diff --git a/doc/source/user_guide/ug_case_settings.rst b/doc/source/user_guide/ug_case_settings.rst index f18ffe03..3dea32fb 100644 --- a/doc/source/user_guide/ug_case_settings.rst +++ b/doc/source/user_guide/ug_case_settings.rst @@ -103,11 +103,11 @@ can be modified as needed. "NBGCLYR", "integer", "number of zbgc layers", "1" "TRZAERO", "0-6", "number of z aerosol tracers", "0" "TRALG", "0,1,2,3", "number of algal tracers", "0" - "TRDOC", "0,1,2,3", "number of dissolved organic carbon", "0" + "TRDOC", "0,1,2", "number of dissolved organic carbon", "0" "TRDIC", "0,1", "number of dissolved inorganic carbon", "0" "TRDON", "0,1", "number of dissolved organic nitrogen", "0" - "TRFEP", "0,1,2", "number of particulate iron tracers", "0" - "TRFED", "0,1,2", "number of dissolved iron tracers", "0" + "TRFEP", "0,1", "number of particulate iron tracers", "0" + "TRFED", "0,1", "number of dissolved iron tracers", "0" "ICE_SNICARHC", "true,false", "include hardcoded (HC) snicar tables", "false" "ICE_BLDDEBUG", "true,false", "turn on compile debug flags", "false" "ICE_COVERAGE", "true,false", "turn on code coverage flags", "false" @@ -392,19 +392,23 @@ forcing_nml "", "``random``", "wave data file is provided, sea surface height generated using random number (multiple iterations of wave fracture)", "" "``ycycle``", "integer", "number of years in forcing data cycle", "1" "", "", "", "" + +* = If Icepack is run stand-alone and wave_spec_type is not set to none, then a fixed wave spectrum is defined in the code to use for testing. As with other input data, this spectrum should not be used for production runs or publications. zbgc_nml ~~~~~~~~~~~~~~~~~~~~~~~~~ +.. _tab-bio-tracers-namelist2: + .. csv-table:: **zbgc_nml namelist options** :header: "variable", "options/format", "description", "default value" - :widths: 15, 15, 30, 15 + :widths: 15, 15, 30, 15 "", "", "", "" "``algaltype_diatoms``", "real", "mobility type between stationary and mobile algal diatoms", "0.0" "``algaltype_phaeo``", "real", "mobility type between stationary and mobile algal phaeocystis", "0.0" "``algaltype_sp``", "real", "mobility type between stationary and mobile small plankton", "0.0" - "``algal_vel``", "real", ":cite:`Lavoie05`", "1.0e-7" + "``algal_vel``", "real", "maximum speed of algae (m/s) :cite:`Lavoie05`", "1.0e-7" "``alpha2max_low_diatoms``", "real", "light limitation diatoms 1/(W/m^2)", "0.3" "``alpha2max_low_phaeo``", "real", "light limitation phaeocystis 1/(W/m^2)", "0.17" "``alpha2max_low_sp``", "real", "light limitation small plankton 1/(W/m^2)", "0.2" @@ -417,7 +421,7 @@ zbgc_nml "``chlabs_diatoms``", "real", "chl absorbtion diatoms 1/m/(mg/m^3)", "0.03" "``chlabs_phaeo``", "real", "chl absorbtion phaeocystis 1/m/(mg/m^3)", "0.05" "``chlabs_sp``", "real", "chl absorbtion small plankton 1/m/(mg/m^3)", "0.01" - "``dEdd_algae``", "logical", "", "``.false.``" + "``dEdd_algae``", "logical", "include ice bgc and/or aerosols in radiative transfer", "``.false.