fa\ :sup:3\ ps

fa\ :sup:3\ ps - Fully automated adsorption analysis in porous solids.

Automated high throughput structure adsorption analysis and library of python code for further customising simulations.

This code was written by Tom Daff as a member of the Woo Lab (http://titan.chem.uottawa.ca) between 2010 and 2015. Since then the development has continued in the Lab, so please contact someone there for more information as this version will lack any updates since then.

Although the key Monte Carlo code must also be obtained from the Woo Lab, this code contains interfaces to several codes (VASP, SIESTA, GULP, GROMACS, CIF files, ...), integration with batch queue systems, analysis methods for porous solids that can easily be used on their own or transplanted into someone else's code.

The code is unfortunately not a complete showcase of best development practices (i.e. not pip install compliant, thoroughly tested, or fully modularised, ...), but there is a faps2.0 branch that shows the what the future could have been if time was available in unlimited quantities!

Documentation

Documentation is available online at: https://faps.readthedocs.io

Complete documentation is included in the docs directory and must be built with sphinx before use. The documentation requires the sphinxcontrib.bibtex and numpydoc extensions to compile successfully (pip install sphinxcontrib-bibtex --user and pip install numpydoc --user will install these for the current user). Any missing faps dependencies may also result in missing parts of the API documentation.

Running the command make html will generate a _build directory that contains a file index.html which can be viewed in any web browser.

If this has been installed on your machine, the documentation may be available with the commands faps-doc or faps-man.

Installation

Faps requires Python 2.7 or 3.3+. Some older versions were compatible with Python 2.4, but support for ancient Pythons has now been dropped.

Obtain a copy of the package, put it somewhere and make a link to the faps.py file in your $PATH. Edit 'site.ini' in the installation directory to customize all simulations for the machine you will be running on (an example file is included).

For the web interface, you can also create a link to the file web/fapweb.py.

Some features require third party modules to function correctly. Most optional:

• numpy : required for most numerical operations
• sqlalchemy : (optional) reading and writing to the fapswitch database format
• scipy : (optional) required for binding site location
• flask : (optional) only needed for the web interface, with either one of gevent or tornado.

Running

Simulations require a structure. Executing the script in the working directory of the structure will try to automatically run all steps for a complete analysis.

Disclaimer

This software was designed for our own research purposes and we make no claims about the suitability for any other purpose.

See the license (BSD 3-clause) for further information.