Remove unnecessary config.h includes

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

diff --git a/src/gromacs/gmxana/gmx_disre.c b/src/gromacs/gmxana/gmx_disre.c
index 6f05124b440f6ae85edcb5405260c4574661463c..4852d3616ba03fcde44ebb91a254eba76594768f 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.c
+++ b/src/gromacs/gmxana/gmx_disre.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.
@@ -34,37 +34,42 @@
  * 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 <stdlib.h>
 #include <string.h>
 
-#include "typedefs.h"
-#include "macros.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "vec.h"
-#include "do_fit.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/fileio/confio.h"
-#include "smalloc.h"
-#include "nrnb.h"
-#include "disre.h"
-#include "gromacs/commandline/pargs.h"
-#include "force.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/force.h"
 #include "gstat.h"
-#include "main.h"
+#include "gromacs/legacyheaders/main.h"
 #include "gromacs/fileio/pdbio.h"
-#include "index.h"
-#include "mdatoms.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/legacyheaders/mdatoms.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "mdrun.h"
-#include "names.h"
-#include "gromacs/fileio/matio.h"
-#include "mtop_util.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gmx_ana.h"
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     int  n;
@@ -639,10 +644,10 @@ static void dump_disre_matrix(const char *fn, t_dr_result *dr, int ndr,
         hi = max_dr;
     }
     printf("Highest level in the matrix will be %g\n", hi);
-    fp = ffopen(fn, "w");
+    fp = gmx_ffopen(fn, "w");
     write_xpm(fp, 0, "Distance Violations", "<V> (nm)", "Residue", "Residue",
               n_res, n_res, t_res, t_res, matrix, 0, hi, rlo, rhi, &nlevels);
-    ffclose(fp);
+    gmx_ffclose(fp);
 }
 
 int gmx_disre(int argc, char *argv[])
@@ -727,7 +732,7 @@ int gmx_disre(int argc, char *argv[])
     };
 #define NFILE asize(fnm)
 
-    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;
@@ -801,7 +806,7 @@ int gmx_disre(int argc, char *argv[])
     }
 
     ir.dr_tau = 0.0;
-    init_disres(fplog, &mtop, &ir, NULL, FALSE, &fcd, NULL, FALSE);
+    init_disres(fplog, &mtop, &ir, NULL, &fcd, NULL, FALSE);
 
     natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
     snew(f, 5*natoms);
@@ -829,7 +834,7 @@ int gmx_disre(int argc, char *argv[])
     }
 
     mdatoms = init_mdatoms(fplog, &mtop, ir.efep != efepNO);
-    atoms2md(&mtop, &ir, 0, NULL, 0, mtop.natoms, mdatoms);
+    atoms2md(&mtop, &ir, 0, NULL, mtop.natoms, mdatoms);
     update_mdatoms(mdatoms, ir.fepvals->init_lambda);
     init_nrnb(&nrnb);
     if (ir.ePBC != epbcNONE)
@@ -929,13 +934,13 @@ int gmx_disre(int argc, char *argv[])
         }
         dump_disre_matrix(opt2fn_null("-x", NFILE, fnm), &dr, fcd.disres.nres,
                           j, &top->idef, &mtop, max_dr, nlevels, bThird);
-        ffclose(out);
-        ffclose(aver);
-        ffclose(numv);
-        ffclose(maxxv);
+        gmx_ffclose(out);
+        gmx_ffclose(aver);
+        gmx_ffclose(numv);
+        gmx_ffclose(maxxv);
         if (isize > 0)
         {
-            ffclose(xvg);
+            gmx_ffclose(xvg);
             do_view(oenv, opt2fn("-dr", NFILE, fnm), "-nxy");
         }
         do_view(oenv, opt2fn("-dn", NFILE, fnm), "-nxy");