3. API Documentation¶
The specification for all generated driver and engine classes which are available in scm.input_classes can be found below.
Included for reference are also the base classes from scm.pisa, but a regular user, you should not interact with these classes directly.
3.1. Input Classes¶
3.1.1. Drivers¶
- class ACERXN[source]¶
- Variables:
Product (str | StringKey) – Make one or more product molecule.
Reactant (str | StringKey) – Make one or more reactant molecule.
BasicOptions (ACERXN._BasicOptions) – General options
DistanceOptions (ACERXN._DistanceOptions) –
Engine (EngineBlock) – The input for the computational engine used to compute energy and forces.
GeomGenRelatedScreeningOptions (ACERXN._GeomGenRelatedScreeningOptions) – Details of screening of intermediates in IntermediateGeneration. There are three screening moments: (1) During the propagation process, (2) After propagation but before geometry optimization, and (3) after geometry optimization. The screening options in this block are concerned with (3).
IntermediateGeneration (ACERXN._IntermediateGeneration) – Options used exclusively in intermediate generation (Step 1)
Intermediates (ACERXN._Intermediates) – If needed specify intermediates.
MappingOptions (ACERXN._MappingOptions) – The options used for the chemical distance computations. Currently only used in step2, but in future will also be available in step1.
MatrixRelatedScreeningOptions (ACERXN._MatrixRelatedScreeningOptions) – Details of screening of intermediates in IntermediateGeneration. There are three screening moments: (1) During the propagation process, (2) After propagation but before geometry optimization, and (3) after geometry optimization. The screening options in this block are concerned with (2).
MoleculeSpecificMatrixScreeningOptions (ACERXN._MoleculeSpecificMatrixScreeningOptions) – Molecule specific options that may be moved to System settings in future.
NetworkCreation (ACERXN._NetworkCreation) – Options exclusively used for network creation (Step 2)
NetworkMinimization (ACERXN._NetworkMinimization) – Options exclusively used for network minimization (Step 3)
ReactantFragmentation (ACERXN._ReactantFragmentation) – Details on how the reactant is split into smallest fragments, and how those are assigned charges and stabilities
RedundantOptions (ACERXN._RedundantOptions) – Options that in this version have only one possible value
RunInfo (ACERXN._RunInfo) – General run and file-Info on creating an ACErxn network
System (ACERXN._System) – Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- class _BasicOptions[source]¶
General options
- Variables:
AcceptSaturatedActiveAtoms (BoolType | BoolKey) – Accept atoms as active even if they are fully saturated in the minimal fragments. By default this is turned off.
Covalent_Radii_Coeff (float | FloatKey) – The criterion for if a bond exists between a pair of atom. Example: Let D_ij is distance between atom i and atom j, R_i is covalent radius of atom i and R_j is covalent radius of atom j, if D_ij <= (Covalent_Radii_Coeff) x (R_i + R_j): bond exists else: bond does not exist (Dalton Trans., 2008, 2832-2838).
IM_MaxMolecule (int | IntKey) – It is the number of constituent molecules in one intermediate state.
MaxJobs (int | IntKey) – The number of parallel calculations (geometry optimizations, matrix enumerations, and network construction processes).
MinimumBondOrder (float | FloatKey) – The minimum bond order to be considered a bond
NProc (int | IntKey) – The number of cores that are used for the QM geometry optimization for each molecule.
SaveMoleculelist (BoolType | BoolKey) – Saves both screened and unscreened molecules to list, which is written to the Legacy output as Molecule_list
TotalChargeMethod (Literal["SumofFragments", "Ionic"]) – If SumofFragments the charge of the intermediate (sum of submolecules) is determined by summing the charges of constituent fragments. If Ionic the charge of the molecule is determined using bond orders.
- class _GeomGenRelatedScreeningOptions[source]¶
Details of screening of intermediates in IntermediateGeneration. There are three screening moments: (1) During the propagation process, (2) After propagation but before geometry optimization, and (3) after geometry optimization. The screening options in this block are concerned with (3).
- Variables:
DiscardAcyclic (BoolType | BoolKey) – Rings in the molecule are counted when the SMILES string is created (during 3D structure generation). After geometry optimization the screening of intermediates based on ring count takes place. If set to True, every molecule in intermediate must contain a ring. The default is False.
EnergyScreening (BoolType | BoolKey) – During intermediate generation, after all geometry optimizations are completed, the generated intermediates can optionally be screened based on energy relative to the reactant. The related keyword is ,CutoffWRTReactantEnergy which must be set.
MaxRingNumber (int | IntKey) – Rings in the molecule are counted when the SMILES string is created (during 3D structure generation). After geometry optimization the screening of intermediates based on ring count takes place. If set to a positive integer, then the number of rings in a single (sub)molecule must be smaller than the provided value.
ScreenChangedConnectivity (BoolType | BoolKey) – If the connectivity of an molecule has been changed during the AC->3D process, the corresponding intermediate will be screened.
ScreenErrorTermination (BoolType | BoolKey) – If a calculation (UFF, DFTB, semi-empirical) is terminated with an error, the corresponding intermediate will be screened.
- class _IntermediateGeneration[source]¶
Options used exclusively in intermediate generation (Step 1)
- Variables:
CompareCharge (BoolType | BoolKey) – When deciding if a molecule has already been computed/created, take into account the charge of the molecule
FormBondsWithinFragment (BoolType | BoolKey) – By default, bond-formation or bond-breaking between all atoms within a fragment is excluded in intermediate generation. If this keyword is set to true, it is possible to form new bonds within a fragment (e.g. create a ring from a chain), and to break them again. The original fragment bonds will always remain in tact.
GenXYZ_MaxCycle (int | IntKey) – The number of adjacency matrix (AC) -> 3D process attempts
MaxBondsBroken (int | IntKey) – When generating new intermediates Y from intermediate X, this is the maximum number of bonds that can be broken in X to form Y.
MaxBondsFormed (int | IntKey) – When generating new intermediates Y from intermediate X, this is the maximum number of bonds that can be formed to create Y from X.
MaxPropagation_Iteration (int | IntKey) – The maximum number of iterations in the propagation of intermediates. If set to default value of -1, ACErxn internally sets the value to 100. Generally, enumeration is terminated when no new intermediates are generated.
Module (str | StringKey) – RDKit is the only option. The default in the original version of the code was OpenBabel.
PropagationMethod (Literal["Class", "Function"]) – Uses either the novel BondOrderMatrixGenerator for propagation and geometry recovery, or the old function PropogationFromReactant
ScreenAndOptimizeIntermediates (BoolType | BoolKey) – If set to True, the generated intermediates will be screened based on a large set of criteria, the remaining intermediates will be converted to 3D structures, and optimized. If set to False, this entire step will be skipped, and 3D geometries and energies are never obtained.
UsePlamsParallelization (BoolType | BoolKey) – Use the novel GeometryGenerator class to generate 3D geometries from molecule bond matrices
UseReactantGeometries (BoolType | BoolKey) – Use the geometries for the reactants as passed as input. If not true the reactant geometries will be generated from smiles. Only works in combination with PropagationMethod=class
AmsOptions (ACERXN._IntermediateGeneration._AmsOptions) – Options related to engine calls
GeometryGenerationOptions (ACERXN._IntermediateGeneration._GeometryGenerationOptions) –
PruningOptions (ACERXN._IntermediateGeneration._PruningOptions) – Details of screening of intermediates in IntermediateGeneration. There are three screening moments: (1) During the propagation process, (2) After propagation but before geometry optimization, and (3) after geometry optimization. The screening options in this block are concerned with (1).
- class _AmsOptions[source]¶
Options related to engine calls
- Variables:
KeepAMSFiles (BoolType | BoolKey) – Keep the files of all AMS calculations in the plams_workdir folder
KeepAMSRunning (BoolType | BoolKey) – Keep the AMS driver running in the background during the geometry optimizations
QMcalculation (str | StringKey) – Filename that defines the method to calculate energy of the intermediates. Example: engine.in
UFF_MaxTime (int | IntKey) – It can have zero or positive number. This is the maximum time for UFF during the AC->3D process
- class _GeometryGenerationOptions[source]¶
- Variables:
RDKitLogging (BoolType | BoolKey) – When the smilestrings are converted to coordinates using RDKit, logging can be switched on or off.
SkipPreOptimization (BoolType | BoolKey) – Skip the MM preoptimization step of geometry optimization, and do not use fragments in 3D structure generation. In the old code this was combined with canonical SMILES generation with OpenBabel, but RDKit has no such option.
- class _PruningOptions[source]¶
Details of screening of intermediates in IntermediateGeneration. There are three screening moments: (1) During the propagation process, (2) After propagation but before geometry optimization, and (3) after geometry optimization. The screening options in this block are concerned with (1).
- Variables:
MaxRingSize (int | IntKey) – If the newly generated intermediate (or molecule) contains a ring larger than the provided value, it is screened.
MinRingSize (int | IntKey) – If the newly generated intermediate (or molecule) contains a ring smaller than the provided value, it is screened.
Pruning_Cyclics (BoolType | BoolKey) – If not set to the default value N, it is the number maximum number of rings allowed in an intermediate.
- class _MappingOptions[source]¶
The options used for the chemical distance computations. Currently only used in step2, but in future will also be available in step1.
- Variables:
Digression_Factor (int | IntKey) – It can have positive integer. It is delta in the expression for the maximum chemical distance of an intermediate form reactants and products
Edge_Energy_Threshold (int | IntKey) – Endergonic reactions whose energy difference is higher than Edge_Energy_Threshold are not connected as edges. Currently not in use.
FullMapping (Literal["Net", "Y", "N"]) – Net: When calculating chemical distance, we only consider submolecules that change upon reaction. N: When calculating chemical distance, we only consider some parts of intermediate (based on the keyword Kthneighbor).
Kthneighbor (int | IntKey) – When calculating chemical distance with FullMapping=N, ACErxn only considers atoms that are k unit away from the active atoms. The distance between two atoms are defined as the graphical distance (length of shortest path between two atoms)
MaxDepth_Alpha (int | IntKey) – Completely equivalent to Digression_Factor, with the exception that it is not used with Digression_Screening in step 1.
UseActiveBonds (BoolType | BoolKey) – During the mapping process (computing the chemical distance, assume only the active bonds can be broken or formed)
- class _MatrixRelatedScreeningOptions[source]¶
Details of screening of intermediates in IntermediateGeneration. There are three screening moments: (1) During the propagation process, (2) After propagation but before geometry optimization, and (3) after geometry optimization. The screening options in this block are concerned with (2).
- Variables:
AllowAldehyde (BoolType | BoolKey) – Determines whether aldehyde anions are acceptable intermediates. Screened after propagation, and before geometry optimization.
AllowCarbenes (BoolType | BoolKey) – Allow carbene molecules among the generated intermediates.
AllowChargedAtoms (BoolType | BoolKey) – The atomic charges are automatically estimated during intermediate generation. If this keyword is set to False, then all estimated charges need to be zero.
AllowChargedMolecules (BoolType | BoolKey) – The charges of all newly generated molecules are derived from the fragment charges. If this keyword is set to False, then all molecule charges need to be zero.
ChargeConservation (BoolType | BoolKey) – Ensure that the estimated atomic charges of the newly generated intermediates match the charges of the submolecules. The latter are derived from the fragment charges.
CheckElectronegativity (BoolType | BoolKey) – If an atom has a more positive charge than its more electronegative neighbor, the intermediate state will be screened. (except carbon monoxide). By default this is switched off.
DigressionScreening (BoolType | BoolKey) – If set to True, ACErxn applies digression screening (screening based on the chemical distance of an intermediate from reactant and product) directly following each propagation step for the intermediate generation (before geometry optimization).
DiscardAtomicOverCharge (BoolType | BoolKey) – If set to True, a formal charge for an atom in a molecule smaller than -2 or bigger than +2 will result in screening of the intermediate.
DiscardMolecularOverCharge (BoolType | BoolKey) – If the total charge for an molecule in a intermediate state is smaller than -2 or bigger than +2, it will be screened.
MaxAllowedRadicals (int | IntKey) – If the value is positive, radical species are screened during enumeration. It counts the number of radicals and if the number exceeds the AllowRadical value, the intermediate is screened.
MaxMetalElectronCount (int | IntKey) – It has an integer. It is the maximum number of counted electrons of metal (neutral counting)
MaxTotalRingNumber (int | IntKey) – Before 3D structure generation the number of rings is also computed, using rdkit GetSymmSSSR(). If this key is a positive number, than the total number of rings in an intermediate (sum of submolecules) must be smaller then the provided number.
MetalMaxCoordination (int | IntKey) – Restricts the maximal number of coordinations of transition metals.
MetalMinCoordination (int | IntKey) – Restricts the minimal number of coordinations of transition metals.
MinMetalElectronCount (int | IntKey) – It has an integer. It is the minimum number of counted electrons of metal (neutral counting)
MinTotalRingNumber (int | IntKey) – Before 3D structure generation the number of rings is also computed, using rdkit GetSymmSSSR(). If this key is a positive number, than the total number of rings in an intermediate (sum of submolecules) must be larger then the provided number.
SuperMoleculeCharge (float | FloatKey) – If TotalChargeMethod is set to Ionic, this is the total charge the intermediate (sum of submolecules) always needs to have.
- class _MoleculeSpecificMatrixScreeningOptions[source]¶
Molecule specific options that may be moved to System settings in future.
- Variables:
Elements_NoTerminus (str | StringKey) – The name of an element. In the intermediates, elements of this type need to be bonded to more than 1 other atom. This key can occur multiple times
ForbiddenMetalElectronCount (int | IntKey) – It prevents the metal from having certain electron counts (neutral counting). Multiple values can be provided by repeating this key multiple times. Note: Refer http://www.columbia.edu/cu/chemistry/groups/parkin/mlxz.htm for the statistics of the electron count of each metal.
LigandElectronCount (int | IntKey) – When a transition metal complex is included in the intermediates state a user has to specify the ligand electrons contributed when using the neutral counting method. The key needs to be present a multiple of 2 times (the first instance is the index of an atom and the second is the corresponding electron contribution).
RangeOfValences (ACERXN._MoleculeSpecificMatrixScreeningOptions._RangeOfValences) – The user can provide the maximum and minimum number of bonds an atom of a certain element can have. If not set, default values are used.
- class _NetworkCreation[source]¶
Options exclusively used for network creation (Step 2)
- Variables:
FindDelocalizedBonds (BoolType | BoolKey) – Seems to write information on bond delocalization into the Intermediate objects before the network is created.
Screening (ACERXN._NetworkCreation._Screening) – Options related to the screening of intermediates
- class _Screening[source]¶
Options related to the screening of intermediates
- Variables:
CutoffWRTReactantEnergy (float | FloatKey) – It determines how much higher energy the intermediate state can have than the state of the reactant. If GeomGenRelatedScreeningOptions%EnergyScreening is set to True, then this value is already used at intermediate generation. Unit is kcal/mol.
- class _NetworkMinimization[source]¶
Options exclusively used for network minimization (Step 3)
- class _ReactantFragmentation[source]¶
Details on how the reactant is split into smallest fragments, and how those are assigned charges and stabilities
- Variables:
DepthElectronegativitySearch (int | IntKey) – The atoms in the reactant molecules are assigned charges based on the connectivity of the molecule and the electronegativity of the atoms. By default the electronegativity is assigned simply based on the element, but if the depth is selected larger than 1, the electronegativity of neighboring atoms (up to depth-1) is included in determining the final electronegativity value of the atoms. For example, in a regular C-C bond, the electrons in the bond are distributed equally over the two atoms. But if DepthElectronegativitySearch is selected higher than 1, then breaking the C-C bond in ethanol will result in a negatively charged C-OH group and a carbocation.
- class _RedundantOptions[source]¶
Options that in this version have only one possible value
- Variables:
Bond_Iteration_Method (str | StringKey) – According to the input description by Jin Woo, ‘Propagation’ is the only option, although the default in the ACE code is ‘Binary’
Command (str | StringKey) – Is not relevant when AMS is used
CreateStereoIsomers (BoolType | BoolKey) – If True, stereo-chemistry of stereo centers is considered during 3D conversion. Not supported in current version.
DistanceMethod (str | StringKey) – According to the input description by Jin Woo, ‘ChemDist’ is the only option, although the default in the ACE code is ‘BondSimilarity’
Fragment_number (str | StringKey) – Fragment numbers for the reactive atoms need to be read at the bottom of the input file. Obsolete if not input file is used.
GeomWriteFormat (str | StringKey) – According to the input description by Jin Woo, ‘xyz’ is the only option, although the default in the ACE code is ‘g09’
Reactive_Atoms (str | StringKey) – The atom indices of the reactive atoms in the fragments need to be read at the bottom of the input file. Obsolete if not input file is used
Temperature (float | FloatKey) – It determines the temperature in Kelvin. It is calculation option for semi-empirical or DFTB.
UseFragments (BoolType | BoolKey) – If the conversion from graph to 3D geometry using SMILES does not provide a stable geometry, then the 3D geometry is generated by combining the fragment geometries. If set to False this will be ignored in the new code (setting PropagationMethod to Class), while in the old code (setting PropagationMethod to Function) a method is called that does not seem to exist.
skf_dir (str | StringKey) – It is the path of the directory that contains skf files. It is replaced by the content of the engine file referenced in QMcalculation
BasinHopping (ACERXN._RedundantOptions._BasinHopping) – Options related to Basin Hopping
Miscellaneous (ACERXN._RedundantOptions._Miscellaneous) –
PruningOptions (ACERXN._RedundantOptions._PruningOptions) – Redundant options related to pruning intermediates in step 1 (intermediate generation)
SpeciesNetOptions (ACERXN._RedundantOptions._SpeciesNetOptions) –
- class _RunInfo[source]¶
General run and file-Info on creating an ACErxn network
- Variables:
MinNumberOfShortestPathsWritten (int | IntKey) – The minimum number of shortest paths written to the shortest_paths.rkf file. Only relevant with Steps=All,Steps=MinimizeNetwork, or Steps=AnalyzeNetwork.
RestartDir (str | Path | StringKey) – Path to the folder containing the restart RKF files
Steps (Literal["GenerateIntermediates", "CreateNetwork", "MinimizeNetwork", "AnalyzeNetwork", "All"]) – Which of the three ACErxn steps to run ((1) GenerateIntermediates, (2) CreateNetwork, (3) MinimizeNetwork, (4) AnalyzeNetwork). The default is to run the first three.
UseAllIntermediatesForPaths (BoolType | BoolKey) – If set (default), if two paths are found with the same chemical distance, then only the one including the most intermediates will be kept.
- class _System[source]¶
Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- Variables:
AllowCloseAtoms (BoolType | BoolKey) – If AllowCloseAtoms is set to False, the AMS driver will stop with an error if it detects almost-coinciding atomic coordinates. If set to True, the AMS driver will try to carry on with the calculation.
Charge (float | FloatKey) – The system’s total charge in atomic units.
FractionalCoords (BoolType | BoolKey) – Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
GeometryFile (str | Path | StringKey) – Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds (BoolType | BoolKey) – Whether or not UFF bonds should be guessed.
LatticeStrain (Iterable[float] | FloatListKey) – Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
MapAtomsToUnitCell (BoolType | BoolKey) – For periodic systems the atoms will be moved to the central cell.
ModifyAlternativeElements (BoolType | BoolKey) – When using alternative elements (using the nuclear_charge attribute) set the element to the nearest integer Z. If you specify an H atom with a nuclear_charge of 2.9 it is replaced by a Li atom with the same nuclear charge.
PerturbCoordinates (float | FloatKey) – Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
PerturbLattice (float | FloatKey) – Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
RandomizeAtomOrder (BoolType | BoolKey) – Whether or not the order of the atoms should be randomly changed. Intended for some technical testing purposes only. Does not work with bond information.
ShiftCoordinates (Iterable[float] | FloatListKey) – Translate the atoms by the specified shift (three numbers).
SuperCell (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
SuperCellTrafo (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
Symmetrize (BoolType | BoolKey) – Whether to symmetrize the input structure. This might also rototranslate the structure into a standard orientation. This will symmetrize the atomic coordinates to machine precision. Useful if the system is almost symmetric or to rototranslate a symmetric molecule into a standard orientation.
Symmetry (Literal["AUTO", "NOSYM", "C(LIN)", "D(LIN)", "C(I)", "C(S)", "C(2)", "C(3)", "C(4)", "C(5)", "C(6)", "C(7)", "C(8)", "C(2V)", "C(3V)", "C(4V)", "C(5V)", "C(6V)", "C(7V)", "C(8V)", "C(2H)", "C(3H)", "C(4H)", "C(5H)", "C(6H)", "C(7H)", "C(8H)", "D(2)", "D(3)", "D(4)", "D(5)", "D(6)", "D(7)", "D(8)", "D(2D)", "D(3D)", "D(4D)", "D(5D)", "D(6D)", "D(7D)", "D(8D)", "D(2H)", "D(3H)", "D(4H)", "D(5H)", "D(6H)", "D(7H)", "D(8H)", "I", "I(H)", "O", "O(H)", "T", "T(D)", "T(H)", "S(4)", "S(6)", "S(8)"]) – Use (sub)symmetry with this Schoenflies symbol. Can only be used for molecules. Orientation should be correct for the (sub)symmetry. If used icw Symmetrize, the symmetrization will not reorient the molecule.
Atoms (str | Sequence[str] | FreeBlock) – The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders (str | Sequence[str] | FreeBlock) – Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
DefineRegion (ACERXN._System._DefineRegion) – Defines a region of atoms using more comprehensive selecting methods
ElectrostaticEmbedding (ACERXN._System._ElectrostaticEmbedding) – Container for electrostatic embedding options, which can be combined.
Lattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
LoadForceFieldAtomTypes (ACERXN._System._LoadForceFieldAtomTypes) – This is a mechanism to set the ForceField.Type attribute in the input. This information is currently only used by the ForceField engine.
LoadForceFieldCharges (ACERXN._System._LoadForceFieldCharges) – This is a mechanism to set the ForceField.Charge attribute in the input. This information is currently only used by the ForceField engine.
Region (ACERXN._System._Region) – Properties for each region specified in the Atoms block.
- class _Atoms[source]¶
The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
- class _BondOrders[source]¶
Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
- class _DefineRegion[source]¶
Defines a region of atoms using more comprehensive selecting methods
- Variables:
AtomRange (Iterable[int] | IntListKey) – Specifies a region by selecting all atoms with indices between a certain range (including the beginning and ending index). Input format is: beginIndex endingIndex
Axis (Iterable[float] | FloatListKey) – Specifies a region by selecting all atoms in space above a certain threshold along an user-defined axis. Input format is: X-component, Y-component, Z-component, threshold
Box (Iterable[float] | FloatListKey) – Specifies a region by selecting all atoms that are present inside a box in space. Input format is: Xmin, Xmax, Ymin, Ymax, Zmin, Zmax
- class _ElectrostaticEmbedding[source]¶
Container for electrostatic embedding options, which can be combined.
- Variables:
ElectricField (Iterable[float] | FloatListKey) –
External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.
In atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 … e11 V/m.
Supported by the engines adf, band, dftb and mopac.
For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
MultipolePotential (ACERXN._System._ElectrostaticEmbedding._MultipolePotential) – External point charges (and dipoles).
- class _MultipolePotential[source]¶
External point charges (and dipoles).
- Variables:
ChargeModel (Literal["Point", "Gaussian"]) – A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
ChargeWidth (float | FloatKey) – The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
Coordinates (str | Sequence[str] | FreeBlock) –
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Coordinates[source]¶
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Lattice[source]¶
Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
- class _LoadForceFieldAtomTypes[source]¶
This is a mechanism to set the ForceField.Type attribute in the input. This information is currently only used by the ForceField engine.
- class _LoadForceFieldCharges[source]¶
This is a mechanism to set the ForceField.Charge attribute in the input. This information is currently only used by the ForceField engine.
- Variables:
CheckGeometryRMSD (BoolType | BoolKey) – Whether the geometry RMSD test should be performed, see MaxGeometryRMSD. Otherwise only basic tests are performed, such as number and atom types. Not doing the RMSD test allows you to load molecular charges in a periodic system.
MaxGeometryRMSD (float | FloatKey) – The geometry of the charge producing calculation is compared to the one of the region, and need to be the same within this tolerance.
Region (str | StringKey) – Region for which the charges should be loaded
- class ADFNBO[source]¶
- Variables:
ADFFile (str | StringKey) – Path to TAPE21 file from which adfnbo reads data and to which adfnbo possibly writes data
Copy (BoolType | BoolKey) –
Fock (BoolType | BoolKey) –
Read (BoolType | BoolKey) –
Spherical (BoolType | BoolKey) –
TAPE15File (str | StringKey) – Path to the TAPE15 file from which adfnbo reads data
TestJob (BoolType | BoolKey) – include extra options in FILE47, such as NRT (natural resonance theory) which is expensive for large molecules
Write (BoolType | BoolKey) –
- class AMS[source]¶
- Variables:
EngineRestart (str | Path | StringKey) –
The path to the file from which to restart the engine.
Should be a proper engine result file (like adf.rkf, band.rkf etc), or the name of the results directory containing it.
FallbackSolveAfterEngineFailure (BoolType | BoolKey) – If the engine fails to Solve, try to re-run the Solve without restarting the engine from the previous results. This generally decreases the engine failure rate. Only relevant certain tasks, such as GeometryOptimization, MolecularDynamics, Replay, IRC.
LoadEngine (str | Path | StringKey) – The path to the file from which to load the engine configuration. Replaces the Engine block.
RNGSeed (Iterable[int] | IntListKey) – Initial seed for the (pseudo)random number generator. This should be omitted in most calculations to avoid introducing bias into the results. If this is unset, the generator will be seeded randomly from external sources of entropy. If you want to exactly reproduce an older calculation, set this to the numbers printed in its output.
Task (Literal["GCMC", "GeometryOptimization", "Idle", "IRC", "MolecularDynamics", "NEB", "PESExploration", "PESScan", "Pipe", "Replay", "SinglePoint", "SteepestDescent", "TestEngine", "TestSymmetry", "TransitionStateSearch", "VibrationalAnalysis"]) –
Specify the computational task to perform:
Single Point: keep geometry as is
Geometry Optimization: minimize energy
Transition State: search for a transition state
IRC: intrinsic reaction coordinate
PES Scan: scan the potential energy surface
NEB: Nudged elastic band for reaction path optimization
Vibrational Analysis: perform one of the analysis types selected on the options page
Molecular Dynamics: perform MD simulation
GCMC: Grand Canonical Monte Carlo simulation
PES Exploration: automated potential energy surface exploration
Replay: recompute frames from the trajectory of a previously run job
Test (Literal["Symmetry", "BareSymmetry", "Bonds", "SecondOrderBonds", "AtomTyping", "SystemMatching"]) – various technical tests that will be done for the system
UseSymmetry (BoolType | BoolKey) – Whether to use the system’s symmetry in AMS. Symmetry is recognized within a tolerance as given in the Symmetry key.
BondOrders (AMS._BondOrders) – Configures details regarding the calculation/guessing of bond orders. To request the calculation of bond orders, use the ‘Properties%BondOrders’ key.
Constraints (AMS._Constraints) – The Constraints block allows geometry optimizations and potential energy surface scans with constraints. The constraints do not have to be satisfied at the start of the calculation.
ElasticTensor (AMS._ElasticTensor) – Options for numerical evaluation of the elastic tensor.
Engine (EngineBlock) – The input for the computational engine. The header of the block determines the type of the engine.
EngineAddons (AMS._EngineAddons) – This block configures all the engine add-ons.
EngineDebugging (AMS._EngineDebugging) – This block contains some options useful for debugging the computational engines.
ExitCondition (AMS._ExitCondition) – If any of the specified exitconditions are met, the AMS driver will exit cleanly.
GCMC (AMS._GCMC) –
This block controls the Grand Canonical Monte Carlo (GCMC) task.
By default, molecules are added at random positions in the simulation box. The initial position is controlled by
GeometryOptimization (AMS._GeometryOptimization) – Configures details of the geometry optimization and transition state searches.
IEEEExceptions (AMS._IEEEExceptions) – Whether this works or not depends on the way the program is compiled (compiler and settings). Only useful for developers debugging some numerical issue.
IRC (AMS._IRC) – Configures details of the Intrinsic Reaction Coordinate optimization.
Idle (AMS._Idle) – Configures details of the idle task, which does nothing for a specified amount of time.
LoadSystem (AMS._LoadSystem) – Block that controls reading the chemical system from a KF file instead of the [System] block.
Log (str | Sequence[str] | FreeBlock) – Configures the debugging loggers. Syntax: ‘Level LoggerName’. Possible Levels: All, Debug, Info, Warning, Error, Fatal.
MolecularDynamics (AMS._MolecularDynamics) – Configures molecular dynamics (with the velocity-Verlet algorithm) with and without thermostats. This block allows to specify the details of the molecular dynamics calculation.
Molecules (AMS._Molecules) – Configures details of the molecular composition analysis enabled by the Properties%Molecules block.
NEB (AMS._NEB) – Configures details of the Nudged Elastic Band optimization.
NormalModes (AMS._NormalModes) – Configures details of a normal modes calculation.
NumericalDifferentiation (AMS._NumericalDifferentiation) – Define options for numerical differentiations, that is the numerical calculation of gradients, Hessian and the stress tensor for periodic systems.
NumericalPhonons (AMS._NumericalPhonons) – Configures details of a numerical phonons calculation.
PESExploration (AMS._PESExploration) – Configures details of the automated PES exploration methods.
PESPointCharacter (AMS._PESPointCharacter) – Options for the characterization of PES points.
PESScan (AMS._PESScan) – Configures the details of the potential energy surface scanning task.
Phonons (AMS._Phonons) – Configures the phonons calculation.
Print (AMS._Print) – This block controls the printing of additional information to stdout.
Properties (AMS._Properties) – Configures which AMS level properties to calculate for SinglePoint calculations or other important geometries (e.g. at the end of an optimization).
Raman (AMS._Raman) – Configures details of the Raman or VROA calculation.
Replay (AMS._Replay) – Configures the details of the Replay task.
Restraints (AMS._Restraints) – The Restraints block allows to add soft constraints to the system. A restraint is a potential energy function (a spring) attached to a certain coordinate, for example, an interatomic distance, with its minimum at the specified optimal value. A restraint is defined using one or two parameters: the ForceConstant and, for some types, the F(Inf) value. The ForceConstant parameter corresponds to second derivative of the restraint potential energy d2V(x)/dx^2 for any x (harmonic restraints) or only at at x=0 (other restraints). Here, x is a deviation from the restraint’s optimal value.
RigidMotions (AMS._RigidMotions) – Specify which rigid motions of the total system are allowed. An external field is not considered part of the system. Normally the automatic option is doing what you want. However this feature can be used as a means of geometry constraint.
SCMLibrary (AMS._SCMLibrary) – Technical settings affecting src/lib
SCMMatrix (AMS._SCMMatrix) – Technical settings for programs using the AMT matrix system. Currently this is only used by DFTB
SerializedTensors (AMS._SerializedTensors) – Technical settings affecting the SerializedTensors module, currently only used for HartreeFock
SteepestDescent (AMS._SteepestDescent) – Configures details of the steepest descent task.
Symmetry (AMS._Symmetry) – Specifying details about the details of symmetry detection and usage.
System (AMS._System) – Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
Thermo (AMS._Thermo) – Options for thermodynamic properties (assuming an ideal gas). The properties are computed for all specified temperatures.
TransitionStateSearch (AMS._TransitionStateSearch) – Configures some details of the transition state search.
VibrationalAnalysis (AMS._VibrationalAnalysis) – Input data for all vibrational analysis utilities in the AMS driver.
- class _BondOrders[source]¶
Configures details regarding the calculation/guessing of bond orders. To request the calculation of bond orders, use the ‘Properties%BondOrders’ key.
- Variables:
Method (Literal["Engine", "Guess", "EngineWithGuessFallback"]) –
How to compute the bond orders when they are requested via the ‘Properties%BondOrders’ key.
’Engine’: let the engine compute the bond orders. The specific method used to compute the bond orders depends on the engine selected, and it may be configurable in the engine’s input. Note: the calculation may stop if the engine cannot compute bond orders.
’Guess’: Use a bond guessing algorithm based on the system’s geometry. This is the same algorithm that is used by the Graphical User Interface to guess bonds.
’EngineWithGuessFallback’: let the engine compute the bond orders (same as in ‘Engine’ option) but if the engine did not produce any bond orders, use the bond guessing algorithm as a fallback option.
- class _Constraints[source]¶
The Constraints block allows geometry optimizations and potential energy surface scans with constraints. The constraints do not have to be satisfied at the start of the calculation.
- Variables:
Fix multiple distances using one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3
The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 as well as the angle between them.
The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then any bond between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. If the distance is omitted then the bond length from the initial geometry is used.
Important: only the bonds present in the system at the start of the simulation can be constrained, which means that the bonds may need to be specified in the System block.
Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H
Angle (str | StringKey) – Fix the angle between three atoms. Three atom indices followed by an angle in degrees.
Atom (int | IntKey) – Fix the position of an atom. Just one integer referring to the index of the atom in the [System%Atoms] block.
AtomList (Iterable[int] | IntListKey) – Fix positions of the specified atoms. A list of integers referring to indices of atoms in the [System%Atoms] block.
Block (str | StringKey) – Name of the region to constrain as a rigid block. Regions are specified in the System%Atoms block.
BlockAtoms (Iterable[int] | IntListKey) – List of atom indices for a block constraint, where the internal degrees of freedom are frozen.
Coordinate (str | StringKey) – Fix a particular coordinate of an atom. Atom index followed by (x|y|z).
DifDist (str | StringKey) – Four atom indices i j k l followed by the distance in Angstrom. This will constrain the difference R(ij)-R(kl) at the given value.
Dihedral (str | StringKey) – Fix the dihedral angle between four atoms. Four atom indices followed by an angle in degrees.
Distance (str | StringKey) – Fix the distance between two atoms. Two atom indices followed by the distance in Angstrom.
EqualStrain (str | StringKey) –
Exclusively for lattice optimizations:
Accepts a set of strain components [xx, xy, xz, yy, yz, zz] which are to be kept equal.
The applied strain will be determined by the average of the corresponding stress tensors components.
In AMSinput just check the corresponding check buttons.
FixedRegion (str | StringKey) – Fix positions of all atoms in a region.
FreezeStrain (str | StringKey) –
Exclusively for lattice optimizations:
Freezes any lattice deformation corresponding to a particular component of the strain tensor.
Accepts a set of strain components [xx, xy, xz, yy, yz, zz] to be frozen.
In AMSinput just check the corresponding check buttons.
SumDist (str | StringKey) – Four atom indices i j k l followed by the distance in Angstrom. This will constrain the sum R(ij)+R(kl) at the given value.
- class _ElasticTensor[source]¶
Options for numerical evaluation of the elastic tensor.
- Variables:
ConvergenceQuality (Literal["Normal", "Good", "VeryGood", "Excellent"]) – The tightness of the convergence of the geometry optimizations for each strain deformation. This should not be set higher than the overall convergence quality of the preceding geometry optimization configured by the
GeometryOptimization%Convergence%Qualitykeyword.StrainStepSize (float | FloatKey) – Step size (relative) of strain deformations used for computing the elastic tensor numerically.
Parallel (AMS._ElasticTensor._Parallel) – Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- class _Parallel[source]¶
Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _Engine[source]¶
The input for the computational engine. The header of the block determines the type of the engine.
- class _EngineAddons[source]¶
This block configures all the engine add-ons.
- Variables:
Pressure (float | FloatKey) – Add a hydrostatic pressure term to the engine’s energy and stress tensor. Can only be used for 3D periodic boundary conditions.
AtomEnergies (str | Sequence[str] | FreeBlock) – Add an element-dependent energy per atom. On each line, give the chemical element followed by the energy (in atomic units).
D3Dispersion (AMS._EngineAddons._D3Dispersion) – This block configures the add-on that adds the Grimme D3 dispersion correction to the engine’s energy, gradients, and stress tensor.
D4Dispersion (AMS._EngineAddons._D4Dispersion) – This block configures the addon that adds the Grimme D4(EEQ) dispersion correction to the engine’s energy, gradients, stress tensor and Hessian.
ExternalEngine (AMS._EngineAddons._ExternalEngine) – External engine as an addon
ExternalStress (AMS._EngineAddons._ExternalStress) – This block configures the addon that adds external stress term to the engine’s energy and stress tensor.
PipeEngine (AMS._EngineAddons._PipeEngine) – Pipe engine as an addon
Repulsion (AMS._EngineAddons._Repulsion) – This block configures an addon that adds a repulsive Weeks-Chandler-Andersen potential to all atom pairs.
WallPotential (AMS._EngineAddons._WallPotential) – This block configures the addon that adds a spherical wall potential to the engine’s energy and gradients.
- class _AtomEnergies[source]¶
Add an element-dependent energy per atom. On each line, give the chemical element followed by the energy (in atomic units).
- class _D3Dispersion[source]¶
This block configures the add-on that adds the Grimme D3 dispersion correction to the engine’s energy, gradients, and stress tensor.
- Variables:
Damping (Literal["BJ", "Zero"]) – Type of damping: BJ (Becke-Johnson) or Zero. BJ is recommended for most applications.
Enabled (BoolType | BoolKey) – Enables the D3 dispersion correction addon.
Functional (str | StringKey) – Use the D3 parameterization by Grimme for a given xc-functional. Accepts the same values as the –func command line option of the official dftd3 program. Note: the naming convention is different from elsewhere in the AMS suite. For example, BLYP should be called b-lyp.
a1 (float | FloatKey) – The a1 parameter. Only used if Damping is set to BJ. If set, it overwrites the a1 value for the chosen functional.
a2 (float | FloatKey) – The a2 parameter. Only used if Damping is set to BJ. If set, it overwrites the a2 value for the chosen functional.
alp (float | FloatKey) – The a2 parameter. Only used if Damping is set to BJ. If set, it overwrites the a2 value for the chosen functional.
s6 (float | FloatKey) – The s6 parameter, global scaling parameter. If set, it overwrites the s6 value for the chosen functional.
s8 (float | FloatKey) – The s8 parameter. If set, it overwrites the s8 value for the chosen functional.
sr6 (float | FloatKey) – The sr6 parameter. Only used if Damping is set to Zero. If set, it overwrites the sr6 value for the chosen functional.
- class _D4Dispersion[source]¶
This block configures the addon that adds the Grimme D4(EEQ) dispersion correction to the engine’s energy, gradients, stress tensor and Hessian.
- Variables:
Enabled (BoolType | BoolKey) – Enables the D4 dispersion correction addon.
Functional (Literal["HF", "BLYP", "BPBE", "BP86", "BPW", "LB94", "MPWLYP", "MPWPW91", "OLYP", "OPBE", "PBE", "RPBE", "REVPBE", "PW86PBE", "RPW86PBE", "PW91", "PW91P86", "XLYP", "B97", "TPSS", "REVTPSS", "SCAN", "B1LYP", "B3LYP", "BHLYP", "B1P86", "B3P86", "B1PW91", "B3PW91", "O3LYP", "REVPBE0", "REVPBE38", "PBE0", "PWP1", "PW1PW", "MPW1PW91", "MPW1LYP", "PW6B95", "TPSSH", "TPSS0", "X3LYP", "M06L", "M06", "OMEGAB97", "OMEGAB97X", "CAM-B3LYP", "LC-BLYP", "LH07TSVWN", "LH07SSVWN", "LH12CTSSIRPW92", "LH12CTSSIFPW92", "LH14TCALPBE", "B2PLYP", "B2GPPLYP", "MPW2PLYP", "PWPB95", "DSDBLYP", "DSDPBE", "DSDPBEB95", "DSDPBEP86", "DSDSVWN", "DODBLYP", "DODPBE", "DODPBEB95", "DODPBEP86", "DODSVWN", "PBE02", "PBE0DH", "DFTB(3ob)", "DFTB(mio)", "DFTB(pbc)", "DFTB(matsci)", "DFTB(ob2)", "B1B95", "MPWB1K", "REVTPSSH", "GLYP", "REVPBE0DH", "REVTPSS0", "REVDSDPBEP86", "REVDSDPBEPBE", "REVDSDBLYP", "REVDODPBEP86", "B97M", "OMEGAB97M", "R2SCAN"]) – Use the D4 parameterization by Grimme for a given xc-functional.
Verbosity (Literal["Silent", "Normal", "Verbose", "VeryVerbose"]) – Controls the verbosity of the dftd4 code. Equivalent to the –silent and –verbose command line switches of the official dftd4 program.
a1 (float | FloatKey) – The a1 parameter, see D4 article. The physically reasonable range for a1 is [0.0,1.0]. If set, it overwrites the a1 value for the chosen functional.
a2 (float | FloatKey) – The a2 parameter, see D4 article. The physically reasonable range for a2 is [0.0,7.0]. If set, it overwrites the a2 value for the chosen functional.
s6 (float | FloatKey) – The s6 parameter, see D4 article. The physically reasonable range for s6 is [0.0,1.0]. If set, it overwrites the s6 value for the chosen functional.
s8 (float | FloatKey) – The s8 parameter, see D4 article. The physically reasonable range for s8 is [0.0,3.0]. If set, it overwrites the s8 value for the chosen functional.
s9 (float | FloatKey) – The s9 parameter, see D4 article. If set, it overwrites the s9 value for the chosen functional.
- class _ExternalStress[source]¶
This block configures the addon that adds external stress term to the engine’s energy and stress tensor.
- Variables:
StressTensorVoigt (Iterable[float] | FloatListKey) – The elements of the external stress tensor in Voigt notation. One should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
UpdateReferenceCell (BoolType | BoolKey) – Whether ot not the reference cell should be updated every time the system changes (see documentation).
- class _Repulsion[source]¶
This block configures an addon that adds a repulsive Weeks-Chandler-Andersen potential to all atom pairs.
- Variables:
Enabled (BoolType | BoolKey) –
Enables the repulsive Weeks-Chandler-Andersen potential addon.
When enabled, all atom pairs will experience repulsion E = 4*epsilon*( (sigma/r)^12 - (sigma/r)^6 + 1/4 ) at the distances shorter than about 1.12*sigma.
Epsilon (float | FloatKey) – The epsilon parameter in the potential equation. It is equal to the amount of energy added at r=sigma.
HydrogenSigmaScale (float | FloatKey) – The sigma parameter for a pair of atoms where one of them is hydrogen is scaled with the given factor. For H-H interactions the sigma is scaled with this value squared.
Sigma (float | FloatKey) – The sigma parameter in the potential equation. The potential is exactly zero at the distances larger than about 1.12*sigma
SkinLength (float | FloatKey) – Technical parameter specifying skin length for the neighbor list generation. A larger value increases the neighbor list cutoff (and cost) but reduces the frequency it needs to be re-created.
- class _WallPotential[source]¶
This block configures the addon that adds a spherical wall potential to the engine’s energy and gradients.
- Variables:
Enabled (BoolType | BoolKey) – Enables the wall potential addon. When enabled, a spherical wall of radius [Radius] around the origin will be added. The force due to the potential will decay exponentially inside the wall, will be close to [Prefactor*Gradient] outside and exactly half of that at the wall.
Gradient (float | FloatKey) – The radial gradient outside the sphere.
Prefactor (float | FloatKey) – The multiplier for the overall strength of the potential.
Radius (float | FloatKey) – The radius of the sphere, wherein the potential is close to zero.
- class _EngineDebugging[source]¶
This block contains some options useful for debugging the computational engines.
- Variables:
AlwaysClaimSuccess (BoolType | BoolKey) – If an engine fails, pretend that it worked. This can be useful when you know that an SCF might fail.
CheckInAndOutput (BoolType | BoolKey) – Enables some additional checks on the input and output of an engine, e.g. for NaN values.
ForceContinousPES (BoolType | BoolKey) – If this option is set, the engine will always run in continuous PES mode. For many engines this disables the use of symmetry, as this one always leads to a discontinuous PES around the symmetric points: Basically there is jump in the PES at the point where the symmetry detection starts classifying the system as symmetric. Normally the continuous PES mode of the engine (often disabling the symmetry) is only used when doing numerical derivatives, but this flag forces the engine to continuously run in this mode.
IgnoreEngineSupportsErrors (BoolType | BoolKey) – Pretend as if the engine supports anything requested. Use at your own risk.
IgnoreGradientsRequest (BoolType | BoolKey) – If this option is set, the engine will not do analytical gradients if asked for it, so that gradients will have to be evaluated numerically by AMS.
IgnorePreviousResults (BoolType | BoolKey) – If this option is set, the engine will not receive information from previous calculations. Typically this information is used to restart the self consistent procedure of the engine.
IgnoreStressTensorRequest (BoolType | BoolKey) – If this option is set, the engine will not calculate an analytical stress tensor if asked for it, so that the stress tensor will have to be evaluated numerically by AMS.
NeverQuiet (BoolType | BoolKey) – Makes the engine ignore the request to work quietly.
RandomFailureChance (float | FloatKey) – Makes the engine randomly report failures, even though the results are actually fine. Useful for testing error handling on the application level.
RandomNoiseInEnergy (float | FloatKey) – Adds a random noise to the energy returned by the engine. The random contribution is drawn from [-r,r] where r is the value of this keyword.
RandomNoiseInGradients (float | FloatKey) – Adds a random noise to the gradients returned by the engine. A random number in the range [-r,r] (where r is the value of this keyword) is drawn and added separately to each component of the gradient.
RandomStopChance (float | FloatKey) – Makes the engine randomly stop. Can be used to simulate crashes.
- class _ExitCondition[source]¶
If any of the specified exitconditions are met, the AMS driver will exit cleanly.
- Variables:
Type (Literal["AtomsTooClose", "EngineEnergyUncertainty", "EngineGradientsUncertainty"]) – The type of exitcondition specified
AtomsTooClose (AMS._ExitCondition._AtomsTooClose) – If any pair of atoms is closer than the specified minimum value, the program will exit cleanly.
EngineEnergyUncertainty (AMS._ExitCondition._EngineEnergyUncertainty) – If the engine reports an uncertainty that is too high, the program will exit cleanly.
EngineGradientsUncertainty (AMS._ExitCondition._EngineGradientsUncertainty) – If the engine reports an uncertainty in the magnitude of the nuclear gradient of any atom that is too high, the program will exit cleanly.
- class _AtomsTooClose[source]¶
If any pair of atoms is closer than the specified minimum value, the program will exit cleanly.
- class _GCMC[source]¶
This block controls the Grand Canonical Monte Carlo (GCMC) task.
By default, molecules are added at random positions in the simulation box. The initial position is controlled by
- Variables:
AccessibleVolume (float | FloatKey) – Volume available to GCMC, in cubic Angstroms. AccessibleVolume should be specified for “Accessible” and “FreeAccessible” [VolumeOption].
Ensemble (Literal["Mu-VT", "Mu-PT"]) – Select the MC ensemble: Mu-VT for fixed volume or Mu-PT for variable volume. When the Mu-PT ensemble is selected the [Pressure] and [VolumeChangeMax] should also be specified.
MapAtomsToOriginalCell (BoolType | BoolKey) – Keeps the atom (mostly) in the original cell by mapping them back before the geometry optimizations.
MaxDistance (float | FloatKey) – The max distance to other atoms of the system when adding the molecule.
MinDistance (float | FloatKey) – Keep the minimal distance to other atoms of the system when adding the molecule.
NonAccessibleVolume (float | FloatKey) – Volume not available to GCMC, in cubic Angstroms. NonAccessibleVolume may be specified for the “Free” [VolumeOption] to reduce the accessible volume.
NumAttempts (int | IntKey) – Try inserting/moving the selected molecule up to the specified number of times or until all constraints are satisfied. If all attempts fail a message will be printed and the simulation will stop. If the MaxDistance-MinDistance interval is small this number may have to be large.
Pressure (float | FloatKey) – Pressure used to calculate the energy correction in the Mu-PT ensemble. Set it to zero for incompressible solid systems unless at very high pressures.
Restart (str | Path | StringKey) – Name of an RKF restart file. Upon restart, the information about the GCMC input parameters, the initial system (atomic coordinates, lattice, charge, etc.) and the MC molecules (both already inserted and to be inserted) are read from the restart file. The global GCMC input parameters and the MC Molecules can be modified from input. Any parameter not specified in the input will use its value from the restart file (i.e. not the default value). Molecules found in the restart file do not have to be present as named Systems in the input, however if there is a System present that matches the name of a molecule from restart then the System’s geometry will replace that found in the restart file. It is also possible to specify new Molecules in the input, which will be added to the pool of the MC molecules from restart.
Temperature (float | FloatKey) – Temperature of the simulation. Increase the temperature to improve the chance of accepting steps that result in a higher energy.
UseGCPreFactor (BoolType | BoolKey) – Use the GC pre-exponential factor for probability.
VolumeChangeMax (float | FloatKey) – Fractional value by which logarithm of the volume is allowed to change at each step. The new volume is then calculated as Vnew = exp(random(-1:1)*VolumeChangeMax)*Vold
VolumeOption (Literal["Free", "Total", "Accessible", "FreeAccessible"]) – Specifies the method to calculate the volume used to calculate the GC pre-exponential factor and the energy correction in the Mu-PT ensemble: Free: V = totalVolume - occupiedVolume - NonAccessibleVolume; Total: V = totalVolume; Accessible: V = AccessibleVolume; FreeAccessible: V = AccessibleVolume - occupiedVolume. The AccessibleVolume and NonAccessibleVolume are specified in the input, the occupiedVolume is calculated as a sum of atomic volumes.
Box (AMS._GCMC._Box) –
Boundaries of the insertion space, i.e. coordinates of the origin of an inserted molecule (coordinates of an atom of the inserted system may fall outside the box).
For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom (the system’s bounding box extended by the MaxDistance value by default).
Molecule (AMS._GCMC._Molecule) – This block defines the molecule (or atom) that can be inserted/moved/deleted with the MC method. The coordinates should form a reasonable structure. The MC code uses these coordinates during the insertion step by giving them a random rotation, followed by a random translation to generate a random position of the molecule inside the box. Currently, there is no check to make sure all atoms of the molecule stay inside the simulation box. The program does check that the MaxDistance/MinDistance conditions are satisfied.
Removables (str | Sequence[str] | FreeBlock) – The Removables can be used to specify a list of molecules that can be removed or moved during this GCMC calculation. Molecules are specified one per line in the format following format: MoleculeName atom1 atom2 … The MoleculeName must match a name specified in one of the [Molecule] blocks. The atom indices refer to the whole input System and the number of atoms must match that in the specified Molecule. A suitable Removables block is written to the standard output after each accepted MC move. If you do so then you should also replace the initial atomic coordinates with the ones found in the same file. If a [Restart] key is present then the Removables block is ignored.
SwapAtoms (AMS._GCMC._SwapAtoms) – Experimental: Occasionally swap the coordinates of a random pair of atoms from two regions.
- class _Box[source]¶
Boundaries of the insertion space, i.e. coordinates of the origin of an inserted molecule (coordinates of an atom of the inserted system may fall outside the box).
For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom (the system’s bounding box extended by the MaxDistance value by default).
- Variables:
Amax (float | FloatKey) – Coordinate of the upper bound along the first axis.
Amin (float | FloatKey) – Coordinate of the lower bound along the first axis.
Bmax (float | FloatKey) – Coordinate of the upper bound along the second axis.
Bmin (float | FloatKey) – Coordinate of the lower bound along the second axis.
Cmax (float | FloatKey) – Coordinate of the upper bound along the third axis.
Cmin (float | FloatKey) – Coordinate of the lower bound along the third axis.
- class _Molecule[source]¶
This block defines the molecule (or atom) that can be inserted/moved/deleted with the MC method. The coordinates should form a reasonable structure. The MC code uses these coordinates during the insertion step by giving them a random rotation, followed by a random translation to generate a random position of the molecule inside the box. Currently, there is no check to make sure all atoms of the molecule stay inside the simulation box. The program does check that the MaxDistance/MinDistance conditions are satisfied.
- Variables:
ChemicalPotential (float | FloatKey) –
Chemical potential of the molecule (or atom) reservoir.
- It is used when calculating the Boltzmann accept/reject criteria after a MC move is executed. This value can be derived from first principles using statistical mechanics, or equivalently, it can be determined from thermochemical tables available in literature sources.
For example, the proper chemical potential for a GCMC simulation in which single oxygen atoms are exchanged with a reservoir of O2 gas, should equal 1/2 the chemical potential of O2 at the temperature and pressure of the reservoir:
cmpot = Mu_O(T,P) = 1/2*Mu_O2(T,P) = 1/2 * [Mu_ref(T,P_ref) + kT*Log(P/Pref) - E_diss]
where the reference chemical potential [Mu_ref(T,P_ref)] is the experimentally determined chemical potential of O2 at T and Pref; kT*Log(P/Pref) is the pressure correction to the free energy, and E_diss is the dissociation energy of the O2 molecule.
NoAddRemove (BoolType | BoolKey) –
Set to True to tell the GCMC code to keep the number of molecules/atoms of this type fixed.
It will thus disable Insert/Delete moves on this type, meaning it can only do a displacement move, or volume change move (for an NPT ensemble).
SystemName (str | StringKey) – String ID of a named [System] to be inserted. The lattice specified with this System, if any, is ignored and the main system’s lattice is used instead.
- class _Removables[source]¶
- The Removables can be used to specify a list of molecules that can be removed or moved during this GCMC calculation. Molecules are specified one per line in the format following format:
MoleculeName atom1 atom2 … The MoleculeName must match a name specified in one of the [Molecule] blocks. The atom indices refer to the whole input System and the number of atoms must match that in the specified Molecule. A suitable Removables block is written to the standard output after each accepted MC move. If you do so then you should also replace the initial atomic coordinates with the ones found in the same file. If a [Restart] key is present then the Removables block is ignored.
- class _GeometryOptimization[source]¶
Configures details of the geometry optimization and transition state searches.
- Variables:
CalcPropertiesOnlyIfConverged (BoolType | BoolKey) – Compute the properties requested in the ‘Properties’ block, e.g. Frequencies or Phonons, only if the optimization (or transition state search) converged. If False, the properties will be computed even if the optimization did not converge.
CoordinateType (Literal["Auto", "Delocalized", "Cartesian"]) –
Select the type of coordinates in which to perform the optimization. ‘Auto’ automatically selects the most appropriate CoordinateType for a given Method.
If ‘Auto’ is selected, Delocalized coordinates will be used for the Quasi-Newton method, while Cartesian coordinates will be used for all other methods.
KeepIntermediateResults (BoolType | BoolKey) – Whether the full engine result files of all intermediate steps are stored on disk. By default only the last step is kept, and only if the geometry optimization converged. This can easily lead to huge amounts of data being stored on disk, but it can sometimes be convenient to closely monitor a tricky optimization, e.g. excited state optimizations going through conical intersections, etc. …
MaxIterations (int | IntKey) – The maximum number of geometry iterations allowed to converge to the desired structure.
MaxRestarts (int | IntKey) – If a geometry optimization of a system with no symmetry operators (or with explicitly disabled symmetry:
UseSymmetry False) and enabled PES point characterization converges to a transition state (or higher order saddle point), it can be restarted automatically after a small displacement along the imaginary vibrational mode. In case the restarted optimization again does not find a minimum, this can happen multiple times in succession. This keyword sets the maximum number of restarts. The default value is 0, so the automatic restarting is disabled by default.Method (Literal["Auto", "Quasi-Newton", "FIRE", "L-BFGS", "ConjugateGradients", "Dimer"]) –
Select the optimization algorithm employed for the geometry relaxation. Currently supported are:
the Hessian-based Quasi-Newton-type BFGS algorithm,
the fast inertial relaxation method (FIRE),
the limited-memory BFGS method,
and the conjugate gradients method. The default is to choose an appropriate method automatically based on the engine’s speed, the system size and the supported optimization options.
OptimizeLattice (BoolType | BoolKey) – Whether to also optimize the lattice for periodic structures. This is currently supported with the Quasi-Newton, FIRE, and L-BFGS optimizers.
PretendConverged (BoolType | BoolKey) – Normally a non-converged geometry optimization is considered an error. If this keyword is set to True, the optimizer will only produce a warning and still claim that the optimization is converged. (This is mostly useful for scripting applications, where one might want to consider non-converged optimizations still successful jobs.)
RestartDisplacement (float | FloatKey) – If a geometry optimization of a system with no symmetry operators (or with explicitly disabled symmetry:
UseSymmetry False) and enabled PES point characterization converges to a transition state (or higher order saddle point), it can be restarted automatically after a small displacement along the imaginary vibrational mode. This keywords sets the size of the displacement for the furthest moving atom.Convergence (AMS._GeometryOptimization._Convergence) – Convergence is monitored for up to 4 quantities: the energy change, the Cartesian gradients, the Cartesian step size, and for lattice optimizations the stress energy per atom. Convergence criteria can be specified separately for each of these items.
Dimer (AMS._GeometryOptimization._Dimer) – Options for the Dimer method for transition state search.
EngineAutomations (AMS._GeometryOptimization._EngineAutomations) – The optimizer can change some settings of the engine, based for instance on the error. The idea is to allow the engine to be a bit quicker at the start, and more accurate towards the end. Automations are always engine specific.
FIRE (AMS._GeometryOptimization._FIRE) – This block configures the details of the FIRE optimizer. The keywords name correspond the the symbols used in the article describing the method, see PRL 97, 170201 (2006).
HessianFree (AMS._GeometryOptimization._HessianFree) – Configures details of the Hessian-free (conjugate gradients or L-BFGS) geometry optimizer.
InitialHessian (AMS._GeometryOptimization._InitialHessian) – Options for initial model Hessian when optimizing systems with the Quasi-Newton method.
Quasi-Newton (AMS._GeometryOptimization._Quasi-Newton) – Configures details of the Quasi-Newton geometry optimizer.
- class _Convergence[source]¶
Convergence is monitored for up to 4 quantities: the energy change, the Cartesian gradients, the Cartesian step size, and for lattice optimizations the stress energy per atom. Convergence criteria can be specified separately for each of these items.
- Variables:
Energy (float | FloatKey) – The criterion for changes in the energy. The energy is considered converged when the change in energy is smaller than this threshold times the number of atoms.
Gradients (float | FloatKey) – Threshold for nuclear gradients.
Quality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent", "Custom"]) – A quick way to change convergence thresholds: ‘Good’ will reduce all thresholds by an order of magnitude from their default value. ‘VeryGood’ will tighten them by two orders of magnitude. ‘Basic’ and ‘VeryBasic’ will increase the thresholds by one or two orders of magnitude respectively.
Step (float | FloatKey) – The maximum Cartesian step allowed for a converged geometry.
StressEnergyPerAtom (float | FloatKey) – Threshold used when optimizing the lattice vectors. The stress is considered ‘converged’ when the maximum value of stress_tensor * cell_volume / number_of_atoms is smaller than this threshold (for 2D and 1D systems, the cell_volume is replaced by the cell_area and cell_length respectively).
- class _Dimer[source]¶
Options for the Dimer method for transition state search.
- Variables:
AngleThreshold (float | FloatKey) – The rotation is considered converged when the the rotation angle falls below the specified threshold.
DimerDelta (float | FloatKey) – Euclidian distance between the midpoint and the endpoint.
ExtrapolateForces (BoolType | BoolKey) – Set to false to call engine to calculate forces at the extrapolated rotation angle instead of extrapolating them.
LBFGSMaxVectors (int | IntKey) – Max number of vectors for the L-BFGS algorithm to save.
MaxRotationIterations (int | IntKey) – Maximum number of rotation iterations for a single translation step.
Region (str | StringKey) – Include only atoms of the specified region(s) in the rotations, which allows searching for a transition state involving selected atoms only.
RotationTrustRadius (float | FloatKey) – L-BFGS trust radius during rotation iterations.
TranslationTrustRadius (float | FloatKey) – L-BFGS trust radius during translation iterations.
- class _EngineAutomations[source]¶
The optimizer can change some settings of the engine, based for instance on the error. The idea is to allow the engine to be a bit quicker at the start, and more accurate towards the end. Automations are always engine specific.
- Variables:
Enabled (BoolType | BoolKey) – Whether or not automations are enabled at all.
Gradient (AMS._GeometryOptimization._EngineAutomations._Gradient) – A gradient-based automation.
Iteration (AMS._GeometryOptimization._EngineAutomations._Iteration) – Geometry step based automation.
- class _Gradient[source]¶
A gradient-based automation.
- Variables:
FinalValue (float | FloatKey) – This value will be used whenever the gradient is less than GradientLow
HighGradient (float | FloatKey) – Defines a large gradient. When the actual gradient is between GradientHigh and GradientLow a linear interpolation scheme is used for kT (on a log scale).
InitialValue (float | FloatKey) – This value will be used at the first geometry, and whenever the gradient is higher than GradientHigh
LowGradient (float | FloatKey) – Defines a small gradient, see GradientHigh
UseLogInterpolation (BoolType | BoolKey) – Whether to use interpolation on a log (y) scale or not
Variable (str | StringKey) – variable to be tweaked for the engine.
- class _Iteration[source]¶
Geometry step based automation.
- Variables:
FirstIteration (int | IntKey) – When the actual gradient is between the first and last iteration, a linear interpolation is used.
InitialValue (float | FloatKey) – This value will be used when the iteration number is smaller or equal to FirstIteration
LastIteration (int | IntKey) – Where the automation should reach the FinalValue
UseLogInterpolation (BoolType | BoolKey) – Whether to use interpolation on a log (y) scale or not
Variable (str | StringKey) – variable to be tweaked for the engine.
- class _FIRE[source]¶
This block configures the details of the FIRE optimizer. The keywords name correspond the the symbols used in the article describing the method, see PRL 97, 170201 (2006).
- Variables:
AllowOverallRotation (BoolType | BoolKey) – Whether or not the system is allowed to freely rotate during the optimization. This is relevant when optimizing structures in the presence of external fields.
AllowOverallTranslation (BoolType | BoolKey) – Whether or not the system is allowed to translate during the optimization. This is relevant when optimizing structures in the presence of external fields.
MapAtomsToUnitCell (BoolType | BoolKey) – Map the atoms to the central cell at each geometry step.
NMin (int | IntKey) – Number of steps after stopping before increasing the time step again.
atomMass (float | FloatKey) – Fictitious atomic mass used for all atoms. There is no reason to change this, as it just corresponds to using a different integration timestep.
dtMax (float | FloatKey) – Maximum time step used for the integration. For ReaxFF and APPLE&P, this value is reduced by 50%.
dtStart (float | FloatKey) – Initial time step for the integration.
fAlpha (float | FloatKey) – Reduction factor for the steering coefficient.
fDec (float | FloatKey) – Reduction factor for reducing the time step in case of uphill movement.
fInc (float | FloatKey) – Growth factor for the integration time step.
strainMass (float | FloatKey) – Fictitious relative mass of the lattice degrees of freedom. This controls the stiffness of the lattice degrees of freedom relative to the atomic degrees of freedom, with smaller values resulting in a more aggressive optimization of the lattice.
- class _HessianFree[source]¶
Configures details of the Hessian-free (conjugate gradients or L-BFGS) geometry optimizer.
- Variables:
- class _Step[source]¶
- Variables:
MaxCartesianStep (float | FloatKey) – Limit on a single Cartesian component of the step.
MinRadius (float | FloatKey) – Minimum value for the trust radius.
TrialStep (float | FloatKey) – Length of the finite-difference step when determining curvature. Should be smaller than the step convergence criterion.
TrustRadius (float | FloatKey) – Initial value of the trust radius.
- class _InitialHessian[source]¶
Options for initial model Hessian when optimizing systems with the Quasi-Newton method.
- Variables:
File (str | Path | StringKey) – KF file containing the initial Hessian (or the results dir. containing it). This can be used to load a Hessian calculated in a previously with the [Properties%Hessian] keyword.
Type (Literal["Auto", "UnitMatrix", "Swart", "FromFile", "Calculate", "CalculateWithFastEngine"]) – Select the type of initial Hessian. Auto: let the program pick an initial model Hessian. UnitMatrix: simplest initial model Hessian, just a unit matrix in the optimization coordinates. Swart: model Hessian from M. Swart. FromFile: load the Hessian from the results of a previous calculation (see InitialHessian%File). Calculate: compute the initial Hessian (this may be computationally expensive and it is mostly recommended for TransitionStateSearch calculations). CalculateWithFastEngine: compute the initial Hessian with a faster engine.
- class _Quasi_Newton[source]¶
Configures details of the Quasi-Newton geometry optimizer.
- Variables:
EnforceConstraints (BoolType | BoolKey) – Whether to enforce constraints at each steps exactly or add them to the optimization space as Lagrange multipliers.
MaxGDIISVectors (int | IntKey) – Sets the maximum number of GDIIS vectors. Setting this to a number >0 enables the GDIIS method.
UpdateTSVectorEveryStep (BoolType | BoolKey) – Whether to update the TS reaction coordinate at each step with the current eigenvector.
Step (AMS._GeometryOptimization._Quasi-Newton._Step) –
- class _IEEEExceptions[source]¶
Whether this works or not depends on the way the program is compiled (compiler and settings). Only useful for developers debugging some numerical issue.
- Variables:
All (BoolType | BoolKey) – Activates all IEEEExceptions known to ams, see list below. The corresponding environment variable is SCM_IEEEException_All.
DivideByZero (BoolType | BoolKey) – Stop program when a divide by zero exception occurs. The corresponding environment variable is SCM_IEEEException_DivideByZero.
Invalid (BoolType | BoolKey) – Stop program when an invalid exception occurs. This may be about sqrt(-1)., or 0/0, and generally leads to a NaN. The corresponding environment variable is SCM_IEEEException_Invalid.
Overflow (BoolType | BoolKey) – Stop program when an overflow exception occurs. The corresponding environment variable is SCM_IEEEException_Overflow
Print (BoolType | BoolKey) – Print feedback on activated IEEEExceptions in the logfile. The corresponding environment variable is SCM_IEEEException_Print.
- class _IRC[source]¶
Configures details of the Intrinsic Reaction Coordinate optimization.
- Variables:
CoordinateType (Literal["Cartesian", "Delocalized"]) – Select the type of coordinates in which to perform the optimization. Note that the Delocalized option should be considered experimental.
Direction (Literal["Both", "Forward", "Backward"]) – Select direction of the IRC path. The difference between the Forward and the Backward directions is determined by the sign of the largest component of the vibrational normal mode corresponding to the reaction coordinate at the transition state geometry. The Forward path correspond to the positive sign of the component. If Both is selected then first the Forward path is computed followed by the Backward one.
KeepConvergedResults (BoolType | BoolKey) – Keep the binary RKF result file for every converged IRC point. These files may contain more information than the main ams.rkf result file.
MaxIRCSteps (int | IntKey) – Soft limit on the number of IRC points to compute in each direction. After the specified number of IRC steps the program will switch to energy minimization and complete the path. This option should be used when you are interested only in the reaction path area near the transition state. Note that even if the soft limit has been hit and the calculation has completed, the IRC can still be restarted with a ‘RedoBackward’ or ‘RedoForward’ option.
MaxIterations (int | IntKey) – The maximum number of geometry iterations allowed to converge the inner IRC loop. If optimization does not converge within the specified number of steps, the calculation is aborted.
MaxPoints (int | IntKey) – Hard limit on the number of IRC points to compute in each direction. After the specified number of IRC steps the program will stop with the current direction and switch to the next one. If both ‘MaxPoints’ and ‘MaxIRCSteps’ are set to the same value then ‘MaxPoints’ takes precedence, therefore this option should be used to set a limit on the number of IRC steps if you intend to use the results later for a restart.
MinEnergyProfile (BoolType | BoolKey) – Calculate minimum energy profile (i.e. no mass-weighting) instead of the IRC.
MinPathLength (float | FloatKey) – Minimum length of the path required before switching to energy minimization. Use this to overcome a small kink or a shoulder on the path.
Step (float | FloatKey) – IRC step size in mass-weighted coordinates, sqrt(amu)*bohr. One may have to increase this value when heavy atoms are involved in the reaction, or decrease it if the reactant or products are very close to the transition state.
Convergence (AMS._IRC._Convergence) – Convergence at each given point is monitored for two items: the Cartesian gradient and the calculated step size. Convergence criteria can be specified separately for each of these items. The same criteria are used both in the inner IRC loop and when performing energy minimization at the path ends.
InitialHessian (AMS._IRC._InitialHessian) – Options for initial Hessian at the transition state. The first eigenvalue of the initial Hessian defines direction of the first forward or backward step. This block is ignored when restarting from a previous IRC calculation because the initial Hessian found in the restart file is used.
Restart (AMS._IRC._Restart) – Restart options. Upon restart, the information about the IRC input parameters and the initial system (atomic coordinates, lattice, charge, etc.) is read from the restart file. The IRC input parameters can be modified from input. Except for ‘MaxPoints’ and ‘Direction’ all parameters not specified in the input will use their values from the restart file. The ‘MaxPoints’ and ‘Direction’ will be reset to their respective default values if not specified in the input. By default, the IRC calculation will continue from the point where it left off. However, the ‘RedoForward’ and/or ‘RedoBackward’ option can be used to enforce recalculation of a part of the reaction path, for example, using a different ‘Step’ value.
- class _Convergence[source]¶
Convergence at each given point is monitored for two items: the Cartesian gradient and the calculated step size. Convergence criteria can be specified separately for each of these items. The same criteria are used both in the inner IRC loop and when performing energy minimization at the path ends.
- class _InitialHessian[source]¶
Options for initial Hessian at the transition state. The first eigenvalue of the initial Hessian defines direction of the first forward or backward step. This block is ignored when restarting from a previous IRC calculation because the initial Hessian found in the restart file is used.
- Variables:
File (str | Path | StringKey) – If ‘Type’ is set to ‘FromFile’ then in this key you should specify the RKF file containing the initial Hessian (or the ams results dir. containing it). This can be used to load a Hessian calculated previously with the ‘Properties%Hessian’ keyword. If you want to also use this file for the initial geometry then also specify it in a ‘LoadSystem’ block.
Type (Literal["Calculate", "FromFile"]) – Calculate the exact Hessian for the input geometry or load it from the results of a previous calculation.
- class _Restart[source]¶
Restart options. Upon restart, the information about the IRC input parameters and the initial system (atomic coordinates, lattice, charge, etc.) is read from the restart file. The IRC input parameters can be modified from input. Except for ‘MaxPoints’ and ‘Direction’ all parameters not specified in the input will use their values from the restart file. The ‘MaxPoints’ and ‘Direction’ will be reset to their respective default values if not specified in the input. By default, the IRC calculation will continue from the point where it left off. However, the ‘RedoForward’ and/or ‘RedoBackward’ option can be used to enforce recalculation of a part of the reaction path, for example, using a different ‘Step’ value.
- Variables:
File (str | Path | StringKey) – Name of an RKF restart file generated by a previous IRC calculation. Do not use this key to provide an RKF file generated by a TransitionStateSearch or a SinglePoint calculation, use the ‘LoadSystem’ block instead.
RedoBackward (int | IntKey) – IRC step number to start recalculating the backward path from. By default, if the backward path has not been completed then start after the last completed step. If the backward path has been completed and the ‘RedoBackward’ is omitted then no point on the backward path will be recomputed.
RedoForward (int | IntKey) – IRC step number to start recalculating the forward path from. By default, if the forward path has not been completed then start after the last completed step. If the forward path has been completed and the ‘RedoForward’ is omitted then no point on the forward path will be recomputed.
- class _Idle[source]¶
Configures details of the idle task, which does nothing for a specified amount of time.
- class _LoadSystem[source]¶
Block that controls reading the chemical system from a KF file instead of the [System] block.
- class _Log[source]¶
Configures the debugging loggers. Syntax: ‘Level LoggerName’. Possible Levels: All, Debug, Info, Warning, Error, Fatal.
- class _MolecularDynamics[source]¶
Configures molecular dynamics (with the velocity-Verlet algorithm) with and without thermostats. This block allows to specify the details of the molecular dynamics calculation.
- Variables:
CalcPressure (BoolType | BoolKey) –
Calculate the pressure in periodic systems.
This may be computationally expensive for some engines that require numerical differentiation.
Some other engines can calculate the pressure for negligible additional cost and will always do so, even if this option is disabled.
CopyRestartTrajectory (BoolType | BoolKey) – If the keyword Restart is present, the content of the restartfile is copied to the ams.rkf file.
NSteps (int | IntKey) – The number of steps to be taken in the MD simulation.
Restart (str | Path | StringKey) – The path to the ams.rkf file from which to restart the simulation.
AddMolecules (AMS._MolecularDynamics._AddMolecules) –
This block controls adding molecules to the system (a.k.a. the Molecule Gun). Multiple occurrences of this block are possible.
By default, molecules are added at random positions in the simulation box with velocity matching the current system temperature. The initial position can be modified using one of the following keywords: Coords, CoordsBox, FractionalCoords, FractionalCoordsBox. The Coords and FractionalCoords keys can optionally be accompanied by CoordsSigma or FractionalCoordsSigma, respectively.
ApplyForce (AMS._MolecularDynamics._ApplyForce) – The ApplyForce keyword can be used to apply an arbitrary constant force to a certain (subgroups of) atoms in the system
ApplyVelocity (AMS._MolecularDynamics._ApplyVelocity) – The ApplyVelocity keyword can be used to move an arbitrary group of atoms in the system with a constant net velocity
Barostat (AMS._MolecularDynamics._Barostat) – This block allows to specify the use of a barostat during the simulation.
BinLog (AMS._MolecularDynamics._BinLog) – This block controls writing the BinLog section in ams.rkf, which contains the selected MD state scalars and tensors from every MD step. No per-atom data is written. If you need the per-atom data then you can set the sampling frequency to 1 and get the required data from the MDHistory section. The tensors are written per component, that is, the pressure tensor is written as six variables: PressureTensor_xx, PressureTensor_yy, etc.. To reduce the file size, all data is written in blocks.
BondBoost (AMS._MolecularDynamics._BondBoost) – Forced reaction (bond boost) definitions. Multiple BondBoost blocks may be specified, which will be treated independently.
CRESTMTD (AMS._MolecularDynamics._CRESTMTD) – Input for CREST metadynamics simulation.
CVHD (AMS._MolecularDynamics._CVHD) – Input for the Collective Variable-driven HyperDynamics (CVHD).
CheckTemperature (AMS._MolecularDynamics._CheckTemperature) – Check at every time step if the temperature has exceeded a threshold. If it has, it is assumed the system exploded, and the simulation will stop.
Checkpoint (AMS._MolecularDynamics._Checkpoint) – Sets the frequency for storing the entire MD state necessary for restarting the calculation.
CosineShear (AMS._MolecularDynamics._CosineShear) – Apply an external acceleration to all atoms of a fluid using a periodic (cosine) function along a selected coordinate axis. This induces a periodic shear flow profile which can be used to determine the viscosity.
Deformation (AMS._MolecularDynamics._Deformation) – Deform the periodic lattice of the system during the simulation.
Gravity (AMS._MolecularDynamics._Gravity) – Apply a constant acceleration in -z.
HeatExchange (AMS._MolecularDynamics._HeatExchange) – Input for the heat-exchange non-equilibrium MD (T-NEMD).
InitialVelocities (AMS._MolecularDynamics._InitialVelocities) – Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
MovingRestraints (AMS._MolecularDynamics._MovingRestraints) – Define a set of moving restraints.
PRD (AMS._MolecularDynamics._PRD) – This block is used for Parallel Replica Dynamics simulations.
Plumed (AMS._MolecularDynamics._Plumed) – Input for PLUMED (version 2.5.0). The parallel option is still experimental.
Preserve (AMS._MolecularDynamics._Preserve) – Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.
Print (AMS._MolecularDynamics._Print) – This block controls the printing of additional information to stdout.
ReactionBoost (AMS._MolecularDynamics._ReactionBoost) –
Define a series of transitions between different states of the system.
Each transition is defined by a TargetSystem and by a set of restraints that force the transition.
Reactor (AMS._MolecularDynamics._Reactor) – Define one phase of the nanoreactor. A reactor is a region of space surrounded by an elastic wall. Atoms inside the region are not affected. Atoms outside it will be pushed back with force depending on the [ForceConstant] and the [MassScaled] flag.
ReflectiveWall (AMS._MolecularDynamics._ReflectiveWall) – Apply a reflective wall in space
Remap (AMS._MolecularDynamics._Remap) – Control periodic remapping (backtranslation) of atoms into the PBC box.
RemoveMolecules (AMS._MolecularDynamics._RemoveMolecules) – This block controls removal of molecules from the system. Multiple occurrences of this block are possible.
ReplicaExchange (AMS._MolecularDynamics._ReplicaExchange) – This block is used for (temperature) Replica Exchange MD (Parallel Tempering) simulations.
Shake (AMS._MolecularDynamics._Shake) – Parameters of the Shake/Rattle algorithm.
Thermostat (AMS._MolecularDynamics._Thermostat) – This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’s behavior.
Trajectory (AMS._MolecularDynamics._Trajectory) – Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
fbMC (AMS._MolecularDynamics._fbMC) – This block sets up force bias Monte Carlo interleaved with the molecular dynamics simulation.
- class _AddMolecules[source]¶
This block controls adding molecules to the system (a.k.a. the Molecule Gun). Multiple occurrences of this block are possible.
By default, molecules are added at random positions in the simulation box with velocity matching the current system temperature. The initial position can be modified using one of the following keywords: Coords, CoordsBox, FractionalCoords, FractionalCoordsBox. The Coords and FractionalCoords keys can optionally be accompanied by CoordsSigma or FractionalCoordsSigma, respectively.
- Variables:
AtomTemperature (float | FloatKey) – Add random velocity corresponding to the specified temperature to individual atoms of the molecule. This only affects rotational and internal degrees of freedom, not the net translational velocity of the inserted molecule as set by the other options.
ContactDistance (float | FloatKey) – Translate the bullet along the velocity vector until it comes within ContactDistance of any other atom.
Coords (Iterable[float] | FloatListKey) –
Place molecules at or around the specified Cartesian coordinates.
This setting takes precedence over other ways to specify initial coordinates of the molecule: [CoordsBox], [FractionalCoords], and [FractionalCoordsBox].
CoordsBox (Iterable[float] | FloatListKey) –
Place molecules at random locations inside the specified box in Cartesian coordinates.
Coordinates of the box corners are specified as: Xmin, Xmax, Ymin, Ymax, Zmin, Zmax. This setting is ignored if Coords is used.
In AMSinput, if this field is not empty it will be used instead of the default Coords.
CoordsSigma (Iterable[float] | FloatListKey) – Sigma values (one per Cartesian axis) for a Gauss distribution of the initial coordinates. Can only be used together with Coords.
DeviationAngle (float | FloatKey) – Randomly tilt the shooting direction up to this angle away from the VelocityDirection vector.
Energy (float | FloatKey) – Initial kinetic energy of the molecule in the shooting direction.
EnergySigma (float | FloatKey) – Sigma value for the Gauss distribution of the initial kinetic energy around the specified value. Should only be used together with Energy.
FractionalCoords (Iterable[float] | FloatListKey) – Place molecules at or around the specified fractional coordinates in the main system’s lattice. For non-periodic dimensions a Cartesian value in Angstrom is expected. This setting is ignored if [Coords] or [CoordsBox] is used.
FractionalCoordsBox (Iterable[float] | FloatListKey) –
Place molecules at random locations inside the box specified as fractional coordinates in the main system’s lattice.
Coordinates of the box corners are specified as: Xmin, Xmax, Ymin, Ymax, Zmin, Zmax.
For non-periodic dimensions the Cartesian value in Angstrom is expected.
This setting is ignored if [Coords], [CoordsBox], or [FractionalCoords] is used.
FractionalCoordsSigma (Iterable[float] | FloatListKey) – Sigma values (one per axis) for a Gauss distribution of the initial coordinates. For non-periodic dimensions the Cartesian value in Angstrom is expected. Can only be used together with FractionalCoords.
A molecule is added every [Frequency] steps after the StartStep.
There is never a molecule added at step 0.
MinDistance (float | FloatKey) – Keep the minimal distance to other atoms of the system when adding the molecule.
MoleFraction (float | FloatKey) –
Defines a mixture to be deposited using one AddMolecules block per component.
AMS will randomly alternate between any guns that have MoleFraction set. These need to all have the same settings for StartStep, StopStep and Frequency. Any additional AddMolecules blocks without MoleFraction will remain completely independent.
NumAttempts (int | IntKey) – Try adding the molecule up to the specified number of times or until the MinDistance constraint is satisfied. If all attempts fail a message will be printed and the simulation will continue normally.
Rotate (BoolType | BoolKey) – Rotate the molecule randomly before adding it to the system.
Step number when the first molecule should be added. After that, molecules are added every Frequency steps.
For example, ff StartStep=99 and Frequency=100 then a molecule will be added at steps 99, 199, 299, etc…
No molecule will be added at step 0, so if StartStep=0 the first molecule is added at the step number equal to [Frequency].
StopStep (int | IntKey) – Do not add this molecule after the specified step.
String ID of the [System] that will be added with this ‘gun’.
The lattice specified with this System is ignored and the main system’s lattice is used instead.
AMSinput adds the system at the coordinates of the System (thus setting Coords to the center of the System).
Temperature (float | FloatKey) – Initial energy of the molecule in the shooting direction will correspond to the given temperature.
TemperatureSigma (float | FloatKey) – Sigma value for the Gauss distribution of the initial temperature the specified value. Should only be used together with Temperature.
Velocity (float | FloatKey) – Initial velocity of the molecule in the shooting direction.
VelocityDirection (Iterable[float] | FloatListKey) –
Velocity direction vector for aimed shooting. It will be random if not specified.
In AMSinput add one or two atoms (which may be dummies).
One atom: use vector from center of the system to add to that atom.
Two atoms: use vector from the first to the second atom.
VelocitySigma (float | FloatKey) – Sigma value for the Gauss distribution of the initial velocity around the specified value. Should only be used together with Velocity.
- class _ApplyForce[source]¶
The ApplyForce keyword can be used to apply an arbitrary constant force to a certain (subgroups of) atoms in the system
- Variables:
CalculateViscosity (BoolType | BoolKey) – Calculates Viscosity property yes/no. If yes is chosen, the global viscosity of the system is calculated and written into the RKF-file. The formula used for the viscosity calculation is eta = - Pxz / (dVx/dz)
CalculateViscosityBins (int | IntKey) – Amount of bins used to determine (dVx/dz)
CalculateViscosityEnd (int | IntKey) – end index to select region in space to calculate (dVx/dz)
CalculateViscosityStart (int | IntKey) – Start index to select region in space to calculate (dVx/dz)
Force (Iterable[float] | FloatListKey) – Defines the constant force vector
PerAtom (BoolType | BoolKey) – If enabled, the Force vector is applied separately to every atom in the selected Region, so that the total net force on the Region equals the value of Force times the number of atoms in Region. This was the behavior of ApplyForce in AMS2022. By default, with PerAtom disabled, the Force vector defines the total net force on the Region, so the force applied to each atom equals the value of Force divided by the number of atoms in Region.
Region (str | StringKey) – Apply the constant force to all atoms in this region.
- class _ApplyVelocity[source]¶
The ApplyVelocity keyword can be used to move an arbitrary group of atoms in the system with a constant net velocity
- Variables:
CalculateViscosity (BoolType | BoolKey) – Calculates Viscosity property yes/no. If yes is chosen, the global viscosity of the system is calculated and written into the RKF-file. The formula used for the viscosity calculation is eta = - Pxz / (dVx/dz)
CalculateViscosityBins (int | IntKey) – Amount of bins used to determine (dVx/dz)
CalculateViscosityEnd (int | IntKey) – end index to select region in space to calculate (dVx/dz)
CalculateViscosityStart (int | IntKey) – Start index to select region in space to calculate (dVx/dz)
Components (Literal["X", "Y", "Z", "XY", "YZ", "XZ", "XYZ"]) – Select which components of the Velocity vector are used to set the corresponding components of the net velocity of the specified set of atoms. Any other components of Velocity are ignored and the motion of the selected atoms in those directions is unaffected by ApplyVelocity.
Region (str | StringKey) – Applies the defined velocity to all atoms in this region.
Velocity (Iterable[float] | FloatListKey) – The constant velocity that will be applied to the specified atoms.
- class _Barostat[source]¶
This block allows to specify the use of a barostat during the simulation.
- Variables:
BulkModulus (float | FloatKey) –
An estimate of the bulk modulus (inverse compressibility) of the system for the Berendsen barostat.
This is only used to make Tau correspond to the true observed relaxation time constant. Values are commonly on the order of 10-100 GPa (1e10 to 1e11) for solids and 1 GPa (1e9) for liquids (2.2e9 for water). Use 1e9 to match the behavior of standalone ReaxFF.
ConstantVolume (BoolType | BoolKey) –
Keep the volume constant while allowing the box shape to change.
This is currently supported only by the MTK barostat.
Duration (Iterable[int] | IntListKey) – Specifies how many steps should a transition from a particular pressure to the next one in sequence take.
Equal (Literal["None", "XYZ", "XY", "YZ", "XZ"]) – Enforce equal scaling of the selected set of dimensions. They will be barostatted as one dimension according to the average pressure over the components.
Pressure (Iterable[float] | FloatListKey) –
Specifies the target pressure.
You can specify multiple pressures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one p to the next p (using a linear ramp).
Scale (Literal["XYZ", "Shape", "X", "Y", "Z", "XY", "YZ", "XZ"]) – Dimensions that should be scaled by the barostat to maintain pressure. Selecting Shape means that all three dimensions and also all the cell angles are allowed to change.
Tau (float | FloatKey) – Specifies the time constant of the barostat.
Type (Literal["None", "Berendsen", "MTK"]) – Selects the type of the barostat.
- class _BinLog[source]¶
This block controls writing the BinLog section in ams.rkf, which contains the selected MD state scalars and tensors from every MD step. No per-atom data is written. If you need the per-atom data then you can set the sampling frequency to 1 and get the required data from the MDHistory section. The tensors are written per component, that is, the pressure tensor is written as six variables: PressureTensor_xx, PressureTensor_yy, etc.. To reduce the file size, all data is written in blocks.
- Variables:
BiasEnergy (BoolType | BoolKey) – Write the CVHD bias energy at every time step.
BoostFactor (BoolType | BoolKey) – Write the CVHD boost factor at every time step.
ConservedEnergy (BoolType | BoolKey) – Write the conserved energy value at every time step.
Density (BoolType | BoolKey) – Write the density at every time step.
DipoleMoment (BoolType | BoolKey) – Write the dipole moment at every time step. Each component of the tensor is written in its own variable.
Hypertime (BoolType | BoolKey) – Write the CVHD hypertime at every time step.
KineticEnergy (BoolType | BoolKey) – Write the kinetic energy value at every time step.
MaxBiasEnergy (BoolType | BoolKey) – Write the max CVHD bias energy at every time step.
MaxBoostFactor (BoolType | BoolKey) – Write the max CVHD boost factor at every time step.
PotentialEnergy (BoolType | BoolKey) – Write the potential energy value at every time step.
Pressure (BoolType | BoolKey) – Write the pressure at every time step.
PressureTensor (BoolType | BoolKey) – Write the pressure tensor in Voigt notation at every time step. Each component of the tensor is written in its own variable.
Step (BoolType | BoolKey) – Write the step index during the simulation at every time step.
Temperature (BoolType | BoolKey) – Write the temperature at every time step.
Time (BoolType | BoolKey) – Write the simulation time (fs) at every time step.
TotalEnergy (BoolType | BoolKey) – Write the total energy value at every time step.
Volume (BoolType | BoolKey) – Write the simulation cell volume, area or length, depending on the system periodicity, at every time step.
- class _BondBoost[source]¶
Forced reaction (bond boost) definitions. Multiple BondBoost blocks may be specified, which will be treated independently.
- Variables:
AddBond (str | StringKey) – [Reserved] Add a bond to the system or change its order. Specify two atom indices followed by the bond’s order. The indices indicate positions of the atoms in the AtomNames key. Currently no engine will honor bond changes caused by this key.
DistanceRestraint (str | StringKey) –
Specify two atom indices followed by the target distance in Angstrom, the first parameter and, optionally, the profile type and the second parameter.
For periodic systems, restraints follow the minimum image convention.
Each atom index indicates a position of the corresponding atom in the AtomNames key. Currently recognized restraint profile types: Harmonic (default), Hyperbolic, Erf, GaussianWell. The profile name can optionally be prefixed by “OneSided-”, thus making this particular restraint one-sided. A one-sided restraint will only push or pull the distance towards its target value depending on the sign of the difference between the initial and the target distance. For example, if the initial distance is larger than the target one then the restraint will only push the value down. This is especially useful with moving restraints because then the restraint will effectively disappear as soon as the system crosses a barrier along the reaction path. By default, the restraints are two-sided, which means they will try to keep the distance between the two specified atoms near the (possibly moving) target value. For moving restraints, this means that after crossing a reaction barrier the system will slide slowly towards products held back by the restraints.
The first parameter is the force constant for the Harmonic, Hyperbolic, and Erf profiles, or well depth for GaussianWell. The second parameter is the asymptotic force value F(Inf) for Hyperbolic and Erf profiles, or the factor before x^2 in the exponent for GaussianWell.
Note: the GaussianWell restraint should be used with the Moving flag.
Moving (BoolType | BoolKey) –
Move the restraints created with this BondBoost. The restraint value will start at the current coordinate’s value and will move towards the optimum during the restraint’s lifetime. The increment is calculated from the initial deviation and the [NSteps] parameter.
This feature should be used with the GaussianWell restraint types.
NSteps (int | IntKey) – Number of steps the restraints will remain active until removed. Atoms participating in one reaction are not available for the given number of steps.
NumInstances (int | IntKey) – Number of reactions of this type taking place simultaneously.
RemoveBond (str | StringKey) – [Reserved] Remove a bond from the system. Specify two atom indices. The indices indicate positions of the atoms in the AtomNames key. Currently no engine will honor bond changes caused by this key.
SetAtomName (str | StringKey) – Change the specified atom’s name. Specify atom index followed by the new name. The index indicates position of the atom in the AtomNames key. Note: this action will change the atom name only and not other properties (element name, mass, etc.). This may be useful to change atom names to affect future chain detections. The atom name length is limited to 32 characters.
Units (Literal["Default", "MD"]) – Change energy, force and force constant units in the DistanceRestraint key from the default (atomic units) to those often used in the MD community (based on kcal/mol and Angstrom). Units for the optimum distances are not affected.
Chain (AMS._MolecularDynamics._BondBoost._Chain) – Specifications of a chain of atoms. When a chain is detected the distance restraints will be activated. No other chain of this type will be detected while any restraints for this chain is active.
- class _Chain[source]¶
Specifications of a chain of atoms. When a chain is detected the distance restraints will be activated. No other chain of this type will be detected while any restraints for this chain is active.
- Variables:
AtomNames (str | StringKey) – Atom names specifying the chain. An atom name can optionally be followed by ‘@’ and a region name, in this case only atoms of this type from the given region will be matched. A leading ‘@’ followed by a number indicates that this position in the chain must be occupied by the atom found earlier at the specified position in the chain. For example “O H N C @1” indicates that the last atom in the chain of the five atoms must be the first oxygen, thus defining a 4-membered ring. This is the only way to define a ring because implicit rings will not be detected. For example, “O H N C O” does not include rings.
MaxDistances (Iterable[float] | FloatListKey) – Maximum distances for each pair of atoms in the chain. The number of distances must be one less than the number of AtomNames.
MinDistances (Iterable[float] | FloatListKey) – Minimum distances for each pair of atoms in the chain. The number of distances must be one less than the number of AtomNames.
- class _CRESTMTD[source]¶
Input for CREST metadynamics simulation.
- Variables:
AddEnergy (BoolType | BoolKey) – Add the bias energy to the potential energy (to match the gradients)
Height (float | FloatKey) – The height of the Gaussians added
NGaussiansMax (int | IntKey) – Maximum number of Gaussians stored
Region (str | StringKey) – Restrict the range of atoms for RMSD calculation to the specified region.
RestartFile (str | Path | StringKey) – Filename for file from which to read data on Gaussians placed previously.
Width (float | FloatKey) – The width of the Gaussians added in terms of the RMSD
GaussianScaling (AMS._MolecularDynamics._CRESTMTD._GaussianScaling) – Options for gradual introduction of the Gaussians
- class _CVHD[source]¶
Input for the Collective Variable-driven HyperDynamics (CVHD).
- Variables:
Frequency (int | IntKey) – Frequency of adding a new bias peak, in steps. New bias is deposited every [Frequency] steps after [StartStep] if the following conditions are satisfied: the current CV value is less than 0.9 (to avoid creating barriers at the transition state), the step number is greater than or equal to [StartStep], and the step number is less than or equal to [StopStep].
MaxEvents (int | IntKey) – Max number of events to allow during dynamics. When this number is reached no new bias will be added for this input block.
StartStep (int | IntKey) – If this key is specified, the first bias will be deposited at this step. Otherwise, the first bias peak is added at the step number equal to the Frequency parameter. The bias is never deposited at step 0.
StopStep (int | IntKey) – No bias will be deposited after the specified step. The already deposited bias will continue to be applied until the reaction event occurs. After that no new CVHD will be started. By default, the CVHD runs for the whole duration of the MD calculation.
WaitSteps (int | IntKey) – If the CV value becomes equal to 1 and remains at this value for this many steps then the reaction event is considered having taken place. After this, the collective variable will be reset and the bias will be removed.
Bias (AMS._MolecularDynamics._CVHD._Bias) – The bias is built from a series of Gaussian peaks deposited on the collective variable axis every [Frequency] steps during MD. Each peak is characterized by its (possibly damped) height and the RMS width (standard deviation).
ColVarBB (AMS._MolecularDynamics._CVHD._ColVarBB) – Description of a bond-breaking collective variable (CV) as described in [Bal & Neyts, JCTC, 11 (2015)]. A collective variable may consist of multiple ColVar blocks.
ColVarBM (AMS._MolecularDynamics._CVHD._ColVarBM) – Description of a bond-making collective variable (CV). A collective variable may consist of multiple ColVar blocks.
- class _Bias[source]¶
The bias is built from a series of Gaussian peaks deposited on the collective variable axis every [Frequency] steps during MD. Each peak is characterized by its (possibly damped) height and the RMS width (standard deviation).
- Variables:
DampingTemp (float | FloatKey) – During well-tempered hyperdynamics the height of the added bias is scaled down with an exp(-E/kT) factor [PhysRevLett 100, 020603 (2008)], where E is the current value of the bias at the given CV value and T is the damping temperature DampingTemp. If DampingTemp is zero then no damping is applied.
Delta (float | FloatKey) – Standard deviation parameter of the Gaussian bias peak.
Height (float | FloatKey) – Height of the Gaussian bias peak.
- class _ColVarBB[source]¶
Description of a bond-breaking collective variable (CV) as described in [Bal & Neyts, JCTC, 11 (2015)]. A collective variable may consist of multiple ColVar blocks.
- Variables:
cutoff (float | FloatKey) – Bond order cutoff. Bonds with BO below this value are ignored when creating the initial bond list for the CV. The bond list does not change during lifetime of the variable even if some bond orders drop below the cutoff.
p (int | IntKey) – Exponent value p used to calculate the p-norm for this CV.
rmax (float | FloatKey) – Max bond distance parameter Rmax used for calculating the CV. It should be close to the transition-state distance for the corresponding bond.
rmin (float | FloatKey) – Min bond distance parameter Rmin used for calculating the CV. It should be close to equilibrium distance for the corresponding bond.
at1 (AMS._MolecularDynamics._CVHD._ColVarBB._at1) – Specifies the first bonded atom in the collective variable.
at2 (AMS._MolecularDynamics._CVHD._ColVarBB._at2) – Specifies the second bonded atom in the collective variable.
- class _at1[source]¶
Specifies the first bonded atom in the collective variable.
- Variables:
region (str | StringKey) – Restrict the selection of bonded atoms to a specific region. If this is not set, atoms anywhere in the system will be selected.
symbol (str | StringKey) – Atom type name of the first atom of the bond. The name must be as it appears in the System block. That is, if the atom name contains an extension (e.g C.1) then the full name including the extension must be used here.
- class _at2[source]¶
Specifies the second bonded atom in the collective variable.
- Variables:
region (str | StringKey) – Restrict the selection of bonded atoms to a specific region. If this is not set, atoms anywhere in the system will be selected.
symbol (str | StringKey) – Atom type name of the second atom of the bond. The value is allowed to be the same as [at1], in which case bonds between atoms of the same type will be included.
- class _ColVarBM[source]¶
Description of a bond-making collective variable (CV). A collective variable may consist of multiple ColVar blocks.
- Variables:
cutoff (float | FloatKey) – Bond order cutoff. Bonds with BO above this value are ignored when creating the initial atom-pair list for the CV. The list does not change during lifetime of the variable even if some bond orders rise above the cutoff.
p (int | IntKey) – Exponent value p used to calculate the p-norm for this CV.
rmax (float | FloatKey) – Max bond distance parameter Rmax used for calculating the CV. It should be much larger than the corresponding Rmin.
rmin (float | FloatKey) – Min bond distance parameter Rmin used for calculating the CV. It should be close to the transition-state distance for the corresponding bond.
at1 (AMS._MolecularDynamics._CVHD._ColVarBM._at1) – Specifies selection criteria for the first atom of a pair in the collective variable.
at2 (AMS._MolecularDynamics._CVHD._ColVarBM._at2) – Specifies selection criteria for the second atom of a pair in the collective variable.
- class _at1[source]¶
Specifies selection criteria for the first atom of a pair in the collective variable.
- Variables:
region (str | StringKey) – Restrict the selection to a specific region. If this is not set, atoms anywhere in the system will be selected.
symbol (str | StringKey) – Atom type name of the first atom of the pair. The name must be as it appears in the System block. That is, if the atom name contains an extension (e.g C.1) then the full name including the extension must be used here.
- class _at2[source]¶
Specifies selection criteria for the second atom of a pair in the collective variable.
- Variables:
region (str | StringKey) – Restrict the selection to a specific region. If this is not set, atoms anywhere in the system will be selected.
symbol (str | StringKey) – Atom type name of the second atom of the pair. The value is allowed to be the same as [at1], in which case pairs of atoms of the same type will be included.
- class _CheckTemperature[source]¶
Check at every time step if the temperature has exceeded a threshold. If it has, it is assumed the system exploded, and the simulation will stop.
- class _Checkpoint[source]¶
Sets the frequency for storing the entire MD state necessary for restarting the calculation.
- Variables:
Frequency (int | IntKey) – Write the MD state to the Molecule and MDResults sections on ams.rkf once every N steps. Setting this to zero disables checkpointing during the simulation, but one checkpoint at the very end of the simulation will always be written.
WriteProperties (BoolType | BoolKey) –
Honor top-level Properties input block when writing engine results files.
DEPRECATED: This input option will be removed in AMS2026 and will be considered always enabled. If you rely on it being disabled, please contact support@scm.com.
- class _CosineShear[source]¶
Apply an external acceleration to all atoms of a fluid using a periodic (cosine) function along a selected coordinate axis. This induces a periodic shear flow profile which can be used to determine the viscosity.
- Variables:
Acceleration (float | FloatKey) – Amplitude of the applied cosine shear acceleration profile. The default value should be a rough first guess for water and it needs to be adjusted by experimentation for other systems.
Enabled (BoolType | BoolKey) – Apply a cosine shear acceleration profile for a NEMD calculation of viscosity.
FlowDirection (Iterable[float] | FloatListKey) – The direction in which to apply the shear acceleration, in Cartesian coordinates. The magnitude of this vector is ignored (AMS will normalize it internally). FlowDirection has to be perpendicular to ProfileAxis.
ProfileAxis (Literal["X", "Y", "Z"]) – The Cartesian coordinate axis along which the cosine wave runs
- class _Deformation[source]¶
Deform the periodic lattice of the system during the simulation.
- Variables:
LengthRate (Iterable[float] | FloatListKey) – Relative rate of change of each lattice vector per step.
LengthVelocity (Iterable[float] | FloatListKey) – Change the length of each lattice vector with this velocity. With Type=Exponential, LengthVelocity is divided by the current lattice vector lengths on StartStep to determine a LengthRate, which is then applied on all subsequent steps. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).
Period (float | FloatKey) – Period of oscillation for Type Sine and Cosine.
ScaleAtoms (BoolType | BoolKey) – Scale the atomic positions together with the lattice vectors. Disable this to deform only the lattice, keeping the coordinates of atoms unchanged.
StartStep (int | IntKey) – First step at which the deformation will be applied.
StopStep (int | IntKey) – Last step at which the deformation will be applied. If unset or zero, nSteps will be used instead.
TargetDensity (float | FloatKey) –
Target density of the system to be achieved by StopStep by isotropically rescaling the lattice.
This can only be used for 3D-periodic systems. Note that the selected Type determines how the lengths of the lattice vectors will evolve (linearly or as a sine/cosine), the evolution of the volume or density is thus necessarily non-linear.
TargetLength (Iterable[float] | FloatListKey) – Target lengths of each lattice vector to be achieved by StopStep. The number of values should equal the periodicity of the system. If a value is zero, the corresponding lattice vector will not be modified.
Type (Literal["Linear", "Exponential", "Sine", "Cosine"]) –
Function defining the time dependence of the deformed lattice parameters.
Linear increments the lattice parameters by the same absolute amount every timestep. Exponential multiplies the lattice parameters by the same factor every timestep. Only StrainRate, LengthRate, and LengthVelocity are supported for Type=Exponential. Sine deforms the system from the starting lattice to TargetLattice/TargetLength and then by the same amount to the opposite direction, while Cosine deforms the system from the starting lattice to the target and back.
LatticeVelocity (str | Sequence[str] | FreeBlock) – Velocity of individual lattice vector components in Angstrom/fs. The format is identical to the System%Lattice block. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).
StrainRate (str | Sequence[str] | FreeBlock) – Strain rate matrix to be applied on every step. The format is identical to the System%Lattice block.
TargetLattice (str | Sequence[str] | FreeBlock) – Target lattice vectors to be achieved by StopStep. The format is identical to the System%Lattice block.
- class _LatticeVelocity[source]¶
Velocity of individual lattice vector components in Angstrom/fs. The format is identical to the System%Lattice block. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).
- class _HeatExchange[source]¶
Input for the heat-exchange non-equilibrium MD (T-NEMD).
- Variables:
HeatingRate (float | FloatKey) – Rate at which the energy is added to the Source and removed from the Sink. A heating rate of 1 Hartree/fs equals to about 0.00436 Watt of power being transferred through the system.
Method (Literal["Simple", "HEX", "eHEX"]) –
Heat exchange method used.
Simple: kinetic energy of the atoms of the source and sink regions is modified irrespective of that of the center of mass (CoM) of the region (recommended for solids).
HEX: kinetic energy of the atoms of these regions is modified keeping that of the corresponding CoM constant.
eHEX: an enhanced version of HEX that conserves the total energy better (recommended for gases and liquids).
StartStep (int | IntKey) – Index of the MD step at which the heat exchange will start.
StopStep (int | IntKey) – Index of the MD step at which the heat exchange will stop.
Sink (AMS._MolecularDynamics._HeatExchange._Sink) – Defines the heat sink region (where the heat will be removed).
Source (AMS._MolecularDynamics._HeatExchange._Source) – Defines the heat source region (where the heat will be added).
- class _Sink[source]¶
Defines the heat sink region (where the heat will be removed).
- Variables:
AtomList (Iterable[int] | IntListKey) –
The atoms that are part of the sink.
This key is ignored if the [Box] block or [Region] key is present.
FirstAtom (int | IntKey) – Index of the first atom of the region. This key is ignored if the [Box] block or the [AtomList] key is present.
LastAtom (int | IntKey) – Index of the last atom of the region. This key is ignored if the [Box] block or the [AtomList] key is present.
The region that is the sink.
This key is ignored if the [Box] block is present.
Show (BoolType | BoolKey) – Show the sink in the AMSinput
Box (AMS._MolecularDynamics._HeatExchange._Sink._Box) – Part of the simulation box (in fractional cell coordinates) defining the heat sink. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes.
- class _Box[source]¶
Part of the simulation box (in fractional cell coordinates) defining the heat sink. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes.
- Variables:
Amax (float | FloatKey) – Coordinate of the upper bound along the first axis.
Amin (float | FloatKey) – Coordinate of the lower bound along the first axis.
Bmax (float | FloatKey) – Coordinate of the upper bound along the second axis.
Bmin (float | FloatKey) – Coordinate of the lower bound along the second axis.
Cmax (float | FloatKey) – Coordinate of the upper bound along the third axis.
Cmin (float | FloatKey) – Coordinate of the lower bound along the third axis.
- class _Source[source]¶
Defines the heat source region (where the heat will be added).
- Variables:
AtomList (Iterable[int] | IntListKey) –
The atoms that are part of the source.
This key is ignored if the [Box] block or [Region] key is present.
FirstAtom (int | IntKey) – Index of the first atom of the region. This key is ignored if the [Box] block or the [AtomList] key is present.
LastAtom (int | IntKey) – Index of the last atom of the region. This key is ignored if the [Box] block or the [AtomList] key is present.
The region that is the source.
This key is ignored if the [Box] block is present.
Show (BoolType | BoolKey) – Show the source in the AMSinput
Box (AMS._MolecularDynamics._HeatExchange._Source._Box) – Part of the simulation box (in fractional cell coordinates) defining the heat source. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes. This block is mutually exclusive with the FirstAtom/LastAtom setting.
- class _Box[source]¶
Part of the simulation box (in fractional cell coordinates) defining the heat source. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes. This block is mutually exclusive with the FirstAtom/LastAtom setting.
- Variables:
Amax (float | FloatKey) – Coordinate of the upper bound along the first axis.
Amin (float | FloatKey) – Coordinate of the lower bound along the first axis.
Bmax (float | FloatKey) – Coordinate of the upper bound along the second axis.
Bmin (float | FloatKey) – Coordinate of the lower bound along the second axis.
Cmax (float | FloatKey) – Coordinate of the upper bound along the third axis.
Cmin (float | FloatKey) – Coordinate of the lower bound along the third axis.
- class _InitialVelocities[source]¶
Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- Variables:
File (str | Path | StringKey) – AMS RKF file containing the initial velocities.
RandomVelocitiesMethod (Literal["Exact", "Boltzmann", "Gromacs"]) –
Specifies how are random velocities generated. Three methods are available.
Exact: Velocities are scaled to exactly match set random velocities temperature.
Boltzmann: Velocities are not scaled and sample Maxwell-Boltzmann distribution. However, the distribution is not corrected for constraints.
Gromacs: Velocities are scaled to match set random velocities temperature, but removal of net momentum is performed only after the scaling. Resulting kinetic energy is lower based on how much net momentum the system had.
Temperature (float | FloatKey) –
Sets the temperature for the Maxwell-Boltzmann distribution when the type of the initial velocities is set to random, in which case specifying this key is mandatory.
AMSinput will use the first temperature of the first thermostat as default.
Type (Literal["Zero", "Random", "FromFile", "Input"]) –
Specifies the initial velocities to assign to the atoms. Three methods to assign velocities are available.
Zero: All atom are at rest at the beginning of the calculation.
Random: Initial atom velocities follow a Maxwell-Boltzmann distribution for the temperature given by the [MolecularDynamics%InitialVelocities%Temperature] keyword.
FromFile: Load the velocities from a previous ams result file.
Input: Atom’s velocities are set to the values specified in the [MolecularDynamics%InitialVelocities%Values] block, which can be accessed via the Expert AMS panel in AMSinput.
Values (str | Sequence[str] | FreeBlock) – This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.
- class _Values[source]¶
This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.
- class _MovingRestraints[source]¶
Define a set of moving restraints.
- Variables:
Change (Literal["Linear", "Sine", "Cosine"]) –
Type of function defining how the target restraint value will change over time:
Linear - linearly between the StartValue and EndValue. Sine - oscillating around StartValue with an amplitude equal to the difference between EndValue and StartValue. Cosine - oscillating between StartValue and EndValue.
Name (str | StringKey) – Optional name to be used for plotting.
Period (float | FloatKey) – Period of oscillation for Sine and Cosine change types.
RestraintType (Literal["None", "Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) – Select type of the moving restraint profile. The force for Hyperbolic and Erf is bounded by a user-defined value, the latter converging to it faster than the former. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable.
StartStep (int | IntKey) – First step number at which the restraints will be applied.
StopStep (int | IntKey) – Last step number at which the restraints will be applied.
Distance (AMS._MolecularDynamics._MovingRestraints._Distance) – Define a distance restraint between pair of atoms. For linear-type
Erf (AMS._MolecularDynamics._MovingRestraints._Erf) – Define parameters for the Int(erf) restraint potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
GaussianWell (AMS._MolecularDynamics._MovingRestraints._GaussianWell) – Define parameters in the Gaussian well restraint potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
Harmonic (AMS._MolecularDynamics._MovingRestraints._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
Hyperbolic (AMS._MolecularDynamics._MovingRestraints._Hyperbolic) – Define parameters for the hyperbolic restraint potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
- class _Distance[source]¶
Define a distance restraint between pair of atoms. For linear-type
- class _Erf[source]¶
Define parameters for the Int(erf) restraint potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
- class _GaussianWell[source]¶
Define parameters in the Gaussian well restraint potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
- class _PRD[source]¶
This block is used for Parallel Replica Dynamics simulations.
- Variables:
CorrelatedSteps (int | IntKey) – How many steps to wait for correlated events after detecting an initial event.
DephasingSteps (int | IntKey) – Spend this many steps dephasing the individual replicas after an event.
nReplicas (int | IntKey) – Number of replicas to run in parallel.
BondChange (AMS._MolecularDynamics._PRD._BondChange) – Detect changes to the bonding topology and bond orders returned by the engine.
MolCount (AMS._MolecularDynamics._PRD._MolCount) – Detect changes to the molecular composition of the system.
- class _BondChange[source]¶
Detect changes to the bonding topology and bond orders returned by the engine.
- Variables:
ChangeThreshold (float | FloatKey) – Trigger an event when the bond order of a bond changes from the reference state by more than this value.
DissociationThreshold (float | FloatKey) – Trigger an event when a bond dissociates (its bond order drops below this value while it was above FormationThreshold in the reference state).
FormationThreshold (float | FloatKey) – Trigger an event when a new bond forms (its bond order exceeds this value while it was below DissociationThreshold in the reference state).
- class _Plumed[source]¶
Input for PLUMED (version 2.5.0). The parallel option is still experimental.
- Variables:
Input (str | Sequence[str] | FreeBlock) – Input for PLUMED. Contents of this block is passed to PLUMED as is.
Parallel (AMS._MolecularDynamics._Plumed._Parallel) – Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- class _Parallel[source]¶
Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _Preserve[source]¶
Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.
- Variables:
AngularMomentum (BoolType | BoolKey) – Remove overall angular momentum of the system. This option is ignored for 2D and 3D-periodic systems, and disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).
CenterOfMass (BoolType | BoolKey) – Translate the system to keep its center of mass at the coordinate origin. This option is not very useful for 3D-periodic systems.
Momentum (BoolType | BoolKey) – Remove overall (linear) momentum of the system. This is disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).
- class _ReactionBoost[source]¶
Define a series of transitions between different states of the system.
Each transition is defined by a TargetSystem and by a set of restraints that force the transition.
- Variables:
Change (Literal["TargetCoordinate", "Force", "LogForce"]) –
Select what to change during dynamics.
By default, once the restraints are switched on, AMS will change the restraint’s target coordinate towards its final value.
If the [Force] or [LogForce] option is selected then the target coordinate is set to its final value immediately and instead the restraint force is gradually scaled from 0 to 1. The scaling is either linear (Force) or logarithmic (LogForce).
InitialFraction (float | FloatKey) –
Initial fraction of the boost variable.
At the first boosting step, the restraint’s target value (or force or log(force)) is equal to InitialFraction + 1/NSteps.
InterEquilibrationSteps (int | IntKey) – Number of equilibration steps after reaching a target before setting up restraints for the next one.
MinBondChange (float | FloatKey) – Minimal change in the distance for an individual restraint to be considered bond-breaking/making vs bonded.
MinBondStrength (float | FloatKey) – Minimum strength (usually ranges from 0 to 1) for a bond to be considered.
NSteps (int | IntKey) – Number of steps per target the restraints should be active for.
PreEquilibrationSteps (int | IntKey) – Number of steps before enabling the first set of restraints.
Region (str | StringKey) – Region to which the restraints should be limited.
TargetSystem (str | StringKey) –
The target system’s name for this transition. Multiple targets can be specified to request multiple transitions in one simulation.
Note that only the lattice and the atomic coordinates of the target system are used and other properties (bonds, charge, etc.) are ignored. The target system’s lattice is used only to determine connections and it cannot be restrained.
Type (Literal["None", "Pair", "RMSD"]) –
Reaction Boost uses a series of transitions between different states of the system. Each transition is defined by a TargetSystem and by a set of restraints that force the transition.
Select the type of the restraint set: -None: no Reaction Boost - Pair: use pair restraints - RMSD: use RMSD restraints.
Pair restraints are defined per atom pair while the RMSD defines one collective restraint for all atoms and is thus suitable for very large systems.
The pair restraints are further divided into four sub-types: bonding, non-bonding, bond-breaking and bond-making. The sub-type of restraints for each pair is determined automatically depending on whether the two atoms are bonded in the initial/final state.
Parameters of the pair restraints are defined by [NonBondedRestraints], [BondedRestraints], [BondBreakingRestraints] and [BondMakingRestraints] blocks, while those of the RMSD restraint by the [RMSDRestraint] block.
BondBreakingRestraints (AMS._MolecularDynamics._ReactionBoost._BondBreakingRestraints) –
Define parameters for moving restraints that are added for pairs of atoms that become disconnected during the transition.
It is intended to make sure the corresponding bonds get broken, although this may not always be required because forming other bonds will likely get these bonds broken.
BondMakingRestraints (AMS._MolecularDynamics._ReactionBoost._BondMakingRestraints) –
Define parameters for moving restraints that are added for pairs of atoms that become connected during the transition.
It is intended to make sure the bonds are created as required.
BondedRestraints (AMS._MolecularDynamics._ReactionBoost._BondedRestraints) –
Define parameters for bonded restraints. A bonded restraint is added for each pair of atoms that are bonded both in the current and in the final state.
It is intended to make sure they remain bonded during simulation.
NonBondedRestraints (AMS._MolecularDynamics._ReactionBoost._NonBondedRestraints) –
Define parameters for non-bonded restraints. A non-bonded restraint is added for each pair of atoms that are bonded neither in the current nor in the final state.
It is intended to keep them from forming a bond unintentionally. They are represented by a repulsive potential
RMSDRestraint (AMS._MolecularDynamics._ReactionBoost._RMSDRestraint) – Define a static restraint that pulls each atom to its position in the target system, but in contrast to the individual restraints, the force for this one depends on the total mass-weighted root-mean-squared distance (RMSD) between the two structures.
- class _BondBreakingRestraints[source]¶
Define parameters for moving restraints that are added for pairs of atoms that become disconnected during the transition.
It is intended to make sure the corresponding bonds get broken, although this may not always be required because forming other bonds will likely get these bonds broken.
- Variables:
Type (Literal["None", "Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) –
Select type of the moving restraint profile.
Harmonic: V=0.5*FC*(r-r0)^2
Hyperbolic: V=alpha*(sqrt(1 + beta*x^2) - 1)
Erf: V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI))
GaussianWell: V=WellDepth*(1-exp(-Sigma*(r-r0)^2))
Here beta=ForceConstant/MaxForce, alpha=MaxForce/beta.
The force for Hyperbolic and Erf is bounded by a user-defined value, the latter converging to it faster than the former. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable.
Moving restraints are added for pairs of atoms that become disconnected during the transition.
It is intended to make sure the corresponding bonds get broken, although this may not always be required because forming other bonds will likely get these bonds broken.
Erf (AMS._MolecularDynamics._ReactionBoost._BondBreakingRestraints._Erf) – Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
GaussianWell (AMS._MolecularDynamics._ReactionBoost._BondBreakingRestraints._GaussianWell) – Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
Harmonic (AMS._MolecularDynamics._ReactionBoost._BondBreakingRestraints._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
Hyperbolic (AMS._MolecularDynamics._ReactionBoost._BondBreakingRestraints._Hyperbolic) – Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
Taper (AMS._MolecularDynamics._ReactionBoost._BondBreakingRestraints._Taper) –
- class _Erf[source]¶
Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
- class _GaussianWell[source]¶
Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
- class _Hyperbolic[source]¶
Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
- class _Taper[source]¶
- Variables:
Enabled (BoolType | BoolKey) – Enable tapering of the restraint potential and force between the given range of bond distances. A 7-th order tapering function on the actual (not target!) distance will be used. The MaxDistance must be greater than MinDistance.
MaxDistance (float | FloatKey) – Bond length at which the restraint potential and force decays to zero.
MinDistance (float | FloatKey) – Bond length at which the restraint potential and force will start decaying to zero.
- class _BondMakingRestraints[source]¶
Define parameters for moving restraints that are added for pairs of atoms that become connected during the transition.
It is intended to make sure the bonds are created as required.
- Variables:
Type (Literal["None", "Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) –
Select type of the moving restraint profile.
Harmonic: V=0.5*FC*(r-r0)^2
Hyperbolic: V=alpha*(sqrt(1 + beta*x^2) - 1)
Erf: V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI))
GaussianWell: V=-WellDepth*exp(-Sigma*(r-r0)^2)
Here beta=ForceConstant/MaxForce, alpha=MaxForce/beta.
The force for Hyperbolic and Erf is bounded by a user-defined value. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable.
Moving restraints are added for pairs of atoms that become connected during the transition.
It is intended to make sure the bonds are created as required.
Erf (AMS._MolecularDynamics._ReactionBoost._BondMakingRestraints._Erf) – Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
GaussianWell (AMS._MolecularDynamics._ReactionBoost._BondMakingRestraints._GaussianWell) – Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
Harmonic (AMS._MolecularDynamics._ReactionBoost._BondMakingRestraints._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
Hyperbolic (AMS._MolecularDynamics._ReactionBoost._BondMakingRestraints._Hyperbolic) – Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
- class _Erf[source]¶
Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
- class _GaussianWell[source]¶
Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
- class _BondedRestraints[source]¶
Define parameters for bonded restraints. A bonded restraint is added for each pair of atoms that are bonded both in the current and in the final state.
It is intended to make sure they remain bonded during simulation.
- Variables:
Type (Literal["None", "Harmonic"]) –
Select type of the bonded restraints:
Harmonic: V=0.5*FC*(r-r0)^2
A bonded restraint is added for each pair of atoms that are bonded both in the current and in the final state.
It is intended to make sure they remain bonded during simulation.
Harmonic (AMS._MolecularDynamics._ReactionBoost._BondedRestraints._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
- class _NonBondedRestraints[source]¶
Define parameters for non-bonded restraints. A non-bonded restraint is added for each pair of atoms that are bonded neither in the current nor in the final state.
It is intended to keep them from forming a bond unintentionally. They are represented by a repulsive potential
- Variables:
Type (Literal["None", "Exponential"]) –
Select type of the non-bonded restraints:
Exponential: V=Epsilon*exp(-Sigma*r)
A non-bonded restraint is added for each pair of atoms that are bonded neither in the current nor in the final state.
It is intended to keep them from forming a bond unintentionally. They are represented by a repulsive potential.
Exponential (AMS._MolecularDynamics._ReactionBoost._NonBondedRestraints._Exponential) – Define parameters for the repulsive potential V=Epsilon*exp(-Sigma*r).
- class _RMSDRestraint[source]¶
Define a static restraint that pulls each atom to its position in the target system, but in contrast to the individual restraints, the force for this one depends on the total mass-weighted root-mean-squared distance (RMSD) between the two structures.
- Variables:
Type (Literal["None", "Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) –
Select type of the RMSD restraint profile:
Harmonic: V=0.5*FC*(r-r0)^2
Hyperbolic: V=alpha*(sqrt(1 + beta*x^2) - 1)
Erf: V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI),
GaussianWell: V=-WellDepth*exp(-Sigma*(r-r0)^2)
Here beta=ForceConstant/MaxForce, alpha=MaxForce/beta.
The Harmonic profile can be problematic at large deviations as it may result in large forces. The force for Hyperbolic and Erf is bounded by a user-defined value. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable.
Erf (AMS._MolecularDynamics._ReactionBoost._RMSDRestraint._Erf) – Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
GaussianWell (AMS._MolecularDynamics._ReactionBoost._RMSDRestraint._GaussianWell) – Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
Harmonic (AMS._MolecularDynamics._ReactionBoost._RMSDRestraint._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
Hyperbolic (AMS._MolecularDynamics._ReactionBoost._RMSDRestraint._Hyperbolic) – Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
- class _Erf[source]¶
Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
- class _GaussianWell[source]¶
Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
- class _Reactor[source]¶
Define one phase of the nanoreactor. A reactor is a region of space surrounded by an elastic wall. Atoms inside the region are not affected. Atoms outside it will be pushed back with force depending on the [ForceConstant] and the [MassScaled] flag.
- Variables:
ForceConstant (float | FloatKey) – Force constant of the reactor wall in Hartree/Bohr^2 (or Hartree/Bohr^2/Dalton if [MassScaled] is true).
MassScaled (BoolType | BoolKey) – If this flag is disabled the force on an atom outside of the reactor depends only on the atomic coordinates and the force constant. Otherwise, the force is also multiplied by the mass of the atom. This means that atoms at the same distance from the wall will receive the same accelerate due to the wall potential.
NSteps (int | IntKey) – Number of steps for which the reactor will remain active until disabled. The next reactor will be activated immediately after this. After the last reactor is disabled the cycle will repeat.
- class _ReflectiveWall[source]¶
Apply a reflective wall in space
- Variables:
Axis (Iterable[float] | FloatListKey) – Defines the normal vector perpendicular to the plane of the reflective wall. Any particle moving in this direction will be reflected back.
Direction (Literal["under", "above"]) – Defines the direction of the reflective wall. under will keep the particles under the defined wall, and above will keep the particles above the defined wall
Region (str | StringKey) – Apply the reflective wall to all atoms in this region.
Threshold (float | FloatKey) – Defines the threshold value determining the position of the reflective wall. If the dot product of a position of a particle with Axis exceeds Threshold, the particle will be reflected. This means that the plane of the wall passes through a point given by Axis times Threshold.
- class _Remap[source]¶
Control periodic remapping (backtranslation) of atoms into the PBC box.
- Variables:
Range (Literal["Auto", "ZeroToOne", "PlusMinusHalf", "AroundCenter"]) –
Select the range of fractional coordinates to which atoms are remapped.
Auto: Use PlusMinusHalf if the geometrical center of the starting positions of all atoms lies between -0.25 and 0.25 in fractional coordinates in all periodic directions, ZeroToOne otherwise.
PlusMinusHalf: Remap atoms to lie between -0.5 and 0.5 in fractional coordinates.
ZeroToOne: Remap atoms to lie between 0 and 1 in fractional coordinates.
AroundCenter: Remap atoms to lie within 0.5 in fractional coordinates around the geometrical center of the starting positions of all atoms.
Type (Literal["None", "Atoms"]) –
Select the method used to remap atoms into the unit cell.
None: Disable remapping completely.
Atoms: Remap any atoms that leave the unit cell.
- class _RemoveMolecules[source]¶
This block controls removal of molecules from the system. Multiple occurrences of this block are possible.
- Variables:
Molecular formula of the molecules that should be removed from the system.
The order of elements in the formula is very important and the correct order is: C, H, all other elements in the strictly alphabetic order. Element names are case-sensitive, spaces in the formula are not allowed. Digit ‘1’ must be omitted.
Valid formula examples: C2H6O, H2O, O2S. Invalid formula examples: C2H5OH, H2O1, OH, SO2. Invalid formulas are silently ignored.
Use * to remove any molecule, which must be combined with SinkBox or SafeBox.
Frequency (int | IntKey) – The specified molecules are removed every so many steps after the StartStep. There is never a molecule removed at step 0.
Step number when molecules are removed for the first time. After that, molecules are removed every [Frequency] steps.
For example, if StartStep=99 and Frequency=100 then molecules will be removed at steps 99, 199, 299, etc…
No molecule will be removed at step 0, so if StartStep=0 the first molecules are removed at the step number equal to [Frequency].
StopStep (int | IntKey) – Do not remove the specified molecules after this step.
SafeBox (AMS._MolecularDynamics._RemoveMolecules._SafeBox) – Part of the simulation box where molecules may not be removed. Only one of the SinkBox or SafeBox blocks may be present. If this block is present the molecule will not be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.
SinkBox (AMS._MolecularDynamics._RemoveMolecules._SinkBox) – Part of the simulation box where matching molecules will be removed. By default, molecules matching the formula will be removed regardless of their location. If this block is present then such a molecule will only be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.
- class _SafeBox[source]¶
Part of the simulation box where molecules may not be removed. Only one of the SinkBox or SafeBox blocks may be present. If this block is present the molecule will not be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.
- Variables:
Amax (float | FloatKey) – Coordinate of the upper bound along the first axis.
Amin (float | FloatKey) – Coordinate of the lower bound along the first axis.
Bmax (float | FloatKey) – Coordinate of the upper bound along the second axis.
Bmin (float | FloatKey) – Coordinate of the lower bound along the second axis.
Cmax (float | FloatKey) – Coordinate of the upper bound along the third axis.
Cmin (float | FloatKey) – Coordinate of the lower bound along the third axis.
FractionalCoordsBox (Iterable[float] | FloatListKey) –
Do not remove molecules that are (partly) inside the safe box.
Borders of the safe box specified as: Amin, Amax, Bmin, Bmax, Cmin, Cmax.
For periodic dimensions fractional coordinates between 0 and 1 and for non-periodic dimensions Cartesian values in Angstrom are expected.
- class _SinkBox[source]¶
Part of the simulation box where matching molecules will be removed. By default, molecules matching the formula will be removed regardless of their location. If this block is present then such a molecule will only be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.
- Variables:
Amax (float | FloatKey) – Coordinate of the upper bound along the first axis.
Amin (float | FloatKey) – Coordinate of the lower bound along the first axis.
Bmax (float | FloatKey) – Coordinate of the upper bound along the second axis.
Bmin (float | FloatKey) – Coordinate of the lower bound along the second axis.
Cmax (float | FloatKey) – Coordinate of the upper bound along the third axis.
Cmin (float | FloatKey) – Coordinate of the lower bound along the third axis.
FractionalCoordsBox (Iterable[float] | FloatListKey) –
Remove molecules that are (partly) inside the sink box.
Borders of the sink box specified as: Amin, Amax, Bmin, Bmax, Cmin, Cmax.
For periodic dimensions fractional coordinates between 0 and 1 and for non-periodic dimensions Cartesian values in Angstrom are expected.
- class _ReplicaExchange[source]¶
This block is used for (temperature) Replica Exchange MD (Parallel Tempering) simulations.
- Variables:
AllowWrongResults (BoolType | BoolKey) – Allow combining Replica Exchange with other features when the combination is known to produce physically incorrect results.
Length of the exponentially weighted moving average used to smooth swap probabilities for monitoring.
This value is equal to the inverse of the EWMA mixing factor.
SwapFrequency (int | IntKey) – Attempt an exchange every N steps.
TemperatureFactors (Iterable[float] | FloatListKey) –
This is the ratio of the temperatures of two successive replicas.
The first value sets the temperature of the second replica with respect to the first replica, the second value sets the temperature of the third replica with respect to the second one, and so on. If there are fewer values than nReplicas, the last value of TemperatureFactor is used for all the remaining replicas.
Temperatures (Iterable[float] | FloatListKey) –
List of temperatures for all replicas except for the first one.
This is mutually exclusive with TemperatureFactors. Exactly nReplicas-1 temperature values need to be specified, in increasing order. The temperature of the first replica is given by [Thermostat%Temperature].
nReplicas (int | IntKey) – Number of replicas to run in parallel.
- class _Shake[source]¶
Parameters of the Shake/Rattle algorithm.
- Variables:
Constraint description in one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3
The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 and the angle between them.
The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then all bonds between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. The distance, if present, must be in Angstrom. If it is omitted then the bond length from the initial geometry is used.
Important: only the bonds present in the system at certain points of the simulation (at the start or right after adding/removing atoms) can be constrained, which means that the bonds may need to be specified in the System block.
Warning: the triangles constraint should be used with care because each constrained bond or angle means removing one degree of freedom from the dynamics. When there are too many constraints (for example, “All triangles H C H” in methane) some of them may be linearly dependent, which will lead to an error in the temperature computation.
Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H
ConvergeR2 (float | FloatKey) – Convergence criterion on the max squared difference, in atomic units.
ConvergeRV (float | FloatKey) – Convergence criterion on the orthogonality of the constraint and the relative atomic velocity, in atomic units.
ShakeInitialCoordinates (BoolType | BoolKey) – Apply constraints before computing the first energy and gradients.
- class _Thermostat[source]¶
This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’s behavior.
- Variables:
BerendsenApply (Literal["Local", "Global"]) –
Select how to apply the scaling correction for the Berendsen thermostat:
per-atom-velocity (Local)
on the molecular system as a whole (Global).
ChainLength (int | IntKey) – Number of individual thermostats forming the NHC thermostat
Duration (Iterable[int] | IntListKey) – Specifies how many steps should a transition from a particular temperature to the next one in sequence take.
ExcludedDirection (Literal["None", "X", "Y", "Z"]) – Exclude a component of the velocities from rescaling by the thermostat. For example in NEMD simulations, when a shear force/velocity is applied in the x direction, the x-direction is often excluded from thermostatting. This currently only works for the Nose-Hoover thermostat.
Friction (float | FloatKey) – Friction coefficient used in langevin dynamics
Region (str | StringKey) – The identifier of the region to thermostat. The default * applies the thermostat to the entire system. The value can by a plain region name, or a region expression, e.g. *-myregion to thermostat all atoms that are not in myregion, or regionA+regionB to thermostat the union of the ‘regionA’ and ‘regionB’. Note that if multiple thermostats are used, their regions may not overlap.
ScaleFrequency (int | IntKey) –
Optional parameter used only by the Scale thermostat.
If specified, the thermostat will be applied every N steps, using that step’s ensemble temperature and the specified thermostat temperature to compute the scaling factor.
If not specified, the thermostat will be applied at every step, using the mean temperature of the ensemble and the specified thermostat temperature to compute the scaling factor.
Tau (float | FloatKey) – The time constant of the thermostat.
Temperature (Iterable[float] | FloatListKey) –
The target temperature of the thermostat.
You can specify multiple temperatures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one T to the next T (using a linear ramp). For NHC thermostat, the temperature may not be zero.
Type (Literal["None", "Scale", "Berendsen", "NHC", "Langevin"]) – Selects the type of the thermostat.
- class _Trajectory[source]¶
Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- Variables:
EngineResultsFreq (int | IntKey) – Write MDStep*.rkf files with engine-specific results once every N steps. Setting this to zero disables writing engine results files except for one file at the end of the simulation. If unset or negative, defaults to the value of Checkpoint%Frequency.
ExitConditionFreq (int | IntKey) – Check the exit conditions every N steps. By default this is done every SamplingFreq steps.
PrintFreq (int | IntKey) – Print current thermodynamic properties to the output every N steps. By default this is done every SamplingFreq steps.
SamplingFreq (int | IntKey) – Write the molecular geometry (and possibly other properties) to the ams.rkf file once every N steps.
TProfileGridPoints (int | IntKey) – Number of points in the temperature profile. If TProfileGridPoints > 0, a temperature profile along each of the three lattice axes will be written to the .rkf file. The temperature at a given profile point is calculated as the total temperature of all atoms inside the corresponding slice of the simulation box, time-averaged over all MD steps since the previous snapshot. By default, no profile is generated.
WriteBonds (BoolType | BoolKey) – Write detected bonds to the .rkf file.
WriteCharges (BoolType | BoolKey) – Write current atomic point charges (if available) to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze charges.
WriteCoordinates (BoolType | BoolKey) – Write atomic coordinates to the .rkf file.
WriteEngineGradients (BoolType | BoolKey) – Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.
WriteMolecules (BoolType | BoolKey) – Write the results of molecule analysis to the .rkf file.
WriteVelocities (BoolType | BoolKey) – Write velocities to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze the velocities.
- class _fbMC[source]¶
This block sets up force bias Monte Carlo interleaved with the molecular dynamics simulation.
- Variables:
Frequency (int | IntKey) – Run the fbMC procedure every Frequency MD steps.
MassRoot (float | FloatKey) – Inverse of the exponent used to mass-weight fbMC steps.
NSteps (int | IntKey) – Number of fbMC steps to perform on every invocation of the procedure.
PrintFreq (int | IntKey) – Print current thermodynamic properties to the output every N fbMC steps. This defaults to the PrintFreq set in the Trajectory block. Setting this to zero disables printing fbMC steps.
StartStep (int | IntKey) – First step at which the fbMC procedure may run.
StepLength (float | FloatKey) – Maximum allowed displacement of the lightest atom in the system in each Cartesian coordinate in one fbMC step.
StopStep (int | IntKey) – Last step at which the fbMC procedure may run. If unset or zero, there is no limit.
MolecularMoves (AMS._MolecularDynamics._fbMC._MolecularMoves) – Move molecules as rigid bodies in addition to normal atomic moves.
- class _MolecularMoves[source]¶
Move molecules as rigid bodies in addition to normal atomic moves.
- Variables:
Enabled (BoolType | BoolKey) – Enable moving molecules as rigid bodies based on net forces and torques. Ordinary per-atom displacements will then be based on residual atomic forces.
RotationMethod (Literal["Mees", "Rao"]) – Select the fbMC method used to generate molecular rotation moves.
RotationStepAngle (float | FloatKey) – Maximum allowed angle of rotation of each molecule in one fbMC step.
TranslationStepLength (float | FloatKey) – Maximum allowed displacement of each molecule in each Cartesian coordinate in one fbMC step.
- class _Molecules[source]¶
Configures details of the molecular composition analysis enabled by the Properties%Molecules block.
- Variables:
AdsorptionSupportRegion (str | StringKey) – Select region that will represent a support for adsorption analysis. Adsorbed molecules will receive an ‘(ads)’ suffix after name of the element bonded to the support. Such elements will be listed separate from atoms of the same element not bonded to the support, for example, HOH(ads) for a water molecule bonded to a surface via one of its H atoms.
BondOrderCutoff (float | FloatKey) – Bond order cutoff for analysis of the molecular composition. Bonds with bond order smaller than this value are neglected when determining the molecular composition.
- class _NEB[source]¶
Configures details of the Nudged Elastic Band optimization.
- Variables:
Climbing (BoolType | BoolKey) – Use the climbing image algorithm to drive the highest image to the transition state.
ClimbingThreshold (float | FloatKey) – Climbing image force threshold. If ClimbingThreshold > 0 and the max perpendicular force component is above the threshold then no climbing is performed at this step. This entry can be used to get a better approximation for the reaction path before starting the search for the transition state. A typical value is 0.01 Hartree/Bohr.
DoubleNudge (Literal["None", "Henkelman", "Trygubenko"]) – Type of the double nudging method.
Images (int | IntKey) – Number of NEB images (not counting the chain ends). Using more images will result in a smoother reaction path and can help with convergence problems, but it will also increase the computation time.
Intermediates (str | StringKey) –
Define one or more intermediate systems.
The molecule names are adjusted when saving so that the order of the intermediates is the order as they appear in the list here.
If no intermediate systems are needed, select None
InterpolateInternal (BoolType | BoolKey) – The initial NEB image geometries are calculated by interpolating between the initial and the final state. By default, for non-periodic systems the interpolation is performed in internal coordinates but the user can choose to do it in the Cartesian ones. For periodic systems the interpolation is always done in Cartesian coordinates. If PreOptimizeWithIDPP is set then the path may be further refined using the image-dependent pair potential (IDPP).
InterpolateShortest (BoolType | BoolKey) – Allow interpolation across periodic cell boundaries. Set to false if an atom is intended to move more than half across the simulation box during reaction.
InterpolationOption (int | IntKey) –
Select which internal coordinates will be interpolated:
- 0 - automatic,
1 - only distances, 2 - distances and near-linear valence angles, 3 - distances and all valence angles, 4 - distances and dihedral angles, 99 - all coordinates
Iterations (int | IntKey) – Maximum number of NEB iterations. The default value depends on the number of degrees of freedom (number of images, atoms, periodic dimensions).
Jacobian (float | FloatKey) – Scaling factor used to convert the lattice strain to a NEB coordinate value. Default value: sqrt(N)*(V/N)^(1/d), where V - lattice volume (area for 2D, length for 1D), N - number of atoms, and d - number of periodic dimensions.
MapAtomsToCell (BoolType | BoolKey) – Translate atoms to the [-0.5,0.5] cell before every step. This option cannot be disabled for SS-NEB.
OldTangent (BoolType | BoolKey) – Turn on the old central difference tangent.
OptimizeEnds (BoolType | BoolKey) – Start the NEB with optimization of the reactant and product geometries.
OptimizeLattice (BoolType | BoolKey) – Turn on the solid-state NEB (SS-NEB).
PreOptimizeWithIDPP (BoolType | BoolKey) – (Experimental) When there is only initial and final system available, the image-dependent pair potential (IDPP, doi: 10.1063/1.4878664) can be used to determine the initial NEB path by interpolating all interatomic distances between the two points and optimizing intermediate images towards them. The optimization starts from the geometries obtained using the selected interpolation options.
ReOptimizeEnds (BoolType | BoolKey) – Re-optimize reactant and product geometries upon restart.
Restart (str | Path | StringKey) – Provide an ams.rkf file from a previous NEB calculation to restart from. It can be an unfinished NEB calculation or one performed with different engine parameters.
Skewness (float | FloatKey) – Degree of how much images are shifted towards or away from the TS, which may help tackle problems with a long reaction path (for example involving a loose adsorption complex) without needing too many images. A value greater than 1 will make sure that images are concentrated near the transition state. The optimal value depends on the path length, the number of images (larger [Skewness] may be needed for a longer path and fewer images). Technically [Skewness] is equal to the ratio between the optimized distances to the lower and the higher neighbor image on the path.
Spring (float | FloatKey) – Spring force constant in atomic units.
LoadPath (AMS._NEB._LoadPath) – Provide details about the trajectory to get the initial NEB path from. PESScan and NEB trajectories are supported. Only the last geometry for each point on the trajectory is considered.
Parallel (AMS._NEB._Parallel) – Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- class _LoadPath[source]¶
Provide details about the trajectory to get the initial NEB path from. PESScan and NEB trajectories are supported. Only the last geometry for each point on the trajectory is considered.
- Variables:
File (str | Path | StringKey) –
Provide an ams.rkf file to load the initial path from. All geometries of this calculation, including initial and final, will be taken from the History section of the file.
Note that for a PESScan it should be a 1D path.
Geometries (Iterable[int] | IntListKey) – Raw indices of the geometries from the History section. By default the last geometry of each path point is used.
Points (Iterable[int] | IntListKey) – By default the whole path is used, which may sometimes be not desirable. For example when a PESScan revealed multiple barriers. In this case one can specify indices of the path points to be used. The last geometry of the specified path point will be loaded.
- class _Parallel[source]¶
Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _NormalModes[source]¶
Configures details of a normal modes calculation.
- Variables:
Displacements (Literal["Cartesian", "Symmetric", "Block"]) –
Type of displacements.
In case of symmetric displacements it is possible to choose only the modes that have non-zero IR or Raman intensity.
Block displacements take rigid blocks into account.
Hessian (Literal["Auto", "Analytical", "Numerical"]) – Default Auto means that if possible by the engine the Hessian will be calculated analytically, else the Hessian will be calculated numerically by AMS.
ReScanFreqRange (Iterable[float] | FloatListKey) – Specifies a frequency range within which all modes will be scanned. 2 numbers: an upper and a lower bound.
ReScanModes (BoolType | BoolKey) – Whether or not to scan imaginary modes after normal modes calculation has concluded.
UseSymmetry (BoolType | BoolKey) – Whether or not to exploit the symmetry of the system in the normal modes calculation.
BlockDisplacements (AMS._NormalModes._BlockDisplacements) – Configures details of a Block Normal Modes (a.k.a. Mobile Block Hessian, or MBH) calculation.
SymmetricDisplacements (AMS._NormalModes._SymmetricDisplacements) – Configures details of the calculation of the frequencies and normal modes of vibration in symmetric displacements.
- class _BlockDisplacements[source]¶
Configures details of a Block Normal Modes (a.k.a. Mobile Block Hessian, or MBH) calculation.
- Variables:
AngularDisplacement (float | FloatKey) – Relative step size for rotational degrees of freedom during Block Normal Modes finite difference calculations. It will be scaled with the characteristic block size.
BlockAtoms (Iterable[int] | IntListKey) – List of atoms belonging to a block. You can have multiple BlockAtoms.
BlockRegion (str | StringKey) – The region to to be considered a block. You can have multiple BlockRegions, also in combination with BlockAtoms.
RadialDisplacement (float | FloatKey) – Step size for translational degrees of freedom during Block Normal Modes finite difference calculations.
Parallel (AMS._NormalModes._BlockDisplacements._Parallel) – Configuration for how the individual displacements are calculated in parallel.
- class _Parallel[source]¶
Configuration for how the individual displacements are calculated in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _SymmetricDisplacements[source]¶
Configures details of the calculation of the frequencies and normal modes of vibration in symmetric displacements.
- Variables:
Type (Literal["All", "Infrared", "Raman", "InfraredAndRaman"]) –
For symmetric molecules it is possible to choose only the modes that have non-zero IR or Raman intensity (or either of them) by symmetry.
In order to calculate the Raman intensities the Raman property must be requested.
- class _NumericalDifferentiation[source]¶
Define options for numerical differentiations, that is the numerical calculation of gradients, Hessian and the stress tensor for periodic systems.
- Variables:
NuclearStepSize (float | FloatKey) – Step size for numerical nuclear gradient calculation.
StrainStepSize (float | FloatKey) – Step size (relative) for numerical stress tensor calculation.
UseSymmetry (BoolType | BoolKey) – Whether or not to exploit the symmetry of the system for numerical differentiations.
Parallel (AMS._NumericalDifferentiation._Parallel) – Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- class _Parallel[source]¶
Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _NumericalPhonons[source]¶
Configures details of a numerical phonons calculation.
- Variables:
AutomaticBZPath (BoolType | BoolKey) – If True, compute the phonon dispersion curve for the standard path through the Brillouin zone. If False, you must specify your custom path in the [BZPath] block.
BornEffCharge (float | FloatKey) – Input option to give the Born effective charges of the species.
DielectricConst (float | FloatKey) – Input option to give the static dielectric constant of the species.
DoubleSided (BoolType | BoolKey) – By default a two-sided (or quadratic) numerical differentiation of the nuclear gradients is used. Using a single-sided (or linear) numerical differentiation is computationally faster but much less accurate. Note: In older versions of the program only the single-sided option was available.
Interpolation (int | IntKey) – Use interpolation to generate smooth phonon plots.
KPathFinderConvention (Literal["Setyawan-Curtarolo", "Hinuma"]) –
This option determines how the path through the Brillouin zone is generated when using the automatic k-point mode.
Available options:
Setyawan-Curtarolo(default for 1D and 2D lattices): Uses our built-in KPath program to find a path through high-symmetry points based on the method by Setyawan and Curtarolo (https://doi.org/10.1016/j.commatsci.2010.05.010). For 2D lattices, the path is derived from the intersection of the 3D Brillouin zone with a plane. For 1D lattices, the path is simply Gamma-Z.Hinuma: Uses the external SeeKPath utility to generate the k-path (https://github.com/giovannipizzi/seekpath and https://doi.org/10.1016/j.commatsci.2016.10.015).
MaxTemperature (float | FloatKey) – Maximum temperature for the thermodynamic properties calculation (Internal Energy, Free Energy, Specific Heat, and Entropy). This value sets the upper limit of the temperature range considered. It is used in conjunction with
NTemperaturesto define the temperature grid. The calculation of thermodynamic properties is performed only if the phonon density of states (DOS) is requested (i.e.,Phonons%DOSis set toYes).NDosEnergies (int | IntKey) – Nr. of energies used to calculate the phonon DOS used to integrate thermodynamic properties. For fast compute engines this may become time limiting and smaller values can be tried.
NTemperatures (int | IntKey) – Number of temperature points to use in the thermodynamic properties calculation (Internal Energy, Free Energy, Specific Heat, and Entropy). This value, along with
MaxTemperature, determines the density of the temperature grid. The temperatures will be distributed evenly between 0 Kelvin and ‘MaxTemperature’. The calculation of thermodynamic properties is performed only if the phonon density of states (DOS) is requested (i.e.,Phonons%DOSis set toYes).RequestContinuousPES (BoolType | BoolKey) – Whether or not the engine should be instructed to disable symmetry. AMS versions older than AMS2024 would use the the hard coded value false.
StepSize (float | FloatKey) – Step size to be taken to obtain the force constants (second derivative) from the analytical gradients numerically.
UseSymmetry (BoolType | BoolKey) – Whether or not to exploit the symmetry of the system in the phonon calculation.
BZPath (AMS._NumericalPhonons._BZPath) – If [NumericalPhonons%AutomaticBZPath] is false, the phonon dispersion curve will be computed for the user-defined path in the [BZPath] block. You should define the vertices of your path in fractional coordinates (with respect to the reciprocal lattice vectors) in the [Path] sub-block. If you want to make a jump in your path (i.e. have a discontinuous path), you need to specify a new [Path] sub-block.
Parallel (AMS._NumericalPhonons._Parallel) – Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
SuperCell (str | Sequence[str] | FreeBlock) – Used for the phonon run. The super lattice is expressed in the lattice vectors. Most people will find a diagonal matrix easiest to understand.
- class _BZPath[source]¶
If [NumericalPhonons%AutomaticBZPath] is false, the phonon dispersion curve will be computed for the user-defined path in the [BZPath] block. You should define the vertices of your path in fractional coordinates (with respect to the reciprocal lattice vectors) in the [Path] sub-block. If you want to make a jump in your path (i.e. have a discontinuous path), you need to specify a new [Path] sub-block.
- class _Parallel[source]¶
Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _PESExploration[source]¶
Configures details of the automated PES exploration methods.
- Variables:
CalculateEnergyReferences (BoolType | BoolKey) – Calculates the energy references.
CalculateFragments (BoolType | BoolKey) – Must be used together with an adsorbent set as the StatesAlignment%ReferenceRegion. Runs a final calculation of the adsorbate and adsorbent (marked by the ReferenceRegion) individually. The fragmented state is included in the energy landscape.
DynamicSeedStates (BoolType | BoolKey) – Whether subsequent expeditions may start from states discovered by previous expeditions. This should lead to a more comprehensive exploration of the potential energy surface. Disabling this will focus the PES exploration around the initial seed states.
FiniteDifference (float | FloatKey) – The finite difference distance to use for Dimer, Hessian, Lanczos, and optimization methods.
GenerateSymmetryImages (BoolType | BoolKey) – By activating this option, after concluding the energy landscape exploration process, it will create the complete set of symmetry-related copies by using the symmetry operators of the reference structure. SinglePoint calculations (including gradients and normal modes) are carried out for each new image structure obtained.
Job (Literal["ProcessSearch", "BasinHopping", "SaddleSearch", "LandscapeRefinement", "BindingSites", "NudgedElasticBand", "SystemMatching"]) – Specify the PES exploration job to perform.
NegativeEigenvalueTolerance (float | FloatKey) – The threshold in Hessian eigenvalue below which a mode is considered imaginary, i.e. indicating a transition state. This is a small negative number, as very small negative eigenvalues may be due to numerical noise on an essentially flat PES and do not indicate true transition states. We need a more flexible value for this parameter in PESExploration because the high computational cost of the task typically forces us to reduce the engine precision, which increases the noise in the vibrational frequencies evaluation. [PESPointCharacter%NegativeEigenvalueTolerance] is overridden by this parameter.
NumExpeditions (int | IntKey) – Sets the number of subsequent expeditions our job will consist of. Larger values result in a more comprehensive exploration of the potential energy surface, but will take more computational time.
NumExplorers (int | IntKey) – Sets the number of independent PES explorers dispatched as part of each expedition. Larger values will result in a more comprehensive exploration of the potential energy surface, but will take more computational time. By default an appropriate number of explorers are executed in parallel.
OptTSMethod (Literal["SaddleSearch", "NudgedElasticBand"]) – When the full set of states in the energy landscape are optimized (see PESExploration%Job = GeometryOptimization), transition states can be optimized using either SaddleSearch or NudgedElasticBand methods. SaddleSearch uses information only from the current geometry of the TS; contrary, NudgedElasticBand ignores the current geometry and runs a Nudged-Elastic-Band calculation trying to connect the associated reactants and products if they are available.
Potential (str | StringKey) – The PES to be explored. The default is to use a callback into AMS to evaluate the energy and gradients using an AMS engine. This can be changed here to give access to one of the EON client’s builtin potentials. This has not been well tested by SCM.
RandomSeed (int | IntKey) – Number used to initialize both the EON clients random number generators as well as the AMS global RNG. The latter is normally initialized with the RNGSeed keyword at the root level. Should be used by developers only. May or may not help to make more reproducible regression tests …
SelectedListedAtomsForPESPointCharacter (str | StringKey) – Uses the Hessian matrix elements only for the listed atoms to determine the PES point character of a located state during the exploration. If not specified, the full Hessian is used.
SelectedRegionForPESPointCharacter (str | StringKey) – Uses the Hessian matrix elements only for the atoms in a particular region to determine the PES point character of a located state during the exploration. If not specified, the full Hessian is used.
Temperature (float | FloatKey) – The temperature that the job will run at. This may be used in different ways depending on the job, e.g. acceptance probabilities for Monte-Carlo based jobs, thermostatting for dynamics based jobs, kinetic prefactors for jobs that find transition states. Some jobs may not use this temperature at all.
WriteEngineGradients (BoolType | BoolKey) – Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.
WriteHistory (Literal["None", "Converged", "All"]) – When to write the molecular geometry (and possibly other properties) to the history on the ams.rkf file. The default is to only write the converged geometries to the history. Can be changed to write no frames at all to the history, or write all frames (should only be used when testing because of the performance impact). Note that for parallel calculations, only the first group of processes writes to ams.rkf.
BasinHopping (AMS._PESExploration._BasinHopping) – Configures the details of the Basin Hopping subtask.
BindingSites (AMS._PESExploration._BindingSites) – Options related to the calculation of binding sites.
Debug (AMS._PESExploration._Debug) – ???.
Dynamics (AMS._PESExploration._Dynamics) – ???.
Hessian (AMS._PESExploration._Hessian) – ???.
LandscapeRefinement (AMS._PESExploration._LandscapeRefinement) – Configures details of the energy landscape refinement job.
LoadEnergyLandscape (AMS._PESExploration._LoadEnergyLandscape) – Options related to the loading of an Energy Landscape from a previous calculation.
LoadInitialSystems (AMS._PESExploration._LoadInitialSystems) – Load initial systems from different sources.
NudgedElasticBand (AMS._PESExploration._NudgedElasticBand) – Options for the Nudged Elastic Band (NEB) method.
Optimizer (AMS._PESExploration._Optimizer) – Configures the details of the geometry optimizers used by the PES explorers.
Parallel (AMS._PESExploration._Parallel) – Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
ParallelReplica (AMS._PESExploration._ParallelReplica) – ???.
Prefactor (AMS._PESExploration._Prefactor) – ???.
ProcessSearch (AMS._PESExploration._ProcessSearch) – Input options specific to the process search procedure.
SaddleSearch (AMS._PESExploration._SaddleSearch) – Configuration for the Saddle Search procedure (used in SaddleSearch and ProcessSearch Jobs).
StatesAlignment (AMS._PESExploration._StatesAlignment) – Configures details of how the energy landscape configurations are aligned respect to the main chemical system [System].
StructureComparison (AMS._PESExploration._StructureComparison) – Settings for structure comparison.
- class _BasinHopping[source]¶
Configures the details of the Basin Hopping subtask.
- Variables:
AdjustDisplacement (BoolType | BoolKey) – Automatically adjust the displacement size to meet the target acceptance ratio.
AdjustFraction (float | FloatKey) – The fraction by which to change the step size in order to meet the target acceptance ratio.
AdjustPeriod (int | IntKey) – The number of Monte Carlo steps between adjustments of the step size.
DisplaceAtomsInRegion (str | StringKey) – If you specify a region name here, only the atoms belonging to this region will be displaced during the basin hopping procedure. For more details on regions, see the documentation on the System definition.
Displacement (float | FloatKey) – Displacement in each degree of freedom.
DisplacementAlgorithm (Literal["Standard", "Linear", "Quadratic"]) – Undocumented in EON.
DisplacementDistribution (Literal["Uniform", "Gaussian"]) –
The distribution used for the displacement of each atom.
Gaussian: The value of the
Displacementkeyword serves as the standard deviation of a Gaussian distribution used to draw the nuclear displacements from.A random number is selected uniformly between
-DisplacementandDisplacement.
InitialRandomStructureProbability (float | FloatKey) – Probability to generate an entirely random structure to start the Basin Hopping from.
JumpMax (int | IntKey) – The number of consecutive rejected steps after which jump steps should be taken. This serves to provide a more global search when the structure is stuck in a certain basin. The number of jump steps is assigned in jump_steps. See paper on the Basin Hopping with Occasional Jumping algorithm by Iwamatsu and Okabe: Chem. Phys. Lett. 399 396 (2004)
JumpSteps (int | IntKey) – The number of jump steps to take after the
JumpMaxnumber of consecutive rejections have taken place.MainSystemAsSeed (BoolType | BoolKey) – If true, only the main system will be used as a seed state. The main system is not added to the database.
PESPointCharacterization (BoolType | BoolKey) – If true, a PES point characterization based on a vibrational analysis is carried out to confirm each detected state is an actual local minimum (no imaginary frequencies). Conversely, if this option is false, the PES point characterization is avoided, which will assume that all located states are local minima (zero gradients). Enabling this option is very useful for large systems. It circumvents the need for computing and diagonalizing the Hessian matrix, a typically expensive computational process.
PushApartDistance (float | FloatKey) – Push atoms apart until no atoms are closer than this distance. This criterion is enforced for the initial structure and all those generated by random displacements.
RotateNonListedAtoms (BoolType | BoolKey) – If true, each iteration randomly rotates all atoms as a rigid body, excluding those listed in [BasinHopping%DisplaceListedAtoms], [BasinHopping%DisplaceListedTypes], or [BasinHopping%DisplaceAtomsInRegion].
SignificantStructure (BoolType | BoolKey) – If true, the Significant Structure Basin Hopping (SSBH) variant instead of the Raw Structure Basin Hopping method (RSBH). In SSBH previously found structures are used as initial structures for further displacements, see Chem. Phys. Lett. 289, 463 (1998) for a comparison of the two approaches.
SingleAtomDisplace (BoolType | BoolKey) – If true, only one atom is displaced per step. Otherwise all atoms of the structure are randomly displaced.
Steps (int | IntKey) – Number of displace & optimize Monte-Carlo steps to take.
SwapProbability (float | FloatKey) – The probability in range [0,1] that a swapping step takes place instead of a displacement step. The swap step selects two atoms of different elements and swaps their position.
TargetRatio (float | FloatKey) – The target acceptance ratio that will be used to determine whether to increase or decrease the step size.
WriteUnique (BoolType | BoolKey) – If true, all unique states found will be included in the energy landscape, even the rejected ones. If false, only the lowest energy structure will be included in the energy landscape.
- class _BindingSites[source]¶
Options related to the calculation of binding sites.
- Variables:
Calculate (BoolType | BoolKey) – Calculate binding sites at the end of a job. Not needed for Binding Sites job.
DistanceDifference (float | FloatKey) – If the distance between two mapped binding-sites is larger than this threshold, the binding-sites are considered different. If not specified, its value will set equal to [PESExploration%StructureComparison%DistanceDifference]
MaxCoordinationShellsForLabels (int | IntKey) – The binding site labels are given based on the coordination numbers of shells in the reference region, using the following format: N<int><int>…, e.g., the label ‘N334’ means 3 atoms in the first coordination shell, 3 in the second one, and 4 in the third one. This parameter controls the maximum number of shells to include.
NeighborCutoff (float | FloatKey) – Atoms within this distance of each other are considered neighbors for the calculation of the binding sites. If not specified, its value will set equal to [PESExploration%StructureComparison%NeighborCutoff]
ReferenceRegion (str | StringKey) – Defines the region that is considered as the reference for binding sites detection. Binding sites are projected on this region using the geometry from the reference system. If not specified, its value will set equal to [PESExploration%StatesAlignment%ReferenceRegion]
- class _Dynamics[source]¶
???.
- Variables:
Thermostat (Literal["andersen", "nose_hoover", "langevin", "none"]) – ???.
Andersen (AMS._PESExploration._Dynamics._Andersen) – ???.
Langevin (AMS._PESExploration._Dynamics._Langevin) – ???.
Nose (AMS._PESExploration._Dynamics._Nose) – ???.
- class _LandscapeRefinement[source]¶
Configures details of the energy landscape refinement job.
- Variables:
CalculateOnlyEnergies (BoolType | BoolKey) – If true, the states’ geometry is not optimized, and the final PES point characterization is ignored [PESExploration%LandscapeRefinement%IgnoreFinalPESPointCharacter]. Only energy values are updated using the specified engine. Furthermore, normal modes and associated properties are copied from the previous calculation to avoid the typically high computational effort of the Hessian matrix calculation. Enabling this option implies that RunInitialSinglePoints=’F’, IgnoreFinalPESPointCharacter=’T’.
IgnoreFinalPESPointCharacter (BoolType | BoolKey) – At the end of the energy landscape refinement job, each state is assigned a PES point character (MIN or TS) based on its vibrational frequencies before being included in the final database. States are only added if the PES point character after refinement remains unchanged. However, states are added without verifying if this option is
true. Nonetheless, vibrational frequencies are calculated and stored for future analysis. This option is especially useful when using computationally demanding engines. Because in those cases, precision and computational effort must be balanced, resulting in significant vibrational frequencies inaccuracies.IgnoreFinalPESPointCharacterForFragments (BoolType | BoolKey) – Same as
LandscapeRefinement%IgnoreFinalPESPointCharacterbut regarding the Fragments calculations, see optionLandscapeRefinement%CalculateFragments.RelaxFromSaddlePoint (BoolType | BoolKey) – Relaxes the saddle point geometries following the imaginary mode to get both reactants and products.
RunInitialSinglePoints (BoolType | BoolKey) – If it is
true, just after loading the energy landscape to refine, the single energy point computations are disabled. Be aware that if you enable this, the output file’s ‘Initial Energy Landscape’ section will display incorrect states’ energy values. If the engine requires too much processing power, this option can help you save a small amount of time.TransitionStateSearchMethod (Literal["Auto", "Dimer"]) – Sets the method to refine transition states.
UseReactantsAndProductsForTSs (BoolType | BoolKey) – For the refinement of transition states, the reaction coordinate can be estimated using either the reactants or products (final system). By enabling this option, the difference between the initial and final geometries is utilized as the reaction coordinate. The final system with the lowest RMSD is chosen to determine this coordinate. For more details see the section [TransitionStateSearch].
- class _LoadEnergyLandscape[source]¶
Options related to the loading of an Energy Landscape from a previous calculation.
- Variables:
GenerateSymmetryImages (BoolType | BoolKey) – By activating this option, after loading the energy landscape, it will create the complete set of symmetry-related copies by using the symmetry operators of the reference structure. Be aware that rkf result files of the generated symmetry images are copies from the parent structures but only atomic coordinates are updated.
KeepOnly (Iterable[int] | IntListKey) – Upon loading the Energy Landscape, only keep the states specified here. The states should be specified via a list of integers referring to the indices of the states you want to keep.
