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view on githubraw file Latest commit 5e7acb36 on 2025-07-11 21:23:07 UTC1d947889e4 Oliv*0001 .. include:: ../defs.hrst 0002 faa67d1773 Oliv*0003 .. _sub_phys_pkg_darwin: 0004 1d947889e4 Oliv*0005 DARWIN package 0006 -------------- 0007 faa67d1773 Oliv*0008 The :filelink:`darwin package <pkg/darwin>` models the dynamics of a flexible 0009 number of phyto- and zooplankton and bacteria types, and the nutrient cycles of 0010 carbon, nitrogen, phosphorus, iron and silica. The description of the 0011 ecosystem model is split over a number of pages: 0012 0013 .. toctree:: 0014 :maxdepth: 1 0015 0016 darwin_equations 0017 darwin_growth 8916dab93b Oliv*0018 darwin_cstore faa67d1773 Oliv*0019 darwin_light 0020 darwin_spectral 0021 darwin_uptake 0022 darwin_chl 0023 darwin_remin 0024 darwin_denit 0025 darwin_cdom 3c930300af Oliv*0026 darwin_airsea faa67d1773 Oliv*0027 darwin_carbon 0028 darwin_iron 81872c4188 Oliv*0029 darwin_resp faa67d1773 Oliv*0030 darwin_mort 0031 darwin_exude 0032 darwin_grazing 0033 darwin_bacteria 0034 darwin_temperature 0035 darwin_sink 5e7acb36b1 daat*0036 darwin_dvm faa67d1773 Oliv*0037 darwin_cons 0038 darwin_changes 1d947889e4 Oliv*0039 faa67d1773 Oliv*0040 Plankton and nutrients are represented by their concentration in the ocean, 0041 using the :ref:`sub_phys_pkg_ptracers`. The darwin package uses the following 0042 tracers (or a subset, depending on the configuration): 1d947889e4 Oliv*0043 0044 .. table:: 0045 :widths: auto 0046 3ded9f825b Oliv*0047 +---------------+--------------------------------+---------------------------------------------------------+ 0048 | Name | Units | Description | 0049 +===============+================================+=========================================================+ 0050 | DIC | mmol C m\ :sup:`--3` | concentration of dissolved inorganic carbon | 0051 +---------------+--------------------------------+---------------------------------------------------------+ 0052 | NO3 | mmol N m\ :sup:`--3` | concentration of nitrate | 0053 +---------------+--------------------------------+---------------------------------------------------------+ 0054 | NO2 | mmol N m\ :sup:`--3` | concentration of nitrite | 0055 +---------------+--------------------------------+---------------------------------------------------------+ 0056 | NH4 | mmol N m\ :sup:`--3` | concentration of ammonia | 0057 +---------------+--------------------------------+---------------------------------------------------------+ 0058 | PO4 | mmol P m\ :sup:`--3` | concentration of phosphate | 0059 +---------------+--------------------------------+---------------------------------------------------------+ 0060 | FeT | mmol Fe m\ :sup:`--3` | concentration of total dissolved iron | 0061 +---------------+--------------------------------+---------------------------------------------------------+ 0062 | SiO2 | mmol Si m\ :sup:`--3` | concentration of inorganic silica | 0063 +---------------+--------------------------------+---------------------------------------------------------+ 0064 | DOC | mmol C m\ :sup:`--3` | concentration of dissolved organic carbon | 0065 +---------------+--------------------------------+---------------------------------------------------------+ 0066 | DON | mmol N m\ :sup:`--3` | concentration of dissolved organic nitrogen | 0067 +---------------+--------------------------------+---------------------------------------------------------+ 0068 | DOP | mmol