Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

bug fix in N fixation #81

Merged
merged 1 commit into from
Oct 10, 2024
Merged

bug fix in N fixation #81

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
24 changes: 9 additions & 15 deletions src/Plankton/IronEnergyMode/growth_kernels.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ end

@kernel function calc_PS_kernel!(plank, nuts, p)
i = @index(Global)
@inbounds plank.PS[i] = calc_PS(nuts.par[i], plank.Bm[i], plank.CH[i], plank.Chl[i], plank.qFe[i], p)
@inbounds plank.PS[i] = calc_PS(nuts.par[i], plank.Bm[i], plank.CH[i], plank.Chl[i], plank.qFePS[i], p)
end
function calc_PS!(plank, nuts, p, arch::Architecture)
kernel! = calc_PS_kernel!(device(arch), 256, (size(plank.ac,1)))
Expand Down Expand Up @@ -113,8 +113,8 @@ end
end

##### calculate iron uptake rate (mmolFe/individual/second)
@inline function calc_Fe_uptake(FeT, qFe, Bm, CH, Sz, pop, p, ac, ΔT)
Qfe = qFe/max(1.0f-30, Bm +CH)
@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)
SA = p.SA * Sz^(2/3)
VFe = p.KSAFe * SA * FeT * regQFe * ac
Expand All @@ -129,7 +129,8 @@ end
plank.Bm[i], nuts.pop[i], p, plank.ac[i], ΔT)
@inbounds plank.VPO4[i] = calc_P_uptake(nuts.PO4[i], nuts.T[i], plank.CH[i], plank.qP[i],
plank.Bm[i], nuts.pop[i], p, plank.ac[i], ΔT)
@inbounds plank.VFe[i] = calc_Fe_uptake(nuts.FeT[i], plank.qFe[i], plank.Bm[i], plank.CH[i],
@inbounds plank.VFe[i] = calc_Fe_uptake(nuts.FeT[i], plank.qFe[i], plank.qFePS[i], plank.qFeNR[i],
plank.qFeNF[i], plank.Bm[i], plank.CH[i],
plank.Sz[i], nuts.pop[i], p, plank.ac[i], ΔT)
end
function calc_nuts_uptake!(plank, nuts, p, ΔT, arch::Architecture)
Expand Down Expand Up @@ -246,16 +247,9 @@ end

##### iron allocation
@inline function iron_alloc(par, dpar, qFe, qFePS, qFeNR, qFeNF, p, ΔT)
# photosynthesis - no-diaz + Crocosphaera
reg = shape_func_dec(par, p.Imax, 1.0f-2; pow = 4.0f0)
f_ST2PS_nd = p.k_Fe_ST2PS * reg * qFe * isless(0.0f0, dpar)
f_PS2ST_nd = p.k_Fe_PS2ST * qFePS * (reg * isless(dpar, 0.0f0) + isequal(0.0f0, par))
# photosynthesis - trichodesmium
f_ST2PS_tr = p.k_Fe_ST2PS * qFe * reg * isless(0.0f0, par)
f_PS2ST_tr = p.k_Fe_PS2ST * qFePS * ((1.0f0 - reg) * isless(0.0f0, par) + isequal(0.0f0, par))
# photosynthesis
f_ST2PS = f_ST2PS_nd * (p.is_nr + p.is_croc) + f_ST2PS_tr * p.is_tric
f_PS2ST = f_PS2ST_nd * (p.is_nr + p.is_croc) + f_PS2ST_tr * p.is_tric
f_ST2PS = p.k_Fe_ST2PS * qFe * isless(0.0f0, dpar)
f_PS2ST = p.k_Fe_PS2ST * qFePS * (isless(dpar, 0.0f0) + isequal(0.0f0, par))

# nitrate reduction
f_ST2NR = p.k_Fe_ST2NR * qFe * isequal(0.0f0, par) * p.is_nr
Expand All @@ -265,8 +259,8 @@ end
f_ST2NF_cr = p.k_Fe_ST2NF * qFe * isequal(0.0f0, par)
f_NF2ST_cr = p.k_Fe_NF2ST * qFeNF * isless(0.0f0, par)
# nitrogen fixation - Trichodesmium
f_ST2NF_tr = p.k_Fe_ST2NF * qFe * (1.0f0 - reg)
f_NF2ST_tr = p.k_Fe_NF2ST * qFeNF * reg
f_ST2NF_tr = p.k_Fe_ST2NF * qFe * isless(0.0f0, dpar)
f_NF2ST_tr = p.k_Fe_NF2ST * qFeNF * (isless(dpar, 0.0f0) + isequal(0.0f0, par))
# nitrogen fixation
f_ST2NF = f_ST2NF_cr * p.is_croc + f_ST2NF_tr * p.is_tric
f_NF2ST = f_NF2ST_cr * p.is_croc + f_NF2ST_tr * p.is_tric
Expand Down
Loading