Larixite: Crystal structures for X-ray absorption spectroscopy

Larixite is a Python package to help use crystallographic data to build clusters of atoms to generate inputs for X-ray absorption spectroscopy and other scientific disciplines that use non-crystalline clusters of atoms.

This project includes:

  1. an sqlite3 database of structures from the American Mineralogical Crystal Structure Database (AMCSD).

  2. Python code to convert structures from the AMCSD database, other CIF files, or XYZ coordinates into atomic clusters for XAS calculations with FEFF, FDMNES, and other XAS calculation tools.

  3. A basic web application to guide those conversions. See Larixite WebApp.

Installation

Either install from PyPI with:

> pip install larixite

or download and unpack this code and install with:

> pip install .

Status

Larixite has been in rapid development, but is also a spin-off from code that has been in xraylarch for many years. That is, while many parts of the code are moving rapidly, much of the code is reasonably stable.

Web App

The Larixite WebApp can be run locally for debugging or for local deployment. To do this, install the extra wed dependencies (essentially only Flask is needed) with:

> pip install ".[web]"

and run the script “run_local.py” with:

> python run_local.py

will launch a local web server with the app running at http://127.0.0.1:11564/