Merge pull request #1859 from giacomofiorin/colvars-update (668feb22) · Commits · 郑智淋 / lammps

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

+11.7 KiB (662 KiB)

File changed.

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lib/colvars/Makefile.common

+3 −0

Original line number	Diff line number	Diff line
		@@ -31,6 +31,7 @@ COLVARS_SRCS = \
		colvarbias_meta.cpp \
		colvarbias_restraint.cpp \
		colvarcomp_angles.cpp \
		colvarcomp_apath.cpp \
		colvarcomp_coordnums.cpp \
		colvarcomp.cpp \
		colvarcomp_distances.cpp \
		@@ -41,8 +42,10 @@ COLVARS_SRCS = \
		colvardeps.cpp \
		colvargrid.cpp \
		colvarmodule.cpp \
		colvarparams.cpp \
		colvarparse.cpp \
		colvarproxy.cpp \
		colvarproxy_replicas.cpp \
		colvarscript.cpp \
		colvartypes.cpp \
		colvarvalue.cpp

lib/colvars/Makefile.deps

+46 −191

Original line number	Diff line number	Diff line

		$(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \
		colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
		colvarparse.h colvaratoms.h colvardeps.h
		colvarparse.h colvarparams.h colvaratoms.h colvardeps.h
		$(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \
		colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \
		colvarparse.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 colvarbias.h colvargrid.h colvar_UIestimator.h
		colvarparse.h colvarparams.h colvardeps.h colvarbias_abf.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 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 colvarbias_alb.h
		$(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
		colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvarbias.h \
		colvar.h colvarparse.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
		colvar.h colvarparse.h colvarparams.h colvardeps.h colvargrid.h
		$(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
		colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
		colvarvalue.h colvar.h colvarparse.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 \
		colvarvalue.h colvar.h colvarparse.h colvarparams.h colvardeps.h \
		colvarbias_histogram.h colvarbias.h colvargrid.h
		$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
		colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \
		colvarparse.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
		colvarparse.h colvarparams.h colvardeps.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 colvarbias_restraint.h colvarbias.h colvar.h colvarparse.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
		$(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \
		colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \
		colvarparse.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
		colvarparse.h colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h \
		colvarproxy.h colvar_arithmeticpath.h
		$(COLVARS_OBJ_DIR)colvarcomp_apath.o: colvarcomp_apath.cpp
		$(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \
		colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \
		colvartypes.h colvaratoms.h colvarproxy.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
		colvartypes.h colvarparams.h colvaratoms.h colvarproxy.h colvardeps.h \
		colvar.h colvarcomp.h colvar_arithmeticpath.h
		$(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \
		colvars_version.h colvarvalue.h colvartypes.h colvar.h colvarparse.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
		colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
		colvar_arithmeticpath.h
		$(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \
		colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
		colvarparse.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
		colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
		colvaratoms.h colvarproxy.h colvar_arithmeticpath.h
		$(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp
		$(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \
		colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
		colvarparse.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
		colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
		colvaratoms.h colvarproxy.h colvar_arithmeticpath.h
		$(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \
		colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
		colvarparse.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
		colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
		colvaratoms.h colvarproxy.h colvar_arithmeticpath.h
		$(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
		colvarvalue.h colvartypes.h colvarparse.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 colvarscript.h colvarbias.h
		colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.h \
		colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
		colvar_arithmeticpath.h colvarscript.h colvarbias.h
		$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \
		colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvardeps.h \
		colvarparse.h
		colvarparse.h colvarparams.h
		$(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \
		colvars_version.h colvarvalue.h colvartypes.h colvarparse.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 colvargrid.h
		colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
		colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
		colvarproxy.h colvar_arithmeticpath.h colvargrid.h
		$(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
		colvars_version.h colvarparse.h colvarvalue.h colvartypes.h \
		colvarproxy.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 colvaratoms.h colvarcomp.h
		colvarparams.h colvarproxy.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 colvaratoms.h colvarcomp.h colvar_arithmeticpath.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 \
		colvars_version.h colvarvalue.h colvartypes.h colvarparse.h
		colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
		colvarparams.h
		$(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \
		colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
		colvarscript.h colvarbias.h colvar.h colvarparse.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
		colvarscript.h colvarbias.h colvar.h colvarparse.h colvarparams.h \
		colvardeps.h colvaratoms.h
		$(COLVARS_OBJ_DIR)colvarproxy_replicas.o: colvarproxy_replicas.cpp \
		colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
		colvarvalue.h
		$(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarscript.h \
		colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
		colvarbias.h colvar.h colvarparse.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 colvar.h colvarparse.h colvarparams.h colvardeps.h \
		colvarproxy.h
		$(COLVARS_OBJ_DIR)colvartypes.o: colvartypes.cpp colvarmodule.h \
		colvars_version.h colvartypes.h colvarparse.h colvarvalue.h
		colvars_version.h colvartypes.h colvarparse.h colvarvalue.h \
		colvarparams.h
		$(COLVARS_OBJ_DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h \
		colvars_version.h colvarvalue.h colvartypes.h

lib/colvars/colvar.cpp

+164 −29

File changed.

Preview size limit exceeded, changes collapsed.

lib/colvars/colvar.h

+50 −23

Original line number	Diff line number	Diff line
		@@ -2,7 +2,7 @@

		// This file is part of the Collective Variables module (Colvars).
		// The original version of Colvars and its updates are located at:
		// https://github.com/colvars/colvars
		// https://github.com/Colvars/colvars
		// Please update all Colvars source files before making any changes.
		// If you wish to distribute your changes, please submit them to the
		// Colvars repository at GitHub.
		@@ -217,11 +217,11 @@ public:
		/// should equal the system force plus \link f \endlink
		colvarvalue ft;


		/// Period, if this variable is periodic
		cvm::real period;
		cvm::real wrap_center;

		/// Center of wrapping, if this variable is periodic
		cvm::real wrap_center;

		/// \brief Expand the boundaries of multiples of width, to keep the
		/// value always within range
		@@ -233,8 +233,6 @@ public:
		colvarvalue lower_wall;
		/// \brief Force constant for the lower boundary potential (\|x-xb\|^2)
		cvm::real lower_wall_k;
		/// \brief Whether this colvar has a hard lower boundary
		bool hard_lower_boundary;

		/// \brief Location of the upper boundary
		colvarvalue upper_boundary;
		@@ -242,8 +240,6 @@ public:
		colvarvalue upper_wall;
		/// \brief Force constant for the upper boundary potential (\|x-xb\|^2)
		cvm::real upper_wall_k;
		/// \brief Whether this colvar has a hard upper boundary
		bool hard_upper_boundary;

		/// \brief Is the interval defined by the two boundaries periodic?
		bool periodic_boundaries() const;
		@@ -356,7 +352,7 @@ public:
		/// colvar::update()) to the external degrees of freedom
		void communicate_forces();

		/// \brief Enables and disables individual CVCs based on flags
		/// \brief Enables and disables individual CVCs based on the given array
		int set_cvc_flags(std::vector<bool> const &flags);

		/// \brief Updates the flags in the CVC objects, and their number
		@@ -365,7 +361,23 @@ public:
		/// \brief Modify the configuration of CVCs (currently, only base class data)
		int update_cvc_config(std::vector<std::string> const &confs);

		/// Whether this named parameter exists (in the first and only component)
		int cvc_param_exists(std::string const &param_name);

		/// Get the value of the named parameter (from the first and only component)
		cvm::real get_cvc_param(std::string const &param_name);

		/// Get a pointer to the named parameter (from the first and only component)
		void const *get_cvc_param_ptr(std::string const &param_name);

		/// Pointer to the derivative of the variable with respect to param_name
		colvarvalue const *get_cvc_param_grad(std::string const &param_name);

