Allow UPF pseudos input. (#195)

- Add `aiida-pseudo` and `upf-to-json` dependencies.
- Update pre-commit settings.

.flake8

@@ -3,8 +3,8 @@
 # rather than using the flake8 default of 79:
 max-line-length = 88
 extend-ignore =
- E501 # Line length handled by black.
- W503 # Line break before binary operator, preferred formatting for black.
- E203 # Whitespace before ':', preferred formatting for black.
+ E501
+ W503
+ E203
 exclude =
  docs/source/conf.py

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 ---
 repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.2.0
+ rev: v4.4.0
  hooks:
 
  - id: check-json
@@ -16,32 +16,32 @@ repos:
  exclude: *exclude_pre_commit_hooks
 
  - repo: https://github.com/psf/black
- rev: 22.3.0
+ rev: 23.7.0
  hooks:
  - id: black
  language_version: python3 # Should be a command that runs python3.6+
  exclude: aiida_cp2k/workchains/base.py
 
  - repo: https://github.com/PyCQA/flake8
- rev: 4.0.1
+ rev: 6.1.0
  hooks:
  - id: flake8
  args: [--count, --show-source, --statistics]
 
  - repo: https://github.com/pycqa/isort
- rev: 5.10.1
+ rev: 5.12.0
  hooks:
  - id: isort
  args: [--profile, black, --filter-files]
 
  - repo: https://github.com/asottile/pyupgrade
- rev: v2.32.1
+ rev: v3.10.1
  hooks:
  - id: pyupgrade
  args: [--py37-plus]
 
  - repo: https://github.com/pre-commit/mirrors-mypy
- rev: v0.961
+ rev: v1.5.1
  hooks:
  - id: mypy
  additional_dependencies:

aiida_cp2k/calculations/__init__.py

@@ -6,12 +6,14 @@
 ###############################################################################
 """AiiDA-CP2K input plugin."""
 
+import json
 from operator import add
 
 from aiida.common import CalcInfo, CodeInfo, InputValidationError
 from aiida.engine import CalcJob
 from aiida.orm import Dict, RemoteData, SinglefileData
 from aiida.plugins import DataFactory
+from upf_to_json import upf_to_json
 
 from ..utils import Cp2kInput
 from ..utils.datatype_helpers import (
@@ -26,6 +28,7 @@
 BandsData = DataFactory("array.bands") # pylint: disable=invalid-name
 StructureData = DataFactory("structure") # pylint: disable=invalid-name
 KpointsData = DataFactory("array.kpoints") # pylint: disable=invalid-name
+UpfData = DataFactory("pseudo.upf") # pylint: disable=invalid-name
 
 
 class Cp2kCalculation(CalcJob):
@@ -105,6 +108,14 @@ def define(cls, spec):
  ),
  )
 
+ spec.input_namespace(
+ "pseudos_upf",
+ valid_type=UpfData,
+ dynamic=True,
+ required=True,
+ help="A mapping of `UpfData` nodes onto the kind name to which they should apply.",
+ )
+
  # Specify default parser.
  spec.input(
  "metadata.options.parser_name",
@@ -262,6 +273,12 @@ def prepare_for_submission(self, folder):
  )
  write_pseudos(inp, self.inputs.pseudos, folder)
 
+ if "pseudos_upf" in self.inputs:
+ for atom_kind, pseudo in self.inputs.pseudos_upf.items():
+ pseudo_dict = upf_to_json(pseudo.get_content(), atom_kind)
+ with folder.open(atom_kind + ".json", "w") as fobj:
+ fobj.write(json.dumps(pseudo_dict, indent=2))
+
  # Kpoints.
  if "kpoints" in self.inputs:
  try:

examples/gaussian_datatypes/gdt_data.py

@@ -74,7 +74,9 @@ def load_data(prefix="MY-"):
  p.element: p
  for p in Pseudo.from_cp2k(fhandle_pseudo, duplicate_handling="error")
  }
- except UniquenessError: # if the user already ran the script, fetch the data from the db instead
+ except (
+ UniquenessError
+ ): # if the user already ran the script, fetch the data from the db instead
  bsets = {
  "H": BasisSet.get("H", f"{prefix}AUTO-DZVP-MOLOPT-GTH"),
  "O": BasisSet.get("O", f"{prefix}AUTO-DZVP-MOLOPT-SR-GTH"),

pyproject.toml

@@ -25,6 +25,8 @@ dependencies = [
  "ase",
  "ruamel.yaml>=0.16.5",
  "cp2k-output-tools",
+ "aiida-pseudo~=0.6",
+ "upf-to-json>=0.9",
 ]
 
 [[project.authors]]