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
This commit is contained in:
Giacomo Fiorin
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@ -15,7 +15,7 @@ else
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COLVARS_DEBUG_INCFLAGS = -DCOLVARS_DEBUG
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endif
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COLVARS_INCFLAGS = $(COLVARS_DEBUG_INCFLAGS) $(COLVARS_PYTHON_INCFLAGS)
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COLVARS_INCFLAGS = -DCOLVARS_LAMMPS $(COLVARS_DEBUG_INCFLAGS) $(COLVARS_PYTHON_INCFLAGS) -I../../src
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.SUFFIXES:
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@ -4,79 +4,227 @@ $(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \
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colvarproxy_tcl.h colvarproxy_volmaps.h colvarparse.h colvarparams.h \
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colvaratoms.h colvardeps.h
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$(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \
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colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
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colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h colvarparse.h \
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colvarparams.h colvardeps.h colvarbias_abf.h colvarbias.h colvargrid.h \
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colvar_UIestimator.h
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colvars_version.h colvar.h colvarvalue.h colvartypes.h colvarparse.h \
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colvarparams.h colvardeps.h lepton/include/Lepton.h \
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lepton/include/lepton/CompiledExpression.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/windowsIncludes.h \
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lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/ExpressionProgram.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/Exception.h \
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lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
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colvarbias_abf.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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colvarbias.h colvargrid.h colvar_UIestimator.h
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$(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \
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colvars_version.h colvarbias.h colvar.h colvarvalue.h colvartypes.h \
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colvarparse.h colvarparams.h colvardeps.h colvarbias_alb.h
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colvarparse.h colvarparams.h colvardeps.h lepton/include/Lepton.h \
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lepton/include/lepton/CompiledExpression.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/windowsIncludes.h \
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lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/ExpressionProgram.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/Exception.h \
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lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
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colvarbias_alb.h
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$(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
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colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
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colvarproxy_tcl.h colvarproxy_volmaps.h colvarbias.h colvar.h \
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colvarparse.h colvarparams.h colvardeps.h colvargrid.h
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colvarparse.h colvarparams.h colvardeps.h lepton/include/Lepton.h \
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lepton/include/lepton/CompiledExpression.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/windowsIncludes.h \
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lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/ExpressionProgram.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/Exception.h \
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lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
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colvargrid.h
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$(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
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colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
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colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h \
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colvarparse.h colvarparams.h colvardeps.h colvarbias_histogram.h \
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colvarbias.h colvargrid.h
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colvarparse.h colvarparams.h colvardeps.h lepton/include/Lepton.h \
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lepton/include/lepton/CompiledExpression.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/windowsIncludes.h \
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lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/ExpressionProgram.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/Exception.h \
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lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
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colvarbias_histogram.h colvarbias.h colvargrid.h
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$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
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colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
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colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h colvarparse.h \
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colvarparams.h colvardeps.h colvarbias_meta.h colvarbias.h colvargrid.h
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colvarparams.h colvardeps.h lepton/include/Lepton.h \
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lepton/include/lepton/CompiledExpression.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/windowsIncludes.h \
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lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/ExpressionProgram.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/Exception.h \
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lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
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colvarbias_meta.h colvarbias.h colvargrid.h
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$(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
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colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
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colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
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colvarparams.h colvardeps.h
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colvarparams.h colvardeps.h lepton/include/Lepton.h \
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lepton/include/lepton/CompiledExpression.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/windowsIncludes.h \
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lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/ExpressionProgram.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/Exception.h \
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lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h
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$(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \
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colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \
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colvarparse.h colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h \
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colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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colvar_arithmeticpath.h colvar_geometricpath.h
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colvarparse.h colvarparams.h colvardeps.h lepton/include/Lepton.h \
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lepton/include/lepton/CompiledExpression.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/windowsIncludes.h \
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lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/ExpressionProgram.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/Exception.h \
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lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
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colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
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colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
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$(COLVARS_OBJ_DIR)colvarcomp_apath.o: colvarcomp_apath.cpp colvarmodule.h \
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colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
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colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
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colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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colvar_arithmeticpath.h colvar_geometricpath.h
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colvarparams.h colvar.h colvardeps.h lepton/include/Lepton.h \
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lepton/include/lepton/CompiledExpression.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/windowsIncludes.h \
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lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/ExpressionProgram.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/Exception.h \
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lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
