* 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 <string.h>
-#include "macros.h"
-#include "vec.h"
-#include "sysstuff.h"
-#include "typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/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"
int **nmat, **totnmat;
real *mean_n;
int *tot_n;
- matrix box;
+ matrix box = {{0}};
output_env_t oenv;
gmx_rmpbc_t gpbc = NULL;
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE, NFILE, fnm,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm,
asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;