Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_spatial.c

diff --git a/src/gromacs/gmxana/gmx_spatial.c b/src/gromacs/gmxana/gmx_spatial.c
index 78a64e4cf0f82ff766b874466978dd2ef0719dde..600608d2e322611aba964abde422bf08db57bc9b 100644 (file)
--- a/src/gromacs/gmxana/gmx_spatial.c
+++ b/src/gromacs/gmxana/gmx_spatial.c
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2007,2008,2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2007,2008,2009,2010,2011,2012,2013,2014, 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.
@@ -32,34 +32,25 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
+#include "gmxpre.h"
 
+#include <math.h>
+#include <stdlib.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "vec.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include <math.h>
-#include "index.h"
-#include "pbc.h"
-#include "rmpbc.h"
-#include "gmx_ana.h"
-#include "macros.h"
-
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/smalloc.h"
 
 static const double bohr = 0.529177249;  /* conversion factor to compensate for VMD plugin conversion... */
 
-static void mequit(void)
-{
-    printf("Memory allocation error\n");
-    exit(1);
-}
-
 int gmx_spatial(int argc, char *argv[])
 {
     const char     *desc[] = {
@@ -218,25 +209,13 @@ int gmx_spatial(int argc, char *argv[])
         MINBIN[i] -= (double)iNAB*rBINWIDTH;
         nbin[i]    = (long)ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH);
     }
-    bin = (long ***)malloc(nbin[XX]*sizeof(long **));
-    if (!bin)
-    {
-        mequit();
-    }
+    snew(bin, nbin[XX]);
     for (i = 0; i < nbin[XX]; ++i)
     {
-        bin[i] = (long **)malloc(nbin[YY]*sizeof(long *));
-        if (!bin[i])
-        {
-            mequit();
-        }
+        snew(bin[i], nbin[YY]);
         for (j = 0; j < nbin[YY]; ++j)
         {
-            bin[i][j] = (long *)calloc(nbin[ZZ], sizeof(long));
-            if (!bin[i][j])
-            {
-                mequit();
-            }
+            snew(bin[i][j], nbin[ZZ]);
         }
     }
     copy_mat(box, box_pbc);
@@ -320,7 +299,7 @@ int gmx_spatial(int argc, char *argv[])
     }
 
     /* OUTPUT */
-    flp = ffopen("grid.cube", "w");
+    flp = gmx_ffopen("grid.cube", "w");
     fprintf(flp, "Spatial Distribution Function\n");
     fprintf(flp, "test\n");
     fprintf(flp, "%5d%12.6f%12.6f%12.6f\n", nidxp, (MINBIN[XX]+(minx+iIGNOREOUTER)*rBINWIDTH)*10./bohr, (MINBIN[YY]+(miny+iIGNOREOUTER)*rBINWIDTH)*10./bohr, (MINBIN[ZZ]+(minz+iIGNOREOUTER)*rBINWIDTH)*10./bohr);
@@ -449,7 +428,7 @@ int gmx_spatial(int argc, char *argv[])
         }
         fprintf(flp, "\n");
     }
-    ffclose(flp);
+    gmx_ffclose(flp);
 
     /* printf("x=%d to %d\n",minx,maxx); */
     /* printf("y=%d to %d\n",miny,maxy); */