doc/phys_pkgs/darwin_denit.rst

1d947889e4 Oliv*0001 .. include:: ../defs.hrst
                0002
                0003 .. _Denitrification:
                0004
                0005 Denitrification
                0006 ^^^^^^^^^^^^^^^
                0007
                0008 When :varlink:`DARWIN_ALLOW_DENIT` is defined in DARWIN_OPTIONS.h,
                0009 denitrification occurs, provided
                0010 :math:`{\mathrm{O}}_2<{\mathrm{O}}_2^{{\text{crit}}}`,
                0011
                0012 .. math::
                0013
faa67d1773 Oliv*0014      D_{\op{NH4}} &= R_{\op{DON}} + [R_{\op{PON}}]
1d947889e4 Oliv*0015
faa67d1773 Oliv*0016      D_{\op{NO3}} &= R^{\mathrm{NO3}:\mathrm{P}}_{\op{denit}} \cdot \bigl(
                0017                          R_{\op{DOP}} + [R_{\op{POP}}] \bigr)
1d947889e4 Oliv*0018
                0019 (the particulate organic terms are not present with :varlink:`DARWIN_ALLOW_CDOM`).
                0020
                0021 The diagnostic 'Denit' is this:
                0022
                0023 .. math::
                0024
faa67d1773 Oliv*0025      \op{Denit} = R^{\mathrm{N}:\mathrm{P}}_{\op{denit}} \bigl(
                0026                       R_{\op{DOP}} + [R_{\op{POP}}] \bigr)
1d947889e4 Oliv*0027
                0028
faa67d1773 Oliv*0029 Also, when :math:`{\mathrm{O}}_2<{\mathrm{O}}_2^{{\text{crit}}}` and
1d947889e4 Oliv*0030 :math:`\op{NO}_3<\op{NO}_3^{{\text{crit}}}`, all remineralization,
                0031 denitrification and CDOM degradation (except bleaching) stops.
faa67d1773 Oliv*0032 Bacteria are not affected.
                0033
                0034 .. csv-table:: Denitrification parameters
                0035    :delim: &
                0036    :widths: 16,12,12,15,45
                0037    :class: longtable
                0038    :header: Param, Symbol, Default, Units, Description
                0039
                0040    :varlink:`denit_NP`  & :math:`R^{\mathrm{N}:\mathrm{P}}_{\op{denit}}`   & 120.0 & mmol N / mmol P               & ratio of n to p in denitrification process
                0041    :varlink:`denit_NO3` & :math:`R^{\mathrm{NO3}:\mathrm{P}}_{\op{denit}}` & 104.0 & mmol N / mmol P               & ratio of NO3 uptake to phos remineralization in denitrification
                0042    :varlink:`O2crit`    & :math:`\mathrm{O}_2^{\op{crit}}`                 & 6.0   & mmol O\ :sub:`2` m\ :sup:`-3` & critical oxygen for O2/NO3 remineralization
                0043    :varlink:`NO3crit`   & :math:`\op{NO}_3^{\op{crit}}`                    & 0.01  & mmol N m\ :sup:`-3`           & critical nitrate below which no denit (or remin) happens