# -*- 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, CalcJobNode
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
[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': {}
}
_wf_default = {
'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],
'serial': False,
'soc_off': [],
'inpxml_changes': [],
}
@classmethod
def define(cls, spec):
super(FleurMaeWorkChain, cls).define(spec)
spec.expose_inputs(FleurScfWorkChain, 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._wf_default)
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 inputs.scf:
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 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
remote_node = self.inputs.remote
for link in remote_node.get_incoming().all():
if isinstance(link.node, CalcJobNode):
parent_calc_node = link.node
retrieved_node = parent_calc_node.get_outgoing().get_node_by_label('retrieved')
fleurin = FleurinpData(files=['inp.xml'], node=retrieved_node)
# 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,
serial=self.ctx.wf_dict['serial'])
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,
serial=self.ctx.wf_dict['serial'])
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 = []
htr_to_ev = 27.21138602
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.energy_units
minenergy = min(t_energydict)
if e_u == 'Htr' or '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