def pwout2dict(fname, **kwargs):
""" Extract available information from pw.x .out file.
Parameters:
fname (str/list): filename or list of filenames to scrape as a
QuantumEspresso pw.x output.
"""
flines, fname = get_flines_extension_agnostic(fname, ["out", "in"])
pwout = {}
pwout['source'] = [fname]
try:
# grab file owner username
from pwd import getpwuid
pwout['user'] = getpwuid(stat(fname).st_uid).pw_name
except Exception:
pwout['user'] = '******'
if 'CollCode' in fname:
pwout['icsd'] = fname.split('CollCode')[-1]
for ind, line in enumerate(reversed(flines)):
ind = len(flines) - 1 - ind
if 'cell_parameters' in line.lower() and 'angstrom' in line.lower(
) and 'lattice_cart' not in pwout:
pwout['lattice_cart'] = []
for j in range(3):
line = flines[ind + j + 1].strip().split()
pwout['lattice_cart'].append(list(map(float, line)))
pwout['cell_volume'] = cart2volume(pwout['lattice_cart'])
elif 'atomic_positions' in line.lower(
) and 'positions_frac' not in pwout:
pwout['positions_frac'] = []
pwout['atom_types'] = []
j = 1
while True:
if 'End final coordinates' in flines[j + ind]:
break
else:
try:
line = flines[j + ind].strip().split()
pwout['atom_types'].append(line[0])
pwout['positions_frac'].append(
list(map(float, line[1:5])))
j += 1
except Exception:
break
pwout['num_atoms'] = len(pwout['atom_types'])
elif 'final enthalpy' in line.lower() and 'enthalpy' not in pwout:
pwout['enthalpy'] = RY_TO_EV * float(line.lower().split()[-2])
elif 'total stress' in line.lower() and 'pressure' not in pwout:
pwout['pressure'] = KBAR_TO_GPA * float(line.lower().split()[-1])
elif all(key in pwout for key in
['enthalpy', 'pressure', 'lattice_cart', 'positions_frac']):
break
# get abc lattice
pwout['lattice_abc'] = cart2abc(pwout['lattice_cart'])
# calculate stoichiometry
pwout['stoichiometry'] = defaultdict(float)
for atom in pwout['atom_types']:
if atom not in pwout['stoichiometry']:
pwout['stoichiometry'][atom] = 0
pwout['stoichiometry'][atom] += 1
gcd_val = 0
for atom in pwout['atom_types']:
if gcd_val == 0:
gcd_val = pwout['stoichiometry'][atom]
else:
gcd_val = gcd(pwout['stoichiometry'][atom], gcd_val)
# convert stoichiometry to tuple for fryan
temp_stoich = []
for key, value in pwout['stoichiometry'].items():
if float(value) / gcd_val % 1 != 0:
temp_stoich.append([key, float(value) / gcd_val])
else:
temp_stoich.append([key, value / gcd_val])
pwout['stoichiometry'] = temp_stoich
atoms_per_fu = 0
for elem in pwout['stoichiometry']:
atoms_per_fu += elem[1]
pwout['num_fu'] = len(pwout['atom_types']) / atoms_per_fu
return pwout, True
def magres2dict(fname, **kwargs):
""" Extract available information from .magres file. Assumes units of
Angstrom and ppm for relevant quantities.
