eabf.h

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//
// The extended adaptive biasing force method has been contributed to NAMD by the following authors:
//
//    Haohao Fu and Christophe Chipot
//    Laboratoire International Associ\'e
//    Centre National de la Recherche Scientifique et University of Illinois at Urbana--Champaign
//    Unit\'e Mixte de Recherche No. 7565, Universit\'e de Lorraine
//    B.P. 70239, 54506 Vand\oe uvre-lès-Nancy cedex, France
//
// Copyright 2016, Centre National de la Recherche Scientifique
//

#ifndef EABF_H
#define EABF_H

#include <iostream>
#include <string>
#include <sstream>
#include <vector>
class ofstream_namd;

class eABF
{
public:
        eABF() {}
        eABF(const std::string& _outputfile,
                const int _outputfreq,
                const bool _restart, const std::string& _inputfile,
                const bool _outputgrad, const int _gradfreq, const double _temperature):
                outputfile(_outputfile), outputfreq(_outputfreq), restart(_restart), inputfile(_inputfile),
                outputgrad(_outputgrad), gradfreq(_gradfreq), temperature(_temperature)
        {}
        virtual ~eABF() {}

        // called by colvar each step, update the sampling point
        virtual bool update(const std::string&) = 0;

        // merge another file, used when reading another file
        bool mergefile(const std::string& inputname, const std::string& outputname)
        {
                this->inputfile = inputname;
                this->readfile();
                std::string temp = this->outputfile;
                this->outputfile = outputname;
                this->writefile();
                this->calpmf();
                this->outputfile = temp;
                return true;
        }

        // which coloum in the string provided by colvar is used
    bool setcolumn(std::vector<int> col)
        {
                this->col = col;
                return true;
        }

protected:
        // the colvar setting
        std::vector<double> lowerboundary;
        std::vector<double> upperboundary;
        std::vector<double> width;

        // the restart (output) file generated by parseABF
        std::string outputfile;

        // the frequency writing a restart file
        int outputfreq;

        // whether restart
        bool restart;

        // the restart input file
        std::string inputfile;

        // whether output gradient and pmf
        bool outputgrad;

        // the frequency writing grad and pmf file
        int gradfreq;

        // the temperature of simulation
        double temperature;

        // internal variables
        std::vector<int> max;        // the max index of the RC
        std::vector<int> min;        // the min index of the RC
        std::vector<int> bins;     // the number of bins

        std::vector<double> krestr; // force constant

        //    need to be defined
        // countall; // the distribution of samples, needed for eABF
        // sumx; // the sum of x in each bin, needed for eABF
        // sumx2; // the sum of x^2, needed for eABF
        // county; // the distribution in each bin, needed for eABF
        int line; // the number of non-zero countall

        std::vector<int> col;    // the column read by the program

        // initialize the variables
        virtual bool initialize() = 0;

        // read variables from a restart file
        virtual bool readfile() = 0;

        // write restart file
        virtual bool writefile() const = 0;

        // write the head of the pmf file
        virtual bool writehead(ofstream_namd&) const = 0;

        // calculate grad and pmf
        virtual bool calpmf() const = 0;

};

#endif // EABF_H