From 7e984bfa2ca1fa276ee01e6823eb990b0b0cefa1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 27 Dec 2022 11:16:09 -0500 Subject: [PATCH] update traditional make build support for shaking Lepton between LEPTON and COLVARS --- lib/colvars/Makefile.common | 21 +- lib/colvars/Makefile.deps | 697 +++++++++++++++++-------------- lib/colvars/Makefile.lepton.deps | 50 --- lib/colvars/README | 33 +- src/COLVARS/Install.sh | 18 +- 5 files changed, 398 insertions(+), 421 deletions(-) delete mode 100644 lib/colvars/Makefile.lepton.deps diff --git a/lib/colvars/Makefile.common b/lib/colvars/Makefile.common index 31a93652ae..f6d6ba84bb 100644 --- a/lib/colvars/Makefile.common +++ b/lib/colvars/Makefile.common @@ -61,22 +61,12 @@ COLVARS_SRCS = \ colvarvalue.cpp \ colvar_neuralnetworkcompute.cpp -LEPTON_SRCS = \ - lepton/src/CompiledExpression.cpp \ - lepton/src/CompiledVectorExpression.cpp \ - lepton/src/ExpressionProgram.cpp \ - lepton/src/ExpressionTreeNode.cpp \ - lepton/src/Operation.cpp \ - lepton/src/ParsedExpression.cpp \ - lepton/src/Parser.cpp - # Allow to selectively turn off Lepton ifeq ($(COLVARS_LEPTON),no) LEPTON_INCFLAGS = COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o) else -LEPTON_INCFLAGS = -Ilepton/include -DLEPTON -COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o) $(LEPTON_SRCS:.cpp=.o) +LEPTON_INCFLAGS = -I../lepton/include -DLEPTON endif @@ -97,12 +87,3 @@ Makefile.deps: $(COLVARS_SRCS) include Makefile.deps -Makefile.lepton.deps: $(LEPTON_SRCS) - @echo > $@ - @for src in $^ ; do \ - obj=`basename $$src .cpp`.o ; \ - $(CXX) $(CXXFLAGS) -MM $(LEPTON_INCFLAGS) \ - -MT '$$(COLVARS_OBJ_DIR)'$$obj $$src >> $@ ; \ - done - -include Makefile.lepton.deps diff --git a/lib/colvars/Makefile.deps b/lib/colvars/Makefile.deps index d26df41995..6619653af0 100644 --- a/lib/colvars/Makefile.deps +++ b/lib/colvars/Makefile.deps @@ -5,327 +5,367 @@ $(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \ colvaratoms.h colvardeps.h $(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \ colvars_version.h colvar.h colvarvalue.h colvartypes.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_abf.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \ - colvarbias.h colvargrid.h colvar_UIestimator.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_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 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 + 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 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 + 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 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_histogram.h colvarbias.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 colvarbias_histogram.h colvarbias.h \ + colvargrid.h $(COLVARS_OBJ_DIR)colvarbias_histogram_reweight_amd.o: \ colvarbias_histogram_reweight_amd.cpp \ colvarbias_histogram_reweight_amd.h colvarbias_histogram.h colvarbias.h \ colvar.h colvarmodule.h colvars_version.h colvarvalue.h colvartypes.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 colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.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 colvarproxy.h \ + colvarproxy_tcl.h colvarproxy_volmaps.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 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 + 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 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 + 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_alchlambda.o: colvarcomp_alchlambda.cpp \ colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \ colvarparse.h colvarparams.h colvar.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 + ../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 $(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 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 + 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 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 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 + colvarparams.h colvar.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 $(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 + ../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 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 + 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 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 \ - 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 + ../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 $(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 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 + colvarparams.h colvar.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 $(COLVARS_OBJ_DIR)colvarcomp_neuralnetwork.o: \ colvarcomp_neuralnetwork.cpp colvarmodule.h colvars_version.h \ colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.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 \ + 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 \ colvar_neuralnetworkcompute.h $(COLVARS_OBJ_DIR)colvarcomp_combination.o: colvarcomp_combination.cpp \ colvarcomp.h colvarmodule.h colvars_version.h colvar.h colvarvalue.h \ colvartypes.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 \ - colvaratoms.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \ - colvar_arithmeticpath.h colvar_geometricpath.