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colvar_grid_gradient Class Reference

Class for accumulating the gradient of a scalar function on a grid. More...

#include <colvargrid.h>

Inheritance diagram for colvar_grid_gradient:

List of all members.

Public Methods
	colvar_grid_gradient ()
	Default constructor. More...
virtual	~colvar_grid_gradient ()
	Destructor. More...
	colvar_grid_gradient (std::vector< int > const &nx_i)
	Constructor from specific sizes arrays. More...
	colvar_grid_gradient (std::vector< colvar * > &colvars)
	Constructor from a vector of colvars. More...
	colvar_grid_gradient (std::string &filename)
	Constructor from a multicol file. More...
virtual std::istream &	read_multicol (std::istream &is, bool add=false)
	Read a grid written by write_multicol(), incrementin if data is true. More...
virtual int	read_multicol (std::string const &filename, std::string description="grid file", bool add=false)
	Read a grid written by write_multicol(), incrementin if data is true. More...
virtual std::ostream &	write_multicol (std::ostream &os) const
	Write grid in a format which is both human-readable and gnuplot-friendly. More...
virtual int	write_multicol (std::string const &filename, std::string description="grid file") const
	Write grid in a format which is both human-readable and gnuplot-friendly. More...
virtual std::ostream &	write_opendx (std::ostream &os) const
	Write the grid data without labels, as they are represented in memory. More...
virtual int	write_opendx (std::string const &filename, std::string description="grid file") const
	Write the grid data without labels, as they are represented in memory. More...
void	vector_value (std::vector< int > const &ix, std::vector< cvm::real > &v) const
	\brief Get a vector with the binned value(s) indexed by ix, normalized if applicable. More...
void	acc_value (std::vector< int > const &ix, std::vector< colvarvalue > const &values)
	\brief Accumulate the value. More...
void	acc_force (std::vector< int > const &ix, cvm::real const *forces)
	\brief Accumulate the gradient based on the force (i.e. sums the opposite of the force). More...
void	acc_force_weighted (std::vector< int > const &ix, cvm::real const *forces, cvm::real weight)
	\brief Accumulate the gradient based on the force (i.e. sums the opposite of the force) with a non-integer weight. More...
virtual cvm::real	value_output (std::vector< int > const &ix, size_t const &imult=0) const
	\brief Return the value of the function at ix divided by its number of samples (if the count grid is defined). More...
virtual void	value_input (std::vector< int > const &ix, cvm::real const &new_value, size_t const &imult=0, bool add=false)
	\brief Get the value from a formatted output and transform it into the internal representation (it may have been rescaled or manipulated). More...
cvm::real	average ()
	Compute and return average value for a 1D gradient grid. More...
void	write_1D_integral (std::ostream &os)
	\brief If the grid is 1-dimensional, integrate it and write the integral to a file. More...
Public Attributes
colvar_grid_count *	samples
	\brief Provide the sample count by which each binned value should be divided. More...
colvar_grid_scalar *	weights
	\brief Provide the floating point weights by which each binned value should be divided (alternate to samples, only one should be non-null). More...

Detailed Description

Class for accumulating the gradient of a scalar function on a grid.

Definition at line 1446 of file colvargrid.h.

Constructor & Destructor Documentation

colvar_grid_gradient::colvar_grid_gradient ( )

Default constructor.

Definition at line 199 of file colvargrid.C.
References NULL.

virtual colvar_grid_gradient::~colvar_grid_gradient ( ) [inline, virtual]

Destructor.

Definition at line 1462 of file colvargrid.h.

colvar_grid_gradient::colvar_grid_gradient ( std::vector< int > const & nx_i )

Constructor from specific sizes arrays.

Definition at line 205 of file colvargrid.C.
References NULL, and size.

colvar_grid_gradient::colvar_grid_gradient ( std::vector< colvar * > & colvars )

Constructor from a vector of colvars.

