#include "gmxpre.h"
#include "config.h"
-#include <math.h>
-/*#define HAVE_NN_LOOPS*/
+#include <math.h>
#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/correl.h"
+#include "gromacs/gmxana/geminate.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/math/units.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 "gromacs/legacyheaders/viewit.h"
-#include "gstat.h"
-#include "gromacs/utility/cstringutil.h"
#include "gromacs/pbcutil/pbc.h"
-#include "correl.h"
-#include "gmx_ana.h"
-#include "geminate.h"
-
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+
+/*#define HAVE_NN_LOOPS*/
typedef short int t_E;
typedef int t_EEst;
for (i = 0; i < isize[grp]; i++)
{
fprintf(fp, (i%15) ? " " : "\n");
- fprintf(fp, " %4u", index[grp][i]+1);
+ fprintf(fp, " %4d", index[grp][i]+1);
}
fprintf(fp, "\n");
/*
{
for (j = 0; (j < hb->d.nhydro[i]); j++)
{
- fprintf(fp, " %4u %4u", hb->d.don[i]+1,
+ fprintf(fp, " %4d %4d", hb->d.don[i]+1,
hb->d.hydro[i][j]+1);
}
fprintf(fp, "\n");
if (hb->a.grp[i] == grp)
{
fprintf(fp, (i%15 && !first) ? " " : "\n");
- fprintf(fp, " %4u", hb->a.acc[i]+1);
+ fprintf(fp, " %4d", hb->a.acc[i]+1);
first = FALSE;
}
}
sprintf(as, "%s", mkatomname(atoms, aaa));
if (bContact)
{
- fprintf(fp, " %6u %6u\n", ddd+1, aaa+1);
+ fprintf(fp, " %6d %6d\n", ddd+1, aaa+1);
if (fplog)
{
fprintf(fplog, "%12s %12s\n", ds, as);
{
hhh = hb->d.hydro[i][m];
sprintf(hs, "%s", mkatomname(atoms, hhh));
- fprintf(fp, " %6u %6u %6u\n", ddd+1, hhh+1, aaa+1);
+ fprintf(fp, " %6d %6d %6d\n", ddd+1, hhh+1, aaa+1);
if (fplog)
{
fprintf(fplog, "%12s %12s %12s\n", ds, hs, as);
};
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 },
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);