Keywords

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.