Definition at line 211 of file colvargrid.C.
References NULL, and size.

colvar_grid_gradient::colvar_grid_gradient ( std::string & filename )

Constructor from a multicol file.

Definition at line 218 of file colvargrid.C.
References colvarproxy_io::close_input_stream, COLVARS_INPUT_ERROR, colvarmodule::error, colvarproxy_io::input_stream, colvar_grid< cvm::real >::lower_boundaries, colvarmodule::main, colvar_grid< cvm::real >::mult, colvar_grid< cvm::real >::nd, NULL, colvar_grid< cvm::real >::periodic, colvarmodule::proxy, read_multicol, colvar_grid< cvm::real >::setup, and colvar_grid< cvm::real >::widths.

Member Function Documentation

void colvar_grid_gradient::acc_force ( std::vector< int > const & ix,

cvm::real const * forces

) [inline]

\brief Accumulate the gradient based on the force (i.e. sums the opposite of the force).

Definition at line 1530 of file colvargrid.h.
References colvar_grid< cvm::real >::address, colvar_grid< cvm::real >::data, colvar_grid_count::incr_count, and colvar_grid< cvm::real >::mult.
Referenced by colvarbias_meta::project_hills, and colvarbias_abf::update.

void colvar_grid_gradient::acc_force_weighted ( std::vector< int > const & ix,

cvm::real const * forces,

cvm::real weight

) [inline]

\brief Accumulate the gradient based on the force (i.e. sums the opposite of the force) with a non-integer weight.

Definition at line 1540 of file colvargrid.h.
References colvar_grid_scalar::acc_value, colvar_grid< cvm::real >::address, colvar_grid< cvm::real >::data, and colvar_grid< cvm::real >::mult.

void colvar_grid_gradient::acc_value ( std::vector< int > const & ix,

std::vector< colvarvalue > const & values

) [inline]

\brief Accumulate the value.

Definition at line 1520 of file colvargrid.h.
References colvar_grid< cvm::real >::address, colvar_grid< cvm::real >::data, colvar_grid_count::incr_count, and colvar_grid< cvm::real >::mult.
Referenced by colvarbias_ti::update_system_forces.

cvm::real colvar_grid_gradient::average ( ) [inline]

Compute and return average value for a 1D gradient grid.

Definition at line 1586 of file colvargrid.h.
References colvar_grid< cvm::real >::incr, colvar_grid< cvm::real >::index_ok, n, colvar_grid< cvm::real >::nd, colvar_grid< cvm::real >::new_index, colvar_grid< cvm::real >::nx, colvarmodule::real, colvar_grid< cvm::real >::value, and colvar_grid< size_t >::value.
Referenced by integrate_potential::integrate, colvarbias_abf::update, and write_1D_integral.

int colvar_grid_gradient::read_multicol ( std::string const & filename,

std::string description = "grid file",

bool add = false

) [virtual]

Read a grid written by write_multicol(), incrementin if data is true.

Reimplemented from colvar_grid< cvm::real >.
Definition at line 289 of file colvargrid.C.
References colvar_grid::read_multicol.

std::istream & colvar_grid_gradient::read_multicol ( std::istream & is,

bool add = false

) [virtual]

Read a grid written by write_multicol(), incrementin if data is true.

Reimplemented from colvar_grid< cvm::real >.
Definition at line 284 of file colvargrid.C.
References colvar_grid::read_multicol.
Referenced by colvar_grid_gradient.

virtual void colvar_grid_gradient::value_input ( std::vector< int > const & ix,

cvm::real const & new_value,

size_t const & imult = 0,

bool add = false

) [inline, virtual]

\brief Get the value from a formatted output and transform it into the internal representation (it may have been rescaled or manipulated).

