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

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

diff --git a/src/gromacs/gmxana/gmx_helixorient.c b/src/gromacs/gmxana/gmx_helixorient.c
index 29a44bb1a94db871c514daf7cd9e8a20a331f377..dfd3a1f7cfc7c7bc2948a523db111fde4433f370 100644 (file)
--- a/src/gromacs/gmxana/gmx_helixorient.c
+++ b/src/gromacs/gmxana/gmx_helixorient.c
@@ -34,29 +34,26 @@
  * 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 "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "xvgr.h"
-#include "gromacs/commandline/pargs.h"
-#include "string2.h"
-#include "vec.h"
-#include "index.h"
-#include "pbc.h"
-#include "gmx_fatal.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
 #include "gstat.h"
-#include "pbc.h"
-#include "do_fit.h"
 #include "gmx_ana.h"
 
-#include "gromacs/fileio/futil.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/math/do_fit.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_helixorient(int argc, char *argv[])
 {
@@ -152,7 +149,7 @@ int gmx_helixorient(int argc, char *argv[])
 #define NPA asize(pa)
 
     t_filenm fnm[] = {
-        { efTPX, NULL, NULL, ffREAD },
+        { efTPR, NULL, NULL, ffREAD },
         { efTRX, "-f", NULL, ffREAD },
         { efNDX, NULL, NULL, ffOPTRD },
         { efDAT, "-oaxis",    "helixaxis", ffWRITE },
@@ -166,13 +163,13 @@ int gmx_helixorient(int argc, char *argv[])
     };
 #define NFILE asize(fnm)
 
-    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
+    if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
                            NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;
     }
 
-    top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+    top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
 
     for (i = 0; i < 3; i++)
     {
@@ -223,16 +220,16 @@ int gmx_helixorient(int argc, char *argv[])
 
     natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
 
-    fpaxis    = ffopen(opt2fn("-oaxis", NFILE, fnm), "w");
-    fpcenter  = ffopen(opt2fn("-ocenter", NFILE, fnm), "w");
-    fprise    = ffopen(opt2fn("-orise", NFILE, fnm), "w");
-    fpradius  = ffopen(opt2fn("-oradius", NFILE, fnm), "w");
-    fptwist   = ffopen(opt2fn("-otwist", NFILE, fnm), "w");
-    fpbending = ffopen(opt2fn("-obending", NFILE, fnm), "w");
+    fpaxis    = gmx_ffopen(opt2fn("-oaxis", NFILE, fnm), "w");
+    fpcenter  = gmx_ffopen(opt2fn("-ocenter", NFILE, fnm), "w");
+    fprise    = gmx_ffopen(opt2fn("-orise", NFILE, fnm), "w");
+    fpradius  = gmx_ffopen(opt2fn("-oradius", NFILE, fnm), "w");
+    fptwist   = gmx_ffopen(opt2fn("-otwist", NFILE, fnm), "w");
+    fpbending = gmx_ffopen(opt2fn("-obending", NFILE, fnm), "w");
 
-    fptheta1 = ffopen("theta1.xvg", "w");
-    fptheta2 = ffopen("theta2.xvg", "w");
-    fptheta3 = ffopen("theta3.xvg", "w");
+    fptheta1 = gmx_ffopen("theta1.xvg", "w");
+    fptheta2 = gmx_ffopen("theta2.xvg", "w");
+    fptheta3 = gmx_ffopen("theta3.xvg", "w");
 
     if (bIncremental)
     {
@@ -513,17 +510,17 @@ int gmx_helixorient(int argc, char *argv[])
 
     gmx_rmpbc_done(gpbc);
 
-    ffclose(fpaxis);
-    ffclose(fpcenter);
-    ffclose(fptilt);
-    ffclose(fprotation);
-    ffclose(fprise);
-    ffclose(fpradius);
-    ffclose(fptwist);
-    ffclose(fpbending);
-    ffclose(fptheta1);
-    ffclose(fptheta2);
-    ffclose(fptheta3);
+    gmx_ffclose(fpaxis);
+    gmx_ffclose(fpcenter);
+    gmx_ffclose(fptilt);
+    gmx_ffclose(fprotation);
+    gmx_ffclose(fprise);
+    gmx_ffclose(fpradius);
+    gmx_ffclose(fptwist);
+    gmx_ffclose(fpbending);
+    gmx_ffclose(fptheta1);
+    gmx_ffclose(fptheta2);
+    gmx_ffclose(fptheta3);
 
     close_trj(status);