Remove unnecessary config.h includes

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

diff --git a/src/gromacs/gmxana/gmx_order.c b/src/gromacs/gmxana/gmx_order.c
index ecb42bccfd6197666545f3bedce68ed8024d7b5a..0c6e723316b6730e4c603b296c2de4e5e8f00bb5 100644 (file)
--- a/src/gromacs/gmxana/gmx_order.c
+++ b/src/gromacs/gmxana/gmx_order.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 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.
@@ -34,31 +34,30 @@
  * 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 <ctype.h>
-
-#include "sysstuff.h"
 #include <string.h>
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gstat.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/commandline/pargs.h"
-#include "index.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/confio.h"
 #include "cmat.h"
 #include "gmx_ana.h"
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 /****************************************************************************/
 /* This program calculates the order parameter per atom for an interface or */
@@ -327,8 +326,8 @@ static void calc_tetra_order_parm(const char *fnNDX, const char *fnTPS,
     sfree(index);
     sfree(isize);
 
-    ffclose(fpsg);
-    ffclose(fpsk);
+    gmx_ffclose(fpsg);
+    gmx_ffclose(fpsk);
 
     fpsg = xvgropen(sgslfn,
                     "S\\sg\\N Angle Order Parameter / Slab", "(nm)", "S\\sg\\N",
@@ -343,8 +342,8 @@ static void calc_tetra_order_parm(const char *fnNDX, const char *fnTPS,
         fprintf(fpsk, "%10g  %10g\n", (i+0.5)*box[slice_dim][slice_dim]/nslice,
                 sk_slice_tot[i]/nframes);
     }
-    ffclose(fpsg);
-    ffclose(fpsk);
+    gmx_ffclose(fpsg);
+    gmx_ffclose(fpsk);
 }
 
 
@@ -357,7 +356,7 @@ static void print_types(atom_id index[], atom_id a[], int ngrps,
     fprintf(stderr, "Using following groups: \n");
     for (i = 0; i < ngrps; i++)
     {
-        fprintf(stderr, "Groupname: %s First atomname: %s First atomnr %u\n",
+        fprintf(stderr, "Groupname: %s First atomname: %s First atomnr %d\n",
                 groups[i], *(top->atoms.atomname[a[index[i]]]), a[index[i]]);
     }
     fprintf(stderr, "\n");
@@ -832,8 +831,8 @@ void order_plot(rvec order[], real *slOrder[], const char *afile, const char *bf
                                                         0.333 * order[atom][YY]));
         }
 
-        ffclose(ord);
-        ffclose(slOrd);
+        gmx_ffclose(ord);
+        gmx_ffclose(slOrd);
     }
 }
 
@@ -978,7 +977,7 @@ int gmx_order(int argc, char *argv[])
     const char   *sgfnm, *skfnm, *ndxfnm, *tpsfnm, *trxfnm;
     output_env_t  oenv;
 
-    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, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;