Update Colvars to version 2020-09-17

Small changes

Implement global map of components (@HanatoK)
https://github.com/Colvars/colvars/pull/363

Format code examples with colored background (@giacomofiorin)
https://github.com/Colvars/colvars/pull/361

replaced jacobi() with an open-source version (@jewettaij)
https://github.com/Colvars/colvars/pull/360

lib/colvars/Makefile.common

@@ -15,7 +15,7 @@ else
 COLVARS_DEBUG_INCFLAGS = -DCOLVARS_DEBUG
 endif
 
-COLVARS_INCFLAGS = $(COLVARS_DEBUG_INCFLAGS) $(COLVARS_PYTHON_INCFLAGS)
+COLVARS_INCFLAGS = -DCOLVARS_LAMMPS $(COLVARS_DEBUG_INCFLAGS) $(COLVARS_PYTHON_INCFLAGS) -I../../src
 
 
 .SUFFIXES:

lib/colvars/Makefile.deps

@@ -4,79 +4,227 @@ $(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \
  colvarproxy_tcl.h colvarproxy_volmaps.h colvarparse.h colvarparams.h \
  colvaratoms.h colvardeps.h
 $(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \
- colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
+ colvars_version.h colvar.h colvarvalue.h colvartypes.h colvarparse.h \
- colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h colvarparse.h \
+ colvarparams.h colvardeps.h lepton/include/Lepton.h \
- colvarparams.h colvardeps.h colvarbias_abf.h colvarbias.h colvargrid.h \
+ lepton/include/lepton/CompiledExpression.h \
- colvar_UIestimator.h
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarbias_abf.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
+ colvarbias.h colvargrid.h colvar_UIestimator.h
 $(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \
  colvars_version.h colvarbias.h colvar.h colvarvalue.h colvartypes.h \
- colvarparse.h colvarparams.h colvardeps.h colvarbias_alb.h
+ colvarparse.h colvarparams.h colvardeps.h lepton/include/Lepton.h \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarbias_alb.h
 $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
  colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
  colvarproxy_tcl.h colvarproxy_volmaps.h colvarbias.h colvar.h \
- colvarparse.h colvarparams.h colvardeps.h colvargrid.h
+ colvarparse.h colvarparams.h colvardeps.h lepton/include/Lepton.h \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvargrid.h
 $(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
  colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
  colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h \
- colvarparse.h colvarparams.h colvardeps.h colvarbias_histogram.h \
+ colvarparse.h colvarparams.h colvardeps.h lepton/include/Lepton.h \
- colvarbias.h colvargrid.h
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarbias_histogram.h colvarbias.h colvargrid.h
 $(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
  colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
  colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h colvarparse.h \
- colvarparams.h colvardeps.h colvarbias_meta.h colvarbias.h colvargrid.h
+ colvarparams.h colvardeps.h lepton/include/Lepton.h \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarbias_meta.h colvarbias.h colvargrid.h
 $(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
  colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
  colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h \
  colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
- colvarparams.h colvardeps.h
+ colvarparams.h colvardeps.h lepton/include/Lepton.h \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h
 $(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \
  colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \
- colvarparse.h colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h \
+ colvarparse.h colvarparams.h colvardeps.h lepton/include/Lepton.h \
- colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
+ lepton/include/lepton/CompiledExpression.h \
- colvar_arithmeticpath.h colvar_geometricpath.h
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
+ colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarcomp_apath.o: colvarcomp_apath.cpp colvarmodule.h \
  colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
- colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
+ colvarparams.h colvar.h colvardeps.h lepton/include/Lepton.h \
- colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
+ lepton/include/lepton/CompiledExpression.h \
- colvar_arithmeticpath.h colvar_geometricpath.h
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
+ colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \
  colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \
  colvartypes.h colvarparams.h colvaratoms.h colvarproxy.h \
  colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h colvar.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
  colvarcomp.h colvar_arithmeticpath.h colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \
  colvars_version.h colvarvalue.h colvartypes.h colvar.h colvarparse.h \
- colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
+ colvarparams.h colvardeps.h lepton/include/Lepton.h \
- colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \
+ lepton/include/lepton/CompiledExpression.h \
- colvar_geometricpath.h
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
+ colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \
  colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
- colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
+ colvarparse.h colvarparams.h colvar.h colvardeps.h \
- colvaratoms.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
- colvar_arithmeticpath.h colvar_geometricpath.h
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
+ colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp colvarmodule.h \
  colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
- colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
+ colvarparams.h colvar.h colvardeps.h lepton/include/Lepton.h \
- colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
+ lepton/include/lepton/CompiledExpression.h \
- colvar_arithmeticpath.h colvar_geometricpath.h
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
+ colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \
  colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
- colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
+ colvarparse.h colvarparams.h colvar.h colvardeps.h \
- colvaratoms.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
- colvar_arithmeticpath.h colvar_geometricpath.h
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
+ colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \
  colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
- colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
+ colvarparse.h colvarparams.h colvar.h colvardeps.h \
- colvaratoms.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
- colvar_arithmeticpath.h colvar_geometricpath.h
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
+ colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarcomp_volmaps.o: colvarcomp_volmaps.cpp \
  colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
- colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
+ colvarparse.h colvarparams.h colvar.h colvardeps.h \
- colvaratoms.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
- colvar_arithmeticpath.h colvar_geometricpath.h
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
+ colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
  colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.h \
- colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
+ colvardeps.h lepton/include/Lepton.h \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
  colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h \
  colvarscript.h colvarbias.h colvarscript_commands.h \
  colvarscript_commands_colvar.h colvarscript_commands_bias.h
@@ -86,18 +234,38 @@ $(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \
  colvarparams.h
 $(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \
  colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
- colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
+ colvarparams.h colvar.h colvardeps.h lepton/include/Lepton.h \
- colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
+ lepton/include/lepton/CompiledExpression.h \
- colvar_arithmeticpath.h colvar_geometricpath.h colvargrid.h
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
+ colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h \
+ colvargrid.h
 $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
  colvars_version.h colvarparse.h colvarvalue.h colvartypes.h \
  colvarparams.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
- colvar.h colvardeps.h colvarbias.h colvarbias_abf.h colvargrid.h \
+ colvar.h colvardeps.h lepton/include/Lepton.h \
- colvar_UIestimator.h colvarbias_alb.h colvarbias_histogram.h \
+ lepton/include/lepton/CompiledExpression.h \
- colvarbias_meta.h colvarbias_restraint.h colvarscript.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
- colvarscript_commands.h colvarscript_commands_colvar.h \
+ lepton/include/lepton/windowsIncludes.h \
- colvarscript_commands_bias.h colvaratoms.h colvarcomp.h \
+ lepton/include/lepton/CustomFunction.h \
- colvar_arithmeticpath.h colvar_geometricpath.h
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarbias.h colvarbias_abf.h colvargrid.h colvar_UIestimator.h \
+ colvarbias_alb.h colvarbias_histogram.h colvarbias_meta.h \
+ colvarbias_restraint.h colvarscript.h colvarscript_commands.h \
+ colvarscript_commands_colvar.h colvarscript_commands_bias.h \
+ colvaratoms.h colvarcomp.h colvar_arithmeticpath.h \
+ colvar_geometricpath.h
 $(COLVARS_OBJ_DIR)colvarparams.o: colvarparams.cpp colvarmodule.h \
  colvars_version.h colvarvalue.h colvartypes.h colvarparams.h
 $(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
@@ -107,6 +275,15 @@ $(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \
  colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
  colvarproxy_tcl.h colvarproxy_volmaps.h colvarscript.h colvarbias.h \
  colvar.h colvarparse.h colvarparams.h colvardeps.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
  colvarscript_commands.h colvarscript_commands_colvar.h \
  colvarscript_commands_bias.h colvaratoms.h
 $(COLVARS_OBJ_DIR)colvarproxy_replicas.o: colvarproxy_replicas.cpp \
@@ -122,28 +299,66 @@ $(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarproxy.h \
  colvarmodule.h colvars_version.h colvartypes.h colvarvalue.h \
  colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h colvarparse.h \
  colvarparams.h colvarscript.h colvarbias.h colvar.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
  colvarscript_commands.h colvarscript_commands_colvar.h \
  colvarscript_commands_bias.h
 $(COLVARS_OBJ_DIR)colvarscript_commands.o: colvarscript_commands.cpp \
  colvarproxy.h colvarmodule.h colvars_version.h colvartypes.h \
  colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h \
  colvarparse.h colvarparams.h colvarscript.h colvarbias.h colvar.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
  colvarscript_commands.h colvarscript_commands_colvar.h \
  colvarscript_commands_bias.h
 $(COLVARS_OBJ_DIR)colvarscript_commands_bias.o: \
  colvarscript_commands_bias.cpp colvarproxy.h colvarmodule.h \
  colvars_version.h colvartypes.h colvarvalue.h colvarproxy_tcl.h \
  colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h \
- colvarscript.h colvarbias.h colvar.h colvarscript_commands.h \
+ colvarscript.h colvarbias.h colvar.h lepton/include/Lepton.h \
- colvarscript_commands_colvar.h colvarscript_commands_bias.h
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarscript_commands.h colvarscript_commands_colvar.h \
+ colvarscript_commands_bias.h
 $(COLVARS_OBJ_DIR)colvarscript_commands_colvar.o: \
  colvarscript_commands_colvar.cpp colvarproxy.h colvarmodule.h \
  colvars_version.h colvartypes.h colvarvalue.h colvarproxy_tcl.h \
  colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h \
- colvarscript.h colvarbias.h colvar.h colvarscript_commands.h \
+ colvarscript.h colvarbias.h colvar.h lepton/include/Lepton.h \
- colvarscript_commands_colvar.h colvarscript_commands_bias.h
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarscript_commands.h colvarscript_commands_colvar.h \
+ colvarscript_commands_bias.h
 $(COLVARS_OBJ_DIR)colvartypes.o: colvartypes.cpp colvarmodule.h \
  colvars_version.h colvartypes.h colvarparse.h colvarvalue.h \
- colvarparams.h
+ colvarparams.h ../../src/math_eigen.h
 $(COLVARS_OBJ_DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h \
  colvars_version.h colvarvalue.h colvartypes.h

