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 (vector< Value * > tmpvalues, Communicator &cc)
	create a bias representation from a list of pointer to values More...

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

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

	BiasRepresentation (vector< Value * > tmpvalues, Communicator &cc, vector< string > gmin, vector< string > gmax, vector< unsigned > nbin, 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 (vector< string > gmin, vector< string > gmax, 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...

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

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

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

const 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 (vector< double > &vmin, vector< double > &vmax, 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_

vector< Value * >	values

vector< string >	names

vector< KernelFunctions * >	hills

vector< double >	biasf

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

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

create a bias representation from a list of pointer to values

the constructor here

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

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

overload the constructor: add the sigma at constructor time

PLMD::BiasRepresentation::BiasRepresentation	(	vector< Value * >	tmpvalues,
		Communicator &	cc,
		vector< string >	gmin,
		vector< string >	gmax,
		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

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

create a histogram with grid representation and sigmas in input

overload the constructor with some external sigmas: needed for histogram

PLMD::BiasRepresentation::~BiasRepresentation ( )

destructor

Member Function Documentation

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

add the grid to the representation

void PLMD::BiasRepresentation::clear ( )

clear the representation (grid included)

Grid * PLMD::BiasRepresentation::getGridPtr ( )

get the pointer to the grid

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

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

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

get the name of the i-th value

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

get the names of the variables

unsigned PLMD::BiasRepresentation::getNumberOfDimensions ( )

retrieve the number of dimension of the representation

int PLMD::BiasRepresentation::getNumberOfKernels ( )

get the number of kernels contained in the representation

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

get a pointer to a specific value

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

get the pointer to the values

bool PLMD::BiasRepresentation::hasSigmaInInput ( )

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

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

check if the representation is rescaled to the bias

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

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

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

get a new histogram point from a file

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

set the flag that rescales the free energy to the bias

Member Data Documentation

vector<double> PLMD::BiasRepresentation::biasf

private

Grid* PLMD::BiasRepresentation::BiasGrid_

private

bool PLMD::BiasRepresentation::doInt_

private

bool PLMD::BiasRepresentation::hasgrid

private

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

private

vector<double> PLMD::BiasRepresentation::histosigma

private

double PLMD::BiasRepresentation::lowI_

private

Communicator& PLMD::BiasRepresentation::mycomm

private

vector<string> PLMD::BiasRepresentation::names

private

int PLMD::BiasRepresentation::ndim

private

bool PLMD::BiasRepresentation::rescaledToBias

private

double PLMD::BiasRepresentation::uppI_

private

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

Member Function Documentation

Member Data Documentation