Path (str | Path | StringKey) – AMS results folder to load an energy landscape from. In the text input file, you may alternatively specify a
.confile in the native EON format.Remove (Iterable[int] | IntListKey) – Upon loading the Energy Landscape, remove (i.e. do not load) the states specified here. The states should be specified via a list of integers referring to the indices of the states you want to remove (i.e. the states you don’t want to load).
RemoveWithNoBindingSites (BoolType | BoolKey) – Upon loading the Energy Landscape, it removes states with no associated binding sites. Associated transition states are also removed. This is an advantageous option to remove physisorbed states automatically. Notice that it requires that the previous calculation was executed, enabling the option [BindingSites%Calculate].
SeedStates (Iterable[int] | IntListKey) – By default when you start a new PES Exploration from a loaded Energy Landscape, expeditions can start from any of the loaded minima. By using this input option, you can instruct the program to only use some of the states as ‘expedition starting point’. The states that serve as ‘expedition starting points’ should be specified via a list of integers referring to the indices of the states.
- class _LoadInitialSystems[source]¶
Load initial systems from different sources.
- Variables:
FromKFHistory (AMS._PESExploration._LoadInitialSystems._FromKFHistory) – Load initial systems from the History section of kf files.
- class _NudgedElasticBand[source]¶
Options for the Nudged Elastic Band (NEB) method.
- Variables:
ClimbingImageConvergedOnly (BoolType | BoolKey) – ???.
ClimbingImageMethod (BoolType | BoolKey) – Use the climbing image algorithm to drive the highest image to the transition state.
ConvergedForce (float | FloatKey) – Convergence threshold for nuclear gradients. Note: Special value of -1.0 means using the same convergence criterion as the PES explorer’s geometry optimizer.
DoublyNudged (BoolType | BoolKey) – ???.
DoublyNudgedSwitching (BoolType | BoolKey) – ???.
ElasticBand (BoolType | BoolKey) – ???.
Images (int | IntKey) – Number of NEB images between the two endpoints.
MaxIterations (int | IntKey) – Maximum number of NEB iterations.
OldTangent (BoolType | BoolKey) – Use the old central difference tangent.
- class _Optimizer[source]¶
Configures the details of the geometry optimizers used by the PES explorers.
- Variables:
ConvergedForce (float | FloatKey) – Convergence threshold for nuclear gradients.
ConvergenceMetric (Literal["norm", "max_atom", "max_component"]) – Determines how the EON client checks the convergence of the forces.
normuses the Frobenius norm of the (3,nFreeAtoms) forces array.max_atomtakes the maximum norm2 of the nFreeAtoms individual force vectors on the free atoms.max_componentjust takes the maximum of all elements in the array. Don’t change this at the moment, as it will break snapshot writing to the history section of ams.rkf.MaxIterations (int | IntKey) – Maximum number of iterations allowed for optimizations.
Method (Literal["CG", "QM", "LBFGS", "FIRE", "SD"]) – Select the method for geometry optimizations.
CG (AMS._PESExploration._Optimizer._CG) – ???.
LBFGS (AMS._PESExploration._Optimizer._LBFGS) – ???.
QM (AMS._PESExploration._Optimizer._QM) – ???.
SD (AMS._PESExploration._Optimizer._SD) – ???.
- class _Parallel[source]¶
Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _ParallelReplica[source]¶
???.
- class _Prefactor[source]¶
???.
- Variables:
Rate (Literal["HTST", "QQHTST", "None"]) – Calculates reaction rate pre-exponential factors via: HTST (Harmonic Transition State Theory), QQHTST (quasi-quantum HTST), or None (disable calculation).
- class _ProcessSearch[source]¶
Input options specific to the process search procedure.
- Variables:
MinimizationOffset (float | FloatKey) – After a saddle is found, images are placed on either side of the saddle along the mode and minimized to ensure that the saddle is connected to the original minimum and to locate the product state. MinimizationOffset is the distance those images are displaced from the saddle.
MinimizeFirst (BoolType | BoolKey) – If true, every time a process search is run by a client the reactant will be minimized first before doing any saddle searches.
- class _SaddleSearch[source]¶
Configuration for the Saddle Search procedure (used in SaddleSearch and ProcessSearch Jobs).
- Variables:
ConvergedForce (float | FloatKey) – Convergence threshold for nuclear gradients. Note: Special value of -1.0 means using the same convergence criterion as the PES explorer’s geometry optimizer.
DisplaceAllAtoms (BoolType | BoolKey) – ???.
DisplaceAllListed (BoolType | BoolKey) – ???.
DisplaceAlongNormalModesActiveModes (str | StringKey) – Sets the active modes to be used when the option [SaddleSearch%DisplaceAlongNormalModesWeight] is enabled. e.g. 1,2,3,5. By default, all normal modes are considered active.
DisplaceAlongNormalModesWeight (float | FloatKey) – The probability of generating a displacement resulting in a random linear combination of the normal modes specified in [SaddleSearch%DisplaceAlongNormalModesActiveModes]. This parameter is a numeric value that should fall within the interval [0.0, 1.0].
DisplaceAtomsInRegion (str | StringKey) – A string corresponding to the name of a region. When performing the initial random displacement, only displace atoms in the specified region.
DisplaceAtomsInRegionWeight (float | FloatKey) – The probability of generating a displacement involving only atoms from the region specified in [SaddleSearch%DisplaceAtomsInRegion]. This parameter is a numeric value that should fall within the interval [0.0, 1.0].
DisplaceLeastCoordinatedWeight (float | FloatKey) – Relative probability to displace with an epicenter that has a coordination number equal to the least-coordinated atom in the configuration.
DisplaceListedAtomWeight (float | FloatKey) – Relative probability to displace with an epicenter listed in displace_atomlist.
DisplaceListedAtoms (str | StringKey) – Sets the active atoms to be used when the option [SaddleSearch%DisplaceAlongNormalModesWeight] is enabled. e.g. 1,2,3,5. By default, all normal modes are considered active.
DisplaceListedTypeWeight (float | FloatKey) – Relative probability to displace with an epicenter listed in displace_typelist.
DisplaceMagnitude (float | FloatKey) – The standard deviation of the Gaussian displacement in each degree of freedom for the selected atoms.
DisplaceNotFCCHCPWeight (float | FloatKey) – Relative probability to displace with an epicenter that is not FCC or HCP coordinated.
DisplaceRadius (float | FloatKey) – Atoms within this distance of the epicenter will be displaced.
DisplaceRandomWeight (float | FloatKey) – Relative probability to displace with a random epicenter.
DisplaceUnderCoordinatedWeight (float | FloatKey) – Relative probability to displace with an epicenter with a coordination equal to or less than displace_max_coordination.
MaxEnergy (float | FloatKey) – The energy (relative to the starting point of the saddle search) at which a saddle search explorer considers the search bad and terminates it.
MaxIterations (int | IntKey) – Maximum number of iterations for each saddle search run.
Method (Literal["min_mode", "dynamics", "basin_hopping", "bgsd"]) – Which saddle search method to use.
MinEnergyBarrier (float | FloatKey) – Minimum energy barrier to accept a new transition state.
MinModeMethod (Literal["dimer", "lanczos"]) – The minimum-mode following method to use.
RandomMode (BoolType | BoolKey) – ???.
RelaxFromSaddlePoint (BoolType | BoolKey) – Relaxes the saddle point geometries following the imaginary mode to get both reactants and products.
RemoveRotation (BoolType | BoolKey) – ???.
ZeroModeAbortCurvature (float | FloatKey) – The threshold in the frequency below which the minimum mode is considered zero. The calculation is aborted if the negative mode becomes zero.
- class _StatesAlignment[source]¶
Configures details of how the energy landscape configurations are aligned respect to the main chemical system [System].
- Variables:
DistanceDifference (float | FloatKey) – If the distance between two mapped atoms is larger than this threshold, the configuration is considered not aligned. If not specified, its value will set equal to [PESExploration%StructureComparison%DistanceDifference]
ReferenceRegion (str | StringKey) – Defines the region that is considered as the reference for alignments. Atoms outside this region are ignored in the alignments.
RemoveUnaligned (BoolType | BoolKey) – ???.
- class _StructureComparison[source]¶
Settings for structure comparison.
- Variables:
CheckRotation (BoolType | BoolKey) – Rotates the system optimally before comparing structures. The default is to do this only for molecular systems when there are no fixed atom constraints.
CheckSymmetry (BoolType | BoolKey) – Considers that two systems are equal if they are equivalent by symmetry.
CovalentScale (float | FloatKey) – Scale factor for the covalent distances used in the neighboring detection. Only used if [StructureComparison%UseCovalent] is enabled. This is an experimental feature!
DistanceDifference (float | FloatKey) – If the distance between two mapped atoms is larger than this threshold, the two configurations are considered different structures.
EnergyDifference (float | FloatKey) – If the energy difference between two configurations is larger than this threshold, the two configurations are considered to be different structures.
IndistinguishableAtoms (BoolType | BoolKey) – If yes, the order of the atoms does not affect the structural comparison. Atoms of the same element are then indistinguishable.
NeighborCutoff (float | FloatKey) – Atoms within this distance of each other are considered neighbors.
RemoveTranslation (BoolType | BoolKey) – Translates the system optimally before comparing structures. The default is to do this only when there are no fixed atom constraints.
UseCovalent (BoolType | BoolKey) – Atoms are considered neighbors if the distance between them is lower than [StructureComparison%CovalentScale] times the covalent distance calculated following M. O’Keeffe and N.E. Brese, J. Am. Chem.Soc. 113 (1991) 3226. This is an experimental feature!
- class _PESPointCharacter[source]¶
Options for the characterization of PES points.
- Variables:
Displacement (float | FloatKey) – Controls the size of the displacements used for numerical differentiation: The displaced geometries are calculated by taking the original coordinates and adding the mass-weighted mode times the reduced mass of the mode times the value of this keyword.
NegativeEigenvalueTolerance (float | FloatKey) – The threshold in Hessian eigenvalue below which a mode is considered imaginary, i.e. indicating a transition state. This is a small negative number, as very small negative eigenvalues may be due to numerical noise on an essentially flat PES and do not indicate true transition states.
NegativeFrequenciesTolerance (float | FloatKey) – The threshold in frequencies below which a mode is considered imaginary, i.e. indicating a transition state. Deprecated. Use NegativeEigenvalueTolerance instead.
NumberOfModes (int | IntKey) – The number of (lowest) eigenvalues that should be checked.
Tolerance (float | FloatKey) – Convergence tolerance for residual in iterative Davidson diagonalization.
- class _PESScan[source]¶
Configures the details of the potential energy surface scanning task.
- Variables:
CalcPropertiesAtPESPoints (BoolType | BoolKey) – Whether to perform an additional calculation with properties on all the sampled points of the PES. If this option is enabled AMS will produce a separate engine output file for every sampled PES point.
FillUnconvergedGaps (BoolType | BoolKey) – After the initial pass over the PES, restart the unconverged points from converged neighboring points.
ScanCoordinate (AMS._PESScan._ScanCoordinate) – Specifies a coordinate along which the potential energy surface is scanned. If this block contains multiple entries, these coordinates will be varied and scanned together as if they were one. Note that there can be only one ScanCoordinate containing a lattice scan in any PES scan job.
- class _ScanCoordinate[source]¶
Specifies a coordinate along which the potential energy surface is scanned. If this block contains multiple entries, these coordinates will be varied and scanned together as if they were one. Note that there can be only one ScanCoordinate containing a lattice scan in any PES scan job.
- Variables:
Angle (str | StringKey) – Scan the angle between three atoms. Three atom indices followed by two real numbers delimiting the transit range in degrees.
CellVolumeRange (Iterable[float] | FloatListKey) – Two numbers for the initial and final cell volume. The cell is scaled isotropically between these values. Can not be used together with any other coordinate within the same ScanCoordinate block.
CellVolumeScalingRange (Iterable[float] | FloatListKey) – Two scaling factors for the initial and final cell volume. A value of ‘0.9 1.1’ would result in an isotropic scaling between 90% and 110% of the cell volume of the input system. Can not be used together with any other coordinate within the same ScanCoordinate block.
Coordinate (str | StringKey) – Scan a particular coordinate of an atom. Atom index followed by (x|y|z) followed by two real numbers delimiting the transit range.
DifDist (str | StringKey) – Scan the difference distance between two pairs of atoms, R(12)-R(34). Four atom indices followed by two real numbers delimiting the transit range in Angstrom.
Dihedral (str | StringKey) – Scan the dihedral angle between four atoms. Four atom indices followed by two real numbers delimiting the transit angle in degrees.
Distance (str | StringKey) – Scan the distance between two atoms. Two atom indices followed by two real numbers delimiting the transit distance in Angstrom.
FromStrainVoigt (Iterable[float] | FloatListKey) – The elements of the initial lattice strain in Voigt notation. One should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems. Has to be used in combination with the ToStrainVoigt keyword and no other coordinate within the same ScanCoordinate block.
LatticeARange (Iterable[float] | FloatListKey) – Scans the length of the first lattice vector. Can be combined with the LatticeBRange and LatticeCRange keywords, but no other coordinates within the same ScanCoordinate.
LatticeBRange (Iterable[float] | FloatListKey) – Scans the length of the second lattice vector. Can be combined with the LatticeARange and LatticeCRange keyword, but no other coordinates within the same ScanCoordinate..
LatticeCRange (Iterable[float] | FloatListKey) – Scans the length of the third lattice vector. Can be combined with the LatticeARange and LatticeBRange keyword, but no other coordinates within the same ScanCoordinate..
SumDist (str | StringKey) – Scan the sum of distances between two pairs of atoms, R(12)+R(34). Four atom indices followed by two real numbers delimiting the transit range in Angstrom.
ToStrainVoigt (Iterable[float] | FloatListKey) – The elements of the final lattice strain in Voigt notation. One should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
nPoints (int | IntKey) – The number of points along the scanned coordinate. Must be greater or equal 2.
FromLattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors to start the scan at. Has to be used in combination with the ToLattice keyword and no other coordinate within the same ScanCoordinate block. Unit can be specified in the header. Default unit is Angstrom.
ToLattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors to end the scan at. Unit can be specified in the header. Default unit is Angstrom.
- class _Phonons[source]¶
Configures the phonons calculation.
- Variables:
BandStructure (BoolType | BoolKey) – Calculates and saves the phonon band structure for visualization. Further configuration options for analytical calculations may be available in the engine-specific settings (
Phonons%BandStructure).DOS (BoolType | BoolKey) – Calculates and saves the phonon density of states (DOS) for visualization. Further configuration options for analytical calculations may be available in the engine-specific settings (
Phonons%DOS).Method (Literal["Auto", "Analytical", "Numerical"]) – Determines how phonons are calculated.
Autoselects the analytical method if supported by the engine, otherwise it defaults to numerical calculation. Configure numerical parameters in theNumericalPhononssection. Engine-specific options for analytical phonon calculations may be available inEngine%Phonons.
- class _Print[source]¶
This block controls the printing of additional information to stdout.
- Variables:
Timers (Literal["None", "Normal", "Detail", "TooMuchDetail"]) – Printing timing details to see how much time is spend in which part of the code.
- class _Properties[source]¶
Configures which AMS level properties to calculate for SinglePoint calculations or other important geometries (e.g. at the end of an optimization).
- Variables:
BondOrders (BoolType | BoolKey) –
Requests the engine to calculate bond orders.
For MM engines these might just be the defined bond orders that go into the force-field, while for QM engines, this might trigger a bond order analysis based on the electronic structure. For engines that do not have a bond order analysis method, a bond guessing algorithm will be used. See also the input options in the BondOrders block.
Charges (BoolType | BoolKey) – Requests the engine to calculate the atomic charges.
DipoleGradients (BoolType | BoolKey) – Requests the engine to calculate the nuclear gradients of the electric dipole moment of the molecule. This can only be requested for non-periodic systems.
DipoleMoment (BoolType | BoolKey) – Requests the engine to calculate the electric dipole moment of the molecule. This can only be requested for non-periodic systems.
ElasticTensor (BoolType | BoolKey) – Calculate the elastic tensor.
GSES (BoolType | BoolKey) – Requests the engine to calculate the gradients of ground to excited state properties.
Gradients (BoolType | BoolKey) – Calculate the nuclear gradients.
Hessian (BoolType | BoolKey) – Whether or not to calculate the Hessian.
Molecules (BoolType | BoolKey) – Requests an analysis of the molecular components of a system, based on the bond orders calculated by the engine.
NormalModes (BoolType | BoolKey) – Calculate the frequencies and normal modes of vibration, as well as the corresponding IR intensities, if the engine supports these calculations natively or can calculate dipole moments.
OrbitalsInfo (BoolType | BoolKey) – Basic molecular orbitals information: orbital energies, occupations, HOMO, LUMO and HOMO-LUMO gap.
Other (BoolType | BoolKey) – Other (engine specific) properties. Details are configured in the engine block.
PESPointCharacter (BoolType | BoolKey) – Determine whether the sampled PES point is a minimum or saddle point. Note that for large systems this does not entail the calculation of the full Hessian and can therefore be used to quickly confirm the success of a geometry optimization or transition state search.
Phonons (BoolType | BoolKey) – Calculate the phonons (for periodic systems).
Polarizability (BoolType | BoolKey) – Requests the engine to calculate the polarizability tensor of the system.
Raman (BoolType | BoolKey) – Requests calculation of Raman intensities for vibrational normal modes.
SelectedRegionForHessian (str | StringKey) – Compute the Hessian matrix elements only for the atoms in a particular region. If not specified, the Hessian will be computed for all atoms.
StressTensor (BoolType | BoolKey) – Calculate the stress tensor.
UncertaintyScore (BoolType | BoolKey) – Request the engine to state how (un)certain it is about its results. Higher number means less certain but specific implementation depends on engine.
VCD (BoolType | BoolKey) – Requests calculation of VCD for vibrational normal modes.
VROA (BoolType | BoolKey) – Requests calculation of VROA for vibrational normal modes.
- class _Raman[source]¶
Configures details of the Raman or VROA calculation.
- Variables:
FreqRange (Iterable[float] | FloatListKey) – Specifies a frequency range within which all modes will be scanned. 2 numbers: an upper and a lower bound.
IncidentFrequency (float | FloatKey) – Frequency of incident light.
LifeTime (float | FloatKey) – Specify the resonance peak width (damping) in Hartree units. Typically the lifetime of the excited states is approximated with a common phenomenological damping parameter. Values are best obtained by fitting absorption data for the molecule, however, the values do not vary a lot between similar molecules, so it is not hard to estimate values. A typical value is 0.004 Hartree.
- class _Replay[source]¶
Configures the details of the Replay task.
- Variables:
Atoms (Iterable[int] | IntListKey) – List of atom indices to include in the replay. All other atoms will be removed before the calculation of energy (and possible other properties). If this keyword is not specified, all atoms will be used for the replay. This keyword can currently not be used for trajectory with a changing number of atoms between frames, e.g. MD trajectories with molecule guns and sinks.
File (str | Path | StringKey) – Provide an ams.rkf file (or a .results folder) from a previously run job to replay. The file needs to contain a History section.
Frames (Iterable[int] | IntListKey) –
List of frames from the History section to recompute.
If not specified the recomputed frames are determined automatically based on the task of the job that is being replayed: PES scans and NEB calculations will only have the converged points replayed, while all other tasks will have all frames recomputed.
Specifying the frames to recompute in the input is probably only useful when replaying trajectories from MolecularDynamics calculations.
StoreAllResultFiles (BoolType | BoolKey) –
If this option is enabled AMS will produce a separate engine output file for every replayed frame.
While basic properties like energy, gradients, stress tensor, etc. are stored anyway on the History section in the AMS driver output file (if they were requested in the Properties block), engine specific properties (e.g. excitations energies from ADF) will only be available if the full result files are stored.
- class _Restraints[source]¶
The Restraints block allows to add soft constraints to the system. A restraint is a potential energy function (a spring) attached to a certain coordinate, for example, an interatomic distance, with its minimum at the specified optimal value. A restraint is defined using one or two parameters: the ForceConstant and, for some types, the F(Inf) value. The ForceConstant parameter corresponds to second derivative of the restraint potential energy d2V(x)/dx^2 for any x (harmonic restraints) or only at at x=0 (other restraints). Here, x is a deviation from the restraint’s optimal value.
- Variables:
Angle (str | StringKey) – Specify three atom indices i j k followed by an angle in degrees and, optionally, by the ForceConstant (default is 0.3 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the i-j-k angle at the given value. For periodic systems this restraint follows the minimum image convention.
DifDist (str | StringKey) – Specify four atom indices i j k l followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the difference R(ij)-R(kl) at the given value. For periodic systems this restraint follows the minimum image convention.
Dihedral (str | StringKey) – Specify four atom indices i j k l followed by an angle in degrees and, optionally, by the ForceConstant (default is 0.1 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the i-j-k-l dihedral angle at the given value. For periodic systems this restraint follows the minimum image convention.
Distance (str | StringKey) – Specify two atom indices followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the distance between the two specified atoms at the given value. For periodic systems this restraint follows the minimum image convention.
FInfinity (float | FloatKey) –
Specify the default asymptotic value for the restraint force for the Hyperbolic and Erf profiles, in Hartree/Bohr or Hartree/radian.
A per-restraint value can be specified after the profile type on the corresponding restraint line.
Profile (Literal["Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) –
Select the default type of restraint profile.
The harmonic profile is most suitable for geometry optimizations but may result is very large forces that can be problematic in molecular dynamic.
For MD simulations the Hyperbolic or Erf may be more suitable because the restraint force is bounded by a user-defined value.
A per-restraint profile type can be specified after the ForceConstant value on the corresponding restraint line.
SumDist (str | StringKey) – Specify four atom indices i j k l followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the sum R(ij)+R(kl) at the given value. For periodic systems this restraint follows the minimum image convention.
Units (Literal["Default", "MD"]) – Change units for energy, force and force constant values from the default (atomic units) to those often used in the MD community (based on kcal/mol and Angstrom). Units for the optimal distances are not affected and are always Angstrom.
- class _RigidMotions[source]¶
Specify which rigid motions of the total system are allowed. An external field is not considered part of the system. Normally the automatic option is doing what you want. However this feature can be used as a means of geometry constraint.
- Variables:
AllowRotations (Literal["Auto", "None", "All", "X", "Y", "Z", "XY", "XZ", "YZ"]) – Which overall rotations of the system are allowed
AllowTranslations (Literal["Auto", "None", "All", "X", "Y", "Z", "XY", "XZ", "YZ"]) – Which overall transitions of the system are allowed
Tolerance (float | FloatKey) – Tolerance for detecting linear molecules. A large value means larger deviation from linearity is permitted.
- class _SCMLibrary[source]¶
Technical settings affecting src/lib
- Variables:
ShellBasedNAFS (BoolType | BoolKey) – Assume that the NAFS are ordered by shell, this allows for a faster evaluation.
- class _SCMMatrix[source]¶
Technical settings for programs using the AMT matrix system. Currently this is only used by DFTB
- Variables:
Type (Literal["Auto", "Reference", "ScaLapack", "Elpa"]) – Determines which implementation is used to support the AbstractMatrixType.
DistributedMatrix (AMS._SCMMatrix._DistributedMatrix) – Technical settings for Distributed matrices
- class _SerializedTensors[source]¶
Technical settings affecting the SerializedTensors module, currently only used for HartreeFock
- Variables:
AllowZeroSize (BoolType | BoolKey) – When the data is blocked, can the size be zero?
IntegerDataBlockSize (int | IntKey) – Integer (meta) data per tensor may be aligned by using a blockSize, only relevant when sparseness is used.
RealDataBlockSize (int | IntKey) – Real data per tensor may be aligned by using a blockSize
SparseDataImplementation (int | IntKey) –
use three ftlDynArrays per tensor. 2) use one big shared array.
- class _System[source]¶
Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- Variables:
AllowCloseAtoms (BoolType | BoolKey) – No longer functional. Just here for backwards compatibility.
Charge (float | FloatKey) – The system’s total charge in atomic units.
FractionalCoords (BoolType | BoolKey) – Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
GeometryFile (str | Path | StringKey) – Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds (BoolType | BoolKey) – Equivalent to ‘Modify%GuessBonds’. Please update input file to use ‘Modify’ block instead.
LatticeStrain (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%LatticeStrain’. Please update input file to use ‘Modify’ block instead.
MapAtomsToUnitCell (BoolType | BoolKey) – Equivalent to ‘Modify%MapAtomsToUnitCell’. Please update input file to use ‘Modify’ block instead.
PerturbCoordinates (float | FloatKey) – Equivalent to ‘Modify%PerturbCoordinates’. Please update input file to use ‘Modify’ block instead.
PerturbLattice (float | FloatKey) – Equivalent to ‘Modify%PerturbLattice’. Please update input file to use ‘Modify’ block instead.
ShiftCoordinates (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%Translate’, but in the unit of bohr by default. Please update input file to use ‘Modify’ block instead.
SuperCell (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCell’. Please update input file to use ‘Modify’ block instead.
SuperCellTrafo (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCellTrafo’. Please update input file to use ‘Modify’ block instead.
Symmetrize (BoolType | BoolKey) – Equivalent to ‘Modify%Symmetrize’. Please update input file to use ‘Modify’ block instead.
Atoms (str | Sequence[str] | FreeBlock) – The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders (str | Sequence[str] | FreeBlock) – Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
ElectrostaticEmbedding (AMS._System._ElectrostaticEmbedding) – Container for electrostatic embedding options, which can be combined.
Lattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
Modify (AMS._System._Modify) – Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- class _Atoms[source]¶
The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
- class _BondOrders[source]¶
Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
- class _ElectrostaticEmbedding[source]¶
Container for electrostatic embedding options, which can be combined.
- Variables:
ElectricField (Iterable[float] | FloatListKey) –
External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.
In atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 … e11 V/m.
Supported by the engines adf, band, dftb and mopac.
For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
MultipolePotential (AMS._System._ElectrostaticEmbedding._MultipolePotential) – External point charges (and dipoles).
- class _MultipolePotential[source]¶
External point charges (and dipoles).
- Variables:
ChargeModel (Literal["Point", "Gaussian"]) – A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
ChargeWidth (float | FloatKey) – The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
Coordinates (str | Sequence[str] | FreeBlock) –
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Coordinates[source]¶
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Lattice[source]¶
Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
- class _Modify[source]¶
Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- Variables:
EnableAtomicProperties (Literal["gui", "adf", "band", "forcefield", "dftb", "reaxff", "qe"]) – Enables an atomic property group. This is only necessary if you want a group enabled, but no atom in the input is using any property from that group.
GuessBonds (BoolType | BoolKey) – Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.
LatticeStrain (Iterable[float] | FloatListKey) – Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
MapAtomsToUnitCell (Iterable[float] | FloatListKey) – For periodic systems the atoms will be moved to the central unit cell where all their fractional coordinates are in the range [start_range,start_range+1). No mapping will take place along non-periodic directions. If just a single number is given, it corresponds to start_range. If multiple numbers are given, they should match the number of lattice vectors and will be used as start ranges along the individual lattice vectors. If no number is given at all, the mapping will be done to the [-0.5:0.5) cell.
PerturbCoordinates (float | FloatKey) – Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
PerturbLattice (float | FloatKey) – Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
SuperCell (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
SuperCellTrafo (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
Symmetrize (BoolType | BoolKey) – Symmetrizes the atomic coordinates to machine precision and rototranslates the molecule to the AMS standard orientation. This allows optimal use of the system’s symmetry for calculations with the AMS driver and its engines.
Translate (Iterable[float] | FloatListKey) – Translate all atoms by a vector.
- class _Thermo[source]¶
Options for thermodynamic properties (assuming an ideal gas). The properties are computed for all specified temperatures.
- Variables:
Pressure (float | FloatKey) – The pressure at which the thermodynamic properties are computed.
Temperatures (Iterable[float] | FloatListKey) – List of temperatures at which the thermodynamic properties will be calculated.
UseSymmetryForEntropy (BoolType | BoolKey) – Use symmetry for the calculation of rotational entropy.
LowFrequencyCorrector (AMS._Thermo._LowFrequencyCorrector) – Options for the dampener-powered free rotor interpolator that corrects thermodynamic quantities for low frequencies. See DOI:10.1021/jp509921r and DOI:10.1002/chem.201200497.
- class _LowFrequencyCorrector[source]¶
Options for the dampener-powered free rotor interpolator that corrects thermodynamic quantities for low frequencies. See DOI:10.1021/jp509921r and DOI:10.1002/chem.201200497.
- Variables:
Alpha (float | FloatKey) – The exponent term used in the dampener.
Frequency (float | FloatKey) – The frequency around which the dampener interpolates between harmonic oscillator and free rotor quantities.
MomentOfInertia (float | FloatKey) – The moment of inertia used to restrict entropy results for very small frequencies (generally around less than 1 cm-1).
- class _TransitionStateSearch[source]¶
Configures some details of the transition state search.
- Variables:
ModeToFollow (int | IntKey) – In case of Transition State Search, here you can specify the index of the normal mode to follow (1 is the mode with the lowest frequency).
ReactionCoordinate (AMS._TransitionStateSearch._ReactionCoordinate) – Specify components of the transition state reaction coordinate (TSRC) as a linear combination of internal coordinates (distances or angles).
- class _ReactionCoordinate[source]¶
Specify components of the transition state reaction coordinate (TSRC) as a linear combination of internal coordinates (distances or angles).
- Variables:
Angle (str | StringKey) – The TSRC contains the valence angle between the given atoms. Three atom indices followed by the weight.
Block (str | StringKey) – Name of the region. Only atoms of the region will be included in the TSRC. It is useful when computing the reaction coordinate from the initial Hessian, in which case only part of the Hessian will be analyzed.
BlockAtoms (Iterable[int] | IntListKey) – List of atom indices. Only the listed atoms will be included in the TSRC. It is useful when computing the reaction coordinate from the initial Hessian, in which case only part of the Hessian will be analyzed.
Coordinate (str | StringKey) – The TSRC contains Cartesian displacement of an atom: atom index followed by [x|y|z] and the weight.
Dihedral (str | StringKey) – The TSRC contains the dihedral angle between the given atoms. Four atom indices followed by the weight.
Distance (str | StringKey) – The TSRC contains the distance between the given atoms. Two atom indices followed by the weight.
- class _VibrationalAnalysis[source]¶
Input data for all vibrational analysis utilities in the AMS driver.
- Variables:
Displacement (float | FloatKey) – Step size for finite difference calculations.
Quiet (BoolType | BoolKey) – Suppress run-time output
Type (Literal["ModeScanning", "ModeTracking", "ModeRefinement", "VibronicStructure", "VibronicStructureTracking", "VibronicStructureRefinement", "ResonanceRaman"]) – Specifies the type of vibrational analysis that should be performed
VSTRestartFile (str | Path | StringKey) – Path to a .rkf file containing restart information for VST.
AbsorptionSpectrum (AMS._VibrationalAnalysis._AbsorptionSpectrum) – Settings related to the integration of the spectrum for vibronic tasks.
ExcitationSettings (AMS._VibrationalAnalysis._ExcitationSettings) – Block that contains settings related to the excitation for vibronic tasks.
ModeTracking (AMS._VibrationalAnalysis._ModeTracking) – Input data for Mode Tracking.
NormalModes (AMS._VibrationalAnalysis._NormalModes) – All input related to processing of normal modes. Not available for vibronic structure tracking (as no modes are required there).
ResonanceRaman (AMS._VibrationalAnalysis._ResonanceRaman) – Block that contains settings for the calculation of Resonance Raman calculations
- class _AbsorptionSpectrum[source]¶
Settings related to the integration of the spectrum for vibronic tasks.
- Variables:
AbsorptionRange (Iterable[float] | FloatListKey) – Specifies frequency range of the vibronic absorption spectrum to compute. 2 numbers: an upper and a lower bound.
FrequencyGridPoints (int | IntKey) – Number of grid points to use for the spectrum
IntegrationThreshold (float | FloatKey) – Value of exponential damping in absorption cross-section used to define upper integration limit.
SpectrumOffset (Literal["absolute", "relative"]) – Specifies whether provided frequency range are absolute frequencies or frequencies relative to computed 0-0 excitation energy.
TimeStep (float | FloatKey) – Value of time step for spectrum integration.
- class _ExcitationSettings[source]¶
Block that contains settings related to the excitation for vibronic tasks.
- Variables:
EnergyInline (float | FloatKey) – Vertical excitation energy, used when [ExcitationInfo] = [Inline].
ExcitationFile (str | Path | StringKey) – Path to a .rkf/.t21 file containing the excited state information (gradients, transition dipoles and energies).
ExcitationInputFormat (Literal["File", "Inline"]) – Select how the application should retrieve the excited state information (energy, gradient).
GradientInline (str | Sequence[str] | FreeBlock) – Excited state gradient at ground state equilibrium geometry, used when [ExcitationInfo] = [Inline].
Singlet (str | Sequence[str] | FreeBlock) – Symmetry labels + integer indices of desired singlet transitions (VG-FC absorption spectra support only 1 at a time)
Triplet (str | Sequence[str] | FreeBlock) – Symmetry labels + integer indices of desired triplet transitions (VG-FC absorption spectra support only 1 at a time)
- class _GradientInline[source]¶
Excited state gradient at ground state equilibrium geometry, used when [ExcitationInfo] = [Inline].
- class _ModeTracking[source]¶
Input data for Mode Tracking.
- Variables:
GramSchmidt (BoolType | BoolKey) – Turn on/off gram-schmidt orthogonalization of new vectors to alter convergence.
GramSchmidtIterations (int | IntKey) – Maximum number of gram-schmidt orthogonalization steps per iteration.
GramSchmidtTolerance (float | FloatKey) – Tolerance for checking orthogonality when expanding the basis.
HessianGuess (Literal["Unit", "File", "CalculateWithFastEngine", "Inline"]) – Sets how to obtain the guess for the Hessian used in the preconditioner (if one is to be used).
HessianPath (str | Path | StringKey) – Path to a .rkf file containing the initial guess for the Hessian, used when [HessianGuess] = [File]. It may also be the name of the results folder containing the engine file.
MaxIterations (int | IntKey) – Maximum number of allowed iterations.
RemoveRigids (BoolType | BoolKey) – Orthogonalize tracked vectors against rigid modes
ToleranceForBasis (float | FloatKey) – Convergence tolerance for the contribution of the newest basis vector to the tracked mode.
ToleranceForNorm (float | FloatKey) – Convergence tolerance for residual RMS value.
ToleranceForResidual (float | FloatKey) – Convergence tolerance for the maximum component of the residual vector.
ToleranceForSpectrum (float | FloatKey) – Convergence tolerance for the spectrum in Vibronic Structure Tracking.
TrackingMethod (Literal["OverlapInitial", "DifferenceInitial", "FreqInitial", "IRInitial", "OverlapPrevious", "DifferencePrevious", "FreqPrevious", "IRPrevious", "HighestFreq", "HighestIR", "LowestFreq", "LowestResidual"]) – Set the tracking method that will be used. Vibronic Structure Tracking uses Largest Displacement.
UpdateMethod (Literal["JD", "D", "I"]) – Chooses the method for expanding the Krylov subspace: (I) No preconditioner (VST default), (D) Davidson or (JD) vdVorst-Sleijpen variant of Jacobi-Davidson (Mode tracking default).
HessianInline (str | Sequence[str] | FreeBlock) – Initial guess for the (non-mass-weighted) Hessian in a 3N x 3N block, used when [HessianGuess] = [Inline].
- class _NormalModes[source]¶
All input related to processing of normal modes. Not available for vibronic structure tracking (as no modes are required there).
- Variables:
MassWeightInlineMode (BoolType | BoolKey) – MODE TRACKING ONLY: The supplied modes must be mass-weighted. This tells the program to mass-weight the supplied modes in case this has not yet been done. (True means the supplied modes will be mass-weighted by the program, e.g. the supplied modes are non-mass-weighted.)
ModeFile (str | Path | StringKey) – Path to a .rkf or .t21 file containing the modes which are to be scanned. Which modes will be scanned is selected using the criteria from the [ModeSelect] block.) This key is optional for Resonance Raman and Vibronic Structure. These methods can also calculate the modes using the engine.
ModeInputFormat (Literal["File", "Inline", "Hessian"]) – Set how the initial guesses for the modes are supplied. Only mode tracking supports the Inline and Hessian options.
ScanModes (BoolType | BoolKey) – Supported by: Mode Tracking, Mode Refinement, Vibronic Structure Refinement: If enabled an additional displacement will be performed along the new modes at the end of the calculation to obtain refined frequencies and IR intensities. Equivalent to running the output file of the mode tracking calculation through the AMS ModeScanning task.
ModeInline (str | Sequence[str] | FreeBlock) – MODE TRACKING ONLY: Coordinates of the mode which will be tracked in a N x 3 block (same as for atoms), used when [ModeInputFormat] = [Inline]. Rows must be ordered in the same way as in the [System%Atoms] block. Mode Tracking only.
ModeSelect (AMS._VibrationalAnalysis._NormalModes._ModeSelect) – Pick which modes to read from file.
- class _ModeInline[source]¶
MODE TRACKING ONLY: Coordinates of the mode which will be tracked in a N x 3 block (same as for atoms), used when [ModeInputFormat] = [Inline]. Rows must be ordered in the same way as in the [System%Atoms] block. Mode Tracking only.
- class _ModeSelect[source]¶
Pick which modes to read from file.
- Variables:
DisplacementBound (float | FloatKey) – Vibronic Structure (Refinement), Resonance Raman: Select all modes with a dimensionless oscillator displacement greater than the specified value.
FreqAndIRRange (Iterable[float] | FloatListKey) – Specifies a combined frequency and IR intensity range within which all modes will be selected. First 2 numbers are the frequency range in cm-1, last 2 numbers are the IR intensity range in km/mol.
FreqRange (Iterable[float] | FloatListKey) – Specifies a frequency range within which all modes will be selected. 2 numbers: an upper and a lower bound. Calculating all modes higher than some frequency can be achieved by making the upper bound very large.
Full (BoolType | BoolKey) – Select all modes. This only make sense for Mode Scanning calculations.
HighFreq (int | IntKey) – Select the N modes with the highest frequencies.
HighIR (int | IntKey) – Select the N modes with the largest IR intensities.
IRRange (Iterable[float] | FloatListKey) – Specifies an IR intensity range within which all modes will be selected. 2 numbers: an upper and a lower bound.
ImFreq (BoolType | BoolKey) – Select all modes with imaginary frequencies.
LargestDisplacement (int | IntKey) – Vibronic Structure (Refinement), Resonance Raman: Select the N modes with the largest VG-FC displacement.
LowFreq (int | IntKey) – Select the N modes with the lowest frequencies. Includes imaginary modes which are recorded with negative frequencies.
LowFreqNoIm (int | IntKey) – Select the N modes with the lowest non-negative frequencies. Imaginary modes have negative frequencies and are thus omitted here.
LowIR (int | IntKey) – Select the N modes with the smallest IR intensities.
ModeNumber (Iterable[int] | IntListKey) – Indices of the modes to select.
- class _ResonanceRaman[source]¶
Block that contains settings for the calculation of Resonance Raman calculations
- Variables:
IncidentFrequency (float | FloatKey) – Frequency of incident light. Also used to determine most important excitation in case more than one is provided.
LifeTime (float | FloatKey) – Lifetime of Raman excited state.
MaximumStates (int | IntKey) – Maximum number of final states included in the spectrum.
RamanOrder (int | IntKey) – Order up to which to compute Raman transitions
RamanRange (Iterable[float] | FloatListKey) – Specifies frequency range of the Raman spectrum to compute. 2 numbers: an upper and a lower bound.
- class AMSBatch[source]¶
- Variables:
EngineRestart (str | Path | StringKey) –
The path to the file from which to restart the engine.
Should be a proper engine result file (like adf.rkf, band.rkf etc), or the name of the results directory containing it.
FallbackSolveAfterEngineFailure (BoolType | BoolKey) – If the engine fails to Solve, try to re-run the Solve without restarting the engine from the previous results. This generally decreases the engine failure rate. Only relevant certain tasks, such as GeometryOptimization, MolecularDynamics, Replay, IRC.
LoadEngine (str | Path | StringKey) – The path to the file from which to load the engine configuration. Replaces the Engine block.
RNGSeed (Iterable[int] | IntListKey) – Initial seed for the (pseudo)random number generator. This should be omitted in most calculations to avoid introducing bias into the results. If this is unset, the generator will be seeded randomly from external sources of entropy. If you want to exactly reproduce an older calculation, set this to the numbers printed in its output.
Task (Literal["GCMC", "GeometryOptimization", "Idle", "IRC", "MolecularDynamics", "NEB", "PESExploration", "PESScan", "Pipe", "Replay", "SinglePoint", "SteepestDescent", "TestEngine", "TestSymmetry", "TransitionStateSearch", "VibrationalAnalysis"]) –
Specify the computational task to perform:
Single Point: keep geometry as is
Geometry Optimization: minimize energy
Transition State: search for a transition state
IRC: intrinsic reaction coordinate
PES Scan: scan the potential energy surface
NEB: Nudged elastic band for reaction path optimization
Vibrational Analysis: perform one of the analysis types selected on the options page
Molecular Dynamics: perform MD simulation
GCMC: Grand Canonical Monte Carlo simulation
PES Exploration: automated potential energy surface exploration
Replay: recompute frames from the trajectory of a previously run job
Test (Literal["Symmetry", "BareSymmetry", "Bonds", "SecondOrderBonds", "AtomTyping", "SystemMatching"]) – various technical tests that will be done for the system
UseSymmetry (BoolType | BoolKey) – Whether to use the system’s symmetry in AMS. Symmetry is recognized within a tolerance as given in the Symmetry key.
BondOrders (AMSBatch._BondOrders) – Configures details regarding the calculation/guessing of bond orders. To request the calculation of bond orders, use the ‘Properties%BondOrders’ key.
Constraints (AMSBatch._Constraints) – The Constraints block allows geometry optimizations and potential energy surface scans with constraints. The constraints do not have to be satisfied at the start of the calculation.
ElasticTensor (AMSBatch._ElasticTensor) – Options for numerical evaluation of the elastic tensor.
Engine (EngineBlock) – The input for the computational engine. The header of the block determines the type of the engine.
EngineAddons (AMSBatch._EngineAddons) – This block configures all the engine add-ons.
EngineDebugging (AMSBatch._EngineDebugging) – This block contains some options useful for debugging the computational engines.
ExitCondition (AMSBatch._ExitCondition) – If any of the specified exitconditions are met, the AMS driver will exit cleanly.
GCMC (AMSBatch._GCMC) –
This block controls the Grand Canonical Monte Carlo (GCMC) task.
By default, molecules are added at random positions in the simulation box. The initial position is controlled by
GeometryOptimization (AMSBatch._GeometryOptimization) – Configures details of the geometry optimization and transition state searches.
IEEEExceptions (AMSBatch._IEEEExceptions) – Whether this works or not depends on the way the program is compiled (compiler and settings). Only useful for developers debugging some numerical issue.
IRC (AMSBatch._IRC) – Configures details of the Intrinsic Reaction Coordinate optimization.
Idle (AMSBatch._Idle) – Configures details of the idle task, which does nothing for a specified amount of time.
LoadSystem (AMSBatch._LoadSystem) – Block that controls reading the chemical system from a KF file instead of the [System] block.
Log (str | Sequence[str] | FreeBlock) – Configures the debugging loggers. Syntax: ‘Level LoggerName’. Possible Levels: All, Debug, Info, Warning, Error, Fatal.
MolecularDynamics (AMSBatch._MolecularDynamics) – Configures molecular dynamics (with the velocity-Verlet algorithm) with and without thermostats. This block allows to specify the details of the molecular dynamics calculation.
Molecules (AMSBatch._Molecules) – Configures details of the molecular composition analysis enabled by the Properties%Molecules block.
NEB (AMSBatch._NEB) – Configures details of the Nudged Elastic Band optimization.
NormalModes (AMSBatch._NormalModes) – Configures details of a normal modes calculation.
NumericalDifferentiation (AMSBatch._NumericalDifferentiation) – Define options for numerical differentiations, that is the numerical calculation of gradients, Hessian and the stress tensor for periodic systems.
NumericalPhonons (AMSBatch._NumericalPhonons) – Configures details of a numerical phonons calculation.
PESExploration (AMSBatch._PESExploration) – Configures details of the automated PES exploration methods.
PESPointCharacter (AMSBatch._PESPointCharacter) – Options for the characterization of PES points.
PESScan (AMSBatch._PESScan) – Configures the details of the potential energy surface scanning task.
Phonons (AMSBatch._Phonons) – Configures the phonons calculation.
Print (AMSBatch._Print) – This block controls the printing of additional information to stdout.
Properties (AMSBatch._Properties) – Configures which AMS level properties to calculate for SinglePoint calculations or other important geometries (e.g. at the end of an optimization).
Raman (AMSBatch._Raman) – Configures details of the Raman or VROA calculation.
Replay (AMSBatch._Replay) – Configures the details of the Replay task.
Restraints (AMSBatch._Restraints) – The Restraints block allows to add soft constraints to the system. A restraint is a potential energy function (a spring) attached to a certain coordinate, for example, an interatomic distance, with its minimum at the specified optimal value. A restraint is defined using one or two parameters: the ForceConstant and, for some types, the F(Inf) value. The ForceConstant parameter corresponds to second derivative of the restraint potential energy d2V(x)/dx^2 for any x (harmonic restraints) or only at at x=0 (other restraints). Here, x is a deviation from the restraint’s optimal value.
RigidMotions (AMSBatch._RigidMotions) – Specify which rigid motions of the total system are allowed. An external field is not considered part of the system. Normally the automatic option is doing what you want. However this feature can be used as a means of geometry constraint.
SCMLibrary (AMSBatch._SCMLibrary) – Technical settings affecting src/lib
SCMMatrix (AMSBatch._SCMMatrix) – Technical settings for programs using the AMT matrix system. Currently this is only used by DFTB
SerializedTensors (AMSBatch._SerializedTensors) – Technical settings affecting the SerializedTensors module, currently only used for HartreeFock
SteepestDescent (AMSBatch._SteepestDescent) – Configures details of the steepest descent task.
Symmetry (AMSBatch._Symmetry) – Specifying details about the details of symmetry detection and usage.
System (AMSBatch._System) – Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
SystemsFromConformers (AMSBatch._SystemsFromConformers) – Constructs a series of systems (with identifiers ‘conformer1’, ‘conformer2’, etc.) from a RKF or XYZ file from a Conformers run.
SystemsFromPES (AMSBatch._SystemsFromPES) – Constructs a series of systems (with identifiers ‘system1’, ‘system2’, etc.) from a RKF file from Conformers, PESExploration, or PESScan run.
SystemsFromSMILES (str | Sequence[str] | FreeBlock) – Generates systems from SMILES strings using the plams.from_smiles() functions. Each line should contain first the system identifier separated by a comma from its SMILES string, e.g.: ‘propanol, CCCO’
SystemsFromTrajectory (AMSBatch._SystemsFromTrajectory) – Constructs a series of systems (with identifiers ‘frame1’, ‘frame2’, etc.) from a trajectory file.
Thermo (AMSBatch._Thermo) – Options for thermodynamic properties (assuming an ideal gas). The properties are computed for all specified temperatures.
TransitionStateSearch (AMSBatch._TransitionStateSearch) – Configures some details of the transition state search.
VibrationalAnalysis (AMSBatch._VibrationalAnalysis) – Input data for all vibrational analysis utilities in the AMS driver.
- class _BondOrders[source]¶
Configures details regarding the calculation/guessing of bond orders. To request the calculation of bond orders, use the ‘Properties%BondOrders’ key.
- Variables:
Method (Literal["Engine", "Guess", "EngineWithGuessFallback"]) –
How to compute the bond orders when they are requested via the ‘Properties%BondOrders’ key.
’Engine’: let the engine compute the bond orders. The specific method used to compute the bond orders depends on the engine selected, and it may be configurable in the engine’s input. Note: the calculation may stop if the engine cannot compute bond orders.
’Guess’: Use a bond guessing algorithm based on the system’s geometry. This is the same algorithm that is used by the Graphical User Interface to guess bonds.
’EngineWithGuessFallback’: let the engine compute the bond orders (same as in ‘Engine’ option) but if the engine did not produce any bond orders, use the bond guessing algorithm as a fallback option.
- class _Constraints[source]¶
The Constraints block allows geometry optimizations and potential energy surface scans with constraints. The constraints do not have to be satisfied at the start of the calculation.
- Variables:
Fix multiple distances using one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3
The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 as well as the angle between them.
The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then any bond between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. If the distance is omitted then the bond length from the initial geometry is used.
Important: only the bonds present in the system at the start of the simulation can be constrained, which means that the bonds may need to be specified in the System block.
Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H
Angle (str | StringKey) – Fix the angle between three atoms. Three atom indices followed by an angle in degrees.
Atom (int | IntKey) – Fix the position of an atom. Just one integer referring to the index of the atom in the [System%Atoms] block.
AtomList (Iterable[int] | IntListKey) – Fix positions of the specified atoms. A list of integers referring to indices of atoms in the [System%Atoms] block.
Block (str | StringKey) – Name of the region to constrain as a rigid block. Regions are specified in the System%Atoms block.
BlockAtoms (Iterable[int] | IntListKey) – List of atom indices for a block constraint, where the internal degrees of freedom are frozen.
Coordinate (str | StringKey) – Fix a particular coordinate of an atom. Atom index followed by (x|y|z).
DifDist (str | StringKey) – Four atom indices i j k l followed by the distance in Angstrom. This will constrain the difference R(ij)-R(kl) at the given value.
Dihedral (str | StringKey) – Fix the dihedral angle between four atoms. Four atom indices followed by an angle in degrees.
Distance (str | StringKey) – Fix the distance between two atoms. Two atom indices followed by the distance in Angstrom.
EqualStrain (str | StringKey) –
Exclusively for lattice optimizations:
Accepts a set of strain components [xx, xy, xz, yy, yz, zz] which are to be kept equal.
The applied strain will be determined by the average of the corresponding stress tensors components.
In AMSinput just check the corresponding check buttons.
FixedRegion (str | StringKey) – Fix positions of all atoms in a region.
FreezeStrain (str | StringKey) –
Exclusively for lattice optimizations:
Freezes any lattice deformation corresponding to a particular component of the strain tensor.
Accepts a set of strain components [xx, xy, xz, yy, yz, zz] to be frozen.
In AMSinput just check the corresponding check buttons.
SumDist (str | StringKey) – Four atom indices i j k l followed by the distance in Angstrom. This will constrain the sum R(ij)+R(kl) at the given value.
- class _ElasticTensor[source]¶
Options for numerical evaluation of the elastic tensor.
- Variables:
ConvergenceQuality (Literal["Normal", "Good", "VeryGood", "Excellent"]) – The tightness of the convergence of the geometry optimizations for each strain deformation. This should not be set higher than the overall convergence quality of the preceding geometry optimization configured by the
GeometryOptimization%Convergence%Qualitykeyword.StrainStepSize (float | FloatKey) – Step size (relative) of strain deformations used for computing the elastic tensor numerically.
Parallel (AMSBatch._ElasticTensor._Parallel) – Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- class _Parallel[source]¶
Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _Engine[source]¶
The input for the computational engine. The header of the block determines the type of the engine.
- class _EngineAddons[source]¶
This block configures all the engine add-ons.
- Variables:
Pressure (float | FloatKey) – Add a hydrostatic pressure term to the engine’s energy and stress tensor. Can only be used for 3D periodic boundary conditions.
AtomEnergies (str | Sequence[str] | FreeBlock) – Add an element-dependent energy per atom. On each line, give the chemical element followed by the energy (in atomic units).
D3Dispersion (AMSBatch._EngineAddons._D3Dispersion) – This block configures the add-on that adds the Grimme D3 dispersion correction to the engine’s energy, gradients, and stress tensor.
D4Dispersion (AMSBatch._EngineAddons._D4Dispersion) – This block configures the addon that adds the Grimme D4(EEQ) dispersion correction to the engine’s energy, gradients, stress tensor and Hessian.
ExternalEngine (AMSBatch._EngineAddons._ExternalEngine) – External engine as an addon
ExternalStress (AMSBatch._EngineAddons._ExternalStress) – This block configures the addon that adds external stress term to the engine’s energy and stress tensor.
PipeEngine (AMSBatch._EngineAddons._PipeEngine) – Pipe engine as an addon
Repulsion (AMSBatch._EngineAddons._Repulsion) – This block configures an addon that adds a repulsive Weeks-Chandler-Andersen potential to all atom pairs.
WallPotential (AMSBatch._EngineAddons._WallPotential) – This block configures the addon that adds a spherical wall potential to the engine’s energy and gradients.
- class _AtomEnergies[source]¶
Add an element-dependent energy per atom. On each line, give the chemical element followed by the energy (in atomic units).
- class _D3Dispersion[source]¶
This block configures the add-on that adds the Grimme D3 dispersion correction to the engine’s energy, gradients, and stress tensor.
- Variables:
Damping (Literal["BJ", "Zero"]) – Type of damping: BJ (Becke-Johnson) or Zero. BJ is recommended for most applications.
Enabled (BoolType | BoolKey) – Enables the D3 dispersion correction addon.
Functional (str | StringKey) – Use the D3 parameterization by Grimme for a given xc-functional. Accepts the same values as the –func command line option of the official dftd3 program. Note: the naming convention is different from elsewhere in the AMS suite. For example, BLYP should be called b-lyp.
a1 (float | FloatKey) – The a1 parameter. Only used if Damping is set to BJ. If set, it overwrites the a1 value for the chosen functional.
a2 (float | FloatKey) – The a2 parameter. Only used if Damping is set to BJ. If set, it overwrites the a2 value for the chosen functional.
alp (float | FloatKey) – The a2 parameter. Only used if Damping is set to BJ. If set, it overwrites the a2 value for the chosen functional.
s6 (float | FloatKey) – The s6 parameter, global scaling parameter. If set, it overwrites the s6 value for the chosen functional.
s8 (float | FloatKey) – The s8 parameter. If set, it overwrites the s8 value for the chosen functional.
sr6 (float | FloatKey) – The sr6 parameter. Only used if Damping is set to Zero. If set, it overwrites the sr6 value for the chosen functional.
- class _D4Dispersion[source]¶
This block configures the addon that adds the Grimme D4(EEQ) dispersion correction to the engine’s energy, gradients, stress tensor and Hessian.
- Variables:
Enabled (BoolType | BoolKey) – Enables the D4 dispersion correction addon.
Functional (Literal["HF", "BLYP", "BPBE", "BP86", "BPW", "LB94", "MPWLYP", "MPWPW91", "OLYP", "OPBE", "PBE", "RPBE", "REVPBE", "PW86PBE", "RPW86PBE", "PW91", "PW91P86", "XLYP", "B97", "TPSS", "REVTPSS", "SCAN", "B1LYP", "B3LYP", "BHLYP", "B1P86", "B3P86", "B1PW91", "B3PW91", "O3LYP", "REVPBE0", "REVPBE38", "PBE0", "PWP1", "PW1PW", "MPW1PW91", "MPW1LYP", "PW6B95", "TPSSH", "TPSS0", "X3LYP", "M06L", "M06", "OMEGAB97", "OMEGAB97X", "CAM-B3LYP", "LC-BLYP", "LH07TSVWN", "LH07SSVWN", "LH12CTSSIRPW92", "LH12CTSSIFPW92", "LH14TCALPBE", "B2PLYP", "B2GPPLYP", "MPW2PLYP", "PWPB95", "DSDBLYP", "DSDPBE", "DSDPBEB95", "DSDPBEP86", "DSDSVWN", "DODBLYP", "DODPBE", "DODPBEB95", "DODPBEP86", "DODSVWN", "PBE02", "PBE0DH", "DFTB(3ob)", "DFTB(mio)", "DFTB(pbc)", "DFTB(matsci)", "DFTB(ob2)", "B1B95", "MPWB1K", "REVTPSSH", "GLYP", "REVPBE0DH", "REVTPSS0", "REVDSDPBEP86", "REVDSDPBEPBE", "REVDSDBLYP", "REVDODPBEP86", "B97M", "OMEGAB97M", "R2SCAN"]) – Use the D4 parameterization by Grimme for a given xc-functional.
Verbosity (Literal["Silent", "Normal", "Verbose", "VeryVerbose"]) – Controls the verbosity of the dftd4 code. Equivalent to the –silent and –verbose command line switches of the official dftd4 program.
a1 (float | FloatKey) – The a1 parameter, see D4 article. The physically reasonable range for a1 is [0.0,1.0]. If set, it overwrites the a1 value for the chosen functional.
a2 (float | FloatKey) – The a2 parameter, see D4 article. The physically reasonable range for a2 is [0.0,7.0]. If set, it overwrites the a2 value for the chosen functional.
s6 (float | FloatKey) – The s6 parameter, see D4 article. The physically reasonable range for s6 is [0.0,1.0]. If set, it overwrites the s6 value for the chosen functional.
s8 (float | FloatKey) – The s8 parameter, see D4 article. The physically reasonable range for s8 is [0.0,3.0]. If set, it overwrites the s8 value for the chosen functional.
s9 (float | FloatKey) – The s9 parameter, see D4 article. If set, it overwrites the s9 value for the chosen functional.
- class _ExternalStress[source]¶
This block configures the addon that adds external stress term to the engine’s energy and stress tensor.
- Variables:
StressTensorVoigt (Iterable[float] | FloatListKey) – The elements of the external stress tensor in Voigt notation. One should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
UpdateReferenceCell (BoolType | BoolKey) – Whether ot not the reference cell should be updated every time the system changes (see documentation).
- class _Repulsion[source]¶
This block configures an addon that adds a repulsive Weeks-Chandler-Andersen potential to all atom pairs.
- Variables:
Enabled (BoolType | BoolKey) –
Enables the repulsive Weeks-Chandler-Andersen potential addon.
When enabled, all atom pairs will experience repulsion E = 4*epsilon*( (sigma/r)^12 - (sigma/r)^6 + 1/4 ) at the distances shorter than about 1.12*sigma.
Epsilon (float | FloatKey) – The epsilon parameter in the potential equation. It is equal to the amount of energy added at r=sigma.
HydrogenSigmaScale (float | FloatKey) – The sigma parameter for a pair of atoms where one of them is hydrogen is scaled with the given factor. For H-H interactions the sigma is scaled with this value squared.
Sigma (float | FloatKey) – The sigma parameter in the potential equation. The potential is exactly zero at the distances larger than about 1.12*sigma
SkinLength (float | FloatKey) – Technical parameter specifying skin length for the neighbor list generation. A larger value increases the neighbor list cutoff (and cost) but reduces the frequency it needs to be re-created.
- class _WallPotential[source]¶
This block configures the addon that adds a spherical wall potential to the engine’s energy and gradients.
- Variables:
Enabled (BoolType | BoolKey) – Enables the wall potential addon. When enabled, a spherical wall of radius [Radius] around the origin will be added. The force due to the potential will decay exponentially inside the wall, will be close to [Prefactor*Gradient] outside and exactly half of that at the wall.
Gradient (float | FloatKey) – The radial gradient outside the sphere.
Prefactor (float | FloatKey) – The multiplier for the overall strength of the potential.
Radius (float | FloatKey) – The radius of the sphere, wherein the potential is close to zero.
- class _EngineDebugging[source]¶
This block contains some options useful for debugging the computational engines.
- Variables:
AlwaysClaimSuccess (BoolType | BoolKey) – If an engine fails, pretend that it worked. This can be useful when you know that an SCF might fail.
CheckInAndOutput (BoolType | BoolKey) – Enables some additional checks on the input and output of an engine, e.g. for NaN values.
ForceContinousPES (BoolType | BoolKey) – If this option is set, the engine will always run in continuous PES mode. For many engines this disables the use of symmetry, as this one always leads to a discontinuous PES around the symmetric points: Basically there is jump in the PES at the point where the symmetry detection starts classifying the system as symmetric. Normally the continuous PES mode of the engine (often disabling the symmetry) is only used when doing numerical derivatives, but this flag forces the engine to continuously run in this mode.
IgnoreEngineSupportsErrors (BoolType | BoolKey) – Pretend as if the engine supports anything requested. Use at your own risk.
IgnoreGradientsRequest (BoolType | BoolKey) – If this option is set, the engine will not do analytical gradients if asked for it, so that gradients will have to be evaluated numerically by AMS.
IgnorePreviousResults (BoolType | BoolKey) – If this option is set, the engine will not receive information from previous calculations. Typically this information is used to restart the self consistent procedure of the engine.
IgnoreStressTensorRequest (BoolType | BoolKey) – If this option is set, the engine will not calculate an analytical stress tensor if asked for it, so that the stress tensor will have to be evaluated numerically by AMS.
NeverQuiet (BoolType | BoolKey) – Makes the engine ignore the request to work quietly.
RandomFailureChance (float | FloatKey) – Makes the engine randomly report failures, even though the results are actually fine. Useful for testing error handling on the application level.
RandomNoiseInEnergy (float | FloatKey) – Adds a random noise to the energy returned by the engine. The random contribution is drawn from [-r,r] where r is the value of this keyword.
RandomNoiseInGradients (float | FloatKey) – Adds a random noise to the gradients returned by the engine. A random number in the range [-r,r] (where r is the value of this keyword) is drawn and added separately to each component of the gradient.
RandomStopChance (float | FloatKey) – Makes the engine randomly stop. Can be used to simulate crashes.
- class _ExitCondition[source]¶
If any of the specified exitconditions are met, the AMS driver will exit cleanly.
- Variables:
Type (Literal["AtomsTooClose", "EngineEnergyUncertainty", "EngineGradientsUncertainty"]) – The type of exitcondition specified
AtomsTooClose (AMSBatch._ExitCondition._AtomsTooClose) – If any pair of atoms is closer than the specified minimum value, the program will exit cleanly.
EngineEnergyUncertainty (AMSBatch._ExitCondition._EngineEnergyUncertainty) – If the engine reports an uncertainty that is too high, the program will exit cleanly.
EngineGradientsUncertainty (AMSBatch._ExitCondition._EngineGradientsUncertainty) – If the engine reports an uncertainty in the magnitude of the nuclear gradient of any atom that is too high, the program will exit cleanly.
- class _AtomsTooClose[source]¶
If any pair of atoms is closer than the specified minimum value, the program will exit cleanly.
- class _GCMC[source]¶
This block controls the Grand Canonical Monte Carlo (GCMC) task.
By default, molecules are added at random positions in the simulation box. The initial position is controlled by
- Variables:
AccessibleVolume (float | FloatKey) – Volume available to GCMC, in cubic Angstroms. AccessibleVolume should be specified for “Accessible” and “FreeAccessible” [VolumeOption].
Ensemble (Literal["Mu-VT", "Mu-PT"]) – Select the MC ensemble: Mu-VT for fixed volume or Mu-PT for variable volume. When the Mu-PT ensemble is selected the [Pressure] and [VolumeChangeMax] should also be specified.
MapAtomsToOriginalCell (BoolType | BoolKey) – Keeps the atom (mostly) in the original cell by mapping them back before the geometry optimizations.
MaxDistance (float | FloatKey) – The max distance to other atoms of the system when adding the molecule.
MinDistance (float | FloatKey) – Keep the minimal distance to other atoms of the system when adding the molecule.
NonAccessibleVolume (float | FloatKey) – Volume not available to GCMC, in cubic Angstroms. NonAccessibleVolume may be specified for the “Free” [VolumeOption] to reduce the accessible volume.
NumAttempts (int | IntKey) – Try inserting/moving the selected molecule up to the specified number of times or until all constraints are satisfied. If all attempts fail a message will be printed and the simulation will stop. If the MaxDistance-MinDistance interval is small this number may have to be large.
Pressure (float | FloatKey) – Pressure used to calculate the energy correction in the Mu-PT ensemble. Set it to zero for incompressible solid systems unless at very high pressures.
Restart (str | Path | StringKey) – Name of an RKF restart file. Upon restart, the information about the GCMC input parameters, the initial system (atomic coordinates, lattice, charge, etc.) and the MC molecules (both already inserted and to be inserted) are read from the restart file. The global GCMC input parameters and the MC Molecules can be modified from input. Any parameter not specified in the input will use its value from the restart file (i.e. not the default value). Molecules found in the restart file do not have to be present as named Systems in the input, however if there is a System present that matches the name of a molecule from restart then the System’s geometry will replace that found in the restart file. It is also possible to specify new Molecules in the input, which will be added to the pool of the MC molecules from restart.
Temperature (float | FloatKey) – Temperature of the simulation. Increase the temperature to improve the chance of accepting steps that result in a higher energy.
UseGCPreFactor (BoolType | BoolKey) – Use the GC pre-exponential factor for probability.
VolumeChangeMax (float | FloatKey) – Fractional value by which logarithm of the volume is allowed to change at each step. The new volume is then calculated as Vnew = exp(random(-1:1)*VolumeChangeMax)*Vold
VolumeOption (Literal["Free", "Total", "Accessible", "FreeAccessible"]) – Specifies the method to calculate the volume used to calculate the GC pre-exponential factor and the energy correction in the Mu-PT ensemble: Free: V = totalVolume - occupiedVolume - NonAccessibleVolume; Total: V = totalVolume; Accessible: V = AccessibleVolume; FreeAccessible: V = AccessibleVolume - occupiedVolume. The AccessibleVolume and NonAccessibleVolume are specified in the input, the occupiedVolume is calculated as a sum of atomic volumes.
Box (AMSBatch._GCMC._Box) –
Boundaries of the insertion space, i.e. coordinates of the origin of an inserted molecule (coordinates of an atom of the inserted system may fall outside the box).
For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom (the system’s bounding box extended by the MaxDistance value by default).
Molecule (AMSBatch._GCMC._Molecule) – This block defines the molecule (or atom) that can be inserted/moved/deleted with the MC method. The coordinates should form a reasonable structure. The MC code uses these coordinates during the insertion step by giving them a random rotation, followed by a random translation to generate a random position of the molecule inside the box. Currently, there is no check to make sure all atoms of the molecule stay inside the simulation box. The program does check that the MaxDistance/MinDistance conditions are satisfied.
Removables (str | Sequence[str] | FreeBlock) – The Removables can be used to specify a list of molecules that can be removed or moved during this GCMC calculation. Molecules are specified one per line in the format following format: MoleculeName atom1 atom2 … The MoleculeName must match a name specified in one of the [Molecule] blocks. The atom indices refer to the whole input System and the number of atoms must match that in the specified Molecule. A suitable Removables block is written to the standard output after each accepted MC move. If you do so then you should also replace the initial atomic coordinates with the ones found in the same file. If a [Restart] key is present then the Removables block is ignored.
SwapAtoms (AMSBatch._GCMC._SwapAtoms) – Experimental: Occasionally swap the coordinates of a random pair of atoms from two regions.
- class _Box[source]¶
Boundaries of the insertion space, i.e. coordinates of the origin of an inserted molecule (coordinates of an atom of the inserted system may fall outside the box).
For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom (the system’s bounding box extended by the MaxDistance value by default).
- Variables:
Amax (float | FloatKey) – Coordinate of the upper bound along the first axis.
Amin (float | FloatKey) – Coordinate of the lower bound along the first axis.
Bmax (float | FloatKey) – Coordinate of the upper bound along the second axis.
Bmin (float | FloatKey) – Coordinate of the lower bound along the second axis.
Cmax (float | FloatKey) – Coordinate of the upper bound along the third axis.
Cmin (float | FloatKey) – Coordinate of the lower bound along the third axis.
- class _Molecule[source]¶
This block defines the molecule (or atom) that can be inserted/moved/deleted with the MC method. The coordinates should form a reasonable structure. The MC code uses these coordinates during the insertion step by giving them a random rotation, followed by a random translation to generate a random position of the molecule inside the box. Currently, there is no check to make sure all atoms of the molecule stay inside the simulation box. The program does check that the MaxDistance/MinDistance conditions are satisfied.
- Variables:
ChemicalPotential (float | FloatKey) –
Chemical potential of the molecule (or atom) reservoir.
- It is used when calculating the Boltzmann accept/reject criteria after a MC move is executed. This value can be derived from first principles using statistical mechanics, or equivalently, it can be determined from thermochemical tables available in literature sources.
For example, the proper chemical potential for a GCMC simulation in which single oxygen atoms are exchanged with a reservoir of O2 gas, should equal 1/2 the chemical potential of O2 at the temperature and pressure of the reservoir:
cmpot = Mu_O(T,P) = 1/2*Mu_O2(T,P) = 1/2 * [Mu_ref(T,P_ref) + kT*Log(P/Pref) - E_diss]
where the reference chemical potential [Mu_ref(T,P_ref)] is the experimentally determined chemical potential of O2 at T and Pref; kT*Log(P/Pref) is the pressure correction to the free energy, and E_diss is the dissociation energy of the O2 molecule.
NoAddRemove (BoolType | BoolKey) –
Set to True to tell the GCMC code to keep the number of molecules/atoms of this type fixed.
It will thus disable Insert/Delete moves on this type, meaning it can only do a displacement move, or volume change move (for an NPT ensemble).
SystemName (str | StringKey) – String ID of a named [System] to be inserted. The lattice specified with this System, if any, is ignored and the main system’s lattice is used instead.
- class _Removables[source]¶
- The Removables can be used to specify a list of molecules that can be removed or moved during this GCMC calculation. Molecules are specified one per line in the format following format:
MoleculeName atom1 atom2 … The MoleculeName must match a name specified in one of the [Molecule] blocks. The atom indices refer to the whole input System and the number of atoms must match that in the specified Molecule. A suitable Removables block is written to the standard output after each accepted MC move. If you do so then you should also replace the initial atomic coordinates with the ones found in the same file. If a [Restart] key is present then the Removables block is ignored.
- class _GeometryOptimization[source]¶
Configures details of the geometry optimization and transition state searches.
- Variables:
CalcPropertiesOnlyIfConverged (BoolType | BoolKey) – Compute the properties requested in the ‘Properties’ block, e.g. Frequencies or Phonons, only if the optimization (or transition state search) converged. If False, the properties will be computed even if the optimization did not converge.
CoordinateType (Literal["Auto", "Delocalized", "Cartesian"]) –
Select the type of coordinates in which to perform the optimization. ‘Auto’ automatically selects the most appropriate CoordinateType for a given Method.
If ‘Auto’ is selected, Delocalized coordinates will be used for the Quasi-Newton method, while Cartesian coordinates will be used for all other methods.
KeepIntermediateResults (BoolType | BoolKey) – Whether the full engine result files of all intermediate steps are stored on disk. By default only the last step is kept, and only if the geometry optimization converged. This can easily lead to huge amounts of data being stored on disk, but it can sometimes be convenient to closely monitor a tricky optimization, e.g. excited state optimizations going through conical intersections, etc. …
MaxIterations (int | IntKey) – The maximum number of geometry iterations allowed to converge to the desired structure.
MaxRestarts (int | IntKey) – If a geometry optimization of a system with no symmetry operators (or with explicitly disabled symmetry:
UseSymmetry False) and enabled PES point characterization converges to a transition state (or higher order saddle point), it can be restarted automatically after a small displacement along the imaginary vibrational mode. In case the restarted optimization again does not find a minimum, this can happen multiple times in succession. This keyword sets the maximum number of restarts. The default value is 0, so the automatic restarting is disabled by default.Method (Literal["Auto", "Quasi-Newton", "FIRE", "L-BFGS", "ConjugateGradients", "Dimer"]) –
Select the optimization algorithm employed for the geometry relaxation. Currently supported are:
the Hessian-based Quasi-Newton-type BFGS algorithm,
the fast inertial relaxation method (FIRE),
the limited-memory BFGS method,
and the conjugate gradients method. The default is to choose an appropriate method automatically based on the engine’s speed, the system size and the supported optimization options.
OptimizeLattice (BoolType | BoolKey) – Whether to also optimize the lattice for periodic structures. This is currently supported with the Quasi-Newton, FIRE, and L-BFGS optimizers.
PretendConverged (BoolType | BoolKey) – Normally a non-converged geometry optimization is considered an error. If this keyword is set to True, the optimizer will only produce a warning and still claim that the optimization is converged. (This is mostly useful for scripting applications, where one might want to consider non-converged optimizations still successful jobs.)
RestartDisplacement (float | FloatKey) – If a geometry optimization of a system with no symmetry operators (or with explicitly disabled symmetry:
UseSymmetry False) and enabled PES point characterization converges to a transition state (or higher order saddle point), it can be restarted automatically after a small displacement along the imaginary vibrational mode. This keywords sets the size of the displacement for the furthest moving atom.Convergence (AMSBatch._GeometryOptimization._Convergence) – Convergence is monitored for up to 4 quantities: the energy change, the Cartesian gradients, the Cartesian step size, and for lattice optimizations the stress energy per atom. Convergence criteria can be specified separately for each of these items.
Dimer (AMSBatch._GeometryOptimization._Dimer) – Options for the Dimer method for transition state search.
EngineAutomations (AMSBatch._GeometryOptimization._EngineAutomations) – The optimizer can change some settings of the engine, based for instance on the error. The idea is to allow the engine to be a bit quicker at the start, and more accurate towards the end. Automations are always engine specific.
FIRE (AMSBatch._GeometryOptimization._FIRE) – This block configures the details of the FIRE optimizer. The keywords name correspond the the symbols used in the article describing the method, see PRL 97, 170201 (2006).
HessianFree (AMSBatch._GeometryOptimization._HessianFree) – Configures details of the Hessian-free (conjugate gradients or L-BFGS) geometry optimizer.
InitialHessian (AMSBatch._GeometryOptimization._InitialHessian) – Options for initial model Hessian when optimizing systems with the Quasi-Newton method.
Quasi-Newton (AMSBatch._GeometryOptimization._Quasi-Newton) – Configures details of the Quasi-Newton geometry optimizer.
- class _Convergence[source]¶
Convergence is monitored for up to 4 quantities: the energy change, the Cartesian gradients, the Cartesian step size, and for lattice optimizations the stress energy per atom. Convergence criteria can be specified separately for each of these items.
- Variables:
Energy (float | FloatKey) – The criterion for changes in the energy. The energy is considered converged when the change in energy is smaller than this threshold times the number of atoms.
Gradients (float | FloatKey) – Threshold for nuclear gradients.
Quality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent", "Custom"]) – A quick way to change convergence thresholds: ‘Good’ will reduce all thresholds by an order of magnitude from their default value. ‘VeryGood’ will tighten them by two orders of magnitude. ‘Basic’ and ‘VeryBasic’ will increase the thresholds by one or two orders of magnitude respectively.
Step (float | FloatKey) – The maximum Cartesian step allowed for a converged geometry.
StressEnergyPerAtom (float | FloatKey) – Threshold used when optimizing the lattice vectors. The stress is considered ‘converged’ when the maximum value of stress_tensor * cell_volume / number_of_atoms is smaller than this threshold (for 2D and 1D systems, the cell_volume is replaced by the cell_area and cell_length respectively).
- class _Dimer[source]¶
Options for the Dimer method for transition state search.
- Variables:
AngleThreshold (float | FloatKey) – The rotation is considered converged when the the rotation angle falls below the specified threshold.
DimerDelta (float | FloatKey) – Euclidian distance between the midpoint and the endpoint.
ExtrapolateForces (BoolType | BoolKey) – Set to false to call engine to calculate forces at the extrapolated rotation angle instead of extrapolating them.
LBFGSMaxVectors (int | IntKey) – Max number of vectors for the L-BFGS algorithm to save.
MaxRotationIterations (int | IntKey) – Maximum number of rotation iterations for a single translation step.
Region (str | StringKey) – Include only atoms of the specified region(s) in the rotations, which allows searching for a transition state involving selected atoms only.
RotationTrustRadius (float | FloatKey) – L-BFGS trust radius during rotation iterations.
TranslationTrustRadius (float | FloatKey) – L-BFGS trust radius during translation iterations.
- class _EngineAutomations[source]¶
The optimizer can change some settings of the engine, based for instance on the error. The idea is to allow the engine to be a bit quicker at the start, and more accurate towards the end. Automations are always engine specific.
- Variables:
Enabled (BoolType | BoolKey) – Whether or not automations are enabled at all.
Gradient (AMSBatch._GeometryOptimization._EngineAutomations._Gradient) – A gradient-based automation.
Iteration (AMSBatch._GeometryOptimization._EngineAutomations._Iteration) – Geometry step based automation.
- class _Gradient[source]¶
A gradient-based automation.
- Variables:
FinalValue (float | FloatKey) – This value will be used whenever the gradient is less than GradientLow
HighGradient (float | FloatKey) – Defines a large gradient. When the actual gradient is between GradientHigh and GradientLow a linear interpolation scheme is used for kT (on a log scale).
InitialValue (float | FloatKey) – This value will be used at the first geometry, and whenever the gradient is higher than GradientHigh
LowGradient (float | FloatKey) – Defines a small gradient, see GradientHigh
UseLogInterpolation (BoolType | BoolKey) – Whether to use interpolation on a log (y) scale or not
Variable (str | StringKey) – variable to be tweaked for the engine.
- class _Iteration[source]¶
Geometry step based automation.
- Variables:
FirstIteration (int | IntKey) – When the actual gradient is between the first and last iteration, a linear interpolation is used.
InitialValue (float | FloatKey) – This value will be used when the iteration number is smaller or equal to FirstIteration
LastIteration (int | IntKey) – Where the automation should reach the FinalValue
UseLogInterpolation (BoolType | BoolKey) – Whether to use interpolation on a log (y) scale or not
Variable (str | StringKey) – variable to be tweaked for the engine.
- class _FIRE[source]¶
This block configures the details of the FIRE optimizer. The keywords name correspond the the symbols used in the article describing the method, see PRL 97, 170201 (2006).
- Variables:
AllowOverallRotation (BoolType | BoolKey) – Whether or not the system is allowed to freely rotate during the optimization. This is relevant when optimizing structures in the presence of external fields.
AllowOverallTranslation (BoolType | BoolKey) – Whether or not the system is allowed to translate during the optimization. This is relevant when optimizing structures in the presence of external fields.
MapAtomsToUnitCell (BoolType | BoolKey) – Map the atoms to the central cell at each geometry step.
NMin (int | IntKey) – Number of steps after stopping before increasing the time step again.
atomMass (float | FloatKey) – Fictitious atomic mass used for all atoms. There is no reason to change this, as it just corresponds to using a different integration timestep.
dtMax (float | FloatKey) – Maximum time step used for the integration. For ReaxFF and APPLE&P, this value is reduced by 50%.
dtStart (float | FloatKey) – Initial time step for the integration.
fAlpha (float | FloatKey) – Reduction factor for the steering coefficient.
fDec (float | FloatKey) – Reduction factor for reducing the time step in case of uphill movement.
fInc (float | FloatKey) – Growth factor for the integration time step.
strainMass (float | FloatKey) – Fictitious relative mass of the lattice degrees of freedom. This controls the stiffness of the lattice degrees of freedom relative to the atomic degrees of freedom, with smaller values resulting in a more aggressive optimization of the lattice.
- class _HessianFree[source]¶
Configures details of the Hessian-free (conjugate gradients or L-BFGS) geometry optimizer.
- Variables:
- class _Step[source]¶
- Variables:
MaxCartesianStep (float | FloatKey) – Limit on a single Cartesian component of the step.
MinRadius (float | FloatKey) – Minimum value for the trust radius.
TrialStep (float | FloatKey) – Length of the finite-difference step when determining curvature. Should be smaller than the step convergence criterion.
TrustRadius (float | FloatKey) – Initial value of the trust radius.
- class _InitialHessian[source]¶
Options for initial model Hessian when optimizing systems with the Quasi-Newton method.
- Variables:
File (str | Path | StringKey) – KF file containing the initial Hessian (or the results dir. containing it). This can be used to load a Hessian calculated in a previously with the [Properties%Hessian] keyword.
Type (Literal["Auto", "UnitMatrix", "Swart", "FromFile", "Calculate", "CalculateWithFastEngine"]) – Select the type of initial Hessian. Auto: let the program pick an initial model Hessian. UnitMatrix: simplest initial model Hessian, just a unit matrix in the optimization coordinates. Swart: model Hessian from M. Swart. FromFile: load the Hessian from the results of a previous calculation (see InitialHessian%File). Calculate: compute the initial Hessian (this may be computationally expensive and it is mostly recommended for TransitionStateSearch calculations). CalculateWithFastEngine: compute the initial Hessian with a faster engine.
- class _Quasi_Newton[source]¶
Configures details of the Quasi-Newton geometry optimizer.
- Variables:
EnforceConstraints (BoolType | BoolKey) – Whether to enforce constraints at each steps exactly or add them to the optimization space as Lagrange multipliers.
MaxGDIISVectors (int | IntKey) – Sets the maximum number of GDIIS vectors. Setting this to a number >0 enables the GDIIS method.
UpdateTSVectorEveryStep (BoolType | BoolKey) – Whether to update the TS reaction coordinate at each step with the current eigenvector.
Step (AMSBatch._GeometryOptimization._Quasi-Newton._Step) –
- class _IEEEExceptions[source]¶
Whether this works or not depends on the way the program is compiled (compiler and settings). Only useful for developers debugging some numerical issue.
- Variables:
All (BoolType | BoolKey) – Activates all IEEEExceptions known to ams, see list below. The corresponding environment variable is SCM_IEEEException_All.
DivideByZero (BoolType | BoolKey) – Stop program when a divide by zero exception occurs. The corresponding environment variable is SCM_IEEEException_DivideByZero.
Invalid (BoolType | BoolKey) – Stop program when an invalid exception occurs. This may be about sqrt(-1)., or 0/0, and generally leads to a NaN. The corresponding environment variable is SCM_IEEEException_Invalid.
Overflow (BoolType | BoolKey) – Stop program when an overflow exception occurs. The corresponding environment variable is SCM_IEEEException_Overflow
Print (BoolType | BoolKey) – Print feedback on activated IEEEExceptions in the logfile. The corresponding environment variable is SCM_IEEEException_Print.
- class _IRC[source]¶
Configures details of the Intrinsic Reaction Coordinate optimization.
- Variables:
CoordinateType (Literal["Cartesian", "Delocalized"]) – Select the type of coordinates in which to perform the optimization. Note that the Delocalized option should be considered experimental.
Direction (Literal["Both", "Forward", "Backward"]) – Select direction of the IRC path. The difference between the Forward and the Backward directions is determined by the sign of the largest component of the vibrational normal mode corresponding to the reaction coordinate at the transition state geometry. The Forward path correspond to the positive sign of the component. If Both is selected then first the Forward path is computed followed by the Backward one.
KeepConvergedResults (BoolType | BoolKey) – Keep the binary RKF result file for every converged IRC point. These files may contain more information than the main ams.rkf result file.
MaxIRCSteps (int | IntKey) – Soft limit on the number of IRC points to compute in each direction. After the specified number of IRC steps the program will switch to energy minimization and complete the path. This option should be used when you are interested only in the reaction path area near the transition state. Note that even if the soft limit has been hit and the calculation has completed, the IRC can still be restarted with a ‘RedoBackward’ or ‘RedoForward’ option.
MaxIterations (int | IntKey) – The maximum number of geometry iterations allowed to converge the inner IRC loop. If optimization does not converge within the specified number of steps, the calculation is aborted.
MaxPoints (int | IntKey) – Hard limit on the number of IRC points to compute in each direction. After the specified number of IRC steps the program will stop with the current direction and switch to the next one. If both ‘MaxPoints’ and ‘MaxIRCSteps’ are set to the same value then ‘MaxPoints’ takes precedence, therefore this option should be used to set a limit on the number of IRC steps if you intend to use the results later for a restart.
MinEnergyProfile (BoolType | BoolKey) – Calculate minimum energy profile (i.e. no mass-weighting) instead of the IRC.
MinPathLength (float | FloatKey) – Minimum length of the path required before switching to energy minimization. Use this to overcome a small kink or a shoulder on the path.
Step (float | FloatKey) – IRC step size in mass-weighted coordinates, sqrt(amu)*bohr. One may have to increase this value when heavy atoms are involved in the reaction, or decrease it if the reactant or products are very close to the transition state.
Convergence (AMSBatch._IRC._Convergence) – Convergence at each given point is monitored for two items: the Cartesian gradient and the calculated step size. Convergence criteria can be specified separately for each of these items. The same criteria are used both in the inner IRC loop and when performing energy minimization at the path ends.
InitialHessian (AMSBatch._IRC._InitialHessian) – Options for initial Hessian at the transition state. The first eigenvalue of the initial Hessian defines direction of the first forward or backward step. This block is ignored when restarting from a previous IRC calculation because the initial Hessian found in the restart file is used.
Restart (AMSBatch._IRC._Restart) – Restart options. Upon restart, the information about the IRC input parameters and the initial system (atomic coordinates, lattice, charge, etc.) is read from the restart file. The IRC input parameters can be modified from input. Except for ‘MaxPoints’ and ‘Direction’ all parameters not specified in the input will use their values from the restart file. The ‘MaxPoints’ and ‘Direction’ will be reset to their respective default values if not specified in the input. By default, the IRC calculation will continue from the point where it left off. However, the ‘RedoForward’ and/or ‘RedoBackward’ option can be used to enforce recalculation of a part of the reaction path, for example, using a different ‘Step’ value.
- class _Convergence[source]¶
Convergence at each given point is monitored for two items: the Cartesian gradient and the calculated step size. Convergence criteria can be specified separately for each of these items. The same criteria are used both in the inner IRC loop and when performing energy minimization at the path ends.
- class _InitialHessian[source]¶
Options for initial Hessian at the transition state. The first eigenvalue of the initial Hessian defines direction of the first forward or backward step. This block is ignored when restarting from a previous IRC calculation because the initial Hessian found in the restart file is used.
- Variables:
File (str | Path | StringKey) – If ‘Type’ is set to ‘FromFile’ then in this key you should specify the RKF file containing the initial Hessian (or the ams results dir. containing it). This can be used to load a Hessian calculated previously with the ‘Properties%Hessian’ keyword. If you want to also use this file for the initial geometry then also specify it in a ‘LoadSystem’ block.
Type (Literal["Calculate", "FromFile"]) – Calculate the exact Hessian for the input geometry or load it from the results of a previous calculation.
- class _Restart[source]¶
Restart options. Upon restart, the information about the IRC input parameters and the initial system (atomic coordinates, lattice, charge, etc.) is read from the restart file. The IRC input parameters can be modified from input. Except for ‘MaxPoints’ and ‘Direction’ all parameters not specified in the input will use their values from the restart file. The ‘MaxPoints’ and ‘Direction’ will be reset to their respective default values if not specified in the input. By default, the IRC calculation will continue from the point where it left off. However, the ‘RedoForward’ and/or ‘RedoBackward’ option can be used to enforce recalculation of a part of the reaction path, for example, using a different ‘Step’ value.
- Variables:
File (str | Path | StringKey) – Name of an RKF restart file generated by a previous IRC calculation. Do not use this key to provide an RKF file generated by a TransitionStateSearch or a SinglePoint calculation, use the ‘LoadSystem’ block instead.
RedoBackward (int | IntKey) – IRC step number to start recalculating the backward path from. By default, if the backward path has not been completed then start after the last completed step. If the backward path has been completed and the ‘RedoBackward’ is omitted then no point on the backward path will be recomputed.
RedoForward (int | IntKey) – IRC step number to start recalculating the forward path from. By default, if the forward path has not been completed then start after the last completed step. If the forward path has been completed and the ‘RedoForward’ is omitted then no point on the forward path will be recomputed.
- class _Idle[source]¶
Configures details of the idle task, which does nothing for a specified amount of time.
- class _LoadSystem[source]¶
Block that controls reading the chemical system from a KF file instead of the [System] block.
- class _Log[source]¶
Configures the debugging loggers. Syntax: ‘Level LoggerName’. Possible Levels: All, Debug, Info, Warning, Error, Fatal.
- class _MolecularDynamics[source]¶
Configures molecular dynamics (with the velocity-Verlet algorithm) with and without thermostats. This block allows to specify the details of the molecular dynamics calculation.
- Variables:
CalcPressure (BoolType | BoolKey) –
Calculate the pressure in periodic systems.
This may be computationally expensive for some engines that require numerical differentiation.
Some other engines can calculate the pressure for negligible additional cost and will always do so, even if this option is disabled.
CopyRestartTrajectory (BoolType | BoolKey) – If the keyword Restart is present, the content of the restartfile is copied to the ams.rkf file.
NSteps (int | IntKey) – The number of steps to be taken in the MD simulation.
Restart (str | Path | StringKey) – The path to the ams.rkf file from which to restart the simulation.
AddMolecules (AMSBatch._MolecularDynamics._AddMolecules) –
This block controls adding molecules to the system (a.k.a. the Molecule Gun). Multiple occurrences of this block are possible.
By default, molecules are added at random positions in the simulation box with velocity matching the current system temperature. The initial position can be modified using one of the following keywords: Coords, CoordsBox, FractionalCoords, FractionalCoordsBox. The Coords and FractionalCoords keys can optionally be accompanied by CoordsSigma or FractionalCoordsSigma, respectively.
ApplyForce (AMSBatch._MolecularDynamics._ApplyForce) – The ApplyForce keyword can be used to apply an arbitrary constant force to a certain (subgroups of) atoms in the system
ApplyVelocity (AMSBatch._MolecularDynamics._ApplyVelocity) – The ApplyVelocity keyword can be used to move an arbitrary group of atoms in the system with a constant net velocity
Barostat (AMSBatch._MolecularDynamics._Barostat) – This block allows to specify the use of a barostat during the simulation.
BinLog (AMSBatch._MolecularDynamics._BinLog) – This block controls writing the BinLog section in ams.rkf, which contains the selected MD state scalars and tensors from every MD step. No per-atom data is written. If you need the per-atom data then you can set the sampling frequency to 1 and get the required data from the MDHistory section. The tensors are written per component, that is, the pressure tensor is written as six variables: PressureTensor_xx, PressureTensor_yy, etc.. To reduce the file size, all data is written in blocks.
BondBoost (AMSBatch._MolecularDynamics._BondBoost) – Forced reaction (bond boost) definitions. Multiple BondBoost blocks may be specified, which will be treated independently.
CRESTMTD (AMSBatch._MolecularDynamics._CRESTMTD) – Input for CREST metadynamics simulation.
CVHD (AMSBatch._MolecularDynamics._CVHD) – Input for the Collective Variable-driven HyperDynamics (CVHD).
CheckTemperature (AMSBatch._MolecularDynamics._CheckTemperature) – Check at every time step if the temperature has exceeded a threshold. If it has, it is assumed the system exploded, and the simulation will stop.
Checkpoint (AMSBatch._MolecularDynamics._Checkpoint) – Sets the frequency for storing the entire MD state necessary for restarting the calculation.
CosineShear (AMSBatch._MolecularDynamics._CosineShear) – Apply an external acceleration to all atoms of a fluid using a periodic (cosine) function along a selected coordinate axis. This induces a periodic shear flow profile which can be used to determine the viscosity.
Deformation (AMSBatch._MolecularDynamics._Deformation) – Deform the periodic lattice of the system during the simulation.
Gravity (AMSBatch._MolecularDynamics._Gravity) – Apply a constant acceleration in -z.
HeatExchange (AMSBatch._MolecularDynamics._HeatExchange) – Input for the heat-exchange non-equilibrium MD (T-NEMD).
InitialVelocities (AMSBatch._MolecularDynamics._InitialVelocities) – Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
MovingRestraints (AMSBatch._MolecularDynamics._MovingRestraints) – Define a set of moving restraints.
PRD (AMSBatch._MolecularDynamics._PRD) – This block is used for Parallel Replica Dynamics simulations.
Plumed (AMSBatch._MolecularDynamics._Plumed) – Input for PLUMED (version 2.5.0). The parallel option is still experimental.
Preserve (AMSBatch._MolecularDynamics._Preserve) – Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.
Print (AMSBatch._MolecularDynamics._Print) – This block controls the printing of additional information to stdout.
ReactionBoost (AMSBatch._MolecularDynamics._ReactionBoost) –
Define a series of transitions between different states of the system.
Each transition is defined by a TargetSystem and by a set of restraints that force the transition.
Reactor (AMSBatch._MolecularDynamics._Reactor) – Define one phase of the nanoreactor. A reactor is a region of space surrounded by an elastic wall. Atoms inside the region are not affected. Atoms outside it will be pushed back with force depending on the [ForceConstant] and the [MassScaled] flag.
ReflectiveWall (AMSBatch._MolecularDynamics._ReflectiveWall) – Apply a reflective wall in space
Remap (AMSBatch._MolecularDynamics._Remap) – Control periodic remapping (backtranslation) of atoms into the PBC box.
RemoveMolecules (AMSBatch._MolecularDynamics._RemoveMolecules) – This block controls removal of molecules from the system. Multiple occurrences of this block are possible.
ReplicaExchange (AMSBatch._MolecularDynamics._ReplicaExchange) – This block is used for (temperature) Replica Exchange MD (Parallel Tempering) simulations.
Shake (AMSBatch._MolecularDynamics._Shake) – Parameters of the Shake/Rattle algorithm.
Thermostat (AMSBatch._MolecularDynamics._Thermostat) – This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’s behavior.
Trajectory (AMSBatch._MolecularDynamics._Trajectory) – Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
fbMC (AMSBatch._MolecularDynamics._fbMC) – This block sets up force bias Monte Carlo interleaved with the molecular dynamics simulation.
- class _AddMolecules[source]¶
This block controls adding molecules to the system (a.k.a. the Molecule Gun). Multiple occurrences of this block are possible.
By default, molecules are added at random positions in the simulation box with velocity matching the current system temperature. The initial position can be modified using one of the following keywords: Coords, CoordsBox, FractionalCoords, FractionalCoordsBox. The Coords and FractionalCoords keys can optionally be accompanied by CoordsSigma or FractionalCoordsSigma, respectively.
- Variables:
AtomTemperature (float | FloatKey) – Add random velocity corresponding to the specified temperature to individual atoms of the molecule. This only affects rotational and internal degrees of freedom, not the net translational velocity of the inserted molecule as set by the other options.
ContactDistance (float | FloatKey) – Translate the bullet along the velocity vector until it comes within ContactDistance of any other atom.
Coords (Iterable[float] | FloatListKey) –
Place molecules at or around the specified Cartesian coordinates.
This setting takes precedence over other ways to specify initial coordinates of the molecule: [CoordsBox], [FractionalCoords], and [FractionalCoordsBox].
CoordsBox (Iterable[float] | FloatListKey) –
Place molecules at random locations inside the specified box in Cartesian coordinates.
Coordinates of the box corners are specified as: Xmin, Xmax, Ymin, Ymax, Zmin, Zmax. This setting is ignored if Coords is used.
In AMSinput, if this field is not empty it will be used instead of the default Coords.
CoordsSigma (Iterable[float] | FloatListKey) – Sigma values (one per Cartesian axis) for a Gauss distribution of the initial coordinates. Can only be used together with Coords.
DeviationAngle (float | FloatKey) – Randomly tilt the shooting direction up to this angle away from the VelocityDirection vector.
Energy (float | FloatKey) – Initial kinetic energy of the molecule in the shooting direction.
EnergySigma (float | FloatKey) – Sigma value for the Gauss distribution of the initial kinetic energy around the specified value. Should only be used together with Energy.
FractionalCoords (Iterable[float] | FloatListKey) – Place molecules at or around the specified fractional coordinates in the main system’s lattice. For non-periodic dimensions a Cartesian value in Angstrom is expected. This setting is ignored if [Coords] or [CoordsBox] is used.
FractionalCoordsBox (Iterable[float] | FloatListKey) –
Place molecules at random locations inside the box specified as fractional coordinates in the main system’s lattice.
Coordinates of the box corners are specified as: Xmin, Xmax, Ymin, Ymax, Zmin, Zmax.
For non-periodic dimensions the Cartesian value in Angstrom is expected.
This setting is ignored if [Coords], [CoordsBox], or [FractionalCoords] is used.
FractionalCoordsSigma (Iterable[float] | FloatListKey) – Sigma values (one per axis) for a Gauss distribution of the initial coordinates. For non-periodic dimensions the Cartesian value in Angstrom is expected. Can only be used together with FractionalCoords.
A molecule is added every [Frequency] steps after the StartStep.
There is never a molecule added at step 0.
MinDistance (float | FloatKey) – Keep the minimal distance to other atoms of the system when adding the molecule.
MoleFraction (float | FloatKey) –
Defines a mixture to be deposited using one AddMolecules block per component.
AMS will randomly alternate between any guns that have MoleFraction set. These need to all have the same settings for StartStep, StopStep and Frequency. Any additional AddMolecules blocks without MoleFraction will remain completely independent.
NumAttempts (int | IntKey) – Try adding the molecule up to the specified number of times or until the MinDistance constraint is satisfied. If all attempts fail a message will be printed and the simulation will continue normally.
Rotate (BoolType | BoolKey) – Rotate the molecule randomly before adding it to the system.
Step number when the first molecule should be added. After that, molecules are added every Frequency steps.
For example, ff StartStep=99 and Frequency=100 then a molecule will be added at steps 99, 199, 299, etc…
No molecule will be added at step 0, so if StartStep=0 the first molecule is added at the step number equal to [Frequency].
StopStep (int | IntKey) – Do not add this molecule after the specified step.
String ID of the [System] that will be added with this ‘gun’.
The lattice specified with this System is ignored and the main system’s lattice is used instead.
AMSinput adds the system at the coordinates of the System (thus setting Coords to the center of the System).
Temperature (float | FloatKey) – Initial energy of the molecule in the shooting direction will correspond to the given temperature.
TemperatureSigma (float | FloatKey) – Sigma value for the Gauss distribution of the initial temperature the specified value. Should only be used together with Temperature.
Velocity (float | FloatKey) – Initial velocity of the molecule in the shooting direction.
VelocityDirection (Iterable[float] | FloatListKey) –
Velocity direction vector for aimed shooting. It will be random if not specified.
In AMSinput add one or two atoms (which may be dummies).
One atom: use vector from center of the system to add to that atom.
Two atoms: use vector from the first to the second atom.
VelocitySigma (float | FloatKey) – Sigma value for the Gauss distribution of the initial velocity around the specified value. Should only be used together with Velocity.
- class _ApplyForce[source]¶
The ApplyForce keyword can be used to apply an arbitrary constant force to a certain (subgroups of) atoms in the system
- Variables:
CalculateViscosity (BoolType | BoolKey) – Calculates Viscosity property yes/no. If yes is chosen, the global viscosity of the system is calculated and written into the RKF-file. The formula used for the viscosity calculation is eta = - Pxz / (dVx/dz)
CalculateViscosityBins (int | IntKey) – Amount of bins used to determine (dVx/dz)
CalculateViscosityEnd (int | IntKey) – end index to select region in space to calculate (dVx/dz)
CalculateViscosityStart (int | IntKey) – Start index to select region in space to calculate (dVx/dz)
Force (Iterable[float] | FloatListKey) – Defines the constant force vector
PerAtom (BoolType | BoolKey) – If enabled, the Force vector is applied separately to every atom in the selected Region, so that the total net force on the Region equals the value of Force times the number of atoms in Region. This was the behavior of ApplyForce in AMS2022. By default, with PerAtom disabled, the Force vector defines the total net force on the Region, so the force applied to each atom equals the value of Force divided by the number of atoms in Region.
Region (str | StringKey) – Apply the constant force to all atoms in this region.
- class _ApplyVelocity[source]¶
The ApplyVelocity keyword can be used to move an arbitrary group of atoms in the system with a constant net velocity
- Variables:
CalculateViscosity (BoolType | BoolKey) – Calculates Viscosity property yes/no. If yes is chosen, the global viscosity of the system is calculated and written into the RKF-file. The formula used for the viscosity calculation is eta = - Pxz / (dVx/dz)
CalculateViscosityBins (int | IntKey) – Amount of bins used to determine (dVx/dz)
CalculateViscosityEnd (int | IntKey) – end index to select region in space to calculate (dVx/dz)
CalculateViscosityStart (int | IntKey) – Start index to select region in space to calculate (dVx/dz)
Components (Literal["X", "Y", "Z", "XY", "YZ", "XZ", "XYZ"]) – Select which components of the Velocity vector are used to set the corresponding components of the net velocity of the specified set of atoms. Any other components of Velocity are ignored and the motion of the selected atoms in those directions is unaffected by ApplyVelocity.
Region (str | StringKey) – Applies the defined velocity to all atoms in this region.
Velocity (Iterable[float] | FloatListKey) – The constant velocity that will be applied to the specified atoms.
- class _Barostat[source]¶
This block allows to specify the use of a barostat during the simulation.
- Variables:
BulkModulus (float | FloatKey) –
An estimate of the bulk modulus (inverse compressibility) of the system for the Berendsen barostat.
This is only used to make Tau correspond to the true observed relaxation time constant. Values are commonly on the order of 10-100 GPa (1e10 to 1e11) for solids and 1 GPa (1e9) for liquids (2.2e9 for water). Use 1e9 to match the behavior of standalone ReaxFF.
ConstantVolume (BoolType | BoolKey) –
Keep the volume constant while allowing the box shape to change.
This is currently supported only by the MTK barostat.
Duration (Iterable[int] | IntListKey) – Specifies how many steps should a transition from a particular pressure to the next one in sequence take.
Equal (Literal["None", "XYZ", "XY", "YZ", "XZ"]) – Enforce equal scaling of the selected set of dimensions. They will be barostatted as one dimension according to the average pressure over the components.
Pressure (Iterable[float] | FloatListKey) –
Specifies the target pressure.
You can specify multiple pressures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one p to the next p (using a linear ramp).
Scale (Literal["XYZ", "Shape", "X", "Y", "Z", "XY", "YZ", "XZ"]) – Dimensions that should be scaled by the barostat to maintain pressure. Selecting Shape means that all three dimensions and also all the cell angles are allowed to change.
Tau (float | FloatKey) – Specifies the time constant of the barostat.
Type (Literal["None", "Berendsen", "MTK"]) – Selects the type of the barostat.
- class _BinLog[source]¶
This block controls writing the BinLog section in ams.rkf, which contains the selected MD state scalars and tensors from every MD step. No per-atom data is written. If you need the per-atom data then you can set the sampling frequency to 1 and get the required data from the MDHistory section. The tensors are written per component, that is, the pressure tensor is written as six variables: PressureTensor_xx, PressureTensor_yy, etc.. To reduce the file size, all data is written in blocks.
- Variables:
BiasEnergy (BoolType | BoolKey) – Write the CVHD bias energy at every time step.
BoostFactor (BoolType | BoolKey) – Write the CVHD boost factor at every time step.
ConservedEnergy (BoolType | BoolKey) – Write the conserved energy value at every time step.
Density (BoolType | BoolKey) – Write the density at every time step.
DipoleMoment (BoolType | BoolKey) – Write the dipole moment at every time step. Each component of the tensor is written in its own variable.
Hypertime (BoolType | BoolKey) – Write the CVHD hypertime at every time step.
KineticEnergy (BoolType | BoolKey) – Write the kinetic energy value at every time step.
MaxBiasEnergy (BoolType | BoolKey) – Write the max CVHD bias energy at every time step.
MaxBoostFactor (BoolType | BoolKey) – Write the max CVHD boost factor at every time step.
PotentialEnergy (BoolType | BoolKey) – Write the potential energy value at every time step.
Pressure (BoolType | BoolKey) – Write the pressure at every time step.
PressureTensor (BoolType | BoolKey) – Write the pressure tensor in Voigt notation at every time step. Each component of the tensor is written in its own variable.
Step (BoolType | BoolKey) – Write the step index during the simulation at every time step.
Temperature (BoolType | BoolKey) – Write the temperature at every time step.
Time (BoolType | BoolKey) – Write the simulation time (fs) at every time step.
TotalEnergy (BoolType | BoolKey) – Write the total energy value at every time step.
Volume (BoolType | BoolKey) – Write the simulation cell volume, area or length, depending on the system periodicity, at every time step.
- class _BondBoost[source]¶
Forced reaction (bond boost) definitions. Multiple BondBoost blocks may be specified, which will be treated independently.
- Variables:
AddBond (str | StringKey) – [Reserved] Add a bond to the system or change its order. Specify two atom indices followed by the bond’s order. The indices indicate positions of the atoms in the AtomNames key. Currently no engine will honor bond changes caused by this key.
DistanceRestraint (str | StringKey) –
Specify two atom indices followed by the target distance in Angstrom, the first parameter and, optionally, the profile type and the second parameter.
For periodic systems, restraints follow the minimum image convention.
Each atom index indicates a position of the corresponding atom in the AtomNames key. Currently recognized restraint profile types: Harmonic (default), Hyperbolic, Erf, GaussianWell. The profile name can optionally be prefixed by “OneSided-”, thus making this particular restraint one-sided. A one-sided restraint will only push or pull the distance towards its target value depending on the sign of the difference between the initial and the target distance. For example, if the initial distance is larger than the target one then the restraint will only push the value down. This is especially useful with moving restraints because then the restraint will effectively disappear as soon as the system crosses a barrier along the reaction path. By default, the restraints are two-sided, which means they will try to keep the distance between the two specified atoms near the (possibly moving) target value. For moving restraints, this means that after crossing a reaction barrier the system will slide slowly towards products held back by the restraints.
The first parameter is the force constant for the Harmonic, Hyperbolic, and Erf profiles, or well depth for GaussianWell. The second parameter is the asymptotic force value F(Inf) for Hyperbolic and Erf profiles, or the factor before x^2 in the exponent for GaussianWell.
Note: the GaussianWell restraint should be used with the Moving flag.
Moving (BoolType | BoolKey) –
Move the restraints created with this BondBoost. The restraint value will start at the current coordinate’s value and will move towards the optimum during the restraint’s lifetime. The increment is calculated from the initial deviation and the [NSteps] parameter.
This feature should be used with the GaussianWell restraint types.
NSteps (int | IntKey) – Number of steps the restraints will remain active until removed. Atoms participating in one reaction are not available for the given number of steps.
NumInstances (int | IntKey) – Number of reactions of this type taking place simultaneously.
RemoveBond (str | StringKey) – [Reserved] Remove a bond from the system. Specify two atom indices. The indices indicate positions of the atoms in the AtomNames key. Currently no engine will honor bond changes caused by this key.
SetAtomName (str | StringKey) – Change the specified atom’s name. Specify atom index followed by the new name. The index indicates position of the atom in the AtomNames key. Note: this action will change the atom name only and not other properties (element name, mass, etc.). This may be useful to change atom names to affect future chain detections. The atom name length is limited to 32 characters.
Units (Literal["Default", "MD"]) – Change energy, force and force constant units in the DistanceRestraint key from the default (atomic units) to those often used in the MD community (based on kcal/mol and Angstrom). Units for the optimum distances are not affected.
Chain (AMSBatch._MolecularDynamics._BondBoost._Chain) – Specifications of a chain of atoms. When a chain is detected the distance restraints will be activated. No other chain of this type will be detected while any restraints for this chain is active.
- class _Chain[source]¶
Specifications of a chain of atoms. When a chain is detected the distance restraints will be activated. No other chain of this type will be detected while any restraints for this chain is active.
- Variables:
AtomNames (str | StringKey) – Atom names specifying the chain. An atom name can optionally be followed by ‘@’ and a region name, in this case only atoms of this type from the given region will be matched. A leading ‘@’ followed by a number indicates that this position in the chain must be occupied by the atom found earlier at the specified position in the chain. For example “O H N C @1” indicates that the last atom in the chain of the five atoms must be the first oxygen, thus defining a 4-membered ring. This is the only way to define a ring because implicit rings will not be detected. For example, “O H N C O” does not include rings.
MaxDistances (Iterable[float] | FloatListKey) – Maximum distances for each pair of atoms in the chain. The number of distances must be one less than the number of AtomNames.
MinDistances (Iterable[float] | FloatListKey) – Minimum distances for each pair of atoms in the chain. The number of distances must be one less than the number of AtomNames.
- class _CRESTMTD[source]¶
Input for CREST metadynamics simulation.
- Variables:
AddEnergy (BoolType | BoolKey) – Add the bias energy to the potential energy (to match the gradients)
Height (float | FloatKey) – The height of the Gaussians added
NGaussiansMax (int | IntKey) – Maximum number of Gaussians stored
Region (str | StringKey) – Restrict the range of atoms for RMSD calculation to the specified region.
RestartFile (str | Path | StringKey) – Filename for file from which to read data on Gaussians placed previously.
Width (float | FloatKey) – The width of the Gaussians added in terms of the RMSD
GaussianScaling (AMSBatch._MolecularDynamics._CRESTMTD._GaussianScaling) – Options for gradual introduction of the Gaussians
- class _CVHD[source]¶
Input for the Collective Variable-driven HyperDynamics (CVHD).
- Variables:
Frequency (int | IntKey) – Frequency of adding a new bias peak, in steps. New bias is deposited every [Frequency] steps after [StartStep] if the following conditions are satisfied: the current CV value is less than 0.9 (to avoid creating barriers at the transition state), the step number is greater than or equal to [StartStep], and the step number is less than or equal to [StopStep].
MaxEvents (int | IntKey) – Max number of events to allow during dynamics. When this number is reached no new bias will be added for this input block.
StartStep (int | IntKey) – If this key is specified, the first bias will be deposited at this step. Otherwise, the first bias peak is added at the step number equal to the Frequency parameter. The bias is never deposited at step 0.
StopStep (int | IntKey) – No bias will be deposited after the specified step. The already deposited bias will continue to be applied until the reaction event occurs. After that no new CVHD will be started. By default, the CVHD runs for the whole duration of the MD calculation.
WaitSteps (int | IntKey) – If the CV value becomes equal to 1 and remains at this value for this many steps then the reaction event is considered having taken place. After this, the collective variable will be reset and the bias will be removed.
Bias (AMSBatch._MolecularDynamics._CVHD._Bias) – The bias is built from a series of Gaussian peaks deposited on the collective variable axis every [Frequency] steps during MD. Each peak is characterized by its (possibly damped) height and the RMS width (standard deviation).
ColVarBB (AMSBatch._MolecularDynamics._CVHD._ColVarBB) – Description of a bond-breaking collective variable (CV) as described in [Bal & Neyts, JCTC, 11 (2015)]. A collective variable may consist of multiple ColVar blocks.
ColVarBM (AMSBatch._MolecularDynamics._CVHD._ColVarBM) – Description of a bond-making collective variable (CV). A collective variable may consist of multiple ColVar blocks.
- class _Bias[source]¶
The bias is built from a series of Gaussian peaks deposited on the collective variable axis every [Frequency] steps during MD. Each peak is characterized by its (possibly damped) height and the RMS width (standard deviation).
- Variables:
DampingTemp (float | FloatKey) – During well-tempered hyperdynamics the height of the added bias is scaled down with an exp(-E/kT) factor [PhysRevLett 100, 020603 (2008)], where E is the current value of the bias at the given CV value and T is the damping temperature DampingTemp. If DampingTemp is zero then no damping is applied.
Delta (float | FloatKey) – Standard deviation parameter of the Gaussian bias peak.
Height (float | FloatKey) – Height of the Gaussian bias peak.
- class _ColVarBB[source]¶
Description of a bond-breaking collective variable (CV) as described in [Bal & Neyts, JCTC, 11 (2015)]. A collective variable may consist of multiple ColVar blocks.
- Variables:
cutoff (float | FloatKey) – Bond order cutoff. Bonds with BO below this value are ignored when creating the initial bond list for the CV. The bond list does not change during lifetime of the variable even if some bond orders drop below the cutoff.
p (int | IntKey) – Exponent value p used to calculate the p-norm for this CV.
rmax (float | FloatKey) – Max bond distance parameter Rmax used for calculating the CV. It should be close to the transition-state distance for the corresponding bond.
rmin (float | FloatKey) – Min bond distance parameter Rmin used for calculating the CV. It should be close to equilibrium distance for the corresponding bond.
at1 (AMSBatch._MolecularDynamics._CVHD._ColVarBB._at1) – Specifies the first bonded atom in the collective variable.
at2 (AMSBatch._MolecularDynamics._CVHD._ColVarBB._at2) – Specifies the second bonded atom in the collective variable.
- class _at1[source]¶
Specifies the first bonded atom in the collective variable.
- Variables:
region (str | StringKey) – Restrict the selection of bonded atoms to a specific region. If this is not set, atoms anywhere in the system will be selected.
symbol (str | StringKey) – Atom type name of the first atom of the bond. The name must be as it appears in the System block. That is, if the atom name contains an extension (e.g C.1) then the full name including the extension must be used here.
- class _at2[source]¶
Specifies the second bonded atom in the collective variable.
- Variables:
region (str | StringKey) – Restrict the selection of bonded atoms to a specific region. If this is not set, atoms anywhere in the system will be selected.
symbol (str | StringKey) – Atom type name of the second atom of the bond. The value is allowed to be the same as [at1], in which case bonds between atoms of the same type will be included.
- class _ColVarBM[source]¶
Description of a bond-making collective variable (CV). A collective variable may consist of multiple ColVar blocks.
- Variables:
cutoff (float | FloatKey) – Bond order cutoff. Bonds with BO above this value are ignored when creating the initial atom-pair list for the CV. The list does not change during lifetime of the variable even if some bond orders rise above the cutoff.
p (int | IntKey) – Exponent value p used to calculate the p-norm for this CV.
rmax (float | FloatKey) – Max bond distance parameter Rmax used for calculating the CV. It should be much larger than the corresponding Rmin.
rmin (float | FloatKey) – Min bond distance parameter Rmin used for calculating the CV. It should be close to the transition-state distance for the corresponding bond.
at1 (AMSBatch._MolecularDynamics._CVHD._ColVarBM._at1) – Specifies selection criteria for the first atom of a pair in the collective variable.
at2 (AMSBatch._MolecularDynamics._CVHD._ColVarBM._at2) – Specifies selection criteria for the second atom of a pair in the collective variable.
- class _at1[source]¶
Specifies selection criteria for the first atom of a pair in the collective variable.
- Variables:
region (str | StringKey) – Restrict the selection to a specific region. If this is not set, atoms anywhere in the system will be selected.
symbol (str | StringKey) – Atom type name of the first atom of the pair. The name must be as it appears in the System block. That is, if the atom name contains an extension (e.g C.1) then the full name including the extension must be used here.
- class _at2[source]¶
Specifies selection criteria for the second atom of a pair in the collective variable.
- Variables:
region (str | StringKey) – Restrict the selection to a specific region. If this is not set, atoms anywhere in the system will be selected.
symbol (str | StringKey) – Atom type name of the second atom of the pair. The value is allowed to be the same as [at1], in which case pairs of atoms of the same type will be included.
- class _CheckTemperature[source]¶
Check at every time step if the temperature has exceeded a threshold. If it has, it is assumed the system exploded, and the simulation will stop.
- class _Checkpoint[source]¶
Sets the frequency for storing the entire MD state necessary for restarting the calculation.
- Variables:
Frequency (int | IntKey) – Write the MD state to the Molecule and MDResults sections on ams.rkf once every N steps. Setting this to zero disables checkpointing during the simulation, but one checkpoint at the very end of the simulation will always be written.
WriteProperties (BoolType | BoolKey) –
Honor top-level Properties input block when writing engine results files.
DEPRECATED: This input option will be removed in AMS2026 and will be considered always enabled. If you rely on it being disabled, please contact support@scm.com.
- class _CosineShear[source]¶
Apply an external acceleration to all atoms of a fluid using a periodic (cosine) function along a selected coordinate axis. This induces a periodic shear flow profile which can be used to determine the viscosity.
- Variables:
Acceleration (float | FloatKey) – Amplitude of the applied cosine shear acceleration profile. The default value should be a rough first guess for water and it needs to be adjusted by experimentation for other systems.
Enabled (BoolType | BoolKey) – Apply a cosine shear acceleration profile for a NEMD calculation of viscosity.
FlowDirection (Iterable[float] | FloatListKey) – The direction in which to apply the shear acceleration, in Cartesian coordinates. The magnitude of this vector is ignored (AMS will normalize it internally). FlowDirection has to be perpendicular to ProfileAxis.
ProfileAxis (Literal["X", "Y", "Z"]) – The Cartesian coordinate axis along which the cosine wave runs
- class _Deformation[source]¶
Deform the periodic lattice of the system during the simulation.
- Variables:
LengthRate (Iterable[float] | FloatListKey) – Relative rate of change of each lattice vector per step.
LengthVelocity (Iterable[float] | FloatListKey) – Change the length of each lattice vector with this velocity. With Type=Exponential, LengthVelocity is divided by the current lattice vector lengths on StartStep to determine a LengthRate, which is then applied on all subsequent steps. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).
Period (float | FloatKey) – Period of oscillation for Type Sine and Cosine.
ScaleAtoms (BoolType | BoolKey) – Scale the atomic positions together with the lattice vectors. Disable this to deform only the lattice, keeping the coordinates of atoms unchanged.
StartStep (int | IntKey) – First step at which the deformation will be applied.
StopStep (int | IntKey) – Last step at which the deformation will be applied. If unset or zero, nSteps will be used instead.
TargetDensity (float | FloatKey) –
Target density of the system to be achieved by StopStep by isotropically rescaling the lattice.
This can only be used for 3D-periodic systems. Note that the selected Type determines how the lengths of the lattice vectors will evolve (linearly or as a sine/cosine), the evolution of the volume or density is thus necessarily non-linear.
TargetLength (Iterable[float] | FloatListKey) – Target lengths of each lattice vector to be achieved by StopStep. The number of values should equal the periodicity of the system. If a value is zero, the corresponding lattice vector will not be modified.
Type (Literal["Linear", "Exponential", "Sine", "Cosine"]) –
Function defining the time dependence of the deformed lattice parameters.
Linear increments the lattice parameters by the same absolute amount every timestep. Exponential multiplies the lattice parameters by the same factor every timestep. Only StrainRate, LengthRate, and LengthVelocity are supported for Type=Exponential. Sine deforms the system from the starting lattice to TargetLattice/TargetLength and then by the same amount to the opposite direction, while Cosine deforms the system from the starting lattice to the target and back.
LatticeVelocity (str | Sequence[str] | FreeBlock) – Velocity of individual lattice vector components in Angstrom/fs. The format is identical to the System%Lattice block. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).
StrainRate (str | Sequence[str] | FreeBlock) – Strain rate matrix to be applied on every step. The format is identical to the System%Lattice block.
TargetLattice (str | Sequence[str] | FreeBlock) – Target lattice vectors to be achieved by StopStep. The format is identical to the System%Lattice block.
- class _LatticeVelocity[source]¶
Velocity of individual lattice vector components in Angstrom/fs. The format is identical to the System%Lattice block. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).
- class _HeatExchange[source]¶
Input for the heat-exchange non-equilibrium MD (T-NEMD).
- Variables:
HeatingRate (float | FloatKey) – Rate at which the energy is added to the Source and removed from the Sink. A heating rate of 1 Hartree/fs equals to about 0.00436 Watt of power being transferred through the system.
Method (Literal["Simple", "HEX", "eHEX"]) –
Heat exchange method used.
Simple: kinetic energy of the atoms of the source and sink regions is modified irrespective of that of the center of mass (CoM) of the region (recommended for solids).
HEX: kinetic energy of the atoms of these regions is modified keeping that of the corresponding CoM constant.
eHEX: an enhanced version of HEX that conserves the total energy better (recommended for gases and liquids).
StartStep (int | IntKey) – Index of the MD step at which the heat exchange will start.
StopStep (int | IntKey) – Index of the MD step at which the heat exchange will stop.
Sink (AMSBatch._MolecularDynamics._HeatExchange._Sink) – Defines the heat sink region (where the heat will be removed).
Source (AMSBatch._MolecularDynamics._HeatExchange._Source) – Defines the heat source region (where the heat will be added).
- class _Sink[source]¶
Defines the heat sink region (where the heat will be removed).
- Variables:
AtomList (Iterable[int] | IntListKey) –
The atoms that are part of the sink.
This key is ignored if the [Box] block or [Region] key is present.
FirstAtom (int | IntKey) – Index of the first atom of the region. This key is ignored if the [Box] block or the [AtomList] key is present.
LastAtom (int | IntKey) – Index of the last atom of the region. This key is ignored if the [Box] block or the [AtomList] key is present.
The region that is the sink.
This key is ignored if the [Box] block is present.
Show (BoolType | BoolKey) – Show the sink in the AMSinput
Box (AMSBatch._MolecularDynamics._HeatExchange._Sink._Box) – Part of the simulation box (in fractional cell coordinates) defining the heat sink. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes.
- class _Box[source]¶
Part of the simulation box (in fractional cell coordinates) defining the heat sink. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes.
- Variables:
Amax (float | FloatKey) – Coordinate of the upper bound along the first axis.
Amin (float | FloatKey) – Coordinate of the lower bound along the first axis.
Bmax (float | FloatKey) – Coordinate of the upper bound along the second axis.
Bmin (float | FloatKey) – Coordinate of the lower bound along the second axis.
Cmax (float | FloatKey) – Coordinate of the upper bound along the third axis.
Cmin (float | FloatKey) – Coordinate of the lower bound along the third axis.
- class _Source[source]¶
Defines the heat source region (where the heat will be added).
- Variables:
AtomList (Iterable[int] | IntListKey) –
The atoms that are part of the source.
This key is ignored if the [Box] block or [Region] key is present.
FirstAtom (int | IntKey) – Index of the first atom of the region. This key is ignored if the [Box] block or the [AtomList] key is present.
LastAtom (int | IntKey) – Index of the last atom of the region. This key is ignored if the [Box] block or the [AtomList] key is present.
The region that is the source.
This key is ignored if the [Box] block is present.
Show (BoolType | BoolKey) – Show the source in the AMSinput
Box (AMSBatch._MolecularDynamics._HeatExchange._Source._Box) – Part of the simulation box (in fractional cell coordinates) defining the heat source. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes. This block is mutually exclusive with the FirstAtom/LastAtom setting.
- class _Box[source]¶
Part of the simulation box (in fractional cell coordinates) defining the heat source. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes. This block is mutually exclusive with the FirstAtom/LastAtom setting.
- Variables:
Amax (float | FloatKey) – Coordinate of the upper bound along the first axis.
Amin (float | FloatKey) – Coordinate of the lower bound along the first axis.
Bmax (float | FloatKey) – Coordinate of the upper bound along the second axis.
Bmin (float | FloatKey) – Coordinate of the lower bound along the second axis.
Cmax (float | FloatKey) – Coordinate of the upper bound along the third axis.
Cmin (float | FloatKey) – Coordinate of the lower bound along the third axis.
- class _InitialVelocities[source]¶
Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- Variables:
File (str | Path | StringKey) – AMS RKF file containing the initial velocities.
RandomVelocitiesMethod (Literal["Exact", "Boltzmann", "Gromacs"]) –
Specifies how are random velocities generated. Three methods are available.
Exact: Velocities are scaled to exactly match set random velocities temperature.
Boltzmann: Velocities are not scaled and sample Maxwell-Boltzmann distribution. However, the distribution is not corrected for constraints.
Gromacs: Velocities are scaled to match set random velocities temperature, but removal of net momentum is performed only after the scaling. Resulting kinetic energy is lower based on how much net momentum the system had.
Temperature (float | FloatKey) –
Sets the temperature for the Maxwell-Boltzmann distribution when the type of the initial velocities is set to random, in which case specifying this key is mandatory.
AMSinput will use the first temperature of the first thermostat as default.
Type (Literal["Zero", "Random", "FromFile", "Input"]) –
Specifies the initial velocities to assign to the atoms. Three methods to assign velocities are available.
Zero: All atom are at rest at the beginning of the calculation.
Random: Initial atom velocities follow a Maxwell-Boltzmann distribution for the temperature given by the [MolecularDynamics%InitialVelocities%Temperature] keyword.
FromFile: Load the velocities from a previous ams result file.
Input: Atom’s velocities are set to the values specified in the [MolecularDynamics%InitialVelocities%Values] block, which can be accessed via the Expert AMS panel in AMSinput.
Values (str | Sequence[str] | FreeBlock) – This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.
- class _Values[source]¶
This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.
- class _MovingRestraints[source]¶
Define a set of moving restraints.
- Variables:
Change (Literal["Linear", "Sine", "Cosine"]) –
Type of function defining how the target restraint value will change over time:
Linear - linearly between the StartValue and EndValue. Sine - oscillating around StartValue with an amplitude equal to the difference between EndValue and StartValue. Cosine - oscillating between StartValue and EndValue.
Name (str | StringKey) – Optional name to be used for plotting.
Period (float | FloatKey) – Period of oscillation for Sine and Cosine change types.
RestraintType (Literal["None", "Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) – Select type of the moving restraint profile. The force for Hyperbolic and Erf is bounded by a user-defined value, the latter converging to it faster than the former. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable.
StartStep (int | IntKey) – First step number at which the restraints will be applied.
StopStep (int | IntKey) – Last step number at which the restraints will be applied.
Distance (AMSBatch._MolecularDynamics._MovingRestraints._Distance) – Define a distance restraint between pair of atoms. For linear-type
Erf (AMSBatch._MolecularDynamics._MovingRestraints._Erf) – Define parameters for the Int(erf) restraint potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
GaussianWell (AMSBatch._MolecularDynamics._MovingRestraints._GaussianWell) – Define parameters in the Gaussian well restraint potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
Harmonic (AMSBatch._MolecularDynamics._MovingRestraints._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
Hyperbolic (AMSBatch._MolecularDynamics._MovingRestraints._Hyperbolic) – Define parameters for the hyperbolic restraint potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
- class _Distance[source]¶
Define a distance restraint between pair of atoms. For linear-type
- class _Erf[source]¶
Define parameters for the Int(erf) restraint potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
- class _GaussianWell[source]¶
Define parameters in the Gaussian well restraint potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
- class _PRD[source]¶
This block is used for Parallel Replica Dynamics simulations.
- Variables:
CorrelatedSteps (int | IntKey) – How many steps to wait for correlated events after detecting an initial event.
DephasingSteps (int | IntKey) – Spend this many steps dephasing the individual replicas after an event.
nReplicas (int | IntKey) – Number of replicas to run in parallel.
BondChange (AMSBatch._MolecularDynamics._PRD._BondChange) – Detect changes to the bonding topology and bond orders returned by the engine.
MolCount (AMSBatch._MolecularDynamics._PRD._MolCount) – Detect changes to the molecular composition of the system.
- class _BondChange[source]¶
Detect changes to the bonding topology and bond orders returned by the engine.
- Variables:
ChangeThreshold (float | FloatKey) – Trigger an event when the bond order of a bond changes from the reference state by more than this value.
DissociationThreshold (float | FloatKey) – Trigger an event when a bond dissociates (its bond order drops below this value while it was above FormationThreshold in the reference state).
FormationThreshold (float | FloatKey) – Trigger an event when a new bond forms (its bond order exceeds this value while it was below DissociationThreshold in the reference state).
- class _Plumed[source]¶
Input for PLUMED (version 2.5.0). The parallel option is still experimental.
- Variables:
Input (str | Sequence[str] | FreeBlock) – Input for PLUMED. Contents of this block is passed to PLUMED as is.
Parallel (AMSBatch._MolecularDynamics._Plumed._Parallel) – Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- class _Parallel[source]¶
Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _Preserve[source]¶
Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.
- Variables:
AngularMomentum (BoolType | BoolKey) – Remove overall angular momentum of the system. This option is ignored for 2D and 3D-periodic systems, and disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).
CenterOfMass (BoolType | BoolKey) – Translate the system to keep its center of mass at the coordinate origin. This option is not very useful for 3D-periodic systems.
Momentum (BoolType | BoolKey) – Remove overall (linear) momentum of the system. This is disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).
- class _ReactionBoost[source]¶
Define a series of transitions between different states of the system.
Each transition is defined by a TargetSystem and by a set of restraints that force the transition.
- Variables:
Change (Literal["TargetCoordinate", "Force", "LogForce"]) –
Select what to change during dynamics.
By default, once the restraints are switched on, AMS will change the restraint’s target coordinate towards its final value.
If the [Force] or [LogForce] option is selected then the target coordinate is set to its final value immediately and instead the restraint force is gradually scaled from 0 to 1. The scaling is either linear (Force) or logarithmic (LogForce).
InitialFraction (float | FloatKey) –
Initial fraction of the boost variable.
At the first boosting step, the restraint’s target value (or force or log(force)) is equal to InitialFraction + 1/NSteps.
InterEquilibrationSteps (int | IntKey) – Number of equilibration steps after reaching a target before setting up restraints for the next one.
MinBondChange (float | FloatKey) – Minimal change in the distance for an individual restraint to be considered bond-breaking/making vs bonded.
MinBondStrength (float | FloatKey) – Minimum strength (usually ranges from 0 to 1) for a bond to be considered.
NSteps (int | IntKey) – Number of steps per target the restraints should be active for.
PreEquilibrationSteps (int | IntKey) – Number of steps before enabling the first set of restraints.
Region (str | StringKey) – Region to which the restraints should be limited.
TargetSystem (str | StringKey) –
The target system’s name for this transition. Multiple targets can be specified to request multiple transitions in one simulation.
Note that only the lattice and the atomic coordinates of the target system are used and other properties (bonds, charge, etc.) are ignored. The target system’s lattice is used only to determine connections and it cannot be restrained.
Type (Literal["None", "Pair", "RMSD"]) –
Reaction Boost uses a series of transitions between different states of the system. Each transition is defined by a TargetSystem and by a set of restraints that force the transition.
Select the type of the restraint set: -None: no Reaction Boost - Pair: use pair restraints - RMSD: use RMSD restraints.
Pair restraints are defined per atom pair while the RMSD defines one collective restraint for all atoms and is thus suitable for very large systems.
The pair restraints are further divided into four sub-types: bonding, non-bonding, bond-breaking and bond-making. The sub-type of restraints for each pair is determined automatically depending on whether the two atoms are bonded in the initial/final state.
Parameters of the pair restraints are defined by [NonBondedRestraints], [BondedRestraints], [BondBreakingRestraints] and [BondMakingRestraints] blocks, while those of the RMSD restraint by the [RMSDRestraint] block.
BondBreakingRestraints (AMSBatch._MolecularDynamics._ReactionBoost._BondBreakingRestraints) –
Define parameters for moving restraints that are added for pairs of atoms that become disconnected during the transition.
It is intended to make sure the corresponding bonds get broken, although this may not always be required because forming other bonds will likely get these bonds broken.
BondMakingRestraints (AMSBatch._MolecularDynamics._ReactionBoost._BondMakingRestraints) –
Define parameters for moving restraints that are added for pairs of atoms that become connected during the transition.
It is intended to make sure the bonds are created as required.
BondedRestraints (AMSBatch._MolecularDynamics._ReactionBoost._BondedRestraints) –
Define parameters for bonded restraints. A bonded restraint is added for each pair of atoms that are bonded both in the current and in the final state.
It is intended to make sure they remain bonded during simulation.
NonBondedRestraints (AMSBatch._MolecularDynamics._ReactionBoost._NonBondedRestraints) –
Define parameters for non-bonded restraints. A non-bonded restraint is added for each pair of atoms that are bonded neither in the current nor in the final state.
It is intended to keep them from forming a bond unintentionally. They are represented by a repulsive potential
RMSDRestraint (AMSBatch._MolecularDynamics._ReactionBoost._RMSDRestraint) – Define a static restraint that pulls each atom to its position in the target system, but in contrast to the individual restraints, the force for this one depends on the total mass-weighted root-mean-squared distance (RMSD) between the two structures.
- class _BondBreakingRestraints[source]¶
Define parameters for moving restraints that are added for pairs of atoms that become disconnected during the transition.
It is intended to make sure the corresponding bonds get broken, although this may not always be required because forming other bonds will likely get these bonds broken.
- Variables:
Type (Literal["None", "Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) –
Select type of the moving restraint profile.
Harmonic: V=0.5*FC*(r-r0)^2
Hyperbolic: V=alpha*(sqrt(1 + beta*x^2) - 1)
Erf: V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI))
GaussianWell: V=WellDepth*(1-exp(-Sigma*(r-r0)^2))
Here beta=ForceConstant/MaxForce, alpha=MaxForce/beta.
The force for Hyperbolic and Erf is bounded by a user-defined value, the latter converging to it faster than the former. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable.
Moving restraints are added for pairs of atoms that become disconnected during the transition.
It is intended to make sure the corresponding bonds get broken, although this may not always be required because forming other bonds will likely get these bonds broken.
Erf (AMSBatch._MolecularDynamics._ReactionBoost._BondBreakingRestraints._Erf) – Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
GaussianWell (AMSBatch._MolecularDynamics._ReactionBoost._BondBreakingRestraints._GaussianWell) – Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
Harmonic (AMSBatch._MolecularDynamics._ReactionBoost._BondBreakingRestraints._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
Hyperbolic (AMSBatch._MolecularDynamics._ReactionBoost._BondBreakingRestraints._Hyperbolic) – Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
Taper (AMSBatch._MolecularDynamics._ReactionBoost._BondBreakingRestraints._Taper) –
- class _Erf[source]¶
Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
- class _GaussianWell[source]¶
Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
- class _Hyperbolic[source]¶
Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
- class _Taper[source]¶
- Variables:
Enabled (BoolType | BoolKey) – Enable tapering of the restraint potential and force between the given range of bond distances. A 7-th order tapering function on the actual (not target!) distance will be used. The MaxDistance must be greater than MinDistance.
MaxDistance (float | FloatKey) – Bond length at which the restraint potential and force decays to zero.
MinDistance (float | FloatKey) – Bond length at which the restraint potential and force will start decaying to zero.
- class _BondMakingRestraints[source]¶
Define parameters for moving restraints that are added for pairs of atoms that become connected during the transition.
It is intended to make sure the bonds are created as required.
- Variables:
Type (Literal["None", "Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) –
Select type of the moving restraint profile.
Harmonic: V=0.5*FC*(r-r0)^2
Hyperbolic: V=alpha*(sqrt(1 + beta*x^2) - 1)
Erf: V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI))
GaussianWell: V=-WellDepth*exp(-Sigma*(r-r0)^2)
Here beta=ForceConstant/MaxForce, alpha=MaxForce/beta.
The force for Hyperbolic and Erf is bounded by a user-defined value. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable.
Moving restraints are added for pairs of atoms that become connected during the transition.
It is intended to make sure the bonds are created as required.
Erf (AMSBatch._MolecularDynamics._ReactionBoost._BondMakingRestraints._Erf) – Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
GaussianWell (AMSBatch._MolecularDynamics._ReactionBoost._BondMakingRestraints._GaussianWell) – Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
Harmonic (AMSBatch._MolecularDynamics._ReactionBoost._BondMakingRestraints._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
Hyperbolic (AMSBatch._MolecularDynamics._ReactionBoost._BondMakingRestraints._Hyperbolic) – Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
- class _Erf[source]¶
Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
- class _GaussianWell[source]¶
Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
- class _BondedRestraints[source]¶
Define parameters for bonded restraints. A bonded restraint is added for each pair of atoms that are bonded both in the current and in the final state.
It is intended to make sure they remain bonded during simulation.
- Variables:
Type (Literal["None", "Harmonic"]) –
Select type of the bonded restraints:
Harmonic: V=0.5*FC*(r-r0)^2
A bonded restraint is added for each pair of atoms that are bonded both in the current and in the final state.
It is intended to make sure they remain bonded during simulation.
Harmonic (AMSBatch._MolecularDynamics._ReactionBoost._BondedRestraints._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
- class _NonBondedRestraints[source]¶
Define parameters for non-bonded restraints. A non-bonded restraint is added for each pair of atoms that are bonded neither in the current nor in the final state.
It is intended to keep them from forming a bond unintentionally. They are represented by a repulsive potential
- Variables:
Type (Literal["None", "Exponential"]) –
Select type of the non-bonded restraints:
Exponential: V=Epsilon*exp(-Sigma*r)
A non-bonded restraint is added for each pair of atoms that are bonded neither in the current nor in the final state.
It is intended to keep them from forming a bond unintentionally. They are represented by a repulsive potential.
Exponential (AMSBatch._MolecularDynamics._ReactionBoost._NonBondedRestraints._Exponential) – Define parameters for the repulsive potential V=Epsilon*exp(-Sigma*r).
- class _RMSDRestraint[source]¶
Define a static restraint that pulls each atom to its position in the target system, but in contrast to the individual restraints, the force for this one depends on the total mass-weighted root-mean-squared distance (RMSD) between the two structures.
- Variables:
Type (Literal["None", "Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) –
Select type of the RMSD restraint profile:
Harmonic: V=0.5*FC*(r-r0)^2
Hyperbolic: V=alpha*(sqrt(1 + beta*x^2) - 1)
Erf: V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI),
GaussianWell: V=-WellDepth*exp(-Sigma*(r-r0)^2)
Here beta=ForceConstant/MaxForce, alpha=MaxForce/beta.
The Harmonic profile can be problematic at large deviations as it may result in large forces. The force for Hyperbolic and Erf is bounded by a user-defined value. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable.
Erf (AMSBatch._MolecularDynamics._ReactionBoost._RMSDRestraint._Erf) – Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
GaussianWell (AMSBatch._MolecularDynamics._ReactionBoost._RMSDRestraint._GaussianWell) – Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
Harmonic (AMSBatch._MolecularDynamics._ReactionBoost._RMSDRestraint._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
Hyperbolic (AMSBatch._MolecularDynamics._ReactionBoost._RMSDRestraint._Hyperbolic) – Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
- class _Erf[source]¶
Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
- class _GaussianWell[source]¶
Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
- class _Reactor[source]¶
Define one phase of the nanoreactor. A reactor is a region of space surrounded by an elastic wall. Atoms inside the region are not affected. Atoms outside it will be pushed back with force depending on the [ForceConstant] and the [MassScaled] flag.
- Variables:
ForceConstant (float | FloatKey) – Force constant of the reactor wall in Hartree/Bohr^2 (or Hartree/Bohr^2/Dalton if [MassScaled] is true).
MassScaled (BoolType | BoolKey) – If this flag is disabled the force on an atom outside of the reactor depends only on the atomic coordinates and the force constant. Otherwise, the force is also multiplied by the mass of the atom. This means that atoms at the same distance from the wall will receive the same accelerate due to the wall potential.
NSteps (int | IntKey) – Number of steps for which the reactor will remain active until disabled. The next reactor will be activated immediately after this. After the last reactor is disabled the cycle will repeat.
- class _ReflectiveWall[source]¶
Apply a reflective wall in space
- Variables:
Axis (Iterable[float] | FloatListKey) – Defines the normal vector perpendicular to the plane of the reflective wall. Any particle moving in this direction will be reflected back.
Direction (Literal["under", "above"]) – Defines the direction of the reflective wall. under will keep the particles under the defined wall, and above will keep the particles above the defined wall
Region (str | StringKey) – Apply the reflective wall to all atoms in this region.
Threshold (float | FloatKey) – Defines the threshold value determining the position of the reflective wall. If the dot product of a position of a particle with Axis exceeds Threshold, the particle will be reflected. This means that the plane of the wall passes through a point given by Axis times Threshold.
- class _Remap[source]¶
Control periodic remapping (backtranslation) of atoms into the PBC box.
- Variables:
Range (Literal["Auto", "ZeroToOne", "PlusMinusHalf", "AroundCenter"]) –
Select the range of fractional coordinates to which atoms are remapped.
Auto: Use PlusMinusHalf if the geometrical center of the starting positions of all atoms lies between -0.25 and 0.25 in fractional coordinates in all periodic directions, ZeroToOne otherwise.
PlusMinusHalf: Remap atoms to lie between -0.5 and 0.5 in fractional coordinates.
ZeroToOne: Remap atoms to lie between 0 and 1 in fractional coordinates.
AroundCenter: Remap atoms to lie within 0.5 in fractional coordinates around the geometrical center of the starting positions of all atoms.
Type (Literal["None", "Atoms"]) –
Select the method used to remap atoms into the unit cell.
None: Disable remapping completely.
Atoms: Remap any atoms that leave the unit cell.
- class _RemoveMolecules[source]¶
This block controls removal of molecules from the system. Multiple occurrences of this block are possible.
- Variables:
Molecular formula of the molecules that should be removed from the system.
The order of elements in the formula is very important and the correct order is: C, H, all other elements in the strictly alphabetic order. Element names are case-sensitive, spaces in the formula are not allowed. Digit ‘1’ must be omitted.
Valid formula examples: C2H6O, H2O, O2S. Invalid formula examples: C2H5OH, H2O1, OH, SO2. Invalid formulas are silently ignored.
Use * to remove any molecule, which must be combined with SinkBox or SafeBox.
Frequency (int | IntKey) – The specified molecules are removed every so many steps after the StartStep. There is never a molecule removed at step 0.
Step number when molecules are removed for the first time. After that, molecules are removed every [Frequency] steps.
For example, if StartStep=99 and Frequency=100 then molecules will be removed at steps 99, 199, 299, etc…
No molecule will be removed at step 0, so if StartStep=0 the first molecules are removed at the step number equal to [Frequency].
StopStep (int | IntKey) – Do not remove the specified molecules after this step.
SafeBox (AMSBatch._MolecularDynamics._RemoveMolecules._SafeBox) – Part of the simulation box where molecules may not be removed. Only one of the SinkBox or SafeBox blocks may be present. If this block is present the molecule will not be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.
SinkBox (AMSBatch._MolecularDynamics._RemoveMolecules._SinkBox) – Part of the simulation box where matching molecules will be removed. By default, molecules matching the formula will be removed regardless of their location. If this block is present then such a molecule will only be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.
- class _SafeBox[source]¶
Part of the simulation box where molecules may not be removed. Only one of the SinkBox or SafeBox blocks may be present. If this block is present the molecule will not be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.
- Variables:
Amax (float | FloatKey) – Coordinate of the upper bound along the first axis.
Amin (float | FloatKey) – Coordinate of the lower bound along the first axis.
Bmax (float | FloatKey) – Coordinate of the upper bound along the second axis.
Bmin (float | FloatKey) – Coordinate of the lower bound along the second axis.
Cmax (float | FloatKey) – Coordinate of the upper bound along the third axis.
Cmin (float | FloatKey) – Coordinate of the lower bound along the third axis.
FractionalCoordsBox (Iterable[float] | FloatListKey) –
Do not remove molecules that are (partly) inside the safe box.
Borders of the safe box specified as: Amin, Amax, Bmin, Bmax, Cmin, Cmax.
For periodic dimensions fractional coordinates between 0 and 1 and for non-periodic dimensions Cartesian values in Angstrom are expected.
- class _SinkBox[source]¶
Part of the simulation box where matching molecules will be removed. By default, molecules matching the formula will be removed regardless of their location. If this block is present then such a molecule will only be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.
- Variables:
Amax (float | FloatKey) – Coordinate of the upper bound along the first axis.
Amin (float | FloatKey) – Coordinate of the lower bound along the first axis.
Bmax (float | FloatKey) – Coordinate of the upper bound along the second axis.
Bmin (float | FloatKey) – Coordinate of the lower bound along the second axis.
Cmax (float | FloatKey) – Coordinate of the upper bound along the third axis.
Cmin (float | FloatKey) – Coordinate of the lower bound along the third axis.
FractionalCoordsBox (Iterable[float] | FloatListKey) –
Remove molecules that are (partly) inside the sink box.
Borders of the sink box specified as: Amin, Amax, Bmin, Bmax, Cmin, Cmax.
For periodic dimensions fractional coordinates between 0 and 1 and for non-periodic dimensions Cartesian values in Angstrom are expected.
- class _ReplicaExchange[source]¶
This block is used for (temperature) Replica Exchange MD (Parallel Tempering) simulations.
- Variables:
AllowWrongResults (BoolType | BoolKey) – Allow combining Replica Exchange with other features when the combination is known to produce physically incorrect results.
Length of the exponentially weighted moving average used to smooth swap probabilities for monitoring.
This value is equal to the inverse of the EWMA mixing factor.
SwapFrequency (int | IntKey) – Attempt an exchange every N steps.
TemperatureFactors (Iterable[float] | FloatListKey) –
This is the ratio of the temperatures of two successive replicas.
The first value sets the temperature of the second replica with respect to the first replica, the second value sets the temperature of the third replica with respect to the second one, and so on. If there are fewer values than nReplicas, the last value of TemperatureFactor is used for all the remaining replicas.
Temperatures (Iterable[float] | FloatListKey) –
List of temperatures for all replicas except for the first one.
This is mutually exclusive with TemperatureFactors. Exactly nReplicas-1 temperature values need to be specified, in increasing order. The temperature of the first replica is given by [Thermostat%Temperature].
nReplicas (int | IntKey) – Number of replicas to run in parallel.
- class _Shake[source]¶
Parameters of the Shake/Rattle algorithm.
- Variables:
Constraint description in one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3
The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 and the angle between them.
The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then all bonds between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. The distance, if present, must be in Angstrom. If it is omitted then the bond length from the initial geometry is used.
Important: only the bonds present in the system at certain points of the simulation (at the start or right after adding/removing atoms) can be constrained, which means that the bonds may need to be specified in the System block.
Warning: the triangles constraint should be used with care because each constrained bond or angle means removing one degree of freedom from the dynamics. When there are too many constraints (for example, “All triangles H C H” in methane) some of them may be linearly dependent, which will lead to an error in the temperature computation.
Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H
ConvergeR2 (float | FloatKey) – Convergence criterion on the max squared difference, in atomic units.
ConvergeRV (float | FloatKey) – Convergence criterion on the orthogonality of the constraint and the relative atomic velocity, in atomic units.
ShakeInitialCoordinates (BoolType | BoolKey) – Apply constraints before computing the first energy and gradients.
- class _Thermostat[source]¶
This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’s behavior.
- Variables:
BerendsenApply (Literal["Local", "Global"]) –
Select how to apply the scaling correction for the Berendsen thermostat:
per-atom-velocity (Local)
on the molecular system as a whole (Global).
ChainLength (int | IntKey) – Number of individual thermostats forming the NHC thermostat
Duration (Iterable[int] | IntListKey) – Specifies how many steps should a transition from a particular temperature to the next one in sequence take.
ExcludedDirection (Literal["None", "X", "Y", "Z"]) – Exclude a component of the velocities from rescaling by the thermostat. For example in NEMD simulations, when a shear force/velocity is applied in the x direction, the x-direction is often excluded from thermostatting. This currently only works for the Nose-Hoover thermostat.
Friction (float | FloatKey) – Friction coefficient used in langevin dynamics
Region (str | StringKey) – The identifier of the region to thermostat. The default * applies the thermostat to the entire system. The value can by a plain region name, or a region expression, e.g. *-myregion to thermostat all atoms that are not in myregion, or regionA+regionB to thermostat the union of the ‘regionA’ and ‘regionB’. Note that if multiple thermostats are used, their regions may not overlap.
ScaleFrequency (int | IntKey) –
Optional parameter used only by the Scale thermostat.
If specified, the thermostat will be applied every N steps, using that step’s ensemble temperature and the specified thermostat temperature to compute the scaling factor.
If not specified, the thermostat will be applied at every step, using the mean temperature of the ensemble and the specified thermostat temperature to compute the scaling factor.
Tau (float | FloatKey) – The time constant of the thermostat.
Temperature (Iterable[float] | FloatListKey) –
The target temperature of the thermostat.
You can specify multiple temperatures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one T to the next T (using a linear ramp). For NHC thermostat, the temperature may not be zero.
Type (Literal["None", "Scale", "Berendsen", "NHC", "Langevin"]) – Selects the type of the thermostat.
- class _Trajectory[source]¶
Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- Variables:
EngineResultsFreq (int | IntKey) – Write MDStep*.rkf files with engine-specific results once every N steps. Setting this to zero disables writing engine results files except for one file at the end of the simulation. If unset or negative, defaults to the value of Checkpoint%Frequency.
ExitConditionFreq (int | IntKey) – Check the exit conditions every N steps. By default this is done every SamplingFreq steps.
PrintFreq (int | IntKey) – Print current thermodynamic properties to the output every N steps. By default this is done every SamplingFreq steps.
SamplingFreq (int | IntKey) – Write the molecular geometry (and possibly other properties) to the ams.rkf file once every N steps.
TProfileGridPoints (int | IntKey) – Number of points in the temperature profile. If TProfileGridPoints > 0, a temperature profile along each of the three lattice axes will be written to the .rkf file. The temperature at a given profile point is calculated as the total temperature of all atoms inside the corresponding slice of the simulation box, time-averaged over all MD steps since the previous snapshot. By default, no profile is generated.
WriteBonds (BoolType | BoolKey) – Write detected bonds to the .rkf file.
WriteCharges (BoolType | BoolKey) – Write current atomic point charges (if available) to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze charges.
WriteCoordinates (BoolType | BoolKey) – Write atomic coordinates to the .rkf file.
WriteEngineGradients (BoolType | BoolKey) – Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.
WriteMolecules (BoolType | BoolKey) – Write the results of molecule analysis to the .rkf file.
WriteVelocities (BoolType | BoolKey) – Write velocities to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze the velocities.
- class _fbMC[source]¶
This block sets up force bias Monte Carlo interleaved with the molecular dynamics simulation.
- Variables:
Frequency (int | IntKey) – Run the fbMC procedure every Frequency MD steps.
MassRoot (float | FloatKey) – Inverse of the exponent used to mass-weight fbMC steps.
NSteps (int | IntKey) – Number of fbMC steps to perform on every invocation of the procedure.
PrintFreq (int | IntKey) – Print current thermodynamic properties to the output every N fbMC steps. This defaults to the PrintFreq set in the Trajectory block. Setting this to zero disables printing fbMC steps.
StartStep (int | IntKey) – First step at which the fbMC procedure may run.
StepLength (float | FloatKey) – Maximum allowed displacement of the lightest atom in the system in each Cartesian coordinate in one fbMC step.
StopStep (int | IntKey) – Last step at which the fbMC procedure may run. If unset or zero, there is no limit.
MolecularMoves (AMSBatch._MolecularDynamics._fbMC._MolecularMoves) – Move molecules as rigid bodies in addition to normal atomic moves.
- class _MolecularMoves[source]¶
Move molecules as rigid bodies in addition to normal atomic moves.
- Variables:
Enabled (BoolType | BoolKey) – Enable moving molecules as rigid bodies based on net forces and torques. Ordinary per-atom displacements will then be based on residual atomic forces.
RotationMethod (Literal["Mees", "Rao"]) – Select the fbMC method used to generate molecular rotation moves.
RotationStepAngle (float | FloatKey) – Maximum allowed angle of rotation of each molecule in one fbMC step.
TranslationStepLength (float | FloatKey) – Maximum allowed displacement of each molecule in each Cartesian coordinate in one fbMC step.
- class _Molecules[source]¶
Configures details of the molecular composition analysis enabled by the Properties%Molecules block.
- Variables:
AdsorptionSupportRegion (str | StringKey) – Select region that will represent a support for adsorption analysis. Adsorbed molecules will receive an ‘(ads)’ suffix after name of the element bonded to the support. Such elements will be listed separate from atoms of the same element not bonded to the support, for example, HOH(ads) for a water molecule bonded to a surface via one of its H atoms.
BondOrderCutoff (float | FloatKey) – Bond order cutoff for analysis of the molecular composition. Bonds with bond order smaller than this value are neglected when determining the molecular composition.
- class _NEB[source]¶
Configures details of the Nudged Elastic Band optimization.
- Variables:
Climbing (BoolType | BoolKey) – Use the climbing image algorithm to drive the highest image to the transition state.
ClimbingThreshold (float | FloatKey) – Climbing image force threshold. If ClimbingThreshold > 0 and the max perpendicular force component is above the threshold then no climbing is performed at this step. This entry can be used to get a better approximation for the reaction path before starting the search for the transition state. A typical value is 0.01 Hartree/Bohr.
DoubleNudge (Literal["None", "Henkelman", "Trygubenko"]) – Type of the double nudging method.
Images (int | IntKey) – Number of NEB images (not counting the chain ends). Using more images will result in a smoother reaction path and can help with convergence problems, but it will also increase the computation time.
Intermediates (str | StringKey) –
Define one or more intermediate systems.
The molecule names are adjusted when saving so that the order of the intermediates is the order as they appear in the list here.
If no intermediate systems are needed, select None
InterpolateInternal (BoolType | BoolKey) – The initial NEB image geometries are calculated by interpolating between the initial and the final state. By default, for non-periodic systems the interpolation is performed in internal coordinates but the user can choose to do it in the Cartesian ones. For periodic systems the interpolation is always done in Cartesian coordinates. If PreOptimizeWithIDPP is set then the path may be further refined using the image-dependent pair potential (IDPP).
InterpolateShortest (BoolType | BoolKey) – Allow interpolation across periodic cell boundaries. Set to false if an atom is intended to move more than half across the simulation box during reaction.
InterpolationOption (int | IntKey) –
Select which internal coordinates will be interpolated:
- 0 - automatic,
1 - only distances, 2 - distances and near-linear valence angles, 3 - distances and all valence angles, 4 - distances and dihedral angles, 99 - all coordinates
Iterations (int | IntKey) – Maximum number of NEB iterations. The default value depends on the number of degrees of freedom (number of images, atoms, periodic dimensions).
Jacobian (float | FloatKey) – Scaling factor used to convert the lattice strain to a NEB coordinate value. Default value: sqrt(N)*(V/N)^(1/d), where V - lattice volume (area for 2D, length for 1D), N - number of atoms, and d - number of periodic dimensions.
MapAtomsToCell (BoolType | BoolKey) – Translate atoms to the [-0.5,0.5] cell before every step. This option cannot be disabled for SS-NEB.
OldTangent (BoolType | BoolKey) – Turn on the old central difference tangent.
OptimizeEnds (BoolType | BoolKey) – Start the NEB with optimization of the reactant and product geometries.
OptimizeLattice (BoolType | BoolKey) – Turn on the solid-state NEB (SS-NEB).
PreOptimizeWithIDPP (BoolType | BoolKey) – (Experimental) When there is only initial and final system available, the image-dependent pair potential (IDPP, doi: 10.1063/1.4878664) can be used to determine the initial NEB path by interpolating all interatomic distances between the two points and optimizing intermediate images towards them. The optimization starts from the geometries obtained using the selected interpolation options.
ReOptimizeEnds (BoolType | BoolKey) – Re-optimize reactant and product geometries upon restart.
Restart (str | Path | StringKey) – Provide an ams.rkf file from a previous NEB calculation to restart from. It can be an unfinished NEB calculation or one performed with different engine parameters.
Skewness (float | FloatKey) – Degree of how much images are shifted towards or away from the TS, which may help tackle problems with a long reaction path (for example involving a loose adsorption complex) without needing too many images. A value greater than 1 will make sure that images are concentrated near the transition state. The optimal value depends on the path length, the number of images (larger [Skewness] may be needed for a longer path and fewer images). Technically [Skewness] is equal to the ratio between the optimized distances to the lower and the higher neighbor image on the path.
Spring (float | FloatKey) – Spring force constant in atomic units.
LoadPath (AMSBatch._NEB._LoadPath) – Provide details about the trajectory to get the initial NEB path from. PESScan and NEB trajectories are supported. Only the last geometry for each point on the trajectory is considered.
Parallel (AMSBatch._NEB._Parallel) – Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- class _LoadPath[source]¶
Provide details about the trajectory to get the initial NEB path from. PESScan and NEB trajectories are supported. Only the last geometry for each point on the trajectory is considered.
- Variables:
File (str | Path | StringKey) –
Provide an ams.rkf file to load the initial path from. All geometries of this calculation, including initial and final, will be taken from the History section of the file.
Note that for a PESScan it should be a 1D path.
Geometries (Iterable[int] | IntListKey) – Raw indices of the geometries from the History section. By default the last geometry of each path point is used.
Points (Iterable[int] | IntListKey) – By default the whole path is used, which may sometimes be not desirable. For example when a PESScan revealed multiple barriers. In this case one can specify indices of the path points to be used. The last geometry of the specified path point will be loaded.
- class _Parallel[source]¶
Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _NormalModes[source]¶
Configures details of a normal modes calculation.
- Variables:
Displacements (Literal["Cartesian", "Symmetric", "Block"]) –
Type of displacements.
In case of symmetric displacements it is possible to choose only the modes that have non-zero IR or Raman intensity.
Block displacements take rigid blocks into account.
Hessian (Literal["Auto", "Analytical", "Numerical"]) – Default Auto means that if possible by the engine the Hessian will be calculated analytically, else the Hessian will be calculated numerically by AMS.
ReScanFreqRange (Iterable[float] | FloatListKey) – Specifies a frequency range within which all modes will be scanned. 2 numbers: an upper and a lower bound.
ReScanModes (BoolType | BoolKey) – Whether or not to scan imaginary modes after normal modes calculation has concluded.
UseSymmetry (BoolType | BoolKey) – Whether or not to exploit the symmetry of the system in the normal modes calculation.
BlockDisplacements (AMSBatch._NormalModes._BlockDisplacements) – Configures details of a Block Normal Modes (a.k.a. Mobile Block Hessian, or MBH) calculation.
SymmetricDisplacements (AMSBatch._NormalModes._SymmetricDisplacements) – Configures details of the calculation of the frequencies and normal modes of vibration in symmetric displacements.
- class _BlockDisplacements[source]¶
Configures details of a Block Normal Modes (a.k.a. Mobile Block Hessian, or MBH) calculation.
- Variables:
AngularDisplacement (float | FloatKey) – Relative step size for rotational degrees of freedom during Block Normal Modes finite difference calculations. It will be scaled with the characteristic block size.
BlockAtoms (Iterable[int] | IntListKey) – List of atoms belonging to a block. You can have multiple BlockAtoms.
BlockRegion (str | StringKey) – The region to to be considered a block. You can have multiple BlockRegions, also in combination with BlockAtoms.
RadialDisplacement (float | FloatKey) – Step size for translational degrees of freedom during Block Normal Modes finite difference calculations.
Parallel (AMSBatch._NormalModes._BlockDisplacements._Parallel) – Configuration for how the individual displacements are calculated in parallel.
- class _Parallel[source]¶
Configuration for how the individual displacements are calculated in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _SymmetricDisplacements[source]¶
Configures details of the calculation of the frequencies and normal modes of vibration in symmetric displacements.
- Variables:
Type (Literal["All", "Infrared", "Raman", "InfraredAndRaman"]) –
For symmetric molecules it is possible to choose only the modes that have non-zero IR or Raman intensity (or either of them) by symmetry.
In order to calculate the Raman intensities the Raman property must be requested.
- class _NumericalDifferentiation[source]¶
Define options for numerical differentiations, that is the numerical calculation of gradients, Hessian and the stress tensor for periodic systems.
- Variables:
NuclearStepSize (float | FloatKey) – Step size for numerical nuclear gradient calculation.
StrainStepSize (float | FloatKey) – Step size (relative) for numerical stress tensor calculation.
UseSymmetry (BoolType | BoolKey) – Whether or not to exploit the symmetry of the system for numerical differentiations.
Parallel (AMSBatch._NumericalDifferentiation._Parallel) – Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- class _Parallel[source]¶
Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _NumericalPhonons[source]¶
Configures details of a numerical phonons calculation.
- Variables:
AutomaticBZPath (BoolType | BoolKey) – If True, compute the phonon dispersion curve for the standard path through the Brillouin zone. If False, you must specify your custom path in the [BZPath] block.
BornEffCharge (float | FloatKey) – Input option to give the Born effective charges of the species.
DielectricConst (float | FloatKey) – Input option to give the static dielectric constant of the species.
DoubleSided (BoolType | BoolKey) – By default a two-sided (or quadratic) numerical differentiation of the nuclear gradients is used. Using a single-sided (or linear) numerical differentiation is computationally faster but much less accurate. Note: In older versions of the program only the single-sided option was available.
Interpolation (int | IntKey) – Use interpolation to generate smooth phonon plots.
KPathFinderConvention (Literal["Setyawan-Curtarolo", "Hinuma"]) –
This option determines how the path through the Brillouin zone is generated when using the automatic k-point mode.
