Add ElectronicDOS and XASSpectra properties (#54)

* Added .pyenv to .gitignore

* Change inheritance of OrbitalsState and AtomsState to Entity

* Added FermiLevel, ChemicalPotential, ElectronicDensityOfStates, XASSpectra to outputs list

Deleted custom_physical_property from Outputs

* Added todos in PhysicalProperty

Added note to change iri and rank to m_def definitions

* Added properties/spectral_profile.py and properties/energies.py modules

Added SpectralProfile, DOSProfile, ElectronicDensityOfStates, XASSpectra in the spectral_profile.py module

* Added conftest generate_simulation, generate_model_system, generate_simulation_electronic_dos fixtures

Testing default iri, name, rank

Fix test_outputs property

 Added testing for spectral_profile classes and methods

* Improved functionalities with @ndaelman-hu comments.

.gitignore

@@ -122,6 +122,7 @@ celerybeat.pid
 # Environments
 .env
 .venv
+.pyenv
 env/
 venv/
 ENV/

src/nomad_simulations/atoms_state.py

@@ -25,12 +25,13 @@
 
 from nomad.metainfo import Quantity, SubSection, MEnum, Section, Context
 from nomad.datamodel.data import ArchiveSection
+from nomad.datamodel.metainfo.basesections import Entity
 from nomad.datamodel.metainfo.annotations import ELNAnnotation
 
 from .utils import RussellSaundersState
 
 
-class OrbitalsState(ArchiveSection):
+class OrbitalsState(Entity):
     """
     A base section used to define the orbital state of an atom.
     """
@@ -537,7 +538,7 @@ def normalize(self, archive, logger) -> None:
                 )
 
 
-class AtomsState(ArchiveSection):
+class AtomsState(Entity):
     """
     A base section to define each atom state information.
     """

src/nomad_simulations/outputs.py

@@ -28,6 +28,10 @@
 from .numerical_settings import SelfConsistency
 from .properties import (
     ElectronicBandGap,
+    FermiLevel,
+    ChemicalPotential,
+    ElectronicDensityOfStates,
+    XASSpectra,
 )
 
 
@@ -53,20 +57,22 @@ class Outputs(ArchiveSection):
         a_eln=ELNAnnotation(component='ReferenceEditQuantity'),
     )
 
-    custom_physical_property = SubSection(
-        sub_section=PhysicalProperty.m_def,
-        repeats=True,
-        description="""
-        A custom physical property used to store properties not yet covered by the NOMAD schema.
-        """,
-    )
-
     # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
     # List of properties
     # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
 
+    fermi_level = SubSection(sub_section=FermiLevel.m_def, repeats=True)
+
+    chemical_potential = SubSection(sub_section=ChemicalPotential.m_def, repeats=True)
+
     electronic_band_gap = SubSection(sub_section=ElectronicBandGap.m_def, repeats=True)
 
+    electronic_dos = SubSection(
+        sub_section=ElectronicDensityOfStates.m_def, repeats=True
+    )
+
+    xas_spectra = SubSection(sub_section=XASSpectra.m_def, repeats=True)
+
     # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
     # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
 

src/nomad_simulations/physical_property.py

@@ -51,6 +51,9 @@ class PhysicalProperty(ArchiveSection):
     string identifiers and quantities for referencing and establishing the character of a physical property.
     """
 
+    # TODO add `errors`
+    # TODO add `smearing`
+
     name = Quantity(
         type=str,
         description="""

src/nomad_simulations/properties/__init__.py

@@ -16,4 +16,11 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from .energies import FermiLevel, ChemicalPotential
 from .band_gap import ElectronicBandGap
+from .spectral_profile import (
+    SpectralProfile,
+    DOSProfile,
+    ElectronicDensityOfStates,
+    XASSpectra,
+)

src/nomad_simulations/properties/band_gap.py

@@ -31,6 +31,8 @@ class ElectronicBandGap(PhysicalProperty):
     Energy difference between the highest occupied electronic state and the lowest unoccupied electronic state.
     """
 
+    # ! implement `iri` and `rank` as part of `m_def = Section()`
+
     iri = 'http://fairmat-nfdi.eu/taxonomy/ElectronicBandGap'
 
     type = Quantity(

src/nomad_simulations/properties/energies.py

@@ -0,0 +1,79 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import numpy as np
+
+from nomad.metainfo import Quantity, Section, Context
+
+from ..physical_property import PhysicalProperty
+
+
+class FermiLevel(PhysicalProperty):
+    """
+    Energy required to add or extract a charge from a material at zero temperature. It can be also defined as the chemical potential at zero temperature.
+    """
+
+    # ! implement `iri` and `rank` as part of `m_def = Section()`
+
+    iri = 'http://fairmat-nfdi.eu/taxonomy/FermiLevel'
+
+    value = Quantity(
+        type=np.float64,
+        unit='joule',
+        description="""
+        The value of the Fermi level.
+        """,
+    )
+
+    def __init__(
+        self, m_def: Section = None, m_context: Context = None, **kwargs
+    ) -> None:
+        super().__init__(m_def, m_context, **kwargs)
+        self.rank = []
+        self.name = self.m_def.name
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+
+class ChemicalPotential(PhysicalProperty):
+    """
+    Free energy cost of adding or extracting a particle from a thermodynamic system.
+    """
+
+    # ! implement `iri` and `rank` as part of `m_def = Section()`
+
+    iri = 'http://fairmat-nfdi.eu/taxonomy/ChemicalPotential'
+
+    value = Quantity(
+        type=np.float64,
+        unit='joule',
+        description="""
+        The value of the chemical potential.
+        """,
+    )
+
+    def __init__(
+        self, m_def: Section = None, m_context: Context = None, **kwargs
+    ) -> None:
+        super().__init__(m_def, m_context, **kwargs)
+        self.rank = []
+        self.name = self.m_def.name
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)