		/// Set the named parameter in the first and only component to the given value
		int set_cvc_param(std::string const &param_name, void const *new_value);

		protected:

		/// \brief Number of CVC objects with an active flag
		size_t n_active_cvcs;

		@@ -380,11 +392,24 @@ protected:

		public:

		/// \brief Return the number of CVC objects defined
		inline size_t num_cvcs() const { return cvcs.size(); }
		/// \brief Number of dimensions of the value of this colvar
		inline size_t num_dimensions() const
		{
		return value().size();
		}

		/// \brief Return the number of CVC objects with an active flag (as set by update_cvc_flags)
		inline size_t num_active_cvcs() const { return n_active_cvcs; }
		/// \brief Number of CVC objects defined
		inline size_t num_cvcs() const
		{
		return cvcs.size();
		}

		/// \brief number of CVC objects with an active flag (as set by
		/// update_cvc_flags)
		inline size_t num_active_cvcs() const
		{
		return n_active_cvcs;
		}

		/// \brief Use the internal metrics (as from \link colvar::cvc
		/// \endlink objects) to calculate square distances and gradients
		@@ -413,22 +438,20 @@ public:
		/// Handles correctly symmetries and periodic boundary conditions
		void wrap(colvarvalue &x_unwrapped) const;


		/// Read the analysis tasks
		int parse_analysis(std::string const &conf);

		/// Perform analysis tasks
		int analyze();


		/// Read the value from a collective variable trajectory file
		std::istream & read_traj(std::istream &is);

		/// Output formatted values to the trajectory file
		std::ostream & write_traj(std::ostream &os);
		/// Write a label to the trajectory file (comment line)
		std::ostream & write_traj_label(std::ostream &os);


		/// Read the collective variable from a restart file
		std::istream & read_restart(std::istream &is);
		/// Write the collective variable to a restart file
		@@ -437,8 +460,8 @@ public:
		/// Write output files (if defined, e.g. in analysis mode)
		int write_output_files();


		protected:

		/// Previous value (to calculate velocities during analysis)
		colvarvalue x_old;

		@@ -530,11 +553,12 @@ protected:
		/// Calculate the running average and its standard deviation
		int calc_runave();

		/// If extended Lagrangian active: colvar energies (kinetic and harmonic potential)
		/// If extended Lagrangian active: colvar kinetic energy
		cvm::real kinetic_energy;
		/// If extended Lagrangian active: colvar harmonic potential
		cvm::real potential_energy;
		public:

		public:

		// collective variable component base class
		class cvc;
		@@ -577,6 +601,8 @@ public:
		class CVBasedPath;
		class gspathCV;
		class gzpathCV;
		class aspathCV;
		class azpathCV;

		// non-scalar components
		class distance_vec;
		@@ -596,7 +622,6 @@ protected:
		/// in all cvcs (called when enabling f_cv_collect_gradients)
		void build_atom_list(void);

		private:
		/// Name of scripted function to be used
		std::string scripted_function;

		@@ -620,6 +645,7 @@ private:
		#endif

		public:

		/// \brief Sorted array of (zero-based) IDs for all atoms involved
		std::vector<int> atom_ids;

		@@ -628,34 +654,35 @@ public:
		/// For scalar variables only!
		std::vector<cvm::rvector> atomic_gradients;

		inline size_t n_components() const {
		return cvcs.size();
		}

		/// \brief Get vector of vectors of atom IDs for all atom groups
		virtual std::vector<std::vector<int> > get_atom_lists();
		};


		inline cvm::real const & colvar::force_constant() const
		{
		return ext_force_k;
		}


		inline colvarvalue const & colvar::value() const
		{
		return x_reported;
		}


		inline colvarvalue const & colvar::actual_value() const
		{
		return x;
		}


		inline colvarvalue const & colvar::run_ave() const
		{
		return runave;
		}


		inline colvarvalue const & colvar::velocity() const
		{
		return v_reported;

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