Keywords¶

Links to manual entries¶

ams:

ams_interactive:

Stop	StopProperties

amsbatch:

SystemsFromTrajectory

analysis:

chemtrayzer2:

conformers:

oled-deposition:

oled-properties:

pipe:

WorkerCommand

Summary of all keywords¶

BondOrders

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

Method

Type: Multiple Choice
Default value: EngineWithGuessFallback
Options: [Engine, Guess, EngineWithGuessFallback]
Description: How to compute the bond orders when they are requested via the ‘Properties%BondOrders’ key. ‘Engine’: let the engine compute the bond orders. The specific method used to compute the bond orders depends on the engine selected, and it may be configurable in the engine’s input. Note: the calculation may stop if the engine cannot compute bond orders. ‘Guess’: Use a bond guessing algorithm based on the system’s geometry. This is the same algorithm that is used by the Graphical User Interface to guess bonds. ‘EngineWithGuessFallback’: let the engine compute the bond orders (same as in ‘Engine’ option) but if the engine did not produce any bond orders, use the bond guessing algorithm as a fallback opion.

Constraints

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

All

Type: String
Recurring: True
Description: Fix multiple distances using one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3 The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 as well as the angle between them. The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then any bond between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. If the distance is omitted then the bond length from the initial geometry is used. Important: only the bonds present in the system at the start of the simulation can be constrained, which means that the bonds may need to be specified in the System block. Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H

Angle

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

Atom

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

AtomList

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

Block

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

BlockAtoms

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

Coordinate

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

DifDist

Type: String
Recurring: True
Description: Four atom indices i j k l followed by the distance in Angstrom. This will constrain the difference R(ij)-R(kl) at the given value.

Dihedral

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

Distance

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

EqualStrain

Type: String
Description: Exclusively for lattice optimizations: Accepts a set of strain components [xx, xy, xz, yy, yz, zz] which are to be kept equal. The applied strain will be determined by the average of the corresponding stress tensors components. In AMSinput just check the corresponding check buttons.

FixedRegion

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

FreezeStrain

Type: String
Description: Exclusively for lattice optimizations: Freezes any lattice deformation corresponding to a particular component of the strain tensor. Accepts a set of strain components [xx, xy, xz, yy, yz, zz] to be frozen. In AMSinput just check the corresponding check buttons.

SumDist

Type: String
Recurring: True
Description: Four atom indices i j k l followed by the distance in Angstrom. This will constrain the sum R(ij)+R(kl) at the given value.

ElasticTensor

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

ConvergenceQuality

Type: Multiple Choice
Default value: Good
Options: [Normal, Good, VeryGood]
GUI name: Convergence
Description: The tightness of the convergence of the geometry optimizations for each strain deformation. This should not be set higher than the overall convergence quality of the preceeding geometry optimization configured by the GeometryOptimization%Convergence%Quality keyword.

Parallel

Type: Block
Description: Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.

nCoresPerGroup

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

nGroups

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

nNodesPerGroup

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

StrainStepSize

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

Engine

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

EngineAddons

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

AtomEnergies

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

D3Dispersion

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

Damping

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

Enabled

Type: Bool
Default value: No
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. When enabled, a spherical wall of radius [Radius] around the origin will be added. The force due to the potential will decay exponentially inside the wall, will be close to [Prefactor*Gradient] outside and exactly half of that at the wall.

Gradient

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

Prefactor

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

Radius

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

EngineDebugging

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

AlwaysClaimSuccess

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

CheckInAndOutput

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

ForceContinousPES

Type: Bool
Default value: No
Description: If this option is set, the engine will always run in continuous PES mode. For many engines this disables the use of symmetry, as this one always leads to a discontinuous PES around the symmetric points: Basically there is jump in the PES at the point where the symmetry detection starts classifying the system as symmetric. Normally the continuous PES mode of the engine (often disabling the symmetry) is only used when doing numerical derivatives, but this flag forces the engine to continuously run in this mode.

IgnoreGradientsRequest

Type: Bool
Default value: No
Description: If this option is set, the engine will not do analytical gradients if asked for it, so that gradients will have to be evaluated numerically by AMS.

IgnorePreviousResults

Type: Bool
Default value: No
Description: If this option is set, the engine will not receive information from previous calculations. Typically this information is used to restart the self consistent procedure of the engine.

IgnoreStressTensorRequest

Type: Bool
Default value: No
Description: If this option is set, the engine will not calculate an analytical stress tensor if asked for it, so that the stress tensor will have to be evaluated numerically by AMS.

NeverQuiet

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

RandomFailureChance

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

RandomNoiseInEnergy

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

RandomNoiseInGradients

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

RandomStopChance

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

EngineRestart

Type: String
Description: The path to the file from which to restart the engine. Should be a proper engine result file (like adf.rkf, band.rkf etc), or the name of the results directory containing it.

ExitCondition

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

AtomsTooClose

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

MinimumDistance

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

PairCalculation

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

Type

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

FallbackSolveAfterEngineFailure

Type: Bool
Default value: Yes
Description: If the engine fails to Solve, try to re-run the Solve without restarting the engine from the previous results. This generally decreases the engine falure rate. Only relevant certain tasks, such as GeometryOptimization, MolecularDynamics, Replay, IRC.

