Revert "added changes for rgroup killingfreq and proportional killing"

This reverts commit 5a043cc.

ST_indivs.c

@@ -44,7 +44,7 @@ void indiv_proportion_Kill( IndivType *ndv, int killType,RealF proportKilled);
 /*********** Locally Used Function Declarations ************/
 /***********************************************************/
 static IndivType *_create ( void);
-void _delete (IndivType *ndv);
+static void _delete (IndivType *ndv);
 
 /***********************************************************/
 /****************** Begin Function Code ********************/
@@ -204,8 +204,9 @@ void indiv_proportion_Kill( IndivType *ndv, int killType, RealF proportKilled){
 	/* Chris Bennett @ LTER-CSU 6/15/2000
 	 * 09/23/15 -AT  -Added proportionKilled           */
 	/*------------------------------------------------------*/
-
-   if (ndv->age > Species[ndv->myspecies]->max_age)
+
+
+	if (ndv->age > Species[ndv->myspecies]->max_age)
 	{
 		LogError(logfp, LOGWARN,
 				"%s dies older than max_age (%d > %d). Iter=%d, Year=%d\n",
@@ -219,15 +220,14 @@ void indiv_proportion_Kill( IndivType *ndv, int killType, RealF proportKilled){
 
 	species_Update_Kills(ndv->myspecies, ndv->age);
 
-	if (proportKilled > 0.99)
+	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);
 	}
 }
@@ -260,7 +260,7 @@ void indiv_Kill_Complete( IndivType *ndv, int killType) {
 }
 
 /**************************************************************/
-void _delete (IndivType *ndv) {
+static void _delete (IndivType *ndv) {
 /*======================================================*/
 /* PURPOSE */
 /* Local routine to remove the data object of an individual.

ST_mortality.c

@@ -203,32 +203,22 @@ void mort_EndOfYear( void) {
   GrpIndex rg;
   GroupType *g;
 
-	ForEachGroup(rg)
-	{
-		g = RGroup[rg];
-
-		if (GT(g->killfreq, 0.))
-		{
-			if (LT(g->killfreq, 1.0))
-			{
-				if (RandUni() <= g->killfreq)
-				{
-					g->killyr = Globals.currYear;
-				}
-			}
-			else if ((Globals.currYear - (g->startyr -1)) % (IntU) g->killfreq  == 0)
-			{
-				g->killyr = Globals.currYear;
-			}
-		}	
-
-		if (Globals.currYear == RGroup[rg]->extirp)
-			rgroup_Extirpate(rg);
-		else if (Globals.currYear == RGroup[rg]->killyr){		
-			RGroup_Kill(rg);
-		}
-
-	}
+  ForEachGroup(rg) { g = RGroup[rg];
+
+    if ( GT( g->killfreq, 0.) ) {
+      if ( LT(g->killfreq, 1.0) ) {
+        if (RandUni() <= g->killfreq)
+          g->killyr = Globals.currYear;
+      } else if ( (Globals.currYear - g->startyr) % (IntU)g->killfreq == 0) {
+        g->killyr = Globals.currYear;
+      }
+    }
+
+    if (Globals.currYear == RGroup[rg]->extirp)
+       rgroup_Extirpate( rg );
+    else if (Globals.currYear == RGroup[rg]->killyr)
+       RGroup_Kill( rg );
+  }
 
    _kill_extra_growth();
    _kill_annuals();

ST_params.c

@@ -981,7 +981,8 @@ static void _rgroup_add1( char name[], RealF space, RealF density,
   RGroup[rg]->use_mort      = itob(mort);
   RGroup[rg]->veg_prod_type = veg_prod_type;
   RGroup[rg]->proportion_killed = prop_killed;
-  RGroup[rg]->proportion_recovered = prop_recovered;  
+  RGroup[rg]->proportion_recovered = prop_recovered;
+  printf("grp= %d prop_killed= %f, prop_recovery=%f \n",rg, RGroup[rg]->proportion_killed,RGroup[rg]->proportion_recovered );
 
 
   RGroup[rg]->extirpated    = FALSE;

ST_resgroups.c

@@ -798,9 +798,7 @@ void RGroup_Update_Newsize( GrpIndex rg) {
   /* 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;
-
-//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;
+  RGroup[rg]->relsize = sumsize / (RealF) RGroup[rg]->max_spp;
 
   if (RGroup[rg]->max_age != 1) {
     /* compute the contribution of each indiv to the group's size */

ST_species.c

@@ -33,8 +33,6 @@ 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       */
@@ -272,12 +270,6 @@ void Species_Update_Newsize( SppIndex sp, RealF newsize ) {
     newsize = -Species[sp]->relsize;
 
   Species[sp]->relsize += newsize;
-
-  if(LT(Species[sp]->relsize, 0.0) || ZERO(Species[sp]->relsize)){
-	 //Warning:ST_Species.c Species_Update_Newsize() Species[sp]->relsize is either zero or negative
-	  Species[sp]->relsize = 0.0;
-  }
-
   RGroup_Update_Newsize(rg);
 
   if ( Species[sp]->max_age != 1) {
@@ -380,13 +372,6 @@ 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) {
@@ -397,26 +382,13 @@ void Species_Proportion_Kill (const SppIndex sp, int killType, RealF proportionK
 	      indiv_proportion_Kill( p, killType,proportionKilled);
 	      p = t;
 	    }
-	  }	
-
-  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);
-	}
+	  }
+
+	  if (proportionKilled > 0.999)
+	  	{
+		  rgroup_DropSpecies(sp);
+	  	}
 
-#undef xF_DELTA
-#undef xD_DELTA
-#undef ZERO
 
 }