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fbdd3978bd Oliv*0001 .. include:: ../defs.hrst
0002
0003 .. _sub_phys_pkgs_darwin_sediments:
0004
0005 Sediments
0006 ^^^^^^^^^
0007
0008 The iron sediment source is discussed in
0009 :numref:`ssub_phys_pkgs_darwin_iron_sedimentation`.
0010
0011 Two versions of the RADI metamodel for sediments are supported: Defining
0012 :varlink:`DARWIN_ALLOW_RADIv1` in DARWIN_OPTIONS.h activates version 1
0013 :cite:`sulpis:22`; Version 2 :cite:`van_der_zant:2026` is activated by
0014 :varlink:`DARWIN_ALLOW_RADIv2`. Both require :varlink:`DARWIN_BOTTOM_SINK` to
0015 be defined.
0016
0017 RADI v1
0018 '''''''
0019
0020 Sediment fluxes are based on modeled sinking fluxes of POC and PIC into the
0021 bottom, see :eq:`eq_darwin_sink`.
0022
0023 DIC, alkalinity and oxygen fluxes can be out of the sediment (positive) or
0024 burial into the sediment (negative):
0025
0026 .. math::
0027 F^{\mathrm{sed}}_{\mathrm{DIC}} = \left( a_1 \Omega_{\mathrm{C}} c
0028 + b_1 F^{\mathrm{sink}}_{\mathrm{POC}}
0029 + c_1 F^{\mathrm{sink}}_{\mathrm{PIC}}
0030 + d_1 c \right) f^{\mathrm{Tcorr}}_{\mathrm{DIC}}
0031
0032 .. math::
0033 F^{\mathrm{sed}}_{\mathrm{ALK}} = \left( a_2 \Omega_{\mathrm{C}} c
0034 + b_2 F^{\mathrm{sink}}_{\mathrm{POC}}
0035 + c_2 F^{\mathrm{sink}}_{\mathrm{PIC}}
0036 + d_2 c \right) f^{\mathrm{Tcorr}}_{\mathrm{ALK}}
0037
0038 .. math::
0039 F^{\mathrm{sed}}_{\mathrm{O2}} = \left( a_3 \Omega_{\mathrm{C}} c
0040 + b_3 F^{\mathrm{sink}}_{\mathrm{POC}}
0041 + c_3 F^{\mathrm{sink}}_{\mathrm{PIC}}
0042 + d_3 c \right) f^{\mathrm{Tcorr}}_{\mathrm{O2}}
0043
0044 POC and Calcite fluxes are burial-only (always negative):
0045
0046 .. math::
0047 F^{\mathrm{sed}}_{\mathrm{POC}} = \min\left(0, - \left( a_4 \Omega_{\mathrm{C}} c
0048 + b_4 F^{\mathrm{sink}}_{\mathrm{POC}}
0049 + c_4 F^{\mathrm{sink}}_{\mathrm{PIC}}
0050 + d_4 c \right) \right)
0051
0052 .. math::
0053 F^{\mathrm{sed}}_{\mathrm{Clc}} = \min\left(0, - \left( a_5 \Omega_{\mathrm{C}} c
0054 + b_5 F^{\mathrm{sink}}_{\mathrm{POC}}
0055 + c_5 F^{\mathrm{sink}}_{\mathrm{PIC}}
0056 + d_5 c \right) \right)
0057
0058 DIC, ALK and O2 fluxes are enhanced at higher temperatures:
0059
0060 .. math::
0061 f^{\mathrm{Tcorr}}_{\mathrm{O2}} &= \frac{0.031558 + 0.001428\cdot|T|}{0.0335572}
0062
0063 f^{\mathrm{Tcorr}}_{\mathrm{DIC}} &= \frac{0.015179 + 0.000795\cdot|T|}{0.016292}
0064
0065 f^{\mathrm{Tcorr}}_{\mathrm{ALK}} &= \frac{0.015179 + 0.000795\cdot|T|}{0.016292}
