Atomic Environment Visualization using Pythia (aevispy)

This package finds and colors different coordination environments in a given structure. The common use case is the outputs from MD simulations, where there are different coordination environments present in the output. This uses descriptors from the Pythia package (https://github.com/glotzerlab/pythia/tree/master) and uses Gaussian Mixture Model for unsupervised classification of the environments. The input file number of expected environments (used to specify clusters) are required arguments.

Demo

YouTube

How to install aevispy locally

cd into the project directory:

bash cd aevispy

Create and activate a new conda environment:

bash conda create -n aevispy_env python=3.8 conda activate aevispy_env

Method 1: Install your package with dependencies sourced from pip

It's simple. The only command required is the following:

bash pip install .

The above command will automatically install the dependencies listed in requirements/pip.txt.

Verify your package has been installed

Verify the installation:

bash pip list

Run

To get started, type

``` aevispy -h

usage: aevispy [-h] [-d [...]] [-s [...]] [-f] input_filename envs [envs ...]

Command line tool for AEVisPy

The following descriptor options are available.
Default is 11 (all descriptors)

1 .  amean
2 .  bispectrum_sphs
3 .  neighborhood_angle_sorted
4 .  neighborhood_distance_sorted
5 .  neighborhood_range_angle_singvals
6 .  neighborhood_range_distance_singvals
7 .  normalized_radial_distance
8 .  spherical_harmonics_abs_neighbor_average
9 .  steinhardt_q
10.  voronoi_angle_histogram
11.  all of the above

positional arguments: input_filename Path to the input file envs Number of environments. e.g. 4 or 4 6

optional arguments: -h, --help show this help message and exit -d [ ...], --desc [ ...] Descriptors. e.g. 4 or 4 6 -s [ ...], --supercell [ ...] Multipliers for making super cell. e.g. 2 2 2 or 2 -f , --frame Frame number to get from gsd file. ```

To color your own files, run

aevispy my_structure.cif number_of_envs_expected ...optional options

e.g.

aevispy CrFe.cif 4 -s 3 -d 8 9

Example Output

After running the command, you will get an output similar to the following: