def enumerate_structures(self, spacegroups=None):
if 'icsd' in self.source:
# First take experimental structures
OI = OqmdInterface()
print('Enumerating experimental prototypes')
chemical_formulas = get_formulas(self.elements,
self.stoichiometries)
for chemical_formula in chemical_formulas:
OI.store_enumeration(filename=self.db_filename,
chemical_formula=chemical_formula,
max_atoms=self.max_atoms)
# Enumerate prototypes as a next step
# experimental structures will not be overwritten.
if 'prototypes' in self.source:
print('Enumerating Prototypes')
for stoichiometry in self.stoichiometries:
self.enumerate_prototypes(stoichiometry, spacegroups)
AE = AtomsEnumeration(self.elements, self.max_atoms, spacegroups)
print('Enumerating atoms')
AE.store_atom_enumeration(filename=self.db_filename,
multithread=False,
max_candidates=1)
def test_unique_prototypes(self):
O = OqmdInterface()
p = O.get_distinct_prototypes(chemical_formula='NiCuCN',
max_atoms=8)
assert(len(p) == 19)
print('{} distinct prototypes found'.format(len(p)))
def test_get_same_formula(self):
# Should get same formula if exists
O = OqmdInterface()
atoms_data = O.get_atoms_for_prototype(chemical_formula='TiO2',
proto_name='AB2_2_a_f_136')[0]
assert atoms_data['chemical_formula'] == atoms_data['original_formula']
def get_structures_from_protosearch(formulas,
source='icsd',
db_interface=None):
"""
Calls protosearch to get the hypothetical structures.
Args:
formulas ([str]): list of chemical formulas from which
to generate candidate structures
source (str): project name in OQMD to be used as source.
Defaults to ICSD.
db_interface (DbInterface): interface to OQMD database
by default uses the one pulled from data.matr.io
Returns:
(pandas.DataFrame) hypothetical pymatgen structures
generated and their unique ids from protosearch
TODO:
- For efficiency, n_max_atoms can be handled within OqmdInterface
"""
if db_interface is None:
cache_matrio_data("oqmd_ver3.db")
oqmd_db_path = os.path.join(CAMD_CACHE, "oqmd_ver3.db")
db_interface = OqmdInterface(oqmd_db_path)
dataframes = [
db_interface.create_proto_data_set(source=source,
chemical_formula=formula)
for formula in formulas
]
_structures = pd.concat(dataframes)
# Drop bad structures
_structures.dropna(axis=0, how='any', inplace=True)
# conversion to pymatgen structures
ase_adap = AseAtomsAdaptor()
pmg_structures = [
ase_adap.get_structure(_structures.iloc[i]['atoms'])
for i in range(len(_structures))
]
_structures['pmg_structures'] = pmg_structures
# The uuid below is probably an overkill. But want the strings
# to be unique. Sometimes in spaces with similar stoichiometries
# they may clash e.g. IrSb2O2 and Ir2SbO2 may end up producing
# the same string, despite different substitutions on same structure.
# We should figure out a way to get the right order from protosearch.
structure_uids = [
_structures.iloc[i]['proto_name'].replace('_', '-') + '-' +
'-'.join(pmg_structures[i].symbol_set) + '-' +
str(uuid.uuid4()).replace('-', '')[:6] for i in range(len(_structures))
]
_structures.index = structure_uids
return _structures
def test_create_proto_dataset(self):
O = OqmdInterface()
atoms_list = O.create_proto_data_set(chemical_formula='FeO6',
max_atoms=7)
assert len(atoms_list) == 5
for atoms in atoms_list["atoms"][:5]:
assert atoms.get_number_of_atoms() == 7
assert atoms.get_chemical_symbols().count('Fe') == 1
assert atoms.get_chemical_symbols().count('O') == 6
def test_substitute_atoms(self):
O = OqmdInterface()
atoms_data = O.get_atoms_for_prototype(chemical_formula='TiMoO2',
proto_name='ABC2_2_a_c_f_194')[0]
atoms = atoms_data['atoms']
atoms_list = O.substitute_atoms(
atoms, new_symbols=['Nb', 'V', 'O', 'O'])
assert len(atoms_list) == 2
def test_unique(self):
# AB == BA - one structure
O = OqmdInterface()
atoms_data = O.get_atoms_for_prototype(chemical_formula='TiMo',
proto_name='AB_4_ab_ab_186')
atoms = [a['atoms'] for a in atoms_data]
assert len(atoms) == 1
# ABC3 != BAC3 - two structures
atoms_data = O.get_atoms_for_prototype(chemical_formula='TiMoO3',
proto_name='ABC3_1_a_a_b_160')
atoms = [a['atoms'] for a in atoms_data]
assert len(atoms) == 2
def get_structures_from_protosearch(formulas,
source="icsd",
db_interface=None):
"""
Calls protosearch to get the hypothetical structures.
Args:
formulas ([str]): list of chemical formulas from which
to generate candidate structures
source (str): project name in OQMD to be used as source.
Defaults to ICSD.
db_interface (DbInterface): interface to OQMD database
by default uses the one pulled from data.matr.io
Returns:
(pandas.DataFrame) hypothetical pymatgen structures
generated and their unique ids from protosearch
"""
if db_interface is None:
db_interface = OqmdInterface(source)
dataframes = [
db_interface.create_proto_data_set(chemical_formula=formula)
for formula in formulas
]
_structures = pd.concat(dataframes)
# Drop bad structures
_structures.dropna(axis=0, how="any", inplace=True)
# conversion to pymatgen structures
ase_adap = AseAtomsAdaptor()
pmg_structures = [
ase_adap.get_structure(_structures.iloc[i]["atoms"])
for i in range(len(_structures))
]
_structures["structure"] = pmg_structures
# This is for compatibility with Mc1, which doesn't allow
# underscores
structure_uids = [
_structures.iloc[i]["structure_name"].replace('_', '-')
for i in range(len(_structures))
]
_structures.index = structure_uids
return _structures
def test_store_enumeration(self):
O = OqmdInterface()
O.store_enumeration(filename='test.db',
chemical_formula='FeO6',
max_atoms=7)
def test_unique_prototypes2(self):
O = OqmdInterface()
p = O.get_distinct_prototypes(chemical_formula='TiO2')
print(len(p))