XHARPy (X-ray diffraction data Hirshfeld Atom Refinement in Python) is a pure Python library that enables refinement with custom atomic form factors from various sources.
This is the first refinement library to implement the calculation of atomic form factors from periodic PAW-DFT calculations. Additionally, there are experimental implementations of atomic form factor determinations with Quantum Espresso, NoSpherA2/Orca and the possibility to refine against .tsc files. Independent atom model for comparison and debugging is also available.
The library has been written with extensibility in mind. You can look at the f0j_sources folder for examples how to write a new atomic form factor source. If you want to develop without touching the library itself you can have a look at the custom_function_source, This source exposes the functions, that are called during the refinement.
Refinement itself relies heavily on JAX for the automatic generation of gradients. This means that new features only have to be implemented in the loss function. No explicit gradients are needed.
If you have used the library in your research, please cite the paper where it was originally published:
Ruth, P.N., Herbst-Irmer, R. & Stalke, D. (2022). IUCrJ, 9, 286-297. https://doi.org/10.1107/S2052252522001385
Creation of this library was only possible due the generous support of the Research Training Group BENCh at the University of Göttingen, which is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 389479699/GRK245
An online version of the documentation is available at:
https://xharpy.readthedocs.org
With the sphinx package and the sphinx-rtd-theme installed you can compile the
documentation using make html in the doc directory.
- The following packages in the following versions were used for development
- For atomic form factor calculation in GPAW
- gpaw = 21.6.0
- For atomic form factor calculation in Quantum Espresso (experimental)
- qe = 7.0
- For difference electron density calculation
- cctbx = 2021.11
This does not mean, that the library will not work with other versions. I tried not to use the newest of features, but I do not have the means/time to test how much older or newer the versions can be before things start to break.