GASP is a genetic algorithm for structure and phase prediction written in Python and interfaced to GULP, LAMMPS and VASP. It can search for the structures of clusters, 2D materials, wires, and bulk materials and do both fixed-composition and phase diagram searches.

Getting GASP

It is easiest to install GASP and all its dependencies into a conda environment. GASP makes extensive use of pymatgen, an open source Python library for materials analysis, and these instructions have been adapted from pymatgen. More details on installing pymatgen can be found at http://pymatgen.org/installation.html.

If pymatgen is already installed, steps 1-3 may be skipped.

1. Install conda

Download and install the version of conda for your operating system from http://conda.pydata.org/miniconda.html. Although GASP is compatible with both Python 2.7 and 3.6, pymatgen recommends using Python 3.6.

For Windows, make sure you have the Miniconda3 installer, and simply double-click the .exe file.

For Mac or Linux, run the bash script:

# if Mac
bash Miniconda3-latest-MacOSX-x86_64.sh

# if Linux
bash Miniconda3-latest-Linux-x86_64.sh

The installer will ask you to approve the terms of the license and then tell you where the installation will be located. The default location is fine, so press Enter. Finally, the installer will ask if you would like it to add the install location to your PATH by prepending a line to your .bash_profile (for Mac) or .bashrc (for Linux) file. Type 'yes' and press Enter.

After completing the installation, create a new terminal in order for the environment variables added by conda to be loaded.

2. Create a conda environment

To create a new conda environment named 'my_gasp', type:

conda create --name my_gasp python=3.6

When conda asks you:

proceed ([y]/n)?

Type 'y' and press Enter.

Now activate the environment so that packages can be installed into it:

# if Mac or Linux
source activate my_gasp

# if Windows
activate my_gasp

3. Install pymatgen and its dependencies

pymatgen recommends using the gcc compiler. To do so, type:

export CC=gcc

Install numpy, scipy, matplotlib and pymatgen with pip:

pip install numpy
pip install scipy
pip install matplotlib
pip install pymatgen

When searching for clusters and wires, GASP uses features of pymatgen that depend on openbabel. So if you plan to use GASP to search for clusters or wires, install openbabel in your conda environment:

conda install -c openbabel openbabel

For Mac, an additional step is needed in order to use the scripts included with GASP for making plots. These scripts depend on the matplotlib library, which requires a framework build of Python to run properly on Mac OS X. However, a regular Python build comes with conda by default. To install a framework build in your conda environment, type:

conda install python.app

See the 'Visualizing output' section of the the usage file for more information on making plots.

4. Install GASP-python

Clone the repository from github:

git clone https://github.com/henniggroup/GASP-python.git

Move into the 'GASP-python' directory and run the setup.py script:

cd GASP-python
python setup.py develop

Using GASP

See the usage file.

License

GASP-python is released under the MIT License:

Copyright (c) 2016-2017 Henniggroup Cornell/University of Florida

Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including without limitation the rights to
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
the Software, and to permit persons to whom the Software is furnished to do so,
subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Contributing

We try to follow the PEP8 coding style used by pymatgen: http://pymatgen.org/contributing.html#coding-guidelines.

Authors

Benjamin Revard

William W. Tipton

Richard G. Hennig

How to cite

DOI: 10.5281/zenodo.2554076

BibTex entry for the Github repository:

@misc{GASP-Python,
  title        = {Genetic algorithm for structure and phase prediction},
  author       = {B. C. Revard, W. W. Tipton, and R. G. Hennig},
  year         = 2018,
  publisher    = {GitHub},
  journal      = {GitHub repository},
  howpublished = {\url{https://github.com/henniggroup/GASP-python}},
  url          = {https://github.com/henniggroup/GASP-python},
  doi          = {10.5281/zenodo.2554076}
}