lib/colvars/colvar.cpp

@@ -18,7 +18,9 @@
 #include "colvarcomp.h"
 #include "colvarscript.h"
 
-
+#if (__cplusplus >= 201103L)
+std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>> colvar::global_cvc_map = std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>>();
+#endif
 
 colvar::colvar()
 {
@@ -724,15 +726,15 @@ int colvar::init_output_flags(std::string const &conf)
   return COLVARS_OK;
 }
 
-
-
-
 // read the configuration and set up corresponding instances, for
 // each type of component implemented
 template<typename def_class_name> int colvar::init_components_type(std::string const &conf,
                                                                    char const * /* def_desc */,
                                                                    char const *def_config_key)
 {
+#if (__cplusplus >= 201103L)
+  global_cvc_map[def_config_key] = [](const std::string& cvc_conf){return new def_class_name(cvc_conf);};
+#endif
   size_t def_count = 0;
   std::string def_conf = "";
   size_t pos = 0;

lib/colvars/colvar.h

@@ -12,6 +12,11 @@
 
 #include <iostream>
 
+#if (__cplusplus >= 201103L)
+#include <map>
+#include <functional>
+#endif
+
 #include "colvarmodule.h"
 #include "colvarvalue.h"
 #include "colvarparse.h"
@@ -114,6 +119,7 @@ public:
 
   /// List of biases that depend on this colvar
   std::vector<colvarbias *> biases;
+
 protected:
 
 
@@ -605,6 +611,14 @@ public:
   // components that do not handle any atoms directly
   class map_total;
 
+  /// getter of the global cvc map
+#if (__cplusplus >= 201103L)
+  /// A global mapping of cvc names to the cvc constructors
+  static const std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>>& get_global_cvc_map() {
+      return global_cvc_map;
+  }
+#endif
+
 protected:
 
   /// \brief Array of \link colvar::cvc \endlink objects
@@ -639,6 +653,11 @@ protected:
   double dev_null;
 #endif
 
+#if (__cplusplus >= 201103L)
+  /// A global mapping of cvc names to the cvc constructors
+  static std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>> global_cvc_map;
+#endif
+
 public:
 
   /// \brief Sorted array of (zero-based) IDs for all atoms involved

lib/colvars/colvarcomp.h

@@ -1493,8 +1493,6 @@ class colvar::linearCombination
   : public colvar::cvc
 {
 protected:
-    /// Map from string to the types of colvar components
-    std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>> string_cv_map;
     /// Sub-colvar components
     std::vector<colvar::cvc*> cv;
     /// If all sub-cvs use explicit gradients then we also use it
@@ -1514,8 +1512,6 @@ class colvar::CVBasedPath
   : public colvar::cvc
 {
 protected:
-    /// Map from string to the types of colvar components
-    std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>> string_cv_map;
     /// Sub-colvar components
     std::vector<colvar::cvc*> cv;
     /// Reference colvar values from path

lib/colvars/colvarcomp_gpath.cpp

@@ -19,10 +19,6 @@
 #include "colvar.h"
 #include "colvarcomp.h"
 
-namespace GeometricPathCV {
-void init_string_cv_map(std::map<std::string, std::function<colvar::cvc* (const std::string& conf)>>& string_cv_map);
-}
-
 bool compareColvarComponent(colvar::cvc *i, colvar::cvc *j)
 {
     return i->name < j->name;
@@ -406,9 +402,8 @@ void colvar::gzpath::apply_force(colvarvalue const &force) {
 }
 
 colvar::linearCombination::linearCombination(std::string const &conf): cvc(conf) {
-    GeometricPathCV::init_string_cv_map(string_cv_map);
     // Lookup all available sub-cvcs
-    for (auto it_cv_map = string_cv_map.begin(); it_cv_map != string_cv_map.end(); ++it_cv_map) {
+    for (auto it_cv_map = colvar::get_global_cvc_map().begin(); it_cv_map != colvar::get_global_cvc_map().end(); ++it_cv_map) {
         if (key_lookup(conf, it_cv_map->first.c_str())) {
             std::vector<std::string> sub_cvc_confs;
             get_key_string_multi_value(conf, it_cv_map->first.c_str(), sub_cvc_confs);
@@ -506,9 +501,8 @@ void colvar::linearCombination::apply_force(colvarvalue const &force) {
 }
 
 colvar::CVBasedPath::CVBasedPath(std::string const &conf): cvc(conf) {
-    GeometricPathCV::init_string_cv_map(string_cv_map);
     // Lookup all available sub-cvcs
-    for (auto it_cv_map = string_cv_map.begin(); it_cv_map != string_cv_map.end(); ++it_cv_map) {
+    for (auto it_cv_map = colvar::get_global_cvc_map().begin(); it_cv_map != colvar::get_global_cvc_map().end(); ++it_cv_map) {
         if (key_lookup(conf, it_cv_map->first.c_str())) {
             std::vector<std::string> sub_cvc_confs;
             get_key_string_multi_value(conf, it_cv_map->first.c_str(), sub_cvc_confs);
@@ -909,33 +903,4 @@ void colvar::gzpathCV::apply_force(colvarvalue const &force) {
     }
 }
 
-void GeometricPathCV::init_string_cv_map(std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>>& string_cv_map) {
-    string_cv_map["distance"]              = [](const std::string& conf){return new colvar::distance(conf);};
-    string_cv_map["dihedral"]              = [](const std::string& conf){return new colvar::dihedral(conf);};
-    string_cv_map["angle"]                 = [](const std::string& conf){return new colvar::angle(conf);};
-    string_cv_map["rmsd"]                  = [](const std::string& conf){return new colvar::rmsd(conf);};
-    string_cv_map["gyration"]              = [](const std::string& conf){return new colvar::gyration(conf);};
-    string_cv_map["inertia"]               = [](const std::string& conf){return new colvar::inertia(conf);};
-    string_cv_map["inertiaZ"]              = [](const std::string& conf){return new colvar::inertia_z(conf);};
-    string_cv_map["tilt"]                  = [](const std::string& conf){return new colvar::tilt(conf);};
-    string_cv_map["distanceZ"]             = [](const std::string& conf){return new colvar::distance_z(conf);};
-    string_cv_map["distanceXY"]            = [](const std::string& conf){return new colvar::distance_xy(conf);};
-    string_cv_map["polarTheta"]            = [](const std::string& conf){return new colvar::polar_theta(conf);};
-    string_cv_map["polarPhi"]              = [](const std::string& conf){return new colvar::polar_phi(conf);};
-    string_cv_map["distanceVec"]           = [](const std::string& conf){return new colvar::distance_vec(conf);};
-    string_cv_map["orientationAngle"]      = [](const std::string& conf){return new colvar::orientation_angle(conf);};
-    string_cv_map["distancePairs"]         = [](const std::string& conf){return new colvar::distance_pairs(conf);};
-    string_cv_map["dipoleMagnitude"]       = [](const std::string& conf){return new colvar::dipole_magnitude(conf);};
-    string_cv_map["coordNum"]              = [](const std::string& conf){return new colvar::coordnum(conf);};
-    string_cv_map["selfCoordNum"]          = [](const std::string& conf){return new colvar::selfcoordnum(conf);};
-    string_cv_map["dipoleAngle"]           = [](const std::string& conf){return new colvar::dipole_angle(conf);};
-    string_cv_map["orientation"]           = [](const std::string& conf){return new colvar::orientation(conf);};
-    string_cv_map["orientationProj"]       = [](const std::string& conf){return new colvar::orientation_proj(conf);};
-    string_cv_map["eigenvector"]           = [](const std::string& conf){return new colvar::eigenvector(conf);};
-    string_cv_map["cartesian"]             = [](const std::string& conf){return new colvar::cartesian(conf);};
-    string_cv_map["alpha"]                 = [](const std::string& conf){return new colvar::alpha_angles(conf);};
-    string_cv_map["dihedralPC"]            = [](const std::string& conf){return new colvar::dihedPC(conf);};
-    string_cv_map["linearCombination"]     = [](const std::string& conf){return new colvar::linearCombination(conf);};
-}
-
 #endif

lib/colvars/colvars_version.h

@@ -1,3 +1,3 @@
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2020-07-07"
+#define COLVARS_VERSION "2020-09-17"
 #endif

lib/colvars/colvartypes.cpp

@@ -14,25 +14,19 @@
 #include "colvartypes.h"
 #include "colvarparse.h"
 
+#ifdef COLVARS_LAMMPS
+// Use open-source Jacobi implementation
+#include "math_eigen_impl.h"
+#else
+// Fall back to NR routine
+#include "nr_jacobi.h"
+#endif
+
 
 bool      colvarmodule::rotation::monitor_crossings = false;
 cvm::real colvarmodule::rotation::crossing_threshold = 1.0E-02;
 
 
-namespace  {
-
-/// Numerical recipes diagonalization
-static int jacobi(cvm::real **a, cvm::real *d, cvm::real **v, int *nrot);
-
-/// Eigenvector sort
-static int eigsrt(cvm::real *d, cvm::real **v);
-
-/// Transpose the matrix
-static int transpose(cvm::real **v);
-
-}
-
-
 std::string cvm::rvector::to_simple_string() const
 {
   std::ostringstream os;
@@ -248,6 +242,66 @@ cvm::quaternion::position_derivative_inner(cvm::rvector const &pos,
 // Seok C, Dill KA.  Using quaternions to calculate RMSD.  J Comput
 // Chem. 25(15):1849-57 (2004) DOI: 10.1002/jcc.20110 PubMed: 15376254
 