Available options:
Setyawan-Curtarolo(default for 1D and 2D lattices): Uses our built-in KPath program to find a path through high-symmetry points based on the method by Setyawan and Curtarolo (https://doi.org/10.1016/j.commatsci.2010.05.010). For 2D lattices, the path is derived from the intersection of the 3D Brillouin zone with a plane. For 1D lattices, the path is simply Gamma-Z.Hinuma: Uses the external SeeKPath utility to generate the k-path (https://github.com/giovannipizzi/seekpath and https://doi.org/10.1016/j.commatsci.2016.10.015).
MaxTemperature (float | FloatKey) – Maximum temperature for the thermodynamic properties calculation (Internal Energy, Free Energy, Specific Heat, and Entropy). This value sets the upper limit of the temperature range considered. It is used in conjunction with
NTemperaturesto define the temperature grid. The calculation of thermodynamic properties is performed only if the phonon density of states (DOS) is requested (i.e.,Phonons%DOSis set toYes).NDosEnergies (int | IntKey) – Nr. of energies used to calculate the phonon DOS used to integrate thermodynamic properties. For fast compute engines this may become time limiting and smaller values can be tried.
NTemperatures (int | IntKey) – Number of temperature points to use in the thermodynamic properties calculation (Internal Energy, Free Energy, Specific Heat, and Entropy). This value, along with
MaxTemperature, determines the density of the temperature grid. The temperatures will be distributed evenly between 0 Kelvin and ‘MaxTemperature’. The calculation of thermodynamic properties is performed only if the phonon density of states (DOS) is requested (i.e.,Phonons%DOSis set toYes).RequestContinuousPES (BoolType | BoolKey) – Whether or not the engine should be instructed to disable symmetry. AMS versions older than AMS2024 would use the the hard coded value false.
StepSize (float | FloatKey) – Step size to be taken to obtain the force constants (second derivative) from the analytical gradients numerically.
UseSymmetry (BoolType | BoolKey) – Whether or not to exploit the symmetry of the system in the phonon calculation.
BZPath (AMSBatch._NumericalPhonons._BZPath) – If [NumericalPhonons%AutomaticBZPath] is false, the phonon dispersion curve will be computed for the user-defined path in the [BZPath] block. You should define the vertices of your path in fractional coordinates (with respect to the reciprocal lattice vectors) in the [Path] sub-block. If you want to make a jump in your path (i.e. have a discontinuous path), you need to specify a new [Path] sub-block.
Parallel (AMSBatch._NumericalPhonons._Parallel) – Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
SuperCell (str | Sequence[str] | FreeBlock) – Used for the phonon run. The super lattice is expressed in the lattice vectors. Most people will find a diagonal matrix easiest to understand.
- class _BZPath[source]¶
If [NumericalPhonons%AutomaticBZPath] is false, the phonon dispersion curve will be computed for the user-defined path in the [BZPath] block. You should define the vertices of your path in fractional coordinates (with respect to the reciprocal lattice vectors) in the [Path] sub-block. If you want to make a jump in your path (i.e. have a discontinuous path), you need to specify a new [Path] sub-block.
- class _Parallel[source]¶
Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _PESExploration[source]¶
Configures details of the automated PES exploration methods.
- Variables:
CalculateEnergyReferences (BoolType | BoolKey) – Calculates the energy references.
CalculateFragments (BoolType | BoolKey) – Must be used together with an adsorbent set as the StatesAlignment%ReferenceRegion. Runs a final calculation of the adsorbate and adsorbent (marked by the ReferenceRegion) individually. The fragmented state is included in the energy landscape.
DynamicSeedStates (BoolType | BoolKey) – Whether subsequent expeditions may start from states discovered by previous expeditions. This should lead to a more comprehensive exploration of the potential energy surface. Disabling this will focus the PES exploration around the initial seed states.
FiniteDifference (float | FloatKey) – The finite difference distance to use for Dimer, Hessian, Lanczos, and optimization methods.
GenerateSymmetryImages (BoolType | BoolKey) – By activating this option, after concluding the energy landscape exploration process, it will create the complete set of symmetry-related copies by using the symmetry operators of the reference structure. SinglePoint calculations (including gradients and normal modes) are carried out for each new image structure obtained.
Job (Literal["ProcessSearch", "BasinHopping", "SaddleSearch", "LandscapeRefinement", "BindingSites", "NudgedElasticBand", "SystemMatching"]) – Specify the PES exploration job to perform.
NegativeEigenvalueTolerance (float | FloatKey) – The threshold in Hessian eigenvalue below which a mode is considered imaginary, i.e. indicating a transition state. This is a small negative number, as very small negative eigenvalues may be due to numerical noise on an essentially flat PES and do not indicate true transition states. We need a more flexible value for this parameter in PESExploration because the high computational cost of the task typically forces us to reduce the engine precision, which increases the noise in the vibrational frequencies evaluation. [PESPointCharacter%NegativeEigenvalueTolerance] is overridden by this parameter.
NumExpeditions (int | IntKey) – Sets the number of subsequent expeditions our job will consist of. Larger values result in a more comprehensive exploration of the potential energy surface, but will take more computational time.
NumExplorers (int | IntKey) – Sets the number of independent PES explorers dispatched as part of each expedition. Larger values will result in a more comprehensive exploration of the potential energy surface, but will take more computational time. By default an appropriate number of explorers are executed in parallel.
OptTSMethod (Literal["SaddleSearch", "NudgedElasticBand"]) – When the full set of states in the energy landscape are optimized (see PESExploration%Job = GeometryOptimization), transition states can be optimized using either SaddleSearch or NudgedElasticBand methods. SaddleSearch uses information only from the current geometry of the TS; contrary, NudgedElasticBand ignores the current geometry and runs a Nudged-Elastic-Band calculation trying to connect the associated reactants and products if they are available.
Potential (str | StringKey) – The PES to be explored. The default is to use a callback into AMS to evaluate the energy and gradients using an AMS engine. This can be changed here to give access to one of the EON client’s builtin potentials. This has not been well tested by SCM.
RandomSeed (int | IntKey) – Number used to initialize both the EON clients random number generators as well as the AMS global RNG. The latter is normally initialized with the RNGSeed keyword at the root level. Should be used by developers only. May or may not help to make more reproducible regression tests …
SelectedListedAtomsForPESPointCharacter (str | StringKey) – Uses the Hessian matrix elements only for the listed atoms to determine the PES point character of a located state during the exploration. If not specified, the full Hessian is used.
SelectedRegionForPESPointCharacter (str | StringKey) – Uses the Hessian matrix elements only for the atoms in a particular region to determine the PES point character of a located state during the exploration. If not specified, the full Hessian is used.
Temperature (float | FloatKey) – The temperature that the job will run at. This may be used in different ways depending on the job, e.g. acceptance probabilities for Monte-Carlo based jobs, thermostatting for dynamics based jobs, kinetic prefactors for jobs that find transition states. Some jobs may not use this temperature at all.
WriteEngineGradients (BoolType | BoolKey) – Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.
WriteHistory (Literal["None", "Converged", "All"]) – When to write the molecular geometry (and possibly other properties) to the history on the ams.rkf file. The default is to only write the converged geometries to the history. Can be changed to write no frames at all to the history, or write all frames (should only be used when testing because of the performance impact). Note that for parallel calculations, only the first group of processes writes to ams.rkf.
BasinHopping (AMSBatch._PESExploration._BasinHopping) – Configures the details of the Basin Hopping subtask.
BindingSites (AMSBatch._PESExploration._BindingSites) – Options related to the calculation of binding sites.
Debug (AMSBatch._PESExploration._Debug) – ???.
Dynamics (AMSBatch._PESExploration._Dynamics) – ???.
Hessian (AMSBatch._PESExploration._Hessian) – ???.
LandscapeRefinement (AMSBatch._PESExploration._LandscapeRefinement) – Configures details of the energy landscape refinement job.
LoadEnergyLandscape (AMSBatch._PESExploration._LoadEnergyLandscape) – Options related to the loading of an Energy Landscape from a previous calculation.
LoadInitialSystems (AMSBatch._PESExploration._LoadInitialSystems) – Load initial systems from different sources.
NudgedElasticBand (AMSBatch._PESExploration._NudgedElasticBand) – Options for the Nudged Elastic Band (NEB) method.
Optimizer (AMSBatch._PESExploration._Optimizer) – Configures the details of the geometry optimizers used by the PES explorers.
Parallel (AMSBatch._PESExploration._Parallel) – Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
ParallelReplica (AMSBatch._PESExploration._ParallelReplica) – ???.
Prefactor (AMSBatch._PESExploration._Prefactor) – ???.
ProcessSearch (AMSBatch._PESExploration._ProcessSearch) – Input options specific to the process search procedure.
SaddleSearch (AMSBatch._PESExploration._SaddleSearch) – Configuration for the Saddle Search procedure (used in SaddleSearch and ProcessSearch Jobs).
StatesAlignment (AMSBatch._PESExploration._StatesAlignment) – Configures details of how the energy landscape configurations are aligned respect to the main chemical system [System].
StructureComparison (AMSBatch._PESExploration._StructureComparison) – Settings for structure comparison.
- class _BasinHopping[source]¶
Configures the details of the Basin Hopping subtask.
- Variables:
AdjustDisplacement (BoolType | BoolKey) – Automatically adjust the displacement size to meet the target acceptance ratio.
AdjustFraction (float | FloatKey) – The fraction by which to change the step size in order to meet the target acceptance ratio.
AdjustPeriod (int | IntKey) – The number of Monte Carlo steps between adjustments of the step size.
DisplaceAtomsInRegion (str | StringKey) – If you specify a region name here, only the atoms belonging to this region will be displaced during the basin hopping procedure. For more details on regions, see the documentation on the System definition.
Displacement (float | FloatKey) – Displacement in each degree of freedom.
DisplacementAlgorithm (Literal["Standard", "Linear", "Quadratic"]) – Undocumented in EON.
DisplacementDistribution (Literal["Uniform", "Gaussian"]) –
The distribution used for the displacement of each atom.
Gaussian: The value of the
Displacementkeyword serves as the standard deviation of a Gaussian distribution used to draw the nuclear displacements from.A random number is selected uniformly between
-DisplacementandDisplacement.
InitialRandomStructureProbability (float | FloatKey) – Probability to generate an entirely random structure to start the Basin Hopping from.
JumpMax (int | IntKey) – The number of consecutive rejected steps after which jump steps should be taken. This serves to provide a more global search when the structure is stuck in a certain basin. The number of jump steps is assigned in jump_steps. See paper on the Basin Hopping with Occasional Jumping algorithm by Iwamatsu and Okabe: Chem. Phys. Lett. 399 396 (2004)
JumpSteps (int | IntKey) – The number of jump steps to take after the
JumpMaxnumber of consecutive rejections have taken place.MainSystemAsSeed (BoolType | BoolKey) – If true, only the main system will be used as a seed state. The main system is not added to the database.
PESPointCharacterization (BoolType | BoolKey) – If true, a PES point characterization based on a vibrational analysis is carried out to confirm each detected state is an actual local minimum (no imaginary frequencies). Conversely, if this option is false, the PES point characterization is avoided, which will assume that all located states are local minima (zero gradients). Enabling this option is very useful for large systems. It circumvents the need for computing and diagonalizing the Hessian matrix, a typically expensive computational process.
PushApartDistance (float | FloatKey) – Push atoms apart until no atoms are closer than this distance. This criterion is enforced for the initial structure and all those generated by random displacements.
RotateNonListedAtoms (BoolType | BoolKey) – If true, each iteration randomly rotates all atoms as a rigid body, excluding those listed in [BasinHopping%DisplaceListedAtoms], [BasinHopping%DisplaceListedTypes], or [BasinHopping%DisplaceAtomsInRegion].
SignificantStructure (BoolType | BoolKey) – If true, the Significant Structure Basin Hopping (SSBH) variant instead of the Raw Structure Basin Hopping method (RSBH). In SSBH previously found structures are used as initial structures for further displacements, see Chem. Phys. Lett. 289, 463 (1998) for a comparison of the two approaches.
SingleAtomDisplace (BoolType | BoolKey) – If true, only one atom is displaced per step. Otherwise all atoms of the structure are randomly displaced.
Steps (int | IntKey) – Number of displace & optimize Monte-Carlo steps to take.
SwapProbability (float | FloatKey) – The probability in range [0,1] that a swapping step takes place instead of a displacement step. The swap step selects two atoms of different elements and swaps their position.
TargetRatio (float | FloatKey) – The target acceptance ratio that will be used to determine whether to increase or decrease the step size.
WriteUnique (BoolType | BoolKey) – If true, all unique states found will be included in the energy landscape, even the rejected ones. If false, only the lowest energy structure will be included in the energy landscape.
- class _BindingSites[source]¶
Options related to the calculation of binding sites.
- Variables:
Calculate (BoolType | BoolKey) – Calculate binding sites at the end of a job. Not needed for Binding Sites job.
DistanceDifference (float | FloatKey) – If the distance between two mapped binding-sites is larger than this threshold, the binding-sites are considered different. If not specified, its value will set equal to [PESExploration%StructureComparison%DistanceDifference]
MaxCoordinationShellsForLabels (int | IntKey) – The binding site labels are given based on the coordination numbers of shells in the reference region, using the following format: N<int><int>…, e.g., the label ‘N334’ means 3 atoms in the first coordination shell, 3 in the second one, and 4 in the third one. This parameter controls the maximum number of shells to include.
NeighborCutoff (float | FloatKey) – Atoms within this distance of each other are considered neighbors for the calculation of the binding sites. If not specified, its value will set equal to [PESExploration%StructureComparison%NeighborCutoff]
ReferenceRegion (str | StringKey) – Defines the region that is considered as the reference for binding sites detection. Binding sites are projected on this region using the geometry from the reference system. If not specified, its value will set equal to [PESExploration%StatesAlignment%ReferenceRegion]
- class _Dynamics[source]¶
???.
- Variables:
Thermostat (Literal["andersen", "nose_hoover", "langevin", "none"]) – ???.
Andersen (AMSBatch._PESExploration._Dynamics._Andersen) – ???.
Langevin (AMSBatch._PESExploration._Dynamics._Langevin) – ???.
Nose (AMSBatch._PESExploration._Dynamics._Nose) – ???.
- class _LandscapeRefinement[source]¶
Configures details of the energy landscape refinement job.
- Variables:
CalculateOnlyEnergies (BoolType | BoolKey) – If true, the states’ geometry is not optimized, and the final PES point characterization is ignored [PESExploration%LandscapeRefinement%IgnoreFinalPESPointCharacter]. Only energy values are updated using the specified engine. Furthermore, normal modes and associated properties are copied from the previous calculation to avoid the typically high computational effort of the Hessian matrix calculation. Enabling this option implies that RunInitialSinglePoints=’F’, IgnoreFinalPESPointCharacter=’T’.
IgnoreFinalPESPointCharacter (BoolType | BoolKey) – At the end of the energy landscape refinement job, each state is assigned a PES point character (MIN or TS) based on its vibrational frequencies before being included in the final database. States are only added if the PES point character after refinement remains unchanged. However, states are added without verifying if this option is
true. Nonetheless, vibrational frequencies are calculated and stored for future analysis. This option is especially useful when using computationally demanding engines. Because in those cases, precision and computational effort must be balanced, resulting in significant vibrational frequencies inaccuracies.IgnoreFinalPESPointCharacterForFragments (BoolType | BoolKey) – Same as
LandscapeRefinement%IgnoreFinalPESPointCharacterbut regarding the Fragments calculations, see optionLandscapeRefinement%CalculateFragments.RelaxFromSaddlePoint (BoolType | BoolKey) – Relaxes the saddle point geometries following the imaginary mode to get both reactants and products.
RunInitialSinglePoints (BoolType | BoolKey) – If it is
true, just after loading the energy landscape to refine, the single energy point computations are disabled. Be aware that if you enable this, the output file’s ‘Initial Energy Landscape’ section will display incorrect states’ energy values. If the engine requires too much processing power, this option can help you save a small amount of time.TransitionStateSearchMethod (Literal["Auto", "Dimer"]) – Sets the method to refine transition states.
UseReactantsAndProductsForTSs (BoolType | BoolKey) – For the refinement of transition states, the reaction coordinate can be estimated using either the reactants or products (final system). By enabling this option, the difference between the initial and final geometries is utilized as the reaction coordinate. The final system with the lowest RMSD is chosen to determine this coordinate. For more details see the section [TransitionStateSearch].
- class _LoadEnergyLandscape[source]¶
Options related to the loading of an Energy Landscape from a previous calculation.
- Variables:
GenerateSymmetryImages (BoolType | BoolKey) – By activating this option, after loading the energy landscape, it will create the complete set of symmetry-related copies by using the symmetry operators of the reference structure. Be aware that rkf result files of the generated symmetry images are copies from the parent structures but only atomic coordinates are updated.
KeepOnly (Iterable[int] | IntListKey) – Upon loading the Energy Landscape, only keep the states specified here. The states should be specified via a list of integers referring to the indices of the states you want to keep.
Path (str | Path | StringKey) – AMS results folder to load an energy landscape from. In the text input file, you may alternatively specify a
.confile in the native EON format.Remove (Iterable[int] | IntListKey) – Upon loading the Energy Landscape, remove (i.e. do not load) the states specified here. The states should be specified via a list of integers referring to the indices of the states you want to remove (i.e. the states you don’t want to load).
RemoveWithNoBindingSites (BoolType | BoolKey) – Upon loading the Energy Landscape, it removes states with no associated binding sites. Associated transition states are also removed. This is an advantageous option to remove physisorbed states automatically. Notice that it requires that the previous calculation was executed, enabling the option [BindingSites%Calculate].
SeedStates (Iterable[int] | IntListKey) – By default when you start a new PES Exploration from a loaded Energy Landscape, expeditions can start from any of the loaded minima. By using this input option, you can instruct the program to only use some of the states as ‘expedition starting point’. The states that serve as ‘expedition starting points’ should be specified via a list of integers referring to the indices of the states.
- class _LoadInitialSystems[source]¶
Load initial systems from different sources.
- Variables:
FromKFHistory (AMSBatch._PESExploration._LoadInitialSystems._FromKFHistory) – Load initial systems from the History section of kf files.
- class _NudgedElasticBand[source]¶
Options for the Nudged Elastic Band (NEB) method.
- Variables:
ClimbingImageConvergedOnly (BoolType | BoolKey) – ???.
ClimbingImageMethod (BoolType | BoolKey) – Use the climbing image algorithm to drive the highest image to the transition state.
ConvergedForce (float | FloatKey) – Convergence threshold for nuclear gradients. Note: Special value of -1.0 means using the same convergence criterion as the PES explorer’s geometry optimizer.
DoublyNudged (BoolType | BoolKey) – ???.
DoublyNudgedSwitching (BoolType | BoolKey) – ???.
ElasticBand (BoolType | BoolKey) – ???.
Images (int | IntKey) – Number of NEB images between the two endpoints.
MaxIterations (int | IntKey) – Maximum number of NEB iterations.
OldTangent (BoolType | BoolKey) – Use the old central difference tangent.
- class _Optimizer[source]¶
Configures the details of the geometry optimizers used by the PES explorers.
- Variables:
ConvergedForce (float | FloatKey) – Convergence threshold for nuclear gradients.
ConvergenceMetric (Literal["norm", "max_atom", "max_component"]) – Determines how the EON client checks the convergence of the forces.
normuses the Frobenius norm of the (3,nFreeAtoms) forces array.max_atomtakes the maximum norm2 of the nFreeAtoms individual force vectors on the free atoms.max_componentjust takes the maximum of all elements in the array. Don’t change this at the moment, as it will break snapshot writing to the history section of ams.rkf.MaxIterations (int | IntKey) – Maximum number of iterations allowed for optimizations.
Method (Literal["CG", "QM", "LBFGS", "FIRE", "SD"]) – Select the method for geometry optimizations.
CG (AMSBatch._PESExploration._Optimizer._CG) – ???.
LBFGS (AMSBatch._PESExploration._Optimizer._LBFGS) – ???.
QM (AMSBatch._PESExploration._Optimizer._QM) – ???.
SD (AMSBatch._PESExploration._Optimizer._SD) – ???.
- class _Parallel[source]¶
Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _ParallelReplica[source]¶
???.
- class _Prefactor[source]¶
???.
- Variables:
Rate (Literal["HTST", "QQHTST", "None"]) – Calculates reaction rate pre-exponential factors via: HTST (Harmonic Transition State Theory), QQHTST (quasi-quantum HTST), or None (disable calculation).
- class _ProcessSearch[source]¶
Input options specific to the process search procedure.
- Variables:
MinimizationOffset (float | FloatKey) – After a saddle is found, images are placed on either side of the saddle along the mode and minimized to ensure that the saddle is connected to the original minimum and to locate the product state. MinimizationOffset is the distance those images are displaced from the saddle.
MinimizeFirst (BoolType | BoolKey) – If true, every time a process search is run by a client the reactant will be minimized first before doing any saddle searches.
- class _SaddleSearch[source]¶
Configuration for the Saddle Search procedure (used in SaddleSearch and ProcessSearch Jobs).
- Variables:
ConvergedForce (float | FloatKey) – Convergence threshold for nuclear gradients. Note: Special value of -1.0 means using the same convergence criterion as the PES explorer’s geometry optimizer.
DisplaceAllAtoms (BoolType | BoolKey) – ???.
DisplaceAllListed (BoolType | BoolKey) – ???.
DisplaceAlongNormalModesActiveModes (str | StringKey) – Sets the active modes to be used when the option [SaddleSearch%DisplaceAlongNormalModesWeight] is enabled. e.g. 1,2,3,5. By default, all normal modes are considered active.
DisplaceAlongNormalModesWeight (float | FloatKey) – The probability of generating a displacement resulting in a random linear combination of the normal modes specified in [SaddleSearch%DisplaceAlongNormalModesActiveModes]. This parameter is a numeric value that should fall within the interval [0.0, 1.0].
DisplaceAtomsInRegion (str | StringKey) – A string corresponding to the name of a region. When performing the initial random displacement, only displace atoms in the specified region.
DisplaceAtomsInRegionWeight (float | FloatKey) – The probability of generating a displacement involving only atoms from the region specified in [SaddleSearch%DisplaceAtomsInRegion]. This parameter is a numeric value that should fall within the interval [0.0, 1.0].
DisplaceLeastCoordinatedWeight (float | FloatKey) – Relative probability to displace with an epicenter that has a coordination number equal to the least-coordinated atom in the configuration.
DisplaceListedAtomWeight (float | FloatKey) – Relative probability to displace with an epicenter listed in displace_atomlist.
DisplaceListedAtoms (str | StringKey) – Sets the active atoms to be used when the option [SaddleSearch%DisplaceAlongNormalModesWeight] is enabled. e.g. 1,2,3,5. By default, all normal modes are considered active.
DisplaceListedTypeWeight (float | FloatKey) – Relative probability to displace with an epicenter listed in displace_typelist.
DisplaceMagnitude (float | FloatKey) – The standard deviation of the Gaussian displacement in each degree of freedom for the selected atoms.
DisplaceNotFCCHCPWeight (float | FloatKey) – Relative probability to displace with an epicenter that is not FCC or HCP coordinated.
DisplaceRadius (float | FloatKey) – Atoms within this distance of the epicenter will be displaced.
DisplaceRandomWeight (float | FloatKey) – Relative probability to displace with a random epicenter.
DisplaceUnderCoordinatedWeight (float | FloatKey) – Relative probability to displace with an epicenter with a coordination equal to or less than displace_max_coordination.
MaxEnergy (float | FloatKey) – The energy (relative to the starting point of the saddle search) at which a saddle search explorer considers the search bad and terminates it.
MaxIterations (int | IntKey) – Maximum number of iterations for each saddle search run.
Method (Literal["min_mode", "dynamics", "basin_hopping", "bgsd"]) – Which saddle search method to use.
MinEnergyBarrier (float | FloatKey) – Minimum energy barrier to accept a new transition state.
MinModeMethod (Literal["dimer", "lanczos"]) – The minimum-mode following method to use.
RandomMode (BoolType | BoolKey) – ???.
RelaxFromSaddlePoint (BoolType | BoolKey) – Relaxes the saddle point geometries following the imaginary mode to get both reactants and products.
RemoveRotation (BoolType | BoolKey) – ???.
ZeroModeAbortCurvature (float | FloatKey) – The threshold in the frequency below which the minimum mode is considered zero. The calculation is aborted if the negative mode becomes zero.
- class _StatesAlignment[source]¶
Configures details of how the energy landscape configurations are aligned respect to the main chemical system [System].
- Variables:
DistanceDifference (float | FloatKey) – If the distance between two mapped atoms is larger than this threshold, the configuration is considered not aligned. If not specified, its value will set equal to [PESExploration%StructureComparison%DistanceDifference]
ReferenceRegion (str | StringKey) – Defines the region that is considered as the reference for alignments. Atoms outside this region are ignored in the alignments.
RemoveUnaligned (BoolType | BoolKey) – ???.
- class _StructureComparison[source]¶
Settings for structure comparison.
- Variables:
CheckRotation (BoolType | BoolKey) – Rotates the system optimally before comparing structures. The default is to do this only for molecular systems when there are no fixed atom constraints.
CheckSymmetry (BoolType | BoolKey) – Considers that two systems are equal if they are equivalent by symmetry.
CovalentScale (float | FloatKey) – Scale factor for the covalent distances used in the neighboring detection. Only used if [StructureComparison%UseCovalent] is enabled. This is an experimental feature!
DistanceDifference (float | FloatKey) – If the distance between two mapped atoms is larger than this threshold, the two configurations are considered different structures.
EnergyDifference (float | FloatKey) – If the energy difference between two configurations is larger than this threshold, the two configurations are considered to be different structures.
IndistinguishableAtoms (BoolType | BoolKey) – If yes, the order of the atoms does not affect the structural comparison. Atoms of the same element are then indistinguishable.
NeighborCutoff (float | FloatKey) – Atoms within this distance of each other are considered neighbors.
RemoveTranslation (BoolType | BoolKey) – Translates the system optimally before comparing structures. The default is to do this only when there are no fixed atom constraints.
UseCovalent (BoolType | BoolKey) – Atoms are considered neighbors if the distance between them is lower than [StructureComparison%CovalentScale] times the covalent distance calculated following M. O’Keeffe and N.E. Brese, J. Am. Chem.Soc. 113 (1991) 3226. This is an experimental feature!
- class _PESPointCharacter[source]¶
Options for the characterization of PES points.
- Variables:
Displacement (float | FloatKey) – Controls the size of the displacements used for numerical differentiation: The displaced geometries are calculated by taking the original coordinates and adding the mass-weighted mode times the reduced mass of the mode times the value of this keyword.
NegativeEigenvalueTolerance (float | FloatKey) – The threshold in Hessian eigenvalue below which a mode is considered imaginary, i.e. indicating a transition state. This is a small negative number, as very small negative eigenvalues may be due to numerical noise on an essentially flat PES and do not indicate true transition states.
NegativeFrequenciesTolerance (float | FloatKey) – The threshold in frequencies below which a mode is considered imaginary, i.e. indicating a transition state. Deprecated. Use NegativeEigenvalueTolerance instead.
NumberOfModes (int | IntKey) – The number of (lowest) eigenvalues that should be checked.
Tolerance (float | FloatKey) – Convergence tolerance for residual in iterative Davidson diagonalization.
- class _PESScan[source]¶
Configures the details of the potential energy surface scanning task.
- Variables:
CalcPropertiesAtPESPoints (BoolType | BoolKey) – Whether to perform an additional calculation with properties on all the sampled points of the PES. If this option is enabled AMS will produce a separate engine output file for every sampled PES point.
FillUnconvergedGaps (BoolType | BoolKey) – After the initial pass over the PES, restart the unconverged points from converged neighboring points.
ScanCoordinate (AMSBatch._PESScan._ScanCoordinate) – Specifies a coordinate along which the potential energy surface is scanned. If this block contains multiple entries, these coordinates will be varied and scanned together as if they were one. Note that there can be only one ScanCoordinate containing a lattice scan in any PES scan job.
- class _ScanCoordinate[source]¶
Specifies a coordinate along which the potential energy surface is scanned. If this block contains multiple entries, these coordinates will be varied and scanned together as if they were one. Note that there can be only one ScanCoordinate containing a lattice scan in any PES scan job.
- Variables:
Angle (str | StringKey) – Scan the angle between three atoms. Three atom indices followed by two real numbers delimiting the transit range in degrees.
CellVolumeRange (Iterable[float] | FloatListKey) – Two numbers for the initial and final cell volume. The cell is scaled isotropically between these values. Can not be used together with any other coordinate within the same ScanCoordinate block.
CellVolumeScalingRange (Iterable[float] | FloatListKey) – Two scaling factors for the initial and final cell volume. A value of ‘0.9 1.1’ would result in an isotropic scaling between 90% and 110% of the cell volume of the input system. Can not be used together with any other coordinate within the same ScanCoordinate block.
Coordinate (str | StringKey) – Scan a particular coordinate of an atom. Atom index followed by (x|y|z) followed by two real numbers delimiting the transit range.
DifDist (str | StringKey) – Scan the difference distance between two pairs of atoms, R(12)-R(34). Four atom indices followed by two real numbers delimiting the transit range in Angstrom.
Dihedral (str | StringKey) – Scan the dihedral angle between four atoms. Four atom indices followed by two real numbers delimiting the transit angle in degrees.
Distance (str | StringKey) – Scan the distance between two atoms. Two atom indices followed by two real numbers delimiting the transit distance in Angstrom.
FromStrainVoigt (Iterable[float] | FloatListKey) – The elements of the initial lattice strain in Voigt notation. One should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems. Has to be used in combination with the ToStrainVoigt keyword and no other coordinate within the same ScanCoordinate block.
LatticeARange (Iterable[float] | FloatListKey) – Scans the length of the first lattice vector. Can be combined with the LatticeBRange and LatticeCRange keywords, but no other coordinates within the same ScanCoordinate.
LatticeBRange (Iterable[float] | FloatListKey) – Scans the length of the second lattice vector. Can be combined with the LatticeARange and LatticeCRange keyword, but no other coordinates within the same ScanCoordinate..
LatticeCRange (Iterable[float] | FloatListKey) – Scans the length of the third lattice vector. Can be combined with the LatticeARange and LatticeBRange keyword, but no other coordinates within the same ScanCoordinate..
SumDist (str | StringKey) – Scan the sum of distances between two pairs of atoms, R(12)+R(34). Four atom indices followed by two real numbers delimiting the transit range in Angstrom.
ToStrainVoigt (Iterable[float] | FloatListKey) – The elements of the final lattice strain in Voigt notation. One should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
nPoints (int | IntKey) – The number of points along the scanned coordinate. Must be greater or equal 2.
FromLattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors to start the scan at. Has to be used in combination with the ToLattice keyword and no other coordinate within the same ScanCoordinate block. Unit can be specified in the header. Default unit is Angstrom.
ToLattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors to end the scan at. Unit can be specified in the header. Default unit is Angstrom.
- class _Phonons[source]¶
Configures the phonons calculation.
- Variables:
BandStructure (BoolType | BoolKey) – Calculates and saves the phonon band structure for visualization. Further configuration options for analytical calculations may be available in the engine-specific settings (
Phonons%BandStructure).DOS (BoolType | BoolKey) – Calculates and saves the phonon density of states (DOS) for visualization. Further configuration options for analytical calculations may be available in the engine-specific settings (
Phonons%DOS).Method (Literal["Auto", "Analytical", "Numerical"]) – Determines how phonons are calculated.
Autoselects the analytical method if supported by the engine, otherwise it defaults to numerical calculation. Configure numerical parameters in theNumericalPhononssection. Engine-specific options for analytical phonon calculations may be available inEngine%Phonons.
- class _Print[source]¶
This block controls the printing of additional information to stdout.
- Variables:
Timers (Literal["None", "Normal", "Detail", "TooMuchDetail"]) – Printing timing details to see how much time is spend in which part of the code.
- class _Properties[source]¶
Configures which AMS level properties to calculate for SinglePoint calculations or other important geometries (e.g. at the end of an optimization).
- Variables:
BondOrders (BoolType | BoolKey) –
Requests the engine to calculate bond orders.
For MM engines these might just be the defined bond orders that go into the force-field, while for QM engines, this might trigger a bond order analysis based on the electronic structure. For engines that do not have a bond order analysis method, a bond guessing algorithm will be used. See also the input options in the BondOrders block.
Charges (BoolType | BoolKey) – Requests the engine to calculate the atomic charges.
DipoleGradients (BoolType | BoolKey) – Requests the engine to calculate the nuclear gradients of the electric dipole moment of the molecule. This can only be requested for non-periodic systems.
DipoleMoment (BoolType | BoolKey) – Requests the engine to calculate the electric dipole moment of the molecule. This can only be requested for non-periodic systems.
ElasticTensor (BoolType | BoolKey) – Calculate the elastic tensor.
GSES (BoolType | BoolKey) – Requests the engine to calculate the gradients of ground to excited state properties.
Gradients (BoolType | BoolKey) – Calculate the nuclear gradients.
Hessian (BoolType | BoolKey) – Whether or not to calculate the Hessian.
Molecules (BoolType | BoolKey) – Requests an analysis of the molecular components of a system, based on the bond orders calculated by the engine.
NormalModes (BoolType | BoolKey) – Calculate the frequencies and normal modes of vibration, as well as the corresponding IR intensities, if the engine supports these calculations natively or can calculate dipole moments.
OrbitalsInfo (BoolType | BoolKey) – Basic molecular orbitals information: orbital energies, occupations, HOMO, LUMO and HOMO-LUMO gap.
Other (BoolType | BoolKey) – Other (engine specific) properties. Details are configured in the engine block.
PESPointCharacter (BoolType | BoolKey) – Determine whether the sampled PES point is a minimum or saddle point. Note that for large systems this does not entail the calculation of the full Hessian and can therefore be used to quickly confirm the success of a geometry optimization or transition state search.
Phonons (BoolType | BoolKey) – Calculate the phonons (for periodic systems).
Polarizability (BoolType | BoolKey) – Requests the engine to calculate the polarizability tensor of the system.
Raman (BoolType | BoolKey) – Requests calculation of Raman intensities for vibrational normal modes.
SelectedRegionForHessian (str | StringKey) – Compute the Hessian matrix elements only for the atoms in a particular region. If not specified, the Hessian will be computed for all atoms.
StressTensor (BoolType | BoolKey) – Calculate the stress tensor.
UncertaintyScore (BoolType | BoolKey) – Request the engine to state how (un)certain it is about its results. Higher number means less certain but specific implementation depends on engine.
VCD (BoolType | BoolKey) – Requests calculation of VCD for vibrational normal modes.
VROA (BoolType | BoolKey) – Requests calculation of VROA for vibrational normal modes.
- class _Raman[source]¶
Configures details of the Raman or VROA calculation.
- Variables:
FreqRange (Iterable[float] | FloatListKey) – Specifies a frequency range within which all modes will be scanned. 2 numbers: an upper and a lower bound.
IncidentFrequency (float | FloatKey) – Frequency of incident light.
LifeTime (float | FloatKey) – Specify the resonance peak width (damping) in Hartree units. Typically the lifetime of the excited states is approximated with a common phenomenological damping parameter. Values are best obtained by fitting absorption data for the molecule, however, the values do not vary a lot between similar molecules, so it is not hard to estimate values. A typical value is 0.004 Hartree.
- class _Replay[source]¶
Configures the details of the Replay task.
- Variables:
Atoms (Iterable[int] | IntListKey) – List of atom indices to include in the replay. All other atoms will be removed before the calculation of energy (and possible other properties). If this keyword is not specified, all atoms will be used for the replay. This keyword can currently not be used for trajectory with a changing number of atoms between frames, e.g. MD trajectories with molecule guns and sinks.
File (str | Path | StringKey) – Provide an ams.rkf file (or a .results folder) from a previously run job to replay. The file needs to contain a History section.
Frames (Iterable[int] | IntListKey) –
List of frames from the History section to recompute.
If not specified the recomputed frames are determined automatically based on the task of the job that is being replayed: PES scans and NEB calculations will only have the converged points replayed, while all other tasks will have all frames recomputed.
Specifying the frames to recompute in the input is probably only useful when replaying trajectories from MolecularDynamics calculations.
StoreAllResultFiles (BoolType | BoolKey) –
If this option is enabled AMS will produce a separate engine output file for every replayed frame.
While basic properties like energy, gradients, stress tensor, etc. are stored anyway on the History section in the AMS driver output file (if they were requested in the Properties block), engine specific properties (e.g. excitations energies from ADF) will only be available if the full result files are stored.
- class _Restraints[source]¶
The Restraints block allows to add soft constraints to the system. A restraint is a potential energy function (a spring) attached to a certain coordinate, for example, an interatomic distance, with its minimum at the specified optimal value. A restraint is defined using one or two parameters: the ForceConstant and, for some types, the F(Inf) value. The ForceConstant parameter corresponds to second derivative of the restraint potential energy d2V(x)/dx^2 for any x (harmonic restraints) or only at at x=0 (other restraints). Here, x is a deviation from the restraint’s optimal value.
- Variables:
Angle (str | StringKey) – Specify three atom indices i j k followed by an angle in degrees and, optionally, by the ForceConstant (default is 0.3 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the i-j-k angle at the given value. For periodic systems this restraint follows the minimum image convention.
DifDist (str | StringKey) – Specify four atom indices i j k l followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the difference R(ij)-R(kl) at the given value. For periodic systems this restraint follows the minimum image convention.
Dihedral (str | StringKey) – Specify four atom indices i j k l followed by an angle in degrees and, optionally, by the ForceConstant (default is 0.1 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the i-j-k-l dihedral angle at the given value. For periodic systems this restraint follows the minimum image convention.
Distance (str | StringKey) – Specify two atom indices followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the distance between the two specified atoms at the given value. For periodic systems this restraint follows the minimum image convention.
FInfinity (float | FloatKey) –
Specify the default asymptotic value for the restraint force for the Hyperbolic and Erf profiles, in Hartree/Bohr or Hartree/radian.
A per-restraint value can be specified after the profile type on the corresponding restraint line.
Profile (Literal["Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) –
Select the default type of restraint profile.
The harmonic profile is most suitable for geometry optimizations but may result is very large forces that can be problematic in molecular dynamic.
For MD simulations the Hyperbolic or Erf may be more suitable because the restraint force is bounded by a user-defined value.
A per-restraint profile type can be specified after the ForceConstant value on the corresponding restraint line.
SumDist (str | StringKey) – Specify four atom indices i j k l followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the sum R(ij)+R(kl) at the given value. For periodic systems this restraint follows the minimum image convention.
Units (Literal["Default", "MD"]) – Change units for energy, force and force constant values from the default (atomic units) to those often used in the MD community (based on kcal/mol and Angstrom). Units for the optimal distances are not affected and are always Angstrom.
- class _RigidMotions[source]¶
Specify which rigid motions of the total system are allowed. An external field is not considered part of the system. Normally the automatic option is doing what you want. However this feature can be used as a means of geometry constraint.
- Variables:
AllowRotations (Literal["Auto", "None", "All", "X", "Y", "Z", "XY", "XZ", "YZ"]) – Which overall rotations of the system are allowed
AllowTranslations (Literal["Auto", "None", "All", "X", "Y", "Z", "XY", "XZ", "YZ"]) – Which overall transitions of the system are allowed
Tolerance (float | FloatKey) – Tolerance for detecting linear molecules. A large value means larger deviation from linearity is permitted.
- class _SCMLibrary[source]¶
Technical settings affecting src/lib
- Variables:
ShellBasedNAFS (BoolType | BoolKey) – Assume that the NAFS are ordered by shell, this allows for a faster evaluation.
- class _SCMMatrix[source]¶
Technical settings for programs using the AMT matrix system. Currently this is only used by DFTB
- Variables:
Type (Literal["Auto", "Reference", "ScaLapack", "Elpa"]) – Determines which implementation is used to support the AbstractMatrixType.
DistributedMatrix (AMSBatch._SCMMatrix._DistributedMatrix) – Technical settings for Distributed matrices
- class _SerializedTensors[source]¶
Technical settings affecting the SerializedTensors module, currently only used for HartreeFock
- Variables:
AllowZeroSize (BoolType | BoolKey) – When the data is blocked, can the size be zero?
IntegerDataBlockSize (int | IntKey) – Integer (meta) data per tensor may be aligned by using a blockSize, only relevant when sparseness is used.
RealDataBlockSize (int | IntKey) – Real data per tensor may be aligned by using a blockSize
SparseDataImplementation (int | IntKey) –
use three ftlDynArrays per tensor. 2) use one big shared array.
- class _System[source]¶
Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- Variables:
AllowCloseAtoms (BoolType | BoolKey) – No longer functional. Just here for backwards compatibility.
Charge (float | FloatKey) – The system’s total charge in atomic units.
FractionalCoords (BoolType | BoolKey) – Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
GeometryFile (str | Path | StringKey) – Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds (BoolType | BoolKey) – Equivalent to ‘Modify%GuessBonds’. Please update input file to use ‘Modify’ block instead.
LatticeStrain (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%LatticeStrain’. Please update input file to use ‘Modify’ block instead.
MapAtomsToUnitCell (BoolType | BoolKey) – Equivalent to ‘Modify%MapAtomsToUnitCell’. Please update input file to use ‘Modify’ block instead.
PerturbCoordinates (float | FloatKey) – Equivalent to ‘Modify%PerturbCoordinates’. Please update input file to use ‘Modify’ block instead.
PerturbLattice (float | FloatKey) – Equivalent to ‘Modify%PerturbLattice’. Please update input file to use ‘Modify’ block instead.
ShiftCoordinates (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%Translate’, but in the unit of bohr by default. Please update input file to use ‘Modify’ block instead.
SuperCell (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCell’. Please update input file to use ‘Modify’ block instead.
SuperCellTrafo (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCellTrafo’. Please update input file to use ‘Modify’ block instead.
Symmetrize (BoolType | BoolKey) – Equivalent to ‘Modify%Symmetrize’. Please update input file to use ‘Modify’ block instead.
Atoms (str | Sequence[str] | FreeBlock) – The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders (str | Sequence[str] | FreeBlock) – Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
ElectrostaticEmbedding (AMSBatch._System._ElectrostaticEmbedding) – Container for electrostatic embedding options, which can be combined.
Lattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
Modify (AMSBatch._System._Modify) – Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- class _Atoms[source]¶
The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
- class _BondOrders[source]¶
Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
- class _ElectrostaticEmbedding[source]¶
Container for electrostatic embedding options, which can be combined.
- Variables:
ElectricField (Iterable[float] | FloatListKey) –
External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.
In atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 … e11 V/m.
Supported by the engines adf, band, dftb and mopac.
For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
MultipolePotential (AMSBatch._System._ElectrostaticEmbedding._MultipolePotential) – External point charges (and dipoles).
- class _MultipolePotential[source]¶
External point charges (and dipoles).
- Variables:
ChargeModel (Literal["Point", "Gaussian"]) – A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
ChargeWidth (float | FloatKey) – The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
Coordinates (str | Sequence[str] | FreeBlock) –
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Coordinates[source]¶
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Lattice[source]¶
Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
- class _Modify[source]¶
Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- Variables:
EnableAtomicProperties (Literal["gui", "adf", "band", "forcefield", "dftb", "reaxff", "qe"]) – Enables an atomic property group. This is only necessary if you want a group enabled, but no atom in the input is using any property from that group.
GuessBonds (BoolType | BoolKey) – Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.
LatticeStrain (Iterable[float] | FloatListKey) – Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
MapAtomsToUnitCell (Iterable[float] | FloatListKey) – For periodic systems the atoms will be moved to the central unit cell where all their fractional coordinates are in the range [start_range,start_range+1). No mapping will take place along non-periodic directions. If just a single number is given, it corresponds to start_range. If multiple numbers are given, they should match the number of lattice vectors and will be used as start ranges along the individual lattice vectors. If no number is given at all, the mapping will be done to the [-0.5:0.5) cell.
PerturbCoordinates (float | FloatKey) – Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
PerturbLattice (float | FloatKey) – Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
SuperCell (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
SuperCellTrafo (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
Symmetrize (BoolType | BoolKey) – Symmetrizes the atomic coordinates to machine precision and rototranslates the molecule to the AMS standard orientation. This allows optimal use of the system’s symmetry for calculations with the AMS driver and its engines.
Translate (Iterable[float] | FloatListKey) – Translate all atoms by a vector.
- class _SystemsFromConformers[source]¶
Constructs a series of systems (with identifiers ‘conformer1’, ‘conformer2’, etc.) from a RKF or XYZ file from a Conformers run.
- class _SystemsFromPES[source]¶
Constructs a series of systems (with identifiers ‘system1’, ‘system2’, etc.) from a RKF file from Conformers, PESExploration, or PESScan run.
- class _SystemsFromSMILES[source]¶
Generates systems from SMILES strings using the plams.from_smiles() functions. Each line should contain first the system identifier separated by a comma from its SMILES string, e.g.: ‘propanol, CCCO’
- class _SystemsFromTrajectory[source]¶
Constructs a series of systems (with identifiers ‘frame1’, ‘frame2’, etc.) from a trajectory file.
- Variables:
File (str | Path | StringKey) – A path to an RKF or concatenated XYZ file.
Frames (Iterable[int] | IntListKey) – List of frames to load from the file. If not specified, all frames will be loaded.
- class _Thermo[source]¶
Options for thermodynamic properties (assuming an ideal gas). The properties are computed for all specified temperatures.
- Variables:
Pressure (float | FloatKey) – The pressure at which the thermodynamic properties are computed.
Temperatures (Iterable[float] | FloatListKey) – List of temperatures at which the thermodynamic properties will be calculated.
UseSymmetryForEntropy (BoolType | BoolKey) – Use symmetry for the calculation of rotational entropy.
LowFrequencyCorrector (AMSBatch._Thermo._LowFrequencyCorrector) – Options for the dampener-powered free rotor interpolator that corrects thermodynamic quantities for low frequencies. See DOI:10.1021/jp509921r and DOI:10.1002/chem.201200497.
- class _LowFrequencyCorrector[source]¶
Options for the dampener-powered free rotor interpolator that corrects thermodynamic quantities for low frequencies. See DOI:10.1021/jp509921r and DOI:10.1002/chem.201200497.
- Variables:
Alpha (float | FloatKey) – The exponent term used in the dampener.
Frequency (float | FloatKey) – The frequency around which the dampener interpolates between harmonic oscillator and free rotor quantities.
MomentOfInertia (float | FloatKey) – The moment of inertia used to restrict entropy results for very small frequencies (generally around less than 1 cm-1).
- class _TransitionStateSearch[source]¶
Configures some details of the transition state search.
- Variables:
ModeToFollow (int | IntKey) – In case of Transition State Search, here you can specify the index of the normal mode to follow (1 is the mode with the lowest frequency).
ReactionCoordinate (AMSBatch._TransitionStateSearch._ReactionCoordinate) – Specify components of the transition state reaction coordinate (TSRC) as a linear combination of internal coordinates (distances or angles).
- class _ReactionCoordinate[source]¶
Specify components of the transition state reaction coordinate (TSRC) as a linear combination of internal coordinates (distances or angles).
- Variables:
Angle (str | StringKey) – The TSRC contains the valence angle between the given atoms. Three atom indices followed by the weight.
Block (str | StringKey) – Name of the region. Only atoms of the region will be included in the TSRC. It is useful when computing the reaction coordinate from the initial Hessian, in which case only part of the Hessian will be analyzed.
BlockAtoms (Iterable[int] | IntListKey) – List of atom indices. Only the listed atoms will be included in the TSRC. It is useful when computing the reaction coordinate from the initial Hessian, in which case only part of the Hessian will be analyzed.
Coordinate (str | StringKey) – The TSRC contains Cartesian displacement of an atom: atom index followed by [x|y|z] and the weight.
Dihedral (str | StringKey) – The TSRC contains the dihedral angle between the given atoms. Four atom indices followed by the weight.
Distance (str | StringKey) – The TSRC contains the distance between the given atoms. Two atom indices followed by the weight.
- class _VibrationalAnalysis[source]¶
Input data for all vibrational analysis utilities in the AMS driver.
- Variables:
Displacement (float | FloatKey) – Step size for finite difference calculations.
Quiet (BoolType | BoolKey) – Suppress run-time output
Type (Literal["ModeScanning", "ModeTracking", "ModeRefinement", "VibronicStructure", "VibronicStructureTracking", "VibronicStructureRefinement", "ResonanceRaman"]) – Specifies the type of vibrational analysis that should be performed
VSTRestartFile (str | Path | StringKey) – Path to a .rkf file containing restart information for VST.
AbsorptionSpectrum (AMSBatch._VibrationalAnalysis._AbsorptionSpectrum) – Settings related to the integration of the spectrum for vibronic tasks.
ExcitationSettings (AMSBatch._VibrationalAnalysis._ExcitationSettings) – Block that contains settings related to the excitation for vibronic tasks.
ModeTracking (AMSBatch._VibrationalAnalysis._ModeTracking) – Input data for Mode Tracking.
NormalModes (AMSBatch._VibrationalAnalysis._NormalModes) – All input related to processing of normal modes. Not available for vibronic structure tracking (as no modes are required there).
ResonanceRaman (AMSBatch._VibrationalAnalysis._ResonanceRaman) – Block that contains settings for the calculation of Resonance Raman calculations
- class _AbsorptionSpectrum[source]¶
Settings related to the integration of the spectrum for vibronic tasks.
- Variables:
AbsorptionRange (Iterable[float] | FloatListKey) – Specifies frequency range of the vibronic absorption spectrum to compute. 2 numbers: an upper and a lower bound.
FrequencyGridPoints (int | IntKey) – Number of grid points to use for the spectrum
IntegrationThreshold (float | FloatKey) – Value of exponential damping in absorption cross-section used to define upper integration limit.
SpectrumOffset (Literal["absolute", "relative"]) – Specifies whether provided frequency range are absolute frequencies or frequencies relative to computed 0-0 excitation energy.
TimeStep (float | FloatKey) – Value of time step for spectrum integration.
- class _ExcitationSettings[source]¶
Block that contains settings related to the excitation for vibronic tasks.
- Variables:
EnergyInline (float | FloatKey) – Vertical excitation energy, used when [ExcitationInfo] = [Inline].
ExcitationFile (str | Path | StringKey) – Path to a .rkf/.t21 file containing the excited state information (gradients, transition dipoles and energies).
ExcitationInputFormat (Literal["File", "Inline"]) – Select how the application should retrieve the excited state information (energy, gradient).
GradientInline (str | Sequence[str] | FreeBlock) – Excited state gradient at ground state equilibrium geometry, used when [ExcitationInfo] = [Inline].
Singlet (str | Sequence[str] | FreeBlock) – Symmetry labels + integer indices of desired singlet transitions (VG-FC absorption spectra support only 1 at a time)
Triplet (str | Sequence[str] | FreeBlock) – Symmetry labels + integer indices of desired triplet transitions (VG-FC absorption spectra support only 1 at a time)
- class _GradientInline[source]¶
Excited state gradient at ground state equilibrium geometry, used when [ExcitationInfo] = [Inline].
- class _ModeTracking[source]¶
Input data for Mode Tracking.
- Variables:
GramSchmidt (BoolType | BoolKey) – Turn on/off gram-schmidt orthogonalization of new vectors to alter convergence.
GramSchmidtIterations (int | IntKey) – Maximum number of gram-schmidt orthogonalization steps per iteration.
GramSchmidtTolerance (float | FloatKey) – Tolerance for checking orthogonality when expanding the basis.
HessianGuess (Literal["Unit", "File", "CalculateWithFastEngine", "Inline"]) – Sets how to obtain the guess for the Hessian used in the preconditioner (if one is to be used).
HessianPath (str | Path | StringKey) – Path to a .rkf file containing the initial guess for the Hessian, used when [HessianGuess] = [File]. It may also be the name of the results folder containing the engine file.
MaxIterations (int | IntKey) – Maximum number of allowed iterations.
RemoveRigids (BoolType | BoolKey) – Orthogonalize tracked vectors against rigid modes
ToleranceForBasis (float | FloatKey) – Convergence tolerance for the contribution of the newest basis vector to the tracked mode.
ToleranceForNorm (float | FloatKey) – Convergence tolerance for residual RMS value.
ToleranceForResidual (float | FloatKey) – Convergence tolerance for the maximum component of the residual vector.
ToleranceForSpectrum (float | FloatKey) – Convergence tolerance for the spectrum in Vibronic Structure Tracking.
TrackingMethod (Literal["OverlapInitial", "DifferenceInitial", "FreqInitial", "IRInitial", "OverlapPrevious", "DifferencePrevious", "FreqPrevious", "IRPrevious", "HighestFreq", "HighestIR", "LowestFreq", "LowestResidual"]) – Set the tracking method that will be used. Vibronic Structure Tracking uses Largest Displacement.
UpdateMethod (Literal["JD", "D", "I"]) – Chooses the method for expanding the Krylov subspace: (I) No preconditioner (VST default), (D) Davidson or (JD) vdVorst-Sleijpen variant of Jacobi-Davidson (Mode tracking default).
HessianInline (str | Sequence[str] | FreeBlock) – Initial guess for the (non-mass-weighted) Hessian in a 3N x 3N block, used when [HessianGuess] = [Inline].
- class _NormalModes[source]¶
All input related to processing of normal modes. Not available for vibronic structure tracking (as no modes are required there).
- Variables:
MassWeightInlineMode (BoolType | BoolKey) – MODE TRACKING ONLY: The supplied modes must be mass-weighted. This tells the program to mass-weight the supplied modes in case this has not yet been done. (True means the supplied modes will be mass-weighted by the program, e.g. the supplied modes are non-mass-weighted.)
ModeFile (str | Path | StringKey) – Path to a .rkf or .t21 file containing the modes which are to be scanned. Which modes will be scanned is selected using the criteria from the [ModeSelect] block.) This key is optional for Resonance Raman and Vibronic Structure. These methods can also calculate the modes using the engine.
ModeInputFormat (Literal["File", "Inline", "Hessian"]) – Set how the initial guesses for the modes are supplied. Only mode tracking supports the Inline and Hessian options.
ScanModes (BoolType | BoolKey) – Supported by: Mode Tracking, Mode Refinement, Vibronic Structure Refinement: If enabled an additional displacement will be performed along the new modes at the end of the calculation to obtain refined frequencies and IR intensities. Equivalent to running the output file of the mode tracking calculation through the AMS ModeScanning task.
ModeInline (str | Sequence[str] | FreeBlock) – MODE TRACKING ONLY: Coordinates of the mode which will be tracked in a N x 3 block (same as for atoms), used when [ModeInputFormat] = [Inline]. Rows must be ordered in the same way as in the [System%Atoms] block. Mode Tracking only.
ModeSelect (AMSBatch._VibrationalAnalysis._NormalModes._ModeSelect) – Pick which modes to read from file.
- class _ModeInline[source]¶
MODE TRACKING ONLY: Coordinates of the mode which will be tracked in a N x 3 block (same as for atoms), used when [ModeInputFormat] = [Inline]. Rows must be ordered in the same way as in the [System%Atoms] block. Mode Tracking only.
- class _ModeSelect[source]¶
Pick which modes to read from file.
- Variables:
DisplacementBound (float | FloatKey) – Vibronic Structure (Refinement), Resonance Raman: Select all modes with a dimensionless oscillator displacement greater than the specified value.
FreqAndIRRange (Iterable[float] | FloatListKey) – Specifies a combined frequency and IR intensity range within which all modes will be selected. First 2 numbers are the frequency range in cm-1, last 2 numbers are the IR intensity range in km/mol.
FreqRange (Iterable[float] | FloatListKey) – Specifies a frequency range within which all modes will be selected. 2 numbers: an upper and a lower bound. Calculating all modes higher than some frequency can be achieved by making the upper bound very large.
Full (BoolType | BoolKey) – Select all modes. This only make sense for Mode Scanning calculations.
HighFreq (int | IntKey) – Select the N modes with the highest frequencies.
HighIR (int | IntKey) – Select the N modes with the largest IR intensities.
IRRange (Iterable[float] | FloatListKey) – Specifies an IR intensity range within which all modes will be selected. 2 numbers: an upper and a lower bound.
ImFreq (BoolType | BoolKey) – Select all modes with imaginary frequencies.
LargestDisplacement (int | IntKey) – Vibronic Structure (Refinement), Resonance Raman: Select the N modes with the largest VG-FC displacement.
LowFreq (int | IntKey) – Select the N modes with the lowest frequencies. Includes imaginary modes which are recorded with negative frequencies.
LowFreqNoIm (int | IntKey) – Select the N modes with the lowest non-negative frequencies. Imaginary modes have negative frequencies and are thus omitted here.
LowIR (int | IntKey) – Select the N modes with the smallest IR intensities.
ModeNumber (Iterable[int] | IntListKey) – Indices of the modes to select.
- class _ResonanceRaman[source]¶
Block that contains settings for the calculation of Resonance Raman calculations
- Variables:
IncidentFrequency (float | FloatKey) – Frequency of incident light. Also used to determine most important excitation in case more than one is provided.
LifeTime (float | FloatKey) – Lifetime of Raman excited state.
MaximumStates (int | IntKey) – Maximum number of final states included in the spectrum.
RamanOrder (int | IntKey) – Order up to which to compute Raman transitions
RamanRange (Iterable[float] | FloatListKey) – Specifies frequency range of the Raman spectrum to compute. 2 numbers: an upper and a lower bound.
- class AMSInteractive[source]¶
- Variables:
Stop (BoolType | BoolKey) – Makes the AMS driver stop execution in an ordered manner at the next opportunity. This will not interrupt the execution in the middle of the numerical calculation of a PES point property (e.g. a Hessian).
StopProperties (BoolType | BoolKey) – Makes the AMS driver stop execution during the evaluation of PES point properties. This may for example be used to interrupt the numerical calculation of a Hessian. Note that this just works at the level of the loops used for the numerical calculation of the properties, so engines which calculate a property analytically may not be interruptible using this keyword. It is recommended to use this keyword in combination with the generic
Stopkeyword.
- class Analysis[source]¶
- Variables:
Task (Literal["RadialDistribution", "Histogram", "AutoCorrelation", "MeanSquareDisplacement", "AverageBinPlot"]) – The analysis task.
Title (str | StringKey) – Title to identify the analysis run. Only used by the GUI.
AutoCorrelation (Analysis._AutoCorrelation) – All input related to auto correlation functions.
AverageBinPlot (Analysis._AverageBinPlot) – All input related to velocity profile
Histogram (Analysis._Histogram) – All input related to histograms.
LoadSystem (Analysis._LoadSystem) – Block that controls reading the chemical system from a KF file instead of the [System] block.
MeanSquareDisplacement (Analysis._MeanSquareDisplacement) – All input related to mean square displacement functions.
Print (Analysis._Print) – This block controls the printing of additional information to stdout.
RadialDistribution (Analysis._RadialDistribution) – All input related to radial distribution functions.
System (Analysis._System) – Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
TrajectoryInfo (Analysis._TrajectoryInfo) – All the info regarding the reading of the trajectory files.
- class _AutoCorrelation[source]¶
All input related to auto correlation functions.
- Variables:
ComputeStandardDeviation (BoolType | BoolKey) – Compute the standard deviation of the autocorrelation function. This will slow down the calculation by approximately a factor 2. The standard deviation takes into account the variance introduced by both the simulation time and by the contributing atoms.
DataReading (Literal["Auto", "AtOnce", "BlockWise"]) – The KF data can be read in and handled once, or blockwise. The former is memory intensive, but mostly faster. If Auto is selected, the data is read at once if it is less than 1 GB, and blockwise if it is more.
LimitMaxFrame (BoolType | BoolKey) – If set to true (default), the program will exit if MaxFrame is selected larger than half the provided number of frames. This limit is only active is UseAllValues is set to false.
MaxCorrelationTime (float | FloatKey) – The maximum correlation time in fs. The default is half the simulation time, except when the PressureTensor is read from the ams.rkf, in which case it is 10 percent of the simulation time. The PressureTensor is read when the Properties PressureTensor, Viscosity, or ViscosityFromBinLog are selected.
MaxFrame (int | IntKey) – The maximum number of frames for which the autocorrelation function will be computed. The default is half of the number of provided frames. Determines the same settings as MaxCorrelationTime. If both are set, MaxCorrelationTime will take precedence.
NPointsHighestFreq (int | IntKey) – The number of points (timesteps) used for the highest frequency displayed in spectrum. This determines up to which frequency the spectrum is displayed. If the spacing between time-steps used for the ACF is 1 fs, then by default the maximum frequency displayed is 0.25 fs-1 (or 8339 cm-1). This corresponds to a (default) value of NPointsHighestFreq of 4. A higher number selected here, will result in a lower maximum frequency returned by the program. The lowest possible value (spectrum up to highest possible frequency) is 2.
PerElement (BoolType | BoolKey) – Compute ACF for all elements in the system. Any other settings in the block will be used.
Property (Literal["Velocities", "DipoleMomentFromCharges", "DiffusionCoefficient", "DipoleDerivativeFromCharges", "PressureTensor", "Viscosity", "DipoleMomentFromBinLog", "ViscosityFromBinLog"]) – Compute the ACF either from velocities (from rkf), the dipole moment (from coordinates and atomic charges in rkf), the dipole moment derivative (from velocities and atomic charges in rkf), from the pressure tensor (from rkf), or from values specified in input. Selecting DiffusionCoefficient is equivalent to selecting Velocities. The default, DipoleDerivativeFromCharges, results in the computation of an IR spectrum.DipoleMomentFromBinLog and ViscosityFromBinLog allow the relevant properties (dipole moment and pressure tensor respectively) to be read from the BinLog section of the trajectory file. In the BinLog section requested properties are stored every step (even if SamplingFreq was set to a higher number than 1) but only if this was specifically requested at the start of the MD simulation.
UnwrapCoordinates (Literal["Auto", "Yes", "No"]) – If the coordinates are involved in the requested property, those coordinates are wrapped into the box at each time step. If set to true, this keyword unwraps those coordinates so that the trajectory is continuous. If not provided the code uses automatic defaults.
UseAllValues (BoolType | BoolKey) – By default the same number of values are used for each t-step in the ACF. This has the advantage that all values in the ACF are equally reliable, but it does mean that for the smaller timesteps much of the data is not used. To switch this off and use all data, UseAllValues can be set to true
WritePropertyToKF (BoolType | BoolKey) – Write the selected property to the KF files for every requested frame
Atoms (Analysis._AutoCorrelation._Atoms) – Relevant if Property is set to Velocities, DipoleMomentFromCharges, DipoleDerivativeFromCharges, or DiffusionCoefficient. Atom numbers or elements for the set of atoms for which the property is read/computed. By default all atoms are used.
UseTimeDerivative (Analysis._AutoCorrelation._UseTimeDerivative) – Possibly use the time derivative of the selected property (e.g. velocity or dipole moments).
VecElements (Analysis._AutoCorrelation._VecElements) – A set of indices referring to a subset of the property vector. Works in combination with the atoms block. For example, in combination with the property Velocities, the Atoms block allows the selection of a subset of atoms, while the VecElelements block allows the selection of a subset of vector elements (e.g. 1 and 2 for the elements x and y).
- class _Atoms[source]¶
Relevant if Property is set to Velocities, DipoleMomentFromCharges, DipoleDerivativeFromCharges, or DiffusionCoefficient. Atom numbers or elements for the set of atoms for which the property is read/computed. By default all atoms are used.
- class _UseTimeDerivative[source]¶
Possibly use the time derivative of the selected property (e.g. velocity or dipole moments).
- class _VecElements[source]¶
A set of indices referring to a subset of the property vector. Works in combination with the atoms block. For example, in combination with the property Velocities, the Atoms block allows the selection of a subset of atoms, while the VecElelements block allows the selection of a subset of vector elements (e.g. 1 and 2 for the elements x and y).
- class _AverageBinPlot[source]¶
All input related to velocity profile
- Variables:
Atoms (Analysis._AverageBinPlot._Atoms) – Relevant if Properties are atom dependent. Atom numbers or elements for the set of atoms for which the property is read/computed. By default all atoms are used.
Property (Analysis._AverageBinPlot._Property) – Property to be plotted along the Y-axis
XProperty (Analysis._AverageBinPlot._XProperty) – Property to be plotted along the Y-axis
- class _Atoms[source]¶
Relevant if Properties are atom dependent. Atom numbers or elements for the set of atoms for which the property is read/computed. By default all atoms are used.
- class _Property[source]¶
Property to be plotted along the Y-axis
- Variables:
Axis (Iterable[float] | FloatListKey) – If defined the dot_product along this axis will be taken. Otherwise, the length of the property vector will be used.
Name (Literal["FrictionCoefficient", "Viscosity", "Velocities", "EngineGradients"]) – Name of the property
- class _XProperty[source]¶
Property to be plotted along the Y-axis
- Variables:
Name (Literal["Time", "Coords"]) – Timestep used for the plotting
VecElements (Analysis._AverageBinPlot._XProperty._VecElements) – A set of indices referring to a subset of the property vector. Works in combination with the atoms block. For example, in combination with the property Velocities, the Atoms block allows the selection of a subset of atoms, while the VecElelements block allows the selection of a subset of vector elements (e.g. 1 and 2 for the elements x and y).
- class _VecElements[source]¶
A set of indices referring to a subset of the property vector. Works in combination with the atoms block. For example, in combination with the property Velocities, the Atoms block allows the selection of a subset of atoms, while the VecElelements block allows the selection of a subset of vector elements (e.g. 1 and 2 for the elements x and y).
- class _Histogram[source]¶
All input related to histograms.
- Variables:
KeepRemainder (BoolType | BoolKey) – Place the values that fall outside the range in an extra bin (on the right).
Normalized (BoolType | BoolKey) – Give the normalized histogram.
Axes (Analysis._Histogram._Axes) – Specifications for the histogram axes.
- class _Axes[source]¶
Specifications for the histogram axes.
- Variables:
Axis (Analysis._Histogram._Axes._Axis) – Specifications for a single histogram axis.
- class _Axis[source]¶
Specifications for a single histogram axis.
- Variables:
NBins (int | IntKey) – The number of bins along the histogram axis.
Range (Iterable[float] | FloatListKey) – Either one, two, or three real values. If one it is the stepsize. If two, it is the minimum value and the maximum value. If three, it is the minimum value, the maximum value, and the stepsize. The stepsize overrides NBins.
Variable (str | StringKey) – The quantity along the histogram axis.
Atoms (Analysis._Histogram._Axes._Axis._Atoms) – Relevant if variable has a value per atom (e.g. Coords, Velocities). This block specifies indices or elements for the set of atoms for which the variable is to be read. By default all atoms are used.
VecElements (Analysis._Histogram._Axes._Axis._VecElements) – A set of indices referring to a subset of a vector. If the variable to be plotted has non-scalar values per step, then this block allows the selection of a subset of vector elements (e.g. 1 and 2 for the x and y values). Can be used in combination with the Atoms block.
- class _Atoms[source]¶
Relevant if variable has a value per atom (e.g. Coords, Velocities). This block specifies indices or elements for the set of atoms for which the variable is to be read. By default all atoms are used.
- class _LoadSystem[source]¶
Block that controls reading the chemical system from a KF file instead of the [System] block.
- class _MeanSquareDisplacement[source]¶
All input related to mean square displacement functions.
- Variables:
ComputeStandardDeviation (BoolType | BoolKey) – Compute the standard deviation of the mean square displacement. This will slow down the calculation by approximately a factor 2. The standard deviation takes into account the variance introduced by both the simulation time and by the contributing atoms.
DataReading (Literal["Auto", "AtOnce", "BlockWise"]) – The KF data can be read in and handled once, or blockwise. The former is memory intensive, but mostly faster. If Auto is selected, the data is read at once if it is less than 1 GB, and blockwise if it is more.
LimitMaxFrame (BoolType | BoolKey) – If set to true (default), the program will exit if MaxFrame is selected larger than half the provided number of frames. This limit is only active is UseAllValues is set to false.
MaxCorrelationTime (float | FloatKey) – The maximum correlation time in fs. The default is half the simulation time.
MaxFrame (int | IntKey) – The maximum number of frames for which the mean square displacement function will be computed. The default is half of the number of provided frames. Determines the same settings as MaxCorrelationTime. If both are set, MaxCorrelationTime will take precedence.
PerElement (BoolType | BoolKey) – Compute MSD for all elements in the system. Any other settings in thie block will be used.
Property (Literal["Coords", "DiffusionCoefficient", "Conductivity"]) – Compute the MSD from the property selected here (from rkf). Selecting DiffusionCoefficient is equivalent to selecting the property Coords.
StartTimeSlope (float | FloatKey) – The MSD has a nonlinear regime at short timescales, and a linear regime at long timescales. To determine the slope, the starting point for the linear regime has to be determined. This keyword sets the starting time in fs. If set to zero, the starttime will be automatically determined.
UnwrapCoordinates (Literal["Auto", "Yes", "No"]) – If the coordinates are involved in the requested property, those coordinates are wrapped into the box at each time step. If set to true, this keyword unwraps those coordinates so that the trajectory is continuous. If not provided the code uses automatic defaults.
UseAllValues (BoolType | BoolKey) – By default the same number of values are used for each t-step in the MSD. This has the advantage that all values in the MSD are equally reliable, but it does mean that for the smaller timesteps much of the data is not used. To switch this off and use all data, UseAllValues can be set to true
WritePropertyToKF (BoolType | BoolKey) – Write the selected property to the KF files for every requested frame
Atoms (Analysis._MeanSquareDisplacement._Atoms) – Relevant if Property is set to any quantity that is available per atom (Coords, DiffusionCoefficient). Atom numbers or elements for the set of atoms for which the property is read/computed are provided here. By default all atoms are used.
UseMolecularCentersOfMass (Analysis._MeanSquareDisplacement._UseMolecularCentersOfMass) – Specifications on using the center of mass coordinates per molecule instead of coordinates per atom. Only relevant for properties that rely on coordinates: Coords, DiffusionCoefficient, and Conductivity.
VecElements (Analysis._MeanSquareDisplacement._VecElements) – A set of indices referring to a subset of the property vector. Works in combination with the atoms block. For example, in combination with the property Coords, the Atoms block allows the selection of a subset of atoms, while the VecElelements block allows the selection of a subset of vector elements (e.g. 1 and 2 for the elements x and y).
- class _Atoms[source]¶
Relevant if Property is set to any quantity that is available per atom (Coords, DiffusionCoefficient). Atom numbers or elements for the set of atoms for which the property is read/computed are provided here. By default all atoms are used.
- class _UseMolecularCentersOfMass[source]¶
Specifications on using the center of mass coordinates per molecule instead of coordinates per atom. Only relevant for properties that rely on coordinates: Coords, DiffusionCoefficient, and Conductivity.
- Variables:
CheckForBondChanges (BoolType | BoolKey) – Check for each frame if the bonds still correspond to the input bonds. If they changed, an error is thrown. If this is set to false, it is assumed that the molecules stay in tact.
Enabled (BoolType | BoolKey) – Use the center of mass coordinates per molecule. Only relevant for properties that rely on coordinates: Coords, DiffusionCoefficient, and Conductivity. The bonds from the MD input system are used.
- class _VecElements[source]¶
A set of indices referring to a subset of the property vector. Works in combination with the atoms block. For example, in combination with the property Coords, the Atoms block allows the selection of a subset of atoms, while the VecElelements block allows the selection of a subset of vector elements (e.g. 1 and 2 for the elements x and y).
- class _Print[source]¶
This block controls the printing of additional information to stdout.
- Variables:
Timers (Literal["None", "Normal", "Detail", "TooMuchDetail"]) – Printing timing details to see how much time is spend in which part of the code.
- class _RadialDistribution[source]¶
All input related to radial distribution functions.
- Variables:
AssumeNoSystemChanges (BoolType | BoolKey) – The system (bonds and atoms) do not change during the simulation, so no checks are needed.
DistanceTypeSelection (Literal["All", "InterMolecular", "IntraMolecular"]) – Select only a certain type of interatomic distances.
KeepRemainder (BoolType | BoolKey) – Place the values that fall outside the range in an extra bin (on the right).
PairwisePerElement (BoolType | BoolKey) – Compute RDF for all element pairs (for all atoms in the system). Any other settings in the block will be used.
Range (Iterable[float] | FloatListKey) – Either one, two, or three real values. If one it is the stepsize. If two, it is the minimum value and the maximum value. If three, it is the minimum value, the maximum value, and the stepsize. The stepsize overrides NBins.
AtomsFrom (Analysis._RadialDistribution._AtomsFrom) – Atom numbers or elements for the first set of atoms in the radial distribution.
AtomsTo (Analysis._RadialDistribution._AtomsTo) – Atom numbers or elements for the second set of atoms in the radial distribution.
- class _System[source]¶
Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- Variables:
AllowCloseAtoms (BoolType | BoolKey) – No longer functional. Just here for backwards compatibility.
Charge (float | FloatKey) – The system’s total charge in atomic units.
FractionalCoords (BoolType | BoolKey) – Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
GeometryFile (str | Path | StringKey) – Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds (BoolType | BoolKey) – Equivalent to ‘Modify%GuessBonds’. Please update input file to use ‘Modify’ block instead.
LatticeStrain (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%LatticeStrain’. Please update input file to use ‘Modify’ block instead.
MapAtomsToUnitCell (BoolType | BoolKey) – Equivalent to ‘Modify%MapAtomsToUnitCell’. Please update input file to use ‘Modify’ block instead.
PerturbCoordinates (float | FloatKey) – Equivalent to ‘Modify%PerturbCoordinates’. Please update input file to use ‘Modify’ block instead.
PerturbLattice (float | FloatKey) – Equivalent to ‘Modify%PerturbLattice’. Please update input file to use ‘Modify’ block instead.
ShiftCoordinates (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%Translate’, but in the unit of bohr by default. Please update input file to use ‘Modify’ block instead.
SuperCell (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCell’. Please update input file to use ‘Modify’ block instead.
SuperCellTrafo (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCellTrafo’. Please update input file to use ‘Modify’ block instead.
Symmetrize (BoolType | BoolKey) – Equivalent to ‘Modify%Symmetrize’. Please update input file to use ‘Modify’ block instead.
Atoms (str | Sequence[str] | FreeBlock) – The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders (str | Sequence[str] | FreeBlock) – Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
ElectrostaticEmbedding (Analysis._System._ElectrostaticEmbedding) – Container for electrostatic embedding options, which can be combined.
Lattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
Modify (Analysis._System._Modify) – Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- class _Atoms[source]¶
The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
- class _BondOrders[source]¶
Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
- class _ElectrostaticEmbedding[source]¶
Container for electrostatic embedding options, which can be combined.
- Variables:
ElectricField (Iterable[float] | FloatListKey) –
External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.
In atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 … e11 V/m.
Supported by the engines adf, band, dftb and mopac.
For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
MultipolePotential (Analysis._System._ElectrostaticEmbedding._MultipolePotential) – External point charges (and dipoles).
- class _MultipolePotential[source]¶
External point charges (and dipoles).
- Variables:
ChargeModel (Literal["Point", "Gaussian"]) – A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
ChargeWidth (float | FloatKey) – The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
Coordinates (str | Sequence[str] | FreeBlock) –
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Coordinates[source]¶
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Lattice[source]¶
Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
- class _Modify[source]¶
Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- Variables:
EnableAtomicProperties (Literal["gui", "adf", "band", "forcefield", "dftb", "reaxff", "qe"]) – Enables an atomic property group. This is only necessary if you want a group enabled, but no atom in the input is using any property from that group.
GuessBonds (BoolType | BoolKey) – Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.
LatticeStrain (Iterable[float] | FloatListKey) – Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
MapAtomsToUnitCell (Iterable[float] | FloatListKey) – For periodic systems the atoms will be moved to the central unit cell where all their fractional coordinates are in the range [start_range,start_range+1). No mapping will take place along non-periodic directions. If just a single number is given, it corresponds to start_range. If multiple numbers are given, they should match the number of lattice vectors and will be used as start ranges along the individual lattice vectors. If no number is given at all, the mapping will be done to the [-0.5:0.5) cell.
PerturbCoordinates (float | FloatKey) – Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
PerturbLattice (float | FloatKey) – Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
SuperCell (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
SuperCellTrafo (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
Symmetrize (BoolType | BoolKey) – Symmetrizes the atomic coordinates to machine precision and rototranslates the molecule to the AMS standard orientation. This allows optimal use of the system’s symmetry for calculations with the AMS driver and its engines.
Translate (Iterable[float] | FloatListKey) – Translate all atoms by a vector.
- class _TrajectoryInfo[source]¶
All the info regarding the reading of the trajectory files.
- Variables:
NBlocksToCompare (int | IntKey) – Get an error estimate by comparing histograms for NBLocks time blocks of the trajectory.
Trajectory (Analysis._TrajectoryInfo._Trajectory) – All info regarding the reading of a single trajectory file.
- class _Trajectory[source]¶
All info regarding the reading of a single trajectory file.
- Variables:
KFFilename (str | Path | StringKey) – The name of the AMS trajectory file.
Range (Iterable[int] | IntListKey) – One or two values: start frame, and optionally end frame. By default the first and last frame are read.
StepSize (int | IntKey) – The step size at which frames are read from the RKF (default 1, every frame is read).
- class AtomTyping[source]¶
- Variables:
AntechamberTask (Literal["GeometryOptimization", "SinglePoint"]) – If antechamber is invoked to guess atomtypes and charges (GAFF force field), select the task for charge guessing with MOPAC
KeepAntechamberFolder (BoolType | BoolKey) – If atom-typing is performed with antechamber, keep the folder after the call to antechamber
Type (Literal["GAFF", "UFF", "APPLE&P", "UFFAutograf"]) – The forcefield type for which atomtyping should be performed
LoadSystem (AtomTyping._LoadSystem) – Block that controls reading the chemical system from a KF file instead of the [System] block.
System (AtomTyping._System) – Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- class _LoadSystem[source]¶
Block that controls reading the chemical system from a KF file instead of the [System] block.
- class _System[source]¶
Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- Variables:
AllowCloseAtoms (BoolType | BoolKey) – No longer functional. Just here for backwards compatibility.
Charge (float | FloatKey) – The system’s total charge in atomic units.
FractionalCoords (BoolType | BoolKey) – Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
GeometryFile (str | Path | StringKey) – Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds (BoolType | BoolKey) – Equivalent to ‘Modify%GuessBonds’. Please update input file to use ‘Modify’ block instead.
LatticeStrain (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%LatticeStrain’. Please update input file to use ‘Modify’ block instead.
MapAtomsToUnitCell (BoolType | BoolKey) – Equivalent to ‘Modify%MapAtomsToUnitCell’. Please update input file to use ‘Modify’ block instead.
PerturbCoordinates (float | FloatKey) – Equivalent to ‘Modify%PerturbCoordinates’. Please update input file to use ‘Modify’ block instead.
PerturbLattice (float | FloatKey) – Equivalent to ‘Modify%PerturbLattice’. Please update input file to use ‘Modify’ block instead.
ShiftCoordinates (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%Translate’, but in the unit of bohr by default. Please update input file to use ‘Modify’ block instead.
SuperCell (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCell’. Please update input file to use ‘Modify’ block instead.
SuperCellTrafo (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCellTrafo’. Please update input file to use ‘Modify’ block instead.
Symmetrize (BoolType | BoolKey) – Equivalent to ‘Modify%Symmetrize’. Please update input file to use ‘Modify’ block instead.
Atoms (str | Sequence[str] | FreeBlock) – The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders (str | Sequence[str] | FreeBlock) – Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
ElectrostaticEmbedding (AtomTyping._System._ElectrostaticEmbedding) – Container for electrostatic embedding options, which can be combined.
Lattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
Modify (AtomTyping._System._Modify) – Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- class _Atoms[source]¶
The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
- class _BondOrders[source]¶
Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
- class _ElectrostaticEmbedding[source]¶
Container for electrostatic embedding options, which can be combined.
- Variables:
ElectricField (Iterable[float] | FloatListKey) –
External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.
In atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 … e11 V/m.
Supported by the engines adf, band, dftb and mopac.
For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
MultipolePotential (AtomTyping._System._ElectrostaticEmbedding._MultipolePotential) – External point charges (and dipoles).
- class _MultipolePotential[source]¶
External point charges (and dipoles).
- Variables:
ChargeModel (Literal["Point", "Gaussian"]) – A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
ChargeWidth (float | FloatKey) – The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
Coordinates (str | Sequence[str] | FreeBlock) –
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Coordinates[source]¶
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Lattice[source]¶
Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
- class _Modify[source]¶
Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- Variables:
EnableAtomicProperties (Literal["gui", "adf", "band", "forcefield", "dftb", "reaxff", "qe"]) – Enables an atomic property group. This is only necessary if you want a group enabled, but no atom in the input is using any property from that group.
GuessBonds (BoolType | BoolKey) – Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.
LatticeStrain (Iterable[float] | FloatListKey) – Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
MapAtomsToUnitCell (Iterable[float] | FloatListKey) – For periodic systems the atoms will be moved to the central unit cell where all their fractional coordinates are in the range [start_range,start_range+1). No mapping will take place along non-periodic directions. If just a single number is given, it corresponds to start_range. If multiple numbers are given, they should match the number of lattice vectors and will be used as start ranges along the individual lattice vectors. If no number is given at all, the mapping will be done to the [-0.5:0.5) cell.
PerturbCoordinates (float | FloatKey) – Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
PerturbLattice (float | FloatKey) – Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
SuperCell (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
SuperCellTrafo (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
Symmetrize (BoolType | BoolKey) – Symmetrizes the atomic coordinates to machine precision and rototranslates the molecule to the AMS standard orientation. This allows optimal use of the system’s symmetry for calculations with the AMS driver and its engines.
Translate (Iterable[float] | FloatListKey) – Translate all atoms by a vector.
- class CPL[source]¶
- Variables:
ADFFile (str | StringKey) – Path to TAPE21 file from which cpl reads data and to which cpl writes data
ALTRHOF (BoolType | BoolKey) –
CALCV2007 (BoolType | BoolKey) – compatibility with older versions of CPL that did not use the SAPA approximation but always calculated the potential during the CPL run, which is inconsistent with SAPA settings in ADF
Diagonal (BoolType | BoolKey) –
Diffuse (BoolType | BoolKey) –
FORCECONVERGE (BoolType | BoolKey) –
FULLNBO (BoolType | BoolKey) –
Fractional (BoolType | BoolKey) – Allow Fractional occupations
GGA (BoolType | BoolKey) – Use first-order GGA potential instead of the first-order VWN potential
LinearScaling (BoolType | BoolKey) –
MODEBUG (BoolType | BoolKey) –
NBODEBUG (BoolType | BoolKey) –
NEWCPKS (BoolType | BoolKey) –
NoFDKERN (BoolType | BoolKey) –
NoGGAPot (BoolType | BoolKey) –
NoKMat (BoolType | BoolKey) –
NoTKINFDKERN (BoolType | BoolKey) –
NoXCFDKERN (BoolType | BoolKey) –
OLDCPKS (BoolType | BoolKey) –
OldCode (BoolType | BoolKey) – Use old code
PSOFirst (BoolType | BoolKey) –
SPINCURRENTS (BoolType | BoolKey) –
TAPE10File (str | StringKey) – Path to the TAPE10 file from which cpl reads data
Hyperfine (CPL._Hyperfine) – control the computation of the NSSCCs
NMRCoupling (CPL._NMRCoupling) – control the computation of the NSSCCs
ZFS (CPL._ZFS) – ZFS branch of the code
- class _Hyperfine[source]¶
control the computation of the NSSCCs
- Variables:
ADFGUI (BoolType | BoolKey) –
Atoms (Iterable[int] | IntListKey) –
Enabled (BoolType | BoolKey) –
FC (BoolType | BoolKey) –
NOFC (BoolType | BoolKey) –
NOPSOSO (BoolType | BoolKey) –
NOSD (BoolType | BoolKey) –
Nuclei (Iterable[int] | IntListKey) –
PSOSO (BoolType | BoolKey) –
SD (BoolType | BoolKey) –
SCF (CPL._Hyperfine._SCF) –
- class _NMRCoupling[source]¶
control the computation of the NSSCCs
- Variables:
ADFGUI (BoolType | BoolKey) –
ALDA (BoolType | BoolKey) –
AtomPert (Iterable[int] | IntListKey) –
AtomResp (Iterable[int] | IntListKey) –
Contributions (str | StringKey) – Analyze orbital contributions
DSO (BoolType | BoolKey) –
FC (BoolType | BoolKey) –
Internal (BoolType | BoolKey) –
NOFC (BoolType | BoolKey) –
NOSD (BoolType | BoolKey) –
Nuclei (Iterable[int] | IntListKey) –
PSO (BoolType | BoolKey) –
PertAllAtomsOfType (str | StringKey) – Space separated list of type of perturbing nuclei (like H, C, P) for which the NMR spin-spin coupling should be calculated.
RespAllAtomsOfType (str | StringKey) – Space separated list of type of responding nuclei (like H, C, P) for which the NMR spin-spin coupling should be calculated.
SD (BoolType | BoolKey) –
XAlpha (BoolType | BoolKey) –
SCF (CPL._NMRCoupling._SCF) –
- class Chemtrayzer2[source]¶
- Variables:
PrintDebug (BoolType | BoolKey) – Print extra debug information to the terminal.
Analysis (Chemtrayzer2._Analysis) – Statistical post-detection analysis, includes reaction coefficients calculation.
MoleculeIdentifier (Chemtrayzer2._MoleculeIdentifier) – Settings for the subgraph identification of molecules and reactions.
Output (Chemtrayzer2._Output) – Settings for program output and output file generation.
ReactionDetection (Chemtrayzer2._ReactionDetection) – Parameters for the the reaction detection algorithm.
Trajectory (Chemtrayzer2._Trajectory) – Info regarding the trajectory to analyze.
- class _Analysis[source]¶
Statistical post-detection analysis, includes reaction coefficients calculation.
- Variables:
PerformAnalysis (BoolType | BoolKey) – Determine the reaction rate coefficients and statistical errors for the detected reactions.
RateConfidence (float | FloatKey) – Upper and lower bounds to the rate coefficients will be calculated for this confidence (0 < confidence < 1), assuming a Poisson distribution of the number of reactive events. A value of 0.9 means that the kinetics of 90% of events of one reaction can be described by a coefficient between the bounds.
- class _MoleculeIdentifier[source]¶
Settings for the subgraph identification of molecules and reactions.
- Variables:
MaxDepth (int | IntKey) – The maximum number of layers the algorithm goes along bonds, starting from one atom when generating hashes for one atom. The entire molecule hash is built from the atom hashes, so this setting influences the identification of atom neighborhoods.
UseBondOrders (BoolType | BoolKey) – Consider bond orders in the identifier.
UseHs (BoolType | BoolKey) – Consider number of hydrogens of atoms in the identifier.
UseRings (BoolType | BoolKey) – Consider ring membership of atoms in the identifier.
WindowDepth (int | IntKey) – The maximum number of layers the algorithm goes along bonds starting from the reactive atoms when generating hashes for the entire molecule. With this setting, the identifier can be limited to only a part of the molecule.
- class _Output[source]¶
Settings for program output and output file generation.
- Variables:
CreateLegacyOutput (BoolType | BoolKey) – Whether to save the reactions, species, and rates as ‘reac.reac.tab’, ‘reac.spec.tab’, and ‘reac.rate.tab’ in the same format as ChemTraYzer 1.
ShowReactionGraph (BoolType | BoolKey) – Whether or not to show the reaction graph at the end of the calculation. Requires the python library matplotlib to be installed.
WriteEventsPerTime (BoolType | BoolKey) – Write two .csv files that contain the number of reactions in every frame (reaction_events_per_time.csv) and the number of bond changes in every frame(bond_change_events_per_time.csv)
WriteKF (BoolType | BoolKey) – Whether to write output to KF
WriteMolPopulation (BoolType | BoolKey) – Write two .csv files: (1) mol_statistics.csv, which contains basic population statistics (counts, averages) for each unique species over the entire trajectory; and (2) mol_population.csv, which provides the count of each unique species in every frame.
WriteReactions (BoolType | BoolKey) – Write two .csv files that contain information about (1) all unique reactions (reactions.csv); and (2) all individual reaction events (reaction_events.csv).
WriteXYZFiles (BoolType | BoolKey) – Write XYZ files (geometries) for detected species and XYZ movies for detected reactions into a subfolder named ‘xyz’.
- class _ReactionDetection[source]¶
Parameters for the the reaction detection algorithm.
- Variables:
BondBreakingThreshold (float | FloatKey) – The bond-order threshold for bond breaking. If the bond order of a bond goes below this value, the bond is considered broken.
BondFormationThreshold (float | FloatKey) – The bond-order threshold for bond formation. If the bond order between two atoms goes above this value, then this will be considered to be a new bond.
InitialBondThreshold (float | FloatKey) – The bond-order threshold for determining the connectivity for the first frame of the simulation. If not specified, the value in BondFormationThreshold will be used instead.
TStable (float | FloatKey) – The minimum time for a molecule to be considered stable.
- class Conductance[source]¶
- Variables:
EnergyGrid (Conductance._EnergyGrid) – Energy grid for Transmission Function
Files (Conductance._Files) – path of files
Output (Conductance._Output) – options describing what should be printed
Physics (Conductance._Physics) – Block describing the physics of the system
Technical (Conductance._Technical) – options describing technical parts of the calculation
- class _Files[source]¶
path of files
- class _Output[source]¶
options describing what should be printed
- Variables:
OldOutput (BoolType | BoolKey) –
- class _Physics[source]¶
Block describing the physics of the system
- Variables:
FermiEnergy (Conductance._Physics._FermiEnergy) – Block describing the physics of the system
- class _Technical[source]¶
options describing technical parts of the calculation
- Variables:
Eta (float | FloatKey) – To avoid poles of the Green’s function, a small imaginary number is added to the energy
overwriteLeads (BoolType | BoolKey) – If true, Hamiltonians H_L and H_R are taken from the DFTB-leads calculation. If False, they are taken from the DFTB scattering-region calculation
setOffDiagonalToZero (BoolType | BoolKey) – If true, H_LR and S_LR are explicitly set to zero. If False, they are taken from the DFTB scattering-region calculation.
- class Conformers[source]¶
- Variables:
InputConformersSet (str | Path | StringKey) –
The path to a file containing a set of conformers.
The file should be either an ‘conformers.rkf’ file (i.e. the results file of conformers), a concatenated .xyz file, a .sdf file, or even .dcd file. In the case of a .dcd file, an additional System block is required. If the specified file does not contain energies in the AMS conformers format (as produced by the conformers tool), all conformer energies will be set to zero.
You can specify multiple input conformers sets by including the InputConformersSet keyword multiple times.
InputMaxConfs (int | IntKey) – The maximum number of conformers to carry forward when loading conformer sets. If this input is not specified, this limit will not be imposed.
InputMaxEnergy (float | FloatKey) – Threshold for filtering out high-energy conformers when loading conformers sets using the InputConformerSet keyword. Conformers with an larger relative energy will not be loaded.
RNGSeed (int | IntKey) – Initial seed for the (pseudo)random number generator. If this is unset, the generator will be seeded randomly from external sources of entropy and the generated conformers will be non-deterministic.
Task (Literal["Generate", "Optimize", "Filter", "Score", "Expand"]) –
The task to be performed by the Conformers tool.
’Generate’: given a molecule, generate a set of conformers. Note: this task will automatically optimize, filter and score the conformers.
’Optimize’: given a previously generated set of conformers, optimize, filter and score the structures using the specified engine.
’Filter’: given one or more previously generated set of conformers, merge them into a single conformer set and filter out duplicate conformers. Note: this will not optimize or re-score the conformers.
’Score’ given one or more previously generated set of conformers, re-score them by computing the energy using the specified engine. Note: this will only do a single point calculation, and will not optimize the structures.
In case of ‘Optimize’, ‘Filter’ and ‘Score’ you can specify the input conformer set(s) using the ‘InputConformersSet’ keyword.
Constraints (Conformers._Constraints) – The Constraints block allows geometry optimizations and potential energy surface scans with constraints. The constraints do not have to be satisfied at the start of the calculation.
Engine (EngineBlock) – The input for the computational engine used to compute energy and forces.
EngineAddons (Conformers._EngineAddons) – This block configures all the engine add-ons.
Equivalence (Conformers._Equivalence) – Options for the procedure determining whether two structures are equivalent or distinct conformers.
Expander (Conformers._Expander) –
Options for the conformer expander. The Expander expands an existing conformer set, by adding new conformers to it. The new conformers are generated from the original conformers in the set. Unlike the generators, the outcome of an expander is therefore very dependent on the input conformations.
The GC generator uses a genetic algorithm to create a combinatorial expansion by combining local substructures. The MD expander start MD simulations from the conformers in the set, and extracts snapshots to create new conformers. Both these expanders are part of the CREST generator.
Filter (Conformers._Filter) – Options for the conformer filtering.
Generator (Conformers._Generator) – Options for the conformer generator.
GeometryOptimization (Conformers._GeometryOptimization) – Some options / details regarding the optimization procedure.
LoadSystem (Conformers._LoadSystem) – Block that controls reading the chemical system from a KF file instead of the [System] block.
Output (Conformers._Output) – Options regarding the output and result files.
Restraints (Conformers._Restraints) – The Restraints block allows to add soft constraints to the system. A restraint is a potential energy function (a spring) attached to a certain coordinate, for example, an interatomic distance, with its minimum at the specified optimal value. A restraint is defined using one or two parameters: the ForceConstant and, for some types, the F(Inf) value. The ForceConstant parameter corresponds to second derivative of the restraint potential energy d2V(x)/dx^2 for any x (harmonic restraints) or only at at x=0 (other restraints). Here, x is a deviation from the restraint’s optimal value.
Rotamers (Conformers._Rotamers) – Options for the treatment of Grimme-rotamers.
System (Conformers._System) – Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- class _Constraints[source]¶
The Constraints block allows geometry optimizations and potential energy surface scans with constraints. The constraints do not have to be satisfied at the start of the calculation.
- Variables:
Fix multiple distances using one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3
The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 as well as the angle between them.
The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then any bond between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. If the distance is omitted then the bond length from the initial geometry is used.
Important: only the bonds present in the system at the start of the simulation can be constrained, which means that the bonds may need to be specified in the System block.
Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H
Angle (str | StringKey) – Fix the angle between three atoms. Three atom indices followed by an angle in degrees.
Atom (int | IntKey) – Fix the position of an atom. Just one integer referring to the index of the atom in the [System%Atoms] block.
AtomList (Iterable[int] | IntListKey) – Fix positions of the specified atoms. A list of integers referring to indices of atoms in the [System%Atoms] block.
Block (str | StringKey) – Name of the region to constrain as a rigid block. Regions are specified in the System%Atoms block.
BlockAtoms (Iterable[int] | IntListKey) – List of atom indices for a block constraint, where the internal degrees of freedom are frozen.
Coordinate (str | StringKey) – Fix a particular coordinate of an atom. Atom index followed by (x|y|z).
DifDist (str | StringKey) – Four atom indices i j k l followed by the distance in Angstrom. This will constrain the difference R(ij)-R(kl) at the given value.
Dihedral (str | StringKey) – Fix the dihedral angle between four atoms. Four atom indices followed by an angle in degrees.
Distance (str | StringKey) – Fix the distance between two atoms. Two atom indices followed by the distance in Angstrom.
EqualStrain (str | StringKey) –
Exclusively for lattice optimizations:
Accepts a set of strain components [xx, xy, xz, yy, yz, zz] which are to be kept equal.
The applied strain will be determined by the average of the corresponding stress tensors components.
In AMSinput just check the corresponding check buttons.
FixedRegion (str | StringKey) – Fix positions of all atoms in a region.
FreezeStrain (str | StringKey) –
Exclusively for lattice optimizations:
Freezes any lattice deformation corresponding to a particular component of the strain tensor.
Accepts a set of strain components [xx, xy, xz, yy, yz, zz] to be frozen.
In AMSinput just check the corresponding check buttons.
SumDist (str | StringKey) – Four atom indices i j k l followed by the distance in Angstrom. This will constrain the sum R(ij)+R(kl) at the given value.
- class _EngineAddons[source]¶
This block configures all the engine add-ons.
- Variables:
Pressure (float | FloatKey) – Add a hydrostatic pressure term to the engine’s energy and stress tensor. Can only be used for 3D periodic boundary conditions.
AtomEnergies (str | Sequence[str] | FreeBlock) – Add an element-dependent energy per atom. On each line, give the chemical element followed by the energy (in atomic units).
D3Dispersion (Conformers._EngineAddons._D3Dispersion) – This block configures the add-on that adds the Grimme D3 dispersion correction to the engine’s energy, gradients, and stress tensor.
D4Dispersion (Conformers._EngineAddons._D4Dispersion) – This block configures the addon that adds the Grimme D4(EEQ) dispersion correction to the engine’s energy, gradients, stress tensor and Hessian.
ExternalEngine (Conformers._EngineAddons._ExternalEngine) – External engine as an addon
ExternalStress (Conformers._EngineAddons._ExternalStress) – This block configures the addon that adds external stress term to the engine’s energy and stress tensor.
PipeEngine (Conformers._EngineAddons._PipeEngine) – Pipe engine as an addon
Repulsion (Conformers._EngineAddons._Repulsion) – This block configures an addon that adds a repulsive Weeks-Chandler-Andersen potential to all atom pairs.
WallPotential (Conformers._EngineAddons._WallPotential) – This block configures the addon that adds a spherical wall potential to the engine’s energy and gradients.
- class _AtomEnergies[source]¶
Add an element-dependent energy per atom. On each line, give the chemical element followed by the energy (in atomic units).
- class _D3Dispersion[source]¶
This block configures the add-on that adds the Grimme D3 dispersion correction to the engine’s energy, gradients, and stress tensor.
- Variables:
Damping (Literal["BJ", "Zero"]) – Type of damping: BJ (Becke-Johnson) or Zero. BJ is recommended for most applications.
Enabled (BoolType | BoolKey) – Enables the D3 dispersion correction addon.
Functional (str | StringKey) – Use the D3 parameterization by Grimme for a given xc-functional. Accepts the same values as the –func command line option of the official dftd3 program. Note: the naming convention is different from elsewhere in the AMS suite. For example, BLYP should be called b-lyp.
a1 (float | FloatKey) – The a1 parameter. Only used if Damping is set to BJ. If set, it overwrites the a1 value for the chosen functional.
a2 (float | FloatKey) – The a2 parameter. Only used if Damping is set to BJ. If set, it overwrites the a2 value for the chosen functional.
alp (float | FloatKey) – The a2 parameter. Only used if Damping is set to BJ. If set, it overwrites the a2 value for the chosen functional.
s6 (float | FloatKey) – The s6 parameter, global scaling parameter. If set, it overwrites the s6 value for the chosen functional.
s8 (float | FloatKey) – The s8 parameter. If set, it overwrites the s8 value for the chosen functional.
sr6 (float | FloatKey) – The sr6 parameter. Only used if Damping is set to Zero. If set, it overwrites the sr6 value for the chosen functional.
- class _D4Dispersion[source]¶
This block configures the addon that adds the Grimme D4(EEQ) dispersion correction to the engine’s energy, gradients, stress tensor and Hessian.
- Variables:
Enabled (BoolType | BoolKey) – Enables the D4 dispersion correction addon.
Functional (Literal["HF", "BLYP", "BPBE", "BP86", "BPW", "LB94", "MPWLYP", "MPWPW91", "OLYP", "OPBE", "PBE", "RPBE", "REVPBE", "PW86PBE", "RPW86PBE", "PW91", "PW91P86", "XLYP", "B97", "TPSS", "REVTPSS", "SCAN", "B1LYP", "B3LYP", "BHLYP", "B1P86", "B3P86", "B1PW91", "B3PW91", "O3LYP", "REVPBE0", "REVPBE38", "PBE0", "PWP1", "PW1PW", "MPW1PW91", "MPW1LYP", "PW6B95", "TPSSH", "TPSS0", "X3LYP", "M06L", "M06", "OMEGAB97", "OMEGAB97X", "CAM-B3LYP", "LC-BLYP", "LH07TSVWN", "LH07SSVWN", "LH12CTSSIRPW92", "LH12CTSSIFPW92", "LH14TCALPBE", "B2PLYP", "B2GPPLYP", "MPW2PLYP", "PWPB95", "DSDBLYP", "DSDPBE", "DSDPBEB95", "DSDPBEP86", "DSDSVWN", "DODBLYP", "DODPBE", "DODPBEB95", "DODPBEP86", "DODSVWN", "PBE02", "PBE0DH", "DFTB(3ob)", "DFTB(mio)", "DFTB(pbc)", "DFTB(matsci)", "DFTB(ob2)", "B1B95", "MPWB1K", "REVTPSSH", "GLYP", "REVPBE0DH", "REVTPSS0", "REVDSDPBEP86", "REVDSDPBEPBE", "REVDSDBLYP", "REVDODPBEP86", "B97M", "OMEGAB97M", "R2SCAN"]) – Use the D4 parameterization by Grimme for a given xc-functional.
Verbosity (Literal["Silent", "Normal", "Verbose", "VeryVerbose"]) – Controls the verbosity of the dftd4 code. Equivalent to the –silent and –verbose command line switches of the official dftd4 program.
a1 (float | FloatKey) – The a1 parameter, see D4 article. The physically reasonable range for a1 is [0.0,1.0]. If set, it overwrites the a1 value for the chosen functional.
a2 (float | FloatKey) – The a2 parameter, see D4 article. The physically reasonable range for a2 is [0.0,7.0]. If set, it overwrites the a2 value for the chosen functional.
s6 (float | FloatKey) – The s6 parameter, see D4 article. The physically reasonable range for s6 is [0.0,1.0]. If set, it overwrites the s6 value for the chosen functional.
s8 (float | FloatKey) – The s8 parameter, see D4 article. The physically reasonable range for s8 is [0.0,3.0]. If set, it overwrites the s8 value for the chosen functional.
s9 (float | FloatKey) – The s9 parameter, see D4 article. If set, it overwrites the s9 value for the chosen functional.
- class _ExternalStress[source]¶
This block configures the addon that adds external stress term to the engine’s energy and stress tensor.
- Variables:
StressTensorVoigt (Iterable[float] | FloatListKey) – The elements of the external stress tensor in Voigt notation. One should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
UpdateReferenceCell (BoolType | BoolKey) – Whether ot not the reference cell should be updated every time the system changes (see documentation).
- class _Repulsion[source]¶
This block configures an addon that adds a repulsive Weeks-Chandler-Andersen potential to all atom pairs.
- Variables:
Enabled (BoolType | BoolKey) –
Enables the repulsive Weeks-Chandler-Andersen potential addon.
When enabled, all atom pairs will experience repulsion E = 4*epsilon*( (sigma/r)^12 - (sigma/r)^6 + 1/4 ) at the distances shorter than about 1.12*sigma.
Epsilon (float | FloatKey) – The epsilon parameter in the potential equation. It is equal to the amount of energy added at r=sigma.
HydrogenSigmaScale (float | FloatKey) – The sigma parameter for a pair of atoms where one of them is hydrogen is scaled with the given factor. For H-H interactions the sigma is scaled with this value squared.
Sigma (float | FloatKey) – The sigma parameter in the potential equation. The potential is exactly zero at the distances larger than about 1.12*sigma
SkinLength (float | FloatKey) – Technical parameter specifying skin length for the neighbor list generation. A larger value increases the neighbor list cutoff (and cost) but reduces the frequency it needs to be re-created.
- class _WallPotential[source]¶
This block configures the addon that adds a spherical wall potential to the engine’s energy and gradients.
- Variables:
Enabled (BoolType | BoolKey) – Enables the wall potential addon. When enabled, a spherical wall of radius [Radius] around the origin will be added. The force due to the potential will decay exponentially inside the wall, will be close to [Prefactor*Gradient] outside and exactly half of that at the wall.
Gradient (float | FloatKey) – The radial gradient outside the sphere.
Prefactor (float | FloatKey) – The multiplier for the overall strength of the potential.
Radius (float | FloatKey) – The radius of the sphere, wherein the potential is close to zero.
- class _Equivalence[source]¶
Options for the procedure determining whether two structures are equivalent or distinct conformers.
- Variables:
AcceptAll (BoolType | BoolKey) – If set to True, add any candidate to the set without checks of connectivity changes, stereo- or cis/trans isomerization, or duplication.
AcceptBondchanges (BoolType | BoolKey) – If set to True, perform all checks of a new conformer candidate, except for the connectivity check.
AcceptIsomers (BoolType | BoolKey) – If set to True, perform all checks of a new conformer candidate, except for the stereo- or cis/trans isomerization check.
CheckForDuplicates (BoolType | BoolKey) – If set to True, check any new conformer candidate for duplication, and only accept unique conformers. If set to False, accept duplicates into the set.
EnableSwapping (BoolType | BoolKey) – If set to True, a conformer candidate will replace another conformer if it is deemed a duplicate but with slightly lower energy.
LogDuplicates (BoolType | BoolKey) – If set to True, print information on equivalence to logfile and standard output.
Method (Literal["AMS", "TFD", "RMSD", "CREST"]) –
Method used to determine (and filter out) equivalent conformers.
The CREST equivalence method relies on rotational constants comparisons. For this reason, conformers with the same rotational constants (such as mirror images) will be considered equivalent conformers.
The AMS equivalence method uses a distance matrix and dihedrals to compare conformers. This equivalence method can be computationally expensive for large molecules.
The TFD equivalence method uses the Torsion Fingerprint Difference as implemented in RDKit.
The RMSD equivalence method uses the RDKit GetBestRMS implementation.
Reorder (BoolType | BoolKey) – Reorder conformers based on energy, whenever a new conformer is added.
Verbose (BoolType | BoolKey) – If set to True, print errors in adding conformer candidates to the logfile.
AMS (Conformers._Equivalence._AMS) – Options for the AMS method of checking equivalence. This method uses the atomic distance matrices and the torsion angles between heavy atoms to determine if conformer candidates are duplicates.
CREST (Conformers._Equivalence._CREST) – Options for the CREST method of checking equivalence. This method uses the rotational constants of conformer candidates to determine if they are duplicates.
RMSD (Conformers._Equivalence._RMSD) – Options for the RMSD method of checking equivalence. This method uses the RDKit implementation of GetBestRMS, which enumerates over atomic permutations for pairs of geometries to detect duplicates based on the RMSD value.
TFD (Conformers._Equivalence._TFD) – Options for the TFD method of checking equivalence. This method uses the Torsion Finger Print method to determine if two conformer candidates are duplicates.
- class _AMS[source]¶
Options for the AMS method of checking equivalence. This method uses the atomic distance matrices and the torsion angles between heavy atoms to determine if conformer candidates are duplicates.
- Variables:
DihedralThreshold (float | FloatKey) – Maximum difference a dihedral can have for a conformer to be considered a duplicate.
DistanceThreshold (float | FloatKey) – Maximum difference a distance between two atoms can have for a conformer to be considered a duplicate.
EnergyThreshold (float | FloatKey) – The energy difference beyond which two conformers are always considered distinct.
IrrelevantAtoms (Iterable[int] | IntListKey) – To detect equivalence, only a subset of atoms is used. The atoms that are excluded from equivalence comparison should be specified here. By default only non-hydrogen atoms will be used for the comparison. Numbering starts at 0.
StoreRotamers (BoolType | BoolKey) – Whether or not rotamers (permutations of the conformers) should be stored in the conformers object. If set to yes, writing the rotamers to file still needs to be explicitly enabled. Storing the rotamers considerably slows down the conformer filtering process.
UseTorsions (BoolType | BoolKey) – To detect equivalence, a two-step procedure is followed. First the permutation of atoms with the best match is determined, and then this permutation is used to see if distances and torsion angles are within the threshold values. For the first step by default both the distance matrices and the torsion angles aere used as well, but this is time consuming. By settings this key to False, only the distance matrix will be used for this first step. As a result it may happen that geometries that are actually equivalent will be accepted as unique conformers, but this will only happen for very symmetric molecules.
- class _CREST[source]¶
Options for the CREST method of checking equivalence. This method uses the rotational constants of conformer candidates to determine if they are duplicates.
- Variables:
BconstScalingFactor (float | FloatKey) – This is the scaling factor of the rotational constant difference used only for cluster analysis. This is not used to determine conformer equivalence (see ScaledBconstSettings). However, if FollowPaper is set to True, then this value IS used to determine conformer equivalence.
EnergyThreshold (float | FloatKey) – The energy difference beyond which two conformers are always considered distinct.
FollowPaper (BoolType | BoolKey) – By default this code uses a procedure to determine equivalence that is as close as possible to the procedure followed by Grimmes crest code. However, when this flag is turned on, then the procedure as described by the CREST paper (DOI: 10.1039/c9cp06869d) is followed. If set to True, then the rotational constant difference threshold used to determine equivalence is BconstScalingFactor, and not BconstThreshold.
RMSDThreshold (float | FloatKey) – Threshold for the RMSD between two conformers that determines if they are duplicates or rotamers (according to the CREST rotamer definition.)
SizeThreshold (float | FloatKey) – An additional threshold based on the difference between distance matrices. This is used to determine if two geometries are duplicates or rotamers.
StoreRotamers (BoolType | BoolKey) – Whether or not rotamers (permutations of the conformers) should be stored in the conformers object. If set to yes, writing the rotamers to file still needs to be explicitly enabled. Storing the rotamers considerably slows down the conformer filtering process.
ScaledRotationalConstantSettings (Conformers._Equivalence._CREST._ScaledRotationalConstantSettings) – By default, the equivalence of two geometries is determined mainly by comparing the rotational constants, and weighing the difference based on the average anisotropy of the two systems. This procedure has several settings that can be user defined.
- class _ScaledRotationalConstantSettings[source]¶
By default, the equivalence of two geometries is determined mainly by comparing the rotational constants, and weighing the difference based on the average anisotropy of the two systems. This procedure has several settings that can be user defined.
- Variables:
BthrMax (float | FloatKey) – Maximum rotational constant threshold due to anisotropy.
BthrShift (float | FloatKey) – Shift in the error function used to compute modified rotational constant threshold, based on anisotropy.
RotationalConstantThreshold (float | FloatKey) – Threshold for the difference in rotational constants that determines if two geometries are duplicates. The threshold is weighed by the anisotropy of the systems. Note: in the grimme code they use 0.01 as bconst_threshold, but this leads to a lot of misclassifications (i.e. different conformers are classified as equivalent rotamers) So, here we use a smaller default value.
- class _RMSD[source]¶
Options for the RMSD method of checking equivalence. This method uses the RDKit implementation of GetBestRMS, which enumerates over atomic permutations for pairs of geometries to detect duplicates based on the RMSD value.
- class _TFD[source]¶
Options for the TFD method of checking equivalence. This method uses the Torsion Finger Print method to determine if two conformer candidates are duplicates.
- Variables:
EnergyThreshold (float | FloatKey) – The energy difference beyond which two conformers are always considered distinct.
TFDThreshold (float | FloatKey) – Threshold on the torsion fingerprint difference to determine if two geometries represent the same conformer. This value is unit-less.
UseEnergyThreshold (BoolType | BoolKey) – Accept all conformers with an energy difference greater than the energy threshold as unique, without TFD testing.
UseWeights (BoolType | BoolKey) – Use the weights of the torsion angles to compute the torsion fingerprint difference (all determined by RDKit).
- class _Expander[source]¶
Options for the conformer expander. The Expander expands an existing conformer set, by adding new conformers to it. The new conformers are generated from the original conformers in the set. Unlike the generators, the outcome of an expander is therefore very dependent on the input conformations.
The GC generator uses a genetic algorithm to create a combinatorial expansion by combining local substructures. The MD expander start MD simulations from the conformers in the set, and extracts snapshots to create new conformers. Both these expanders are part of the CREST generator.
- Variables:
AdjustInputBonds (BoolType | BoolKey) – If geometry optimization of the initial conformer results in bond changes, adjust the reference connectivity. If the changes are too severe, the calculation will stop.
MaxEnergy (float | FloatKey) – Threshold for filtering out high-energy conformers. If the relative energy of a conformer with respect to the lowest conformer is larger than this value, the conformer will be discarded.
Method (Literal["MD", "GC"]) – Method used to generate the conformers.
RNGSeed (int | IntKey) – Initial guesses for conformers can be randomly generated by RDKit, using the ETKDG algorithm. For reproducibility, a random number seed can be provided here.
Verbose (BoolType | BoolKey) – If set to True, print additional info about conformer equivalence to standard output.
GC (Conformers._Expander._GC) – Options for the genetic algorithm for combinatorial expansion of conformer geometries. This generator only works if a non-zero set of conformers is already provided.
MD (Conformers._Expander._MD) – Produces conformers by running a set of MD simulations at different elevated temperatures, extracting snapshots, and optimizing those.
Preoptimization (Conformers._Expander._Preoptimization) – If this block is enabled geometries will be preoptimized. After preoptimization the high energy conformers will be discarded, and then from the remaining set the unoptimized geometries will be optimized at higher level. This is to prevent the preoptimizer from collapsing different conformers into a single false minimum. As a result, preoptimization is only useful if MaxEnergy is chosen low.
RDKitETKDG (Conformers._Expander._RDKitETKDG) – Settings for the call to RDKits ETKDG conformer generator tool.
- class _GC[source]¶
Options for the genetic algorithm for combinatorial expansion of conformer geometries. This generator only works if a non-zero set of conformers is already provided.
- Variables:
ClashThreshold (float | FloatKey) – Newly generated geometries are only accepted if the increase in coordination number per atom is below this threshold..
CoordnumThreshold (float | FloatKey) – Distance squared threshold, above which the coordination number can be neglected in Angstrom**2.
GCNgeomsFactor (float | FloatKey) – Parameter used to determine the maximum number of geometries that this generator is allowed to produce.
MaxGCenergy (float | FloatKey) – The maximum energy (relative to the lowest in the set) of the conformers we are going to use for expansion. The default is 6.0 kcal/mol, but if MaxEnergy was set, then that value is used.
Parallel (BoolType | BoolKey) – Determines if the combinatorial expansion of conformers should be performed in parallel or not (default: True).
RMSDThreshold (float | FloatKey) – Newly generated geometries are only considered unique if their RMSD from all other newly generated geometries is larger than this threshold.
- class _MD[source]¶
Produces conformers by running a set of MD simulations at different elevated temperatures, extracting snapshots, and optimizing those.
- Variables:
Blocksize (int | IntKey) – The interval between the trajectory snapshots written to file that are extracted and optimized. By default all written snapshots are extracted.
Multiples (int | IntKey) – The number of MD simulations per selected temperature and starting geometry. The default is 1.
Ngeoms (int | IntKey) – At each temperature, MD simulations are started from Ngeoms different starting geometries. The starting geometries are extracted from the provided conformer set. If the conformer set is empty, then no more than a single geometry per temperature can be provided, limiting the total number of MD simulations.
Temperatures (Iterable[float] | FloatListKey) – The list of different temperatures at which MD simulations are run.
UseShake (BoolType | BoolKey) – Constrain all -H bonds with shake. If turned on, the MD timestep is automatically increased.
UseXtb (BoolType | BoolKey) – Use Grimmes XTB code to perform the MD simulations instead of AMS
MolecularDynamics (Conformers._Expander._MD._MolecularDynamics) – Configures molecular dynamics (with the velocity-Verlet algorithm) with and without thermostats. This block allows to specify the details of the molecular dynamics calculation. Default values will be ignored.
- class _MolecularDynamics[source]¶
Configures molecular dynamics (with the velocity-Verlet algorithm) with and without thermostats. This block allows to specify the details of the molecular dynamics calculation. Default values will be ignored.
- Variables:
NSteps (int | IntKey) – The number of steps to be taken in the MD simulation.
Restart (str | Path | StringKey) – The path to the ams.rkf file from which to restart the simulation.
Checkpoint (Conformers._Expander._MD._MolecularDynamics._Checkpoint) – Sets the frequency for storing the entire MD state necessary for restarting the calculation.
InitialVelocities (Conformers._Expander._MD._MolecularDynamics._InitialVelocities) – Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
Preserve (Conformers._Expander._MD._MolecularDynamics._Preserve) – Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.
Print (Conformers._Expander._MD._MolecularDynamics._Print) – This block controls the printing of additional information to stdout.
Shake (Conformers._Expander._MD._MolecularDynamics._Shake) – Parameters of the Shake/Rattle algorithm.
Thermostat (Conformers._Expander._MD._MolecularDynamics._Thermostat) – This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’s behavior.
Trajectory (Conformers._Expander._MD._MolecularDynamics._Trajectory) – Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- class _Checkpoint[source]¶
Sets the frequency for storing the entire MD state necessary for restarting the calculation.
- Variables:
Frequency (int | IntKey) – Write the MD state to the Molecule and MDResults sections on ams.rkf once every N steps. Setting this to zero disables checkpointing during the simulation, but one checkpoint at the very end of the simulation will always be written.
WriteProperties (BoolType | BoolKey) –
Honor top-level Properties input block when writing engine results files.
DEPRECATED: This input option will be removed in AMS2026 and will be considered always enabled. If you rely on it being disabled, please contact support@scm.com.
- class _InitialVelocities[source]¶
Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- Variables:
File (str | Path | StringKey) – AMS RKF file containing the initial velocities.
RandomVelocitiesMethod (Literal["Exact", "Boltzmann", "Gromacs"]) –
Specifies how are random velocities generated. Three methods are available.
Exact: Velocities are scaled to exactly match set random velocities temperature.
Boltzmann: Velocities are not scaled and sample Maxwell-Boltzmann distribution. However, the distribution is not corrected for constraints.
Gromacs: Velocities are scaled to match set random velocities temperature, but removal of net momentum is performed only after the scaling. Resulting kinetic energy is lower based on how much net momentum the system had.
Temperature (float | FloatKey) –
Sets the temperature for the Maxwell-Boltzmann distribution when the type of the initial velocities is set to random, in which case specifying this key is mandatory.
AMSinput will use the first temperature of the first thermostat as default.
Type (Literal["Zero", "Random", "FromFile", "Input"]) –
Specifies the initial velocities to assign to the atoms. Three methods to assign velocities are available.
Zero: All atom are at rest at the beginning of the calculation.
Random: Initial atom velocities follow a Maxwell-Boltzmann distribution for the temperature given by the [MolecularDynamics%InitialVelocities%Temperature] keyword.
FromFile: Load the velocities from a previous ams result file.
Input: Atom’s velocities are set to the values specified in the [MolecularDynamics%InitialVelocities%Values] block, which can be accessed via the Expert AMS panel in AMSinput.
Values (str | Sequence[str] | FreeBlock) – This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.
- class _Values[source]¶
This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.
- class _Preserve[source]¶
Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.
- Variables:
AngularMomentum (BoolType | BoolKey) – Remove overall angular momentum of the system. This option is ignored for 2D and 3D-periodic systems, and disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).
CenterOfMass (BoolType | BoolKey) – Translate the system to keep its center of mass at the coordinate origin. This option is not very useful for 3D-periodic systems.
Momentum (BoolType | BoolKey) – Remove overall (linear) momentum of the system. This is disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).
- class _Shake[source]¶
Parameters of the Shake/Rattle algorithm.
- Variables:
Constraint description in one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3
The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 and the angle between them.
The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then all bonds between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. The distance, if present, must be in Angstrom. If it is omitted then the bond length from the initial geometry is used.
Important: only the bonds present in the system at certain points of the simulation (at the start or right after adding/removing atoms) can be constrained, which means that the bonds may need to be specified in the System block.
Warning: the triangles constraint should be used with care because each constrained bond or angle means removing one degree of freedom from the dynamics. When there are too many constraints (for example, “All triangles H C H” in methane) some of them may be linearly dependent, which will lead to an error in the temperature computation.
Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H
ConvergeR2 (float | FloatKey) – Convergence criterion on the max squared difference, in atomic units.
ConvergeRV (float | FloatKey) – Convergence criterion on the orthogonality of the constraint and the relative atomic velocity, in atomic units.
ShakeInitialCoordinates (BoolType | BoolKey) – Apply constraints before computing the first energy and gradients.
- class _Thermostat[source]¶
This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’s behavior.
- Variables:
BerendsenApply (Literal["Local", "Global"]) –
Select how to apply the scaling correction for the Berendsen thermostat:
per-atom-velocity (Local)
on the molecular system as a whole (Global).
ChainLength (int | IntKey) – Number of individual thermostats forming the NHC thermostat
Duration (Iterable[int] | IntListKey) – Specifies how many steps should a transition from a particular temperature to the next one in sequence take.
ExcludedDirection (Literal["None", "X", "Y", "Z"]) – Exclude a component of the velocities from rescaling by the thermostat. For example in NEMD simulations, when a shear force/velocity is applied in the x direction, the x-direction is often excluded from thermostatting. This currently only works for the Nose-Hoover thermostat.
Friction (float | FloatKey) – Friction coefficient used in langevin dynamics
Region (str | StringKey) – The identifier of the region to thermostat. The default * applies the thermostat to the entire system. The value can by a plain region name, or a region expression, e.g. *-myregion to thermostat all atoms that are not in myregion, or regionA+regionB to thermostat the union of the ‘regionA’ and ‘regionB’. Note that if multiple thermostats are used, their regions may not overlap.
ScaleFrequency (int | IntKey) –
Optional parameter used only by the Scale thermostat.
If specified, the thermostat will be applied every N steps, using that step’s ensemble temperature and the specified thermostat temperature to compute the scaling factor.
If not specified, the thermostat will be applied at every step, using the mean temperature of the ensemble and the specified thermostat temperature to compute the scaling factor.
Tau (float | FloatKey) – The time constant of the thermostat.
Temperature (Iterable[float] | FloatListKey) –
The target temperature of the thermostat.
You can specify multiple temperatures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one T to the next T (using a linear ramp). For NHC thermostat, the temperature may not be zero.
Type (Literal["None", "Scale", "Berendsen", "NHC", "Langevin"]) – Selects the type of the thermostat.
- class _Trajectory[source]¶
Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- Variables:
EngineResultsFreq (int | IntKey) – Write MDStep*.rkf files with engine-specific results once every N steps. Setting this to zero disables writing engine results files except for one file at the end of the simulation. If unset or negative, defaults to the value of Checkpoint%Frequency.
ExitConditionFreq (int | IntKey) – Check the exit conditions every N steps. By default this is done every SamplingFreq steps.
PrintFreq (int | IntKey) – Print current thermodynamic properties to the output every N steps. By default this is done every SamplingFreq steps.
SamplingFreq (int | IntKey) – Write the molecular geometry (and possibly other properties) to the ams.rkf file once every N steps.
TProfileGridPoints (int | IntKey) – Number of points in the temperature profile. If TProfileGridPoints > 0, a temperature profile along each of the three lattice axes will be written to the .rkf file. The temperature at a given profile point is calculated as the total temperature of all atoms inside the corresponding slice of the simulation box, time-averaged over all MD steps since the previous snapshot. By default, no profile is generated.
WriteBonds (BoolType | BoolKey) – Write detected bonds to the .rkf file.
WriteCharges (BoolType | BoolKey) – Write current atomic point charges (if available) to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze charges.
WriteCoordinates (BoolType | BoolKey) – Write atomic coordinates to the .rkf file.
WriteEngineGradients (BoolType | BoolKey) – Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.
WriteMolecules (BoolType | BoolKey) – Write the results of molecule analysis to the .rkf file.
WriteVelocities (BoolType | BoolKey) – Write velocities to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze the velocities.
- class _Preoptimization[source]¶
If this block is enabled geometries will be preoptimized. After preoptimization the high energy conformers will be discarded, and then from the remaining set the unoptimized geometries will be optimized at higher level. This is to prevent the preoptimizer from collapsing different conformers into a single false minimum. As a result, preoptimization is only useful if MaxEnergy is chosen low.
- Variables:
Enable (BoolType | BoolKey) – Perform preoptimization at a low level of accuracy.
PreoptFactor (int | IntKey) – This factor is multiplied with MaxEnergy, to determine which high energy conformers can be discarded after preoptimization.
Engine (EngineBlock) – The engine specifics to be used for preoptimization.
- class _RDKitETKDG[source]¶
Settings for the call to RDKits ETKDG conformer generator tool.
- Variables:
BestRMSDThreshold (float | FloatKey) – After ETKDG conformer generation by RDKit, RDKit can be used to remove duplicates via the BestRMS algorithm. This filter does exactly the same as the RMSD equivalence detector in the Equivalence block.
ConstrainedAtoms (Iterable[int] | IntListKey) – The indices of the atoms to constrain during ETKDG conformer generation. The atom numbering starts at zero.
Forcefield (Literal["None", "UFF", "MMFF"]) – The name of the RDKit forcefield to use for geometry optimization at the end of ETKDG conformer generation (by default no geometry optimization is performed). Using the RDKit internal optimization may make the subsequent geometry optimizations with AMS faster.
Parallel (BoolType | BoolKey) – Experimental: Parallelize the RDKit generation step by calling the RDKit conformer generation method in parallel from multiple processes.
RMSDThreshold (float | FloatKey) – Root Mean Square deviation threshold for removing similar/equivalent conformations during the RDKit ETKDG procedure. By default there is no pruning (value: -1).
UseExpTorsionAnglePrefs (str | StringKey) – Impose experimental torsion angle preferences in RDKit ETKDG conformer generation. By default the RDKit version determines whether or not to switch this on.
- class _Filter[source]¶
Options for the conformer filtering.
- Variables:
MaxEnergy (float | FloatKey) – Threshold for filtering out high-energy conformers. If the relative energy of a conformer with respect to the lowest conformer is larger than this value, the conformer will be discarded.
RemoveNonMinima (BoolType | BoolKey) – For the final set of conformers, explicitly check that the geometry corresponds to a local minimum, and remove it if it does not. Note: this will run a PES point characterization, which can be computationally expensive!
- class _Generator[source]¶
Options for the conformer generator.
- Variables:
AdjustInputBonds (BoolType | BoolKey) – If geometry optimization of the initial conformer results in bond changes, adjust the reference connectivity. If the changes are too severe, the calculation will stop.
MaxEnergy (float | FloatKey) – Threshold for filtering out high-energy conformers. If the relative energy of a conformer with respect to the lowest conformer is larger than this value, the conformer will be discarded.
Method (Literal["RDKit", "CREST", "METADYNAMICS", "ANNEALING", "TORSION"]) –
Method used to generate the conformers.
The RDKit generator is based on random distance matrix method. This is the recommended (and default) method.
The CREST Generator uses a multi-step workflow with meta-dynamics simulations to explore the conformers space of a molecule. This can be a powerful conformer search method, but it is generally computationally expensive compared to the RDKit generator.
The ANNEALING generator performs a simulated annealing simulation to explore conformer space.
RNGSeed (int | IntKey) – Initial guesses for conformers can be randomly generated by RDKit, using the ETKDG algorithm. For reproducibility, a random number seed can be provided here.
Verbose (BoolType | BoolKey) – If set to True, print additional info about conformer equivalence to standard output.
ANNEALING (Conformers._Generator._ANNEALING) – Options for the annealing generator. This generator creates conformers by performing a simulated annealing simulation.
CREST (Conformers._Generator._CREST) – Options for the CREST generator. The CREST generator performs a set of metadynamics simulations (using the METADYNAMICS generator), then a set of MD simulations (using the MD expander), and finally it does a combinatorial expansion of the generated conformers using the GC expander. This sequence is repeated in an iterative fashion until the lowest energy conformer no longer changes.
METADYNAMICS (Conformers._Generator._METADYNAMICS) – Produces conformers by running a set of CREST-RMSD metadynamics simulations with different biases, extracting snapshots, and optimizing those.
Preoptimization (Conformers._Generator._Preoptimization) – If this block is enabled geometries will be preoptimized. After preoptimization the high energy conformers will be discarded, and then from the remaining set the unoptimized geometries will be optimized at higher level. This is to prevent the preoptimizer from collapsing different conformers into a single false minimum. As a result, preoptimization is only useful if MaxEnergy is chosen low.
RDKit (Conformers._Generator._RDKit) – Options for the RDKit generator. This generator produces initial guesses for conformers using the RDKit ETKDG method, followed by AMS geometry optimizations.
RDKitETKDG (Conformers._Generator._RDKitETKDG) – Settings for the call to RDKits ETKDG conformer generator tool.
TORSION (Conformers._Generator._TORSION) – Options for the TorsionGenerator, which generates geometries by enumerative rotation around rotatable bonds. This is the slowest of all generator, and quickly becomes infeasible for large systems. Currently does not work for systems with interconnected rings.
- class _ANNEALING[source]¶
Options for the annealing generator. This generator creates conformers by performing a simulated annealing simulation.
- Variables:
Blocksize (int | IntKey) – The spacing between the number of frames stored on the MD trajectory file, that will be used to generate conformers.
Temperatures (Iterable[float] | FloatListKey) – The minimum and maximum temperature of the annealing simulation. The simulation will start at the highest temperature, and cool down to the lowest.
UseShake (BoolType | BoolKey) – Constrain all -H bonds with shake. If turned on, the MD timestep is automatically increased.
MolecularDynamics (Conformers._Generator._ANNEALING._MolecularDynamics) – Configures molecular dynamics (with the velocity-Verlet algorithm) with and without thermostats. This block allows to specify the details of the molecular dynamics calculation. Default values will be ignored.
- class _MolecularDynamics[source]¶
Configures molecular dynamics (with the velocity-Verlet algorithm) with and without thermostats. This block allows to specify the details of the molecular dynamics calculation. Default values will be ignored.
- Variables:
NSteps (int | IntKey) – The number of steps to be taken in the MD simulation.
Restart (str | Path | StringKey) – The path to the ams.rkf file from which to restart the simulation.
Checkpoint (Conformers._Generator._ANNEALING._MolecularDynamics._Checkpoint) – Sets the frequency for storing the entire MD state necessary for restarting the calculation.
InitialVelocities (Conformers._Generator._ANNEALING._MolecularDynamics._InitialVelocities) – Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
Preserve (Conformers._Generator._ANNEALING._MolecularDynamics._Preserve) – Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.
Print (Conformers._Generator._ANNEALING._MolecularDynamics._Print) – This block controls the printing of additional information to stdout.
Shake (Conformers._Generator._ANNEALING._MolecularDynamics._Shake) – Parameters of the Shake/Rattle algorithm.
Thermostat (Conformers._Generator._ANNEALING._MolecularDynamics._Thermostat) – This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’s behavior.
Trajectory (Conformers._Generator._ANNEALING._MolecularDynamics._Trajectory) – Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- class _Checkpoint[source]¶
Sets the frequency for storing the entire MD state necessary for restarting the calculation.
- Variables:
Frequency (int | IntKey) – Write the MD state to the Molecule and MDResults sections on ams.rkf once every N steps. Setting this to zero disables checkpointing during the simulation, but one checkpoint at the very end of the simulation will always be written.
WriteProperties (BoolType | BoolKey) –
Honor top-level Properties input block when writing engine results files.
DEPRECATED: This input option will be removed in AMS2026 and will be considered always enabled. If you rely on it being disabled, please contact support@scm.com.
- class _InitialVelocities[source]¶
Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- Variables:
File (str | Path | StringKey) – AMS RKF file containing the initial velocities.
RandomVelocitiesMethod (Literal["Exact", "Boltzmann", "Gromacs"]) –
Specifies how are random velocities generated. Three methods are available.
Exact: Velocities are scaled to exactly match set random velocities temperature.
Boltzmann: Velocities are not scaled and sample Maxwell-Boltzmann distribution. However, the distribution is not corrected for constraints.
Gromacs: Velocities are scaled to match set random velocities temperature, but removal of net momentum is performed only after the scaling. Resulting kinetic energy is lower based on how much net momentum the system had.
Temperature (float | FloatKey) –
Sets the temperature for the Maxwell-Boltzmann distribution when the type of the initial velocities is set to random, in which case specifying this key is mandatory.
AMSinput will use the first temperature of the first thermostat as default.
Type (Literal["Zero", "Random", "FromFile", "Input"]) –
Specifies the initial velocities to assign to the atoms. Three methods to assign velocities are available.
Zero: All atom are at rest at the beginning of the calculation.
Random: Initial atom velocities follow a Maxwell-Boltzmann distribution for the temperature given by the [MolecularDynamics%InitialVelocities%Temperature] keyword.
FromFile: Load the velocities from a previous ams result file.
Input: Atom’s velocities are set to the values specified in the [MolecularDynamics%InitialVelocities%Values] block, which can be accessed via the Expert AMS panel in AMSinput.
Values (str | Sequence[str] | FreeBlock) – This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.
- class _Values[source]¶
This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.
- class _Preserve[source]¶
Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.
- Variables:
AngularMomentum (BoolType | BoolKey) – Remove overall angular momentum of the system. This option is ignored for 2D and 3D-periodic systems, and disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).
CenterOfMass (BoolType | BoolKey) – Translate the system to keep its center of mass at the coordinate origin. This option is not very useful for 3D-periodic systems.
Momentum (BoolType | BoolKey) – Remove overall (linear) momentum of the system. This is disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).
- class _Shake[source]¶
Parameters of the Shake/Rattle algorithm.
- Variables:
Constraint description in one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3
The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 and the angle between them.
The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then all bonds between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. The distance, if present, must be in Angstrom. If it is omitted then the bond length from the initial geometry is used.
Important: only the bonds present in the system at certain points of the simulation (at the start or right after adding/removing atoms) can be constrained, which means that the bonds may need to be specified in the System block.
Warning: the triangles constraint should be used with care because each constrained bond or angle means removing one degree of freedom from the dynamics. When there are too many constraints (for example, “All triangles H C H” in methane) some of them may be linearly dependent, which will lead to an error in the temperature computation.
Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H
ConvergeR2 (float | FloatKey) – Convergence criterion on the max squared difference, in atomic units.
ConvergeRV (float | FloatKey) – Convergence criterion on the orthogonality of the constraint and the relative atomic velocity, in atomic units.
ShakeInitialCoordinates (BoolType | BoolKey) – Apply constraints before computing the first energy and gradients.
- class _Thermostat[source]¶
This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’s behavior.
- Variables:
BerendsenApply (Literal["Local", "Global"]) –
Select how to apply the scaling correction for the Berendsen thermostat:
per-atom-velocity (Local)
on the molecular system as a whole (Global).
ChainLength (int | IntKey) – Number of individual thermostats forming the NHC thermostat
Duration (Iterable[int] | IntListKey) – Specifies how many steps should a transition from a particular temperature to the next one in sequence take.
ExcludedDirection (Literal["None", "X", "Y", "Z"]) – Exclude a component of the velocities from rescaling by the thermostat. For example in NEMD simulations, when a shear force/velocity is applied in the x direction, the x-direction is often excluded from thermostatting. This currently only works for the Nose-Hoover thermostat.
Friction (float | FloatKey) – Friction coefficient used in langevin dynamics
Region (str | StringKey) – The identifier of the region to thermostat. The default * applies the thermostat to the entire system. The value can by a plain region name, or a region expression, e.g. *-myregion to thermostat all atoms that are not in myregion, or regionA+regionB to thermostat the union of the ‘regionA’ and ‘regionB’. Note that if multiple thermostats are used, their regions may not overlap.
ScaleFrequency (int | IntKey) –
Optional parameter used only by the Scale thermostat.
If specified, the thermostat will be applied every N steps, using that step’s ensemble temperature and the specified thermostat temperature to compute the scaling factor.
If not specified, the thermostat will be applied at every step, using the mean temperature of the ensemble and the specified thermostat temperature to compute the scaling factor.
Tau (float | FloatKey) – The time constant of the thermostat.
Temperature (Iterable[float] | FloatListKey) –
The target temperature of the thermostat.
You can specify multiple temperatures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one T to the next T (using a linear ramp). For NHC thermostat, the temperature may not be zero.
Type (Literal["None", "Scale", "Berendsen", "NHC", "Langevin"]) – Selects the type of the thermostat.
- class _Trajectory[source]¶
Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- Variables:
EngineResultsFreq (int | IntKey) – Write MDStep*.rkf files with engine-specific results once every N steps. Setting this to zero disables writing engine results files except for one file at the end of the simulation. If unset or negative, defaults to the value of Checkpoint%Frequency.
ExitConditionFreq (int | IntKey) – Check the exit conditions every N steps. By default this is done every SamplingFreq steps.
PrintFreq (int | IntKey) – Print current thermodynamic properties to the output every N steps. By default this is done every SamplingFreq steps.
SamplingFreq (int | IntKey) – Write the molecular geometry (and possibly other properties) to the ams.rkf file once every N steps.
TProfileGridPoints (int | IntKey) – Number of points in the temperature profile. If TProfileGridPoints > 0, a temperature profile along each of the three lattice axes will be written to the .rkf file. The temperature at a given profile point is calculated as the total temperature of all atoms inside the corresponding slice of the simulation box, time-averaged over all MD steps since the previous snapshot. By default, no profile is generated.
WriteBonds (BoolType | BoolKey) – Write detected bonds to the .rkf file.
WriteCharges (BoolType | BoolKey) – Write current atomic point charges (if available) to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze charges.
WriteCoordinates (BoolType | BoolKey) – Write atomic coordinates to the .rkf file.
WriteEngineGradients (BoolType | BoolKey) – Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.
WriteMolecules (BoolType | BoolKey) – Write the results of molecule analysis to the .rkf file.
WriteVelocities (BoolType | BoolKey) – Write velocities to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze the velocities.
- class _CREST[source]¶
Options for the CREST generator. The CREST generator performs a set of metadynamics simulations (using the METADYNAMICS generator), then a set of MD simulations (using the MD expander), and finally it does a combinatorial expansion of the generated conformers using the GC expander. This sequence is repeated in an iterative fashion until the lowest energy conformer no longer changes.
- Variables:
ConvergenceQualityCrude (Literal["Normal", "Good", "VeryGood", "Excellent", "None"]) – The tightness of the convergence of the crude geometry pre-optimizations. If set to none it will be selected two levels below ConvergenceQuality.
ConvergenceQualityTight (Literal["Normal", "Good", "VeryGood", "Excellent", "None"]) – The tightness of the convergence of the final geometry optimizations. If set to none it will be selected the same as ConvergenceQuality.
GCStep (BoolType | BoolKey) – Wether or not to include the combinatorial expansion of the conformers using the GC Generator. For big systems this step can be very time consuming. By default it is set to True.
NCycles (int | IntKey) – The maximum number of CREST cycles (by default the number is 10). If the lowest conformer energy converges before then, Crest exits.
UseShake (BoolType | BoolKey) – Wether or not SHAKE should be turned on in the MD and Metadynamics simulations. If this is turned on, the MD timestep is automatically increased (from 2 to 5 fs).
- class _METADYNAMICS[source]¶
Produces conformers by running a set of CREST-RMSD metadynamics simulations with different biases, extracting snapshots, and optimizing those.
- Variables:
Blocksize (int | IntKey) – The interval between the trajectory snapshots written to file that are extracted and optimized. By default all written snapshots are extracted.
ConvergenceQualityCrude (Literal["normal", "good", "verygood", "excellent", "none"]) – The tightness of the convergence of the crude geometry pre-optimizations. If set to none it will be selected two levels below ConvergenceQuality.
MaxHeight (float | FloatKey) – The maximum Gaussian height used in a metadynamics simulation.
MaxWidth (float | FloatKey) – The maximum Gaussian width used in a metadynamics simulation.
MinHeight (float | FloatKey) – The minimum Gaussian height used in a metadynamics simulation.
NCycles (int | IntKey) – The maximum number of cycles of metadynamics simulations. The generator stops when either this number is reached, or the conformer set is stable.
NWidthsHeights (Iterable[int] | IntListKey) – The number of different Gaussian widths and heights respectively used in the metadynamics simulations. By default 4 different widths are used and 3 different heights, resulting in 12 different metadynamics simulations.
Restartdir (str | StringKey) – A PLAMS folder containing the results from a previous conformers generation using the METADYNAMICS generator.
SimulationSuccessFraction (float | FloatKey) – The fraction of planned metadynamics steps that has to have succeeded in order for the metadynamics iteration to be considered a success.
UseShake (BoolType | BoolKey) – Constrain all -H bonds with shake. If turned on, the MD timestep is automatically increased.
UseXtb (BoolType | BoolKey) – Use Grimmes xTB code to perform the MD simulations instead of AMS
WidthIncrement (float | FloatKey) – The increment between Gaussian widths used in subsequent metadynamics simulations.
AdditionalGaussians (Conformers._Generator._METADYNAMICS._AdditionalGaussians) – An additional set of Gaussian widths and heights, each representing the Gaussians of a single additional metadynamics simulation. By default, if nothing is provided, then two Gaussians are used: ([(width:0.1 Angstrom, height:0.001 Hartree), (width:0.8 Angstrom, height:0.005 Hartree)])
MolecularDynamics (Conformers._Generator._METADYNAMICS._MolecularDynamics) – Configures molecular dynamics (with the velocity-Verlet algorithm) with and without thermostats. This block allows to specify the details of the molecular dynamics calculation. Default values will be ignored.
- class _AdditionalGaussians[source]¶
An additional set of Gaussian widths and heights, each representing the Gaussians of a single additional metadynamics simulation. By default, if nothing is provided, then two Gaussians are used: ([(width:0.1 Angstrom, height:0.001 Hartree), (width:0.8 Angstrom, height:0.005 Hartree)])
- class _MolecularDynamics[source]¶
Configures molecular dynamics (with the velocity-Verlet algorithm) with and without thermostats. This block allows to specify the details of the molecular dynamics calculation. Default values will be ignored.
- Variables:
NSteps (int | IntKey) – The number of steps to be taken in the MD simulation.
Restart (str | Path | StringKey) – The path to the ams.rkf file from which to restart the simulation.
Checkpoint (Conformers._Generator._METADYNAMICS._MolecularDynamics._Checkpoint) – Sets the frequency for storing the entire MD state necessary for restarting the calculation.
InitialVelocities (Conformers._Generator._METADYNAMICS._MolecularDynamics._InitialVelocities) – Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
Preserve (Conformers._Generator._METADYNAMICS._MolecularDynamics._Preserve) – Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.
Print (Conformers._Generator._METADYNAMICS._MolecularDynamics._Print) – This block controls the printing of additional information to stdout.
Shake (Conformers._Generator._METADYNAMICS._MolecularDynamics._Shake) – Parameters of the Shake/Rattle algorithm.
Thermostat (Conformers._Generator._METADYNAMICS._MolecularDynamics._Thermostat) – This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’s behavior.
Trajectory (Conformers._Generator._METADYNAMICS._MolecularDynamics._Trajectory) – Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- class _Checkpoint[source]¶
Sets the frequency for storing the entire MD state necessary for restarting the calculation.
- Variables:
Frequency (int | IntKey) – Write the MD state to the Molecule and MDResults sections on ams.rkf once every N steps. Setting this to zero disables checkpointing during the simulation, but one checkpoint at the very end of the simulation will always be written.
WriteProperties (BoolType | BoolKey) –
Honor top-level Properties input block when writing engine results files.
DEPRECATED: This input option will be removed in AMS2026 and will be considered always enabled. If you rely on it being disabled, please contact support@scm.com.
- class _InitialVelocities[source]¶
Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- Variables:
File (str | Path | StringKey) – AMS RKF file containing the initial velocities.
RandomVelocitiesMethod (Literal["Exact", "Boltzmann", "Gromacs"]) –
Specifies how are random velocities generated. Three methods are available.
Exact: Velocities are scaled to exactly match set random velocities temperature.
Boltzmann: Velocities are not scaled and sample Maxwell-Boltzmann distribution. However, the distribution is not corrected for constraints.
Gromacs: Velocities are scaled to match set random velocities temperature, but removal of net momentum is performed only after the scaling. Resulting kinetic energy is lower based on how much net momentum the system had.
Temperature (float | FloatKey) –
Sets the temperature for the Maxwell-Boltzmann distribution when the type of the initial velocities is set to random, in which case specifying this key is mandatory.
AMSinput will use the first temperature of the first thermostat as default.
Type (Literal["Zero", "Random", "FromFile", "Input"]) –
Specifies the initial velocities to assign to the atoms. Three methods to assign velocities are available.
Zero: All atom are at rest at the beginning of the calculation.
Random: Initial atom velocities follow a Maxwell-Boltzmann distribution for the temperature given by the [MolecularDynamics%InitialVelocities%Temperature] keyword.
FromFile: Load the velocities from a previous ams result file.
Input: Atom’s velocities are set to the values specified in the [MolecularDynamics%InitialVelocities%Values] block, which can be accessed via the Expert AMS panel in AMSinput.
Values (str | Sequence[str] | FreeBlock) – This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.
- class _Values[source]¶
This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.
- class _Preserve[source]¶
Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.
- Variables:
AngularMomentum (BoolType | BoolKey) – Remove overall angular momentum of the system. This option is ignored for 2D and 3D-periodic systems, and disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).
CenterOfMass (BoolType | BoolKey) – Translate the system to keep its center of mass at the coordinate origin. This option is not very useful for 3D-periodic systems.
Momentum (BoolType | BoolKey) – Remove overall (linear) momentum of the system. This is disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).
- class _Shake[source]¶
Parameters of the Shake/Rattle algorithm.
- Variables:
Constraint description in one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3
The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 and the angle between them.
The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then all bonds between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. The distance, if present, must be in Angstrom. If it is omitted then the bond length from the initial geometry is used.
Important: only the bonds present in the system at certain points of the simulation (at the start or right after adding/removing atoms) can be constrained, which means that the bonds may need to be specified in the System block.
Warning: the triangles constraint should be used with care because each constrained bond or angle means removing one degree of freedom from the dynamics. When there are too many constraints (for example, “All triangles H C H” in methane) some of them may be linearly dependent, which will lead to an error in the temperature computation.
Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H
ConvergeR2 (float | FloatKey) – Convergence criterion on the max squared difference, in atomic units.
ConvergeRV (float | FloatKey) – Convergence criterion on the orthogonality of the constraint and the relative atomic velocity, in atomic units.
ShakeInitialCoordinates (BoolType | BoolKey) – Apply constraints before computing the first energy and gradients.
- class _Thermostat[source]¶
This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’s behavior.
- Variables:
BerendsenApply (Literal["Local", "Global"]) –
Select how to apply the scaling correction for the Berendsen thermostat:
per-atom-velocity (Local)
on the molecular system as a whole (Global).
ChainLength (int | IntKey) – Number of individual thermostats forming the NHC thermostat
Duration (Iterable[int] | IntListKey) – Specifies how many steps should a transition from a particular temperature to the next one in sequence take.
ExcludedDirection (Literal["None", "X", "Y", "Z"]) – Exclude a component of the velocities from rescaling by the thermostat. For example in NEMD simulations, when a shear force/velocity is applied in the x direction, the x-direction is often excluded from thermostatting. This currently only works for the Nose-Hoover thermostat.
Friction (float | FloatKey) – Friction coefficient used in langevin dynamics
Region (str | StringKey) – The identifier of the region to thermostat. The default * applies the thermostat to the entire system. The value can by a plain region name, or a region expression, e.g. *-myregion to thermostat all atoms that are not in myregion, or regionA+regionB to thermostat the union of the ‘regionA’ and ‘regionB’. Note that if multiple thermostats are used, their regions may not overlap.
ScaleFrequency (int | IntKey) –
Optional parameter used only by the Scale thermostat.
If specified, the thermostat will be applied every N steps, using that step’s ensemble temperature and the specified thermostat temperature to compute the scaling factor.
If not specified, the thermostat will be applied at every step, using the mean temperature of the ensemble and the specified thermostat temperature to compute the scaling factor.
Tau (float | FloatKey) – The time constant of the thermostat.
Temperature (Iterable[float] | FloatListKey) –
The target temperature of the thermostat.
You can specify multiple temperatures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one T to the next T (using a linear ramp). For NHC thermostat, the temperature may not be zero.
Type (Literal["None", "Scale", "Berendsen", "NHC", "Langevin"]) – Selects the type of the thermostat.
- class _Trajectory[source]¶
Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- Variables:
EngineResultsFreq (int | IntKey) – Write MDStep*.rkf files with engine-specific results once every N steps. Setting this to zero disables writing engine results files except for one file at the end of the simulation. If unset or negative, defaults to the value of Checkpoint%Frequency.
ExitConditionFreq (int | IntKey) – Check the exit conditions every N steps. By default this is done every SamplingFreq steps.
PrintFreq (int | IntKey) – Print current thermodynamic properties to the output every N steps. By default this is done every SamplingFreq steps.
SamplingFreq (int | IntKey) – Write the molecular geometry (and possibly other properties) to the ams.rkf file once every N steps.
TProfileGridPoints (int | IntKey) – Number of points in the temperature profile. If TProfileGridPoints > 0, a temperature profile along each of the three lattice axes will be written to the .rkf file. The temperature at a given profile point is calculated as the total temperature of all atoms inside the corresponding slice of the simulation box, time-averaged over all MD steps since the previous snapshot. By default, no profile is generated.
WriteBonds (BoolType | BoolKey) – Write detected bonds to the .rkf file.
WriteCharges (BoolType | BoolKey) – Write current atomic point charges (if available) to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze charges.
WriteCoordinates (BoolType | BoolKey) – Write atomic coordinates to the .rkf file.
WriteEngineGradients (BoolType | BoolKey) – Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.
WriteMolecules (BoolType | BoolKey) – Write the results of molecule analysis to the .rkf file.
WriteVelocities (BoolType | BoolKey) – Write velocities to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze the velocities.
- class _Preoptimization[source]¶
If this block is enabled geometries will be preoptimized. After preoptimization the high energy conformers will be discarded, and then from the remaining set the unoptimized geometries will be optimized at higher level. This is to prevent the preoptimizer from collapsing different conformers into a single false minimum. As a result, preoptimization is only useful if MaxEnergy is chosen low.
- Variables:
Enable (BoolType | BoolKey) – Perform preoptimization at a low level of accuracy.
PreoptFactor (int | IntKey) – This factor is multiplied with MaxEnergy, to determine which high energy conformers can be discarded after preoptimization.
Engine (EngineBlock) – The engine specifics to be used for preoptimization.
- class _RDKit[source]¶
Options for the RDKit generator. This generator produces initial guesses for conformers using the RDKit ETKDG method, followed by AMS geometry optimizations.
- Variables:
InitialNConformers (int | IntKey) – Number of geometries initially created by RDKit, before AMS geometry optimization and filtering. If not set, the number will be automatically set, based on the number of rotational bonds.
MaxConfs (int | IntKey) – If InitialNConformers is not set, then the number of conformers will be automatically set, with a maximum of MaxConfs.
MinConfs (int | IntKey) – If InitialNConformers is not set, then the number of conformers will be automatically set, with a minimum of MinConfs.
NconfsEstimationFactor (int | IntKey) – If InitialNConformers is not set, then the number of conformers will be automatically set based on the number of rotational bonds. The resulting number is then multiplied by this factor (default: 100), to ensure that enough conformers will be created.
Restartdir (str | StringKey) – A PLAMS folder containing the results from a previous conformers generation using this same generator. Currently only used to reread the initial conformers created by RDKit.
Restartfilename (str | StringKey) – The name of the file containing geometries generated by RDKits ETKDG algorithm, in the Restartdir folder.
- class _RDKitETKDG[source]¶
Settings for the call to RDKits ETKDG conformer generator tool.
- Variables:
BestRMSDThreshold (float | FloatKey) – After ETKDG conformer generation by RDKit, RDKit can be used to remove duplicates via the BestRMS algorithm. This filter does exactly the same as the RMSD equivalence detector in the Equivalence block.
ConstrainedAtoms (Iterable[int] | IntListKey) – The indices of the atoms to constrain during ETKDG conformer generation.
Forcefield (Literal["None", "UFF", "MMFF"]) – The name of the RDKit forcefield to use for geometry optimization at the end of ETKDG conformer generation (by default no geometry optimization is performed). Using the RDKit internal optimization may make the subsequent geometry optimizations with AMS faster.
Parallel (BoolType | BoolKey) – Experimental: Parallelize the RDKit generation step by calling the RDKit conformer generation method in parallel from multiple processes.
RMSDThreshold (float | FloatKey) – Root Mean Square deviation threshold for removing similar/equivalent conformations during the RDKit ETKDG procedure. By default there is no pruning (value: -1).
UseExpTorsionAnglePrefs (str | StringKey) – Impose experimental torsion angle preferences in RDKit ETKDG conformer generation. By default the RDKit version determines whether or not to switch this on.
- class _TORSION[source]¶
Options for the TorsionGenerator, which generates geometries by enumerative rotation around rotatable bonds. This is the slowest of all generator, and quickly becomes infeasible for large systems. Currently does not work for systems with interconnected rings.
- Variables:
BondDistortionThreshold (float | FloatKey) – A factor multiplied by the original bondlength, used to check if a geometry is not too distorted. A new geometry is discarded if any of the bonds have become longer than this value times the original bond length.
Dtheta (float | FloatKey) – The angle over which the bonds are rotated, in order to create a new conformer.
TruncateRingtorsions (BoolType | BoolKey) – In producing conformers for rings, one can rotate over all the bonds in the ring, or one can save time by excluding the last three bonds in the ring, which share atoms with the first bonds in the ring. This should yield identical results, and by default this is done.
- class _GeometryOptimization[source]¶
Some options / details regarding the optimization procedure.
- Variables:
ConvergenceQuality (Literal["Normal", "Good", "VeryGood", "Excellent"]) – The tightness of the convergence of the geometry optimizations. Lower quality levels may lead to badly converged geometries being classified as distinct conformers.
Keep (Literal["None", "all"]) – Keep all the output files of the geometry optimizations. If set to ‘all’, must be used in combination with Output%KeepWorkDir.
MaxConvergenceTime (Literal["Default", "High"]) – The number of iterations for the geometry optimization, based on the number of atoms in the system. The default value is the general AMS value for geometry optimization. Often, for conformer generation, it needs to be set higher.
MaxOptimizations (int | IntKey) – Set a maximum to the number of geometries accepted for optimization at once, per AMSWorker (so should be multiplied by the number of cores used). If not set, the disc size requirements can become too large.
OptimizationMethod (Literal["Auto", "Quasi-Newton", "FIRE", "L-BFGS", "ConjugateGradients", "Dimer"]) –
Select the optimization algorithm employed for the geometry relaxation. Currently supported are:
the Hessian-based Quasi-Newton-type BFGS algorithm,
the fast inertial relaxation method (FIRE),
the limited-memory BFGS method,
and the conjugate gradients method. The default is Quasi-Newton, which gives the most reliable results for conformers. The Auto method leaves it to the AMS GeometryOptimization task to select a method.
UseAMSWorker (BoolType | BoolKey) – Whether the set of optimizations should be run via the AMSWorkerPool or via regular AMSJobs.
GeometryOptimization (Conformers._GeometryOptimization._GeometryOptimization) – Configures details of the geometry optimization and transition state searches.
WriteGeometries (Conformers._GeometryOptimization._WriteGeometries) – Determines if and where optimized geometries will be written to file during optimization. When the AMSWorker is used, then the write interval depends on MaxOptimizations. If enabled, must be used in combination with Output%KeepWorkDir.
- class _GeometryOptimization[source]¶
Configures details of the geometry optimization and transition state searches.
- Variables:
CalcPropertiesOnlyIfConverged (BoolType | BoolKey) – Compute the properties requested in the ‘Properties’ block, e.g. Frequencies or Phonons, only if the optimization (or transition state search) converged. If False, the properties will be computed even if the optimization did not converge.
CoordinateType (Literal["Auto", "Delocalized", "Cartesian"]) –
Select the type of coordinates in which to perform the optimization. ‘Auto’ automatically selects the most appropriate CoordinateType for a given Method.
If ‘Auto’ is selected, Delocalized coordinates will be used for the Quasi-Newton method, while Cartesian coordinates will be used for all other methods.
KeepIntermediateResults (BoolType | BoolKey) – Whether the full engine result files of all intermediate steps are stored on disk. By default only the last step is kept, and only if the geometry optimization converged. This can easily lead to huge amounts of data being stored on disk, but it can sometimes be convenient to closely monitor a tricky optimization, e.g. excited state optimizations going through conical intersections, etc. …
MaxIterations (int | IntKey) – The maximum number of geometry iterations allowed to converge to the desired structure.
MaxRestarts (int | IntKey) – If a geometry optimization of a system with no symmetry operators (or with explicitly disabled symmetry:
UseSymmetry False) and enabled PES point characterization converges to a transition state (or higher order saddle point), it can be restarted automatically after a small displacement along the imaginary vibrational mode. In case the restarted optimization again does not find a minimum, this can happen multiple times in succession. This keyword sets the maximum number of restarts. The default value is 0, so the automatic restarting is disabled by default.Method (Literal["Auto", "Quasi-Newton", "FIRE", "L-BFGS", "ConjugateGradients", "Dimer"]) –
Select the optimization algorithm employed for the geometry relaxation. Currently supported are:
the Hessian-based Quasi-Newton-type BFGS algorithm,
the fast inertial relaxation method (FIRE),
the limited-memory BFGS method,
and the conjugate gradients method. The default is to choose an appropriate method automatically based on the engine’s speed, the system size and the supported optimization options.
OptimizeLattice (BoolType | BoolKey) – Whether to also optimize the lattice for periodic structures. This is currently supported with the Quasi-Newton, FIRE, and L-BFGS optimizers.
PretendConverged (BoolType | BoolKey) – Normally a non-converged geometry optimization is considered an error. If this keyword is set to True, the optimizer will only produce a warning and still claim that the optimization is converged. (This is mostly useful for scripting applications, where one might want to consider non-converged optimizations still successful jobs.)
RestartDisplacement (float | FloatKey) – If a geometry optimization of a system with no symmetry operators (or with explicitly disabled symmetry:
UseSymmetry False) and enabled PES point characterization converges to a transition state (or higher order saddle point), it can be restarted automatically after a small displacement along the imaginary vibrational mode. This keywords sets the size of the displacement for the furthest moving atom.Convergence (Conformers._GeometryOptimization._GeometryOptimization._Convergence) – Convergence is monitored for up to 4 quantities: the energy change, the Cartesian gradients, the Cartesian step size, and for lattice optimizations the stress energy per atom. Convergence criteria can be specified separately for each of these items.
Dimer (Conformers._GeometryOptimization._GeometryOptimization._Dimer) – Options for the Dimer method for transition state search.
EngineAutomations (Conformers._GeometryOptimization._GeometryOptimization._EngineAutomations) – The optimizer can change some settings of the engine, based for instance on the error. The idea is to allow the engine to be a bit quicker at the start, and more accurate towards the end. Automations are always engine specific.
FIRE (Conformers._GeometryOptimization._GeometryOptimization._FIRE) – This block configures the details of the FIRE optimizer. The keywords name correspond the the symbols used in the article describing the method, see PRL 97, 170201 (2006).
HessianFree (Conformers._GeometryOptimization._GeometryOptimization._HessianFree) – Configures details of the Hessian-free (conjugate gradients or L-BFGS) geometry optimizer.
InitialHessian (Conformers._GeometryOptimization._GeometryOptimization._InitialHessian) – Options for initial model Hessian when optimizing systems with the Quasi-Newton method.
Quasi-Newton (Conformers._GeometryOptimization._GeometryOptimization._Quasi-Newton) – Configures details of the Quasi-Newton geometry optimizer.
- class _Convergence[source]¶
Convergence is monitored for up to 4 quantities: the energy change, the Cartesian gradients, the Cartesian step size, and for lattice optimizations the stress energy per atom. Convergence criteria can be specified separately for each of these items.
- Variables:
Energy (float | FloatKey) – The criterion for changes in the energy. The energy is considered converged when the change in energy is smaller than this threshold times the number of atoms.
Gradients (float | FloatKey) – Threshold for nuclear gradients.
Quality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent", "Custom"]) – A quick way to change convergence thresholds: ‘Good’ will reduce all thresholds by an order of magnitude from their default value. ‘VeryGood’ will tighten them by two orders of magnitude. ‘Basic’ and ‘VeryBasic’ will increase the thresholds by one or two orders of magnitude respectively.
Step (float | FloatKey) – The maximum Cartesian step allowed for a converged geometry.
StressEnergyPerAtom (float | FloatKey) – Threshold used when optimizing the lattice vectors. The stress is considered ‘converged’ when the maximum value of stress_tensor * cell_volume / number_of_atoms is smaller than this threshold (for 2D and 1D systems, the cell_volume is replaced by the cell_area and cell_length respectively).
- class _Dimer[source]¶
Options for the Dimer method for transition state search.
- Variables:
AngleThreshold (float | FloatKey) – The rotation is considered converged when the the rotation angle falls below the specified threshold.
DimerDelta (float | FloatKey) – Euclidian distance between the midpoint and the endpoint.
ExtrapolateForces (BoolType | BoolKey) – Set to false to call engine to calculate forces at the extrapolated rotation angle instead of extrapolating them.
LBFGSMaxVectors (int | IntKey) – Max number of vectors for the L-BFGS algorithm to save.
MaxRotationIterations (int | IntKey) – Maximum number of rotation iterations for a single translation step.
Region (str | StringKey) – Include only atoms of the specified region(s) in the rotations, which allows searching for a transition state involving selected atoms only.
RotationTrustRadius (float | FloatKey) – L-BFGS trust radius during rotation iterations.
TranslationTrustRadius (float | FloatKey) – L-BFGS trust radius during translation iterations.
- class _EngineAutomations[source]¶
The optimizer can change some settings of the engine, based for instance on the error. The idea is to allow the engine to be a bit quicker at the start, and more accurate towards the end. Automations are always engine specific.
- Variables:
Enabled (BoolType | BoolKey) – Whether or not automations are enabled at all.
Gradient (Conformers._GeometryOptimization._GeometryOptimization._EngineAutomations._Gradient) – A gradient-based automation.
Iteration (Conformers._GeometryOptimization._GeometryOptimization._EngineAutomations._Iteration) – Geometry step based automation.
- class _Gradient[source]¶
A gradient-based automation.
- Variables:
FinalValue (float | FloatKey) – This value will be used whenever the gradient is less than GradientLow
HighGradient (float | FloatKey) – Defines a large gradient. When the actual gradient is between GradientHigh and GradientLow a linear interpolation scheme is used for kT (on a log scale).
InitialValue (float | FloatKey) – This value will be used at the first geometry, and whenever the gradient is higher than GradientHigh
LowGradient (float | FloatKey) – Defines a small gradient, see GradientHigh
UseLogInterpolation (BoolType | BoolKey) – Whether to use interpolation on a log (y) scale or not
Variable (str | StringKey) – variable to be tweaked for the engine.
- class _Iteration[source]¶
Geometry step based automation.
- Variables:
FirstIteration (int | IntKey) – When the actual gradient is between the first and last iteration, a linear interpolation is used.
InitialValue (float | FloatKey) – This value will be used when the iteration number is smaller or equal to FirstIteration
LastIteration (int | IntKey) – Where the automation should reach the FinalValue
UseLogInterpolation (BoolType | BoolKey) – Whether to use interpolation on a log (y) scale or not
Variable (str | StringKey) – variable to be tweaked for the engine.
- class _FIRE[source]¶
This block configures the details of the FIRE optimizer. The keywords name correspond the the symbols used in the article describing the method, see PRL 97, 170201 (2006).
- Variables:
AllowOverallRotation (BoolType | BoolKey) – Whether or not the system is allowed to freely rotate during the optimization. This is relevant when optimizing structures in the presence of external fields.
AllowOverallTranslation (BoolType | BoolKey) – Whether or not the system is allowed to translate during the optimization. This is relevant when optimizing structures in the presence of external fields.
MapAtomsToUnitCell (BoolType | BoolKey) – Map the atoms to the central cell at each geometry step.
NMin (int | IntKey) – Number of steps after stopping before increasing the time step again.
atomMass (float | FloatKey) – Fictitious atomic mass used for all atoms. There is no reason to change this, as it just corresponds to using a different integration timestep.
dtMax (float | FloatKey) – Maximum time step used for the integration. For ReaxFF and APPLE&P, this value is reduced by 50%.
dtStart (float | FloatKey) – Initial time step for the integration.
fAlpha (float | FloatKey) – Reduction factor for the steering coefficient.
fDec (float | FloatKey) – Reduction factor for reducing the time step in case of uphill movement.
fInc (float | FloatKey) – Growth factor for the integration time step.
strainMass (float | FloatKey) – Fictitious relative mass of the lattice degrees of freedom. This controls the stiffness of the lattice degrees of freedom relative to the atomic degrees of freedom, with smaller values resulting in a more aggressive optimization of the lattice.
- class _HessianFree[source]¶
Configures details of the Hessian-free (conjugate gradients or L-BFGS) geometry optimizer.
- Variables:
Step (Conformers._GeometryOptimization._GeometryOptimization._HessianFree._Step) –
- class _Step[source]¶
- Variables:
MaxCartesianStep (float | FloatKey) – Limit on a single Cartesian component of the step.
MinRadius (float | FloatKey) – Minimum value for the trust radius.
TrialStep (float | FloatKey) – Length of the finite-difference step when determining curvature. Should be smaller than the step convergence criterion.
TrustRadius (float | FloatKey) – Initial value of the trust radius.
- class _InitialHessian[source]¶
Options for initial model Hessian when optimizing systems with the Quasi-Newton method.
- Variables:
File (str | Path | StringKey) – KF file containing the initial Hessian (or the results dir. containing it). This can be used to load a Hessian calculated in a previously with the [Properties%Hessian] keyword.
Type (Literal["Auto", "UnitMatrix", "Swart", "FromFile", "Calculate", "CalculateWithFastEngine"]) – Select the type of initial Hessian. Auto: let the program pick an initial model Hessian. UnitMatrix: simplest initial model Hessian, just a unit matrix in the optimization coordinates. Swart: model Hessian from M. Swart. FromFile: load the Hessian from the results of a previous calculation (see InitialHessian%File). Calculate: compute the initial Hessian (this may be computationally expensive and it is mostly recommended for TransitionStateSearch calculations). CalculateWithFastEngine: compute the initial Hessian with a faster engine.
- class _Quasi_Newton[source]¶
Configures details of the Quasi-Newton geometry optimizer.
- Variables:
EnforceConstraints (BoolType | BoolKey) – Whether to enforce constraints at each steps exactly or add them to the optimization space as Lagrange multipliers.
MaxGDIISVectors (int | IntKey) – Sets the maximum number of GDIIS vectors. Setting this to a number >0 enables the GDIIS method.
UpdateTSVectorEveryStep (BoolType | BoolKey) – Whether to update the TS reaction coordinate at each step with the current eigenvector.
Step (Conformers._GeometryOptimization._GeometryOptimization._Quasi-Newton._Step) –
- class _LoadSystem[source]¶
Block that controls reading the chemical system from a KF file instead of the [System] block.
- class _Output[source]¶
Options regarding the output and result files.
- Variables:
KeepWorkDir (BoolType | BoolKey) – Do not remove the working directories after the conformer generation is finished.
rkf (BoolType | BoolKey) – Save the final conformers in .rkf format. The file ‘conformers.rkf’ will be located in the results directory. You can visualize this file using the AMSMovie GUI module.
sdf (BoolType | BoolKey) – Save the final conformers in .sdf format. The file ‘conformers.sdf’ will be located in the results directory.
xyz (BoolType | BoolKey) – Save the final conformers in .xyz format. The file ‘conformers.xyz’ will be located in the results directory.
- class _Restraints[source]¶
The Restraints block allows to add soft constraints to the system. A restraint is a potential energy function (a spring) attached to a certain coordinate, for example, an interatomic distance, with its minimum at the specified optimal value. A restraint is defined using one or two parameters: the ForceConstant and, for some types, the F(Inf) value. The ForceConstant parameter corresponds to second derivative of the restraint potential energy d2V(x)/dx^2 for any x (harmonic restraints) or only at at x=0 (other restraints). Here, x is a deviation from the restraint’s optimal value.
- Variables:
Angle (str | StringKey) – Specify three atom indices i j k followed by an angle in degrees and, optionally, by the ForceConstant (default is 0.3 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the i-j-k angle at the given value. For periodic systems this restraint follows the minimum image convention.
DifDist (str | StringKey) – Specify four atom indices i j k l followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the difference R(ij)-R(kl) at the given value. For periodic systems this restraint follows the minimum image convention.
Dihedral (str | StringKey) – Specify four atom indices i j k l followed by an angle in degrees and, optionally, by the ForceConstant (default is 0.1 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the i-j-k-l dihedral angle at the given value. For periodic systems this restraint follows the minimum image convention.
Distance (str | StringKey) – Specify two atom indices followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the distance between the two specified atoms at the given value. For periodic systems this restraint follows the minimum image convention.
FInfinity (float | FloatKey) –
Specify the default asymptotic value for the restraint force for the Hyperbolic and Erf profiles, in Hartree/Bohr or Hartree/radian.
A per-restraint value can be specified after the profile type on the corresponding restraint line.
Profile (Literal["Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) –
Select the default type of restraint profile.
The harmonic profile is most suitable for geometry optimizations but may result is very large forces that can be problematic in molecular dynamic.
For MD simulations the Hyperbolic or Erf may be more suitable because the restraint force is bounded by a user-defined value.
A per-restraint profile type can be specified after the ForceConstant value on the corresponding restraint line.
SumDist (str | StringKey) – Specify four atom indices i j k l followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the sum R(ij)+R(kl) at the given value. For periodic systems this restraint follows the minimum image convention.
Units (Literal["Default", "MD"]) – Change units for energy, force and force constant values from the default (atomic units) to those often used in the MD community (based on kcal/mol and Angstrom). Units for the optimal distances are not affected and are always Angstrom.
- class _System[source]¶
Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- Variables:
AllowCloseAtoms (BoolType | BoolKey) – No longer functional. Just here for backwards compatibility.
Charge (float | FloatKey) – The system’s total charge in atomic units.
FractionalCoords (BoolType | BoolKey) – Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
GeometryFile (str | Path | StringKey) – Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds (BoolType | BoolKey) – Equivalent to ‘Modify%GuessBonds’. Please update input file to use ‘Modify’ block instead.
LatticeStrain (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%LatticeStrain’. Please update input file to use ‘Modify’ block instead.
MapAtomsToUnitCell (BoolType | BoolKey) – Equivalent to ‘Modify%MapAtomsToUnitCell’. Please update input file to use ‘Modify’ block instead.
PerturbCoordinates (float | FloatKey) – Equivalent to ‘Modify%PerturbCoordinates’. Please update input file to use ‘Modify’ block instead.
PerturbLattice (float | FloatKey) – Equivalent to ‘Modify%PerturbLattice’. Please update input file to use ‘Modify’ block instead.
ShiftCoordinates (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%Translate’, but in the unit of bohr by default. Please update input file to use ‘Modify’ block instead.
SuperCell (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCell’. Please update input file to use ‘Modify’ block instead.
SuperCellTrafo (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCellTrafo’. Please update input file to use ‘Modify’ block instead.
Symmetrize (BoolType | BoolKey) – Equivalent to ‘Modify%Symmetrize’. Please update input file to use ‘Modify’ block instead.
Atoms (str | Sequence[str] | FreeBlock) – The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders (str | Sequence[str] | FreeBlock) – Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
ElectrostaticEmbedding (Conformers._System._ElectrostaticEmbedding) – Container for electrostatic embedding options, which can be combined.
Lattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
Modify (Conformers._System._Modify) – Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- class _Atoms[source]¶
The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
- class _BondOrders[source]¶
Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
- class _ElectrostaticEmbedding[source]¶
Container for electrostatic embedding options, which can be combined.
- Variables:
ElectricField (Iterable[float] | FloatListKey) –
External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.
In atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 … e11 V/m.
Supported by the engines adf, band, dftb and mopac.
For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
MultipolePotential (Conformers._System._ElectrostaticEmbedding._MultipolePotential) – External point charges (and dipoles).
- class _MultipolePotential[source]¶
External point charges (and dipoles).
- Variables:
ChargeModel (Literal["Point", "Gaussian"]) – A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
ChargeWidth (float | FloatKey) – The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
Coordinates (str | Sequence[str] | FreeBlock) –
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Coordinates[source]¶
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Lattice[source]¶
Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
- class _Modify[source]¶
Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- Variables:
EnableAtomicProperties (Literal["gui", "adf", "band", "forcefield", "dftb", "reaxff", "qe"]) – Enables an atomic property group. This is only necessary if you want a group enabled, but no atom in the input is using any property from that group.
GuessBonds (BoolType | BoolKey) – Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.
LatticeStrain (Iterable[float] | FloatListKey) – Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
MapAtomsToUnitCell (Iterable[float] | FloatListKey) – For periodic systems the atoms will be moved to the central unit cell where all their fractional coordinates are in the range [start_range,start_range+1). No mapping will take place along non-periodic directions. If just a single number is given, it corresponds to start_range. If multiple numbers are given, they should match the number of lattice vectors and will be used as start ranges along the individual lattice vectors. If no number is given at all, the mapping will be done to the [-0.5:0.5) cell.
PerturbCoordinates (float | FloatKey) – Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
PerturbLattice (float | FloatKey) – Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
SuperCell (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
SuperCellTrafo (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
Symmetrize (BoolType | BoolKey) – Symmetrizes the atomic coordinates to machine precision and rototranslates the molecule to the AMS standard orientation. This allows optimal use of the system’s symmetry for calculations with the AMS driver and its engines.
Translate (Iterable[float] | FloatListKey) – Translate all atoms by a vector.
- class DENSF[source]¶
- Variables:
ADFFile (str | StringKey) – Path to the TAPE21 file from which densf reads the input data
COSMO (BoolType | BoolKey) –
Convert (BoolType | BoolKey) –
CubInput (str | StringKey) – If the CubInput keyword is present then the grid as specified in the file is used to calculate all requested quantities. Any volume data found in the cube file is also saved in the output file. NOTE: CUBINPUT option cannot be used with a pre-existing TAPE41 file because they both specify the grid, which may lead to a conflict.
CubOutput (str | StringKey) – Presence of the CubOutput keyword tells densf to save all computed quantities as cube files using file as filename prefix. The prefix can also contain a complete path including directories. For example, specifying the following in the densf input
DEBUGRISM (BoolType | BoolKey) –
DualDescriptor (BoolType | BoolKey) –
FOD (BoolType | BoolKey) –
InputFile (str | StringKey) – Path to the TAPE21 file from which densf reads the input data
OutputFile (str | StringKey) – Path to the (possibly existing) TAPE41 file. If the file exists, densf will read grid specifications from it ignoring GRID keyword in the input. Computed quantities are saved in the file overwriting existing data with the same name, if any
POLTDDFT (int | IntKey) – Frequency point for transition density
QP (BoolType | BoolKey) –
RISM (BoolType | BoolKey) –
Ridge (BoolType | BoolKey) –
SEDD (BoolType | BoolKey) –
TAPE16File (str | StringKey) – Path to the TAPE16 file from which densf reads the input data
VTKFile (str | StringKey) – Specifies path to a file in the format readable by VTK directly. This option exists primarily for better integration with AMS-GUI and the user should not specify it.
IrrepDensity (str | Sequence[str] | FreeBlock) – Select particular symmetry to compute the electron density for.
TransitionDensity (str | Sequence[str] | FreeBlock) – Select particular excitations to calculate the transition density for. Format: SS|ST SymLabel Index
Units (DENSF._Units) – Definitions of the units.
- class FCF[source]¶
- Variables:
Convergence (float | FloatKey) – Minimum fraction of the FC factors sum to be calculated
DeltaClass (float | FloatKey) – Minimum gain in FCF between classes to continue calculation
Lambda (float | FloatKey) – Optional. The minimum value of the electron-phonon coupling for a mode to be taken into account in the calculation. Together with the MODES option, this provides a way to significantly reduce the total number of Franck-Condon factors. As with the MODES option, always check if the results do not change too much.
Modes (Iterable[int] | IntListKey) – Optional. The first and last mode to be taken into account in the calculation. By default, all modes are taken into account. This option can be used to effectively specify and energy range for the Franck-Condon factors. When using this options, always check if the results (electron-phonon couplings, ground state to ground overlap integral, average sum of Franck-Condon factors, etc.) do not change too much.
NumericalQuality (Literal["0-0", "Basic", "Normal", "Good", "Excellent"]) – Set the quality of several technical aspects of an FC calculation, including details for the prescreening, the amount of computed integrals, the maximum integral class evaluated, as well as the convergence criteria.
Rotate (BoolType | BoolKey) – Recommended to be used. Rotate the geometries to maximize the overlap of the nuclear coordinates.
State1 (str | StringKey) – Filename of the result files of a numerical or analytical frequency calculation for the first (initial) state.
State2 (str | StringKey) – Filename of the result files of a numerical or analytical frequency calculation for the second (final) state.
States (str | StringKey) – The filenames of two results files of a numerical or analytical frequency calculation. The calculations must have been performed on the same molecule, i.e. the type, mass and order of occurrence of all the atoms (or fragments) has to be the same in both files.
Translate (BoolType | BoolKey) – Recommended to be used. Move the center of mass of both geometries to the origin.
Prescreening (FCF._Prescreening) – Optional. Controls the details of the FC factors prescreening algorithm
Printing (FCF._Printing) – Optional. Printing Options.
Spectrum (FCF._Spectrum) – Optional. Controls the details of the spectrum calculation
- class _Prescreening[source]¶
Optional. Controls the details of the FC factors prescreening algorithm
- Variables:
Class1 (int | IntKey) – Maximum quantum number for Class 1 FC integrals
Class2 (int | IntKey) – Maximum quantum number for Class 2 FC integrals
MaxClass (int | IntKey) – Maximum class of integrals to be computed
MaxFCI (int | IntKey) – Maximum number of FC integrals to be computed for each Class (in millions)
- class _Spectrum[source]¶
Optional. Controls the details of the spectrum calculation
- Variables:
HWHM (float | FloatKey) – Half-Width at Half-Maximum for the spectral lineshape function
LineShape (Literal["Stick", "Gaussian", "Lorentzian"]) – Type of lineshape function
SpcMax (float | FloatKey) – Maximum absolute energy difference between the states relative to the 0-0 transition
SpcMin (float | FloatKey) – Minimum absolute energy difference between the states relative to the 0-0 transition
Type (Literal["Absorption", "Emission"]) – Type of spectrum
- class Green[source]¶
- Variables:
DOS (str | StringKey) – Enables the calculation of the density of states. The string specifies the TAPE21 file containing the result of an ADF calculation of the extended molecule (performed with SYMMETRY NOSYM)
ETA (float | FloatKey) – The imaginary energy, or the distance from the real axis, in the calculation of the Green’s function. The value needs to be a small positive number to prevent singularities in the calculation.
Eps (str | StringKey) – mineps maxeps numeps: The energy range for which either the self-energy matrices or the DOS and transmission have to be calculated. The range consists of numeps (<=1) points running from mineps to maxeps inclusive.
SO (Iterable[float] | FloatListKey) –
Left (Green._Left) – Specify the left self-energies used in a calculation of the DOS and transmission. If a filename is specified in the header, the self-energy matrices are read from that file.
Right (Green._Right) – Specify the right self-energies used in a calculation of the DOS and transmission. If a filename is specified in the header, the self-energy matrices are read from that file.
Surface (Green._Surface) – Enables the calculation of the self-energy matrices. The filename in the header specifies the TAPE21 file resulting from an ADF calculation of the contacts
- class _Left[source]¶
Specify the left self-energies used in a calculation of the DOS and transmission. If a filename is specified in the header, the self-energy matrices are read from that file.
- class LFDFT[source]¶
- Variables:
ADFFile (str | StringKey) – Path to TAPE21 file from which lfdft reads data and to which lfdft writes data
BField (Iterable[float] | FloatListKey) – Include a finite magnetic Field. For MCD calculations include a magnetic field in the z-direction. The DegeneracyThreshold should be small to see the splitting of levels due to the magnetic field.
DEBUG (BoolType | BoolKey) – debug
DegeneracyThreshold (float | FloatKey) – Energy difference threshold to determine degenerate levels
MOIND (Iterable[int] | IntListKey) – The indices of the MOs that participate for shell 1.
MOIND1 (Iterable[int] | IntListKey) – The indices of the MOs that participate for shell 1.
MOIND2 (Iterable[int] | IntListKey) – The indices of the MOs that participate for shell 2.
MOIND3 (Iterable[int] | IntListKey) – The indices of the MOs that participate for shell 3.
MOIND4 (Iterable[int] | IntListKey) – The indices of the MOs that participate for shell 4.
NLVAL (Iterable[int] | IntListKey) – n and l value of shell 1.
NLVAL1 (Iterable[int] | IntListKey) – n and l value of shell 1.
NLVAL2 (Iterable[int] | IntListKey) – n and l value of shell 2.
NLVAL3 (Iterable[int] | IntListKey) – n and l value of shell 3.
NLVAL4 (Iterable[int] | IntListKey) – n and l value of shell 4.
SOC (Iterable[float] | FloatListKey) – Include Spin-Orbit coupling for the shells, scaling it with the specified factor(s).
SOCType (LFDFT._SOCType) – Choose the type of Spin-Orbit coupling calculation used for the shells.
- class _SOCType[source]¶
Choose the type of Spin-Orbit coupling calculation used for the shells.
- Variables:
Shell1 (Literal["ZORA", "Core"]) – Type of Spin-Orbit coupling for the first shell
Shell2 (Literal["ZORA", "Core"]) – Type of Spin-Orbit coupling for the second shell
Shell3 (Literal["ZORA", "Core"]) – Type of Spin-Orbit coupling for the third shell
Shell4 (Literal["ZORA", "Core"]) – Type of Spin-Orbit coupling for the fourth shell
- class NAO[source]¶
- Variables:
RunType (Literal["foo", "bar", "slakotable", "testblas", "testfunctionsetdotproduct", "testfunctionsetdotproduct2", "testlinalg", "testsyscalls", "testabstractmatrix"]) –
usesymmetry (BoolType | BoolKey) –
System (NAO._System) – Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
TestParameters (NAO._TestParameters) –
aimcriticalpoints (NAO._aimcriticalpoints) –
beckegridconfig (NAO._beckegridconfig) –
grid (NAO._grid) –
programmer (NAO._programmer) –
slakotableconfig (NAO._slakotableconfig) –
thresholds (NAO._thresholds) –
zlmfit (NAO._zlmfit) – Options for the density fitting scheme ‘ZlmFit’.
- class _System[source]¶
Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- Variables:
AllowCloseAtoms (BoolType | BoolKey) – No longer functional. Just here for backwards compatibility.
Charge (float | FloatKey) – The system’s total charge in atomic units.
FractionalCoords (BoolType | BoolKey) – Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
GeometryFile (str | Path | StringKey) – Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds (BoolType | BoolKey) – Equivalent to ‘Modify%GuessBonds’. Please update input file to use ‘Modify’ block instead.
LatticeStrain (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%LatticeStrain’. Please update input file to use ‘Modify’ block instead.
MapAtomsToUnitCell (BoolType | BoolKey) – Equivalent to ‘Modify%MapAtomsToUnitCell’. Please update input file to use ‘Modify’ block instead.
PerturbCoordinates (float | FloatKey) – Equivalent to ‘Modify%PerturbCoordinates’. Please update input file to use ‘Modify’ block instead.
PerturbLattice (float | FloatKey) – Equivalent to ‘Modify%PerturbLattice’. Please update input file to use ‘Modify’ block instead.
ShiftCoordinates (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%Translate’, but in the unit of bohr by default. Please update input file to use ‘Modify’ block instead.
SuperCell (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCell’. Please update input file to use ‘Modify’ block instead.
SuperCellTrafo (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCellTrafo’. Please update input file to use ‘Modify’ block instead.
Symmetrize (BoolType | BoolKey) – Equivalent to ‘Modify%Symmetrize’. Please update input file to use ‘Modify’ block instead.
Atoms (str | Sequence[str] | FreeBlock) – The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders (str | Sequence[str] | FreeBlock) – Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
ElectrostaticEmbedding (NAO._System._ElectrostaticEmbedding) – Container for electrostatic embedding options, which can be combined.
Lattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
Modify (NAO._System._Modify) – Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- class _Atoms[source]¶
The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
- class _BondOrders[source]¶
Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
- class _ElectrostaticEmbedding[source]¶
Container for electrostatic embedding options, which can be combined.
- Variables:
ElectricField (Iterable[float] | FloatListKey) –
External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.
In atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 … e11 V/m.
Supported by the engines adf, band, dftb and mopac.
For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
MultipolePotential (NAO._System._ElectrostaticEmbedding._MultipolePotential) – External point charges (and dipoles).
- class _MultipolePotential[source]¶
External point charges (and dipoles).
- Variables:
ChargeModel (Literal["Point", "Gaussian"]) – A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
ChargeWidth (float | FloatKey) – The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
Coordinates (str | Sequence[str] | FreeBlock) –
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Coordinates[source]¶
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Lattice[source]¶
Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
- class _Modify[source]¶
Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- Variables:
EnableAtomicProperties (Literal["gui", "adf", "band", "forcefield", "dftb", "reaxff", "qe"]) – Enables an atomic property group. This is only necessary if you want a group enabled, but no atom in the input is using any property from that group.
GuessBonds (BoolType | BoolKey) – Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.
LatticeStrain (Iterable[float] | FloatListKey) – Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
MapAtomsToUnitCell (Iterable[float] | FloatListKey) – For periodic systems the atoms will be moved to the central unit cell where all their fractional coordinates are in the range [start_range,start_range+1). No mapping will take place along non-periodic directions. If just a single number is given, it corresponds to start_range. If multiple numbers are given, they should match the number of lattice vectors and will be used as start ranges along the individual lattice vectors. If no number is given at all, the mapping will be done to the [-0.5:0.5) cell.
PerturbCoordinates (float | FloatKey) – Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
PerturbLattice (float | FloatKey) – Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
SuperCell (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
SuperCellTrafo (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
Symmetrize (BoolType | BoolKey) – Symmetrizes the atomic coordinates to machine precision and rototranslates the molecule to the AMS standard orientation. This allows optimal use of the system’s symmetry for calculations with the AMS driver and its engines.
Translate (Iterable[float] | FloatListKey) – Translate all atoms by a vector.
- class _programmer[source]¶
- Variables:
UseSharedMemoryForSandwiching (BoolType | BoolKey) –
calcdipole (BoolType | BoolKey) –
dynamicblockiterator (BoolType | BoolKey) –
exactsharedarraylocking (BoolType | BoolKey) –
functionsetdotproductemploysym (BoolType | BoolKey) –
functionsetoverlapemploysym (BoolType | BoolKey) –
functionsetoverlaplockcolumn (BoolType | BoolKey) –
randomlypermuteblocks (BoolType | BoolKey) –
usenewtailroutines (BoolType | BoolKey) –
usesharedmemory (BoolType | BoolKey) –
- class _slakotableconfig[source]¶
- Variables:
debug (BoolType | BoolKey) –
grid (NAO._slakotableconfig._grid) –
repweights (NAO._slakotableconfig._repweights) –
- class NMR[source]¶
- Variables:
ADFFile (str | StringKey) – Path to TAPE21 file from which nmr reads data and to which nmr writes data
AllInOne (BoolType | BoolKey) – Tensor in one step
FakeSO (BoolType | BoolKey) –
Fractional (BoolType | BoolKey) –
HFAtomsPerPass (int | IntKey) – Memory usage option for old HF scheme
HFMaxMemory (int | IntKey) – Memory usage option for old HF scheme
NBO (BoolType | BoolKey) –
NoScale (BoolType | BoolKey) –
PNMRFile (str | StringKey) – Path to file that contains pNMR data
RecalculateTAPE10 (BoolType | BoolKey) –
Scaled (BoolType | BoolKey) –
TAPE10File (str | StringKey) – Path to the TAPE10 file from which nmr reads data
Temperature (float | FloatKey) – Temperature (Kelvin) for temperature dependent part shielding tensor.
Analysis (NMR._Analysis) – Block for analysis options.
NMR (NMR._NMR) – Main NMR options.
- class _Analysis[source]¶
Block for analysis options.
- Variables:
Components (BoolType | BoolKey) – The components keyword is optional and enables an analysis not only of the isotropic shielding but also of the diagonal Cartesian components of the tensor XX, YY, and ZZ). In order to analyze the principal shielding tensor components with canonical MOs you can calculate the shielding tensor first with the NMR code, rotate the molecule such that the principal axes system aligns with the Cartesian coordinate system, and then repeat the NMR calculation with the analysis features switched on.
FakeSO (BoolType | BoolKey) –
NoPrincipal (BoolType | BoolKey) – Do not transform to principal axes for analysis
Print (float | FloatKey) – The print keyword selects printout of contributions relative to the total diamagnetic, paramagnetic. For example in case of print 0.01 only contributions greater than 1% are printed. Set to zero to print ALL contributions.
ZSOAO2007 (BoolType | BoolKey) –
canonical (BoolType | BoolKey) – It enables an analysis of the shielding in terms of the canonical MOs.
nbo (BoolType | BoolKey) –
- class _NMR[source]¶
Main NMR options.
- Variables:
ADFGUI (BoolType | BoolKey) –
AllAtomsOfType (str | StringKey) – Space separated list of type of nuclei (like H, C, P) for which the NMR shielding should be calculated. In addition to Nuc or Atoms.
This key controls the MO analysis. Its value should be an integer, which then specifies that the first so many MOs are to be analyzed.
Default no Analysis.
The value of this analysis subkey in the block key NMR is somewhat limited. The separate ANALYSIS block key can give more analysis of the NMR chemical shielding.
Atoms (Iterable[int] | IntListKey) – This subkey ATOMS specifies for which nuclei the NMR shielding is calculated. Default all nuclei are calculated, i.e. as for omitting the subkeys ATOMS and NUC. The numbers refer to the input ordering in the ADF calculation. Use the subkey NUC to specify the nuclei according to the internal NMR numbers of the atoms.
Calc (str | StringKey) – The sub key Calc controls what is actually calculated. All: Implies all of the other options to this key. Para: The paramagnetic part, Dia: The diamagnetic part, FC: The Fermi-contact part in case of the Pauli Hamiltonian, SO: The Fermi-contact part in case of the ZORA Hamiltonian.
GFactors (BoolType | BoolKey) – Calculate g-factors
Nuc (Iterable[int] | IntListKey) – This subkey NUC specifies for which nuclei the NMR shielding is calculated. Default all nuclei are calculated, i.e. as for omitting the subkeys ATOMS and NUC. Else you may use this options by simply typing Nuc in the NMR block (without any further data); this means: for no nuclei at all. Alternatively you may type the index of the atom(s) you want to see analyzed. Default all nuclei are calculated, i.e. as for omitting this subkey. The numbers refer to the internal numbering of the nuclei as it appears somewhere early in the general ADF output. This internal numbering is also the internal NMR numbering, but it is not necessarily the same as the input ordering. Use the subkey ATOMS to specify the nuclei according to this input ordering in the ADF calculation. Note that the number of nuclei has a significant consequence for the total CPU time.
Out (str | StringKey) – Controls printed output. Options: All: All the other options, ISO: Isotropic shielding constants, Tens: Shielding tensors, Eig: Eigenvectors, U1: The U1 Matrix, F1: The first order change in the Fock matrix, S1: The first order change in the Overlap matrix, AOP: The paramagnetic AO matrix (= the matrix in the representation of elementary atomic basis functions), AOD: The diamagnetic AO matrix, AOF: The Fermi-contact AO matrix, Refs: Literature references, INFO: General information.
SCF (float | FloatKey) – Convergence threshold for CPKS cycle
U1K (str | StringKey) – Determines which terms are included in the calculation of the U1 matrix (first order changes in MO coefficients). Best: The best (recommended) options for each relativistic option are included for this subkey. Implies None for non-relativistic and scalar relativistic ZORA, SO + SOFULL for spin-orbit coupled ZORA, and MV + Dar for the Pauli Hamiltonian. None: Implies none of the other options to this key. All: Implies all the other options to this key. MV: The mass-velocity term. Dar: The Darwin term. ZMAN: The Spin-Zeeman term (can be included only in case of spin-orbit coupled Pauli Hamiltonian). SO: ZORA spin-orbit part. SOFULL: ZORA spin-orbit part.
Use (str | StringKey) – The subkey Use controls some optional options. FXC: Improves the exchange-correlation kernel used, as was implemented by J. Autschbach [http://dx.doi.org/10.1080/00268976.2013.796415]. Important only in case of spin-orbit coupled calculations. This may give some (small) gauge dependent results when using this. Important option that should be seriously considered and has been advocated in Ref [http://dx.doi.org/10.1080/00268976.2013.796415]. SCALED: Implies the scaled ZORA method, which gives (slightly) gauge dependent results. Note that in case of the ZORA Hamiltonian default the unscaled ZORA method is used. For chemical shifts, only compare results with the same options. SO1C: Before ADF2008.01 in the the spin-orbit term a 1-center approximation was used, which does not suffer from gauge dependence. This 1-center approximation can be used with USE SO1C.
Ghosts (str | Sequence[str] | FreeBlock) – The subkey GHOSTS is a block type subkey. The format is Ghosts | xx1 yy1 zz1 | xx2 yy2 zz2 | … | SubEnd
- class OLEDDepostion[source]¶
- Variables:
RestartWorkdir (str | Path | StringKey) – Uses the data from the working directory of a previously run deposition workflow for restarting. Under the hood this uses the normal rerun-prevention available in PLAMS: it may reuse results from old jobs instead of running them again.
Box (OLEDDepostion._Box) – Specifications of the box into which the material is deposited.
Deposition (OLEDDepostion._Deposition) – Specifies the details of how molecules are deposited.
LAMMPSOffload (OLEDDepostion._LAMMPSOffload) – Offload the calculation to LAMMPS via AMSPipe.
LoadSystem (OLEDDepostion._LoadSystem) – Block that controls reading the chemical system from a KF file instead of the [System] block.
Molecule (OLEDDepostion._Molecule) – Specification of the molecule to be deposited.
System (OLEDDepostion._System) – Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- class _Box[source]¶
Specifications of the box into which the material is deposited.
- Variables:
Size (Iterable[float] | FloatListKey) – Specify the desired size of the box. The final deposited box may have a different size. The x- and y-axis are perpendicular to the direction of deposition, so these may be regarded as the width of the growing layer. The z-axis is the direction along which the deposition happens, so this determines the thickness of the deposited layer. Note that the x- and y-axis will be ignored if a custom substrate is used: the are of the box is then determined by the lattice of the substrate. The z-axis can still be freely chosen, but should be large enough that there is enough space for the substrate itself and to deposit more molecules on top of it.
Substrate (Literal["Graphene", "Custom"]) – The substrate on which to grow the layer.
SubstrateSystem (str | StringKey) – String ID of a named [System] to be used as a substrate. (This is only used when the Substrate key is set to Custom.)
- class _Deposition[source]¶
Specifies the details of how molecules are deposited.
- Variables:
ConstrainHXBonds (BoolType | BoolKey) – Constrain the bond length for all H-* bonds (i.e. any bond to a hydrogen atom). Doing this allows choosing a larger time step. If this option is disabled, the TimeStep needs to be reduced manually.
Frequency (int | IntKey) – The frequency in MD steps at which new molecules will be added to the system.
NumMolecules (int | IntKey) – The number of molecules that we will try to deposit. If not specified the number will be determined automatically such that the box becomes approximately full.
Temperature (float | FloatKey) – The temperature at which the deposition happens.
- class _LAMMPSOffload[source]¶
Offload the calculation to LAMMPS via AMSPipe.
- Variables:
Enabled (BoolType | BoolKey) – Enable offloading the force field evaluation to LAMMPS instead of handling it internally in AMS.
UseGPU (BoolType | BoolKey) – Accelerate LAMMPS calculations using a GPU. Requires a LAMMPS library built with the GPU package.
UseGPUForKSpace (BoolType | BoolKey) – When UseGPU is enabled, also use the GPU to accelerate reciprocal space electrostatic interactions. Disabling this can improve performance on less powerful GPUs.
UseGPUForNeighbor (BoolType | BoolKey) – When UseGPU is enabled, also use the GPU to accelerate neighbor searches. Disabling this can improve performance on less powerful GPUs.
UseOpenMP (BoolType | BoolKey) – Parallelize LAMMPS calculations using OpenMP threading. Requires a LAMMPS library built with the OMP package.
- class _LoadSystem[source]¶
Block that controls reading the chemical system from a KF file instead of the [System] block.
- class _Molecule[source]¶
Specification of the molecule to be deposited.
- Variables:
MoleFraction (float | FloatKey) – The relative occurrence of the molecule with regard to other deposited species. Only relevant for mixed molecule depositions.
SystemName (str | StringKey) – String ID of a named [System] to be inserted. The lattice specified with this System, if any, is ignored and the main system’s lattice is used instead.
- class _System[source]¶
Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- Variables:
AllowCloseAtoms (BoolType | BoolKey) – No longer functional. Just here for backwards compatibility.
Charge (float | FloatKey) – The system’s total charge in atomic units.
FractionalCoords (BoolType | BoolKey) – Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
GeometryFile (str | Path | StringKey) – Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds (BoolType | BoolKey) – Equivalent to ‘Modify%GuessBonds’. Please update input file to use ‘Modify’ block instead.
LatticeStrain (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%LatticeStrain’. Please update input file to use ‘Modify’ block instead.
MapAtomsToUnitCell (BoolType | BoolKey) – Equivalent to ‘Modify%MapAtomsToUnitCell’. Please update input file to use ‘Modify’ block instead.
PerturbCoordinates (float | FloatKey) – Equivalent to ‘Modify%PerturbCoordinates’. Please update input file to use ‘Modify’ block instead.
PerturbLattice (float | FloatKey) – Equivalent to ‘Modify%PerturbLattice’. Please update input file to use ‘Modify’ block instead.
ShiftCoordinates (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%Translate’, but in the unit of bohr by default. Please update input file to use ‘Modify’ block instead.
SuperCell (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCell’. Please update input file to use ‘Modify’ block instead.
SuperCellTrafo (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCellTrafo’. Please update input file to use ‘Modify’ block instead.
Symmetrize (BoolType | BoolKey) – Equivalent to ‘Modify%Symmetrize’. Please update input file to use ‘Modify’ block instead.
Atoms (str | Sequence[str] | FreeBlock) – The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders (str | Sequence[str] | FreeBlock) – Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
ElectrostaticEmbedding (OLEDDepostion._System._ElectrostaticEmbedding) – Container for electrostatic embedding options, which can be combined.
Lattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
Modify (OLEDDepostion._System._Modify) – Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- class _Atoms[source]¶
The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
- class _BondOrders[source]¶
Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
- class _ElectrostaticEmbedding[source]¶
Container for electrostatic embedding options, which can be combined.
- Variables:
ElectricField (Iterable[float] | FloatListKey) –
External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.
In atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 … e11 V/m.
Supported by the engines adf, band, dftb and mopac.
For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
MultipolePotential (OLEDDepostion._System._ElectrostaticEmbedding._MultipolePotential) – External point charges (and dipoles).
- class _MultipolePotential[source]¶
External point charges (and dipoles).
- Variables:
ChargeModel (Literal["Point", "Gaussian"]) – A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
ChargeWidth (float | FloatKey) – The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
Coordinates (str | Sequence[str] | FreeBlock) –
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Coordinates[source]¶
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Lattice[source]¶
Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
- class _Modify[source]¶
Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- Variables:
EnableAtomicProperties (Literal["gui", "adf", "band", "forcefield", "dftb", "reaxff", "qe"]) – Enables an atomic property group. This is only necessary if you want a group enabled, but no atom in the input is using any property from that group.
GuessBonds (BoolType | BoolKey) – Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.
LatticeStrain (Iterable[float] | FloatListKey) – Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
MapAtomsToUnitCell (Iterable[float] | FloatListKey) – For periodic systems the atoms will be moved to the central unit cell where all their fractional coordinates are in the range [start_range,start_range+1). No mapping will take place along non-periodic directions. If just a single number is given, it corresponds to start_range. If multiple numbers are given, they should match the number of lattice vectors and will be used as start ranges along the individual lattice vectors. If no number is given at all, the mapping will be done to the [-0.5:0.5) cell.
PerturbCoordinates (float | FloatKey) – Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
PerturbLattice (float | FloatKey) – Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
SuperCell (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
SuperCellTrafo (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
Symmetrize (BoolType | BoolKey) – Symmetrizes the atomic coordinates to machine precision and rototranslates the molecule to the AMS standard orientation. This allows optimal use of the system’s symmetry for calculations with the AMS driver and its engines.
Translate (Iterable[float] | FloatListKey) – Translate all atoms by a vector.
- class OLEDProperties[source]¶
- Variables:
CoresPerJob (int | IntKey) – The number of CPU cores used for each job in the workflow. Combined with the total number of cores used (set by the
NSCMenvironment variable or the-ncommand line argument), this indirectly determines the number of simultaneously running jobs. The default value should usually be a good choice. When changing this value, make sure you are using all allocated cores by setting a value that divides the total number of cores, as well as the number of cores on each node.LogProgressEvery (float | FloatKey) – How often to print progress information to the logfile.
NumAdditionalOrbitalEnergies (int | IntKey) – The number of additional orbital energies to write to the HDF5 file. A value of N means to write everything up to HOMO-N and LUMO+N.
NumExcitations (int | IntKey) – The number of exited states to calculate. By default the S_1 and T_1 states will be calculated. The calculation of excited states is currently only supported for systems with a closed-shell ground state.
NumSelectedMoleculesPerSpecies (int | IntKey) – Number of molecules per species to calculate properties for. Around 50 molecules per species should be enough to estimate distribution means and standard deviations as input for the Bumblebee KMC code. Mutually exclusive with the
SelectedMoleculeskeyword. If neither this key norSelectedMoleculesis present, all molecules will be selected.OccupationSmearing (Literal["None", "Ions", "All"]) – Determines for which systems the electron smearing feature in ADF will be used. If enabled, the molecular orbital occupations will be smeared out with a 300K Fermi-Dirac distribution. This makes SCF convergence easier, as the occupation of energetically close orbitals does not jump when their energetic order flips. See the ADF manual for details. It is recommended to keep this option enabled for the ionic systems, which are more likely to suffer from difficult SCF convergence.
Relax (Literal["None", "Neutral", "All"]) –
Which geometries to relax prior to taking the energy differences for the calculation of ionization potential and electron affinity. The relaxation is done at the DFTB level using the GFN1-xTB model Hamiltonian with electrostatic embedding in a UFF environment.
None: Use the geometries directly from the input.
Neutral: Relax the uncharged molecule and use its optimized geometry for the neutral as well as the ionic systems. This gives (approximately) the vertical ionization potential and electron affinity.
All: Individually relax the neutral systems and the ions before calculating the total energies. This gives (approximately) the adiabatic ionization potential and electron affinity.
Restart (str | Path | StringKey) – The HDF5 file from a previous calculation on the same morphology. Data already calculated on the restart file will just be copied over and not be recalculated.
SelectedMolecules (Iterable[int] | IntListKey) – Indices of the molecules to calculate properties for. Note that indexing starts at 0. Mutually exclusive with the
NumSelectedMoleculesPerSpecieskeyword. If neither this key norNumSelectedMoleculesPerSpeciesis present, all molecules will be selected.StoreResultFiles (Literal["None", "Failed", "All"]) – Whether to keep the full result files from all the individual jobs. By default the result files from all jobs for a particular molecule will be deleted after all relevant results have been extracted and stored on the HDF5 file. Note that keeping the full results for all molecules can easily require hundreds of gigabytes of storage space.
Embedding (OLEDProperties._Embedding) – Configures details of how the environment is taken into account.
GW (OLEDProperties._GW) – Perform a GW calculation. G0W0 is the default for GW%SelfConsistency.
LoadSystem (OLEDProperties._LoadSystem) – Block that controls reading the chemical system from a KF file instead of the [System] block.
MBPT (OLEDProperties._MBPT) – Technical aspects of the MP2 algorithm.
System (OLEDProperties._System) – Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
TransferIntegrals (OLEDProperties._TransferIntegrals) – Configures the details of the calculation of electron and hole transfer integrals.
- class _Embedding[source]¶
Configures details of how the environment is taken into account.
- Variables:
Charges (Literal["DFTB", "DFT"]) –
Which atomic charges to use for the DRF embedding.
DFTB: Use the self-consistent Mulliken charges from a quick DFTB calculation with the GFN1-xTB model.
DFT: Use the MDC-D charges from a relatively quick DFT calculation using LDA and a DZP basis set.
Cutoff (float | FloatKey) – The cutoff distance determining which molecules will be considered the environment of the central molecule. The maximum possible cutoff distance is half the length of the smallest lattice vector. The distance can be measured using different metrics, see the
Metrickeyword.Metric (Literal["CoM", "Atoms", "Atoms_noH"]) –
The metric used to calculate the distance between two molecules.
CoM: use the distance between the centers of mass of the two molecules.
Atoms: Use the distance between the two closest atoms of two molecules.
Atoms_noH: Use the distance between the closest non-hydrogen atoms of the two molecules.
Type (Literal["None", "DRF"]) – The type of embedding used to simulate the molecular environment.
- class _GW[source]¶
Perform a GW calculation. G0W0 is the default for GW%SelfConsistency.
- Variables:
AdaptiveMixing (Iterable[float] | FloatListKey) –
Requests to use adaptive mixing instead of DIIS and sets the staring mixing parameter for mixing of Green’s function in case of self-consistency.
Adapative mixing is recommended in case a qsGW calculation does not converge with DIIS.
It is ignored in non-selfconsistent calculation and overwritten by DIIS when DIIS is also present.
DIIS (int | IntKey) – Requests to use DIIS. This is the Default. Number of expansion coefficients can be requested as well. Ignored in non-selfconsistent calculation
Enabled (BoolType | BoolKey) – Enable the calculation of the GW quasi-particle energies.
ExpansionOrder (int | IntKey) – Order of the expansion of the screened interaction on the SOS-GF(n) method. order 2 (=SOS-GF2) is the default
FixedGridSizes (BoolType | BoolKey) – In a self-consistent GW calculation, recalculate Grids but keep them the same size during the SCF procedure.
FixedGrids (BoolType | BoolKey) – In a self-consistent GW calculation, do not recalculate Grids. Can be useful in case of convergence problems. Only relevant for qsGW and qsGW0. In case of evGW and evGW0, the grids are always kept fixed.
G3W2 (Literal["Full", "Diagonal", "Perturbative"]) – Only relevant when self-energy is one of GF2 or G3W2: Full requests that the second-order term is evaluated for the full self-energy matrix. This is very expensive and should only be done for small systems. Diagonal requests, that only the Diagonal of the self-energy matrix is updated. Perturbative means, that only a second-order screened exchange correction is evaluated after the GW calculation is completed. For a G0W0 calculation, all of these options are equivalent.
LinearMixing (Iterable[float] | FloatListKey) –
Requests to use linear mixing instead of DIIS and sets the mixing parameter for linear mixing of Green’s function in case of self-consistency.
It is ignored in non-selfconsistent calculation and overwritten by DIIS when DIIS is also present.
LinearizeQPequations (BoolType | BoolKey) –
Instead of solving the non-linear QP equations in a G0W0 (or evGW calculation) by bisection exacly, linearize them by first-order Taylor expansion.
This is not recommended since it does not save computational time when used together with analytical continuation (as implemented in AMS). It might however be useful for benchmarking or for validating results.
If the results os the linearization differ by a lot (for instance, more than 0.1 eV in frontier QP energies) from the non-linearized results, this might indicate that the GW calculation is not reliable.
OffDiagonalEFermi (BoolType | BoolKey) – Analytically continue the off-diagonal elements of the KSF2 qsGW Hamiltonian at the Fermi-energy instead of omega=0. Typically leads to slightly lower QP energies, i.e. higher ionization potentials. The HOMO-LUMO gaps are typically not affected.
Polarizability (Literal["RPA", "BSE", "G4W1", "G4V1", "TDHF"]) –
Sets the expression for the Polarizability used in the GW calculation.
RPA is the Default and amounts to a standard GW calculation.
BSE denotes screening in the Bethe-Salpeter-equation formalism.
PrintAllSolutions (BoolType | BoolKey) – Print out all solutions for all requested states. Detects multiple solutions of the QP equations.
PrintImaginaryAxisData (BoolType | BoolKey) – If true, print out the self-energy on the imaginary axis.
PrintSpectralFunction (BoolType | BoolKey) – Plot the self-energy as a function of frequency. Automatically done in case of analytical continuation. However, this is expensive in the analytical integration formalism.
PrintZfactor (BoolType | BoolKey) –
QPHamiltonian (Literal["KSF1", "KSF2", "SRG", "LQSGW"]) –
The quasi-particle Hamiltonian can be constructed in different ways.
KSF1 refers to the original construction by Kotani, Van Schilfgaarde anf Faleev (KSF) which is also implemented in TURBOMOLE.
KSF2 refers to an alternative construction by KSF.
KSF1 is not recommended since it is numerically less stable than KSF2 in case analytical continuation is used (the default).
In case the analytical integration algorithm is used, only KSF1 is implemented. Therefore, make sure that KSF1 is specified. The results are typically very similar.
The QP energies at which the matrix elements are evaluated can be tweaked further, see the two subsequent keys: However, KSF2 is recommended since it typically leads to QP energies with the best agreement with experiment.
Ignored when not a quasi-particle self-consistent GW calculation is performed
Scaling (float | FloatKey) – Scale factor for the polarizability in the screened interaction SOS-GF2. Default = 1.0 (corresponds to no scaling)
ScissorShift (BoolType | BoolKey) –
Only calculate the HOMO and LUMO QP energies and shift the remaining QP energies by the same amount.
This is a rather crude approximation and not recommended.
It might again be useful for benchmarking purposes.
SelfConsistency (Literal["None", "G0W0", "EVGW0", "EVGW", "QSGW0", "QSGW"]) –
Sets the level of self-consistency in a GW calculation.
G0W0 calculates a one-shot, perturbative correction to the KS eigenvalues.
In evGW and evGW0, the quasi-particle energies are updated until self-consistency is reached.
evGW0 requests that the Green’s function is evaluated self-consistently but not the screened interaction.
In qsGW, the density is updated as well, however, the self-energy is mapped to a static effective potential and the Dyson equation is solved by diagonalization instead of inversion. The results of a qsGW are independent of the choice of the underlying exchange-correlation functional and are usually the most accurate ones.
The same is done in qsGW0, but the screened interaction is not updated.
SelfConsistentSigmaVertex (BoolType | BoolKey) – If active, evaluate the vertex correction in Sigma in qsGW self-consistent. Only supported for GWGammaInf so far
SelfEnergy (Literal["HF", "GW", "G3W2", "SOSEX", "GWGamma", "G3W2dynamic", "GWGammaInf", "GWGammaInfDyn"]) –
Controls the form of the self-energy.
GW is the default and corresponds to the standard GW calculation.
G3W2 is a GW calculation plus a perturbative second-order statically screened exchange correction (second order expansion in the self-energy). Note, that there the self-energy is always static.
TabulateGridPoints (BoolType | BoolKey) – pretabulate grid points for numerical integration.
nIterations (Iterable[int] | IntListKey) –
The maximum number of iterations within the (partially or fully) self-consistent GW calculation has to converge.
Ignored when Formalism is set to G0W0
nLowest (int | IntKey) – Number of lowest occupied QP levels to be evaluated, overwrites nStates’
Number of Quasiparticle States to be printed to output.
The default is 5 states which in this case means that min(5, Number of particle states) occupied and min(5, Number of hole states) hole states are printed. The whole list of states can be printed by setting this parameter to -1’
preconditionQSGW (BoolType | BoolKey) –
If true, the QSGW equations are solved but prior to each diagonalization, i.e. a G0W0 calculation is performed to find the optimal QP energies at which to analytically continue the self-energy.
This is in principle a more consistent construction than KSF1 or KSF2 since the diagonal elements are consistent with G0W0.
In KSF1 and KSF2, the diagonal elements are evaluated at the QP energies from the previous iteration which is equivalent to a zeroth-order Taylor expansion of the diagonal elements around the previous QP energies.Enabling this option typically leads to slightly lower QP energies.
AnalyticalIntegration (OLEDProperties._GW._AnalyticalIntegration) – Use analytical integration to calculate the self-energy. Very slow, unless the system is very small but useful to check the accuracy of the frequency integration
Converge (OLEDProperties._GW._Converge) – Sets convergence criteria for the GW calculation in self-consistent case
- class _AnalyticalIntegration[source]¶
Use analytical integration to calculate the self-energy. Very slow, unless the system is very small but useful to check the accuracy of the frequency integration
- Variables:
Enabled (BoolType | BoolKey) – Enable the calculation of the GW quasi-particle energies via analytical integration.
SpectralFunctionResolution (int | IntKey) – Number of points at which spectral function is evaluated.
TDA (BoolType | BoolKey) – Solve the linear response equations in the Tamm-Dancoff approximation.
Artificial (positive) broadening parameter for evaluation of self-energy in analytical integration.
Ideally should be as small as possible but this might lead to convergence issues in partially self-consistent approaches.
In this case, a value of up to 0.1 is possible.
printBSEexcitationsInLastIteration (BoolType | BoolKey) –
Print out BSE excitations in the last iteration in a qsGW calculation. Can be used in the BAND engine.
In ADF, one should instead just calculate excitation energies using the excitation block.
- class _Converge[source]¶
Sets convergence criteria for the GW calculation in self-consistent case
- Variables:
Density (Iterable[float] | FloatListKey) –
First Criterion for self-consistency procedure to terminate.
Criterion is the trace of the density matrix. Ignored in non-selfconsistent Calculation and in eigenvalue self-consistent GW
It is possible to run a qsGW calculation with an inner SCF loop which updates the static part of the elf-energy only. This can be useful to accelerate the convergence in case linear mixing is used. It is not recommended to use linear mixing, so it is also not recommended to use that inner loop as well. The second number in this list specifies the convergence criterion for the inner SCF loop.
Criterion for self-consistency procedure to terminate.
The self-consistent GW calculation terminates, when the difference between the HOMO QP energies between 2 consecutive iterations is below this number.
The LUMO energy converged faster than the HOMO energy so when the HOMO energy is converged according to this criterion, the LUMO energy will be converged as well.
In non-selfconsistent Calculation, this criterion is ignored.
- class _LoadSystem[source]¶
Block that controls reading the chemical system from a KF file instead of the [System] block.
- class _MBPT[source]¶
Technical aspects of the MP2 algorithm.
- Variables:
Dependency (BoolType | BoolKey) – If true, to improve numerical stability, almost linearly-dependent combination of basis functions are removed from the Green’s function that are used in the MBPT equations. Disabling this key is strongly discouraged. Its value can however be changed. The key to adjust this value is RiHartreeFock%DependencyThreshold
Enabled (BoolType | BoolKey) – Enable the calculation of the MP2 energy.
ExcludeCore (BoolType | BoolKey) –
If active, excludes core states from the calculation of the optimal imaginary time and frequency grids.
The core states are still included in all parts of the calculations.
In case a frozen care calculation is performed, this key is ignored.
For MP2 and double hybrid calculation, it defaults to false. For RPA and GW calculations, it defaults to true.
FitSetQuality (Literal["Auto", "VeryBasic", "Basic", "Normal", "Good", "VeryGood"]) –
Specifies the fit set to be used in the MBPT calculation.
’Normal’ quality is generally sufficient for basis sets up to and including TZ2P.
For larger basis sets (or for benchmarking purposes) a ‘VeryGood’ fit set is recommended. Note that the FitSetQuality heavily influences the computational cost of the calculation.
If not specified or ‘Auto’, the RIHartreeFock%FitSetQuality is used.
Formalism (Literal["Auto", "RI", "LT", "All"]) –
Specifies the formalism for the calculation of the MP2 correlation energy.
’LT’ means Laplace Transformed MP2 (also referred to as AO-PARI-MP2),
’RI’ means that a conventional RI-MP2 is carried out.
If ‘Auto’, LT will be used in case of DOD double hybrids and SOS MP2, and RI will be used in all other cases.
’All’ means that both RI and LT formalisms are used in the calculation.
For a RPA or GW calculation, the formalism is always LT, irrespective of the formalism specified with this key.
FrequencyGridType (Literal["LeastSquare", "GaussLegendre"]) – Use Gauss-legendre grid for imaginary frequency integration in RPA and GW calculations instead of the usually used Least-Square optimized ones. Has the advantage that it can be systematically converged and an arbitrary number of grid points can be used. Typically more grid points will be needed to get the same level of accuracy. However, the convergence of the results with the size of the grid can be more systematic. These grids can only be used when Formalism is set to RI.
IntegrationQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood"]) – Specifies the integration quality to be used in the MBPT calculation. If not specified, the RIHartreeFock%IntegrationQuality is used.
PrintOutSigma (BoolType | BoolKey) – Print out additional output for sigma-functional for parametrization.
SigmaFunctionalParametrization (Literal["W1", "W2", "S1", "S2", "S1re"]) – Only relevant if a sigma-functional calculation is performed. Possible choices for the parametrization of the sigma-functional. Not all options are supported for all functionals.
ThresholdQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Controls the distances between atomic centers for which the product of two basis functions is not fitted any more. Especially for spatially extended, large systems, ‘VERYBASIC’ and ‘BASIC’ can lead to large computational savings, but the fit is also more approximate. If not specified, the RIHartreeFock%ThresholdQuality is used.
UseScaledZORA (BoolType | BoolKey) – If true, use the scaled ZORA orbital energies instead of the ZORA orbital energies in the MBPT equations.
cutOfftransition (float | FloatKey) – Energy above which states are ignored in a MBPT calculation (must be a positive number). The default energy is chosen so high, that all states are included except for the ones which have been removed.
frozencore (BoolType | BoolKey) – Freeze core states in correlation part of MBPT calculation
Number of core states which will be excluded from the correlated calculation.
Will be ignored if frozencore is false.
In case nothing is specified, the number of core levels will be determined automatically.
Needs to be smaller than the number of occupied states.
nFreqIntegration (int | IntKey) – Number of imaginary frequency points for G3W2 integration
nFrequency (int | IntKey) – Number of imaginary frequency points. This key is only relevant for RPA and GW and will be ignored if used in an AO-PARI-MP2 calculation. 12 Points is the default for a RPA calculation. It is technically possible to use a different number of imaginary frequency points than for imaginary time. The maximum number of points which can be requested for imaginary frequency integration is 42. Important note: The computation time and memory requirements roughly scale linearly with the number of imaginary frequency points. However, memory can be an issue for RPA and GW when the number of imaginary frequency points is high. In case a job crashes, it is advised to increase the number of nodes since the necessary memory distributes over all nodes.
nLambda (int | IntKey) – Size of coupling constant integration grid for SOSEX variants in RPA. Default is 4 points
Number of imaginary time points (only relevant in case the Laplace Transformed (LT) formalism is used).
In the many-body-perturbation theory module in ADF, the polarizability (or Kohn-Sham density response function) is evaluated in imaginary time to exploit sparsity in the AO basis. For MP2, this is often referred to as a Laplace transform. For MP2, 9 points are the default. This is a safe choice, guaranteeing accuracies higher than 1 Kj/mol for most systems (For many simple organic systems, 6 points are sufficient for good accuracy).
Only for systems with a very small HOMO-LUMO gap or low-lying core states (heavy elements starting from the 4th row of the periodic table) more points might be necessary.
In principle, the same considerations apply for RPA and GW as well, however, the accuracy requirements are somewhat higher and 12 point are the default for RPA. In a GW calculation, the number of points is adjusted according to the numerical quality. Using less than 9 points is strongly discouraged except for the simplest molecules.
In ADF2019, it can happen that the algorithm determining the imaginary time grid does not converge. In this case, the usual reason is that the number of points is too small and more points need to be specified. Starting from AMS2020, this does not happen any more. In case the imaginary time grid does not converge, the number of points is automatically adjusted until it does.
The computation time of AO-PARI-MP2, RPA, and GW scales linearly with the number of imaginary time points.
useGreenXgrids (BoolType | BoolKey) – Use GreenX library to generate grid points. This is recommended for larger number of grid points (> 20). Up to 34 points can be requested.
- class _System[source]¶
Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- Variables:
AllowCloseAtoms (BoolType | BoolKey) – No longer functional. Just here for backwards compatibility.
Charge (float | FloatKey) – The system’s total charge in atomic units.
FractionalCoords (BoolType | BoolKey) – Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
GeometryFile (str | Path | StringKey) – Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds (BoolType | BoolKey) – Equivalent to ‘Modify%GuessBonds’. Please update input file to use ‘Modify’ block instead.
LatticeStrain (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%LatticeStrain’. Please update input file to use ‘Modify’ block instead.
MapAtomsToUnitCell (BoolType | BoolKey) – Equivalent to ‘Modify%MapAtomsToUnitCell’. Please update input file to use ‘Modify’ block instead.
PerturbCoordinates (float | FloatKey) – Equivalent to ‘Modify%PerturbCoordinates’. Please update input file to use ‘Modify’ block instead.
PerturbLattice (float | FloatKey) – Equivalent to ‘Modify%PerturbLattice’. Please update input file to use ‘Modify’ block instead.
ShiftCoordinates (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%Translate’, but in the unit of bohr by default. Please update input file to use ‘Modify’ block instead.
SuperCell (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCell’. Please update input file to use ‘Modify’ block instead.
SuperCellTrafo (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCellTrafo’. Please update input file to use ‘Modify’ block instead.
Symmetrize (BoolType | BoolKey) – Equivalent to ‘Modify%Symmetrize’. Please update input file to use ‘Modify’ block instead.
Atoms (str | Sequence[str] | FreeBlock) – The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders (str | Sequence[str] | FreeBlock) – Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
ElectrostaticEmbedding (OLEDProperties._System._ElectrostaticEmbedding) – Container for electrostatic embedding options, which can be combined.
Lattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
Modify (OLEDProperties._System._Modify) – Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- class _Atoms[source]¶
The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
- class _BondOrders[source]¶
Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
- class _ElectrostaticEmbedding[source]¶
Container for electrostatic embedding options, which can be combined.
- Variables:
ElectricField (Iterable[float] | FloatListKey) –
External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.
In atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 … e11 V/m.
Supported by the engines adf, band, dftb and mopac.
For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
MultipolePotential (OLEDProperties._System._ElectrostaticEmbedding._MultipolePotential) – External point charges (and dipoles).
- class _MultipolePotential[source]¶
External point charges (and dipoles).
- Variables:
ChargeModel (Literal["Point", "Gaussian"]) – A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
ChargeWidth (float | FloatKey) – The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
Coordinates (str | Sequence[str] | FreeBlock) –
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Coordinates[source]¶
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Lattice[source]¶
Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
- class _Modify[source]¶
Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- Variables:
EnableAtomicProperties (Literal["gui", "adf", "band", "forcefield", "dftb", "reaxff", "qe"]) – Enables an atomic property group. This is only necessary if you want a group enabled, but no atom in the input is using any property from that group.
GuessBonds (BoolType | BoolKey) – Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.
LatticeStrain (Iterable[float] | FloatListKey) – Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
MapAtomsToUnitCell (Iterable[float] | FloatListKey) – For periodic systems the atoms will be moved to the central unit cell where all their fractional coordinates are in the range [start_range,start_range+1). No mapping will take place along non-periodic directions. If just a single number is given, it corresponds to start_range. If multiple numbers are given, they should match the number of lattice vectors and will be used as start ranges along the individual lattice vectors. If no number is given at all, the mapping will be done to the [-0.5:0.5) cell.
PerturbCoordinates (float | FloatKey) – Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
PerturbLattice (float | FloatKey) – Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
SuperCell (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
SuperCellTrafo (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
Symmetrize (BoolType | BoolKey) – Symmetrizes the atomic coordinates to machine precision and rototranslates the molecule to the AMS standard orientation. This allows optimal use of the system’s symmetry for calculations with the AMS driver and its engines.
Translate (Iterable[float] | FloatListKey) – Translate all atoms by a vector.
- class _TransferIntegrals[source]¶
Configures the details of the calculation of electron and hole transfer integrals.
- Variables:
Type (Literal["None", "DFTB", "Fast", "Full"]) – The method used for the calculation of the transfer integrals.
Exclude (OLEDProperties._TransferIntegrals._Exclude) – Configures which dimers NOT to calculate transfer integrals for.
Include (OLEDProperties._TransferIntegrals._Include) – Configures which dimers transfer integrals are calculated for.
- class _Exclude[source]¶
Configures which dimers NOT to calculate transfer integrals for.
- Variables:
Cutoff (float | FloatKey) – Exclude dimers for which the distance is larger than this threshold. Acts as a quick pre-screening to reduce the number of dimers to calculate transfer integrals for.
Metric (Literal["CoM", "Atoms", "Atoms_noH"]) –
The metric used to calculate the distance between two molecules.
CoM: use the distance between the centers of mass of the two molecules.
Atoms: Use the distance between the two closest atoms of two molecules.
Atoms_noH: Use the distance between the closest non-hydrogen atoms of the two molecules.
- class _Include[source]¶
Configures which dimers transfer integrals are calculated for.
- Variables:
Cutoff (float | FloatKey) – Transfer integrals will be calculated for all molecule pairs within a cutoff distance from each other. This distance can be measured using different metrics, see the corresponding
Metrickeyword.Metric (Literal["CoM", "Atoms", "Atoms_noH"]) –
The metric used to calculate the distance between two molecules.
CoM: use the distance between the centers of mass of the two molecules.
Atoms: Use the distance between the two closest atoms of two molecules.
Atoms_noH: Use the distance between the closest non-hydrogen atoms of the two molecules.
- class ParAMS[source]¶
- Variables:
ApplyStoppersToBestOptimizer (BoolType | BoolKey) – By default the stoppers are not applied to the best optimizer (the one who has seen the best value thus far). This is because many stoppers are based on comparisons to the best optimizer, and in most scenarios one would like to keep a well-performing optimizer alive. For some stopper configurations this paradigm does not make sense and we would prefer to apply the stoppers equally to all optimizers.
CheckStopperInterval (int | IntKey) – Number of loss function evaluations between evaluations of the stopper conditions.
EndTimeout (float | FloatKey) –
The amount of time the manager will wait trying to smoothly join each optimizer at the end of the run. If exceeded the manager will abandon the optimizer and shutdown. This can raise errors from the abandoned threads, but may be needed to ensure the manager closes and does not hang.
This option is often needed if the Scipy optimizers are being used and should be set to a low value.
EngineCollection (str | StringKey) – Path to (optional) JobCollection Engines YAML file.
EvaluateLoss (BoolType | BoolKey) –
Evaluate the loss function based on the job results. This will produce the same output files as Task Optimization. If No, this will be skipped and only the jobs will be run (and saved).
Warning: If both Store Jobs and Evaluate Loss are No then this task will not produce any output.
ExitConditionBooleanCombination (str | StringKey) –
If multiple ExitConditions are used, this key indicates how their evaluations relate to one another.
Use an integer to refer to a exit condition (defined by order in input file).
Recognizes the symbols: ( ) & |
E.g. (1 & 2) | 3.
Defaults to an OR combination of all selected exit conditions.
FilterInfiniteValues (BoolType | BoolKey) –
If Yes, removes points from the calculation with non-finite loss values.
Non-finite points can cause numerical issues in the sensitivity calculation.
GlompoLogging (BoolType | BoolKey) – Include status and progress information from the optimization manager in the printstreams.
GlompoSummaryFiles (Literal["None", "1", "2", "3", "4"]) –
Indicates what GloMPO-style outputs you would like saved to disk. Higher values also save all lower level information.
Available options: • None: Nothing is saved. • 1: YAML file with summary info about the optimization settings, performance and the result. • 2: PNG file showing the trajectories of the optimizers. • 3: HDF5 file containing iteration history for each optimizer. • 4: More detailed HDF5 log including the residual results for each optimizer, data set and iteration.
JobCollection (str | StringKey) – Path to JobCollection YAML file.
MoreExtractorsPath (str | Path | StringKey) – Path to directory with extractors.
NumberBootstraps (int | IntKey) –
Number of repeats of the calculation with different sub-samples.
A small spread from a large number of bootstraps provides confidence on the estimation of the sensitivity.
NumberCalculationSamples (int | IntKey) –
Number of samples from the full set available to use in the calculation.
If not specified or -1, uses all available points. For the sensitivity calculation, this will be redrawn for every bootstrap.
NumberSamples (int | IntKey) – Number of samples to generate during the sampling procedure.
PLAMSWorkingDirectory (str | Path | StringKey) – Path to PLAMS working directory to temporarily hold Job results files.
ParameterInterface (str | StringKey) – Path to parameter interface YAML file.
PrintStatusInterval (float | FloatKey) – Number of seconds between printing of a status summary.
RandomSeed (int | IntKey) – Random seed to use during the sampling procedure (for reproducibility).
RestartDirectory (str | Path | StringKey) –
Specify a directory to continue interrupted GenerateReference or SinglePoint calculations. The directory depends on the task:
GenerateReference: results/reference_jobs SinglePoint: results/single_point/jobs
Note: If you use the GUI this directory will be COPIED into the results folder and the name will be prepended with ‘dep-’. This can take up a lot of disk space, so you may want to remove the ‘dep-’ folder after the job has finished.
ResultsDirectory (str | Path | StringKey) – Directory in which output files will be created.
ResumeCheckpoint (str | Path | StringKey) – Path to checkpoint file from which a previous optimization can be resumed.
RunReweightCalculation (BoolType | BoolKey) –
Run a more expensive sensitivity calculation that will also return suggested weights for the training set which will produce more balanced sensitivities between all the parameters.
Note: The Gaussian kernel is recommended for the loss values kernel in this case.
RunSampling (BoolType | BoolKey) –
Produce a set of samples of the loss function and active parameters. Samples from the parameter space are drawn from a uniform random distribution.
Such a set of samples serves as the input to the sensitivity calculation.
SampleWithReplacement (BoolType | BoolKey) –
Sample from the available data with or without replacement.
This only has an effect if the number of samples for the calculation is less than the total number available otherwise replace is Yes by necessity.
SamplesDirectory (str | Path | StringKey) –
Path to an ‘optimization’ directory containing the results of a previously run sampling.
First looks for a ‘glompo_log.h5’ file. If not found, will look for ‘running_loss.txt’ and ‘running_active_parameters.txt’ in a sub-directory. The sub-directory used will depend on the DataSet Name.
For the Reweight calculation only a ‘glompo_log.h5’ file (with residuals) may be used.
SaveResiduals (BoolType | BoolKey) –
During the sampling, save the individual difference between reference and predicted values for every sample and training set item. Required for the Reweight calculation, and will be automatically activated if the reweight calculation is requested.
Saving and analyzing the residuals can provide valuable insight into your training set, but can quickly occupy a large amount of disk space. Only save the residuals if you would like to run the reweight calculation or have a particular reason to do so.
Scaler (Literal["Linear", "Std", "None", "Optimizers"]) –
Type of scaling applied to the parameters. A scaled input space is needed by many optimization algorithms.
Available options: • Linear: Scale all parameters between 0 and 1. • Std: Scale all parameters between -1 and 1. • None: Applies no scaling. • Optimizers (Default): Does not specify a scaling at the manager level, but allows the selection to be governed by the optimizer/s. If they do not require any particular scaler, then ‘linear’ is selected as the ultimate fallback.
SetToAnalyze (Literal["TrainingSet", "ValidationSet"]) – Name of the data set to use for the sensitivity analysis.
ShareBestEvaluationBetweenOptimizers (BoolType | BoolKey) –
Share new best evaluations from one optimizer to another.
Some algorithms can use this information to accelerate their own convergence. However, optimizers typically have to be configured to receive and handle the information.
This option can work very well with CMA-ES injections.
SkipX0 (BoolType | BoolKey) –
Do not evaluate the initial parameters before starting the optimization.
If the initial parameters evaluated and do not return a finite loss function value, the optimization will abort. A non-infinite value typically indicates crashed jobs.
SplitPrintstreams (BoolType | BoolKey) – Split print statements from each optimizer to separate files.
StopperBooleanCombination (str | StringKey) –
If multiple Stoppers are used this is required to indicate how their evaluations relate to one another.
Use an integer to refer to a stopper (defined by order in input file).
Recognizes the symbols: ( ) & |
E.g. (1 & 2) | 3.
Defaults to an OR combination of all selected stoppers.
StoreJobs (Literal["Auto", "Yes", "No"]) –
Keeps the results files for each of the jobs. If No, all pipeable jobs will be run through the AMS Pipe and no files will be saved (not even the ones not run through the pipe). If Auto, the pipeable jobs are run through the pipe and the results of nonpipeable jobs are saved to disk. If Yes, no jobs are run through the pipe and all job results are stored on disk.
Warning: If both Store Jobs and Evaluate Loss are No then task SinglePoint will not produce any output.
Task (Literal["Optimization", "GenerateReference", "SinglePoint", "Sensitivity", "MachineLearning"]) –
Task to run.
Available options: •MachineLearning: Optimization for machine learning models. •Optimization: Global optimization powered by GloMPO •Generate Reference: Run jobs with reference engine to get reference values •Single Point: Evaluate the current configuration of jobs, training data, and parameters •Sensitivity: Measure the sensitivity of the loss function to each of the active parameters
Validation (float | FloatKey) – Fraction of the training set to be used as a validation set. Will be ignored if a validation set has been explicitly defined.
CheckpointControl (ParAMS._CheckpointControl) – Settings to control the production of checkpoints from which the optimization can be resumed.
Constraints (str | Sequence[str] | FreeBlock) –
Parameter constraint rules to apply to the loss function. One per line. Use ‘p’ to reference the parameter set. You may use indices or names in square brackets to refer to a specific variable.
Note, that indices are absolute i.e., they do not reference the active subset of parameters.
Eg: p[0]>=p[2] p[‘O:p_boc2’]==p[‘H:p_boc2’]
ControlOptimizerSpawning (ParAMS._ControlOptimizerSpawning) – Control the spawning of optimizers. Note, this is different from ExitConditions. These simply stop new optimizers from spawning, but leave existing ones untouched. ExitConditions shutdown active optimizers and stop the optimization.
DataSet (ParAMS._DataSet) – Configuration settings for each data set in the optimization.
Engine (EngineBlock) – If set, use this engine for the ParAMS SinglePoint. Mutually exclusive with EngineCollection.
ExitCondition (ParAMS._ExitCondition) – A condition used to stop the optimization when it returns true.
Generator (ParAMS._Generator) – A Generator used to produce x0 starting points for the optimizers.
LoggingInterval (ParAMS._LoggingInterval) – Number of function evaluations between every log to file.
LossValuesKernel (ParAMS._LossValuesKernel) – Kernel applied to the parameters for which sensitivity is being measured.
MachineLearning (ParAMS._MachineLearning) – Options for Task MachineLearning.
Optimizer (ParAMS._Optimizer) – An optimizer which may be used during the optimization.
OptimizerSelector (ParAMS._OptimizerSelector) – If multiple Optimizers are included, then this block must be included and configures the Selector which will choose between them.
ParallelLevels (ParAMS._ParallelLevels) – Distribution of threads/processes between the parallelization levels.
ParametersKernel (ParAMS._ParametersKernel) – Kernel applied to the parameters for which sensitivity is being measured.
Stopper (ParAMS._Stopper) – A Stopper used to terminate optimizers early.
- class _CheckpointControl[source]¶
Settings to control the production of checkpoints from which the optimization can be resumed.
- Variables:
AtEnd (BoolType | BoolKey) – Create a checkpoint when the exit condition/s are triggered.
AtInitialisation (BoolType | BoolKey) – Create a checkpoint immediately at the start of an optimization.
CheckpointingDirectory (str | Path | StringKey) – Directory in which the checkpoints will be saved. Defaults to ‘checkpoints’ in the results directory
EveryFunctionCalls (int | IntKey) –
Create a checkpoint every n function evaluations.
If not specified or -1, checkpoints are not created based on function calls.
EverySeconds (float | FloatKey) –
Create a checkpoint every n seconds.
If not specified or -1, a checkpoint is not created based time.
Number of earlier checkpoints to keep. Older ones are deleted when a new one is created. -1 does not delete any previous checkpoints, and 0 retains only the most recent checkpoint.
This number excludes the most recent checkpoint which is obviously always retained! So the actual number of files will be larger than this number by one.
NamingFormat (str | StringKey) –
Convention used to name the checkpoints.
The following special keys are supported: • %(date): Current calendar date in YYYYMMDD format • %(year): Year formatted to YYYY • %(yr): Year formatted to YY • %(month): Numerical month formatted to MM • %(day): Calendar day of the month formatted to DD • %(time): Current calendar time formatted to HHMMSS (24-hour style) • %(hour): Hour formatted to HH (24-hour style) • %(min): Minutes formatted to MM • %(sec): Seconds formatted to SS • %(count): Index count of the number of checkpoints constructed. Starts at zero, formatted to 3 digits.
RaiseFail (BoolType | BoolKey) – Raise an error and stop the optimization if a checkpoint fails to be constructed, otherwise issue a warning and continue the optimization.
- class _Constraints[source]¶
Parameter constraint rules to apply to the loss function. One per line. Use ‘p’ to reference the parameter set. You may use indices or names in square brackets to refer to a specific variable.
Note, that indices are absolute i.e., they do not reference the active subset of parameters.
Eg: p[0]>=p[2] p[‘O:p_boc2’]==p[‘H:p_boc2’]
- class _ControlOptimizerSpawning[source]¶
Control the spawning of optimizers. Note, this is different from ExitConditions. These simply stop new optimizers from spawning, but leave existing ones untouched. ExitConditions shutdown active optimizers and stop the optimization.
- Variables:
MaxEvaluations (int | IntKey) –
No new optimizers will be started after this number of function evaluations has been used.
Note, this is different from the equivalent exit condition which would terminate existing optimizers rather than simply not allowing new ones to spawn.
MaxOptimizers (int | IntKey) –
No new optimizers will be started after this number has been spawned.
Note, this is different from the equivalent exit condition which would terminate existing optimizers rather than simply not allowing new ones to spawn.
- class _DataSet[source]¶
Configuration settings for each data set in the optimization.
- Variables:
BatchSize (int | IntKey) – Number of data set entries to be evaluated per epoch. Default 0 means all entries.
EvaluateEvery (int | IntKey) –
This data set is evaluated every n evaluations of the training set.
This will always be set to 1 for the training set. For other data sets it will be adjusted to the closest multiple of LoggingInterval%General, i.e., you cannot evaluate an extra data set more frequently than you log it.
LossFunction (Literal["mae", "rmse", "sse", "sae"]) –
Loss function used to quantify the error between model and reference values. This becomes the minimization task.
Available options: • mae: Mean absolute error • rmse: Root mean squared error • sse: Sum of squared errors • sae: Sum of absolute errors
MaxJobs (int | IntKey) – Limit each evaluation to a subset of n jobs. Default 0 meaning all jobs are used.
MaxJobsShuffle (BoolType | BoolKey) – Use a different job subset every for every evaluation.
Unique data set identifier.
The first occurrence of DataSet will always be called training_set. The second will always be called validation_set. These cannot be overwritten.
Later occurrences will default to data_set_xx where xx starts at 03 and increments from there. This field can be used to customize the latter names.
UsePipe (BoolType | BoolKey) – Use AMS Pipe for suitable jobs to speed-up evaluation.
- class _Engine[source]¶
If set, use this engine for the ParAMS SinglePoint. Mutually exclusive with EngineCollection.
- class _ExitCondition[source]¶
A condition used to stop the optimization when it returns true.
- Variables:
MaxOptimizersConverged (int | IntKey) –
Return True after n optimizers have converged normally.
An optimizer that has ‘converged’ is distinct from an optimizer that was shutdown via the Stopper settings (i.e. ‘stopped’).
MaxOptimizersStarted (int | IntKey) –
Return True after n optimizers have been started.
Note, this is best used in combination with other conditions because it will stop the optimization as soon as the correct number have been started and not allow newly spawned optimizer to iterate at all.
MaxOptimizersStopped (int | IntKey) –
Return True after n optimizers have been stopped.
An optimizer that has been ‘stopped’ is distinct from an optimizer that stopped due to its internal convergence conditions (i.e., ‘converged’).
MaxTotalFunctionCalls (int | IntKey) – Return True after n function calls have been executed.
TargetFunctionValue (float | FloatKey) – Return True after an optimizer finds a function value less than or equal to n.
TimeLimit (float | FloatKey) –
Return True after the entire optimization has been running for n seconds.
Note, this is NOT the time for any particular optimizer.
See also: Time Limit Through Restarts
TimeLimitThroughRestarts (float | FloatKey) –
Return True after the sum-total of all optimization runs (i.e., through all restarts) has been running for n seconds.
Note, this is NOT the time for any particular optimizer.
See also: Time Limit
Type (Literal["TimeLimit", "MaxTotalFunctionCalls", "MaxOptimizersStarted", "MaxOptimizersConverged", "MaxOptimizersStopped", "StopsAfterConvergence", "TimeLimitThroughRestarts", "TargetFunctionValue"]) –
A condition used to stop the optimization when it returns true.
Available options: • Time Limit: Limit the optimization walltime. • Max Function Calls: Stop the optimization after a certain number of loss function evaluations. • Max Optimizers Started: Shutdown after a certain number of optimizers have been spawned. • Max Optimizers Converged: Shutdown when optimizers have converged via their own internal conditions. • Max Optimizers Stopped: Shutdown when the Stopping configuration has resulted in a number of optimizers being stopped. • Stops After Convergence: Stop when some optimizers have converged and others have been stopped. • Time Limit Through Restarts: Limit the total cumulative walltime across multiple restarts of the optimization. • Target Function Value: Shutdown when a small enough loss function value is found.
StopsAfterConvergence (ParAMS._ExitCondition._StopsAfterConvergence) – Returns True when at least n_a optimizers have been stopped after n_b optimizers have converged.
- class _Generator[source]¶
A Generator used to produce x0 starting points for the optimizers.
- Variables:
Type (Literal["Incumbent", "ExploreExploit", "Perturbation", "Random", "SinglePoint"]) –
Algorithm used to pick starting points for the optimizers.
Available options: • Incumbent: Optimizers will be started at the best point seen thus far by any optimizer. First point is random. • ExploreExploit: Early starting points are random, but later points are closer to good minima. • Perturbation: Each starting point is a drawn from a multivariate Gaussian distribution centred at the initial parameter set. • Random: Optimizers are started at random locations in parameter space. • SinglePoint: All optimizers are started at the initial parameter values.
ExploreExploit (ParAMS._Generator._ExploreExploit) – Blends a randomly generated point with the location of an existing optimizer, based on the time progress through the optimization. The optimizer is chosen based on a weighted roulette selection based on their function value. Early in the optimization optimizers are started randomly, and later they are started near previously found good minima.
Perturbation (ParAMS._Generator._Perturbation) – Randomly generates parameter vectors from a multivariate normal distribution around the starting parameters.
- class _ExploreExploit[source]¶
Blends a randomly generated point with the location of an existing optimizer, based on the time progress through the optimization. The optimizer is chosen based on a weighted roulette selection based on their function value. Early in the optimization optimizers are started randomly, and later they are started near previously found good minima.
- Variables:
Focus (float | FloatKey) – The blend parameter between random point and incumbent points. Used as follows: p=(f_calls / max_f_calls) ** focus
MaxFunctionCalls (int | IntKey) – Maximum function calls allowed for the optimization, at and beyond this point there is a 100% chance that a previously evaluated point will be returned by the generator. If the optimization is not limited by the number of function calls, provide an estimate.
- class _LoggingInterval[source]¶
Number of function evaluations between every log to file.
- Variables:
The number of function evaluations between flushes of the output streams to disk.
If Flush = General, then files will be flushed after every logged call.
The number of function evaluations between writes to stdout, running_loss.txt, running_stats.txt and all latest/ and best/ files.
This is also the interval with which the validation set will be evaluated and logged.
History (int | IntKey) – The number of function evaluations between saves to the history directory with copies of latest/.
Parameters (int | IntKey) – The number of function evaluations between writes to running_active_parameters.txt.
- class _LossValuesKernel[source]¶
Kernel applied to the parameters for which sensitivity is being measured.
- Variables:
Cut-off parameter for the Threshold kernel between zero and one.
All loss values are scaled by taking the logarithm and then adjusted to a range between zero and one. This parameter is a value within this scaled space.
Gamma (float | FloatKey) – Bandwidth parameter for the conjunctive-Gaussian kernel.
Bandwidth parameter for the Gaussian kernel.
If not specified or -1, calculates a reasonable default based on the number of parameters being tested.
Type (Literal["Gaussian", "ConjunctiveGaussian", "Threshold", "Polynomial", "Linear"]) – Name of the kernel to applied to the parameters for which sensitivity is being measured.
Polynomial (ParAMS._LossValuesKernel._Polynomial) – Settings for the Polynomial kernel.
- class _MachineLearning[source]¶
Options for Task MachineLearning.
- Variables:
Backend (Literal["Custom", "M3GNet", "NequIP", "Test"]) – The backend to use. You must separately install the backend before running a training job.
CommitteeSize (int | IntKey) – The number of independently trained ML potentials.
LoadModel (str | Path | StringKey) – Load a previously fitted model from a ParAMS results directory. A ParAMS results directory should contain two subdirectories
optimizationandsettings_and_initial_data. This option ignores all settings inside model blocks.MaxEpochs (int | IntKey) – Set the maximum number of epochs a backend should perform.
RunAMSAtEnd (BoolType | BoolKey) – Whether to run the (committee) ML potential through AMS at the end. This will create the energy/forces scatter plots for the final trained model.
Custom (ParAMS._MachineLearning._Custom) – Set up a custom fitting program within ParAMS
LossCoeffs (ParAMS._MachineLearning._LossCoeffs) – Modify the coefficients for the machine learning loss function. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
M3GNet (ParAMS._MachineLearning._M3GNet) – Options for M3GNet fitting.
NequIP (ParAMS._MachineLearning._NequIP) – Options for NequIP fitting.
Target (ParAMS._MachineLearning._Target) – Target values for stopping training. If both the training and validation metrics are smaller than the specified values, the training will stop early. Only supported by the M3GNet backend.
- class _LossCoeffs[source]¶
Modify the coefficients for the machine learning loss function. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
- Variables:
AverageForcePerAtom (BoolType | BoolKey) – For each force data entry, divide the loss contribution by the number of concomittent atoms. This is the same as the behavior for ParAMS Optimization, but it is turned off by default in Task MachineLearning. For machine learning, setting this to ‘No’ can be better since larger molecules will contribute more to the loss. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
Energy (float | FloatKey) – Coefficient for the contribution of loss due to the energy. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
Forces (float | FloatKey) – Coefficient for the contribution of loss due to the forces. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
- class _M3GNet[source]¶
Options for M3GNet fitting.
- Variables:
LearningRate (float | FloatKey) – Learning rate for the M3GNet weight optimization.
Model (Literal["UniversalPotential", "Custom", "ModelDir"]) – How to specify the model for the M3GNet backend. Either a Custom model can be made from scratch or an existing model directory can be loaded to obtain the model settings.
ModelDir (str | Path | StringKey) – Path to the directory defining the model. This folder should contain the files: ‘checkpoint’, ‘m3gnet.data-00000-of-00001’, ‘ m3gnet.index’ and ‘m3gnet.json’
Custom (ParAMS._MachineLearning._M3GNet._Custom) – Specify a custom M3GNet model.
UniversalPotential (ParAMS._MachineLearning._M3GNet._UniversalPotential) – Settings for (transfer) learning with the M3GNet Universal Potential.
- class _Custom[source]¶
Specify a custom M3GNet model.
- Variables:
MaxL (int | IntKey) – Include spherical components up to order MaxL. Higher gives a better angular resolution, but increases computational cost substantially.
MaxN (int | IntKey) – Include radial components up to the MaxN’th root of the spherical Bessel function. Higher gives a better radial resolution, but increases computational cost substantially.
NumNeurons (int | IntKey) – Number of neurons in each layer.
ThreebodyCutoff (float | FloatKey) – Cutoff radius of the three-body interaction.
- class _UniversalPotential[source]¶
Settings for (transfer) learning with the M3GNet Universal Potential.
- Variables:
Featurizer (BoolType | BoolKey) – Train the Featurizer layer of the M3GNet universal potential.
Final (BoolType | BoolKey) – Train the Final layer of the M3GNet universal potential.
GraphLayer1 (BoolType | BoolKey) – Train the first Graph layer of the M3GNet universal potential.
GraphLayer2 (BoolType | BoolKey) – Train the second Graph layer of the M3GNet universal potential.
GraphLayer3 (BoolType | BoolKey) – Train the third Graph layer of the M3GNet universal potential.
ThreeDInteractions1 (BoolType | BoolKey) – Train the first ThreeDInteractions (three-body terms) layer of the M3GNet universal potential.
ThreeDInteractions2 (BoolType | BoolKey) – Train the second ThreeDInteractions (three-body terms) layer of the M3GNet universal potential.
ThreeDInteractions3 (BoolType | BoolKey) – Train the third ThreeDInteractions (three-body terms) layer of the M3GNet universal potential.
Version (Literal["2022"]) – Which version of the M3GNet Universal Potential to use.
- class _NequIP[source]¶
Options for NequIP fitting.
- Variables:
LearningRate (float | FloatKey) – Learning rate for the NequIP weight optimization
Model (Literal["Custom", "ModelFile"]) – How to specify the model for the NequIP backend. Either a Custom model can be made from scratch or an existing ‘model.pth’ file can be loaded to obtain the model settings.
ModelFile (str | Path | StringKey) – Path to the model.pth file defining the model.
UseRescalingFromLoadedModel (BoolType | BoolKey) – When loading a model with LoadModel or NequiP%ModelFile do not recalculate the dataset rescaling but use the value from the loaded model.
Custom (ParAMS._MachineLearning._NequIP._Custom) – Specify a custom NequIP model.
- class _Custom[source]¶
Specify a custom NequIP model.
- class _Target[source]¶
Target values for stopping training. If both the training and validation metrics are smaller than the specified values, the training will stop early. Only supported by the M3GNet backend.
- Variables:
Forces (ParAMS._MachineLearning._Target._Forces) – Forces (as reported by the backend)
- class _Optimizer[source]¶
An optimizer which may be used during the optimization.
- Variables:
Type (Literal["AdaptiveRateMonteCarlo", "CMAES", "Nevergrad", "Scipy", "RandomSampling", "GridSampling"]) –
Name of the optimization algorithm or interface.
Available options: • Adaptive Rate Monte Carlo • CMAES (Covariance Matrix Adaptation Evolutionary Strategy) • Nevergrad (Interface to many other algorithms) • Scipy (Interface to classic optimization algorithms) • Random Sampling (Uniform random sampling of the space for later analysis. NOT an actual optimizer) • Grid Sampling (Gridwise sampling of the parameter space for later analysis. NOT and actual optimizer)
AdaptiveRateMonteCarlo (ParAMS._Optimizer._AdaptiveRateMonteCarlo) – Settings for the Adaptive Rate Monte-Carlo optimizer
CMAES (ParAMS._Optimizer._CMAES) – Settings for the Covariance Matrix Adaptation Evolutionary Strategy
GridSampling (ParAMS._Optimizer._GridSampling) – Settings for grid-wise sampling of the parameter space.
Nevergrad (ParAMS._Optimizer._Nevergrad) – Settings for the Nevergrad wrapper which gives access to many optimization algorithms.
RandomSampling (ParAMS._Optimizer._RandomSampling) – Settings for a totally random sampler of the parameter space.
Scipy (ParAMS._Optimizer._Scipy) – Settings for the Scipy wrapper which gives access to many optimization algorithms. For parallel optimizations, Nevergrad is preferred as it provides better control options.
- class _AdaptiveRateMonteCarlo[source]¶
Settings for the Adaptive Rate Monte-Carlo optimizer
- class _CMAES[source]¶
Settings for the Covariance Matrix Adaptation Evolutionary Strategy
- Variables:
ForceInjections (BoolType | BoolKey) –
If Yes, injections of parameter vectors into the solver will be exact, guaranteeing that that solution will be in the next iteration’s population.
If No, the injection will result in a direction relative nudge towards the vector. Forcing the injecting can limit global exploration but non-forced injections may have little effect.
See also glompo.optimizer.cmaes.injectioninterval
InjectionInterval (int | IntKey) –
Number of iterations between injections of the incumbent solution into the sampled population. Defaults to 0, i.e., no injections are performed.
Injections can be helpful in increasing the convergence speed and nudging optimizers toward a solution. This is a form of elitism and will limit exploration.
Of particular interest is pairing this key with glompo.ShareBestEvaluationBetweenOptimizers. In this case the incumbent that is injected comes from other optimizers run in parallel. This can help nudge optimizers towards better solutions while dramatically improving convergence speed.
See also glompo.optimizer.cmaes.forceinjections
KeepFiles (BoolType | BoolKey) – Keep CMA specific history files about the state of the covariance matrix and other algorithm variables.
MinSigma (float | FloatKey) – Convergence condition to terminate the optimization when the standard deviation of the sampling distribution falls below this value.
Number of function evaluations per CMA-ES iteration.
If not specified or -1, then the population size will equal the number of workers available to the optimizer. This is computationally efficient but not algorithmically efficient.
A value of zero or one will set the population size to the value suggested by CMA based on the dimensionality of the problem. This produces the best algorithm performance but may be computationally inefficient if resources are left idling while waiting for other evaluations to complete.
Note: a population of one is not allowed by CMA, therefore, it is changed to the algorithm default. This also means that giving CMA only one worker will also change the popsize to the algorithm default.
Sampler (Literal["full", "vd", "vkd"]) –
Choice of full or restricted Gaussian sampling procedures.
Options: • full: Full sampling procedure • vd: Restricted sampler for VD-CMA (Linear time/space comparison-based natural gradient optimization) • vkd: Restricted sampler for VkD-CMA (Time/space variant of CMA-ES)
Initial standard deviation of the multivariate normal distribution from which trials are drawn.
The recommended range of values for is between 0.01 and 0.5. Lower values sample very locally and converge quickly, higher values sample broadly but will take a long time to converge.
Verbose (BoolType | BoolKey) – Produce a printstream of results from within the optimizer itself.
Settings (str | Sequence[str] | FreeBlock) –
‘argument value’ pairs for extra CMA specific configuration arguments.
See CMAOptimizer API documentation for more details on which options are possible.
- class _Nevergrad[source]¶
Settings for the Nevergrad wrapper which gives access to many optimization algorithms.
- Variables:
Algorithm (Literal["ASCMA2PDEthird", "ASCMADEQRthird", "ASCMADEthird", "AlmostRotationInvariantDE", "AvgMetaLogRecentering", "AvgMetaRecentering", "BO", "CM", "CMA", "CMandAS", "CMandAS2", "CMandAS3", "CauchyLHSSearch", "CauchyOnePlusOne", "CauchyScrHammersleySearch", "Cobyla", "DE", "DiagonalCMA", "DiscreteOnePlusOne", "DoubleFastGADiscreteOnePlusOne", "EDA", "ES", "FCMA", "HaltonSearch", "HaltonSearchPlusMiddlePoint", "HammersleySearch", "HammersleySearchPlusMiddlePoint", "LHSSearch", "LargeHaltonSearch", "LhsDE", "MEDA", "MPCEDA", "MetaLogRecentering", "MetaRecentering", "MixES", "MultiCMA", "MultiScaleCMA", "MutDE", "NGO", "NaiveIsoEMNA", "NaiveTBPSA", "NelderMead", "NoisyBandit", "NoisyDE", "NoisyDiscreteOnePlusOne", "NoisyOnePlusOne", "OAvgMetaLogRecentering", "ORandomSearch", "OScrHammersleySearch", "OnePlusOne", "OptimisticDiscreteOnePlusOne", "OptimisticNoisyOnePlusOne", "PBIL", "PCEDA", "PSO", "ParaPortfolio", "Portfolio", "Powell", "QORandomSearch", "QOScrHammersleySearch", "QrDE", "RCobyla", "RPowell", "RSQP", "RandomSearch", "RandomSearchPlusMiddlePoint", "RealSpacePSO", "RecES", "RecMixES", "RecMutDE", "RecombiningPortfolioOptimisticNoisyDiscreteOnePlusOne", "RotationInvariantDE", "SPSA", "SQP", "SQPCMA", "ScrHaltonSearch", "ScrHaltonSearchPlusMiddlePoint", "ScrHammersleySearch", "ScrHammersleySearchPlusMiddlePoint", "Shiva", "SplitOptimizer", "TBPSA", "TripleCMA", "TwoPointsDE", "cGA", "chainCMAPowel"]) –
Optimization strategy to use.
See Nevergrad documentation for details of the available methods.
Zero (float | FloatKey) – Function value below which the algorithm will terminate.
Settings (str | Sequence[str] | FreeBlock) –
‘argument value’ pairs for extra algorithm-specific configuration arguments.
See Nevergrad API documentation for more details on which options are possible.
- class _Scipy[source]¶
Settings for the Scipy wrapper which gives access to many optimization algorithms. For parallel optimizations, Nevergrad is preferred as it provides better control options.
- Variables:
Algorithm (Literal["Nelder-Mead", "Powell", "CG", "BFGS", "Newton-CG", "L-BFGS-B", "TNC", "COBYLA", "SLSQP", "trust-constr", "dogleg", "trust-ncg", "trust-exact", "trust-krylov"]) –
Optimization strategy to use.
See Scipy documentation for details of the available methods.
Hessian (Literal["2-point", "3-point", "cs"]) – Choice of the Hessian estimation method. Only for Newton-CG, dogleg, trust-ncg, trust-krylov, trust-exact and trust-constr.
Jacobian (Literal["2-point", "3-point", "cs"]) – Choice of gradient estimation method. Only for CG, BFGS, Newton-CG, L-BFGS-B, TNC, SLSQP, dogleg, trust-ncg, trust-krylov, trust-exact and trust-constr.
Tolerance (float | FloatKey) – Tolerance for termination. Interpretation linked to chosen method. See Scipy docs.
Settings (str | Sequence[str] | FreeBlock) –
‘argument value’ pairs for extra algorithm-specific configuration arguments.
See Scipy API documentation for more details on which options are possible.
- class _OptimizerSelector[source]¶
If multiple Optimizers are included, then this block must be included and configures the Selector which will choose between them.
- Variables:
Type (Literal["Cycle", "Random", "Chain"]) –
Name of the algorithm selecting between optimizers.
Available options: • Cycle (Default): Sequential loop through available optimizers. • Random: Optimizers are selected randomly from the available options. • Chain: Time-based progression through the list of available optimizers. The next option will be started once a certain number of loss function evaluations have been used.
Chain (ParAMS._OptimizerSelector._Chain) – Start different optimizers at different points in time based on the number of function evaluations used.
- class _Chain[source]¶
Start different optimizers at different points in time based on the number of function evaluations used.
- Variables:
Thresholds (Iterable[int] | IntListKey) – List of loss function evaluation thresholds which switch to the next optimizer in the list. If there are n optimizers available, then this list should have n-1 thresholds.
- class _ParallelLevels[source]¶
Distribution of threads/processes between the parallelization levels.
- Variables:
CommitteeMembers (int | IntKey) – Maximum number of committee member optimizations to run in parallel. If set to zero will take the minimum of MachineLearning%CommitteeSize and the number of available cores (NSCM)
Cores (int | IntKey) – Number of cores to use per committee member optimization. By default (0) the available cores (NSCM) divided equally among committee members. When using GPU offloading, consider setting this to 1.
Jobs (int | IntKey) – Number of JobCollection jobs to run in parallel for each loss function evaluation.
Optimizations (int | IntKey) – Number of independent optimizers to run in parallel.
ParameterVectors (int | IntKey) –
Number of parameter vectors to try in parallel for each optimizer iteration. This level of parallelism can only be used with optimizers that support parallel optimization!
Default (0) will set this value to the number of cores on the system divided by the number of optimizers run in parallel, i.e., each optimizer will be given an equal share of the resources.
Number of processes (MPI ranks) to spawn for each JobCollection job. This effectively sets the NSCM environment variable for each job.
A value of -1 will disable explicit setting of related variables. We recommend a value of 1 in almost all cases. A value greater than 1 would only be useful if you parametrize DFTB with a serial optimizer and have very few jobs in the job collection.
Number of threads to use for each of the processes. This effectively set the OMP_NUM_THREADS environment variable. Note that the DFTB engine does not use threads, so the value of this variable would not have any effect. We recommend always leaving it at the default value of 1. Please consult the manual of the engine you are parameterizing.
A value of -1 will disable explicit setting of related variables.
- class _ParametersKernel[source]¶
Kernel applied to the parameters for which sensitivity is being measured.
- Variables:
Cut-off parameter for the Threshold kernel between zero and one.
All loss values are scaled by taking the logarithm and then adjusted to a range between zero and one. This parameter is a value within this scaled space.
Gamma (float | FloatKey) – Bandwidth parameter for the conjunctive-Gaussian kernel.
Sigma (float | FloatKey) – Bandwidth parameter for the Gaussian kernel.
Type (Literal["Gaussian", "ConjunctiveGaussian", "Threshold", "Polynomial", "Linear"]) – Name of the kernel to applied to the parameters for which sensitivity is being measured.
Polynomial (ParAMS._ParametersKernel._Polynomial) – Settings for the Polynomial kernel.
- class _Stopper[source]¶
A Stopper used to terminate optimizers early.
- Variables:
MaxFunctionCalls (int | IntKey) –
Returns True after an optimizer has evaluated at least n points.
Use in an AND combination with other stoppers to keep optimizers alive for at least some period of time, or alone or in an OR combination to shut them down after some period of time.
MaxSequentialInvalidPoints (int | IntKey) – Return True if the optimizer has failed to find a finite function value in the last n iterations. Usually indicates a lost optimizer with poor starting point.
OptimizerType (Literal["AdaptiveRateMonteCarlo", "CMAES", "Nevergrad", "Scipy", "RandomSampling", "GridSampling"]) – Intended for use with other stoppers to allow for specific hunting conditions based on the type of optimizer.
Type (Literal["BestFunctionValueUnmoving", "CurrentFunctionValueUnmoving", "MaxSequentialInvalidPoints", "MaxFunctionCalls", "MaxInteroptimizerDistance", "MinStepSize", "TimeAnnealing", "OptimizerType", "ValueAnnealing", "ValidationWorsening"]) –
Conditions used to stop individual optimizers. Only optimizers which have not seen the current best value will be hunted. The ‘best’ optimizer will always be left alive.
Available options: • Best Function Value Unmoving: Shutdown optimizers who haven’t improved their best point in a long time. • Current Function Value Unmoving: Shutdown optimizers which have not changed their currently explored loss function value a lot in a long time. • Max Sequential Invalid Points: Stop optimizers that are stuck in areas of parameter space which return non-finite loss function values. • Max Function Calls: Stop optimizers when they have evaluated the loss function a certain number of times. • Max Interoptimizer Distance: Stop optimizers too close together in parameter space. • Min Step Size: Stop optimizers who are taking very small steps between iterations. • Time Annealing: For use with other conditions. Keep an optimizer alive for longer if it’s relatively new. • Optimizer Type: For use with other conditions. Shutdown optimizers of a specific type. • Value Annealing: For use with other conditions. Keep an optimizer alive if it looks likely to overtake the best optimizer. • Validation Worsening: Stops optimizers which are evaluating points where the validation set loss value is worse than the average of several previously seen ones.
BestFunctionValueUnmoving (ParAMS._Stopper._BestFunctionValueUnmoving) – Return True if an optimizer’s best value has not improved significantly in a given amount of time.
CurrentFunctionValueUnmoving (ParAMS._Stopper._CurrentFunctionValueUnmoving) – Return True if an optimizer’s current function value has not improved significantly in a given amount of time.
MaxInteroptimizerDistance (ParAMS._Stopper._MaxInteroptimizerDistance) – Return True if two optimizers are evaluating points too close to one another in parameter space.
MinStepSize (ParAMS._Stopper._MinStepSize) – Return True if an optimizer’s step size between evaluations is too small.
TimeAnnealing (ParAMS._Stopper._TimeAnnealing) – Keeps optimizers alive based on how long they have been alive. Randomly keeps optimizers alive based on how long (in function evaluations) they have been active. The newer an optimizer is, the more likely it will pass the test and be kept alive. Used to temper very strict termination conditions.
ValidationWorsening (ParAMS._Stopper._ValidationWorsening) – Return True if the loss value of the validation set is increasing.
ValueAnnealing (ParAMS._Stopper._ValueAnnealing) – Intended for use with other stoppers. This condition is unlikely to stop a victim which has a loss function value very near the best seen thus far, but the probability of stopping increases with the difference between them.
- class _BestFunctionValueUnmoving[source]¶
Return True if an optimizer’s best value has not improved significantly in a given amount of time.
- class _CurrentFunctionValueUnmoving[source]¶
Return True if an optimizer’s current function value has not improved significantly in a given amount of time.
- class _MaxInteroptimizerDistance[source]¶
Return True if two optimizers are evaluating points too close to one another in parameter space.
- Variables:
CompareAllOptimizers (BoolType | BoolKey) – If Yes the distance between all optimizer combinations are compared, otherwise worse optimizers are only compared to the best one.
MaxRelativeDistance (float | FloatKey) – Fraction (between 0 and 1) of the maximum distance in the space (from the point at all lower bounds to the point at all upper bounds) below which the optimizers are deemed too close and the victim will be stopped.
- class _MinStepSize[source]¶
Return True if an optimizer’s step size between evaluations is too small.
- class _TimeAnnealing[source]¶
Keeps optimizers alive based on how long they have been alive. Randomly keeps optimizers alive based on how long (in function evaluations) they have been active. The newer an optimizer is, the more likely it will pass the test and be kept alive. Used to temper very strict termination conditions.
- Variables:
CriticalRatio (float | FloatKey) – Critical ratio of function calls between stopper and victim above which the victim is guaranteed to survive. Values lower than one are looser and allow the victim to survive even if it has been in operation longer than the stopper. Values higher than one are stricter and may stop the victim even if it has iterated fewer times than the stopper.
- class _ValidationWorsening[source]¶
Return True if the loss value of the validation set is increasing.
- class ParAMSGenerateReference[source]¶
- Variables:
EngineCollection (str | StringKey) – Path to (optional) JobCollection Engines YAML file.
JobCollection (str | StringKey) – Path to JobCollection YAML file.
ParameterInterface (str | StringKey) – Path to parameter interface YAML file.
RestartDirectory (str | Path | StringKey) –
Specify a directory to continue interrupted GenerateReference or SinglePoint calculations. The directory depends on the task:
GenerateReference: results/reference_jobs SinglePoint: results/single_point/jobs
Note: If you use the GUI this directory will be COPIED into the results folder and the name will be prepended with ‘dep-’. This can take up a lot of disk space, so you may want to remove the ‘dep-’ folder after the job has finished.
ResultsDirectory (str | Path | StringKey) – Directory in which output files will be created.
Task (Literal["Optimization", "GenerateReference", "SinglePoint", "Sensitivity", "MachineLearning"]) –
Task to run.
Available options: •MachineLearning: Optimization for machine learning models. •Optimization: Global optimization powered by GloMPO •Generate Reference: Run jobs with reference engine to get reference values •Single Point: Evaluate the current configuration of jobs, training data, and parameters •Sensitivity: Measure the sensitivity of the loss function to each of the active parameters
DataSet (ParAMSGenerateReference._DataSet) – Configuration settings for each data set in the optimization.
ParallelLevels (ParAMSGenerateReference._ParallelLevels) – Distribution of threads/processes between the parallelization levels.
- class _DataSet[source]¶
Configuration settings for each data set in the optimization.
- Variables:
BatchSize (int | IntKey) – Number of data set entries to be evaluated per epoch. Default 0 means all entries.
EvaluateEvery (int | IntKey) –
This data set is evaluated every n evaluations of the training set.
This will always be set to 1 for the training set. For other data sets it will be adjusted to the closest multiple of LoggingInterval%General, i.e., you cannot evaluate an extra data set more frequently than you log it.
LossFunction (Literal["mae", "rmse", "sse", "sae"]) –
Loss function used to quantify the error between model and reference values. This becomes the minimization task.
Available options: • mae: Mean absolute error • rmse: Root mean squared error • sse: Sum of squared errors • sae: Sum of absolute errors
MaxJobs (int | IntKey) – Limit each evaluation to a subset of n jobs. Default 0 meaning all jobs are used.
MaxJobsShuffle (BoolType | BoolKey) – Use a different job subset every for every evaluation.
Unique data set identifier.
The first occurrence of DataSet will always be called training_set. The second will always be called validation_set. These cannot be overwritten.
Later occurrences will default to data_set_xx where xx starts at 03 and increments from there. This field can be used to customize the latter names.
UsePipe (BoolType | BoolKey) – Use AMS Pipe for suitable jobs to speed-up evaluation.
- class _ParallelLevels[source]¶
Distribution of threads/processes between the parallelization levels.
- Variables:
CommitteeMembers (int | IntKey) – Maximum number of committee member optimizations to run in parallel. If set to zero will take the minimum of MachineLearning%CommitteeSize and the number of available cores (NSCM)
Cores (int | IntKey) – Number of cores to use per committee member optimization. By default (0) the available cores (NSCM) divided equally among committee members. When using GPU offloading, consider setting this to 1.
Jobs (int | IntKey) – Number of JobCollection jobs to run in parallel for each loss function evaluation.
Optimizations (int | IntKey) – Number of independent optimizers to run in parallel.
ParameterVectors (int | IntKey) –
Number of parameter vectors to try in parallel for each optimizer iteration. This level of parallelism can only be used with optimizers that support parallel optimization!
Default (0) will set this value to the number of cores on the system divided by the number of optimizers run in parallel, i.e., each optimizer will be given an equal share of the resources.
Number of processes (MPI ranks) to spawn for each JobCollection job. This effectively sets the NSCM environment variable for each job.
A value of -1 will disable explicit setting of related variables. We recommend a value of 1 in almost all cases. A value greater than 1 would only be useful if you parametrize DFTB with a serial optimizer and have very few jobs in the job collection.
Number of threads to use for each of the processes. This effectively set the OMP_NUM_THREADS environment variable. Note that the DFTB engine does not use threads, so the value of this variable would not have any effect. We recommend always leaving it at the default value of 1. Please consult the manual of the engine you are parameterizing.
A value of -1 will disable explicit setting of related variables.
- class ParAMSMachineLearning[source]¶
- Variables:
EngineCollection (str | StringKey) – Path to (optional) JobCollection Engines YAML file.
JobCollection (str | StringKey) – Path to JobCollection YAML file.
ResultsDirectory (str | Path | StringKey) – Directory in which output files will be created.
Task (Literal["Optimization", "GenerateReference", "SinglePoint", "Sensitivity", "MachineLearning"]) –
Task to run.
Available options: •MachineLearning: Optimization for machine learning models. •Optimization: Global optimization powered by GloMPO •Generate Reference: Run jobs with reference engine to get reference values •Single Point: Evaluate the current configuration of jobs, training data, and parameters •Sensitivity: Measure the sensitivity of the loss function to each of the active parameters
DataSet (ParAMSMachineLearning._DataSet) – Configuration settings for each data set in the optimization.
MachineLearning (ParAMSMachineLearning._MachineLearning) – Options for Task MachineLearning.
ParallelLevels (ParAMSMachineLearning._ParallelLevels) – Distribution of threads/processes between the parallelization levels.
- class _DataSet[source]¶
Configuration settings for each data set in the optimization.
- Variables:
BatchSize (int | IntKey) – Number of data set entries to be evaluated per epoch. Default 0 means all entries.
EvaluateEvery (int | IntKey) –
This data set is evaluated every n evaluations of the training set.
This will always be set to 1 for the training set. For other data sets it will be adjusted to the closest multiple of LoggingInterval%General, i.e., you cannot evaluate an extra data set more frequently than you log it.
LossFunction (Literal["mae", "rmse", "sse", "sae"]) –
Loss function used to quantify the error between model and reference values. This becomes the minimization task.
Available options: • mae: Mean absolute error • rmse: Root mean squared error • sse: Sum of squared errors • sae: Sum of absolute errors
MaxJobs (int | IntKey) – Limit each evaluation to a subset of n jobs. Default 0 meaning all jobs are used.
MaxJobsShuffle (BoolType | BoolKey) – Use a different job subset every for every evaluation.
Unique data set identifier.
The first occurrence of DataSet will always be called training_set. The second will always be called validation_set. These cannot be overwritten.
Later occurrences will default to data_set_xx where xx starts at 03 and increments from there. This field can be used to customize the latter names.
UsePipe (BoolType | BoolKey) – Use AMS Pipe for suitable jobs to speed-up evaluation.
- class _MachineLearning[source]¶
Options for Task MachineLearning.
- Variables:
Backend (Literal["Custom", "M3GNet", "NequIP", "Test"]) – The backend to use. You must separately install the backend before running a training job.
CommitteeSize (int | IntKey) – The number of independently trained ML potentials.
LoadModel (str | Path | StringKey) – Load a previously fitted model from a ParAMS results directory. A ParAMS results directory should contain two subdirectories
optimizationandsettings_and_initial_data. This option ignores all settings inside model blocks.MaxEpochs (int | IntKey) – Set the maximum number of epochs a backend should perform.
RunAMSAtEnd (BoolType | BoolKey) – Whether to run the (committee) ML potential through AMS at the end. This will create the energy/forces scatter plots for the final trained model.
Custom (ParAMSMachineLearning._MachineLearning._Custom) – Set up a custom fitting program within ParAMS
LossCoeffs (ParAMSMachineLearning._MachineLearning._LossCoeffs) – Modify the coefficients for the machine learning loss function. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
M3GNet (ParAMSMachineLearning._MachineLearning._M3GNet) – Options for M3GNet fitting.
NequIP (ParAMSMachineLearning._MachineLearning._NequIP) – Options for NequIP fitting.
Target (ParAMSMachineLearning._MachineLearning._Target) – Target values for stopping training. If both the training and validation metrics are smaller than the specified values, the training will stop early. Only supported by the M3GNet backend.
- class _LossCoeffs[source]¶
Modify the coefficients for the machine learning loss function. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
- Variables:
AverageForcePerAtom (BoolType | BoolKey) – For each force data entry, divide the loss contribution by the number of concomittent atoms. This is the same as the behavior for ParAMS Optimization, but it is turned off by default in Task MachineLearning. For machine learning, setting this to ‘No’ can be better since larger molecules will contribute more to the loss. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
Energy (float | FloatKey) – Coefficient for the contribution of loss due to the energy. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
Forces (float | FloatKey) – Coefficient for the contribution of loss due to the forces. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
- class _M3GNet[source]¶
Options for M3GNet fitting.
- Variables:
LearningRate (float | FloatKey) – Learning rate for the M3GNet weight optimization.
Model (Literal["UniversalPotential", "Custom", "ModelDir"]) – How to specify the model for the M3GNet backend. Either a Custom model can be made from scratch or an existing model directory can be loaded to obtain the model settings.
ModelDir (str | Path | StringKey) – Path to the directory defining the model. This folder should contain the files: ‘checkpoint’, ‘m3gnet.data-00000-of-00001’, ‘ m3gnet.index’ and ‘m3gnet.json’
Custom (ParAMSMachineLearning._MachineLearning._M3GNet._Custom) – Specify a custom M3GNet model.
UniversalPotential (ParAMSMachineLearning._MachineLearning._M3GNet._UniversalPotential) – Settings for (transfer) learning with the M3GNet Universal Potential.
- class _Custom[source]¶
Specify a custom M3GNet model.
- Variables:
MaxL (int | IntKey) – Include spherical components up to order MaxL. Higher gives a better angular resolution, but increases computational cost substantially.
MaxN (int | IntKey) – Include radial components up to the MaxN’th root of the spherical Bessel function. Higher gives a better radial resolution, but increases computational cost substantially.
NumNeurons (int | IntKey) – Number of neurons in each layer.
ThreebodyCutoff (float | FloatKey) – Cutoff radius of the three-body interaction.
- class _UniversalPotential[source]¶
Settings for (transfer) learning with the M3GNet Universal Potential.
- Variables:
Featurizer (BoolType | BoolKey) – Train the Featurizer layer of the M3GNet universal potential.
Final (BoolType | BoolKey) – Train the Final layer of the M3GNet universal potential.
GraphLayer1 (BoolType | BoolKey) – Train the first Graph layer of the M3GNet universal potential.
GraphLayer2 (BoolType | BoolKey) – Train the second Graph layer of the M3GNet universal potential.
GraphLayer3 (BoolType | BoolKey) – Train the third Graph layer of the M3GNet universal potential.
ThreeDInteractions1 (BoolType | BoolKey) – Train the first ThreeDInteractions (three-body terms) layer of the M3GNet universal potential.
ThreeDInteractions2 (BoolType | BoolKey) – Train the second ThreeDInteractions (three-body terms) layer of the M3GNet universal potential.
ThreeDInteractions3 (BoolType | BoolKey) – Train the third ThreeDInteractions (three-body terms) layer of the M3GNet universal potential.
Version (Literal["2022"]) – Which version of the M3GNet Universal Potential to use.
- class _NequIP[source]¶
Options for NequIP fitting.
- Variables:
LearningRate (float | FloatKey) – Learning rate for the NequIP weight optimization
Model (Literal["Custom", "ModelFile"]) – How to specify the model for the NequIP backend. Either a Custom model can be made from scratch or an existing ‘model.pth’ file can be loaded to obtain the model settings.
ModelFile (str | Path | StringKey) – Path to the model.pth file defining the model.
UseRescalingFromLoadedModel (BoolType | BoolKey) – When loading a model with LoadModel or NequiP%ModelFile do not recalculate the dataset rescaling but use the value from the loaded model.
Custom (ParAMSMachineLearning._MachineLearning._NequIP._Custom) – Specify a custom NequIP model.
- class _Custom[source]¶
Specify a custom NequIP model.
- class _Target[source]¶
Target values for stopping training. If both the training and validation metrics are smaller than the specified values, the training will stop early. Only supported by the M3GNet backend.
- Variables:
Forces (ParAMSMachineLearning._MachineLearning._Target._Forces) – Forces (as reported by the backend)
- class _ParallelLevels[source]¶
Distribution of threads/processes between the parallelization levels.
- Variables:
CommitteeMembers (int | IntKey) – Maximum number of committee member optimizations to run in parallel. If set to zero will take the minimum of MachineLearning%CommitteeSize and the number of available cores (NSCM)
Cores (int | IntKey) – Number of cores to use per committee member optimization. By default (0) the available cores (NSCM) divided equally among committee members. When using GPU offloading, consider setting this to 1.
Jobs (int | IntKey) – Number of JobCollection jobs to run in parallel for each loss function evaluation.
Optimizations (int | IntKey) – Number of independent optimizers to run in parallel.
ParameterVectors (int | IntKey) –
Number of parameter vectors to try in parallel for each optimizer iteration. This level of parallelism can only be used with optimizers that support parallel optimization!
Default (0) will set this value to the number of cores on the system divided by the number of optimizers run in parallel, i.e., each optimizer will be given an equal share of the resources.
Number of processes (MPI ranks) to spawn for each JobCollection job. This effectively sets the NSCM environment variable for each job.
A value of -1 will disable explicit setting of related variables. We recommend a value of 1 in almost all cases. A value greater than 1 would only be useful if you parametrize DFTB with a serial optimizer and have very few jobs in the job collection.
Number of threads to use for each of the processes. This effectively set the OMP_NUM_THREADS environment variable. Note that the DFTB engine does not use threads, so the value of this variable would not have any effect. We recommend always leaving it at the default value of 1. Please consult the manual of the engine you are parameterizing.
A value of -1 will disable explicit setting of related variables.
- class ParAMSOptimize[source]¶
- Variables:
ApplyStoppersToBestOptimizer (BoolType | BoolKey) – By default the stoppers are not applied to the best optimizer (the one who has seen the best value thus far). This is because many stoppers are based on comparisons to the best optimizer, and in most scenarios one would like to keep a well-performing optimizer alive. For some stopper configurations this paradigm does not make sense and we would prefer to apply the stoppers equally to all optimizers.
CheckStopperInterval (int | IntKey) – Number of loss function evaluations between evaluations of the stopper conditions.
EndTimeout (float | FloatKey) –
The amount of time the manager will wait trying to smoothly join each optimizer at the end of the run. If exceeded the manager will abandon the optimizer and shutdown. This can raise errors from the abandoned threads, but may be needed to ensure the manager closes and does not hang.
This option is often needed if the Scipy optimizers are being used and should be set to a low value.
EngineCollection (str | StringKey) – Path to (optional) JobCollection Engines YAML file.
ExitConditionBooleanCombination (str | StringKey) –
If multiple ExitConditions are used, this key indicates how their evaluations relate to one another.
Use an integer to refer to a exit condition (defined by order in input file).
Recognizes the symbols: ( ) & |
E.g. (1 & 2) | 3.
Defaults to an OR combination of all selected exit conditions.
GlompoLogging (BoolType | BoolKey) – Include status and progress information from the optimization manager in the printstreams.
GlompoSummaryFiles (Literal["None", "1", "2", "3", "4"]) –
Indicates what GloMPO-style outputs you would like saved to disk. Higher values also save all lower level information.
Available options: • None: Nothing is saved. • 1: YAML file with summary info about the optimization settings, performance and the result. • 2: PNG file showing the trajectories of the optimizers. • 3: HDF5 file containing iteration history for each optimizer. • 4: More detailed HDF5 log including the residual results for each optimizer, data set and iteration.
JobCollection (str | StringKey) – Path to JobCollection YAML file.
MoreExtractorsPath (str | Path | StringKey) – Path to directory with extractors.
PLAMSWorkingDirectory (str | Path | StringKey) – Path to PLAMS working directory to temporarily hold Job results files.
ParameterInterface (str | StringKey) – Path to parameter interface YAML file.
PrintStatusInterval (float | FloatKey) – Number of seconds between printing of a status summary.
ResultsDirectory (str | Path | StringKey) – Directory in which output files will be created.
ResumeCheckpoint (str | Path | StringKey) – Path to checkpoint file from which a previous optimization can be resumed.
Scaler (Literal["Linear", "Std", "None", "Optimizers"]) –
Type of scaling applied to the parameters. A scaled input space is needed by many optimization algorithms.
Available options: • Linear: Scale all parameters between 0 and 1. • Std: Scale all parameters between -1 and 1. • None: Applies no scaling. • Optimizers (Default): Does not specify a scaling at the manager level, but allows the selection to be governed by the optimizer/s. If they do not require any particular scaler, then ‘linear’ is selected as the ultimate fallback.
ShareBestEvaluationBetweenOptimizers (BoolType | BoolKey) –
Share new best evaluations from one optimizer to another.
Some algorithms can use this information to accelerate their own convergence. However, optimizers typically have to be configured to receive and handle the information.
This option can work very well with CMA-ES injections.
SkipX0 (BoolType | BoolKey) –
Do not evaluate the initial parameters before starting the optimization.
If the initial parameters evaluated and do not return a finite loss function value, the optimization will abort. A non-infinite value typically indicates crashed jobs.
SplitPrintstreams (BoolType | BoolKey) – Split print statements from each optimizer to separate files.
StopperBooleanCombination (str | StringKey) –
If multiple Stoppers are used this is required to indicate how their evaluations relate to one another.
Use an integer to refer to a stopper (defined by order in input file).
Recognizes the symbols: ( ) & |
E.g. (1 & 2) | 3.
Defaults to an OR combination of all selected stoppers.
Task (Literal["Optimization", "GenerateReference", "SinglePoint", "Sensitivity", "MachineLearning"]) –
Task to run.
Available options: •MachineLearning: Optimization for machine learning models. •Optimization: Global optimization powered by GloMPO •Generate Reference: Run jobs with reference engine to get reference values •Single Point: Evaluate the current configuration of jobs, training data, and parameters •Sensitivity: Measure the sensitivity of the loss function to each of the active parameters
Validation (float | FloatKey) – Fraction of the training set to be used as a validation set. Will be ignored if a validation set has been explicitly defined.
CheckpointControl (ParAMSOptimize._CheckpointControl) – Settings to control the production of checkpoints from which the optimization can be resumed.
Constraints (str | Sequence[str] | FreeBlock) –
Parameter constraint rules to apply to the loss function. One per line. Use ‘p’ to reference the parameter set. You may use indices or names in square brackets to refer to a specific variable.
Note, that indices are absolute i.e., they do not reference the active subset of parameters.
Eg: p[0]>=p[2] p[‘O:p_boc2’]==p[‘H:p_boc2’]
ControlOptimizerSpawning (ParAMSOptimize._ControlOptimizerSpawning) – Control the spawning of optimizers. Note, this is different from ExitConditions. These simply stop new optimizers from spawning, but leave existing ones untouched. ExitConditions shutdown active optimizers and stop the optimization.
DataSet (ParAMSOptimize._DataSet) – Configuration settings for each data set in the optimization.
ExitCondition (ParAMSOptimize._ExitCondition) – A condition used to stop the optimization when it returns true.
Generator (ParAMSOptimize._Generator) – A Generator used to produce x0 starting points for the optimizers.
LoggingInterval (ParAMSOptimize._LoggingInterval) – Number of function evaluations between every log to file.
Optimizer (ParAMSOptimize._Optimizer) – An optimizer which may be used during the optimization.
OptimizerSelector (ParAMSOptimize._OptimizerSelector) – If multiple Optimizers are included, then this block must be included and configures the Selector which will choose between them.
ParallelLevels (ParAMSOptimize._ParallelLevels) – Distribution of threads/processes between the parallelization levels.
Stopper (ParAMSOptimize._Stopper) – A Stopper used to terminate optimizers early.
- class _CheckpointControl[source]¶
Settings to control the production of checkpoints from which the optimization can be resumed.
- Variables:
AtEnd (BoolType | BoolKey) – Create a checkpoint when the exit condition/s are triggered.
AtInitialisation (BoolType | BoolKey) – Create a checkpoint immediately at the start of an optimization.
CheckpointingDirectory (str | Path | StringKey) – Directory in which the checkpoints will be saved. Defaults to ‘checkpoints’ in the results directory
EveryFunctionCalls (int | IntKey) –
Create a checkpoint every n function evaluations.
If not specified or -1, checkpoints are not created based on function calls.
EverySeconds (float | FloatKey) –
Create a checkpoint every n seconds.
If not specified or -1, a checkpoint is not created based time.
Number of earlier checkpoints to keep. Older ones are deleted when a new one is created. -1 does not delete any previous checkpoints, and 0 retains only the most recent checkpoint.
This number excludes the most recent checkpoint which is obviously always retained! So the actual number of files will be larger than this number by one.
NamingFormat (str | StringKey) –
Convention used to name the checkpoints.
The following special keys are supported: • %(date): Current calendar date in YYYYMMDD format • %(year): Year formatted to YYYY • %(yr): Year formatted to YY • %(month): Numerical month formatted to MM • %(day): Calendar day of the month formatted to DD • %(time): Current calendar time formatted to HHMMSS (24-hour style) • %(hour): Hour formatted to HH (24-hour style) • %(min): Minutes formatted to MM • %(sec): Seconds formatted to SS • %(count): Index count of the number of checkpoints constructed. Starts at zero, formatted to 3 digits.
RaiseFail (BoolType | BoolKey) – Raise an error and stop the optimization if a checkpoint fails to be constructed, otherwise issue a warning and continue the optimization.
- class _Constraints[source]¶
Parameter constraint rules to apply to the loss function. One per line. Use ‘p’ to reference the parameter set. You may use indices or names in square brackets to refer to a specific variable.
Note, that indices are absolute i.e., they do not reference the active subset of parameters.
Eg: p[0]>=p[2] p[‘O:p_boc2’]==p[‘H:p_boc2’]
- class _ControlOptimizerSpawning[source]¶
Control the spawning of optimizers. Note, this is different from ExitConditions. These simply stop new optimizers from spawning, but leave existing ones untouched. ExitConditions shutdown active optimizers and stop the optimization.
- Variables:
MaxEvaluations (int | IntKey) –
No new optimizers will be started after this number of function evaluations has been used.
Note, this is different from the equivalent exit condition which would terminate existing optimizers rather than simply not allowing new ones to spawn.
MaxOptimizers (int | IntKey) –
No new optimizers will be started after this number has been spawned.
Note, this is different from the equivalent exit condition which would terminate existing optimizers rather than simply not allowing new ones to spawn.
- class _DataSet[source]¶
Configuration settings for each data set in the optimization.
- Variables:
BatchSize (int | IntKey) – Number of data set entries to be evaluated per epoch. Default 0 means all entries.
EvaluateEvery (int | IntKey) –
This data set is evaluated every n evaluations of the training set.
This will always be set to 1 for the training set. For other data sets it will be adjusted to the closest multiple of LoggingInterval%General, i.e., you cannot evaluate an extra data set more frequently than you log it.
LossFunction (Literal["mae", "rmse", "sse", "sae"]) –
Loss function used to quantify the error between model and reference values. This becomes the minimization task.
Available options: • mae: Mean absolute error • rmse: Root mean squared error • sse: Sum of squared errors • sae: Sum of absolute errors
MaxJobs (int | IntKey) – Limit each evaluation to a subset of n jobs. Default 0 meaning all jobs are used.
MaxJobsShuffle (BoolType | BoolKey) – Use a different job subset every for every evaluation.
Unique data set identifier.
The first occurrence of DataSet will always be called training_set. The second will always be called validation_set. These cannot be overwritten.
Later occurrences will default to data_set_xx where xx starts at 03 and increments from there. This field can be used to customize the latter names.
UsePipe (BoolType | BoolKey) – Use AMS Pipe for suitable jobs to speed-up evaluation.
- class _ExitCondition[source]¶
A condition used to stop the optimization when it returns true.
- Variables:
MaxOptimizersConverged (int | IntKey) –
Return True after n optimizers have converged normally.
An optimizer that has ‘converged’ is distinct from an optimizer that was shutdown via the Stopper settings (i.e. ‘stopped’).
MaxOptimizersStarted (int | IntKey) –
Return True after n optimizers have been started.
Note, this is best used in combination with other conditions because it will stop the optimization as soon as the correct number have been started and not allow newly spawned optimizer to iterate at all.
MaxOptimizersStopped (int | IntKey) –
Return True after n optimizers have been stopped.
An optimizer that has been ‘stopped’ is distinct from an optimizer that stopped due to its internal convergence conditions (i.e., ‘converged’).
MaxTotalFunctionCalls (int | IntKey) – Return True after n function calls have been executed.
TargetFunctionValue (float | FloatKey) – Return True after an optimizer finds a function value less than or equal to n.
TimeLimit (float | FloatKey) –
Return True after the entire optimization has been running for n seconds.
Note, this is NOT the time for any particular optimizer.
See also: Time Limit Through Restarts
TimeLimitThroughRestarts (float | FloatKey) –
Return True after the sum-total of all optimization runs (i.e., through all restarts) has been running for n seconds.
Note, this is NOT the time for any particular optimizer.
See also: Time Limit
Type (Literal["TimeLimit", "MaxTotalFunctionCalls", "MaxOptimizersStarted", "MaxOptimizersConverged", "MaxOptimizersStopped", "StopsAfterConvergence", "TimeLimitThroughRestarts", "TargetFunctionValue"]) –
A condition used to stop the optimization when it returns true.
Available options: • Time Limit: Limit the optimization walltime. • Max Function Calls: Stop the optimization after a certain number of loss function evaluations. • Max Optimizers Started: Shutdown after a certain number of optimizers have been spawned. • Max Optimizers Converged: Shutdown when optimizers have converged via their own internal conditions. • Max Optimizers Stopped: Shutdown when the Stopping configuration has resulted in a number of optimizers being stopped. • Stops After Convergence: Stop when some optimizers have converged and others have been stopped. • Time Limit Through Restarts: Limit the total cumulative walltime across multiple restarts of the optimization. • Target Function Value: Shutdown when a small enough loss function value is found.
StopsAfterConvergence (ParAMSOptimize._ExitCondition._StopsAfterConvergence) – Returns True when at least n_a optimizers have been stopped after n_b optimizers have converged.
- class _Generator[source]¶
A Generator used to produce x0 starting points for the optimizers.
- Variables:
Type (Literal["Incumbent", "ExploreExploit", "Perturbation", "Random", "SinglePoint"]) –
Algorithm used to pick starting points for the optimizers.
Available options: • Incumbent: Optimizers will be started at the best point seen thus far by any optimizer. First point is random. • ExploreExploit: Early starting points are random, but later points are closer to good minima. • Perturbation: Each starting point is a drawn from a multivariate Gaussian distribution centred at the initial parameter set. • Random: Optimizers are started at random locations in parameter space. • SinglePoint: All optimizers are started at the initial parameter values.
ExploreExploit (ParAMSOptimize._Generator._ExploreExploit) – Blends a randomly generated point with the location of an existing optimizer, based on the time progress through the optimization. The optimizer is chosen based on a weighted roulette selection based on their function value. Early in the optimization optimizers are started randomly, and later they are started near previously found good minima.
Perturbation (ParAMSOptimize._Generator._Perturbation) – Randomly generates parameter vectors from a multivariate normal distribution around the starting parameters.
- class _ExploreExploit[source]¶
Blends a randomly generated point with the location of an existing optimizer, based on the time progress through the optimization. The optimizer is chosen based on a weighted roulette selection based on their function value. Early in the optimization optimizers are started randomly, and later they are started near previously found good minima.
- Variables:
Focus (float | FloatKey) – The blend parameter between random point and incumbent points. Used as follows: p=(f_calls / max_f_calls) ** focus
MaxFunctionCalls (int | IntKey) – Maximum function calls allowed for the optimization, at and beyond this point there is a 100% chance that a previously evaluated point will be returned by the generator. If the optimization is not limited by the number of function calls, provide an estimate.
- class _LoggingInterval[source]¶
Number of function evaluations between every log to file.
- Variables:
The number of function evaluations between flushes of the output streams to disk.
If Flush = General, then files will be flushed after every logged call.
The number of function evaluations between writes to stdout, running_loss.txt, running_stats.txt and all latest/ and best/ files.
This is also the interval with which the validation set will be evaluated and logged.
History (int | IntKey) – The number of function evaluations between saves to the history directory with copies of latest/.
Parameters (int | IntKey) – The number of function evaluations between writes to running_active_parameters.txt.
- class _Optimizer[source]¶
An optimizer which may be used during the optimization.
- Variables:
Type (Literal["AdaptiveRateMonteCarlo", "CMAES", "Nevergrad", "Scipy", "RandomSampling", "GridSampling"]) –
Name of the optimization algorithm or interface.
Available options: • Adaptive Rate Monte Carlo • CMAES (Covariance Matrix Adaptation Evolutionary Strategy) • Nevergrad (Interface to many other algorithms) • Scipy (Interface to classic optimization algorithms) • Random Sampling (Uniform random sampling of the space for later analysis. NOT an actual optimizer) • Grid Sampling (Gridwise sampling of the parameter space for later analysis. NOT and actual optimizer)
AdaptiveRateMonteCarlo (ParAMSOptimize._Optimizer._AdaptiveRateMonteCarlo) – Settings for the Adaptive Rate Monte-Carlo optimizer
CMAES (ParAMSOptimize._Optimizer._CMAES) – Settings for the Covariance Matrix Adaptation Evolutionary Strategy
GridSampling (ParAMSOptimize._Optimizer._GridSampling) – Settings for grid-wise sampling of the parameter space.
Nevergrad (ParAMSOptimize._Optimizer._Nevergrad) – Settings for the Nevergrad wrapper which gives access to many optimization algorithms.
RandomSampling (ParAMSOptimize._Optimizer._RandomSampling) – Settings for a totally random sampler of the parameter space.
Scipy (ParAMSOptimize._Optimizer._Scipy) – Settings for the Scipy wrapper which gives access to many optimization algorithms. For parallel optimizations, Nevergrad is preferred as it provides better control options.
- class _AdaptiveRateMonteCarlo[source]¶
Settings for the Adaptive Rate Monte-Carlo optimizer
- class _CMAES[source]¶
Settings for the Covariance Matrix Adaptation Evolutionary Strategy
- Variables:
ForceInjections (BoolType | BoolKey) –
If Yes, injections of parameter vectors into the solver will be exact, guaranteeing that that solution will be in the next iteration’s population.
If No, the injection will result in a direction relative nudge towards the vector. Forcing the injecting can limit global exploration but non-forced injections may have little effect.
See also glompo.optimizer.cmaes.injectioninterval
InjectionInterval (int | IntKey) –
Number of iterations between injections of the incumbent solution into the sampled population. Defaults to 0, i.e., no injections are performed.
Injections can be helpful in increasing the convergence speed and nudging optimizers toward a solution. This is a form of elitism and will limit exploration.
Of particular interest is pairing this key with glompo.ShareBestEvaluationBetweenOptimizers. In this case the incumbent that is injected comes from other optimizers run in parallel. This can help nudge optimizers towards better solutions while dramatically improving convergence speed.
See also glompo.optimizer.cmaes.forceinjections
KeepFiles (BoolType | BoolKey) – Keep CMA specific history files about the state of the covariance matrix and other algorithm variables.
MinSigma (float | FloatKey) – Convergence condition to terminate the optimization when the standard deviation of the sampling distribution falls below this value.
Number of function evaluations per CMA-ES iteration.
If not specified or -1, then the population size will equal the number of workers available to the optimizer. This is computationally efficient but not algorithmically efficient.
A value of zero or one will set the population size to the value suggested by CMA based on the dimensionality of the problem. This produces the best algorithm performance but may be computationally inefficient if resources are left idling while waiting for other evaluations to complete.
Note: a population of one is not allowed by CMA, therefore, it is changed to the algorithm default. This also means that giving CMA only one worker will also change the popsize to the algorithm default.
Sampler (Literal["full", "vd", "vkd"]) –
Choice of full or restricted Gaussian sampling procedures.
Options: • full: Full sampling procedure • vd: Restricted sampler for VD-CMA (Linear time/space comparison-based natural gradient optimization) • vkd: Restricted sampler for VkD-CMA (Time/space variant of CMA-ES)
Initial standard deviation of the multivariate normal distribution from which trials are drawn.
The recommended range of values for is between 0.01 and 0.5. Lower values sample very locally and converge quickly, higher values sample broadly but will take a long time to converge.
Verbose (BoolType | BoolKey) – Produce a printstream of results from within the optimizer itself.
Settings (str | Sequence[str] | FreeBlock) –
‘argument value’ pairs for extra CMA specific configuration arguments.
See CMAOptimizer API documentation for more details on which options are possible.
- class _Nevergrad[source]¶
Settings for the Nevergrad wrapper which gives access to many optimization algorithms.
- Variables:
Algorithm (Literal["ASCMA2PDEthird", "ASCMADEQRthird", "ASCMADEthird", "AlmostRotationInvariantDE", "AvgMetaLogRecentering", "AvgMetaRecentering", "BO", "CM", "CMA", "CMandAS", "CMandAS2", "CMandAS3", "CauchyLHSSearch", "CauchyOnePlusOne", "CauchyScrHammersleySearch", "Cobyla", "DE", "DiagonalCMA", "DiscreteOnePlusOne", "DoubleFastGADiscreteOnePlusOne", "EDA", "ES", "FCMA", "HaltonSearch", "HaltonSearchPlusMiddlePoint", "HammersleySearch", "HammersleySearchPlusMiddlePoint", "LHSSearch", "LargeHaltonSearch", "LhsDE", "MEDA", "MPCEDA", "MetaLogRecentering", "MetaRecentering", "MixES", "MultiCMA", "MultiScaleCMA", "MutDE", "NGO", "NaiveIsoEMNA", "NaiveTBPSA", "NelderMead", "NoisyBandit", "NoisyDE", "NoisyDiscreteOnePlusOne", "NoisyOnePlusOne", "OAvgMetaLogRecentering", "ORandomSearch", "OScrHammersleySearch", "OnePlusOne", "OptimisticDiscreteOnePlusOne", "OptimisticNoisyOnePlusOne", "PBIL", "PCEDA", "PSO", "ParaPortfolio", "Portfolio", "Powell", "QORandomSearch", "QOScrHammersleySearch", "QrDE", "RCobyla", "RPowell", "RSQP", "RandomSearch", "RandomSearchPlusMiddlePoint", "RealSpacePSO", "RecES", "RecMixES", "RecMutDE", "RecombiningPortfolioOptimisticNoisyDiscreteOnePlusOne", "RotationInvariantDE", "SPSA", "SQP", "SQPCMA", "ScrHaltonSearch", "ScrHaltonSearchPlusMiddlePoint", "ScrHammersleySearch", "ScrHammersleySearchPlusMiddlePoint", "Shiva", "SplitOptimizer", "TBPSA", "TripleCMA", "TwoPointsDE", "cGA", "chainCMAPowel"]) –
Optimization strategy to use.
See Nevergrad documentation for details of the available methods.
Zero (float | FloatKey) – Function value below which the algorithm will terminate.
Settings (str | Sequence[str] | FreeBlock) –
‘argument value’ pairs for extra algorithm-specific configuration arguments.
See Nevergrad API documentation for more details on which options are possible.
- class _Scipy[source]¶
Settings for the Scipy wrapper which gives access to many optimization algorithms. For parallel optimizations, Nevergrad is preferred as it provides better control options.
- Variables:
Algorithm (Literal["Nelder-Mead", "Powell", "CG", "BFGS", "Newton-CG", "L-BFGS-B", "TNC", "COBYLA", "SLSQP", "trust-constr", "dogleg", "trust-ncg", "trust-exact", "trust-krylov"]) –
Optimization strategy to use.
See Scipy documentation for details of the available methods.
Hessian (Literal["2-point", "3-point", "cs"]) – Choice of the Hessian estimation method. Only for Newton-CG, dogleg, trust-ncg, trust-krylov, trust-exact and trust-constr.
Jacobian (Literal["2-point", "3-point", "cs"]) – Choice of gradient estimation method. Only for CG, BFGS, Newton-CG, L-BFGS-B, TNC, SLSQP, dogleg, trust-ncg, trust-krylov, trust-exact and trust-constr.
Tolerance (float | FloatKey) – Tolerance for termination. Interpretation linked to chosen method. See Scipy docs.
Settings (str | Sequence[str] | FreeBlock) –
‘argument value’ pairs for extra algorithm-specific configuration arguments.
See Scipy API documentation for more details on which options are possible.
- class _OptimizerSelector[source]¶
If multiple Optimizers are included, then this block must be included and configures the Selector which will choose between them.
- Variables:
Type (Literal["Cycle", "Random", "Chain"]) –
Name of the algorithm selecting between optimizers.
Available options: • Cycle (Default): Sequential loop through available optimizers. • Random: Optimizers are selected randomly from the available options. • Chain: Time-based progression through the list of available optimizers. The next option will be started once a certain number of loss function evaluations have been used.
Chain (ParAMSOptimize._OptimizerSelector._Chain) – Start different optimizers at different points in time based on the number of function evaluations used.
- class _Chain[source]¶
Start different optimizers at different points in time based on the number of function evaluations used.
- Variables:
Thresholds (Iterable[int] | IntListKey) – List of loss function evaluation thresholds which switch to the next optimizer in the list. If there are n optimizers available, then this list should have n-1 thresholds.
- class _ParallelLevels[source]¶
Distribution of threads/processes between the parallelization levels.
- Variables:
CommitteeMembers (int | IntKey) – Maximum number of committee member optimizations to run in parallel. If set to zero will take the minimum of MachineLearning%CommitteeSize and the number of available cores (NSCM)
Cores (int | IntKey) – Number of cores to use per committee member optimization. By default (0) the available cores (NSCM) divided equally among committee members. When using GPU offloading, consider setting this to 1.
Jobs (int | IntKey) – Number of JobCollection jobs to run in parallel for each loss function evaluation.
Optimizations (int | IntKey) – Number of independent optimizers to run in parallel.
ParameterVectors (int | IntKey) –
Number of parameter vectors to try in parallel for each optimizer iteration. This level of parallelism can only be used with optimizers that support parallel optimization!
Default (0) will set this value to the number of cores on the system divided by the number of optimizers run in parallel, i.e., each optimizer will be given an equal share of the resources.
Number of processes (MPI ranks) to spawn for each JobCollection job. This effectively sets the NSCM environment variable for each job.
A value of -1 will disable explicit setting of related variables. We recommend a value of 1 in almost all cases. A value greater than 1 would only be useful if you parametrize DFTB with a serial optimizer and have very few jobs in the job collection.
Number of threads to use for each of the processes. This effectively set the OMP_NUM_THREADS environment variable. Note that the DFTB engine does not use threads, so the value of this variable would not have any effect. We recommend always leaving it at the default value of 1. Please consult the manual of the engine you are parameterizing.
A value of -1 will disable explicit setting of related variables.
- class _Stopper[source]¶
A Stopper used to terminate optimizers early.
- Variables:
MaxFunctionCalls (int | IntKey) –
Returns True after an optimizer has evaluated at least n points.
Use in an AND combination with other stoppers to keep optimizers alive for at least some period of time, or alone or in an OR combination to shut them down after some period of time.
MaxSequentialInvalidPoints (int | IntKey) – Return True if the optimizer has failed to find a finite function value in the last n iterations. Usually indicates a lost optimizer with poor starting point.
OptimizerType (Literal["AdaptiveRateMonteCarlo", "CMAES", "Nevergrad", "Scipy", "RandomSampling", "GridSampling"]) – Intended for use with other stoppers to allow for specific hunting conditions based on the type of optimizer.
Type (Literal["BestFunctionValueUnmoving", "CurrentFunctionValueUnmoving", "MaxSequentialInvalidPoints", "MaxFunctionCalls", "MaxInteroptimizerDistance", "MinStepSize", "TimeAnnealing", "OptimizerType", "ValueAnnealing", "ValidationWorsening"]) –
Conditions used to stop individual optimizers. Only optimizers which have not seen the current best value will be hunted. The ‘best’ optimizer will always be left alive.
Available options: • Best Function Value Unmoving: Shutdown optimizers who haven’t improved their best point in a long time. • Current Function Value Unmoving: Shutdown optimizers which have not changed their currently explored loss function value a lot in a long time. • Max Sequential Invalid Points: Stop optimizers that are stuck in areas of parameter space which return non-finite loss function values. • Max Function Calls: Stop optimizers when they have evaluated the loss function a certain number of times. • Max Interoptimizer Distance: Stop optimizers too close together in parameter space. • Min Step Size: Stop optimizers who are taking very small steps between iterations. • Time Annealing: For use with other conditions. Keep an optimizer alive for longer if it’s relatively new. • Optimizer Type: For use with other conditions. Shutdown optimizers of a specific type. • Value Annealing: For use with other conditions. Keep an optimizer alive if it looks likely to overtake the best optimizer. • Validation Worsening: Stops optimizers which are evaluating points where the validation set loss value is worse than the average of several previously seen ones.
BestFunctionValueUnmoving (ParAMSOptimize._Stopper._BestFunctionValueUnmoving) – Return True if an optimizer’s best value has not improved significantly in a given amount of time.
CurrentFunctionValueUnmoving (ParAMSOptimize._Stopper._CurrentFunctionValueUnmoving) – Return True if an optimizer’s current function value has not improved significantly in a given amount of time.
MaxInteroptimizerDistance (ParAMSOptimize._Stopper._MaxInteroptimizerDistance) – Return True if two optimizers are evaluating points too close to one another in parameter space.
MinStepSize (ParAMSOptimize._Stopper._MinStepSize) – Return True if an optimizer’s step size between evaluations is too small.
TimeAnnealing (ParAMSOptimize._Stopper._TimeAnnealing) – Keeps optimizers alive based on how long they have been alive. Randomly keeps optimizers alive based on how long (in function evaluations) they have been active. The newer an optimizer is, the more likely it will pass the test and be kept alive. Used to temper very strict termination conditions.
ValidationWorsening (ParAMSOptimize._Stopper._ValidationWorsening) – Return True if the loss value of the validation set is increasing.
ValueAnnealing (ParAMSOptimize._Stopper._ValueAnnealing) – Intended for use with other stoppers. This condition is unlikely to stop a victim which has a loss function value very near the best seen thus far, but the probability of stopping increases with the difference between them.
- class _BestFunctionValueUnmoving[source]¶
Return True if an optimizer’s best value has not improved significantly in a given amount of time.
- class _CurrentFunctionValueUnmoving[source]¶
Return True if an optimizer’s current function value has not improved significantly in a given amount of time.
- class _MaxInteroptimizerDistance[source]¶
Return True if two optimizers are evaluating points too close to one another in parameter space.
- Variables:
CompareAllOptimizers (BoolType | BoolKey) – If Yes the distance between all optimizer combinations are compared, otherwise worse optimizers are only compared to the best one.
MaxRelativeDistance (float | FloatKey) – Fraction (between 0 and 1) of the maximum distance in the space (from the point at all lower bounds to the point at all upper bounds) below which the optimizers are deemed too close and the victim will be stopped.
- class _MinStepSize[source]¶
Return True if an optimizer’s step size between evaluations is too small.
- class _TimeAnnealing[source]¶
Keeps optimizers alive based on how long they have been alive. Randomly keeps optimizers alive based on how long (in function evaluations) they have been active. The newer an optimizer is, the more likely it will pass the test and be kept alive. Used to temper very strict termination conditions.
- Variables:
CriticalRatio (float | FloatKey) – Critical ratio of function calls between stopper and victim above which the victim is guaranteed to survive. Values lower than one are looser and allow the victim to survive even if it has been in operation longer than the stopper. Values higher than one are stricter and may stop the victim even if it has iterated fewer times than the stopper.
- class _ValidationWorsening[source]¶
Return True if the loss value of the validation set is increasing.
- class ParAMSSensitivity[source]¶
- Variables:
EngineCollection (str | StringKey) – Path to (optional) JobCollection Engines YAML file.
FilterInfiniteValues (BoolType | BoolKey) –
If Yes, removes points from the calculation with non-finite loss values.
Non-finite points can cause numerical issues in the sensitivity calculation.
JobCollection (str | StringKey) – Path to JobCollection YAML file.
NumberBootstraps (int | IntKey) –
Number of repeats of the calculation with different sub-samples.
A small spread from a large number of bootstraps provides confidence on the estimation of the sensitivity.
NumberCalculationSamples (int | IntKey) –
Number of samples from the full set available to use in the calculation.
If not specified or -1, uses all available points. For the sensitivity calculation, this will be redrawn for every bootstrap.
NumberSamples (int | IntKey) – Number of samples to generate during the sampling procedure.
ParameterInterface (str | StringKey) – Path to parameter interface YAML file.
RandomSeed (int | IntKey) – Random seed to use during the sampling procedure (for reproducibility).
ResultsDirectory (str | Path | StringKey) – Directory in which output files will be created.
RunReweightCalculation (BoolType | BoolKey) –
Run a more expensive sensitivity calculation that will also return suggested weights for the training set which will produce more balanced sensitivities between all the parameters.
Note: The Gaussian kernel is recommended for the loss values kernel in this case.
RunSampling (BoolType | BoolKey) –
Produce a set of samples of the loss function and active parameters. Samples from the parameter space are drawn from a uniform random distribution.
Such a set of samples serves as the input to the sensitivity calculation.
SampleWithReplacement (BoolType | BoolKey) –
Sample from the available data with or without replacement.
This only has an effect if the number of samples for the calculation is less than the total number available otherwise replace is Yes by necessity.
SamplesDirectory (str | Path | StringKey) –
Path to an ‘optimization’ directory containing the results of a previously run sampling.
First looks for a ‘glompo_log.h5’ file. If not found, will look for ‘running_loss.txt’ and ‘running_active_parameters.txt’ in a sub-directory. The sub-directory used will depend on the DataSet Name.
For the Reweight calculation only a ‘glompo_log.h5’ file (with residuals) may be used.
SaveResiduals (BoolType | BoolKey) –
During the sampling, save the individual difference between reference and predicted values for every sample and training set item. Required for the Reweight calculation, and will be automatically activated if the reweight calculation is requested.
Saving and analyzing the residuals can provide valuable insight into your training set, but can quickly occupy a large amount of disk space. Only save the residuals if you would like to run the reweight calculation or have a particular reason to do so.
SetToAnalyze (Literal["TrainingSet", "ValidationSet"]) – Name of the data set to use for the sensitivity analysis.
Task (Literal["Optimization", "GenerateReference", "SinglePoint", "Sensitivity", "MachineLearning"]) –
Task to run.
Available options: •MachineLearning: Optimization for machine learning models. •Optimization: Global optimization powered by GloMPO •Generate Reference: Run jobs with reference engine to get reference values •Single Point: Evaluate the current configuration of jobs, training data, and parameters •Sensitivity: Measure the sensitivity of the loss function to each of the active parameters
DataSet (ParAMSSensitivity._DataSet) – Configuration settings for each data set in the optimization.
LossValuesKernel (ParAMSSensitivity._LossValuesKernel) – Kernel applied to the parameters for which sensitivity is being measured.
ParametersKernel (ParAMSSensitivity._ParametersKernel) – Kernel applied to the parameters for which sensitivity is being measured.
- class _DataSet[source]¶
Configuration settings for each data set in the optimization.
- Variables:
BatchSize (int | IntKey) – Number of data set entries to be evaluated per epoch. Default 0 means all entries.
EvaluateEvery (int | IntKey) –
This data set is evaluated every n evaluations of the training set.
This will always be set to 1 for the training set. For other data sets it will be adjusted to the closest multiple of LoggingInterval%General, i.e., you cannot evaluate an extra data set more frequently than you log it.
LossFunction (Literal["mae", "rmse", "sse", "sae"]) –
Loss function used to quantify the error between model and reference values. This becomes the minimization task.
Available options: • mae: Mean absolute error • rmse: Root mean squared error • sse: Sum of squared errors • sae: Sum of absolute errors
MaxJobs (int | IntKey) – Limit each evaluation to a subset of n jobs. Default 0 meaning all jobs are used.
MaxJobsShuffle (BoolType | BoolKey) – Use a different job subset every for every evaluation.
Unique data set identifier.
The first occurrence of DataSet will always be called training_set. The second will always be called validation_set. These cannot be overwritten.
Later occurrences will default to data_set_xx where xx starts at 03 and increments from there. This field can be used to customize the latter names.
UsePipe (BoolType | BoolKey) – Use AMS Pipe for suitable jobs to speed-up evaluation.
- class _LossValuesKernel[source]¶
Kernel applied to the parameters for which sensitivity is being measured.
- Variables:
Cut-off parameter for the Threshold kernel between zero and one.
All loss values are scaled by taking the logarithm and then adjusted to a range between zero and one. This parameter is a value within this scaled space.
Gamma (float | FloatKey) – Bandwidth parameter for the conjunctive-Gaussian kernel.
Bandwidth parameter for the Gaussian kernel.
If not specified or -1, calculates a reasonable default based on the number of parameters being tested.
Type (Literal["Gaussian", "ConjunctiveGaussian", "Threshold", "Polynomial", "Linear"]) – Name of the kernel to applied to the parameters for which sensitivity is being measured.
Polynomial (ParAMSSensitivity._LossValuesKernel._Polynomial) – Settings for the Polynomial kernel.
- class _ParametersKernel[source]¶
Kernel applied to the parameters for which sensitivity is being measured.
- Variables:
Cut-off parameter for the Threshold kernel between zero and one.
All loss values are scaled by taking the logarithm and then adjusted to a range between zero and one. This parameter is a value within this scaled space.
Gamma (float | FloatKey) – Bandwidth parameter for the conjunctive-Gaussian kernel.
Sigma (float | FloatKey) – Bandwidth parameter for the Gaussian kernel.
Type (Literal["Gaussian", "ConjunctiveGaussian", "Threshold", "Polynomial", "Linear"]) – Name of the kernel to applied to the parameters for which sensitivity is being measured.
Polynomial (ParAMSSensitivity._ParametersKernel._Polynomial) – Settings for the Polynomial kernel.
- class ParAMSSinglePoint[source]¶
- Variables:
EngineCollection (str | StringKey) – Path to (optional) JobCollection Engines YAML file.
EvaluateLoss (BoolType | BoolKey) –
Evaluate the loss function based on the job results. This will produce the same output files as Task Optimization. If No, this will be skipped and only the jobs will be run (and saved).
Warning: If both Store Jobs and Evaluate Loss are No then this task will not produce any output.
JobCollection (str | StringKey) – Path to JobCollection YAML file.
ParameterInterface (str | StringKey) – Path to parameter interface YAML file.
RestartDirectory (str | Path | StringKey) –
Specify a directory to continue interrupted GenerateReference or SinglePoint calculations. The directory depends on the task:
GenerateReference: results/reference_jobs SinglePoint: results/single_point/jobs
Note: If you use the GUI this directory will be COPIED into the results folder and the name will be prepended with ‘dep-’. This can take up a lot of disk space, so you may want to remove the ‘dep-’ folder after the job has finished.
ResultsDirectory (str | Path | StringKey) – Directory in which output files will be created.
StoreJobs (Literal["Auto", "Yes", "No"]) –
Keeps the results files for each of the jobs. If No, all pipeable jobs will be run through the AMS Pipe and no files will be saved (not even the ones not run through the pipe). If Auto, the pipeable jobs are run through the pipe and the results of nonpipeable jobs are saved to disk. If Yes, no jobs are run through the pipe and all job results are stored on disk.
Warning: If both Store Jobs and Evaluate Loss are No then task SinglePoint will not produce any output.
Task (Literal["Optimization", "GenerateReference", "SinglePoint", "Sensitivity", "MachineLearning"]) –
Task to run.
Available options: •MachineLearning: Optimization for machine learning models. •Optimization: Global optimization powered by GloMPO •Generate Reference: Run jobs with reference engine to get reference values •Single Point: Evaluate the current configuration of jobs, training data, and parameters •Sensitivity: Measure the sensitivity of the loss function to each of the active parameters
DataSet (ParAMSSinglePoint._DataSet) – Configuration settings for each data set in the optimization.
Engine (EngineBlock) – If set, use this engine for the ParAMS SinglePoint. Mutually exclusive with EngineCollection.
ParallelLevels (ParAMSSinglePoint._ParallelLevels) – Distribution of threads/processes between the parallelization levels.
- class _DataSet[source]¶
Configuration settings for each data set in the optimization.
- Variables:
BatchSize (int | IntKey) – Number of data set entries to be evaluated per epoch. Default 0 means all entries.
EvaluateEvery (int | IntKey) –
This data set is evaluated every n evaluations of the training set.
This will always be set to 1 for the training set. For other data sets it will be adjusted to the closest multiple of LoggingInterval%General, i.e., you cannot evaluate an extra data set more frequently than you log it.
LossFunction (Literal["mae", "rmse", "sse", "sae"]) –
Loss function used to quantify the error between model and reference values. This becomes the minimization task.
Available options: • mae: Mean absolute error • rmse: Root mean squared error • sse: Sum of squared errors • sae: Sum of absolute errors
MaxJobs (int | IntKey) – Limit each evaluation to a subset of n jobs. Default 0 meaning all jobs are used.
MaxJobsShuffle (BoolType | BoolKey) – Use a different job subset every for every evaluation.
Unique data set identifier.
The first occurrence of DataSet will always be called training_set. The second will always be called validation_set. These cannot be overwritten.
Later occurrences will default to data_set_xx where xx starts at 03 and increments from there. This field can be used to customize the latter names.
UsePipe (BoolType | BoolKey) – Use AMS Pipe for suitable jobs to speed-up evaluation.
- class _Engine[source]¶
If set, use this engine for the ParAMS SinglePoint. Mutually exclusive with EngineCollection.
- class _ParallelLevels[source]¶
Distribution of threads/processes between the parallelization levels.
- Variables:
CommitteeMembers (int | IntKey) – Maximum number of committee member optimizations to run in parallel. If set to zero will take the minimum of MachineLearning%CommitteeSize and the number of available cores (NSCM)
Cores (int | IntKey) – Number of cores to use per committee member optimization. By default (0) the available cores (NSCM) divided equally among committee members. When using GPU offloading, consider setting this to 1.
Jobs (int | IntKey) – Number of JobCollection jobs to run in parallel for each loss function evaluation.
Optimizations (int | IntKey) – Number of independent optimizers to run in parallel.
ParameterVectors (int | IntKey) –
Number of parameter vectors to try in parallel for each optimizer iteration. This level of parallelism can only be used with optimizers that support parallel optimization!
Default (0) will set this value to the number of cores on the system divided by the number of optimizers run in parallel, i.e., each optimizer will be given an equal share of the resources.
Number of processes (MPI ranks) to spawn for each JobCollection job. This effectively sets the NSCM environment variable for each job.
A value of -1 will disable explicit setting of related variables. We recommend a value of 1 in almost all cases. A value greater than 1 would only be useful if you parametrize DFTB with a serial optimizer and have very few jobs in the job collection.
Number of threads to use for each of the processes. This effectively set the OMP_NUM_THREADS environment variable. Note that the DFTB engine does not use threads, so the value of this variable would not have any effect. We recommend always leaving it at the default value of 1. Please consult the manual of the engine you are parameterizing.
A value of -1 will disable explicit setting of related variables.
- class PreAmsifiedADF[source]¶
- Variables:
A1Fit (float | FloatKey) – STO-Fit keyword: distance between atoms, in Angstrom. The symmetric fit approximation is applied only for atoms farther apart.
AOMat2File (BoolType | BoolKey) – Write PMatrix, Fock matrix, and overlap matrix on AO basis to file for future analysis purposes
AORCOnly (BoolType | BoolKey) –
AORXCOnly (BoolType | BoolKey) –
AORun (BoolType | BoolKey) –
AccurateGradients (BoolType | BoolKey) – Print the nuclear gradients with more digits than usual.
AddDiffuseFit (BoolType | BoolKey) – STO-Fit keyword: One can get more diffuse fit functions by setting this to True.
AllDipMat (BoolType | BoolKey) – Print all dipole matrix elements between occupied and virtual Kohn-Sham orbitals.
AllPoints (BoolType | BoolKey) – ADF makes use of symmetry in the numerical integrations. Points are generated for the irreducible wedge, a symmetry unique sub region of space. Optionally the symmetry equivalent points are also used. This is achieved by setting this key to True.
AllWaals (BoolType | BoolKey) –
AltLinVXC (BoolType | BoolKey) –
AltOrthon (BoolType | BoolKey) –
AltRhof (BoolType | BoolKey) –
AnaPol (BoolType | BoolKey) –
Balance (BoolType | BoolKey) – Measure the actual speed of the nodes in the parallel machine
BasValZero (BoolType | BoolKey) – Debug option
Blapt (BoolType | BoolKey) –
BoySold (BoolType | BoolKey) –
C2Coef (BoolType | BoolKey) – Print C2Coef to output
CM5 (BoolType | BoolKey) – Calculate the charge model 5 (CM5) analysis.
CalcOverlapOnly (BoolType | BoolKey) – Calculate overlaps of primitive basis and stops after computing them.
CalcTotalEnergy (BoolType | BoolKey) – Whether or not to calculate the total energy.
Charge (Iterable[float] | FloatListKey) – Controls the net charge of the molecule and the net spin polarization. First number: The net total charge of the molecule, Second number: The net total spin polarization: the number of spin-alpha electrons in excess of spin-beta electrons. Specification is only meaningful in a spin-unrestricted calculation. However, specification is not meaningful in an unrestricted Spin-Orbit coupled calculation using the (non-)collinear approximation.
ChkDisFal (BoolType | BoolKey) –
ColTDDFT (BoolType | BoolKey) –
Collinear (BoolType | BoolKey) – Use collinear approximation (only relevant in the case of Spin-Orbit coupling).
CommTiming (BoolType | BoolKey) –
ComplexAcl (BoolType | BoolKey) –
CoreTables (BoolType | BoolKey) –
CoulombFit (BoolType | BoolKey) –
Create (str | StringKey) – Keywords for create run. {Atomtype Datafile}
DFTBParams (BoolType | BoolKey) –
DRho241 (BoolType | BoolKey) –
DeltaEpStrip (BoolType | BoolKey) –
DensPrep (BoolType | BoolKey) –
Diffuse (BoolType | BoolKey) –
DipoleLength (BoolType | BoolKey) – Use dipole-length elements for perturbing (external) integrals in CURRENT response
DipoleResponse (BoolType | BoolKey) –
EGOXAlpha (BoolType | BoolKey) –
EnergyTest (BoolType | BoolKey) –
ExactDensity (BoolType | BoolKey) – Use the exact density (as opposed to the fitted density) for the computation of the exchange-correlation potential
ExtendPopAn (BoolType | BoolKey) –
ExtendedPopan (BoolType | BoolKey) – Calculate the Mayer bond orders and Mulliken atom-atom populations per l-value
FitAlfa (BoolType | BoolKey) –
FitExcit (BoolType | BoolKey) –
Fitelstat (BoolType | BoolKey) –
Fithyppol (BoolType | BoolKey) –
Fitmeta (BoolType | BoolKey) –
Fitsecder (BoolType | BoolKey) –
ForceALDA (BoolType | BoolKey) – In spin-flip TDDFT, the XC kernel can be calculated directly from the XC potential. To use the LDA potential for the XC kernel, which roughly corresponds to the ALDA in ordinary TDDFT, one must specify the key
FragMetaGGAToten (BoolType | BoolKey) – By setting this to true the difference in the metahybrid or metagga exchange-correlation energies between the molecule and its fragments will be calculated using the molecular integration grid, which is more accurate than the default, but is much more time consuming.
FullFock (BoolType | BoolKey) – Calculate the full Fock matrix each SCF iteration (instead of the difference with the previous cycle).
FullSCF (BoolType | BoolKey) –
FullTotEn (BoolType | BoolKey) –
Fuzzy_BO (BoolType | BoolKey) –
GSCorr (BoolType | BoolKey) – The singlet ground state is included, which means that spin-orbit coupling can also have some effect on energy of the ground state. The spin-orbit matrix in this case is on basis of the ground state and the singlet and triplet excited states.
GZip (str | StringKey) – GZip the corresponding tape (possibly working only for TAPE21)
GaugeOrigin (Iterable[float] | FloatListKey) – Untested and undocumented
Gradient (BoolType | BoolKey) –
Force calculation of gradients of the total energy with respect to the nuclear coordinates, just as in a geometry optimization.
This is useful if you want to perform a single point calculation and get gradients for that specific geometry.
HFAtomsPerPass (int | IntKey) – Memory usage option for old HF scheme
HFDependency (BoolType | BoolKey) – Untested and undocumented
HFMaxMemory (int | IntKey) – Memory usage option for old HF scheme
HartreeFock (BoolType | BoolKey) – Compute hybrid meta-GGA energy functionals (if METAGGA key is True)
HessTest (BoolType | BoolKey) – Print the force field derived initial Hessian.
Hilbert (BoolType | BoolKey) –
IgnoreOverlap (BoolType | BoolKey) –
ImportEmbPot (str | StringKey) – File containing an external embedding potential (FDE calculations only)
KSSpectrum (BoolType | BoolKey) –
LB4 (BoolType | BoolKey) –
Lap1 (BoolType | BoolKey) –
LinTermVXC (BoolType | BoolKey) –
MBlockBig (BoolType | BoolKey) –
MBlockSmall (BoolType | BoolKey) –
MOExactDensity (BoolType | BoolKey) –
MetaGGA (BoolType | BoolKey) –
NewDIIS (BoolType | BoolKey) –
NoBeckeGrid (BoolType | BoolKey) –
NoESRfcsd (BoolType | BoolKey) –
NoESRpso (BoolType | BoolKey) –
NoFDEPot (BoolType | BoolKey) –
NoFragDp (BoolType | BoolKey) –
NoGTerm (BoolType | BoolKey) –
NoSharedArrays (BoolType | BoolKey) –
NoSymFit (BoolType | BoolKey) –
NoTotEn (BoolType | BoolKey) –
NoUpdFac (BoolType | BoolKey) –
NonCollinear (BoolType | BoolKey) – Use non-collinear approximation (only relevant in the case of Spin-Orbit coupling).
NuclearModel (Literal["PointCharge", "Gaussian"]) –
Model for the nuclear charge distribution.
To see effects from your choice you will need to use a basis set with extra steep functions. For some elements you can find these in the ZORA/jcpl basis directory.
NumericalQuality (Literal["Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Set the quality of several important technical aspects of an ADF calculation (with the notable exception of the basis set). It sets the quality of: BeckeGrid (numerical integration) and ZlmFit (density fitting). Note: the quality defined in the block of a specific technical aspects supersedes the value defined in NumericalQuality (e.g. if I specify ‘NumericalQuality Basic’ and ‘BeckeGrid%Quality Good’, the quality of the BeckeGrid will be ‘Good’)
OrbitalsCoulombInteraction (Iterable[int] | IntListKey) – Compute the Coulomb interaction energy between the density of two orbitals. After the key, specify the indices of the two orbitals for which you want to compute the Coulomb interaction energy. Can only be used for spin-restricted calculations. Cannot be used in case of Symmetry (use Symmetry NoSym).
OrthFragPrep (BoolType | BoolKey) –
ProgConv (BoolType | BoolKey) –
QTens (BoolType | BoolKey) – Calculate the the Nuclear Electric Quadrupole Hyperfine interaction (Q-tensor, NQCC, NQI), related to the Electric Field Gradient (EFG).
RConfine (Iterable[float] | FloatListKey) – Untested and undocumented
RESTOCC (BoolType | BoolKey) –
ReducedMass (BoolType | BoolKey) – Print reduced mass for each normal mode
Relativistic (str | StringKey) – instructs ADF to take relativistic effects into account.
RemoveAllFragVirtuals (BoolType | BoolKey) –
SFTDDFT (BoolType | BoolKey) – Calculate spin-flip excitation energies (requires TDA and FORCEALDA keys).
SOMCD (BoolType | BoolKey) –
SOUExact (BoolType | BoolKey) –
STContrib (BoolType | BoolKey) –
STOFit (BoolType | BoolKey) –
SharcOverlap (BoolType | BoolKey) –
Symmetry (str | StringKey) – The Schonfliess symmetry symbol. A tolerance can be supplied.
TDA (BoolType | BoolKey) – Use the Tamm-Dancoff approximation (TDA) (requires the EXCITATION block key)
TDDFTSO (BoolType | BoolKey) –
TotalEnergy (BoolType | BoolKey) –
Calculate the total energy.
Normally only the bonding energy with respect to the fragments is calculated.
The total energy will be less accurate then the bonding energy (about two decimal places), and is not compatible with some options.
In most cases the total energy will not be needed.
TransferIntegrals (BoolType | BoolKey) –
Calculate the charge transfer integrals, spatial overlap integrals and site energies.
Charge transfer integrals can be used in models that calculate transport properties.
Unrestricted (BoolType | BoolKey) – By default, a spin-restricted calculation is performed where the spin alpha and spin beta orbitals are spatially the same.
UnrestrictedFragments (BoolType | BoolKey) –
Use fragments calculated a spin-unrestricted calculation: the spin alpha and spin beta orbitals may be spatially different.
The total spin polarization of your fragments must match the spin polarization of your final molecule.
UsePseudoDiag (BoolType | BoolKey) –
UseSPCode (BoolType | BoolKey) – Use Patchkovskii routines for PBE
VCD (BoolType | BoolKey) – Calculate rotational strength during an analytical frequencies calculation.
VectorLength (int | IntKey) – Specify a different batch size for the integration points here (default: 128 on most machines and 2047 on vector machines).
ZExact (BoolType | BoolKey) –
gpuenabled (BoolType | BoolKey) –
grad_no_fragment_potentials (BoolType | BoolKey) –
grad_trf_btrf (BoolType | BoolKey) –
hydrogenbonds (BoolType | BoolKey) –
nocalcs2 (BoolType | BoolKey) –
nodrop (BoolType | BoolKey) –
noerror (BoolType | BoolKey) –
nogiao (BoolType | BoolKey) –
nomorton (BoolType | BoolKey) –
nopm5rho (BoolType | BoolKey) –
notstcoe (BoolType | BoolKey) –
nouseactivefrag (BoolType | BoolKey) –
novkpot (BoolType | BoolKey) –
noxcprint (BoolType | BoolKey) –
oldblockedsmat (BoolType | BoolKey) –
oldorthon (BoolType | BoolKey) –
peano (BoolType | BoolKey) –
plap3 (BoolType | BoolKey) –
prepvibron (BoolType | BoolKey) –
prtallten (BoolType | BoolKey) –
prtiao (BoolType | BoolKey) –
quild_nocoords_in_log (BoolType | BoolKey) –
readepsilons (BoolType | BoolKey) –
readfcfile (BoolType | BoolKey) –
rhobelpotimport (BoolType | BoolKey) –
riskyfast (BoolType | BoolKey) –
scaledkinfunctionals (BoolType | BoolKey) –
sfguess (BoolType | BoolKey) –
sfotrans (BoolType | BoolKey) –
skipcoulombpot (BoolType | BoolKey) –
skorthon (BoolType | BoolKey) –
solv (BoolType | BoolKey) –
soux (BoolType | BoolKey) –
souy (BoolType | BoolKey) –
sozero (BoolType | BoolKey) –
switchcoe (BoolType | BoolKey) –
symexcit (BoolType | BoolKey) –
symresp (BoolType | BoolKey) –
testaor (BoolType | BoolKey) –
testfit (BoolType | BoolKey) –
testjob (BoolType | BoolKey) –
testpscharge (BoolType | BoolKey) –
testsub1 (BoolType | BoolKey) –
totenskip (BoolType | BoolKey) –
trustsfguess (BoolType | BoolKey) –
userlegmn (BoolType | BoolKey) –
usesumfragp (BoolType | BoolKey) –
xonly (BoolType | BoolKey) –
xyonly (BoolType | BoolKey) –
xzonly (BoolType | BoolKey) –
yonly (BoolType | BoolKey) –
yzonly (BoolType | BoolKey) –
zonly (BoolType | BoolKey) –
AOResponse (PreAmsifiedADF._AOResponse) – If the block key AORESPONSE is used, by default, the polarizability is calculated. Note that if the molecule has symmetry the key ALLPOINTS should be included
AnalyticalFreq (PreAmsifiedADF._AnalyticalFreq) – Calculate the harmonic frequencies analytically
Aromaticity (str | Sequence[str] | FreeBlock) – Calculate aromaticity indicators, i.e. the matrix of localization/delocalization indices (LI-DI), Iring (ring index) and MCI (multi center index) aromaticity indices.
Basis (str | Sequence[str] | FreeBlock) – Not to be used. Use $ADFBIN/adf (NOT adf.exe!) to run this job
BeckeGrid (PreAmsifiedADF._BeckeGrid) – Options for the numerical integration grid.
CDFT (PreAmsifiedADF._CDFT) – CDFT is a tool for carrying out DFT calculations in the presence of a constraint.
CVNDFT (PreAmsifiedADF._CVNDFT) – The CVNDFT block key regulates the execution of the CV(n)-DFT code, which calculates the singlet or triplet electronic excitations for the closed shell molecules.
ConceptualDFT (PreAmsifiedADF._ConceptualDFT) – Conceptual DFT Properties
ConstructPot (PreAmsifiedADF._ConstructPot) – Reads a density from a TAPE41 file and constructs numerically the corresponding potential to it
CorePotentials (str | Sequence[str] | FreeBlock) – With the key COREPOTENTIALS you specify the core file and (optionally) which sections pertain to the distinct atom types in the molecule.
CurrentResponse (PreAmsifiedADF._CurrentResponse) –
Dependency (PreAmsifiedADF._Dependency) –
EPrint (PreAmsifiedADF._EPrint) – Print switches that require more specification than just off or on
ESR (PreAmsifiedADF._ESR) –
ETSNOCV (PreAmsifiedADF._ETSNOCV) – Perform ETS-NOCV analysis.
ElectronTransfer (PreAmsifiedADF._ElectronTransfer) –
Excitations (PreAmsifiedADF._Excitations) – Excitation energies: UV/Vis
ExcitedGO (PreAmsifiedADF._ExcitedGO) – Excited state geometry optimization
Externals (str | Sequence[str] | FreeBlock) – Legacy support of the older DRF code
FDE (PreAmsifiedADF._FDE) – Frozen Density Embedding options
Fragments (str | Sequence[str] | FreeBlock) – Definitions of the fragment type/files: {FragmentName FragmentFile}. In the block header one can specify the directory where the fragment files are located
GUIBonds (str | Sequence[str] | FreeBlock) – The bonds used by the GUI (this does not affect the ADF calculation in any way)
Geometry (PreAmsifiedADF._Geometry) – Geometry Optimizations procedure
HessDiag (PreAmsifiedADF._HessDiag) – Diagonal Hessian elements… Placeholder
IQA (PreAmsifiedADF._IQA) – Bond energy decomposition based on the interacting quantum atoms (IQA) approach and using QTAIM real-space partition.
Integration (str | Sequence[str] | FreeBlock) – Options for the obsolete Voronoi numerical integration scheme
IrrepOccupations (str | Sequence[str] | FreeBlock) – Explicit occupation numbers per irrep
LinearScaling (PreAmsifiedADF._LinearScaling) –
MDC (PreAmsifiedADF._MDC) – Options for Multipole Derived Charges (MDC)
MP2 (PreAmsifiedADF._MP2) – Technical aspects of the MP2 algorithm.
ModifyExcitation (PreAmsifiedADF._ModifyExcitation) –
PertLoc (PreAmsifiedADF._PertLoc) – Perturbed localized molecular orbitals, correct to first order in an applied field, can be calculated in case of AORESPONSE. Can be used if the applied field changes the density in first order.
PointCharges (str | Sequence[str] | FreeBlock) – Point charges: {x y z q}
PolTDDFT (PreAmsifiedADF._PolTDDFT) – TODO!
QTAIM (PreAmsifiedADF._QTAIM) – This block is used to request a topological analysis of the gradient field of the electron density, also known as the Bader’s analysis. If this block is specified without any sub-key, only local properties are calculated.
RIHartreeFock (PreAmsifiedADF._RIHartreeFock) –
RISM (str | Sequence[str] | FreeBlock) – 3D-RISM-related input keys.
RadialCoreGrid (PreAmsifiedADF._RadialCoreGrid) – For each atom the charge densities and the coulomb potentials of frozen core and valence electrons are computed in a radial grid. The radial grid consists of a sequence of r-values, defined by a smallest value, a constant multiplication factor to obtain each successive r-value, and the total number of points. Equivalently it can be characterized by the smallest r-value, the largest r-value, and the number of points; from these data the program computes then the constant multiplication factor.
Response (PreAmsifiedADF._Response) – The calculation of frequency-dependent (hyper)polarizabilities and related properties (Raman, ORD)
Restart (PreAmsifiedADF._Restart) – Options for restarts
SCF (PreAmsifiedADF._SCF) – Control aspects of the Self Consistent Field procedure
SOPert (PreAmsifiedADF._SOPert) –
SelectExcitation (PreAmsifiedADF._SelectExcitation) –
Solvation (PreAmsifiedADF._Solvation) –
SubExci (PreAmsifiedADF._SubExci) – Subsystem TDDFT (FDE)
SubResponse (str | Sequence[str] | FreeBlock) – Untested and undocumented
TSRC (str | Sequence[str] | FreeBlock) – Transition State Reaction Coordinate (TSRC)
Tails (PreAmsifiedADF._Tails) – Obsolete option for linear scaling and distance effects. We recommend using the LinearScaling key instead.
Thermo (PreAmsifiedADF._Thermo) – At the end of a completed Frequencies calculation, a survey is given of thermodynamic properties: Heat Capacity, Internal Energy, Entropy. The computed results assume an ideal gas, and electronic contributions are ignored. The latter is a serious omission if the electronic configuration is (almost) degenerate, but the effect is small whenever the energy difference with the next state is large compared to the vibrational frequencies
Units (PreAmsifiedADF._Units) – Definitions of the units.
Vibron (PreAmsifiedADF._Vibron) – Resonance Raman Input options
XC (PreAmsifiedADF._XC) – Definition of the XC.
XES (PreAmsifiedADF._XES) – X-ray emission spectroscopy
ZlmFit (PreAmsifiedADF._ZlmFit) – Options for the density fitting scheme ‘ZlmFit’.
- class _AOResponse[source]¶
If the block key AORESPONSE is used, by default, the polarizability is calculated. Note that if the molecule has symmetry the key ALLPOINTS should be included
- Variables:
2ANTISYM (BoolType | BoolKey) –
ALDA (BoolType | BoolKey) – Use ALDA only
Alpha (BoolType | BoolKey) – Calculate linear response
Beta (BoolType | BoolKey) – Will use 2n+1 rule to calculate beta.
CALCTRANSFORMPROP (str | StringKey) – Transformation Properties of Polarizabilities
CHANGESIGN (BoolType | BoolKey) –
Components (str | StringKey) – Limit the tensor components to the specified ones. Using this option may save the computation time. Options: XX, XY, XZ, YX, YY, YZ, ZX, ZY, ZZ
Cubic (BoolType | BoolKey) – Calculate cubic response
Damp (float | FloatKey) – Specify damping for non-acceleration iteration
DoNothing (BoolType | BoolKey) – Do nothing.
EFIOR (BoolType | BoolKey) –
EFISHG (BoolType | BoolKey) –
EFPLOT (BoolType | BoolKey) –
EOPE (BoolType | BoolKey) –
FULLMAT (BoolType | BoolKey) –
FitAODeriv (BoolType | BoolKey) – Use FITAODERIV for Coulomb potential
FreqRange (str | StringKey) – Usage: FREQRANGE freq1 freqN TotFreq units. This key is useful when it is necessary to specify more than 20 equally spaced frequencies for the response calculations. The first frequency is freq1 and the last one is freqN. The total number of frequencies including the first and the last one is TotFreq. The last item specifies the units: EV, HARTREE or ANGSTROM
Frequency (str | StringKey) – Usage: FREQUENCY Nfreq freq1 freq2 … freqN units. To calculate time-dependent properties, one needs to specify frequency of perturbation field. Here Nfreq specifies the number of frequencies that follow. The last item on the line specifies the units and is one of EV, HARTREE, ANGSTROM
GIAO (BoolType | BoolKey) – Use gauge-included atomic orbitals
Gamma (BoolType | BoolKey) – Will use 2n+1 rule to calculate gamma.
HirshPol (BoolType | BoolKey) – Hirshfeld Polarizability of fragments
IDRI (BoolType | BoolKey) –
LifeTime (float | FloatKey) – Specify the resonance peak width (damping) in Hartree units. Typically the lifetime of the excited states is approximated with a common phenomenological damping parameter. Values are best obtained by fitting absorption data for the molecule, however, the values do not vary a lot between similar molecules, so it is not hard to estimate values. A value of 0.004 Hartree was used in Ref. [266].
MagOptRot (BoolType | BoolKey) – Calculate magneto-optical rotation
MagneticPert (BoolType | BoolKey) – Use magnetic field as a perturbation
NBO (BoolType | BoolKey) – Perform NBO analysis
NoCore (BoolType | BoolKey) – if NOCORE is set we skip the core potential in diamagnetic term and/or in the unperturbed density of the CPKS solvers
OCCOCC (BoolType | BoolKey) – occ-occ block response (not GIAO) - Experimental
OKE (BoolType | BoolKey) –
ONLYANTISYM (BoolType | BoolKey) –
ONLYSYM (BoolType | BoolKey) –
OPTICALR (BoolType | BoolKey) –
OnlyPot (BoolType | BoolKey) – Calculation only potential for debugging purposes
OpticalRotation (BoolType | BoolKey) – Calculate optical rotation
PBE0LDA (BoolType | BoolKey) –
QuadBeta (BoolType | BoolKey) – Quadrupole operators with beta tensor
QuadPert (BoolType | BoolKey) – Calculate quadrupole-quadrupole polarizability
Quadratic (BoolType | BoolKey) – Calculate quadratic response
Quadrupole (BoolType | BoolKey) – Calculate dipole-quadrupole polarizability
REVPBE (BoolType | BoolKey) –
Raman (BoolType | BoolKey) –
SCF (str | StringKey) – Specify CPKS parameters such as the degree of convergence and the maximum number of iterations: NOCYC - disable self-consistence altogetherNOACCEL - disable convergence accelerationCONV - convergence criterion for CPKS. The default value is 10-6 . The value is relative to the uncoupled result (i.e. to the value without self-consistence).ITER - maximum number of CPKS iterations, 50 by default.Specifying ITER=0 has the same effect as specifying NOCYC.
SHG (BoolType | BoolKey) –
STATIC (BoolType | BoolKey) –
THG (BoolType | BoolKey) –
TPA (BoolType | BoolKey) –
Traceless (BoolType | BoolKey) – Traceless quadrupole tensors
USEHP (BoolType | BoolKey) –
VROA (BoolType | BoolKey) – Calculate Vibrational Raman Optical Activity.
VelocityOrd (BoolType | BoolKey) – Use VelocityOrd without GIAOs
XAlpha (BoolType | BoolKey) – Xalpha potential
- class _AnalyticalFreq[source]¶
Calculate the harmonic frequencies analytically
- Variables:
B1Thresh (float | FloatKey) – MMGF_DENB1 and MMGF_GRADB1 cutoff values
Check_CPKS_From_Iteration (int | IntKey) – Solution of the CPKS equations is an iterative process, and convergence is achieved if the difference between U1 matrix of successive iterations falls below a certain threshold. This key can be used to determine at which iteration the checking should start taking place.
Debug (str | StringKey) – For debugging purposes. Options: fit, hessian, b1, densities, numbers, symmetry, all.
Hessian (Literal["reflect", "average"]) – Whether the final Hessian is obtained by reflecting or averaging?
Max_CPKS_Iterations (int | IntKey) – Calculating the analytical frequencies requires the solution of the Coupled Perturbed Kohn-Sham (CPKS) equations, which is an iterative process. If convergence is not achieved (a warning will be printed in the output if this is the case) then this subkey can be used to increase the number of iterations, although convergence is not guaranteed. The user required accuracy of the U1 matrix, as well as the ADF integration accuracy, can effect the rates of convergence.
Nuc (Iterable[int] | IntListKey) – By default, when calculating the frequencies analytically, the derivatives of the energy with respect to all nuclei are calculated. This gives a complete Hessian (second derivative) matrix, from which the vibrational frequencies of the molecule can be calculated. However, there may be certain cases where only derivatives with respect to a subset of all the nuclei are required. In this case it is a considerable saving in time if only a partial Hessian is calculated. With this subkey, a list of the nuclei for which the derivatives are required can be specified. However, the frequencies in this case are not the vibrational frequencies of the molecule, but may be used in guiding certain transition state searches
Print (str | StringKey) – Primarily for debugging purposes. Options: eigs, u1, parts, raw_freq. Choosing EIGS results in the print out of the MO eigenvectors, while U1 results in the print out of the U1 matrices. Except for small molecules this will result in a lot of data being output, and so they are not recommended. Choosing PARTS results in the print out of various sub-hessians that add up to give the final analytical hessian. RAW_FREQ gives the eigenvalues of the initial force matrix, which are essentially the frequencies before rotational and translational degrees of freedom have been removed from the force matrix.
U1_Accuracy (float | FloatKey) – Solution of the CPKS equations is an iterative process, and convergence is achieved if the difference between U1 matrix of successive iterations falls below a certain threshold. This subkey can be used to set the threshold. The accuracy of the U1 will be 10**(-x). So, the higher the number the more accurate the U1 will be. While this parameter effects the accuracy of the frequencies, other factors also effect the accuracy of the frequencies, especially the ADF integration accuracy.
- class _Aromaticity[source]¶
Calculate aromaticity indicators, i.e. the matrix of localization/delocalization indices (LI-DI), Iring (ring index) and MCI (multi center index) aromaticity indices.
- class _BeckeGrid[source]¶
Options for the numerical integration grid.
- Variables:
AllowAngularBoost (BoolType | BoolKey) – Allow automatic augmentation of the Lebedev spherical grid for highly coordinated atoms.
InnerShellsPruning (BoolType | BoolKey) – Allow automatic pruning of the Lebedev spherical grid for shells close to the nuclei.
PartitionFunPruning (BoolType | BoolKey) – Allow pruning of integration points based on the value of the partition function.
QPNear (float | FloatKey) – Only relevant if you have specified point charges in the input file. ADF generates grids only about those point charges that are close to any real atoms. The criterion, input with the qpnear subkey, is the closest distance between the point charge at hand and any real atom. Any input value is interpreted in the unit-of-length specified with the Units key
Quality (Literal["Auto", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Quality of the integration grid. For a description of the various qualities and the associated numerical accuracy see reference. If ‘Auto’, the quality defined in the ‘NumericalQuality’ will be used.
RadialGridBoost (float | FloatKey) – The number of radial grid points will be boosted by this factor. Some XC functionals require very accurate radial integration grids, so BAND will automatically boost the radial grid by a factor 3 for the following numerically sensitive functionals: LibXC M05, LibXC M05-2X, LibXC M06-2X, LibXC M06-HF, LibXC M06-L, LibXC M08-HX, LibXC M08-SO, LibXC M11-L, LibXC MS0, LibXC MS1, LibXC MS2, LibXC MS2H, LibXC MVS, LibXC MVSH, LibXC N12, LibXC N12-SX, LibXC SOGGA11, LibXC SOGGA11-X, LibXC TH1, LibXC TH2, LibXC WB97, LibXC WB97X, MetaGGA M06L, MetaHybrid M06-2X, MetaHybrid M06-HF, MetaGGA MVS.
AtomDepQuality (str | Sequence[str] | FreeBlock) – One can define a different grid quality for each atom.
- class _CDFT[source]¶
CDFT is a tool for carrying out DFT calculations in the presence of a constraint.
- Variables:
AllAtoms (BoolType | BoolKey) – If AllAtoms is true, then TheAtoms is overridden and all the atoms in the active fragment are included in the set.
AnalyticalHessian (int | IntKey) – This will calculate the analytical derivative of the energy w.r.t. the Lagrange multiplier up to the specified SCF iteration. This key is not recommended due to the high computational cost that comes with it. The calculation is equivalent to a ground state Hessian, and it is carried out with the full sum-over-states formula.
ChargeAndSpin (BoolType | BoolKey) – will constrain both the charge and the spin
Constraints (Iterable[float] | FloatListKey) – The values of the constraints. If CHARGEANDSPIN, constraints to the alpha and beta electrons need to be specified sequentially. One more electron => CONSTRAINTS -1.0. One less electron => CONSTRAINTS 1.0. If the CDFT type is EXCITEDCDFT, CONSTRAINTS=1.0 is recommended. Other values are technically possible but have not been tested yet.
DoNotOptimize (BoolType | BoolKey) – If true, the multipliers chosen in INITIALMULTIPLIERS will not be optimized and will be constant throughout the entire SCF procedure.
ExcitedCDFT (BoolType | BoolKey) – will generate an excited state with CONSTRAINTS number of ALPHA electrons constrained to occupy the virtual space of a ground state reference calculation. EXCITEDCDFT has never been tested in closed-shell systems.
InitialMultipliers (Iterable[float] | FloatListKey) – If available, a guess for the Lagrange multipliers can be entered.
MaxIter (int | IntKey) – Maximum number of CDFT iterations. CDFT carries out a loop nested inside the SCF cycle.
Metric (BoolType | BoolKey) – metric parameter p, d and m that characterizes the quality of the XCDFT excitation.
NAtomsPerSet (Iterable[int] | IntListKey) – The number of atoms in each moiety (set).
NConstraints (int | IntKey) – This specifies the number of sets of atoms to be considered. For example, if the user wishes to constrain a positive charge on one part of the system, and a negative charge on another part, NCONSTRAINTS should be set to two. There is no limit on the number of constraints. However, SCF convergence becomes an issue with more than 2 constraints. Note: NCONSTRAINTS>1 is untested.
OnlyCharge (BoolType | BoolKey) – Will constrain only the charge, letting spin relax (and potentially delocalize)
OnlySpin (BoolType | BoolKey) – Will constrain only the spin
PopType (Literal["yukawalike", "fuzzyvoronoibecke", "fuzzyvoronoifermi"]) – The population analysis chosen for determining the constraint.
Print (Literal["low", "medium", "high"]) – Print level and debugging.
SelfConsistent (BoolType | BoolKey) – Self-Consistent CDFT
StepSize (float | FloatKey) – The amount of the Lagrange multipliers step taken in each CDFT iteration
TheAtoms (Iterable[int] | IntListKey) – The atom numbers of the moieties in the input geometry order. If NCONSTRAINTS is larger than 1, the sets of atoms are entered as a single list.
Threshold (float | FloatKey) – The threshold for convergence of the CDFT constraints. The tighter the SCF convergence criteria, the tighter the THRESHOLD should be.
- class _CVNDFT[source]¶
The CVNDFT block key regulates the execution of the CV(n)-DFT code, which calculates the singlet or triplet electronic excitations for the closed shell molecules.
- Variables:
Tolerance (float | FloatKey) – The convergence criterion, i.e. the SCF-CV(infinity)-DFT procedure stops when the given accuracy is achieved.
CV_DFT (PreAmsifiedADF._CVNDFT._CV_DFT) – The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
DSCF_CV_DFT (PreAmsifiedADF._CVNDFT._DSCF_CV_DFT) – The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
RSCF_CV_DFT (PreAmsifiedADF._CVNDFT._RSCF_CV_DFT) – The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
R_CV_DFT (PreAmsifiedADF._CVNDFT._R_CV_DFT) – The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
SCF_CV_DFT (PreAmsifiedADF._CVNDFT._SCF_CV_DFT) – The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
- class _CV_DFT[source]¶
The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
- Variables:
InitGuess (Literal["TDDFT", "SOR"]) – Initial guess
- class _DSCF_CV_DFT[source]¶
The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
- Variables:
DampOrbRelax (float | FloatKey) – The mix_relax parameter defines the relative weight of the new relaxation vector that is added to the one from the previous iteration.
DampVariable (BoolType | BoolKey) – Damping condition
InitGuess (Literal["TDDFT", "SOR"]) – Initial guess
Optimize (Literal["SVD", "SOR", "COL"]) – Gradient optimization method
RelaxAlpha (int | IntKey) – The SCF cycle number at which the relaxation of alpha orbitals starts.
RelaxBeta (int | IntKey) – The SCF cycle number at which the relaxation of beta orbitals starts.
- class _RSCF_CV_DFT[source]¶
The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
- Variables:
DampOrbRelax (float | FloatKey) – The mix_relax parameter defines the relative weight of the new relaxation vector that is added to the one from the previous iteration.
DampVariable (BoolType | BoolKey) – Damping condition
InitGuess (Literal["TDDFT", "SOR"]) – Initial guess
RelaxAlpha (int | IntKey) – The SCF cycle number at which the relaxation of alpha orbitals starts.
RelaxBeta (int | IntKey) – The SCF cycle number at which the relaxation of beta orbitals starts.
- class _R_CV_DFT[source]¶
The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
- Variables:
DampOrbRelax (float | FloatKey) – The mix_relax parameter defines the relative weight of the new relaxation vector that is added to the one from the previous iteration.
DampVariable (BoolType | BoolKey) – Damping condition
InitGuess (Literal["TDDFT", "SOR"]) – Initial guess
RelaxAlpha (int | IntKey) – The SCF cycle number at which the relaxation of alpha orbitals starts.
RelaxBeta (int | IntKey) – The SCF cycle number at which the relaxation of beta orbitals starts.
- class _ConceptualDFT[source]¶
Conceptual DFT Properties
- Variables:
AnalysisLevel (Literal["Normal", "Extended", "Full"]) –
Set the level of the ConceptualDFT analysis:
Normal - global descriptors only,
Extended - both global and condensed (QTAIM) local descriptors,
Full - all descriptors including non local ones.
AtomsToDo (Iterable[int] | IntListKey) – Define a subset of atoms for which properties are calculated. If the [Domains] block is present then this list specifies which atoms are used to define the domains bounding box.
Electronegativity (BoolType | BoolKey) – Calculate atomic electronegativities. Requires an all-electron calculation (no frozen core), triggers the TotalEnergy and increases the [AnalysisLevel] to at least Extended.
Enabled (BoolType | BoolKey) – Calculate Conceptual DFT properties.
Domains (PreAmsifiedADF._ConceptualDFT._Domains) – Calculate integrated properties for the domains (same sign) of the dual descriptor.
- class _Domains[source]¶
Calculate integrated properties for the domains (same sign) of the dual descriptor.
- Variables:
Border (float | FloatKey) – Set the extent of the Cartesian grid. Extent is the distance between a face of the grid’s bounding box and the most outlying atom in the corresponding direction. If the [AtomsToDo] key is present, the bounding box is created around the specified atoms.
Display (float | FloatKey) – Domains for which the integrated DD value is smaller (in magnitude) than the specified value are omitted from the printed output.
Enabled (BoolType | BoolKey) – Calculate properties of reactivity domains.
Ensemble (Literal["Canonical", "GrandCanonical"]) – Statistical ensemble for DD domains. Canonical: DD values are calculated using the statistical canonical ensemble. GrandCanonical: DD values are calculated using the statistical grand canonical ensemble. The grand canonical DD corresponds to (S^2 f(2) - (gamma/eta^3) f^0), where f(2) is the canonical DD, gamma and eta - the hyper-hardness and hardness of the chemical system, respectively, and f^0 is the mean Fukui function. This statistical ensemble is a natural choice when comparing two chemical systems with a different number of electrons.
Radius (float | FloatKey) – This option adds a sphere around each nucleus, excluding all points inside it. This can help to separate domains around an atom or to exclude core electrons. Be careful when using this option. In particular, the radius of the sphere should exceed two or three times the [Spacing] value to be effective. By default, no spheres are added.
Spacing (float | FloatKey) – Specifies spacing (distance between neighboring points) of the rectangular Cartesian grid used when searching for DD domains. It may be useful to specify a smaller value (or increase the size of the grid, see [Border] key) if a substantial part of the electronic density is accounted for.
Threshold (float | FloatKey) – Arbitrary value of dual descriptor used to separate DD domains (values below this threshold are ignored).
- class _ConstructPot[source]¶
Reads a density from a TAPE41 file and constructs numerically the corresponding potential to it
- class _CorePotentials[source]¶
With the key COREPOTENTIALS you specify the core file and (optionally) which sections pertain to the distinct atom types in the molecule.
- class _CurrentResponse[source]¶
- class _Dependency[source]¶
- Variables:
bas (float | FloatKey) – A criterion applied to the overlap matrix of unoccupied normalized SFOs. Eigenvectors corresponding to smaller eigenvalues are eliminated from the valence space. Note: if you choose a very coarse value, you will remove too many degrees of freedom in the basis set, while if you choose it too strict, the numerical problems may not be countered adequately.
eig (float | FloatKey) – Merely a technical parameter. When the DEPENDENCY key is activated, any rejected basis functions (i.e.: linear combinations that correspond with small eigenvalues in the virtual SFOs overlap matrix) are normally processed until diagonalization of the Fock matrix takes place. At that point, all matrix elements corresponding to rejected functions are set to zero (off-diagonal) and BigEig (diagonal).
fit (float | FloatKey) – Similar to Dependency%bas. The criterion is now applied to the overlap matrix of fit functions. The fit coefficients, which give the approximate expansion of the charge density in terms of the fit functions (for the evaluation of the coulomb potential) are set to zero for fit functions (i.e.: combinations of) corresponding to small-eigenvalue eigenvectors of the fit overlap matrix.
- class _EPrint[source]¶
Print switches that require more specification than just off or on
- Variables:
AtomPop (str | StringKey) – Mulliken population analysis on a per-atom basis
BASPop (str | StringKey) – Mulliken population analysis on a per-bas-function basis
Frag (str | StringKey) – Building of the molecule from fragments
FragPop (str | StringKey) – Mulliken population analysis on a per fragment basis
Freq (str | StringKey) – Intermediate results in the computation of frequencies (see debug: freq).
GeoStep (str | StringKey) – Geometry updates (Optimization, Transition State, …)
OrbPopEr (str | StringKey) – Energy Range (ER) in hartree units for the OrbPop subkey
Repeat (str | StringKey) – Repetition of output in Geometry iterations (SCF, optimization, …)
SFO (str | StringKey) – Information related to the Symmetrized Fragment Orbitals and the analysis
OrbPop (str | Sequence[str] | FreeBlock) – (Mulliken type) population analysis for individual MOs
- class _ETSNOCV[source]¶
Perform ETS-NOCV analysis.
- Variables:
EKMin (float | FloatKey) – The threshold for orbital interaction energy contributions corresponding to deformation density components originating from each NOCV-pairs
ENOCV (float | FloatKey) – The threshold for NOCV-eigenvalues
Enabled (BoolType | BoolKey) – Perform ETS-NOCV analysis.
RhoKMin (float | FloatKey) – The threshold for population analysis of each deformation density contribution in terms of individual SFOs.
- class _Excitations[source]¶
Excitation energies: UV/Vis
- Variables:
ALLXASMOMENTS (BoolType | BoolKey) – To be used in combination with XAS. This will print out all the individual transition moments used within the calculation of the total oscillator strength
ALLXASQUADRUPOLE (BoolType | BoolKey) – To be used in combination with XAS.This will print out the individual oscillator strength components to the total oscillator strength.
Allowed (BoolType | BoolKey) – Treat only those irreducible representations for which the oscillator strengths will be nonzero (as opposed to all)
AlsoRestricted (BoolType | BoolKey) – Include also excitation energies in which a spin-restricted exchange-correlation kernel is used
Analytical (BoolType | BoolKey) – The required integrals for the CD spectrum are calculated analytically, instead of numerically. Only used in case of CD spectrum
CDSpectrum (BoolType | BoolKey) – Compute the rotatory strengths for the calculated excitations, in order to simulate Circular Dichroism (CD) spectra
Descriptors (BoolType | BoolKey) – Compute charge-transfer descriptors and SFO analysis
Descriptors_CT_AT_Rab (float | FloatKey) – Atomic distance criterion used for the calculation of CT_AT descriptors
FullKernel (BoolType | BoolKey) – Use the non-ALDA kernel (with XCFUN)
Iterations (int | IntKey) – The maximum number of attempts within which the Davidson algorithm has to converge
KFWrite (int | IntKey) – If kfwrite is 0 then do not write contributions, transition densities, and restart vectors to TAPE21, since this can lead to a huge TAPE21, especially if many excitations are calculated. 3 means that contributions, transition densities, and restart vectors are written to TAPE21.
Lowest (Iterable[int] | IntListKey) – Number of lowest excitations to compute
NTO (BoolType | BoolKey) – Compute the Natural Transition Orbitals
OnlySing (BoolType | BoolKey) – Compute only singlet-singlet excitations
OnlyTrip (BoolType | BoolKey) – Compute only singlet-triplet excitations
Orthonormality (float | FloatKey) – The Davidson algorithm orthonormalizes its trial vectors. Increasing the default orthonormality criterion increases the CPU time somewhat, but is another useful check on the reliability of the results.
SFOAnalysis (BoolType | BoolKey) – Do SFO analysis
STDA (BoolType | BoolKey) – Simplified Tamm-Dancoff approach
STDDFT (BoolType | BoolKey) – Simplified time-dependent DFT
ScaleCoul (float | FloatKey) – Scaling of Coulomb kernel with scale parameter
ScaleHF (float | FloatKey) – Scaling of the HF part of the kernel with scale parameter
ScaleXC (float | FloatKey) – Scaling of the XC-kernel (excluding a possible HF-part) with scale parameter
Select (str | StringKey) – Rather than selecting the first nmcdterm transitions for consideration individual transitions can be selected through the SELECT keyword
SingleOrbTrans (BoolType | BoolKey) – keyword to use only orbital energy differences
TD-DFTB (BoolType | BoolKey) – Use the molecular orbitals from a DFT ground state calculation as input to an excited state calculation with TD-DFTB coupling matrices
Vectors (int | IntKey) – The maximum number of trial vectors in the Davidson algorithm for which space is allocated. If this number is small less memory will be needed, but the trial vector space is smaller and has to be collapsed more often, at the expense of CPU time. The default if usually adequate.
Velocity (BoolType | BoolKey) – calculates the dipole-velocity representation of the oscillator strength. If applicable, the dipole-velocity representation of the rotatory strength is calculated. Default the dipole-length representation of the oscillator strength and rotatory strength is calculated
XAS (BoolType | BoolKey) – calculation of the higher order multipole moment integrals and the calculation of the quadrupole oscillator strengths. This will only print the total oscillator strength and the excitation energy.
Davidson (str | Sequence[str] | FreeBlock) – Use the Davidson procedure
Exact (str | Sequence[str] | FreeBlock) – The most straightforward procedure is a direct diagonalization of the matrix from which the excitation energies and oscillator strengths are obtained. Since the matrix may become very large, this option is possible only for very small molecules
- class _ExcitedGO[source]¶
Excited state geometry optimization
- Variables:
ALLGRADIENTS (BoolType | BoolKey) –
EigenFollow (BoolType | BoolKey) – This key tries to follow the eigenvector in excited state geometry optimizations
Output (int | IntKey) – The amount of output printed. A higher value requests more detailed output
Singlet (BoolType | BoolKey) – Singlet-singlet excitation is considered
State (str | StringKey) – Choose the excitation for which the gradient is to be evaluated: ‘STATE Irreplab nstate’. Irreplab is the label from the TDDFT calculation. NOTE: the TDDFT module uses a different notation for some representation names, for example, A’ is used instead of AA. nstate: This value indicates that the nstate-th transition of symmetry Irreplab is to be evaluated. Default is the first fully symmetric transition.
Triplet (BoolType | BoolKey) – Singlet-triplet excitation is considered
CPKS (PreAmsifiedADF._ExcitedGO._CPKS) – Some control parameters for the CPKS(Z-vector) part of the TDDFT gradients calculation
- class _CPKS[source]¶
Some control parameters for the CPKS(Z-vector) part of the TDDFT gradients calculation
- Variables:
Eps (float | FloatKey) – Convergence requirement of the CPKS
IterOut (int | IntKey) – Details of the CPKS calculation are printed every iter iterations
NoPreConiter (int | IntKey) – maximum number of iterations allowed for the unpreconditioned solver.
PreConiter (int | IntKey) – maximum number of iterations allowed for the preconditioned solver
- class _FDE[source]¶
Frozen Density Embedding options
- Variables:
AMOLFDE (BoolType | BoolKey) – placeholder
CAPPOTBASIS (BoolType | BoolKey) – placeholder
CAPPOTDIIS (BoolType | BoolKey) – placeholder
CAPPOTLINESEARCH (BoolType | BoolKey) – placeholder
CJCORR (float | FloatKey) – Option to switch on a long-distance correction
Coulomb (BoolType | BoolKey) – Neglecting completely vt[rhoA,rhoB] (vt[rhoA,rhoB] equals zero) together with the exchange-correlation component of the embedding potential introduced by Wesolowski and Warshel.
Dipole (BoolType | BoolKey) – placeholder
E00 (BoolType | BoolKey) – placeholder
ENERGY (BoolType | BoolKey) – placeholder
EXTERNALORTHO (float | FloatKey) – Used to specify the use of external orthogonality (EO) in the FDE block
EXTPRINTENERGY (BoolType | BoolKey) – placeholder
FULLGRID (BoolType | BoolKey) – placeholder
FreezeAndThawCycles (int | IntKey) – This keyword duplicates RelaxCycles
FreezeAndThawPostSCF (BoolType | BoolKey) – This keyword duplicates RelaxPostSCF
GGA97 (BoolType | BoolKey) – placeholder
GGAPotCFD (str | StringKey) – The correlation approximant is used in the construction of the embedding potential. The same correlation approximants as in the XC key are available.
GGAPotXFD (str | StringKey) – The exchange approximant is used in the construction of the embedding potential. The same exchange approximants as in the XC key are available.
LLP91 (BoolType | BoolKey) – placeholder
LLP91S (BoolType | BoolKey) – placeholder
NOCAPSEPCONV (BoolType | BoolKey) – placeholder
NOFDKERN (BoolType | BoolKey) – placeholder
OL91A (BoolType | BoolKey) – placeholder
OL91B (BoolType | BoolKey) – placeholder
ONEGRID (BoolType | BoolKey) – placeholder
P92 (BoolType | BoolKey) – placeholder
PBE2 (BoolType | BoolKey) – placeholder
PBE3 (BoolType | BoolKey) – placeholder
PBE4 (BoolType | BoolKey) – placeholder
PDFT (BoolType | BoolKey) – placeholder
PRINTEACHCYCLE (BoolType | BoolKey) – placeholder
PRINTRHO2 (BoolType | BoolKey) – placeholder
PW86K (BoolType | BoolKey) – placeholder
PW91K (BoolType | BoolKey) – placeholder
PW91Kscaled (BoolType | BoolKey) – placeholder
RHO1FITTED (BoolType | BoolKey) – placeholder
RelaxCycles (int | IntKey) – This gives the maximum number of freeze-and-thaw cycles that are performed for this fragment. If the maximum number given in the FDE block is smaller, or if convergence is reached earlier, then fewer cycles are performed.
RelaxPostSCF (BoolType | BoolKey) – this option is included, several post-SCF properties will be calculated after each freeze-and-thaw cycle. These are otherwise only calculated in the last cycle.
SDFTEnergy (BoolType | BoolKey) – placeholder
SHORTPRINTENERGY (BoolType | BoolKey) – placeholder
TF9W (BoolType | BoolKey) – placeholder
THAKKAR92 (BoolType | BoolKey) – placeholder
THOMASFERMI (BoolType | BoolKey) – Local-density-approximation form of vt[rhoA,rhoB] derived from Thomas-Fermi expression for Ts[rho]
TW02 (BoolType | BoolKey) – placeholder
WEIZ (BoolType | BoolKey) – placeholder
XCFun (BoolType | BoolKey) – Use XCFUN for nonadditive functionals
- class _Fragments[source]¶
Definitions of the fragment type/files: {FragmentName FragmentFile}. In the block header one can specify the directory where the fragment files are located
- class _GUIBonds[source]¶
The bonds used by the GUI (this does not affect the ADF calculation in any way)
- class _Geometry[source]¶
Geometry Optimizations procedure
- Variables:
Branch (Literal["New", "Old"]) – Code branch to be used.
Constraints (Literal["FullConverge", "PartialConverge"]) – Choice between enforcing constraints at each steps exactly or adding them to the optimization space as Lagrange multipliers.
GEigenvalueThreshold (float | FloatKey) – Threshold for delocalized coordinates singular value decomposition eigenvalues
GO (BoolType | BoolKey) – Just for compatibility. It is not actually parsed
GeoOpt (BoolType | BoolKey) – Just for compatibility. It is not actually parsed
HessUpd (Literal["Automatic", "BFGS", "MS", "DFP", "FS", "FARKAS", "FARKAS-BOFILL", "BOFILL", "HOSHINO", "POWELL", "BAKKEN-HELGAKER", "NONE"]) – Specifies how the Hessian matrix is updated, using the gradient values of the current and the previous geometry
ImplicitHessianUpdate (BoolType | BoolKey) – Placeholder
InitHess (str | StringKey) – read a Hessian from a text files. The only argument is the name of the file containing the initial Hessian. The Hessian must be given in full, in non-mass-weighted Cartesian coordinates, and in atomic units.
Iterations (Iterable[int] | IntListKey) – The maximum number of geometry iterations allowed to locate the desired structure. The default is max(30,2*Nfree), where Nfree is the number of free variables, which is typically close to 3*N(atoms).
NEBOptEnds (BoolType | BoolKey) – Optimize end points
QuasiNewton (Literal["HighOrder", "Standard"]) –
SP (BoolType | BoolKey) – Single point
Vibron (BoolType | BoolKey) – Placeholder
Converge (PreAmsifiedADF._Geometry._Converge) – Convergence criteria
DIIS (PreAmsifiedADF._Geometry._DIIS) – DIIS options
Frequencies (PreAmsifiedADF._Geometry._Frequencies) – Calculation of frequencies via numerical differentiation
IRC (PreAmsifiedADF._Geometry._IRC) – Intrinsic Reaction Coordinates
Step (PreAmsifiedADF._Geometry._Step) – Controls that changes in geometry from one cycle to another are not too large
TransitionState (PreAmsifiedADF._Geometry._TransitionState) – Transition state search
- class _Converge[source]¶
Convergence criteria
- Variables:
Angle (float | FloatKey) – Refers to changes in bond- and dihedral angles, in degrees. This is only meaningful if optimization takes place in Z-matrix coordinates
E (float | FloatKey) – The criterion for changes in the energy
Grad (float | FloatKey) – The criterion for the nuclear gradients
Rad (float | FloatKey) – Refers to changes in the Cartesian coordinates or bond lengths, depending on in what coordinates you optimize
- class _Frequencies[source]¶
Calculation of frequencies via numerical differentiation
- Variables:
Allowed (BoolType | BoolKey) – Another advantage of the symmetric displacements is that only a subset of frequencies can be calculated. The ALLOWED option requests computation of only IR-visible frequencies. This option is only useful for symmetric molecules where it can be a big time-saver.
DisAng (float | FloatKey) – The displacements of the coordinates (angle)
DisRad (float | FloatKey) – The displacements of the coordinates (Cartesian and bond length)
NoScan (BoolType | BoolKey) – Placeholder
NumDif (int | IntKey) – Must have the value between 1 and 4 and specifies the type of numerical differentiation that is applied to compute the force constants from gradients in slightly displaced geometries
ScanAll (BoolType | BoolKey) – Placeholder
ScanRange (Iterable[float] | FloatListKey) – Placeholder
Symm (BoolType | BoolKey) – Frequencies are calculated in symmetric displacements
- class _IRC[source]¶
Intrinsic Reaction Coordinates
- Variables:
Backward (BoolType | BoolKey) – Do backward path from the Transition State
Forward (BoolType | BoolKey) – Do forward path from the Transition State
HessianEigenvector (int | IntKey) – Defines how the initial direction of the path is chosen to move away from the Transition State. It does not imply whether the first step along this direction is taken positively or negatively. See for this aspect the section about Forward/Backward IRC paths. The admissible values for start are: Grad: compute the gradient and take that direction right from the start. Obviously, if we start perfectly at the Transition State this will be meaningless since the gradient vanishes there completely. Read : the initial path direction is read in with the key IRCstart, see the section IRC Start Direction. Hess n : the initial path coincides with the n-th Hessian eigenvector (ordered by ascending eigenvalues); n must be an integer in the appropriate range. The default (omission of any start specification at all) is the first Hessian eigenvector, presumably corresponding to the path over the Transition State (negative Hessian eigenvalue!).
Points (int | IntKey) – The maximum number of IRC points computed in the run, for both paths together and including the initial (TS) central point (as far as applicable).
Start (Literal["Hess", "Read", "Grad"]) – Defines how the initial direction of the path is chosen to move away from the Transition State
Step (float | FloatKey) – The (initial) step length when proceeding from one IRC point to another along the path.
StepMax (float | FloatKey) – The maximum step length that the program will select in the step-adjusting algorithm (the program will wither use the default or 10 times the initial step length, whichever is larger)
StepMin (float | FloatKey) – (the program will wither use the default or 0.3 times the initial step length, whichever is smaller)
- class _IQA[source]¶
Bond energy decomposition based on the interacting quantum atoms (IQA) approach and using QTAIM real-space partition.
- Variables:
AtomsToDo (Iterable[int] | IntListKey) –
Define a subset of atoms for which the IQA atom-atom interactions are calculated.
If left empty, all atoms will be included.
Enabled (BoolType | BoolKey) – Calculate the bond energy decomposition using the interacting quantum atoms (IQA) approach and the QTAIM real-space partitioning.
Interactions (Literal["intra", "inter", "all"]) – Placeholder
Print (Literal["Normal", "Verbose", "Debug"]) –
For each atom pair, print energy terms:
Normal: total, covalent and ionic terms,
Verbose: all terms.
- class _LinearScaling[source]¶
- Variables:
Cutoff_Coulomb (float | FloatKey) – determines the radii for the fit functions in the evaluation of the (short-range part of) the Coulomb potential.
Cutoff_Fit (float | FloatKey) – determines how many atom pairs are taken into account in the calculation of the fit integrals and the density fit procedure. If the value is too low, charge will not be conserved and the density fitting procedure will become unreliable. This parameter is relevant for the timings of the FITINT and RHOFIH routines of ADF.
Cutoff_Multipoles (float | FloatKey) – determines the cut-offs in the multipole (long-range) part of the Coulomb potential
Overlap_Int (float | FloatKey) – determines the overlap criterion for pairs of AOs in the calculation of the Fock-matrix in a block of points. Indirectly it determines what the cut-off radii for AO’s should be. The value of ovint has a strong influence on the timing for the evaluation of the Fock matrix, which is very important for the overall timings
ProgConv (float | FloatKey) – determines how the overall accuracy changes during the SCF procedure
- class _MDC[source]¶
Options for Multipole Derived Charges (MDC)
- class _MP2[source]¶
Technical aspects of the MP2 algorithm.
- Variables:
Debug (BoolType | BoolKey) – Enable MP2 debug output.
Enabled (BoolType | BoolKey) – Enable the calculation of the MP2 energy.
FitSetQuality (Literal["Auto", "VeryBasic", "Basic", "Normal", "Good", "VeryGood"]) – Specifies the fit set to be used in the MP2 calculation. ‘Normal’ quality is generally sufficient for basis sets up to and including TZ2P. For larger basis sets (or for benchmarking purposes) a ‘VeryGood’ fit set is recommended. Note that the FitSetQuality heavily influences the computational cost of the calculation. If not specified or ‘Auto’, the RIHartreeFock%FitSetQuality is used.
Formalism (Literal["Auto", "RI", "LT", "All"]) – Specifies the formalism for the calculation of the MP2 correlation energy. ‘LT’ means Laplace Transformed MP2 (also referred to as AO-PARI-MP2), ‘RI’ means that a conventional RI-MP2 is carried out. If ‘Auto’, LT will be used in case of DOD double hybrids and SOS MP2, and RI will be used in all other cases. ‘All’ means that both RI and LT formalisms are used in the calculation.
IntegrationQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood"]) – Specifies the integration quality to be used in the MP2 calculation. If not specified, the RIHartreeFock%IntegrationQuality is used.
Memory (BoolType | BoolKey) – If true, the more memory efficient variant of the algorithm is invoked (only implemented for SOS)
MultipoleApproximation (BoolType | BoolKey) – If true, the multipole approximation for distant centers will be used.
ThresholdQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood"]) – Controls the distances between atomic centers for which the product of two basis functions is not fitted any more. Especially for spatially extended, large systems, ‘VERYBASIC’ and ‘BASIC’ can lead to large computational savings, but the fit is also more approximate. This keyword is only meaningful when the LT formalism is used. If not specified, the RIHartreeFock%ThresholdQuality is used.
ThresholdQualityHalf (float | FloatKey) – Specifies the treshold for neglecting half-transformed fit coefficients. (only relevant if the LT formalism is used). In the AO-PARI-MP2 algorithm, fit coefficients are contracted with so-called pseudo density matrices. If all elements of the resulting half-transformed fitfunction tensor are smaller than the values specified with ‘ThresholdQualityHalf’, all following tensor-contractions with this tensor are not carried out. This keyword is only relevant for very large and spatially extended systems. A low value, i.e. 1.0E-6, can lead to a linear-scaling evaluation of the opposite-spin MP2 energy, but also results in rather inaccurate results.
ThresholdQualityHalfTimesC (float | FloatKey) – Specifies the treshold for neglecting products of halt-transformed fit-coefficients with fitfunctions.
nLaplace (int | IntKey) – Number of laplace points (only relevant in case the Laplace Transformed (LT) formalism is used). Transforming the MP2 equations to the AO basis requires the numerical evaluation of an integral (often referred to as a Laplace transform). 9 points is a rather safe choice, guaranteeing for practically all systems a good accuracy. Only for systems with a very small HOMO-LUMO gap more points might be necessary. For many systems, 6 points are sufficient for good accuracy. The computation time of a AO-PARI-MP2 calculation scales linearly with the number of quadrature points. If the HOMO-LUMO gap approaches zero, it is possible that the algorithm determining the weights for the quadrature points does not converge. In these cases, the double-hybrid calculation is not meaningful anyway, as a non-zero HOMO-LUMO gap is required for accurate MP2 energies.
- class _ModifyExcitation[source]¶
- Variables:
GRIMMEPERTC (BoolType | BoolKey) –
NOGRIMMEPERTC (BoolType | BoolKey) –
OscStrength (float | FloatKey) – Use only pairs of an occupied and virtual orbital as guess vectors, for which the oscillator strength of the single-orbital transition is larger than this value
SetLargeEnergy (float | FloatKey) – The orbital energies of the uninteresting occupied orbitals are changed to -epsbig Hartree, and the orbital energies of the uninteresting virtual orbitals are changed to epsbig Hartree
SetOccEnergy (float | FloatKey) – All occupied orbitals that have to be used will change their orbital energy to this value. In practice only useful if one has selected one occupied orbital energy, and one want to change this to another value. Default: the orbital energies of the occupied orbitals that are used are not changed.
UseOccRange (Iterable[float] | FloatListKey) – Use only occupied orbitals which have orbital energies between the two numbers.
UseOccVirtNumbers (Iterable[int] | IntListKey) – Use only pairs of an occupied and virtual orbital as guess vectors, for which in the sorted list of the orbital energy differences, the number of the single-orbital transition is between the two numbers.
UseOccVirtRange (Iterable[float] | FloatListKey) – Use only pairs of an occupied and virtual orbital, for which the orbital energy difference is between the two numbers
UseScaledZORA (BoolType | BoolKey) – Use everywhere the scaled ZORA orbital energies instead of the ZORA orbital energies in the TDDFT equations. This can improve deep core excitation energies. Only valid if ZORA is used.
UseVirtRange (Iterable[float] | FloatListKey) – Use only virtual orbitals which have orbital energies between the two numbers
UseOccupied (str | Sequence[str] | FreeBlock) – Use only the occupied orbitals which are specified
UseVirtual (str | Sequence[str] | FreeBlock) – Use only the virtual orbitals which are specified
- class _PertLoc[source]¶
Perturbed localized molecular orbitals, correct to first order in an applied field, can be calculated in case of AORESPONSE. Can be used if the applied field changes the density in first order.
- Variables:
Alfa (BoolType | BoolKey) – Analyze the static or dynamic polarizability
BField (BoolType | BoolKey) – The perturbation is a magnetic field. Should be consistent with AORESPONSE
Beta (BoolType | BoolKey) – Analyze the optical rotation parameter beta. The relation to G’ is beta = -G’/omega. The optical rotation parameter beta is calculated directly and has a well-defined static limit, i.e. omega can be zero or non-zero
Diag (BoolType | BoolKey) – Only analyze the diagonal of the response tensor
Dynamic (BoolType | BoolKey) – Should be used for a frequency dependent perturbation field.
EField (BoolType | BoolKey) – The perturbation is an electric field
Fulltens (BoolType | BoolKey) – The full tensor is analyzed
GPrime (BoolType | BoolKey) – Analyze the G’ (gyration) tensor, for optical rotation dispersion. Requires a frequency dependent perturbation field, with a frequency (omega) unequal to zero.
Static (BoolType | BoolKey) – should be used for a static field
- class _PolTDDFT[source]¶
TODO!
- Variables:
CutOff (float | FloatKey) – For a given point in the spectrum, only include pairs of an occupied and virtual orbital, for which the orbital energy difference is lower than the energy of the point in the spectrum plus cutoff.
Enabled (BoolType | BoolKey) – Calculate UV/Vis and CD spectrum from the imaginary part of the polarizability tensor at any given photon energy. This avoids the bottleneck of Davidson diagonalization.
FreqRange (str | StringKey) – Keyword FREQRANGE is used to specify the equally spaced points in the spectrum for which one would like to calculate the complex dynamical polarizability. The first point is eVi (0 eV by default) and the last one is eVf (5 eV by default). The total number of points in the spectrum is nfreq (100 by default).
KGrid (str | StringKey) – Keyword KGRID is used to discretize the energy scale for calculating the complex dynamical polarizability. Only pairs of an occupied and virtual orbital are included, for which the orbital energy difference is lower than eVgrid (9 eV by default). Ngrid is the number of points within the energy grid (180 by default).
Lambda (float | FloatKey) – Jacob’s scaling factor for the study of plasmonic resonances. This factor, 0<lambda<1, turns on the coupling matrix K.
Lifetime (float | FloatKey) – Specify the resonance peak width (damping). Typically the lifetime of the excited states is approximated with a common phenomenological damping parameter. Values are best obtained by fitting absorption data for the molecule, however, the values do not vary a lot between similar molecules, so it is not hard to estimate values.
Velocity (BoolType | BoolKey) – If True, ADF calculates the dipole moment in velocity gauge. If false: dipole-length representation is used
Irrep (str | Sequence[str] | FreeBlock) – Subblock key for selecting which symmetry irreps of the excitations to calculate (all excitations by default). In the subkey data block list the symmetry irrep labels, like B1, for example
- class _QTAIM[source]¶
This block is used to request a topological analysis of the gradient field of the electron density, also known as the Bader’s analysis. If this block is specified without any sub-key, only local properties are calculated.
- Variables:
AnalysisLevel (Literal["Normal", "Extended", "Full"]) –
Set the level of the QTAIM analysis:
Normal - topology analysis and properties at the density critical points,
Extended - same as Normal plus condensed atomic descriptors,
Full - same as Extended plus non-local descriptors.
AtomsToDo (Iterable[int] | IntListKey) – List of atoms for which condensed descriptors are to be calculated. By default all atoms are included.
Enabled (BoolType | BoolKey) – Calculate QTAIM (also known as Bader) properties.
Energy (BoolType | BoolKey) – Calculate atomic energies. Requires an all-electron calculation (no frozen core), triggers the TotalEnergy and increases the [AnalysisLevel] to at least Extended.
Spacing (float | FloatKey) – Specifies spacing of the initial Cartesian grid when searching for critical points. It may be useful to specify a smaller value than the default if some critical points are missed. This will result in a more accurate but slower calculation.
- class _RIHartreeFock[source]¶
- Variables:
DependencyThreshold (float | FloatKey) –
To improve numerical stability, almost linearly-dependent combination of basis functions are removed from the Hartree-Fock exchange matrix.
If you obtain unphysically large bond energy in an Hybrid calculation, you might try setting the DependencyThreshold to a larger value (e.g. 3.0E-3)
FitSetQuality (Literal["Auto", "VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) –
The quality of auxiliary fit set employed in the RI scheme.
If ‘Auto’, the value of the RIHartreeFock Quality option will be used.
Normal quality is generally sufficient for basis sets up to and including TZ2P.
For larger basis sets (or for benchmarking purposes) a VeryGood fit set is recommended.
Note that the FitSetQuality heavily influences the computational cost of the calculation.
IntegrationQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Quality of the numerical integration for evaluating the integrals between basis functions and fit functions. If IntegrationQuality is not defined in input, the value defined in RIHartreeFock%Quality will be used.
Quality (Literal["Auto", "VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Numerical accuracy of the RI procedure. If ‘Auto’, the quality specified in the ‘NumericalQuality’ will be used.
ResponseQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Numerical accuracy of the RI procedure for the Response module.
ThresholdQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Linear scaling thresholds (also used for determining at what range the multiple approximation is used). To disable all linear scaling thresholds set this to Excellent.
UseMe (BoolType | BoolKey) – Set to False if you want to use the old RI scheme
AtomDepQuality (str | Sequence[str] | FreeBlock) – One can define a different fit-set quality for each atom. The syntax for this free block is ‘iAtom quality’, where iAtom is the index of the atom in input order.
- class _RadialCoreGrid[source]¶
For each atom the charge densities and the coulomb potentials of frozen core and valence electrons are computed in a radial grid. The radial grid consists of a sequence of r-values, defined by a smallest value, a constant multiplication factor to obtain each successive r-value, and the total number of points. Equivalently it can be characterized by the smallest r-value, the largest r-value, and the number of points; from these data the program computes then the constant multiplication factor.
- class _Response[source]¶
The calculation of frequency-dependent (hyper)polarizabilities and related properties (Raman, ORD)
- Variables:
ALLCOMPONENTS (BoolType | BoolKey) –
ALLHYPER (BoolType | BoolKey) –
ALPHAINANG (BoolType | BoolKey) –
ANALYTIC (BoolType | BoolKey) –
AllCycles (BoolType | BoolKey) – Convergence printout
AllTensor (BoolType | BoolKey) – Higher dispersion coefficients are also calculated
C8 (BoolType | BoolKey) –
CUTTAILS (BoolType | BoolKey) –
DYNAHYP (BoolType | BoolKey) –
Dipole (BoolType | BoolKey) –
FXCDRCONV (BoolType | BoolKey) –
FXCLB (BoolType | BoolKey) –
Hartree (BoolType | BoolKey) –
IFILES (int | IntKey) – Integration run including external files. Used for Van der Waals dispersion coefficients calculations.
KSORBRUN (BoolType | BoolKey) –
MAGNETICPERT (BoolType | BoolKey) –
NOFXCDR (BoolType | BoolKey) –
NUMERIC (BoolType | BoolKey) –
OPTICALROTATION (BoolType | BoolKey) –
Octupole (BoolType | BoolKey) –
Quadrupole (BoolType | BoolKey) –
Raman (BoolType | BoolKey) –
STARTREALGR (BoolType | BoolKey) –
SYMRUN (BoolType | BoolKey) –
Temperature (float | FloatKey) – Wavelength of incoming light is equal to the wavelength at which the calculation is performed and temperature is equal to room temperature (300K) Total Raman band is default, not the Q-branch of diatomic. (Relevant for Raman scattering cross section)
VERDET (float | FloatKey) – For numerical differentiation d alfa(omega) /d omega, needed for Verdet constant, the default frequencies are omega + dverdt and omega - dverdt
- class _Restart[source]¶
Options for restarts
- Variables:
File (str | StringKey) – The name of a file with restart data. The path (absolute or relative) to the file must be included if the file is not local to the directory where the calculation executes.
NoExc (BoolType | BoolKey) – Do not use any Excitation data from the restart file.
NoGeo (BoolType | BoolKey) – Do not use the geometry - Cartesian, Z-matrix, etc. coordinates - from the restart file
NoHes (BoolType | BoolKey) – Do not use any Hessian from the restart file.
NoOrb (BoolType | BoolKey) – Do not use orbitals from the restart file
NoSCF (BoolType | BoolKey) – Do not use any fit coefficients from the restart file as a first approximation to the (fitted) SCF density for the new calculation. Instead, the sum-of-fragments density will be used, as in a non-restart run. Note, typically noSCF should be used in combination with noORB.
NoSmear (BoolType | BoolKey) – Do not use any electron smearing data from the restart file.
SpinFlip (Iterable[int] | IntListKey) – Indices of atoms in for which the flipping will be performed
- class _SCF[source]¶
Control aspects of the Self Consistent Field procedure
- Variables:
AccelerationMethod (Literal["ADIIS", "fDIIS", "LISTb", "LISTf", "LISTi", "MESA", "SDIIS"]) –
SCF acceleration method.
The default method is ADIIS, which is actually a mix of A-DIIS and SDIIS: A-DIIS is used at the start of the SCF and SDIIS is used closer to convergence, with a smooth switching function.
The other methods are from the LIST family developed by Alex Wang and co-workers. They may perform better than the default in some situations.
Setting AccelerationMethod to SDIIS effectively disables A-DIIS and is equivalent to the legacy mixing+DIIS method.
Converge (Iterable[float] | FloatListKey) –
The criterion to stop the SCF updates.
The tested error is the commutator of the Fock matrix and the P-matrix (=density matrix in the representation of the basis functions) from which the F-matrix was obtained. This commutator is zero when absolute self-consistency is reached. Convergence is considered reached when the maximum element falls below SCFcnv and the norm of the matrix below 10*SCFcnv. The default is fairly strict.
A second criterion which plays a role when the SCF procedure has difficulty converging. When in any SCF procedure the currently applicable criterion does not seem to be achievable, the program stops the SCF. When the secondary criterion (sconv2) has been met, only a warning is issued and the program continues normally.
EDIIS (BoolType | BoolKey) – Use the Energy-DIIS SCF acceleration method. This key also triggers the OldSCF. The Energy-DIIS should not be used because it is not supported by the new SCF module, is not any better than methods from the LIST family and can be very slow.
Iterations (int | IntKey) – The maximum number of SCF cycles allowed.
The level shifting parameter.
The diagonal elements of the Fock matrix, in the representation of the orbitals of the previous iteration, are raised by vshift hartree energy units for the virtual orbitals. This may help to solve convergence problems when during the SCF iterations charge is sloshing back and forth between different orbitals that are close in energy and all located around the Fermi level.
Level shifting is not supported in the case of Spin-Orbit coupling.
At the moment properties that use virtuals, like excitation energies, response properties, NMR calculations, will give incorrect results if level shifting is applied.
LShift_cyc (int | IntKey) – Specifies that level shifting is not turned on before the given SCF cycle number (for the start-up geometry).
LShift_err (float | FloatKey) – Specifies that level shifting will be turned off by the program as soon as the SCF error drops below a threshold.
Mixing (float | FloatKey) – When none of the SCF acceleration methods is active, the next Fock matrix is determined F = mixing * F_n + (1-mixing)F_(n-1).
Mixing1 (float | FloatKey) – The mixing parameter at the 1st SCF cycle.
NoADIIS (BoolType | BoolKey) – Disables A-DIIS and switches SCF to a damping+DIIS scheme.
OldSCF (BoolType | BoolKey) –
Disable the default SCF algorithm and use the old SCF algorithm.
The default SCF improves performance for big systems on big machines (when your calculation uses many tasks).
It is also recommended for machines with slow disk I/O as it writes less data to disk.
The default convergence method supported is A-DIIS, but LISTi is also supported.
ScalableSCF (BoolType | BoolKey) – Use new scalable scf.
ScalableSO (BoolType | BoolKey) – Use new scalable scf.
ADIIS (PreAmsifiedADF._SCF._ADIIS) – Settings for the ADIIS method.
ARH (PreAmsifiedADF._SCF._ARH) – The Augmented Roothaan-Hall method has been developed by T. Helgaker and coworkers.
DIIS (PreAmsifiedADF._SCF._DIIS) – The maximum number of SCF cycles allowed.
- class _ADIIS[source]¶
Settings for the ADIIS method.
- Variables:
If ErrMax > Thresh1 then only A-DIIS coefficients are used to determine the next Fock matrix.
Below this threshold a weighted mix of A-DIIS and DIIS coefficients will be used.
If ErrMax < Thresh2 then only SDIIS coefficients are used.
Below this threshold a weighted mix of A-DIIS and DIIS coefficients will be used.
- class _ARH[source]¶
The Augmented Roothaan-Hall method has been developed by T. Helgaker and coworkers.
- Variables:
CGiter (int | IntKey) – Sets the maximum number of micro-iterations.
Conv (float | FloatKey) – ARH convergence criterion. When the RMS gradient and its maximum components are both lower than the criterion, the ARH procedure will be considered converged.
Enabled (BoolType | BoolKey) – Use ARH.
Final (BoolType | BoolKey) –
If enabled, only one Fock matrix diagonalization will be performed after the ARH solution is found to get the orbitals. No further SCF iterations will be performed.
If not enabled, the regular SCF method will continue after the ARH solution is found.
Iter (int | IntKey) – Maximum number of ARH iteration to perform. Please note that in difficult cases a huge number of iterations may be required for complete SCF convergence
NOTRANSPCG (BoolType | BoolKey) –
The number of saved density and Fock matrices used for augmentation of the electronic Hessian.
A larger value should be used in difficult cases when the number of orbitals very close to the Fermi level is large.
NoPrecond (BoolType | BoolKey) –
PRECOND (BoolType | BoolKey) –
SHIFTED (BoolType | BoolKey) –
SWITCHING (BoolType | BoolKey) –
Turn OFF to avoid switching from the normal CG to a trust-radius minimization in reduced space.
Turning off this option helps to reduce the total number of SCF cycles is some cases.
Thus, if this option is turned off a NOSWITCHING key will be added (see User’s Guide).
TRANSPCG (BoolType | BoolKey) –
- class _DIIS[source]¶
The maximum number of SCF cycles allowed.
- Variables:
BFac (float | FloatKey) – By default, the latest vector is not favored in the DIIS algorithm (value 0.0). A sensible value would be 0.2.
CX (float | FloatKey) – The DIIS space is reduced when very large DIIS coefficients appear. The value is the threshold.
CXX (float | FloatKey) – When very large DIIS coefficients appear, switch to traditional damping. The value is the threshold.
Cyc (int | IntKey) – When A-DIIS is disabled, the Pulay DIIS will start at this iteration irrespective of the DIIS OK value.
N (int | IntKey) – The number of expansion vectors used for accelerating the SCF. The number of previous cycles taken into the linear combination is then n-1 (the new computed potential is also involved in the linear combination)
Ok (float | FloatKey) – The Pulay DIIS starting criterion, when A-DIIS is disabled,
- class _SelectExcitation[source]¶
- Variables:
GRIMMEPERTC (BoolType | BoolKey) –
NOGRIMMEPERTC (BoolType | BoolKey) –
OscStrength (float | FloatKey) – Use only pairs of an occupied and virtual orbital as guess vectors, for which the oscillator strength of the single-orbital transition is larger than this value
SetLargeEnergy (float | FloatKey) – The orbital energies of the uninteresting occupied orbitals are changed to -epsbig Hartree, and the orbital energies of the uninteresting virtual orbitals are changed to epsbig Hartree
SetOccEnergy (float | FloatKey) – All occupied orbitals that have to be used will change their orbital energy to this value. In practice only useful if one has selected one occupied orbital energy, and one want to change this to another value. Default: the orbital energies of the occupied orbitals that are used are not changed.
UseOccRange (Iterable[float] | FloatListKey) – Use only occupied orbitals which have orbital energies between the two numbers.
UseOccVirtNumbers (Iterable[int] | IntListKey) – Use only pairs of an occupied and virtual orbital as guess vectors, for which in the sorted list of the orbital energy differences, the number of the single-orbital transition is between the two numbers.
UseOccVirtRange (Iterable[float] | FloatListKey) – Use only pairs of an occupied and virtual orbital, for which the orbital energy difference is between the two numbers
UseScaledZORA (BoolType | BoolKey) – Use everywhere the scaled ZORA orbital energies instead of the ZORA orbital energies in the TDDFT equations. This can improve deep core excitation energies. Only valid if ZORA is used.
UseVirtRange (Iterable[float] | FloatListKey) – Use only virtual orbitals which have orbital energies between the two numbers
UseOccupied (str | Sequence[str] | FreeBlock) – Use only the occupied orbitals which are specified
UseVirtual (str | Sequence[str] | FreeBlock) – Use only the virtual orbitals which are specified
- class _Solvation[source]¶
- Variables:
Ass (BoolType | BoolKey) –
COSKFAtoms (Iterable[int] | IntListKey) – This subkey COSKFATOMS specifies for which nuclei the segments in the COSMO section of the COSKF file should be used. Default all nuclei should be used, i.e. as for omitting the subkey COSKFATOMS. The numbers refer to the input ordering in the ADF calculation.
CsmRsp (BoolType | BoolKey) –
Lpr (BoolType | BoolKey) –
NoAss (BoolType | BoolKey) –
NoCsmRsp (BoolType | BoolKey) –
NoLpr (BoolType | BoolKey) –
NoPVec (BoolType | BoolKey) –
PVec (BoolType | BoolKey) –
PrintSM12 (BoolType | BoolKey) –
Surf (Literal["wsurf", "asurf", "esurf", "klamt", "delley", "wsurf nokeep", "asurf nokeep", "esurf nokeep", "klamt nokeep", "delley nokeep"]) – Defines the type of cavity to be used.
- class _SubExci[source]¶
Subsystem TDDFT (FDE)
- Variables:
CICoupl (BoolType | BoolKey) – Within the Tamm-Dancoff Approximation, the couplings between localized excited states on different subsystems correspond directly to so-called exciton couplings. The CICOUPL keyword, in conjunction with TDA, prints these exciton couplings. It is also possible to use CICOUPL with full FDEc-TDDFT. In that case, the excitonic couplings between monomers are reconstructed from an effective 2x2 CIS-like eigenvalue problem.
COULKERNEL (BoolType | BoolKey) –
COUPLBLOCK (BoolType | BoolKey) –
COUPLSYS (Iterable[int] | IntListKey) –
CThres (float | FloatKey) – all excitations of all subsystems (present on the fragment TAPE21 files) with an excitation energy that differs by less than coupling_threshold. From one of the reference states are selected to be included in the coupling. Note that additional excited states of system 1 may be included here.
DIPVEL (BoolType | BoolKey) –
DiagType (Literal["EXACT"]) –
ETHRES (float | FloatKey) – Threshold for effective coupling
FULLGRID (BoolType | BoolKey) –
InvGuess (Literal["EigVal-OrbDiff", "OrbDiff-OrbDiff", "Exact"]) – Type of states to be coupled
LOCALFXCK (BoolType | BoolKey) –
Lowest (int | IntKey) – The selection of the excited states to be coupled consists of two steps
NOINTERSOLV (BoolType | BoolKey) –
NOSOLVCCHECK (BoolType | BoolKey) –
ONEGRID (BoolType | BoolKey) –
OptStates (Iterable[int] | IntListKey) – If the keyword OPTSTATES is given, only those excited states of the first subsystem are considered as reference states that are given in this list.
PFRAGOUT (BoolType | BoolKey) –
SFThres (float | FloatKey) – To reduce the computational effort, it is possible to ignore the effect of orbital pairs with coefficients less than solutionfactor_threshold in the solution factors (TDDFT eigenvectors) of the underlying uncoupled calculation in the construction of the exact trial densities during the calculation of the coupling matrix elements. These orbital pair contributions are not ignored in the subsequent calculation of transition moments, oscillator, and rotational strengths.
SMARTGRID (BoolType | BoolKey) –
Stat2CPL (Literal["OnlyKnown"]) – Type of states to be coupled
TCOMEGA (BoolType | BoolKey) – Transpose construction of Omega matrix
TDA (BoolType | BoolKey) – TDA specifies the use of the Tamm-Dancoff-Approximation (Tamm-Dancoff approximation) in the underlying uncoupled FDE-TDDFT calculations. Contrary to the full SUBEXCI-TDDFT variant, SUBEXCI-TDA allows for the usage of hybrid functionals in the underlying uncoupled FDE-TDDFT calculations.
TKINKERNEL (BoolType | BoolKey) –
XCKERNEL (BoolType | BoolKey) –
- class _Tails[source]¶
Obsolete option for linear scaling and distance effects. We recommend using the LinearScaling key instead.
- Variables:
Bas (float | FloatKey) – Parameter related to the threshold for the calculation of basis functions on a block of integration points. A higher value implies higher precision. The default depends on the Integration numerical quality.
Fit (float | FloatKey) – Parameter related to the threshold for the calculation of fit functions on a block of integration points. A higher value implies higher precision. The default depends on the Integration numerical quality.
- class _Thermo[source]¶
At the end of a completed Frequencies calculation, a survey is given of thermodynamic properties: Heat Capacity, Internal Energy, Entropy. The computed results assume an ideal gas, and electronic contributions are ignored. The latter is a serious omission if the electronic configuration is (almost) degenerate, but the effect is small whenever the energy difference with the next state is large compared to the vibrational frequencies
- Variables:
P (float | FloatKey) – The Pressure. A zero or negative pressure is adjusted by the program to a (very) small number 1e-4
TMax (float | FloatKey) – Maximum temperature for the temperature range.
TMin (float | FloatKey) – Minimum temperature for the temperature range.
The number of steps by which the temperature interval is scanned.
By default (value 0) it is computed by the program from the temperature range (TMin, Tmax), such that the step size is as close as possible to 10 K. Note that the number of temperatures for which the calculations are done is one more than the number of temperature steps.
- class _Units[source]¶
Definitions of the units.
- Variables:
angle (Literal["degree", "radian"]) – Units of angles
length (Literal["bohr", "angstrom"]) – Units of length
- class _Vibron[source]¶
Resonance Raman Input options
- Variables:
CALCCC (BoolType | BoolKey) – use ADF routines to calculate coupling constants (they only work for the linear coupling constants)
CDVIBRON (BoolType | BoolKey) – CD spectra calculations
CGRAD (BoolType | BoolKey) – calculate ground-state gradients in VIBRON runs
DOMODES (Iterable[int] | IntListKey) –
DONTMODES (Iterable[int] | IntListKey) –
DONTSTEPS (Iterable[int] | IntListKey) –
DOSTEPS (Iterable[int] | IntListKey) –
ELTHRES (float | FloatKey) – lower boundary for excitation energy
EUTHRES (float | FloatKey) – upper boundary for excitation energy
EXTAPE (str | StringKey) – excited state symmetry information input file
HARMGR (BoolType | BoolKey) – use harmonic approximation for ground state energy
IGNORECHECK (BoolType | BoolKey) – ignore safety checks
NDTYPE (int | IntKey) – by default, always use 3-point central differences (i.e. two sided), but only compute linear couplings
NMTape (str | StringKey) – It specifies the name of a TAPE21 file from a previous frequency calculation. This TAPE21 file is needed to read the normal modes w.r.t. which the derivatives are computed. I.e., a separate frequency calculation must be carried out first.
NOINV (BoolType | BoolKey) – inversion of initial sadiab
NOTONLYSYM (BoolType | BoolKey) –
ONLYSYM (BoolType | BoolKey) – calculate displacements along symmetric modes
PDEBUG (BoolType | BoolKey) –
PESCAN (Iterable[int] | IntListKey) –
PURIFY (BoolType | BoolKey) – purify excitation energies for excited states (leads to errors for non-totally symmetric modes in degenerate systems)
RESRAMAN (BoolType | BoolKey) – perform resonance Raman calculations
SAVEREFAO (BoolType | BoolKey) – save reference AO vectors
STOPAT (int | IntKey) – debug option: stop at a particular geometry step
STPSIZE (float | FloatKey) – Step size for numerical differentiation
SelState (Iterable[int] | IntListKey) – For advanced users it is furthermore possible to pick out certain states from the energy window, and only perform the mapping (and diabatization, if requested) and differentiation for them. Here list includes the number (in ascending excitation energy) of the excited state at the reference (equilibrium) structure.
TRANSDEF (BoolType | BoolKey) – use transpose definition of overlap matrix
USERAWDAT (BoolType | BoolKey) –
WINTREAT (str | StringKey) – do not increase energy window upon change of state no.
WRTMAG (BoolType | BoolKey) –
EShift (str | Sequence[str] | FreeBlock) – Empirical vertical shifts for the excitation energies
UsSym (str | Sequence[str] | FreeBlock) – user-specified symmetry of excited states (at reference geometry)
- class _XC[source]¶
Definition of the XC.
- Variables:
DoubleHybrid (str | StringKey) – Specifies the double hybrid functional that should be used during the SCF.
EmpiricalScaling (Literal["None", "SOS", "SCS", "SCSMI"]) – Calculate the (SOS/SCS/SCSMI)-MP2 correlation energy.
GGA (str | StringKey) – Specifies the GGA part of the XC Functional
HartreeFock (BoolType | BoolKey) – Use the Hartree-Fock exchange should be used during the SCF.
Hybrid (str | StringKey) – Specifies the hybrid functional that should be used during the SCF.
LDA (str | StringKey) – Defines the LDA part of the XC functional
LibXC (str | StringKey) – Use the LibXC library with the specified functional.
MP2 (BoolType | BoolKey) – Calculate the MP2 correlation energy after the HF SCF is completed.
MetaGGA (str | StringKey) – Specifies that a meta-GGA should be used during the SCF
MetaHybrid (str | StringKey) – Specifies the meta-hybrid functional that should be used during the SCF.
NoLibXC (BoolType | BoolKey) – Prevent the usage of the LibXC library
OEP (str | StringKey) – Defines the optimized effective potential expanded into a set of the fit functions
RangeSep (str | StringKey) – Range separated hybrids parameters
XCFun (BoolType | BoolKey) – Use the XCFun library
- class _XES[source]¶
X-ray emission spectroscopy
- Variables:
AllXESMoments (BoolType | BoolKey) – Print out all the individual transition moments used within the calculation of the total oscillator strength
AllXESQuadrupole (BoolType | BoolKey) – Print out the individual oscillator strength components to the total oscillator strength
selection of the acceptor orbital for the calculation of the emission oscillator strengths. For example ‘CoreHole A1 2’ calculates oscillator strengths to the orbital 2 in irrep A1.
In ADFinput you may also use the notation 2A1 (so first the orbital number, next the symmetry)
Enabled (BoolType | BoolKey) –
Calculate the X-ray emission energies to a core orbital.
By default it calculates the emission to the first orbital in the first symmetry.
- class _ZlmFit[source]¶
Options for the density fitting scheme ‘ZlmFit’.
- Variables:
AllowBoost (BoolType | BoolKey) – Allow automatic atom-dependent tuning of maximum l of spherical harmonics expansion. Whether or not this boost is needed for a given atom is based on an heuristic estimate of how complex the density around that atom is.
DensityThreshold (float | FloatKey) – Threshold below which the electron density is considered to be negligible.
Pruning (BoolType | BoolKey) –
Quality (Literal["Auto", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Quality of the density-fitting approximation. For a description of the various qualities and the associated numerical accuracy see reference. If ‘Auto’, the quality defined in the ‘NumericalQuality’ will be used.
AtomDepQuality (str | Sequence[str] | FreeBlock) – One can specify different ZlmFit-quality for different atoms, The syntax for this free block is ‘iAtom quality’, where iAtom is the index of the atom in input order. For the atoms that are not present in the AtomDepQuality sub-block, the quality defined in the Quality key will be used.
- class _AtomDepQuality[source]¶
One can specify different ZlmFit-quality for different atoms, The syntax for this free block is ‘iAtom quality’, where iAtom is the index of the atom in input order. For the atoms that are not present in the AtomDepQuality sub-block, the quality defined in the Quality key will be used.
- class ReactionsDiscovery[source]¶
- Variables:
Engine (EngineBlock) – The input for the computational engine for the MolecularDynamics and NetworkExtraction tasks. The header of the block determines the type of the engine.
LoadSystem (ReactionsDiscovery._LoadSystem) – Block that controls reading the chemical system from a KF file instead of the [System] block.
MolecularDynamics (ReactionsDiscovery._MolecularDynamics) – Settings for reactive molecular dynamics.
NetworkExtraction (ReactionsDiscovery._NetworkExtraction) – Options for extracting the reactive network from MD trajectories
ProductRanking (ReactionsDiscovery._ProductRanking) – Options for ranking of the intermediates by stability
System (ReactionsDiscovery._System) – Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- class _Engine[source]¶
The input for the computational engine for the MolecularDynamics and NetworkExtraction tasks. The header of the block determines the type of the engine.
- class _LoadSystem[source]¶
Block that controls reading the chemical system from a KF file instead of the [System] block.
- class _MolecularDynamics[source]¶
Settings for reactive molecular dynamics.
- Variables:
Enabled (BoolType | BoolKey) – Whether to run molecular dynamics.
NumSimulations (int | IntKey) – Total number of MD simulations to run.
Type (Literal["NanoReactorOld", "LatticeDeformationOld", "NanoReactor", "LatticeDeformation", "Restart"]) – The type of molecular dynamics.
UseDeuterium (BoolType | BoolKey) – If true, all hydrogen atoms will be replaced by deuterium during the MD. This helps to slow down the motion of the hydrogen atoms. This options does not affect the density you should insert in BuildSystem%Density. However, it does affect the density on the resulting MD trajectory file.
BondOrders (ReactionsDiscovery._MolecularDynamics._BondOrders) – Details regarding the calculation/guessing of bond orders during Molecular Dynamics. The bond changes during the MD are later analyzed in the Network Extraction step.
BuildSystem (ReactionsDiscovery._MolecularDynamics._BuildSystem) – Build the initial system for molecular dynamics with packmol. If
MolecularDynamics%Typeis set toRestart, then BuildSystem is ignored.LatticeDeformation (ReactionsDiscovery._MolecularDynamics._LatticeDeformation) – Option for the reactive molecular dynamics.
NanoReactor (ReactionsDiscovery._MolecularDynamics._NanoReactor) – Option for the reactive molecular dynamics.
Restart (ReactionsDiscovery._MolecularDynamics._Restart) – Settings for restarting MD simulations.
- class _BondOrders[source]¶
Details regarding the calculation/guessing of bond orders during Molecular Dynamics. The bond changes during the MD are later analyzed in the Network Extraction step.
- Variables:
Method (Literal["Guess", "EngineWithGuessFallback"]) –
How to compute the bond orders.
’Guess’: Use a bond guessing algorithm based on the system’s geometry. This is the same algorithm that is used by the Graphical User Interface to guess bonds.
’EngineWithGuessFallback’: let the engine compute the bond orders but if the engine did not produce any bond orders, use the bond guessing algorithm as a fallback option.
- class _BuildSystem[source]¶
Build the initial system for molecular dynamics with packmol. If
MolecularDynamics%Typeis set toRestart, then BuildSystem is ignored.- Variables:
Density (float | FloatKey) – The initial density of the system. This should be the lowest density (corresponding to the largest volume) that you want the system to have. The standard atomic masses are used when building the system.
Enabled (BoolType | BoolKey) – If True, build the initial system using packmol. If False, a System block must be provided with the initial system.
Equilibration (BoolType | BoolKey) – Whether to run a short 250 fs equilibration simulation on the packmol-built structure.
NumAtoms (int | IntKey) – Approximate total number of atoms in each MD simulation.
Molecule (ReactionsDiscovery._MolecularDynamics._BuildSystem._Molecule) – A molecule to put in the MD simulation.
- class _Molecule[source]¶
A molecule to put in the MD simulation.
- Variables:
MoleFraction (float | FloatKey) – Mole fraction of the molecule (the mole fractions of the various molecules will be normalized, so only the relative MoleFraction values matter)
SMILES (str | StringKey) – The SMILES string of the molecules.
SystemID (str | StringKey) – The ID of the corresponding System (i.e. the header of the corresponding System block).
- class _LatticeDeformation[source]¶
Option for the reactive molecular dynamics.
- Variables:
MinVolumeFraction (float | FloatKey) – The minimum (compressed) volume of the system, as a fraction of the initial (maximum) system volume.
NumCycles (int | IntKey) – How many compression-expansion cycles to perform.
Period (float | FloatKey) – The period with which the lattice will oscillate in femtoseconds.
Temperature (float | FloatKey) – Thermostat temperature during the MD simulation.
- class _NanoReactor[source]¶
Option for the reactive molecular dynamics.
- Variables:
DiffusionTime (float | FloatKey) – The length of the diffusion phase in femtoseconds.
InitialRadius (float | FloatKey) – The radius of the initial (spherical) system. If
BuildSystemis used, the value is ignored (then the value is automatically determined). IfBuildSystemis not used, then a guess for theInitialRadiuswill be made if it is not specified.MinVolumeFraction (float | FloatKey) – The minimum (compressed) volume of the system, as a fraction of the initial (maximum) system volume.
NumCycles (int | IntKey) – How many compression-expansion cycles to perform.
Temperature (float | FloatKey) – Temperature during the diffusion phase. The temperature during the compression phase will be much higher as a result of the inward acceleration.
- class _Restart[source]¶
Settings for restarting MD simulations.
- Variables:
Directory (str | Path | StringKey) – Directory containing a previous Reactions Discovery calculation with MD simulations that were not finished. Note: This directory will be scanned recursively for ams.rkf files!
NSteps (int | IntKey) – Number of MD steps. If left empty, the number of MD steps from the original MD trajectory will be used. Note that you need to manually increase this number if you want to continue finished simulations.
- class _NetworkExtraction[source]¶
Options for extracting the reactive network from MD trajectories
- Variables:
Enabled (BoolType | BoolKey) – Whether to perform network extraction.
ExtractFromFailedMDJobs (BoolType | BoolKey) – Whether to extract from failed/crashed MD jobs (by default, only successful jobs are used)
MDTrajectories (str | Path | StringKey) – If MolecularDynamics%Enabled is False, this directory will be recursively scanned for ams.rkf files containing MD trajectories. All found trajectories will be used for the analysis. It should typically be a Reactions Discovery results directory containing finished MD simulations.
StoreGeometryOptimizationResults (BoolType | BoolKey) – Many AMS calculations are performed to analyse whether detected molecules are stable. Enabling this option will store all those calculations on disk, which can be helpful to understand why a molecule was not considered stable or why a calculation failed, but it will make the NetworkExtraction much slower and can take up large amounts of disk space.
UseCharges (BoolType | BoolKey) – Use engine-calculated charges if they exist on the MD trajectory files for the NetworkExtraction
Print (ReactionsDiscovery._NetworkExtraction._Print) – Printing details
- class _Print[source]¶
Printing details
- Variables:
FilterFluctuations (BoolType | BoolKey) – If true, do not print molecules that are only part of recrossing reactions.
MaxReactionOrder (int | IntKey) – If the reaction order is larger than this value, the reaction will not be printed.
MinReactionsThreshold (int | IntKey) – If a molecule is involved in fewer reaction than this value, skip printing the results corresponding to it. To print all molecules, set this value to 0.
SkipRareReactions (BoolType | BoolKey) – If true,reduce the output by filtering out rare reactions. If false, always print all reactions.
- class _ProductRanking[source]¶
Options for ranking of the intermediates by stability
- Variables:
BalanceFromNetwork (BoolType | BoolKey) – Use the network to determine the balanced reaction from the initial reactants to each stable product. This is not the default. By default, a balanced equation is determined directly by using the other stable products as possible side products.
DiscardIons (BoolType | BoolKey) – Remove all ions from the final product list
Enabled (BoolType | BoolKey) – Whether to perform ranking of the reaction network.
MaxBalancedReactions (int | IntKey) – The maximum number of stable products used to find a balanced reaction equation for each one.
ReactionNetwork (str | Path | StringKey) – Directory containing a previous Reactions Discovery calculation with ‘NetworkExtraction%Enabled Yes’
Temperature (float | FloatKey) – Temperature used to compute reaction rates from reaction energies of reactions in the reaction network.
WritePaths (BoolType | BoolKey) – Write full paths to the reaction network for each molecule.
- class _System[source]¶
Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- Variables:
AllowCloseAtoms (BoolType | BoolKey) – No longer functional. Just here for backwards compatibility.
Charge (float | FloatKey) – The system’s total charge in atomic units.
FractionalCoords (BoolType | BoolKey) – Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
GeometryFile (str | Path | StringKey) – Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds (BoolType | BoolKey) – Equivalent to ‘Modify%GuessBonds’. Please update input file to use ‘Modify’ block instead.
LatticeStrain (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%LatticeStrain’. Please update input file to use ‘Modify’ block instead.
MapAtomsToUnitCell (BoolType | BoolKey) – Equivalent to ‘Modify%MapAtomsToUnitCell’. Please update input file to use ‘Modify’ block instead.
PerturbCoordinates (float | FloatKey) – Equivalent to ‘Modify%PerturbCoordinates’. Please update input file to use ‘Modify’ block instead.
PerturbLattice (float | FloatKey) – Equivalent to ‘Modify%PerturbLattice’. Please update input file to use ‘Modify’ block instead.
ShiftCoordinates (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%Translate’, but in the unit of bohr by default. Please update input file to use ‘Modify’ block instead.
SuperCell (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCell’. Please update input file to use ‘Modify’ block instead.
SuperCellTrafo (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCellTrafo’. Please update input file to use ‘Modify’ block instead.
Symmetrize (BoolType | BoolKey) – Equivalent to ‘Modify%Symmetrize’. Please update input file to use ‘Modify’ block instead.
Atoms (str | Sequence[str] | FreeBlock) – The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders (str | Sequence[str] | FreeBlock) – Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
ElectrostaticEmbedding (ReactionsDiscovery._System._ElectrostaticEmbedding) – Container for electrostatic embedding options, which can be combined.
Lattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
Modify (ReactionsDiscovery._System._Modify) – Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- class _Atoms[source]¶
The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
- class _BondOrders[source]¶
Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
- class _ElectrostaticEmbedding[source]¶
Container for electrostatic embedding options, which can be combined.
- Variables:
ElectricField (Iterable[float] | FloatListKey) –
External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.
In atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 … e11 V/m.
Supported by the engines adf, band, dftb and mopac.
For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
MultipolePotential (ReactionsDiscovery._System._ElectrostaticEmbedding._MultipolePotential) – External point charges (and dipoles).
- class _MultipolePotential[source]¶
External point charges (and dipoles).
- Variables:
ChargeModel (Literal["Point", "Gaussian"]) – A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
ChargeWidth (float | FloatKey) – The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
Coordinates (str | Sequence[str] | FreeBlock) –
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Coordinates[source]¶
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Lattice[source]¶
Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
- class _Modify[source]¶
Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- Variables:
EnableAtomicProperties (Literal["gui", "adf", "band", "forcefield", "dftb", "reaxff", "qe"]) – Enables an atomic property group. This is only necessary if you want a group enabled, but no atom in the input is using any property from that group.
GuessBonds (BoolType | BoolKey) – Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.
LatticeStrain (Iterable[float] | FloatListKey) – Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
MapAtomsToUnitCell (Iterable[float] | FloatListKey) – For periodic systems the atoms will be moved to the central unit cell where all their fractional coordinates are in the range [start_range,start_range+1). No mapping will take place along non-periodic directions. If just a single number is given, it corresponds to start_range. If multiple numbers are given, they should match the number of lattice vectors and will be used as start ranges along the individual lattice vectors. If no number is given at all, the mapping will be done to the [-0.5:0.5) cell.
PerturbCoordinates (float | FloatKey) – Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
PerturbLattice (float | FloatKey) – Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
SuperCell (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
SuperCellTrafo (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
Symmetrize (BoolType | BoolKey) – Symmetrizes the atomic coordinates to machine precision and rototranslates the molecule to the AMS standard orientation. This allows optimal use of the system’s symmetry for calculations with the AMS driver and its engines.
Translate (Iterable[float] | FloatListKey) – Translate all atoms by a vector.
- class RedoxPotential[source]¶
- Variables:
Method (Literal["DC", "TC", "TC-COSMORS", "Screening"]) –
Specify the method to use to calculate the redox potential.
DC: Direct calculation TC: Thermodynamic cycle TC-COSMORS: Thermodynamic cycle using COSMO-RS Screening: Quick method using lower level of theory (GFN1-xTB)
Mode (Literal["Oxidation", "Reduction"]) – Specify whether to do reduction or oxidation
System (RedoxPotential._System) – Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- class _System[source]¶
Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- Variables:
AllowCloseAtoms (BoolType | BoolKey) – No longer functional. Just here for backwards compatibility.
Charge (float | FloatKey) – The system’s total charge in atomic units.
FractionalCoords (BoolType | BoolKey) – Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
GeometryFile (str | Path | StringKey) – Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds (BoolType | BoolKey) – Equivalent to ‘Modify%GuessBonds’. Please update input file to use ‘Modify’ block instead.
LatticeStrain (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%LatticeStrain’. Please update input file to use ‘Modify’ block instead.
MapAtomsToUnitCell (BoolType | BoolKey) – Equivalent to ‘Modify%MapAtomsToUnitCell’. Please update input file to use ‘Modify’ block instead.
PerturbCoordinates (float | FloatKey) – Equivalent to ‘Modify%PerturbCoordinates’. Please update input file to use ‘Modify’ block instead.
PerturbLattice (float | FloatKey) – Equivalent to ‘Modify%PerturbLattice’. Please update input file to use ‘Modify’ block instead.
ShiftCoordinates (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%Translate’, but in the unit of bohr by default. Please update input file to use ‘Modify’ block instead.
SuperCell (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCell’. Please update input file to use ‘Modify’ block instead.
SuperCellTrafo (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCellTrafo’. Please update input file to use ‘Modify’ block instead.
Symmetrize (BoolType | BoolKey) – Equivalent to ‘Modify%Symmetrize’. Please update input file to use ‘Modify’ block instead.
Atoms (str | Sequence[str] | FreeBlock) – The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders (str | Sequence[str] | FreeBlock) – Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
ElectrostaticEmbedding (RedoxPotential._System._ElectrostaticEmbedding) – Container for electrostatic embedding options, which can be combined.
Lattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
Modify (RedoxPotential._System._Modify) – Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- class _Atoms[source]¶
The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
- class _BondOrders[source]¶
Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
- class _ElectrostaticEmbedding[source]¶
Container for electrostatic embedding options, which can be combined.
- Variables:
ElectricField (Iterable[float] | FloatListKey) –
External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.
In atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 … e11 V/m.
Supported by the engines adf, band, dftb and mopac.
For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
MultipolePotential (RedoxPotential._System._ElectrostaticEmbedding._MultipolePotential) – External point charges (and dipoles).
- class _MultipolePotential[source]¶
External point charges (and dipoles).
- Variables:
ChargeModel (Literal["Point", "Gaussian"]) – A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
ChargeWidth (float | FloatKey) – The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
Coordinates (str | Sequence[str] | FreeBlock) –
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Coordinates[source]¶
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Lattice[source]¶
Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
- class _Modify[source]¶
Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- Variables:
EnableAtomicProperties (Literal["gui", "adf", "band", "forcefield", "dftb", "reaxff", "qe"]) – Enables an atomic property group. This is only necessary if you want a group enabled, but no atom in the input is using any property from that group.
GuessBonds (BoolType | BoolKey) – Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.
LatticeStrain (Iterable[float] | FloatListKey) – Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
MapAtomsToUnitCell (Iterable[float] | FloatListKey) – For periodic systems the atoms will be moved to the central unit cell where all their fractional coordinates are in the range [start_range,start_range+1). No mapping will take place along non-periodic directions. If just a single number is given, it corresponds to start_range. If multiple numbers are given, they should match the number of lattice vectors and will be used as start ranges along the individual lattice vectors. If no number is given at all, the mapping will be done to the [-0.5:0.5) cell.
PerturbCoordinates (float | FloatKey) – Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
PerturbLattice (float | FloatKey) – Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
SuperCell (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
SuperCellTrafo (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
Symmetrize (BoolType | BoolKey) – Symmetrizes the atomic coordinates to machine precision and rototranslates the molecule to the AMS standard orientation. This allows optimal use of the system’s symmetry for calculations with the AMS driver and its engines.
Translate (Iterable[float] | FloatListKey) – Translate all atoms by a vector.
- class SGF[source]¶
- Variables:
SurfaceGF (SGF._SurfaceGF) –
TightBinding (SGF._TightBinding) –
- class SimpleActiveLearning[source]¶
- Variables:
RNGSeed (Iterable[int] | IntListKey) – Initial seed for the (pseudo)random number generator. This should be omitted in most calculations to avoid introducing bias into the results. If this is unset, the generator will be seeded randomly from external sources of entropy. If you want to exactly reproduce an older calculation, set this to the numbers printed in its output.
Task (Literal["MolecularDynamics"]) – The task to perform.
ActiveLearning (SimpleActiveLearning._ActiveLearning) – Settings for Active Learning
Constraints (SimpleActiveLearning._Constraints) – The Constraints block allows geometry optimizations and potential energy surface scans with constraints. The constraints do not have to be satisfied at the start of the calculation.
Engine (EngineBlock) – The reference engine settings.
LoadSystem (SimpleActiveLearning._LoadSystem) – Block that controls reading the chemical system from a KF file instead of the [System] block.
MachineLearning (SimpleActiveLearning._MachineLearning) – Options for Task MachineLearning.
MolecularDynamics (SimpleActiveLearning._MolecularDynamics) – Settings for Molecular Dynamics
ParallelLevels (SimpleActiveLearning._ParallelLevels) – Distribution of threads/processes between the parallelization levels.
System (SimpleActiveLearning._System) – Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- class _ActiveLearning[source]¶
Settings for Active Learning
- Variables:
JobPrefix (str | StringKey) – Jobs added to the job collection will receive this prefix. Example: set to
water_to get jobs likewater_step1_attempt1_frame001. If the prefix does not end with an underscore_, one will be automatically added.MaxAttemptsPerStep (int | IntKey) – Maximum number of attempts per active learning step. If this number is exceeded, the active learning will continue to the next step even if the potential is not accurate enough according to the criteria. If the default value is exceeded, it probably means that the criteria are too strict.
MaxReferenceCalculationsPerAttempt (int | IntKey) – Maximum number of reference calculations per attempt. For successful attempts, only a single reference calculation is performed. For very short active learning steps, fewer calculations are done than the number specified.
RestartDirectory (str | Path | StringKey) –
Directory to restart from. It should be a
jobname.resultsfolder containing the filesimple_active_learning.rkf.This will continue an interrupted Active Learning workflow and ignore all other input settings.
To reuse reference data from a previous workflow, instead use the
ActiveLearning%InitialReferenceDatablock. To reuse a previously trained model, instead use theMachineLearning%LoadModelkey.AtEnd (SimpleActiveLearning._ActiveLearning._AtEnd) – What to do at the end of the active learning loop.
FromScratchTraining (SimpleActiveLearning._ActiveLearning._FromScratchTraining) – Custom options when training ‘from scratch’ (not restarting).
InitialReferenceData (SimpleActiveLearning._ActiveLearning._InitialReferenceData) – Options for loading reference data.
ReasonableSimulationCriteria (SimpleActiveLearning._ActiveLearning._ReasonableSimulationCriteria) – Criteria for determining whether a simulation is reasonable. If any of the criteria are exceeded, this will be reported as ‘ENERGY_UNCERTAINTY’, ‘TEMPERATURE’, etc., with capital letters in the output. If a simulation is unreasonable, it will never lead to an increase of the Step, even if the number of attempts exceeds
MaxAttemptsPerStep.Save (SimpleActiveLearning._ActiveLearning._Save) – The files/directories on disk to keep. If you set these options to
All, a lot of output will be created. This output is usually not necessary but can be used for debugging purposes, or to better understand what the workflow is doing.Steps (SimpleActiveLearning._ActiveLearning._Steps) – Settings to determine the number of MD steps per active learning step.
SuccessCriteria (SimpleActiveLearning._ActiveLearning._SuccessCriteria) – Criteria for determining whether an active learning step was successful. These criteria compare one or more reference calculations to the predictions. If any of the criteria are exceeded, the active learning loop will reparametrize the model and repeat the step.
- class _AtEnd[source]¶
What to do at the end of the active learning loop.
- Variables:
RerunSimulation (BoolType | BoolKey) – Rerun the MD simulation (folder:
final_production_simulation) using the last set of parameters. This guarantees that the entire trajectory is calculated using the same model / potential energy surface, and that the trajectory has a consistent sampling frequency. This means that it can be used with all MD postanalysis tools.RetrainModel (BoolType | BoolKey) – Train a final model (folder:
final_training) using all reference (training and validation) data, including any reference calculations that have not yet been trained to.
- class _FromScratchTraining[source]¶
Custom options when training ‘from scratch’ (not restarting).
- Variables:
Enabled (BoolType | BoolKey) – With the given probability, start parameter training from the original starting point (from ‘scratch’) instead of restarting from the previous step/attempt.
EpochMultiplier (float | FloatKey) – The maximum number of epochs is multiplier by this number when training from scratch. When not restarting from the previous parameters, it is usually a good idea to train for more epochs.
Probability (float | FloatKey) – With the given probability, start parameter training from the original starting point (from ‘scratch’) instead of restarting from the previous step/attempt.
- class _InitialReferenceData[source]¶
Options for loading reference data.
- Variables:
Generate (SimpleActiveLearning._ActiveLearning._InitialReferenceData._Generate) –
How to generate initial reference data from the initial structure. Can also be combined with the
Loadblock.The purpose of these options is to get some initial reference structures/data around the current structure that can be used for Step 1 of the active learning loop.
The
ReferenceMDoption will be automatically enabled if no data is otherwise loaded or generated.Load (SimpleActiveLearning._ActiveLearning._InitialReferenceData._Load) – How to load initial reference data from other sources. Can also be combined with the
Generateblock
- class _Generate[source]¶
How to generate initial reference data from the initial structure. Can also be combined with the
Loadblock.The purpose of these options is to get some initial reference structures/data around the current structure that can be used for Step 1 of the active learning loop.
The
ReferenceMDoption will be automatically enabled if no data is otherwise loaded or generated.- Variables:
M3GNetShortMD (SimpleActiveLearning._ActiveLearning._InitialReferenceData._Generate._M3GNetShortMD) – Structure sampler using M3GNet-UP-2022
ReferenceMD (SimpleActiveLearning._ActiveLearning._InitialReferenceData._Generate._ReferenceMD) – Run a very short MD simulation using the reference engine.
- class _M3GNetShortMD[source]¶
Structure sampler using M3GNet-UP-2022
- Variables:
Enabled (BoolType | BoolKey) – Run 300 steps with M3GNet-UP-2022 at T=600 K. If the system is 3D-periodic the density will be scanned around the initial value. Extract 5 frames and run reference calculations on those.
- class _Load[source]¶
How to load initial reference data from other sources. Can also be combined with the
Generateblock- Variables:
Directory (str | Path | StringKey) –
Directory containing initial reference data. It can be * a ParAMS input directory or a
stepX_attemptY_reference_datadirectory containing the files job_collection.yaml, training_set.yaml, and validation_set.yaml. * a ParAMS results directory.If a directory is specified here it will be used instead of the data from a previously loaded model.
FromPreviousModel (BoolType | BoolKey) –
If
MachineLearning%LoadModelis set, reuse reference data from that ParAMS run.If
MachineLearning%LoadModelis not set, or ifDirectoryis specified, then this input option is ignored.
- class _ReasonableSimulationCriteria[source]¶
Criteria for determining whether a simulation is reasonable. If any of the criteria are exceeded, this will be reported as ‘ENERGY_UNCERTAINTY’, ‘TEMPERATURE’, etc., with capital letters in the output. If a simulation is unreasonable, it will never lead to an increase of the Step, even if the number of attempts exceeds
MaxAttemptsPerStep.- Variables:
Distance (SimpleActiveLearning._ActiveLearning._ReasonableSimulationCriteria._Distance) – Stop the simulation if any interatomic distance is smaller than the specified value.
EnergyUncertainty (SimpleActiveLearning._ActiveLearning._ReasonableSimulationCriteria._EnergyUncertainty) – Stop the simulation if the uncertainty in the energy is too high. Currently only applicable when training committees.
GradientsUncertainty (SimpleActiveLearning._ActiveLearning._ReasonableSimulationCriteria._GradientsUncertainty) – Stop the simulation if the uncertainty in the gradients (forces) is too high. Currently only applicable when training committees.
Temperature (SimpleActiveLearning._ActiveLearning._ReasonableSimulationCriteria._Temperature) – Discard all frames after the temperature has reached the specified value.
- class _Distance[source]¶
Stop the simulation if any interatomic distance is smaller than the specified value.
- class _EnergyUncertainty[source]¶
Stop the simulation if the uncertainty in the energy is too high. Currently only applicable when training committees.
- Variables:
Enabled (BoolType | BoolKey) – Stop the simulation if the uncertainty in the energy is too high. Currently only applicable when training committees. If CommitteeSize = 1 then this keyword has no effect.
MaxValue (float | FloatKey) – Threshold for allowed [energy uncertainty divided by
Normalization].Normalization (float | FloatKey) – Normalize (divide) the energy uncertainty by this number before comparing to the specified threshold. If not specified, it will become the number of atoms.
- class _Save[source]¶
The files/directories on disk to keep. If you set these options to
All, a lot of output will be created. This output is usually not necessary but can be used for debugging purposes, or to better understand what the workflow is doing.- Variables:
ReferenceCalculations (Literal["None", "All"]) – The reference calculation directories (
initial_reference_calculationsorstepX_attemptY_ref_calcZ) including the original input and output. These directories may take up a lot of disk space and are not kept by default. Enable this option if you need to investigate why reference calculations fail (incorrect input, SCF convergence problems, …), or if you want to keep them for some other reason. Note: The output used for parametrization (energy, forces) is always stored in the ReferenceData (training and validation sets).ReferenceData (Literal["Latest", "All"]) – The reference data directories (
stepX_attemptY_reference_data) containing the training and validation sets in ParAMS .yaml format (and ASE .xyz format). These can be opened in the ParAMS GUI or used as input for ParAMS.TrainingDirectories (Literal["Latest", "All"]) – The ParAMS training directories (
stepX_attemptY_training).Trajectories (Literal["Latest", "All"]) – The MD trajectory calculation directories (
stepX_attemptY_simulation) using the trained ML potential. Note: the trajectories in these directories are the entire trajectories from the beginning of the simulation.
- class _Steps[source]¶
Settings to determine the number of MD steps per active learning step.
- Variables:
List (Iterable[int] | IntListKey) – List of MD frame indices, for example
10 50 200 1000 10000 100000. Only indices smaller thanMolecularDynamics%NStepsare considered. Note: the final frame of the MD simulation is always considered to be the end of a step and does not need to be specified here.Type (Literal["Geometric", "List", "Linear"]) – How to determine the number of MD steps per active learning step.
Geometric (SimpleActiveLearning._ActiveLearning._Steps._Geometric) – Options for geometric.
Linear (SimpleActiveLearning._ActiveLearning._Steps._Linear) – Options for linear.
- class _SuccessCriteria[source]¶
Criteria for determining whether an active learning step was successful. These criteria compare one or more reference calculations to the predictions. If any of the criteria are exceeded, the active learning loop will reparametrize the model and repeat the step.
- Variables:
Energy (SimpleActiveLearning._ActiveLearning._SuccessCriteria._Energy) – Conditions to decide whether the calculated energy is are accurate enough with respect to reference energies.
Forces (SimpleActiveLearning._ActiveLearning._SuccessCriteria._Forces) – Conditions to decide whether calculated forces are accurate enough with respect to reference forces.
- class _Energy[source]¶
Conditions to decide whether the calculated energy is are accurate enough with respect to reference energies.
- Variables:
Enabled (BoolType | BoolKey) – Enable energy checking during the active learning.
Normalization (float | FloatKey) – Normalize (divide) energies by this number before comparing to the specified thresholds. If not specified, it will become the number of atoms.
Relative (float | FloatKey) –
|ΔΔE|/Normalization: Maximum allowed difference between the calculated relative reference energies and relative predicted energies. The relative energies are calculated for the current structure with respect to the structure in the previous reference calculation. ΔE_ref = E_ref(current) - E_ref(previous). ΔE_pred = E_pred(current) - E_pred(previous).|ΔΔE| = |ΔE_pred - ΔE_ref|Total (float | FloatKey) –
|ΔE|/Normalization: Maximum allowed total energy difference between the reference and predicted energy. This criterion is mostly useful when restarting a workflow from a previously trained model but on a new stoichiometry / system, for which the total energy prediction may be very far from the target. The default value is quite large so it is normally not exceeded.|∆E| = |E_pred - E_ref|
- class _Forces[source]¶
Conditions to decide whether calculated forces are accurate enough with respect to reference forces.
- Variables:
Enabled (BoolType | BoolKey) – Enable checking the forces during the active learning.
MaxDeviationForZeroForce (float | FloatKey) – The maximum allowed deviation between a calculated force component and the corresponding reference force component. For larger reference forces, the allowed deviation will also be larger (see the documentation). If any deviation is larger than the (magnitude-dependent) threshold, the active learning step will be repeated after a reparametrization.
MaxMAE (float | FloatKey) – Maximum allowed mean absolute error when comparing reference and predicted forces for a single frame at the end of an active learning step. If the obtained MAE is larger than this threshold, the active learning step will be repeated after a reparametrization.
MinR2 (float | FloatKey) – Minimum allowed value for R^2 when comparing reference and predicted forces for a single frame at the end of an active learning step. If the obtained R^2 is smaller than this threshold, the active learning step will be repeated after a reparametrization. Note that if you have very small forces (for example by running the active learning at a very low temperature or starting from a geometry-optimized structure), then you should decrease the MinR2 since it is difficult for the ML model predict very small forces accurately.
- class _Constraints[source]¶
The Constraints block allows geometry optimizations and potential energy surface scans with constraints. The constraints do not have to be satisfied at the start of the calculation.
- Variables:
Fix multiple distances using one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3
The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 as well as the angle between them.
The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then any bond between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. If the distance is omitted then the bond length from the initial geometry is used.
Important: only the bonds present in the system at the start of the simulation can be constrained, which means that the bonds may need to be specified in the System block.
Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H
Angle (str | StringKey) – Fix the angle between three atoms. Three atom indices followed by an angle in degrees.
Atom (int | IntKey) – Fix the position of an atom. Just one integer referring to the index of the atom in the [System%Atoms] block.
AtomList (Iterable[int] | IntListKey) – Fix positions of the specified atoms. A list of integers referring to indices of atoms in the [System%Atoms] block.
Block (str | StringKey) – Name of the region to constrain as a rigid block. Regions are specified in the System%Atoms block.
BlockAtoms (Iterable[int] | IntListKey) – List of atom indices for a block constraint, where the internal degrees of freedom are frozen.
Coordinate (str | StringKey) – Fix a particular coordinate of an atom. Atom index followed by (x|y|z).
DifDist (str | StringKey) – Four atom indices i j k l followed by the distance in Angstrom. This will constrain the difference R(ij)-R(kl) at the given value.
Dihedral (str | StringKey) – Fix the dihedral angle between four atoms. Four atom indices followed by an angle in degrees.
Distance (str | StringKey) – Fix the distance between two atoms. Two atom indices followed by the distance in Angstrom.
EqualStrain (str | StringKey) –
Exclusively for lattice optimizations:
Accepts a set of strain components [xx, xy, xz, yy, yz, zz] which are to be kept equal.
The applied strain will be determined by the average of the corresponding stress tensors components.
In AMSinput just check the corresponding check buttons.
FixedRegion (str | StringKey) – Fix positions of all atoms in a region.
FreezeStrain (str | StringKey) –
Exclusively for lattice optimizations:
Freezes any lattice deformation corresponding to a particular component of the strain tensor.
Accepts a set of strain components [xx, xy, xz, yy, yz, zz] to be frozen.
In AMSinput just check the corresponding check buttons.
SumDist (str | StringKey) – Four atom indices i j k l followed by the distance in Angstrom. This will constrain the sum R(ij)+R(kl) at the given value.
- class _LoadSystem[source]¶
Block that controls reading the chemical system from a KF file instead of the [System] block.
- class _MachineLearning[source]¶
Options for Task MachineLearning.
- Variables:
Backend (Literal["Custom", "M3GNet", "NequIP", "Test"]) – The backend to use. You must separately install the backend before running a training job.
CommitteeSize (int | IntKey) – The number of independently trained ML potentials.
LoadModel (str | Path | StringKey) – Load a previously fitted model from a ParAMS results directory. A ParAMS results directory should contain two subdirectories
optimizationandsettings_and_initial_data. This option ignores all settings inside model blocks.MaxEpochs (int | IntKey) – Set the maximum number of epochs a backend should perform.
RunAMSAtEnd (BoolType | BoolKey) – Whether to run the (committee) ML potential through AMS at the end. This will create the energy/forces scatter plots for the final trained model.
Custom (SimpleActiveLearning._MachineLearning._Custom) – Set up a custom fitting program within ParAMS
LossCoeffs (SimpleActiveLearning._MachineLearning._LossCoeffs) – Modify the coefficients for the machine learning loss function. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
M3GNet (SimpleActiveLearning._MachineLearning._M3GNet) – Options for M3GNet fitting.
NequIP (SimpleActiveLearning._MachineLearning._NequIP) – Options for NequIP fitting.
Target (SimpleActiveLearning._MachineLearning._Target) – Target values for stopping training. If both the training and validation metrics are smaller than the specified values, the training will stop early. Only supported by the M3GNet backend.
- class _LossCoeffs[source]¶
Modify the coefficients for the machine learning loss function. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
- Variables:
AverageForcePerAtom (BoolType | BoolKey) – For each force data entry, divide the loss contribution by the number of concomittent atoms. This is the same as the behavior for ParAMS Optimization, but it is turned off by default in Task MachineLearning. For machine learning, setting this to ‘No’ can be better since larger molecules will contribute more to the loss. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
Energy (float | FloatKey) – Coefficient for the contribution of loss due to the energy. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
Forces (float | FloatKey) – Coefficient for the contribution of loss due to the forces. For backends that support weights, this is on top of the supplied dataset weights and sigmas.
- class _M3GNet[source]¶
Options for M3GNet fitting.
- Variables:
LearningRate (float | FloatKey) – Learning rate for the M3GNet weight optimization.
Model (Literal["UniversalPotential", "Custom", "ModelDir"]) – How to specify the model for the M3GNet backend. Either a Custom model can be made from scratch or an existing model directory can be loaded to obtain the model settings.
ModelDir (str | Path | StringKey) – Path to the directory defining the model. This folder should contain the files: ‘checkpoint’, ‘m3gnet.data-00000-of-00001’, ‘ m3gnet.index’ and ‘m3gnet.json’
Custom (SimpleActiveLearning._MachineLearning._M3GNet._Custom) – Specify a custom M3GNet model.
UniversalPotential (SimpleActiveLearning._MachineLearning._M3GNet._UniversalPotential) – Settings for (transfer) learning with the M3GNet Universal Potential.
- class _Custom[source]¶
Specify a custom M3GNet model.
- Variables:
MaxL (int | IntKey) – Include spherical components up to order MaxL. Higher gives a better angular resolution, but increases computational cost substantially.
MaxN (int | IntKey) – Include radial components up to the MaxN’th root of the spherical Bessel function. Higher gives a better radial resolution, but increases computational cost substantially.
NumNeurons (int | IntKey) – Number of neurons in each layer.
ThreebodyCutoff (float | FloatKey) – Cutoff radius of the three-body interaction.
- class _UniversalPotential[source]¶
Settings for (transfer) learning with the M3GNet Universal Potential.
- Variables:
Featurizer (BoolType | BoolKey) – Train the Featurizer layer of the M3GNet universal potential.
Final (BoolType | BoolKey) – Train the Final layer of the M3GNet universal potential.
GraphLayer1 (BoolType | BoolKey) – Train the first Graph layer of the M3GNet universal potential.
GraphLayer2 (BoolType | BoolKey) – Train the second Graph layer of the M3GNet universal potential.
GraphLayer3 (BoolType | BoolKey) – Train the third Graph layer of the M3GNet universal potential.
ThreeDInteractions1 (BoolType | BoolKey) – Train the first ThreeDInteractions (three-body terms) layer of the M3GNet universal potential.
ThreeDInteractions2 (BoolType | BoolKey) – Train the second ThreeDInteractions (three-body terms) layer of the M3GNet universal potential.
ThreeDInteractions3 (BoolType | BoolKey) – Train the third ThreeDInteractions (three-body terms) layer of the M3GNet universal potential.
Version (Literal["2022"]) – Which version of the M3GNet Universal Potential to use.
- class _NequIP[source]¶
Options for NequIP fitting.
- Variables:
LearningRate (float | FloatKey) – Learning rate for the NequIP weight optimization
Model (Literal["Custom", "ModelFile"]) – How to specify the model for the NequIP backend. Either a Custom model can be made from scratch or an existing ‘model.pth’ file can be loaded to obtain the model settings.
ModelFile (str | Path | StringKey) – Path to the model.pth file defining the model.
UseRescalingFromLoadedModel (BoolType | BoolKey) – When loading a model with LoadModel or NequiP%ModelFile do not recalculate the dataset rescaling but use the value from the loaded model.
Custom (SimpleActiveLearning._MachineLearning._NequIP._Custom) – Specify a custom NequIP model.
- class _Custom[source]¶
Specify a custom NequIP model.
- class _Target[source]¶
Target values for stopping training. If both the training and validation metrics are smaller than the specified values, the training will stop early. Only supported by the M3GNet backend.
- Variables:
Forces (SimpleActiveLearning._MachineLearning._Target._Forces) – Forces (as reported by the backend)
- class _MolecularDynamics[source]¶
Settings for Molecular Dynamics
- Variables:
CalcPressure (BoolType | BoolKey) –
Calculate the pressure in periodic systems.
This may be computationally expensive for some engines that require numerical differentiation.
Some other engines can calculate the pressure for negligible additional cost and will always do so, even if this option is disabled.
CopyRestartTrajectory (BoolType | BoolKey) – If the keyword Restart is present, the content of the restartfile is copied to the ams.rkf file.
NSteps (int | IntKey) – The number of steps to be taken in the MD simulation.
Restart (str | Path | StringKey) – The path to the ams.rkf file from which to restart the simulation.
AddMolecules (SimpleActiveLearning._MolecularDynamics._AddMolecules) –
This block controls adding molecules to the system (a.k.a. the Molecule Gun). Multiple occurrences of this block are possible.
By default, molecules are added at random positions in the simulation box with velocity matching the current system temperature. The initial position can be modified using one of the following keywords: Coords, CoordsBox, FractionalCoords, FractionalCoordsBox. The Coords and FractionalCoords keys can optionally be accompanied by CoordsSigma or FractionalCoordsSigma, respectively.
ApplyForce (SimpleActiveLearning._MolecularDynamics._ApplyForce) – The ApplyForce keyword can be used to apply an arbitrary constant force to a certain (subgroups of) atoms in the system
ApplyVelocity (SimpleActiveLearning._MolecularDynamics._ApplyVelocity) – The ApplyVelocity keyword can be used to move an arbitrary group of atoms in the system with a constant net velocity
Barostat (SimpleActiveLearning._MolecularDynamics._Barostat) – This block allows to specify the use of a barostat during the simulation.
BinLog (SimpleActiveLearning._MolecularDynamics._BinLog) – This block controls writing the BinLog section in ams.rkf, which contains the selected MD state scalars and tensors from every MD step. No per-atom data is written. If you need the per-atom data then you can set the sampling frequency to 1 and get the required data from the MDHistory section. The tensors are written per component, that is, the pressure tensor is written as six variables: PressureTensor_xx, PressureTensor_yy, etc.. To reduce the file size, all data is written in blocks.
BondBoost (SimpleActiveLearning._MolecularDynamics._BondBoost) – Forced reaction (bond boost) definitions. Multiple BondBoost blocks may be specified, which will be treated independently.
CRESTMTD (SimpleActiveLearning._MolecularDynamics._CRESTMTD) – Input for CREST metadynamics simulation.
CVHD (SimpleActiveLearning._MolecularDynamics._CVHD) – Input for the Collective Variable-driven HyperDynamics (CVHD).
CheckTemperature (SimpleActiveLearning._MolecularDynamics._CheckTemperature) – Check at every time step if the temperature has exceeded a threshold. If it has, it is assumed the system exploded, and the simulation will stop.
Checkpoint (SimpleActiveLearning._MolecularDynamics._Checkpoint) – Sets the frequency for storing the entire MD state necessary for restarting the calculation.
CosineShear (SimpleActiveLearning._MolecularDynamics._CosineShear) – Apply an external acceleration to all atoms of a fluid using a periodic (cosine) function along a selected coordinate axis. This induces a periodic shear flow profile which can be used to determine the viscosity.
Deformation (SimpleActiveLearning._MolecularDynamics._Deformation) – Deform the periodic lattice of the system during the simulation.
Gravity (SimpleActiveLearning._MolecularDynamics._Gravity) – Apply a constant acceleration in -z.
HeatExchange (SimpleActiveLearning._MolecularDynamics._HeatExchange) – Input for the heat-exchange non-equilibrium MD (T-NEMD).
InitialVelocities (SimpleActiveLearning._MolecularDynamics._InitialVelocities) – Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
MovingRestraints (SimpleActiveLearning._MolecularDynamics._MovingRestraints) – Define a set of moving restraints.
PRD (SimpleActiveLearning._MolecularDynamics._PRD) – This block is used for Parallel Replica Dynamics simulations.
Plumed (SimpleActiveLearning._MolecularDynamics._Plumed) – Input for PLUMED (version 2.5.0). The parallel option is still experimental.
Preserve (SimpleActiveLearning._MolecularDynamics._Preserve) – Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.
Print (SimpleActiveLearning._MolecularDynamics._Print) – This block controls the printing of additional information to stdout.
ReactionBoost (SimpleActiveLearning._MolecularDynamics._ReactionBoost) –
Define a series of transitions between different states of the system.
Each transition is defined by a TargetSystem and by a set of restraints that force the transition.
Reactor (SimpleActiveLearning._MolecularDynamics._Reactor) – Define one phase of the nanoreactor. A reactor is a region of space surrounded by an elastic wall. Atoms inside the region are not affected. Atoms outside it will be pushed back with force depending on the [ForceConstant] and the [MassScaled] flag.
ReflectiveWall (SimpleActiveLearning._MolecularDynamics._ReflectiveWall) – Apply a reflective wall in space
Remap (SimpleActiveLearning._MolecularDynamics._Remap) – Control periodic remapping (backtranslation) of atoms into the PBC box.
RemoveMolecules (SimpleActiveLearning._MolecularDynamics._RemoveMolecules) – This block controls removal of molecules from the system. Multiple occurrences of this block are possible.
ReplicaExchange (SimpleActiveLearning._MolecularDynamics._ReplicaExchange) – This block is used for (temperature) Replica Exchange MD (Parallel Tempering) simulations.
Shake (SimpleActiveLearning._MolecularDynamics._Shake) – Parameters of the Shake/Rattle algorithm.
Thermostat (SimpleActiveLearning._MolecularDynamics._Thermostat) – This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’s behavior.
Trajectory (SimpleActiveLearning._MolecularDynamics._Trajectory) – Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
fbMC (SimpleActiveLearning._MolecularDynamics._fbMC) – This block sets up force bias Monte Carlo interleaved with the molecular dynamics simulation.
- class _AddMolecules[source]¶
This block controls adding molecules to the system (a.k.a. the Molecule Gun). Multiple occurrences of this block are possible.
By default, molecules are added at random positions in the simulation box with velocity matching the current system temperature. The initial position can be modified using one of the following keywords: Coords, CoordsBox, FractionalCoords, FractionalCoordsBox. The Coords and FractionalCoords keys can optionally be accompanied by CoordsSigma or FractionalCoordsSigma, respectively.
- Variables:
AtomTemperature (float | FloatKey) – Add random velocity corresponding to the specified temperature to individual atoms of the molecule. This only affects rotational and internal degrees of freedom, not the net translational velocity of the inserted molecule as set by the other options.
ContactDistance (float | FloatKey) – Translate the bullet along the velocity vector until it comes within ContactDistance of any other atom.
Coords (Iterable[float] | FloatListKey) –
Place molecules at or around the specified Cartesian coordinates.
This setting takes precedence over other ways to specify initial coordinates of the molecule: [CoordsBox], [FractionalCoords], and [FractionalCoordsBox].
CoordsBox (Iterable[float] | FloatListKey) –
Place molecules at random locations inside the specified box in Cartesian coordinates.
Coordinates of the box corners are specified as: Xmin, Xmax, Ymin, Ymax, Zmin, Zmax. This setting is ignored if Coords is used.
In AMSinput, if this field is not empty it will be used instead of the default Coords.
CoordsSigma (Iterable[float] | FloatListKey) – Sigma values (one per Cartesian axis) for a Gauss distribution of the initial coordinates. Can only be used together with Coords.
DeviationAngle (float | FloatKey) – Randomly tilt the shooting direction up to this angle away from the VelocityDirection vector.
Energy (float | FloatKey) – Initial kinetic energy of the molecule in the shooting direction.
EnergySigma (float | FloatKey) – Sigma value for the Gauss distribution of the initial kinetic energy around the specified value. Should only be used together with Energy.
FractionalCoords (Iterable[float] | FloatListKey) – Place molecules at or around the specified fractional coordinates in the main system’s lattice. For non-periodic dimensions a Cartesian value in Angstrom is expected. This setting is ignored if [Coords] or [CoordsBox] is used.
FractionalCoordsBox (Iterable[float] | FloatListKey) –
Place molecules at random locations inside the box specified as fractional coordinates in the main system’s lattice.
Coordinates of the box corners are specified as: Xmin, Xmax, Ymin, Ymax, Zmin, Zmax.
For non-periodic dimensions the Cartesian value in Angstrom is expected.
This setting is ignored if [Coords], [CoordsBox], or [FractionalCoords] is used.
FractionalCoordsSigma (Iterable[float] | FloatListKey) – Sigma values (one per axis) for a Gauss distribution of the initial coordinates. For non-periodic dimensions the Cartesian value in Angstrom is expected. Can only be used together with FractionalCoords.
A molecule is added every [Frequency] steps after the StartStep.
There is never a molecule added at step 0.
MinDistance (float | FloatKey) – Keep the minimal distance to other atoms of the system when adding the molecule.
MoleFraction (float | FloatKey) –
Defines a mixture to be deposited using one AddMolecules block per component.
AMS will randomly alternate between any guns that have MoleFraction set. These need to all have the same settings for StartStep, StopStep and Frequency. Any additional AddMolecules blocks without MoleFraction will remain completely independent.
NumAttempts (int | IntKey) – Try adding the molecule up to the specified number of times or until the MinDistance constraint is satisfied. If all attempts fail a message will be printed and the simulation will continue normally.
Rotate (BoolType | BoolKey) – Rotate the molecule randomly before adding it to the system.
Step number when the first molecule should be added. After that, molecules are added every Frequency steps.
For example, ff StartStep=99 and Frequency=100 then a molecule will be added at steps 99, 199, 299, etc…
No molecule will be added at step 0, so if StartStep=0 the first molecule is added at the step number equal to [Frequency].
StopStep (int | IntKey) – Do not add this molecule after the specified step.
String ID of the [System] that will be added with this ‘gun’.
The lattice specified with this System is ignored and the main system’s lattice is used instead.
AMSinput adds the system at the coordinates of the System (thus setting Coords to the center of the System).
Temperature (float | FloatKey) – Initial energy of the molecule in the shooting direction will correspond to the given temperature.
TemperatureSigma (float | FloatKey) – Sigma value for the Gauss distribution of the initial temperature the specified value. Should only be used together with Temperature.
Velocity (float | FloatKey) – Initial velocity of the molecule in the shooting direction.
VelocityDirection (Iterable[float] | FloatListKey) –
Velocity direction vector for aimed shooting. It will be random if not specified.
In AMSinput add one or two atoms (which may be dummies).
One atom: use vector from center of the system to add to that atom.
Two atoms: use vector from the first to the second atom.
VelocitySigma (float | FloatKey) – Sigma value for the Gauss distribution of the initial velocity around the specified value. Should only be used together with Velocity.
- class _ApplyForce[source]¶
The ApplyForce keyword can be used to apply an arbitrary constant force to a certain (subgroups of) atoms in the system
- Variables:
CalculateViscosity (BoolType | BoolKey) – Calculates Viscosity property yes/no. If yes is chosen, the global viscosity of the system is calculated and written into the RKF-file. The formula used for the viscosity calculation is eta = - Pxz / (dVx/dz)
CalculateViscosityBins (int | IntKey) – Amount of bins used to determine (dVx/dz)
CalculateViscosityEnd (int | IntKey) – end index to select region in space to calculate (dVx/dz)
CalculateViscosityStart (int | IntKey) – Start index to select region in space to calculate (dVx/dz)
Force (Iterable[float] | FloatListKey) – Defines the constant force vector
PerAtom (BoolType | BoolKey) – If enabled, the Force vector is applied separately to every atom in the selected Region, so that the total net force on the Region equals the value of Force times the number of atoms in Region. This was the behavior of ApplyForce in AMS2022. By default, with PerAtom disabled, the Force vector defines the total net force on the Region, so the force applied to each atom equals the value of Force divided by the number of atoms in Region.
Region (str | StringKey) – Apply the constant force to all atoms in this region.
- class _ApplyVelocity[source]¶
The ApplyVelocity keyword can be used to move an arbitrary group of atoms in the system with a constant net velocity
- Variables:
CalculateViscosity (BoolType | BoolKey) – Calculates Viscosity property yes/no. If yes is chosen, the global viscosity of the system is calculated and written into the RKF-file. The formula used for the viscosity calculation is eta = - Pxz / (dVx/dz)
CalculateViscosityBins (int | IntKey) – Amount of bins used to determine (dVx/dz)
CalculateViscosityEnd (int | IntKey) – end index to select region in space to calculate (dVx/dz)
CalculateViscosityStart (int | IntKey) – Start index to select region in space to calculate (dVx/dz)
Components (Literal["X", "Y", "Z", "XY", "YZ", "XZ", "XYZ"]) – Select which components of the Velocity vector are used to set the corresponding components of the net velocity of the specified set of atoms. Any other components of Velocity are ignored and the motion of the selected atoms in those directions is unaffected by ApplyVelocity.
Region (str | StringKey) – Applies the defined velocity to all atoms in this region.
Velocity (Iterable[float] | FloatListKey) – The constant velocity that will be applied to the specified atoms.
- class _Barostat[source]¶
This block allows to specify the use of a barostat during the simulation.
- Variables:
BulkModulus (float | FloatKey) –
An estimate of the bulk modulus (inverse compressibility) of the system for the Berendsen barostat.
This is only used to make Tau correspond to the true observed relaxation time constant. Values are commonly on the order of 10-100 GPa (1e10 to 1e11) for solids and 1 GPa (1e9) for liquids (2.2e9 for water). Use 1e9 to match the behavior of standalone ReaxFF.
ConstantVolume (BoolType | BoolKey) –
Keep the volume constant while allowing the box shape to change.
This is currently supported only by the MTK barostat.
Duration (Iterable[int] | IntListKey) – Specifies how many steps should a transition from a particular pressure to the next one in sequence take.
Equal (Literal["None", "XYZ", "XY", "YZ", "XZ"]) – Enforce equal scaling of the selected set of dimensions. They will be barostatted as one dimension according to the average pressure over the components.
Pressure (Iterable[float] | FloatListKey) –
Specifies the target pressure.
You can specify multiple pressures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one p to the next p (using a linear ramp).
Scale (Literal["XYZ", "Shape", "X", "Y", "Z", "XY", "YZ", "XZ"]) – Dimensions that should be scaled by the barostat to maintain pressure. Selecting Shape means that all three dimensions and also all the cell angles are allowed to change.
Tau (float | FloatKey) – Specifies the time constant of the barostat.
Type (Literal["None", "Berendsen", "MTK"]) – Selects the type of the barostat.
- class _BinLog[source]¶
This block controls writing the BinLog section in ams.rkf, which contains the selected MD state scalars and tensors from every MD step. No per-atom data is written. If you need the per-atom data then you can set the sampling frequency to 1 and get the required data from the MDHistory section. The tensors are written per component, that is, the pressure tensor is written as six variables: PressureTensor_xx, PressureTensor_yy, etc.. To reduce the file size, all data is written in blocks.
- Variables:
BiasEnergy (BoolType | BoolKey) – Write the CVHD bias energy at every time step.
BoostFactor (BoolType | BoolKey) – Write the CVHD boost factor at every time step.
ConservedEnergy (BoolType | BoolKey) – Write the conserved energy value at every time step.
Density (BoolType | BoolKey) – Write the density at every time step.
DipoleMoment (BoolType | BoolKey) – Write the dipole moment at every time step. Each component of the tensor is written in its own variable.
Hypertime (BoolType | BoolKey) – Write the CVHD hypertime at every time step.
KineticEnergy (BoolType | BoolKey) – Write the kinetic energy value at every time step.
MaxBiasEnergy (BoolType | BoolKey) – Write the max CVHD bias energy at every time step.
MaxBoostFactor (BoolType | BoolKey) – Write the max CVHD boost factor at every time step.
PotentialEnergy (BoolType | BoolKey) – Write the potential energy value at every time step.
Pressure (BoolType | BoolKey) – Write the pressure at every time step.
PressureTensor (BoolType | BoolKey) – Write the pressure tensor in Voigt notation at every time step. Each component of the tensor is written in its own variable.
Step (BoolType | BoolKey) – Write the step index during the simulation at every time step.
Temperature (BoolType | BoolKey) – Write the temperature at every time step.
Time (BoolType | BoolKey) – Write the simulation time (fs) at every time step.
TotalEnergy (BoolType | BoolKey) – Write the total energy value at every time step.
Volume (BoolType | BoolKey) – Write the simulation cell volume, area or length, depending on the system periodicity, at every time step.
- class _BondBoost[source]¶
Forced reaction (bond boost) definitions. Multiple BondBoost blocks may be specified, which will be treated independently.
- Variables:
AddBond (str | StringKey) – [Reserved] Add a bond to the system or change its order. Specify two atom indices followed by the bond’s order. The indices indicate positions of the atoms in the AtomNames key. Currently no engine will honor bond changes caused by this key.
DistanceRestraint (str | StringKey) –
Specify two atom indices followed by the target distance in Angstrom, the first parameter and, optionally, the profile type and the second parameter.
For periodic systems, restraints follow the minimum image convention.
Each atom index indicates a position of the corresponding atom in the AtomNames key. Currently recognized restraint profile types: Harmonic (default), Hyperbolic, Erf, GaussianWell. The profile name can optionally be prefixed by “OneSided-”, thus making this particular restraint one-sided. A one-sided restraint will only push or pull the distance towards its target value depending on the sign of the difference between the initial and the target distance. For example, if the initial distance is larger than the target one then the restraint will only push the value down. This is especially useful with moving restraints because then the restraint will effectively disappear as soon as the system crosses a barrier along the reaction path. By default, the restraints are two-sided, which means they will try to keep the distance between the two specified atoms near the (possibly moving) target value. For moving restraints, this means that after crossing a reaction barrier the system will slide slowly towards products held back by the restraints.
The first parameter is the force constant for the Harmonic, Hyperbolic, and Erf profiles, or well depth for GaussianWell. The second parameter is the asymptotic force value F(Inf) for Hyperbolic and Erf profiles, or the factor before x^2 in the exponent for GaussianWell.
Note: the GaussianWell restraint should be used with the Moving flag.
Moving (BoolType | BoolKey) –
Move the restraints created with this BondBoost. The restraint value will start at the current coordinate’s value and will move towards the optimum during the restraint’s lifetime. The increment is calculated from the initial deviation and the [NSteps] parameter.
This feature should be used with the GaussianWell restraint types.
NSteps (int | IntKey) – Number of steps the restraints will remain active until removed. Atoms participating in one reaction are not available for the given number of steps.
NumInstances (int | IntKey) – Number of reactions of this type taking place simultaneously.
RemoveBond (str | StringKey) – [Reserved] Remove a bond from the system. Specify two atom indices. The indices indicate positions of the atoms in the AtomNames key. Currently no engine will honor bond changes caused by this key.
SetAtomName (str | StringKey) – Change the specified atom’s name. Specify atom index followed by the new name. The index indicates position of the atom in the AtomNames key. Note: this action will change the atom name only and not other properties (element name, mass, etc.). This may be useful to change atom names to affect future chain detections. The atom name length is limited to 32 characters.
Units (Literal["Default", "MD"]) – Change energy, force and force constant units in the DistanceRestraint key from the default (atomic units) to those often used in the MD community (based on kcal/mol and Angstrom). Units for the optimum distances are not affected.
Chain (SimpleActiveLearning._MolecularDynamics._BondBoost._Chain) – Specifications of a chain of atoms. When a chain is detected the distance restraints will be activated. No other chain of this type will be detected while any restraints for this chain is active.
- class _Chain[source]¶
Specifications of a chain of atoms. When a chain is detected the distance restraints will be activated. No other chain of this type will be detected while any restraints for this chain is active.
- Variables:
AtomNames (str | StringKey) – Atom names specifying the chain. An atom name can optionally be followed by ‘@’ and a region name, in this case only atoms of this type from the given region will be matched. A leading ‘@’ followed by a number indicates that this position in the chain must be occupied by the atom found earlier at the specified position in the chain. For example “O H N C @1” indicates that the last atom in the chain of the five atoms must be the first oxygen, thus defining a 4-membered ring. This is the only way to define a ring because implicit rings will not be detected. For example, “O H N C O” does not include rings.
MaxDistances (Iterable[float] | FloatListKey) – Maximum distances for each pair of atoms in the chain. The number of distances must be one less than the number of AtomNames.
MinDistances (Iterable[float] | FloatListKey) – Minimum distances for each pair of atoms in the chain. The number of distances must be one less than the number of AtomNames.
- class _CRESTMTD[source]¶
Input for CREST metadynamics simulation.
- Variables:
AddEnergy (BoolType | BoolKey) – Add the bias energy to the potential energy (to match the gradients)
Height (float | FloatKey) – The height of the Gaussians added
NGaussiansMax (int | IntKey) – Maximum number of Gaussians stored
Region (str | StringKey) – Restrict the range of atoms for RMSD calculation to the specified region.
RestartFile (str | Path | StringKey) – Filename for file from which to read data on Gaussians placed previously.
Width (float | FloatKey) – The width of the Gaussians added in terms of the RMSD
GaussianScaling (SimpleActiveLearning._MolecularDynamics._CRESTMTD._GaussianScaling) – Options for gradual introduction of the Gaussians
- class _CVHD[source]¶
Input for the Collective Variable-driven HyperDynamics (CVHD).
- Variables:
Frequency (int | IntKey) – Frequency of adding a new bias peak, in steps. New bias is deposited every [Frequency] steps after [StartStep] if the following conditions are satisfied: the current CV value is less than 0.9 (to avoid creating barriers at the transition state), the step number is greater than or equal to [StartStep], and the step number is less than or equal to [StopStep].
MaxEvents (int | IntKey) – Max number of events to allow during dynamics. When this number is reached no new bias will be added for this input block.
StartStep (int | IntKey) – If this key is specified, the first bias will be deposited at this step. Otherwise, the first bias peak is added at the step number equal to the Frequency parameter. The bias is never deposited at step 0.
StopStep (int | IntKey) – No bias will be deposited after the specified step. The already deposited bias will continue to be applied until the reaction event occurs. After that no new CVHD will be started. By default, the CVHD runs for the whole duration of the MD calculation.
WaitSteps (int | IntKey) – If the CV value becomes equal to 1 and remains at this value for this many steps then the reaction event is considered having taken place. After this, the collective variable will be reset and the bias will be removed.
Bias (SimpleActiveLearning._MolecularDynamics._CVHD._Bias) – The bias is built from a series of Gaussian peaks deposited on the collective variable axis every [Frequency] steps during MD. Each peak is characterized by its (possibly damped) height and the RMS width (standard deviation).
ColVarBB (SimpleActiveLearning._MolecularDynamics._CVHD._ColVarBB) – Description of a bond-breaking collective variable (CV) as described in [Bal & Neyts, JCTC, 11 (2015)]. A collective variable may consist of multiple ColVar blocks.
ColVarBM (SimpleActiveLearning._MolecularDynamics._CVHD._ColVarBM) – Description of a bond-making collective variable (CV). A collective variable may consist of multiple ColVar blocks.
- class _Bias[source]¶
The bias is built from a series of Gaussian peaks deposited on the collective variable axis every [Frequency] steps during MD. Each peak is characterized by its (possibly damped) height and the RMS width (standard deviation).
- Variables:
DampingTemp (float | FloatKey) – During well-tempered hyperdynamics the height of the added bias is scaled down with an exp(-E/kT) factor [PhysRevLett 100, 020603 (2008)], where E is the current value of the bias at the given CV value and T is the damping temperature DampingTemp. If DampingTemp is zero then no damping is applied.
Delta (float | FloatKey) – Standard deviation parameter of the Gaussian bias peak.
Height (float | FloatKey) – Height of the Gaussian bias peak.
- class _ColVarBB[source]¶
Description of a bond-breaking collective variable (CV) as described in [Bal & Neyts, JCTC, 11 (2015)]. A collective variable may consist of multiple ColVar blocks.
- Variables:
cutoff (float | FloatKey) – Bond order cutoff. Bonds with BO below this value are ignored when creating the initial bond list for the CV. The bond list does not change during lifetime of the variable even if some bond orders drop below the cutoff.
p (int | IntKey) – Exponent value p used to calculate the p-norm for this CV.
rmax (float | FloatKey) – Max bond distance parameter Rmax used for calculating the CV. It should be close to the transition-state distance for the corresponding bond.
rmin (float | FloatKey) – Min bond distance parameter Rmin used for calculating the CV. It should be close to equilibrium distance for the corresponding bond.
at1 (SimpleActiveLearning._MolecularDynamics._CVHD._ColVarBB._at1) – Specifies the first bonded atom in the collective variable.
at2 (SimpleActiveLearning._MolecularDynamics._CVHD._ColVarBB._at2) – Specifies the second bonded atom in the collective variable.
- class _at1[source]¶
Specifies the first bonded atom in the collective variable.
- Variables:
region (str | StringKey) – Restrict the selection of bonded atoms to a specific region. If this is not set, atoms anywhere in the system will be selected.
symbol (str | StringKey) – Atom type name of the first atom of the bond. The name must be as it appears in the System block. That is, if the atom name contains an extension (e.g C.1) then the full name including the extension must be used here.
- class _at2[source]¶
Specifies the second bonded atom in the collective variable.
- Variables:
region (str | StringKey) – Restrict the selection of bonded atoms to a specific region. If this is not set, atoms anywhere in the system will be selected.
symbol (str | StringKey) – Atom type name of the second atom of the bond. The value is allowed to be the same as [at1], in which case bonds between atoms of the same type will be included.
- class _ColVarBM[source]¶
Description of a bond-making collective variable (CV). A collective variable may consist of multiple ColVar blocks.
- Variables:
cutoff (float | FloatKey) – Bond order cutoff. Bonds with BO above this value are ignored when creating the initial atom-pair list for the CV. The list does not change during lifetime of the variable even if some bond orders rise above the cutoff.
p (int | IntKey) – Exponent value p used to calculate the p-norm for this CV.
rmax (float | FloatKey) – Max bond distance parameter Rmax used for calculating the CV. It should be much larger than the corresponding Rmin.
rmin (float | FloatKey) – Min bond distance parameter Rmin used for calculating the CV. It should be close to the transition-state distance for the corresponding bond.
at1 (SimpleActiveLearning._MolecularDynamics._CVHD._ColVarBM._at1) – Specifies selection criteria for the first atom of a pair in the collective variable.
at2 (SimpleActiveLearning._MolecularDynamics._CVHD._ColVarBM._at2) – Specifies selection criteria for the second atom of a pair in the collective variable.
- class _at1[source]¶
Specifies selection criteria for the first atom of a pair in the collective variable.
- Variables:
region (str | StringKey) – Restrict the selection to a specific region. If this is not set, atoms anywhere in the system will be selected.
symbol (str | StringKey) – Atom type name of the first atom of the pair. The name must be as it appears in the System block. That is, if the atom name contains an extension (e.g C.1) then the full name including the extension must be used here.
- class _at2[source]¶
Specifies selection criteria for the second atom of a pair in the collective variable.
- Variables:
region (str | StringKey) – Restrict the selection to a specific region. If this is not set, atoms anywhere in the system will be selected.
symbol (str | StringKey) – Atom type name of the second atom of the pair. The value is allowed to be the same as [at1], in which case pairs of atoms of the same type will be included.
- class _CheckTemperature[source]¶
Check at every time step if the temperature has exceeded a threshold. If it has, it is assumed the system exploded, and the simulation will stop.
- class _Checkpoint[source]¶
Sets the frequency for storing the entire MD state necessary for restarting the calculation.
- Variables:
Frequency (int | IntKey) – Write the MD state to the Molecule and MDResults sections on ams.rkf once every N steps. Setting this to zero disables checkpointing during the simulation, but one checkpoint at the very end of the simulation will always be written.
WriteProperties (BoolType | BoolKey) –
Honor top-level Properties input block when writing engine results files.
DEPRECATED: This input option will be removed in AMS2026 and will be considered always enabled. If you rely on it being disabled, please contact support@scm.com.
- class _CosineShear[source]¶
Apply an external acceleration to all atoms of a fluid using a periodic (cosine) function along a selected coordinate axis. This induces a periodic shear flow profile which can be used to determine the viscosity.
- Variables:
Acceleration (float | FloatKey) – Amplitude of the applied cosine shear acceleration profile. The default value should be a rough first guess for water and it needs to be adjusted by experimentation for other systems.
Enabled (BoolType | BoolKey) – Apply a cosine shear acceleration profile for a NEMD calculation of viscosity.
FlowDirection (Iterable[float] | FloatListKey) – The direction in which to apply the shear acceleration, in Cartesian coordinates. The magnitude of this vector is ignored (AMS will normalize it internally). FlowDirection has to be perpendicular to ProfileAxis.
ProfileAxis (Literal["X", "Y", "Z"]) – The Cartesian coordinate axis along which the cosine wave runs
- class _Deformation[source]¶
Deform the periodic lattice of the system during the simulation.
- Variables:
LengthRate (Iterable[float] | FloatListKey) – Relative rate of change of each lattice vector per step.
LengthVelocity (Iterable[float] | FloatListKey) – Change the length of each lattice vector with this velocity. With Type=Exponential, LengthVelocity is divided by the current lattice vector lengths on StartStep to determine a LengthRate, which is then applied on all subsequent steps. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).
Period (float | FloatKey) – Period of oscillation for Type Sine and Cosine.
ScaleAtoms (BoolType | BoolKey) – Scale the atomic positions together with the lattice vectors. Disable this to deform only the lattice, keeping the coordinates of atoms unchanged.
StartStep (int | IntKey) – First step at which the deformation will be applied.
StopStep (int | IntKey) – Last step at which the deformation will be applied. If unset or zero, nSteps will be used instead.
TargetDensity (float | FloatKey) –
Target density of the system to be achieved by StopStep by isotropically rescaling the lattice.
This can only be used for 3D-periodic systems. Note that the selected Type determines how the lengths of the lattice vectors will evolve (linearly or as a sine/cosine), the evolution of the volume or density is thus necessarily non-linear.
TargetLength (Iterable[float] | FloatListKey) – Target lengths of each lattice vector to be achieved by StopStep. The number of values should equal the periodicity of the system. If a value is zero, the corresponding lattice vector will not be modified.
Type (Literal["Linear", "Exponential", "Sine", "Cosine"]) –
Function defining the time dependence of the deformed lattice parameters.
Linear increments the lattice parameters by the same absolute amount every timestep. Exponential multiplies the lattice parameters by the same factor every timestep. Only StrainRate, LengthRate, and LengthVelocity are supported for Type=Exponential. Sine deforms the system from the starting lattice to TargetLattice/TargetLength and then by the same amount to the opposite direction, while Cosine deforms the system from the starting lattice to the target and back.
LatticeVelocity (str | Sequence[str] | FreeBlock) – Velocity of individual lattice vector components in Angstrom/fs. The format is identical to the System%Lattice block. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).
StrainRate (str | Sequence[str] | FreeBlock) – Strain rate matrix to be applied on every step. The format is identical to the System%Lattice block.
TargetLattice (str | Sequence[str] | FreeBlock) – Target lattice vectors to be achieved by StopStep. The format is identical to the System%Lattice block.
- class _LatticeVelocity[source]¶
Velocity of individual lattice vector components in Angstrom/fs. The format is identical to the System%Lattice block. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).
- class _HeatExchange[source]¶
Input for the heat-exchange non-equilibrium MD (T-NEMD).
- Variables:
HeatingRate (float | FloatKey) – Rate at which the energy is added to the Source and removed from the Sink. A heating rate of 1 Hartree/fs equals to about 0.00436 Watt of power being transferred through the system.
Method (Literal["Simple", "HEX", "eHEX"]) –
Heat exchange method used.
Simple: kinetic energy of the atoms of the source and sink regions is modified irrespective of that of the center of mass (CoM) of the region (recommended for solids).
HEX: kinetic energy of the atoms of these regions is modified keeping that of the corresponding CoM constant.
eHEX: an enhanced version of HEX that conserves the total energy better (recommended for gases and liquids).
StartStep (int | IntKey) – Index of the MD step at which the heat exchange will start.
StopStep (int | IntKey) – Index of the MD step at which the heat exchange will stop.
Sink (SimpleActiveLearning._MolecularDynamics._HeatExchange._Sink) – Defines the heat sink region (where the heat will be removed).
