eABF1D Class Reference

#include <eabf1D.h>

Inheritance diagram for eABF1D:

Public Member Functions
	eABF1D ()
	eABF1D (const double _lowerboundary, const double _upperboundary, const double _width, const double _krestr, const std::string &_outputfile, const int _outputfreq, const bool _restart, const std::string &_inputfile, const bool _outputgrad, const int _gradfreq, const double _temperature)
virtual	~eABF1D ()
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)

Protected Member Functions
bool	initialize ()
bool	readfile ()
bool	writefile () const
bool	writehead (ofstream_namd &) const
bool	calpmf () const
int	convertscale (double lowerboundary, int window) const

Protected Attributes
std::vector< std::vector< int > >	countall
std::vector< double >	sumx
std::vector< double >	sumx2
std::vector< int >	county
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 eabf1D.h.

Constructor & Destructor Documentation

eABF1D() [1/2]

eABF1D::eABF1D ( )

inline

Definition at line 26 of file eabf1D.h.

{}

eABF1D() [2/2]

eABF1D::eABF1D	(	const double	_lowerboundary,
		const double	_upperboundary,
		const double	_width,
		const double	_krestr,
		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 eabf1D.C.

References initialize(), eABF::krestr, eABF::lowerboundary, readfile(), eABF::restart, eABF::upperboundary, and eABF::width.

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

~eABF1D()

virtual eABF1D::~eABF1D ( )

inlinevirtual

Definition at line 39 of file eabf1D.h.

{}

Member Function Documentation

calpmf()

bool eABF1D::calpmf ( ) const

protectedvirtual

Implements eABF.

Definition at line 197 of file eabf1D.C.

References eABF::bins, eabffunc::BOLTZMANN, countall, county, eABF::krestr, eABF::lowerboundary, eABF::min, eABF::outputfile, sumx, sumx2, eABF::temperature, eABF::upperboundary, eABF::width, and writehead().

Referenced by update().

{
        // implementation of YangWei's estimator
        // mimic Jerome's script
        int norm;
        std::vector<double> x_av(bins[0]);
        std::vector<double> sigma2(bins[0]);
        for (int biny = 0; biny < bins[0]; biny++)
        {
                norm = county[biny] > 0 ? county[biny] : 1;
                x_av[biny] = sumx[biny] / norm;
                sigma2[biny] = sumx2[biny] / norm - x_av[biny] * x_av[biny];
        }

        static std::string gridfilename = outputfile + ".grad";
        static std::string histfilename = outputfile + ".hist.grad";
        static std::string pmffilename = outputfile + ".pmf";
        static std::string countfilename = outputfile + ".count";

        ofstream_namd ofile(gridfilename.c_str(),".old");
        ofstream_namd ofile_hist(histfilename.c_str(), std::ios::app);
        ofstream_namd ofile_pmf(pmffilename.c_str(),".old");
        ofstream_namd ofile_count(countfilename.c_str(),".old");

        writehead(ofile);
        writehead(ofile_hist);
        writehead(ofile_count);

        ofile_pmf << lowerboundary[0] << " 0.0" << std::endl;

        double pmf = 0, pmf_x = 0;
        double x, y, av, diff_av, grad;
        for (int binx = 0; binx < bins[0]; binx++)
        {
                x = (binx + min[0] + 0.5) * width[0];
                norm = 0;
                av = 0;
                diff_av = 0;

                for (int biny = 0; biny < bins[0]; biny++)
                {
                        y = (biny + min[0] + 0.5) * width[0];
                        norm += countall[binx][biny];

