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colvarbias_meta::hill Class Reference

\brief A hill for the metadynamics bias. More...

#include <colvarbias_meta.h>

List of all members.

Public Methods
	hill (cvm::step_number it, cvm::real W, std::vector< colvarvalue > const &cv_values, std::vector< cvm::real > const &cv_sigmas, std::string const &replica="")
	Constructor of a hill object Parameters: it  Step number at which the hill was added W  Weight of the hill (energy units) cv_values  Array of collective variable values cv_sigmas  Array of collective variable values replica  ID of the replica that creates the hill (optional). More...
	hill (colvarbias_meta::hill const &h)
	Copy constructor. More...
	~hill ()
	Destructor. More...
hill &	operator= (colvarbias_meta::hill const &h)
	Assignment operator. More...
cvm::real	energy ()
	Get the energy. More...
cvm::real	energy (cvm::real const &new_weight)
	Get the energy using another hill weight. More...
cvm::real const &	value ()
	Get the current hill value. More...
void	value (cvm::real const &new_value)
	Set the hill value as specified. More...
cvm::real	weight ()
	Get the weight. More...
void	scale (cvm::real const &new_scale_fac)
	Scale the weight with this factor (by default 1.0 is used). More...
std::vector< colvarvalue > &	center ()
	Get the center of the hill. More...
colvarvalue &	center (size_t const &i)
	Get the i-th component of the center. More...
std::string	output_traj ()
	Represent the hill ina string suitable for a trajectory file. More...
Protected Attributes
cvm::step_number	it
	Time step at which this hill was added. More...
cvm::real	hill_value
	Value of the hill function (ranges between 0 and 1). More...
cvm::real	sW
	Scale factor, which could be modified at runtime (default: 1). More...
cvm::real	W
	Maximum height in energy of the hill. More...
std::vector< colvarvalue >	centers
	Centers of the hill in the collective variable space. More...
std::vector< cvm::real >	sigmas
	Half-widths of the hill in the collective variable space. More...
std::string	replica
	Identity of the replica who added this hill. More...
Friends
class	colvarbias_meta
bool	operator< (hill const &h1, hill const &h2)
	Comparison operator. More...
bool	operator<= (hill const &h1, hill const &h2)
	Comparison operator. More...
bool	operator> (hill const &h1, hill const &h2)
	Comparison operator. More...
bool	operator>= (hill const &h1, hill const &h2)
	Comparison operator. More...
bool	operator== (hill const &h1, hill const &h2)
	Comparison operator. More...
std::ostream &	operator<< (std::ostream &os, hill const &h)
	Write the hill to an output stream. More...

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Detailed Description

\brief A hill for the metadynamics bias.

Definition at line 267 of file colvarbias_meta.h.

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Constructor & Destructor Documentation

colvarbias_meta::hill::hill (  cvm::step_number    it, cvm::real    W, std::vector< colvarvalue > const &    cv_values, std::vector< cvm::real > const &    cv_sigmas, std::string const &    replica = "" )

Constructor of a hill object Parameters: it  Step number at which the hill was added W  Weight of the hill (energy units) cv_values  Array of collective variable values cv_sigmas  Array of collective variable values replica  ID of the replica that creates the hill (optional). Definition at line 1982 of file colvarbias_meta.C. References centers, colvarmodule::debug, hill_value, it, colvarmodule::log, sigmas, size, colvarmodule::to_str, and W.

colvarbias_meta::hill::hill (  colvarbias_meta::hill const &    h )

Copy constructor. Definition at line 2010 of file colvarbias_meta.C. References hill_value, and it.

colvarbias_meta::hill::~hill (    )

Destructor. Definition at line 2038 of file colvarbias_meta.C.

