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 629f221d0b6dc4ad02fb2d560860845d9e0587a6..e13434df5543e92f9d6659320b0a1836c13aaabc 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjcat.c
+++ b/src/gromacs/gmxana/gmx_trjcat.c
@@ -34,36 +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 "gromacs/utility/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 "rmpbc.h"
-#include "pbc.h"
-#include "xvgr.h"
-#include "gmx_ana.h"
-
-#include "gmx_fatal.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
@@ -506,7 +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;
@@ -590,7 +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++)
             {