def run_task(self, fw_spec):
lammps_input_set = self["lammps_input_set"]
input_filename = self["input_filename"]
data_filename = self.get("data_filename", None)
if isinstance(lammps_input_set.lammps_data, dict):
lammps_input_set.lammps_data = LammpsData.from_dict(
lammps_input_set.lammps_data)
lammps_input_set.write_input(input_filename, data_filename)
def writeLammpsStruct(struct, args):
from pymatgen.io.lammps.data import LammpsData
from pymatgen import Element
from json import dumps, loads
# Get the LammpsData object
lammps_dict = LammpsData.from_structure(struct,
atom_style="atomic").as_dict()
# Relabel the atom types in the LammpsData object
masses = {
"columns": ["mass"],
"index": [val for val in range(1,
len(args["atom_mapping"]) + 1)]
}
mass_data = [None] * len(args["atom_mapping"])
for key in args["atom_mapping"].keys():
mass_data[args["atom_mapping"][key]] = [Element(key).atomic_mass]
masses["data"] = mass_data
lammps_dict["masses"] = dumps(masses)
atoms = loads(lammps_dict["atoms"])
try:
for i in range(len(atoms["data"])):
atoms["data"][i][0] = args["atom_mapping"][
struct[i].species_string] + 1
except KeyError as e:
raise Exception(
"{} Missing From atom_mapping Keyword from Input File".format(
e.args[0]))
# Move the correct labels back to the LammpsData object
lammps_dict["atoms"] = dumps(atoms)
LammpsData.from_dict(lammps_dict).write_file("atom.data",
distance=16,
velocity=16,
charge=16)
return
def test_json_dict(self):
encoded = json.dumps(self.ethane.as_dict())
decoded = json.loads(encoded)
c2h6 = LammpsData.from_dict(decoded)
pd.testing.assert_frame_equal(c2h6.masses, self.ethane.masses)
pd.testing.assert_frame_equal(c2h6.atoms, self.ethane.atoms)
ff = self.ethane.force_field
key, target_df = random.sample(ff.items(), 1)[0]
self.assertIsNone(
pd.testing.assert_frame_equal(c2h6.force_field[key], target_df, check_dtype=False),
key,
)
topo = self.ethane.topology
key, target_df = random.sample(topo.items(), 1)[0]
self.assertIsNone(pd.testing.assert_frame_equal(c2h6.topology[key], target_df), key)
def test_json_dict(self):
encoded = json.dumps(self.ethane.as_dict())
decoded = json.loads(encoded)
c2h6 = LammpsData.from_dict(decoded)
pd.testing.assert_frame_equal(c2h6.masses, self.ethane.masses)
pd.testing.assert_frame_equal(c2h6.atoms, self.ethane.atoms)
ff = self.ethane.force_field
key, target_df = random.sample(ff.items(), 1)[0]
self.assertIsNone(
pd.testing.assert_frame_equal(c2h6.force_field[key], target_df,
check_dtype=False),
key
)
topo = self.ethane.topology
key, target_df = random.sample(topo.items(), 1)[0]
self.assertIsNone(
pd.testing.assert_frame_equal(c2h6.topology[key], target_df),
key
)