git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8162 f3b2605a-c512-4ea7-a41b-209d697bcdaa

lib/colvars/colvarbias.h

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+#ifndef COLVARBIAS_H
+#define COLVARBIAS_H
+
+#include "colvar.h"
+#include "colvarparse.h"
+
+
+/// \brief Collective variable bias, base class
+class colvarbias : public colvarparse {
+public:
+
+  /// Numeric id of this bias
+  int            id;
+
+  /// Name of this bias
+  std::string    name;
+  
+  /// Add a new collective variable to this bias
+  void add_colvar (std::string const &cv_name);
+
+  /// Retrieve colvar values and calculate their biasing forces
+  /// Return bias energy
+  virtual cvm::real update() = 0;
+
+  /// Load new configuration - force constant and/or centers only
+  virtual void change_configuration(std::string const &conf);
+
+  /// Calculate change in energy from using alternate configuration
+  virtual cvm::real energy_difference(std::string const &conf);
+
+  /// Perform analysis tasks
+  virtual inline void analyse() {}
+
+  /// Send forces to the collective variables
+  void communicate_forces();
+
+  /// \brief Constructor
+  /// 
+  /// The constructor of the colvarbias base class is protected, so
+  /// that it can only be called from inherited classes
+  colvarbias (std::string const &conf, char const *key);
+
+  /// Default constructor
+  colvarbias();
+
+  /// Destructor
+  virtual inline ~colvarbias() {}
+
+  /// Read the bias configuration from a restart file
+  virtual std::istream & read_restart (std::istream &is) = 0;
+
+  /// Write the bias configuration to a restart file
+  virtual std::ostream & write_restart (std::ostream &os) = 0;
+
+protected:
+
+  /// \brief Pointers to collective variables to which the bias is
+  /// applied; current values and metric functions will be obtained
+  /// through each colvar object
+  std::vector<colvar *>    colvars;
+
+  /// \brief Current forces from this bias to the colvars
+  std::vector<colvarvalue> colvar_forces;
+
+  /// \brief Current energy of this bias (colvar_forces should be
+  /// obtained by deriving this)
+  cvm::real                bias_energy;
+
+  /// \brief Whether this bias has already accumulated information
+  /// (when relevant)
+  bool                     has_data;
+
+};
+
+
+/// \brief Harmonic restraint, optionally moving towards a target
+/// (implementation of \link colvarbias \endlink)
+class colvarbias_harmonic : public colvarbias {
+
+public:
+
+  /// Retrieve colvar values and calculate their biasing forces
+  virtual cvm::real update();
+
+  /// Load new configuration - force constant and/or centers only
+  virtual void change_configuration(std::string const &conf);
+
+  /// Calculate change in energy from using alternate configuration
+  virtual cvm::real energy_difference(std::string const &conf);
+
+  /// Read the bias configuration from a restart file
+  virtual std::istream & read_restart (std::istream &is);
+
+  /// Write the bias configuration to a restart file
+  virtual std::ostream & write_restart (std::ostream &os);
+
+  /// \brief Constructor
+  colvarbias_harmonic (std::string const &conf, char const *key);
+
+  /// Destructor
+  virtual inline ~colvarbias_harmonic() {}
+
+
+protected:
+
+  /// \brief Restraint centers
+  std::vector<colvarvalue> colvar_centers;
+
+  /// \brief Restraint centers without wrapping or constraints applied
+  std::vector<colvarvalue> colvar_centers_raw;
+
+  /// \brief Restraint force constant
+  cvm::real force_k;
+
+  /// \brief Moving target?
+  bool b_chg_centers;
+
+  /// \brief Changing force constant?
+  bool b_chg_force_k;
+
+  /// \brief Restraint force constant (target value)
+  cvm::real target_force_k;
+
+  /// \brief Equilibration steps for restraint FE calculation through TI
+  cvm::real target_equil_steps;
+
+  /// \brief Restraint force constant (starting value)
+  cvm::real starting_force_k;
+
+  /// \brief Lambda-schedule for custom varying force constant
+  std::vector<cvm::real> lambda_schedule;
+
+  /// \brief New restraint centers
+  std::vector<colvarvalue> target_centers;
+
+  /// \brief Amplitude of the restraint centers' increment at each step
+  /// (or stage) towards the new values (calculated from target_nsteps)
+  std::vector<colvarvalue> centers_incr;
+
+  /// \brief Exponent for varying the force constant
+  cvm::real force_k_exp;
+
+  /// \brief Number of steps required to reach the target force constant
+  /// or restraint centers
+  size_t target_nsteps;
+
+  /// \brief Number of stages over which to perform the change
+  /// If zero, perform a continuous change
+  size_t target_nstages;
+
+  /// \brief Number of current stage of the perturbation
+  size_t stage;
+  
+  /// \brief Intermediate quantity to compute the restraint free energy
+  /// (in TI, would be the accumulating FE derivative)
+  cvm::real restraint_FE;
+};
+
+
+#endif
+
+
+
+// Emacs
+// Local Variables:
+// mode: C++
+// End: