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.
All
Type:String
Recurring:True
Description:Fix multiple distances using one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3 The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 as well as the angle between them. The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then any bond between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. If the distance is omitted then the bond length from the initial geometry is used. Important: only the bonds present in the system at the start of the simulation can be constrained, which means that the bonds may need to be specified in the System block. Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H
Angle
Type:String
Recurring:True
Description:Fix the angle between three atoms. Three atom indices followed by an angle in degrees.
Atom
Type:Integer
Recurring:True
Description:Fix the position of an atom. Just one integer referring to the index of the atom in the [System%Atoms] block.
AtomList
Type:Integer List
Recurring:True
Description:Fix positions of the specified atoms. A list of integers referring to indices of atoms in the [System%Atoms] block.
Block
Type:String
Recurring:True
Description:Name of the region to constrain as a rigid block. Regions are specified in the System%Atoms block.
BlockAtoms
Type:Integer List
Recurring:True
Description:List of atom indices for a block constraint, where the internal degrees of freedom are frozen.
Coordinate
Type:String
Recurring:True
Description:Fix a particular coordinate of an atom. Atom index followed by (x|y|z).
DifDist
Type:String
Recurring:True
Description:Four atom indices i j k l followed by the distance in Angstrom. This will constrain the difference R(ij)-R(kl) at the given value.
Dihedral
Type:String
Recurring:True
Description:Fix the dihedral angle between four atoms. Four atom indices followed by an angle in degrees.
Distance
Type:String
Recurring:True
Description:Fix the distance between two atoms. Two atom indices followed by the distance in Angstrom.
EqualStrain
Type:String
Description:Exclusively for lattice optimizations: Accepts a set of strain components [xx, xy, xz, yy, yz, zz] which are to be kept equal. The applied strain will be determined by the average of the corresponding stress tensors components. In AMSinput just check the corresponding check buttons.
FixedRegion
Type:String
Recurring:True
Description:Fix positions of all atoms in a region.
FreezeStrain
Type:String
Description:Exclusively for lattice optimizations: Freezes any lattice deformation corresponding to a particular component of the strain tensor. Accepts a set of strain components [xx, xy, xz, yy, yz, zz] to be frozen. In AMSinput just check the corresponding check buttons.
SumDist
Type:String
Recurring:True
Description:Four atom indices i j k l followed by the distance in Angstrom. This will constrain the sum R(ij)+R(kl) at the given value.
ElasticTensor
Type:Block
Description:Options for numerical evaluation of the elastic tensor.
MaxGradientForGeoOpt
Type:Float
Default value:0.0001
Unit:Hartree/Angstrom
GUI name:Maximum nuclear gradient
Description:Maximum nuclear gradient for the relaxation of the internal degrees of freedom of strained systems.
Parallel
Type:Block
Description:Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
nCoresPerGroup
Type:Integer
GUI name:Cores per group
Description:Number of cores in each working group.
nGroups
Type:Integer
GUI name:Number of groups
Description:Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup
Type:Integer
GUI name:Nodes per group
Description:Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
StrainStepSize
Type:Float
Default value:0.001
Description:Step size (relative) of strain deformations used for computing the elastic tensor numerically.
Engine
Type:Block
Description:The input for the computational engine. The header of the block determines the type of the engine.
EngineAddons
Type:Block
Description:This block configures all the engine add-ons.
AtomEnergies
Type:Non-standard block
Description:Add an element-dependent energy per atom. On each line, give the chemical element followed by the energy (in atomic units).
D3Dispersion
Type:Block
Description:This block configures the add-on that adds the Grimme D3 dispersion correction to the engine’s energy, gradients, and stress tensor.
Damping
Type:Multiple Choice
Default value:BJ
Options:[BJ, Zero]
Description:Type of damping: BJ (Becke-Johnson) or Zero. BJ is recommended for most applications.
Enabled
Type:Bool
Default value:No
Description:Enables the D3 dispersion correction addon.
Functional
Type:String
Default value:PBE
Description:Use the D3 parameterization by Grimme for a given xc-functional. Accepts the same values as the –func command line option of the official dftd3 program. Note: the naming convention is different from elsewhere in the AMS suite. For example, BLYP should be called b-lyp.
a1
Type:Float
Description:The a1 parameter. Only used if Damping is set to BJ. If set, it overwrites the a1 value for the chosen functional.
a2
Type:Float
Description:The a2 parameter. Only used if Damping is set to BJ. If set, it overwrites the a2 value for the chosen functional.
s6
Type:Float
Description:The s6 parameter, global scaling parameter. If set, it overwrites the s6 value for the chosen functional.
s8
Type:Float
Description:The s8 parameter. If set, it overwrites the s8 value for the chosen functional.
sr6
Type:Float
Description:The sr6 parameter. Only used if Damping is set to Zero. If set, it overwrites the sr6 value for the chosen functional.
D4Dispersion
Type:Block
Description:This block configures the addon that adds the Grimme D4(EEQ) dispersion correction to the engine’s energy, gradients, stress tensor and Hessian.
Enabled
Type:Bool
Default value:No
Description:Enables the D4 dispersion correction addon.
Functional
Type:Multiple Choice
Default value:PBE
Options:[HF, BLYP, BPBE, BP86, BPW, LB94, MPWLYP, MPWPW91, OLYP, OPBE, PBE, RPBE, REVPBE, PW86PBE, RPW86PBE, PW91, PW91P86, XLYP, B97, TPSS, REVTPSS, SCAN, B1LYP, B3LYP, BHLYP, B1P86, B3P86, B1PW91, B3PW91, O3LYP, REVPBE0, REVPBE38, PBE0, PWP1, PW1PW, MPW1PW91, MPW1LYP, PW6B95, TPSSH, TPSS0, X3LYP, M06L, M06, OMEGAB97, OMEGAB97X, CAM-B3LYP, LC-BLYP, LH07TSVWN, LH07SSVWN, LH12CTSSIRPW92, LH12CTSSIFPW92, LH14TCALPBE, B2PLYP, B2GPPLYP, MPW2PLYP, PWPB95, DSDBLYP, DSDPBE, DSDPBEB95, DSDPBEP86, DSDSVWN, DODBLYP, DODPBE, DODPBEB95, DODPBEP86, DODSVWN, PBE02, PBE0DH, DFTB(3ob), DFTB(mio), DFTB(pbc), DFTB(matsci), DFTB(ob2), B1B95, MPWB1K, REVTPSSH, GLYP, REVPBE0DH, REVTPSS0, REVDSDPBEP86, REVDSDPBEPBE, REVDSDBLYP, REVDODPBEP86, B97M, OMEGAB97M, R2SCAN]
Description:Use the D4 parameterization by Grimme for a given xc-functional.
Verbosity
Type:Multiple Choice
Default value:Silent
Options:[Silent, Normal, Verbose, VeryVerbose]
Description:Controls the verbosity of the dftd4 code. Equivalent to the –silent and –verbose command line switches of the official dftd4 program.
a1
Type:Float
Description:The a1 parameter, see D4 article. The physically reasonable range for a1 is [0.0,1.0]. If set, it overwrites the a1 value for the chosen functional.
a2
Type:Float
Description:The a2 parameter, see D4 article. The physically reasonable range for a2 is [0.0,7.0]. If set, it overwrites the a2 value for the chosen functional.
s6
Type:Float
Description:The s6 parameter, see D4 article. The physically reasonable range for s6 is [0.0,1.0]. If set, it overwrites the s6 value for the chosen functional.
s8
Type:Float
Description:The s8 parameter, see D4 article. The physically reasonable range for s8 is [0.0,3.0]. If set, it overwrites the s8 value for the chosen functional.
s9
Type:Float
Description:The s9 parameter, see D4 article. If set, it overwrites the s9 value for the chosen functional.
ExternalEngine
Type:Block
Description:External engine as an addon
Execute
Type:String
GUI name:Execute
Description:execute command
ExternalStress
Type:Block
Description:This block configures the addon that adds external stress term to the engine’s energy and stress tensor.
StressTensorVoigt
Type:Float List
Unit:a.u.
GUI name:External stress tensor
Description:The elements of the external stress tensor in Voigt notation. One should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
UpdateReferenceCell
Type:Bool
Default value:No
Description:Whether ot not the reference cell should be updated every time the system changes (see documentation).
PipeEngine
Type:Block
Description:Pipe engine as an addon
WorkerCommand
Type:String
GUI name:Worker command
Description:pipe worker command
Pressure
Type:Float
Default value:0.0
Unit:GPa
Description:Add a hydrostatic pressure term to the engine’s energy and stress tensor. Can only be used for 3D periodic boundary conditions.
WallPotential
Type:Block
Description:This block configures the addon that adds a spherical wall potential to the engine’s energy and gradients.
Enabled
Type:Bool
Default value:No
Description:Enables the wall potential addon.
Gradient
Type:Float
Default value:10.0
Unit:1/Angstrom
Description:The radial gradient outside the sphere.
Prefactor
Type:Float
Default value:0.01
Unit:Hartree
Description:The multiplier for the overall strength of the potential.
Radius
Type:Float
Default value:30.0
Unit:Angstrom
Description:The radius of the sphere, wherein the potential is close to zero.
EngineDebugging
Type:Block
Description:This block contains some options useful for debugging the computational engines.
CheckInAndOutput
Type:Bool
Default value:No
Description:Enables some additional checks on the input and output of and engine, e.g. for NaN values.
ForceContinousPES
Type:Bool
Default value:No
Description:If this option is set, the engine will always run in continuous PES mode. For many engines this disables the use of symmetry, as this one always leads to a discontinuous PES around the symmetric points: Basically there is jump in the PES at the point where the symmetry detection starts classifying the system as symmetric. Normally the continuous PES mode of the engine (often disabling the symmetry) is only used when doing numerical derivatives, but this flag forces the engine to continuously run in this mode.
IgnoreGradientsRequest
Type:Bool
Default value:No
Description:If this option is set, the engine will not do analytical gradients if asked for it, so that gradients will have to be evaluated numerically by AMS.
IgnorePreviousResults
Type:Bool
Default value:No
Description:If this option is set, the engine will not receive information from previous calculations. Typically this information is used to restart the self consistent procedure of the engine.
IgnoreStressTensorRequest
Type:Bool
Default value:No
Description:If this option is set, the engine will not calculate an analytical stress tensor if asked for it, so that the stress tensor will have to be evaluated numerically by AMS.
NeverQuiet
Type:Bool
Default value:No
Description:Makes the engine ignore the request to work quietly.
RandomFailureChance
Type:Float
Default value:0.0
Description:Makes the engine randomly report failures, even though the results are actually fine. Useful for testing error handling on the application level.
RandomNoiseInEnergy
Type:Float
Default value:0.0
Unit:Hartree
Description:Adds a random noise to the energy returned by the engine. The random contribution is drawn from [-r,r] where r is the value of this keyword.
RandomNoiseInGradients
Type:Float
Default value:0.0
Unit:Hartree/Angstrom
Description:Adds a random noise to the gradients returned by the engine. A random number in the range [-r,r] (where r is the value of this keyword) is drawn and added separately to each component of the gradient.
RandomStopChance
Type:Float
Default value:0.0
Description:Makes the engine randomly stop. Can be used to simulate crashes.
EngineRestart
Type:String
Description:The path to the file from which to restart the engine. Should be a proper engine result file (like adf.rkf, band.rkf etc), or the name of the results directory containing it.
GCMC
Type:Block
Description:This block controls the Grand Canonical Monte Carlo (GCMC) task. By default, molecules are added at random positions in the simulation box. The initial position is controlled by
AccessibleVolume
Type:Float
Default value:0.0
Description:Volume available to GCMC, in cubic Angstroms. AccessibleVolume should be specified for “Accessible” and “FreeAccessible” [VolumeOption].
Box
Type:Block
Description:Boundaries of the insertion space, i.e. coordinates of the origin of an inserted molecule (coordinates of an atom of the inserted system may fall outside the box). For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom (the system’s bounding box extended by the MaxDistance value by default).
Amax
Type:Float
Description:Coordinate of the upper bound along the first axis.
Amin
Type:Float
Description:Coordinate of the lower bound along the first axis.
Bmax
Type:Float
Description:Coordinate of the upper bound along the second axis.
Bmin
Type:Float
Description:Coordinate of the lower bound along the second axis.
Cmax
Type:Float
Description:Coordinate of the upper bound along the third axis.
Cmin
Type:Float
Description:Coordinate of the lower bound along the third axis.
Ensemble
Type:Multiple Choice
Default value:Mu-VT
Options:[Mu-VT, Mu-PT]
Description:Select the MC ensemble: Mu-VT for fixed volume or Mu-PT for variable volume. When the Mu-PT ensemble is selected the [Pressure] and [VolumeChangeMax] should also be specified.
Iterations
Type:Integer
GUI name:Number of GCMC iterations
Description:Number of GCMC moves.
MapAtomsToOriginalCell
Type:Bool
Default value:Yes
Description:Keeps the atom (mostly) in the original cell by mapping them back before the geometry optimizations.
MaxDistance
Type:Float
Default value:3.0
Unit:Angstrom
GUI name:Add molecules within
Description:The max distance to other atoms of the system when adding the molecule.
MinDistance
Type:Float
Default value:0.3
Unit:Angstrom
GUI name:Add molecules not closer than
Description:Keep the minimal distance to other atoms of the system when adding the molecule.
Molecule
Type:Block
Recurring:True
GUI name:Molecules
Description:This block defines the molecule (or atom) that can be inserted/moved/deleted with the MC method. The coordinates should form a reasonable structure. The MC code uses these coordinates during the insertion step by giving them a random rotation, followed by a random translation to generate a random position of the molecule inside the box. Currently, there is no check to make sure all atoms of the molecule stay inside the simulation box. The program does check that the MaxDistance/MinDistance conditions are satisfied.
ChemicalPotential
Type:Float
Unit:Hartree
Description:Chemical potential of the molecule (or atom) reservoir. It is used when calculating the Boltzmann accept/reject criteria after a MC move is executed. This value can be derived from first principles using statistical mechanics, or equivalently, it can be determined from thermochemical tables available in literature sources. For example, the proper chemical potential for a GCMC simulation in which single oxygen atoms are exchanged with a reservoir of O2 gas, should equal 1/2 the chemical potential of O2 at the temperature and pressure of the reservoir: cmpot = Mu_O(T,P) = 1/2*Mu_O2(T,P) = 1/2 * [Mu_ref(T,P_ref) + kT*Log(P/Pref) - E_diss] where the reference chemical potential [Mu_ref(T,P_ref)] is the experimentally determined chemical potential of O2 at T and Pref; kT*Log(P/Pref) is the pressure correction to the free energy, and E_diss is the dissociation energy of the O2 molecule.
NoAddRemove
Type:Bool
Default value:No
GUI name:Fix molecule
Description:Set to True to tell the GCMC code to keep the number of molecules/atoms of this type fixed. It will thus disable Insert/Delete moves on this type, meaning it can only do a displacement move, or volume change move (for an NPT ensemble).
SystemName
Type:String
GUI name:Molecule
Description:String ID of a named [System] to be inserted. The lattice specified with this System, if any, is ignored and the main system’s lattice is used instead.
NonAccessibleVolume
Type:Float
Default value:0.0
GUI name:Non-accessible volume
Description:Volume not available to GCMC, in cubic Angstroms. NonAccessibleVolume may be specified for the “Free” [VolumeOption] to reduce the accessible volume.
