diff --git a/Plant.jl b/Plant.jl
index 9c3aea8910ac1947c74b6e60104cf256993554a4..0e1da152c2e9e470d752a2e794b4f81e48fdbc30 100644
--- a/Plant.jl
+++ b/Plant.jl
@@ -65,76 +65,52 @@ module Plant
abstract type PhotosynthesisOrgan <: GrowingOrgan end # Organs that can photosynthesize
@with_kw mutable struct OrganInfo
- BB::BranchBase
- Species::Int64
- PlantNumber::Int64
- Order::Int64
+ BB::BranchBase # Every organ belongs to a specific branch which has a branch base object that stores variables of that branch
+ Species::Int64 # Species number to which organ belongs
+ PlantNumber::Int64 # Plant number to which organ belongs
+ Order::Int64 # Order, nr of branches removed from main stem (0: main stem)
- Age::Int64 = 0
- AgeDD::Float64 = 0.0
+ Age::Int64 = 0 # Age in days
+ AgeDD::Float64 = 0.0 # Age in degree days
end
@with_kw mutable struct GrowthVars
- PotentialBiomass::Float64
- GrowthDuration::Float64
- MaxGrowthAge::Float64
- GrowthRespiration::Float64
- MaxSinkStrength::Float64
-
- Biomass::Float64 = 0.0
- Growth::Float64 = 0.0
- SinkStrength::Float64 = 0.0
- AssimilatesAvailable::Float64 = 0.0
- AssimilatesAllocated::Float64 = 0.0
- Area::Float64 = 0.0
+ PotentialBiomass::Float64 # Potential maximum biomass of organ
+ GrowthDuration::Float64 # Duration of organ growth (days)
+ MaxGrowthAge::Float64 # Age of organ at which organ growth is highest
+ GrowthRespiration::Float64 # Growth respiration of organ (fraction of biomass)
+ MaxSinkStrength::Float64 # Maximum possible sink strength of organ
+
+ Biomass::Float64 = 0.0 # Biomass of organ (g)
+ Growth::Float64 = 0.0 # Growth rate of organ at current time point
+ SinkStrength::Float64 = 0.0 # Sink strength of organ at current time point
+ AssimilatesAvailable::Float64 = 0.0 # Amount of assimilates that are available for organ growth at this time step (mg)
+ AssimilatesAllocated::Float64 = 0.0 # Amount of assimilates that are allocated for organ growth at this time step (mg)
+ Area::Float64 = 0.0 # Area of organ
end
@with_kw mutable struct PhotosynthesisVars
- Assimilated::Float64 = 0.0
+ Assimilated::Float64 = 0.0 # Amount of CO2 acquired at current time point (mol CO2)
end
# Define internode
@with_kw mutable struct Internode <: PhotosynthesisOrgan
- OI::OrganInfo
- GV::GrowthVars
- PV::PhotosynthesisVars
- #BB::BranchBase # Every internode belongs to a specific branch which has a branch base object that stores variables of that branch
- #Species::Int64 # Species number to which internode belongs
- #PlantNumber::Int64 # Plant number to which internode belongs
- #Order::Int64 # Order of internode, nr of branches removed from main stem (0: main stem)
+ OI::OrganInfo # Object containing general organ information
+ GV::GrowthVars # Object containing growth variables
+ PV::PhotosynthesisVars # Object containing photosynthesis variables
SIL::Float64 # Specific internode length: ratio of internode length per biomass (mm/mg) // Parameter
- #PotentialBiomass::Float64 # Potential maximum biomass of internode // Parameter
- #GrowthDuration::Float64 # Duration of internode growth (days) // Parameter
- #MaxGrowthAge::Float64 # Age of internode at which internode growth is highest // Parameter
- #GrowthRespiration::Float64 # Growth respiration of internode (fraction of biomass) // Parameter
- #MaxSinkStrength::Float64 # Maximum possible sink strength of internode
-
- #Age::Int64 = 0 # Age of internode in days
- #AgeDD::Float64 = 0.0 # Age of internode in degree days
+
Length::Float64 = 0.0 # Length of internode
- Width::Float64 = 0.0 # Width of internode
- #Biomass::Float64 = 0.0 # Biomass of internode (g)
- #Growth::Float64 = 0.0 # Growth rate of internode at current time point
- #SinkStrength::Float64 = 0.0 # Sink strength of internode at current time point
- #AssimilatesAvailable::Float64 = 0.0 # Amount of assimilates that are available for internode growth at this time step (mg)
- #AssimilatesAllocated::Float64 = 0.0 # Amount of assimilates that are allocated for internode growth at this time step (mg)
- #Area::Float64 = 0.0 # Area of internode
- #Assimilated::Float64 = 0.0 # Amount of CO2 acquired at current time point (mol CO2)
+ Width::Float64 = 0.0 # Width of internode
end
# Define meristem, the organ that is the source of phytomer creation
@with_kw mutable struct Meristem <: Organ
- OI::OrganInfo
- #BB::BranchBase # Every meristem belongs to a specific branch which has a branch base object that stores variables of that branch
- #Species::Int64 # Species number to which meristem belongs
- #PlantNumber::Int64 # Plant number to which meristem belongs
+ OI::OrganInfo # Object containing general organ information
Phyllotaxis::Float64 # Phyllotaxis for phytomer construction (degrees) // Parameter
- #Order::Int64 # Order of meristem, nr of branches removed from main stem (0: main stem)
Rank::Int64 # Phytomer rank of meristem
ParentRank::Int64 = 0 # Rank of parent phytomer
- #Age::Int64 = 0 # Age of meristem in days
- #AgeDD::Float64 = 0.0 # Age of meristem in degree days
Dormant::Bool = true # Whether the meristem can develop
Dominance::Float64 = 0.0 # Dominance of the meristem, deciding factor in branching
PhytomerNumber::Int64 = 0 # Number of phytomers from meristem to base
@@ -142,30 +118,12 @@ module Plant
# Define leaf
@with_kw mutable struct Leaf <: PhotosynthesisOrgan
- OI::OrganInfo
- GV::GrowthVars
- PV::PhotosynthesisVars
- #BB::BranchBase # Every leaf belongs to a specific branch which has a branch base object that stores variables of that branch
- #Species::Int64 # Species number to which leaf belongs
- #PlantNumber::Int64 # Plant number to which leaf belongs
- #Order::Int64 # Order of leaf, nr of branches removed from main stem (0: main stem)
+ OI::OrganInfo # Object containing general organ information
+ GV::GrowthVars # Object containing growth variables
+ PV::PhotosynthesisVars # Object containing photosynthesis variables
Angle::Float64 # Angle of leaf insertion at phytomer construction // Parameter?
- #PotentialBiomass::Float64 # Potential maximum biomass of leaf // Parameter
- #GrowthDuration::Float64 # Duration of leaf growth (days) // Parameter
- #MaxGrowthAge::Float64 # Age of leaf at which leaf growth is highest // Parameter
- #GrowthRespiration::Float64 # Growth respiration of leaf (fraction of biomass) // Parameter
- #MaxSinkStrength::Float64 # Maximum possible sink strength of leaf
-
- #Age::Int64 = 0 # Age of leaf in days
- #AgeDD::Float64 = 0.0 # Age of leaf in degree days
+
Size::Float64 = 0.0 # Size of leaf
- #Biomass::Float64 = 0.0 # Biomass of leaf (g)
- #Growth::Float64 = 0.0 # Growth rate of leaf at current time point
- #SinkStrength::Float64 = 0.0 # Sink strength of leaf at current time point
- #AssimilatesAvailable::Float64 = 0.0 # Amount of assimilates that are available for leaf growth at this time step (mg)
- #AssimilatesAllocated::Float64 = 0.0 # Amount of assimilates that are allocated for leaf growth at this time step (mg)
- #Area::Float64 = 0.0 # Area of leaf
- #Assimilated::Float64 = 0.0 # Amount of CO2 acquired at current time point (mol CO2)
end
@with_kw mutable struct Seed <: VPL.Node
@@ -174,12 +132,7 @@ module Plant
Endosperm::Float64 # Biomass in seed (mg)
end
- ##
- ##
- ## TRY MACROS. SEE BOOKMARK
- ##
- ##
-
+ # Add methods for getproperty function such that the composite fields can be accessed directly
function Base.getproperty(O::Organ, S::Symbol)
if hasfield(OrganInfo, S)
return getfield(O.OI, S)
@@ -192,22 +145,6 @@ module Plant
end
end
- #=function Base.getproperty(GO::GrowingOrgan, S::Symbol)
- if hasfield(GrowthVars, S)
- return getfield(GO.GV, S)
- else
- return getfield(GO, S)
- end
- end
-
- function Base.getproperty(PO::PhotosynthesisOrgan, S::Symbol)
- if hasfield(PhotosynthesisVars, S)
- return getfield(PO.PV, S)
- else
- return getfield(PO, S)
- end
- end
- =#
function Base.setproperty!(O::Organ, S::Symbol, X)
if hasfield(OrganInfo, S)
return setfield!(O.OI, S, X)
@@ -220,23 +157,6 @@ module Plant
end
end
- #=function Base.setproperty!(GO::GrowingOrgan, S::Symbol, X)
- if hasfield(GrowthVars, S)
- return setfield!(GO.GV, S, X)
- else
- return setfield!(GO, S, X)
- end
- end
-
- function Base.setproperty!(PO::PhotosynthesisOrgan, S::Symbol, X)
- if hasfield(PhotosynthesisVars, S)
- return setfield!(PO.PV, S, X)
- else
- return setfield!(PO, S, X)
- end
- end
- =#
-
# Define organ creation functions
function createInternode(MR, BB, Order)
Species = data(MR).Species
@@ -332,10 +252,10 @@ module Plant
Leaves = apply(Plant, getLeaf)
SourceStrength::Float64 = 0.0
if length(Internodes) > 0
- SourceStrength += sum([x.SinkStrength for x in Internodes])
+ SourceStrength += sum([x.Assimilated for x in Internodes])
end
if length(Leaves) > 0
- SourceStrength += sum([x.SinkStrength for x in Leaves])
+ SourceStrength += sum([x.Assimilated for x in Leaves])
end
PB.Substrates = max(((SourceStrength * MassCO2 * 0.001) - (PB.Respiration * PB.Biomass)) * ConversionCO2 + PB.ReservePool, 0)
if length(Internodes) + length(Leaves) > 0