Source code for aiida_kkr.workflows.gf_writeout

# -*- coding: utf-8 -*-
In this module you find the base workflow for writing out the kkr_flexfiles and
some helper methods to do so with AiiDA
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from aiida.orm import Code, load_node, Bool
from aiida.engine import WorkChain, ToContext, if_
from import kkrparams
from import test_and_get_codenode, get_parent_paranode, update_params_wf, get_inputs_kkr
from aiida_kkr.calculations.kkr import KkrCalculation
from aiida_kkr.calculations import KkrimpCalculation
from aiida.engine import CalcJob
from aiida.orm import CalcJobNode
from import get_Ry2eV
from aiida.orm import WorkChainNode, RemoteData, StructureData, Dict, FolderData
from aiida.common.exceptions import InputValidationError
from import create_out_dict_node
from import get_username
from aiida_kkr.workflows.dos import kkr_dos_wc
import os

__copyright__ = (u"Copyright (c), 2018, Forschungszentrum Jülich GmbH, "
                 "IAS-1/PGI-1, Germany. All rights reserved.")
__license__ = "MIT license, see LICENSE.txt file"
__version__ = "0.5.5"
__contributors__ = (u"Fabian Bertoldo", u"Philipp Rüßmann")

# ToDo: add more default values to wf_parameters

[docs]class kkr_flex_wc(WorkChain): """ Workchain of a kkr_flex calculation to calculate the Green function with KKR starting from the RemoteData node of a previous calculation (either Voronoi or KKR). :param options: (Dict), Workchain specifications :param wf_parameters: (Dict), Workflow parameters that deviate from previous KKR RemoteData :param remote_data: (RemoteData), mandatory; from a converged KKR calculation :param kkr: (Code), mandatory; KKR code running the flexfile writeout :param impurity_info: Dict, mandatory: node specifying information of the impurities in the system :return workflow_info: (Dict), Information of workflow results like success, last result node, list with convergence behavior :return GF_host_remote: (RemoteData), host GF of the system """ _workflowversion = __version__ _wf_label = 'kkr_flex_wc' _wf_description = 'Workflow for a KKR flex calculation starting from RemoteData node of previous converged KKR calculation' _options_default = {'queue_name' : '', # Queue name to submit jobs too 'resources': {"num_machines": 1}, # resources to allowcate for the job 'max_wallclock_seconds' : 60*60, # walltime after which the job gets killed (gets parsed to KKR)} 'custom_scheduler_commands' : '', # some additional scheduler commands 'withmpi' : True} # execute KKR with mpi or without _wf_default = {'ef_shift': 0. , # set costum absolute E_F (in eV) 'dos_run': False, # activate a DOS run with the parameters given in the dos_params input 'retrieve_kkrflex': True, # retrieve the DOS files or only keep them on the computer (move to KkrimpCalculation._DIRNAME_GF_UPLOAD on the remote computer's working dir), needs to use the same computer for GF writeout as for the KKRimp calculation! } # add defaults of dos_params since they are passed onto that workflow _wf_default['dos_params'] = kkr_dos_wc.get_wf_defaults(silent=True)
[docs] @classmethod def get_wf_defaults(self): """ Print and return _wf_defaults dictionary. Can be used to easily create set of wf_parameters. returns _wf_defaults """ print('Version of workflow: {}'.format(self._workflowversion)) return self._wf_default
[docs] @classmethod def define(cls, spec): """ Defines the outline of the workflow """ # Take input of the workflow or use defaults defined above super(kkr_flex_wc, cls).define(spec) spec.input("kkr", valid_type=Code, required=True) spec.input("options", valid_type=Dict, required=False, default=lambda: Dict(dict=cls._options_default)) spec.input("wf_parameters", valid_type=Dict, required=False) spec.input("remote_data", valid_type=RemoteData, required=True) spec.input("impurity_info", valid_type=Dict, required=True) spec.input("params_kkr_overwrite", valid_type=Dict, required=False, help="Set some input parameters of the KKR calculation.") # Here the structure of the workflow is defined spec.outline( cls.start, if_(cls.validate_input)( cls.set_params_flex, # TODO: encapsulate this in restarting mechanism (should be a base class of workflows that start calculations) # i.e. use base_restart_calc workchain as parent cls.get_flex, # calculate host GF and kkr-flexfiles cls.move_kkrflex_files, # maybe move them on the remote folder to some other directory ), cls.return_results) # ToDo: improve