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

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_dipoles.cpp

diff --git a/src/gromacs/gmxana/gmx_dipoles.cpp b/src/gromacs/gmxana/gmx_dipoles.cpp
index ae7a8ac8d7b26eb4036e54cc196bc97a26336d13..68e338fe04be79a85f0791000612763be85e6277 100644 (file)
--- a/src/gromacs/gmxana/gmx_dipoles.cpp
+++ b/src/gromacs/gmxana/gmx_dipoles.cpp
@@ -36,7 +36,6 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
 #include <string.h>
 #include <math.h>
 
@@ -44,7 +43,6 @@
 
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/bondf.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/legacyheaders/txtdump.h"
@@ -60,6 +58,7 @@
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/fileio/trxio.h"
 
+#include "gromacs/bonded/bonded.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/xvgr.h"
@@ -1591,7 +1590,7 @@ int gmx_dipoles(int argc, char *argv[])
     t_filenm       fnm[] = {
         { efEDR, "-en", NULL,         ffOPTRD },
         { efTRX, "-f", NULL,           ffREAD },
-        { efTPX, NULL, NULL,           ffREAD },
+        { efTPR, NULL, NULL,           ffREAD },
         { efNDX, NULL, NULL,           ffOPTRD },
         { efXVG, "-o",   "Mtot",       ffWRITE },
         { efXVG, "-eps", "epsilon",    ffWRITE },
@@ -1615,7 +1614,7 @@ int gmx_dipoles(int argc, char *argv[])
 
     npargs = asize(pa);
     ppa    = add_acf_pargs(&npargs, pa);
-    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, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;
@@ -1665,7 +1664,7 @@ int gmx_dipoles(int argc, char *argv[])
     }
 
     snew(top, 1);
-    ePBC = read_tpx_top(ftp2fn(efTPX, NFILE, fnm), NULL, box,
+    ePBC = read_tpx_top(ftp2fn(efTPR, NFILE, fnm), NULL, box,
                         &natoms, NULL, NULL, NULL, top);
 
     snew(gnx, ncos);