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colvarbias_reweightaMD Class Reference

Reweighted histogram for accelerated molecular dynamics (aMD) or Gaussian aMD (GaMD). More...

#include <colvarbias_histogram_reweight_amd.h>

Inheritance diagram for colvarbias_reweightaMD:

List of all members.

Public Methods
	colvarbias_reweightaMD (char const *key)
virtual	~colvarbias_reweightaMD ()
virtual int	init (std::string const &conf)
	\brief Parse config string and (re)initialize. More...
virtual int	update ()
	Retrieve colvar values and calculate their biasing forces Some implementations may use calc_energy() and calc_forces(). More...
virtual int	write_output_files ()
	Write any output files that this bias may have (e.g. PMF files). More...
void	hist_to_pmf (colvar_grid_scalar hist, const colvar_grid_scalar hist_count) const
	@brief convert histogram to PMF by taking logarithm and multiplying it with -1/beta am[in,out] hist the origin histogram and also the output PMF @param[in] hist_count the sampling or biased histogram. More...
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 calculate the cumulant expansion to second order am[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. More...
virtual int	write_exponential_reweighted_pmf (const std::string &p_output_prefix, bool keep_open=false)
	@brief output the PMF by the exponential average estimator am[in] p_output_prefix the prefix of the output file @param[in] keep_open Allow writing the history of the PMF. More...
virtual int	write_cumulant_expansion_pmf (const std::string &p_output_prefix, bool keep_open=false)
	@brief output the PMF by the cumulant expansion estimator am[in] p_output_prefix the prefix of the output file @param[in] keep_open Allow writing the history of the expansion. More...
virtual int	write_count (const std::string &p_output_prefix, bool keep_open=false)
	@brief output the biased sampling am[in] p_output_prefix the prefix of the output file @param[in] keep_open Allow writing the history of the samples. More...
Protected Methods
virtual std::istream &	read_state_data (std::istream &is)
	save and restore. More...
virtual std::ostream &	write_state_data (std::ostream &os)
	Write all mutable data not already written by get_state_params(). More...
Protected Attributes
std::vector< int >	previous_bin
	Current accelMD factor is the from previous frame. More...
colvarmodule::step_number	start_after_steps
	Start collecting samples after N steps. More...
bool	b_use_cumulant_expansion
	Use cumulant expansion to second order? More...
colvar_grid_scalar *	grid_count
colvar_grid_scalar *	grid_dV
colvar_grid_scalar *	grid_dV_square
size_t	history_freq
	Number of timesteps between recording data in history files (if non-zero). More...
bool	b_history_files
bool	b_write_gradients
	Write gradients of the PMF? More...

Detailed Description

Reweighted histogram for accelerated molecular dynamics (aMD) or Gaussian aMD (GaMD).

Definition at line 17 of file colvarbias_histogram_reweight_amd.h.

Constructor & Destructor Documentation

colvarbias_reweightaMD::colvarbias_reweightaMD ( char const * key )

Definition at line 13 of file colvarbias_histogram_reweight_amd.C.
References NULL.

colvarbias_reweightaMD::~colvarbias_reweightaMD ( ) [virtual]

Definition at line 20 of file colvarbias_histogram_reweight_amd.C.
References grid_count, grid_dV, grid_dV_square, and NULL.

Member Function Documentation

void colvarbias_reweightaMD::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 calculate the cumulant expansion to second order
am[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.

Definition at line 326 of file colvarbias_histogram_reweight_amd.C.
References colvarproxy_system::boltzmann, colvarmodule::exp, colvarmodule::main, colvarmodule::proxy, colvar_grid< cvm::real >::raw_data_num, colvar_grid< cvm::real >::set_value, colvarproxy_system::target_temperature, and colvar_grid< cvm::real >::value.
Referenced by write_cumulant_expansion_pmf.

void colvarbias_reweightaMD::hist_to_pmf ( colvar_grid_scalar * hist,

const colvar_grid_scalar * hist_count

) const

@brief convert histogram to PMF by taking logarithm and multiplying it with -1/beta
am[in,out] hist the origin histogram and also the output PMF @param[in] hist_count the sampling or biased
histogram.

Definition at line 275 of file colvarbias_histogram_reweight_amd.C.
References colvarproxy_system::boltzmann, colvarmodule::logn, colvarmodule::main, colvarmodule::proxy, colvar_grid< cvm::real >::raw_data_num, colvar_grid< cvm::real >::set_value, colvarproxy_system::target_temperature, and colvar_grid< cvm::real >::value.
Referenced by write_cumulant_expansion_pmf, and write_exponential_reweighted_pmf.

int colvarbias_reweightaMD::init ( std::string const & conf ) [virtual]

\brief Parse config string and (re)initialize.

Reimplemented from colvarbias_histogram.
Definition at line 51 of file colvarbias_histogram_reweight_amd.C.
References b_history_files, b_use_cumulant_expansion, b_write_gradients, colvarmodule::cite_feature, colvarbias::colvars, COLVARS_INPUT_ERROR, conf, colvarmodule::error, colvarparse::get_keyval, colvarbias_histogram::grid, grid_count, grid_dV, grid_dV_square, history_freq, colvarbias_histogram::init, colvarmodule::main, colvarbias::num_variables, previous_bin, colvar_grid< cvm::real >::request_actual_value, and start_after_steps.

std::istream & colvarbias_reweightaMD::read_state_data ( std::istream & is ) [protected, virtual]

save and restore.

Reimplemented from colvarbias_histogram.
Definition at line 362 of file colvarbias_histogram_reweight_amd.C.
References colvarbias_histogram::grid, grid_count, grid_dV, grid_dV_square, colvar_grid< cvm::real >::read_raw, and colvarbias::read_state_data_key.

int colvarbias_reweightaMD::update ( ) [virtual]

Retrieve colvar values and calculate their biasing forces Some implementations may use calc_energy() and calc_forces().

