Source code for aiida_fleur.workflows.ssdisp
###############################################################################
# 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 'FleurSSDispWorkChain' for the calculation of
spin spiral dispersion using scalar-relatevistic Hamiltonian.
"""
import copy
from typing import Type
from lxml import etree
from ase.dft.kpoints import monkhorst_pack
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, KpointsData
from aiida.common import AttributeDict
from aiida.common.exceptions import NotExistent
from masci_tools.util.constants import HTR_TO_EV
from aiida_fleur.tools.common_fleur_wf import test_and_get_codenode
from aiida_fleur.tools.common_fleur_wf import get_inputs_fleur
from aiida_fleur.workflows.scf import FleurScfWorkChain
from aiida_fleur.data.fleurinpmodifier import FleurinpModifier, inpxml_changes
from aiida_fleur.workflows.base_fleur import FleurBaseWorkChain
from aiida_fleur.data.fleurinp import FleurinpData, get_fleurinp_from_remote_data
[docs]class FleurSSDispWorkChain(WorkChain):
"""
This workflow calculates spin spiral dispersion 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 = {
'beta': {
'all': 1.57079
},
'prop_dir': [1.0, 0.0, 0.0],
'q_vectors': [[0.0, 0.0, 0.0], [0.125, 0.0, 0.0], [0.250, 0.0, 0.0], [0.375, 0.0, 0.0]],
'ref_qss': [0.0, 0.0, 0.0],
'add_comp_para': {
'only_even_MPI': False,
'max_queue_nodes': 20,
'max_queue_wallclock_sec': 86400
},
'kmesh_force_theorem': None,
'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_ssdisp_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(f'INFO: started Spin Stiffness calculation workflow version {self._workflowversion}\n')
self.ctx.info = []
self.ctx.warnings = []
self.ctx.errors = []
self.ctx.energy_dict = []
# 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 = f'ERROR: input wf_parameters for SSDisp contains extra keys: {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 wf_default.items():
wf_dict[key] = wf_dict.get(key, val)
self.ctx.wf_dict = wf_dict
if wf_dict['ref_qss'] != wf_dict['q_vectors'][0]:
error = ('The first q_vector of the forceTheorem step has to be equal to'
'the q vector of the reference calculation.')
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 defaultoptions.items():
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')
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 converge_scf(self):
"""
Converge charge density for collinear case which is a reference for futher
spin spiral calculations.
"""
inputs = self.get_inputs_scf()
res = self.submit(FleurScfWorkChain, **inputs)
return ToContext(reference=res)
[docs] def get_inputs_scf(self):
"""
Initialize inputs for the scf cycle
"""
input_scf = AttributeDict(self.exposed_inputs(FleurScfWorkChain, namespace='scf'))
input_scf.metadata.label = 'reference_scf_SSDisp'
input_scf.metadata.description = ('The SCF workchain converging reference charge'
' density for Spin Spiral Dispersion')
if 'wf_parameters' not in input_scf:
scf_wf_dict = {}
else:
scf_wf_dict = input_scf.wf_parameters.get_dict()
with inpxml_changes(scf_wf_dict) as fm:
if [x for x in self.ctx.wf_dict['ref_qss'] if x != 0]:
fm.set_inpchanges({'qss': self.ctx.wf_dict['ref_qss'], 'l_noco': True, 'ctail': False, 'l_ss': True})
else:
fm.set_inpchanges({'qss': ' 0.0 0.0 0.0 ', 'l_noco': False, 'ctail': True, 'l_ss': False})
# change beta parameter
for key, val in self.ctx.wf_dict['beta'].items():
fm.set_atomgroup_label(key, {'nocoParams': {'beta': val}})
input_scf.wf_parameters = Dict(scf_wf_dict)
if 'structure' in input_scf: # add info about spin spiral propagation
if 'calc_parameters' in input_scf:
calc_parameters = input_scf.calc_parameters.get_dict()
else:
calc_parameters = {}
calc_parameters['qss'] = {
'x': self.ctx.wf_dict['prop_dir'][0],
'y': self.ctx.wf_dict['prop_dir'][1],
'z': self.ctx.wf_dict['prop_dir'][2]
}
input_scf.calc_parameters = Dict(calc_parameters)
return input_scf
[docs] def change_fleurinp(self):
"""
This routine sets somethings in the fleurinp file before running a fleur
calculation.