NumAttempts
Type:Integer
Default value:1000
GUI name:Max tries
Description:Try inserting/moving the selected molecule up to the specified number of times or until all constraints are satisfied. If all attempts fail a message will be printed and the simulation will stop. If the MaxDistance-MinDistance interval is small this number may have to be large.
Pressure
Type:Float
Default value:0.0
Unit:Pascal
Description:Pressure used to calculate the energy correction in the Mu-PT ensemble. Set it to zero for incompressible solid systems unless at very high pressures.
Removables
Type:Non-standard block
Description:The Removables can be used to specify a list of molecules that can be removed or moved during this GCMC calculation. Molecules are specified one per line in the format following format: MoleculeName atom1 atom2 … The MoleculeName must match a name specified in one of the [Molecule] blocks. The atom indices refer to the whole input System and the number of atoms must match that in the specified Molecule. A suitable Removables block is written to the standard output after each accepted MC move. If you do so then you should also replace the initial atomic coordinates with the ones found in the same file. If a [Restart] key is present then the Removables block is ignored.
Restart
Type:String
Description:Name of an RKF restart file. Upon restart, the information about the GCMC input parameters, the initial system (atomic coordinates, lattice, charge, etc.) and the MC molecules (both already inserted and to be inserted) are read from the restart file. The global GCMC input parameters and the MC Molecules can be modified from input. Any parameter not specified in the input will use its value from the restart file (i.e. not the default value). Molecules found in the restart file do not have to be present as named Systems in the input, however if there is a System present that matches the name of a molecule from restart then the System’s geometry will replace that found in the restart file. It is also possible to specify new Molecules in the input, which will be added to the pool of the MC molecules from restart.
SwapAtoms
Type:Block
Description:Experimental: Occasionally swap the coordinates of a random pair of atoms from two regions.
Probability
Type:Float
Default value:0.0
Description:Probability of performing a swap move instead of any other GCMC move in a single GCMC iteration.
Regions
Type:String
Description:Names of two regions to swap between (separated by a space).
Temperature
Type:Float
Default value:300.0
Unit:Kelvin
Description:Temperature of the simulation. Increase the temperature to improve the chance of accepting steps that result in a higher energy.
UseGCPreFactor
Type:Bool
Default value:Yes
GUI name:Use GC prefactor
Description:Use the GC pre-exponential factor for probability.
VolumeChangeMax
Type:Float
Default value:0.05
Description:Fractional value by which logarithm of the volume is allowed to change at each step. The new volume is then calculated as Vnew = exp(random(-1:1)*VolumeChangeMax)*Vold
VolumeOption
Type:Multiple Choice
Default value:Free
Options:[Free, Total, Accessible, FreeAccessible]
GUI name:Volume method
Description:Specifies the method to calculate the volume used to calculate the GC pre-exponential factor and the energy correction in the Mu-PT ensemble: Free: V = totalVolume - occupiedVolume - NonAccessibleVolume; Total: V = totalVolume; Accessible: V = AccessibleVolume; FreeAccessible: V = AccessibleVolume - occupiedVolume. The AccessibleVolume and NonAccessibleVolume are specified in the input, the occupiedVolume is calculated as a sum of atomic volumes.
GeometryOptimization
Type:Block
Description:Configures details of the geometry optimization and transition state searches.
CalcPropertiesOnlyIfConverged
Type:Bool
Default value:Yes
Description:Compute the properties requested in the ‘Properties’ block, e.g. Frequencies or Phonons, only if the optimization (or transition state search) converged. If False, the properties will be computed even if the optimization did not converge.
Convergence
Type:Block
Description:Convergence is monitored for up to 4 quantities: the energy change, the Cartesian gradients, the Cartesian step size, and for lattice optimizations the stress energy per atom. Convergence criteria can be specified separately for each of these items.
Energy
Type:Float
Default value:1e-05
Unit:Hartree
GUI name:Energy convergence
Description:The criterion for changes in the energy. The energy is considered converged when the change in energy is smaller than this threshold times the number of atoms.
Gradients
Type:Float
Default value:0.001
Unit:Hartree/Angstrom
GUI name:Gradient convergence
Description:Threshold for nuclear gradients.
Step
Type:Float
Default value:0.01
Unit:Angstrom
GUI name:Step convergence
Description:The maximum Cartesian step allowed for a converged geometry.
StressEnergyPerAtom
Type:Float
Default value:0.0005
Unit:Hartree
Description:Threshold used when optimizing the lattice vectors. The stress is considered ‘converged’ when the maximum value of stress_tensor * cell_volume / number_of_atoms is smaller than this threshold (for 2D and 1D systems, the cell_volume is replaced by the cell_area and cell_length respectively).
CoordinateType
Type:Multiple Choice
Default value:Auto
Options:[Auto, Delocalized, Cartesian]
GUI name:Optimization space
Description:Select the type of coordinates in which to perform the optimization. ‘Auto’ automatically selects the most appropriate CoordinateType for a given Method. If ‘Auto’ is selected, Delocalized coordinates will be used for the Quasi-Newton and SCMGO methods, while Cartesian coordinates will be used for all other methods.
EngineAutomations
Type:Block
Description:The optimizer can change some settings of the engine, based for instance on the error. The idea is to allow the engine to be a bit quicker at the start, and more accurate towards the end. Automations are always engine specific.
Enabled
Type:Bool
Default value:Yes
Description:Whether or not autotions are enabled at all.
Gradient
Type:Block
Recurring:True
Description:A gradient-based automation.
FinalValue
Type:Float
Description:This value will be used whenever the gradient is less than GradientLow
HighGradient
Type:Float
Default value:1.0
Unit:Hartree/Angstrom
Description:Defines a large gradient. When the actual gradient is between GradientHigh and GradientLow a linear interpolation scheme is used for kT (on a log scale).
InitialValue
Type:Float
Description:This value will be used at the first geometry, and whenever the gradient is higher than GradientHigh
LowGradient
Type:Float
Default value:1.0
Unit:Hartree/Angstrom
Description:Defines a small gradient, see GradientHigh
UseLogInterpolation
Type:Bool
Default value:Yes
Description:Whether to use interpolation on a log (y) scale or not
Variable
Type:String
Default value:
Description:variable to be tweaked for the engine.
Iteration
Type:Block
Recurring:True
Description:Geometry step based automation.
FinalValue
Type:Float
Description:
FirstIteration
Type:Integer
Default value:1
Description:When the actual gradient is between the first and last iteration, a linear interpolation is used.
InitialValue
Type:Float
Description:This value will be used when the iteration number is smaller or equal to FirstIteration
LastIteration
Type:Integer
Default value:10
Description:Where the automation should reach the FinalValue
UseLogInterpolation
Type:Bool
Default value:Yes
Description:Whether to use interpolation on a log (y) scale or not
Variable
Type:String
Default value:
Description:variable to be tweaked for the engine.
FIRE
Type:Block
Description:This block configures the details of the FIRE optimizer. The keywords name correspond the the symbols used in the article describing the method, see PRL 97, 170201 (2006).
AllowOverallRotation
Type:Bool
Default value:Yes
Description:Whether or not the system is allowed to freely rotate during the optimization. This is relevant when optimizing structures in the presence of external fields.
AllowOverallTranslation
Type:Bool
Default value:No
Description:Whether or not the system is allowed to translate during the optimization. This is relevant when optimizing structures in the presence of external fields.
MapAtomsToUnitCell
Type:Bool
Default value:No
Description:Map the atoms to the central cell at each geometry step.
NMin
Type:Integer
Default value:5
Description:Number of steps after stopping before increasing the time step again.
alphaStart
Type:Float
Default value:0.1
Description:Steering coefficient.
dtMax
Type:Float
Default value:1.0
Unit:Femtoseconds
Description:Maximum time step used for the integration.
dtStart
Type:Float
Default value:0.25
Unit:Femtoseconds
Description:Initial time step for the integration.
fAlpha
Type:Float
Default value:0.99
Description:Reduction factor for the steering coefficient.
fDec
Type:Float
Default value:0.5
Description:Reduction factor for reducing the time step in case of uphill movement.
fInc
Type:Float
Default value:1.1
Description:Growth factor for the integration time step.
strainMass
Type:Float
Default value:0.5
Description:Fictitious relative mass of the lattice degrees of freedom. This controls the stiffness of the lattice degrees of freedom relative to the atomic degrees of freedom, with smaller values resulting in a more aggressive optimization of the lattice.
HessianFree
Type:Block
Description:Configures details of the Hessian-free (conjugate gradients or L-BFGS) geometry optimizer.
Step
Type:Block
Description:
MaxCartesianStep
Type:Float
Default value:0.1
Unit:Angstrom
Description:Limit on a single Cartesian component of the step.
MinRadius
Type:Float
Default value:0.0
Unit:Angstrom
Description:Minimum value for the trust radius.
TrialStep
Type:Float
Default value:0.0005
Unit:Angstrom
Description:Length of the finite-difference step when determining curvature. Should be smaller than the step convergence criterion.
TrustRadius
Type:Float
Default value:0.2
Unit:Angstrom
Description:Initial value of the trust radius.
InitialHessian
Type:Block
Description:Options for initial model Hessian when optimizing systems with either the Quasi-Newton or the SCMGO method.
File
Type:String
GUI name:Initial Hessian from
Description:KF file containing the initial Hessian (or the results dir. containing it). This can be used to load a Hessian calculated in a previously with the [Properties%Hessian] keyword.
Type
Type:Multiple Choice
Default value:Auto
Options:[Auto, UnitMatrix, Swart, FromFile, Calculate, CalculateWithFastEngine]
GUI name:Initial Hessian
Description:Select the type of initial Hessian. Auto: let the program pick an initial model Hessian. UnitMatrix: simplest initial model Hessian, just a unit matrix in the optimization coordinates. Swart: model Hessian from M. Swart. FromFile: load the Hessian from the results of a previous calculation (see InitialHessian%File). Calculate: compute the initial Hessian (this may be computationally expensive and it is mostly recommended for TransitionStateSearch calculations). CalculateWithFastEngine: compute the initial Hessian with a faster engine.
KeepIntermediateResults
Type:Bool
Default value:No
Description:Whether the full engine result files of all intermediate steps are stored on disk. By default only the last step is kept, and only if the geometry optimization converged. This can easily lead to huge amounts of data being stored on disk, but it can sometimes be convenient to closely monitor a tricky optimization, e.g. excited state optimizations going through conical intersections, etc. …
MaxIterations
Type:Integer
GUI name:Maximum number of iterations
Description:The maximum number of geometry iterations allowed to converge to the desired structure.
MaxRestarts
Type:Integer
Default value:0
Description:If a geometry optimization of a system with no symmetry operators (or with explicitly disabled symmetry: UseSymmetry False) and enabled PES point characterization converges to a transition state (or higher order saddle point), it can be restarted automatically after a small displacement along the imaginary vibrational mode. In case the restarted optimization again does not find a minimum, this can happen multiple times in succession. This keyword sets the maximum number of restarts. The default value is 0, so the automatic restarting is disabled by default.
Method
Type:Multiple Choice
Default value:Auto
Options:[Auto, Quasi-Newton, SCMGO, FIRE, L-BFGS, ConjugateGradients]
GUI name:Optimization method
Description:Select the optimization algorithm employed for the geometry relaxation. Currently supported are: the Hessian-based Quasi-Newton-type BFGS algorithm, the experimental SCMGO optimizer, the fast inertial relaxation method (FIRE), the limited-memory BFGS method, and the conjugate gradients method. The default is to choose an appropriate method automatically based on the engine’s speed, the system size and the supported optimization options.
OptimizeLattice
Type:Bool
Default value:No
Description:Whether to also optimize the lattice for periodic structures. This is currently only supported with the Quasi-Newton, FIRE, L-BFGS and SCMGO optimizers.
PretendConverged
Type:Bool
Default value:No
Description:Normally a non-converged geometry optimization is considered an error. If this keyword is set to True, the optimizer will only produce a warning and still claim that the optimization is converged. (This is mostly useful for scripting applications, where one might want to consider non-converged optimizations still successful jobs.)
Quasi-Newton
Type:Block
Description:Configures details of the Quasi-Newton geometry optimizer.
MaxGDIISVectors
Type:Integer
Default value:0
Description:Sets the maximum number of GDIIS vectors. Setting this to a number >0 enables the GDIIS method.
Step
Type:Block
Description:
TrustRadius
Type:Float
Description:Initial value of the trust radius.
VaryTrustRadius
Type:Bool
Description:Whether to allow the trust radius to change during optimization. By default True during energy minimization and False during transition state search.
UpdateTSVectorEveryStep
Type:Bool
Default value:Yes
GUI name:Update TSRC vector every step
Description:Whether to update the TS reaction coordinate at each step with the current eigenvector.
RestartDisplacement
Type:Float
Default value:0.05
Unit:Angstrom
Description:If a geometry optimization of a system with no symmetry operators (or with explicitly disabled symmetry: UseSymmetry False) and enabled PES point characterization converges to a transition state (or higher order saddle point), it can be restarted automatically after a small displacement along the imaginary vibrational mode. This keywords sets the size of the displacement for the furthest moving atom.
SCMGO
Type:Block
Description:Configures details SCMGO.
ContractPrimitives
Type:Bool
Default value:Yes
Description:Form non-redundant linear combinations of primitive coordinates sharing the same central atom
NumericalBMatrix
Type:Bool
Default value:No
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:Yes
Description:Whether or not the trust radius can be updated during the optimization.
logSCMGO
Type:Bool
Default value:No
Description:Verbose output of SCMGO internal data
testSCMGO
Type:Bool
Default value:No
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
GUI name:Gradient convergence
Description:Convergence criterion for the max component of the residual energy gradient.
Step
Type:Float
Default value:0.001
Unit:Angstrom
GUI name:Step convergence
Description:Convergence criterion for the max component of the step in the optimization coordinates.
CoordinateType
Type:Multiple Choice
Default value:Cartesian
Options:[Cartesian, Delocalized]
GUI name:Coordinates used for optimization
Description:Select the type of coordinates in which to perform the optimization. Note that the Delocalized option should be considered experimental.
Direction
Type:Multiple Choice
Default value:Both
Options:[Both, Forward, Backward]
Description:Select direction of the IRC path. The difference between the Forward and the Backward directions is determined by the sign of the largest component of the vibrational normal mode corresponding to the reaction coordinate at the transition state geometry. The Forward path correspond to the positive sign of the component. If Both is selected then first the Forward path is computed followed by the Backward one.
InitialHessian
Type:Block
Description:Options for initial Hessian at the transition state. The first eigenvalue of the initial Hessian defines direction of the first forward or backward step. This block is ignored when restarting from a previous IRC calculation because the initial Hessian found in the restart file is used.
File
Type:String
GUI name:File
Description:If ‘Type’ is set to ‘FromFile’ then in this key you should specify the RKF file containing the initial Hessian (or the ams results dir. containing it). This can be used to load a Hessian calculated previously with the ‘Properties%Hessian’ keyword. If you want to also use this file for the initial geometry then also specify it in a ‘LoadSystem’ block.
Type
Type:Multiple Choice
Default value:Calculate
Options:[Calculate, FromFile]
GUI name:Initial Hessian
Description:Calculate the exact Hessian for the input geometry or load it from the results of a previous calculation.
