Enable energy range around the Fermi level

* This PR fixes the existing `align_to_fermi` attribute. It was implemented as a top level argument in the previous version, however, it was only expected in the parameter dictionaries of `dos` and `projwfc`. Hence, it was never used as intended.

* Further bugs in the input generation were fixed

* The existing `align_to_fermi` input is replaced by `energy_range_vs_fermi`, which is a `List` that can optionally specify the energy range around the Fermi level that should be covered by the DOS and PDOS.

Co-authored-by: Sebastiaan Huber <mail@sphuber.net>

Author: t-reents

src/aiida_quantumespresso/workflows/pdos.py

@@ -10,10 +10,10 @@
 
 Additional functionality:
 
-- Setting ``'align_to_fermi': True`` in the inputs will ensure that the energy range is centred around the Fermi
-  energy when `Emin` and `Emax` are provided for both the `dos` and `projwfc` inputs. This is useful when you are only
-  interested in a certain energy range around the Fermi energy. By default the energy range is extracted from the
-  NSCF calculation.
+- Setting ``'energy_range_vs_fermi'`` in the inputs allows to specify an energy range around the Fermi level that should
+    be covered by the DOS and PDOS. This is useful when you are only interested in a certain energy range around the
+    Fermi energy. By default, this is not specified and the energy range given in the `dos.x` and `projwfc.x`
+    inputs will be used.
 
 Storage memory management:
 
@@ -97,7 +97,6 @@ def validate_inputs(value, _):
 
     - Check that either the `scf` or `nscf.pw.parent_folder` inputs is provided.
     - Check that the `Emin`, `Emax` and `DeltaE` inputs are the same for the `dos` and `projwfc` namespaces.
-    - Check that `Emin` and `Emax` are provided in case `align_to_fermi` is set to `True`.
     """
     # Check that either the `scf` input or `nscf.pw.parent_folder` is provided.
     import warnings
@@ -113,10 +112,13 @@ def validate_inputs(value, _):
         if value['dos']['parameters']['DOS'].get(par, None) != value['projwfc']['parameters']['PROJWFC'].get(par, None):
             return f'The `{par}`` parameter has to be equal for the `dos` and `projwfc` inputs.'
 
-    if value.get('align_to_fermi', False):
+    if value.get('energy_range_vs_fermi', False):
         for par in ['Emin', 'Emax']:
-            if value['dos']['parameters']['DOS'].get(par, None) is None:
-                return f'The `{par}`` parameter must be set in case `align_to_fermi` is set to `True`.'
+            if value['dos']['parameters']['DOS'].get(par, None):
+                warnings.warn(
+                    f'The `{par}` parameter and `energy_range_vs_fermi` were specified.'
+                    'The value in `energy_range_vs_fermi` will be used.'
+                )
 
     if 'nbands_factor' in value and 'nbnd' in value['nscf']['pw']['parameters'].base.attributes.get('SYSTEM', {}):
         return PdosWorkChain.exit_codes.ERROR_INVALID_INPUT_NUMBER_OF_BANDS.message
@@ -160,6 +162,17 @@ def validate_projwfc(value, _):
     jsonschema.validate(value['parameters'].get_dict()['PROJWFC'], get_parameter_schema())
 
 
+def validate_energy_range_vs_fermi(value, _):
+    """Validate specified energy_range_vs_fermi.
+
+    - List needs to consist of two float values.
+    """
+    if len(value) != 2:
+        return f'`energy_range_vs_fermi` should be a `List` of length two, but got: {value}'
+    if not all(isinstance(val, (float, int)) for val in value):
+        return f'`energy_range_vs_fermi` should be a `List` of floats, but got: {value}'
+
+
 def clean_calcjob_remote(node):
     """Clean the remote directory of a ``CalcJobNode``."""
     cleaned = False
@@ -220,14 +233,15 @@ def define(cls, spec):
             help='Terminate workchain steps before submitting calculations (test purposes only).'
         )
         spec.input(
-            'align_to_fermi',
-            valid_type=orm.Bool,
+            'energy_range_vs_fermi',
+            valid_type=orm.List,
+            required=False,
             serializer=to_aiida_type,
-            default=lambda: orm.Bool(False),
+            validator=validate_energy_range_vs_fermi,
             help=(
-                'If true, Emin=>Emin-Efermi & Emax=>Emax-Efermi, where Efermi is taken from the `nscf` calculation. '
-                'Note that it only makes sense to align `Emax` and `Emin` to the fermi level in case they are actually '
-                'provided by in the `dos` and `projwfc` inputs, since otherwise the '
+                'Energy range with respect to the Fermi level that should be covered in DOS and PROJWFC calculation.'
+                'If not specified but Emin and Emax are specified in the input parameters, these values will be used.'
+                'Otherwise, the default values are extracted from the NSCF calculation.'
             )
         )
         spec.input('nbands_factor', valid_type=orm.Float, required=False,
@@ -383,6 +397,9 @@ def setup(self):
         """Initialize context variables that are used during the logical flow of the workchain."""
         self.ctx.serial_clean = 'serial_clean' in self.inputs and self.inputs.serial_clean.value
         self.ctx.dry_run = 'dry_run' in self.inputs and self.inputs.dry_run.value
+        self.ctx.energy_range_vs_fermi = (
+            self.inputs.energy_range_vs_fermi if 'energy_range_vs_fermi' in self.inputs else None
+            )
 
