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

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

diff --git a/src/gromacs/gmxana/gmx_sans.c b/src/gromacs/gmxana/gmx_sans.c
index 6ba73e33befc543e877f7ab3dc8d588105aafa09..a91af5888bbf27e5308f0ba395065c145ff9086d 100644 (file)
--- a/src/gromacs/gmxana/gmx_sans.c
+++ b/src/gromacs/gmxana/gmx_sans.c
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -33,30 +33,28 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
 
-#include <ctype.h>
-#include "smalloc.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "xvgr.h"
-#include "copyrite.h"
-#include "gromacs/commandline/pargs.h"
-#include "index.h"
+#include "config.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/topology/index.h"
 #include "gstat.h"
 #include "gmx_ana.h"
 #include "nsfactor.h"
 
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/matio.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
 
 int gmx_sans(int argc, char *argv[])
 {
@@ -148,7 +146,7 @@ int gmx_sans(int argc, char *argv[])
 #define NFILE asize(fnm)
 
     t_filenm   fnm[] = {
-        { efTPX,  "-s",       NULL,       ffREAD },
+        { efTPR,  "-s",       NULL,       ffREAD },
         { efTRX,  "-f",       NULL,       ffREAD },
         { efNDX,  NULL,       NULL,       ffOPTRD },
         { efDAT,  "-d",       "nsfactor", ffOPTRD },
@@ -160,7 +158,7 @@ int gmx_sans(int argc, char *argv[])
 
     nthreads = gmx_omp_get_max_threads();
 
-    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;
@@ -219,7 +217,7 @@ int gmx_sans(int argc, char *argv[])
 
     /* Try to read files */
     fnDAT = ftp2fn(efDAT, NFILE, fnm);
-    fnTPX = ftp2fn(efTPX, NFILE, fnm);
+    fnTPX = ftp2fn(efTPR, NFILE, fnm);
     fnTRX = ftp2fn(efTRX, NFILE, fnm);
 
     gnsf = gmx_neutronstructurefactors_init(fnDAT);