* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "xvgr.h"
-#include "copyrite.h"
-#include "gromacs/commandline/pargs.h"
-#include "index.h"
+#include "config.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/topology/index.h"
#include "gstat.h"
#include "gmx_ana.h"
#include "nsfactor.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/matio.h"
+#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
int gmx_sans(int argc, char *argv[])
{
#define NFILE asize(fnm)
t_filenm fnm[] = {
- { efTPX, "-s", NULL, ffREAD },
+ { efTPR, "-s", NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efDAT, "-d", "nsfactor", ffOPTRD },
nthreads = gmx_omp_get_max_threads();
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
/* Try to read files */
fnDAT = ftp2fn(efDAT, NFILE, fnm);
- fnTPX = ftp2fn(efTPX, NFILE, fnm);
+ fnTPX = ftp2fn(efTPR, NFILE, fnm);
fnTRX = ftp2fn(efTRX, NFILE, fnm);
gnsf = gmx_neutronstructurefactors_init(fnDAT);