{ "-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)"},
#endif
- /* The ballistic/geminate fitting will be taken away temporarily sue to problems with stability. */
-/* { "-NN", FALSE, etENUM, {NNtype}, */
-/* "HIDDENDo a full all vs all loop and estimate the interaction energy instead of having a binary existence function for hydrogen bonds. NOT FULLY TESTED YET! DON'T USE IT!"}, */
-/* { "-gemfit", FALSE, etBOOL, {&bGemFit}, */
-/* "With -gemainate != none: fit ka and kd to the ACF"}, */
-/* { "-gemlogstart", FALSE, etREAL, {&logAfterTime}, */
-/* "HIDDENWith -gemfit: After this time (ps) the data points fitted to will be equidistant in log-time."}, */
-/* { "-gemnp", FALSE, etINT, {&nFitPoints}, */
-/* "HIDDENNuber of points in the ACF used to fit rev. gem. recomb. model"}, */
-/* { "-ballistic", FALSE, etBOOL, {&bBallistic}, */
-/* "Calculate and remove ultrafast \"ballistic\" component in the ACF"}, */
-/* { "-ballisticlen", FALSE, etREAL, {&gemBallistic}, */
-/* "HIDDENFitting interval for the ultrafast \"ballistic\" component in ACF"}, */
-/* { "-nbalexp", FALSE, etINT, {&nBalExp}, */
-/* "HIDDENNumber of exponentials to fit when removing the ballistic component"}, */
-/* { "-ballisticDt", FALSE, etBOOL, {&bBallisticDt}, */
-/* "HIDDENIf TRUE, finding of the fastest ballistic component will be based on the time derivative at t=0, " */
-/* "while if FALSE, it will be based on the exponent alone (like in Markovitch 2008)"} */
};
const char *bugs[] = {
"The option [TT]-sel[tt] that used to work on selected hbonds is out of order, and therefore not available for the time being."
bMerge = TRUE;
}
}
- } else
- printf("No geminate recombination.\n");
-
+ }
+
/* process input */
- bSelected = opt2bSet("-sel",NFILE,fnm);
+ bSelected = FALSE;
ccut = cos(acut*DEG2RAD);
if (bContact) {
if (bSelected)
- gmx_fatal(FARGS,"Can not analyze selected contacts: turn off -sel");
+ gmx_fatal(FARGS,"Can not analyze selected contacts.");
if (!bDA) {
gmx_fatal(FARGS,"Can not analyze contact between H and A: turn off -noda");
}
}
#ifndef HAVE_LIBGSL
- printf("NO GSL! Can't find and take away ballistic term in ACF without GSL\n.");
+ /* Don't pollute stdout with information about external libraries.
+ *
+ * printf("NO GSL! Can't find and take away ballistic term in ACF without GSL\n.");
+ */
#endif
/* Initiate main data structure! */
bGem);
#ifdef HAVE_OPENMP
- printf("Compiled with OpenMP (%i)\n", _OPENMP);
+ /* Same thing here. There is no reason whatsoever to write the specific version of
+ * OpenMP used for compilation to stdout for normal usage.
+ *
+ * printf("Compiled with OpenMP (%i)\n", _OPENMP);
+ */
#endif
/* if (bContact && bGem) */