Many and poorly formatted debug print statements

- addressing #126
- revert commit (or comment printf's out) once issue is resolved

- to recreate my output in the comments, run with `model.in`:
 # niter nyrs  seed
 1 100 3

ST_indivs.c

@@ -308,12 +308,19 @@ void indiv_proportion_Recovery( IndivType *ndv, int killType,RealF proportionRec
 
    // using  individual killing year old real size and reduction for making base for calculating proportional recovery
 	RealF prev_reduction = ndv->prv_yr_relsize * proportionKilled;
-  	RealF increase = prev_reduction * proportionRecovery;
+	RealF increase = prev_reduction * proportionRecovery;
 	ndv->relsize = ndv->relsize + increase;
 	Species_Update_Newsize(ndv->myspecies, increase);
 
 	if (ZERO(ndv->relsize) || LT(ndv->relsize, 0.0))
 	{
+    // this should never happend because `increase` should always be positive
+    LogError(logfp, LOGWARN, "'indiv_proportion_Recovery': an individual of "\
+      "%s reached relsize of 0 and is removed (increase = %.3f): for " \
+      "killType = %d, proportionKilled = %.2f, proportionRecovery = %.2f",
+      Species[ndv->myspecies]->name, increase,
+      killType, proportionKilled, proportionRecovery);
+
 		_delete(ndv);
 	}
 	#undef xF_DELTA
@@ -343,16 +350,35 @@ void indiv_Kill_Complete( IndivType *ndv, int killType) {
  // if(!UseGrid)
 //	  insertIndivKill(ndv->id,killType);
   species_Update_Kills(ndv->myspecies, ndv->age);
+
+if (Species[ndv->myspecies]->res_grp == 6 && Species[ndv->myspecies]->sp_num == 11) {
+printf("'indiv_Kill_Complete' after 'species_Update_Kills': \n" \
+  "\t%s, relsize = %.2f, est_count = %d\n" \
+  "\t%s, relsize = %.2f, ndv->relsize = %.2f, est_count = %d\n",
+  RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+  Species[11]->name, Species[11]->relsize, ndv->relsize, Species[11]->est_count);
+}
+
   Species_Update_Newsize(ndv->myspecies, -ndv->relsize);
-  _delete(ndv);
+
+if (Species[ndv->myspecies]->res_grp == 6 && Species[ndv->myspecies]->sp_num == 11) {
+printf("'indiv_Kill_Complete' after 'Species_Update_Newsize': \n" \
+  "\t%s, relsize = %.2f, est_count = %d\n" \
+  "\t%s, relsize = %.2f, est_count = %d\n",
+  RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+  Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+}
+
+  _delete(ndv); // `_delete` updates the Species[ndv->myspecies]->est_count, i.e., removes one individual
 
 }
 
 /**************************************************************/
 void _delete (IndivType *ndv) {
 /*======================================================*/
 /* PURPOSE */
-/* Local routine to remove the data object of an individual.
+/* Local routine to remove the data object of an individual and update
+ * the number of individuals `Species[ndv->myspecies]->est_count`
  * Called from indiv_Kill_Complete().
 */
 /* HISTORY */
@@ -387,9 +413,13 @@ void _delete (IndivType *ndv) {
       ndv->Next->Prev = ndv->Prev;
   }
 
-  if( --s->est_count == 0)
+  // update Species[ndv->myspecies]->est_count, i.e.,
+  // remove one individual from tally
+  if( --s->est_count == 0) {
+    // if there are no individual left of this species, then remove species
+    // from resource group and update `est_count` of the resource group
     rgroup_DropSpecies(sp);
-
+  }
 
   if ((s->est_count > 0 && s->IndvHead == NULL)
      || (s->est_count == 0 && s->IndvHead != NULL))

ST_main.c

@@ -195,45 +195,121 @@ int main(int argc, char **argv) {
 		/* ------  Begin running the model ------ */
 		for (year = 1; year <= Globals.runModelYears; year++) {
 
-      //printf("------------------------Repetition/year = %d / %d\n", iter, year);
+      printf("------------------------Repetition/year = %d / %d\n", iter, year);
 
 			Globals.currYear = year;
 
 			rgroup_Establish();
+      printf("'main' after 'rgroup_Establish': \n" \
+        "\t%s, relsize = %.2f, est_count = %d\n" \
+        "\t%s, relsize = %.2f, est_count = %d\n",
+        RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+        Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+      check_sizes("'main' after 'rgroup_Establish'");
 
 			Env_Generate();
 
 			rgroup_PartResources();
+      printf("'main' after 'rgroup_PartResources': \n" \
+        "\t%s, relsize = %.2f, est_count = %d\n" \
+        "\t%s, relsize = %.2f, est_count = %d\n",
+        RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+        Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+      check_sizes("'main' after 'rgroup_PartResources'");
 
 #ifdef STEPWAT
 			if (!isnull(SXW.debugfile) ) SXW_PrintDebug(0);
 #endif
 
 			rgroup_Grow();
+      printf("'main' after 'rgroup_Grow': \n" \
+        "\t%s, relsize = %.2f, est_count = %d\n" \
+        "\t%s, relsize = %.2f, est_count = %d\n",
+        RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+        Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+      check_sizes("'main' after 'rgroup_Grow'");
 
 			mort_Main(&killedany);
+      printf("'main' after 'mort_Main': \n" \
+        "\t%s, relsize = %.2f, est_count = %d\n" \
+        "\t%s, relsize = %.2f, est_count = %d\n",
+        RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+        Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+      check_sizes("'main' after 'mort_Main'");
 
 			rgroup_IncrAges();
+      printf("'main' after 'rgroup_IncrAges': \n" \
+        "\t%s, relsize = %.2f, est_count = %d\n" \
+        "\t%s, relsize = %.2f, est_count = %d\n",
+        RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+        Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+      check_sizes("'main' after 'rgroup_IncrAges'");
 
       // Added functions for Grazing and mort_end_year as proportional killing effect before exporting biomass end of the year
 			grazing_EndOfYear();
-                        save_annual_species_relsize();
+      printf("'main' after 'grazing_EndOfYear': \n" \
+        "\t%s, relsize = %.2f, est_count = %d\n" \
+        "\t%s, relsize = %.2f, est_count = %d\n",
+        RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+        Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+      check_sizes("'main' after 'grazing_EndOfYear'");
+
+
+      save_annual_species_relsize();
+      printf("'main' after 'save_annual_species_relsize': \n" \
+        "\t%s, relsize = %.2f, est_count = %d\n" \
+        "\t%s, relsize = %.2f, est_count = %d\n",
+        RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+        Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+      check_sizes("'main' after 'save_annual_species_relsize'");
+
 
 			mort_EndOfYear();
+      printf("'main' after 'mort_EndOfYear': \n" \
+        "\t%s, relsize = %.2f, est_count = %d\n" \
+        "\t%s, relsize = %.2f, est_count = %d\n",
+        RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+        Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+      check_sizes("'main' after 'mort_EndOfYear'");
 
 			stat_Collect(year);
+      printf("'main' after 'stat_Collect': \n" \
+        "\t%s, relsize = %.2f, est_count = %d\n" \
+        "\t%s, relsize = %.2f, est_count = %d\n",
+        RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+        Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+      check_sizes("'main' after 'stat_Collect'");
 
 			if (BmassFlags.yearly)
 				output_Bmass_Yearly(year);
 
        // Moved kill annual and kill extra growth after we export biomass, and recovery of biomass after fire before the next year
 			_kill_annuals();
-			 proportion_Recovery();
+      printf("'main' after '_kill_annuals': \n" \
+        "\t%s, relsize = %.2f, est_count = %d\n" \
+        "\t%s, relsize = %.2f, est_count = %d\n",
+        RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+        Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+      check_sizes("'main' after '_kill_annuals'");
+
+			proportion_Recovery();
+      printf("'main' after 'proportion_Recovery': \n" \
+        "\t%s, relsize = %.2f, est_count = %d\n" \
+        "\t%s, relsize = %.2f, est_count = %d\n",
+        RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+        Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+      check_sizes("'main' after 'proportion_Recovery'");
+
 			_kill_extra_growth();
 
 			// Check that relsizes match up at end of year after extra growth is removed
 			// may want to wrap this in #ifdef DEBUG once problem is fixed
 			check_sizes("'main' at end of year");
+      printf("'main' after '_kill_extra_growth': \n" \
+        "\t%s, relsize = %.2f, est_count = %d\n" \
+        "\t%s, relsize = %.2f, est_count = %d\n",
+        RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+        Species[11]->name, Species[11]->relsize, Species[11]->est_count);
 		} /* end model run for this year*/
 
 		if (MortFlags.summary) {
@@ -550,15 +626,15 @@ void check_sizes(const char *chkpt) {
 
       if (LT(diff, fabs(spsize - Species[sp]->relsize)) ) {
         LogError(stdout, LOGWARN, "%s (%d:%d): SP: \"%s\" size error: "
-                                  "SP=%.9f, ndv=%.9f\n",
+                                  "SP=%.3f, ndv=%.3f",
                 chkpt, Globals.currIter, Globals.currYear,
                 Species[sp]->name, Species[sp]->relsize, spsize);
       }
     }
 
     if ( LT(diff, fabs(rgsize -RGroup[rg]->relsize)) ) {
       LogError(stdout, LOGWARN, "%s (%d:%d): RG \"%s\" size error: "
-                                "RG=%.9f, ndv=%.9f\n",
+                                "RG=%.3f, ndv=%.3f",
               chkpt, Globals.currIter, Globals.currYear,
               RGroup[rg]->name, RGroup[rg]->relsize, rgsize);
     }

ST_mortality.c

@@ -148,6 +148,13 @@ void mort_Main( Bool *killed) {
     if ( GT(g->pr, 1.0) ) {
        if (++g->yrs_neg_pr >= g->max_stretch)
           _no_resources( rg);
+
+if (rg == 6) printf("'mort_Main' after '_no_resources': \n" \
+  "\t%s, relsize = %.2f, est_count = %d\n" \
+  "\t%s, relsize = %.2f, est_count = %d\n",
+  RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+  Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+
     } else {
       g->yrs_neg_pr = 0;
     }
@@ -157,7 +164,21 @@ void mort_Main( Bool *killed) {
       /* Take care of mortality types 1 and 2*/
       if ( g->use_mort ) {
         _age_independent( sp );
+
+if (rg == 6 && sp == 11) printf("'mort_Main' after '_age_independent': \n" \
+  "\t%s, relsize = %.2f, est_count = %d\n" \
+  "\t%s, relsize = %.2f, est_count = %d\n",
+  RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+  Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+
         _slow_growth( sp );
+
+if (rg == 6 && sp == 11) printf("'mort_Main' after '_slow_growth': \n" \
+  "\t%s, relsize = %.2f, est_count = %d\n" \
+  "\t%s, relsize = %.2f, est_count = %d\n",
+  RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+  Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+
       }
       /* now deal with succulents problems*/
       if (g->succulent
@@ -176,6 +197,13 @@ void mort_Main( Bool *killed) {
         case Burrow:
              _burrow( sp);
              break;
+
+if (rg == 6 && sp == 11) printf("'mort_Main' after 'Plot.disturbance': \n" \
+  "\t%s, relsize = %.2f, est_count = %d\n" \
+  "\t%s, relsize = %.2f, est_count = %d\n",
+  RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+  Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+
       }
 
     } /* end for each species*/
@@ -598,14 +626,52 @@ static void _age_independent( const SppIndex sp) {
       kills[++k] = ndv;
   }
 
+if (Species[sp]->res_grp == 6 && sp == 11) {
+  int kk = 0;
+  printf("'_age_independent': individuals of %s/%s with relsize = %.2f\n",
+    RGroup[6]->name, Species[11]->name, Species[11]->relsize);
+
+  ForEachIndiv (ndv, Species[sp]) {
+    printf("\t%d, relsize = %.2f\n",
+      kk, ndv->relsize);
+    kk++;
+  }
+
+  printf("'_age_independent': individuals of %s/%s slated to kill\n",
+    RGroup[6]->name, Species[11]->name);
+
+  for( n=0; n <= k; n++ ) {
+    printf("\t%d, relsize = %.2f\n", n, kills[n]->relsize);
+  }
+}
+
+
   for( n=0; n <= k; n++ ) {
+    printf("'_age_independent' calling 'indiv_Kill_Complete': n=%d <= k=%d\n", n, k);
     indiv_Kill_Complete(kills[n], 9);
   }
 
+if (Species[sp]->res_grp == 6 && sp == 11) {
+  printf("'_age_independent' after 'indiv_Kill_Complete': \n" \
+  "\t%s, relsize = %.2f, est_count = %d\n" \
+  "\t%s, relsize = %.2f, est_count = %d\n",
+  RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+  Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+}
 
   if (k >= 0) _SomeKillage = TRUE;
 
   Mem_Free(kills);
+
+
+if (Species[sp]->res_grp == 6 && sp == 11) {
+  printf("'_age_independent' after 'Mem_Free': \n" \
+  "\t%s, relsize = %.2f, est_count = %d\n" \
+  "\t%s, relsize = %.2f, est_count = %d\n",
+  RGroup[6]->name, RGroup[6]->relsize, RGroup[6]->est_count,
+  Species[11]->name, Species[11]->relsize, Species[11]->est_count);
+}
+
 }
 
 /***********************************************************/