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(t_complex *in1, t_complex *in2)
  69 {
  70     t_complex res;
  71     res.re  = in1->re *  in2->re + in1->im * in2->im;
  72     res.im  = in1->re * -in2->im + in1->im * in2->re;
  73     in1->re = res.re;
  74     in1->im = res.im;
  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     t_complex *     in1, * in2;
  91
  92     snew(in1, size);
  93     snew(in2, size);
  94
  95     for (i = 0; i < n; i++)
  96     {
  97         in1[i].re  = f[i];
  98         in1[i].im  = 0;
  99         in2[i].re  = g[i];
 100         in2[i].im  = 0;
 101     }
 102     for (; i < size; i++)
 103     {
 104         in1[i].re  = 0;
 105         in1[i].im  = 0;
 106         in2[i].re  = 0;
 107         in2[i].im  = 0;
 108     }
 109     gmx_fft_1d(fft, GMX_FFT_FORWARD, in1, in1);
 110     gmx_fft_1d(fft, GMX_FFT_FORWARD, in2, in2);
 111
 112     for (i = 0; i < size; i++)
 113     {
 114         complexConjugatMult(&in1[i], &in2[i]);
 115         in1[i].re /= size;
 116     }
 117     gmx_fft_1d(fft, GMX_FFT_BACKWARD, in1, in1);
 118
 119     for (i = 0; i < n; i++)
 120     {
 121         corr[i] = in1[i].re;
 122     }
 123
 124     sfree(in1);
 125     sfree(in2);
 126
 127 }
 128
 129 void cross_corr(int n, real f[], real g[], real corr[])
 130 {
 131     gmx_fft_t fft;
 132     gmx_fft_init_1d(&fft, zeroPaddingSize(n), GMX_FFT_FLAG_CONSERVATIVE);
 133     cross_corr_low( n,  f,  g, corr, fft);
 134     gmx_fft_destroy(fft);
 135     gmx_fft_cleanup();
 136 }
 137
 138 void many_cross_corr(int nFunc, int * nData, real ** f, real ** g, real ** corr)
 139 {
 140 #pragma omp parallel
 141     //gmx_fft_t is not thread safe, so structure are allocated per thread.
 142     {
 143         int i;
 144
 145 #pragma omp for
 146         for (i = 0; i < nFunc; i++)
 147         {
 148             try
 149             {
 150                 gmx_fft_t fft;
 151                 gmx_fft_init_1d(&fft, zeroPaddingSize(nData[i]), GMX_FFT_FLAG_CONSERVATIVE);
 152                 cross_corr_low( nData[i],  f[i],  g[i], corr[i], fft);
 153                 gmx_fft_destroy(fft);
 154             }
 155             GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
 156         }
 157     }
 158     gmx_fft_cleanup();
 159
 160 }