0066
0067 These are normalized to 1 at :math:`|T|=1.4`.
0068
0069
0070 .. rst-class:: right-align-secondright-col
0071
0072 .. csv-table:: RADI sediment metamodel version 1 parameters
0073 :delim: &
0074 :widths: auto
0075 :header: Name, Symbol, Default, Units
0076 :name: phys_pkg_darwin_radiv1_parameters
0077
0078 :varlink:`sed_a1` & :math:`a_1` & --0.101 &
0079 :varlink:`sed_b1` & :math:`b_1` & 1.040 &
0080 :varlink:`sed_c1` & :math:`c_1` & 0.128 &
0081 :varlink:`sed_d1` & :math:`d_1` & 0.125 &
0082 :varlink:`sed_a2` & :math:`a_2` & --0.225 &
0083 :varlink:`sed_b2` & :math:`b_2` & 0.581 &
0084 :varlink:`sed_c2` & :math:`c_2` & 0.273 &
0085 :varlink:`sed_d2` & :math:`d_2` & 0.211 &
0086 :varlink:`sed_a3` & :math:`a_3` & --0.018 &
0087 :varlink:`sed_b3` & :math:`b_3` & --0.800 &
0088 :varlink:`sed_c3` & :math:`c_3` & 0.011 &
0089 :varlink:`sed_d3` & :math:`d_3` & --0.033 &
0090 :varlink:`sed_a4` & :math:`a_4` & 0.000 &
0091 :varlink:`sed_b4` & :math:`b_4` & 0.027 &
0092 :varlink:`sed_c4` & :math:`c_4` & 0.012 &
0093 :varlink:`sed_d4` & :math:`d_4` & --0.001 &
0094 :varlink:`sed_a5` & :math:`a_5` & 0.117 &
0095 :varlink:`sed_b5` & :math:`b_5` & --0.251 &
0096 :varlink:`sed_c5` & :math:`c_5` & 0.852 &
0097 :varlink:`sed_d5` & :math:`d_5` & --0.127 &
0098 :varlink:`sed_c` & :math:`c` & 3.17E-5 & mmol m\ :sup:`-2` s\ :sup:`-1`
0099
0100
0101 RADI v2
0102 '''''''
0103
0104 Sediment fluxes into the water column (if positive) or burial into the sediment
0105 (if negative) are parametrized in terms of modeled sinking fluxes into the
0106 bottom, see :eq:`eq_darwin_sink`,
0107
0108 .. math::
0109 F^{\mathrm{sed}}_{\mathrm{DIC}} &= a_1 + b_1 |T| + c_1 \Omega_{\mathrm{C}}
0110 + d_1 \left( F^{\mathrm{sink}}_{\mathrm{POC}}
0111 + F^{\mathrm{sink}}_{\mathrm{plank,C}}
0112 \right)
0113 + e_1 F^{\mathrm{sink}}_{\mathrm{PIC}}
0114
0115 F^{\mathrm{sed}}_{\mathrm{ALK}} &= a_2 + b_2 |T| + c_2 \Omega_{\mathrm{C}}
0116 + d_2 \left( F^{\mathrm{sink}}_{\mathrm{POC}}
0117 + F^{\mathrm{sink}}_{\mathrm{plank,C}}
0118 \right)
0119 + e_2 F^{\mathrm{sink}}_{\mathrm{PIC}}
0120
0121 F^{\mathrm{sed}}_{\mathrm{O2}} &= a_3 + b_3 |T| + c_3 \Omega_{\mathrm{C}}
0122 + d_3 \left( F^{\mathrm{sink}}_{\mathrm{POC}}
0123 + F^{\mathrm{sink}}_{\mathrm{plank,C}}
0124 \right)
0125 + e_3 F^{\mathrm{sink}}_{\mathrm{PIC}}
0126
0127 F^{\mathrm{sed}}_{\mathrm{NO3}} &= a_4
0128 + b_4 \left( F^{\mathrm{sink}}_{\mathrm{PON}}
0129 + F^{\mathrm{sink}}_{\mathrm{plank,N}}
0130 \right)
0131 + c_4 F_{\mathrm{DIC}}
0132 + d_4 F_{\mathrm{O2}}
0133
0134 &\quad + e_4 |T| F_{\mathrm{DIC}}
0135 + f_4 |T| F_{\mathrm{O2}}
0136 + g_4 F_{\mathrm{DIC}} F_{\mathrm{O2}}
0137
0138 F^{\mathrm{sed}}_{\mathrm{PO4}} &= a_5 + b_5 |T| + c_5 \Omega_{\mathrm{C}}
0139 + d_5 \left( F^{\mathrm{sink}}_{\mathrm{POP}}
0140 + F^{\mathrm{sink}}_{\mathrm{plank,P}}
0141 \right)
0142 + e_5 F^{\mathrm{sink}}_{\mathrm{PIC}}
0143
0144 F^{\mathrm{sed}}_{\mathrm{NH4}} &= a_6 + b_6 |T| + c_6 \Omega_{\mathrm{C}}
