Merge pull request #121 from benrich37/loose-infile-parsing

Ignorable infile errors

Author: benrich37

src/pymatgen/io/jdftx/inputs.py

@@ -180,6 +180,7 @@ def from_dict(cls, d: dict[str, Any], validate_value_boundaries=True) -> JDFTXIn
             instance.validate_boundaries()
         return instance
 
+    # TODO: This can be cleaned up by generalizing kwargs that are passed to from_str
     @classmethod
     def from_file(
         cls,
@@ -309,6 +310,7 @@ def from_str(
         sort_tags: bool = True,
         path_parent: Path | None = None,
         validate_value_boundaries: bool = True,
+        skip_invalid_tags: bool = False,
     ) -> JDFTXInfile:
         """Read a JDFTXInfile object from a string.
 
@@ -329,9 +331,17 @@ def from_str(
         params: dict[str, Any] = {}
         # process all tag value lines using specified tag formats in MASTER_TAG_LIST
         for line in lines:
-            tag_object, tag, value = cls._preprocess_line(line)
-            processed_value = tag_object.read(tag, value)
-            params = cls._store_value(params, tag_object, tag, processed_value)  # this will change with tag categories
+            try:
+                tag_object, tag, value = cls._preprocess_line(line)
+                processed_value = tag_object.read(tag, value)
+                params = cls._store_value(
+                    params, tag_object, tag, processed_value
+                )  # this will change with tag categories
+            except ValueError as e:
+                if skip_invalid_tags:
+                    warnings.warn(f"Skipping invalid tag line: '{line}'. Error: {e}", stacklevel=2)
+                    continue
+                raise
         pop_idcs = []
         if "include" in params:
             for i, filename in enumerate(params["include"]):

src/pymatgen/io/jdftx/jdftxoutfileslice.py

@@ -428,7 +428,7 @@ def _set_internal_infile(self, text: list[str]) -> None:
         if end_line_idx is None:
             raise ValueError("Calculation did not begin for this out file slice.")
         self.infile = JDFTXInfile.from_str(
-            "\n".join(text[start_line_idx:end_line_idx]), validate_value_boundaries=False
+            "\n".join(text[start_line_idx:end_line_idx]), validate_value_boundaries=False, skip_invalid_tags=True
         )
         self.constant_lattice = True
         if "lattice-minimize" in self.infile: