3e89b270fd
Notable features are the umbrella-integration based free energy estimator for eABF, and the traditional thermodynamic integration estimator now available for umbrella sampling, SMD, metadynamics. Also included are several small fixes. Below is a list of relevant commits in the Colvars repository since the last update. 321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin] 26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin] cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin] 0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin] 28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin] 92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin] 12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin] fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin] c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin] cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin] a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin] b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin] 1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin] 03a61a4 2017-04-06 Add UI-based estimator [fhh2626] ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas] 1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]
362 lines
11 KiB
C++
362 lines
11 KiB
C++
// -*- c++ -*-
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// This file is part of the Collective Variables module (Colvars).
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// The original version of Colvars and its updates are located at:
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// https://github.com/colvars/colvars
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// Please update all Colvars source files before making any changes.
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// If you wish to distribute your changes, please submit them to the
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// Colvars repository at GitHub.
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#ifndef COLVARBIAS_RESTRAINT_H
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#define COLVARBIAS_RESTRAINT_H
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#include "colvarbias.h"
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/// \brief Most general definition of a colvar restraint:
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/// see derived classes for specific types
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/// (implementation of \link colvarbias \endlink)
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class colvarbias_restraint
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: public virtual colvarbias,
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public virtual colvarbias_ti
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{
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public:
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/// Retrieve colvar values and calculate their biasing forces
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virtual int update();
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/// Load new configuration - force constant and/or centers only
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virtual int change_configuration(std::string const &conf) { return COLVARS_NOT_IMPLEMENTED; }
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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) { return 0.0; }
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virtual std::string const get_state_params() const;
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virtual int set_state_params(std::string const &conf);
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// virtual std::ostream & write_state_data(std::ostream &os);
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// virtual std::istream & read_state_data(std::istream &os);
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virtual std::ostream & write_state(std::ostream &os);
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virtual std::istream & read_state(std::istream &is);
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virtual std::ostream & write_traj_label(std::ostream &os);
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virtual std::ostream & write_traj(std::ostream &os);
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/// \brief Constructor
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colvarbias_restraint(char const *key);
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virtual int init(std::string const &conf);
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virtual ~colvarbias_restraint();
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protected:
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/// \brief Potential function for the i-th colvar
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virtual cvm::real restraint_potential(size_t i) const = 0;
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/// \brief Force function for the i-th colvar
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virtual colvarvalue const restraint_force(size_t i) const = 0;
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/// \brief Derivative of the potential function with respect to the force constant
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virtual cvm::real d_restraint_potential_dk(size_t i) const = 0;
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};
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/// Definition and parsing of the restraint centers
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class colvarbias_restraint_centers
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: public virtual colvarbias_restraint
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{
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public:
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colvarbias_restraint_centers(char const *key);
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virtual int init(std::string const &conf);
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virtual int change_configuration(std::string const &conf);
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protected:
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/// \brief Restraint centers
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std::vector<colvarvalue> colvar_centers;
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};
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/// Definition and parsing of the force constant
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class colvarbias_restraint_k
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: public virtual colvarbias_restraint
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{
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public:
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colvarbias_restraint_k(char const *key);
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virtual int init(std::string const &conf);
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virtual int change_configuration(std::string const &conf);
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protected:
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/// \brief Restraint force constant
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cvm::real force_k;
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};
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/// Options to change the restraint configuration over time (shared between centers and k moving)
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class colvarbias_restraint_moving
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: public virtual colvarparse, public virtual colvardeps {
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public:
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colvarbias_restraint_moving(char const *key);
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// Note: despite the diamond inheritance, most of this function gets only executed once
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virtual int init(std::string const &conf);
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virtual int update() { return COLVARS_OK; }
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virtual int change_configuration(std::string const &conf) { return COLVARS_NOT_IMPLEMENTED; }
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virtual std::string const get_state_params() const;
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virtual int set_state_params(std::string const &conf);
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protected:
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/// \brief Moving target?
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bool b_chg_centers;
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/// \brief Changing force constant?
