Added energies.py and FermiLevel and ChemicalPotential

Added SpectralProfile, ElectronicDensityOfStates, XASSpectra in spectral_profile.py

Check iri assignement in __init__ in PhysicalProperty

Fixed ElectronicBandGap

src/nomad_simulations/outputs.py

@@ -26,7 +26,13 @@
 from .model_system import ModelSystem
 from .physical_property import PhysicalProperty
 from .numerical_settings import SelfConsistency
-from .properties import ElectronicBandGap
+from .properties import (
+    ElectronicBandGap,
+    FermiLevel,
+    ChemicalPotential,
+    ElectronicDensityOfStates,
+    XASSpectra,
+)
 
 
 class Outputs(ArchiveSection):
@@ -64,6 +70,18 @@ class Outputs(ArchiveSection):
     # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
     electronic_band_gap = SubSection(sub_section=ElectronicBandGap.m_def, repeats=True)
 
+    fermi_level = SubSection(sub_section=FermiLevel.m_def, repeats=True)
+
+    chemical_potential = SubSection(sub_section=ChemicalPotential.m_def, repeats=True)
+
+    electronic_dos = SubSection(
+        sub_section=ElectronicDensityOfStates.m_def, repeats=True
+    )
+
+    xas_spectra = SubSection(sub_section=XASSpectra.m_def, repeats=True)
+    # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
+    # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
+
     def set_model_system_ref(self) -> Optional[ModelSystem]:
         if self.m_parent is not None:
             model_systems = self.m_parent.model_system

src/nomad_simulations/physical_property.py

@@ -208,7 +208,10 @@ def _new_value(self) -> Quantity:
 
     def __init__(self, m_def: Section = None, m_context: Context = None, **kwargs):
         super().__init__(m_def, m_context, **kwargs)
-        # self._new_value = self._new_value
+        if self.iri is None:
+            logger.warning(
+                'The used property is not defined in the FAIRmat taxonomy (https://fairmat-nfdi.github.io/fairmat-taxonomy/). You can contribute there if you want to extend the list of available materials properties.'
+            )
 
     def __setattr__(self, name: str, val: Any) -> None:
         # For the special case of `value`, its `shape` needs to be defined from `_full_shape`

src/nomad_simulations/properties/__init__.py

@@ -16,5 +16,6 @@
 # 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
+from .spectral_profile import SpectralProfile, ElectronicDensityOfStates, XASSpectra

src/nomad_simulations/properties/band_gap.py

@@ -21,7 +21,6 @@
 import pint
 from typing import Optional
 
-from nomad.units import ureg
 from nomad.metainfo import Quantity, MEnum, Section, Context
 
 from ..physical_property import PhysicalProperty
@@ -32,7 +31,7 @@ class ElectronicBandGap(PhysicalProperty):
     Energy difference between the highest occupied electronic state and the lowest unoccupied electronic state.
     """
 
-    iri = 'https://fairmat-nfdi.github.io/fairmat-taxonomy/#/ElectronicBandGap'
+    iri = 'https://fairmat-nfdi.github.io/fairmat-taxonomy/ElectronicBandGap'
 
     # ? can `type` change character depending on the `variables`?
     type = Quantity(
@@ -69,7 +68,7 @@ class ElectronicBandGap(PhysicalProperty):
 
     value = Quantity(
         type=np.float64,
-        unit='joule',
+        unit='joule',  # ! this units need to be fixed when we have dynamical units
         description="""
         The value of the `ElectronicBandGap`.
         """,

src/nomad_simulations/properties/energies.py

@@ -0,0 +1,69 @@
+#
+# 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.
+    """
+
+    iri = 'https://fairmat-nfdi.github.io/fairmat-taxonomy/FermiLevel'
+
+    value = Quantity(
+        type=np.float64,
+        unit='joule',  # ! this units need to be fixed when we have dynamical units
+        description="""
+        Value of the Fermi level.
+        """,
+    )
+
+    def __init__(self, m_def: Section = None, m_context: Context = None, **kwargs):
+        super().__init__(m_def, m_context, **kwargs)
+        self.rank = []  # ? Is this here or in the attrs instantiation better?
+
+    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.
+    """
+
+    iri = 'https://fairmat-nfdi.github.io/fairmat-taxonomy/ChemicalPotential'
+
+    value = Quantity(
+        type=np.float64,
+        unit='joule',  # ! this units need to be fixed when we have dynamical units
+        description="""
+        Value of the chemical potential.
+        """,
+    )
+
+    def __init__(self, m_def: Section = None, m_context: Context = None, **kwargs):
+        super().__init__(m_def, m_context, **kwargs)
+        self.rank = []  # ? Is this here or in the attrs instantiation better?
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)

src/nomad_simulations/properties/spectral_profile.py

@@ -22,7 +22,6 @@
 import pint
 
 from nomad.units import ureg
-from nomad.datamodel.data import ArchiveSection
 from nomad.metainfo import (
     Quantity,
     SubSection,
@@ -32,38 +31,42 @@
     JSON,
 )
 
-from ..outputs import resolve_output_value, Outputs, PhysicalProperty, FermiLevel
+from ..physical_property import PhysicalProperty
 
 
-class SpectralProfile(Outputs):
+class SpectralProfile(PhysicalProperty):
     """
     A base section used to define the spectral profile.
     """
 
-    intensities = Quantity(
+    value = Quantity(
         type=np.float64,
-        shape=['*'],
         description="""
-        Intensities in arbitrary units.
+        Value of the intensities of a spectral profile in arbitrary units.
         """,
     )
 
