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Introduction

gpxrdpy

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

Usage

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 found in the ugent pyiron branch.

Requirements

  • pyobjcryst - Python bindings to ObjCryst++, the Object-Oriented Crystallographic Library
    (see https://github.com/diffpy/pyobjcryst)
  • numpy - library for computing in python
  • scipy - library for scientific computing in python
  • matplotlib - library for plotting in python
  • h5py - library for storing data in python