"Atomic democracy" for site analysis of surfaces and bulks with known lattice structure(s).
Built on sitator, which provides a general framework for site analysis.
surfator depends on sitator.
(sitator's optional dependencies are not required.)
Once sitator is installed, surfator is installed like any other Python package:
$ git clone https://github.com/mir-group/surfator.git
$ cd surfator/
$ pip install .Please see our preprint for a full description of the atomic democracy algorithm (Methods -> Clamping):
Evolution of Metastable Structures in Bimetallic Catalysts from Microscopy and Machine-Learning Molecular Dynamics
Jin Soo Lim, Jonathan Vandermause, Matthijs A. van Spronsen, Albert Musaelian, Christopher R. O’Connor, Tobias Egle, Yu Xie, Lixin Sun, Nicola Molinari, Jacob Florian, Kaining Duanmu, Robert J. Madix, Philippe Sautet, Cynthia M. Friend, Boris Kozinsky
Documentation of parameters can be found in docstrings in the source.
This software is made available under the MIT License. See LICENSE for details.