error codes spec.exit_code(101, 'ERROR_INVALID_INPUT_IMP_INFO', message="ERROR: the 'impurity_info' input Dict node could not be used") spec.exit_code(102, 'ERROR_INVALID_INPUT_KKR', message="ERROR: the code you provided for kkr does not use the plugin kkr.kkr") spec.exit_code(103, 'ERROR_INVALID_INPUT_REMOTE_DATA', message="ERROR: No remote_data was provided as Input") spec.exit_code(104, 'ERROR_INVALID_CALC_PARAMETERS', message='ERROR: calc_parameters given are not consistent! Hint: did you give an unknown keyword?') spec.exit_code(105, 'ERROR_CALC_PARAMETERS_INCOMPLETE', message='ERROR: calc_parameters misses keys') spec.exit_code(106, 'ERROR_KKR_CALCULATION_FAILED', message='ERROR: KKR calculation to write out kkrflex files unsuccessful') # specify the outputs #spec.output('remote_folder', valid_type=RemoteData) spec.output('workflow_info', valid_type=Dict) spec.output('GF_host_remote', valid_type=RemoteData)
[docs] def start(self): """ init context and some parameters """'INFO: started KKR flex workflow version {}' ''.format(self._workflowversion)) ####### init ####### # internal para / control para self.ctx.abort = False # input both wf and options parameters options_dict = self.inputs.options.get_dict() if 'wf_parameters' in self.inputs: wf_dict = self.inputs.wf_parameters.get_dict() if wf_dict == {}: wf_dict = self._wf_default'INFO: using default wf parameters') else: wf_dict = self._wf_default'INFO: using default wf parameters') if options_dict == {}: options_dict = self._options_default'INFO: using default options parameters') # set values, or defaults # ToDo: arrange option assignment differently (look at from aiida-fleur) 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('max_wallclock_seconds', self._options_default['max_wallclock_seconds']) self.ctx.queue = options_dict.get('queue_name', self._options_default['queue_name']) self.ctx.custom_scheduler_commands = options_dict.get('custom_scheduler_commands', self._options_default['custom_scheduler_commands']) self.ctx.ef_shift = wf_dict.get('ef_shift', self._wf_default['ef_shift']) self.ctx.dos_run = wf_dict.get('dos_run', self._wf_default['dos_run']) self.ctx.dos_params_dict = wf_dict.get('dos_params', self._wf_default['dos_params']) # fill missing key, value pairs with defaults for k,v in self._wf_default['dos_params'].items(): if k not in self.ctx.dos_params_dict.keys(): self.ctx.dos_params_dict[k] = v self.ctx.description_wf = self.inputs.get('description', self._wf_description) self.ctx.label_wf = self.inputs.get('label', self._wf_label) self.ctx.retrieve_kkrflex = wf_dict.get('retrieve_kkrflex', self._wf_default['retrieve_kkrflex'])'INFO: use the following parameter:\n' 'withmpi: {}\n' 'Resources: {}\n' 'Walltime (s): {}\n' 'queue name: {}\n' 'scheduler command: {}\n' 'description: {}\n' 'label: {}\n'.format(self.ctx.withmpi, self.ctx.resources, self.ctx.max_wallclock_seconds, self.ctx.queue, self.ctx.custom_scheduler_commands, self.ctx.description_wf, self.ctx.label_wf)) # return para/vars self.ctx.successful = True self.ctx.errors = [] self.ctx.formula = ''
[docs] def validate_input(self): """ Validate input """ inputs = self.inputs input_ok = True if not 'impurity_info' in inputs: input_ok = False return self.exit_codes.ERROR_INVALID_INPUT_IMP_INFO if 'remote_data' in inputs: input_ok = True else: input_ok = False return self.exit_codes.ERROR_INVALID_REMOTE_DATA # extract correct remote folder of last calculation if input remote_folder node # is not from KKRCalculation but kkr_scf_wc workflow input_remote = self.inputs.remote_data # check if input_remote has single KKRCalculation parent parents = input_remote.get_incoming(node_class=CalcJobNode) nparents = len(parents.all_link_labels()) if nparents!=1: # extract parent workflow and get uuid of last calc from output node parent_workflow = input_remote.inputs.last_RemoteData if not isinstance(parent_workflow, WorkChainNode): raise InputValidationError("Input remote_data node neither output of a KKR calculation nor of kkr_scf_wc workflow") parent_workflow_out = parent_workflow.outputs.output_kkr_scf_wc_ParameterResults uuid_last_calc = parent_workflow_out.get_dict().get('last_calc_nodeinfo').get('uuid') last_calc = load_node(uuid_last_calc) if not isinstance(last_calc, KkrCalculation): raise InputValidationError("Extracted last_calc node not of type KkrCalculation: check remote_data input node") # overwrite remote_data node with extracted remote folder output_remote = last_calc.outputs.remote_folder self.inputs.remote_data = output_remote if 'kkr' in inputs: try: test_and_get_codenode(inputs.kkr, 'kkr.kkr', use_exceptions=True) except ValueError: error = ("The code you provided for kkr does not " "use the plugin kkr.kkr") self.ctx.errors.append(error) input_ok = False return self.exit_codes.ERROR_INVALID_INPUT_KKR # set self.ctx.input_params_KKR self.ctx.input_params_KKR = get_parent_paranode(self.inputs.remote_data) if input_ok:'INFO: checking inputs successful') return input_ok
