Embed atomify with base64 simulation data

EMBEDDING.md

@@ -0,0 +1,208 @@
+# Atomify Embedding
+
+Atomify now supports embedding simulations directly in web pages using base64-encoded simulation data. This allows you to share complete simulations (including all required files) through a single URL parameter.
+
+## How it Works
+
+The embedding system uses a protobuf-like schema to serialize simulation data into a compact base64 format that can be passed as a URL parameter. This includes:
+
+- Simulation metadata (id, title, description, keywords)
+- All simulation files (LAMMPS input scripts, data files, force field files, etc.)
+- Analysis descriptions and Jupyter notebooks
+
+## Usage
+
+### Basic Usage
+
+To embed a simulation, add the `embeddedSimulationData` parameter to the Atomify URL:
+
+```
+https://your-atomify-host.com/?embeddedSimulationData=<base64-encoded-simulation>
+```
+
+### Creating Embedded Simulations
+
+#### From Scratch
+
+```typescript
+import { createSimulationDataFromFiles, generateEmbeddedUrl } from './utils/embedding';
+
+const lammpsScript = `
+# Simple LJ particles simulation
+units lj
+atom_style atomic
+dimension 3
+boundary p p p
+
+region box block 0 10 0 10 0 10
+create_box 1 box
+create_atoms 1 random 100 12345 box
+
+mass 1 1.0
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+velocity all create 1.0 12345
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+thermo 100
+run 1000
+`;
+
+const simulationData = createSimulationDataFromFiles(
+  'simple-lj',
+  'Simple LJ Particles',
+  'A basic simulation of Lennard-Jones particles.',
+  'simple.in',
+  {
+    'simple.in': lammpsScript
+  },
+  {
+    keywords: ['lennard jones', 'basic'],
+    analysisDescription: '# Simple LJ Simulation\nThis is a basic example.'
+  }
+);
+
+const embeddedUrl = generateEmbeddedUrl('https://your-atomify-host.com', simulationData);
+```
+
+#### From Existing Atomify Simulation
+
+```typescript
+import { generateEmbeddedUrlFromAtomifySimulation } from './utils/embedding';
+
+const existingSimulation = {
+  id: "diffusion",
+  title: "Diffusion",
+  description: "Measure diffusion coefficient using MSD.",
+  inputScript: "simple_diffusion.in",
+  keywords: ["lennard jones", "diffusion"],
+  files: [
+    {
+      fileName: "simple_diffusion.in",
+      url: "examples/diffusion/diffusion/simple_diffusion.in"
+    }
+  ]
+};
+
+const embeddedUrl = await generateEmbeddedUrlFromAtomifySimulation(
+  'https://your-atomify-host.com', 
+  existingSimulation
+);
+```
+
+## Features
+
+- **Complete simulation packaging**: All files are embedded, no external dependencies
+- **Automatic loading**: Simulations start automatically when the embedded URL is accessed
+- **No network requests**: All simulation data is self-contained in the URL
+- **Compatible with existing features**: Analysis notebooks, multiple files, etc.
+
+## URL Parameters
+
+| Parameter | Description | Required |
+|-----------|-------------|----------|
+| `embeddedSimulationData` | Base64-encoded simulation data | Yes (for base64 embedding) |
+| `embeddedSimulationUrl` | URL to examples JSON (legacy) | No |
+| `simulationIndex` | Index in examples array (legacy) | No |
+
+## Schema
+
+The embedding uses the following schema structure:
+
+```typescript
+interface SimulationData {
+  id: string;
+  title: string;
+  description: string;
+  analysisDescription?: string;
+  analysisScript?: string;
+  inputScript: string;
+  keywords: string[];
+  files: { [key: string]: SimulationFile };
+}
+
+interface SimulationFile {
+  content?: 
+    | { $case: 'text'; text: string }
+    | { $case: 'data'; data: Uint8Array };
+}
+```
+
+## Backwards Compatibility
+
+The original embedding method using `embeddedSimulationUrl` and `simulationIndex` parameters is still supported for backwards compatibility.
