# chemistry.tools documentation

Build, test and run chemical software. Practical guides from a first job to reproducible scientific pipelines.

- [How the job system works](https://docs.chemistry.tools/text/start/job-system.md): Understand what a job is, how the queue matches work to workers, and how Programs, pipelines and files fit together.
- [Run your first job](https://docs.chemistry.tools/text/start/first-job.md): Run a Python script locally, submit it to a remote worker and download its output files.
- [Make a function reusable](https://docs.chemistry.tools/text/start/reusable-programs.md): Add typed inputs and outputs to a Python function, publish it once and call it from the CLI or Python.
- [Build a scientific pipeline](https://docs.chemistry.tools/text/start/pipelines.md): Chain calculation, verification and save steps, or fan out across inputs in parallel.
- [Optimize a structure](https://docs.chemistry.tools/text/science/structures.md): Run an ASE geometry optimization and save the relaxed coordinates, trajectory and convergence report.
- [Build a reaction network](https://docs.chemistry.tools/text/science/networks.md): Validate starting species and elementary steps, save sourced proposals and attach calculation evidence.
- [Run molecular simulations](https://docs.chemistry.tools/text/science/simulations.md): Submit an MD configuration that simulates trajectories, parses reaction events and publishes observations.
- [Search and verify a transition state](https://docs.chemistry.tools/text/science/transition-states.md): Submit a TS search strategy, run strict Hessian/IRC verification and publish the result.
- [Evaluate DFT energies](https://docs.chemistry.tools/text/science/dft.md): Compute single-point DFT energies on stored reactant, TS and product geometries.
- [Simulate a reaction network](https://docs.chemistry.tools/text/science/kinetics.md): Integrate a kinetic ODE model inside a job and save the concentration trace and mass-balance check.
- [Create an algorithm benchmark](https://docs.chemistry.tools/text/test/benchmarks.md): Define a dataset, score candidate outputs against reference answers and rank algorithm versions.
- [Test parsers and TS strategies](https://docs.chemistry.tools/text/test/algorithms.md): Evaluate a custom trajectory parser or TS search strategy against a frozen benchmark dataset.
- [Measure throughput and efficiency](https://docs.chemistry.tools/text/test/throughput.md): Break wall-clock time into queue, setup, compute and verification so you optimize the real bottleneck.
- [Connect a worker](https://docs.chemistry.tools/text/operate/workers.md): Create a worker invitation, enroll a machine into a pool and start accepting jobs.
- [Choose code and dependencies](https://docs.chemistry.tools/text/operate/environments.md): Pick the right packaging mode for standalone scripts, Python packages, native profiles and containers.
- [Share and stream scientific datasets](https://docs.chemistry.tools/text/operate/files.md): Write Parquet datasets, share accepted files between jobs and choose between partial reads and full downloads.
- [Inspect and recover a run](https://docs.chemistry.tools/text/operate/recovery.md): Check status, inspect failure logs and retry failed stages without repeating completed upstream work.
- [Use the local development stack](https://docs.chemistry.tools/text/operate/local-development.md): Start the local API, database, scheduler, storage and CPU worker on your machine.

Human guides: https://docs.chemistry.tools