def load_data(self):
_data = self.load(list_of_datasets=["dw"])
_num_atoms = _data["datasets"]["dw"].shape[0]
_dw_crystal_data = AbinsModules.DWSingleCrystalData(temperature=self._temperature, num_atoms=_num_atoms)
_dw_crystal_data.set(items=_data["datasets"]["dw"])
_crystal_data = AbinsModules.SingleCrystalData()
_crystal_data.set(abins_data=self._abins_data, dw_crystal_data=_dw_crystal_data)
return _crystal_data
def _calculate_dw(self):
"""
The Debye-Waller coefficients are calculated atom by atom.
For each atom they consist in a 3X3 matrix. The Debye-Waller factors are given in atomic units.
Working equation implemented according to:
https://forge.epn-campus.eu/html/ab2tds/debye_waller.html
"""
dw = AbinsModules.DWSingleCrystalData(temperature=self._temperature,
num_atoms=self._num_atoms)
data = self._abins_data.extract()
num_atoms = len(data["atoms_data"])
mass_hartree_factor = np.asarray([
1.0 / (data["atoms_data"]["atom_%s" % atom]["mass"] * 2)
for atom in range(num_atoms)
])
temperature_hartree = self._temperature * AbinsModules.AbinsConstants.K_2_HARTREE
coth_factor = 1.0 / (2.0 * temperature_hartree
) # coth( coth_factor * omega)
k_points = [str(k) for k in range(self._num_k)]
frequencies_hartree = data["k_points_data"]["frequencies"]
atomic_displacements = data["k_points_data"]["atomic_displacements"]
weights = data["k_points_data"]["weights"]
coth_over_omega = {}
for k in k_points:
tanh = np.tanh(np.multiply(coth_factor, frequencies_hartree[k]))
coth_over_omega[k] = np.divide(
1.0, np.multiply(tanh,
frequencies_hartree[k])) # coth(...)/omega
atomic_displacements[k] = atomic_displacements[
k] / AbinsModules.AbinsConstants.ATOMIC_LENGTH_2_ANGSTROM
# num_freq -- number of phonons
# dim -- size of displacement vector for one atom (dim = 3)
# item_k [dim, dim]
item_k = np.zeros((3, 3), dtype=AbinsModules.AbinsConstants.FLOAT_TYPE
) # stores DW for one atom
for num in range(self._num_atoms):
item_k.fill(
0.0
) # erase stored information so that it can be filled with content for the next atom
for k in k_points:
disp = atomic_displacements[k][num]
# temp_1 [freq, dim dim]
temp_1 = np.einsum(
'kij,k->kij',
np.einsum('ki, kj->kij', disp, disp.conjugate()).real,
coth_over_omega[k])
# temp2 [dim, dim]
temp_2 = np.sum(temp_1, axis=0)
np.add(item_k, np.multiply(temp_2, weights[k]), item_k)
np.multiply(item_k, mass_hartree_factor[num], item_k)
# noinspection PyProtectedMember
dw._append(item=item_k, num_atom=num)
return dw
