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| [](https://github.com/cmelab/flowerMD/actions/workflows/pytest.yml) | ||
| [](https://codecov.io/gh/cmelab/flowerMD) | ||
| [](https://anaconda.org/conda-forge/flowermd) | ||
| [](https://anaconda.org/conda-forge/flowermd) | ||
| ## flowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics | ||
| flowerMD is a modular “wrapper” package for molecular dynamics (MD) | ||
| simulation pipeline development, designed to enable fast, reproducible, | ||
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| ensemble, and allowing for growth on an as-needed basis. | ||
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| Installing flowermd | ||
| =================== | ||
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| ## Installation | ||
| Installing `flowermd` from the `conda-forge` channel can be achieved by adding `conda-forge` to your channels with: | ||
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| ### 1. Clone this repository: ### | ||
| ``` | ||
| conda config --add channels conda-forge | ||
| conda config --set channel_priority strict | ||
| ``` | ||
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| Once the `conda-forge` channel has been enabled, `flowermd` can be installed with `conda`: | ||
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| ``` | ||
| conda install flowermd | ||
| ``` | ||
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| or with `mamba`: | ||
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| ``` | ||
| mamba install flowermd | ||
| ``` | ||
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| **Installing from source for development:** | ||
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| Clone this repository: | ||
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| ``` | ||
| git clone [email protected]:cmelab/flowerMD.git | ||
| cd flowerMD | ||
| ``` | ||
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| ### 2. Set up and activate environment: ### | ||
| #### a. Using HOOMD-blue from conda: | ||
| Set up and activate environment: | ||
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| ``` | ||
| conda env create -f environment-cpu.yml | ||
| conda env create -f environment-dev.yml | ||
| conda activate flowermd | ||
| python -m pip install . | ||
| python -m pip install -e . | ||
| ``` | ||
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| ## Basic Usage | ||
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| name: flowermd | ||
| channels: | ||
| - conda-forge | ||
| dependencies: | ||
| - foyer | ||
| - fresnel | ||
| - freud >=2.13.1 | ||
| - gmso >=0.11.2 | ||
| - gsd >=3.0 | ||
| - hoomd=4.3=*cpu* | ||
| - mbuild >=0.16.4 | ||
| - numpy | ||
| - openbabel | ||
| - pip | ||
| - py3Dmol | ||
| - pytest | ||
| - pytest-cov | ||
| - python >=3.10 | ||
| - fresnel >=0.13.5 | ||
| - cmeutils >=1.0 | ||
| - grits >=0.3.0 |