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https://github.com/balaranjan/coord_env_analysis

https://github.com/balaranjan/coord_env_analysis

Science Score: 26.0%

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Repository

Basic Info
  • Host: GitHub
  • Owner: balaranjan
  • Language: Python
  • Default Branch: main
  • Size: 1.13 MB
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  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
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Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme

README.md

This repository contains scripts to find coordination environments of interest. This repository is under development. The following scripts are available now.

  1. plotcappedprisms/ - find capped-prism environments in bi-layered compounds.

    Install the required libraries listed in requirements.txt and then type python overlay_plot_capped_prisms.py path prism_nums to get started.
    Type python overlay_plot_capped_prisms.py -h to get an overview of inputs and options.
    The path can be either a single .cif file or a directory containing multiple cif files. sgs.csv contains the Hermann–Mauguin notation and their latex formatting. Extend this list as required. colors.csv contains the assigned color-group for each element. Extend this list as required.

``` $:~/16plotcustom$ python overlayplotcappedprisms.py -h usage: overlayplotcappedprisms.py [-h] [-p] [-f] [-m] [-w] [-s] [-i] [-l] path

Script to plot capped-prisms in bi-layered compounds.

positional arguments: path path to CIF or folder containing multiple CIFs

options: -h, --help show this help message and exit -p , --prisms set the numbers for prisms (3 for trigonal, 4 for square, 5 for pentagonal, etc.) eg. 3,4 (default) -f , --fixlength fix the length of shortest side -m , --markersize set marker size eg. 1 -w , --line_width set line width eg. 3.0 -s , --sites select sites to plot eg. Si1 Al1 -i, --invert invert the layers -l, --label label the sites

Output images will be (over)written inside images folder in the current directory. CIFs encountering errors will be written to errors.txt ```
2. innerCN/ finds the inner coordination numbers using the d/dmin method. This code can run in parallel and the output containing filename, center atom, its Wyckoff, neghbor formula will be saved as .csv file.

3. linear_groups - finds the linear M-M-M units made of same element.

Owner

  • Name: Balaranjan Selvaratnam
  • Login: balaranjan
  • Kind: user

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Dependencies

plot_capped_prisms/requirements.txt pypi
  • cifkit ==0.0.1
  • matplotlib ==3.10.1
  • numpy ==2.2.4
  • pandas ==2.2.3
  • scipy ==1.15.2