Commit 9427fc50 authored by Giacomo Fiorin's avatar Giacomo Fiorin
Browse files

Update Colvars library to version 2020-01-27 

One new feature (arithmetic path variables) and several smaller enhancements
or bugfixes.

    Fix error check when loading an old state file
    https://github.com/Colvars/colvars/pull/317

    Get default values for grid boundaries when available
    https://github.com/Colvars/colvars/pull/310

    Allow redefining existing index groups (warn when this happens)
    https://github.com/Colvars/colvars/pull/302

    Simplified replica communication syntax in metadynamics
    https://github.com/Colvars/colvars/pull/301

    Obtain the bias_energy for ABF biases
    https://github.com/Colvars/colvars/pull/294

    Fix reading path file with vector CVCs
    https://github.com/Colvars/colvars/pull/288

    Fix segfault at deleting CVBasedPath
    https://github.com/Colvars/colvars/pull/286

    Parrinello's (arithmetic) pathCV in CV space
    https://github.com/Colvars/colvars/pull/274

    Fix race condition when starting a bundle of walkers
    https://github.com/Colvars/colvars/pull/279
parent 5eef3b18

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

+11.7 KiB (662 KiB)

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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.

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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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