From 93cc51fe733abf33e19bc8d5c2c60e3eecbed1a6 Mon Sep 17 00:00:00 2001 From: jlinmod <134327817+jlinmod@users.noreply.github.com> Date: Thu, 18 Jul 2024 17:40:55 -0400 Subject: [PATCH 1/2] Update marbl_ciso_interior_tendency_mod.F90 Fixed comments, eps_aq_g equation error (Zhang et al., 1995), and cell surface area unit conversion fix for calcifier (Popp et al., 1998). --- src/marbl_ciso_interior_tendency_mod.F90 | 47 ++++++++++++++---------- 1 file changed, 27 insertions(+), 20 deletions(-) diff --git a/src/marbl_ciso_interior_tendency_mod.F90 b/src/marbl_ciso_interior_tendency_mod.F90 index 9e1839ce..c8eef908 100644 --- a/src/marbl_ciso_interior_tendency_mod.F90 +++ b/src/marbl_ciso_interior_tendency_mod.F90 @@ -38,7 +38,7 @@ module marbl_ciso_interior_tendency_mod !----------------------------------------------------------------------- real (r8), parameter :: c14_halflife_years = 5730.0_r8 !C14 half file - real (r8) :: c14_lambda_inv_sec ! Decay variable in seconds + real (r8) :: c14_lambda_inv_sec ! Decay variable in 1/seconds (convert 5730 year decay to seconds) contains @@ -97,8 +97,8 @@ subroutine marbl_ciso_interior_tendency_compute( & real (r8), dimension(autotroph_cnt) :: & cell_active_C_uptake, & ! ratio of active carbon uptake to carbon fixation - cell_surf, & ! surface areas of cells ( m2 ) - cell_carb_cont, & ! cell carbon content ( mol C cell-1 ) + cell_surf, & ! surface areas of cells ( m^2 ) + cell_carb_cont, & ! cell carbon content ( mol C cell^-1 ) cell_radius, & ! cell radius ( um ) cell_permea, & ! cell wall permeability to CO2(aq) (m/s) cell_eps_fix ! fractionation effect of carbon fixation @@ -128,16 +128,16 @@ subroutine marbl_ciso_interior_tendency_compute( & R14C_zoototC ! 14C/12C in total zooplankton real (r8), dimension(autotroph_cnt, marbl_domain%km) :: & - Ca13CO3_PROD, & ! prod. of 13C CaCO3 by small phyto (mmol CaCO3/m^3/sec) - Ca14CO3_PROD, & ! prod. of 13C CaCO3 by small phyto (mmol CaCO3/m^3/sec) + Ca13CO3_PROD, & ! prod. of 13C CaCO3 by small phyto (mmol Ca13CO3/m^3/sec) + Ca14CO3_PROD, & ! prod. of 14C CaCO3 by small phyto (mmol Ca14CO3/m^3/sec) eps_autotroph, & ! Permil fractionation (or discrimination factor) for Carbon autotroph types sp, diat, diaz mui_to_co2star, & ! Carbon autotroph instanteous growth rate over [CO2*] (m^3 /mmol C /s) - R13C_photoC, & ! 13C/12C in Carbon autotroph C-fixation (mmol C/m^3/sec) - R13C_autotroph, & ! 13C/12C in total small phytoplankton - photo13C, & ! Carbon autotroph 13C-fixation (mmol C/m^3/sec) - photo14C, & ! Carbon autotroph 14C-fixation (mmol C/m^3/sec) - R14C_photoC, & ! 14C/12C in Carbon autotroph C-fixation (mmol C/m^3/sec) - R14C_autotroph, & ! 14C/12C in total small phytoplankton + R13C_photoC, & ! 13C/12C in Carbon autotroph C-fixation (mmol 13C/m^3/sec) + R13C_autotroph, & ! 13C/12C in total small phytoplankton (mmol 13C/m^3/sec) + photo13C, & ! Carbon autotroph 13C-fixation (mmol 13C/m^3/sec) + photo14C, & ! Carbon autotroph 14C-fixation (mmol 14C/m^3/sec) + R14C_photoC, & ! 14C/12C in Carbon autotroph C-fixation (mmol 14C/m^3/sec) + R14C_autotroph, & ! 