Atomic

Turn your vault into a semantically-connected, AI-augmented knowledge graph. Atomic syncs your notes to an Atomic server and gives you semantic search, similar-note discovery, AI-generated wiki articles, an agentic chat over your notes, and a spatial knowledge-graph canvas — all from inside Obsidian.

What you get

• Semantic search — find notes by meaning, not keywords. Hybrid keyword + vector search with snippet previews.
• Live sync — notes sync to Atomic in the background as you write, with content hashing to skip unchanged files.
• Similar notes — a sidebar that surfaces the most semantically related notes to whatever you're editing.
• Wiki articles — LLM-synthesized summaries organized by your tag hierarchy, with inline citations back to source notes.
• Chat — an agentic RAG assistant that searches your vault mid-conversation. Scope to a tag or go vault-wide.
• Knowledge-graph canvas — a spatial, force-directed view of your notes and how they connect.

Requirements

You need a running Atomic server that your vault can reach. You have two options:

1. Atomic desktop app — install Atomic on the same machine. It runs a local server automatically; copy an API token from its settings.
2. Self-hosted server — run atomic-server on your machine or a server you control. See the main repo for setup.

Atomic needs an LLM provider (OpenRouter or a local Ollama) configured on the server side for embedding, tagging, wiki generation, and chat.

Install

From Community Plugins (recommended once published):

1. Open Obsidian → Settings → Community plugins → Browse
2. Search for "Atomic" and install
3. Enable the plugin

Manual install:

1. Download manifest.json, main.js, and styles.css from the latest release
2. Copy them to <vault>/.obsidian/plugins/atomic/
3. Reload Obsidian and enable Atomic in Community plugins

First-run setup

When you enable the plugin, a setup wizard walks you through three steps:

1. Connect — paste your server URL (e.g. http://localhost:8080) and API token, then press Test Connection.
2. Index — upload your existing notes. Progress bars show upload, embedding, and auto-tagging. You can continue in the background at any time.
3. Done — shortcuts for the main features are shown. Close the wizard and you're ready.

You can re-open the wizard any time via the command palette: Atomic: Setup Wizard.

Commands

Settings

Open Settings → Atomic to configure:

Privacy & data handling

• Notes you sync leave your vault. They are sent to the Atomic server you configure, which in turn sends them to the LLM/embedding provider configured on that server (OpenRouter or a local Ollama).
• The API token is stored in plaintext in <vault>/.obsidian/plugins/atomic/data.json, per Obsidian's plugin-data model. Treat the token like a password and avoid committing your .obsidian/ folder to public repos.
• Your data stays under your control when you self-host Atomic and pair it with a local Ollama — nothing leaves your machine.
• Excluded paths (.obsidian/, .trash/, .git/, node_modules/, plus anything you add) are never uploaded.

Troubleshooting

• "Connection failed" — confirm the server is running and reachable at the configured URL, and that the token is valid.
• Notes aren't syncing — check that Auto Sync is on, or run Atomic: Sync Current Note manually. Files matching an exclude pattern won't sync.
• Similar notes / wiki is empty — embedding and tagging run asynchronously after upload. Give large vaults a few minutes to finish the pipeline.
• Mobile — the plugin is marked desktop-friendly; mobile support depends on your server being reachable from the device.

Development

cd plugins/obsidian-plugin
npm install
npm run dev      # Watch mode
npm run build    # Type-check + production bundle

For live testing, symlink the plugin into a test vault:

ln -s "$(pwd)" /path/to/vault/.obsidian/plugins/atomic

Source files (all in src/):

• main.ts — plugin entry, command registration, view registration
• atomic-client.ts — HTTP client for atomic-server
• ws-client.ts — WebSocket subscriber for pipeline events
• sync-engine.ts / sync-state.ts — file-watching, hashing, upload
• onboarding-modal.ts — setup wizard
• settings.ts — settings tab
• search-modal.ts, similar-view.ts, wiki-view.ts, chat-view.ts, canvas-view.ts — feature UI

Issues & contributions

Report bugs and feature requests at github.com/kenforthewin/atomic/issues. PRs welcome.

License

MIT.