\(\newcommand{\p}[1]{\frac{\partial }{\partial #1}}\) \(\newcommand{\pp}[2]{\frac{\partial #1}{\partial #2}}\) \(\newcommand{\dd}[2]{\frac{d #1}{d #2}}\) \(\newcommand{\h}{\frac{1}{2}}\) \(\newcommand{\op}[1]{\operatorname{#1}}\)

8.7.3.21. Conservation of chemical elements¶

The ecosystem equations cycle the chemical elements C, N, P, Fe, Si, oxygen and alkalinity in a conservative way, with a few exceptions. Conservation can be monitored by defining DARWIN_ALLOW_CONS. This will trigger writing of a text file darwin_cons_X.txt for each element X that contains the total amount and global mean for each iteration. Non-conservation can arise in a number of ways:

If DARWIN_BOTTOM_SINK is defined, particulate organic matter and plankton can sink into the bottom where they are presumed to be sedimentized and no longer accounted for.

With an implicit linear free surface, there is tracer non-conservation at the surface. This can be corrected by setting darwin_linFSConserv to true, see section below.

With DARWIN_ALLOW_CARBON defined, there are carbon and oxygen fluxes through the sea surface. If ALLOW_OLD_VIRTUALFLUX is defined, there will also be corrective surface fluxes for carbon and alkalinity corresponding to changes in salinity at the free surface, see Carbon chemistry.

With ironFile set, there will be an iron flux through the sea surface. Furthermore, if DARWIN_MINFE is defined, the total inorganic iron tracer is adjusted so that free iron does not exceed freefemax. With DARWIN_PART_SCAV defined, some free iron is scavenged and lost. And finally, if fesedflux (or fesedflux_pcm if DARWIN_IRON_SED_SOURCE_VARIABLE is defined) is set, there is an iron source from sediment at the bottom of the ocean.

Diazotrophs can take up molecular nitrogen, which is not accounted for in the model. Conversely, with DARWIN_ALLOW_DENIT defined, ammonia and nitrate will be turned into molecular nitrogen, see Section 8.7.3.9. These sources and sinks of nitrogen are logged in the file darwin_cons_N.txt in separate columns. Note that they are tendencies while the global totals and means are snapshots in time.

In order to visualize where tracer non-conservation occurs, it is useful to write out all ecosystem tendency diagnostics, gDAR##, and then add up the ones contributing to each element, i.e.,

DIC, DOC, POC, PIC, CDOM*R_CP_CDOM, c₁, …	for C
NO3, NO2, NH4, DON, PON, CDOM*R_NP_CDOM, n₁, …	for N
PO4, DOP, POP, CDOM, p₁, …	for P
FeT, DOFe, POFe, CDOM*R_FeP_CDOM, fe₁, …	for Fe
SiO2, POSi, si₁, …	for Si
O2	for oxygen
Alk	for alkalinity

Without DARWIN_ALLOW_NQUOTA, n₁ has to be replaced by c₁*R_NC₁, etc. Note that gDAR## contain all the above-mentioned sources of non-conservation except the limit on free iron. There are also separate diagnostics for the rates of nitrogen fixation, Nfix, and denitrification, DenitN. The surface flux of soluble iron is given in sfcSolFe, that of CO2 in fluxCO2. The change of oxygen in the surface layer due to air-sea exchange is given in gO2surf, that of alkalinity due to virtual flux is given in gALKsurf, and the change of DIC due to both regular and virtual surface fluxes in gDICsurf.

8.7.3.21.1. Linear free surface¶

When a linear free surface is used (implicitFreeSurface is set), tracers are not conserved as the moving sea surface is not explicitly represented in the model. With DARWIN_linFSConserve set, this non-conservation is fixed globally for each element represented in the ecosystem model (carbon, nitrogen, phosphorus, iron, silica, Alkalinity and oxygen). For each of these elements, the total tracer lost at the surface is computed and added back into the corresponding inorganic tracer (DIC, NO3, PO4, FeT, DSi, Alk and O2), spread out evenly over the entire 3-dimensional domain.

Table 8.59 Linear-free-surface parameters¶
Param	Default	Description
DARWIN_linFSConserve	.FALSE.	whether to correct for linear-free-surface non-conservation