https://github.com/open2c/polychrom-hoomd
https://github.com/open2c/polychrom-hoomd
Last synced: about 1 year ago
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- Host: GitHub
- URL: https://github.com/open2c/polychrom-hoomd
- Owner: open2c
- License: mit
- Created: 2023-03-27T20:39:00.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2025-01-29T00:40:59.000Z (over 1 year ago)
- Last Synced: 2025-04-24T01:13:54.135Z (about 1 year ago)
- Language: Python
- Size: 69 MB
- Stars: 7
- Watchers: 9
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# polychrom-hoomd
[**HOOMD-blue**](https://hoomd-blue.readthedocs.io/en/v3.11.0/)-based package for coarse-grained polymer and chromosome simulations.
## Installation
You may use the provided `environment.yml` file to create a conda environment `polychrom-hoomd` including all required software packages:
~~~shell
conda env create -f environment.yml
conda activate polychrom-hoomd
~~~
Note that this environment should be built on a node with GPU access (and CUDA). HOOMD may silently default to CPU version if this is not the case.
Following which the code may be installed as usual,
~~~shell
python3 -m pip install -e .
~~~
## Usage
See the attached Jupyter notebook tutorials within the `examples` directory.