add Bacteria in CarbonMode (#85)

Add bacteria in CarbonMode, which light is not required for growth.

Author: zhenwu0728

src/Parameters/param_default.jl

@@ -300,6 +300,7 @@ function phyt_params_default(N::Int64, mode::CarbonMode)
         "grazFracC" => [0.7],     # Fraction goes into dissolved organic pool
         "mortFracC" => [0.5],     # Fraction goes into dissolved organic pool
         "thermal"   => [1.0],     # thermal damage, 1 for on, 0 for off
+        "is_bact"   => [0.0],     # is this specis bacteria or not, 1 for bacteria, 0 for phytoplankton
     )
 
     if N == 1

src/Plankton/CarbonMode/growth_kernels.jl

@@ -28,12 +28,9 @@ end
 ##### calculate photosynthesis rate (mmolC/individual/second)
 @inline function calc_photosynthesis(par, T, Chl, Bm, Bd, p)
     αI  = par * p.α * p.Φ
-    if p.thermal == 1.0f0
-        PCm = p.PCmax * tempFunc(T, p)
-    else
-        PCm = p.PCmax * tempFunc_PS(T, p)
-    end
-    PS  = PCm * (1.0f0 - exp(-αI / max(1.0f-30, PCm) * Chl / max(1.0f-30, Bm))) * max(0.0f0, Bm - Bd)
+    PCm = p.PCmax * (tempFunc(temp, p) * p.thermal + tempFunc_PS(temp, p) * (1.0f0 - p.thermal))
+    light_limit = 1.0f0 - exp(-αI / max(1.0f-30, PCm) * Chl / max(1.0f-30, Bm))
+    PS  = PCm * max(0.0f0, Bm - Bd) * (light_limit * (1.0f0 - p.is_bact) + p.is_bact)
     return PS
 end
 

src/Plankton/CarbonMode/plankton_generation.jl

@@ -12,7 +12,8 @@ function construct_plankton(arch::Architecture, sp::Int, params::Dict, maxN::Int
     data = replace_storage(array_type(arch), rawdata)
 
     param_names=(:Nsuper, :Cquota, :mean, :var, :α, :Φ, :Topt, :Tmax, :Ea, :PCmax, :Chl2C, :respir, :f_T2B,
-                 :grz_P, :dvid_type, :dvid_P, :dvid_reg, :dvid_reg2, :mort_P, :mort_reg, :grazFracC, :mortFracC, :thermal)
+                 :grz_P, :dvid_type, :dvid_P, :dvid_reg, :dvid_reg2, :mort_P, :mort_reg, :grazFracC, :mortFracC,
+                 :thermal, :is_bact)
 
     pkeys = collect(keys(params))
     tmp = zeros(length(param_names))