R/pft.coms.r
In manfredo89/ED2io: Manages Input/Output for Ecosystem Demography 2 Model
#==========================================================================================#
#==========================================================================================#
# This module contains several parameters used in the Farquar Leuning photosynthesis #
# solver. The following references are used as a departing point: #
# - M09 - Medvigy, D.M., S. C. Wofsy, J. W. Munger, D. Y. Hollinger, P. R. Moorcroft, #
# 2009: Mechanistic scaling of ecosystem function and dynamics in space and time: #
# Ecosystem Demography model version 2. J. Geophys. Res., 114, G01002, #
# doi:10.1029/2008JG000812. #
# - M06 - Medvigy, D.M., 2006: The State of the Regional Carbon Cycle: results from a #
# constrained coupled ecosystem-atmosphere model, 2006. Ph.D. dissertation, #
# Harvard University, Cambridge, MA, 322pp. #
# - M01 - Moorcroft, P. R., G. C. Hurtt, S. W. Pacala, 2001: A method for scaling #
# vegetation dynamics: the ecosystem demography model, Ecological Monographs, 71, #
# 557-586. #
# - F96 - Foley, J. A., I. Colin Prentice, N. Ramankutty, S. Levis, D. Pollard, S. Sitch, #
# A. Haxeltime, 1996: An integrated biosphere model of land surface processes, #
# terrestrial carbon balance, and vegetation dynamics. Glob. Biogeochem. Cycles, #
# 10, 603-602. #
# - L95 - Leuning, R., F. M. Kelliher, D. G. G. de Pury, E. D. Schulze, 1995: Leaf #
# nitrogen, photosynthesis, conductance, and transpiration: scaling from leaves to #
# canopies. Plant, Cell, and Environ., 18, 1183-1200. #
# - C91 - Collatz, G. J., J. T. Ball, C. Grivet, J. A. Berry, 1991: Physiological and #
# environmental regulation of stomatal conductance, photosynthesis and #
# transpiration: A model that includes a laminar boundary layer. Agric. For. #
# Meteor., 53, 107-136. #
# - B01 - Bernacchi, C. J., E. L. Singsaas, C. Pimentel, A. R. Portis Jr., S. P. Long, #
# 2001: Improved temperature response functions for models of Rubisco-limited #
# photosynthesis. Plant, Cell and Environ., 24, 253-259. #
# - B02 - Bernacchi, C. J., A. R. Portis, H. Nakano, S. von Caemmerer, S. P. Long, #
# 2002: Temperature response of mesophyll conductance. Implications for the #
# determination of Rubisco enzyme kinetics and for limitations to photosynthesis #
# in vivo. Plant physiol., 130, 1992-1998. #
#------------------------------------------------------------------------------------------#
#' @include rconstants.r
#'
#'
#'
if (! "npft" %in% ls()) npft = 17
#----- Fudging parameters to try to tune photosynthesis. ----------------------------------#
if (! "alpha.c3" %in% ls()){
alpha.c3 <<- 0.08
}else{
alpha.c3 <<- alpha.c3
}#end if
if (! "alpha.c4" %in% ls()){
alpha.c4 <<- 0.053
}else{
alpha.c4 <<- alpha.c4
}#end if
if (! "vmfact.c3" %in% ls()){
vmfact.c3 <<- 1.0
}else{
vmfact.c3 <<- vmfact.c3
}#end if
if (! "vmfact.c4" %in% ls()){
vmfact.c4 <<- 1.0
}else{
vmfact.c4 <<- vmfact.c4
}#end if
if (! "mphoto.c3" %in% ls()){
mphoto.c3 <<- 8.0
}else{
mphoto.c3 <<- mphoto.c3
}#end if
if (! "mphoto.aa" %in% ls()){
mphoto.aa <<- 6.4
}else{
mphoto.aa <<- mphoto.aa
}#end if
if (! "mphoto.c4" %in% ls()){
mphoto.c4 <<- 4.0
}else{
mphoto.c4 <<- mphoto.c4
}#end if
if (! "gamma.c3" %in% ls()){
gamma.c3 <<- 0.020
}else{
gamma.c3 <<- gamma.c3
}#end if
if (! "gamma.aa" %in% ls()){
gamma.aa <<- 0.028
}else{
gamma.aa <<- gamma.aa
}#end if
if (! "gamma.c4" %in% ls()){
gamma.c4 <<- 0.040
}else{
gamma.c4 <<- gamma.c4
}#end if
if (! "d0.grass" %in% ls()){
d0.grass <<- 0.01
}else{
d0.grass <<- d0.grass
}#end if
if (! "d0.tree" %in% ls()){
d0.tree <<- 0.01
}else{
d0.tree <<- d0.tree
}#end if
if (! "klowin" %in% ls()){
klowin <<- 18000.
}else{
klowin <<- klowin
}#end if
if (! "base.c3" %in% ls()){
base.c3 <<- 2.4
}else{
base.c3 <<- base.c3
}#end if
if (! "base.c4" %in% ls()){
base.c4 <<- 2.0
}else{
base.c4 <<- base.c4
}#end if
if (! "b.c3" %in% ls()){
b.c3 <<- 10000.
}else{
b.c3 <<- b.c3
}#end if
if (! "b.aa" %in% ls()){
b.aa <<- 1000.
}else{
b.aa <<- b.aa
}#end if
if (! "b.c4" %in% ls()){
b.c4 <<- 8000.
}else{
b.c4 <<- b.c4
}#end if
if (! "orient.tree" %in% ls()){
orient.tree <<- 0.00
}else{
orient.tree <<- orient.tree
}#end if
if (! "orient.aa" %in% ls()){
orient.aa <<- 0.00
}else{
orient.aa <<- orient.aa
}#end if
if (! "orient.grass" %in% ls()){
orient.grass <<- 0.00
}else{
orient.grass <<- orient.grass
}#end if
if (! "clumping.tree" %in% ls()){
clumping.tree <<- 0.735
}else{
clumping.tree <<- clumping.tree
}#end if
if (! "clumping.aa" %in% ls()){
clumping.aa <<- 0.735
}else{
clumping.aa <<- clumping.aa
}#end if
if (! "clumping.grass" %in% ls()){
clumping.grass <<- 1.0
}else{
clumping.grass <<- clumping.grass
}#end if
if (! "lwidth.grass" %in% ls()){
lwidth.grass <<- 0.05
}else{
lwidth.grass <<- lwidth.grass
}#end if
if (! "lwidth.bltree" %in% ls()){
lwidth.bltree <<- 0.10
}else{
lwidth.bltree <<- lwidth.bltree
}#end if
if (! "lwidth.nltree" %in% ls()){
lwidth.nltree <<- 0.05
}else{
lwidth.nltree <<- lwidth.nltree
}#end if
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# The following parameter is the k coefficient in Foley et al. (1996) that is used to #
# determine the CO2-limited photosynthesis for C4 grasses. #
#------------------------------------------------------------------------------------------#
klowco2 <<- klowin * mmco2 /mmdry # Coefficient for low CO2 [ mol/mol]
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# These parameters will be assigned to the PFT structure. Notice that depending on the #
# physiology method (Foley or Collatz), some of them will be used, and some of them will #
# not. #
#------------------------------------------------------------------------------------------#
vm.hor <<- 3000. # Ref. exp. coeff. for carboxylase fctn. [ K]
vm.base.c3 <<- base.c3 # Base Vm for C3 - Collatz et al. (1991) [mol/m2/s]
vm.base.c4 <<- base.c4 # Base Vm for C4 - Collatz et al. (1992) [mol/m2/s]
vm.decay.a <<- 220000. # Decay function for warm temperatures -- A [ J/mol]
vm.decay.b <<- 695. # Decay function for warm temperatures -- B [ J/mol/K]
vm.tcold.c3temp <<- 4.7137
vm.tcold.c3trop <<- 8.0
vm.tcold.aa <<- 4.7137
vm.tcold.c4 <<- 8.0
vm.thot.c3 <<- 45.0
vm.thot.aa <<- 45.0
vm.thot.c4 <<- 45.0
vm.decay.e.c3 <<- 0.4
vm.decay.e.aa <<- 0.4
vm.decay.e.c4 <<- 0.4
lr.hor <<- 3000. # Ref. exp. coeff. for carboxylase fctn. [ K]
lr.base.c3 <<- base.c3
lr.base.c4 <<- base.c4
lr.tcold.c3temp <<- vm.tcold.c3temp
lr.tcold.c3trop <<- vm.tcold.c3trop
lr.tcold.aa <<- vm.tcold.aa
lr.tcold.c4 <<- vm.tcold.c4
lr.thot.c3 <<- vm.thot.c3
lr.thot.aa <<- vm.thot.aa
lr.thot.c4 <<- vm.thot.c3
lr.decay.e.c3 <<- 0.4
lr.decay.e.aa <<- 0.4
lr.decay.e.c4 <<- 0.4
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# Define some common values to make it easier to change the list below... #
#------------------------------------------------------------------------------------------#
C2B <<- 2.0
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# These variables define the allometry to use #
# 0 - ED-2.1 #
# 1 - a. AGB is based on Baker et al. (2004), Chave formula, keeping the same Bleaf as #
# ED-2.1 and Bdead to make up the difference. #
# b. Use the crown area as in Poorter et al. (2006) for tropical PFTs #
# c. Use a simple rooting depth ranging from 0.5 to 5.0 #
# 2 - Same as 1, but using the height as in Poorter et al. (2006) for tropical PFTs, and #
# finding a fit similar to Baker et al. (2004) that doesn't depend on height, using #
# Saldarriaga et al. (1988) as a starting point. #
#------------------------------------------------------------------------------------------#
if ("iallom" %in% ls()){
iallom <<- iallom
}else{
iallom <<- 3
}#end if
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# These constants will help defining the allometric parameters for IALLOM 1 and 2. #
#------------------------------------------------------------------------------------------#
odead.small = c( -1.11382700, 2.44048300, 2.18063200)
odead.large = c( 0.13625460, 2.42173900, 6.94835320)
ndead.small = c( -1.26395300, 2.43236100, 1.80180100)
ndead.large = c( -0.83468050, 2.42557360, 2.68228050)
nleaf = c( 0.01925119, 0.97494935, 2.58585087)
uleaf = c( -1.09254800, 1.28505100, 3.199019 )
ncrown.area = c( 0.11842950, 1.05211970)
#------------------------------------------------------------------------------------------#
#----- Define reference height and coefficients for tropical allometry. -------------------#
if (iallom %in% c(0,1)){
hgt.ref.trop = NA
b1Ht.trop = 0.37 * log(10)
b2Ht.trop = 0.64
}else if (iallom %in% c(2,3)){
hgt.ref.trop = 61.7
b1Ht.trop = 0.0352
b2Ht.trop = 0.694
}#end if
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# The following variables will define the PFT characteristics regarding the #
# photosynthesis. #
#------------------------------------------------------------------------------------------#
pft01 = list( name = "C4 grass"
, key = "C4G"
, colour = "#E5E503"
, tropical = TRUE
, liana = FALSE
, pathway = 4
, d0 = d0.grass
, vm.hor = vm.hor
, vm.base = vm.base.c4
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c4 + t00
, vm.high.temp = vm.thot.c4 + t00
, vm.decay.e = vm.decay.e.c4
, lr.hor = lr.hor
, lr.base = lr.base.c4
, lr.low.temp = lr.tcold.c4 + t00
, lr.high.temp = lr.thot.c4 + t00
, lr.decay.e = lr.decay.e.c4
, vm0 = 12.5 * vmfact.c4 * umol.2.mol
, m = mphoto.c4
, alpha = alpha.c4
, b = b.c4 * umol.2.mol
, gamma.resp = gamma.c4
, effarea.transp = 1.0
, rho = 0.20
, leaf.turnover.rate = 2.0
, root.turnover.rate = 2.0
, SLA = 22.7
, hgt.ref = hgt.ref.trop
, b1Ht = b1Ht.trop
, b2Ht = b2Ht.trop
, b1Bl.small = NA
, b2Bl.small = NA
, b1Bl.large = NA
, b2Bl.large = NA
, bleaf.adult = NA
, b1Bs.small = NA
, b2Bs.small = NA
, b1Bs.large = NA
, b2Bs.large = NA
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.99
, b2Cl = 1.00
, b1WAI = 0.00
, b2WAI = 1.00
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 0.5
, hgt.max = 1.5
, qroot = 1.0
, qsw = 22.0 / 3900.
, agf.bs = 0.7
, orient.factor = orient.grass
, clumping.factor = clumping.grass
, leaf.width = lwidth.grass
, init.density = 0.1
, veg.hcap.min = 3.68093E+00
)
pft02 = list( name = "Early tropical"
, key = "ETR"
, colour = "#9FFF8C"
, tropical = TRUE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3trop + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3trop + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 18.75 * vmfact.c3 * umol.2.mol
, m = mphoto.c3
, alpha = alpha.c3
, b = b.c3 * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = 0.53
, leaf.turnover.rate = 1.0
, root.turnover.rate = 1.0
, SLA = NA
, hgt.ref = hgt.ref.trop
, b1Ht = b1Ht.trop
, b2Ht = b2Ht.trop
, b1Bl.small = NA
, b2Bl.small = NA
, b1Bl.large = NA
, b2Bl.large = NA
, bleaf.adult = NA
, b1Bs.small = NA
, b2Bs.small = NA
, b1Bs.large = NA
, b2Bs.large = NA
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0192 * 0.5
, b2WAI = 2.0947
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 0.5
, hgt.max = 35.0
, qroot = 1.0
, qsw = 16.0 / 3900.
, agf.bs = 0.7
, orient.factor = orient.tree
, clumping.factor = clumping.tree
, leaf.width = lwidth.bltree
, init.density = 0.1
, veg.hcap.min = 9.75446E+00
)
pft03 = list( name = "Mid tropical"
, key = "MTR"
, colour = "#44CC29"
, tropical = TRUE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3trop + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3trop + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 12.5 * vmfact.c3 * umol.2.mol
, m = mphoto.c3
, alpha = alpha.c3
, b = b.c3 * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = 0.71
, leaf.turnover.rate = 0.50
, root.turnover.rate = 0.50
, SLA = NA
, hgt.ref = hgt.ref.trop
, b1Ht = b1Ht.trop
, b2Ht = b2Ht.trop
, b1Bl.small = NA
, b2Bl.small = NA
, b1Bl.large = NA
, b2Bl.large = NA
, bleaf.adult = NA
, b1Bs.small = NA
, b2Bs.small = NA
, b1Bs.large = NA
, b2Bs.large = NA
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0192 * 0.5
, b2WAI = 2.0947
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 0.5
, hgt.max = 35.0
, qroot = 1.0
, qsw = 11.6 / 3900.
, agf.bs = 0.7
, orient.factor = orient.tree
, clumping.factor = clumping.tree
, leaf.width = lwidth.bltree
, init.density = 0.1
, veg.hcap.min = 1.30673E+01
)
pft04 = list( name = "Late tropical"
, key = "LTR"
, colour = "#137300"
, tropical = TRUE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3trop + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3trop + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 6.25 * vmfact.c3 * umol.2.mol
, m = mphoto.c3
, alpha = alpha.c3
, b = b.c3 * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = 0.90
, leaf.turnover.rate = 1./3.
, root.turnover.rate = 1./3.
, SLA = NA
, hgt.ref = hgt.ref.trop
, b1Ht = b1Ht.trop
, b2Ht = b2Ht.trop
, b1Bl.small = NA
, b2Bl.small = NA
, b1Bl.large = NA
, b2Bl.large = NA
, bleaf.adult = NA
, b1Bs.small = NA
, b2Bs.small = NA
, b1Bs.large = NA
, b2Bs.large = NA
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0192 * 0.5
, b2WAI = 2.0947
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 0.5
, hgt.max = 35.0
, qroot = 1.0
, qsw = 9.67 / 3900.
, agf.bs = 0.7
, orient.factor = orient.tree
, clumping.factor = clumping.tree
, leaf.width = lwidth.bltree
, init.density = 0.1
, veg.hcap.min = 1.65642E+01
)
pft05 = list( name = "Temperate C3 Grass"
, key = "TTG"
, colour = "#B2B224"
, tropical = FALSE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3temp + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3temp + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 18.3 * umol.2.mol
, m = mphoto.c3
, alpha = alpha.c3
, b = b.c3 * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = 0.32
, leaf.turnover.rate = 2.0
, root.turnover.rate = 2.0
, SLA = 22.0
, hgt.ref = 0.0
, b1Ht = 0.4778
, b2Ht = -0.750
, b1Bl.small = 0.08
, b2Bl.small = 1.00
, b1Bl.large = 0.08
, b2Bl.large = 1.00
, bleaf.adult = NA
, b1Bs.small = 1.e-5
, b2Bs.small = 1.0
, b1Bs.large = 1.e-5
, b2Bs.large = 1.0
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.99
, b2Cl = 1.0
, b1WAI = 0.0
, b2WAI = 1.0
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 0.15
, hgt.max = 0.95 * 0.4778
, qroot = 1.0
, qsw = 22.0 / 3900.
, agf.bs = 0.7
, orient.factor = -0.30
, clumping.factor = 1.00
, leaf.width = lwidth.grass
, init.density = 0.1
, veg.hcap.min = 9.16551E+00
)
pft06 = list( name = "North Pine"
, key = "NPN"
, colour = "#0066CC"
, tropical = FALSE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3temp + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3temp + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 15.625 * 0.7264 * umol.2.mol
, m = mphoto.c3 * 6.3949 / 8.0
, alpha = alpha.c3
, b = 1000. * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 2.0
, rho = NA
, leaf.turnover.rate = 1./3.
, root.turnover.rate = 3.927218
, SLA = 6.0
, hgt.ref = 1.3
, b1Ht = 27.14
, b2Ht = -0.03884
, b1Bl.small = 0.024
, b2Bl.small = 1.899
, b1Bl.large = 0.024
, b2Bl.large = 1.899
, bleaf.adult = NA
, b1Bs.small = 0.147
, b2Bs.small = 2.238
, b1Bs.large = 0.147
, b2Bs.large = 2.238
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0553 * 0.5
, b2WAI = 1.9769
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 1.5
, hgt.max = 0.999 * 27.14
, qroot = 0.3463
, qsw = 6.0 / 3900.
, agf.bs = 0.7
, orient.factor = 0.01
, clumping.factor = 0.735
, leaf.width = lwidth.nltree
, init.density = 0.1
, veg.hcap.min = 2.34683E-01
)
pft07 = list( name = "South Pine"
, key = "SPN"
, colour = "#99CCFF"
, tropical = FALSE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3temp + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3temp + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 15.625 * 0.7264 * umol.2.mol
, m = mphoto.c3 * 6.3949 / 8.0
, alpha = alpha.c3
, b = 1000. * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 2.0
, rho = NA
, leaf.turnover.rate = 1./3.
, root.turnover.rate = 4.117847
, SLA = 9.0
, hgt.ref = 1.3
, b1Ht = 27.14
, b2Ht = -0.03884
, b1Bl.small = 0.024
, b2Bl.small = 1.899
, b1Bl.large = 0.024
, b2Bl.large = 1.899
, bleaf.adult = NA
, b1Bs.small = 0.147
, b2Bs.small = 2.238
, b1Bs.large = 0.147
, b2Bs.large = 2.238
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0553 * 0.5
, b2WAI = 1.9769
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 1.5
, hgt.max = 0.999 * 27.14
, qroot = 0.3463
, qsw = 9.0 / 3900.
, agf.bs = 0.7
, orient.factor = 0.01
, clumping.factor = 0.735
, leaf.width = lwidth.nltree
, init.density = 0.1
, veg.hcap.min = 2.34683E-01
)
pft08 = list( name = "Late conifer"
, key = "LCN"
, colour = "#00407F"
, tropical = FALSE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3temp + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3temp + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 6.25 * 0.7264 * umol.2.mol
, m = mphoto.c3 * 6.3949 / 8.0
, alpha = alpha.c3
, b = 1000. * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 2.0
, rho = NA
, leaf.turnover.rate = 1./3.
