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PLMD::BiasRepresentation Class Reference

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...
 
ValuegetPtrToValue (unsigned i)
 get a pointer to a specific value More...
 
GridgetGridPtr ()
 get the pointer to the grid More...
 
KernelFunctionsreadFromPoint (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
 
Communicatormycomm
 
GridBiasGrid_
 

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: