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fix to prevent overly efficient iron uptake/scavenging and early onset of aggregation/sinking in warm water #101

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Oct 31, 2024
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fix to prevent overly efficient iron uptake/scavenging and early onset of aggregation/sinking in warm water #101

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e46d29d
fix to prevent overly efficient iron uptake/scavenging and early onse…
charliestock Oct 7, 2024
2b29556
added growth > 0 condition for iron uptake
charliestock Oct 21, 2024
9468189
change default frac_mu_stress from 0.25 to 0.4
charliestock Oct 30, 2024
16d5688
Update reference answer
yichengt900 Oct 30, 2024
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16 changes: 8 additions & 8 deletions .github/ref/OM4.single_column.COBALT.p4/docker-linux-gnu/ocean.stats
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
Step, Day, Truncs, Energy/Mass, Maximum CFL, Mean Sea Level, Total Mass, Mean Salin, Mean Temp, Frac Mass Err, Salin Err, Temp Err
[days] [m2 s-2] [Nondim] [m] [kg] [PSU] [degC] [Nondim] [PSU] [degC]
0, 731595.000, 0, En 0.0000000000000000E+00, CFL 0.00000, SL -0.0000E+00, M 6.97073E+15, S 35.2427, T 6.2462, Me 0.00E+00, Se 0.00E+00, Te 0.00E+00
6, 731595.250, 0, En 1.9430731566557828E-06, CFL 0.00273, SL -1.0976E-03, M 6.97073E+15, S 35.2427, T 6.2460, Me -8.57E-10, Se -2.86E-07, Te -2.66E-06
12, 731595.500, 0, En 4.1720928837009248E-06, CFL 0.00286, SL -2.1342E-03, M 6.97073E+15, S 35.2427, T 6.2457, Me -7.46E-10, Se -6.81E-07, Te -6.81E-06
18, 731595.750, 0, En 1.1711233584828893E-05, CFL 0.00771, SL -3.2696E-03, M 6.97073E+15, S 35.2427, T 6.2459, Me -7.01E-10, Se -9.90E-07, Te -1.00E-05
24, 731596.000, 0, En 2.3222260224258834E-05, CFL 0.00834, SL -4.4878E-03, M 6.97072E+15, S 35.2427, T 6.2457, Me -1.14E-09, Se -1.40E-06, Te -1.42E-05
30, 731596.250, 0, En 2.8141564688335571E-05, CFL 0.00697, SL -5.5233E-03, M 6.97072E+15, S 35.2428, T 6.2454, Me -1.17E-09, Se -1.93E-06, Te -1.96E-05
36, 731596.500, 0, En 3.5463133196222812E-05, CFL 0.00719, SL -6.4934E-03, M 6.97072E+15, S 35.2428, T 6.2451, Me -1.19E-09, Se -2.38E-06, Te -2.42E-05
42, 731596.750, 0, En 4.0871903202982405E-05, CFL 0.00769, SL -7.1812E-03, M 6.97072E+15, S 35.2428, T 6.2453, Me -1.11E-09, Se -2.80E-06, Te -2.86E-05
48, 731597.000, 0, En 4.6240478947958968E-05, CFL 0.00900, SL -7.7400E-03, M 6.97072E+15, S 35.2428, T 6.2453, Me -8.74E-10, Se -3.06E-06, Te -3.14E-05
6, 731595.250, 0, En 1.9430731566546388E-06, CFL 0.00273, SL -1.0976E-03, M 6.97073E+15, S 35.2427, T 6.2460, Me -8.57E-10, Se -2.86E-07, Te -2.66E-06
12, 731595.500, 0, En 4.1720467725151035E-06, CFL 0.00286, SL -2.1342E-03, M 6.97073E+15, S 35.2427, T 6.2457, Me -7.46E-10, Se -6.81E-07, Te -6.81E-06
18, 731595.750, 0, En 1.1685557354771320E-05, CFL 0.00769, SL -3.2696E-03, M 6.97073E+15, S 35.2427, T 6.2459, Me -7.01E-10, Se -9.90E-07, Te -1.00E-05
24, 731596.000, 0, En 2.3175399507961748E-05, CFL 0.00833, SL -4.4877E-03, M 6.97072E+15, S 35.2427, T 6.2457, Me -1.14E-09, Se -1.40E-06, Te -1.42E-05
30, 731596.250, 0, En 2.8121131207009207E-05, CFL 0.00696, SL -5.5232E-03, M 6.97072E+15, S 35.2428, T 6.2454, Me -1.17E-09, Se -1.93E-06, Te -1.96E-05
36, 731596.500, 0, En 3.5453054955347525E-05, CFL 0.00719, SL -6.4933E-03, M 6.97072E+15, S 35.2428, T 6.2451, Me -1.19E-09, Se -2.38E-06, Te -2.42E-05
42, 731596.750, 0, En 4.0859910168740299E-05, CFL 0.00767, SL -7.1811E-03, M 6.97072E+15, S 35.2428, T 6.2453, Me -1.11E-09, Se -2.80E-06, Te -2.86E-05
48, 731597.000, 0, En 4.6183029943438057E-05, CFL 0.00894, SL -7.7396E-03, M 6.97072E+15, S 35.2428, T 6.2453, Me -8.74E-10, Se -3.06E-06, Te -3.14E-05
21 changes: 12 additions & 9 deletions generic_tracers/generic_COBALT.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -906,20 +906,20 @@ subroutine user_add_params(param_file)
! Phytoplankton mortality terms differ by whether they are density-dependent (i.e., linear versus quadratic),
! temperature-dependent, and whether they vary depending on the condition (or stress) of the phytoplankton. The
! level of stress is defined based on the achieved growth rate relative to the maximum growth rate. By default,
! stress-dependent mortality begins to increase from 0 when this ratio falls below 0.25 (frac_mu_stress = 0.25).