"""
magres = defaultdict(list)
flines, fname = get_flines_extension_agnostic(fname, "magres")
magres['source'] = [fname]
# grab file owner username
try:
from pwd import getpwuid
magres['user'] = getpwuid(stat(fname).st_uid).pw_name
except Exception:
magres['user'] = '******'
magres['magres_units'] = dict()
for line_no, line in enumerate(flines):
line = line.lower().strip()
if line in ['<atoms>', '[atoms]']:
i = 1
while flines[line_no +
i].strip().lower() not in ['</atoms>', '[/atoms]']:
split_line = flines[line_no + i].split()
if not split_line:
i += 1
continue
if i > len(flines):
raise RuntimeError("Something went wrong in reader loop")
if split_line[0] == 'units':
magres['magres_units'][split_line[1]] = split_line[2]
elif 'lattice' in split_line:
lattice = split_line[1:]
for j in range(3):
magres['lattice_cart'].append([
float(elem) for elem in lattice[j * 3:(j + 1) * 3]
])
magres['lattice_abc'] = cart2abc(magres['lattice_cart'])
elif 'atom' in split_line:
atom = split_line
magres['atom_types'].append(atom[1])
magres['positions_abs'].append(
[float(elem) for elem in atom[-3:]])
i += 1
break
if "atom_types" in magres:
magres['num_atoms'] = len(magres['atom_types'])
magres['positions_frac'] = cart2frac(magres['lattice_cart'],
magres['positions_abs'])
magres['stoichiometry'] = get_stoich(magres['atom_types'])
for line_no, line in enumerate(flines):
line = line.lower().strip()
if line in ['<magres>', '[magres]']:
i = 1
while flines[line_no +
i].strip().lower() not in ['</magres>', '[/magres]']:
split_line = flines[line_no + i].split()
if not split_line:
i += 1
continue
if i > len(flines):
raise RuntimeError("Something went wrong in reader loop")
if split_line[0] == 'units':
magres['magres_units'][split_line[1]] = split_line[2]
elif 'sus' in split_line:
magres["susceptibility_tensor"] = np.array(
[float(val) for val in split_line[1:]]).reshape(3, 3)
elif 'ms' in split_line:
ms = np.array([float(val)
for val in split_line[3:]]).reshape(3, 3)
s_iso = np.trace(ms) / 3
# find eigenvalues of symmetric part of shielding and order them to calc anisotropy eta
symmetric_shielding = _symmetrise_tensor(ms)
s_yy, s_xx, s_zz = _get_haeberlen_eigs(symmetric_shielding)
s_aniso = s_zz - (s_xx + s_yy) / 2.0
asymm = (s_yy - s_xx) / (s_zz - s_iso)
# convert from reduced anistropy to CSA
magres["magnetic_shielding_tensors"].append(ms)
magres["chemical_shielding_isos"].append(s_iso)
magres["chemical_shift_anisos"].append(s_aniso)
magres["chemical_shift_asymmetries"].append(asymm)
elif "efg" in split_line:
efg = np.array([float(val)
for val in split_line[3:]]).reshape(3, 3)
species = split_line[1]
eigs = _get_haeberlen_eigs(efg)
v_zz, eta = eigs[2], (eigs[0] - eigs[1]) / eigs[2]
# calculate C_Q in MHz
quadrupole_moment = ELECTRIC_QUADRUPOLE_MOMENTS.get(
species, 1.0)
C_Q = ((ELECTRON_CHARGE * v_zz * quadrupole_moment *
EFG_AU_TO_SI * BARN_TO_M2) /
(PLANCK_CONSTANT * 1e6))
magres["electric_field_gradient"].append(efg)
magres["quadrupolar_couplings"].append(C_Q)
magres["quadrupolar_asymmetries"].append(eta)
i += 1
for line_no, line in enumerate(flines):
line = line.lower().strip()
if line in ['<calculation>', '[calculation]']:
i = 1
while flines[line_no + i].strip().lower() not in [
'</calculation>', '[/calculation]'
]:
if i > len(flines):
raise RuntimeError("Something went wrong in reader loop")
# space important as it excludes other calc_code_x variables
if 'calc_code ' in flines[line_no + i]:
magres['calculator'] = flines[line_no + i].split()[1]
if 'calc_code_version' in flines[line_no + i]:
magres['calculator_version'] = flines[line_no +
i].split()[1]
i += 1
return dict(magres), True
def cif2dict(fname, **kwargs):
""" Extract available information from .cif file and store as a
dictionary. Raw cif data is stored under the `'_cif'` key. Symmetric
sites are expanded by the symmetry operations and their occupancies
are tracked.