Source (SimpleActiveLearning._MolecularDynamics._HeatExchange._Source) – Defines the heat source region (where the heat will be added).
- class _Sink[source]¶
Defines the heat sink region (where the heat will be removed).
- Variables:
AtomList (Iterable[int] | IntListKey) –
The atoms that are part of the sink.
This key is ignored if the [Box] block or [Region] key is present.
FirstAtom (int | IntKey) – Index of the first atom of the region. This key is ignored if the [Box] block or the [AtomList] key is present.
LastAtom (int | IntKey) – Index of the last atom of the region. This key is ignored if the [Box] block or the [AtomList] key is present.
The region that is the sink.
This key is ignored if the [Box] block is present.
Show (BoolType | BoolKey) – Show the sink in the AMSinput
Box (SimpleActiveLearning._MolecularDynamics._HeatExchange._Sink._Box) – Part of the simulation box (in fractional cell coordinates) defining the heat sink. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes.
- class _Box[source]¶
Part of the simulation box (in fractional cell coordinates) defining the heat sink. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes.
- Variables:
Amax (float | FloatKey) – Coordinate of the upper bound along the first axis.
Amin (float | FloatKey) – Coordinate of the lower bound along the first axis.
Bmax (float | FloatKey) – Coordinate of the upper bound along the second axis.
Bmin (float | FloatKey) – Coordinate of the lower bound along the second axis.
Cmax (float | FloatKey) – Coordinate of the upper bound along the third axis.
Cmin (float | FloatKey) – Coordinate of the lower bound along the third axis.
- class _Source[source]¶
Defines the heat source region (where the heat will be added).
- Variables:
AtomList (Iterable[int] | IntListKey) –
The atoms that are part of the source.
This key is ignored if the [Box] block or [Region] key is present.
FirstAtom (int | IntKey) – Index of the first atom of the region. This key is ignored if the [Box] block or the [AtomList] key is present.
LastAtom (int | IntKey) – Index of the last atom of the region. This key is ignored if the [Box] block or the [AtomList] key is present.
The region that is the source.
This key is ignored if the [Box] block is present.
Show (BoolType | BoolKey) – Show the source in the AMSinput
Box (SimpleActiveLearning._MolecularDynamics._HeatExchange._Source._Box) – Part of the simulation box (in fractional cell coordinates) defining the heat source. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes. This block is mutually exclusive with the FirstAtom/LastAtom setting.
- class _Box[source]¶
Part of the simulation box (in fractional cell coordinates) defining the heat source. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes. This block is mutually exclusive with the FirstAtom/LastAtom setting.
- Variables:
Amax (float | FloatKey) – Coordinate of the upper bound along the first axis.
Amin (float | FloatKey) – Coordinate of the lower bound along the first axis.
Bmax (float | FloatKey) – Coordinate of the upper bound along the second axis.
Bmin (float | FloatKey) – Coordinate of the lower bound along the second axis.
Cmax (float | FloatKey) – Coordinate of the upper bound along the third axis.
Cmin (float | FloatKey) – Coordinate of the lower bound along the third axis.
- class _InitialVelocities[source]¶
Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- Variables:
File (str | Path | StringKey) – AMS RKF file containing the initial velocities.
RandomVelocitiesMethod (Literal["Exact", "Boltzmann", "Gromacs"]) –
Specifies how are random velocities generated. Three methods are available.
Exact: Velocities are scaled to exactly match set random velocities temperature.
Boltzmann: Velocities are not scaled and sample Maxwell-Boltzmann distribution. However, the distribution is not corrected for constraints.
Gromacs: Velocities are scaled to match set random velocities temperature, but removal of net momentum is performed only after the scaling. Resulting kinetic energy is lower based on how much net momentum the system had.
Temperature (float | FloatKey) –
Sets the temperature for the Maxwell-Boltzmann distribution when the type of the initial velocities is set to random, in which case specifying this key is mandatory.
AMSinput will use the first temperature of the first thermostat as default.
Type (Literal["Zero", "Random", "FromFile", "Input"]) –
Specifies the initial velocities to assign to the atoms. Three methods to assign velocities are available.
Zero: All atom are at rest at the beginning of the calculation.
Random: Initial atom velocities follow a Maxwell-Boltzmann distribution for the temperature given by the [MolecularDynamics%InitialVelocities%Temperature] keyword.
FromFile: Load the velocities from a previous ams result file.
Input: Atom’s velocities are set to the values specified in the [MolecularDynamics%InitialVelocities%Values] block, which can be accessed via the Expert AMS panel in AMSinput.
Values (str | Sequence[str] | FreeBlock) – This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.
- class _Values[source]¶
This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.
- class _MovingRestraints[source]¶
Define a set of moving restraints.
- Variables:
Change (Literal["Linear", "Sine", "Cosine"]) –
Type of function defining how the target restraint value will change over time:
Linear - linearly between the StartValue and EndValue. Sine - oscillating around StartValue with an amplitude equal to the difference between EndValue and StartValue. Cosine - oscillating between StartValue and EndValue.
Name (str | StringKey) – Optional name to be used for plotting.
Period (float | FloatKey) – Period of oscillation for Sine and Cosine change types.
RestraintType (Literal["None", "Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) – Select type of the moving restraint profile. The force for Hyperbolic and Erf is bounded by a user-defined value, the latter converging to it faster than the former. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable.
StartStep (int | IntKey) – First step number at which the restraints will be applied.
StopStep (int | IntKey) – Last step number at which the restraints will be applied.
Distance (SimpleActiveLearning._MolecularDynamics._MovingRestraints._Distance) – Define a distance restraint between pair of atoms. For linear-type
Erf (SimpleActiveLearning._MolecularDynamics._MovingRestraints._Erf) – Define parameters for the Int(erf) restraint potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
GaussianWell (SimpleActiveLearning._MolecularDynamics._MovingRestraints._GaussianWell) – Define parameters in the Gaussian well restraint potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
Harmonic (SimpleActiveLearning._MolecularDynamics._MovingRestraints._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
Hyperbolic (SimpleActiveLearning._MolecularDynamics._MovingRestraints._Hyperbolic) – Define parameters for the hyperbolic restraint potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
- class _Distance[source]¶
Define a distance restraint between pair of atoms. For linear-type
- class _Erf[source]¶
Define parameters for the Int(erf) restraint potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
- class _GaussianWell[source]¶
Define parameters in the Gaussian well restraint potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
- class _PRD[source]¶
This block is used for Parallel Replica Dynamics simulations.
- Variables:
CorrelatedSteps (int | IntKey) – How many steps to wait for correlated events after detecting an initial event.
DephasingSteps (int | IntKey) – Spend this many steps dephasing the individual replicas after an event.
nReplicas (int | IntKey) – Number of replicas to run in parallel.
BondChange (SimpleActiveLearning._MolecularDynamics._PRD._BondChange) – Detect changes to the bonding topology and bond orders returned by the engine.
MolCount (SimpleActiveLearning._MolecularDynamics._PRD._MolCount) – Detect changes to the molecular composition of the system.
- class _BondChange[source]¶
Detect changes to the bonding topology and bond orders returned by the engine.
- Variables:
ChangeThreshold (float | FloatKey) – Trigger an event when the bond order of a bond changes from the reference state by more than this value.
DissociationThreshold (float | FloatKey) – Trigger an event when a bond dissociates (its bond order drops below this value while it was above FormationThreshold in the reference state).
FormationThreshold (float | FloatKey) – Trigger an event when a new bond forms (its bond order exceeds this value while it was below DissociationThreshold in the reference state).
- class _Plumed[source]¶
Input for PLUMED (version 2.5.0). The parallel option is still experimental.
- Variables:
Input (str | Sequence[str] | FreeBlock) – Input for PLUMED. Contents of this block is passed to PLUMED as is.
Parallel (SimpleActiveLearning._MolecularDynamics._Plumed._Parallel) – Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- class _Parallel[source]¶
Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _Preserve[source]¶
Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.
- Variables:
AngularMomentum (BoolType | BoolKey) – Remove overall angular momentum of the system. This option is ignored for 2D and 3D-periodic systems, and disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).
CenterOfMass (BoolType | BoolKey) – Translate the system to keep its center of mass at the coordinate origin. This option is not very useful for 3D-periodic systems.
Momentum (BoolType | BoolKey) – Remove overall (linear) momentum of the system. This is disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).
- class _ReactionBoost[source]¶
Define a series of transitions between different states of the system.
Each transition is defined by a TargetSystem and by a set of restraints that force the transition.
- Variables:
Change (Literal["TargetCoordinate", "Force", "LogForce"]) –
Select what to change during dynamics.
By default, once the restraints are switched on, AMS will change the restraint’s target coordinate towards its final value.
If the [Force] or [LogForce] option is selected then the target coordinate is set to its final value immediately and instead the restraint force is gradually scaled from 0 to 1. The scaling is either linear (Force) or logarithmic (LogForce).
InitialFraction (float | FloatKey) –
Initial fraction of the boost variable.
At the first boosting step, the restraint’s target value (or force or log(force)) is equal to InitialFraction + 1/NSteps.
InterEquilibrationSteps (int | IntKey) – Number of equilibration steps after reaching a target before setting up restraints for the next one.
MinBondChange (float | FloatKey) – Minimal change in the distance for an individual restraint to be considered bond-breaking/making vs bonded.
MinBondStrength (float | FloatKey) – Minimum strength (usually ranges from 0 to 1) for a bond to be considered.
NSteps (int | IntKey) – Number of steps per target the restraints should be active for.
PreEquilibrationSteps (int | IntKey) – Number of steps before enabling the first set of restraints.
Region (str | StringKey) – Region to which the restraints should be limited.
TargetSystem (str | StringKey) –
The target system’s name for this transition. Multiple targets can be specified to request multiple transitions in one simulation.
Note that only the lattice and the atomic coordinates of the target system are used and other properties (bonds, charge, etc.) are ignored. The target system’s lattice is used only to determine connections and it cannot be restrained.
Type (Literal["None", "Pair", "RMSD"]) –
Reaction Boost uses a series of transitions between different states of the system. Each transition is defined by a TargetSystem and by a set of restraints that force the transition.
Select the type of the restraint set: -None: no Reaction Boost - Pair: use pair restraints - RMSD: use RMSD restraints.
Pair restraints are defined per atom pair while the RMSD defines one collective restraint for all atoms and is thus suitable for very large systems.
The pair restraints are further divided into four sub-types: bonding, non-bonding, bond-breaking and bond-making. The sub-type of restraints for each pair is determined automatically depending on whether the two atoms are bonded in the initial/final state.
Parameters of the pair restraints are defined by [NonBondedRestraints], [BondedRestraints], [BondBreakingRestraints] and [BondMakingRestraints] blocks, while those of the RMSD restraint by the [RMSDRestraint] block.
BondBreakingRestraints (SimpleActiveLearning._MolecularDynamics._ReactionBoost._BondBreakingRestraints) –
Define parameters for moving restraints that are added for pairs of atoms that become disconnected during the transition.
It is intended to make sure the corresponding bonds get broken, although this may not always be required because forming other bonds will likely get these bonds broken.
BondMakingRestraints (SimpleActiveLearning._MolecularDynamics._ReactionBoost._BondMakingRestraints) –
Define parameters for moving restraints that are added for pairs of atoms that become connected during the transition.
It is intended to make sure the bonds are created as required.
BondedRestraints (SimpleActiveLearning._MolecularDynamics._ReactionBoost._BondedRestraints) –
Define parameters for bonded restraints. A bonded restraint is added for each pair of atoms that are bonded both in the current and in the final state.
It is intended to make sure they remain bonded during simulation.
NonBondedRestraints (SimpleActiveLearning._MolecularDynamics._ReactionBoost._NonBondedRestraints) –
Define parameters for non-bonded restraints. A non-bonded restraint is added for each pair of atoms that are bonded neither in the current nor in the final state.
It is intended to keep them from forming a bond unintentionally. They are represented by a repulsive potential
RMSDRestraint (SimpleActiveLearning._MolecularDynamics._ReactionBoost._RMSDRestraint) – Define a static restraint that pulls each atom to its position in the target system, but in contrast to the individual restraints, the force for this one depends on the total mass-weighted root-mean-squared distance (RMSD) between the two structures.
- class _BondBreakingRestraints[source]¶
Define parameters for moving restraints that are added for pairs of atoms that become disconnected during the transition.
It is intended to make sure the corresponding bonds get broken, although this may not always be required because forming other bonds will likely get these bonds broken.
- Variables:
Type (Literal["None", "Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) –
Select type of the moving restraint profile.
Harmonic: V=0.5*FC*(r-r0)^2
Hyperbolic: V=alpha*(sqrt(1 + beta*x^2) - 1)
Erf: V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI))
GaussianWell: V=WellDepth*(1-exp(-Sigma*(r-r0)^2))
Here beta=ForceConstant/MaxForce, alpha=MaxForce/beta.
The force for Hyperbolic and Erf is bounded by a user-defined value, the latter converging to it faster than the former. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable.
Moving restraints are added for pairs of atoms that become disconnected during the transition.
It is intended to make sure the corresponding bonds get broken, although this may not always be required because forming other bonds will likely get these bonds broken.
Erf (SimpleActiveLearning._MolecularDynamics._ReactionBoost._BondBreakingRestraints._Erf) – Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
GaussianWell (SimpleActiveLearning._MolecularDynamics._ReactionBoost._BondBreakingRestraints._GaussianWell) – Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
Harmonic (SimpleActiveLearning._MolecularDynamics._ReactionBoost._BondBreakingRestraints._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
Hyperbolic (SimpleActiveLearning._MolecularDynamics._ReactionBoost._BondBreakingRestraints._Hyperbolic) – Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
Taper (SimpleActiveLearning._MolecularDynamics._ReactionBoost._BondBreakingRestraints._Taper) –
- class _Erf[source]¶
Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
- class _GaussianWell[source]¶
Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
- class _Hyperbolic[source]¶
Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
- class _Taper[source]¶
- Variables:
Enabled (BoolType | BoolKey) – Enable tapering of the restraint potential and force between the given range of bond distances. A 7-th order tapering function on the actual (not target!) distance will be used. The MaxDistance must be greater than MinDistance.
MaxDistance (float | FloatKey) – Bond length at which the restraint potential and force decays to zero.
MinDistance (float | FloatKey) – Bond length at which the restraint potential and force will start decaying to zero.
- class _BondMakingRestraints[source]¶
Define parameters for moving restraints that are added for pairs of atoms that become connected during the transition.
It is intended to make sure the bonds are created as required.
- Variables:
Type (Literal["None", "Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) –
Select type of the moving restraint profile.
Harmonic: V=0.5*FC*(r-r0)^2
Hyperbolic: V=alpha*(sqrt(1 + beta*x^2) - 1)
Erf: V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI))
GaussianWell: V=-WellDepth*exp(-Sigma*(r-r0)^2)
Here beta=ForceConstant/MaxForce, alpha=MaxForce/beta.
The force for Hyperbolic and Erf is bounded by a user-defined value. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable.
Moving restraints are added for pairs of atoms that become connected during the transition.
It is intended to make sure the bonds are created as required.
Erf (SimpleActiveLearning._MolecularDynamics._ReactionBoost._BondMakingRestraints._Erf) – Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
GaussianWell (SimpleActiveLearning._MolecularDynamics._ReactionBoost._BondMakingRestraints._GaussianWell) – Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
Harmonic (SimpleActiveLearning._MolecularDynamics._ReactionBoost._BondMakingRestraints._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
Hyperbolic (SimpleActiveLearning._MolecularDynamics._ReactionBoost._BondMakingRestraints._Hyperbolic) – Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
- class _Erf[source]¶
Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
- class _GaussianWell[source]¶
Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
- class _BondedRestraints[source]¶
Define parameters for bonded restraints. A bonded restraint is added for each pair of atoms that are bonded both in the current and in the final state.
It is intended to make sure they remain bonded during simulation.
- Variables:
Type (Literal["None", "Harmonic"]) –
Select type of the bonded restraints:
Harmonic: V=0.5*FC*(r-r0)^2
A bonded restraint is added for each pair of atoms that are bonded both in the current and in the final state.
It is intended to make sure they remain bonded during simulation.
Harmonic (SimpleActiveLearning._MolecularDynamics._ReactionBoost._BondedRestraints._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
- class _NonBondedRestraints[source]¶
Define parameters for non-bonded restraints. A non-bonded restraint is added for each pair of atoms that are bonded neither in the current nor in the final state.
It is intended to keep them from forming a bond unintentionally. They are represented by a repulsive potential
- Variables:
Type (Literal["None", "Exponential"]) –
Select type of the non-bonded restraints:
Exponential: V=Epsilon*exp(-Sigma*r)
A non-bonded restraint is added for each pair of atoms that are bonded neither in the current nor in the final state.
It is intended to keep them from forming a bond unintentionally. They are represented by a repulsive potential.
Exponential (SimpleActiveLearning._MolecularDynamics._ReactionBoost._NonBondedRestraints._Exponential) – Define parameters for the repulsive potential V=Epsilon*exp(-Sigma*r).
- class _RMSDRestraint[source]¶
Define a static restraint that pulls each atom to its position in the target system, but in contrast to the individual restraints, the force for this one depends on the total mass-weighted root-mean-squared distance (RMSD) between the two structures.
- Variables:
Type (Literal["None", "Harmonic", "Hyperbolic", "Erf", "GaussianWell"]) –
Select type of the RMSD restraint profile:
Harmonic: V=0.5*FC*(r-r0)^2
Hyperbolic: V=alpha*(sqrt(1 + beta*x^2) - 1)
Erf: V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI),
GaussianWell: V=-WellDepth*exp(-Sigma*(r-r0)^2)
Here beta=ForceConstant/MaxForce, alpha=MaxForce/beta.
The Harmonic profile can be problematic at large deviations as it may result in large forces. The force for Hyperbolic and Erf is bounded by a user-defined value. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable.
Erf (SimpleActiveLearning._MolecularDynamics._ReactionBoost._RMSDRestraint._Erf) – Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
GaussianWell (SimpleActiveLearning._MolecularDynamics._ReactionBoost._RMSDRestraint._GaussianWell) – Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
Harmonic (SimpleActiveLearning._MolecularDynamics._ReactionBoost._RMSDRestraint._Harmonic) – Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.
Hyperbolic (SimpleActiveLearning._MolecularDynamics._ReactionBoost._RMSDRestraint._Hyperbolic) – Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta
- class _Erf[source]¶
Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.
- class _GaussianWell[source]¶
Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).
- class _Reactor[source]¶
Define one phase of the nanoreactor. A reactor is a region of space surrounded by an elastic wall. Atoms inside the region are not affected. Atoms outside it will be pushed back with force depending on the [ForceConstant] and the [MassScaled] flag.
- Variables:
ForceConstant (float | FloatKey) – Force constant of the reactor wall in Hartree/Bohr^2 (or Hartree/Bohr^2/Dalton if [MassScaled] is true).
MassScaled (BoolType | BoolKey) – If this flag is disabled the force on an atom outside of the reactor depends only on the atomic coordinates and the force constant. Otherwise, the force is also multiplied by the mass of the atom. This means that atoms at the same distance from the wall will receive the same accelerate due to the wall potential.
NSteps (int | IntKey) – Number of steps for which the reactor will remain active until disabled. The next reactor will be activated immediately after this. After the last reactor is disabled the cycle will repeat.
- class _ReflectiveWall[source]¶
Apply a reflective wall in space
- Variables:
Axis (Iterable[float] | FloatListKey) – Defines the normal vector perpendicular to the plane of the reflective wall. Any particle moving in this direction will be reflected back.
Direction (Literal["under", "above"]) – Defines the direction of the reflective wall. under will keep the particles under the defined wall, and above will keep the particles above the defined wall
Region (str | StringKey) – Apply the reflective wall to all atoms in this region.
Threshold (float | FloatKey) – Defines the threshold value determining the position of the reflective wall. If the dot product of a position of a particle with Axis exceeds Threshold, the particle will be reflected. This means that the plane of the wall passes through a point given by Axis times Threshold.
- class _Remap[source]¶
Control periodic remapping (backtranslation) of atoms into the PBC box.
- Variables:
Range (Literal["Auto", "ZeroToOne", "PlusMinusHalf", "AroundCenter"]) –
Select the range of fractional coordinates to which atoms are remapped.
Auto: Use PlusMinusHalf if the geometrical center of the starting positions of all atoms lies between -0.25 and 0.25 in fractional coordinates in all periodic directions, ZeroToOne otherwise.
PlusMinusHalf: Remap atoms to lie between -0.5 and 0.5 in fractional coordinates.
ZeroToOne: Remap atoms to lie between 0 and 1 in fractional coordinates.
AroundCenter: Remap atoms to lie within 0.5 in fractional coordinates around the geometrical center of the starting positions of all atoms.
Type (Literal["None", "Atoms"]) –
Select the method used to remap atoms into the unit cell.
None: Disable remapping completely.
Atoms: Remap any atoms that leave the unit cell.
- class _RemoveMolecules[source]¶
This block controls removal of molecules from the system. Multiple occurrences of this block are possible.
- Variables:
Molecular formula of the molecules that should be removed from the system.
The order of elements in the formula is very important and the correct order is: C, H, all other elements in the strictly alphabetic order. Element names are case-sensitive, spaces in the formula are not allowed. Digit ‘1’ must be omitted.
Valid formula examples: C2H6O, H2O, O2S. Invalid formula examples: C2H5OH, H2O1, OH, SO2. Invalid formulas are silently ignored.
Use * to remove any molecule, which must be combined with SinkBox or SafeBox.
Frequency (int | IntKey) – The specified molecules are removed every so many steps after the StartStep. There is never a molecule removed at step 0.
Step number when molecules are removed for the first time. After that, molecules are removed every [Frequency] steps.
For example, if StartStep=99 and Frequency=100 then molecules will be removed at steps 99, 199, 299, etc…
No molecule will be removed at step 0, so if StartStep=0 the first molecules are removed at the step number equal to [Frequency].
StopStep (int | IntKey) – Do not remove the specified molecules after this step.
SafeBox (SimpleActiveLearning._MolecularDynamics._RemoveMolecules._SafeBox) – Part of the simulation box where molecules may not be removed. Only one of the SinkBox or SafeBox blocks may be present. If this block is present the molecule will not be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.
SinkBox (SimpleActiveLearning._MolecularDynamics._RemoveMolecules._SinkBox) – Part of the simulation box where matching molecules will be removed. By default, molecules matching the formula will be removed regardless of their location. If this block is present then such a molecule will only be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.
- class _SafeBox[source]¶
Part of the simulation box where molecules may not be removed. Only one of the SinkBox or SafeBox blocks may be present. If this block is present the molecule will not be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.
- Variables:
Amax (float | FloatKey) – Coordinate of the upper bound along the first axis.
Amin (float | FloatKey) – Coordinate of the lower bound along the first axis.
Bmax (float | FloatKey) – Coordinate of the upper bound along the second axis.
Bmin (float | FloatKey) – Coordinate of the lower bound along the second axis.
Cmax (float | FloatKey) – Coordinate of the upper bound along the third axis.
Cmin (float | FloatKey) – Coordinate of the lower bound along the third axis.
FractionalCoordsBox (Iterable[float] | FloatListKey) –
Do not remove molecules that are (partly) inside the safe box.
Borders of the safe box specified as: Amin, Amax, Bmin, Bmax, Cmin, Cmax.
For periodic dimensions fractional coordinates between 0 and 1 and for non-periodic dimensions Cartesian values in Angstrom are expected.
- class _SinkBox[source]¶
Part of the simulation box where matching molecules will be removed. By default, molecules matching the formula will be removed regardless of their location. If this block is present then such a molecule will only be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.
- Variables:
Amax (float | FloatKey) – Coordinate of the upper bound along the first axis.
Amin (float | FloatKey) – Coordinate of the lower bound along the first axis.
Bmax (float | FloatKey) – Coordinate of the upper bound along the second axis.
Bmin (float | FloatKey) – Coordinate of the lower bound along the second axis.
Cmax (float | FloatKey) – Coordinate of the upper bound along the third axis.
Cmin (float | FloatKey) – Coordinate of the lower bound along the third axis.
FractionalCoordsBox (Iterable[float] | FloatListKey) –
Remove molecules that are (partly) inside the sink box.
Borders of the sink box specified as: Amin, Amax, Bmin, Bmax, Cmin, Cmax.
For periodic dimensions fractional coordinates between 0 and 1 and for non-periodic dimensions Cartesian values in Angstrom are expected.
- class _ReplicaExchange[source]¶
This block is used for (temperature) Replica Exchange MD (Parallel Tempering) simulations.
- Variables:
AllowWrongResults (BoolType | BoolKey) – Allow combining Replica Exchange with other features when the combination is known to produce physically incorrect results.
Length of the exponentially weighted moving average used to smooth swap probabilities for monitoring.
This value is equal to the inverse of the EWMA mixing factor.
SwapFrequency (int | IntKey) – Attempt an exchange every N steps.
TemperatureFactors (Iterable[float] | FloatListKey) –
This is the ratio of the temperatures of two successive replicas.
The first value sets the temperature of the second replica with respect to the first replica, the second value sets the temperature of the third replica with respect to the second one, and so on. If there are fewer values than nReplicas, the last value of TemperatureFactor is used for all the remaining replicas.
Temperatures (Iterable[float] | FloatListKey) –
List of temperatures for all replicas except for the first one.
This is mutually exclusive with TemperatureFactors. Exactly nReplicas-1 temperature values need to be specified, in increasing order. The temperature of the first replica is given by [Thermostat%Temperature].
nReplicas (int | IntKey) – Number of replicas to run in parallel.
- class _Shake[source]¶
Parameters of the Shake/Rattle algorithm.
- Variables:
Constraint description in one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3
The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 and the angle between them.
The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then all bonds between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. The distance, if present, must be in Angstrom. If it is omitted then the bond length from the initial geometry is used.
Important: only the bonds present in the system at certain points of the simulation (at the start or right after adding/removing atoms) can be constrained, which means that the bonds may need to be specified in the System block.
Warning: the triangles constraint should be used with care because each constrained bond or angle means removing one degree of freedom from the dynamics. When there are too many constraints (for example, “All triangles H C H” in methane) some of them may be linearly dependent, which will lead to an error in the temperature computation.
Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H
ConvergeR2 (float | FloatKey) – Convergence criterion on the max squared difference, in atomic units.
ConvergeRV (float | FloatKey) – Convergence criterion on the orthogonality of the constraint and the relative atomic velocity, in atomic units.
ShakeInitialCoordinates (BoolType | BoolKey) – Apply constraints before computing the first energy and gradients.
- class _Thermostat[source]¶
This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’s behavior.
- Variables:
BerendsenApply (Literal["Local", "Global"]) –
Select how to apply the scaling correction for the Berendsen thermostat:
per-atom-velocity (Local)
on the molecular system as a whole (Global).
ChainLength (int | IntKey) – Number of individual thermostats forming the NHC thermostat
Duration (Iterable[int] | IntListKey) – Specifies how many steps should a transition from a particular temperature to the next one in sequence take.
ExcludedDirection (Literal["None", "X", "Y", "Z"]) – Exclude a component of the velocities from rescaling by the thermostat. For example in NEMD simulations, when a shear force/velocity is applied in the x direction, the x-direction is often excluded from thermostatting. This currently only works for the Nose-Hoover thermostat.
Friction (float | FloatKey) – Friction coefficient used in langevin dynamics
Region (str | StringKey) – The identifier of the region to thermostat. The default * applies the thermostat to the entire system. The value can by a plain region name, or a region expression, e.g. *-myregion to thermostat all atoms that are not in myregion, or regionA+regionB to thermostat the union of the ‘regionA’ and ‘regionB’. Note that if multiple thermostats are used, their regions may not overlap.
ScaleFrequency (int | IntKey) –
Optional parameter used only by the Scale thermostat.
If specified, the thermostat will be applied every N steps, using that step’s ensemble temperature and the specified thermostat temperature to compute the scaling factor.
If not specified, the thermostat will be applied at every step, using the mean temperature of the ensemble and the specified thermostat temperature to compute the scaling factor.
Tau (float | FloatKey) – The time constant of the thermostat.
Temperature (Iterable[float] | FloatListKey) –
The target temperature of the thermostat.
You can specify multiple temperatures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one T to the next T (using a linear ramp). For NHC thermostat, the temperature may not be zero.
Type (Literal["None", "Scale", "Berendsen", "NHC", "Langevin"]) – Selects the type of the thermostat.
- class _Trajectory[source]¶
Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
- Variables:
EngineResultsFreq (int | IntKey) – Write MDStep*.rkf files with engine-specific results once every N steps. Setting this to zero disables writing engine results files except for one file at the end of the simulation. If unset or negative, defaults to the value of Checkpoint%Frequency.
ExitConditionFreq (int | IntKey) – Check the exit conditions every N steps. By default this is done every SamplingFreq steps.
PrintFreq (int | IntKey) – Print current thermodynamic properties to the output every N steps. By default this is done every SamplingFreq steps.
SamplingFreq (int | IntKey) – Write the molecular geometry (and possibly other properties) to the ams.rkf file once every N steps.
TProfileGridPoints (int | IntKey) – Number of points in the temperature profile. If TProfileGridPoints > 0, a temperature profile along each of the three lattice axes will be written to the .rkf file. The temperature at a given profile point is calculated as the total temperature of all atoms inside the corresponding slice of the simulation box, time-averaged over all MD steps since the previous snapshot. By default, no profile is generated.
WriteBonds (BoolType | BoolKey) – Write detected bonds to the .rkf file.
WriteCharges (BoolType | BoolKey) – Write current atomic point charges (if available) to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze charges.
WriteCoordinates (BoolType | BoolKey) – Write atomic coordinates to the .rkf file.
WriteEngineGradients (BoolType | BoolKey) – Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.
WriteMolecules (BoolType | BoolKey) – Write the results of molecule analysis to the .rkf file.
WriteVelocities (BoolType | BoolKey) – Write velocities to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze the velocities.
- class _fbMC[source]¶
This block sets up force bias Monte Carlo interleaved with the molecular dynamics simulation.
- Variables:
Frequency (int | IntKey) – Run the fbMC procedure every Frequency MD steps.
MassRoot (float | FloatKey) – Inverse of the exponent used to mass-weight fbMC steps.
NSteps (int | IntKey) – Number of fbMC steps to perform on every invocation of the procedure.
PrintFreq (int | IntKey) – Print current thermodynamic properties to the output every N fbMC steps. This defaults to the PrintFreq set in the Trajectory block. Setting this to zero disables printing fbMC steps.
StartStep (int | IntKey) – First step at which the fbMC procedure may run.
StepLength (float | FloatKey) – Maximum allowed displacement of the lightest atom in the system in each Cartesian coordinate in one fbMC step.
StopStep (int | IntKey) – Last step at which the fbMC procedure may run. If unset or zero, there is no limit.
MolecularMoves (SimpleActiveLearning._MolecularDynamics._fbMC._MolecularMoves) – Move molecules as rigid bodies in addition to normal atomic moves.
- class _MolecularMoves[source]¶
Move molecules as rigid bodies in addition to normal atomic moves.
- Variables:
Enabled (BoolType | BoolKey) – Enable moving molecules as rigid bodies based on net forces and torques. Ordinary per-atom displacements will then be based on residual atomic forces.
RotationMethod (Literal["Mees", "Rao"]) – Select the fbMC method used to generate molecular rotation moves.
RotationStepAngle (float | FloatKey) – Maximum allowed angle of rotation of each molecule in one fbMC step.
TranslationStepLength (float | FloatKey) – Maximum allowed displacement of each molecule in each Cartesian coordinate in one fbMC step.
- class _ParallelLevels[source]¶
Distribution of threads/processes between the parallelization levels.
- Variables:
CommitteeMembers (int | IntKey) – Maximum number of committee member optimizations to run in parallel. If set to zero will take the minimum of MachineLearning%CommitteeSize and the number of available cores (NSCM)
Cores (int | IntKey) – Number of cores to use per committee member optimization. By default (0) the available cores (NSCM) divided equally among committee members. When using GPU offloading, consider setting this to 1.
Jobs (int | IntKey) – Number of JobCollection jobs to run in parallel for each loss function evaluation.
Optimizations (int | IntKey) – Number of independent optimizers to run in parallel.
ParameterVectors (int | IntKey) –
Number of parameter vectors to try in parallel for each optimizer iteration. This level of parallelism can only be used with optimizers that support parallel optimization!
Default (0) will set this value to the number of cores on the system divided by the number of optimizers run in parallel, i.e., each optimizer will be given an equal share of the resources.
Number of processes (MPI ranks) to spawn for each JobCollection job. This effectively sets the NSCM environment variable for each job.
A value of -1 will disable explicit setting of related variables. We recommend a value of 1 in almost all cases. A value greater than 1 would only be useful if you parametrize DFTB with a serial optimizer and have very few jobs in the job collection.
Number of threads to use for each of the processes. This effectively set the OMP_NUM_THREADS environment variable. Note that the DFTB engine does not use threads, so the value of this variable would not have any effect. We recommend always leaving it at the default value of 1. Please consult the manual of the engine you are parameterizing.
A value of -1 will disable explicit setting of related variables.
- class _System[source]¶
Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- Variables:
AllowCloseAtoms (BoolType | BoolKey) – No longer functional. Just here for backwards compatibility.
Charge (float | FloatKey) – The system’s total charge in atomic units.
FractionalCoords (BoolType | BoolKey) – Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
GeometryFile (str | Path | StringKey) – Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds (BoolType | BoolKey) – Equivalent to ‘Modify%GuessBonds’. Please update input file to use ‘Modify’ block instead.
LatticeStrain (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%LatticeStrain’. Please update input file to use ‘Modify’ block instead.
MapAtomsToUnitCell (BoolType | BoolKey) – Equivalent to ‘Modify%MapAtomsToUnitCell’. Please update input file to use ‘Modify’ block instead.
PerturbCoordinates (float | FloatKey) – Equivalent to ‘Modify%PerturbCoordinates’. Please update input file to use ‘Modify’ block instead.
PerturbLattice (float | FloatKey) – Equivalent to ‘Modify%PerturbLattice’. Please update input file to use ‘Modify’ block instead.
ShiftCoordinates (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%Translate’, but in the unit of bohr by default. Please update input file to use ‘Modify’ block instead.
SuperCell (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCell’. Please update input file to use ‘Modify’ block instead.
SuperCellTrafo (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCellTrafo’. Please update input file to use ‘Modify’ block instead.
Symmetrize (BoolType | BoolKey) – Equivalent to ‘Modify%Symmetrize’. Please update input file to use ‘Modify’ block instead.
Atoms (str | Sequence[str] | FreeBlock) – The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders (str | Sequence[str] | FreeBlock) – Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
ElectrostaticEmbedding (SimpleActiveLearning._System._ElectrostaticEmbedding) – Container for electrostatic embedding options, which can be combined.
Lattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
Modify (SimpleActiveLearning._System._Modify) – Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- class _Atoms[source]¶
The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
- class _BondOrders[source]¶
Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
- class _ElectrostaticEmbedding[source]¶
Container for electrostatic embedding options, which can be combined.
- Variables:
ElectricField (Iterable[float] | FloatListKey) –
External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.
In atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 … e11 V/m.
Supported by the engines adf, band, dftb and mopac.
For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
MultipolePotential (SimpleActiveLearning._System._ElectrostaticEmbedding._MultipolePotential) – External point charges (and dipoles).
- class _MultipolePotential[source]¶
External point charges (and dipoles).
- Variables:
ChargeModel (Literal["Point", "Gaussian"]) – A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
ChargeWidth (float | FloatKey) – The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
Coordinates (str | Sequence[str] | FreeBlock) –
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Coordinates[source]¶
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Lattice[source]¶
Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
- class _Modify[source]¶
Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- Variables:
EnableAtomicProperties (Literal["gui", "adf", "band", "forcefield", "dftb", "reaxff", "qe"]) – Enables an atomic property group. This is only necessary if you want a group enabled, but no atom in the input is using any property from that group.
GuessBonds (BoolType | BoolKey) – Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.
LatticeStrain (Iterable[float] | FloatListKey) – Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
MapAtomsToUnitCell (Iterable[float] | FloatListKey) – For periodic systems the atoms will be moved to the central unit cell where all their fractional coordinates are in the range [start_range,start_range+1). No mapping will take place along non-periodic directions. If just a single number is given, it corresponds to start_range. If multiple numbers are given, they should match the number of lattice vectors and will be used as start ranges along the individual lattice vectors. If no number is given at all, the mapping will be done to the [-0.5:0.5) cell.
PerturbCoordinates (float | FloatKey) – Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
PerturbLattice (float | FloatKey) – Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
SuperCell (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
SuperCellTrafo (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
Symmetrize (BoolType | BoolKey) – Symmetrizes the atomic coordinates to machine precision and rototranslates the molecule to the AMS standard orientation. This allows optimal use of the system’s symmetry for calculations with the AMS driver and its engines.
Translate (Iterable[float] | FloatListKey) – Translate all atoms by a vector.
- class Symmetrize[source]¶
- Variables:
LoadSystem (Symmetrize._LoadSystem) – Block that controls reading the chemical system from a KF file instead of the [System] block.
Symmetry (Symmetrize._Symmetry) – Specifying details about the details of symmetry detection and usage.
System (Symmetrize._System) – Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- class _LoadSystem[source]¶
Block that controls reading the chemical system from a KF file instead of the [System] block.
- class _System[source]¶
Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
- Variables:
AllowCloseAtoms (BoolType | BoolKey) – No longer functional. Just here for backwards compatibility.
Charge (float | FloatKey) – The system’s total charge in atomic units.
FractionalCoords (BoolType | BoolKey) – Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
GeometryFile (str | Path | StringKey) – Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds (BoolType | BoolKey) – Equivalent to ‘Modify%GuessBonds’. Please update input file to use ‘Modify’ block instead.
LatticeStrain (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%LatticeStrain’. Please update input file to use ‘Modify’ block instead.
MapAtomsToUnitCell (BoolType | BoolKey) – Equivalent to ‘Modify%MapAtomsToUnitCell’. Please update input file to use ‘Modify’ block instead.
PerturbCoordinates (float | FloatKey) – Equivalent to ‘Modify%PerturbCoordinates’. Please update input file to use ‘Modify’ block instead.
PerturbLattice (float | FloatKey) – Equivalent to ‘Modify%PerturbLattice’. Please update input file to use ‘Modify’ block instead.
ShiftCoordinates (Iterable[float] | FloatListKey) – Equivalent to ‘Modify%Translate’, but in the unit of bohr by default. Please update input file to use ‘Modify’ block instead.
SuperCell (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCell’. Please update input file to use ‘Modify’ block instead.
SuperCellTrafo (Iterable[int] | IntListKey) – Equivalent to ‘Modify%SuperCellTrafo’. Please update input file to use ‘Modify’ block instead.
Symmetrize (BoolType | BoolKey) – Equivalent to ‘Modify%Symmetrize’. Please update input file to use ‘Modify’ block instead.
Atoms (str | Sequence[str] | FreeBlock) – The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders (str | Sequence[str] | FreeBlock) – Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
ElectrostaticEmbedding (Symmetrize._System._ElectrostaticEmbedding) – Container for electrostatic embedding options, which can be combined.
Lattice (str | Sequence[str] | FreeBlock) – Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
Modify (Symmetrize._System._Modify) – Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- class _Atoms[source]¶
The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
- class _BondOrders[source]¶
Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
- class _ElectrostaticEmbedding[source]¶
Container for electrostatic embedding options, which can be combined.
- Variables:
ElectricField (Iterable[float] | FloatListKey) –
External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.
In atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 … e11 V/m.
Supported by the engines adf, band, dftb and mopac.
For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
MultipolePotential (Symmetrize._System._ElectrostaticEmbedding._MultipolePotential) – External point charges (and dipoles).
- class _MultipolePotential[source]¶
External point charges (and dipoles).
- Variables:
ChargeModel (Literal["Point", "Gaussian"]) – A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
ChargeWidth (float | FloatKey) – The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
Coordinates (str | Sequence[str] | FreeBlock) –
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Coordinates[source]¶
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
- class _Lattice[source]¶
Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
- class _Modify[source]¶
Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
- Variables:
EnableAtomicProperties (Literal["gui", "adf", "band", "forcefield", "dftb", "reaxff", "qe"]) – Enables an atomic property group. This is only necessary if you want a group enabled, but no atom in the input is using any property from that group.
GuessBonds (BoolType | BoolKey) – Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.
LatticeStrain (Iterable[float] | FloatListKey) – Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
MapAtomsToUnitCell (Iterable[float] | FloatListKey) – For periodic systems the atoms will be moved to the central unit cell where all their fractional coordinates are in the range [start_range,start_range+1). No mapping will take place along non-periodic directions. If just a single number is given, it corresponds to start_range. If multiple numbers are given, they should match the number of lattice vectors and will be used as start ranges along the individual lattice vectors. If no number is given at all, the mapping will be done to the [-0.5:0.5) cell.
PerturbCoordinates (float | FloatKey) – Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
PerturbLattice (float | FloatKey) – Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
SuperCell (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
SuperCellTrafo (Iterable[int] | IntListKey) – Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
Symmetrize (BoolType | BoolKey) – Symmetrizes the atomic coordinates to machine precision and rototranslates the molecule to the AMS standard orientation. This allows optimal use of the system’s symmetry for calculations with the AMS driver and its engines.
Translate (Iterable[float] | FloatListKey) – Translate all atoms by a vector.
3.1.2. Engines¶
- class ADF[source]¶
- Variables:
A1Fit (float | FloatKey) – STO-Fit keyword: distance between atoms, in Angstrom. The symmetric fit approximation is applied only for atoms farther apart.
AOMat2File (BoolType | BoolKey) – Write PMatrix, Fock matrix, and overlap matrix on AO basis to file for future analysis purposes
AORCOnly (BoolType | BoolKey) – Debug option AOResponse.
AORXCOnly (BoolType | BoolKey) – Debug option AOResponse.
AORun (BoolType | BoolKey) – Expert option not to write orbitals to file for TDDFT.
AccurateGradients (BoolType | BoolKey) – Print the nuclear gradients with more digits than usual.
AddDiffuseFit (BoolType | BoolKey) – STO-Fit keyword: One can get more diffuse fit functions by setting this to True.
AllDipMat (BoolType | BoolKey) – Print all dipole matrix elements between occupied and virtual Kohn-Sham orbitals.
AllPoints (BoolType | BoolKey) – ADF makes use of symmetry in the numerical integrations. Points are generated for the irreducible wedge, a symmetry unique sub region of space. Optionally the symmetry equivalent points are also used. This is achieved by setting this key to True.
AllWaals (BoolType | BoolKey) – Expert to write all van der Waals tensors in Response..
Allow (str | StringKey) – Controlled aborts can in some cases be overruled. Of course, the checks have been inserted for good reasons and one should realize that ignoring them probably produces incorrect results or may lead to a program-crash.
AltLinVXC (BoolType | BoolKey) –
AltOrthon (BoolType | BoolKey) – Expert option for alternative orthogonalization.
AltRhof (BoolType | BoolKey) – Expert option for Response.
AtomicChargesTypeForAMS (Literal["Mulliken", "Hirshfeld", "CM5", "Voronoi", "MDC-M", "MDC-D", "MDC-Q", "QTAIM"]) –
Type of atomic charges to be used by AMS.
Note that some of these atomic charges are computed and printed by default in ADF.
Hirshfeld charges are available only for default atomic fragments.
Balance (BoolType | BoolKey) – Measure the actual speed of the nodes in the parallel machine
BasValZero (BoolType | BoolKey) – Debug option
Blapt (BoolType | BoolKey) – Debug option for calculating post-SCF functional.
BoysOld (BoolType | BoolKey) – Option for localizing orbitals using old scheme.
C2Coef (BoolType | BoolKey) – Print C2Coef to output
CM5 (BoolType | BoolKey) – Calculate the charge model 5 (CM5) analysis.
CalcOverlapOnly (BoolType | BoolKey) – Calculate overlaps of primitive basis and stops after computing them.
CalcTotalEnergy (BoolType | BoolKey) – Whether or not to calculate the total energy.
ChkDisFal (BoolType | BoolKey) – Debug option not to ise distance effects, probably not working correct anymore.
ColTDDFT (BoolType | BoolKey) – Debug option to see the effect of a collinear kernel TDDFT in case of spin-orbit coupling
CommTiming (BoolType | BoolKey) – Only perform parallel timing test on the gather, broadcast and combine routines.
ComplexAcl (BoolType | BoolKey) – Expert key for AOresponse spin-orbit coupled.
CoreTables (BoolType | BoolKey) – Undocumented and unused option for using CoreTables.
CoulombFit (BoolType | BoolKey) – Undocumented and unused option for using old HF exchange integrals also for Coulomb.
Create (str | StringKey) – Keywords for create run. {Atomtype Datafile}
DRho241 (BoolType | BoolKey) – Debug key for Response.
Debug (str | StringKey) – The amount of printed output is regulated with the keys Print, NoPrint, EPrint and Debug.
DeltaEpStrip (BoolType | BoolKey) – TDDFT Excitations expert key.
DensPrep (BoolType | BoolKey) – Undocumented option for FDE for sum-of-fragments density in SCF.
Diffuse (BoolType | BoolKey) – Adding diffuse integration points in case of the old Voronoi numerical integration grid.
DipoleLength (BoolType | BoolKey) – Use dipole-length elements for perturbing (external) integrals in CURRENT response
DipoleResponse (BoolType | BoolKey) –
DumpBasisOnly (BoolType | BoolKey) – Dump basis and fit set files use for each atom.
EGOXAlpha (BoolType | BoolKey) – Debug key for excited GO in excitations.
EnergyTest (BoolType | BoolKey) – Expert key for total energy.
ExactDensity (BoolType | BoolKey) – Use the exact density (as opposed to the fitted density) for the computation of the exchange-correlation potential
ExtendedPopan (BoolType | BoolKey) – Calculate the Mayer bond orders and Mulliken atom-atom populations per l-value
FitAlfa (BoolType | BoolKey) – Debug key for Response.
FitExcit (BoolType | BoolKey) –
FitFile (str | StringKey) – Only to be used in Create runs for STOFIT. Specify a file on which the fit functions are specified.
Fitelstat (BoolType | BoolKey) – In energy decomposition analysis use fitted density for electrostatic energy.
Fithyppol (BoolType | BoolKey) – Use fitted density in TDDFT for hyperpolarizability calculation.
Fitmeta (BoolType | BoolKey) – SCF: use fitted density for post-SCF meta-GGA functionals.
Fitsecder (BoolType | BoolKey) – SCF: use fitted density for second derivative density.
ForceALDA (BoolType | BoolKey) – In spin-flip TDDFT, the XC kernel can be calculated directly from the XC potential. To use the LDA potential for the XC kernel, which roughly corresponds to the ALDA in ordinary TDDFT, one must specify the key
FragMetaGGAToten (BoolType | BoolKey) – By setting this to true the difference in the metahybrid or metagga exchange-correlation energies between the molecule and its fragments will be calculated using the molecular integration grid, which is more accurate than the default, but is much more time consuming.
FullFock (BoolType | BoolKey) – Calculate the full Fock matrix each SCF iteration (instead of the difference with the previous cycle).
FullTotEn (BoolType | BoolKey) –
Fuzzy_BO (BoolType | BoolKey) –
GZip (str | StringKey) – GZip the corresponding tape (possibly working only for TAPE21)
Gradient (BoolType | BoolKey) –
Force calculation of gradients of the total energy with respect to the nuclear coordinates, just as in a geometry optimization.
This is useful if you want to perform a single point calculation and get gradients for that specific geometry.
HFAtomsPerPass (int | IntKey) – Memory usage option for old HF scheme
HFDependency (BoolType | BoolKey) – Extra Dependency trick for old Hartree-Fock exchange integrals.
HFMaxMemory (int | IntKey) – Memory usage option for old HF scheme
HartreeFock (BoolType | BoolKey) – Compute hybrid meta-GGA energy functionals (if METAGGA key is True)
Hilbert (BoolType | BoolKey) – Option for localization of numerical integration points.
IgnoreOverlap (BoolType | BoolKey) – Expert option. Ignore that atoms are close.
ImportEmbPot (str | StringKey) – File containing an external embedding potential (FDE calculations only)
ImportGrid (str | StringKey) – FDE option for importing numerical integration grid.
IntegralsToFile (Literal["None", "FCIdump", "Dirac", "SERENITY"]) – Write all 4-center integrals to direct access file (DIRAC). or in FCIdump/Serenity format. Default is None
KSSpectrum (BoolType | BoolKey) – Old key. TDDFT excitations, calculate single-orbital transitions.
LB4 (BoolType | BoolKey) – Debug option for unrestricted spin-orbit coupling.
Lap1 (BoolType | BoolKey) – Debug option for calculating post-SCF functional.
MBlockSmall (BoolType | BoolKey) – For TDDFT excitations with Davidson: Option to use only 1 extra trial vector at a time.
MOExactDensity (BoolType | BoolKey) – In SCF use exact density for MOs.
MetaGGA (BoolType | BoolKey) –
NewDIIS (BoolType | BoolKey) – For old SCF routine: use newDIIS.
NoBeckeGrid (BoolType | BoolKey) – If true ADF will use the Voronoi numerical integration grid.
NoFDEPot (BoolType | BoolKey) – Expert FDE option.
NoFragDp (BoolType | BoolKey) – Debug option for orthogonalization and dependency.
NoGTerm (BoolType | BoolKey) – Debug option in Response.
NoPrint (str | StringKey) – The amount of printed output is regulated with the keys Print, NoPrint, EPrint and Debug.
NoSharedArrays (BoolType | BoolKey) – To disable the use of shared memory.
NoSymFit (BoolType | BoolKey) – Do not use only an A1 symmetric fit.
NoTotEn (BoolType | BoolKey) –
NuclearModel (Literal["PointCharge", "Gaussian"]) –
Model for the nuclear charge distribution.
To see effects from your choice you will need to use a basis set with extra steep functions. For example you can find these in the ZORA/TZ2P-J basis directory.
NumericalQuality (Literal["Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Set the quality of several important technical aspects of an ADF calculation (with the notable exception of the basis set). It sets the quality of: BeckeGrid (numerical integration) and ZlmFit (density fitting). Note: the quality defined in the block of a specific technical aspects supersedes the value defined in NumericalQuality (e.g. if I specify ‘NumericalQuality Basic’ and ‘BeckeGrid%Quality Good’, the quality of the BeckeGrid will be ‘Good’)
OrbitalsCoulombInteraction (Iterable[int] | IntListKey) – Compute the Coulomb interaction energy between the density of two orbitals. After the key, specify the indices of the two orbitals for which you want to compute the Coulomb interaction energy. Can only be used for spin-restricted calculations. Cannot be used in case of Symmetry (use Symmetry NoSym).
OrthFragPrep (BoolType | BoolKey) – Expert FDE option.
PartialZORA (str | StringKey) – Untested and undocumented key to use partial ZORA.
Print (str | StringKey) – The amount of printed output is regulated with the keys Print, NoPrint, EPrint and Debug.
ProgConv (BoolType | BoolKey) – Use progressive convergence in SCF, icw LinearScaling%ProgConv not equal 0.
QTens (BoolType | BoolKey) – Calculate the the Nuclear Electric Quadrupole Hyperfine interaction (Q-tensor, NQCC, NQI), related to the Electric Field Gradient (EFG).
RConfine (Iterable[float] | FloatListKey) – Used for making confinement potential in order to make DFTB parameters. Obsolete.
RESPPMATSAVE (BoolType | BoolKey) – Needed for SubResponse (EO) calculations. Hacked by JN. Restored by Pengchong Liu
RESTOCC (BoolType | BoolKey) –
RemoveAllFragVirtuals (BoolType | BoolKey) – Remove all virtual fragment orbitals.
RemoveOtherFragVirtuals (BoolType | BoolKey) – Remove all virtual fragment orbitals, except on first fragment.
ResponseFormalism (Literal["Auto", "Response", "AOResponse"]) – Set to RESPONSE or AORESPONSE.
SFTDDFT (BoolType | BoolKey) – Calculate spin-flip excitation energies (requires TDA and FORCEALDA keys).
SOMCD (BoolType | BoolKey) – MCD option. Required for a calculation of MCD temperature-dependent C terms. The calculation must be an unrestricted and scalar relativistic ZORA.
STContrib (BoolType | BoolKey) – For an analysis of spin-orbit coupled excitations in terms of scalar relativistic singlet and triplet excitations. In order to get this analysis one needs to perform a scalar relativistic TDDFT calculation of excitation energies on the closed shell molecule first, and use the resulting adf.rkf as a fragment in the spin-orbit coupled TDDFT calculation of excitation energies, including this keyword STCONTRIB.
STOFit (BoolType | BoolKey) – Computation of the Coulomb potential with the pair fit method.
Save (str | StringKey) – A sequence of file names separated by blanks or commas. Possible file names are TAPE10, TAPE13, TAPE14.
SharcOverlap (BoolType | BoolKey) –
Skip (str | StringKey) – Expert key. To restrict which parts of the program are actually executed.
SpinPolarization (float | FloatKey) – The spin polarization of the system, which is the number of spin-alpha electrons in excess of spin-beta electrons. Specification is only meaningful in a spin-unrestricted calculation. However, specification is not meaningful in an unrestricted Spin-Orbit coupled calculation using the (non-)collinear approximation.
Symmetry (Literal["AUTO", "NOSYM", "ATOM", "C(LIN)", "D(LIN)", "C(I)", "C(S)", "C(2)", "C(2V)", "C(3V)", "C(4V)", "C(5V)", "C(6V)", "C(7V)", "C(8V)", "C(2H)", "D(2)", "D(3)", "D(4)", "D(5)", "D(6)", "D(7)", "D(8)", "D(2D)", "D(3D)", "D(4D)", "D(5D)", "D(6D)", "D(7D)", "D(8D)", "D(2H)", "D(3H)", "D(4H)", "D(5H)", "D(6H)", "D(7H)", "D(8H)", "O(H)", "T(D)"]) – Use (sub)symmetry with this Schoenflies symbol. Can only be used for molecules. Orientation should be correct for the (sub)symmetry. Coordinates must be symmetric within SymmetryTolerance.
SymmetryTolerance (float | FloatKey) – Tolerance used to detect symmetry in the system. If symmetry Schoenflies symbol is specified, the coordinates must be symmetric within this tolerance.
TDA (BoolType | BoolKey) – Use the Tamm-Dancoff approximation (TDA) (requires the EXCITATIONS block key)
TDDFTSO (BoolType | BoolKey) –
TIDegeneracyThreshold (float | FloatKey) – If the orbital energy of the fragment MO is within this threshold with fragment HOMO or LUMO energy, then this fragment MO is included in the calculation of the transfer integrals. Relevant in case there is (near) degeneracy.
TotalEnergy (BoolType | BoolKey) –
Calculate the total energy.
Normally only the bonding energy with respect to the fragments is calculated.
The total energy will be less accurate then the bonding energy (about two decimal places), and is not compatible with some options.
In most cases the total energy will not be needed.
TransferIntegrals (BoolType | BoolKey) –
Calculate the charge transfer integrals, spatial overlap integrals and site energies.
Charge transfer integrals can be used in models that calculate transport properties.
Unrestricted (BoolType | BoolKey) – By default, a spin-restricted calculation is performed where the spin alpha and spin beta orbitals are spatially the same.
UnrestrictedFragments (BoolType | BoolKey) –
Use fragments calculated a spin-unrestricted calculation: the spin alpha and spin beta orbitals may be spatially different.
The total spin polarization of your fragments must match the spin polarization of your final molecule.
UsePseudoDiag (BoolType | BoolKey) – Expert option for diagonalization in SCF.
UseSPCode (BoolType | BoolKey) – Use Patchkovskii routines for PBE
VectorLength (int | IntKey) – Specify a different batch size for the integration points here (default: 128 on most machines and 2047 on vector machines).
ZExact (BoolType | BoolKey) – Expert option in TDDFT excitations.
ZFS (str | StringKey) – Calculate the zero-field splitting (ZFS) of an open shell ground state. An unrestricted calculation is required and a spin larger than 1/2, and no no spatial degeneracy. Scalar relativistic ZORA is required.
grad_no_fragment_potentials (BoolType | BoolKey) – FDE option.
hydrogenbonds (BoolType | BoolKey) – Option for SFO population analysis to print small numbers.
nocalcs2 (BoolType | BoolKey) – Do not calculate expectation value S**2 (spin).
nomorton (BoolType | BoolKey) – Debug option for localization of numerical integration points.
nopm5rho (BoolType | BoolKey) – Debug option for response.
notstcoe (BoolType | BoolKey) – Option not to test orthonormal basis set.
nouseactivefrag (BoolType | BoolKey) – Do not use orbital data from active fragment in first cycle SCF.
novkpot (BoolType | BoolKey) – Debug option for AOResponse.
noxcprint (BoolType | BoolKey) – Do not print XC energy terms.
oldblockedsmat (BoolType | BoolKey) – Use old way to calculate overlap matrix.
oldorthon (BoolType | BoolKey) – Use old orthogonalization routine.
plap3 (BoolType | BoolKey) – Debug option for calculating post-SCF functional.
prtallten (BoolType | BoolKey) – Debug option for response.
readepsilons (BoolType | BoolKey) – Debug option for TDDFT. Read extra orbitals.
rhobelpotimport (BoolType | BoolKey) – Key for FDE-MD.
riskyfast (BoolType | BoolKey) – Debug option to skip some post-SCF properties, like bond energy.
scaledkinfunctionals (BoolType | BoolKey) – FDE option.
sfotrans (BoolType | BoolKey) – Old key for SFO analysis TDDFT excitations.
skorthon (BoolType | BoolKey) – Debug option to skip ETALOW.
sozero (BoolType | BoolKey) – Debug option to set spin-orbit matrix to zero.
switchcoe (BoolType | BoolKey) – Debug option for orthogonalization.
symexcit (BoolType | BoolKey) – Debug option for TDDFT excitations.
symresp (BoolType | BoolKey) – Debug option for TDDFT response.
testsub1 (BoolType | BoolKey) – Debug option excitations and subexci.
totenskip (BoolType | BoolKey) – Debug option to skip toten.
useortp (BoolType | BoolKey) – Use orth density matrices instead of previous density matrix.
usesumfragp (BoolType | BoolKey) – Use sum fragment density matrices instead of previous density matrix.
xonly (BoolType | BoolKey) – Option for spin-orbit coupled AOresponse.
xyonly (BoolType | BoolKey) – Option for spin-orbit coupled AOresponse.
xzonly (BoolType | BoolKey) – Option for spin-orbit coupled AOresponse.
yonly (BoolType | BoolKey) – Option for spin-orbit coupled AOresponse.
yzonly (BoolType | BoolKey) – Option for spin-orbit coupled AOresponse.
zonly (BoolType | BoolKey) – Option for spin-orbit coupled AOresponse.
AOResponse (ADF._AOResponse) – If the block key AORESPONSE is used, by default, the polarizability is calculated. Note that if the molecule has symmetry the key ALLPOINTS should be included
AnalyticalFreq (ADF._AnalyticalFreq) – Define options for analytical frequencies.
Aromaticity (ADF._Aromaticity) – Calculate aromaticity indicators, i.e. the matrix of localization/delocalization indices (LI-DI), Iring (ring index) and MCI (multi center index) aromaticity indices.
Basis (ADF._Basis) – Definition of the basis set
BeckeGrid (ADF._BeckeGrid) – Options for the numerical integration grid.
BondOrders (ADF._BondOrders) – Options for the calculation of bond orders. Note: the calculation of bond orders should be requested via the Properties%BondOrders input option in the AMS driver input.
CDFT (ADF._CDFT) – CDFT is a tool for carrying out DFT calculations in the presence of a constraint.
CVNDFT (ADF._CVNDFT) – The CVNDFT block key regulates the execution of the CV(n)-DFT code, which calculates the singlet or triplet electronic excitations for the closed shell molecules.
ConceptualDFT (ADF._ConceptualDFT) – Conceptual DFT Properties
ConstructPot (ADF._ConstructPot) – Reads a density from a TAPE41 file and constructs numerically the corresponding potential to it
CorePotentials (str | Sequence[str] | FreeBlock) – With the key COREPOTENTIALS you specify the core file and (optionally) which sections pertain to the distinct atom types in the molecule.
CurrentResponse (ADF._CurrentResponse) –
DIMPAR (str | Sequence[str] | FreeBlock) – In this block, the parameters for the DIM atoms are defined in DIM/QM calculations.
Dependency (ADF._Dependency) –
EPrint (ADF._EPrint) – Print switches that require more specification than just off or on
ESR (ADF._ESR) –
ETSNOCV (ADF._ETSNOCV) – Perform ETS-NOCV analysis.
ElectronTransfer (ADF._ElectronTransfer) – Block key for charge transfer integrals with FDE.
Excitations (ADF._Excitations) – Excitation energies: UV/Vis
ExcitedEDA (ADF._ExcitedEDA) – Options for excited energy decomposition (EDA).
ExcitedGO (ADF._ExcitedGO) – Excited state geometry optimization
ExcitonTransfer (ADF._ExcitonTransfer) – Block key for exciton transfer integrals with ROSE or FOCDFT.
Externals (str | Sequence[str] | FreeBlock) – Legacy support of the older DRF code.
FDE (ADF._FDE) – Frozen Density Embedding options
FDEFragments (str | Sequence[str] | FreeBlock) – Definitions of the FDE fragment types.
FOCDFT (ADF._FOCDFT) – Localize orbitals on fragments and constrain charge and spin polarization on fragments.
FragOccupations (str | Sequence[str] | FreeBlock) – Simulation of unrestricted fragments with the key FRAGOCCUPATIONS. Fragments need to be calculated spin-restricted. One can specify occupation numbers as if these fragments are calculated spin-unrestricted. The sum of spin-alpha and spin-beta occupations must, for each fragment orbital in each irrep separately, be equal to the total spin-restricted occupation of that orbital in the fragment.
Fragments (str | Sequence[str] | FreeBlock) – Definitions of the fragment type/files: {FragmentName FragmentFile}. In the block header one can specify the directory where the fragment files are located
GPU (ADF._GPU) – Set GPU options
GW (ADF._GW) – Perform a GW calculation. G0W0 is the default for GW%SelfConsistency.
IQA (ADF._IQA) – Total energy decomposition based on the interacting quantum atoms (IQA) approach and using QTAIM real-space partition.
Integration (ADF._Integration) – Options for the Voronoi numerical integration scheme
IrrepOccupations (str | Sequence[str] | FreeBlock) – Explicit occupation numbers per irrep
LinearScaling (ADF._LinearScaling) –
LocOrb (str | Sequence[str] | FreeBlock) – The computation of localized orbitals is controlled with this block-type key
MBPT (ADF._MBPT) – Technical aspects of the MP2 algorithm.
MDC (ADF._MDC) – Options for Multipole Derived Charges (MDC)
ModifyExcitation (ADF._ModifyExcitation) –
ModifyStartPotential (str | Sequence[str] | FreeBlock) – Modify the starting spin-dependent potential for unrestricted calculations.
Nanoparticle (ADF._Nanoparticle) – To include the presence of a nanoparticle near the system
PertLoc (ADF._PertLoc) – Perturbed localized molecular orbitals, correct to first order in an applied field, can be calculated in case of AORESPONSE. Can be used if the applied field changes the density in first order.
PolTDDFT (ADF._PolTDDFT) – POLTDDFT is a fast algorithm to solve the TDDFT equations in the space of the density fitting auxiliary basis set. The (real and imaginary part of the) diagonal of the polarizability tensor and rotatory strengths will be calculated, which can be used to calculate the photoabsorption and circular dichroism (CD) spectra.
QMFQ (ADF._QMFQ) – Block input key for QM/FQ(FMu).
QTAIM (ADF._QTAIM) – This block is used to request a topological analysis of the gradient field of the electron density, also known as the Bader’s analysis. If this block is specified without any sub-key, only local properties are calculated.
RIHartreeFock (ADF._RIHartreeFock) –
RISM (str | Sequence[str] | FreeBlock) – 3D-RISM-related input keys.
ROSE (ADF._ROSE) – Options for orbital localization
RadialCoreGrid (ADF._RadialCoreGrid) – For each atom the charge densities and the coulomb potentials of frozen core and valence electrons are computed in a radial grid. The radial grid consists of a sequence of r-values, defined by a smallest value, a constant multiplication factor to obtain each successive r-value, and the total number of points. Equivalently it can be characterized by the smallest r-value, the largest r-value, and the number of points; from these data the program computes then the constant multiplication factor.
Relativity (ADF._Relativity) – Options for relativistic effects.
RemoveFragOrbitals (str | Sequence[str] | FreeBlock) – Block key to remove selected virtual fragment orbitals.
Response (ADF._Response) – The calculation of frequency-dependent (hyper)polarizabilities and related properties (Raman, ORD)
Restart (ADF._Restart) – Options for restarts
SCF (ADF._SCF) – Control aspects of the Self Consistent Field procedure
SCRF (str | Sequence[str] | FreeBlock) – SCRF is no longer supported. Use AMS2023 or earlier.
SOPert (ADF._SOPert) – Key for perturbative inclusion of spin-orbit coupling.
SelectExcitation (ADF._SelectExcitation) –
SlaterDeterminants (str | Sequence[str] | FreeBlock) – The calculation of the one-determinant states based on the AOC reference state is controlled with this key.
Solvation (ADF._Solvation) –
SpinOrbitMagnetization (ADF._SpinOrbitMagnetization) – Starting artificial spin-orbit magnetization at first SCF cycle
SubExci (ADF._SubExci) – Subsystem TDDFT (FDE)
SubResponse (str | Sequence[str] | FreeBlock) – Untested and undocumented
Tails (ADF._Tails) – Obsolete option for linear scaling and distance effects. We recommend using the LinearScaling key instead.
VSCRF (str | Sequence[str] | FreeBlock) – VSCRF is no longer supported. Use AMS2023 or earlier.
XC (ADF._XC) – Definition of the XC.
XES (ADF._XES) – X-ray emission spectroscopy
ZlmFit (ADF._ZlmFit) – Options for the density fitting scheme ‘ZlmFit’.
- class _AOResponse[source]¶
If the block key AORESPONSE is used, by default, the polarizability is calculated. Note that if the molecule has symmetry the key ALLPOINTS should be included
- Variables:
2ANTISYM (BoolType | BoolKey) –
ALDA (BoolType | BoolKey) – Use ALDA only
Alpha (BoolType | BoolKey) – Calculate linear response
Beta (BoolType | BoolKey) – Will use 2n+1 rule to calculate beta.
CALCTRANSFORMPROP (str | StringKey) – Transformation Properties of Polarizabilities
CHANGESIGN (BoolType | BoolKey) –
Components (str | StringKey) – Limit the tensor components to the specified ones. Using this option may save the computation time. Options: XX, XY, XZ, YX, YY, YZ, ZX, ZY, ZZ
Cubic (BoolType | BoolKey) – Calculate cubic response
Damp (float | FloatKey) – Specify damping for non-acceleration iteration
DoNothing (BoolType | BoolKey) – Do nothing.
EFIOR (BoolType | BoolKey) –
EFISHG (BoolType | BoolKey) –
EFPLOT (BoolType | BoolKey) –
EOPE (BoolType | BoolKey) –
FitAODeriv (BoolType | BoolKey) – Use FITAODERIV for Coulomb potential
Frequencies (Iterable[float] | FloatListKey) – List of frequencies of incident light, the perturbing field, at which the time-dependent properties will be calculated.
GIAO (BoolType | BoolKey) – Use gauge-included atomic orbitals
Gamma (BoolType | BoolKey) – Will use 2n+1 rule to calculate gamma.
HirshPol (BoolType | BoolKey) – Hirshfeld Polarizability of fragments
IDRI (BoolType | BoolKey) –
LifeTime (float | FloatKey) – Specify the resonance peak width (damping) in Hartree units. Typically the lifetime of the excited states is approximated with a common phenomenological damping parameter. Values are best obtained by fitting absorption data for the molecule, however, the values do not vary a lot between similar molecules, so it is not hard to estimate values. A value of 0.004 Hartree was used in Ref. [266].
MagOptRot (BoolType | BoolKey) – Calculate magneto-optical rotation
MagneticPert (BoolType | BoolKey) – Use magnetic field as a perturbation
NBO (BoolType | BoolKey) – Perform NBO analysis
NoCore (BoolType | BoolKey) – if NOCORE is set we skip the core potential in diamagnetic term and/or in the unperturbed density of the CPKS solvers
OCCOCC (BoolType | BoolKey) – occ-occ block response (not GIAO) - Experimental
OKE (BoolType | BoolKey) –
ONLYANTISYM (BoolType | BoolKey) –
ONLYSYM (BoolType | BoolKey) –
OPTICALR (BoolType | BoolKey) –
OnlyPot (BoolType | BoolKey) – Calculation only potential for debugging purposes
OpticalRotation (BoolType | BoolKey) – Calculate optical rotation
PBE0LDA (BoolType | BoolKey) –
QuadBeta (BoolType | BoolKey) – Quadrupole operators with beta tensor
QuadPert (BoolType | BoolKey) – Calculate quadrupole-quadrupole polarizability
Quadratic (BoolType | BoolKey) – Calculate quadratic response
Quadrupole (BoolType | BoolKey) – Calculate dipole-quadrupole polarizability
REVPBE (BoolType | BoolKey) –
Raman (BoolType | BoolKey) –
SCF (str | StringKey) – Specify CPKS parameters such as the degree of convergence and the maximum number of iterations: NOCYC - disable self-consistence altogetherNOACCEL - disable convergence accelerationCONV - convergence criterion for CPKS. The default value is 10-6 . The value is relative to the uncoupled result (i.e. to the value without self-consistence).ITER - maximum number of CPKS iterations, 50 by default.Specifying ITER=0 has the same effect as specifying NOCYC.
SHG (BoolType | BoolKey) –
STATIC (BoolType | BoolKey) –
THG (BoolType | BoolKey) –
TPA (BoolType | BoolKey) –
Traceless (BoolType | BoolKey) – Traceless quadrupole tensors
VROA (BoolType | BoolKey) – Calculate Vibrational Raman Optical Activity.
VelocityOrd (BoolType | BoolKey) – Use VelocityOrd without GIAOs
XAlpha (BoolType | BoolKey) – Xalpha potential
EFG (ADF._AOResponse._EFG) – Perform a Mulliken type analysis of the EFG principal components, and an analysis in terms of canonical MOs.
- class _EFG[source]¶
Perform a Mulliken type analysis of the EFG principal components, and an analysis in terms of canonical MOs.
- Variables:
Atom (int | IntKey) – The number of the nucleus at which the EFG is to be analyzed (ADF input ordering).
Dump (BoolType | BoolKey) – Dump EFG data to file.
NBO (BoolType | BoolKey) – Perform an NBO/NLMO analysis of the EFG. Requires a series of calculations. See documentation.
Nuc (int | IntKey) – The number of the nucleus at which the EFG is to be analyzed (ADF internal atom ordering).
Thresh (float | FloatKey) – The threshold for printing the EFG-NBO contributions. The default is 0.05, which means that only orbitals with absolute value contribution larger than 5% of the total EFG are printed. To increase the number of contributions printed, specify a smaller threshold.
- class _AnalyticalFreq[source]¶
Define options for analytical frequencies.
- Variables:
B1Thresh (float | FloatKey) – MMGF_DENB1 and MMGF_GRADB1 cutoff values
Check_CPKS_From_Iteration (int | IntKey) – Solution of the CPKS equations is an iterative process, and convergence is achieved if the difference between U1 matrix of successive iterations falls below a certain threshold. This key can be used to determine at which iteration the checking should start taking place.
Debug (str | StringKey) – For debugging purposes. Options: fit, hessian, b1, densities, numbers, symmetry, all.
Hessian (Literal["reflect", "average"]) – Whether the final Hessian is obtained by reflecting or averaging?
Max_CPKS_Iterations (int | IntKey) – Calculating the analytical frequencies requires the solution of the Coupled Perturbed Kohn-Sham (CPKS) equations, which is an iterative process. If convergence is not achieved (a warning will be printed in the output if this is the case) then this subkey can be used to increase the number of iterations, although convergence is not guaranteed. The user required accuracy of the U1 matrix, as well as the ADF integration accuracy, can effect the rates of convergence.
Nuc (Iterable[int] | IntListKey) – By default, when calculating the frequencies analytically, the derivatives of the energy with respect to all nuclei are calculated. This gives a complete Hessian (second derivative) matrix, from which the vibrational frequencies of the molecule can be calculated. However, there may be certain cases where only derivatives with respect to a subset of all the nuclei are required. In this case it is a considerable saving in time if only a partial Hessian is calculated. With this subkey, a list of the nuclei for which the derivatives are required can be specified. However, the frequencies in this case are not the vibrational frequencies of the molecule, but may be used in guiding certain transition state searches
Print (str | StringKey) – Primarily for debugging purposes. Options: eigs, u1, parts. Choosing EIGS results in the print out of the MO eigenvectors, while U1 results in the print out of the U1 matrices. Except for small molecules this will result in a lot of data being output, and so they are not recommended. Choosing PARTS results in the print out of various sub-hessians that add up to give the final analytical hessian.
PrintNormalModeAnalysis (BoolType | BoolKey) – Request ADF to print analysis of the normal modes independently of AMS.
U1_Accuracy (float | FloatKey) – Solution of the CPKS equations is an iterative process, and convergence is achieved if the difference between U1 matrix of successive iterations falls below a certain threshold. This subkey can be used to set the threshold. The accuracy of the U1 will be 10**(-x). So, the higher the number the more accurate the U1 will be. While this parameter effects the accuracy of the frequencies, other factors also effect the accuracy of the frequencies, especially the ADF integration accuracy.
- class _Aromaticity[source]¶
Calculate aromaticity indicators, i.e. the matrix of localization/delocalization indices (LI-DI), Iring (ring index) and MCI (multi center index) aromaticity indices.
- Variables:
RingAtoms (Iterable[int] | IntListKey) – List of the atom numbers that form a ring. For each ring a separate line.
- class _Basis[source]¶
Definition of the basis set
- Variables:
Core (Literal["None", "Small", "Medium", "Large"]) –
Select the size of the frozen core you want to use.
Small and Large will be interpreted within the basis sets available (of the selected quality), and might refer to the same core in some cases.
If you specify ‘None’ you are guaranteed to have an all-electron basis set.
CreateOutput (BoolType | BoolKey) – If true, the output of the atomic create runs will be printed to standard output. If false, it will be saved to the file CreateAtoms.out in the AMS results folder.
FitType (Literal["Auto", "SZ", "DZ", "DZP", "TZP", "TZ2P", "QZ4P", "TZ2P+", "TZ2P-J", "QZ4P-J", "ZORA/SZ", "ZORA/DZ", "ZORA/DZP", "ZORA/TZP", "ZORA/TZ2P", "ZORA/QZ4P", "ZORA/TZ2P+", "ZORA/TZ2P-J", "ZORA/QZ4P-J", "ZORA/jcpl", "AUG/ASZ", "AUG/ADZ", "AUG/ADZP", "AUG/ATZP", "AUG/ATZ2P", "ET/ET-pVQZ", "ET/ET-QZ+5P", "ET/ET-QZ3P", "ET/ET-QZ3P-1DIFFUSE", "ET/ET-QZ3P-2DIFFUSE", "ET/ET-QZ3P-3DIFFUSE"]) –
Expert option.
Select the auxiliary fit to be used for STOfit or old Hartree-Fock RI scheme.
The fit set for a given atom is taken from the all-electron basis set file for the specified choice, for the same element as the atom.
By default (Auto) the fit set is taken from the original basis set file.
Path (str | StringKey) – The name of an alternative directory with basis sets to use. ADF looks for appropriate basis sets only within this directory. Default $AMSRESOURCES/ADF.
Type (Literal["SZ", "DZ", "DZP", "TZP", "TZ2P", "QZ4P", "TZ2P+", "TZ2P-J", "QZ4P-J", "mTZ2P", "ZORA/SZ", "ZORA/DZ", "ZORA/DZP", "ZORA/TZP", "ZORA/TZ2P", "ZORA/QZ4P", "ZORA/TZ2P+", "ZORA/TZ2P-J", "ZORA/QZ4P-J", "ZORA/mTZ2P", "ZORA/jcpl", "AUG/ASZ", "AUG/ADZ", "AUG/ADZP", "AUG/ATZP", "AUG/ATZ2P", "ET/ET-pVQZ", "ET/ET-QZ+5P", "ET/ET-QZ3P", "ET/ET-QZ3P-1DIFFUSE", "ET/ET-QZ3P-2DIFFUSE", "ET/ET-QZ3P-3DIFFUSE", "Corr/TZ3P", "Corr/QZ6P", "Corr/ATZ3P", "Corr/AQZ6P", "Corr/dATZ3P", "Corr/dAQZ6P", "POLTDDFT/DZ", "POLTDDFT/DZP", "POLTDDFT/TZP"]) –
Select the basis set to use.
SZ: Single Z DZ: Double Z DZP: Double Z, 1 polarization function TZP: Triple Z, 1 polarization function TZ2P: Triple Z, 2 polarization functions QZ4P: Quad Z, 4 pol functions, all-electron AUG: Augmented (extra diffuse functions) ET: Even tempered all electron basis sets J: Extra tight functions
These descriptions are meant to give an indication of the quality, but remember that ADF uses Slater type functions.
For standard calculations (energies, geometries, etc.) the relative quality is:
SZ < DZ < DZP < TZP < TZ2P < ET-pVQZ < QZ4P
The basis set chosen will apply to all atom types in your molecule. If no matching basis set is found, ADF will try to use a basis set of better quality.
For TDDFT applications and small negatively charged atoms or molecules, use basis sets with extra diffuse functions.
J: TZ2P-J, QZ4P-J: for use in ESR hyperfine or NMR spin-spin couplings.
Use the Basis panel to select a basis set per atom type, and to see what basis set actually will be used.
PerAtomType (ADF._Basis._PerAtomType) – Defines the basis set for all atoms of a particular type.
PerRegion (ADF._Basis._PerRegion) – Defines the basis set for all atoms in a region. If specified, this overwrites the values set with the Basis%Type and Basis%PerAtomType keywords for atoms in that region. Note that if this keyword is used multiple times, the chosen regions may not overlap.
- class _PerAtomType[source]¶
Defines the basis set for all atoms of a particular type.
- Variables:
Core (Literal["None", "Small", "Medium", "Large"]) – Size of the frozen core.
File (str | Path | StringKey) – The path of the basis set file (the path can either absolute or relative to $AMSRESOURCES/ADF). Note that one should include ZORA in the path for relativistic calculations, for example ‘ZORA/QZ4P/Au’. Specifying the path to the basis file explicitly overrides the automatic basis file selection via the Type and Core subkeys.
Symbol (str | StringKey) – The symbol for which to define the basis set.
Type (Literal["SZ", "DZ", "DZP", "TZP", "TZ2P", "QZ4P", "TZ2P+", "TZ2P-J", "QZ4P-J", "mTZ2P", "ZORA/SZ", "ZORA/DZ", "ZORA/DZP", "ZORA/TZP", "ZORA/TZ2P", "ZORA/QZ4P", "ZORA/TZ2P+", "ZORA/TZ2P-J", "ZORA/QZ4P-J", "ZORA/mTZ2P", "ZORA/jcpl", "AUG/ASZ", "AUG/ADZ", "AUG/ADZP", "AUG/ATZP", "AUG/ATZ2P", "ET/ET-pVQZ", "ET/ET-QZ+5P", "ET/ET-QZ3P", "ET/ET-QZ3P-1DIFFUSE", "ET/ET-QZ3P-2DIFFUSE", "ET/ET-QZ3P-3DIFFUSE", "Corr/TZ3P", "Corr/QZ6P", "Corr/ATZ3P", "Corr/AQZ6P", "Corr/dATZ3P", "Corr/dAQZ6P", "POLTDDFT/DZ", "POLTDDFT/DZP", "POLTDDFT/TZP"]) – The basis sets to be used.
- class _PerRegion[source]¶
Defines the basis set for all atoms in a region. If specified, this overwrites the values set with the Basis%Type and Basis%PerAtomType keywords for atoms in that region. Note that if this keyword is used multiple times, the chosen regions may not overlap.
- Variables:
Core (Literal["None", "Small", "Medium", "Large"]) – Size of the frozen core.
File (str | Path | StringKey) – The path of the basis set file (the path can either absolute or relative to $AMSRESOURCES/ADF). Note that one should include ZORA in the path for relativistic calculations, for example ‘ZORA/QZ4P/Au’. Specifying the path to the basis file explicitly overrides the automatic basis file selection via the Type and Core subkeys.
Region (str | StringKey) – The identifier of the region for which to define the basis set. Note that this may also be a region expression, e.g. ‘myregion+myotherregion’ (the union of two regions).
Type (Literal["SZ", "DZ", "DZP", "TZP", "TZ2P", "QZ4P", "TZ2P+", "TZ2P-J", "QZ4P-J", "mTZ2P", "ZORA/SZ", "ZORA/DZ", "ZORA/DZP", "ZORA/TZP", "ZORA/TZ2P", "ZORA/QZ4P", "ZORA/TZ2P+", "ZORA/TZ2P-J", "ZORA/QZ4P-J", "ZORA/mTZ2P", "ZORA/jcpl", "AUG/ASZ", "AUG/ADZ", "AUG/ADZP", "AUG/ATZP", "AUG/ATZ2P", "ET/ET-pVQZ", "ET/ET-QZ+5P", "ET/ET-QZ3P", "ET/ET-QZ3P-1DIFFUSE", "ET/ET-QZ3P-2DIFFUSE", "ET/ET-QZ3P-3DIFFUSE", "Corr/TZ3P", "Corr/QZ6P", "Corr/ATZ3P", "Corr/AQZ6P", "Corr/dATZ3P", "Corr/dAQZ6P", "POLTDDFT/DZ", "POLTDDFT/DZP", "POLTDDFT/TZP"]) – The basis sets to be used.
- class _BeckeGrid[source]¶
Options for the numerical integration grid.
- Variables:
AllowAngularBoost (BoolType | BoolKey) – Allow automatic augmentation of the Lebedev spherical grid for highly coordinated atoms.
InnerShellsPruning (BoolType | BoolKey) – Allow automatic pruning of the Lebedev spherical grid for shells close to the nuclei.
PartitionFunPruning (BoolType | BoolKey) – Allow pruning of integration points based on the value of the partition function.
QPNear (float | FloatKey) – Only relevant if you have specified point charges in the input file. ADF generates grids only about those point charges that are close to any real atoms. The criterion, input with the qpnear subkey, is the closest distance between the point charge at hand and any real atom.
Quality (Literal["Auto", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Quality of the integration grid. For a description of the various qualities and the associated numerical accuracy see reference. If ‘Auto’, the quality defined in the ‘NumericalQuality’ will be used.
RadialGridBoost (float | FloatKey) – The number of radial grid points will be boosted by this factor. Some XC functionals require very accurate radial integration grids, so ADF will automatically boost the radial grid by a factor 3 for the following numerically sensitive functionals: LibXC M05, LibXC M05-2X, LibXC M06-2X, LibXC M06-HF, LibXC M06-L, LibXC M08-HX, LibXC M08-SO, LibXC M11-L, LibXC MS0, LibXC MS1, LibXC MS2, LibXC MS2H, LibXC MVS, LibXC MVSH, LibXC N12, LibXC N12-SX, LibXC SOGGA11, LibXC SOGGA11-X, LibXC TH1, LibXC TH2, LibXC WB97, LibXC WB97X, MetaGGA M06L, MetaHybrid M06-2X, MetaHybrid M06-HF, MetaGGA MVS.
QualityPerRegion (ADF._BeckeGrid._QualityPerRegion) – Sets the grid quality for all atoms in a region. If specified, this overwrites the globally set quality.
- class _BondOrders[source]¶
Options for the calculation of bond orders. Note: the calculation of bond orders should be requested via the Properties%BondOrders input option in the AMS driver input.
- Variables:
Calculate (BoolType | BoolKey) – Whether or not the bond orders should be calculated. This is for internal use/debug purposes, except for multi-atomic fragments. In case of atomic fragments one should request the bond orders at the AMS driver level via the Properties%BondOrders input option. For multi-atomic fragments, however, one should not request the bond orders at the AMS driver level, but instead use this key.
PrintAll (BoolType | BoolKey) – If ‘Yes’, all five types of bond orders (i.e. Nalewajski-Mrozek-1,2 & 3, Mayer and Gopinathan-Jug) will be printed to the output. Otherwise only the Nalewajski-Mrozek-3 and the type requested in BondOrders%TypeForAMS will be printed.
PrintTolerance (float | FloatKey) – Only bond orders larger than this threshold will be printed in the output (this treshold applies only to the printing in the ‘BOND-ORDER ANALYSIS’ section of the ADF output.
TypeForAMS (Literal["Nalewajski-Mrozek-1", "Nalewajski-Mrozek-2", "Nalewajski-Mrozek-3", "Mayer", "Gopinathan-Jug"]) –
The type of bond order that will be saved, printed and used by AMS.
Nalewajski-Mrozek-1,2: bond orders calculated from two-electron valence indices based on partitioning of tr(Delta_P^2) using 3-index set or 4-index set respectively. Nalewajski-Mrozek-3: bond-orders calculated from valence indices based on partitioning of tr(P*Delta_P). Inter-atomic bond orders are not defined with non-atomic fragments.
- class _CDFT[source]¶
CDFT is a tool for carrying out DFT calculations in the presence of a constraint.
- Variables:
AllAtoms (BoolType | BoolKey) – If AllAtoms is true, then TheAtoms is overridden and all the atoms in the active fragment are included in the set.
AnalyticalHessian (int | IntKey) – This will calculate the analytical derivative of the energy w.r.t. the Lagrange multiplier up to the specified SCF iteration. This key is not recommended due to the high computational cost that comes with it. The calculation is equivalent to a ground state Hessian, and it is carried out with the full sum-over-states formula.
ChargeAndSpin (BoolType | BoolKey) – will constrain both the charge and the spin
Constraints (Iterable[float] | FloatListKey) – The values of the constraints. If CHARGEANDSPIN, constraints to the alpha and beta electrons need to be specified sequentially. One more electron => CONSTRAINTS -1.0. One less electron => CONSTRAINTS 1.0. If the CDFT type is EXCITEDCDFT, CONSTRAINTS=1.0 is recommended. Other values are technically possible but have not been tested yet.
DoNotOptimize (BoolType | BoolKey) – If true, the multipliers chosen in INITIALMULTIPLIERS will not be optimized and will be constant throughout the entire SCF procedure.
ExcitedCDFT (BoolType | BoolKey) – will generate an excited state with CONSTRAINTS number of ALPHA electrons constrained to occupy the virtual space of a ground state reference calculation. This is the essence of the eXcited Constrained DFT (XCDFT) method(P. Ramos, M. Pavanello, Low-lying excited states by constrained DFT, Journal of Chemical Physics 148, 144103 (2018) https://doi.org/10.1063/1.5018615) for the calculation of low-lying single excitations. XCDFT is found to correctly reproduce the energy surface topology at conical intersections between the ground state and the first singly excited state and can also accounts for the condensed phase effects in solvated chromophores where typical Delta SCF methods variationally collapse.
InitialMultipliers (Iterable[float] | FloatListKey) – If available, a guess for the Lagrange multipliers can be entered.
MaxIter (int | IntKey) – Maximum number of CDFT iterations. CDFT carries out a loop nested inside the SCF cycle.
Metric (BoolType | BoolKey) – Relevant for XCDFT. In the XCDFT method orthogonality is not imposed between the KS-orbitals of ground and excited states. If METRIC is specified, the degree of mixing of the single excited state with the ground state or high-order excitations is calculated. Three parameters are calculated: p, m and d. The parameters p and m will give information about the amount of mixing with the ground state, while parameter d will determine the mixing with high order excitations. Additional information about the origin of these parameters can be found in the literature (P. Ramos, M. Pavanello, Low-lying excited states by constrained DFT, Journal of Chemical Physics 148, 144103 (2018) https://doi.org/10.1063/1.5018615)
NAtomsPerSet (Iterable[int] | IntListKey) – The number of atoms in each moiety (set).
NConstraints (int | IntKey) – This specifies the number of sets of atoms to be considered. For example, if the user wishes to constrain a positive charge on one part of the system, and a negative charge on another part, NCONSTRAINTS should be set to two. There is no limit on the number of constraints. However, SCF convergence becomes an issue with more than 2 constraints. Note: NCONSTRAINTS>1 is untested.
OnlyCharge (BoolType | BoolKey) – Will constrain only the charge, letting spin relax (and potentially delocalize)
OnlySpin (BoolType | BoolKey) – Will constrain only the spin
PopType (Literal["yukawalike", "fuzzyvoronoibecke", "fuzzyvoronoifermi"]) – The population analysis chosen for determining the constraint.
Print (Literal["low", "medium", "high"]) – Print level and debugging.
SelfConsistent (BoolType | BoolKey) – Self-Consistent CDFT
StepSize (float | FloatKey) – The amount of the Lagrange multipliers step taken in each CDFT iteration
TheAtoms (Iterable[int] | IntListKey) – The atom numbers of the moieties in the input geometry order. If NCONSTRAINTS is larger than 1, the sets of atoms are entered as a single list.
Threshold (float | FloatKey) – The threshold for convergence of the CDFT constraints. The tighter the SCF convergence criteria, the tighter the THRESHOLD should be.
- class _CVNDFT[source]¶
The CVNDFT block key regulates the execution of the CV(n)-DFT code, which calculates the singlet or triplet electronic excitations for the closed shell molecules.
- Variables:
Tolerance (float | FloatKey) – The convergence criterion, i.e. the SCF-CV(infinity)-DFT procedure stops when the given accuracy is achieved.
CV_DFT (ADF._CVNDFT._CV_DFT) – The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
DSCF_CV_DFT (ADF._CVNDFT._DSCF_CV_DFT) – The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
RSCF_CV_DFT (ADF._CVNDFT._RSCF_CV_DFT) – The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
R_CV_DFT (ADF._CVNDFT._R_CV_DFT) – The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
SCF_CV_DFT (ADF._CVNDFT._SCF_CV_DFT) – The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
- class _CV_DFT[source]¶
The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
- Variables:
InitGuess (Literal["TDDFT", "SOR"]) – Initial guess
- class _DSCF_CV_DFT[source]¶
The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
- Variables:
DampOrbRelax (float | FloatKey) – The mix_relax parameter defines the relative weight of the new relaxation vector that is added to the one from the previous iteration.
DampVariable (BoolType | BoolKey) – Damping condition
InitGuess (Literal["TDDFT", "SOR"]) – Initial guess
Optimize (Literal["SVD", "SOR", "COL"]) – Gradient optimization method
RelaxAlpha (int | IntKey) – The SCF cycle number at which the relaxation of alpha orbitals starts.
RelaxBeta (int | IntKey) – The SCF cycle number at which the relaxation of beta orbitals starts.
- class _RSCF_CV_DFT[source]¶
The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
- Variables:
DampOrbRelax (float | FloatKey) – The mix_relax parameter defines the relative weight of the new relaxation vector that is added to the one from the previous iteration.
DampVariable (BoolType | BoolKey) – Damping condition
InitGuess (Literal["TDDFT", "SOR"]) – Initial guess
RelaxAlpha (int | IntKey) – The SCF cycle number at which the relaxation of alpha orbitals starts.
RelaxBeta (int | IntKey) – The SCF cycle number at which the relaxation of beta orbitals starts.
- class _R_CV_DFT[source]¶
The simplest case: the TDDFT transition density U-vector is substituted into the infinite order CV(infinity)-DFT excitation energy
- Variables:
DampOrbRelax (float | FloatKey) – The mix_relax parameter defines the relative weight of the new relaxation vector that is added to the one from the previous iteration.
DampVariable (BoolType | BoolKey) – Damping condition
InitGuess (Literal["TDDFT", "SOR"]) – Initial guess
RelaxAlpha (int | IntKey) – The SCF cycle number at which the relaxation of alpha orbitals starts.
RelaxBeta (int | IntKey) – The SCF cycle number at which the relaxation of beta orbitals starts.
- class _ConceptualDFT[source]¶
Conceptual DFT Properties
- Variables:
AnalysisLevel (Literal["Normal", "Extended", "Full"]) –
Set the level of the ConceptualDFT analysis:
Normal - global descriptors only,
Extended - both global and condensed (QTAIM) local descriptors,
Full - all descriptors including non local ones.
AtomsToDo (Iterable[int] | IntListKey) – Define a subset of atoms for which properties are calculated. If the [Domains] block is present then this list specifies which atoms are used to define the domains bounding box.
Electronegativity (BoolType | BoolKey) – Calculate atomic electronegativities. Requires an all-electron calculation (no frozen core), triggers the TotalEnergy and increases the [AnalysisLevel] to at least Extended.
Enabled (BoolType | BoolKey) – Calculate Conceptual DFT properties.
Domains (ADF._ConceptualDFT._Domains) – Calculate integrated properties for the domains (same sign) of the dual descriptor.
- class _Domains[source]¶
Calculate integrated properties for the domains (same sign) of the dual descriptor.
- Variables:
Border (float | FloatKey) – Set the extent of the Cartesian grid. Extent is the distance between a face of the grid’s bounding box and the most outlying atom in the corresponding direction. If the [AtomsToDo] key is present, the bounding box is created around the specified atoms.
Display (float | FloatKey) – Domains for which the integrated DD value is smaller (in magnitude) than the specified value are omitted from the printed output.
Enabled (BoolType | BoolKey) – Calculate properties of reactivity domains.
Ensemble (Literal["Canonical", "GrandCanonical"]) – Statistical ensemble for DD domains. Canonical: DD values are calculated using the statistical canonical ensemble. GrandCanonical: DD values are calculated using the statistical grand canonical ensemble. The grand canonical DD corresponds to (S^2 f(2) - (gamma/eta^3) f^0), where f(2) is the canonical DD, gamma and eta - the hyper-hardness and hardness of the chemical system, respectively, and f^0 is the mean Fukui function. This statistical ensemble is a natural choice when comparing two chemical systems with a different number of electrons.
Radius (float | FloatKey) – This option adds a sphere around each nucleus, excluding all points inside it. This can help to separate domains around an atom or to exclude core electrons. Be careful when using this option. In particular, the radius of the sphere should exceed two or three times the [Spacing] value to be effective. By default, no spheres are added.
Spacing (float | FloatKey) – Specifies spacing (distance between neighboring points) of the rectangular Cartesian grid used when searching for DD domains. It may be useful to specify a smaller value (or increase the size of the grid, see [Border] key) if a substantial part of the electronic density is accounted for.
Threshold (float | FloatKey) – Arbitrary value of dual descriptor used to separate DD domains (values below this threshold are ignored).
- class _ConstructPot[source]¶
Reads a density from a TAPE41 file and constructs numerically the corresponding potential to it
- class _CorePotentials[source]¶
With the key COREPOTENTIALS you specify the core file and (optionally) which sections pertain to the distinct atom types in the molecule.
- class _CurrentResponse[source]¶
- class _DIMPAR[source]¶
In this block, the parameters for the DIM atoms are defined in DIM/QM calculations.
- class _Dependency[source]¶
- Variables:
Enabled (BoolType | BoolKey) – Used to make the basis or fit set linearly independent, up to the threshold specified below. This is typically important when you have many diffuse functions in your basis or fit set.
A criterion applied to the overlap matrix of unoccupied normalized SFOs. Eigenvectors corresponding to smaller eigenvalues are eliminated from the valence space.
Note: if you choose a very coarse value, you will remove too many degrees of freedom in the basis set, while if you choose it too strict, the numerical problems may not be countered adequately.
Merely a technical parameter. When the DEPENDENCY key is activated, any rejected basis functions (i.e.: linear combinations that correspond with small eigenvalues in the virtual SFOs overlap matrix) are normally processed until diagonalization of the Fock matrix takes place. At that point, all matrix elements corresponding to rejected functions are set to zero (off-diagonal) and BigEig (diagonal).
In AMSinput you must check the Fix Linear dependency check box for this option to be used.
Similar to Dependency%bas.
The criterion is now applied to the overlap matrix of fit functions.
The fit coefficients, which give the approximate expansion of the charge density in terms of the fit functions (for the evaluation of the coulomb potential) are set to zero for fit functions (i.e.: combinations of) corresponding to small-eigenvalue eigenvectors of the fit overlap matrix.
- class _EPrint[source]¶
Print switches that require more specification than just off or on
- Variables:
AtomPop (str | StringKey) – Mulliken population analysis on a per-atom basis
BASPop (str | StringKey) – Mulliken population analysis on a per-bas-function basis
Frag (str | StringKey) – Building of the molecule from fragments
FragPop (str | StringKey) – Mulliken population analysis on a per fragment basis
Freq (str | StringKey) – Intermediate results in the computation of frequencies (see debug: freq).
GeoStep (str | StringKey) – Geometry updates (Optimization, Transition State, …)
OrbPopEr (str | StringKey) – Energy Range (ER) in hartree units for the OrbPop subkey
Repeat (str | StringKey) – Repetition of output in Geometry iterations (SCF, optimization, …)
SFO (str | StringKey) – Information related to the Symmetrized Fragment Orbitals and the analysis
OrbPop (str | Sequence[str] | FreeBlock) – (Mulliken type) population analysis for individual MOs
- class _ESR[source]¶
- Variables:
AnaPol (BoolType | BoolKey) – Expert option for ESR.
Enabled (BoolType | BoolKey) – Calculate ESR (g- and/or A tensors)
GaugeOrigin (Iterable[float] | FloatListKey) – Can be used in ESR to set gauge origin.
NoESRfcsd (BoolType | BoolKey) – Debug option in ESR.
NoESRpso (BoolType | BoolKey) – Debug option in ESR.
PARANMR (BoolType | BoolKey) – Paramagnetic part NMR shielding.
nogiao (BoolType | BoolKey) – Debug option for ESR g-tensor
- class _ETSNOCV[source]¶
Perform ETS-NOCV analysis.
- Variables:
DEBUGTV (BoolType | BoolKey) – For T/V debugging
EKMin (float | FloatKey) – The threshold for orbital interaction energy contributions corresponding to deformation density components originating from each NOCV-pairs
ENOCV (float | FloatKey) – The threshold for NOCV-eigenvalues
Enabled (BoolType | BoolKey) – Perform ETS-NOCV analysis.
RhoKMin (float | FloatKey) – The threshold for population analysis of each deformation density contribution in terms of individual SFOs.
TVanalysis (BoolType | BoolKey) – Perform T/V decomposition
- class _Excitations[source]¶
Excitation energies: UV/Vis
- Variables:
AAS (BoolType | BoolKey) – Use the molecular orbitals from a DFT ground state calculation as input to an excited state calculation with TDDFT-aas coupling matrices
AASALPHA (float | FloatKey) – optimal alpha value for TDDFT-aas method
ALLXASMOMENTS (BoolType | BoolKey) – To be used in combination with XAS. This will print out all the individual transition moments used within the calculation of the total oscillator strength
ALLXASQUADRUPOLE (BoolType | BoolKey) – To be used in combination with XAS.This will print out the individual oscillator strength components to the total oscillator strength.
Allowed (BoolType | BoolKey) – Treat only those irreducible representations for which the oscillator strengths will be nonzero (as opposed to all)
AlsoRestricted (BoolType | BoolKey) – Include also excitation energies in which a spin-restricted exchange-correlation kernel is used
Analytical (BoolType | BoolKey) – The required integrals for the CD spectrum are calculated analytically, instead of numerically. Only used in case of CD spectrum
BSE (BoolType | BoolKey) – Solve the static Bethe-Salpeter equation based on a GW calculation
BSEscreening (BoolType | BoolKey) – Solve the static Bethe-Salpeter equation based on a GW-BSE calculation, i.e. the screening entering the excitation calculation is calculated at the BSE level of theory instead of the RPA.
CDSpectrum (BoolType | BoolKey) – Compute the rotatory strengths for the calculated excitations, in order to simulate Circular Dichroism (CD) spectra
DBSE (BoolType | BoolKey) – Solve the dynamic Bethe-Salpeter equation based on a GW calculation in the diagonal approximation for the GW kernel
Descriptors (BoolType | BoolKey) – Compute charge-transfer descriptors and SFO analysis
Descriptors_CT_AT_Rab (float | FloatKey) – Atomic distance criterion used for the calculation of CT_AT descriptors
ESESTDM (BoolType | BoolKey) – Compute transition dipole moments between excited states
FullKernel (BoolType | BoolKey) – Use the non-ALDA kernel (with XCFUN)
HDA (BoolType | BoolKey) –
Activate the diagonal HF exchange approximation.
This is only relevant if a (meta-)hybrid is used in the SCF.
HDA_CutOff (float | FloatKey) – This is cutoff based on differences in energy between eps_virt-eps_occ, to reduce number of diagonal HF exchange integrals.
Iterations (int | IntKey) – The maximum number of attempts within which the Davidson algorithm has to converge
KFWrite (int | IntKey) – If kfwrite is 0 then do not write contributions, transition densities, and restart vectors to TAPE21, since this can lead to a huge TAPE21, especially if many excitations are calculated. 3 means that contributions, transition densities, and restart vectors are written to TAPE21.
Lowest (Iterable[int] | IntListKey) – Number of lowest excitations to compute
MAXPRINTED (int | IntKey) – The maximum number of printed contributions
NTO (BoolType | BoolKey) – Compute the Natural Transition Orbitals
N_HDA_integral (int | IntKey) – Maximum number of HDA integrals
Nospinsocd (BoolType | BoolKey) – Turn off calculation of spin operator matrices in spin-orbit relativistic CD spectrum calculations
OnlySing (BoolType | BoolKey) – Compute only singlet-singlet excitations
OnlyTrip (BoolType | BoolKey) – Compute only singlet-triplet excitations
Orthonormality (float | FloatKey) – The Davidson algorithm orthonormalizes its trial vectors. Increasing the default orthonormality criterion increases the CPU time somewhat, but is another useful check on the reliability of the results.
SDKernelType (Literal["Collinear", "NonCollinear", "QuasiNonCollinear"]) – Choose specific kernel approximation in case of ROKS-SD-TDA or ROKS-SD-CIS.
SFOAnalysis (BoolType | BoolKey) – Do SFO analysis
STDA (BoolType | BoolKey) – Simplified Tamm-Dancoff approach
STDDFT (BoolType | BoolKey) – Simplified time-dependent DFT
ScaleCoul (float | FloatKey) – Scaling of Coulomb kernel with scale parameter
ScaleHF (float | FloatKey) – Scaling of the HF part of the kernel with scale parameter
ScaleXC (float | FloatKey) – Scaling of the XC-kernel (excluding a possible HF-part) with scale parameter
Select (str | StringKey) – Rather than selecting the first nmcdterm transitions for consideration individual transitions can be selected through the SELECT keyword
SingleOrbTrans (BoolType | BoolKey) – keyword to use only orbital energy differences
TD-DFTB (BoolType | BoolKey) – Use the molecular orbitals from a DFT ground state calculation as input to an excited state calculation with TD-DFTB coupling matrices
TDA-DFTB (BoolType | BoolKey) – Use the molecular orbitals from a DFT ground state calculation as input to an excited state calculation with TDA-DFTB coupling matrices
THRESHPRINTED (float | FloatKey) – Loop until 100 x THRESHPRINTED percent of the transition is found or MAXPRINTED contributions are printed
Vectors (int | IntKey) – The maximum number of trial vectors in the Davidson algorithm for which space is allocated. If this number is small less memory will be needed, but the trial vector space is smaller and has to be collapsed more often, at the expense of CPU time. The default if usually adequate.
Velocity (BoolType | BoolKey) – Calculates the dipole-velocity representation of the oscillator strength. If applicable, the dipole-velocity representation of the rotatory strength is calculated. Default the dipole-length representation of the oscillator strength and rotatory strength is calculated
XAS (BoolType | BoolKey) – Calculation of the higher order multipole moment integrals and the calculation of the quadrupole oscillator strengths. This will only print the total oscillator strength and the excitation energy.
Davidson (str | Sequence[str] | FreeBlock) – Use the Davidson procedure
Exact (str | Sequence[str] | FreeBlock) – The most straightforward procedure is a direct diagonalization of the matrix from which the excitation energies and oscillator strengths are obtained. Since the matrix may become very large, this option is possible only for very small molecules
RoksTddftType (ADF._Excitations._RoksTddftType) – Excitation energies from RoksTddft: UV/Vis
- class _Exact[source]¶
The most straightforward procedure is a direct diagonalization of the matrix from which the excitation energies and oscillator strengths are obtained. Since the matrix may become very large, this option is possible only for very small molecules
- class _RoksTddftType[source]¶
Excitation energies from RoksTddft: UV/Vis
- Variables:
Calculate (Literal["None", "SD", "SS", "SU", "SD-SS", "SS-SU", "SD-SS-SU"]) – Specifies the types of RoksTddft methods to target several target spins: spin-down (SD), same-spin (SS), and/or spin-up (SU).
SDType (Literal["None", "SD-TDA", "SD-CIS", "QSD-TDA"]) – Specifies the flavor to be used in the case of SD-type RoksTddft
SSType (Literal["None", "R-TDA", "S-TDA", "X-TDA"]) – Specifies the flavor to be used in the case of SS-type RoksTddft
SUType (Literal["None", "SF-TDA"]) – Specifies the flavor to be used in the case of SF-type RoksTddft
- class _ExcitedEDA[source]¶
Options for excited energy decomposition (EDA).
- Variables:
Calc (Literal["None", "Electrostatic", "Pauli", "All"]) –
None: No calculation of parts of excited EDA.
Electrostatic: calculate electrostatic part EDA excited state.
Pauli: calculate Pauli repulsion part of excited state.
ElectrostaticFile (str | StringKey) – Path to adf.rkf file from which ADF reads electrostatic part excited EDA.
PauliFile (str | StringKey) – Path to adf.rkf file from which ADF reads Pauli repulsion part excited EDA.
- class _ExcitedGO[source]¶
Excited state geometry optimization
- Variables:
ALLGRADIENTS (BoolType | BoolKey) –
EigenFollow (BoolType | BoolKey) – This key tries to follow the eigenvector in excited state geometry optimizations
Output (int | IntKey) – The amount of output printed. A higher value requests more detailed output
Singlet (BoolType | BoolKey) – Singlet-singlet excitation is considered
State (str | StringKey) – Choose the excitation for which the gradient is to be evaluated: ‘State Irreplab nstate’. ‘Irreplab’ is the label from the TDDFT calculation. NOTE: the TDDFT module uses a different notation for some representation names, for example, A’ is used instead of AA. ‘nstate’: this value indicates that the nstate-th transition of symmetry Irreplab is to be evaluated. Default is the first fully symmetric transition.
Triplet (BoolType | BoolKey) – Singlet-triplet excitation is considered
CPKS (ADF._ExcitedGO._CPKS) – Some control parameters for the CPKS(Z-vector) part of the TDDFT gradients calculation
- class _CPKS[source]¶
Some control parameters for the CPKS(Z-vector) part of the TDDFT gradients calculation
- Variables:
Eps (float | FloatKey) – Convergence requirement of the CPKS
IterOut (int | IntKey) – Details of the CPKS calculation are printed every iter iterations
NoPreConiter (int | IntKey) – maximum number of iterations allowed for the unpreconditioned solver.
PreConiter (int | IntKey) – maximum number of iterations allowed for the preconditioned solver
- class _ExcitonTransfer[source]¶
Block key for exciton transfer integrals with ROSE or FOCDFT.
- Variables:
CoupleFinalStates (BoolType | BoolKey) – Calculate delocalized excited states in the basis of the localized excited states that are calculated, thus couple the localized excited states.
Debug (BoolType | BoolKey) – Print extra output for debug purposes
FullRun (BoolType | BoolKey) – Include run without restriction of localization of occupied and/or virtual orbitals.
LocalCouplingsOnly (BoolType | BoolKey) – Only account for couplings between local diabatic states
Localize (Literal["OccupiedOnly", "OccupiedAndVirtual"]) – Localize OccupiedAndVirtual means that separately purely localized excitations and purely charge-transfer excitations are calculated. Localize OccupiedOnly means that an excitation may have local and charge-transfer character, but the excitation only has contributions from occupied orbitals on one fragment. Only relevant in case block key FOCDFT is used or ROSE orbitals are used.
Lowest (Iterable[int] | IntListKey) – Number of lowest excitations to compute for each fragment. These are purely local excitations if the Localize OccupiedAndVirtual key is specified.
LowestCT (Iterable[int] | IntListKey) – Number of lowest charge-transfer excitations to compute for each fragment. Only relevant if the Localize OccupiedAndVirtual key is also specified.
Output (Literal["AllCouplings", "FilteredCouplings", "AllAndFilteredCouplings"]) – Amount of output
SecondOrder (BoolType | BoolKey) – Include 2nd-order correction to electronic couplings
UseFragments (Iterable[int] | IntListKey) – In case of Rose or FOCDFT only, one can specify the fragment numbers of 2 fragments. Then calculate only excitations from occupied orbitals on fragment one to virtual orbitals on fragment two. If not specified calculate all possible excitations.
FilteredCouplings (ADF._ExcitonTransfer._FilteredCouplings) – Details on filter used for electronic couplings in the output
- class _FilteredCouplings[source]¶
Details on filter used for electronic couplings in the output
- Variables:
MaxEnergy (float | FloatKey) – Max. energy (in eV) of diabatic states
MaxEnergyDiff (float | FloatKey) – Max. energy difference (in eV) between diabatic states
MinCoupling (float | FloatKey) – Min. coupling value (in meV) that is printed
MinEnergy (float | FloatKey) – Min. energy (in eV) of diabatic states
- class _FDE[source]¶
Frozen Density Embedding options
- Variables:
AMOLFDE (BoolType | BoolKey) – placeholder
CAPPOTBASIS (BoolType | BoolKey) – placeholder
CAPPOTLINESEARCH (BoolType | BoolKey) – placeholder
CJCORR (float | FloatKey) – Option to switch on a long-distance correction
Coulomb (BoolType | BoolKey) – Neglecting completely vt[rhoA,rhoB] (vt[rhoA,rhoB] equals zero) together with the exchange-correlation component of the embedding potential introduced by Wesolowski and Warshel.
Dipole (BoolType | BoolKey) – placeholder
E00 (BoolType | BoolKey) – placeholder
ENERGY (BoolType | BoolKey) – placeholder
EXTERNALORTHO (float | FloatKey) – Used to specify the use of external orthogonality (EO) in the FDE block
EXTPRINTENERGY (BoolType | BoolKey) – placeholder
FULLGRID (BoolType | BoolKey) – placeholder
FreezeAndThawCycles (int | IntKey) – This keyword duplicates RelaxCycles
FreezeAndThawPostSCF (BoolType | BoolKey) – This keyword duplicates RelaxPostSCF
GGA97 (BoolType | BoolKey) – placeholder
GGAPotCFD (str | StringKey) – The correlation approximant is used in the construction of the embedding potential. The same correlation approximants as in the XC key are available.
GGAPotXFD (str | StringKey) – The exchange approximant is used in the construction of the embedding potential. The same exchange approximants as in the XC key are available.
LLP91 (BoolType | BoolKey) – placeholder
LLP91S (BoolType | BoolKey) – placeholder
NOCAPSEPCONV (BoolType | BoolKey) – placeholder
NOFDKERN (BoolType | BoolKey) – placeholder
OL91A (BoolType | BoolKey) – placeholder
OL91B (BoolType | BoolKey) – placeholder
ONEGRID (BoolType | BoolKey) – placeholder
P92 (BoolType | BoolKey) – placeholder
PBE2 (BoolType | BoolKey) – placeholder
PBE3 (BoolType | BoolKey) – placeholder
PBE4 (BoolType | BoolKey) – placeholder
PDFT (BoolType | BoolKey) – placeholder
PRINTEACHCYCLE (BoolType | BoolKey) – placeholder
PRINTRHO2 (BoolType | BoolKey) – placeholder
PW86K (BoolType | BoolKey) – placeholder
PW91K (BoolType | BoolKey) – placeholder
PW91Kscaled (BoolType | BoolKey) – placeholder
RHO1FITTED (BoolType | BoolKey) – placeholder
RelaxCycles (int | IntKey) – This gives the maximum number of freeze-and-thaw cycles that are performed for this fragment. If the maximum number given in the FDE block is smaller, or if convergence is reached earlier, then fewer cycles are performed.
RelaxPostSCF (BoolType | BoolKey) – this option is included, several post-SCF properties will be calculated after each freeze-and-thaw cycle. These are otherwise only calculated in the last cycle.
SDFTEnergy (BoolType | BoolKey) – placeholder
SHORTPRINTENERGY (BoolType | BoolKey) – placeholder
TF9W (BoolType | BoolKey) – placeholder
THAKKAR92 (BoolType | BoolKey) – placeholder
THOMASFERMI (BoolType | BoolKey) – Local-density-approximation form of vt[rhoA,rhoB] derived from Thomas-Fermi expression for Ts[rho]
TW02 (BoolType | BoolKey) – placeholder
WEIZ (BoolType | BoolKey) – placeholder
XCFun (BoolType | BoolKey) – Use XCFUN for nonadditive functionals
- class _FOCDFT[source]¶
Localize orbitals on fragments and constrain charge and spin polarization on fragments.
- Variables:
Charge (Iterable[float] | FloatListKey) – Constrain charge on fragments. Number of charges should be the same as number of fragments, and sum should add up to total charge.
Debug (BoolType | BoolKey) – Debug.
SpinPolarization (Iterable[float] | FloatListKey) – Constrain spin polarization on fragments. Number of spin polarization values should be the same as number of fragments, and sum should add up to total spin polarization. Calculation should be spin unrestricted.
ElectronTransfer (ADF._FOCDFT._ElectronTransfer) –
- class _ElectronTransfer[source]¶
- Variables:
Charge (Iterable[float] | FloatListKey) – Constrain charge on fragments for the second calculation. Number of charges should be the same as number of fragments, and sum should add up to total charge.
OffDiagonalHF (BoolType | BoolKey) – Off diagonal HF matrix elements.
OffDiagonalHFValue (float | FloatKey) – Amount of HF in case off diagonal HF matrix elements.
SpinPolarization (Iterable[float] | FloatListKey) – Constrain spin polarization on fragments for the second calculation. Number of spin polarization values should be the same as number of fragments, and sum should add up to total spin polarization. Calculation should be spin unrestricted.
- class _FragOccupations[source]¶
Simulation of unrestricted fragments with the key FRAGOCCUPATIONS. Fragments need to be calculated spin-restricted. One can specify occupation numbers as if these fragments are calculated spin-unrestricted. The sum of spin-alpha and spin-beta occupations must, for each fragment orbital in each irrep separately, be equal to the total spin-restricted occupation of that orbital in the fragment.
- class _Fragments[source]¶
Definitions of the fragment type/files: {FragmentName FragmentFile}. In the block header one can specify the directory where the fragment files are located
- class _GPU[source]¶
Set GPU options
- Variables:
Enabled (BoolType | BoolKey) – Use a CUDA-compatible GPU.
UseDevices (Iterable[int] | IntListKey) – Use only specified devices for this calculation. Multiple devices will be distributed evenly among MPI ranks.
- class _GW[source]¶
Perform a GW calculation. G0W0 is the default for GW%SelfConsistency.
- Variables:
AdaptiveMixing (Iterable[float] | FloatListKey) –
Requests to use adaptive mixing instead of DIIS and sets the staring mixing parameter for mixing of Green’s function in case of self-consistency.
Adapative mixing is recommended in case a qsGW calculation does not converge with DIIS.
It is ignored in non-selfconsistent calculation and overwritten by DIIS when DIIS is also present.
DIIS (int | IntKey) – Requests to use DIIS. This is the Default. Number of expansion coefficients can be requested as well. Ignored in non-selfconsistent calculation
Enabled (BoolType | BoolKey) – Enable the calculation of the GW quasi-particle energies.
ExpansionOrder (int | IntKey) – Order of the expansion of the screened interaction on the SOS-GF(n) method. order 2 (=SOS-GF2) is the default
FixedGridSizes (BoolType | BoolKey) – In a self-consistent GW calculation, recalculate Grids but keep them the same size during the SCF procedure.
FixedGrids (BoolType | BoolKey) – In a self-consistent GW calculation, do not recalculate Grids. Can be useful in case of convergence problems. Only relevant for qsGW and qsGW0. In case of evGW and evGW0, the grids are always kept fixed.
G3W2 (Literal["Full", "Diagonal", "Perturbative"]) – Only relevant when self-energy is one of GF2 or G3W2: Full requests that the second-order term is evaluated for the full self-energy matrix. This is very expensive and should only be done for small systems. Diagonal requests, that only the Diagonal of the self-energy matrix is updated. Perturbative means, that only a second-order screened exchange correction is evaluated after the GW calculation is completed. For a G0W0 calculation, all of these options are equivalent.
LinearMixing (Iterable[float] | FloatListKey) –
Requests to use linear mixing instead of DIIS and sets the mixing parameter for linear mixing of Green’s function in case of self-consistency.
It is ignored in non-selfconsistent calculation and overwritten by DIIS when DIIS is also present.
LinearizeQPequations (BoolType | BoolKey) –
Instead of solving the non-linear QP equations in a G0W0 (or evGW calculation) by bisection exacly, linearize them by first-order Taylor expansion.
This is not recommended since it does not save computational time when used together with analytical continuation (as implemented in AMS). It might however be useful for benchmarking or for validating results.
If the results os the linearization differ by a lot (for instance, more than 0.1 eV in frontier QP energies) from the non-linearized results, this might indicate that the GW calculation is not reliable.
OffDiagonalEFermi (BoolType | BoolKey) – Analytically continue the off-diagonal elements of the KSF2 qsGW Hamiltonian at the Fermi-energy instead of omega=0. Typically leads to slightly lower QP energies, i.e. higher ionization potentials. The HOMO-LUMO gaps are typically not affected.
Polarizability (Literal["RPA", "BSE", "G4W1", "G4V1", "TDHF"]) –
Sets the expression for the Polarizability used in the GW calculation.
RPA is the Default and amounts to a standard GW calculation.
BSE denotes screening in the Bethe-Salpeter-equation formalism.
PrintAllSolutions (BoolType | BoolKey) – Print out all solutions for all requested states. Detects multiple solutions of the QP equations.
PrintImaginaryAxisData (BoolType | BoolKey) – If true, print out the self-energy on the imaginary axis.
PrintSpectralFunction (BoolType | BoolKey) – Plot the self-energy as a function of frequency. Automatically done in case of analytical continuation. However, this is expensive in the analytical integration formalism.
PrintZfactor (BoolType | BoolKey) –
QPHamiltonian (Literal["KSF1", "KSF2", "SRG", "LQSGW"]) –
The quasi-particle Hamiltonian can be constructed in different ways.
KSF1 refers to the original construction by Kotani, Van Schilfgaarde anf Faleev (KSF) which is also implemented in TURBOMOLE.
KSF2 refers to an alternative construction by KSF.
KSF1 is not recommended since it is numerically less stable than KSF2 in case analytical continuation is used (the default).
In case the analytical integration algorithm is used, only KSF1 is implemented. Therefore, make sure that KSF1 is specified. The results are typically very similar.
The QP energies at which the matrix elements are evaluated can be tweaked further, see the two subsequent keys: However, KSF2 is recommended since it typically leads to QP energies with the best agreement with experiment.
Ignored when not a quasi-particle self-consistent GW calculation is performed
Scaling (float | FloatKey) – Scale factor for the polarizability in the screened interaction SOS-GF2. Default = 1.0 (corresponds to no scaling)
ScissorShift (BoolType | BoolKey) –
Only calculate the HOMO and LUMO QP energies and shift the remaining QP energies by the same amount.
This is a rather crude approximation and not recommended.
It might again be useful for benchmarking purposes.
SelfConsistency (Literal["None", "G0W0", "EVGW0", "EVGW", "QSGW0", "QSGW"]) –
Sets the level of self-consistency in a GW calculation.
G0W0 calculates a one-shot, perturbative correction to the KS eigenvalues.
In evGW and evGW0, the quasi-particle energies are updated until self-consistency is reached.
evGW0 requests that the Green’s function is evaluated self-consistently but not the screened interaction.
In qsGW, the density is updated as well, however, the self-energy is mapped to a static effective potential and the Dyson equation is solved by diagonalization instead of inversion. The results of a qsGW are independent of the choice of the underlying exchange-correlation functional and are usually the most accurate ones.
The same is done in qsGW0, but the screened interaction is not updated.
SelfConsistentSigmaVertex (BoolType | BoolKey) – If active, evaluate the vertex correction in Sigma in qsGW self-consistent. Only supported for GWGammaInf so far
SelfEnergy (Literal["HF", "GW", "G3W2", "SOSEX", "GWGamma", "G3W2dynamic", "GWGammaInf", "GWGammaInfDyn"]) –
Controls the form of the self-energy.
GW is the default and corresponds to the standard GW calculation.
G3W2 is a GW calculation plus a perturbative second-order statically screened exchange correction (second order expansion in the self-energy). Note, that there the self-energy is always static.
TabulateGridPoints (BoolType | BoolKey) – pretabulate grid points for numerical integration.
nIterations (Iterable[int] | IntListKey) –
The maximum number of iterations within the (partially or fully) self-consistent GW calculation has to converge.
Ignored when Formalism is set to G0W0
nLowest (int | IntKey) – Number of lowest occupied QP levels to be evaluated, overwrites nStates’
Number of Quasiparticle States to be printed to output.
The default is 5 states which in this case means that min(5, Number of particle states) occupied and min(5, Number of hole states) hole states are printed. The whole list of states can be printed by setting this parameter to -1’
preconditionQSGW (BoolType | BoolKey) –
If true, the QSGW equations are solved but prior to each diagonalization, i.e. a G0W0 calculation is performed to find the optimal QP energies at which to analytically continue the self-energy.
This is in principle a more consistent construction than KSF1 or KSF2 since the diagonal elements are consistent with G0W0.
In KSF1 and KSF2, the diagonal elements are evaluated at the QP energies from the previous iteration which is equivalent to a zeroth-order Taylor expansion of the diagonal elements around the previous QP energies.Enabling this option typically leads to slightly lower QP energies.
AnalyticalIntegration (ADF._GW._AnalyticalIntegration) – Use analytical integration to calculate the self-energy. Very slow, unless the system is very small but useful to check the accuracy of the frequency integration
Converge (ADF._GW._Converge) – Sets convergence criteria for the GW calculation in self-consistent case
- class _AnalyticalIntegration[source]¶
Use analytical integration to calculate the self-energy. Very slow, unless the system is very small but useful to check the accuracy of the frequency integration
- Variables:
Enabled (BoolType | BoolKey) – Enable the calculation of the GW quasi-particle energies via analytical integration.
SpectralFunctionResolution (int | IntKey) – Number of points at which spectral function is evaluated.
TDA (BoolType | BoolKey) – Solve the linear response equations in the Tamm-Dancoff approximation.
Artificial (positive) broadening parameter for evaluation of self-energy in analytical integration.
Ideally should be as small as possible but this might lead to convergence issues in partially self-consistent approaches.
In this case, a value of up to 0.1 is possible.
printBSEexcitationsInLastIteration (BoolType | BoolKey) –
Print out BSE excitations in the last iteration in a qsGW calculation. Can be used in the BAND engine.
In ADF, one should instead just calculate excitation energies using the excitation block.
- class _Converge[source]¶
Sets convergence criteria for the GW calculation in self-consistent case
- Variables:
Density (Iterable[float] | FloatListKey) –
First Criterion for self-consistency procedure to terminate.
Criterion is the trace of the density matrix. Ignored in non-selfconsistent Calculation and in eigenvalue self-consistent GW
It is possible to run a qsGW calculation with an inner SCF loop which updates the static part of the elf-energy only. This can be useful to accelerate the convergence in case linear mixing is used. It is not recommended to use linear mixing, so it is also not recommended to use that inner loop as well. The second number in this list specifies the convergence criterion for the inner SCF loop.
Criterion for self-consistency procedure to terminate.
The self-consistent GW calculation terminates, when the difference between the HOMO QP energies between 2 consecutive iterations is below this number.
The LUMO energy converged faster than the HOMO energy so when the HOMO energy is converged according to this criterion, the LUMO energy will be converged as well.
In non-selfconsistent Calculation, this criterion is ignored.
- class _IQA[source]¶
Total energy decomposition based on the interacting quantum atoms (IQA) approach and using QTAIM real-space partition.
- Variables:
AtomsToDo (Iterable[int] | IntListKey) –
Define a subset of atoms for which the IQA atom-atom interactions are calculated (no intra-atomic terms).
If left empty, all atoms will be included (full IQA).
Enabled (BoolType | BoolKey) – Calculate the total energy decomposition using the interacting quantum atoms (IQA) approach and the QTAIM real-space partitioning.
Interactions (Literal["inter", "all", "debug"]) – Placeholder
Print (Literal["normal", "verbose"]) – Minimal output (default) or verbose mode (detailed energy decomposition)
- class _Integration[source]¶
Options for the Voronoi numerical integration scheme
- Variables:
ACCINT (Iterable[float] | FloatListKey) – The main precision parameter Its value defines the number of significant digits by which an internal set of standard integrals must be evaluated. The number and distribution of integration points is tuned accordingly. For normal applications this should yield a nearly optimal (given the underlying method) generation of points and weights. The default depends on the run type.
ACCOUT (float | FloatKey) – The region of space further away from the atoms, outside the polyhedrons, has its own precision parameter. By default accout=accint.
ACCPYR (float | FloatKey) – Similarly this subkey sets the test level for the parts of the pyramids outside the atomic sphere. Default: accpyr=accint.
ACCPYU (float | FloatKey) – The truncated pyramids are mathematically transformed into unit cubes. A product Gauss integration formula is applied to the cubes, with three (test precision) parameters for the three dimensions. Accpyw controls the direction that is essentially the radial integration from the surface of the atomic sphere to the base of the pyramid. The other two control the orthogonal directions (angular). By default all three equal accpyr.
ACCPYV (float | FloatKey) – The truncated pyramids are mathematically transformed into unit cubes. A product Gauss integration formula is applied to the cubes, with three (test precision) parameters for the three dimensions. Accpyw controls the direction that is essentially the radial integration from the surface of the atomic sphere to the base of the pyramid. The other two control the orthogonal directions (angular). By default all three equal accpyr.
ACCPYW (float | FloatKey) – The truncated pyramids are mathematically transformed into unit cubes. A product Gauss integration formula is applied to the cubes, with three (test precision) parameters for the three dimensions. Accpyw controls the direction that is essentially the radial integration from the surface of the atomic sphere to the base of the pyramid. The other two control the orthogonal directions (angular). By default all three equal accpyr.
ACCSPH (float | FloatKey) – The polyhedron method of generating integration points partitions space in atomic polyhedrons, partitioned in pyramids with their tops at the atom in the center of the polyhedron. A core like atomic sphere is constructed around the atom; this truncates the tops of the pyramids. accsph specifies the test precision for the generation of points within the spheres. By default accsph=accint.
DISHUL (float | FloatKey) – Sets the distance between the outermost nuclei of the molecule and the boundary planes that define the boundary between the polyhedrons and the outer region. By default dishul=2.3*R, where R is the radius of the largest atomic sphere in the molecule.
FRANGE (float | FloatKey) – The outward range of the outer region: integration is not performed to infinity but to a distance frange from the outermost atoms, where all functions can be assumed to be essentially zero. By default frange is derived both from accint, the general precision parameter, and from the present chemical elements: heavier atoms have longer-range functions than hydrogen say. The precise relations can be found in the implementation.
LINROT (int | IntKey) – This parameter is significant only for symmetries with an axis of infinite rotational symmetry: C and D It is the highest rotational quantum number around this axis that occurs among the integrands. This depends on the employed basis functions and fit functions. By default the program finds this out for itself.
LINTEG (Iterable[int] | IntListKey) – The maximum angular momentum quantum number of integrands centered on an atom of that type (one value for each atom type). This depends on the basis functions and on the fit functions. By default the program checks the function sets and sets the linteg values accordingly. This subkey is applied for the generation of grid points in the atomic spheres.
NOUTER (int | IntKey) – This outer region is treated by a product formula: outwards times parallel. The latter involves two dimensions: the surface of the molecule say. The outward integration is performed with Gauss-Legendre quadrature, in a few separate steps. The lengths of the steps are not equal, they increase by constant factors. The total length is fixed. The number of steps is controlled with this subkey; default: 2.
OUTPAR (float | FloatKey) – Similarly the integration in the directions parallel to the surface of the atomic system is controlled by a parameter. See the implementation for details.
OUTRAD (float | FloatKey) – The parameter that defines the number of Gauss-Legendre integration points for each outward step. The precise relation between the actual number of points and this subkey, and the default relation between outrad and accout can be found in the implementation.
QPNEAR (float | FloatKey) – If you specify point charges in the input file, there are two considerations implied for the numerical integration grid. First, since the point charges create a Coulomb singularity. The integrands (of for instance the basis function products against the Coulomb potential) can only be evaluated with high precision if the grid around the point charges has spherical symmetry and uses local spherical coordinates, exactly as is done for the atomic nuclei. Second, the point charges do not carry fit or basis functions, hence they play only a role in the more diffuse tails of the actual functions involved in integrals. Therefore, a relative low precision of the integral part close to the point charge may have little effect on the total integration accuracy. Since additional ‘spherical centers’ with their own surrounding grids increase the total number of points significantly, typically a few thousands per Coulomb center, this may result in high computational effort. Therefore, the program generates spherical grids only about those point charges that are close to the other atoms. The criterion, input with the qpnear subkey, is the closest distance between the point charge at hand and any real atom. Default 4.0 Angstrom.
RSPHER (Iterable[float] | FloatListKey) – Gives the radii of the atomic spheres, one value for each atom type. By default, the radii are derived from the chemical element (heavier atoms get larger spheres) and from the environment: the sphere must not be too large for the atomic cell (polyhedron).
- class _LinearScaling[source]¶
- Variables:
Cutoff_Coulomb (float | FloatKey) – determines the radii for the fit functions in the evaluation of the (short-range part of) the Coulomb potential.
Cutoff_Fit (float | FloatKey) – determines how many atom pairs are taken into account in the calculation of the fit integrals and the density fit procedure. If the value is too low, charge will not be conserved and the density fitting procedure will become unreliable. This parameter is relevant for the timings of the FITINT and RHOFIH routines of ADF.
Cutoff_Multipoles (float | FloatKey) – determines the cut-offs in the multipole (long-range) part of the Coulomb potential
Overlap_Int (float | FloatKey) – determines the overlap criterion for pairs of AOs in the calculation of the Fock-matrix in a block of points. Indirectly it determines what the cut-off radii for AO’s should be. The value of ovint has a strong influence on the timing for the evaluation of the Fock matrix, which is very important for the overall timings
ProgConv (float | FloatKey) – determines how the overall accuracy changes during the SCF procedure
- class _MBPT[source]¶
Technical aspects of the MP2 algorithm.
- Variables:
Dependency (BoolType | BoolKey) – If true, to improve numerical stability, almost linearly-dependent combination of basis functions are removed from the Green’s function that are used in the MBPT equations. Disabling this key is strongly discouraged. Its value can however be changed. The key to adjust this value is RiHartreeFock%DependencyThreshold
Enabled (BoolType | BoolKey) – Enable the calculation of the MP2 energy.
ExcludeCore (BoolType | BoolKey) –
If active, excludes core states from the calculation of the optimal imaginary time and frequency grids.
The core states are still included in all parts of the calculations.
In case a frozen care calculation is performed, this key is ignored.
For MP2 and double hybrid calculation, it defaults to false. For RPA and GW calculations, it defaults to true.
FitSetQuality (Literal["Auto", "VeryBasic", "Basic", "Normal", "Good", "VeryGood"]) –
Specifies the fit set to be used in the MBPT calculation.
’Normal’ quality is generally sufficient for basis sets up to and including TZ2P.
For larger basis sets (or for benchmarking purposes) a ‘VeryGood’ fit set is recommended. Note that the FitSetQuality heavily influences the computational cost of the calculation.
If not specified or ‘Auto’, the RIHartreeFock%FitSetQuality is used.
Formalism (Literal["Auto", "RI", "LT", "All"]) –
Specifies the formalism for the calculation of the MP2 correlation energy.
’LT’ means Laplace Transformed MP2 (also referred to as AO-PARI-MP2),
’RI’ means that a conventional RI-MP2 is carried out.
If ‘Auto’, LT will be used in case of DOD double hybrids and SOS MP2, and RI will be used in all other cases.
’All’ means that both RI and LT formalisms are used in the calculation.
For a RPA or GW calculation, the formalism is always LT, irrespective of the formalism specified with this key.
FrequencyGridType (Literal["LeastSquare", "GaussLegendre"]) – Use Gauss-legendre grid for imaginary frequency integration in RPA and GW calculations instead of the usually used Least-Square optimized ones. Has the advantage that it can be systematically converged and an arbitrary number of grid points can be used. Typically more grid points will be needed to get the same level of accuracy. However, the convergence of the results with the size of the grid can be more systematic. These grids can only be used when Formalism is set to RI.
IntegrationQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood"]) – Specifies the integration quality to be used in the MBPT calculation. If not specified, the RIHartreeFock%IntegrationQuality is used.
PrintOutSigma (BoolType | BoolKey) – Print out additional output for sigma-functional for parametrization.
SigmaFunctionalParametrization (Literal["W1", "W2", "S1", "S2", "S1re"]) – Only relevant if a sigma-functional calculation is performed. Possible choices for the parametrization of the sigma-functional. Not all options are supported for all functionals.
ThresholdQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Controls the distances between atomic centers for which the product of two basis functions is not fitted any more. Especially for spatially extended, large systems, ‘VERYBASIC’ and ‘BASIC’ can lead to large computational savings, but the fit is also more approximate. If not specified, the RIHartreeFock%ThresholdQuality is used.
UseScaledZORA (BoolType | BoolKey) – If true, use the scaled ZORA orbital energies instead of the ZORA orbital energies in the MBPT equations.
cutOfftransition (float | FloatKey) – Energy above which states are ignored in a MBPT calculation (must be a positive number). The default energy is chosen so high, that all states are included except for the ones which have been removed.
frozencore (BoolType | BoolKey) – Freeze core states in correlation part of MBPT calculation
Number of core states which will be excluded from the correlated calculation.
Will be ignored if frozencore is false.
In case nothing is specified, the number of core levels will be determined automatically.
Needs to be smaller than the number of occupied states.
nFreqIntegration (int | IntKey) – Number of imaginary frequency points for G3W2 integration
nFrequency (int | IntKey) – Number of imaginary frequency points. This key is only relevant for RPA and GW and will be ignored if used in an AO-PARI-MP2 calculation. 12 Points is the default for a RPA calculation. It is technically possible to use a different number of imaginary frequency points than for imaginary time. The maximum number of points which can be requested for imaginary frequency integration is 42. Important note: The computation time and memory requirements roughly scale linearly with the number of imaginary frequency points. However, memory can be an issue for RPA and GW when the number of imaginary frequency points is high. In case a job crashes, it is advised to increase the number of nodes since the necessary memory distributes over all nodes.
nLambda (int | IntKey) – Size of coupling constant integration grid for SOSEX variants in RPA. Default is 4 points
Number of imaginary time points (only relevant in case the Laplace Transformed (LT) formalism is used).
In the many-body-perturbation theory module in ADF, the polarizability (or Kohn-Sham density response function) is evaluated in imaginary time to exploit sparsity in the AO basis. For MP2, this is often referred to as a Laplace transform. For MP2, 9 points are the default. This is a safe choice, guaranteeing accuracies higher than 1 Kj/mol for most systems (For many simple organic systems, 6 points are sufficient for good accuracy).
Only for systems with a very small HOMO-LUMO gap or low-lying core states (heavy elements starting from the 4th row of the periodic table) more points might be necessary.
In principle, the same considerations apply for RPA and GW as well, however, the accuracy requirements are somewhat higher and 12 point are the default for RPA. In a GW calculation, the number of points is adjusted according to the numerical quality. Using less than 9 points is strongly discouraged except for the simplest molecules.
In ADF2019, it can happen that the algorithm determining the imaginary time grid does not converge. In this case, the usual reason is that the number of points is too small and more points need to be specified. Starting from AMS2020, this does not happen any more. In case the imaginary time grid does not converge, the number of points is automatically adjusted until it does.
The computation time of AO-PARI-MP2, RPA, and GW scales linearly with the number of imaginary time points.
useGreenXgrids (BoolType | BoolKey) – Use GreenX library to generate grid points. This is recommended for larger number of grid points (> 20). Up to 34 points can be requested.
- class _MDC[source]¶
Options for Multipole Derived Charges (MDC)
- class _ModifyExcitation[source]¶
- Variables:
GRIMMEPERTC (BoolType | BoolKey) –
NOGRIMMEPERTC (BoolType | BoolKey) –
OscStrength (float | FloatKey) – Use only pairs of an occupied and virtual orbital as guess vectors, for which the oscillator strength of the single-orbital transition is larger than this value
SetLargeEnergy (float | FloatKey) – The orbital energies of the uninteresting occupied orbitals are changed to -epsbig Hartree, and the orbital energies of the uninteresting virtual orbitals are changed to epsbig Hartree
SetOccEnergy (float | FloatKey) – All occupied orbitals that have to be used will change their orbital energy to this value. In practice only useful if one has selected one occupied orbital energy, and one want to change this to another value. Default: the orbital energies of the occupied orbitals that are used are not changed.
UseOccRange (Iterable[float] | FloatListKey) – Use only occupied orbitals which have orbital energies between the two numbers.
UseOccVirtNumbers (Iterable[int] | IntListKey) – Use only pairs of an occupied and virtual orbital as guess vectors, for which in the sorted list of the orbital energy differences, the number of the single-orbital transition is between the two numbers.
UseOccVirtRange (Iterable[float] | FloatListKey) – Use only pairs of an occupied and virtual orbital, for which the orbital energy difference is between the two numbers
UseScaledZORA (BoolType | BoolKey) – Use everywhere the scaled ZORA orbital energies instead of the ZORA orbital energies in the TDDFT equations. This can improve deep core excitation energies. Only valid if ZORA is used.
UseVirtRange (Iterable[float] | FloatListKey) – Use only virtual orbitals which have orbital energies between the two numbers
UseOccupied (str | Sequence[str] | FreeBlock) – Use only the occupied orbitals which are specified
UseVirtual (str | Sequence[str] | FreeBlock) – Use only the virtual orbitals which are specified
- class _ModifyStartPotential[source]¶
Modify the starting spin-dependent potential for unrestricted calculations.
- class _Nanoparticle[source]¶
To include the presence of a nanoparticle near the system
- Variables:
TransitionPotential (BoolType | BoolKey) – Evaluate the transition potential due to a nanoparticle
- class _PertLoc[source]¶
Perturbed localized molecular orbitals, correct to first order in an applied field, can be calculated in case of AORESPONSE. Can be used if the applied field changes the density in first order.
- Variables:
Alfa (BoolType | BoolKey) – Analyze the static or dynamic polarizability
BField (BoolType | BoolKey) – The perturbation is a magnetic field. Should be consistent with AORESPONSE
Beta (BoolType | BoolKey) – Analyze the optical rotation parameter beta. The relation to G’ is beta = -G’/omega. The optical rotation parameter beta is calculated directly and has a well-defined static limit, i.e. omega can be zero or non-zero
Diag (BoolType | BoolKey) – Only analyze the diagonal of the response tensor
Dynamic (BoolType | BoolKey) – Should be used for a frequency dependent perturbation field.
EField (BoolType | BoolKey) – The perturbation is an electric field
Fulltens (BoolType | BoolKey) – The full tensor is analyzed
GPrime (BoolType | BoolKey) – Analyze the G’ (gyration) tensor, for optical rotation dispersion. Requires a frequency dependent perturbation field, with a frequency (omega) unequal to zero.
Static (BoolType | BoolKey) – should be used for a static field
- class _PolTDDFT[source]¶
POLTDDFT is a fast algorithm to solve the TDDFT equations in the space of the density fitting auxiliary basis set. The (real and imaginary part of the) diagonal of the polarizability tensor and rotatory strengths will be calculated, which can be used to calculate the photoabsorption and circular dichroism (CD) spectra.
- Variables:
Analysis (BoolType | BoolKey) – An analysis of the absorption and CD spectrum in terms of single orbital transitions.
CutOff (float | FloatKey) – For a given point in the spectrum, only include pairs of an occupied and virtual orbital, for which the orbital energy difference is lower than the energy of the point in the spectrum plus cutoff.
Enabled (BoolType | BoolKey) – Calculate UV/Vis and CD spectrum from the imaginary part of the polarizability tensor at any given photon energy. This avoids the bottleneck of Davidson diagonalization.
FreqRange (Iterable[float] | FloatListKey) – Specifies a frequency range of frequencies of incident light, the perturbing field, at which the complex dynamical polarizability will be calculated. 2 numbers: an upper and a lower bound. Use subkey NFreq to specify the number of frequencies.
HDA_fitted (BoolType | BoolKey) – Use fit functions to calculate HDA (Hybrid diagonal approximation), only relevant for hybrids.
KGrid (float | FloatKey) – Keyword KGRID is used to discretize the energy scale for calculating the complex dynamical polarizability. Only pairs of an occupied and virtual orbital are included, for which the orbital energy difference is lower than this value. Use key NGRID to set the number of points within the energy grid.
Jacob’s scaling factor for the study of plasmonic resonances.
This factor, 0<lambda<1, turns on the coupling matrix K.
Specify the resonance peak width (damping).
Typically the lifetime of the excited states is approximated with a common phenomenological damping parameter. Values are best obtained by fitting absorption data for the molecule, however, the values do not vary a lot between similar molecules, so it is not hard to estimate values.
NFreq (int | IntKey) – NFreq is the number of frequencies of incident light, the perturbing field, at which the complex dynamical polarizability will be calculated. Use FreqRange to specify the frequency range.
NGrid (int | IntKey) – Ngrid is the number of points within the energy grid.
N_FitOrb (int | IntKey) – The number of vectors containing the coefficients we use to expand the projection of each fitting function over the electron density (of a particular molecular orbital) as a linear combination of overlap matrices between fitting functions pair
Print_Int_Time (int | IntKey) – Print detailed timing during calculation of integrals of Tape63 and Tape64
RegionsForAnalysis (str | StringKey) – Names of regions for analysis per region using the fragment projection analysis approach. Will split the absorption and CD spectrum in region_i -> region_j terms.
Velocity (BoolType | BoolKey) –
If True, ADF calculates the dipole moment in velocity gauge.
If false: dipole-length representation is used
Irrep (str | Sequence[str] | FreeBlock) – Subblock key for selecting which symmetry irreps of the excitations to calculate (all excitations by default). In the subkey data block list the symmetry irrep labels, like B1, for example
- class _QMFQ[source]¶
Block input key for QM/FQ(FMu).
- Variables:
DEBUG (BoolType | BoolKey) – The DEBUG subkey will print additional information from the FQ subroutines.
FDERESP (BoolType | BoolKey) – In response calculations (TD), the polarization contribution of the FDE part is introduced at the FQ level [See F. Egidi et al. J. Chem. Phys. 2021, 154, 164107].
Forcefield (Literal["FQ", "FQ_RQ", "FQFMU", "FQFMU_RQRMU", "NOPOL"]) – Version of the FQ family of polarizable forcefields
Frozen (BoolType | BoolKey) – Expert option. Do not introduce polarization effect in response calculations.
Kernel (Literal["OHNO", "COUL", "GAUS"]) – Expert option. KERNEL can be used to choose the functional form of the charge-charge interaction kernel between MM atoms. Recommended is to use the default OHNO. The COUL screening is the standard Coulomb interaction 1/r. The OHNO choice introduce the Ohno functional (see [K. Ohno, Theoret. Chim. Acta 2, 219 (1964)]), which depends on a parameter n that is set equal to 2. Finally, the GAUS screening models each FQ charge by means of a spherical Gaussian-type distribution, and the interaction kernel is obtained accordingly. For QM/FQFMU only GAUS SCREEN is implemented.
MolCharge (float | FloatKey) – Total charge of each fragment (FQ only)
NOGROUNDSTATE (BoolType | BoolKey) – Avoid introducing FQ effects on ground state calculations
NonEle (Literal["LJ", "None"]) – Whether to include non-electrostatic contributions to the energy. Default is the Lennard-Jones (LJ) model.
QMSCREEN (Literal["ERF", "EXP", "GAUS", "NONE"]) – Expert option. QMSCREEN can be used to choose the functional form of the charge-charge interaction kernel between MM atoms and the QM density. The screening types available are ERF (error function), EXP (exponential), GAUS (Gaussian), or NONE. The default is GAUS.
QMSCREENFACTOR (float | FloatKey) – Expert option. Sets the QM/MM interaction kernel screening length. Recommended is to use the default value 0.2 with the GAUS QM/MM screening function.
AtomType (ADF._QMFQ._AtomType) – Definition of atomic types in MM environment
Coords (str | Sequence[str] | FreeBlock) – Coordinates and fragment information (FQ only)
Repulsion (ADF._QMFQ._Repulsion) – Definition of parameters for Pauli repulsion (see JCTC ….)
Solver (ADF._QMFQ._Solver) –
- class _AtomType[source]¶
Definition of atomic types in MM environment
- class _Repulsion[source]¶
Definition of parameters for Pauli repulsion (see JCTC ….)
- Variables:
AtomDistance (float | FloatKey) – Each fictitious Slater function is added only if the associated MM atom is closer than the AtomDistance threshold (in Angstrom) to a QM atom
Basis (ADF._QMFQ._Repulsion._Basis) – Slater type basis function to add on a specific atom type in the environment.
- class _QTAIM[source]¶
This block is used to request a topological analysis of the gradient field of the electron density, also known as the Bader’s analysis. If this block is specified without any sub-key, only local properties are calculated.
- Variables:
AnalysisLevel (Literal["Normal", "Extended", "Full"]) –
Set the level of the QTAIM analysis:
Normal - topology analysis and properties at the density critical points,
Extended - same as Normal plus condensed atomic descriptors,
Full - same as Extended plus non-local descriptors.
AtomsToDo (Iterable[int] | IntListKey) – List of atoms for which condensed descriptors are to be calculated. By default all atoms are included.
Enabled (BoolType | BoolKey) – Calculate QTAIM (also known as Bader) properties.
Energy (BoolType | BoolKey) – Calculate atomic energies. Requires an all-electron calculation (no frozen core), triggers the TotalEnergy and increases the [AnalysisLevel] to at least Extended.
Source (BoolType | BoolKey) – Calculate the Source Function at BCPs and RCPs.
Spacing (float | FloatKey) – Specifies spacing of the initial Cartesian grid when searching for critical points. It may be useful to specify a smaller value than the default if some critical points are missed. This will result in a more accurate but slower calculation.
- class _RIHartreeFock[source]¶
- Variables:
DependencyCoreRange (float | FloatKey) – Basis functions may be given a core character based on the range. For now only active in Band and only if present in the input
DependencyThreshold (float | FloatKey) –
To improve numerical stability, almost linearly-dependent combination of basis functions are removed from the Hartree-Fock exchange matrix.
If you obtain unphysically large bond energy in an Hybrid calculation, or an unphysically low correlation energy in an RPA, MP2, or double hybrid calculation, you might try setting the DependencyThreshold to a larger value (e.g. 3.0E-3)
Note, that in GW calculations and GW-BSE calculations the default for this key is 5.0e-3.
DoAlternativeDependencyTrick (BoolType | BoolKey) – Only applies to band. Do trick on the density matrix being input to HFEval, rather than on the K-matrix.
DoDependencyTrick (BoolType | BoolKey) – Available only in BAND, turns on and off the RIHartreeFock dependency trick.
FitSetQuality (Literal["Auto", "VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent", "FromBasisProducts"]) –
The quality of auxiliary fit set employed in the RI scheme.
If ‘Auto’, the value of the RIHartreeFock Quality option will be used.
Normal quality is generally sufficient for basis sets up to and including TZ2P.
For larger basis sets (or for benchmarking purposes) a VeryGood fit set is recommended.
Note that the FitSetQuality heavily influences the computational cost of the calculation.
IntegrationQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Quality of the numerical integration for evaluating the integrals between basis functions and fit functions. If IntegrationQuality is not defined in input, the value defined in RIHartreeFock%Quality will be used.
Quality (Literal["Auto", "VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Numerical accuracy of the RI procedure. If ‘Auto’, the quality specified in the ‘NumericalQuality’ will be used.
ResponseQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Numerical accuracy of the RI procedure for the Response module.
ThresholdQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Linear scaling thresholds (also used for determining at what range the multiple approximation is used). To disable all linear scaling thresholds set this to Excellent.
UseCoulombMetricForDependency (BoolType | BoolKey) – Use Coulomb metric for the Dependency Trick (band only)
UseMe (BoolType | BoolKey) – Set to False if you want to use the old RI scheme (ADF only)
ExplicitThresholds (ADF._RIHartreeFock._ExplicitThresholds) – Override the thresholds as implied by the ThresholdQuality.
FitGenerationDetails (ADF._RIHartreeFock._FitGenerationDetails) – Technical details about how the RI Hartree-Fock fit functions are generated.
QualityPerRegion (ADF._RIHartreeFock._QualityPerRegion) – Sets the fit-set quality for all atoms in a region. If specified, this overwrites the globally set quality.
- class _FitGenerationDetails[source]¶
Technical details about how the RI Hartree-Fock fit functions are generated.
- Variables:
BoostL (BoolType | BoolKey) –
Add extra max(l)+1 diffuse function
When l denotes the highest angular momentum present in the primary basis,
FromBasisProducts will generate auxiliary fit functions with up to 2l angular momentum.
When this key is set to true, the maximum angular momentum in the auxiliary fit set becomes 2l+2.
Typically, this option is not needed and when precision issues arise, it is rather advised to adjust the OneCenterDependencyThreshold key to a smaller value.
LapackWorkAround (BoolType | BoolKey) – GetFitFunctionsForAtomType diagonalization done with Lapack instead of Scalapack
Method (Literal["Auto", "FromBasisProducts"]) –
The way in which fit functions are generated. The main distinction is whether it depends on the basis functions used.
When FromBasisProducts is used, the auxiliary basis is generated directly from the products of primary basis functions.
This has the advantage that the auxiliary fit adapts automatically to the basis set size.
Especially for basis sets of QZ quality or larger, this is often necessary to obtain highly precise correlation energies using RPA or double hybrids
FromBasisProducts option is also useful for GW or BSE calculations with basis sets of QZ quality or larger.
OneCenterDependencyThreshold (float | FloatKey) –
This key is only active when FromBasisProducts is chosen as method to generate the auxiliary basis.
This threshold controls the size, and at the samw time, the precision of the auxiliary basis set. A smaller number leads to a larger auxiliary fit set.
The default value of 1e-8 is typically sufficient to converge correlation energies and QP energies to a very high precision.
It corresponds to an auxiliary basis which is typically 8-9 times larger than the primary basis.
UseBandRadialGrid (BoolType | BoolKey) –
Only applies to band. The band logarithmic grid ranges (by default) from 1e-6 to 100 with 3000 points. Otherwise 300 points will be used.
For 0-periodicity (molecules) it is advisable to set this key to false since lots of memory is needed to evaluate all necessary integrals.
- class _ROSE[source]¶
Options for orbital localization
- Variables:
Additional_virtuals_cutoff (float | FloatKey) – Specifies the energy threshold to determine the number of additional hard virtuals to localize for the supermolecule. If not specified the default value is used.
Exponent (int | IntKey) – The value of the exponent (for the default Pipek-Mezey type of localization, the exponent is equal to 2. A higher value of 3 or 4 is sometimes useful.).
Frag_bias (Iterable[float] | FloatListKey) – Expert key. Specifies the bias applied to each fragment when assigning the localized orbitals to a particular fragment. Use a negative value for default behavior for a given fragment. If not specified, or if the number of items is unequal the number of fragments, a default bias is used.
Frag_threshold (float | FloatKey) – Specifies energy threshold to determine number of reference hard virtuals to use for the fragments (needed to localize the additional hard virtuals). The total number of reference virtuals should be larger than the number of virtual MOs to localize (similar to having more reference valence orbitals than occupied valence orbitals to localize), so it is advisable to use a relatively high value for this parameter. If not specified the default value is used.
Frag_valence (Iterable[int] | IntListKey) – Expert key. Specifies the number of valence orbitals for each fragment. Use a negative value for default behavior for a given fragment. If not specified, or if the number of items is unequal the number of fragments, by default the code generates the valence space for each fragment as the sum of valence orbitals of individual atoms within each fragment.
FragmentFile (str | Path | StringKey) – Path (either absolute or relative) of each fragment file. The number of fragments used to project on will be number of occurrences of this key.
GWenergies (BoolType | BoolKey) – Use GW energies instead of DFT energies.
GWorbitals (BoolType | BoolKey) – Use GW orbitals instead of DFT orbitals.
Version (Literal["Stndrd_2013", "Simple_2013", "Simple_2014"]) – Expert key, specifies version of the IAO generation. If not specified a default value is used.
nfragments (int | IntKey) – Expert key, preferably use the FragmentFile key for each fragment instead, and do not use this key. If the FragmentFile key is not used, then with this key one can specify the number of fragments used to project on. If this key is used the fragment file names should be called frag1.rkf, frag2.rkf, etcetera, and should be present at the directory where ams is started.
- class _RadialCoreGrid[source]¶
For each atom the charge densities and the coulomb potentials of frozen core and valence electrons are computed in a radial grid. The radial grid consists of a sequence of r-values, defined by a smallest value, a constant multiplication factor to obtain each successive r-value, and the total number of points. Equivalently it can be characterized by the smallest r-value, the largest r-value, and the number of points; from these data the program computes then the constant multiplication factor.
- class _Relativity[source]¶
Options for relativistic effects.
- Variables:
Formalism (Literal["Pauli", "ZORA", "X2C", "RA-X2C"]) –
Note that if Level is None, no relativistic effects are taken into account, irrespective of the chosen formalism.
Pauli stands for the Pauli Hamiltonian.
ZORA means the Zero Order Regular Approximated Hamiltonian, recommended.
X2C and RA-X2C both stand for an exact transformation of the 4-component Dirac equation to 2-components.
X2C is the modified Dirac equation by Dyall.
RA-X2C is the regular approach to the modified Dirac equation.
Level (Literal["None", "Scalar", "Spin-Orbit"]) –
None: No relativistic effects.
Scalar: Scalar relativistic. This option comes at very little cost.
Spin-Orbit: Spin-orbit coupled. This is the best level of theory, but it is (4-8 times) more expensive than a normal calculation. Spin-orbit effects are generally quite small, unless there are very heavy atoms in your system, especially with p valence electrons (like Pb).
See also the SpinOrbitMagnetization subkey.
Potential (Literal["MAPA", "SAPA"]) – Starting from ADF2017 instead of SAPA (the Sum of neutral Atomic potential Approximation) MAPA is used by default for ZORA. The MAPA (the Minimum of neutral Atomic potential Approximation) at a point is the minimum of the neutral Atomic potentials at that point. Advantage of MAPA over SAPA is that the gauge dependence of ZORA is reduced. The ZORA gauge dependency is small for almost all properties, except for the electron density very close to a heavy nucleus. The electron density very close to a heavy nucleus can be used for the interpretation of isomer shifts in Mossbauer spectroscopy.
SOUExact (BoolType | BoolKey) – Expert option for unrestricted spin-orbit coupled calculations.
SpinOrbitMagnetization (Literal["NonCollinear", "Collinear", "CollinearX", "CollinearY", "CollinearZ"]) –
Relevant only for spin-orbit coupling and if unrestricted key has been activated.
Most XC functionals have as one ingredient the spin polarization in case of unrestricted calculations. Normally the direction of the spin quantization axis is arbitrary and conveniently chosen to be the z-axis.
However, in a spin-orbit calculation the direction matters, and it is arbitrary to put the z-component of the magnetization vector into the XC functional. There is also the exotic option to choose the quantization axis along the x or y axis.
It is also possible to plug the size of the magnetization vector into the XC functional. This is called the non-collinear approach.
NonCollinear: the non-collinear method.
CollinearXYZ: use the x, y, or z component as spin polarization for the XC functional.
Collinear: the same as CollinearZ.
- class _Response[source]¶
The calculation of frequency-dependent (hyper)polarizabilities and related properties (Raman, ORD)
- Variables:
ALLCOMPONENTS (BoolType | BoolKey) –
ALLHYPER (BoolType | BoolKey) –
ALPHAINANG (BoolType | BoolKey) –
ANALYTIC (BoolType | BoolKey) –
AllCycles (BoolType | BoolKey) – Convergence printout
AllTensor (BoolType | BoolKey) – Higher dispersion coefficients are also calculated
C8 (BoolType | BoolKey) –
CUTTAILS (BoolType | BoolKey) –
DYNAHYP (BoolType | BoolKey) –
Dipole (BoolType | BoolKey) –
Frequencies (Iterable[float] | FloatListKey) – List of frequencies of incident light, the perturbing field, at which the time-dependent properties will be calculated.
IFILES (int | IntKey) – Integration run including external files. Used for Van der Waals dispersion coefficients calculations.
KSORBRUN (BoolType | BoolKey) –
MAGNETICPERT (BoolType | BoolKey) –
NUMERIC (BoolType | BoolKey) –
OPTICALROTATION (BoolType | BoolKey) –
Octupole (BoolType | BoolKey) –
Quadrupole (BoolType | BoolKey) –
Raman (BoolType | BoolKey) –
STARTREALGR (BoolType | BoolKey) –
SYMRUN (BoolType | BoolKey) –
Temperature (float | FloatKey) – Wavelength of incoming light is equal to the wavelength at which the calculation is performed and temperature is equal to room temperature (300K) Total Raman band is default, not the Q-branch of diatomic. (Relevant for Raman scattering cross section)
VERDET (float | FloatKey) – For numerical differentiation d alfa(omega) /d omega, needed for Verdet constant, the default frequencies are omega + dverdt and omega - dverdt
- class _Restart[source]¶
Options for restarts
- Variables:
NoOrb (BoolType | BoolKey) – Do not use orbitals from the restart file
NoSCF (BoolType | BoolKey) – Do not use any fit coefficients from the restart file as a first approximation to the (fitted) SCF density for the new calculation. Instead, the sum-of-fragments density will be used, as in a non-restart run. Note, typically noSCF should be used in combination with noORB.
NoSmear (BoolType | BoolKey) – Do not use any electron smearing data from the restart file.
SpinFlip (Iterable[int] | IntListKey) – Select the atoms for which the spin is to be flipped upon restart.
- class _SCF[source]¶
Control aspects of the Self Consistent Field procedure
- Variables:
AccelerationMethod (Literal["ADIIS", "fDIIS", "LISTb", "LISTf", "LISTi", "MESA", "SDIIS"]) –
SCF acceleration method.
The default method is ADIIS, which is actually a mix of A-DIIS and SDIIS: A-DIIS is used at the start of the SCF and SDIIS is used closer to convergence, with a smooth switching function.
The other methods are from the LIST family developed by Alex Wang and co-workers. They may perform better than the default in some situations.
Setting AccelerationMethod to SDIIS effectively disables A-DIIS and is equivalent to the legacy mixing+DIIS method.
Converge (Iterable[float] | FloatListKey) –
The criterion to stop the SCF updates.
The tested error is the commutator of the Fock matrix and the P-matrix (=density matrix in the representation of the basis functions) from which the F-matrix was obtained. This commutator is zero when absolute self-consistency is reached. Convergence is considered reached when the maximum element falls below SCFcnv and the norm of the matrix below 10*SCFcnv. The default is fairly strict.