P m\ :sup:`--3` | concentration of dissolved organic phosphorus | 0069 +---------------+--------------------------------+---------------------------------------------------------+ 0070 | DOFe | mmol Fe m\ :sup:`--3` | concentration of dissolved organic iron | 0071 +---------------+--------------------------------+---------------------------------------------------------+ 0072 | POC | mmol C m\ :sup:`--3` | concentration of particulate organic carbon | 0073 +---------------+--------------------------------+---------------------------------------------------------+ 0074 | PON | mmol N m\ :sup:`--3` | concentration of particulate organic nitrogen | 0075 +---------------+--------------------------------+---------------------------------------------------------+ 0076 | POP | mmol P m\ :sup:`--3` | concentration of particulate organic phosphorus | 0077 +---------------+--------------------------------+---------------------------------------------------------+ 0078 | POFe | mmol Fe m\ :sup:`--3` | concentration of particulate organic iron | 0079 +---------------+--------------------------------+---------------------------------------------------------+ 0080 | POSi | mmol Si m\ :sup:`--3` | concentration of particulate organic silica | 0081 +---------------+--------------------------------+---------------------------------------------------------+ 0082 | PIC | mmol C m\ :sup:`--3` | concentration of particulate inorganic carbon | 0083 +---------------+--------------------------------+---------------------------------------------------------+ 0084 | ALK | meq m\ :sup:`--3` | alkalinity | 0085 +---------------+--------------------------------+---------------------------------------------------------+ 0086 | O2 | mmol O\ :sub:`2` m\ :sup:`--3` | concentration of oxygen | 0087 +---------------+--------------------------------+---------------------------------------------------------+ 0088 | CDOM | mmol C m\ :sup:`--3` | concentration of colored dissolved organic matter [#a]_ | 0089 | | | | 0090 | | (mmol P m\ :sup:`--3`) | | 0091 +---------------+--------------------------------+---------------------------------------------------------+ 0092 | c\ :sub:`j` | mmol C m\ :sup:`--3` | concentration of carbon in plankton type j | 0093 +---------------+--------------------------------+---------------------------------------------------------+ 0094 | n\ :sub:`j` | mmol N m\ :sup:`--3` | concentration of nitrogen in plankton type j | 0095 +---------------+--------------------------------+---------------------------------------------------------+ 0096 | p\ :sub:`j` | mmol P m\ :sup:`--3` | concentration of phosphorus in plankton type j | 0097 +---------------+--------------------------------+---------------------------------------------------------+ 0098 | fe\ :sub:`j` | mmol Fe m\ :sup:`--3` | concentration of iron in plankton type j | 0099 +---------------+--------------------------------+---------------------------------------------------------+ 0100 | si\ :sub:`j` | mmol Si m\ :sup:`--3` | concentration of silica in plankton type j | 0101 +---------------+--------------------------------+---------------------------------------------------------+ 0102 | Chl\ :sub:`j` | mg Chl a m\ :sup:`--3` | concentration of Chlorophyll-a in plankton type j | 0103 +---------------+--------------------------------+---------------------------------------------------------+ 0104 0105 .. [#a] units of CDOM are mmol C m\ :sup:`--3` if #define DARWIN_CDOM_UNITS_CARBON (default), 0106 mmol P m\ :sup:`--3` otherwise 1d947889e4 Oliv*0107 0108 Phyto- and zooplankton are not distinguished except that certain source terms 0109 will not be active, dependening on whether a plankton type can engage in 0110 photosynthesis, grazing, etc. This makes it very simple to include, for 0111 instance, mixotrophy in the model. 