KeepConvergedResults
Type:Bool
Default value:Yes
Description:Keep the binary RKF result file for every converged IRC point. These files may contain more information than the main ams.rkf result file.
MaxIRCSteps
Type:Integer
GUI name:Maximum IRC steps
Description:Soft limit on the number of IRC points to compute in each direction. After the specified number of IRC steps the program will switch to energy minimization and complete the path. This option should be used when you are interested only in the reaction path area near the transition state. Note that even if the soft limit has been hit and the calculation has completed, the IRC can still be restarted with a ‘RedoBackward’ or ‘RedoForward’ option.
MaxIterations
Type:Integer
Default value:300
GUI name:Maximum iterations
Description:The maximum number of geometry iterations allowed to converge the inner IRC loop. If optimization does not converge within the specified number of steps, the calculation is aborted.
MaxPoints
Type:Integer
Default value:100
GUI name:Maximum points
Description:Hard limit on the number of IRC points to compute in each direction. After the specified number of IRC steps the program will stop with the current direction and switch to the next one. If both ‘MaxPoints’ and ‘MaxIRCSteps’ are set to the same value then ‘MaxPoints’ takes precedence, therefore this option should be used to set a limit on the number of IRC steps if you intend to use the results later for a restart.
MinEnergyProfile
Type:Bool
Default value:No
GUI name:Minimum energy profile
Description:Calculate minimum energy profile (i.e. no mass-weighting) instead of the IRC.
MinPathLength
Type:Float
Default value:0.1
Unit:Angstrom
Description:Minimum length of the path required before switching to energy minimization. Use this to overcome a small kink or a shoulder on the path.
Restart
Type:Block
Description:Restart options. Upon restart, the information about the IRC input parameters and the initial system (atomic coordinates, lattice, charge, etc.) is read from the restart file. The IRC input parameters can be modified from input. Except for ‘MaxPoints’ and ‘Direction’ all parameters not specified in the input will use their values from the restart file. The ‘MaxPoints’ and ‘Direction’ will be reset to their respective default values if not specified in the input. By default, the IRC calculation will continue from the point where it left off. However, the ‘RedoForward’ and/or ‘RedoBackward’ option can be used to enforce recalculation of a part of the reaction path, for example, using a different ‘Step’ value.
File
Type:String
GUI name:Restart
Description:Name of an RKF restart file generated by a previous IRC calculation. Do not use this key to provide an RKF file generated by a TransitionStateSearch or a SinglePoint calculation, use the ‘LoadSystem’ block instead.
RedoBackward
Type:Integer
Default value:0
Description:IRC step number to start recalculating the backward path from. By default, if the backward path has not been completed then start after the last completed step. If the backward path has been completed and the ‘RedoBackward’ is omitted then no point on the backward path will be recomputed.
RedoForward
Type:Integer
Default value:0
Description:IRC step number to start recalculating the forward path from. By default, if the forward path has not been completed then start after the last completed step. If the forward path has been completed and the ‘RedoForward’ is omitted then no point on the forward path will be recomputed.
Step
Type:Float
Default value:0.2
GUI name:Step size
Description:IRC step size in mass-weighted coordinates, sqrt(amu)*bohr. One may have to increase this value when heavy atoms are involved in the reaction, or decrease it if the reactant or products are very close to the transition state.
LoadEngine
Type:String
Description:The path to the file from which to load the engine configuration. Replaces the Engine block.
LoadSystem
Type:Block
Recurring:True
Description:Block that controls reading the chemical system from a KF file instead of the [System] block.
File
Type:String
Description:The path of the KF file from which to load the system. It may also be the results directory containing it.
Section
Type:String
Default value:Molecule
Description:The section on the KF file from which to load the system.
Log
Type:Non-standard block
Description:Configures the debugging loggers. Syntax: ‘Level LoggerName’. Possible Levels: All, Debug, Info, Warning, Error, Fatal.
MolecularDynamics
Type:Block
Description:Configures molecular dynamics (with the velocity-Verlet algorithm) with and without thermostats. This block allows to specify the details of the molecular dynamics calculation.
AddMolecules
Type:Block
Recurring:True
GUI name:Add molecules
Description:This block controls adding molecules to the system (a.k.a. the Molecule Gun). Multiple occurrences of this block are possible. By default, molecules are added at random positions in the simulation box with velocity matching the current system temperature. The initial position can be modified using one of the following keywords: Coords, CoordsBox, FractionalCoords, FractionalCoordsBox. The Coords and FractionalCoords keys can optionally be accompanied by CoordsSigma or FractionalCoordsSigma, respectively.
AtomTemperature
Type:Float
Default value:0.0
Unit:Kelvin
Description:Add random velocity corresponding to the specified temperature to individual atoms of the molecule. This only affects rotational and internal degrees of freedom, not the net translational velocity of the inserted molecule as set by the other options.
ContactDistance
Type:Float
Default value:0.0
Unit:Angstrom
Description:Translate the bullet along the velocity vector until it comes within ContactDistance of any other atom.
Coords
Type:Float List
Unit:Angstrom
Description:Place molecules at or around the specified Cartesian coordinates. This setting takes precedence over other ways to specify initial coordinates of the molecule: [CoordsBox], [FractionalCoords], and [FractionalCoordsBox].
CoordsBox
Type:Float List
Unit:Angstrom
Description:Place molecules at random locations inside the specified box in Cartesian coordinates. Coordinates of the box corners are specified as: Xmin, Xmax, Ymin, Ymax, Zmin, Zmax. This setting is ignored if Coords is used. In AMSinput, if this field is not empty it will be used instead of the default Coords.
CoordsSigma
Type:Float List
Unit:Angstrom
Description:Sigma values (one per Cartesian axis) for a Gauss distribution of the initial coordinates. Can only be used together with Coords.
DeviationAngle
Type:Float
Default value:0.0
Unit:Degree
Description:Randomly tilt the shooting direction up to this angle away from the VelocityDirection vector.
Energy
Type:Float
Unit:Hartree
Description:Initial kinetic energy of the molecule in the shooting direction.
EnergySigma
Type:Float
Default value:0.0
Unit:Hartree
Description:Sigma value for the Gauss distribution of the initial kinetic energy around the specified value. Should only be used together with Energy.
FractionalCoords
Type:Float List
Description:Place molecules at or around the specified fractional coordinates in the main system’s lattice. For non-periodic dimensions a Cartesian value in Angstrom is expected. This setting is ignored if [Coords] or [CoordsBox] is used.
FractionalCoordsBox
Type:Float List
Description:Place molecules at random locations inside the box specified as fractional coordinates in the main system’s lattice. Coordinates of the box corners are specified as: Xmin, Xmax, Ymin, Ymax, Zmin, Zmax. For non-periodic dimensions the Cartesian value in Angstrom is expected. This setting is ignored if [Coords], [CoordsBox], or [FractionalCoords] is used.
FractionalCoordsSigma
Type:Float List
Description:Sigma values (one per axis) for a Gauss distribution of the initial coordinates. For non-periodic dimensions the Cartesian value in Angstrom is expected. Can only be used together with FractionalCoords.
Frequency
Type:Integer
Default value:0
Description:A molecule is added every [Frequency] steps after the StartStep. There is never a molecule added at step 0.
MinDistance
Type:Float
Default value:0.0
Unit:Angstrom
Description:Keep the minimal distance to other atoms of the system when adding the molecule.
MoleFraction
Type:Float
Description:Defines a mixture to be deposited using one AddMolecules block per component. AMS will randomly alternate between any guns that have MoleFraction set. These need to all have the same settings for StartStep, StopStep and Frequency. Any additional AddMolecules blocks without MoleFraction will remain completely independent.
NumAttempts
Type:Integer
Default value:10
Description:Try adding the molecule up to the specified number of times or until the MinDistance constraint is satisfied. If all attempts fail a message will be printed and the simulation will continue normally.
Rotate
Type:Bool
Default value:No
Description:Rotate the molecule randomly before adding it to the system.
StartStep
Type:Integer
Default value:0
Description:Step number when the first molecule should be added. After that, molecules are added every Frequency steps. For example, ff StartStep=99 and Frequency=100 then a molecule will be added at steps 99, 199, 299, etc… No molecule will be added at step 0, so if StartStep=0 the first molecule is added at the step number equal to [Frequency].
StopStep
Type:Integer
Description:Do not add this molecule after the specified step.
System
Type:String
Description:String ID of the [System] that will be added with this ‘gun’. The lattice specified with this System is ignored and the main system’s lattice is used instead. AMSinput adds the system at the coordinates of the System (thus setting Coords to the center of the System).
Temperature
Type:Float
Unit:Kelvin
Description:Initial energy of the molecule in the shooting direction will correspond to the given temperature.
TemperatureSigma
Type:Float
Default value:0.0
Unit:Kelvin
Description:Sigma value for the Gauss distribution of the initial temperature the specified value. Should only be used together with Temperature.
Velocity
Type:Float
Unit:Angstrom/fs
Description:Initial velocity of the molecule in the shooting direction.
VelocityDirection
Type:Float List
Description:Velocity direction vector for aimed shooting. It will be random if not specified. In AMSinput add one or two atoms (which may be dummies). One atom: use vector from center of the system to add to that atom. Two atoms: use vector from the first to the second atom.
VelocitySigma
Type:Float
Default value:0.0
Unit:Angstrom/fs
Description:Sigma value for the Gauss distribution of the initial velocity around the specified value. Should only be used together with Velocity.
ApplyForce
Type:Block
Recurring:True
Description:The ApplyForce keyword can be used to apply shear stress to a system by applying a constant force to a certain (subgroups of) atoms in the system
AtomList
Type:Integer List
Recurring:True
Description:Apply the constant force to the specified atoms. A list of integers referring to indices of atoms in the [System%Atoms] block.
CosineShear
Type:Block
Description:Periodic Perturbation can be used to add force using a periodic function along a certain axis in the system
Axis
Type:Float List
Recurring:False
Description:The axis along which to apply the cosinus wave
Direction
Type:Integer
Recurring:False
Description:The direction along which to apply the streaming velocity, 1 = x-direction, 2 = y-direction, 3 = z-direction
Magnitude
Type:Float
Unit:Angstrom
Recurring:False
Description:Magnitude of the cosinus wave function
FixedRegion
Type:String
Recurring:True
Description:Apply the constant force to all atoms in a region.
Force
Type:Float List
Unit:Hartree/Bohr
Description:Defines the constant force vector
ApplyVelocity
Type:Block
Recurring:True
Description:The ApplyVelocity keyword can be used to apply shear stress to a system by moving certain (subgroups of) atoms in the system at a constant velocity
AtomList
Type:Integer List
Recurring:True
Description:Applies the shearing velocity to the specified atoms. A list of integers referring to indices of atoms in the [System%Atoms] block.
CosineShear
Type:Block
Description:Periodic Perturbation can be used to add streaming velocities using a periodic function along a certain axis in the system
Axis
Type:Float List
Recurring:False
Description:The axis along which to apply the cosinus wave
Direction
Type:Integer
Recurring:False
Description:The direction along which to apply the streaming velocity, 1 = x-direction, 2 = y-direction, 3 = z-direction
Magnitude
Type:Float
Unit:Angstrom
Recurring:False
Description:Magnitude of the cosinus wave function
FixedRegion
Type:String
Recurring:True
Description:Applies the shearing velocity to all atoms in a region.
Velocity
Type:Float List
Unit:Angstrom/fs
Recurring:False
Description:The constant velocity that will be applied to the specified atoms. Only nonzero components of this vector are used to set the corresponding components of the net velocity of the specified set of atoms. Any zero components of this velocity vector leave the corresponding component of the net velocity unaffected.
Barostat
Type:Block
Description:This block allows to specify the use of a barostat during the simulation.
BulkModulus
Type:Float
Default value:2200000000.0
Unit:Pascal
Description:An estimate of the bulk modulus (inverse compressibility) of the system for the Berendsen barostat. This is only used to make Tau correspond to the true observed relaxation time constant. Values are commonly on the order of 10-100 GPa (1e10 to 1e11) for solids and 1 GPa (1e9) for liquids (2.2e9 for water). Use 1e9 to match the behavior of standalone ReaxFF.
ConstantVolume
Type:Bool
Default value:No
Description:Keep the volume constant while allowing the box shape to change. This is currently supported only by the MTK barostat.
Duration
Type:Integer List
Description:Specifies how many steps should a transition from a particular pressure to the next one in sequence take.
Equal
Type:Multiple Choice
Default value:None
Options:[None, XYZ, XY, YZ, XZ]
Description:Enforce equal scaling of the selected set of dimensions. They will be barostatted as one dimension according to the average pressure over the components.
Pressure
Type:Float List
Unit:Pascal
Description:Specifies the target pressure. You can specify multiple pressures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one p to the next p (using a linear ramp).
Scale
Type:Multiple Choice
Default value:XYZ
Options:[XYZ, Shape, X, Y, Z, XY, YZ, XZ]
Description:Dimensions that should be scaled by the barostat to maintain pressure. Selecting Shape means that all three dimensions and also all the cell angles are allowed to change.
Tau
Type:Float
Unit:Femtoseconds
GUI name:Damping constant
Description:Specifies the time constant of the barostat.
Type
Type:Multiple Choice
Default value:None
Options:[None, Berendsen, MTK]
GUI name:Barostat
Description:Selects the type of the barostat.
BondBoost
Type:Block
Recurring:True
Description:Forced reaction (bond boost) definitions. Multiple BondBoost blocks may be specified, which will be treated independently.
Chain
Type:Block
Description:Specifications of a chain of atoms. When a chain is detected the distance restraints will be activated. No other chain of this type will be detected while any restraints for this chain is active.
AtomNames
Type:String
Description:Atom names specifying the chain. An atom name can optionally be followed by ‘@’ and a region name, in this case only atoms of this type from the given region will be matched. A leading ‘@’ followed by a number indicates that this position in the chain must be occupied by the atom found earlier at the specified position in the chain. For example “O H N C @1” indicates that the last atom in the chain of the five atoms must be the first oxygen, thus defining a 4-membered ring. This is the only way to define a ring because implicit rings will not be detected. For example, “O H N C O” does not include rings.
MaxDistances
Type:Float List
Unit:Angstrom
Description:Maximum distances for each pair of atoms in the chain. The number of distances must be one less than the number of AtomNames.
MinDistances
Type:Float List
Unit:Angstrom
Description:Minimum distances for each pair of atoms in the chain. The number of distances must be one less than the number of AtomNames.
DistanceRestraint
Type:String
Recurring:True
Description:Specify two atom indices followed by the optimum distance in Angstrom, the first parameter and, optionally, the profile type and the second parameter. This restraint will try to keep the distance between the two specified atoms at the given value. For periodic systems this restraint follows the minimum image convention. Each atom index indicates a position of the corresponding atom in the AtomNames key. Currently recognized restraint profile types: Harmonic (default), Hyperbolic, Erf, GaussianWell. The first parameter is the force constant for the Harmonic, Hyperbolic, and Erf profiles, or well depth for GaussianWell. The second parameter is the asymptotic force value F(Inf) for Hyperbolic and Erf profiles, or the factor before x^2 in the exponent for GaussianWell. Note: the GaussianWell restraint should be used with the Moving flag.
