def bands_to_bandsdata(bands_info, kpoints, bands):
"""
Convert the result of parser_dot_bands into a BandsData object
:param bands_info: A dictionary of the informations of the bands file.
contains field such as eferemi, units, cell
:param kpoints: An array of the kpoints of the bands, rows are
(kindex, kx, ky, kz, weight)
:param bands: The actual bands array
:return: A BandsData object
:rtype: ``aiida.orm.bands.data.array.bands.BandsData``
"""
bands_node = BandsData()
# Extract the index of the kpoints
kpn_array = np.asarray(kpoints)
k_index = kpn_array[:, 0]
# We need to restore the order of the kpoints
k_sort = np.argsort(k_index)
# Sort the kpn_array
kpn_array = kpn_array[k_sort]
_weights = kpn_array[:, -1]
kpts = kpn_array[:, 1:-1]
bands_node.set_kpoints(kpts, weights=_weights)
# Sort the bands to match the order of the kpoints
bands_array = np.asarray(bands)[k_sort]
# We need to swap the axes from kpt,spin,engs to spin,kpt,engs
bands_array = bands_array.swapaxes(0, 1)
# Squeeze the first dimension e.g when there is a single spin
if bands_array.shape[0] == 1:
bands_array = bands_array[0]
bands_array = bands_array * units['Eh']
bands_info = dict(bands_info) # Create a copy
# Convert the units for the fermi energies
if isinstance(bands_info['efermi'], list):
bands_info['efermi'] = [x * units['Eh'] for x in bands_info['efermi']]
else:
bands_info['efermi'] = bands_info['efermi'] * units['Eh']
bands_node.set_bands(bands_array, units="eV")
# PBC is always true as this is PW DFT....
bands_node.set_cell(bands_info['cell'], pbc=(True, True, True))
# Store information from *.bands in the attributes
# This is needs as we need to know the number of electrons
# and the fermi energy
for key, value in bands_info.items():
bands_node.set_attribute(key, value)
return bands_node
def bands_from_castepbin(seedname, fmanager):
"""
Acquire and prepare bands data from the castep_bin file instead
"""
with fmanager.open(seedname + '.castep_bin', 'rb') as handle:
binfile = CastepbinFile(fileobj=handle)
bands_node = BandsData()
kidx = binfile.kpoints_indices
sort_idx = np.argsort(kidx)
# Generated sorted arrays
kpoints = binfile.kpoints[sort_idx, :]
weights = binfile.kpoint_weights[sort_idx].astype(float)
eigenvalues = binfile.eigenvalues[:, sort_idx, :]
occupancies = binfile.occupancies[:, sort_idx, :]
efermi = binfile.fermi_energy
bands_node.set_kpoints(kpoints, weights=weights)
bands_node.set_bands(eigenvalues, occupations=occupancies, units="eV")
bands_node.set_cell(binfile.cell, pbc=(True, True, True))
bands_node.set_attribute('efermi', efermi)
return bands_node
def _aiida_bands_data(self, data, cell, kpoints_dict):
if not data:
return False
kpt_idx = sorted(data.keys()) # list of kpoint indices
try:
k_list = [kpoints_dict[i]
for i in kpt_idx] # list of k-point triplet
except KeyError:
# kpoint triplets are not present (true for .qp and so on, can not use BandsData)
# We use the internal Yambo Format [ [Eo_1, Eo_2,... ], ...[So_1,So_2,] ]
# QP_TABLE [[ib_1,ik_1,isp_1] ,[ib_n,ik_n,isp_n]]
# Each entry in DATA has corresponding legend in QP_TABLE that defines its details
# like ib= Band index, ik= kpoint index, isp= spin polarization index.
# Eo_1 => at ib_1, ik_1 isp_1.
pdata = ArrayData()
QP_TABLE = []
ORD = []
Eo = []
E_minus_Eo = []
So = []
Z = []
for ky in data.keys(): # kp == kpoint index as a string 1,2,..
for ind in range(len(data[ky]['Band'])):
try:
Eo.append(data[ky]['Eo'][ind])
except KeyError:
pass
try:
E_minus_Eo.append(data[ky]['E-Eo'][ind])
except KeyError:
pass
try:
So.append(data[ky]['Sc|Eo'][ind])
except KeyError:
pass
try:
Z.append(data[ky]['Z'][ind])
except KeyError:
pass
ik = int(ky)
ib = data[ky]['Band'][ind]
isp = 0
if 'Spin_Pol' in list(data[ky].keys()):
isp = data[ky]['Spin_Pol'][ind]
QP_TABLE.append([ik, ib, isp])
pdata.set_array('Eo', numpy.array(Eo))
pdata.set_array('E_minus_Eo', numpy.array(E_minus_Eo))
pdata.set_array('So', numpy.array(So))
pdata.set_array('Z', numpy.array(Z))
pdata.set_array('qp_table', numpy.array(QP_TABLE))
return pdata
quasiparticle_bands = BandsData()
quasiparticle_bands.set_cell(cell)
quasiparticle_bands.set_kpoints(k_list, cartesian=True)
# labels will come from any of the keys in the nested kp_point data,
# there is a uniform set of observables for each k-point, ie Band, Eo, ...
# ***FIXME BUG does not seem to handle spin polarizes at all when constructing bandsdata***
bands_labels = [
legend for legend in sorted(data[list(data.keys())[0]].keys())
]
append_list = [[] for i in bands_labels]
for kp in kpt_idx:
for i in range(len(bands_labels)):
append_list[i].append(data[kp][bands_labels[i]])
generalised_bands = [numpy.array(it) for it in append_list]
quasiparticle_bands.set_bands(bands=generalised_bands,
units='eV',
labels=bands_labels)
return quasiparticle_bands