def calculate_trim_wf(self):
"""Launch a pw_bands calculation on the TRIM points for the structure."""
self.report(
'Using parities at TRIM points to calculatte Z2 invariant.')
kpoints = generate_trim(self.ctx.current_structure,
self.inputs.dimensionality)
inputs = AttributeDict(
self.exposed_inputs(PwBaseWorkChain, namespace='band'))
inputs.clean_workdir = self.inputs.clean_workdir
inputs.pw.code = self.inputs.pw_code
inputs.pw.structure = self.ctx.current_structure
inputs.pw.parameters = inputs.pw.parameters.get_dict()
inputs.pw.parameters.setdefault('CONTROL', {})
inputs.pw.parameters['CONTROL']['calculation'] = 'bands'
inputs.pw.parent_folder = self.ctx.scf_folder
inputs.kpoints = kpoints
inputs = prepare_process_inputs(PwBaseWorkChain, inputs)
running = self.submit(PwBaseWorkChain, **inputs)
self.report('launching PwBaseWorkChain<{}> in {} mode'.format(
running.pk, 'bands'))
return ToContext(workchain_trim=running)
def run_nscf_crop(self):
"""Run the PwBaseWorkChain in nscf mode along the path of high-symmetry determined by seekpath."""
inputs = AttributeDict(self.exposed_inputs(PwBaseWorkChain, namespace='nscf_crop'))
inputs.metadata.call_link_label = 'nscf_crop'
# inputs.pw.metadata.options.max_wallclock_seconds *= 4
# inputs.kpoints_distance = self.inputs.kpoints_distance
inputs.pw.structure = self.ctx.current_structure
inputs.pw.parent_folder = self.ctx.current_folder
inputs.pw.parameters = inputs.pw.parameters.get_dict()
inputs.pw.parameters.setdefault('CONTROL', {})
inputs.pw.parameters.setdefault('SYSTEM', {})
inputs.pw.parameters.setdefault('ELECTRONS', {})
# The following flags always have to be set in the parameters, regardless of what caller specified in the inputs
inputs.pw.parameters['CONTROL']['calculation'] = 'nscf'
inputs.pop('kpoints_distance', None)
inputs.kpoints = self.ctx.kpoint_crop
# Only set the following parameters if not directly explicitly defined in the inputs
# inputs.pw.parameters['ELECTRONS'].setdefault('diagonalization', 'cg')
# inputs.pw.parameters['ELECTRONS'].setdefault('diago_full_acc', True)
# If `nbands_factor` is defined in the inputs we set the `nbnd` parameter
if 'nbands_factor_crop' in self.inputs:
factor = self.inputs.nbands_factor_crop.value
parameters = self.ctx.workchain_scf.outputs.output_parameters.get_dict()
if int(parameters['number_of_spin_components']) > 1:
nspin_factor = 2
else:
nspin_factor = 1
nbands = int(parameters['number_of_bands'])
nelectron = int(parameters['number_of_electrons'])
nbnd = max(
int(0.5 * nelectron * nspin_factor * factor),
int(0.5 * nelectron * nspin_factor) + 4 * nspin_factor,
nbands)
inputs.pw.parameters['SYSTEM']['nbnd'] = nbnd
# Otherwise set the current number of bands, unless explicitly set in the inputs
else:
inputs.pw.parameters['SYSTEM'].setdefault('nbnd', self.ctx.current_number_of_bands)
inputs = prepare_process_inputs(PwBaseWorkChain, inputs)
running = self.submit(PwBaseWorkChain, **inputs)
self.report('launching PwBaseWorkChain<{}> in {} mode for CROP grid'.format(running.pk, 'nscf'))
return ToContext(workchain_nscf_crop=running)
def first_bands_step(self):
"""Do a bandcalculation using the kpoints provided in `starting_kpoints`."""
