Resolve "Adding reduce and descriptive formula to the GUI search"

Closes #1255 (closed)

Adds also a fix in the formula normalizer of the Perovskite Database to return the proper chemical_formula_reduced

nomad/datamodel/metainfo/eln/perovskite_solar_cell_database/__init__.py

@@ -1560,7 +1560,7 @@ Ozone
     def normalize(self, archive, logger):
         from .formula_normalizer import PerovskiteFormulaNormalizer
-        from ase.formula import Formula
+        from ase import Atoms
         addSolarCell(archive)
@@ -1603,14 +1603,15 @@ Ozone
             if archive.results.material.functional_type is None:
                 archive.results.material.functional_type = ['semiconductor', 'solar cell']
-            if archive.results.material.chemical_formula_reduced is None:
+            if self.composition_long_form:
                 formula_cleaner = PerovskiteFormulaNormalizer(self.composition_long_form)
                 final_formula = formula_cleaner.clean_formula()
-                archive.results.material.chemical_formula_reduced = final_formula[0]
-                chemical_formula_reduced = archive.results.material.chemical_formula_reduced
+                chemical_formula_reduced = final_formula[0]
                 archive.results.material.elements = final_formula[1]
                 try:
-                    archive.results.material.chemical_formula_hill = Formula(chemical_formula_reduced).format('hill')
+                    atoms = Atoms(chemical_formula_reduced)
+                    archive.results.material.chemical_formula_hill = atoms.get_chemical_formula(mode='hill')
+                    archive.results.material.chemical_formula_reduced = atoms.get_chemical_formula(mode='reduce')
                     archive.results.material.chemical_formula_descriptive = self.composition_long_form
                 except Exception as e:
                     logger.warn('could not analyse chemical formula', exc_info=e)

[Lauri Himanen]

Could you try here if our custom formula class (atomutils.Formula) does the job correctly? It is designed to write the formulas in a way where they are compatible with our metainfo definitions. I think it would be good if we used the same implementation everywhere where we need these formulas. So simply try:

try:
    formula = atomutils.Formula(chemical_formula_reduced)
    archive.results.material.chemical_formula_hill = formula.format('hill')
    archive.results.material.chemical_formula_reduced = formula.format('reduce')
    ...

[Jose Marquez Prieto]

I would say we do this merge as it is. Then, when we correct the Formula class from atomutils we also correct all the normalizers with formulas. Maybe we even need a Formula normalizer inside all the normalizers getting formulas in the system?

To document the current problem, three different ways to get the formulas in the "correct" formats:

from nomad.atomutils import Formula
from pymatgen.core import Composition
from ase import Atoms

formula = 'H12C2I6N2Pb2'

print('nomad atomutils')
print('Hill: ' + Formula(formula).format('hill'))
print('reduced: ' + Formula(formula).format('reduce'))

print('pymatgen')
composition = Composition(formula)
print('Hill: ' + composition.hill_formula)
print('reduced: ' + composition.reduced_formula)

print('ASE')
atoms = Atoms(formula)
print('Hill: ' + atoms.get_chemical_formula(mode='hill'))
print('reduced: ' + atoms.get_chemical_formula(mode='reduce'))

Returns

nomad atomutils
Hill: C2H12I6N2Pb2
reduced: C2H12I6N2Pb2
pymatgen
Hill: C2 H12 I6 N2 Pb2
reduced: H6PbCI3N
ASE
Hill: C2H12I6N2Pb2
reduced: H12C2I6N2Pb2