Reimplemented from colvarbias_histogram.
Definition at line 83 of file colvarbias_histogram_reweight_amd.C.
References colvar_grid_scalar::acc_value, colvarbias_histogram::bin, colvarproxy_system::boltzmann, colvarbias_histogram::colvar_array_size, colvar_grid< cvm::real >::current_bin_scalar, colvarmodule::debug, colvarmodule::get_error, colvarbias_histogram::grid, grid_count, grid_dV, grid_dV_square, colvar_grid< cvm::real >::index_ok, colvarmodule::log, colvarmodule::logn, colvarmodule::main, colvarbias::num_variables, previous_bin, colvarmodule::proxy, start_after_steps, colvarmodule::step_relative, colvarproxy_system::target_temperature, and colvarbias::update.

int colvarbias_reweightaMD::write_count ( const std::string & p_output_prefix,

bool keep_open = false

) [virtual]

@brief output the biased sampling
am[in] p_output_prefix the prefix of the output file @param[in] keep_open Allow writing the history of the
samples.

Definition at line 261 of file colvarbias_histogram_reweight_amd.C.
References COLVARS_FILE_ERROR, grid_count, colvarmodule::log, and colvar_grid_scalar::write_multicol.
Referenced by write_output_files.

int colvarbias_reweightaMD::write_cumulant_expansion_pmf ( const std::string & p_output_prefix,

bool keep_open = false

) [virtual]

@brief output the PMF by the cumulant expansion estimator
am[in] p_output_prefix the prefix of the output file @param[in] keep_open Allow writing the history of the
expansion.

Definition at line 225 of file colvarbias_histogram_reweight_amd.C.
References COLVARS_FILE_ERROR, compute_cumulant_expansion_factor, colvar_grid_scalar::gradient_finite_diff, grid_count, grid_dV, grid_dV_square, hist_to_pmf, colvar_grid< cvm::real >::incr, colvar_grid< cvm::real >::index_ok, colvarmodule::log, colvar_grid< cvm::real >::multiplicity, n, colvar_grid< cvm::real >::new_index, colvar_grid< cvm::real >::set_value, colvar_grid_gradient::write_multicol, and colvar_grid_scalar::write_multicol.
Referenced by write_output_files.

int colvarbias_reweightaMD::write_output_files ( ) [virtual]

Write any output files that this bias may have (e.g. PMF files).

Reimplemented from colvarbias_histogram.
Definition at line 147 of file colvarbias_histogram_reweight_amd.C.
References b_history_files, colvarmodule::get_error, history_freq, colvarbias::name, colvarmodule::output_prefix, colvarmodule::step_absolute, write_count, write_cumulant_expansion_pmf, and write_exponential_reweighted_pmf.

std::ostream & colvarbias_reweightaMD::write_state_data ( std::ostream & os ) [protected, virtual]

Write all mutable data not already written by get_state_params().

Reimplemented from colvarbias_histogram.
Definition at line 346 of file colvarbias_histogram_reweight_amd.C.
References colvarbias_histogram::grid, grid_count, grid_dV, grid_dV_square, and colvar_grid< cvm::real >::write_raw.

Member Data Documentation

bool colvarbias_reweightaMD::b_history_files [protected]

Definition at line 83 of file colvarbias_histogram_reweight_amd.h.
Referenced by init, and write_output_files.

bool colvarbias_reweightaMD::b_use_cumulant_expansion [protected]

Use cumulant expansion to second order?

Definition at line 76 of file colvarbias_histogram_reweight_amd.h.
Referenced by init.

bool colvarbias_reweightaMD::b_write_gradients [protected]

Write gradients of the PMF?

Definition at line 86 of file colvarbias_histogram_reweight_amd.h.
Referenced by init.

colvar_grid_scalar* colvarbias_reweightaMD::grid_count [protected]

Definition at line 77 of file colvarbias_histogram_reweight_amd.h.
Referenced by init, read_state_data, update, write_count, write_cumulant_expansion_pmf, write_exponential_reweighted_pmf, write_state_data, and ~colvarbias_reweightaMD.

colvar_grid_scalar* colvarbias_reweightaMD::grid_dV [protected]

Definition at line 78 of file colvarbias_histogram_reweight_amd.h.
Referenced by init, read_state_data, update, write_cumulant_expansion_pmf, write_state_data, and ~colvarbias_reweightaMD.

colvar_grid_scalar* colvarbias_reweightaMD::grid_dV_square [protected]

Definition at line 79 of file colvarbias_histogram_reweight_amd.h.
Referenced by init, read_state_data, update, write_cumulant_expansion_pmf, write_state_data, and ~colvarbias_reweightaMD.

size_t colvarbias_reweightaMD::history_freq [protected]

Number of timesteps between recording data in history files (if non-zero).

Definition at line 82 of file colvarbias_histogram_reweight_amd.h.
Referenced by init, and write_output_files.

std::vector<int> colvarbias_reweightaMD::previous_bin [protected]

Current accelMD factor is the from previous frame.

Definition at line 71 of file colvarbias_histogram_reweight_amd.h.
Referenced by init, and update.

colvarmodule::step_number colvarbias_reweightaMD::start_after_steps [protected]

Start collecting samples after N steps.

Definition at line 73 of file colvarbias_histogram_reweight_amd.h.
Referenced by init, and update.

The documentation for this class was generated from the following files:

Generated on Sun Apr 28 02:45:51 2024 for VMD (current) by

colvarbias_reweightaMD Class Reference

Public Methods

Protected Methods

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation