Synopsis

A species of molecule (base class).

A Species object contains a description of the molecular structure of a species of molecule within a mixture, as well the number of molecules of that species for which space is allocated in the simulation. The class Species is a base class that is flexible enough to describe any molecule. Subclasses of Species (e.g., Homopolymer or Diblock) describe more specific types of molecule.

See also: Simp::Species

Parameters

The default parameter file format for an instance of the Species base class is:

Species{
  moleculeCapcacity  int
  nAtom              int
  atomTypeIds        Array int[nAtom]
  [nBond              int]
  (speciesBonds      Array SpeciesGroup<2>[nBond])
  [nAngle             int]
  (speciesAngles     Array SpeciesGroup<3>[nAngle])
  [nDihedral          int]
  (speciesDihedrals  Array SpeciesGroup<4>[nAngle])
}

Square brackets indicate optional paramters. The parameters nBond, nAngle, and nDihedral are all optional parameters, as indicated by the use of square brackets. These parameters are each set to zero by default (i.e., if not present), to indicate that there are no bonds, angles, or dihedrals, respectively. Parentheses indicate conditional parameters, which are required if and only if one an associated optional parameters is present and is assigned a positive value. Specifically:

Parameter speciesBonds is required if and only if (iff) nBond > 0.
Parameter speciesAngles is required if and only if (iff) nAngle > 0.
Parameter speciesDihedrals is required if and only if (iff) nDihedrals > 0.

Parameter atomTypeIds is an array of integers, formatted one per line, that give the type ids of all of the atoms in a molecule. Parameter speciesBonds, if present, is an array of nBond SpeciesGroup<2> objects, with one such object per line. The text format for each SpeciesGroup<2> object contains integer identifiers for the two atoms in a bond followed by a corresponding bond type id, separated by spaces. Similarly, the parameter speciesAngles, if present, is an an array of nAngle SpeciesGroups<3> objects, one per line, each of which describes an angle group of three atoms in a file format containing the three atom ids for the atoms in the group followed by an angle type id.

For example, the following parameter file block describes a species of linear trimer molecules containing three atoms (atom ids 0,1, and 2) connected by two bonds (between atoms 0 and 1 and between atoms 1 and 2) and a single angle group involving all three atoms, but not dihedral group.

Species{
   moleculeCapacity     200
   nAtom                  2
   nBond                  2
   nAngle                 1
   nDihedral              0
   atomTypeIds            1
                          2
                          1
   speciesBonds           0    1    0
                          1    2    0
   speciesAngles          0    1    2    1
}

In this species, atoms 0 and 2 are of atom type 1, while atom 2 is of atom type 2. Both bonds are of bond type 0, and the single angle group is of angle type 1. No speciesDihedral array is shown because nDihedral = 0.

The parameter meanings are as follows:

moleculeCapacity	number of molecules for which memory is allocated	required
nAtom	number of atoms per molecule	required
nBond	number of bonds per molecule	required
nAngle	number of covalent angle groups per molecule	required
nDihedral	number of dihedral groups per molecule	required
atomTypeIds	array of monomer type ids for specific atoms	required
speciesBonds	array of SpeciesGroup<2> bond descriptors	conditional
speciesAngles	array of SpeciesGroup<3> angle group descriptors	conditional
speciesDihedrals	array of SpeciesGroup<4> dihedral group descriptors	conditional

Each array of SpeciesGroup<N> objects must be present if and only if the number of groups of the specified type (i.e,. the value of nBond, nAngle, or nDihedral) is greater than zero.

The text representation for a single SpeciesGroup<N> object is also described here.