Remove unnecessary config.h includes

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

diff --git a/src/gromacs/gmxana/gmx_vanhove.c b/src/gromacs/gmxana/gmx_vanhove.c
index dbb21a59783b3382a218368426569a0b06c66519..781fc5cf1f37f22d329395c82682f2799f4bec41 100644 (file)
--- a/src/gromacs/gmxana/gmx_vanhove.c
+++ b/src/gromacs/gmxana/gmx_vanhove.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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.
@@ -34,27 +34,26 @@
  * 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 <string.h>
-#include <ctype.h>
+#include <assert.h>
 #include <math.h>
+#include <stdlib.h>
+#include <string.h>
 
-#include "sysstuff.h"
-#include "smalloc.h"
-#include "macros.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/commandline/pargs.h"
-#include "maths.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "typedefs.h"
-#include "xvgr.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gstat.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/fileio/matio.h"
 #include "gmx_ana.h"
 
@@ -148,7 +147,7 @@ int gmx_vanhove(int argc, char *argv[])
     FILE        *fp;
     t_rgb        rlo = {1, 1, 1}, rhi = {0, 0, 0};
 
-    if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+    if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;
@@ -200,6 +199,7 @@ int gmx_vanhove(int argc, char *argv[])
             srenew(sbox, nalloc);
             srenew(sx, nalloc);
         }
+        assert(time != NULL); assert(sbox != NULL);
 
         time[nfr] = t;
         copy_mat(box, sbox[nfr]);
@@ -425,22 +425,25 @@ int gmx_vanhove(int argc, char *argv[])
         {
             ticky[i] = i*rbin;
         }
-        fp = ffopen(matfile, "w");
+        fp = gmx_ffopen(matfile, "w");
         write_xpm(fp, MAT_SPATIAL_Y, "Van Hove function", "G (1/nm)",
                   sbin == 0 ? "time (ps)" : "sqrt(time) (ps^1/2)", "r (nm)",
                   mat_nx, nbin, tickx, ticky, mat, 0, matmax, rlo, rhi, &nlev);
-        ffclose(fp);
+        gmx_ffclose(fp);
     }
 
     if (orfile)
     {
         fp = xvgropen(orfile, "Van Hove function", "r (nm)", "G (nm\\S-1\\N)", oenv);
-        fprintf(fp, "@ subtitle \"for particles in group %s\"\n", grpname);
+        if (output_env_get_print_xvgr_codes(oenv))
+        {
+            fprintf(fp, "@ subtitle \"for particles in group %s\"\n", grpname);
+        }
         snew(legend, nr);
         for (fbin = 0; fbin < nr; fbin++)
         {
             sprintf(buf, "%g ps", (fbin + 1)*fshift*dt);
-            legend[fbin] = strdup(buf);
+            legend[fbin] = gmx_strdup(buf);
         }
         xvgr_legend(fp, nr, (const char**)legend, oenv);
         for (i = 0; i < nalloc; i++)
@@ -453,19 +456,22 @@ int gmx_vanhove(int argc, char *argv[])
             }
             fprintf(fp, "\n");
         }
-        ffclose(fp);
+        gmx_ffclose(fp);
     }
 
     if (otfile)
     {
         sprintf(buf, "Probability of moving less than %g nm", rint);
         fp = xvgropen(otfile, buf, "t (ps)", "", oenv);
-        fprintf(fp, "@ subtitle \"for particles in group %s\"\n", grpname);
+        if (output_env_get_print_xvgr_codes(oenv))
+        {
+            fprintf(fp, "@ subtitle \"for particles in group %s\"\n", grpname);
+        }
         for (f = 0; f <= ftmax; f++)
         {
             fprintf(fp, "%g %g\n", f*dt, (real)pt[f]/(tcount[f]*isize));
         }
-        ffclose(fp);
+        gmx_ffclose(fp);
     }
 
     do_view(oenv, matfile, NULL);