Sort all includes in src/gromacs

[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 6fee2d60a64d1818309ce068857f4d11366b1698..06911ed582214ded1cc8209f72bbfe11e3a569bb 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 "gromacs/commandline/pargs.h"
-#include "copyrite.h"
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "physics.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "index.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "gstat.h"
-#include "gromacs/utility/cstringutil.h"
-#include "pbc.h"
-#include "correl.h"
-#include "gmx_ana.h"
-#include "geminate.h"
+#include <math.h>
 
-#include "gromacs/fileio/futil.h"
+#include "gromacs/commandline/pargs.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 "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+
+/*#define HAVE_NN_LOOPS*/
 
 typedef short int t_E;
 typedef int t_EEst;
@@ -1183,7 +1183,7 @@ static void add_dh(t_donors *ddd, int id, int ih, int grp, unsigned char *databl
 {
     int i;
 
-    if (ISDON(datable[id]) || !datable)
+    if (!datable || ISDON(datable[id]))
     {
         if (ddd->dptr[id] == NOTSET)   /* New donor */
         {
@@ -2543,13 +2543,16 @@ static void parallel_print(int *data, int nThreads)
 
 static void normalizeACF(real *ct, real *gt, int nhb, int len)
 {
-    real ct_fac, gt_fac;
+    real ct_fac, gt_fac = 0;
     int  i;
 
     /* Xu and Berne use the same normalization constant */
 
     ct_fac = 1.0/ct[0];
-    gt_fac = (nhb == 0) ? 0 : 1.0/(real)nhb;
+    if (nhb != 0)
+    {
+        gt_fac = 1.0/(real)nhb;
+    }
 
     printf("Normalization for c(t) = %g for gh(t) = %g\n", ct_fac, gt_fac);
     for (i = 0; i < len; i++)
@@ -3634,7 +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 },
@@ -3706,7 +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;
@@ -3819,7 +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);
@@ -4604,7 +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);
@@ -4617,6 +4620,7 @@ int gmx_hbond(int argc, char *argv[])
         {
             t_matrix mat;
             int      id, ia, hh, x, y;
+            mat.flags = mat.y0 = 0;
 
             if ((nframes > 0) && (hb->nrhb > 0))
             {
@@ -4743,9 +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)