A second criterion which plays a role when the SCF procedure has difficulty converging. When in any SCF procedure the currently applicable criterion does not seem to be achievable, the program stops the SCF. When the secondary criterion (sconv2) has been met, only a warning is issued and the program continues normally.
EDIIS (BoolType | BoolKey) – Use the Energy-DIIS SCF acceleration method. This key also triggers the OldSCF. The Energy-DIIS should not be used because it is not supported by the new SCF module, is not any better than methods from the LIST family and can be very slow.
Iterations (int | IntKey) – The maximum number of SCF cycles allowed.
The level shifting parameter.
The diagonal elements of the Fock matrix, in the representation of the orbitals of the previous iteration, are raised by vshift hartree energy units for the virtual orbitals. This may help to solve convergence problems when during the SCF iterations charge is sloshing back and forth between different orbitals that are close in energy and all located around the Fermi level.
Level shifting is not supported in the case of Spin-Orbit coupling.
At the moment properties that use virtuals, like excitation energies, response properties, NMR calculations, will give incorrect results if level shifting is applied.
LShift_cyc (int | IntKey) – Specifies that level shifting is not turned on before the given SCF cycle number (for the start-up geometry).
LShift_err (float | FloatKey) – Specifies that level shifting will be turned off by the program as soon as the SCF error drops below a threshold.
Mixing (float | FloatKey) – When none of the SCF acceleration methods is active, the next Fock matrix is determined F = mixing * F_n + (1-mixing)F_(n-1).
Mixing1 (float | FloatKey) – The mixing parameter at the 1st SCF cycle.
NoADIIS (BoolType | BoolKey) – Disables A-DIIS and switches SCF to a damping+DIIS scheme.
OldSCF (BoolType | BoolKey) –
Disable the default SCF algorithm and use the old SCF algorithm.
The default SCF improves performance for big systems on big machines (when your calculation uses many tasks).
It is also recommended for machines with slow disk I/O as it writes less data to disk.
The default convergence method supported is A-DIIS, but LISTi is also supported.
ScalableSCF (BoolType | BoolKey) – Use new scalable scf.
ScalableSO (BoolType | BoolKey) – Use new scalable scf for spin-orbit coupling.
ADIIS (ADF._SCF._ADIIS) – Settings for the ADIIS method.
ARH (ADF._SCF._ARH) – The Augmented Roothaan-Hall method has been developed by T. Helgaker and coworkers.
DIIS (ADF._SCF._DIIS) – The maximum number of SCF cycles allowed.
ROSCF (ADF._SCF._ROSCF) – Settings for the ROSCF method.
- class _ADIIS[source]¶
Settings for the ADIIS method.
- Variables:
If ErrMax > Thresh1 then only A-DIIS coefficients are used to determine the next Fock matrix.
Below this threshold a weighted mix of A-DIIS and DIIS coefficients will be used.
If ErrMax < Thresh2 then only SDIIS coefficients are used.
Below this threshold a weighted mix of A-DIIS and DIIS coefficients will be used.
- class _ARH[source]¶
The Augmented Roothaan-Hall method has been developed by T. Helgaker and coworkers.
- Variables:
CGiter (int | IntKey) – Sets the maximum number of micro-iterations.
Conv (float | FloatKey) – ARH convergence criterion. When the RMS gradient and its maximum components are both lower than the criterion, the ARH procedure will be considered converged.
Enabled (BoolType | BoolKey) – Use ARH.
Final (BoolType | BoolKey) –
If enabled, only one Fock matrix diagonalization will be performed after the ARH solution is found to get the orbitals. No further SCF iterations will be performed.
If not enabled, the regular SCF method will continue after the ARH solution is found.
Iter (int | IntKey) – Maximum number of ARH iteration to perform. Please note that in difficult cases a huge number of iterations may be required for complete SCF convergence
NOTRANSPCG (BoolType | BoolKey) –
The number of saved density and Fock matrices used for augmentation of the electronic Hessian.
A larger value should be used in difficult cases when the number of orbitals very close to the Fermi level is large.
NoPrecond (BoolType | BoolKey) –
PRECOND (BoolType | BoolKey) –
SHIFTED (BoolType | BoolKey) –
SWITCHING (BoolType | BoolKey) –
Turn OFF to avoid switching from the normal CG to a trust-radius minimization in reduced space.
Turning off this option helps to reduce the total number of SCF cycles is some cases.
Thus, if this option is turned off a NOSWITCHING key will be added (see User’s Guide).
TRANSPCG (BoolType | BoolKey) –
- class _DIIS[source]¶
The maximum number of SCF cycles allowed.
- Variables:
BFac (float | FloatKey) – By default, the latest vector is not favored in the DIIS algorithm (value 0.0). A sensible value would be 0.2.
CX (float | FloatKey) – The DIIS space is reduced when very large DIIS coefficients appear. The value is the threshold.
CXX (float | FloatKey) – When very large DIIS coefficients appear, switch to traditional damping. The value is the threshold.
Cyc (int | IntKey) – When A-DIIS is disabled, the Pulay DIIS will start at this iteration irrespective of the DIIS OK value.
N (int | IntKey) – The number of expansion vectors used for accelerating the SCF. The number of previous cycles taken into the linear combination is then n-1 (the new computed potential is also involved in the linear combination)
Ok (float | FloatKey) – The Pulay DIIS starting criterion, when A-DIIS is disabled,
- class _ROSCF[source]¶
Settings for the ROSCF method.
- Variables:
Alpha (Iterable[float] | FloatListKey) – Coefficients to build the alpha-spin orbital contribution to the diagonal closed-, open-, and virtual-shell blocks of the Fock matrix. The beta-spin orbital contributions are 1.0 minus the alpha ones.
- class _SOPert[source]¶
Key for perturbative inclusion of spin-orbit coupling.
- Variables:
EShift (float | FloatKey) – The actually calculated eigenvalues are calculated up to the maximum singlet-singlet or singlet-triplet scalar relativistic excitation energy plus eshift (in Hartree).
GSCorr (BoolType | BoolKey) – The singlet ground state is included, which means that spin-orbit coupling can also have some effect on energy of the ground state. The spin-orbit matrix in this case is on basis of the ground state and the singlet and triplet excited states.
NCalc (int | IntKey) – Number of spin-orbit coupled excitation energies to be calculated. Default (and maximum) value: 4 times the number of scalar relativistic singlet-singlet excitations.
error (BoolType | BoolKey) – Debug option for perturbative spin-orbit coupling.
- class _SelectExcitation[source]¶
- Variables:
GRIMMEPERTC (BoolType | BoolKey) –
NOGRIMMEPERTC (BoolType | BoolKey) –
OscStrength (float | FloatKey) – Use only pairs of an occupied and virtual orbital as guess vectors, for which the oscillator strength of the single-orbital transition is larger than this value
SetLargeEnergy (float | FloatKey) – The orbital energies of the uninteresting occupied orbitals are changed to -epsbig Hartree, and the orbital energies of the uninteresting virtual orbitals are changed to epsbig Hartree
SetOccEnergy (float | FloatKey) – All occupied orbitals that have to be used will change their orbital energy to this value. In practice only useful if one has selected one occupied orbital energy, and one want to change this to another value. Default: the orbital energies of the occupied orbitals that are used are not changed.
UseOccRange (Iterable[float] | FloatListKey) – Use only occupied orbitals which have orbital energies between the two numbers.
UseOccVirtNumbers (Iterable[int] | IntListKey) – Use only pairs of an occupied and virtual orbital as guess vectors, for which in the sorted list of the orbital energy differences, the number of the single-orbital transition is between the two numbers.
UseOccVirtRange (Iterable[float] | FloatListKey) – Use only pairs of an occupied and virtual orbital, for which the orbital energy difference is between the two numbers
UseScaledZORA (BoolType | BoolKey) – Use everywhere the scaled ZORA orbital energies instead of the ZORA orbital energies in the TDDFT equations. This can improve deep core excitation energies. Only valid if ZORA is used.
UseVirtRange (Iterable[float] | FloatListKey) – Use only virtual orbitals which have orbital energies between the two numbers
UseOccupied (str | Sequence[str] | FreeBlock) – Use only the occupied orbitals which are specified
UseVirtual (str | Sequence[str] | FreeBlock) – Use only the virtual orbitals which are specified
- class _SlaterDeterminants[source]¶
The calculation of the one-determinant states based on the AOC reference state is controlled with this key.
- class _Solvation[source]¶
- Variables:
Ass (BoolType | BoolKey) –
COSKFAtoms (Iterable[int] | IntListKey) – This subkey COSKFATOMS specifies for which nuclei the segments in the COSMO section of the COSKF file should be used. Default all nuclei should be used, i.e. as for omitting the subkey COSKFATOMS. The numbers refer to the input ordering in the ADF calculation.
CsmRsp (BoolType | BoolKey) –
Lpr (BoolType | BoolKey) –
NoAss (BoolType | BoolKey) –
NoCsmRsp (BoolType | BoolKey) –
NoLpr (BoolType | BoolKey) –
NoPVec (BoolType | BoolKey) –
PVec (BoolType | BoolKey) –
PrintSM12 (BoolType | BoolKey) –
SM12SolvationPotential (Literal["cm5", "chelpg"]) – Partial Charges to use in SCRF for SM12
Surf (Literal["wsurf", "asurf", "esurf", "klamt", "delley", "wsurf nokeep", "asurf nokeep", "esurf nokeep", "klamt nokeep", "delley nokeep"]) – Defines the type of cavity to be used.
- class _SpinOrbitMagnetization[source]¶
Starting artificial spin-orbit magnetization at first SCF cycle
- Variables:
Strength (float | FloatKey) – Strength of artificial spin-polarization at first SCF cycle
PerRegion (ADF._SpinOrbitMagnetization._PerRegion) – Defines the starting spin-polarization direction for all atoms in a region. Note that if this keyword is used multiple times, the chosen regions may not overlap.
- class _PerRegion[source]¶
Defines the starting spin-polarization direction for all atoms in a region. Note that if this keyword is used multiple times, the chosen regions may not overlap.
- Variables:
Direction (Iterable[float] | FloatListKey) – The starting spin-polarization direction for a region.
Region (str | StringKey) – The identifier of the region for which to define the starting spin-polarization direction.
Strength (float | FloatKey) – Strength of artificial spin-polarization in this region
- class _SubExci[source]¶
Subsystem TDDFT (FDE)
- Variables:
CICoupl (BoolType | BoolKey) – Within the Tamm-Dancoff Approximation, the couplings between localized excited states on different subsystems correspond directly to so-called exciton couplings. The CICOUPL keyword, in conjunction with TDA, prints these exciton couplings. It is also possible to use CICOUPL with full FDEc-TDDFT. In that case, the excitonic couplings between monomers are reconstructed from an effective 2x2 CIS-like eigenvalue problem.
COULKERNEL (BoolType | BoolKey) –
COUPLBLOCK (BoolType | BoolKey) –
COUPLSYS (Iterable[int] | IntListKey) –
CThres (float | FloatKey) – all excitations of all subsystems (present on the fragment TAPE21 files) with an excitation energy that differs by less than coupling_threshold. From one of the reference states are selected to be included in the coupling. Note that additional excited states of system 1 may be included here.
DIPVEL (BoolType | BoolKey) –
DiagType (Literal["EXACT"]) –
ETHRES (float | FloatKey) – Threshold for effective coupling
FULLGRID (BoolType | BoolKey) –
InvGuess (Literal["EigVal-OrbDiff", "OrbDiff-OrbDiff", "Exact"]) – Type of states to be coupled
LOCALFXCK (BoolType | BoolKey) –
Lowest (int | IntKey) – The selection of the excited states to be coupled consists of two steps
NOINTERSOLV (BoolType | BoolKey) –
NOSOLVCCHECK (BoolType | BoolKey) –
ONEGRID (BoolType | BoolKey) –
OptStates (Iterable[int] | IntListKey) – If the keyword OPTSTATES is given, only those excited states of the first subsystem are considered as reference states that are given in this list.
PFRAGOUT (BoolType | BoolKey) –
SFThres (float | FloatKey) – To reduce the computational effort, it is possible to ignore the effect of orbital pairs with coefficients less than solutionfactor_threshold in the solution factors (TDDFT eigenvectors) of the underlying uncoupled calculation in the construction of the exact trial densities during the calculation of the coupling matrix elements. These orbital pair contributions are not ignored in the subsequent calculation of transition moments, oscillator, and rotational strengths.
SMARTGRID (BoolType | BoolKey) –
Stat2CPL (Literal["OnlyKnown"]) – Type of states to be coupled
TCOMEGA (BoolType | BoolKey) – Transpose construction of Omega matrix
TDA (BoolType | BoolKey) – TDA specifies the use of the Tamm-Dancoff-Approximation (Tamm-Dancoff approximation) in the underlying uncoupled FDE-TDDFT calculations. Contrary to the full SUBEXCI-TDDFT variant, SUBEXCI-TDA allows for the usage of hybrid functionals in the underlying uncoupled FDE-TDDFT calculations.
TKINKERNEL (BoolType | BoolKey) –
XCKERNEL (BoolType | BoolKey) –
- class _Tails[source]¶
Obsolete option for linear scaling and distance effects. We recommend using the LinearScaling key instead.
- Variables:
Bas (float | FloatKey) – Parameter related to the threshold for the calculation of basis functions on a block of integration points. A higher value implies higher precision. The default depends on the Integration numerical quality.
Fit (float | FloatKey) – Parameter related to the threshold for the calculation of fit functions on a block of integration points. A higher value implies higher precision. The default depends on the Integration numerical quality.
- class _XC[source]¶
Definition of the XC.
- Variables:
DoubleHybrid (str | StringKey) – Specifies the double hybrid functional that should be used during the SCF.
EmpiricalScaling (Literal["None", "SOS", "SCS", "SCSMI"]) – Calculate the (SOS/SCS/SCSMI)-MP2 correlation energy.
GALITSKIIMIGDAL (BoolType | BoolKey) – Calculate the Galitskii-Migdal correlation energy after the SCF is completed.
GCPparameters (str | StringKey) – Applying parameters for the geometrical counter poise correction.
GGA (str | StringKey) – Specifies the GGA part of the XC Functional
HartreeFock (BoolType | BoolKey) – Use the Hartree-Fock exchange should be used during the SCF.
Hybrid (str | StringKey) – Specifies the hybrid functional that should be used during the SCF.
LDA (str | StringKey) – Defines the LDA part of the XC functional
LibXC (str | StringKey) – Use the LibXC library with the specified functional.
MP2 (BoolType | BoolKey) – Calculate the MP2 correlation energy after the HF SCF is completed.
MetaGGA (str | StringKey) – Specifies that a meta-GGA should be used during the SCF
MetaHybrid (str | StringKey) – Specifies the meta-hybrid functional that should be used during the SCF.
NoLibXC (BoolType | BoolKey) – Prevent the usage of the LibXC library
OEP (str | StringKey) – Defines the optimized effective potential expanded into a set of the fit functions
RPA (Literal["None", "Direct", "Sigma", "SOSEX", "SOSSX"]) – Specifies that RPA is used an possibly also a post-RPA method. By default, RPA is not used.
RangeSep (str | StringKey) – Range separated hybrids parameters
XCFun (BoolType | BoolKey) – Use the XCFun library
gCP (str | StringKey) – Use the geometrical counter poise correction.
- class _XES[source]¶
X-ray emission spectroscopy
- Variables:
AllXESMoments (BoolType | BoolKey) – Print out all the individual transition moments used within the calculation of the total oscillator strength
AllXESQuadrupole (BoolType | BoolKey) – Print out the individual oscillator strength components to the total oscillator strength
selection of the acceptor orbital for the calculation of the emission oscillator strengths. For example ‘CoreHole A1 2’ calculates oscillator strengths to the orbital 2 in irrep A1.
In AMSinput you may also use the notation 2A1 (so first the orbital number, next the symmetry)
Enabled (BoolType | BoolKey) –
Calculate the X-ray emission energies to a core orbital.
By default it calculates the emission to the first orbital in the first symmetry.
- class _ZlmFit[source]¶
Options for the density fitting scheme ‘ZlmFit’.
- Variables:
AllowBoost (BoolType | BoolKey) – Allow automatic atom-dependent tuning of maximum l of spherical harmonics expansion. Whether or not this boost is needed for a given atom is based on an heuristic estimate of how complex the density around that atom is.
DensityThreshold (float | FloatKey) – Threshold below which the electron density is considered to be negligible.
Pruning (BoolType | BoolKey) –
Quality (Literal["Auto", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Quality of the density-fitting approximation. For a description of the various qualities and the associated numerical accuracy see reference. If ‘Auto’, the quality defined in the ‘NumericalQuality’ will be used.
QualityPerRegion (ADF._ZlmFit._QualityPerRegion) – Sets the ZlmFit quality for all atoms in a region. If specified, this overwrites the globally set quality.
- class ASE[source]¶
- Variables:
AllASEResults (BoolType | BoolKey) – Return all ASE results that are not also part of AMSResults. These values can be found in ase.rkf without any unit conversions.
ArgumentsFromFile (str | Path | StringKey) – Specify the path to a yaml or python file defining the arguments to the function or class defined in Calculator or Callable.
File (str | Path | StringKey) –
Specify the path to a Python file. This file should contain a callable (e.g. function or class) named get_calculator that returns an ASE Calculator and uses the arguments defined in Arguments or ArgumentsFromFile.
You can find examples of suitable calculator.py files (possibly requiring additional installations of packages) in
$AMSHOME/scripting/scm/external_engines/backends.Specify the module and name of a Calculator installed in the used Python stack. This is case sensitive.
Builtin ASE examples: ase.calculators.emt.EMT
Other examples requiring special installations: scm.external_engines.backends._psi4.calculator.get_calculator scm.external_engines.backends._tblite.calculator.get_calculator scm.external_engines.backends._mace.calculator.get_calculator
Performance (Literal["Fast", "ForceField", "DFTB", "DFT", "Slow"]) – Choose which option most accurately corresponds to how long a calculation with the calculator takes.
Results (str | StringKey) – The data of this key in the results dictionary of the Calculator is stored in the engine rkf. Multiple results keys can be specified. This is case sensitive.
Type (Literal["File", "Import"]) – Select how to specify which calculator to use.
Arguments (str | Sequence[str] | FreeBlock) –
Arguments to the function or constructor initializing the Calculator. Give each argument on a separate line. This is case sensitive.
Note: Do not perform any Python imports here. Only use Python builtin types. Arguments containing paths must be absolute.
Example: cutoff = 3.14 title = ‘my_string’ my_list_arg = [1, 4, 5] options_dictionary = {‘key1’: 11, ‘key2’: 22} my_boolean_flag = True my_path = ‘/this/must/be/an/absolute/path’
Python (ASE._Python) – Specify which Python to run.
- class _Arguments[source]¶
Arguments to the function or constructor initializing the Calculator. Give each argument on a separate line. This is case sensitive.
Note: Do not perform any Python imports here. Only use Python builtin types. Arguments containing paths must be absolute.
Example: cutoff = 3.14 title = ‘my_string’ my_list_arg = [1, 4, 5] options_dictionary = {‘key1’: 11, ‘key2’: 22} my_boolean_flag = True my_path = ‘/this/must/be/an/absolute/path’
- class _Python[source]¶
Specify which Python to run.
- Variables:
Name of conda environment. Only used when
Python%Type = Conda. You may also define the conda environment setting the environment variable SCM_ASE_PYTHON_TYPE=conda:name-of-environment.If the value is an absolute path it will be executed with
conda run -p, otherwise it is assumed to be a name of a conda environment that can be executed withconda run -n.The
condaexecutable shell script must exist on your$PATH. To see available environments, runconda env list.Type (Literal["amspython", "Conda", "Current"]) – Type of Python environment. If
Conda, set the name or path of the environment underPython%Conda. IfCurrent, the defaultpython(orpython.exeon Windows) command will be used.
- class BAND[source]¶
- Variables:
Allow (str | StringKey) – Debugging feature to let the program continue even when intermediate results seem to be wrong or very inaccurate
BerryPhase (BoolType | BoolKey) – Boolean that determines whether the dipole as determined through the Berry phase approach should be calculated.
CPVector (int | IntKey) – The code is vectorized and this key can be used to set the vector length
Debug (str | StringKey) – Enables debug printing for the subroutine name(s) specified here.
DefaultsConvention (str | StringKey) – There has been a big change in many default settings with the 2014 release. This lets you switch to the old defaults.
DumpBasisOnly (BoolType | BoolKey) – Dump basis and fit set files use for each atom.
EigThreshold (float | FloatKey) – Threshold for printing the eigenvectors coefficients (Print Eigens)
EnforcedSpinPolarization (float | FloatKey) –
Enforce a specific spin-polarization instead of occupying according to the aufbau principle. The spin-polarization is the difference between the number of alpha and beta electron.
Thus, a value of 1 means that there is one more alpha electron than beta electrons.
The number may be anything, including zero, which may be of interest when searching for a spin-flipped pair, that may otherwise end up in the (more stable) parallel solution.
FormFactors (int | IntKey) – Number of stars of K-vectors for which the form factors are computed
IntegrationMethod (Literal["Becke", "Voronoi"]) – Choose the real-space numerical integration method. Note: the Voronoi integration scheme is deprecated.
KGrpX (int | IntKey) – Absolute upper bound on the number of k-points processed together. This only affects the computational performance.
ModifyAlternativeElements (BoolType | BoolKey) – When using alternative elements (using the nuclear_charge attribute) set the element to the nearest integer Z. If you specify an H atom with a nuclear_charge of 2.9 it is replaced by a Li atom with the same nuclear charge.
NUElstat (int | IntKey) – Number of outward (parabolic) integration points (for elliptical integration of the electrostatic interaction)
NVElstat (int | IntKey) – Number of angular (elliptic) integration points (for elliptical integration of the electrostatic interaction)
NeutralizingDensity (Literal["None", "rho(atoms)", "rho(valence/atoms)", "rho(neutralizing/atoms)", "rho(homogeneous)"]) – For charged systems an artificial compensating density can be used to make it neutral again. This fictitious density only affects the Coulomb potential. For charged periodic systems neutralization is required, as otherwise the Coulomb potential diverges.
NuclearModel (Literal["PointCharge", "Gaussian", "Uniform"]) –
Specify what model to use for the nucleus.
For the Gaussian model the nuclear radius is calculated according to the work of Visscher and Dyall (L. Visscher, and K.G. Dyall, Dirac-Fock atomic electronic structure calculations using different nuclear charge distributions, Atomic Data and Nuclear Data Tables 67, 207 (1997))
NumericalQuality (Literal["Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Set the quality of several important technical aspects of a BAND calculation (with the notable exception of the basis set). It sets the quality of: BeckeGrid (numerical integration), ZlmFit (density fitting), KSpace (reciprocal space integration), and SoftConfinement (basis set confinement). Note: the quality defined in the block of a specific technical aspects supersedes the value defined in NumericalQuality (e.g. if I specify ‘NumericalQuality Basic’ and ‘BeckeGrid%Quality Good’, the quality of the BeckeGrid will be ‘Good’)
PEDA (BoolType | BoolKey) – If present in combination with the fragment block, the decomposition of the interaction energy between fragments is invoked.
PopThreshold (float | FloatKey) – Threshold for printing Mulliken population terms. Works with ‘Print orbpop’
PotentialNoise (float | FloatKey) – The initial potential for the SCF procedure is constructed from a sum-of-atoms density. Added to this is some small noise in the numerical values of the potential in the points of the integration grid. The purpose of the noise is to help the program break the initial symmetry, if that would lower the energy, by effectively inducing small differences between (initially) degenerate orbitals.
Print (str | StringKey) – One or more strings (separated by blanks) from a pre-defined set may be typed after the key. This induces printing of various kinds of information, usually only used for debugging and checking. The set of recognized strings frequently changes (mainly expands) in the course of software-developments. Useful arguments may be symmetry, and fit.
Save (str | StringKey) – Save scratch files or extra data that would be otherwise deleted at the end of the calculation. e.g. ‘TAPE10’ (containing the integration grid) or ‘DensityMatrix’
SelectedAtoms (Iterable[int] | IntListKey) – With this key you can select atoms. This has an effect on a few of options, like NMR and EFG.
Skip (str | StringKey) – Skip the specified part of the Band calculation (expert/debug option).
StopAfter (str | StringKey) – Specifies that the program is stopped after execution of a specified program-part (subroutine).
StoreHamAsMol (BoolType | BoolKey) – Undocumented, used for (at least) NEGF.
StoreHamiltonian (BoolType | BoolKey) – Undocumented.
StoreHamiltonian2 (BoolType | BoolKey) – determine the tight-binding representation of the overlap an fock matrix. Used for (at least) NEGF.
SubSymmetry (Iterable[int] | IntListKey) – The indices of the symmetry operators to maintain.
Title (str | StringKey) – Title of the calculation, which will be printed in the output file.
Unrestricted (BoolType | BoolKey) – Controls whether Band should perform a spin-unrestricted calculation. Spin-unrestricted calculations are computationally roughly twice as expensive as spin-restricted.
UnrestrictedOnlyReference (BoolType | BoolKey) – Undocumented.
UnrestrictedReference (BoolType | BoolKey) – Undocumented.
UnrestrictedStartup (BoolType | BoolKey) – Undocumented.
UseInversionSymmetryInReciprocalSpace (BoolType | BoolKey) – Whether to use inversion symmetry in reciprocal space. This is almost always a valid assumption.
UseSymmetry (BoolType | BoolKey) – Whether or not to exploit symmetry during the calculation.
AIMCriticalPoints (BAND._AIMCriticalPoints) – Compute the critical points of the density (Atoms In Molecules). The algorithm starts from a regular mesh of points, and from each of these it walks towards its corresponding critical point.
ATensor (BAND._ATensor) – Hyperfine A-tensor.
Align (BAND._Align) – Alignment of the potential of the system. Old NEGF.
AtomType (BAND._AtomType) – Explicit basis set definition for given atom type.
BField (BAND._BField) – The effect of a magnetic filed can be approximated by the following potential: mu * sigma_i * B, where mu is the Bohr magneton, sigma_i are the Pauli matrices and B is the magnetic field
BZPath (BAND._BZPath) – Definition of the user-defined path in the Brillouin zone for band structure plotting.
BandStructure (BAND._BandStructure) – Options for the calculation of the band structure.
Basis (BAND._Basis) – Definition of the basis set
BasisMisc (BAND._BasisMisc) – Miscellaneous options related to basis
BeckeGrid (BAND._BeckeGrid) – Options for the numerical integration grid, which is a refined version of the fuzzy cells integration scheme developed by Becke.
Bias (BAND._Bias) – Old NEGF. No longer supported
CDFT (BAND._CDFT) – Constrained DFT Implementation in Transport. Old NEGF.
Comment (str | Sequence[str] | FreeBlock) – The content of this block will be copied to the output header as a comment to the calculation.
Convergence (BAND._Convergence) – Options and parameters related to the convergence behavior of the SCF procedure.
DFTBConfinementPotential (BAND._DFTBConfinementPotential) – Specify the confinement potentials (used for DFTB parametrization)
DIIS (BAND._DIIS) – Parameters for the DIIS procedure to obtain the SCF solution
DIRIS (BAND._DIRIS) – Same options as DIIS key, except that this one applies to the DIIS procedure used in the Dirac subprogram, for numerical single atom calculations, which constructs the radial tables for the NAOs.
DOS (BAND._DOS) – Density-Of-States (DOS) options
DensityPlot (str | Sequence[str] | FreeBlock) – Plots of the density. Goes together with the Restart%DensityPlot and Grid keys.
Dependency (BAND._Dependency) – Criteria for linear dependency of the basis and fit set
DiracOptions (BAND._DiracOptions) – Options for the atomic Dirac calculations.
Dispersion (BAND._Dispersion) – Technical options for dispersion-corrected functionals.
DosBas (str | Sequence[str] | FreeBlock) – Used to specify the fragment basis for the DOS.
EFG (BAND._EFG) – The electronic charge density causes an electric field, and the gradient of this field couples with the nuclear quadrupole moment, that some (non-spherical) nuclei have and can be measured by several spectroscopic techniques. The EFG tensor is the second derivative of the Coulomb potential at the nuclei. For each atom it is a 3x3 symmetric and traceless matrix. Diagonalization of this matrix gives three eigenvalues, which are usually ordered by their decreasing absolute size and denoted as V_{xx}, V_{yy}, V_{zz}. The result is summarized by the largest eigenvalue and the asymmetry parameter.
ESR (BAND._ESR) – Zeeman g-tensor. The Zeeman g-tensor is implemented using two-component approach of Van Lenthe and co-workers in which the g-tensor is computed from a pair of spinors related to each other by time-reversal symmetry. Note: the following options are necessary for ESR: ‘Relativistic zora spin’ and ‘Kspace 1’
EffectiveMass (BAND._EffectiveMass) –
In a semi-conductor, the mobility of electrons and holes is related to the curvature of the bands at the top of the valence band and the bottom of the conduction band.
With the effective mass option, this curvature is obtained by numerical differentiation.
The estimation is done with the specified step size, and twice the specified step size, and both results are printed to give a hint on the accuracy. The easiest way to use this key is to enabled it without specifying any extra options.
ElectronHole (BAND._ElectronHole) – Allows one to specify an occupied band which shall be depopulated, where the electrons are then moved to the Fermi level. For a spin-restricted calculation 2 electrons are shifted and for a spin-unrestricted calculation only one electron is shifted.
EmbeddingPotential (BAND._EmbeddingPotential) – An external potential can be read in and will be added to the effective Kohn-Sham potential. It has to be on the becke grid
Excitations (BAND._Excitations) – Excitation energies: UV/Vis
Fermi (BAND._Fermi) – Technical parameter used in determining the Fermi energy, which is carried out at each cycle of the SCF procedure.
FermiSurface (BAND._FermiSurface) – Calculation of the Fermi surface for metals
FitMethod (BAND._FitMethod) – Undocumented
FracOp (BAND._FracOp) – Parameters from input for fractional occupations
FragOccupations (str | Sequence[str] | FreeBlock) – Undocumented
Fragment (BAND._Fragment) – Defines a fragment. You can define several fragments for a calculation.
FragmentEnergyTerms (str | Sequence[str] | FreeBlock) – Undocumented
FuzzyPotential (str | Sequence[str] | FreeBlock) – Atomic (fuzzy cell) based, external, electric potential. See example.
FuzzyUnitCellGrid (BAND._FuzzyUnitCellGrid) – Undocumented.
GMix (BAND._GMix) – Undocumented. Old NEGF.
GW (BAND._GW) – Perform a GW calculation. G0W0 is the default for GW%SelfConsistency.
Gate (BAND._Gate) – Undocumented. Old NEGF.
Gradients (BAND._Gradients) – Options for nuclear gradients and strain derivatives calculations.
Grid (BAND._Grid) – Options for the regular grid used for plotting (e.g. density plot). Used ICW the restart option.
GridBasedAIM (BAND._GridBasedAIM) – Invoke the ultra fast grid based Bader analysis.
GrossPopulations (str | Sequence[str] | FreeBlock) – Partial DOS (pDOS) are generated for the gross populations listed under this key. See example.
HardConfinement (BAND._HardConfinement) – Obsolete basis functions confinement method. Use SoftConfinement instead.
HubbardU (BAND._HubbardU) – Options for Hubbard-corrected DFT calculations.
Integration (BAND._Integration) – Options for the Voronoi numerical integration scheme. Deprecated. Use BeckeGrid instead.
KSpace (BAND._KSpace) – Options for the k-space integration (i.e. the grid used to sample the Brillouin zone)
LDOS (BAND._LDOS) – Local Density-Of-States information. This can be used to generate STM images in the Tersoff-Hamann approximation (see https://doi.org/10.1103/PhysRevB.31.805)
MBPT (BAND._MBPT) – Technical aspects of the MP2 algorithm.
MolecularNMR (BAND._MolecularNMR) – Options for the calculations of the NMR shielding tensor for molecules, excluding periodic systems. Implements the Schreckenbach method like ADF.
MultiSecantConfig (BAND._MultiSecantConfig) – Parameters for the Multi-secant SCF convergence method.
NEGF (BAND._NEGF) – Options for the NEGF (non-equilibrium green function) transport calculation.
NMR (BAND._NMR) – Options for the calculations of the NMR shielding tensor.
NOCVOrbitalPlot (str | Sequence[str] | FreeBlock) – Goes together with the Restart%NOCVOrbitalPlot and Grid keys. See example.
NOCVdRhoPlot (str | Sequence[str] | FreeBlock) – Goes together with the Restart%NOCVdRhoPlot and Grid keys. See example.
NOPROrbitalPlot (str | Sequence[str] | FreeBlock) – Undocumented.
NOPRdRhoPlot (str | Sequence[str] | FreeBlock) – Undocumented.
NeutralizingDensityDetails (BAND._NeutralizingDensityDetails) –
NewResponse (BAND._NewResponse) – The TD-CDFT calculation to obtain the dielectric function is computed when this block is present in the input. Several important settings can be defined here.
NewResponseKSpace (BAND._NewResponseKSpace) – Modify the details for the integration weights evaluation in reciprocal space for each single-particle transition. Only influencing the NewResponse code.
NewResponseSCF (BAND._NewResponseSCF) – Details for the linear-response self-consistent optimization cycle. Only influencing the NewResponse code.
NonCollinearMagnetizationModule (BAND._NonCollinearMagnetizationModule) – Undocumented.
Occupations (str | Sequence[str] | FreeBlock) – Allows one to input specific occupations numbers. Applies only for calculations that use only one k-point (i.e. pseudo-molecule calculations). See example.
OldResponse (BAND._OldResponse) – Options for the old TD-CDFT implementation.
OrbitalLabels (str | Sequence[str] | FreeBlock) – Undocumented.
OrbitalPlot (str | Sequence[str] | FreeBlock) – Goes together with the Restart%OrbitalPlot and Grid keys. See Example.
Output (BAND._Output) – Control the output.
OverlapPopulations (str | Sequence[str] | FreeBlock) – Overlap population weighted DOS (OPWDOS), also known as the crystal orbital overlap population (COOP).
PEDANOCV (BAND._PEDANOCV) – Options for the decomposition of the orbital relaxation (pEDA).
PEDANOPR (BAND._PEDANOPR) – Undocumented.
PeriodicRIHartreeFock (BAND._PeriodicRIHartreeFock) – Technical options for periodic Hartree Fock.
PeriodicSolvation (BAND._PeriodicSolvation) – Additional options for simulations of periodic structures with solvation.
Programmer (BAND._Programmer) – Miscellaneous technical options.
PropertiesAtNuclei (str | Sequence[str] | FreeBlock) – A number of properties can be obtained near the nucleus. An average is taken over a tiny sphere around the nucleus. The following properties are available: vxc[rho(fit)], rho(fit), rho(scf), v(coulomb/scf), rho(deformation/fit), rho(deformation/scf).
RIHartreeFock (BAND._RIHartreeFock) –
RadialDefaults (BAND._RadialDefaults) – Options for the logarithmic radial grid of the basis functions used in the subprogram Dirac
Relativity (BAND._Relativity) – Options for relativistic effects.
ResponseInducedDensityPlot (str | Sequence[str] | FreeBlock) – Goes together with Restart%ResponseInducedDensityPlot and Grid.
Restart (BAND._Restart) – Tells the program that it should restart with the restart file, and what to restart.
SCF (BAND._SCF) – Controls technical SCF parameters.
Screening (BAND._Screening) – For the periodic solvation potential and for the old (not default anymore) fitting method, BAND performs lattice summations which are in practice truncated. The precision of the lattice summations is controlled by the options in this block.
SlakoConfig (BAND._SlakoConfig) – Undocumented.
SoftConfinement (BAND._SoftConfinement) – In order to make the basis functions more compact, the radial part of the basis functions is multiplied by a Fermi-Dirac (FD) function (this ‘confinement’ is done for efficiency and numerical stability reasons). A FD function goes from one to zero, controlled by two parameters. It has a value 0.5 at Radius, and the decay width is Delta.
Solvation (BAND._Solvation) – Options for the COSMO (Conductor like Screening Model) solvation model.
SolvationSM12 (BAND._SolvationSM12) – Options for Solvation Model 12 (SM12).
StrainDerivatives (BAND._StrainDerivatives) – Undocumented.
Tails (BAND._Tails) – Ignore function tails.
TechnicalCOSMO (BAND._TechnicalCOSMO) – Some options to develop cosmo for charged periodic systems
TestParameters (BAND._TestParameters) – Undocumented.
Transport (BAND._Transport) – Old NEGF. No longer supported
XC (BAND._XC) – Exchange Correlation functionals
ZlmFit (BAND._ZlmFit) – Options for the density fitting scheme ‘ZlmFit’.
- class _AIMCriticalPoints[source]¶
Compute the critical points of the density (Atoms In Molecules). The algorithm starts from a regular mesh of points, and from each of these it walks towards its corresponding critical point.
- Variables:
Enabled (BoolType | BoolKey) – Compute the critical points of the density (Atoms In Molecules). The algorithm starts from a regular mesh of points, and from each of these it walks towards its corresponding critical point.
EqvPointsTol (float | FloatKey) – If the distance between two critical points is smaller than this value, the two critical points are considered to be the same point.
GridPadding (float | FloatKey) – How much extra space is added to the starting guess domain in the search for the critical points
GridSpacing (float | FloatKey) – The distance between the initial trial points.
- class _ATensor[source]¶
Hyperfine A-tensor.
- Variables:
Enabled (BoolType | BoolKey) –
Compute the hyperfine A-tensor.
Note: Unrestricted calculation is required.
- class _Align[source]¶
Alignment of the potential of the system. Old NEGF.
- class _AtomType[source]¶
Explicit basis set definition for given atom type.
- Variables:
AutomaticGaussians (str | Sequence[str] | FreeBlock) – Definition of the automatic gaussians
BasisFunctions (str | Sequence[str] | FreeBlock) – Definition of the extra Slater-type orbitals
ContractedGaussians (str | Sequence[str] | FreeBlock) – Definition of the contracted gaussians
Dirac (str | Sequence[str] | FreeBlock) – Specification of the numerical (‘Herman-Skillman’) free atom, which defines the initial guess for the SCF density, and which also (optionally) supplies Numerical Atomic Orbitals (NOs) as basis functions
FitFunctions (str | Sequence[str] | FreeBlock) – Slater-type fit functions. Obsolete feature.
- class _BField[source]¶
The effect of a magnetic filed can be approximated by the following potential: mu * sigma_i * B, where mu is the Bohr magneton, sigma_i are the Pauli matrices and B is the magnetic field
- Variables:
Bx (float | FloatKey) – Value of the x component of the BField
By (float | FloatKey) – Value of the y component of the BField
Bz (float | FloatKey) – Value of the z component of the BField
Dipole (BoolType | BoolKey) – Use an atomic dipole as magnetic field instead of a uniform magnetic field.
DipoleAtom (int | IntKey) – Atom on which the magnetic dipole should be centered (if using the dipole option)
Method (Literal["NR_SDOTB", "NR_LDOTB", "NR_SDOTB_LDOTB"]) –
There are two terms coupling to an external magnetic field.
One is the intrinsic spin of the electron, called S-dot-B, the other one is the orbital momentum call L-dot-B.
The L.B is implemented non-relativistically, using GIAOs in the case of a homogeneous magnetic field (not for the dipole case).
Unit (Literal["tesla", "a.u."]) – Unit of magnetic filed. The a.u. is the SI version of a.u.
- class _BZPath[source]¶
Definition of the user-defined path in the Brillouin zone for band structure plotting.
- Variables:
- class _BandStructure[source]¶
Options for the calculation of the band structure.
- Variables:
Automatic (BoolType | BoolKey) –
If True, BAND will automatically generate the standard path through the Brillouin zone.
If False BAND will use the user-defined path in BZPath.
Step (in reciprocal space) for band structure interpolation.
Using a smaller number (e.g. 0.03) will result in smoother band curves at the cost of an increased computation time.
Enabled (BoolType | BoolKey) – If True, Band will calculate the band structure and save it to file for visualization.
EnergyAboveFermi (float | FloatKey) – Bands with minimum energy larger then FermiEnergy + EnergyAboveFermi are not saved to file. Increasing the value of EnergyAboveFermi will result in more unoccupied bands to be saved to file for visualization.
EnergyBelowFermi (float | FloatKey) – Bands with maximum energy smaller then FermiEnergy - EnergyBelowFermi are not saved to file. Increasing the value of EnergyBelowFermi will result in more occupied core bands to be saved to file for visualization. Note: EnergyBelowFermi should be a positive number!
FatBands (BoolType | BoolKey) –
If True, BAND will compute the fat bands (only if BandStructure%Enabled is True).
The Fat Bands are the periodic equivalent of the Mulliken population analysis.
KPathFinderConvention (Literal["Setyawan-Curtarolo", "Hinuma"]) –
This option determines how the path through the Brillouin zone is generated when using the automatic k-point mode.
Available options:
Setyawan-Curtarolo(default for 1D and 2D lattices): Uses our built-in KPath program to find a path through high-symmetry points based on the method by Setyawan and Curtarolo (https://doi.org/10.1016/j.commatsci.2010.05.010). For 2D lattices, the path is derived from the intersection of the 3D Brillouin zone with a plane. For 1D lattices, the path is simply Gamma-Z.Hinuma: Uses the external SeeKPath utility to generate the k-path (https://github.com/giovannipizzi/seekpath and https://doi.org/10.1016/j.commatsci.2016.10.015).
UseSymmetry (BoolType | BoolKey) –
If True, only the irreducible wedge of the Wigner-Seitz cell is sampled.
If False, the whole (inversion-unique) Wigner-Seitz cell is sampled.
Note: The Symmetry key does not influence the symmetry of the band structure sampling. Only available for Setyawan and Curtarolo convention (see
KPathFinderConvention).
- class _Basis[source]¶
Definition of the basis set
- Variables:
Core (Literal["None", "Small", "Medium", "Large"]) –
Select the size of the frozen core you want to use.
Small, Medium, and Large will be interpreted within the basis sets available (of the selected quality), and might refer to the same core in some cases.
Folder (str | Path | StringKey) – Path to a folder containing the basis set files. This can be used for special use-defined basis sets. Cannot be used in combination with ‘Type’
Type (Literal["SZ", "DZ", "DZP", "TZP", "TZ2P", "QZ4P", "QZ5P", "V", "STO/TZ2P", "STO/SZ", "STO/DZ", "STO/DZP", "STO/QZ4P", "AUTOGAUSS", "CORR/QZ6P", "CORR/TZ3P", "CORR/QZ6P_GH", "CORR/TZ3P_G", "GTO/CC-PWCVQZ", "GTO/CC-PV5Z", "GTO/DEF2-QZVPPD", "GTO/CC-PV6Z", "GTO/CC-PVQZ", "GTO/CC-PVTZ", "GTO/CC-PVDZ", "GTO/DEF2-SVP", "GTO/DEF2-TZVP", "GTO/DEF2-TZVPP", "GTO/DEF2-QZVP", "GTO/AUG-CC-PVDZ", "GTO/AUG-CC-PVTZ", "GTO/AUG-CC-PVQZ", "GTO/POB-TZVP"]) –
Select the basis set to use.
SZ : Single Z DZ : Double Z DZP : Double Z, 1 polarization function TZP : Triple Z, 1 polarization function TZ2P : Triple Z, 2 polarization functions QZ4P : Quadruple Z, 4 polarization function
The basis set chosen will apply to all atoms in your structure. If a matching basis is not found a better type might be used.
PerAtomType (BAND._Basis._PerAtomType) – Defines the basis set for all atoms of a particular type.
PerRegion (BAND._Basis._PerRegion) – Defines the basis set for all atoms in a region. If specified, this overwrites the values set with the Basis%Type and Basis%PerAtomType keywords for atoms in that region. Note that if this keyword is used multiple times, the chosen regions may not overlap.
- class _PerAtomType[source]¶
Defines the basis set for all atoms of a particular type.
- Variables:
Core (Literal["None", "Small", "Medium", "Large"]) – Size of the frozen core.
File (str | Path | StringKey) – The path to the basis set file. The path can be absolute or relative to $AMSRESOURCES/Band. Specifying the path to the basis file explicitly overrides the automatic basis file selection via the Type and Core subkeys.
Symbol (str | StringKey) – The symbol for which to define the basis set.
Type (Literal["SZ", "DZ", "DZP", "TZP", "TZ2P", "QZ4P", "V"]) – The basis sets to be used.
- class _PerRegion[source]¶
Defines the basis set for all atoms in a region. If specified, this overwrites the values set with the Basis%Type and Basis%PerAtomType keywords for atoms in that region. Note that if this keyword is used multiple times, the chosen regions may not overlap.
- Variables:
Core (Literal["None", "Small", "Medium", "Large"]) – Size of the frozen core.
File (str | Path | StringKey) – The path to the basis set file. The path can be absolute or relative to $AMSRESOURCES/Band. Specifying the path to the basis file explicitly overrides the automatic basis file selection via the Type and Core subkeys.
Region (str | StringKey) – The identifier of the region for which to define the basis set. Note that this may also be a region expression, e.g. ‘myregion+myotherregion’ (the union of two regions).
Type (Literal["SZ", "DZ", "DZP", "TZP", "TZ2P", "QZ4P", "V"]) – The basis sets to be used.
- class _BeckeGrid[source]¶
Options for the numerical integration grid, which is a refined version of the fuzzy cells integration scheme developed by Becke.
- Variables:
AllowAngularBoost (BoolType | BoolKey) – Allow automatic augmentation of the Lebedev spherical grid for highly coordinated atoms.
CutOffDistancePointCharges (float | FloatKey) – In case of external point charges the grid puts also centers there. For charges far away from the QM density this is not needed.
InnerShellsPruning (BoolType | BoolKey) – Allow automatic pruning of the Lebedev spherical grid for shells close to the nuclei.
PartitionFunPruning (BoolType | BoolKey) – Allow pruning of integration points based on the value of the partition function.
Quality (Literal["Auto", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Quality of the integration grid. For a description of the various qualities and the associated numerical accuracy see reference. If ‘Auto’, the quality defined in the ‘NumericalQuality’ will be used.
RadialGridBoost (float | FloatKey) – The number of radial grid points will be boosted by this factor. Some XC functionals require very accurate radial integration grids, so BAND will automatically boost the radial grid by a factor 3 for the following numerically sensitive functionals: LibXC M05, LibXC M05-2X, LibXC M06-2X, LibXC M06-HF, LibXC M06-L, LibXC M08-HX, LibXC M08-SO, LibXC M11-L, LibXC MS0, LibXC MS1, LibXC MS2, LibXC MS2H, LibXC MVS, LibXC MVSH, LibXC N12, LibXC N12-SX, LibXC SOGGA11, LibXC SOGGA11-X, LibXC TH1, LibXC TH2, LibXC WB97, LibXC WB97X, MetaGGA M06L, MetaHybrid M06-2X, MetaHybrid M06-HF, MetaGGA MVS.
UserCoreL (int | IntKey) – Technical grid parameter: Lebedev angular grid order for core shells.
UserExterL (int | IntKey) – Technical grid parameter: Lebedev angular grid order for exterl shells.
UserInter1l (int | IntKey) – Technical grid parameter: Lebedev angular grid order for first inner core shells.
UserInter2l (int | IntKey) – Technical grid parameter: Lebedev angular grid order for second inner core shells.
UserRadMulFactor (float | FloatKey) – Technical grid parameter: Multiplication factor for number of radial grid points.
QualityPerRegion (BAND._BeckeGrid._QualityPerRegion) – Sets the grid quality for all atoms in a region. If specified, this overwrites the globally set quality.
- class _Bias[source]¶
Old NEGF. No longer supported
- class _CDFT[source]¶
Constrained DFT Implementation in Transport. Old NEGF.
- class _Comment[source]¶
The content of this block will be copied to the output header as a comment to the calculation.
- class _Convergence[source]¶
Options and parameters related to the convergence behavior of the SCF procedure.
- Variables:
Criterion (float | FloatKey) – Criterion for termination of the SCF procedure. The default depends on the NumericalQuality and on the number of atoms in the system. Can be used for EngineAutomations
CriterionFactor (float | FloatKey) – Multiply Criterion (which depends on system and quality) with this factor. Can be used for EngineAutomations
Degenerate (str | StringKey) – Smooths (slightly) occupation numbers around the Fermi level, so as to insure that nearly-degenerate states get (nearly-) identical occupations. Be aware: In case of problematic SCF convergence the program will turn this key on automatically, unless the key ‘Nodegenerate’ is set in input. The smoothing depends on the argument to this key, which can be considered a ‘degeneration width’. When the argument reads default, the program will use the value 1e-4 a.u. for the energy width.
ElectronicTemperature (float | FloatKey) – (KT) Specify this key for a gradient independent electronic temperature
InitialDensity (Literal["rho", "psi", "frompot"]) – The SCF is started with a guess of the density. There are the following choices RHO: the sum of atomic density. PSI: construct an initial eigensystem by occupying the atomic orbitals. The guessed eigensystem is orthonormalized, and from this the density is calculated/
LessDegenerate (BoolType | BoolKey) – If smoothing of occupations over nearly degenerate orbitals is applied (see Degenerate key), then, if this key is set in the input file, the program will limit the smoothing energy range to 1e-4 a.u. as soon as the SCF has converged ‘halfway’, i.e. when the SCF error has decreased to the square root of its convergence criterion.
ModestCriterion (float | FloatKey) – If this is specified band will consider the SCF converged if the error is below this criterion (after using the maximum number of iterations).
NoDegenerate (BoolType | BoolKey) – This key prevents any internal automatic setting of the key DEGENERATE.
NumBoltz (int | IntKey) – The electronic temperature is done with a Riemann Stieltjes numerical integration, between zero and one occupation. This defines the number of points to be used.
SpinFlip (Iterable[int] | IntListKey) – List here the atoms for which you want the initial spin polarization to be flipped. This way you can distinguish between ferromagnetic and anti ferromagnetic states. Currently, it is not allowed to give symmetry equivalent atoms a different spin orientation. To achieve that you have to break the symmetry.
SpinFlipEnabled (BoolType | BoolKey) – If set to False, the keys SpinFlip and SpinFlipRegion are ignored. Only useful/convenient when trying to compare in a script the effect of spin flip.
SpinFlipRegion (str | StringKey) – Specify here the region for which you want the initial spin polarization to be flipped. This way you can distinguish between ferromagnetic and anti ferromagnetic states. Currently, it is not allowed to give symmetry equivalent atoms a different spin orientation. To achieve that you have to break the symmetry.
StartWithMaxSpin (BoolType | BoolKey) – To break the initial perfect symmetry of up and down densities there are two strategies. One is to occupy the numerical orbitals in a maximum spin configuration. The alternative is to add a constant to the potential. See also Vsplit key.
StartWithMaxSpinForSO (BoolType | BoolKey) – Same as the StartWithMaxSpin option. In case of spin-orbit band always used to split the potential. Now will use maxspin in case of SpinFlip. With this option it will always do that.
- class _DFTBConfinementPotential[source]¶
Specify the confinement potentials (used for DFTB parametrization)
- class _DIIS[source]¶
Parameters for the DIIS procedure to obtain the SCF solution
- Variables:
Adaptable (BoolType | BoolKey) – Change automatically the value of dimix during the SCF.
CHuge (float | FloatKey) – When the largest coefficient in the DIIS expansion exceeds this value, damping is applied
CLarge (float | FloatKey) – When the largest DIIS coefficient exceeds this value, the oldest DIIS vector is removed and the procedure re-applied
Condition (float | FloatKey) – The condition number of the DIIS matrix, the largest eigenvalue divided by the smallest, must not exceed this value. If this value is exceeded, this vector will be removed.
DiMix (float | FloatKey) – Mixing parameter for the DIIS procedure
DiMixMax (float | FloatKey) – For adaptive diis: A negative value means automatic, see DiMixatnvctrx. If positive it is an absolute upper bound for (adaptive) dimix
DiMixMin (float | FloatKey) – An absolute lower bound for adaptive dimix.
DiMixatnvctrx (float | FloatKey) – Adaptive dimix. When only one vector is used the maximum is one, when the full history is used it is this value (Exponential decay).
EDIIS (BoolType | BoolKey) – Use EDIIS
NCycleDamp (int | IntKey) – Number of initial iterations where damping is applied, before any DIIS is considered
NVctrx (int | IntKey) – Maximum number of DIIS expansion vectors
Variant (Literal["DIIS", "LISTi", "LISTb", "LISTd"]) – Which variant to use. In case of problematic SCF convergence, first try MultiSecant, and if that does not work the LISTi is the advised method. Note: LIST is computationally more expensive per SCF iteration than DIIS.
- class _DIRIS[source]¶
Same options as DIIS key, except that this one applies to the DIIS procedure used in the Dirac subprogram, for numerical single atom calculations, which constructs the radial tables for the NAOs.
- class _DOS[source]¶
Density-Of-States (DOS) options
- Variables:
AbsoluteMaxMin (BoolType | BoolKey) – When DOS%Min and DOS%Max are used: should they be absolute or relative to the fermi level.
CalcDOS (BoolType | BoolKey) – Whether or not to calculate the density of states.
CalcPDOS (BoolType | BoolKey) – Whether or not to calculate the partial DOS (projections on basis functions). This can be significantly more expensive than calculating the total DOS
CalcPopulationAnalysis (BoolType | BoolKey) – Whether or not to calculate the population analysis. Population analysis can become very expensive when there are many symmetry operators, such as in a super cell.
CompensateDeltaE (BoolType | BoolKey) – Only relevant when IntegrateDeltaE=yes. If set to true then after integrating each interval over DeltaE the result is divided by DeltaE, so that the unit is DOS.
DeltaE (float | FloatKey) – Energy step for the DOS grid. Using a smaller value (e.g. half the default value) will result in a finer sampling of the DOS.
Enabled (BoolType | BoolKey) – Obsolete key whether or not to calculate the density of states.
Energies (int | IntKey) – Number of equidistant energy-values for the DOS grid. This keyword is superseded by the ‘DeltaE’ keyword.
File (str | Path | StringKey) – Write the DOS (plain text format) to the specified file instead of writing it to the standard output.
IntegrateDeltaE (BoolType | BoolKey) – This subkey handles which algorithm is used to calculate the data-points in the plotted DOS. If true, the data-points represent an integral over the states in an energy interval. Here, the energy interval depends on the number of Energies and the user-defined upper and lower energy for the calculation of the DOS. The result has as unit [number of states / (energy interval * unit cell)]. If false, the data-points do represent the number of states for a specific energy and the resulting plot is equal to the DOS per unit cell (unit: [1/energy]). Since the resulting plot can be a wild function and one might miss features of the DOS due to the step length between the energies, the default is set to the integration algorithm.
Max (float | FloatKey) – User defined upper bound energy (with respect to the Fermi energy)
Min (float | FloatKey) – User defined lower bound energy (with respect to the Fermi energy)
ReduceSymmetryOperatorsForIBZExpansion (BoolType | BoolKey) – To expand the eigensystem to the whole BZ either all or a minimal set can be used. If it can be reduced this is the faster option.
StoreCoopPerBasPair (BoolType | BoolKey) – Calculate the COOP (crystal orbital overlap population).
UseSharedArrays (BoolType | BoolKey) – Undocumented.
- class _DensityPlot[source]¶
Plots of the density. Goes together with the Restart%DensityPlot and Grid keys.
- class _Dependency[source]¶
Criteria for linear dependency of the basis and fit set
- Variables:
AllowBasisDependency (BoolType | BoolKey) – Project out the dependent part of the basis set (associated with small eigenvalues of the overlap matrix).
Basis (float | FloatKey) – Criteria for linear dependency of the basis: smallest eigenvalue of the overlap matrix of normalized Bloch functions.
Core (float | FloatKey) – The program verifies that the frozen core approximation is reasonable, by checking the smallest eigen value of the overlap matrix of the core (Bloch) orbitals (which should ideally be one) is bigger than this criterion.
CoreValence (float | FloatKey) – Criterion for dependency of the core functions on the valence basis. The maximum overlap between any two normalized functions in the two respective function spaces should not exceed 1.0-corevalence
Fit (float | FloatKey) – Criterion for dependency of the total set of fit functions. The value monitored is the smallest eigenvalue of the overlap matrix of normalized Bloch sums of symmetrized fit functions.
KeepShapeForDependencyFix (BoolType | BoolKey) – If AllowBasisDependency=true, this triggers the most simple fix, where all matrices retain their shape.
- class _DiracOptions[source]¶
Options for the atomic Dirac calculations.
- Variables:
DumpAllTables (BoolType | BoolKey) – Dump many functions during the SCF on a file call dirac.rkf. Works only for one atom. xxx
UseDidervInDigradRel (BoolType | BoolKey) – For scalar zora dv/dr is used to get the analytical second derivative of the large component. It can also be obtained by numerical differentiation of dpsi/dr
convergence (float | FloatKey) – Convergence criterion, based on input/output density difference.
maxcycles (int | IntKey) – Maximum number of self-consistent attempts to be made.
spinor (BoolType | BoolKey) – Undocumented.
- class _EFG[source]¶
The electronic charge density causes an electric field, and the gradient of this field couples with the nuclear quadrupole moment, that some (non-spherical) nuclei have and can be measured by several spectroscopic techniques. The EFG tensor is the second derivative of the Coulomb potential at the nuclei. For each atom it is a 3x3 symmetric and traceless matrix. Diagonalization of this matrix gives three eigenvalues, which are usually ordered by their decreasing absolute size and denoted as V_{xx}, V_{yy}, V_{zz}. The result is summarized by the largest eigenvalue and the asymmetry parameter.
- Variables:
Enabled (BoolType | BoolKey) – Compute the EFG tensor (for nuclear quadrupole interaction).
- class _ESR[source]¶
Zeeman g-tensor. The Zeeman g-tensor is implemented using two-component approach of Van Lenthe and co-workers in which the g-tensor is computed from a pair of spinors related to each other by time-reversal symmetry. Note: the following options are necessary for ESR: ‘Relativistic zora spin’ and ‘Kspace 1’
- Variables:
Enabled (BoolType | BoolKey) –
Compute Zeeman g-tensor.
The Zeeman g-tensor is implemented using two-component approach of Van Lenthe and co-workers in which the g-tensor is computed from a pair of spinors related to each other by time-reversal symmetry.
Note: the following options are necessary for ESR: ‘Relativistic zora spin’ and ‘Kspace 1’
- class _EffectiveMass[source]¶
In a semi-conductor, the mobility of electrons and holes is related to the curvature of the bands at the top of the valence band and the bottom of the conduction band.
With the effective mass option, this curvature is obtained by numerical differentiation.
The estimation is done with the specified step size, and twice the specified step size, and both results are printed to give a hint on the accuracy. The easiest way to use this key is to enabled it without specifying any extra options.
- Variables:
Enabled (BoolType | BoolKey) – Compute the EffectiveMass.
KPointCoord (Iterable[float] | FloatListKey) – Coordinate of the k-points for which you would like to compute the effective mass.
NumAbove (int | IntKey) – Number of bands to take into account above the Fermi level.
NumBelow (int | IntKey) – Number of bands to take into account below the Fermi level.
StepSize (float | FloatKey) – Size of the step taken in reciprocal space to perform the numerical differentiation
UseBandStructureInfoFromPath (BoolType | BoolKey) – The (automatic) location of the HOMO and LUMO can be determined via band interpolation, or from the path as used by the BandStructure feature. The latter works better when they are located on the path. See also comments in the BandStructure block. To reproduce results from before ams2025 set to no.
- class _ElectronHole[source]¶
Allows one to specify an occupied band which shall be depopulated, where the electrons are then moved to the Fermi level. For a spin-restricted calculation 2 electrons are shifted and for a spin-unrestricted calculation only one electron is shifted.
- class _EmbeddingPotential[source]¶
An external potential can be read in and will be added to the effective Kohn-Sham potential. It has to be on the becke grid
- class _Excitations[source]¶
Excitation energies: UV/Vis
- Variables:
BSE (BoolType | BoolKey) – Solve the static Bethe-Salpeter equation based on a GW calculation
- class _Fermi[source]¶
Technical parameter used in determining the Fermi energy, which is carried out at each cycle of the SCF procedure.
- Variables:
Delta (float | FloatKey) – Convergence criterion: upper and lower bounds for the Fermi energy and the corresponding integrated charge volumes must be equal within delta.
Eps (float | FloatKey) – After convergence of the Fermi energy search procedure, a final estimate is defined by interpolation and the corresponding integrated charge volume is tested. It should be exact, to machine precision. Tested is that it deviates not more than eps.
MaxTry (int | IntKey) – Maximum number of attempts to locate the Fermi energy. The procedure is iterative in nature, narrowing the energy band in which the Fermi energy must lie, between an upper and a lower bound. If the procedure has not converged sufficiently within MaxTry iterations, the program takes a reasonable value and constructs the charge density by interpolation between the functions corresponding to the last used upper and lower bounds for the Fermi energy.
RefinePostSCFFactor (int | IntKey) – Use a finer k-grid after the scf to calculate a refined fermi level. Makes only sense for metals. Works like DoubleCount. Use 1,2,3
- class _FermiSurface[source]¶
Calculation of the Fermi surface for metals
- Variables:
AvoidDuplicates (BoolType | BoolKey) – Undocumented.
CaseA (BoolType | BoolKey) – Undocumented.
CaseB (BoolType | BoolKey) – Undocumented.
CaseC (BoolType | BoolKey) – Undocumented.
ConjugateGradient (BoolType | BoolKey) – Undocumented.
Enabled (BoolType | BoolKey) – Calculate the Fermi surface if the system has no band gap (i.e. is a metal). The result can be visualized with amsbands.
KIntegForSymmetricKGrid (int | IntKey) – If the (default) regular k-grid is used, a symmetric one is created to determine the Fermi surface. If this key is not specified an automatic value of kInteg is used. Odd values trigger quadratic interpolation.
NMesh (int | IntKey) – Improves the matching of the interpolated quadratic surface. For better results it makes more sense to increases KIntegForSymmetricKGrid.
UniqueWedgeOnly (BoolType | BoolKey) – Undocumented.
- class _FitMethod[source]¶
Undocumented
- Variables:
ConstrainCharge (BoolType | BoolKey) – Undocumented
ConstrainWiths (BoolType | BoolKey) – Undocumented
PruneDivisions (BoolType | BoolKey) – Undocumented
RepeatDivisions (BoolType | BoolKey) – Undocumented
StoreFinalFitTra (BoolType | BoolKey) – Undocumented
UseSharedarrays (BoolType | BoolKey) – Undocumented
- class _Fragment[source]¶
Defines a fragment. You can define several fragments for a calculation.
- Variables:
Filename (str | StringKey) – Filename of the fragment. Absolute path or path relative to the executing directory.
AtomMapping (str | Sequence[str] | FreeBlock) – Format ‘indexFragAt indexCurrentAt’. One has to associate the atoms of the fragment to the atoms of the current calculation. So, for each atom of the fragment the indexFragAt has to be associated uniquely to the indexCurrentAt for the current calculation.
Labels (str | Sequence[str] | FreeBlock) – This gives the possibility to introduce labels for the fragment orbitals. See examples.
- class _FuzzyPotential[source]¶
Atomic (fuzzy cell) based, external, electric potential. See example.
- class _FuzzyUnitCellGrid[source]¶
Undocumented.
- Variables:
CellPartitionInterpolationCubic (BoolType | BoolKey) – Undocumented.
CellPartitionInterpolationMesh (int | IntKey) – Undocumented.
CentralizeNaturalLSG (BoolType | BoolKey) – Undocumented.
InterpolateCellPartition (BoolType | BoolKey) – Undocumented.
PruneLatticeSummedGrid (BoolType | BoolKey) – Undocumented.
ReduceAccuracyLSG (BoolType | BoolKey) – Undocumented.
SimpleLatticeSummedGrid (BoolType | BoolKey) – Undocumented.
- class _GW[source]¶
Perform a GW calculation. G0W0 is the default for GW%SelfConsistency.
- Variables:
AdaptiveMixing (Iterable[float] | FloatListKey) –
Requests to use adaptive mixing instead of DIIS and sets the staring mixing parameter for mixing of Green’s function in case of self-consistency.
Adapative mixing is recommended in case a qsGW calculation does not converge with DIIS.
It is ignored in non-selfconsistent calculation and overwritten by DIIS when DIIS is also present.
DIIS (int | IntKey) – Requests to use DIIS. This is the Default. Number of expansion coefficients can be requested as well. Ignored in non-selfconsistent calculation
Enabled (BoolType | BoolKey) – Enable the calculation of the GW quasi-particle energies.
ExpansionOrder (int | IntKey) – Order of the expansion of the screened interaction on the SOS-GF(n) method. order 2 (=SOS-GF2) is the default
FixedGridSizes (BoolType | BoolKey) – In a self-consistent GW calculation, recalculate Grids but keep them the same size during the SCF procedure.
FixedGrids (BoolType | BoolKey) – In a self-consistent GW calculation, do not recalculate Grids. Can be useful in case of convergence problems. Only relevant for qsGW and qsGW0. In case of evGW and evGW0, the grids are always kept fixed.
G3W2 (Literal["Full", "Diagonal", "Perturbative"]) – Only relevant when self-energy is one of GF2 or G3W2: Full requests that the second-order term is evaluated for the full self-energy matrix. This is very expensive and should only be done for small systems. Diagonal requests, that only the Diagonal of the self-energy matrix is updated. Perturbative means, that only a second-order screened exchange correction is evaluated after the GW calculation is completed. For a G0W0 calculation, all of these options are equivalent.
LinearMixing (Iterable[float] | FloatListKey) –
Requests to use linear mixing instead of DIIS and sets the mixing parameter for linear mixing of Green’s function in case of self-consistency.
It is ignored in non-selfconsistent calculation and overwritten by DIIS when DIIS is also present.
LinearizeQPequations (BoolType | BoolKey) –
Instead of solving the non-linear QP equations in a G0W0 (or evGW calculation) by bisection exacly, linearize them by first-order Taylor expansion.
This is not recommended since it does not save computational time when used together with analytical continuation (as implemented in AMS). It might however be useful for benchmarking or for validating results.
If the results os the linearization differ by a lot (for instance, more than 0.1 eV in frontier QP energies) from the non-linearized results, this might indicate that the GW calculation is not reliable.
OffDiagonalEFermi (BoolType | BoolKey) – Analytically continue the off-diagonal elements of the KSF2 qsGW Hamiltonian at the Fermi-energy instead of omega=0. Typically leads to slightly lower QP energies, i.e. higher ionization potentials. The HOMO-LUMO gaps are typically not affected.
Polarizability (Literal["RPA", "BSE", "G4W1", "G4V1", "TDHF"]) –
Sets the expression for the Polarizability used in the GW calculation.
RPA is the Default and amounts to a standard GW calculation.
BSE denotes screening in the Bethe-Salpeter-equation formalism.
PrintAllSolutions (BoolType | BoolKey) – Print out all solutions for all requested states. Detects multiple solutions of the QP equations.
PrintImaginaryAxisData (BoolType | BoolKey) – If true, print out the self-energy on the imaginary axis.
PrintSpectralFunction (BoolType | BoolKey) – Plot the self-energy as a function of frequency. Automatically done in case of analytical continuation. However, this is expensive in the analytical integration formalism.
PrintZfactor (BoolType | BoolKey) –
QPHamiltonian (Literal["KSF1", "KSF2", "SRG", "LQSGW"]) –
The quasi-particle Hamiltonian can be constructed in different ways.
KSF1 refers to the original construction by Kotani, Van Schilfgaarde anf Faleev (KSF) which is also implemented in TURBOMOLE.
KSF2 refers to an alternative construction by KSF.
KSF1 is not recommended since it is numerically less stable than KSF2 in case analytical continuation is used (the default).
In case the analytical integration algorithm is used, only KSF1 is implemented. Therefore, make sure that KSF1 is specified. The results are typically very similar.
The QP energies at which the matrix elements are evaluated can be tweaked further, see the two subsequent keys: However, KSF2 is recommended since it typically leads to QP energies with the best agreement with experiment.
Ignored when not a quasi-particle self-consistent GW calculation is performed
Scaling (float | FloatKey) – Scale factor for the polarizability in the screened interaction SOS-GF2. Default = 1.0 (corresponds to no scaling)
ScissorShift (BoolType | BoolKey) –
Only calculate the HOMO and LUMO QP energies and shift the remaining QP energies by the same amount.
This is a rather crude approximation and not recommended.
It might again be useful for benchmarking purposes.
SelfConsistency (Literal["None", "G0W0", "EVGW0", "EVGW", "QSGW0", "QSGW"]) –
Sets the level of self-consistency in a GW calculation.
G0W0 calculates a one-shot, perturbative correction to the KS eigenvalues.
In evGW and evGW0, the quasi-particle energies are updated until self-consistency is reached.
evGW0 requests that the Green’s function is evaluated self-consistently but not the screened interaction.
In qsGW, the density is updated as well, however, the self-energy is mapped to a static effective potential and the Dyson equation is solved by diagonalization instead of inversion. The results of a qsGW are independent of the choice of the underlying exchange-correlation functional and are usually the most accurate ones.
The same is done in qsGW0, but the screened interaction is not updated.
SelfConsistentSigmaVertex (BoolType | BoolKey) – If active, evaluate the vertex correction in Sigma in qsGW self-consistent. Only supported for GWGammaInf so far
SelfEnergy (Literal["HF", "GW", "G3W2", "SOSEX", "GWGamma", "G3W2dynamic", "GWGammaInf", "GWGammaInfDyn"]) –
Controls the form of the self-energy.
GW is the default and corresponds to the standard GW calculation.
G3W2 is a GW calculation plus a perturbative second-order statically screened exchange correction (second order expansion in the self-energy). Note, that there the self-energy is always static.
TabulateGridPoints (BoolType | BoolKey) – pretabulate grid points for numerical integration.
nIterations (Iterable[int] | IntListKey) –
The maximum number of iterations within the (partially or fully) self-consistent GW calculation has to converge.
Ignored when Formalism is set to G0W0
nLowest (int | IntKey) – Number of lowest occupied QP levels to be evaluated, overwrites nStates’
Number of Quasiparticle States to be printed to output.
The default is 5 states which in this case means that min(5, Number of particle states) occupied and min(5, Number of hole states) hole states are printed. The whole list of states can be printed by setting this parameter to -1’
preconditionQSGW (BoolType | BoolKey) –
If true, the QSGW equations are solved but prior to each diagonalization, i.e. a G0W0 calculation is performed to find the optimal QP energies at which to analytically continue the self-energy.
This is in principle a more consistent construction than KSF1 or KSF2 since the diagonal elements are consistent with G0W0.
In KSF1 and KSF2, the diagonal elements are evaluated at the QP energies from the previous iteration which is equivalent to a zeroth-order Taylor expansion of the diagonal elements around the previous QP energies.Enabling this option typically leads to slightly lower QP energies.
AnalyticalIntegration (BAND._GW._AnalyticalIntegration) – Use analytical integration to calculate the self-energy. Very slow, unless the system is very small but useful to check the accuracy of the frequency integration
Converge (BAND._GW._Converge) – Sets convergence criteria for the GW calculation in self-consistent case
- class _AnalyticalIntegration[source]¶
Use analytical integration to calculate the self-energy. Very slow, unless the system is very small but useful to check the accuracy of the frequency integration
- Variables:
Enabled (BoolType | BoolKey) – Enable the calculation of the GW quasi-particle energies via analytical integration.
SpectralFunctionResolution (int | IntKey) – Number of points at which spectral function is evaluated.
TDA (BoolType | BoolKey) – Solve the linear response equations in the Tamm-Dancoff approximation.
Artificial (positive) broadening parameter for evaluation of self-energy in analytical integration.
Ideally should be as small as possible but this might lead to convergence issues in partially self-consistent approaches.
In this case, a value of up to 0.1 is possible.
printBSEexcitationsInLastIteration (BoolType | BoolKey) –
Print out BSE excitations in the last iteration in a qsGW calculation. Can be used in the BAND engine.
In ADF, one should instead just calculate excitation energies using the excitation block.
- class _Converge[source]¶
Sets convergence criteria for the GW calculation in self-consistent case
- Variables:
Density (Iterable[float] | FloatListKey) –
First Criterion for self-consistency procedure to terminate.
Criterion is the trace of the density matrix. Ignored in non-selfconsistent Calculation and in eigenvalue self-consistent GW
It is possible to run a qsGW calculation with an inner SCF loop which updates the static part of the elf-energy only. This can be useful to accelerate the convergence in case linear mixing is used. It is not recommended to use linear mixing, so it is also not recommended to use that inner loop as well. The second number in this list specifies the convergence criterion for the inner SCF loop.
Criterion for self-consistency procedure to terminate.
The self-consistent GW calculation terminates, when the difference between the HOMO QP energies between 2 consecutive iterations is below this number.
The LUMO energy converged faster than the HOMO energy so when the HOMO energy is converged according to this criterion, the LUMO energy will be converged as well.
In non-selfconsistent Calculation, this criterion is ignored.
- class _Gradients[source]¶
Options for nuclear gradients and strain derivatives calculations.
- Variables:
AccurateNucGradKin (BoolType | BoolKey) – Undocumented.
AddCoulombAndXC (BoolType | BoolKey) – Undocumented.
CoreOrthPartialInt (BoolType | BoolKey) – Undocumented.
FastNucGradRho (BoolType | BoolKey) – Undocumented.
MetaGGAUpdateOption (int | IntKey) – How to update metaGGA nuclear gradient terms. Option 1 is the original implementation. Option 2 is faster and requires less memory
NeglectCoreCoreTerm (BoolType | BoolKey) – Undocumented.
NucGradAtomGroupSize (int | IntKey) – Avoid handling the nuclear gradient of the basis set of all atoms at once. A negative value means: handle all at once. Currently only affects MetaGGA calculations.
StrainDerivatives (BoolType | BoolKey) – Undocumented.
StrainDerunitcellintegraloption (int | IntKey) – Undocumented.
StrainDerwholespaceintegraloption (int | IntKey) – Undocumented.
ViaVOC (BoolType | BoolKey) – Undocumented.
WipeOneCenterTerms (BoolType | BoolKey) – Undocumented.
- class _Grid[source]¶
Options for the regular grid used for plotting (e.g. density plot). Used ICW the restart option.
- Variables:
ExtendX (float | FloatKey) – Extend the default regular grid along the x-direction by the specified amount: [x_min, x_max] => [x_min - ExtendX/2, x_max + ExtendX/2].
ExtendY (float | FloatKey) – Extend the default regular grid along the y-direction by the specified amount: [y_min, y_max] => [y_min - ExtendY/2, y_max + ExtendY/2].
ExtendZ (float | FloatKey) – Extend the default regular grid along the z-direction by the specified amount: [z_min, z_max] => [z_min - ExtendZ/2, z_max + ExtendZ/2].
FileName (str | StringKey) – Read in the grid from a file. The file format of the grid is: three numbers per line (defining the x, y and z coordinates of the points).
Type (Literal["coarse", "medium", "fine"]) – The default regular grids.
UserDefined (str | Sequence[str] | FreeBlock) – One can define the regular grid specification in this block. See example. Default unit is Bohr
- class _GridBasedAIM[source]¶
Invoke the ultra fast grid based Bader analysis.
- Variables:
Enabled (BoolType | BoolKey) – Invoke the ultra fast grid based Bader analysis.
Iterations (int | IntKey) – The maximum number of steps that may be taken to find the nuclear attractor for a grid point.
SmallDensity (float | FloatKey) – Value below which the density is ignored. This should not be chosen too small because it may lead to unassignable grid points.
UseStartDensity (BoolType | BoolKey) – Whether the analysis is performed on the startup density (True) or on the final density (False).
- class _GrossPopulations[source]¶
Partial DOS (pDOS) are generated for the gross populations listed under this key. See example.
- class _HardConfinement[source]¶
Obsolete basis functions confinement method. Use SoftConfinement instead.
- class _HubbardU[source]¶
Options for Hubbard-corrected DFT calculations.
- Variables:
Enabled (BoolType | BoolKey) – Whether or not to apply the Hubbard Hamiltonian. Can be useful to turn of Hubbard in a script with a single variable.
IgnoreForPEDA (BoolType | BoolKey) – Ignore the hubbard energy term when calculating the energy of psi_0 for the energy decomposition analysis (EDA).
LValue (str | StringKey) – For each atom type specify the l value (0 - s orbitals, 1 - p orbitals, 2 - d orbitals). A negative value is interpreted as no l-value.
PrintOccupations (BoolType | BoolKey) – Whether or not to print the occupations during the SCF.
UValue (str | StringKey) – For each atom type specify the U value (in atomic units). A value of 0.0 is interpreted as no U.
UseDiagonalOccupations (BoolType | BoolKey) – Undocumented.
UseNAO (BoolType | BoolKey) – Undocumented.
Atom (BAND._HubbardU._Atom) – Specify Hubbard parameters (U,l) for a certain element
Region (BAND._HubbardU._Region) – Specify Hubbard parameters (U,l) for all atoms in a certain region
- class _Integration[source]¶
Options for the Voronoi numerical integration scheme. Deprecated. Use BeckeGrid instead.
- Variables:
AccInt (float | FloatKey) – General parameter controlling the accuracy of the Voronoi integration grid. A value of 3 would be basic quality and a value of 7 would be good quality.
AccOut (float | FloatKey) – Integration accuracy for the outer region.
AccSph (float | FloatKey) – Integration accuracy for the atomic sphere regions.
AllElectron (BoolType | BoolKey) – Undocumented.
Slow (BoolType | BoolKey) – Undocumented.
TSTF (BoolType | BoolKey) – Undocumented.
- class _KSpace[source]¶
Options for the k-space integration (i.e. the grid used to sample the Brillouin zone)
- Variables:
Analytical (BoolType | BoolKey) –
For analytical integration the BZ is split into simplices, whereover the bands are interpolated, ater which the integrals can be performed analytically.
Alternatively, the set of eigenvalues in the discrete set of k-points are just handled as distinct molecular orbitals.
Using analytical=no can improve SCF convergence in combination with smearing/temperature.
Quality (Literal["Auto", "GammaOnly", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) –
Select the quality of the K-space grid used to sample the Brillouin Zone. If ‘Auto’, the quality defined in the ‘NumericalQuality’ will be used. If ‘GammaOnly’, only one point (the gamma point) will be used.
The actual number of K points generated depends on this option and on the size of the unit cell. The larger the real space cell, the fewer K points will be generated.
The CPU-time and accuracy strongly depend on this option.
Type (Literal["Regular", "Symmetric"]) –
The type of k-space integration grid used to sample the Brillouin zone (BZ) used.
’Regular’: simple regular grid.
’Symmetric’: symmetric grid for the irreducible wedge of the first BZ (useful when high-symmetry points in the BZ are needed to capture the correct physics of the system, graphene being a notable example).
Regular (BAND._KSpace._Regular) – Options for the regular k-space integration grid.
Symmetric (BAND._KSpace._Symmetric) – Options for the symmetric k-space integration grid.
- class _Regular[source]¶
Options for the regular k-space integration grid.
- Variables:
DoubleCount (int | IntKey) – Increase for each dimension the grid. A sequence of doubling, with a special meaning for grid with odd numbers. Useful when checking k-space convergence.
NumberOfPoints (Iterable[int] | IntListKey) –
Use a regular grid with the specified number of k-points along each reciprocal lattice vector.
For 1D periodic systems you should specify only one number, for 2D systems two numbers, and for 3D systems three numbers.
PreferEvenNumberOfPoints (BoolType | BoolKey) – In case of an automatic grid normally odd numbers will be generated (1,3,5,9), suitable for a quadratic grid. With this option the suggested odd numbers will be increased by one, unless it is one.
SplitCubeInSix (BoolType | BoolKey) – Undocumented.
SplitLongest (BoolType | BoolKey) – Undocumented.
- class _Symmetric[source]¶
Options for the symmetric k-space integration grid.
- Variables:
Specify the accuracy for the Symmetric method.
1: absolutely minimal (only the G-point is used) 2: linear tetrahedron method, coarsest spacing 3: quadratic tetrahedron method, coarsest spacing 4,6,… (even): linear tetrahedron method 5,7…. (odd): quadratic method
The tetrahedron method is usually by far inferior.
- class _LDOS[source]¶
Local Density-Of-States information. This can be used to generate STM images in the Tersoff-Hamann approximation (see https://doi.org/10.1103/PhysRevB.31.805)
- class _MBPT[source]¶
Technical aspects of the MP2 algorithm.
- Variables:
Dependency (BoolType | BoolKey) – If true, to improve numerical stability, almost linearly-dependent combination of basis functions are removed from the Green’s function that are used in the MBPT equations. Disabling this key is strongly discouraged. Its value can however be changed. The key to adjust this value is RiHartreeFock%DependencyThreshold
Enabled (BoolType | BoolKey) – Enable the calculation of the MP2 energy.
ExcludeCore (BoolType | BoolKey) –
If active, excludes core states from the calculation of the optimal imaginary time and frequency grids.
The core states are still included in all parts of the calculations.
In case a frozen care calculation is performed, this key is ignored.
For MP2 and double hybrid calculation, it defaults to false. For RPA and GW calculations, it defaults to true.
FitSetQuality (Literal["Auto", "VeryBasic", "Basic", "Normal", "Good", "VeryGood"]) –
Specifies the fit set to be used in the MBPT calculation.
’Normal’ quality is generally sufficient for basis sets up to and including TZ2P.
For larger basis sets (or for benchmarking purposes) a ‘VeryGood’ fit set is recommended. Note that the FitSetQuality heavily influences the computational cost of the calculation.
If not specified or ‘Auto’, the RIHartreeFock%FitSetQuality is used.
Formalism (Literal["Auto", "RI", "LT", "All"]) –
Specifies the formalism for the calculation of the MP2 correlation energy.
’LT’ means Laplace Transformed MP2 (also referred to as AO-PARI-MP2),
’RI’ means that a conventional RI-MP2 is carried out.
If ‘Auto’, LT will be used in case of DOD double hybrids and SOS MP2, and RI will be used in all other cases.
’All’ means that both RI and LT formalisms are used in the calculation.
For a RPA or GW calculation, the formalism is always LT, irrespective of the formalism specified with this key.
FrequencyGridType (Literal["LeastSquare", "GaussLegendre"]) – Use Gauss-legendre grid for imaginary frequency integration in RPA and GW calculations instead of the usually used Least-Square optimized ones. Has the advantage that it can be systematically converged and an arbitrary number of grid points can be used. Typically more grid points will be needed to get the same level of accuracy. However, the convergence of the results with the size of the grid can be more systematic. These grids can only be used when Formalism is set to RI.
IntegrationQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood"]) – Specifies the integration quality to be used in the MBPT calculation. If not specified, the RIHartreeFock%IntegrationQuality is used.
PrintOutSigma (BoolType | BoolKey) – Print out additional output for sigma-functional for parametrization.
SigmaFunctionalParametrization (Literal["W1", "W2", "S1", "S2", "S1re"]) – Only relevant if a sigma-functional calculation is performed. Possible choices for the parametrization of the sigma-functional. Not all options are supported for all functionals.
ThresholdQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Controls the distances between atomic centers for which the product of two basis functions is not fitted any more. Especially for spatially extended, large systems, ‘VERYBASIC’ and ‘BASIC’ can lead to large computational savings, but the fit is also more approximate. If not specified, the RIHartreeFock%ThresholdQuality is used.
UseScaledZORA (BoolType | BoolKey) – If true, use the scaled ZORA orbital energies instead of the ZORA orbital energies in the MBPT equations.
cutOfftransition (float | FloatKey) – Energy above which states are ignored in a MBPT calculation (must be a positive number). The default energy is chosen so high, that all states are included except for the ones which have been removed.
frozencore (BoolType | BoolKey) – Freeze core states in correlation part of MBPT calculation
Number of core states which will be excluded from the correlated calculation.
Will be ignored if frozencore is false.
In case nothing is specified, the number of core levels will be determined automatically.
Needs to be smaller than the number of occupied states.
nFreqIntegration (int | IntKey) – Number of imaginary frequency points for G3W2 integration
nFrequency (int | IntKey) – Number of imaginary frequency points. This key is only relevant for RPA and GW and will be ignored if used in an AO-PARI-MP2 calculation. 12 Points is the default for a RPA calculation. It is technically possible to use a different number of imaginary frequency points than for imaginary time. The maximum number of points which can be requested for imaginary frequency integration is 42. Important note: The computation time and memory requirements roughly scale linearly with the number of imaginary frequency points. However, memory can be an issue for RPA and GW when the number of imaginary frequency points is high. In case a job crashes, it is advised to increase the number of nodes since the necessary memory distributes over all nodes.
nLambda (int | IntKey) – Size of coupling constant integration grid for SOSEX variants in RPA. Default is 4 points
Number of imaginary time points (only relevant in case the Laplace Transformed (LT) formalism is used).
In the many-body-perturbation theory module in ADF, the polarizability (or Kohn-Sham density response function) is evaluated in imaginary time to exploit sparsity in the AO basis. For MP2, this is often referred to as a Laplace transform. For MP2, 9 points are the default. This is a safe choice, guaranteeing accuracies higher than 1 Kj/mol for most systems (For many simple organic systems, 6 points are sufficient for good accuracy).
Only for systems with a very small HOMO-LUMO gap or low-lying core states (heavy elements starting from the 4th row of the periodic table) more points might be necessary.
In principle, the same considerations apply for RPA and GW as well, however, the accuracy requirements are somewhat higher and 12 point are the default for RPA. In a GW calculation, the number of points is adjusted according to the numerical quality. Using less than 9 points is strongly discouraged except for the simplest molecules.
In ADF2019, it can happen that the algorithm determining the imaginary time grid does not converge. In this case, the usual reason is that the number of points is too small and more points need to be specified. Starting from AMS2020, this does not happen any more. In case the imaginary time grid does not converge, the number of points is automatically adjusted until it does.
The computation time of AO-PARI-MP2, RPA, and GW scales linearly with the number of imaginary time points.
useGreenXgrids (BoolType | BoolKey) – Use GreenX library to generate grid points. This is recommended for larger number of grid points (> 20). Up to 34 points can be requested.
- class _MolecularNMR[source]¶
Options for the calculations of the NMR shielding tensor for molecules, excluding periodic systems. Implements the Schreckenbach method like ADF.
- Variables:
Enabled (BoolType | BoolKey) – Compute NMR shielding.
- class _MultiSecantConfig[source]¶
Parameters for the Multi-secant SCF convergence method.
- Variables:
CMax (float | FloatKey) – Maximum coefficient allowed in expansion
InitialSigmaN (float | FloatKey) – This is a lot like a mix factor: bigger means bolder
MaxSigmaN (float | FloatKey) – Upper bound for the SigmaN parameter
MaxVectors (int | IntKey) – Maximum number of previous cycles to be used
MinSigmaN (float | FloatKey) – Lower bound for the SigmaN parameter
PredictGreed (BoolType | BoolKey) – Currently not used.
Renormalize (BoolType | BoolKey) – Whether to renormalize matrix An with Psi. Affects regularization.
SigmaRegularize (float | FloatKey) – Prevent division by zero by adding a small number. Makes most sense when using renormalization.
Tweak1 (BoolType | BoolKey) – Stick closer too the article: sigmaN < R abs(p)/abs(g) rather than sigmaN < R abs(u)/abs(p), where u is the unpredicted part, p the predicted part and g is the current error
Tweak2 (BoolType | BoolKey) – assume x = x + H error rather than x = x - H error
Variant (Literal["MSB2"]) – There are several version of the Multi secant method.
- class _NEGF[source]¶
Options for the NEGF (non-equilibrium green function) transport calculation.
- Variables:
AlignChargeTol (float | FloatKey) – In an alignment run you want to get the number of electrons in the center right. This number specifies the criterion for that.
AlignmentFile (str | StringKey) – Band result file (.rkf) corresponding to the alignment calculation.
Alpha (float | FloatKey) – A charge error needs to be translated in a potential shift. DeltaV = alpha * DeltaQ
ApplyShift1 (BoolType | BoolKey) – Apply the main shift, obtained from comparing matrix elements in the leads with those from the tight-binding run. Strongly recommended.
ApplyShift2 (BoolType | BoolKey) – Apply the smaller alignment shift. This requires an extra alignment run. Usually this shift is smaller.
AutoContour (BoolType | BoolKey) – Use automatic contour integral.
BiasPotential (float | FloatKey) – Apply a bias potential (atomic units). Can be negative. One has to specify the ramp potential with the FuzzyPotential key. This is mostly conveniently done with the GUI.
BoundOccupationMethod (int | IntKey) – See text. Only relevant with NonEqDensityMethod equal 2 or 3.
CDIIS (BoolType | BoolKey) – Make the normal DIIS procedure aware of the align charge error
CheckOverlapTol (float | FloatKey) – BAND checks how well the TB overlap matrix S(R=0) represents the overlap matrix in the lead region. Elements corresponding to the outer layer are neglected, because when using a frozen core they have bigger errors.
ContourQuality (Literal["basic", "normal", "good", "verygood"]) – The density matrix is calculated numerically via a contour integral. Changing the quality influences the number of points. This influences a lot the performance.
DEContourInt (float | FloatKey) – The energy interval for the contour grid. Defaults depends on the contour quality
DERealAxisInt (float | FloatKey) – The energy interval for the real axis grid. Defaults depends on the contour quality.
DoAlignment (BoolType | BoolKey) – Set this to True if you want to do an align run. Between the leads there should be lead material. The GUI can be of help here.
EMax (float | FloatKey) – The maximum energy for the transmission grid (with respect to the Fermi level of the lead)
EMin (float | FloatKey) – The minimum energy for the transmission grid (with respect to the Fermi level of the lead)
Eta (float | FloatKey) – Small value used for the contour integral: stay at least this much above the real axis. This value is also used for the evaluation of the Transmission and dos.
IgnoreOuterLayer (BoolType | BoolKey) – Whether or not to ignore the outer layer.
LeadFile (str | StringKey) – File containing the tight binding representation of the lead.
NE (int | IntKey) – The number of energies for the transmission energy grid.
OverwriteLeadFock (BoolType | BoolKey) – Undocumented.
SGFFile (str | StringKey) – The result from the SGF program. Contains the Fermi energy of the lead.
YContourInt (float | FloatKey) – The density is calculated via a contour integral. This value specifies how far above the real axis the (horizontal part of the) contour runs. The value is rounded in such a way that it goes exactly halfway between two Fermi poles. There is a trade off: making it bigger makes the integrand more smooth, but the number of enclosed poles increases. For low temperatures it makes sense to lower this value, and use a smaller deContourInt.
YRealaxisInt (float | FloatKey) – The non-Equilibrium density is calculated near the real axis.
- class _NMR[source]¶
Options for the calculations of the NMR shielding tensor.
- Variables:
Correct_rmu (BoolType | BoolKey) – Undocumented.
Correction_r (BoolType | BoolKey) – Undocumented.
Debug_r_corr (BoolType | BoolKey) – Undocumented.
Enabled (BoolType | BoolKey) – Compute NMR shielding.
NMRAtom (int | IntKey) – The index of the atom atom (in input order) for which NMR should be computed.
Numeric (BoolType | BoolKey) – Undocumented.
Obsolete (BoolType | BoolKey) – Undocumented.
OnlyNDimBasPnt (BoolType | BoolKey) – Undocumented.
Original (BoolType | BoolKey) – Undocumented.
PrintK (BoolType | BoolKey) – Undocumented.
Print_jp (BoolType | BoolKey) – Print paramagnetic current.
SharedArrayColumnLock (BoolType | BoolKey) – Undocumented.
SuperCell (BoolType | BoolKey) – This is the switch between the two methods, either the super cell (true), or the single-dipole method (false)
Test (BoolType | BoolKey) – Key for printing all intrinsic tensors.
Test_E (BoolType | BoolKey) – Test of energy levels.
Test_S (BoolType | BoolKey) – Test of overlap matrix.
UseSharedMemory (BoolType | BoolKey) – Whether or not to use shared memory in the NMR calculation.
- class _NOCVOrbitalPlot[source]¶
Goes together with the Restart%NOCVOrbitalPlot and Grid keys. See example.
- class _NOCVdRhoPlot[source]¶
Goes together with the Restart%NOCVdRhoPlot and Grid keys. See example.
- class _NeutralizingDensityDetails[source]¶
- Variables:
DiffuseFactor (float | FloatKey) – The bigger this number, the more diffuse (extended) the neutralizing density becomes. Works only for rho(neutralizing/atoms)
IncludeSelfTerm (BoolType | BoolKey) – The energy should contain the self term for consistent energy and gradients.
HomogeneousDensity (BAND._NeutralizingDensityDetails._HomogeneousDensity) – xxx
- class _NewResponse[source]¶
The TD-CDFT calculation to obtain the dielectric function is computed when this block is present in the input. Several important settings can be defined here.
- Variables:
ActiveESpace (float | FloatKey) – Modifies the energy threshold (DeltaE^{max}_{thresh} = omega_{high} + ActiveESpace) for which single orbital transitions (DeltaEpsilon_{ia} = Epsilon_{a}^{virtual} - Epsilon_{i}^{occupied}) are taken into account.
ActiveXYZ (str | StringKey) – Expects a string consisting of three letters of either ‘T’ (for true) or ‘F’ (for false) where the first is for the X-, the second for the Y- and the third for the Z-component of the response properties. If true, then the response properties for this component will be evaluated.
DensityCutOff (float | FloatKey) – For 1D and 2D systems the unit cell volume is undefined. Here, the volume is calculated as the volume bordered by the isosurface for the value DensityCutoff of the total density.
EShift (float | FloatKey) – Energy shift of the virtual crystal orbitals.
FreqHigh (float | FloatKey) – Upper limit of the frequency range for which response properties are calculated (omega_{high}).
FreqLow (float | FloatKey) – Lower limit of the frequency range for which response properties are calculated. (omega_{low})
NFreq (int | IntKey) – Number of frequencies for which a linear response TD-CDFT calculation is performed.
BugFixes (BAND._NewResponse._BugFixes) – Allows the user to control bug fixes to check older results
- class _BugFixes[source]¶
Allows the user to control bug fixes to check older results
- Variables:
CopyTiaOldAlda (BoolType | BoolKey) – NFreq was reduced by one in case of old alda. Does not influence the calculation, but changes band.rkf used by the gui
NoScissorsInJia (BoolType | BoolKey) – The scissors operator lifts the virtual eigenvalues, but this should not be done while calculating the Jia matrix. Relates (logically inversely) to OldResponse%Bugfixes%NewAldaShift.
PotTimesTwo (BoolType | BoolKey) – Undocumented.
SignJia2 (BoolType | BoolKey) – Undocumented.
SwapPiaPai (BoolType | BoolKey) – Undocumented.
WeightsTimesTwo (BoolType | BoolKey) – Multiply k-space weights times two. No effect when UseOldResponseWeights=yes
- class _NewResponseKSpace[source]¶
Modify the details for the integration weights evaluation in reciprocal space for each single-particle transition. Only influencing the NewResponse code.
- Variables:
Eta (float | FloatKey) – Defines the small, finite imaginary number i*eta which is necessary in the context of integration weights for single-particle transitions in reciprocal space.
HardIntegral (BoolType | BoolKey) – Undocumented.
SubSimp (int | IntKey) – determines into how many sub-integrals each integration around a k point is split. This is only true for so-called quadratic integration grids. The larger the number the better the convergence behavior for the sampling in reciprocal space. Note: the computing time for the weights is linear for 1D, quadratic for 2D and cubic for 3D!
UseOldResponseWeights (BoolType | BoolKey) – Call the old code to generate the response weights. If true then all other arguments of NewResponseKSpace are ignored
- class _NewResponseSCF[source]¶
Details for the linear-response self-consistent optimization cycle. Only influencing the NewResponse code.
- Variables:
Bootstrap (int | IntKey) – defines if the Berger2015 kernel (Bootstrap 1) is used or not (Bootstrap 0). If you chose the Berger2015 kernel, you have to set NewResponseSCF%XC to ‘0’. Since it shall be used in combination with the bare Coulomb response only. Note: The evaluation of response properties using the Berger2015 is recommend for 3D systems only!
COApproach (BoolType | BoolKey) – The program automatically decides to calculate the integrals and induced densities via the Bloch expanded atomic orbitals (AO approach) or via the cyrstal orbitals (CO approach). The option COApproach overrules this decision.
COApproachBoost (BoolType | BoolKey) –
Keeps the grid data of the Crystal Orbitals in memory.
Requires significantly more memory for a speedup of the calculation. One might have to use multiple computing nodes to not run into memory problems.
Criterion (float | FloatKey) –
For the SCF convergence the RMS of the induced density change is tested. If this value is below the Criterion the SCF is finished.
Furthermore, one can find the calculated electric susceptibility for each SCF step in the output and can therefore decide if the default value is too loose or too strict.
LowFreqAlgo (BoolType | BoolKey) – Numerically more stable results for frequencies lower than 1.0 eV. Note: for a graphene monolayer the conical intersection results in a very small band gap (zero band gap semi-conductor). This leads ta a failing low frequency algorithm. One can then chose to use the algorithm as originally proposed by Kootstra by setting the input value to false. But, this can result in unreliable results for frequencies lower than 1.0 eV!
NCycle (int | IntKey) – Number of SCF cycles for each frequency to be evaluated.
XC (int | IntKey) – Influences if the bare induced Coulomb response (XC 0) is used for the effective, induced potential or the induced potential derived from the ALDA kernel as well (XC 1).
DIIS (BAND._NewResponseSCF._DIIS) – Parameters influencing the DIIS self-consistency method
- class _DIIS[source]¶
Parameters influencing the DIIS self-consistency method
- Variables:
Enabled (BoolType | BoolKey) – If not enabled simple mixing without DIIS acceleration will be used.
MaxSamples (int | IntKey) – Specifies the maximum number of samples considered during the direct inversion of iteration of subspace (DIIS) extrapolation of the atomic charges during the SCC iterations. A smaller number of samples potentially leads to a more aggressive convergence acceleration, while a larger number often guarantees a more stable iteration. Due to often occurring linear dependencies within the set of sample vectors, the maximum number of samples is reached only in very rare cases.
MaximumCoefficient (float | FloatKey) – When the diis expansion coefficients exceed this threshold, the solution is rejected. The vector space is too crowded. The oldest vector is discarded, and the expansion is re-evaluated.
MinSamples (int | IntKey) – When bigger than one, this affects the shrinking of the DIIS space on linear dependence. It will not reduce to a smaller space than MinSamples unless there is extreme dependency.
MixingFactor (float | FloatKey) – The parameter used to mix the DIIS linear combination of previously sampled atomic charge vectors with an analogous linear combination of charge vectors resulting from population analysis combination. It can assume real values between 0 and 1.
- class _NonCollinearMagnetizationModule[source]¶
Undocumented.
- Variables:
DoBackForthTest (BoolType | BoolKey) – Transform 2x2 matrices to the Pauli vector representation and back.
DotProductBugfix (BoolType | BoolKey) – About a forgotten dagger in the dot product code.
SignFix (BoolType | BoolKey) – Try to get a sign in the up and down projections. Otherwise the size of m is by definition always in the up direction, i.e. only the size of m matters.
- class _Occupations[source]¶
Allows one to input specific occupations numbers. Applies only for calculations that use only one k-point (i.e. pseudo-molecule calculations). See example.
- class _OldResponse[source]¶
Options for the old TD-CDFT implementation.
- Variables:
Berger2015 (BoolType | BoolKey) – Use the parameter-free polarization functional by A. Berger (Phys. Rev. Lett. 115, 137402). This is possible for 3D insulators and metals. Note: The evaluation of response properties using the Berger2015 is recommend for 3D systems only!
CNT (BoolType | BoolKey) – Use the CNT parametrization for the longitudinal and transverse kernels of the XC kernel of the homogeneous electron gas. Use this in conjunction with the NewVK option.
CNVI (float | FloatKey) – The first convergence criterion for the change in the fit coefficients for the fit functions, when fitting the density.
CNVJ (float | FloatKey) – the second convergence criterion for the change in the fit coefficients for the fit functions, when fitting the density.
Ebndtl (float | FloatKey) – the energy band tolerance, for determination which routines to use for calculating the numerical integration weights, when the energy band posses no or to less dispersion.
Enabled (BoolType | BoolKey) – If true, the response function will be calculated using the old TD-CDFT implementation
Endfr (float | FloatKey) – The upper bound frequency of the frequency range over which the dielectric function is calculated
Ifxc (int | IntKey) – Integer defining the XC kernel. 0: ALDA, 1: Freq. dependent, 2: LB94
Isz (int | IntKey) – Integer indicating whether or not scalar zeroth order relativistic effects are included in the TDCDFT calculation. 0 = relativistic effects are not included, 1 = relativistic effects are included. The current implementation does NOT work with the option XC%SpinOrbitMagnetization equal NonCollinear
Iyxc (int | IntKey) – integer for printing yxc-tensor (see http://aip.scitation.org/doi/10.1063/1.1385370). 0 = not printed, 1 = printed.
Mac (BoolType | BoolKey) – Undocumented.
MinDIISSpace (int | IntKey) – Ensure that the size of the DIIS space does not shrink below this value (if bigger than one). It seems that DIIS with two vectors never converges. Setting this to 3 is reasonable
Nct (BoolType | BoolKey) – Undocumented.
NewVK (BoolType | BoolKey) – Use the slightly modified version of the VK kernel (see https://aip.scitation.org/doi/10.1063/1.1385370). When using this option one uses effectively the static option, even for metals, so one should check carefully the convergence with the KSPACE parameter.
Newalda (BoolType | BoolKey) – Undocumented.
Nfreq (int | IntKey) – the number of frequencies for which a linear response TD-CDFT calculation is performed.
NonLoc (BoolType | BoolKey) – Undocumented.
QV (BoolType | BoolKey) – Use the QV parametrization for the longitudinal and transverse kernels of the XC kernel of the homogeneous electron gas. Use this in conjunction with the NewVK option. (see reference).
QV0 (BoolType | BoolKey) – Undocumented.
Rice (BoolType | BoolKey) – Undocumented.
Shift (float | FloatKey) – energy shift for the virtual crystal orbitals.
Static (BoolType | BoolKey) – An alternative method that allows an analytic evaluation of the static response (normally the static response is approximated by a finite small frequency value). This option should only be used for non-relativistic calculations on insulators, and it has no effect on metals. Note: experience shows that KSPACE convergence can be slower.
Strtfr (float | FloatKey) – is the lower bound frequency of the frequency range over which the dielectric function is calculated.
VK (BoolType | BoolKey) – Undocumented.
BugFixes (BAND._OldResponse._BugFixes) – Allows the user to control bug fixes to check older results
- class _Output[source]¶
Control the output.
- Variables:
Print (BAND._Output._Print) –
- class _OverlapPopulations[source]¶
Overlap population weighted DOS (OPWDOS), also known as the crystal orbital overlap population (COOP).
- class _PEDANOCV[source]¶
Options for the decomposition of the orbital relaxation (pEDA).
- Variables:
EigvalThresh (float | FloatKey) – The threshold controls that for all NOCV deformation densities with NOCV eigenvalues larger than EigvalThresh the energy contribution will be calculated and the respective pEDA-NOCV results will be printed in the output
Enabled (BoolType | BoolKey) – If true in combination with the fragment blocks and the pEDA key, the decomposition of the orbital relaxation term is performed.
- class _PeriodicRIHartreeFock[source]¶
Technical options for periodic Hartree Fock.
- Variables:
AllowLinearScaling (BoolType | BoolKey) – Use function ranges and multipoles.
AllowMultipoleExpansion (BoolType | BoolKey) – Use the multipole expansion if possible.
AllowOddKGrid (BoolType | BoolKey) – Allow the user to specify an odd k-grid. This does not work well with HartreeFock.
AllowPartialMultipoleExpansion (BoolType | BoolKey) – Use the partial multipole expansion if possible. This has only effect if AllowMultipoleExpansion=yes.
AnalyzeCells (BoolType | BoolKey) – Determine the cell loop ranges needed and stop.
AvoidPeriodicKMatR (BoolType | BoolKey) – Undocumented.
AvoidPeriodicPMatR (BoolType | BoolKey) – Undocumented.
CellLoopPrecision (Literal["Minimal", "Medium", "Full"]) – The range of the density matrix, R(P), combined with the range of basis products, R(C), determines the cell range contributing to the exchange matrix. The cell range used is. Minimal: R(P). Medium: R(P)+R(C). All: R(P)+2R(C)
CheckRelativeLatticeIndex (BoolType | BoolKey) – Compare result of fast and slow routine to obtain the relative lattice index.
ExactLMaxMultiPerAtom (BoolType | BoolKey) – Used to be a hardcodes lMaxMulti=3. If specified it is determined per atom from the RIHF fit functions.
FitCoeffThreshold (float | FloatKey) – Threshold to be applied for the fit coefficients, ignore blocks for which all (abs) elements are smaller than this threshold.
Iterator (Literal["Auto", "Static", "Hybrid", "Dynamic"]) – With the option Dynamic one thread may be sacrified to distribute the work, and is the default when using more than 16 cores, otherwise Hybrid is used. With Hybrid more detailed timings are possible, even if using more than one (shared memory) node.
M1Threshold (float | FloatKey) – Threshold to be applied for the M1 matrix appearing in the I,II, and III terms. A negative value means no threshold.
MaxCellForP (int | IntKey) – Apply a maximum to the the number of cells for P(R), mostly useful for 1D systems.
MergeIterators (BoolType | BoolKey) – If true, calculate terms I,II,III,and IV in parallel, otherwise term IV is done separately.
NCellsToUse (int | IntKey) – Hack to explicitly control the number of cells to be used.
PrintKDistanceDecay (BoolType | BoolKey) – The decay of the norm of K with respect to the distance cell order.
PrintKShellDecay (BoolType | BoolKey) – The decay of the norm of K with respect to the shell cell order.
PrintKTopoDecay (BoolType | BoolKey) – The decay of the norm of K with respect to the topological cell order.
RemapPMatR (BoolType | BoolKey) – Possibly move elements from one cell to another, minimizing the distance between the atom pairs.
RemapPMatRNew (BoolType | BoolKey) – Possibly move elements from one cell to another, minimizing the distance between the atom pairs.
SaveKMatR (BoolType | BoolKey) – Undocumented.
SortFitFunctions (BoolType | BoolKey) – Sort the RIHartreeFock fit functions per atom, based on the range. This is needed when allowing for partial multipole atom pairs.
SupportPostProcessing (BoolType | BoolKey) – Store some info in a RIHartreeFock section, that can be useful for python post processing/analysis.
UpdateVersion (int | IntKey) – Which implementation to use for the update123 and update4 routines.
UseHalfKGrid (BoolType | BoolKey) – Let all RIHF settings be based on the assumption that the k-grid was twice as coarse. What will be more accurate is P(R), but it gets the range as if the coarser k-grid was used.
UseHelper (BoolType | BoolKey) – Provide the RIHartreeFock with knowledge about loop bounds.
UseInverseCellSymmetry (BoolType | BoolKey) – If true, only half of the K(R) is calculated, and the rest is obtained from K(-R)=transpose(K(R)).
UseLatticeShiftForPairs (BoolType | BoolKey) – Apply a pair based minimum image convention.
UseM1V (BoolType | BoolKey) – Multiply M1 by V, being faster for term II.
lMaxMulti (int | IntKey) – Apply a maximum to the lMaxMulti. If negative the key is ignored.
BugFixes (BAND._PeriodicRIHartreeFock._BugFixes) – Allows the user to control bug fixes to check older results
- class _PeriodicSolvation[source]¶
Additional options for simulations of periodic structures with solvation.
- Variables:
NStar (int | IntKey) – This option, expecting an integer number (>2), handles the accuracy for the construction of the COMSO surface. The larger the given number the more accurate the construction.
RemovePointsWithNegativeZ (BoolType | BoolKey) –
Whether the COSMO surface is constructed on both sides of a surface.
If one is only interested in the solvation effect on the upper side of a surface (in the Z direction), then this option should be set to ‘True’
RestartPoints (BoolType | BoolKey) – Undocumented.
RestartWithPointApprox (BoolType | BoolKey) – Undocumented.
ReusePoints (BoolType | BoolKey) – Undocumented.
SmartScreening (BoolType | BoolKey) – Undocumented.
SymmetrizeSurfacePoints (BoolType | BoolKey) – Whether or not the COSMO point should be symmetrized
- class _Programmer[source]¶
Miscellaneous technical options.
- Variables:
Allowtailsforresponse (BoolType | BoolKey) – Undocumented.
Atomicenergyinmolgrid (BoolType | BoolKey) – Undocumented.
BandEigSysOption (int | IntKey) –
orig version, 2) uses SCMMatrix.
Basgrad (BoolType | BoolKey) – Undocumented.
Baskin (BoolType | BoolKey) – Undocumented.
Bassecder (BoolType | BoolKey) – Undocumented.
Calctau (BoolType | BoolKey) – Undocumented.
Didervcompat (BoolType | BoolKey) – Undocumented.
DiracPotentialCutoff (float | FloatKey) – When V (times R) is smaller than this, set potential to zero. (coulomb potential of spherical atoms in dirac routine)
DirectBas (BoolType | BoolKey) – Calculate basis functions and their derivatives on the fly, and do not store basis functions on disk.
Directfit (BoolType | BoolKey) – Undocumented.
Dkbas (BoolType | BoolKey) – Undocumented.
DynamicBlockIterator (BoolType | BoolKey) – This causes the iteration over the blocks to be dynamic. Technically all grid based functions will be stored in shared arrays. Might be faster when there is load imbalance. Can be considered for large/sparse systems. Does not work too wel with too many cores per node.
Enablescratcharraymodule (BoolType | BoolKey) – Undocumented.
Exactgradrho (BoolType | BoolKey) – Undocumented.
Exactgradrhopostscf (BoolType | BoolKey) – Undocumented.
Exactrho (BoolType | BoolKey) – Undocumented.
Exactsharedarraylocking (BoolType | BoolKey) – Undocumented.
Fastatmfnc (BoolType | BoolKey) – Undocumented.
Fastfitort (BoolType | BoolKey) – Undocumented.
Fitgrad (BoolType | BoolKey) – Undocumented.
Frageif (BoolType | BoolKey) – Undocumented.
Functionsetdotproductemploysym (BoolType | BoolKey) – Undocumented.
Functionsetincrementkeepsorted (BoolType | BoolKey) – Undocumented.
Functionsetoverlapemploysym (BoolType | BoolKey) – Undocumented.
Functionsetoverlaplockcolumn (BoolType | BoolKey) – Undocumented.
HuntForSpinorbitBug (BoolType | BoolKey) – On some platforms either the Lowdin ortho fails or the CheckCore.
KMIOMaxSectionSize (float | FloatKey) – Normally this should be the maximum number of elements that a kf varialbe can hold.
Kinviagrad (BoolType | BoolKey) – Undocumented.
KmioFinalStorageMode (int | IntKey) – How the eigensystem is saved at the end of the calculation on the main result file.
Kmioforcecomplex (BoolType | BoolKey) – Undocumented.
LogGap (BoolType | BoolKey) – Show the band gap in the logfile at each cycle.
Mapatomstounitcell (BoolType | BoolKey) – Undocumented.
Oldgetvocbasis (BoolType | BoolKey) – Undocumented.
OptimizePointDistribution (BoolType | BoolKey) – Undocumented.
Pmathistory (BoolType | BoolKey) – Undocumented.
PrepareBasLinAlgOption (int | IntKey) – Variations for the matrix processing part of PrepareBas. Possible values: 1 or 2.
RemoveRigidMotions (BoolType | BoolKey) – Whether or not to remove rigid motions from gradient.
ReorderPoints (BoolType | BoolKey) – Whether or not to reorder the real space points by localization.
Rhograd (BoolType | BoolKey) – Undocumented.
SharedMemorySandwichingThreshold (int | IntKey) –
When the nr. of basis functions exceeds this threshold shared memory will be used to calculate matrix elements.
Unless UseSharedMemoryForSandwiching is explicitly set in the input.
StopAfterFirstEigsys (BoolType | BoolKey) – Stop after the first call to eigsys is completed, useful for timings, in particular for HartreeFock.
StoreDOSPerBas (BoolType | BoolKey) – Whether or not to store the parial DOS per basis function. This allows you to view any partial DOS with amsspectra and amsbands. Requires the CalcPDOS option to be on.
StoreOrbitals (BoolType | BoolKey) – Copy information on band.rkf needed for orbital plotting and restarts. This can be a lot of information. DOS and BandStructure require StoreOrbitals=true.
StoreZlmFitEachSCFCycle (BoolType | BoolKey) – Write ZlmFit info to band.rkf, normally only done at the last cycle.
Storebandinternalham (BoolType | BoolKey) – Undocumented.
Storeoriginalbloch (BoolType | BoolKey) – Undocumented.
UpdateSTDVec (BoolType | BoolKey) – Shift atoms so that center of mass is at zero. As a results the detected symmetry may be higher.
UseDiracCoulomb (BoolType | BoolKey) – Affects dirac subroutine. In 2023 a spline-based routine was made replacing the original code that employed a (necessary) 10-6 CutOff. To emulate pre ams2023 calculations set this key to false.
UseSharedMemoryForSandwiching (BoolType | BoolKey) –
When calculating matrix elements the array will be shared. This saves memory at the cost of locking overhead.
If not specified this will depend on the threshold SharedMemorySandwichingThreshold
UseTurnoverRuleForXcMatrix (BoolType | BoolKey) – Undocumented.
UseTurnoverRuleForXcMatrixDirac (BoolType | BoolKey) – Affects which potential to use in Dirac in case of libxc and UseTurnoverRuleForXcMatrix=true.
Usenewtailroutines (BoolType | BoolKey) – Undocumented.
Usesharedmemory (BoolType | BoolKey) –
When running more then one task, share memory between those tasks. This saves a lot of memory.
Only disable it in case of problems.
Usestofit (BoolType | BoolKey) – Undocumented.
Usezlmfit (BoolType | BoolKey) – Undocumented.
VOCBasEvaluator4OptimizeOrdering (BoolType | BoolKey) – Make sure that the sparse functions are ordered (idtail is ascending).
Wipeonecenterterms (BoolType | BoolKey) – Undocumented.
- class _PropertiesAtNuclei[source]¶
A number of properties can be obtained near the nucleus. An average is taken over a tiny sphere around the nucleus. The following properties are available: vxc[rho(fit)], rho(fit), rho(scf), v(coulomb/scf), rho(deformation/fit), rho(deformation/scf).
- class _RIHartreeFock[source]¶
- Variables:
DependencyCoreRange (float | FloatKey) – Basis functions may be given a core character based on the range. For now only active in Band and only if present in the input
DependencyThreshold (float | FloatKey) –
To improve numerical stability, almost linearly-dependent combination of basis functions are removed from the Hartree-Fock exchange matrix.
If you obtain unphysically large bond energy in an Hybrid calculation, or an unphysically low correlation energy in an RPA, MP2, or double hybrid calculation, you might try setting the DependencyThreshold to a larger value (e.g. 3.0E-3)
Note, that in GW calculations and GW-BSE calculations the default for this key is 5.0e-3.
DoAlternativeDependencyTrick (BoolType | BoolKey) – Only applies to band. Do trick on the density matrix being input to HFEval, rather than on the K-matrix.
DoDependencyTrick (BoolType | BoolKey) – Available only in BAND, turns on and off the RIHartreeFock dependency trick.
FitSetQuality (Literal["Auto", "VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent", "FromBasisProducts"]) –
The quality of auxiliary fit set employed in the RI scheme.
If ‘Auto’, the value of the RIHartreeFock Quality option will be used.
Normal quality is generally sufficient for basis sets up to and including TZ2P.
For larger basis sets (or for benchmarking purposes) a VeryGood fit set is recommended.
Note that the FitSetQuality heavily influences the computational cost of the calculation.
IntegrationQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Quality of the numerical integration for evaluating the integrals between basis functions and fit functions. If IntegrationQuality is not defined in input, the value defined in RIHartreeFock%Quality will be used.
Quality (Literal["Auto", "VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Numerical accuracy of the RI procedure. If ‘Auto’, the quality specified in the ‘NumericalQuality’ will be used.
ResponseQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Numerical accuracy of the RI procedure for the Response module.
ThresholdQuality (Literal["VeryBasic", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Linear scaling thresholds (also used for determining at what range the multiple approximation is used). To disable all linear scaling thresholds set this to Excellent.
UseCoulombMetricForDependency (BoolType | BoolKey) – Use Coulomb metric for the Dependency Trick (band only)
UseMe (BoolType | BoolKey) – Set to False if you want to use the old RI scheme (ADF only)
ExplicitThresholds (BAND._RIHartreeFock._ExplicitThresholds) – Override the thresholds as implied by the ThresholdQuality.
FitGenerationDetails (BAND._RIHartreeFock._FitGenerationDetails) – Technical details about how the RI Hartree-Fock fit functions are generated.
QualityPerRegion (BAND._RIHartreeFock._QualityPerRegion) – Sets the fit-set quality for all atoms in a region. If specified, this overwrites the globally set quality.
- class _FitGenerationDetails[source]¶
Technical details about how the RI Hartree-Fock fit functions are generated.
- Variables:
BoostL (BoolType | BoolKey) –
Add extra max(l)+1 diffuse function
When l denotes the highest angular momentum present in the primary basis,
FromBasisProducts will generate auxiliary fit functions with up to 2l angular momentum.
When this key is set to true, the maximum angular momentum in the auxiliary fit set becomes 2l+2.
Typically, this option is not needed and when precision issues arise, it is rather advised to adjust the OneCenterDependencyThreshold key to a smaller value.
LapackWorkAround (BoolType | BoolKey) – GetFitFunctionsForAtomType diagonalization done with Lapack instead of Scalapack
Method (Literal["Auto", "FromBasisProducts"]) –
The way in which fit functions are generated. The main distinction is whether it depends on the basis functions used.
When FromBasisProducts is used, the auxiliary basis is generated directly from the products of primary basis functions.
This has the advantage that the auxiliary fit adapts automatically to the basis set size.
Especially for basis sets of QZ quality or larger, this is often necessary to obtain highly precise correlation energies using RPA or double hybrids
FromBasisProducts option is also useful for GW or BSE calculations with basis sets of QZ quality or larger.
OneCenterDependencyThreshold (float | FloatKey) –
This key is only active when FromBasisProducts is chosen as method to generate the auxiliary basis.
This threshold controls the size, and at the samw time, the precision of the auxiliary basis set. A smaller number leads to a larger auxiliary fit set.
The default value of 1e-8 is typically sufficient to converge correlation energies and QP energies to a very high precision.
It corresponds to an auxiliary basis which is typically 8-9 times larger than the primary basis.
UseBandRadialGrid (BoolType | BoolKey) –
Only applies to band. The band logarithmic grid ranges (by default) from 1e-6 to 100 with 3000 points. Otherwise 300 points will be used.
For 0-periodicity (molecules) it is advisable to set this key to false since lots of memory is needed to evaluate all necessary integrals.
- class _RadialDefaults[source]¶
Options for the logarithmic radial grid of the basis functions used in the subprogram Dirac
- Variables:
AdjustRMinForFunctional (BoolType | BoolKey) – Some functionals have numerically unstable potentials near the nucleus for light elements: Enlarge rmin for lighter elements. If not specified then the option will be set for the OLYP and HTBS functionals
DiDervViaSpline (BoolType | BoolKey) – replace old diderv with DiDervViaSpline
NR (int | IntKey) – Number of radial points. With very high values (like 30000) the Dirac subprogram may not converge.
NRPerType (Iterable[int] | IntListKey) – If present overrides NR. The list needs to be as long as there are atom types
RMax (float | FloatKey) – Upper bound of the logarithmic radial grid
RMin (float | FloatKey) – Lower bound of the logarithmic radial grid
RMinPerType (Iterable[float] | FloatListKey) – If specified overrides RMin. The list needs to be as long as there are atom types (different elements)
- class _Relativity[source]¶
Options for relativistic effects.
- Variables:
Level (Literal["None", "Scalar", "Spin-Orbit"]) –
None: No relativistic effects.
Scalar: Scalar relativistic ZORA. This option comes at very little cost.
SpinOrbit: Spin-orbit coupled ZORA. This is the best level of theory, but it is (4-8 times) more expensive than a normal calculation. Spin-orbit effects are generally quite small, unless there are very heavy atoms in your system, especially with p valence electrons (like Pb).
See also the SpinOrbitMagnetization key.
Potential (Literal["APA", "SAPA"]) – Undocumented
- class _ResponseInducedDensityPlot[source]¶
Goes together with Restart%ResponseInducedDensityPlot and Grid.
- class _Restart[source]¶
Tells the program that it should restart with the restart file, and what to restart.
- Variables:
BandStructure (BoolType | BoolKey) – Calculate the band structure from a previous calculation. Does not work with model potentials and Hubbard.
COSMO (BoolType | BoolKey) – Restart the COSMO charges.
CheckAtomicPositions (BoolType | BoolKey) – If set to True: For restarting the SCF the atomic positions will be checked, and may not deviate too much.
DOS (BoolType | BoolKey) – Calculate the DOS from a previous calculation. Does not work with model potentials and Hubbard.
DensityPlot (BoolType | BoolKey) – Goes together with the DensityPlot block and Grid blocks
FermiSurface (BoolType | BoolKey) – Undocumented.
File (str | Path | StringKey) – Name of the restart file. The file should be a band.rkf file from a previous run.
IgnoreBadGeometry (BoolType | BoolKey) – Undocumented.
LoadEigenSystem (BoolType | BoolKey) – At each step of the SCF load the section eigensystem from the restart file, forcing constant eigenvalues and vectors.
NOCVOrbitalPlot (BoolType | BoolKey) – Goes together with the NOCVOrbitalPlot and Grid blocks.
NOCVdRhoPlot (BoolType | BoolKey) – Goes together with the NOCVdRhoPlot and Grid blocks.
NoPrdRhoPlot (BoolType | BoolKey) – Undocumented.
NoprOrbitalPlot (BoolType | BoolKey) – Undocumented.
OrbitalPlot (BoolType | BoolKey) – Goes together with the OrbitalPlot and Grid
ResponseInducedDensityPlot (BoolType | BoolKey) – Goes together with the ResponseInducedDensityPlot and Grid blocks.
SCF (BoolType | BoolKey) – Continue the SCF procedure using the orbital coefficients and occupations from the restart file.
UseDensityMatrix (BoolType | BoolKey) – If set to True: For restarting the SCF the density matrix will be used. Requires you to set ‘Save DensityMatrix’ in the previous run.
VTKFile (str | StringKey) – If specified a vtk file with be created with this name. If the extension is ‘.txt’, a text file is created. Setting it to ‘CUBE’ one or more (one for each component) files in the cube format are generated with an automatic naming scheme.
VoronoiGrid (BoolType | BoolKey) – Copy the section Num In Params to the current file.
- class _SCF[source]¶
Controls technical SCF parameters.
- Variables:
ApplyVSplitToDensity (BoolType | BoolKey) – Undocumented.
Eigenstates (BoolType | BoolKey) – The program knows two alternative ways to evaluate the charge density iteratively in the SCF procedure: from the P-matrix, and directly from the squared occupied eigenstates. By default the program actually uses both at least one time and tries to take the most efficient. If present, Eigenstates turns off this comparison and lets the program stick to one method (from the eigenstates).
Iterations (int | IntKey) – The maximum number of SCF iterations to be performed.
LoadPreviousSCFMixing (BoolType | BoolKey) – Load dimix and mixing from the previous SCF procedure, for instance during a geometry optimization.
Method (Literal["DIIS", "MultiSecant", "MultiStepper"]) – Choose the general scheme used to converge the density in the SCF. In case of scf problems one can try the MultiSecant alternative at no extra cost per SCF cycle. For more details see the DIIS and MultiSecantConfig block.
Mixing (float | FloatKey) – Initial ‘damping’ parameter in the SCF procedure, for the iterative update of the potential: new potential = old potential + mix (computed potential-old potential). Note: the program automatically adapts Mixing during the SCF iterations, in an attempt to find the optimal mixing value.
MultiStepperPresetPath (str | Path | StringKey) – Name of file containing a SCFMultiStepper key block. This will be used if no Explicit SCFMultiStepper block is in the input, and Method=MultiStepper. If the path is not absolute, it is relative to $AMSHOME/data/presets/multi_stepper’
NComponentsForNonColDIIS (int | IntKey) – For a non-collinear calculation: use all 8 components for the DIIS error metric. Possible choices: 2,4,8. With option=2 information is discarded. Option=4 or 8 are nearly identical except that the off diag weights are a bit different. Before the key was introduced two components were used.
NewEigenstates (BoolType | BoolKey) – Undocumented.
NewPMatrix (BoolType | BoolKey) – Undocumented.
PMatrix (BoolType | BoolKey) – If present, evaluate the charge density from the P-matrix. See also the key Eigenstates.
PrintAllOccupiedBands (BoolType | BoolKey) – When printing the ranges of the bands, include all occupied ones.
PrintAllVirtualBands (BoolType | BoolKey) – When printing the ranges of the bands, include all virtual ones.
PrintAlwaysBandRanges (BoolType | BoolKey) – Normally the ranges of the bands are only printed at the last SCF cycle
Rate (float | FloatKey) – Minimum rate of convergence for the SCF procedure. If progress is too slow the program will take measures (such as smearing out occupations around the Fermi level, see key Degenerate of block Convergence) or, if everything seems to fail, it will stop
SkipDiagonalization (BoolType | BoolKey) – Undocumented.
VSplit (float | FloatKey) – To disturb degeneracy of alpha and beta spin MOs the value of this key is added to the beta spin potential at the startup.
SCFMultiStepper (BAND._SCF._SCFMultiStepper) – To solve the self-consistent problem multiple steppers can be tried during stints using the ones that give the best progress.
- class _SCFMultiStepper[source]¶
To solve the self-consistent problem multiple steppers can be tried during stints using the ones that give the best progress.
- Variables:
AlwaysChangeStepper (BoolType | BoolKey) – When the progress is fine there is no reason to change the stepper. In practice this is always set to true, because also the Stepper%ExpectedSlope can be used to achieve similar behavior.
ErrorGrowthAbortFactor (float | FloatKey) – Abort stint when the error grows too much, compared to the error at the start of the stint.
FractionalStepFactor (float | FloatKey) – Multiply the step by this factor. If smaller than zero this is not used.
MinStintCyclesForAbort (int | IntKey) – Look at ErrorGrowthAbortFactor only when a number of steps has been completed since the start of the stint. A value of 0 means always.
StintLength (int | IntKey) – A stepper is active during a number of SCF cycles, called a stint.
UsePreviousStintForErrorGrowthAbort (BoolType | BoolKey) – The error is normally checked against the first error of the stint. With this option that will be the one from the previous stint, if performed with the same stepper.
Stepper (BAND._SCF._SCFMultiStepper._Stepper) –
??
- class _Stepper[source]¶
??
- Variables:
AbortSlope (float | FloatKey) – If the slope (at the end of a stint) is larger than this: abort the stepper
AlwaysAbortAtBeginOfStint (BoolType | BoolKey) – For debugging only: no matter what abort this stepper at the begin of the stint (doing only one step).
AlwaysAbortAtEndOfStint (BoolType | BoolKey) – For debugging only: no matter what abort this stepper at the end of the stint.
ErrorGrowthAbortFactor (float | FloatKey) – Abort stint when the error grows too much, compared to the error at the start of the stint. Overrides global ErrorGrowthAbortFactor when set to a value > 0
ExpectedSlope (float | FloatKey) – If the slope of the total SCF is better than this keep on going.
FractionalStepFactor (float | FloatKey) – Multiply the step by this factor. If smaller than zero this is not used.
InitialMixFromPreviousStint (BoolType | BoolKey) – Similar to MixFromPreviousStint, but only done the first time that a stepper is used.
MaxInitialError (float | FloatKey) – Only use the stepper when error is smaller than this.
MaxIterationNumber (int | IntKey) – Stepper will only be active for iterations smaller than this number. (Negative value means: Ignore this option)
MaxStintNumber (int | IntKey) – Stepper will only be active for stints smaller than this number. (Negative value means: Ignore this option)
MaxStints (int | IntKey) – Maximum number of stints that a stepper should be used.
MinInitialError (float | FloatKey) – Only use the stepper when error is larger than this.
MinIterationNumber (int | IntKey) – Stepper will only be active for iterations larger than this number.
MinStintCyclesForAbort (int | IntKey) – Look at ErrorGrowthAbortFactor only when a number of steps has been completed since the start of the stint. A value of 0 means always. Overrides global value.
MinStintNumber (int | IntKey) – Stepper will only be active for stints larger than this number.
MixFromPreviousStint (BoolType | BoolKey) – When starting a new stint use the mix from the previous stepper, even if it is of another type.
DIISStepper (BAND._SCF._SCFMultiStepper._Stepper._DIISStepper) – DIIS stepper
MixAdapter (BAND._SCF._SCFMultiStepper._Stepper._MixAdapter) – Generic mix adapter
MixStepper (BAND._SCF._SCFMultiStepper._Stepper._MixStepper) – Simple mixing stepper, only using the previous (in/out) density.
MultiSecantStepper (BAND._SCF._SCFMultiStepper._Stepper._MultiSecantStepper) – Multi secant stepper.
- class _DIISStepper[source]¶
DIIS stepper
- Variables:
EDIIS (BoolType | BoolKey) – Use energy DIIS. The energy is used as extra info and only interpolation is done (all coefficients in the interval [0,1]).
EDIISAlpha (float | FloatKey) – The extra energy vector is weighed by this factor. .
MaxBMatrixRange (float | FloatKey) – If larger than zero: limit the ratio between the oldest and last diagonal B matrix element.
MaxCoefficient (float | FloatKey) – The largest allowed value of the expansion coefficients. If exceed the number of vectors is reduces until the criterion is met.
MaxConditionNumber (float | FloatKey) – If larger than zero: check condition number of the B matrix. If too large reduce nVectors.
MaxVectors (int | IntKey) – Maximum number of previous densities to be used (size of the history).
MinLastCoefficient (float | FloatKey) – If larger than zero: If the most recent vector gets a (abs) coefficient smaller than this the mix is boosted.
MinVectors (int | IntKey) – Try to prevent to make nVectors shrink below this value, by allowing for significantly larger coefficients.
Mix (float | FloatKey) – Also known as greed. It determines the amount of output density to be used. May be changed by the MixAdapter.
RescaleBMatrix (BoolType | BoolKey) – Rescale the B matrix so that is’s values are of the same order as those of the constraints.
UseHalfMixForFirstCycle (BoolType | BoolKey) – Use half the mix factor at iteration 1 (if applicable).
- class _MixAdapter[source]¶
Generic mix adapter
- Variables:
CorrelateMixWithSlope (BoolType | BoolKey) – For the last two mixing factors the one with the best slope is preferred.
ErrorGrowthPanicFactor (float | FloatKey) – When the error increases more than this factor, this mix is reduced a lot.
GrowWhenSpaceGrows (BoolType | BoolKey) – Has only effect when the error goes down. If nVectors increases grow the mix factor, otherwise do not change the mix
GrowthFactor (float | FloatKey) – When the mix is considered too low it is multiplied by this factor. Otherwise it is divided by it.
MaxMix (float | FloatKey) – Do not grow the mix above this value.
MinMix (float | FloatKey) – Do not shrink the mix below this value.
NTrialMixFactors (int | IntKey) – Only used with Type=Trial. Must be an odd number.
TrialMode (Literal["CurrentMixCentered", "FullRange"]) – How are the NTrialMixFactors chosen?
Type (Literal["Error", "Energy", "UnpredictedStep", "Trial"]) – Adapt the mix factor based on the observed progress (slope).
- class _MultiSecantStepper[source]¶
Multi secant stepper.
- Variables:
AlphaMSR1 (float | FloatKey) – For the MSR1 variant: W = Y + alpha S.
MaxConditionNumber (float | FloatKey) – If set larger than zero this condition number of the matrix to be inverted will be checked. If exceeded the space is reduced.
PredictGreed (BoolType | BoolKey) – Try to predict the optimal greed.
ScaleYTY (BoolType | BoolKey) – Scale matrix before inversion
SigmaRegularize (float | FloatKey) – Prevent division by zero by adding a small number. Makes most sense when using renormalization.
Variant (Literal["MSB1", "MSB2", "MSR1", "MSR1s"]) – There are several version of the Multi secant method.
- class _Screening[source]¶
For the periodic solvation potential and for the old (not default anymore) fitting method, BAND performs lattice summations which are in practice truncated. The precision of the lattice summations is controlled by the options in this block.
- Variables:
CutOff (float | FloatKey) – Criterion for negligibility of tails in the construction of Bloch sums. Default depends on Accuracy.
DMadel (float | FloatKey) – One of the parameters that define the screening of Coulomb-potentials in lattice sums. Depends by default on Accuracy, rmadel, and rcelx. One should consult the literature for more information
LatticeBased (BoolType | BoolKey) – Undocumented.
NoDirectionalScreening (BoolType | BoolKey) – Real space lattice sums of slowly (or non-) convergent terms, such as the Coulomb potential, are computed by a screening technique. In previous releases, the screening was applied to all (long-range) Coulomb expressions. Screening is only applied in the periodicity directions. This key restores the original situation: screening in all directions
RCelx (float | FloatKey) – Max. distance of lattice site from which tails of atomic functions will be taken into account for the Bloch sums. Default depends on Accuracy.
RMadel (float | FloatKey) – One of the parameters that define screening of the Coulomb potentials in lattice summations. Depends by default on Accuracy, dmadel, rcelx. One should consult the literature for more information.
- class _SoftConfinement[source]¶
In order to make the basis functions more compact, the radial part of the basis functions is multiplied by a Fermi-Dirac (FD) function (this ‘confinement’ is done for efficiency and numerical stability reasons). A FD function goes from one to zero, controlled by two parameters. It has a value 0.5 at Radius, and the decay width is Delta.
- Variables:
Analytical (BoolType | BoolKey) – Undocumented
AssumeLatticeDependent (BoolType | BoolKey) – Bit of a hack to store the fact that the confinement was affected by the lattice. This allows later for disabling analytical stress if so.
Delta (float | FloatKey) – Explicitly specify the delta parameter of the Fermi-Dirac function (if not specified, it will be 0.1*Radius).
Quality (Literal["Auto", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) –
In order to make the basis functions more compact, the radial part of the basis functions is multiplied by a Fermi-Dirac (FD) function (this ‘confinement’ is done for efficiency and numerical stability reasons). A FD function goes from one to zero, controlled by two parameters. It has a value 0.5 at Radius, and the decay width is Delta.
This key sets the two parameters ‘Radius’ and ‘Delta’.
Basic: Radius=7.0, Delta=0.7; Normal: Radius=10.0, Delta=1.0; Good: Radius=20.0, Delta=2.0; VeryGood and Excellent: no confinement at all.
If ‘Auto’, the quality defined in the ‘NumericalQuality’ will be used.
Radius (float | FloatKey) – Explicitly specify the radius parameter of the Fermi-Dirac function.
- class _Solvation[source]¶
Options for the COSMO (Conductor like Screening Model) solvation model.
- Variables:
CVec (Literal["EXACT", "FITPOT"]) –
Choose how to calculate the Coulomb interaction matrix between the molecule and the point charges on the surface:
EXACT: use exact density, and integrate against the potential of the point charges. This may have inaccuracies when integration points are close to the point charges.
FITPOT: evaluate the molecular potential at the positions of the point charges, and multiply with these charges.
Enabled (BoolType | BoolKey) – Use the Conductor like Screening Model (COSMO) to include solvent effects.
SCF (Literal["VAR", "PERT", "NONE"]) – Determine the point charges either Variational (VAR) or after the SCF as a Perturbation (PERT).
Surf (Literal["Delley", "Wsurf", "Asurf", "Esurf", "Klamt"]) –
Within the COSMO model the molecule is contained in a molecule shaped cavity.
Select one of the following surfaces to define the cavity:
Wsurf: Van der Waals surface
Asurf: solvent accessible surface
Esurf: solvent excluding surface
Klamt: Klamt surface
Delley: Delley surface.
Charge (BAND._Solvation._Charge) – Select the algorithm to determine the charges.
Radii (str | Sequence[str] | FreeBlock) – The values are the radii of the atomic spheres. If not specified the default values are those by Allinger. Format: ‘AtomType value’. e.g.: ‘H 0.7’
Solvent (BAND._Solvation._Solvent) – Solvent details
- class _Charge[source]¶
Select the algorithm to determine the charges.
- Variables:
Conv (float | FloatKey) – Charge convergence threshold in iterative COSMO solution.
Corr (BoolType | BoolKey) – Correct for outlying charge.
Iter (int | IntKey) – Maximum number of iterations to solve COSMO equations.
Method (Literal["CONJ", "INVER"]) –
INVER: matrix inversion, CONJ: biconjugate gradient method.
The CONJ method is guaranteed to converge with small memory requirements and is normally the preferred method.
- class _Radii[source]¶
The values are the radii of the atomic spheres. If not specified the default values are those by Allinger. Format: ‘AtomType value’. e.g.: ‘H 0.7’
- class _Solvent[source]¶
Solvent details
- Variables:
Del (float | FloatKey) – Del is the value of Klamt’s delta_sol parameter, only relevant in case of Klamt surface.
Emp (float | FloatKey) – Emp is the empirical scaling factor x for the energy scaling.
Eps (float | FloatKey) – User-defined dielectric constant of the solvent (overrides the Eps value of the solvent defined in ‘Name’)
Name (Literal["AceticAcid", "Acetone", "Acetonitrile", "Ammonia", "Aniline", "Benzene", "BenzylAlcohol", "Bromoform", "Butanol", "isoButanol", "tertButanol", "CarbonDisulfide", "CarbonTetrachloride", "Chloroform", "Cyclohexane", "Cyclohexanone", "Dichlorobenzene", "DiethylEther", "Dioxane", "DMFA", "DMSO", "Ethanol", "EthylAcetate", "Dichloroethane", "EthyleneGlycol", "Formamide", "FormicAcid", "Glycerol", "HexamethylPhosphoramide", "Hexane", "Hydrazine", "Methanol", "MethylEthylKetone", "Dichloromethane", "Methylformamide", "Methypyrrolidinone", "Nitrobenzene", "Nitrogen", "Nitromethane", "PhosphorylChloride", "IsoPropanol", "Pyridine", "Sulfolane", "Tetrahydrofuran", "Toluene", "Triethylamine", "TrifluoroaceticAcid", "Water"]) – Name of a pre-defined solvent. A solvent is characterized by the dielectric constant (Eps) and the solvent radius (Rad).
Rad (float | FloatKey) – User-defined radius of the solvent molecule (overrides the Rad value of the solvent defined in ‘Name’).
- class _SolvationSM12[source]¶
Options for Solvation Model 12 (SM12).
- Variables:
ARO (float | FloatKey) – Square of the fraction of non-hydrogen atoms in the solvent that are aromatic carbon atoms (carbon aromaticity)
Acid (float | FloatKey) – Abraham hydrogen bond acidity parameter
Base (float | FloatKey) – Abraham hydrogen bond basicity parameter
BornC (float | FloatKey) – Coulomb constant for General Born Approximation
Chgal (float | FloatKey) – Exponential of Pauli’s bond order
Debug (str | StringKey) – Prints a lot of information about every pass on CDS and ENP code, keywords: ENP, CDS
Enabled (BoolType | BoolKey) – Whether to use the Solvation Model 12 (SM12) in the calculation.
HALO (float | FloatKey) – Square of the fraction of non-hydrogen atoms in the solvent molecule that are F, Cl, or Br (electronegative halogenicity)
PostSCF (BoolType | BoolKey) – Whether to apply the solvation potential during the SCF or only calculate the solvation energy after the SCF.
PrintSM12 (BoolType | BoolKey) – Prints out an in-depth breakdown of solvation energies
RadSolv (float | FloatKey) – The radius distance between the solute and solvent
Solv (Literal["ACETICACID", "ACETONITRILE", "ACETOPHENONE", "ANILINE", "ANISOLE", "BENZENE", "BENZONITRILE", "BENZYLALCOHOL", "BROMOBENZENE", "BROMOETHANE", "BROMOFORM", "BROMOOCTANE", "N-BUTANOL", "SEC-BUTANOL", "BUTANONE", "BUTYLACETATE", "N-BUTYLBENZENE", "SEC-BUTYLBENZENE", "T-BUTYLBENZENE", "CARBONDISULFIDE", "CARBONTETRACHLORIDE", "CHLOROBENZENE", "CHLOROFORM", "CHLOROHEXANE", "M-CRESOL", "CYCLOHEXANE", "CYCLOHEXANONE", "DECALIN", "DECANE", "DECANOL", "1-2-DIBROMOETHANE", "DIBUTYLETHER", "O-DICHLOROBENZENE", "1-2-DICHLOROETHANE", "DIETHYLETHER", "DIISOPROPYLETHER", "N-N-DIMETHYLACETAMIDE", "N-N-DIMETHYLFORMAMIDE", "2-6-DIMETHYLPYRIDINE", "DIMETHYLSULFOXIDE", "DODECANE", "ETHANOL", "ETHOXYBENZENE", "ETHYLACETATE", "ETHYLBENZENE", "FLUOROBENZENE", "1-FLUORO-N-OCTANE", "HEPTANE", "HEPTANOL", "HEXADECANE", "HEXADECYLIODIDE", "HEXANE", "HEXANOL", "IODOBENZENE", "ISOBUTANOL", "ISOOCTANE", "ISOPROPANOL", "ISOPROPYLBENZENE", "P-ISOPROPYLTOLUENE", "MESITYLENE", "METHANOL", "METHOXYETHANOL", "METHYLENECHLORIDE", "N-METHYLFORMAMIDE", "2-METHYLPYRIDINE", "4-METHYL-2-PENTANONE", "NITROBENZENE", "NITROETHANE", "NITROMETHANE", "O-NITROTOLUENE", "NONANE", "NONANOL", "OCTANE", "OCTANOL", "PENTADECANE", "PENTANE", "PENTANOL", "PERFLUOROBENZENE", "PHENYLETHER", "PROPANOL", "PYRIDINE", "TETRACHLOROETHENE", "TETRAHYDROFURAN", "TETRAHYDROTHIOPHENEDIOXIDE", "TETRALIN", "TOLUENE", "TRIBUTYLPHOSPHATE", "TRIETHYLAMINE", "1-2-4-TRIMETHYLBENZENE", "UNDECANE", "WATER", "XYLENE", "1-2-DIBROMOETHANE_WATER", "1-2-DICHLOROETHANE_WATER", "BENZENE_WATER", "CARBONTETRACHLORIDE_WATER", "CHLOROBENZENE_WATER", "CHLOROFORM_WATER", "CYCLOHEXANE_WATER", "DIBUTYLETHER_WATER", "DIETHYLETHER_WATER", "ETHYLACETATE_WATER", "HEPTANE_WATER", "HEXANE_WATER", "NITROBENZENE_WATER", "OCTANOL_WATER"]) – List of predefined solvents
SuperTrafoDiag (int | IntKey) – Used for the generation of the super cell.
SuperTrafoDiagCM5 (int | IntKey) – Used for the generation of the super cell with CM5 charges.
Tens (float | FloatKey) – Macroscopic surface tension of the solvent at the air/solvent interface at 298K (cal*mol^-1*Ang^-2)
BornRadiusConfig (BAND._SolvationSM12._BornRadiusConfig) –
TopologicalExtrapolation (BAND._SolvationSM12._TopologicalExtrapolation) – Method to extrapolate the long range Coulomb potential, needed for periodic calculations
- class _TopologicalExtrapolation[source]¶
Method to extrapolate the long range Coulomb potential, needed for periodic calculations
- Variables:
FirstCell (int | IntKey) – First cell for the topological extrapolation of the long range part of the Coulomb Potential.
LastCell (int | IntKey) – Last cell for the topological extrapolation of the long range part of the Coulomb Potential.
Order (int | IntKey) – Order of the topological extrapolation of the long range part of the Coulomb Potential.
- class _StrainDerivatives[source]¶
Undocumented.
- Variables:
Analytical (BoolType | BoolKey) – Whether or not to use analytical strain derivatives. By default this is determined automatically, and used if possible.
AnalyticalElectrostatic (BoolType | BoolKey) – Undocumented.
Analyticalkinetic (BoolType | BoolKey) – Undocumented.
Analyticalpulay (BoolType | BoolKey) – Undocumented.
Analyticalxc (BoolType | BoolKey) – Undocumented.
CalcRhoDef0FitError (BoolType | BoolKey) – Does not affect the results, but prints the fit error and a first order error estimation for the stress. Can be very expensive.
Fitrho0prune (BoolType | BoolKey) – Undocumented.
Kinviadagger (BoolType | BoolKey) – Undocumented.
Naiveelstat (BoolType | BoolKey) – Undocumented.
NoPairSetKCoordsToZero (BoolType | BoolKey) – This used to be the case, do not know why. It seems to have no effect.
Numericaldefdef (BoolType | BoolKey) – Undocumented.
Numericaldefdeflong (BoolType | BoolKey) – Undocumented.
Renormalizechargefitrho0 (BoolType | BoolKey) – Undocumented.
Shiftmultipoleorigin (BoolType | BoolKey) – Undocumented.
Skipinlgwsmodule (BoolType | BoolKey) – Undocumented.
SubtractAtomicXC (BoolType | BoolKey) – Derive stress from xc energy difference of molecule versus atoms.
Usesymmetry (BoolType | BoolKey) – Undocumented.
Usevstrainderrho (BoolType | BoolKey) – Undocumented.
- class _Tails[source]¶
Ignore function tails.
- Variables:
Bas (float | FloatKey) – Cut off the basis functions when smaller than the specified threshold.
Confine (float | FloatKey) – Define a soft confinement radius for all functions. The value can be chosen larger than Tails%Bas. It never exceeds the SoftConfinement%Radius value.
Coulomb (BoolType | BoolKey) – ToDo
Rosa (BoolType | BoolKey) – Increase the radius of contracted functions. A factor is used that decays from 2 to 1.
Verbose (BoolType | BoolKey) – Feedback, in particular on the confinement.
- class _TechnicalCOSMO[source]¶
Some options to develop cosmo for charged periodic systems
- Variables:
AddCOSMOPotentialToZlmFit (BoolType | BoolKey) – Should the cosmo potential be calculated via ZlmFit?. Merely for technical tests
CalcEnergyForChargedPeriodicCase (BoolType | BoolKey) – Use new energy expression suitable for charged periodic systems.
ChargeConstraintViaEnergy (BoolType | BoolKey) – The charge constraint can be done via a Lagrange multiplier, or by eliminating one charge from the energy.
ExcludeNuBugFix (BoolType | BoolKey) – There was a bug skipping for all nu==mu, not checking icell = 1
ExtrapolateChargeDerivativePotential (BoolType | BoolKey) – Use topological extrapolation for the calculation of the charge derivative of the (surface) potential.
IncludeCOSMOPotentialInZlmFit (BoolType | BoolKey) – Solve COSMO and include cosmo pot in ZlmFit potential. This makes sense for the charge periodic COSMO case.
NeutralizeSurfaceCharges (BoolType | BoolKey) – Add Q/N to surface charges.
SolveChargesForChargedPeriodicCase (BoolType | BoolKey) – Use new energy expression suitable for charged periodic systems to determine the charges.
UseFullEnergyExpression (BoolType | BoolKey) – Use the energy expression that is valid for any q vector.
- class _Transport[source]¶
Old NEGF. No longer supported
- Variables:
c1atoms (int | IntKey) – count of number of atoms considered as contact 1
c2atoms (int | IntKey) – count of number of atoms considered as contact 2
defersigma (BoolType | BoolKey) – decides whether to load sigmas on the fly
easynegf (BoolType | BoolKey) – Undocumented.
freezestop (int | IntKey) – controls how long you might whether deltaphi0 floats in transport
hmatmixsteps (int | IntKey) – controls over how many steps to mix in bulk hmats after freezestop
nematoms (int | IntKey) – count of number of atoms considered as extended molecule
noshiftfloat (BoolType | BoolKey) – turns off deltaphi0 floating calculation in transport
screw (BoolType | BoolKey) – controls negfs ability to adapt the scf, diis mixing parameters
testmatch (BoolType | BoolKey) – controls whether we should do extensive testing of hmat matches
unresleads (BoolType | BoolKey) – turns on unrestricted calculation for the leads in transport
wbl (BoolType | BoolKey) – sets wide band limit coupling parameter
wblflat (float | FloatKey) – decides whether to do wbl with flat imaginary constant part, and sets it
wblimonly (BoolType | BoolKey) – decides whether to do wbl sigma(fermi) with only imaginary part
wblplotonly (BoolType | BoolKey) – decides whether to turn wbl of any kind off in scf cycle
wblrescale (BoolType | BoolKey) – decides whether to do wbl sigma rescaled from ellipse to flat band
- class _XC[source]¶
Exchange Correlation functionals
- Variables:
DoubleHybrid (str | StringKey) – Specifies the double hybrid functional that should be used during the SCF.
EmpiricalScaling (Literal["None", "SOS", "SCS", "SCSMI"]) – Calculate the (SOS/SCS/SCSMI)-MP2 correlation energy.
GALITSKIIMIGDAL (BoolType | BoolKey) – Calculate the Galitskii-Migdal correlation energy after the SCF is completed.
GLLBKParameter (float | FloatKey) – K parameter for the GLLB functionals. See equation (20) of the paper.
HartreeFock (BoolType | BoolKey) – Stand alone HF calculation.
MP2 (BoolType | BoolKey) – Calculate the MP2 correlation energy after the HF SCF is completed.
RPA (Literal["None", "Direct", "Sigma", "SOSEX", "SOSSX"]) – Specifies that RPA is used an possibly also a post-RPA method. By default, direct RPA is used
RangeSeparation (str | StringKey) – Intended to be used with HartreeFock (or hybrid functionals). Example: OMEGA= 0.110000 ALPHA= 0.250000 BETA= -0.250000 ERF-SHORTRANGE
allowany (BoolType | BoolKey) – Undocumented.
dispersion (str | StringKey) – The dispersion correction model to be used.
libxc (str | StringKey) – Functional using the LicXC library.
libxcdensitythreshold (float | FloatKey) – Density threshold for LibXC functionals.
model (str | StringKey) – Model potential. The possible choices are LB94, GLLB-SC, BGLLB-VWN, and BGLLB-LYP
spinorbitmagnetization (str | StringKey) – Type of Spin-Orbit magnetization.
tb_mbjafactor (float | FloatKey) – a parameter for the TB-MBJ model potential.
tb_mbjbfactor (float | FloatKey) – b parameter for the TB-MBJ model potential..
tb_mbjcfactor (float | FloatKey) – c parameter for the TB-MBJ model potential..
tb_mbjefactor (float | FloatKey) – e parameter for the TB-MBJ model potential..
usexcfun (BoolType | BoolKey) – Whether ot not the XCFun library should be used.
xcfun (BoolType | BoolKey) – Functional for the XCFun library.
DFTHalf (BAND._XC._DFTHalf) – DFT-1/2 method for band gaps. See PRB vol 78,125116 2008. This method can be used in combination with any functional. For each active atom type (see ActiveAtomType) Band will perform SCF calculations at different screening cut-off values (see ScreeningCutOffs) and pick the cut-off value that maximizes the band gap. If multiple atom types are active, the screening cut-off optimizations are done one type at the time (in the same order as the ActiveAtomType blocks appear in the input).
- class _DFTHalf[source]¶
DFT-1/2 method for band gaps. See PRB vol 78,125116 2008. This method can be used in combination with any functional. For each active atom type (see ActiveAtomType) Band will perform SCF calculations at different screening cut-off values (see ScreeningCutOffs) and pick the cut-off value that maximizes the band gap. If multiple atom types are active, the screening cut-off optimizations are done one type at the time (in the same order as the ActiveAtomType blocks appear in the input).
- Variables:
Enabled (BoolType | BoolKey) – Whether the DFT-1/2 method will be used.
Prepare (BoolType | BoolKey) – Analyze the band structure to determine reasonable settings for an DFT-1/2 calculation. If this is possible the list of active atom types is written to the output. This can be used in a next run as the values for ActiveAtomType. The DFTHalf%Enabled key should be set to false
SelfConsistent (BoolType | BoolKey) – Apply the extra potential during the SCF, or only afterwards. Applying DFT-1/2 only post SCF increases the band gap, compared to the self-consistent one.
ActiveAtomType (BAND._XC._DFTHalf._ActiveAtomType) – Use the DFT-1/2 method for the atom-type specified in this block.
- class _ActiveAtomType[source]¶
Use the DFT-1/2 method for the atom-type specified in this block.
- Variables:
AtomType (str | StringKey) – Atom-type to use. You can activate all atom-types by specifying ‘All’.
IonicCharge (float | FloatKey) – The amount of charge to be removed from the atomic HOMO.
ScreeningCutOffs (Iterable[float] | FloatListKey) – List of screening cut-offs (to screen the asymptotic IonicCharge/r potential). Band will loop over these values and find the cut-off that maximizes the band-gap. If only one number is provided, Band will simply use that value.
- class _ZlmFit[source]¶
Options for the density fitting scheme ‘ZlmFit’.
- Variables:
AllowBoost (BoolType | BoolKey) – Allow automatic atom-dependent tuning of maximum l of spherical harmonics expansion. Whether or not this boost is needed for a given atom is based on an heuristic estimate of how complex the density around that atom is.
DensityThreshold (float | FloatKey) – Threshold below which the electron density is considered to be negligible. Depends on Quality and is normally 1.0e-7
FGaussianW (float | FloatKey) – Only for 3D periodic systems. Width of the Gaussian functions replacing the S and P Zlms for Fourier transform.
FGridSpacing (float | FloatKey) – Only for 3D periodic systems. Spacing for the Fourier grid. By default, this depends on the quality.
FKSpaceCutOff (float | FloatKey) – Only for 3D periodic systems. Cut-off of the grid in k-space for the Fourier transform.
FirstTopoCell (int | IntKey) – First cell for the topological extrapolation of the long range part of the Coulomb Potential.
GridAngOrder (int | IntKey) – Lebedev angular order for the fitting grid.
GridRadialFactor (float | FloatKey) – User defined value for determining how many radial points are used in the interpolation grid. By default, this depends on the quality, and normally is 1.0
LMargin (int | IntKey) – User-defined l-margin, i.e., l_max for fitting is max(lMargin + l_max_basis_function, 2*l_max_basis_function). Depends on Quality and normally is 4
LastTopoCell (int | IntKey) – Last cell for the topological extrapolation of the long range part of the Coulomb Potential.
NumStarsPartitionFun (int | IntKey) – Number of cell stars to consider when computing the partition function.
OrderTopoTrick (int | IntKey) – Order of the topological extrapolation of the long range part of the Coulomb Potential.
PartitionFunThreshold (float | FloatKey) – Threshold for the partition functions: if an integration point has a partition function weight smaller than this threshold, it will be discarded.
PotentialThreshold (float | FloatKey) – Depends on the Quality. For band it is normally 1.0e-8, ten times smaller than for molecules.
Pruning (BoolType | BoolKey) – Undocumented. Depends on the Quality, normally true
Quality (Literal["Auto", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Quality of the density-fitting approximation. For a description of the various qualities and the associated numerical accuracy see reference. If ‘Auto’, the quality defined in the ‘NumericalQuality’ will be used.
UseBlockProperty (BoolType | BoolKey) – Undocumented.
QualityPerRegion (BAND._ZlmFit._QualityPerRegion) – Sets the ZlmFit quality for all atoms in a region. If specified, this overwrites the globally set quality.
- class DFTB[source]¶
- Variables:
DispersionCorrection (Literal["None", "Auto", "UFF", "ULG", "D2", "D3-BJ", "D4"]) –
This key is used to specify an empirical dispersion model. Please refer to the DFTB documentation for details on the different methods.
By default no dispersion correction will be applied. Setting this to auto applies the dispersion correction recommended in the DFTB parameter set’s metainfo file. Note that the D3-BJ dispersion correction is enabled by default when using the GFN1-xTB model Hamiltonian, but can be disabled manually by setting this keyword to None.
Model (Literal["DFTB", "DFTB0", "DFTB1", "SCC-DFTB", "DFTB2", "DFTB3", "GFN1-xTB", "NonSCC-GFN1-xTB"]) –
Selects the Hamiltonian used in the DFTB calculation: - DFTB/DFTB0/DFTB1 for classic DFTB without a self-consistent charge cycle - SCC-DFTB/DFTB2 with a self-consistency loop for the Mulliken charges - DFTB3 for additional third-order contributions. - GFN1-xTB for Grimme’s extended tight-binding model in the GFN1 version. - NonSCC-GFN1-xTB for a less accurate but faster version of GFN1-xTB without a self-consistency cycle
The choice has to be supported by the selected parameter set.
NumericalQuality (Literal["Basic", "Normal", "Good", "VeryGood", "Excellent"]) – Set the quality of some technical aspects of a DFTB calculation. It sets the quality of: KSpace (reciprocal space integration). Note: the quality defined in the block of a specific technical aspects supersedes the value defined in NumericalQuality (e.g. if I specify ‘NumericalQuality Basic’ and ‘KSpace%Quality Good’, the quality of the KSpace will be ‘Good’)
RadialExtrapolation (Literal["Auto", "ScreenTail", "None", "Linear", "Original", "Improved", "Bezier"]) – Advanced control option. Overrides the extrapolation method for Slater-Koster grid values between the end of the tabulated grid and the cutoff distance (value for which atoms are considered too far to interact). Depending on the structure of your Slater-Koster tables, a different radial extrapolation method may be needed in order to guarantee correct behavior, in particular for large and periodic systems. See the DFTB documentation for a description of the various available methods.
ResourcesDir (str | Path | StringKey) – The directory containing the parameter files. The path can be absolute or relative. Relative paths starting with ./ are considered relative to the directory in which the calculation is started, otherwise they are considered relative to $AMSRESOURCES/DFTB. This key is required for the Slater-Koster based DFTB models, but optional for xTB.
StoreMatrices (BoolType | BoolKey) – Determines whether the Hamiltonian and overlap matrices are stored in the binary result file.
StoreOrbitals (BoolType | BoolKey) – Determines whether the orbital coefficients are stored in the binary result file. They are needed for displaying orbitals and densities in amsview.
UnpairedElectrons (int | IntKey) –
This specifies the number of unpaired electrons (not the multiplicity!).
This number will then be used in the orbital-filling strategy. Has to be compatible with the total number of electrons, meaning it must be an even number if the total number of electrons is even and odd if the total number is odd. Must be an integer value.
Note that this does not activate spin polarization, it only affects the filling of the orbitals.
UseSymmetry (BoolType | BoolKey) –
KSpace (DFTB._KSpace) – Options for the k-space integration (i.e. the grid used to sample the Brillouin zone)
Occupation (DFTB._Occupation) – Configures the details of how the molecular orbitals are occupied with electrons.
Periodic (DFTB._Periodic) – Block that sets various details of the calculation only relevant for periodic systems.
Properties (DFTB._Properties) – DFTB can calculate various properties of the simulated system. This block configures which properties will be calculated.
QMFQ (DFTB._QMFQ) – Block input key for QM/FQ(FMu).
Repulsion (DFTB._Repulsion) – Configures various details of the repulsive potential.
SCC (DFTB._SCC) – This optional section configures various details of the self-consistent charge cycle. If the model Hamiltonian does not need a self-consistent solution (e.g. plain DFTB0), none of this information is used and the entire section will be ignored.
Solvation (DFTB._Solvation) – Generalized Born solvation model with Solvent Accessible Surface Area (GBSA).
Technical (DFTB._Technical) – This optional section is about technical aspects of the program that should not concern the normal user.
XTBConfig (DFTB._XTBConfig) – This block allows for minor tweaking.