, root.turnover.rate = 3.800132
, SLA = 10.0
, hgt.ref = 1.3
, b1Ht = 22.79
, b2Ht = -0.04445
, b1Bl.small = 0.0454
, b2Bl.small = 1.6829
, b1Bl.large = 0.0454
, b2Bl.large = 1.6829
, bleaf.adult = NA
, b1Bs.small = 0.1617
, b2Bs.small = 2.1536
, b1Bs.large = 0.1617
, b2Bs.large = 2.1536
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0553 * 0.5
, b2WAI = 1.9769
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 1.5
, hgt.max = 0.999 * 22.79
, qroot = 0.3463
, qsw = 10.0 / 3900.
, agf.bs = 0.7
, orient.factor = 0.01
, clumping.factor = 0.735
, leaf.width = lwidth.nltree
, init.density = 0.1
, veg.hcap.min = 6.80074E-01
)
pft09 = list( name = "Early hardwood"
, key = "EHW"
, colour = "#FF999B"
, tropical = FALSE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3temp + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3temp + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 18.25 * 1.1171 * umol.2.mol
, m = mphoto.c3 * 6.3949 / 8.0
, alpha = alpha.c3
, b = 20000. * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = NA
, leaf.turnover.rate = NA
, root.turnover.rate = 5.772506
, SLA = 30.0
, hgt.ref = 1.3
, b1Ht = 22.6799
, b2Ht = -0.06534
, b1Bl.small = 0.0129
, b2Bl.small = 1.7477
, b1Bl.large = 0.0129
, b2Bl.large = 1.7477
, bleaf.adult = NA
, b1Bs.small = 0.02648
, b2Bs.small = 2.95954
, b1Bs.large = 0.02648
, b2Bs.large = 2.95954
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0192 * 0.5
, b2WAI = 2.0947
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 1.5
, hgt.max = 0.999 * 22.6799
, qroot = 1.1274
, qsw = 30.0 / 3900.
, agf.bs = 0.7
, orient.factor = 0.25
, clumping.factor = 0.84
, leaf.width = lwidth.bltree
, init.density = 0.1
, veg.hcap.min = 8.95049E-02
)
pft10 = list( name = "Mid hardwood"
, key = "MHW"
, colour = "#E5171A"
, tropical = FALSE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3temp + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3temp + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 15.625 * 1.1171 * umol.2.mol
, m = mphoto.c3 * 6.3949 / 8.0
, alpha = alpha.c3
, b = 20000. * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = NA
, leaf.turnover.rate = NA
, root.turnover.rate = 5.083700
, SLA = 24.2
, hgt.ref = 1.3
, b1Ht = 25.18
, b2Ht = -0.04964
, b1Bl.small = 0.048
, b2Bl.small = 1.455
, b1Bl.large = 0.048
, b2Bl.large = 1.455
, bleaf.adult = NA
, b1Bs.small = 0.1617
, b2Bs.small = 2.4572
, b1Bs.large = 0.1617
, b2Bs.large = 2.4572
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0192 * 0.5
, b2WAI = 2.0947
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 1.5
, hgt.max = 0.999 * 25.18
, qroot = 1.1274
, qsw = 24.2 / 3900.
, agf.bs = 0.7
, orient.factor = 0.25
, clumping.factor = 0.84
, leaf.width = lwidth.bltree
, init.density = 0.1
, veg.hcap.min = 7.65271E-01
)
pft11 = list( name = "Late hardwood"
, key = "LHW"
, colour = "#990003"
, tropical = FALSE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3temp + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3temp + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 6.25 * 1.1171 * umol.2.mol
, m = mphoto.c3 * 6.3949 / 8.0
, alpha = alpha.c3
, b = 20000. * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = NA
, leaf.turnover.rate = NA
, root.turnover.rate = 5.070992
, SLA = 60.0
, hgt.ref = 1.3
, b1Ht = 23.3874
, b2Ht = -0.05404
, b1Bl.small = 0.017
, b2Bl.small = 1.731
, b1Bl.large = 0.017
, b2Bl.large = 1.731
, bleaf.adult = NA
, b1Bs.small = 0.235
, b2Bs.small = 2.2518
, b1Bs.large = 0.235
, b2Bs.large = 2.2518
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0192 * 0.5
, b2WAI = 2.0947
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 1.5
, hgt.max = 0.999 * 23.3874
, qroot = 1.1274
, qsw = 60.0 / 3900.
, agf.bs = 0.7
, orient.factor = 0.25
, clumping.factor = 0.84
, leaf.width = lwidth.bltree
, init.density = 0.1
, veg.hcap.min = 1.60601E-01
)
pft12 = pft05; pft12$name = "C3 crop" ; pft12$key = "CC3"; pft12$colour="#A38FCC"
pft13 = pft05; pft13$name = "C3 pasture"; pft13$key = "PC3"; pft13$colour="#7F40FF"
pft14 = pft01; pft14$name = "C4 crop" ; pft14$key = "CC4"; pft14$colour="#A1E5CF"
pft15 = pft01; pft15$name = "C4 pasture"; pft15$key = "PC4"; pft15$colour="#6B998A"
pft16 = list( name = "C3 grass"
, key = "C3G"
, colour = "#F2F291"
, tropical = TRUE
, liana = FALSE
, pathway = 3
, d0 = d0.grass
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3trop + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3trop + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 20.833333333 * vmfact.c3 * umol.2.mol
, m = mphoto.c3
, alpha = alpha.c3
, b = b.c3 * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = 0.20
, leaf.turnover.rate = 2.0
, root.turnover.rate = 2.0
, SLA = 22.7
, hgt.ref = hgt.ref.trop
, b1Ht = b1Ht.trop
, b2Ht = b2Ht.trop
, b1Bl.small = NA
, b2Bl.small = NA
, b1Bl.large = NA
, b2Bl.large = NA
, bleaf.adult = NA
, b1Bs.small = NA
, b2Bs.small = NA
, b1Bs.large = NA
, b2Bs.large = NA
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.99
, b2Cl = 1.00
, b1WAI = 0.0
, b2WAI = 1.0
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 0.5
, hgt.max = 1.5
, qroot = 1.0
, qsw = 22.0 / 3900.
, agf.bs = 0.7
, orient.factor = orient.grass
, clumping.factor = clumping.grass
, leaf.width = lwidth.grass
, init.density = 0.1
, veg.hcap.min = 3.68093E+00
)
pft17 = list( name = "Lianas"
, key = "Lia"
, colour = "#1E64C8"
, tropical = TRUE
, liana = TRUE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.aa + t00
, vm.high.temp = vm.thot.aa + t00
, vm.decay.e = vm.decay.e.aa
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.aa + t00
, lr.high.temp = lr.thot.aa + t00
, lr.decay.e = lr.decay.e.aa
, vm0 = 18.75 * vmfact.c3 * umol.2.mol
, m = mphoto.aa
, alpha = alpha.c3
, b = b.aa * umol.2.mol
, gamma.resp = gamma.aa
, effarea.transp = 1.0
, rho = 0.46
, leaf.turnover.rate = 1.27
, root.turnover.rate = 1.27
, SLA = NA
, hgt.ref = hgt.ref.trop
, b1Ht = 0.1136442
, b2Ht = 0.8675
, b1Bl.small = NA
, b2Bl.small = NA
, b1Bl.large = NA
, b2Bl.large = NA
, bleaf.adult = NA
, b1Bs.small = NA
, b2Bs.small = NA
, b1Bs.large = NA
, b2Bs.large = NA
, b1Ca = 2.490154
, b2Ca = 1.26254364
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0192 * 0.5
, b2WAI = 2.0947
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 0.5
, hgt.max = 35.0
, qroot = 1.0
, qsw = 17.88 / 3900.
, agf.bs = 0.7
, orient.factor = orient.aa
, clumping.factor = clumping.aa
, leaf.width = lwidth.nltree
, init.density = 0.1
, veg.hcap.min = 9.93851E+00
)
pft18 = pft07; pft18$name = "Total" ; pft18$key = "ALL"; pft18$colour="#404040"
#------------------------------------------------------------------------------------------#
#----- Build the structure of photosynthesis parameters by PFT. ---------------------------#
pft = list()
for (p in 1:(npft+1)){
ppp = substring(100+p,2,3)
phph = paste("pft",ppp,sep="")
if (p == 1){
pft = get(phph)
}else{
phmerge = get(phph)
for (n in union(names(pft),names(phmerge))){
pft[[n]] = c(pft[[n]],phmerge[[n]])
} #end for
}# end if
} #end for
#----- Minimum and Maximum DBH. -----------------------------------------------------------#
pft$dbh.min = rep(NA,times=npft+1)
pft$dbh.crit = rep(NA,times=npft+1)
pft$dbh.adult = rep(NA,times=npft+1)
for (ipft in sequence(npft)){
if (pft$tropical[ipft]){
if (iallom %in% c(0,1)){
pft$dbh.min [ipft] = exp((log(pft$hgt.min[ipft])-pft$b1Ht[ipft])/pft$b2Ht[ipft])
pft$dbh.crit[ipft] = exp((log(pft$hgt.max[ipft])-pft$b1Ht[ipft])/pft$b2Ht[ipft])
}else if (iallom %in% c(2,3)){
pft$dbh.min [ipft] = ( log( pft$hgt.ref[ipft]
/ ( pft$hgt.ref[ipft] - pft$hgt.min[ipft]) )
/ pft$b1Ht[ipft] ) ^ (1.0 / pft$b2Ht[ipft])
pft$dbh.crit[ipft] = ( log( pft$hgt.ref[ipft]
/ ( pft$hgt.ref[ipft] - pft$hgt.max[ipft]) )
/ pft$b1Ht[ipft] ) ^ (1.0 / pft$b2Ht[ipft])
}#end if
}else{
pft$dbh.min [ipft] = ( log(1.0 - (pft$hgt.min[ipft]-pft$hgt.ref[ipft])
/ pft$b1Ht[ipft] ) / pft$b2Ht[ipft] )
pft$dbh.crit[ipft] = ( log(1.0 - (pft$hgt.max[ipft]-pft$hgt.ref[ipft])
/ pft$b1Ht[ipft]) / pft$b2Ht[ipft] )
}#end if
pft$dbh.adult[ipft] = 10.0
}#end for
pft$dbh.crit[17] = 26
pft$dbh.adult[17] = 1.81
#------------------------------------------------------------------------------------------#
# Specific leaf area for those PFTs whose specific leaf area depends on the leaf turn- #
# over rate. #
#------------------------------------------------------------------------------------------#
#pft$SLA = rep(NA,times=npft+1)
for (ipft in sequence(npft)){
if (is.na(pft$SLA[ipft])){
pft$SLA[ipft] = ( 10^( (2.4 - 0.46 * log10(12./pft$leaf.turnover.rate[ipft])))
* C2B * 0.1 )
}#end if
}#end for
#------------------------------------------------------------------------------------------#
#----- Constants shared by both bdead and bleaf -------------------------------------------#
a1 = -1.981
b1 = 1.047
dcrit = 100.0
#----- Constants used by bdead only -------------------------------------------------------#
c1d = 0.572
d1d = 0.931
a2d = -1.086
b2d = 0.876
c2d = 0.604
d2d = 0.871
#----- Constants used by bleaf only -------------------------------------------------------#
c1l = -0.584
d1l = 0.550
a2l = -4.111
b2l = 0.605
c2l = 0.848
d2l = 0.438
#------------------------------------------------------------------------------------------#
for (ipft in sequence(npft)){
if (pft$tropical[ipft]){
#------------------------------------------------------------------------------------#
# Fill in the leaf biomass parameters. #
#------------------------------------------------------------------------------------#
if (iallom %in% c(0,1)){
#---- ED-2.1 allometry. ----------------------------------------------------------#
pft$b1Bl.small [ipft] = exp(a1 + c1l * pft$b1Ht[ipft] + d1l * log(pft$rho[ipft]))
aux = ( (a2l - a1) + pft$b1Ht[ipft] * (c2l - c1l)
+ log(pft$rho[ipft]) * (d2l - d1l)) * (1.0/log(dcrit))
pft$b2Bl.small [ipft] = C2B * b2l + c2l * pft$b2Ht[ipft] + aux
pft$b1Bl.large [ipft] = pft$b1Bl.small[ipft]
pft$b2Bl.large [ipft] = pft$b2Bl.small[ipft]
pft$bleaf.adult[ipft] = ( pft$b1Bl.large[ipft] / C2B
* pft$dbh.adult [ipft] ^ pft$b2Bl.large[ipft] )
}else if(iallom %in% c(2)){
pft$b1Bl.small [ipft] = C2B * exp(nleaf[1]) * pft$rho[ipft] / nleaf[3]
pft$b2Bl.small [ipft] = nleaf[2]
pft$b1Bl.large [ipft] = pft$b1Bl.small[ipft]
pft$b2Bl.large [ipft] = pft$b2Bl.small[ipft]
pft$bleaf.adult[ipft] = ( pft$b1Bl.large[ipft] / C2B
* pft$dbh.adult [ipft] ^ pft$b2Bl.large[ipft] )
}else if(iallom %in% c(3)){
#---------------------------------------------------------------------------------#
# Use Lescure et al. (1983) for large trees, assume minimum leaf biomass for #
# mid-successional to be 50gC/plant and interpolate biomass for saplings using a #
# log-linear function. #
#---------------------------------------------------------------------------------#
pft$b1Bl.large [ipft] = 0.00873 * pft$SLA[3] / pft$SLA[ipft] # * C2B
pft$b2Bl.large [ipft] = 2.1360
bleaf.sapling = 0.02 * C2B * pft$SLA[3] / pft$SLA[ipft]
pft$bleaf.adult[ipft] = ( pft$b1Bl.large[ipft] / C2B
* pft$dbh.adult [ipft] ^ pft$b2Bl.large[ipft] )
pft$b2Bl.small [ipft] = ( log(pft$bleaf.adult[ipft]/bleaf.sapling)
/ log(pft$dbh.adult[ipft]/pft$dbh.min[ipft]) )
pft$b1Bl.small [ipft] = ( pft$bleaf.adult[ipft] * C2B
/ pft$dbh.adult[ipft] ^ pft$b2Bl.small[ipft] )
}#end if
#------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------#
# Fill in the structural biomass parameters. #
#------------------------------------------------------------------------------------#
if (iallom %in% c(0)){
#---- ED-2.1 allometry. ----------------------------------------------------------#
pft$b1Bs.small[ipft] = exp(a1 + c1d * pft$b1Ht[ipft] + d1d * log(pft$rho[ipft]))
pft$b1Bs.large[ipft] = exp(a1 + c1d * log(pft$hgt.max[ipft])
+ d1d * log(pft$rho[ipft]))
aux = ( (a2d - a1) + pft$b1Ht[ipft] * (c2d - c1d)
+ log(pft$rho[ipft]) * (d2d - d1d) ) * (1.0/log(dcrit))
pft$b2Bs.small[ipft] = C2B * b2d + c2d * pft$b2Ht[ipft] + aux
aux = ( (a2d - a1) + log(pft$hgt.max[ipft]) * (c2d - c1d)
+ log(pft$rho[ipft]) * (d2d - d1d)) * (1.0/log(dcrit))
pft$b2Bs.large[ipft] = C2B * b2d + aux
}else if (iallom %in% c(1)){
#---- Based on modified Chave et al. (2001) allometry. ---------------------------#
pft$b1Bs.small[ipft] = C2B * exp(odead.small[1]) * pft$rho[ipft] / odead.small[3]
pft$b2Bs.small[ipft] = odead.small[2]
pft$b1Bs.large[ipft] = C2B * exp(odead.large[1]) * pft$rho[ipft] / odead.large[3]
pft$b2Bs.large[ipft] = odead.large[2]
}else if (iallom %in% c(2,3)){
#---- Based an alternative modification of Chave et al. (2001) allometry. --------#
pft$b1Bs.small[ipft] = C2B * exp(ndead.small[1]) * pft$rho[ipft] / ndead.small[3]
pft$b2Bs.small[ipft] = ndead.small[2]
pft$b1Bs.large[ipft] = C2B * exp(ndead.large[1]) * pft$rho[ipft] / ndead.large[3]
pft$b2Bs.large[ipft] = ndead.large[2]
}#end if
#------------------------------------------------------------------------------------#
pft$b1Bs.small[17] = 0.2749
pft$b1Bs.large[17] = pft$b1Bs.small[17]
pft$b2Bs.small[17] = 2.69373
pft$b2Bs.large[17] = pft$b2Bs.small[17]
pft$b1Bl.small[17] = pft$b1Bl.small[2]
pft$b2Bl.small[17] = pft$b2Bl.small[2]
pft$b1Bl.large[17] = 0.0856
pft$b2Bl.large[17] = 2.0
#------------------------------------------------------------------------------------#
# Replace the coefficients if we are going to use Poorter et al. (2006) #
# parameters for crown area. #
#------------------------------------------------------------------------------------#
if (iallom %in% c(0,1)){
pft$b1Ca[ipft] = exp(-1.853) * exp(pft$b1Ht[ipft]) ^ 1.888
pft$b2Ca[ipft] = pft$b2Ht[ipft] * 1.888
}else if (iallom %in% c(2,3)){
pft$b1Ca[ipft] = exp(ncrown.area[1])
pft$b2Ca[ipft] = ncrown.area[2]
}#end if
pft$b2Ca[17] = 1.26254364
#------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------#
# Replace the coefficients for WAI in case iallom is 3. #
# These numbers come from fitting Chambers et al. (2001) and Chambers et al. (2004) #
# allometries for stem area index. #
#------------------------------------------------------------------------------------#
if (iallom %in% c(3)){
pft$b1WAI[ipft] = 0.11 * pft$SLA[ipft] * pft$b1Bl.large[ipft]
pft$b2WAI[ipft] = pft$b2Bl.large[ipft]
}#end if
#------------------------------------------------------------------------------------#
}else{
pft$bleaf.adult[ipft] = ( pft$b1Bl.large[ipft] / C2B
* pft$dbh.adult [ipft] ^ pft$b2Bl.large[ipft] )
}#end if (pft$tropical[ipft])
#---------------------------------------------------------------------------------------#
}#end for (ipft in sequence(npft))
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# Rooting depth coefficients. #
#------------------------------------------------------------------------------------------#
pft$b1Rd = rep(NA,times=npft+1)
if (iallom %in% c(0)){
#----- Original ED-2.1 scheme, based on standing volume. -------------------------------#
pft$b1Rd[ 1:17] = NA
pft$b1Rd[ 1] = -0.700
pft$b1Rd[ 2:4] = -exp(0.545 * log(10.))
pft$b1Rd[ 5] = -0.700
pft$b1Rd[ 6:11] = -exp(0.545 * log(10.))
pft$b1Rd[12:16] = -0.700
pft$b1Rd[ 17] = -exp(0.545 * log(10.))
pft$b2Rd[ 1:17] = NA
pft$b2Rd[ 1] = 0.000
pft$b2Rd[ 2:4] = 0.277
pft$b2Rd[ 5] = 0.000
pft$b2Rd[ 6:11] = 0.277
pft$b2Rd[12:16] = 0.000
pft$b2Rd[ 17] = 0.277
}else if (iallom %in% c(1,2,3)){
#----- Simple allometry (0.5 m for seedlings, 5.0m for 35-m trees. ---------------------#
pft$b1Rd[1:17] = -1.1140580
pft$b2Rd[1:17] = 0.4223014
}#end if
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# Minimum bleaf and leaf area index that is resolvable. #
#------------------------------------------------------------------------------------------#
pft$bleaf.min = c(dbh2bl(dbh=pft$dbh.min[1:npft],ipft=1:npft),NA)
pft$lai.min = onesixth * pft$init.dens * pft$bleaf.min * pft$SLA
#------------------------------------------------------------------------------------------#
pft$dbh.min[c(2,3,4)]=10.0
pft$dbh.min[17]=2.0
#----- Make it global. --------------------------------------------------------------------#
pft <<- pft
#------------------------------------------------------------------------------------------#
manfredo89/ED2io documentation built on May 21, 2019, 11:24 a.m.
