* 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 <math.h>
+#include "gmxpre.h"
-/*#define HAVE_NN_LOOPS*/
+#include "config.h"
-#include "gromacs/commandline/pargs.h"
-#include "copyrite.h"
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "physics.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "index.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "gstat.h"
-#include "gromacs/utility/cstringutil.h"
-#include "pbc.h"
-#include "correl.h"
-#include "gmx_ana.h"
-#include "geminate.h"
+#include <math.h>
-#include "gromacs/fileio/futil.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/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+
+/*#define HAVE_NN_LOOPS*/
typedef short int t_E;
typedef int t_EEst;
{
int i;
- if (ISDON(datable[id]) || !datable)
+ if (!datable || ISDON(datable[id]))
{
if (ddd->dptr[id] == NOTSET) /* New donor */
{
static void normalizeACF(real *ct, real *gt, int nhb, int len)
{
- real ct_fac, gt_fac;
+ real ct_fac, gt_fac = 0;
int i;
/* Xu and Berne use the same normalization constant */
ct_fac = 1.0/ct[0];
- gt_fac = (nhb == 0) ? 0 : 1.0/(real)nhb;
+ if (nhb != 0)
+ {
+ gt_fac = 1.0/(real)nhb;
+ }
printf("Normalization for c(t) = %g for gh(t) = %g\n", ct_fac, gt_fac);
for (i = 0; i < len; i++)
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);
"HIDDENDffusion coefficient to use in the reversible geminate recombination kinetic model. If negative, then it will be fitted to the ACF along with ka and kd."},
#ifdef GMX_OPENMP
{ "-nthreads", FALSE, etINT, {&nThreads},
- "Number of threads used for the parallel loop over autocorrelations. nThreads <= 0 means maximum number of threads. Requires linking with OpenMP. The number of threads is limited by the number of processors (before OpenMP v.3 ) or environment variable OMP_THREAD_LIMIT (OpenMP v.3)"},
+ "Number of threads used for the parallel loop over autocorrelations. nThreads <= 0 means maximum number of threads. Requires linking with OpenMP. The number of threads is limited by the number of cores (before OpenMP v.3 ) or environment variable OMP_THREAD_LIMIT (OpenMP v.3)"},
#endif
};
const char *bugs[] = {
};
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);
gmx_fatal(FARGS, "Could not initiate t_gemParams params.");
}
}
- gemstring = strdup(gemType[hb->per->gemtype]);
+ gemstring = gmx_strdup(gemType[hb->per->gemtype]);
do_hbac(opt2fn("-ac", NFILE, fnm), hb, nDump,
bMerge, bContact, fit_start, temp, r2cut > 0, smooth_tail_start, oenv,
gemstring, nThreads, NN, bBallistic, bGemFit);
{
t_matrix mat;
int id, ia, hh, x, y;
+ mat.flags = mat.y0 = 0;
if ((nframes > 0) && (hb->nrhb > 0))
{
if (USE_THIS_GROUP(j) )
{
sprintf(buf, "Donors %s", grpnames[j]);
- legnames[i++] = strdup(buf);
+ legnames[i++] = gmx_strdup(buf);
sprintf(buf, "Acceptors %s", grpnames[j]);
- legnames[i++] = strdup(buf);
+ legnames[i++] = gmx_strdup(buf);
}
}
if (i != nleg)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff