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Tentative changes from final version used for photoacclimation experiments #12

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78 changes: 39 additions & 39 deletions generic_tracers/generic_COBALT.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -248,8 +248,8 @@ module generic_COBALT
si_2_n_max, &
si_2_n_static, &
thetamax, &
bresp_frac_mixed, &
bresp_frac_strat, &
bresp_frac_norm, &
bresp_frac_stress, &
sink_max, &
agg, &
frac_mu_stress, &
Expand Down Expand Up @@ -6272,36 +6272,36 @@ subroutine user_add_params
! Phytoplankton light limitation/growth rate
!-----------------------------------------------------------------------
!
call g_tracer_add_param('alpha_Di_hl', phyto(DIAZO)%alpha_hl, 0.4e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Lg_hl', phyto(LARGE)%alpha_hl, 0.4e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Md_hl', phyto(MEDIUM)%alpha_hl, 0.8e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Sm_hl', phyto(SMALL)%alpha_hl, 1.6e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Di_ll', phyto(DIAZO)%alpha_ll, 0.8e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Lg_ll', phyto(LARGE)%alpha_ll, 0.8e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Md_ll', phyto(MEDIUM)%alpha_ll, 1.6e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Sm_ll', phyto(SMALL)%alpha_ll, 3.2e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Di_hl', phyto(DIAZO)%alpha_hl, 0.6e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Lg_hl', phyto(LARGE)%alpha_hl, 0.6e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Md_hl', phyto(MEDIUM)%alpha_hl, 1.2e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Sm_hl', phyto(SMALL)%alpha_hl, 2.4e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Di_ll', phyto(DIAZO)%alpha_ll, 0.6e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Lg_ll', phyto(LARGE)%alpha_ll, 0.6e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Md_ll', phyto(MEDIUM)%alpha_ll, 1.2e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('alpha_Sm_ll', phyto(SMALL)%alpha_ll, 2.4e-5 * 2.77e18 / 6.022e17)! g C g Chl-1 sec-1 (W m-2)-1
call g_tracer_add_param('kappa_eppley', cobalt%kappa_eppley, 0.063) ! deg C-1
call g_tracer_add_param('P_C_max_Di_hl', phyto(DIAZO)%P_C_max_hl, 0.6/sperd) ! s-1
call g_tracer_add_param('P_C_max_Lg_hl', phyto(LARGE)%P_C_max_hl, 1.0/sperd) ! s-1
call g_tracer_add_param('P_C_max_Md_hl', phyto(MEDIUM)%P_C_max_hl, 1.1/sperd) ! s-1
call g_tracer_add_param('P_C_max_Sm_hl', phyto(SMALL)%P_C_max_hl, 1.0/sperd) ! s-1
call g_tracer_add_param('P_C_max_Di_ll', phyto(DIAZO)%P_C_max_ll, 0.3/sperd) ! s-1
call g_tracer_add_param('P_C_max_Lg_ll', phyto(LARGE)%P_C_max_ll, 0.5/sperd) ! s-1
call g_tracer_add_param('P_C_max_Md_ll', phyto(MEDIUM)%P_C_max_ll, 0.55/sperd) ! s-1
call g_tracer_add_param('P_C_max_Sm_ll', phyto(SMALL)%P_C_max_ll, 0.5/sperd) ! s-1
call g_tracer_add_param('numlightadapt', cobalt%numlightadapt, 10) ! dimensionless
