Avoid error in acos and asin with fast-math#776
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by returning hardcoded values on boundaries -1 and 1
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giacomofiorin
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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
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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
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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
acmnpv
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Nov 7, 2025
This update introduces some new features (flexible definition of CV grids), significant
performance improvements by switching to a structure-of-arrays (SOA) memory layout, and bugfixes
for several use cases.
The following is a list of pull requests affecting GROMACS merged into the Colvars repository
since 2024-11-14:
- 873 test: Functional test for atomPermutation
Colvars/colvars#873 (@HanatoK, @jhenin)
- 868 Fix debug gradients recalc gradients
Colvars/colvars#868 (@HanatoK)
- 866 Make non-MTS colvars always awake
Colvars/colvars#866 (@jhenin)
- 856 Fix cut and paste error in dipole_angle gradients
Colvars/colvars#856 (@giacomofiorin)
- 854 fix: update the total charge and total mass from AOS to SOA
Colvars/colvars#854 (@HanatoK)
- 851 Moving harmonic walls - unify moving restraint logic
Colvars/colvars#851 (@jhenin, @giacomofiorin, @OmriShf)
- 849 opt: optimize the forces or gradients from q to the fitting group
Colvars/colvars#849 (@HanatoK)
- 856 Fix cut and paste error in dipole_angle gradients
Colvars/colvars#856 (@giacomofiorin)
- 854 fix: update the total charge and total mass from AOS to SOA
Colvars/colvars#854 (@HanatoK)
- 847 Define version numbers outside of headers
Colvars/colvars#847 (@giacomofiorin)
- 839 Optimize the calculation of fit gradients and update the documentation (fix #560)
Colvars/colvars#839 (@HanatoK, @jhenin)
- 838 More functional tests
Colvars/colvars#838 (@jhenin, @giacomofiorin)
- 835 Initialize quaternions to zero, rotations to unity
Colvars/colvars#835 (@jhenin)
- 831 Gradient tests and bugfix
Colvars/colvars#831 (@jhenin, @HanatoK)
- 829 fix: try fixing the orientation sign
Colvars/colvars#829 (@HanatoK)
- 828 fix: fix the gradients of the eigenvector CVC
Colvars/colvars#828 (@HanatoK, @jhenin)
- 824 fix: fix a potential issue of "fit gradients" for non-scalar components with only centering but not rotating
Colvars/colvars#824 (@HanatoK, @jhenin)
- 822 Documentation for torchann and a minor change
Colvars/colvars#822 (@zwpku)
- 814 Add regression test for multiple-walkers metadynamics in GROMACS
Colvars/colvars#814 (@giacomofiorin)
- 808 fix: fix the calculation of bias factor with off-grid hills
Colvars/colvars#808 (@HanatoK)
- 799 Weighted Poisson integration
Colvars/colvars#799 (@jhenin)
- 798 Rename m_output_index to output_component in torchANN
Colvars/colvars#798 (@giacomofiorin)
- 797 Add torchANN documentation
Colvars/colvars#797 (@giacomofiorin)
- 794 Correctly implement parallel OPES
Colvars/colvars#794 (@HanatoK, @jhenin)
- 788 Change the atom group to SOA
Colvars/colvars#788 (@HanatoK, @giacomofiorin, @jhenin)
- 780 Add an option to parallelize the inner loops instead of CVCs
Colvars/colvars#780 (@HanatoK, @giacomofiorin)
- 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)
- 757 Fix MSVC OpenMP issue
Colvars/colvars#757 (@HanatoK)
- 755 Fix indentation of 'Init CVC' message in standard output
Colvars/colvars#755 (@jhenin)
- 752 New tool poisson_integrator_conv
Colvars/colvars#752 (@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)
- 733 Custom grids for all biases
Colvars/colvars#733 (@giacomofiorin, @jhenin)
Authors: @giacomofiorin, @HanatoK, @jhenin, @zwpku, @OmriShf
Closes #560
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by returning hardcoded values on boundaries -1 and 1
Compared with previous fix #768 this is more radical: