bug fix & remove unused parameters

JuliaOcean · May 14, 2024 · a188468 · a188468
1 parent 548136e
commit a188468
Show file tree

Hide file tree

Showing 3 changed files with 11 additions and 16 deletions.
diff --git a/src/Parameters/param_default.jl b/src/Parameters/param_default.jl
@@ -106,11 +106,8 @@ function phyt_params_default(N::Int64, mode::MacroMolecularMode)
         "KsatPO4"  => [0.003],   # Half-saturation coeff (mmol P/m³)
         "KsatDOC"  => [0.0],     # Half-saturation coeff (mmol C/m³)
         "NSTmax"   => [0.12],    # Maximum N reserve in total N (mmol N/mmol N)
-        "NSTmin"   => [0.01],    # Minimum N reserve in total N (mmol N/mmol N)
         "PSTmax"   => [0.70],    # Maximum P reserve in total P (mmol P/mmol P)
-        "PSTmin"   => [0.40],    # Minimum P reserve in total P (mmol P/mmol P)
         "CHmax"    => [0.4],     # Maximum Carbohydrate in cell (mmol C/mmol C)
-        "CHmin"    => [0.1],     # Minimum Carbohydrate in cell (mmol C/mmol C)
         "respir"   => [1.2e-6],  # Respiration rate(per second)
         "k_pro"    => [6.0e-5],  # Protein synthesis rate (mmol C/mmol C/second)
         "k_sat_pro"=> [4.5e-13], # Hafl saturation constent for protein synthesis (mmol C/cell)
@@ -168,12 +165,9 @@ function phyt_params_default(N::Int64, mode::QuotaMode)
         "KsatNO3"  => [0.010],   # Half-saturation coeff (mmol N/m³)
         "KsatPO4"  => [0.003],   # Half-saturation coeff (mmol P/m³)
         "KsatDOC"  => [0.0],     # Half-saturation coeff (mmol C/m³)
-        "Nqmax"    => [0.12],    # Maximum N quota in cell (mmol N/mmol C)
-        "Nqmin"    => [0.05],    # Minimum N quota in cell (mmol N/mmol C)
-        "Pqmax"    => [0.01],    # Maximum P quota in cell (mmol P/mmol C)
-        "Pqmin"    => [0.004],   # Minimum P quota in cell (mmol P/mmol C)
+        "Nqmax"    => [0.25],    # Maximum N quota in cell (mmol N/mmol C)
+        "Pqmax"    => [0.02],    # Maximum P quota in cell (mmol P/mmol C)
         "Cqmax"    => [0.4],     # Maximum C quota in cell (mmol C/mmol C)
-        "Cqmin"    => [0.1],     # Minimum C quota in cell (mmol C/mmol C)
         "k_mtb"    => [3.5e-5],  # Metabolic rate (per second)
         "respir"   => [1.2e-6],  # Respiration rate(per second)
         "Chl2N"    => [3.0],     # Maximum Chla:N ratio in phytoplankton

diff --git a/src/Plankton/MacroMolecularMode/plankton_generation.jl b/src/Plankton/MacroMolecularMode/plankton_generation.jl
@@ -16,7 +16,7 @@ function construct_plankton(arch::Architecture, sp::Int, params::Dict, maxN::Int
     param_names=(:Nsuper, :C_DNA, :var, :PRO2DNA, :RNA2DNA, :CH2DNA, :Chl2DNA,
                  :α, :Φ, :Topt, :Tmax, :Ea,
                  :PCmax, :VDOCmax, :VNO3max, :VNH4max, :VPO4max, :KsatDOC, :KsatNH4, :KsatNO3,
-                 :KsatPO4, :CHmax, :CHmin, :NSTmax, :NSTmin, :PSTmax, :PSTmin,
+                 :KsatPO4, :CHmax, :NSTmax, :PSTmax,
                  :Chl2N, :R_NC_PRO, :R_NC_DNA, :R_NC_RNA, :R_PC_DNA, :R_PC_RNA, :respir,
                  :k_pro, :k_sat_pro, :k_rna, :k_sat_rna, :k_dna, :k_sat_dna, 
                  :dvid_P, :grz_P, :mort_P, :mort_reg, :grazFracC, :grazFracN, :grazFracP,

diff --git a/src/Plankton/QuotaMode/plankton_generation.jl b/src/Plankton/QuotaMode/plankton_generation.jl
@@ -14,7 +14,7 @@ function construct_plankton(arch::Architecture, sp::Int, params::Dict, maxN::Int
 
     param_names=(:Nsuper, :Cquota, :mean, :var, :Chl2Cint, :α, :Φ, :Topt, :Tmax, :Ea,
                  :PCmax, :VDOCmax, :VNO3max, :VNH4max, :VPO4max,
-                 :KsatDOC, :KsatNH4, :KsatNO3, :KsatPO4, :Cqmax, :Cqmin, :Nqmax, :Nqmin, :Pqmax, :Pqmin,
+                 :KsatDOC, :KsatNH4, :KsatNO3, :KsatPO4, :Cqmax, :Nqmax, :Pqmax,
                  :Chl2N, :R_NC, :R_PC, :k_mtb, :respir, :grz_P, :dvid_type, :dvid_P, :dvid_reg, :dvid_reg2,
                  :mort_P, :mort_reg, :grazFracC, :grazFracN, :grazFracP, :mortFracC, :mortFracN, :mortFracP, :ther_mort)
 
@@ -37,11 +37,10 @@ function generate_plankton!(plank, N::Int, g::AbstractGrid, arch::Architecture)
     Cquota = plank.p.Cquota
     Nsuper = plank.p.Nsuper
     cqmax = plank.p.Cqmax
-    cqmin = plank.p.Cqmin
     nqmax = plank.p.Nqmax
-    nqmin = plank.p.Nqmin
     pqmax = plank.p.Pqmax
-    pqmin = plank.p.Pqmin
+    R_NC = plank.p.R_NC
+    R_PC = plank.p.R_PC
     Chl2Cint = plank.p.Chl2Cint
 
     plank.data.ac[1:N]  .= 1.0f0                                                      # activity
@@ -62,9 +61,11 @@ function generate_plankton!(plank, N::Int, g::AbstractGrid, arch::Architecture)
     plank.data.iS  .= max.(1.0f0, plank.data.iS .* var .+ mean) .* plank.data.ac      # init_size
     plank.data.Sz  .= copy(plank.data.iS)                                             # size
     plank.data.Bm  .= Cquota .* plank.data.Sz .* Nsuper                               # Bm
-    plank.data.Cq  .=(plank.data.Cq .* (cqmax - cqmin)  .+ cqmin) .* plank.data.Bm    # Cq
-    plank.data.Nq  .=(plank.data.Nq .* (nqmax - nqmin)  .+ nqmin) .* plank.data.Bm    # Nq
-    plank.data.Pq  .=(plank.data.Pq .* (pqmax - pqmin)  .+ pqmin) .* plank.data.Bm    # Pq
+    plank.data.Cq  .=plank.data.Cq .* cqmax .* plank.data.Bm                          # Cq
+    plank.data.Nq  .=plank.data.Nq .* (nqmax .* (plank.data.Bm .+ plank.data.Cq) .- 
+                                        plank.data.Bm .* R_NC)                        # Nq
+    plank.data.Pq  .=plank.data.Pq .* (pqmax .* (plank.data.Bm .+ plank.data.Cq) .- 
+                                        plank.data.Bm .* R_PC)                        # Nq
     plank.data.Chl .= plank.data.Bm .* Chl2Cint                                       # Chl
 
     mask_individuals!(plank.data, g, N, arch)