CIF2Dist 0.2.0

CIF2Dist is a python application to calculate the number and distance of coordination spheres of atoms in a lattice based on a cif.

CIF2Dist

CIF2Dist is a command-line tool and python package for calculating interatomic distances from a CIF (crystallography information file). It is authored by Marco Gurbisz and Tom Förster.

Installation

To use CIF2Dist, you need

• Python 3.8 or later installed
• pip (Python's package installer)

For installation, you can either

1. clone the git repository and install the package locally:

git clone https://github.com/MGurbisz/CIF2Dist.git
cd CIF2Dist
pip install .

2. Or install using pip directly

pip install CIF2Dist

Then run from command line

CIF2Dist --help

If the CIF2Dist command is not found, you may need to add Python's Scripts Folder to your Path: For Windows, search for 'Environment Variables' and open 'Edit the system environment variables'. There open 'Environment Variables'. Under 'User Variables' find Path and click Edit. Select 'New' and add this:

%LOCALAPPDATA%\Packages\PythonSoftwareFoundation.Python.3.###\LocalCache\local-packages\Python3###\Scripts

Alternatively, you can run it using:

python -m cif2dist.cli --help

Input

Input a CIF using its path and filename, and specify a site with -s to calculate the distance to its neighbors. This specification can be the Wyckoff site (e. g. '4a') or Wyckoff letter (e. g. 'a'), the site's name (e. g. 'Y1'), or the element (e. g. 'Y') if it is unambiguous (i .e there is only one site for this element).

Arguments

The tool supports multiple Arguments

Help --help, -h

Displays the help site and exits

Version --version, -v

Displays the version number and exits

Center site --site, -s

Specifies center site for calculation. See Subsection 'Input'

Cutoff Distance --cutoff, -c

Specifies cutoff distance for the calculation. The default value is 10 Ångstrom.

Filter --filter, -f

Specifies the output filter. It accepts Wyckoff sites and letters, site labels and elements. The output will contain the specified site distances only.

Output

After running the code, you'll get an output file called 'summary.txt'. It contains the Site labels, the number of atoms on this site at the same distance and then the distance itself in Å all separated by a tab space character.