Accept UpfData to contruct builder

pyproject.toml

@@ -74,3 +74,6 @@ filterwarnings = [
     'ignore:Object of type .* not in session, .* operation along .* will not proceed:sqlalchemy.exc.SAWarning',
     'ignore:The `Code` class is deprecated.*:aiida.common.warnings.AiidaDeprecationWarning',
 ]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+]

src/aiida_sssp_workflow/protocol/convergence.yml

@@ -1,14 +1,14 @@
 ---
-acwf:
-    name: acwf
-    description: The protocol where input parameters bring from AiiDA common workflow (ACWF).
+balanced:
+    name: balanced
+    description: The balanced protocol from Gabriel
 
     base:   # base parameters is inherit by other process
         occupations: smearing
         degauss: 0.02   # balanced protocol of qe -> gabriel
         smearing: fd
-        conv_thr_per_atom: 1.0e-10
-        kpoints_distance: 0.15  # balanced protocol of qe -> gabriel
+        conv_thr_per_atom: 1.0e-8
+        kpoints_distance: 0.2  # balanced protocol of qe -> gabriel
         mixing_beta: 0.4
 
     cohesive_energy:
@@ -35,43 +35,41 @@ acwf:
         scale_count: 7
         scale_increment: 0.02
 
+acwf:
+    name: acwf
+    description: The parameters of EOS is exactly the same as it used in nat.phys.rev 2024 paper.
+
+    base:   # base parameters is inherit by other process
+        occupations: smearing
+        degauss: 0.0045   # balanced protocol of qe -> gabriel
+        smearing: fd
+        conv_thr_per_atom: 1.0e-10
+        kpoints_distance: 0.06  # balanced protocol of qe -> gabriel
+        mixing_beta: 0.4
+
+    cohesive_energy:
+        atom_smearing: gaussian
+        vacuum_length: 12.0
+
+    phonon_frequencies:
+        qpoints_list:
+            - [0.5, 0.5, 0.5]
+        epsilon: false
+        tr2_ph: 1.0e-16
+
+    pressure:
+        scale_count: 7
+        scale_increment: 0.02
+
+    bands:
+        init_nbands_factor: 3.0
+        fermi_shift: 10.0
+        kpoints_distance_scf: 0.15
+        kpoints_distance_bands: 0.15
 
-#moderate:
-#    name: moderate
-#    description: The protocol where input parameters bring from aiidaqe moderate protocol. Only for QE >= 6.8
-#
-#    base:   # base parameters is inherit by other process
-#        occupations: smearing
-#        degauss: 0.01
-#        smearing: cold
-#        conv_thr_per_atom: 1.0e-10
-#        kpoints_distance: 0.15
-#
-#    cohesive_energy:
-#        atom_smearing: gaussian
-#        vacuum_length: 12.0
-#
-#    phonon_frequencies:
-#        qpoints_list:
-#            - [0.5, 0.5, 0.5]
-#        epsilon: false
-#        tr2_ph: 1.0e-16
-#
-#    pressure:
-#        scale_count: 7
-#        scale_increment: 0.02
-#        mixing_beta: 0.4
-#
-#    bands:
-#        init_nbands_factor: 3.0
-#        fermi_shift: 10.0
-#        kpoints_distance_scf: 0.15
-#        kpoints_distance_bands: 0.15
-#
-#    eos:
-#        scale_count: 7
-#        scale_increment: 0.02
-#        mixing_beta: 0.4
+    eos:
+        scale_count: 7
+        scale_increment: 0.02
 
 test:
     name: test-only

src/aiida_sssp_workflow/workflows/convergence/_base.py

@@ -6,13 +6,14 @@
 The detail parameters for different properties are defined in the subclass that inherit this base class.
 """
 
