fix(lammps): reject mismatched explicit masses

Reject explicit system["masses"] arrays unless they match atom_names exactly to avoid silently truncating and mis-mapping LAMMPS Masses entries. Add a regression test covering the mismatched-length case.

Authored by OpenClaw (model: custom-chat-jinzhezeng-group/gpt-5.4)

Author: njzjz-bot

dpdata/lammps/lmp.py

@@ -502,11 +502,24 @@ def _get_lammps_masses(system) -> np.ndarray | None:
     np.ndarray or None
         Per-type masses aligned with ``atom_names``. Returns ``None`` when the
         masses cannot be determined safely.
+
+    Raises
+    ------
+    ValueError
+        If explicit ``system["masses"]`` is present but does not match the
+        length of ``atom_names``.
     """
     atom_names = system["atom_names"]
     masses = system.get("masses")
-    if masses is not None and len(masses) >= len(atom_names):
-        return np.asarray(masses[: len(atom_names)], dtype=float)
+    if masses is not None:
+        masses = np.asarray(masses, dtype=float)
+        if masses.ndim != 1 or len(masses) != len(atom_names):
+            raise ValueError(
+                'Explicit system["masses"] must be a 1D array with the same '
+                'length as system["atom_names"] to write the LAMMPS Masses '
+                "section."
+            )
+        return masses
 
     if not all(name in ELEMENTS for name in atom_names):
         return None

tests/test_lammps_lmp_dump.py

@@ -128,6 +128,15 @@ def test_dump_unknown_types_skips_masses(self):
 
         self.assertNotIn("Masses\n", content)
 
+    def test_dump_rejects_mismatched_explicit_masses(self):
+        system = dpdata.System(POSCAR_CONF_LMP, type_map=["O", "H"])
+        system.data["masses"] = np.array([15.9994, 1.00794, 99.0])
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            output = os.path.join(tmpdir, "tmp_bad_masses.lmp")
+            with self.assertRaisesRegex(ValueError, r'system\["masses"\]'):
+                system.to_lammps_lmp(output)
+
 
 if __name__ == "__main__":
     unittest.main()