Fix ICC warnings

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

diff --git a/src/gromacs/gmxana/gmx_hbond.c b/src/gromacs/gmxana/gmx_hbond.c
index e9bc54aaf6e2f65fb662cb3bf156ce6dc3eecbe2..5d960071a7e80b64503180e44fe66f79180081b9 100644 (file)
--- a/src/gromacs/gmxana/gmx_hbond.c
+++ b/src/gromacs/gmxana/gmx_hbond.c
@@ -34,36 +34,36 @@
  * 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 <math.h>
+#include "gmxpre.h"
 
-/*#define HAVE_NN_LOOPS*/
+#include "config.h"
+
+#include <math.h>
 
 #include "gromacs/commandline/pargs.h"
-#include "copyrite.h"
-#include "txtdump.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/correl.h"
+#include "gromacs/gmxana/geminate.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/units.h"
-#include "macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
-#include "viewit.h"
-#include "gstat.h"
-#include "gromacs/utility/cstringutil.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "correl.h"
-#include "gmx_ana.h"
-#include "geminate.h"
-
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
 #include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+
+/*#define HAVE_NN_LOOPS*/
 
 typedef short int t_E;
 typedef int t_EEst;
@@ -3386,7 +3386,7 @@ static void dump_hbmap(t_hbdata *hb,
         for (i = 0; i < isize[grp]; i++)
         {
             fprintf(fp, (i%15) ? " " : "\n");
-            fprintf(fp, " %4u", index[grp][i]+1);
+            fprintf(fp, " %4d", index[grp][i]+1);
         }
         fprintf(fp, "\n");
         /*
@@ -3402,7 +3402,7 @@ static void dump_hbmap(t_hbdata *hb,
                 {
                     for (j = 0; (j < hb->d.nhydro[i]); j++)
                     {
-                        fprintf(fp, " %4u %4u", hb->d.don[i]+1,
+                        fprintf(fp, " %4d %4d", hb->d.don[i]+1,
                                 hb->d.hydro[i][j]+1);
                     }
                     fprintf(fp, "\n");
@@ -3415,7 +3415,7 @@ static void dump_hbmap(t_hbdata *hb,
                 if (hb->a.grp[i] == grp)
                 {
                     fprintf(fp, (i%15 && !first) ? " " : "\n");
-                    fprintf(fp, " %4u", hb->a.acc[i]+1);
+                    fprintf(fp, " %4d", hb->a.acc[i]+1);
                     first = FALSE;
                 }
             }
@@ -3446,7 +3446,7 @@ static void dump_hbmap(t_hbdata *hb,
                     sprintf(as, "%s", mkatomname(atoms, aaa));
                     if (bContact)
                     {
-                        fprintf(fp, " %6u %6u\n", ddd+1, aaa+1);
+                        fprintf(fp, " %6d %6d\n", ddd+1, aaa+1);
                         if (fplog)
                         {
                             fprintf(fplog, "%12s  %12s\n", ds, as);
@@ -3456,7 +3456,7 @@ static void dump_hbmap(t_hbdata *hb,
                     {
                         hhh = hb->d.hydro[i][m];
                         sprintf(hs, "%s", mkatomname(atoms, hhh));
-                        fprintf(fp, " %6u %6u %6u\n", ddd+1, hhh+1, aaa+1);
+                        fprintf(fp, " %6d %6d %6d\n", ddd+1, hhh+1, aaa+1);
                         if (fplog)
                         {
                             fprintf(fplog, "%12s  %12s  %12s\n", ds, hs, as);
@@ -3637,7 +3637,7 @@ int gmx_hbond(int argc, char *argv[])
     };
     t_filenm    fnm[] = {
         { efTRX, "-f",   NULL,     ffREAD  },
-        { efTPX, NULL,   NULL,     ffREAD  },
+        { efTPR, NULL,   NULL,     ffREAD  },
         { efNDX, NULL,   NULL,     ffOPTRD },
         /*    { efNDX, "-sel", "select", ffOPTRD },*/
         { efXVG, "-num", "hbnum",  ffWRITE },
@@ -3709,7 +3709,7 @@ int gmx_hbond(int argc, char *argv[])
     npargs = asize(pa);
     ppa    = add_acf_pargs(&npargs, pa);
 
-    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE, NFILE, fnm, npargs,
+    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, npargs,
                            ppa, asize(desc), desc, asize(bugs), bugs, &oenv))
     {
         return 0;
@@ -3822,7 +3822,7 @@ int gmx_hbond(int argc, char *argv[])
     hb = mk_hbdata(bHBmap, opt2bSet("-dan", NFILE, fnm), bMerge || bContact, bGem, gemmode);
 
     /* get topology */
-    read_tpx_top(ftp2fn(efTPX, NFILE, fnm), &ir, box, &natoms, NULL, NULL, NULL, &top);
+    read_tpx_top(ftp2fn(efTPR, NFILE, fnm), &ir, box, &natoms, NULL, NULL, NULL, &top);
 
     snew(grpnames, grNR);
     snew(index, grNR);
@@ -4607,7 +4607,7 @@ int gmx_hbond(int argc, char *argv[])
                     gmx_fatal(FARGS, "Could not initiate t_gemParams params.");
                 }
             }
-            gemstring = strdup(gemType[hb->per->gemtype]);
+            gemstring = gmx_strdup(gemType[hb->per->gemtype]);
             do_hbac(opt2fn("-ac", NFILE, fnm), hb, nDump,
                     bMerge, bContact, fit_start, temp, r2cut > 0, smooth_tail_start, oenv,
                     gemstring, nThreads, NN, bBallistic, bGemFit);
@@ -4747,9 +4747,9 @@ int gmx_hbond(int argc, char *argv[])
             if (USE_THIS_GROUP(j) )
             {
                 sprintf(buf, "Donors %s", grpnames[j]);
-                legnames[i++] = strdup(buf);
+                legnames[i++] = gmx_strdup(buf);
                 sprintf(buf, "Acceptors %s", grpnames[j]);
-                legnames[i++] = strdup(buf);
+                legnames[i++] = gmx_strdup(buf);
             }
         }
         if (i != nleg)