- Flesh out business logic in OpenMX parser

- Rewrite business logic to use `n_excited_electrons` in the `VASP` parser

electronicparsers/openmx/parser.py

@@ -83,7 +83,7 @@
 
 core_hole_parser = TextParser(quantities=[
     Quantity('core_hole', rf'(\d+)\s+({element})\s+(\d+)',
-             repeats=True),
+             repeats=False),  # TODO: consider `repeats = True` case
 ])
 
 
@@ -326,17 +326,35 @@ def parse_species(self, definitions: list[str], logger: logging.Logger) -> tuple
             logger.error(f'Unknown exchange-correlation functional: {_definitions[2]}')
 
         # evaluate core_hole
-        try:
-            nq, lq = _extract_core_hole(_definitions[1]).groups()
+        quantum_nums_flag = _extract_core_hole(_definitions[1])  # this checks the PAO, the PP is only necessary for the final state
+        if quantum_nums_flag:
+            quantum_nums = quantum_nums_flag.groups()
             core_hole = CoreHole(
-                n_quantum_number = int(nq),
-                l_quantum_number = l_mapping[lq],
-                occupation = 0.,
+                n_quantum_number=int(quantum_nums[0]),
             )
-        except AttributeError:
-            pass
-        except KeyError:
-            logger.error(f'Unknown l-quantum symbol: {lq}')
+            try:
+                core_hole.l_quantum_number = l_mapping[quantum_nums[1]]
+            except KeyError:
+                logger.error(f'Unknown l-quantum symbol: {quantum_nums[1]}')
+
+            core_hole_flags = mainfile_parser.results.get('core_hole')
+            if core_hole_flags:
+                core_hole.dscf_state = 'final'
+                spinpol = mainfile_parser.get('scf.SpinPolarization', '').lower()
+                if spinpol == 'on':
+                    core_hole.n_electrons_excited = 1.
+                    core_hole.ms_quantum_bool = not bool(int(core_hole_flags.results['core_hole'][2] / core_hole.degeneracy))
+                elif spinpol == 'off':
+                    core_hole.n_electrons_excited = 2.  # TODO: verify
+                    logger.warning('''
+                    Unexpected spin-restricted setting when using final-state core-hole computation.
+                    This is not recommended by the manual. For now assuming double electron (bosonic) excitation.
+                    ''')
+                else:
+                    logger.warning('Could not set all quantum numbers: non-collinear calculations not yet supported')
+            else:
+                core_hole.dscf_state = 'initial'  # this will be a hook in $\Delta$-SCF
+                core_hole.n_electrons_excited = 0.
 
         return pseudopotential, core_hole
 

electronicparsers/vasp/parser.py

@@ -1377,27 +1377,19 @@ def parse_core_hole(self) -> (Union[CoreHole, None], Union[AtomsGroup, None], in
 
         source = self.parser.incar
 
-        # setup `CoreHole` parameters
-        corehole_map = {
-            'n_quantum_number': source.get('CLN', 1),
-            'l_quantum_number': source.get('CLL', 0),
-            'occupation': source.get('CLZ', 0.),  # tested with VASP 6.4.1
-        }
-
-        core_hole = CoreHole(**corehole_map)
-        core_hole.occupation = core_hole.degeneracy - core_hole.occupation
-        if core_hole.occupation < 0.:
-            self.logger.warning('Core hole occupation is negative. Setting to 0.')  # TODO: check if this is correct
-            core_hole.occupation = 0.
-
         # setup `AtomsGroup` parameters
         elem_id = source.get('CLNT', 1) - 1
         elem_ids = [int(x) for x in self.parser.atom_info['atomtypes']['atomspertype']]
         lower_range = elem_ids[elem_id - 1] if elem_id > 1 else 0
         atom_ids = list(range(lower_range, elem_ids[elem_id]))
 
         return (
-            core_hole,
+            CoreHole(
+                n_quantum_number=source.get('CLN', 1),
+                l_quantum_number=source.get('CLL', 0),
+                n_electrons_excited=source.get('CLZ', 0.),  # tested with VASP 6.4.1
+                dscf_state='final',
+            ),
             AtomsGroup(
                 label='core-hole',
                 type='active_orbital',
@@ -1552,7 +1544,7 @@ def parse_method(self) -> dict[str, Any]:
             except AttributeError:
                 break
             try:
-                species_electrons += param.core_hole.degeneracy - param.core_hole.occupation  # same, regardless of spin-orbital or not
+                species_electrons -= param.core_hole.n_electrons_excited
             except AttributeError:
                 pass
             neutral_count += species_electrons * n_atoms
@@ -1640,6 +1632,7 @@ def parse_system(n_calc):
                 sec_system.x_vasp_nose_thermostat = nose
 
             # Check for core-holes
+            ## note that this check should be added to `parse_core_hole` if other kinds of atom_parameters are set
             if self.parser.incar.get('ICORELEVEL', 0) == 2:
                 core_hole, core_hole_group, corehole_id = self.parse_core_hole()
                 self.archive.run[-1].method[-1].atom_parameters[corehole_id].core_hole = core_hole