AllocateYr <- function(share,clim,site,veg,rstep,CN_Mode) {
#
# Annual C allocation for the PnET ecosystem model.
#


#global veg site clim share rstep CN_Mode

share$NPPFolYr <- share$FolProdCYr / veg$CFracBiomass
share$NPPWoodYr <- share$WoodProdCYr / veg$CFracBiomass
share$NPPRootYr <- share$RootProdCYr / veg$CFracBiomass

if ( share$DwaterIx > 0) {
  AvgDWater <- share$Dwatertot / share$DwaterIx
}else{
  AvgDWater <- 1.0
}#end

if ( share$PosCBalMassIx > 0) {
  avgPCBM <- (share$PosCBalMassTot / share$PosCBalMassIx)
}else{
  avgPCBM <- share$FolMass
}#end

# Simplif (ied below) {
#EnvMaxFol <- (AvgDWater * avgPCBM) * (1.0 + (veg$FolRelGrowMax * share$LightEffMin))
#SppMaxFol <- avgPCBM * (1.0 + (veg$FolRelGrowMax * share$LightEffMin))
#veg$FolMassMax <- min(EnvMaxFol, SppMaxFol)

# Simpler form of above (Note: AvgDWater <= 1.0)
share$FolMassMax <- (AvgDWater * avgPCBM) * (1.0 + (veg$FolRelGrowMax * share$LightEffMin))
#Zaixing suggests thinking of FolRelGrowMax as inverse of leaf lifespan

# Check for a disturbance year
FolRegen<-100 #Hard coded value, not clear what it does (used post disturbance)
BiomLossFrac<-0
for (  i in 1 : length(site$distyear) ) {
  if ( clim$year[rstep]==site$distyear[i]) {
    BiomLossFrac <- site$distintensity[i]
    share$FolMassMax <- max(share$FolMassMax * (1 - BiomLossFrac), FolRegen)
    break
  }#end
}#end

share$FolMassMin <- (share$FolMassMax - share$FolMassMax * (1.0 / veg$FolReten))
share$BudC <- ((share$FolMassMax - share$FolMass) * veg$CFracBiomass)
#share$BudC <- veg$LeafAlloc * share$PlantC * 0.5
  
if ( share$BudC < 0) {
  share$BudC <- 0
}#end

share$PlantC <- share$PlantC - share$BudC
if (veg$PFT==4)
{
  share$RootC = share$RootC + (1.0 - veg$PlantCReserveFrac) * share$PlantC; #mimicks root allocation
  share$PlantC = share$PlantC * veg$PlantCReserveFrac; #mimicks root allocation
}
else
{
  share$WoodC <- (1.0 - veg$PlantCReserveFrac) * share$PlantC
  share$PlantC <- share$PlantC - share$WoodC
}

if ( share$WoodC < (veg$MinWoodFolRatio * share$BudC)) {
  TotalC <- share$WoodC + share$BudC
  share$WoodC <- TotalC * (veg$MinWoodFolRatio / (1.0 + veg$MinWoodFolRatio))
  share$BudC <- TotalC - share$WoodC
  share$FolMassMax <- share$FolMass + (share$BudC / veg$CFracBiomass)
  share$FolMassMin <- (share$FolMassMax - share$FolMassMax * (1.0 / veg$FolReten))
}#end

# NEP calculation for PnET-II
share$NEP <- share$TotPsn - share$WoodMRespYr - share$WoodGRespYr - share$FolGRespYr - share$SoilRespYr

# PnET-CN Only -----------------------------------------------------------------
if ( CN_Mode==1) {
  if ( share$PlantN > veg$MaxNStore) {
    share$PlantN <- veg$MaxNStore
  }#end

  share$NRatio <- 1 + (share$PlantN / veg$MaxNStore) * veg$FolNConRange

  if ( share$NRatio < 1) {
    share$NRatio <- 1
  }#end

  if ( share$NRatio > (1 + veg$FolNConRange)) {
    share$NRatio <- 1 + veg$FolNConRange
  }#end

  share$BudN <- (share$BudC / veg$CFracBiomass) * veg$FLPctN * (1 / veg$FolNRetrans) * share$NRatio

  if ( share$BudN > share$PlantN) {
    if ( share$PlantN < 0) {
      share$BudC <- share$BudC * 0.1
      share$BudN <- share$BudN * 0.1
    }else{
      share$BudC <- share$BudC * (share$PlantN / share$BudN)
      share$BudN <- share$BudN * (share$PlantN / share$BudN)
    }#end
  }#end

  FolNConOld <- share$FolNCon
  if((share$FolMass + (share$BudC / veg$CFracBiomass))>0)
  {
    folnconnew <- (share$FolMass * (share$FolNCon / 100) + share$BudN) / (share$FolMass + (share$BudC / veg$CFracBiomass)) * 100
  }else{
    folnconnew = 0
  }
  share$FolNCon <- folnconnew
  
  share$PlantN <- share$PlantN - share$BudN
  
  if ( share$NRatio < 1) {
    share$NRatioNit <- 0
  }else{
    nr <- max((share$NRatio - 1 - (veg$FolNConRange / 3)), 0)
    share$NRatioNit <- min((nr / (0.6667 * veg$FolNConRange))^2,1)
  }#end

  if ( share$PlantN > veg$MaxNStore) {
    share$NH4 <- share$NH4 + (share$PlantN - veg$MaxNStore)
    share$PlantN <- veg$MaxNStore
  }#end

  share$RootNSinkEff <- sqrt(1 - (share$PlantN / veg$MaxNStore))

  # Annual total variables for PnET-CN
  share$NEP <- share$TotPsn - share$SoilDecRespYr - share$WoodDecRespYr - share$WoodMRespYr - share$WoodGRespYr - share$FolGRespYr - share$RootMRespYr - share$RootGRespYr
  share$FolN <- (share$FolMass * share$FolNCon / 100)
  share$FolC <- share$FolMass * veg$CFracBiomass
  share$TotalN <- share$FolN + share$WoodMassN + share$RootMassN + share$HON + share$NH4 + share$NO3 + share$BudN + share$DeadWoodN + share$PlantN
  share$TotalM <- (share$BudC / veg$CFracBiomass) + share$FolMass + (share$WoodMass + share$WoodC / veg$CFracBiomass) + share$RootMass + share$DeadWoodM + share$HOM + (share$PlantC / veg$CFracBiomass)

}#end
# ------------------------------------------------------------------------------

 return(share)
}