def run_pdos(self):
"""Run the `PdosWorkChain`."""
inputs = AttributeDict(
self.exposed_inputs(PdosWorkChain, namespace="pdos"))
inputs.metadata.call_link_label = "pdos"
inputs.structure = self.ctx.current_structure
inputs.nscf.pw.parameters = inputs.nscf.pw.parameters.get_dict()
if self.ctx.current_number_of_bands:
inputs.nscf.pw.parameters.setdefault("SYSTEM", {}).setdefault(
"nbnd", self.ctx.current_number_of_bands)
if self.ctx.scf_parent_folder:
inputs.pop("scf")
inputs.nscf.pw.parent_folder = self.ctx.scf_parent_folder
else:
if "kpoints_distance_override" in self.inputs:
inputs.scf.kpoints_distance = self.inputs.kpoints_distance_override
if "degauss_override" in self.inputs:
inputs.scf.pw.parameters = inputs.scf.pw.parameters.get_dict()
inputs.scf.pw.parameters.setdefault(
"SYSTEM",
{})["degauss"] = self.inputs.degauss_override.value
inputs = prepare_process_inputs(PdosWorkChain, inputs)
running = self.submit(PdosWorkChain, **inputs)
self.report(f"launching PdosWorkChain<{running.pk}>")
return ToContext(workchain_pdos=running)
def run_relax(self):
"""Run the `PwRelaxWorkChain`."""
inputs = AttributeDict(
self.exposed_inputs(PwRelaxWorkChain, namespace="relax"))
inputs.metadata.call_link_label = "relax"
inputs.structure = self.ctx.current_structure
if "kpoints_distance_override" in self.inputs:
inputs.base.kpoints_distance = self.inputs.kpoints_distance_override
if "base_scf" in inputs:
inputs.base_scf.kpoints_distance = self.inputs.kpoints_distance_override
if "degauss_override" in self.inputs:
inputs.base.pw.parameters = inputs.base.pw.parameters.get_dict()
inputs.base.pw.parameters.setdefault(
"SYSTEM", {})["degauss"] = self.inputs.degauss_override.value
if "base_scf" in inputs:
inputs.base_scf_params.pw.parameters = (
inputs.base_scf_params.pw.parameters.get_dict())
inputs.base_scf_params.pw.parameters.setdefault(
"SYSTEM",
{})["degauss"] = self.inputs.degauss_override.value
inputs = prepare_process_inputs(PwRelaxWorkChain, inputs)
running = self.submit(PwRelaxWorkChain, **inputs)
self.report(f"launching PwRelaxWorkChain<{running.pk}>")
return ToContext(workchain_relax=running)
def get_inputs_first_scf(self):
"""
Initialize inputs for the first iteration.
"""
input_scf = AttributeDict(
self.exposed_inputs(FleurScfWorkChain, namespace='scf'))
input_scf.metadata.label = 'SCF_forces'
input_scf.metadata.description = 'The SCF workchain converging forces, part of the Relax'
if self.ctx.wf_dict['break_symmetry']:
calc_para = None
if 'calc_parameters' in input_scf:
calc_para = input_scf.calc_parameters
# currently we always break the full symmetry
break_dict = Dict(dict={'atoms': ['all']}) # for provenance
broken_sys = break_symmetry_wf(input_scf.structure,
wf_para=break_dict,
parameterdata=calc_para)
input_scf.structure = broken_sys['new_structure']
input_scf.calc_parameters = broken_sys['new_parameters']
if 'wf_parameters' not in input_scf:
scf_wf_dict = {}
else:
scf_wf_dict = input_scf.wf_parameters.get_dict()
if 'inpxml_changes' not in scf_wf_dict:
scf_wf_dict['inpxml_changes'] = []
scf_wf_dict['mode'] = 'force'
if self.ctx.wf_dict['film_distance_relaxation']:
scf_wf_dict['inpxml_changes'].append(('set_atomgr_att', {
'attributedict': {
'force': [('relaxXYZ', 'FFT')]
},
'species': 'all'
}))
for specie_off in self.ctx.wf_dict['atoms_off']:
scf_wf_dict['inpxml_changes'].append(('set_atomgr_att_label', {
'attributedict': {
'force': [('relaxXYZ', 'FFF')]
},
'atom_label': specie_off
}))
scf_wf_dict['inpxml_changes'].append(('set_atomgr_att_label', {
'attributedict': {
'force': [('relaxXYZ', 'FFF')]
},
'atom_label': '49'
}))
input_scf.wf_parameters = Dict(dict=scf_wf_dict)
return input_scf
def run_relax(self):
"""Run the PwRelaxWorkChain to run a relax PwCalculation."""
