eABF2D Class Reference

#include <eabf2D.h>

Inheritance diagram for eABF2D:

Public Member Functions
	eABF2D (const double _lowerboundary, const double _upperboundary, const double _width, const double _krestr, const double _lowerboundary2, const double _upperboundary2, const double _width2, const double _krestr2, const std::string &_outputfile, const int _outputfreq, const bool _restart, const std::string &_inputfile, const bool _outputgrad, const int _gradfreq, const double _temperature)
virtual	~eABF2D ()
bool	update (const std::string &)
Public Member Functions inherited from eABF
	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)
virtual	~eABF ()
bool	mergefile (const std::string &inputname, const std::string &outputname)
bool	setcolumn (std::vector< int > col)

Additional Inherited Members
Protected Attributes inherited from eABF
std::vector< double >	lowerboundary
std::vector< double >	upperboundary
std::vector< double >	width
std::string	outputfile
int	outputfreq
bool	restart
std::string	inputfile
bool	outputgrad
int	gradfreq
double	temperature
std::vector< int >	max
std::vector< int >	min
std::vector< int >	bins
std::vector< double >	krestr
int	line
std::vector< int >	col

Detailed Description

Definition at line 23 of file eabf2D.h.

Constructor & Destructor Documentation

eABF2D::eABF2D	(	const double	_lowerboundary,
		const double	_upperboundary,
		const double	_width,
		const double	_krestr,
		const double	_lowerboundary2,
		const double	_upperboundary2,
		const double	_width2,
		const double	_krestr2,
		const std::string &	_outputfile,
		const int	_outputfreq,
		const bool	_restart,
		const std::string &	_inputfile,
		const bool	_outputgrad,
		const int	_gradfreq,
		const double	_temperature
	)

Definition at line 28 of file eabf2D.C.

References eABF::krestr, eABF::lowerboundary, eABF::restart, eABF::upperboundary, and eABF::width.

                                   :
        eABF(_outputfile, _outputfreq, _restart, _inputfile, _outputgrad, _gradfreq, _temperature)
{
        lowerboundary.push_back(_lowerboundary);
        lowerboundary.push_back(_lowerboundary2);
        upperboundary.push_back(_upperboundary);
        upperboundary.push_back(_upperboundary2);
        width.push_back(_width);
        width.push_back(_width2);
        krestr.push_back(_krestr);
        krestr.push_back(_krestr2);
        this->initialize();
        this->restart = _restart;
    if(restart == true)
        this->readfile();
}

virtual eABF2D::~eABF2D ( )

inlinevirtual

Definition at line 43 of file eabf2D.h.

References eABF::bins.

    {
                for (int i = 0; i < bins[0] * bins[0]; i++)
                        delete[] countall[i];
                delete[] countall;
    }

Member Function Documentation

bool eABF2D::update ( const std::string &  colvarstring )

virtual

Implements eABF.

Definition at line 92 of file eabf2D.C.

References eabffunc::chartodouble(), eabffunc::chartoint(), eABF::col, eABF::gradfreq, eABF::line, eABF::min, eABF::outputfreq, eABF::outputgrad, eabffunc::split(), and eABF::width.

{
    // this is the string obtained from colvar each step
    // the format of this string is the same as those in colvar.traj file

        std::vector<std::string> data;
        eabffunc::split(colvarstring, data);

    int step;

    double abf_force;
    double eabf_force;
    double abf_force2;
    double eabf_force2;

        step = eabffunc::chartoint(data[0]);
        abf_force = eabffunc::chartodouble(data[col[0]]);
        eabf_force = eabffunc::chartodouble(data[col[1]]);
        abf_force2 = eabffunc::chartodouble(data[col[2]]);
        eabf_force2 = eabffunc::chartodouble(data[col[3]]);


        if (abf_force > 150 && eabf_force < -150)
                eabf_force += 360;
        else if (abf_force < -150 && eabf_force > 150)
                eabf_force -= 360;

        if (abf_force2 > 150 && eabf_force2 < -150)
                eabf_force2 += 360;
        else if (abf_force2 < -150 && eabf_force2 > 150)
        eabf_force2 -= 360;

        int binx = int(floor(abf_force / width[0])) - min[0];
        int biny = int(floor(eabf_force / width[0])) - min[0];
        int binx2 = int(floor(abf_force2 / width[1])) - min[1];
        int biny2 = int(floor(eabf_force2 / width[1])) - min[1];

        if (step%outputfreq == 0)
    {
        writefile();
    }

        if (outputgrad == true && (step%gradfreq) == 0)
    {
        calpmf();
    }


        if (binx < 0 || binx >= bins[0] || biny < 0 || biny >= bins[0] || binx2 < 0 || binx2 >= bins[1] || biny2 < 0 || biny2 >= bins[1])
                return false;
    else
    {
        // distribution
                countall[binx*bins[0] + biny][binx2*bins[1] + biny2]++;

        // if this is the first time add "countall", then the line in outputfile will increase
                if (countall[binx*bins[0] + biny][binx2*bins[1] + biny2] == 1)
                        line++;
        county[biny][biny2]++;
    }

    sumx1[biny][biny2] += abf_force;
    sumx21[biny][biny2] += abf_force * abf_force;
    sumx2[biny][biny2] += abf_force2;
        sumx22[biny][biny2] += abf_force2 * abf_force2;


    // TODO: add convergence judgement
    return true;
}

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The documentation for this class was generated from the following files:

• eabf2D.h
• eabf2D.C