From d5c3c883eda0c5df2f281fe3b7c42a4621ae240c Mon Sep 17 00:00:00 2001 From: Jusong Yu Date: Wed, 12 Jun 2024 17:36:37 +0200 Subject: [PATCH] Refactoring transferibility verification workflow --- pyproject.toml | 2 +- .../{precision.yml => transferability.yml} | 0 ...v0.1.upf => N.us.pbe.z_5.ld1.psl.v0.1.upf} | 0 .../O.nc.pbe.z_6.oncvpsp3.dojo.v0.4.1-std.upf | 2755 +++++++++++++++++ ...0.1.upf => O.paw.pbe.z_6.ld1.psl.v0.1.upf} | 0 src/aiida_sssp_workflow/utils/pseudo.py | 93 + src/aiida_sssp_workflow/utils/structure.py | 8 +- src/aiida_sssp_workflow/workflows/common.py | 26 - .../workflows/convergence/_base.py | 4 +- .../workflows/evaluate/_metric.py | 2 +- .../workflows/measure/__init__.py | 42 +- .../workflows/measure/precision.py | 403 --- .../workflows/measure/report.py | 24 + .../workflows/measure/transferability.py | 468 +++ tests/conftest.py | 12 + tests/utils/__init__.py | 0 tests/utils/test_pseudo.py | 48 +- tests/workflows/convergence/__init__.py | 0 tests/workflows/convergence/test_base.py | 2 +- tests/workflows/convergence/test_report.py | 14 +- tests/workflows/measure/test_report.py | 38 + .../workflows/measure/test_transferability.py | 102 + ...builder_default_args_passing_NC_False_.yml | 20 + ...uilder_default_args_passing_SSSP_True_.yml | 20 + .../test_transferability/test_run_default.yml | 29 + ...est_run_default_check_inner_eos_inputs.yml | 29 + 26 files changed, 3666 insertions(+), 475 deletions(-) rename src/aiida_sssp_workflow/protocol/{precision.yml => transferability.yml} (100%) rename src/aiida_sssp_workflow/statics/upf/{N.us.z_5.ld1.psl.v0.1.upf => N.us.pbe.z_5.ld1.psl.v0.1.upf} (100%) create mode 100644 src/aiida_sssp_workflow/statics/upf/O.nc.pbe.z_6.oncvpsp3.dojo.v0.4.1-std.upf rename src/aiida_sssp_workflow/statics/upf/{O.paw.z_6.ld1.psl.v0.1.upf => O.paw.pbe.z_6.ld1.psl.v0.1.upf} (100%) delete mode 100644 src/aiida_sssp_workflow/workflows/measure/precision.py create mode 100644 src/aiida_sssp_workflow/workflows/measure/report.py create mode 100644 src/aiida_sssp_workflow/workflows/measure/transferability.py create mode 100644 tests/utils/__init__.py create mode 100644 tests/workflows/convergence/__init__.py create mode 100644 tests/workflows/measure/test_report.py create mode 100644 tests/workflows/measure/test_transferability.py create mode 100644 tests/workflows/measure/test_transferability/test_builder_default_args_passing_NC_False_.yml create mode 100644 tests/workflows/measure/test_transferability/test_builder_default_args_passing_SSSP_True_.yml create mode 100644 tests/workflows/measure/test_transferability/test_run_default.yml create mode 100644 tests/workflows/measure/test_transferability/test_run_default_check_inner_eos_inputs.yml diff --git a/pyproject.toml b/pyproject.toml index 634ca24d..a2cee82b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -43,7 +43,7 @@ aiida-sssp-workflow = "aiida_sssp_workflow.cli:cmd_root" "sssp_workflow.birch_murnaghan_fit" = "aiida_sssp_workflow.calculations.birch_murnaghan_fit:birch_murnaghan_fit" [project.entry-points."aiida.workflows"] -"sssp_workflow.measure_precision" = "aiida_sssp_workflow.workflows.measure.precision:PrecisionMeasureWorkChain" +"sssp_workflow.measure.transferability" = "aiida_sssp_workflow.workflows.measure.transferability:EOSTransferabilityWorkChain" "sssp_workflow.measure_bands" = "aiida_sssp_workflow.workflows.measure.bands:BandsMeasureWorkChain" "sssp_workflow.convergence.caching" = "aiida_sssp_workflow.workflows.convergence.caching:_CachingConvergenceWorkChain" "sssp_workflow.convergence.eos" = "aiida_sssp_workflow.workflows.convergence.eos:ConvergenceEOSWorkChain" diff --git a/src/aiida_sssp_workflow/protocol/precision.yml b/src/aiida_sssp_workflow/protocol/transferability.yml similarity index 100% rename from src/aiida_sssp_workflow/protocol/precision.yml rename to src/aiida_sssp_workflow/protocol/transferability.yml diff --git a/src/aiida_sssp_workflow/statics/upf/N.us.z_5.ld1.psl.v0.1.upf b/src/aiida_sssp_workflow/statics/upf/N.us.pbe.z_5.ld1.psl.v0.1.upf similarity index 100% rename from src/aiida_sssp_workflow/statics/upf/N.us.z_5.ld1.psl.v0.1.upf rename to src/aiida_sssp_workflow/statics/upf/N.us.pbe.z_5.ld1.psl.v0.1.upf diff --git a/src/aiida_sssp_workflow/statics/upf/O.nc.pbe.z_6.oncvpsp3.dojo.v0.4.1-std.upf b/src/aiida_sssp_workflow/statics/upf/O.nc.pbe.z_6.oncvpsp3.dojo.v0.4.1-std.upf new file mode 100644 index 00000000..11acdf12 --- /dev/null +++ b/src/aiida_sssp_workflow/statics/upf/O.nc.pbe.z_6.oncvpsp3.dojo.v0.4.1-std.upf @@ -0,0 +1,2755 @@ + + + +This pseudopotential file has been produced using the code +ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) +scalar-relativistic version 3.3.0 08/16/2017 by D. R. Hamann +The code is available through a link at URL www.mat-simresearch.com. +Documentation with the package provides a full discription of the +input data below. + + +While it is not required under the terms of the GNU GPL, it is +suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) +in any publication using these pseudopotentials. + + +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile +O 8.00 1 2 4 upf +# +# n l f energy (Ha) +1 0 2.00 +2 0 2.00 +2 1 4.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax +2 +# +# l, rc, ep, ncon, nbas, qcut +0 1.35000 -0.88057 4 8 8.40000 +1 1.45000 -0.33187 4 8 9.30000 +2 1.25000 0.10000 4 8 6.00000 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 +4 5 1.20000 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl +0 2 1.00000 +1 2 1.00000 +2 1 1.00000 +# +# MODEL CORE CHARGE +# icmod, fcfact, rcfact +3 4.00000 1.50000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh +-12.00 12.00 0.02 +# +# OUTPUT GRID +# rlmax, drl +6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf +0 +# nvcnf +# n l f + + + + + + + + +0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700 +0.0800 0.0900 0.1000 0.1100 0.1200 0.1300 0.1400 0.1500 +0.1600 0.1700 0.1800 0.1900 0.2000 0.2100 0.2200 0.2300 +0.2400 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similarity index 100% rename from src/aiida_sssp_workflow/statics/upf/O.paw.z_6.ld1.psl.v0.1.upf rename to src/aiida_sssp_workflow/statics/upf/O.paw.pbe.z_6.ld1.psl.v0.1.upf diff --git a/src/aiida_sssp_workflow/utils/pseudo.py b/src/aiida_sssp_workflow/utils/pseudo.py index 371308e1..2a5795c6 100644 --- a/src/aiida_sssp_workflow/utils/pseudo.py +++ b/src/aiida_sssp_workflow/utils/pseudo.py @@ -1,6 +1,16 @@ from pydantic import BaseModel +from importlib import resources +from enum import Enum from pseudo_parser.upf_parser import parse +from aiida.plugins import DataFactory + +UpfData = DataFactory("pseudo.upf") + + +class CurateType(Enum): + SSSP = "sssp" + NC = "nc" class PseudoInfo(BaseModel): @@ -43,3 +53,86 @@ def parse_std_filename(filename: str, extension: str = "upf") -> PseudoInfo: type=type, z_valence=int(num_of_valence), ) + + +def compute_total_nelectrons(configuration, pseudos): + """Compute the number of electrons of oxide configurations with pseudos + + This function is limited to only computer the total number of electrons of oxides. + """ + if len(pseudos) != 2: + raise ValueError( + f"There are {len(pseudos)} != 2 pseudos, we expect for binary oxides." + ) + + z_O = None + z_X = None + for e, p in pseudos.items(): + if e == "O": + z_O = p.z_valence + else: + z_X = p.z_valence + + if z_O is None or z_X is None: + raise ValueError( + "Either `O` or `X` pseudos not read properly to get number of valence electrons." + ) + + if configuration == "XO": + return z_X + z_O + + elif configuration == "XO2": + return z_X + z_O * 2 + + elif configuration == "XO3": + return z_X + z_O * 3 + + elif configuration == "X2O": + return z_X * 2 + z_O + + elif configuration == "X2O3": + return z_X * 4 + z_O * 6 + + elif configuration == "X2O5": + return z_X * 4 + z_O * 10 + else: + raise ValueError( + f"Cannot compute the number electrons of configuration {configuration}." + ) + + +def get_pseudo_O(curate_type: CurateType | str = CurateType.SSSP): + """Return pseudo of oxygen for oxides""" + match curate_type: + case CurateType.SSSP: + import_path = resources.path( + "aiida_sssp_workflow.statics.upf", "O.paw.pbe.z_6.ld1.psl.v0.1.upf" + ) + with import_path as psp_path, open(psp_path, "rb") as stream: + pseudo = UpfData(stream) + ecutwfc, ecutrho = 70.0, 560.0 + case CurateType.NC: + import_path = resources.path( + "aiida_sssp_workflow.statics.upf", + "O.nc.pbe.z_6.oncvpsp3.dojo.v0.4.1-std.upf", + ) + with import_path as psp_path, open(psp_path, "rb") as stream: + pseudo = UpfData(stream) + ecutwfc, ecutrho = 80.0, 320.0 + case _: + raise ValueError(f"Unknown curate_type = {curate_type}") + + return pseudo, ecutwfc, ecutrho + + +# XXX: should do the same as pseudo_O when using for LAN-Nitride band structure calculation. +# Depend on the target curate library type we use the corresponding N pseudos. +def get_pseudo_N(): + """Return pseudo of nitrogen for lanthanide nitrides""" + import_path = resources.path( + "aiida_sssp_workflow.statics.upf", "N.us.pbe.z_5.ld1.psl.v0.1.upf" + ) + with import_path as psp_path, open(psp_path, "rb") as stream: + pseudo_N = UpfData(stream) + + return pseudo_N, 55.0, 330.0 diff --git a/src/aiida_sssp_workflow/utils/structure.py b/src/aiida_sssp_workflow/utils/structure.py index 83fb3baa..60737cc0 100644 --- a/src/aiida_sssp_workflow/utils/structure.py +++ b/src/aiida_sssp_workflow/utils/structure.py @@ -13,6 +13,10 @@ UNARIE_CONFIGURATIONS = ["BCC", "FCC", "SC", "DC"] ACWF_CONFIGURATIONS = OXIDE_CONFIGURATIONS + UNARIE_CONFIGURATIONS +VALID_CONFIGURATIONS = ( + ACWF_CONFIGURATIONS # FIXME: should also have GS for bands and LANN +) + @calcfunction def get_default_configuration(element: orm.Str, property: orm.Str) -> orm.Str: @@ -40,7 +44,7 @@ def _get_default_configuration(element: str, property: str) -> str: @calcfunction def get_standard_structure( - element: orm.Str, configuration=orm.Str + element: orm.Str, configuration: orm.Str ) -> orm.StructureData: try: ase_structure = _get_standard_structure(element.value, configuration.value) @@ -59,7 +63,7 @@ def get_standard_structure( return structure -def _get_standard_structure(element: str, configuration=str) -> Atoms: +def _get_standard_structure(element: str, configuration: str) -> Atoms: """ Create an ASE structure from property and configuration and element. diff --git a/src/aiida_sssp_workflow/workflows/common.py b/src/aiida_sssp_workflow/workflows/common.py index e1044e01..91289978 100644 --- a/src/aiida_sssp_workflow/workflows/common.py +++ b/src/aiida_sssp_workflow/workflows/common.py @@ -1,10 +1,6 @@ -import importlib from typing import Optional from aiida import orm -from aiida.plugins import DataFactory - -UpfData = DataFactory("pseudo.upf") def get_extra_parameters_for_lanthanides(element, nbnd) -> dict: @@ -35,28 +31,6 @@ def get_extra_parameters_for_lanthanides(element, nbnd) -> dict: return extra_parameters -def get_pseudo_N(): - """Return pseudo of nitrogen for lanthanide nitrides""" - import_path = importlib.resources.path( - "aiida_sssp_workflow.statics.upf", "N.us.z_5.ld1.psl.v0.1.upf" - ) - with import_path as psp_path, open(psp_path, "rb") as stream: - pseudo_N = UpfData(stream) - - return pseudo_N - - -def get_pseudo_O(): - """Return pseudo of oxygen for oxides""" - import_path = importlib.resources.path( - "aiida_sssp_workflow.statics.upf", "O.paw.z_6.ld1.psl.v0.1.upf" - ) - with import_path as psp_path, open(psp_path, "rb") as stream: - pseudo_O = UpfData(stream) - - return pseudo_O - - def clean_workdir(node: orm.CalcJobNode) -> Optional[int]: """clean remote workdir of nonmenon calcjob""" # I have to do only clean nonmenon calcjob since I regard it as a bug that diff --git a/src/aiida_sssp_workflow/workflows/convergence/_base.py b/src/aiida_sssp_workflow/workflows/convergence/_base.py index 0863c739..0ee27a7b 100644 --- a/src/aiida_sssp_workflow/workflows/convergence/_base.py +++ b/src/aiida_sssp_workflow/workflows/convergence/_base.py @@ -120,7 +120,7 @@ def define(cls, spec): ) spec.output( - "convergence_report", + "report", valid_type=orm.Dict, required=True, help="The output report of convergence verification, it is a dict contains the full information of convergence test, the mapping of cutoffs to the UUID of the evaluation workchain etc.", @@ -413,7 +413,7 @@ def inspect_convergence(self): raise e else: self.out( - "convergence_report", + "report", orm.Dict(dict=validated_report.model_dump()).store(), ) diff --git a/src/aiida_sssp_workflow/workflows/evaluate/_metric.py b/src/aiida_sssp_workflow/workflows/evaluate/_metric.py index a09d6780..0754dbfa 100644 --- a/src/aiida_sssp_workflow/workflows/evaluate/_metric.py +++ b/src/aiida_sssp_workflow/workflows/evaluate/_metric.py @@ -15,7 +15,7 @@ class MetricWorkChain(SelfCleanWorkChain): - """WorkChain calculate the bands for certain pseudopotential""" + """WorkChain running EOS workflow and compute nu/delta values""" @classmethod def define(cls, spec): diff --git a/src/aiida_sssp_workflow/workflows/measure/__init__.py b/src/aiida_sssp_workflow/workflows/measure/__init__.py index d94c2dcc..321257b7 100644 --- a/src/aiida_sssp_workflow/workflows/measure/__init__.py +++ b/src/aiida_sssp_workflow/workflows/measure/__init__.py @@ -14,16 +14,6 @@ class _BaseMeasureWorkChain(SelfCleanWorkChain): """Base Measure Workchain since bands measure and precision measure share same input ports""" - # ECUT for oxygen, remember to update this if the oxygen pseudo is changed - # Currently the oxygen pseudo is `O.paw.z_6.ld1.psl.v0.1.upf` - _O_ECUTWFC = 70.0 - _O_ECUTRHO = 560.0 - - # ECUT for nitrogen, remember to update this if the nitrogen pseudo is changed - # Currently the nitrogen pseudo is `N.us.z_5.ld1.psl.v0.1.upf` - _N_ECUTWFC = 55.0 - _N_ECUTRHO = 330.0 - @classmethod def define(cls, spec): """Define the process specification.""" @@ -33,18 +23,26 @@ def define(cls, spec): help='The `pw.x` code use for the `PwCalculation`.') spec.input('pseudo', valid_type=UpfData, required=True, help='Pseudopotential to be verified') - spec.input('oxygen_pseudo', valid_type=UpfData, required=False) - spec.input('oxygen_ecutwfc', valid_type=orm.Float, required=False) - spec.input('oxygen_ecutrho', valid_type=orm.Float, required=False) + spec.input('oxygen_pseudo', valid_type=UpfData, required=True) + spec.input('oxygen_ecutwfc', valid_type=orm.Float, required=True) + spec.input('oxygen_ecutrho', valid_type=orm.Float, required=True) spec.input('protocol', valid_type=orm.Str, required=True, help='The