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USER-CGDNA oxRNA2 Implementation #1772
This pull request is for the implementation of the oxRNA2 model for RNA.
Oliver Henrich, Department of Physics, University of Strathclyde, Glasgow, UK
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).
Some code of the oxDNA and oxDNA2 implementation has been modified, but backward compatibility is fully retained.
The model has been verified against the standalone code and previous tests.
Post Submission Checklist
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[x] The feature or features in this pull request is complete
(I can't remember if I commented already. Forgive me if this gets posted twice.)
(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.