Dependencies: update to aiida-pseudo==0.4.0

This new minor version comes with some significant changes:

 * All format specific pseudopotential family subclasses have been
   removed, for example, `UpfFamily` no longer exists. The format of
   the pseudos in a family are now stored as an extra and can be
   retrieved through the `pseudo_type` property. The command line
   option param type `PseudoFamilyType` was updated to reflect these
   changes.

 * The recommended cutoffs for families are now always stored in
   electronvolt. They therefore have to be converted explicitly to
   Rydberg before they are passed to the calculations.

aiida_quantumespresso/cli/calculations/cp.py

@@ -23,6 +23,8 @@ def launch_calculation(code, structure, pseudo_family, max_num_machines, max_wal
  """Run a CpCalculation."""
  from aiida.orm import Dict
  from aiida.plugins import CalculationFactory
+ from qe_tools import CONSTANTS
+
  from aiida_quantumespresso.utils.resources import get_default_options
 
  cutoff_wfc, cutoff_rho = pseudo_family.get_recommended_cutoffs(structure=structure)
@@ -38,8 +40,8 @@ def launch_calculation(code, structure, pseudo_family, max_num_machines, max_wal
  'nstep': 10,
  },
  'SYSTEM': {
- 'ecutwfc': cutoff_wfc,
- 'ecutrho': cutoff_rho,
+ 'ecutwfc': cutoff_wfc / CONSTANTS.ry_to_ev,
+ 'ecutrho': cutoff_rho / CONSTANTS.ry_to_ev,
  'nr1b': 24,
  'nr2b': 24,
  'nr3b': 24,

aiida_quantumespresso/cli/calculations/neb.py

@@ -59,6 +59,8 @@ def launch_calculation(
  """
  from aiida.orm import Dict
  from aiida.plugins import CalculationFactory
+ from qe_tools import CONSTANTS
+
  from aiida_quantumespresso.utils.resources import get_default_options
 
  cutoff_wfc, cutoff_rho = pseudo_family.get_recommended_cutoffs(structure=structures[0])
@@ -68,8 +70,8 @@ def launch_calculation(
  'calculation': 'relax',
  },
  'SYSTEM': {
- 'ecutwfc': ecutwfc or cutoff_wfc,
- 'ecutrho': ecutrho or cutoff_rho,
+ 'ecutwfc': ecutwfc or cutoff_wfc / CONSTANTS.ry_to_ev,
+ 'ecutrho': ecutrho or cutoff_rho / CONSTANTS.ry_to_ev,
  }
  }
 

aiida_quantumespresso/cli/calculations/pw.py

@@ -58,6 +58,8 @@ def launch_calculation(
  """Run a PwCalculation."""
  from aiida.orm import Dict, KpointsData
  from aiida.plugins import CalculationFactory
+ from qe_tools import CONSTANTS
+
  from aiida_quantumespresso.utils.resources import get_default_options
 
  cutoff_wfc, cutoff_rho = pseudo_family.get_recommended_cutoffs(structure=structure)
@@ -67,8 +69,8 @@ def launch_calculation(
  'calculation': mode,
  },
  'SYSTEM': {
- 'ecutwfc': ecutwfc or cutoff_wfc,
- 'ecutrho': ecutrho or cutoff_rho,
+ 'ecutwfc': ecutwfc or cutoff_wfc / CONSTANTS.ry_to_ev,
+ 'ecutrho': ecutrho or cutoff_rho / CONSTANTS.ry_to_ev,
  }
  }
 

aiida_quantumespresso/cli/utils/options.py

@@ -13,6 +13,11 @@
 class PseudoFamilyType(types.GroupParamType):
  """Subclass of `GroupParamType` in order to be able to print warning with instructions."""
 