+from typing import Union
 from pathlib import Path
 from abc import ABCMeta, abstractmethod
 
 from aiida import orm
 from aiida.engine import append_
-from aiida.plugins import DataFactory
 from aiida.engine import ProcessBuilder
+from aiida_pseudo.data.pseudo import UpfData
 
 from aiida_sssp_workflow.utils import (
     get_default_configuration,
@@ -24,8 +25,6 @@
 from aiida_sssp_workflow.workflows import SelfCleanWorkChain
 from aiida_sssp_workflow.workflows.convergence.report import ConvergenceReport
 
-UpfData = DataFactory("pseudo.upf")
-
 
 class abstract_attribute(object):
     """lazy variable check: https://stackoverflow.com/a/32536493"""
@@ -210,7 +209,7 @@ def prepare_evaluate_builder(self, ecutwfc: int, ecutrho: int) -> dict:
     @classmethod
     def get_builder(
         cls,
-        pseudo: Path,
+        pseudo: Union[Path, UpfData],
         protocol: str,
         cutoff_list: list,
         configuration: str,
@@ -219,7 +218,11 @@ def get_builder(
         """Generate builder for the generic convergence workflow"""
         builder = super().get_builder()
         builder.protocol = orm.Str(protocol)
-        builder.pseudo = UpfData.get_or_create(pseudo)
+
+        if isinstance(pseudo, Path):
+            builder.pseudo = UpfData.get_or_create(pseudo)
+        else:
+            builder.pseudo = pseudo
 
         if ret := is_valid_cutoff_list(cutoff_list):
             raise ValueError(ret)

src/aiida_sssp_workflow/workflows/convergence/eos.py

@@ -4,9 +4,11 @@
 """
 
 from pathlib import Path
+from typing import Union
 
 from aiida import orm
 from aiida.engine import ProcessBuilder
+from aiida_pseudo.data.pseudo import UpfData
 
 from aiida_sssp_workflow.utils import get_default_mpi_options
 from aiida_sssp_workflow.workflows.convergence._base import _BaseConvergenceWorkChain
@@ -45,7 +47,7 @@ def define(cls, spec):
     @classmethod
     def get_builder(
         cls,
-        pseudo: Path,
+        pseudo: Union[Path, UpfData],
         protocol: str,
         cutoff_list: list,
         configuration: str,

tests/conftest.py

@@ -7,6 +7,7 @@
 
 from aiida import orm
 from aiida.orm.utils.managers import NodeLinksManager
+from aiida.engine import ProcessBuilder
 
 pytest_plugins = ["aiida.manage.tests.pytest_fixtures"]
 
@@ -62,12 +63,69 @@ def _pseudo_path(element="Al"):
     return _pseudo_path
 
 
+def _serialize_data(data):
+    from aiida.orm import (
+        AbstractCode,
+        BaseType,
+        Data,
+        Dict,
+        KpointsData,
+        List,
+        RemoteData,
+        SinglefileData,
+    )
+    from aiida.plugins import DataFactory
+
+    StructureData = DataFactory("core.structure")
+    UpfData = DataFactory("pseudo.upf")
+
+    if isinstance(data, dict):
+        return {key: _serialize_data(value) for key, value in data.items()}
+
+    if isinstance(data, BaseType):
+        return data.value
+
+    if isinstance(data, AbstractCode):
+        return data.full_label
+
+    if isinstance(data, Dict):
+        return data.get_dict()
+
+    if isinstance(data, List):
+        return data.get_list()
+
+    if isinstance(data, StructureData):
+        return data.get_formula()
+
+    if isinstance(data, UpfData):
+        return f"{data.element}<md5={data.md5}>"
+
+    if isinstance(data, RemoteData):
+        # For `RemoteData` we compute the hash of the repository. The value returned by `Node._get_hash` is not
+        # useful since it includes the hash of the absolute filepath and the computer UUID which vary between tests
+        return data.base.repository.hash()
+
+    if isinstance(data, KpointsData):
+        try:
+            return data.get_kpoints()
+        except AttributeError:
+            return data.get_kpoints_mesh()
+
+    if isinstance(data, SinglefileData):
+        return data.get_content()
+
+    if isinstance(data, Data):
+        return data.base.caching._get_hash()
+
+    return data
+
+
 @pytest.fixture
 def serialize_inputs():
     """Serialize the given process inputs into a dictionary with nodes turned into their value representation.
     (Borrowed from aiida-quantumespresso/tests/conftest.py::serialize_builder)
 
