\hypertarget{classNegativeFreeEnergy}{
\subsection{NegativeFreeEnergy Class Reference}
\label{classNegativeFreeEnergy}\index{NegativeFreeEnergy@{NegativeFreeEnergy}}
}


Class for computing the negitve free energy using thermodynamic integration.  


Inheritance diagram for NegativeFreeEnergy:\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[height=2.000000cm]{classNegativeFreeEnergy}
\end{center}
\end{figure}
\subsubsection*{Public Member Functions}
\begin{DoxyCompactItemize}
\item 
\hyperlink{classNegativeFreeEnergy_a848303f87467c22716b292f0acb30798}{NegativeFreeEnergy} (const \hyperlink{classDataForMCMC}{DataForMCMC} \&d)
\item 
double \hyperlink{classNegativeFreeEnergy_a267e5220250091e3673302d76c7111ba}{variance\_\-from\_\-sample} (double sample, double \hyperlink{classDataForMCMC_aec3a6d4e2a675e7f402ae38e342f4994}{samples}, double base\_\-sigma, double scale\_\-pow) const 
\item 
double \hyperlink{classNegativeFreeEnergy_a0840071c0e2eccada3fea1eca7f9457a}{compute\_\-with\_\-mask} (const Vector$<$$>$ \&spots, const vector$<$ vector$<$ int $>$ $>$ \&spot\_\-pixels) const 
\item 
double \hyperlink{classNegativeFreeEnergy_ab20dafb28f4f1b962f3f6a112f81e77c}{operator()} (const Vector$<$$>$ \&spots) const 
\item 
\hyperlink{structMT19937}{MT19937} \& \hyperlink{classDataForMCMC_a075edc255ded434adab5dc29818ac36f}{get\_\-rng} () const 
\end{DoxyCompactItemize}
\subsubsection*{Protected Attributes}
\begin{DoxyCompactItemize}
\item 
const vector$<$ ImageRef $>$ \& \hyperlink{classDataForMCMC_ab2e18ea9907dbf6c802377805f41b39c}{pixels}
\item 
const vector$<$ vector$<$ double $>$ $>$ \& \hyperlink{classDataForMCMC_af938cc0cf40b14c954121da40acddde8}{pixel\_\-intensities}
\item 
const double \hyperlink{classDataForMCMC_ad6f046e65d3fb7dfed4d1df300df4530}{mu\_\-brightness}
\item 
const double \hyperlink{classDataForMCMC_a00058a98358c328fcf6223d216d7f8d3}{sigma\_\-brightness}
\item 
const double \hyperlink{classDataForMCMC_ae2cdad8d7062a79b3ea33d2a962ac1e7}{mu\_\-blur}
\item 
const double \hyperlink{classDataForMCMC_a8fd8eb85c9ab7e89d80dbb9259c31a9c}{sigma\_\-blur}
\item 
const double \hyperlink{classDataForMCMC_a3e343a540b3ea41d9124fbad4549d8cc}{variance}
\item 
const int \hyperlink{classDataForMCMC_aec3a6d4e2a675e7f402ae38e342f4994}{samples}
\item 
const int \hyperlink{classDataForMCMC_a83103f72475b121baabd05e9b8df1008}{sample\_\-iterations}
\item 
const Matrix$<$ 3 $>$ \hyperlink{classDataForMCMC_a9a6d87f160124548bc024d3729104d1c}{A}
\item 
const Vector$<$ 3 $>$ \hyperlink{classDataForMCMC_a0f6b8af3c843069f6d9f0ea16deffe48}{pi}
\item 
\hyperlink{structMT19937}{MT19937} \& \hyperlink{classDataForMCMC_abae93ccf7880ba57a5cbb322e69e6f16}{rng}
\end{DoxyCompactItemize}


\subsubsection{Detailed Description}
Class for computing the negitve free energy using thermodynamic integration. 

Definition at line 280 of file multispot5.cc.



