def _generate(fout):
f_mol = '{}/molecules.json'.format(ROOT)
box = 50
molecules = MoleculeFactory(_parse_molecules(f_mol), box=box).molecules
system = System(50, molecules=molecules)
config = ConfigFile(system, comment='Statistical Star Co-Polyelectrolyte in Neutral system')
config.write(fout)
def _generate(fout):
f_mol = '{}/molecules.json'.format(ROOT)
box = 50
molecules = MoleculeFactory(_parse_molecules(f_mol), box=box).molecules
system = System(box, molecules=molecules)
config = ConfigFile(system, comment='Real condensation system')
config.write(fout)
def _generate(fout):
f_mol = '{}/molecules.json'.format(ROOT)
box = 50
molecules = MoleculeFactory(_parse_molecules(f_mol), box=box).molecules
system = System(box, molecules=molecules)
config = ConfigFile(system, comment='Many diblock Star CoPolyelectrolytes in Neutral system')
config.write(fout)
def _generate(fout):
f_mol = '{}/molecules.json'.format(ROOT)
box = 50
lpe, salt = MoleculeFactory(_parse_molecules(f_mol), box=box).molecules
system = System(50, molecules=[lpe, salt])
system.neutralise(salt)
config = ConfigFile(system,
comment='Linear Polyelectrolyte in Neutral system')
config.write(fout)
def test_configuration(delete: bool = True):
item = {'molecule': 'dna', 'lam': 10}
molecule = LinearPolyelectrolyte(item)
system = System(10., molecules=[molecule])
# try all styles except dihedral
for style in STYLES:
if style == 'dihedral': continue
config_file = ConfigFile(system, style=style)
OUT = FOLDER / f'lammps.{style}.conf'
OUT.unlink(missing_ok=True)
config_file.write(OUT)
if delete:
OUT.unlink()
return
def _generate(fout):
f_mol = '{}/molecules.json'.format(ROOT)
molecules = MoleculeFactory(_parse_molecules(f_mol)).molecules
system = System(50, molecules=molecules)
config = ConfigFile(system, comment='Neutral Linear Polymer')
config.write(fout)