From b0694e4e7354e4975eebcdf8e176d08b86a4ef35 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 11 Jun 2025 18:09:40 -0400
Subject: [PATCH] add support for dipoles section

---
 src/molecule.cpp                | 59 +++++++++++++++++++++++++++++++--
 tools/json/molecule-schema.json | 23 +++++++++++++
 2 files changed, 79 insertions(+), 3 deletions(-)

diff --git a/src/molecule.cpp b/src/molecule.cpp
index 33f227a41c..f50eccc9d5 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -651,8 +651,61 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
           id, secfmt[0], secfmt[1]);
     }
   }
+
   // dipoles
 
+  if (muflag) {
+
+    for (int i = 0; i < 4; ++i) secfmt[i] = moldata["dipoles"]["format"][i];
+    if ((secfmt[0] == "atom-id") && (secfmt[1] == "mux") && (secfmt[2] == "muy") &&
+        (secfmt[3] == "muz")) {
+
+      memset(count, 0, natoms * sizeof(count));
+      for (const auto &c : moldata["dipoles"]["data"]) {
+        if (c.size() < 4)
+          error->all(
+              FLERR, Error::NOLASTLINE,
+              "Molecule template {}: missing data in \"dipoles\" section of molecule JSON data: {}",
+              id, to_string(c));
+        if (!c[0].is_number_integer())
+          error->all(
+              FLERR, Error::NOLASTLINE,
+              "Molecule template {}: invalid atom-id in \"dipoles\" section of molecule JSON "
+              "data: {}",
+              id, to_string(c[0]));
+
+        const int iatom = int(c[0]) - 1;
+        if ((iatom < 0) || (iatom >= natoms))
+          error->all(
+              FLERR, Error::NOLASTLINE,
+              "Molecule template {}: invalid atom-id {} in dipoles section of molecule JSON data",
+              id, iatom + 1);
+        count[iatom]++;
+        mu[iatom][0] = c[1];
+        mu[iatom][1] = c[2];
+        mu[iatom][2] = c[3];
+        mu[iatom][0] *= sizescale;
+        mu[iatom][1] *= sizescale;
+        mu[iatom][2] *= sizescale;
+      }
+
+      // checks
+      for (int i = 0; i < natoms; i++) {
+        if (count[i] == 0) {
+          error->all(FLERR, Error::NOLASTLINE,
+                     "Molecule template {}: atom {} missing in \"dipoles\" JSON section", id,
+                     i + 1);
+        }
+      }
+    } else {
+      error->all(
+          FLERR, Error::NOLASTLINE,
+          "Molecule template {}: Expected \"dipoles\" format [\"atom-id\",\"mux\",\"muy\",\"muz\"] "
+          "but found [\"{}\",\"{}\",\"{}\",\"{}\"]",
+          id, secfmt[0], secfmt[1], secfmt[2], secfmt[3]);
+    }
+  }
+
   // masses
 
   if (rmassflag) {
@@ -1590,9 +1643,9 @@ void Molecule::dipoles(char *line)
         error->all(FLERR, fileiarg, "Invalid atom index in Dipoles section of molecule file");
 
       count[iatom]++;
-      mu[iatom][0] = values.next_double();
-      mu[iatom][1] = values.next_double();
-      mu[iatom][2] = values.next_double();
+      mu[iatom][0] = values.next_double() * sizescale;
+      mu[iatom][1] = values.next_double() * sizescale;
+      mu[iatom][2] = values.next_double() * sizescale;
     }
   } catch (TokenizerException &e) {
     error->all(FLERR, fileiarg, "Invalid line in Dipoles section of molecule file: {}\n{}", e.what(), line);
diff --git a/tools/json/molecule-schema.json b/tools/json/molecule-schema.json
index bb2c95ce57..51616931e8 100644
--- a/tools/json/molecule-schema.json
+++ b/tools/json/molecule-schema.json
@@ -143,6 +143,29 @@
             },
             "required": ["format", "data"]
         },
+        "dipoles": {
+            "type": "object",
+            "properties": {
+                "format": {
+                    "type": "array",
+                    "const": ["atom-id", "mux", "muy", "muz"]
+                },
+                "data": {
+                    "type": "array",
+                    "items": {
+                        "type": "array",
+                        "prefixItems": [
+                            {"type": "integer"},
+                            {"type": "number"},
+                            {"type": "number"},
+                            {"type": "number"}
+                        ],
+                        "items": false
+                    }
+                }
+            },
+            "required": ["format", "data"]
+        },
         "diameters": {
             "type": "object",
             "properties": {