From: Rossen Apostolov <rossen@kth.se>
Date: Wed, 3 Jun 2015 10:13:01 +0000 (+0200)
Subject: Converted correlationfuntcions to C++.
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=3dadfbb969e79953a942885fb931908a36fcaf08;hp=4bd00f0d606ba94e0e61994c087369ee125297b2;p=alexxy%2Fgromacs.git

Converted correlationfuntcions to C++.

Change-Id: If5a478eb05fc295670cfa982525838c5e1e255b7
---

diff --git a/src/gromacs/correlationfunctions/CMakeLists.txt b/src/gromacs/correlationfunctions/CMakeLists.txt
index 6c6718af5d..88d3bd88b3 100644
--- a/src/gromacs/correlationfunctions/CMakeLists.txt
+++ b/src/gromacs/correlationfunctions/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2014, by the GROMACS development team, led by
+# Copyright (c) 2014,2015, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -32,7 +32,7 @@
 # To help us fund GROMACS development, we humbly ask that you cite
 # the research papers on the package. Check out http://www.gromacs.org.
 
-file(GLOB GMXCORRFUNC_SOURCES *.c *.cpp)
+file(GLOB GMXCORRFUNC_SOURCES *.cpp)
 file(GLOB LMFIT_SOURCES ${CMAKE_SOURCE_DIR}/src/external/lmfit/*.c)
 
 set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${GMXCORRFUNC_SOURCES}  ${LMFIT_SOURCES} PARENT_SCOPE)
diff --git a/src/gromacs/correlationfunctions/autocorr.c b/src/gromacs/correlationfunctions/autocorr.cpp
similarity index 97%
rename from src/gromacs/correlationfunctions/autocorr.c
rename to src/gromacs/correlationfunctions/autocorr.cpp
index 72966978ce..7cdf48d577 100644
--- a/src/gromacs/correlationfunctions/autocorr.c
+++ b/src/gromacs/correlationfunctions/autocorr.cpp
@@ -45,10 +45,13 @@
 
 #include "autocorr.h"
 
-#include <math.h>
 #include <stdio.h>
 #include <string.h>
 
+#include <cmath>
+
+#include <algorithm>
+
 #include "gromacs/correlationfunctions/expfit.h"
 #include "gromacs/correlationfunctions/integrate.h"
 #include "gromacs/correlationfunctions/manyautocorrelation.h"
@@ -87,16 +90,12 @@ static void low_do_four_core(int nfour, int nframes, real c1[], real cfour[],
                              int nCos)
 {
     int  i = 0;
-    int  fftcode;
-    real aver, *ans;
 
-    aver = 0.0;
     switch (nCos)
     {
         case enNorm:
             for (i = 0; (i < nframes); i++)
             {
-                aver    += c1[i];
                 cfour[i] = c1[i];
             }
             break;
@@ -116,7 +115,7 @@ static void low_do_four_core(int nfour, int nframes, real c1[], real cfour[],
             gmx_fatal(FARGS, "nCos = %d, %s %d", nCos, __FILE__, __LINE__);
     }
 
-    fftcode = many_auto_correl(1, nframes, nfour, &cfour);
+    many_auto_correl(1, nframes, nfour, &cfour);
 }
 
