def test_pair_coeffs(self):
natoms, natom_types, atomic_masses_dict = \
LammpsForceFieldData.get_basic_system_info(self.dmoe)
# atom_types = list(atomic_masses_dict.keys())
ans_atomtype_ids = [x[0] for x in atomic_masses_dict.values()]
pair_coeffs = self.lammps_ff_data.pair_coeffs
atomtype_ids = [x[0] for x in pair_coeffs]
self.assertEqual(ans_atomtype_ids, atomtype_ids)
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 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 test_system_info_with_ff_map(self):
natoms, natom_types, atomic_masses_dict = \
LammpsForceFieldData.get_basic_system_info(self.polymer_linear_ff_decorated)
ans_atom_masses_dict = OrderedDict([('H2', [1, 1.00794]),
('H3', [2, 1.00794]),
('C2', [3, 12.0107]),
('C3', [4, 12.0107]),
('O', [5, 15.9994])])
self.assertEqual(natoms, 51)
self.assertEqual(natom_types, 5)
self.assertEqual(atomic_masses_dict.keys(), ans_atom_masses_dict.keys())
for k, v in atomic_masses_dict.items():
self.assertEqual(ans_atom_masses_dict[k][1], v[1])
