def test_nio_sto3g_afm():
path = os.path.join(TEST_DIR, "input_files", 'nio_sto3g_afm.crystal.d12')
with open(path) as f:
input_str = f.read()
output_dict, basis_sets, atom_props = extract_data(input_str)
assert len(basis_sets) == 2
assert atom_props == {'spin_alpha': [1], 'spin_beta': [2]}
assert output_dict == {
'scf': {
'single': 'UHF',
'numerical': {
'FMIXING': 30
},
'post_scf': ['PPAN'],
'spinlock': {
'SPINLOCK': [0, 15]
},
'k_points': (8, 8)
},
'title': 'NiO Bulk with AFM spin'
}
def test_mgo_sto3g_scf():
path = os.path.join(TEST_DIR, "input_files", 'mgo_sto3g_scf.crystal.d12')
with open(path) as f:
input_str = f.read()
output_dict, basis_sets, atom_props = extract_data(input_str)
assert len(basis_sets) == 2
assert atom_props == {}
assert output_dict == {'scf': {'k_points': (8, 8)}, 'title': 'MgO bulk'}
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
def test_full_read(input_str):
output_dict, basis_sets, atom_props = extract_data(input_str)
assert len(basis_sets) == 2
assert atom_props == {
'fragment': [1, 3],
'ghosts': [5, 6],
'spin_alpha': [1, 3],
'spin_beta': [2, 4]
}
expected = {
"title": "a title",
"geometry": {
"info_print": ["ATOMSYMM", "SYMMOPS"],
"info_external": ["STRUCPRT"],
"optimise": {
"type": "FULLOPTG",
"hessian": "HESSIDEN",
"gradient": "NUMGRATO",
"info_print": ["PRINTOPT", "PRINTFORCES"],
"convergence": {
"TOLDEG": 0.0003,
"TOLDEX": 0.0012,
"TOLDEE": 7,
"MAXCYCLE": 50,
"FINALRUN": 4
},
}
},
"basis_set": {
"CHARGED": True,
},
"scf": {
"dft": {
"xc": ["LDA", "PZ"],
# or
# "xc": "HSE06",
# or
# "xc": {
# "LSRSH-PBE": [0.11, 0.25, 0.00001]
# },
"SPIN": True,
"grid": "XLGRID",
"grid_weights": "BECKE",
"numerical": {
"TOLLDENS": 6,
"TOLLGRID": 14,
"LIMBEK": 400
}
},
# or
# "single": "UHF",
"k_points": [8, 8],
"numerical": {
"BIPOLAR": [18, 14],
"BIPOSIZE": 4000000,
"EXCHSIZE": 4000000,
"EXCHPERM": True,
"ILASIZE": 6000,
"INTGPACK": 0,
"MADELIND": 50,
"POLEORDR": 4,
"TOLINTEG": [6, 6, 6, 6, 12],
"TOLPSEUD": 6,
"FMIXING": 0,
"MAXCYCLE": 50,
"TOLDEE": 6,
"LEVSHIFT": [2, 1],
"SMEAR": 0.1
},
"fock_mixing": "DIIS",
# or
# "fock_mixing": ["BROYDEN", 0.0001, 50, 2],
"spinlock": {
"SPINLOCK": [1, 10]
},
"post_scf": ["GRADCAL", "PPAN"]
}
}
assert edict.diff(output_dict, expected) == {}
def test_read_fail(input_str):
input_str = input_str.replace("PPAN", "WRONG")
with pytest.raises(NotImplementedError):
extract_data(input_str)