Sort all includes in src/gromacs

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

diff --git a/src/gromacs/gmxana/gmx_trjcat.c b/src/gromacs/gmxana/gmx_trjcat.c
index be102c28b394bf2bcecb818b6fa2c7647b1016ac..e13434df5543e92f9d6659320b0a1836c13aaabc 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjcat.c
+++ b/src/gromacs/gmxana/gmx_trjcat.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.
@@ -34,37 +34,32 @@
  * 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 <math.h>
-#include "macros.h"
-#include "sysstuff.h"
-#include "smalloc.h"
-#include "typedefs.h"
+#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/tngio.h"
 #include "gromacs/fileio/tngio_for_tools.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/confio.h"
-#include "names.h"
-#include "index.h"
-#include "vec.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xtcio.h"
-#include "do_fit.h"
-#include "rmpbc.h"
-#include "gromacs/fileio/g87io.h"
-#include "pbc.h"
-#include "xvgr.h"
-#include "gromacs/fileio/xdrf.h"
-#include "gmx_ana.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 #define TIME_EXPLICIT 0
 #define TIME_CONTINUE 1
@@ -507,7 +502,7 @@ int gmx_trjcat(int argc, char *argv[])
 
 #define NFILE asize(fnm)
 
-    if (!parse_common_args(&argc, argv, PCA_BE_NICE | PCA_TIME_UNIT, NFILE, fnm,
+    if (!parse_common_args(&argc, argv, PCA_TIME_UNIT, NFILE, fnm,
                            asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;
@@ -591,7 +586,7 @@ int gmx_trjcat(int argc, char *argv[])
     {
         if (nfile_out != nset)
         {
-            char *buf = strdup(fnms_out[0]);
+            char *buf = gmx_strdup(fnms_out[0]);
             snew(fnms_out, nset);
             for (i = 0; (i < nset); i++)
             {
@@ -690,26 +685,9 @@ int gmx_trjcat(int argc, char *argv[])
                 /* Fails if last frame is incomplete
                  * We can't do anything about it without overwriting
                  * */
-                if (filetype == efXTC)
-                {
-                    lasttime =
-                        xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
-                                                    gmx_fio_getxdr(stfio),
-                                                    fr.natoms, &bOK);
-                    fr.time = lasttime;
-                    if (!bOK)
-                    {
-                        gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
-                    }
-                }
-                else if (filetype == efTNG)
+                if (filetype == efXTC || filetype == efTNG)
                 {
-                    tng_trajectory_t tng = trx_get_tng(status);
-                    if (!tng)
-                    {
-                        gmx_fatal(FARGS, "Error opening TNG file.");
-                    }
-                    lasttime = gmx_tng_get_time_of_final_frame(tng);
+                    lasttime = trx_get_time_of_final_frame(status);
                     fr.time  = lasttime;
                 }
                 else
@@ -730,14 +708,8 @@ int gmx_trjcat(int argc, char *argv[])
                 {
                     gmx_fatal(FARGS, "Overwrite only supported for XTC." );
                 }
-                last_frame_time =
-                    xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
-                                                gmx_fio_getxdr(stfio),
-                                                fr.natoms, &bOK);
-                if (!bOK)
-                {
-                    gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
-                }
+                last_frame_time = trx_get_time_of_final_frame(status);
+
                 /* xtc_seek_time broken for trajectories containing only 1 or 2 frames
                  *     or when seek time = 0 */
                 if (nfile_in > 1 && settime[1] < last_frame_time+timest[0]*0.5)