\subsubsection{Constructor \& Destructor Documentation}
\hypertarget{classNegativeFreeEnergy_a848303f87467c22716b292f0acb30798}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{NegativeFreeEnergy}]{\setlength{\rightskip}{0pt plus 5cm}NegativeFreeEnergy::NegativeFreeEnergy (
\begin{DoxyParamCaption}
\item[{const {\bf DataForMCMC} \&}]{d}
\end{DoxyParamCaption}
)\hspace{0.3cm}{\ttfamily  \mbox{[}inline\mbox{]}}}}
\label{classNegativeFreeEnergy_a848303f87467c22716b292f0acb30798}

\begin{DoxyParams}{Parameters}
{\em d} & Necessary data \\
\hline
\end{DoxyParams}


Definition at line 285 of file multispot5.cc.


\begin{DoxyCode}
    :DataForMCMC(d)
    {
    }
\end{DoxyCode}


\subsubsection{Member Function Documentation}
\hypertarget{classNegativeFreeEnergy_a267e5220250091e3673302d76c7111ba}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!variance\_\-from\_\-sample@{variance\_\-from\_\-sample}}
\index{variance\_\-from\_\-sample@{variance\_\-from\_\-sample}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{variance\_\-from\_\-sample}]{\setlength{\rightskip}{0pt plus 5cm}double NegativeFreeEnergy::variance\_\-from\_\-sample (
\begin{DoxyParamCaption}
\item[{double}]{sample, }
\item[{double}]{samples, }
\item[{double}]{base\_\-sigma, }
\item[{double}]{scale\_\-pow}
\end{DoxyParamCaption}
) const\hspace{0.3cm}{\ttfamily  \mbox{[}inline\mbox{]}}}}
\label{classNegativeFreeEnergy_a267e5220250091e3673302d76c7111ba}


Give the noise variance given a sample number and growth parameters. 


\begin{DoxyParams}{Parameters}
{\em sample} & Sample number \\
\hline
{\em samples} & Total number of samples \\
\hline
{\em base\_\-sigma} & Starting value of sigme \\
\hline
{\em scale\_\-pow} & Exponent scaling \\
\hline
\end{DoxyParams}


Definition at line 295 of file multispot5.cc.



References sq().


\begin{DoxyCode}
    {
        double scale = pow(1.25, sample * 1. / samples * scale_pow);
        double sigma = base_sigma * scale;
        double new_variance = sq(sigma);

        return new_variance;
    }
\end{DoxyCode}
\hypertarget{classNegativeFreeEnergy_a0840071c0e2eccada3fea1eca7f9457a}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!compute\_\-with\_\-mask@{compute\_\-with\_\-mask}}
\index{compute\_\-with\_\-mask@{compute\_\-with\_\-mask}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{compute\_\-with\_\-mask}]{\setlength{\rightskip}{0pt plus 5cm}double NegativeFreeEnergy::compute\_\-with\_\-mask (
\begin{DoxyParamCaption}
\item[{const Vector$<$$>$ \&}]{spots, }
\item[{const vector$<$ vector$<$ int $>$ $>$ \&}]{spot\_\-pixels}
\end{DoxyParamCaption}
) const\hspace{0.3cm}{\ttfamily  \mbox{[}inline\mbox{]}}}}
\label{classNegativeFreeEnergy_a0840071c0e2eccada3fea1eca7f9457a}


Estimate free energy using the Slow Growth Thermodynamic Integration method given in Probalistic Inference Using Markov Chain Monte Carlo Methods, Radford. 

M. Neal, 1993 Except using a 5 point stencil instead of forward differenceing in Eq 6.30 
\begin{DoxyParams}{Parameters}
{\em spots} & list of spots \\
\hline
{\em spot\_\-pixels} & Mask around each spot to use to save on computation \\
\hline
\end{DoxyParams}


Definition at line 309 of file multispot5.cc.



References Kahan::add(), SampledMultispot::compute\_\-spot\_\-intensity(), DataForMCMC::get\_\-rng(), log\_\-log\_\-normal(), SampledMultispot::GibbsSampler2::next(), SampledMultispot::GibbsSampler2::sample\_\-intensities(), SampledMultispot::GibbsSampler2::set\_\-variance(), spots\_\-to\_\-vector(), and sq().



Referenced by FitSpots::try\_\-modifying\_\-model().


\begin{DoxyCode}
    {
        //Estimate free energy using the Slow Growth Thermodynamic Integration me
      thod given in
        //Probalistic Inference Using Markov Chain Monte Carlo Methods, Radford. 
      M. Neal, 1993
        //Except using a 5 point stencil instead of forward differenceing in Eq 6
      .30
        double base_sigma = sqrt(variance); // should be 1
        double scale_pow = 100.0;

        const unsigned int nspots  = spots.size()/4;
        const unsigned int nframes = pixel_intensities.size();
        const unsigned int npixels = pixels.size();
        assert(spots.size() %4 == 0);
        assert(spot_pixels.size() == nspots);

        //Compute the intensities and derivatives for all spot
        vector<vector<double> > spot_intensity; //[spot][pixel]
        for(unsigned int i=0; i < nspots; i++)
            spot_intensity.push_back(compute_spot_intensity(pixels, spots.slice<D
      ynamic,4>(i*4,4)));
        
        GibbsSampler2 sampler(pixel_intensities, spot_intensity, spots_to_vector(
      spots), spot_pixels, A, pi, variance, sample_iterations);

        double sum = 0;
        Kahan ksum;
        for(int sample=0; sample < samples; sample++)
        {
            //Compute the positions of the surrounding steps
            double var1 = variance_from_sample(sample-2, samples, base_sigma, sca
      le_pow);
            double var2 = variance_from_sample(sample-1, samples, base_sigma, sca
      le_pow);
            double var3 = variance_from_sample(sample+1, samples, base_sigma, sca
      le_pow);
            double var4 = variance_from_sample(sample+2, samples, base_sigma, sca
      le_pow);

            //Take a sample
            sampler.set_variance(var2);
            sampler.next(DataForMCMC::get_rng());
            
            //Compute the SSD. This is fixed regardless of sigma.   
            double err_sum=0;
            for(unsigned int frame=0; frame < nframes; frame++)
                for(unsigned int pixel=0; pixel < npixels; pixel++)
                    err_sum -= sq(pixel_intensities[frame][pixel] - sampler.sampl
      e_intensities()[frame][pixel]);
            
            //Compute the derivative using a five point stencil
            //This could be done in a better but less clear way
            double e1 = err_sum / (2*var1) - npixels*nframes*::log(2*M_PI*var1)/2
      ;
            double e2 = err_sum / (2*var2) - npixels*nframes*::log(2*M_PI*var2)/2
      ;
            double e3 = err_sum / (2*var3) - npixels*nframes*::log(2*M_PI*var3)/2
      ;
            double e4 = err_sum / (2*var4) - npixels*nframes*::log(2*M_PI*var4)/2
      ;
            sum += (-e1 + 8*e2 - 8*e3 + e4)/12;

            ksum.add(-e1/12);
            ksum.add(8*e2/12);
            ksum.add(-8*e3/12);
            ksum.add(e4/12);
        }

        double log_final = (log(variance_from_sample(samples, samples, base_sigma
      , scale_pow)*2*M_PI)/2) * npixels * nframes;
        
        double priors=0;
        for(unsigned int i=0; i < nspots; i++)
        {
            priors += log_log_normal(spots[i*4+0], mu_brightness, 
      sigma_brightness);
            priors += log_log_normal(spots[i*4+1], mu_blur, sigma_blur);
        }

        /*cout << "Thermo:\n";
        cout << "sum: " << sum -log_final << endl;
        cout << "kah: " << ksum.sum -log_final << endl;
        cout << "priors: " << priors + sum -log_final << endl;
        cout << "   kah: " << priors + ksum.sum -log_final << endl;
*/
        //cout << log_final << endl;
        //cout << sum + log_final << endl;
        
        
        sampler.set_variance(variance);
        return -(sum+priors - log_final);
    }
\end{DoxyCode}
\hypertarget{classNegativeFreeEnergy_ab20dafb28f4f1b962f3f6a112f81e77c}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!operator()@{operator()}}
\index{operator()@{operator()}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{operator()}]{\setlength{\rightskip}{0pt plus 5cm}double NegativeFreeEnergy::operator() (
\begin{DoxyParamCaption}
\item[{const Vector$<$$>$ \&}]{spots}
\end{DoxyParamCaption}
) const\hspace{0.3cm}{\ttfamily  \mbox{[}inline\mbox{]}}}}
\label{classNegativeFreeEnergy_ab20dafb28f4f1b962f3f6a112f81e77c}


Estimate free energy using the Slow Growth Thermodynamic Integration method given in Probalistic Inference Using Markov Chain Monte Carlo Methods, Radford. 