-    intensities_units = Quantity(
-        type=str,
-        description="""
-        Unit using the pint UnitRegistry() notation for the `intensities`. Example, if the spectra `is_derived`
-        from the imaginary part of the dielectric function, `intensities_units` are `'F/m'`.
-        """,
-    )
+    # TODO implement this in PhysicalProperty (similar to shape)
+    # value_units = Quantity(
+    #     type=str,
+    #     description="""
+    #     Unit using the pint UnitRegistry() notation for the `value`. Example, if the spectra `is_derived`
+    #     from the imaginary part of the dielectric function, `value` are `'F/m'`.
+    #     """,
+    # )
+
+    def __init__(self, m_def: Section = None, m_context: Context = None, **kwargs):
+        super().__init__(m_def, m_context, **kwargs)
+        self.rank = []  # ? Is this here or in the attrs instantiation better?
 
     def is_valid_spectral_profile(self) -> bool:
         """
-        Check if the spectral profile is valid, i.e., if the `intensities` are defined positive.
+        Check if the spectral profile is valid, i.e., if all `value` are defined positive.
 
         Returns:
             (bool): True if the spectral profile is valid, False otherwise.
         """
-        if (self.intensities < 0.0).any():
+        if (self.value < 0.0).any():
             return False
         return True
 
@@ -77,45 +80,21 @@ def normalize(self, archive, logger) -> None:
             return
 
 
-class ElectronicSpectralProfile(SpectralProfile):
+class ElectronicDensityOfStates(SpectralProfile):
     """
-    A base section used to define the electronic spectral profile variables. These are defined as the excitation energies.
+    Electronic Density of States (DOS).
     """
 
-    n_energies = Quantity(
-        type=np.int32,
-        shape=[],
-        description="""
-        Number of energies.
-        """,
-    )
-
-    energies = Quantity(
-        type=np.float64,
-        shape=['n_energies'],
-        unit='joule',
-        description="""
-        Energies.
-        """,
-    )
+    iri = 'http://fairmat-nfdi.eu/taxonomy/ElectronicDensityOfStates'
 
-    energies_origin = Quantity(
-        type=np.float64,
-        unit='joule',
+    spin_channel = Quantity(
+        type=np.int32,
         description="""
-        Origin of reference for the energies.
+        Spin channel of the corresponding DOS. It can take values of 0 or 1. This quantity is set only if
+        `ModelMethod.is_spin_polarized` is `True`.
         """,
     )
 
-    def normalize(self, archive, logger) -> None:
-        super().normalize(archive, logger)
-
-
-class ElectronicDOS(ElectronicSpectralProfile):
-    """
-    Electronic Density of States (DOS).
-    """
-
     fermi_level = Quantity(
         type=np.float64,
         unit='joule',
@@ -129,14 +108,6 @@ class ElectronicDOS(ElectronicSpectralProfile):
         """,
     )
 
-    spin_channel = Quantity(
-        type=np.int32,
-        description="""
-        Spin channel of the corresponding DOS. It can take values of 0 or 1. This quantity is set only if
-        `ModelMethod.is_spin_polarized` is `True`.
-        """,
-    )
-
     normalization_factor = Quantity(
         type=np.float64,
         description="""
@@ -146,16 +117,15 @@ class ElectronicDOS(ElectronicSpectralProfile):
         """,
     )
 
-    intensities_integrated = Quantity(
+    value_integrated = Quantity(
         type=np.float64,
-        shape=['n_energies'],
         description="""
         The cumulative intensities integrated from from the lowest (most negative) energy to the `fermi_level`.
         """,
     )
 
     projected_dos = SubSection(
-        sub_section=ElectronicSpectralProfile.m_def,
+        sub_section=SpectralProfile.m_def,
         repeats=True,
         description="""
         Projected DOS. It can be species- (same elements in the unit cell), atom- (different elements in the unit cell),
@@ -170,7 +140,6 @@ class ElectronicDOS(ElectronicSpectralProfile):
 
     def __init__(self, m_def: Section = None, m_context: Context = None, **kwargs):
         super().__init__(m_def, m_context, **kwargs)
-        # Set the name of the section
         self.name = self.m_def.name
 
     def resolve_fermi_level(self) -> Optional[np.float64]:
@@ -181,9 +150,9 @@ def resolve_fermi_level(self) -> Optional[np.float64]:
             (Optional[np.float64]): The resolved Fermi level.
         """
         fermi_level = self.fermi_level
-        if fermi_level is None:
-            fermi_level = resolve_output_value(self, FermiLevel)
-        return fermi_level
+        # if fermi_level is None:
+        #     fermi_level = resolve_output_value(self, FermiLevel)
+        # return fermi_level
 
     def check_spin_polarized(self) -> bool:
         """
@@ -234,23 +203,25 @@ def normalize(self, archive, logger) -> None:
         self.energies_origin = self.resolve_energies_origin()
 
 
-class XASSpectra(ElectronicSpectralProfile):
+class XASSpectra(SpectralProfile):
     """
     X-ray Absorption Spectra (XAS).
     """
 
     xanes_spectra = SubSection(
-        sub_section=ElectronicSpectralProfile.m_def,
+        sub_section=SpectralProfile.m_def,
         description="""
         X-ray Absorption Near Edge Structure (XANES) spectra.
         """,
+        repeats=False,
     )
 
     exafs_spectra = SubSection(
-        sub_section=ElectronicSpectralProfile.m_def,
+        sub_section=SpectralProfile.m_def,
         description="""
         Extended X-ray Absorption Fine Structure (EXAFS) spectra.
         """,
+        repeats=False,
     )
 
     def __init__(self, m_def: Section = None, m_context: Context = None, **kwargs):