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added LD potential and wrote html-style doc #1666

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merged 6 commits into from Sep 19, 2019

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commented Sep 9, 2019

Summary

New manybody mean-field potential suitable for capturing manybody effects in bottom-up CG models of liquids (and possibly peptides too). Re-submitting the PR after completing cosmetic changes and adding html style documentation per previous PR #1658

Author(s)
Tanmoy Sanyal
Chemical Engineering, UC Santa Barbara
currently at Bioengineering, UC San Francisco
email: tanmoy dot 7989 at gmail.com

David Rosenberger
Computational Physical Chemistry, TU Darmstadt
email: rosenberger at cpc.tu-darmstadt.de

Prof. M. Scott Shell
Chemical Engineering, UC Santa Barbara
email: shell at engineering.ucsb.edu

Licensing

By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).

Backward Compatibility

Backwards compatible (tested upto 15May2015 version)

Implementation Notes

The code draws heavily from the pair_eam styles. For further information please read the manual pdf. Two example systems have been provided and tested in both serial and mpi modes.

Post Submission Checklist

Please check the fields below as they are completed after the pull request has been submitted. Delete lines that don't apply

  • The feature or features in this pull request is complete
  • Licensing information is complete
  • Corresponding author information is complete
  • The source code follows the LAMMPS formatting guidelines
  • Suitable new documentation files and/or updates to the existing docs are included
  • The added/updated documentation is integrated and tested with the documentation build system
  • The feature has been verified to work with the conventional build system
  • The feature has been verified to work with the CMake based build system
  • A package specific README file has been included or updated
  • One or more example input decks are included

Further Information, Files, and Links

Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)

References

  1. Sanyal and Shell, Coarse-grained models using local density potentials optimized with the relative entropy: Application to implicit solvation}, Journal of Chemical Physics, 2016, 145 (3), 034109

  2. Sanyal and Shell, Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy, Journal of Physical Chemistry B, 122 (21), 5678-5693

  3. Rosenberger, Sanyal, Shell and van der Vegt, Transferability of local density assisted implicit solvation models for homogenenous fluid mixtures, Journal of Chemical Physics, 2019, 151 (4), 044111

@tanmoy7989 tanmoy7989 requested a review from rbberger as a code owner Sep 9, 2019
…ache; added this to the false_positives.txt file
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commented Sep 10, 2019

Can't fix the doc building error. I ran txt2html on doc/src/pair_local_density.txt and it ran flawlessly, but here I end up with an "unexpected section title or transition" in the rst rendering from the .txt file, which I don't understand fully (since I don't know much about the new rst system for direct conversion to Sphinx type manuals)

akohlmey added 2 commits Sep 11, 2019
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commented Sep 11, 2019

Can't fix the doc building error. I ran txt2html on doc/src/pair_local_density.txt and it ran flawlessly, but here I end up with an "unexpected section title or transition" in the rst rendering from the .txt file, which I don't understand fully (since I don't know much about the new rst system for direct conversion to Sphinx type manuals)

fixed the issue by replacing an unnumbered list with a pre-formatted block. also integrated the pair style doc file into the manual by adding links and including it to certain files.

@akohlmey akohlmey self-assigned this Sep 11, 2019
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commented Sep 11, 2019

Cool. Thanks Axel!

@akohlmey akohlmey requested review from athomps and sjplimp Sep 18, 2019
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just a couple minor suggestions

doc/src/pair_local_density.txt Outdated Show resolved Hide resolved
src/USER-MISC/pair_local_density.cpp Show resolved Hide resolved
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commented Sep 18, 2019

Thanks for adding the pair style to LAMMPS. Doc page looks nicely
complete, and thanks for including examples.

@akohlmey akohlmey dismissed sjplimp’s stale review Sep 19, 2019

requested changes have been implemented

@akohlmey akohlmey requested a review from sjplimp Sep 19, 2019
@akohlmey akohlmey merged commit ed6dd1a into lammps:master Sep 19, 2019
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