Moving
Type:Bool
Default value:No
GUI name:Move restraint
Description:Move the restraints created with this BondBoost. The restraint value will start at the currect coordinate’s value and will move towards the optimum during the restraint’s lifetime. The increment is calculated from the initial deviation and the [NSteps] parameter. This feature should be used with the GaussianWell restraint types.
NSteps
Type:Integer
GUI name:Boost lifetime
Description:Number of steps the restraints will remain active until removed. Atoms participating in one reaction are not available for the given number of steps.
NumInstances
Type:Integer
Default value:1
GUI name:Number of instances
Description:Number of reactions of this type taking place simultaneously.
Units
Type:Multiple Choice
Default value:Default
Options:[Default, MD]
GUI name:Restr. parameter units
Description:Change energy, force and force constant units in the DistanceRestraint key from the default (atomic units) to those often used in the MD community (based on kcal/mol and Angstrom). Units for the optimum distances are not affected.
CRESTMTD
Type:Block
GUI name:CREST_MTD
Description:Input for CREST metadynamics simulation.
AddEnergy
Type:Bool
Default value:No
Description:Add the bias energy to the potential energy (to match the gradients)
GaussianScaling
Type:Block
Description:Options for gradual introduction of the Gaussians
ScaleGaussians
Type:Bool
Default value:Yes
Description:Introduce the Gaussians gradually, using a scaling function
ScalingSlope
Type:Float
Default value:0.03
Description:Slope of the scaling function for the Gaussians with respect to time
Height
Type:Float
Unit:Hartree
Description:The height of the Gaussians added
NGaussiansMax
Type:Integer
Description:Maximum number of Gaussians stored
NSteps
Type:Integer
Description:Interval of Gaussian placement
RestartFile
Type:String
Description:Filename for file from which to read data on Gaussians placed previously.
Width
Type:Float
Unit:Bohr
Description:The width of the Gaussians added in terms of the RMSD
CVHD
Type:Block
Recurring:True
GUI name:CVHD
Description:Input for the Collective Variable-driven HyperDynamics (CVHD).
Bias
Type:Block
Description:The bias is built from a series of Gaussian peaks deposited on the collective variable axis every [Frequency] steps during MD. Each peak is characterized by its (possibly damped) height and the RMS width (standard deviation).
DampingTemp
Type:Float
Default value:0.0
Unit:Kelvin
GUI name:Bias damping T
Description:During well-tempered hyperdynamics the height of the added bias is scaled down with an exp(-E/kT) factor [PhysRevLett 100, 020603 (2008)], where E is the current value of the bias at the given CV value and T is the damping temperature DampingTemp. If DampingTemp is zero then no damping is applied.
Delta
Type:Float
Description:Standard deviation parameter of the Gaussian bias peak.
Height
Type:Float
Unit:Hartree
Description:Height of the Gaussian bias peak.
ColVarBB
Type:Block
Recurring:True
GUI name:Collective Variable
Description:Description of a bond-breaking collective variable (CV) as described in [Bal & Neyts, JCTC, 11 (2015)]. A collective variable may consist of multiple ColVar blocks.
at1
Type:Block
Description:Specifies the first bonded atom in the collective variable.
region
Type:String
Default value:*
Description:Restrict the selection of bonded atoms to a specific region. If this is not set, atoms anywhere in the system will be selected.
symbol
Type:String
Description:Atom type name of the first atom of the bond. The name must be as it appears in the System block. That is, if the atom name contains an extension (e.g C.1) then the full name including the extension must be used here.
at2
Type:Block
Description:Specifies the second bonded atom in the collective variable.
region
Type:String
Default value:*
Description:Restrict the selection of bonded atoms to a specific region. If this is not set, atoms anywhere in the system will be selected.
symbol
Type:String
Description:Atom type name of the second atom of the bond. The value is allowed to be the same as [at1], in which case bonds between atoms of the same type will be included.
cutoff
Type:Float
Default value:0.3
GUI name:Bond order cutoff
Description:Bond order cutoff. Bonds with BO below this value are ignored when creating the initial bond list for the CV. The bond list does not change during lifetime of the variable even if some bond orders drop below the cutoff.
p
Type:Integer
Default value:6
GUI name:Exponent p
Description:Exponent value p used to calculate the p-norm for this CV.
rmax
Type:Float
Unit:Angstrom
GUI name:R max
Description:Max bond distance parameter Rmax used for calculating the CV. It should be close to the transition-state distance for the corresponding bond.
rmin
Type:Float
Unit:Angstrom
GUI name:R min
Description:Min bond distance parameter Rmin used for calculating the CV. It should be close to equilibrium distance for the corresponding bond.
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:No
GUI name:Calculate pressure
Description:Calculate the pressure in periodic systems. This may be computationally expensive for some engines that require numerical differentiation. Some other engines can calculate the pressure for negligible additional cost and will always do so, even if this option is disabled.
Checkpoint
Type:Block
Description:Sets the frequency for storing the entire MD state necessary for restarting the calculation.
Frequency
Type:Integer
Default value:1000
GUI name:Checkpoint frequency
Description:Write the MD state and engine-specific data to the respective .rkf files once every N steps.
WriteProperties
Type:Bool
Default value:No
Description:Write the properties from the properties section to the ChecoPoint file once every N steps.
Deformation
Type:Block
Recurring:True
Description:Deform the periodic lattice of the system during the simulation.
LatticeVelocity
Type:Non-standard block
Description:Velocity of individual lattice vector components in Angstrom/fs. The format is identical to the System%Lattice block. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).
LengthRate
Type:Float List
Default value:[0.0, 0.0, 0.0]
Description:Relative rate of change of each lattice vector per step.
LengthVelocity
Type:Float List
Default value:[0.0, 0.0, 0.0]
Unit:Angstrom/fs
Description:Change the length of each lattice vector with this velocity. With Type=Exponential, LengthVelocity is divided by the current lattice vector lengths on StartStep to determine a LengthRate, which is then applied on all subsequent steps. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).
Period
Type:Float
Unit:Femtoseconds
Description:Period of oscillation for Type Sine and Cosine.
ScaleAtoms
Type:Bool
Default value:Yes
Description:Scale the atomic positions together with the lattice vectors. Disable this to deform only the lattice, keeping the coordinates of atoms unchanged.
StartStep
Type:Integer
Default value:1
Description:First step at which the deformation will be applied.
StopStep
Type:Integer
Default value:0
Description:Last step at which the deformation will be applied. If unset or zero, nSteps will be used instead.
StrainRate
Type:Non-standard block
Description:Strain rate matrix to be applied on every step. The format is identical to the System%Lattice block.
TargetLattice
Type:Non-standard block
Description:Target lattice vectors to be achieved by StopStep. The format is identical to the System%Lattice block.
TargetLength
Type:Float List
Default value:[0.0, 0.0, 0.0]
Unit:Angstrom
Description:Target lengths of each lattice vector to be achieved by StopStep. The number of values should equal the periodicity of the system. If a value is zero, the corresponding lattice vector will not be modified.
Type
Type:Multiple Choice
Default value:Linear
Options:[Linear, Exponential, Sine, Cosine]
Description:Function defining the time dependence of the deformed lattice parameters. Linear increments the lattice parameters by the same absolute amount every timestep. Exponential multiplies the lattice parameters by the same factor every timestep. Only StrainRate, LengthRate, and LengthVelocity are supported for Type=Exponential. Sine deforms the system from the starting lattice to TargetLattice/TargetLength and then by the same amount to the opposite direction, while Cosine deforms the system from the starting lattice to the target and back.
Gravity
Type:Block
Description:Apply a constant acceleration in -z.
Acceleration
Type:Float
Default value:0.0
Unit:Angstrom/fs^2
Description:Magnitude of the applied acceleration.
HeatExchange
Type:Block
Recurring:True
GUI name:Heat exchange
Description:Input for the heat-exchange non-equilibrium MD (T-NEMD).
HeatingRate
Type:Float
Unit:Hartree/fs
Description:Rate at which the energy is added to the Source and removed from the Sink. A heating rate of 1 Hartree/fs equals to about 0.00436 Watt of power being transferred through the system.
Method
Type:Multiple Choice
Default value:Simple
Options:[Simple, HEX, eHEX]
Description:Heat exchange method used. Simple: kinetic energy of the atoms of the source and sink regions is modified irrespective of that of the center of mass (CoM) of the region (recommended for solids). HEX: kinetic energy of the atoms of these regions is modified keeping that of the corresponding CoM constant. eHEX: an enhanced version of HEX that conserves the total energy better (recommended for gases and liquids).
Sink
Type:Block
Description:Defines the heat sink region (where the heat will be removed).
AtomList
Type:Integer List
GUI name:Sink region
Description:The atoms that are part of the sink. This key is ignored if the [Box] block or [Region] key is present.
Box
Type:Block
Description:Part of the simulation box (in fractional cell coordinates) defining the heat sink. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes.
Amax
Type:Float
Default value:1.0
Description:Coordinate of the upper bound along the first axis.
Amin
Type:Float
Default value:0.0
Description:Coordinate of the lower bound along the first axis.
Bmax
Type:Float
Default value:1.0
Description:Coordinate of the upper bound along the second axis.
Bmin
Type:Float
Default value:0.0
Description:Coordinate of the lower bound along the second axis.
Cmax
Type:Float
Default value:1.0
Description:Coordinate of the upper bound along the third axis.
Cmin
Type:Float
Default value:0.0
Description:Coordinate of the lower bound along the third axis.
Region
Type:String
GUI name:Sink region
Description:The region that is the sink. This key is ignored if the [Box] block is present.
Source
Type:Block
Description:Defines the heat source region (where the heat will be added).
AtomList
Type:Integer List
GUI name:Source region
Description:The atoms that are part of the source. This key is ignored if the [Box] block or [Region] key is present.
Box
Type:Block
Description:Part of the simulation box (in fractional cell coordinates) defining the heat source. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes. This block is mutually exclusive with the FirstAtom/LastAtom setting.
Amax
Type:Float
Default value:1.0
Description:Coordinate of the upper bound along the first axis.
Amin
Type:Float
Default value:0.0
Description:Coordinate of the lower bound along the first axis.
Bmax
Type:Float
Default value:1.0
Description:Coordinate of the upper bound along the second axis.
Bmin
Type:Float
Default value:0.0
Description:Coordinate of the lower bound along the second axis.
Cmax
Type:Float
Default value:1.0
Description:Coordinate of the upper bound along the third axis.
Cmin
Type:Float
Default value:0.0
Description:Coordinate of the lower bound along the third axis.
Region
Type:String
GUI name:Source region
Description:The region that is the source. This key is ignored if the [Box] block is present.
StartStep
Type:Integer
Default value:0
Description:Index of the MD step at which the heat exchange will start.
StopStep
Type:Integer
Description:Index of the MD step at which the heat exchange will stop.
InitialVelocities
Type:Block
Description:Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
File
Type:String
Description:AMS RKF file containing the initial velocities.
Temperature
Type:Float
Unit:Kelvin
GUI name:Initial temperature
Description:Sets the temperature for the Maxwell-Boltzmann distribution when the type of the initial velocities is set to random, in which case specifying this key is mandatory. AMSinput will use the first temperature of the first thermostat as default.
Type
Type:Multiple Choice
Default value:Random
Options:[Zero, Random, FromFile, Input]
GUI name:Initial velocities
Description:Specifies the initial velocities to assign to the atoms. Three methods to assign velocities are available. Zero: All atom are at rest at the beginning of the calculation. Random: Initial atom velocities follow a Maxwell-Boltzmann distribution for the temperature given by the [MolecularDynamics%InitialVelocities%Temperature] keyword. FromFile: Load the velocities from a previous ams result file. Input: Atom’s velocities are set to the values specified in the [MolecularDynamics%InitialVelocities%Values] block, which can be accessed via the Expert AMS panel in AMSinput.
Values
Type:Non-standard block
Description:This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.
NSteps
Type:Integer
Default value:1000
GUI name:Number of steps
Description:The number of steps to be taken in the MD simulation.
Plumed
Type:Block
Description:Input for PLUMED. The parallel option is still experimental.
Input
Type:Non-standard block
Description:Input for PLUMED. Contents of this block is passed to PLUMED as is.
Parallel
Type:Block
Description:Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
nCoresPerGroup
Type:Integer
GUI name:Cores per group
Description:Number of cores in each working group.
nGroups
Type:Integer
GUI name:Number of groups
Description:Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup
Type:Integer
GUI name:Nodes per group
Description:Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
Preserve
Type:Block
Description:Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.
AngularMomentum
Type:Bool
Default value:Yes
GUI name:: Angular momentum
Description:Remove overall angular momentum of the system. This option is ignored for 2D and 3D-periodic systems.
CenterOfMass
Type:Bool
Default value:No
GUI name:: Center of mass
Description:Translate the system to keep its center of mass at the coordinate origin. This option is not very useful for 3D-periodic systems.
Momentum
Type:Bool
Default value:Yes
GUI name:Preserve: Total momentum
Description:Remove overall (linear) momentum of the system.
Print
Type:Block
Description:This block controls the printing of additional information to stdout.
System
Type:Bool
Default value:No
Description:Print the chemical system before and after the simulation.
Velocities
Type:Bool
Default value:No
Description:Print the atomic velocities before and after the simulation.
ReflectiveWall
Type:Block
Recurring:True
Description:Apply a reflective wall in space
AtomList
Type:Integer List
Recurring:True
Description:Apply the reflective wall to the specified atoms. A list of integers referring to indices of atoms in the [System%Atoms] block.
Axis
Type:Float List
Unit:Angstrom
Description:Defines the normal vector perpendicular to the plane of the reflective wall. Any particle moving in this direction will be reflected back.
FixedRegion
Type:String
Recurring:True
Description:Apply the reflective wall to all atoms in a region.
Threshold
Type:Float
Unit:Angstrom
Description:Defines the threshold value determining the position of the reflective wall. If the dot product of a position of a particle with Axis exceeds Threshold, the particle will be reflected. This means that the plane of the wall passes through a point given by Axis times Threshold.
Remap
Type:Block
Description:Control periodic remapping (backtranslation) of atoms into the PBC box.
Type
Type:Multiple Choice
Default value:Atoms
Options:[None, Atoms]
Description:Select the method used to remap atoms into the unit cell. None: Disable remapping completely. Atoms: Remap any atoms that leave the unit cell.
RemoveMolecules
Type:Block
Recurring:True
GUI name:Remove molecules
Description:This block controls removal of molecules from the system. Multiple occurrences of this block are possible.
Formula
Type:String
Description:Molecular formula of the molecules that should be removed from the system. The order of elements in the formula is very important and the correct order is: C, H, all other elements in the strictly alphabetic order. Element names are case-sensitive, spaces in the formula are not allowed. Digit ‘1’ must be omitted. Valid formula examples: C2H6O, H2O, O2S. Invalid formula examples: C2H5OH, H2O1, OH, SO2. Invalid formulas are silently ignored. Use * to remove any molecule, which must be combined with SinkBox or SafeBox.
Frequency
Type:Integer
Default value:0
Description:The specified molecules are removed every so many steps after the StartStep. There is never a molecule removed at step 0.
SafeBox
Type:Block
Description:Part of the simulation box where molecules may not be removed. Only one of the SinkBox or SafeBox blocks may be present. If this block is present the molecule will not be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.
Amax
Type:Float
Description:Coordinate of the upper bound along the first axis.
Amin
Type:Float
Description:Coordinate of the lower bound along the first axis.
