Molecule¶

class openfts.molecule.Bead(label=None, bead_species=None, volume_frac=None, ncopies=None)¶

Molecule Bead

Parameters:

label (string) – label for this molecule, defaults to molX
bead_species (string) – Species type of bead
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.

Example (python):

fts.add_molecule(type='Bead',bead_species='A',volume_frac=0.5)

Example (json):

"molecule0": {
  "bead_species": "A",
  "type": "Bead",
  "volume_frac": 0.5
},

class openfts.molecule.PolymerLinearContinuous(label=None, volume_frac=None, ncopies=None, nblocks=None, block_species=None, block_fractions=None, alpha=None, ds=None)¶

Molecule Polymer Linear (continuous)

Parameters:

label (string) – label for this molecule
alpha (float) – Relative length of molecule. \(\alpha = N / N_{ref}\)
ds (float) – Contour step size
volume_frac (float) – Volume fraction of molecule in the simulation. Must be 0-1.
ncopies (float) – number of copies of molecule 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.molecules.append(openfts.molecule.PolymerLinearContinuous(alpha=1.0,ds=0.01,nblocks=2,block_fractions=[0.5, 0.5],block_species=['A', 'B'],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
},

class openfts.molecule.PolymerLinearDiscrete(label=None, volume_frac=None, ncopies=None, nblocks=None, block_species=None, block_fractions=None, nbeads=None, monomer_sequence=None)¶

Molecule Polymer Linear (discrete)

Parameters:

label (string) – label for this molecule
nbeads (int) – Number of beads in discrete chain
volume_frac (float) – Volume fraction of molecule in the simulation. Must be 0-1.
ncopies (float) – number of copies of molecule in the simulation. Note that either volume_frac or ncopies can be specified, not both.

There are two options to initialize the polymer sequence

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.
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
},

class openfts.molecule.PolymerCombContinuous(label=None, volume_frac=None, backbone=None, **kwargs)¶

Molecule Polymer Comb (continuous)

Parameters:

label (string) – label for this molecule
volume_frac (float) – Volume fraction of moleculeX in the simulation. Must be 0-1.
backbone (json object or dict) – Backbone chain information. Required arguments depend on chain_type specified earlier. For example, if chain_type=discrete the arguments nbeads, nblocks, block_species, block_fractions (or monomer_sequence) must be specified. See molecule.PolymerLinearContinuous and molecule.PolymerLinearDiscrete for required arguments.
sidechainX (json object) – Sidechain information of sidechainX where X starts at 1. In each sidechainX object, all information of the corresponding chain_type must be specified (see backbone argument above). Additionally, the following argument must also be specified:
graft_locations (list int) – the indicies of backbone sites that this sidechain will be grafted to. Indexing starts at 0.

(python):

fts.molecules.append(openfts.molecule.PolymerCombContinuous(volume_frac=1.0,
                     backbone=dict(ds=0.01,alpha=0.6,nblocks=1,block_fractions=[1.0],block_species=['A']),
                     sidechain1=dict(ds=0.01,alpha=0.2,nblocks=1,block_fractions=[1.0],block_species=['A'],
                     graft_locations=[0,60])))

json:

"molecules": {
  "molecule0": {
    "backbone": {
      "alpha": 0.6,
      "block_fractions": [
        1.0
      ],
      "block_species": [
        "A"
      ],
      "ds": 0.01,
      "nblocks": 1
    },
    "chain_type": "continuous",
    "sidechain1": {
      "alpha": 0.2,
      "block_fractions": [
        1.0
      ],
      "block_species": [
        "A"
      ],
      "ds": 0.01,
      "graft_locations": [
        0,
        60
      ],
      "nblocks": 1
    },
    "type": "PolymerComb",
    "volume_frac": 1.0
  },
  ...
},

class openfts.molecule.PolymerCombDiscrete(label=None, volume_frac=None, backbone=None, **kwargs)¶

Molecule Polymer Comb (discrete)

Parameters:

label (string) – label for this molecule
volume_frac (float) – Volume fraction of moleculeX in the simulation. Must be 0-1.
backbone (json object or dict) – Backbone chain information. Required arguments depend on chain_type specified earlier. For example, if chain_type=discrete the arguments nbeads, nblocks, block_species, block_fractions (or monomer_sequence) must be specified. See molecule.PolymerLinearContinuous and molecule.PolymerLinearDiscrete for required arguments.
sidechainX (json object) – Sidechain information of sidechainX where X starts at 1. In each sidechainX object, all information of the corresponding chain_type must be specified (see backbone argument above). Additionally, the following argument must also be specified:
graft_locations (list int) – the indicies of backbone sites that this sidechain will be grafted to. Indexing starts at 0.

Example (python):

# this creates an A-B bottlebrush
fA = 0.5  # fraction of A beads
N_BB = 50 # backbone length
N_SC = 10 # sidechain length
B_graft_start = int(fA*N_BB)

fts.add_molecule(type='PolymerComb',\
    chain_type='discrete',\
    backbone=dict(nbeads=N_BB,nblocks=2,block_fractions=[fA, 1-fA],block_species=['A', 'B']),\
    sidechain1=dict(nbeads=N_SC,nblocks=1,block_fractions=[1.0],block_species=['A'], graft_locations=list(range(0,B_graft_start))),\
    sidechain2=dict(nbeads=N_SC,nblocks=1,block_fractions=[1.0],block_species=['B'], graft_locations=list(range(B_graft_start,N_BB))),\
    volume_frac=1.0)

Example (json):

"molecules": {
  "molecule0": {
    "backbone": {
      "block_fractions": [0.5,0.5],
      "block_species": ["A","B"],
      "nbeads": 50,
      "nblocks": 2
    },
    "chain_type": "discrete",
    "sidechain1": {
      "block_fractions": [1.0],
      "block_species": ["A"],
      "graft_locations": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24],
      "nbeads": 10,
      "nblocks": 1
    },
    "sidechain2": {
      "block_fractions": [1.0],
      "block_species": ["B"],
      "graft_locations": [25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49],
      "nbeads": 10,
      "nblocks": 1
    },
    "type": "PolymerComb",
    "volume_frac": 1.0
  },
  "nmolecule": 1
},