Sort all includes in src/gromacs

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

diff --git a/src/gromacs/gmxana/gmx_clustsize.c b/src/gromacs/gmxana/gmx_clustsize.c
index ae5a1ec58e17260230aec020f2f8947b6d384bd5..2f9d219d7d7a489a0e0bcbcc73b1958d0b0ea806 100644 (file)
--- a/src/gromacs/gmxana/gmx_clustsize.c
+++ b/src/gromacs/gmxana/gmx_clustsize.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2007, 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.
@@ -34,37 +34,30 @@
  * 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 <ctype.h>
-
-#include "string2.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "rmpbc.h"
+
 #include "gromacs/commandline/pargs.h"
-#include "xvgr.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "index.h"
-#include "smalloc.h"
-#include "calcgrid.h"
-#include "nrnb.h"
-#include "physics.h"
-#include "coulomb.h"
-#include "pme.h"
-#include "gstat.h"
-#include "gromacs/fileio/matio.h"
-#include "mtop_util.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 static void clust_size(const char *ndx, const char *trx, const char *xpm,
                        const char *xpmw, const char *ncl, const char *acl,
@@ -123,7 +116,7 @@ static void clust_size(const char *ndx, const char *trx, const char *xpm,
         read_tpxheader(tpr, &tpxh, TRUE, &version, &generation);
         if (tpxh.natoms != natoms)
         {
-            gmx_fatal(FARGS, "tpr (%d atoms) and xtc (%d atoms) do not match!",
+            gmx_fatal(FARGS, "tpr (%d atoms) and trajectory (%d atoms) do not match!",
                       tpxh.natoms, natoms);
         }
         ePBC = read_tpx(tpr, NULL, NULL, &natoms, NULL, NULL, NULL, mtop);
@@ -153,7 +146,7 @@ static void clust_size(const char *ndx, const char *trx, const char *xpm,
         {
             index[i] = i;
         }
-        gname = strdup("mols");
+        gname = gmx_strdup("mols");
     }
     else
     {
@@ -339,16 +332,16 @@ static void clust_size(const char *ndx, const char *trx, const char *xpm,
     }
     while (read_next_frame(oenv, status, &fr));
     close_trx(status);
-    ffclose(fp);
-    ffclose(gp);
-    ffclose(hp);
-    ffclose(tp);
+    gmx_ffclose(fp);
+    gmx_ffclose(gp);
+    gmx_ffclose(hp);
+    gmx_ffclose(tp);
 
     gmx_mtop_atomlookup_destroy(alook);
 
     if (max_clust_ind >= 0)
     {
-        fp = ffopen(mcn, "w");
+        fp = gmx_ffopen(mcn, "w");
         fprintf(fp, "[ max_clust ]\n");
         for (i = 0; (i < nindex); i++)
         {
@@ -367,7 +360,7 @@ static void clust_size(const char *ndx, const char *trx, const char *xpm,
                 }
             }
         }
-        ffclose(fp);
+        gmx_ffclose(fp);
     }
 
     /* Print the real distribution cluster-size/numer, averaged over the trajectory. */
@@ -385,7 +378,7 @@ static void clust_size(const char *ndx, const char *trx, const char *xpm,
         nhisto += (int)((j+1)*nelem/n_x);
     }
     fprintf(fp, "%5d  %8.3f\n", j+1, 0.0);
-    ffclose(fp);
+    gmx_ffclose(fp);
 
     fprintf(stderr, "Total number of atoms in clusters =  %d\n", nhisto);
 
@@ -407,11 +400,11 @@ static void clust_size(const char *ndx, const char *trx, const char *xpm,
     }
     fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
     cmid = 1;
-    fp   = ffopen(xpm, "w");
+    fp   = gmx_ffopen(xpm, "w");
     write_xpm3(fp, 0, "Cluster size distribution", "# clusters", timebuf, "Size",
                n_x, max_size, t_x, t_y, cs_dist, 0, cmid, cmax,
                rlo, rmid, rhi, &nlevels);
-    ffclose(fp);
+    gmx_ffclose(fp);
     cmid = 100.0;
     cmax = 0.0;
     for (i = 0; (i < n_x); i++)
@@ -427,11 +420,11 @@ static void clust_size(const char *ndx, const char *trx, const char *xpm,
         }
     }
     fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
-    fp = ffopen(xpmw, "w");
+    fp = gmx_ffopen(xpmw, "w");
     write_xpm3(fp, 0, "Weighted cluster size distribution", "Fraction", timebuf,
                "Size", n_x, max_size, t_x, t_y, cs_dist, 0, cmid, cmax,
                rlo, rmid, rhi, &nlevels);
-    ffclose(fp);
+    gmx_ffclose(fp);
 
     sfree(clust_index);
     sfree(clust_size);
@@ -509,7 +502,7 @@ int gmx_clustsize(int argc, char *argv[])
 #define NFILE asize(fnm)
 
     if (!parse_common_args(&argc, argv,
-                           PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+                           PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
                            NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;