+
+## Browser Console Utility
+
+When you have a simulation loaded in Atomify, you can generate an embedded URL directly from the browser console:
+
+```javascript
+// In the browser console while a simulation is loaded:
+const embeddedUrl = window.generateEmbeddedUrl();
+// This will log the embedded URL and return it
+```
+
+## Complete Example
+
+Here's a complete example showing how to create and use an embedded simulation:
+
+```javascript
+// 1. Create a simple simulation in the browser console
+const createSimulationDataFromFiles = window.createSimulationDataFromFiles;
+const generateEmbeddedUrl = window.generateEmbeddedUrlFn;
+
+const lammpsScript = `
+units lj
+atom_style atomic
+dimension 3
+boundary p p p
+
+region box block 0 10 0 10 0 10
+create_box 1 box
+create_atoms 1 random 100 12345 box
+
+mass 1 1.0
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+velocity all create 1.0 12345
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+thermo 100
+run 1000
+`;
+
+const simulationData = createSimulationDataFromFiles(
+  'demo-lj',
+  'Demo LJ Particles',
+  'A demonstration of Lennard-Jones particles.',
+  'demo.in',
+  { 'demo.in': lammpsScript },
+  { keywords: ['demo', 'lennard jones'] }
+);
+
+const embeddedUrl = generateEmbeddedUrl(window.location.origin, simulationData);
+console.log('Embedded URL:', embeddedUrl);
+
+// 2. Copy the URL and paste it in a new browser tab
+// 3. The simulation will automatically load and start
+```
+
+## Integration in External Websites
+
+To embed Atomify simulations in external websites, you can create embedded URLs and use them in iframes:
+
+```html
+<iframe 
+  src="https://atomify.com/?embeddedSimulationData=<your-base64-data>"
+  width="100%" 
+  height="600px"
+  frameborder="0">
+</iframe>
+```
+
+When accessed, embedded URLs will automatically load and start the simulation in an optimized embedded view.

build/asset-manifest.json

@@ -0,0 +1,74 @@
+{
+  "files": {
+    "main.css": "/atomify/static/css/main.377843dd.css",
+    "main.js": "/atomify/static/js/main.45b37aeb.js",
+    "static/media/codicon.ttf": "/atomify/static/media/codicon.b797181c93b3755f4fa1.ttf",
+    "static/media/KaTeX_AMS-Regular.ttf": "/atomify/static/media/KaTeX_AMS-Regular.853be92419a6c3766b9a.ttf",
+    "static/media/KaTeX_Main-Regular.ttf": "/atomify/static/media/KaTeX_Main-Regular.9eba1d77abcf2aa6e94e.ttf",
+    "static/media/KaTeX_Main-Bold.ttf": "/atomify/static/media/KaTeX_Main-Bold.8169508bf58f8bd92ad8.ttf",
+    "static/media/KaTeX_Main-Italic.ttf": "/atomify/static/media/KaTeX_Main-Italic.fa675e5e4bec9eb250b6.ttf",
+    "static/media/KaTeX_AMS-Regular.woff": "/atomify/static/media/KaTeX_AMS-Regular.d562e886c52f12660a41.woff",
+    "static/media/KaTeX_Main-BoldItalic.ttf": "/atomify/static/media/KaTeX_Main-BoldItalic.828abcb200061cffbaae.ttf",
+    "static/media/KaTeX_Math-Italic.ttf": "/atomify/static/media/KaTeX_Math-Italic.8a5f936332e8028c7278.ttf",
+    "static/media/KaTeX_Math-BoldItalic.ttf": "/atomify/static/media/KaTeX_Math-BoldItalic.bf2d440b3a42ea78a998.ttf",
+    "static/media/KaTeX_Main-Regular.woff": "/atomify/static/media/KaTeX_Main-Regular.4f35fbcc9ee8614c2bcc.woff",
+    "static/media/KaTeX_Main-Bold.woff": "/atomify/static/media/KaTeX_Main-Bold.0c3b8929d377c0e9b2f3.woff",
+    "static/media/KaTeX_AMS-Regular.woff2": "/atomify/static/media/KaTeX_AMS-Regular.73ea273a72f4aca30ca5.woff2",
+    "static/media/KaTeX_Typewriter-Regular.ttf": "/atomify/static/media/KaTeX_Typewriter-Regular.c5c02d763c89380dcb4e.ttf",
+    "static/media/KaTeX_Main-Regular.woff2": "/atomify/static/media/KaTeX_Main-Regular.f650f111a3b890d116f1.woff2",
+    "static/media/KaTeX_Main-Bold.woff2": "/atomify/static/media/KaTeX_Main-Bold.39890742bc957b368704.woff2",
+    "static/media/KaTeX_SansSerif-Bold.ttf": "/atomify/static/media/KaTeX_SansSerif-Bold.5b49f4993ae22d7975b4.ttf",
+    "static/media/KaTeX_SansSerif-Italic.ttf": "/atomify/static/media/KaTeX_SansSerif-Italic.b257a18c016f37ee4543.ttf",
+    "static/media/KaTeX_Main-Italic.woff": "/atomify/static/media/KaTeX_Main-Italic.fd947498bc16392e76c2.woff",
+    "static/media/KaTeX_Fraktur-Bold.ttf": "/atomify/static/media/KaTeX_Fraktur-Bold.4c761b3711973ab04edf.ttf",
+    "static/media/KaTeX_Fraktur-Regular.ttf": "/atomify/static/media/KaTeX_Fraktur-Regular.ed305b5434865e06ffde.ttf",
+    "static/media/KaTeX_SansSerif-Regular.ttf": "/atomify/static/media/KaTeX_SansSerif-Regular.2f7bc363fc5424ebda59.ttf",
+    "static/media/KaTeX_Main-BoldItalic.woff": "/atomify/static/media/KaTeX_Main-BoldItalic.428978dc7837d46de091.woff",
+    "static/media/KaTeX_Math-Italic.woff": "/atomify/static/media/KaTeX_Math-Italic.96759856b4e70f3a8338.woff",
+    "static/media/KaTeX_Math-BoldItalic.woff": "/atomify/static/media/KaTeX_Math-BoldItalic.3f07ed67f06c720120ce.woff",
+    "static/media/KaTeX_Main-Italic.woff2": "/atomify/static/media/KaTeX_Main-Italic.fe2176f79edaa716e621.woff2",
+    "static/media/KaTeX_Main-BoldItalic.woff2": "/atomify/static/media/KaTeX_Main-BoldItalic.20f389c4120be058d80a.woff2",
+    "static/media/KaTeX_Script-Regular.ttf": "/atomify/static/media/KaTeX_Script-Regular.fc9ba5249878cd8f8d88.ttf",
+    "static/media/KaTeX_Math-Italic.woff2": "/atomify/static/media/KaTeX_Math-Italic.6d3d25f4820d0da8f01f.woff2",
+    "static/media/KaTeX_Math-BoldItalic.woff2": "/atomify/static/media/KaTeX_Math-BoldItalic.dcbcbd93bac0470b462d.woff2",
+    "static/media/KaTeX_Typewriter-Regular.woff": "/atomify/static/media/KaTeX_Typewriter-Regular.4c6b94fd1d07f8beff7c.woff",
+    "static/media/KaTeX_SansSerif-Bold.woff": "/atomify/static/media/KaTeX_SansSerif-Bold.b9cd458ac6d5889ff9c3.woff",
+    "static/media/KaTeX_SansSerif-Italic.woff": "/atomify/static/media/KaTeX_SansSerif-Italic.8d593cfaa96238d5e2f8.woff",
+    "static/media/KaTeX_Typewriter-Regular.woff2": "/atomify/static/media/KaTeX_Typewriter-Regular.c295e7f71970f03c0549.woff2",
+    "static/media/KaTeX_Fraktur-Bold.woff": "/atomify/static/media/KaTeX_Fraktur-Bold.354501bac435c3264834.woff",
+    "static/media/KaTeX_Fraktur-Regular.woff": "/atomify/static/media/KaTeX_Fraktur-Regular.6fdf0ac577be0ba82a4c.woff",
+    "static/media/KaTeX_Caligraphic-Bold.ttf": "/atomify/static/media/KaTeX_Caligraphic-Bold.7489a2fbfb9bfe704420.ttf",
+    "static/media/KaTeX_Caligraphic-Regular.ttf": "/atomify/static/media/KaTeX_Caligraphic-Regular.7e873d3833eb108a0758.ttf",
+    "static/media/KaTeX_SansSerif-Regular.woff": "/atomify/static/media/KaTeX_SansSerif-Regular.02271ec5cb9f5b4588ac.woff",
+    "static/media/KaTeX_Size1-Regular.ttf": "/atomify/static/media/KaTeX_Size1-Regular.6de7d4b539221a49e9e2.ttf",
+    "static/media/KaTeX_SansSerif-Bold.woff2": "/atomify/static/media/KaTeX_SansSerif-Bold.95591a929f0d32aa282a.woff2",
+    "static/media/KaTeX_SansSerif-Italic.woff2": "/atomify/static/media/KaTeX_SansSerif-Italic.7d393d382f3e7fb1c637.woff2",
+    "static/media/KaTeX_Size2-Regular.ttf": "/atomify/static/media/KaTeX_Size2-Regular.57f5c1837853986ea1db.ttf",
+    "static/media/KaTeX_Fraktur-Bold.woff2": "/atomify/static/media/KaTeX_Fraktur-Bold.931d67ea207ab37ee693.woff2",