Bmax
Type:Float
Description:Coordinate of the upper bound along the second axis.
Bmin
Type:Float
Description:Coordinate of the lower bound along the second axis.
Cmax
Type:Float
Description:Coordinate of the upper bound along the third axis.
Cmin
Type:Float
Description:Coordinate of the lower bound along the third axis.
FractionalCoordsBox
Type:Float List
GUI name:Safe box
Description:Do not remove molecules that are (partly) inside the safe box. Borders of the safe box specified as: Amin, Amax, Bmin, Bmax, Cmin, Cmax. For periodic dimensions fractional coordinates between 0 and 1 and for non-periodic dimensions Cartesian values in Angstrom are expected.
SinkBox
Type:Block
Description:Part of the simulation box where matching molecules will be removed. By default, molecules matching the formula will be removed regardless of their location. If this block is present then such a molecule will only be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.
Amax
Type:Float
Description:Coordinate of the upper bound along the first axis.
Amin
Type:Float
Description:Coordinate of the lower bound along the first axis.
Bmax
Type:Float
Description:Coordinate of the upper bound along the second axis.
Bmin
Type:Float
Description:Coordinate of the lower bound along the second axis.
Cmax
Type:Float
Description:Coordinate of the upper bound along the third axis.
Cmin
Type:Float
Description:Coordinate of the lower bound along the third axis.
FractionalCoordsBox
Type:Float List
GUI name:Sink box
Description:Remove molecules that are (partly) inside the sink box. Borders of the sink box specified as: Amin, Amax, Bmin, Bmax, Cmin, Cmax. For periodic dimensions fractional coordinates between 0 and 1 and for non-periodic dimensions Cartesian values in Angstrom are expected.
StartStep
Type:Integer
Default value:0
Description:Step number when molecules are removed for the first time. After that, molecules are removed every [Frequency] steps. For example, if StartStep=99 and Frequency=100 then molecules will be removed at steps 99, 199, 299, etc… No molecule will be removed at step 0, so if StartStep=0 the first molecules are removed at the step number equal to [Frequency].
StopStep
Type:Integer
Description:Do not remove the specified molecules after this step.
ReplicaExchange
Type:Block
Description:This block is used for (temperature) Replica Exchange MD (Parallel Tempering) simulations.
AllowWrongResults
Type:Bool
Default value:No
Description:Allow combining Replica Exchange with other features when the combination is known to produce physically incorrect results.
EWMALength
Type:Integer
Default value:10
Description:Length of the exponentially weighted moving average used to smooth swap probabilities for monitoring. This value is equal to the inverse of the EWMA mixing factor.
SwapFrequency
Type:Integer
Default value:100
Description:Attempt an exchange every N steps.
TemperatureFactors
Type:Float List
Description:This is the ratio of the temperatures of two successive replicas. The first value sets the temperature of the second replica with respect to the first replica, the second value sets the temperature of the third replica with respect to the second one, and so on. If there are fewer values than nReplicas, the last value of TemperatureFactor is used for all the remaining replicas.
Temperatures
Type:Float List
Description:List of temperatures for all replicas except for the first one. This is mutually exclusive with TemperatureFactors. Exactly nReplicas-1 temperature values need to be specified, in increasing order. The temperature of the first replica is given by [Thermostat%Temperature].
nReplicas
Type:Integer
Default value:1
GUI name:Number of replicas
Description:Number of replicas to run in parallel.
Restart
Type:String
GUI name:Restart from
Description:The path to the ams.rkf file from which to restart the simulation.
Shake
Type:Block
Description:Parameters of the Shake/Rattle algorithm.
All
Type:String
Recurring:True
GUI name:Constrain all
Description:Constraint description in one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3 The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 and the angle between them. The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then all bonds between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. The distance, if present, must be in Angstrom. If it is omitted then the bond length from the initial geometry is used. Important: only the bonds present in the system at certain points of the simulation (at the start or right after adding/removing atoms) can be constrained, which means that the bonds may need to be specified in the System block. Warning: the triangles constraint should be used with care because each constrained bond or angle means removing one degree of freedom from the dynamics. When there are too many constraints (for example, “All triangles H C H” in methane) some of them may be linearly dependent, which will lead to an error in the temperature computation. Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H
ConvergeR2
Type:Float
Default value:1e-08
Description:Convergence criterion on the max squared difference, in atomic units.
ConvergeRV
Type:Float
Default value:1e-08
Description:Convergence criterion on the orthogonality of the constraint and the relative atomic velocity, in atomic units.
Iterations
Type:Integer
Default value:100
Description:Number of iterations.
ShakeInitialCoordinates
Type:Bool
Default value:Yes
Description:Apply constraints before computing the first energy and gradients.
Thermostat
Type:Block
Recurring:True
Description:This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’ behavior.
BerendsenApply
Type:Multiple Choice
Default value:Global
Options:[Local, Global]
GUI name:Apply Berendsen
Description:Select how to apply the scaling correction for the Berendsen thermostat: - per-atom-velocity (Local) - on the molecular system as a whole (Global).
ChainLength
Type:Integer
Default value:10
GUI name:NHC chain length
Description:Number of individual thermostats forming the NHC thermostat
Duration
Type:Integer List
GUI name:Duration(s)
Description:Specifies how many steps should a transition from a particular temperature to the next one in sequence take.
Region
Type:String
Default value:*
Description:The identifier of the region to thermostat. The default ‘*’ applies the thermostat to the entire system. The value can by a plain region name, or a region expression, e.g. ‘*-myregion’ to thermostat all atoms that are not in myregion, or ‘regionA+regionB’ to thermostat the union of the ‘regionA’ and ‘regionB’. Note that if multiple thermostats are used, their regions may not overlap.
Tau
Type:Float
Unit:Femtoseconds
GUI name:Damping constant
Description:The time constant of the thermostat.
Temperature
Type:Float List
Unit:Kelvin
GUI name:Temperature(s)
Description:The target temperature of the thermostat. You can specify multiple temperatures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one T to the next T (using a linear ramp). For NHC thermostat, the temperature may not be zero.
Type
Type:Multiple Choice
Default value:None
Options:[None, Berendsen, NHC]
GUI name:Thermostat
Description:Selects the type of the thermostat.
TimeStep
Type:Float
Default value:0.25
Unit:Femtoseconds
Description:The time difference per step.
Trajectory
Type:Block
Description:Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.
PrintFreq
Type:Integer
GUI name:Printing frequency
Description:Print current thermodynamic properties to the output every N steps. By default this is done every SamplingFreq steps.
SamplingFreq
Type:Integer
Default value:100
GUI name:Sample frequency
Description:Write the the molecular geometry (and possibly other properties) to the .rkf file once every N steps.
TProfileGridPoints
Type:Integer
Default value:0
Description:Number of points in the temperature profile. If TProfileGridPoints > 0, a temperature profile along each of the three lattice axes will be written to the .rkf file. The temperature at a given profile point is calculated as the total temperature of all atoms inside the corresponding slice of the simulation box, time-averaged over all MD steps since the previous snapshot.​ By default, no profile is generated.
WriteBonds
Type:Bool
Default value:Yes
Description:Write detected bonds to the .rkf file.
WriteCharges
Type:Bool
Default value:Yes
Description:Write current atomic point charges (if available) to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze charges.
WriteEngineGradients
Type:Bool
Default value:No
Description:Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.
WriteMolecules
Type:Bool
Default value:Yes
Description:Write the results of molecule analysis to the .rkf file.
WriteVelocities
Type:Bool
Default value:Yes
Description:Write velocities to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze the velocities.
fbMC
Type:Block
Recurring:True
GUI name:fbMC
Description:This block sets up force bias Monte Carlo interleaved with the molecular dynamics simulation.
Frequency
Type:Integer
Default value:1
Description:Run the fbMC procedure every Frequency MD steps.
MassRoot
Type:Float
Default value:2.0
Description:Inverse of the exponent used to mass-weight fbMC steps.
MolecularMoves
Type:Block
Description:Move molecules as rigid bodies in addition to normal atomic moves.
Enabled
Type:Bool
Default value:No
GUI name:Enable molecular moves
Description:Enable moving molecules as rigid bodies based on net forces and torques. Ordinary per-atom displacements will then be based on residual atomic forces.
RotationStepAngle
Type:Float
Default value:0.1
Unit:Radian
Description:Maximum allowed angle of rotation of each molecule in one fbMC step.
TranslationStepLength
Type:Float
Default value:0.1
Unit:Angstrom
Description:Maximum allowed displacement of each molecule in each Cartesian coordinate in one fbMC step.
NSteps
Type:Integer
GUI name:Number of steps
Description:Number of fbMC steps to perform on every invocation of the procedure.
PrintFreq
Type:Integer
GUI name:Printing frequency
Description:Print current thermodynamic properties to the output every N fbMC steps. This defaults to the PrintFreq set in the Trajectory block. Setting this to zero disables printing fbMC steps.
StartStep
Type:Integer
Default value:1
Description:First step at which the fbMC procedure may run.
StepLength
Type:Float
Default value:0.1
Unit:Angstrom
Description:Maximum allowed displacement of the lightest atom in the system in each Cartesian coordinate in one fbMC step.
StopStep
Type:Integer
Default value:0
Description:Last step at which the fbMC procedure may run. If unset or zero, there is no limit.
Temperature
Type:Float
Unit:Kelvin
Description:Temperature used for fbMC.
Molecules
Type:Block
Description:Configures details of the molecular composition analysis enabled by the Properties%Molecules block.
AdsorptionSupportRegion
Type:String
GUI name:Adsorption support region
Description:Select region that will represent a support for adsorption analysis. Adsorbed molecules will receive an ‘(ads)’ suffix after name of the element bonded to the support. Such elements will be listed separate from atoms of the same element not bonded to the support, for example, HOH(ads) for a water molecule bonded to a surface via one of its H atoms.
BondOrderCutoff
Type:Float
Default value:0.5
Description:Bond order cutoff for analysis of the molecular composition. Bonds with bond order smaller than this value are neglected when determining the molecular composition.
NEB
Type:Block
Description:Configures details of the Nudged Elastic Band optimization.
Climbing
Type:Bool
Default value:Yes
GUI name:Climb highest image to TS
Description:Use the climbing image algorithm to drive the highest image to the transition state.
ClimbingThreshold
Type:Float
Default value:0.0
Unit:Hartree/Bohr
GUI name:CI force threshold
Description:Climbing image force threshold. If ClimbingThreshold > 0 and the max perpendicular force component is above the threshold then no climbing is performed at this step. This entry can be used to get a better approximation for the reaction path before starting the search for the transition state. A typical value is 0.01 Hartree/Bohr.
Images
Type:Integer
Default value:8
GUI name:Number of images
Description:Number of NEB images (not counting the chain ends). Using more images will result in a smoother reaction path and can help with convergence problems, but it will also increase the computation time.
InterpolateInternal
Type:Bool
Default value:Yes
GUI name:Interpolate in Internal coordinates
Description:The initial NEB image geometries are calculated by interpolating between the initial and the final state. By default, for non-periodic systems the interpolation is performed in Internal coordinates but the user can choose to do it in the Cartesian ones. For periodic systems the interpolation is always done in Cartesian coordinates.
InterpolateShortest
Type:Bool
Default value:Yes
GUI name:Interpolate across cell boundary
Description:Allow interpolation across periodic cell boundaries. Set to false if an atom is intended to move more than half across the simulation box during reaction.
Iterations
Type:Integer
GUI name:Maximum number of iterations
Description:Maximum number of NEB iterations. The default value depends on the number of degrees of freedom (number of images, atoms, periodic dimensions).
Jacobian
Type:Float
GUI name:Jacobian value
Description:Scaling factor used to convert the lattice strain to a NEB coordinate value. Default value: sqrt(N)*(V/N)^(1/d), where V - lattice volume (area for 2D, length for 1D), N - number of atoms, and d - number of periodic dimensions.
MapAtomsToCell
Type:Bool
Default value:Yes
GUI name:Map atoms to cell
Description:Translate atoms to the [-0.5,0.5] cell before every step. This option cannot be disabled for SS-NEB.
OldTangent
Type:Bool
Default value:No
GUI name:Use old tangent
Description:Turn on the old central difference tangent.
OptimizeEnds
Type:Bool
Default value:Yes
GUI name:Optimize reactants/products
Description:Start the NEB with optimization of the reactant and product geometries.
OptimizeLattice
Type:Bool
Default value:No
GUI name:Optimize lattice
Description:Turn on the solid-state NEB (SS-NEB).
Parallel
Type:Block
Description:Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
nCoresPerGroup
Type:Integer
GUI name:Cores per group
Description:Number of cores in each working group.
nGroups
Type:Integer
GUI name:Number of groups
Description:Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup
Type:Integer
GUI name:Nodes per group
Description:Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
ReOptimizeEnds
Type:Bool
Default value:No
GUI name:Re-optimize reactants/products
Description:Re-optimize reactant and product geometries upon restart.
Restart
Type:String
GUI name:Restart from
Description:Provide an ams.rkf file from a previous NEB calculation to restart from. It can be an unfinished NEB calculation or one performed with different engine parameters.
Skewness
Type:Float
Default value:1.0
GUI name:Skewness
Description:Degree of how much images are shifted towards or away from the TS, which may help tackle problems with a long reaction path (for example involving a loose adsorption complex) without needing too many images. A value greater than 1 will make sure that images are concentrated near the transition state. The optimal value depends on the path length, the number of images (larger [Skewness] may be needed for a longer path and fewer images). Technically [Skewness] is equal to the ratio between the optimized distances to the lower and the higher neighbor image on the path.
Spring
Type:Float
Default value:1.0
Unit:Hartree/Bohr^2
GUI name:Spring value
Description:Spring force constant in atomic units.
NormalModes
Type:Block
Description:Configures details of a normal modes calculation.
BlockDisplacements
Type:Block
Description:Configures details of a Block Normal Modes (a.k.a. Mobile Block Hessian, or MBH) calculation.
AngularDisplacement
Type:Float
Default value:0.5
Unit:Degree
Description:Relative step size for rotational degrees of freedom during Block Normal Modes finite difference calculations. It will be scaled with the characteristic block size.
BlockAtoms
Type:Integer List
Recurring:True
Description:List of atoms belonging to a block. You can have multiple BlockAtoms.
BlockRegion
Type:String
Recurring:True
Description:The region to to be considered a block. You can have multiple BlockRegions, also in combination with BlockAtoms.
Parallel
Type:Block
Description:Configuration for how the individual displacements are calculated in parallel.
nCoresPerGroup
Type:Integer
Description:Number of cores in each working group.
nGroups
Type:Integer
Description:Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup
Type:Integer
GUI name:Cores per task
Description:Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
RadialDisplacement
Type:Float
Default value:0.005
Unit:Angstrom
Description:Step size for translational degrees of freedom during Block Normal Modes finite difference calculations.
Displacements
Type:Multiple Choice
Default value:Cartesian
Options:[Cartesian, Symmetric, Block]
GUI name:Displacements
Description:Type of displacements. In case of symmetric displacements it is possible to choose only the modes that have non-zero IR or Raman intensity. Block displacements take rigid blocks into account.
Hessian
Type:Multiple Choice
Default value:Auto
Options:[Auto, Analytical, Numerical]
Description:Default Auto means that if possible by the engine the Hessian will be calculated analytically, else the Hessian will be calculated numerically by AMS.
