expanded normalize function for different cases and added comments

src/nomad_parser_vasp/parsers/xml_parser.py

@@ -13,7 +13,6 @@
 from nomad_parser_vasp.schema_packages.vasp_schema import (
     HartreeDCEnergy,
     TotalEnergy,
-    UnknownEnergy,
     XCdcEnergy,
 )
 
@@ -44,6 +43,9 @@ def xml_get(path: str, slicer=slice(0, 1), fallback=None):
             except KeyError:
                 return fallback
 
+        ####################################################
+        # Parse the basic program, method, and system data #
+        ####################################################
         archive.data = Simulation(
             program=Program(
                 name='VASP',
@@ -88,20 +90,44 @@ def xml_get(path: str, slicer=slice(0, 1), fallback=None):
                 ModelSystem(cell=[AtomicCell(positions=positions)])
             )
 
+        #####################################################
+        # Get the energy data from the raw simulation files #
+        #####################################################
         total_energy = xml_get("i[@name='e_fr_energy']", slice(-2, -1))
-        total_energy = total_energy[0] if total_energy else None
+        total_energy = total_energy[0] * ureg.eV if total_energy else None
         hartreedc = xml_get("i[@name='hartreedc']", slice(-2, -1))
-        hartreedc = hartreedc[0] if hartreedc else None
+        hartreedc = hartreedc[0] * ureg.eV if hartreedc else None
         xcdc = xml_get("i[@name='XCdc']", slice(-2, -1))
-        xcdc = xcdc[0] if xcdc else None
+        xcdc = xcdc[0] * ureg.eV if xcdc else None
 
+        ####################################################
+        # Create the outputs section, populate it with the #
+        # parsed energies, and add it to the archive       #
+        ####################################################
         output = Outputs()
         archive.data.outputs.append(output)
-        output.total_energy.append(TotalEnergy(value=total_energy * ureg.eV))
+        output.total_energy.append(TotalEnergy(value=total_energy))
+        output.total_energy[0].contributions.append(HartreeDCEnergy(value=hartreedc))
+        output.total_energy[0].contributions.append(XCdcEnergy(value=xcdc))
+
+        ##############################################################
+        # Add a new contribution to the total energy that quantifies #
+        # its unknown contributions (3 ways, choose 1)               #
+        ##############################################################
+
+        # Case 1: Add UnknownEnergy to contribution list in the parser with a value
+        from nomad_parser_vasp.schema_packages.vasp_schema import UnknownEnergy
 
         output.total_energy[0].contributions.append(
-            HartreeDCEnergy(value=hartreedc * ureg.eV)
+            UnknownEnergy(value=(total_energy - hartreedc - xcdc))
         )
-        output.total_energy[0].contributions.append(XCdcEnergy(value=xcdc * ureg.eV))
+        # Expected Results: normalizer does not change the value of UnknownEnergy
+
+        # Case 2: Add UnknownEnergy to contribution list in the parser but without a value
+        # from nomad_parser_vasp.schema_packages.vasp_schema import UnknownEnergy
+
+        # output.total_energy[0].contributions.append(UnknownEnergy(value=None))
+        # Expected Results: UnknownEnergy value is calculated by the normalizer and placed into this section
 
-        output.total_energy[0].contributions.append(UnknownEnergy(value=None))
+        # Case 3: Don't include UnknownEnergy in parsing
+        # Expected Results: UnknownEnergy is added to contribution list by the normalizer

src/nomad_parser_vasp/schema_packages/vasp_schema.py

@@ -58,15 +58,23 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
             return
 
         value = self.value
+        unknown_exists = False
+        unknown_has_value = False
         i_unknown = None
         for i_cont, contribution in enumerate(self.contributions):
             if contribution.name == 'UnknownEnergy':
+                unknown_exists = True
                 i_unknown = i_cont
+                unknown_has_value = True if contribution.value else False
 
             if not contribution.value:
                 continue
 
             value -= contribution.value
 
-        if i_unknown:
-            self.contributions[i_unknown].value = value
+        if unknown_exists:
+            if not unknown_has_value:
+                self.contributions[i_unknown].value = value
+        else:
+            self.contributions.append(UnknownEnergy(value=value))
+            self.contributions[-1].normalize(archive, logger)