Skip to content

Commit

Permalink
fix respiration
Browse files Browse the repository at this point in the history
  • Loading branch information
@zhenwu0728
zhenwu0728 committed Nov 14, 2024
1 parent 490269e commit 2cf3edb
Showing 1 changed file with 37 additions and 42 deletions.
79 changes: 37 additions & 42 deletions src/Plankton/IronEnergyMode/growth_kernels.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -36,17 +36,15 @@ function calc_PS!(plank, nuts, p, arch::Architecture)
end

##### calculate respiration (mmolC/individual/second)
@inline function calc_respir(CH, En, T, p, ac, ΔT)
reg = shape_func_dec_alt(En, p.Enmax * p.Nsuper, 1.0f-2)
RS = max(0.0f0, CH) * reg * p.k_rs * tempFunc(T, p) * ac
@inline function calc_respir(CH, Bm, T, p, ac, ΔT)
RS = Bm * p.k_rs * tempFunc(T, p) * ac
RS = min(RS, CH/ΔT) # double check CH is not over consumed
ERS = RS * p.e_rs * ac
return RS, ERS
end

@kernel function calc_respiration_kernel!(plank, nuts, p, ΔT)
i = @index(Global)
@inbounds plank.RS[i], plank.ERS[i] = calc_respir(plank.CH[i], plank.En[i],
@inbounds plank.RS[i], plank.ERS[i] = calc_respir(plank.CH[i], plank.Bm[i],
nuts.T[i], p, plank.ac[i], ΔT)
end
function calc_repiration!(plank, nuts, p, ΔT, arch::Architecture)
Expand All @@ -68,24 +66,22 @@ function update_state_1!(plank, ΔT, arch::Architecture)
end

##### calculate carbon fixation rate (mmolC/individual/second)
@inline function calc_CF(En, CH, Bm, temp, p, ac, ΔT)
@inline function calc_CF(En, CH, Bm, T, p, ac)
Qc = CH/max(1.0f-30, Bm + CH)
regQC = shape_func_dec(Qc, p.CHmax, 1.0f-4)
regEn = shape_func_inc_alt(En, p.Enmax * p.Nsuper, 1.0f-4)
CF = p.k_cf * regQC * regEn * tempFunc_PS(temp, p) * Bm * ac
CF = min(CF, En/p.e_cf/ΔT)
regQC = shape_func_dec(Qc, p.CHmax, 1.0f-4, pow = 2.0f0)
regEn = shape_func_inc_alt(En, p.Enmax * p.Nsuper, 1.0f-2, pow = 2.0f0)
CF = p.k_cf * regQC * regEn * tempFunc_PS(T, p) * Bm * ac
ECF = CF * p.e_cf * ac
return CF, ECF
end

@kernel function calc_carbon_fixation_kernel!(plank, nuts, p, ΔT)
@kernel function calc_carbon_fixation_kernel!(plank, nuts, p)
i = @index(Global)
@inbounds plank.CF[i], plank.ECF[i] = calc_CF(plank.En[i], plank.CH[i], plank.Bm[i],
nuts.T[i], p, plank.ac[i], ΔT)
nuts.T[i], p, plank.ac[i])
end
function calc_carbon_fixation!(plank, nuts, p, ΔT, arch::Architecture)
function calc_carbon_fixation!(plank, nuts, p, arch::Architecture)
kernel! = calc_carbon_fixation_kernel!(device(arch), 256, (size(plank.ac,1)))
kernel!(plank, nuts, p, ΔT)
kernel!(plank, nuts, p)
return nothing
end

Expand Down Expand Up @@ -115,8 +111,8 @@ end

##### calculate iron uptake rate (mmolFe/individual/second)
@inline function calc_Fe_uptake(FeT, qFe, qFePS, qFeNR, qFeNF, Bm, CH, Sz, pop, p, ac, ΔT)
Qfe = (qFe + qFePS + qFeNF + qFeNR)/max(1.0f-30, Bm +CH)
regQFe = shape_func_dec(Qfe, p.qFemax, 1.0f-4)
Qfe = (qFe + qFePS + qFeNF + qFeNR)/max(1.0f-30, Bm + CH)
regQFe = shape_func_dec(Qfe, p.qFemax, 1.0f-4, pow = 2.0f0)
SA = p.SA * Sz^(2/3)
VFe = p.KSAFe * SA * FeT * regQFe * ac
return min(VFe, FeT/ΔT/max(1.0f0,pop))
Expand Down Expand Up @@ -157,50 +153,49 @@ function update_state_2!(plank, ΔT, arch::Architecture)
end

