this class implements a general purpose class that aims to provide a Grid/list transparently add gaussians to a bias More...

#include <BiasRepresentation.h>

Public Member Functions
	BiasRepresentation (const std::vector< Value *> &tmpvalues, Communicator &cc)
	create a bias representation from a list of pointer to values More...

	BiasRepresentation (const std::vector< Value *> &tmpvalues, Communicator &cc, const std::vector< double > &sigma)
	create a bias using explicit sigma in input (needed for histogram building) More...

	BiasRepresentation (const std::vector< Value *> &tmpvalues, Communicator &cc, const std::vector< std::string > &gmin, const std::vector< std::string > &gmax, const std::vector< unsigned > &nbin, bool doInt, double lowI_, double uppI_)
	create a bias containing a grid representation More...

	BiasRepresentation (const std::vector< Value *> &tmpvalues, Communicator &cc, const std::vector< std::string > &gmin, const std::vector< std::string > &gmax, const std::vector< unsigned > &nbin, const std::vector< double > &sigma)
	create a histogram with grid representation and sigmas in input More...

	~BiasRepresentation ()
	destructor More...

unsigned	getNumberOfDimensions ()
	retrieve the number of dimension of the representation More...

void	addGrid (const std::vector< std::string > &gmin, const std::vector< std::string > &gmax, const std::vector< unsigned > &nbin)
	add the grid to the representation More...

void	pushKernel (IFile *ff)
	push a kernel on the representation (includes widths and height) More...

void	setRescaledToBias (bool rescaled)
	set the flag that rescales the free energy to the bias More...

const bool &	isRescaledToBias ()
	check if the representation is rescaled to the bias More...

bool	hasSigmaInInput ()
	check if the sigma values are already provided (in case of a histogram representation with input sigmas) More...

std::vector< std::string >	getNames ()
	get the names of the variables More...

const std::vector< Value * > &	getPtrToValues ()
	get the pointer to the values More...

int	getNumberOfKernels ()
	get the number of kernels contained in the representation More...

const std::string &	getName (unsigned i)
	get the name of the i-th value More...

Value *	getPtrToValue (unsigned i)
	get a pointer to a specific value More...

Grid *	getGridPtr ()
	get the pointer to the grid More...

KernelFunctions *	readFromPoint (IFile *ifile)
	get a new histogram point from a file More...

void	getMinMaxBin (std::vector< double > &vmin, std::vector< double > &vmax, std::vector< unsigned > &vbin)
	get an automatic min/max from the set so to know how to configure the grid More...

void	clear ()
	clear the representation (grid included) More...

Private Attributes
int	ndim

bool	hasgrid

bool	rescaledToBias

bool	doInt_

double	lowI_

double	uppI_

std::vector< Value * >	values

std::vector< std::string >	names

std::vector< KernelFunctions * >	hills

std::vector< double >	biasf

std::vector< double >	histosigma

Communicator &	mycomm

Grid *	BiasGrid_

Detailed Description

this class implements a general purpose class that aims to provide a Grid/list transparently add gaussians to a bias

Constructor & Destructor Documentation

◆ BiasRepresentation() [1/4]

PLMD::BiasRepresentation::BiasRepresentation	(	const std::vector< Value *> &	tmpvalues,
		Communicator &	cc
	)

create a bias representation from a list of pointer to values

the constructor here

◆ BiasRepresentation() [2/4]

PLMD::BiasRepresentation::BiasRepresentation	(	const std::vector< Value *> &	tmpvalues,
		Communicator &	cc,
		const std::vector< double > &	sigma
	)

create a bias using explicit sigma in input (needed for histogram building)

overload the constructor: add the sigma at constructor time

◆ BiasRepresentation() [3/4]

PLMD::BiasRepresentation::BiasRepresentation	(	const std::vector< Value *> &	tmpvalues,
		Communicator &	cc,
		const std::vector< std::string > &	gmin,
		const std::vector< std::string > &	gmax,
		const std::vector< unsigned > &	nbin,
		bool	doInt,
		double	lowI_,
		double	uppI_
	)

create a bias containing a grid representation

overload the constructor: add the grid at constructor time

◆ BiasRepresentation() [4/4]

PLMD::BiasRepresentation::BiasRepresentation	(	const std::vector< Value *> &	tmpvalues,
		Communicator &	cc,
		const std::vector< std::string > &	gmin,
		const std::vector< std::string > &	gmax,
		const std::vector< unsigned > &	nbin,
		const std::vector< double > &	sigma
	)

create a histogram with grid representation and sigmas in input

overload the constructor with some external sigmas: needed for histogram

◆ ~BiasRepresentation()

PLMD::BiasRepresentation::~BiasRepresentation ( )

destructor

Member Function Documentation

◆ addGrid()

void PLMD::BiasRepresentation::addGrid	(	const std::vector< std::string > &	gmin,
		const std::vector< std::string > &	gmax,
		const std::vector< unsigned > &	nbin
	)

add the grid to the representation

◆ clear()

void PLMD::BiasRepresentation::clear ( )

clear the representation (grid included)

◆ getGridPtr()

Grid * PLMD::BiasRepresentation::getGridPtr ( )

get the pointer to the grid

◆ getMinMaxBin()

void PLMD::BiasRepresentation::getMinMaxBin	(	std::vector< double > &	vmin,
		std::vector< double > &	vmax,
		std::vector< unsigned > &	vbin
	)

get an automatic min/max from the set so to know how to configure the grid

◆ getName()

const string & PLMD::BiasRepresentation::getName ( unsigned i )

get the name of the i-th value

◆ getNames()

vector< string > PLMD::BiasRepresentation::getNames ( )

get the names of the variables

◆ getNumberOfDimensions()

unsigned PLMD::BiasRepresentation::getNumberOfDimensions ( )

retrieve the number of dimension of the representation

◆ getNumberOfKernels()

int PLMD::BiasRepresentation::getNumberOfKernels ( )

get the number of kernels contained in the representation

◆ getPtrToValue()

Value * PLMD::BiasRepresentation::getPtrToValue ( unsigned i )

get a pointer to a specific value

◆ getPtrToValues()

const vector< Value * > & PLMD::BiasRepresentation::getPtrToValues ( )

get the pointer to the values

◆ hasSigmaInInput()

bool PLMD::BiasRepresentation::hasSigmaInInput ( )

check if the sigma values are already provided (in case of a histogram representation with input sigmas)

◆ isRescaledToBias()

const bool & PLMD::BiasRepresentation::isRescaledToBias ( )

check if the representation is rescaled to the bias

◆ pushKernel()

void PLMD::BiasRepresentation::pushKernel ( IFile * ff )

push a kernel on the representation (includes widths and height)

◆ readFromPoint()

KernelFunctions * PLMD::BiasRepresentation::readFromPoint ( IFile * ifile )

get a new histogram point from a file

◆ setRescaledToBias()

void PLMD::BiasRepresentation::setRescaledToBias ( bool rescaled )

set the flag that rescales the free energy to the bias

Member Data Documentation

◆ biasf

std::vector<double> PLMD::BiasRepresentation::biasf

private

◆ BiasGrid_

Grid* PLMD::BiasRepresentation::BiasGrid_

private

◆ doInt_

bool PLMD::BiasRepresentation::doInt_

private

◆ hasgrid

bool PLMD::BiasRepresentation::hasgrid

private

◆ hills

std::vector<KernelFunctions*> PLMD::BiasRepresentation::hills

private

◆ histosigma

std::vector<double> PLMD::BiasRepresentation::histosigma

private

◆ lowI_

double PLMD::BiasRepresentation::lowI_

private

◆ mycomm

Communicator& PLMD::BiasRepresentation::mycomm

private

◆ names

std::vector<std::string> PLMD::BiasRepresentation::names

private

◆ ndim

int PLMD::BiasRepresentation::ndim

private

◆ rescaledToBias

bool PLMD::BiasRepresentation::rescaledToBias

private

◆ uppI_

double PLMD::BiasRepresentation::uppI_

private

◆ values

std::vector<Value*> PLMD::BiasRepresentation::values

private

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

tools/BiasRepresentation.h
tools/BiasRepresentation.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ BiasRepresentation() [1/4]

◆ BiasRepresentation() [2/4]

◆ BiasRepresentation() [3/4]

◆ BiasRepresentation() [4/4]

◆ ~BiasRepresentation()

Member Function Documentation

◆ addGrid()

◆ clear()

◆ getGridPtr()

◆ getMinMaxBin()

◆ getName()

◆ getNames()

◆ getNumberOfDimensions()

◆ getNumberOfKernels()

◆ getPtrToValue()

◆ getPtrToValues()

◆ hasSigmaInInput()

◆ isRescaledToBias()

◆ pushKernel()

◆ readFromPoint()

◆ setRescaledToBias()

Member Data Documentation

◆ biasf

◆ BiasGrid_

◆ doInt_

◆ hasgrid

◆ hills

◆ histosigma

◆ lowI_

◆ mycomm

◆ names

◆ ndim

◆ rescaledToBias

◆ uppI_

◆ values