Configuration

Atomic has two kinds of configuration:

• Server configuration - command-line flags and environment variables that control how atomic-server starts.
• Runtime settings - key-value settings stored in the registry or data database and editable through the UI/API.

Command-Line Options

atomic-server [GLOBAL_OPTIONS] <COMMAND>

Global options:
  --data-dir <path>       Directory containing registry.db and data databases
  --db-path <path>        Deprecated; use --data-dir

Commands:
  serve                   Start the HTTP server
  token                   Manage API tokens

Serve Options

atomic-server --data-dir ./data serve \
  --bind 0.0.0.0 \
  --port 8080 \
  --public-url https://atomic.example.com \
  --setup-token "$ATOMIC_SETUP_TOKEN"

Flag	Env Var	Default	Description
--port		8080	Port to listen on
--bind		127.0.0.1	Address to bind to
--public-url	PUBLIC_URL	unset	Public URL used for OAuth/MCP discovery
--storage	ATOMIC_STORAGE	sqlite	Storage backend: sqlite or postgres
--database-url	ATOMIC_DATABASE_URL	unset	Postgres connection string when using Postgres
--setup-token	ATOMIC_SETUP_TOKEN	unset	Token required to claim a fresh instance through the setup UI
--dangerously-skip-setup-token	ATOMIC_DANGEROUSLY_SKIP_SETUP_TOKEN	false	Insecurely allow first-run setup claims without a setup token

Use --bind 0.0.0.0 only when the server should accept connections from outside the host or container network. Put it behind a reverse proxy for public deployments. Set ATOMIC_SETUP_TOKEN before using the setup UI on a fresh server:

export ATOMIC_SETUP_TOKEN="$(openssl rand -base64 24)"

--dangerously-skip-setup-token is intended only for trusted development environments. With that flag enabled, any client that can reach an unclaimed server can claim it.

Token Command Options

The token command must point at the same data directory or storage backend as the server:

atomic-server --data-dir ./data token create --name "my-laptop"
atomic-server --data-dir ./data token list
atomic-server --data-dir ./data token revoke <token-id>

For Postgres:

ATOMIC_STORAGE=postgres \
ATOMIC_DATABASE_URL=postgres://user:pass@host:5432/atomic \
atomic-server token list

Runtime Settings

Runtime settings are available through:

• The Settings UI
• GET /api/settings
• PUT /api/settings/{key}
• SQLite/Postgres direct inspection for operators

Important settings include:

Key	Purpose
provider	openrouter, ollama, or OpenAI-compatible provider selection
embedding_model	OpenRouter embedding model
tagging_model	OpenRouter tagging model
wiki_model	Wiki and briefing model
chat_model	Chat model
auto_tagging_enabled	Enables or disables automatic tagging
ollama_host	Ollama server URL
openai_compat_base_url	OpenAI-compatible API base URL
task.daily_briefing.enabled	Enables scheduled briefings
task.daily_briefing.interval_hours	Briefing interval
task.draft_pipeline.enabled	Enables scheduled draft pipeline processing

Inspect SQLite settings:

sqlite3 databases/registry.db "SELECT key, value FROM settings;"

Registry vs Data Databases

Atomic uses a registry database plus one or more data databases. Global settings and API tokens live in the registry. Atoms, tags, chunks, wiki articles, conversations, feeds, and briefings live in data databases.

For multi-database deployments, background jobs and per-database state are isolated by database. See Multi-Database.

Health and Docs

Public endpoints useful for operations:

• GET /health
• GET /api/docs
• GET /api/docs/openapi.json

Authenticated status endpoints:

• GET /api/embeddings/status
• GET /api/embeddings/status/all
• GET /api/logs

Related

• Docker Compose
• Token Management
• Data and Backups