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Add user yaff #1297

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merged 6 commits into from Jan 24, 2019

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stevenvdb commented Jan 22, 2019

Purpose

Some new styles are implemented which are used in force fields generated by QuickFF, mainly aimed at the simulation of metal-organic frameworks.

Author(s)

Steven Vandenbrande, Center for Molecular Modeling, Ghent University

Backward Compatibility

Backward compatibiliy is maintained.

Implementation Notes

All changes to the code are isolated in the USER-YAFF package. Correctness of energies, forces and virials was checked by comparing with the implementation of these styles in YAFF, our in-house MD code.
I could not figure out how the .tex files in doc/src/Eqs are automatically converted to jpg. I converted the new files myself, so the resulting .jpg files look a but different from the others.

Post Submission Checklist

Please check the fields below as they are completed

  • The feature or features in this pull request is complete
  • Suitable new documentation files and/or updates to the existing docs are included
  • One or more example input decks are included
  • The source code follows the LAMMPS formatting guidelines (unsure)

Further Information, Files, and Links

The styles implemented in the USER-YAFF package are all present in YAFF: https://github.com/molmod/yaff
Force fields employing these styles can be generated using QuickFF: http://dx.doi.org/10.1002/jcc.23877 and http://dx.doi.org/10.1002/jcc.25173

@akohlmey akohlmey self-assigned this Jan 22, 2019

@akohlmey akohlmey added this to the Stable Release Spring 2019 milestone Jan 22, 2019

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akohlmey commented Jan 22, 2019

@stevenvdb thanks for your submission. As for creating the equation image files, I use:

pdflatex formula.tex
pdftoppm formula.pdf | pnmcrop | pnmtojpeg > formula.jpg

As for adding to the documentation, the corresponding integration test fails, most likely due to false positives from the spell checker. Please do: cd doc; make spelling and check what the warnings are and either make corrections or add the false positives to doc/utils/sphinx-config/false_positives.txt.
Also, please check with make html if the typesetting for your added doc files works and that there are no complaints about link target problems. Same for make pdf, where there must me no complaints about non-ASCII characters and no warnings about missing files. I will have a close look at the code itself later today or tomorrow, when I have more time.

@stevenvdb stevenvdb requested a review from rbberger as a code owner Jan 22, 2019

@stevenvdb stevenvdb requested a review from junghans as a code owner Jan 22, 2019

@akohlmey akohlmey merged commit 985913b into lammps:master Jan 24, 2019

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@stevenvdb stevenvdb referenced this pull request Jan 24, 2019

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Fix mistake in mixing rules for mm3/switch3 #1301

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