                        if (sigma2[biny] > 0.00001 || sigma2[biny] < -0.00001)
                        {
                                av += countall[binx][biny] * (x - x_av[biny]) / sigma2[biny];
                        }
                        else if (countall[binx][biny] > 1)
                        {
                                // TODO, print error
                        }
                        diff_av += countall[binx][biny] * (x - y);
                }

                diff_av /= (norm > 0 ? norm : 1);
                av = eabffunc::BOLTZMANN * temperature * av / (norm > 0 ? norm : 1);
                grad = av - krestr[0] * diff_av;


                if (x >= lowerboundary[0] && x < upperboundary[0])
                {
                        ofile << x << " " << grad << std::endl;
                        ofile_hist << x << " " << grad << std::endl;
                        pmf += grad * width[0];
                        pmf_x = x + 0.5 * width[0];
                        ofile_pmf << pmf_x << " " << pmf << std::endl;
                        ofile_count << x << " " << norm << std::endl;
                        // TODO, rescale the pmf file to prevent negetive free energy
                }
        }
        ofile.close();
        ofile_pmf.close();
        ofile_hist.close();
        ofile_count.close();
        return true;
}

convertscale()

int eABF1D::convertscale ( double  lowerboundary, int  window  ) const

inlineprotected

Definition at line 60 of file eabf1D.h.

References eABF::lowerboundary, and eABF::width.

Referenced by readfile().

        {
                return int((lowerboundary - this->lowerboundary[0]) / width[0] + window);
        }

initialize()

bool eABF1D::initialize ( void  )

protectedvirtual

Implements eABF.

Definition at line 45 of file eabf1D.C.

References eABF::bins, countall, county, eabffunc::doubletoint(), eABF::line, eABF::lowerboundary, eABF::max, eABF::min, sumx, sumx2, eABF::upperboundary, and eABF::width.

Referenced by eABF1D().

{
        // calculate the number of bins in the calculation
        // the bins is equal to "real bins + 20" to prevent boundary effect
    min.push_back(eabffunc::doubletoint(lowerboundary[0] / width[0]) - 10);
    max.push_back(eabffunc::doubletoint(upperboundary[0] / width[0]) + 10);
        bins.push_back(max[0] - min[0]);

    // initialize the distribution of "countall"
        for (int i = 0; i < bins[0]; i++)
    {
                countall.push_back(std::vector<int>(bins[0], 0));
    }

    // initialize other variables
        sumx = std::vector<double>(bins[0], 0);
        sumx2 = std::vector<double>(bins[0], 0);
        county = std::vector<int>(bins[0], 0);
    line = 0;
    return true;
}

readfile()

bool eABF1D::readfile ( )

protectedvirtual

Implements eABF.

Definition at line 123 of file eabf1D.C.

References convertscale(), countall, county, eABF::inputfile, eABF::krestr, eABF::line, sumx, sumx2, and eABF::temperature.

Referenced by eABF1D().

{
    std::ifstream file(inputfile.c_str(), std::ios::in);

    // output file format: (also see writefile function)
    // (number of lines) lowerboundary width (number of bins) krestr temperature
        // (normalized CV) (normalized extended CV) numbers
        // ......  "only non-zero value is recorded here"
        // (normalized CV) sumx sumx2 county
        // ......
    int temp_line, temp_bins;
    double temp_lowerboundary, temp_width;
        file >> temp_line >> temp_lowerboundary >> temp_width >> temp_bins >> krestr[0] >> temperature;

    temp_bins = temp_bins + 20;

        int x = 0, y = 0, temp_countall;
        for (int i = 0; i < temp_line; i++)
    {
                file >> x >> y;
                file >> temp_countall;
                //if (x > temp_bins - 10 || x < 10)
                //      continue;
        ;
                if (countall[convertscale(temp_lowerboundary, x)][convertscale(temp_lowerboundary, y)] == 0)
                        line++;
        countall[convertscale(temp_lowerboundary,x)][convertscale(temp_lowerboundary,y)] += temp_countall;
    }

        double temp_sumx, temp_sumx2;
        int temp_county;
        for (int i = 0; i < temp_bins; i++)
    {
                file >> x >> temp_sumx >> temp_sumx2 >> temp_county;
                //if (x > temp_bins - 10 || x < 10)
                //      continue;
        ;
                sumx[convertscale(temp_lowerboundary, x)] += temp_sumx;
                sumx2[convertscale(temp_lowerboundary, x)] += temp_sumx2;
                county[convertscale(temp_lowerboundary, x)] += temp_county;
    }

    file.close();
    return true;
}

update()

bool eABF1D::update ( const std::string &  colvarstring )

virtual

Implements eABF.

Definition at line 67 of file eabf1D.C.

References eABF::bins, calpmf(), eabffunc::chartodouble(), eabffunc::chartoint(), eABF::col, countall, county, eABF::gradfreq, eABF::line, eABF::min, eABF::outputfreq, eABF::outputgrad, eabffunc::split(), sumx, sumx2, eABF::width, and writefile().

{
    // 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);  // split the string to a vector<string>

    int step;

    double abf_force;       // the value of the two columns characterizing the value of CV and extended CV
    double eabf_force;

        step = eabffunc::chartoint(data[0]);    // read the variables fron the "colvarstring"
        abf_force = eabffunc::chartodouble(data[col[0]]);
        eabf_force = eabffunc::chartodouble(data[col[1]]);


        // for dihedral RC, it is possible that abf_force = 179 and eabf_force = -179, should correct it
    if(abf_force > 150 && eabf_force < -150)
        eabf_force += 360;
    else if(abf_force < -150 && eabf_force > 150)
        eabf_force -= 360;

        // normalize the index of the value of CV and extended CV
        int binx = int(floor(abf_force / width[0])) - min[0];
        int biny = int(floor(eabf_force / width[0])) - min[0];

    // update the 
        if (binx < 0 || binx >= bins[0] || biny < 0 || biny >= bins[0])
        return false;
    else
    {
                countall[binx][biny]++;
        // if this is the first time add "countall", then the line in outputfile will increase
        if(countall[binx][biny]==1)
            line++;
        county[biny]++;
    }

    sumx[biny] += abf_force;
    sumx2[biny] += abf_force * abf_force;

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

    if(outputgrad==1&&(step%gradfreq)==0)
    {
        calpmf();
    }

    return true;
}

writefile()

bool eABF1D::writefile ( ) const

protectedvirtual

Implements eABF.

Definition at line 169 of file eabf1D.C.

References eABF::bins, countall, county, eABF::krestr, eABF::line, eABF::lowerboundary, eABF::outputfile, sumx, sumx2, eABF::temperature, and eABF::width.

Referenced by update().

{
    ofstream_namd file(outputfile.c_str(),".old");
    file<<std::setprecision(15);

        file << line << " " << lowerboundary[0] << " " << width[0] << " " << bins[0] - 20 << " " << krestr[0] << " " << temperature << std::endl;

        for (int i = 0; i < bins[0]; i++)
                for (int j = 0; j < bins[0]; j++)
                        if (countall[i][j] != 0)
                                // the number of line should be "this->line", I guess :)
                                file << i << " " << j << " " << countall[i][j] << std::endl;

        for (int i = 0; i < bins[0]; i++)
                file << i << " " << sumx[i] << " " << sumx2[i] << " " << county[i] << " " << std::endl;

    file.close();
    return true;
}

writehead()

bool eABF1D::writehead ( ofstream_namd &  os ) const

protectedvirtual

Implements eABF.

Definition at line 189 of file eabf1D.C.

References eABF::bins, eABF::lowerboundary, and eABF::width.

Referenced by calpmf().

{
        os << "# 1" << std::endl;
        os << "# " << lowerboundary[0] << " " << width[0] << " " << bins[0] - 20 << " " << 0 << std::endl;
        os << std::endl;
    return true;
}

Member Data Documentation

countall

std::vector<std::vector<int> > eABF1D::countall

protected

Definition at line 45 of file eabf1D.h.

Referenced by calpmf(), initialize(), readfile(), update(), and writefile().

county

std::vector<int> eABF1D::county

protected

Definition at line 48 of file eabf1D.h.

Referenced by calpmf(), initialize(), readfile(), update(), and writefile().

sumx

std::vector<double> eABF1D::sumx

protected

Definition at line 46 of file eabf1D.h.

Referenced by calpmf(), initialize(), readfile(), update(), and writefile().

sumx2

std::vector<double> eABF1D::sumx2

protected

Definition at line 47 of file eabf1D.h.

Referenced by calpmf(), initialize(), readfile(), update(), and writefile().

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

• eabf1D.h
• eabf1D.C