protocol which define input calculation parameters.') - spec.input('wavefunction_cutoff', valid_type=orm.Float, required=True, help='The wavefunction cutoff.') spec.input('configurations', valid_type=orm.List, required=False) + spec.input('wavefunction_cutoff', valid_type=orm.Float, required=True, help='The wavefunction cutoff.') spec.input('charge_density_cutoff', valid_type=orm.Float, required=True, help='The charge density cutoff.') - spec.input('options', valid_type=orm.Dict, required=True, - help='Optional `options` to use for the `PwCalculations`.') - spec.input('parallelization', valid_type=orm.Dict, required=True, - help='Parallelization options for the `PwCalculations`.') + spec.input( + "parallelization", + valid_type=orm.Dict, + required=False, + help="The parallelization settings for the `PwCalculation`.", + ) + spec.input( + "mpi_options", + valid_type=orm.Dict, + required=False, + help="The MPI options for the `PwCalculation`.", + ) def _get_pw_cutoff( self, structure: orm.StructureData, ecutwfc: float, ecutrho: float @@ -52,12 +50,8 @@ def _get_pw_cutoff( """Get cutoff pair, if strcture contains oxygen or nitrogen, need to use the max between pseudo cutoff and the O/N cutoff. """ - if "oxygen_pseudo" in self.inputs: - o_ecutwfc = self.inputs.oxygen_ecutwfc.value - o_ecutrho = self.inputs.oxygen_ecutrho.value - else: - o_ecutwfc = self._O_ECUTWFC - o_ecutrho = self._O_ECUTRHO + o_ecutwfc = self.inputs.oxygen_ecutwfc.value + o_ecutrho = self.inputs.oxygen_ecutrho.value elements = set(structure.get_symbols_set()) if "O" in elements: diff --git a/src/aiida_sssp_workflow/workflows/measure/precision.py b/src/aiida_sssp_workflow/workflows/measure/precision.py deleted file mode 100644 index cca5dd63..00000000 --- a/src/aiida_sssp_workflow/workflows/measure/precision.py +++ /dev/null @@ -1,403 +0,0 @@ -# -*- coding: utf-8 -*- -"""Workchain to calculate delta factor of specific psp""" - -from aiida import orm -from aiida.plugins import DataFactory - -from aiida_sssp_workflow.utils import ( - ACTINIDE_ELEMENTS, - LANTHANIDE_ELEMENTS, - MAGNETIC_ELEMENTS, - NO_GS_CONF_ELEMENTS, - OXIDE_CONFIGURATIONS, - UNARIE_CONFIGURATIONS, - get_magnetic_inputs, - get_protocol, - get_standard_structure, - reset_pseudos_for_magnetic, - update_dict, -) -from aiida_sssp_workflow.workflows.common import ( - get_extra_parameters_for_lanthanides, - get_pseudo_N, - get_pseudo_O, -) -from aiida_sssp_workflow.workflows.evaluate._metric import MetricWorkChain -from aiida_sssp_workflow.workflows.measure import _BaseMeasureWorkChain -from pseudo_parser.upf_parser import parse_element, parse_pseudo_type - -UpfData = DataFactory("pseudo.upf") - - -class PrecisionMeasureWorkChain(_BaseMeasureWorkChain): - """Workchain to calculate delta factor of specific pseudopotential""" - - # pylint: disable=too-many-instance-attributes - - _OXIDE_CONFIGURATIONS = OXIDE_CONFIGURATIONS - - # _UNARIE_GS_CONFIGURATIONS = UNARIE_CONFIGURATIONS + ["GS"] - # For now, we decide not include the GS configuration since the reference data from sci 2016 paper use - # the different parameters compared with the aiida common workflow. So the result will be different. - _UNARIE_GS_CONFIGURATIONS = UNARIE_CONFIGURATIONS - - _NBANDS_FACTOR_FOR_LAN = 1.5 - - @classmethod - def define(cls, spec): - """Define the process specification.""" - # yapf: disable - super().define(spec) - - spec.outline( - cls.setup, - cls.setup_pw_parameters_from_protocol, - cls.setup_configurations, - cls.run_metric, - cls.inspect_metric, - cls.finalize, - ) - # namespace for storing all detail of run on each configuration - for configuration in cls._OXIDE_CONFIGURATIONS + cls._UNARIE_GS_CONFIGURATIONS + ["RE"]: - spec.expose_outputs(MetricWorkChain, namespace=configuration, - namespace_options={ - 'help': f'Delta calculation result of {configuration} EOS.', - 'required': False, - }) - - spec.output('output_parameters', - help='The summary output parameters of all delta measures to describe the precision of EOS compare ' - ' with the AE equation of state.') - spec.exit_code(401, 'ERROR_METRIC_WORKCHAIN_NOT_FINISHED_OK', message='The metric workchain of configuration {confs} not finished ok.') - # yapf: enable - - def _setup_pseudo_and_configuration(self): - """Depend on the element set the proper pseudo and configuration list""" - - # this is the pseudo dict for the element - self.ctx.pseudos_unary = {self.ctx.element: self.inputs.pseudo} - - # for the oxide, need to pseudo of oxygen, - # the pseudo is the one select after the oxygen verification and - # store in the `statics/upf/O.**.upf` - if "oxygen_pseudo" in self.inputs: - pseudo_O = self.inputs.oxygen_pseudo - else: - pseudo_O = get_pseudo_O() - self.ctx.pseudos_oxide = { - self.ctx.element: self.inputs.pseudo, - "O": pseudo_O, - } - - # For oxygen, still run for oxides but use only the pseudo. - if self.ctx.element == "O": - self.ctx.pseudos_oxide = { - self.ctx.element: self.inputs.pseudo, - } - - # Structures for delta factor calculation as provided in - # http:// molmod.ugent.be/deltacodesdft/ - # Exception for lanthanides use nitride structures from - # https://doi.org/10.1016/j.commatsci.2014.07.030 and from - # common-workflow set from acwf paper xsf files all store in `statics/structures`. - # keys here are: BCC, FCC, SC, Diamond, XO, XO2, XO3, X2O, X2O3, X2O5, RE (Lanthanide that will use RE-N), GS - if self.ctx.element in NO_GS_CONF_ELEMENTS + ACTINIDE_ELEMENTS: - # Don't have ground state structure for At, Fr, Ra - self.ctx.configuration_list = ( - self._OXIDE_CONFIGURATIONS + UNARIE_CONFIGURATIONS - ) - elif self.ctx.element in LANTHANIDE_ELEMENTS: - self.ctx.configuration_list = ( - self._OXIDE_CONFIGURATIONS + UNARIE_CONFIGURATIONS + ["RE"] - ) - else: - self.ctx.configuration_list = ( - self._OXIDE_CONFIGURATIONS + self._UNARIE_GS_CONFIGURATIONS - ) - - # set structures except RARE earth element and actinides elements with will be set independently - # in sepecific step. Other wise, the gs structure is request but not provided, which - # will raise error. - self.ctx.structures = dict() - for configuration in self.ctx.configuration_list: - self.ctx.structures[configuration] = get_standard_structure( - self.ctx.element, - prop="delta", - configuration=configuration, - ) - - def setup(self): - """ - This step contains all preparation before actaul setup, e.g. set - the context of element, base_structure, base pw_parameters and pseudos. - """ - # parse pseudo and output its header information - content = self.inputs.pseudo.get_content() - self.ctx.element = parse_element(content) - self.ctx.pseudo_type = parse_pseudo_type(content) - - self.ctx.pw_parameters = {} - - self._setup_pseudo_and_configuration() - - # set up the ecutwfc and ecutrho - self.ctx.ecutwfc = self.inputs.wavefunction_cutoff.value - self.ctx.ecutrho = self.inputs.charge_density_cutoff.value - - def setup_pw_parameters_from_protocol(self): - """Input validation""" - # pylint: disable=invalid-name, attribute-defined-outside-init - - # Read from protocol if parameters not set from inputs - protocol = get_protocol(category="precision", name=self.inputs.protocol.value) - self._DEGAUSS = protocol["degauss"] - self._OCCUPATIONS = protocol["occupations"] - self._SMEARING = protocol["smearing"] - self._CONV_THR_PER_ATOM = protocol["conv_thr_per_atom"] - self._MIXING_BETA = protocol["mixing_beta"] - self.ctx.kpoints_distance = self._KDISTANCE = protocol["kpoints_distance"] - self.ctx.scale_count = self._SCALE_COUNT = protocol["scale_count"] - self.ctx.scale_increment = self._SCALE_INCREMENT = protocol["scale_increment"] - - parameters = { - "CONTROL": { - "calculation": "scf", - "disk_io": "nowf", # safe to hard-code, this will never be the parent calculation of other calculations - }, - "SYSTEM": { - "degauss": self._DEGAUSS, - "occupations": self._OCCUPATIONS, - "smearing": self._SMEARING, - }, - "ELECTRONS": { - "conv_thr": self._CONV_THR_PER_ATOM, - "mixing_beta": self._MIXING_BETA, - }, - } - - self.ctx.pw_parameters = update_dict(self.ctx.pw_parameters, parameters) - - self.logger.info(f"The pw parameters for EOS step is: {self.ctx.pw_parameters}") - - def setup_configurations(self): - # narrow the configuration list by protocol - # this is used for test protocol which only has limited configurations to be verified - if "configurations" in self.inputs: - clist = self.inputs.configurations.get_list() - else: - clist = self.ctx.configuration_list - - for key in list(self.ctx.structures.keys()): - if key not in clist: - self.ctx.structures.pop(key) - - @staticmethod - def _compute_nelectrons_of_oxide(configuration, z_O, z_X): - """Will return the number of electrons of oxide configurations with pseudos - z_O is the number of electrons of oxygen pseudo - z_X is the number of electrons of X pseudo - """ - if configuration == "XO": - return z_X + z_O - - elif configuration == "XO2": - return z_X + z_O * 2 - - elif configuration == "XO3": - return z_X + z_O * 3 - - elif configuration == "X2O": - return z_X * 2 + z_O - - elif configuration == "X2O3": - return z_X * 4 + z_O * 6 - - elif configuration == "X2O5": - return z_X * 4 + z_O * 10 - - else: - raise ValueError( - f"Cannot compute the number electrons of configuration {configuration} with z_O={z_O} and z_X={z_X}." - ) - - def _get_inputs(self, structure, configuration): - """Set pw parameters and pseudos based on configuration and structure""" - if configuration in self._OXIDE_CONFIGURATIONS: - # pseudos for oxides - pseudos = self.ctx.pseudos_oxide - pw_parameters = self.ctx.pw_parameters - kpoints_distance = self.ctx.kpoints_distance - - # need also increase nbands for Rare-earth oxides. - # See https://github.com/aiidateam/aiida-sssp-workflow/issues/161 - # This is not easy to be set in the rare-earth step since it will - # finally act on here - if self.ctx.element in LANTHANIDE_ELEMENTS: - nbnd_factor = self._NBANDS_FACTOR_FOR_LAN - pseudo_O = get_pseudo_O() - pseudo_RE = self.inputs.pseudo - nbnd = ( - nbnd_factor - * int( - self._compute_nelectrons_of_oxide( - configuration, pseudo_O.z_valence, pseudo_RE.z_valence - ) - ) - // 2 - ) - pw_parameters["SYSTEM"]["nbnd"] = int(nbnd) - - if configuration in self._UNARIE_GS_CONFIGURATIONS: # include regular 'GS' - # pseudos for BCC, FCC, SC, Diamond and TYPYCAL configurations - pseudos = self.ctx.pseudos_unary - pw_parameters = self.ctx.pw_parameters - kpoints_distance = self.ctx.kpoints_distance - - if configuration == "GS" and self.ctx.element in MAGNETIC_ELEMENTS: - # specific setting for magnetic elements gs since mag on - - # reconstruct configuration, O1, O2 for sites - ( - structure, - pw_magnetic_parameters, - ) = get_magnetic_inputs(structure) - - # override pseudos setting - # required for O, Mn, Cr where the kind names varies for sites - self.ctx.pseudos_magnetic = reset_pseudos_for_magnetic( - self.inputs.pseudo, structure - ) - - pseudos = self.ctx.pseudos_magnetic - pw_parameters = update_dict(self.ctx.pw_parameters, pw_magnetic_parameters) - - if configuration == "RE": - # pseudos for nitrides - pseudo_N = get_pseudo_N() - pseudo_RE = self.inputs.pseudo - self.ctx.pseudos_nitride = {"N": pseudo_N, self.ctx.element: pseudo_RE} - pseudos = self.ctx.pseudos_nitride - - # perticular parameters for RE-N - # Since the reference data is from https://doi.org/10.1016/j.commatsci.2014.07.030 - # Here I need to use the same input parameters - nbnd_factor = self._NBANDS_FACTOR_FOR_LAN - nbnd = nbnd_factor * (pseudo_N.z_valence + pseudo_RE.z_valence) - - pw_parameters = self.ctx.pw_parameters - # Set the namespace directly will override the original value set in `self.ctx.pw_parameters` - pw_parameters = update_dict( - self.ctx.pw_parameters, - get_extra_parameters_for_lanthanides(self.ctx.element, nbnd), - ) - pw_parameters["SYSTEM"]["occupations"] = "tetrahedra" - pw_parameters["SYSTEM"].pop("smearing") - - # sparse kpoints, we use tetrahedra occupation - kpoints_distance = self.ctx.kpoints_distance + 0.1 - - ecutwfc, ecutrho = self._get_pw_cutoff( - structure, self.ctx.ecutwfc, self.ctx.ecutrho - ) - parameters = { - "SYSTEM": { - "ecutwfc": round(ecutwfc, 1), - "ecutrho": round(ecutrho, 1), - }, - } - parameters = update_dict(parameters, pw_parameters) - - # conv_thr is extensive, like the total energy so we need to scale it with the number of atoms - natoms = len(structure.sites) - parameters["ELECTRONS"]["conv_thr"] = ( - parameters["ELECTRONS"]["conv_thr"] * natoms - ) - - inputs = { - "eos": { - "metadata": {"call_link_label": "delta_EOS"}, - "structure": structure, - "kpoints_distance": orm.Float(kpoints_distance), - "scale_count": orm.Int(self.ctx.scale_count), - "scale_increment": orm.Float(self.ctx.scale_increment), - "pw": { - "code": self.inputs.code, - "pseudos": pseudos, - "parameters": orm.Dict(dict=parameters), - "metadata": { - "options": self.inputs.options.get_dict(), - }, - "parallelization": self.inputs.parallelization, - }, - }, - "element": orm.Str(self.ctx.element), - "configuration": orm.Str(configuration), - "clean_workdir": self.inputs.clean_workdir, - } - - return inputs - - def run_metric(self): - """run eos workchain""" - - for configuration, structure in self.ctx.structures.items(): - inputs = self._get_inputs(structure, configuration) - - future = self.submit(MetricWorkChain, **inputs) - self.report( - f"launching DeltaWarkChain<{future.pk}> for {configuration} structure." - ) - - self.to_context(**{f"{configuration}_metric": future}) - - def inspect_metric(self): - """Inspect the results of MetricWorkChain""" - failed_configuration_lst = list() - for configuration in self.ctx.structures.keys(): - workchain = self.ctx[f"{configuration}_metric"] - - if not workchain.is_finished_ok: - self.logger.warning( - f"MetricWorkChain of {configuration} failed with exit status {workchain.exit_status}" - ) - failed_configuration_lst.append(configuration) - - self.out_many( - self.exposed_outputs( - workchain, - MetricWorkChain, - namespace=configuration, - ) - ) - - if failed_configuration_lst: - return self.exit_codes.ERROR_METRIC_WORKCHAIN_NOT_FINISHED_OK.format( - confs=f"{failed_configuration_lst}", - ) - - def finalize(self): - """calculate the delta factor""" - output_parameters = {} - - for configuration in self.ctx.configuration_list: - try: - output = self.outputs[configuration].get("output_parameters") - except KeyError: - self.logger.warning( - f"Can not get the key {configuration} from outputs, not verify or failed." - ) - continue - - try: - output_parameters[configuration] = { - "delta": output["delta"], - "delta/natoms": output["delta/natoms"], - "nu": output["rel_errors_vec_length"], - } - except KeyError: - self.logger.warning( - "Can not get the metric, check EOS result or directly recalculate metric from EOS." - ) - continue - - self.out("output_parameters", orm.Dict(dict=output_parameters).store()) diff --git a/src/aiida_sssp_workflow/workflows/measure/report.py b/src/aiida_sssp_workflow/workflows/measure/report.py new file mode 100644 index 00000000..f0621aa9 --- /dev/null +++ b/src/aiida_sssp_workflow/workflows/measure/report.py @@ -0,0 +1,24 @@ +from pydantic import BaseModel, field_validator + +from aiida_sssp_workflow.utils.structure import VALID_CONFIGURATIONS + + +class SingleEOSEntry(BaseModel): + uuid: str + exit_status: int + + +class TransferabilityReport(BaseModel): + eos_dict: dict[str, SingleEOSEntry] + + @classmethod + def construct(cls, eos_dict: dict[str, dict]): + """Construct the TransferabilityReport from dict data.""" + + return cls(eos_dict={k: SingleEOSEntry(**v) for (k, v) in eos_dict.items()}) + + @field_validator("eos_dict") + def validate_eos_dict(cls, d): + if not all(k in VALID_CONFIGURATIONS for k in d.keys()): + raise ValueError(f"configuration should be one of {VALID_CONFIGURATIONS}") + return d diff --git a/src/aiida_sssp_workflow/workflows/measure/transferability.py b/src/aiida_sssp_workflow/workflows/measure/transferability.py new file mode 100644 index 00000000..635e1ab9 --- /dev/null +++ b/src/aiida_sssp_workflow/workflows/measure/transferability.py @@ -0,0 +1,468 @@ +# -*- coding: utf-8 -*- +"""Workchain to calculate delta factor of specific psp""" + +from pathlib import Path + +from aiida import orm +from aiida.engine import ProcessBuilder +from aiida_pseudo.data.pseudo import UpfData + +from aiida_sssp_workflow.utils import ( + ACTINIDE_ELEMENTS, + LANTHANIDE_ELEMENTS, + NO_GS_CONF_ELEMENTS, + OXIDE_CONFIGURATIONS, + UNARIE_CONFIGURATIONS, + get_protocol, + get_standard_structure, +) +from aiida_sssp_workflow.utils import get_default_mpi_options +from aiida_sssp_workflow.utils.pseudo import ( + extract_pseudo_info, + compute_total_nelectrons, + get_pseudo_O, + CurateType, +) +from aiida_sssp_workflow.workflows.evaluate._metric import MetricWorkChain +from aiida_sssp_workflow.workflows.measure import _BaseMeasureWorkChain +from aiida_sssp_workflow.workflows.measure.report import TransferabilityReport + + +class EOSTransferabilityWorkChain(_BaseMeasureWorkChain): + """Workchain run EOS on 10 structures and compute nu/delta metric factor""" + + # pylint: disable=too-many-instance-attributes + + _OXIDE_CONFIGURATIONS = OXIDE_CONFIGURATIONS + + # _UNARIE_GS_CONFIGURATIONS = UNARIE_CONFIGURATIONS + ["GS"] + # For now, we decide not include the GS configuration since the reference data from sci 2016 paper use + # the different parameters compared with the aiida common workflow. So the result will be different. + _UNARIE_GS_CONFIGURATIONS = UNARIE_CONFIGURATIONS + + _NBANDS_FACTOR_FOR_LAN = 2.0 + + _EVALUATE_WORKCHAIN = MetricWorkChain + + @classmethod + def define(cls, spec): + """Define the process specification.""" + super().define(spec) + + spec.outline( + cls._setup_pseudos, + cls._setup_protocol, + cls._setup_configurations, + cls.run_transferability, + cls.inspect_transferability, + cls._finalize, + ) + # namespace for storing all detail of run on each configuration + for configuration in ( + cls._OXIDE_CONFIGURATIONS + cls._UNARIE_GS_CONFIGURATIONS + ["RE"] + ): + spec.expose_outputs( + MetricWorkChain, + namespace=configuration, + namespace_options={ + "help": f"Delta calculation result of {configuration} EOS.", + "required": False, + }, + ) + + spec.output( + "report", + valid_type=orm.Dict, + required=True, + help="The output report of convergence verification, it is a dict contains the full information of convergence test, the mapping of cutoffs to the UUID of the evaluation workchain etc.", + ) + spec.exit_code( + 401, + "ERROR_METRIC_WORKCHAIN_NOT_FINISHED_OK", + message="The metric workchain of configuration {confs} not finished ok.", + ) + + def _setup_configurations(self): + """Get the configuration and the corresponding structure to run.""" + # Structures for delta factor calculation as provided in + # http:// molmod.ugent.be/deltacodesdft/ + # Exception for lanthanides use nitride structures from + # https://doi.org/10.1016/j.commatsci.2014.07.030 and from + # common-workflow set from acwf paper xsf files all store in `statics/structures`. + # keys here are: BCC, FCC, SC, Diamond, XO, XO2, XO3, X2O, X2O3, X2O5, RE (Lanthanide that will use RE-N), GS + # XXX: at the moment all three if..else cases give the same configuration_list since we didn't consider the GS configuration. + if self.ctx.element in NO_GS_CONF_ELEMENTS + ACTINIDE_ELEMENTS: + # Don't have ground state structure for At, Fr, Ra + # We didn't consider the ground state structure from sci.2016 in transferability verification. + self.ctx.configuration_list = ( + self._OXIDE_CONFIGURATIONS + UNARIE_CONFIGURATIONS + ) + elif self.ctx.element in LANTHANIDE_ELEMENTS: + self.ctx.configuration_list = ( + self._OXIDE_CONFIGURATIONS + + UNARIE_CONFIGURATIONS # TODO: add back?? + ["RE"] + ) + else: + self.ctx.configuration_list = ( + self._OXIDE_CONFIGURATIONS + UNARIE_CONFIGURATIONS + ) + + # narrow the configuration from input by popping up confs not passing into + if "configurations" in self.inputs: + clist = self.inputs.configurations.get_list() + else: + clist = self.ctx.configuration_list + + # set structures except RARE earth element and actinides elements with will be set independently + # in sepecific step. Other wise, the gs structure is request but not provided, which + # will raise error. + self.ctx.configuration_structure_mapping = dict() + for c in clist: + self.ctx.configuration_structure_mapping[c] = get_standard_structure( + self.ctx.element, + configuration=c, + ) + + for key in list(self.ctx.configuration_structure_mapping.keys()): + if key not in clist: + self.ctx.configuration_structure_mapping.pop(key) + + # Used for _finalize check + self.ctx.final_verified_configurations = clist + + def _setup_pseudos(self): + """Setup pseudos""" + pseudo_info = extract_pseudo_info( + self.inputs.pseudo.get_content(), + ) + self.ctx.element = pseudo_info.element + self.ctx.pseudos = {self.ctx.element: self.inputs.pseudo} + + # this is the pseudo dict for the element + self.ctx.pseudos_unary = {self.ctx.element: self.inputs.pseudo} + + pseudo_O = self.inputs.oxygen_pseudo + + self.ctx.pseudos_oxide = { + self.ctx.element: self.inputs.pseudo, + "O": pseudo_O, + } + + # For oxygen, still run for oxides but use only the pseudo. + if self.ctx.element == "O": + self.ctx.pseudos_oxide = { + "O": self.inputs.pseudo, + } + + def get_pseudos(self, configuration) -> dict: + """Syntax sugar to get the pseudos from configuration""" + if configuration in self._OXIDE_CONFIGURATIONS: + # pseudos for oxides + pseudos = self.ctx.pseudos_oxide + + elif configuration in self._UNARIE_GS_CONFIGURATIONS: + # pseudos for BCC, FCC, SC, Diamond and TYPYCAL configurations + pseudos = self.ctx.pseudos_unary + + else: + raise