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Update iron scavening docs
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# Conflicts:
#	doc/phys_pkgs/darwin_iron.rst
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jahn committed Jan 4, 2023
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20 changes: 20 additions & 0 deletions doc/manual_references.bib
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Expand Up @@ -1747,6 +1747,16 @@ @Article{parekh:2004
doi = {10.1029/2003GB002061}
}

@Article{parekh:2005,
author = {Parekh, P. and Follows, M. J. and Boyle, E. A.},
title = {Decoupling of iron and phosphate in the global ocean},
journal = {Global Biogeochemical Cycles},
year = {2005},
volume = {19},
pages = {},
doi = {10.1029/2004GB002280}
}

@Article{parkinson:79,
author = {Parkinson, C. L. and W. M. Washington},
title = {A Large-Scale Numerical Model of Sea Ice},
Expand Down Expand Up @@ -1866,6 +1876,16 @@ @Article{ringeisen:20
doi = {10.5194/tc-2020-153}
}

@Article{rios:1998,
author = {Ríos, A. F. and Fraga, F. and Pérez, F. F. and Figueiras, F. G.},
title = {Chemical composition of phytoplankton and {Particulate} {Organic} {Matter} in the {Ría} de {Vigo} ({NW} {Spain})},
journal = {Sciencia Marina},
volume = {6 2},
number = {3},
year = {1998},
pages = {257--271},
}

@Article{roach:15,
author = {Roach, C. J. and H. E. Phillips and N. L. Bindoff and S. R. Rintoul},
year = 2015,
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10 changes: 6 additions & 4 deletions doc/phys_pkgs/darwin.rst
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Expand Up @@ -362,13 +362,15 @@ General parameters are set in namelist :varlink:`DARWIN_PARAMS`:
:varlink:`uptakeTempAe` & 0.0 & 1/K & temperature coefficient for uptake (TEMP_VERSION 4)
:varlink:`alpfe` & 0.04 & & solubility of Fe dust
:varlink:`scav` & 0.4/year & 1/s & fixed iron scavenging rate
:varlink:`scav_tau` & 0.2 & & factor for converting Th scavenging rates to iron ones
:varlink:`scav_inter` & 0.079 / day & L\ :sup:`e` mg\ :sup:`-e` s\ :sup:`-1` & intercept of scavenging power law (e=e\ :sub:`scav`)
:varlink:`scav_exp` & 0.58 & & exponent of scavenging power law
:varlink:`scav_POC_wgt` & 0.02173 & g/mmol |nbsp| C & weight POC contributes to POM
:varlink:`scav_POSi_wgt` & 0.069 & g/mmol |nbsp| Si & weight POSi contributes to POM
:varlink:`scav_PIC_wgt` & 0.100 & g/mmol |nbsp| C & weight PIC contributes to POM
:varlink:`ligand_tot` & 1D-3 & mol/m\ :sup:`3` & total ligand concentration
:varlink:`ligand_stab` & 2D5 & m\ :sup:`3`/mol & ligand stability rate ratio
:varlink:`freefemax` & 0.4D-3 & mol/m\ :sup:`3` & max concentration of free iron
:varlink:`scav_rat` & 0.005 / day & 1/s & rate of POM-based iron scavenging
:varlink:`scav_inter` & 0.079 & & intercept of scavenging power law
:varlink:`scav_exp` & 0.58 & & exponent of scavenging power law
:varlink:`scav_R_POPPOC` & 1.1321D-4 & mmol P / mmol C & POP\:POC ratio for :varlink:`DARWIN_PART_SCAV_POP`
:varlink:`depthfesed` & -1.0 & m & depth above which to add sediment source (was -1000)
:varlink:`fesedflux` & 1D-3 / day & mmol Fe /m\ :sup:`2`/s & fixed iron flux from sediment
:varlink:`fesedflux_pcm` & 0.68D-3 & mmol Fe / mmol C & iron input per POC sinking into bottom for :varlink:`DARWIN_IRON_SED_SOURCE_VARIABLE`
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66 changes: 51 additions & 15 deletions doc/phys_pkgs/darwin_iron.rst
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Expand Up @@ -88,21 +88,42 @@ The scavenging rate for free iron is
.. math::
r_{{\text{scav}}}= \begin{cases}
r_{{\text{scav}}}I_{{\text{scav}}}\op{POC}^{e_{{\text{scav}}}}
& \text{for POM-based scavenging,} \\
\op{scav}
& \text{for constant scavenging.}
& \text{for fixed-rate scavenging,} \\
\tau_{{\text{scav}}}I_{{\text{scav}}}\op{POM}^{e_{{\text{scav}}}}
& \text{for particle-based scavenging.}
\end{cases}
To select POM-based scavenging, #define :varlink:`DARWIN_PART_SCAV`.
If :varlink:`DARWIN_PART_SCAV_POP` is defined, :math:`\op{POC}` is
replaced by :math:`\op{POP}\!/R^{\op{POP}:\op{POC}}_{{\text{scav}}}`.
To select particle-based scavenging following Parekh et al. (2005)
:cite:`parekh:2005`, define :varlink:`DARWIN_PART_SCAV`. POM is the
concentration of particulate organic matter in units of mg/L. It is
parameterized in terms of POC, POSi and PIC,

The concentration of free iron is determined following
Parekh et al. (2004) :cite:`parekh:2004` and
Dutkiewicz et al. (2005) :cite:`dutkiewicz:2005`. Free dissolved iron,
Fe', is assumed to be in equilibrium with dissolved iron bound
to ligands, FeL,
.. math::
\op{POM} = w^{\text{scav}}_{\text{POC}} \op{POC}
+ w^{\text{scav}}_{\text{POSi}} \op{POSi}
+ w^{\text{scav}}_{\text{PIC}} \op{PIC}
\;.
The value for :math:`w^{\text{scav}}_{\text{POC}}` is taken from Rios et al.
(1998) :cite:`rios:1998` as the weight of as detritus without opal per mol of
carbon. :math:`w^{\text{scav}}_{\text{POSi}}` and
:math:`w^{\text{scav}}_{\text{PIC}}` are just the molecular weights of opal
(per mol Si) and calcium carbonate, see
:numref:`tab_phys_pkgs_darwin_iron_params`.

