Sort all includes in src/gromacs

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

diff --git a/src/gromacs/gmxana/gmx_dyecoupl.c b/src/gromacs/gmxana/gmx_dyecoupl.c
index 5eebeb12320eae0bac99a2ff48b77554efdd08dc..57f2e47dca8b9ede552df98a1397cd453f999249 100644 (file)
--- a/src/gromacs/gmxana/gmx_dyecoupl.c
+++ b/src/gromacs/gmxana/gmx_dyecoupl.c
@@ -32,17 +32,20 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-#include "copyrite.h"
-#include "gromacs/fileio/filenm.h"
-#include "macros.h"
-#include "pbc.h"
-#include "gromacs/utility/smalloc.h"
+#include "gmxpre.h"
+
 #include "gromacs/commandline/pargs.h"
-#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_dyecoupl(int argc, char *argv[])
 {
@@ -98,7 +101,6 @@ int gmx_dyecoupl(int argc, char *argv[])
     int          ndon, nacc;
     atom_id     *donindex, *accindex;
     char        *grpnm;
-    t_atoms     *atoms = NULL;
     t_trxstatus *status;
     t_trxframe   fr;
 
@@ -126,7 +128,8 @@ int gmx_dyecoupl(int argc, char *argv[])
                 rrange, krange, rincr, kincr, Rfrac;
     int         rkcount = 0, rblocksallocated = 0, kblocksallocated = 0;
 
-    if (!parse_common_args(&argc, argv, PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE, NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+    if (!parse_common_args(&argc, argv, PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT,
+                           NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;
     }
@@ -162,10 +165,10 @@ int gmx_dyecoupl(int argc, char *argv[])
     }
 
     printf("Select group with donor atom pairs defining the transition moment\n");
-    get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &ndon, &donindex, &grpnm);
+    get_index(NULL, ftp2fn_null(efNDX, NFILE, fnm), 1, &ndon, &donindex, &grpnm);
 
     printf("Select group with acceptor atom pairs defining the transition moment\n");
-    get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &nacc, &accindex, &grpnm);
+    get_index(NULL, ftp2fn_null(efNDX, NFILE, fnm), 1, &nacc, &accindex, &grpnm);
 
     /*check if groups are identical*/
     grident = TRUE;