R Package Documentation
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#==========================================================================================#
#==========================================================================================#
# This module contains several parameters used in the Farquar Leuning photosynthesis #
# solver. The following references are used as a departing point: #
# - M09 - Medvigy, D.M., S. C. Wofsy, J. W. Munger, D. Y. Hollinger, P. R. Moorcroft, #
# 2009: Mechanistic scaling of ecosystem function and dynamics in space and time: #
# Ecosystem Demography model version 2. J. Geophys. Res., 114, G01002, #
# doi:10.1029/2008JG000812. #
# - M06 - Medvigy, D.M., 2006: The State of the Regional Carbon Cycle: results from a #
# constrained coupled ecosystem-atmosphere model, 2006. Ph.D. dissertation, #
# Harvard University, Cambridge, MA, 322pp. #
# - M01 - Moorcroft, P. R., G. C. Hurtt, S. W. Pacala, 2001: A method for scaling #
# vegetation dynamics: the ecosystem demography model, Ecological Monographs, 71, #
# 557-586. #
# - F96 - Foley, J. A., I. Colin Prentice, N. Ramankutty, S. Levis, D. Pollard, S. Sitch, #
# A. Haxeltime, 1996: An integrated biosphere model of land surface processes, #
# terrestrial carbon balance, and vegetation dynamics. Glob. Biogeochem. Cycles, #
# 10, 603-602. #
# - L95 - Leuning, R., F. M. Kelliher, D. G. G. de Pury, E. D. Schulze, 1995: Leaf #
# nitrogen, photosynthesis, conductance, and transpiration: scaling from leaves to #
# canopies. Plant, Cell, and Environ., 18, 1183-1200. #
# - C91 - Collatz, G. J., J. T. Ball, C. Grivet, J. A. Berry, 1991: Physiological and #
# environmental regulation of stomatal conductance, photosynthesis and #
# transpiration: A model that includes a laminar boundary layer. Agric. For. #
# Meteor., 53, 107-136. #
# - B01 - Bernacchi, C. J., E. L. Singsaas, C. Pimentel, A. R. Portis Jr., S. P. Long, #
# 2001: Improved temperature response functions for models of Rubisco-limited #
# photosynthesis. Plant, Cell and Environ., 24, 253-259. #
# - B02 - Bernacchi, C. J., A. R. Portis, H. Nakano, S. von Caemmerer, S. P. Long, #
# 2002: Temperature response of mesophyll conductance. Implications for the #
# determination of Rubisco enzyme kinetics and for limitations to photosynthesis #
# in vivo. Plant physiol., 130, 1992-1998. #
#------------------------------------------------------------------------------------------#
#' @include rconstants.r
#'
#'
#'
if (! "npft" %in% ls()) npft = 17
#----- Fudging parameters to try to tune photosynthesis. ----------------------------------#
if (! "alpha.c3" %in% ls()){
alpha.c3 <<- 0.08
}else{
alpha.c3 <<- alpha.c3
}#end if
if (! "alpha.c4" %in% ls()){
alpha.c4 <<- 0.053
}else{
alpha.c4 <<- alpha.c4
}#end if
if (! "vmfact.c3" %in% ls()){
vmfact.c3 <<- 1.0
}else{
vmfact.c3 <<- vmfact.c3
}#end if
if (! "vmfact.c4" %in% ls()){
vmfact.c4 <<- 1.0
}else{
vmfact.c4 <<- vmfact.c4
}#end if
if (! "mphoto.c3" %in% ls()){
mphoto.c3 <<- 8.0
}else{
mphoto.c3 <<- mphoto.c3
}#end if
if (! "mphoto.aa" %in% ls()){
mphoto.aa <<- 6.4
}else{
mphoto.aa <<- mphoto.aa
}#end if
if (! "mphoto.c4" %in% ls()){
mphoto.c4 <<- 4.0
}else{
mphoto.c4 <<- mphoto.c4
}#end if
if (! "gamma.c3" %in% ls()){
gamma.c3 <<- 0.020
}else{
gamma.c3 <<- gamma.c3
}#end if
if (! "gamma.aa" %in% ls()){
gamma.aa <<- 0.028
}else{
gamma.aa <<- gamma.aa
}#end if
if (! "gamma.c4" %in% ls()){
gamma.c4 <<- 0.040
}else{
gamma.c4 <<- gamma.c4
}#end if
if (! "d0.grass" %in% ls()){
d0.grass <<- 0.01
}else{
d0.grass <<- d0.grass
}#end if
if (! "d0.tree" %in% ls()){
d0.tree <<- 0.01
}else{
d0.tree <<- d0.tree
}#end if
if (! "klowin" %in% ls()){
klowin <<- 18000.
}else{
klowin <<- klowin
}#end if
if (! "base.c3" %in% ls()){
base.c3 <<- 2.4
}else{
base.c3 <<- base.c3
}#end if
if (! "base.c4" %in% ls()){
base.c4 <<- 2.0
}else{
base.c4 <<- base.c4
}#end if
if (! "b.c3" %in% ls()){
b.c3 <<- 10000.
}else{
b.c3 <<- b.c3
}#end if
if (! "b.aa" %in% ls()){
b.aa <<- 1000.
}else{
b.aa <<- b.aa
}#end if
if (! "b.c4" %in% ls()){
b.c4 <<- 8000.
}else{
b.c4 <<- b.c4
}#end if
if (! "orient.tree" %in% ls()){
orient.tree <<- 0.00
}else{
orient.tree <<- orient.tree
}#end if
if (! "orient.aa" %in% ls()){
orient.aa <<- 0.00
}else{
orient.aa <<- orient.aa
}#end if
if (! "orient.grass" %in% ls()){
orient.grass <<- 0.00
}else{
orient.grass <<- orient.grass
}#end if
if (! "clumping.tree" %in% ls()){
clumping.tree <<- 0.735
}else{
clumping.tree <<- clumping.tree
}#end if
if (! "clumping.aa" %in% ls()){
clumping.aa <<- 0.735
}else{
clumping.aa <<- clumping.aa
}#end if
if (! "clumping.grass" %in% ls()){
clumping.grass <<- 1.0
}else{
clumping.grass <<- clumping.grass
}#end if
if (! "lwidth.grass" %in% ls()){
lwidth.grass <<- 0.05
}else{
lwidth.grass <<- lwidth.grass
}#end if
if (! "lwidth.bltree" %in% ls()){
lwidth.bltree <<- 0.10
}else{
lwidth.bltree <<- lwidth.bltree
}#end if
if (! "lwidth.nltree" %in% ls()){
lwidth.nltree <<- 0.05
}else{
lwidth.nltree <<- lwidth.nltree
}#end if
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# The following parameter is the k coefficient in Foley et al. (1996) that is used to #
# determine the CO2-limited photosynthesis for C4 grasses. #
#------------------------------------------------------------------------------------------#
klowco2 <<- klowin * mmco2 /mmdry # Coefficient for low CO2 [ mol/mol]
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# These parameters will be assigned to the PFT structure. Notice that depending on the #
# physiology method (Foley or Collatz), some of them will be used, and some of them will #
# not. #
#------------------------------------------------------------------------------------------#
vm.hor <<- 3000. # Ref. exp. coeff. for carboxylase fctn. [ K]
vm.base.c3 <<- base.c3 # Base Vm for C3 - Collatz et al. (1991) [mol/m2/s]
vm.base.c4 <<- base.c4 # Base Vm for C4 - Collatz et al. (1992) [mol/m2/s]
vm.decay.a <<- 220000. # Decay function for warm temperatures -- A [ J/mol]
vm.decay.b <<- 695. # Decay function for warm temperatures -- B [ J/mol/K]
vm.tcold.c3temp <<- 4.7137
vm.tcold.c3trop <<- 8.0
vm.tcold.aa <<- 4.7137
vm.tcold.c4 <<- 8.0
vm.thot.c3 <<- 45.0
vm.thot.aa <<- 45.0
vm.thot.c4 <<- 45.0
vm.decay.e.c3 <<- 0.4
vm.decay.e.aa <<- 0.4
vm.decay.e.c4 <<- 0.4
lr.hor <<- 3000. # Ref. exp. coeff. for carboxylase fctn. [ K]
lr.base.c3 <<- base.c3
lr.base.c4 <<- base.c4
lr.tcold.c3temp <<- vm.tcold.c3temp
lr.tcold.c3trop <<- vm.tcold.c3trop
lr.tcold.aa <<- vm.tcold.aa
lr.tcold.c4 <<- vm.tcold.c4
lr.thot.c3 <<- vm.thot.c3
lr.thot.aa <<- vm.thot.aa
lr.thot.c4 <<- vm.thot.c3
lr.decay.e.c3 <<- 0.4
lr.decay.e.aa <<- 0.4
lr.decay.e.c4 <<- 0.4
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# Define some common values to make it easier to change the list below... #
#------------------------------------------------------------------------------------------#
C2B <<- 2.0
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# These variables define the allometry to use #
# 0 - ED-2.1 #
# 1 - a. AGB is based on Baker et al. (2004), Chave formula, keeping the same Bleaf as #
# ED-2.1 and Bdead to make up the difference. #
# b. Use the crown area as in Poorter et al. (2006) for tropical PFTs #
# c. Use a simple rooting depth ranging from 0.5 to 5.0 #
# 2 - Same as 1, but using the height as in Poorter et al. (2006) for tropical PFTs, and #
# finding a fit similar to Baker et al. (2004) that doesn't depend on height, using #
# Saldarriaga et al. (1988) as a starting point. #
#------------------------------------------------------------------------------------------#
if ("iallom" %in% ls()){
iallom <<- iallom
}else{
iallom <<- 3
}#end if
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# These constants will help defining the allometric parameters for IALLOM 1 and 2. #
#------------------------------------------------------------------------------------------#
odead.small = c( -1.11382700, 2.44048300, 2.18063200)
odead.large = c( 0.13625460, 2.42173900, 6.94835320)
ndead.small = c( -1.26395300, 2.43236100, 1.80180100)
ndead.large = c( -0.83468050, 2.42557360, 2.68228050)
nleaf = c( 0.01925119, 0.97494935, 2.58585087)
uleaf = c( -1.09254800, 1.28505100, 3.199019 )
ncrown.area = c( 0.11842950, 1.05211970)
#------------------------------------------------------------------------------------------#
#----- Define reference height and coefficients for tropical allometry. -------------------#
if (iallom %in% c(0,1)){
hgt.ref.trop = NA
b1Ht.trop = 0.37 * log(10)
b2Ht.trop = 0.64
}else if (iallom %in% c(2,3)){
hgt.ref.trop = 61.7
b1Ht.trop = 0.0352
b2Ht.trop = 0.694
}#end if
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# The following variables will define the PFT characteristics regarding the #
# photosynthesis. #
#------------------------------------------------------------------------------------------#
pft01 = list( name = "C4 grass"
, key = "C4G"
, colour = "#E5E503"
, tropical = TRUE
, liana = FALSE
, pathway = 4
, d0 = d0.grass
, vm.hor = vm.hor
, vm.base = vm.base.c4
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c4 + t00
, vm.high.temp = vm.thot.c4 + t00
, vm.decay.e = vm.decay.e.c4
, lr.hor = lr.hor
, lr.base = lr.base.c4
, lr.low.temp = lr.tcold.c4 + t00
, lr.high.temp = lr.thot.c4 + t00
, lr.decay.e = lr.decay.e.c4
, vm0 = 12.5 * vmfact.c4 * umol.2.mol
, m = mphoto.c4
, alpha = alpha.c4
, b = b.c4 * umol.2.mol
, gamma.resp = gamma.c4
, effarea.transp = 1.0
, rho = 0.20
, leaf.turnover.rate = 2.0
, root.turnover.rate = 2.0
, SLA = 22.7
, hgt.ref = hgt.ref.trop
, b1Ht = b1Ht.trop
, b2Ht = b2Ht.trop
, b1Bl.small = NA
, b2Bl.small = NA
, b1Bl.large = NA
, b2Bl.large = NA
, bleaf.adult = NA
, b1Bs.small = NA
, b2Bs.small = NA
, b1Bs.large = NA
, b2Bs.large = NA
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.99
, b2Cl = 1.00
, b1WAI = 0.00
, b2WAI = 1.00
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 0.5
, hgt.max = 1.5
, qroot = 1.0
, qsw = 22.0 / 3900.
