def _parse_stdout(self, out_folder):
"""CP2K output parser"""
from aiida.orm import BandsData, Dict
# pylint: disable=protected-access
fname = self.node.process_class._DEFAULT_OUTPUT_FILE
if fname not in out_folder._repository.list_object_names():
raise OutputParsingError("Cp2k output file not retrieved")
abs_fn = os.path.join(
out_folder._repository._get_base_folder().abspath, fname)
with io.open(abs_fn, mode="r", encoding="utf-8") as fobj:
result_dict = parse_cp2k_output(fobj)
if "nwarnings" not in result_dict:
raise OutputParsingError("CP2K did not finish properly.")
if "kpoint_data" in result_dict:
bnds = BandsData()
bnds.set_kpoints(result_dict["kpoint_data"]["kpoints"])
bnds.labels = result_dict["kpoint_data"]["labels"]
bnds.set_bands(
result_dict["kpoint_data"]["bands"],
units=result_dict["kpoint_data"]["bands_unit"],
)
self.out("output_bands", bnds)
del result_dict["kpoint_data"]
self.out("output_parameters", Dict(dict=result_dict))
def example_bands_v2(fresh_aiida_env):
"""Example eigen values and occupations"""
from aiida.orm import BandsData
bdata = BandsData()
bdata.set_kpoints([[0, 0, 0], [0.25, 0.25, 0.25]])
occ = np.array([[1, 1, 1, 0, 0, 0], [1, 1, 1, 0, 0, 0]], dtype=np.float64)
eigen = np.array([[-1, -1, -1, 0, 0, 0], [-0.5, -0.5, -0.5, 0, 0, 0]])
bdata.set_bands(bands=eigen, occupations=occ)
return bdata
def _parse_stdout(self):
"""Advanced CP2K output file parser."""
from aiida.orm import BandsData
from aiida_cp2k.utils import parse_cp2k_output_advanced
fname = self.node.process_class._DEFAULT_OUTPUT_FILE # pylint: disable=protected-access
if fname not in self.retrieved.list_object_names():
raise OutputParsingError("Cp2k output file not retrieved")
try:
output_string = self.retrieved.get_object_content(fname)
except IOError:
return self.exit_codes.ERROR_OUTPUT_STDOUT_READ
result_dict = parse_cp2k_output_advanced(output_string)
# nwarnings is the last thing to be printed in th eCP2K output file:
# if it is not there, CP2K didn't finish properly
if 'nwarnings' not in result_dict:
raise OutputParsingError("CP2K did not finish properly.")
if "aborted" in result_dict:
return self.exit_codes.ERROR_OUTPUT_CONTAINS_ABORT
# Compute the bandgap for Spin1 and Spin2 if eigen was parsed (works also with smearing!)
if 'eigen_spin1_au' in result_dict:
if result_dict['dft_type'] == "RKS":
result_dict['eigen_spin2_au'] = result_dict['eigen_spin1_au']
lumo_spin1_idx = result_dict['init_nel_spin1']
lumo_spin2_idx = result_dict['init_nel_spin2']
if (lumo_spin1_idx > len(result_dict['eigen_spin1_au'])-1) or \
(lumo_spin2_idx > len(result_dict['eigen_spin2_au'])-1):
#electrons jumped from spin1 to spin2 (or opposite): assume last eigen is lumo
lumo_spin1_idx = len(result_dict['eigen_spin1_au']) - 1
lumo_spin2_idx = len(result_dict['eigen_spin2_au']) - 1
homo_spin1 = result_dict['eigen_spin1_au'][lumo_spin1_idx - 1]
homo_spin2 = result_dict['eigen_spin2_au'][lumo_spin2_idx - 1]
lumo_spin1 = result_dict['eigen_spin1_au'][lumo_spin1_idx]
lumo_spin2 = result_dict['eigen_spin2_au'][lumo_spin2_idx]
result_dict['bandgap_spin1_au'] = lumo_spin1 - homo_spin1
result_dict['bandgap_spin2_au'] = lumo_spin2 - homo_spin2
if "kpoint_data" in result_dict:
bnds = BandsData()
bnds.set_kpoints(result_dict["kpoint_data"]["kpoints"])
bnds.labels = result_dict["kpoint_data"]["labels"]
bnds.set_bands(
result_dict["kpoint_data"]["bands"],
units=result_dict["kpoint_data"]["bands_unit"],
)
self.out("output_bands", bnds)
del result_dict["kpoint_data"]
self.out("output_parameters", Dict(dict=result_dict))
return None
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 _parse_stdout(self, out_folder):
"""Advanced CP2K output file parser"""
from aiida.orm import BandsData
from .parser_functions import parse_cp2k_output_advanced
# pylint: disable=protected-access
fname = self.node.process_class._DEFAULT_OUTPUT_FILE
if fname not in out_folder._repository.list_object_names():
raise OutputParsingError("Cp2k output file not retrieved")
abs_fn = os.path.join(
out_folder._repository._get_base_folder().abspath, fname)
with io.open(abs_fn, mode="r", encoding="utf-8") as fobj:
result_dict = parse_cp2k_output_advanced(fobj)
# nwarnings is the last thing to be printed in th eCP2K output file:
# if it is not there, CP2K didn't finish properly
if 'nwarnings' not in result_dict:
raise OutputParsingError("CP2K did not finish properly.")
# Compute the bandgap for Spin1 and Spin2 if eigen was parsed (works also with smearing!)
if 'eigen_spin1_au' in result_dict:
if result_dict['dft_type'] == "RKS":
result_dict['eigen_spin2_au'] = result_dict['eigen_spin1_au']
lumo_spin1_idx = result_dict['init_nel_spin1']
lumo_spin2_idx = result_dict['init_nel_spin2']
if (lumo_spin1_idx > len(result_dict['eigen_spin1_au'])-1) or \
(lumo_spin2_idx > len(result_dict['eigen_spin2_au'])-1):
#electrons jumped from spin1 to spin2 (or opposite): assume last eigen is lumo
lumo_spin1_idx = len(result_dict['eigen_spin1_au']) - 1
lumo_spin2_idx = len(result_dict['eigen_spin2_au']) - 1
homo_spin1 = result_dict['eigen_spin1_au'][lumo_spin1_idx - 1]
homo_spin2 = result_dict['eigen_spin2_au'][lumo_spin2_idx - 1]
lumo_spin1 = result_dict['eigen_spin1_au'][lumo_spin1_idx]
lumo_spin2 = result_dict['eigen_spin2_au'][lumo_spin2_idx]
result_dict['bandgap_spin1_au'] = lumo_spin1 - homo_spin1
result_dict['bandgap_spin2_au'] = lumo_spin2 - homo_spin2
if "kpoint_data" in result_dict:
bnds = BandsData()
bnds.set_kpoints(result_dict["kpoint_data"]["kpoints"])
bnds.labels = result_dict["kpoint_data"]["labels"]
bnds.set_bands(
result_dict["kpoint_data"]["bands"],
units=result_dict["kpoint_data"]["bands_unit"],
)
self.out("output_bands", bnds)
del result_dict["kpoint_data"]
self.out("output_parameters", Dict(dict=result_dict))
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 spin_dependent_subparser(out_info_dict):
"""This find the projection and bands arrays from the out_file and out_info_dict. Used to handle the different
possible spin-cases in a convenient manner.
:param out_info_dict: contains various technical internals useful in parsing
:return: ProjectionData, BandsData parsed from out_file
"""
out_file = out_info_dict['out_file']
spin_down = out_info_dict['spin_down']
od = out_info_dict #using a shorter name for convenience
# regular expressions needed for later parsing
WaveFraction1_re = re.compile(r'\=(.*?)\*') # state composition 1
WaveFractionremain_re = re.compile(r'\+(.*?)\*') # state comp 2
FunctionId_re = re.compile(r'\#(.*?)\]') # state identity
# primes arrays for the later parsing
num_wfc = len(od['wfc_lines'])
bands = np.zeros([od['k_states'], od['num_bands']])
projection_arrays = np.zeros([od['k_states'], od['num_bands'], num_wfc])
try:
for i in range(od['k_states']):
if spin_down:
i += od['k_states']
# grabs band energy
for j in range(i * od['num_bands'], (i + 1) * od['num_bands'], 1):
out_ind = od['e_lines'][j]
try:
# post ~6.3 output format "e ="
val = out_file[out_ind].split()[2]
float(val)
except ValueError:
# pre ~6.3 output format? "==== e("
val = out_file[out_ind].split()[4]
bands[i % od['k_states']][j % od['num_bands']] = val
#subloop grabs pdos
wave_fraction = []
wave_id = []
for k in range(od['e_lines'][j] + 1, od['psi_lines'][j], 1):
out_line = out_file[k]
wave_fraction += WaveFraction1_re.findall(out_line)
wave_fraction += WaveFractionremain_re.findall(out_line)
wave_id += FunctionId_re.findall(out_line)
if len(wave_id) != len(wave_fraction):
raise IndexError
for l in range(len(wave_id)):
wave_id[l] = int(wave_id[l])
wave_fraction[l] = float(wave_fraction[l])
#sets relevant values in pdos_array
projection_arrays[i % od['k_states']][j % od['num_bands']][
wave_id[l] - 1] = wave_fraction[l]
except IndexError:
raise QEOutputParsingError(
'the standard out file does not comply with the official documentation.'
)
bands_data = BandsData()
# Attempts to retrieve the kpoints from the parent calc
parent_calc = out_info_dict['parent_calc']
try:
parent_kpoints = parent_calc.get_incoming(
link_label_filter='kpoints').one().node
except ValueError:
raise QEOutputParsingError(
'The parent had no input kpoints! Cannot parse from this!')
try:
if len(od['k_vect']) != len(parent_kpoints.get_kpoints()):
raise AttributeError
bands_data.set_kpointsdata(parent_kpoints)
except AttributeError:
bands_data.set_kpoints(od['k_vect'].astype(float))
bands_data.set_bands(bands, units='eV')
orbitals = out_info_dict['orbitals']
if len(orbitals) != np.shape(projection_arrays[0, 0, :])[0]:
raise QEOutputParsingError('There was an internal parsing error, '
' the projection array shape does not agree'
' with the number of orbitals')
projection_data = ProjectionData()
projection_data.set_reference_bandsdata(bands_data)
projections = [projection_arrays[:, :, i] for i in range(len(orbitals))]
# Do the bands_check manually here
for projection in projections:
if np.shape(projection) != np.shape(bands):
raise AttributeError('Projections not the same shape as the bands')
#insert here some logic to assign pdos to the orbitals
pdos_arrays = spin_dependent_pdos_subparser(out_info_dict)
energy_arrays = [out_info_dict['energy']] * len(orbitals)
projection_data.set_projectiondata(orbitals,
list_of_projections=projections,
list_of_energy=energy_arrays,
list_of_pdos=pdos_arrays,
bands_check=False)
# pdos=pdos_arrays
return bands_data, projection_data
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
def _get_output_nodes(self, output_path, messages_path, xml_path,
json_path, bands_path):
"""
Extracts output nodes from the standard output and standard error
files. (And XML and JSON files)
"""
from aiida.orm import TrajectoryData
import re
parser_version = '1.0.1'
parser_info = {}
parser_info['parser_info'] = 'AiiDA Siesta Parser V. {}'.format(
parser_version)
parser_info['parser_warnings'] = []
#No need for checks anymore
xmldoc = get_parsed_xml_doc(xml_path)
in_struc = self.node.inputs.structure
try:
in_settings = self.node.inputs.settings
except exceptions.NotExistent:
in_settings = None
result_dict = get_dict_from_xml_doc(xmldoc)
# Add timing information
#if json_path is None:
###TODO###
#Not sure how to implement what once was logger.info
#Also not sure I understood the purpose of this file
if json_path is not None:
from .json_time import get_timing_info
global_time, timing_decomp = get_timing_info(json_path)
if global_time is None:
raise OutputParsingError(
"Cannot fully parse the time.json file")
else:
result_dict["global_time"] = global_time
result_dict["timing_decomposition"] = timing_decomp
# Add warnings
if messages_path is None:
# Perhaps using an old version of Siesta
warnings_list = ['WARNING: No MESSAGES file...']
else:
successful, warnings_list = self.get_warnings_from_file(
messages_path)
###TODO### or maybe not
#How do we process this successfull booelan?
result_dict["warnings"] = warnings_list
# Add parser info dictionary
parsed_dict = dict(
list(result_dict.items()) + list(parser_info.items()))
output_data = Dict(dict=parsed_dict)
self.out('output_parameters', output_data)
# If the structure has changed, save it
if is_variable_geometry(xmldoc):
# Get the input structure to copy its site names,
# as the CML file traditionally contained only the
# atomic symbols.
#
struc = get_last_structure(xmldoc, in_struc)
# result_list.append((self.get_linkname_outstructure(),struc))
self.out(self.get_linkname_outstructure(), struc)
# Save forces and stress in an ArrayData object
forces, stress = get_final_forces_and_stress(xmldoc)
if forces is not None and stress is not None:
# from aiida.orm.nodes.array import ArrayData
from aiida.orm import ArrayData
arraydata = ArrayData()
arraydata.set_array('forces', np.array(forces))
arraydata.set_array('stress', np.array(stress))
# result_list.append((self.get_linkname_fs_and_stress(),arraydata))
self.out(self.get_linkname_fs_and_stress(), arraydata)
# Parse band-structure information if available
if bands_path is not None:
bands, coords = self.get_bands(bands_path)
from aiida.orm import BandsData
arraybands = BandsData()
f = self.node.inputs.bandskpoints #Temporary workaround due to a bug
#f._set_reciprocal_cell() #in KpointData (issue #2749)
arraybands.set_kpoints(f.get_kpoints(cartesian=True))
arraybands.labels = f.labels
arraybands.set_bands(bands, units="eV")
self.out(self.get_linkname_bands(), arraybands)
bandsparameters = Dict(dict={"kp_coordinates": coords})
self.out(self.get_linkname_bandsparameters(), bandsparameters)
return result_dict
def _parse_gsr(self):
"""Abinit GSR parser."""
# Output GSR Abinit NetCDF file - Default name is aiidao_GSR.nc
fname = f'{self.node.get_attribute("prefix")}o_GSR.nc'
# Absolute path of the folder in which aiidao_GSR.nc is stored
path = self.node.get_remote_workdir()
if fname not in self.retrieved.list_object_names():
return self.exit_codes.ERROR_MISSING_OUTPUT_FILES
with abilab.abiopen(path + '/' + fname) as gsr:
gsr_data = {
'abinit_version':
gsr.abinit_version,
'cart_stress_tensor':
gsr.cart_stress_tensor.tolist(),
'cart_stress_tensor' + UNITS_SUFFIX:
DEFAULT_STRESS_UNITS,
'is_scf_run':
bool(gsr.is_scf_run),
# 'cart_forces': gsr.cart_forces.tolist(),
# 'cart_forces' + units_suffix: DEFAULT_FORCE_UNITS,
'forces':
gsr.cart_forces.tolist(), # backwards compatibility
'forces' + UNITS_SUFFIX:
DEFAULT_FORCE_UNITS,
'energy':
float(gsr.energy),
'energy' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_localpsp':
float(gsr.energy_terms.e_localpsp),
'e_localpsp' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_eigenvalues':
float(gsr.energy_terms.e_eigenvalues),
'e_eigenvalues' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_ewald':
float(gsr.energy_terms.e_ewald),
'e_ewald' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_hartree':
float(gsr.energy_terms.e_hartree),
'e_hartree' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_corepsp':
float(gsr.energy_terms.e_corepsp),
'e_corepsp' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_corepspdc':
float(gsr.energy_terms.e_corepspdc),
'e_corepspdc' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_kinetic':
float(gsr.energy_terms.e_kinetic),
'e_kinetic' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_nonlocalpsp':
float(gsr.energy_terms.e_nonlocalpsp),
'e_nonlocalpsp' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_entropy':
float(gsr.energy_terms.e_entropy),
'e_entropy' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'entropy':
float(gsr.energy_terms.entropy),
'entropy' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_xc':
float(gsr.energy_terms.e_xc),
'e_xc' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_xcdc':
float(gsr.energy_terms.e_xcdc),
'e_xcdc' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_paw':
float(gsr.energy_terms.e_paw),
'e_paw' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_pawdc':
float(gsr.energy_terms.e_pawdc),
'e_pawdc' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_elecfield':
float(gsr.energy_terms.e_elecfield),
'e_elecfield' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_magfield':
float(gsr.energy_terms.e_magfield),
'e_magfield' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_fermie':
float(gsr.energy_terms.e_fermie),
'e_fermie' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_sicdc':
float(gsr.energy_terms.e_sicdc),
'e_sicdc' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_exactX':
float(gsr.energy_terms.e_exactX),
'e_exactX' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'h0':
float(gsr.energy_terms.h0),
'h0' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_electronpositron':
float(gsr.energy_terms.e_electronpositron),
'e_electronpositron' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'edc_electronpositron':
float(gsr.energy_terms.edc_electronpositron),
'edc_electronpositron' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e0_electronpositron':
float(gsr.energy_terms.e0_electronpositron),
'e0_electronpositron' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'e_monopole':
float(gsr.energy_terms.e_monopole),
'e_monopole' + UNITS_SUFFIX:
DEFAULT_ENERGY_UNITS,
'pressure':
float(gsr.pressure),
'pressure' + UNITS_SUFFIX:
DEFAULT_STRESS_UNITS
}
try:
# will return an integer 0 if non-magnetic calculation is run; convert it to a float
total_magnetization = float(gsr.ebands.get_collinear_mag())
gsr_data['total_magnetization'] = total_magnetization
gsr_data['total_magnetization' +
UNITS_SUFFIX] = DEFAULT_MAGNETIZATION_UNITS
except ValueError as valerr:
# get_collinear_mag will raise ValueError if it doesn't know what to do
if 'Cannot calculate collinear magnetization' in valerr.args[
0]:
pass
else:
raise valerr
try:
bands_data = BandsData()
bands_data.set_kpoints(gsr.ebands.kpoints.get_cart_coords())
bands_data.set_bands(np.array(gsr.ebands.eigens),
units=str(gsr.ebands.eigens.unit))
self.out('output_bands', bands_data)
except: # pylint: disable=bare-except
pass
self.out('output_parameters', Dict(dict=gsr_data))