leaf area growth rates

NEWS.md

@@ -7,6 +7,7 @@
 - Infiltration excess, saturation excess and capillarity rise reported
 - Lateral water flows and water table depth as inputs
 - Soil output revision
+- Evaluation of moisture in multiple soil layers
 
 # Version 4.0.0
 - Options leafCavitationEffects and stemCavitationEffects for Sperry

R/defaultControl.R

@@ -133,7 +133,7 @@
 #'       \item{\code{minimumRelativeStarchForGrowth [= 0.50]}: Default minimum concentration of storage carbon (starch), relative to the maximum storage capacity, for sapwood growth to occur, when not specified via SpParams (\code{RSSG}). }
 #'       \item{\code{constructionCosts [= c(leaf = 1.5, sapwood = 1.47, fineroot = 1.30)]}: Default construction costs, including respiration and structural carbon, per dry weight of new tissue (g gluc · g dry -1) when not specified via SpParams (\code{CCleaf}, \code{CCsapwood} and \code{CCfineroot}).}
 #'       \item{\code{senescenceRates [= c(sapwood = 0.0001261398, fineroot = 0.001897231)]}: Default senescence rates (day-1) for sapwood and fineroots when not specified via SpParams (\code{SRsapwood} and \code{SRfineroot}). Defaults are equivalent to 9\%, 5\% and 50\% annual turnover for gymnosperm sapwood, angiosperm sapwood and fine roots, respectively.}
-#'       \item{\code{maximumRelativeGrowthRates [=   c(leaf = 0.03, cambium = 0.005, sapwood = 0.002, fineroot = 0.1)]}: Default maximum relative growth rates for leaves (m2 leaf ·cm-2 sapwood· day-1), tree sapwood (cm2 sapwood· cm-1 cambium · day-1), shrub sapwood (cm2 sapwood ·cm-2 sapwood· day-1) and fine roots (g dw · g dw -1 · day -1) when not specified via SpParams (\code{RGRleafmax}, \code{RGRcambiummax} , \code{RGRsapwoodmax} and \code{RGRfinerootmax}, respectively).}
+#'       \item{\code{maximumRelativeGrowthRates [=   c(leaf = 0.09, cambium = 0.005, sapwood = 0.002, fineroot = 0.1)]}: Default maximum relative growth rates for leaves (m2 leaf ·cm-2 sapwood· day-1), tree sapwood (cm2 sapwood· cm-1 cambium · day-1), shrub sapwood (cm2 sapwood ·cm-2 sapwood· day-1) and fine roots (g dw · g dw -1 · day -1) when not specified via SpParams (\code{RGRleafmax}, \code{RGRcambiummax} , \code{RGRsapwoodmax} and \code{RGRfinerootmax}, respectively).}
 #'       \item{\code{mortalityMode [= "density/deterministic"]}: String describing how mortality is applied. Current accepted values are combinations of "cohort" vs "density" (for whole-cohort mortality vs reduction of stem density) and "deterministic" vs. "stochastic".}
 #'       \item{\code{mortalityBaselineRate [= 0.0015]}: Default deterministic proportion or probability specifying the baseline reduction of cohort's density occurring in a year (for \code{mortalityMode = "density/deterministic" or "density/stochastic").}}
 #'       \item{\code{mortalityRelativeSugarThreshold [= 0.4]}: Threshold of stem sugar concentration relative to the equilibrium sugar concentration, resulting in an increased starvation mortality rate/probability whenever levels are below.}
@@ -274,7 +274,7 @@ defaultControl<-function(transpirationMode = "Granier") {
                              fineroot = 1.30), #  g gluc · g dw -1
     senescenceRates = list(sapwood = 0.000135, # day-1 Equivalent to annual 4.8% 1-(1-0.048)^(1.0/365)
                       fineroot = 0.001897231), #day-1 Equivalent to annual 50% 1-(1-0.5)^(1.0/365)
-    maximumRelativeGrowthRates = list(leaf = 0.03, # m2 leaf ·cm-2 sapwood· day-1
+    maximumRelativeGrowthRates = list(leaf = 0.09, # m2 leaf ·cm-2 sapwood· day-1
                                       cambium = 0.0025, # cm2 sapwood ·cm-1 cambium· day-1
                                       sapwood = 0.002, # cm2 sapwood ·cm-2 sapwood· day-1
                                       fineroot = 0.1), # g dw · g dw -1 · day -1

src/growth.cpp

@@ -479,7 +479,7 @@ List growthDayInner(List x, NumericVector meteovec,
 
   //Values at the end of the day (after calling spwb)
   NumericVector StemPLC = Rcpp::as<Rcpp::NumericVector>(internalWater["StemPLC"]);
-  NumericVector PlantPsi, psiApoLeaf, psiApoStem, psiSympLeaf, psiSympStem;
+  NumericVector PlantPsi, psiApoLeaf, psiApoStem, psiSympLeaf, psiSympStem, psiRootCrown;
   NumericVector LeafPLC = Rcpp::as<Rcpp::NumericVector>(internalWater["LeafPLC"]);
   if(transpirationMode=="Granier") {
     PlantPsi  = Rcpp::as<Rcpp::NumericVector>(internalWater["PlantPsi"]);
@@ -493,6 +493,7 @@ List growthDayInner(List x, NumericVector meteovec,
       psiApoStem = Rcpp::as<Rcpp::NumericVector>(internalWater["StemPsi"]);
       psiSympLeaf = Rcpp::as<Rcpp::NumericVector>(internalWater["LeafPsi"]);
     }
+    psiRootCrown = Rcpp::as<Rcpp::NumericVector>(internalWater["RootCrownPsi"]);
     psiSympStem = Rcpp::as<Rcpp::NumericVector>(internalWater["StemSympPsi"]);
   }
 
@@ -739,8 +740,8 @@ List growthDayInner(List x, NumericVector meteovec,
         for(int l=0;l<numLayers;l++) rfineroot[l] = std::min(rcellmax, relative_expansion_rate(psiSoil[l] ,tday, -1.0 ,0.5,0.05,5.0));
         // if(j==0) Rcout<<j<< " Psi:"<< PlantPsi[j]<< " r:"<< rcambiumcell<<"\n";
       } else {
-        rleafcell = std::min(rcellmax, relative_expansion_rate(psiSympLeaf[j] ,tcan_day, -1.0, 0.5,0.05,5.0));
-        rcambiumcell = std::min(rcellmax, relative_expansion_rate(psiSympStem[j] ,tcan_day, -1.0, 0.5,0.05,5.0));
+        rleafcell = std::min(rcellmax, relative_expansion_rate(psiRootCrown[j] ,tcan_day, -1.0, 0.5,0.05,5.0));
+        rcambiumcell = std::min(rcellmax, relative_expansion_rate(psiRootCrown[j] ,tcan_day, -1.0, 0.5,0.05,5.0));
         for(int l=0;l<numLayers;l++) rfineroot[l] = std::min(rcellmax, relative_expansion_rate(RhizoPsi(j,l) ,Tsoil[l], -1.0, 0.5,0.05,5.0));
         // if(j==0) Rcout<<j<< " Psi:"<< psiSympStem[j]<< " pi0:"<< " r:"<< rcambiumcell<<"\n";
       }