Inputs density and pseed changed to units of # / m2 (#350)

fix inconsistencies in units between documentation, inputs, and how the code uses these variables:
- inputs are in units of number per square meter (so that these inputs do not depend on plot size)
- internally, code converts these to number per plot (because that is the unit of the simulation)

ST_params.c

@@ -904,8 +904,9 @@ 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]->baseline_min_res_req = space;
@@ -1103,7 +1104,8 @@ 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_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
@@ -181,7 +181,7 @@ struct resourcegroup_st {
   RealF baseline_min_res_req,  /* 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 */

testing.sagebrush.master/Stepwat_Inputs/Input/rgroup.in

@@ -14,9 +14,9 @@
 # name = a name to give the group (12 chars)
 # space = proportion of the resource space used by the group.
 #         this must sum to 1.0
-# density = relative number of mature individuals per plot, reassigned to max_density in the model code
-# maxest = maximum species that can establish in a given year, 
-#          this value cannot be greater than the number of species assigned 
+# density = number of mature individuals per square-meter, converted to `max_density` (in units of plants per plot) in the model code
+# maxest = maximum species that can establish in a given year,
+#          this value cannot be greater than the number of species assigned
 #          to the resource group in the species.in file
 # slow = slow growth rate, defines when to count stretched years
 # stretch  = max yrs resources can be stretched before low-resource mortality occurs.

testing.sagebrush.master/Stepwat_Inputs/Input/species.in

@@ -50,7 +50,7 @@
 #       along with the mean (pestab), is used to calculate the two shape parameters: alpha and beta. 
 #       Default value: 0.0001. NOTE: var must be < pestab * (1-pestab) or alpha and/or beta will be negative,
 #       we will no longer be meeting the assumptions of a beta distribution, and the code will fail.
-# pseed = the average number of seeds produced by annual species per 1g of biomass, per 1m^2 and per year.
+# pseed = the 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)
 
 ###PARAMETER SOURCES     
 #TM - eind values are density values taken from Adler datasets from Idaho. Species vuoc (1090), bogr, spcr, brar (2080), are from Karl et al 1999