GPU coordnum#940
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According to the CUDA API documentation, this could improve the performance.
Keep in mind that not every CVC use CUDA graphs for the GPU implementation. Consequently, whether to use CUDA graphs or not is considered to be an implementation detail. This commit strips the CUDA graphs in colvar::cvc to a separate class to colvar_gpu_calc.*. The RMSD GPU code is modified to use it.
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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This PR should wait for #919 and #938. #919 is necessary for wrapping the distances using the internal PBC function on GPU. This PR is independent from #926.
Regarding the pairlist implementation, the GPU kernels in this PR try to match the CPU pairlist, which is slow for the time being. A better option is to implement at least a NAMD-style GPU pairlist, but since Colvars (i) does not allow atoms in an atom group to be reordered, and (ii) uses only a single cutoff for both the switching function and the pairlist, it is impossible or very diffcult to do so.