ModelSystem should contain cell and not atomic_cell (#20)

Changed ModelSystem.atomic_cell to ModelSystem.cell

Fix name definitions in inherited Cell and NumericalSettings classes

src/nomad_simulations/model_method.py

@@ -15,24 +15,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-#
-# 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
 import pint
@@ -71,7 +53,6 @@ class NumericalSettings(ArchiveSection):
         `NumericalSettings` section. Possible values: "KMesh", "FrequencyMesh", "TimeMesh",
         "SelfConsistency", "BasisSet".
         """,
-        a_eln=ELNAnnotation(component='StringEditQuantity'),
     )
 
     def normalize(self, archive, logger) -> None:
@@ -317,6 +298,11 @@ class KMesh(Mesh):
 
     # TODO add extraction of `high_symmetry_points` using BandStructureNormalizer idea (left for later when defining outputs.py)
 
+    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_points_and_offset(
         self, logger: BoundLogger
     ) -> Tuple[Optional[List[np.ndarray]], Optional[np.ndarray]]:
@@ -420,9 +406,6 @@ def resolve_k_line_density(
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
-        # Set the name of the section
-        self.name = self.m_def.name if self.name is None else self.name
-
         # If `grid` is not defined, we do not normalize the KMesh
         if self.grid is None:
             logger.warning('Could not find `KMesh.grid`.')
@@ -452,12 +435,14 @@ class QuasiparticlesFrequencyMesh(Mesh):
         """,
     )
 
+    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 normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
-        # Set the name of the section
-        self.name = self.m_def.name if self.name is None else self.name
-
 
 class SelfConsistency(NumericalSettings):
     """
@@ -511,22 +496,27 @@ class SelfConsistency(NumericalSettings):
         """,
     )
 
+    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 normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
-        # Set the name of the section
-        self.name = self.m_def.name if self.name is None else self.name
-
 
 class BasisSet(NumericalSettings):
     """"""
 
     # TODO work on this base section (@ndaelman-hu)
-    def normalize(self, archive, logger) -> None:
-        super().normalize(archive, logger)
 
+    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 if self.name is None else self.name
+        self.name = self.m_def.name
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
 
 
 class ModelMethod(ArchiveSection):

src/nomad_simulations/model_system.py

@@ -55,7 +55,7 @@
 from nomad.units import ureg
 from nomad.atomutils import Formula, get_normalized_wyckoff, search_aflow_prototype
 
-from nomad.metainfo import Quantity, SubSection, SectionProxy, MEnum
+from nomad.metainfo import Quantity, SubSection, SectionProxy, MEnum, Section, Context
 from nomad.datamodel.data import ArchiveSection
 from nomad.datamodel.metainfo.basesections import Entity, System
 from nomad.datamodel.metainfo.annotations import ELNAnnotation
@@ -224,6 +224,14 @@ class Cell(GeometricSpace):
     A base section used to specify the cell quantities of a system at a given moment in time.
     """
 
+    name = Quantity(
+        type=str,
+        description="""
+        Name of the specific cell section. This is typically used to easy identification of the
+        `Cell` section. Possible values: "AtomicCell".
+        """,
+    )
+
     type = Quantity(
         type=MEnum('original', 'primitive', 'conventional'),
         description="""
@@ -327,6 +335,11 @@ class AtomicCell(Cell):
         """,
     )
 
+    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 to_ase_atoms(self, logger: BoundLogger) -> Optional[ase.Atoms]:
         """
         Generates an ASE Atoms object with the most basic information from the parsed `AtomicCell`
@@ -373,6 +386,9 @@ def to_ase_atoms(self, logger: BoundLogger) -> Optional[ase.Atoms]:
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+        # Set the name of the section
+        self.name = self.m_def.name if self.name is None else self.name
+
 
 class Symmetry(ArchiveSection):
     """
@@ -629,22 +645,18 @@ def resolve_bulk_symmetry(
 
