def test_compress():
top = Topology.open(cwd + '/files/10-H2O-5-C3H6.lmp', improper_center=3)
molecules = top.molecules
for mol in molecules[4:]:
for atom in mol.atoms:
atom.charge *= 2
top = Topology.open(cwd + '/files/Im11.zmat')
molecules += top.molecules
top = Topology.open(cwd + '/files/10-H2O-5-C3H6.lmp', improper_center=3)
molecules += top.molecules
top = Topology.open(cwd + '/files/Im11.zmat')
molecules += top.molecules
top = Topology()
top.update_molecules(molecules)
mols_unique = top.get_unique_molecules()
for mol, count in mols_unique.items():
print(str(mol), count)
assert list(mols_unique.values()) == [4, 6, 5, 1, 10, 5, 1]
if args.ljscale is not None:
scaler = PaduaLJScaler(args.ljscale)
scaler.scale(ff)
if args.scaleeps != 1.0 or args.scalesig != 1.0:
for vdw in list(ff.vdw_terms.values()) + list(ff.pairwise_vdw_terms.values()):
if vdw.type1 in args.scaleignoreatom or vdw.type2 in args.scaleignoreatom:
continue
if args.scaleeps != 1.0:
vdw.epsilon *= args.scaleeps
vdw.comments.append('eps*%.3f' % args.scaleeps)
if args.scalesig != 1.0:
vdw.sigma *= args.scalesig
vdw.comments.append('sig*%.3f' % args.scalesig)
mol_count = top.get_unique_molecules(deepcopy=False)
for mol in mol_count.keys():
mol: Molecule
logger.info('Processing %s ...' % str(mol))
if typer is not None:
try:
typer.type_molecule(mol)
except TypingNotSupportedError as e:
pass
except TypingUndefinedError as e:
xyz = '_typing_' + mol.name + '.xyz'
Topology([mol]).write(xyz)
logger.error('Failed typing %s: %s. Check %s' % (mol, str(e), xyz))
sys.exit(1)
if mol.n_atom > 1 and mol.n_bond == 0:
