Kokkos charmmfsw pair and dihedral styles #4030
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…t lammps scripts generated by charmm-gui.org can be run without tweaks
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alphataubio
changed the title
…jtype].lj3:params(itype,jtype).lj3)" in compute_evdwl
// superclass destructor from KSPACE/pair_lj_charmmfsw_coul_long.cpp:81 // resets force->qqr2e = force->qqr2e_lammps_real at end of timestep 0 // causing ~E-6 errors for steps 1,2,... everywhere in this class when // running kokkos with openmp (and probably with GPUs also). // // WORKAROUND: for now until guidance from lammps devs is to // reset it back force->qqr2e = force->qqr2e_charmm_real here.
//
// force->qqr2e = force->qqr2e_lammps_real
//
// at end of timestep 0 causing ~E-6 errors for steps 1,2,...
// everywhere in pair_lj_charmmfsw_coul_long_kokkos when
// running kokkos with openmp (and probably with GPUs also).
//
// WORKAROUND: for now until guidance from lammps devs is to
// comment out this line here (commit to be reversed later).
//force->qqr2e = force->qqr2e_lammps_real;
This reverts commit de1f6ee. my first idea to reset back force->qqr2e = force->qqr2e_charmm_real didnt work because class destructor gets called first THEN superclass destructor gets called
alphataubio
changed the title
This reverts commit f113ec8.
…ubio/lammps-alphataubio into alphataubio-charmmfsw-kk
- gathered all tutorial like discussion, equations, and plot for old charmm and new charmmfsw into howto - added equations and another plot for charmmfsw - charmmgui 1HVN and 2CV5 examples
checked in as a separate commit, if maintainer doesnt approve, then easy to revert atomically. if maintainer approves, then ill add mentions to examples/README and Examples.rst, and anywhere else needed
…ded note box to use tip3 with charmm
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@alphataubio this now gives correct numerics on the GPU for my test, and does not hang. |
stanmoore1
requested changes
Jan 8, 2024
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@alphataubio overall this is almost ready to merge, just a few minor change requests.
stanmoore1
approved these changes
Jan 8, 2024
ndtrung81
approved these changes
Jan 10, 2024
sjplimp
approved these changes
Jan 10, 2024
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for documentation purposes and reproducibility later, im attaching to this PR mathematica notebook used to create plots. had to use zip because .nb files not allowed on github |
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Summary
add pair/lj/charmmfsw/coul/long/kk and dihedral/charmmfsw/kk
Related Issue(s)
https://matsci.org/t/charmmfsw-pair-style-and-gpu-acceleration/39482
Author(s)
Mitch Murphy, alphataubio.com, alphataubio@gmail.com
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
n/a
Implementation Notes
*** DRAFT VERSION 1 (lots of comments to be removed just before merge) ***
(1) first draft version of PairLJCharmmfswCoulLongKokkos exactly same as PairLJCharmmCoulLongKokkos but with new class name. compiles without errors or warnings
method: track changes from serial kspace pair_lj_charmm_coul_long to pair_lj_charmmfsw_coul_long and apply to PairLJCharmmfswCoulLongKokkos
% diff pair_lj_charmm_coul_long.h pair_lj_charmmfsw_coul_long.h
Post Submission Checklist
Further Information, Files, and Links
My test input is a protein-dna simulation (1HVN), the smallest number of atoms available on PDB with at least one protein, at least one dna, and no modified engineered residues. 1HVN lammps input scripts created by charmm-gui.org:
1hvn-lammps-charmm.zip
1hvn-lammps-charmmfsw.zip