def setUp(self):
with open(os.path.join(test_dir, 'test_toec_data.json')) as f:
self.data_dict = json.load(f)
self.strains = [Strain(sm) for sm in self.data_dict['strains']]
self.pk_stresses = [Stress(d) for d in self.data_dict['pk_stresses']]
self.c2 = self.data_dict["C2_raw"]
self.c3 = self.data_dict["C3_raw"]
self.exp = ElasticTensorExpansion.from_voigt([self.c2, self.c3])
self.cu = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.623),
["Cu"], [[0] * 3])
indices = [(0, 0), (0, 1), (3, 3)]
values = [167.8, 113.5, 74.5]
cu_c2 = ElasticTensor.from_values_indices(values,
indices,
structure=self.cu,
populate=True)
indices = [(0, 0, 0), (0, 0, 1), (0, 1, 2), (0, 3, 3), (0, 5, 5),
(3, 4, 5)]
values = [-1507., -965., -71., -7., -901., 45.]
cu_c3 = Tensor.from_values_indices(values,
indices,
structure=self.cu,
populate=True)
self.exp_cu = ElasticTensorExpansion([cu_c2, cu_c3])
cu_c4 = Tensor.from_voigt(self.data_dict["Cu_fourth_order"])
self.exp_cu_4 = ElasticTensorExpansion([cu_c2, cu_c3, cu_c4])
warnings.simplefilter("ignore")
def setUp(self):
with open(os.path.join(test_dir, 'test_toec_data.json')) as f:
self.data_dict = json.load(f)
self.strains = [Strain(sm) for sm in self.data_dict['strains']]
self.pk_stresses = [Stress(d) for d in self.data_dict['pk_stresses']]
self.c2 = self.data_dict["C2_raw"]
self.c3 = self.data_dict["C3_raw"]
self.exp = ElasticTensorExpansion.from_voigt([self.c2, self.c3])
self.cu = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.623),
["Cu"], [[0]*3])
indices = [(0, 0), (0, 1), (3, 3)]
values = [167.8, 113.5, 74.5]
cu_c2 = ElasticTensor.from_values_indices(values, indices, structure=self.cu,
populate=True)
indices = [(0, 0, 0), (0, 0, 1), (0, 1, 2),
(0, 3, 3), (0, 5, 5), (3, 4, 5)]
values = [-1507., -965., -71., -7., -901., 45.]
cu_c3 = Tensor.from_values_indices(values, indices, structure=self.cu,
populate=True)
self.exp_cu = ElasticTensorExpansion([cu_c2, cu_c3])
cu_c4 = Tensor.from_voigt(self.data_dict["Cu_fourth_order"])
self.exp_cu_4 = ElasticTensorExpansion([cu_c2, cu_c3, cu_c4])
warnings.simplefilter("ignore")
def test_init(self):
cijkl = Tensor.from_voigt(self.c2)
cijklmn = Tensor.from_voigt(self.c3)
exp = ElasticTensorExpansion([cijkl, cijklmn])
from_voigt = ElasticTensorExpansion.from_voigt([self.c2, self.c3])
self.assertEqual(exp.order, 3)
def process_item(self, item):
docs, material_dict = item
grouped = group_by_material_id(material_dict, docs, 'input_structure')
formula = docs[0]['pretty_formula']
if not grouped:
formula = Structure.from_dict(list(
material_dict.values())[0]).composition.reduced_formula
logger.debug("No material match for {}".format(formula))
# For now just do the most recent one that's not failed
# TODO: better sorting of docs
all_docs = []
for task_id, elastic_docs in grouped.items():
elastic_docs = sorted(elastic_docs,
key=lambda x:
(x['order'], x['state'], x['completed_at']))
grouped_by_order = {
k: list(v)
for k, v in groupby(elastic_docs, key=lambda x: x['order'])
}
soec_docs = grouped_by_order.get(2)
toec_docs = grouped_by_order.get(3)
if soec_docs:
final_doc = soec_docs[-1]
else:
final_doc = toec_docs[-1]
structure = Structure.from_dict(final_doc['optimized_structure'])
formula = structure.composition.reduced_formula
elements = [s.symbol for s in structure.composition.elements]
chemsys = '-'.join(elements)
# Issue warning if relaxed structure differs
warnings = final_doc.get('warnings') or []
opt = Structure.from_dict(final_doc['optimized_structure'])
init = Structure.from_dict(final_doc['input_structure'])
# TODO: are these the right params?
if not StructureMatcher().fit(init, opt):
warnings.append("Inequivalent optimization structure")
material_mag = CollinearMagneticStructureAnalyzer(
opt).ordering.value
material_mag = mag_types[material_mag]
if final_doc['magnetic_type'] != material_mag:
warnings.append("Elastic magnetic phase is {}".format(
final_doc['magnetic_type']))
warnings = warnings or None
# Filter for failure and warnings
k_vrh = final_doc['k_vrh']
if k_vrh < 0 or k_vrh > 600:
state = 'failed'
elif warnings is not None:
state = 'warning'
else:
state = 'successful'
final_doc.update({"warnings": warnings})
elastic_summary = {
'task_id': task_id,
'all_elastic_fits': elastic_docs,
'elasticity': final_doc,
'spacegroup': init.get_space_group_info()[0],
'magnetic_type': final_doc['magnetic_type'],
'pretty_formula': formula,
'chemsys': chemsys,
'elements': elements,
'last_updated': self.elasticity.lu_field,
'state': state
}
if toec_docs:
# TODO: this should be a bit more refined
final_toec_doc = deepcopy(toec_docs[-1])
et_exp = ElasticTensorExpansion.from_voigt(
final_toec_doc['elastic_tensor_expansion'])
symbol_dict = et_exp[1].zeroed(1e-2).get_symbol_dict()
final_toec_doc.update({"symbol_dict": symbol_dict})
set_(elastic_summary, "elasticity.third_order", final_toec_doc)
all_docs.append(jsanitize(elastic_summary))
# elastic_summary.update(final_doc)
return all_docs
def test_init(self):
cijkl = Tensor.from_voigt(self.c2)
cijklmn = Tensor.from_voigt(self.c3)
exp = ElasticTensorExpansion([cijkl, cijklmn])
from_voigt = ElasticTensorExpansion.from_voigt([self.c2, self.c3])
self.assertEqual(exp.order, 3)