14C/12C in total small phytoplankton (mmol 14C/m^3/sec) autotrophCaCO3_d13C, & ! d13C of autotrophCaCO3 autotrophCaCO3_d14C, & ! d14C of autotrophCaCO3 autotroph_d13C, & ! d13C of autotroph C @@ -148,16 +148,16 @@ subroutine marbl_ciso_interior_tendency_compute( & real (r8), dimension(marbl_domain%km) :: & frac_co3, & ! carbonate fraction fCO3 = [CO3--]/DIC CO2STAR_int, & ! [CO2*] water (mmol/m^3) in interior domain (not only surface) - DO13Ctot_prod, & ! production of 13C DOCtot (mmol C/m^3/sec) - DO13Ctot_remin, & ! remineralization of 13C DOCtot (mmol C/m^3/sec) + DO13Ctot_prod, & ! production of 13C DOCtot (mmol 13C/m^3/sec) + DO13Ctot_remin, & ! remineralization of 13C DOCtot (mmol 13C/m^3/sec) eps_aq_g, & ! equilibrium fractionation (CO2_gaseous <-> CO2_aq) eps_dic_g, & ! equilibrium fractionation between total DIC and gaseous CO2 - alpha_aq_g, & ! eps = ( alpa -1 ) * 1000 - alpha_dic_g, & ! eps = ( alpa -1 ) * 1000 + alpha_aq_g, & ! eps = ( alpha -1 ) * 1000 + alpha_dic_g, & ! eps = ( alpha -1 ) * 1000 delta_C13_Corg, & ! deltaC13 of Net Primary Production delta_C13_CO2STAR, & ! deltaC13 of CO2* - DO14Ctot_prod, & ! production of 13C DOCtot (mmol C/m^3/sec) - DO14Ctot_remin, & ! remineralization of 13C DOCtot (mmol C/m^3/sec) + DO14Ctot_prod, & ! production of 13C DOCtot (mmol 14C/m^3/sec) + DO14Ctot_remin, & ! remineralization of 13C DOCtot (mmol 14C/m^3/sec) alpha_aq_g_14c, & ! alpha for 14C, with fractionation twice as large as for 13C alpha_dic_g_14c, & ! alpha for 14C, with fractionation twice as large as for 13C delta_C14_CO2STAR, & ! deltaC14 of CO2* @@ -184,7 +184,7 @@ subroutine marbl_ciso_interior_tendency_compute( & DOCtot_remin => interior_tendency_share%DOCtot_remin_fields, & ! INPUT remineralization of DOCtot (mmol C/m^3/sec) DOCtot_loc => interior_tendency_share%DOCtot_loc_fields, & ! INPUT local copy of model DOCtot - DO13Ctot_loc => tracer_local(marbl_tracer_indices%DO13Ctot_ind,:), & ! local copy of model DO14Ctot + DO13Ctot_loc => tracer_local(marbl_tracer_indices%DO13Ctot_ind,:), & ! local copy of model DO13Ctot DO14Ctot_loc => tracer_local(marbl_tracer_indices%DO14Ctot_ind,:), & ! local copy of model DO14Ctot DIC_loc => tracer_local(marbl_tracer_indices%DIC_ind,:), & ! INPUT local copy of model DIC DI13C_loc => tracer_local(marbl_tracer_indices%DI13C_ind,:), & ! local copy of model DI13C @@ -332,7 +332,7 @@ subroutine marbl_ciso_interior_tendency_compute( & ! Fractionation is twice as large for 14C compared to 13C !----------------------------------------------------------------------- - eps_aq_g(k) = 0.0049_r8 * temperature(k) - 1.31_r8 + eps_aq_g(k) = -0.0049_r8 * temperature(k) - 1.31_r8 eps_dic_g(k) = 0.014_r8 * temperature(k) * frac_co3(k) - 0.105_r8 * temperature(k) + 10.53_r8 alpha_aq_g(k) = c1 + eps_aq_g(k) / c1000 @@ -833,7 +833,7 @@ subroutine setup_cell_attributes(ciso_fract_factors, & ! convert pgC to molC : ! Mc = 12 g / mol ! Mc = 12 e12 pg / mol !---------------------------------------------------------------------------------------- ! cell_active_C_uptake(auto_ind) = 0.0_r9 ! ratio of active carbon uptake to carbon fixation - ! cell_surf(auto_ind) = 3886.0_r8 ! surface areas of cells ( m2 ) + ! cell_surf(auto_ind) = 3.886e-9_r8 ! surface areas of cells ( m2 ) ! cell_carb_cont(auto_ind) = 1.68e-10_r8 ! cell carbon content ( mol C cell-1 ) ! cell_radius(auto_ind) = ! cell radius ( um ) ! cell_permea(auto_ind) = 1.1e-5_r8 ! cell wall permeability to CO2(aq) (m/s) @@ -947,6 +947,13 @@ subroutine fract_keller_morel( & !--------------------------------------------------------------------- ! cellular carbon content ( mol C ) ! volume in um^3 + ! + ! Qc based on Dieter A. Wolf-Gladrow, Ulf Riebeseel, Steffen Burkhardt and Jelle Buma (1999) + ! Direct effects of CO2 concentration on growth and isotopic composition of marine plankton, based on + ! + ! Strathmann, 1967: Estimating the organic carbon content of phytoplankton from cell volume + ! or plasma volume + !--------------------------------------------------------------------- if ( cell_carb_cont > c0 ) then From c40e8acd2184d85810fc770513fbd8667922271c Mon Sep 17 00:00:00 2001 From: jlinmod <134327817+jlinmod@users.noreply.github.com> Date: Thu, 19 Sep 2024 09:03:44 -0400 Subject: [PATCH 2/2] Update marbl_ciso_interior_tendency_mod.F90 9-19-24 --- src/marbl_ciso_interior_tendency_mod.F90 | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/marbl_ciso_interior_tendency_mod.F90 b/src/marbl_ciso_interior_tendency_mod.F90 index c8eef908..ea577d2f 100644 --- a/src/marbl_ciso_interior_tendency_mod.F90 +++ b/src/marbl_ciso_interior_tendency_mod.F90 @@ -325,6 +325,8 @@ subroutine marbl_ciso_interior_tendency_compute( & !----------------------------------------------------------------------- ! discrimination factors of carbone chemistry based on ! Zhang et al, 1995, Geochim. et Cosmochim. Acta, 59 (1), 107-114 + ! Note: there is a discrepancy between the figure caption and the abstract of the paper, + ! the typo is in the abstract, no negative 0.0049 ! ! eps = permil fractionation and alpha is the fractionation factor ! with eps =(alpha - 1) *1000 @@ -332,7 +334,7 @@ subroutine marbl_ciso_interior_tendency_compute( & ! Fractionation is twice as large for 14C compared to 13C !----------------------------------------------------------------------- - eps_aq_g(k) = -0.0049_r8 * temperature(k) - 1.31_r8 + eps_aq_g(k) = 0.0049_r8 * temperature(k) - 1.31_r8 eps_dic_g(k) = 0.014_r8 * temperature(k) * frac_co3(k) - 0.105_r8 * temperature(k) + 10.53_r8 alpha_aq_g(k) = c1 + eps_aq_g(k) / c1000 @@ -833,7 +835,7 @@ subroutine setup_cell_attributes(ciso_fract_factors, & ! convert pgC to molC : ! Mc = 12 g / mol ! Mc = 12 e12 pg / mol !---------------------------------------------------------------------------------------- ! cell_active_C_uptake(auto_ind) = 0.0_r9 ! ratio of active carbon uptake to carbon fixation - ! cell_surf(auto_ind) = 3.886e-9_r8 ! surface areas of cells ( m2 ) + ! cell_surf(auto_ind) = 3886.0_r8 ! surface areas of cells ( m2 ) ! cell_carb_cont(auto_ind) = 1.68e-10_r8 ! cell carbon content ( mol C cell-1 ) ! cell_radius(auto_ind) = ! cell radius ( um ) ! cell_permea(auto_ind) = 1.1e-5_r8 ! cell wall permeability to CO2(aq) (m/s)