Warning, /doc/phys_pkgs/darwin_cons.rst is written in an unsupported language. File is not indexed.
view on githubraw file Latest commit faa67d17 on 2022-01-31 17:00:48 UTC
faa67d1773 Oliv*0001 .. include:: ../defs.hrst
0002
0003 .. _para_phys_pkg_darwin_cons:
0004
0005 Conservation of chemical elements
0006 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
0007
0008 The ecosystem equations cycle the chemical elements C, N, P, Fe, Si, oxygen and
0009 alkalinity in a conservative way, with a few exceptions. Conservation can be
0010 monitored by defining :varlink:`DARWIN_ALLOW_CONS`. This will trigger writing
0011 of a text file darwin_cons_X.txt for each element X that contains the total
0012 amount and global mean for each iteration. Non-conservation can arise in a
0013 number of ways:
0014
0015 If :varlink:`DARWIN_BOTTOM_SINK` is defined, particulate organic matter and
0016 plankton can sink into the bottom where they are presumed to be sedimentized
0017 and no longer accounted for.
0018
0019 With an implicit linear free surface, there is tracer non-conservation at the
0020 surface. This can be corrected by setting :varlink:`darwin_linFSConserv` to
0021 true, see section below.
0022
0023 With :varlink:`DARWIN_ALLOW_CARBON` defined, there are carbon and oxygen fluxes
0024 through the sea surface. If :varlink:`ALLOW_OLD_VIRTUALFLUX` is defined, there
0025 will also be corrective surface fluxes for carbon and alkalinity corresponding
0026 to changes in salinity at the free surface, see :ref:`CarbonChemistry`.
0027
0028
0029 With :varlink:`ironFile` set, there will be an iron flux through the sea
0030 surface. Furthermore, if :varlink:`DARWIN_MINFE` is defined, the total
0031 inorganic iron tracer is adjusted so that free iron does not exceed
0032 :varlink:`freefemax`. With :varlink:`DARWIN_PART_SCAV` defined, some free iron
0033 is scavenged and lost. And finally, if :varlink:`fesedflux` (or
0034 :varlink:`fesedflux_pcm` if :varlink:`DARWIN_IRON_SED_SOURCE_VARIABLE` is
0035 defined) is set, there is an iron source from sediment at the bottom of the
0036 ocean.
0037
0038 Diazotrophs can take up molecular nitrogen, which is not accounted for in the
0039 model. Conversely, with :varlink:`DARWIN_ALLOW_DENIT` defined, ammonia and
0040 nitrate will be turned into molecular nitrogen, see :numref:`Denitrification`.
0041 These sources and sinks of nitrogen are logged in the file darwin_cons_N.txt
0042 in separate columns. Note that they are tendencies while the global totals and
0043 means are snapshots in time.
0044
0045 In order to visualize where tracer non-conservation occurs, it is useful to
0046 write out all ecosystem tendency diagnostics, gDAR##, and then add up the ones
0047 contributing to each element, i.e.,
0048
0049 .. csv-table::
0050 :delim: &
0051 :widths: auto
0052
0053 DIC, DOC, POC, PIC, CDOM*R_CP_CDOM, c\ :sub:`1`, ... & for C
0054 NO3, NO2, NH4, DON, PON, CDOM*R_NP_CDOM, n\ :sub:`1`, ... & for N
0055 PO4, DOP, POP, CDOM, p\ :sub:`1`, ... & for P
0056 FeT, DOFe, POFe, CDOM*R_FeP_CDOM, fe\ :sub:`1`, ... & for Fe
0057 SiO2, POSi, si\ :sub:`1`, ... & for Si
0058 O2 & for oxygen
0059 Alk & for alkalinity
0060
0061 Without :varlink:`DARWIN_ALLOW_NQUOTA`, n\ :sub:`1` has to be replaced by
0062 c\ :sub:`1`\*R_NC\ :sub:`1`, etc. Note that gDAR## contain all the
0063 above-mentioned sources of non-conservation except the limit on free iron.
0064 There are also separate diagnostics for the rates of nitrogen fixation, Nfix,
0065 and denitrification, DenitN. The surface flux of soluble iron is given in
0066 sfcSolFe, that of CO2 in fluxCO2. The change of oxygen in the surface layer
0067 due to air-sea exchange is given in gO2surf, that of alkalinity due to virtual
0068 flux is given in gALKsurf, and the change of DIC due to both regular and
0069 virtual surface fluxes in gDICsurf.
0070
0071
0072 Linear free surface
0073 '''''''''''''''''''
0074
0075 When a linear free surface is used (:varlink:`implicitFreeSurface` is set),
0076 tracers are not conserved as the moving sea surface is not explicitly
0077 represented in the model. With :varlink:`DARWIN_linFSConserve` set, this
0078 non-conservation is fixed globally for each element represented in the
0079 ecosystem model (carbon, nitrogen, phosphorus, iron, silica, Alkalinity and
0080 oxygen). For each of these elements, the total tracer lost at the surface is
0081 computed and added back into the corresponding inorganic tracer (DIC, NO3, PO4,
0082 FeT, DSi, Alk and O2), spread out evenly over the entire 3-dimensional
0083 domain.
0084
0085 .. csv-table:: Linear-free-surface parameters
0086 :delim: &
0087 :widths: auto
0088 :class: longtable
0089 :header: Param, Default, Description
0090
0091 :varlink:`DARWIN_linFSConserve` & .FALSE. & whether to correct for linear-free-surface non-conservation
