Remove .tpa, .tpb, .tpx, .trj files. Part of #1500.

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

diff --git a/src/gromacs/gmxana/gmx_disre.c b/src/gromacs/gmxana/gmx_disre.c
index 84ebace731160fcc9af9dd0d38caab3cec4c1c1d..d7e1dd8af8e04a5a8ab76444975d9f3908da4a0f 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.c
+++ b/src/gromacs/gmxana/gmx_disre.c
@@ -34,38 +34,42 @@
  * 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 <stdlib.h>
 #include <string.h>
 
-#include "typedefs.h"
-#include "macros.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "vec.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/utility/smalloc.h"
-#include "nrnb.h"
-#include "disre.h"
-#include "gromacs/commandline/pargs.h"
-#include "force.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/force.h"
 #include "gstat.h"
-#include "main.h"
+#include "gromacs/legacyheaders/main.h"
 #include "gromacs/fileio/pdbio.h"
-#include "index.h"
-#include "mdatoms.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/legacyheaders/mdatoms.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "mdrun.h"
-#include "names.h"
-#include "gromacs/fileio/matio.h"
-#include "mtop_util.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gmx_ana.h"
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/xvgr.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     int  n;
@@ -713,7 +717,7 @@ int gmx_disre(int argc, char *argv[])
     gmx_rmpbc_t     gpbc = NULL;
 
     t_filenm        fnm[] = {
-        { efTPX, NULL, NULL, ffREAD },
+        { efTPR, NULL, NULL, ffREAD },
         { efTRX, "-f", NULL, ffREAD },
         { efXVG, "-ds", "drsum",  ffWRITE },
         { efXVG, "-da", "draver", ffWRITE },
@@ -728,7 +732,7 @@ int gmx_disre(int argc, char *argv[])
     };
 #define NFILE asize(fnm)
 
-    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;
@@ -741,9 +745,9 @@ int gmx_disre(int argc, char *argv[])
         init5(ntop);
     }
 
-    read_tpxheader(ftp2fn(efTPX, NFILE, fnm), &header, FALSE, NULL, NULL);
+    read_tpxheader(ftp2fn(efTPR, NFILE, fnm), &header, FALSE, NULL, NULL);
     snew(xtop, header.natoms);
-    read_tpx(ftp2fn(efTPX, NFILE, fnm), &ir, box, &ntopatoms, xtop, NULL, NULL, &mtop);
+    read_tpx(ftp2fn(efTPR, NFILE, fnm), &ir, box, &ntopatoms, xtop, NULL, NULL, &mtop);
     bPDB = opt2bSet("-q", NFILE, fnm);
     if (bPDB)
     {