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Chemistry and Aerosol","monthly_downloads":3203,"total_dependent_repos":1,"total_dependent_packages":1,"readme":"pyrcel: cloud parcel model\n==========================\n\n![sample parcel model run](https://raw.githubusercontent.com/darothen/pyrcel/master/docs/assets/figures/basic_run.png)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20870343.svg)](https://zenodo.org/badge/latestdoi/12927551)[![PyPI Version](https://badge.fury.io/py/pyrcel.svg)](https://badge.fury.io/py/pyrcel)[![CI](https://github.com/darothen/pyrcel/actions/workflows/ci.yml/badge.svg)](https://github.com/darothen/pyrcel/actions/workflows/ci.yml)[![Documentation Status](https://readthedocs.org/projects/pyrcel/badge/?version=stable)](https://pyrcel.readthedocs.io/en/latest/)\n\n\n`pyrcel` is a simple, adiabatic cloud parcel model for use in\naerosol-cloud interaction studies. [Rothenberg and Wang (2016)](http://journals.ametsoc.org/doi/full/10.1175/JAS-D-15-0223.1) discuss the model in detail and its improvements over [Nenes et al (2001)][nenes2001]:\n\n* Implementation of κ-Köhler theory for condensation physics ([Petters and Kreidenweis, 2007][pk2007])\n* Extension of model to handle arbitrary sectional representations of aerosol populations, based on user-controlled empirical or parameterized size distributions\n* JAX/[diffrax][diffrax]-based numerical core — differentiable, batchable, GPU-ready, with no Fortran/SUNDIALS dependency\n\n[Detailed documentation is available](https://pyrcel.readthedocs.io/en/latest/), including a [scientific description](https://pyrcel.readthedocs.io/en/latest/user_guide/sci_descr/), [installation details](https://pyrcel.readthedocs.io/en/latest/getting_started/installation/), and a [basic example](https://pyrcel.readthedocs.io/en/latest/examples/basic_run/).\n\n\u003e [!WARNING]\n\u003e **Version 2.0 Notice**\n\u003e\n\u003e This is **pyrcel v2.0**, a major new release with more features, greater flexibility, and a JAX-based differentiable kernel. However, there are several **breaking changes** compared to version 1.3.x.\n\u003e\n\u003e Please review the [migration guide](https://pyrcel.readthedocs.io/en/latest/user_guide/migration/) to update your code.\n\u003e\n\u003e If you wish to continue using the legacy (v1.3.x) model, you can install it from PyPI by pinning the version:\n\u003e\n\u003e ```shell\n\u003e pip install \"pyrcel\u003c2\"\n\u003e ```\n\n\nQuick Start\n-----------\n\nThe easiest way to run `pyrcel` from source is with [`uv`](https://docs.astral.sh/uv/):\n\n```shell\n$ git clone https://github.com/darothen/pyrcel.git \u0026\u0026 cd pyrcel\n$ uv run python examples/basic_run.py\n```\n\n`uv` will automatically create an isolated environment and install all dependencies.\nThe first call compiles JAX kernels; subsequent calls are fast.\n\nUsage\n-----\n\n```python\nimport pyrcel as pm\n\nsulfate = pm.AerosolSpecies(\n    \"sulfate\", pm.Lognorm(mu=0.05, sigma=2.0, N=1000.0), kappa=0.54, bins=50\n)\nmodel = pm.ParcelModel([sulfate], V=1.0, T0=283.0, S0=-0.02, P0=85000.0, console=True)\noutput = model.run(t_end=300.0, output_dt=10.0, terminate=True, live=True)\n\nprint(f\"S_max  = {output.summary['S_max']*100:.3f} %\")\nprint(f\"N_act  = {output.Nd:.3e} m⁻³\")\n```\n\nKey capabilities:\n\n* **Autodiff** — exact gradients of `S_max` w.r.t. updraft speed, initial conditions,\n  accommodation coefficient, and aerosol properties via `jax.grad`.\n* **Batching / GPU** — `jax.vmap` runs ensembles of parcels in one compiled call;\n  pass `device=\"gpu\"` to `ParcelModel` for CUDA acceleration.\n* **Time-varying updraft** — pass a `pyrcel.InterpolatedUpdraft(ts=..., vs=...)` as `V`.\n* **Flexible output** — `output.to_pandas()`, `.to_xarray()`, `.to_netcdf()`, `.to_parquet()`.\n\nThe differentiable core (`pyrcel.integrator`, `pyrcel.equilibrate`) is usable directly\nfor `jit`/`grad`/`vmap`; `ParcelModel` is the interactive convenience layer (console\noutput, progress meter, post-solve summary table).\n\nInstallation\n------------\n\n**From PyPI (recommended):**\n\n```shell\n$ pip install pyrcel\n```\n\nJAX (CPU) is included by default. No extras needed for standard use.\n\n**From source:**\n\n```shell\n$ git clone https://github.com/darothen/pyrcel.git \u0026\u0026 cd pyrcel\n$ uv sync\n$ uv run python examples/basic_run.py\n```\n\n**GPU support (CUDA 12):**\n\n```shell\n$ pip install \"pyrcel[gpu]\"\n```\n\nRequirements\n------------\n\n* Python \u003e= 3.11\n* [JAX](https://docs.jax.dev/) \u003e= 0.4.38\n* [diffrax](https://docs.kidger.site/diffrax/) \u003e= 0.6.2\n* [equinox](https://docs.kidger.site/equinox/) \u003e= 0.11.10\n* [optimistix](https://docs.kidger.site/optimistix/) \u003e= 0.0.7\n* NumPy, SciPy, pandas, polars, xarray\n\nDevelopment\n-----------\n\nClone the repo and install with dev dependencies:\n\n```shell\n$ git clone https://github.com/darothen/pyrcel.git \u0026\u0026 cd pyrcel\n$ uv sync --extra test\n$ prek install   # installs the git pre-commit hook (requires prek: https://prek.j178.dev)\n```\n\nRun the fast test suite:\n\n```shell\n$ uv run pytest tests/ -m \"not slow\"\n```\n\nLint and format are handled automatically by `prek` on commit, or run manually:\n\n```shell\n$ prek run --all-files\n```\n\nPlease fork this repository if you intend to develop the model further so that the\ncode's provenance can be maintained.\n\nLicense / Usage\n---------------\n\n[All scientific code should be licensed](http://www.astrobetter.com/the-whys-and-hows-of-licensing-scientific-code/). This code is released under the New BSD (3-clause) [license](LICENSE.md).\n\nIf you use this for any scientific work resulting in a publication, please cite our\noriginal publication detailing the model:\n\n```\n@article {\n      author = \"Daniel Rothenberg and Chien Wang\",\n      title = \"Metamodeling of Droplet Activation for Global Climate Models\",\n      journal = \"Journal of the Atmospheric Sciences\",\n      year = \"2016\",\n      publisher = \"American Meteorological Society\",\n      address = \"Boston MA, USA\",\n      volume = \"73\",\n      number = \"3\",\n      doi = \"10.1175/JAS-D-15-0223.1\",\n      pages= \"1255 - 1272\",\n      url = \"https://journals.ametsoc.org/view/journals/atsc/73/3/jas-d-15-0223.1.xml\"\n}\n```\nAdditionally, please consider citing the bespoke DOI for the\n[specific release version of pyrcel](https://zenodo.org/records/20693507)\nthat you used during your research (or the base version you modified). This\nallows us to track adoption and use of specific model versions over time.\n\n[author_email]: mailto:daniel@danielrothenberg.com\n[nenes2001]: https://onlinelibrary.wiley.com/doi/abs/10.1034/j.1600-0889.2001.d01-12.x\n[pk2007]: http://www.atmos-chem-phys.net/7/1961/2007/acp-7-1961-2007.html\n[diffrax]: https://docs.kidger.site/diffrax/\n[jax]: https://docs.jax.dev/\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["optimize","archiving","transforms","measur","generic","observation","compose","conversion","projection","animals"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/123985","html_url":"https://ost.ecosyste.ms/projects/123985"}