BiasRepresentation.h

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/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   Copyright (c) 2013 The plumed team
   (see the PEOPLE file at the root of the distribution for a list of names)

   See http://www.plumed-code.org for more information.

   This file is part of plumed, version 2.0.

   plumed is free software: you can redistribute it and/or modify
   it under the terms of the GNU Lesser General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.

   plumed is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU Lesser General Public License for more details.

   You should have received a copy of the GNU Lesser General Public License
   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#ifndef __PLUMED_tools_BiasRepresentation_h
#define __PLUMED_tools_BiasRepresentation_h

#include "Exception.h"
#include "KernelFunctions.h"
#include "File.h"
#include "Grid.h"
#include <iostream>

using namespace std;

namespace PLMD{

//+PLUMEDOC INTERNAL biasrepresentation 
/*

*/
//+ENDPLUMEDOC

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

class BiasRepresentation {
  public:
          /// create a bias representation from a list of pointer to values
          BiasRepresentation(vector<Value*> tmpvalues, Communicator &cc  ); 
          /// create a bias using explicit sigma in input (needed for histogram building) 
          BiasRepresentation(vector<Value*> tmpvalues, Communicator &cc  ,  vector<double> sigma); 
          /// create a bias containing a grid representation 
          BiasRepresentation(vector<Value*> tmpvalues, Communicator &cc , vector<string> gmin, vector<string> gmax, vector<unsigned> nbin );
          /// create a histogram with grid representation and sigmas in input
          BiasRepresentation(vector<Value*> tmpvalues, Communicator &cc , vector<string> gmin, vector<string> gmax, vector<unsigned> nbin , vector<double> sigma);
          /// destructor
          ~BiasRepresentation();
          /// retrieve the number of dimension of the representation
          unsigned      getNumberOfDimensions();
          /// add the grid to the representation
          void          addGrid( vector<string> gmin, vector<string> gmax, vector<unsigned> nbin );
          /// push a kernel on the representation (includes widths and height)
          void          pushKernel( IFile * ff);
          /// set the flag that rescales the free energy to the bias 
          void          setRescaledToBias(bool rescaled);
          /// check if the representation is rescaled to the bias 
          const bool &  isRescaledToBias();
          /// check if the sigma values are already provided (in case of a histogram representation with input sigmas)
          bool          hasSigmaInInput();
          /// get the names of the variables
          vector<string> getNames();
          /// get the pointer to the values 
          const vector<Value*> & getPtrToValues();
          /// get the number of kernels contained in the representation
          int           getNumberOfKernels();
          /// get the name of the i-th value
          const string & getName(unsigned i);
          /// get a pointer to a specific value
          Value*        getPtrToValue(unsigned i);
          /// get the pointer to the grid
          Grid*         getGridPtr();
          /// get a new histogram point from a file 
          KernelFunctions* readFromPoint(IFile *ifile); 
          /// get an automatic min/max from the set so to know how to configure the grid
          void getMinMaxBin(vector<double> &vmin, vector<double> &vmax, vector<unsigned> &vbin);
          /// clear the representation (grid included)
          void clear(); 
  private:
    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_;
};

}

#endif