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)
	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

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

Definition at line 45 of file BiasRepresentation.h.

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

Definition at line 37 of file BiasRepresentation.cpp.

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

Definition at line 45 of file BiasRepresentation.cpp.

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

create a bias containing a grid representation

overload the constructor: add the grid at constructor time

Definition at line 53 of file BiasRepresentation.cpp.

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

Definition at line 63 of file BiasRepresentation.cpp.

PLMD::BiasRepresentation::~BiasRepresentation ( )

destructor

Definition at line 73 of file BiasRepresentation.cpp.

Member Function Documentation

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

add the grid to the representation

Definition at line 78 of file BiasRepresentation.cpp.

void PLMD::BiasRepresentation::clear ( )

clear the representation (grid included)

Definition at line 248 of file BiasRepresentation.cpp.

Grid * PLMD::BiasRepresentation::getGridPtr ( )

get the pointer to the grid

Definition at line 210 of file BiasRepresentation.cpp.

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

Definition at line 214 of file BiasRepresentation.cpp.

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

get the name of the i-th value

Definition at line 104 of file BiasRepresentation.cpp.

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

get the names of the variables

Definition at line 101 of file BiasRepresentation.cpp.

unsigned PLMD::BiasRepresentation::getNumberOfDimensions ( )

retrieve the number of dimension of the representation

Definition at line 98 of file BiasRepresentation.cpp.

int PLMD::BiasRepresentation::getNumberOfKernels ( )

get the number of kernels contained in the representation

Definition at line 207 of file BiasRepresentation.cpp.

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

get a pointer to a specific value

Definition at line 111 of file BiasRepresentation.cpp.

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

get the pointer to the values

Definition at line 108 of file BiasRepresentation.cpp.

bool PLMD::BiasRepresentation::hasSigmaInInput ( )

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

Definition at line 87 of file BiasRepresentation.cpp.

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

check if the representation is rescaled to the bias

Definition at line 94 of file BiasRepresentation.cpp.

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

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

Definition at line 123 of file BiasRepresentation.cpp.

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

get a new histogram point from a file

Definition at line 115 of file BiasRepresentation.cpp.

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

set the flag that rescales the free energy to the bias

Definition at line 90 of file BiasRepresentation.cpp.

Member Data Documentation

vector<double> PLMD::BiasRepresentation::biasf

private

Definition at line 94 of file BiasRepresentation.h.

Grid* PLMD::BiasRepresentation::BiasGrid_

private

Definition at line 97 of file BiasRepresentation.h.

bool PLMD::BiasRepresentation::hasgrid

private

Definition at line 89 of file BiasRepresentation.h.

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

private

Definition at line 93 of file BiasRepresentation.h.

vector<double> PLMD::BiasRepresentation::histosigma

private

Definition at line 95 of file BiasRepresentation.h.

Communicator& PLMD::BiasRepresentation::mycomm

private

Definition at line 96 of file BiasRepresentation.h.

vector<string> PLMD::BiasRepresentation::names

private

Definition at line 92 of file BiasRepresentation.h.

int PLMD::BiasRepresentation::ndim

private

Definition at line 88 of file BiasRepresentation.h.

bool PLMD::BiasRepresentation::rescaledToBias

private

Definition at line 90 of file BiasRepresentation.h.

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

private

Definition at line 91 of file BiasRepresentation.h.

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