def test_parse_formula(self):
elements_dict = {
'Ca': 1,
'Ti': 1,
'O': 3,
}
self.assertEqual(pmutt.parse_formula('CaTiO3'), elements_dict)
elements_dict = {
'H': 1,
'F': 1,
}
self.assertEqual(pmutt.parse_formula('HF'), elements_dict)
elements_dict = {
'H': 8,
'C': 3,
}
self.assertEqual(pmutt.parse_formula('CH3CH2CH3'), elements_dict)
def set_formula(formula, output_structure):
"""Parses stoichiometric formula unit and assigns to output_structure
Parameters
----------
formula : str
Stoichiometric formula unit. e.g. H2O
Note that an element cannot be specified multiple times.
e.g. CH3OH is not supported
output_structure : dict
Structure to assign value. Will assign to
output_structure['elements']
"""
elements = parse_formula(formula=formula)
output_structure['elements'] = elements
def __init__(self,
name=None,
trans_model=EmptyMode(),
vib_model=EmptyMode(),
rot_model=EmptyMode(),
elec_model=EmptyMode(),
nucl_model=EmptyMode(),
misc_models=None,
elements=None,
references=None,
smiles=None,
notes=None,
**kwargs):
self.name = name
self.smiles = smiles
self.notes = notes
self.references = references
self.trans_model = _check_obj(trans_model, **kwargs)
self.vib_model = _check_obj(vib_model, **kwargs)
self.rot_model = _check_obj(rot_model, **kwargs)
self.elec_model = _check_obj(elec_model, **kwargs)
self.nucl_model = _check_obj(nucl_model, **kwargs)
# Assign elements from Atoms if necessary
if elements is None:
try:
elements = parse_formula( \
kwargs['atoms'].get_chemical_formula('hill'))
except KeyError:
pass
self.elements = elements
# Assign misc models
# TODO misc models can not be initialized by passing the class
# because all the models will have the same attributes. Figure out
# a way to pass them. Perhaps have a dictionary that contains the
# attributes separated by species
self.misc_models = _check_iterable_attr(misc_models)