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 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 \ - 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 + ../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 $(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 \ - 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 + ../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 $(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 \ - 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 + ../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 $(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \ colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.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 + 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 $(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \ colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \ colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h colvarparse.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 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 \ - colvargrid.h + colvarparams.h colvar.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 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 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.h colvarbias_abf.h colvargrid.h colvar_UIestimator.h \ - colvarbias_alb.h colvarbias_histogram.h \ - colvarbias_histogram_reweight_amd.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 colvarmodule_refs.h + colvar.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.h colvarbias_abf.h \ + colvargrid.h colvar_UIestimator.h colvarbias_alb.h \ + colvarbias_histogram.h colvarbias_histogram_reweight_amd.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 colvarmodule_refs.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 \ @@ -335,17 +375,19 @@ $(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 colvarmodule_utils.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 colvarmodule_utils.h $(COLVARS_OBJ_DIR)colvarproxy_replicas.o: colvarproxy_replicas.cpp \ colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \ colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h @@ -360,64 +402,68 @@ $(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 + ../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 + ../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 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 + 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_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 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 + 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)colvartypes.o: colvartypes.cpp colvarmodule.h \ colvars_version.h colvartypes.h colvarparse.h colvarvalue.h \ colvarparams.h ../../src/math_eigen_impl.h @@ -425,14 +471,15 @@ $(COLVARS_OBJ_DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h \ colvars_version.h colvarvalue.h colvartypes.h $(COLVARS_OBJ_DIR)colvar_neuralnetworkcompute.o: \ colvar_neuralnetworkcompute.cpp colvar_neuralnetworkcompute.h \ - lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ - lepton/include/lepton/ExpressionTreeNode.h \ - lepton/include/lepton/windowsIncludes.h \ - lepton/include/lepton/CustomFunction.h \ - lepton/include/lepton/ExpressionProgram.h \ - lepton/include/lepton/ExpressionTreeNode.h \ - lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ - lepton/include/lepton/Exception.h \ - lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ - colvarparse.h colvarmodule.h colvars_version.h colvarvalue.h \ - colvartypes.h colvarparams.h + ../lepton/include/Lepton.h ../lepton/include/lepton/CompiledExpression.h \ + ../lepton/include/lepton/ExpressionTreeNode.h \ + ../lepton/include/lepton/windowsIncludes.h \ + ../lepton/include/lepton/CustomFunction.h \ + ../lepton/include/lepton/ExpressionProgram.h \ + ../lepton/include/lepton/ExpressionTreeNode.h \ + ../lepton/include/lepton/Operation.h \ + ../lepton/include/lepton/CustomFunction.h \ + ../lepton/include/lepton/Exception.h \ + ../lepton/include/lepton/ParsedExpression.h \ + ../lepton/include/lepton/Parser.h colvarparse.h colvarmodule.h \ + colvars_version.h colvarvalue.h colvartypes.h colvarparams.h diff --git a/lib/colvars/Makefile.lepton.deps b/lib/colvars/Makefile.lepton.deps deleted file mode 100644 index 4546339de6..0000000000 --- a/lib/colvars/Makefile.lepton.deps +++ /dev/null @@ -1,50 +0,0 @@ - -$(COLVARS_OBJ_DIR)CompiledExpression.o: lepton/src/CompiledExpression.cpp \ - lepton/include/lepton/CompiledExpression.h \ - lepton/include/lepton/ExpressionTreeNode.h \ - lepton/include/lepton/windowsIncludes.h \ - lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ - lepton/include/lepton/Exception.h \ - lepton/include/lepton/ParsedExpression.h -$(COLVARS_OBJ_DIR)CompiledVectorExpression.o: \ - lepton/src/CompiledVectorExpression.cpp \ - lepton/include/lepton/CompiledVectorExpression.h \ - lepton/include/lepton/ExpressionTreeNode.h \ - lepton/include/lepton/windowsIncludes.h \ - lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ - lepton/include/lepton/Exception.h \ - lepton/include/lepton/ParsedExpression.h -$(COLVARS_OBJ_DIR)ExpressionProgram.o: lepton/src/ExpressionProgram.cpp \ - lepton/include/lepton/ExpressionProgram.h \ - lepton/include/lepton/ExpressionTreeNode.h \ - lepton/include/lepton/windowsIncludes.h \ - lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ - lepton/include/lepton/Exception.h \ - lepton/include/lepton/ParsedExpression.h -$(COLVARS_OBJ_DIR)ExpressionTreeNode.o: lepton/src/ExpressionTreeNode.cpp \ - lepton/include/lepton/ExpressionTreeNode.h \ - lepton/include/lepton/windowsIncludes.h \ - lepton/include/lepton/Exception.h lepton/include/lepton/Operation.h \ - lepton/include/lepton/CustomFunction.h lepton/include/lepton/Exception.h -$(COLVARS_OBJ_DIR)Operation.o: lepton/src/Operation.cpp \ - lepton/include/lepton/Operation.h \ - lepton/include/lepton/windowsIncludes.h \ - lepton/include/lepton/CustomFunction.h lepton/include/lepton/Exception.h \ - lepton/include/lepton/ExpressionTreeNode.h lepton/src/MSVC_erfc.h -$(COLVARS_OBJ_DIR)ParsedExpression.o: lepton/src/ParsedExpression.cpp \ - lepton/include/lepton/ParsedExpression.h \ - lepton/include/lepton/ExpressionTreeNode.h \ - lepton/include/lepton/windowsIncludes.h \ - lepton/include/lepton/CompiledExpression.h \ - lepton/include/lepton/CompiledVectorExpression.h \ - lepton/include/lepton/ExpressionProgram.h \ - lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \ - lepton/include/lepton/Exception.h -$(COLVARS_OBJ_DIR)Parser.o: lepton/src/Parser.cpp \ - lepton/include/lepton/Parser.h lepton/include/lepton/windowsIncludes.h \ - lepton/include/lepton/CustomFunction.h lepton/include/lepton/Exception.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/ExpressionTreeNode.h diff --git a/lib/colvars/README b/lib/colvars/README index eeba557ce3..cd1e08b6de 100644 --- a/lib/colvars/README +++ b/lib/colvars/README @@ -35,39 +35,32 @@ The reference article is: The Colvars library can be built for the most part with all major versions of the C++ language. -A few of the most recent features require C++11 support. In particular, the -library is optionally built together with the -"Lepton"_https://simtk.org/projects/lepton library, a copy of which is also -included in the LAMMPS distribution. Lepton implements the -"customFunction"_http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction -feature, and requires C++11 support. - -See "here"_https://colvars.github.io/README-c++11.html for a detailed list of -C++11-only features. - +A few of the most recent features require C++11 support, which is also required +by LAMMPS, so no additional notes are needed. ## How to build (CMake) This is the recommended build recipe: no additional settings are normally needed besides "-D PKG_COLVARS=yes". -Building and linking of Lepton (or other C++11-only features) is enabled -automatically when compilation is carried out with C++11 support, and disabled -otherwise. Optionally, Lepton build may be manually controlled with the flag -"-D COLVARS_LEPTON=yes|no". - +Linking to the Lepton library, which is also used by the LEPTON LAMMPS package, +is enabled automatically. Optionally, support for Lepton within Colvars may +be manually controlled with theCMake setting "-D COLVARS_LEPTON=yes|no". ## How to build (traditional make) -Before building LAMMPS, one must build the Colvars library in lib/colvars. +Before building LAMMPS, one must build the Colvars library in lib/colvars +and the Lepton library in lib/lepton. For building Lepton please see the +README.md file in the lib/lepton folder. -This can be done manually in the same folder by using or adapting one of the -provided Makefiles: for example, Makefile.g++ for the GNU compiler. +Building the Colvars library can be done manually in the respective +folders by using or adapting one of the provided Makefiles: for example, +Makefile.g++ for the GNU compiler. In general, it is safer to use build setting consistent with the rest of LAMMPS. This is best carried out from the LAMMPS src directory using a -command like these, which simply invoke the lib/colvars/Install.py script with -the specified args: +command like these, which simply invoke the lib/colvars/Install.py script +with the specified args: make lib-colvars # print help message make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") diff --git a/src/COLVARS/Install.sh b/src/COLVARS/Install.sh index ebabfd7a1e..6b9b9febe0 100755 --- a/src/COLVARS/Install.sh +++ b/src/COLVARS/Install.sh @@ -38,12 +38,12 @@ if (test $1 = 1) then if (test -e ../Makefile.package) then sed -i -e 's/[^ \t]*colvars[^ \t]* //g' ../Makefile.package - sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/colvars |' ../Makefile.package - sed -i -e 's|^PKG_PATH =[ \t]*|&-L..\/..\/lib\/colvars$(LIBOBJDIR) |' ../Makefile.package - sed -i -e 's|^PKG_LIB =[ \t]*|&-lcolvars |' ../Makefile.package - sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(colvars_SYSINC) |' ../Makefile.package - sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(colvars_SYSLIB) |' ../Makefile.package - sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(colvars_SYSPATH) |' ../Makefile.package + sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/colvars -I..\/..\/lib\/lepton\/include |' ../Makefile.package + sed -i -e 's|^PKG_PATH =[ \t]*|&-L..\/..\/lib\/colvars$(LIBOBJDIR) -L..\/..\/lib\/lepton$(LIBOBJDIR) |' ../Makefile.package + sed -i -e 's|^PKG_LIB =[ \t]*|&-lcolvars -llepton|' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(colvars_SYSINC) $(lepton_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(colvars_SYSLIB) $(lepton_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(colvars_SYSPATH) $(lepton_SYSPATH) |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then @@ -51,6 +51,12 @@ if (test $1 = 1) then # multiline form needed for BSD sed on Macs sed -i -e '4 i \ include ..\/..\/lib\/colvars\/Makefile.lammps +' ../Makefile.package.settings + + sed -i -e '/^[ \t]*include.*lepton.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ +include ..\/..\/lib\/lepton\/Makefile.lammps ' ../Makefile.package.settings fi