Local Atomic Motif Isolator

Overview

This repo includes the LAM and LAMisolator classes, which allow for LAM isolation. The LAMplotter class contains some methods for computing histograms and plotting the density isosurfaces via the Mayavi API.

Dependencies

You will need to have numpy, scipy and mayavi installed. Personally, I used pythonxy for the aforementioned dependencies on Windows. If you're on Linux, I'll assume that you know how to apt-get or pip.

Additionally, you must install PeriodicCKDTree.

Usage

Build the local_atomic_motif.py file, to ensure that nothing crazy is going on. Depending on the permissions with which you run the script, you may want to manually add a build/ directory to the same location as the LAM Python files.

Next, run the local_atomic_motif_isolator.py, followed by the local_atomic_motif_plotter.py. Do not be surprised by long runtimes.

The LAMisolator and LAMplotter both include functions called full_compute(), which should work as-is.