call g_tracer_add_param('P_C_max_Di_ll', phyto(DIAZO)%P_C_max_ll, 0.6/sperd) ! s-1
call g_tracer_add_param('P_C_max_Lg_ll', phyto(LARGE)%P_C_max_ll, 1.0/sperd) ! s-1
call g_tracer_add_param('P_C_max_Md_ll', phyto(MEDIUM)%P_C_max_ll, 1.1/sperd) ! s-1
call g_tracer_add_param('P_C_max_Sm_ll', phyto(SMALL)%P_C_max_ll, 1.0/sperd) ! s-1
call g_tracer_add_param('numlightadapt', cobalt%numlightadapt, 2) ! dimensionless
call g_tracer_add_param('thetamax_Di', phyto(DIAZO)%thetamax, 0.035) ! g Chl g C-1
call g_tracer_add_param('thetamax_Lg', phyto(LARGE)%thetamax, 0.07) ! g Chl g C-1
call g_tracer_add_param('thetamax_Md', phyto(MEDIUM)%thetamax, 0.045) ! g Chl g C-1
call g_tracer_add_param('thetamax_Sm', phyto(SMALL)%thetamax, 0.035) ! g Chl g C-1
call g_tracer_add_param('bresp_frac_mixed_Di', phyto(DIAZO)%bresp_frac_mixed,0.02) ! none
call g_tracer_add_param('bresp_frac_mixed_Lg', phyto(LARGE)%bresp_frac_mixed,0.02) ! none
call g_tracer_add_param('bresp_frac_mixed_Md', phyto(MEDIUM)%bresp_frac_mixed,0.02) ! none
call g_tracer_add_param('bresp_frac_mixed_Sm', phyto(SMALL)%bresp_frac_mixed,0.02) ! none
call g_tracer_add_param('bresp_frac_strat_Di', phyto(DIAZO)%bresp_frac_strat,0.01) ! none
call g_tracer_add_param('bresp_frac_strat_Lg', phyto(LARGE)%bresp_frac_strat,0.01) ! none
call g_tracer_add_param('bresp_frac_strat_Md', phyto(MEDIUM)%bresp_frac_strat,0.01) ! none
call g_tracer_add_param('bresp_frac_strat_Sm', phyto(SMALL)%bresp_frac_strat,0.01) ! none
call g_tracer_add_param('bresp_frac_stress_Di', phyto(DIAZO)%bresp_frac_stress,0.01) ! none
call g_tracer_add_param('bresp_frac_stress_Lg', phyto(LARGE)%bresp_frac_stress,0.01) ! none
call g_tracer_add_param('bresp_frac_stress_Md', phyto(MEDIUM)%bresp_frac_stress,0.01) ! none
call g_tracer_add_param('bresp_frac_stress_Sm', phyto(SMALL)%bresp_frac_stress,0.01) ! none
call g_tracer_add_param('bresp_frac_norm_Di', phyto(DIAZO)%bresp_frac_norm,0.01) ! none
call g_tracer_add_param('bresp_frac_norm_Lg', phyto(LARGE)%bresp_frac_norm,0.01) ! none
call g_tracer_add_param('bresp_frac_norm_Md', phyto(MEDIUM)%bresp_frac_norm,0.01) ! none
call g_tracer_add_param('bresp_frac_norm_Sm', phyto(SMALL)%bresp_frac_norm,0.01) ! none
call g_tracer_add_param('sink_max_Di', phyto(DIAZO)%sink_max,1.0/sperd) ! m sec-1
call g_tracer_add_param('sink_max_Lg', phyto(LARGE)%sink_max,5.0/sperd) ! m sec-1
call g_tracer_add_param('sink_max_Md', phyto(MEDIUM)%sink_max,1.0/sperd) ! m sec-1
Expand All @@ -6312,7 +6312,7 @@ subroutine user_add_params
call g_tracer_add_param('gamma_irr_aclm', cobalt%gamma_irr_aclm, 1.0 / sperd) ! s-1
call g_tracer_add_param('gamma_irr_mem_dp',cobalt%gamma_irr_mem_dp,0.1/sperd) ! s-1
call g_tracer_add_param('gamma_mu_mem', cobalt%gamma_mu_mem, 1.0 / sperd) ! s-1
call g_tracer_add_param('ml_aclm_efold', cobalt%ml_aclm_efold, 4.6) ! dimensionless
call g_tracer_add_param('ml_aclm_efold', cobalt%ml_aclm_efold, 999.0) ! dimensionless
call g_tracer_add_param('zmld_ref', cobalt%zmld_ref, 10.0) ! m
call g_tracer_add_param('densdiff_mld', cobalt%densdiff_mld, 0.03) ! kg m-3
call g_tracer_add_param('irrad_day_thresh', cobalt%irrad_day_thresh, 1.0 ) ! watts m-2
Expand Down Expand Up @@ -6341,14 +6341,14 @@ subroutine user_add_params
call g_tracer_add_param('p_2_n_min_Di', phyto(DIAZO)%p_2_n_min,1.0/40.0 ) ! mol P mol N-1
call g_tracer_add_param('p_2_n_slope_Di', phyto(DIAZO)%p_2_n_slope, 0.0*1.0e6) ! mol P mol N-1 mol P-1 kg
call g_tracer_add_param('p_2_n_max_Di', phyto(DIAZO)%p_2_n_max,1.0/40.0 ) ! mol P mol N-1
call g_tracer_add_param('p_2_n_min_Sm', phyto(SMALL)%p_2_n_min,1.0/31.0 ) ! mol P mol N-1
call g_tracer_add_param('p_2_n_slope_Sm', phyto(SMALL)%p_2_n_slope, 0.048*1.0e6) ! mol P mol N-1 mol P-1 kg
call g_tracer_add_param('p_2_n_max_Sm', phyto(SMALL)%p_2_n_max,1.0/20.0 ) ! mol P mol N-1
call g_tracer_add_param('p_2_n_min_Md', phyto(MEDIUM)%p_2_n_min,1.0/31.0 ) ! mol P mol N-1
call g_tracer_add_param('p_2_n_slope_Md', phyto(MEDIUM)%p_2_n_slope, 0.048*1.0e6) ! mol P mol N-1 mol P-1 kg
call g_tracer_add_param('p_2_n_max_Md', phyto(MEDIUM)%p_2_n_max,1.0/16.0 ) ! mol P mol N-1
call g_tracer_add_param('p_2_n_min_Lg', phyto(LARGE)%p_2_n_min,1.0/31.0 ) ! mol P mol N-1
call g_tracer_add_param('p_2_n_slope_Lg', phyto(LARGE)%p_2_n_slope, 0.048*1.0e6) ! mol P mol N-1 mol P-1 kg
call g_tracer_add_param('p_2_n_min_Sm', phyto(SMALL)%p_2_n_min,1.0/23.0 ) ! mol P mol N-1
call g_tracer_add_param('p_2_n_slope_Sm', phyto(SMALL)%p_2_n_slope, 0.0*1.0e6) ! mol P mol N-1 mol P-1 kg
call g_tracer_add_param('p_2_n_max_Sm', phyto(SMALL)%p_2_n_max,1.0/23.0 ) ! mol P mol N-1
call g_tracer_add_param('p_2_n_min_Md', phyto(MEDIUM)%p_2_n_min,1.0/18.0 ) ! mol P mol N-1
call g_tracer_add_param('p_2_n_slope_Md', phyto(MEDIUM)%p_2_n_slope, 0.0*1.0e6) ! mol P mol N-1 mol P-1 kg
call g_tracer_add_param('p_2_n_max_Md', phyto(MEDIUM)%p_2_n_max,1.0/18.0 ) ! mol P mol N-1
call g_tracer_add_param('p_2_n_min_Lg', phyto(LARGE)%p_2_n_min,1.0/14.0 ) ! mol P mol N-1
call g_tracer_add_param('p_2_n_slope_Lg', phyto(LARGE)%p_2_n_slope, 0.0*1.0e6) ! mol P mol N-1 mol P-1 kg
Comment on lines +6344 to +6351
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I think I see what's going on here now... this is effectively disabling the variable n:p, right? So this should not be merged.

call g_tracer_add_param('p_2_n_max_Lg', phyto(LARGE)%p_2_n_max,1.0/14.0 ) ! mol P mol N-1
call g_tracer_add_param('si_2_n_static_Lg', phyto(LARGE)%si_2_n_static, 2.0) ! mol Si mol N-1
call g_tracer_add_param('si_2_n_static_Md', phyto(MEDIUM)%si_2_n_static, 2.0) ! mol Si mol N-1
Expand All @@ -6363,7 +6363,7 @@ subroutine user_add_params
!-----------------------------------------------------------------------
!
call g_tracer_add_param('q_p_2_n_smz',zoo(1)%q_p_2_n, 1.0/20.0) ! mol P mol N-1
call g_tracer_add_param('q_p_2_n_mdz',zoo(2)%q_p_2_n, 1.0/18.0) ! mol P mol N-1
call g_tracer_add_param('q_p_2_n_mdz',zoo(2)%q_p_2_n, 1.0/16.0) ! mol P mol N-1
call g_tracer_add_param('q_p_2_n_lgz',zoo(3)%q_p_2_n, 1.0/16.0) ! mol P mol N-1
!
!-----------------------------------------------------------------------
Expand Down Expand Up @@ -6585,7 +6585,7 @@ subroutine user_add_params
call g_tracer_add_param('jpo4_iceberg_ratio', cobalt%jpo4_iceberg_ratio,1.1e-7) ! mol P kg-1 ice melt
call g_tracer_add_param('fe_coast', cobalt%fe_coast,0.0 ) ! mol Fe m kg-1 s-1
call g_tracer_add_param('alpha_fescav',cobalt%alpha_fescav, 0.0/spery) ! sec-1
call g_tracer_add_param('beta_fescav',cobalt%beta_fescav, 2.5e9/spery ) ! sec-1 (mole ndet kg-1)-1
call g_tracer_add_param('beta_fescav',cobalt%beta_fescav, 3.5e9/spery ) ! sec-1 (mole ndet kg-1)-1
call g_tracer_add_param('remin_eff_fedet',cobalt%remin_eff_fedet, 0.25) ! unitless
call g_tracer_add_param('io_fescav',cobalt%io_fescav, 10.0 ) ! watts m-2
call g_tracer_add_param('kfe_eq_lig_ll',cobalt%kfe_eq_lig_ll, 1.0e12) ! mol lig-1 kg
Expand Down Expand Up @@ -8277,7 +8277,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
min(phyto(n)%po4lim(i,j,k), phyto(n)%def_fe(i,j,k))
do n= 2, NUM_PHYTO !{
phyto(n)%liebig_lim(i,j,k) = min(phyto(n)%no3lim(i,j,k)+phyto(n)%nh4lim(i,j,k),&
phyto(n)%po4lim(i,j,k), max(phyto(n)%def_fe(i,j,k),phyto(n)%felim(i,j,k)))
phyto(n)%po4lim(i,j,k), phyto(n)%def_fe(i,j,k))
enddo !} n
enddo; enddo ; enddo !} i,j,k
!
Expand Down Expand Up @@ -8492,9 +8492,9 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
! maximum photosynthetic rate laters to give units of day-1
!
if (k.le.kblt(i,j)) then
bresp_temp = phyto(n)%bresp_frac_mixed*cobalt%expkT(i,j,k)
bresp_temp = phyto(n)%bresp_frac_stress*cobalt%expkT(i,j,k)
else
bresp_temp = phyto(n)%bresp_frac_strat*cobalt%expkT(i,j,k)
bresp_temp = phyto(n)%bresp_frac_norm*cobalt%expkT(i,j,k)
endif
! adjust basal respiration to maintain small refuge
bresp_temp = bresp_temp*phyto(n)%f_n(i,j,k)/(cobalt%refuge_conc+phyto(n)%f_n(i,j,k))
Expand Down Expand Up @@ -9257,7 +9257,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
!

do n = 1,NUM_PHYTO !{
growth_ratio = min(max(phyto(n)%f_mu_mem(i,j,k),0.0)/ &
growth_ratio = min(phyto(n)%f_mu_mem(i,j,k)/ &
(phyto(n)%frac_mu_stress*phyto(n)%P_C_max(i,j,k)*cobalt%expkT(i,j,k)),1.0)
phyto(n)%stress_fac(i,j,k) = (1.0-growth_ratio)**2
phyto(n)%jaggloss_n(i,j,k) = phyto(n)%stress_fac(i,j,k)*phyto(n)%agg*phyto(n)%f_n(i,j,k)**2.0
Expand Down Expand Up @@ -9745,7 +9745,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,h
cobalt%jfe_ads(i,j,k) = cobalt%alpha_fescav*cobalt%feprime(i,j,k) + &
cobalt%beta_fescav*cobalt%feprime(i,j,k)*cobalt%f_ndet(i,j,k)
else
cobalt%jfe_ads(i,j,k) = 2.0*(cobalt%alpha_fescav*cobalt%feprime(i,j,k) + &
cobalt%jfe_ads(i,j,k) = 10.0*(cobalt%alpha_fescav*cobalt%feprime(i,j,k) + &
cobalt%beta_fescav*cobalt%feprime(i,j,k)*cobalt%f_ndet(i,j,k))
endif
cobalt%jfe_ads(i,j,k) = min(cobalt%jfe_ads(i,j,k),cobalt%f_fed(i,j,k)/(2.0*dt))
Expand Down
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