+ def __init__(self, pseudo_types=None, **kwargs):
+ """Construct a new instance."""
+ super().__init__(**kwargs)
+ self._pseudo_types = pseudo_types
+
  @decorators.with_dbenv()
  def convert(self, value, param, ctx):
  """Convert the value to actual pseudo family instance."""
@@ -28,16 +33,23 @@ def convert(self, value, param, ctx):
  raise click.BadParameter( # pylint: disable=raise-missing-from
  f'`{value}` is not of a supported pseudopotential family type.\nTo install a supported '
  'pseudofamily, use the `aiida-pseudo` plugin. See the following link for detailed instructions:\n\n'
- ' https://github.com/aiidateam/aiida-quantumespresso#pseudo-potentials'
+ ' https://github.com/aiidateam/aiida-quantumespresso#pseudopotentials'
  )
 
+ if self._pseudo_types is not None and group.pseudo_type not in self._pseudo_types:
+ pseudo_types = ', '.join(self._pseudo_types)
+ raise click.BadParameter(
+ f'family `{group.label}` contains pseudopotentials of the wrong type `{group.pseudo_type}`.\nOnly the '
+ f'following types are supported: {pseudo_types}'
+ )
+
  return group
 
 
 PSEUDO_FAMILY = OverridableOption(
  '-F',
  '--pseudo-family',
- type=PseudoFamilyType(sub_classes=('aiida.groups:pseudo.family.upf', 'aiida.groups:pseudo.family.sssp')),
+ type=PseudoFamilyType(sub_classes=('aiida.groups:pseudo.family',), pseudo_types=('pseudo.upf',)),
  required=True,
  help='Select a pseudopotential family.'
 )

aiida_quantumespresso/cli/workflows/pw/bands.py

@@ -40,6 +40,8 @@ def launch_workflow(
  # pylint: disable=too-many-statements
  from aiida.orm import Bool, Float, Dict
  from aiida.plugins import WorkflowFactory
+ from qe_tools import CONSTANTS
+
  from aiida_quantumespresso.utils.resources import get_default_options, get_automatic_parallelization_options
 
  builder = WorkflowFactory('quantumespresso.pw.bands').get_builder()
@@ -48,8 +50,8 @@ def launch_workflow(
 
  parameters = {
  'SYSTEM': {
- 'ecutwfc': ecutwfc or cutoff_wfc,
- 'ecutrho': ecutrho or cutoff_rho,
+ 'ecutwfc': ecutwfc or cutoff_wfc / CONSTANTS.ry_to_ev,
+ 'ecutrho': ecutrho or cutoff_rho / CONSTANTS.ry_to_ev,
  },
  }
 

aiida_quantumespresso/cli/workflows/pw/base.py

@@ -40,6 +40,8 @@ def launch_workflow(
  """Run a `PwBaseWorkChain`."""
  from aiida.orm import Bool, Float, Dict
  from aiida.plugins import WorkflowFactory
+ from qe_tools import CONSTANTS
+
  from aiida_quantumespresso.utils.resources import get_default_options, get_automatic_parallelization_options
 
  builder = WorkflowFactory('quantumespresso.pw.base').get_builder()
@@ -48,8 +50,8 @@ def launch_workflow(
 
  parameters = {
  'SYSTEM': {
- 'ecutwfc': ecutwfc or cutoff_wfc,
- 'ecutrho': ecutrho or cutoff_rho,
+ 'ecutwfc': ecutwfc or cutoff_wfc / CONSTANTS.ry_to_ev,
+ 'ecutrho': ecutrho or cutoff_rho / CONSTANTS.ry_to_ev,
  },
  }
 

aiida_quantumespresso/cli/workflows/pw/relax.py

@@ -47,6 +47,7 @@ def launch_workflow(
  """Run a `PwRelaxWorkChain`."""
  from aiida.orm import Bool, Float, Dict, Str
  from aiida.plugins import WorkflowFactory
+ from qe_tools import CONSTANTS
 
  from aiida_quantumespresso.common.types import RelaxType
  from aiida_quantumespresso.utils.resources import get_default_options, get_automatic_parallelization_options
@@ -57,8 +58,8 @@ def launch_workflow(
 
  parameters = {
  'SYSTEM': {
- 'ecutwfc': ecutwfc or cutoff_wfc,
- 'ecutrho': ecutrho or cutoff_rho,
+ 'ecutwfc': ecutwfc or cutoff_wfc / CONSTANTS.ry_to_ev,
+ 'ecutrho': ecutrho or cutoff_rho / CONSTANTS.ry_to_ev,
  },
  }
 

aiida_quantumespresso/workflows/pw/base.py

@@ -17,7 +17,6 @@
 from ..protocols.utils import ProtocolMixin
 
 PwCalculation = CalculationFactory('quantumespresso.pw')
-UpfFamily = GroupFactory('pseudo.family.upf')
 SsspFamily = GroupFactory('pseudo.family.sssp')
 
 
@@ -140,6 +139,7 @@ def get_builder_from_protocol(
  guess for the magnetization is automatically set in case this argument is not provided.
  :return: a process builder instance with all inputs defined ready for launch.
  """
+ from qe_tools import CONSTANTS
  from aiida_quantumespresso.workflows.protocols.utils import get_starting_magnetization
 
  if isinstance(code, str):
@@ -168,18 +168,17 @@ def get_builder_from_protocol(
  nkinds = len(structure.kinds)
 
  try:
- types = (UpfFamily, SsspFamily)
- pseudo_family = orm.QueryBuilder().append(types, filters={'label': pseudo_family}).one()[0]
+ pseudo_family = orm.QueryBuilder().append(SsspFamily, filters={'label': pseudo_family}).one()[0]
  except exceptions.NotExistent as exception:
  raise ValueError(f'required pseudo family `{pseudo_family}` is not installed') from exception
 
- cutoffs = pseudo_family.get_recommended_cutoffs(structure=structure)
+ cutoff_wfc, cutoff_rho = pseudo_family.get_recommended_cutoffs(structure=structure)
 
  parameters = inputs['pw']['parameters']
  parameters['CONTROL']['etot_conv_thr'] = natoms * meta_parameters['etot_conv_thr_per_atom']
  parameters['ELECTRONS']['conv_thr'] = natoms * meta_parameters['conv_thr_per_atom']
- parameters['SYSTEM']['ecutwfc'] = cutoffs[0]
- parameters['SYSTEM']['ecutrho'] = cutoffs[1]
+ parameters['SYSTEM']['ecutwfc'] = cutoff_wfc / CONSTANTS.ry_to_ev
+ parameters['SYSTEM']['ecutrho'] = cutoff_rho / CONSTANTS.ry_to_ev
 
  if electronic_type is ElectronicType.INSULATOR:
  parameters['SYSTEM']['occupations'] = 'fixed'

setup.json

@@ -89,8 +89,8 @@
  ]
  },
  "install_requires": [
- "aiida_core[atomic_tools]~=1.4,>=1.4.2",
- "aiida-pseudo~=0.3.0",
+ "aiida_core[atomic_tools]~=1.4,>=1.4.4",
+ "aiida-pseudo~=0.4.0",
  "packaging",
  "qe-tools~=2.0rc1",
  "xmlschema~=1.2,>=1.2.5",

tests/conftest.py

@@ -293,35 +293,6 @@ def _generate_upf_data(element):
  return _generate_upf_data
 
 
-@pytest.fixture
-def generate_upf_family(tmp_path, generate_upf_data):
- """Return a factory for a `UpfFamily` instance."""
-
- def _generate_upf_family(label='family', elements=('Si',)):
- """Return an instance of `UpfFamily` or subclass containing the given elements.
-
- :param elements: optional list of elements to include instead of all the available ones
- :return: the pseudo family
- """
- from aiida_pseudo.groups.family import UpfFamily
-
- cutoffs = {}
-
- for element in elements:
- upf = generate_upf_data(element)
- with open(os.path.join(tmp_path, f'{element}.upf'), 'wb') as handle:
- with upf.open(mode='rb') as source:
- handle.write(source.read())
- cutoffs[element] = {'cutoff_wfc': 1.0, 'cutoff_rho': 2.0}
-
- family = UpfFamily.create_from_folder(str(tmp_path), label)
- family.set_cutoffs({'standard': cutoffs})
-
- return family
-
- return _generate_upf_family
-
-
 @pytest.fixture
 def generate_structure():
  """Return a `StructureData` representing bulk silicon."""