def test_polymer_chain_topologies(self):
topology_random = Topology.from_molecule(self.peo_polymer.molecule,
tol=0.1)
topology_linear = Topology.from_molecule(
self.peo_polymer_linear.molecule, tol=0.1)
self.assertNotEqual(topology_linear.bonds, topology_random.bonds)
self.assertNotEqual(topology_linear.angles, topology_random.angles)
self.assertNotEqual(topology_linear.dihedrals,
topology_random.dihedrals)
def setUp(self):
self.polymer_linear = Molecule.from_file(
os.path.join(test_dir, "polymer_linear.xyz"))
charges = [-0.1187, 0.0861, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.1187, 0.0861,
0.0861, 0.0861]
ff_map = ["C3", "H3", "H3", "H3", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C2", "H2",
"H2", "C2", "H2", "H2", "O", "C3", "H3", "H3", "H3"]
self.polymer_linear.add_site_property("charge", charges)
self.polymer_linear.add_site_property("ff_map", ff_map)
self.topology = Topology.from_molecule(self.polymer_linear)
self.forcefield = ForceField.from_file(
os.path.join(test_dir, "ffmap_data.yaml"))
box_size = [[0.0, 50],
[0.0, 50],
[0.0, 50]]
self.lammps_ff_data = LammpsForceFieldData.from_forcefield_and_topology(
[self.polymer_linear], [1], box_size, self.polymer_linear,
self.forcefield, [self.topology])
def test_atoms_data_with_ff_map(self):
natoms, natom_types, atomic_masses_dict = \
LammpsForceFieldData.get_basic_system_info(self.polymer_linear_ff_decorated)
topology = Topology.from_molecule(self.polymer_linear_ff_decorated,
ff_map="ff_map")
atoms_data, molid_to_atomid = LammpsForceFieldData.get_atoms_data(
[self.polymer_linear_ff_decorated], [1],
self.polymer_linear_ff_decorated, atomic_masses_dict, [topology])
for i, atom in enumerate(atoms_data):
key = self.polymer_linear_ff_decorated[i].ff_map
self.assertEqual(atom[2], atomic_masses_dict[key][0])
def setUpClass(cls):
polymer_chain = Molecule.from_file(os.path.join(test_dir, "polymer_chain.xyz"))
polymer_linear = Molecule.from_file(os.path.join(test_dir, "polymer_linear.xyz"))
cls.polymer_matrix = Molecule.from_file(os.path.join(test_dir, "polymer_matrix.xyz"))
charges = [-0.1187, 0.0861, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861,
0.0861, -0.0326, 0.0861, 0.0861, -0.2792, -0.1187, 0.0861,
0.0861, 0.0861]
polymer_linear.add_site_property("charge", charges)
topology = Topology.from_molecule(polymer_linear)
cls.polymer_linear_ff_decorated = Molecule.from_file(
os.path.join(test_dir,"polymer_linear.xyz"))
ff_map = ['C2', 'H3', 'H2', 'H3', 'O', 'C3', 'H2', 'H3', 'C2', 'H3',
'H2', 'O', 'C2', 'H3', 'H2', 'C3', 'H2', 'H3', 'O', 'C3',
'H2', 'H3', 'C2', 'H3', 'H2', 'O', 'C2', 'H3', 'H2', 'C3',
'H2', 'H3', 'O', 'C3', 'H2', 'H3', 'C2', 'H3', 'H2', 'O',
'C2', 'H3', 'H2', 'C3', 'H2', 'H3', 'O', 'C3', 'H2', 'H3', 'H2']
cls.polymer_linear_ff_decorated.add_site_property("ff_map", ff_map)
atoms = OrderedDict([("C", "C"), ("H", "H"), ("O", "O")])
bonds = OrderedDict([((u'C', u'O'), [1000, 1.4115]),
((u'C', u'H'), [1000, 1.1041]),
((u'C', u'C'), [1000, 1.5075])])
pairs = OrderedDict([((u'O', u'O'), [75844.8, 0.2461, 396.9]),
((u'H', u'H'), [2649.6, 0.2674, 27.22]),
((u'C', u'C'), [14976.0, 0.3236, 637.6])])
angles = OrderedDict([((u'C', u'C', u'H'), [42.9, 110.1]),
((u'H', u'C', u'H'), [38.5, 109.47]),
((u'H', u'C', u'O'), [56.0, 109.48]),
((u'C', u'C', u'O'), [86.0, 108.54]),
((u'C', u'O', u'C'), [74.5, 108.05])])
dihedrals = OrderedDict([((u'H', u'C', u'O', u'C'), [0.0, 0.0, -0.73, 0.0]),
((u'H', u'C', u'C', u'H'), [0.0, 0.0, 0.28, 0.0]),
((u'C', u'C', u'O', u'C'), [1.76, 0.67, 0.04, 0.0]),
((u'H', u'C', u'C', u'O'), [0.0, 0.0, 0.28, 0.0]),
((u'O', u'C', u'C', u'O'), [0.41, -2.1, -0.6, -0.82])])
forcefield = ForceField(atoms, bonds, angles, dihedrals=dihedrals, pairs=pairs)
cls.molecules = [polymer_chain] * 3
cls.mols_number = [7, 3, 1]
box_size = [[0.0, 50], [0.0, 50], [0.0, 50]]
cls.topologies = [topology] * len(cls.molecules)
cls.lammps_ff_data_1 = LammpsForceFieldData.from_forcefield_and_topology(
cls.molecules, cls.mols_number, box_size, cls.polymer_matrix,
forcefield, cls.topologies)
def test_atoms_data_with_ff_map(self):
natoms, natom_types, atomic_masses_dict = \
LammpsForceFieldData.get_basic_system_info(self.polymer_linear_ff_decorated)
topology = Topology.from_molecule(self.polymer_linear_ff_decorated,
ff_map="ff_map")
atoms_data, molid_to_atomid = LammpsForceFieldData.get_atoms_data(
[self.polymer_linear_ff_decorated], [1],
self.polymer_linear_ff_decorated, atomic_masses_dict,
[topology])
for i, atom in enumerate(atoms_data):
key = self.polymer_linear_ff_decorated[i].ff_map
self.assertEqual(atom[2], atomic_masses_dict[key][0])
def _get_gaussian_ff_top_single(self, filename=None):
"""
run antechamber using gaussian output file, then run parmchk
to generate missing force field parameters. Store and return
the force field and topology information in ff_mol.
Args:
filename: gaussian output file of the molecule
Returns:
Amberff namedtuple object that contains information on force field and
topology
"""
scratch = tempfile.gettempdir()
Amberff = namedtuple("Amberff", ["force_field", "topology"])
with ScratchDir(scratch,
copy_from_current_on_enter=True,
copy_to_current_on_exit=True) as d:
# self._convert_to_pdb(mol, 'mol.pdb')
# self.molname = filename.split('.')[0]
self._run_antechamber(filename)
self._run_parmchk()
# if antechamber can't find parameters go to gaff_example.dat
try:
top = Topology.from_file('mol.rtf')
except TopCorruptionException:
correct_corrupted_top_files('mol.rtf', 'gaff_data.txt')
top = Topology.from_file('mol.rtf')
try:
gff = ForceField.from_file('mol.frcmod')
except FFCorruptionException:
correct_corrupted_frcmod_files('ANTECHAMBER.FRCMOD',
'gaff_data.txt')
gff = ForceField.from_file('ANTECHAMBER.FRCMOD')
# gff.set_atom_mappings('ANTECHAMBER_AC.AC')
# gff.read_charges()
# decorate the molecule with the sire property "atomname"
#mol.add_site_property("atomname", (list(gff.atom_index.values())))
return Amberff(gff, top)
def get_packmol_wf(input_file, user_settings, constituent_molecules, packing_config, forcefield,
final_box_size, ff_site_property=None, tolerance=2.0, filetype="xyz",
control_params=None, lammps_cmd="lmp_serial", dump_filenames=None, db_file=None,
name="Packmol Lammps Wflow"):
"""
Returns workflow that uses Packmol to pack the constituent molecules into the given
configuration and then run lammps on the final packed molecule. Useful for
polymer studies.
