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Post-processing suite for ePolyScat calculations (Matlab & Python).

Project description

Post-processing suite for ePolyScat calculations.

ePSproc scripts are designed for photoionization studies. The scripts were originally written for Matlab (2009 - 2016); a Python version is currently under (heavy) development (Aug. 2019), and will be the main version in future.

Source code is available on Github.

Ongoing documentation is on Read the Docs.

For more background, and details on the Matlab version, see the software metapaper for ePSproc (Aug. 2016), ePSproc: Post-processing suite for ePolyScat electron-molecule scattering calculations, on Authorea or arXiv 1611.04043.

https://epsproc.readthedocs.io/en/latest/_images/output_12_2.png

Installation

From source: simply download from Github. See specific version notes below for more details on the source code.

Python:

$ pip install ePSproc

Main requirements are Xarray (>= 0.12.2), and Moble’s spherical functions (quaternion based) (tested with v2019.7.12.23.25.11). See the individual package docs for full instructions - one option is via conda-forge: (Update Sept. 2019 - Xarray v0.13.0 is now on the main Anaconda channel.)

.. $ conda install -c conda-forge xarray=0.12.3
$ conda install -c conda-forge spherical_functions

The usual SciPy stack is also used (numpy, matplotlib etc.) - see requirements.txt for full list - plus some optional packages for additional functionality.

Python

Functionality:

  • Read raw photoionization matrix elements from ePS output files with “dumpIdy” segments
  • Calculate MF-PADs from the matrix elements (ePSproc_MFPAD.m, see also ePSproc_NO2_MFPADs_demo.m)
  • Plot MF-PADs
  • Calculate MF-$beta_{LM}$ parameters
  • Distirbution via PyPi (latest stable version) .`
  • Under development: additional functionality and distribution via PyPi.

See the demo Jupyter notebooks for example usage:

Source:

Full function documentation.

Matlab

Functionality:

  • Read raw photoionization matrix elements from ePS output files with “dumpIdy” segments
  • Calculate MF-PADs from the matrix elements (ePSproc_MFPAD.m, see also ePSproc_NO2_MFPADs_demo.m)
  • Plot MF-PADs
  • Plot X-sects
  • (Beta testing): Calculate MF-BLMs from matrix elements, see ePSproc_MFBLM.m
  • (Under development): Calculate AF-BLMs from matrix elements.

Source:

  • /matlab: stable matlab code (as per release v1.0.1).
    • a set of functions for processing (ePSproc*.m files)
    • a script showing demo calculations, ePSproc_NO2_MFPADs_demo.m
  • /docs/additional contains:
    • the benchmark results from these calculations, ePSproc_NO2_testing_summary_250915.pdf
    • additional notes on ePS photoionization matrix elements, ePSproc_scattering_theory_ePS_notes_011015.pdf.

See ePSproc: Post-processing suite for ePolyScat electron-molecule scattering calculations for more details.

Resources

An ongoing repository of ePS results can be found on OSF.

ePolyScat

For details about ePolyScat (ePS), a tool for computation of electron-molecule scattering, see:

  • ePS website & manual, maintained by R.R. Lucchese.
  • Calculation of low-energy elastic cross sections for electron-CF4 scattering, F. A. Gianturco, R. R. Lucchese, and N. Sanna, J. Chem. Phys. 100, 6464 (1994), http://dx.doi.org/10.1063/1.467237
  • Cross section and asymmetry parameter calculation for sulfur 1s photoionization of SF6, A. P. P. Natalense and R. R. Lucchese, J. Chem. Phys. 111, 5344 (1999), http://dx.doi.org/10.1063/1.479794

Future aims

  • Add capabilities, including more general processing, and for other phenomena (e.g. recombination matrix elements for high-harmonic generation, aligned-frame calculations)
  • Tidy and streamline code (yep)
  • Extend & update notes and benchmark calculations
  • Port to non-commercial run-time engines, e.g. python

Citation

If you make use of ePSproc in your research, please cite it.

Cite the software directly via either Github or Figshare repositories for the software (note same DOI for both):

@misc{ePSprocGithub,
  title={ePSproc: Post-processing for ePolyScat},
  url={https://github.com/phockett/ePSproc},
  DOI={10.6084/m9.figshare.3545639},
  publisher={Github},
  howpublished = {\url{https://github.com/phockett/ePSproc}},
  author={Hockett, Paul},
  year={2016},
  commit = {30158eb3fbba41d0a4c3a973744f28b7187e6ee2}
}

@misc{ePSprocFigshare,
  title={ePSproc: Post-processing for ePolyScat},
  url={https://figshare.com/articles/ePSproc_Post-processing_for_ePolyScat_v1_0_0_/3545639/4},
  DOI={10.6084/m9.figshare.3545639},
  publisher={Figshare},
  author={Hockett, Paul},
  year={2016}
}

… or the software paper (Authorea/arXiv):

@article{ePSprocPaper,
  title={ePSproc: Post-processing for ePolyScat electron-molecule scattering calculations},
  url={https://www.authorea.com/users/71114/articles/122402-epsproc-post-processing-suite-for-epolyscat-electron-molecule-scattering-calculations},
  DOI={10.22541/au.156754490.06103020},
  journal = {Authorea/arXiv e-prints},
  publisher={Authorea/arXiv},
  author={Hockett, Paul},
  year={2016},
  archivePrefix = {arXiv},
  eprint = {1611.04043},
  primaryClass = {physics.comp-ph},
  eid = {arXiv:1611.04043},
  pages = {arXiv:1611.04043}
}

(Citation styles for software from StackExchange.)

Acknowledgements

Special thanks to R.R. Lucchese and coworkers for ePolyScat.

Thanks to the multiple collaborators and co-authors who encouraged and suggested the cavilier use of ePS “out of the box”, for many different problems incorporating electron scattering and photoionization. This spirit of “shoot first, ask questions later” indeed raised many questions which, eventually, necessitated proper use of ePS and careful post-processing of the results, and sharpened related foundational expertise - efforts well worth making.

Thanks, finally, and of course, to those supporting scientific software development and infrastructure (and making it easy!), including Github, Read the Docs, Pypi, SciPy etc. etc. In particular the python version of this project makes use of Xarray, and Moble’s spherical functions (& quaternion).

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