[docs] def set_params_flex(self): """ Take input parameter node and change to input from wf_parameter and options """'INFO: setting parameters ...') input_links = {} params = self.ctx.input_params_KKR input_dict = params.get_dict() para_check = kkrparams() # step 1: try to fill keywords try: for key, val in input_dict.items(): para_check.set_value(key, val, silent=True) except: return self.exit_codes.ERROR_INVALID_CALC_PARAMETERS # step 2: check if all mandatory keys are there label = '' descr = '' missing_list = para_check.get_missing_keys(use_aiida=True) if missing_list != []: kkrdefaults = kkrparams.get_KKRcalc_parameter_defaults()[0] kkrdefaults_updated = [] for key_default, val_default in list(kkrdefaults.items()): if key_default in missing_list: para_check.set_value(key_default, kkrdefaults.get(key_default), silent=True) kkrdefaults_updated.append(key_default) missing_list.remove(key_default) if len(missing_list)>0:'ERROR: calc_parameters misses keys: {}'.format(missing_list)) return self.exit_codes.ERROR_CALC_PARAMETERS_INCOMPLETE else:'updated KKR parameter node with default values: {}'.format(kkrdefaults_updated)) label = 'add_defaults_' descr = 'added missing default keys, ' # updatedict contains all things that will be updated with update_params_wf later on updatedict = {} runopt = para_check.get_dict().get('RUNOPT', None) if runopt is None: runopt = [] # overwrite some parameters of the KKR calculation by hand before setting mandatory keys if "params_kkr_overwrite" in self.inputs: for key, val in self.inputs.params_kkr_overwrite.get_dict().items(): if key != runopt: updatedict[key] = val else: runopt = val'INFO: overwriting KKR parameter: {} with {} from params_kkr_overwrite input node'.format(key, val)) input_links['params_kkr_overwrite'] = self.inputs.params_kkr_overwrite runopt = [i.strip() for i in runopt] if 'KKRFLEX' not in runopt: runopt.append('KKRFLEX') updatedict['RUNOPT'] = runopt'INFO: RUNOPT set to: {}'.format(runopt)) if 'wf_parameters' in self.inputs: # extract Fermi energy in Ry remote_data_parent = self.inputs.remote_data parent_calc = remote_data_parent.get_incoming(link_label_filter='remote_folder').first().node ef = parent_calc.outputs.output_parameters.get_dict().get('fermi_energy') if self.ctx.dos_run: # convert emin, emax to Ry units emin = ef + self.ctx.dos_params_dict['emin']/get_Ry2eV() emax = ef + self.ctx.dos_params_dict['emax']/get_Ry2eV() # set dos params for key, val in {'EMIN': emin, 'EMAX': emax, 'NPT2': self.ctx.dos_params_dict['nepts'], 'NPOL': 0, 'NPT1': 0, 'NPT3': 0, 'BZDIVIDE': self.ctx.dos_params_dict['kmesh'], 'IEMXD': self.ctx.dos_params_dict['nepts'], 'TEMPR': self.ctx.dos_params_dict['tempr']}.items(): updatedict[key] = val elif self.ctx.ef_shift != 0: # get Fermi energy shift in eV ef_shift = self.ctx.ef_shift #set new E_F in eV # calculate new Fermi energy in Ry ef_new = (ef + ef_shift)'INFO: ef_old + ef_shift = ef_new: {} eV + {} eV = {} eV'.format(ef*get_Ry2eV(), ef_shift, ef_new*get_Ry2eV())) updatedict['ef_set'] = ef_new #construct the final param node containing all of the params updatenode = Dict(dict=updatedict) updatenode.label = label+'KKRparam_flex' updatenode.description = descr+'KKR parameter node extracted from parent parameters and wf_parameter and options input node.' paranode_flex = update_params_wf(self.ctx.input_params_KKR, updatenode, **input_links) self.ctx.flex_kkrparams = paranode_flex self.ctx.flex_runopt = runopt'INFO: Updated params= {}'.format(paranode_flex.get_dict()))
