| Name | jaxincell JSON |
| Version |
0.5
JSON |
| download |
| home_page | None |
| Summary | JAX-in-Cell: Particle-in-Cell code in JAX |
| upload_time | 2025-03-14 03:29:45 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.5 |
| license | MIT License
Copyright (c) 2024 uwplasma
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
|
| keywords |
plasma
physics
simulation
jax
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
jax
jaxlib
jax_tqdm
matplotlib
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
<p align="center">
<img src="https://raw.githubusercontent.com/uwplasma/JAX-in-Cell/refs/heads/main/docs/JAX-in-Cell_logo.png" align="center" width="30%">
</p>
<!-- <p align="center"><h3 align="center">JAX-IN-CELL</h1></p> -->
<p align="center">
<em><code>❯ jaxincell: 1D particle-in-cell code in JAX to perform simulation of plasmas</code></em>
</p>
<p align="center">
<img src="https://img.shields.io/github/license/uwplasma/JAX-in-Cell?style=default&logo=opensourceinitiative&logoColor=white&color=0080ff" alt="license">
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<img src="https://github.com/uwplasma/JAX-in-Cell/actions/workflows/build_test.yml/badge.svg" alt="Build Status">
</a>
<a href="https://codecov.io/gh/uwplasma/JAX-in-Cell">
<img src="https://codecov.io/gh/uwplasma/JAX-in-Cell/branch/main/graph/badge.svg" alt="Coverage">
</a>
<a href="https://jax-in-cell.readthedocs.io/en/latest/?badge=latest">
<img src="https://readthedocs.org/projects/jax-in-cell/badge/?version=latest" alt="Documentation Status">
</a>
</p>
<p align="center"><!-- default option, no dependency badges. -->
</p>
<p align="center">
<!-- default option, no dependency badges. -->
</p>
<br>
## Table of Contents
- [ Overview](#-overview)
- [ Features](#-features)
- [ Project Structure](#-project-structure)
- [ Project Index](#-project-index)
- [ Getting Started](#-getting-started)
- [ Prerequisites](#-prerequisites)
- [ Installation](#-installation)
- [ Usage](#-usage)
- [ Testing](#-testing)
- [ Project Roadmap](#-project-roadmap)
- [ Contributing](#-contributing)
- [ License](#-license)
- [ Acknowledgments](#-acknowledgments)
---
## Overview
JAX-in-Cell is an open-source project in Python that uses JAX to speedup simulations, leading to a simple to use, fast and concise code. It can be imported in a Python script using the **jaxincell** package, or run directly in the command line as `jaxincell`. To install it, use
```sh
pip install jaxincell
```
Alternatively, you can install the Python dependencies `jax`, `jax_tqdm` and `matplotlib`, and run the [example script](example_script.py) in the repository after downloading it as
```sh
git clone https://github.com/uwplasma/JAX-in-Cell
python example_script.py
```
This allows JAX-in-Cell to be run without any installation.
The project can be downloaded in its [GitHub repository](https://github.com/uwplasma/JAX-in-Cell)
</code>
---
## Features
JAX-in-Cell can run in CPUs, GPUs and TPUs, has autodifferentiation and just-in-time compilation capabilities, is based on rigorous testing, uses CI/CD via GitHub actions and has detailed documentation.
Currently, it evolves particles using the non-relativisic Lorentz force $\mathbf F = q (\mathbf E + \mathbf v \times \mathbf B)$, and evolves the electric $\mathbf E$ and magnetic $\mathbf B$ field using Maxwell's equations.
Plenty of examples are provided in the `examples` folder, and the documentation can be found in [Read the Docs](https://jax-in-cell.readthedocs.io/).
