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