5. ACErxn Settings¶

ACErxn has a very large number of possible settings. As usual in AMS applications, the settings can be provided in an input text file in AMS format, or as PLAMS Settings object if the program is used as a Python library.

Generally the default values will do, and the settings don’t need to be specified. A few of the most commonly used keywords are selected below.

5.1. Common Keywords¶

The block RunInfo describes which of the three ACErxn steps (intermediate generation, network creation, network minimization) should be performed, and if appropriate, where the restart information can be found.

RunInfo
   MinNumberOfShortestPathsWritten integer
   RestartDir string
   Steps [GenerateIntermediates | CreateNetwork | MinimizeNetwork | AnalyzeNetwork | All]
End

RunInfo

Type: Block
Description: General run and file-Info on creating an ACErxn network

MinNumberOfShortestPathsWritten

Type: Integer
Default value: 5
Description: The minimum number of shortest paths written to the shortest_paths.rkf file. Only relevant with Steps=All,Steps=MinimizeNetwork, or Steps=AnalyzeNetwork.

RestartDir

Type: String
Default value
GUI name: Restart directory
Description: Path to the folder containing the restart RKF files

Steps

Type: Multiple Choice
Default value: All
Options: [GenerateIntermediates, CreateNetwork, MinimizeNetwork, AnalyzeNetwork, All]
Description: Which of the three ACErxn steps to run ((1) GenerateIntermediates, (2) CreateNetwork, (3) MinimizeNetwork, (4) AnalyzeNetwork). The default is to run the first three.

In the block BasicOptions the key MaxJobs determines the number of parallel processes spawned in the parallelized parts of the program.

BasicOptions
   MaxJobs integer
End

BasicOptions

Type: Block
Description: General options

MaxJobs

Type: Integer
Description: The number of parallel calculations (geometry optimizations, matrix enumerations, and network construction processes).

In the block InterrmediateGeneration the subblock AmsOptions specifies details about the calls to AMS (geometry optimizations), stating whether the AMS driver should keep running in the background (default), or if a new AMS process should be created for each geometry optimization. In addition it can be specified wether AMS output files should be kept or thrown away (default).

IntermediateGeneration
   AmsOptions
      KeepAMSFiles Yes/No
      KeepAMSRunning Yes/No
   End
End

IntermediateGeneration

Type: Block
Description: Options used exclusively in intermediate generation (Step 1)

AmsOptions

Type: Block
Description: Options related to engine calls

KeepAMSFiles

Type: Bool
Default value: No
GUI name: Keep AMS files
Description: Keep the files of all AMS calculations in the plams_workdir folder

KeepAMSRunning

Type: Bool
Default value: Yes
GUI name: Keep AMS running
Description: Keep the AMS driver running in the background during the geometry optimizations

By default the ACErxn code will never try to form or break bonds within a fragment in the intermediate generation process. There are many situation where the user may wish to override this, and this can be done with the keyword FormBondsWithinFragment in the block IntermediateGeneration.

IntermediateGeneration
   FormBondsWithinFragment Yes/No
End

IntermediateGeneration

Type: Block
Description: Options used exclusively in intermediate generation (Step 1)

FormBondsWithinFragment

Type: Bool
Default value: No
Description: By default, bond-formation or bond-breaking between all atoms within a fragment is excluded in intermediate generation. If this keyword is set to true, it is possible to form new bonds within a fragment (e.g. create a ring from a chain), and to break them again. The original fragment bonds will always remain in tact.

5.2. Summary of all keywords¶

BasicOptions

Type: Block
Description: General options

AcceptSaturatedActiveAtoms

Type: Bool
Default value: No
Description: Accept atoms as active even if they are fully saturated in the minimal fragments. By default this is turned off.

Covalent_Radii_Coeff

Type: Float
Default value: 1.1
Description: The criterion for if a bond exists between a pair of atom. Example: Let D_ij is distance between atom i and atom j, R_i is covalent radius of atom i and R_j is covalent radius of atom j, if D_ij <= (Covalent_Radii_Coeff) x (R_i + R_j): bond exists else: bond does not exist (Dalton Trans., 2008, 2832-2838).

IM_MaxMolecule

Type: Integer
Default value: 10000
Description: It is the number of constituent molecules in one intermediate state.

MaxJobs

Type: Integer
Description: The number of parallel calculations (geometry optimizations, matrix enumerations, and network construction processes).

NProc

Type: Integer
Default value: 1
Description: The number of cores that are used for the QM geometry optimization for each molecule.

TotalChargeMethod

Type: Multiple Choice
Default value: SumofFragments
Options: [SumofFragments, Ionic]
Description: If SumofFragments the charge of the intermediate (sum of submolecules) is determined by summing the charges of constituent fragments. If Ionic the charge of the molecule is determined using bond orders.

DistanceOptions

Type: Block
Description

BDE_scaling

Type: Float
Default value: 0.01
Description

Engine

Type: Block
Recurring: True
Description: The input for the computational engine used to compute energy and forces.

GeomGenRelatedScreeningOptions

Type: Block
Description: Details of screening of intermediates in IntermediateGeneration. There are three screening moments: (1) During the propagation process, (2) After propagation but before geometry optimization, and (3) after geometry optimization. The screening options in this block are concerned with (3).

DiscardAcyclic

Type: Bool
Default value: No
Description: Rings in the molecule are counted when the SMILES string is created (during 3D structure generation). After geometry optimization the screening of intermediates based on ring count takes place. If set to True, every molecule in intermediate must contain a ring. The default is False.

EnergyScreening

Type: Bool
Default value: No
Description: During intermediate generation, after all geometry optimizations are completed, the generated intermediates can optionally be screened based on energy relative to the reactant. The related keyword is ,CutoffWRTReactantEnergy which must be set.

MaxRingNumber

Type: Integer
Default value: -1
Description: Rings in the molecule are counted when the SMILES string is created (during 3D structure generation). After geometry optimization the screening of intermediates based on ring count takes place. If set to a positive integer, then the number of rings in a single (sub)molecule must be smaller than the provided value.

ScreenChangedConnectivity

Type: Bool
Default value: Yes
Description: If the connectivity of an molecule has been changed during the AC->3D process, the corresponding intermediate will be screened.

ScreenErrorTermination

Type: Bool
Default value: No
Description: If a calculation (UFF, DFTB, semi-empirical) is terminated with an error, the corresponding intermediate will be screened.

IntermediateGeneration

Type: Block
Description: Options used exclusively in intermediate generation (Step 1)

AmsOptions

Type: Block
Description: Options related to engine calls

KeepAMSFiles

Type: Bool
Default value: No
GUI name: Keep AMS files
Description: Keep the files of all AMS calculations in the plams_workdir folder

KeepAMSRunning

Type: Bool
Default value: Yes
GUI name: Keep AMS running
Description: Keep the AMS driver running in the background during the geometry optimizations

CompareCharge

Type: Bool
Default value: No
Description: When deciding if a molecule has already been computed/created, take into account the charge of the molecule

FormBondsWithinFragment

Type: Bool
Default value: No
Description: By default, bond-formation or bond-breaking between all atoms within a fragment is excluded in intermediate generation. If this keyword is set to true, it is possible to form new bonds within a fragment (e.g. create a ring from a chain), and to break them again. The original fragment bonds will always remain in tact.

GenXYZ_MaxCycle

Type: Integer
Default value: 2
Description: The number of adjacency matrix (AC) -> 3D process attempts

GeometryGenerationOptions

Type: Block
Description

RDKitLogging

Type: Bool
Default value: No
Description: When the smilestrings are converted to coordinates using RDKit, logging can be switched on or off.

MaxBondsBroken

Type: Integer
Default value: 2
Description: When generating new intermediates Y from intermediate X, this is the maximum number of bonds that can be broken in X to form Y.

MaxBondsFormed

Type: Integer
Default value: 2
Description: When generating new intermediates Y from intermediate X, this is the maximum number of bonds that can be formed to create Y from X.

MaxPropagation_Iteration

Type: Integer
Default value: -1
Description: The maximum number of iterations in the propagation of intermediates. If set to default value of -1, ACErxn internally sets the value to 100. Generally, enumeration is terminated when no new intermediates are generated.

PropagationMethod

Type: Multiple Choice
Default value: Class
Options: [Class, Function]
Description: Uses either the novel BondOrderMatrixGenerator for propagation and geometry recovery, or the old function PropogationFromReactant

PruningOptions

Type: Block
Description: Details of screening of intermediates in IntermediateGeneration. There are three screening moments: (1) During the propagation process, (2) After propagation but before geometry optimization, and (3) after geometry optimization. The screening options in this block are concerned with (1).

MaxRingSize

Type: Integer
Default value: 10000
Description: If the newly generated intermediate (or molecule) contains a ring larger than the provided value, it is screened.

MinRingSize

Type: Integer
Default value: 3
Description: If the newly generated intermediate (or molecule) contains a ring smaller than the provided value, it is screened.