---
## Project Structure
```sh
└── JAX-in-Cell/
├── LICENSE
├── docs
├── examples
│ ├── Landau_damping.py
│ ├── Langmuir_wave.py
│ ├── ion-acoustic_wave.py
│ ├── two-stream_instability.py
│ ├── auto-differentiability.py
│ ├── scaling_energy_time.py
│ └── optimize_two_stream_saturation.py
├── jaxincell
│ ├── boundary_conditions.py
│ ├── constants.py
│ ├── diagnostics.py
│ ├── fields.py
│ ├── particles.py
│ ├── plot.py
│ ├── simulation.py
│ └── sources.py
├── main.py
└── tests
└── test_simulation.py
```
---
## Getting Started
### Prerequisites
- **Programming Language:** Python
Besides Python, JAX-in-Cell has minimum requirements. These are stated in [requirements.txt](requirements.txt), and consist of the Python libraries `jax`, `jax_tqdm` and `matplotlib`.
### Installation
Install JAX-in-Cell using one of the following methods:
**Using PyPi:**
1. Install JAX-in-Cell from anywhere in the terminal:
```sh
pip install jaxincell
```
**Build from source:**
1. Clone the JAX-in-Cell repository:
```sh
git clone https://github.com/uwplasma/JAX-in-Cell
```
2. Navigate to the project directory:
```sh
cd JAX-in-Cell
```
3. Install the project dependencies:
```sh
pip install -r /path/to/requirements.txt
```
4. Install JAX-in-Cell:
```sh
pip install -e .
```
### Usage
To run a simple case of JAX-in-Cell, you can simply call `jaxincell` from the terminal
```sh
jaxincell
```
This runs JAX-in-Cell using standard input parameters of Landau damping. To change input parameters, use a TOML file similar to the [example input](example_input.toml) present in the repository as
```sh
jaxincell example_input.toml
```
Additionally, it can be run inside a script, as shown in the [example script](example_script.py) file
```sh
python example_script.py
```
There, you can find most of the input parameters needed to run many test cases, as well as resolution parameters.
The `jaxincell` package has a single function `simulation()` that takes as arguments a dictionary input_parameters, the number of grid points, number of pseudoelectrons, total number of time steps, and the field solver to use.
In the [example script](example_script.py) file we write as inline comments the meaning of each input parameter.
### Testing
Run the test suite using the following command:
```sh
pytest .
```
---
## Project Roadmap
- [X] **`Task 1`**: <strike>Run PIC simulation using several field solvers.</strike>
- [ ] **`Task 2`**: Finalize example scripts and their documentation.
- [ ] **`Task 3`**: Implement a relativistic equation of motion.
- [ ] **`Task 4`**: Implement collisions to allow the plasma to relax to a Maxwellian.
- [ ] **`Task 5`**: Implement guiding-center equations of motion.
- [ ] **`Task 6`**: Implement an implicit time-stepping algorithm.
- [ ] **`Task 7`**: Generalize JAX-in-Cell to 2D.
---
## Contributing
- **💬 [Join the Discussions](https://github.com/uwplasma/JAX-in-Cell/discussions)**: Share your insights, provide feedback, or ask questions.
- **🐛 [Report Issues](https://github.com/uwplasma/JAX-in-Cell/issues)**: Submit bugs found or log feature requests for the `JAX-in-Cell` project.
- **💡 [Submit Pull Requests](https://github.com/uwplasma/JAX-in-Cell/blob/main/CONTRIBUTING.md)**: Review open PRs, and submit your own PRs.
<details closed>
<summary>Contributing Guidelines</summary>
1. **Fork the Repository**: Start by forking the project repository to your github account.
2. **Clone Locally**: Clone the forked repository to your local machine using a git client.
```sh
git clone https://github.com/uwplasma/JAX-in-Cell
```
3. **Create a New Branch**: Always work on a new branch, giving it a descriptive name.
```sh
git checkout -b new-feature-x
```
4. **Make Your Changes**: Develop and test your changes locally.
5. **Commit Your Changes**: Commit with a clear message describing your updates.
```sh
git commit -m 'Implemented new feature x.'
```
6. **Push to github**: Push the changes to your forked repository.
```sh
git push origin new-feature-x
```
7. **Submit a Pull Request**: Create a PR against the original project repository. Clearly describe the changes and their motivations.
8. **Review**: Once your PR is reviewed and approved, it will be merged into the main branch. Congratulations on your contribution!
</details>
<details closed>
<summary>Contributor Graph</summary>
<br>
<p align="left">
<a href="https://github.com{/uwplasma/JAX-in-Cell/}graphs/contributors">
<img src="https://contrib.rocks/image?repo=uwplasma/JAX-in-Cell">
</a>
</p>
</details>
---
## License
This project is protected under the MIT License. For more details, refer to the [LICENSE](LICENSE) file.
---
## Acknowledgments
- This code was inspired by a previous implementation of a PIC code in JAX by Sean Lim [here](https://github.com/SeanLim2101/PiC-Code-Jax).
- We acknowledge the help of the whole [UWPlasma](https://rogerio.physics.wisc.edu/) plasma group.
---
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"description": "<p align=\"center\">\n <img src=\"https://raw.githubusercontent.com/uwplasma/JAX-in-Cell/refs/heads/main/docs/JAX-in-Cell_logo.png\" align=\"center\" width=\"30%\">\n</p>\n<!-- <p align=\"center\"><h3 align=\"center\">JAX-IN-CELL</h1></p> -->\n<p align=\"center\">\n\t<em><code>\u276f jaxincell: 1D particle-in-cell code in JAX to perform simulation of plasmas</code></em>\n</p>\n<p align=\"center\">\n\t<img src=\"https://img.shields.io/github/license/uwplasma/JAX-in-Cell?style=default&logo=opensourceinitiative&logoColor=white&color=0080ff\" alt=\"license\">\n\t<img src=\"https://img.shields.io/github/last-commit/uwplasma/JAX-in-Cell?style=default&logo=git&logoColor=white&color=0080ff\" alt=\"last-commit\">\n\t<img src=\"https://img.shields.io/github/languages/top/uwplasma/JAX-in-Cell?style=default&color=0080ff\" alt=\"repo-top-language\">\n\t<a href=\"https://github.com/uwplasma/JAX-in-Cell/actions/workflows/build_test.yml\">\n\t\t<img src=\"https://github.com/uwplasma/JAX-in-Cell/actions/workflows/build_test.yml/badge.svg\" alt=\"Build Status\">\n\t</a>\n\t<a href=\"https://codecov.io/gh/uwplasma/JAX-in-Cell\">\n\t\t<img src=\"https://codecov.io/gh/uwplasma/JAX-in-Cell/branch/main/graph/badge.svg\" alt=\"Coverage\">\n\t</a>\n\t<a href=\"https://jax-in-cell.readthedocs.io/en/latest/?badge=latest\">\n\t\t<img src=\"https://readthedocs.org/projects/jax-in-cell/badge/?version=latest\" alt=\"Documentation Status\">\n\t</a>\n\n</p>\n<p align=\"center\"><!-- default option, no dependency badges. -->\n</p>\n<p align=\"center\">\n\t<!-- default option, no dependency badges. -->\n</p>\n<br>\n\n\n## Table of Contents\n\n- [ Overview](#-overview)\n- [ Features](#-features)\n- [ Project Structure](#-project-structure)\n - [ Project Index](#-project-index)\n- [ Getting Started](#-getting-started)\n - [ Prerequisites](#-prerequisites)\n - [ Installation](#-installation)\n - [ Usage](#-usage)\n - [ Testing](#-testing)\n- [ Project Roadmap](#-project-roadmap)\n- [ Contributing](#-contributing)\n- [ License](#-license)\n- [ Acknowledgments](#-acknowledgments)\n\n---\n\n## Overview\n\nJAX-in-Cell is an open-source project in Python that uses JAX to speedup simulations, leading to a simple to use, fast and concise code. It can be imported in a Python script using the **jaxincell** package, or run directly in the command line as `jaxincell`. To install it, use\n\n ```sh\n pip install jaxincell\n ```\n\nAlternatively, you can install the Python dependencies `jax`, `jax_tqdm` and `matplotlib`, and run the [example script](example_script.py) in the repository after downloading it as\n\n ```sh\n git clone https://github.com/uwplasma/JAX-in-Cell\n python example_script.py\n ```\n\nThis allows JAX-in-Cell to be run without any installation.