GCMC

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

AccessibleVolume

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

Box

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

Amax

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

Amin

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

Bmax

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

Bmin

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

Cmax

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

Cmin

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

Ensemble

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

Iterations

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

MapAtomsToOriginalCell

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

MaxDistance

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

MinDistance

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

Molecule

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

ChemicalPotential

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

NoAddRemove

Type: Bool
Default value: No
GUI name: Fix molecule
Description: Set to True to tell the GCMC code to keep the number of molecules/atoms of this type fixed. It will thus disable Insert/Delete moves on this type, meaning it can only do a displacement move, or volume change move (for an NPT ensemble).

SystemName

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

NonAccessibleVolume

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

NumAttempts

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

Pressure

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

Removables

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

Restart

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

SwapAtoms

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

Probability

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

Regions

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

Temperature

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

UseGCPreFactor

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

VolumeChangeMax

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

VolumeOption

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

GeometryOptimization

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

CalcPropertiesOnlyIfConverged

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

Convergence

Type: Block
Description: Convergence is monitored for up to 4 quantities: the energy change, the Cartesian gradients, the Cartesian step size, and for lattice optimizations the stress energy per atom. Convergence criteria can be specified separately for each of these items.

Energy

Type: Float
Default value: 1e-05
Unit: Hartree
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.

Quality

Type: Multiple Choice
Default value: Custom
Options: [VeryBasic, Basic, Normal, Good, VeryGood, Custom]
GUI name: Convergence
Description: A quick way to change convergence thresholds: ‘Good’ will reduce all thresholds by an order of magnitude from their default value. ‘VeryGood’ will tighten them by two orders of magnitude. ‘Basic’ and ‘VeryBasic’ will increase the thresholds by one or two orders of magnitude respectively.

Step

Type: Float
Default value: 0.01
Unit: Angstrom
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. For ReaxFF and APPLE&P, this value is reduced by 50%.

dtStart

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

fAlpha

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

fDec

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

fInc

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

strainMass

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

HessianFree

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

Step

Type: Block
Description

MaxCartesianStep

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

MinRadius

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

TrialStep

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

TrustRadius

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

InitialHessian

Type: Block
Description: Options for initial model Hessian when optimizing systems with 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 an arbitrary constant force to a certain (subgroups of) atoms in the system

Force

Type: Float List
Unit: Hartree/Bohr
Description: Defines the constant force vector

PerAtom

Type: Bool
Default value: No
Description: If enabled, the Force vector is applied separately to every atom in the selected Region, so that the total net force on the Region equals the value of Force times the number of atoms in Region. This was the behaviour of ApplyForce in AMS2022. By default, with PerAtom disabled, the Force vector defines the total net force on the Region, so the force applied to each atom equals the value of Force divided by the number of atoms in Region.

Region

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

ApplyVelocity

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

Components

Type: Multiple Choice
Default value: XY
Options: [X, Y, Z, XY, YZ, XZ, XYZ]
Description: Select which components of the Velocity vector are used to set the corresponding components of the net velocity of the specified set of atoms. Any other components of Velocity are ignored and the motion of the selected atoms in those directions is unaffected by ApplyVelocity.

Region

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

Velocity

Type: Float List
Unit: Angstrom/fs
Recurring: False
Description: The constant velocity that will be applied to the specified atoms.

Barostat

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

BulkModulus

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

ConstantVolume

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

Duration

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

Equal

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

Pressure

Type: Float List
Unit: Pascal
Description: Specifies the target pressure. You can specify multiple pressures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one p to the next p (using a linear ramp).

Scale

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

Tau

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

Type

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

BinLog

Type: Block
Description: This block controls writing the BinLog section in ams.rkf, which contains the selected MD state scalars and tensors from every MD step. No per-atom data is written. If you need the per-atom data then you can set the sampling frequency to 1 and get the required data from the MDHistory section. The tensors are written per component, that is, the pressure tensor is written as six variables: PressureTensor_xx, PressureTensor_yy, etc.. To reduce the file size, all data is written in blocks.

BiasEnergy

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

BoostFactor

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

ConservedEnergy

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

Density

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

Hypertime

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

KineticEnergy

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

MaxBiasEnergy

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

MaxBoostFactor

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

PotentialEnergy

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

Pressure

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

PressureTensor

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

Step

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

Temperature

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

Time

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

TotalEnergy

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

Volume

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

BondBoost

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

Chain

Type: Block
Description: Specifications of a chain of atoms. When a chain is detected the distance restraints will be activated. No other chain of this type will be detected while any restraints for this chain is active.

AtomNames

Type: String
Description: Atom names specifying the chain. An atom name can optionally be followed by ‘@’ and a region name, in this case only atoms of this type from the given region will be matched. A leading ‘@’ followed by a number indicates that this position in the chain must be occupied by the atom found earlier at the specified position in the chain. For example “O H N C @1” indicates that the last atom in the chain of the five atoms must be the first oxygen, thus defining a 4-membered ring. This is the only way to define a ring because implicit rings will not be detected. For example, “O H N C O” does not include rings.

MaxDistances

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

MinDistances

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

DistanceRestraint

Type: String
Recurring: True
Description: Specify two atom indices followed by the optimum distance in Angstrom, the first parameter and, optionally, the profile type and the second parameter. This restraint will try to keep the distance between the two specified atoms at the given value. For periodic systems this restraint follows the minimum image convention. Each atom index indicates a position of the corresponding atom in the AtomNames key. Currently recognized restraint profile types: Harmonic (default), Hyperbolic, Erf, GaussianWell. The first parameter is the force constant for the Harmonic, Hyperbolic, and Erf profiles, or well depth for GaussianWell. The second parameter is the asymptotic force value F(Inf) for Hyperbolic and Erf profiles, or the factor before x^2 in the exponent for GaussianWell. Note: the GaussianWell restraint should be used with the Moving flag.

Moving

Type: Bool
Default value: No
GUI name: Move restraint
Description: Move the restraints created with this BondBoost. The restraint value will start at the 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

Region

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

RestartFile

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

Width

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

CVHD

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

Bias

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

DampingTemp

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

Delta

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

Height

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

ColVarBB

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

at1

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

region

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

symbol

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

at2

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

region

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

symbol

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

cutoff

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

p

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

rmax

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

rmin

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

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.

CopyRestartTrajectory

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

CosineShear

Type: Block
Description: Apply an external acceleration to all atoms of a fluid using a periodic (cosine) function along a selected coordinate axis. This induces a periodic shear flow profile which can be used to determine the viscosity.

Acceleration

Type: Float
Default value: 5e-06
Unit: Angstrom/fs^2
Description: Amplitude of the applied cosine shear acceleration profile. The default value should be a rough first guess for water and it needs to be adjusted by experimentation for other systems.

Enabled

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

FlowDirection

Type: Float List
Default value: [1.0, 0.0, 0.0]
Description: The direction in which to apply the shear acceleration, in Cartesian coordinates. The magnitude of this vector is ignored (AMS will normalize it internally). FlowDirection has to be perpendicular to ProfileAxis.

ProfileAxis

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

Deformation

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

LatticeVelocity

Type: Non-standard block
Description: Velocity of individual lattice vector components in Angstrom/fs. The format is identical to the System%Lattice block. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).

LengthRate

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

LengthVelocity

Type: Float List
Default value: [0.0, 0.0, 0.0]
Unit: Angstrom/fs
Description: Change the length of each lattice vector with this velocity. With Type=Exponential, LengthVelocity is divided by the current lattice vector lengths on StartStep to determine a LengthRate, which is then applied on all subsequent steps. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).

Period

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

ScaleAtoms

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

StartStep

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

StopStep

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

StrainRate

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

TargetLattice

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

TargetLength

Type: Float List
Default value: [0.0, 0.0, 0.0]
Unit: Angstrom
Description: Target lengths of each lattice vector to be achieved by StopStep. The number of values should equal the periodicity of the system. If a value is zero, the corresponding lattice vector will not be modified.

Type

Type: Multiple Choice
Default value: Linear
Options: [Linear, Exponential, Sine, Cosine]
Description: Function defining the time dependence of the deformed lattice parameters. Linear increments the lattice parameters by the same absolute amount every timestep. Exponential multiplies the lattice parameters by the same factor every timestep. Only StrainRate, LengthRate, and LengthVelocity are supported for Type=Exponential. Sine deforms the system from the starting lattice to TargetLattice/TargetLength and then by the same amount to the opposite direction, while Cosine deforms the system from the starting lattice to the target and back.

Gravity

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

Acceleration

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

HeatExchange

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

HeatingRate

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

Method

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

Sink

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

AtomList

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

Box

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

Amax

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

Amin

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

Bmax

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

Bmin

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

Cmax

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

Cmin

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

Region

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

Source

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

AtomList

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

Box

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

Amax

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

Amin

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

Bmax

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

Bmin

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

Cmax

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

Cmin

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

Region

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

StartStep

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

StopStep

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

InitialVelocities

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

File

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

RandomVelocitiesMethod

Type: Multiple Choice
Default value: Exact
Options: [Exact, Boltzmann, Gromacs]
GUI name: Velocity randomization method
Description: Specifies how are random velocities generated. Three methods are available. Exact: Velocities are scaled to exactly match set random velocities temperature. Boltzmann: Velocities are not scaled and sample Maxwell-Boltzmann distribution. However, the distribution is not corrected for constraints. Gromacs: Velocities are scaled to match set random velocities temperature, but removal of net momentum is performed only after the scaling. Resulting kinetic energy is lower based on how much net momentum the system had.

Temperature

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

Type

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

Values

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

NSteps

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

Plumed

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

Input

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

Parallel

Type: Block
Description: Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.

nCoresPerGroup

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

nGroups

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

nNodesPerGroup

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

Preserve

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

AngularMomentum

Type: Bool
Default value: Yes
GUI name: : Angular momentum
Description: Remove overall angular momentum of the system. This option is ignored for 2D and 3D-periodic systems, and disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).

CenterOfMass

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

Momentum

Type: Bool
Default value: Yes
GUI name: Preserve: Total momentum
Description: Remove overall (linear) momentum of the system. This is disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).

Print

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

System

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

Velocities

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

Reactor

Type: Block
Recurring: True
Description: Define one phase of the nanoreactor. A reactor is a region of space surrounded by an elastic wall. Atoms inside the region are not affected. Atoms outside it will be pushed back with force depending on the [ForceConstant] and the [MassScaled] flag.

ForceConstant

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

MassScaled

Type: Bool
Default value: Yes
GUI name: Scale force by mass
Description: If this flag is disabled the force on an atom outside of the reactor depends only on the atomic coordinates and the force constant. Otherwise, the force is also multiplied by the mass of the atom. This means that atoms at the same distance from the wall will receive the same accelerate due to the wall potential.

NSteps

Type: Integer
GUI name: Reactor lifetime
Description: Number of steps for which the reactor will remain active until disabled. The next reactor will be activated immediately after this. After the last reactor is disabled the cycle will repeat.

Radius

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

ReflectiveWall

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

Axis

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

Region

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

Threshold

Type: Float
Unit: Angstrom
Description: Defines the threshold value determining the position of the reflective wall. If the dot product of a position of a particle with Axis exceeds Threshold, the particle will be reflected. This means that the plane of the wall passes through a point given by Axis times Threshold.

Remap

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

Type

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

RemoveMolecules

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

Formula

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

Frequency

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

SafeBox

Type: Block
Description: Part of the simulation box where molecules may not be removed. Only one of the SinkBox or SafeBox blocks may be present. If this block is present the molecule will not be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.

Amax

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

Amin

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

Bmax

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

Bmin

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

Cmax

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

Cmin

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

FractionalCoordsBox

Type: Float List
GUI name: Safe box
Description: Do not remove molecules that are (partly) inside the safe box. Borders of the safe box specified as: Amin, Amax, Bmin, Bmax, Cmin, Cmax. For periodic dimensions fractional coordinates between 0 and 1 and for non-periodic dimensions Cartesian values in Angstrom are expected.

SinkBox

Type: Block
Description: Part of the simulation box where matching molecules will be removed. By default, molecules matching the formula will be removed regardless of their location. If this block is present then such a molecule will only be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.

Amax

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

Amin

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

Bmax

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

Bmin

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

Cmax

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

Cmin

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

FractionalCoordsBox

Type: Float List
GUI name: Sink box
Description: Remove molecules that are (partly) inside the sink box. Borders of the sink box specified as: Amin, Amax, Bmin, Bmax, Cmin, Cmax. For periodic dimensions fractional coordinates between 0 and 1 and for non-periodic dimensions Cartesian values in Angstrom are expected.

StartStep

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

StopStep

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

ReplicaExchange

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

AllowWrongResults

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

EWMALength

Type: Integer
Default value: 10
Description: Length of the exponentially weighted moving average used to smooth swap probabilities for monitoring. This value is equal to the inverse of the EWMA mixing factor.

SwapFrequency

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

TemperatureFactors

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

Temperatures

Type: Float List
Description: List of temperatures for all replicas except for the first one. This is mutually exclusive with TemperatureFactors. Exactly nReplicas-1 temperature values need to be specified, in increasing order. The temperature of the first replica is given by [Thermostat%Temperature].

nReplicas

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

Restart

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

Shake

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

All

Type: String
Recurring: True
GUI name: Constrain all
Description: Constraint description in one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3 The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 and the angle between them. The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then all bonds between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. The distance, if present, must be in Angstrom. If it is omitted then the bond length from the initial geometry is used. Important: only the bonds present in the system at certain points of the simulation (at the start or right after adding/removing atoms) can be constrained, which means that the bonds may need to be specified in the System block. Warning: the triangles constraint should be used with care because each constrained bond or angle means removing one degree of freedom from the dynamics. When there are too many constraints (for example, “All triangles H C H” in methane) some of them may be linearly dependent, which will lead to an error in the temperature computation. Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H

ConvergeR2

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

ConvergeRV

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

Iterations

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

ShakeInitialCoordinates

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

Thermostat

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

BerendsenApply

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

ChainLength

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

Duration

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

Region

Type: String
Default value: *
Description: The identifier of the region to thermostat. The default ‘*’ applies the thermostat to the entire system. The value can by a plain region name, or a region expression, e.g. ‘*-myregion’ to thermostat all atoms that are not in myregion, or ‘regionA+regionB’ to thermostat the union of the ‘regionA’ and ‘regionB’. Note that if multiple thermostats are used, their regions may not overlap.

Tau

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

Temperature

Type: Float List
Unit: Kelvin
GUI name: Temperature(s)
Description: The target temperature of the thermostat. You can specify multiple temperatures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one T to the next T (using a linear ramp). For NHC thermostat, the temperature may not be zero.

Type

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

TimeStep

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

Trajectory

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

PrintFreq

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

SamplingFreq

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

TProfileGridPoints

Type: Integer
Default value: 0
Description: Number of points in the temperature profile. If TProfileGridPoints > 0, a temperature profile along each of the three lattice axes will be written to the .rkf file. The temperature at a given profile point is calculated as the total temperature of all atoms inside the corresponding slice of the simulation box, time-averaged over all MD steps since the previous snapshot. By default, no profile is generated.