Parameters:
fname (str/list): filename or list of filenames of .cif file(s)
(with or without extension).
Returns:
(dict/str, bool): if successful, a dictionary containing scraped
data and True, if not, then an error string and False.
"""
flines, fname = get_flines_extension_agnostic(fname, "cif")
doc = dict()
cif_dict = _cif_parse_raw(flines)
doc['_cif'] = cif_dict
doc['source'] = [str(Path(fname).resolve())]
doc['atom_types'] = []
atom_labels = cif_dict.get("_atom_site_type_symbol", False)
if not atom_labels:
atom_labels = cif_dict.get("_atom_site_label", False)
if not atom_labels:
raise RuntimeError(f"Unable to find atom types in cif file {fname}.")
for atom in atom_labels:
symbol = ''
for character in atom:
if not character.isalpha():
break
else:
symbol += character
doc['atom_types'].append(symbol)
doc['positions_frac'] = [list(map(lambda x: float(x.split('(')[0]), vector)) for vector in
zip(cif_dict['_atom_site_fract_x'],
cif_dict['_atom_site_fract_y'],
cif_dict['_atom_site_fract_z'])]
if '_atom_site_occupancy' in cif_dict:
doc['site_occupancy'] = [float(x.split('(')[0]) for x in cif_dict['_atom_site_occupancy']]
else:
doc['site_occupancy'] = [1.0 for _ in doc['positions_frac']]
if '_atom_site_symmetry_multiplicity' in cif_dict:
doc['site_multiplicity'] = [float(x.split('(')[0]) for x in cif_dict['_atom_site_symmetry_multiplicity']]
else:
doc['site_multiplicity'] = [1.0 for _ in doc['positions_frac']]
doc['lattice_abc'] = [list(map(_cif_parse_float_with_errors,
[cif_dict['_cell_length_a'],
cif_dict['_cell_length_b'],
cif_dict['_cell_length_c']])),
list(map(_cif_parse_float_with_errors,
[cif_dict['_cell_angle_alpha'],
cif_dict['_cell_angle_beta'],
cif_dict['_cell_angle_gamma']]))]
doc['lattice_cart'] = abc2cart(doc['lattice_abc'])
doc['cell_volume'] = cart2volume(doc['lattice_cart'])
doc['stoichiometry'] = _cif_disordered_stoichiometry(doc)
doc['num_atoms'] = len(doc['positions_frac'])
if '_space_group_symop_operation_xyz' in doc['_cif'] and '_symmetry_equiv_pos_as_xyz' not in doc['_cif']:
doc["_cif"]["_symmetry_equiv_pos_as_xyz"] = doc["_cif"]["_space_group_symop_operation_xyz"]
if '_symmetry_equiv_pos_as_xyz' in doc['_cif']:
_cif_set_unreduced_sites(doc)
try:
doc['space_group'] = get_spacegroup_spg(doc, check_occ=False)
except RuntimeError:
pass
return doc, True
def magres2dict(fname, **kwargs):
""" Extract available information from .magres file. Assumes units of
Angstrom and ppm for relevant quantities.
