Source code for aiida_fleur.workflows.dos

# -*- 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/                               #
###############################################################################
"""
This is the worklfow 'dos' for the Fleur code, which calculates a
density of states (DOS).
"""
from __future__ import absolute_import
from __future__ import print_function
import os.path
import six

from aiida.plugins import DataFactory
from aiida.orm import Code, StructureData, Dict, RemoteData
from aiida.engine import WorkChain, ToContext
from aiida.engine import submit
#from aiida.work.process_registry import ProcessRegistry
from aiida_fleur.calculation.fleur import FleurCalculation
from aiida_fleur.data.fleurinpmodifier import FleurinpModifier
from aiida_fleur.tools.common_fleur_wf import get_inputs_fleur
from aiida_fleur.tools.common_fleur_wf import test_and_get_codenode
from aiida_fleur.data.fleurinp import FleurinpData


[docs]class fleur_dos_wc(WorkChain): """ This workflow calculated a DOS from a Fleur calculation :Params: a Fleurcalculation node :returns: Success, last result node, list with convergence behavior wf_parameters: { 'tria', 'nkpts', 'sigma', 'emin', 'emax'} defaults : tria = True, nkpts = 800, sigma=0.005, emin= -0.3, emax = 0.8 """ _workflowversion = '0.3.3' _default_options = { 'resources': { 'num_machines': 1 }, 'max_wallclock_seconds': 60 * 60, 'queue_name': '', 'custom_scheduler_commands': '', # 'max_memory_kb' : None, 'import_sys_environment': False, 'environment_variables': {} } _default_wf_para = { 'tria': True, 'nkpts': 800, 'sigma': 0.005, 'emin': -0.30, 'emax': 0.80, 'add_comp_para': { 'serial': False, 'only_even_MPI': False, 'max_queue_nodes': 20, 'max_queue_wallclock_sec': 86400 } }
[docs] @classmethod def define(cls, spec): super().define(spec) spec.input('wf_parameters', valid_type=Dict, required=False, default=lambda: Dict(dict=cls._default_wf_para)) spec.input('calc_parameters', valid_type=Dict, required=False) spec.input('settings', valid_type=Dict, required=False) spec.input('options', valid_type=Dict, required=False, default=lambda: Dict(dict=cls._default_options)) spec.input('fleurinp', valid_type=FleurinpData, required=False) # TODO ggf run convergence first spec.input('remote_data', valid_type=RemoteData, required=False) #spec.input("inpgen", valid_type=Code, required=False) spec.input('fleur', valid_type=Code, required=True) spec.outline(cls.start, cls.create_new_fleurinp, cls.run_fleur, cls.return_results)
# spec.dynamic_output()
[docs] def start(self): ''' check parameters, what condictions? complete? check input nodes ''' # input check ### ? or done automaticly, how optional? # check if fleuinp corresponds to fleur_calc self.report('Started dos workflow version {}' # "Workchain node identifiers: ")#{}" ''.format(self._workflowversion)) # ProcessRegistry().current_calc_node)) self.ctx.fleurinp1 = '' self.ctx.last_calc = None self.ctx.successful = False self.ctx.warnings = [] wf_dict = self.inputs.wf_parameters.get_dict() # if MPI in code name, execute parallel self.ctx.serial = wf_dict.get('serial', False) # set values, or defaults self.ctx.max_number_runs = wf_dict.get('fleur_runmax', 4) inputs = self.inputs if 'options' in inputs: self.ctx.options = inputs.options.get_dict() if 'remote_data' in inputs: self.ctx.remote = inputs.remote_data 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) self.report(error) return 1
[docs] def create_new_fleurinp(self): """ create a new fleurinp from the old with certain parameters """ # TODO allow change of kpoint mesh?, tria? wf_dict = self.inputs.wf_parameters.get_dict() nkpts = wf_dict.get('nkpts', 800) # how can the user say he want to use the given kpoint mesh, ZZ nkpts : False/0 tria = wf_dict.get('tria', True) sigma = wf_dict.get('sigma', 0.005) emin = wf_dict.get('emin', -0.30) emax = wf_dict.get('emax', 0.80) fleurmode = FleurinpModifier(self.inputs.fleurinp) # change_dict = {'dos': True, 'ndir' : -1, 'minEnergy' : self.inputs.wf_parameters.get_dict().get('minEnergy', -0.30000000), # 'maxEnergy' : self.inputs.wf_parameters.get_dict().get('manEnergy','0.80000000'), # 'sigma' : self.inputs.wf_parameters.get_dict().get('sigma', '0.00500000')} change_dict = {'dos': True, 'ndir': -1, 'minEnergy': emin, 'maxEnergy': emax, 'sigma': sigma} fleurmode.set_inpchanges(change_dict) if tria: change_dict = {'mode': 'tria'} fleurmode.set_inpchanges(change_dict) if nkpts: fleurmode.set_nkpts(count=nkpts) # fleurinp_new.replace_tag() fleurmode.show(validate=True, display=False) # needed? fleurinp_new = fleurmode.freeze() self.ctx.fleurinp1 = fleurinp_new
# print(fleurinp_new) # print(fleurinp_new.folder.get_subfolder('path').get_abs_path(''))
[docs] def run_fleur(self): """ run a FLEUR calculation """ fleurin = self.ctx.fleurinp1 remote = self.inputs.remote_data code = self.inputs.fleur options = self.ctx.options inputs = get_inputs_fleur(code, remote, fleurin, options, add_comp_para=self.ctx.wf_dict['add_comp_para']) future = submit(FleurCalculation, **inputs) return ToContext(last_calc=future) # calcs.append(future),
[docs] def return_results(self): ''' return the results of the calculations ''' # TODO more here self.report('Dos workflow Done') # self.report('A DOS was calculated for calculation {} and is found under pk=, ' # 'calculation {}')#.format(self.ctx.last_calc, ctx['last_calc'] ) # check if dos file exists: if not succesful = False # TODO be careful with general DOS.X dosfilename = 'DOS.1' # ['DOS.1', 'DOS.2', ...] # TODO this should be easier... dosfilepath = self.ctx.last_calc.get_outputs_dict()['retrieved'].folder.get_subfolder('path').get_abs_path( dosfilename) print(dosfilepath) # dosfilepath = "path to dosfile" # Array? if os.path.isfile(dosfilepath): self.ctx.successful = True else: dosfilepath = None self.report('!NO DOS.1 file was found, something went wrong!') outputnode_dict = {} outputnode_dict['workflow_name'] = self.__class__.__name__ outputnode_dict['workflow_version'] = self._workflowversion outputnode_dict['Warnings'] = self.ctx.warnings outputnode_dict['successful'] = self.ctx.successful #outputnode_dict['last_calc_pk'] = self.ctx.last_calc.pk #outputnode_dict['last_calc_uuid'] = self.ctx.last_calc.uuid outputnode_dict['dosfile'] = dosfilepath # add nkpoints, emin, emax, sigma, tria # print outputnode_dict outputnode = Dict(dict=outputnode_dict) outdict = {} # TODO parse dos to dosnode #dosnode = '' #outdict['output_band'] = dosnode # or if spin =2 #outdict['output_band1'] = dosnode1 #outdict['output_band2'] = dosnode2 outdict['output_dos_wc_para'] = outputnode # print outdict for k, v in six.iteritems(outdict): self.out(k, v)