"""
self.report('INFO: run change_fleurinp')
if self.ctx.scf_needed: # use fleurinp from scf wc
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: # use the given fleurinp
fleurin = self.inputs.fleurinp
else: # or generate a new one from inp.xml located in the remote folder
fleurin = get_fleurinp_from_remote_data(self.inputs.remote)
# copy inpchanges from wf parameters
with inpxml_changes(self.ctx.wf_dict) as fm:
fm.set_complex_tag('spinSpiralDispersion', {'q': self.ctx.wf_dict['q_vectors']}, create=True)
fm.set_inpchanges({'itmax': 1, 'l_noco': True, 'ctail': False, 'l_ss': True})
if self.ctx.wf_dict['kmesh_force_theorem'] is not None:
kmesh = KpointsData()
kmesh.set_kpoints(monkhorst_pack(self.ctx.wf_dict['kmesh_force_theorem']))
kmesh.store()
fm.set_kpointsdata(kmesh.uuis, switch=True, kpoint_type='mesh')
# change beta parameter
for label, beta in self.ctx.wf_dict['beta'].items():
fm.set_atomgroup_label(label, {'nocoParams': {'beta': beta}})
fleurmode = FleurinpModifier(fleurin)
try:
fleurmode.add_task_list(self.ctx.wf_dict['inpxml_changes'])
except (ValueError, TypeError) as exc:
error = ('ERROR: Changing the inp.xml file failed. Tried to apply inpxml_changes'
f', which failed with {exc}. I abort, good luck next time!')
self.control_end_wc(error)
return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED
# 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
except (ValueError, TypeError) as exc:
error = ('ERROR: input, user wanted inp.xml changes could not be applied.'
f'The following error was raised {exc}')
self.control_end_wc(error)
return self.exit_codes.ERROR_CHANGING_FLEURINPUT_FAILED
# apply
out = fleurmode.freeze()
self.ctx.fleurinp = out
[docs] def force_after_scf(self):
'''
This routine uses the force theorem to calculate energies dispersion of
spin spirals. The force theorem calculations implemented into the FLEUR
code. Hence a single iteration FLEUR input file having <forceTheorem> tag
has to be created and submitted.
'''
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()
if 'total_energy' not in outpara:
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 = '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 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 = 'SSDisp_force_theorem'
description = 'This is the force theorem calculation for Spin Spiral Dispersion.'
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 = []
try:
calculation = self.ctx.f_t
if not calculation.is_finished_ok:
message = f'ERROR: Force theorem Fleur calculation failed somehow it has exit status {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:
out_dict = calculation.outputs.output_parameters.dict
t_energydict = out_dict.spst_force_evsum
e_u = out_dict.spst_force_units
# Find a minimal value of SpSp and count it as 0
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]
self.ctx.energy_dict = t_energydict
except AttributeError:
message = ('Did not manage to read evSum or energy units after FT calculation.')
self.control_end_wc(message)
return self.exit_codes.ERROR_FORCE_THEOREM_FAILED
[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, # parse from fleurinp or remove
'is_it_force_theorem': True,
'energies': self.ctx.energy_dict,
'q_vectors': self.ctx.wf_dict['q_vectors'],
'energy_units': 'eV',
'info': self.ctx.info,
'warnings': self.ctx.warnings,
'errors': self.ctx.errors
}
out = save_output_node(Dict(dict=out))
self.out('output_ssdisp_wc_para', out)
[docs] def control_end_wc(self, errormsg):
"""
Controlled way to shutdown the workchain. It will initialize the output nodes
The shutdown of the workchain will has to be done afterwards
"""
self.report(errormsg) # because return_results still fails sometimes
self.ctx.errors.append(errormsg)
self.return_results()
[docs]@cf
def save_output_node(out):
"""
This calcfunction saves the out dict in the db
"""
out_wc = out.clone()
return out_wc