Move calcfunctions to aiida_quantumespresso.calculations.functions

Since they are calculation functions they do not belong in the workflow
module. To not break backwards-compatibility the original modules import
the functions from their new location and emit a `Warning`. Note that we
explicitly do not use a `DeprecationWarning` since those are
automatically filtered in Python 3.

aiida_quantumespresso/calculations/functions/create_kpoints_from_distance.py

@@ -0,0 +1,37 @@
+# -*- coding: utf-8 -*-
+"""Calculation function to compute a k-point mesh for a structure with a guaranteed minimum k-point distance."""
+from aiida.engine import calcfunction
+
+
+@calcfunction
+def create_kpoints_from_distance(structure, distance, force_parity):
+ """Generate a uniformly spaced kpoint mesh for a given structure.
+
+ The spacing between kpoints in reciprocal space is guaranteed to be at least the defined distance.
+
+ :param structure: the StructureData to which the mesh should apply
+ :param distance: a Float with the desired distance between kpoints in reciprocal space
+ :param force_parity: a Bool to specify whether the generated mesh should maintain parity
+ :returns: a KpointsData with the generated mesh
+ """
+ from numpy import linalg
+ from aiida.orm import KpointsData
+
+ epsilon = 1E-5
+
+ kpoints = KpointsData()
+ kpoints.set_cell_from_structure(structure)
+ kpoints.set_kpoints_mesh_from_density(distance.value, force_parity=force_parity.value)
+
+ lengths_vector = [linalg.norm(vector) for vector in structure.cell]
+ lengths_kpoint = kpoints.get_kpoints_mesh()[0]
+
+ is_symmetric_cell = all(abs(length - lengths_vector[0]) < epsilon for length in lengths_vector)
+ is_symmetric_mesh = all(length == lengths_kpoint[0] for length in lengths_kpoint)
+
+ # If the vectors of the cell all have the same length, the kpoint mesh should be isotropic as well
+ if is_symmetric_cell and not is_symmetric_mesh:
+ nkpoints = max(lengths_kpoint)
+ kpoints.set_kpoints_mesh([nkpoints, nkpoints, nkpoints])
+
+ return kpoints

aiida_quantumespresso/calculations/functions/seekpath_structure_analysis.py

@@ -0,0 +1,31 @@
+# -*- coding: utf-8 -*-
+"""Calcfunction to primitivize a structure and return high symmetry k-point path through its Brillouin zone."""
+from aiida.engine import calcfunction
+from aiida.orm import Data
+
+
+@calcfunction
+def seekpath_structure_analysis(structure, **kwargs):
+ """Primitivize the structure with SeeKpath and generate the high symmetry k-point path through its Brillouin zone.
+
+ This calcfunction will take a structure and pass it through SeeKpath to get the normalized primitive cell and the
+ path of high symmetry k-points through its Brillouin zone. Note that the returned primitive cell may differ from the
+ original structure in which case the k-points are only congruent with the primitive cell.
+
+ The keyword arguments can be used to specify various Seekpath parameters, such as:
+
+ with_time_reversal: True
+ reference_distance: 0.025
+ recipe: 'hpkot'
+ threshold: 1e-07
+ symprec: 1e-05
+ angle_tolerance: -1.0
+
+ Note that exact parameters that are available and their defaults will depend on your Seekpath version.
+ """
+ from aiida.tools import get_explicit_kpoints_path
+
+ # All keyword arugments should be `Data` node instances of base type and so should have the `.value` attribute
+ unwrapped_kwargs = {key: node.value for key, node in kwargs.items() if isinstance(node, Data)}
+
+ return get_explicit_kpoints_path(structure, **unwrapped_kwargs)

aiida_quantumespresso/workflows/functions/create_kpoints_from_distance.py

@@ -1,37 +1,12 @@
 # -*- coding: utf-8 -*-
 """Calculation function to compute a k-point mesh for a structure with a guaranteed minimum k-point distance."""
-from aiida.engine import calcfunction
-
-
-@calcfunction
-def create_kpoints_from_distance(structure, distance, force_parity):
- """Generate a uniformly spaced kpoint mesh for a given structure.
-
- The spacing between kpoints in reciprocal space is guaranteed to be at least the defined distance.
-
- :param structure: the StructureData to which the mesh should apply
- :param distance: a Float with the desired distance between kpoints in reciprocal space
- :param force_parity: a Bool to specify whether the generated mesh should maintain parity
- :returns: a KpointsData with the generated mesh
- """
- from numpy import linalg
- from aiida.orm import KpointsData
-
- epsilon = 1E-5
-
- kpoints = KpointsData()
- kpoints.set_cell_from_structure(structure)
- kpoints.set_kpoints_mesh_from_density(distance.value, force_parity=force_parity.value)
-
- lengths_vector = [linalg.norm(vector) for vector in structure.cell]
- lengths_kpoint = kpoints.get_kpoints_mesh()[0]
-
- is_symmetric_cell = all(abs(length - lengths_vector[0]) < epsilon for length in lengths_vector)
- is_symmetric_mesh = all(length == lengths_kpoint[0] for length in lengths_kpoint)
-
- # If the vectors of the cell all have the same length, the kpoint mesh should be isotropic as well
- if is_symmetric_cell and not is_symmetric_mesh:
- nkpoints = max(lengths_kpoint)
- kpoints.set_kpoints_mesh([nkpoints, nkpoints, nkpoints])
-
- return kpoints
+# pylint: disable=unused-import
+import warnings
+from aiida_quantumespresso.calculations.functions.create_kpoints_from_distance import create_kpoints_from_distance
+
+warnings.warn(
+ 'This module is deprecated and will be removed soon.\nPlease use instead the new module:\n'
+ 'from aiida_quantumespresso.calculations.functions.create_kpoints_from_distance import create_kpoints_from_distance'
+ "\nOr use the entry point with the factory: CalculationFactory('quantumespresso.create_kpoints_from_distance')",
+ FutureWarning
+)

aiida_quantumespresso/workflows/functions/seekpath_structure_analysis.py

@@ -1,31 +1,12 @@
 # -*- coding: utf-8 -*-
 """Calcfunction to primitivize a structure and return high symmetry k-point path through its Brillouin zone."""
-from aiida.engine import calcfunction
-from aiida.orm import Data
-
-
-@calcfunction
-def seekpath_structure_analysis(structure, **kwargs):
- """Primitivize the structure with SeeKpath and generate the high symmetry k-point path through its Brillouin zone.
-
- This calcfunction will take a structure and pass it through SeeKpath to get the normalized primitive cell and the
- path of high symmetry k-points through its Brillouin zone. Note that the returned primitive cell may differ from the
- original structure in which case the k-points are only congruent with the primitive cell.
-
- The keyword arguments can be used to specify various Seekpath parameters, such as:
-
- with_time_reversal: True
- reference_distance: 0.025
- recipe: 'hpkot'
- threshold: 1e-07
- symprec: 1e-05
- angle_tolerance: -1.0
-
- Note that exact parameters that are available and their defaults will depend on your Seekpath version.
- """
- from aiida.tools import get_explicit_kpoints_path
-
- # All keyword arugments should be `Data` node instances of base type and so should have the `.value` attribute
- unwrapped_kwargs = {key: node.value for key, node in kwargs.items() if isinstance(node, Data)}
-
- return get_explicit_kpoints_path(structure, **unwrapped_kwargs)
+# pylint: disable=unused-import
+import warnings
+from aiida_quantumespresso.calculations.functions.seekpath_structure_analysis import seekpath_structure_analysis
+
+warnings.warn(
+ 'This module is deprecated and will be removed soon.\nPlease use instead the new module:\n'
+ 'from aiida_quantumespresso.calculations.functions.seekpath_structure_analysis import seekpath_structure_analysis'
+ "\nOr use the entry point with the factory: CalculationFactory('quantumespresso.seekpath_structure_analysis')",
+ FutureWarning
+)

aiida_quantumespresso/workflows/pw/bands.py

@@ -5,8 +5,8 @@
 from aiida.plugins import WorkflowFactory
 from aiida.engine import WorkChain, ToContext, if_
 
+from aiida_quantumespresso.calculations.functions.seekpath_structure_analysis import seekpath_structure_analysis
 from aiida_quantumespresso.utils.mapping import prepare_process_inputs
-from aiida_quantumespresso.workflows.functions.seekpath_structure_analysis import seekpath_structure_analysis
 
 PwBaseWorkChain = WorkflowFactory('quantumespresso.pw.base')
 PwRelaxWorkChain = WorkflowFactory('quantumespresso.pw.relax')

aiida_quantumespresso/workflows/pw/base.py

@@ -5,14 +5,14 @@
 from aiida.engine import ToContext, if_, while_
 from aiida.plugins import CalculationFactory
 
