9427fc50a5
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
89 lines
2.6 KiB
C++
89 lines
2.6 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_ALB_H
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#define COLVARBIAS_ALB_H
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#include "colvar.h"
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#include "colvarbias.h"
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class colvarbias_alb : public colvarbias {
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public:
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colvarbias_alb(char const *key);
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virtual ~colvarbias_alb();
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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_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 centers
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std::vector<colvarvalue> colvar_centers;
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/// \brief colvar parameters, used for calculating the gradient/variance
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std::vector<cvm::real> means;
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std::vector<cvm::real> ssd; // SSD = sum of squares of differences from mean
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int update_calls;
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///\brief how often to update coupling constant
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int update_freq;
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///\brief Estimated range of coupling constant values in kT
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std::vector<cvm::real> max_coupling_range;
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//\brief Estimated max for how quickly the rate can change in kT / time
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std::vector<cvm::real> max_coupling_rate;
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/// \brief accumated couping force; used in stochastic online gradient descent algorithm
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std::vector<cvm::real> coupling_accum;
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/// \brief coupling constant
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std::vector<cvm::real> set_coupling;
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/// \brief current coupling constant, which is ramped up during equilibration to coupling
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std::vector<cvm::real> current_coupling;
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/// \brief how quickly to change the coupling constant
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std::vector<cvm::real> coupling_rate;
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// \brief if we're equilibrating our estimates or collecting data
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bool b_equilibration;
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// \brief If the coupling range should be increased
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bool b_hard_coupling_range;
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/// \brief flag for outputting colvar centers
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bool b_output_centers;
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/// \brief flag for outputting current gradient
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bool b_output_grad;
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/// \brief flag for outputting coupling constant
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bool b_output_coupling;
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cvm::real restraint_potential(cvm::real k, const colvar* x, const colvarvalue& xcenter) const;
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/// \brief Force function
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colvarvalue restraint_force(cvm::real k, const colvar* x, const colvarvalue& xcenter) const;
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///\brief Unit scaling
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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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