* 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 "sysstuff.h"
#include <string.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "princ.h"
-#include "rmpbc.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+
#include "gromacs/commandline/pargs.h"
-#include "index.h"
-#include "gmx_ana.h"
#include "gromacs/fileio/trxio.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/****************************************************************************/
/* This program calculates the ordering of water molecules across a box, as */
{ efTRX, "-f", NULL, ffREAD }, /* trajectory file */
{ efNDX, NULL, NULL, ffREAD }, /* index file */
{ efNDX, "-nm", NULL, ffOPTRD }, /* index with micelle atoms */
- { efTPX, NULL, NULL, ffREAD }, /* topology file */
+ { efTPR, NULL, NULL, ffREAD }, /* topology file */
{ efXVG, "-o", "order", ffWRITE }, /* xvgr output file */
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE, NFILE,
+ PCA_CAN_VIEW | PCA_CAN_TIME, NFILE,
fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
bMicel = opt2bSet("-nm", NFILE, fnm);
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &ngx, &index, &grpname);