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

Project description

Documentation Status

A post-processing suite for ePolyScat calculations, and general tool for photoionzation 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 (2019 to date), and is now the main/preferred version.

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. For data platform and related experimental tools, see the Photoelectron Metrolgy toolkit.

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

Getting Started

To get started, see the demo Jupyter notebooks for example usage:

Installation (Python)

Basics:

  • From source: simply download from Github and use locally, or run pip install git+https://github.com/phockett/ePSproc.git.

  • From Pypi pip install ePSproc

See the extended installation notes for more details & options.

Python

Functionality:

  • Plot basic properties (cross-secions, anisotropy parameters) from ePS GetCro outputs.

  • Read raw photoionization matrix elements from ePS output files with dumpIdy segments.

  • Process matrix elements:

    • Plot matrix elements.

    • Calculate MF-PADs from the matrix elements.

    • Calculate MF, LF and AF $beta_{LM}$ from the matrix elements.

    • Plot $beta_{LM}$ & PADs.

  • Distirbution via PyPi (latest stable version) .

  • Docs on Read the Docs .

Source:

Full function documentation.

Matlab (legacy code)

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.

For more details see

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.

Resources

An ongoing repository of ePS results can be found at ePSdata (as of Jan 2020, this replaces the previous repository 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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