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colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
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colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
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$(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \
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colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \
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colvartypes.h colvarparams.h colvaratoms.h colvarproxy.h \
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colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h colvar.h \
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lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/windowsIncludes.h \
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lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/ExpressionProgram.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/Exception.h \
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lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
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colvarcomp.h colvar_arithmeticpath.h colvar_geometricpath.h
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$(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \
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colvars_version.h colvarvalue.h colvartypes.h colvar.h colvarparse.h \
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colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
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colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \
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colvar_geometricpath.h
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colvarparams.h colvardeps.h lepton/include/Lepton.h \
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lepton/include/lepton/CompiledExpression.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/windowsIncludes.h \
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lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/ExpressionProgram.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/Exception.h \
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lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
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colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
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colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
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$(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \
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colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
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colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
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colvaratoms.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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colvar_arithmeticpath.h colvar_geometricpath.h
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colvarparse.h colvarparams.h colvar.h colvardeps.h \
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lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/windowsIncludes.h \
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lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/ExpressionProgram.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/Exception.h \
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lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
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colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
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colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
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$(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp colvarmodule.h \
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colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
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colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
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colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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colvar_arithmeticpath.h colvar_geometricpath.h
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colvarparams.h colvar.h colvardeps.h lepton/include/Lepton.h \
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lepton/include/lepton/CompiledExpression.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/windowsIncludes.h \
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lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/ExpressionProgram.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/Exception.h \
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lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
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colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
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colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
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$(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \
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colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
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colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
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colvaratoms.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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colvar_arithmeticpath.h colvar_geometricpath.h
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colvarparse.h colvarparams.h colvar.h colvardeps.h \
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lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/windowsIncludes.h \
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lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/ExpressionProgram.h \
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lepton/include/lepton/ExpressionTreeNode.h \
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lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
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lepton/include/lepton/Exception.h \
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lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
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colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
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colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h
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$(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \
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colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
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colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
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colvaratoms.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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||||
colvar_arithmeticpath.h colvar_geometricpath.h
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||||
colvarparse.h colvarparams.h colvar.h colvardeps.h \
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||||
lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
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||||
lepton/include/lepton/ExpressionTreeNode.h \
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||||
lepton/include/lepton/windowsIncludes.h \
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||||
lepton/include/lepton/CustomFunction.h \
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||||
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 \
|
||||
colvaratoms.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||
colvar_arithmeticpath.h colvar_geometricpath.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
|
||||
$(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 \
|
||||
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 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
|
||||
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_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_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 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
|
||||
colvarparams.h ../../src/math_eigen.h
|
||||
$(COLVARS_OBJ_DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h \
|
||||
colvars_version.h colvarvalue.h colvartypes.h
|
||||
|
||||
@ -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;
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -1,3 +1,3 @@
|
||||
#ifndef COLVARS_VERSION
|
||||
#define COLVARS_VERSION "2020-07-07"
|
||||
#define COLVARS_VERSION "2020-09-17"
|
||||
#endif
|
||||
|
||||
@ -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)
|
||||
@ -291,8 +345,10 @@ void colvarmodule::rotation::compute_overlap_matrix()
|
||||
}
|
||||
|
||||
|
||||
void colvarmodule::rotation::diagonalize_matrix(
|
||||
cvm::matrix2d<cvm::real> &m,
|
||||
#ifndef COLVARS_LAMMPS
|
||||
namespace {
|
||||
|
||||
void diagonalize_matrix(cvm::matrix2d<cvm::real> &m,
|
||||
cvm::vector1d<cvm::real> &eigval,
|
||||
cvm::matrix2d<cvm::real> &eigvec)
|
||||
{
|
||||
@ -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
|
||||
|
||||
@ -1389,30 +1389,16 @@ public:
|
||||
std::vector<atom_pos> const &pos2);
|
||||
|
||||
/// Default constructor
|
||||
inline rotation()
|
||||
: b_debug_gradients(false)
|
||||
{}
|
||||
rotation();
|
||||
|
||||
/// Constructor after a quaternion
|
||||
inline rotation(cvm::quaternion const &qi)
|
||||
: q(qi),
|
||||
b_debug_gradients(false)
|
||||
{
|
||||
}
|
||||
rotation(cvm::quaternion const &qi);
|
||||
|
||||
/// Constructor after an axis of rotation and an angle (in radians)
|
||||
inline 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);
|
||||
}
|
||||
rotation(cvm::real angle, cvm::rvector const &axis);
|
||||
|
||||
/// 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())
|
||||
static void diagonalize_matrix(cvm::matrix2d<cvm::real> &m,
|
||||
cvm::vector1d<cvm::real> &eigval,
|
||||
cvm::matrix2d<cvm::real> &eigvec);
|
||||
/// Pointer to instance of Jacobi solver
|
||||
void *jacobi;
|
||||
};
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user