inputs = AttributeDict(self.exposed_inputs(PwRelaxWorkChain, namespace='relax'))
inputs.structure = self.ctx.current_structure
running = self.submit(PwRelaxWorkChain, **inputs)
self.report('launching PwRelaxWorkChain<{}>'.format(running.pk))
return ToContext(workchain_relax=running)
def run_relax(self):
"""Run the PwRelaxWorkChain to run a relax PwCalculation."""
inputs = AttributeDict(self.exposed_inputs(PwRelaxWorkChain, namespace='relax'))
inputs.metadata.call_link_label = 'relax'
inputs.structure = self.ctx.current_structure
running = self.submit(PwRelaxWorkChain, **inputs)
self.report(f'launching PwRelaxWorkChain<{running.pk}>')
return ToContext(workchain_relax=running)
def run_find_crossings(self):
"""Run the FindCrossingsWorkChain to find bands crossings."""
inputs = AttributeDict(
self.exposed_inputs(FindCrossingsWorkChain, namespace='find'))
inputs.structure = self.ctx.current_structure
inputs.code = self.inputs.pw_code
running = self.submit(FindCrossingsWorkChain, **inputs)
self.report('launching FindCrossingsWorkChain<{}>'.format(running.pk))
return ToContext(workchain_find=running)
def prepare_z2pack(self):
"""Prepare the inputs for the z2pack calculations."""
inputs = AttributeDict(
self.exposed_inputs(Z2packBaseWorkChain, namespace='z2pack_base'))
inputs.pw_code = self.inputs.pw_code
inputs.structure = self.ctx.current_structure
inputs.parent_folder = self.ctx.remote_scf
self.ctx.inputs = inputs
self.ctx.iteration = 0
self.ctx.max_iteration = len(self.ctx.crossings)
self.ctx.workchain_z2pack = []
def prepare_eos(self):
"""
Initialize inputs for eos workflow:
wf_param, options, calculation parameters, codes, structure
"""
inputs = AttributeDict(self.exposed_inputs(FleurEosWorkChain, namespace='eos'))
inputs.metadata.label = 'EOS_substrate'
inputs.metadata.description = 'The EOS workchain finding equilibrium substrate'
# Here wf_dict nodes appears out of nowwhere.
inputs.structure = create_substrate_bulk(Dict(dict=self.ctx.wf_dict))
if not isinstance(inputs.structure, StructureData):
return inputs, inputs.structure # exit code thrown in create_substrate_bulk
return inputs, None
def prepare_z2pack(self):
"""Prepare the inputs for the z2ack calculation."""
self.report('Using z2pack to calculatte Z2 invariant.')
inputs = AttributeDict(
self.exposed_inputs(Z2packBaseWorkChain, namespace='z2pack_base'))
inputs.pw_code = self.inputs.pw_code
inputs.structure = self.ctx.current_structure
inputs.parent_folder = self.ctx.scf_folder
settings = inputs.z2pack.z2pack_settings.get_dict()
settings.update({
'dimension_mode': '2D',
'invariant': 'Z2',
})
self.ctx.inputs = inputs
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)