diff --git a/index.html b/index.html
index bf6efd99..f2a7762d 100644
--- a/index.html
+++ b/index.html
@@ -21,7 +21,7 @@
-
+
diff --git a/public/examples/diffusion/large_diffusion/large_diffusion.in b/public/examples/diffusion/large_diffusion/large_diffusion.in
new file mode 100644
index 00000000..487ce5fd
--- /dev/null
+++ b/public/examples/diffusion/large_diffusion/large_diffusion.in
@@ -0,0 +1,65 @@
+# Large system: run with KOKKOS multithreading (Atomify detects this line)
+suffix kk
+
+# Atomify commands start with #/
+
+# Move camera to a nice position
+#/camera position 50.0 72.7 221.7
+#/camera target 45.7 51.3 35.0
+
+# Set atom size and color
+#/atom 1 1.0 #ffffff
+#/atom 2 1.5 #ff0000
+
+variable L equal 50.0
+variable Lhalf equal $(0.5*v_L)
+variable thickness equal 2.0
+
+units lj
+atom_style atomic
+lattice fcc 0.5
+
+# Create regions to place atoms
+variable left equal 0.5*$L-0.5*${thickness}
+variable right equal 0.5*$L+0.5*${thickness}
+region system block 0 $L 0 $L 0 ${Lhalf}
+region boxinside block ${left} ${right} 0 $L 0 ${Lhalf}
+region boxoutside block ${left} ${right} 0 $L 0 ${Lhalf} side out
+
+# Create a box with 2 atom types in the region system
+create_box 2 system
+# Create atoms of type 1 inside the inner region
+create_atoms 1 region boxinside
+# Create atoms of type 2 inside the outer region
+create_atoms 2 region boxoutside
+
+# Set atom masses
+mass 1 1.0
+mass 2 4.0
+
+# Give initial velocity, T=3.00, seed = 1337
+velocity all create 3.00 1337 loop geom
+
+# Choose LJ with 2.5sigma cutoff
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+neigh_modify every 1 delay 0 check yes
+
+# Create two groups for computing diffusion coefficients
+group light type 1
+group heavy type 2
+
+# Measure mean square displacement and diffusion coefficient
+compute msd_light light msd com yes
+variable diffusion_coeff_light equal c_msd_light[4]/6/(step*dt+1.0e-6)
+variable msd_light equal c_msd_light[4]
+
+compute msd_heavy heavy msd com yes
+variable msd_heavy equal c_msd_heavy[4]
+variable diffusion_coeff_heavy equal c_msd_heavy[4]/6/(step*dt+1.0e-6)
+
+thermo 100
+thermo_style custom step v_diffusion_coeff_light v_msd_light v_diffusion_coeff_heavy v_msd_heavy
+fix 1 all nve
+compute displace all displace/atom
+run 10000
\ No newline at end of file
diff --git a/public/examples/diffusion/large_diffusion/large_diffusion.png b/public/examples/diffusion/large_diffusion/large_diffusion.png
new file mode 100644
index 00000000..87cfa359
Binary files /dev/null and b/public/examples/diffusion/large_diffusion/large_diffusion.png differ
diff --git a/public/examples/examples.json b/public/examples/examples.json
index b1b41cc6..33ec712f 100644
--- a/public/examples/examples.json
+++ b/public/examples/examples.json
@@ -21,6 +21,26 @@
}
]
},
+ {
+ "id": "large_diffusion",
+ "title": "Large diffusion",
+ "description": "A large version of the diffusion example (~250,000 atoms) that runs multithreaded with KOKKOS. The white atoms have mass 1 while the red atoms have mass 4.",
+ "analysisDescription": "# About this simulation\nWe simulate two Lennard Jones particle types with masses 1.0 and 4.0. The diffusion coefficient [https://en.wikipedia.org/wiki/Mass_diffusivity](scales like) D$\\propto 1/\\sqrt{m}$, so we should see a factor 2 higher diffusion coefficient for the small molecules.",
+ "imageUrl": "diffusion/large_diffusion/large_diffusion.png",
+ "inputScript": "large_diffusion.in",
+ "keywords": [
+ "lennard jones",
+ "diffusion",
+ "kokkos",
+ "large"
+ ],
+ "files": [
+ {
+ "fileName": "large_diffusion.in",
+ "url": "diffusion/large_diffusion/large_diffusion.in"
+ }
+ ]
+ },
{
"id": "2d-msd-diffusion",
"title": "2D diffusion coefficient MSD",
@@ -40,34 +60,34 @@
"url": "diffusion/2d-msd-diffusion/2d-msd-diffusion.in"
},
{
- "fileName": "2d-msd-diffusion.ipynb",
- "url": "diffusion/2d-msd-diffusion/2d-msd-diffusion.ipynb"
- }
+ "fileName": "2d-msd-diffusion.ipynb",
+ "url": "diffusion/2d-msd-diffusion/2d-msd-diffusion.ipynb"
+ }
]
},
{
- "id": "2d-vacf-diffusion",
- "title": "2D diffusion coefficient VACF",
- "description": "We measure the diffusion coefficient using the velocity auto correlation function.",
- "analysisDescription": "# About this simulation\nWe measure the diffusion coefficient using the velocity auto correlation function.",
- "analysisScript": "2d-vacf-diffusion.ipynb",
- "imageUrl": "diffusion/2d-vacf-diffusion/2d-vacf-diffusion.png",
- "inputScript": "2d-vacf-diffusion.in",
- "keywords": [
- "lennard jones",
- "diffusion",
- "velocity autocorrelation function"
- ],
- "files": [
- {
- "fileName": "2d-vacf-diffusion.in",
- "url": "diffusion/2d-vacf-diffusion/2d-vacf-diffusion.in"
- },
- {
- "fileName": "2d-vacf-diffusion.ipynb",
- "url": "diffusion/2d-vacf-diffusion/2d-vacf-diffusion.ipynb"
- }
- ]
+ "id": "2d-vacf-diffusion",
+ "title": "2D diffusion coefficient VACF",
+ "description": "We measure the diffusion coefficient using the velocity auto correlation function.",
+ "analysisDescription": "# About this simulation\nWe measure the diffusion coefficient using the velocity auto correlation function.",
+ "analysisScript": "2d-vacf-diffusion.ipynb",
+ "imageUrl": "diffusion/2d-vacf-diffusion/2d-vacf-diffusion.png",
+ "inputScript": "2d-vacf-diffusion.in",
+ "keywords": [
+ "lennard jones",
+ "diffusion",
+ "velocity autocorrelation function"
+ ],
+ "files": [
+ {
+ "fileName": "2d-vacf-diffusion.in",
+ "url": "diffusion/2d-vacf-diffusion/2d-vacf-diffusion.in"
+ },
+ {
+ "fileName": "2d-vacf-diffusion.ipynb",
+ "url": "diffusion/2d-vacf-diffusion/2d-vacf-diffusion.ipynb"
+ }
+ ]
},
{
"id": "proteinfolding",
@@ -1410,4 +1430,4 @@
]
}
]
-}
\ No newline at end of file
+}
diff --git a/vite.config.ts b/vite.config.ts
index e1007365..c0791add 100644
--- a/vite.config.ts
+++ b/vite.config.ts
@@ -1,11 +1,45 @@
-import { defineConfig } from "vite";
+import { createRequire } from "node:module";
+import { createReadStream, statSync } from "node:fs";
+import { defineConfig, type Plugin } from "vite";
import react from "@vitejs/plugin-react";
import basicSsl from "@vitejs/plugin-basic-ssl";
+/**
+ * Dev-only: serve the ~43 MB lammps-atomify.js emscripten module RAW.
+ * The worker loads it via `?url` + fetch-as-blob (see lammps.worker.ts) —
+ * it is never bundled — but Vite's dev transform would otherwise rewrite it
+ * and append an inline sourcemap, inflating the download to ~460 MB (which
+ * can crash the tab). This middleware runs before Vite's transform and
+ * streams the file as-is. `?url`/`?import` requests (the tiny URL-shim
+ * module) still go through Vite untouched.
+ */
+function serveLammpsModuleRaw(): Plugin {
+ return {
+ name: "serve-lammps-atomify-raw",
+ apply: "serve",
+ configureServer(server) {
+ const require = createRequire(import.meta.url);
+ // Resolve via the package's exports map (the raw dist path is not an
+ // exported subpath).
+ const filePath = require.resolve("lammps.js/wasm-atomify");
+ server.middlewares.use((req, res, next) => {
+ const url = req.url ?? "";
+ if (!url.includes("lammps-atomify.js") || url.includes("?")) {
+ return next();
+ }
+ res.setHeader("Content-Type", "text/javascript");
+ res.setHeader("Content-Length", statSync(filePath).size);
+ createReadStream(filePath).pipe(res);
+ });
+ },
+ };
+}
+
// https://vitejs.dev/config/
export default defineConfig({
plugins: [
react(),
+ serveLammpsModuleRaw(),
// Only enable HTTPS if HTTPS environment variable is set
...(process.env.HTTPS === "true" ? [basicSsl()] : []),
],