Molecule Polymer Linear (continuous)

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 continuous (as documented here) or discrete.

  • alpha (float) - Relative length of molecule. \(\alpha = N / N_{ref}\)

  • ds (float) - Contour step size

  • 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.

  • 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.

Example (python):

fts.add_molecule(alpha=1.0,ds=0.01,nblocks=2,block_fractions=[0.5, 0.5],block_species=['A', 'B'],type='PolymerLinear',chain_type='continuous',volume_frac=1.0)

Example (json):

"molecules": {
  "molecule0": {
    "alpha": 1.0,
    "ds": 0.01,
    "nblocks": 2,
    "block_fractions": [0.5, 0.5],
    "block_species": ["A","B"],
    "type": "PolymerLinear",
    "chain_type": "continuous",
    "volume_frac": 1.0
  },
  "nmolecule": 1
},

Molecule Polymer Continuous Formalism

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