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Add the Wien2kCommonRelaxWorkChain
First implementation of the common relax work chain for WIEN2k. This also includes the `moderate` protocol, used for the oxides verification project. Co-authored-by: Oleg Rubel <[email protected]> Co-authored-by: Marnik Bercx <[email protected]> Co-authored-by: Emanuele Bosoni <[email protected]>
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‎aiida_common_workflows/workflows/relax/wien2k/__init__.py‎

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# -*- coding: utf-8 -*-
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# pylint: disable=undefined-variable
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"""Module with the implementations of the common structure relaxation workchain for Siesta."""
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from .generator import *
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from .workchain import *
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__all__ = (generator.__all__ + workchain.__all__)

‎aiida_common_workflows/workflows/relax/wien2k/generator.py‎

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# -*- coding: utf-8 -*-
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"""Implementation of `aiida_common_workflows.common.relax.generator.CommonRelaxInputGenerator` for Wien2k."""
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import os
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from aiida import engine, orm, plugins
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import yaml
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from aiida_common_workflows.common import ElectronicType, RelaxType, SpinType
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from aiida_common_workflows.generators import ChoiceType, CodeType
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from ..generator import CommonRelaxInputGenerator
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__all__ = ('Wien2kCommonRelaxInputGenerator',)
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StructureData = plugins.DataFactory('structure')
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class Wien2kCommonRelaxInputGenerator(CommonRelaxInputGenerator):
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"""Generator of inputs for the Wien2kCommonRelaxWorkChain"""
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_default_protocol = 'moderate'
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def __init__(self, *args, **kwargs):
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"""Construct an instance of the input generator, validating the class attributes."""
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self._initialize_protocols()
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super().__init__(*args, **kwargs)
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def _initialize_protocols(self):
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"""Initialize the protocols class attribute by parsing them from the configuration file."""
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_filepath = os.path.join(os.path.dirname(__file__), 'protocol.yml')
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with open(_filepath, encoding='utf-8') as _thefile:
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self._protocols = yaml.full_load(_thefile)
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@classmethod
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def define(cls, spec):
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"""Define the specification of the input generator.
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The ports defined on the specification are the inputs that will be accepted by the ``get_builder`` method.
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"""
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super().define(spec)
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spec.inputs['spin_type'].valid_type = ChoiceType((SpinType.NONE,))
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spec.inputs['relax_type'].valid_type = ChoiceType((RelaxType.NONE,))
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spec.inputs['electronic_type'].valid_type = ChoiceType((ElectronicType.METAL, ElectronicType.INSULATOR))
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spec.inputs['engines']['relax']['code'].valid_type = CodeType('wien2k-run123_lapw')
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def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:
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"""Construct a process builder based on the provided keyword arguments.
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The keyword arguments will have been validated against the input generator specification.
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"""
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structure = kwargs['structure']
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engines = kwargs['engines']
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protocol = kwargs['protocol']
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reference_workchain = kwargs.get('reference_workchain', None)
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electronic_type = kwargs['electronic_type']
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# Checks
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if protocol not in self.get_protocol_names():
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import warnings
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warnings.warn(f'no protocol implemented with name {protocol}, using default moderate')
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protocol = self.get_default_protocol_name()
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if not all(x in engines.keys() for x in ['relax']):
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raise ValueError('The `engines` dictionary must contain "relax" as outermost key')
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# construct input for run123_lapw
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inpdict = orm.Dict(
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dict={
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'-red': self._protocols[protocol]['parameters']['red'],
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'-i': self._protocols[protocol]['parameters']['max-scf-iterations'],
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'-ec': self._protocols[protocol]['parameters']['scf-ene-tol-Ry'],
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'-cc': self._protocols[protocol]['parameters']['scf-charge-tol'],
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'-fermits': self._protocols[protocol]['parameters']['fermi-temp-Ry'],
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'-nokshift': self._protocols[protocol]['parameters']['nokshift'],
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'-noprec': self._protocols[protocol]['parameters']['noprec'],
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'-numk': self._protocols[protocol]['parameters']['numk'],
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'-numk2': self._protocols[protocol]['parameters']['numk2'],
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'-p': self._protocols[protocol]['parameters']['parallel'],
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}
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)
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if electronic_type == ElectronicType.INSULATOR:
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inpdict['-nometal'] = True
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if reference_workchain: # ref. workchain is passed as input
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# derive Rmt's from the ref. workchain and pass as input
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w2k_wchain = reference_workchain.get_outgoing(node_class=orm.WorkChainNode).one().node
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ref_wrkchn_res_dict = w2k_wchain.outputs.workchain_result.get_dict()
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rmt = ref_wrkchn_res_dict['Rmt']
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atm_lbl = ref_wrkchn_res_dict['atom_labels']
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if len(rmt) != len(atm_lbl):
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raise ValueError(f'The list of rmt radii does not match the list of elements: {rmt} and {atm_lbl}')
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inpdict['-red'] = ','.join([f'{a}:{r}' for a, r in zip(atm_lbl, rmt)])
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# derive k mesh from the ref. workchain and pass as input
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if 'kmesh3' in ref_wrkchn_res_dict and ref_wrkchn_res_dict['kmesh3']: # check if kmesh3 is in results dict
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inpdict['-numk'] = '0' + ' ' + ref_wrkchn_res_dict['kmesh3']
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if 'kmesh3k' in ref_wrkchn_res_dict and ref_wrkchn_res_dict['kmesh3k'
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]: # check if kmesh3k is in results dict
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inpdict['-numk2'] = '0' + ' ' + ref_wrkchn_res_dict['kmesh3k']
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if 'fftmesh3k' in ref_wrkchn_res_dict and ref_wrkchn_res_dict['fftmesh3k'
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]: # check if fftmesh3k is in results dict
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inpdict['-fft'] = ref_wrkchn_res_dict['fftmesh3k']
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# res = NodeNumberJobResource(num_machines=8, num_mpiprocs_per_machine=1, num_cores_per_mpiproc=1)
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builder = self.process_class.get_builder()
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builder.aiida_structure = structure
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builder.code = engines['relax']['code'] # load wien2k-run123_lapw code
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builder.options = orm.Dict(dict=engines['relax']['options'])
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builder.inpdict = inpdict
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return builder

‎aiida_common_workflows/workflows/relax/wien2k/protocol.yml‎

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moderate:
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description: 'A standard list of inputs for Wienk.'
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parameters:
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red: '3'
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max-scf-iterations: '100'
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scf-ene-tol-Ry: '0.000001'
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scf-charge-tol: '0.000001'
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fermi-temp-Ry: '0.0045'
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nokshift: True
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noprec: '2'
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numk: '-1 0.0317506'
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numk2: '-1 0.023812976204734406'
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parallel: False

‎aiida_common_workflows/workflows/relax/wien2k/workchain.py‎

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# -*- coding: utf-8 -*-
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"""Implementation of `aiida_common_workflows.common.relax.workchain.CommonRelaxWorkChain` for Wien2k."""
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from aiida import orm
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from aiida.engine import calcfunction
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from aiida.plugins import WorkflowFactory
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from ..workchain import CommonRelaxWorkChain
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from .generator import Wien2kCommonRelaxInputGenerator
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__all__ = ('Wien2kCommonRelaxWorkChain',)
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@calcfunction
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def get_energy(pardict):
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"""Extract the energy from the `workchain_result` dictionary (Ry -> eV)"""
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return orm.Float(pardict['EtotRyd'] * 13.605693122994)
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class Wien2kCommonRelaxWorkChain(CommonRelaxWorkChain):
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"""Implementation of `aiida_common_workflows.common.relax.workchain.CommonRelaxWorkChain` for WIEN2k."""
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_process_class = WorkflowFactory('wien2k.scf123_wf')
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_generator_class = Wien2kCommonRelaxInputGenerator
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def convert_outputs(self):
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"""Convert the outputs of the sub workchain to the common output specification."""
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self.report('Relaxation task concluded sucessfully, converting outputs')
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self.out('total_energy', get_energy(self.ctx.workchain.outputs.workchain_result))
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self.out('relaxed_structure', self.ctx.workchain.outputs.aiida_structure_out)

‎pyproject.toml‎

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'aiida-quantumespresso~=3.4,>=3.4.1',
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'aiida-siesta>=1.2.0',
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'aiida-vasp~=2.2',
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'aiida-wien2k~=0.1.1',
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'aiida-ase',
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'pymatgen>=2022.1.20',
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'numpy<1.24.0',
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'common_workflows.relax.siesta' = 'aiida_common_workflows.workflows.relax.siesta.workchain:SiestaCommonRelaxWorkChain'
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'common_workflows.relax.vasp' = 'aiida_common_workflows.workflows.relax.vasp.workchain:VaspCommonRelaxWorkChain'
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'common_workflows.relax.gpaw' = 'aiida_common_workflows.workflows.relax.gpaw.workchain:GpawCommonRelaxWorkChain'
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'common_workflows.relax.wien2k' = 'aiida_common_workflows.workflows.relax.wien2k.workchain:Wien2kCommonRelaxWorkChain'
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'common_workflows.bands.siesta' = 'aiida_common_workflows.workflows.bands.siesta.workchain:SiestaCommonBandsWorkChain'
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[tool.flit.module]

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