M. Neal, 1993 Except using a 5 point stencil instead of forward differenceing in Eq 6.30 
\begin{DoxyParams}{Parameters}
{\em spots} & list of spots \\
\hline
\end{DoxyParams}


Definition at line 391 of file multispot5.cc.



References Kahan::add(), SampledMultispot::compute\_\-spot\_\-intensity(), DataForMCMC::get\_\-rng(), log\_\-log\_\-normal(), SampledMultispot::GibbsSampler::next(), SampledMultispot::GibbsSampler::sample\_\-intensities(), SampledMultispot::GibbsSampler::set\_\-variance(), spots\_\-to\_\-vector(), and sq().


\begin{DoxyCode}
    {
        double base_sigma = sqrt(variance); // should be 1
        double scale_pow = 100.0;

        const unsigned int nspots  = spots.size()/4;
        const unsigned int nframes = pixel_intensities.size();
        const unsigned int npixels = pixels.size();
        assert(spots.size() %4 == 0);

        //Compute the intensities and derivatives for all spot
        vector<vector<double> > spot_intensity; //[spot][pixel]
        for(unsigned int i=0; i < nspots; i++)
            spot_intensity.push_back(compute_spot_intensity(pixels, spots.slice<D
      ynamic,4>(i*4,4)));
        
        GibbsSampler sampler(pixel_intensities, spot_intensity, spots_to_vector(s
      pots), A, pi, variance, sample_iterations);

        double sum = 0;
        Kahan ksum;
        for(int sample=0; sample < samples; sample++)
        {
            //Compute the positions of the surrounding steps
            double var1 = variance_from_sample(sample-2, samples, base_sigma, sca
      le_pow);
            double var2 = variance_from_sample(sample-1, samples, base_sigma, sca
      le_pow);
            double var3 = variance_from_sample(sample+1, samples, base_sigma, sca
      le_pow);
            double var4 = variance_from_sample(sample+2, samples, base_sigma, sca
      le_pow);

            //Take a sample
            sampler.set_variance(var2);
            sampler.next(DataForMCMC::get_rng());
            
            //Compute the SSD. This is fixed regardless of sigma.   
            double err_sum=0;
            for(unsigned int frame=0; frame < nframes; frame++)
                for(unsigned int pixel=0; pixel < npixels; pixel++)
                    err_sum -= sq(pixel_intensities[frame][pixel] - sampler.sampl
      e_intensities()[frame][pixel]);
            
            //Compute the derivative using a five point stencil
            //This could be done in a better but less clear way
            double e1 = err_sum / (2*var1) - npixels*nframes*::log(2*M_PI*var1)/2
      ;
            double e2 = err_sum / (2*var2) - npixels*nframes*::log(2*M_PI*var2)/2
      ;
            double e3 = err_sum / (2*var3) - npixels*nframes*::log(2*M_PI*var3)/2
      ;
            double e4 = err_sum / (2*var4) - npixels*nframes*::log(2*M_PI*var4)/2
      ;
            sum += (-e1 + 8*e2 - 8*e3 + e4)/12;

            ksum.add(-e1/12);
            ksum.add(8*e2/12);
            ksum.add(-8*e3/12);
            ksum.add(e4/12);
        }

        double log_final = (log(variance_from_sample(samples, samples, base_sigma
      , scale_pow)*2*M_PI)/2) * npixels * nframes;
        
        double priors=0;
        for(unsigned int i=0; i < nspots; i++)
        {
            priors += log_log_normal(spots[i*4+0], mu_brightness, 
      sigma_brightness);
            priors += log_log_normal(spots[i*4+1], mu_blur, sigma_blur);
        }

