1. Calculating minimum atomic distances in a set of structures
This bash script calculates the minimum atomic distance (Å) for each structure in a given set by generating its radial distribution function using Atomsk and finding the first non-zero element. The results are listed in the ‚output_all.txt‘ file, with the first column containing the structure name and the second column showing the minimum atomic distance.
Prerequisities
- Bash
- Atomsk
- Python 3.x
Usage
The following is a bash script, run it with:
sudo chmod +x minimum_distance.sh
./minimum_distance.sh
Place the script into the folder containing the structures and run it. In the same folder, the output file ‚output_all.txt‘ will be created.
Example of content of the output file 'output_all.txt', listing the name of the characterized structure and its corresponding minimum atomic distance in Å:
