src/gromacs/correlationfunctions/crosscorr.cpp

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  35 /*! \internal
  36  * \file
  37  * \brief
  38  * Implements routine for computing a cross correlation between two data sets
  39  *
  40  * \author David van der Spoel <david.vanderspoel@icm.uu.se>
  41  * \ingroup module_correlationfunctions
  42  */
  43 #include "gmxpre.h"
  44
  45 #include "crosscorr.h"
  46
  47 #include "gromacs/fft/fft.h"
  48 #include "gromacs/utility/exceptions.h"
  49 #include "gromacs/utility/smalloc.h"
  50
  51 /*! \brief
  52  * return the size witch the array should be after zero padding
  53  *
  54  * \param[in] n Factor to multiply by 2
  55  * \return zeroPaddingSize
  56  */
  57 static int zeroPaddingSize(int n)
  58 {
  59     return 2*n;
  60 }
  61
  62 /*! \brief
  63  * Compute complex conjugate. Output in the first input variable.
  64  *
  65  * \param[in] in1 first complex number
  66  * \param[in] in2 second complex number
  67  */
  68 static void complexConjugatMult(double in1[], double in2[])
  69 {
  70     double res[2];
  71     res[0]  = in1[0] * in2[0] + in1[1] * in2[1];
  72     res[1]  = in1[0] * -in2[1] + in1[1] * in2[0];
  73     in1[0]  = res[0];
  74     in1[1]  = res[1];
  75 }
  76
  77 /*! \brief
  78  * Compute one cross correlation corr = f x g using FFT.
  79  *
  80  * \param[in] n number of data point
  81  * \param[in] f first function
  82  * \param[in] g second function
  83  * \param[out] corr output correlation
  84  * \param[in] fft FFT data structure
  85  */
  86 static void cross_corr_low(int n, real f[], real g[], real corr[], gmx_fft_t fft)
  87 {
  88     int             i;
  89     const int       size = zeroPaddingSize(n);
  90     double    **    in1, ** in2;
  91     snew(in1, size);
  92     snew(in2, size);
  93
  94     for (i = 0; i < size; i++)
  95     {
  96         snew(in1[i], 2);
  97         snew(in2[i], 2);
  98     }
  99
 100     for (i = 0; i < n; i++)
 101     {
 102         in1[i][0]  = (double)f[i];
 103         in1[i][1]  = 0;
 104         in2[i][0]  = (double)g[i];
 105         in2[i][1]  = 0;
 106     }
 107     for (; i < size; i++)
 108     {
 109         in1[i][0]  = 0;
 110         in1[i][1]  = 0;
 111         in2[i][0]  = 0;
 112         in2[i][1]  = 0;
 113     }
 114
 115
 116     gmx_fft_1d(fft, GMX_FFT_FORWARD, in1, in1);
 117     gmx_fft_1d(fft, GMX_FFT_FORWARD, in2, in2);
 118
 119     for (i = 0; i < size; i++)
 120     {
 121         complexConjugatMult(in1[i], in2[i]);
 122         in1[i][0] /= size;
 123     }
 124     gmx_fft_1d(fft, GMX_FFT_BACKWARD, in1, in1);
 125
 126     for (i = 0; i < n; i++)
 127     {
 128         corr[i] = (real)(in1[i][0]);
 129     }
 130
 131     for (i = 0; i < size; i++)
 132     {
 133         sfree(in1[i]);
 134         sfree(in2[i]);
 135     }
 136
 137     sfree(in1);
 138     sfree(in2);
 139
 140 }
 141
 142 void cross_corr(int n, real f[], real g[], real corr[])
 143 {
 144     gmx_fft_t fft;
 145     gmx_fft_init_1d(&fft, zeroPaddingSize(n), GMX_FFT_FLAG_CONSERVATIVE);
 146     cross_corr_low( n,  f,  g, corr, fft);
 147     gmx_fft_destroy(fft);
 148     gmx_fft_cleanup();
 149 }
 150
 151 void many_cross_corr(int nFunc, int * nData, real ** f, real ** g, real ** corr)
 152 {
 153 #pragma omp parallel
 154     //gmx_fft_t is not thread safe, so structure are allocated per thread.
 155     {
 156         int i;
 157
 158 #pragma omp for
 159         for (i = 0; i < nFunc; i++)
 160         {
 161             try
 162             {
 163                 gmx_fft_t fft;
 164                 gmx_fft_init_1d(&fft, zeroPaddingSize(nData[i]), GMX_FFT_FLAG_CONSERVATIVE);
 165                 cross_corr_low( nData[i],  f[i],  g[i], corr[i], fft);
 166                 gmx_fft_destroy(fft);
 167             }
 168             GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
 169         }
 170     }
 171     gmx_fft_cleanup();
 172
 173 }