[docs] def get_flex(self): """ Submit a KKRFLEX calculation """ label = 'KKRFLEX calc.' description = 'KKRFLEX calculation to write out host GF' code = self.inputs.kkr remote = self.inputs.remote_data params = self.ctx.flex_kkrparams imp_info = self.inputs.impurity_info options = {"max_wallclock_seconds": self.ctx.max_wallclock_seconds, "resources": self.ctx.resources, "queue_name": self.ctx.queue} if self.ctx.custom_scheduler_commands: options["custom_scheduler_commands"] = self.ctx.custom_scheduler_commands inputs = get_inputs_kkr(code, remote, options, label, description, parameters=params, serial=(not self.ctx.withmpi), imp_info=imp_info) # add retrieve_kkrflex to inputs inputs.retrieve_kkrflex = Bool(self.ctx.retrieve_kkrflex) # run the KKRFLEX calculation'INFO: doing calculation') flexrun = self.submit(KkrCalculation, **inputs) return ToContext(flexrun=flexrun)
[docs] def move_kkrflex_files(self): """ Move the kkrflex files from the remote folder to KkrimpCalculation._DIRNAME_GF_UPLOAD on the remote computer's working dir. This skips retrieval to the file repository and reduces cluttering the database. """ # skip this if we want to retrieve the data to the file repository if not self.ctx.retrieve_kkrflex and self.ctx.flexrun.is_finished_ok: # get name where GF is uploaded to gf_upload_path = KkrimpCalculation._DIRNAME_GF_UPLOAD # extract computer info computer = computername = # set upload dir (get the remote username and try 5 times if there was a connection error remote_user = get_username(computer) workdir = computer.get_workdir().format(username=remote_user) gf_upload_path = os.path.join(workdir, gf_upload_path)'move kkrflex files to: '+ computername) # extract absolute filepath of retrieved dir, used as source to upload kkrflex_* files from abspath_remote = self.ctx.flexrun.outputs.remote_folder.get_remote_path() abspath_tmat = os.path.join(abspath_remote, KkrimpCalculation._KKRFLEX_TMAT) abspath_gmat = os.path.join(abspath_remote, KkrimpCalculation._KKRFLEX_GREEN) # extract uuid (used as filename for remote dir) uuid_retrieved = self.ctx.flexrun.outputs.retrieved.uuid gf_upload_path = os.path.join(gf_upload_path, uuid_retrieved) # open connection to computer and upload files with computer.get_transport() as connection: if not connection.isdir(gf_upload_path):'move kkrflex_tmat and green to: ' + gf_upload_path) # create directory connection.makedirs(gf_upload_path, ignore_existing=True) abspath_tmat_new = os.path.join(gf_upload_path, KkrimpCalculation._KKRFLEX_TMAT) abspath_gmat_new = os.path.join(gf_upload_path, KkrimpCalculation._KKRFLEX_GREEN) # create a symlink to to original dir to be able to find it easily connection.symlink(os.path.join(abspath_remote, 'out_kkr'), os.path.join(gf_upload_path, 'out_kkr')) # copy files connection.copyfile(abspath_tmat, abspath_tmat_new) connection.copyfile(abspath_gmat, abspath_gmat_new) # remove from remote_folder and replace by a symlink to save space on remote connection.remove(abspath_tmat) connection.remove(abspath_gmat) connection.symlink(abspath_tmat_new, abspath_tmat) connection.symlink(abspath_gmat_new, abspath_gmat) else:'dir exsists already, skip moving the kkrflex_tmat and green files to: ' + gf_upload_path)
[docs] def return_results(self): """ Return the results of the KKRFLEX calculation. This should run through and produce output nodes even if everything failed, therefore it only uses results from context. """ # capture error of unsuccessful flexrun if not self.ctx.flexrun.is_finished_ok: self.ctx.successful = False return self.exit_codes.ERROR_KKR_CALCULATION_FAILED # create dict to store results of workflow output outputnode_dict = {} outputnode_dict['workflow_name'] = self.__class__.__name__ outputnode_dict['workflow_version'] = self._workflowversion outputnode_dict['withmpi'] = self.ctx.withmpi outputnode_dict['resources'] = self.ctx.resources outputnode_dict['max_wallclock_seconds'] = self.ctx.max_wallclock_seconds outputnode_dict['queue_name'] = self.ctx.queue outputnode_dict['custom_scheduler_commands'] = self.ctx.custom_scheduler_commands outputnode_dict['successful'] = self.ctx.successful outputnode_dict['pk_flexcalc'] = outputnode_dict['list_of_errors'] = self.ctx.errors # create results node with calcfuntion for data provenance outputnode = create_out_dict_node(Dict(dict=outputnode_dict), GF_host_remote=self.ctx.flexrun.outputs.remote_folder) outputnode.label = 'kkr_flex_wc_results' outputnode.description = '' # return Dict node containing information about previous calculation self.out('workflow_info', outputnode) # return retrieved data from kkrflex calculation self.out('GF_host_remote', self.ctx.flexrun.outputs.remote_folder)'INFO: created GF writeout result nodes')"INFO: done with KKRFLEX GF writeout workflow!\n")
#"Successful run: {}".format(has_flexrun))