feat: enable rendering of walls defined in LAMMPS

cpp/lammpsweb/lammpsweb.cpp

@@ -24,6 +24,7 @@
 #include "error.h"
 #include "neigh_list.h"
 #include "fix_atomify.h"
+#include "fix_wall.h"
 
 using namespace std;
 
@@ -674,3 +675,73 @@ void LAMMPSWeb::step() {
 void LAMMPSWeb::runCommand(std::string command) {
   lammps_commands_string((void *)m_lmp, command.c_str());
 }
+
+int LAMMPSWeb::getDimension() {
+  if (!m_lmp) {
+    return 3; // default to 3D
+  }
+  return m_lmp->domain->dimension;
+}
+
+std::vector<WallInfo> LAMMPSWeb::getWalls() {
+  std::vector<WallInfo> walls;
+
+  if (!m_lmp) {
+    return walls;
+  }
+
+  LAMMPS_NS::Domain *domain = m_lmp->domain;
+  domain->box_corners();
+
+  // Loop through all fixes to find FixWall instances
+  for (int i = 0; i < m_lmp->modify->nfix; i++) {
+    LAMMPS_NS::Fix *lmpFix = m_lmp->modify->fix[i];
+    LAMMPS_NS::FixWall *fixWall = dynamic_cast<LAMMPS_NS::FixWall*>(lmpFix);
+
+    if (!fixWall) {
+      continue;
+    }
+
+    // Extract wall data from this FixWall instance
+    for (int m = 0; m < fixWall->nwall; m++) {
+      int which = fixWall->wallwhich[m];
+      int style = fixWall->xstyle[m];
+
+      // Skip NONE and VARIABLE styles
+      // NONE=0, EDGE=1, CONSTANT=2, VARIABLE=3
+      if (style == 0 || style == 3) { // NONE or VARIABLE
+        continue;
+      }
+
+      double position;
+      if (style == 1) { // EDGE style
+        int dim = which / 2;
+        int side = which % 2;
+        if (side == 0) {
+          position = domain->boxlo[dim];
+        } else {
+          position = domain->boxhi[dim];
+        }
+      } else if (style == 2) { // CONSTANT style
+        position = fixWall->coord0[m];
+      } else {
+        // Unknown style, skip
+        continue;
+      }
+
+      // Get cutoff (it's protected, so we'll use 0 as default)
+      // For visualization, the exact cutoff isn't critical
+      double wallCutoff = 0.0;
+
+      WallInfo wall;
+      wall.which = which;
+      wall.style = style;
+      wall.position = position;
+      wall.cutoff = wallCutoff;
+
+      walls.push_back(wall);
+    }
+  }
+
+  return walls;
+}

cpp/lammpsweb/lammpsweb.h

@@ -7,9 +7,11 @@
 #include "atomify_compute.h"
 #include "atomify_fix.h"
 #include "atomify_variable.h"
+#include "fix_wall.h"
 #include <iostream>
 #include <string>
 #include <map>
+#include <vector>
 
 #ifdef __EMSCRIPTEN__
   #include <emscripten.h>
@@ -18,6 +20,13 @@
   using namespace emscripten;
 #endif
 
+struct WallInfo {
+  int which;       // 0-5 (XLO, XHI, YLO, YHI, ZLO, ZHI)
+  int style;       // 0-3 (NONE, EDGE, CONSTANT, VARIABLE)
+  double position; // current wall position
+  double cutoff;   // interaction range
+};
+
 class LAMMPSWeb
 {
 private:
@@ -90,6 +99,9 @@ class LAMMPSWeb
   void syncFixes();
   void syncVariables();
 
+  int getDimension();
+  std::vector<WallInfo> getWalls();
+
   LAMMPS_NS::Fix* findFixByIdentifier(std::string identifier);
   LAMMPS_NS::Compute* findComputeByIdentifier(std::string identifier);
   int findFixIndex(std::string identifier);
@@ -145,7 +157,15 @@ EMSCRIPTEN_BINDINGS(LAMMPSWeb)
     .function("runCommand", &LAMMPSWeb::runCommand)
 
     .function("computeBonds", &LAMMPSWeb::computeBonds)
-    .function("computeParticles", &LAMMPSWeb::computeParticles);
+    .function("computeParticles", &LAMMPSWeb::computeParticles)
+    .function("getDimension", &LAMMPSWeb::getDimension)
+    .function("getWalls", &LAMMPSWeb::getWalls);
+  class_<WallInfo>("WallInfo")
+    .constructor<>()
+    .property("which", &WallInfo::which)
+    .property("style", &WallInfo::style)
+    .property("position", &WallInfo::position)
+    .property("cutoff", &WallInfo::cutoff);
   class_<Modify>("Modify")
     .function("getName", &Modify::getName)
     .function("getClearPerSync", &Modify::getClearPerSync)
@@ -179,6 +199,7 @@ EMSCRIPTEN_BINDINGS(LAMMPSWeb)
   register_vector<Fix>("vector<Fix>");
   register_vector<Compute>("vector<Compute>");
   register_vector<float>("vector<float>");
+  register_vector<WallInfo>("vector<WallInfo>");
 }
 #endif
 #endif

public/examples/examples.json

@@ -1370,6 +1370,44 @@
                     "url": "reaxff/ZnOH2/param.qeq"
                 }
             ]
+        },
+        {
+            "id": "2d-lj-walls",
+            "title": "2D LJ particles with walls",
+            "description": "Lennard-Jones particles confined by LJ93 potential walls in 2D. Demonstrates wall rendering as thick slabs visible from the side view.",
+            "imageUrl": "walls/2d-lj-walls/2d-lj-walls.png",
+            "inputScript": "2d-lj-walls.in",
+            "keywords": [
+                "lennard jones",
+                "wall",
+                "lj93",
+                "2d"
+            ],
+            "files": [
+                {
+                    "fileName": "2d-lj-walls.in",
+                    "url": "walls/2d-lj-walls/2d-lj-walls.in"
+                }
+            ]
+        },
+        {
+            "id": "3d-lj-walls",
+            "title": "3D LJ particles with walls",
+            "description": "Lennard-Jones particles confined by LJ93 potential walls in 3D. Demonstrates transparent wall rendering in 3D mode.",
+            "imageUrl": "walls/3d-lj-walls/3d-lj-walls.png",
+            "inputScript": "3d-lj-walls.in",
+            "keywords": [
+                "lennard jones",
+                "wall",
+                "lj93",
+                "3d"
+            ],
+            "files": [
+                {
+                    "fileName": "3d-lj-walls.in",
+                    "url": "walls/3d-lj-walls/3d-lj-walls.in"
+                }
+            ]
         }
     ]
 }

public/examples/walls/2d-lj-walls/2d-lj-walls.in

@@ -0,0 +1,46 @@
+#/camera position 3.0 1.5 60.1
+#/camera target 4.1 -0.7 -2.6
+#/atom 1 1.0 #a1a1a1
+#/atom 2 3.0 #6EBFC0
+
+# This LAMMPS input script simulates LJ particles with reflecting walls in 2D
+# Demonstrates wall rendering in 2D mode
+
+# main parameters
+units lj
+dimension 2
+atom_style atomic
+pair_style lj/cut 2.5
+boundary f f p  # Fixed X and Y (for walls), periodic Z (required for 2D)
+
+# create system and insert atoms
+region myreg block -30 30 -30 30 -0.5 0.5
+create_box 2 myreg
+create_atoms 1 random 1500 341341 myreg
+create_atoms 2 random 100 127569 myreg
+
+# atom settings
+mass 1 1
+mass 2 1
+pair_coeff 1 1 1.0 1.0
+pair_coeff 2 2 0.5 3.0
+neigh_modify every 1 delay 5 check yes
+
+# Add walls before minimization to prevent atoms from escaping
+fix mywalls all wall/lj93 xlo EDGE 1.0 1.0 2.5 xhi EDGE 1.0 1.0 2.5 ylo EDGE 1.0 1.0 2.5 yhi EDGE 1.0 1.0 2.5
+
+# minimisation
+minimize 1.0e-4 1.0e-6 1000 10000
+
+# dynamics
+fix mynve all nve
+fix mylgv all langevin 1.0 1.0 0.1 1530917
+fix myefn all enforce2d
+timestep 0.005
+
+# outputs
+thermo 10
+thermo_style one
+
+# run
+run 1000

public/examples/walls/3d-lj-walls/3d-lj-walls.in

@@ -0,0 +1,41 @@
+#/atom 1 2.0 #a1a1a1
+
+#/camera position -20 20 20
+#/camera target 0 0 0
+
+# This LAMMPS input script demonstrates wall collisions with 5 non-interacting particles
+# Particles bounce off LJ93 potential walls in 3D
+
+# main parameters
+units lj
+dimension 3
+atom_style atomic
+pair_style none  # No pair interactions - particles only interact with walls
+boundary f f f  # Fixed boundaries (non-periodic) for walls
+
+# create system and insert atoms
+# Smaller box for easier visualization
+region myreg block -10 10 -10 10 -10 10
+create_box 1 myreg
+region atomreg block -8 8 -8 8 -8 8  # Leave gap for wall cutoff
+create_atoms 1 random 5 341341 atomreg
+
+# atom settings
+mass 1 1
+
+# Add walls before setting velocities
+fix mywalls all wall/lj93 xlo EDGE 1.0 1.0 2.5 xhi EDGE 1.0 1.0 2.5 ylo EDGE 1.0 1.0 2.5 yhi EDGE 1.0 1.0 2.5 zlo EDGE 1.0 1.0 2.5 zhi EDGE 1.0 1.0 2.5
+
+# Set random initial velocities so particles bounce off walls
+velocity all create 2.0 341341 rot yes dist gaussian
+
+# dynamics
+fix mynve all nve
+timestep 0.005
+
+# outputs
+thermo 100
+thermo_style one
+
+# run
+run 10000

src/containers/Settings.tsx

@@ -124,6 +124,21 @@ const Settings = ({ open, onClose }: SettingsProps) => {
           Show simulation box
         </Checkbox>
 
+        <div style={{ marginTop: "8px" }}>
+          <Checkbox
+            checked={renderSettings.showWalls}
+            onChange={(e) =>
+              handleSettingChange(
+                "showWalls",
+                e.target.checked,
+                "Settings.Render.ShowWalls",
+              )
+            }
+          >
+            Show walls
+          </Checkbox>
+        </div>
+
         <div style={{ marginTop: "8px" }}>
           <Checkbox
             checked={renderSettings.orthographic}