##### nitrate reduction (mmolN/individual/second)
@inline function calc_NO3_reduction(En, qNO3, qNH4, qFeNR, Bm, CH, p, ac, ΔT)
@inline function calc_NR(En, qNO3, qNH4, qFeNR, Bm, CH, T, p, ac, ΔT)
Qn = qNH4/max(1.0f-30, Bm + CH)
reg = shape_func_dec(Qn, p.qNH4max, 1.0f-4)
reg = shape_func_dec(Qn, p.qNH4max, 1.0f-4, pow = 2.0f0)
Qfe_NR = qFeNR / max(1.0f-30, Bm + CH)
regEn = shape_func_inc_alt(En, p.Enmax * p.Nsuper, 1.0f-4)
NR = p.k_nr * reg * regEn * qNO3 * Qfe_NR / max(1.0f-30, Qfe_NR + p.KfeNR) * ac
regEn = shape_func_inc_alt(En, p.Enmax * p.Nsuper, 1.0f-3, pow = 2.0f0)
Ksat = Qfe_NR / max(1.0f-30, Qfe_NR + p.KfeNR)
NR = p.k_nr * reg * regEn * qNO3 * Ksat * tempFunc(T, p) * ac
NR = min(NR, qNO3/ΔT) # double check qNO3 are not over consumed
ENR = NR * p.e_nr * ac
return NR * p.is_nr, ENR * p.is_nr
end

@kernel function calc_NO3_reduc_kernel!(plank, p, ΔT)
@kernel function calc_NO3_reduction_kernel!(plank, nuts, p, ΔT)
i = @index(Global)
@inbounds plank.NR[i], plank.ENR[i] = calc_NO3_reduction(plank.En[i], plank.qNO3[i], plank.qNH4[i],
plank.qFeNR[i], plank.Bm[i], plank.CH[i],
p, plank.ac[i], ΔT)
@inbounds plank.NR[i], plank.ENR[i] = calc_NR(plank.En[i], plank.qNO3[i], plank.qNH4[i],
plank.qFeNR[i], plank.Bm[i], plank.CH[i],
nuts.T[i], p, plank.ac[i], ΔT)
end
function calc_NO3_reduc!(plank, p, ΔT, arch::Architecture)
kernel! = calc_NO3_reduc_kernel!(device(arch), 256, (size(plank.ac,1)))
kernel!(plank, p, ΔT)
function calc_NO3_reduction!(plank, nuts, p, ΔT, arch::Architecture)
kernel! = calc_NO3_reduction_kernel!(device(arch), 256, (size(plank.ac,1)))
kernel!(plank, nuts, p, ΔT)
return nothing
end

##### nitrogen fixation (mmolN/individual/second)
@inline function calc_Nfixation(En, qNH4, qFeNF, Bm, CH, p, ac, ΔT)
@inline function calc_NF(En, qNH4, qFeNF, Bm, CH, T, p, ac)
Qn = qNH4/max(1.0f-30, Bm + CH)
reg = shape_func_dec(Qn, p.qNH4max, 1.0f-4)
reg = shape_func_dec(Qn, p.qNH4max, 1.0f-4, pow = 2.0f0)
Qfe_NF = qFeNF / max(1.0f-30, Bm + CH)
regEn = shape_func_inc_alt(En, p.Enmax * p.Nsuper, 1.0f-4)
NF = p.k_nf * reg * regEn * Qfe_NF / max(1.0f-30, Qfe_NF + p.KfeNF) * Bm * ac
NF = min(NF, En/p.e_nf/ΔT)
regEn = shape_func_inc_alt(En, p.Enmax * p.Nsuper, 1.0f-3, pow = 2.0f0)
Ksat = Qfe_NF / max(1.0f-30, Qfe_NF + p.KfeNF)
NF = p.k_nf * reg * regEn * Ksat * tempFunc(T, p) * Bm * ac
ENF = NF * p.e_nf * ac
return NF * (p.is_croc + p.is_tric), ENF * (p.is_croc + p.is_tric)
end

@kernel function calc_Nfix_kernel!(plank, p, ΔT)
@kernel function calc_nitrogen_fixation_kernel!(plank, nuts, p)
i = @index(Global)
@inbounds plank.NF[i], plank.ENF[i] = calc_Nfixation(plank.En[i], plank.qNH4[i],
plank.qFeNF[i], plank.Bm[i], plank.CH[i],
p, plank.ac[i], ΔT)
@inbounds plank.NF[i], plank.ENF[i] = calc_NF(plank.En[i], plank.qNH4[i],
plank.qFeNF[i], plank.Bm[i], plank.CH[i],
nuts.T[i], p, plank.ac[i])
end
function calc_Nfix!(plank, p, ΔT, arch::Architecture)
kernel! = calc_Nfix_kernel!(device(arch), 256, (size(plank.ac,1)))
kernel!(plank, p, ΔT)
function calc_nitrogen_fixation!(plank, nuts, p, arch::Architecture)
kernel! = calc_nitrogen_fixation_kernel!(device(arch), 256, (size(plank.ac,1)))
kernel!(plank, nuts, p)
return nothing
end

Expand Down

0 comments on commit 2cf3edb

Please sign in to comment.