Keywords¶

Links to manual entries¶

ams:

ams_interactive:

Stop	StopProperties

amsbatch:

SystemsFromTrajectory

analysis:

conformers:

pipe:

WorkerCommand

Summary of all keywords¶

ams¶

BondOrders

Type: Block
Description: Configures details regarding the calculation/guessing of bond orders. To request the calculation of bond orders, use the ‘Properties%BondOrders’ key.

Method

Type: Multiple Choice
Default value: EngineWithGuessFallback
Options: [Engine, Guess, EngineWithGuessFallback]
Description: 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.

Constraints

Type: Block
Description: 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.

All

Type: String
Recurring: True
Description: 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

Type: String
Recurring: True
Description: Fix the angle between three atoms. Three atom indices followed by an angle in degrees.

Atom

Type: Integer
Recurring: True
Description: Fix the position of an atom. Just one integer referring to the index of the atom in the [System%Atoms] block.

AtomList

Type: Integer List
Recurring: True
Description: Fix positions of the specified atoms. A list of integers referring to indices of atoms in the [System%Atoms] block.

Block

Type: String
Recurring: True
Description: Name of the region to constrain as a rigid block. Regions are specified in the System%Atoms block.

BlockAtoms

Type: Integer List
Recurring: True
Description: List of atom indices for a block constraint, where the internal degrees of freedom are frozen.

Coordinate

Type: String
Recurring: True
Description: Fix a particular coordinate of an atom. Atom index followed by (x|y|z).

DifDist

Type: String
Recurring: True
Description: 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

Type: String
Recurring: True
Description: Fix the dihedral angle between four atoms. Four atom indices followed by an angle in degrees.

Distance

Type: String
Recurring: True
Description: Fix the distance between two atoms. Two atom indices followed by the distance in Angstrom.

EqualStrain

Type: String
Description: 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

Type: String
Recurring: True
Description: Fix positions of all atoms in a region.

FreezeStrain

Type: String
Description: 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

Type: String
Recurring: True
Description: 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.

ElasticTensor

Type: Block
Description: Options for numerical evaluation of the elastic tensor.

ConvergenceQuality

Type: Multiple Choice
Default value: Good
Options: [Normal, Good, VeryGood]
GUI name: Convergence
Description: 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%Quality keyword.

Parallel

Type: Block
Description: 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.

nCoresPerGroup

Type: Integer
GUI name: Cores per group
Description: Number of cores in each working group.

nGroups

Type: Integer
GUI name: Number of groups
Description: Total number of processor groups. This is the number of tasks that will be executed in parallel.

nNodesPerGroup

Type: Integer
GUI name: Nodes per group
Description: 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.

StrainStepSize

Type: Float
Default value: 0.001
Description: Step size (relative) of strain deformations used for computing the elastic tensor numerically.

Engine

Type: Block
Description: The input for the computational engine. The header of the block determines the type of the engine.

EngineAddons

Type: Block
Description: This block configures all the engine add-ons.

AtomEnergies

Type: Non-standard block
Description: Add an element-dependent energy per atom. On each line, give the chemical element followed by the energy (in atomic units).

D3Dispersion

Type: Block
Description: This block configures the add-on that adds the Grimme D3 dispersion correction to the engine’s energy, gradients, and stress tensor.

Damping

Type: Multiple Choice
Default value: BJ
Options: [BJ, Zero]
Description: Type of damping: BJ (Becke-Johnson) or Zero. BJ is recommended for most applications.

Enabled

Type: Bool
Default value: No
GUI name: D3 dispersion
Description: Enables the D3 dispersion correction addon.

Functional

Type: String
Default value: PBE
Description: 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

Type: Float
Description: The a1 parameter. Only used if Damping is set to BJ. If set, it overwrites the a1 value for the chosen functional.

a2

Type: Float
Description: The a2 parameter. Only used if Damping is set to BJ. If set, it overwrites the a2 value for the chosen functional.

s6

Type: Float
Description: The s6 parameter, global scaling parameter. If set, it overwrites the s6 value for the chosen functional.

s8

Type: Float
Description: The s8 parameter. If set, it overwrites the s8 value for the chosen functional.

sr6

Type: Float
Description: The sr6 parameter. Only used if Damping is set to Zero. If set, it overwrites the sr6 value for the chosen functional.

D4Dispersion

Type: Block
Description: This block configures the addon that adds the Grimme D4(EEQ) dispersion correction to the engine’s energy, gradients, stress tensor and Hessian.

Enabled

Type: Bool
Default value: No
GUI name: D4 dispersion
Description: Enables the D4 dispersion correction addon.

Functional

Type: Multiple Choice
Default value: PBE
Options: [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]
Description: Use the D4 parameterization by Grimme for a given xc-functional.

Verbosity

Type: Multiple Choice
Default value: Silent
Options: [Silent, Normal, Verbose, VeryVerbose]
Description: Controls the verbosity of the dftd4 code. Equivalent to the –silent and –verbose command line switches of the official dftd4 program.

a1

Type: Float
Description: 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

Type: Float
Description: 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

Type: Float
Description: 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

Type: Float
Description: 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

Type: Float
Description: The s9 parameter, see D4 article. If set, it overwrites the s9 value for the chosen functional.

ExternalEngine

Type: Block
Description: External engine as an addon

Execute

Type: String
GUI name: Execute
Description: execute command

ExternalStress

Type: Block
Description: This block configures the addon that adds external stress term to the engine’s energy and stress tensor.

StressTensorVoigt

Type: Float List
Unit: Hartree/Bohr^3
GUI name: External stress tensor
Description: 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

Type: Bool
Default value: No
Description: Whether ot not the reference cell should be updated every time the system changes (see documentation).

PipeEngine

Type: Block
Description: Pipe engine as an addon

WorkerCommand

Type: String
GUI name: Worker command
Description: pipe worker command

Pressure

Type: Float
Default value: 0.0
Unit: GPa
Description: Add a hydrostatic pressure term to the engine’s energy and stress tensor. Can only be used for 3D periodic boundary conditions.

Repulsion

Type: Block
Description: This block configures an addon that adds a repulsive Weeks-Chandler-Andersen potential to all atom pairs.

Enabled

Type: Bool
Default value: No
GUI name: Repulsion
Description: 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

Type: Float
Default value: 0.01
Unit: Hartree
Description: The epsilon parameter in the potential equation. It is equal to the amount of energy added at r=sigma.

HydrogenSigmaScale

Type: Float
Default value: 0.75
Unit: Angstrom
Description: 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

Type: Float
Default value: 0.55
Unit: Angstrom
Description: The sigma parameter in the potential equation. The potential is exactly zero at the distances larger than about 1.12*sigma

SkinLength

Type: Float
Default value: 2.0
Unit: Angstrom
Description: 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.

WallPotential

Type: Block
Description: This block configures the addon that adds a spherical wall potential to the engine’s energy and gradients.

Enabled

Type: Bool
Default value: No
Description: 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

Type: Float
Default value: 10.0
Unit: 1/Angstrom
Description: The radial gradient outside the sphere.

Prefactor

Type: Float
Default value: 0.01
Unit: Hartree
Description: The multiplier for the overall strength of the potential.

Radius

Type: Float
Default value: 30.0
Unit: Angstrom
Value Range: value > 0
Description: The radius of the sphere, wherein the potential is close to zero.

EngineDebugging

Type: Block
Description: This block contains some options useful for debugging the computational engines.

AlwaysClaimSuccess

Type: Bool
Default value: No
Description: If an engine fails, pretend that it worked. This can be useful when you know that an SCF might fail.

CheckInAndOutput

Type: Bool
Default value: No
Description: Enables some additional checks on the input and output of an engine, e.g. for NaN values.

ForceContinousPES

Type: Bool
Default value: No
Description: 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.

IgnoreGradientsRequest

Type: Bool
Default value: No
Description: 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

Type: Bool
Default value: No
Description: 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

Type: Bool
Default value: No
Description: 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

Type: Bool
Default value: No
Description: Makes the engine ignore the request to work quietly.

RandomFailureChance

Type: Float
Default value: 0.0
Description: Makes the engine randomly report failures, even though the results are actually fine. Useful for testing error handling on the application level.

RandomNoiseInEnergy

Type: Float
Default value: 0.0
Unit: Hartree
Description: 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

Type: Float
Default value: 0.0
Unit: Hartree/Angstrom
Description: 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

Type: Float
Default value: 0.0
Description: Makes the engine randomly stop. Can be used to simulate crashes.

EngineRestart

Type: String
Description: 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.

ExitCondition

Type: Block
Recurring: True
Description: If any of the specified exitconditions are met, the AMS driver will exit cleanly.

AtomsTooClose

Type: Block
Description: If any pair of atoms is closer than the specified minimum value, the program will exit cleanly.

MinimumDistance

Type: Float
Default value: 0.7
Unit: Angstrom
Description: Two atoms closer than this threshold value are considered too close.

PairCalculation

Type: Multiple Choice
Default value: NeighborList
Options: [NeighborList, DistanceMatrix]
Description: Two atoms closer than this threshold value are considered too close.

EngineEnergyUncertainty

Type: Block
Description: If the engine reports an uncertainty that is too high, the program will exit cleanly.

MaxUncertainty

Type: Float
Default value: 0.001
Unit: Hartree
Description: Threshold for Engine Energy Uncertainty divided by Normalization (by default the number of atoms)

Normalization

Type: Float
Value Range: value >= 0.0
Description: Divide the reported Engine Energy Uncertainty by this normalization. Will divide by the number of atoms if unset.

EngineGradientsUncertainty

Type: Block
Description: 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.

MaxUncertainty

Type: Float
Default value: 0.01580221
Unit: Hartree/Angstrom
Description: Threshold for Engine Gradients Uncertainty.

Type

Type: Multiple Choice
Default value: AtomsTooClose
Options: [AtomsTooClose, EngineEnergyUncertainty, EngineGradientsUncertainty]
Description: The type of exitcondition specified

FallbackSolveAfterEngineFailure

Type: Bool
Default value: Yes
Description: 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.

GCMC

Type: Block
Description: 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

AccessibleVolume

Type: Float
Default value: 0.0
Description: Volume available to GCMC, in cubic Angstroms. AccessibleVolume should be specified for “Accessible” and “FreeAccessible” [VolumeOption].

Box

Type: Block
Description: 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).

Amax

Type: Float
Description: Coordinate of the upper bound along the first axis.

Amin

Type: Float
Description: Coordinate of the lower bound along the first axis.

Bmax

Type: Float
Description: Coordinate of the upper bound along the second axis.

Bmin

Type: Float
Description: Coordinate of the lower bound along the second axis.

Cmax

Type: Float
Description: Coordinate of the upper bound along the third axis.

Cmin

Type: Float
Description: Coordinate of the lower bound along the third axis.

Ensemble

Type: Multiple Choice
Default value: Mu-VT
Options: [Mu-VT, Mu-PT]
Description: 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.

Iterations

Type: Integer
GUI name: Number of GCMC iterations
Description: Number of GCMC moves.

MapAtomsToOriginalCell

Type: Bool
Default value: Yes
Description: Keeps the atom (mostly) in the original cell by mapping them back before the geometry optimizations.

MaxDistance

Type: Float
Default value: 3.0
Unit: Angstrom
GUI name: Add molecules within
Description: The max distance to other atoms of the system when adding the molecule.

MinDistance

Type: Float
Default value: 0.3
Unit: Angstrom
GUI name: Add molecules not closer than
Description: Keep the minimal distance to other atoms of the system when adding the molecule.

Molecule

Type: Block
Recurring: True
GUI name: Molecules
Description: 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.

ChemicalPotential

Type: Float
Unit: Hartree
Description: 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

Type: Bool
Default value: No
GUI name: Fix molecule
Description: 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

Type: String
GUI name: Molecule
Description: 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.

NonAccessibleVolume

Type: Float
Default value: 0.0
GUI name: Non-accessible volume
Description: Volume not available to GCMC, in cubic Angstroms. NonAccessibleVolume may be specified for the “Free” [VolumeOption] to reduce the accessible volume.

NumAttempts

Type: Integer
Default value: 1000
GUI name: Max tries
Description: 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

Type: Float
Default value: 0.0
Unit: Pascal
Description: 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.

Removables

Type: Non-standard block
Description: 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.

Restart

Type: String
Description: 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.

SwapAtoms

Type: Block
Description: Experimental: Occasionally swap the coordinates of a random pair of atoms from two regions.

Probability

Type: Float
Default value: 0.0
Description: Probability of performing a swap move instead of any other GCMC move in a single GCMC iteration.

Regions

Type: String
Description: Names of two regions to swap between (separated by a space).

Temperature

Type: Float
Default value: 300.0
Unit: Kelvin
Description: Temperature of the simulation. Increase the temperature to improve the chance of accepting steps that result in a higher energy.

UseGCPreFactor

Type: Bool
Default value: Yes
GUI name: Use GC prefactor
Description: Use the GC pre-exponential factor for probability.

VolumeChangeMax

Type: Float
Default value: 0.05
Description: 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

Type: Multiple Choice
Default value: Free
Options: [Free, Total, Accessible, FreeAccessible]
GUI name: Volume method
Description: 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.

GeometryOptimization

Type: Block
Description: Configures details of the geometry optimization and transition state searches.

CalcPropertiesOnlyIfConverged

Type: Bool
Default value: Yes
Description: 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.

Convergence

Type: Block
Description: 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.

Energy

Type: Float
Default value: 1e-05
Unit: Hartree
Value Range: value > 0
GUI name: Energy convergence
Description: 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

Type: Float
Default value: 0.001
Unit: Hartree/Angstrom
Value Range: value > 0
GUI name: Gradient convergence
Description: Threshold for nuclear gradients.

Quality

Type: Multiple Choice
Default value: Custom
Options: [VeryBasic, Basic, Normal, Good, VeryGood, Custom]
GUI name: Convergence
Description: 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

Type: Float
Default value: 0.01
Unit: Angstrom
Value Range: value > 0
GUI name: Step convergence
Description: The maximum Cartesian step allowed for a converged geometry.

StressEnergyPerAtom

Type: Float
Default value: 0.0005
Unit: Hartree
Value Range: value > 0
Description: 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).

CoordinateType

Type: Multiple Choice
Default value: Auto
Options: [Auto, Delocalized, Cartesian]
GUI name: Optimization space
Description: 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.

Dimer

Type: Block
Description: Options for the Dimer method for transition state search.

AngleThreshold

Type: Float
Default value: 1.0
Unit: Degree
Description: The rotation is considered converged when the the rotation angle falls below the specified threshold.

DimerDelta

Type: Float
Default value: 0.01
Unit: Angstrom
Description: Euclidian distance between the midpoint and the endpoint.

ExtrapolateForces

Type: Bool
Default value: Yes
Description: Set to false to call engine to calculate forces at the extrapolated rotation angle instead of extrapolating them.

LBFGSMaxVectors

Type: Integer
Default value: 10
Description: Max number of vectors for the L-BFGS algorithm to save.

MaxRotationIterations

Type: Integer
Default value: 10
Description: Maximum number of rotation iterations for a single translation step.

Region

Type: String
Default value: *
Description: Include only atoms of the specified region(s) in the rotations, which allows searching for a transition state involving selected atoms only.

RotationTrustRadius

Type: Float
Default value: 0.1
Unit: Angstrom
Description: L-BFGS trust radius during rotation iterations.

TranslationTrustRadius

Type: Float
Default value: 0.1
Unit: Angstrom
Description: L-BFGS trust radius during translation iterations.

EngineAutomations

Type: Block
Description: 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.

Enabled

Type: Bool
Default value: Yes
Description: Whether or not automations are enabled at all.

Gradient

Type: Block
Recurring: True
Description: A gradient-based automation.

FinalValue

Type: Float
Description: This value will be used whenever the gradient is less than GradientLow

HighGradient

Type: Float
Default value: 1.0
Unit: Hartree/Angstrom
Description: 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

Type: Float
Description: This value will be used at the first geometry, and whenever the gradient is higher than GradientHigh

LowGradient

Type: Float
Default value: 1.0
Unit: Hartree/Angstrom
Description: Defines a small gradient, see GradientHigh

UseLogInterpolation

Type: Bool
Default value: Yes
Description: Whether to use interpolation on a log (y) scale or not

Variable

Type: String
Default value
Description: variable to be tweaked for the engine.

Iteration

Type: Block
Recurring: True
Description: Geometry step based automation.

FinalValue

Type: Float
Description

FirstIteration

Type: Integer
Default value: 1
Description: When the actual gradient is between the first and last iteration, a linear interpolation is used.

InitialValue

Type: Float
Description: This value will be used when the iteration number is smaller or equal to FirstIteration

LastIteration

Type: Integer
Default value: 10
Description: Where the automation should reach the FinalValue

UseLogInterpolation

Type: Bool
Default value: Yes
Description: Whether to use interpolation on a log (y) scale or not

Variable

Type: String
Default value
Description: variable to be tweaked for the engine.

FIRE

Type: Block
Description: 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).

AllowOverallRotation

Type: Bool
Default value: Yes
Description: 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

Type: Bool
Default value: No
Description: 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

Type: Bool
Default value: No
Description: Map the atoms to the central cell at each geometry step.

NMin

Type: Integer
Default value: 5
Description: Number of steps after stopping before increasing the time step again.

alphaStart

Type: Float
Default value: 0.1
Description: Steering coefficient.

dtMax

Type: Float
Default value: 1.0
Unit: Femtoseconds
Description: Maximum time step used for the integration. For ReaxFF and APPLE&P, this value is reduced by 50%.

dtStart

Type: Float
Default value: 0.25
Unit: Femtoseconds
Description: Initial time step for the integration.

fAlpha

Type: Float
Default value: 0.99
Description: Reduction factor for the steering coefficient.

fDec

Type: Float
Default value: 0.5
Description: Reduction factor for reducing the time step in case of uphill movement.

fInc

Type: Float
Default value: 1.1
Description: Growth factor for the integration time step.

strainMass

Type: Float
Default value: 0.5
Description: 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.

HessianFree

Type: Block
Description: Configures details of the Hessian-free (conjugate gradients or L-BFGS) geometry optimizer.

Step

Type: Block
Description

MaxCartesianStep

Type: Float
Default value: 0.1
Unit: Angstrom
Description: Limit on a single Cartesian component of the step.

MinRadius

Type: Float
Default value: 0.0
Unit: Angstrom
Description: Minimum value for the trust radius.

TrialStep

Type: Float
Default value: 0.0005
Unit: Angstrom
Description: Length of the finite-difference step when determining curvature. Should be smaller than the step convergence criterion.

TrustRadius

Type: Float
Default value: 0.2
Unit: Angstrom
Description: Initial value of the trust radius.

InitialHessian

Type: Block
Description: Options for initial model Hessian when optimizing systems with the Quasi-Newton method.

File

Type: String
GUI name: Initial Hessian from
Description: 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

Type: Multiple Choice
Default value: Auto
Options: [Auto, UnitMatrix, Swart, FromFile, Calculate, CalculateWithFastEngine]
GUI name: Initial Hessian
Description: 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.

KeepIntermediateResults

Type: Bool
Default value: No
Description: 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

Type: Integer
Value Range: value >= 0
GUI name: Maximum number of iterations
Description: The maximum number of geometry iterations allowed to converge to the desired structure.

MaxRestarts

Type: Integer
Default value: 0
Description: 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

Type: Multiple Choice
Default value: Auto
Options: [Auto, Quasi-Newton, FIRE, L-BFGS, ConjugateGradients, Dimer]
GUI name: Optimization method
Description: 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

Type: Bool
Default value: No
Description: Whether to also optimize the lattice for periodic structures. This is currently supported with the Quasi-Newton, FIRE, and L-BFGS optimizers.

PretendConverged

Type: Bool
Default value: No
Description: 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.)

Quasi-Newton

Type: Block
Description: Configures details of the Quasi-Newton geometry optimizer.

MaxGDIISVectors

Type: Integer
Default value: 0
Description: Sets the maximum number of GDIIS vectors. Setting this to a number >0 enables the GDIIS method.

Step

Type: Block
Description

TrustRadius

Type: Float
Description: Initial value of the trust radius.

VaryTrustRadius

Type: Bool
Description: Whether to allow the trust radius to change during optimization. By default True during energy minimization and False during transition state search.

UpdateTSVectorEveryStep

Type: Bool
Default value: Yes
GUI name: Update TSRC vector every step
Description: Whether to update the TS reaction coordinate at each step with the current eigenvector.

RestartDisplacement

Type: Float
Default value: 0.05
Unit: Angstrom
Description: 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.

IRC

Type: Block
Description: Configures details of the Intrinsic Reaction Coordinate optimization.

Convergence

Type: Block
Description: 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.

Gradients

Type: Float
Default value: 0.001
Unit: Hartree/Angstrom
GUI name: Gradient convergence
Description: Convergence criterion for the max component of the residual energy gradient.

Step

Type: Float
Default value: 0.001
Unit: Angstrom
GUI name: Step convergence
Description: Convergence criterion for the max component of the step in the optimization coordinates.

CoordinateType

Type: Multiple Choice
Default value: Cartesian
Options: [Cartesian, Delocalized]
GUI name: Coordinates used for optimization
Description: Select the type of coordinates in which to perform the optimization. Note that the Delocalized option should be considered experimental.

Direction

Type: Multiple Choice
Default value: Both
Options: [Both, Forward, Backward]
Description: 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.

InitialHessian

Type: Block
Description: 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.

File

Type: String
GUI name: File
Description: 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

Type: Multiple Choice
Default value: Calculate
Options: [Calculate, FromFile]
GUI name: Initial Hessian
Description: Calculate the exact Hessian for the input geometry or load it from the results of a previous calculation.

KeepConvergedResults

Type: Bool
Default value: Yes
Description: 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

Type: Integer
GUI name: Maximum IRC steps
Description: 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

Type: Integer
Default value: 300
GUI name: Maximum iterations
Description: 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

Type: Integer
Default value: 100
GUI name: Maximum points
Description: 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

Type: Bool
Default value: No
GUI name: Minimum energy profile
Description: Calculate minimum energy profile (i.e. no mass-weighting) instead of the IRC.

MinPathLength

Type: Float
Default value: 0.1
Unit: Angstrom
Description: Minimum length of the path required before switching to energy minimization. Use this to overcome a small kink or a shoulder on the path.

Restart

Type: Block
Description: 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.

File

Type: String
GUI name: Restart
Description: 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

Type: Integer
Default value: 0
Description: 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

Type: Integer
Default value: 0
Description: 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.

Step

Type: Float
Default value: 0.2
GUI name: Step size
Description: 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.

LoadEngine

Type: String
Description: The path to the file from which to load the engine configuration. Replaces the Engine block.

LoadSystem

Type: Block
Recurring: True
Description: Block that controls reading the chemical system from a KF file instead of the [System] block.

File

Type: String
Description: The path of the KF file from which to load the system. It may also be the results directory containing it.

Section

Type: String
Default value: Molecule
Description: The section on the KF file from which to load the system.

Log

Type: Non-standard block
Description: Configures the debugging loggers. Syntax: ‘Level LoggerName’. Possible Levels: All, Debug, Info, Warning, Error, Fatal.

MolecularDynamics

Type: Block
Description: Configures molecular dynamics (with the velocity-Verlet algorithm) with and without thermostats. This block allows to specify the details of the molecular dynamics calculation.

AddMolecules

Type: Block
Recurring: True
GUI name: Add molecules
Description: 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.

AtomTemperature

Type: Float
Default value: 0.0
Unit: Kelvin
Description: 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

Type: Float
Default value: 0.0
Unit: Angstrom
Description: Translate the bullet along the velocity vector until it comes within ContactDistance of any other atom.

Coords

Type: Float List
Unit: Angstrom
Description: 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

Type: Float List
Unit: Angstrom
Description: 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

Type: Float List
Unit: Angstrom
Description: Sigma values (one per Cartesian axis) for a Gauss distribution of the initial coordinates. Can only be used together with Coords.

DeviationAngle

Type: Float
Default value: 0.0
Unit: Degree
Description: Randomly tilt the shooting direction up to this angle away from the VelocityDirection vector.

Energy

Type: Float
Unit: Hartree
Description: Initial kinetic energy of the molecule in the shooting direction.

EnergySigma

Type: Float
Default value: 0.0
Unit: Hartree
Description: Sigma value for the Gauss distribution of the initial kinetic energy around the specified value. Should only be used together with Energy.

FractionalCoords

Type: Float List
Description: 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

Type: Float List
Description: 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

Type: Float List
Description: 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.

Frequency

Type: Integer
Default value: 0
Description: A molecule is added every [Frequency] steps after the StartStep. There is never a molecule added at step 0.

MinDistance

Type: Float
Default value: 0.0
Unit: Angstrom
Description: Keep the minimal distance to other atoms of the system when adding the molecule.

MoleFraction

Type: Float
Description: 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

Type: Integer
Default value: 10
Description: 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

Type: Bool
Default value: No
Description: Rotate the molecule randomly before adding it to the system.

StartStep

Type: Integer
Default value: 0
Description: 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

Type: Integer
Description: Do not add this molecule after the specified step.

System

Type: String
Description: 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

Type: Float
Unit: Kelvin
Description: Initial energy of the molecule in the shooting direction will correspond to the given temperature.

TemperatureSigma

Type: Float
Default value: 0.0
Unit: Kelvin
Description: Sigma value for the Gauss distribution of the initial temperature the specified value. Should only be used together with Temperature.

Velocity

Type: Float
Unit: Angstrom/fs
Description: Initial velocity of the molecule in the shooting direction.

VelocityDirection

Type: Float List
Description: 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

Type: Float
Default value: 0.0
Unit: Angstrom/fs
Description: Sigma value for the Gauss distribution of the initial velocity around the specified value. Should only be used together with Velocity.

ApplyForce

Type: Block
Recurring: True
Description: The ApplyForce keyword can be used to apply an arbitrary constant force to a certain (subgroups of) atoms in the system

Force

Type: Float List
Default value: [0.0, 0.0, 0.0]
Unit: Hartree/Bohr
Description: Defines the constant force vector

PerAtom

Type: Bool
Default value: No
Description: 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

Type: String
Recurring: True
Description: Apply the constant force to all atoms in this region.

ApplyVelocity

Type: Block
Recurring: True
Description: The ApplyVelocity keyword can be used to move an arbitrary group of atoms in the system with a constant net velocity

Components

Type: Multiple Choice
Default value: XY
Options: [X, Y, Z, XY, YZ, XZ, XYZ]
Description: 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

Type: String
Recurring: True
Description: Applies the defined velocity to all atoms in this region.

Velocity

Type: Float List
Default value: [0.0, 0.0, 0.0]
Unit: Angstrom/fs
Recurring: False
Description: The constant velocity that will be applied to the specified atoms.

Barostat

Type: Block
Description: This block allows to specify the use of a barostat during the simulation.

BulkModulus

Type: Float
Default value: 2200000000.0
Unit: Pascal
Description: 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

Type: Bool
Default value: No
Description: Keep the volume constant while allowing the box shape to change. This is currently supported only by the MTK barostat.

Duration

Type: Integer List
Description: Specifies how many steps should a transition from a particular pressure to the next one in sequence take.

Equal

Type: Multiple Choice
Default value: None
Options: [None, XYZ, XY, YZ, XZ]
Description: 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

Type: Float List
Unit: Pascal
Description: 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

Type: Multiple Choice
Default value: XYZ
Options: [XYZ, Shape, X, Y, Z, XY, YZ, XZ]
Description: 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

Type: Float
Unit: Femtoseconds
GUI name: Damping constant
Description: Specifies the time constant of the barostat.

Type

Type: Multiple Choice
Default value: None
Options: [None, Berendsen, MTK]
GUI name: Barostat
Description: Selects the type of the barostat.

BinLog

Type: Block
Description: 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.

BiasEnergy

Type: Bool
Default value: No
Description: Write the CVDH bias energy.

BoostFactor

Type: Bool
Default value: No
Description: Write the CVDH boost factor.

ConservedEnergy

Type: Bool
Default value: No
Description: Write the conserved energy value.

Density

Type: Bool
Default value: No
Description: Write the density.

DipoleMoment

Type: Bool
Default value: No
Description: Write the dipole moment. Each component of the tensor is written in its own variable.

Hypertime

Type: Bool
Default value: No
Description: Write the CVDH hypertime.

KineticEnergy

Type: Bool
Default value: No
Description: Write the kinetic energy value.

MaxBiasEnergy

Type: Bool
Default value: No
Description: Write the max CVDH bias energy.

MaxBoostFactor

Type: Bool
Default value: No
Description: Write the max CVDH boost factor.

PotentialEnergy

Type: Bool
Default value: No
Description: Write the potential energy value.

Pressure

Type: Bool
Default value: No
Description: Write the pressure.

PressureTensor

Type: Bool
Default value: No
Description: Write the pressure tensor in Voigt notation. Each component of the tensor is written in its own variable.

Step

Type: Bool
Default value: No
Description: Write the step index during the simulation.

Temperature

Type: Bool
Default value: No
Description: Write the temperature.

Time

Type: Bool
Default value: No
Description: Write the simulation time (fs).

TotalEnergy

Type: Bool
Default value: No
Description: Write the total energy value.

Volume

Type: Bool
Default value: No
Description: Write the simulation cell volume, area or length, depending on the system periodicity.

BondBoost

Type: Block
Recurring: True
Description: Forced reaction (bond boost) definitions. Multiple BondBoost blocks may be specified, which will be treated independently.

Chain

Type: Block
Description: 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.

AtomNames

Type: String
Description: 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

Type: Float List
Unit: Angstrom
Description: Maximum distances for each pair of atoms in the chain. The number of distances must be one less than the number of AtomNames.

MinDistances

Type: Float List
Unit: Angstrom
Description: Minimum distances for each pair of atoms in the chain. The number of distances must be one less than the number of AtomNames.

DistanceRestraint

Type: String
Recurring: True
Description: Specify two atom indices followed by the optimum distance in Angstrom, the first parameter and, optionally, the profile type and the second parameter. 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. 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 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

Type: Bool
Default value: No
GUI name: Move restraint
Description: 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

Type: Integer
GUI name: Boost lifetime
Description: 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

Type: Integer
Default value: 1
GUI name: Number of instances
Description: Number of reactions of this type taking place simultaneously.

Units

Type: Multiple Choice
Default value: Default
Options: [Default, MD]
GUI name: Restr. parameter units
Description: 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.

CRESTMTD

Type: Block
GUI name: CREST_MTD
Description: Input for CREST metadynamics simulation.

AddEnergy

Type: Bool
Default value: No
Description: Add the bias energy to the potential energy (to match the gradients)

GaussianScaling

Type: Block
Description: Options for gradual introduction of the Gaussians

ScaleGaussians

Type: Bool
Default value: Yes
Description: Introduce the Gaussians gradually, using a scaling function

ScalingSlope

Type: Float
Default value: 0.03
Description: Slope of the scaling function for the Gaussians with respect to time

Height

Type: Float
Unit: Hartree
Description: The height of the Gaussians added

NGaussiansMax

Type: Integer
Description: Maximum number of Gaussians stored

NSteps

Type: Integer
Description: Interval of Gaussian placement

Region

Type: String
Default value: *
Description: Restrict the range of atoms for RMSD calculation to the specified region.

RestartFile

Type: String
Description: Filename for file from which to read data on Gaussians placed previously.

Width

Type: Float
Unit: Bohr
Description: The width of the Gaussians added in terms of the RMSD

CVHD

Type: Block
Recurring: True
GUI name: CVHD
Description: Input for the Collective Variable-driven HyperDynamics (CVHD).

Bias

Type: Block
Description: 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).

DampingTemp

Type: Float
Default value: 0.0
Unit: Kelvin
GUI name: Bias damping T
Description: 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

Type: Float
Description: Standard deviation parameter of the Gaussian bias peak.

Height

Type: Float
Unit: Hartree
Description: Height of the Gaussian bias peak.

ColVarBB

Type: Block
Recurring: True
GUI name: Collective Variable
Description: 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.

at1

Type: Block
Description: Specifies the first bonded atom in the collective variable.

region

Type: String
Default value: *
Description: Restrict the selection of bonded atoms to a specific region. If this is not set, atoms anywhere in the system will be selected.

symbol

Type: String
Description: 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.

at2

Type: Block
Description: Specifies the second bonded atom in the collective variable.

region

Type: String
Default value: *
Description: Restrict the selection of bonded atoms to a specific region. If this is not set, atoms anywhere in the system will be selected.

symbol

Type: String
Description: 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.

cutoff

Type: Float
Default value: 0.3
GUI name: Bond order cutoff
Description: 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

Type: Integer
Default value: 6
GUI name: Exponent p
Description: Exponent value p used to calculate the p-norm for this CV.

rmax

Type: Float
Unit: Angstrom
GUI name: R max
Description: Max bond distance parameter Rmax used for calculating the CV. It should be close to the transition-state distance for the corresponding bond.

rmin

Type: Float
Unit: Angstrom
GUI name: R min
Description: Min bond distance parameter Rmin used for calculating the CV. It should be close to equilibrium distance for the corresponding bond.

ColVarBM

Type: Block
Recurring: True
GUI name: Collective Variable
Description: Description of a bond-making collective variable (CV). A collective variable may consist of multiple ColVar blocks.

at1

Type: Block
Description: Specifies selection criteria for the first atom of a pair in the collective variable.

region

Type: String
Default value: *
Description: Restrict the selection to a specific region. If this is not set, atoms anywhere in the system will be selected.

symbol

Type: String
Description: 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.

at2

Type: Block
Description: Specifies selection criteria for the second atom of a pair in the collective variable.

region

Type: String
Default value: *
Description: Restrict the selection to a specific region. If this is not set, atoms anywhere in the system will be selected.

symbol

Type: String
Description: 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.

cutoff

Type: Float
Default value: 0.3
GUI name: Bond order cutoff
Description: 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

Type: Integer
Default value: 6
GUI name: Exponent p
Description: Exponent value p used to calculate the p-norm for this CV.

rmax

Type: Float
Unit: Angstrom
GUI name: R max
Description: Max bond distance parameter Rmax used for calculating the CV. It should be much larger than the corresponding Rmin.

rmin

Type: Float
Unit: Angstrom
GUI name: R min
Description: Min bond distance parameter Rmin used for calculating the CV. It should be close to the transition-state distance for the corresponding bond.

Frequency

Type: Integer
Description: 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

Type: Integer
Default value: 0
Description: Max number of events to allow during dynamics. When this number is reached no new bias will be added for this input block.

StartStep

Type: Integer
Description: 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

Type: Integer
Description: 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

Type: Integer
Description: 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.

CalcPressure

Type: Bool
Default value: No
GUI name: Calculate pressure
Description: 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.

Checkpoint

Type: Block
Description: Sets the frequency for storing the entire MD state necessary for restarting the calculation.

Frequency

Type: Integer
Default value: 1000
GUI name: Checkpoint frequency
Description: Write the MD state and engine-specific data to the respective .rkf files once every N steps.

WriteProperties

Type: Bool
Default value: No
Description: Write the properties from the properties section to the ChecoPoint file once every N steps.

CopyRestartTrajectory

Type: Bool
Default value: No
Description: If the keyword Restart is present, the content of the restartfile is copied to the ams.rkf file.

CosineShear

Type: Block
Description: 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.

Acceleration

Type: Float
Default value: 5e-06
Unit: Angstrom/fs^2
Description: 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

Type: Bool
Default value: No
GUI name: Enable cosine shear
Description: Apply a cosine shear acceleration profile for a NEMD calculation of viscosity.

FlowDirection

Type: Float List
Default value: [1.0, 0.0, 0.0]
Description: 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

Type: Multiple Choice
Default value: Z
Options: [X, Y, Z]
Description: The Cartesian coordinate axis along which the cosine wave runs

Deformation

Type: Block
Recurring: True
Description: Deform the periodic lattice of the system during the simulation.

LatticeVelocity

Type: Non-standard block
Description: 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).

LengthRate

Type: Float List
Default value: [0.0, 0.0, 0.0]
Description: Relative rate of change of each lattice vector per step.

LengthVelocity

Type: Float List
Default value: [0.0, 0.0, 0.0]
Unit: Angstrom/fs
Description: 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

Type: Float
Unit: Femtoseconds
Description: Period of oscillation for Type Sine and Cosine.

ScaleAtoms

Type: Bool
Default value: Yes
Description: Scale the atomic positions together with the lattice vectors. Disable this to deform only the lattice, keeping the coordinates of atoms unchanged.

StartStep

Type: Integer
Default value: 1
Description: First step at which the deformation will be applied.

StopStep

Type: Integer
Default value: 0
Description: Last step at which the deformation will be applied. If unset or zero, nSteps will be used instead.

StrainRate

Type: Non-standard block
Description: Strain rate matrix to be applied on every step. The format is identical to the System%Lattice block.

TargetLattice

Type: Non-standard block
Description: Target lattice vectors to be achieved by StopStep. The format is identical to the System%Lattice block.

TargetLength

Type: Float List
Default value: [0.0, 0.0, 0.0]
Unit: Angstrom
Description: 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

Type: Multiple Choice
Default value: Linear
Options: [Linear, Exponential, Sine, Cosine]
Description: 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.

Gravity

Type: Block
Description: Apply a constant acceleration in -z.

Acceleration

Type: Float
Default value: 0.0
Unit: Angstrom/fs^2
Description: Magnitude of the applied acceleration.

HeatExchange

Type: Block
Recurring: True
GUI name: Heat exchange
Description: Input for the heat-exchange non-equilibrium MD (T-NEMD).

HeatingRate

Type: Float
Unit: Hartree/fs
Description: 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

Type: Multiple Choice
Default value: Simple
Options: [Simple, HEX, eHEX]
Description: 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).

Sink

Type: Block
Description: Defines the heat sink region (where the heat will be removed).

AtomList

Type: Integer List
GUI name: Sink region
Description: The atoms that are part of the sink. This key is ignored if the [Box] block or [Region] key is present.

Box

Type: Block
Description: 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.

Amax

Type: Float
Default value: 1.0
Description: Coordinate of the upper bound along the first axis.

Amin

Type: Float
Default value: 0.0
Description: Coordinate of the lower bound along the first axis.

Bmax

Type: Float
Default value: 1.0
Description: Coordinate of the upper bound along the second axis.

Bmin

Type: Float
Default value: 0.0
Description: Coordinate of the lower bound along the second axis.

Cmax

Type: Float
Default value: 1.0
Description: Coordinate of the upper bound along the third axis.

Cmin

Type: Float
Default value: 0.0
Description: Coordinate of the lower bound along the third axis.

Region

Type: String
GUI name: Sink region
Description: The region that is the sink. This key is ignored if the [Box] block is present.

Source

Type: Block
Description: Defines the heat source region (where the heat will be added).

AtomList

Type: Integer List
GUI name: Source region
Description: The atoms that are part of the source. This key is ignored if the [Box] block or [Region] key is present.

Box

Type: Block
Description: 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.

Amax

Type: Float
Default value: 1.0
Description: Coordinate of the upper bound along the first axis.

Amin

Type: Float
Default value: 0.0
Description: Coordinate of the lower bound along the first axis.

Bmax

Type: Float
Default value: 1.0
Description: Coordinate of the upper bound along the second axis.

Bmin

Type: Float
Default value: 0.0
Description: Coordinate of the lower bound along the second axis.

Cmax

Type: Float
Default value: 1.0
Description: Coordinate of the upper bound along the third axis.

Cmin

Type: Float
Default value: 0.0
Description: Coordinate of the lower bound along the third axis.

Region

Type: String
GUI name: Source region
Description: The region that is the source. This key is ignored if the [Box] block is present.

StartStep

Type: Integer
Default value: 0
Description: Index of the MD step at which the heat exchange will start.

StopStep

Type: Integer
Description: Index of the MD step at which the heat exchange will stop.

InitialVelocities

Type: Block
Description: Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.

File

Type: String
Description: AMS RKF file containing the initial velocities.

RandomVelocitiesMethod

Type: Multiple Choice
Default value: Exact
Options: [Exact, Boltzmann, Gromacs]
GUI name: Velocity randomization method
Description: 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

Type: Float
Unit: Kelvin
GUI name: Initial temperature
Description: 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

Type: Multiple Choice
Default value: Random
Options: [Zero, Random, FromFile, Input]
GUI name: Initial velocities
Description: 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

Type: Non-standard block
Description: 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.

MovingRestraints

Type: Block
Recurring: True
Description: Define a set of moving restraints.

Change

Type: Multiple Choice
Default value: Linear
Options: [Linear, Sine, Cosine]
GUI name: Move type
Description: 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.

Distance

Type: Block
Recurring: True
Description: Define a distance restraint between pair of atoms. For linear-type

Atom1

Type: Integer
Description: First atom of the distance restraint.

Atom2

Type: Integer
Description: Second atom of the distance restraint.

EndValue

Type: Float
Unit: Angstrom
Description: Linear: final target distance. Sine: target distance at 1/4 of the period. Cosine: target distance at 1/2 of the period.

StartValue

Type: Float
Unit: Angstrom
Description: Initial target distance.

Erf

Type: Block
Description: 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.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
GUI name: Erf force constant
Description: The force constant (second derivative of the potential) at the optimum point.

MaxForce

Type: Float
Default value: 0.05
Unit: Hartree/Bohr
GUI name: Erf F(Inf)
Description: Asymptotic value of the force at the infinity.

GaussianWell

Type: Block
Description: Define parameters in the Gaussian well restraint potential V=-WellDepth*exp(-Sigma*(r-r0)^2).

Sigma

Type: Float
Default value: 1.0
Unit: 1/Bohr^2
GUI name: Gaussian well sigma
Description: Sigma parameter in the potential expression.

WellDepth

Type: Float
Default value: 1.0
Unit: Hartree
GUI name: Gaussian well depth
Description: WellDepth parameter in the potential expression.

Harmonic

Type: Block
Description: Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
GUI name: Harmonic force constant
Description: The FC parameter of the harmonic potential.

Hyperbolic

Type: Block
Description: 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

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
GUI name: Hyperbolic force constant
Description: The force constant (second derivative of the potential) at the optimum point.

MaxForce

Type: Float
Default value: 0.05
Unit: Hartree/Bohr
GUI name: Hyperbolic F(Inf)
Description: Asymptotic value of the force at the infinity.

Name

Type: String
GUI name: Name
Description: Optional name to be used for plotting.

Period

Type: Float
Default value: 0.0
Unit: Femtoseconds
Description: Period of oscillation for Sine and Cosine change types.

RestraintType

Type: Multiple Choice
Default value: None
Options: [None, Harmonic, Hyperbolic, Erf, GaussianWell]
GUI name: Restraint type
Description: 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

Type: Integer
Default value: 1
GUI name: Start step
Description: First step number at which the restraints will be applied.

StopStep

Type: Integer
Default value: 0
GUI name: End step
Description: Last step number at which the restraints will be applied.

NSteps

Type: Integer
Default value: 1000
GUI name: Number of steps
Description: The number of steps to be taken in the MD simulation.

Plumed

Type: Block
Description: Input for PLUMED. The parallel option is still experimental.

Input

Type: Non-standard block
Description: Input for PLUMED. Contents of this block is passed to PLUMED as is.

Parallel

Type: Block
Description: 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.

nCoresPerGroup

Type: Integer
GUI name: Cores per group
Description: Number of cores in each working group.

nGroups

Type: Integer
GUI name: Number of groups
Description: Total number of processor groups. This is the number of tasks that will be executed in parallel.

nNodesPerGroup

Type: Integer
GUI name: Nodes per group
Description: 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.

Preserve

Type: Block
Description: Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.

AngularMomentum

Type: Bool
Default value: Yes
GUI name: : Angular momentum
Description: 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

Type: Bool
Default value: No
GUI name: : Center of mass
Description: Translate the system to keep its center of mass at the coordinate origin. This option is not very useful for 3D-periodic systems.

Momentum

Type: Bool
Default value: Yes
GUI name: Preserve: Total momentum
Description: 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).

Print

Type: Block
Description: This block controls the printing of additional information to stdout.

System

Type: Bool
Default value: No
Description: Print the chemical system before and after the simulation.

Velocities

Type: Bool
Default value: No
Description: Print the atomic velocities before and after the simulation.

ReactionBoost

Type: Block
GUI name: Reaction Boost
Description: 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.

BondBreakingRestraints

Type: Block
Description: 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.

Erf

Type: Block
Description: 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.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The force constant (second derivative of the potential) at the optimum point.

MaxForce

Type: Float
Default value: 0.05
Unit: Hartree/Bohr
Description: Asymptotic value of the force at the infinity.

GaussianWell

Type: Block
Description: Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).

Sigma

Type: Float
Default value: 1.0
Unit: 1/Bohr^2
Description: Sigma parameter in the potential expression.

WellDepth

Type: Float
Default value: 1.0
Unit: Hartree
Description: WellDepth parameter in the potential expression.

Harmonic

Type: Block
Description: Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The FC parameter of the harmonic potential.

Hyperbolic

Type: Block
Description: 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

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The force constant (second derivative of the potential) at the optimum point.

MaxForce

Type: Float
Default value: 0.05
Unit: Hartree/Bohr
Description: Asymptotic value of the force at the infinity.

Taper

Type: Block
Description

Enabled

Type: Bool
Default value: No
GUI name: Tapering
Description: 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

Type: Float
Default value: 0.0
Unit: Angstrom
GUI name: End tapering at
Description: Bond length at which the restraint potential and force decays to zero.

MinDistance

Type: Float
Default value: 0.0
Unit: Angstrom
GUI name: Start tapering at
Description: Bond length at which the restraint potential and force will start decaying to zero.

Type

Type: Multiple Choice
Default value: Erf
Options: [None, Harmonic, Hyperbolic, Erf, GaussianWell]
GUI name: Bond breaking restraints
Description: 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 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.

BondMakingRestraints

Type: Block
Description: 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.

Erf

Type: Block
Description: 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.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The force constant (second derivative of the potential) at the optimum point.

MaxForce

Type: Float
Default value: 0.05
Unit: Hartree/Bohr
Description: Asymptotic value of the force at the infinity.

GaussianWell

Type: Block
Description: Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).

Sigma

Type: Float
Default value: 1.0
Unit: 1/Bohr^2
Description: Sigma parameter in the potential expression.

WellDepth

Type: Float
Default value: 1.0
Unit: Hartree
Description: WellDepth parameter in the potential expression.

Harmonic

Type: Block
Description: Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The FC parameter of the harmonic potential.

Hyperbolic

Type: Block
Description: 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

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The force constant (second derivative of the potential) at the optimum point.

MaxForce

Type: Float
Default value: 0.05
Unit: Hartree/Bohr
Description: Asymptotic value of the force at the infinity.

Type

Type: Multiple Choice
Default value: Erf
Options: [None, Harmonic, Hyperbolic, Erf, GaussianWell]
GUI name: Bond making restraints
Description: 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.

BondedRestraints

Type: Block
Description: 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.

Harmonic

Type: Block
Description: Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The FC parameter of the harmonic potential.

Type

Type: Multiple Choice
Default value: None
Options: [None, Harmonic]
GUI name: Bonded restraints
Description: 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.

Change

Type: Multiple Choice
Default value: TargetCoordinate
Options: [TargetCoordinate, Force, LogForce]
GUI name: Move type
Description: 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

Type: Float
Default value: 0.0
Description: 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

Type: Integer
Default value: 0
Description: Number of equilibration steps after reaching a target before setting up restraints for the next one.

MinBondChange

Type: Float
Default value: 1.0
Unit: Bohr
Description: Minimal change in the distance for an individual restraint to be considered bond-breaking/making vs bonded.

MinBondStrength

Type: Float
Default value: 0.5
Description: Minimum strength (usually ranges from 0 to 1) for a bond to be considered.

NSteps

Type: Integer
Default value: 500
GUI name: Steps per target
Description: Number of steps per target the restraints should be active for.

NonBondedRestraints

Type: Block
Description: 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

Exponential

Type: Block
Description: Define parameters for the repulsive potential V=Epsilon*exp(-Sigma*r).

Epsilon

Type: Float
Default value: 1.0
Unit: Hartree
Description: Epsilon parameter in the repulsive potential expression.

Sigma

Type: Float
Default value: 1.0
Unit: 1/Bohr
Description: Sigma parameter in the repulsive potential expression.

Type

Type: Multiple Choice
Default value: None
Options: [None, Exponential]
GUI name: Non-bonded restraints
Description: 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.

PreEquilibrationSteps

Type: Integer
Default value: 0
Description: Number of steps before enabling the first set of restraints.

RMSDRestraint

Type: Block
GUI name: RMSD restraint
Description: 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.

Erf

Type: Block
Description: 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.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The force constant (second derivative of the potential) at the optimum point.

MaxForce

Type: Float
Default value: 0.05
Unit: Hartree/Bohr
Description: Asymptotic value of the force at the infinity.

GaussianWell

Type: Block
Description: Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).

Sigma

Type: Float
Default value: 1.0
Unit: 1/Bohr^2
Description: Sigma parameter in the potential expression.

WellDepth

Type: Float
Default value: 1.0
Unit: Hartree
Description: WellDepth parameter in the potential expression.

Harmonic

Type: Block
Description: Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The FC parameter of the harmonic potential.

Hyperbolic

Type: Block
Description: 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

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The force constant (second derivative of the potential) at the optimum point.

MaxForce

Type: Float
Default value: 0.05
Unit: Hartree/Bohr
Description: Asymptotic value of the force at the infinity.

Type

Type: Multiple Choice
Default value: None
Options: [None, Harmonic, Hyperbolic, Erf, GaussianWell]
GUI name: Type
Description: 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.

Region

Type: String
Default value: *
GUI name: Region
Description: Region to which the restraints should be limited.

TargetSystem

Type: String
Recurring: True
GUI name: Target system
Description: 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

Type: Multiple Choice
Default value: None
Options: [None, Pair, RMSD]
GUI name: Restraint set type
Description: 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.

Reactor

Type: Block
Recurring: True
Description: 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.

ForceConstant

Type: Float
GUI name: Reactor force constant
Description: Force constant of the reactor wall in Hartree/Bohr^2 (or Hartree/Bohr^2/Dalton if [MassScaled] is true).

MassScaled

Type: Bool
Default value: Yes
GUI name: Scale force by mass
Description: 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

Type: Integer
GUI name: Reactor lifetime
Description: 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.

Radius

Type: Float
Unit: Angstrom
GUI name: Reactor radius
Description: Radius of the reactor sphere.

ReflectiveWall

Type: Block
Recurring: True
Description: Apply a reflective wall in space

Axis

Type: Float List
Unit: Angstrom
Description: Defines the normal vector perpendicular to the plane of the reflective wall. Any particle moving in this direction will be reflected back.

Region

Type: String
Recurring: True
Description: Apply the reflective wall to all atoms in this region.

Threshold

Type: Float
Unit: Angstrom
Description: 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.

Remap

Type: Block
Description: Control periodic remapping (backtranslation) of atoms into the PBC box.

Type

Type: Multiple Choice
Default value: Atoms
Options: [None, Atoms]
Description: Select the method used to remap atoms into the unit cell. None: Disable remapping completely. Atoms: Remap any atoms that leave the unit cell.

RemoveMolecules

Type: Block
Recurring: True
GUI name: Remove molecules
Description: This block controls removal of molecules from the system. Multiple occurrences of this block are possible.

Formula

Type: String
Description: 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

Type: Integer
Default value: 0
Description: The specified molecules are removed every so many steps after the StartStep. There is never a molecule removed at step 0.

SafeBox

Type: Block
Description: 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.

Amax

Type: Float
Description: Coordinate of the upper bound along the first axis.

Amin

Type: Float
Description: Coordinate of the lower bound along the first axis.

Bmax

Type: Float
Description: Coordinate of the upper bound along the second axis.

Bmin

Type: Float
Description: Coordinate of the lower bound along the second axis.

Cmax

Type: Float
Description: Coordinate of the upper bound along the third axis.

Cmin

Type: Float
Description: Coordinate of the lower bound along the third axis.

FractionalCoordsBox

Type: Float List
GUI name: Safe box
Description: 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.

SinkBox

Type: Block
Description: 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.

Amax

Type: Float
Description: Coordinate of the upper bound along the first axis.

Amin

Type: Float
Description: Coordinate of the lower bound along the first axis.

Bmax

Type: Float
Description: Coordinate of the upper bound along the second axis.

Bmin

Type: Float
Description: Coordinate of the lower bound along the second axis.

Cmax

Type: Float
Description: Coordinate of the upper bound along the third axis.

Cmin

Type: Float
Description: Coordinate of the lower bound along the third axis.

FractionalCoordsBox

Type: Float List
GUI name: Sink box
Description: 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.

StartStep

Type: Integer
Default value: 0
Description: 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

Type: Integer
Description: Do not remove the specified molecules after this step.

ReplicaExchange

Type: Block
Description: This block is used for (temperature) Replica Exchange MD (Parallel Tempering) simulations.

AllowWrongResults

Type: Bool
Default value: No
Description: Allow combining Replica Exchange with other features when the combination is known to produce physically incorrect results.

EWMALength

Type: Integer
Default value: 10
Description: 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

Type: Integer
Default value: 100
Description: Attempt an exchange every N steps.

TemperatureFactors

Type: Float List
Description: 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

Type: Float List
Description: 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

Type: Integer
Default value: 1
GUI name: Number of replicas
Description: Number of replicas to run in parallel.

Restart

Type: String
GUI name: Restart from
Description: The path to the ams.rkf file from which to restart the simulation.

Shake

Type: Block
Description: Parameters of the Shake/Rattle algorithm.

All

Type: String
Recurring: True
GUI name: Constrain all
Description: 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

Type: Float
Default value: 1e-08
Description: Convergence criterion on the max squared difference, in atomic units.

ConvergeRV

Type: Float
Default value: 1e-08
Description: Convergence criterion on the orthogonality of the constraint and the relative atomic velocity, in atomic units.

Iterations

Type: Integer
Default value: 100
Description: Number of iterations.

ShakeInitialCoordinates

Type: Bool
Default value: Yes
Description: Apply constraints before computing the first energy and gradients.

Thermostat

Type: Block
Recurring: True
Description: 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’ behavior.

BerendsenApply

Type: Multiple Choice
Default value: Global
Options: [Local, Global]
GUI name: Apply Berendsen
Description: Select how to apply the scaling correction for the Berendsen thermostat: - per-atom-velocity (Local) - on the molecular system as a whole (Global).

ChainLength

Type: Integer
Default value: 10
GUI name: NHC chain length
Description: Number of individual thermostats forming the NHC thermostat

Duration

Type: Integer List
GUI name: Duration(s)
Description: Specifies how many steps should a transition from a particular temperature to the next one in sequence take.

Region

Type: String
Default value: *
Description: 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.

Tau

Type: Float
Unit: Femtoseconds
GUI name: Damping constant
Description: The time constant of the thermostat.

Temperature

Type: Float List
Unit: Kelvin
GUI name: Temperature(s)
Description: 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

Type: Multiple Choice
Default value: None
Options: [None, Berendsen, NHC]
GUI name: Thermostat
Description: Selects the type of the thermostat.

TimeStep

Type: Float
Default value: 0.25
Unit: Femtoseconds
Description: The time difference per step.

Trajectory

Type: Block
Description: Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.

ExitConditionFreq

Type: Integer
GUI name: Exit condition frequency
Description: Check the exit conditions every N steps. By default this is done every SamplingFreq steps.

PrintFreq

Type: Integer
GUI name: Printing frequency
Description: Print current thermodynamic properties to the output every N steps. By default this is done every SamplingFreq steps.

SamplingFreq

Type: Integer
Default value: 100
GUI name: Sample frequency
Description: Write the the molecular geometry (and possibly other properties) to the .rkf file once every N steps.

TProfileGridPoints

Type: Integer
Default value: 0
Description: 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

Type: Bool
Default value: Yes
Description: Write detected bonds to the .rkf file.

WriteCharges

Type: Bool
Default value: Yes
Description: 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

Type: Bool
Default value: Yes
Description: Write atomic coordinates to the .rkf file.

WriteEngineGradients

Type: Bool
Default value: No
Description: Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.

WriteMolecules

Type: Bool
Default value: Yes
Description: Write the results of molecule analysis to the .rkf file.

WriteVelocities

Type: Bool
Default value: Yes
Description: Write velocities to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze the velocities.

fbMC

Type: Block
Recurring: True
GUI name: fbMC
Description: This block sets up force bias Monte Carlo interleaved with the molecular dynamics simulation.

Frequency

Type: Integer
Default value: 1
Description: Run the fbMC procedure every Frequency MD steps.

MassRoot

Type: Float
Default value: 2.0
Description: Inverse of the exponent used to mass-weight fbMC steps.

MolecularMoves

Type: Block
Description: Move molecules as rigid bodies in addition to normal atomic moves.

Enabled

Type: Bool
Default value: No
GUI name: Enable molecular moves
Description: Enable moving molecules as rigid bodies based on net forces and torques. Ordinary per-atom displacements will then be based on residual atomic forces.

RotationStepAngle

Type: Float
Default value: 0.1
Unit: Radian
Description: Maximum allowed angle of rotation of each molecule in one fbMC step.

TranslationStepLength

Type: Float
Default value: 0.1
Unit: Angstrom
Description: Maximum allowed displacement of each molecule in each Cartesian coordinate in one fbMC step.

NSteps

Type: Integer
GUI name: Number of steps
Description: Number of fbMC steps to perform on every invocation of the procedure.

PrintFreq

Type: Integer
GUI name: Printing frequency
Description: 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

Type: Integer
Default value: 1
Description: First step at which the fbMC procedure may run.

StepLength

Type: Float
Default value: 0.1
Unit: Angstrom
Description: Maximum allowed displacement of the lightest atom in the system in each Cartesian coordinate in one fbMC step.

StopStep

Type: Integer
Default value: 0
Description: Last step at which the fbMC procedure may run. If unset or zero, there is no limit.

Temperature

Type: Float
Unit: Kelvin
Description: Temperature used for fbMC.

Molecules

Type: Block
Description: Configures details of the molecular composition analysis enabled by the Properties%Molecules block.

AdsorptionSupportRegion

Type: String
GUI name: Adsorption support region
Description: 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

Type: Float
Default value: 0.5
Description: Bond order cutoff for analysis of the molecular composition. Bonds with bond order smaller than this value are neglected when determining the molecular composition.

NEB

Type: Block
Description: Configures details of the Nudged Elastic Band optimization.

Climbing

Type: Bool
Default value: Yes
GUI name: Climb highest image to TS
Description: Use the climbing image algorithm to drive the highest image to the transition state.

ClimbingThreshold

Type: Float
Default value: 0.0
Unit: Hartree/Bohr
GUI name: CI force threshold
Description: 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.

Images

Type: Integer
Default value: 8
GUI name: Number of images
Description: 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.

InterpolateInternal

Type: Bool
Default value: Yes
GUI name: Interpolate in Internal coordinates
Description: 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

Type: Bool
Default value: Yes
GUI name: Interpolate across cell boundary
Description: 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.

Iterations

Type: Integer
GUI name: Maximum number of iterations
Description: Maximum number of NEB iterations. The default value depends on the number of degrees of freedom (number of images, atoms, periodic dimensions).

Jacobian

Type: Float
GUI name: Jacobian value
Description: 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.

LoadPath

Type: Block
Description: 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.

File

Type: String
GUI name: Initial path file
Description: 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

Type: Integer List
GUI name: Raw geometry indices
Description: Raw indices of the geometries from the History section. By default the last geometry of each path point is used.

Points

Type: Integer List
GUI name: Path points
Description: 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.

MapAtomsToCell

Type: Bool
Default value: Yes
GUI name: Map atoms to cell
Description: Translate atoms to the [-0.5,0.5] cell before every step. This option cannot be disabled for SS-NEB.

OldTangent

Type: Bool
Default value: No
GUI name: Use old tangent
Description: Turn on the old central difference tangent.

OptimizeEnds

Type: Bool
Default value: Yes
GUI name: Optimize reactants/products
Description: Start the NEB with optimization of the reactant and product geometries.

OptimizeLattice

Type: Bool
Default value: No
GUI name: Optimize lattice
Description: Turn on the solid-state NEB (SS-NEB).

Parallel

Type: Block
Description: 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.

nCoresPerGroup

Type: Integer
GUI name: Cores per group
Description: Number of cores in each working group.

nGroups

Type: Integer
GUI name: Number of groups
Description: Total number of processor groups. This is the number of tasks that will be executed in parallel.

nNodesPerGroup

Type: Integer
GUI name: Nodes per group
Description: 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.

PreOptimizeWithIDPP

Type: Bool
Default value: No
GUI name: Use IDPP
Description: (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

Type: Bool
Default value: No
GUI name: Re-optimize reactants/products
Description: Re-optimize reactant and product geometries upon restart.

Restart

Type: String
GUI name: Restart from
Description: 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

Type: Float
Default value: 1.0
GUI name: Skewness
Description: 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

Type: Float
Default value: 1.0
Unit: Hartree/Bohr^2
GUI name: Spring value
Description: Spring force constant in atomic units.

NormalModes

Type: Block
Description: Configures details of a normal modes calculation.

BlockDisplacements

Type: Block
Description: Configures details of a Block Normal Modes (a.k.a. Mobile Block Hessian, or MBH) calculation.

AngularDisplacement

Type: Float
Default value: 0.5
Unit: Degree
Description: 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

Type: Integer List
Recurring: True
Description: List of atoms belonging to a block. You can have multiple BlockAtoms.

BlockRegion

Type: String
Recurring: True
Description: The region to to be considered a block. You can have multiple BlockRegions, also in combination with BlockAtoms.

Parallel

Type: Block
Description: Configuration for how the individual displacements are calculated in parallel.

nCoresPerGroup

Type: Integer
Description: Number of cores in each working group.

nGroups

Type: Integer
Description: Total number of processor groups. This is the number of tasks that will be executed in parallel.

nNodesPerGroup

Type: Integer
GUI name: Cores per task
Description: 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.

RadialDisplacement

Type: Float
Default value: 0.005
Unit: Angstrom
Description: Step size for translational degrees of freedom during Block Normal Modes finite difference calculations.

Displacements

Type: Multiple Choice
Default value: Cartesian
Options: [Cartesian, Symmetric, Block]
GUI name: Displacements
Description: 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

Type: Multiple Choice
Default value: Auto
Options: [Auto, Analytical, Numerical]
Description: 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

Type: Float List
Default value: [-10000000.0, 10.0]
Unit: cm-1
Recurring: True
GUI name: Re-scan range
Description: Specifies a frequency range within which all modes will be scanned. 2 numbers: an upper and a lower bound.

ReScanModes

Type: Bool
Default value: Yes
GUI name: Re-scan modes
Description: Whether or not to scan imaginary modes after normal modes calculation has concluded.

SymmetricDisplacements

Type: Block
Description: Configures details of the calculation of the frequencies and normal modes of vibration in symmetric displacements.

Type

Type: Multiple Choice
Default value: All
Options: [All, Infrared, Raman, InfraredAndRaman]
GUI name: Symm Frequencies
Description: 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.

NumericalDifferentiation

Type: Block
Description: Define options for numerical differentiations, that is the numerical calculation of gradients, Hessian and the stress tensor for periodic systems.

NuclearStepSize

Type: Float
Default value: 0.005
Unit: Bohr
Description: Step size for numerical nuclear gradient calculation.

Parallel

Type: Block
Description: 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.

nCoresPerGroup

Type: Integer
GUI name: Cores per group
Description: Number of cores in each working group.

nGroups

Type: Integer
GUI name: Number of groups
Description: Total number of processor groups. This is the number of tasks that will be executed in parallel.

nNodesPerGroup

Type: Integer
GUI name: Nodes per group
Description: 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.

StrainStepSize

Type: Float
Default value: 0.001
Description: Step size (relative) for numerical stress tensor calculation.

NumericalPhonons

Type: Block
Description: Configures details of a numerical phonons calculation.

AutomaticBZPath

Type: Bool
Default value: Yes
GUI name: Automatic BZ path
Description: 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.

BZPath

Type: Block
Description: 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.

Path

Type: Non-standard block
Recurring: True
Description: A section of a k space path. This block should contain multiple lines, and in each line you should specify one vertex of the path in fractional coordinates. Optionally, you can add text labels for your vertices at the end of each line.

BornEffCharge

Type: Float
Default value: 0.0
Description: Input option to give the Born effective charges of the species.

DielectricConst

Type: Float
Default value: 1.0
Description: Input option to give the static dielectric constant of the species.

DoubleSided

Type: Bool
Default value: Yes
Description: 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

Type: Integer
Default value: 100
Description: Use interpolation to generate smooth phonon plots.

NDosEnergies

Type: Integer
Default value: 1000
Description: 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.

Parallel

Type: Block
Description: 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.

nCoresPerGroup

Type: Integer
GUI name: Cores per group
Description: Number of cores in each working group.

nGroups

Type: Integer
GUI name: Number of groups
Description: Total number of processor groups. This is the number of tasks that will be executed in parallel.

nNodesPerGroup

Type: Integer
GUI name: Nodes per group
Description: 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.

StepSize

Type: Float
Default value: 0.04
Unit: Angstrom
Description: Step size to be taken to obtain the force constants (second derivative) from the analytical gradients numerically.

SuperCell

Type: Non-standard block
Description: Used for the phonon run. The super lattice is expressed in the lattice vectors. Most people will find a diagonal matrix easiest to understand.

PESExploration

Type: Block
Description: Configures details of the automated PES exploration methods.

BasinHopping

Type: Block
Description: Configures the details of the Basin Hopping subtask.

DisplaceAtomsInRegion

Type: String
Default value
Description: 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

Type: Float
Default value: 0.5
Unit: Angstrom
Description: Displacement in each degree of freedom.

MainSystemAsSeed

Type: Bool
Default value: No
Description: If true, only the main system will be used as a seed state. The main system is not added to the database.

PESPointCharacterization

Type: Bool
Default value: Yes
Description: 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

Type: Float
Default value: 0.4
Unit: Angstrom
Description: 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.

Steps

Type: Integer
Default value: 20
Description: Number of displace & optimize Monte-Carlo steps to take.

BindingSites

Type: Block
Description: Options related to the calculation of binding sites.

Calculate

Type: Bool
Default value: No
Description: Calculate binding sites at the end of a job. Not needed for Binding Sites job.

DistanceDifference

Type: Float
Default value: -1.0
Unit: Angstrom
Description: 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

Type: Integer
Default value: 3
Description: 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

Type: Float
Default value: -1.0
Unit: Angstrom
Description: 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

Type: String
Default value
Description: 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]

CalculateEnergyReferences

Type: Bool
Default value: No
Description: Calculates the energy references.

CalculateFragments

Type: Bool
Default value: No
Description: 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.

Debug

Type: Block
Description: ???.

DynamicSeedStates

Type: Bool
Default value: Yes
Description: 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.

Dynamics

Type: Block
Description: ???.

Andersen

Type: Block
Description: ???.

Alpha

Type: Float
Default value: 1.0
Description: ???.

CollisionPeriod

Type: Float
Default value: 100.0
Description: ???.

Langevin

Type: Block
Description: ???.

Friction

Type: Float
Default value: 0.01
Description: ???.

Nose

Type: Block
Description: ???.

Mass

Type: Float
Default value: 1.0
Description: ???.

Thermostat

Type: Multiple Choice
Default value: none
Options: [andersen, nose_hoover, langevin, none]
Description: ???.

Time

Type: Float
Default value: 1000.0
Description: ???.

TimeStep

Type: Float
Default value: 1.0
Description: ???.

FiniteDifference

Type: Float
Default value: 0.0026458861
Unit: Angstrom
Description: The finite difference distance to use for Dimer, Hessian, Lanczos, and optimization methods.

Hessian

Type: Block
Description: ???.

AtomList

Type: String
Default value: all
Description: ???.

ZeroFreqValue

Type: Float
Default value: 1e-06
Description: ???.

Job

Type: Multiple Choice
Options: [ProcessSearch, BasinHopping, SaddleSearch, LandscapeRefinement, BindingSites]
Description: Specify the PES exploration job to perform.

LandscapeRefinement

Type: Block
Description: Configures details of the energy landscape refinement job.

CalculateOnlyEnergies

Type: Bool
Default value: No
Description: 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

Type: Bool
Default value: No
Description: 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

Type: Bool
Default value: No
Description: Same as LandscapeRefinement%IgnoreFinalPESPointCharacter but regarding the Fragments calculations, see option LandscapeRefinement%CalculateFragments.

RelaxFromSaddlePoint

Type: Bool
Default value: No
Description: Relaxes the saddle point geometries following the imaginary mode to get both reactants and products.

RunInitialSinglePoints

Type: Bool
Default value: Yes
Description: 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

Type: Multiple Choice
Default value: Auto
Options: [Auto, Dimer]
Description: Sets the method to refine transition states.

LoadEnergyLandscape

Type: Block
Description: Options related to the loading of an Energy Landscape from a previous calculation.

GenerateSymmetryImages

Type: Bool
Default value: No
Description: 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

Type: Integer List
GUI name: List of states to keep
Description: 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

Type: String
GUI name: Load energy landscape from
Description: AMS results folder to load an energy landscape from. In the text input file, you may alternatively specify a .con file in the native EON format.

Remove

Type: Integer List
GUI name: List of states to remove
Description: 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

Type: Bool
Default value: No
Description: 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

Type: Integer List
GUI name: List of seed states
Description: 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.

NegativeEigenvalueTolerance

Type: Float
Default value: -0.0005
Unit: Hartree/Bohr^2
Description: 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.

NudgedElasticBand

Type: Block
Description: Options for the Nudged Elastic Band (NEB) method.

ClimbingImageMethod

Type: Bool
Default value: Yes
Description: Use the climbing image algorithm to drive the highest image to the transition state.

ConvergedForce

Type: Float
Default value: -1.0
Unit: eV/Angstrom
Description: Convergence threshold for nuclear gradients. Note: Special value of -1.0 means using the same convergence criterion as the PES explorer’s geometry optimizer.

Images

Type: Integer
Default value: 5
Description: Number of NEB images between the two endpoints.

MaxIterations

Type: Integer
Default value: 500
Description: Maximum number of NEB iterations.

OldTangent

Type: Bool
Default value: No
Description: Use the old central difference tangent.

Spring

Type: Float
Default value: 5.0
Unit: eV/Ang^2
Description: Spring force constant.

NumExpeditions

Type: Integer
Default value: 1
Description: 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

Type: Integer
Default value: 1
Description: 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

Type: Multiple Choice
Default value: SaddleSearch
Options: [SaddleSearch, NudgedElasticBand]
Description: 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.

Optimizer

Type: Block
Description: Configures the details of the geometry optimizers used by the PES explorers.

ConvergedForce

Type: Float
Default value: 0.005
Unit: eV/Angstrom
Description: Convergence threshold for nuclear gradients.

MaxIterations

Type: Integer
Default value: 400
Description: Maximum number of iterations allowed for optimizations.

Method

Type: Multiple Choice
Default value: CG
Options: [CG, QM, LBFGS, FIRE, SD]
Description: Select the method for geometry optimizations.

Parallel

Type: Block
Description: 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.

nCoresPerGroup

Type: Integer
GUI name: Cores per group
Description: Number of cores in each working group.

nGroups

Type: Integer
GUI name: Number of groups
Description: Total number of processor groups. This is the number of tasks that will be executed in parallel.

nNodesPerGroup

Type: Integer
GUI name: Nodes per group
Description: 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.

ParallelReplica

Type: Block
Description: ???.

DephaseLoopMax

Type: Integer
Default value: 5
Description: ???.

DephaseLoopStop

Type: Bool
Default value: No
Description: ???.

DephaseTime

Type: Float
Default value: 1000.0
Description: ???.

PostTransitionTime

Type: Float
Default value: 1000.0
Description: ???.

RefineTransition

Type: Bool
Default value: Yes
Description: ???.

StateCheckInterval

Type: Float
Default value: 1000.0
Description: ???.

StateSaveInterval

Type: Float
Default value: -1.0
Description: ???.

StopAfterTransition

Type: Bool
Default value: No
Description: ???.

Prefactor

Type: Block
Description: ???.

Rate

Type: Multiple Choice
Default value: HTST
Options: [HTST, QQHTST]
Description: Calculates the pre-exponential factors of the Reaction Rates using either Harmonic Transition State Theory (HTST) or quasi-quantum HTST (QQHTST).

ProcessSearch

Type: Block
Description: Input options specific to the process search procedure.

MinimizationOffset

Type: Float
Default value: 0.2
Description: 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.

RandomSeed

Type: Integer
Description: 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 …

SaddleSearch

Type: Block
Description: Configuration for the Saddle Search procedure (used in SaddleSearch and ProcessSearch Jobs).

ConvergedForce

Type: Float
Default value: -1.0
Unit: eV/Angstrom
Description: Convergence threshold for nuclear gradients. Note: Special value of -1.0 means using the same convergence criterion as the PES explorer’s geometry optimizer.

DisplaceAlongNormalModesActiveModes

Type: String
Default value
Description: 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

Type: Float
Default value: 0.0
Description: 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

Type: String
Default value
Description: A string corresponding to the name of a region. When performing the initial random displacement, only displace atoms in the specified region.

DisplaceAtomsInRegionWeight

Type: Float
Default value: 0.0
Description: 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].

DisplaceListedAtoms

Type: String
Default value
Description: 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.

DisplaceListedTypes

Type: String
Default value
Description: ???.

DisplaceMagnitude

Type: Float
Default value: 0.1
Unit: Angstrom
Description: The standard deviation of the Gaussian displacement in each degree of freedom for the selected atoms.

DisplaceRadius

Type: Float
Default value: 4.0
Unit: Angstrom
Description: Atoms within this distance of the epicenter will be displaced.

MaxEnergy

Type: Float
Default value: 20.0
Unit: eV
Description: 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

Type: Integer
Default value: 400
Description: Maximum number of iterations for each saddle search run.

MinEnergyBarrier

Type: Float
Default value: 0.001
Unit: eV
Description: Minimum energy barrier to accept a new transition state.

MinModeMethod

Type: Multiple Choice
Default value: dimer
Options: [dimer, lanczos]
Description: The minimum-mode following method to use.

RelaxFromSaddlePoint

Type: Bool
Default value: No
Description: Relaxes the saddle point geometries following the imaginary mode to get both reactants and products.

ZeroModeAbortCurvature

Type: Float
Default value: 0.01
Unit: eV/Angstrom^2
Description: The threshold in the frequency below which the minimum mode is considered zero. The calculation is aborted if the negative mode becomes zero.

SelectedListedAtomsForPESPointCharacter

Type: String
Default value
Description: 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

Type: String
Default value
Description: 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.

StatesAlignment

Type: Block
Description: Configures details of how the energy landscape configurations are aligned respect to the main chemical system [System].

DistanceDifference

Type: Float
Default value: -1.0
Unit: Angstrom
Description: 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

Type: String
Default value
Description: Defines the region that is considered as the reference for alignments. Atoms outside this region are ignored in the alignments.

StructureComparison

Type: Block
Description: Settings for structure comparison.

CheckRotation

Type: Bool
Description: 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

Type: Bool
Default value: No
Description: Considers that two systems are equal if they are equivalent by symmetry.

DistanceDifference

Type: Float
Default value: 0.1
Unit: Angstrom
Description: If the distance between two mapped atoms is larger than this threshold, the two configurations are considered different structures.

EnergyDifference

Type: Float
Default value: 0.01
Unit: eV
Description: If the energy difference between two configurations is larger than this threshold, the two configurations are considered to be different structures.

IndistinguishableAtoms

Type: Bool
Default value: Yes
Description: If yes, the order of the atoms does not affect the structural comparison. Atoms of the same element are then indistinguishable.

NeighborCutoff

Type: Float
Default value: 3.3
Unit: Angstrom
Description: Atoms within this distance of each other are considered neighbors.

RemoveTranslation

Type: Bool
Description: Translates the system optimally before comparing structures. The default is to do this only when there are no fixed atom constraints.

Temperature

Type: Float
Default value: 300.0
Unit: Kelvin
Description: 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

Type: Bool
Default value: No
Description: Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.

WriteHistory

Type: Multiple Choice
Default value: Converged
Options: [None, Converged, All]
Description: 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.

PESPointCharacter

Type: Block
Description: Options for the characterization of PES points.

Displacement

Type: Float
Default value: 0.04
Description: 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

Type: Float
Default value: -0.0001
Unit: Hartree/Bohr^2
Description: 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.

NumberOfModes

Type: Integer
Default value: 2
Description: The number of (lowest) eigenvalues that should be checked.

Tolerance

Type: Float
Default value: 0.016
Description: Convergence tolerance for residual in iterative Davidson diagonalization.

PESScan

Type: Block
Description: Configures the details of the potential energy surface scanning task.

CalcPropertiesAtPESPoints

Type: Bool
Default value: No
Description: 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

Type: Bool
Default value: Yes
Description: After the initial pass over the PES, restart the unconverged points from converged neighboring points.

ScanCoordinate

Type: Block
Recurring: True
Description: 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.

Angle

Type: String
Recurring: True
Description: Scan the angle between three atoms. Three atom indices followed by two real numbers delimiting the transit range in degrees.

CellVolumeRange

Type: Float List
Unit: Angstrom^3
Description: 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

Type: Float List
Description: 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

Type: String
Recurring: True
Description: Scan a particular coordinate of an atom. Atom index followed by (x|y|z) followed by two real numbers delimiting the transit range.

DifDist

Type: String
Recurring: True
Description: 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

Type: String
Recurring: True
Description: Scan the dihedral angle between four atoms. Four atom indices followed by two real numbers delimiting the transit angle in degrees.

Distance

Type: String
Recurring: True
Description: Scan the distance between two atoms. Two atom indices followed by two real numbers delimiting the transit distance in Angstrom.

FromLattice

Type: Non-standard block
Description: 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.

FromStrainVoigt

Type: Float List
Description: 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

Type: Float List
Unit: Angstrom
Description: 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

Type: Float List
Unit: Angstrom
Description: 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

Type: Float List
Unit: Angstrom
Description: 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

Type: String
Recurring: True
Description: 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.

ToLattice

Type: Non-standard block
Description: Up to three lattice vectors to end the scan at. Unit can be specified in the header. Default unit is Angstrom.

ToStrainVoigt

Type: Float List
Description: 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

Type: Integer
Default value: 10
Description: The number of points along the scanned coordinate. Must be greater or equal 2.

Print

Type: Block
Description: This block controls the printing of additional information to stdout.

Timers

Type: Multiple Choice
Default value: None
Options: [None, Normal, Detail, TooMuchDetail]
Description: Printing timing details to see how much time is spend in which part of the code.

Properties

Type: Block
Description: Configures which AMS level properties to calculate for SinglePoint calculations or other important geometries (e.g. at the end of an optimization).

BondOrders

Type: Bool
Default value: No
Description: 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

Type: Bool
Default value: No
Description: Requests the engine to calculate the atomic charges.

DipoleGradients

Type: Bool
Default value: No
Description: 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

Type: Bool
Default value: No
Description: Requests the engine to calculate the electric dipole moment of the molecule. This can only be requested for non-periodic systems.

ElasticTensor

Type: Bool
Default value: No
Description: Calculate the elastic tensor.

GSES

Type: Bool
Default value: No
Description: Requests the engine to calculate the gradients of ground to excited state properties.

Gradients

Type: Bool
Default value: No
GUI name: Nuclear gradients
Description: Calculate the nuclear gradients.

Hessian

Type: Bool
Default value: No
Description: Whether or not to calculate the Hessian.

Molecules

Type: Bool
Default value: No
Description: Requests an analysis of the molecular components of a system, based on the bond orders calculated by the engine.

NormalModes

Type: Bool
Default value: No
GUI name: Frequencies
Description: Calculate the frequencies and normal modes of vibration, and for molecules also the corresponding IR intensities if the engine supports the calculation of dipole moments.

OrbitalsInfo

Type: Bool
Default value: No
Description: Basic molecular orbitals information: orbital energies, occupations, HOMO, LUMO and HOMO-LUMO gap.

Other

Type: Bool
Default value: Yes
Description: Other (engine specific) properties. Details are configured in the engine block.

PESPointCharacter

Type: Bool
Default value: No
GUI name: Characterize PES point
Description: 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

Type: Bool
Default value: No
Description: Calculate the phonons (for periodic systems).

Polarizability

Type: Bool
Default value: No
Description: Requests the engine to calculate the polarizability tensor of the system.

Raman

Type: Bool
Default value: No
Description: Requests calculation of Raman intensities for vibrational normal modes.

SelectedRegionForHessian

Type: String
GUI name: Hessian only for
Description: 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

Type: Bool
Default value: No
GUI name: Stress tensor
Description: Calculate the stress tensor.

VCD

Type: Bool
Default value: No
Description: Requests calculation of VCD for vibrational normal modes.

VROA

Type: Bool
Default value: No
Description: Requests calculation of VROA for vibrational normal modes.

Raman

Type: Block
Description: Configures details of the Raman or VROA calculation.

FreqRange

Type: Float List
Unit: cm-1
Recurring: True
GUI name: Frequency range
Description: Specifies a frequency range within which all modes will be scanned. 2 numbers: an upper and a lower bound.

IncidentFrequency

Type: Float
Default value: 0.0
Unit: eV
Description: Frequency of incident light.

LifeTime

Type: Float
Default value: 0.0
Unit: hartree
Description: 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.

Replay

Type: Block
Description: Configures the details of the Replay task.

File

Type: String
GUI name: Restart from
Description: 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

Type: Integer List
Description: 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

Type: Bool
Default value: No
Description: 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.

Restraints

Type: Block
Description: 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.

Angle

Type: String
Recurring: True
Description: 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

Type: String
Recurring: True
Description: 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

Type: String
Recurring: True
Description: 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

Type: String
Recurring: True
Description: 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

Type: Float
Default value: 1.0
GUI name: Default F(inf)
Description: 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

Type: Multiple Choice
Default value: Harmonic
Options: [Harmonic, Hyperbolic, Erf, GaussianWell]
GUI name: Default restraint profile
Description: 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

Type: String
Recurring: True
Description: 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

Type: Multiple Choice
Default value: Default
Options: [Default, MD]
GUI name: Units
Description: 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.

RigidMotions

Type: Block
Description: 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.

AllowRotations

Type: Multiple Choice
Default value: Auto
Options: [Auto, None, All, X, Y, Z, XY, XZ, YZ]
Description: Which overall rotations of the system are allowed

AllowTranslations

Type: Multiple Choice
Default value: Auto
Options: [Auto, None, All, X, Y, Z, XY, XZ, YZ]
Description: Which overall transitions of the system are allowed

Tolerance

Type: Float
Default value: 1e-06
Description: Tolerance for detecting linear molecules. A large value means larger deviation from linearity is permitted.

RNGSeed

Type: Integer List
Description: 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.

SCMMatrix

Type: Block
Description: Technical settings for programs using the AMT matrix system. Currently this is only used by DFTB

DistributedMatrix

Type: Block
Description: Technical settings for Distributed matrices

ColBlockSize

Type: Integer
Default value: 64
Description: See comment of RowBlockSize.

RowBlockSize

Type: Integer
Default value: 64
Description: The matrix is divided into blocks of size RowBlockSize x ColBlockSize. The smaller the blocks the better the distribution, but at the expense of increased communication overhead

Type

Type: Multiple Choice
Default value: Elpa
Options: [Auto, Reference, ScaLapack, Elpa]
Description: Determines which implementation is used to support the AbstractMatrixType.

Symmetry

Type: Block
Description: Specifying details about the details of symmetry detection and usage.

SymmetrizeTolerance

Type: Float
Default value: 0.05
Description: Tolerance used to detect symmetry in case symmetrize is requested.

Tolerance

Type: Float
Default value: 1e-07
Description: Tolerance used to detect symmetry in the system.

System

Type: Block
Recurring: True
Description: 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.

AllowCloseAtoms

Type: Bool
Default value: No
Description: 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.

Atoms

Type: Non-standard block
Description: The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.

BondOrders

Type: Non-standard block
Description: 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.

Charge

Type: Float
Default value: 0.0
GUI name: Total charge
Description: The system’s total charge in atomic units.

ElectrostaticEmbedding

Type: Block
Description: Container for electrostatic embedding options, which can be combined.

ElectricField

Type: Float List
Unit: V/Angstrom
Description: 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

Type: Block
Description: External point charges (and dipoles).

ChargeModel

Type: Multiple Choice
Default value: Point
Options: [Point, Gaussian]
Description: A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.

ChargeWidth

Type: Float
Default value: -1.0
Description: 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

Type: Non-standard block
Description: 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.

FractionalCoords

Type: Bool
Default value: No
Description: 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

Type: String
Description: Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz

GuessBonds

Type: Bool
Default value: No
Description: Whether or not UFF bonds should be guessed.

Lattice

Type: Non-standard block
Description: Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.

LatticeStrain

Type: Float List
Description: 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.

LoadForceFieldAtomTypes

Type: Block
Description: This is a mechanism to set the ForceField.Type attribute in the input. This information is currently only used by the ForceField engine.

File

Type: String
Description: Name of the (kf) file. It needs to be the result of a forcefield calculation.

LoadForceFieldCharges

Type: Block
Recurring: True
Description: This is a mechanism to set the ForceField.Charge attribute in the input. This information is currently only used by the ForceField engine.

CheckGeometryRMSD

Type: Bool
Default value: No
Description: 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.

File

Type: String
Description: Name of the (kf) file

MaxGeometryRMSD

Type: Float
Default value: 0.1
Unit: Angstrom
Description: 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

Type: String
Default value: *
Description: Region for which the charges should be loaded

Section

Type: String
Default value: AMSResults
Description: Section name of the kf file

Variable

Type: String
Default value: Charges
Description: Variable name of the kf file

MapAtomsToUnitCell

Type: Bool
Default value: No
Description: For periodic systems the atoms will be moved to the central cell.

ModifyAlternativeElements

Type: Bool
Default value: No
Description: 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

Type: Float
Default value: 0.0
Unit: Angstrom
Description: 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

Type: Float
Default value: 0.0
Description: 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

Type: Bool
Default value: No
Description: 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.

Region

Type: Block
Recurring: True
Description: Properties for each region specified in the Atoms block.

Properties

Type: Non-standard block
Description: Properties for each region specified in the Atoms block.

ShiftCoordinates

Type: Float List
Unit: Bohr
Description: Translate the atoms by the specified shift (three numbers).

SuperCell

Type: Integer List
Description: 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

Type: Integer List
Description: 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

Type: Bool
Default value: No
Description: 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

Type: Multiple Choice
Default value: AUTO
Options: [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)]
Description: 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.

Task

Type: Multiple Choice
Options: [GCMC, GeometryOptimization, IRC, MolecularDynamics, NEB, PESExploration, PESScan, Replay, SinglePoint, TransitionStateSearch, VibrationalAnalysis]
Description: 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

Thermo

Type: Block
Description: Options for thermodynamic properties (assuming an ideal gas). The properties are computed for all specified temperatures.

LowFrequencyCorrector

Type: Block
Description: 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.

Alpha

Type: Float
Default value: 4.0
Description: The exponent term used in the dampener.

Frequency

Type: Float
Default value: 100.0
Unit: cm-1
Description: The frequency around which the dampener interpolates between harmonic oscillator and free rotor quantities.

MomentOfInertia

Type: Float
Default value: 1e-44
Unit: kg m^2
GUI name: Averaging Moment of Inertia
Description: The moment of inertia used to restrict entropy results for very small frequencies (generally around less than 1 cm-1).

Pressure

Type: Float
Default value: 1.0
Unit: atm
Description: The pressure at which the thermodynamic properties are computed.

Temperatures

Type: Float List
Default value: [298.15]
Unit: Kelvin
Value Range: value >= 0
Description: List of temperatures at which the thermodynamic properties will be calculated.

TransitionStateSearch

Type: Block
Description: Configures some details of the transition state search.

ModeToFollow

Type: Integer
Default value: 1
Description: 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

Type: Block
Description: Specify components of the transition state reaction coordinate (TSRC) as a linear combination of internal coordinates (distances or angles).

Angle

Type: String
Recurring: True
Description: The TSRC contains the valence angle between the given atoms. Three atom indices followed by the weight.

Block

Type: String
Recurring: True
Description: 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

Type: Integer List
Value Range: value > 0
Recurring: True
Description: 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

Type: String
Recurring: True
Description: The TSRC contains Cartesian displacement of an atom: atom index followed by [x|y|z] and the weight.

Dihedral

Type: String
Recurring: True
Description: The TSRC contains the dihedral angle between the given atoms. Four atom indices followed by the weight.

Distance

Type: String
Recurring: True
Description: The TSRC contains the distance between the given atoms. Two atom indices followed by the weight.

UseSymmetry

Type: Bool
Default value: Yes
Description: Whether to use the system’s symmetry in AMS. Symmetry is recognized within a tolerance as given in the Symmetry key.

VibrationalAnalysis

Type: Block
Description: Input data for all vibrational analysis utilities in the AMS driver.

AbsorptionSpectrum

Type: Block
Description: Settings related to the integration of the spectrum for vibronic tasks.

AbsorptionRange

Type: Float List
Default value: [-200.0, 4000.0]
Unit: cm-1
Recurring: True
Description: Specifies frequency range of the vibronic absorption spectrum to compute. 2 numbers: an upper and a lower bound.

FrequencyGridPoints

Type: Integer
Default value: 400
Description: Number of grid points to use for the spectrum

LineWidth

Type: Float
Default value: 200.0
Unit: cm-1
Description: Lorentzian line-width.

SpectrumOffset

Type: Multiple Choice
Default value: relative
Options: [absolute, relative]
Description: Specifies whether provided frequency range are absolute frequencies or frequencies relative to computed 0-0 excitation energy.

Displacement

Type: Float
Unit: Bohr
Description: Step size for finite difference calculations.

ExcitationSettings

Type: Block
Description: Block that contains settings related to the excitation for vibronic tasks.

EnergyInline

Type: Float
Unit: hartree
Description: Vertical excitation energy, used when [ExcitationInfo] = [Inline].

ExcitationFile

Type: String
Description: Path to a .rkf/.t21 file containing the excited state information (gradients, transition dipoles and energies).

ExcitationInputFormat

Type: Multiple Choice
Default value: File
Options: [File, Inline]
Description: Select how the application should retrieve the excited state information (energy, gradient).

GradientInline

Type: Non-standard block
Description: Excited state gradient at ground state equilibrium geometry, used when [ExcitationInfo] = [Inline].

Singlet

Type: Non-standard block
Description: Symmetry labels + integer indices of desired singlet transitions (VG-FC absorption spectra support only 1 at a time)

Triplet

Type: Non-standard block
Description: Symmetry labels + integer indices of desired triplet transitions (VG-FC absorption spectra support only 1 at a time)

ModeTracking

Type: Block
Description: Input data for Mode Tracking.

HessianGuess

Type: Multiple Choice
Default value: CalculateWithFastEngine
Options: [Unit, File, CalculateWithFastEngine]
GUI name: Guess Hessian
Description: Sets how to obtain the guess for the Hessian used in the preconditioner (if one is to be used).

HessianInline

Type: Non-standard block
Description: Initial guess for the (non-mass-weighted) Hessian in a 3N x 3N block, used when [HessianGuess] = [Inline].

HessianPath

Type: String
Description: 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.

ToleranceForBasis

Type: Float
Default value: 0.0001
Description: Convergence tolerance for the contribution of the newest basis vector to the tracked mode.

ToleranceForNorm

Type: Float
Default value: 0.0005
Description: Convergence tolerance for residual RMS value.

ToleranceForResidual

Type: Float
Default value: 0.0005
Description: Convergence tolerance for the maximum component of the residual vector.

ToleranceForSpectrum

Type: Float
Default value: 0.01
Description: Convergence tolerance for the spectrum in Vibronic Structure Tracking.

TrackingMethod

Type: Multiple Choice
Default value: OverlapInitial
Options: [OverlapInitial, DifferenceInitial, FreqInitial, IRInitial, OverlapPrevious, DifferencePrevious, FreqPrevious, IRPrevious, HighestFreq, HighestIR, LowestFreq, LowestResidual]
Description: Set the tracking method that will be used. Vibronic Structure Tracking uses Largest Displacement.

UpdateMethod

Type: Multiple Choice
Options: [JD, D, I]
Description: 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).

NormalModes

Type: Block
Description: All input related to processing of normal modes. Not available for vibronic structure tracking (as no modes are required there).

MassWeightInlineMode

Type: Bool
Default value: Yes
Description: 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

Type: String
Description: 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.

ModeInline

Type: Non-standard block
Recurring: True
Description: 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.

ModeInputFormat

Type: Multiple Choice
Default value: File
Options: [File, Inline, Hessian]
GUI name: Tracked mode source
Description: Set how the initial guesses for the modes are supplied. Only mode tracking supports the Inline and Hessian options.

ModeSelect

Type: Block
Description: Pick which modes to read from file.

DisplacementBound

Type: Float
Description: Vibronic Structure (Refinement), Resonance Raman: Select all modes with a dimensionless oscillator displacement greater than the specified value.

FreqAndIRRange

Type: Float List
Recurring: True
Description: 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

Type: Float List
Unit: cm-1
Recurring: True
Description: 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

Type: Bool
Default value: No
GUI name: All modes
Description: Select all modes. This only make sense for Mode Scanning calculations.

HighFreq

Type: Integer
GUI name: # High frequencies
Description: Select the N modes with the highest frequencies.

HighIR

Type: Integer
GUI name: # High IR
Description: Select the N modes with the largest IR intensities.

IRRange

Type: Float List
Unit: km/mol
Recurring: True
Description: Specifies an IR intensity range within which all modes will be selected. 2 numbers: an upper and a lower bound.

ImFreq

Type: Bool
Default value: No
GUI name: All imaginary frequencies
Description: Select all modes with imaginary frequencies.

LargestDisplacement

Type: Integer
Description: Vibronic Structure (Refinement), Resonance Raman: Select the N modes with the largest VG-FC displacement.

LowFreq

Type: Integer
GUI name: # Low frequencies
Description: Select the N modes with the lowest frequencies. Includes imaginary modes which are recorded with negative frequencies.

LowFreqNoIm

Type: Integer
GUI name: # Low positive frequencies
Description: Select the N modes with the lowest non-negative frequencies. Imaginary modes have negative frequencies and are thus omitted here.

LowIR

Type: Integer
GUI name: # Low IR
Description: Select the N modes with the smallest IR intensities.

ModeNumber

Type: Integer List
GUI name: Mode numbers
Description: Indices of the modes to select.

ScanModes

Type: Bool
Default value: No
GUI name: Scan after refining
Description: 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.

ResonanceRaman

Type: Block
Description: Block that contains settings for the calculation of Resonance Raman calculations

IncidentFrequency

Type: Float
Unit: cm-1
Description: Frequency of incident light. Also used to determine most important excitation in case more than one is provided.

LifeTime

Type: Float
Default value: 0.00045
Unit: hartree
Description: Lifetime of Raman excited state.

RamanOrder

Type: Integer
Default value: 2
Description: Order up to which to compute Raman transitions

RamanRange

Type: Float List
Default value: [0.0, 2000.0]
Unit: cm-1
Recurring: True
Description: Specifies frequency range of the Raman spectrum to compute. 2 numbers: an upper and a lower bound.

Type

Type: Multiple Choice
Options: [ModeScanning, ModeTracking, ModeRefinement, VibronicStructure, VibronicStructureTracking, VibronicStructureRefinement, ResonanceRaman]
Description: Specifies the type of vibrational analysis that should be performed

VSTRestartFile

Type: String
Description: Path to a .rkf file containing restart information for VST.

analysis¶

AutoCorrelation

Type: Block
Recurring: True
Description: All input related to auto correlation functions.

Atoms

Type: Block
Description: 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.

Atom

Type: Integer
Recurring: True
Description: Atom number.

Element

Type: String
Recurring: True
Description: Element Symbol Atom.

Region

Type: String
Recurring: True
Description: Region name.

DataReading

Type: Multiple Choice
Default value: Auto
Options: [Auto, AtOnce, BlockWise]
Description: 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.

InputValues

Type: Block
Description: Relevant if Property is set to InputValues. All input values (a vector on each line) need to be provided in this block, using the keyword Values (possibly multiple times).

Values

Type: Float List
Recurring: True
Description: The values at each step (on a single line)

MaxCorrelationTime

Type: Float
Description: 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

Type: Integer
Description: 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

Type: Integer
Default value: 4
Description: 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

Type: Bool
Default value: No
Description: Compute ACF for all elements in the system. Any other settings in the block will be used.

Property

Type: Multiple Choice
Default value: DipoleDerivativeFromCharges
Options: [Velocities, DipoleMomentFromCharges, DiffusionCoefficient, DipoleDerivativeFromCharges, PressureTensor, Viscosity, DipoleMomentFromBinLog, ViscosityFromBinLog]
Description: 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.

TimeStep

Type: Float
Description: Relevant if Property is set to InputValues. The time separating the entries (in fs). If Property is set to any of the other quantities, it can be read from an RKF file, and the timestep is read from the RKF file as well. The read value then overrides this keyword.

UnwrapCoordinates

Type: Multiple Choice
Default value: Auto
Options: [Auto, Yes, No]
Description: 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

Type: Bool
Default value: No
Description: 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

UseTimeDerivative

Type: Block
Description: Possibly use the time derivative of the selected property (e.g. velocity or dipole moments).

Enabled

Type: Bool
Default value: No
Description: Enable the use of the time derivative of the property.

VecElements

Type: Block
Description: 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). Currently not implemented with InputValues.

Index

Type: Integer
Recurring: True
Description: Element of the property vector.

WritePropertyToKF

Type: Bool
Default value: No
Description: Write the selected property to the KF files for every requested frame

AverageBinPlot

Type: Block
Recurring: True
Description: All input related to velocity profile

Atoms

Type: Block
Description: 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.

Atom

Type: Integer
Recurring: True
Description: Atom number.

Element

Type: String
Recurring: True
Description: Element Symbol Atom.

Region

Type: String
Recurring: True
Description: Region name.

Nbins

Type: Integer
Default value: 10
Description: Number of bins that are plotted

Property

Type: Block
Description: Property to be plotted along the Y-axis

Axis

Type: Float List
Description: If defined the dot_product along this axis will be taken. Otherwise, the length of the property vector will be used.

Name

Type: Multiple Choice
Options: [FrictionCoefficient, Viscosity, Velocities, EngineGradients]
Description: Name of the property

XProperty

Type: Block
Description: Property to be plotted along the Y-axis

Name

Type: Multiple Choice
Default value: Time
Options: [Time, Coords]
Description: Timestep used for the plotting

VecElements

Type: Block
Description: 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). Currently not implemented with InputValues.

Index

Type: Integer
Default value: 3
Description: Element of the x_property, in case it is a vector (For Coords: 1 for X, 2 for Y, 3 for Z).

Histogram

Type: Block
Recurring: True
Description: All input related to histograms.

Axes

Type: Block
Description: Specifications for the histogram axes.

Axis

Type: Block
Recurring: True
Description: Specifications for a single histogram axis.

Atoms

Type: Block
Description: 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.

Atom

Type: Integer
Recurring: True
Description: Atom index.

Element

Type: String
Recurring: True
Description: Element Symbol Atom.

Region

Type: String
Recurring: True
Description: Region name

NBins

Type: Integer
Default value: 100
Description: The number of bins along the histogram axis.

Range

Type: Float List
Description: 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

Type: String
Description: The quantity along the histogram axis.

VecElements

Type: Block
Description: 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.

Index

Type: Integer
Recurring: True
Description: Element of the property vector.

KeepRemainder

Type: Bool
Default value: No
Description: Place the values that fall outside the range in an extra bin (on the right).

Normalized

Type: Bool
Default value: No
Description: Give the normalized histogram.

MeanSquareDisplacement

Type: Block
Recurring: True
Description: All input related to auto correlation functions.

Atoms

Type: Block
Description: 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.

Atom

Type: Integer
Recurring: True
Description: Atom number.

Element

Type: String
Recurring: True
Description: Element Symbol Atom.

Region

Type: String
Recurring: True
Description: Region name.

DataReading

Type: Multiple Choice
Default value: Auto
Options: [Auto, AtOnce, BlockWise]
Description: 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.

InputValues

Type: Block
Description: Relevant if Property is set to InputValues. All input values (a vector on each line) need to be provided in this block, using the keyword Values (possibly multiple times).

Values

Type: Float List
Recurring: True
Description: The values at each step (on a single line)

MaxCorrelationTime

Type: Float
Description: The maximum correlation time in fs. The default is half the simulation time.

MaxFrame

Type: Integer
Description: 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

Type: Bool
Default value: No
Description: Compute MSD for all elements in the system. Any other settings in thie block will be used.

Property

Type: Multiple Choice
Default value: Coords
Options: [Coords, DiffusionCoefficient, Conductivity]
Description: Compute the MSD from the property selected here (from rkf). Selecting DiffusionCoefficient is equivalent to selecting the property Coords.

StartTimeSlope

Type: Float
Default value: 0.0
Description: 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.

TimeStep

Type: Float
Description: Relevant if Property is set to InputValues. The time separating the entries (in fs). If Property is set to any of the other quantities, it can be read from an RKF file, and the timestep is read from the RKF file as well. The read value then overrides this keyword.

UnwrapCoordinates

Type: Multiple Choice
Default value: Auto
Options: [Auto, Yes, No]
Description: 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

Type: Bool
Default value: No
Description: 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

VecElements

Type: Block
Description: 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). Currently not implemented with InputValues.

Index

Type: Integer
Recurring: True
Description: Element of the property vector.

WritePropertyToKF

Type: Bool
Default value: No
Description: Write the selected property to the KF files for every requested frame

Print

Type: Block
Description: This block controls the printing of additional information to stdout.

Timers

Type: Multiple Choice
Default value: None
Options: [None, Normal, Detail, TooMuchDetail]
Description: Printing timing details to see how much time is spend in which part of the code.

RadialDistribution

Type: Block
Recurring: True
Description: All input related to radial distribution functions.

AtomsFrom

Type: Block
Description: Atom numbers or elements for the first set of atoms in the radial distribution.

Atom

Type: Integer
Default value: 0
Recurring: True
Description: Atom number.

Element

Type: String
Recurring: True
Description: Element Symbol Atom.

Region

Type: String
Recurring: True
Description: Region name.

AtomsTo

Type: Block
Description: Atom numbers or elements for the second set of atoms in the radial distribution.

Atom

Type: Integer
Default value: 0
Recurring: True
Description: Atom number.

Element

Type: String
Recurring: True
Description: Element Symbol Atom.

Region

Type: String
Recurring: True
Description: Region name.

DistanceTypeSelection

Type: Multiple Choice
Default value: All
Options: [All, InterMolecular, IntraMolecular]
Description: Select only a certain type of interatomic distances.

KeepRemainder

Type: Bool
Default value: No
Description: Place the values that fall outside the range in an extra bin (on the right).

NBins

Type: Integer
Default value: 1000
Description: The number of bins in the histogram.

PairwisePerElement

Type: Bool
Default value: No
Description: Compute RDF for all element pairs (for all atoms in the system). Any other settings in the block will be used.

Range

Type: Float List
Description: 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.

Task

Type: Multiple Choice
Options: [RadialDistribution, Histogram, AutoCorrelation, MeanSquareDisplacement, AverageBinPlot]
Description: The analysis task.

TrajectoryInfo

Type: Block
Description: All the info regarding the reading of the trajectory files.

NBlocksToCompare

Type: Integer
Default value: 1
Description: Get an error estimate by comparing histograms for NBLocks time blocks of the trajectory.

Trajectory

Type: Block
Recurring: True
Description: All info regarding the reading of a single trajectory file.

KFFilename

Type: String
Default value: ams.rkf
Description: The name of the AMS trajectory file.

Range

Type: Integer List
Description: One or two values: start frame, and optionally end frame. By default the first and last frame are read.

StepSize

Type: Integer
Default value: 1
Description: The step size at which frames are read from the RKF (default 1, every frame is read).

chemtrayzer2¶

Analysis

Type: Block
Description: Statistical post-detection analysis, includes reaction coefficients calculation.

PerformAnalysis

Type: Bool
Default value: Yes
Description: Determine the reaction rate coefficients and statistical errors for the detected reactions.

RateConfidence

Type: Float
Default value: 0.9
Description: 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.

MoleculeIdentifier

Type: Block
Description: Settings for the subgraph identification of molecules and reactions.

MaxDepth

Type: Integer
Default value: 2
Description: 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

Type: Bool
Default value: No
Description: Consider bond orders in the identifier.

UseHs

Type: Bool
Default value: No
GUI name: Use Hs
Description: Consider number of hydrogens of atoms in the identifier.

UseRings

Type: Bool
Default value: Yes
Description: Consider ring membership of atoms in the identifier.

WindowDepth

Type: Integer
Default value: 5
Description: 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.

Output

Type: Block
Description: Settings for program output and output file generation.

CreateLegacyOutput

Type: Bool
Default value: No
Description: 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

Type: Bool
Default value: No
Description: Whether or not to show the reaction graph at the end of the calculation. Requires the python library matplotlib to be installed.

WriteEventsPerTime

Type: Bool
Default value: No
Description: 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

Type: Bool
Default value: No
Description: Whether to write output to KF

WriteMolPopulation

Type: Bool
Default value: No
Description: 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

Type: Bool
Default value: Yes
Description: Write two .csv files that contain information about (1) all unique reactions (reactions.csv); and (2) all individual reaction events (reaction_events.csv).

WriteXYZFiles

Type: Bool
Default value: No
Description: Write XYZ files (geometries) for detected species and XYZ movies for detected reactions into a subfolder named ‘xyz’.

PrintDebug

Type: Bool
Default value: No
Description: Print extra debug information to the terminal.

ReactionDetection

Type: Block
Description: Parameters for the the reaction detection algorithm.

BondBreakingThreshold

Type: Float
Default value: 0.3
Description: The bond-order threshold for bond breaking. If the bond order of a bond goes below this value, the bond is considered broken.

BondFormationThreshold

Type: Float
Default value: 0.8
Description: 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

Type: Float
Description: 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

Type: Float
Default value: 10.0
Unit: fs
GUI name: T stable
Description: The minimum time for a molecule to be considered stable.

Trajectory

Type: Block
Description: Info regarding the trajectory to analyze.

FinalFrame

Type: Integer
Default value: -1
Description: Last frame of the trajectory to analyze.

FirstFrame

Type: Integer
Default value: 1
Description: First frame of the trajectory to analyze.

Path

Type: String
Description: The path to ams results dir of an AMS calculation. This folder must contain a ams.rkf file.

conformers¶

Constraints

Type: Block
Description: 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.

All

Type: String
Recurring: True
Description: 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

Type: String
Recurring: True
Description: Fix the angle between three atoms. Three atom indices followed by an angle in degrees.

Atom

Type: Integer
Recurring: True
Description: Fix the position of an atom. Just one integer referring to the index of the atom in the [System%Atoms] block.

AtomList

Type: Integer List
Recurring: True
Description: Fix positions of the specified atoms. A list of integers referring to indices of atoms in the [System%Atoms] block.

Block

Type: String
Recurring: True
Description: Name of the region to constrain as a rigid block. Regions are specified in the System%Atoms block.

BlockAtoms

Type: Integer List
Recurring: True
Description: List of atom indices for a block constraint, where the internal degrees of freedom are frozen.

Coordinate

Type: String
Recurring: True
Description: Fix a particular coordinate of an atom. Atom index followed by (x|y|z).

DifDist

Type: String
Recurring: True
Description: 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

Type: String
Recurring: True
Description: Fix the dihedral angle between four atoms. Four atom indices followed by an angle in degrees.

Distance

Type: String
Recurring: True
Description: Fix the distance between two atoms. Two atom indices followed by the distance in Angstrom.

EqualStrain

Type: String
Description: 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

Type: String
Recurring: True
Description: Fix positions of all atoms in a region.

FreezeStrain

Type: String
Description: 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

Type: String
Recurring: True
Description: 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.

Engine

Type: Block
Description: The input for the computational engine used to compute energy and forces.

EngineAddons

Type: Block
Description: This block configures all the engine add-ons.

AtomEnergies

Type: Non-standard block
Description: Add an element-dependent energy per atom. On each line, give the chemical element followed by the energy (in atomic units).

D3Dispersion

Type: Block
Description: This block configures the add-on that adds the Grimme D3 dispersion correction to the engine’s energy, gradients, and stress tensor.

Damping

Type: Multiple Choice
Default value: BJ
Options: [BJ, Zero]
Description: Type of damping: BJ (Becke-Johnson) or Zero. BJ is recommended for most applications.

Enabled

Type: Bool
Default value: No
GUI name: D3 dispersion
Description: Enables the D3 dispersion correction addon.

Functional

Type: String
Default value: PBE
Description: 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

Type: Float
Description: The a1 parameter. Only used if Damping is set to BJ. If set, it overwrites the a1 value for the chosen functional.

a2

Type: Float
Description: The a2 parameter. Only used if Damping is set to BJ. If set, it overwrites the a2 value for the chosen functional.

s6

Type: Float
Description: The s6 parameter, global scaling parameter. If set, it overwrites the s6 value for the chosen functional.

s8

Type: Float
Description: The s8 parameter. If set, it overwrites the s8 value for the chosen functional.

sr6

Type: Float
Description: The sr6 parameter. Only used if Damping is set to Zero. If set, it overwrites the sr6 value for the chosen functional.

D4Dispersion

Type: Block
Description: This block configures the addon that adds the Grimme D4(EEQ) dispersion correction to the engine’s energy, gradients, stress tensor and Hessian.

Enabled

Type: Bool
Default value: No
GUI name: D4 dispersion
Description: Enables the D4 dispersion correction addon.

Functional

Type: Multiple Choice
Default value: PBE
Options: [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]
Description: Use the D4 parameterization by Grimme for a given xc-functional.

Verbosity

Type: Multiple Choice
Default value: Silent
Options: [Silent, Normal, Verbose, VeryVerbose]
Description: Controls the verbosity of the dftd4 code. Equivalent to the –silent and –verbose command line switches of the official dftd4 program.

a1

Type: Float
Description: 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

Type: Float
Description: 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

Type: Float
Description: 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

Type: Float
Description: 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

Type: Float
Description: The s9 parameter, see D4 article. If set, it overwrites the s9 value for the chosen functional.

ExternalEngine

Type: Block
Description: External engine as an addon

Execute

Type: String
GUI name: Execute
Description: execute command

ExternalStress

Type: Block
Description: This block configures the addon that adds external stress term to the engine’s energy and stress tensor.

StressTensorVoigt

Type: Float List
Unit: Hartree/Bohr^3
GUI name: External stress tensor
Description: 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

Type: Bool
Default value: No
Description: Whether ot not the reference cell should be updated every time the system changes (see documentation).

PipeEngine

Type: Block
Description: Pipe engine as an addon

WorkerCommand

Type: String
GUI name: Worker command
Description: pipe worker command

Pressure

Type: Float
Default value: 0.0
Unit: GPa
Description: Add a hydrostatic pressure term to the engine’s energy and stress tensor. Can only be used for 3D periodic boundary conditions.

Repulsion

Type: Block
Description: This block configures an addon that adds a repulsive Weeks-Chandler-Andersen potential to all atom pairs.

Enabled

Type: Bool
Default value: No
GUI name: Repulsion
Description: 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

Type: Float
Default value: 0.01
Unit: Hartree
Description: The epsilon parameter in the potential equation. It is equal to the amount of energy added at r=sigma.

HydrogenSigmaScale

Type: Float
Default value: 0.75
Unit: Angstrom
Description: 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

Type: Float
Default value: 0.55
Unit: Angstrom
Description: The sigma parameter in the potential equation. The potential is exactly zero at the distances larger than about 1.12*sigma

SkinLength

Type: Float
Default value: 2.0
Unit: Angstrom
Description: 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.

WallPotential

Type: Block
Description: This block configures the addon that adds a spherical wall potential to the engine’s energy and gradients.

Enabled

Type: Bool
Default value: No
Description: 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

Type: Float
Default value: 10.0
Unit: 1/Angstrom
Description: The radial gradient outside the sphere.

Prefactor

Type: Float
Default value: 0.01
Unit: Hartree
Description: The multiplier for the overall strength of the potential.

Radius

Type: Float
Default value: 30.0
Unit: Angstrom
Value Range: value > 0
Description: The radius of the sphere, wherein the potential is close to zero.

Equivalence

Type: Block
Description: Options for the procedure determining whether two structures are equivalent or distinct conformers.

AMS

Type: Block
Description: 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.

DihedralThreshold

Type: Float
Default value: 30.0
Description: Maximum difference a dihedral can have for a conformer to be considered a duplicate.

DistanceThreshold

Type: Float
Default value: 0.1
Description: Maximum difference a distance between two atoms can have for a conformer to be considered a duplicate.

EnergyThreshold

Type: Float
Default value: 0.2
Unit: kcal/mol
Description: The energy difference beyond which two conformers are always considered distinct.

IrrelevantAtoms

Type: Integer List
Description: 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.

AcceptAll

Type: Bool
Default value: No
Description: If set to True, add any candidate to the set without checks of connectivity changes, stereo- or cis/trans isomerization, or duplication.

AcceptIsomers

Type: Bool
Default value: No
Description: If set to True, perform all checks of a new conformer candidate, except for the stereo- or cis/trans isomerization check.

CREST

Type: Block
Description: Options for the CREST method of checking equivalence. This method uses the rotational constants of conformer candidates to determine if they are duplicates.

EnergyThreshold

Type: Float
Default value: 0.05
Unit: kcal/mol
Description: The energy difference beyond which two conformers are always considered distinct.

RMSDThreshold

Type: Float
Default value: 0.125
Description: Threshold for the RMSD between two conformers that determines if they are duplicates or rotamers (according to the CREST rotamer definition.)

ScaledRotationalConstantSettings

Type: Block
Description: 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.

RotationalConstantThreshold

Type: Float
Default value: 0.003
Description: 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.

CheckForDuplicates

Type: Bool
Default value: Yes
Description: 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.

Method

Type: Multiple Choice
Default value: CREST
Options: [AMS, TFD, RMSD, CREST]
GUI name: Equivalence method
Description: 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.

RMSD

Type: Block
Description: 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.

EnergyThreshold

Type: Float
Default value: 0.05
Unit: kcal/mol
Description: The energy difference beyond which two conformers are always considered distinct.

RMSDThreshold

Type: Float
Default value: 0.125
Description: Threshold on the RMSD difference to determine if two geometries represent the same conformer. This value is in Angstrom.

Reorder

Type: Bool
Default value: Yes
Description: Reorder conformers based on energy, whenever a new conformer is added.

TFD

Type: Block
Description: Options for the TFD method of checking equivalence. This method uses the Torsion Finger Print method to determine if two conformer candidates are duplicates.

EnergyThreshold

Type: Float
Default value: 0.05
Unit: kcal/mol
Description: The energy difference beyond which two conformers are always considered distinct.

TFDThreshold

Type: Float
Default value: 0.05
Description: Threshold on the torsion fingerprint difference to determine if two geometries represent the same conformer. This value is unit-less.

Expander

Type: Block
Description: 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.

GC

Type: Block
Description: 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.

MaxGCenergy

Type: Float
Default value: 6.0
Description: 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

Type: Bool
Default value: Yes
Description: Determines if the combinatorial expansion of conformers should be performed in parallel or not (default: True).

RMSDThreshold

Type: Float
Default value: 0.25
Description: Newly generated geometries are only considered unique if their RMSD from all other newly generated geometries is larger than this threshold.

MD

Type: Block
Description: Produces conformers by running a set of MD simulations at different elevated temperatures, extracting snapshots, and optimizing those.

MolecularDynamics

Type: Block
Description: 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.

Checkpoint

Type: Block
Description: Sets the frequency for storing the entire MD state necessary for restarting the calculation.

Frequency

Type: Integer
Default value: 1000
GUI name: Checkpoint frequency
Description: Write the MD state and engine-specific data to the respective .rkf files once every N steps.

WriteProperties

Type: Bool
Default value: No
Description: Write the properties from the properties section to the ChecoPoint file once every N steps.

InitialVelocities

Type: Block
Description: Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.

File

Type: String
Description: AMS RKF file containing the initial velocities.

RandomVelocitiesMethod

Type: Multiple Choice
Default value: Exact
Options: [Exact, Boltzmann, Gromacs]
GUI name: Velocity randomization method
Description: 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

Type: Float
Unit: Kelvin
GUI name: Initial temperature
Description: 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

Type: Multiple Choice
Default value: Random
Options: [Zero, Random, FromFile, Input]
GUI name: Initial velocities
Description: 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

Type: Non-standard block
Description: 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.

NSteps

Type: Integer
Default value: 1000
GUI name: Number of steps
Description: The number of steps to be taken in the MD simulation.

Preserve

Type: Block
Description: Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.

AngularMomentum

Type: Bool
Default value: Yes
GUI name: : Angular momentum
Description: 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

Type: Bool
Default value: No
GUI name: : Center of mass
Description: Translate the system to keep its center of mass at the coordinate origin. This option is not very useful for 3D-periodic systems.

Momentum

Type: Bool
Default value: Yes
GUI name: Preserve: Total momentum
Description: 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).

Print

Type: Block
Description: This block controls the printing of additional information to stdout.

System

Type: Bool
Default value: No
Description: Print the chemical system before and after the simulation.

Velocities

Type: Bool
Default value: No
Description: Print the atomic velocities before and after the simulation.

Restart

Type: String
GUI name: Restart from
Description: The path to the ams.rkf file from which to restart the simulation.

Shake

Type: Block
Description: Parameters of the Shake/Rattle algorithm.

All

Type: String
Recurring: True
GUI name: Constrain all
Description: 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

Type: Float
Default value: 1e-08
Description: Convergence criterion on the max squared difference, in atomic units.

ConvergeRV

Type: Float
Default value: 1e-08
Description: Convergence criterion on the orthogonality of the constraint and the relative atomic velocity, in atomic units.

Iterations

Type: Integer
Default value: 100
Description: Number of iterations.

ShakeInitialCoordinates

Type: Bool
Default value: Yes
Description: Apply constraints before computing the first energy and gradients.

Thermostat

Type: Block
Recurring: True
Description: 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’ behavior.

BerendsenApply

Type: Multiple Choice
Default value: Global
Options: [Local, Global]
GUI name: Apply Berendsen
Description: Select how to apply the scaling correction for the Berendsen thermostat: - per-atom-velocity (Local) - on the molecular system as a whole (Global).

ChainLength

Type: Integer
Default value: 10
GUI name: NHC chain length
Description: Number of individual thermostats forming the NHC thermostat

Duration

Type: Integer List
GUI name: Duration(s)
Description: Specifies how many steps should a transition from a particular temperature to the next one in sequence take.

Region

Type: String
Default value: *
Description: 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.

Tau

Type: Float
Unit: Femtoseconds
GUI name: Damping constant
Description: The time constant of the thermostat.

Temperature

Type: Float List
Unit: Kelvin
GUI name: Temperature(s)
Description: 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

Type: Multiple Choice
Default value: None
Options: [None, Berendsen, NHC]
GUI name: Thermostat
Description: Selects the type of the thermostat.

TimeStep

Type: Float
Default value: 0.25
Unit: Femtoseconds
Description: The time difference per step.

Trajectory

Type: Block
Description: Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.

ExitConditionFreq

Type: Integer
GUI name: Exit condition frequency
Description: Check the exit conditions every N steps. By default this is done every SamplingFreq steps.

PrintFreq

Type: Integer
GUI name: Printing frequency
Description: Print current thermodynamic properties to the output every N steps. By default this is done every SamplingFreq steps.

SamplingFreq

Type: Integer
Default value: 100
GUI name: Sample frequency
Description: Write the the molecular geometry (and possibly other properties) to the .rkf file once every N steps.

TProfileGridPoints

Type: Integer
Default value: 0
Description: 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

Type: Bool
Default value: Yes
Description: Write detected bonds to the .rkf file.

WriteCharges

Type: Bool
Default value: Yes
Description: 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

Type: Bool
Default value: Yes
Description: Write atomic coordinates to the .rkf file.

WriteEngineGradients

Type: Bool
Default value: No
Description: Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.

WriteMolecules

Type: Bool
Default value: Yes
Description: Write the results of molecule analysis to the .rkf file.

WriteVelocities

Type: Bool
Default value: Yes
Description: Write velocities to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze the velocities.

Ngeoms

Type: Integer
Default value: 4
Description: 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

Type: Float List
Default value: [400.0, 500.0]
Unit: Kelvin
Description: The list of different temperatures at which MD simulations are run.

UseShake

Type: Bool
Default value: No
Description: Constrain all -H bonds with shake. If turned on, the MD timestep is automatically increased.

MaxEnergy

Type: Float
Unit: kcal/mol
Description: 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

Type: Multiple Choice
Default value: GC
Options: [MD, GC]
GUI name: Generator method
Description: Method used to generate the conformers.

Preoptimization

Type: Block
Description: 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.

Enable

Type: Bool
Default value: No
Description: Perform preoptimization at a low level of accuracy.

Engine

Type: Block
Description: The engine specifics to be used for preoptimization.

PreoptFactor

Type: Integer
Default value: 2
Description: This factor is multiplied with MaxEnergy, to determine which high energy conformers can be discarded after preoptimization.

RDKitETKDG

Type: Block
Description: Settings for the call to RDKits ETKDG conformer generator tool.

BestRMSDThreshold

Type: Float
Default value: -1.0
Description: 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.

Forcefield

Type: Multiple Choice
Default value: None
Options: [None, UFF, MMFF]
Description: 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

Type: Bool
Default value: No
Description: Experimental: Parallelize the RDKit generation step by calling the RDKit conformer generation method in parallel from multiple processes.

RMSDThreshold

Type: Float
Default value: -1.0
Description: Root Mean Square deviation threshold for removing similar/equivalent conformations during the RDKit ETKDG procedure. By default there is no pruning (value: -1).

UseExpTorsionAnglePrefs

Type: String
Default value: default
Description: Impose experimental torsion angle preferences in RDKit ETKDG conformer generation. By default the RDKit version determines whether or not to switch this on.

RNGSeed

Type: Integer
Description: Initial guesses for conformers can be randomly generated by RDKit, using the ETKDG algorithm. For reproducibility, a random number seed can be provided here.

Filter

Type: Block
Description: Options for the conformer filtering.

MaxEnergy

Type: Float
Unit: kcal/mol
Description: 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

Type: Bool
Default value: No
Description: 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!

Generator

Type: Block
Description: Options for the conformer generator.

ANNEALING

Type: Block
Description: Options for the annealing generator. This generator creates conformers by performing a simulated annealing simulation.

MolecularDynamics

Type: Block
Description: 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.

Checkpoint

Type: Block
Description: Sets the frequency for storing the entire MD state necessary for restarting the calculation.

Frequency

Type: Integer
Default value: 1000
GUI name: Checkpoint frequency
Description: Write the MD state and engine-specific data to the respective .rkf files once every N steps.

WriteProperties

Type: Bool
Default value: No
Description: Write the properties from the properties section to the ChecoPoint file once every N steps.

InitialVelocities

Type: Block
Description: Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.

File

Type: String
Description: AMS RKF file containing the initial velocities.

RandomVelocitiesMethod

Type: Multiple Choice
Default value: Exact
Options: [Exact, Boltzmann, Gromacs]
GUI name: Velocity randomization method
Description: 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

Type: Float
Unit: Kelvin
GUI name: Initial temperature
Description: 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

Type: Multiple Choice
Default value: Random
Options: [Zero, Random, FromFile, Input]
GUI name: Initial velocities
Description: 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

Type: Non-standard block
Description: 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.

NSteps

Type: Integer
Default value: 1000
GUI name: Number of steps
Description: The number of steps to be taken in the MD simulation.

Preserve

Type: Block
Description: Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.

AngularMomentum

Type: Bool
Default value: Yes
GUI name: : Angular momentum
Description: 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

Type: Bool
Default value: No
GUI name: : Center of mass
Description: Translate the system to keep its center of mass at the coordinate origin. This option is not very useful for 3D-periodic systems.

Momentum

Type: Bool
Default value: Yes
GUI name: Preserve: Total momentum
Description: 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).

Print

Type: Block
Description: This block controls the printing of additional information to stdout.

System

Type: Bool
Default value: No
Description: Print the chemical system before and after the simulation.

Velocities

Type: Bool
Default value: No
Description: Print the atomic velocities before and after the simulation.

Restart

Type: String
GUI name: Restart from
Description: The path to the ams.rkf file from which to restart the simulation.

Shake

Type: Block
Description: Parameters of the Shake/Rattle algorithm.

All

Type: String
Recurring: True
GUI name: Constrain all
Description: 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

Type: Float
Default value: 1e-08
Description: Convergence criterion on the max squared difference, in atomic units.

ConvergeRV

Type: Float
Default value: 1e-08
Description: Convergence criterion on the orthogonality of the constraint and the relative atomic velocity, in atomic units.

Iterations

Type: Integer
Default value: 100
Description: Number of iterations.

ShakeInitialCoordinates

Type: Bool
Default value: Yes
Description: Apply constraints before computing the first energy and gradients.

Thermostat

Type: Block
Recurring: True
Description: 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’ behavior.

BerendsenApply

Type: Multiple Choice
Default value: Global
Options: [Local, Global]
GUI name: Apply Berendsen
Description: Select how to apply the scaling correction for the Berendsen thermostat: - per-atom-velocity (Local) - on the molecular system as a whole (Global).

ChainLength

Type: Integer
Default value: 10
GUI name: NHC chain length
Description: Number of individual thermostats forming the NHC thermostat

Duration

Type: Integer List
GUI name: Duration(s)
Description: Specifies how many steps should a transition from a particular temperature to the next one in sequence take.

Region

Type: String
Default value: *
Description: 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.

Tau

Type: Float
Unit: Femtoseconds
GUI name: Damping constant
Description: The time constant of the thermostat.

Temperature

Type: Float List
Unit: Kelvin
GUI name: Temperature(s)
Description: 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

Type: Multiple Choice
Default value: None
Options: [None, Berendsen, NHC]
GUI name: Thermostat
Description: Selects the type of the thermostat.

TimeStep

Type: Float
Default value: 0.25
Unit: Femtoseconds
Description: The time difference per step.

Trajectory

Type: Block
Description: Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.

ExitConditionFreq

Type: Integer
GUI name: Exit condition frequency
Description: Check the exit conditions every N steps. By default this is done every SamplingFreq steps.

PrintFreq

Type: Integer
GUI name: Printing frequency
Description: Print current thermodynamic properties to the output every N steps. By default this is done every SamplingFreq steps.

SamplingFreq

Type: Integer
Default value: 100
GUI name: Sample frequency
Description: Write the the molecular geometry (and possibly other properties) to the .rkf file once every N steps.

TProfileGridPoints

Type: Integer
Default value: 0
Description: 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

Type: Bool
Default value: Yes
Description: Write detected bonds to the .rkf file.

WriteCharges

Type: Bool
Default value: Yes
Description: 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

Type: Bool
Default value: Yes
Description: Write atomic coordinates to the .rkf file.

WriteEngineGradients

Type: Bool
Default value: No
Description: Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.

WriteMolecules

Type: Bool
Default value: Yes
Description: Write the results of molecule analysis to the .rkf file.

WriteVelocities

Type: Bool
Default value: Yes
Description: Write velocities to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze the velocities.

Temperatures

Type: Float List
Default value: [298.0, 798.0]
Unit: Kelvin
Description: The minimum and maximum temperature of the annealing simulation. The simulation will start at the highest temperature, and cool down to the lowest.

UseShake

Type: Bool
Default value: No
Description: Constrain all -H bonds with shake. If turned on, the MD timestep is automatically increased.

CREST

Type: Block
Description: 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.

ConvergenceQualityCrude

Type: Multiple Choice
Default value: None
Options: [Normal, Good, VeryGood, Excellent, None]
Description: The tightness of the convergence of the crude geometry pre-optimizations. If set to none it will be selected two levels below ConvergenceQuality.

ConvergenceQualityTight

Type: Multiple Choice
Default value: None
Options: [Normal, Good, VeryGood, Excellent, None]
Description: The tightness of the convergence of the final geometry optimizations. If set to none it will be selected the same as ConvergenceQuality.

GCStep

Type: Bool
Default value: Yes
Description: 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

Type: Integer
Default value: 10
Description: The maximum number of CREST cycles (by default the number is 10). If the lowest conformer energy converges before then, Crest exits.

UseShake

Type: Bool
Default value: Yes
Description: 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).

METADYNAMICS

Type: Block
Description: Produces conformers by running a set of CREST-RMSD metadynamics simulations with different biases, extracting snapshots, and optimizing those.

ConvergenceQualityCrude

Type: Multiple Choice
Default value: none
Options: [normal, good, verygood, excellent, none]
Description: The tightness of the convergence of the crude geometry pre-optimizations. If set to none it will be selected two levels below ConvergenceQuality.

MolecularDynamics

Type: Block
Description: 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.

Checkpoint

Type: Block
Description: Sets the frequency for storing the entire MD state necessary for restarting the calculation.

Frequency

Type: Integer
Default value: 1000
GUI name: Checkpoint frequency
Description: Write the MD state and engine-specific data to the respective .rkf files once every N steps.

WriteProperties

Type: Bool
Default value: No
Description: Write the properties from the properties section to the ChecoPoint file once every N steps.

InitialVelocities

Type: Block
Description: Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.

File

Type: String
Description: AMS RKF file containing the initial velocities.

RandomVelocitiesMethod

Type: Multiple Choice
Default value: Exact
Options: [Exact, Boltzmann, Gromacs]
GUI name: Velocity randomization method
Description: 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

Type: Float
Unit: Kelvin
GUI name: Initial temperature
Description: 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

Type: Multiple Choice
Default value: Random
Options: [Zero, Random, FromFile, Input]
GUI name: Initial velocities
Description: 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

Type: Non-standard block
Description: 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.

NSteps

Type: Integer
Default value: 1000
GUI name: Number of steps
Description: The number of steps to be taken in the MD simulation.

Preserve

Type: Block
Description: Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.

AngularMomentum

Type: Bool
Default value: Yes
GUI name: : Angular momentum
Description: 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

Type: Bool
Default value: No
GUI name: : Center of mass
Description: Translate the system to keep its center of mass at the coordinate origin. This option is not very useful for 3D-periodic systems.

Momentum

Type: Bool
Default value: Yes
GUI name: Preserve: Total momentum
Description: 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).

Print

Type: Block
Description: This block controls the printing of additional information to stdout.

System

Type: Bool
Default value: No
Description: Print the chemical system before and after the simulation.

Velocities

Type: Bool
Default value: No
Description: Print the atomic velocities before and after the simulation.

Restart

Type: String
GUI name: Restart from
Description: The path to the ams.rkf file from which to restart the simulation.

Shake

Type: Block
Description: Parameters of the Shake/Rattle algorithm.

All

Type: String
Recurring: True
GUI name: Constrain all
Description: 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

Type: Float
Default value: 1e-08
Description: Convergence criterion on the max squared difference, in atomic units.

ConvergeRV

Type: Float
Default value: 1e-08
Description: Convergence criterion on the orthogonality of the constraint and the relative atomic velocity, in atomic units.

Iterations

Type: Integer
Default value: 100
Description: Number of iterations.

ShakeInitialCoordinates

Type: Bool
Default value: Yes
Description: Apply constraints before computing the first energy and gradients.

Thermostat

Type: Block
Recurring: True
Description: 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’ behavior.

BerendsenApply

Type: Multiple Choice
Default value: Global
Options: [Local, Global]
GUI name: Apply Berendsen
Description: Select how to apply the scaling correction for the Berendsen thermostat: - per-atom-velocity (Local) - on the molecular system as a whole (Global).

ChainLength

Type: Integer
Default value: 10
GUI name: NHC chain length
Description: Number of individual thermostats forming the NHC thermostat

Duration

Type: Integer List
GUI name: Duration(s)
Description: Specifies how many steps should a transition from a particular temperature to the next one in sequence take.

Region

Type: String
Default value: *
Description: 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.

Tau

Type: Float
Unit: Femtoseconds
GUI name: Damping constant
Description: The time constant of the thermostat.

Temperature

Type: Float List
Unit: Kelvin
GUI name: Temperature(s)
Description: 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

Type: Multiple Choice
Default value: None
Options: [None, Berendsen, NHC]
GUI name: Thermostat
Description: Selects the type of the thermostat.

TimeStep

Type: Float
Default value: 0.25
Unit: Femtoseconds
Description: The time difference per step.

Trajectory

Type: Block
Description: Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.

ExitConditionFreq

Type: Integer
GUI name: Exit condition frequency
Description: Check the exit conditions every N steps. By default this is done every SamplingFreq steps.

PrintFreq

Type: Integer
GUI name: Printing frequency
Description: Print current thermodynamic properties to the output every N steps. By default this is done every SamplingFreq steps.

SamplingFreq

Type: Integer
Default value: 100
GUI name: Sample frequency
Description: Write the the molecular geometry (and possibly other properties) to the .rkf file once every N steps.

TProfileGridPoints

Type: Integer
Default value: 0
Description: 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

Type: Bool
Default value: Yes
Description: Write detected bonds to the .rkf file.

WriteCharges

Type: Bool
Default value: Yes
Description: 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

Type: Bool
Default value: Yes
Description: Write atomic coordinates to the .rkf file.

WriteEngineGradients

Type: Bool
Default value: No
Description: Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.

WriteMolecules

Type: Bool
Default value: Yes
Description: Write the results of molecule analysis to the .rkf file.

WriteVelocities

Type: Bool
Default value: Yes
Description: Write velocities to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze the velocities.

NCycles

Type: Integer
Default value: 5
Description: The maximum number of cycles of metadynamics simulations. The generator stops when either this number is reached, or the conformer set is stable.

NWidthsHeights

Type: Integer List
Default value: [4, 3]
Description: 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.

SimulationSuccessFraction

Type: Float
Default value: 0.4
Description: The fraction of planned metadynamics steps that has to have succeeded in order for the metadynamics iteration to be considered a success.

UseShake

Type: Bool
Default value: No
Description: Constrain all -H bonds with shake. If turned on, the MD timestep is automatically increased.

MaxEnergy

Type: Float
Unit: kcal/mol
Description: 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

Type: Multiple Choice
Default value: RDKit
Options: [RDKit, CREST, ANNEALING]
GUI name: Generator method
Description: 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.

Preoptimization

Type: Block
Description: 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.

Enable

Type: Bool
Default value: No
Description: Perform preoptimization at a low level of accuracy.

Engine

Type: Block
Description: The engine specifics to be used for preoptimization.

PreoptFactor

Type: Integer
Default value: 2
Description: This factor is multiplied with MaxEnergy, to determine which high energy conformers can be discarded after preoptimization.

RDKit

Type: Block
Description: Options for the RDKit generator. This generator produces initial guesses for conformers using the RDKit ETKDG method, followed by AMS geometry optimizations.

InitialNConformers

Type: Integer
GUI name: Initial no. of conformers
Description: 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

Type: Integer
Default value: 5000
Description: If InitialNConformers is not set, then the number of conformers will be automatically set, with a maximum of MaxConfs.

MinConfs

Type: Integer
Default value: 10
Description: If InitialNConformers is not set, then the number of conformers will be automatically set, with a minimum of MinConfs.

NconfsEstimationFactor

Type: Integer
Default value: 100
Description: 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.

RDKitETKDG

Type: Block
Description: Settings for the call to RDKits ETKDG conformer generator tool.

BestRMSDThreshold

Type: Float
Default value: -1.0
Description: 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

Type: Integer List
Description: The indices of the atoms to constrain during ETKDG conformer generation.

Forcefield

Type: Multiple Choice
Default value: None
Options: [None, UFF, MMFF]
Description: 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

Type: Bool
Default value: No
Description: Experimental: Parallelize the RDKit generation step by calling the RDKit conformer generation method in parallel from multiple processes.

RMSDThreshold

Type: Float
Default value: -1.0
Description: Root Mean Square deviation threshold for removing similar/equivalent conformations during the RDKit ETKDG procedure. By default there is no pruning (value: -1).

UseExpTorsionAnglePrefs

Type: String
Default value: default
Description: Impose experimental torsion angle preferences in RDKit ETKDG conformer generation. By default the RDKit version determines whether or not to switch this on.

RNGSeed

Type: Integer
Description: Initial guesses for conformers can be randomly generated by RDKit, using the ETKDG algorithm. For reproducibility, a random number seed can be provided here.

TORSION

Type: Block
Description: 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.

Dtheta

Type: Float
Default value: 60.0
Description: The angle over which the bonds are rotated, in order to create a new conformer.

GeometryOptimization

Type: Block
Description: Some options / details regarding the optimization procedure.

ConvergenceQuality

Type: Multiple Choice
Default value: VeryGood
Options: [Normal, Good, VeryGood, Excellent]
GUI name: Convergence
Description: The tightness of the convergence of the geometry optimizations. Lower quality levels may lead to badly converged geometries being classified as distinct conformers.

GeometryOptimization

Type: Block
Description: Configures details of the geometry optimization and transition state searches.

CalcPropertiesOnlyIfConverged

Type: Bool
Default value: Yes
Description: 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.

Convergence

Type: Block
Description: 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.

Energy

Type: Float
Default value: 1e-05
Unit: Hartree
Value Range: value > 0
GUI name: Energy convergence
Description: 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

Type: Float
Default value: 0.001
Unit: Hartree/Angstrom
Value Range: value > 0
GUI name: Gradient convergence
Description: Threshold for nuclear gradients.

Quality

Type: Multiple Choice
Default value: Custom
Options: [VeryBasic, Basic, Normal, Good, VeryGood, Custom]
GUI name: Convergence
Description: 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

Type: Float
Default value: 0.01
Unit: Angstrom
Value Range: value > 0
GUI name: Step convergence
Description: The maximum Cartesian step allowed for a converged geometry.

StressEnergyPerAtom

Type: Float
Default value: 0.0005
Unit: Hartree
Value Range: value > 0
Description: 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).

CoordinateType

Type: Multiple Choice
Default value: Auto
Options: [Auto, Delocalized, Cartesian]
GUI name: Optimization space
Description: 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.

Dimer

Type: Block
Description: Options for the Dimer method for transition state search.

AngleThreshold

Type: Float
Default value: 1.0
Unit: Degree
Description: The rotation is considered converged when the the rotation angle falls below the specified threshold.

DimerDelta

Type: Float
Default value: 0.01
Unit: Angstrom
Description: Euclidian distance between the midpoint and the endpoint.

ExtrapolateForces

Type: Bool
Default value: Yes
Description: Set to false to call engine to calculate forces at the extrapolated rotation angle instead of extrapolating them.

LBFGSMaxVectors

Type: Integer
Default value: 10
Description: Max number of vectors for the L-BFGS algorithm to save.

MaxRotationIterations

Type: Integer
Default value: 10
Description: Maximum number of rotation iterations for a single translation step.

Region

Type: String
Default value: *
Description: Include only atoms of the specified region(s) in the rotations, which allows searching for a transition state involving selected atoms only.

RotationTrustRadius

Type: Float
Default value: 0.1
Unit: Angstrom
Description: L-BFGS trust radius during rotation iterations.

TranslationTrustRadius

Type: Float
Default value: 0.1
Unit: Angstrom
Description: L-BFGS trust radius during translation iterations.

EngineAutomations

Type: Block
Description: 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.

Enabled

Type: Bool
Default value: Yes
Description: Whether or not automations are enabled at all.

Gradient

Type: Block
Recurring: True
Description: A gradient-based automation.

FinalValue

Type: Float
Description: This value will be used whenever the gradient is less than GradientLow

HighGradient

Type: Float
Default value: 1.0
Unit: Hartree/Angstrom
Description: 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

Type: Float
Description: This value will be used at the first geometry, and whenever the gradient is higher than GradientHigh

LowGradient

Type: Float
Default value: 1.0
Unit: Hartree/Angstrom
Description: Defines a small gradient, see GradientHigh

UseLogInterpolation

Type: Bool
Default value: Yes
Description: Whether to use interpolation on a log (y) scale or not

Variable

Type: String
Default value
Description: variable to be tweaked for the engine.

Iteration

Type: Block
Recurring: True
Description: Geometry step based automation.

FinalValue

Type: Float
Description

FirstIteration

Type: Integer
Default value: 1
Description: When the actual gradient is between the first and last iteration, a linear interpolation is used.

InitialValue

Type: Float
Description: This value will be used when the iteration number is smaller or equal to FirstIteration

LastIteration

Type: Integer
Default value: 10
Description: Where the automation should reach the FinalValue

UseLogInterpolation

Type: Bool
Default value: Yes
Description: Whether to use interpolation on a log (y) scale or not

Variable

Type: String
Default value
Description: variable to be tweaked for the engine.

FIRE

Type: Block
Description: 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).

AllowOverallRotation

Type: Bool
Default value: Yes
Description: 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

Type: Bool
Default value: No
Description: 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

Type: Bool
Default value: No
Description: Map the atoms to the central cell at each geometry step.

NMin

Type: Integer
Default value: 5
Description: Number of steps after stopping before increasing the time step again.

alphaStart

Type: Float
Default value: 0.1
Description: Steering coefficient.

dtMax

Type: Float
Default value: 1.0
Unit: Femtoseconds
Description: Maximum time step used for the integration. For ReaxFF and APPLE&P, this value is reduced by 50%.

dtStart

Type: Float
Default value: 0.25
Unit: Femtoseconds
Description: Initial time step for the integration.

fAlpha

Type: Float
Default value: 0.99
Description: Reduction factor for the steering coefficient.

fDec

Type: Float
Default value: 0.5
Description: Reduction factor for reducing the time step in case of uphill movement.

fInc

Type: Float
Default value: 1.1
Description: Growth factor for the integration time step.

strainMass

Type: Float
Default value: 0.5
Description: 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.

HessianFree

Type: Block
Description: Configures details of the Hessian-free (conjugate gradients or L-BFGS) geometry optimizer.

Step

Type: Block
Description

MaxCartesianStep

Type: Float
Default value: 0.1
Unit: Angstrom
Description: Limit on a single Cartesian component of the step.

MinRadius

Type: Float
Default value: 0.0
Unit: Angstrom
Description: Minimum value for the trust radius.

TrialStep

Type: Float
Default value: 0.0005
Unit: Angstrom
Description: Length of the finite-difference step when determining curvature. Should be smaller than the step convergence criterion.

TrustRadius

Type: Float
Default value: 0.2
Unit: Angstrom
Description: Initial value of the trust radius.

InitialHessian

Type: Block
Description: Options for initial model Hessian when optimizing systems with the Quasi-Newton method.

File

Type: String
GUI name: Initial Hessian from
Description: 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

Type: Multiple Choice
Default value: Auto
Options: [Auto, UnitMatrix, Swart, FromFile, Calculate, CalculateWithFastEngine]
GUI name: Initial Hessian
Description: 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.

KeepIntermediateResults

Type: Bool
Default value: No
Description: 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

Type: Integer
Value Range: value >= 0
GUI name: Maximum number of iterations
Description: The maximum number of geometry iterations allowed to converge to the desired structure.

MaxRestarts

Type: Integer
Default value: 0
Description: 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

Type: Multiple Choice
Default value: Auto
Options: [Auto, Quasi-Newton, FIRE, L-BFGS, ConjugateGradients, Dimer]
GUI name: Optimization method
Description: 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

Type: Bool
Default value: No
Description: Whether to also optimize the lattice for periodic structures. This is currently supported with the Quasi-Newton, FIRE, and L-BFGS optimizers.

PretendConverged

Type: Bool
Default value: No
Description: 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.)

Quasi-Newton

Type: Block
Description: Configures details of the Quasi-Newton geometry optimizer.

MaxGDIISVectors

Type: Integer
Default value: 0
Description: Sets the maximum number of GDIIS vectors. Setting this to a number >0 enables the GDIIS method.

Step

Type: Block
Description

TrustRadius

Type: Float
Description: Initial value of the trust radius.

VaryTrustRadius

Type: Bool
Description: Whether to allow the trust radius to change during optimization. By default True during energy minimization and False during transition state search.

UpdateTSVectorEveryStep

Type: Bool
Default value: Yes
GUI name: Update TSRC vector every step
Description: Whether to update the TS reaction coordinate at each step with the current eigenvector.

RestartDisplacement

Type: Float
Default value: 0.05
Unit: Angstrom
Description: 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.

Keep

Type: Multiple Choice
Default value: None
Options: [None, all]
Description: Keep all the output files of the geometry optimizations. If set to ‘all’, must be used in combination with Output%KeepWorkDir.

MaxConvergenceTime

Type: Multiple Choice
Default value: Default
Options: [Default, High]
Description: 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

Type: Integer
Default value: 1000
Description: 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

Type: Multiple Choice
Default value: Quasi-Newton
Options: [Auto, Quasi-Newton, FIRE, L-BFGS, ConjugateGradients, Dimer]
Description: 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

Type: Bool
Default value: Yes
Description: Whether the set of optimizations should be run via the AMSWorkerPool or via regular AMSJobs.

WriteGeometries

Type: Block
Description: 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.

Dirname

Type: String
Default value: conf_tmpdir
Description: The name of the folder that should contain the optimized geometries.

Enabled

Type: Bool
Default value: No
Description: Enables or disables the periodic writing of optimized geometries to file

InputConformersSet

Type: String
Recurring: True
Description: 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) or a concatenated .xyz file. You can specify multiple input conformers sets by including the InputConformersSet keyword multiple times.

InputMaxConfs

Type: Integer
Description: 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

Type: Float
Unit: kcal/mol
Description: 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.

LoadSystem

Type: Block
Recurring: True
Description: Block that controls reading the chemical system from a KF file instead of the [System] block.

File

Type: String
Description: The path of the KF file from which to load the system. It may also be the results directory containing it.

Section

Type: String
Default value: Molecule
Description: The section on the KF file from which to load the system.

Output

Type: Block
Description: Options regarding the output and result files.

KeepWorkDir

Type: Bool
Default value: No
Description: Do not remove the working directories after the conformer generation is finished.

rkf

Type: Bool
Default value: Yes
Description: 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

Type: Bool
Default value: Yes
Description: Save the final conformers in .sdf format. The file ‘conformers.sdf’ will be located in the results directory.

xyz

Type: Bool
Default value: Yes
Description: Save the final conformers in .xyz format. The file ‘conformers.xyz’ will be located in the results directory.

Restraints

Type: Block
Description: 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.

Angle

Type: String
Recurring: True
Description: 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

Type: String
Recurring: True
Description: 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

Type: String
Recurring: True
Description: 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

Type: String
Recurring: True
Description: 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

Type: Float
Default value: 1.0
GUI name: Default F(inf)
Description: 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

Type: Multiple Choice
Default value: Harmonic
Options: [Harmonic, Hyperbolic, Erf, GaussianWell]
GUI name: Default restraint profile
Description: 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

Type: String
Recurring: True
Description: 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

Type: Multiple Choice
Default value: Default
Options: [Default, MD]
GUI name: Units
Description: 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.

RNGSeed

Type: Integer
Description: 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.

System

Type: Block
Recurring: True
Description: 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.

AllowCloseAtoms

Type: Bool
Default value: No
Description: 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.

Atoms

Type: Non-standard block
Description: The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.

BondOrders

Type: Non-standard block
Description: 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.

Charge

Type: Float
Default value: 0.0
GUI name: Total charge
Description: The system’s total charge in atomic units.

ElectrostaticEmbedding

Type: Block
Description: Container for electrostatic embedding options, which can be combined.

ElectricField

Type: Float List
Unit: V/Angstrom
Description: 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

Type: Block
Description: External point charges (and dipoles).

ChargeModel

Type: Multiple Choice
Default value: Point
Options: [Point, Gaussian]
Description: A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.

ChargeWidth

Type: Float
Default value: -1.0
Description: 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

Type: Non-standard block
Description: 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.

FractionalCoords

Type: Bool
Default value: No
Description: 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

Type: String
Description: Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz

GuessBonds

Type: Bool
Default value: No
Description: Whether or not UFF bonds should be guessed.

Lattice

Type: Non-standard block
Description: Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.

LatticeStrain

Type: Float List
Description: 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.

LoadForceFieldAtomTypes

Type: Block
Description: This is a mechanism to set the ForceField.Type attribute in the input. This information is currently only used by the ForceField engine.

File

Type: String
Description: Name of the (kf) file. It needs to be the result of a forcefield calculation.

LoadForceFieldCharges

Type: Block
Recurring: True
Description: This is a mechanism to set the ForceField.Charge attribute in the input. This information is currently only used by the ForceField engine.

CheckGeometryRMSD

Type: Bool
Default value: No
Description: 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.

File

Type: String
Description: Name of the (kf) file

MaxGeometryRMSD

Type: Float
Default value: 0.1
Unit: Angstrom
Description: 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

Type: String
Default value: *
Description: Region for which the charges should be loaded

Section

Type: String
Default value: AMSResults
Description: Section name of the kf file

Variable

Type: String
Default value: Charges
Description: Variable name of the kf file

MapAtomsToUnitCell

Type: Bool
Default value: No
Description: For periodic systems the atoms will be moved to the central cell.

ModifyAlternativeElements

Type: Bool
Default value: No
Description: 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

Type: Float
Default value: 0.0
Unit: Angstrom
Description: 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

Type: Float
Default value: 0.0
Description: 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

Type: Bool
Default value: No
Description: 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.

Region

Type: Block
Recurring: True
Description: Properties for each region specified in the Atoms block.

Properties

Type: Non-standard block
Description: Properties for each region specified in the Atoms block.

ShiftCoordinates

Type: Float List
Unit: Bohr
Description: Translate the atoms by the specified shift (three numbers).

SuperCell

Type: Integer List
Description: 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

Type: Integer List
Description: 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

Type: Bool
Default value: No
Description: 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

Type: Multiple Choice
Default value: AUTO
Options: [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)]
Description: 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.

Task

Type: Multiple Choice
Default value: Generate
Options: [Generate, Optimize, Filter, Score, Expand]
Description: 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.

fcf¶

See FCF manual page

oled-deposition¶

Box

Type: Block
Description: Specifications of the box into which the material is deposited.

Size

Type: Float List
Default value: [60.0, 60.0, 120.0]
Unit: Angstrom
GUI name: Box size
Description: 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

Type: Multiple Choice
Default value: Graphene
Options: [Graphene, Custom]
Description: The substrate on which to grow the layer.

SubstrateSystem

Type: String
GUI name: Custom substrate
Description: String ID of a named [System] to be used as a substrate. (This is only used when the Substrate key is set to Custom.)

Deposition

Type: Block
Description: Specifies the details of how molecules are deposited.

ConstrainHXBonds

Type: Bool
Default value: Yes
GUI name: Constrain H-* bonds
Description: 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

Type: Integer
Default value: 10000
Description: The frequency in MD steps at which new molecules will be added to the system.

NumMolecules

Type: Integer
Description: 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

Type: Float
Default value: 600.0
Description: The temperature at which the deposition happens.

TimeStep

Type: Float
Default value: 1.0
Unit: Femtoseconds
Description: The time difference per step.

LAMMPSOffload

Type: Block
Description: Offload the calculation to LAMMPS via AMSPipe.

Enabled

Type: Bool
Default value: No
Description: Enable offloading the force field evaluation to LAMMPS instead of handling it internally in AMS.

UseGPU

Type: Bool
Default value: No
GUI name: Use GPU
Description: Accelerate LAMMPS calculations using a GPU. Requires a LAMMPS library built with the GPU package.

UseOpenMP

Type: Bool
Default value: No
GUI name: Use OpenMP
Description: Parallelize LAMMPS calculations using OpenMP threading. Requires a LAMMPS library built with the OMP package.

LoadSystem

Type: Block
Recurring: True
Description: Block that controls reading the chemical system from a KF file instead of the [System] block.

File

Type: String
Description: The path of the KF file from which to load the system. It may also be the results directory containing it.

Section

Type: String
Default value: Molecule
Description: The section on the KF file from which to load the system.

Molecule

Type: Block
Recurring: True
GUI name: Molecules
Description: Specification of the molecule to be deposited.

MoleFraction

Type: Float
Default value: 1.0
GUI name: Molar fraction
Description: The relative occurrence of the molecule with regard to other deposited species. Only relevant for mixed molecule depositions.

SystemName

Type: String
GUI name: Molecule
Description: 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.

RestartWorkdir

Type: String
Description: 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.

System

Type: Block
Recurring: True
Description: 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.

AllowCloseAtoms

Type: Bool
Default value: No
Description: 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.

Atoms

Type: Non-standard block
Description: The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.

BondOrders

Type: Non-standard block
Description: 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.

Charge

Type: Float
Default value: 0.0
GUI name: Total charge
Description: The system’s total charge in atomic units.

ElectrostaticEmbedding

Type: Block
Description: Container for electrostatic embedding options, which can be combined.

ElectricField

Type: Float List
Unit: V/Angstrom
Description: 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

Type: Block
Description: External point charges (and dipoles).

ChargeModel

Type: Multiple Choice
Default value: Point
Options: [Point, Gaussian]
Description: A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.

ChargeWidth

Type: Float
Default value: -1.0
Description: 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

Type: Non-standard block
Description: 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.

FractionalCoords

Type: Bool
Default value: No
Description: 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

Type: String
Description: Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz

GuessBonds

Type: Bool
Default value: No
Description: Whether or not UFF bonds should be guessed.

Lattice

Type: Non-standard block
Description: Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.

LatticeStrain

Type: Float List
Description: 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.

LoadForceFieldAtomTypes

Type: Block
Description: This is a mechanism to set the ForceField.Type attribute in the input. This information is currently only used by the ForceField engine.

File

Type: String
Description: Name of the (kf) file. It needs to be the result of a forcefield calculation.

LoadForceFieldCharges

Type: Block
Recurring: True
Description: This is a mechanism to set the ForceField.Charge attribute in the input. This information is currently only used by the ForceField engine.

CheckGeometryRMSD

Type: Bool
Default value: No
Description: 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.

File

Type: String
Description: Name of the (kf) file

MaxGeometryRMSD

Type: Float
Default value: 0.1
Unit: Angstrom
Description: 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

Type: String
Default value: *
Description: Region for which the charges should be loaded

Section

Type: String
Default value: AMSResults
Description: Section name of the kf file

Variable

Type: String
Default value: Charges
Description: Variable name of the kf file

MapAtomsToUnitCell

Type: Bool
Default value: No
Description: For periodic systems the atoms will be moved to the central cell.

ModifyAlternativeElements

Type: Bool
Default value: No
Description: 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

Type: Float
Default value: 0.0
Unit: Angstrom
Description: 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

Type: Float
Default value: 0.0
Description: 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

Type: Bool
Default value: No
Description: 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.

Region

Type: Block
Recurring: True
Description: Properties for each region specified in the Atoms block.

Properties

Type: Non-standard block
Description: Properties for each region specified in the Atoms block.

ShiftCoordinates

Type: Float List
Unit: Bohr
Description: Translate the atoms by the specified shift (three numbers).

SuperCell

Type: Integer List
Description: 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

Type: Integer List
Description: 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

Type: Bool
Default value: No
Description: 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

Type: Multiple Choice
Default value: AUTO
Options: [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)]
Description: 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.

oled-properties¶

CoresPerJob

Type: Integer
Default value: 8
Description: The number of CPU cores used for each job in the workflow. Combined with the total number of cores used (set by the NSCM environment variable or the -n command 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.

Embedding

Type: Block
Description: Configures details of how the environment is taken into account.

Charges

Type: Multiple Choice
Default value: DFT
Options: [DFTB, DFT]
Description: 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

Type: Float
Default value: 15.0
Unit: Angstrom
Description: 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 Metric keyword.

Metric

Type: Multiple Choice
Default value: Atoms
Options: [CoM, Atoms, Atoms_noH]
Description: 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

Type: Multiple Choice
Default value: DRF
Options: [None, DRF]
Description: The type of embedding used to simulate the molecular environment.

GW

Type: Block
Description: Instruct ADF to perform a G0W0 calculation.

AdaptiveMixing

Type: Float List
Description: 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.

AnalyticalIntegration

Type: Block
Description: 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

Enabled

Type: Bool
Default value: No
GUI name: analytical integration
Description: Enable the calculation of the GW quasi-particle energies via analytical integration.

Polarizability

Type: Multiple Choice
Default value: RPA
Options: [RPA, BSE]
Description: 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.

PrintSpectralFunction

Type: Bool
Default value: No
Description: 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.

SpectralFunctionResolution

Type: Integer
Default value: 800
Description: Number of points at which spectral function is evaluated.

TDA

Type: Bool
Default value: No
Description: Solve the linear response equations in the Tamm-Dancoff approximation.

eta

Type: Float
Default value: 0.001
Description: 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.

Converge

Type: Block
Description: Sets convergence criteria for the GW calculation in self-consistent case

Density

Type: Float List
Default value: [1e-08, 1e-05]
Description: 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.

HOMO

Type: Float
Default value: 0.003
Unit: eV
GUI name: HOMO energy convergence
Description: 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.

DIIS

Type: Integer
Default value: 10
Description: Requests to use DIIS. This is the Default. Number of expansion coefficients can be requested as well. Ignored in non-selfconsistent calculation

Enabled

Type: Bool
Default value: No
GUI name: Calculate GW quasi-particle energies
Description: Enable the calculation of the GW quasi-particle energies.

FixedGrids

Type: Bool
Default value: No
Description: 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.

LinearMixing

Type: Float List
Description: 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

Type: Bool
Default value: No
Description: Instead of solving the non-linear QP equations in a G0W0 (or evGW calculation) by bisection exactly, 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

Type: Bool
Default value: No
Description: 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.

PrintAllSolutions

Type: Bool
Default value: No
Description: Print out all solutions for all requested states. Detects multiple solutions of the QP equations.

QPHamiltonian

Type: Multiple Choice
Default value: KSF2
Options: [KSF1, KSF2, SRG, LQSGW]
Description: 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. 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

ScissorShift

Type: Bool
Default value: No
Description: 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

Type: Multiple Choice
Default value: G0W0
Options: [G0W0, EVGW0, EVGW, QSGW0, QSGW]
Description: 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.

SelfEnergy

Type: Multiple Choice
Default value: GW
Options: [HF, GW, G3W2, SOSEX, GWGamma, G3W2dynamic]
Description: 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.

nIterations

Type: Integer List
Default value: [10]
GUI name: Number of iterations
Description: 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

Type: Integer
Default value: 1
GUI name: N Lowest
Description: Number of lowest occupied QP levels to be evaluated, overwrites nStates’

nStates

Type: Integer
Default value: 5
GUI name: N states
Description: 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

Type: Bool
Default value: No
Description: 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.

LoadSystem

Type: Block
Recurring: True
Description: Block that controls reading the chemical system from a KF file instead of the [System] block.

File

Type: String
Description: The path of the KF file from which to load the system. It may also be the results directory containing it.

Section

Type: String
Default value: Molecule
Description: The section on the KF file from which to load the system.

LogProgressEvery

Type: Float
Default value: 600.0
Unit: Seconds
Description: How often to print progress information to the logfile.

NumAdditionalOrbitalEnergies

Type: Integer
Default value: 1
Description: 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

Type: Integer
Default value: 1
Description: 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.

OccupationSmearing

Type: Multiple Choice
Default value: Ions
Options: [None, Ions, All]
Description: 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

Type: Multiple Choice
Default value: All
Options: [None, Neutral, All]
Description: 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

Type: String
Description: 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

Type: Integer List
Description: Indices of the molecules to calculate properties for. If not present, all molecules will be used. Note that indexing starts at 0.

StoreResultFiles

Type: Multiple Choice
Default value: Failed
Options: [None, Failed, All]
Description: 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.

System

Type: Block
Recurring: True
Description: 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.

AllowCloseAtoms

Type: Bool
Default value: No
Description: 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.

Atoms

Type: Non-standard block
Description: The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.

BondOrders

Type: Non-standard block
Description: 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.

Charge

Type: Float
Default value: 0.0
GUI name: Total charge
Description: The system’s total charge in atomic units.

ElectrostaticEmbedding

Type: Block
Description: Container for electrostatic embedding options, which can be combined.

ElectricField

Type: Float List
Unit: V/Angstrom
Description: 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

Type: Block
Description: External point charges (and dipoles).

ChargeModel

Type: Multiple Choice
Default value: Point
Options: [Point, Gaussian]
Description: A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.

ChargeWidth

Type: Float
Default value: -1.0
Description: 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

Type: Non-standard block
Description: 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.

FractionalCoords

Type: Bool
Default value: No
Description: 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

Type: String
Description: Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz

GuessBonds

Type: Bool
Default value: No
Description: Whether or not UFF bonds should be guessed.

Lattice

Type: Non-standard block
Description: Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.

LatticeStrain

Type: Float List
Description: 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.

LoadForceFieldAtomTypes

Type: Block
Description: This is a mechanism to set the ForceField.Type attribute in the input. This information is currently only used by the ForceField engine.

File

Type: String
Description: Name of the (kf) file. It needs to be the result of a forcefield calculation.

LoadForceFieldCharges

Type: Block
Recurring: True
Description: This is a mechanism to set the ForceField.Charge attribute in the input. This information is currently only used by the ForceField engine.

CheckGeometryRMSD

Type: Bool
Default value: No
Description: 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.

File

Type: String
Description: Name of the (kf) file

MaxGeometryRMSD

Type: Float
Default value: 0.1
Unit: Angstrom
Description: 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

Type: String
Default value: *
Description: Region for which the charges should be loaded

Section

Type: String
Default value: AMSResults
Description: Section name of the kf file

Variable

Type: String
Default value: Charges
Description: Variable name of the kf file

MapAtomsToUnitCell

Type: Bool
Default value: No
Description: For periodic systems the atoms will be moved to the central cell.

ModifyAlternativeElements

Type: Bool
Default value: No
Description: 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

Type: Float
Default value: 0.0
Unit: Angstrom
Description: 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

Type: Float
Default value: 0.0
Description: 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

Type: Bool
Default value: No
Description: 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.

Region

Type: Block
Recurring: True
Description: Properties for each region specified in the Atoms block.

Properties

Type: Non-standard block
Description: Properties for each region specified in the Atoms block.

ShiftCoordinates

Type: Float List
Unit: Bohr
Description: Translate the atoms by the specified shift (three numbers).

SuperCell

Type: Integer List
Description: 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

Type: Integer List
Description: 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

Type: Bool
Default value: No
Description: 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

Type: Multiple Choice
Default value: AUTO
Options: [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)]
Description: 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.

TransferIntegrals

Type: Block
Description: Configures the details of the calculation of electron and hole transfer integrals.

Exclude

Type: Block
Description: Configures which dimers NOT to calculate transfer integrals for.

Cutoff

Type: Float
Default value: 4.0
Unit: Angstrom
GUI name: Exclude beyond
Description: 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

Type: Multiple Choice
Default value: Atoms
Options: [CoM, Atoms, Atoms_noH]
Description: 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.

Include

Type: Block
Description: Configures which dimers transfer integrals are calculated for.

Cutoff

Type: Float
Default value: 4.0
Unit: Angstrom
GUI name: Include within
Description: 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 Metric keyword.

Metric

Type: Multiple Choice
Default value: Atoms
Options: [CoM, Atoms, Atoms_noH]
Description: 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

Type: Multiple Choice
Default value: Fast
Options: [None, Fast, Full]
Description: The method used for the calculation of the transfer integrals.