From faa1dbc19d91a79e00dd29b9a6e3409fd56e912c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 14 Jun 2025 11:48:11 -0400
Subject: [PATCH] add missing type check and setting of ntypes for json data
 molecules

---
 src/molecule.cpp | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/molecule.cpp b/src/molecule.cpp
index fdfbe8fce8..c59dca424d 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -483,11 +483,18 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
       count[iatom]++;
     }
     // checks
+    ntypes = 0;
     for (int i = 0; i < natoms; i++) {
       if (count[i] == 0) {
         error->all(FLERR, Error::NOLASTLINE,
                    "Molecule template {}: atom {} missing in \"types\" JSON section", id, i + 1);
       }
+      for (int i = 0; i < natoms; i++) {
+        if ((type[i] <= 0) || (domain->box_exist && (type[i] > atom->ntypes)))
+          error->all(FLERR, fileiarg, "Invalid atom type {} for atom {} in molecule file", type[i],
+                     i + 1);
+        ntypes = MAX(ntypes, type[i]);
+      }
     }
   } else {
     error->all(FLERR, Error::NOLASTLINE,