clancyLab-squid 2.0.12

A set of modules to aid in atomistic and molecular simulations.

Squid is an open-source molecular simulation codebase developed by the Clancy Lab at the Johns Hopkins University. The codebase includes simplified Molecular Dynamics (MD) and Density Functional Theory (DFT) simulation submission, as well as other utilities such as file I/O and post-processing.

Installing

For most, the easiest way to install squid is to use pip install:

[user@local]~% pip install clancylab-squid

If you wish, you may also clone the repository though:

[user@local]~% cd ~; git clone https://github.com/ClancyLab/squid.git

Contributing

If you would like to be an active developer within the Clancy Group, please contact the project maintainer to be added as a collaborator on the project. Otherwise, you are welcome to submit pull requests as you see fit, and they will be addressed.

Documentation

Documentation is necessary, and the following steps MUST be followed during contribution of new code:

Setup

1. Download Sphinx. This can be done simply if you have pip installed via pip install -U Sphinx

2. Wherever you have squid installed, you want another folder called squid-docs (NOT as a subfolder of squid).

[user@local]~% cd ~; mkdir squid-docs; cd squid-docs; git clone -b gh-pages [e-mail]:clancylab/squid.git html

3. Forever more just ignore that directory (don’t delete it though)

Adding Documentation

Documentation is done using ReStructuredText format docstrings, the Sphinx python package, and indices with autodoc extensions. To add more documentation, first add the file to be included in docs/source/conf.py under os.path.abspath(‘example/dir/to/script.py’). Secondly, ensure that you have proper docstrings in the python file, and finally run make full to re-generate the documentation and commit it to your local branch, as well as the git gh-pages branch.

For anymore information on documentation, the tutorial follwed can be found here.