0112 0113 0114 Compiling and Running 0115 ~~~~~~~~~~~~~~~~~~~~~ 0116 0117 Compiling 0118 ^^^^^^^^^ 0119 0120 Include the word ``darwin`` in ``packages.conf`` in your code directory. 0121 This will automatically turn on gchem, ptracers and exf. 0122 0123 Set compile-time options for darwin in file 0124 :filelink:`~pkg/darwin/DARWIN_OPTIONS.h` (see table below). 0125 0126 Adjust the number of plankton types, functional groups, autotrophs, 0127 grazers, prey and optical types in :filelink:`~pkg/darwin/DARWIN_SIZE.h`. 0128 0129 You will also have to adjust the number of passive tracers in 0130 :filelink:`~pkg/ptracers/PTRACERS_SIZE.h`. You can run 0131 :filelink:`tools/darwin/mkdarwintracers` in your code 0132 directory (after adjusting :filelink:`~pkg/darwin/DARWIN_OPTIONS.h` and 0133 :filelink:`~pkg/darwin/DARWIN_SIZE.h`) 0134 to find out how many ptracers you will need and what they are. 0135 0136 In :filelink:`~pkg/gchem/GCHEM_OPTIONS.h` you need to define 0137 :varlink:`GCHEM_SEPARATE_FORCING`. 0138 0139 In :filelink:`~pkg/exf/EXF_OPTIONS.h` you may want to undef 0140 :varlink:`ALLOW_CLIMSST_RELAXATION` and :varlink:`ALLOW_CLIMSSS_RELAXATION`. 0141 0142 To use spectral light, compile the radtrans package, see 0143 :numref:`sub_phys_pkg_radtrans`. 0144 0145 .. tabularcolumns:: |l|l| 0146 0147 .. csv-table:: Darwin package CPP options 0148 :delim: & 0149 :widths: auto 0150 :class: longtable 0151 :header: CPP option, description 0152 0153 :varlink:`DARWIN_ALLOW_NQUOTA` & enable nitrogen quotas for all plankton 0154 :varlink:`DARWIN_ALLOW_PQUOTA` & enable phosphorus quotas for all plankton 0155 :varlink:`DARWIN_ALLOW_FEQUOTA` & enable iron quotas for all plankton 0156 :varlink:`DARWIN_ALLOW_SIQUOTA` & enable silica quotas for all plankton 0157 :varlink:`DARWIN_ALLOW_CHLQUOTA` & enable chlorophyll quotas for all *phototrophs* 0158 :varlink:`DARWIN_ALLOW_CDOM` & enable a dynamic CDOM tracer faa67d1773 Oliv*0159 :varlink:`DARWIN_CDOM_UNITS_CARBON` & measure CDOM in units of mmol C/m\ :sup:`3` and follow organic carbon instead of phosphorus 3c930300af Oliv*0160 :varlink:`DARWIN_ALLOW_CSTORE` & enable internal carbon store and exudation for all phototrophs 0161 :varlink:`DARWIN_ALLOW_CSTORE_DIAGS` & enable diagnostics for internal carbon store 1d947889e4 Oliv*0162 :varlink:`DARWIN_ALLOW_CARBON` & enable air-sea carbon exchange and ALK and O\ :math:`_2` tracers 3c930300af Oliv*0163 :varlink:`DARWIN_SOLVESAPHE` & compile Munhoven "Solvesaphe" pH/pOC2 solver package faa67d1773 Oliv*0164 :varlink:`DARWIN_TOTALPHSCALE` & consistently use the total pH scale for carbon chemistry coefficients 3c930300af Oliv*0165 :varlink:`DARWIN_USE_PLOAD` & take atmospheric pressure from coupled atmospheric model 5be9e53640 Oliv*0166 :varlink:`DARWIN_ALLOW_RADIv1` & enable RADI sediment metamodel version 1 0167 :varlink:`DARWIN_ALLOW_RADIv2` & enable RADI sediment metamodel version 2 1d947889e4 Oliv*0168 :varlink:`DARWIN_ALLOW_DENIT` & enable denitrification code 0169 :varlink:`DARWIN_ALLOW_EXUDE` & enable exudation of individual quotas 0170 :varlink:`ALLOW_OLD_VIRTUALFLUX` & enable old virtualflux code for DIC and ALK 0171 :varlink:`DARWIN_NITRATE_FELIMIT` & reduce nitrate uptake by iron limitation factor 0172 :varlink:`DARWIN_BOTTOM_SINK` & allow organic matter to sink into bottom (sedimentize) a3709ed096 Oliv*0173 :varlink:`DARWIN_NUTRIENT_RUNOFF` & include code for reading nutrient runoff from files 1d947889e4 Oliv*0174 :varlink:`DARWIN_AVPAR` & compute average PAR in layer, assuming exponential decay (%) 0175 :varlink:`DARWIN_ALLOW_GEIDER` & enable GEIDER light code (required for radtrans)** Warning **
