* 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 "index.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "names.h"
-#include "typedefs.h"
-#include "gromacs/gmxpreprocess/readir.h"
+
#include "gromacs/commandline/pargs.h"
-#include "gromacs/math/vec.h"
-#include "mtop_util.h"
-#include "checkpoint.h"
+#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/enxio.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/state.h"
+#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define RANGECHK(i, n) if ((i) >= (n)) gmx_fatal(FARGS, "Your index file contains atomnumbers (e.g. %d)\nthat are larger than the number of atoms in the tpr file (%d)", (i), (n))
char buf[200], buf2[200];
output_env_t oenv;
t_filenm fnm[] = {
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efTRN, "-f", NULL, ffOPTRD },
{ efEDR, "-e", NULL, ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
- { efTPX, "-o", "tpxout", ffWRITE }
+ { efTPR, "-o", "tprout", ffWRITE }
};
#define NFILE asize(fnm)
bTime = opt2parg_bSet("-time", asize(pa), pa);
bTraj = (opt2bSet("-f", NFILE, fnm) || bTime);
- top_fn = ftp2fn(efTPX, NFILE, fnm);
+ top_fn = ftp2fn(efTPR, NFILE, fnm);
fprintf(stderr, "Reading toplogy and stuff from %s\n", top_fn);
snew(ir, 1);