# Keywords¶

## Summary of all keywords¶

Constraints
Type: Block 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.
Angle
Type: String True Fix the angle between three atoms. Three atom indices followed by an angle in degrees.
Atom
Type: Integer True 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 True Fix positions of the specified atoms. A list of integers referring to indices of atoms in the [System%Atoms] block.
Block
Type: String True Name of the region to constrain as a rigid block. Regions are specified in the System%Atoms block.
BlockAtoms
Type: Integer List True List of atom indices for a block constraint, where the internal degrees of freedom are frozen.
Coordinate
Type: String True Fix a particular coordinate of an atom. Atom index followed by (x|y|z).
DifDist
Type: String True 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 True Fix the dihedral angle between four atoms. Four atom indices followed by an angle in degrees.
Distance
Type: String True Fix the distance between two atoms. Two atom indices followed by the distance in Angstrom.
EqualStrain
Type: String 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 True Fix positions of all atoms in a region.
FreezeStrain
Type: String 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 True 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 Options for numerical evaluation of the elastic tensor.
MaxGradientForGeoOpt
Type: Float 0.0001 Hartree/Angstrom Maximum nuclear gradient Maximum nuclear gradient for the relaxation of the internal degrees of freedom of strained systems.
Parallel
Type: Block 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 Cores per group Number of cores in each working group.
nGroups
Type: Integer Number of groups Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup
Type: Integer Nodes per group 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 0.001 Step size (relative) of strain deformations used for computing the elastic tensor numerically.
Engine
Type: Block The input for the computational engine. The header of the block determines the type of the engine.
EngineAddons
Type: Block This block configures all the engine add-ons.
AtomEnergies
Type: Non-standard block Add an element-dependent energy per atom. On each line, give the chemical element followed by the energy (in atomic units).
D3Dispersion
Type: Block 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 BJ [BJ, Zero] Type of damping: BJ (Becke-Johnson) or Zero. BJ is recommended for most applications.
Enabled
Type: Bool No Enables the D3 dispersion correction addon.
Functional
Type: String PBE 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 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 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 The s6 parameter, global scaling parameter. If set, it overwrites the s6 value for the chosen functional.
s8
Type: Float The s8 parameter. If set, it overwrites the s8 value for the chosen functional.
sr6
Type: Float 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 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 No Enables the D4 dispersion correction addon.
Functional
Type: Multiple Choice PBE [HF, BLYP, BPBE, BP86, BPW, LB94, MPWLYP, MPWPW91, OLYP, OPBE, PBE, RPBE, REVPBE, PW86PBE, RPW86PBE, PW91, PW91P86, XLYP, B97, TPSS, REVTPSS, SCAN, B1LYP, B3LYP, BHLYP, B1P86, B3P86, B1PW91, B3PW91, O3LYP, REVPBE0, REVPBE38, PBE0, PWP1, PW1PW, MPW1PW91, MPW1LYP, PW6B95, TPSSH, TPSS0, X3LYP, M06L, M06, OMEGAB97, OMEGAB97X, CAM-B3LYP, LC-BLYP, LH07TSVWN, LH07SSVWN, LH12CTSSIRPW92, LH12CTSSIFPW92, LH14TCALPBE, B2PLYP, B2GPPLYP, MPW2PLYP, PWPB95, DSDBLYP, DSDPBE, DSDPBEB95, DSDPBEP86, DSDSVWN, DODBLYP, DODPBE, DODPBEB95, DODPBEP86, DODSVWN, PBE02, PBE0DH, DFTB(3ob), DFTB(mio), DFTB(pbc), DFTB(matsci), DFTB(ob2), B1B95, MPWB1K, REVTPSSH, GLYP, REVPBE0DH, REVTPSS0, REVDSDPBEP86, REVDSDPBEPBE, REVDSDBLYP, REVDODPBEP86, B97M, OMEGAB97M, R2SCAN] Use the D4 parameterization by Grimme for a given xc-functional.
Verbosity
Type: Multiple Choice Silent [Silent, Normal, Verbose, VeryVerbose] Controls the verbosity of the dftd4 code. Equivalent to the –silent and –verbose command line switches of the official dftd4 program.
a1
Type: Float 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 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 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 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 The s9 parameter, see D4 article. If set, it overwrites the s9 value for the chosen functional.
ExternalEngine
Type: Block External engine as an addon
Execute
Type: String Execute execute command
ExternalStress
Type: Block This block configures the addon that adds external stress term to the engine’s energy and stress tensor.
StressTensorVoigt
Type: Float List a.u. External stress tensor 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 No Whether ot not the reference cell should be updated every time the system changes (see documentation).
PipeEngine
Type: Block Pipe engine as an addon
WorkerCommand
Type: String Worker command pipe worker command
Pressure
Type: Float 0.0 GPa Add a hydrostatic pressure term to the engine’s energy and stress tensor. Can only be used for 3D periodic boundary conditions.
WallPotential
Type: Block This block configures the addon that adds a spherical wall potential to the engine’s energy and gradients.
Enabled
Type: Bool No Enables the wall potential addon.
Gradient
Prefactor
Type: Float 0.01 Hartree The multiplier for the overall strength of the potential.
Radius
Type: Float 30.0 Angstrom The radius of the sphere, wherein the potential is close to zero.
EngineDebugging
Type: Block This block contains some options useful for debugging the computational engines.
CheckInAndOutput
Type: Bool No Enables some additional checks on the input and output of and engine, e.g. for NaN values.
ForceContinousPES
Type: Bool No 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 No 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 No 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 No 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 No Makes the engine ignore the request to work quietly.
RandomFailureChance
Type: Float 0.0 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 0.0 Hartree 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 0.0 Hartree/Angstrom 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 0.0 Makes the engine randomly stop. Can be used to simulate crashes.
EngineRestart
Type: String 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.
GCMC
Type: Block 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 0.0 Volume available to GCMC, in cubic Angstroms. AccessibleVolume should be specified for “Accessible” and “FreeAccessible” [VolumeOption].
Box
Type: Block 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 Coordinate of the upper bound along the first axis.
Amin
Type: Float Coordinate of the lower bound along the first axis.
Bmax
Type: Float Coordinate of the upper bound along the second axis.
Bmin
Type: Float Coordinate of the lower bound along the second axis.
Cmax
Type: Float Coordinate of the upper bound along the third axis.
Cmin
Type: Float Coordinate of the lower bound along the third axis.
Ensemble
Type: Multiple Choice Mu-VT [Mu-VT, Mu-PT] Select the MC ensemble: Mu-VT for fixed volume or Mu-PT for variable volume. When the Mu-PT ensemble is selected the [Pressure] and [VolumeChangeMax] should also be specified.
Iterations
Type: Integer Number of GCMC iterations Number of GCMC moves.
MapAtomsToOriginalCell
Type: Bool Yes Keeps the atom (mostly) in the original cell by mapping them back before the geometry optimizations.
MaxDistance
Type: Float 3.0 Angstrom Add molecules within The max distance to other atoms of the system when adding the molecule.
MinDistance
Type: Float 0.3 Angstrom Add molecules not closer than Keep the minimal distance to other atoms of the system when adding the molecule.
Molecule
Type: Block True Molecules 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 Hartree 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 No Fix molecule 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 Molecule 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 0.0 Non-accessible volume Volume not available to GCMC, in cubic Angstroms. NonAccessibleVolume may be specified for the “Free” [VolumeOption] to reduce the accessible volume.
NumAttempts
Type: Integer 1000 Max tries 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 0.0 Pascal 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 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 Name of an RKF restart file. Upon restart, the information about the GCMC input parameters, the initial system (atomic coordinates, lattice, charge, etc.) and the MC molecules (both already inserted and to be inserted) are read from the restart file. The global GCMC input parameters and the MC Molecules can be modified from input. Any parameter not specified in the input will use its value from the restart file (i.e. not the default value). Molecules found in the restart file do not have to be present as named Systems in the input, however if there is a System present that matches the name of a molecule from restart then the System’s geometry will replace that found in the restart file. It is also possible to specify new Molecules in the input, which will be added to the pool of the MC molecules from restart.
Temperature
Type: Float 300.0 Kelvin Temperature of the simulation. Increase the temperature to improve the chance of accepting steps that result in a higher energy.
UseGCPreFactor
Type: Bool Yes Use GC prefactor Use the GC pre-exponential factor for probability.
VolumeChangeMax
Type: Float 0.05 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 Free [Free, Total, Accessible, FreeAccessible] Volume method 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 Configures details of the geometry optimization and transition state searches.
CalcPropertiesOnlyIfConverged
Type: Bool Yes 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 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 1e-05 Hartree Energy convergence 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
Step
Type: Float 0.01 Angstrom Step convergence The maximum Cartesian step allowed for a converged geometry.
StressEnergyPerAtom
Type: Float 0.0005 Hartree 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 Auto [Auto, Delocalized, Cartesian] Optimization space 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 and SCMGO methods, while Cartesian coordinates will be used for all other methods.
EngineAutomations
Type: Block 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 Yes Whether or not autotions are enabled at all.
Gradient
Type: Block True A gradient-based automation.
FinalValue
Type: Float This value will be used whenever the gradient is less than GradientLow
HighGradient
Type: Float 1.0 Hartree/Angstrom 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 This value will be used at the first geometry, and whenever the gradient is higher than GradientHigh
LowGradient
UseLogInterpolation
Type: Bool Yes Whether to use interpolation on a log (y) scale or not
Variable
Type: String variable to be tweaked for the engine.
Iteration
Type: Block True Geometry step based automation.
FinalValue
Type: Float
FirstIteration
Type: Integer 1 When the actual gradient is between the first and last iteration, a linear interpolation is used.
InitialValue
Type: Float This value will be used when the iteration number is smaller or equal to FirstIteration
LastIteration
Type: Integer 10 Where the automation should reach the FinalValue
UseLogInterpolation
Type: Bool Yes Whether to use interpolation on a log (y) scale or not
Variable
Type: String variable to be tweaked for the engine.
FIRE
Type: Block 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 Yes 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 No 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 No Map the atoms to the central cell at each geometry step.
NMin
Type: Integer 5 Number of steps after stopping before increasing the time step again.
alphaStart
Type: Float 0.1 Steering coefficient.
dtMax
Type: Float 1.0 Femtoseconds Maximum time step used for the integration.
dtStart
Type: Float 0.25 Femtoseconds Initial time step for the integration.
fAlpha
Type: Float 0.99 Reduction factor for the steering coefficient.
fDec
Type: Float 0.5 Reduction factor for reducing the time step in case of uphill movement.
fInc
Type: Float 1.1 Growth factor for the integration time step.
strainMass
Type: Float 0.5 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 Configures details of the Hessian-free (conjugate gradients or L-BFGS) geometry optimizer.
Step
Type: Block
MaxCartesianStep
Type: Float 0.1 Angstrom Limit on a single Cartesian component of the step.
MinRadius
Type: Float 0.0 Angstrom Minimum value for the trust radius.
TrialStep
Type: Float 0.0005 Angstrom Length of the finite-difference step when determining curvature. Should be smaller than the step convergence criterion.
TrustRadius
Type: Float 0.2 Angstrom Initial value of the trust radius.
InitialHessian
Type: Block Options for initial model Hessian when optimizing systems with either the Quasi-Newton or the SCMGO method.
File
Type: String Initial Hessian from 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 Auto [Auto, UnitMatrix, Swart, FromFile, Calculate, CalculateWithFastEngine] Initial Hessian 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 No 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 Maximum number of iterations The maximum number of geometry iterations allowed to converge to the desired structure.
Method
Type: Multiple Choice Auto [Auto, Quasi-Newton, SCMGO, FIRE, L-BFGS, ConjugateGradients] Optimization method Select the optimization algorithm employed for the geometry relaxation. Currently supported are: the Hessian-based Quasi-Newton-type BFGS algorithm, the experimental SCMGO optimizer, 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 No Whether to also optimize the lattice for periodic structures. This is currently only supported with the Quasi-Newton, FIRE, L-BFGS and SCMGO optimizers.
PretendConverged
Type: Bool No 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 Configures details of the Quasi-Newton geometry optimizer.
MaxGDIISVectors
Type: Integer 0 Sets the maximum number of GDIIS vectors. Setting this to a number >0 enables the GDIIS method.
Step
Type: Block
TrustRadius
Type: Float Initial value of the trust radius.
UpdateTSVectorEveryStep
Type: Bool Yes Update TSRC vector every step Whether to update the TS reaction coordinate at each step with the current eigenvector.
SCMGO
Type: Block Configures details SCMGO.
ContractPrimitives
Type: Bool Yes Form non-redundant linear combinations of primitive coordinates sharing the same central atom
NumericalBMatrix
Type: Bool No Calculation of the B-matrix, i.e. Jacobian of internal coordinates in terms of numerical differentiations
Step
Type: Block
TrustRadius
Type: Float 0.2 Initial value of the trust radius.
VariableTrustRadius
Type: Bool Yes Whether or not the trust radius can be updated during the optimization.
logSCMGO
Type: Bool No Verbose output of SCMGO internal data
testSCMGO
Type: Bool No Run SCMGO in test mode.
IRC
Type: Block Configures details of the Intrinsic Reaction Coordinate optimization.
Convergence
Type: Block 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 0.001 Hartree/Angstrom Gradient convergence Convergence criterion for the max component of the residual energy gradient.
Step
Type: Float 0.001 Angstrom Step convergence Convergence criterion for the max component of the step in the optimization coordinates.
CoordinateType
Type: Multiple Choice Cartesian [Cartesian, Delocalized] Coordinates used for optimization Select the type of coordinates in which to perform the optimization. Note that the Delocalized option should be considered experimental.
Direction
Type: Multiple Choice Both [Both, Forward, Backward] Select direction of the IRC path. The difference between the Forward and the Backward directions is determined by the sign of the largest component of the vibrational normal mode corresponding to the reaction coordinate at the transition state geometry. The Forward path correspond to the positive sign of the component. If Both is selected then first the Forward path is computed followed by the Backward one.
InitialHessian
Type: Block 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 File 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 Calculate [Calculate, FromFile] Initial Hessian Calculate the exact Hessian for the input geometry or load it from the results of a previous calculation.
KeepConvergedResults
Type: Bool Yes 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 Maximum IRC steps 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 300 Maximum iterations 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 100 Maximum points 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 No Minimum energy profile Calculate minimum energy profile (i.e. no mass-weighting) instead of the IRC.
MinPathLength
Type: Float 0.1 Angstrom 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 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 Restart 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 0 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 0 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 0.2 Step size 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 The path to the file from which to load the engine configuration. Replaces the Engine block.
LoadSystem
Type: Block True Block that controls reading the chemical system from a KF file instead of the [System] block.
File
Type: String The path of the KF file from which to load the system. It may also be the results directory containing it.
Section
Type: String Molecule The section on the KF file from which to load the system.
Log
Type: Non-standard block Configures the debugging loggers. Syntax: ‘Level LoggerName’. Possible Levels: All, Debug, Info, Warning, Error, Fatal.
MolecularDynamics
Type: Block 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 True Add molecules 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 0.0 Kelvin 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 0.0 Angstrom Translate the bullet along the velocity vector until it comes within ContactDistance of any other atom.
Coords
Type: Float List Angstrom 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 Angstrom 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 Angstrom Sigma values (one per Cartesian axis) for a Gauss distribution of the initial coordinates. Can only be used together with Coords.
DeviationAngle
Type: Float 0.0 Degree Randomly tilt the shooting direction up to this angle away from the VelocityDirection vector.
Energy
Type: Float Hartree Initial kinetic energy of the molecule in the shooting direction.
EnergySigma
Type: Float 0.0 Hartree 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 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 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 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 0 A molecule is added every [Frequency] steps after the StartStep. There is never a molecule added at step 0.
MinDistance
Type: Float 0.0 Angstrom Keep the minimal distance to other atoms of the system when adding the molecule.
NumAttempts
Type: Integer 10 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 No Rotate the molecule randomly before adding it to the system.
StartStep
Type: Integer 0 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 Do not add this molecule after the specified step.
System
Type: String 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 Kelvin Initial energy of the molecule in the shooting direction will correspond to the given temperature.
TemperatureSigma
Type: Float 0.0 Kelvin Sigma value for the Gauss distribution of the initial temperature the specified value. Should only be used together with Temperature.
Velocity
Type: Float Angstrom/fs Initial velocity of the molecule in the shooting direction.
VelocityDirection
Type: Float List 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 0.0 Angstrom/fs Sigma value for the Gauss distribution of the initial velocity around the specified value. Should only be used together with Velocity.
Barostat
Type: Block This block allows to specify the use of a barostat during the simulation.
BulkModulus
Type: Float 2200000000.0 Pascal 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 No Keep the volume constant while allowing the box shape to change. This is currently supported only by the MTK barostat.
Duration
Type: Integer List Specifies how many steps should a transition from a particular pressure to the next one in sequence take.
Equal
Type: Multiple Choice None [None, XYZ, XY, YZ, XZ] Enforce equal scaling of the selected set of dimensions. They will be barostatted as one dimension according to the average pressure over the components.
Pressure
Type: Float List Pascal 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 XYZ [XYZ, Shape, X, Y, Z, XY, YZ, XZ] Dimensions that should be scaled by the barostat to maintain pressure. Selecting Shape means that all three dimensions and also all the cell angles are allowed to change.
Tau
Type: Float Femtoseconds Damping constant Specifies the time constant of the barostat.
Type
Type: Multiple Choice None [None, Berendsen, MTK] Barostat Selects the type of the barostat.
BondBoost
Type: Block True Forced reaction (bond boost) definitions. Multiple BondBoost blocks may be specified, which will be treated independently.
Chain
Type: Block 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 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 Angstrom 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 Angstrom 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 True Specify two atom indices followed by the distance in Angstrom, the ForceConstant (in a.u.) and, optionally, the 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. Each index indicates position of the corresponding atom in the AtomNames key. Currently recognized restraint profile types: Harmonic (default), Hyperbolic, Erf.
NSteps
Type: Integer Boost lifetime 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 1 Number of instances Number of reactions of this type taking place simultaneously.
CRESTMTD
Type: Block CREST_MTD Input for CREST metadynamics simulation.
AddEnergy
Type: Bool No Add the bias energy to the potential energy (to match the gradients)
GaussianScaling
Type: Block Options for gradual introduction of the Gaussians
ScaleGaussians
Type: Bool Yes Introduce the Gaussians gradually, using a scaling function
ScalingSlope
Type: Float 0.03 Slope of the scaling function for the Gaussians with respect to time
Height
Type: Float Hartree The height of the Gaussians added
NGaussiansMax
Type: Integer Maximum number of Gaussians stored
NSteps
Type: Integer Interval of Gaussian placement
RestartFile
Type: String Filename for file from which to read data on Gaussians placed previously.
Width
Type: Float Bohr The width of the Gaussians added in terms of the RMSD
CVHD
Type: Block True CVHD Input for the Collective Variable-driven HyperDynamics (CVHD).
Bias
Type: Block 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 0.0 Kelvin Bias damping T 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 Standard deviation parameter of the Gaussian bias peak.
Height
Type: Float Hartree Height of the Gaussian bias peak.
ColVarBB
Type: Block True Collective Variable 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 Specifies the first bonded atom in the collective variable.
region
Type: String * 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 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 Specifies the second bonded atom in the collective variable.
region
Type: String * 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 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 0.3 Bond order cutoff 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 6 Exponent p Exponent value p used to calculate the p-norm for this CV.
rmax
Type: Float Angstrom R max 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 Angstrom R min Min bond distance parameter Rmin used for calculating the CV. It should be close to equilibrium distance for the corresponding bond.
Frequency
Type: Integer 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].
StartStep
Type: Integer 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 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 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 No 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 Sets the frequency for storing the entire MD state necessary for restarting the calculation.
Frequency
Type: Integer 1000 Checkpoint frequency Write the MD state and engine-specific data to the respective .rkf files once every N steps.
WriteProperties
Type: Bool No Write the properties from the properties section to the ChecoPoint file once every N steps.
Deformation
Type: Block True Deform the periodic lattice of the system during the simulation.
LatticeVelocity
Type: Non-standard block 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 [0.0, 0.0, 0.0] Relative rate of change of each lattice vector per step.
LengthVelocity
Type: Float List [0.0, 0.0, 0.0] Angstrom/fs 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 Femtoseconds Period of oscillation for Type Sine and Cosine.
ScaleAtoms
Type: Bool Yes 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 1 First step at which the deformation will be applied.
StopStep
Type: Integer 0 Last step at which the deformation will be applied. If unset or zero, nSteps will be used instead.
StrainRate
Type: Non-standard block Strain rate matrix to be applied on every step. The format is identical to the System%Lattice block.
TargetLattice
Type: Non-standard block Target lattice vectors to be achieved by StopStep. The format is identical to the System%Lattice block.
TargetLength
Type: Float List [0.0, 0.0, 0.0] Angstrom 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 Linear [Linear, Exponential, Sine, Cosine] Function defining the time dependence of the deformed lattice parameters. Linear increments the lattice parameters by the same absolute amount every timestep. Exponential multiplies the lattice parameters by the same factor every timestep. Only StrainRate, LengthRate, and LengthVelocity are supported for Type=Exponential. Sine deforms the system from the starting lattice to TargetLattice/TargetLength and then by the same amount to the opposite direction, while Cosine deforms the system from the starting lattice to the target and back.
Gravity
Type: Block Apply a constant acceleration in -z.
Acceleration
Type: Float 0.0 Angstrom/fs^2 Magnitude of the applied acceleration.
HeatExchange
Type: Block True Heat exchange Input for the heat-exchange non-equilibrium MD (T-NEMD).
HeatingRate
Type: Float Hartree/fs 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 Simple [Simple, HEX, eHEX] Heat exchange method used. Simple: kinetic energy of the atoms of the source and sink regions is modified irrespective of that of the center of mass (CoM) of the region (recommended for solids). HEX: kinetic energy of the atoms of these regions is modified keeping that of the corresponding CoM constant. eHEX: an enhanced version of HEX that conserves the total energy better (recommended for gases and liquids).
Sink
Type: Block Defines the heat sink region (where the heat will be removed).
AtomList
Type: Integer List Sink region The atoms that are part of the sink. This key is ignored if the [Box] block or [Region] key is present.
Box
Type: Block 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 1.0 Coordinate of the upper bound along the first axis.
Amin
Type: Float 0.0 Coordinate of the lower bound along the first axis.
Bmax
Type: Float 1.0 Coordinate of the upper bound along the second axis.
Bmin
Type: Float 0.0 Coordinate of the lower bound along the second axis.
Cmax
Type: Float 1.0 Coordinate of the upper bound along the third axis.
Cmin
Type: Float 0.0 Coordinate of the lower bound along the third axis.
Region
Type: String Sink region The region that is the sink. This key is ignored if the [Box] block is present.
Source
Type: Block Defines the heat source region (where the heat will be added).
AtomList
Type: Integer List Source region The atoms that are part of the source. This key is ignored if the [Box] block or [Region] key is present.
Box
Type: Block 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 1.0 Coordinate of the upper bound along the first axis.
Amin
Type: Float 0.0 Coordinate of the lower bound along the first axis.
Bmax
Type: Float 1.0 Coordinate of the upper bound along the second axis.
Bmin
Type: Float 0.0 Coordinate of the lower bound along the second axis.
Cmax
Type: Float 1.0 Coordinate of the upper bound along the third axis.
Cmin
Type: Float 0.0 Coordinate of the lower bound along the third axis.
Region
Type: String Source region The region that is the source. This key is ignored if the [Box] block is present.
StartStep
Type: Integer 0 Index of the MD step at which the heat exchange will start.
StopStep
Type: Integer Index of the MD step at which the heat exchange will stop.
InitialVelocities
Type: Block Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
File
Type: String AMS RKF file containing the initial velocities.
Temperature
Type: Float Kelvin Initial temperature 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 Random [Zero, Random, FromFile, Input] Initial velocities 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 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 1000 Number of steps The number of steps to be taken in the MD simulation.
Plumed
Type: Block Input for PLUMED. The parallel option is still experimental.
Input
Type: Non-standard block Input for PLUMED. Contents of this block is passed to PLUMED as is.
Parallel
Type: Block 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 Cores per group Number of cores in each working group.
nGroups
Type: Integer Number of groups Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup
Type: Integer Nodes per group 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 Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.
AngularMomentum
Type: Bool Yes : Angular momentum Remove overall angular momentum of the system. This option is ignored for 2D and 3D-periodic systems.
CenterOfMass
Type: Bool No : Center of mass 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 Yes Preserve: Total momentum Remove overall (linear) momentum of the system.
Print
Type: Block This block controls the printing of additional information to stdout.
System
Type: Bool No Print the chemical system before and after the simulation.
Velocities
Type: Bool No Print the atomic velocities before and after the simulation.
Remap
Type: Block Control periodic remapping (backtranslation) of atoms into the PBC box.
Type
Type: Multiple Choice Atoms [None, Atoms] Select the method used to remap atoms into the unit cell. None: Disable remapping completely. Atoms: Remap any atoms that leave the unit cell.
RemoveMolecules
Type: Block True Remove molecules This block controls removal of molecules from the system. Multiple occurrences of this block are possible.
Formula
Type: String 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 0 The specified molecules are removed every so many steps after the StartStep. There is never a molecule removed at step 0.
SafeBox
Type: Block 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 Coordinate of the upper bound along the first axis.
Amin
Type: Float Coordinate of the lower bound along the first axis.
Bmax
Type: Float Coordinate of the upper bound along the second axis.
Bmin
Type: Float Coordinate of the lower bound along the second axis.
Cmax
Type: Float Coordinate of the upper bound along the third axis.
Cmin
Type: Float Coordinate of the lower bound along the third axis.
FractionalCoordsBox
Type: Float List Safe box 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 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 Coordinate of the upper bound along the first axis.
Amin
Type: Float Coordinate of the lower bound along the first axis.
Bmax
Type: Float Coordinate of the upper bound along the second axis.
Bmin
Type: Float Coordinate of the lower bound along the second axis.
Cmax
Type: Float Coordinate of the upper bound along the third axis.
Cmin
Type: Float Coordinate of the lower bound along the third axis.
FractionalCoordsBox
Type: Float List Sink box 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 0 Step number when molecules are removed for the first time. After that, molecules are removed every [Frequency] steps. For example, if StartStep=99 and Frequency=100 then molecules will be removed at steps 99, 199, 299, etc… No molecule will be removed at step 0, so if StartStep=0 the first molecules are removed at the step number equal to [Frequency].
StopStep
Type: Integer Do not remove the specified molecules after this step.
ReplicaExchange
Type: Block This block is used for (temperature) Replica Exchange MD (Parallel Tempering) simulations.
AllowWrongResults
Type: Bool No Allow combining Replica Exchange with other features when the combination is known to produce physically incorrect results.
EWMALength
Type: Integer 10 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 100 Attempt an exchange every N steps.
TemperatureFactors
Type: Float List 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 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 1 Number of replicas Number of replicas to run in parallel.
Restart
Type: String Restart from The path to the ams.rkf file from which to restart the simulation.
Thermostat
Type: Block True 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 Global [Local, Global] Apply Berendsen 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 10 NHC chain length Number of individual thermostats forming the NHC thermostat
Duration
Type: Integer List Duration(s) Specifies how many steps should a transition from a particular temperature to the next one in sequence take.
Region
Type: String * 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 Femtoseconds Damping constant The time constant of the thermostat.
Temperature
Type: Float List Kelvin Temperature(s) 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 None [None, Berendsen, NHC] Thermostat Selects the type of the thermostat.
TimeStep
Type: Float 0.25 Femtoseconds The time difference per step.
Trajectory
Type: Block Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
PrintFreq
Type: Integer Printing frequency Print current thermodynamic properties to the output every N steps. By default this is done every SamplingFreq steps.
SamplingFreq
Type: Integer 100 Sample frequency Write the the molecular geometry (and possibly other properties) to the .rkf file once every N steps.
TProfileGridPoints
Type: Integer 0 Number of points in the temperature profile. If TProfileGridPoints > 0, a temperature profile along each of the three unit cell axes will be written to the .rkf file. By default, no profile is generated.
WriteBonds
Type: Bool Yes Write detected bonds to the .rkf file.
WriteCharges
Type: Bool Yes 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.
WriteGradients
Type: Bool No Write gradients (negative of the atomic forces) to the .rkf file.
WriteMolecules
Type: Bool Yes Write the results of molecule analysis to the .rkf file.
WriteVelocities
Type: Bool Yes Write velocities to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze the velocities.
fbMC
Type: Block True fbMC This block sets up force bias Monte Carlo interleaved with the molecular dynamics simulation.
Frequency
Type: Integer 1 Run the fbMC procedure every Frequency MD steps.
MassRoot
Type: Float 2.0 Inverse of the exponent used to mass-weight fbMC steps.
NSteps
Type: Integer Number of steps Number of fbMC steps to perform on every invocation of the procedure.
PrintFreq
Type: Integer Printing frequency 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 1 First step at which the fbMC procedure may run.
StepLength
Type: Float 0.1 Angstrom Maximum allowed displacement of the lightest atom in the system in each Cartesian coordinate in one fbMC step.
StopStep
Type: Integer 0 Last step at which the fbMC procedure may run. If unset or zero, there is no limit.
Temperature
Type: Float Kelvin Temperature used for fbMC.
Molecules
Type: Block Configures details of the molecular composition analysis enabled by the Properties%Molecules block.
AdsorptionSupportRegion
Type: String Adsorption support region 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 0.5 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 Configures details of the Nudged Elastic Band optimization.
Climbing
Type: Bool Yes Climb highest image to TS Use the climbing image algorithm to drive the highest image to the transition state.
ClimbingThreshold
Type: Float 0.0 Hartree/Bohr CI force threshold 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 8 Number of images 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 Yes Interpolate in Internal coordinates 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.
InterpolateShortest
Type: Bool Yes Interpolate across cell boundary 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 Maximum number of iterations 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 Jacobian value Scaling factor used to convert the lattice strain to a NEB coordinate value. Default value: sqrt(N)*(V/N)^(1/d), where V - lattice volume (area for 2D, length for 1D), N - number of atoms, and d - number of periodic dimensions.
MapAtomsToCell
Type: Bool Yes Map atoms to cell Translate atoms to the [-0.5,0.5] cell before every step. This option cannot be disabled for SS-NEB.
OldTangent
Type: Bool No Use old tangent Turn on the old central difference tangent.
OptimizeEnds
Type: Bool Yes Optimize reactants/products Start the NEB with optimization of the reactant and product geometries.
OptimizeLattice
Type: Bool No Optimize lattice Turn on the solid-state NEB (SS-NEB).
Parallel
Type: Block 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 Cores per group Number of cores in each working group.
nGroups
Type: Integer Number of groups Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup
Type: Integer Nodes per group 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.
ReOptimizeEnds
Type: Bool No Re-optimize reactants/products Re-optimize reactant and product geometries upon restart.
Restart
Type: String Restart from 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 1.0 Skewness 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 1.0 Hartree/Bohr^2 Spring value Spring force constant in atomic units.
NormalModes
Type: Block Configures details of a normal modes calculation.
BlockDisplacements
Type: Block Configures details of a Block Normal Modes (a.k.a. Mobile Block Hessian, or MBH) calculation.
AngularDisplacement
Type: Float 0.5 Degree 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 True List of atoms belonging to a block. You can have multiple BlockAtoms.
BlockRegion
Type: String True The region to to be considered a block. You can have multiple BlockRegions, also in combination with BlockAtoms.
Parallel
Type: Block Configuration for how the individual displacements are calculated in parallel.
nCoresPerGroup
Type: Integer Number of cores in each working group.
nGroups
Type: Integer Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup
Type: Integer Cores per task 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 0.005 Angstrom Step size for translational degrees of freedom during Block Normal Modes finite difference calculations.
Displacements
Type: Multiple Choice Cartesian [Cartesian, Symmetric, Block] Displacements 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 Auto [Auto, Analytical, Numerical] Default Auto means that if possible by the engine the Hessian will be calculated analytically, else the Hessian will be calculated numerically by AMS.
ReScanFreqRange
Type: Float List [-10000000.0, 10.0] cm-1 True Re-scan range Specifies a frequency range within which all modes will be scanned. 2 numbers: an upper and a lower bound.
ReScanModes
Type: Bool Yes Re-scan modes Whether or not to scan imaginary modes after normal modes calculation has concluded.
SymmetricDisplacements
Type: Block Configures details of the calculation of the frequencies and normal modes of vibration in symmetric displacements.
Type
Type: Multiple Choice All [All, Infrared, Raman, InfraredAndRaman] Symm Frequencies 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 Define options for numerical differentiations, that is the numerical calculation of gradients, Hessian and the stress tensor for periodic systems.
NuclearStepSize
Type: Float 0.005 Bohr Step size for numerical nuclear gradient calculation.
Parallel
Type: Block 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 Cores per group Number of cores in each working group.
nGroups
Type: Integer Number of groups Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup
Type: Integer Nodes per group 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 0.001 Step size (relative) for numerical stress tensor calculation.
NumericalPhonons
Type: Block Configures details of a numerical phonons calculation.
AutomaticBZPath
Type: Bool Yes Automatic BZ path 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 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 True 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 0.0 Input option to give the Born effective charges of the species.
DielectricConst
Type: Float 1.0 Input option to give the static dielectric constant of the species.
DoubleSided
Type: Bool Yes 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 100 Use interpolation to generate smooth phonon plots.
NDosEnergies
Type: Integer 1000 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 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 Cores per group Number of cores in each working group.
nGroups
Type: Integer Number of groups Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup
Type: Integer Nodes per group 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 0.04 Angstrom Step size to be taken to obtain the force constants (second derivative) from the analytical gradients numerically.
SuperCell
Type: Non-standard block 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 Configures details of the automated PES exploration methods.
BasinHopping
Type: Block Configures the details of the Basin Hopping subtask.
DisplaceAtomsInRegion
Type: String 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 0.5 Angstrom Displacement in each degree of freedom.
PushApartDistance
Type: Float 0.4 Angstrom 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 20 Number of displace & optimize Monte-Carlo steps to take.
BindingSites
Type: Block Options related to the calculation of binding sites.
AllowDisconnected
Type: Bool No Allow disconnected binding sites.
Calculate
Type: Bool No Calculate binding sites at the end of a job. Not needed for Binding Sites job.
DistanceDifference
Type: Float -1.0 Angstrom 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]
Debug
Type: Block ???.
DynamicSeedStates
Type: Bool Yes 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 ???.
Andersen
Type: Block ???.
Alpha
Type: Float 1.0 ???.
CollisionPeriod
Type: Float 100.0 ???.
Langevin
Type: Block ???.
Friction
Type: Float 0.01 ???.
Nose
Type: Block ???.
Mass
Type: Float 1.0 ???.
Thermostat
Type: Multiple Choice none [andersen, nose_hoover, langevin, none] ???.
Time
Type: Float 1000.0 ???.
TimeStep
Type: Float 1.0 ???.
FiniteDifference
Type: Float 0.01 Angstrom The finite difference distance to use for Dimer, Hessian, Lanczos, and optimization methods.
Hessian
Type: Block ???.
AtomList
Type: String all ???.
ZeroFreqValue
Type: Float 1e-06 ???.
Job
Type: Multiple Choice [ProcessSearch, BasinHopping, SaddleSearch, LandscapeRefinement, BindingSites] Specify the PES exploration job to perform.
LoadEnergyLandscape
Type: Block Options related to the loading of an Energy Landscape from a previous calculation.
KeepOnly
Type: Integer List List of states to keep 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 Load energy landscape from The path to load an energy landscape from. Accepts either AMS result folders, or .con files in the native EON format (only available through the text input file).
Remove
Type: Integer List List of states to remove 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).
SeedStates
Type: Integer List List of seed states 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.
NudgedElasticBand
Type: Block Options for the Nudged Elastic Band (NEB) method.
ClimbingImageMethod
Type: Bool Yes Use the climbing image algorithm to drive the highest image to the transition state.
ConvergedForce
Type: Float -1.0 eV/Angstrom 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 5 Number of NEB images between the two endpoints.
MaxIterations
Type: Integer 500 Maximum number of NEB iterations.
OldTangent
Type: Bool No Use the old central difference tangent.
Spring
Type: Float 5.0 eV/Ang^2 Spring force constant.
NumExpeditions
Type: Integer 1 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 1 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 SaddleSearch [SaddleSearch, NudgedElasticBand] When the full set of states in the energy landscape are optimized (see PESExploration%Job = GeometryOptimization), transition states can be optimized using either SaddleSearch or NudgedElasticBand methods. SaddleSearch uses information only from the current geometry of the TS; contrary, NudgedElasticBand ignores the current geometry and runs a Nudged-Elastic-Band calculation trying to connect the associated reactants and products if they are available.
Optimizer
Type: Block Configures the details of the geometry optimizers used by the PES explorers.
ConvergedForce
Type: Float 0.005 eV/Angstrom Convergence threshold for nuclear gradients.
MaxIterations
Type: Integer 400 Maximum number of iterations allowed for optimizations.
Method
Type: Multiple Choice CG [CG, QM, LBFGS, FIRE, SD] Select the method for geometry optimizations.
Parallel
Type: Block 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 Cores per group Number of cores in each working group.
nGroups
Type: Integer Number of groups Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup
Type: Integer Nodes per group 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 ???.
DephaseLoopMax
Type: Integer 5 ???.
DephaseLoopStop
Type: Bool No ???.
DephaseTime
Type: Float 1000.0 ???.
PostTransitionTime
Type: Float 1000.0 ???.
RefineTransition
Type: Bool Yes ???.
StateCheckInterval
Type: Float 1000.0 ???.
StateSaveInterval
Type: Float -1.0 ???.
StopAfterTransition
Type: Bool No ???.
Prefactor
Type: Block ???.
DefaultValue
Type: Float 1000000000000.0 ???.
ProcessSearch
Type: Block Input options specific to the process search procedure.
MinimizationOffset
Type: Float 0.2 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.
SaddleSearch
Type: Block Configuration for the Saddle Search procedure (used in SaddleSearch and ProcessSearch Jobs).
DisplaceAtomsInRegion
Type: String A string corresponding to the name of a region. When performing the initial random displacement, only displace atoms in the specified region. This can help the Saddle Search procedure to start off in a desired region of the PES.
DisplaceMagnitude
Type: Float 0.1 The standard deviation of the Gaussian displacement in each degree of freedom for the selected atoms.
MaxEnergy
Type: Float 20.0 eV 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 400 Maximum number of iterations for each saddle search run.
MinModeMethod
Type: Multiple Choice dimer [dimer, lanczos] The minimum-mode following method to use.
StatesAlignment
Type: Block Configures details of how the energy landscape configurations are aligned respect to the main chemical system [System].
DistanceDifference
Type: Float -1.0 Angstrom 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 Defines the region that is considered as the reference for alignments. Atoms outside this region are ignored in the alignments. TODO: Description of which PES exploration jobs actually use this …
StructureComparison
Type: Block Settings for structure comparison.
CheckRotation
Type: Bool Rotates the system optimally before comparing structures. The default is to do this only for molecular systems when there are no fixed atom constraints.
DistanceDifference
Type: Float 0.1 Angstrom If the distance between two mapped atoms is larger than this threshold, the two configurations are considered different structures.
EnergyDifference
Type: Float 0.01 eV If the energy difference between two configurations is larger than this threshold, the two configurations are considered to be different structures.
IndistinguishableAtoms
Type: Bool Yes If yes, the order of the atoms does not affect the structural comparison. Atoms of the same element are then indistinguishable.
NeighborCutoff
Type: Float 3.3 Angstrom Atoms within this distance of each other are considered neighbors.
RemoveTranslation
Type: Bool Translates the system optimally before comparing structures. The default is to do this only when there are no fixed atom constraints.
Temperature
Type: Float 300.0 Kelvin 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.
WriteHistory
Type: Multiple Choice Converged [None, Converged, All] When to write the molecular geometry (and possibly other properties) to the history on the ams.rkf file. The default is to only write the converged geometries to the history. Changed to write either all frames or not frames at all to the history. Note that for parallel calculations, only the first group of processes writes to ams.rkf.
PESPointCharacter
Type: Block Options for the characterization of PES points.
Displacement
Type: Float 0.04 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.
NegativeFrequenciesTolerance
Type: Float -10.0 cm-1 The threshold in frequency below which a mode is considered imaginary, i.e. indicating a transition state. This is a small negative number, as very small negative frequencies are normally due to numerical noise on an essentially flat PES and do not indicate true transition states.
NumberOfModes
Type: Integer 2 The number of (lowest) eigenvalues that should be checked.
Tolerance
Type: Float 0.016 Convergence tolerance for residual in iterative Davidson diagonalization.
PESScan
Type: Block Configures the details of the potential energy surface scanning task.
CalcPropertiesAtPESPoints
Type: Bool No 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 Yes After the initial pass over the PES, restart the unconverged points from converged neighboring points.
ScanCoordinate
Type: Block True 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.
Angle
Type: String True Scan the angle between three atoms. Three atom indices followed by two real numbers delimiting the transit range in degrees.
Coordinate
Type: String True 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 True 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 True Scan the dihedral angle between four atoms. Four atom indices followed by two real numbers delimiting the transit angle in degrees.
Distance
Type: String True Scan the distance between two atoms. Two atom indices followed by two real numbers delimiting the transit distance in Angstrom.
SumDist
Type: String True 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.
nPoints
Type: Integer 10 The number of points along the scanned coordinate. Must be greater or equal 2.
Print
Type: Block This block controls the printing of additional information to stdout.
Timers
Type: Multiple Choice None [None, Normal, Detail, TooMuchDetail] Printing timing details to see how much time is spend in which part of the code.
Properties
Type: Block 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 No 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.
Charges
Type: Bool No Requests the engine to calculate the atomic charges.
DipoleGradients
Type: Bool No 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 No Requests the engine to calculate the electric dipole moment of the molecule. This can only be requested for non-periodic systems.
ElasticTensor
Type: Bool No Calculate the elastic tensor.
Gradients
Hessian
Type: Bool No Whether or not to calculate the Hessian.
Molecules
Type: Bool No Requests an analysis of the molecular components of a system, based on the bond orders calculated by the engine.
NormalModes
Type: Bool No Frequencies 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.
Other
Type: Bool Yes Other (engine specific) properties. Details are configured in the engine block.
PESPointCharacter
Type: Bool No Characterize PES point 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 No Calculate the phonons (for periodic systems).
Polarizability
Type: Bool No Requests the engine to calculate the polarizability tensor of the system.
Raman
Type: Bool No Requests calculation of Raman intensities for vibrational normal modes.
SelectedRegionForHessian
Type: String Hessian only for 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 No Stress tensor Calculate the stress tensor.
VCD
Type: Bool No Requests calculation of VCD for vibrational normal modes.
VROA
Type: Bool No Requests calculation of VROA for vibrational normal modes.
Raman
Type: Block Configures details of the Raman or VROA calculation.
FreqRange
Type: Float List cm-1 True Frequency range Specifies a frequency range within which all modes will be scanned. 2 numbers: an upper and a lower bound.
IncidentFrequency
Type: Float 0.0 eV Frequency of incident light.
LifeTime
Type: Float 0.0 hartree 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.
Restraints
Type: Block 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 True 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 True 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 True 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 True 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 1.0 Default F(inf) 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 Harmonic [Harmonic, Hyperbolic, Erf] Default restraint profile 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 True 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.
RigidMotions
Type: Block 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 Auto [Auto, None, All, X, Y, Z, XY, XZ, YZ] Which overall rotations of the system are allowed
AllowTranslations
Type: Multiple Choice Auto [Auto, None, All, X, Y, Z, XY, XZ, YZ] Which overall transitions of the system are allowed
Tolerance
Type: Float 1e-06 Tolerance for detecting linear molecules. A large value means larger deviation from linearity is permitted.
RNGSeed
Type: Integer List 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 Technical settings for programs using the AMT matrix system. Currently this is only used by DFTB
DistributedMatrix
Type: Block Technical settings for Distributed matrices
ColBlockSize
Type: Integer 64 See comment of RowBlockSize.
RowBlockSize
Type: Integer 64 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 Elpa [Auto, Reference, ScaLapack, Elpa] Determines which implementation is used to support the AbstractMatrixType.
Symmetry
Type: Block Specifying details about the details of symmetry detection and usage.
SymmetrizeTolerance
Type: Float 0.05 Tolerance used to detect symmetry in case symmetrize is requested.
Tolerance
Type: Float 1e-07 Tolerance used to detect symmetry in the system.
System
Type: Block True 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 No 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 The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders
Type: Non-standard block Defined bond orders. May by used by MM engines.
Charge
Type: Float 0.0 Total charge The system’s total charge in atomic units.
ElectrostaticEmbedding
Type: Block Container for electrostatic embedding options, which can be combined.
ElectricField
Type: Float List V/Angstrom External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å. In atomic units: Hartree/(e bohr) = 27.211 V/bohr; 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 External point charges (and dipoles).
ChargeModel
Type: Multiple Choice Point [Point, Gaussian] The charges may represented as simple points (with a singular potential at the charge location) or may represented by a spherical Gaussian distribution.
ChargeWidth
Type: Float -1.0 A 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 Positions (in Å) and values of multipole charges, one per line. Each line describes a singe point charge like: x y z q, or x y z q py pz px. Here x, y, z are the coordinates, q is the charge (in atomic units of charge) and py, pz, px are the (optional) dipole components (in atomic units, i.e. e/Bohr). Periodic systems are not supported.
FractionalCoords
Type: Bool No 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 Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds
Type: Bool No Whether or not UFF bonds should be guessed.
Lattice
Type: Non-standard block Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
LatticeStrain
Type: Float List 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 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 Name of the (kf) file. It needs to be the result of a forcefield calculation.
LoadForceFieldCharges
Type: Block True 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 No 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 Name of the (kf) file
MaxGeometryRMSD
Type: Float 0.1 Angstrom 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 * Region for which the charges should be loaded
Section
Type: String AMSResults Section name of the kf file
Variable
Type: String Charges Variable name of the kf file
MapAtomsToUnitCell
Type: Bool No For periodic systems the atoms will be moved to the central cell.
PerturbCoordinates
Type: Float 0.0 Angstrom 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 0.0 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 No Whether or not the order of the atoms should be randomly changed. Intended for some technical testing purposes only. Does not work with bond information.
ShiftCoordinates
Type: Float List Bohr Translate the atoms by the specified shift (three numbers).
SuperCell
Type: Integer List 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 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 No 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 AUTO [AUTO, NOSYM, C(LIN), D(LIN), C(I), C(S), C(2), C(3), C(4), C(5), C(6), C(7), C(8), C(2V), C(3V), C(4V), C(5V), C(6V), C(7V), C(8V), C(2H), C(3H), C(4H), C(5H), C(6H), C(7H), C(8H), D(2), D(3), D(4), D(5), D(6), D(7), D(8), D(2D), D(3D), D(4D), D(5D), D(6D), D(7D), D(8D), D(2H), D(3H), D(4H), D(5H), D(6H), D(7H), D(8H), I, I(H), O, O(H), T, T(D), T(H), S(4), S(6), S(8)] Use (sub)symmetry with this Schoenflies symbol. Can only be used for molecules. Orientation should be correct for the (sub)symmetry. If used icw Symmetrize, the symmetrization will not reorient the molecule.
Task
Type: Multiple Choice [SinglePoint, GeometryOptimization, TransitionStateSearch, IRC, PESScan, NEB, VibrationalAnalysis, MolecularDynamics, GCMC, PESExploration] Specify the computational task to perform: • Single Point: keep geometry as is • Geometry Optimization: optimize the geometry • Transition State: search for the 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
Thermo
Type: Block Options for thermodynamic properties (assuming an ideal gas). The properties are computed for all specified temperatures.
LowFrequencyCorrector
Type: Block 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 4.0 The exponent term used in the dampener.
Frequency
Type: Float 100.0 cm-1 The frequency around which the dampener interpolates between harmonic oscillator and free rotor quantities.
MomentOfInertia
Type: Float 1e-44 kg m^2 Averaging Moment of Inertia The moment of inertia used to restrict entropy results for very small frequencies (generally around less than 1 cm-1).
Pressure
Type: Float 1.0 atm The pressure at which the thermodynamic properties are computed.
Temperatures
Type: Float List [298.15] Kelvin List of temperatures at which the thermodynamic properties will be calculated.
TransitionStateSearch
Type: Block Configures some details of the transition state search.
ModeToFollow
Type: Integer 1 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 Specify components of the transition state reaction coordinate (TSRC) as a linear combination of internal coordinates (distances or angles).
Angle
Type: String True The TSRC contains the valence angle between the given atoms. Three atom indices followed by the weight.
Dihedral
Type: String True The TSRC contains the dihedral angle between the given atoms. Four atom indices followed by the weight.
Distance
Type: String True The TSRC contains the distance between the given atoms. Two atom indices followed by the weight.
UseSymmetry
Type: Bool Yes Whether to use the system’s symmetry in AMS. Symmetry is recognized within a tolerance as given in the Symmetry key.
VibrationalAnalysis
Type: Block Input data for all vibrational analysis utilities in the AMS driver.
AbsorptionSpectrum
Type: Block Settings related to the integration of the spectrum for vibronic tasks.
AbsorptionRange
Type: Float List [-200.0, 4000.0] cm-1 True Specifies frequency range of the vibronic absorption spectrum to compute. 2 numbers: an upper and a lower bound.
FrequencyGridPoints
Type: Integer 400 Number of grid points to use for the spectrum
LineWidth
Type: Float 200.0 cm-1 Lorentzian line-width.
SpectrumOffset
Type: Multiple Choice relative [absolute, relative] Specifies whether provided frequency range are absolute frequencies or frequencies relative to computed 0-0 excitation energy.
Displacement
Type: Float Step size for finite difference calculations.
ExcitationSettings
Type: Block Block that contains settings related to the excitation for vibronic tasks.
EnergyInline
Type: Float hartree Vertical excitation energy, used when [ExcitationInfo] = [Inline].
ExcitationFile
Type: String Path to a .rkf/.t21 file containing the excited state information (gradients, transition dipoles and energies).
ExcitationInputFormat
Type: Multiple Choice File [File, Inline] Select how the application should retrieve the excited state information (energy, gradient).
GradientInline
Type: Non-standard block Excited state gradient at ground state equilibrium geometry, used when [ExcitationInfo] = [Inline].
Singlet
Type: Non-standard block Symmetry labels + integer indices of desired singlet transitions (VG-FC absorption spectra support only 1 at a time)
Triplet
Type: Non-standard block Symmetry labels + integer indices of desired triplet transitions (VG-FC absorption spectra support only 1 at a time)
ModeTracking
Type: Block Input data for Mode Tracking.
HessianGuess
Type: Multiple Choice CalculateWithFastEngine [Unit, File, CalculateWithFastEngine] Guess Hessian Sets how to obtain the guess for the Hessian used in the preconditioner (if one is to be used).
HessianInline
Type: Non-standard block Initial guess for the (non-mass-weighted) Hessian in a 3N x 3N block, used when [HessianGuess] = [Inline].
HessianPath
Type: String 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 0.0001 Convergence tolerance for the contribution of the newest basis vector to the tracked mode.
ToleranceForNorm
Type: Float 0.0005 Convergence tolerance for residual RMS value.
ToleranceForResidual
Type: Float 0.0005 Convergence tolerance for the maximum component of the residual vector.
ToleranceForSpectrum
Type: Float 0.01 Convergence tolerance for the spectrum in Vibronic Structure Tracking.
TrackingMethod
Type: Multiple Choice OverlapInitial [OverlapInitial, DifferenceInitial, FreqInitial, IRInitial, OverlapPrevious, DifferencePrevious, FreqPrevious, IRPrevious, HighestFreq, HighestIR, LowestFreq, LowestResidual] Set the tracking method that will be used. Vibronic Structure Tracking uses Largest Displacement.
UpdateMethod
Type: Multiple Choice [JD, D, I] Chooses the method for expanding the Krylov subspace: (I) No preconditioner (VST default), (D) Davidson or (JD) vdVorst-Sleijpen variant of Jacobi-Davidson (Mode tracking default).
NormalModes
Type: Block All input related to processing of normal modes. Not available for vibronic structure tracking (as no modes are required there).
MassWeightInlineMode
Type: Bool Yes 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 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 True 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 File [File, Inline, Hessian] Tracked mode source Set how the initial guesses for the modes are supplied. Only mode tracking supports the Inline and Hessian options.
ModeSelect
Type: Block Pick which modes to read from file.
DisplacementBound
Type: Float Vibronic Structure (Refinement), Resonance Raman: Select all modes with a dimensionless oscillator displacement greater than the specified value.
FreqAndIRRange
Type: Float List cm-1 and km/mol True Specifies a combined frequency and IR intensity range within which all modes will be selected. First 2 numbers are the frequency range, last 2 numbers are the IR intensity range.
FreqRange
Type: Float List cm-1 True 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 No All modes Select all modes. This only make sense for Mode Scanning calculations.
HighFreq
Type: Integer # High frequencies Select the N modes with the highest frequencies.
HighIR
Type: Integer # High IR Select the N modes with the largest IR intensities.
IRRange
Type: Float List km/mol True Specifies an IR intensity range within which all modes will be selected. 2 numbers: an upper and a lower bound.
ImFreq
Type: Bool No All imaginary frequencies Select all modes with imaginary frequencies.
LargestDisplacement
Type: Integer Vibronic Structure (Refinement), Resonance Raman: Select the N modes with the largest VG-FC displacement.
LowFreq
Type: Integer # Low frequencies Select the N modes with the lowest frequencies. Includes imaginary modes which are recorded with negative frequencies.
LowFreqNoIm
Type: Integer # Low positive frequencies Select the N modes with the lowest non-negative frequencies. Imaginary modes have negative frequencies and are thus omitted here.
LowIR
Type: Integer # Low IR Select the N modes with the smallest IR intensities.
ModeNumber
Type: Integer List Mode numbers Indices of the modes to select.
ScanModes
Type: Bool No Scan after refining 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 Block that contains settings for the calculation of Resonance Raman calculations
IncidentFrequency
Type: Float cm-1 Frequency of incident light. Also used to determine most important excitation in case more than one is provided.
LifeTime
Type: Float 0.00045 hartree Lifetime of Raman excited state.
RamanOrder
Type: Integer 2 Order up to which to compute Raman transitions
RamanRange
Type: Float List [0.0, 2000.0] cm-1 True Specifies frequency range of the Raman spectrum to compute. 2 numbers: an upper and a lower bound.
Type
Type: Multiple Choice [ModeScanning, ModeTracking, ModeRefinement, VibronicStructure, VibronicStructureTracking, VibronicStructureRefinement, ResonanceRaman] Specifies the type of vibrational analysis that should be performed
VSTRestartFile
Type: String Path to a .rkf file containing restart information for VST.