From 12f256bc74792a1cf052b2989e0c20a4c2d38346 Mon Sep 17 00:00:00 2001
From: Maxwell-Rosen <mrquell@gmail.com>
Date: Mon, 22 Jun 2026 16:17:14 -0700
Subject: [PATCH 1/2] Refactor mpack map creation to handle duplicate keys and
 ensure unique entries

---
 core/zero/util.c | 90 +++++++++++++++++++++++++++++-------------------
 1 file changed, 55 insertions(+), 35 deletions(-)

diff --git a/core/zero/util.c b/core/zero/util.c
index 2bcc40cf02..4b67f666c7 100644
--- a/core/zero/util.c
+++ b/core/zero/util.c
@@ -514,45 +514,65 @@ gkyl_msgpack_create_union(int numlist_union, int *nvals_union, const struct gkyl
   mpack_writer_t writer;
   mpack_writer_init_growable(&writer, &mdata->meta, &mdata->meta_sz);
 
-  mpack_build_map(&writer);  
+  // Flatten the union of lists so we can detect duplicate keys. MessagePack
+  // maps must have unique keys; a map with duplicates is rejected by the
+  // reader (mpack_error_data), which would silently corrupt every lookup.
+  int nvals_tot = 0;
+  for (int j=0; j<numlist_union; ++j)
+    nvals_tot += nvals_union[j];
 
-  for (int j=0; j<numlist_union; ++j) {
+  const struct gkyl_msgpack_map_elem *flat[nvals_tot];
+  int fidx = 0;
+  for (int j=0; j<numlist_union; ++j)
+    for (int i=0; i<nvals_union[j]; ++i)
+      flat[fidx++] = &elist_union[j][i];
+
+  mpack_build_map(&writer);
+
+  for (int k=0; k<nvals_tot; ++k) {
+    // Keep only the last occurrence of each key (later lists override earlier
+    // ones), so the emitted map never contains duplicate keys.
+    bool overridden = false;
+    for (int m=k+1; m<nvals_tot; ++m) {
+      if (strcmp(flat[k]->key, flat[m]->key) == 0) {
+        overridden = true;
+        break;
+      }
+    }
+    if (overridden)
+      continue;
 
-    int nvals = nvals_union[j];
-    const struct gkyl_msgpack_map_elem *elist = elist_union[j];
+    const struct gkyl_msgpack_map_elem *elem = flat[k];
+    mpack_write_cstr(&writer, elem->key);
 
-    for (int i=0; i<nvals; ++i) {
-      mpack_write_cstr(&writer, elist[i].key);
-  
-      switch (elist[i].elem_type) {
-        case GKYL_MP_BOOL:
-          mpack_write_bool(&writer, elist[i].bval);
-          break;
-  
-        case GKYL_MP_UNSIGNED_INT:
-          mpack_write_u64(&writer, elist[i].uval);
-          break;
-  
-        case GKYL_MP_INT:
-          mpack_write_i64(&writer, elist[i].ival);
-          break;
-  
-        case GKYL_MP_FLOAT:
-          mpack_write_float(&writer, elist[i].fval);
-          break;
-  
-        case GKYL_MP_DOUBLE:
-          mpack_write_double(&writer, elist[i].dval);
-          break;
-  
-        case GKYL_MP_STRING:
-          mpack_write_cstr(&writer, elist[i].cval);
-          break;
+    switch (elem->elem_type) {
+      case GKYL_MP_BOOL:
+        mpack_write_bool(&writer, elem->bval);
+        break;
 
-        default:
-          assert(false); // NYI.
-          break;
-      }
+      case GKYL_MP_UNSIGNED_INT:
+        mpack_write_u64(&writer, elem->uval);
+        break;
+
+      case GKYL_MP_INT:
+        mpack_write_i64(&writer, elem->ival);
+        break;
+
+      case GKYL_MP_FLOAT:
+        mpack_write_float(&writer, elem->fval);
+        break;
+
+      case GKYL_MP_DOUBLE:
+        mpack_write_double(&writer, elem->dval);
+        break;
+
+      case GKYL_MP_STRING:
+        mpack_write_cstr(&writer, elem->cval);
+        break;
+
+      default:
+        assert(false); // NYI.
+        break;
     }
   }
 

From 235c1c88d870a87ca66976b3e4944d889e8e1154 Mon Sep 17 00:00:00 2001
From: Maxwell-Rosen <mrquell@gmail.com>
Date: Mon, 22 Jun 2026 16:22:35 -0700
Subject: [PATCH 2/2] Update jacobtot_inv_file_name in initialization from file
 for consistency

---
 core/zero/util.c                           | 5 -----
 gyrokinetic/creg/rt_gk_wham_1xIC_2x2v_p1.c | 4 ++--
 2 files changed, 2 insertions(+), 7 deletions(-)

diff --git a/core/zero/util.c b/core/zero/util.c
index 4b67f666c7..07806aed6a 100644
--- a/core/zero/util.c
+++ b/core/zero/util.c
@@ -514,9 +514,6 @@ gkyl_msgpack_create_union(int numlist_union, int *nvals_union, const struct gkyl
   mpack_writer_t writer;
   mpack_writer_init_growable(&writer, &mdata->meta, &mdata->meta_sz);
 
-  // Flatten the union of lists so we can detect duplicate keys. MessagePack
-  // maps must have unique keys; a map with duplicates is rejected by the
-  // reader (mpack_error_data), which would silently corrupt every lookup.
   int nvals_tot = 0;
   for (int j=0; j<numlist_union; ++j)
     nvals_tot += nvals_union[j];
@@ -530,8 +527,6 @@ gkyl_msgpack_create_union(int numlist_union, int *nvals_union, const struct gkyl
   mpack_build_map(&writer);
 
   for (int k=0; k<nvals_tot; ++k) {
-    // Keep only the last occurrence of each key (later lists override earlier
-    // ones), so the emitted map never contains duplicate keys.
     bool overridden = false;
     for (int m=k+1; m<nvals_tot; ++m) {
       if (strcmp(flat[k]->key, flat[m]->key) == 0) {
diff --git a/gyrokinetic/creg/rt_gk_wham_1xIC_2x2v_p1.c b/gyrokinetic/creg/rt_gk_wham_1xIC_2x2v_p1.c
index 253cc7887f..43ca8cf397 100644
--- a/gyrokinetic/creg/rt_gk_wham_1xIC_2x2v_p1.c
+++ b/gyrokinetic/creg/rt_gk_wham_1xIC_2x2v_p1.c
@@ -819,7 +819,7 @@ int main(int argc, char **argv)
       .init_from_file = {
         .type = GKYL_IC_IMPORT_F,
         .file_name = "gk_wham_1x2v_p1-elc_0.gkyl",
-        // .jacobtot_inv_file_name = "gk_wham_1x2v_p1-jacobtot_inv.gkyl",
+        .jacobtot_inv_file_name = "gk_wham_1x2v_p1-geo_int_jacobtot_inv.gkyl",
       },
 
       .mapc2p = {
@@ -887,7 +887,7 @@ int main(int argc, char **argv)
       .init_from_file = {
         .type = GKYL_IC_IMPORT_F,
         .file_name = "gk_wham_1x2v_p1-ion_0.gkyl",
-        .jacobtot_inv_file_name = "gk_wham_1x2v_p1-jacobtot_inv.gkyl",
+        .jacobtot_inv_file_name = "gk_wham_1x2v_p1-geo_int_jacobtot_inv.gkyl",
       },
 
       .scale_with_polarization = true,