Args:
input_file (str): path to lammps input(or template) file.
user_settings (dict): if the input_file is a tempalte file then this dict contains
the key value pairs for the template file.
constituent_molecules ([Molecules]): list of pymatgen Molecule objects
packing_config ([dict]): list of configuration dictionaries, one for each constituent molecule.
forcefield (ForceField): pymatgen.io.lammps.forcefield.ForceField object
final_box_size ([list]): list of list of low and high values for each dimension [[xlow, xhigh], ...]
ff_site_property (str): the name of the site property used for forcefield mapping
tolerance (float): packmol tolerance
filetype (str): packmol i/o file type.
control_params (dict): packmol control params
lammps_cmd (string): lammps command to run (skip the input file).
dump_filenames ([str]): list of dump file names
db_file (string): path to the db file.
name (str): workflow name
Returns:
Workflow
"""
packmol_output_file = "packed.{}".format(filetype)
mols_number = [mol_config["number"] for mol_config in packing_config]
topologies = []
for mol in constituent_molecules:
topologies.append(Topology.from_molecule(mol, ff_map=ff_site_property))
fw_packmol = PackmolFW(constituent_molecules, packing_config, tolerance=tolerance, filetype=filetype,
control_params=control_params, copy_to_current_on_exit=True,
output_file=packmol_output_file, site_property=ff_site_property),
fw_lammps = LammpsForceFieldFW(input_file, packmol_output_file, forcefield, final_box_size,
topologies=topologies, constituent_molecules=constituent_molecules,
mols_number=mols_number, user_settings=user_settings,
ff_site_property=ff_site_property, input_filename="lammps.in",
lammps_cmd=lammps_cmd, db_file=db_file, log_filename="lammps.log",
dump_filenames=dump_filenames, parents=[fw_packmol])
return Workflow([fw_packmol, fw_lammps], name=name)
def test_topology(self):
atoms = [['H', 'H'], ['H', 'H'], ['H', 'H'], ['H', 'H'], ['H', 'H'],
['C', 'C'], ['O', 'O'], ['C', 'C'], ['C', 'C'], ['O', 'O']]
bonds = [[11, 19, ('C', 'H')], [12, 13, ('O', 'C')],
[13, 20, ('C', 'H')], [13, 21, ('C', 'H')],
[19, 22, ('H', 'C')], [22, 23, ('C', 'O')],
[22, 29, ('C', 'H')], [23, 24, ('O', 'C')],
[24, 25, ('C', 'C')], [24, 30, ('C', 'H')]]
angles = [[8, 9, 10, ('C', 'O', 'C')], [9, 10, 11, ('O', 'C', 'C')],
[9, 10, 16, ('O', 'C', 'H')], [9, 10, 17, ('O', 'C', 'H')],
[11, 10, 16, ('C', 'C', 'H')], [11, 10, 17, ('C', 'C', 'H')],
[10, 11, 12, ('C', 'C', 'O')], [10, 11, 18, ('C', 'C', 'H')],
[10, 11, 19, ('C', 'C', 'H')], [16, 10, 17, ('H', 'C', 'H')]]
dihedrals = [[8, 9, 10, 16, ('C', 'O', 'C', 'H')],
[8, 9, 10, 17, ('C', 'O', 'C', 'H')],
[15, 8, 9, 10, ('H', 'C', 'O', 'C')],
[9, 10, 11, 12, ('O', 'C', 'C', 'O')],
[9, 10, 11, 18, ('O', 'C', 'C', 'H')],
[9, 10, 11, 19, ('O', 'C', 'C', 'H')],
[10, 11, 12, 13, ('C', 'C', 'O', 'C')],