WriteBonds

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

WriteCharges

Type: Bool
Default value: Yes
Description: Write current atomic point charges (if available) to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze charges.

WriteCoordinates

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

WriteEngineGradients

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

WriteMolecules

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

WriteVelocities

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

fbMC

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

Frequency

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

MassRoot

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

MolecularMoves

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

Enabled

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

RotationStepAngle

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

TranslationStepLength

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

NSteps

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

PrintFreq

Type: Integer
GUI name: Printing frequency
Description: Print current thermodynamic properties to the output every N fbMC steps. This defaults to the PrintFreq set in the Trajectory block. Setting this to zero disables printing fbMC steps.

StartStep

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

StepLength

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

StopStep

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

Temperature

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

Molecules

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

AdsorptionSupportRegion

Type: String
GUI name: Adsorption support region
Description: Select region that will represent a support for adsorption analysis. Adsorbed molecules will receive an ‘(ads)’ suffix after name of the element bonded to the support. Such elements will be listed separate from atoms of the same element not bonded to the support, for example, HOH(ads) for a water molecule bonded to a surface via one of its H atoms.

BondOrderCutoff

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

NEB

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

Climbing

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

ClimbingThreshold

Type: Float
Default value: 0.0
Unit: Hartree/Bohr
GUI name: CI force threshold
Description: Climbing image force threshold. If ClimbingThreshold > 0 and the max perpendicular force component is above the threshold then no climbing is performed at this step. This entry can be used to get a better approximation for the reaction path before starting the search for the transition state. A typical value is 0.01 Hartree/Bohr.

Images

Type: Integer
Default value: 8
GUI name: Number of images
Description: Number of NEB images (not counting the chain ends). Using more images will result in a smoother reaction path and can help with convergence problems, but it will also increase the computation time.

InterpolateInternal

Type: Bool
Default value: Yes
GUI name: Interpolate in Internal coordinates
Description: The initial NEB image geometries are calculated by interpolating between the initial and the final state. By default, for non-periodic systems the interpolation is performed in Internal coordinates but the user can choose to do it in the Cartesian ones. For periodic systems the interpolation is always done in Cartesian coordinates.

InterpolateShortest

Type: Bool
Default value: Yes
GUI name: Interpolate across cell boundary
Description: Allow interpolation across periodic cell boundaries. Set to false if an atom is intended to move more than half across the simulation box during reaction.

Iterations

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

Jacobian

Type: Float
GUI name: Jacobian value
Description: Scaling factor used to convert the lattice strain to a NEB coordinate value. Default value: sqrt(N)*(V/N)^(1/d), where V - lattice volume (area for 2D, length for 1D), N - number of atoms, and d - number of periodic dimensions.

LoadPath

Type: Block
Description: Provide details about the trajectory to get the initial NEB path from. PESScan and NEB trajectories are supported. Only the last geometry for each point on the trajectory is considered.

File

Type: String
GUI name: Initial path file
Description: Provide an ams.rkf file to load the initial path from. All geometries of this calculation, including initial and final, will be taken from the History section of the file. Note that for a PESScan it should be a 1D path.

Geometries

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

Points

Type: Integer List
GUI name: Path points
Description: By default the whole path is used, which may sometimes be not desirable. For example when a PESScan revealed multiple barriers. In this case one can specify indices of the path points to be used. The last geometry of the specified path point will be loaded.

MapAtomsToCell

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

OldTangent

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

OptimizeEnds

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

OptimizeLattice

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

Parallel

Type: Block
Description: Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.

nCoresPerGroup

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

nGroups

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

nNodesPerGroup

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

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.

Calculate

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

DistanceDifference

Type: Float
Default value: -1.0
Unit: Angstrom
Description: If the distance between two mapped binding-sites is larger than this threshold, the binding-sites are considered different. If not specified, its value will set equal to [PESExploration%StructureComparison%DistanceDifference]

MaxCoordinationShellsForLabels

Type: Integer
Default value: 3
Description: The binding site labels are given based on the coordination numbers of shells in the reference region, using the following format: N<int><int>…, e.g., the label ‘N334’ means 3 atoms in the first coordination shell, 3 in the second one, and 4 in the third one. This parameter controls the maximum number of shells to include.

NeighborCutoff

Type: Float
Default value: -1.0
Unit: Angstrom
Description: Atoms within this distance of each other are considered neighbors for the calculation of the binding sites. If not specified, its value will set equal to [PESExploration%StructureComparison%NeighborCutoff]

ReferenceRegion

Type: String
Default value
Description: Defines the region that is considered as the reference for binding sites detection. Binding sites are projected on this region using the geometry from the reference system. If not specified, its value will set equal to [PESExploration%StatesAlignment%ReferenceRegion]

CalculateFragments

Type: Bool
Default value: No
Description: Must be used together with an adsorbent set as the StatesAlignment%ReferenceRegion. Runs a final calculation of the adsorbate and adsorbent (marked by the ReferenceRegion) individually. The fragmented state is included in the energy landscape.

Debug

Type: Block
Description: ???.