ValueError(f"can not find pseudos for {configuration}") + + return pseudos + + def _setup_protocol(self): + """unzip and parse protocol parameters to context""" + protocol = get_protocol( + category="transferability", name=self.inputs.protocol.value + ) + self.ctx.protocol = protocol + + @property + def protocol(self): + """Syntax sugar for self.ctx.protocol""" + if "protocol" not in self.ctx: + raise AttributeError( + "protocol is not set in the context, your step must after _setup_protocol" + ) + + return self.ctx.protocol + + @classmethod + def get_builder( + cls, + pseudo: Path | UpfData, + protocol: str, + wavefunction_cutoff: float, + charge_density_cutoff: float, + code: orm.AbstractCode, + configurations: list | None = None, + curate_type: str | None = None, # sssp -> pslib O; nc -> dojo O + oxygen_pseudo: Path | UpfData | None = None, + oxygen_ecutwfc: float | None = None, + oxygen_ecutrho: float | None = None, + parallelization: dict | None = None, + mpi_options: dict | None = None, + clean_workdir: bool = True, # default to clean workdir + ) -> ProcessBuilder: + """Return a builder to run this EOS convergence workchain""" + builder = super().get_builder() + builder.protocol = orm.Str(protocol) + if isinstance(pseudo, Path): + builder.pseudo = UpfData.get_or_create(pseudo) + else: + builder.pseudo = pseudo + builder.wavefunction_cutoff = orm.Float(wavefunction_cutoff) + builder.charge_density_cutoff = orm.Float(charge_density_cutoff) + builder.code = code + + if configurations is not None: + builder.configurations = orm.List(configurations) + + # When both oxygen_pseudo and curate_type are set, use oxygen_pseudo which is more explicit + if oxygen_pseudo is not None: + if oxygen_ecutwfc is None or oxygen_ecutrho is None: + raise ValueError( + "oxygen_ecutwfc and oxygen_ecutrho need to pass along with oxygen_pseudo." + ) + + _oxygen_pseudo = oxygen_pseudo + _oxygen_ecutwfc = orm.Float(oxygen_ecutwfc) + _oxygen_ecutrho = orm.Float(oxygen_ecutrho) + elif curate_type is not None: + match curate_type.lower(): + case "sssp": + ct = CurateType.SSSP + case "nc": + ct = CurateType.NC + case _: + ct = curate_type + + _oxygen_pseudo, _oxygen_ecutwfc, _oxygen_ecutrho = get_pseudo_O(ct) + else: + raise ValueError("Set at least curate_type or oxygen_pseudo.") + + if isinstance(_oxygen_pseudo, Path): + builder.oxygen_pseudo = UpfData.get_or_create(_oxygen_pseudo) + else: + builder.oxygen_pseudo = _oxygen_pseudo + + builder.oxygen_ecutwfc = orm.Float(_oxygen_ecutwfc) + builder.oxygen_ecutrho = orm.Float(_oxygen_ecutrho) + + # Set the default label and description + # The default label is set to be the base file name of PP + # The description include which configuration and which protocol is using. + builder.metadata.call_link_label = "transferability_eos" + builder.metadata.label = ( + pseudo.filename if isinstance(pseudo, UpfData) else pseudo.name + ) + builder.metadata.description = ( + f"""Run on protocol '{protocol}' | configurations '{configurations if configurations is not None else "all"}' | """ + f"with oxygen_pseudo '{builder.oxygen_pseudo.filename}' | base (ecutwfc, ecutrho) = ({wavefunction_cutoff}, {charge_density_cutoff})" + ) + builder.clean_workdir = orm.Bool(clean_workdir) + builder.code = code + + if parallelization: + builder.parallelization = orm.Dict(parallelization) + else: + builder.parallelization = orm.Dict() + + if mpi_options: + builder.mpi_options = orm.Dict(mpi_options) + else: + builder.mpi_options = orm.Dict(get_default_mpi_options()) + + return builder + + def prepare_evaluate_builder( + self, configuration: str, structure: orm.StructureData + ): + """Set pw parameters and pseudos based on configuration and structure""" + # set up the ecutwfc and ecutrho + ecutwfc = self.inputs.wavefunction_cutoff.value + ecutrho = self.inputs.charge_density_cutoff.value + + # Read from protocol if parameters not set from inputs + protocol = self.protocol + natoms = len(structure.sites) + + # Cutoff is depend on the structure + ecutwfc, ecutrho = self._get_pw_cutoff( + structure, + ecutwfc, + ecutrho, + ) + + pw_parameters = { + "CONTROL": { + "calculation": "scf", + "disk_io": "nowf", + }, + "SYSTEM": { + "degauss": protocol["degauss"], + "occupations": protocol["occupations"], + "smearing": protocol["smearing"], + "ecutwfc": round(ecutwfc), + "ecutrho": round(ecutrho), + }, + "ELECTRONS": { + "conv_thr": protocol["conv_thr_per_atom"] * natoms, + "mixing_beta": protocol["mixing_beta"], + }, + } + + pseudos = self.get_pseudos(configuration) + + # Increase nbands for Rare-earth oxides which help the electronic step convergence. + # See https://github.com/aiidateam/aiida-sssp-workflow/issues/161 + # This is not easy to be set in the rare-earth step since it will + # finally act on here + if ( + self.ctx.element in LANTHANIDE_ELEMENTS + and configuration in self._OXIDE_CONFIGURATIONS + ): + nbnd_factor = self._NBANDS_FACTOR_FOR_LAN + nbnd = ( + nbnd_factor + * int( + compute_total_nelectrons( + configuration, + pseudos, + ) + ) + // 2 + ) + pw_parameters["SYSTEM"]["nbnd"] = int(nbnd) + + builder = self._EVALUATE_WORKCHAIN.get_builder() + + builder.clean_workdir = ( + self.inputs.clean_workdir + ) # sync with the main workchain + + builder.element = orm.Str(self.ctx.element) + builder.configuration = orm.Str(configuration) + + builder.eos.metadata.call_link_label = "transferability_EOS" + builder.eos.structure = structure + builder.eos.kpoints_distance = orm.Float(protocol["kpoints_distance"]) + builder.eos.scale_count = orm.Int(protocol["scale_count"]) + builder.eos.scale_increment = orm.Float(protocol["scale_increment"]) + + # pw + builder.eos.pw["code"] = self.inputs.code + builder.eos.pw["pseudos"] = pseudos + builder.eos.pw["parameters"] = orm.Dict(dict=pw_parameters) + builder.eos.pw["parallelization"] = self.inputs.parallelization + builder.eos.pw["metadata"]["options"] = self.inputs.mpi_options.get_dict() + + return builder + + # if configuration == "GS" and self.ctx.element in MAGNETIC_ELEMENTS: + # # specific setting for magnetic elements gs since mag on + # + # # reconstruct configuration, O1, O2 for sites + # ( + # structure, + # pw_magnetic_parameters, + # ) = get_magnetic_inputs(structure) + # + # # override pseudos setting + # # required for O, Mn, Cr where the kind names varies for sites + # self.ctx.pseudos_magnetic = reset_pseudos_for_magnetic( + # self.inputs.pseudo, structure + # ) + # + # pseudos = self.ctx.pseudos_magnetic + # pw_parameters = update_dict(self.ctx.pw_parameters, pw_magnetic_parameters) + # + # if configuration == "RE": + # # pseudos for nitrides + # pseudo_N = get_pseudo_N() + # pseudo_RE = self.inputs.pseudo + # self.ctx.pseudos_nitride = {"N": pseudo_N, self.ctx.element: pseudo_RE} + # pseudos = self.ctx.pseudos_nitride + # + # # perticular parameters for RE-N + # # Since the reference data is from https://doi.org/10.1016/j.commatsci.2014.07.030 + # # Here I need to use the same input parameters + # nbnd_factor = self._NBANDS_FACTOR_FOR_LAN + # nbnd = nbnd_factor * (pseudo_N.z_valence + pseudo_RE.z_valence) + # + # pw_parameters = self.ctx.pw_parameters + # # Set the namespace directly will override the original value set in `self.ctx.pw_parameters` + # pw_parameters = update_dict( + # self.ctx.pw_parameters, + # get_extra_parameters_for_lanthanides(self.ctx.element, nbnd), + # ) + # pw_parameters["SYSTEM"]["occupations"] = "tetrahedra" + # pw_parameters["SYSTEM"].pop("smearing") + # + # # sparse kpoints, we use tetrahedra occupation + # kpoints_distance = self.ctx.kpoints_distance + 0.1 + + def run_transferability(self): + """run eos workchain""" + + for ( + configuration, + structure, + ) in self.ctx.configuration_structure_mapping.items(): + builder = self.prepare_evaluate_builder(configuration, structure) + + future = self.submit(builder) + + self.report( + f"launching DeltaWarkChain<{future.pk}> for {configuration} structure." + ) + + self.to_context(**{f"{configuration}_metric": future}) + + def inspect_transferability(self): + """Inspect the results of MetricWorkChain""" + failed_configuration_lst = list() + transferability_reports = {} + for configuration in self.ctx.configuration_structure_mapping.keys(): + child = self.ctx[f"{configuration}_metric"] + + if not child.is_finished_ok: + self.logger.warning( + f"MetricWorkChain of {configuration} failed with exit status {child.exit_status}" + ) + failed_configuration_lst.append(configuration) + + self.out_many( + self.exposed_outputs( + child, + MetricWorkChain, + namespace=configuration, + ) + ) + + _report = { + "uuid": child.uuid, + "exit_status": child.exit_status, + } + + transferability_reports[configuration] = _report + + if failed_configuration_lst: + return self.exit_codes.ERROR_METRIC_WORKCHAIN_NOT_FINISHED_OK.format( + confs=f"{failed_configuration_lst}", + ) + + try: + validated_report = TransferabilityReport.construct(transferability_reports) + self.report("TransferabilityReport report is validated.") + except Exception as e: + self.report(f"TransferabilityReport report is not validated: {e}") + raise e + else: + self.out( + "report", + orm.Dict(dict=validated_report.model_dump()).store(), + ) + + def _finalize(self): + """calculate the delta factor""" + # TODO: see what need to be added here diff --git a/tests/conftest.py b/tests/conftest.py index 3adab7c1..4c753f65 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -4,6 +4,8 @@ import os import pytest from pathlib import Path +import uuid +import hashlib from aiida import orm from aiida.orm.utils.managers import NodeLinksManager @@ -14,6 +16,14 @@ STATICS_DIR = Path(__file__).parent / "_statics" +@pytest.fixture +def generate_uuid(): + def _generate_uuid(seed="0"): + return str(uuid.UUID(hashlib.md5(seed.encode()).hexdigest())) + + return _generate_uuid + + @pytest.fixture(scope="function") def code_generator(aiida_localhost): """For quantum espresso codes generator""" @@ -55,6 +65,8 @@ def pseudo_path(): def _pseudo_path(element="Al"): if element == "Al": path = STATICS_DIR / "upf" / "Al.paw.pbe.z_3.ld1.psl.v0.1.upf" + elif element == "O_nc": + path = STATICS_DIR / "upf" / "O.nc.pbe.z_6.oncvpsp3.dojo.v0.4.1-std.upf" else: raise ValueError(f"pseudo for {element} not found") diff --git a/tests/utils/__init__.py b/tests/utils/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/tests/utils/test_pseudo.py b/tests/utils/test_pseudo.py index ec859dba..7ffd5077 100644 --- a/tests/utils/test_pseudo.py +++ b/tests/utils/test_pseudo.py @@ -1,10 +1,15 @@ """Test ``utils.pseudo`` module.""" -from pathlib import Path - import pytest +from pathlib import Path from aiida_sssp_workflow.utils import extract_pseudo_info, parse_std_filename +from aiida_sssp_workflow.utils.pseudo import ( + compute_total_nelectrons, + get_pseudo_O, + get_pseudo_N, + CurateType, +) upf_folder = Path(__file__).parent.parent / "_statics" / "upf" upf_files = list(upf_folder.glob("*.upf")) @@ -23,3 +28,42 @@ def test_extract_pseudo_info(file): info_from_filename = parse_std_filename(file.name) assert info_from_text == info_from_filename + + +@pytest.mark.parametrize( + "curate_type, expected_filename", + [ + (CurateType.SSSP, "O.paw.pbe.z_6.ld1.psl.v0.1.upf"), + (CurateType.NC, "O.nc.pbe.z_6.oncvpsp3.dojo.v0.4.1-std.upf"), + ], +) +def test_get_pseudo_O(curate_type, expected_filename): + """Test get_pseudo_O for different curate type""" + pseudo, _, _ = get_pseudo_O(curate_type) + + assert pseudo.filename == expected_filename + + +def test_get_pseudo_O_unknown_type(): + """Test raise when curate_type is unknown + + We have type annotation for the function but python does not prevent user from passing wrong type. + """ + with pytest.raises(ValueError, match="Unknown curate_type"): + get_pseudo_O("unknown") + + +def test_compute_total_nelectrons(): + """Test util function computer_total_nelectrons""" + pseudo_O, _, _ = get_pseudo_O() + pseudo_N, _, _ = get_pseudo_N() + + for configuration, pseudos, n_total in [ + ("XO", {"O": pseudo_O, "N": pseudo_N}, 11), + ("XO2", {"O": pseudo_O, "N": pseudo_N}, 17), + ("XO3", {"O": pseudo_O, "N": pseudo_N}, 23), + ("X2O", {"O": pseudo_O, "N": pseudo_N}, 16), + ("X2O3", {"O": pseudo_O, "N": pseudo_N}, 56), + ("X2O5", {"O": pseudo_O, "N": pseudo_N}, 80), + ]: + assert compute_total_nelectrons(configuration, pseudos) == n_total diff --git a/tests/workflows/convergence/__init__.py b/tests/workflows/convergence/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/tests/workflows/convergence/test_base.py b/tests/workflows/convergence/test_base.py index 598c0f14..5c10e0f7 100644 --- a/tests/workflows/convergence/test_base.py +++ b/tests/workflows/convergence/test_base.py @@ -58,7 +58,7 @@ def test_run_default( assert node.label == "Al.paw.pbe.z_3.ld1.psl.v0.1.upf" assert "DC" in node.description and "test" in node.description - validated_report = ConvergenceReport.construct(**result["convergence_report"]) + validated_report = ConvergenceReport.construct(**result["report"]) assert validated_report.reference == validated_report.convergence_list[-1] diff --git a/tests/workflows/convergence/test_report.py b/tests/workflows/convergence/test_report.py index 3971d0c6..5a67ee37 100644 --- a/tests/workflows/convergence/test_report.py +++ b/tests/workflows/convergence/test_report.py @@ -1,16 +1,4 @@ -import uuid -import hashlib -import pytest - -from aiida_sssp_workflow.workflows.convergence._base import ConvergenceReport - - -@pytest.fixture -def generate_uuid(): - def _generate_uuid(seed="0"): - return str(uuid.UUID(hashlib.md5(seed.encode()).hexdigest())) - - return _generate_uuid +from aiida_sssp_workflow.workflows.convergence.report import ConvergenceReport def test_point_run_report_entry(generate_uuid): diff --git a/tests/workflows/measure/test_report.py b/tests/workflows/measure/test_report.py new file mode 100644 index 00000000..3c79e82a --- /dev/null +++ b/tests/workflows/measure/test_report.py @@ -0,0 +1,38 @@ +import pytest + +from aiida_sssp_workflow.workflows.measure.report import TransferabilityReport + + +def test_construct_report_entry(generate_uuid): + """Test convergence report model""" + report1 = { + "uuid": generate_uuid("1"), + "exit_status": 0, + } + + report2 = { + "uuid": generate_uuid("2"), + "exit_status": 0, + } + + expected_report = TransferabilityReport.construct({"XO": report1, "SC": report2}) + + # regression test + got_report = TransferabilityReport.construct(**expected_report.model_dump()) + + assert got_report == expected_report + + +def