Added check_archive to utils and normalize() of atoms_state.py and mo…

…del_system.py classes

src/nomad_simulations/atoms_state.py

@@ -46,7 +46,7 @@
 from nomad.datamodel.data import ArchiveSection
 from nomad.datamodel.metainfo.annotations import ELNAnnotation
 
-from .utils import RussellSaundersState
+from .utils import RussellSaundersState, check_archive
 
 
 class OrbitalsState(ArchiveSection):
@@ -308,6 +308,8 @@ def resolve_degeneracy(self) -> Optional[int]:
         return degeneracy
 
     def normalize(self, archive, logger) -> None:
+        if not check_archive(archive, logger):
+            return
         super().normalize(archive, logger)
 
         # General checks for physical quantum numbers and symbols
@@ -387,6 +389,8 @@ def resolve_occupation(self, logger: BoundLogger) -> Optional[np.float64]:
         return None
 
     def normalize(self, archive, logger) -> None:
+        if not check_archive(archive, logger):
+            return
         super().normalize(archive, logger)
 
         # Check if n_excited_electrons is between 0 and 1
@@ -555,6 +559,8 @@ def resolve_u_effective(self, logger: BoundLogger) -> Optional[np.float64]:
         return self.u_interaction - self.j_local_exchange_interaction
 
     def normalize(self, archive, logger) -> None:
+        if not check_archive(archive, logger):
+            return
         super().normalize(archive, logger)
 
         # Obtain (u, up, j_hunds_coupling) from slater_integrals
@@ -663,6 +669,8 @@ def resolve_atomic_number(self, logger: BoundLogger) -> Optional[int]:
         return None
 
     def normalize(self, archive, logger) -> None:
+        if not check_archive(archive, logger):
+            return
         super().normalize(archive, logger)
 
         # Get chemical_symbol from atomic_number and viceversa

src/nomad_simulations/model_system.py

@@ -61,7 +61,7 @@
 from nomad.datamodel.metainfo.annotations import ELNAnnotation
 
 from .atoms_state import AtomsState
-from .utils import get_sibling_section, is_not_representative
+from .utils import get_sibling_section, is_not_representative, check_archive
 
 
 class GeometricSpace(Entity):
@@ -209,6 +209,9 @@ def get_geometric_space_for_atomic_cell(self, logger: BoundLogger) -> None:
         self.volume = cell.volume * ureg.angstrom**3
 
     def normalize(self, archive, logger) -> None:
+        if not check_archive(archive, logger):
+            return
+
         # Skip normalization for `Entity`
         try:
             self.get_geometric_space_for_atomic_cell(logger)
@@ -290,6 +293,8 @@ class Cell(GeometricSpace):
     )
 
     def normalize(self, archive, logger) -> None:
+        if not check_archive(archive, logger):
+            return
         super().normalize(archive, logger)
 
 
@@ -371,6 +376,8 @@ def to_ase_atoms(self, logger: BoundLogger) -> Optional[ase.Atoms]:
         return ase_atoms
 
     def normalize(self, archive, logger) -> None:
+        if not check_archive(archive, logger):
+            return
         super().normalize(archive, logger)
 
 
@@ -629,6 +636,8 @@ def resolve_bulk_symmetry(
         return primitive_atomic_cell, conventional_atomic_cell
 
     def normalize(self, archive, logger) -> None:
+        if not check_archive(archive, logger):
+            return
         atomic_cell = get_sibling_section(
             section=self, sibling_section_name='atomic_cell', logger=logger
         )
@@ -718,6 +727,8 @@ def resolve_chemical_formulas(self, formula: Formula) -> None:
         self.anonymous = formula.format('anonymous')
 
     def normalize(self, archive, logger) -> None:
+        if not check_archive(archive, logger):
+            return
         atomic_cell = get_sibling_section(
             section=self, sibling_section_name='atomic_cell', logger=logger
         )
@@ -963,6 +974,8 @@ def resolve_system_type_and_dimensionality(
         return system_type, dimensionality
 
     def normalize(self, archive, logger) -> None:
+        if not check_archive(archive, logger):
+            return
         super().normalize(archive, logger)
 
         # We don't need to normalize if the system is not representative

src/nomad_simulations/utils/__init__.py

@@ -16,4 +16,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .utils import get_sibling_section, RussellSaundersState, is_not_representative
+from .utils import (
+    get_sibling_section,
+    RussellSaundersState,
+    is_not_representative,
+    check_archive,
+)

src/nomad_simulations/utils/utils.py

@@ -126,3 +126,20 @@ def is_not_representative(model_system, logger: BoundLogger = None):
         logger.warning('The `ModelSystem` was not found to be representative.')
         return True
     return False
+
+
+def check_archive(archive: ArchiveSection, logger: BoundLogger = None):
+    """
+    Checks if the given `Archive` is empty and logs a warning.
+
+    Args:
+        archive (ArchiveSection): The `ArchiveSection` to check.
+        logger (BoundLogger): The logger to log messages.
+
+    Returns:
+        (bool): True if the archive is empty, False otherwise.
+    """
+    if not archive:
+        logger.warning('The `archive` is empty.')
+        return False
+    return True