CIF2Dist 0.2.2

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 3.9 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

Use CIF2Dist as a package

To use CIF2Dist inside a virtual environment (venv) use the following inside your project directory:

python -m venv venv
venv\Scripts\activate # On Windows
venv/bin/activate # On macOS, GNU Linux
python -m pip install cif2dist
python -m myscript

Inside your script make sure to use:

import cif2dist
from cif2dist.core import compute_distances

compute_distances is the main funtion of this package and is defined as:

def compute_distances(cif_path, user_site: str, cutoff_dist: float, filter: str) -> list[tuple[str, int, float]]:

Input

Input a CIF using its path and filename, and specify a site with -s to calculate the distance to its neighbors. For the stom site input you can use the atom label (e. g. "Y1") directly. Otherwise stating the Wyckoff site (e. g. '4a') or Wyckoff letter (e. g. 'a') or the element (e. g. 'Y') can be done, if it's unambiguous (i. e. there is only one match for the input and a atom label).

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.

No Version Check --no-version-check

Disables automatic version check.

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.