ScreenAndOptimizeIntermediates

Type: Bool
Default value: Yes
Description: If set to True, the generated intermediates will be screened based on a large set of criteria, the remaining intermediates will be converted to 3D structures, and optimized. If set to False, this entire step will be skipped, and 3D geometries and energies are never obtained.

UsePlamsParallelization

Type: Bool
Default value: Yes
Description: Use the novel GeometryGenerator class to generate 3D geometries from molecule bond matrices

UseReactantGeometries

Type: Bool
Default value: Yes
Description: Use the geometries for the reactants as passed as input. If not true the reactant geometries will be generated from smiles. Only works in combination with PropagationMethod=class

MappingOptions

Type: Block
Description: The options used for the chemical distance computations. Currently only used in step2, but in future will also be available in step1.

Digression_Factor

Type: Integer
Default value: -100
Description: It can have positive integer. It is delta in the expression for the maximum chemical distance of an intermediate form reactants and products

FullMapping

Type: Multiple Choice
Default value: Net
Options: [Net, Y, N]
Description: Net: When calculating chemical distance, we only consider submolecules that change upon reaction. N: When calculating chemical distance, we only consider some parts of intermediate (based on the keyword Kthneighbor).

Kthneighbor

Type: Integer
Default value: 1
Description: When calculating chemical distance with FullMapping=N, ACErxn only considers atoms that are k unit away from the active atoms. The distance between two atoms are defined as the graphical distance (length of shortest path between two atoms)

UseActiveBonds

Type: Bool
Default value: Yes
Description: During the mapping process (computing the chemical distance, assume only the active bonds can be broken or formed)

MatrixRelatedScreeningOptions

Type: Block
Description: Details of screening of intermediates in IntermediateGeneration. There are three screening moments: (1) During the propagation process, (2) After propagation but before geometry optimization, and (3) after geometry optimization. The screening options in this block are concerned with (2).

AllowAldehyde

Type: Bool
Default value: Yes
Description: Determines whether aldehyde anions are acceptable intermediates. Screened after propagation, and before geometry optimization.

AllowCarbenes

Type: Bool
Default value: Yes
Description: Allow carbene molecules among the generated intermediates.

AllowChargedAtoms

Type: Bool
Default value: Yes
Description: The atomic charges are automatically estimated during intermediate generation. If this keyword is set to False, then all estimated charges need to be zero.

AllowChargedMolecules

Type: Bool
Default value: Yes
Description: The charges of all newly generated molecules are derived from the fragment charges. If this keyword is set to False, then all molecule charges need to be zero.

ChargeConservation

Type: Bool
Default value: Yes
Description: Ensure that the estimated atomic charges of the newly generated intermediates match the charges of the submolecules. The latter are derived from the fragment charges.

CheckElectronegativity

Type: Bool
Default value: No
Description: If an atom has a more positive charge than its more electronegative neighbor, the intermediate state will be screened. (except carbon monoxide). By default this is switched off.

DigressionScreening

Type: Bool
Default value: No
Description: If set to True, ACErxn applies digression screening (screening based on the chemical distance of an intermediate from reactant and product) directly following each propagation step for the intermediate generation (before geometry optimization).

DiscardAtomicOverCharge

Type: Bool
Default value: No
Description: If set to True, a formal charge for an atom in a molecule smaller than -2 or bigger than +2 will result in screening of the intermediate.

DiscardMolecularOverCharge

Type: Bool
Default value: No
Description: If the total charge for an molecule in a intermediate state is smaller than -2 or bigger than +2, it will be screened.

MaxAllowedRadicals

Type: Integer
Default value: -1
Description: If the value is positive, radical species are screened during enumeration. It counts the number of radicals and if the number exceeds the AllowRadical value, the intermediate is screened.

MaxMetalElectronCount

Type: Integer
Default value: 100
Description: It has an integer. It is the maximum number of counted electrons of metal (neutral counting)

MaxTotalRingNumber

Type: Integer
Default value: 100000
Description: Before 3D structure generation the number of rings is also computed, using rdkit GetSymmSSSR(). If this key is a positive number, than the total number of rings in an intermediate (sum of submolecules) must be smaller then the provided number.

MetalMaxCoordination

Type: Integer
Default value: -1
Description: Restricts the maximal number of coordinations of transition metals.

MetalMinCoordination

Type: Integer
Default value: -1
Description: Restricts the minimal number of coordinations of transition metals.