+    "static/media/KaTeX_Fraktur-Regular.woff2": "/atomify/static/media/KaTeX_Fraktur-Regular.172d3529b26f8cedef6b.woff2",
+    "static/media/KaTeX_Script-Regular.woff": "/atomify/static/media/KaTeX_Script-Regular.073b3402d036714b4370.woff",
+    "static/media/KaTeX_Size4-Regular.ttf": "/atomify/static/media/KaTeX_Size4-Regular.4ad7c7e8bb8d10a34bb7.ttf",
+    "static/media/KaTeX_SansSerif-Regular.woff2": "/atomify/static/media/KaTeX_SansSerif-Regular.cd5e231e0cc53b2cb2c0.woff2",
+    "static/media/KaTeX_Script-Regular.woff2": "/atomify/static/media/KaTeX_Script-Regular.c81d1b2a4b75d3eded60.woff2",
+    "static/media/KaTeX_Caligraphic-Bold.woff": "/atomify/static/media/KaTeX_Caligraphic-Bold.d757c535a2e5902f1325.woff",
+    "static/media/KaTeX_Caligraphic-Regular.woff": "/atomify/static/media/KaTeX_Caligraphic-Regular.db074fa22cf224af93d7.woff",
+    "static/media/KaTeX_Size3-Regular.ttf": "/atomify/static/media/KaTeX_Size3-Regular.8d6b6822586eea3d3b20.ttf",
+    "static/media/KaTeX_Caligraphic-Bold.woff2": "/atomify/static/media/KaTeX_Caligraphic-Bold.a1abf90dfd72792a577a.woff2",
+    "static/media/KaTeX_Caligraphic-Regular.woff2": "/atomify/static/media/KaTeX_Caligraphic-Regular.d6484fce1ef428d5bd94.woff2",
+    "static/media/KaTeX_Size1-Regular.woff": "/atomify/static/media/KaTeX_Size1-Regular.0108e89c9003e8c14ea3.woff",
+    "static/media/KaTeX_Size2-Regular.woff": "/atomify/static/media/KaTeX_Size2-Regular.3a99e70aee4076660d38.woff",
+    "static/media/KaTeX_Size4-Regular.woff": "/atomify/static/media/KaTeX_Size4-Regular.aeffd8025cba3647f1a6.woff",
+    "static/media/KaTeX_Size1-Regular.woff2": "/atomify/static/media/KaTeX_Size1-Regular.6eec866c69313624be60.woff2",
+    "static/media/KaTeX_Size2-Regular.woff2": "/atomify/static/media/KaTeX_Size2-Regular.2960900c4f271311eb36.woff2",
+    "static/media/KaTeX_Size4-Regular.woff2": "/atomify/static/media/KaTeX_Size4-Regular.e418bf257af1052628d8.woff2",
+    "static/media/KaTeX_Size3-Regular.woff": "/atomify/static/media/KaTeX_Size3-Regular.7947224e8a9914fa332b.woff",
+    "static/media/KaTeX_Size3-Regular.woff2": "/atomify/static/media/KaTeX_Size3-Regular.e1951519f6f0596f7356.woff2",
+    "index.html": "/atomify/index.html",
+    "main.377843dd.css.map": "/atomify/static/css/main.377843dd.css.map",
+    "main.45b37aeb.js.map": "/atomify/static/js/main.45b37aeb.js.map"
+  },
+  "entrypoints": [
+    "static/css/main.377843dd.css",
+    "static/js/main.45b37aeb.js"
+  ]
+}

build/examples/diffusion/2d-msd-diffusion/2d-msd-diffusion.in

@@ -0,0 +1,53 @@
+# Move camera to a nice position
+#/camera position 33.5 39.0 47.8
+#/camera target 34.9 38.2 10.1
+
+# Set atom size and color
+#/atom 1 1.0 #ffffff
+
+variable x equal 40
+variable y equal 40
+
+variable rho equal 0.6
+variable t equal 1.0
+variable rc equal 2.5
+
+# problem setup
+
+units lj
+dimension 2
+atom_style atomic
+neigh_modify delay 0 every 1
+
+lattice sq2 ${rho}
+region simbox block 0 $x 0 $y -0.1 0.1
+create_box 1 simbox
+create_atoms 1 box
+
+pair_style lj/cut ${rc}
+pair_coeff * * 1 1
+
+mass * 1.0
+velocity all create $t 97287
+
+fix nve all nve
+fix langevin all langevin $t $t 0.1 498094
+fix enforce2d all enforce2d
+# equilibration run
+
+run 2000
+unfix langevin
+
+# data gathering run
+
+reset_timestep 0
+
+# factor of 4 in 2 variables is for 2d
+compute msd all msd com yes
+variable diffusioncoeff equal c_msd[4]/4/(step*dt+1.0e-6)
+
+thermo_style custom step temp c_msd[4] v_diffusioncoeff
+compute displacement all displace/atom
+
+thermo 25
+run 10000