``" "``dmspdtype``", "real", "mobility type between stationary and mobile dmspd", "0.0" "``dmspptype``", "real", "mobility type between stationary and mobile dmspp", "0.5" "``doctype_l``", "real", "mobility type between stationary and mobile doc lipids", "0.0" @@ -427,14 +431,14 @@ zbgc_nml "``fedtype_1``", "real", "mobility type between stationary and mobile fed lipids", "0.0" "``feptype_1``", "real", "mobility type between stationary and mobile fep lipids", "0.5" "``frazil_scav``", "real", "increase in initial bio bracer from ocean scavenging", "0.8" - "``fr_dFe``", "real", "fraction of remineralized nitrogen in units of algal iron", "1.0" + "``fr_dFe``", "real", "fraction of remineralized iron from algae", "1.0" "``fr_graze_diatoms``", "real", "fraction grazed diatoms", "0.19" "``fr_graze_e``", "real", "fraction of assimilation excreted", "0.5" "``fr_graze_phaeo``", "real", "fraction grazed phaeocystis", "0.19" "``fr_graze_s``", "real", "fraction of grazing spilled or slopped", "0.5" "``fr_graze_sp``", "real", "fraction grazed small plankton", "0.19" "``fr_mort2min``", "real", "fractionation of mortality to Am", "0.9" - "``fr_resp``", "real", "frac of algal growth lost due to respiration", "0.05" + "``fr_resp``", "real", "fraction of algal growth lost due to respiration", "0.05" "``fr_resp_s``", "real", "DMSPd fraction of respiration loss as DMSPd", "0.9" "``fsal``", "real", "salinity limitation ppt", "1.0" "``F_abs_chl_diatoms``", "real", "scales absorbed radiation for dEdd chl diatoms", "2.0" @@ -446,7 +450,7 @@ zbgc_nml "``f_don_protein``", "real", "fraction of spilled grazing to proteins", "0.6" "``f_exude_l``", "real", "fraction of exudation to DOC lipids", "1.0" "``f_exude_s``", "real", "fraction of exudation to DOC saccharids", "1.0" - "``grid_o``", "real", "z biology for bottom flux", "0.006" + "``grid_o``", "real", "z biology length scale for bottom flux (m)", "0.006" "``grid_oS``", "real", "DEPRECATED", "" "``grow_Tdep_diatoms``", "real", "temperature dependence growth diatoms per degC", "0.063" "``grow_Tdep_phaeo``", "real", "temperature dependence growth phaeocystis per degC", "0.063" @@ -472,14 +476,14 @@ zbgc_nml "``K_Sil_phaeo``", "real", "silicate half saturation phaeocystis mmol/m^3", "0.0" "``K_Sil_sp``", "real", "silicate half saturation small plankton mmol/m^3", "0.0" "``kn_bac_protein``", "real", "bacterial degradation of DON per day", "0.2" - "``l_sk``", "real", "characteristic diffusive scale in m", "20.0" + "``l_sk``", "real", "characteristic diffusive scale in m", "2.0" "``l_skS``", "real", "DEPRECATED", "" "``max_dfe_doc1``", "real", "max ratio of dFe to saccharides in the ice in nm Fe / muM C", "0.2" "``max_loss``", "real", "restrict uptake to percent of remaining value", "0.9" - "``modal_aero``", "logical", "modal aersols", "``.false.``" - "``mort_pre_diatoms``", "real", "mortality diatoms", "0.007" - "``mort_pre_phaeo``", "real", "mortality phaeocystis", "0.007" - "``mort_pre_sp``", "real", "mortality small plankton", "0.007" + "``modal_aero``", "logical", "modal aerosols", "``.false.