darwin3 |
|
|
|
|||
Warning, /doc/phys_pkgs/darwin_carbon.rst is written in an unsupported language. File is not indexed.
view on githubraw file Latest commit 5be9e536 on 2025-03-13 14:15:58 UTC1d947889e4 Oliv*0001 .. include:: ../defs.hrst 0002 0003 .. _CarbonChemistry: 0004 0005 Carbon chemistry 0006 ^^^^^^^^^^^^^^^^ 0007 3c930300af Oliv*0008 Carbon chemistry options 0009 '''''''''''''''''''''''' 0010 0011 The following preprocessor options affect the computation of pH, 0012 :math:`[\mathrm{CO}_2^*]` and :math:`[\mathrm{CO}_3^{2-}]`: 0013 0014 .. tabularcolumns:: |l|l| 0015 0016 .. csv-table:: CPP options for carbon chemistry 0017 :delim: & 0018 :widths: auto 0019 :class: longtable 0020 :header: CPP option, description 0021 0022 :varlink:`DARWIN_ALLOW_CARBON` & enable air-sea carbon exchange and ALK and O\ :sub:`2` tracers 0023 :varlink:`DARWIN_SOLVESAPHE` & compile Munhoven "Solvesaphe" pH/pCO\ :sub:`2` solver package 0024 :varlink:`DARWIN_TOTALPHSCALE` & consistently use the total pH scale for carbon chemistry coefficients 5be9e53640 Oliv*0025 :varlink:`DARWIN_ALLOW_RADIv1` & enable RADI sediment metamodel version 1 0026 :varlink:`DARWIN_ALLOW_RADIv2` & enable RADI sediment metamodel version 2 3c930300af Oliv*0027 0028 :varlink:`DARWIN_ALLOW_CARBON` is required to enable the computation 0029 of pH, :math:`[\mathrm{CO}_2^*]` and :math:`[\mathrm{CO}_3^{2-}]` values. If 0030 :varlink:`DARWIN_SOLVESAPHE` is defined, the coefficients for the carbon solver 0031 are computed following to Munhoven (2013) :cite:`munhoven:13`, otherwise 0032 according to Follows et al. (2006) :cite:`follows:06`. In this case, 0033 :varlink:`DARWIN_TOTALPHSCALE` can be defined to ensure all computations 5be9e53640 Oliv*0034 consistently use the total pH scale. :varlink:`DARWIN_ALLOW_RADIv1` activates 0035 version 1 of the RADI sediment model following :cite:`sulpis:22`. Version 2 0036 is activated by :varlink:`DARWIN_ALLOW_RADIv2`. 3c930300af Oliv*0037 0038 The run-time parameter :varlink:`selectPHsolver` decides which pH solver to use: 0039 0040 .. table:: 0041 0042 +----------------+----------------------------------+ 0043 | selectPHsolver | meaning | 0044 +================+==================================+ 0045 | 0 (default) | use Follows et al. (2006) solver | 0046 +----------------+----------------------------------+ 0047 | 1 | use the GENERAL solver | 0048 +----------------+----------------------------------+ 0049 | 2 | use SEC solver | 0050 +----------------+----------------------------------+ 0051 | 3 | use FAST solver routine | 0052 +----------------+----------------------------------+ 0053 0054 All options except '0' require :varlink:`DARWIN_SOLVESAPHE` to be defined. 0055 Note that if the Follows et al. solver is selected with 0056 :varlink:`DARWIN_SOLVESAPHE`, the dissociation coefficients from Solvesaphe 0057 will be used. More Solvesaphe parameters: 0058 0059 .. csv-table:: 0060 :delim: & 0061 :widths: auto 0062 :header: selectBTconst, estimates borate concentration from salinity 0063 0064 1 (default) & use default formulation of Uppström (1974) :cite:`uppstrom:74` (same as S/R CARBON_COEFFS) 0065 2 & use new formulation from Lee et al (2010) :cite:`lee:10` 0066 0067 .. csv-table:: 0068 :delim: & 0069 :widths: auto 0070 :header: selectFTconst, estimates fluoride concentration from salinity 0071 0072 1 (default) & use default formulation of Riley (1965) :cite:`riley:65` (same as S/R CARBON_COEFFS) 0073 2 & use new formulation from Culkin (1965) :cite:`culkin:65` 0074 0075 .. csv-table:: 0076 :delim: & 0077 :widths: auto 0078 :header: selectHFconst, sets the first dissociation constant for hydrogen fluoride 0079 0080 1 (default) & use default Dickson and Riley (1979) :cite:`dickson:79` (same as S/R CARBON_COEFFS) 0081 2 & use new formulation of Perez and Fraga (1987) :cite:`perez:87` 0082 0083 .. csv-table:: 0084 :delim: & 0085 :widths: auto 0086 :header: selectK1K2const, sets the 1rst and 2nd dissociation constants of carbonic acid 0087 0088 1 (default) & use default formulation of Millero (1995) :cite:`millero:95` with data from Mehrbach et al. (1973) :cite:`mehrbach:73` (same as S/R CARBON_COEFFS) 0089 2 & use formulation of Roy et al. (1993) :cite:`roy:93` 0090 3 & use "combination" formulation of Millero (1995) :cite:`millero:95` 0091 4 & use formulation of Luecker et al. (2000) :cite:`lueker:00` 0092 5 & use formulation of Millero (2010) :cite:`millero:10b` 0093 6 & use formulation of Waters, Millero, Woosley (2014) :cite:`waters:13,waters:14` 0094 0095 The input parameters for the carbon solver are salinity, temperature, DIC, 0096 alkalinity, phosphate and silica. Limits are applied to all these quantities 0097 to ensure convergence. The corresponsing parameters are shown in 0098 :numref:`phys_pkg_darwin_carbon_parameters`. There is a separate set of 0099 parameters for the initialization phase which is treated differently from calls 0100 to the solver during the run: the Follows et al. solver is called 10 times in 0101 order to allow the solution to converge. The Munhoven solvers have a special 0102 initialization routine. faa67d1773 Oliv*0103 0104 .. csv-table:: Carbon parameters 3c930300af Oliv*0105 :delim: & 0106 :widths: 20,11,11,17,41 0107 :header: Name, Symbol, Default, Units, Description 0108 :name: phys_pkg_darwin_carbon_parameters 0109 0110 :varlink:`surfSaltMinInit` & & 4.0 & g/kg & limits for carbon solver input at initialization 0111 :varlink:`surfSaltMaxInit` & & 50.0 & g/kg & ... 0112 :varlink:`surfTempMinInit` & & --4.0 & °C & 0113 :varlink:`surfTempMaxInit` & & 39.0 & °C & 0114 :varlink:`surfDICMinInit` & & 10.0 & mmol C m\ :sup:`-3` & 0115 :varlink:`surfDICMaxInit` & & 4000.0 & mmol C m\ :sup:`-3` & 0116 :varlink:`surfALKMinInit` & & 10.0 & meq m\ :sup:`-3` & 0117 :varlink:`surfALKMaxInit` & & 4000.0 & meq m\ :sup:`-3` & 0118 :varlink:`surfPO4MinInit` & & 1D-10 & mmol P m\ :sup:`-3` & 0119 :varlink:`surfPO4MaxInit` & & 10.0 & mmol P m\ :sup:`-3` & 0120 :varlink:`surfSiMinInit` & & 1D-8 & mmol Si m\ :sup:`-3` & 0121 :varlink:`surfSiMaxInit` & & 500.0 & mmol Si m\ :sup:`-3` & 0122 :varlink:`surfSaltMin` & & 4.0 & g/kg & limits for carbon solver input during run 0123 :varlink:`surfSaltMax` & & 50.0 & g/kg & ... 0124 :varlink:`surfTempMin` & & --4.0 & °C & 0125 :varlink:`surfTempMax` & & 39.0 & °C & 0126 :varlink:`surfDICMin` & & 400.0 & mmol C m\ :sup:`-3` & 0127 :varlink:`surfDICMax` & & 4000.0 & mmol C m\ :sup:`-3` & 0128 :varlink:`surfALKMin` & & 400.0 & meq m\ :sup:`-3` & 0129 :varlink:`surfALKMax` & & 4000.0 & meq m\ :sup:`-3` & 0130 :varlink:`surfPO4Min` & & 1D-10 & mmol P m\ :sup:`-3` & 0131 :varlink:`surfPO4Max` & & 10.0 & mmol P m\ :sup:`-3` & 0132 :varlink:`surfSiMin` & & 1D-8 & mmol Si m\ :sup:`-3` & 0133 :varlink:`surfSiMax` & & 500.0 & mmol Si m\ :sup:`-3` & 0134 0135 0136 Calcite dissolution 0137 ''''''''''''''''''' 0138 0139 The parameter :varlink:`darwin_disscSelect` determines the calcite dissolution** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 141.
