Homopolymer

Synopsis

Linear chain of atoms of the same type.

A homopolymer is a chain of nAtom atoms with the same atomType (i.e., the same type id) connected by bonds of the same bondType.

If the code is compiled with angle potentials enabled (i.e., with SIMP_ANGLE defined), a Hompolymer may optionally have a bending potential between each sequence of three consecutive atoms. All angle potentials, if present, are characterized by the same angle potential type id, and are thus described by the same parameters.

If the code is compiled with dihedral potentials enabled (i.e., with SIMP_DIHEDRAL defined), a Hompolymer may optionally have a dihedral potential between each sequence of four consecutive atoms. All dihedral potentials, if present, are characterized by the same angle potential type id, and are thus described by the same parameters.

See also

Simp::Homopolymer

Parameters

Homopolymerhe parameter file format is:

Homopolymer{
  moleculeCapacity  int
  nAtom             int
  atomType          int
  bondType          int
  [hasAngles        bool]
  (angleType        int)
  [hasDihedrals     bool]
  (dihedralType     int)
}

Square brackets indicate optional parameters, while parentheses indicate parameters whose presence or absence is conditional on the presence or absence or values of earlier parameters, as discussed in more detail below.

Parameters related angle and dihedral potentials (the last four parameters in this format) are valid only if the code has been compiled with angle and dihedral potentials enabled, respectively.

When the code is compiled with the relevant parameters enabled, the boolean parameters hasAngles and hasDihedrals are optional, and are both taken to be false by default if absent. The conditional parameters angleType and dihedral type are required if any and only if the following conditions are satisfied:

• Parameter angleType is required if and only if (iff) parameter hasAngles is present in the file and set to true.
• Parameter dihedral Type is required if and only if (iff) parameter hasAngles is present and true.

The parameter meanings are as follows:

moleculeCapacity	number of molecules for which memory is allocated	required
nAtom	number of atoms (monomers) in chain	required
atomType	monomer type id of all monomers	required
bondType	bond type id of all bonds	required
hasAngles	true iff molecule has angle potentials	optional (default false)
angleType	angle type id of all angle potentials	conditional
hasDihedrals	true iff molecule has dihedral potentials	optional (default false)
dihedralType	dihedral type id of all dihedral potentials	conditional

A parameter block to describe a flexible chain, with no angle or dihedral potentials, needs to include only the first three parameters. A parameter block to describe a work like chain must also include hasAngles, which should be set true, and an angleType parameter. A parameter block to describe a homogeneous polymer with angle and dihedral potentials must include all 7 possible parameters.