test_raise_when_configuration_not_valid(generate_uuid): + report1 = { + "uuid": generate_uuid("1"), + "exit_status": 0, + } + + report2 = { + "uuid": generate_uuid("2"), + "exit_status": 0, + } + + with pytest.raises(ValueError, match="should be one of"): + TransferabilityReport.construct({"XO": report1, "WRONG": report2}) diff --git a/tests/workflows/measure/test_transferability.py b/tests/workflows/measure/test_transferability.py new file mode 100644 index 00000000..e60281da --- /dev/null +++ b/tests/workflows/measure/test_transferability.py @@ -0,0 +1,102 @@ +import pytest + +from aiida import orm +from aiida.plugins import DataFactory, WorkflowFactory +from aiida.engine import ProcessBuilder, run_get_node + +from aiida_sssp_workflow.workflows.measure.report import TransferabilityReport + +UpfData = DataFactory("pseudo.upf") + + +@pytest.mark.slow +def test_run_default_check_inner_eos_inputs( + pseudo_path, code_generator, serialize_inputs, data_regression +): + """Test running the caching convergence workflow. + Used to test basic things of _base convergence workchain such as the + output ports are correct and the report is correct in the format. + """ + _WorkChain = WorkflowFactory("sssp_workflow.measure.transferability") + + builder: ProcessBuilder = _WorkChain.get_builder( + pseudo=pseudo_path("Al"), + protocol="test", + configurations=["SC", "XO"], + wavefunction_cutoff=25, + charge_density_cutoff=100, + oxygen_pseudo=pseudo_path("O_nc"), + oxygen_ecutwfc=30, + oxygen_ecutrho=120, + code=code_generator("pw"), + clean_workdir=True, + ) + + # run the workchain + result, node = run_get_node(builder) + + assert node.is_finished_ok + assert node.label == "Al.paw.pbe.z_3.ld1.psl.v0.1.upf" + assert "SC" in node.description and "XO" in node.description + assert "(25, 100)" in node.description + assert "test" in node.description + + # Check the first EOS (SC) use (25, 100) cutoffs + pw_parameters_SC = node.called[2].inputs.eos.pw.parameters + assert isinstance(pw_parameters_SC["SYSTEM"]["ecutwfc"], int) + assert pw_parameters_SC["SYSTEM"]["ecutwfc"] == 25 + assert pw_parameters_SC["SYSTEM"]["ecutrho"] == 100 + + # Check the first EOS (XO) use (30, 120) cutoffs + pw_parameters_XO = node.called[3].inputs.eos.pw.parameters + assert isinstance(pw_parameters_XO["SYSTEM"]["ecutwfc"], int) + assert pw_parameters_XO["SYSTEM"]["ecutwfc"] == 30 + assert pw_parameters_XO["SYSTEM"]["ecutrho"] == 120 + + assert "SC" in result + assert "XO" in result + assert "report" in result + + validated_report = TransferabilityReport.construct(**result["report"]) + + assert {"SC", "XO"} == set(validated_report.eos_dict.keys()) + + assert validated_report.eos_dict["SC"].exit_status == 0 + assert validated_report.eos_dict["XO"].exit_status == 0 + + # From the report can get the uuid of the evaluate workchain + # test that the pw inputs are from the protocol (convergence/base) + xo_evaluate_node = orm.load_node(validated_report.eos_dict["XO"].uuid) + + data_regression.check(serialize_inputs(xo_evaluate_node.inputs)) + + +@pytest.mark.parametrize( + "curate_type,clean_workdir", + [ + ("SSSP", True), + ("NC", False), + ], +) +def test_builder_default_args_passing( + curate_type, + clean_workdir, + pseudo_path, + code_generator, + serialize_builder, + data_regression, +): + """Test transferability workflow builder is correctly created with default args""" + _WorkChain = WorkflowFactory("sssp_workflow.measure.transferability") + + builder: ProcessBuilder = _WorkChain.get_builder( + pseudo=pseudo_path("Al"), + protocol="test", + wavefunction_cutoff=25, + charge_density_cutoff=100, + code=code_generator("pw"), + curate_type=curate_type, + clean_workdir=clean_workdir, + ) + + data_regression.check(serialize_builder(builder)) diff --git a/tests/workflows/measure/test_transferability/test_builder_default_args_passing_NC_False_.yml b/tests/workflows/measure/test_transferability/test_builder_default_args_passing_NC_False_.yml new file mode 100644 index 00000000..387eac80 --- /dev/null +++ b/tests/workflows/measure/test_transferability/test_builder_default_args_passing_NC_False_.yml @@ -0,0 +1,20 @@ +charge_density_cutoff: 100.0 +clean_workdir: false +code: pw-docker@localhost +metadata: + call_link_label: transferability_eos + description: Run on protocol 'test' | configurations 'all' | with oxygen_pseudo + 'O.nc.pbe.z_6.oncvpsp3.dojo.v0.4.1-std.upf' | base (ecutwfc, ecutrho) = (25, 100) + label: Al.paw.pbe.z_3.ld1.psl.v0.1.upf +mpi_options: + max_wallclock_seconds: 1800 + resources: + num_machines: 1 + withmpi: false +oxygen_ecutrho: 320.0 +oxygen_ecutwfc: 80.0 +oxygen_pseudo: O +parallelization: {} +protocol: test +pseudo: Al +wavefunction_cutoff: 25.0 diff --git a/tests/workflows/measure/test_transferability/test_builder_default_args_passing_SSSP_True_.yml b/tests/workflows/measure/test_transferability/test_builder_default_args_passing_SSSP_True_.yml new file mode 100644 index 00000000..bfb4ef40 --- /dev/null +++ b/tests/workflows/measure/test_transferability/test_builder_default_args_passing_SSSP_True_.yml @@ -0,0 +1,20 @@ +charge_density_cutoff: 100.0 +clean_workdir: true +code: pw-docker@localhost +metadata: + call_link_label: transferability_eos + description: Run on protocol 'test' | configurations 'all' | with oxygen_pseudo + 'O.paw.pbe.z_6.ld1.psl.v0.1.upf' | base (ecutwfc, ecutrho) = (25, 100) + label: Al.paw.pbe.z_3.ld1.psl.v0.1.upf +mpi_options: + max_wallclock_seconds: 1800 + resources: + num_machines: 1 + withmpi: false +oxygen_ecutrho: 560.0 +oxygen_ecutwfc: 70.0 +oxygen_pseudo: O +parallelization: {} +protocol: test +pseudo: Al +wavefunction_cutoff: 25.0 diff --git a/tests/workflows/measure/test_transferability/test_run_default.yml b/tests/workflows/measure/test_transferability/test_run_default.yml new file mode 100644 index 00000000..6bc4acb2 --- /dev/null +++ b/tests/workflows/measure/test_transferability/test_run_default.yml @@ -0,0 +1,29 @@ +clean_workdir: true +configuration: XO +element: Al +eos: + clean_workdir: false + kpoints_distance: 0.5 + max_iterations: 5 + pw: + code: pw-docker@localhost + parallelization: {} + parameters: + CONTROL: + calculation: scf + disk_io: nowf + ELECTRONS: + conv_thr: 2.0e-06 + mixing_beta: 0.4 + SYSTEM: + degauss: 0.0045 + ecutrho: 120 + ecutwfc: 30 + occupations: smearing + smearing: fd + pseudos: + Al: Al + O: O + scale_count: 5 + scale_increment: 0.02 + structure: AlO diff --git a/tests/workflows/measure/test_transferability/test_run_default_check_inner_eos_inputs.yml b/tests/workflows/measure/test_transferability/test_run_default_check_inner_eos_inputs.yml new file mode 100644 index 00000000..6bc4acb2 --- /dev/null +++ b/tests/workflows/measure/test_transferability/test_run_default_check_inner_eos_inputs.yml @@ -0,0 +1,29 @@ +clean_workdir: true +configuration: XO +element: Al +eos: + clean_workdir: false + kpoints_distance: 0.5 + max_iterations: 5 + pw: + code: pw-docker@localhost + parallelization: {} + parameters: + CONTROL: + calculation: scf + disk_io: nowf + ELECTRONS: + conv_thr: 2.0e-06 + mixing_beta: 0.4 + SYSTEM: + degauss: 0.0045 + ecutrho: 120 + ecutwfc: 30 + occupations: smearing + smearing: fd + pseudos: + Al: Al + O: O + scale_count: 5 + scale_increment: 0.02 + structure: AlO