0145 + d_6 \left( F^{\mathrm{sink}}_{\mathrm{PON}}
0146 + F^{\mathrm{sink}}_{\mathrm{plank,N}}
0147 \right)
0148 + e_6 F^{\mathrm{sink}}_{\mathrm{PIC}}
0149
0150
0151 .. rst-class:: right-align-right-col
0152
0153 .. csv-table:: RADI sediment metamodel version 2 parameters
0154 :delim: &
0155 :widths: auto
0156 :header: Name, Symbol, Default
0157 :name: phys_pkg_darwin_radiv2_parameters
0158
0159 :varlink:`sed_globala1` & :math:`a_1` & 2.07E-5
0160 :varlink:`sed_globalb1` & :math:`b_1` & --5.64E-7
0161 :varlink:`sed_globalc1` & :math:`c_1` & --5.42E-6
0162 :varlink:`sed_globald1` & :math:`d_1` & 1.45
0163 :varlink:`sed_globale1` & :math:`e_1` & 4.19E-1
0164 :varlink:`sed_globala2` & :math:`a_2` & 1.55E-5
0165 :varlink:`sed_globalb2` & :math:`b_2` & --2.94E-7
0166 :varlink:`sed_globalc2` & :math:`c_2` & --6.55E-6
0167 :varlink:`sed_globald2` & :math:`d_2` & 5.83E-1
0168 :varlink:`sed_globale2` & :math:`e_2` & 1.38E-1
0169 :varlink:`sed_globala3` & :math:`a_3` & --1.35E-5
0170 :varlink:`sed_globalb3` & :math:`b_3` & 5.08E-8
0171 :varlink:`sed_globalc3` & :math:`c_3` & 1.79E-6
0172 :varlink:`sed_globald3` & :math:`d_3` & --1.07
0173 :varlink:`sed_globale3` & :math:`e_3` & --4.47E-1
0174 :varlink:`sed_globala4` & :math:`a_4` & 3.0E-6
0175 :varlink:`sed_globalb4` & :math:`b_4` & --7.14E-1
0176 :varlink:`sed_globalc4` & :math:`c_4` & 1.94E-1
0177 :varlink:`sed_globald4` & :math:`d_4` & 2.81E-1
0178 :varlink:`sed_globale4` & :math:`e_4` & --2.21E-2
0179 :varlink:`sed_globalf4` & :math:`f_4` & --2.97E-2
0180 :varlink:`sed_globalg4` & :math:`g_4` & --3.20E2
0181 :varlink:`sed_globala5` & :math:`a_5` & --2.42E-7
0182 :varlink:`sed_globalb5` & :math:`b_5` & 1.54E-8
0183 :varlink:`sed_globalc5` & :math:`c_5` & --4.77E-8
0184 :varlink:`sed_globald5` & :math:`d_5` & 1.64
0185 :varlink:`sed_globale5` & :math:`e_5` & 1.20E-2
0186 :varlink:`sed_globala6` & :math:`a_6` & --3.87E-6
0187 :varlink:`sed_globalb6` & :math:`b_6` & 9.15E-8
0188 :varlink:`sed_globalc6` & :math:`c_6` & --7.26E-7
0189 :varlink:`sed_globald6` & :math:`d_6` & 1.73
0190 :varlink:`sed_globale6` & :math:`e_6` & 1.51E-1
0191
0192
0193 Diagnostics
0194 '''''''''''
0195
0196 Diagnostics available with :varlink:`DARWIN_ALLOW_RADIv1`:
0197
0198 .. tabularcolumns:: |\Y{.16}|\Y{.16}|\Y{.18}|\Y{.5}|
0199
0200 .. csv-table:: RADI sediment model version 1 diagnostic fields
0201 :delim: &
0202 :widths: auto
0203 :class: longtable
0204 :header: Name, Code, Units, Description
0205
0206 DICFsed & ``SM______U1`` & mmol C/m\ :sup:`2`/s & DIC sediment flux, :math:`F^{\mathrm{sed}}_{\mathrm{DIC}}`
0207 ALKFsed & ``SM______U1`` & meq/m\ :sup:`2`/s & ALK sediment flux, :math:`F^{\mathrm{sed}}_{\mathrm{ALK}}`
0208 O2Fsed & ``SM______U1`` & mmol O\ :sub:`2` /m\ :sup:`2`/s & O\ :sub:`2` sediment flux, :math:`F^{\mathrm{sed}}_{\mathrm{O2}}`
0209 POCFbur & ``SM______U1`` & mmol C/m\ :sup:`2`/s & POC buried flux, :math:`F^{\mathrm{sed}}_{\mathrm{POC}}` (negative!)