DynamicSeedStates

Type: Bool
Default value: Yes
Description: Whether subsequent expeditions may start from states discovered by previous expeditions. This should lead to a more comprehensive exploration of the potential energy surface. Disabling this will focus the PES exploration around the initial seed states.

Dynamics

Type: Block
Description: ???.

Andersen

Type: Block
Description: ???.

Alpha

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

CollisionPeriod

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

Langevin

Type: Block
Description: ???.

Friction

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

Nose

Type: Block
Description: ???.

Mass

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

Thermostat

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

Time

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

TimeStep

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

FiniteDifference

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

Hessian

Type: Block
Description: ???.

AtomList

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

ZeroFreqValue

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

Job

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

LandscapeRefinement

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

IgnoreFinalPESPointCharacter

Type: Bool
Default value: No
Description: At the end of the energy landscape refinement job, each state is assigned a PES point character (MIN or TS) based on its vibrational frequencies before being included in the final database. States are only added if the PES point character after refinement remains unchanged. However, states are added without verifying if this option is true. Nonetheless, vibrational frequencies are calculated and stored for future analysis. This option is especially useful when using computationally demanding engines. Because in those cases, precision and computational effort must be balanced, resulting in significant vibrational frequencies inaccuracies.

RunInitialSinglePoints

Type: Bool
Default value: Yes
Description: If it is true, just after loading the energy landscape to refine, the single energy point computations are disabled. Be aware that if you enable this, the output file’s ‘Initial Energy Landscape’ section will display incorrect states’ energy values. If the engine requires too much processing power, this option can help you save a small amount of time.

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.

NegativeEigenvalueTolerance

Type: Float
Default value: -0.0005
Unit: Hartree/Bohr^2
Description: The threshold in Hessian eigenvalue below which a mode is considered imaginary, i.e. indicating a transition state. This is a small negative number, as very small negative eigenvalues may be due to numerical noise on an essentially flat PES and do not indicate true transition states. We need a more flexible value for this parameter in PESExploration because the high computational cost of the task typically forces us to reduce the engine precision, which increases the noise in the vibrational frequencies evaluation. [PESPointCharacter%NegativeEigenvalueTolerance] is overridden by this parameter.

NudgedElasticBand

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

ClimbingImageMethod

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

ConvergedForce

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

Images

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

MaxIterations

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

OldTangent

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

Spring

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

NumExpeditions

Type: Integer
Default value: 1
Description: Sets the number of subsequent expeditions our job will consist of. Larger values result in a more comprehensive exploration of the potential energy surface, but will take more computational time.

NumExplorers

Type: Integer
Default value: 1
Description: Sets the number of independent PES explorers dispatched as part of each expedition. Larger values will result in a more comprehensive exploration of the potential energy surface, but will take more computational time. By default an appropriate number of explorers are executed in parallel.

OptTSMethod

Type: Multiple Choice
Default value: SaddleSearch
Options: [SaddleSearch, NudgedElasticBand]
Description: When the full set of states in the energy landscape are optimized (see PESExploration%Job = GeometryOptimization), transition states can be optimized using either SaddleSearch or NudgedElasticBand methods. SaddleSearch uses information only from the current geometry of the TS; contrary, NudgedElasticBand ignores the current geometry and runs a Nudged-Elastic-Band calculation trying to connect the associated reactants and products if they are available.

Optimizer

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

ConvergedForce

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

MaxIterations

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

Method

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

Parallel

Type: Block
Description: Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.

nCoresPerGroup

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

nGroups

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

nNodesPerGroup

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

ParallelReplica

Type: Block
Description: ???.

DephaseLoopMax

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

DephaseLoopStop

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

DephaseTime

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

PostTransitionTime

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

RefineTransition

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

StateCheckInterval

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

StateSaveInterval

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

StopAfterTransition

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

Prefactor

Type: Block
Description: ???.

Rate

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

ProcessSearch

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

MinimizationOffset

Type: Float
Default value: 0.2
Description: After a saddle is found, images are placed on either side of the saddle along the mode and minimized to ensure that the saddle is connected to the original minimum and to locate the product state. MinimizationOffset is the distance those images are displaced from the saddle.

RandomSeed

Type: Integer
Description: Number used to initialize both the EON clients random number generators as well as the AMS global RNG. The latter is normally initialized with the RNGSeed keyword at the root level. Should be used by developers only. May or may not help to make more reproducible regression tests …

SaddleSearch

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

ConvergedForce

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

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: 0.001
Unit: eV
Description: Minimum energy barrier to accept a new transition state.

MinModeMethod

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

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.

NegativeEigenvalueTolerance

Type: Float
Default value: -0.0001
Unit: Hartree/Bohr^2
Description: The threshold in Hessian eigenvalue below which a mode is considered imaginary, i.e. indicating a transition state. This is a small negative number, as very small negative eigenvalues may be due to numerical noise on an essentially flat PES and do not indicate true transition states.

NumberOfModes

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

Tolerance

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

PESScan

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

CalcPropertiesAtPESPoints

Type: Bool
Default value: No
Description: Whether to perform an additional calculation with properties on all the sampled points of the PES. If this option is enabled AMS will produce a separate engine output file for every sampled PES point.