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0176 :varlink:`DARWIN_GEIDER_RHO_SYNTH` & use ρ instead of acclimated Chl:C for chlorophyll synthesis 0177 :varlink:`DARWIN_CHL_INIT_LEGACY` & initialize chlorophyll as in darwin2 0178 :varlink:`DARWIN_SCATTER_CHL` & scattering coefficients are per Chlorophyll 0179 :varlink:`DARWIN_DIAG_IOP` & make diagnostics for instrinsic optical properties available 0180 :varlink:`DARWIN_GRAZING_SWITCH` & enable quadratic grazing as in darwin2+quota 0181 :varlink:`DARWIN_ALLOMETRIC_PALAT` & compute palatability from size ratios 0182 :varlink:`DARWIN_NOZOOTEMP` & turn off grazing temperature dependence 0183 :varlink:`DARWIN_NOTEMP` & turn off all temperature dependence 0184 :varlink:`DARWIN_TEMP_VERSION` & select temperature version: 1, 2 or 3 0185 :varlink:`DARWIN_TEMP_RANGE` & restrict phytoplankton growth to a temperature range 0186 :varlink:`DARWIN_MINFE` & restrict maximum free iron (sic) 0187 :varlink:`DARWIN_PART_SCAV` & enable particle scavenging code 0188 :varlink:`DARWIN_IRON_SED_SOURCE_VARIABLE` & enable variable iron sediment source 9f79ba70a9 Oliv*0189 :varlink:`DARWIN_ALLOW_HYDROTHERMAL_VENTS` & include code for iron input from hydrothermal vents 5a1d3d992b Oliv*0190 :varlink:`DARWIN_DIAG_PERTYPE` & enable per-type diagnostics PP####, GR####, GrGn#### a3709ed096 Oliv*0191 :varlink:`DARWIN_DIAG_TENDENCIES` & enable diagnostics for many tendency terms 1d947889e4 Oliv*0192 :varlink:`DARWIN_DEBUG` & turn on debugging output 0193 :varlink:`DARWIN_ALLOW_CONS` & compute and print global element totals 0194 :varlink:`DARWIN_UNUSED` & value for unused traits 0195 0196 The following options are used for random trait generation (as in darwin2): 0197 0198 .. tabularcolumns:: |l|L| 0199 0200 .. csv-table:: 0201 :delim: & 0202 :widths: auto 0203 :header: CPP option, description 0204 0205 :varlink:`DARWIN_RANDOM_TRAITS` & assign traits based on random numbers as in darwin2 0206 :varlink:`DARWIN_TWO_SPECIES_SETUP` & set traits for darwin2 2-species setup (requires :varlink:`DARWIN_RANDOM_TRAITS`) 0207 :varlink:`DARWIN_NINE_SPECIES_SETUP` & set traits for darwin2 9-species setup (requires :varlink:`DARWIN_RANDOM_TRAITS`) 0208 :varlink:`DARWIN_ALLOW_DIAZ` & enable diazotrophy when using :varlink:`DARWIN_RANDOM_TRAITS` 0209 0210 Random trait generation is supported mainly for backwards compatibility. 0211 0212 Running 0213 ^^^^^^^ 0214 0215 You will need to set ``useDARWIN=.TRUE.`` in ``data.gchem`` (and turn on 0216 gchem, ptracers, exf, etc.in ``data.pkg``). 