0210 CALFbur & ``SM______U1`` & mmol C/m\ :sup:`2`/s & Calcite buried flux, :math:`F^{\mathrm{sed}}_{\mathrm{CAL}}` (negative!)
0211 sedFlPOC & ``SM_P____U1`` & mmol C/m\ :sup:`2`/s & POC flux from water column to sediment, :math:`F^{\mathrm{sink}}_{\mathrm{POC}}`
0212 sedFlPIC & ``SM_P____U1`` & mmol C/m\ :sup:`2`/s & PIC flux from water column to sediment, :math:`F^{\mathrm{sink}}_{\mathrm{PIC}}`
0213 TcorrO2 & ``SM_P____M1`` & 1 & Temperature correction factor for diffusive O\ :sub:`2` flux
0214 TcorrALK & ``SM_P____M1`` & 1 & Temperature correction factor for diffusive ALK flux
0215 TcorrDIC & ``SM_P____M1`` & 1 & Temperature correction factor for diffusive DIC flux
0216 OmegCbot & ``SM_P____M1`` & 1 & Calcite saturation ratio above the seabed
0217
0218 Diagnostics available with :varlink:`DARWIN_ALLOW_RADIv2`:
0219
0220 .. tabularcolumns:: |\Y{.16}|\Y{.16}|\Y{.18}|\Y{.5}|
0221
0222 .. csv-table:: RADI sediment model version 2 diagnostic fields
0223 :delim: &
0224 :widths: auto
0225 :class: longtable
0226 :header: Name, Code, Units, Description
0227
0228 DICFsed & ``SM______U1`` & mmol C/m\ :sup:`2`/s & DIC sediment flux, :math:`F^{\mathrm{sed}}_{\mathrm{DIC}}`
0229 ALKFsed & ``SM______U1`` & meq/m\ :sup:`2`/s & ALK sediment flux, :math:`F^{\mathrm{sed}}_{\mathrm{ALK}}`
0230 O2Fsed & ``SM______U1`` & mmol O\ :sub:`2` /m\ :sup:`2`/s & O\ :sub:`2` sediment flux, :math:`F^{\mathrm{sed}}_{\mathrm{O2}}`
0231 NO3Fsed & ``SM______U1`` & mmol N/m\ :sup:`2`/s & NO3 sediment flux, :math:`F^{\mathrm{sed}}_{\mathrm{NO3}}`
0232 PO4Fsed & ``SM______U1`` & mmol P/m\ :sup:`2`/s & PO4 sediment flux, :math:`F^{\mathrm{sed}}_{\mathrm{PO3}}`
0233 NH4Fsed & ``SM______U1`` & mmol N/m\ :sup:`2`/s & NH4 sediment flux, :math:`F^{\mathrm{sed}}_{\mathrm{NH4}}`
0234 sedFlPOC & ``SM_P____U1`` & mmol C/m\ :sup:`2`/s & POC flux from water column to sediment, :math:`F^{\mathrm{sink}}_{\mathrm{POC}}`
0235 sedFlPIC & ``SM_P____U1`` & mmol C/m\ :sup:`2`/s & PIC flux from water column to sediment, :math:`F^{\mathrm{sink}}_{\mathrm{PIC}}`
0236 sedFlPOP & ``SM_P____U1`` & mmol P/m\ :sup:`2`/s & POP flux from water column to sediment, :math:`F^{\mathrm{sink}}_{\mathrm{POP}}`
0237 sedFlPON & ``SM_P____U1`` & mmol N/m\ :sup:`2`/s & PON flux from water column to sediment, :math:`F^{\mathrm{sink}}_{\mathrm{PON}}`
0238 sedFplkC & ``SM_P____U1`` & mmol C/m\ :sup:`2`/s & C flux from bottom sink plankton to sed, :math:`F^{\mathrm{sink}}_{\mathrm{plank,C}}`
0239 sedFplkN & ``SM_P____U1`` & mmol N/m\ :sup:`2`/s & N flux from bottom sink plankton to sed, :math:`F^{\mathrm{sink}}_{\mathrm{plank,N}}`
0240 sedFplkP & ``SM_P____U1`` & mmol P/m\ :sup:`2`/s & P flux from bottom sink plankton to sed, :math:`F^{\mathrm{sink}}_{\mathrm{plank,P}}`
0241 OmegCbot & ``SM_P____M1`` & 1 & Calcite saturation ratio above the seabed
0242
