Source code for aiida_fleur.workflows.mae

# -*- coding: utf-8 -*-
###############################################################################
# Copyright (c), Forschungszentrum Jülich GmbH, IAS-1/PGI-1, Germany.         #
#                All rights reserved.                                         #
# This file is part of the AiiDA-FLEUR package.                               #
#                                                                             #
# The code is hosted on GitHub at https://github.com/JuDFTteam/aiida-fleur    #
# For further information on the license, see the LICENSE.txt file            #
# For further information please visit http://www.flapw.de or                 #
# http://aiida-fleur.readthedocs.io/en/develop/                               #
###############################################################################
"""
    In this module you find the workflow 'FleurMaeWorkChain' for the calculation of
    Magnetic Anisotropy Energy via the force theorem.
"""

from __future__ import absolute_import
import copy

import six
#from six.moves import map
from lxml import etree

from aiida.engine import WorkChain, ToContext, if_
from aiida.engine import calcfunction as cf
from aiida.orm import Code, load_node
from aiida.orm import RemoteData, Dict
from aiida.common import AttributeDict
from aiida.common.exceptions import NotExistent

from aiida_fleur.tools.common_fleur_wf import test_and_get_codenode, get_inputs_fleur
from aiida_fleur.workflows.scf import FleurScfWorkChain
from aiida_fleur.workflows.base_fleur import FleurBaseWorkChain
from aiida_fleur.data.fleurinpmodifier import FleurinpModifier
from aiida_fleur.data.fleurinp import FleurinpData, get_fleurinp_from_remote_data
from aiida_fleur.common.constants import HTR_TO_EV


[docs]class FleurMaeWorkChain(WorkChain): """ This workflow calculates the Magnetic Anisotropy Energy of a structure. """ _workflowversion = '0.3.0' _default_options = { 'resources': { 'num_machines': 1, 'num_mpiprocs_per_machine': 1 }, 'max_wallclock_seconds': 2 * 60 * 60, 'queue_name': '', 'custom_scheduler_commands': '', 'import_sys_environment': False, 'environment_variables': {} } _default_wf_para = { 'sqa_ref': [0.7, 0.7], 'use_soc_ref': False, 'sqas_theta': [0.0, 1.57079, 1.57079], 'sqas_phi': [0.0, 0.0, 1.57079], 'add_comp_para': { 'serial': False, 'only_even_MPI': False, 'max_queue_nodes': 20, 'max_queue_wallclock_sec': 86400 }, 'soc_off': [], 'inpxml_changes': [], }
[docs] @classmethod def define(cls, spec): super().define(spec) spec.expose_inputs(FleurScfWorkChain, namespace_options={ 'required': False, 'populate_defaults': False }, namespace='scf') spec.input('wf_parameters', valid_type=Dict, required=False) spec.input('fleur', valid_type=Code, required=True) spec.input('remote', valid_type=RemoteData, required=False) spec.input('fleurinp', valid_type=FleurinpData, required=False) spec.input('options', valid_type=Dict, required=False) spec.outline(cls.start, if_(cls.scf_needed)( cls.converge_scf, cls.force_after_scf, ).else_( cls.force_wo_scf, ), cls.get_results, cls.return_results) spec.output('output_mae_wc_para', valid_type=Dict) # exit codes spec.exit_code(230, 'ERROR_INVALID_INPUT_PARAM', message='Invalid workchain parameters.') spec.exit_code(231, 'ERROR_INVALID_INPUT_CONFIG', message='Invalid input configuration.') spec.exit_code(233, 'ERROR_INVALID_CODE_PROVIDED', message='Invalid code node specified, check inpgen and fleur code nodes.') spec.exit_code(235, 'ERROR_CHANGING_FLEURINPUT_FAILED', message='Input file modification failed.') spec.exit_code(236, 'ERROR_INVALID_INPUT_FILE', message="Input file was corrupted after user's modifications.") spec.exit_code(334, 'ERROR_REFERENCE_CALCULATION_FAILED', message='Reference calculation failed.') spec.exit_code(335, 'ERROR_REFERENCE_CALCULATION_NOREMOTE', message='Found no reference calculation remote repository.') spec.exit_code(336, 'ERROR_FORCE_THEOREM_FAILED', message='Force theorem calculation failed.')
[docs] def start(self): """ Retrieve and initialize paramters of the WorkChain """ self.report('INFO: started Magnetic Anisotropy Energy calculation workflow version {}\n' ''.format(self._workflowversion)) self.ctx.info = [] self.ctx.warnings = [] self.ctx.errors = [] self.ctx.t_energydict = [] self.ctx.mae_thetas = [] self.ctx.mae_phis = [] self.ctx.fleuroutuuid = None # initialize the dictionary using defaults if no wf paramters are given wf_default = copy.deepcopy(self._default_wf_para) if 'wf_parameters' in self.inputs: wf_dict = self.inputs.wf_parameters.get_dict() else: wf_dict = wf_default extra_keys = [] for key in wf_dict.keys(): if key not in wf_default.keys(): extra_keys.append(key) if extra_keys: error = 'ERROR: input wf_parameters for MAE contains extra keys: {}'.format(extra_keys) self.report(error) return self.exit_codes.ERROR_INVALID_INPUT_PARAM # extend wf parameters given by user using defaults for key, val in six.iteritems(wf_default): wf_dict[key] = wf_dict.get(key, val) self.ctx.wf_dict = wf_dict # switch off SOC on an atom specie for atom_label in self.ctx.wf_dict['soc_off']: self.ctx.wf_dict['inpxml_changes'].append(('set_species_label', { 'at_label': atom_label, 'attributedict': { 'special': { 'socscale': 0.0 } }, 'create': True })) # Check if sqas_theta and sqas_phi have the same length if len(self.ctx.wf_dict.get('sqas_theta')) != len(self.ctx.wf_dict.get('sqas_phi')): error = ('Number of sqas_theta has to be equal to the number of sqas_phi') self.control_end_wc(error) return self.exit_codes.ERROR_INVALID_INPUT_PARAM # initialize the dictionary using defaults if no options are given defaultoptions = self._default_options if 'options' in self.inputs: options = self.inputs.options.get_dict() else: options = defaultoptions # extend options given by user using defaults for key, val in six.iteritems(defaultoptions): options[key] = options.get(key, val) self.ctx.options = options # Check if user gave valid fleur executable inputs = self.inputs if 'fleur' in inputs: try: test_and_get_codenode(inputs.fleur, 'fleur.fleur', use_exceptions=True) except ValueError: error = ('The code you provided for FLEUR does not use the plugin fleur.fleur') self.control_end_wc(error) return self.exit_codes.ERROR_INVALID_CODE_PROVIDED # Check if user gave an input setup making any sense if 'scf' in inputs: self.ctx.scf_needed = True if 'remote' in inputs: error = 'ERROR: you gave SCF input + remote for the FT' self.control_end_wc(error) return self.exit_codes.ERROR_INVALID_INPUT_CONFIG if 'fleurinp' in inputs: error = 'ERROR: you gave SCF input + fleurinp for the FT' self.control_end_wc(error) return self.exit_codes.ERROR_INVALID_INPUT_CONFIG elif 'remote' not in inputs: error = 'ERROR: you gave neither SCF input nor remote for the FT' self.control_end_wc(error) return self.exit_codes.ERROR_INVALID_INPUT_CONFIG else: self.ctx.scf_needed = False
[docs] def scf_needed(self): """ Returns True if SCF WC is needed. """ return self.ctx.scf_needed
[docs] def converge_scf(self): """ Converge charge density with or without SOC. Submit a single Fleur calculation to obtain a reference for further force theorem calculations. """ inputs = self.get_inputs_scf() res = self.submit(FleurScfWorkChain, **inputs) return ToContext(reference=res)
[docs] def get_inputs_scf(self): """ Initialize inputs for scf workflow: wf_param, options, calculation parameters, codes, structure """ input_scf = AttributeDict(self.exposed_inputs(FleurScfWorkChain, namespace='scf')) 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'] = [] soc = self.ctx.wf_dict.get('sqa_ref') if not self.ctx.wf_dict.get('use_soc_ref'): scf_wf_dict['inpxml_changes'].append(('set_inpchanges', {'change_dict': {'l_soc': False}})) else: # set soc parameters explicitly changes_dict = {'theta': soc[0], 'phi': soc[1], 'l_soc': True} scf_wf_dict['inpxml_changes'].append(('set_inpchanges', {'change_dict': changes_dict})) input_scf.wf_parameters = Dict(dict=scf_wf_dict) if 'structure' in input_scf: if 'calc_parameters' in input_scf: calc_parameters = input_scf.calc_parameters.get_dict() else: calc_parameters = {} calc_parameters['soc'] = {'theta': soc[0], 'phi': soc[1]} input_scf.calc_parameters = Dict(dict=calc_parameters) return input_scf
[docs] def change_fleurinp(self): """ This routine sets somethings in the fleurinp file before running a fleur calculation. """ if self.ctx.scf_needed: try: fleurin = self.ctx.reference.outputs.fleurinp except NotExistent: error = 'Fleurinp generated in the reference calculation is not found.' self.control_end_wc(error) return self.exit_codes.ERROR_REFERENCE_CALCULATION_FAILED else: if 'fleurinp' in self.inputs: fleurin = self.inputs.fleurinp else: # In this case only remote is given # fleurinp data has to be generated from the remote inp.xml file fleurin = get_fleurinp_from_remote_data(self.inputs.remote) # copy default changes fchanges = self.ctx.wf_dict.get('inpxml_changes', []) # add forceTheorem tag into inp.xml fchanges.extend([ ('create_tag', { 'xpath': '/fleurInput', 'newelement': 'forceTheorem' }), ('create_tag', { 'xpath': '/fleurInput/forceTheorem', 'newelement': 'MAE' }), ('xml_set_attribv_occ', { 'xpathn': '/fleurInput/forceTheorem/MAE', 'attributename': 'theta', 'attribv': ' '.join(six.moves.map(str, self.ctx.wf_dict.get('sqas_theta'))) }), ('xml_set_attribv_occ', { 'xpathn': '/fleurInput/forceTheorem/MAE', 'attributename': 'phi', 'attribv': ' '.join(six.moves.map(str, self.ctx.wf_dict.get('sqas_phi'))) }), ('set_inpchanges', { 'change_dict': { 'itmax': 1, 'l_soc': True } }), ]) if fchanges: # change inp.xml file fleurmode = FleurinpModifier(fleurin) avail_ac_dict = fleurmode.get_avail_actions() # apply further user dependend changes for change in fchanges: function = change[0] para = change[1] method = avail_ac_dict.get(function, None) if not method: error = ("ERROR: Input 'inpxml_changes', function {} " 'is not known to fleurinpmodifier class, ' 'please check/test your input. I abort...' ''.format(function)) self.control_end_wc(error) return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED else: # apply change method(**para) # validate? try: fleurmode.show(display=False, validate=True) except etree.DocumentInvalid: error = ('ERROR: input, user wanted inp.xml changes did not validate') self.report(error) return self.exit_codes.ERROR_INVALID_INPUT_FILE # apply out = fleurmode.freeze() self.ctx.fleurinp = out return else: # otherwise do not change the inp.xml self.ctx.fleurinp = fleurin return
[docs] def force_after_scf(self): """ Calculate energy of a system for given SQAs using the force theorem. Converged reference is stored in self.ctx['xyz']. """ calc = self.ctx.reference if not calc.is_finished_ok: message = ('The reference SCF calculation was not successful.') self.control_end_wc(message) return self.exit_codes.ERROR_REFERENCE_CALCULATION_FAILED try: outpara_node = calc.outputs.output_scf_wc_para except NotExistent: message = ('The reference SCF calculation failed, no scf output node.') self.control_end_wc(message) return self.exit_codes.ERROR_REFERENCE_CALCULATION_FAILED outpara = outpara_node.get_dict() t_e = outpara.get('total_energy', 'failed') if not isinstance(t_e, float): message = ('Did not manage to extract float total energy from the reference SCF calculation.') self.control_end_wc(message) return self.exit_codes.ERROR_REFERENCE_CALCULATION_FAILED self.report('INFO: run Force theorem calculations') status = self.change_fleurinp() if status: return status fleurin = self.ctx.fleurinp # Do not copy mixing_history* files from the parent settings = {'remove_from_remotecopy_list': ['mixing_history*']} # Retrieve remote folder of the reference calculation pk_last = 0 scf_ref_node = load_node(calc.pk) for i in scf_ref_node.called: if i.node_type == 'process.workflow.workchain.WorkChainNode.': if i.process_class is FleurBaseWorkChain: if pk_last < i.pk: pk_last = i.pk try: remote = load_node(pk_last).outputs.remote_folder except AttributeError: message = ('Found no remote folder of the reference scf calculation.') self.control_end_wc(message) return self.exit_codes.ERROR_REFERENCE_CALCULATION_NOREMOTE label = 'MAE_force_theorem' description = 'This is the force theorem calculation for MAE.' code = self.inputs.fleur options = self.ctx.options.copy() inputs_builder = get_inputs_fleur(code, remote, fleurin, options, label, description, settings, add_comp_para=self.ctx.wf_dict['add_comp_para']) future = self.submit(FleurBaseWorkChain, **inputs_builder) return ToContext(f_t=future)
[docs] def force_wo_scf(self): """ Submit FLEUR force theorem calculation using input remote """ self.report('INFO: run Force theorem calculations') status = self.change_fleurinp() if status: return status fleurin = self.ctx.fleurinp # Do not copy mixing_history* files from the parent settings = {'remove_from_remotecopy_list': ['mixing_history*']} # Retrieve remote folder from the inputs remote = self.inputs.remote label = 'Force_theorem_calculation' description = 'This is a force theorem calculation for all SQA' code = self.inputs.fleur options = self.ctx.options.copy() inputs_builder = get_inputs_fleur(code, remote, fleurin, options, label, description, settings, add_comp_para=self.ctx.wf_dict['add_comp_para']) future = self.submit(FleurBaseWorkChain, **inputs_builder) return ToContext(f_t=future)
[docs] def get_results(self): """ Generates results of the workchain. """ t_energydict = [] mae_thetas = [] mae_phis = [] fleur_output_uuid = None try: calculation = self.ctx.f_t if not calculation.is_finished_ok: message = ('ERROR: Force theorem Fleur calculation failed somehow it has ' 'exit status {}'.format(calculation.exit_status)) self.control_end_wc(message) return self.exit_codes.ERROR_FORCE_THEOREM_FAILED except AttributeError: message = 'ERROR: Something went wrong I do not have a force theorem Fleur calculation' self.control_end_wc(message) return self.exit_codes.ERROR_FORCE_THEOREM_FAILED try: fleurout = calculation.outputs.output_parameters fleur_output_uuid = fleurout.uuid out_dict = fleurout.dict t_energydict = out_dict.mae_force_evsum mae_thetas = out_dict.mae_force_theta mae_phis = out_dict.mae_force_phi e_u = out_dict.mae_force_units minenergy = min(t_energydict) if e_u in ['Htr', 'htr']: t_energydict = [HTR_TO_EV * (x - minenergy) for x in t_energydict] else: t_energydict = [(x - minenergy) for x in t_energydict] except AttributeError as e_message: message = ('Did not manage to read evSum or energy units after FT calculation. {}'.format(e_message)) self.control_end_wc(message) return self.exit_codes.ERROR_FORCE_THEOREM_FAILED self.ctx.t_energydict = t_energydict self.ctx.mae_thetas = mae_thetas self.ctx.mae_phis = mae_phis self.ctx.fleuroutuuid = fleur_output_uuid
[docs] def return_results(self): """ This function outputs results of the wc """ out = { 'workflow_name': self.__class__.__name__, 'workflow_version': self._workflowversion, # 'initial_structure': self.inputs.structure.uuid, 'is_it_force_theorem': True, 'maes': self.ctx.t_energydict, 'theta': self.ctx.mae_thetas, 'phi': self.ctx.mae_phis, 'mae_units': 'eV', 'info': self.ctx.info, 'warnings': self.ctx.warnings, 'errors': self.ctx.errors } # ensure provenance of output nodes out_dict = {'out': Dict(dict=out)} if self.ctx.fleuroutuuid is not None: out_dict['last_fleur_out'] = load_node(self.ctx.fleuroutuuid) out_nodes = save_mae_output_node(**out_dict) out = out_nodes.get('output_mae_wc_para') # make wc return out node self.out('output_mae_wc_para', out)
[docs] def control_end_wc(self, errormsg): """ Controlled way to shutdown the workchain. will initialize the output nodes The shutdown of the workchain will has to be done afterwards """ self.report(errormsg) # because return_results still fails somewhen self.ctx.errors.append(errormsg) self.return_results()
[docs]@cf def save_mae_output_node(**kwargs): """ This is a pseudo cf, to create the right graph structure of AiiDA. This calcfunction will create the output node in the database. It also connects the output_node to all nodes the information comes from. So far it is just also parsed in as argument, because so far we are to lazy to put most of the code overworked from return_results in here. """ for key, val in six.iteritems(kwargs): if key == 'out': # should be always there outpara = val outdict = {} # clone, because we rather produce the same node twice then have a circle in the database for outputnode = outpara.clone() outputnode.label = 'output_mae_wc_para' outputnode.description = ('Contains magnetic anisotropy results and information of an FleurMaeWorkChain run.') outdict['output_mae_wc_para'] = outputnode return outdict