{"id":18378016,"url":"https://github.com/barbagroup/bempp_exafmm_paper","last_synced_at":"2025-04-06T21:32:02.003Z","repository":{"id":53512231,"uuid":"313656574","full_name":"barbagroup/bempp_exafmm_paper","owner":"barbagroup","description":"Manuscript repository for our research paper, including reproducibility packages for all results, and latex source files.","archived":false,"fork":false,"pushed_at":"2023-08-20T21:23:25.000Z","size":16172,"stargazers_count":6,"open_issues_count":14,"forks_count":2,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-03-22T07:22:54.698Z","etag":null,"topics":["bem","biophysics","electrostatics","fmm"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/barbagroup.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-11-17T15:10:00.000Z","updated_at":"2023-10-31T12:39:30.000Z","dependencies_parsed_at":"2024-11-06T00:31:45.953Z","dependency_job_id":"ba4edd7b-7611-4603-9580-202857ff79f2","html_url":"https://github.com/barbagroup/bempp_exafmm_paper","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/barbagroup%2Fbempp_exafmm_paper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/barbagroup%2Fbempp_exafmm_paper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/barbagroup%2Fbempp_exafmm_paper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/barbagroup%2Fbempp_exafmm_paper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/barbagroup","download_url":"https://codeload.github.com/barbagroup/bempp_exafmm_paper/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247555505,"owners_count":20957780,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bem","biophysics","electrostatics","fmm"],"created_at":"2024-11-06T00:30:12.389Z","updated_at":"2025-04-06T21:32:01.144Z","avatar_url":"https://github.com/barbagroup.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# High-productivity, high-performance workflow for virus-scale electrostatic simulations with Bempp-Exafmm\n\n**Tingyu Wang, Christopher D. Cooper, Timo Betcke, Lorena A. Barba**\n\nManuscript repository, including all source files for the text and reproducibility packages for all figures.\n\nPreprint on [arxiv:2103.01048](https://arxiv.org/abs/2103.01048)\n\n- Submitted: 20 March 2021; first revision request: 26 April 2021 (4 peer-review reports provided)\n  - submitted version is tagged release [v2.0](https://github.com/barbagroup/bempp_exafmm_paper/releases/tag/v2.0) \n- Revision submitted: 26 May 2021; request for information from the editors: 8 July 2021.\n  - resubmission version is tagged release [v2.1](https://github.com/barbagroup/bempp_exafmm_paper/releases/tag/v2.1) \n- Reply to the editor first sent on 12 July.\n  - 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.\n- 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.\n- Email to EiC on Oct. 15, 2021: see [comment](https://github.com/barbagroup/bempp_exafmm_paper/issues/15#issuecomment-1364748153) on issue #15.\n- Revision submitted **Dec. 7, 2021**\n- First rejection decision: February 15, 2022 (see issue [#19](https://github.com/barbagroup/bempp_exafmm_paper/issues/19))\n- Appeal, with new evidence, rebuttal and revision: Sep 5, 2022\n- Second rejection decision: December 5, 2022\n\n\n## Reproducibility package archives\n\nSee the [README in the repro-pack folder](https://github.com/barbagroup/bempp_exafmm_paper/tree/master/repro-pack) for instructions.\n\n- 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)\n\n- 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)\n\n## Software\n\n- [Exafmm-t](https://github.com/exafmm/exafmm-t) (BSD 3-Clause License)\n   - [Documentation](https://exafmm.github.io/exafmm-t/)\n   - _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\n- [Bempp-cl](https://github.com/bempp/bempp-cl) (MIT License)\n   - [Installing Bempp](http://bempp.com/installation.html)\n   - _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\n\n### LICENSE\n**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. \nBut 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.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbarbagroup%2Fbempp_exafmm_paper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbarbagroup%2Fbempp_exafmm_paper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbarbagroup%2Fbempp_exafmm_paper/lists"}