Modified CifParser.check() as one possible solution for issue materialsproject#3626 (materialsproject#3628)

* Modified check method of CifParser as one possible way to fix issue 3626.

* Reincluded all CifParser check() checks but for relative stoichiometry in case of missing formula keys.

* Added CifParser test for skipping relative stoichiometry check in case of missing formula keys and for appending a warning to self.warnings in this case.

* Refactor CifParser.check

* tighter warning test

---------

Co-authored-by: Janosh Riebesell <[email protected]>

Author: kaueltzen

pymatgen/io/cif.py

@@ -1313,13 +1313,6 @@ def has_errors(self):
     def check(self, structure: Structure) -> str | None:
         """Check whether a structure constructed from CIF passes sanity checks.
 
-        Args:
-            structure (Structure) : structure created from CIF
-
-        Returns:
-            str | None: If any check fails, on output, returns a human-readable str for the
-                reason why (e.g., which elements are missing). Returns None if all checks pass.
-
         Checks:
             - Composition from CIF is valid
             - CIF composition contains only valid elements
@@ -1329,19 +1322,30 @@ def check(self, structure: Structure) -> str | None:
             -  CIF and structure have same relative stoichiometry. Thus
                 if CIF reports stoichiometry LiFeO, and the structure has
                 composition (LiFeO)4, this check passes.
+
+        Args:
+            structure (Structure) : structure created from CIF
+
+        Returns:
+            str | None: If any check fails, on output, returns a human-readable str for the
+                reason why (e.g., which elements are missing). Returns None if all checks pass.
         """
         failure_reason = None
 
         cif_as_dict = self.as_dict()
         head_key = next(iter(cif_as_dict))
 
         cif_formula = None
+        check_stoichiometry = True
         for key in ("_chemical_formula_sum", "_chemical_formula_structural"):
             if cif_as_dict[head_key].get(key):
                 cif_formula = cif_as_dict[head_key][key]
                 break
 
+        # In case of missing CIF formula keys, get non-stoichiometric formula from
+        # unique sites and skip relative stoichiometry check (added in gh-3628)
         if cif_formula is None and cif_as_dict[head_key].get("_atom_site_type_symbol"):
+            check_stoichiometry = False
             cif_formula = " ".join(cif_as_dict[head_key]["_atom_site_type_symbol"])
 
         try:
@@ -1370,17 +1374,20 @@ def check(self, structure: Structure) -> str | None:
             failure_reason = f"Missing elements {missing_str} {addendum}"
 
         elif not all(struct_comp[elt] - orig_comp[elt] == 0 for elt in orig_comp):
-            # Check that stoichiometry is same, i.e., same relative ratios of elements
-            ratios = {elt: struct_comp[elt] / orig_comp[elt] for elt in orig_comp_elts}
-
-            same_stoich = all(
-                abs(ratios[elt_a] - ratios[elt_b]) < self.comp_tol
-                for elt_a in orig_comp_elts
-                for elt_b in orig_comp_elts
-            )
+            if check_stoichiometry:
+                # Check that CIF/PMG stoichiometry has same relative ratios of elements
+                ratios = {elt: struct_comp[elt] / orig_comp[elt] for elt in orig_comp_elts}
+
+                same_stoich = all(
+                    abs(ratios[elt_a] - ratios[elt_b]) < self.comp_tol
+                    for elt_a in orig_comp_elts
+                    for elt_b in orig_comp_elts
+                )
 
-            if not same_stoich:
-                failure_reason = f"Incorrect stoichiometry:\n  CIF={orig_comp}\n  PMG={struct_comp}\n  {ratios=}"
+                if not same_stoich:
+                    failure_reason = f"Incorrect stoichiometry:\n  CIF={orig_comp}\n  PMG={struct_comp}\n  {ratios=}"
+            else:
+                self.warnings += ["Skipping relative stoichiometry check because CIF does not contain formula keys."]
 
         return failure_reason
 

tests/io/test_cif.py

@@ -193,6 +193,7 @@ def test_cif_parser(self):
 
         with open(f"{TEST_FILES_DIR}/FePO4.cif") as cif_file:
             cif_str = cif_file.read()
+
         parser = CifParser.from_str(cif_str)
         struct = parser.parse_structures(primitive=False)[0]
         assert struct.formula == "Fe4 P4 O16"
@@ -933,6 +934,14 @@ def test_invalid_cif_composition(self):
         failure_reason = cif.check(Structure.from_file(f"{TEST_FILES_DIR}/LiFePO4.cif"))
         assert failure_reason == "'X' is not a valid Element"
 
+    def test_skipping_relative_stoichiometry_check(self):
+        cif = CifParser(f"{TEST_FILES_DIR}/Li10GeP2S12.cif")
+        struct = cif.parse_structures()[0]
+        failure_reason = cif.check(struct)
+        assert failure_reason is None
+        assert len(cif.warnings) == 2
+        assert cif.warnings[-1] == "Skipping relative stoichiometry check because CIF does not contain formula keys."
+
     def test_cif_writer_site_properties(self):
         # check CifWriter(write_site_properties=True) adds Structure site properties to
         # CIF with _atom_site_ prefix