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USER-CGDNA oxRNA2 Implementation #1772

Merged
merged 13 commits into from Dec 6, 2019
Merged

USER-CGDNA oxRNA2 Implementation #1772

merged 13 commits into from Dec 6, 2019

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@ohenrich
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ohenrich commented Nov 15, 2019

Summary

This pull request is for the implementation of the oxRNA2 model for RNA.

Author(s)

Oliver Henrich, Department of Physics, University of Strathclyde, Glasgow, UK

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

Some code of the oxDNA and oxDNA2 implementation has been modified, but backward compatibility is fully retained.

Implementation Notes

The model has been verified against the standalone code and previous tests.

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

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

@ohenrich ohenrich changed the title oxRNA2 Implementation USER-CGDNA oxRNA2 Implementation Nov 15, 2019
ohenrich added 4 commits Nov 15, 2019
This reverts commit 2d6e84e.
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jewettaij commented Nov 16, 2019

(I can't remember if I commented already. Forgive me if this gets posted twice.)
Thanks for submitting this. I look forward to using it and I'll definitely let you know when we have a cool example for people to play with.

(Incidentally, don't worry about getting this to work with KOKKOS. You mentioned this in our email correspondence. Last I checked, KOKKOS does not support hybrid pair_styles, and USER-CGDNA and oxDNA requires a pair_style hybrid/overlay. More generally, lack of hybrid support is a problem for people who use exotic coarse-grained models. Thankfully, the GPU package has not been abandoned. My sincere gratitude to the folks who are maintaining it.)

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ohenrich commented Nov 16, 2019

(Incidentally, don't worry about getting this to work with KOKKOS. You mentioned this in our email correspondence. Last I checked, KOKKOS does not support hybrid pair_styles, and USER-CGDNA and oxDNA requires a pair_style hybrid/overlay. More generally, lack of hybrid support is a problem for people who use exotic coarse-grained models. Thankfully, the GPU package has not been abandoned. My sincere gratitude to the folks who are maintaining it.)

Thanks, Andrew. I know that the KOKKOS package has severe limitations in its current form. From what I can see it looks as if hybrid styles among pair styles are supported. What is less clear to me is whether hybrid atom types are supported. For USER-CGDNA we need atom_style hybrid bond ellipsoid and I don't think aspherical particles are in any way supported at the moment.

I wanted to get in touch with the core developers to find out what the option are and whether some of these limitations will be mitigated in due course as KOKKOS is a core package after all.

@rbberger rbberger self-assigned this Nov 26, 2019
@rbberger rbberger requested a review from akohlmey Nov 27, 2019
@rbberger rbberger merged commit e68824a into lammps:master Dec 6, 2019
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