ReScanFreqRange
Type:Float List
Default value:[-10000000.0, 10.0]
Unit:cm-1
Recurring:True
GUI name:Re-scan range
Description:Specifies a frequency range within which all modes will be scanned. 2 numbers: an upper and a lower bound.
ReScanModes
Type:Bool
Default value:Yes
GUI name:Re-scan modes
Description:Whether or not to scan imaginary modes after normal modes calculation has concluded.
SymmetricDisplacements
Type:Block
Description:Configures details of the calculation of the frequencies and normal modes of vibration in symmetric displacements.
Type
Type:Multiple Choice
Default value:All
Options:[All, Infrared, Raman, InfraredAndRaman]
GUI name:Symm Frequencies
Description:For symmetric molecules it is possible to choose only the modes that have non-zero IR or Raman intensity (or either of them) by symmetry. In order to calculate the Raman intensities the Raman property must be requested.
NumericalDifferentiation
Type:Block
Description:Define options for numerical differentiations, that is the numerical calculation of gradients, Hessian and the stress tensor for periodic systems.
NuclearStepSize
Type:Float
Default value:0.005
Unit:Bohr
Description:Step size for numerical nuclear gradient calculation.
Parallel
Type:Block
Description:Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
nCoresPerGroup
Type:Integer
GUI name:Cores per group
Description:Number of cores in each working group.
nGroups
Type:Integer
GUI name:Number of groups
Description:Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup
Type:Integer
GUI name:Nodes per group
Description:Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
StrainStepSize
Type:Float
Default value:0.001
Description:Step size (relative) for numerical stress tensor calculation.
NumericalPhonons
Type:Block
Description:Configures details of a numerical phonons calculation.
AutomaticBZPath
Type:Bool
Default value:Yes
GUI name:Automatic BZ path
Description:If True, compute the phonon dispersion curve for the standard path through the Brillouin zone. If False, you must specify your custom path in the [BZPath] block.
BZPath
Type:Block
Description:If [NumericalPhonons%AutomaticBZPath] is false, the phonon dispersion curve will be computed for the user-defined path in the [BZPath] block. You should define the vertices of your path in fractional coordinates (with respect to the reciprocal lattice vectors) in the [Path] sub-block. If you want to make a jump in your path (i.e. have a discontinuous path), you need to specify a new [Path] sub-block.
Path
Type:Non-standard block
Recurring:True
Description:A section of a k space path. This block should contain multiple lines, and in each line you should specify one vertex of the path in fractional coordinates. Optionally, you can add text labels for your vertices at the end of each line.
BornEffCharge
Type:Float
Default value:0.0
Description:Input option to give the Born effective charges of the species.
DielectricConst
Type:Float
Default value:1.0
Description:Input option to give the static dielectric constant of the species.
DoubleSided
Type:Bool
Default value:Yes
Description:By default a two-sided (or quadratic) numerical differentiation of the nuclear gradients is used. Using a single-sided (or linear) numerical differentiation is computationally faster but much less accurate. Note: In older versions of the program only the single-sided option was available.
Interpolation
Type:Integer
Default value:100
Description:Use interpolation to generate smooth phonon plots.
NDosEnergies
Type:Integer
Default value:1000
Description:Nr. of energies used to calculate the phonon DOS used to integrate thermodynamic properties. For fast compute engines this may become time limiting and smaller values can be tried.
Parallel
Type:Block
Description:Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
nCoresPerGroup
Type:Integer
GUI name:Cores per group
Description:Number of cores in each working group.
nGroups
Type:Integer
GUI name:Number of groups
Description:Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup
Type:Integer
GUI name:Nodes per group
Description:Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
StepSize
Type:Float
Default value:0.04
Unit:Angstrom
Description:Step size to be taken to obtain the force constants (second derivative) from the analytical gradients numerically.
SuperCell
Type:Non-standard block
Description:Used for the phonon run. The super lattice is expressed in the lattice vectors. Most people will find a diagonal matrix easiest to understand.
PESExploration
Type:Block
Description:Configures details of the automated PES exploration methods.
BasinHopping
Type:Block
Description:Configures the details of the Basin Hopping subtask.
DisplaceAtomsInRegion
Type:String
Default value:
Description:If you specify a region name here, only the atoms belonging to this region will be displaced during the basin hopping procedure. For more details on regions, see the documentation on the System definition.
Displacement
Type:Float
Default value:0.5
Unit:Angstrom
Description:Displacement in each degree of freedom.
PushApartDistance
Type:Float
Default value:0.4
Unit:Angstrom
Description:Push atoms apart until no atoms are closer than this distance. This criterion is enforced for the initial structure and all those generated by random displacements.
Steps
Type:Integer
Default value:20
Description:Number of displace & optimize Monte-Carlo steps to take.
BindingSites
Type:Block
Description:Options related to the calculation of binding sites.
AllowDisconnected
Type:Bool
Default value:No
Description:Allow disconnected binding sites.
Calculate
Type:Bool
Default value:No
Description:Calculate binding sites at the end of a job. Not needed for Binding Sites job.
DistanceDifference
Type:Float
Default value:-1.0
Unit:Angstrom
Description:If the distance between two mapped binding-sites is larger than this threshold, the binding-sites are considered different. If not specified, its value will set equal to [PESExploration%StructureComparison%DistanceDifference]
NeighborCutoff
Type:Float
Default value:-1.0
Unit:Angstrom
Description:The binding sites labels are given based on the number of neighbor atoms (in the reference region) within this distance. If not specified, its value will set equal to [PESExploration%StructureComparison%NeighborCutoff]
CalculateFragments
Type:Bool
Default value:No
Description:Must be used together with an adsorbent set as the StatesAlignment%ReferenceRegion. Runs a final calculation of the adsorbate and adsorbent (marked by the ReferenceRegion) individually. The fragmented state is included in the energy landscape.
Debug
Type:Block
Description:???.
DynamicSeedStates
Type:Bool
Default value:Yes
Description:Whether subsequent expeditions may start from states discovered by previous expeditions. This should lead to a more comprehensive exploration of the potential energy surface. Disabling this will focus the PES exploration around the initial seed states.
Dynamics
Type:Block
Description:???.
Andersen
Type:Block
Description:???.
Alpha
Type:Float
Default value:1.0
Description:???.
CollisionPeriod
Type:Float
Default value:100.0
Description:???.
Langevin
Type:Block
Description:???.
Friction
Type:Float
Default value:0.01
Description:???.
Nose
Type:Block
Description:???.
Mass
Type:Float
Default value:1.0
Description:???.
Thermostat
Type:Multiple Choice
Default value:none
Options:[andersen, nose_hoover, langevin, none]
Description:???.
Time
Type:Float
Default value:1000.0
Description:???.
TimeStep
Type:Float
Default value:1.0
Description:???.
FiniteDifference
Type:Float
Default value:0.01
Unit:Angstrom
Description:The finite difference distance to use for Dimer, Hessian, Lanczos, and optimization methods.
Hessian
Type:Block
Description:???.
AtomList
Type:String
Default value:all
Description:???.
ZeroFreqValue
Type:Float
Default value:1e-06
Description:???.
Job
Type:Multiple Choice
Options:[ProcessSearch, BasinHopping, SaddleSearch, LandscapeRefinement, BindingSites]
Description:Specify the PES exploration job to perform.
LoadEnergyLandscape
Type:Block
Description:Options related to the loading of an Energy Landscape from a previous calculation.
KeepOnly
Type:Integer List
GUI name:List of states to keep
Description:Upon loading the Energy Landscape, only keep the states specified here. The states should be specified via a list of integers referring to the indices of the states you want to keep.
Path
Type:String
GUI name:Load energy landscape from
Description:The path to load an energy landscape from. Accepts either AMS result folders, or .con files in the native EON format (only available through the text input file).
Remove
Type:Integer List
GUI name:List of states to remove
Description:Upon loading the Energy Landscape, remove (i.e. do not load) the states specified here. The states should be specified via a list of integers referring to the indices of the states you want to remove (i.e. the states you don’t want to load).
SeedStates
Type:Integer List
GUI name:List of seed states
Description:By default when you start a new PES Exploration from a loaded Energy Landscape, expeditions can start from any of the loaded minima. By using this input option, you can instruct the program to only use some of the states as ‘expedition starting point’. The states that serve as ‘expedition starting points’ should be specified via a list of integers referring to the indices of the states.
NudgedElasticBand
Type:Block
Description:Options for the Nudged Elastic Band (NEB) method.
ClimbingImageMethod
Type:Bool
Default value:Yes
Description:Use the climbing image algorithm to drive the highest image to the transition state.
ConvergedForce
Type:Float
Default value:-1.0
Unit:eV/Angstrom
Description:Convergence threshold for nuclear gradients. Note: Special value of -1.0 means using the same convergence criterion as the PES explorer’s geometry optimizer.
Images
Type:Integer
Default value:5
Description:Number of NEB images between the two endpoints.
MaxIterations
Type:Integer
Default value:500
Description:Maximum number of NEB iterations.
OldTangent
Type:Bool
Default value:No
Description:Use the old central difference tangent.
Spring
Type:Float
Default value:5.0
Unit:eV/Ang^2
Description:Spring force constant.
NumExpeditions
Type:Integer
Default value:1
Description:Sets the number of subsequent expeditions our job will consist of. Larger values result in a more comprehensive exploration of the potential energy surface, but will take more computational time.
NumExplorers
Type:Integer
Default value:1
Description:Sets the number of independent PES explorers dispatched as part of each expedition. Larger values will result in a more comprehensive exploration of the potential energy surface, but will take more computational time. By default an appropriate number of explorers are executed in parallel.
OptTSMethod
Type:Multiple Choice
Default value:SaddleSearch
Options:[SaddleSearch, NudgedElasticBand]
Description:When the full set of states in the energy landscape are optimized (see PESExploration%Job = GeometryOptimization), transition states can be optimized using either SaddleSearch or NudgedElasticBand methods. SaddleSearch uses information only from the current geometry of the TS; contrary, NudgedElasticBand ignores the current geometry and runs a Nudged-Elastic-Band calculation trying to connect the associated reactants and products if they are available.
Optimizer
Type:Block
Description:Configures the details of the geometry optimizers used by the PES explorers.
ConvergedForce
Type:Float
Default value:0.005
Unit:eV/Angstrom
Description:Convergence threshold for nuclear gradients.
MaxIterations
Type:Integer
Default value:400
Description:Maximum number of iterations allowed for optimizations.
Method
Type:Multiple Choice
Default value:CG
Options:[CG, QM, LBFGS, FIRE, SD]
Description:Select the method for geometry optimizations.
Parallel
Type:Block
Description:Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.
nCoresPerGroup
Type:Integer
GUI name:Cores per group
Description:Number of cores in each working group.
nGroups
Type:Integer
GUI name:Number of groups
Description:Total number of processor groups. This is the number of tasks that will be executed in parallel.
nNodesPerGroup
Type:Integer
GUI name:Nodes per group
Description:Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.
ParallelReplica
Type:Block
Description:???.
DephaseLoopMax
Type:Integer
Default value:5
Description:???.
DephaseLoopStop
Type:Bool
Default value:No
Description:???.
DephaseTime
Type:Float
Default value:1000.0
Description:???.
PostTransitionTime
Type:Float
Default value:1000.0
Description:???.
RefineTransition
Type:Bool
Default value:Yes
Description:???.
StateCheckInterval
Type:Float
Default value:1000.0
Description:???.
StateSaveInterval
Type:Float
Default value:-1.0
Description:???.
StopAfterTransition
Type:Bool
Default value:No
Description:???.
Prefactor
Type:Block
Description:???.
Rate
Type:Multiple Choice
Default value:HTST
Options:[HTST, QQHTST]
Description:Calculates the pre-exponential factors of the Reaction Rates using either Harmonic Transition State Theory (HTST) or quasi-quantum HTST (QQHTST).
ProcessSearch
Type:Block
Description:Input options specific to the process search procedure.
MinimizationOffset
Type:Float
Default value:0.2
Description:After a saddle is found, images are placed on either side of the saddle along the mode and minimized to ensure that the saddle is connected to the original minimum and to locate the product state. MinimizationOffset is the distance those images are displaced from the saddle.
SaddleSearch
Type:Block
Description:Configuration for the Saddle Search procedure (used in SaddleSearch and ProcessSearch Jobs).
ConvergedForce
Type:Float
Default value:-1.0
Unit:eV/Angstrom
Description:Convergence threshold for nuclear gradients. Note: Special value of -1.0 means using the same convergence criterion as the PES explorer’s geometry optimizer.
DisplaceAtomsInRegion
Type:String
Default value:
Description:A string corresponding to the name of a region. When performing the initial random displacement, only displace atoms in the specified region. This can help the Saddle Search procedure to start off in a desired region of the PES.
DisplaceMagnitude
Type:Float
Default value:0.1
Unit:Angstrom
Description:The standard deviation of the Gaussian displacement in each degree of freedom for the selected atoms.
MaxEnergy
Type:Float
Default value:20.0
Unit:eV
Description:The energy (relative to the starting point of the saddle search) at which a saddle search explorer considers the search bad and terminates it.
MaxIterations
Type:Integer
Default value:400
Description:Maximum number of iterations for each saddle search run.
MinEnergyBarrier
Type:Float
Default value:0.0
Unit:eV
Description:Minimum energy barrier to accept a new transition state.
MinModeMethod
Type:Multiple Choice
Default value:dimer
Options:[dimer, lanczos]
Description:The minimum-mode following method to use.
StatesAlignment
Type:Block
Description:Configures details of how the energy landscape configurations are aligned respect to the main chemical system [System].
DistanceDifference
Type:Float
Default value:-1.0
Unit:Angstrom
Description:If the distance between two mapped atoms is larger than this threshold, the configuration is considered not aligned. If not specified, its value will set equal to [PESExploration%StructureComparison%DistanceDifference]
ReferenceRegion
Type:String
Default value:
Description:Defines the region that is considered as the reference for alignments. Atoms outside this region are ignored in the alignments.
StructureComparison
Type:Block
Description:Settings for structure comparison.
CheckRotation
Type:Bool
Description:Rotates the system optimally before comparing structures. The default is to do this only for molecular systems when there are no fixed atom constraints.
CheckSymmetry
Type:Bool
Default value:No
Description:Considers that two systems are equal if they are equivalent by symmetry.
DistanceDifference
Type:Float
Default value:0.1
Unit:Angstrom
Description:If the distance between two mapped atoms is larger than this threshold, the two configurations are considered different structures.
EnergyDifference
Type:Float
Default value:0.01
Unit:eV
Description:If the energy difference between two configurations is larger than this threshold, the two configurations are considered to be different structures.
IndistinguishableAtoms
Type:Bool
Default value:Yes
Description:If yes, the order of the atoms does not affect the structural comparison. Atoms of the same element are then indistinguishable.
NeighborCutoff
Type:Float
Default value:3.3
Unit:Angstrom
Description:Atoms within this distance of each other are considered neighbors.
RemoveTranslation
Type:Bool
Description:Translates the system optimally before comparing structures. The default is to do this only when there are no fixed atom constraints.
Temperature
Type:Float
Default value:300.0
Unit:Kelvin
Description:The temperature that the job will run at. This may be used in different ways depending on the job, e.g. acceptance probabilities for Monte-Carlo based jobs, thermostatting for dynamics based jobs, kinetic prefactors for jobs that find transition states. Some jobs may not use this temperature at all.
