* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "config.h"
#include <math.h>
/*#define HAVE_NN_LOOPS*/
#include "gromacs/commandline/pargs.h"
-#include "copyrite.h"
-#include "txtdump.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/txtdump.h"
#include "gromacs/math/units.h"
-#include "macros.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/topology/index.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/math/vec.h"
#include "gromacs/fileio/xvgr.h"
-#include "viewit.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gstat.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/pbcutil/pbc.h"
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
/* { efNDX, "-sel", "select", ffOPTRD },*/
{ efXVG, "-num", "hbnum", ffWRITE },
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE, NFILE, fnm, npargs,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, npargs,
ppa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
hb = mk_hbdata(bHBmap, opt2bSet("-dan", NFILE, fnm), bMerge || bContact, bGem, gemmode);
/* get topology */
- read_tpx_top(ftp2fn(efTPX, NFILE, fnm), &ir, box, &natoms, NULL, NULL, NULL, &top);
+ read_tpx_top(ftp2fn(efTPR, NFILE, fnm), &ir, box, &natoms, NULL, NULL, NULL, &top);
snew(grpnames, grNR);
snew(index, grNR);