{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# About ePSdata\n", "21/01/20" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Overview" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* [ePolyScat](http://www.chem.tamu.edu/rgroup/lucchese/ePolyScat.E3.manual/manual.html) (ePS) is an open-source tool for numerical computation of electron-molecule scattering & photoionization by Lucchese & coworkers. For more details try: \n", " \n", " * The [ePolyScat website and manual](http://www.chem.tamu.edu/rgroup/lucchese/ePolyScat.E3.manual/manual.html).\n", " * *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\n", " * *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\n", " \n", " " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* [ePSproc](https://epsproc.readthedocs.io) is an open-source tool for post-processing & visualisation of ePS results, aimed primarily at photoionization studies.\n", " \n", " * Ongoing documentation is on [Read the Docs](https://epsproc.readthedocs.io).\n", " * Source code is [available on Github](https://github.com/phockett/ePSproc).\n", " * For more background, see the software metapaper for the original release of ePSproc (Aug. 2016): *ePSproc: Post-processing suite for ePolyScat electron-molecule scattering calculations*, on [Authorea](https://www.authorea.com/users/71114/articles/122402/_show_article) or [arXiv 1611.04043](https://arxiv.org/abs/1611.04043).\n", " \n", " " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* ePSdata is an open-data/open-science collection of ePS + ePSproc results.\n", "\n", " * ePSdata collects ePS datasets, post-processed via ePSproc (Python) in [Jupyter notebooks](https://jupyter.org), for a full open-data/open-science transparent pipeline.\n", " * ePSdata is currently (Jan 2020) collecting existing calculations from 2010 - 2019, from the [femtolabs at NRC](http://femtolab.ca), with one notebook per ePS job.\n", " * In future, ePSdata pages will be automatically generated from ePS jobs (via the ePSman toolset, currently in development), for immediate dissemination to the research community.\n", " * Source notebooks are available on the [Github project pages](https://github.com/phockett/ePSdata/), and notebooks + datasets via [Zenodo repositories](https://about.zenodo.org) (one per dataset). Each notebook + dataset is given a Zenodo DOI for full traceability, and notebooks are versioned on Github.\n", " * Note: ePSdata may also be linked or mirrored on the existing [ePolyScat Collected Results OSF project](https://osf.io/psjxt/), but will effectively supercede those pages.\n", " * All results are released under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 (CC BY-NC-SA 4.0) license, and are part of our ongoing [Open Science initiative](http://femtolab.ca/?p=877)." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![ePSproc demo](https://epsproc.readthedocs.io/en/latest/_images/output_12_2.png)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![Zenodo_badge](https://about.zenodo.org/static/img/logos/zenodo-gradient-round.svg)\n", "![CC_badge](https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png)\n", "\n", "\"Zenodo\" \"Creative" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Demos" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "For an introduction to ePS and ePSproc, see:\n", "\n", "* Sample ePS jobs from the [ePolyScat website and manual](http://www.chem.tamu.edu/rgroup/lucchese/ePolyScat.E3.manual/manual.html)\n", "\n", "* Demos for ePSproc: \n", " * [Basic use demo](https://epsproc.readthedocs.io/en/latest/ePSproc_demo_Aug2019/ePSproc_demo_Aug2019.html)\n", " * [$\\beta_{lm}$ calculations demo](https://epsproc.readthedocs.io/en/latest/ePSproc_BLM_calc_demo_Sept2019_rst/ePSproc_BLM_calc_demo_Sept2019.html)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "(More demos coming soon.)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Workflow\n", "\n", "The general workflow for photoionization calculations plus post-processing is shown below. This pipeline involves a range of code suites, as shown in the main workflow; some additional details are also illustrated." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![ePS_workflow](_figs/ePSworkflow_170220.gv.png)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The basic ePSproc workflow (from the [original software metapaper]((https://www.authorea.com/users/71114/articles/122402/_show_article)) is shown below: essentially, the ePS output file is parsed for photoionization matrix elements, and ancillary data; the matrix elements are the used to calculate properties of interest, such as photoionziation cross-sections and MF-PADs. For ePSdata, this workflow is applied to each ePS dataset, with a Jupyter notebook as a template. The completed analysis & dataset is then uploaded to Zenodo, and HTML version to ePSdata." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![ePSproc workflow](https://www.authorea.com/users/71114/articles/122402/master/file/figures/ePSproc_workflow_fig_040816/ePSproc_workflow_fig_040816.png)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Citation & acknowledgements" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Each notebook & dataset has a DOI, see the [citations page](https://phockett.github.io/ePSdata/cite.html) for further details." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Motivation" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Scientific\n", "\n", "* Platform development for quantum metrology with photoelectrons; see, for example: \n", " * [Phase-sensitive Photoelectron Metrology (video, 2017)](https://vimeo.com/223603377) \n", " * [Quantum Metrology with Photoelectron (books, 2018)](http://femtolab.ca/?p=1030).\n", " * [Molecular Frame Reconstruction Using Time-Domain Photoionization Interferometry. Marceau et. al. (2017). Physical Review Letters, 119(8), 083401](https://doi.org/10.1103/PhysRevLett.119.083401)\n", "* Theory and method development.\n", "* Bridge-building and method unification between theory and experiment.\n", "* Lowering the barrier to entry for photoionization studies.\n", "* Sharing and disemination of computational results and data, which would not otherwise be subject to \"traditional\" publication, and just sit on a hard-drive.\n", "* General good scientific practice and open science..." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Platform development for quantum metrology with photoelectrons: figures below show existing and new platform schematics. In the former case, theory and experiment are treated separately, and compared at the level of observables; in the latter lower-level comparisons are possible and aid analysis.\n", "![Existing platform schema](_figs/photoionization_theory_expt_290120.gv.png)\n", "![Quantum metrology platform schema](_figs/QM_unified_schema_130220.gv.png)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "" ] }, { "cell_type": "markdown", "metadata": {}, "source": [] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Science policy/open science\n", "\n", "* All things open: open data, open science, open source software. (See further reading below, and also the [Open Science Initiative](http://femtolab.ca/?p=877)).\n", "* Reproducibility, and avoiding the reproducibility crises.\n", "* Transparency, and making full computational results stacks available. \n", "* Building a community resource.\n", "\n", "Some further reading on these topics, in no particular order:\n", "\n", "* [*Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research.* Stodden, V., & Miguez, S. (2014). Journal of Open Research Software, 2(1), e21](https://doi.org/10.5334/jors.ay)\n", "* [*Taking up TOP*. McNutt, M. (2016). Science, 352(6290)](http://science.sciencemag.org/content/352/6290/1147.full)\n", "* [*The State of Open Data Report*. (2016)](https://figshare.com/articles/The_State_of_Open_Data_Report/4036398)\n", "* [*Promoting an open research culture.* Nosek et. al. (2015). Science, 348(6242), 1422–1425.](https://doi.org/10.1126/science.aab2374)\n", "* [*Publish your computer code: it is good enough.* Barnes, N. (2010). Nature, 467(7317), 753.](https://doi.org/10.1038/467753a)\n", "* [*Community Recommendations for Sustainable Scientific Software.* Downs, R. R., Lenhardt, W. C., Robinson, E., Davis, E., & Weber, N. (2015). Journal of Open Research Software, 3(1).](https://doi.org/10.5334/jors.bt)\n", "\n", "For more general discussion, tools and further resources, see, for example: \n", "\n", "* [Science 2.0 (Wikipedia)](https://en.m.wikipedia.org/wiki/Science_2.0)\n", "* [Center for Open Science](https://cos.io/)\n", "* [Reproducible Research and Data Analysis module at Open Science MOOC](https://opensciencemooc.eu/modules/reproducible-research-and-data-analysis/) (includes many more tools, links and references, [many other modules are available too](https://opensciencemooc.eu)).\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Open" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Notes" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "- Web pages are auto-generated from source Jupyter notebooks: please [raise any issues on Github](https://github.com/phockett/ePSdata/issues/new/choose).\n", "- Figures may appear small due to HTML template constraints, but opening in a new window or downloading will provide the high-res source. (This will be fixed at some point in the future...)\n" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.7.4" } }, "nbformat": 4, "nbformat_minor": 4 }