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

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

diff --git a/src/gromacs/gmxana/gmx_dos.c b/src/gromacs/gmxana/gmx_dos.c
index f4f9a0932f6151602a7d57c8c001747abc521745..07439151bc47948254d0bfb5265cf17923b82e28 100644 (file)
--- a/src/gromacs/gmxana/gmx_dos.c
+++ b/src/gromacs/gmxana/gmx_dos.c
@@ -32,29 +32,28 @@
  * 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 <stdio.h>
+#include "gmxpre.h"
+
 #include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 
 #include "gromacs/fileio/confio.h"
-#include "copyrite.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gstat.h"
-#include "macros.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/utilities.h"
-#include "physics.h"
-#include "index.h"
-#include "smalloc.h"
+#include "gromacs/math/units.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
-#include <string.h>
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "correl.h"
 #include "gmx_ana.h"
 #include "gromacs/fft/fft.h"
@@ -222,8 +221,11 @@ static void dump_fy(output_env_t oenv, real toler)
     DD = pow(10.0, 0.125);
     fp = xvgropen("fy.xvg", "Fig. 2, Lin2003a", "Delta", "y or fy", oenv);
     xvgr_legend(fp, asize(leg), leg, oenv);
-    fprintf(fp, "@    world 1e-05, 0, 1000, 1\n");
-    fprintf(fp, "@    xaxes scale Logarithmic\n");
+    if (output_env_get_print_xvgr_codes(oenv))
+    {
+        fprintf(fp, "@    world 1e-05, 0, 1000, 1\n");
+        fprintf(fp, "@    xaxes scale Logarithmic\n");
+    }
     for (Delta = 1e-5; (Delta <= 1000); Delta *= DD)
     {
         f = calc_fluidicity(Delta, toler);
@@ -303,7 +305,7 @@ int gmx_dos(int argc, char *argv[])
 
     t_filenm            fnm[] = {
         { efTRN, "-f",    NULL,    ffREAD  },
-        { efTPX, "-s",    NULL,    ffREAD  },
+        { efTPR, "-s",    NULL,    ffREAD  },
         { efNDX, NULL,    NULL,    ffOPTRD },
         { efXVG, "-vacf", "vacf",  ffWRITE },
         { efXVG, "-mvacf", "mvacf", ffWRITE },
@@ -319,7 +321,7 @@ int gmx_dos(int argc, char *argv[])
 
     npargs = asize(pa);
     ppa    = add_acf_pargs(&npargs, pa);
-    if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+    if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
                            NFILE, fnm, npargs, ppa, asize(desc), desc,
                            asize(bugs), bugs, &oenv))
     {
@@ -340,7 +342,7 @@ int gmx_dos(int argc, char *argv[])
     please_cite(fplog, "Pascal2011a");
     please_cite(fplog, "Caleman2011b");
 
-    read_tps_conf(ftp2fn(efTPX, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
+    read_tps_conf(ftp2fn(efTPR, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
                   TRUE);
     V     = det(box);
     tmass = 0;