"""
magres = defaultdict(list)
flines, fname = get_flines_extension_agnostic(fname, "magres")
magres['source'] = [fname]
# grab file owner username
try:
magres['user'] = getpwuid(stat(fname).st_uid).pw_name
except Exception:
magres['user'] = '******'
magres['magres_units'] = dict()
for line_no, line in enumerate(flines):
line = line.lower().strip()
if line in ['<atoms>', '[atoms]']:
i = 1
while flines[line_no +
i].strip().lower() not in ['</atoms>', '[/atoms]']:
split_line = flines[line_no + i].split()
if not split_line:
i += 1
continue
if i > len(flines):
raise RuntimeError("Something went wrong in reader loop")
if split_line[0] == 'units':
magres['magres_units'][split_line[1]] = split_line[2]
elif 'lattice' in flines[line_no + i]:
lattice = flines[line_no + i].split()[1:]
for j in range(3):
magres['lattice_cart'].append([
float(elem) for elem in lattice[j * 3:(j + 1) * 3]
])
magres['lattice_abc'] = cart2abc(magres['lattice_cart'])
elif 'atom' in flines[line_no + i]:
atom = flines[line_no + i].split()
magres['atom_types'].append(atom[1])
magres['positions_abs'].append(
[float(elem) for elem in atom[-3:]])
i += 1
break
magres['num_atoms'] = len(magres['atom_types'])
magres['positions_frac'] = cart2frac(magres['lattice_cart'],
magres['positions_abs'])
magres['stoichiometry'] = get_stoich(magres['atom_types'])
for line_no, line in enumerate(flines):
line = line.lower().strip()
if line in ['<magres>', '[magres]']:
i = 1
while flines[line_no +
i].strip().lower() not in ['</magres>', '[/magres]']:
split_line = flines[line_no + i].split()
if not split_line:
i += 1
continue
if i > len(flines):
raise RuntimeError("Something went wrong in reader loop")
if split_line[0] == 'units':
magres['magres_units'][split_line[1]] = split_line[2]
elif 'sus' in flines[line_no + i]:
sus = flines[line_no + i].split()[1:]
for j in range(3):
magres['susceptibility_tensor'].append(
[float(val) for val in sus[3 * j:3 * (j + 1)]])
elif 'ms' in flines[line_no + i]:
ms = flines[line_no + i].split()[3:]
magres['magnetic_shielding_tensors'].append([])
for j in range(3):
magres['magnetic_shielding_tensors'][-1].append(
[float(val) for val in ms[3 * j:3 * (j + 1)]])
magres['chemical_shielding_isos'].append(0)
magres['chemical_shift_anisos'].append(0)
magres['chemical_shift_asymmetries'].append(0)
for j in range(3):
magres['chemical_shielding_isos'][-1] += magres[
'magnetic_shielding_tensors'][-1][j][j] / 3
# find eigenvalues of symmetric part of shielding and order them to calc anisotropy eta
symmetric_shielding = (
0.5 *
(magres['magnetic_shielding_tensors'][-1] + np.asarray(
magres['magnetic_shielding_tensors'][-1]).T))
eig_vals, eig_vecs = np.linalg.eig(symmetric_shielding)
eig_vals, eig_vecs = zip(
*sorted(zip(eig_vals, eig_vecs),
key=lambda eig: abs(eig[0] - magres[
'chemical_shielding_isos'][-1])))
# Haeberlen convention: |s_zz - s_iso| >= |s_xx - s_iso| >= |s_yy - s_iso|
s_yy, s_xx, s_zz = eig_vals
s_iso = magres['chemical_shielding_isos'][-1]
# convert from reduced anistropy to CSA
magres['chemical_shift_anisos'][-1] = s_zz - (s_xx +
s_yy) / 2.0
magres['chemical_shift_asymmetries'][-1] = (
s_yy - s_xx) / (s_zz - s_iso)
i += 1
for line_no, line in enumerate(flines):
line = line.lower().strip()
if line in ['<calculation>', '[calculation]']:
i = 1
while flines[line_no + i].strip().lower() not in [
'</calculation>', '[/calculation]'
]:
if i > len(flines):
raise RuntimeError("Something went wrong in reader loop")
# space important as it excludes other calc_code_x variables
if 'calc_code ' in flines[line_no + i]:
magres['calculator'] = flines[line_no + i].split()[1]
if 'calc_code_version' in flines[line_no + i]:
magres['calculator_version'] = flines[line_no +
i].split()[1]
i += 1
return magres, True