+from aiida_quantumespresso.calculations.functions.create_kpoints_from_distance import create_kpoints_from_distance
 from aiida_quantumespresso.common.workchain.utils import register_error_handler, ErrorHandlerReport
 from aiida_quantumespresso.common.workchain.base.restart import BaseRestartWorkChain
 from aiida_quantumespresso.utils.defaults.calculation import pw as qe_defaults
 from aiida_quantumespresso.utils.mapping import update_mapping, prepare_process_inputs
 from aiida_quantumespresso.utils.pseudopotential import validate_and_prepare_pseudos_inputs
 from aiida_quantumespresso.utils.resources import get_default_options, get_pw_parallelization_parameters
 from aiida_quantumespresso.utils.resources import cmdline_remove_npools, create_scheduler_resources
-from aiida_quantumespresso.workflows.functions.create_kpoints_from_distance import create_kpoints_from_distance
 
 PwCalculation = CalculationFactory('quantumespresso.pw')
 

setup.json

@@ -13,19 +13,21 @@
  "entry_points": {
  "aiida.calculations": [
  "quantumespresso.cp = aiida_quantumespresso.calculations.cp:CpCalculation",
+ "quantumespresso.create_kpoints_from_distance = aiida_quantumespresso.calculations.functions.create_kpoints_from_distance:create_kpoints_from_distance",
  "quantumespresso.dos = aiida_quantumespresso.calculations.dos:DosCalculation",
+ "quantumespresso.epw = aiida_quantumespresso.calculations.epw:EpwCalculation",
  "quantumespresso.matdyn = aiida_quantumespresso.calculations.matdyn:MatdynCalculation",
  "quantumespresso.namelists = aiida_quantumespresso.calculations.namelists:NamelistsCalculation",
  "quantumespresso.neb = aiida_quantumespresso.calculations.neb:NebCalculation",
  "quantumespresso.ph = aiida_quantumespresso.calculations.ph:PhCalculation",
  "quantumespresso.pp = aiida_quantumespresso.calculations.pp:PpCalculation",
+ "quantumespresso.projwfc = aiida_quantumespresso.calculations.projwfc:ProjwfcCalculation",
  "quantumespresso.pw = aiida_quantumespresso.calculations.pw:PwCalculation",
- "quantumespresso.epw = aiida_quantumespresso.calculations.epw:EpwCalculation",
  "quantumespresso.pw2gw = aiida_quantumespresso.calculations.pw2gw:Pw2gwCalculation",
- "quantumespresso.projwfc = aiida_quantumespresso.calculations.projwfc:ProjwfcCalculation",
  "quantumespresso.pw2wannier90 = aiida_quantumespresso.calculations.pw2wannier90:Pw2wannier90Calculation",
+ "quantumespresso.pwimmigrant = aiida_quantumespresso.calculations.pwimmigrant:PwimmigrantCalculation",
  "quantumespresso.q2r = aiida_quantumespresso.calculations.q2r:Q2rCalculation",
- "quantumespresso.pwimmigrant = aiida_quantumespresso.calculations.pwimmigrant:PwimmigrantCalculation"
+ "quantumespresso.seekpath_structure_analysis = aiida_quantumespresso.calculations.functions.seekpath_structure_analysis:seekpath_structure_analysis"
  ],
  "aiida.data": [
  "quantumespresso.force_constants = aiida_quantumespresso.data.force_constants:ForceConstantsData"

tests/calculations/test_autoinvalidate_cache.py

@@ -1,16 +1,12 @@
 # -*- coding: utf-8 -*-
 """Test the automatic 'invalidates_cache' attribute for exit codes."""
-from distutils.version import StrictVersion # pylint: disable=import-error,no-name-in-module
-
+import inspect
 import pytest
 
-import aiida
+from aiida.engine import CalcJob
 from aiida.plugins import CalculationFactory
 from aiida.plugins.entry_point import get_entry_point_names
 
-if StrictVersion(aiida.__version__) < StrictVersion('1.1.0'):
- pytest.skip("The 'invalidates_cache' feature is only available on AiiDA 1.1+", allow_module_level=True)
-
 QE_CALC_ENTRY_POINT_NAMES = [
  ep_name for ep_name in get_entry_point_names(group='aiida.calculations') if ep_name.startswith('quantumespresso')
 ]
@@ -28,9 +24,14 @@ def test_exit_code_invalidates_cache(entry_point_name):
  Test that the 'invalidates_cache' attribute of exit codes is automatically
  set according to the status integer.
  """
- calc_class = CalculationFactory(entry_point_name)
+ entry_point = CalculationFactory(entry_point_name)
+
+ if not inspect.isclass(entry_point) or not issubclass(entry_point, CalcJob):
+ return
+
  overrides = EXPLICIT_OVERRIDES.get(entry_point_name, [])
- for exit_code in calc_class.exit_codes.values():
+
+ for exit_code in entry_point.exit_codes.values():
  if exit_code.status not in overrides:
  if exit_code.status < 400:
  assert exit_code.invalidates_cache