Species Block

Defines a single molecular/atomic species

Overview

The Species block completely defines an atomic or molecular species for use in a simulation. This description includes:the atomic contents, their connectivity

The block keyword itself takes a single (required) argument - the name of the species. This name is used to reference the species when, for example, constructing a configuration.

For more information see the section on setting up species.

Keywords

Keyword Arguments Default Description
Angle i
j
k
form
[parameters]		 – Create an intramolecular angle definition between the three atom indices i-j-k, and with the named functional form and parameters. The functional form may instead be replaced with the name of an existing master term preceded with an ampersand (@), in which case the master term form and parameters will be used for this interaction.
Atom index
element
x
y
z
type
[q]		 – Creates a new atom with integer index and chemical element at the x, y, and z coordinates specified, and with the associated atom type (or None). Optionally, the atomic charge q may be provided if required. Alternatively, the atomic charge may be specified for the atom with the Charge keyword.
Bond i
j
form
[parameters]		 – Create an intramolecular bond definition between the two atom indices i-j, and with the named functional form and parameters. The functional form may instead be replaced with the name of an existing master term preceded with an ampersand (@), in which case the master term form and parameters will be used for this interaction.
BondType i
j
type
 – Explicitly sets the bond type between the atoms i and j to be of the specified type. The bond must already exist.
Charge i
q		 – Sets the atomic charge of the atom with index i to q. Alternatively, the atomic charge may be specified as the last argument to the Atom keyword.
CoordinateSets CoordinatesFileAndFormat – Sets a file from which coordinates for the species are read in, and which are used when adding multiple copies of the species to a configuration in its generator definition.
EndSpecies – Indicates the end of the current Species block.
Forcefield name – Applies inter- and intramolecular terms from the named forcefield to the Species, overwriting any that previously exist.
Improper i
j
k
l
form
[parameters]		 – Create an intramolecular improper torsion definition between the four atom indices i-j-k-l (where i is the central atom), and with the named functional form and parameters. The functional form may instead be replaced with the name of an existing master term preceded with an ampersand (@), in which case the master term form and parameters will be used for this interaction.
Isotopologue name
type=Z ...		 – Create an isotopologue called name, with isotopes assigned to atom types by their Z value.
Site name – Begin a site block defining a reference site on the species in terms of its atoms for use in the analysis modules.
Torsion i
j
k
l
form
[parameters]		 – Create an intramolecular torsion (dihedral angle) definition between the four atom indices i-j-k-l, and with the named functional form and parameters. The functional form may instead be replaced with the name of an existing master term preceded with an ampersand (@), in which case the master term form and parameters will be used for this interaction.

Examples

Water

Species  'Water'
  Atom    1    O     5.139     5.968     0.000  'OW'    -0.82
  Atom    2    H     3.924     5.424     0.000  'HW'     0.41
  Atom    3    H     6.088     5.120     0.000  'HW'     0.41

  Bond    1    2  Harmonic  4431.530     0.976
  Bond    3    1  Harmonic  4431.530     0.976

  Angle    3    1    2  Harmonic   317.566   107.134

  Isotopologue  'Deuterated'  HW=2

  Site  'COM'
    Origin  1  2  3
    OriginMassWeighted  True
    XAxis  1
    YAxis  3
  EndSite

EndSpecies

Water (with master terms)

Master
  Bond  'HW-OW'  Harmonic  4431.530     0.976
  Angle  'HW-OW-HW'  Harmonic   317.566   107.134
EndMaster

Species  'Water'
  Atom    1    O     5.139     5.968     0.000  'OW'    -0.82
  Atom    2    H     3.924     5.424     0.000  'HW'     0.41
  Atom    3    H     6.088     5.120     0.000  'HW'     0.41

  Bond    1    2  @HW-OW
  Bond    3    1  @HW-OW

  Angle    3    1    2  @HW-OW-HW

  ...

EndSpecies
Last modified November 20, 2024: Updating Developer Docs (#1545) (19274c2)