diff --git a/doc/source/science_guide/sg_bgc.rst b/doc/source/science_guide/sg_bgc.rst index 73a6ea0c..236133a8 100755 --- a/doc/source/science_guide/sg_bgc.rst +++ b/doc/source/science_guide/sg_bgc.rst @@ -429,7 +429,7 @@ section :ref:`reactions`. .. _zbgc: -Vertical BGC (''zbgc'') +Vertical BGC ("zbgc") ~~~~~~~~~~~~~~~~~~~~~~~ In order to solve for the vertically resolved biogeochemistry, several @@ -1016,7 +1016,7 @@ are true). "DMSPd", "DMSPdin", "`tr_bgc_DMS`", "dissolved DMSP", ":math:`mmol` :math:`S/m^3`" "DMS", "DMSin", "`tr_bgc_DMS`", "DMS", ":math:`mmol` :math:`S/m^3`" "PON", "PON :math:`^a`", "`tr_bgc_PON`", "passive mobile tracer", ":math:`mmol` :math:`N/m^3`" - "hum", "hum :math:`^{a}`", "`tr_bgc_hum`", "refractive dissolved organic carbon", ":math:`mmol C` :math:`/m^3`" + "hum", "hum :math:`^{a}`", "`tr_bgc_hum`", "refractory dissolved organic carbon", ":math:`mmol C` :math:`/m^3`" "BC (1)", "zaero(1) :math:`^a`", "`tr_zaero`", "black carbon species 1", ":math:`kg` :math:`/m^3`" "BC (2)", "zaero(2) :math:`^a`", "`tr_zaero`", "black carbon species 2", ":math:`kg` :math:`/m^3`" "dust (1)", "zaero(3) :math:`^a`", "`tr_zaero`", "dust species 1", ":math:`kg` :math:`/m^3`" @@ -1101,13 +1101,6 @@ lipids. The :math:`{\mbox{DOC}}^i` equation is: \begin{aligned} \frac{\Delta {\mbox{DOC}}^i}{dt} & = & R_{{\mbox{DOC}}} = f^i_{cg}(graze^{tot} + M_{ort}^{tot} - f_{ng}\mu^{tot} - \frac{DON_{source}}{dt}) R^i_{c:n}-[{\mbox{DOC}}]k^i_{cb} \\ & = & R_{{\mbox{DOC}}} = f^i_{cg}(graze^{tot} + M_{ort}^{tot} - f_{ng}\mu^{tot} - \frac{DON_{source}}{dt}) R^i_{c:n} - \frac{DOC_{loss}}{dt}\end{aligned} - -Dissolved inorganic carbon closes the carbon loop. The :math:`{\mbox{DIC}}` - -.. math:: - - \begin{aligned} - \frac{\Delta {\mbox{DIC}}^i}{dt} & = & \frac{DOC_{loss}}{dt}\end{aligned} Silicate has no biochemical source terms within the ice and is lost only through algal uptake: @@ -1128,16 +1121,16 @@ and particulate iron is .. math:: \begin{aligned} - \frac{\Delta_{fe}{\mbox{fed}}}{dt} & = & -\frac{[{\mbox{fed}}]}{\tau_{fe}} \nonumber \\ - \frac{\Delta_{fe}{\mbox{fep}}}{dt} & = & \frac{[{\mbox{fed}}]}{\tau_{fe}}\end{aligned} + \frac{\tilde{\Delta} {\mbox{fed}}}{dt} & = & -\frac{[{\mbox{fed}}]}{\tau_{fe}} \nonumber \\ + \frac{\tilde{\Delta} {\mbox{fep}}}{dt} & = & \frac{[{\mbox{fed}}]}{\tau_{fe}}\end{aligned} for values less than :math:`r^{max}_{fed:doc}`. .. math:: \begin{aligned} - \frac{\Delta_{fe}{\mbox{fed}}}{dt} & = & \frac{[{\mbox{fep}}]}{\tau_{fe}} \nonumber \\ - \frac{\Delta_{fe}{\mbox{fep}}}{dt} & = & -\frac{[{\mbox{fep}}]}{\tau_{fe}}\end{aligned} + \frac{\tilde{\Delta} {\mbox{fed}}}{dt} & = & \frac{[{\mbox{fep}}]}{\tau_{fe}} \nonumber \\ + \frac{\tilde{\Delta} {\mbox{fep}}}{dt} & = & -\frac{[{\mbox{fep}}]}{\tau_{fe}}\end{aligned} Very long timescales :math:`\tau_{fe}` will remove this source/sink term. The default value is currently set at 3065 days to turn off this @@ -1151,7 +1144,7 @@ remineralization is \begin{aligned} \frac{\Delta {\mbox{fed}}}{dt} & = & R_{{\mbox{fed}}} = -U^{tot}_{{\mbox{fed}}} + f_{fa}R_{fe:n}N_{remin} - + \frac{\Delta_{fe}{\mbox{fed}}}{dt}\end{aligned} + + \frac{\tilde{\Delta}{\mbox{fed}}}{dt}\end{aligned} Particulate iron also includes a source term from algal mortality and grazing that is not immediately bioavailable. The full equation for @@ -1161,7 +1154,7 @@ grazing that is not immediately bioavailable. The full equation for \begin{aligned} \frac{\Delta {\mbox{fep}}}{dt} & = & R_{{\mbox{fep}}} = R_{fe:n}[\frac{\mbox{Z}_{oo}}{dt} + (1-f_{fa})]N_{remin} - + \frac{\Delta_{fe}{\mbox{fep}}}{dt}\end{aligned} + + \frac{\tilde{\Delta}{\mbox{fep}}}{dt}\end{aligned} The sulfur cycle includes :math:`{\mbox{DMS}}` and dissolved DMSP (:math:`{\mbox{DMSPd}}`). Particulate DMSP is assumed to be proportional @@ -1176,14 +1169,14 @@ to the algal concentration, i.e. +f_{nm}M_{ort} ] - \frac{[{\mbox{DMSPd}}]}{\tau_{dmsp}} \nonumber \\ \frac{\Delta {\mbox{DMS}}}{dt} & = & R_{{\mbox{DMS}}} = y_{dms}\frac{[{\mbox{DMSPd}}]}{\tau_{dmsp}} - \frac{[{\mbox{DMS}}]}{\tau_{dms}}\end{aligned} -The dissolved inorganic carbon tracer, :math:`{\mbox{DIC}}`, currently serves to conserve carbon in sea ice. There is no alkalinity tracer nor precipitated forms of carbonate that would be needed for solving the carbonate chemistry. In addition, :math:`{\mbox{DIC}}` never limits photosynthesis in this formulation and carbon to nitrogen ratios for each algal species are fixed at run-time. In the event that :math:`{\mbox{DIC}}` algal requirements exceed the available in situ concentration at a given timestep, the demand is met by an assumed ocean flux into the sea ice. :math:`{\mbox{DIC}}` reactive sources are equivalent to the remineralized losses of :math:`{\mbox{DON}}_{loss} = [{\mbox{DON}}] k_{nb}` +The dissolved inorganic carbon tracer, :math:`{\mbox{DIC}}`, currently serves to conserve carbon in sea ice. There is no alkalinity tracer nor precipitated forms of carbonate that would be needed for solving the carbonate chemistry. In addition, :math:`{\mbox{DIC}}` never limits photosynthesis in this formulation and carbon to nitrogen ratios for each algal species are fixed at run-time. In the event that :math:`{\mbox{DIC}}` algal requirements exceed the available in situ concentration at a given timestep, the demand is met by an assumed ocean flux into the sea ice. :math:`{\mbox{DIC}}` reactive sources are equivalent to the remineralized losses of :math:`{\mbox{DON}}_{loss} = [{\mbox{DON}}] k_{nb}` and :math:`{\mbox{DOC}}^{tot}_{loss} = \sum^{i} [{\mbox{DOC}}]_i (k_{bac})_i` The :math:`{\mbox{DIC}}` reaction equation is .. math:: \begin{aligned} - \frac{\Delta {\mbox{DIC}}}{dt} & = & R_{{\mbox{DIC}}} = {\mbox{DON}}_{loss} * R_{C2N:DON} -\sum^{algae} [(1-fr_{resp})*grow_{N} * R_{C:N}]\end{aligned} + \frac{\Delta {\mbox{DIC}}}{dt} & = & R_{{\mbox{DIC}}} = {\mbox{DON}}_{loss} * R_{C2N:DON} + {\mbox{DOC}}^{tot}_{loss}-\sum^{algae} [(1-fr_{resp})*grow_{N} * R_{C:N}]\end{aligned} where the summation is over all algal groups, :math:`R_{C:N}` is the carbon to nitrogen ratio of each algal group :math:`{\mbox{N}}`, and :math:`R_{C2N:DON}` is the carbon to nitrogen ratio of :math:`{\mbox{DON}}`.