FillUnconvergedGaps

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

ScanCoordinate

Type: Block
Recurring: True
Description: Specifies a coordinate along which the potential energy surface is scanned. If this block contains multiple entries, these coordinates will be varied and scanned together as if they were one. Note that there can be only one ScanCoordinate containing a lattice scan in any PES scan job.

Angle

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

CellVolumeRange

Type: Float List
Unit: Angstrom^3
Description: Two numbers for the initial and final cell volume. The cell is scaled isotropically between these values. Can not be used together with any other coordinate within the same ScanCoordinate block.

CellVolumeScalingRange

Type: Float List
Description: Two scaling factors for the initial and final cell volume. A value of ‘0.9 1.1’ would result in an isotropic scaling between 90% and 110% of the cell volume of the input system. Can not be used together with any other coordinate within the same ScanCoordinate block.

Coordinate

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

DifDist

Type: String
Recurring: True
Description: Scan the difference distance between two pairs of atoms, R(12)-R(34). Four atom indices followed by two real numbers delimiting the transit range in Angstrom.

Dihedral

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

Distance

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

FromLattice

Type: Non-standard block
Description: Up to three lattice vectors to start the scan at. Has to be used in combination with the ToLattice keyword and no other coordinate within the same ScanCoordinate block. Unit can be specified in the header. Default unit is Angstrom.

FromStrainVoigt

Type: Float List
Description: The elements of the initial lattice strain in Voigt notation. One should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems. Has to be used in combination with the ToStrainVoigt keyword and no other coordinate within the same ScanCoordinate block.

LatticeARange

Type: Float List
Unit: Angstrom
Description: Scans the length of the first lattice vector. Can be combined with the LatticeBRange and LatticeCRange keywords, but no other coordinates within the same ScanCoordinate.

LatticeBRange

Type: Float List
Unit: Angstrom
Description: Scans the length of the second lattice vector. Can be combined with the LatticeARange and LatticeCRange keyword, but no other coordinates within the same ScanCoordinate..

LatticeCRange

Type: Float List
Unit: Angstrom
Description: Scans the length of the third lattice vector. Can be combined with the LatticeARange and LatticeBRange keyword, but no other coordinates within the same ScanCoordinate..

SumDist

Type: String
Recurring: True
Description: Scan the sum of distances between two pairs of atoms, R(12)+R(34). Four atom indices followed by two real numbers delimiting the transit range in Angstrom.

ToLattice

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

ToStrainVoigt

Type: Float List
Description: The elements of the final lattice strain in Voigt notation. One should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.

nPoints

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

Print

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

Timers

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

Properties

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

BondOrders

Type: Bool
Default value: No
Description: Requests the engine to calculate bond orders. For MM engines these might just be the defined bond orders that go into the force-field, while for QM engines, this might trigger a bond order analysis based on the electronic structure. For engines that do not have a bond order analysis method, a bond guessing algorithm will be used. See also the input options in the BondOrders block.

Charges

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

DipoleGradients

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

DipoleMoment

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

ElasticTensor

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

GSES

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

Gradients

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

Hessian

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

Molecules

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

NormalModes

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

OrbitalsInfo

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

Other

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

PESPointCharacter

Type: Bool
Default value: No
GUI name: Characterize PES point
Description: Determine whether the sampled PES point is a minimum or saddle point. Note that for large systems this does not entail the calculation of the full Hessian and can therefore be used to quickly confirm the success of a geometry optimization or transition state search.

Phonons

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

Polarizability

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

Raman

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

SelectedRegionForHessian

Type: String
GUI name: Hessian only for
Description: Compute the Hessian matrix elements only for the atoms in a particular region. If not specified, the Hessian will be computed for all atoms.

StressTensor

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

VCD

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

VROA

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

Raman

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

FreqRange

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

IncidentFrequency

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

LifeTime

Type: Float
Default value: 0.0
Unit: hartree
Description: Specify the resonance peak width (damping) in Hartree units. Typically the lifetime of the excited states is approximated with a common phenomenological damping parameter. Values are best obtained by fitting absorption data for the molecule, however, the values do not vary a lot between similar molecules, so it is not hard to estimate values. A typical value is 0.004 Hartree.

Replay

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

File

Type: String
GUI name: Restart from
Description: Provide an ams.rkf file (or a .results folder) from a previously run job to replay. The file needs to contain a History section.

Frames

Type: Integer List
Description: List of frames from the History section to recompute. If not specified the recomputed frames are determined automatically based on the task of the job that is being replayed: PES scans and NEB calculations will only have the converged points replayed, while all other tasks will have all frames recomputed. Specifying the frames to recompute in the input is probably only useful when replaying trajectories from MolecularDynamics calculations.

StoreAllResultFiles

Type: Bool
Default value: No
Description: If this option is enabled AMS will produce a separate engine output file for every replayed frame. While basic properties like energy, gradients, stress tensor, etc. are stored anyway on the History section in the AMS driver output file (if they were requested in the Properties block), engine specific properties (e.g. excitations energies from ADF) will only be available if the full result files are stored.

Restraints

Type: Block
Description: The Restraints block allows to add soft constraints to the system. A restraint is a potential energy function (a spring) attached to a certain coordinate, for example, an interatomic distance, with its minimum at the specified optimal value. A restraint is defined using one or two parameters: the ForceConstant and, for some types, the F(Inf) value. The ForceConstant parameter corresponds to second derivative of the restraint potential energy d2V(x)/dx^2 for any x (harmonic restraints) or only at at x=0 (other restraints). Here, x is a deviation from the restraint’s optimal value.

Angle

Type: String
Recurring: True
Description: Specify three atom indices i j k followed by an angle in degrees and, optionally, by the ForceConstant (default is 0.3 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the i-j-k angle at the given value. For periodic systems this restraint follows the minimum image convention.

DifDist

Type: String
Recurring: True
Description: Specify four atom indices i j k l followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the difference R(ij)-R(kl) at the given value. For periodic systems this restraint follows the minimum image convention.

Dihedral

Type: String
Recurring: True
Description: Specify four atom indices i j k l followed by an angle in degrees and, optionally, by the ForceConstant (default is 0.1 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the i-j-k-l dihedral angle at the given value. For periodic systems this restraint follows the minimum image convention.

Distance

Type: String
Recurring: True
Description: Specify two atom indices followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the distance between the two specified atoms at the given value. For periodic systems this restraint follows the minimum image convention.

FInfinity

Type: Float
Default value: 1.0
GUI name: Default F(inf)
Description: Specify the default asymptotic value for the restraint force for the Hyperbolic and Erf profiles, in Hartree/Bohr or Hartree/radian. A per-restraint value can be specified after the profile type on the corresponding restraint line.

Profile

Type: Multiple Choice
Default value: Harmonic
Options: [Harmonic, Hyperbolic, Erf, GaussianWell]
GUI name: Default restraint profile
Description: Select the default type of restraint profile. The harmonic profile is most suitable for geometry optimizations but may result is very large forces that can be problematic in molecular dynamic. For MD simulations the Hyperbolic or Erf may be more suitable because the restraint force is bounded by a user-defined value. A per-restraint profile type can be specified after the ForceConstant value on the corresponding restraint line.

SumDist

Type: String
Recurring: True
Description: Specify four atom indices i j k l followed by the distance in Angstrom and, optionally, by the ForceConstant (default is 1.0 in a.u.), profile type and F(Inf) (in a.u.). This restraint will try to keep the sum R(ij)+R(kl) at the given value. For periodic systems this restraint follows the minimum image convention.

Units

Type: Multiple Choice
Default value: Default
Options: [Default, MD]
GUI name: Units
Description: Change units for energy, force and force constant values from the default (atomic units) to those often used in the MD community (based on kcal/mol and Angstrom). Units for the optimal distances are not affected and are always Angstrom.

RigidMotions

Type: Block
Description: Specify which rigid motions of the total system are allowed. An external field is not considered part of the system. Normally the automatic option is doing what you want. However this feature can be used as a means of geometry constraint.

AllowRotations

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

AllowTranslations

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

Tolerance

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

RNGSeed

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

SCMMatrix

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

DistributedMatrix

Type: Block
Description: Technical settings for Distributed matrices

ColBlockSize

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

RowBlockSize

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

Type

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

Symmetry

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

SymmetrizeTolerance

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

Tolerance

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

System

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

AllowCloseAtoms

Type: Bool
Default value: No
Description: If AllowCloseAtoms is set to False, the AMS driver will stop with an error if it detects almost-coinciding atomic coordinates. If set to True, the AMS driver will try to carry on with the calculation.

Atoms

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

BondOrders

Type: Non-standard block
Description: Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.

Charge

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

ElectrostaticEmbedding

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

ElectricField

Type: Float List
Unit: V/Angstrom
Description: External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å. In atomic units: Hartree/(e bohr) = 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
Unit: Bohr
Description: Step size for finite difference calculations.

ExcitationSettings

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

EnergyInline

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

ExcitationFile

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

ExcitationInputFormat

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

GradientInline

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

Singlet

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

Triplet

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

ModeTracking

Type: Block
Description: Input data for Mode Tracking.

HessianGuess

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

HessianInline

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

HessianPath

Type: String
Description: Path to a .rkf file containing the initial guess for the Hessian, used when [HessianGuess] = [File]. It may also be the name of the results folder containing the engine file.

ToleranceForBasis

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

ToleranceForNorm

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

ToleranceForResidual

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

ToleranceForSpectrum

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

TrackingMethod

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

UpdateMethod

Type: Multiple Choice
Options: [JD, D, I]
Description: Chooses the method for expanding the Krylov subspace: (I) No preconditioner (VST default), (D) Davidson or (JD) vdVorst-Sleijpen variant of Jacobi-Davidson (Mode tracking default).

NormalModes

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

MassWeightInlineMode

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

ModeFile

Type: String
Description: Path to a .rkf or .t21 file containing the modes which are to be scanned. Which modes will be scanned is selected using the criteria from the [ModeSelect] block.) This key is optional for Resonance Raman and Vibronic Structure. These methods can also calculate the modes using the engine.

ModeInline

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

ModeInputFormat

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

ModeSelect

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

DisplacementBound

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

FreqAndIRRange

Type: Float List
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.

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