Remove unnecessary config.h includes

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

diff --git a/src/gromacs/gmxana/gmx_rms.c b/src/gromacs/gmxana/gmx_rms.c
index 90605021a4c891c0b2e9a1b7f4019d98edaccd80..24af686324c5c1ba96a3c2dc424c946abf0dc117 100644 (file)
--- a/src/gromacs/gmxana/gmx_rms.c
+++ b/src/gromacs/gmxana/gmx_rms.c
@@ -34,28 +34,28 @@
  * 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 "gmxpre.h"
 
-#include "gromacs/utility/smalloc.h"
 #include <math.h>
-#include "macros.h"
-#include "typedefs.h"
-#include "xvgr.h"
-#include "copyrite.h"
+#include <stdlib.h>
+
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/commandline/pargs.h"
-#include "vec.h"
-#include "index.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "princ.h"
-#include "rmpbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "cmat.h"
-#include "viewit.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gmx_ana.h"
 
 #include "gromacs/math/do_fit.h"
@@ -228,7 +228,7 @@ int gmx_rms(int argc, char *argv[])
     int             ePBC;
     t_iatom        *iatom = NULL;
 
-    matrix          box;
+    matrix          box = {{0}};
     rvec           *x, *xp, *xm = NULL, **mat_x = NULL, **mat_x2, *mat_x2_j = NULL, vec1,
                     vec2;
     t_trxstatus    *status;
@@ -268,8 +268,8 @@ int gmx_rms(int argc, char *argv[])
     };
 #define NFILE asize(fnm)
 
-    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW
-                           | PCA_BE_NICE, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
+    if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
+                           NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
                            &oenv))
     {
         return 0;