Reimplemented from colvar_grid< cvm::real >.
Definition at line 1565 of file colvargrid.h.
References colvar_grid< cvm::real >::address, colvar_grid< cvm::real >::data, colvar_grid< cvm::real >::has_data, colvar_grid_count::new_count, and colvar_grid< size_t >::value.

virtual cvm::real colvar_grid_gradient::value_output ( std::vector< int > const & ix,

size_t const & imult = 0

) const [inline, virtual]

\brief Return the value of the function at ix divided by its number of samples (if the count grid is defined).

Reimplemented from colvar_grid< cvm::real >.
Definition at line 1551 of file colvargrid.h.
References colvar_grid< cvm::real >::address, colvar_grid< cvm::real >::data, colvarmodule::real, and colvar_grid< size_t >::value.
Referenced by integrate_potential::integrate.

void colvar_grid_gradient::vector_value ( std::vector< int > const & ix,

std::vector< cvm::real > & v

) const [inline]

\brief Get a vector with the binned value(s) indexed by ix, normalized if applicable.

Definition at line 1497 of file colvargrid.h.
References colvar_grid< cvm::real >::mult, colvar_grid< size_t >::value, and colvar_grid< cvm::real >::value.
Referenced by colvarbias_abf::update.

void colvar_grid_gradient::write_1D_integral ( std::ostream & os )

\brief If the grid is 1-dimensional, integrate it and write the integral to a file.

Definition at line 319 of file colvargrid.C.
References average, bin, colvar_grid< cvm::real >::cv, colvarmodule::error, colvar_grid< cvm::real >::incr, colvar_grid< cvm::real >::index_ok, colvar_grid< cvm::real >::new_index, colvar_grid< cvm::real >::nx, colvar_grid< cvm::real >::periodic, colvarmodule::real, samples, colvar_grid< cvm::real >::value, and colvar_grid< size_t >::value.
Referenced by colvarbias_ti::write_output_files.

int colvar_grid_gradient::write_multicol ( std::string const & filename,

std::string description = "grid file"

) const [virtual]

Write grid in a format which is both human-readable and gnuplot-friendly.

Reimplemented from colvar_grid< cvm::real >.
Definition at line 301 of file colvargrid.C.
References colvar_grid::write_multicol.

std::ostream & colvar_grid_gradient::write_multicol ( std::ostream & os ) const [virtual]

Write grid in a format which is both human-readable and gnuplot-friendly.

Reimplemented from colvar_grid< cvm::real >.
Definition at line 296 of file colvargrid.C.
References colvar_grid::write_multicol.
Referenced by colvarbias_reweightaMD::write_cumulant_expansion_pmf, colvarbias_reweightaMD::write_exponential_reweighted_pmf, and colvarbias_ti::write_output_files.

int colvar_grid_gradient::write_opendx ( std::string const & filename,

std::string description = "grid file"

) const [virtual]

Write the grid data without labels, as they are represented in memory.

Reimplemented from colvar_grid< cvm::real >.
Definition at line 312 of file colvargrid.C.
References colvar_grid::write_opendx.

std::ostream & colvar_grid_gradient::write_opendx ( std::ostream & os ) const [virtual]

Write the grid data without labels, as they are represented in memory.

Reimplemented from colvar_grid< cvm::real >.
Definition at line 307 of file colvargrid.C.
References colvar_grid::write_opendx.

Member Data Documentation

colvar_grid_count* colvar_grid_gradient::samples

\brief Provide the sample count by which each binned value should be divided.

Definition at line 1452 of file colvargrid.h.
Referenced by integrate_potential::get_grad, colvarbias_abf::init, colvarbias_ti::init_grids, and write_1D_integral.

colvar_grid_scalar* colvar_grid_gradient::weights

\brief Provide the floating point weights by which each binned value should be divided (alternate to samples, only one should be non-null).

Definition at line 1456 of file colvargrid.h.

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

Generated on Fri Nov 8 02:46:44 2024 for VMD (current) by

colvar_grid_gradient Class Reference

Public Methods

Public Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation