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https://github.com/barbagroup/bempp_exafmm_paper

Manuscript repository for our research paper, including reproducibility packages for all results, and latex source files.
https://github.com/barbagroup/bempp_exafmm_paper

bem biophysics electrostatics fmm

Last synced: about 2 months ago
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Manuscript repository for our research paper, including reproducibility packages for all results, and latex source files.

Host: GitHub
URL: https://github.com/barbagroup/bempp_exafmm_paper
Owner: barbagroup
Created: 2020-11-17T15:10:00.000Z (about 4 years ago)
Default Branch: master
Last Pushed: 2023-08-20T21:23:25.000Z (over 1 year ago)
Last Synced: 2024-03-26T15:40:21.736Z (9 months ago)
Topics: bem, biophysics, electrostatics, fmm
Language: Jupyter Notebook
Homepage:
Size: 15.4 MB
Stars: 6
Watchers: 6
Forks: 2
Open Issues: 14
Metadata Files:
- Readme: README.md

Awesome Lists containing this project

README

        # High-productivity, high-performance workflow for virus-scale electrostatic simulations with Bempp-Exafmm

**Tingyu Wang, Christopher D. Cooper, Timo Betcke, Lorena A. Barba**

Manuscript repository, including all source files for the text and reproducibility packages for all figures.

Preprint on [arxiv:2103.01048](https://arxiv.org/abs/2103.01048)

- Submitted: 20 March 2021; first revision request: 26 April 2021 (4 peer-review reports provided)

  - submitted version is tagged release [v2.0](https://github.com/barbagroup/bempp_exafmm_paper/releases/tag/v2.0) 

- Revision submitted: 26 May 2021; request for information from the editors: 8 July 2021.

  - resubmission version is tagged release [v2.1](https://github.com/barbagroup/bempp_exafmm_paper/releases/tag/v2.1) 

- Reply to the editor first sent on 12 July.

  - 31 July: EiC writes that after discussion with the editorial team, they would like to send our replies to Reviewers 1 and 3, and requests these in PDF. Responses in HackMD for [Reviewer 1](https://hackmd.io/DG_f3UiMSsaAHukBp1SmVQ) and [Reviewer 3](https://hackmd.io/e--_niKFRtWDqKBdGncy5g). Sent to editor 2 August.

- New review comments provided 21 September, with request to respond. See issue [#15] (https://github.com/barbagroup/bempp_exafmm_paper/issues/15) for editorial letter. Issues 16,17,18 address reviewer comments.

- Email to EiC on Oct. 15, 2021: see [comment](https://github.com/barbagroup/bempp_exafmm_paper/issues/15#issuecomment-1364748153) on issue #15.

- Revision submitted **Dec. 7, 2021**

- First rejection decision: February 15, 2022 (see issue [#19](https://github.com/barbagroup/bempp_exafmm_paper/issues/19))

- Appeal, with new evidence, rebuttal and revision: Sep 5, 2022

- Second rejection decision: December 5, 2022

## Reproducibility package archives

See the [README in the repro-pack folder](https://github.com/barbagroup/bempp_exafmm_paper/tree/master/repro-pack) for instructions.

- Wang, Tingyu, Cooper, Christopher D., Betcke, Timo, Barba, Lorena A., High-productivity, high-performance workflow for virus-scale electrostatic simulations with Bempp-Exafmm (manuscript and repro-pack), (2021). [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4815402.svg)](https://doi.org/10.5281/zenodo.4815402)

- Wang, Tingyu, Cooper, Christopher D., Betcke, Timo, Barba, Lorena A., High-productivity, high-performance workflow for virus-scale electrostatic simulations with Bempp-Exafmm (meshes and pqr files), (2021). [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4568768.svg)](https://doi.org/10.5281/zenodo.4568768)

## Software

- [Exafmm-t](https://github.com/exafmm/exafmm-t) (BSD 3-Clause License)

   - [Documentation](https://exafmm.github.io/exafmm-t/)

   - _Citation:_ Wang et al., (2021). ExaFMM: a high-performance fast multipole method library with C++ and Python interfaces. Journal of Open Source Software, 6(61), 3145, https://doi.org/10.21105/joss.03145

- [Bempp-cl](https://github.com/bempp/bempp-cl) (MIT License)

   - [Installing Bempp](http://bempp.com/installation.html)

   - _Citation:_ Betcke et al., (2021). Bempp-cl: A fast Python based just-in-time compiling boundary element library.. Journal of Open Source Software, 6(59), 2879, https://doi.org/10.21105/joss.02879

### LICENSE

**Not all content in this repository is open source.** The Python code for creating the figures is shared under a BSD3 License. The written content in any Jupyter Notebooks is shared under a Creative Commons Attribution (CC-BY) license. 

But please note that _the manuscript text is not open source;_ we reserve rights to the article content, which will be submitted for publication in a journal. Only fair use applies in this case.