def test_cart2frac(self):
lattice_cart = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
positions_abs = [1, 1, 1]
self.assertEqual(cart2frac(lattice_cart, positions_abs),
[0.5, 0.5, 0.5])
lattice_cart = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
positions_abs = [[1, 1, 1]]
self.assertEqual(cart2frac(lattice_cart, positions_abs),
[[0.5, 0.5, 0.5]])
lattice_cart = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
positions_abs = [[2, 2, 2], [1, 1, 1]]
self.assertEqual(cart2frac(lattice_cart, positions_abs),
[[1, 1, 1], [0.5, 0.5, 0.5]])
def positions_frac(self):
""" Return list of fractional positions. """
from matador.utils.cell_utils import cart2frac
if 'positions_frac' not in self._data:
self._data['positions_frac'] = cart2frac(self.cell.lattice_cart,
self.positions_abs)
return self._data['positions_frac']
def optimade_to_basic_cif(structure):
""" A simple CIF creator that is enough to trick ChemDoodle. """
cif_string = ""
lattice_abc = cart2abc(structure.attributes.lattice_vectors)
positions_frac = cart2frac(
structure.attributes.lattice_vectors,
structure.attributes.cartesian_site_positions,
)
cif_string += f"_cell_length_a {lattice_abc[0][0]}\n"
cif_string += f"_cell_length_b {lattice_abc[0][1]}\n"
cif_string += f"_cell_length_c {lattice_abc[0][2]}\n"
cif_string += f"_cell_angle_alpha {lattice_abc[1][0]}\n"
cif_string += f"_cell_angle_beta {lattice_abc[1][1]}\n"
cif_string += f"_cell_angle_gamma {lattice_abc[1][2]}\n"
cif_string += "loop_\n"
cif_string += "_atom_site_label\n"
cif_string += "_atom_site_symbol\n"
cif_string += "_atom_site_fract_x\n"
cif_string += "_atom_site_fract_y\n"
cif_string += "_atom_site_fract_z\n"
for atom, pos in zip(structure.attributes.species_at_sites, positions_frac):
cif_string += f"{atom} {atom} {pos[0]} {pos[1]} {pos[2]}\n"
return cif_string
def test_conversion_transitivity(self):
""" Test that cart2frac(frac2cart(A)) == A. """
castep_fname = REAL_PATH + "data/Na3Zn4-swap-ReOs-OQMD_759599.castep"
test_doc, s = castep2dict(castep_fname, db=True, verbosity=VERBOSITY)
lattice_cart = test_doc["lattice_cart"]
positions_frac = test_doc["positions_frac"]
np.testing.assert_almost_equal(
cart2frac(lattice_cart, frac2cart(lattice_cart, positions_frac)),
positions_frac,
decimal=10,
)
def test_cart2abc(self):
castep_fname = REAL_PATH + "data/Na3Zn4-swap-ReOs-OQMD_759599.castep"
self.assertTrue(os.path.isfile(castep_fname))
test_doc, s = castep2dict(castep_fname, db=True, verbosity=VERBOSITY)
try:
self.assertTrue(
np.allclose(test_doc["lattice_abc"],
cart2abc(test_doc["lattice_cart"])),
msg="Conversion cart2abc failed.",
)
self.assertTrue(
np.allclose(
cart2abc(test_doc["lattice_cart"]),
cart2abc(abc2cart(test_doc["lattice_abc"])),
),
msg="Conversion abc2cart failed.",
)
self.assertAlmostEqual(
test_doc["cell_volume"],
cart2volume(test_doc["lattice_cart"]),
msg="Failed to calculate volume from lattice vectors.",
places=5,
)
self.assertIsInstance(test_doc["lattice_abc"],
list,
msg="Failed abc numpy cast to list")
self.assertIsInstance(
test_doc["lattice_cart"],
list,
msg="Failed cartesian numpy cast to list",
)
cart_pos = frac2cart(test_doc["lattice_cart"],
test_doc["positions_frac"])
back2frac = cart2frac(test_doc["lattice_cart"], cart_pos)
np.testing.assert_array_almost_equal(back2frac,
test_doc["positions_frac"])
except AssertionError:
print("cart:", test_doc["lattice_cart"],
abc2cart(test_doc["lattice_abc"]))
print("abc:", test_doc["lattice_abc"],
cart2abc(test_doc["lattice_cart"]))
print(
"volume:",
test_doc["cell_volume"],
cart2volume(test_doc["lattice_cart"]),
)
raise AssertionError
def set_position(self, position, units):
if len(position) != 3 or not all(
isinstance(p, (float, int)) for p in position):
raise RuntimeError(
'CrystalSite position has wrong shape: {}'.format(position))
if not hasattr(self, '_coords'):
self._coords = dict()
if units == 'fractional':
self._coords['fractional'] = wrap_frac_coords(
[float(pos) for pos in position], remove=False)
elif units == 'cartesian':
self._coords['fractional'] = wrap_frac_coords(cart2frac(
self.lattice, self.coords),
remove=False)
else:
raise RuntimeError(
'Unit system {} not understood, expecting `fractional`/`cartesian`'
.format(units))
def relax(self):
from ase.optimize import LBFGS
cached = sys.__stdout__
try:
optimizer = LBFGS(self.ucf)
optimizer.logfile = None
optimised = optimizer.run(fmax=0.05, steps=100)
except Exception:
optimised = False
self.doc["optimised"] = bool(optimised)
self.doc["positions_abs"] = self.atoms.get_positions().tolist()
self.doc["lattice_cart"] = self.atoms.get_cell().tolist()
self.doc["lattice_abc"] = cart2abc(self.doc["lattice_cart"])
self.doc["positions_frac"] = cart2frac(self.doc["lattice_cart"],
self.doc["positions_abs"])
self.doc["enthalpy_per_atom"] = float(self.calc.results["energy"] /
len(self.doc["atom_types"]))
self.doc["enthalpy"] = float(self.calc.results["energy"])
self.queue.put(self.doc)
sys.stdout = cached
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 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