, agf.bs = 0.7
, orient.factor = orient.grass
, clumping.factor = clumping.grass
, leaf.width = lwidth.grass
, init.density = 0.1
, veg.hcap.min = 3.68093E+00
)
pft02 = list( name = "Early tropical"
, key = "ETR"
, colour = "#9FFF8C"
, tropical = TRUE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3trop + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3trop + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 18.75 * vmfact.c3 * umol.2.mol
, m = mphoto.c3
, alpha = alpha.c3
, b = b.c3 * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = 0.53
, leaf.turnover.rate = 1.0
, root.turnover.rate = 1.0
, SLA = NA
, hgt.ref = hgt.ref.trop
, b1Ht = b1Ht.trop
, b2Ht = b2Ht.trop
, b1Bl.small = NA
, b2Bl.small = NA
, b1Bl.large = NA
, b2Bl.large = NA
, bleaf.adult = NA
, b1Bs.small = NA
, b2Bs.small = NA
, b1Bs.large = NA
, b2Bs.large = NA
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0192 * 0.5
, b2WAI = 2.0947
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 0.5
, hgt.max = 35.0
, qroot = 1.0
, qsw = 16.0 / 3900.
, agf.bs = 0.7
, orient.factor = orient.tree
, clumping.factor = clumping.tree
, leaf.width = lwidth.bltree
, init.density = 0.1
, veg.hcap.min = 9.75446E+00
)
pft03 = list( name = "Mid tropical"
, key = "MTR"
, colour = "#44CC29"
, tropical = TRUE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3trop + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3trop + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 12.5 * vmfact.c3 * umol.2.mol
, m = mphoto.c3
, alpha = alpha.c3
, b = b.c3 * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = 0.71
, leaf.turnover.rate = 0.50
, root.turnover.rate = 0.50
, SLA = NA
, hgt.ref = hgt.ref.trop
, b1Ht = b1Ht.trop
, b2Ht = b2Ht.trop
, b1Bl.small = NA
, b2Bl.small = NA
, b1Bl.large = NA
, b2Bl.large = NA
, bleaf.adult = NA
, b1Bs.small = NA
, b2Bs.small = NA
, b1Bs.large = NA
, b2Bs.large = NA
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0192 * 0.5
, b2WAI = 2.0947
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 0.5
, hgt.max = 35.0
, qroot = 1.0
, qsw = 11.6 / 3900.
, agf.bs = 0.7
, orient.factor = orient.tree
, clumping.factor = clumping.tree
, leaf.width = lwidth.bltree
, init.density = 0.1
, veg.hcap.min = 1.30673E+01
)
pft04 = list( name = "Late tropical"
, key = "LTR"
, colour = "#137300"
, tropical = TRUE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3trop + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3trop + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 6.25 * vmfact.c3 * umol.2.mol
, m = mphoto.c3
, alpha = alpha.c3
, b = b.c3 * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = 0.90
, leaf.turnover.rate = 1./3.
, root.turnover.rate = 1./3.
, SLA = NA
, hgt.ref = hgt.ref.trop
, b1Ht = b1Ht.trop
, b2Ht = b2Ht.trop
, b1Bl.small = NA
, b2Bl.small = NA
, b1Bl.large = NA
, b2Bl.large = NA
, bleaf.adult = NA
, b1Bs.small = NA
, b2Bs.small = NA
, b1Bs.large = NA
, b2Bs.large = NA
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0192 * 0.5
, b2WAI = 2.0947
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 0.5
, hgt.max = 35.0
, qroot = 1.0
, qsw = 9.67 / 3900.
, agf.bs = 0.7
, orient.factor = orient.tree
, clumping.factor = clumping.tree
, leaf.width = lwidth.bltree
, init.density = 0.1
, veg.hcap.min = 1.65642E+01
)
pft05 = list( name = "Temperate C3 Grass"
, key = "TTG"
, colour = "#B2B224"
, tropical = FALSE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3temp + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3temp + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 18.3 * umol.2.mol
, m = mphoto.c3
, alpha = alpha.c3
, b = b.c3 * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = 0.32
, leaf.turnover.rate = 2.0
, root.turnover.rate = 2.0
, SLA = 22.0
, hgt.ref = 0.0
, b1Ht = 0.4778
, b2Ht = -0.750
, b1Bl.small = 0.08
, b2Bl.small = 1.00
, b1Bl.large = 0.08
, b2Bl.large = 1.00
, bleaf.adult = NA
, b1Bs.small = 1.e-5
, b2Bs.small = 1.0
, b1Bs.large = 1.e-5
, b2Bs.large = 1.0
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.99
, b2Cl = 1.0
, b1WAI = 0.0
, b2WAI = 1.0
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 0.15
, hgt.max = 0.95 * 0.4778
, qroot = 1.0
, qsw = 22.0 / 3900.
, agf.bs = 0.7
, orient.factor = -0.30
, clumping.factor = 1.00
, leaf.width = lwidth.grass
, init.density = 0.1
, veg.hcap.min = 9.16551E+00
)
pft06 = list( name = "North Pine"
, key = "NPN"
, colour = "#0066CC"
, tropical = FALSE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3temp + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3temp + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 15.625 * 0.7264 * umol.2.mol
, m = mphoto.c3 * 6.3949 / 8.0
, alpha = alpha.c3
, b = 1000. * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 2.0
, rho = NA
, leaf.turnover.rate = 1./3.
, root.turnover.rate = 3.927218
, SLA = 6.0
, hgt.ref = 1.3
, b1Ht = 27.14
, b2Ht = -0.03884
, b1Bl.small = 0.024
, b2Bl.small = 1.899
, b1Bl.large = 0.024
, b2Bl.large = 1.899
, bleaf.adult = NA
, b1Bs.small = 0.147
, b2Bs.small = 2.238
, b1Bs.large = 0.147
, b2Bs.large = 2.238
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0553 * 0.5
, b2WAI = 1.9769
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 1.5
, hgt.max = 0.999 * 27.14
, qroot = 0.3463
, qsw = 6.0 / 3900.
, agf.bs = 0.7
, orient.factor = 0.01
, clumping.factor = 0.735
, leaf.width = lwidth.nltree
, init.density = 0.1
, veg.hcap.min = 2.34683E-01
)
pft07 = list( name = "South Pine"
, key = "SPN"
, colour = "#99CCFF"
, tropical = FALSE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3temp + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3temp + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 15.625 * 0.7264 * umol.2.mol
, m = mphoto.c3 * 6.3949 / 8.0
, alpha = alpha.c3
, b = 1000. * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 2.0
, rho = NA
, leaf.turnover.rate = 1./3.
, root.turnover.rate = 4.117847
, SLA = 9.0
, hgt.ref = 1.3
, b1Ht = 27.14
, b2Ht = -0.03884
, b1Bl.small = 0.024
, b2Bl.small = 1.899
, b1Bl.large = 0.024
, b2Bl.large = 1.899
, bleaf.adult = NA
, b1Bs.small = 0.147
, b2Bs.small = 2.238
, b1Bs.large = 0.147
, b2Bs.large = 2.238
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0553 * 0.5
, b2WAI = 1.9769
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 1.5
, hgt.max = 0.999 * 27.14
, qroot = 0.3463
, qsw = 9.0 / 3900.
, agf.bs = 0.7
, orient.factor = 0.01
, clumping.factor = 0.735
, leaf.width = lwidth.nltree
, init.density = 0.1
, veg.hcap.min = 2.34683E-01
)
pft08 = list( name = "Late conifer"
, key = "LCN"
, colour = "#00407F"
, tropical = FALSE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3temp + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3temp + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 6.25 * 0.7264 * umol.2.mol
, m = mphoto.c3 * 6.3949 / 8.0
, alpha = alpha.c3
, b = 1000. * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 2.0
, rho = NA
, leaf.turnover.rate = 1./3.
, root.turnover.rate = 3.800132
, SLA = 10.0
, hgt.ref = 1.3
, b1Ht = 22.79
, b2Ht = -0.04445
, b1Bl.small = 0.0454
, b2Bl.small = 1.6829
, b1Bl.large = 0.0454
, b2Bl.large = 1.6829
, bleaf.adult = NA
, b1Bs.small = 0.1617
, b2Bs.small = 2.1536
, b1Bs.large = 0.1617
, b2Bs.large = 2.1536
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0553 * 0.5
, b2WAI = 1.9769
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 1.5
, hgt.max = 0.999 * 22.79
, qroot = 0.3463
, qsw = 10.0 / 3900.