+#ifdef COLVARS_LAMMPS
+namespace {
+  inline void *new_Jacobi_solver(int size) {
+    return reinterpret_cast<void *>(new MathEigen::Jacobi<cvm::real,
+                                    cvm::vector1d<cvm::real> &,
+                                    cvm::matrix2d<cvm::real> &>(4));
+  }
+}
+#endif
+
+
+colvarmodule::rotation::rotation()
+{
+  b_debug_gradients = false;
+#ifdef COLVARS_LAMMPS
+  jacobi = new_Jacobi_solver(4);
+#else
+  jacobi = NULL;
+#endif
+}
+
+
+colvarmodule::rotation::rotation(cvm::quaternion const &qi)
+  : q(qi)
+{
+  b_debug_gradients = false;
+#ifdef COLVARS_LAMMPS
+  jacobi = new_Jacobi_solver(4);
+#else
+  jacobi = NULL;
+#endif
+}
+
+
+colvarmodule::rotation::rotation(cvm::real angle, cvm::rvector const &axis)
+{
+  b_debug_gradients = false;
+  cvm::rvector const axis_n = axis.unit();
+  cvm::real const sina = cvm::sin(angle/2.0);
+  q = cvm::quaternion(cvm::cos(angle/2.0),
+                      sina * axis_n.x, sina * axis_n.y, sina * axis_n.z);
+#ifdef COLVARS_LAMMPS
+  jacobi = new_Jacobi_solver(4);
+#else
+  jacobi = NULL;
+#endif
+}
+
+
+colvarmodule::rotation::~rotation()
+{
+#ifdef COLVARS_LAMMPS
+  delete reinterpret_cast<
+    MathEigen::Jacobi<cvm::real,
+                      cvm::vector1d<cvm::real> &,
+                      cvm::matrix2d<cvm::real> &> *>(jacobi);
+#endif
+}
+
+
 void colvarmodule::rotation::build_correlation_matrix(
                                         std::vector<cvm::atom_pos> const &pos1,
                                         std::vector<cvm::atom_pos> const &pos2)
@@ -291,10 +345,12 @@ void colvarmodule::rotation::compute_overlap_matrix()
 }
 
 
-void colvarmodule::rotation::diagonalize_matrix(
+#ifndef COLVARS_LAMMPS
-                                            cvm::matrix2d<cvm::real> &m,
+namespace {
-                                            cvm::vector1d<cvm::real> &eigval,
+
-                                            cvm::matrix2d<cvm::real> &eigvec)
+void diagonalize_matrix(cvm::matrix2d<cvm::real> &m,
+                        cvm::vector1d<cvm::real> &eigval,
+                        cvm::matrix2d<cvm::real> &eigvec)
 {
   eigval.resize(4);
   eigval.reset();
@@ -303,15 +359,15 @@ void colvarmodule::rotation::diagonalize_matrix(
 
   // diagonalize
   int jac_nrot = 0;
-  if (jacobi(m.c_array(), eigval.c_array(), eigvec.c_array(), &jac_nrot) !=
+  if (NR_Jacobi::jacobi(m.c_array(), eigval.c_array(), eigvec.c_array(), &jac_nrot) !=
       COLVARS_OK) {
-    cvm::error("Too many iterations in routine jacobi.\n"
+    cvm::error("Too many iterations in jacobi diagonalization.\n"
                "This is usually the result of an ill-defined set of atoms for "
                "rotational alignment (RMSD, rotateReference, etc).\n");
   }
-  eigsrt(eigval.c_array(), eigvec.c_array());
+  NR_Jacobi::eigsrt(eigval.c_array(), eigvec.c_array());
   // jacobi saves eigenvectors by columns
-  transpose(eigvec.c_array());
+  NR_Jacobi::transpose(eigvec.c_array());
 
   // normalize eigenvectors
   for (size_t ie = 0; ie < 4; ie++) {
@@ -327,6 +383,9 @@ void colvarmodule::rotation::diagonalize_matrix(
   }
 }
 
+}
+#endif
+
 
 // Calculate the rotation, plus its derivatives
 
@@ -349,7 +408,28 @@ void colvarmodule::rotation::calc_optimal_rotation(
     cvm::log("S     = "+cvm::to_str(S_backup, cvm::cv_width, cvm::cv_prec)+"\n");
   }
 
