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38 * Implements routine for computing a cross correlation between two data sets
40 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
41 * \ingroup module_correlationfunctions
45 #include "crosscorr.h"
47 #include "gromacs/fft/fft.h"
48 #include "gromacs/legacyheaders/macros.h"
49 #include "gromacs/utility/smalloc.h"
52 * return the size witch the array should be after zero padding
54 * \param[in] n Factor to multiply by 2
55 * \return zeroPaddingSize
57 static int zeroPaddingSize(int n)
63 * Compute complex conjugate. Output in the first input variable.
65 * \param[in] in1 first complex number
66 * \param[in] in2 second complex number
68 static void complexConjugatMult(double in1[], double in2[])
71 res[0] = in1[0] * in2[0] + in1[1] * in2[1];
72 res[1] = in1[0] * -in2[1] + in1[1] * in2[0];
78 * Compute one cross correlation corr = f x g using FFT.
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
86 static void cross_corr_low(int n, real f[], real g[], real corr[], gmx_fft_t fft)
89 const int size = zeroPaddingSize(n);
90 double ** in1, ** in2;
94 for (i = 0; i < size; i++)
100 for (i = 0; i < n; i++)
102 in1[i][0] = (double)f[i];
104 in2[i][0] = (double)g[i];
107 for (; i < size; i++)
116 gmx_fft_1d(fft, GMX_FFT_FORWARD, in1, in1);
117 gmx_fft_1d(fft, GMX_FFT_FORWARD, in2, in2);
119 for (i = 0; i < size; i++)
121 complexConjugatMult(in1[i], in2[i]);
124 gmx_fft_1d(fft, GMX_FFT_BACKWARD, in1, in1);
126 for (i = 0; i < n; i++)
128 corr[i] = (real)(in1[i][0]);
131 for (i = 0; i < size; i++)
142 void cross_corr(int n, real f[], real g[], real corr[])
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);
151 void many_cross_corr(int nFunc, int * nData, real ** f, real ** g, real ** corr)
154 //gmx_fft_t is not thread safe, so structure are allocated per thread.
159 for (i = 0; i < nFunc; i++)
162 gmx_fft_init_1d(&fft, zeroPaddingSize(nData[i]), GMX_FFT_FLAG_CONSERVATIVE);
163 cross_corr_low( nData[i], f[i], g[i], corr[i], fft);
164 gmx_fft_destroy(fft);