0217 0218 Runtime Parameters 0219 '''''''''''''''''' 0220 0221 Runtime parameters are set in ``data.darwin`` in these namelists: 0222 0223 .. csv-table:: 0224 :delim: & 0225 :widths: auto 0226 :header: Namelist, Description 0227 0228 :varlink:`DARWIN_FORCING_PARAMS` & parameters related to forcing and initialization 0229 :varlink:`DARWIN_INTERP_PARAMS` & parameters for interpolation of forcing fields (only used if :varlink:`USE_EXF_INTERPOLATION` is defined) 0230 :varlink:`DARWIN_PARAMS` & general parameters (not per-plankton traits) 0231 :varlink:`DARWIN_CDOM_PARAMS` & parameters for dynamic CDOM 0232 :varlink:`DARWIN_RADTRANS_PARAMS` & parameters for radiative transer 0233 :varlink:`DARWIN_RANDOM_PARAMS` & parameters for randomly generated traits (deprecated) 0234 :varlink:`DARWIN_TRAIT_PARAMS` & parameters for trait generation (allometric and functional groups) 0235 0236 Set initial values/files for the tracers in ``data.ptracers``. You can 0237 generate a template by running :filelink:`tools/darwin/mkdarwintracers` in your** Warning **
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0238 code directory (get help with the ‘-h’ option). 0239 0240 You may generate a minimal file ``data.diagnostics`` with all the darwin 0241 tracers by running :filelink:`tools/darwin/mkdiagnosticsdata` in your input/run 0242 directory. 0243 0244 Forcing fields are read in using the exf package. File names and forcing 0245 parameters are given in namelist :varlink:`DARWIN_FORCING_PARAMS` in 0246 ``data.darwin``. For light, ice area and wind speed, the following 0247 alternative sources can be given: 0248 0249 .. csv-table:: Namelist DARWIN_FORCING_PARAMS 0250 :delim: & 0251 :widths: auto 0252 :header: Name, Default, Description 0253 0254 :varlink:`darwin_useQsw` & .FALSE. & whether to use model shortwave radiation for light 0255 :varlink:`darwin_useSEAICE` & .FALSE. & whether to use ice area from the seaice package 0256 :varlink:`darwin_useEXFwind` & .FALSE. & whether to use wind speed from the exf package 0257 0258 The forcing fields are: 0259 0260 .. tabularcolumns:: |\Y{.09}|\Y{.09}|\Y{.17}|\Y{.65}| 0261 0262 .. csv-table:: Darwin forcing fields 0263 :delim: & 0264 :widths: auto 0265 :class: longtable 0266 :header: Name, Default, Units, Description 0267 61dd464eee Oliv*0268 iron & 0.0 & mmol Fe m\ :sup:`--2` s\ :sup:`--1` & iron input through sea surface, will be multiplied by solubility :varlink:`alpfe`** Warning **
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0269 PAR & 0.0 & μEin m\ :sup:`--2` s\ :sup:`--1` & Photosynthetically active radiation below sea surface; not used with the radtrans package 0270 ice & 0.0 & m\ :sup:`2`\ /m\ :sup:`2` & fraction of surface covered by ice; used to reduce non-spectral light and for carbon and oxygen surface forcing; for spectral light, ice fraction has to be given in ``data.radtrans`` 0271 wind & 5.0 & m/s & wind speed; used for carbon and oxygen surface forcing 0272 pCO2 & 278E-6 & atm & partial pressure of atmospheric CO\ :sub:`2`; used for carbon and oxygen surface forcing 9f79ba70a9 Oliv*0273 ventHe3 & 0.0 & mmol |nbsp| :sup:`3`\ He m\ :sup:`--2` s\ :sup:`--1` & Helium-3 flux from hydrothermal vents; used for iron input 61dd464eee Oliv*0274 DOCrunoff & 0.0 & mmol C m\ :sup:`--2` s\ :sup:`--1` & surface flux of DOC from runoff 0275 DONrunoff & 0.0 & mmol N m\ :sup:`--2` s\ :sup:`--1` & surface flux of DON from runoff 0276 DOPrunoff & 0.0 & mmol P m\ :sup:`--2` s\ :sup:`--1` & surface flux of DOP from runoff 0277 DINrunoff & 0.0 & mmol N m\ :sup:`--2` s\ :sup:`--1` & surface flux of DIN from runoff 0278 IPrunoff & 0.0 & mmol P m\ :sup:`--2` s\ :sup:`--1` & surface flux of IP from runoff 0279 DSirunoff & 0.0 & mmol Si m\ :sup:`--2` s\ :sup:`--1` & surface flux of DSi from runoff 0280 POCrunoff & 0.0 & mmol C m\ :sup:`--2` s\ :sup:`--1` & surface flux of POC from runoff 0281 PONrunoff & 0.0 & mmol N m\ :sup:`--2` s\ :sup:`--1` & surface flux of PON from runoff 0282 POPrunoff & 0.0 & mmol P m\ :sup:`--2` s\ :sup:`--1` & surface flux of POP from runoff 0283 DICrunoff & 0.0 & mmol C m\ :sup:`--2` s\ :sup:`--1` & surface flux of DIC from runoff 1d947889e4 Oliv*0284 0285 Each forcing field has a set of parameters in :varlink:`DARWIN_FORCING_PARAMS`. 0286 These work as in the exf package, see 0287 :numref:`tab_phys_pkg_exf_runtime_attributes`. For instance, for PAR they are: 0288** Warning **
