def create_cif_data(cls):
"""Create CifData object."""
with tempfile.NamedTemporaryFile(mode='w+') as fhandle:
filename = fhandle.name
fhandle.write(cls.valid_sample_cif_str)
fhandle.flush()
a_cif = CifData(file=filename,
source={
'version': '1234',
'db_name': 'COD',
'id': '0000001'
})
a_cif.store()
g_ne = Group(label='non_empty_group')
g_ne.store()
g_ne.add_nodes(a_cif)
g_e = Group(label='empty_group')
g_e.store()
cls.cif = a_cif
return {
DummyVerdiDataListable.NODE_ID_STR: a_cif.id,
DummyVerdiDataListable.NON_EMPTY_GROUP_ID_STR: g_ne.id,
DummyVerdiDataListable.EMPTY_GROUP_ID_STR: g_e.id
}
def get_cif_node(self, store=False, parse_policy='lazy'):
"""
Creates a CIF node, that can be used in AiiDA workflow.
:return: :py:class:`aiida.orm.nodes.data.cif.CifData` object
"""
from aiida.orm.nodes.data.cif import CifData
import tempfile
cifnode = None
with tempfile.NamedTemporaryFile(mode='w+') as f:
f.write(self.cif)
f.flush()
cifnode = CifData(file=f.name,
source=self.source,
parse_policy=parse_policy)
# Maintaining backwards-compatibility. Parameter 'store' should
# be removed in the future, as the new node can be stored later.
if store:
cifnode.store()
return cifnode
def test_extract_structure_info(clear_database_aiida_fleur, generate_structure,
generate_work_chain_node, fixture_localhost):
"""
I do not test 'extras' here due to some kind of bug
"""
from aiida_fleur.tools.data_handling import extract_structure_info
from aiida_fleur.tools.common_aiida import create_group
from aiida_fleur.tools.read_cif_folder import wf_struc_from_cif
from aiida.orm import CalcFunctionNode, load_node, CifData
from aiida.common import LinkType
pks = []
uuids = []
for i in range(3):
structure_bulk = generate_structure()
structure_bulk.append_atom(position=(i, 0., -1.99285), symbols='Se')
structure_bulk.store()
pks.append(structure_bulk.pk)
uuids.append(structure_bulk.uuid)
cif_data = CifData(file=TEST_CIF)
cif_data.store()
cif_structure = wf_struc_from_cif(cif_data)
print(cif_structure.get_incoming().all())
# create CalcFunction having StructureData input
calc_function = CalcFunctionNode()
calc_function.set_attribute('process_label', 'test_label')
calc_function.add_incoming(structure_bulk,
link_type=LinkType.INPUT_CALC,
link_label='test_calcfundtion')
calc_function.store()
# create WorkChainNode scf having StructureData input
scf_wc = generate_work_chain_node(computer=fixture_localhost,
entry_point_name='aiida_fleur.scf',
inputs={'structure': load_node(pks[1])})
scf_wc.store()
scf_wc.set_attribute('process_label', 'fleur_scf_wc')
# create a group
group = create_group(name='test_group',
nodes=pks[:2],
description='test_description')
result = extract_structure_info(keys=[
'uuid', 'formula', 'pk', 'symmetry', 'pbc', 'volume', 'total_energy',
'child_nodes', 'natoms', 'group', 'label', 'description', 'cif_file',
'cif_number', 'cif_uuid', 'cif_ref', 'calcfunctions', 'band', 'dos',
'eos', 'init_cls', 'corehole', 'primitive', 'cell', 'scf'
])
# print(result)
# assert 0
correct_result = [
sorted({
'formula': 'AlB2',
'pk': cif_structure.pk,
'uuid': cif_structure.uuid,
'natoms': 3,
'cell':
'[[3.009, 0.0, 0.0], [-1.5045, 2.6058704399874, 0.0], [0.0, 0.0, 3.262]]',
'pbc': '(True, True, True)',
'label': '',
'description': '',
# 'extras': "{{'_aiida_hash': {0}}}".format(cif_structure.get_hash()),
'symmetry': 'Amm2 (38)',
'volume': 25.57755127009385,
'child_nodes': 0,
'primitive': False,
'cif_file': ['AlB.cif', cif_data.uuid],
'group': [],
'scf': [],
'band': [],
'dos': [],
'eos': [],
'init_cls': [],
'corehole': [],
'calcfunctions': [[], []],
}),
sorted({
'formula': 'SeSi2',
'pk': pks[2],
'uuid': uuids[2],
'natoms': 3,
'cell':
'[[2.715, 2.715, 0.0], [2.715, 0.0, 2.715], [0.0, 2.715, 2.715]]',
'pbc': '(True, True, True)',
'label': '',
'description': '',
# 'extras': "{{'_aiida_hash': {0}}}".format(load_node(pks[2]).get_hash()),
'symmetry': 'P1 (1)',
'volume': 40.02575174999999,
'child_nodes': 1,
'primitive': False,
'cif_file': ['', ''],
'group': [],
'scf': [],
'band': [],
'dos': [],
'eos': [],
'init_cls': [],
'corehole': [],
'calcfunctions': [[calc_function.uuid], ['test_label']],
}),
sorted({
'formula': 'SeSi2',
'pk': pks[1],
'uuid': uuids[1],
'natoms': 3,
'cell':
'[[2.715, 2.715, 0.0], [2.715, 0.0, 2.715], [0.0, 2.715, 2.715]]',
'pbc': '(True, True, True)',
'label': '',
'description': '',
# 'extras': "{{'_aiida_hash': {0}}}".format(load_node(pks[1]).get_hash()),
'symmetry': 'P1 (1)',
'volume': 40.02575174999999,
'child_nodes': 1,
'primitive': False,
'cif_file': ['', ''],
'group': ['test_group'],
'scf': [scf_wc.uuid],
'band': [],
'dos': [],
'eos': [],
'init_cls': [],
'corehole': [],
'calcfunctions': [[], []],
}),
sorted({
'formula': 'SeSi2',
'pk': pks[0],
'uuid': uuids[0],
'natoms': 3,
'cell':
'[[2.715, 2.715, 0.0], [2.715, 0.0, 2.715], [0.0, 2.715, 2.715]]',
'pbc': '(True, True, True)',
'label': '',
'description': '',
# 'extras': "{{'_aiida_hash': {0}}}".format(load_node(pks[0]).get_hash),
'symmetry': 'Imm2 (44)',
'volume': 40.02575174999999,
'child_nodes': 0,
'primitive': False,
'cif_file': ['', ''],
'group': ['test_group'],
'scf': [],
'band': [],
'dos': [],
'eos': [],
'init_cls': [],
'corehole': [],
'calcfunctions': [[], []],
})
]
for i in result:
assert sorted(i) in correct_result