0140 rate law. A value of ‘0’ gives a constant dissolution rate, 0141 0142 .. math:: 0143 0144 D_{\mathrm{PIC}} = \kappa^{\mathrm{diss}}_{\mathrm{C}} \cdot \op{PIC} 0145 \;. 0146** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 148.
0147 A value of ‘1’ gives the power law of Keir (1980) :cite:`keir:80`, 0148 0149 .. math:: 0150 0151 D_{\mathrm{PIC}} = \kappa_{\text{Keir}} (1 - \Omega_{\mathrm{C}})^{e_{\text{Keir}}} \cdot \op{PIC} 0152 \;, 0153** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 155.
0154 a value of ‘2’ the double power law of Naviaux (2019) :cite:`naviaux:19`, 0155 0156 .. math:: 0157 0158 D_{\mathrm{PIC}} = \op{PIC} \cdot \begin{cases} 0159 5.22\cdot 10^{-9} (1 - \Omega_{\mathrm{C}})^{0.11} 0160 &\text{for } \Omega_{\mathrm{C}} > 0.8272 \;, \\ 0161 1.65\cdot 10^{-5} (1 - \Omega_{\mathrm{C}})^{4.7} 0162 &\text{for } \Omega_{\mathrm{C}} \le 0.8272 \;. 0163 \end{cases} 0164 0165 Here, 0166 0167 .. math:: 0168 0169 \Omega_{\mathrm{C}} = \frac{[\op{Ca}^{2+}] [\op{CO}_3^{2-}]}{K_{\mathrm{sp}}^{\mathrm{calc}}} 0170 0171 and the concentration of calcium is parameterized as a function of salinity. 0172 With :varlink:`DARWIN_SOLVESAPHE`, 0173 0174 .. math:: 0175 0176 [\op{Ca}^{2+}] = 0.010282\frac{S}{35} 0177 \;, 0178 0179 otherwise, 0180 0181 .. math:: 0182 0183 [\op{Ca}^{2+}] = 0.01028\frac{S}{35} 0184 \;. 0185 0186 0187 .. csv-table:: Calcite dissolution parameters 0188 :delim: & 0189 :widths: 23,12,15,10,40 0190 :header: Name, Symbol, Default, Units, Description 0191 :name: phys_pkg_darwin_calcite_parameters 0192 0193 :varlink:`darwin_disscSelect` & & 0 & & choose calcite dissolution rate law 0194 & & & & 0: constant 0195 & & & & 1: Keir 0196 & & & & 2: Naviaux 0197 :varlink:`Kdissc` & :math:`\kappa^{\mathrm{diss}}_{\mathrm{C}}` & 1/(300 days) & 1/s & constant calcite dissolution rate 0198 :varlink:`darwin_KeirCoeff` & :math:`\kappa_{\text{Keir}}` & e\ :sup:`7.177` /100/86400 & 1/s & Keir rate factor 0199 :varlink:`darwin_KeirExp` & :math:`e_{\text{Keir}}` & 4.54 & & Keir rate exponent 0200 0201 0202 .. _CarbonChemistryDiagnostics: 0203 0204 Diagnostics 0205 ''''''''''' 0206 0207 Diagnostics available with :varlink:`DARWIN_ALLOW_CARBON`: 0208 0209 .. tabularcolumns:: |\Y{.16}|\Y{.16}|\Y{.18}|\Y{.5}| 0210 0211 .. csv-table:: Darwin package carbon diagnostic fields faa67d1773 Oliv*0212 :delim: & 0213 :widths: auto 3c930300af Oliv*0214 :class: longtable 0215 :header: Name, Code, Units, Description 0216 0217 apCO2 & ``SM_P____L1`` & atm & atmospheric pCO\ :sub:`2` 0218 apCO2sat & ``SM_P____L1`` & atm & atmospheric pCO\ :sub:`2` sat 0219 pH & ``SMR_____MR`` & 1 & pH 0220 pCO2 & ``SMRP____MR`` & atm & Partial Pressure of CO\ :sub:`2` in the ocean 0221 CO3 & ``SMR_____MR`` & mol/kg & Concentration of carbonate 0222 KspTPClc & ``SMR_____MR`` & mol\ :sup:`2`/kg\ :sup:`2` & Solubility product for calcite 0223 OmegaC & ``SMR_____MR`` & 1 & Calcite saturation ratio 0224 fugfCO2 & ``SM_P____L1`` & 1 & Fugacity factor of CO\ :sub:`2` at surface 0225 fCO2 & ``SM_P____L1`` & atm & Fugacity of CO\ :sub:`2` (atm) 0226 fluxCO2 & ``SM______L1`` & mmol C/m\ :sup:`2`/s & Flux of CO\ :sub:`2` - air-sea exch 0227 fluxO2 & ``SM______L1`` & mmol O\ :sub:`2` /m\ :sup:`2`/s & Flux of O\ :sub:`2` - air-sea exch 0228 VfluxCO2 & ``SM______L1`` & mmol C/m\ :sup:`2`/s & Virtual flux of CO\ :sub:`2` 0229 VfluxAlk & ``SM______L1`` & meq/m\ :sup:`2`/s & Virtual flux of alkalinity 0230 gDICsurf & ``SM______L1`` & mmol C/m\ :sup:`3`/s & Tendency of DIC due to air-sea exch + oldvirt.flux 0231 gALKsurf & ``SM______L1`` & meq/m\ :sup:`3`/s & Tendency of ALK due to oldvirt.flux 0232 gO2surf & ``SM______L1`` & mmol O\ :sub:`2` /m\ :sup:`3`/s & Tendency of O\ :sub:`2` due to air-sea exch 0233 C_DIC & ``SMR_____MR`` & mmol C/m\ :sup:`3`/s & Consumption of DIC 0234 C_DICPIC & ``SMR_____MR`` & mmol C/m\ :sup:`3`/s & Consumption of DIC due to PIC 0235 respDIC & ``SMR_____MR`` & mmol C/m\ :sup:`3`/s & DIC due to respiration 0236 rDIC_DOC & ``SMR_____MR`` & mmol C/m\ :sup:`3`/s & DIC due to remineralization of DOC 0237 rDIC_POC & ``SMR_____MR`` & mmol C/m\ :sup:`3`/s & DIC due to remineralization of POC 0238 dDIC_PIC & ``SMR_____MR`` & mmol C/m\ :sup:`3`/s & DIC due to dissolution of PIC 0239 C_ALK & ``SMR_____MR`` & meq/m\ :sup:`3`/s & Consumption of alkalinity 0240 S_ALK & ``SMR_____MR`` & meq/m\ :sup:`3`/s & Non-transport source of alkalinity 0241 C_O2 & ``SMR_____MR`` & mmol O\ :sub:`2` /m\ :sup:`3`/s & Consumption of oxygen 0242 S_O2 & ``SMR_____MR`` & mmol O\ :sub:`2` /m\ :sup:`3`/s & Non-transport source of oxygen 0243 0244 The sign convention for the fluxCO2, gDICsurf, gALKsurf and gO2surf diagnostics 0245 is such that positive values increase the concentration in the ocean. Note 0246 that the units vary: gDICsurf, gALKsurf and gO2surf are tracer tendencies, 0247 i.e., change rates of concentration, while fluxCO2 is a flux per area of 0248 sea surface. 0249 5be9e53640 Oliv*0250 Diagnostics available with :varlink:`DARWIN_ALLOW_RADIv1`: 3c930300af Oliv*0251 0252 .. tabularcolumns:: |\Y{.16}|\Y{.16}|\Y{.18}|\Y{.5}| 0253 5be9e53640 Oliv*0254 .. csv-table:: RADI sediment model version 1 diagnostic fields 3c930300af Oliv*0255 :delim: & 0256 :widths: auto 0257 :class: longtable 0258 :header: Name, Code, Units, Description 0259 0260 DICFsed & ``SM______U1`` & mmol C/m\ :sup:`2`/s & DIC sediment flux 0261 ALKFsed & ``SM______U1`` & meq/m\ :sup:`2`/s & ALK sediment flux 0262 O2Fsed & ``SM______U1`` & mmol O\ :sub:`2` /m\ :sup:`2`/s & O\ :sub:`2` sediment flux 0263 POCFbur & ``SM______U1`` & mmol C/m\ :sup:`2`/s & POC buried flux 0264 CALFbur & ``SM______U1`` & mmol C/m\ :sup:`2`/s & Calcite buried flux 0265 sedFlPOC & ``SM_P____U1`` & mmol C/m\ :sup:`2`/s & POC flux from water column to sediment 0266 sedFlPIC & ``SM_P____U1`` & mmol C/m\ :sup:`2`/s & PIC flux from water column to sediment 0267 TcorrO2 & ``SM_P____M1`` & 1 & Temperature correction factor for diffusive O\ :sub:`2` flux 0268 TcorrALK & ``SM_P____M1`` & 1 & Temperature correction factor for diffusive ALK flux 0269 TcorrDIC & ``SM_P____M1`` & 1 & Temperature correction factor for diffusive DIC flux 0270 OmegCbot & ``SM_P____M1`` & 1 & Calcite saturation ratio above the seabed 0271 5be9e53640 Oliv*0272 Diagnostics available with :varlink:`DARWIN_ALLOW_RADIv2`: 0273 0274 .. tabularcolumns:: |\Y{.16}|\Y{.16}|\Y{.18}|\Y{.5}| 0275 0276 .. csv-table:: RADI sediment model version 2 diagnostic fields 0277 :delim: & 0278 :widths: auto 0279 :class: longtable 0280 :header: Name, Code, Units, Description 0281 0282 DICFsed & ``SM______U1`` & mmol C/m\ :sup:`2`/s & DIC sediment flux 0283 ALKFsed & ``SM______U1`` & meq/m\ :sup:`2`/s & ALK sediment flux 0284 O2Fsed & ``SM______U1`` & mmol O\ :sub:`2` /m\ :sup:`2`/s & O\ :sub:`2` sediment flux 0285 NO3Fsed & ``SM______U1`` & mmol N/m\ :sup:`2`/s & NO3 sediment flux 0286 PO4Fsed & ``SM______U1`` & mmol P/m\ :sup:`2`/s & PO4 sediment flux 0287 NH4Fsed & ``SM______U1`` & mmol N/m\ :sup:`2`/s & NH4 sediment flux 0288 sedFlPOC & ``SM_P____U1`` & mmol C/m\ :sup:`2`/s & POC flux from water column to sediment 0289 sedFlPIC & ``SM_P____U1`` & mmol C/m\ :sup:`2`/s & PIC flux from water column to sediment 0290 sedFlPOP & ``SM_P____U1`` & mmol P/m\ :sup:`2`/s & POP flux from water column to sediment 0291 sedFlPON & ``SM_P____U1`` & mmol N/m\ :sup:`2`/s & PON flux from water column to sediment 0292 sedFplkC & ``SM_P____U1`` & mmol C/m\ :sup:`2`/s & C flux from bottom sink plankton to sed 0293 sedFplkN & ``SM_P____U1`` & mmol N/m\ :sup:`2`/s & N flux from bottom sink plankton to sed 0294 sedFplkP & ``SM_P____U1`` & mmol P/m\ :sup:`2`/s & P flux from bottom sink plankton to sed 0295 OmegCbot & ``SM_P____M1`` & 1 & Calcite saturation ratio above the seabed 0296
| [ Source navigation ] | [ Diff markup ] | [ Identifier search ] | [ general search ] |
|
This page was automatically generated from https://github.com/darwinproject/darwin3 by the 2.3.7-MITgcm-0.1 LXR engine. The LXR team |
|