MinMetalElectronCount

Type: Integer
Default value: 0
Description: It has an integer. It is the minimum number of counted electrons of metal (neutral counting)

MinTotalRingNumber

Type: Integer
Default value: -1
Description: Before 3D structure generation the number of rings is also computed, using rdkit GetSymmSSSR(). If this key is a positive number, than the total number of rings in an intermediate (sum of submolecules) must be larger then the provided number.

SuperMoleculeCharge

Type: Float
Description: If TotalChargeMethod is set to Ionic, this is the total charge the intermediate (sum of submolecules) always needs to have.

MoleculeSpecificMatrixScreeningOptions

Type: Block
Description: Molecule specific options that may be moved to System settings in future.

Elements_NoTerminus

Type: String
Recurring: True
Description: The name of an element. In the intermediates, elements of this type need to be bonded to more than 1 other atom. This key can occur multiple times

ForbiddenMetalElectronCount

Type: Integer
Recurring: True
Description: It prevents the metal from having certain electron counts (neutral counting). Multiple values can be provided by repeating this key multiple times. Note: Refer http://www.columbia.edu/cu/chemistry/groups/parkin/mlxz.htm for the statistics of the electron count of each metal.

LigandElectronCount

Type: Integer
Recurring: True
Description: When a transition metal complex is included in the intermediates state a user has to specify the ligand electrons contributed when using the neutral counting method. The key needs to be present a multiple of 2 times (the first instance is the index of an atom and the second is the corresponding electron contribution).

RangeOfValences

Type: Block
Recurring: True
Description: The user can provide the maximum and minimum number of bonds an atom of a certain element can have. If not set, default values are used.

Element

Type: String
Description: The element for which the maximum and/or minimum allowed number of bonds is set.

MaxNumberOfBonds

Type: Integer
Description: The maximum number of bonds allowed for this element.

MinNumberOfBonds

Type: Integer
Description: The minimum number of bonds allowed for this element.

NetworkCreation

Type: Block
Description: Options exclusively used for network creation (Step 2)

FindDelocalizedBonds

Type: Bool
Default value: No
Description: Seems to write information on bond delocalization into the Intermediate objects before the network is created.

Screening

Type: Block
Description: Options related to the screening of intermediates

CutoffWRTReactantEnergy

Type: Float
Description: It determines how much higher energy the intermediate state can have than the state of the reactant. If GeomGenRelatedScreeningOptions%EnergyScreening is set to True, then this value is already used at intermediate generation. Unit is kcal/mol.

NetworkMinimization

Type: Block
Description: Options exclusively used for network minimization (Step 3)

Barrier_cutoff

Type: Float
Default value: 0.0
Description

Pathlength_cutoff

Type: Integer
Default value: -1
Description: If this value is positive, only those paths are collected whose lengths are less than or equal to the given value in step3.

YenKSP_K

Type: Integer
Default value: 1
Description: For given value k, the kth shortest paths are extracted in the final step of ACErxn.

ReactantFragmentation

Type: Block
Description: Details on how the reactant is split into smallest fragments, and how those are assigned charges and stabilities

DepthElectronegativitySearch

Type: Integer
Default value: 1
Description: The atoms in the reactant molecules are assigned charges based on the connectivity of the molecule and the electronegativity of the atoms. By default the electronegativity is assigned simply based on the element, but if the depth is selected larger than 1, the electronegativity of neighboring atoms (up to depth-1) is included in determining the final electronegativity value of the atoms. For example, in a regular C-C bond, the electrons in the bond are distributed equally over the two atoms. But if DepthElectronegativitySearch is selected higher than 1, then breaking the C-C bond in ethanol will result in a negatively charged C-OH group and a carbocation.

RunInfo

Type: Block
Description: General run and file-Info on creating an ACErxn network

MinNumberOfShortestPathsWritten

Type: Integer
Default value: 5
Description: The minimum number of shortest paths written to the shortest_paths.rkf file. Only relevant with Steps=All,Steps=MinimizeNetwork, or Steps=AnalyzeNetwork.

RestartDir

Type: String
Default value
GUI name: Restart directory
Description: Path to the folder containing the restart RKF files

Steps

Type: Multiple Choice
Default value: All
Options: [GenerateIntermediates, CreateNetwork, MinimizeNetwork, AnalyzeNetwork, All]
Description: Which of the three ACErxn steps to run ((1) GenerateIntermediates, (2) CreateNetwork, (3) MinimizeNetwork, (4) AnalyzeNetwork). The default is to run the first three.

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.