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// -*- c++ -*-
// 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
// 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.
#ifndef COLVARBIAS_HISTOGRAM_REWEIGHT_AMD
#define COLVARBIAS_HISTOGRAM_REWEIGHT_AMD
#include "colvarbias_histogram.h"
/// Reweighted histogram for accelerated molecular dynamics (aMD) or
/// Gaussian aMD (GaMD)
class colvarbias_reweightaMD : public colvarbias_histogram {
public:
colvarbias_reweightaMD(char const *key);
virtual ~colvarbias_reweightaMD();
virtual int init(std::string const &conf) override;
virtual int update() override;
virtual int write_output_files() override;
/// @brief convert histogram to PMF by taking logarithm and multiplying
/// it with -1/beta
/// @param[in,out] hist the origin histogram and also the output PMF
/// @param[in] hist_count the sampling or biased histogram
void hist_to_pmf(
colvar_grid_scalar* hist,
const colvar_grid_scalar* hist_count) const;
/// @brief calculate the cumulant expansion to second order
/// @param[in] hist_dV the histogram of the boosting potential, ΔV(ξ)
/// @param[in] hist_dV_square the histogram of the square of boosting
/// potential
/// @param[in] hist_count the sampling or biased histogram
/// @param[out] cumulant_expansion_factor the factor of the cumulant
/// expansion to second order
void compute_cumulant_expansion_factor(
const colvar_grid_scalar* hist_dV,
const colvar_grid_scalar* hist_dV_square,
const colvar_grid_scalar* hist_count,
colvar_grid_scalar* cumulant_expansion_factor) const;
/// @brief output the PMF by the exponential average estimator
/// @param[in] p_output_prefix the prefix of the output file
/// @param[in] keep_open Allow writing the history of the PMF
virtual int write_exponential_reweighted_pmf(
const std::string& p_output_prefix, bool keep_open = false);
/// @brief output the PMF by the cumulant expansion estimator
/// @param[in] p_output_prefix the prefix of the output file
/// @param[in] keep_open Allow writing the history of the expansion
virtual int write_cumulant_expansion_pmf(
const std::string& p_output_prefix, bool keep_open = false);
/// @brief output the biased sampling
/// @param[in] p_output_prefix the prefix of the output file
/// @param[in] keep_open Allow writing the history of the samples
virtual int write_count(
const std::string& p_output_prefix, bool keep_open = false);
protected:
/// Current accelMD factor is the from previous frame
std::vector<int> previous_bin;
/// Start collecting samples after N steps
colvarmodule::step_number start_after_steps;
/// Use cumulant expansion to second order?
bool b_use_cumulant_expansion;
colvar_grid_scalar* grid_count;
colvar_grid_scalar* grid_dV;
colvar_grid_scalar* grid_dV_square;
/// Number of timesteps between recording data in history files (if non-zero)
size_t history_freq;
bool b_history_files;
/// Write gradients of the PMF?
bool b_write_gradients;
template <typename OST> OST & write_state_data_template_(OST& os);
template <typename IST> IST & read_state_data_template_(IST& is);
/// save and restore
virtual std::istream & read_state_data(std::istream &is) override;
virtual cvm::memory_stream & read_state_data(cvm::memory_stream &is) override;
virtual std::ostream & write_state_data(std::ostream &os) override;
virtual cvm::memory_stream & write_state_data(cvm::memory_stream &os) override;
private:
/// temporary grids for evaluating PMFs
colvar_grid_scalar *pmf_grid_exp_avg;
colvar_grid_scalar *pmf_grid_cumulant;
colvar_grid_gradient *grad_grid_exp_avg;
colvar_grid_gradient *grad_grid_cumulant;
};
#endif // COLVARBIAS_HISTOGRAM_REWEIGHT_AMD
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