usnistgov/PACCS

paccs: Python Analysis of Colloidal Crystal Structures.

This is paccs, a colloidal crystal structure analysis, generation, optimization, and visualization library written in Python. It supports stochastic optimization of periodic multicomponent systems in two and three dimensions, as well as the generation of candidate structures in two dimensions using wallpaper groups. A module is included to permit simple parallelization of large generation and optimization jobs, as well as the collection and filtering of the output of these jobs into a single database.

Getting started

Once you've obtained a copy of the repository for yourself, take note that:

• As well as an installation of Python 3, paccs requires the presence of
  some additional packages listed in the requirements.txt file. We recommend
  installing these dependencies by obtaining a distribution of
  Miniconda and using
  conda install ...; note that python-constraint is unavailable through conda and must be installed with pip.

    $ cat requirements.txt
        cython
        mayavi
        numpy
        plotly
        python-constraint
        scikit-learn
        scipy
        sphinx
        sphinx_rtd_theme

• It is recommended that you use the latest version of Python 3 as well as the latest versions of all of the requirements. You can leave out one or both of mayavi and plotly if you don't want to use the visualization frontends enabled when they are present.

• Building the paccs package can be accomplished by executing the shell script install in the package root directory. With no options, the package will be built and tested automatically. A few options are available to skip parts of the build or control build options for testing purposes; see install -h for a list.

    $ ./install -h
        Accepted options:
            -c  Skip compilation
            -d  Skip documentation generation
            -u  Skip unit testing
            -p  Compile with Cython profiling information

• The compiled modules will be placed in the lib directory. This is the directory you should add to your PYTHONPATH to use paccs.

To start working, you can either import paccs or from paccs import * once the libraries are in your path, or use the script bin/paccssh. This script will find and load paccs and then start a Python interactive session (or an IPython interactive session if IPython is available).

Documentation

The build process automatically creates HTML documentation inside docs/build/html. Information on the paccs API, as well as how to use paccs to accomplish various common tasks, is available here.

Other information

Please see the LICENSE file for package license information.