# jaxonomy

> Jaxonomy — block-diagram simulation for hybrid dynamical systems (JAX, NumPy API, tutorials, examples, and API reference).

Jaxonomy is a JAX-native Python engine for simulating hybrid dynamical systems built as block diagrams — wired blocks, continuous and discrete state, zero-crossing events, and acausal multi-physics networks (electrical, mechanical, thermal, hydraulic). Every simulation is JIT-compilable, vmap-batchable, and differentiable end to end, so calibration, trajectory optimization and controller tuning are ordinary gradient-based optimizations over the simulation itself. It ships 150+ library blocks including LQR, MPC, PID and Kalman/EKF/UKF, plus FMI 2.0 co-simulation and a reduced-order-modeling suite. MIT licensed.

## Start here

- [Jaxonomy documentation](https://py.jaxonomy.com/index.md): What Jaxonomy is, how to install it, and where to go next.
- [Using Jaxonomy from an AI agent](https://py.jaxonomy.com/agents/index.md): Operating manual for AI agents using Jaxonomy — when to use it, when to reach for something else instead, the core API surface, and the known pitfalls that break a first script.
- [Installation](https://py.jaxonomy.com/installation/index.md): Install, optional extras, and development installs.
- [MCP server](https://py.jaxonomy.com/mcp/index.md): The MCP server that lets an agent drive the engine directly — install, client configuration, the seven tools it exposes, and what they cannot do.

## API reference

- [Framework](https://py.jaxonomy.com/framework/index.md): DiagramBuilder, LeafSystem, ports, Context, dependency tickets.
- [Block library](https://py.jaxonomy.com/library/index.md): The standard block library.
- [Simulation](https://py.jaxonomy.com/simulation/index.md): simulate, solvers, SimulatorOptions, results handling.
- [Optimization](https://py.jaxonomy.com/optimization/index.md): Training and optimization helpers.
- [Analysis](https://py.jaxonomy.com/analysis/index.md): Linearization, frequency response, influence graphs.

## Guides and scope

- [Tutorials](https://py.jaxonomy.com/tutorials/index.md): Index of the tutorial notebooks.
- [Example notebooks](https://py.jaxonomy.com/examples/index.md): Index of the applied example notebooks.
- [Scope — PINNs & PDEs](https://py.jaxonomy.com/scope/pinn/index.md): What Jaxonomy does and does not do for PINNs and PDEs.
- [Scope — ROM & surrogates](https://py.jaxonomy.com/scope/rom/index.md): Reduced-order modeling and surrogates.
- [Public benchmarks](https://py.jaxonomy.com/benchmarks/index.md): Performance benchmarks and how to read them.
- [Distributed ensemble](https://py.jaxonomy.com/distributed/index.md): Batch and distributed simulation.
- [Persistent JIT cache](https://py.jaxonomy.com/jit_cache/index.md): JIT caching behaviour.
- [Memory footprint](https://py.jaxonomy.com/memory/index.md): Memory footprint and recorder buffers.
- [About](https://py.jaxonomy.com/about/index.md): Project scope, provenance, and licensing.