 /*! \brief Routine to comput ACF without FFT. */
@@ -577,8 +576,8 @@ void low_do_autocorr(const char *fn, const output_env_t oenv, const char *title,
     }
     if (bFour)
     {
-        c0 = log((double)nframes)/log(2.0);
-        k  = c0;
+        c0 = std::log(static_cast<double>(nframes))/std::log(2.0);
+        k  = static_cast<int>(c0);
         if (k < c0)
         {
             k++;
@@ -606,10 +605,9 @@ void low_do_autocorr(const char *fn, const output_env_t oenv, const char *title,
      * In this loop the actual correlation functions are computed, but without
      * normalizing them.
      */
-    k = max(1, pow(10, (int)(log(nitem)/log(100))));
-    for (i = 0; i < nitem; i++)
+    for (int i = 0; i < nitem; i++)
     {
-        if (bVerbose && ((i%k == 0 || i == nitem-1)))
+        if (bVerbose && (((i % 100) == 0) || (i == nitem-1)))
         {
             fprintf(stderr, "\rThingie %d", i+1);
         }
@@ -660,10 +658,10 @@ void low_do_autocorr(const char *fn, const output_env_t oenv, const char *title,
         else
         {
             sum = print_and_integrate(fp, nout, dt, c1[0], NULL, 1);
-            if (bVerbose)
-            {
-                printf("Correlation time (integral over corrfn): %g (ps)\n", sum);
-            }
+        }
+        if (bVerbose)
+        {
+            printf("Correlation time (integral over corrfn): %g (ps)\n", sum);
         }
     }
     else
diff --git a/src/gromacs/correlationfunctions/crosscorr.c b/src/gromacs/correlationfunctions/crosscorr.cpp
similarity index 98%
rename from src/gromacs/correlationfunctions/crosscorr.c
rename to src/gromacs/correlationfunctions/crosscorr.cpp
index 1911b5b41e..b588bd8f86 100644
--- a/src/gromacs/correlationfunctions/crosscorr.c
+++ b/src/gromacs/correlationfunctions/crosscorr.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
diff --git a/src/gromacs/correlationfunctions/integrate.c b/src/gromacs/correlationfunctions/integrate.cpp
similarity index 98%
rename from src/gromacs/correlationfunctions/integrate.c
rename to src/gromacs/correlationfunctions/integrate.cpp
index dc0a7ae083..d58c5add9d 100644
--- a/src/gromacs/correlationfunctions/integrate.c
+++ b/src/gromacs/correlationfunctions/integrate.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
diff --git a/src/gromacs/correlationfunctions/manyautocorrelation.c b/src/gromacs/correlationfunctions/manyautocorrelation.cpp
similarity index 89%
rename from src/gromacs/correlationfunctions/manyautocorrelation.c
rename to src/gromacs/correlationfunctions/manyautocorrelation.cpp
index c4fb7db465..8474c867a3 100644
--- a/src/gromacs/correlationfunctions/manyautocorrelation.c
+++ b/src/gromacs/correlationfunctions/manyautocorrelation.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -43,10 +43,13 @@
 
 #include "manyautocorrelation.h"
 
-#include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
 
+#include <cmath>
+
+#include <algorithm>
+
 #include "gromacs/fft/fft.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/utility/gmxomp.h"
@@ -57,7 +60,7 @@ int many_auto_correl(int nfunc, int ndata, int nfft, real **c)
     #pragma omp parallel
     {
         typedef real complex[2];
-        int          i, t, j, fftcode;
+        int          i, j;
         gmx_fft_t    fft1;
         complex     *in, *out;
         int          i0, i1;
@@ -70,9 +73,9 @@ int many_auto_correl(int nfunc, int ndata, int nfft, real **c)
             // fprintf(stderr, "There are %d threads for correlation functions\n", nthreads);
         }
         i0 = thread_id*nfunc/nthreads;
-        i1 = min(nfunc, (thread_id+1)*nfunc/nthreads);
+        i1 = std::min(nfunc, (thread_id+1)*nfunc/nthreads);
 
-        fftcode = gmx_fft_init_1d(&fft1, nfft, GMX_FFT_FLAG_CONSERVATIVE);
+        gmx_fft_init_1d(&fft1, nfft, GMX_FFT_FLAG_CONSERVATIVE);
         /* Allocate temporary arrays */
         snew(in, nfft);
         snew(out, nfft);
@@ -88,7 +91,7 @@ int many_auto_correl(int nfunc, int ndata, int nfft, real **c)
                 in[j][0] = in[j][1] = 0;
             }
 
-            fftcode = gmx_fft_1d(fft1, GMX_FFT_BACKWARD, (void *)in, (void *)out);
+            gmx_fft_1d(fft1, GMX_FFT_BACKWARD, (void *)in, (void *)out);
             for (j = 0; j < nfft; j++)
             {
                 in[j][0] = (out[j][0]*out[j][0] + out[j][1]*out[j][1])/nfft;
@@ -99,7 +102,7 @@ int many_auto_correl(int nfunc, int ndata, int nfft, real **c)
                 in[j][0] = in[j][1] = 0;
             }
 
-            fftcode = gmx_fft_1d(fft1, GMX_FFT_FORWARD, (void *)in, (void *)out);
+            gmx_fft_1d(fft1, GMX_FFT_FORWARD, (void *)in, (void *)out);
             for (j = 0; (j < nfft); j++)
             {
                 c[i][j] = out[j][0]/ndata;
diff --git a/src/gromacs/correlationfunctions/polynomials.c b/src/gromacs/correlationfunctions/polynomials.cpp
similarity index 97%
rename from src/gromacs/correlationfunctions/polynomials.c
rename to src/gromacs/correlationfunctions/polynomials.cpp
index c5f499a17d..18765ab1ff 100644
--- a/src/gromacs/correlationfunctions/polynomials.c
+++ b/src/gromacs/correlationfunctions/polynomials.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.