From 3cb63e452a8a5798d0b2b319ac0d58e6c502270c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20R=C3=BC=C3=9Fmann?= Date: Fri, 31 May 2024 06:45:11 +0000 Subject: [PATCH] Improvements and bug fixes - Allow to set energy range from input - Fix input of 'retrieve_kkrflex' - Cleanup in workflow --- aiida_kkr/workflows/kkr_STM.py | 117 ++++++++++----------------------- 1 file changed, 33 insertions(+), 84 deletions(-) diff --git a/aiida_kkr/workflows/kkr_STM.py b/aiida_kkr/workflows/kkr_STM.py index 032d397c..591b3cee 100644 --- a/aiida_kkr/workflows/kkr_STM.py +++ b/aiida_kkr/workflows/kkr_STM.py @@ -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 @@ -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') @@ -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 ) @@ -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 @@ -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 @@ -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 @@ -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( @@ -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']) @@ -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): @@ -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: @@ -450,6 +411,7 @@ 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 @@ -457,18 +419,16 @@ def STM_lmdos_run(self): ) # 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. @@ -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 @@ -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'