1. Installation

1.1. Dependencies

MicMec 1.0 has been developed with Python 3.7 and 3.8 in mind. It has been confirmed to work with the following combination of packages:

  • python 3.8.10

  • numpy 1.22.4

  • molmod 1.4.8

  • scipy 1.8.1

  • cython 0.29.30

  • matplotlib 3.5.2

  • h5py 3.7.0

  • jax 0.3.13 (optional)

  • jaxlib 0.3.10 (optional)

  • sphinx 5.0.2 (optional)

  • setuptools 63.0.1 (optional)

Sphinx is used for documentation, while JAX (with CUDA[CPU]) is used for automatic differentiation and just-in-time compilation. Sphinx and JAX are entirely optional and do not affect the core routines of MicMec. SetupTools is also optional.

1.2. Installation

MicMec can be installed manually by cloning the entire GitHub repository into a pre-existing directory on your Python path, for instance, micmec.

git clone https://github.com/Jlvdwall/micmec.git micmec
python

>>> import sys
>>> repo = "micmec"
>>> any((repo == directory[-len(repo):]) for directory in sys.path)

The Python code checks whether the repository directory (micmec in this case) is on your Python path. If it is not, you must add it to the path by editing your .bashrc or .profile script. With that, you can use MicMec to its fullest extent. As a bonus, you can install MicMec locally, by performing the following commands.

cd micmec
pip install .
pip list

That will add MicMec to the list of installed packages.