Sort all includes in src/gromacs

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

diff --git a/src/gromacs/gmxana/gmx_mindist.c b/src/gromacs/gmxana/gmx_mindist.c
index 8fbb7d3712a6b426e4743d5e5b8adebadf2677dd..920f6cc3a7465e6044e37091d1786049027016b7 100644 (file)
--- a/src/gromacs/gmxana/gmx_mindist.c
+++ b/src/gromacs/gmxana/gmx_mindist.c
@@ -34,29 +34,27 @@
  * 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 "sysstuff.h"
 #include <string.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.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/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "rmpbc.h"
-#include "gmx_ana.h"
-#include "names.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 static void periodic_dist(int ePBC,
@@ -363,7 +361,7 @@ void dist_plot(const char *fn, const char *afile, const char *dfile,
         {
             snew(leg, 1);
             sprintf(buf, "Internal in %s", grpn[0]);
-            leg[0] = strdup(buf);
+            leg[0] = gmx_strdup(buf);
             xvgr_legend(dist, 0, (const char**)leg, oenv);
             if (num)
             {
@@ -378,7 +376,7 @@ void dist_plot(const char *fn, const char *afile, const char *dfile,
                 for (k = i+1; (k < ng); k++, j++)
                 {
                     sprintf(buf, "%s-%s", grpn[i], grpn[k]);
-                    leg[j] = strdup(buf);
+                    leg[j] = gmx_strdup(buf);
                 }
             }
             xvgr_legend(dist, j, (const char**)leg, oenv);
@@ -394,7 +392,7 @@ void dist_plot(const char *fn, const char *afile, const char *dfile,
         for (i = 0; (i < ng-1); i++)
         {
             sprintf(buf, "%s-%s", grpn[0], grpn[i+1]);
-            leg[i] = strdup(buf);
+            leg[i] = gmx_strdup(buf);
         }
         xvgr_legend(dist, ng-1, (const char**)leg, oenv);
         if (num)
@@ -713,7 +711,7 @@ int gmx_mindist(int argc, char *argv[])
 #define NFILE asize(fnm)
 
     if (!parse_common_args(&argc, argv,
-                           PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+                           PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
     {
         return 0;