WriteHistory
Type:Multiple Choice
Default value:Converged
Options:[None, Converged, All]
Description:When to write the molecular geometry (and possibly other properties) to the history on the ams.rkf file. The default is to only write the converged geometries to the history. Can be changed to write no frames at all to the history, or write all frames (should only be used when testing because of the performance impact). Note that for parallel calculations, only the first group of processes writes to ams.rkf.
PESPointCharacter
Type:Block
Description:Options for the characterization of PES points.
Displacement
Type:Float
Default value:0.04
Description:Controls the size of the displacements used for numerical differentiation: The displaced geometries are calculated by taking the original coordinates and adding the mass-weighted mode times the reduced mass of the mode times the value of this keyword.
NegativeFrequenciesTolerance
Type:Float
Default value:-10.0
Unit:cm-1
Description:The threshold in frequency below which a mode is considered imaginary, i.e. indicating a transition state. This is a small negative number, as very small negative frequencies are normally due to numerical noise on an essentially flat PES and do not indicate true transition states.
NumberOfModes
Type:Integer
Default value:2
Description:The number of (lowest) eigenvalues that should be checked.
Tolerance
Type:Float
Default value:0.016
Description:Convergence tolerance for residual in iterative Davidson diagonalization.
PESScan
Type:Block
Description:Configures the details of the potential energy surface scanning task.
CalcPropertiesAtPESPoints
Type:Bool
Default value:No
Description:Whether to perform an additional calculation with properties on all the sampled points of the PES. If this option is enabled AMS will produce a separate engine output file for every sampled PES point.
FillUnconvergedGaps
Type:Bool
Default value:Yes
Description:After the initial pass over the PES, restart the unconverged points from converged neighboring points.
ScanCoordinate
Type:Block
Recurring:True
Description:Specifies a coordinate along which the potential energy surface is scanned. If this block contains multiple entries, these coordinates will be varied and scanned together as if they were one. Note that there can be only one ScanCoordinate containing a lattice scan in any PES scan job.
Angle
Type:String
Recurring:True
Description:Scan the angle between three atoms. Three atom indices followed by two real numbers delimiting the transit range in degrees.
CellVolumeRange
Type:Float List
Unit:Angstrom^3
Description:Two numbers for the initial and final cell volume. The cell is scaled isotropically between these values. Can not be used together with any other coordinate within the same ScanCoordinate block.
CellVolumeScalingRange
Type:Float List
Description:Two scaling factors for the initial and final cell volume. A value of ‘0.9 1.1’ would result in an isotropic scaling between 90% and 110% of the cell volume of the input system. Can not be used together with any other coordinate within the same ScanCoordinate block.
Coordinate
Type:String
Recurring:True
Description:Scan a particular coordinate of an atom. Atom index followed by (x|y|z) followed by two real numbers delimiting the transit range.
DifDist
Type:String
Recurring:True
Description:Scan the difference distance between two pairs of atoms, R(12)-R(34). Four atom indices followed by two real numbers delimiting the transit range in Angstrom.
Dihedral
Type:String
Recurring:True
Description:Scan the dihedral angle between four atoms. Four atom indices followed by two real numbers delimiting the transit angle in degrees.
Distance
Type:String
Recurring:True
Description:Scan the distance between two atoms. Two atom indices followed by two real numbers delimiting the transit distance in Angstrom.
FromLattice
Type:Non-standard block
Description:Up to three lattice vectors to start the scan at. Has to be used in combination with the ToLattice keyword and no other coordinate within the same ScanCoordinate block. Unit can be specified in the header. Default unit is Angstrom.
FromStrainVoigt
Type:Float List
Description:The elements of the initial lattice strain in Voigt notation. One should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems. Has to be used in combination with the ToStrainVoigt keyword and no other coordinate within the same ScanCoordinate block.
LatticeARange
Type:Float List
Unit:Angstrom
Description:Scans the length of the first lattice vector. Can be combined with the LatticeBRange and LatticeCRange keywords, but no other coordinates within the same ScanCoordinate.
LatticeBRange
Type:Float List
Unit:Angstrom
Description:Scans the length of the second lattice vector. Can be combined with the LatticeARange and LatticeCRange keyword, but no other coordinates within the same ScanCoordinate..
LatticeCRange
Type:Float List
Unit:Angstrom
Description:Scans the length of the third lattice vector. Can be combined with the LatticeARange and LatticeBRange keyword, but no other coordinates within the same ScanCoordinate..
SumDist
Type:String
Recurring:True
Description:Scan the sum of distances between two pairs of atoms, R(12)+R(34). Four atom indices followed by two real numbers delimiting the transit range in Angstrom.
ToLattice
Type:Non-standard block
Description:Up to three lattice vectors to end the scan at. Unit can be specified in the header. Default unit is Angstrom.
ToStrainVoigt
Type:Float List
Description:The elements of the final lattice strain in Voigt notation. One should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
nPoints
Type:Integer
Default value:10
Description:The number of points along the scanned coordinate. Must be greater or equal 2.
Print
Type:Block
Description:This block controls the printing of additional information to stdout.
Timers
Type:Multiple Choice
Default value:None
Options:[None, Normal, Detail, TooMuchDetail]
Description:Printing timing details to see how much time is spend in which part of the code.
Properties
Type:Block
Description:Configures which AMS level properties to calculate for SinglePoint calculations or other important geometries (e.g. at the end of an optimization).
BondOrders
Type:Bool
Default value:No
Description:Requests the engine to calculate bond orders. For MM engines these might just be the defined bond orders that go into the force-field, while for QM engines, this might trigger a bond order analysis based on the electronic structure.
Charges
Type:Bool
Default value:No
Description:Requests the engine to calculate the atomic charges.
DipoleGradients
Type:Bool
Default value:No
Description:Requests the engine to calculate the nuclear gradients of the electric dipole moment of the molecule. This can only be requested for non-periodic systems.
DipoleMoment
Type:Bool
Default value:No
Description:Requests the engine to calculate the electric dipole moment of the molecule. This can only be requested for non-periodic systems.
ElasticTensor
Type:Bool
Default value:No
Description:Calculate the elastic tensor.
GSES
Type:Bool
Default value:No
Description:Requests the engine to calculate the gradients of ground to excited state properties.
Gradients
Type:Bool
Default value:No
GUI name:Nuclear gradients
Description:Calculate the nuclear gradients.
Hessian
Type:Bool
Default value:No
Description:Whether or not to calculate the Hessian.
Molecules
Type:Bool
Default value:No
Description:Requests an analysis of the molecular components of a system, based on the bond orders calculated by the engine.
NormalModes
Type:Bool
Default value:No
GUI name:Frequencies
Description:Calculate the frequencies and normal modes of vibration, and for molecules also the corresponding IR intensities if the engine supports the calculation of dipole moments.
Other
Type:Bool
Default value:Yes
Description:Other (engine specific) properties. Details are configured in the engine block.
PESPointCharacter
Type:Bool
Default value:No
GUI name:Characterize PES point
Description:Determine whether the sampled PES point is a minimum or saddle point. Note that for large systems this does not entail the calculation of the full Hessian and can therefore be used to quickly confirm the success of a geometry optimization or transition state search.
Phonons
Type:Bool
Default value:No
Description:Calculate the phonons (for periodic systems).
Polarizability
Type:Bool
Default value:No
Description:Requests the engine to calculate the polarizability tensor of the system.
Raman
Type:Bool
Default value:No
Description:Requests calculation of Raman intensities for vibrational normal modes.
SelectedRegionForHessian
Type:String
GUI name:Hessian only for
Description:Compute the Hessian matrix elements only for the atoms in a particular region. If not specified, the Hessian will be computed for all atoms.
StressTensor
Type:Bool
Default value:No
GUI name:Stress tensor
Description:Calculate the stress tensor.
VCD
Type:Bool
Default value:No
Description:Requests calculation of VCD for vibrational normal modes.
VROA
Type:Bool
Default value:No
Description:Requests calculation of VROA for vibrational normal modes.
Raman
Type:Block
Description:Configures details of the Raman or VROA calculation.
FreqRange
Type:Float List
Unit:cm-1
Recurring:True
GUI name:Frequency range
Description:Specifies a frequency range within which all modes will be scanned. 2 numbers: an upper and a lower bound.
IncidentFrequency
Type:Float
Default value:0.0
Unit:eV
Description:Frequency of incident light.
LifeTime
Type:Float
Default value:0.0
Unit:hartree
Description:Specify the resonance peak width (damping) in Hartree units. Typically the lifetime of the excited states is approximated with a common phenomenological damping parameter. Values are best obtained by fitting absorption data for the molecule, however, the values do not vary a lot between similar molecules, so it is not hard to estimate values. A typical value is 0.004 Hartree.
Replay
Type:Block
Description:Configures the details of the Replay task.
File
Type:String
GUI name:Restart from
Description:Provide an ams.rkf file (or a .results folder) from a previously run job to replay. The file needs to contain a History section.
Frames
Type:Integer List
Description:List of frames from the History section to recompute. If not specified the recomputed frames are determined automatically based on the task of the job that is being replayed: PES scans and NEB calculations will only have the converged points replayed, while all other tasks will have all frames recomputed. Specifying the frames to recompute in the input is probably only useful when replaying trajectories from MolecularDynamics calculations.
StoreAllResultFiles
Type:Bool
Default value:No
Description:If this option is enabled AMS will produce a separate engine output file for every replayed frame. While basic properties like energy, gradients, stress tensor, etc. are stored anyway on the History section in the AMS driver output file (if they were requested in the Properties block), engine specific properties (e.g. excitations energies from ADF) will only be available if the full result files are stored.
Restraints
Type:Block
Description:The Restraints block allows to add soft constraints to the system. A restraint is a potential energy function (a spring) attached to a certain coordinate, for example, an interatomic distance, with its minimum at the specified optimal value. A restraint is defined using one or two parameters: the ForceConstant and, for some types, the F(Inf) value. The ForceConstant parameter corresponds to second derivative of the restraint potential energy d2V(x)/dx^2 for any x (harmonic restraints) or only at at x=0 (other restraints). Here, x is a deviation from the restraint’s optimal value.
Angle
Type:String
Recurring:True
Description:Specify three atom indices i j k followed by an angle in degrees and, optionally, by the ForceConstant (default is 0.3 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the i-j-k angle at the given value. For periodic systems this restraint follows the minimum image convention.
DifDist
Type:String
Recurring:True
Description:Specify four atom indices i j k l followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the difference R(ij)-R(kl) at the given value. For periodic systems this restraint follows the minimum image convention.
Dihedral
Type:String
Recurring:True
Description:Specify four atom indices i j k l followed by an angle in degrees and, optionally, by the ForceConstant (default is 0.1 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the i-j-k-l dihedral angle at the given value. For periodic systems this restraint follows the minimum image convention.
Distance
Type:String
Recurring:True
Description:Specify two atom indices followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the distance between the two specified atoms at the given value. For periodic systems this restraint follows the minimum image convention.
FInfinity
Type:Float
Default value:1.0
GUI name:Default F(inf)
Description:Specify the default asymptotic value for the restraint force for the Hyperbolic and Erf profiles, in Hartree/Bohr or Hartree/radian. A per-restraint value can be specified after the profile type on the corresponding restraint line.
Profile
Type:Multiple Choice
Default value:Harmonic
Options:[Harmonic, Hyperbolic, Erf, GaussianWell]
GUI name:Default restraint profile
Description:Select the default type of restraint profile. The harmonic profile is most suitable for geometry optimizations but may result is very large forces that can be problematic in molecular dynamic. For MD simulations the Hyperbolic or Erf may be more suitable because the restraint force is bounded by a user-defined value. A per-restraint profile type can be specified after the ForceConstant value on the corresponding restraint line.
SumDist
Type:String
Recurring:True
Description:Specify four atom indices i j k l followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the sum R(ij)+R(kl) at the given value. For periodic systems this restraint follows the minimum image convention.
Units
Type:Multiple Choice
Default value:Default
Options:[Default, MD]
GUI name:Units
Description:Change units for energy, force and force constant values from the default (atomic units) to those often used in the MD community (based on kcal/mol and Angstrom). Units for the optimal distances are not affected and are always Angstrom.
RigidMotions
Type:Block
Description:Specify which rigid motions of the total system are allowed. An external field is not considered part of the system. Normally the automatic option is doing what you want. However this feature can be used as a means of geometry constraint.
AllowRotations
Type:Multiple Choice
Default value:Auto
Options:[Auto, None, All, X, Y, Z, XY, XZ, YZ]
Description:Which overall rotations of the system are allowed
AllowTranslations
Type:Multiple Choice
Default value:Auto
Options:[Auto, None, All, X, Y, Z, XY, XZ, YZ]
Description:Which overall transitions of the system are allowed
Tolerance
Type:Float
Default value:1e-06
Description:Tolerance for detecting linear molecules. A large value means larger deviation from linearity is permitted.
RNGSeed
Type:Integer List
Description:Initial seed for the (pseudo)random number generator. This should be omitted in most calculations to avoid introducing bias into the results. If this is unset, the generator will be seeded randomly from external sources of entropy. If you want to exactly reproduce an older calculation, set this to the numbers printed in its output.
SCMMatrix
Type:Block
Description:Technical settings for programs using the AMT matrix system. Currently this is only used by DFTB
DistributedMatrix
Type:Block
Description:Technical settings for Distributed matrices
ColBlockSize
Type:Integer
Default value:64
Description:See comment of RowBlockSize.
RowBlockSize
Type:Integer
Default value:64
Description:The matrix is divided into blocks of size RowBlockSize x ColBlockSize. The smaller the blocks the better the distribution, but at the expense of increased communication overhead
Type
Type:Multiple Choice
Default value:Elpa
Options:[Auto, Reference, ScaLapack, Elpa]
Description:Determines which implementation is used to support the AbstractMatrixType.
Symmetry
Type:Block
Description:Specifying details about the details of symmetry detection and usage.
SymmetrizeTolerance
Type:Float
Default value:0.05
Description:Tolerance used to detect symmetry in case symmetrize is requested.
Tolerance
Type:Float
Default value:1e-07
Description:Tolerance used to detect symmetry in the system.
System
Type:Block
Recurring:True
Description:Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
AllowCloseAtoms
Type:Bool
Default value:No
Description:If AllowCloseAtoms is set to False, the AMS driver will stop with an error if it detects almost-coinciding atomic coordinates. If set to True, the AMS driver will try to carry on with the calculation.
Atoms
Type:Non-standard block
Description:The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
BondOrders
Type:Non-standard block
Description:Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
Charge
Type:Float
Default value:0.0
GUI name:Total charge
Description:The system’s total charge in atomic units.
ElectrostaticEmbedding
Type:Block
Description:Container for electrostatic embedding options, which can be combined.
ElectricField
Type:Float List
Unit:V/Angstrom
Description:External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å. In atomic units: Hartree/(e bohr) = 14.39964 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 … e11 V/m. Supported by the engines adf, band, dftb and mopac. For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
MultipolePotential
Type:Block
Description:External point charges (and dipoles).
ChargeModel
Type:Multiple Choice
Default value:Point
Options:[Point, Gaussian]
Description:A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
ChargeWidth
Type:Float
Default value:-1.0
Description:The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
Coordinates
Type:Non-standard block
Description:Positions and values of the multipoles, one per line. Each line has the following format: x y z q, or x y z q µx µy µz. Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr). Periodic systems are not supported.
FractionalCoords
Type:Bool
Default value:No
Description:Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
GeometryFile
Type:String
Description:Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
GuessBonds
Type:Bool
Default value:No
Description:Whether or not UFF bonds should be guessed.
Lattice
Type:Non-standard block
Description:Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
LatticeStrain
Type:Float List
Description:Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
LoadForceFieldAtomTypes
Type:Block
Description:This is a mechanism to set the ForceField.Type attribute in the input. This information is currently only used by the ForceField engine.
File
Type:String
Description:Name of the (kf) file. It needs to be the result of a forcefield calculation.
LoadForceFieldCharges
Type:Block
Recurring:True
Description:This is a mechanism to set the ForceField.Charge attribute in the input. This information is currently only used by the ForceField engine.
CheckGeometryRMSD
Type:Bool
Default value:No
Description:Whether the geometry RMSD test should be performed, see MaxGeometryRMSD. Otherwise only basic tests are performed, such as number and atom types. Not doing the RMSD test allows you to load molecular charges in a periodic system.
File
Type:String
Description:Name of the (kf) file
MaxGeometryRMSD
Type:Float
Default value:0.1
Unit:Angstrom
Description:The geometry of the charge producing calculation is compared to the one of the region, and need to be the same within this tolerance.
Region
Type:String
Default value:*
Description:Region for which the charges should be loaded
Section
Type:String
Default value:AMSResults
Description:Section name of the kf file
Variable
Type:String
Default value:Charges
Description:Variable name of the kf file
MapAtomsToUnitCell
Type:Bool
Default value:No
Description:For periodic systems the atoms will be moved to the central cell.
ModifyAlternativeElements
Type:Bool
Default value:No
Description:When using alternative elements (using the nuclear_charge attribute) set the element to the nearest integer Z. If you specify an H atom with a nuclear_charge of 2.9 it is replaced by a Li atom with the same nuclear charge.
PerturbCoordinates
Type:Float
Default value:0.0
Unit:Angstrom
Description:Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
PerturbLattice
Type:Float
Default value:0.0
Description:Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
RandomizeAtomOrder
Type:Bool
Default value:No
Description:Whether or not the order of the atoms should be randomly changed. Intended for some technical testing purposes only. Does not work with bond information.
Region
Type:Block
Recurring:True
Description:Properties for each region specified in the Atoms block.
Properties
Type:Non-standard block
Description:Properties for each region specified in the Atoms block.
ShiftCoordinates
Type:Float List
Unit:Bohr
Description:Translate the atoms by the specified shift (three numbers).
SuperCell
Type:Integer List
Description:Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
SuperCellTrafo
Type:Integer List
Description:Create a supercell of the input system (only possible for periodic systems) \(\vec{a}_i' = \sum_j T_{ij} \vec{a}_j\). The integer numbers represent the supercell transformation \(T_{ij}\): 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
Symmetrize
Type:Bool
Default value:No
Description:Whether to symmetrize the input structure. This might also rototranslate the structure into a standard orientation. This will symmetrize the atomic coordinates to machine precision. Useful if the system is almost symmetric or to rototranslate a symmetric molecule into a standard orientation.
Symmetry
Type:Multiple Choice
Default value:AUTO
Options:[AUTO, NOSYM, C(LIN), D(LIN), C(I), C(S), C(2), C(3), C(4), C(5), C(6), C(7), C(8), C(2V), C(3V), C(4V), C(5V), C(6V), C(7V), C(8V), C(2H), C(3H), C(4H), C(5H), C(6H), C(7H), C(8H), D(2), D(3), D(4), D(5), D(6), D(7), D(8), D(2D), D(3D), D(4D), D(5D), D(6D), D(7D), D(8D), D(2H), D(3H), D(4H), D(5H), D(6H), D(7H), D(8H), I, I(H), O, O(H), T, T(D), T(H), S(4), S(6), S(8)]
Description:Use (sub)symmetry with this Schoenflies symbol. Can only be used for molecules. Orientation should be correct for the (sub)symmetry. If used icw Symmetrize, the symmetrization will not reorient the molecule.
Task
Type:Multiple Choice
Options:[GCMC, GeometryOptimization, IRC, MolecularDynamics, NEB, PESExploration, PESScan, Replay, SinglePoint, TransitionStateSearch, VibrationalAnalysis]
Description:Specify the computational task to perform: • Single Point: keep geometry as is • Geometry Optimization: optimize the geometry • Transition State: search for the transition state • IRC: intrinsic reaction coordinate • PES Scan: scan the potential energy surface • NEB: Nudged elastic band for reaction path optimization • Vibrational Analysis: perform one of the analysis types selected on the options page • Molecular Dynamics: perform MD simulation • GCMC: Grand Canonical Monte Carlo simulation • PES Exploration: automated potential energy surface exploration • Replay: Recompute frames from the trajectory of a previously run job
Thermo
Type:Block
Description:Options for thermodynamic properties (assuming an ideal gas). The properties are computed for all specified temperatures.
LowFrequencyCorrector
Type:Block
Description:Options for the dampener-powered free rotor interpolator that corrects thermodynamic quantities for low frequencies. See DOI:10.1021/jp509921r and DOI:10.1002/chem.201200497.
Alpha
Type:Float
Default value:4.0
Description:The exponent term used in the dampener.
Frequency
Type:Float
Default value:100.0
Unit:cm-1
Description:The frequency around which the dampener interpolates between harmonic oscillator and free rotor quantities.
MomentOfInertia
Type:Float
Default value:1e-44
Unit:kg m^2
GUI name:Averaging Moment of Inertia
Description:The moment of inertia used to restrict entropy results for very small frequencies (generally around less than 1 cm-1).
Pressure
Type:Float
Default value:1.0
Unit:atm
Description:The pressure at which the thermodynamic properties are computed.
Temperatures
Type:Float List
Default value:[298.15]
Unit:Kelvin
Description:List of temperatures at which the thermodynamic properties will be calculated.
TransitionStateSearch
Type:Block
Description:Configures some details of the transition state search.
ModeToFollow
Type:Integer
Default value:1
Description:In case of Transition State Search, here you can specify the index of the normal mode to follow (1 is the mode with the lowest frequency).
ReactionCoordinate
Type:Block
Description:Specify components of the transition state reaction coordinate (TSRC) as a linear combination of internal coordinates (distances or angles).
Angle
Type:String
Recurring:True
Description:The TSRC contains the valence angle between the given atoms. Three atom indices followed by the weight.
Coordinate
Type:String
Recurring:True
Description:The TSRC contains Cartesian displacement of an atom: atom index followed by [x|y|z] and the weight.
Dihedral
Type:String
Recurring:True
Description:The TSRC contains the dihedral angle between the given atoms. Four atom indices followed by the weight.
Distance
Type:String
Recurring:True
Description:The TSRC contains the distance between the given atoms. Two atom indices followed by the weight.
UseSymmetry
Type:Bool
Default value:Yes
Description:Whether to use the system’s symmetry in AMS. Symmetry is recognized within a tolerance as given in the Symmetry key.
VibrationalAnalysis
Type:Block
Description:Input data for all vibrational analysis utilities in the AMS driver.
AbsorptionSpectrum
Type:Block
Description:Settings related to the integration of the spectrum for vibronic tasks.
AbsorptionRange
Type:Float List
Default value:[-200.0, 4000.0]
Unit:cm-1
Recurring:True
Description:Specifies frequency range of the vibronic absorption spectrum to compute. 2 numbers: an upper and a lower bound.
FrequencyGridPoints
Type:Integer
Default value:400
Description:Number of grid points to use for the spectrum
LineWidth
Type:Float
Default value:200.0
Unit:cm-1
Description:Lorentzian line-width.
SpectrumOffset
Type:Multiple Choice
Default value:relative
Options:[absolute, relative]
Description:Specifies whether provided frequency range are absolute frequencies or frequencies relative to computed 0-0 excitation energy.
Displacement
Type:Float
Description:Step size for finite difference calculations.
ExcitationSettings
Type:Block
Description:Block that contains settings related to the excitation for vibronic tasks.
EnergyInline
Type:Float
Unit:hartree
Description:Vertical excitation energy, used when [ExcitationInfo] = [Inline].
ExcitationFile
Type:String
Description:Path to a .rkf/.t21 file containing the excited state information (gradients, transition dipoles and energies).
ExcitationInputFormat
Type:Multiple Choice
Default value:File
Options:[File, Inline]
Description:Select how the application should retrieve the excited state information (energy, gradient).
GradientInline
Type:Non-standard block
Description:Excited state gradient at ground state equilibrium geometry, used when [ExcitationInfo] = [Inline].
Singlet
Type:Non-standard block
Description:Symmetry labels + integer indices of desired singlet transitions (VG-FC absorption spectra support only 1 at a time)
Triplet
Type:Non-standard block
Description:Symmetry labels + integer indices of desired triplet transitions (VG-FC absorption spectra support only 1 at a time)
ModeTracking
Type:Block
Description:Input data for Mode Tracking.
HessianGuess
Type:Multiple Choice
Default value:CalculateWithFastEngine
Options:[Unit, File, CalculateWithFastEngine]
GUI name:Guess Hessian
Description:Sets how to obtain the guess for the Hessian used in the preconditioner (if one is to be used).
HessianInline
Type:Non-standard block
Description:Initial guess for the (non-mass-weighted) Hessian in a 3N x 3N block, used when [HessianGuess] = [Inline].
HessianPath
Type:String
Description:Path to a .rkf file containing the initial guess for the Hessian, used when [HessianGuess] = [File]. It may also be the name of the results folder containing the engine file.
ToleranceForBasis
Type:Float
Default value:0.0001
Description:Convergence tolerance for the contribution of the newest basis vector to the tracked mode.
ToleranceForNorm
Type:Float
Default value:0.0005
Description:Convergence tolerance for residual RMS value.
ToleranceForResidual
Type:Float
Default value:0.0005
Description:Convergence tolerance for the maximum component of the residual vector.
ToleranceForSpectrum
Type:Float
Default value:0.01
Description:Convergence tolerance for the spectrum in Vibronic Structure Tracking.
TrackingMethod
Type:Multiple Choice
Default value:OverlapInitial
Options:[OverlapInitial, DifferenceInitial, FreqInitial, IRInitial, OverlapPrevious, DifferencePrevious, FreqPrevious, IRPrevious, HighestFreq, HighestIR, LowestFreq, LowestResidual]
Description:Set the tracking method that will be used. Vibronic Structure Tracking uses Largest Displacement.
UpdateMethod
Type:Multiple Choice
Options:[JD, D, I]
Description:Chooses the method for expanding the Krylov subspace: (I) No preconditioner (VST default), (D) Davidson or (JD) vdVorst-Sleijpen variant of Jacobi-Davidson (Mode tracking default).
NormalModes
Type:Block
Description:All input related to processing of normal modes. Not available for vibronic structure tracking (as no modes are required there).
MassWeightInlineMode
Type:Bool
Default value:Yes
Description:MODE TRACKING ONLY: The supplied modes must be mass-weighted. This tells the program to mass-weight the supplied modes in case this has not yet been done. (True means the supplied modes will be mass-weighted by the program, e.g. the supplied modes are non-mass-weighted.)
ModeFile
Type:String
Description:Path to a .rkf or .t21 file containing the modes which are to be scanned. Which modes will be scanned is selected using the criteria from the [ModeSelect] block.) This key is optional for Resonance Raman and Vibronic Structure. These methods can also calculate the modes using the engine.
ModeInline
Type:Non-standard block
Recurring:True
Description:MODE TRACKING ONLY: Coordinates of the mode which will be tracked in a N x 3 block (same as for atoms), used when [ModeInputFormat] = [Inline]. Rows must be ordered in the same way as in the [System%Atoms] block. Mode Tracking only.
ModeInputFormat
Type:Multiple Choice
Default value:File
Options:[File, Inline, Hessian]
GUI name:Tracked mode source
Description:Set how the initial guesses for the modes are supplied. Only mode tracking supports the Inline and Hessian options.
ModeSelect
Type:Block
Description:Pick which modes to read from file.
DisplacementBound
Type:Float
Description:Vibronic Structure (Refinement), Resonance Raman: Select all modes with a dimensionless oscillator displacement greater than the specified value.
FreqAndIRRange
Type:Float List
Unit:cm-1 and km/mol
Recurring:True
Description:Specifies a combined frequency and IR intensity range within which all modes will be selected. First 2 numbers are the frequency range, 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 selected. 2 numbers: an upper and a lower bound. Calculating all modes higher than some frequency can be achieved by making the upper bound very large.
Full
Type:Bool
Default value:No
GUI name:All modes
Description:Select all modes. This only make sense for Mode Scanning calculations.
HighFreq
Type:Integer
GUI name:# High frequencies
Description:Select the N modes with the highest frequencies.
HighIR
Type:Integer
GUI name:# High IR
Description:Select the N modes with the largest IR intensities.
IRRange
Type:Float List
Unit:km/mol
Recurring:True
Description:Specifies an IR intensity range within which all modes will be selected. 2 numbers: an upper and a lower bound.
ImFreq
Type:Bool
Default value:No
GUI name:All imaginary frequencies
Description:Select all modes with imaginary frequencies.
LargestDisplacement
Type:Integer
Description:Vibronic Structure (Refinement), Resonance Raman: Select the N modes with the largest VG-FC displacement.
LowFreq
Type:Integer
GUI name:# Low frequencies
Description:Select the N modes with the lowest frequencies. Includes imaginary modes which are recorded with negative frequencies.
LowFreqNoIm
Type:Integer
GUI name:# Low positive frequencies
Description:Select the N modes with the lowest non-negative frequencies. Imaginary modes have negative frequencies and are thus omitted here.
LowIR
Type:Integer
GUI name:# Low IR
Description:Select the N modes with the smallest IR intensities.
ModeNumber
Type:Integer List
GUI name:Mode numbers
Description:Indices of the modes to select.
ScanModes
Type:Bool
Default value:No
GUI name:Scan after refining
Description:Supported by: Mode Tracking, Mode Refinement, Vibronic Structure Refinement: If enabled an additional displacement will be performed along the new modes at the end of the calculation to obtain refined frequencies and IR intensities. Equivalent to running the output file of the mode tracking calculation through the AMS ModeScanning task.
ResonanceRaman
Type:Block
Description:Block that contains settings for the calculation of Resonance Raman calculations
IncidentFrequency
Type:Float
Unit:cm-1
Description:Frequency of incident light. Also used to determine most important excitation in case more than one is provided.
LifeTime
Type:Float
Default value:0.00045
Unit:hartree
Description:Lifetime of Raman excited state.
RamanOrder
Type:Integer
Default value:2
Description:Order up to which to compute Raman transitions
RamanRange
Type:Float List
Default value:[0.0, 2000.0]
Unit:cm-1
Recurring:True
Description:Specifies frequency range of the Raman spectrum to compute. 2 numbers: an upper and a lower bound.
Type
Type:Multiple Choice
Options:[ModeScanning, ModeTracking, ModeRefinement, VibronicStructure, VibronicStructureTracking, VibronicStructureRefinement, ResonanceRaman]
Description:Specifies the type of vibrational analysis that should be performed
VSTRestartFile
Type:String
Description:Path to a .rkf file containing restart information for VST.