adding changes for propostional killling with kill year and kill freq…

…uency in rgroup

ST_indivs.c

@@ -44,7 +44,9 @@ void indiv_proportion_Kill( IndivType *ndv, int killType,RealF proportionKilled)
 /*********** Locally Used Function Declarations ************/
 /***********************************************************/
 static IndivType *_create ( void);
-static void _delete (IndivType *ndv);
+
+//_delete function also called from ST_species.c
+void _delete (IndivType *ndv);
 
 /***********************************************************/
 /****************** Begin Function Code ********************/
@@ -193,7 +195,7 @@ Bool indiv_Kill_Partial( MortalityType code,
   return( result);
 }
 
-void indiv_proportion_Kill( IndivType *ndv, int killType,RealF proportionKilled){
+void indiv_proportion_Kill( IndivType *ndv, int killType,RealF proportKilled){
 	/*======================================================*/
 	/* PURPOSE */
 	/* Remove individual proportionally and adjust relative sizes of the
@@ -212,19 +214,23 @@ void indiv_proportion_Kill( IndivType *ndv, int killType,RealF proportionKilled)
 	                    ndv->age, Species[ndv->myspecies]->max_age,
 	                    Globals.currIter, Globals.currYear);
 	  }
-	  if(!UseGrid)
-		  insertIndivKill(ndv->id,killType);
-
-	  species_Update_Kills(ndv->myspecies, ndv->age);
-
-	  if(proportionKilled >0.999){
-		   Species_Update_Newsize(ndv->myspecies, -ndv->relsize);
-		  _delete(ndv);
-	  }else{
-		  RealF newSize = -(ndv->relsize * proportionKilled);
-		  printf("\n proportionKilled = %f, oldSize = %f, newSize for reduction = %f \n", ndv->relsize, newSize);
-		  Species_Update_Newsize(ndv->myspecies, newSize);
-	  }
+
+	  if (!UseGrid)
+	  		insertIndivKill(ndv->id, killType);
+
+	  	species_Update_Kills(ndv->myspecies, ndv->age);
+
+	  	if (proportKilled > 0.999)
+	  	{
+	  		Species_Update_Newsize(ndv->myspecies, -ndv->relsize);
+	  		_delete(ndv);
+	  	}
+	  	else
+	  	{
+	  		RealF newSize = -(ndv->relsize * proportKilled);
+	  		ndv->relsize = ndv->relsize + newSize;
+	  		Species_Update_Newsize(ndv->myspecies, newSize);
+	  	}
 
 }
 
@@ -256,7 +262,7 @@ void indiv_Kill_Complete( IndivType *ndv, int killType) {
 }
 
 /**************************************************************/
-static void _delete (IndivType *ndv) {
+void _delete (IndivType *ndv) {
 /*======================================================*/
 /* PURPOSE */
 /* Local routine to remove the data object of an individual.

ST_mortality.c

@@ -209,7 +209,7 @@ void mort_EndOfYear( void) {
       if ( LT(g->killfreq, 1.0) ) {
         if (RandUni() <= g->killfreq)
           g->killyr = Globals.currYear;
-      } else if ( (Globals.currYear - g->startyr) % (IntU)g->killfreq == 0) {
+      } else if ( (Globals.currYear - (g->startyr-1)) % (IntU)g->killfreq == 0) {
         g->killyr = Globals.currYear;
       }
     }

ST_resgroups.c

@@ -797,8 +797,21 @@ void RGroup_Update_Newsize( GrpIndex rg) {
   /* first get group's relative size adjusted for num indivs */
   /* ie, groupsize=1 when 1 indiv of each species is present */
   /* ie each indiv is an equivalent contributor, not based on biomass */
-  ForEachEstSpp( sp, rg, n) sumsize += Species[sp]->relsize;
-  RGroup[rg]->relsize = sumsize / (RealF) RGroup[rg]->max_spp;
+	ForEachEstSpp( sp, rg, n)
+		sumsize += Species[sp]->relsize;
+
+	if (RGroup[rg]->est_count < 0)
+		RGroup[rg]->est_count = 0;
+
+	if (RGroup[rg]->est_count == 0 || LT(sumsize, 0.0))
+	{
+		RGroup[rg]->relsize = 0.0;
+	}
+	else
+	{
+		//For calculating rgroup relSize, sumsize should be divide by no of current established species in rgroup rather than total no of species in rgroup.
+		RGroup[rg]->relsize = sumsize / (RealF) RGroup[rg]->est_count;
+	}
 
