Merge feature_space into master

ST_indivs.c

@@ -225,7 +225,6 @@ void indiv_proportion_Kill(IndivType *ndv, int killType, RealF proportKilled)
 	//	insertIndivKill(ndv->id, killType);
 
     //kill indiv Proportionally or adjust their real size irrespective of being annual or perennial, both will have this effect
-	species_Update_Kills(ndv->myspecies, ndv->age);
 	// saving killing year real size here that is going to use for calculating next year proportional recovery
 	ndv->prv_yr_relsize = ndv->relsize;
 
@@ -238,6 +237,8 @@ void indiv_proportion_Kill(IndivType *ndv, int killType, RealF proportKilled)
 	if (ZERO(ndv->relsize) || LT(ndv->relsize, 0.0))
 	{
 		ndv->relsize =0.0;
+		// increase mortality count only if relsize has become zero due to fire
+		species_Update_Kills(ndv->myspecies, ndv->age);
 	}
 
 	#undef xF_DELTA

ST_mortality.c

@@ -146,6 +146,10 @@ void mort_Main( Bool *killed) {
     /* annuals are not subject to these sources of mortality and instead die in _kill_annuals */
     if (g->max_age == 1) continue;  
 
+    /* Calculate PR at the functional group level: resources required/resources available */
+    g->pr = ZRO(g->res_avail) ? 0. : g->res_required / g->res_avail;
+    //printf("g->pr after = %f\n,Group = %s \n",RGroup[rg]->name,  g->pr);/* kill plants if low resources for consecutive years */
+
     /* kill plants if low resources for consecutive years */
     /* increment yrs_neg_pr if pr > 1, else zero it. */
     /* one good year cancels all previous bad years. */

ST_params.c

@@ -909,10 +909,12 @@ static void _rgroup_add1( char name[], RealF space, RealF density,
   RGroup[rg]->grp_num       = rg;
   RGroup[rg]->max_stretch   = (IntS) stretch;
   RGroup[rg]->max_spp_estab = (IntS) estab;
-  RGroup[rg]->max_density   = density;
-  RGroup[rg]->max_per_sqm   = density / Globals.plotsize;
+  // input of `density` is in units of [# / m2]; convert to units of [# / plot]
+  RGroup[rg]->max_density   = density * Globals.plotsize; // density per plot
+  RGroup[rg]->max_per_sqm   = density; // density per square-meter
   RGroup[rg]->use_mort      = itob(mort);
   RGroup[rg]->slowrate      = slow;
+  RGroup[rg]->space = space;
   RGroup[rg]->min_res_req   = space;
   RGroup[rg]->est_annually  = itob(estann);
   RGroup[rg]->startyr       = styr;
@@ -1107,7 +1109,8 @@ static void _species_init( void) {
       Species[sp]->received_prob = 0;
       Species[sp]->cohort_surv = cohort;
       Species[sp]->var = var;
-      Species[sp]->pseed = pseed / Globals.plotsize;
+      // input of `pseed` is in units of [# / m2]; convert to units of [# / plot]
+      Species[sp]->pseed = pseed * Globals.plotsize;
 /*      Species[sp]->ann_mort_prob = (age > 0)
                                          ? -log(cohort)/age
                                          : 0.0;

ST_resgroups.c

@@ -100,10 +100,6 @@ void rgroup_PartResources(void) {
             LogError(logfp, LOGWARN, "RGroup %s : res_avail is Zero and res_required > 0", g->name);
         }
 
-        /* Calculate PR at the functional group level: resources required/resources available */
-        g->pr = ZRO(g->res_avail) ? 0. : g->res_required / g->res_avail;
-        //printf("g->pr = %f\n,Group = %s \n",RGroup[rg]->name,  g->pr);
-
         /* If relsize>0 and individuals are established, reset noplants from TRUE to FALSE */
         if (GT(getRGroupRelsize(rg), 0.))
             noplants = FALSE;
@@ -257,7 +253,7 @@ static void _res_part_extra(RealF extra, RealF size[]) {
             continue;
 
         /* Check to avoid dividing by 0 */
-        if (sum_size == 0.)
+        if (ZRO(sum_size))
             req_prop = 0.;
 
         /* Calculate proportional biomass of each group out of the total biomass
@@ -267,9 +263,10 @@ static void _res_part_extra(RealF extra, RealF size[]) {
 
         /* If the group can use extra resources, divide out extra based on
          * proportional biomass */
-        if (g->use_extra_res)
+        if (g->use_extra_res) {
             g->res_extra = req_prop * extra;
-
+            g->res_avail += g->res_extra;
+        }
         /* If the group can't use extra resources, set res_extra to 0 */
         else
             g->res_extra = 0.;
@@ -384,7 +381,7 @@ void rgroup_ResPartIndiv(void) {
 
                     /* If individuals already have the resources they require do 
                      * not assign extra */
-                    if (ndv->res_avail == ndv->res_required) {
+                    if (GE(ndv->res_avail, ndv->res_required)) {
                         ndv->res_extra = 0.0;
                         //printf("ndv->res_extra = %f\n", ndv->res_extra);
                     }
@@ -471,8 +468,7 @@ void rgroup_Grow(void) {
                 continue;
 
             /* Modify growth rate by temperature calculated in Env_Generate() */
-            if (s->tempclass != NoSeason)
-                tgmod = Env.temp_reduction[s->tempclass];
+            tgmod = (s->tempclass == NoSeason) ? 1. : Env.temp_reduction[s->tempclass];
 
             /* Now increase size of the individual plants of current species */
             ForEachIndiv(ndv, s) {
@@ -616,6 +612,8 @@ void rgroup_Establish(void) {
     /*------------------------------------------------------*/
 
     IntS i, num_est; /* number of individuals of sp. that establish*/
+    RealF
+      used_space = 0; /* sums up all of the space that is currently used */
     GrpIndex rg;
     SppIndex sp;
     GroupType *g;
@@ -634,6 +632,7 @@ void rgroup_Establish(void) {
             continue;
 
         g->regen_ok = TRUE; /* default */
+        g->min_res_req = g->space; /* reset min_res_req, if it was modified last year */
 
         if (Globals.currYear < RGroup[rg]->startyr) {
             g->regen_ok = FALSE;
@@ -652,7 +651,6 @@ void rgroup_Establish(void) {
                 if (Species[sp]->max_age == 1) {
                     //printf("Globals.currYear = %hu, call to _add_annuals sp=%d Species[sp]->lastyear_relsize : %.5f \n", Globals.currYear, sp, Species[sp]->lastyear_relsize);
                     num_est = _add_annuals(rg, sp, Species[sp]->lastyear_relsize);
-                    //  printf("g->seedbank annuals=%d \n",g->seedbank);
                 }
 
                     /* Establishment for species that belong to perennial functional groups*/
@@ -670,8 +668,32 @@ void rgroup_Establish(void) {
 
             } /* end ForEachGroupSpp() */
         }
+
+        // sum up min_res_req in case we need to redistribute min_res_req
+        if (g->est_count > 0) {
+            used_space += g->min_res_req;
+        } else {
+            // this group needs no resources because it is not established.
+            g->min_res_req = 0;
+        }
     } /* end ForEachGroup() */
+
+    // If there is unused (or too much used) space we need to redistribute
+    if (!EQ(used_space, 1.0)) {
+      //printf("\nYear %d: used_space = %f\n", Globals.currYear, used_space);
+
+      ForEachGroup(rg) {
+        g = RGroup[rg];
+        /* Redistribute the unused (or too much used) space to all groups that
+           are established */
+        if (g->est_count > 0) {
+          //printf("%s before: %f -- ", g->name, g->min_res_req);
+          g->min_res_req = g->min_res_req / used_space;
+        }
+      }
+    }
 }
+
 /***********************************************************/
 void rgroup_IncrAges(void)
 {
@@ -717,17 +739,18 @@ void rgroup_IncrAges(void)
 /* Sums relsize for all individuals in all species in RGroup rg.
    param rg = RGroup index.
    Return: RGroup relsize. */
+
 RealF getRGroupRelsize(GrpIndex rg){
     Int n;
 	SppIndex sp;
 	double sum = 0.0;
 
     ForEachEstSpp( sp, rg, n){
-		sum += getSpeciesRelsize(sp);
+	sum += getSpeciesRelsize(sp);
     }
 
     if(RGroup[rg]->est_count > 0){
-        return (RealF) sum / (RealF) RGroup[rg]->est_count;
+        return (RealF) sum;
     } else {
         return 0;
     }

ST_structs.h

@@ -90,7 +90,7 @@ struct species_st {
         estabs,        /* number of individuals established in iter */
         *seedprod,    /* annuals: array of previous years' seed production (size = viable_yrs)*/
          seedbank,
-         pseed;
+         pseed;       /* average number of seeds produced by annual species per 1g of biomass, per 1m^2 and per year (internally re-calculated as seeds per 1 g biomass per plot and per year) */
   RealF lastyear_relsize,    /* relsize from the previous year, used for annual establishment */
         extragrowth,   /* amt of superfluous growth from extra resources */
 	received_prob,	//the chance that this species received seeds this year... only applicable if using seed dispersal and gridded option
@@ -180,9 +180,10 @@ struct resourcegroup_st {
 		grazingfrq,     /* grazing effect on group at this frequency: <1=prob, >1=# years */
         grazingfreq_startyr;/* start year for grazing frequency*/
   SppIndex *species; /*list of spp belonging to this grp*/
-  RealF min_res_req,  /* input from table */
+  RealF space,  /* input from table */
+        min_res_req,  /* input from table, rescaled if an rgroup is not established */
         max_density,  /* number of mature plants per plot allowed */
-        max_per_sqm,  /* convert density and plotsize to max plants/m^2 */
+        max_per_sqm,  /* density of mature plants in units of plants / m^2 */
         max_bmass,    /* sum of mature biomass for all species in group */
         killfreq,       /* kill group at this frequency: <1=prob, >1=# years */
         ignition,       /* cheatgrass biomass (g/m2) that triggers potential ignition of a wildfire */