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Member Function Documentation

colvarvalue& colvarbias_meta::hill::center (  size_t const &    i )  [inline]

Get the i-th component of the center. Definition at line 359 of file colvarbias_meta.h.

std::vector<colvarvalue>& colvarbias_meta::hill::center (    )  [inline]

Get the center of the hill. Definition at line 353 of file colvarbias_meta.h.

cvm::real colvarbias_meta::hill::energy (  cvm::real const &    new_weight )  [inline]

Get the energy using another hill weight. Definition at line 323 of file colvarbias_meta.h.

cvm::real colvarbias_meta::hill::energy (    )  [inline]

Get the energy. Definition at line 317 of file colvarbias_meta.h.

colvarbias_meta::hill & colvarbias_meta::hill::operator= (  colvarbias_meta::hill const &    h )

Assignment operator. Definition at line 2024 of file colvarbias_meta.C. References centers, hill_value, it, replica, sigmas, sW, and W.

std::string colvarbias_meta::hill::output_traj (    )

Represent the hill ina string suitable for a trajectory file. Definition at line 1951 of file colvarbias_meta.C. References centers, it, sigmas, and W.

void colvarbias_meta::hill::scale (  cvm::real const &    new_scale_fac )  [inline]

Scale the weight with this factor (by default 1.0 is used). Definition at line 347 of file colvarbias_meta.h.

void colvarbias_meta::hill::value (  cvm::real const &    new_value )  [inline]

Set the hill value as specified. Definition at line 335 of file colvarbias_meta.h.

cvm::real const& colvarbias_meta::hill::value (    )  [inline]

Get the current hill value. Definition at line 329 of file colvarbias_meta.h.

cvm::real colvarbias_meta::hill::weight (    )  [inline]

Get the weight. Definition at line 341 of file colvarbias_meta.h.

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Friends And Related Function Documentation

friend class colvarbias_meta [friend]

Definition at line 294 of file colvarbias_meta.h.

bool operator< (  hill const &    h1, hill const &    h2 )  [friend]

Comparison operator. Definition at line 365 of file colvarbias_meta.h.

std::ostream& operator<< (  std::ostream &    os, hill const &    h )  [friend]

Write the hill to an output stream. Definition at line 2042 of file colvarbias_meta.C.

bool operator<= (  hill const &    h1, hill const &    h2 )  [friend]

Comparison operator. Definition at line 372 of file colvarbias_meta.h.

bool operator== (  hill const &    h1, hill const &    h2 )  [friend]

Comparison operator. Definition at line 393 of file colvarbias_meta.h.

bool operator> (  hill const &    h1, hill const &    h2 )  [friend]

Comparison operator. Definition at line 379 of file colvarbias_meta.h.

bool operator>= (  hill const &    h1, hill const &    h2 )  [friend]

Comparison operator. Definition at line 386 of file colvarbias_meta.h.

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Member Data Documentation

std::vector<colvarvalue> colvarbias_meta::hill::centers [protected]

Centers of the hill in the collective variable space. Definition at line 284 of file colvarbias_meta.h. Referenced by colvarbias_meta::add_hill, hill, operator<<, operator=, and output_traj.

cvm::real colvarbias_meta::hill::hill_value [protected]

Value of the hill function (ranges between 0 and 1). Definition at line 275 of file colvarbias_meta.h. Referenced by hill, and operator=.

cvm::step_number colvarbias_meta::hill::it [protected]

Time step at which this hill was added. Definition at line 272 of file colvarbias_meta.h. Referenced by operator<<, operator=, and output_traj.

std::string colvarbias_meta::hill::replica [protected]

Identity of the replica who added this hill. Definition at line 290 of file colvarbias_meta.h. Referenced by operator<<, and operator=.

std::vector<cvm::real> colvarbias_meta::hill::sigmas [protected]

Half-widths of the hill in the collective variable space. Definition at line 287 of file colvarbias_meta.h. Referenced by hill, operator<<, operator=, and output_traj.

cvm::real colvarbias_meta::hill::sW [protected]

Scale factor, which could be modified at runtime (default: 1). Definition at line 278 of file colvarbias_meta.h. Referenced by operator=.

cvm::real colvarbias_meta::hill::W [protected]

Maximum height in energy of the hill. Definition at line 281 of file colvarbias_meta.h. Referenced by hill, operator<<, operator=, and output_traj.

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

• colvarbias_meta.h
• colvarbias_meta.C

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