\n\nThe project can be downloaded in its [GitHub repository](https://github.com/uwplasma/JAX-in-Cell)\n</code>\n\n---\n\n## Features\n\nJAX-in-Cell can run in CPUs, GPUs and TPUs, has autodifferentiation and just-in-time compilation capabilities, is based on rigorous testing, uses CI/CD via GitHub actions and has detailed documentation.\n\nCurrently, it evolves particles using the non-relativisic Lorentz force $\\mathbf F = q (\\mathbf E + \\mathbf v \\times \\mathbf B)$, and evolves the electric $\\mathbf E$ and magnetic $\\mathbf B$ field using Maxwell's equations.\n\nPlenty of examples are provided in the `examples` folder, and the documentation can be found in [Read the Docs](https://jax-in-cell.readthedocs.io/).\n\n---\n\n## Project Structure\n\n```sh\n\u2514\u2500\u2500 JAX-in-Cell/\n \u251c\u2500\u2500 LICENSE\n \u251c\u2500\u2500 docs\n \u251c\u2500\u2500 examples\n \u2502 \u251c\u2500\u2500 Landau_damping.py\n \u2502 \u251c\u2500\u2500 Langmuir_wave.py\n \u2502 \u251c\u2500\u2500 ion-acoustic_wave.py\n\t\u2502 \u251c\u2500\u2500 two-stream_instability.py\n\t\u2502 \u251c\u2500\u2500 auto-differentiability.py\n\t\u2502 \u251c\u2500\u2500 scaling_energy_time.py\n \u2502 \u2514\u2500\u2500 optimize_two_stream_saturation.py\n \u251c\u2500\u2500 jaxincell\n \u2502 \u251c\u2500\u2500 boundary_conditions.py\n \u2502 \u251c\u2500\u2500 constants.py\n \u2502 \u251c\u2500\u2500 diagnostics.py\n \u2502 \u251c\u2500\u2500 fields.py\n \u2502 \u251c\u2500\u2500 particles.py\n \u2502 \u251c\u2500\u2500 plot.py\n \u2502 \u251c\u2500\u2500 simulation.py\n \u2502 \u2514\u2500\u2500 sources.py\n \u251c\u2500\u2500 main.py\n \u2514\u2500\u2500 tests\n \u2514\u2500\u2500 test_simulation.py\n```\n\n---\n## Getting Started\n\n### Prerequisites\n\n- **Programming Language:** Python\n\nBesides Python, JAX-in-Cell has minimum requirements. These are stated in [requirements.txt](requirements.txt), and consist of the Python libraries `jax`, `jax_tqdm` and `matplotlib`.\n\n### Installation\n\nInstall JAX-in-Cell using one of the following methods:\n\n**Using PyPi:**\n\n1. Install JAX-in-Cell from anywhere in the terminal:\n```sh\npip install jaxincell\n```\n\n**Build from source:**\n\n1. Clone the JAX-in-Cell repository:\n```sh\ngit clone https://github.com/uwplasma/JAX-in-Cell\n```\n\n2. Navigate to the project directory:\n```sh\ncd JAX-in-Cell\n```\n\n3. Install the project dependencies:\n\n```sh\npip install -r /path/to/requirements.txt\n```\n\n4. Install JAX-in-Cell:\n\n```sh\npip install -e .\n```\n\n### Usage\nTo run a simple case of JAX-in-Cell, you can simply call `jaxincell` from the terminal\n```sh\njaxincell\n```\n\nThis runs JAX-in-Cell using standard input parameters of Landau damping. To change input parameters, use a TOML file similar to the [example input](example_input.toml) present in the repository as\n\n```sh\njaxincell example_input.toml\n```\n\nAdditionally, it can be run inside a script, as shown in the [example script](example_script.py) file\n```sh\npython example_script.py\n```\n\nThere, you can find most of the input parameters needed to run many test cases, as well as resolution parameters.\nThe `jaxincell` package has a single function `simulation()` that takes as arguments a dictionary input_parameters, the number of grid points, number of pseudoelectrons, total number of time steps, and the field solver to use.\n\nIn the [example script](example_script.py) file we write as inline comments the meaning of each input parameter.