* 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 <stdio.h>
#include <string.h>
-#include "main.h"
-#include "macros.h"
-#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "gmx_fatal.h"
-#include "atomprop.h"
-#include "vec.h"
-#include "pbc.h"
-#include "physics.h"
-#include "index.h"
-#include "gromacs/utility/smalloc.h"
-#include "names.h"
-#include "mtop_util.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/xtcio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
#include "compare.h"
typedef struct {
int gmx_check(int argc, char *argv[])
{
const char *desc[] = {
- "[THISMODULE] reads a trajectory ([TT].trj[tt], [TT].trr[tt] or ",
- "[TT].xtc[tt]), an energy file ([TT].ene[tt] or [TT].edr[tt])",
+ "[THISMODULE] reads a trajectory ([TT].tng[tt], [TT].trr[tt] or ",
+ "[TT].xtc[tt]), an energy file ([TT].edr[tt])",
"or an index file ([TT].ndx[tt])",
"and prints out useful information about them.[PAR]",
"Option [TT]-c[tt] checks for presence of coordinates,",
"file are indeed correct in the trajectory. If not you may have",
"non-matching files due to e.g. deshuffling or due to problems with",
"virtual sites. With these flags, [TT]gmx check[tt] provides a quick check for such problems.[PAR]",
- "The program can compare two run input ([TT].tpr[tt], [TT].tpb[tt] or",
- "[TT].tpa[tt]) files",
+ "The program can compare two run input ([TT].tpr[tt])",
+ "files",
"when both [TT]-s1[tt] and [TT]-s2[tt] are supplied.",
"Similarly a pair of trajectory files can be compared (using the [TT]-f2[tt]",
"option), or a pair of energy files (using the [TT]-e2[tt] option).[PAR]",
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffOPTRD },
{ efTRX, "-f2", NULL, ffOPTRD },
- { efTPX, "-s1", "top1", ffOPTRD },
- { efTPX, "-s2", "top2", ffOPTRD },
+ { efTPR, "-s1", "top1", ffOPTRD },
+ { efTPR, "-s2", "top2", ffOPTRD },
{ efTPS, "-c", NULL, ffOPTRD },
{ efEDR, "-e", NULL, ffOPTRD },
{ efEDR, "-e2", "ener2", ffOPTRD },
}
else if (fn2)
{
- fprintf(stderr, "Please give me TWO trajectory (.xtc/.trr/.trj) files!\n");
+ fprintf(stderr, "Please give me TWO trajectory (.xtc/.trr/.tng) files!\n");
}
fn1 = opt2fn_null("-s1", NFILE, fnm);
}
else if ((fn1 && !opt2fn_null("-f", NFILE, fnm)) || (!fn1 && fn2))
{
- fprintf(stderr, "Please give me TWO run input (.tpr/.tpa/.tpb) files\n"
+ fprintf(stderr, "Please give me TWO run input (.tpr) files\n"
"or specify the -m flag to generate a methods.tex file\n");
}