The old (and deprecated) formulation of scavenging in terms of POP can be
recovered by defining :varlink:`DARWIN_PART_SCAV_POP`, in which case
:math:`\op{POM}` is replaced by
:math:`\op{POP}\!/R^{\op{POP}:\op{POC}}_{{\text{scav}}}`. Parameter names and
defaults are different in this case, see
:numref:`tab_phys_pkgs_darwin_scav_pop`.

The concentration of free iron, Fe', is determined following Parekh et al.
(2004) :cite:`parekh:2004` and Dutkiewicz et al. (2005)
:cite:`dutkiewicz:2005`. Free dissolved iron is assumed to be in equilibrium
with dissolved iron bound to ligands, FeL,

.. math:: \op{Fe}' + L' \rightleftharpoons \op{FeL}

Expand Down Expand Up @@ -133,6 +154,7 @@ and after each biogeochemical subtimestep.
:delim: &
:widths: auto
:header: Parameter, Symbol, Default, Units, Description
:name: tab_phys_pkgs_darwin_iron_params

:varlink:`alpfe` & :math:`\alpha_{\op{Fe}}` & 0.04 & & solubility of Fe dust
:varlink:`depthfesed` & :math:`d_{\op{sed}}` & -1.0 & m & depth above which to add sediment source
Expand All @@ -144,10 +166,24 @@ and after each biogeochemical subtimestep.
:varlink:`solFeVent` & :math:`\alpha_{\op{Fe}}^{\op{vents}}` & 0.002 & & solubility of iron from hydrothermal vents
:varlink:`R_FeHe3_vent` & :math:`R^{\op{Fe:^3He}}_{\op{vents}}` & 4.5E8 & mol Fe / mol :sup:`3`\ He & Fe:\ :sup:`3`\ He ratio for hydrothermal vents
:varlink:`scav` & scav & 0.4/year & 1/s & fixed iron scavenging rate
:varlink:`scav_rat` & :math:`r_{\op{scav}}` & 0.005 / day & 1/s & rate of POM-based iron scavenging
:varlink:`scav_inter` & :math:`I_{\op{scav}}` & 0.079 & & intercept of scavenging power law
:varlink:`scav_tau` & :math:`\tau_{\op{scav}}` & 0.2 & & factor for converting Th scavenging rates to iron ones
:varlink:`scav_inter` & :math:`I_{\op{scav}}` & 0.079 / day & L\ :sup:`e` mg\ :sup:`-e` s\ :sup:`-1` & intercept of scavenging power law (e=e\ :sub:`scav`)
:varlink:`scav_exp` & :math:`e_{\op{scav}}` & 0.58 & & exponent of scavenging power law
:varlink:`scav_R_POPPOC` & :math:`R^{\op{POP:POC}}_{\op{scav}}` & 1.1321E-4 & mmol P / mmol C & POP\:POC ratio for :varlink:`DARWIN_PART_SCAV_POP`
:varlink:`scav_POC_wgt` & :math:`w^{\op{scav}}_{\op{POC}}` & 0.02173 & g/mmol |nbsp| C & weight POC contributes to POM
:varlink:`scav_POSi_wgt` & :math:`w^{\op{scav}}_{\op{POSi}}` & 0.069 & g/mmol |nbsp| Si & weight POSi contributes to POM
:varlink:`scav_PIC_wgt` & :math:`w^{\op{scav}}_{\op{PIC}}` & 0.100 & g/mmol |nbsp| C & weight PIC contributes to POM
:varlink:`ligand_tot` & :math:`L_{\op{T}}` & 1E-3 & mmol/m\ :sup:`3` & total ligand concentration
:varlink:`ligand_stab` & :math:`\beta_{\op{stab}}` & .2E6 & m\ :sup:`3`/mmol & ligand stability rate ratio
:varlink:`ligand_stab` & :math:`\beta_{\op{stab}}` & 0.2E6 & m\ :sup:`3`/mmol & ligand stability rate ratio
:varlink:`freefemax` & :math:`\op{Fe}'_{\op{max}}` & 0.4E-3 & mmol/m\ :sup:`3` & max concentration of free iron


.. csv-table:: Iron parameters for :varlink:`DARWIN_PART_SCAV_POP`
:delim: &
:widths: auto
:header: Parameter, Symbol, Default, Units, Description
:name: tab_phys_pkgs_darwin_scav_pop

:varlink:`scav_rat` & :math:`\tau_{\op{scav}}` & 0.005 / day & 1/s & rate factor
:varlink:`scav_inter` & :math:`I_{\op{scav}}` & 0.079 & L\ :sup:`e` mg\ :sup:`-e` & intercept of scavenging power law (e=e\ :sub:`scav`)
:varlink:`scav_exp` & :math:`e_{\op{scav}}` & 0.58 & & exponent of scavenging power law
:varlink:`scav_R_POPPOC` & :math:`R^{\op{POP:POC}}_{\op{scav}}` & 1.1321E-4 & mmol |nbsp| P / g & POP\:POC ratio

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