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
+
+
+
+
+
+
+
+
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+1.0402791645E-05 1.0232603014E-05 1.0065200420E-05 9.9005382321E-06
+9.7385715649E-06 9.5792562698E-06 9.4225489209E-06 9.2684068038E-06
+9.1167879037E-06 8.9676508939E-06 8.8209551204E-06 8.6766605867E-06
+8.5347279828E-06 8.3951186259E-06 8.2577944667E-06 8.1227180793E-06
+7.9898526507E-06 7.8591619710E-06 7.7306104235E-06 7.6041629747E-06
+7.4797851651E-06 7.3574430950E-06 7.2371034143E-06 7.1187333456E-06
+7.0023006336E-06 6.8877735515E-06 6.7751208923E-06 6.6643119598E-06
+6.5553165610E-06 6.4481049973E-06 6.3426480563E-06 6.2389170043E-06
+
+
diff --git a/src/aiida_sssp_workflow/statics/upf/O.paw.z_6.ld1.psl.v0.1.upf b/src/aiida_sssp_workflow/statics/upf/O.paw.pbe.z_6.ld1.psl.v0.1.upf
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