     def normalize(self, archive, logger) -> None:
         atomic_cell = get_sibling_section(
-            section=self, sibling_section_name='atomic_cell', logger=logger
+            section=self, sibling_section_name='cell', logger=logger
         )
         if self.m_parent.type == 'bulk':
             # Adding the newly calculated primitive and conventional cells to the ModelSystem
             (
                 primitive_atomic_cell,
                 conventional_atomic_cell,
             ) = self.resolve_bulk_symmetry(atomic_cell, logger)
-            self.m_parent.m_add_sub_section(
-                ModelSystem.atomic_cell, primitive_atomic_cell
-            )
-            self.m_parent.m_add_sub_section(
-                ModelSystem.atomic_cell, conventional_atomic_cell
-            )
+            self.m_parent.m_add_sub_section(ModelSystem.cell, primitive_atomic_cell)
+            self.m_parent.m_add_sub_section(ModelSystem.cell, conventional_atomic_cell)
             # Reference to the standarized cell, and if not, fallback to the originally parsed one
-            self.atomic_cell_ref = self.m_parent.atomic_cell[-1]
+            self.atomic_cell_ref = self.m_parent.cell[-1]
 
 
 class ChemicalFormula(ArchiveSection):
@@ -718,7 +730,7 @@ def resolve_chemical_formulas(self, formula: Formula) -> None:
 
     def normalize(self, archive, logger) -> None:
         atomic_cell = get_sibling_section(
-            section=self, sibling_section_name='atomic_cell', logger=logger
+            section=self, sibling_section_name='cell', logger=logger
         )
         ase_atoms = atomic_cell.to_ase_atoms(logger)
         formula = None
@@ -858,7 +870,7 @@ class ModelSystem(System):
         """,
     )
 
-    atomic_cell = SubSection(sub_section=AtomicCell.m_def, repeats=True)
+    cell = SubSection(sub_section=Cell.m_def, repeats=True)
 
     symmetry = SubSection(sub_section=Symmetry.m_def, repeats=True)
 
@@ -966,29 +978,30 @@ def normalize(self, archive, logger) -> None:
             return
 
         # Extracting ASE Atoms object from the originally parsed AtomicCell section
-        if self.atomic_cell is None:
+        if self.cell is None:
             self.logger.warning(
                 'Could not find the originally parsed atomic system. `Symmetry` and `ChemicalFormula` extraction is thus not run.'
             )
             return
-        self.atomic_cell[0].type = 'original'
-        ase_atoms = self.atomic_cell[0].to_ase_atoms(logger)
-        if not ase_atoms:
-            return
-
-        # Resolving system `type`, `dimensionality`, and Symmetry section (if this last
-        # one does not exists already)
-        original_atom_positions = self.atomic_cell[0].positions
-        if original_atom_positions is not None:
-            self.type = 'unavailable' if not self.type else self.type
-            (
-                self.type,
-                self.dimensionality,
-            ) = self.resolve_system_type_and_dimensionality(ase_atoms, logger)
-            # Creating and normalizing Symmetry section
-            if self.type == 'bulk' and self.symmetry is not None:
-                sec_symmetry = self.m_create(Symmetry)
-                sec_symmetry.normalize(archive, logger)
+        if self.cell[0].name == 'AtomicCell':
+            self.cell[0].type = 'original'
+            ase_atoms = self.cell[0].to_ase_atoms(logger)
+            if not ase_atoms:
+                return
+
+            # Resolving system `type`, `dimensionality`, and Symmetry section (if this last
+            # one does not exists already)
+            original_atom_positions = self.cell[0].positions
+            if original_atom_positions is not None:
+                self.type = 'unavailable' if not self.type else self.type
+                (
+                    self.type,
+                    self.dimensionality,
+                ) = self.resolve_system_type_and_dimensionality(ase_atoms, logger)
+                # Creating and normalizing Symmetry section
+                if self.type == 'bulk' and self.symmetry is not None:
+                    sec_symmetry = self.m_create(Symmetry)
+                    sec_symmetry.normalize(archive, logger)
 
         # Creating and normalizing ChemicalFormula section
         # TODO add support for fractional formulas (possibly add `AtomicCell.concentrations` for each species)