-    :param builder: the process builder to serialize
+    :param input: the process inputs of type NodeManegerLink to serialize
     :return: dictionary
     """
 
@@ -136,3 +194,18 @@ def _serialize_inputs(inputs: NodeLinksManager):
         return _serialize_data(_inputs)
 
     return _serialize_inputs
+
+
+@pytest.fixture
+def serialize_builder():
+    """Serialize the builder into a dictionary with nodes turned into their value representation.
+    (Borrowed from aiida-quantumespresso/tests/conftest.py::serialize_builder)
+
+    :param builder: the process builder to serialize
+    :return: dictionary
+    """
+
+    def _serialize_builder(builder: ProcessBuilder):
+        return _serialize_data(builder._inputs(prune=True))
+
+    return _serialize_builder

tests/workflows/convergence/test_base.py

@@ -9,6 +9,7 @@
 UpfData = DataFactory("pseudo.upf")
 
 
+@pytest.mark.slow
 @pytest.mark.parametrize(
     "entry_point",
     [
@@ -62,5 +63,35 @@ def test_run_default(
     data_regression.check(serialize_inputs(ref_evaluate_node.inputs))
 
 
+@pytest.mark.parametrize(
+    "entry_point,clean_workdir",
+    [
+        ("sssp_workflow.convergence.eos", True),
+        ("sssp_workflow.convergence.eos", False),
+    ],
+)
+def test_builder_pseudo_as_upfdata(
+    entry_point,
+    clean_workdir,
+    pseudo_path,
+    code_generator,
+    serialize_builder,
+    data_regression,
+):
+    _ConvergencWorkChain = WorkflowFactory(entry_point)
+    pseudo = UpfData.get_or_create(pseudo_path("Al"))
+
+    builder: ProcessBuilder = _ConvergencWorkChain.get_builder(
+        pseudo=pseudo,
+        protocol="test",
+        cutoff_list=[(20, 80), (30, 120)],
+        configuration="DC",
+        code=code_generator("pw"),
+        clean_workdir=clean_workdir,
+    )
+
+    data_regression.check(serialize_builder(builder))
+
+
 # TODO: test not clean workdir
 # TODO: test validator of _base convergence workchain working as expected

tests/workflows/convergence/test_base/test_builder_pseudo_as_upfdata_sssp_workflow_convergence_eos_False_.yml

@@ -0,0 +1,18 @@
+clean_workdir: false
+code: pw-docker@localhost
+configuration: DC
+cutoff_list:
+- - 20
+  - 80
+- - 30
+  - 120
+metadata:
+  call_link_label: caching
+mpi_options:
+  max_wallclock_seconds: 1800
+  resources:
+    num_machines: 1
+  withmpi: false
+parallelization: {}
+protocol: test
+pseudo: Al<md5=a2ca6568aad2214016a12794e7e55b1e>

tests/workflows/convergence/test_base/test_builder_pseudo_as_upfdata_sssp_workflow_convergence_eos_True_.yml

@@ -0,0 +1,18 @@
+clean_workdir: true
+code: pw-docker@localhost
+configuration: DC
+cutoff_list:
+- - 20
+  - 80
+- - 30
+  - 120
+metadata:
+  call_link_label: caching
+mpi_options:
+  max_wallclock_seconds: 1800
+  resources:
+    num_machines: 1
+  withmpi: false
+parallelization: {}
+protocol: test
+pseudo: Al<md5=a2ca6568aad2214016a12794e7e55b1e>