From 1eb49f3248790086c61220c86ee8b17820927445 Mon Sep 17 00:00:00 2001
From: Cursor Agent <cursoragent@cursor.com>
Date: Sun, 30 Nov 2025 08:39:23 +0000
Subject: [PATCH 1/2] Refactor: Use 'tag' instead of 'id' for atom extraction

Co-authored-by: andershaf <andershaf@gmail.com>
---
 cpp/lammpsweb/lammpsweb.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cpp/lammpsweb/lammpsweb.cpp b/cpp/lammpsweb/lammpsweb.cpp
index 921c8f5d..44582d86 100644
--- a/cpp/lammpsweb/lammpsweb.cpp
+++ b/cpp/lammpsweb/lammpsweb.cpp
@@ -575,7 +575,7 @@ long LAMMPSWeb::getPositionsPointer() {
 }
 
 long LAMMPSWeb::getIdPointer() {
-  auto ptr = lammps_extract_atom((void *)m_lmp, "id");
+  auto ptr = lammps_extract_atom((void *)m_lmp, "tag");
 
   return reinterpret_cast<long>(ptr);
 }

From 9ecd09e1f794ce67de3490de4b59332fc6655e03 Mon Sep 17 00:00:00 2001
From: Cursor Agent <cursoragent@cursor.com>
Date: Sun, 30 Nov 2025 08:43:57 +0000
Subject: [PATCH 2/2] feat: Add getTagPointer and use tag for particle IDs

Co-authored-by: andershaf <andershaf@gmail.com>
---
 cpp/lammpsweb/lammpsweb.cpp            | 11 +++++++++++
 cpp/lammpsweb/lammpsweb.h              |  2 ++
 src/modifiers/syncparticlesmodifier.ts | 11 ++++++++---
 src/types.ts                           |  1 +
 4 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/cpp/lammpsweb/lammpsweb.cpp b/cpp/lammpsweb/lammpsweb.cpp
index 44582d86..9ce4baf9 100644
--- a/cpp/lammpsweb/lammpsweb.cpp
+++ b/cpp/lammpsweb/lammpsweb.cpp
@@ -575,7 +575,18 @@ long LAMMPSWeb::getPositionsPointer() {
 }
 
 long LAMMPSWeb::getIdPointer() {
+  auto ptr = lammps_extract_atom((void *)m_lmp, "id");
+
+  return reinterpret_cast<long>(ptr);
+}
+
+long LAMMPSWeb::getTagPointer() {
   auto ptr = lammps_extract_atom((void *)m_lmp, "tag");
+  
+  // Tag may not exist for all atom styles, return 0 if not available
+  if (!ptr) {
+    return 0;
+  }
 
   return reinterpret_cast<long>(ptr);
 }
diff --git a/cpp/lammpsweb/lammpsweb.h b/cpp/lammpsweb/lammpsweb.h
index 86239f15..004b3627 100644
--- a/cpp/lammpsweb/lammpsweb.h
+++ b/cpp/lammpsweb/lammpsweb.h
@@ -65,6 +65,7 @@ class LAMMPSWeb
   long getBondsDistanceMapPointer();
   long getPositionsPointer();
   long getIdPointer();
+  long getTagPointer();
   long getTypePointer();
   long getBondsPosition1Pointer();
   long getBondsPosition2Pointer();
@@ -129,6 +130,7 @@ EMSCRIPTEN_BINDINGS(LAMMPSWeb)
     .function("getPositionsPointer", &LAMMPSWeb::getPositionsPointer)
     .function("getBondsDistanceMapPointer", &LAMMPSWeb::getBondsDistanceMapPointer)
     .function("getIdPointer", &LAMMPSWeb::getIdPointer)
+    .function("getTagPointer", &LAMMPSWeb::getTagPointer)
     .function("getTypePointer", &LAMMPSWeb::getTypePointer)
     .function("getCellMatrixPointer", &LAMMPSWeb::getCellMatrixPointer)
     .function("getOrigoPointer", &LAMMPSWeb::getOrigoPointer)
diff --git a/src/modifiers/syncparticlesmodifier.ts b/src/modifiers/syncparticlesmodifier.ts
index 7a4ad840..4ad5a069 100644
--- a/src/modifiers/syncparticlesmodifier.ts
+++ b/src/modifiers/syncparticlesmodifier.ts
@@ -48,7 +48,12 @@ class SyncParticlesModifier extends Modifier {
 
     const positionsPtr = input.lammps.getPositionsPointer() / 4;
     const typePtr = input.lammps.getTypePointer() / 4;
-    const idPtr = input.lammps.getIdPointer() / 4;
+
+    // Try to use tag first (persistent particle identifier), fallback to id if not available
+    const tagPtr = input.lammps.getTagPointer();
+    const particleIdPtr =
+      tagPtr !== 0 ? tagPtr / 4 : input.lammps.getIdPointer() / 4;
+
     const positionsSubarray = input.wasm.HEAPF32.subarray(
       positionsPtr,
       positionsPtr + 3 * numParticles,
@@ -58,8 +63,8 @@ class SyncParticlesModifier extends Modifier {
       typePtr + numParticles,
     ) as Int32Array;
     const idSubarray = input.wasm.HEAP32.subarray(
-      idPtr,
-      idPtr + numParticles,
+      particleIdPtr,
+      particleIdPtr + numParticles,
     ) as Int32Array;
 
     newParticles.positions.set(positionsSubarray);
diff --git a/src/types.ts b/src/types.ts
index a942c77d..873a300e 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -24,6 +24,7 @@ export type LammpsWeb = {
 
   getPositionsPointer: () => number;
   getIdPointer: () => number;
+  getTagPointer: () => number;
   getTypePointer: () => number;
   getCellMatrixPointer: () => number;
   getOrigoPointer: () => number;