README.md

Python wrapper for PXRD pattern calculation based on pyobjcryst. There are four main usages:

• calculate PXRD pattern based on cif file - calc
• compare two PXRD patterns based on .tsv files - comp
• fit a background profile - background
• average PXRD pattern over the course of a trajectory (.h5) - average

Each of these modes can be called using the main script, for which a specific --help has been implemented.
Usage:

gpxrd.py mode [<options>]

Warning: the average mode is deprecated in favor of the included gpxrd_average.sh script, as the current backend suffers from some kind of memory error.
Usage:

gpxrd_average.sh file.h5 nr_snapshots

The default values for the run_up_time and exp_filename should be altered within this bash script before execution.

A version of gpxrdpy is also implemented in pyiron at https://github.com/SanderBorgmans/pyiron/tree/hpc_ugent_2020. An example notebook, created as supporting information for this paper, can be found in the notebooks folder. In this notebook, static and dynamic simulations are performed, and provided as input to the gpxrdpy module of pyiron.

How to cite

[1] S. Borgmans, S.M.J. Rogge, J.S. De Vos, C.V. Stevens, P. Van Der Voort, V. Van Speybroeck. Quantifying the Likelihood of Structural Models through a Dynamically Enhanced Powder X-Ray Diffraction Protocol. Angew. Chem. Int. Ed., 60, 16 (2021). https://doi.org/10.1002/anie.202017153

Requirements

• pyobjcryst - Python bindings to ObjCryst++, the Object-Oriented Crystallographic Library (see https://github.com/diffpy/pyobjcryst)
• numpy - library for scientific computing in python
• scipy - library for scientific computing in python
• molmod - collection of molecular modelling tools for python (https://github.com/molmod/molmod)

Additional installation instructions can be found in the documentation.