Merge release-5-0 into master

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

diff --git a/src/gromacs/gmxana/gmx_mdmat.c b/src/gromacs/gmxana/gmx_mdmat.c
index 029edf26c28abb9980bf2972a55f3cf4386f370f..2918ce8d3afe73ac2f9bf03bdc22ead187210817 100644 (file)
--- a/src/gromacs/gmxana/gmx_mdmat.c
+++ b/src/gromacs/gmxana/gmx_mdmat.c
@@ -42,21 +42,20 @@
 #include <string.h>
 
 #include "macros.h"
-#include "vec.h"
-#include "sysstuff.h"
+#include "gromacs/math/vec.h"
 #include "typedefs.h"
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/matio.h"
-#include "xvgr.h"
-#include "index.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "rmpbc.h"
-#include "pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gmx_ana.h"
 
 
@@ -224,7 +223,7 @@ int gmx_mdmat(int argc, char *argv[])
     int          **nmat, **totnmat;
     real          *mean_n;
     int           *tot_n;
-    matrix         box;
+    matrix         box = {{0}};
     output_env_t   oenv;
     gmx_rmpbc_t    gpbc = NULL;