From a88261f9100ce491b50bd3549058441e8a243514 Mon Sep 17 00:00:00 2001
From: Erik Lindahl <lindahl@cbr.su.se>
Date: Wed, 1 Sep 2010 20:56:08 +0200
Subject: [PATCH] Removed lots of unnecessary messages to stdout from g_hbond

---
 src/tools/gmx_hbond.c | 38 +++++++++++++-------------------------
 1 file changed, 13 insertions(+), 25 deletions(-)

diff --git a/src/tools/gmx_hbond.c b/src/tools/gmx_hbond.c
index a4b2a2e44b..a347b58fdd 100644
--- a/src/tools/gmx_hbond.c
+++ b/src/tools/gmx_hbond.c
@@ -3192,24 +3192,6 @@ int gmx_hbond(int argc,char *argv[])
         { "-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."
@@ -3336,23 +3318,25 @@ int gmx_hbond(int argc,char *argv[])
                 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! */
@@ -3363,7 +3347,11 @@ int gmx_hbond(int argc,char *argv[])
               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) */
-- 
2.11.4.GIT