   if (RGroup[rg]->max_age != 1) {
     /* compute the contribution of each indiv to the group's size */
@@ -1044,7 +1057,6 @@ void RGroup_Kill( GrpIndex rg) {
 
 	ForEachEstSpp2( rg, i)
 	      Species_Proportion_Kill(RGroup[rg]->est_spp[i], 6,RGroup[rg]->proportion_killed);
-		//Species_Kill(RGroup[rg]->est_spp[i], 6);
 }
 
 /**********************************************************/

ST_species.c

@@ -33,6 +33,8 @@ Bool indiv_New( SppIndex sp);
 void indiv_Kill_Complete( IndivType *ndv, int killType);
 void indiv_proportion_Kill( IndivType *ndv, int killType,RealF proportionKilled);
 
+void _delete (IndivType *ndv);
+
 /*------------------------------------------------------*/
 /* Modular functions only used on one or two specific   */
 /* places; that is, they are not generally useful       */
@@ -372,22 +374,44 @@ void Species_Proportion_Kill (const SppIndex sp, int killType, RealF proportionK
 	 */
 
 	/*------------------------------------------------------*/
+#define xF_DELTA (20*F_DELTA)
+#define xD_DELTA (20*D_DELTA)
+#define ZERO(x) \
+( (sizeof(x) == sizeof(float)) \
+  ? ((x)>-xF_DELTA && (x)<xF_DELTA) \
+  : ((x)>-xD_DELTA && (x)<xD_DELTA) )
+
 	  IndivType *p = Species[sp]->IndvHead,
 	            *t;
 
-
 	  if (Species[sp]->max_age == 1) {
 	    Species_Update_Newsize(sp, -Species[sp]->relsize);
 	  } else {
 	    while(p) {
 	      t = p->Next;
-	      //indiv_Kill_Complete( p, killType);
 	      indiv_proportion_Kill( p, killType,proportionKilled);
 	      p = t;
 	    }
 	  }
 
-	  rgroup_DropSpecies(sp);
+	  if ( LT(Species[sp]->relsize, 0.0)  || ZERO(Species[sp]->relsize) )
+		{
+		//"Warning:ST_species.c Species_Proportion_Kill()  Species[sp]->relsize is either zero or negative so deleting all the individual in species and making species rel_size to zero
+		    Species[sp]->relsize = 0.0 ;
+			IndivType *p1 = Species[sp]->IndvHead, *t1;
+
+			while (p1)
+			{
+				t1 = p1->Next;
+				_delete(p);
+				p1 = t1;
+			}
+			rgroup_DropSpecies(sp);
+		}
+
+	#undef xF_DELTA
+	#undef xD_DELTA
+	#undef ZERO
 
 }
 

testing.sagebrush.MT_drs/Stepwat Inputs/Input/rgroup.in

@@ -49,7 +49,9 @@
 #         into ephemeral (this year's) biomass by
 #         grams_extra_biomass = mm_extra_ppt * xgrow_factor
 # veg_prod_type = 1 for tree, 2 for shrub, & 3 for grass.  Refer to soilwat's VegProd types in VegProd.h.
-#
+# proportion_killed = proportionally killed all members of the group at end of the given kill year.
+# proportion_recovered =
+
 #TM - density values from Biondini et al 1998 - used density% in Table 2 for p.cool.forb (Achillea millefolium) and
 #	p.warm.forb (Grindelia squarrosa)
 #TM - density values for annual cool grasses from (http://www.fs.fed.us/database/feis/plants/graminoid/brojap/all.html) converted 56 stems/sqft to stems/sqmeter