Update Colvars library to version 2025-04-18
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 https://github.com/Colvars/colvars/pull/752 (@jhenin) - 733 Custom grids for all biases https://github.com/Colvars/colvars/pull/733 (@giacomofiorin, @jhenin) - 776 Avoid error in acos and asin with fast-math https://github.com/Colvars/colvars/pull/776 (@jhenin) - 773 fix: fix the clang build test failure of OPES https://github.com/Colvars/colvars/pull/773 (@HanatoK) - 768 fix: clamp the input values of asin and acos in case of fast math on aarch64 https://github.com/Colvars/colvars/pull/768 (@HanatoK) - 761 Add debug code for the Jacobi failure https://github.com/Colvars/colvars/pull/761 (@HanatoK) - 759 min_image fix; Saves long runs from crashes; https://github.com/Colvars/colvars/pull/759 (@PolyachenkoYA) - 757 Fix MSVC OpenMP issue https://github.com/Colvars/colvars/pull/757 (@HanatoK) - 755 Fix indentation of 'Init CVC' message in standard output https://github.com/Colvars/colvars/pull/755 (@jhenin) - 750 Optimize and simplify the calculation of dihedral gradients https://github.com/Colvars/colvars/pull/750 (@HanatoK) - 749 Add references to new Colvars paper https://github.com/Colvars/colvars/pull/749 (@jhenin, @giacomofiorin) - 740 Report the specific C++ standard at init time, stop warning about C++97/03 https://github.com/Colvars/colvars/pull/740 (@giacomofiorin) - 731 Improve detection of hard/mathematical boundaries https://github.com/Colvars/colvars/pull/731 (@giacomofiorin) - 729 Optimize the fit gradients https://github.com/Colvars/colvars/pull/729 (@HanatoK, @jhenin) - 728 Fix undefined behavior when getting the current working directory from std::filesystem https://github.com/Colvars/colvars/pull/728 (@giacomofiorin) - 727 Add patchversion scripting command https://github.com/Colvars/colvars/pull/727 (@giacomofiorin) - 724 Fix gradients and metric functions of distanceDir https://github.com/Colvars/colvars/pull/724 (@giacomofiorin) - 715 Add missing rotation in orientation component https://github.com/Colvars/colvars/pull/715 (@giacomofiorin) - 713 fix: try to solve #87 for non-scala components https://github.com/Colvars/colvars/pull/713 (@HanatoK) - 709 Implementation of OPES in Colvars https://github.com/Colvars/colvars/pull/709 (@HanatoK, @giacomofiorin, @jhenin) - 706 BUGFIX for Segmentation fault in colvarbias_meta::calc_energy() with useGrids off https://github.com/Colvars/colvars/pull/706 (@alphataubio) - 570 enable use of CVs defined by PyTorch neural network models https://github.com/Colvars/colvars/pull/570 (@zwpku, @giacomofiorin, @HanatoK, @jhenin) Authors: @alphataubio, @EzryStIago, @giacomofiorin, @HanatoK, @jhenin, @PolyachenkoYA, @zwpku
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@ -261,7 +261,6 @@ int colvar::cvc::init_dependencies() {
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require_feature_children(f_cvc_explicit_gradient, f_ag_explicit_gradient);
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init_feature(f_cvc_inv_gradient, "inverse_gradient", f_type_dynamic);
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require_feature_self(f_cvc_inv_gradient, f_cvc_gradient);
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init_feature(f_cvc_debug_gradient, "debug_gradient", f_type_user);
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require_feature_self(f_cvc_debug_gradient, f_cvc_gradient);
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@ -525,7 +524,7 @@ void colvar::cvc::calc_force_invgrads()
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void colvar::cvc::calc_Jacobian_derivative()
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{
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cvm::error("Error: calculation of inverse gradients is not implemented "
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cvm::error("Error: calculation of Jacobian derivatives is not implemented "
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"for colvar components of type \""+function_type()+"\".\n",
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COLVARS_NOT_IMPLEMENTED);
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}
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@ -533,8 +532,10 @@ void colvar::cvc::calc_Jacobian_derivative()
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void colvar::cvc::calc_fit_gradients()
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{
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for (size_t ig = 0; ig < atom_groups.size(); ig++) {
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atom_groups[ig]->calc_fit_gradients();
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if (is_enabled(f_cvc_explicit_gradient)) {
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for (size_t ig = 0; ig < atom_groups.size(); ig++) {
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atom_groups[ig]->calc_fit_gradients();
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}
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}
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}
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