, agf.bs = 0.7
, orient.factor = 0.01
, clumping.factor = 0.735
, leaf.width = lwidth.nltree
, init.density = 0.1
, veg.hcap.min = 6.80074E-01
)
pft09 = list( name = "Early hardwood"
, key = "EHW"
, colour = "#FF999B"
, tropical = FALSE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3temp + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3temp + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 18.25 * 1.1171 * umol.2.mol
, m = mphoto.c3 * 6.3949 / 8.0
, alpha = alpha.c3
, b = 20000. * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = NA
, leaf.turnover.rate = NA
, root.turnover.rate = 5.772506
, SLA = 30.0
, hgt.ref = 1.3
, b1Ht = 22.6799
, b2Ht = -0.06534
, b1Bl.small = 0.0129
, b2Bl.small = 1.7477
, b1Bl.large = 0.0129
, b2Bl.large = 1.7477
, bleaf.adult = NA
, b1Bs.small = 0.02648
, b2Bs.small = 2.95954
, b1Bs.large = 0.02648
, b2Bs.large = 2.95954
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0192 * 0.5
, b2WAI = 2.0947
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 1.5
, hgt.max = 0.999 * 22.6799
, qroot = 1.1274
, qsw = 30.0 / 3900.
, agf.bs = 0.7
, orient.factor = 0.25
, clumping.factor = 0.84
, leaf.width = lwidth.bltree
, init.density = 0.1
, veg.hcap.min = 8.95049E-02
)
pft10 = list( name = "Mid hardwood"
, key = "MHW"
, colour = "#E5171A"
, tropical = FALSE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3temp + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3temp + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 15.625 * 1.1171 * umol.2.mol
, m = mphoto.c3 * 6.3949 / 8.0
, alpha = alpha.c3
, b = 20000. * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = NA
, leaf.turnover.rate = NA
, root.turnover.rate = 5.083700
, SLA = 24.2
, hgt.ref = 1.3
, b1Ht = 25.18
, b2Ht = -0.04964
, b1Bl.small = 0.048
, b2Bl.small = 1.455
, b1Bl.large = 0.048
, b2Bl.large = 1.455
, bleaf.adult = NA
, b1Bs.small = 0.1617
, b2Bs.small = 2.4572
, b1Bs.large = 0.1617
, b2Bs.large = 2.4572
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0192 * 0.5
, b2WAI = 2.0947
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 1.5
, hgt.max = 0.999 * 25.18
, qroot = 1.1274
, qsw = 24.2 / 3900.
, agf.bs = 0.7
, orient.factor = 0.25
, clumping.factor = 0.84
, leaf.width = lwidth.bltree
, init.density = 0.1
, veg.hcap.min = 7.65271E-01
)
pft11 = list( name = "Late hardwood"
, key = "LHW"
, colour = "#990003"
, tropical = FALSE
, liana = FALSE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3temp + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3temp + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 6.25 * 1.1171 * umol.2.mol
, m = mphoto.c3 * 6.3949 / 8.0
, alpha = alpha.c3
, b = 20000. * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = NA
, leaf.turnover.rate = NA
, root.turnover.rate = 5.070992
, SLA = 60.0
, hgt.ref = 1.3
, b1Ht = 23.3874
, b2Ht = -0.05404
, b1Bl.small = 0.017
, b2Bl.small = 1.731
, b1Bl.large = 0.017
, b2Bl.large = 1.731
, bleaf.adult = NA
, b1Bs.small = 0.235
, b2Bs.small = 2.2518
, b1Bs.large = 0.235
, b2Bs.large = 2.2518
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0192 * 0.5
, b2WAI = 2.0947
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 1.5
, hgt.max = 0.999 * 23.3874
, qroot = 1.1274
, qsw = 60.0 / 3900.
, agf.bs = 0.7
, orient.factor = 0.25
, clumping.factor = 0.84
, leaf.width = lwidth.bltree
, init.density = 0.1
, veg.hcap.min = 1.60601E-01
)
pft12 = pft05; pft12$name = "C3 crop" ; pft12$key = "CC3"; pft12$colour="#A38FCC"
pft13 = pft05; pft13$name = "C3 pasture"; pft13$key = "PC3"; pft13$colour="#7F40FF"
pft14 = pft01; pft14$name = "C4 crop" ; pft14$key = "CC4"; pft14$colour="#A1E5CF"
pft15 = pft01; pft15$name = "C4 pasture"; pft15$key = "PC4"; pft15$colour="#6B998A"
pft16 = list( name = "C3 grass"
, key = "C3G"
, colour = "#F2F291"
, tropical = TRUE
, liana = FALSE
, pathway = 3
, d0 = d0.grass
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.c3trop + t00
, vm.high.temp = vm.thot.c3 + t00
, vm.decay.e = vm.decay.e.c3
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.c3trop + t00
, lr.high.temp = lr.thot.c3 + t00
, lr.decay.e = lr.decay.e.c3
, vm0 = 20.833333333 * vmfact.c3 * umol.2.mol
, m = mphoto.c3
, alpha = alpha.c3
, b = b.c3 * umol.2.mol
, gamma.resp = gamma.c3
, effarea.transp = 1.0
, rho = 0.20
, leaf.turnover.rate = 2.0
, root.turnover.rate = 2.0
, SLA = 22.7
, hgt.ref = hgt.ref.trop
, b1Ht = b1Ht.trop
, b2Ht = b2Ht.trop
, b1Bl.small = NA
, b2Bl.small = NA
, b1Bl.large = NA
, b2Bl.large = NA
, bleaf.adult = NA
, b1Bs.small = NA
, b2Bs.small = NA
, b1Bs.large = NA
, b2Bs.large = NA
, b1Ca = 2.490154
, b2Ca = 0.8068806
, b1Cl = 0.99
, b2Cl = 1.00
, b1WAI = 0.0
, b2WAI = 1.0
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 0.5
, hgt.max = 1.5
, qroot = 1.0
, qsw = 22.0 / 3900.
, agf.bs = 0.7
, orient.factor = orient.grass
, clumping.factor = clumping.grass
, leaf.width = lwidth.grass
, init.density = 0.1
, veg.hcap.min = 3.68093E+00
)
pft17 = list( name = "Lianas"
, key = "Lia"
, colour = "#1E64C8"
, tropical = TRUE
, liana = TRUE
, pathway = 3
, d0 = d0.tree
, vm.hor = vm.hor
, vm.base = vm.base.c3
, vm.decay.a = vm.decay.a
, vm.decay.b = vm.decay.b
, vm.low.temp = vm.tcold.aa + t00
, vm.high.temp = vm.thot.aa + t00
, vm.decay.e = vm.decay.e.aa
, lr.hor = lr.hor
, lr.base = lr.base.c3
, lr.low.temp = lr.tcold.aa + t00
, lr.high.temp = lr.thot.aa + t00
, lr.decay.e = lr.decay.e.aa
, vm0 = 18.75 * vmfact.c3 * umol.2.mol
, m = mphoto.aa
, alpha = alpha.c3
, b = b.aa * umol.2.mol
, gamma.resp = gamma.aa
, effarea.transp = 1.0
, rho = 0.46
, leaf.turnover.rate = 1.27
, root.turnover.rate = 1.27
, SLA = NA
, hgt.ref = hgt.ref.trop
, b1Ht = 0.1136442
, b2Ht = 0.8675
, b1Bl.small = NA
, b2Bl.small = NA
, b1Bl.large = NA
, b2Bl.large = NA
, bleaf.adult = NA
, b1Bs.small = NA
, b2Bs.small = NA
, b1Bs.large = NA
, b2Bs.large = NA
, b1Ca = 2.490154
, b2Ca = 1.26254364
, b1Cl = 0.3106775
, b2Cl = 1.098
, b1WAI = 0.0192 * 0.5
, b2WAI = 2.0947
, b1Vol = 0.65 * pi * 0.11 * 0.11
, b2Vol = 2.0
, hgt.min = 0.5
, hgt.max = 35.0
, qroot = 1.0
, qsw = 17.88 / 3900.