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bool b_chg_force_k;
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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 Lambda-schedule for custom varying force constant
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std::vector<cvm::real> lambda_schedule;
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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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long target_nsteps;
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};
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/// Options to change the restraint centers over time
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class colvarbias_restraint_centers_moving
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: public virtual colvarbias_restraint_centers,
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public virtual colvarbias_restraint_moving
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{
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public:
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colvarbias_restraint_centers_moving(char const *key);
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virtual int init(std::string const &conf);
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virtual int update();
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virtual int change_configuration(std::string const &conf) { return COLVARS_NOT_IMPLEMENTED; }
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virtual std::string const get_state_params() const;
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virtual int set_state_params(std::string const &conf);
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virtual std::ostream & write_traj_label(std::ostream &os);
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virtual std::ostream & write_traj(std::ostream &os);
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protected:
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/// \brief New restraint centers
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std::vector<colvarvalue> target_centers;
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/// \brief Initial value of the restraint centers
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std::vector<colvarvalue> initial_centers;
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/// \brief Amplitude of the restraint centers' increment at each step
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/// towards the new values (calculated from target_nsteps)
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std::vector<colvarvalue> centers_incr;
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/// \brief Update the centers by interpolating between initial and target
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virtual int update_centers(cvm::real lambda);
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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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/// Update the accumulated work
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int update_acc_work();
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};
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/// Options to change the restraint force constant over time
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class colvarbias_restraint_k_moving
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: public virtual colvarbias_restraint_k,
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public virtual colvarbias_restraint_moving
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{
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public:
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colvarbias_restraint_k_moving(char const *key);
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virtual int init(std::string const &conf);
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virtual int update();
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virtual int change_configuration(std::string const &conf) { return COLVARS_NOT_IMPLEMENTED; }
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virtual std::string const get_state_params() const;
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virtual int set_state_params(std::string const &conf);
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virtual std::ostream & write_traj_label(std::ostream &os);
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virtual std::ostream & write_traj(std::ostream &os);
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protected:
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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 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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};
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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
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: public colvarbias_restraint_centers_moving,
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public colvarbias_restraint_k_moving
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{
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public:
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colvarbias_restraint_harmonic(char const *key);
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virtual int init(std::string const &conf);
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virtual int update();
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virtual std::string const get_state_params() const;
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virtual int set_state_params(std::string const &conf);
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virtual std::ostream & write_state_data(std::ostream &os);
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virtual std::istream & read_state_data(std::istream &os);
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virtual std::ostream & write_traj_label(std::ostream &os);
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virtual std::ostream & write_traj(std::ostream &os);
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virtual int change_configuration(std::string const &conf);
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virtual cvm::real energy_difference(std::string const &conf);
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protected:
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virtual cvm::real restraint_potential(size_t i) const;
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virtual colvarvalue const restraint_force(size_t i) const;
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virtual cvm::real d_restraint_potential_dk(size_t i) const;
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};
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/// \brief Wall restraint
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/// (implementation of \link colvarbias_restraint \endlink)
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class colvarbias_restraint_harmonic_walls
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: public colvarbias_restraint_k_moving
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{
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public:
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colvarbias_restraint_harmonic_walls(char const *key);
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virtual int init(std::string const &conf);
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virtual int update();
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virtual void communicate_forces();
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virtual std::string const get_state_params() const;
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virtual int set_state_params(std::string const &conf);
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virtual std::ostream & write_state_data(std::ostream &os);
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virtual std::istream & read_state_data(std::istream &os);
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virtual std::ostream & write_traj_label(std::ostream &os);
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virtual std::ostream & write_traj(std::ostream &os);
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protected:
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/// \brief Location of the lower walls
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std::vector<colvarvalue> lower_walls;
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/// \brief Location of the upper walls
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std::vector<colvarvalue> upper_walls;
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/// \brief If both walls are defined, use this k for the lower
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cvm::real lower_wall_k;
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/// \brief If both walls are defined, use this k for the upper
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cvm::real upper_wall_k;
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virtual cvm::real colvar_distance(size_t i) const;
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virtual cvm::real restraint_potential(size_t i) const;
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virtual colvarvalue const restraint_force(size_t i) const;
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virtual cvm::real d_restraint_potential_dk(size_t i) 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
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: public colvarbias_restraint_centers_moving,
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public colvarbias_restraint_k_moving
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{
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public:
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colvarbias_restraint_linear(char const *key);
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virtual int init(std::string const &conf);
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virtual int update();
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virtual int change_configuration(std::string const &conf);
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virtual cvm::real energy_difference(std::string const &conf);
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virtual std::string const get_state_params() const;
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virtual int set_state_params(std::string const &conf);
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virtual std::ostream & write_state_data(std::ostream &os);
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virtual std::istream & read_state_data(std::istream &os);
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virtual std::ostream & write_traj_label(std::ostream &os);
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virtual std::ostream & write_traj(std::ostream &os);
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protected:
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virtual cvm::real restraint_potential(size_t i) const;
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virtual colvarvalue const restraint_force(size_t i) const;
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virtual cvm::real d_restraint_potential_dk(size_t i) const;
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};
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/// Restrain the 1D histogram of a set of variables (or of a multidimensional one)
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// TODO this could be reimplemented more cleanly as a derived class of both restraint and histogram
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class colvarbias_restraint_histogram : public colvarbias {
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public:
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colvarbias_restraint_histogram(char const *key);
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int init(std::string const &conf);
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~colvarbias_restraint_histogram();
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virtual int update();
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virtual std::istream & read_restart(std::istream &is);
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virtual std::ostream & write_restart(std::ostream &os);
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virtual std::ostream & write_traj_label(std::ostream &os);
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virtual std::ostream & write_traj(std::ostream &os);
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protected:
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/// Probability density
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cvm::vector1d<cvm::real> p;
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/// Reference probability density
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cvm::vector1d<cvm::real> ref_p;
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/// Difference between probability density and reference
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cvm::vector1d<cvm::real> p_diff;
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/// Lower boundary of the grid
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cvm::real lower_boundary;
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/// Upper boundary of the grid
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cvm::real upper_boundary;
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/// Resolution of the grid
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cvm::real width;
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/// Width of the Gaussians
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cvm::real gaussian_width;
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/// Restraint force constant
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cvm::real force_k;
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/// Write the histogram to a file
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bool b_write_histogram;
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};
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#endif
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