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Improvements and bug fixes
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- Allow to set energy range from input
- Fix input of 'retrieve_kkrflex'
- Cleanup in workflow
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@PhilippRue
PhilippRue committed May 31, 2024
1 parent 9d595b4 commit 3cb63e4
Showing 1 changed file with 33 additions and 84 deletions.
117 changes: 33 additions & 84 deletions aiida_kkr/workflows/kkr_STM.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
__copyright__ = (u'Copyright (c), 2024, Forschungszentrum Jülich GmbH, '
'IAS-1/PGI-1, Germany. All rights reserved.')
__license__ = 'MIT license, see LICENSE.txt file'
__version__ = '0.1.0'
__version__ = '0.1.1'
__contributors__ = (u'Raffaele Aliberti', u'David Antognini Silva', u'Philipp Rüßmann')
_VERBOSE_ = True

Expand Down Expand Up @@ -175,9 +175,8 @@ def define(cls, spec):
spec.exit_code(102, 'ERROR_NO_IMP_POT_SFD', 'No impurity node has been given in the intput')
spec.exit_code(103, 'ERROR_NO_IMPURITY_INFO', 'No impurity info has been given in the input')
spec.exit_code(
104, 'ERROR_NO_DATA_FOR_THE_GF_STEP',
"""Neither the kkrflex files nor the KKR builder have been given. Please
provide already converged kkrflex files, or the kkr builder to evaluate them"""
104, 'ERROR_NO_DATA_FOR_THE_GF_STEP', """Neither the kkrflex files nor the KKR builder have been given.
Please provide already converged kkrflex files, or the kkr builder to evaluate them"""
)
spec.exit_code(201, 'ERROR_IMP_SUB_WORKFLOW_FAILURE', 'A step in the kkr_imp_dos workflow has failed')

Expand All @@ -186,10 +185,7 @@ def define(cls, spec):
cls.start,
# We first aggregate all the impurity data
# The gf is then used to evaluate the STM lmdos
#cls.gf_writeout_run,
cls.STM_lmdos_run,
# Data aggregator, used to make the final result more user friendly
# cls.finalize_results,
cls.results
)

Expand All @@ -204,9 +200,7 @@ def combine_potentials(self, host_structure, impurity_to_combine, da, db):
tip_position['ilayer'] = self.inputs.tip_position['ilayer']
tip_position['da'] = da
tip_position['db'] = db
#print(impurity_to_combine.get_dict())
imp_info = self.inputs.imp_info #(impurity to combine)
#host_remote = self.inputs.host_remote

combined_imp_info = get_imp_info_add_position(Dict(tip_position), host_structure, imp_info)
# Since the objects in AiiDA are immutable we have to create a new dictionary and then convert
Expand All @@ -218,27 +212,9 @@ def combine_potentials(self, host_structure, impurity_to_combine, da, db):

for key in impurity_to_combine.keys():
if key == 'Zimp':
#print(impurity_to_combine[key])
impurity_to_combine[key].append(combined_imp_info[key][-1])
#if key == 'Rimp_rel':
# np.append(impurity_to_combine[key], [combined_imp_info[key][-1]], axis=0)
# print(impurity_to_combine[key])
else:
#print(combined_imp_info[key][-1])
impurity_to_combine[key] = np.append(impurity_to_combine[key], [combined_imp_info[key][-1]], axis=0)
#print(impurity_to_combine[key])

#new_combined_imp_info[

#new_combined_imp_info[key] = impurity_to_combine[key].tolist()
#new_combined_imp_info[key].append(combined_imp_info[key][-1].tolist())
#new_combined_imp_info[key] = new_combined_imp_info[key].tolist()
#else:
# # Here we have lists of list that we need to confront
# new_combined_imp_info[key] = impurity_to_combine[key]
# set_tmp = [set(row) for row in impurity_to_combine[key]]
#
# new_combined_imp_info[key] += [row for row in combined_imp_info[key] if set(row) not in set_tmp]

# Convert to an AiiDA Dictionary
new_combined_imp_info = impurity_to_combine
Expand All @@ -255,15 +231,12 @@ def combine_nodes(self, host_calc, node_to_combine, da, db):
Here we create a combined potential node from the host potential (no impurity)
and from the impurity potential
"""
#imp_potential_node = self.inputs.imp_potential_node # (node_to_combine).
#host_remote = self.inputs.host_remote # the remote host structure remains the same.