[10, 11, 19, 22, ('C', 'C', 'H', 'C')],
[16, 10, 11, 12, ('H', 'C', 'C', 'O')],
[16, 10, 11, 18, ('H', 'C', 'C', 'H')]]
self.assertEqual(len(self.topology.atoms), 44)
self.assertEqual(len(self.topology.bonds), 50)
self.assertEqual(len(self.topology.angles), 123)
self.assertEqual(len(self.topology.dihedrals), 175)
self.assertEqual(self.topology.atoms[17:27], atoms)
self.assertEqual(self.topology.bonds[17:27], bonds)
self.assertEqual(self.topology.angles[17:27], angles)
self.assertEqual(self.topology.dihedrals[17:27], dihedrals)
monomer_charges = [
-0.118700, -0.279200, -0.032600, -0.118700, -0.279200, -0.032600,
0.086100, 0.086100, 0.086100, 0.086100, 0.086100, 0.086100,
0.086100, 0.086100
]
monomer_atoms = [['C', 'C'], ['O', 'O'], ['C', 'C'], ['C', 'C'],
['O', 'O'], ['C', 'C'], ['H', 'H'], ['H', 'H'],
['H', 'H'], ['H', 'H'], ['H', 'H'], ['H', 'H'],
['H', 'H'], ['H', 'H']]
self.monomer.add_site_property("charge", monomer_charges)
monomer_topology = Topology.from_molecule(self.monomer, tol=0.1)
self.assertEqual(monomer_topology.atoms, monomer_atoms)
self.assertEqual(monomer_topology.charges, monomer_charges)
def test_topology(self):
atoms = [['H', 'H'], ['H', 'H'], ['H', 'H'], ['H', 'H'], ['H', 'H'],
['C', 'C'], ['O', 'O'], ['C', 'C'], ['C', 'C'], ['O', 'O']]
bonds = [[11, 19, ('C', 'H')], [12, 13, ('O', 'C')],
[13, 20, ('C', 'H')], [13, 21, ('C', 'H')],
[19, 22, ('H', 'C')], [22, 23, ('C', 'O')],
[22, 29, ('C', 'H')], [23, 24, ('O', 'C')],
[24, 25, ('C', 'C')], [24, 30, ('C', 'H')]]
angles = [[8, 9, 10, ('C', 'O', 'C')], [9, 10, 11, ('O', 'C', 'C')],
[9, 10, 16, ('O', 'C', 'H')], [9, 10, 17, ('O', 'C', 'H')],
[11, 10, 16, ('C', 'C', 'H')], [11, 10, 17, ('C', 'C', 'H')],
[10, 11, 12, ('C', 'C', 'O')], [10, 11, 18, ('C', 'C', 'H')],
[10, 11, 19, ('C', 'C', 'H')], [16, 10, 17, ('H', 'C', 'H')]]
dihedrals = [[8, 9, 10, 16, ('C', 'O', 'C', 'H')],
[8, 9, 10, 17, ('C', 'O', 'C', 'H')],
[15, 8, 9, 10, ('H', 'C', 'O', 'C')],
[9, 10, 11, 12, ('O', 'C', 'C', 'O')],
[9, 10, 11, 18, ('O', 'C', 'C', 'H')],
[9, 10, 11, 19, ('O', 'C', 'C', 'H')],
[10, 11, 12, 13, ('C', 'C', 'O', 'C')],
[10, 11, 19, 22, ('C', 'C', 'H', 'C')],
[16, 10, 11, 12, ('H', 'C', 'C', 'O')],
[16, 10, 11, 18, ('H', 'C', 'C', 'H')]]
self.assertEqual(len(self.topology.atoms), 44)
self.assertEqual(len(self.topology.bonds), 50)
self.assertEqual(len(self.topology.angles), 123)
self.assertEqual(len(self.topology.dihedrals), 175)
self.assertEqual(self.topology.atoms[17:27], atoms)
self.assertEqual(self.topology.bonds[17:27], bonds)
self.assertEqual(self.topology.angles[17:27], angles)
self.assertEqual(self.topology.dihedrals[17:27], dihedrals)
monomer_charges = [-0.118700, -0.279200, -0.032600, -0.118700,
-0.279200, -0.032600, 0.086100, 0.086100,
0.086100, 0.086100,0.086100, 0.086100,
0.086100, 0.086100]