self.ctx.iteration += 1
inputs = AttributeDict(deep_copy(self.ctx.inputs))
inputs.kpoints = self.inputs.starting_kpoints
try:
kpt = inputs.kpoints.get_kpoints()
except:
kpt = inputs.kpoints.get_kpoints_mesh(print_list=True)
nkpt = len(kpt)
if 'settings' in inputs.pw:
settings = inputs.pw.settings.get_dict()
if 'cmdline' in settings:
ptr = settings['cmdline']
npools = None
if '-npools' in ptr:
i = ptr.index('-npools')
npools = int(ptr[i + 1])
elif '-nk' in ptr:
i = ptr.index('-nk')
npools = int(ptr[i + 1])
if not npools is None and npools > nkpt:
self.report('WARNING: npools={} > nkpt={}'.format(
npools, nkpt))
for n in range(nkpt, 0, -1):
if npools % n == 0:
ptr[i + 1] = str(n)
self.report('... reducing npools to {}.'.format(n))
break
inputs.pw.settings = settings
inputs = prepare_process_inputs(PwBaseWorkChain, inputs)
running = self.submit(PwBaseWorkChain, **inputs)
self.report(
'launching PwBaseWorkChain<{}> in {} mode, iteration {}'.format(
running.pk, 'bands', self.ctx.iteration))
return ToContext(workchain_bands=append_(running))
def run_nscf(self):
"""Run the PwBaseWorkChain in bands mode along the path of high-symmetry determined by seekpath."""
inputs = AttributeDict(self.exposed_inputs(PwBaseWorkChain, namespace='nscf'))
inputs.metadata.call_link_label = 'nscf'
inputs.kpoints = self.ctx.bands_kpoints
inputs.pw.structure = self.ctx.current_structure
inputs.pw.parent_folder = self.ctx.current_folder
inputs.pw.parameters = inputs.pw.parameters.get_dict()
inputs.pw.parameters.setdefault('CONTROL', {})
inputs.pw.parameters.setdefault('SYSTEM', {})
inputs.pw.parameters.setdefault('ELECTRONS', {})
# The following flags always have to be set in the parameters, regardless of what caller specified in the inputs
inputs.pw.parameters['CONTROL']['calculation'] = 'nscf'
# Only set the following parameters if not directly explicitly defined in the inputs
inputs.pw.parameters['ELECTRONS'].setdefault('diagonalization', 'cg')
inputs.pw.parameters['ELECTRONS'].setdefault('diago_full_acc', True)
# If `nbands_factor` is defined in the inputs we set the `nbnd` parameter
factor = 1.2
parameters = self.ctx.workchain_scf.outputs.output_parameters.get_dict()
if int(parameters['number_of_spin_components']) > 1:
nspin_factor = 2
else:
nspin_factor = 1
nbands = int(parameters['number_of_bands'])
nelectron = int(parameters['number_of_electrons'])
nbnd = max(
int(0.5 * nelectron * nspin_factor * factor),
int(0.5 * nelectron * nspin_factor) + 4 * nspin_factor, nbands
)
inputs.pw.parameters['SYSTEM']['nbnd'] = nbnd
inputs.pw.parameters['SYSTEM']['nosym'] = True
inputs = prepare_process_inputs(PwBaseWorkChain, inputs)
running = self.submit(PwBaseWorkChain, **inputs)
self.report(f'launching PwBaseWorkChain<{running.pk}> in nscf mode')
return ToContext(workchain_nscf=running)
def setup_bands(self):
"""Set the inputs for the `bands` calculation."""
inputs = AttributeDict(
self.exposed_inputs(PwBaseWorkChain, namespace='bands'))
inputs.pw.code = self.inputs.code
inputs.kpoints = self.ctx.kpt_data
inputs.pw.pseudos = self.inputs.pseudos
inputs.pw.structure = self.inputs.structure
inputs.pw.parent_folder = self.ctx.remote
inputs.clean_workdir = self.inputs.clean_workdir
inputs.pw.parameters = inputs.pw.parameters.get_dict()
inputs.pw.parameters.setdefault('CONTROL', {})
inputs.pw.parameters['CONTROL']['calculation'] = 'bands'
inputs.pw.parameters['SYSTEM']['nosym'] = True
inputs = prepare_process_inputs(PwBaseWorkChain, inputs)
self.ctx.inputs = inputs
def run_bands(self):
"""Run the PwBaseWorkChain in bands mode along the path of high-symmetry determined by seekpath."""
# Get info from SCF on number of electrons and number of spin components
scf_out_dict = self.ctx.workchain_scf.outputs.output_parameters.get_dict()
nelectron = int(scf_out_dict['number_of_electrons'])
nspin = int(scf_out_dict['number_of_spin_components'])
nbands = max(
int(0.5 * nelectron * nspin * self.inputs.nbands_factor.value),
int(0.5 * nelectron * nspin) + 4 * nspin)
inputs = AttributeDict(self.exposed_inputs(PwBaseWorkChain, namespace='bands'))
inputs.pw.parameters = inputs.pw.parameters.get_dict()
inputs.pw.parameters.setdefault('CONTROL', {})
inputs.pw.parameters.setdefault('SYSTEM', {})
inputs.pw.parameters.setdefault('ELECTRONS', {})
inputs.pw.parameters['CONTROL']['restart_mode'] = 'restart'
inputs.pw.parameters['CONTROL']['calculation'] = 'bands'
inputs.pw.parameters['ELECTRONS']['diagonalization'] = 'cg'
inputs.pw.parameters['ELECTRONS']['diago_full_acc'] = True
inputs.pw.parameters['SYSTEM']['nbnd'] = nbands
if 'kpoints' not in self.inputs.bands:
inputs.kpoints = self.ctx.kpoints_path
inputs.pw.structure = self.ctx.current_structure
inputs.pw.parent_folder = self.ctx.current_folder
inputs = prepare_process_inputs(PwBaseWorkChain, inputs)
running = self.submit(PwBaseWorkChain, **inputs)
self.report('launching PwBaseWorkChain<{}> in {} mode'.format(running.pk, 'bands'))
return ToContext(workchain_bands=running)
def run_wannier90_pp(self):
"""The input of wannier90 calculation is build here.
:return: [description]
:rtype: [type]
"""
inputs = AttributeDict(
self.exposed_inputs(Wannier90Calculation, namespace='wannier90'))
inputs.structure = self.ctx.current_structure
parameters = inputs.parameters.get_dict()
# get nscf kmesh
inputs.kpoints = self.ctx.workchain_nscf.inputs.kpoints
# the input kpoints of nscf is an explicitly generated list of kpoints,
# we mush retrieve the original kmesh, and explicitly set w90 mp_grid keyword
parameters['mp_grid'] = self.ctx.nscf_kmesh.get_kpoints_mesh()[0]
# check num_bands, exclude_bands, nscf nbnd
nbnd = self.ctx.workchain_nscf.outputs.output_parameters.get_dict(
)['number_of_bands']
num_ex_bands = len(get_exclude_bands(inputs.parameters.get_dict()))
parameters['num_bands'] = nbnd - num_ex_bands
# set num_wann for auto_projections
if self.ctx.auto_projections:
if self.inputs.only_valence:
parameters['num_wann'] = parameters['num_bands']
inputs.parameters = orm.Dict(dict=parameters)
else:
inputs.parameters = orm.Dict(dict=parameters)
inputs.parameters = update_w90_params_numwann(
inputs.parameters,
self.ctx.calc_projwfc.outputs.projections)
self.report(
'number of Wannier functions extracted from projections: '
+ str(inputs.parameters['num_wann']))
# get scf Fermi energy
try:
energies_relative_to_fermi = self.inputs.get(
'wannier_energies_relative_to_fermi')
inputs.parameters = update_w90_params_fermi(
inputs.parameters,
self.ctx.workchain_scf.outputs.output_parameters,
energies_relative_to_fermi)
except TypeError:
self.report("Error in retriving the SCF Fermi energy "
"from pk: {}".format(self.ctx.workchain_scf))
return self.exit_codes.ERROR_SUB_PROCESS_FAILED_WANNIER90PP
#Check if settings is given in input
try:
settings = inputs['settings'].get_dict()
except KeyError:
settings = {}
settings['postproc_setup'] = True
inputs['settings'] = settings
inputs = prepare_process_inputs(Wannier90Calculation, inputs)
running = self.submit(Wannier90Calculation, **inputs)
self.report(
'wannier90 postproc step - launching Wannier90Calculation<{}> in postproc mode'
.format(running.pk))
return ToContext(calc_wannier90_pp=running)
def run_nscf(self):
"""
Run the PwBaseWorkChain in nscf mode
"""
inputs = AttributeDict(
self.exposed_inputs(PwBaseWorkChain, namespace='nscf'))
inputs.pw.structure = self.ctx.current_structure
inputs.pw.parent_folder = self.ctx.current_folder
inputs.pw.parameters = inputs.pw.parameters.get_dict()
inputs.pw.parameters.setdefault('CONTROL', {})
inputs.pw.parameters.setdefault('SYSTEM', {})
inputs.pw.parameters.setdefault('ELECTRONS', {})
inputs.pw.parameters['CONTROL']['restart_mode'] = 'from_scratch'
inputs.pw.parameters['CONTROL']['calculation'] = 'nscf'
inputs.pw.parameters['SYSTEM']['nosym'] = True
inputs.pw.parameters['SYSTEM']['noinv'] = True
inputs.pw.parameters['ELECTRONS']['diagonalization'] = 'cg'
inputs.pw.parameters['ELECTRONS']['diago_full_acc'] = True
if self.inputs.only_valence:
inputs.pw.parameters['SYSTEM']['occupations'] = 'fixed'
inputs.pw.parameters['SYSTEM'].pop(
'smearing', None) # pop None to avoid KeyError
inputs.pw.parameters['SYSTEM'].pop(
'degauss', None) # pop None to avoid KeyError
# inputs.pw.pseudos is an AttributeDict, but calcfunction only accepts
# orm.Data, so we unpack it to pass in orm.UpfData
inputs.pw.parameters = update_nscf_num_bands(
orm.Dict(dict=inputs.pw.parameters),
self.ctx.workchain_scf.outputs.output_parameters,
self.ctx.current_structure, self.inputs.only_valence,
**inputs.pw.pseudos)
self.report('nscf number of bands set as ' +
str(inputs.pw.parameters['SYSTEM']['nbnd']))
# check kmesh
try:
inputs.kpoints
except AttributeError:
# then kpoints_distance must exists, since this is ensured by inputs check of this workchain
from aiida_quantumespresso.workflows.functions.create_kpoints_from_distance import create_kpoints_from_distance
force_parity = inputs.get('kpoints_force_parity', orm.Bool(False))
kmesh = create_kpoints_from_distance(self.ctx.current_structure,
inputs.kpoints_distance,
force_parity)
#kpoints_data = orm.KpointsData()
# kpoints_data.set_cell_from_structure(self.ctx.current_structure)
# kmesh = kpoints_data.set_kpoints_mesh_from_density(inputs.kpoints_distance.value)
else:
try:
inputs.kpoints.get_kpoints_mesh()
except AttributeError:
self.report("nscf only support `mesh' type KpointsData")
return self.exit_codes.ERROR_SUB_PROCESS_FAILED_NSCF
else:
kmesh = inputs.kpoints
# convert kmesh to explicit list, since auto generated kpoints
# maybe different between QE & Wannier90. Here we explicitly
# generate a list of kpoint to avoid discrepencies between
# QE's & Wannier90's automatically generated kpoints.
self.ctx.nscf_kmesh = kmesh # store it since it will be used by w90
inputs.kpoints = convert_kpoints_mesh_to_list(kmesh)
inputs = prepare_process_inputs(PwBaseWorkChain, inputs)
running = self.submit(PwBaseWorkChain, **inputs)
self.report(
'nscf step - launching PwBaseWorkChain<{}> in {} mode'.format(
running.pk, 'nscf'))
return ToContext(workchain_nscf=running)