# Since the objects in AiiDA are immutable we have to create a new dictionary and then convert
# it to the right AiiDA type

tip_position = {}
tip_position['ilayer'] = self.inputs.tip_position['ilayer'
] # for now we require that the z position remains the same.
# for now we require that the z position remains the same.
tip_position['ilayer'] = self.inputs.tip_position['ilayer']
tip_position['da'] = da
tip_position['db'] = db

Expand Down Expand Up @@ -297,7 +270,6 @@ def start(self):
self.report('INFO: usign defalut wf parameters')

# In this section we assign the computational resources to the builder

self.ctx.withmpi = options_dict.get('withmpi', self._options_default['withmpi'])
self.ctx.resources = options_dict.get('resources', self._options_default['resources'])
self.ctx.max_wallclock_seconds = options_dict.get(
Expand All @@ -316,7 +288,7 @@ def start(self):
})

# Set workflow parameters for the KKR imputrity calculations
"""This part is really important, this should always be set to True for an STM calculation"""
# This part is really important, this should always be set to True for an STM calculation
self.ctx.lmdos = wf_param_dict.get('lmdos', self._wf_default['lmdos'])

self.ctx.retrieve_kkrflex = wf_param_dict.get('retrieve_kkrflex', self._wf_default['retrieve_kkrflex'])
Expand All @@ -335,40 +307,30 @@ def start(self):
self.ctx.description_wf = self.inputs.get('description', self._wf_description)
self.ctx.label_wf = self.inputs.get('label', self._wf_label)

message = f"""
INFO: use the following parameter:
withmpi: {self.ctx.withmpi}
Resources: {self.ctx.resources}
Walltime (s): {self.ctx.max_wallclock_seconds}
queue name: {self.ctx.queue}
scheduler command: {self.ctx.custom_scheduler_commands}
description: {self.ctx.description_wf}
label: {self.ctx.label_wf}
"""
print(message)
self.report(message)

# return para/vars
self.ctx.successful = True
self.ctx.errors = []
self.ctx.formula = ''
if _VERBOSE_:
message = f"""
INFO: use the following parameter:
withmpi: {self.ctx.withmpi}
Resources: {self.ctx.resources}
Walltime (s): {self.ctx.max_wallclock_seconds}
queue name: {self.ctx.queue}
scheduler command: {self.ctx.custom_scheduler_commands}
description: {self.ctx.description_wf}
label: {self.ctx.label_wf}
"""
self.report(message)

def validate_input(self):

"""Check if inputs are valid"""
inputs = self.inputs
inputs_ok = True
gf_writeout_calc = None

if not 'imp_potential_node' in inputs:
inputs_ok = False
return self.exit_codes.ERROR_NO_IMP_POT_SFD # pylint: disable=no-member

if not 'imp_info' in inputs:
inputs_ok = False
return self.exit_codes.ERROR_NO_IMP_INFO # pylint: disable=no-member

if not 'kkrflex_files' and 'kkr' in inputs:
inputs_ok = False
return self.exit_codes.ERROR_NO_DATA_FOR_THE_GF_STEP # pylint: disable=no-member

def impurity_cluster_evaluation(self):
Expand Down Expand Up @@ -397,7 +359,6 @@ def impurity_cluster_evaluation(self):

# Since the combine tools use the element already in the units of da and db, we use a helper function
# to have the indices of the linear combination of the used position vectors in the base of the Bravais lattice.

