def test_prepare_and_validate(new_database, new_workdir):
"""test preparation of inputs"""
code = get_main_code(new_workdir)
inparams = {"scf.k_points": (8, 8)}
from aiida.orm import DataFactory, CalculationFactory
StructureData = DataFactory('structure')
atoms = crystal(symbols=[12, 8],
basis=[[0, 0, 0], [0.5, 0.5, 0.5]],
spacegroup=225,
cellpar=[4.21, 4.21, 4.21, 90, 90, 90])
instruct = StructureData(ase=atoms)
from aiida_crystal17.workflows.symmetrise_3d_struct import (
run_symmetrise_3d_structure)
instruct, settings = run_symmetrise_3d_structure(instruct)
calc_cls = CalculationFactory('crystal17.main')
calc_cls.prepare_and_validate(inparams, instruct, settings, flattened=True)
def create_inputs(inpath, outpath):
""" create ``crystal17.main`` input nodes from an existing run
NB: none of the nodes are stored, also
existing basis will be retrieved if availiable
:param inpath: path to .d12 file
:param outpath: path to .out file
:return: dictionary of inputs, with keys 'structure', 'parameters', 'settings', 'structure', 'basis'
"""
from aiida.orm import DataFactory, CalculationFactory
calc_cls = CalculationFactory('crystal17.main')
basis_cls = DataFactory('crystal17.basisset')
struct_cls = DataFactory('structure')
structsettings_cls = DataFactory('crystal17.structsettings')
inputs = {}
with open(inpath) as f:
d12content = f.read()
output_dict, basis_sets, atom_props = extract_data(d12content)
cryparse = CrystalOutputPlugin()
if not os.path.exists(outpath):
raise OutputParsingError(
"The raw data file does not exist: {}".format(outpath))
with open(outpath) as f:
try:
data = cryparse.read_file(f, log_warnings=False)
except IOError as err:
raise OutputParsingError(
"Error in CRYSTAL 17 run output: {}".format(err))
# we retrieve the initial primitive geometry and symmetry
atoms = _create_atoms(data)
# convert fragment (i.e. unfixed) to fixed
if "fragment" in atom_props:
frag = atom_props.pop("fragment")
atom_props["fixed"] = [
i + 1 for i in range(atoms.get_number_of_atoms())
if i + 1 not in frag
]
atoms.set_tags(_create_tags(atom_props, atoms))
structure = struct_cls(ase=atoms)
inputs['structure'] = structure
settings_dict = {"kinds": {}}
for key, vals in atom_props.items():
settings_dict["kinds"][key] = [
structure.sites[i - 1].kind_name for i in vals
]
settings_dict["operations"] = data["initial"]["primitive_symmops"]
# TODO retrieve centering code, crystal system and spacegroup
settings_dict["space_group"] = 1
settings_dict["crystal_type"] = 1
settings_dict["centring_code"] = 1
settings = structsettings_cls(data=settings_dict)
parameters = calc_cls.prepare_and_validate(output_dict, structure,
settings)
inputs['parameters'] = parameters
inputs['settings'] = settings
inputs["basis"] = {}
for bset in basis_sets:
bfile = tempfile.NamedTemporaryFile(delete=False)
try:
with open(bfile.name, "w") as f:
f.write(bset)
bdata, _ = basis_cls.get_or_create(
bfile.name, use_first=False, store_basis=False)
# TODO report if bases created or retrieved
finally:
os.remove(bfile.name)
inputs["basis"][bdata.element] = bdata
return inputs
