Molecule Polymer Linear (discrete)

Arguments:

  • nmolecule (int) - Number of molecules in simulation

  • moleculeX (json object) - Information about moleculeX where X ranges from 0 to nmolecule-1. In each moleculeX object the following must be specified:

    • type (string) - Type of molecule. Here PolymerLinear

    • label (string) - label for this molecule, defaults to molX

    • chain_type (string) - Type of chain statistics. Either discrete (as documented here) or continuous.

    • nbeads (int) - Number of beads in discrete chain

    • volume_frac (float) - Volume fraction of moleculeX in the simulation. Must be 0-1.

    • ncopies (float) - number of copies of moleculeX in the simulation. Note that either volume_frac or ncopies can be specified, not both.

    • There are two options to initialize the polymer sequence

      1. Initialize by block

      • nblocks (int) - Number of blocks in polymer

      • block_species (list string) - the species of each block. Length is nblocks. Must corresponds to a label entry in Species.

      • block_fractions (list float) - fractional length of each block. Length is nblocks, must sum to 1.

      1. Initialize by monomer sequence

      • monomer_sequence (string) - String of length nbeads where each letter corresponds to a Species label. To use this option, each Species label must be a single character.

Example (python):

# a block polymer
fts.add_molecule(nbeads=100,nblocks=2,block_fractions=[0.5, 0.5],block_species=['A', 'B'],type='PolymerLinear',chain_type='discrete',volume_frac=1.0)

# sequence defined polymer
seq = "AABAAAAAABAAABAABBAAABABBABBABAABBABBBBBBBBBBBBAAA"
fts.add_molecule(nbeads=50,type='PolymerLinear',chain_type='discrete',volume_frac=1.0,monomer_sequence=sv20)

Example (json):

# block polmer
"molecules": {
  "molecule0": {
    "nbeads": 100,
    "nblocks": 2,
    "block_fractions": [0.5, 0.5],
    "block_species": ["A","B"],
    "type": "PolymerLinear",
    "chain_type": "discrete",
    "volume_frac": 1.0
  },
  "nmolecule": 1
},

# sequence defined polymer
"molecules": {
  "molecule0": {
  "chain_type": "discrete",
  "monomer_sequence": "AABAAAAAABAAABAABBAAABABBABBABAABBABBBBBBBBBBBBAAA",
  "nbeads": 50,
  "type": "PolymerLinear",
  "volume_frac": 1.0
  },
  "nmolecule": 1
},

Molecule Polymer Discrete Formalism

TODO should consolidate. For now, see Continuous vs Discrete Chains.