\n\n### Testing\nRun the test suite using the following command:\n```sh\npytest .\n```\n\n---\n## Project Roadmap\n\n- [X] **`Task 1`**: <strike>Run PIC simulation using several field solvers.</strike>\n- [ ] **`Task 2`**: Finalize example scripts and their documentation.\n- [ ] **`Task 3`**: Implement a relativistic equation of motion.\n- [ ] **`Task 4`**: Implement collisions to allow the plasma to relax to a Maxwellian.\n- [ ] **`Task 5`**: Implement guiding-center equations of motion.\n- [ ] **`Task 6`**: Implement an implicit time-stepping algorithm.\n- [ ] **`Task 7`**: Generalize JAX-in-Cell to 2D.\n\n---\n\n## Contributing\n\n- **\ud83d\udcac [Join the Discussions](https://github.com/uwplasma/JAX-in-Cell/discussions)**: Share your insights, provide feedback, or ask questions.\n- **\ud83d\udc1b [Report Issues](https://github.com/uwplasma/JAX-in-Cell/issues)**: Submit bugs found or log feature requests for the `JAX-in-Cell` project.\n- **\ud83d\udca1 [Submit Pull Requests](https://github.com/uwplasma/JAX-in-Cell/blob/main/CONTRIBUTING.md)**: Review open PRs, and submit your own PRs.\n\n<details closed>\n<summary>Contributing Guidelines</summary>\n\n1. **Fork the Repository**: Start by forking the project repository to your github account.\n2. **Clone Locally**: Clone the forked repository to your local machine using a git client.\n ```sh\n git clone https://github.com/uwplasma/JAX-in-Cell\n ```\n3. **Create a New Branch**: Always work on a new branch, giving it a descriptive name.\n ```sh\n git checkout -b new-feature-x\n ```\n4. **Make Your Changes**: Develop and test your changes locally.\n5. **Commit Your Changes**: Commit with a clear message describing your updates.\n ```sh\n git commit -m 'Implemented new feature x.'\n ```\n6. **Push to github**: Push the changes to your forked repository.\n ```sh\n git push origin new-feature-x\n ```\n7. **Submit a Pull Request**: Create a PR against the original project repository. Clearly describe the changes and their motivations.\n8. **Review**: Once your PR is reviewed and approved, it will be merged into the main branch. Congratulations on your contribution!\n</details>\n\n<details closed>\n<summary>Contributor Graph</summary>\n<br>\n<p align=\"left\">\n <a href=\"https://github.com{/uwplasma/JAX-in-Cell/}graphs/contributors\">\n <img src=\"https://contrib.rocks/image?repo=uwplasma/JAX-in-Cell\">\n </a>\n</p>\n</details>\n\n---\n\n## License\n\nThis project is protected under the MIT License. For more details, refer to the [LICENSE](LICENSE) file.\n\n---\n\n## Acknowledgments\n\n- This code was inspired by a previous implementation of a PIC code in JAX by Sean Lim [here](https://github.com/SeanLim2101/PiC-Code-Jax).\n- We acknowledge the help of the whole [UWPlasma](https://rogerio.physics.wisc.edu/) plasma group.\n\n---\n",
"bugtrack_url": null,
"license": "MIT License\n \n Copyright (c) 2024 uwplasma\n \n Permission is hereby granted, free of charge, to any person obtaining a copy\n of this software and associated documentation files (the \"Software\"), to deal\n in the Software without restriction, including without limitation the rights\n to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n copies of the Software, and to permit persons to whom the Software is\n furnished to do so, subject to the following conditions:\n \n The above copyright notice and this permission notice shall be included in all\n copies or substantial portions of the Software.\n \n THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\n SOFTWARE.\n ",
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