``" + "``mort_pre_diatoms``", "real", "mortality diatoms per day", "0.007" + "``mort_pre_phaeo``", "real", "mortality phaeocystis per day", "0.007" + "``mort_pre_sp``", "real", "mortality small plankton per day", "0.007" "``mort_Tdep_diatoms``", "real", "temperature dependence of mortality diatoms per degC", "0.03" "``mort_Tdep_phaeo``", "real", "temperature dependence of mortality phaeocystis per degC", "0.03" "``mort_Tdep_sp``", "real", "temperature dependence of mortality small plankton per degC", "0.03" @@ -488,7 +492,7 @@ zbgc_nml "``mu_max_sp``", "real", "maximum growth rate small plankton per day", "0.41" "``nitratetype``", "real", "mobility type between stationary and mobile nitrate", "-1.0" "``op_dep_min``", "real", "light attenuates for optical depths exceeding min", "0.1" - "``phi_snow``", "real", "snow porosity for brine height tracer", "-0.3" + "``phi_snow``", "real", "snow porosity for brine height tracer (compute from snow density if negative)", "-1.0" "``ratio_chl2N_diatoms``", "real", "algal chl to N in mg/mmol diatoms", "2.1" "``ratio_chl2N_phaeo``", "real", "algal chl to N in mg/mmol phaeocystis", "0.84" "``ratio_chl2N_sp``", "real", "algal chl to N in mg/mmol small plankton", "1.1" @@ -496,12 +500,12 @@ zbgc_nml "``ratio_C2N_phaeo``", "real", "algal C to N in mol/mol phaeocystis", "7.0" "``ratio_C2N_proteins``", "real", "algal C to N in mol/mol proteins", "5.0" "``ratio_C2N_sp``", "real", "algal C to N in mol/mol small plankton", "7.0" - "``ratio_Fe2C_diatoms``", "real", "algal Fe to C in umol/mol diatoms", "0.0033" - "``ratio_Fe2C_phaeo``", "real", "algal Fe to C in umol/mol phaeocystis", "0.1" - "``ratio_Fe2C_sp``", "real", "algal Fe to C in umol/mol small plankton", "0.0033" - "``ratio_Fe2N_diatoms``", "real", "algal Fe to N in umol/mol diatoms", "0.023" - "``ratio_Fe2N_phaeo``", "real", "algal Fe to N in umol/mol phaeocystis", "0.7" - "``ratio_Fe2N_sp``", "real", "algal Fe to N in umol/mol small plankton", "0.023" + "``ratio_Fe2C_diatoms``", "real", "algal Fe to C in mmol/mol diatoms", "0.0033" + "``ratio_Fe2C_phaeo``", "real", "algal Fe to C in mmol/mol phaeocystis", "0.1" + "``ratio_Fe2C_sp``", "real", "algal Fe to C in mmol/mol small plankton", "0.0033" + "``ratio_Fe2N_diatoms``", "real", "algal Fe to N in mmol/mol diatoms", "0.023" + "``ratio_Fe2N_phaeo``", "real", "algal Fe to N in mmol/mol phaeocystis", "0.7" + "``ratio_Fe2N_sp``", "real", "algal Fe to N in mmol/mol small plankton", "0.023" "``ratio_Fe2DOC_s``", "real", "Fe to C of DON saccharids nmol/umol", "0.1" "``ratio_Fe2DOC_l``", "real", "Fe to C of DOC lipids nmol/umol", "0.033" "``ratio_Fe2DON``", "real", "Fe to C of DON nmol/umol", "0.023" @@ -513,29 +517,29 @@ zbgc_nml "``ratio_S2N_sp``", "real", "algal S to N in mol/mol small plankton", "0.03" "``restore_bgc``", "logical", "DEPRECATED", "``.false.``" "``R_dFe2dust``", "real", "g/g :cite:`Tagliabue09`", "0.035" - "``scale_bgc``", "logical", "", "``.false.``" + "``scale_bgc``", "logical", "initialize bgc by scaling with salinity", "``.false.``" "``silicatetype``", "real", "mobility type between stationary and mobile silicate", "-1.0" - "``skl_bgc``", "logical", "DEPRECATED", "``.false.``" - "``solve_zbgc``", "logical", "", "``.false.``" + "``skl_bgc``", "logical", "DEPRECATED: skeletal layer biogeochemistry", "``.false.``" + "``solve_zbgc``", "logical", "solve z-biogeochemistry reactions", "``.false.``" "``solve_zsal``", "logical", "DEPRECATED", "``.false.``" - "``tau_max``", "real", "long time mobile to stationary exchanges", "7776000." - "``tau_min``", "real", "rapid module to stationary exchanges", "3600." + "``tau_max``", "real", "long time mobile to stationary exchanges (s)", "604800.0" + "``tau_min``", "real", "rapid module to stationary exchanges (s)", "3600.0" "``tr_bgc_Am``", "logical", "ammonium tracer", "``.false.``" "``tr_bgc_C``", "logical", "algal carbon tracer", "``.false.``" "``tr_bgc_chl``", "logical", "algal chlorophyll tracer", "``.false.``" "``tr_bgc_DMS``", "logical", "DMS tracer", "``.false.``" "``tr_bgc_DON``", "logical", "DON tracer", "``.false.``" "``tr_bgc_Fe``", "logical", "iron tracer", "``.false.``" - "``tr_bgc_hum``", "logical", "", "``.false.``" - "``tr_bgc_Nit``", "logical", "", "``.false.``" - "``tr_bgc_PON``", "logical", "PON tracer", "``.false.``" + "``tr_bgc_hum``", "logical", "refractory DOC", "``.false.``" + "``tr_bgc_Nit``", "logical", "nitrate tracer", "``.false.``" + "``tr_bgc_PON``", "logical", "Non-reactive nitrate tracer", "``.false.``" "``tr_bgc_Sil``", "logical", "silicate tracer", "``.false.``" "``tr_brine``", "logical", "brine height tracer", "``.false.``" "``tr_zaero``", "logical", "vertical aerosol tracers", "``.false.``" "``t_iron_conv``", "real", "desorption loss pFe to dFe in days", "3065." "``t_sk_conv``", "real", "Stefels conversion time in days", "5.0" "``t_sk_ox``", "real", "DMS oxidation time in days", "12.0" - "``T_max``", "real", "maximum temperature degC", "0.0" + "``T_max``", "real", "maximum brine temperature degC", "0.0" "``y_sk_DMS``", "real", "fraction conversion given high yield", "0.7" "``zaerotype_bc1``", "real", "mobility type between stationary and mobile zaero bc1", "-1.0" "``zaerotype_bc2``", "real", "mobility type between stationary and mobile zaero bc2", "-1.0" @@ -543,7 +547,7 @@ zbgc_nml "``zaerotype_dust2``", "real", "mobility type between stationary and mobile zaero dust2", "-1.0" "``zaerotype_dust3``", "real", "mobility type between stationary and mobile zaero dust3", "-1.0" "``zaerotype_dust4``", "real", "mobility type between stationary and mobile zaero dust4", "-1.0" - "``z_tracers``", "logical", "", "``.false.``" + "``z_tracers``", "logical", "allows vertically resolved bgc and/or z-aerosol tracers", "``.false.``" "", "", "", "" @@ -559,19 +563,18 @@ zbgc_nml .. "``restart_hbrine``", "logical", "", "``.false.``" .. "``solve_zsal``", "logical", "update salinity tracer profile", "``.false.``" .. "TRZS", "0,1", "zsalinity tracer, needs TRBRI=1", "0" - -* = If Icepack is run stand-alone and wave_spec_type is not set to none, then a fixed wave spectrum is defined in the code to use for testing. As with other input data, this spectrum should not be used for production runs or publications. .. _tuning: -BGC Tuning Parameters +BGC Parameter Arrays ------------------------ -Biogeochemical tuning parameters are specified as namelist options in -**icepack\_in**. Table :ref:`tab-bio-tracers2` provides a list of parameters + +Biogeochemical parameter arrays are specified in the code from namelist options in +**icepack\_in**. Table :ref:`tab-bio-tracers2` provides a list of parameter arrays used in the reaction equations, their representation in the code, a -short description of each and the default values. Please keep in mind -that there has only been minimal tuning of the model. +short description of each and the namelist parameters (Table :ref:`tab-bio-tracers-namelist2`) +used in their definition. .. _tab-bio-tracers2: @@ -579,41 +582,22 @@ that there has only been minimal tuning of the model. :header: "Text Variable", "Variable in code", "Description", "Value", "units" :widths: 7, 20, 15, 15, 15 - ":math:`f_{graze}`", "fr\_graze(1:3)", "fraction of growth grazed", "0, 0.1, 0.1", "1" - ":math:`f_{res}`", "fr\_resp", "fraction of growth respired", "0.05", "1" - ":math:`l_{max}`", "max\_loss", "maximum tracer loss fraction", "0.9", "1" - ":math:`m_{pre}`", "mort\_pre(1:3)", "maximum mortality rate", "0.007, 0.007, 0.007", "day\ :math:`^{-1}`" - ":math:`m_{T}`", "mort\_Tdep(1:3)", "mortality temperature decay", "0.03, 0.03, 0.03", ":math:`^o`\ C\ :math:`^{-1}`" - ":math:`T_{max}`", "T\_max", "maximum brine temperature", "0", ":math:`^o`\ C" - ":math:`k_{nitr}`", "k\_nitrif", "nitrification rate", "0", "day\ :math:`^{-1}`" - ":math:`f_{ng}`", "fr\_graze\_e", "fraction of grazing excreted", "0.5", "1" - ":math:`f_{gs}`", "fr\_graze\_s", "fraction of grazing spilled", "0.5", "1" - ":math:`f_{nm}`", "fr\_mort2min", "fraction of mortality to :math:`{\mbox{NH$_4$}}`", "0.5", "1" - ":math:`f_{dg}`", "f\_don", "frac. spilled grazing to :math:`{\mbox{DON}}`", "0.6", "1" - ":math:`k_{nb}`", "kn\_bac :math:`^a`", "bacterial degradation of :math:`{\mbox{DON}}`", "0.03", "day\ :math:`^{-1}`" - ":math:`f_{cg}`", "f\_doc(1:3)", "fraction of mortality to :math:`{\mbox{DOC}}`", "0.4, 0.4, 0.2 ", "1" - ":math:`R_{c:n}^c`", "R\_C2N(1:3)", "algal carbon to nitrogen ratio", "7.0, 7.0, 7.0", "mol/mol" - ":math:`k_{cb}`", "k\_bac1:3\ :math:`^a`", "bacterial degradation of DOC", "0.03, 0.03, 0.03", "day\ :math:`^{-1}`" - ":math:`\tau_{fe}`", "t\_iron\_conv", "conversion time pFe :math:`\leftrightarrow` dFe", "3065.0 ", "day" - ":math:`r^{max}_{fed:doc}`", "max\_dfe\_doc1", "max ratio of dFe to saccharids", "0.1852", "nM Fe\ :math:`/\mu`\ M C" - ":math:`f_{fa}`", "fr\_dFe ", "fraction of remin. N to dFe", "0.3", "1" - ":math:`R_{fe:n}`", "R\_Fe2N(1:3)", "algal Fe to N ratio", "0.023, 0.023, 0.7", "mmol/mol" - ":math:`R_{s:n}`", "R\_S2N(1:3)", "algal S to N ratio", "0.03, 0.03, 0.03", "mol/mol" - ":math:`f_{sr}`", "fr\_resp\_s", "resp. loss as DMSPd", "0.75", "1" - ":math:`\tau_{dmsp}`", "t\_sk\_conv", "Stefels rate", "3.0", "day" - ":math:`\tau_{dms}`", "t\_sk\_ox", "DMS oxidation rate", "10.0", "day" - ":math:`y_{dms}`", "y\_sk\_DMS", "yield for DMS conversion", "0.5", "1" - ":math:`K_{{\mbox{NO$_3$}}}`", "K\_Nit(1:3)", ":math:`{\mbox{NO$_3$}}` half saturation constant", "1,1,1", "mmol/m\ :math:`^{3}`" - ":math:`K_{{\mbox{NH$_4$}}}`", "K\_Am(1:3)", ":math:`{\mbox{NH$_4$}}` half saturation constant", "0.3, 0.3, 0.3", "mmol/m\ :math:`^{-3}`" - ":math:`K_{{\mbox{SiO$_3$}}}`", "K\_Sil(1:3)", "silicate half saturation constant", "4.0, 0, 0", "mmol/m\ :math:`^{-3}`" - ":math:`K_{{\mbox{fed}}}`", "K\_Fe(1:3)", "iron half saturation constant", "1.0, 0.2, 0.1", ":math:`\mu`\ mol/m\ :math:`^{-3}`" - ":math:`op_{min}`", "op\_dep\_min", "boundary for light attenuation", "0.1", "1" - ":math:`chlabs`", "chlabs(1:3)", "light absorption length per chla conc.", "0.03, 0.01, 0.05", "1\ :math:`/`\ m\ :math:`/`\ (mg\ :math:`/`\ m\ :math:`^{3}`)" - ":math:`\alpha`", "alpha2max\_low(1:3)", "light limitation factor", "0.25, 0.25, 0.25", "m\ :math:`^2`/W" - ":math:`\beta`", "beta2max(1:3)", "light inhibition factor", "0.018, 0.0025, 0.01", "m\ :math:`^2`/W" - ":math:`\mu_{max}`", "mu\_max(1:3)", "maximum algal growth rate", "1.44, 0.851, 0.851", "day\ :math:`^{-1}`" - ":math:`\mu_T`", "grow\_Tdep(1:3)", "temperature growth factor", "0.06, 0.06, 0.06", "day\ :math:`^{-1}`" - ":math:`f_{sal}`", "fsal", "salinity growth factor", "1", "1" - ":math:`R_{si:n}`", "R\_Si2N(1:3)", "algal silicate to nitrogen", "1.8, 0, 0", "mol/mol" - -:math:`^a` only (1:2) of DOC and DOC parameters have physical meaning + ":math:`f_{graze}`", "fr\_graze(1:3)", "fraction of growth grazed", "(``fr_graze_diatoms``, ``fr_graze_sp``, ``fr_graze_phaeo``)", "1" + ":math:`m_{pre}`", "mort\_pre(1:3)", "maximum mortality rate", "(``mort_pre_diatoms``, ``mort_pre_sp``, ``mort_pre_phaeo``)", "day\ :math:`^{-1}`" + ":math:`m_{T}`", "mort\_Tdep(1:3)", "mortality temperature decay", "(``mort_Tdep_diatoms``, ``mort_Tdep_sp``, ``mort_Tdep_phaeo``)", ":math:`^o`\ C\ :math:`^{-1}`" + ":math:`f_{cg}`", "f\_doc(1:2)", "fraction of mortality to :math:`{\mbox{DOC}}`", "(``f_doc_s``, ``f_doc_l``)", "1" + ":math:`R_{c:n}`", "R\_C2N(1:3)", "algal carbon to nitrogen ratio", "(``ratio_C2N_diatoms``, ``ratio_C2N_sp``, ``ratio_C2N_phaeo``)", "mol/mol" + ":math:`k_{cb}`", "k\_bac(1:2)", "bacterial degradation of DOC", "(``k_bac_s``, ``k_bac_l``)", "day\ :math:`^{-1}`" + ":math:`R_{fe:n}`", "R\_Fe2N(1:3)", "algal Fe to N ratio", "(``ratio_Fe2N_diatoms``, ``ratio_Fe2N_sp``, ``ratio_Fe2N_phaeo``)", "mmol/mol" + ":math:`R_{s:n}`", "R\_S2N(1:3)", "algal S to N ratio", "(``ratio_S2N_diatoms``, ``ratio_S2N_sp``, ``ratio_S2N_phaeo``)", "mol/mol" + ":math:`K_{{\mbox{NO$_3$}}}`", "K\_Nit(1:3)", ":math:`{\mbox{NO$_3$}}` half saturation constant", "(``K_Nit_diatoms``, ``K_Nit_sp``, ``K_Nit_phaeo``)", "mmol/m\ :math:`^{3}`" + ":math:`K_{{\mbox{NH$_4$}}}`", "K\_Am(1:3)", ":math:`{\mbox{NH$_4$}}` half saturation constant", "(``K_Am_diatoms``, ``K_Am_sp``, ``K_Am_phaeo``)", "mmol/m\ :math:`^{-3}`" + ":math:`K_{{\mbox{SiO$_3$}}}`", "K\_Sil(1:3)", "silicate half saturation constant", "(``K_Sil_diatoms``, ``K_Sil_sp``, ``K_Sil_phaeo``)", "mmol/m\ :math:`^{-3}`" + ":math:`K_{{\mbox{fed}}}`", "K\_Fe(1:3)", "iron half saturation constant", "(``K_Fe_diatoms``, ``K_Fe_sp``, ``K_Fe_phaeo``)", ":math:`\mu`\ mol/m\ :math:`^{-3}`" + ":math:`chlabs`", "chlabs(1:3)", "light absorption length per chla conc.", "(``chlabs_diatoms``, ``chlabs_sp``, ``chlabs_phaeo``)", "1\ :math:`/`\ m\ :math:`/`\ (mg\ :math:`/`\ m\ :math:`^{3}`)" + + ":math:`\alpha`", "alpha2max\_low(1:3)", "light limitation factor", "(``alpha2max_low_diatoms``, ``alpha2max_low_sp``, ``alpha2max_low_phaeo``)", "m\ :math:`^2`/W" + ":math:`\beta`", "beta2max(1:3)", "light inhibition factor", "(``beta2max_diatoms``, ``beta2max_sp``, ``beta2max_phaeo``)", "m\ :math:`^2`/W" + ":math:`\mu_{max}`", "mu\_max(1:3)", "maximum algal growth rate", "(``mu_max_diatoms``, ``mu_max_sp``, ``mu_max_phaeo``)", "day\ :math:`^{-1}`" + ":math:`\mu_T`", "grow\_Tdep(1:3)", "temperature growth factor", "(``grow_Tdep_diatoms``, ``grow_Tdep_sp``, ``grow_Tdep_phaeo``)", "day\ :math:`^{-1}`" + ":math:`R_{si:n}`", "R\_Si2N(1:3)", "algal silicate to nitrogen", "(``ratio_Si2N_diatoms``, ``ratio_Si2N_sp``, ``ratio_Si2N_phaeo``)", "mol/mol"