R/Func_Leaf_FvCB_Model.R

In TEST-BNL/R-Canopy_Photosynthesis: Canopy photosynthesis testbed

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##' 
##' Leaf level FvCB Photosynthesis model (Farquhar et al. 1980)
##' 
##' @title Func_Leaf_FvCB_Photosynthesis_Model
##' 
##' @param Vcmax25 Vcmax at 25 degrees C
##' @param Jmax25 Jmax at 25 degrees C
##' @param Tleaf Leaf temperature in degrees C
##' @param Topt Temperature optimum for Jmax
##' @param I incident light
##' @param Ci internal CO2 concentration in umols/mol or ppm
##' @param Press Atmospheric pressure in Pa
##' @param PSII_in Input PSII for maximum quantum yield
##' @param Phi_in Input curvature factor for light response function
##' 
##' @return List containing: Anet - Net photosynthetic rate (Agross-Rd,umol/m2/s) at leaf temperature, 
##' Agross - Gross photosynthetic rate (umol/m2/s) at leaf temperature, Rd - Leaf respiration rate (umol/m2/s) at leaf temperature, 
##' Wc - Rubisco limited photosynthetic rate (umol/m2/s), Wj - RuBP limited photosynthetic rate (umol/m2/s),
##' Wp - TPU limited photosynthetic rate (0.5*Vcmax, umol/m2/s), Vcmax - Maximum rate of RuBP carboxylation (umol/m2/s) 
##' at leaf temperature, Jmax - Maximum rate of electron transport (umol/m2/s) at leaf temperature,
##' Vo - , Vomax - Maximum rate of oxygen evolution (umol/m2/s) at leaf temperature, Gamma* - at leaf temperature,
##' Kc - , Ko - , PSII - , Phi - at leaf temperature
##' 
##' @examples
##' \dontrun{
##' # Run test leaf photosynthesis simulations
##' file <- system.file('examples/Example_Leaf_Photosynthesis.R',package='CanopyPhotosynthesis')
##' source(file)
##' 
##' }
##' 
##' @references Long and Bernacchi, 2003; Medlyn et al., 2002; Bernacchi et al., 2013
##' 
##' @export
##' @author Jin Wu
##' @author Shawn Serbin
##' 
Func_Leaf_FvCB_Photosynthesis_Model <- function(Vcmax25, Jmax25, Tleaf, Topt, I, 
  Ci, Press, PSII_in, Phi_in) {
  
  # print('Running leaf photosyntheis') cat('Function call was: ',
  # deparse(match.call()), '\n', sep = '')
  num.args <- nargs()
  if (num.args < 9) 
    stop(paste0("Missing function arguments. Number of arguments ", print(num.args), 
      " less than the total required 9"))
  
  Scaled_parameters <- Func_Temperature_Response(Vcmax25, Jmax25, Tleaf, Topt, 
    Press)
  Vcmax <- Scaled_parameters$Vcmax
  Jmax <- Scaled_parameters$Jmax
  Gamma_star <- Scaled_parameters$Gamma_star
  Kc <- Scaled_parameters$Kc
  Ko <- Scaled_parameters$Ko
  PSII <- Scaled_parameters$PSII
  Phi <- Scaled_parameters$Phi
  Rd <- Scaled_parameters$Rd
  Vomax <- Scaled_parameters$Vomax  # TODO: Remove Vo, Vomax from code
  
  # For now we are fixing these at their input values. In the future we can use the
  # temperature scaled values
  PSII <- PSII_in
  Phi <- Phi_in
  # !!!
  
  C <- Ci * Press/(101325)
  O <- 210 * Press/(101325)  # % mmol/mol
  
  # model photosynthesis reference from Bernacchi et al. 2013, Long and Bernacchi
  # 2003
  Wc <- Vcmax * C/(C + Kc * (1 + O/Ko))  # Rubisco limited photosynthesis
  Wp <- 0.5 * Vcmax  # using default or non-direct observed TPU
  
  f <- 0.15  # spectral correction factor
  I_used <- I * (1 - f) * 0.5 * PSII  # the absorbed light used for photosynthesis process
  
  J <- I_used + Jmax - sqrt((I_used + Jmax)^2 - 4 * Phi * I_used * Jmax)
  J <- J/(2 * Phi)
  
  # Equation 6 in Long and Bernacchi, 2003; Multiply limitation states by
  # 1-Gama*/Ci Instead could just use form similar to medlyn et al 2002 where
  # Gamma* has been multiplied through
  Wj <- J * C/(4 * C + 8 * Gamma_star)
  Wc <- Wc * (1 - Gamma_star/C)
  Wj <- Wj * (1 - Gamma_star/C)
  
  # modeled gross photo
  Agross <- min(Wc, Wj, Wp)
  
  # !! WHAT IS THIS FOR?
  Vo <- Vomax * O/(O + Ko * (1 + C/Kc))
  # !!
  
  # modeled net photo
  An <- Agross - Rd
  
  output <- list(Anet = An, Agross = Agross, Rd = Rd, Wc = Wc, Wj = Wj, Wp = Wp, 
    Vcmax = Vcmax, Jmax = Jmax, Vo = Vo, Vomax = Vomax, Gamma_star = Gamma_star, 
    Kc = Kc, Ko = Ko, PSII = PSII, Phi = Phi)
  return(output)
  
}  # End of function
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### EOF