+  S_eigval.resize(4);
+  S_eigvec.resize(4, 4);
+
+#ifdef COLVARS_LAMMPS
+  MathEigen::Jacobi<cvm::real,
+                    cvm::vector1d<cvm::real> &,
+                    cvm::matrix2d<cvm::real> &> *ecalc =
+    reinterpret_cast<MathEigen::Jacobi<cvm::real,
+                                       cvm::vector1d<cvm::real> &,
+                                       cvm::matrix2d<cvm::real> &> *>(jacobi);
+
+  int ierror = ecalc->Diagonalize(S, S_eigval, S_eigvec);
+  if (ierror) {
+    cvm::error("Too many iterations in jacobi diagonalization.\n"
+               "This is usually the result of an ill-defined set of atoms for "
+               "rotational alignment (RMSD, rotateReference, etc).\n");
+  }
+#else
   diagonalize_matrix(S, S_eigval, S_eigvec);
+#endif
+
+
   // eigenvalues and eigenvectors
   cvm::real const L0 = S_eigval[0];
   cvm::real const L1 = S_eigval[1];
@@ -521,7 +601,11 @@ void colvarmodule::rotation::calc_optimal_rotation(
 
         //           cvm::log("S_new = "+cvm::to_str(cvm::to_str (S_new), cvm::cv_width, cvm::cv_prec)+"\n");
 
+#ifdef COLVARS_LAMMPS
+        ecalc->Diagonalize(S_new, S_new_eigval, S_new_eigvec);
+#else
         diagonalize_matrix(S_new, S_new_eigval, S_new_eigvec);
+#endif
 
         cvm::real const &L0_new = S_new_eigval[0];
         cvm::quaternion const Q0_new(S_new_eigvec[0]);
@@ -544,138 +628,3 @@ void colvarmodule::rotation::calc_optimal_rotation(
 
 
 
-// Numerical Recipes routine for diagonalization
-
-#define ROTATE(a,i,j,k,l) g=a[i][j]; \
-  h=a[k][l];                         \
-  a[i][j]=g-s*(h+g*tau);             \
-  a[k][l]=h+s*(g-h*tau);
-
-#define n 4
-
-
-namespace {
-
-int jacobi(cvm::real **a, cvm::real *d, cvm::real **v, int *nrot)
-{
-  int j,iq,ip,i;
-  cvm::real tresh,theta,tau,t,sm,s,h,g,c;
-
-  cvm::vector1d<cvm::real> b(n);
-  cvm::vector1d<cvm::real> z(n);
-
-  for (ip=0;ip<n;ip++) {
-    for (iq=0;iq<n;iq++) {
-      v[ip][iq]=0.0;
-    }
-    v[ip][ip]=1.0;
-  }
-  for (ip=0;ip<n;ip++) {
-    b[ip]=d[ip]=a[ip][ip];
-    z[ip]=0.0;
-  }
-  *nrot=0;
-  for (i=0;i<=50;i++) {
-    sm=0.0;
-    for (ip=0;ip<n-1;ip++) {
-      for (iq=ip+1;iq<n;iq++)
-        sm += cvm::fabs(a[ip][iq]);
-    }
-    if (sm == 0.0) {
-      return COLVARS_OK;
-    }
-    if (i < 4)
-      tresh=0.2*sm/(n*n);
-    else
-      tresh=0.0;
-    for (ip=0;ip<n-1;ip++) {
-      for (iq=ip+1;iq<n;iq++) {
-        g=100.0*cvm::fabs(a[ip][iq]);
-        if (i > 4 && (cvm::real)(cvm::fabs(d[ip])+g) == (cvm::real)cvm::fabs(d[ip])
-            && (cvm::real)(cvm::fabs(d[iq])+g) == (cvm::real)cvm::fabs(d[iq]))
-          a[ip][iq]=0.0;
-        else if (cvm::fabs(a[ip][iq]) > tresh) {
-          h=d[iq]-d[ip];
-          if ((cvm::real)(cvm::fabs(h)+g) == (cvm::real)cvm::fabs(h))
-            t=(a[ip][iq])/h;
-          else {
-            theta=0.5*h/(a[ip][iq]);
-            t=1.0/(cvm::fabs(theta)+cvm::sqrt(1.0+theta*theta));
-            if (theta < 0.0) t = -t;
-          }
-          c=1.0/cvm::sqrt(1+t*t);
-          s=t*c;
-          tau=s/(1.0+c);
-          h=t*a[ip][iq];
-          z[ip] -= h;
-          z[iq] += h;
-          d[ip] -= h;
-          d[iq] += h;
-          a[ip][iq]=0.0;
-          for (j=0;j<=ip-1;j++) {
-            ROTATE(a,j,ip,j,iq)
-              }
-          for (j=ip+1;j<=iq-1;j++) {
-            ROTATE(a,ip,j,j,iq)
-              }
-          for (j=iq+1;j<n;j++) {
-            ROTATE(a,ip,j,iq,j)
-              }
-          for (j=0;j<n;j++) {
-            ROTATE(v,j,ip,j,iq)
-              }
-          ++(*nrot);
-        }
-      }
-    }
-    for (ip=0;ip<n;ip++) {
-      b[ip] += z[ip];
-      d[ip]=b[ip];
-      z[ip]=0.0;
-    }
-  }
-  return COLVARS_ERROR;
-}
-
-
-int eigsrt(cvm::real *d, cvm::real **v)
-{
-  int k,j,i;
-  cvm::real p;
-
-  for (i=0;i<n;i++) {
-    p=d[k=i];
-    for (j=i+1;j<n;j++)
-      if (d[j] >= p) p=d[k=j];
-    if (k != i) {
-      d[k]=d[i];
-      d[i]=p;
-      for (j=0;j<n;j++) {
-        p=v[j][i];
-        v[j][i]=v[j][k];
-        v[j][k]=p;
-      }
-    }
-  }
-  return COLVARS_OK;
-}
-
-
-int transpose(cvm::real **v)
-{
-  cvm::real p;
-  int i,j;
-  for (i=0;i<n;i++) {
-    for (j=i+1;j<n;j++) {
-      p=v[i][j];
-      v[i][j]=v[j][i];
-      v[j][i]=p;
-    }
-  }
-  return COLVARS_OK;
-}
-
-}
-
-#undef n
-#undef ROTATE

lib/colvars/colvartypes.h

@@ -1389,30 +1389,16 @@ public:
                              std::vector<atom_pos> const &pos2);
 
   /// Default constructor
-  inline rotation()
+  rotation();
-    : b_debug_gradients(false)
-  {}
 
   /// Constructor after a quaternion
-  inline rotation(cvm::quaternion const &qi)
+  rotation(cvm::quaternion const &qi);
-    : q(qi),
-      b_debug_gradients(false)
-  {
-  }
 
   /// Constructor after an axis of rotation and an angle (in radians)
-  inline rotation(cvm::real angle, cvm::rvector const &axis)
+  rotation(cvm::real angle, cvm::rvector const &axis);
-    : b_debug_gradients(false)
-  {
-    cvm::rvector const axis_n = axis.unit();
-    cvm::real const sina = cvm::sin(angle/2.0);
-    q = cvm::quaternion(cvm::cos(angle/2.0),
-                        sina * axis_n.x, sina * axis_n.y, sina * axis_n.z);
-  }
 
   /// Destructor
-  inline ~rotation()
+  ~rotation();
-  {}
 
   /// Return the rotated vector
   inline cvm::rvector rotate(cvm::rvector const &v) const
@@ -1432,7 +1418,6 @@ public:
     return q.rotation_matrix();
   }
 
-
   /// \brief Return the spin angle (in degrees) with respect to the
   /// provided axis (which MUST be normalized)
   inline cvm::real spin_angle(cvm::rvector const &axis) const
@@ -1537,10 +1522,8 @@ protected:
   /// Compute the overlap matrix S (used by calc_optimal_rotation())
   void compute_overlap_matrix();
 
-  /// Diagonalize a given matrix m (used by calc_optimal_rotation())
+  /// Pointer to instance of Jacobi solver
-  static void diagonalize_matrix(cvm::matrix2d<cvm::real> &m,
+  void *jacobi;
-                                 cvm::vector1d<cvm::real> &eigval,
-                                 cvm::matrix2d<cvm::real> &eigvec);
 };