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0289 .. csv-table:: Namelist DARWIN_FORCING_PARAMS, cont’d 0290 :delim: & 0291 :widths: auto 0292 :header: Name, Default, Description 0293 0294 :varlink:`PARfile` & ' ' & filename; if left empty no file will be read; PARconst will be used instead 0295 :varlink:`PARconst` & 0.0 & constant that will be used if no file is read 0296 :varlink:`PARperiod` & 0.0 & interval in seconds between two records 0297 :varlink:`PARRepCycle` & :varlink:`repeatPeriod` & repeat cycle in seconds; only available if :varlink:`useExfYearlyFields` is .FALSE. 0298 :varlink:`PARStartTime` & UNSET_RL & time in seconds of first record from the beginning of the model integration or, if useExfYearlyFields, from the beginning of year; computed from PARstartdate* if not given 0299 :varlink:`PARstartdate1` & 0 & date/time of first record when using the cal package; format: YYYYMMDD; start year (YYYY), month (MM), day (YY) 0300 :varlink:`PARstartdate2` & 0 & format: HHMMSS; start hour (HH), minute (MM), second(SS) 0301 :varlink:`PAR_exfremo_intercept` & 0.0 & can be used to remove global mean 0302 :varlink:`PAR_exfremo_slope` & 0.0 & can be used to remove global trend 0303 :varlink:`PARmask` & 'c' & grid point for masking: ' ' = no masking; 'c' = centered mask; 'w' = western mask; 's' = southern 0304 :varlink:`darwin_inscal_PAR` & 1.0 & optional rescaling of input fields to adjust units 0305 61dd464eee Oliv*0306 The parameters darwin_inscal\_Name can be used to convert units. Some examples 0307 are given in :numref:`tab_phys_pkgs_darwin_inscal`. 0308 0309 .. csv-table:: Example unit conversions 0310 :delim: & 0311 :widths: auto 0312 :class: longtable 0313 :header: Field, File units, Scaling factor 0314 :name: tab_phys_pkgs_darwin_inscal 0315 0316 iron & mol Fe m\ :sup:`--2` s\ :sup:`--1` & darwin_inscal_iron = 1000 0317 & kg Fe m\ :sup:`--2` & darwin_inscal_iron = 17906.7 0318 PAR & Ein m\ :sup:`--2` day\ :sup:`--1` & darwin_inscal_PAR = 11.574074074074 0319 0320 Nutrient runoff has some extra parameters: 0321 0322 .. tabularcolumns:: |\Y{.25}|\Y{.12}|\Y{.14}|\Y{.49}| 0323** Warning **
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0324 .. csv-table:: Namelist DARWIN_FORCING_PARAMS, cont’d 0325 :delim: & 0326 :widths: 25,12,14,49 0327 :header: Name, Default, Units, Description 0328 0329 :varlink:`R_ALK_DIC_runoff` & 1.0218 & meq / mmol C & ALK:DIC ratio in runoff 0330 :varlink:`R_NO3_DIN_runoff` & 0.6531 & mmol N / mmol N & NO3 fraction of DIN in runoff 0331 :varlink:`R_NO2_DIN_runoff` & 0.0158 & mmol N / mmol N & NO2 fraction of DIN in runoff 0332 :varlink:`R_NH4_DIN_runoff` & 0.3311 & mmol N / mmol N & NH4 fraction of DIN in runoff 0333 :varlink:`R_DIP_IP_runoff` & 0.333 & mmol P / mmol P & ratio of dissolved to total inorganic P in runoff 0334 :varlink:`R_DFe_DIP_runoff` & 0.0003 & mmol Fe / mmol P & Fe:P ratio for inorganic P in runoff 0335 :varlink:`R_DOFe_DOP_runoff` & 0.0003 & mmol Fe / mmol P & Fe:P ratio for dissolved organic matter in runoff 0336 :varlink:`R_POFe_POP_runoff` & 0.0003 & mmol Fe / mmol P & Fe:P ratio for particulate organic matter in runoff 0337 0338 These govern how the various tracers receive contributions from the runoff files: 0339 0340 .. csv-table:: Runoff forcing-tracer associations 0341 :delim: & 0342 :widths: auto 0343 :header: Tracer, Surface Forcing Field 0344 0345 DOC & DOCrunoff 0346 DON & DONrunoff 0347 DOP & DOPrunoff 0348 NO3 & DINrunoff \* R_NO3_DIN_runoff 0349 NO2 & DINrunoff \* R_NO2_DIN_runoff 0350 NH4 & DINrunoff \* R_NH4_DIN_runoff 0351 PO4 & IPrunoff \* R_DIP_IP_runoff 0352 SiO2 & DSirunoff 0353 POC & POCrunoff 0354 PON & PONrunoff 0355 POP & POPrunoff 0356 DIC & DICrunoff 0357 ALK & DICrunoff \* R_ALK_DIC_runoff 0358 FeT & IPrunoff \* R_DIP_IP_runoff \* R_DFe_DIP_runoff 0359 DOFe & DOPrunoff \* R_DOFe_DOP_runoff 0360 POFe & POPrunoff \* R_POFe_POP_runoff 0361 1d947889e4 Oliv*0362 Interpolation parameters for all forcing fields are set in namelist 0363 :varlink:`DARWIN_INTERP_PARAMS`. See the exf package for how to set them. 0364 0365 0366 General parameters are set in namelist :varlink:`DARWIN_PARAMS`: 0367 0368 .. tabularcolumns:: |\Y{.235}|\Y{.135}|\Y{.14}|\Y{.49}| 0369 0370 .. csv-table:: Namelist DARWIN_PARAMS 0371 :delim: & 0372 :widths: auto 0373 :class: longtable 0374 :header: Name, Default, Units, Description 0375 0376 :varlink:`darwin_seed` & 0 & & seed for random number generator (for :varlink:`DARWIN_RANDOM_TRAITS`) 0377 :varlink:`darwin_strict_check` & .FALSE. & & stop instead of issuing warnings 0378 :varlink:`iDEBUG` & 1 & & index in x dimension for debug prints 0379 :varlink:`jDEBUG` & 1 & & index in y dimension for debug prints 0380 :varlink:`kDEBUG` & 1 & & index in z dimension for debug prints 0381 :varlink:`darwin_pickupSuff` & :varlink:`pickupSuff` & & pickup suffix for darwin; set to ' ' to disable reading at :varlink:`PTRACERS_Iter0` 0382 :varlink:`darwin_linFSConserve` & .FALSE. & & correct non-conservation due to linear free surface (globally) 0383 :varlink:`darwin_read_phos` & .FALSE. & & initial conditions for plankton biomass are in mmol P/m3 0384 :varlink:`darwin_chlInitBalanced` & .FALSE. & & Initialize Chlorophyll to a balanced value following Geider 0385 :varlink:`darwin_chlIter0` & 0 & & Iteration number when to initialize Chlorophyll 0386 :varlink:`katten_w` & 4D-2 & 1/m & atten coefficient water 0387 :varlink:`katten_chl` & 4D-2 & m\ :sup:`2`/mg Chl & atten coefficient chl 0388 :varlink:`parfrac` & 0.4 & & fraction Qsw that is PAR** Warning **
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0389 :varlink:`parconv` & 1/0.2174 & μEin/s/W & conversion from W/m2 to μEin/m2/s 0390 :varlink:`tempnorm` & 0.3 & & set temperature function (was 1.0) 0391 :varlink:`TempAeArr` & -4000.0 & K & slope for pseudo-Arrhenius (TEMP_VERSION 2) 0392 :varlink:`TemprefArr` & 293.15 & K & reference temp for pseudo-Arrhenius (TEMP_VERSION 2) 0393 :varlink:`TempCoeffArr` & 0.5882 & & pre-factor for pseudo-Arrhenius (TEMP_VERSION 2) 09b16dd232 Oliv*0394 :varlink:`reminTempAe` & 0.0438 & 1/K & temperature coefficient for remineralization (TEMP_VERSION 4) 0395 :varlink:`mortTempAe` & 0.0438 & 1/K & temperature coefficient for linear mortality (TEMP_VERSION 4) 0396 :varlink:`mort2TempAe` & 0.0438 & 1/K & temperature coefficient for quadr. mortality (TEMP_VERSION 4) 0397 :varlink:`uptakeTempAe` & 0.0 & 1/K & temperature coefficient for uptake (TEMP_VERSION 4) 1d947889e4 Oliv*0398 :varlink:`alpfe` & 0.04 & & solubility of Fe dust 0399 :varlink:`scav` & 