monomer_atoms = [['C', 'C'], ['O', 'O'], ['C', 'C'], ['C', 'C'],
['O', 'O'], ['C', 'C'], ['H', 'H'], ['H', 'H'],
['H', 'H'], ['H', 'H'], ['H', 'H'], ['H', 'H'],
['H', 'H'], ['H', 'H']]
self.monomer.add_site_property("charge", monomer_charges)
monomer_topology = Topology.from_molecule(self.monomer, tol=0.1)
self.assertEqual(monomer_topology.atoms, monomer_atoms)
self.assertEqual(monomer_topology.charges, monomer_charges)
def setUp(self):
# DMOE = Dimethoxyethane
self.dmoe = Molecule.from_file(os.path.join(test_dir, "dmoe.xyz"))
dmoe_charges = [-0.10, 0.09, 0.09, 0.09,
-0.34, -0.01, 0.09, 0.09,
-0.01, 0.09, 0.09, -0.34,
-0.10, 0.09, 0.09, 0.09]
self.dmoe.add_site_property("charge", dmoe_charges)
ff_map = ["C3", "H3", "H3", "H3",
"O", "C2", "H2", "H2",
"C2", "H2", "H2", "O",
"C3", "H3", "H3", "H3"]
self.dmoe.add_site_property("ff_map", ff_map)
self.topology = Topology.from_molecule(self.dmoe, ff_map="ff_map")
self.forcefield = ForceField.from_file(
os.path.join(test_dir, "ffmap_data.yaml"))
self.box_size = [[0.0, 10], [0.0, 10], [0.0, 10]]
self.lammps_ff_data = \
LammpsForceFieldData.from_forcefield_and_topology(
[self.dmoe], [1], self.box_size, self.dmoe, self.forcefield, [self.topology])
def setUpClass(cls):
atoms = OrderedDict([('hw', 'h'), ('ow', 'o')])
bonds = OrderedDict([((u'hw', u'ow'), [553.0, 0.957]),
((u'hw', u'hw'), [553.0, 1.513])])
angles = OrderedDict([((u'hw', u'ow', u'hw'), [0.0, 104.52])])
vdws = OrderedDict([(u'hw', [0.0, 0.0]), (u'ow', [1.7683, 0.1520])])
forcefield = ForceField(atoms, bonds, angles, vdws=vdws)
h2o_coords = [[9.626, 6.787, 12.673], [9.626, 8.420, 12.673],
[10.203, 7.604, 12.673]]
h2o = Molecule(["H", "H", "O"], h2o_coords)
# h2o, h-o, h-o, h=1, h=2, o=3
top_atoms = [['h', 'hw'], ['o', 'ow']]
top_bonds = [[1, 3, ('hw', 'ow')], [2, 3, ('hw', 'ow')]]
top_angles = [[1, 3, 2, ('hw', 'ow', 'hw')]]
topology = Topology(top_atoms, top_bonds, top_angles)
mols = [h2o]
mols_number = [1]
box_size = [[0.0, 10.0], [0.0, 10.0], [0.0, 10.0]]
molecule = h2o
topologies = [topology]
cls.lammps_ff_data = LammpsForceFieldData.from_forcefield_and_topology(
mols, mols_number, box_size, molecule, forcefield, topologies)
def setUpClass(cls):
polymer = Molecule.from_file(os.path.join(test_dir, "polymer.xyz"))
cls.topology = Topology.from_molecule(polymer, tol=0.1)
cls.forcefield = ForceField.from_file(os.path.join(test_dir,
"ff_data.yaml"))
def test_polymer_chain_topologies(self):
topology_random = Topology.from_molecule(self.peo_polymer.molecule, tol=0.1)
topology_linear = Topology.from_molecule(self.peo_polymer_linear.molecule, tol=0.1)
self.assertNotEqual(topology_linear.bonds, topology_random.bonds)
self.assertNotEqual(topology_linear.angles, topology_random.angles)
self.assertNotEqual(topology_linear.dihedrals, topology_random.dihedrals)
def setUpClass(cls):
polymer = Molecule.from_file(os.path.join(test_dir, "polymer.xyz"))
cls.monomer = Molecule.from_file(os.path.join(test_dir, "monomer.xyz"))
cls.topology = Topology.from_molecule(polymer, tol=0.1)
cls.forcefield = ForceField.from_file(
os.path.join(test_dir, "ff_data.yaml"))
def __init__(self,
input_file,
final_molecule,
forcefield,
box_size,
topologies=None,
constituent_molecules=None,
mols_number=None,
user_settings=None,
ff_site_property=None,
input_filename="lammps.in",
data_filename="lammps.data",
lammps_cmd="lammps",
db_file=None,
parents=None,
log_filename="log.lammps",
dump_filenames=None,
name="LammpsFFFW",
**kwargs):
"""
Write lammps input from forcefield and topology, run lammps, store results. Can be used
with RunPackmol firework.
Args:
input_file (str): path to lammps input(or template) file.
final_molecule (str/Molecule): either path to the moelcule of Molecule object.
forcefield (ForceField): pymatgen.io.lammps.force_field.ForceField object
box_size (list): list of list of low and high values for each dimension [[xlow, xhigh], ...]
topologies ([Topology]): list of pymatgen.io.lammps.topology.Topology objects, one for
each constituent molecule.
constituent_molecules ([Molecule]): list of Molecule objects that make up the final_molecule
mols_number (list): list of number of each constituent moelcule.
user_settings (dict):
ff_site_property (str): the site property used for forcefiled mapping
input_filename (str): name of the input file to be written
data_filename (str):name of the data file to be written
lammps_cmd (str): lammps command run (without the input file)
db_file (str): path to the db settings
parents (list): list of Fireworks
log_filename (str): lammps log file name
dump_filenames (str): list of dump files
name (str): firework name
**kwargs:
"""
user_settings = user_settings or {}
constituent_molecules = constituent_molecules or [final_molecule]
mols_number = mols_number or [1]
topologies = topologies or Topology.from_molecule(
final_molecule, ff_map=ff_site_property)
# one constituent molecule ==> no packmol usage.
tasks = [CopyPackmolOutputs(
calc_loc=True)] if mols_number != [1] else []
tasks.extend([
WriteInputFromForceFieldAndTopology(
input_file=input_file,
final_molecule_path=final_molecule,
constituent_molecules=constituent_molecules,
mols_number=mols_number,
forcefield=forcefield,
topologies=topologies,
input_filename=input_filename,
user_settings=user_settings,
ff_site_property=ff_site_property,
box_size=box_size),
RunLammpsDirect(lammps_cmd=lammps_cmd,
input_filename=input_filename),
LammpsToDB(input_filename=input_filename,
data_filename=data_filename,
log_filename=log_filename,
dump_filenames=dump_filenames,
db_file=db_file,
additional_fields={"task_label": name})
])
super(LammpsForceFieldFW, self).__init__(tasks,
parents=parents,
name=name,
**kwargs)
