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