! stress-dependent mortality begins to increase from 0 when this ratio falls below 0.4 (frac_mu_stress = 0.4).
!
call get_param(param_file, "generic_COBALT", "frac_mu_stress_Sm", phyto(SMALL)%frac_mu_stress, &
"fraction of max growth when stress-dependent losses initiate for small phytoplankton", &
units="none", default=0.25)
units="none", default=0.4)
call get_param(param_file, "generic_COBALT", "frac_mu_stress_Di", phyto(DIAZO)%frac_mu_stress, &
"fraction of max growth when stress-dependent losses initiate for diazotrophs", &
units="none", default=0.25)
units="none", default=0.4)
call get_param(param_file, "generic_COBALT", "frac_mu_stress_Lg", phyto(LARGE)%frac_mu_stress, &
"fraction of max growth when stress-dependent losses initiate for large phytoplankton", &
units="none", default=0.25)
units="none", default=0.4)
call get_param(param_file, "generic_COBALT", "frac_mu_stress_Md", phyto(MEDIUM)%frac_mu_stress, &
"fraction of max growth when stress-dependent losses initiate for medium phytoplankton", &
units="none", default=0.25)
units="none", default=0.4)
!
! Phytoplankton aggregation is a density-dependent (quadratic) mortality term that is more effective for large
! phytoplankton, following Jackson (1990). Aggregation rates increase with stress (e.g., Waite et al, 1992).
Expand Down Expand Up @@ -3423,7 +3423,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
phyto(n)%theta(i,j,k) = theta_temp
phyto(n)%bresp(i,j,k) = bresp_temp*P_C_max_temp
phyto(n)%mu(i,j,k) = P_C_m_temp/(1.0 + cobalt%zeta)*phyto(n)%irrlim(i,j,k) - phyto(n)%bresp(i,j,k)
phyto(n)%P_C_max(i,j,k) = P_C_max_temp*cobalt%expkT(i,j,k)
phyto(n)%P_C_max(i,j,k) = P_C_max_temp
phyto(n)%alpha(i,j,k) = alpha_temp
endif
enddo
Expand Down Expand Up @@ -3514,14 +3514,17 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
!
do k = 1, nk ; do j = jsc, jec ; do i = isc, iec !{
do n = 1, NUM_PHYTO !{
if (phyto(n)%q_fe_2_n(i,j,k).lt.phyto(n)%fe_2_n_max) then
! Take up iron if below maximum guota and day averaged growth is positive
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if ( (phyto(n)%q_fe_2_n(i,j,k).lt.phyto(n)%fe_2_n_max).and.(phyto(n)%f_mu_mem(i,j,k).gt.0.0) ) then
! Scaling fe uptake with the maximum photosynthesis allows for luxury iron uptake when other nutrients
! are limiting but iron is not
! are limiting but iron is not. Added light dependence to prevent excessive iron scavenging while sinking
phyto(n)%juptake_fe(i,j,k) = phyto(n)%P_C_max(i,j,k)*cobalt%expkT(i,j,k)*phyto(n)%f_n(i,j,k)* &
(1.0 - exp(-phyto(n)%alpha(i,j,k)*cobalt%f_irr_aclm(i,j,k)*phyto(n)%theta(i,j,k)/ &
max(phyto(n)%liebig_lim(i,j,k)*phyto(n)%P_C_max(i,j,k)*cobalt%expkT(i,j,k),epsln)))* &
phyto(n)%felim(i,j,k)*cobalt%fe_2_n_upt_fac
phyto(n)%jexuloss_fe(i,j,k) = 0.0
else
! if you've exceeded the maximum quota, stop uptake and exude extra
! if you've exceeded the maximum quota or day averaged growth is negative, stop uptake and exude extra
phyto(n)%juptake_fe(i,j,k) = 0.0
phyto(n)%jexuloss_fe(i,j,k) = cobalt%expkT(i,j,k)*phyto(n)%bresp(i,j,k)*phyto(n)%f_fe(i,j,k)
endif
Expand Down
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