comp_chem_py: python library for computational chemistry

The comp_chem_py package is a collections of python modules and scripts that can be usefull in computational chemistry. The package evolves with my needs in the field. Feel free to re-use and modify as you wish and :ref:`contact` me if you have any question or comment.

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   developer_guide
   comp_chem_utils
   cpmd_scripts
   PDOS

Citation

If you use this library in a program or publication, please add the following reference:

• comp_chem_py, a python library for computational chemistry, Pablo Baudin, (Version vX.Y), (2019). http://doi.org/10.5281/zenodo.2580170

Set up and installation

Dependencies

The comp_chem_py library depends on the following modules:

• scipy_
• numpy_
• matplotlib_
• MySQLdb_

When installing the comp_chem_py library with pip_ those modules will be installed along if needed.

Using git and Linux/UNIX

In order to use the library, first clone it:

git clone --recursive https://gitlab.com/pablobaudin/comp_chem_py.git

Then export the PATH in your ~/.bashrc:

COMP_CHEM_PATH=/path/to/comp_chem_py/root/dir
export PATH=${COMP_CHEM_PATH}/bin:$PATH
export PYTHONPATH=${COMP_CHEM_PATH}/external:$PYTHONPATH
export PYTHONPATH=${COMP_CHEM_PATH}/src:$PYTHONPATH

Using pip

pip_ is the standard Python package manager. To install comp_chem_py with pip_:

pip install comp_chem_py

This will install the comp_chem_py package with all available dependencies as regular pip controlled packages.

Documentation

Please take a look at the code documentation for more details.

.. todo::
   #. Add tests. Maybe with doctest. They should also be included in the setup.py. See,
         https://python-packaging.readthedocs.io/en/latest/testing.html

   #. Consider making comp_chem_utils an external submodule.

   #. test ./setup.py script with pip.

   #. Find out how to deal with the dependency on MySQLdb package.

   #. Add the ebsel package into setup.py using the git repo as,
         dependency_links=['http://github.com/user/repo/tarball/master#egg=package-1.0']

Contact

• Pablo Baudin
• Scientific collatoborator at LCBC EPFL.
• [email protected]