, agf.bs = 0.7
, orient.factor = orient.aa
, clumping.factor = clumping.aa
, leaf.width = lwidth.nltree
, init.density = 0.1
, veg.hcap.min = 9.93851E+00
)
pft18 = pft07; pft18$name = "Total" ; pft18$key = "ALL"; pft18$colour="#404040"
#------------------------------------------------------------------------------------------#
#----- Build the structure of photosynthesis parameters by PFT. ---------------------------#
pft = list()
for (p in 1:(npft+1)){
ppp = substring(100+p,2,3)
phph = paste("pft",ppp,sep="")
if (p == 1){
pft = get(phph)
}else{
phmerge = get(phph)
for (n in union(names(pft),names(phmerge))){
pft[[n]] = c(pft[[n]],phmerge[[n]])
} #end for
}# end if
} #end for
#----- Minimum and Maximum DBH. -----------------------------------------------------------#
pft$dbh.min = rep(NA,times=npft+1)
pft$dbh.crit = rep(NA,times=npft+1)
pft$dbh.adult = rep(NA,times=npft+1)
for (ipft in sequence(npft)){
if (pft$tropical[ipft]){
if (iallom %in% c(0,1)){
pft$dbh.min [ipft] = exp((log(pft$hgt.min[ipft])-pft$b1Ht[ipft])/pft$b2Ht[ipft])
pft$dbh.crit[ipft] = exp((log(pft$hgt.max[ipft])-pft$b1Ht[ipft])/pft$b2Ht[ipft])
}else if (iallom %in% c(2,3)){
pft$dbh.min [ipft] = ( log( pft$hgt.ref[ipft]
/ ( pft$hgt.ref[ipft] - pft$hgt.min[ipft]) )
/ pft$b1Ht[ipft] ) ^ (1.0 / pft$b2Ht[ipft])
pft$dbh.crit[ipft] = ( log( pft$hgt.ref[ipft]
/ ( pft$hgt.ref[ipft] - pft$hgt.max[ipft]) )
/ pft$b1Ht[ipft] ) ^ (1.0 / pft$b2Ht[ipft])
}#end if
}else{
pft$dbh.min [ipft] = ( log(1.0 - (pft$hgt.min[ipft]-pft$hgt.ref[ipft])
/ pft$b1Ht[ipft] ) / pft$b2Ht[ipft] )
pft$dbh.crit[ipft] = ( log(1.0 - (pft$hgt.max[ipft]-pft$hgt.ref[ipft])
/ pft$b1Ht[ipft]) / pft$b2Ht[ipft] )
}#end if
pft$dbh.adult[ipft] = 10.0
}#end for
pft$dbh.crit[17] = 26
pft$dbh.adult[17] = 1.81
#------------------------------------------------------------------------------------------#
# Specific leaf area for those PFTs whose specific leaf area depends on the leaf turn- #
# over rate. #
#------------------------------------------------------------------------------------------#
#pft$SLA = rep(NA,times=npft+1)
for (ipft in sequence(npft)){
if (is.na(pft$SLA[ipft])){
pft$SLA[ipft] = ( 10^( (2.4 - 0.46 * log10(12./pft$leaf.turnover.rate[ipft])))
* C2B * 0.1 )
}#end if
}#end for
#------------------------------------------------------------------------------------------#
#----- Constants shared by both bdead and bleaf -------------------------------------------#
a1 = -1.981
b1 = 1.047
dcrit = 100.0
#----- Constants used by bdead only -------------------------------------------------------#
c1d = 0.572
d1d = 0.931
a2d = -1.086
b2d = 0.876
c2d = 0.604
d2d = 0.871
#----- Constants used by bleaf only -------------------------------------------------------#
c1l = -0.584
d1l = 0.550
a2l = -4.111
b2l = 0.605
c2l = 0.848
d2l = 0.438
#------------------------------------------------------------------------------------------#
for (ipft in sequence(npft)){
if (pft$tropical[ipft]){
#------------------------------------------------------------------------------------#
# Fill in the leaf biomass parameters. #
#------------------------------------------------------------------------------------#
if (iallom %in% c(0,1)){
#---- ED-2.1 allometry. ----------------------------------------------------------#
pft$b1Bl.small [ipft] = exp(a1 + c1l * pft$b1Ht[ipft] + d1l * log(pft$rho[ipft]))
aux = ( (a2l - a1) + pft$b1Ht[ipft] * (c2l - c1l)
+ log(pft$rho[ipft]) * (d2l - d1l)) * (1.0/log(dcrit))
pft$b2Bl.small [ipft] = C2B * b2l + c2l * pft$b2Ht[ipft] + aux
pft$b1Bl.large [ipft] = pft$b1Bl.small[ipft]
pft$b2Bl.large [ipft] = pft$b2Bl.small[ipft]
pft$bleaf.adult[ipft] = ( pft$b1Bl.large[ipft] / C2B
* pft$dbh.adult [ipft] ^ pft$b2Bl.large[ipft] )
}else if(iallom %in% c(2)){
pft$b1Bl.small [ipft] = C2B * exp(nleaf[1]) * pft$rho[ipft] / nleaf[3]
pft$b2Bl.small [ipft] = nleaf[2]
pft$b1Bl.large [ipft] = pft$b1Bl.small[ipft]
pft$b2Bl.large [ipft] = pft$b2Bl.small[ipft]
pft$bleaf.adult[ipft] = ( pft$b1Bl.large[ipft] / C2B
* pft$dbh.adult [ipft] ^ pft$b2Bl.large[ipft] )
}else if(iallom %in% c(3)){
#---------------------------------------------------------------------------------#
# Use Lescure et al. (1983) for large trees, assume minimum leaf biomass for #
# mid-successional to be 50gC/plant and interpolate biomass for saplings using a #
# log-linear function. #
#---------------------------------------------------------------------------------#
pft$b1Bl.large [ipft] = 0.00873 * pft$SLA[3] / pft$SLA[ipft] # * C2B
pft$b2Bl.large [ipft] = 2.1360
bleaf.sapling = 0.02 * C2B * pft$SLA[3] / pft$SLA[ipft]
pft$bleaf.adult[ipft] = ( pft$b1Bl.large[ipft] / C2B
* pft$dbh.adult [ipft] ^ pft$b2Bl.large[ipft] )
pft$b2Bl.small [ipft] = ( log(pft$bleaf.adult[ipft]/bleaf.sapling)
/ log(pft$dbh.adult[ipft]/pft$dbh.min[ipft]) )
pft$b1Bl.small [ipft] = ( pft$bleaf.adult[ipft] * C2B
/ pft$dbh.adult[ipft] ^ pft$b2Bl.small[ipft] )
}#end if
#------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------#
# Fill in the structural biomass parameters. #
#------------------------------------------------------------------------------------#
if (iallom %in% c(0)){
#---- ED-2.1 allometry. ----------------------------------------------------------#
pft$b1Bs.small[ipft] = exp(a1 + c1d * pft$b1Ht[ipft] + d1d * log(pft$rho[ipft]))
pft$b1Bs.large[ipft] = exp(a1 + c1d * log(pft$hgt.max[ipft])
+ d1d * log(pft$rho[ipft]))
aux = ( (a2d - a1) + pft$b1Ht[ipft] * (c2d - c1d)
+ log(pft$rho[ipft]) * (d2d - d1d) ) * (1.0/log(dcrit))
pft$b2Bs.small[ipft] = C2B * b2d + c2d * pft$b2Ht[ipft] + aux
aux = ( (a2d - a1) + log(pft$hgt.max[ipft]) * (c2d - c1d)
+ log(pft$rho[ipft]) * (d2d - d1d)) * (1.0/log(dcrit))
pft$b2Bs.large[ipft] = C2B * b2d + aux
}else if (iallom %in% c(1)){
#---- Based on modified Chave et al. (2001) allometry. ---------------------------#
pft$b1Bs.small[ipft] = C2B * exp(odead.small[1]) * pft$rho[ipft] / odead.small[3]
pft$b2Bs.small[ipft] = odead.small[2]
pft$b1Bs.large[ipft] = C2B * exp(odead.large[1]) * pft$rho[ipft] / odead.large[3]
pft$b2Bs.large[ipft] = odead.large[2]
}else if (iallom %in% c(2,3)){
#---- Based an alternative modification of Chave et al. (2001) allometry. --------#
pft$b1Bs.small[ipft] = C2B * exp(ndead.small[1]) * pft$rho[ipft] / ndead.small[3]
pft$b2Bs.small[ipft] = ndead.small[2]
pft$b1Bs.large[ipft] = C2B * exp(ndead.large[1]) * pft$rho[ipft] / ndead.large[3]
pft$b2Bs.large[ipft] = ndead.large[2]
}#end if
#------------------------------------------------------------------------------------#
pft$b1Bs.small[17] = 0.2749
pft$b1Bs.large[17] = pft$b1Bs.small[17]
pft$b2Bs.small[17] = 2.69373
pft$b2Bs.large[17] = pft$b2Bs.small[17]
pft$b1Bl.small[17] = pft$b1Bl.small[2]
pft$b2Bl.small[17] = pft$b2Bl.small[2]
pft$b1Bl.large[17] = 0.0856
pft$b2Bl.large[17] = 2.0
#------------------------------------------------------------------------------------#
# Replace the coefficients if we are going to use Poorter et al. (2006) #
# parameters for crown area. #
#------------------------------------------------------------------------------------#
if (iallom %in% c(0,1)){
pft$b1Ca[ipft] = exp(-1.853) * exp(pft$b1Ht[ipft]) ^ 1.888
pft$b2Ca[ipft] = pft$b2Ht[ipft] * 1.888
}else if (iallom %in% c(2,3)){
pft$b1Ca[ipft] = exp(ncrown.area[1])
pft$b2Ca[ipft] = ncrown.area[2]
}#end if
pft$b2Ca[17] = 1.26254364
#------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------#
# Replace the coefficients for WAI in case iallom is 3. #
# These numbers come from fitting Chambers et al. (2001) and Chambers et al. (2004) #
# allometries for stem area index. #
#------------------------------------------------------------------------------------#
if (iallom %in% c(3)){
pft$b1WAI[ipft] = 0.11 * pft$SLA[ipft] * pft$b1Bl.large[ipft]
pft$b2WAI[ipft] = pft$b2Bl.large[ipft]
}#end if
#------------------------------------------------------------------------------------#
}else{
pft$bleaf.adult[ipft] = ( pft$b1Bl.large[ipft] / C2B
* pft$dbh.adult [ipft] ^ pft$b2Bl.large[ipft] )
}#end if (pft$tropical[ipft])
#---------------------------------------------------------------------------------------#
}#end for (ipft in sequence(npft))
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# Rooting depth coefficients. #
#------------------------------------------------------------------------------------------#
pft$b1Rd = rep(NA,times=npft+1)
if (iallom %in% c(0)){
#----- Original ED-2.1 scheme, based on standing volume. -------------------------------#
pft$b1Rd[ 1:17] = NA
pft$b1Rd[ 1] = -0.700
pft$b1Rd[ 2:4] = -exp(0.545 * log(10.))
pft$b1Rd[ 5] = -0.700
pft$b1Rd[ 6:11] = -exp(0.545 * log(10.))
pft$b1Rd[12:16] = -0.700
pft$b1Rd[ 17] = -exp(0.545 * log(10.))
pft$b2Rd[ 1:17] = NA
pft$b2Rd[ 1] = 0.000
pft$b2Rd[ 2:4] = 0.277
pft$b2Rd[ 5] = 0.000
pft$b2Rd[ 6:11] = 0.277
pft$b2Rd[12:16] = 0.000
pft$b2Rd[ 17] = 0.277
}else if (iallom %in% c(1,2,3)){
#----- Simple allometry (0.5 m for seedlings, 5.0m for 35-m trees. ---------------------#
pft$b1Rd[1:17] = -1.1140580
pft$b2Rd[1:17] = 0.4223014
}#end if
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# Minimum bleaf and leaf area index that is resolvable. #
#------------------------------------------------------------------------------------------#
pft$bleaf.min = c(dbh2bl(dbh=pft$dbh.min[1:npft],ipft=1:npft),NA)
pft$lai.min = onesixth * pft$init.dens * pft$bleaf.min * pft$SLA
#------------------------------------------------------------------------------------------#
pft$dbh.min[c(2,3,4)]=10.0
pft$dbh.min[17]=2.0
#----- Make it global. --------------------------------------------------------------------#
pft <<- pft
#------------------------------------------------------------------------------------------#
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