- class _KSpace[source]¶
Options for the k-space integration (i.e. the grid used to sample the Brillouin zone)
- Variables:
Analytical (BoolType | BoolKey) –
For analytical integration the BZ is split into simplices, whereover the bands are interpolated, ater which the integrals can be performed analytically.
Alternatively, the set of eigenvalues in the discrete set of k-points are just handled as distinct molecular orbitals.
Using analytical=no can improve SCF convergence in combination with smearing/temperature.
Quality (Literal["Auto", "GammaOnly", "Basic", "Normal", "Good", "VeryGood", "Excellent"]) –
Select the quality of the K-space grid used to sample the Brillouin Zone. If ‘Auto’, the quality defined in the ‘NumericalQuality’ will be used. If ‘GammaOnly’, only one point (the gamma point) will be used.
The actual number of K points generated depends on this option and on the size of the unit cell. The larger the real space cell, the fewer K points will be generated.
The CPU-time and accuracy strongly depend on this option.
Type (Literal["Regular", "Symmetric"]) –
The type of k-space integration grid used to sample the Brillouin zone (BZ) used.
’Regular’: simple regular grid.
’Symmetric’: symmetric grid for the irreducible wedge of the first BZ (useful when high-symmetry points in the BZ are needed to capture the correct physics of the system, graphene being a notable example).
Regular (DFTB._KSpace._Regular) – Options for the regular k-space integration grid.
Symmetric (DFTB._KSpace._Symmetric) – Options for the symmetric k-space integration grid.
- class _Regular[source]¶
Options for the regular k-space integration grid.
- Variables:
DoubleCount (int | IntKey) – Increase for each dimension the grid. A sequence of doubling, with a special meaning for grid with odd numbers. Useful when checking k-space convergence.
NumberOfPoints (Iterable[int] | IntListKey) –
Use a regular grid with the specified number of k-points along each reciprocal lattice vector.
For 1D periodic systems you should specify only one number, for 2D systems two numbers, and for 3D systems three numbers.
PreferEvenNumberOfPoints (BoolType | BoolKey) – In case of an automatic grid normally odd numbers will be generated (1,3,5,9), suitable for a quadratic grid. With this option the suggested odd numbers will be increased by one, unless it is one.
SplitCubeInSix (BoolType | BoolKey) – Undocumented.
SplitLongest (BoolType | BoolKey) – Undocumented.
- class _Symmetric[source]¶
Options for the symmetric k-space integration grid.
- Variables:
Specify the accuracy for the Symmetric method.
1: absolutely minimal (only the G-point is used) 2: linear tetrahedron method, coarsest spacing 3: quadratic tetrahedron method, coarsest spacing 4,6,… (even): linear tetrahedron method 5,7…. (odd): quadratic method
The tetrahedron method is usually by far inferior.
- class _Occupation[source]¶
Configures the details of how the molecular orbitals are occupied with electrons.
- Variables:
KT (float | FloatKey) – (KT) Boltzmann constant times temperature, used for electronic temperature with strategy is auto. The default value is the default value for Temperature*3.166815423e-6. This key and Temperature are mutually exclusive.
NumBoltz (int | IntKey) – The electronic temperature is done with a Riemann Stieltjes numerical integration, between zero and one occupation. This defines the number of points to be used.
Strategy (Literal["Auto", "Aufbau", "Fermi"]) –
This optional key allows to specify the fill strategy to use for the molecular orbitals.
Can either be ‘Aufbau’ for simply filling the energetically lowest orbitals, or ‘Fermi’ for a smeared out Fermi-Dirac occupation. By default the occupation strategy is determined automatically, based on the other settings (such as the number of unpaired electrons).
Temperature (float | FloatKey) – The Fermi temperature used for the Fermi-Dirac distribution. Ignored in case of aufbau occupations.
- class _Periodic[source]¶
Block that sets various details of the calculation only relevant for periodic systems.
- Variables:
BZPath (DFTB._Periodic._BZPath) – If [BandStructure%Automatic] is disabled, DFTB will compute the band structure for the user-defined path in the [BZPath] block. You should define the vertices of your path in fractional coordinates (with respect to the reciprocal lattice vectors) in the [Path] sub-block. If you want to make a jump in your path, you need to specify a new [Path] sub-block.
BandStructure (DFTB._Periodic._BandStructure) – Options for band structure plotting. This has no effect on the calculated energy. [Warning: The band structure is only computed in case of k-space sampling, i.e. it is not computed for Gamma-only calculations (see: Periodic%KSpace).]
DOS (DFTB._Periodic._DOS) – The subkeys of [DOS] allow to customize the calculation of the density of states.
EffectiveMass (DFTB._Periodic._EffectiveMass) –
In a semi-conductor, the mobility of electrons and holes is related to the curvature of the bands at the top of the valence band and the bottom of the conduction band.
With the effective mass option, this curvature is obtained by numerical differentiation.
The estimation is done with the specified step size, and twice the specified step size, and both results are printed to give a hint on the accuracy. By far the most convenient way to use this key is without specifying any options.
- class _BZPath[source]¶
If [BandStructure%Automatic] is disabled, DFTB will compute the band structure for the user-defined path in the [BZPath] block. You should define the vertices of your path in fractional coordinates (with respect to the reciprocal lattice vectors) in the [Path] sub-block. If you want to make a jump in your path, you need to specify a new [Path] sub-block.
- class _BandStructure[source]¶
Options for band structure plotting. This has no effect on the calculated energy. [Warning: The band structure is only computed in case of k-space sampling, i.e. it is not computed for Gamma-only calculations (see: Periodic%KSpace).]
- Variables:
Automatic (BoolType | BoolKey) –
Generate and use the standard path through the Brillouin zone.
If not, use the user defined path (set via Custom path in the GUI, or with the Periodic%BZPath keyword in the run script).
DeltaK (float | FloatKey) – Step size in reciprocal space for band structure interpolation. Using a smaller number will produce smoother band curves at an increased computational time.
Enabled (BoolType | BoolKey) – Whether or not to calculate the band structure.
FatBands (BoolType | BoolKey) –
Control the computation of the fat bands (only when the bandstructure is calculated).
The fat bands are the periodic equivalent of the Mulliken population analysis. The definition of the fat bands can be found in the Band Documentation.
KPathFinderConvention (Literal["Setyawan-Curtarolo", "Hinuma"]) –
This option determines how the path through the Brillouin zone is generated when using the automatic k-point mode.
Available options:
Setyawan-Curtarolo(default for 1D and 2D lattices): Uses our built-in KPath program to find a path through high-symmetry points based on the method by Setyawan and Curtarolo (https://doi.org/10.1016/j.commatsci.2010.05.010). For 2D lattices, the path is derived from the intersection of the 3D Brillouin zone with a plane. For 1D lattices, the path is simply Gamma-Z.Hinuma: Uses the external SeeKPath utility to generate the k-path (https://github.com/giovannipizzi/seekpath and https://doi.org/10.1016/j.commatsci.2016.10.015).
UseSymmetry (BoolType | BoolKey) – If set, only the irreducible wedge of the Wigner-Seitz cell is sampled. If not, the whole (inversion-unique) Wigner-Seitz cell is sampled. Only available for Setyawan and Curtarolo convention (see
KPathFinderConvention).
- class _DOS[source]¶
The subkeys of [DOS] allow to customize the calculation of the density of states.
- Variables:
EMax (float | FloatKey) – Upper end of the energy interval in which the density of states is calculated.
EMin (float | FloatKey) – Lower end of the energy interval in which the density of states is calculated.
Enabled (BoolType | BoolKey) – Whether or not to calculate the DOS. Note that the DOS will always be calculated when also the band structure is calculated.
NSteps (int | IntKey) – The number of energy intervals between [EMin] and [EMax] for which the density of states is calculated.
- class _EffectiveMass[source]¶
In a semi-conductor, the mobility of electrons and holes is related to the curvature of the bands at the top of the valence band and the bottom of the conduction band.
With the effective mass option, this curvature is obtained by numerical differentiation.
The estimation is done with the specified step size, and twice the specified step size, and both results are printed to give a hint on the accuracy. By far the most convenient way to use this key is without specifying any options.
- Variables:
Enabled (BoolType | BoolKey) –
In a semi-conductor, the mobility of electrons and holes is related to the curvature of the bands at the top of the valence band and the bottom of the conduction band.
With the effective mass option, this curvature is obtained by numerical differentiation.
The estimation is done with the specified step size, and twice the specified step size, and both results are printed to give a hint on the accuracy. By far the most convenient way to use this key is without specifying any options.
KPointCoord (Iterable[float] | FloatListKey) – Coordinate of the k-points for which you would like to compute the effective mass.
NumAbove (int | IntKey) – Number of bands to take into account above the Fermi level.
NumBelow (int | IntKey) – Number of bands to take into account below the Fermi level.
StepSize (float | FloatKey) – Size of the step taken in reciprocal space to perform the numerical differentiation
UseBandStructureInfoFromPath (BoolType | BoolKey) – The (automatic) location of the HOMO and LUMO can be determined via band interpolation, or from the path as used by the BandStructure feature. The latter works better when they are located on the path. See also comments in the BandStructure block. To reproduce results from before ams2025 set to no.
- class _Properties[source]¶
DFTB can calculate various properties of the simulated system. This block configures which properties will be calculated.
- Variables:
NBOInput (BoolType | BoolKey) – Whether or not an input file for the NBO program is written to disk as nboInput.FILE47. The input file follows the FILE47 format as described in the NBO6 manual available on nbo6.chem.wisc.edu. By default, only the calculation of the natural bond orbitals and the natural localized molecular orbitals is enabled, but the nboInput.FILE47 file can be edited by hand to enable other analysis models. Please refer to the NBO6 manual for details.
Excitations (DFTB._Properties._Excitations) – Contains all options related to the calculation of excited states, either as simple single orbitals transitions or from a TD-DFTB calculation.
Fragments (DFTB._Properties._Fragments) – Fragment files
RESPONSE (DFTB._Properties._RESPONSE) – Linear response module to compute electric (complex) polarizabilities
- class _Excitations[source]¶
Contains all options related to the calculation of excited states, either as simple single orbitals transitions or from a TD-DFTB calculation.
- Variables:
SingleOrbTrans (DFTB._Properties._Excitations._SingleOrbTrans) – The simplest approximation to the true excitations are the single orbital transitions (sometimes called Kohn-Sham transitions), that is transitions where a single electron is excited from an occupied Kohn-Sham orbital into a virtual orbital. The calculation of these transitions is configured in this section. Note that the SingleOrbTrans section is optional even though the single orbital transitions are also needed for TD-DFTB calculations. If the section is not present all single orbital transitions will still be calculated and used in a subsequent TD-DFTB calculation, but no output will be produced.
TDDFTB (DFTB._Properties._Excitations._TDDFTB) – Calculations with time-dependent DFTB can be configured in the TDDFTB section and should in general give better results than the raw single orbital transitions. TD-DFTB calculates the excitations in the basis of the single orbital transitions, whose calculation is configured in the SingleOrbTrans section. Using a filter in SingleOrbTrans can therefore be used to reduce the size of the basis for TD-DFTB. One possible application of this is to accelerate the calculation of electronic absorption spectra by removing single orbital transitions with small oscillator strengths from the basis. Note that the entire TDDFTB section is optional. If no TDDFTB section is found, the behavior depends on the existence of the SingleOrbTrans section: If no SingleOrbTrans section is found (the Excitations section is completely empty then) a TD-DFTB calculation with default parameters will be performed. If only the SingleOrbTrans section is present no TD-DFTB calculation will be done.
TDDFTBGradients (DFTB._Properties._Excitations._TDDFTBGradients) – This block configures the calculation of analytical gradients for the TD-DFTB excitation energies, which allows the optimization of excited state geometries and the calculation of vibrational frequencies in excited states (see J. Comput. Chem., 28: 2589-2601). If the gradients are calculated, they will automatically be used for geometry optimizations or vibrational frequency calculations, if the corresponding Task is selected and only 1 excitation is selected. Vibrationally resolved UV/Vis spectroscopy (Franck-Condon Factors) can be calculated in combination with the FCF program or using the Vibrational Analysis Tools in AMS. See the ADF documentation on Vibrationally resolved electronic spectra or the AMS documentation for the Vibrational Analysis Tools.
- class _SingleOrbTrans[source]¶
The simplest approximation to the true excitations are the single orbital transitions (sometimes called Kohn-Sham transitions), that is transitions where a single electron is excited from an occupied Kohn-Sham orbital into a virtual orbital. The calculation of these transitions is configured in this section. Note that the SingleOrbTrans section is optional even though the single orbital transitions are also needed for TD-DFTB calculations. If the section is not present all single orbital transitions will still be calculated and used in a subsequent TD-DFTB calculation, but no output will be produced.
- Variables:
Enabled (BoolType | BoolKey) – Calculate the single orbital transitions.
The number of single orbital transitions that are printed to the screen and written to disk.
If not a TD-DFTB calculation, the default is to print the 10 lowest single orbital transitions.
In case of a TD-DFTB calculation it is assumed that the single orbital transitions are only used as an input for TD-DFTB and nothing will be printed unless PrintLowest is specified explicitly.
Filter (DFTB._Properties._Excitations._SingleOrbTrans._Filter) – This section allows to remove single orbital transitions based on certain criteria. All filters are disabled by default.
- class _Filter[source]¶
This section allows to remove single orbital transitions based on certain criteria. All filters are disabled by default.
- Variables:
MinPertCont (float | FloatKey) – The energy range up to which SOTs are considered primary in Grimme’s sTDA based filter.
Removes single orbital transitions with an oscillator strength smaller than this threshold.
A typical value to start (if used at all) would be 1.0e-3.
PrimRange (float | FloatKey) – The energy range up to which SOTs are considered primary in Grimme’s sTDA based filter.
UsePertCorr (BoolType | BoolKey) – The energy range up to which SOTs are considered primary in Grimme’s sTDA based filter.
dEMax (float | FloatKey) – Removes single orbital transitions with an orbital energy difference larger than this threshold.
dEMin (float | FloatKey) – Removes single orbital transitions with an orbital energy difference smaller than this threshold.
- class _TDDFTB[source]¶
Calculations with time-dependent DFTB can be configured in the TDDFTB section and should in general give better results than the raw single orbital transitions. TD-DFTB calculates the excitations in the basis of the single orbital transitions, whose calculation is configured in the SingleOrbTrans section. Using a filter in SingleOrbTrans can therefore be used to reduce the size of the basis for TD-DFTB. One possible application of this is to accelerate the calculation of electronic absorption spectra by removing single orbital transitions with small oscillator strengths from the basis. Note that the entire TDDFTB section is optional. If no TDDFTB section is found, the behavior depends on the existence of the SingleOrbTrans section: If no SingleOrbTrans section is found (the Excitations section is completely empty then) a TD-DFTB calculation with default parameters will be performed. If only the SingleOrbTrans section is present no TD-DFTB calculation will be done.
- Variables:
ATChargeAnalysis (Literal["Mulliken", "Loewdin"]) – Which analysis method to use for the calculation of the atomic transition charges.
Calc (Literal["None", "Singlet", "Triplet"]) – Specifies the multiplicity of the excitations to be calculated.
Diagonalization (Literal["Auto", "Davidson", "Exact"]) –
Select the method used to solve the TD-DFTB eigenvalue equation.
The most straightforward procedure is a direct diagonalization of the matrix from which the excitation energies and oscillator strengths are obtained. Since the matrix grows quickly with system size (number of used single orbital transitions squared), this option is possible only for small molecules.
The alternative is the iterative Davidson method, which finds a few of the lowest excitations within an error tolerance without ever storing the full matrix.
The default is to make this decision automatically based on the system size and the requested number of excitations.
Specifies the number of excitations that are calculated.
Note that in case of the exact diagonalization all excitations are calculated, but only the lowest ones are printed to screen and written to the output file.
Also note that if limited both by number and by energy, (lowest and upto), DFTB will always use whatever results in the smaller number of calculated excitations.
Print (str | StringKey) – Specifies whether to print details on the contribution of the individual single orbital transitions to the calculated excitations.
ScaleKernel (float | FloatKey) –
Set the scaling parameter of the response kernel.
A scaling approach can be used to identify plasmons in molecules. While single-particle excitations are only slightly affected by scaling of the response kernel, plasmonic excitations are sensitive to variations in the scaling parameter. Default no scaling is used (scaling parameter = 1.0)
Set the maximum excitation energy.
Attempts to calculate all excitations up to a given energy by calculating a number of excitations equal to the number of single orbital transitions in this window. This is only approximately correct, so one should always add some safety margin.
Note that if limited both by number and by energy, (lowest and upto), DFTB will always use whatever results in the smaller number of calculated excitations.
DavidsonConfig (DFTB._Properties._Excitations._TDDFTB._DavidsonConfig) – This section contains a number of keywords that can be used to override various internals of the Davidson eigensolver. The default values should generally be fine.
- class _DavidsonConfig[source]¶
This section contains a number of keywords that can be used to override various internals of the Davidson eigensolver. The default values should generally be fine.
- Variables:
ATCharges (Literal["Precalc", "OnTheFly"]) –
Select whether the atomic transition charges are precalculated in advance or reevaluated during the iterations of the Davidson solver.
Precalculating the charges will improve the performance, but requires additional storage.
The default is to precalculate the atomic transition charges, but the precalculation may be disabled if not not enough memory is available.
SafetyMargin (int | IntKey) – The number of eigenvectors the Davidson method will calculate in addition to the ones requested by the user. With the Davidson eigensolver it is generally a good idea to calculate a few more eigenvectors than needed, as depending on the initial guess for the eigenvectors it can happen that the found ones are not exactly the lowest ones. This problem is especially prominent if one wants to calculate only a small number of excitations for a symmetric molecule, where the initial guesses for the eigenvectors might have the wrong symmetry. Note that the additionally calculated excitations will neither be written to the result file nor be visible in the output.
Tolerance (float | FloatKey) – Convergence criterion for the norm of the residual.
- class _TDDFTBGradients[source]¶
This block configures the calculation of analytical gradients for the TD-DFTB excitation energies, which allows the optimization of excited state geometries and the calculation of vibrational frequencies in excited states (see J. Comput. Chem., 28: 2589-2601). If the gradients are calculated, they will automatically be used for geometry optimizations or vibrational frequency calculations, if the corresponding Task is selected and only 1 excitation is selected. Vibrationally resolved UV/Vis spectroscopy (Franck-Condon Factors) can be calculated in combination with the FCF program or using the Vibrational Analysis Tools in AMS. See the ADF documentation on Vibrationally resolved electronic spectra or the AMS documentation for the Vibrational Analysis Tools.
- Variables:
Eigenfollow (BoolType | BoolKey) – If this option is set, DFTB uses the transition density in atomic orbital basis to follow the initially selected excited state during a geometry optimization. This is useful if excited state potential energy surfaces cross each other and you want to follow the surface you started on.
Excitation (Iterable[int] | IntListKey) –
Select which excited states to calculate the gradients for.
Gradients can only be calculated for an excited states that has been calculated using TD-DFTB. Make sure that enough excitations are calculated.
- class _Fragments[source]¶
Fragment files
- Variables:
Analysis (BoolType | BoolKey) – Mulliken population analysis in terms of fragment orbitals.
EMax (float | FloatKey) – Upper end of the energy interval for which the orbitals are analyzed.
Emin (float | FloatKey) – Lower end of the energy interval for which the orbitals are analyzed.
File (str | StringKey) – Path (either absolute or relative) of fragment file
TIDegeneracyThreshold (float | FloatKey) – If the orbital energy of the fragment MO is within this threshold with fragment HOMO or LUMO energy, then this fragment MO is included in the calculation of the transfer integrals. Relevant in case there is (near) degeneracy.
TransferIntegrals (BoolType | BoolKey) –
Calculate the charge transfer integrals, spatial overlap integrals and site energies.
Charge transfer integrals can be used in models that calculate transport properties.
- class _RESPONSE[source]¶
Linear response module to compute electric (complex) polarizabilities
- Variables:
ATChargeAnalysis (Literal["Mulliken", "Loewdin"]) – Which analysis method to use for the calculation of the atomic transition charges.
Frequencies (Iterable[float] | FloatListKey) – List of frequencies of incident light
Solver (DFTB._Properties._RESPONSE._Solver) – Solver details for CPKS
- class _QMFQ[source]¶
Block input key for QM/FQ(FMu).
- Variables:
DEBUG (BoolType | BoolKey) – The DEBUG subkey will print additional information from the FQ subroutines.
Forcefield (Literal["FQ", "FQ_RQ", "FQFMU", "FQFMU_RQRMU", "NOPOL"]) – Version of the FQ family of polarizable forcefields
Frozen (BoolType | BoolKey) – Expert option. Do not introduce polarization effect in response calculations.
Kernel (Literal["OHNO", "COUL", "GAUS"]) – Expert option. KERNEL can be used to choose the functional form of the charge-charge interaction kernel between MM atoms. Recommended is to use the default OHNO. The COUL screening is the standard Coulomb interaction 1/r. The OHNO choice introduce the Ohno functional (see [K. Ohno, Theoret. Chim. Acta 2, 219 (1964)]), which depends on a parameter n that is set equal to 2. Finally, the GAUS screening models each FQ charge by means of a spherical Gaussian-type distribution, and the interaction kernel is obtained accordingly. For QM/FQFMU only GAUS SCREEN is implemented.
MolCharge (float | FloatKey) – Total charge of each fragment (FQ only)
NOGROUNDSTATE (BoolType | BoolKey) – Avoid introducing FQ effects on ground state calculations
NonEle (Literal["LJ", "None"]) – Whether to include non-electrostatic contributions to the energy. Default is the Lennard-Jones (LJ) model.
QMSCREEN (Literal["ERF", "EXP", "GAUS", "NONE"]) – Expert option. QMSCREEN can be used to choose the functional form of the charge-charge interaction kernel between MM atoms and the QM density. The screening types available are ERF (error function), EXP (exponential), GAUS (Gaussian), or NONE. The default is GAUS.
QMSCREENFACTOR (float | FloatKey) – Expert option. Sets the QM/MM interaction kernel screening length. Recommended is to use the default value 0.2 with the GAUS QM/MM screening function.
AtomType (DFTB._QMFQ._AtomType) – Definition of atomic types in MM environment
Coords (str | Sequence[str] | FreeBlock) – Coordinates and fragment information (FQ only)
Solver (DFTB._QMFQ._Solver) –
- class _Repulsion[source]¶
Configures various details of the repulsive potential.
- Variables:
ForcePolynomial (BoolType | BoolKey) – Forces the use of the polynomial repulsion, even if a spline repulsion is present in the Slater-Koster files.
- class _SCC[source]¶
This optional section configures various details of the self-consistent charge cycle. If the model Hamiltonian does not need a self-consistent solution (e.g. plain DFTB0), none of this information is used and the entire section will be ignored.
- Variables:
AdaptiveMixing (BoolType | BoolKey) – Change the mixing parameter based on the monitored energy. A significant increase of energy will strongly reduce the mixing. Then it will slowly grow back to the SCC%Mixing value.
AdaptiveMixingStrategy (int | IntKey) – Currently there are three flavors, 1, 2, and 3. The first is the most conservative. The difference between 2 and 3 is that number 3 decreases the mixing when the energy seems to go up.
AlwaysClaimConvergence (BoolType | BoolKey) – Even if the SCC does not converge, claim convergence.
HXDamping (BoolType | BoolKey) – This option activates the DFTB3 style damping for H-X bonds. Note that this is always enabled if the DFTB%Model key is set to DFTB3. Not used with xTB.
InheritMixFromPreviousResult (BoolType | BoolKey) – For some run types, such as GeometryOptimization, a previous result is available. By using the charges from the previous geometry a better initial guess for the SCC procedure may be obtained. Also the last mix factor from the previous result can be loaded, possibly speeding up the SCC.
Allows to specify the maximum number of SCC iterations. The default should suffice for most standard calculations.
Convergence issues may arise due to the use of the Aufbau occupations for systems with small HOMO-LUMO gaps. In this case the use of a Fermi broadening strategy may improve convergence.
Choosing a smaller mixing parameter (see DFTB%SCC%Mixing) may also help with convergence issues: it often provides a more stable but slower way to converge the SCC cycle.
Method (Literal["DIIS", "MultiStepper"]) – The DIIS option is the old method. The MultiStepper is much more flexible and is controlled by the SCFMultiSolver block
MinimumAdaptiveMixingFactor (float | FloatKey) – In case of AdaptiveMixing the lower bound for the MixingFactor.
MultiStepperPresetPath (str | Path | StringKey) – Name of file containing a SCFMultiStepper key block. This will be used if no Explicit SCFMultiStepper block is in the input, and Method=MultiStepper. If the path is not absolute, it is relative to $AMSHOME/data/presets/multi_stepper’
OrbitalDependent (BoolType | BoolKey) – Activates or disables orbital resolved calculations. If this key is absent the recommended settings from the parameter file’s metainfo.
PrintIterationDetails (BoolType | BoolKey) – Print nIterationsGlobal, etc. to standard output.
SpinOrbit (BoolType | BoolKey) – test
Unrestricted (BoolType | BoolKey) –
Enables spin unrestricted calculations.
Only collinear spin polarization is supported, see Theor Chem Acc (2016) 135: 232, for details.
Must be supported by the chosen parameter set. Not yet compatible with DFTB3, k-space sampling periodic calculations or the xTB models.
Converge (DFTB._SCC._Converge) – Controls the convergence criteria of the SCC cycle.
DIIS (DFTB._SCC._DIIS) – Parameters influencing the DIIS self-consistency method
SCFMultiStepper (DFTB._SCC._SCFMultiStepper) – To solve the self-consistent problem multiple steppers can be tried during stints using the ones that give the best progress.
- class _Converge[source]¶
Controls the convergence criteria of the SCC cycle.
- Variables:
Charge (float | FloatKey) – The maximum change in atomic charges between subsequent SCC iterations. If the charges change less, the SCC cycle is considered converged.
Norm (Literal["L2", "L-Infinity"]) – The LInfinity norm is the more stringent choice. The L2 norm is directly what is optimized by the DIIS procedure, it is scaled by the extra constant factor 2/sqrt(nAtoms).
- class _DIIS[source]¶
Parameters influencing the DIIS self-consistency method
- Variables:
Enabled (BoolType | BoolKey) – If not enabled simple mixing without DIIS acceleration will be used.
MaxSamples (int | IntKey) – Specifies the maximum number of samples considered during the direct inversion of iteration of subspace (DIIS) extrapolation of the atomic charges during the SCC iterations. A smaller number of samples potentially leads to a more aggressive convergence acceleration, while a larger number often guarantees a more stable iteration. Due to often occurring linear dependencies within the set of sample vectors, the maximum number of samples is reached only in very rare cases.
MaximumCoefficient (float | FloatKey) – When the diis expansion coefficients exceed this threshold, the solution is rejected. The vector space is too crowded. The oldest vector is discarded, and the expansion is re-evaluated.
MinSamples (int | IntKey) – When bigger than one, this affects the shrinking of the DIIS space on linear dependence. It will not reduce to a smaller space than MinSamples unless there is extreme dependency.
MixingFactor (float | FloatKey) – The parameter used to mix the DIIS linear combination of previously sampled atomic charge vectors with an analogous linear combination of charge vectors resulting from population analysis combination. It can assume real values between 0 and 1.
- class _SCFMultiStepper[source]¶
To solve the self-consistent problem multiple steppers can be tried during stints using the ones that give the best progress.
- Variables:
AlwaysChangeStepper (BoolType | BoolKey) – When the progress is fine there is no reason to change the stepper. In practice this is always set to true, because also the Stepper%ExpectedSlope can be used to achieve similar behavior.
ErrorGrowthAbortFactor (float | FloatKey) – Abort stint when the error grows too much, compared to the error at the start of the stint.
FractionalStepFactor (float | FloatKey) – Multiply the step by this factor. If smaller than zero this is not used.
MinStintCyclesForAbort (int | IntKey) – Look at ErrorGrowthAbortFactor only when a number of steps has been completed since the start of the stint. A value of 0 means always.
StintLength (int | IntKey) – A stepper is active during a number of SCF cycles, called a stint.
UsePreviousStintForErrorGrowthAbort (BoolType | BoolKey) – The error is normally checked against the first error of the stint. With this option that will be the one from the previous stint, if performed with the same stepper.
Stepper (DFTB._SCC._SCFMultiStepper._Stepper) –
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- class _Stepper[source]¶
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- Variables:
AbortSlope (float | FloatKey) – If the slope (at the end of a stint) is larger than this: abort the stepper
AlwaysAbortAtBeginOfStint (BoolType | BoolKey) – For debugging only: no matter what abort this stepper at the begin of the stint (doing only one step).
AlwaysAbortAtEndOfStint (BoolType | BoolKey) – For debugging only: no matter what abort this stepper at the end of the stint.
ErrorGrowthAbortFactor (float | FloatKey) – Abort stint when the error grows too much, compared to the error at the start of the stint. Overrides global ErrorGrowthAbortFactor when set to a value > 0
ExpectedSlope (float | FloatKey) – If the slope of the total SCF is better than this keep on going.
FractionalStepFactor (float | FloatKey) – Multiply the step by this factor. If smaller than zero this is not used.
InitialMixFromPreviousStint (BoolType | BoolKey) – Similar to MixFromPreviousStint, but only done the first time that a stepper is used.
MaxInitialError (float | FloatKey) – Only use the stepper when error is smaller than this.
MaxIterationNumber (int | IntKey) – Stepper will only be active for iterations smaller than this number. (Negative value means: Ignore this option)
MaxStintNumber (int | IntKey) – Stepper will only be active for stints smaller than this number. (Negative value means: Ignore this option)
MaxStints (int | IntKey) – Maximum number of stints that a stepper should be used.
MinInitialError (float | FloatKey) – Only use the stepper when error is larger than this.
MinIterationNumber (int | IntKey) – Stepper will only be active for iterations larger than this number.
MinStintCyclesForAbort (int | IntKey) – Look at ErrorGrowthAbortFactor only when a number of steps has been completed since the start of the stint. A value of 0 means always. Overrides global value.
MinStintNumber (int | IntKey) – Stepper will only be active for stints larger than this number.
MixFromPreviousStint (BoolType | BoolKey) – When starting a new stint use the mix from the previous stepper, even if it is of another type.
DIISStepper (DFTB._SCC._SCFMultiStepper._Stepper._DIISStepper) – DIIS stepper
MixAdapter (DFTB._SCC._SCFMultiStepper._Stepper._MixAdapter) – Generic mix adapter
MixStepper (DFTB._SCC._SCFMultiStepper._Stepper._MixStepper) – Simple mixing stepper, only using the previous (in/out) density.
MultiSecantStepper (DFTB._SCC._SCFMultiStepper._Stepper._MultiSecantStepper) – Multi secant stepper.
- class _DIISStepper[source]¶
DIIS stepper
- Variables:
EDIIS (BoolType | BoolKey) – Use energy DIIS. The energy is used as extra info and only interpolation is done (all coefficients in the interval [0,1]).
EDIISAlpha (float | FloatKey) – The extra energy vector is weighed by this factor. .
MaxBMatrixRange (float | FloatKey) – If larger than zero: limit the ratio between the oldest and last diagonal B matrix element.
MaxCoefficient (float | FloatKey) – The largest allowed value of the expansion coefficients. If exceed the number of vectors is reduces until the criterion is met.
MaxConditionNumber (float | FloatKey) – If larger than zero: check condition number of the B matrix. If too large reduce nVectors.
MaxVectors (int | IntKey) – Maximum number of previous densities to be used (size of the history).
MinLastCoefficient (float | FloatKey) – If larger than zero: If the most recent vector gets a (abs) coefficient smaller than this the mix is boosted.
MinVectors (int | IntKey) – Try to prevent to make nVectors shrink below this value, by allowing for significantly larger coefficients.
Mix (float | FloatKey) – Also known as greed. It determines the amount of output density to be used. May be changed by the MixAdapter.
RescaleBMatrix (BoolType | BoolKey) – Rescale the B matrix so that is’s values are of the same order as those of the constraints.
UseHalfMixForFirstCycle (BoolType | BoolKey) – Use half the mix factor at iteration 1 (if applicable).
- class _MixAdapter[source]¶
Generic mix adapter
- Variables:
CorrelateMixWithSlope (BoolType | BoolKey) – For the last two mixing factors the one with the best slope is preferred.
ErrorGrowthPanicFactor (float | FloatKey) – When the error increases more than this factor, this mix is reduced a lot.
GrowWhenSpaceGrows (BoolType | BoolKey) – Has only effect when the error goes down. If nVectors increases grow the mix factor, otherwise do not change the mix
GrowthFactor (float | FloatKey) – When the mix is considered too low it is multiplied by this factor. Otherwise it is divided by it.
MaxMix (float | FloatKey) – Do not grow the mix above this value.
MinMix (float | FloatKey) – Do not shrink the mix below this value.
NTrialMixFactors (int | IntKey) – Only used with Type=Trial. Must be an odd number.
TrialMode (Literal["CurrentMixCentered", "FullRange"]) – How are the NTrialMixFactors chosen?
Type (Literal["Error", "Energy", "UnpredictedStep", "Trial"]) – Adapt the mix factor based on the observed progress (slope).
- class _MultiSecantStepper[source]¶
Multi secant stepper.
- Variables:
AlphaMSR1 (float | FloatKey) – For the MSR1 variant: W = Y + alpha S.
MaxConditionNumber (float | FloatKey) – If set larger than zero this condition number of the matrix to be inverted will be checked. If exceeded the space is reduced.
PredictGreed (BoolType | BoolKey) – Try to predict the optimal greed.
ScaleYTY (BoolType | BoolKey) – Scale matrix before inversion
SigmaRegularize (float | FloatKey) – Prevent division by zero by adding a small number. Makes most sense when using renormalization.
Variant (Literal["MSB1", "MSB2", "MSR1", "MSR1s"]) – There are several version of the Multi secant method.
- class _Solvation[source]¶
Generalized Born solvation model with Solvent Accessible Surface Area (GBSA).
- Variables:
GSolvState (Literal["Gas1BarSolvent", "Gas1MSolvent1M", "Gas1BarSolvent1M"]) – Reference state for solvation free energy shift.
Solvent (Literal["None", "Acetone", "Acetonitrile", "Benzene", "CH2Cl2", "CHCl3", "CS2", "DMSO", "Ether", "H2O", "Methanol", "THF", "Toluene"]) – Solvent used in the GBSA implicit solvation model.
SurfaceGrid (Literal["230", "974", "2030", "5810"]) – Number of angular grid points for the construction of the solvent accessible surface area. Usually the default number of grid point suffices, but in case of suspicious behaviors you can increase the number of points.
Temperature (float | FloatKey) – The temperature used when calculating the solvation free energy shift. Only used for ‘Gas1BarSolvent’ and ‘Gas1BarSolvent1M’ GSolvState options.
UseGSASA (BoolType | BoolKey) – Include shift term and G(SASA) terms in the energy and gradient.
- class _Technical[source]¶
This optional section is about technical aspects of the program that should not concern the normal user.
- Variables:
AnalyticalStressTensor (BoolType | BoolKey) – Whether to compute the stress tensor analytically. Note: This can only be used together with Ewald summation as it will give (slightly) wrong results with Madelung screening.
AssumeInsulator (BoolType | BoolKey) – (Expert option) Assume that the material has only fully occupied bands. Only relevant for periodic structures. If you know the material is an insulator this can be a bit faster. Use with care.
MatricesViaFullMaxSize (int | IntKey) – Matrices smaller than this size are constructed via a full matrix. This is faster, but uses more memory in the construction.
ReuseKSpaceConfig (BoolType | BoolKey) – Keep the number of k-points constant during a lattice optimization. Otherwise the PES might display jumps, because the number of points depends on the lattice vector sizes. If this option is on it will always use the number of k-points that was used from a previous result.
UseGeneralizedDiagonalization (BoolType | BoolKey) – Whether or not to use generalized diagonalization. Does not affect the results, but might be faster or slower.
EwaldSummation (DFTB._Technical._EwaldSummation) – Configures the details of the Ewald summation of the Coulomb interaction.
Parallel (DFTB._Technical._Parallel) – Calculation of the orbitals in several k-points is trivially parallel.
Screening (DFTB._Technical._Screening) – For SCC-DFTB in periodic systems the Coulomb interaction can (instead of using Ewald summation) be screened with a Fermi-Dirac like function defined as S(r)=1/(exp((r-r_madel)/d_madel)+1). This section allows to change some details of the screening procedure. Note that Coulomb screening is only used if the Ewald summation is disabled.
- class _EwaldSummation[source]¶
Configures the details of the Ewald summation of the Coulomb interaction.
- Variables:
CellRangeFactor (float | FloatKey) – Smaller values will make the Ewald summation less accurate but faster.
Enabled (BoolType | BoolKey) – Whether to use Ewald summation for the long-range part of the Coulomb interaction. Otherwise screening is used.
Tolerance (float | FloatKey) – Larger values will make the Ewald summation less accurate but faster.
- class _Parallel[source]¶
Calculation of the orbitals in several k-points is trivially parallel.
- Variables:
nCoresPerGroup (int | IntKey) – Number of cores in each working group.
nGroups (int | IntKey) – Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup (int | IntKey) – Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
- class _Screening[source]¶
For SCC-DFTB in periodic systems the Coulomb interaction can (instead of using Ewald summation) be screened with a Fermi-Dirac like function defined as S(r)=1/(exp((r-r_madel)/d_madel)+1). This section allows to change some details of the screening procedure. Note that Coulomb screening is only used if the Ewald summation is disabled.
- class _XTBConfig[source]¶
This block allows for minor tweaking.
- Variables:
SlaterRadialThreshold (float | FloatKey) – Threshold determining the range of the basis functions. Using a larger threshold will speed up the calculation, but will also make the results less accurate.
useXBTerm (BoolType | BoolKey) – Whether to use the Halogen bonding (XB) term. This is not advised as it has a non-continuous PES.
- class External[source]¶
- Variables:
Execute (str | StringKey) – The command to execute to run the external engine. The command is executed in a temporary subdirectory to the results directory.
ExecuteAtEnd (str | StringKey) – The command to execute after the last calculation (e.g. after the final step of a geometry optimization). This can, for example, be used to run a custom analysis tool, or to stop a background process. The command is executed in the results directory.
InputDefinition (str | Path | StringKey) – The JSON file containing the definition of the input for the external engine.
Input (str | Sequence[str] | FreeBlock) – The text input of the engine. This has to match with the JSON input definition set with the InputDefinition keyword.
Supports (External._Supports) – Specifies the capabilities of the external engine.
- class _Input[source]¶
The text input of the engine. This has to match with the JSON input definition set with the InputDefinition keyword.
- class _Supports[source]¶
Specifies the capabilities of the external engine.
- Variables:
DipoleMoment (BoolType | BoolKey) – Whether the external engine can calculate dipole moments.
NonSpecificSystems (BoolType | BoolKey) – Whether the engine can handle calculating any system in any order, or if it is restricted to a single system and only supports changes in the geometry. Engines that only handle a specific system can not be used for tasks such as GCMC, MD calculations with insertions (molecule gun), or numerical phonon calculations.
PeriodicityBulk (BoolType | BoolKey) – Whether the external engine supports 3D periodic systems.
PeriodicityChain (BoolType | BoolKey) – Whether the external engine supports 1D periodic systems, i.e. chains.
PeriodicityNone (BoolType | BoolKey) – Whether the external engine supports non-periodic systems, i.e. molecules.
PeriodicitySlab (BoolType | BoolKey) – Whether the external engine supports 2D periodic systems, i.e. slabs.
- class ForceField[source]¶
- Variables:
AllowMissingParameters (BoolType | BoolKey) – When parameters are not found for bonds, angles, dihedrals, or inversions, the first entry in the database will be used.
AntechamberIntegration (BoolType | BoolKey) – EXPERIMENTAL: Use the Antechamber program to automatically determine atom types for the GAFF force field. This may run a geometry optimization with MOPAC under the hood in order to determine the charges (see keyword AntechamberTask), which might not work for very large systems.
AntechamberTask (Literal["GeometryOptimization", "SinglePoint"]) – If antechamber is invoked to guess atomtypes and charges (GAFF force field), select the task for charge guessing with MOPAC
BondsUsage (Literal["Input", "None", "Guess", "Auto"]) – Controls what bonds are used by the engine. The choice auto means: guess in case there are no bonds. Guessing only happens at the first MD step, or first geometry optimization step.
CheckDuplicateRules (BoolType | BoolKey) – The database could contain duplicate entries. For torsions this is a feature, and the potentials will be added. For all other terms this is no allowed, and if detected the program stops. One should fix the database or set the checking to false. As always the last entry will be used.
DipoleConvergenceThreshold (float | FloatKey) – Convergence criterion for induced point dipoles, in atomic units. When the length of every atomic delta_mu vector between two iterations becomes below the tolerance, the procedure is considered converged.
DoChargeCheck (BoolType | BoolKey) – Check that the sum of atomic (partial) charges equals the total charge of the system.
EngineConstraints (BoolType | BoolKey) – Set to false to ignore constraints implied by the engine.
ForceFieldFile (str | Path | StringKey) – Path to the force field parameter file
ForceFieldPatchFile (str | Path | StringKey) – Present for backwards compatibility. Path to the force field patch parameter file (additional parameters, missing from main file). Cannot be used when atomtypes are guessed.
GuessCharges (BoolType | BoolKey) – Use another engine to calculate/guess the charges to be used by the force field.
KeepAntechamberFolder (BoolType | BoolKey) – If atom-typing is performed with antechamber, keep the folder after the call to antechamber
LinearizationEnergyForRepulsion (float | FloatKey) – The Lennard-Jones potential becomes extremely repulsive at short distances. The distance is determined where the potential reaches this threshold, for smaller distances a linear expression is used, reducing the repulsion.
NeighborListSkin (float | FloatKey) – Thickness of the buffer region added to the NonBondedCutoff when building a neighbor list.
NonBondedCutoff (float | FloatKey) –
Distance beyond which the non-bonded pair interactions (Coulomb and Van der Waals) will be ignored.
The interactions are smoothly damped starting from 0.9*NonBondedCutoff.
Has no effect on the Coulomb term for 3D-periodic systems, as Ewald summation is used.
PairInteractionTapering (Literal["None", "Potential", "Force", "CHARMM", "CHARMM-Force"]) –
Select a method for smoothing non-bonded pair interactions in the distance range between 90% and 100% of the [NonBondedCutoff] to avoid energy and force jump near the cutoff.
Potential - use a 7th order polynomial switching function that has zero 1st, 2nd and 3rd derivatives at both ends of the interval (force matches the energy derivative). Force - the same switching function is applied both to the potential and the force (so the force does not match the energy), which may break the total energy conservation during MD. CHARMM - use a different polynomial that does not have a decaying 2nd derivative at NonBondedCutoff. CHARMM-Force - use the same switching function as CHARMM but apply it both to the energy and the forces.
TaperPairInteractions (BoolType | BoolKey) – Smooth non-bonded pair interactions in the distance range between 90% and 100% of the [NonBondedCutoff] to avoid energy and force jump near the cutoff. See PairInteractionTapering for more precise tuning.
Type (Literal["UFF", "Amber95", "GAFF", "Tripos5.2", "APPLE&P", "UserDefined"]) – Type of force field to be used
Verbosity (Literal["Silent", "Normal", "Verbose", "VeryVerbose"]) – Controls the verbosity of the engine.
APPLE&P (ForceField._APPLE&P) – Options for the APPLE&P force field.
EnergyTerms (ForceField._EnergyTerms) – expert key, that allows you to disable specific energy terms.
EwaldSummation (ForceField._EwaldSummation) – Configures the details of the particle mesh Ewald (PME) summation of the Coulomb interaction.
GAFF (ForceField._GAFF) – Specific keywords for the GAFF force field type
GuessChargesConfig (ForceField._GuessChargesConfig) – Guess charges to be used by the forcefield
LAMMPSOffload (ForceField._LAMMPSOffload) – Offload the calculation to LAMMPS via AMSPipe.
LoadCharges (ForceField._LoadCharges) – Load charges from a file to be used as forcefield charges
SoftCorePotentials (ForceField._SoftCorePotentials) – When performing free energy perturbation the LJ interactions must be scaled by lambda. To avoid numerical instabilities at small lambda, soft-core potentials need to be used (see DOI:10.1021/ct900587b).
UFF (ForceField._UFF) – Option for the UFF force filed.
- class _APPLE_AND_P[source]¶
Options for the APPLE&P force field.
- Variables:
LongRangeCorrection (BoolType | BoolKey) –
Add a long-range dispersion correction to the energy and pressure for 3D-periodic systems.
This correction should be enabled only for a homogeneous liquid.
MuMu14Scaling (float | FloatKey) – Scaling factor for dipole-dipole interactions between atoms connected to 3rd order (via a dihedral).
QMu14Scaling (float | FloatKey) – Scaling factor for charge-dipole interactions between atoms connected to 3rd order (via a dihedral).
QQ14Scaling (float | FloatKey) – Scaling factor for charge-charge interactions between atoms connected to 3rd order (via a dihedral).
RD14Scaling (float | FloatKey) – Scaling factor for repulsion/dispersion interactions between atoms connected to 3rd order (via a dihedral).
TholeParam (float | FloatKey) – (UNUSED) Parameter for the exponential Thole screening for the induced dipole-dipole interactions.
- class _EnergyTerms[source]¶
expert key, that allows you to disable specific energy terms.
- Variables:
Angle (BoolType | BoolKey) – Whether to use angle (bend) energy.
Coulomb (BoolType | BoolKey) – Whether to use coulomb energy.
Dispersion (BoolType | BoolKey) – Whether to use dispersion energy.
Inversion (BoolType | BoolKey) – Whether to use inversion energy.
Stretch (BoolType | BoolKey) – Whether to use stretch energy.
Torsion (BoolType | BoolKey) – Whether to use torsion energy.
- class _EwaldSummation[source]¶
Configures the details of the particle mesh Ewald (PME) summation of the Coulomb interaction.
- Variables:
Alpha (float | FloatKey) – This parameter shifts the workload from real space (smaller alpha) to reciprocal space (larger alpha). Using a larger [Alpha] without decreasing [GridSpacing] may increase the error in the reciprocal-space contribution. Set to zero to disable the reciprocal-space Ewald part. Negative value means the [Alpha] will be determined automatically from the [Tolerance] and [RealSpaceCutoff] values.
Enabled (BoolType | BoolKey) – Set to false to use real-space pair summation instead of the Ewald, which is the default and the only option for molecules, 1D and 2D periodic systems.
GridSpacing (float | FloatKey) – Grid spacing in the particle mesh Ewald method. Smaller grid spacing will make the reciprocal energy calculation more accurate but slower. Using a larger [Alpha] value may require a smaller GridSpacing to be accurate.
RealSpaceCutoff (float | FloatKey) – Set the cutoff value for the real-space summation. Zero means the internal defaults will be used depending on the [Alpha] (if Alpha=0 then the cutoff will be set to 50 Bohr, otherwise to 20 Bohr).
Tolerance (float | FloatKey) – Value of the error function that should be used to determine the cutoff radius for real-space Ewald summation if [Alpha] is set on input. Alternatively, if the [RealSpaceCutoff] is set but [Alpha] is not then the [Tolerance] value affects the [Alpha]. Larger values will make the real-space summation faster but less accurate.
- class _LAMMPSOffload[source]¶
Offload the calculation to LAMMPS via AMSPipe.
- Variables:
Enabled (BoolType | BoolKey) – Enable offloading the force field evaluation to LAMMPS instead of handling it internally in AMS. This is currently only supported for Type=UFF.
UseGPU (BoolType | BoolKey) – Accelerate LAMMPS calculations using a GPU. Requires a LAMMPS library built with the GPU package.
UseGPUForKSpace (BoolType | BoolKey) – When UseGPU is enabled, also use the GPU to accelerate reciprocal space electrostatic interactions. Disabling this can improve performance on less powerful GPUs.
UseGPUForNeighbor (BoolType | BoolKey) – When UseGPU is enabled, also use the GPU to accelerate neighbor searches. Disabling this can improve performance on less powerful GPUs.
UseOpenMP (BoolType | BoolKey) – Parallelize LAMMPS calculations using OpenMP threading. Requires a LAMMPS library built with the OMP package.
WorkerCommand (str | StringKey) – The command to execute to run the external worker. The command is executed in a subdirectory of the results directory. The LAMMPS input commands will be passed to the worker on standard input.
Input (str | Sequence[str] | FreeBlock) – Commands to be passed to LAMMPS to set up the calculation. If this is left empty, AMS will generate a set of commands to set LAMMPS up according to the settings of the ForceField engine. Any LAMMPS commands entered in this input block will be used to set LAMMPS up instead of those generated by AMS. To merge the AMS-generated lines with your customizations, include lines like ‘AMS somelammpskeyword’ anywhere in this block. Any such line will be replaced by the AMS-generated line for ‘somelammpskeyword’. Any text after ‘somelammpskeyword’ will be appended to the generated line verbatim, which can be used to modify the generated command by additional options. A special line ‘AMS everything’ will be replaced by the entire block of AMS-generated commands, except those overridden anywhere in this input block (defined manually or inserted using ‘AMS somelammpskeyword’. Any customized Input block should probably include ‘AMS read_data’ near or at the end to load the AMS-generated data file defining the system.
- class _Input[source]¶
Commands to be passed to LAMMPS to set up the calculation. If this is left empty, AMS will generate a set of commands to set LAMMPS up according to the settings of the ForceField engine. Any LAMMPS commands entered in this input block will be used to set LAMMPS up instead of those generated by AMS. To merge the AMS-generated lines with your customizations, include lines like ‘AMS somelammpskeyword’ anywhere in this block. Any such line will be replaced by the AMS-generated line for ‘somelammpskeyword’. Any text after ‘somelammpskeyword’ will be appended to the generated line verbatim, which can be used to modify the generated command by additional options. A special line ‘AMS everything’ will be replaced by the entire block of AMS-generated commands, except those overridden anywhere in this input block (defined manually or inserted using ‘AMS somelammpskeyword’. Any customized Input block should probably include ‘AMS read_data’ near or at the end to load the AMS-generated data file defining the system.
- class _SoftCorePotentials[source]¶
When performing free energy perturbation the LJ interactions must be scaled by lambda. To avoid numerical instabilities at small lambda, soft-core potentials need to be used (see DOI:10.1021/ct900587b).
- Variables:
Alpha (float | FloatKey) – This parameter determines how far the soft-core potential deviates from the scaled regular LJ potential (at zero the expression is a regular LJ expression).
Enabled (BoolType | BoolKey) – Set to True to use the scaled soft-core LJ potentials.
Lambda (float | FloatKey) – The scaling parameter for the LJ interaction term for free energy perturbation (the window).
- class _UFF[source]¶
Option for the UFF force filed.
- Variables:
AtomTypesFile (str | StringKey) – Expert option: Select the file that defines how UFF determines the atom types
Database (str | StringKey) – Expert option: Select the file that defines the UFF parameters per atom type
ElementsFile (str | StringKey) – Expert option: Select the file that defines the elements known to UFF
IgnoreInputBonds (BoolType | BoolKey) – Developer option: Ignore the bonds from the input. This mean UFF will either reuse bonds from a previous result, or will guess the bonds.
Library (Literal["UFF", "UFF4MOF", "UFF4MOF-II"]) – Selects the used parameter library.
- class GFNFF[source]¶
- Variables:
Accuracy (float | FloatKey) – Expert option: GFNFF accuracy parameter. Several thresholds within GFNFF depend on this accuracy parameter. Must be a positive number. Smaller values of Accuracy will result in larger distance thresholds.
EwaldTolerance (float | FloatKey) – Expert option: Value of the error function that should be used to determine the cutoff radius for real-space Ewald summation if [Alpha] is set on input. Alternatively, if the [RealSpaceCutoff] is set but [Alpha] is not then the [Tolerance] value affects the [Alpha]. Larger values will make the real-space summation faster but less accurate.
ForceFieldFile (str | StringKey) – Path to a GFNFF parameter file
Type (Literal["AngewChem2020", "AngewChem2020_1", "AngewChem2020_2", "Harmonic2020", "FromFile"]) – Type of GFNFF to be used
EnergyTerms (GFNFF._EnergyTerms) – expert key, that allows you to disable specific energy terms.
- class _EnergyTerms[source]¶
expert key, that allows you to disable specific energy terms.
- Variables:
Angle (BoolType | BoolKey) – Whether to use angle (bend) energy.
BondedATM (BoolType | BoolKey) – Whether to use bonded ATM energy.
Coulomb (BoolType | BoolKey) – Whether to use coulomb energy.
Dispersion (BoolType | BoolKey) – Whether to use dispersion energy.
ElectricField (BoolType | BoolKey) – Whether to use external electric field energy.
HBonding (BoolType | BoolKey) – Whether to use hydrogen bonding energy.
Repulsion (BoolType | BoolKey) – Whether to use the repulsion energy.
Solvation (BoolType | BoolKey) – Whether to use solvation energy.
Stretch (BoolType | BoolKey) – Whether to use stretch energy.
Torsion (BoolType | BoolKey) – Whether to use torsion energy.
XBonding (BoolType | BoolKey) – Whether to use halogen bonding energy.
- class Hybrid[source]¶
- Variables:
AllowSanityCheckWarnings (BoolType | BoolKey) – Sanity checks will be performed on the setup. If this option is on, only warnings are printed. If not the program will stop on warnings.
GuessAttributesOnce (BoolType | BoolKey) – If any ForceField subengines are defined, and if automatic atom typing is possible, then the atom typing is done at the level of the Hybrid engine, and not of the ForceField subengines. This ensures that the same atom types and charges are used in each subsystem, so that pair energy terms that should cancel, will cancel. If set to False, then for each energy term the atom types and charges of the subsystem will be determined separately.
RestartSubEngines (BoolType | BoolKey) – Save all the results of the subengines and pass those in a next geometry step or MD step.
TweakRequestForSubEngines (BoolType | BoolKey) – Only request what is really needed, gradients and charges.
Capping (Hybrid._Capping) – This block is about capping details. Capping occurs with hydrogen atoms when a bond is broken between an atom inside the region and one outside.
Committee (Hybrid._Committee) – Settings for using the hybrid engine as a committee. The factors and region for each engine must be the same. When committee is enabled the standard deviation is also reported as the uncertainty.
Energy (Hybrid._Energy) – This block is there to construct the energy.
Engine (EngineBlock) – The input for the computational (sub) engine. The header of the block determines the type of the engine. An optional second word in the header serves as the EngineID, if not present it defaults to the engine name. Currently it is not allowed to have a Hybrid engine as a sub engine.
QMMM (Hybrid._QMMM) – This block is there to identify the QMMM engines.
- class _Capping[source]¶
This block is about capping details. Capping occurs with hydrogen atoms when a bond is broken between an atom inside the region and one outside.
- Variables:
AllowHighBondOrders (BoolType | BoolKey) – Allows capping of interregional aromatic, double and triple bonds. This is normally not a good idea, since the capping is done with hydrogen atoms.
AtomicInfoForCappingAtom (str | StringKey) – The AtomicInfo for the capping atoms. Typically a string like ForceField.Type=X much like forcefield info is entered in the System block for normal atoms.
CappingElement (str | StringKey) – The element to be used for capping. The hydrogen atom has the advantage that it is very small.
CheckCapping (BoolType | BoolKey) – The same outside atom can be involved in multiple capping coordinate definitions. This is not a good idea, and this will not be accepted by using this check.
Distance (float | FloatKey) – A negative value means automatic. In that case the sum of covalent radii is used
Option (Literal["Fractional", "Fixed"]) –
The capping atom is always along the broken bond vector.
The bond distance between the capping atom and the two atoms are obtained from covalent radii, let us call them D1H and D2H.
With option=Fractional the capping is on the bond vector with the fraction D1H/(D1H+D2H).
With the Fixed option it at the distance D1H from atom 1. A distance of zero always means the coordinate of the inside atom.
- class _Committee[source]¶
Settings for using the hybrid engine as a committee. The factors and region for each engine must be the same. When committee is enabled the standard deviation is also reported as the uncertainty.
- Variables:
Enabled (BoolType | BoolKey) – Enable committee
- class _Energy[source]¶
This block is there to construct the energy.
- Variables:
DynamicFactors (Literal["Default", "UseLowestEnergy", "UseHighestEnergy"]) – Default - use factors as set in the corresponding Term blocks; UseLowestEnergy - set all factors to 0 except for that of the engine with the lowest energy, which is set to 1; UseHighestEnergy - set all factors to 0 except for that of the engine with the highest energy, which is set to 1. The last two options make sense only for non-QMMM hybrid calculation (that is, if the QMMM block is not present) and only when using engines whose energies can be compared directly.
Term (Hybrid._Energy._Term) – This block is there to construct the energy term. Can have multiple occurrences
- class _Engine[source]¶
The input for the computational (sub) engine. The header of the block determines the type of the engine. An optional second word in the header serves as the EngineID, if not present it defaults to the engine name. Currently it is not allowed to have a Hybrid engine as a sub engine.
- class _QMMM[source]¶
This block is there to identify the QMMM engines.
- Variables:
Embedding (Literal["Mechanical", "Electrostatic"]) –
Determines how the QM region is embedded into the MM region.
Mechanical embedding embedding can also be achieved using the Energy%Terms keywords, but the common case of a two region mechanical QM/MM embedding is easier to set up using this keyword.
MMCharge (float | FloatKey) – Net charge to be used for the MM region.
MMEngineIsPolarizable (BoolType | BoolKey) – Whether or not the MM engine has dynamic charges (for now not supported at all).
QMCharge (float | FloatKey) – Net charge to be used for the QM region.
QMRegion (str | StringKey) – Identifier for the QM region. The rest of the system is considered the MM region.
UseCappingAtoms (BoolType | BoolKey) – Whether to use capping for broken bonds.
- class MLPotential[source]¶
- Variables:
Backend (Literal["M3GNet", "NequIP", "PiNN", "RuNNerLAMMPS", "SchNetPack", "sGDML", "TorchANI"]) – The machine learning potential backend.
Device (Literal["", "cpu", "cuda:0", "cuda:1", "mps"]) –
Device on which to run the calculation (e.g. cpu, cuda:0).
If empty, the device can be controlled using environment variables for TensorFlow or PyTorch.
MLDistanceUnit (Literal["Auto", "angstrom", "bohr"]) – Unit of distances expected by the ML backend (not the ASE calculator). The ASE calculator may require this information.
MLEnergyUnit (Literal["Auto", "Hartree", "eV", "kcal/mol", "kJ/mol"]) – Unit of energy output by the ML backend (not the unit output by the ASE calculator). The ASE calculator may require this information.
Model (Literal["Custom", "AIMNet2-B973c", "AIMNet2-wB97MD3", "ANI-1ccx", "ANI-1x", "ANI-2x", "M3GNet-UP-2022"]) –
Select a particular parameterization.
ANI-1x and ANI-2x: based on DFT (wB97X) ANI-1cxx: based on DLPNO-CCSD(T)/CBS M3GNet-UP-2022: based on DFT (PBE and PBE+U) data. AIMNet2: based on ωB97m-D3 or B97-3c data.
ANI-1x and ANI-1ccx have been parameterized to give good geometries, vibrational frequencies, and reaction energies for gasphase organic molecules containing H, C, O, and N. ANI-2x can also handle the atoms F, S, and Cl.
M3GNet-UP-2022 is a universal potential (UP) for the entire periodic table and has been primarily trained to crystal data (energies, forces, stresses) from the Materials Project.
AIMNet2 has been parametrized to give good geometries and reaction energies for gasphase molecules and ions containing H, B, C, N, O, F, Si, P, S, Cl, As, Se, Br, I.
Set to Custom to specify the backend and parameter files yourself.
NumThreads (str | StringKey) –
Number of threads.
If not empty, OMP_NUM_THREADS will be set to this number; for PyTorch-engines, torch.set_num_threads() will be called.
ParameterDir (str | Path | StringKey) – Path to a set of parameters for the backend, if it expects to read from a directory.
ParameterFile (str | Path | StringKey) – Path to a set of parameters for the backend, if it expects to read from a file.
Member (MLPotential._Member) – Specify the details of a member of a committee.
- class Mopac[source]¶
- Variables:
CalcLocalOrbitals (BoolType | BoolKey) – Compute and print the localized orbitals, also known as Natural Bond Orbitals (NBO). This is equivalent to the LOCAL mopac keyword.
Debug (BoolType | BoolKey) – Extra debug printing.
Keywords (str | StringKey) – A string containing all the desired custom MOPAC keywords. Basically for anything not directly supported through AMS.
Model (Literal["AM1", "MNDO", "MNDOD", "PM3", "RM1", "PM6", "PM6-D3", "PM6-DH+", "PM6-DH2", "PM6-DH2X", "PM6-D3H4X", "PM7"]) –
Selects the model Hamiltonian to use in the calculation.
- AM1: Use the AM1 Hamiltonian.
MNDO: Use the MNDO Hamiltonian. MNDOD: Use the MNDO-d Hamiltonian. RM1: Use the RM1 Hamiltonian. PM3: Use the MNDO-PM3 Hamiltonian. PM6: Use the PM6 Hamiltonian. PM6-D3: Use the PM6 Hamiltonian with Grimme’s D3 corrections for dispersion. PM6-DH+: Use the PM6 Hamiltonian with corrections for dispersion and hydrogen-bonding. PM6-DH2: Use the PM6 Hamiltonian with corrections for dispersion and hydrogen-bonding. PM6-DH2X: Use PM6 with corrections for dispersion and hydrogen and halogen bonding. PM6-D3H4: Use PM6 with Rezac and Hobza’s D3H4 correction. PM6-D3H4X: Use PM6 with Brahmkshatriya, et al.’s D3H4X correction. PM7: Use the PM7 Hamiltonian. PM7-TS: Use the PM7-TS Hamiltonian (only for barrier heights)
Mozyme (BoolType | BoolKey) – Replace the standard SCF procedure with a localized molecular orbital (LMO) method. The time required for an SCF cycle when Mozyme is used scales linearly with system size.
Sparkles (BoolType | BoolKey) – Represent lanthanides by their fully ionized 3+ sparkles. That is, they have no basis set, and therefore cannot have a charge different from +3. When using sparkles, the geometries of the lanthanides are reproduced with good accuracy, but the heats of formation and electronic properties are not accurate.
UnpairedElectrons (int | IntKey) – If this key is present, a spin-unrestricted calculation with the specified number of unpaired electrons is performed. If this key is not present the number of unpaired electrons is determined automatically (0 for systems with an even number of electrons, 1 for radicals), and a restricted or unrestricted calculation is performed accordingly.
Properties (Mopac._Properties) – MOPAC can calculate various properties of the simulated system. This block configures which properties will be calculated.
SCF (Mopac._SCF) – Options for the self-consistent field procedure.
Solvation (Mopac._Solvation) – Options for the COSMO (Conductor like Screening Model) solvation model.
- class _Properties[source]¶
MOPAC can calculate various properties of the simulated system. This block configures which properties will be calculated.
- Variables:
StaticPolarizability (BoolType | BoolKey) – Calculate the static polarizability. An electric field gradient is applied to the system, and the response is calculated. The dipole and polarizability are calculated two different ways, from the change in heat of formation and from the change in dipole. A measure of the imprecision of the calculation can be obtained by comparing the two quantities.
pKa (BoolType | BoolKey) – If requested, the pKa of hydrogen atoms attached to oxygen atoms is calculated and printed.
- class _SCF[source]¶
Options for the self-consistent field procedure.
- Variables:
CampKingConverger (BoolType | BoolKey) – Use the Camp-King SCF converger. This is a very powerful, but CPU intensive, SCF converger.
ConvergenceThreshold (float | FloatKey) – If the difference in energy between two successive SCF iterations is smaller than this value, the SCF procedure is considered converged.
MaxIterations (int | IntKey) – Maximum number of SCF iterations.
- class _Solvation[source]¶
Options for the COSMO (Conductor like Screening Model) solvation model.
- Variables:
Enabled (BoolType | BoolKey) – Use the Conductor like Screening Model (COSMO) to include solvent effects.
NSPA (Literal["12", "32", "42", "92", "122", "162", "252", "272", "362", "482", "492", "642", "752"]) – Maximum number of COSMO surface points per atom.
Solvent (Mopac._Solvation._Solvent) – Solvent details
- class _Solvent[source]¶
Solvent details
- Variables:
Eps (float | FloatKey) – User-defined dielectric constant of the solvent (overrides the Eps value of the solvent defined in ‘Name’)
Name (Literal["CRS", "AceticAcid", "Acetone", "Acetonitrile", "Ammonia", "Aniline", "Benzene", "BenzylAlcohol", "Bromoform", "Butanol", "isoButanol", "tertButanol", "CarbonDisulfide", "CarbonTetrachloride", "Chloroform", "Cyclohexane", "Cyclohexanone", "Dichlorobenzene", "DiethylEther", "Dioxane", "DMFA", "DMSO", "Ethanol", "EthylAcetate", "Dichloroethane", "EthyleneGlycol", "Formamide", "FormicAcid", "Glycerol", "HexamethylPhosphoramide", "Hexane", "Hydrazine", "Methanol", "MethylEthylKetone", "Dichloromethane", "Methylformamide", "Methypyrrolidinone", "Nitrobenzene", "Nitrogen", "Nitromethane", "PhosphorylChloride", "IsoPropanol", "Pyridine", "Sulfolane", "Tetrahydrofuran", "Toluene", "Triethylamine", "TrifluoroaceticAcid", "Water"]) – Name of a pre-defined solvent. A solvent is characterized by the dielectric constant (Eps) and the solvent radius (Rad).
Rad (float | FloatKey) – User-defined radius of the solvent molecule (overrides the Rad value of the solvent defined in ‘Name’).
- class QuantumESPRESSO[source]¶
- Variables:
CheckInputIncompatibilities (BoolType | BoolKey) – Performs a preliminary check for incompatible input parameters before starting the calculation. If any inconsistencies are detected (e.g., attempting a Raman calculation with spin polarization), the program will stop and report the error. This helps to avoid wasted time and resources by identifying potential issues early on.
K_PointsLabels (str | StringKey) – You can provide labels for your k-points, like
L-GAMMA-X-U-GAMMA, separating each label with a hyphen (-) or a vertical bar (|). For example,L-GAMMA-X-U-GAMMAandL|GAMMA|X|U|GAMMAare both valid. These labels are optional and only used for display purposes when theK_Pointsblock is specified. This option is used only if the header of theK_Pointsblock is notams_kpath. Important: These labels do not determine the actual k-point coordinates. You must specify the k-point coordinates separately within theK_Pointssection.KeepDataFiles (BoolType | BoolKey) – If ‘False’ the program will perform the following actions at the end of the calculation: 1) Remove the ‘prefix.qein’ file, which serves as the QE input file, 2) Delete the output data stored in the ‘prefix.xml’ file, and 3) Clear the contents of the ‘prefix.save’ directory. If you require further details, please refer to the QE user manual in the ‘Data Files’ section. It provides comprehensive information on the specific files and their functionalities. In particular, these files are needed to calculate the bands structure and DOS.
UseBondingEnergy (BoolType | BoolKey) – When enabled, the calculation engine uses the bonding energy (energy difference between the molecule and its constituent atoms) instead of the total energy. This facilitates comparisons of relative stability between molecular configurations. Atomic energies are consistently computed using Gamma-point sampling, Gaussian smearing (degauss = 0.01), and spin-restricted (nSpin = 1) settings within a cubic lattice of 8 angstrom side length to approximate their spherically symmetric ground states. All other parameters for the atomic calculations remain the same as those used for the molecular system.
AVERAGE_X (QuantumESPRESSO._AVERAGE_X) – This section configures the parameters for running the QE-utility
average.x. This utility reads files produce by produced bypp.xand compute planar and macroscopic averages of a quantity (e.g. charge) in real space on a 3D FFT mesh.BandStructure (QuantumESPRESSO._BandStructure) –
This section configures the parameters for calculating the Band Structure. This involves utilizing the following utilities:
kpath: This AMS tool generates an automated high-symmetry k-path in the Brillouin zone.pw.x(with calculation=bands): This utility from Quantum ESPRESSO (QE) performs electronic structure calculations, particularly for bands. For more details see https://www.quantum-espresso.org/Doc/INPUT_PW.htmlbands.x: Another QE utility, which calculates the band structure. For more details see https://www.quantum-espresso.org/Doc/INPUT_BANDS.html.
Control (QuantumESPRESSO._Control) – Keywords from the &CONTROL namelist in the QuantumEspresso input file.
DOS (QuantumESPRESSO._DOS) –
This section configures the parameters for calculating the Density of States (DOS). These are the utilities involved:
kpath: This AMS tool generates an automated high-symmetry k-path in the Brillouin zone.pw.x(withcalculation=nscf): This Quantum ESPRESSO (QE) utility conducts electronic structure calculations, specifically for the non-self-consistent field (nscf) computation.dos.x: A QE utility utilized for post-processing electronic structure calculations. It analyzes the electronic wavefunctions obtained from preceding calculations to determine the density of available electronic states at different energy levels. For more details see https://www.quantum-espresso.org/Doc/INPUT_DOS.htmlprojwfc.x: Another QE utility employed for post-processing electronic structure calculations. It projects the wavefunctions onto atomic orbitals or basis sets, offering insights into the composition and character of electronic states. For more details see https://www.quantum-espresso.org/Doc/INPUT_PROJWFC.html
By default, the calculation sequence follows the order:
kpath -> pw.x(calculation=nscf) -> dos.x. However, enablingDOS%PDOSswitches the calculation to useprojwfc.xinstead ofdos.x. While common parameters can be customized directly in this section, specialized adjustments should be made in either theDOS_XorPROJWFC_Xsection, depending on specific requirements.DOS_X (QuantumESPRESSO._DOS_X) – This section configures the parameters for running the QE-utility
dos.x(see https://www.quantum-espresso.org/Doc/INPUT_DOS.html). This utility calculates the Density of States (DOS), separated into up and down components for DSDA.DYNMAT_X (QuantumESPRESSO._DYNMAT_X) – This section configures the parameters for running the QE utility dynmat.x (see https://www.quantum-espresso.org/Doc/INPUT_DYNMAT.html). This utility is used to ???
Electrons (QuantumESPRESSO._Electrons) – Keywords from the &ELECTRONS namelist in the QuantumEspresso input file.
Hubbard (str | Sequence[str] | FreeBlock) –
Specify parameters for DFT+U models. The type of Hubbard projectors to use (e.g.
atomicorortho-atomic) is specified in the header of this block. Example input:Hubbard ortho-atomic U Fe-3d 3.0 EndMore examples can be found in the documentation.
HubbardU (QuantumESPRESSO._HubbardU) – Specify parameters for DFT+U Models.
K_Points (str | Sequence[str] | FreeBlock) – Specify the k-points to use. Available header values are:
tpiba,automatic,crystal,gamma,tpiba_b,crystal_b,tpiba_c,crystal_c, andams_kpath. See the examples and QE documentation for details. If omitted, onlygammais used. For most cases,automatic(which generates a Monkhorst-Pack grid) is recommended. Note: Gamma-point calculations are significantly faster usinggammathanautomatic, but may not be possible to use for all types of calculations or postprocessing programs.MATDYN_X (QuantumESPRESSO._MATDYN_X) – This section configures the parameters for running the QE utility matdyn.x (see https://www.quantum-espresso.org/Doc/INPUT_MATDYN.html). This utility is used to calculate various phonon-related properties from the real-space interatomic force constants (IFC) produced by q2r.x. These properties include phonon dispersion curves, phonon density of states (DOS), thermodynamic properties (e.g., free energy, entropy), and more.
NormalModes (QuantumESPRESSO._NormalModes) –
This section outlines the configuration of parameters for calculating Normal Modes. The process involves using the following utilities:
ph.x: This utility from Quantum ESPRESSO (QE) calculates phonon frequencies and eigenvectors at specified q-points (wave vectors) using Density Functional Perturbation Theory (DFPT). You can set specific parameters in the sectionPH_X. For more details, see https://www.quantum-espresso.org/Doc/INPUT_PH.html.dynmat.x: This QE utility calculates the infrared (IR) and Raman intensities (oscillator strengths) as well as the normal modes associated with each vibrational frequency. Specific parameters can be set in the sectionDYNMAT_X. The information fromph.x, combined with the phonon frequencies, is used to generate the simulated IR/Raman absorption spectrum. For more details, see https://www.quantum-espresso.org/Doc/INPUT_DYNMAT.html.
If Normal Modes are requested in the main AMS properties section, the program automatically sets
PH_X%asr=Yes,PH_X%epsilon=Yes, andPH_X%trans=Yes. If Raman is requested in the main AMS properties section, it also setsPH_X%lraman=Yesalong with the previous parameters.PH_X (QuantumESPRESSO._PH_X) – This section configures the parameters for running the QE utility ph.x (see https://www.quantum-espresso.org/Doc/INPUT_PH.html). This utility is used for post-processing phonon calculations in Quantum ESPRESSO.
PP_X (QuantumESPRESSO._PP_X) – This section configures the parameters for running the QE-utility
pp.x(see https://www.quantum-espresso.org/Doc/INPUT_PP.html). This utility reads the output produced bypw.x, extracts and calculates the desired quantity/quantities (rho, V, …), and then writes the desired quantity to file in a suitable format for various types of plotting and various plotting programs. Only a few options are supported at the moment.PROJWFC_X (QuantumESPRESSO._PROJWFC_X) – This section configures the parameters for running the QE-utility
projwfc.x(see https://www.quantum-espresso.org/Doc/INPUT_PROJWFC.html). This utility projects wavefunctions onto orthogonalized atomic wavefunctions, calculates Lowdin charges, spilling parameter, projected DOS (separated into up and down components for LSDA).Phonons (QuantumESPRESSO._Phonons) –
This section configures the parameters for calculating the Phonon Structure. This involves utilizing the following utilities:
kpath: This AMS tool generates an automated high-symmetry k-path in the Brillouin zone.ph.x: This utility from Quantum ESPRESSO (QE) calculates phonon frequencies and eigenvectors at specified q-points (wavevectors) using Density Functional Perturbation Theory (DFPT). For more details see https://www.quantum-espresso.org/Doc/INPUT_PH.htmlq2r.x: This QE utility transforms the dynamical matrix from reciprocal space (q-space) to real space (r-space). This is necessary for further post-processing steps. For more details see https://www.quantum-espresso.org/Doc/INPUT_Q2R.html.matdyn.x: This QE utility calculates various phonon-related properties from the real-space dynamical matrix, such as phonon dispersion curves, density of states (DOS), thermodynamic properties, and more. For more details see https://www.quantum-espresso.org/Doc/INPUT_MATDYN.html.
Properties (QuantumESPRESSO._Properties) – Configures which QE level properties to calculate for SinglePoint calculations or other important geometries (e.g. at the end of an optimization).
Pseudopotentials (QuantumESPRESSO._Pseudopotentials) – Selects the pseudopotential to use for the atomic species.
Q2R_X (QuantumESPRESSO._Q2R_X) – This section configures the parameters for running the QE utility q2r.x (see https://www.quantum-espresso.org/Doc/INPUT_Q2R.html). This utility is used to transform the interatomic force constants (IFC) calculated in reciprocal space (q-space) by ph.x into real space (r-space). The real-space IFCs are then used as input for the matdyn.x utility to calculate various phonon-related properties.
Restart (QuantumESPRESSO._Restart) – This section configures restarting a Quantum Espresso calculation from previous data. You can restart from a specific Quantum Espresso results file (e.g., quantumespresso.rkf), or by providing the directory and file prefix of the previous calculation. This is compatible with any stand-alone Quantum Espresso version.
System (QuantumESPRESSO._System) – Keywords from the &SYSTEM namelist in the QuantumEspresso input file.
WorkFunction (QuantumESPRESSO._WorkFunction) –
This section configures the parameters for calculating the Work Function. This involves utilizing the following utilities:
pp.x: Calculates the the electrostatic potential using the results from the last Quantum ESPRESSO calculation.average.x: Performs planar and macroscopic averages of the electrostatic potential along a specified direction, which are crucial for determining the vacuum level and subsequently the work function.
- class _AVERAGE_X[source]¶
This section configures the parameters for running the QE-utility
average.x. This utility reads files produce by produced bypp.xand compute planar and macroscopic averages of a quantity (e.g. charge) in real space on a 3D FFT mesh.- Variables:
awin (float | FloatKey) – The size of the window for macroscopic average (a.u.).
filename (str | StringKey) – List of strings containing the name of the n files.
idir (int | IntKey) – 1,2 or 3. Planar average is done in the plane orthogonal to direction
idir, as defined for the crystal cell.nfile (int | IntKey) – The number of files containing the desired quantities. All files must refer to the same physical system!
npt (int | IntKey) – The number of points for the final interpolation of the planar and macroscopic averages, as written to file. If npt <= N_idir (see below) no interpolation is done, the N_idir FFT points in direction idir are printed.
weight (Iterable[float] | FloatListKey) – List of numbers containing the weights w_n of the quantities read from the files
filename.
- class _BandStructure[source]¶
This section configures the parameters for calculating the Band Structure. This involves utilizing the following utilities:
kpath: This AMS tool generates an automated high-symmetry k-path in the Brillouin zone.pw.x(with calculation=bands): This utility from Quantum ESPRESSO (QE) performs electronic structure calculations, particularly for bands. For more details see https://www.quantum-espresso.org/Doc/INPUT_PW.htmlbands.x: Another QE utility, which calculates the band structure. For more details see https://www.quantum-espresso.org/Doc/INPUT_BANDS.html.
- Variables:
KPathFinderConvention (Literal["Setyawan-Curtarolo", "Hinuma"]) –
This option determines how the path through the Brillouin zone is generated when using the automatic k-point mode.
Available options:
Setyawan-Curtarolo(default for 1D and 2D lattices): Uses our built-in KPath program to find a path through high-symmetry points based on the method by Setyawan and Curtarolo (https://doi.org/10.1016/j.commatsci.2010.05.010). For 2D lattices, the path is derived from the intersection of the 3D Brillouin zone with a plane. For 1D lattices, the path is simplyGAMMA-Z.Hinuma: Uses the external SeeKPath utility to generate the k-path (https://github.com/giovannipizzi/seekpath and https://doi.org/10.1016/j.commatsci.2016.10.015).
K_PointsLabels (str | StringKey) – You can provide labels for your k-points, like
L-GAMMA-X-U-GAMMA, separating each label with a hyphen (-) or a vertical bar (|). For example,L-GAMMA-X-U-GAMMAandL|GAMMA|X|U|GAMMAare both valid. These labels are optional and only used for display purposes when theK_Pointsblock is specified. This option is used only if the header of theBandStructure%K_Pointsblock is notams_kpath. Important: These labels do not determine the actual k-point coordinates. You must specify the k-point coordinates separately within theK_Pointssection.K_PointsStep (float | FloatKey) – Step size in reciprocal space for band structure calculation. Using a smaller number will produce smoother band curves at an increased computational time. This option is used only if the header of the
BandStructure%K_Pointsblock isams_kpath.UseSymmetry (BoolType | BoolKey) – If set, only the irreducible wedge of the Wigner-Seitz cell is sampled. If not, the whole (inversion-unique) Wigner-Seitz cell is sampled. Only available for Setyawan and Curtarolo convention (see
KPathFinderConvention).Number of electronic states (bands) to be calculated. Note that in spin-polarized calculations the number of k-point, not the number of bands per k-point, is doubled.
Default: 20% more (minimum of 4 additional bands) than the number used in the main ‘pw.x’ calculation, regardless of the material’s insulating or metallic nature. Notice that this default is calculated differently than in standard QE.
K_Points (str | Sequence[str] | FreeBlock) – Specify the k-points to use. Choose a header appropriate for your system. Available values are:
tpiba,automatic,crystal,gamma,tpiba_b,crystal_b,tpiba_c,crystal_c, andams_kpath. See the QE documentation for details. If omitted,ams_kpathwill be used for 3D systems, andgammaotherwise. For most cases,ams_kpath(which generates a convenient path along high-symmetry k-points in the Brillouin zone) is recommended.
- class _K_Points[source]¶
Specify the k-points to use. Choose a header appropriate for your system. Available values are:
tpiba,automatic,crystal,gamma,tpiba_b,crystal_b,tpiba_c,crystal_c, andams_kpath. See the QE documentation for details. If omitted,ams_kpathwill be used for 3D systems, andgammaotherwise. For most cases,ams_kpath(which generates a convenient path along high-symmetry k-points in the Brillouin zone) is recommended.
- class _Control[source]¶
Keywords from the &CONTROL namelist in the QuantumEspresso input file.
- Variables:
dipfield (BoolType | BoolKey) –
If True (and
tefieldis True) a dipole correction is also added to the bare ionic potential - implements the recipe of L. Bengtsson, PRB 59, 12301 (1999).See keywords
edir,emaxpos,eopregfor the form of the correction.Must be used ONLY in a slab geometry, for surface calculations, with the discontinuity FALLING IN THE EMPTY SPACE.
disk_io (Literal["High", "Medium", "Low", "NoWf", "Minimal", "None"]) –
Specifies the amount of disk I/O activity:
High: save charge to disk at each SCF step, keep wavefunctions on disk (in ‘distributed’ format), save mixing data as well. Do not use this option unless you have a good reason! It is no longer needed to specify ‘high’ in order to be able to restart from an interrupted calculation (see restart_mode).
Medium: save charge to disk at each SCF step, keep wavefunctions on disk only if more than one k-point, per process is present, otherwise keep them in memory; save them to disk only at the end (in ‘portable’ format).
Low: save charge to disk at each SCF step, keep wavefunctions in memory (for all k-points), save them to disk only at the end (in ‘portable’ format). Reduces I/O but increases memory wrt the previous cases.
NoWf: save to disk only the xml data file and the charge density at convergence, never save wavefunctions. Restarting from an interrupted calculation is not possible with this option.
Minimal: save to disk only the xml data file at convergence.
None: do not save anything to disk.
Default stablished by QE (‘Low’ for the scf case, ‘Medium’ otherwise.)
lelfield (BoolType | BoolKey) –
If True a homogeneous finite electric field described through the modern theory of the polarization is applied.
This is different from setting
tefieldto True!max_seconds (float | FloatKey) –
Jobs stops after max_seconds CPU time. Use this option in conjunction with option restart_mode if you need to
split a job too long to complete into shorter jobs that fit into your batch queues. Warning! Unfortunately, AMS does not yet support restarting an SCF calculation in QE. Therefore, utilizing this option is unhelpful, unless you intend to continue the calculation directly using QE.
tefield (BoolType | BoolKey) –
If True a saw-like potential simulating an electric field is added to the bare ionic potential.
See keywords
edir,eamp,emaxpos,eopregfor the form and size of the added potential.
- class _DOS[source]¶
This section configures the parameters for calculating the Density of States (DOS). These are the utilities involved:
kpath: This AMS tool generates an automated high-symmetry k-path in the Brillouin zone.pw.x(withcalculation=nscf): This Quantum ESPRESSO (QE) utility conducts electronic structure calculations, specifically for the non-self-consistent field (nscf) computation.dos.x: A QE utility utilized for post-processing electronic structure calculations. It analyzes the electronic wavefunctions obtained from preceding calculations to determine the density of available electronic states at different energy levels. For more details see https://www.quantum-espresso.org/Doc/INPUT_DOS.htmlprojwfc.x: Another QE utility employed for post-processing electronic structure calculations. It projects the wavefunctions onto atomic orbitals or basis sets, offering insights into the composition and character of electronic states. For more details see https://www.quantum-espresso.org/Doc/INPUT_PROJWFC.html
By default, the calculation sequence follows the order:
kpath -> pw.x(calculation=nscf) -> dos.x. However, enablingDOS%PDOSswitches the calculation to useprojwfc.xinstead ofdos.x. While common parameters can be customized directly in this section, specialized adjustments should be made in either theDOS_XorPROJWFC_Xsection, depending on specific requirements.- Variables:
Emax (float | FloatKey) – Maximum energy for DOS plot. If unspecified, the upper band value, plus 3 times the value of the gaussian smearing if present, will be used.
Emin (float | FloatKey) – Minimum energy for DOS plot. If unspecified, the lower band value, minus 3 times the value of the gaussian smearing if present, will be used.
K_PointsStep (float | FloatKey) – This option is used only if the header of the
DOS%K_Pointsblock isams_kpath.PDOS (BoolType | BoolKey) – If true, the partial Density-Of-States (projections on atomic basis functions) is calculated and saved for visualization. It uses the QE-utility
projwfc.x. To configure the parameters of the calculation, please modify the options in the the sectionPROJWFC_X.degauss (float | FloatKey) – Gaussian broadening. See more details in sections
DOS_XorPROJWFC_X.Number of electronic states (bands) to be calculated. Note that in spin-polarized calculations the number of k-point, not the number of bands per k-point, is doubled.
Default: 20% more (minimum of 4 additional bands) than the number used in the main ‘pw.x’ calculation, regardless of the material’s insulating or metallic nature. Notice that this default is calculated differently than in standard QE.
ngauss (Literal["0", "SimpleGaussian", "1", "Methfessel-Paxton", "-1", "ColdSmearing", "-99", "Fermi-Dirac", "Default"]) –
Type of gaussian broadening: Available options are:
SimpleGaussian.
Methfessel-Paxton: Methfessel-Paxton of order 1.
ColdSmearing: Marzari-Vanderbilt-DeVita-Payne.
Fermi-Dirac: Fermi-Dirac function.
Default: See more details in sections
DOS_XorPROJWFC_X.
occupations (Literal["Smearing", "Tetrahedra", "Tetrahedra_lin", "Tetrahedra_opt", "Fixed", "Auto"]) –
Available options are:
Smearing: gaussian smearing for metals; see keywords
smearinganddegaussTetrahedra: Tetrahedron method, Bloechl’s version: P.E. Bloechl, PRB 49, 16223 (1994). Requires uniform grid of k-points, to be automatically generated (see
block K_Points). Well suited for calculation of DOS, less so (because not variational) for force/optimization/dynamics calculations.Tetrahedra_lin: Original linear tetrahedron method. To be used only as a reference; the optimized tetrahedron method is more efficient.
Tetrahedra_opt: optimized tetrahedron method, see M. Kawamura, PRB 89, 094515 (2014). Can be used for phonon calculations as well.
Fixed: for insulators with a gap.
Auto: Uses
Tetrahedrafor 3D and 2D systems, andFixedfor 0D and 1D systems.
smearing (Literal["Gaussian", "gauss", "Methfessel-Paxton", "m-p", "mp", "Marzari-Vanderbilt", "cold", "m-v", "mv", "Fermi-Dirac", "f-d", "fd"]) –
Available options are:
Gaussian: ordinary Gaussian spreading
Methfessel-Paxton: first-order spreading (see PRB 40, 3616 (1989))
Marzari-Vanderbilt: cold smearing (see PRL 82, 3296 (1999))
Fermi-Dirac: smearing with Fermi-Dirac function
K_Points (str | Sequence[str] | FreeBlock) – Specify the k-points to use. Choose a header appropriate for your system. Available values are:
tpiba,automatic,crystal,gamma,tpiba_b,crystal_b,tpiba_c,crystal_c, andams_kpath. See the QE documentation for details. If omitted, the k-points specified in the main QE calculation will be used. For most cases,automatic(which generates a Monkhorst-Pack grid) is recommended.
- class _K_Points[source]¶
Specify the k-points to use. Choose a header appropriate for your system. Available values are:
tpiba,automatic,crystal,gamma,tpiba_b,crystal_b,tpiba_c,crystal_c, andams_kpath. See the QE documentation for details. If omitted, the k-points specified in the main QE calculation will be used. For most cases,automatic(which generates a Monkhorst-Pack grid) is recommended.
- class _DOS_X[source]¶
This section configures the parameters for running the QE-utility
dos.x(see https://www.quantum-espresso.org/Doc/INPUT_DOS.html). This utility calculates the Density of States (DOS), separated into up and down components for DSDA.- Variables:
Emax (float | FloatKey) – Maximum energy for DOS plot. If unspecified, the upper band value, plus 3 times the value of the gaussian smearing if present, will be used.
Emin (float | FloatKey) – Minimum energy for DOS plot. If unspecified, the lower band value, minus 3 times the value of the gaussian smearing if present, will be used.
bz_sum (Literal["Smearing", "Tetrahedra", "Tetrahedra_lin", "Tetrahedra_opt", "Default"]) –
Keyword selecting the method for BZ summation. Available options are:
Smearing: Integration using gaussian smearing. In fact currently any string not related to tetrahedra defaults to smearing.
Tetrahedra: Tetrahedron method, Bloechl’s version: P.E. Bloechl, PRB 49, 16223 (1994). Requires uniform grid of k-points, to be automatically generated (see
block K_Points).Tetrahedra_lin: Original linear tetrahedron method. To be used only as a reference; the optimized tetrahedron method is more efficient.
Tetrahedra_opt: Optimized tetrahedron method, see M. Kawamura, PRB 89, 094515 (2014). Default: The default value is
SmearingifDOS_X%degaussis set, otherwise it is influenced by related variables used in the previous ‘pw.x’ run. For more information, consult the original Quantum Espresso documentation at this link: https://www.quantum-espresso.org/Doc/INPUT_DOS.html.
degauss (float | FloatKey) – Gaussian broadening. If not set, the default value is determined by the choice you make for
DOS_X%bz_sum, and it may also be influenced by related variables used in the previous ‘pw.x’ run. For more information, consult the original Quantum Espresso documentation at this link: https://www.quantum-espresso.org/Doc/INPUT_DOS.html.ngauss (Literal["0", "SimpleGaussian", "1", "Methfessel-Paxton", "-1", "ColdSmearing", "-99", "Fermi-Dirac", "Default"]) –
Type of gaussian broadening: Available options are:
SimpleGaussian.
Methfessel-Paxton: Methfessel-Paxton of order 1.
ColdSmearing: Marzari-Vanderbilt-DeVita-Payne.
Fermi-Dirac: Fermi-Dirac function.
Default: The default value is determined by the choices you make for
DOS_X%bz_sumandDOS_X%degauss, and it may also be influenced by related variables used in the previous ‘pw.x’ run. For more information, consult the original Quantum Espresso documentation at this link: https://www.quantum-espresso.org/Doc/INPUT_DOS.html.
- class _DYNMAT_X[source]¶
This section configures the parameters for running the QE utility dynmat.x (see https://www.quantum-espresso.org/Doc/INPUT_DYNMAT.html). This utility is used to ???
- class _Electrons[source]¶
Keywords from the &ELECTRONS namelist in the QuantumEspresso input file.
- Variables:
conv_thr (float | FloatKey) – Convergence threshold for selfconsistency: estimated energy error <
conv_thr. Note thatconv_thris extensive, like the total energy.diagonalization (Literal["Davidson", "David", "ConjugateGradient", "CG", "PPCG", "ParO", "RMM-Davidson", "RMM-ParO"]) –
Available options are:
Davidson: iterative diagonalization with overlap matrix. Fast, may in some rare cases fail.
ConjugateGradient: Conjugate-gradient-like band-by-band diagonalization. MUCH slower than
Davidsonbut uses less memory and is (a little bit) more robust.PPCG: PPCG iterative diagonalization
ParO: ParO iterative diagonalization
RMM-Davidson & RMM-ParO: RMM-DIIS iterative diagonalization. To stabilize the SCF loop RMM-DIIS is alternated with calls to Davidson or ParO solvers.
electron_maxstep (int | IntKey) – Maximum number of iterations in a SCF step.
mixing_beta (float | FloatKey) –
Mixing factor for self-consistency.
Note: the default value in the AMS interface (0.3) is smaller than the default value in pw.x (0.7)
mixing_mode (Literal["Plain", "Thomas-Fermi", "TF", "Local-Thomas-Fermi", "local-TF"]) –
Available options are:
Plain: charge density Broyden mixing
Thomas-Fermi: as above, with simple Thomas-Fermi screening (for highly homogeneous systems)
Local-Thomas-Fermi: as above, with local-density-dependent TF screening (for highly inhomogeneous systems)
mixing_ndim (int | IntKey) – Number of iterations used in mixing scheme. If you are tight with memory, you may reduce it to 4 or so.
scf_must_converge (BoolType | BoolKey) – If .false. do not stop molecular dynamics or ionic relaxation when electron_maxstep is reached. Use with care. Important: When using the AMS interface, setting this to .true. will halt the entire AMS execution if the SCF fails; otherwise, AMS will try to continue using the unconverged results.
startingpot (Literal["atomic", "file"]) –
Available options are:
’atomic’: starting potential from atomic charge superposition.
’file’: start from existing ‘charge-density.xml’ file in the directory specified by variables prefix and outdir. Note: This option applies only to the main and first QE calculation. Once the QE worker is up, the results from the previous step are reused.
startingwfc (Literal["atomic", "atomic+random", "random", "file"]) –
Available options are:
’atomic’: Start from superposition of atomic orbitals. If not enough atomic orbitals are available, fill with random numbers the remaining wfcs. The scf typically starts better with this option, but in some high-symmetry cases one can ‘loose’ valence states, ending up in the wrong ground state.
’atomic+random’: As above, plus a superimposed ‘randomization’ of atomic orbitals. Prevents the ‘loss’ of states mentioned above.
’random’: Start from random wfcs. Slower start of scf but safe. It may also reduce memory usage in conjunction with diagonalization=’cg’.
’file’: Start from an existing wavefunction file in the directory specified by variables prefix and outdir. Note: This option applies only to the main and first QE calculation. Once the QE worker is up, the results from the previous step are reused.
- class _Hubbard[source]¶
Specify parameters for DFT+U models. The type of Hubbard projectors to use (e.g.
atomicorortho-atomic) is specified in the header of this block. Example input:Hubbard ortho-atomic U Fe-3d 3.0 EndMore examples can be found in the documentation.
- class _HubbardU[source]¶
Specify parameters for DFT+U Models.
- Variables:
Projector (Literal["atomic", "ortho-atomic", "norm-atomic", "wf", "pseudo"]) – The Hubbard projector to use.
Parameter (QuantumESPRESSO._HubbardU._Parameter) – Specify parameters for DFT+U Models.
- class _Parameter[source]¶
Specify parameters for DFT+U Models.
- Variables:
AtomType (str | StringKey) – The QE atom type for which this parameter applies.
State (Literal["1s", "2s", "2p", "3s", "3p", "3d", "4s", "4p", "4d", "4f", "5s", "5p", "5d", "5f", "6s", "6p", "6d", "7s", "7p"]) – The state for this parameter applies.
Type (Literal["U", "J", "J0", "B", "V"]) – The type of Hubbard parameter.
- class _K_Points[source]¶
Specify the k-points to use. Available header values are:
tpiba,automatic,crystal,gamma,tpiba_b,crystal_b,tpiba_c,crystal_c, andams_kpath. See the examples and QE documentation for details. If omitted, onlygammais used. For most cases,automatic(which generates a Monkhorst-Pack grid) is recommended. Note: Gamma-point calculations are significantly faster usinggammathanautomatic, but may not be possible to use for all types of calculations or postprocessing programs.
- class _MATDYN_X[source]¶
This section configures the parameters for running the QE utility matdyn.x (see https://www.quantum-espresso.org/Doc/INPUT_MATDYN.html). This utility is used to calculate various phonon-related properties from the real-space interatomic force constants (IFC) produced by q2r.x. These properties include phonon dispersion curves, phonon density of states (DOS), thermodynamic properties (e.g., free energy, entropy), and more.
- Variables:
asr (Literal["no", "simple", "crystal", "all", "one-dim", "zero-dim"]) –
Indicates the type of Acoustic Sum Rule imposed. Allowed values:
’no’: no Acoustic Sum Rules imposed (default)
’simple’: previous implementation of the asr used (3 translational asr imposed by correction of the diagonal elements of the force constants matrix).
’crytal’: 3 translational asr imposed by optimized correction of the force constants (projection).
’all’: 3 translational asr + 3 rotational asr + 15 Huang conditions for vanishing stress tensor, imposed by optimized correction of the force constants (projection). Remember to set write_lr = .true. to write long-range force constants into file when running q2r and set read_lr = .true. when running matdyn in the case of infrared-active solids. (See npj Comput Mater 8, 236 (2022)).
’one-dim’: 3 translational asr + 1 rotational asr imposed by optimized correction of the dyn. mat. (the rotation axis is the direction of periodicity; it will work only if this axis considered is one of the Cartesian axis).
’zero-dim’: 3 translational asr + 3 rotational asr imposed by optimized correction of the dyn. mat.
degauss (float | FloatKey) – DOS broadening in cm-1. Default: 0 - meaning use tetrahedra.
deltaE (float | FloatKey) – Energy step, in cm-1, for DOS calculation: from min to max phonon energy (default: 1 cm-1 if is not specified).
dos (BoolType | BoolKey) – If .true. calculate phonon Density of States (DOS) using tetrahedra and a uniform q-point grid (see below) NB: may not work properly in noncubic materials. If .false. calculate phonon bands from the list of q-points supplied in input (default)
l1 (int | IntKey) – Supercell lattice vectors are original cell vectors times
l1,l2,l3respectively (default: 1)l2 (int | IntKey) – Supercell lattice vectors are original cell vectors times
l1,l2,l3respectively (default: 1)l3 (int | IntKey) – Supercell lattice vectors are original cell vectors times
l1,l2,l3respectively (default: 1)loto_2d (BoolType | BoolKey) – Set to .true. to activate two-dimensional treatment of LO-TO splitting
ndos (int | IntKey) – Number of energy steps for DOS calculations (default: calculated from deltaE if not specified).
nk1 (int | IntKey) – Uniform q-point grid for DOS calculation (includes q=0). First direction. Must be specified if
dos = .true., ignored otherwise.nk2 (int | IntKey) – Uniform q-point grid for DOS calculation (includes q=0). Second direction. Must be specified if
dos = .true., ignored otherwise.nk3 (int | IntKey) – Uniform q-point grid for DOS calculation (includes q=0). Third direction. Must be specified if
dos = .true., ignored otherwise.q_in_cryst_coord (BoolType | BoolKey) – If True, the q-points for the phonon dispersion calculation are given in crystal coordinates (i.e., as fractions of the reciprocal lattice vectors).
Q_Points (str | Sequence[str] | FreeBlock) – Specify the q-points to use for the bands calculation.
- class _NormalModes[source]¶
This section outlines the configuration of parameters for calculating Normal Modes. The process involves using the following utilities:
ph.x: This utility from Quantum ESPRESSO (QE) calculates phonon frequencies and eigenvectors at specified q-points (wave vectors) using Density Functional Perturbation Theory (DFPT). You can set specific parameters in the sectionPH_X. For more details, see https://www.quantum-espresso.org/Doc/INPUT_PH.html.dynmat.x: This QE utility calculates the infrared (IR) and Raman intensities (oscillator strengths) as well as the normal modes associated with each vibrational frequency. Specific parameters can be set in the sectionDYNMAT_X. The information fromph.x, combined with the phonon frequencies, is used to generate the simulated IR/Raman absorption spectrum. For more details, see https://www.quantum-espresso.org/Doc/INPUT_DYNMAT.html.
If Normal Modes are requested in the main AMS properties section, the program automatically sets
PH_X%asr=Yes,PH_X%epsilon=Yes, andPH_X%trans=Yes. If Raman is requested in the main AMS properties section, it also setsPH_X%lraman=Yesalong with the previous parameters.- Variables:
ActiveAtoms (Iterable[int] | IntListKey) – This is a list of atoms to be used in the linear response calculation. It can help estimate modes for a molecule adsorbed on a surface without requiring a full calculation. Please be aware that this is an approximation and may not be reliable. If you perform a linear response calculation for a specific atom, you should also do so for all symmetry-equivalent atoms. This option serves as an interface to the
ph.xoptionnat_todo. This is an experimental feature!ActiveAtomsInRegion (str | StringKey) – Specify the region of atoms to be included in the linear response calculation. It can help estimate modes for a molecule adsorbed on a surface without requiring a full calculation. Please be aware that this is an approximation and may not be reliable. If you perform a linear response calculation for a specific atom, you should also do so for all symmetry-equivalent atoms. This option serves as an interface to the
ph.xoptionnat_todo. This is an experimental feature!asr (Literal["no", "simple", "crystal", "one-dim", "zero-dim"]) – Indicates the type of Acoustic Sum Rule imposed. Allowed values: ‘no’, ‘simple’, ‘crystal’, ‘one-dim’, ‘zero-dim’
tr2_ph (float | FloatKey) – Threshold for self-consistency. It overwrites
PH_X%tr2_ph.xq1 (float | FloatKey) – First component of the phonon wavevector (q-point) at which the IR spectrum is calculated, in units of 2pi/a0 (a0 = lattice parameter). It overwrites
PH_X%xq1.xq2 (float | FloatKey) – Second component of the phonon wavevector (q-point) at which the IR spectrum is calculated, in units of 2pi/a0 (a0 = lattice parameter). It overwrites
PH_X%xq2.xq3 (float | FloatKey) – Third component of the phonon wavevector (q-point) at which the IR spectrum is calculated, in units of 2pi/a0 (a0 = lattice parameter). It overwrites
PH_X%xq3.
- class _PH_X[source]¶
This section configures the parameters for running the QE utility ph.x (see https://www.quantum-espresso.org/Doc/INPUT_PH.html). This utility is used for post-processing phonon calculations in Quantum ESPRESSO.
- Variables:
asr (BoolType | BoolKey) – Apply Acoustic Sum Rule to dynamical matrix, effective charges Works only in conjunction with ‘gamma_gamma’ tricks (see above)
epsil (BoolType | BoolKey) – If .true. in a q=0 calculation for a non metal the macroscopic dielectric constant of the system is computed. Do not set epsil to .true. if you have a metallic system or q/=0: the code will complain and stop.
k1 (int | IntKey) – If specified, triggers a non-self-consistent calculation in ph.x with a separate Monkhorst-Pack k-point grid for phonons. This sets the k-point grid offset along the first reciprocal lattice vector for that grid.
k2 (int | IntKey) – If specified, triggers a non-self-consistent calculation in ph.x with a separate Monkhorst-Pack k-point grid for phonons. This sets the k-point grid offset along the second reciprocal lattice vector for that grid.
k3 (int | IntKey) – If specified, triggers a non-self-consistent calculation in ph.x with a separate Monkhorst-Pack k-point grid for phonons. This sets the k-point grid offset along the third reciprocal lattice vector for that grid.
ldisp (BoolType | BoolKey) – If True, phonon dispersion curves are calculated along specified high-symmetry lines in the Brillouin zone. Requires additional input defining the path.
lraman (BoolType | BoolKey) – If .true. calculate non-resonant Raman coefficients using second-order response as in: M. Lazzeri and F. Mauri, PRL 90, 036401 (2003).
nk1 (int | IntKey) – If specified, triggers a non-self-consistent calculation in ph.x with a separate Monkhorst-Pack k-point grid for phonons. This sets the number of k-points along the first reciprocal lattice vector for that grid.
nk2 (int | IntKey) – If specified, triggers a non-self-consistent calculation in ph.x with a separate Monkhorst-Pack k-point grid for phonons. This sets the number of k-points along the second reciprocal lattice vector for that grid.
nk3 (int | IntKey) – If specified, triggers a non-self-consistent calculation in ph.x with a separate Monkhorst-Pack k-point grid for phonons. This sets the number of k-points along the third reciprocal lattice vector for that grid.
nq1 (int | IntKey) – Sets the number of q-points along the first reciprocal lattice vector for the Monkhorst-Pack q-point grid for phonons. Default 1. Notice that this default is different than in standard QE (default 0).
nq2 (int | IntKey) – Sets the number of q-points along the second reciprocal lattice vector for the Monkhorst-Pack q-point grid for phonons. Default 1. Notice that this default is different than in standard QE (default 0).
nq3 (int | IntKey) – Sets the number of q-points along the third reciprocal lattice vector for the Monkhorst-Pack q-point grid for phonons. Default 1. Notice that this default is different than in standard QE (default 0).
search_sym (BoolType | BoolKey) – Set it to .false. if you want to disable the mode symmetry analysis.
trans (BoolType | BoolKey) – If .false. the phonons are not computed. If trans .and. epsil are both .true., the effective charges are calculated. If ldisp is .true., trans=.false. is overridden (except for the case of electron-phonon calculations)
xq1 (float | FloatKey) – First component of the phonon wavevector, in units of 2pi/a0 (a0 = lattice parameter). Not used if ldisp=.true. or qplot=.true.
xq2 (float | FloatKey) – Second component of the phonon wavevector, in units of 2pi/a0 (a0 = lattice parameter). Not used if ldisp=.true. or qplot=.true.
xq3 (float | FloatKey) – Third component of the phonon wavevector, in units of 2pi/a0 (a0 = lattice parameter). Not used if ldisp=.true. or qplot=.true.
- class _PP_X[source]¶
This section configures the parameters for running the QE-utility
pp.x(see https://www.quantum-espresso.org/Doc/INPUT_PP.html). This utility reads the output produced bypw.x, extracts and calculates the desired quantity/quantities (rho, V, …), and then writes the desired quantity to file in a suitable format for various types of plotting and various plotting programs. Only a few options are supported at the moment.
- class _PROJWFC_X[source]¶
This section configures the parameters for running the QE-utility
projwfc.x(see https://www.quantum-espresso.org/Doc/INPUT_PROJWFC.html). This utility projects wavefunctions onto orthogonalized atomic wavefunctions, calculates Lowdin charges, spilling parameter, projected DOS (separated into up and down components for LSDA).- Variables:
Emax (float | FloatKey) – Maximum energy for DOS plot. If unspecified, the upper band value, plus 3 times the value of the gaussian smearing if present, will be used.
Emin (float | FloatKey) – Minimum energy for DOS plot. If unspecified, the lower band value, minus 3 times the value of the gaussian smearing if present, will be used.
degauss (float | FloatKey) – Gaussian broadening. If not set, the default value is determined by the choice you make for
DOS_X%bz_sum, and it may also be influenced by related variables used in the previous ‘pw.x’ run. For more information, consult the original Quantum Espresso documentation at this link: https://www.quantum-espresso.org/Doc/INPUT_PROJWFC.html.diag_basis (BoolType | BoolKey) – If False, the projections of Kohn-Sham states are done on the orthogonalized atomic orbitals in the global XYZ coordinate frame. If True, the projections of Kohn-Sham states are done on the orthogonalized atomic orbitals that are rotated to the basis in which the atomic occupation matrix is diagonal (i.e. local XYZ coordinate frame).
lsym (BoolType | BoolKey) – If True, the projections are symmetrized, the partial density of states are computed. If False the projections are not symmetrized, the partial DOS can be computed only in the k-resolved case
ngauss (Literal["0", "SimpleGaussian", "1", "Methfessel-Paxton", "-1", "ColdSmearing", "-99", "Fermi-Dirac", "Default"]) –
Type of gaussian broadening: Available options are:
SimpleGaussian.
Methfessel-Paxton: Methfessel-Paxton of order 1.
ColdSmearing: Marzari-Vanderbilt-DeVita-Payne.
Fermi-Dirac: Fermi-Dirac function.
Default: The default value is determined by the choices you make for
DOS_X%bz_sumandDOS_X%degauss, and it may also be influenced by related variables used in the previous ‘pw.x’ run. For more information, consult the original Quantum Espresso documentation at this link: https://www.quantum-espresso.org/Doc/INPUT_PROJWFC.html.
- class _Phonons[source]¶
This section configures the parameters for calculating the Phonon Structure. This involves utilizing the following utilities:
kpath: This AMS tool generates an automated high-symmetry k-path in the Brillouin zone.ph.x: This utility from Quantum ESPRESSO (QE) calculates phonon frequencies and eigenvectors at specified q-points (wavevectors) using Density Functional Perturbation Theory (DFPT). For more details see https://www.quantum-espresso.org/Doc/INPUT_PH.htmlq2r.x: This QE utility transforms the dynamical matrix from reciprocal space (q-space) to real space (r-space). This is necessary for further post-processing steps. For more details see https://www.quantum-espresso.org/Doc/INPUT_Q2R.html.matdyn.x: This QE utility calculates various phonon-related properties from the real-space dynamical matrix, such as phonon dispersion curves, density of states (DOS), thermodynamic properties, and more. For more details see https://www.quantum-espresso.org/Doc/INPUT_MATDYN.html.
- Variables:
MaxTemperature (float | FloatKey) – Maximum temperature for the thermodynamic properties calculation (Internal Energy, Free Energy, Specific Heat, and Entropy). This value sets the upper limit of the temperature range considered. It is used in conjunction with
NTemperaturesto define the temperature grid. The calculation of thermodynamic properties is performed only if the phonon density of states (DOS) is requested (i.e.,Phonons%DOSis set toYes).NTemperatures (int | IntKey) – Number of temperature points to use in the thermodynamic properties calculation (Internal Energy, Free Energy, Specific Heat, and Entropy). This value, along with
MaxTemperature, determines the density of the temperature grid. The temperatures will be distributed evenly between 0 Kelvin and ‘MaxTemperature’. The calculation of thermodynamic properties is performed only if the phonon density of states (DOS) is requested (i.e.,Phonons%DOSis set toYes).asr (Literal["simple", "crystal", "no"]) – Determines the acoustic sum rule (ASR) treatment. It has three options: * ‘simple’: Applies a simplified ASR where the frequencies of the three acoustic modes at q=0 are forced to be zero. * ‘crystal’: Applies the ASR considering the crystal symmetry to impose constraints on the frequencies at q=0. * ‘no’: Does not enforce any ASR. It overwrites
PH_X%asr(setting it to .TRUE. if asr is not ‘no’),Q2R_X%zasr, andMATDYN_X%asr. Notice that the default value is different than in standard QE (default ‘simple’).k1 (int | IntKey) – If specified, triggers a non-self-consistent calculation in ph.x with a separate Monkhorst-Pack k-point grid for phonons. This sets the k-point grid offset along the first reciprocal lattice vector for that grid.
k2 (int | IntKey) – If specified, triggers a non-self-consistent calculation in ph.x with a separate Monkhorst-Pack k-point grid for phonons. This sets the k-point grid offset along the second reciprocal lattice vector for that grid.
k3 (int | IntKey) – If specified, triggers a non-self-consistent calculation in ph.x with a separate Monkhorst-Pack k-point grid for phonons. This sets the k-point grid offset along the third reciprocal lattice vector for that grid.
nk1 (int | IntKey) – If specified, triggers a non-self-consistent calculation in ph.x with a separate Monkhorst-Pack k-point grid for phonons. This sets the number of k-points along the first reciprocal lattice vector for that grid.
nk2 (int | IntKey) – If specified, triggers a non-self-consistent calculation in ph.x with a separate Monkhorst-Pack k-point grid for phonons. This sets the number of k-points along the second reciprocal lattice vector for that grid.
nk3 (int | IntKey) – If specified, triggers a non-self-consistent calculation in ph.x with a separate Monkhorst-Pack k-point grid for phonons. This sets the number of k-points along the third reciprocal lattice vector for that grid.
nq1 (int | IntKey) – Sets the number of q-points along the first reciprocal lattice vector for the Monkhorst-Pack q-point grid for phonons. Default 1. Notice that this default is different than in standard QE (default 0).
nq2 (int | IntKey) – Sets the number of q-points along the second reciprocal lattice vector for the Monkhorst-Pack q-point grid for phonons. Default 1. Notice that this default is different than in standard QE (default 0).
nq3 (int | IntKey) – Sets the number of q-points along the third reciprocal lattice vector for the Monkhorst-Pack q-point grid for phonons. Default 1. Notice that this default is different than in standard QE (default 0).
BandStructure (QuantumESPRESSO._Phonons._BandStructure) – This section configures the parameters for calculating the Phonons Band Structure.
DOS (QuantumESPRESSO._Phonons._DOS) – Configures the parameters for calculating the Phonons DOS.
K_Points (str | Sequence[str] | FreeBlock) – When these block is specified the phonon program (
ph.x) runs a pw non-self consistent calculation with a different k-point grid thant that used for the charge density. The only available header values areautomaticorgamma. See the examples and QE documentation for details. This parameter is equivalent tonk1, nk2, nk3, k1, k2, k3in the QE toolph.x. If omitted,ph.xwill use the same k-point grid used in the main QE calculation.Q_Points (str | Sequence[str] | FreeBlock) – Defines the Monkhorst-Pack grid (no offset) for sampling the Brillouin zone in the phonon calculation. The grid determines the density of q-points at which phonon frequencies will be calculated. It is used when DOS or BandStructure phonon properties are requested. The only available header values are
automaticorgamma. See the examples and QE documentation for details. This parameter is equivalent tonq1, nq2, nq3in the QE toolph.x. If omitted, onlygamma(1 1 1 0 0 0) is used.
- class _BandStructure[source]¶
This section configures the parameters for calculating the Phonons Band Structure.
- Variables:
KPathFinderConvention (Literal["Setyawan-Curtarolo", "Hinuma"]) –
This option determines how the path through the Brillouin zone is generated when using the automatic k-point mode.
Available options:
Setyawan-Curtarolo(default for 1D and 2D lattices): Uses our built-in KPath program to find a path through high-symmetry points based on the method by Setyawan and Curtarolo (https://doi.org/10.1016/j.commatsci.2010.05.010). For 2D lattices, the path is derived from the intersection of the 3D Brillouin zone with a plane. For 1D lattices, the path is simplyGAMMA-Z.Hinuma: Uses the external SeeKPath utility to generate the k-path (https://github.com/giovannipizzi/seekpath and https://doi.org/10.1016/j.commatsci.2016.10.015).
Q_PointsLabels (str | StringKey) – You can provide labels for your q-points, like
L-GAMMA-X-U-GAMMA, separating each label with a hyphen (-) or a vertical bar (|). For example,L-GAMMA-X-U-GAMMAandL|GAMMA|X|U|GAMMAare both valid. These labels are optional and only used for display purposes when theQ_Pointsblock is specified. This option is used only if the header of theQ_Pointsblock is notams_kpath. Important: These labels do not determine the actual k-point coordinates. You must specify the q-point coordinates separately within theQ_Pointssection.Q_PointsStep (float | FloatKey) – This option is used only if the header of the
Phonons%BandStructure%Q_Pointsblock isams_kpath.UseSymmetry (BoolType | BoolKey) – If set, only the irreducible wedge of the Wigner-Seitz cell is sampled. If not, the whole (inversion-unique) Wigner-Seitz cell is sampled. Only available for Setyawan and Curtarolo convention (see
KPathFinderConvention).Q_Points (str | Sequence[str] | FreeBlock) – Specify the q-points to use. Available header values are:
crystal_b, andams_kpath. See the examples and QE documentation for details. If omitted,ams_kpathis used.
- class _DOS[source]¶
Configures the parameters for calculating the Phonons DOS.
- Variables:
degauss (float | FloatKey) – DOS broadening in cm-1. Default: 0 - meaning use tetrahedra. It overwrites
MATDYN_X%degauss.deltaE (float | FloatKey) – Energy step, in cm-1, for DOS calculation: from min to max phonon energy (default: 1 cm-1). It overwrites
MATDYN_X%deltaE.nq1 (int | IntKey) – Uniform q-point grid for DOS calculation (includes q=0). First direction. It overwrites
MATDYN_X%nk1.nq2 (int | IntKey) – Uniform q-point grid for DOS calculation (includes q=0). Second direction. It overwrites
MATDYN_X%nk2.nq3 (int | IntKey) – Uniform q-point grid for DOS calculation (includes q=0). Third direction. It overwrites
MATDYN_X%nk3.Q_Points (str | Sequence[str] | FreeBlock) – Specify the q-points to use. Only the header
automaticis allowed. This option is added for consistency, it is equivalent to setnq1,nq2, andnq3independently.
- class _K_Points[source]¶
When these block is specified the phonon program (
ph.x) runs a pw non-self consistent calculation with a different k-point grid thant that used for the charge density. The only available header values areautomaticorgamma. See the examples and QE documentation for details. This parameter is equivalent tonk1, nk2, nk3, k1, k2, k3in the QE toolph.x. If omitted,ph.xwill use the same k-point grid used in the main QE calculation.
- class _Q_Points[source]¶
Defines the Monkhorst-Pack grid (no offset) for sampling the Brillouin zone in the phonon calculation. The grid determines the density of q-points at which phonon frequencies will be calculated. It is used when DOS or BandStructure phonon properties are requested. The only available header values are
automaticorgamma. See the examples and QE documentation for details. This parameter is equivalent tonq1, nq2, nq3in the QE toolph.x. If omitted, onlygamma(1 1 1 0 0 0) is used.
- class _Properties[source]¶
Configures which QE level properties to calculate for SinglePoint calculations or other important geometries (e.g. at the end of an optimization).
- Variables:
BandStructure (BoolType | BoolKey) – If true, the band structure is calculated and saved for visualization. To configure the parameters of the calculation, please modify the options in the the section ‘BandStructure’.
DOS (BoolType | BoolKey) – If true, the Density-Of-States (DOS) is calculated and saved for visualization. To configure the parameters of the calculation, please modify the options in the the section ‘DOS’.
ForceStopAfterError (BoolType | BoolKey) – If set to true, and a Quantum Espresso property calculation fails, the entire job will stop, preventing any subsequent property calculations from running. If set to false (default), other property calculations will proceed even if one fails.
WorkFunction (BoolType | BoolKey) – If true, the work function is calculated and saved for visualization. To configure the parameters of the calculation, please modify the options in the the section ‘WorkFunction’.
- class _Pseudopotentials[source]¶
Selects the pseudopotential to use for the atomic species.
- Variables:
Database (str | StringKey) – Specifies the file name of the pseudopotential database located in $AMSRESOURCES/QE
Directory (str | Path | StringKey) –
This key is mutually exclusive with the
FamilyandFileskeywords. This key specifies a directory containing label.upf files.Example:
System Atoms H 0 0 0 H 0 0 1 QE.Label=H1 H 0 0 2 QE.Label=H2 C 0 0 3 QE.Label=C1 End EndThis will look for the files H.upf, H1.upf, H2.upf, C1.upf. If H1.upf does not exist, H.upf will be used. If H2.upf does not exist, H.upf will be used. If C1.upf does not exist, C.upf will be used.
Family (Literal["Dojo", "GBRV", "pslibrary-PAW", "pslibrary-US", "SG15", "SSSP-Efficiency", "SSSP-Precision"]) – The pseudopotential family to use. Mutually exclusive with the
FilesandDirectorykeywords.FullyRelativistic (BoolType | BoolKey) – Whether to use fully relativistic pseudopotentials (required for spin-orbit calculations).
Functional (Literal["BLYP", "LDA", "PBE", "PBEsol", "PW91"]) –
Exchange-correlation functional that was used to generate the pseudopotential. Not all choices are valid for all pseudopotential families.
This functional will also be used for the calculation, unless the
input_dftoption is set.Version (str | StringKey) – Version number for pseudopotentials. Currently, must be set to ‘auto’.
Files (QuantumESPRESSO._Pseudopotentials._Files) – Selects the pseudopotentials to use for each atomic species. This key is mutually exclusive with the
FamilyandDirectorykeywords.
- class _Files[source]¶
Selects the pseudopotentials to use for each atomic species. This key is mutually exclusive with the
FamilyandDirectorykeywords.- Variables:
Label (str | StringKey) – Label for an atom corresponding to the QE.Label, or to the element symbol if QE.Label is not set.
Path (str | Path | StringKey) – Path to a .upf file to use as pseudopotential. Relative paths are relative to root of the pseudopotential library shipped with AMS. Prefix a path with ‘./’ to make it relative to the starting directory of your job.
- class _Q2R_X[source]¶
This section configures the parameters for running the QE utility q2r.x (see https://www.quantum-espresso.org/Doc/INPUT_Q2R.html). This utility is used to transform the interatomic force constants (IFC) calculated in reciprocal space (q-space) by ph.x into real space (r-space). The real-space IFCs are then used as input for the matdyn.x utility to calculate various phonon-related properties.
- Variables:
loto_2d (BoolType | BoolKey) – Set to .true. to activate two-dimensional treatment of LO-TO splitting
zasr (Literal["simple", "crystal", "no"]) – Determines the acoustic sum rule (ASR) treatment. It has three options: * ‘simple’: Applies a simplified ASR where the frequencies of the three acoustic modes at q=0 are forced to be zero. * ‘crystal’: Applies the ASR considering the crystal symmetry to impose constraints on the frequencies at q=0. * ‘no’: Does not enforce any ASR.
- class _Restart[source]¶
This section configures restarting a Quantum Espresso calculation from previous data. You can restart from a specific Quantum Espresso results file (e.g., quantumespresso.rkf), or by providing the directory and file prefix of the previous calculation. This is compatible with any stand-alone Quantum Espresso version.
- Variables:
Directory (str | Path | StringKey) – The directory containing the restart files from a previous Quantum Espresso calculation. This typically includes the prefix.save directory with wavefunctions and other data. This option is used in conjunction with the Prefix option.
Path (str | Path | StringKey) – Path to the Quantum Espresso results file (e.g., quantumespresso.rkf) to use to restart the calculation. When this option is used, the directory of the results file is used as the Directory, and the filename (without the .rkf extension) is used as the Prefix. This assumes all restart files (e.g., prefix.save directory) are in the same directory as the results file. This option is equivalent to the EngineRestart option.
Prefix (str | StringKey) – The prefix used for the files in the previous calculation. This is usually the same as the ‘prefix’ specified in the input file of the original calculation. For example, if your files are named ‘my_calc.save’ and ‘my_calc.restart_scf’, the prefix would be ‘my_calc’. This option is used in conjunction with the Directory option.
- class _System[source]¶
Keywords from the &SYSTEM namelist in the QuantumEspresso input file.
- Variables:
assume_isolated (Literal["Auto", "None", "m-p", "mp", "Martyna-Tuckerman", "m-t", "mt", "ESM", "2D"]) –
Used to perform calculation assuming the system to be isolated (a molecule or a cluster in a 3D supercell).
Currently available choices:
Auto: determines the used method based on the periodicity of the system in the AMS driver input. None for systems 3D periodicity, Martyna-Tuckerman for systems without a lattice.
None: regular periodic calculation w/o any correction.
Martyna-Tuckerman: correction to both total energy and scf potential. Adapted from: G.J. Martyna, and M.E. Tuckerman, A reciprocal space based method for treating long range interactions in ab-initio and force-field-based calculation in clusters, J. Chem. Phys. 110, 2810 (1999), [doi:10.1063/1.477923].
ESM: Effective Screening Medium Method. For polarized or charged slab calculation, embeds the simulation cell within an effective semi-infinite medium in the perpendicular direction (along z). Embedding regions can be vacuum or semi-infinite metal electrodes (use esm_bc to choose boundary conditions). If between two electrodes, an optional electric field (esm_efield) may be applied. Method described in M. Otani and O. Sugino, ‘First-principles calculations of charged surfaces and interfaces: A plane-wave nonrepeated slab approach’, PRB 73, 115407 (2006).
2D: Truncation of the Coulomb interaction in the z direction for structures periodic in the x-y plane. Total energy, forces and stresses are computed in a two-dimensional framework. Linear-response calculations () done on top of a self-consistent calculation with this flag will automatically be performed in the 2D framework as well. Please refer to: Sohier, T., Calandra, M., & Mauri, F. (2017), ‘Density functional perturbation theory for gated two-dimensional heterostructures: Theoretical developments and application to flexural phonons in graphene’, PRB, 96, 075448 (2017).
degauss (float | FloatKey) – Value of the gaussian spreading for Brillouin-zone integration in metals.
dftd3_threebody (BoolType | BoolKey) –
Turn three-body terms in Grimme-D3 on.
If False two-body contributions only are computed, using two-body parameters of Grimme-D3.
If dftd3_version is set to
2, three-body contribution is always disabled.dftd3_version (Literal["2", "3", "4", "5", "6"]) –
Version of Grimme implementation of Grimme-D3:
2: Original Grimme-D2 parametrization
3: Grimme-D3 (zero damping)
4: Grimme-D3 (BJ damping)
5: Grimme-D3M (zero damping)
6: Grimme-D3M (BJ damping)
NOTE: not all functionals are parametrized.
Amplitude of the electric field, in Hartree a.u. = = 51.4220632*10^10 V/m.
Used only if
tefieldis enabled.The saw-like potential increases with slope
eampin the region from (emaxpos+eopreg- 1) to (emaxpos), then decreases to 0 until (emaxpos+eopreg), in units of the crystal vector edir.Important: the change of slope of this potential must be located in the empty region, or else unphysical forces will result.
Kinetic energy cutoff for the exact exchange operator in EXX type calculations.
By default this is the same as
ecutrhobut in some EXX calculations, a significant speed-up can be obtained by reducing ecutfock, at the expense of some loss in accuracy.Must be >=
ecutwfc.Not implemented for stress calculation and for US-PP and PAW pseudopotentials.
Use with care, especially in metals where it may give raise to instabilities.
Kinetic energy cutoff for charge density and potential.
If this key is not specified and the
Pseudopotential%Familyrecommends a ratio ofecutrhotoecutwfc, this recommended ratio will be used.If there is no recommended ratio, the default value is
4 x ecutwfc.For norm-conserving pseudopotential you should stick to the default value, you can reduce it by a little but it will introduce noise especially on forces and stress.
If there are ultrasoft PP, a larger value than the default is often desirable (
ecutrho= 8 to 12 timesecutwfc, typically).PAW datasets can often be used at
4 x ecutwfc, but it depends on the shape of augmentation charge: testing is mandatory.The use of gradient-corrected functional, especially in cells with vacuum, or for pseudopotential without non-linear core correction, usually requires an higher values of
ecutrhoto be accurately converged.ecutvcut (float | FloatKey) – Reciprocal space cutoff for correcting Coulomb potential divergencies at small q vectors.
ecutwfc (float | FloatKey) – Kinetic energy cutoff for wavefunctions.
edir (Literal["1", "2", "3", "x", "y", "z"]) –
1(orx), 2 (ory) or 3 (orz). The direction of the electric field or dipole correction is parallel to the bg(:,edir) reciprocal lattice vector.Thus the potential is constant in planes defined by FFT grid points.
Used only if
tefieldis enabled.Position of the maximum of the saw-like potential along crystal axis
edir, within the unit cell, see alsoeopreg.0 <
emaxpos< 1Used only if
tefieldis enabled.Zone in the unit cell where the saw-like potential decreases, see also
amp.Must be in range 0 <
eopreg< 1.Used only if
tefieldis enabled.exx_fraction (float | FloatKey) –
Fraction of EXX for hybrid functional calculations.
In the case of
input_dftset to ‘PBE0’, the default value is 0.25, while forinput_dftset to ‘B3LYP’ theexx_fractiondefault value is 0.20.exxdiv_treatment (Literal["gygi-baldereschi", "vcut_spherical", "vcut_ws", "none"]) –
Specific for EXX. It selects the kind of approach to be used for treating the Coulomb potential divergencies at small q vectors.
gygi-baldereschi: appropriate for cubic and quasi-cubic supercells
vcut_spherical: appropriate for cubic and quasi-cubic supercells
- vcut_ws: appropriate for strongly anisotropic supercells, see also ecutvcut.
none: sets Coulomb potential at G,q=0 to 0.0 (required for GAU-PBE)
Exchange-correlation functional. Some valid values are • pbe • blyp • pbe0 • hse • revpbe • vdw-df-cx. See the documentation for more possible values.
Overrides the value read from pseudopotential files.
lspinorb (BoolType | BoolKey) – if .TRUE. the noncollinear code can use a pseudopotential with spin-orbit.
Number of electronic states (bands) to be calculated. Note that in spin-polarized calculations the number of k-point, not the number of bands per k-point, is doubled.
Default: For an insulator, nbnd = number of valence bands (nbnd = # of electrons /2); for a metal, 20% more (minimum 4 more)
noncolin (BoolType | BoolKey) – If True the program will perform a noncollinear calculation.
nosym (BoolType | BoolKey) – If True, symmetry is not used, and k points are forced to have the symmetry of the Bravais lattice; an automatically generated Monkhorst-Pack grid will contain all points of the grid over the entire Brillouin Zone, plus the points rotated by the symmetries of the Bravais lattice which were not in the original grid. The same applies if a k-point list is provided in input instead of a Monkhorst-Pack grid. Time reversal symmetry is assumed so k and -k are equivalent unless noinv=.true. is specified. This option differs from nosym because it forces k-points in all cases to have the full symmetry of the Bravais lattice (not all uniform grids have such property!)
nqx1 (int | IntKey) – Three-dimensional mesh for q (k1-k2) sampling of the Fock operator (EXX). Can be smaller than the number of k-points. Defaults to the size of the k-point mesh used.
nqx2 (int | IntKey) – Three-dimensional mesh for q (k1-k2) sampling of the Fock operator (EXX). Can be smaller than the number of k-points. Defaults to the size of the k-point mesh used.
nqx3 (int | IntKey) – Three-dimensional mesh for q (k1-k2) sampling of the Fock operator (EXX). Can be smaller than the number of k-points. Defaults to the size of the k-point mesh used.
nr1 (int | IntKey) – Three-dimensional FFT mesh (hard grid) for charge density (and scf potential). If not specified the grid is calculated based on the cutoff for charge density (see also
ecutrho). Note: you must specify all three dimensions for this setting to be used (nr1,nr2,nr3).nr1s (int | IntKey) – Three-dimensional mesh for wavefunction FFT and for the smooth part of charge density ( smooth grid ). Coincides with
nr1,nr2,nr3ifecutrho = 4 * ecutwfc( default ). Note: you must specify all three dimensions for this setting to be used (nr1s,nr2s,nr3s).nr2 (int | IntKey) – Three-dimensional FFT mesh (hard grid) for charge density (and scf potential). If not specified the grid is calculated based on the cutoff for charge density (see also
ecutrho). Note: you must specify all three dimensions for this setting to be used (nr1,nr2,nr3).nr2s (int | IntKey) – Three-dimensional mesh for wavefunction FFT and for the smooth part of charge density ( smooth grid ). Coincides with
nr1,nr2,nr3ifecutrho = 4 * ecutwfc( default ). Note: you must specify all three dimensions for this setting to be used (nr1s,nr2s,nr3s).nr3 (int | IntKey) – Three-dimensional FFT mesh (hard grid) for charge density (and scf potential). If not specified the grid is calculated based on the cutoff for charge density (see also
ecutrho). Note: you must specify all three dimensions for this setting to be used (nr1,nr2,nr3).nr3s (int | IntKey) – Three-dimensional mesh for wavefunction FFT and for the smooth part of charge density ( smooth grid ). Coincides with
nr1,nr2,nr3ifecutrho = 4 * ecutwfc( default ). Note: you must specify all three dimensions for this setting to be used (nr1s,nr2s,nr3s).nspin (Literal["1", "None", "2", "Collinear", "4", "Non-Collinear"]) –
Available options are:
None: not spin-polarized
Collinear: LSDA with magnetization along z-axis
Non-Collinear: any magnetization (equivalent to setting the
noncolinkey to True)
occupations (Literal["Smearing", "Tetrahedra", "Tetrahedra_lin", "Tetrahedra_opt", "Fixed"]) –
Available options are:
Smearing: gaussian smearing for metals; see keywords
smearinganddegaussTetrahedra: Tetrahedron method, Bloechl’s version: P.E. Bloechl, PRB 49, 16223 (1994). Requires uniform grid of k-points, to be automatically generated (see
block K_Points). Well suited for calculation of DOS, less so (because not variational) for force/optimization/dynamics calculations.Tetrahedra_lin: Original linear tetrahedron method. To be used only as a reference; the optimized tetrahedron method is more efficient.
Tetrahedra_opt: optimized tetrahedron method, see M. Kawamura, PRB 89, 094515 (2014). Can be used for phonon calculations as well.
Fixed: for insulators with a gap.
screening_parameter (float | FloatKey) – screening_parameter for HSE like hybrid functionals. For more information, see: J. Chem. Phys. 118, 8207 (2003), doi:10.1063/1.1564060 J. Chem. Phys. 124, 219906 (2006), doi:10.1063/1.2204597
smearing (Literal["Gaussian", "gauss", "Methfessel-Paxton", "m-p", "mp", "Marzari-Vanderbilt", "cold", "m-v", "mv", "Fermi-Dirac", "f-d", "fd"]) –
Available options are:
Gaussian: ordinary Gaussian spreading
Methfessel-Paxton: first-order spreading (see PRB 40, 3616 (1989))
Marzari-Vanderbilt: cold smearing (see PRL 82, 3296 (1999))
Fermi-Dirac: smearing with Fermi-Dirac function
tot_magnetization (float | FloatKey) –
Total majority spin charge minus minority spin charge.
Used to impose a specific total electronic magnetization.
If unspecified then tot_magnetization variable is ignored and the amount of electronic magnetization is determined during the self-consistent cycle.
vdw_corr (Literal["None", "Grimme-D2", "DFT-D", "Grimme-D3", "DFT-D3", "TS", "ts-vdW", "tkatchenko-scheffler", "MBD", "many-body-dispersion", "mbd_vdw", "XDM"]) –
Type of Van der Waals correction. Allowed values:
Grimme-D2: Semiempirical Grimme’s DFT-D2, see S. Grimme, J. Comp. Chem. 27, 1787 (2006) [doi:10.1002/jcc.20495], and V. Barone et al., J. Comp. Chem. 30, 934 (2009) [doi:10.1002/jcc.21112].
Grimme-D3: Semiempirical Grimme’s DFT-D3, see S. Grimme et al, J. Chem. Phys 132, 154104 (2010) [doi:10.1063/1.3382344].
TS: Tkatchenko-Scheffler dispersion corrections with first-principle derived C6 coefficients, see A. Tkatchenko and M. Scheffler, PRL 102, 073005 (2009).
MBD: Many-body dispersion (MBD) correction to long-range interactions, see A. Ambrosetti, A. M. Reilly, R. A. DiStasio, A. Tkatchenko, J. Chem. Phys. 140 18A508 (2014).
XDM: Exchange-hole dipole-moment model, see A. D. Becke et al., J. Chem. Phys. 127, 154108 (2007) [doi:10.1063/1.2795701], and A. Otero de la Roza et al., J. Chem. Phys. 136, 174109 (2012) [doi:10.1063/1.4705760].
Note that non-local functionals (eg vdw-DF) are NOT specified here but using the
input_dftkeyword.x_gamma_extrapolation (BoolType | BoolKey) – Specific for EXX. If .true., extrapolate the G=0 term of the potential (see README in examples/EXX_example for more) Set this to .false. for GAU-PBE.
Damping function parameter a1 (adimensional).
It is NOT necessary to give a value if the functional is one of B86bPBE, PW86PBE, PBE, BLYP. For functionals in this list, the coefficients are given in: http://schooner.chem.dal.ca/wiki/XDM; A. Otero de la Roza, E. R. Johnson, J. Chem. Phys. 138, 204109 (2013) [doi:10.1063/1.4705760]
Damping function parameter a2 (Angstrom).
It is NOT necessary to give a value if the functional is one of B86bPBE, PW86PBE, PBE, BLYP. For functionals in this list, the coefficients are given in: http://schooner.chem.dal.ca/wiki/XDM; A. Otero de la Roza, E. R. Johnson, J. Chem. Phys. 138, 204109 (2013) [doi:10.1063/1.4705760]
starting_magnetization (QuantumESPRESSO._System._starting_magnetization) –
Starting spin polarization for an atomic type in a spin polarized (LSDA or noncollinear/spin-orbit) calculation. Allowed values range between -1 (all spins down for the valence electrons of atom type ‘i’) to 1 (all spins up). If you expect a nonzero magnetization in your ground state, you MUST either specify a nonzero value for at least one atomic type, or constrain the magnetization using keyword
tot_magnetizationfor LSDA,constrained_magnetizationfor noncollinear/spin-orbit calculations. If you don’t, you will get a nonmagnetic (zero magnetization) state. In order to perform LSDA calculations for an antiferromagnetic state, define two different atomic species corresponding to sublattices of the same atomic type.Note: If you fix the magnetization with
tot_magnetization, do not specifystarting_magnetization.Note: In the noncollinear/spin-orbit case, starting with zero starting_magnetization on all atoms imposes time reversal symmetry. The magnetization is never calculated and is set to zero.
- class _starting_magnetization[source]¶
Starting spin polarization for an atomic type in a spin polarized (LSDA or noncollinear/spin-orbit) calculation. Allowed values range between -1 (all spins down for the valence electrons of atom type ‘i’) to 1 (all spins up). If you expect a nonzero magnetization in your ground state, you MUST either specify a nonzero value for at least one atomic type, or constrain the magnetization using keyword
tot_magnetizationfor LSDA,constrained_magnetizationfor noncollinear/spin-orbit calculations. If you don’t, you will get a nonmagnetic (zero magnetization) state. In order to perform LSDA calculations for an antiferromagnetic state, define two different atomic species corresponding to sublattices of the same atomic type.Note: If you fix the magnetization with
tot_magnetization, do not specifystarting_magnetization.Note: In the noncollinear/spin-orbit case, starting with zero starting_magnetization on all atoms imposes time reversal symmetry. The magnetization is never calculated and is set to zero.
- class _WorkFunction[source]¶
This section configures the parameters for calculating the Work Function. This involves utilizing the following utilities:
pp.x: Calculates the the electrostatic potential using the results from the last Quantum ESPRESSO calculation.average.x: Performs planar and macroscopic averages of the electrostatic potential along a specified direction, which are crucial for determining the vacuum level and subsequently the work function.
- Variables:
awin (float | FloatKey) – The size of the window for macroscopic average (a.u.).
centralize (BoolType | BoolKey) – Translates the calculated electrostatic potential along the
idircoordinate, respecting periodic boundary conditions, so that the geometric center of the system is at the center of the coordinate.idir (Literal["1", "2", "3", "x", "y", "z"]) –
1(orx), 2 (ory) or 3 (orz). Planar average is done in the plane orthogonal to directionidir, as defined for the crystal cell. Theidirparameter defaults to the value ofSystem%edirif it’s set. Otherwise,idiris set to 3.npt (int | IntKey) – Number of points used for the final interpolation of the planar and macroscopic averages of the electrostatic potential. This controls the resolution of the averaged potential data. If npt is less than or equal to N_idir (the number of FFT grid points along the specified direction), no interpolation is performed and the raw FFT data is used. The default value is 10 * N_idir, which typically provides sufficient resolution for accurate work function calculations.
- class ReaxFF[source]¶
- Variables:
BondDistanceCutoff (float | FloatKey) – Maximum distance between two atoms to be considered when searching for possible bonds.
BondOrderCutoff (float | FloatKey) – Minimum bond order required for a bond to be considered during the evaluation of the 3- and 4-body potentials.
ComputeAtomicPressure (BoolType | BoolKey) – Compute the virial part of the atomic pressure (the kinetic part cannot be computed by the engine).
FeDimerCorrection (BoolType | BoolKey) – Add a special correction term for Fe-Fe dimers.
ForceField (str | Path | StringKey) – Path to the force field parameter file. The path can be absolute or relative. Relative paths starting with ./ are considered relative to the directory in which the calculation is started, otherwise they are considered relative to $AMSRESOURCES/ForceFields/ReaxFF.
FurmanTorsions (BoolType | BoolKey) – Use (sin(Theta_ijk)*sin(Theta_jkl))^3 instead of sin(Theta_ijk)*sin(Theta_jkl) in the torsion energy term to remove discontinuity in the corresponding force.
NonReactive (BoolType | BoolKey) – Enable the non-reactive mode. Bonds are determined only once at the beginning and subsequent steps only update their bond orders. Thus, no new bonds can form during the simulation, but existing bonds can still stretch and dissociate.
RemapSkin (float | FloatKey) – Thickness of region around the unit cell into which atoms are allowed to move before being internally remapped back into the unit cell.Defaults to VerletListSkin if not set. Should never be smaller than VerletListSkin.
ReturnCorrectedBonds (BoolType | BoolKey) – When enabled, the bonds returned to the driver are based on the final bond orders that include valence-dependent correction terms. Disable this if you want to see the raw uncorrected bond orders instead.
StrongBondCutoff (float | FloatKey) – Minimum bond order required for a bond to be returned to the driver for bonding analysis and molecule detection. Bonds below this threshold are only used to evaluate the potential and not written to result files.
TaperBO (BoolType | BoolKey) – Use tapered bond orders by Furman & Wales (DOI: 10.1021/acs.jpclett.9b02810).
Torsions (Literal["Original", "2013"]) – Version of the torsion potential expression.
VerletListSkin (float | FloatKey) – Thickness of the buffer region added to the force-field-defined non-bonded cutoff radius when building the Verlet list.
Charges (ReaxFF._Charges) – Settings for the polarizable charge model.
- class _Charges[source]¶
Settings for the polarizable charge model.
- Variables:
AllowSmallCellACKS2 (BoolType | BoolKey) – EXPERIMENTAL: Let ACKS2 run even with a periodic cell thinner than the bond softness cutoff.
DisableChecks (BoolType | BoolKey) – Disable checks for suspicious or unphysical charges.
Fix (BoolType | BoolKey) – REB: Fix certain atom charges, if those atoms are specified with MOLCHARGE (not yet possible with AMS-REAXFF
Solver (Literal["Direct", "CG", "MINRESQLP", "SparseCG", "None"]) – Algorithm used to solve the charge equilibration equations.
Constraint (ReaxFF._Charges._Constraint) – Constrain the net charge of a given region.
Converge (ReaxFF._Charges._Converge) – Controls the convergence criteria for charge equilibration.
Predictor (ReaxFF._Charges._Predictor) – Settings for the prediction of new charges before running the solver.
- class VASP[source]¶
- Variables:
CHGCARFile (str | Path | StringKey) – Use a custom CHGCAR file for initializing the charge density. Note: You must also set ICHARG to an appropriate value for this CHGCAR file to be read by VASP.
EnergyChoice (Literal["FreeEnergy", "EnergyWithoutEntropy", "EnergySigmaToZero"]) – The energy from the VASP output which is used with the AMS driver.
EnergyCutoff (float | FloatKey) –
The energy cutoff for the planewave basis set.
VASP keyword: ENCUT
INCARFile (str | Path | StringKey) – Use a custom INCAR file. The keywords NSW, IBRION, ISIF, and LWAV must not be set in this INCAR file, since they are controlled by the AMS driver.
Initialize (str | Path | StringKey) –
Path to a WAVECAR (wavefunction) file from a previous calculation that is used to initialize the present calculation.
If specified, the file will be copied into the new calculation directory and the VASP keyword ISTART will be set to 1.
KPOINTSFile (str | Path | StringKey) – Use a custom KPOINTS file. This will override any other settings related to the k-point sampling.
KPOINTSOrigin (Literal["Gamma-centered", "Monkhorst-Pack"]) –
Type of regular k-point grid. Gamma-centered k-point grids always include the Gamma point, whereas Monkhorst-Pack grids do not include the Gamma point if any of the k-point grid dimensions is even.
To use a custom set of k-points, or to specify paths in the Brillouin zone, prepare such a KPOINTS file manually and set the KPOINTSFile setting.
LDAU (BoolType | BoolKey) – Enables a DFT+U calculation. The options LMAXMIX, LDAUType, LDAUU, LDAUJ, and LDAUL must also be set.
LDAUJ (Iterable[float] | FloatListKey) –
LDAUType (Literal["1", "2", "4"]) –
1: The rotationally invariant DFT+U introduced by Liechtenstein et al. 2: The simplified (rotationally invariant) approach to DFT+U, introduced by Dudarev et al. 4: Same as type 1, but without exchange splitting.
VASP keyword: LDAUTYPE.
LDAUU (Iterable[float] | FloatListKey) –
Occupation (Literal["Gaussian", "Fermi", "1stOrderMethfesselPaxton", "2ndOrderMethfesselPaxton", "TetrahedronMethodWithoutBlochlCorrections", "TetrahedronMethodWithBlochlCorrections"]) –
Type of electronic smearing (fractional occupation scheme).
VASP keyword: ISMEAR
OnlyPreprocessing (BoolType | BoolKey) – If Yes, VASP will not be executed. Instead, the first set of input files (e.g. INCAR, POSCAR, POTCAR, KPOINTS) that would have been read by VASP will be left on disk for inspection.
POTCARFile (str | Path | StringKey) – Use a custom POTCAR file. This will override the POTCAR created from the POTCARLibrary.
POTCARLibrary (str | Path | StringKey) –
Path to the POTCAR (pseudopotential) library, as delivered with VASP. This library must be accessible on the machine currently running AMSinput.
For example, setting this to /library/PBE/PAW/ will use /library/PBE/PAW/Cu/POTCAR as the POTCAR file for Cu atoms by default. Click the arrow to see or change exactly which POTCAR files are used.
Precision (Literal["Single", "Normal", "Accurate"]) – VASP keyword: PREC
SpinPolarization (BoolType | BoolKey) – Determines if a spin-polarized calculation is performed. If set, the VASP keyword ISPIN is set to 2.
Command used to execute VASP.
For example: mpirun -np 4 vasp
Verbosity (BoolType | BoolKey) – If set, more detailed information is printed in the output file.
XC (Literal["Auto", "LDA", "PBE", "PW91", "HF", "PBE0", "HSE06", "B3LYP", "03", "05", "10", "20", "91", "AM", "B3", "B5", "BF", "BO", "CA", "CO", "HL", "MK", "OR", "PE", "PL", "PS", "PZ", "RA", "RE", "RP", "VW", "WI"]) –
The exchange-correlation functional. This setting must be consistent with POTCAR. If your desired functional is not present in the list, choose Auto and set the GGA tag manually under Additional INCAR options. Note: not all functionals are implemented in all versions of VASP.
Auto: The XC functional is determined by the information in POTCAR. The GGA setting is not set. LDA: the VASP GGA setting is set to an empty string. PBE: sets GGA = PE. PW91: sets GGA = 91. HF: Hartree-Fock. Sets LHFCALC = .TRUE, AEXX = 1, ALDAC = 0, AGGAC = 0. PBE0: sets GGA = PE, LHFCALC = .TRUE. HSE06: sets GGA = PE, LHFCALC = .TRUE., HFSCREEN = 0.2. B3LYP: sets LHFCALC = .TRUE., GGA = B3, AEXX = 0.2, AGGAX = 0.72, AGGAC = 0.81, ALDAC = 0.19.
All other options set the VASP GGA setting to the corresponding value. For more information, see the VASP manual.
nk1 (int | IntKey) – Number of k-points in the first dimension
nk2 (int | IntKey) – Number of k-points in the second dimension
nk3 (int | IntKey) – Number of k-points in the third dimension
sk1 (float | FloatKey) – Fractional shift of the k-mesh in the first dimension
sk2 (float | FloatKey) – Fractional shift of the k-mesh in the second dimension
sk3 (float | FloatKey) – Fractional shift of the k-mesh in the third dimension
vdW (Literal["Disable", "DFT-D2", "DFT-D3", "DFT-D3(BJ)", "TS", "TSWithIterativeHirshfeldPartitioning", "ManyBodyDispersionEnergyMethod", "IDVW=4"]) –
The van der Waals correction method.
VASP keyword: IVDW Default: IVDW = 0 (Disable)
Misc (str | Sequence[str] | FreeBlock) –
The contents of this block are copied verbatim into the VASP INCAR file.
Note: do not set NSW, IBRION, ISIF or LWAV in this block, as those keys are set by the AMS driver.
3.2. PISA¶
3.2.1. Entry Module¶
The Entry class is the abstract base class for all input entries. If provides the skeleton for producing input strings and the mechanics for repeated entries. This class is not meant to be used directly.
- _check_unique(meth)[source]¶
Decorator that is used to wrap any
Entrymethod that is not meant for unique entries (like__getitem__)- Parameters:
meth (Callable) –
Entrymethod to decorate- Raises:
ValueError – When wrapped method is called on unique instances of the
Entryobject- Returns:
The wrapped method
- Return type:
Callable
- class Entry[source]¶
Abstract base class serving as the base class for the Block and Key classes. Also handles index notation ‘[]’ for repeated blocks and keys by automatically creating new instances of itself upon indexing.
- __init__(name=None, comment='', hidden=False, unique=True, gui_name=None, default=None, ispath=False, unit='', choices=None, hiddenchoices=None, header=False, ordered=False, isatomlist=False, rootdir=None, engines=None, extra_info=None, gui_type=None, shared_id=None, default_engine=None, range=None, _keyword_dict=None)[source]¶
- Parameters:
name (str | None) –
comment (str) –
hidden (bool) –
unique (bool) –
gui_name (str | None) –
default (Any) –
ispath (bool) –
unit (str) –
header (bool) –
ordered (bool) –
isatomlist (bool) –
rootdir (str | None) –
engines (str | None) –
extra_info (str | None) –
gui_type (str | None) –
shared_id (str | None) –
default_engine (str | None) –
range (str | None) –
- Return type:
None
- property value_changed: bool¶
Property that determines if an entry will be processed by
get_input_string(). Will be set to true if the entry was touched in any way. For keys, this means trying to change their values (even if changed to the default value). For blocks, this means any of their keys were touched in any way.- Returns:
Whether the value of the entry was changed
- Return type:
- get_input_string(indent_lvl=0)[source]¶
Generates a valid AMS input string. Note that this method exists for every entry, but generally as user you want to call it on the highest level
DriverBlockinstance, which will recursively include all its entries.
- abstract _get_single_input_string(indent_lvl=0)[source]¶
This method produces the input string for unique Entries. This is the method that needs to be overwritten to implement specific subclasses, not
get_input_string().
- _get_repeated_input_string(indent_lvl)[source]¶
For repeated entries, simply generate a multiline string by repeatedly calling
get_input_string()for every entry inself._entry_list
3.2.2. Block Module¶
The following classes represent the different types of blocks in the input system. Note that for normal usage, one never needs to instantiate these classes directly. Instead use the autogenerated subclasses present in scm.input_classes.drivers and scm.input_classes.engines.
- class InputParserEngineBlock[source]¶
Simple container for data created by the InputParser for EngineBlocks. Only used in the
Block.from_text()functionality
- class InputParserFreeBlock[source]¶
Simple container for data created by the InputParser for FreeBlocks. Only used in the
Block.from_text()functionality
- class Block[source]¶
Base class representing an input block for AMS.
- _header = ''¶
- property header¶
- static from_def_dict(name, def_dict)[source]¶
Instantiate the relevant
Blockobject from a definition dictionary from the json input definitions. Only used in the autogeneration ofscm.input_classes
- classmethod from_settings(settings)[source]¶
Generate a block object from a settings object. Should only be used for backwards compatibility, e.g. old job classes or recipes that will break on receiving a PISA object. Not guaranteed to always work, since it does a to text input and from text input conversion. Examples:
from scm.input_classes import AMS, DFTB from scm.plams.interfaces.adfsuite.ams import AMSJob from scm.plams.core.settings import Settings settings = Settings() settings.input settings.input.ams.Task = 'GeometryOptimization' settings.input.ams.Properties.NormalModes = 'Yes' settings.input.DFTB.Model = 'SCC-DFTB' ams = AMS.from_settings(settings) # this is supported, but fragile: dftb = DFTB.from_settings(settings) # this is safer: ams = AMS.from_settings(settings) dftb = ams.engine
- Parameters:
cls (type[T_Block]) – Block class you want to generate from settings. Usually should be AMS
settings (Settings) – Settings object to convert from. Should contain ‘input’ attribute.
- Raises:
ValueError – If settings input does not contain ‘input’ attribute
- Returns:
Block object with keys and blocks set according to information in settings object.
- Return type:
T_Block
- classmethod from_text(text)[source]¶
Class method to instantiate a block object from text input. Need to call this on the relevant subclass to work correctly. E.g. for an AMS input string one needs to call AMS.from_text, not Block.from_text
- set_from_input_dict(input_dict)[source]¶
Called from
Block.from_textafter instantiation of the Block to correctly set the values of the key/block attributes as defined in the text input.- Parameters:
input_dict (dict[str, Any]) – dictionary returned by
scm.libbase.InputParser- Raises:
ValueError – When the text input references an Entry not present in the JSON input definitions, would be caused by faulty text input.
- Return type:
None
- property entries: tuple[Entry, ...]¶
Property returning all the entries (blocks and keys) in this block. Return will be sorted with possible engine blocks at the end.
- property _lowercase_dict_entry: dict[str, Entry]¶
Lowercase dictionary of all Entries and their lowercase names, used to check if accessed
Entryattributes in__setattr__()are an incorrect case variation of an existing attributes.
- property _dict_entry: dict[str, Entry]¶
Dictionary of all Entries and their names, to find the proper case names of misspelled Entries in
__setattr__().
- _get_single_input_string(indent_lvl=0)[source]¶
A wrapper that concatenates the outputs of
self._get_block_start,self._get_block_body, andself._get_block_end. Those are the methods to override in the subclasses.
- _get_block_body(indent_lvl)[source]¶
Recursively searches all the key/block attributes build the body by concatenating the outputs of
get_input_stringfor attributes that were changed/touched by the user.
- property value_changed: bool¶
Recursively searches all
Entryattributes to see if any of them hasvalue_changed=True. We consider a key changed if it’s value is changed by the user, even if it is set to the default value. A block is changed when any of its keys or block have their value changed. Used as a condition to include a block in the input string- Returns:
Whether the value of this block is different from the default or touched by the user.
- Return type:
- class EngineBlock[source]¶
Represents engine blocks. Input string will always start with ‘Engine <engine_name>’ and end with ‘EndEngine’
- _get_block_start(indent_lvl)[source]¶
Prefixes the word Engine to the block start line containing the block name
- static _get_engine_class_and_header(header_str)[source]¶
Only used when generating block objects from text input. Separates the engine name from the possible header and looks it up in
scm.input_classes.engine- Parameters:
header_str (str) – Line like
BAND test_headerthat started the engine block in the text input- Raises:
ValueError – When the corresponding engine class can not be found
- Returns:
The Engine class and the possible header
- Return type:
tuple[type[EngineBlock], str | None]
- static _from_input_parser(d)[source]¶
Create an
EngineBlockobject from the output of thescm.libbase.InputParser- Parameters:
d (InputParserEngineBlock) – Dataclass holding the engine block info
- Returns:
EngineBlock object
- Return type:
- comment: Final¶
- unique: Final¶
- gui_name: Final¶
- default: Final¶
- ispath: Final¶
- unit: Final¶
- allow_header: Final¶
- ordered: Final¶
- isatomlist: Final¶
- rootdir: Final¶
- engines: Final¶
- extra_info: Final¶
- gui_type: Final¶
- default_engine: Final¶
- range: Final¶
- _keyword_dict: Final¶
- class DriverBlock[source]¶
Represents the highest level block.
- _get_block_start(indent_lvl)[source]¶
Driver blocks don’t have start line or an end line, simply returns an empty string
- Parameters:
indent_lvl (int) – Indentation level, ignored.
- Returns:
Empty string
- Return type:
Literal[“”]
- _get_block_end(indent_lvl)[source]¶
Driver blocks don’t have start line or an end line, simply returns an empty string
- Parameters:
indent_lvl (int) – Indentation level, ignored.
- Returns:
Empty string
- Return type:
Literal[“”]
- get_input_string(indent_lvl=-1)[source]¶
Generates a valid AMS input string. Note that this method exists for every entry, but generally as user you want to call it on the highest level
DriverBlockinstance, which will recursively include all its entries.
- to_settings()[source]¶
Convert the Block to a PLAMS Settings object. Can be used for Job classes/recipes that don’t support PISA objects. Example:
from scm.input_classes import AMS, DFTB from scm.plams.interfaces.adfsuite.ams import AMSJob from scm.plams.core.settings import Settings ams = AMS() ams.Task = 'SinglePoint' ams.Engine = DFTB() s = Settings() s.input = ams.to_settings() AMSJob(settings=s)
This conversion works via serializing to text and using the libbase InputParser to create a settings object from text. Since this is a bit fragile, only recommended to use this method for backwards compatibility.
- Returns:
Settings object representation of the Block
- Return type:
Settings
- comment: Final¶
- unique: Final¶
- gui_name: Final¶
- default: Final¶
- ispath: Final¶
- unit: Final¶
- allow_header: Final¶
- ordered: Final¶
- isatomlist: Final¶
- rootdir: Final¶
- engines: Final¶
- extra_info: Final¶
- gui_type: Final¶
- default_engine: Final¶
- range: Final¶
- _keyword_dict: Final¶
- class FreeBlock[source]¶
A block that can be assigned a multiline string of an iterable of strings, instead of directly assigning attributes. Will simply result in a series of lines in the input text
- _get_block_body(indent_lvl=0)[source]¶
Simply returns an indented version of the multiline string in
FreeBlock._multiline_string
- set_from_input_dict(input_dict)[source]¶
Called from
Block.from_textafter instantiation of the Block to correctly set the values of the key/block attributes as defined in the text input.- Parameters:
input_dict (dict[str, Any]) – dictionary returned by
scm.libbase.InputParser- Raises:
ValueError – When the text input references an Entry not present in the JSON input definitions, would be caused by faulty text input.
- Return type:
None
- class FixedBlock[source]¶
Standard block with a predefined set of possible keys and blocks.
- comment: Final¶
- unique: Final¶
- gui_name: Final¶
- default: Final¶
- ispath: Final¶
- unit: Final¶
- allow_header: Final¶
- ordered: Final¶
- isatomlist: Final¶
- rootdir: Final¶
- engines: Final¶
- extra_info: Final¶
- gui_type: Final¶
- default_engine: Final¶
- range: Final¶
- _keyword_dict: Final¶
- class InputBlock[source]¶
Identical to the
FreeBlock, but end with EndInput instead of End- comment: Final¶
- unique: Final¶
- gui_name: Final¶
- default: Final¶
- ispath: Final¶
- unit: Final¶
- allow_header: Final¶
- ordered: Final¶
- isatomlist: Final¶
- rootdir: Final¶
- engines: Final¶
- extra_info: Final¶
- gui_type: Final¶
- default_engine: Final¶
- range: Final¶
- _keyword_dict: Final¶
3.2.3. Key Module¶
The following classes represent the different types of keys in the input system. Note that for normal usage, one never needs to instantiate these classes directly. Instead, the autogenerated block classes will have key that attributes that are subclasses of the following classes:
- class Key[source]¶
Base class for all key classes in the input system. Keys are single lines in the text input, with the name of the key, followed by a space, and followed by a string representing the value.
- property val¶
Property representing the key value. Any proposed value will be sent to the abstract method
_convert_val(), which is overwritten in each subclass. Values that cannot be converted to the correct type will be rejected.- Parameters:
value (Any) – Value to set the key with
- _get_single_input_string(indent_lvl=0)[source]¶
This method produces the input string for unique Entries. This is the method that needs to be overwritten to implement specific subclasses, not
get_input_string().
- class FloatKey[source]¶
- class BoolKey[source]¶
- _convert_val(val)[source]¶
Will accept a set of strings and True or False as boolean values. Will not try to convert to
bool, since nearly every python object can be converted to a boolean and passing anything butBoolTyperarely on purpose.- Parameters:
val (BoolType) – value
- Raises:
ValueError – When value is not of type
BoolTypeor a case variation of one of the strings- Returns:
Converted value
- Return type:
- class FloatListKey[source]¶
- class IntListKey[source]¶
- class MultipleChoiceKey[source]¶
- _convert_val(val)[source]¶
Accepts any strings that is equal to (or a case variation of) the list of strings defined in
MultipleChoiceKey.choices.- Parameters:
val (str) – value
- Raises:
ValueError – When val not present in
MultipleChoiceKey.choices- Returns:
Converted value.
- Return type:
- type_hint(k)[source]¶
Provides the proper type hint for key attributes for the autogenerated classes. Keys are type hinted as their actual type, plus the type hint of their value to allow for syntax like:
some_block.some_key = 5
to pass the type hinter, instead of the more cumbersome
some_block.some_key.val = 5
- Parameters:
k (Key) – Key object
- Raises:
NotImplementedError – When providing a key object for which a type hint is not implemented yet.
- Returns:
String describing a type hint
- Return type: