Keywords

Links to manual entries

ElasticTensor EngineDebugging GCMC GeometryOptimization IRC LoadSystem ModeRefinement ModeScanning ModeTracking

MolecularDynamics NormalModes NumericalDifferentiation NumericalPhonons Print Properties System Thermo TransitionStateSearch

Summary of all keywords

Constraints

Type:Block Description:The Constraints block allows geometry optimizations and potential energy surface scans with constraints. The constraints do not have to be satisfied at the start of the calculation.

Angle

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

Atom

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

Block

Type:String Recurring:True Description:Name of the block to constrain as specified in the atom tag within the System%Atoms block.

BlockAtoms

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

Coordinate

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

Dihedral

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

Distance

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

ElasticTensor

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

MaxGradientForGeoOpt

Type:Float Default value:0.0001 Unit:Hartree/Angstrom Description:Maximum nuclear gradient for the relaxation of the internal degrees of freedom of strained systems.

Parallel

Type:Block Description:The evaluation of the elastic tensor via numerical differentiation is an embarrassingly parallel problem. Double parallelization 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 Description:Number of cores in each working group.

nGroups

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

nNodesPerGroup

Type:Integer Description:Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.

StrainStepSize

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

Engine

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

EngineDebugging

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

CheckInAndOutput

Type:Bool Default value:False Description:Enables some additional checks on the input and output of and engine, e.g. for NaN values.

ForceContinousPES

Type:Bool Default value:False Description:If this option is set, the engine will always run in continuous PES mode. For many engines this disables the use of symmetry, as this one always leads to a discontinuous PES around the symmetric points: Basically there is jump in the PES at the point where the symmetry detection starts classifying the system as symmetric. Normally the continuous PES mode of the engine (often disabling the symmetry) is only used when doing numerical derivatives, but this flag forces the engine to continuously run in this mode.

IgnoreGradientsRequest

Type:Bool Default value:False Description:If this option is set, the engine will not do analytical gradients if asked for it, so that gradients will have to be evaluated numerically by AMS.

IgnoreStressTensorRequest

Type:Bool Default value:False Description:If this option is set, the engine will not calculate an analytical stress tensor if asked for it, so that the stress tensor will have to be evaluated numerically by AMS.

RandomFailureChance

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

RandomNoiseInEnergy

Type:Float Default value:0.0 Unit:Hartree Description:Adds a random noise to the energy returned by the engine. The random contribution is drawn from [-r,r] where r is the value of this keyword.

RandomNoiseInGradients

Type:Float Default value:0.0 Unit:Hartree/Angstrom Description:Adds a random noise to the gradients returned by the engine. A random number in the range [-r,r] (where r is the value of this keyword) is drawn and added separately to each component of the gradient.

EngineRestart

Type:String Description:The path to the file from which to restart the engine.

GCMC

Type:Block Description:This block controls the Grand Canonical Monte Carlo (GCMC) task. By default, molecules are added at random positions in the simulation box. The initial position is controlled by

AccessibleVolume

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

Box

Type:Block Description:Boundaries of the insertion space, i.e. coordinates of the origin of an inserted molecule (coordinates of an atom of the inserted system may fall outside the box). For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom (the system’s bounding box extended by the MaxDistance value by default).

Amax

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

Amin

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

Bmax

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

Bmin

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

Cmax

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

Cmin

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

Ensemble

Type:Multiple Choice Default value:Mu-VT Options:[Mu-VT, Mu-PT] Description:Select the MC ensemble: Mu-VT for fixed volume or Mu-PT for variable volume. When the Mu-PT ensemble is selected the [Pressure] and [VolumeChangeMax] should also be specified.

Iterations

Type:Integer Description:Number of GCMC moves.

MapAtomsToOriginalCell

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

MaxDistance

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

MinDistance

Type:Float Default value:0.3 Unit:Angstrom Description:Keep the minimal distance to other atoms of the system when adding the molecule.

Molecule

Type:Block Recurring:True Description:This block defines the molecule (or atom) that can be inserted/moved/deleted with the MC method. The coordinates should form a reasonable structure. The MC code uses these coordinates during the insertion step by giving them a random rotation, followed by a random translation to generate a random position of the molecule inside the box. Currently, there is no check to make sure all atoms of the molecule stay inside the simulation box. The program does check that the MaxDistance/MinDistance conditions are satisfied.

ChemicalPotential

Type:Float Unit:Hartree Description:Chemical potential of the molecule (or atom) reservoir. It is used when calculating the Boltzmann accept/reject criteria after a MC move is executed. This value can be derived from first principles using statistical mechanics, or equivalently, it can be determined from thermochemical tables available in literature sources. For example, the proper chemical potential for a GCMC simulation in which single oxygen atoms are exchanged with a reservoir of O2 gas, should equal 1/2 the chemical potential of O2 at the temperature and pressure of the reservoir: cmpot = Mu_O(T,P) = 1/2*Mu_O2(T,P) = 1/2 * [Mu_ref(T,P_ref) + kT*Log(P/Pref) - E_diss] where the reference chemical potential [Mu_ref(T,P_ref)] is the experimentally determined chemical potential of O2 at T and Pref; kT*Log(P/Pref) is the pressure correction to the free energy, and E_diss is the dissociation energy of the O2 molecule.

NoAddRemove

Type:Bool Default value:False Description:Set to True to tell the GCMC code to keep the number of molecules/atoms of this type fixed. It will thus disable Insert/Delete moves on this type, meaning it can only do a displacement move, or volume change move (for an NPT ensemble).

SystemName

Type:String Description:String ID of a named [System] to be inserted. The lattice specified with this System, if any, is ignored and the main system’s lattice is used instead.

NonAccessibleVolume

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

NumAttempts

Type:Integer Default value:1000 Description:Try inserting/moving the selected molecule up to the specified number of times or until all constraints are satisfied. If all attempts fail a message will be printed and the simulation will stop. If the MaxDistance-MinDistance interval is small this number may have to be large.

Pressure

Type:Float Default value:0.0 Unit:Pascal Description:Pressure used to calculate the energy correction in the Mu-PT ensemble. Set it to zero for incompressible solid systems unless at very high pressures.

Removables

Type:Non-standard block Description:The Removables can be used to specify a list of molecules that can be removed or moved during this GCMC calculation. Molecules are specified one per line in the format following format: MoleculeName atom1 atom2 ... The MoleculeName must match a name specified in one of the [Molecule] blocks. The atom indices refer to the whole input System and the number of atoms must match that in the specified Molecule. A suitable Removables block is written to the standard output after each accepted MC move. If you do so then you should also replace the initial atomic coordinates with the ones found in the same file. If a [Restart] key is present then the Removables block is ignored.

Restart

Type:String Description:Name of an RKF restart file. Upon restart, the information about the GCMC input parameters, the initial system (atomic coordinates, lattice, charge, etc.) and the MC molecules (both already inserted and to be inserted) are read from the restart file. The global GCMC input parameters and the MC Molecules can be modified from input. Any parameter not specified in the input will use its value from the restart file (i.e. not the default value). Molecules found in the restart file do not have to be present as named Systems in the input, however if there is a System present that matches the name of a molecule from restart then the System’s geometry will replace that found in the restart file. It is also possible to specify new Molecules in the input, which will be added to the pool of the MC molecules from restart.

Temperature

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

UseGCPreFactor

Type:Bool Default value:True Description:Use the GC pre-exponential factor for probability.

VolumeChangeMax

Type:Float Default value:0.05 Description:Fractional value by which logarithm of the volume is allowed to change at each step. The new volume is then calculated as Vnew = exp(random(-1:1)*VolumeChangeMax)*Vold

VolumeOption

Type:Multiple Choice Default value:Free Options:[Free, Total, Accessible, FreeAccessible] Description:Specifies the method to calculate the volume used to calculate the GC pre-exponential factor and the energy correction in the Mu-PT ensemble: Free: V = totalVolume - occupiedVolume - NonAccessibleVolume; Total: V = totalVolume; Accessible: V = AccessibleVolume; FreeAccessible: V = AccessibleVolume - occupiedVolume. The AccessibleVolume and NonAccessibleVolume are specified in the input, the occupiedVolume is calculated as a sum of atomic volumes.

GeometryOptimization

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

CalcPropertiesOnlyIfConverged

Type:Bool Default value:True Description:Compute the properties requested in the ‘Properties’ block, e.g. Frequencies or Phonons, only if the optimization (or transition state search) converged. If False, the properties will be computed even if the optimization did not converge.

ConjugateGradients

Type:Block Description:Configures details of the conjugate gradients geometry optimizer.

Step

Type:Block Description:

MinRadius

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

TrustRadius

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

Convergence

Type:Block Description:Convergence is monitored for two items: the energy and the Cartesian gradients. Convergence criteria can be specified separately for each of these items.

Energy

Type:Float Default value:1e-05 Unit:Hartree Description:The criterion for changes in the energy.

Gradients

Type:Float Default value:0.001 Unit:Hartree/Angstrom Description:The criterion for changes in the gradients.

Step

Type:Float Default value:0.001 Unit:Angstrom Description:The maximum Cartesian step allowed for a converged geometry.

CoordinateType

Type:Multiple Choice Default value:Auto Options:[Auto, Delocalized, Cartesian] Description:Select the type of coordinates in which to perform the optimization. If ‘Auto’, delocalized coordinates will be used for molecular systems, while Cartesian coordinates will be used for periodic systems. Optimization in delocalized coordinates [Delocalized] can only be used for geometry optimizations or transition state searches of molecular systems with the Quasi-Newton method. The experimental SCMGO optimizer supports [Delocalized] coordinates for both molecular and periodic systems.

FIRE

Type:Block Description:This block configures the details of the FIRE optimizer. The keywords name correspond the the symbols used in the article describing the method, see PRL 97, 170201 (2006).

MapAtomsToUnitCell

Type:Bool Default value:False Description:Map the atoms to the central cell at each geometry step.

NMin

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

RejectEnergyIncrease

Type:Bool Default value:False Description:Makes the optimizer reject steps that increase the energy. This can speed up convergence, but often causes the optimizer to get stuck on small discontinuities on the potential energy surface. It is therefore disabled by default.

alphaStart

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

dtMax

Type:Float Default value:1.0 Unit:Femtoseconds Description:Maximum time step used for the integration.

dtStart

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

fAlpha

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

fDec

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

fInc

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

strainMass

Type:Float Default value:0.5 Description:Fictitious relative mass of the lattice degrees of freedom. This controls the stiffness of the lattice degrees of freedom relative to the atomic degrees of freedom, with smaller values resulting in a more aggressive optimization of the lattice.

InitialHessian

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

File

Type:String Description:KF file containing the initial Hessian. This can be used to load a Hessian calculated in a previously with the [Properties%Hessian] keyword.

Type

Type:Multiple Choice Default value:Auto Options:[Auto, UnitMatrix, Swart, FromFile, Calculate] Description:Select the type of initial Hessian. Auto: let the program pick an initial model Hessian. UnitMatrix: simplest initial model Hessian, just a unit matrix in the optimization coordinates. Swart: model Hessian from M. Swart. FromFile: load the Hessian from the results of a previous calculation (see InitialHessian%File). Calculate: compute the initial Hessian (this may be computationally expensive and it is mostly recommended for TransitionStateSearch calculations).

KeepIntermediateResults

Type:Bool Default value:False Description:Whether the full engine result files of all intermediate steps are stored on disk. By default only the last step is kept, and only if the geometry optimization converged. This can easily lead to huge amounts of data being stored on disk, but it can sometimes be convenient to closely monitor a tricky optimization, e.g. excited state optimizations going through conical intersections, etc. ...

MaxIterations

Type:Integer Description:The maximum number of geometry iterations allowed to converge to the desired structure.

Method

Type:Multiple Choice Default value:Auto Options:[Auto, Quasi-Newton, SCMGO, FIRE, ConjugateGradients] Description: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), and the conjugate gradients method. The default is to choose an appropriate method automatically based on the engine’s speed, the system size and the supported optimization options.

OptimizeLattice

Type:Bool Default value:False Description:Whether to also optimize the lattice for periodic structures. This is currently only supported with the Quasi-Newton and SCMGO optimizers.

Pressure

Type:Float Default value:0.0 Description:Optimize the structure under pressure (this will only have an effect if you are optimizing the lattice vectors). Currently only working in combination with the Quasi-Newton optimizer. For phase transitions you may consider disabling or breaking the symmetry.

PressureUnit

Type:Multiple Choice Default value:GPa Options:[a.u., Pascal, GPa, atm, bar, kbar] Description:The unit for pressure to be used for optimizations under pressure

Quasi-Newton

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

MaxGDIISVectors

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

Step

Type:Block Description:

TrustRadius

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

SCMGO

Type:Block Description:Configures details SCMGO.

ContractPrimitives

Type:Bool Default value:True Description:Form non-redundant linear combinations of primitive coordinates sharing the same central atom

NumericalBMatrix

Type:Bool Default value:False Description:Calculation of the B-matrix, i.e. Jacobian of internal coordinates in terms of numerical differentiations

Step

Type:Block Description:

TrustRadius

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

VariableTrustRadius

Type:Bool Default value:True Description:Whether or not the trust radius can be updated during the optimization.

logSCMGO

Type:Bool Default value:False Description:Verbose output of SCMGO internal data

testSCMGO

Type:Bool Default value:False Description:Run SCMGO in test mode.

IRC

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

Convergence

Type:Block Description:Convergence at each given point is monitored for two items: the Cartesian gradient and the calculated step size. Convergence criteria can be specified separately for each of these items. The same criteria are used both in the inner IRC loop and when performing energy minimization at the path ends.

Gradients

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

Step

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

CoordinateType

Type:Multiple Choice Default value:Cartesian Options:[Cartesian, Delocalized] Description:Select the type of coordinates in which to perform the optimization. Note that the Delocalized option should be considered experimental. Besides, it is not possible to use delocalized coordinates for periodic systems.

Direction

Type:Multiple Choice Default value:Both Options:[Both, Forward, Backward] Description:Select direction of the IRC path. The difference between the Forward and the Backward directions is determined by the sign of the largest component of the vibrational normal mode corresponding to the reaction coordinate at the transition state geometry. The Forward path correspond to the positive sign of the component. If Both is selected then first the Forward path is computed followed by the Backward one.

InitialHessian

Type:Block Description:Options for initial Hessian at the transition state. The first eigenvalue of the initial Hessian defines direction of the first forward or backward step. This block is ignored when restarting from a previous IRC calculation because the initial Hessian found in the restart file is used.

File

Type:String Description:If ‘Type’ is set to ‘FromFile’ then in this key you should specifiy the RKF file containing the initial Hessian. This can be used to load a Hessian calculated previously with the ‘Properties%Hessian’ keyword. If you want to also use this file for the initial geometry then also specify it in a ‘LoadSystem’ block.

Type

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

KeepConvergedResults

Type:Bool Default value:True Description:Keep the binary RKF result file for every converged IRC point. These files may contain more information than the main ams.rkf result file.

MaxIRCSteps

Type:Integer Description:Soft limit on the number of IRC points to compute in each direction. After the specified number of IRC steps the program will switch to energy minimization and complete the path. This option should be used when you are interested only in the reaction path area near the transition state. Note that even if the soft limit has been hit and the calculation has completed, the IRC can still be restarted with a ‘RedoBackward’ or ‘RedoForward’ option.

MaxIterations

Type:Integer Default value:300 Description:The maximum number of geometry iterations allowed to converge the inner IRC loop. If optimization does not converge within the specified number of steps, the calculation is aborted.

MaxPoints

Type:Integer Default value:100 Description:Hard limit on the number of IRC points to compute in each direction. After the specified number of IRC steps the program will stop with the current direction and switch to the next one. If both ‘MaxPoints’ and ‘MaxIRCSteps’ are set to the same value then ‘MaxPoints’ takes precedence, therefore this option should be used to set a limit on the number of IRC steps if you intend to use the results later for a restart.

MinEnergyProfile

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

MinPathLength

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

Restart

Type:Block Description:Restart options. Upon restart, the information about the IRC input parameters and the initial system (atomic coordinates, lattice, charge, etc.) is read from the restart file. The IRC input parameters can be modified from input. Except for ‘MaxPoints’ and ‘Direction’ all parameters not specified in the input will use their values from the restart file. The ‘MaxPoints’ and ‘Direction’ will be reset to their respective default values if not specified in the input. By default, the IRC calculation will continue from the point where it left off. However, the ‘RedoForward’ and/or ‘RedoBackward’ option can be used to enforce recalculation of a part of the reaction path, for example, using a different ‘Step’ value.

File

Type:String Description:Name of an RKF restart file generated by a previous IRC calculation. Do not use this key to provide an RKF file generated by a TransitionStateSearch or a SinglePoint calculation, use the ‘LoadSystem’ block instead.

RedoBackward

Type:Integer Default value:0 Description:IRC step number to start recalculating the backward path from. By default, if the backward path has not been completed then start after the last completed step. If the backward path has been completed and the ‘RedoBackward’ is omitted then no point on the backward path will be recomputed.

RedoForward

Type:Integer Default value:0 Description:IRC step number to start recalculating the forward path from. By default, if the forward path has not been completed then start after the last completed step. If the forward path has been completed and the ‘RedoForward’ is omitted then no point on the forward path will be recomputed.

Step

Type:Float Default value:0.2 Description:IRC step size in mass-weighted coordinates, sqrt(amu)*bohr. One may have to increase this value when heavy atoms are involved in the reaction, or decrease it if the reactant or products are very close to the transition state.

LoadEngine

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

LoadSystem

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

File

Type:String Description:The path of the KF file from which to load the system.

Section

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

ModeRefinement

Type:Block Description:Input data for ModeRefinement tasks.

Displacement

Type:Float Default value:0.001 Description:Step size for finite difference calculation of frequencies and IR intensities.

ModePath

Type:String Description:Path to a .rkf file containing the modes which are to be scanned. Which modes will be refined is selected using the criteria from the [ModeSelect] block.)

ModeSelect

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

FreqAndIRRange

Type:Float List Unit:cm-1 and km/mol Recurring:True Description:Specifies a combined frequency and IR intensity range within which all modes will be refined. (First 2 numbers are the frequency range, last 2 numbers are the IR intensity range.)

FreqRange

Type:Float List Unit:cm-1 Recurring:True Description:Specifies a frequency range within which all modes will be refined. (2 numbers: a upper and a lower bound.)

Full

Type:Bool Default value:False Description:Refine all modes.

HighFreq

Type:Integer Description:Refine the N modes with the highest frequencies.

HighIR

Type:Integer Description:Refine the N modes with the largest IR intensities.

IRRange

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

ImFreq

Type:Bool Default value:False Description:Refine all modes with imaginary frequencies.

LowFreq

Type:Integer Description:Refine the N modes with the lowest frequencies. (Includes imaginary modes which are recorded with negative frequencies.)

LowFreqNoIm

Type:Integer Description:Refine the N modes with the lowest non-negative frequencies. (Imaginary modes have negative frequencies and are thus omitted here.)

LowIR

Type:Integer Description:Refine the N modes with the smallest IR intensities.

ModeNumber

Type:Integer List Description:Indices of the modes to refine.

ScanModes

Type:Bool Default value:False Description: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.

ModeScanning

Type:Block Description:Input data for the ModeScanning task.

Displacement

Type:Float Default value:0.001 Description:Step size for finite difference calculation of frequencies and IR intensities.

ModePath

Type:String Description:Path to a .rkf file containing the modes which are to be scanned. Which modes will be scanned is selected using the criteria from the [ModeSelect] block.)

ModeSelect

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

FreqAndIRRange

Type:Float List Unit:cm-1 and km/mol Recurring:True Description:Specifies a combined frequency and IR intensity range within which all modes will be scanned. (First 2 numbers are the frequency range, last 2 numbers are the IR intensity range.)

FreqRange

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

Full

Type:Bool Default value:False Description:Scan all modes.

HighFreq

Type:Integer Description:Scan the N modes with the highest frequencies.

HighIR

Type:Integer Description:Scan the N modes with the largest IR intensities.

IRRange

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

ImFreq

Type:Bool Default value:False Description:Scan all modes with imaginary frequencies.

LowFreq

Type:Integer Description:Scan the N modes with the lowest frequencies. (Includes imaginary modes which are recorded with negative frequencies.)

LowFreqNoIm

Type:Integer Description:Scan the N modes with the lowest non-negative frequencies. (Imaginary modes have negative frequencies and are thus omitted here.)

LowIR

Type:Integer Description:Scan the N modes with the smallest IR intensities.

ModeNumber

Type:Integer List Description:Indices of the modes to scan.

ModeTracking

Type:Block Description:Input data for ModeTracking task.

Displacement

Type:Float Default value:0.01 Description:Step size (in Bohr) for finite difference calculation of frequencies and IR intensities during mode tracking iterations.

HessianGuess

Type:Multiple Choice Default value:UFF Options:[Unit, File, UFF, Inline] Description:Sets how to obtain the guess for the Hessian used in the preconditioner.

HessianInline

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

HessianPath

Type:String Description:Path to a .rkf file containing the initial guess for the Hessian, used when [HessianGuess] = [File].

MassWeighInlineMode

Type:Bool Default value:True Description:The supplied modes must be mass-weighed. This tells the program to mass-weigh the supplied modes in case this has not yet been done. (True means the supplied modes will be mass-weighed by the program, e.g. the supplied modes are non-mass-weighed.)

MaxIterations

Type:Integer Description:Maximum number of allowed iterations.

ModeInline

Type:Non-standard block Recurring:True Description:Coordinates of the mode which will be tracked in a N x 3 block (same as for atoms), used when [TrackedMode] = [Inline]. Rows must be ordered in the same way as in the [System%Atoms] block.

ModePath

Type:String Description:Path to a .rkf file containing the modes which are to be tracked. Which modes will be refined is selected using the criteria from the [ModeSelect] block.)

ModeSelect

Type:Block Description:Pick which modes to track from modes generated from Hessian or read from file.

FreqAndIRRange

Type:Float List Unit:cm-1 and km/mol Recurring:True Description:Specifies a combined frequency and IR intensity range within which all modes will be tracked. (First 2 numbers are the frequency range, last 2 numbers are the IR intensity range.)

FreqRange

Type:Float List Unit:cm-1 Recurring:True Description:Specifies a frequency range within which all modes will be tracked. (2 numbers: a upper and a lower bound.)

Full

Type:Bool Default value:False Description:Track all modes.

HighFreq

Type:Integer Description:Track the N modes with the highest frequencies.

HighIR

Type:Integer Description:Track the N modes with the largest IR intensities.

IRRange

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

ImFreq

Type:Bool Default value:False Description:Track all modes with imaginary frequencies.

LowFreq

Type:Integer Description:Track the N modes with the lowest frequencies. (Includes imaginary modes which are recorded with negative frequencies.)

LowFreqNoIm

Type:Integer Description:Track the N modes with the lowest non-negative frequencies. (Imaginary modes have negative frequencies and are thus omitted here.)

LowIR

Type:Integer Description:Track the N modes with the smallest IR intensities.

ModeNumber

Type:Integer List Description:Indices of the modes to track.

ScanModes

Type:Bool Default value:False Description: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.

ToleranceForBasis

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

ToleranceForNorm

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

ToleranceForResidual

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

TrackedMode

Type:Multiple Choice Default value:File Options:[Inline, File, Hessian] Description:Set how the initial guesses for the modes are supplied.

TrackingMethod

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

UpdateMethod

Type:Multiple Choice Default value:JD Options:[JD, D] Description:Chooses the method for expanding the Krylov subspace: (D) Davidson or (JD) vdVorst-Sleijpen variant of Jacobi-Davidson.

MolecularDynamics

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

AddMolecules

Type:Block Recurring:True Description:This block controls adding molecules to the system (a.k.a. the Molecule Gun). Multiple occurrences of this block are possible. By default, molecules are added at random positions in the simulation box with velocity matching the current system temperature. The initial position can be modified using one of the following keywords: Coords, CoordsBox, FractionalCoords, FractionalCoordsBox. The Coords and FractionalCoords keys can optionally be accompanied by CoordsSigma or FractionalCoordsSigma, respectively.

AtomTemperature

Type:Float Default value:0.0 Unit:Kelvin Description:Add random velocity corresponding to the specified temperature to individual atoms of the molecule. The total momentum of the added molecule is not conserved.

Coords

Type:Float List Unit:Angstrom Description:Place molecules at or around the specified Cartesian coordinates. This setting takes precedence over other ways to specify initial coordinates of the molecule: [CoordsBox], [FractionalCoords], and [FractionalCoordsBox].

CoordsBox

Type:Float List Unit:Angstrom Description:Place molecules at random locations inside the specified box in Cartesian coordinates. Coordinates of the box corners are specified as: Xmin, Xmax, Ymin, Ymax, Zmin, Zmax. This setting is ignored if Coords is used. In ADFinput, if this field is not empty it will be used instead of the default Coords.

CoordsSigma

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

Energy

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

EnergySigma

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

FractionalCoords

Type:Float List Description:Place molecules at or around the specified fractional coordinates in the main system’s lattice. For non-periodic dimensions a Cartesian value in Angstrom is expected. This setting is ignored if [Coords] or [CoordsBox] is used.

FractionalCoordsBox

Type:Float List Description:Place molecules at random locations inside the box specified as fractional coordinates in the main system’s lattice. Coordinates of the box corners are specified as: Xmin, Xmax, Ymin, Ymax, Zmin, Zmax. For non-periodic dimensions the Cartesian value in Angstrom is expected. This setting is ignored if [Coords], [CoordsBox], or [FractionalCoords] is used.

FractionalCoordsSigma

Type:Float List Description:Sigma values (one per axis) for a Gauss distribution of the initial coordinates. For non-periodic dimensions the Cartesian value in Angstrom is expected. Can only be used together with FractionalCoords.

Frequency

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

MinDistance

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

NumAttempts

Type:Integer Default value:10 Description:Try adding the molecule up to the specified number of times or until the MinDistance constraint is satisfied. If all attempts fail a message will be printed and the simulation will continue normally.

Rotate

Type:Bool Default value:False Description:Rotate the molecule randomly before adding it to the system.

StartStep

Type:Integer Default value:0 Description:Step number when the first molecule should be added. After that, molecules are added every Frequency steps. For example, ff StartStep=99 and Frequency=100 then a molecule will be added at steps 99, 199, 299, etc... No molecule will be added at step 0, so if StartStep=0 the first molecule is added at the step number equal to [Frequency].

StopStep

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

System

Type:String Description:String ID of the [System] that will be added with this ‘gun’. The lattice specified with this System is ignored and the main system’s lattice is used instead. ADFinput adds the system at the coordinates of the System (thus setting Coords to the center of the System).

Temperature

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

TemperatureSigma

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

Velocity

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

VelocityDirection

Type:Float List Description:Velocity direction vector for aimed shooting. It will be random if not specified. In ADFinput add one or two atoms (which may be dummies). One atom: use vector from center of the system to add to that atom. Two atoms: use vector from the first to the second atom.

VelocitySigma

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

Barostat

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

BulkModulus

Type:Float Default value:2200000000.0 Unit:Pascal Description:An estimate of the bulk modulus (inverse compressibility) of the system for the Berendsen barostat. This is only used to make Tau correspond to the true observed relaxation time constant. Values are commonly on the order of 10-100 GPa (1e10 to 1e11) for solids and 1 GPa (1e9) for liquids (2.2e9 for water). Use 1e9 to match the behavior of standalone ReaxFF.

ConstantVolume

Type:Bool Default value:False Description:Keep the volume constant while allowing the box shape to change. This is currently supported only by the MTK barostat.

Duration

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

Equal

Type:Multiple Choice Default value:None Options:[None, XYZ, XY, YZ, XZ] Description:Enforce equal scaling of the selected set of dimensions. They will be barostatted as one dimension according to the average pressure over the components.

Pressure

Type:Float List Unit:Pascal Description:Specifies the target pressure.

Scale

Type:Multiple Choice Default value:XYZ Options:[XYZ, Shape, X, Y, Z, XY, YZ, XZ] Description:Dimensions that should be scaled by the barostat to maintain pressure. Selecting Shape means that all three dimensions and also all the cell angles are allowed to change.

Tau

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

Type

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

BondOrderCutoff

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

CVHD

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

Bias

Type:Block Description:The bias is built from a series of Gaussian peaks deposited on the collective variable axis every [Frequency] steps during MD. Each peak is characterized by its (possibly damped) height and the RMS width (standard deviation).

DampingTemp

Type:Float Default value:0.0 Unit:Kelvin Description:During well-tempered hyperdynamics the height of the added bias is scaled down with an exp(-E/kT) factor [PhysRevLett 100, 020603 (2008)], where E is the current value of the bias at the given CV value and T is the damping temperature DampingTemp. If DampingTemp is zero then no damping is applied.

Delta

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

Height

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

ColVarBB

Type:Block Recurring:True Description:Description of a bond-breaking collective variable (CV) as described in [Bal & Neyts, JCTC, 11 (2015)]. A collective variable may consist of multiple ColVar blocks.

at1

Type:String Description:Atom type name of the first atom of the bond. The name must be as it appears in the System block. That is, if the atom name contains an extension (e.g C.1) then the full name including the extension must be used here.

at2

Type:String Description:Atom type name of the second atom of the bond. The value is allowed to be the same as [at1], in which case bonds between atoms of the same type will be included.

cutoff

Type:Float Default value:0.3 Description:Bond order cutoff. Bonds with BO below this value are ignored when creating the initial bond list for the CV. The bond list does not change during lifetime of the variable even if some bond orders drop below the cutoff.

p

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

rmax

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

rmin

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

Frequency

Type:Integer Description:Frequency of adding a new bias peak, in steps. New bias is deposited every [Frequency] steps after [StartStep] if the following conditions are satisfied: the current CV value is less than 0.9 (to avoid creating barriers at the transition state), the step number is greater than or equal to [StartStep], and the step number is less than or equal to [StopStep].

StartStep

Type:Integer Description:If this key is specified, the first bias will be deposited at this step. Otherwise, the first bias peak is added at the step number equal to the Frequency parameter. The bias is never deposited at step 0.

StopStep

Type:Integer Description:No bias will be deposited after the specified step. The already deposited bias will continue to be applied until the reaction event occurs. After that no new CVHD will be started. By default, the CVHD runs for the whole duration of the MD calculation.

WaitSteps

Type:Integer Description:If the CV value becomes equal to 1 and remains at this value for this many steps then the reaction event is considered having taken place. After this, the collective variable will be reset and the bias will be removed.

CalcPressure

Type:Bool Default value:False Description:Calculate the pressure in periodic systems. This may be computationally expensive for some engines that require numerical differentiation. Some other engines can calculate the pressure for negligible additional cost and will always do so, even if this option is disabled.

Checkpoint

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

Frequency

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

HeatExchange

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

HeatingRate

Type:Float Unit:Hartree/fs Description:Rate at which the energy is added to the Source and removed from the Sink. A heating rate of 1 Hartree/fs equals to about 0.00436 Watt of power being transfered through the system.

Method

Type:Multiple Choice Default value:Simple Options:[Simple, HEX, eHEX] Description:Heat exchange method used. Simple: kinetic energy of the atoms of the source and sink regions is modified irrespective of that of the center of mass (CoM) of the region (recommended for solids). HEX: kinetic energy of the atoms of these regions is modified keeping that of the corresponding CoM constant. eHEX: an enhanced version of HEX that conserves the total energy better (recommended for gases and liquids).

Sink

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

Box

Type:Block Description:Part of the simulation box (in fractional cell coordinates) defining the heat sink. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes. This block is mutually exclusive with the FirstAtom/LastAtom setting.

Amax

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

Amin

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

Bmax

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

Bmin

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

Cmax

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

Cmin

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

FirstAtom

Type:Integer Description:Index of the first atom of the region. This key is ignored if the [Box] block is present.

LastAtom

Type:Integer Description:Index of the last atom of the region. This key is ignored if the [Box] block is present.

Source

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

Box

Type:Block Description:Part of the simulation box (in fractional cell coordinates) defining the heat source. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes. This block is mutually exclusive with the FirstAtom/LastAtom setting.

Amax

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

Amin

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

Bmax

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

Bmin

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

Cmax

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

Cmin

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

FirstAtom

Type:Integer Description:Index of the first atom of the region. This key is ignored if the [Box] block is present.

LastAtom

Type:Integer Description:Index of the last atom of the region. This key is ignored if the [Box] block is present.

StartStep

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

StopStep

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

InitialVelocities

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

File

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

Temperature

Type:Float Unit:Kelvin Description:Sets the temperature for the Maxwell-Boltzmann distribution when the type of the initial velocities is set to random, in which case specifying this key is mandatory. ADFinput will use the thermostat temperature as default.

Type

Type:Multiple Choice Default value:Random Options:[Zero, Random, FromFile, Input] Description:Specifies the initial velocities to assign to the atoms. Three methods to assign velocities are available. Zero: All atom are at rest at the beginning of the calculation. Random: Initial atom velocities follow a Maxwell-Boltzmann distribution for the temperature given by the [MolecularDynamics%InitialVelocities%Temperature] keyword. FromFile: Load the velocities from a previous ams result file. Input: Atom’s velocities are set to the values specified in the [MolecularDynamics%InitialVelocities%Values] block, which can be accessed via the Expert AMS panel in ADFinput.

Values

Type:Non-standard block Description:This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.

NSteps

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

PRD

Type:Block Description:This block is used for Parallel Replica Dynamics simulations.

BondChange

Type:Block Recurring:True Description:Detect changes to the bonding topology and bond orders returned by the engine.

ChangeThreshold

Type:Float Default value:0.5 Description:Trigger an event when the bond order of a bond changes from the reference state by more than this value.

DissociationThreshold

Type:Float Default value:0.3 Description:Trigger an event when a bond dissociates (its bond order drops below this value while it was above FormationThreshold in the reference state).

FormationThreshold

Type:Float Default value:0.8 Description:Trigger an event when a new bond forms (its bond order exceeds this value while it was below DissociationThreshold in the reference state).

CorrelatedSteps

Type:Integer Default value:100 Description:How many steps to wait for correlated events after detecting an initial event.

DephasingSteps

Type:Integer Default value:100 Description:Spend this many steps dephasing the individual replicas after an event.

MolCount

Type:Block Recurring:True Description:Detect changes to the molecular composition of the system.

nReplicas

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

Plumed

Type:Block Description:Input for PLUMED.

Input

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

Preserve

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

AngularMomentum

Type:Bool Default value:True Description:Remove overall angular momentum of the system. This option is ignored for 2D and 3D-periodic systems.

CenterOfMass

Type:Bool Default value:False Description:Translate the system to keep its center of mass at the coordinate origin. This option is not very useful for 3D-periodic systems.

Momentum

Type:Bool Default value:True Description:Remove overall (linear) momentum of the system.

Print

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

System

Type:Bool Default value:False Description:Print the chemical system before and after the simulation.

Velocities

Type:Bool Default value:False Description:Print the atomic velocities before and after the simulation.

RemoveMolecules

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

Formula

Type:String Description:Molecular formula of the molecules that should be removed from the system. The order of elements in the formula is very important and the correct order is: C, H, all other elements in the strictly alphabetic order. Element names are case-sensitive, spaces in the formula are not allowed. Digit ‘1’ must be omitted. Valid formula examples: C2H6O, H2O, O2S. Invalid formula examples: C2H5OH, H2O1, OH, SO2. Invalid formulas are silently ignored.

Frequency

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

SafeBox

Type:Block Description:Part of the simulation box where molecules may not be removed. Only one of the SinkBox or SafeBox blocks may be present. If this block is present a 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 atomic units.

Amax

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

Amin

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

Bmax

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

Bmin

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

Cmax

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

Cmin

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

SinkBox

Type:Block Description:Part of the simulation box where molecules will be removed. By default, molecules matching the formula will be removed regardless of their location. If this block is present a molecule will 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 atomic units.

Amax

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

Amin

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

Bmax

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

Bmin

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

Cmax

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

Cmin

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

StartStep

Type:Integer Default value:0 Description:Step number when molecules are removed for the first time. After that, molecules are removed every [Frequency] steps. For example, if StartStep=99 and Frequency=100 then molecules will be removed at steps 99, 199, 299, etc... No molecule will be removed at step 0, so if StartStep=0 the first molecules are removed at the step number equal to [Frequency].

StopStep

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

ReplicaExchange

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

SwapFrequency

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

TemperatureFactor

Type:Float List Description:This is the ratio of the temperatures of two successive replicas. The first value sets the temperature of the second replica with respect to the first replica, the second value sets the temperature of the third replica with respect to the second one, and so on. If there are fewer values than nReplicas, the last value of TemperatureFactor is used for all the remaining replicas.

nReplicas

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

Restart

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

Thermostat

Type:Block Recurring:True Description:This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’ behavior.

BerendsenApply

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

ChainLength

Type:Integer Default value:10 Description:Number of individual thermostats forming the NHC thermostat

Duration

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

FirstAtom

Type:Integer Default value:1 Description:Index of the first atom to be thermostatted

LastAtom

Type:Integer Default value:0 Description:Index of the last atom to be thermostatted. A value of zero means the last atom in the system.

Tau

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

Temperature

Type:Float List Unit:Kelvin Description:The target temperature of the thermostat.

Type

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

TimeStep

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

Trajectory

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

SamplingFreq

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

TProfileGridPoints

Type:Integer Default value:0 Description:Number of points in the temperature profile. If TProfileGridPoints is greater than 0 then a temperature profile will be generates along each of the three unit cell axes. By default, no profile is generated.

NormalModes

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

UseSymmetry

Type:Bool Default value:True Description:Whether or not to exploit the symmetry of the system in the normal modes calculation.

NumericalDifferentiation

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

NuclearStepSize

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

Parallel

Type:Block Description:Numerical differentiation is an embarrassingly parallel problem. Double parallelization 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 Description:Number of cores in each working group.

nGroups

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

nNodesPerGroup

Type:Integer Description:Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.

StrainStepSize

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

UseSymmetry

Type:Bool Default value:True Description:Whether or not to exploit the symmetry of the system for numerical differentiations.

NumericalPhonons

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

DoubleSided

Type:Bool Default value:True Description:By default a two-sided (or quadratic) numerical differentiation of the nuclear gradients is used. Using a single-sided (or linear) numerical differentiation is computationally faster but much less accurate. Note: In older versions of the program only the single-sided option was available.

Interpolation

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

NDosEnergies

Type:Integer Default value:1000 Description:Nr. of energies used to calculate the phonon DOS used to integrate thermodynamic properties. For fast compute engines this may become time limiting and smaller values can be tried.

Parallel

Type:Block Description:Computing the phonons via numerical differentiation is an embarrassingly parallel problem. Double parallelization 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. Keep in mind that the displacements for a phonon calculation are done on a super-cell system, so that every task requires more memory than the central point calculated using the primitive cell.

nCoresPerGroup

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

nGroups

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

nNodesPerGroup

Type:Integer Description:Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.

StepSize

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

SuperCell

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

UseSymmetry

Type:Bool Default value:True Description:Whether or not to exploit the symmetry of the system in the phonon calculation.

PESScan

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

CalcPropertiesAtPESPoints

Type:Bool Default value:False Description:Whether to perform an additional calculation with properties on all the sampled points of the PES. If this option is enabled AMS will produce a separate engine output file for every sampled PES point.

FillUnconvergedGaps

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

ScanCoordinate

Type:Block Recurring:True Description:Specifies a coordinate along which the potential energy surface is scanned. If this block contains multiple entries, these coordinates will be varied and scanned together as if they were one.

Angle

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

Coordinate

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

Dihedral

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

Distance

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

nPoints

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

Print

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

Timers

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

Properties

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

BondOrders

Type:Bool Default value:False Description:Requests the engine to calculate bond orders. For MM engines these might just be the defined bond orders that go into the force-field, while for QM engines, this might trigger a bond order analysis based on the electronic structure.

ElasticTensor

Type:Bool Default value:False Description:Whether or not to calculate the elastic tensor.

Gradients

Type:Bool Default value:False Description:Whether or not to calculate the gradients.

Hessian

Type:Bool Default value:False Description:Whether or not to calculate the Hessian.

Molecules

Type:Bool Default value:False Description:Requests an analysis of the molecular components of a system, based on the bond orders calculated by the engine.

NormalModes

Type:Bool Default value:False Description:Whether or not to calculate the normal modes of vibration (and of molecules the corresponding Ir intensities.)

Other

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

Phonons

Type:Bool Default value:False Description:Whether or not to calculate the phonons for periodic systems.

SelectedAtomsForHessian

Type:Integer List Description:Compute the Hessian matrix elements only for the atoms defined in this list (index). If not specified, the Hessian will be computed for all atoms.

StressTensor

Type:Bool Default value:False Description:Whether or not to calculate the stress tensor.

RNGSeed

Type:Integer List Description:Initial seed for the (pseudo)random number generator. This should be omitted in most calculations to avoid introducing bias into the results. If this is unset, the generator will be seeded randomly from external sources of entropy. If you want to exactly reproduce an older calculation, set this to the numbers printed in its output.

Symmetry

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

Tolerance

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

System

Type:Block Recurring:True Description:Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.

AtomMasses

Type:Non-standard block Description:User defined atomic masses.

Atoms

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

BondOrders

Type:Non-standard block Description:Defined bond orders. May by used by MM engines.

Charge

Type:Float Default value:0.0 Description:The system’s total charge in atomic units (only for non-periodic systems).

FractionalCoords

Type:Bool Default value:False Description:Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.

GeometryFile

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

Lattice

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

LatticeStrain

Type:Float List Description:Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.

RandomizeCoordinates

Type:Float Default value:0.0 Unit:Angstrom Description:Apply a random noise to the atomic coordinates. This can be useful if you want to deviate from an ideal symmetric geometry.

RandomizeStrain

Type:Float Default value:0.0 Description:Apply a random strain to the system. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.

SuperCell

Type:Integer List Description:Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).

SuperCellTrafo

Type:Integer List Description:Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).

Task

Type:Multiple Choice Options:[SinglePoint, GeometryOptimization, TransitionStateSearch, PESScan, MolecularDynamics, ModeScanning, ModeRefinement, ModeTracking, GCMC, IRC] Description:This key is used to specify the computational task to perform.

Thermo

Type:Block Description:Options for thermodynamic properties (assuming an ideal gas). The properties are computed for ‘nSteps’ temperatures in the range [TMin,TMax].

Pressure

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

TMax

Type:Float Default value:298.15 Unit:Kelvin Description:Maximum value for the temperature range.

TMin

Type:Float Default value:298.15 Unit:Kelvin Description:Minimum value for the temperature range.

nSteps

Type:Integer Default value:1 Description:The number of temperatures in the range [TMin,TMax].

TransitionStateSearch

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

ModeToFollow

Type:Integer Default value:1 Description:In case of Transition State Search, here you can specify the index of the normal mode to follow (1 is the mode with the lowest frequency).

UseSymmetry

Type:Bool Default value:True Description:Whether to use the system’s symmetry at the application level.