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

• Submitted: 20 March 2021; first revision request: 26 April 2021 (4 peer-review reports provided)
  • submitted version is tagged release v2.0
• Revision submitted: 26 May 2021; request for information from the editors: 8 July 2021.
  • resubmission version is tagged release 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 and Reviewer 3. Sent to editor 2 August.
• New review comments provided 21 September, with request to respond. See issue [#15] (#15) for editorial letter. Issues 16,17,18 address reviewer comments.
• Email to EiC on Oct. 15, 2021: see comment on issue #15.
• Revision submitted Dec. 7, 2021
• First rejection decision: February 15, 2022 (see issue #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 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).

• 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).

Software

• Exafmm-t (BSD 3-Clause License)
  • Documentation
  • 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 (MIT License)
  • Installing Bempp
  • 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.