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
  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

Author: giacomofiorin

cmake/Modules/Packages/COLVARS.cmake

@@ -26,6 +26,11 @@ if(BUILD_OMP)
   target_link_libraries(colvars PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
+if(BUILD_MPI)
+  target_compile_definitions(colvars PUBLIC -DCOLVARS_MPI)
+  target_link_libraries(colvars PUBLIC MPI::MPI_CXX)
+endif()
+
 if(COLVARS_DEBUG)
   # Need to export the define publicly to be valid in interface code
   target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)

doc/src/PDF/colvars-refman-lammps.pdf

@@ -32,6 +32,7 @@ COLVARS_SRCS = \
         colvarbias_histogram_reweight_amd.cpp \
         colvarbias_meta.cpp \
         colvarbias_restraint.cpp \
+        colvarbias_opes.cpp \
         colvarcomp_alchlambda.cpp \
         colvarcomp_angles.cpp \
         colvarcomp_apath.cpp \
@@ -40,6 +41,7 @@ COLVARS_SRCS = \
         colvarcomp_distances.cpp \
         colvarcomp_gpath.cpp \
         colvarcomp_neuralnetwork.cpp \
+        colvarcomp_torchann.cpp \
         colvarcomp_combination.cpp \
         colvarcomp_protein.cpp \
         colvarcomp_rotations.cpp \

lib/colvars/Makefile.common

@@ -52,6 +52,12 @@ $(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
  colvarproxy_tcl.h colvarproxy_volmaps.h colvarvalue.h \
  colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
  colvarparams.h colvardeps.h
+$(COLVARS_OBJ_DIR)colvarbias_opes.o: colvarbias_opes.cpp \
+ colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
+ ../../src/math_eigen_impl.h colvarproxy_io.h colvarproxy_system.h \
+ colvarproxy_tcl.h colvarproxy_volmaps.h colvarvalue.h \
+ colvarbias_opes.h colvarbias.h colvar.h colvarparse.h \
+ colvarparams.h colvardeps.h
 $(COLVARS_OBJ_DIR)colvarcomp_alchlambda.o: colvarcomp_alchlambda.cpp \
  colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
  ../../src/math_eigen_impl.h colvar.h colvarparse.h colvarparams.h \
@@ -101,6 +107,11 @@ $(COLVARS_OBJ_DIR)colvarcomp_neuralnetwork.o: \
  colvarproxy.h colvarproxy_io.h colvarproxy_system.h colvarproxy_tcl.h \
  colvarproxy_volmaps.h colvar_geometricpath.h \
  colvar_neuralnetworkcompute.h
+$(COLVARS_OBJ_DIR)colvarcomp_torchann.o: \
+ colvarcomp_torchann.cpp colvarmodule.h colvars_version.h \
+ colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.h \
+ colvardeps.h colvarcomp.h colvarcomp_torchann.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
+ colvarproxy_system.h colvarproxy_tcl.h 
 $(COLVARS_OBJ_DIR)colvarcomp_combination.o: colvarcomp_combination.cpp \
  colvarcomp.h colvarmodule.h colvars_version.h colvaratoms.h \
  colvarproxy.h colvartypes.h ../../src/math_eigen_impl.h colvarproxy_io.h \
@@ -127,7 +138,7 @@ $(COLVARS_OBJ_DIR)colvarcomp_volmaps.o: colvarcomp_volmaps.cpp \
  colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
  colvarvalue.h colvartypes.h ../../src/math_eigen_impl.h colvarparse.h \
- colvarparams.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
+ colvarparams.h colvarcomp.h colvarcomp_torchann.h colvaratoms.h colvarproxy.h colvarproxy_io.h \
  colvarproxy_system.h colvarproxy_tcl.h colvarproxy_volmaps.h \
  colvardeps.h colvar.h colvar_geometricpath.h colvarbias.h \
  colvars_memstream.h
@@ -152,7 +163,8 @@ $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
  colvarbias_histogram_reweight_amd.h colvarbias_meta.h colvarscript.h \
  colvarscript_commands.h colvarscript_commands_colvar.h \
  colvarscript_commands_bias.h colvaratoms.h colvarcomp.h \
- colvar_geometricpath.h colvars_memstream.h colvarmodule_refs.h
+ colvar_geometricpath.h colvars_memstream.h colvarmodule_refs.h \
+ colvarbias_opes.h
 $(COLVARS_OBJ_DIR)colvarparams.o: colvarparams.cpp colvarmodule.h \
  colvars_version.h colvarvalue.h colvartypes.h \
  ../../src/math_eigen_impl.h colvarparams.h