        /*cout << "Thermo:\n";
        cout << "sum: " << sum -log_final << endl;
        cout << "kah: " << ksum.sum -log_final << endl;
        cout << "priors: " << priors + sum -log_final << endl;
        cout << "   kah: " << priors + ksum.sum -log_final << endl;
*/
        //cout << log_final << endl;
        //cout << sum + log_final << endl;
        
        
        sampler.set_variance(variance);
        return -(sum+priors - log_final);
    }
\end{DoxyCode}
\hypertarget{classDataForMCMC_a075edc255ded434adab5dc29818ac36f}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!get\_\-rng@{get\_\-rng}}
\index{get\_\-rng@{get\_\-rng}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{get\_\-rng}]{\setlength{\rightskip}{0pt plus 5cm}{\bf MT19937}\& DataForMCMC::get\_\-rng (
\begin{DoxyParamCaption}
{}
\end{DoxyParamCaption}
) const\hspace{0.3cm}{\ttfamily  \mbox{[}inline, inherited\mbox{]}}}}
\label{classDataForMCMC_a075edc255ded434adab5dc29818ac36f}


Definition at line 208 of file multispot5.cc.



Referenced by compute\_\-with\_\-mask(), and operator()().


\begin{DoxyCode}
    {
        return rng;
    }
\end{DoxyCode}


\subsubsection{Member Data Documentation}
\hypertarget{classDataForMCMC_ab2e18ea9907dbf6c802377805f41b39c}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!pixels@{pixels}}
\index{pixels@{pixels}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{pixels}]{\setlength{\rightskip}{0pt plus 5cm}const vector$<$ImageRef$>$\& {\bf DataForMCMC::pixels}\hspace{0.3cm}{\ttfamily  \mbox{[}protected, inherited\mbox{]}}}}
\label{classDataForMCMC_ab2e18ea9907dbf6c802377805f41b39c}


Definition at line 198 of file multispot5.cc.

\hypertarget{classDataForMCMC_af938cc0cf40b14c954121da40acddde8}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!pixel\_\-intensities@{pixel\_\-intensities}}
\index{pixel\_\-intensities@{pixel\_\-intensities}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{pixel\_\-intensities}]{\setlength{\rightskip}{0pt plus 5cm}const vector$<$vector$<$double$>$ $>$\& {\bf DataForMCMC::pixel\_\-intensities}\hspace{0.3cm}{\ttfamily  \mbox{[}protected, inherited\mbox{]}}}}
\label{classDataForMCMC_af938cc0cf40b14c954121da40acddde8}


Definition at line 199 of file multispot5.cc.

\hypertarget{classDataForMCMC_ad6f046e65d3fb7dfed4d1df300df4530}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!mu\_\-brightness@{mu\_\-brightness}}
\index{mu\_\-brightness@{mu\_\-brightness}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{mu\_\-brightness}]{\setlength{\rightskip}{0pt plus 5cm}const double {\bf DataForMCMC::mu\_\-brightness}\hspace{0.3cm}{\ttfamily  \mbox{[}protected, inherited\mbox{]}}}}
\label{classDataForMCMC_ad6f046e65d3fb7dfed4d1df300df4530}


Definition at line 200 of file multispot5.cc.

\hypertarget{classDataForMCMC_a00058a98358c328fcf6223d216d7f8d3}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!sigma\_\-brightness@{sigma\_\-brightness}}
\index{sigma\_\-brightness@{sigma\_\-brightness}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{sigma\_\-brightness}]{\setlength{\rightskip}{0pt plus 5cm}const double {\bf DataForMCMC::sigma\_\-brightness}\hspace{0.3cm}{\ttfamily  \mbox{[}protected, inherited\mbox{]}}}}
\label{classDataForMCMC_a00058a98358c328fcf6223d216d7f8d3}


Definition at line 200 of file multispot5.cc.

\hypertarget{classDataForMCMC_ae2cdad8d7062a79b3ea33d2a962ac1e7}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!mu\_\-blur@{mu\_\-blur}}
\index{mu\_\-blur@{mu\_\-blur}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{mu\_\-blur}]{\setlength{\rightskip}{0pt plus 5cm}const double {\bf DataForMCMC::mu\_\-blur}\hspace{0.3cm}{\ttfamily  \mbox{[}protected, inherited\mbox{]}}}}
\label{classDataForMCMC_ae2cdad8d7062a79b3ea33d2a962ac1e7}


Definition at line 200 of file multispot5.cc.

