def test_to_from_dict(self):
d = self.nwi.as_dict()
nwi = NwInput.from_dict(d)
self.assertIsInstance(nwi, NwInput)
#Ensure it is json-serializable.
json.dumps(d)
d = self.nwi_symm.as_dict()
nwi_symm = NwInput.from_dict(d)
self.assertIsInstance(nwi_symm, NwInput)
json.dumps(d)
def test_to_from_dict(self):
d = self.nwi.as_dict()
nwi = NwInput.from_dict(d)
self.assertIsInstance(nwi, NwInput)
# Ensure it is json-serializable.
json.dumps(d)
d = self.nwi_symm.as_dict()
nwi_symm = NwInput.from_dict(d)
self.assertIsInstance(nwi_symm, NwInput)
json.dumps(d)
def _prepare_pymatgen_dict(parameters,struct=None):
from pymatgen.io.nwchem import NwInput
import copy
par = copy.deepcopy(parameters)
add_cell = par.pop('add_cell',False)
if struct:
if add_cell:
par['geometry_options'].append(
'\n system crystal\n'
' lat_a {}\n lat_b {}\n lat_c {}\n'
' alpha {}\n beta {}\n gamma {}\n'
' end'.format(*(struct.cell_lengths+struct.cell_angles)))
if 'mol' not in par:
par['mol'] = {}
if 'sites' not in par['mol']:
par['mol']['sites'] = []
atoms = struct.get_ase()
for i,atom_type in enumerate(atoms.get_chemical_symbols()):
xyz = []
if add_cell:
xyz = atoms.get_scaled_positions()[i]
else:
xyz = atoms.get_positions()[i]
par['mol']['sites'].append({
'species': [ { 'element': atom_type, 'occu': 1 } ],
'xyz': xyz
})
return str(NwInput.from_dict(par))