coeff = tools_STM_scan.find_linear_combination_coefficients(struc_info['plane_vectors'], used_pos)

for element in coeff:
Expand Down Expand Up @@ -450,25 +411,24 @@ def STM_lmdos_run(self):
'nsteps': 1,
'kkr_runmax': 1,
'dos_run': True,
'retrieve_kkrflex': self.ctx.retrieve_kkrflex,
'lmdos': self.ctx.lmdos,
'jij_run': self.ctx.jij_run,
'dos_params': self.ctx.dos_params_dict
}
)

# We want to set the energy to the Fermi level

self.ctx.kkrimp_params_dict['dos_params']['emin'] = 0 - 0.005
self.ctx.kkrimp_params_dict['dos_params']['emax'] = 0 + 0.005
if 'emin' not in self.ctx.dos_params_dict:
self.ctx.kkrimp_params_dict['dos_params']['emin'] = 0 - 0.005
if 'emax' not in self.ctx.dos_params_dict:
self.ctx.kkrimp_params_dict['dos_params']['emax'] = 0 + 0.005

# Finally we overwrite the number of energy points to 1
# This is because we want many epoints around the impurity position

self.ctx.kkrimp_params_dict['dos_params'][
'nepts'] = 7 # Here 7 because of the interpolated files that aren't generated

#builder.metadata.label = label_imp # pylint: disable=no-member
#builder.metadata.description = description_imp # pylint: disable=no-member
if 'nepts' not in self.ctx.dos_params_dict:
self.ctx.kkrimp_params_dict['dos_params'][
'nepts'] = 7 # Here 7 because of the interpolated files that aren't generated

builder.wf_parameters = self.ctx.kkrimp_params_dict
# Host remote files that will be used for the actual plot step.
Expand All @@ -487,13 +447,12 @@ def STM_lmdos_run(self):
calc = self.submit(builder)

message = f"""INFO: running DOS step for an STM measurement (pk: {calc.pk}) at position
(ilayer: {self.inputs.tip_position['ilayer']}, da: {x}, db: {y} )"""
(ilayer: {self.inputs.tip_position['ilayer']}, da: {x}, db: {y} )"""

if 'params_kkr_overwrite' in self.inputs.BdG:
if self.inputs.BdG.params_kkr_overwrite:
message = f"""INFO: runnig DOS step (pk: {calc.pk}) BdG is present"""
message += f'\nINFO: runnig DOS step (pk: {calc.pk}) BdG is present'

print(message)
self.report(message)

# Save the calculated impurity cluster and impurity info in the context
Expand All @@ -503,32 +462,22 @@ def STM_lmdos_run(self):
return ToContext(STM_data=calc)

def results(self):
"""Collect results and return output nodes"""

if not self.ctx.STM_data.is_finished_ok:

message = 'ERROR: sub workflow for STM calculation failed'
print(message)
self.report(message)
self.report('ERROR: sub workflow for STM calculation failed')
return self.exit_codes.ERROR_IMP_SUB_WORKFLOW_FAILURE # pylint: disable=no-member

else:

# Declaring the output
self.out('STM_dos_data', self.ctx.STM_data.outputs.dos_data)
self.out('STM_dos_data_lmdos', self.ctx.STM_data.outputs.dos_data_lm)
#self.out("workflow_info", self.ctx.STM_lmdos.outputs.workflow_info)
self.out('tip_position', self.inputs.tip_position)
try:
if 'gf_dos_remote' in self.ctx.STM_data.outputs:
self.out('kkrflexfiles', self.ctx.STM_data.outputs.gf_dos_remote)
except:
pass

self.out('combined_imp_info', self.ctx.impurity_info)
self.out('combined_imp_potential', self.ctx.imp_pot_sfd)

message = 'INFO: created output nodes for KKR STM workflow.'
print(message)
self.report(message)
self.report('INFO: created output nodes for KKR STM workflow.')

self.report(
'\n'
Expand Down

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