\hypertarget{classDataForMCMC_a8fd8eb85c9ab7e89d80dbb9259c31a9c}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!sigma\_\-blur@{sigma\_\-blur}}
\index{sigma\_\-blur@{sigma\_\-blur}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{sigma\_\-blur}]{\setlength{\rightskip}{0pt plus 5cm}const double {\bf DataForMCMC::sigma\_\-blur}\hspace{0.3cm}{\ttfamily  \mbox{[}protected, inherited\mbox{]}}}}
\label{classDataForMCMC_a8fd8eb85c9ab7e89d80dbb9259c31a9c}


Definition at line 200 of file multispot5.cc.

\hypertarget{classDataForMCMC_a3e343a540b3ea41d9124fbad4549d8cc}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!variance@{variance}}
\index{variance@{variance}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{variance}]{\setlength{\rightskip}{0pt plus 5cm}const double {\bf DataForMCMC::variance}\hspace{0.3cm}{\ttfamily  \mbox{[}protected, inherited\mbox{]}}}}
\label{classDataForMCMC_a3e343a540b3ea41d9124fbad4549d8cc}


Definition at line 201 of file multispot5.cc.

\hypertarget{classDataForMCMC_aec3a6d4e2a675e7f402ae38e342f4994}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!samples@{samples}}
\index{samples@{samples}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{samples}]{\setlength{\rightskip}{0pt plus 5cm}const int {\bf DataForMCMC::samples}\hspace{0.3cm}{\ttfamily  \mbox{[}protected, inherited\mbox{]}}}}
\label{classDataForMCMC_aec3a6d4e2a675e7f402ae38e342f4994}


Definition at line 202 of file multispot5.cc.

\hypertarget{classDataForMCMC_a83103f72475b121baabd05e9b8df1008}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!sample\_\-iterations@{sample\_\-iterations}}
\index{sample\_\-iterations@{sample\_\-iterations}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{sample\_\-iterations}]{\setlength{\rightskip}{0pt plus 5cm}const int {\bf DataForMCMC::sample\_\-iterations}\hspace{0.3cm}{\ttfamily  \mbox{[}protected, inherited\mbox{]}}}}
\label{classDataForMCMC_a83103f72475b121baabd05e9b8df1008}


Definition at line 202 of file multispot5.cc.

\hypertarget{classDataForMCMC_a9a6d87f160124548bc024d3729104d1c}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!A@{A}}
\index{A@{A}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{A}]{\setlength{\rightskip}{0pt plus 5cm}const Matrix$<$3$>$ {\bf DataForMCMC::A}\hspace{0.3cm}{\ttfamily  \mbox{[}protected, inherited\mbox{]}}}}
\label{classDataForMCMC_a9a6d87f160124548bc024d3729104d1c}


Definition at line 203 of file multispot5.cc.

\hypertarget{classDataForMCMC_a0f6b8af3c843069f6d9f0ea16deffe48}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!pi@{pi}}
\index{pi@{pi}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{pi}]{\setlength{\rightskip}{0pt plus 5cm}const Vector$<$3$>$ {\bf DataForMCMC::pi}\hspace{0.3cm}{\ttfamily  \mbox{[}protected, inherited\mbox{]}}}}
\label{classDataForMCMC_a0f6b8af3c843069f6d9f0ea16deffe48}


Definition at line 204 of file multispot5.cc.

\hypertarget{classDataForMCMC_abae93ccf7880ba57a5cbb322e69e6f16}{
\index{NegativeFreeEnergy@{NegativeFreeEnergy}!rng@{rng}}
\index{rng@{rng}!NegativeFreeEnergy@{NegativeFreeEnergy}}
\paragraph[{rng}]{\setlength{\rightskip}{0pt plus 5cm}{\bf MT19937}\& {\bf DataForMCMC::rng}\hspace{0.3cm}{\ttfamily  \mbox{[}protected, inherited\mbox{]}}}}
\label{classDataForMCMC_abae93ccf7880ba57a5cbb322e69e6f16}


Definition at line 205 of file multispot5.cc.



The documentation for this class was generated from the following file:\begin{DoxyCompactItemize}
\item 
\hyperlink{multispot5_8cc}{multispot5.cc}\end{DoxyCompactItemize}