     def serial_clean(self):
         """Return whether dos and projwfc calculations should be run in serial.
@@ -491,9 +508,12 @@ def _generate_dos_inputs(self):
         dos_inputs.parent_folder = self.ctx.nscf_parent_folder
         dos_parameters = self.inputs.dos.parameters.get_dict()
 
-        if dos_parameters.pop('align_to_fermi', False):
-            dos_parameters['DOS']['Emin'] = dos_parameters['Emin'] + self.ctx.nscf_fermi
-            dos_parameters['DOS']['Emax'] = dos_parameters['Emax'] + self.ctx.nscf_fermi
+        if self.ctx.energy_range_vs_fermi:
+            dos_parameters['DOS']['Emin'] = self.ctx.energy_range_vs_fermi[0] + self.ctx.nscf_fermi
+            dos_parameters['DOS']['Emax'] = self.ctx.energy_range_vs_fermi[1] + self.ctx.nscf_fermi
+        else:
+            dos_parameters['DOS'].setdefault('Emin', self.ctx.nscf_emin)
+            dos_parameters['DOS'].setdefault('Emax', self.ctx.nscf_emax)
 
         dos_inputs.parameters = orm.Dict(dos_parameters)
         dos_inputs['metadata']['call_link_label'] = 'dos'
@@ -505,9 +525,12 @@ def _generate_projwfc_inputs(self):
         projwfc_inputs.parent_folder = self.ctx.nscf_parent_folder
         projwfc_parameters = self.inputs.projwfc.parameters.get_dict()
 
-        if projwfc_parameters.pop('align_to_fermi', False):
-            projwfc_parameters['PROJWFC']['Emin'] = projwfc_parameters['Emin'] + self.ctx.nscf_fermi
-            projwfc_parameters['PROJWFC']['Emax'] = projwfc_parameters['Emax'] + self.ctx.nscf_fermi
+        if self.ctx.energy_range_vs_fermi:
+            projwfc_parameters['PROJWFC']['Emin'] = self.ctx.energy_range_vs_fermi[0] + self.ctx.nscf_fermi
+            projwfc_parameters['PROJWFC']['Emax'] = self.ctx.energy_range_vs_fermi[1] + self.ctx.nscf_fermi
+        else:
+            projwfc_parameters['PROJWFC'].setdefault('Emin', self.ctx.nscf_emin)
+            projwfc_parameters['PROJWFC'].setdefault('Emax', self.ctx.nscf_emax)
 
         projwfc_inputs.parameters = orm.Dict(projwfc_parameters)
         projwfc_inputs['metadata']['call_link_label'] = 'projwfc'

tests/conftest.py

@@ -879,8 +879,8 @@ def _generate_workchain_ph(exit_code=None, inputs=None, return_inputs=False):
 def generate_workchain_pdos(generate_workchain, generate_inputs_pw, fixture_code):
     """Generate an instance of a `PdosWorkChain`."""
 
-    def _generate_workchain_pdos():
-        from aiida.orm import Bool, Dict
+    def _generate_workchain_pdos(emin=None, emax=None, energy_range_vs_fermi=None):
+        from aiida.orm import Bool, Dict, List
 
         from aiida_quantumespresso.utils.resources import get_default_options
 
@@ -902,12 +902,15 @@ def _generate_workchain_pdos():
 
         dos_params = {
             'DOS': {
-                'Emin': -10,
-                'Emax': 10,
                 'DeltaE': 0.01,
             }
         }
-        projwfc_params = {'PROJWFC': {'Emin': -10, 'Emax': 10, 'DeltaE': 0.01, 'ngauss': 0, 'degauss': 0.01}}
+        projwfc_params = {'PROJWFC': {'DeltaE': 0.01, 'ngauss': 0, 'degauss': 0.01}}
+
+        if emin and emax:
+            dos_params['DOS'].update({'Emin': emin, 'Emax': emax})
+            projwfc_params['PROJWFC'].update({'Emin': emin, 'Emax': emax})
+
         dos = {
             'code': fixture_code('quantumespresso.dos'),
             'parameters': Dict(dos_params),
@@ -928,9 +931,10 @@ def _generate_workchain_pdos():
             'nscf': nscf,
             'dos': dos,
             'projwfc': projwfc,
-            'align_to_fermi': Bool(True),
             'dry_run': Bool(True)
         }
+        if energy_range_vs_fermi:
+            inputs.update({'energy_range_vs_fermi': List(energy_range_vs_fermi)})
 
         return generate_workchain(entry_point, inputs)
 

tests/workflows/test_pdos.py

@@ -7,6 +7,7 @@
 from aiida.common import LinkType
 from aiida.engine.utils import instantiate_process
 from aiida.manage.manager import get_manager
+import numpy as np
 from plumpy import ProcessState
 import pytest
 
@@ -27,31 +28,39 @@ def instantiate_process_cls(process_cls, inputs):
     return instantiate_process(runner, process_cls, **inputs)
 
 
+def check_pdos_energy_range(dos_inputs, projwfc_inputs, expected_p_dos_inputs):
+    """Check the energy range of the pdos calculation."""
+    # check generated inputs
+    dos_params = dos_inputs.parameters.get_dict()
+    projwfc_params = projwfc_inputs.parameters.get_dict()
+
+    assert np.isclose(dos_params['DOS']['Emin'], expected_p_dos_inputs[0])
+    assert np.isclose(dos_params['DOS']['Emax'], expected_p_dos_inputs[1])
+    assert np.isclose(projwfc_params['PROJWFC']['Emin'], expected_p_dos_inputs[0])
+    assert np.isclose(projwfc_params['PROJWFC']['Emax'], expected_p_dos_inputs[1])
+
+
 @pytest.mark.parametrize(
-    'nscf_output_parameters', [
-        {
-            'fermi_energy': 6.9
-        },
-        {
-            'fermi_energy_down': 5.9,
-            'fermi_energy_up': 6.9
-        },
-    ]
+    'nscf_output_parameters,energy_range_inputs,expected_p_dos_inputs',
+    [({
+        'fermi_energy': 6.9
+    }, (-10, 10, None), (-10, 10)),
+     ({
+         'fermi_energy_down': 5.9,
+         'fermi_energy_up': 6.9
+     }, (None, None, [-10, 10]), (-3.1, 16.9)), ({
+         'fermi_energy': 6.9
+     }, (None, None, None), (-5.64024889, 8.91047649))]
 )
+@pytest.mark.usefixtures('aiida_profile_clean')
 def test_default(
-    generate_workchain_pdos,
-    generate_workchain_pw,
-    fixture_localhost,
-    generate_remote_data,
-    generate_calc_job,
-    generate_calc_job_node,
-    fixture_sandbox,
-    generate_bands_data,
-    nscf_output_parameters,
+    generate_workchain_pdos, generate_workchain_pw, fixture_localhost, generate_remote_data, generate_calc_job,
+    generate_calc_job_node, fixture_sandbox, generate_bands_data, nscf_output_parameters, energy_range_inputs,
+    expected_p_dos_inputs
 ):
     """Test instantiating the WorkChain, then mock its process, by calling methods in the ``spec.outline``."""
 
-    wkchain = generate_workchain_pdos()
+    wkchain = generate_workchain_pdos(*energy_range_inputs)
     assert wkchain.setup() is None
     assert wkchain.serial_clean() is False
 
@@ -93,8 +102,7 @@ def test_default(
     result.store()
     result.base.links.add_incoming(mock_wknode, link_type=LinkType.RETURN, link_label='output_parameters')
 
-    bands_data = generate_bands_data()
-    bands_data.store()
+    bands_data = generate_bands_data().store()
     bands_data.base.links.add_incoming(mock_wknode, link_type=LinkType.RETURN, link_label='output_band')
 
     wkchain.ctx.workchain_nscf = mock_wknode
@@ -104,6 +112,9 @@ def test_default(
 
     # mock run dos and projwfc, and check that their inputs are acceptable
     dos_inputs, projwfc_inputs = wkchain.run_pdos_parallel()
+
+    check_pdos_energy_range(dos_inputs, projwfc_inputs, expected_p_dos_inputs)
+
     generate_calc_job(fixture_sandbox, 'quantumespresso.dos', dos_inputs)
     generate_calc_job(fixture_sandbox, 'quantumespresso.projwfc', projwfc_inputs)