Performance enhancements for USER-DPD, mostly in SSA communication#87
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akohlmey merged 1 commit intolammps:lammps-icmsfrom Jun 10, 2016
Merged
Performance enhancements for USER-DPD, mostly in SSA communication#87akohlmey merged 1 commit intolammps:lammps-icmsfrom
akohlmey merged 1 commit intolammps:lammps-icmsfrom
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1) For an ideal fluid benchmark: ~15% speedup and ~5% memory savings 2) Removes duCond and duMech, and replaces dvSSA with v_t0 (ghosts only) 3) Eliminates the need to transmit deltas and uCond/uMech in forward_comm 4) Reduces adds and loads for computing updated velocities from v + dvSSA
jhenin
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Dec 16, 2024
- 759 min_image fix; Saves long runs from crashes; Colvars/colvars#759 (@PolyachenkoYA) - 728 Fix undefined behavior when getting the current working directory from std::filesystem Colvars/colvars#728 (@giacomofiorin) - 724 Fix gradients and metric functions of distanceDir Colvars/colvars#724 (@giacomofiorin) - 715 Add missing rotation in orientation component Colvars/colvars#715 (@giacomofiorin) - 713 fix: try to solve lammps#87 for non-scala components Colvars/colvars#713 (@HanatoK) - 706 BUGFIX for Segmentation fault in colvarbias_meta::calc_energy() with useGrids off Colvars/colvars#706 (@alphataubio) - 701 Do not try accessing LAMMPS proxy object before allocating it Colvars/colvars#701 (@giacomofiorin) Authors: @alphataubio, @giacomofiorin, @HanatoK, @PolyachenkoYA
giacomofiorin
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Apr 18, 2025
The following is a list of pull requests relevant to LAMMPS in the Colvars repository since 2024-08-06: - 752 New tool poisson_integrator_conv Colvars/colvars#752 (@jhenin) - 733 Custom grids for all biases Colvars/colvars#733 (@giacomofiorin, @jhenin) - 776 Avoid error in acos and asin with fast-math Colvars/colvars#776 (@jhenin) - 773 fix: fix the clang build test failure of OPES Colvars/colvars#773 (@HanatoK) - 768 fix: clamp the input values of asin and acos in case of fast math on aarch64 Colvars/colvars#768 (@HanatoK) - 761 Add debug code for the Jacobi failure Colvars/colvars#761 (@HanatoK) - 759 min_image fix; Saves long runs from crashes; Colvars/colvars#759 (@PolyachenkoYA) - 757 Fix MSVC OpenMP issue Colvars/colvars#757 (@HanatoK) - 755 Fix indentation of 'Init CVC' message in standard output Colvars/colvars#755 (@jhenin) - 750 Optimize and simplify the calculation of dihedral gradients Colvars/colvars#750 (@HanatoK) - 749 Add references to new Colvars paper Colvars/colvars#749 (@jhenin, @giacomofiorin) - 740 Report the specific C++ standard at init time, stop warning about C++97/03 Colvars/colvars#740 (@giacomofiorin) - 731 Improve detection of hard/mathematical boundaries Colvars/colvars#731 (@giacomofiorin) - 729 Optimize the fit gradients Colvars/colvars#729 (@HanatoK, @jhenin) - 728 Fix undefined behavior when getting the current working directory from std::filesystem Colvars/colvars#728 (@giacomofiorin) - 727 Add patchversion scripting command Colvars/colvars#727 (@giacomofiorin) - 724 Fix gradients and metric functions of distanceDir Colvars/colvars#724 (@giacomofiorin) - 715 Add missing rotation in orientation component Colvars/colvars#715 (@giacomofiorin) - 713 fix: try to solve lammps#87 for non-scala components Colvars/colvars#713 (@HanatoK) - 709 Implementation of OPES in Colvars Colvars/colvars#709 (@HanatoK, @giacomofiorin, @jhenin) - 706 BUGFIX for Segmentation fault in colvarbias_meta::calc_energy() with useGrids off Colvars/colvars#706 (@alphataubio) - 570 enable use of CVs defined by PyTorch neural network models Colvars/colvars#570 (@zwpku, @giacomofiorin, @HanatoK, @jhenin) Authors: @alphataubio, @EzryStIago, @giacomofiorin, @HanatoK, @jhenin, @PolyachenkoYA, @zwpku
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giacomofiorin
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Apr 18, 2025
The following is a list of pull requests relevant to LAMMPS in the Colvars repository since 2024-08-06: - 752 New tool poisson_integrator_conv Colvars/colvars#752 (@jhenin) - 733 Custom grids for all biases Colvars/colvars#733 (@giacomofiorin, @jhenin) - 776 Avoid error in acos and asin with fast-math Colvars/colvars#776 (@jhenin) - 773 fix: fix the clang build test failure of OPES Colvars/colvars#773 (@HanatoK) - 768 fix: clamp the input values of asin and acos in case of fast math on aarch64 Colvars/colvars#768 (@HanatoK) - 761 Add debug code for the Jacobi failure Colvars/colvars#761 (@HanatoK) - 759 min_image fix; Saves long runs from crashes; Colvars/colvars#759 (@PolyachenkoYA) - 757 Fix MSVC OpenMP issue Colvars/colvars#757 (@HanatoK) - 755 Fix indentation of 'Init CVC' message in standard output Colvars/colvars#755 (@jhenin) - 750 Optimize and simplify the calculation of dihedral gradients Colvars/colvars#750 (@HanatoK) - 749 Add references to new Colvars paper Colvars/colvars#749 (@jhenin, @giacomofiorin) - 740 Report the specific C++ standard at init time, stop warning about C++97/03 Colvars/colvars#740 (@giacomofiorin) - 731 Improve detection of hard/mathematical boundaries Colvars/colvars#731 (@giacomofiorin) - 729 Optimize the fit gradients Colvars/colvars#729 (@HanatoK, @jhenin) - 728 Fix undefined behavior when getting the current working directory from std::filesystem Colvars/colvars#728 (@giacomofiorin) - 727 Add patchversion scripting command Colvars/colvars#727 (@giacomofiorin) - 724 Fix gradients and metric functions of distanceDir Colvars/colvars#724 (@giacomofiorin) - 715 Add missing rotation in orientation component Colvars/colvars#715 (@giacomofiorin) - 713 fix: try to solve #87 for non-scala components Colvars/colvars#713 (@HanatoK) - 709 Implementation of OPES in Colvars Colvars/colvars#709 (@HanatoK, @giacomofiorin, @jhenin) - 706 BUGFIX for Segmentation fault in colvarbias_meta::calc_energy() with useGrids off Colvars/colvars#706 (@alphataubio) - 570 enable use of CVs defined by PyTorch neural network models Colvars/colvars#570 (@zwpku, @giacomofiorin, @HanatoK, @jhenin) Authors: @alphataubio, @EzryStIago, @giacomofiorin, @HanatoK, @jhenin, @PolyachenkoYA, @zwpku
giacomofiorin
added a commit
to Colvars/lammps
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Apr 30, 2025
The following is a list of pull requests relevant to LAMMPS in the Colvars repository since 2024-08-06: - 752 New tool poisson_integrator_conv Colvars/colvars#752 (@jhenin) - 733 Custom grids for all biases Colvars/colvars#733 (@giacomofiorin, @jhenin) - 776 Avoid error in acos and asin with fast-math Colvars/colvars#776 (@jhenin) - 773 fix: fix the clang build test failure of OPES Colvars/colvars#773 (@HanatoK) - 768 fix: clamp the input values of asin and acos in case of fast math on aarch64 Colvars/colvars#768 (@HanatoK) - 761 Add debug code for the Jacobi failure Colvars/colvars#761 (@HanatoK) - 759 min_image fix; Saves long runs from crashes; Colvars/colvars#759 (@PolyachenkoYA) - 757 Fix MSVC OpenMP issue Colvars/colvars#757 (@HanatoK) - 755 Fix indentation of 'Init CVC' message in standard output Colvars/colvars#755 (@jhenin) - 750 Optimize and simplify the calculation of dihedral gradients Colvars/colvars#750 (@HanatoK) - 749 Add references to new Colvars paper Colvars/colvars#749 (@jhenin, @giacomofiorin) - 740 Report the specific C++ standard at init time, stop warning about C++97/03 Colvars/colvars#740 (@giacomofiorin) - 731 Improve detection of hard/mathematical boundaries Colvars/colvars#731 (@giacomofiorin) - 729 Optimize the fit gradients Colvars/colvars#729 (@HanatoK, @jhenin) - 728 Fix undefined behavior when getting the current working directory from std::filesystem Colvars/colvars#728 (@giacomofiorin) - 727 Add patchversion scripting command Colvars/colvars#727 (@giacomofiorin) - 724 Fix gradients and metric functions of distanceDir Colvars/colvars#724 (@giacomofiorin) - 715 Add missing rotation in orientation component Colvars/colvars#715 (@giacomofiorin) - 713 fix: try to solve lammps#87 for non-scala components Colvars/colvars#713 (@HanatoK) - 709 Implementation of OPES in Colvars Colvars/colvars#709 (@HanatoK, @giacomofiorin, @jhenin) - 706 BUGFIX for Segmentation fault in colvarbias_meta::calc_energy() with useGrids off Colvars/colvars#706 (@alphataubio) - 570 enable use of CVs defined by PyTorch neural network models Colvars/colvars#570 (@zwpku, @giacomofiorin, @HanatoK, @jhenin) Authors: @alphataubio, @EzryStIago, @giacomofiorin, @HanatoK, @jhenin, @PolyachenkoYA, @zwpku
giacomofiorin
added a commit
to Colvars/lammps
that referenced
this pull request
Apr 30, 2025
The following is a list of pull requests relevant to LAMMPS in the Colvars repository since 2024-08-06: - 752 New tool poisson_integrator_conv Colvars/colvars#752 (@jhenin) - 733 Custom grids for all biases Colvars/colvars#733 (@giacomofiorin, @jhenin) - 776 Avoid error in acos and asin with fast-math Colvars/colvars#776 (@jhenin) - 773 fix: fix the clang build test failure of OPES Colvars/colvars#773 (@HanatoK) - 768 fix: clamp the input values of asin and acos in case of fast math on aarch64 Colvars/colvars#768 (@HanatoK) - 761 Add debug code for the Jacobi failure Colvars/colvars#761 (@HanatoK) - 759 min_image fix; Saves long runs from crashes; Colvars/colvars#759 (@PolyachenkoYA) - 757 Fix MSVC OpenMP issue Colvars/colvars#757 (@HanatoK) - 755 Fix indentation of 'Init CVC' message in standard output Colvars/colvars#755 (@jhenin) - 750 Optimize and simplify the calculation of dihedral gradients Colvars/colvars#750 (@HanatoK) - 749 Add references to new Colvars paper Colvars/colvars#749 (@jhenin, @giacomofiorin) - 740 Report the specific C++ standard at init time, stop warning about C++97/03 Colvars/colvars#740 (@giacomofiorin) - 731 Improve detection of hard/mathematical boundaries Colvars/colvars#731 (@giacomofiorin) - 729 Optimize the fit gradients Colvars/colvars#729 (@HanatoK, @jhenin) - 728 Fix undefined behavior when getting the current working directory from std::filesystem Colvars/colvars#728 (@giacomofiorin) - 727 Add patchversion scripting command Colvars/colvars#727 (@giacomofiorin) - 724 Fix gradients and metric functions of distanceDir Colvars/colvars#724 (@giacomofiorin) - 715 Add missing rotation in orientation component Colvars/colvars#715 (@giacomofiorin) - 713 fix: try to solve lammps#87 for non-scala components Colvars/colvars#713 (@HanatoK) - 709 Implementation of OPES in Colvars Colvars/colvars#709 (@HanatoK, @giacomofiorin, @jhenin) - 706 BUGFIX for Segmentation fault in colvarbias_meta::calc_energy() with useGrids off Colvars/colvars#706 (@alphataubio) - 570 enable use of CVs defined by PyTorch neural network models Colvars/colvars#570 (@zwpku, @giacomofiorin, @HanatoK, @jhenin) Authors: @alphataubio, @EzryStIago, @giacomofiorin, @HanatoK, @jhenin, @PolyachenkoYA, @zwpku
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