Added initial modules for ModelMethod and Outputs

Fixed conditions in AtomicCell normalizer

simulationdataschema/general.py

@@ -54,27 +54,20 @@
 from nomad.datamodel.metainfo.basesections import Simulation as BaseSimulation
 from nomad.metainfo import SubSection
 from .model_system import ModelSystem
+from .model_method import ModelMethod
+from .outputs import Outputs
 
 
 class Simulation(BaseSimulation, EntryData):
     """ """
 
     # m_def = Section(extends_base_section=True)
+
     model_system = SubSection(sub_section=ModelSystem.m_def, repeats=True)
-    # method = SubSection(
-    # sub_section=Method.m_def,
-    # description='''
-    # The input methodological parameters used for the computation.
-    # ''',
-    # repeats=True,
-    # )
-    # calculation = SubSection(
-    # sub_section=Calculation.m_def,
-    # description='''
-    # The output of a computation. It can reference a specific system and method section.
-    # ''',
-    # repeats=True,
-    # )
+
+    model_method = SubSection(sub_section=ModelMethod.m_def, repeats=True)
+
+    outputs = SubSection(sub_section=Outputs.m_def, repeats=True)
 
     def _set_system_tree_index(self, system_parent: ModelSystem, tree_index: int = 0):
         for system_child in system_parent.model_system:

simulationdataschema/model_method.py

@@ -0,0 +1,52 @@
+#
+# 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.
+#
+#
+# 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 re
+import numpy as np
+
+from nomad.units import ureg
+from nomad.datamodel.data import ArchiveSection
+from nomad.metainfo import Quantity, SubSection, SectionProxy, MEnum
+
+
+class ModelMethod(ArchiveSection):
+    """ """
+
+    normalizer_level = 1
+
+    def normalize(self, archive, logger):
+        super().normalize(archive, logger)
+        self.logger = logger

simulationdataschema/model_system.py

@@ -258,7 +258,7 @@ def normalize(self, archive, logger):
             return
 
         # If the labels and atomic_numbers are not specified, we return with an error
-        if not self.labels and not self.atomic_numbers:
+        if self.labels is None and self.atomic_numbers is None:
             logger.error(
                 "Could not read parsed AtomicCell.labels or AtomicCell.atomic_positions."
             )
@@ -267,7 +267,7 @@ def normalize(self, archive, logger):
         atomic_numbers = self.atomic_numbers
 
         # Labels
-        if not atomic_labels and atomic_numbers is not None:
+        if atomic_labels is None and atomic_numbers is not None:
             try:
                 atomic_labels = [
                     ase.data.chemical_symbols[number] for number in atomic_numbers
@@ -286,7 +286,7 @@ def normalize(self, archive, logger):
         self.m_cache["ase_atoms"] = ase_atoms
 
         # Atomic numbers
-        if atomic_labels is not None and not atomic_numbers:
+        if atomic_labels is not None and atomic_numbers is None:
             atomic_numbers = ase_atoms.get_atomic_numbers()
         self.atomic_numbers = atomic_numbers
 

simulationdataschema/outputs.py

@@ -0,0 +1,52 @@
+#
+# 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.
+#
+#
+# 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 re
+import numpy as np
+
+from nomad.units import ureg
+from nomad.datamodel.data import ArchiveSection
+from nomad.metainfo import Quantity, SubSection, SectionProxy, MEnum
+
+
+class Outputs(ArchiveSection):
+    """ """
+
+    normalizer_level = 2
+
+    def normalize(self, archive, logger):
+        super().normalize(archive, logger)
+        self.logger = logger