0.4/year & 1/s & fixed iron scavenging rate 4ee77fca61 Oliv*0400 :varlink:`scav_tau` & 0.2 & & factor for converting Th scavenging rates to iron ones 0401 :varlink:`scav_inter` & 0.079 / day & L\ :sup:`e` mg\ :sup:`-e` s\ :sup:`-1` & intercept of scavenging power law (e=e\ :sub:`scav`) 0402 :varlink:`scav_exp` & 0.58 & & exponent of scavenging power law 0403 :varlink:`scav_POC_wgt` & 0.02173 & g/mmol |nbsp| C & weight POC contributes to POM 0404 :varlink:`scav_POSi_wgt` & 0.069 & g/mmol |nbsp| Si & weight POSi contributes to POM 0405 :varlink:`scav_PIC_wgt` & 0.100 & g/mmol |nbsp| C & weight PIC contributes to POM 1d947889e4 Oliv*0406 :varlink:`ligand_tot` & 1D-3 & mol/m\ :sup:`3` & total ligand concentration 0407 :varlink:`ligand_stab` & 2D5 & m\ :sup:`3`/mol & ligand stability rate ratio 0408 :varlink:`freefemax` & 0.4D-3 & mol/m\ :sup:`3` & max concentration of free iron 0409 :varlink:`depthfesed` & -1.0 & m & depth above which to add sediment source (was -1000) 0410 :varlink:`fesedflux` & 1D-3 / day & mmol Fe /m\ :sup:`2`/s & fixed iron flux from sediment 0411 :varlink:`fesedflux_pcm` & 0.68D-3 & mmol Fe / mmol C & iron input per POC sinking into bottom for :varlink:`DARWIN_IRON_SED_SOURCE_VARIABLE` b3165fc3b9 Oliv*0412 :varlink:`fesedflux_min` & 0.5D-3 / day & mmol Fe /s & min iron input rate subtracted from fesedflux_pcm*wc_sink*POC 0413 :varlink:`R_CP_fesed` & 106 & mmol C / mmol P & POC:POP conversion for :varlink:`DARWIN_IRON_SED_SOURCE_POP` 9f79ba70a9 Oliv*0414 :varlink:`depthFeVent` & 750 & m & depth below which iron from hydrothermal vents is added 0415 :varlink:`solFeVent` & 0.002 & & solubility of iron from hydrothermal vents 0416 :varlink:`R_FeHe3_vent` & 4.5E8 & mol Fe / mol :sup:`3`\ He & Fe:\ :sup:`3`\ He ratio for hydrothermal vents 0417 1d947889e4 Oliv*0418 :varlink:`Knita` & 1/(0.5 days) & 1/s & ammonia oxidation rate 0419 :varlink:`Knitb` & 1/(10 days) & 1/s & nitrite oxidation rate** Warning **
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0420 :varlink:`PAR_oxi` & 10 & μEin/m\ :sup:`2`/s & critical light level after which oxidation starts 0421 :varlink:`Kdoc` & 1/(100 days) & 1/s & DOC remineralization rate 0422 :varlink:`Kdop` & 1/(100 days) & 1/s & DON remineralization rate 0423 :varlink:`Kdon` & 1/(100 days) & 1/s & DOP remineralization rate 0424 :varlink:`KdoFe` & 1/(100 days) & 1/s & DOFe remineralization rate 0425 :varlink:`KPOC` & 1/(50 days) & 1/s & POC remineralization rate 0426 :varlink:`KPOP` & :varlink:`KPOC` & 1/s & POP remineralization rate 0427 :varlink:`KPON` & :varlink:`KPOC` & 1/s & PON remineralization rate 0428 :varlink:`KPOFe` & :varlink:`KPOC` & 1/s & POFe remineralization rate 0429 :varlink:`KPOSi` & 1/(300 days) & 1/s & POSi remineralization rate 0430 :varlink:`wC_sink` & 10/day & m/s & sinking velocity for POC 0431 :varlink:`wP_sink` & :varlink:`wC_sink` & m/s & sinking velocity for POP 0432 :varlink:`wN_sink` & :varlink:`wC_sink` & m/s & sinking velocity for PON 0433 :varlink:`wFe_sink` & :varlink:`wC_sink` & m/s & sinking velocity for POFe 0434 :varlink:`wSi_sink` & :varlink:`wC_sink` & m/s & sinking velocity for POSi 0435 :varlink:`wPIC_sink` & 15/day & m/s & sinking velocity for PIC 0436 :varlink:`Kdissc` & 1/(300 days) & 1/s & dissolution rate for PIC 0437 :varlink:`R_OP` & 170 & mmol O\ :sub:`2` / mmol P & O:P ratio for respiration and consumption 0438 :varlink:`R_OC` & 170/120.0 & mmol O\ :sub:`2` / mmol C & NOT USED 0439 :varlink:`m3perkg` & 1 / 1024.5 & m\ :sup:`3`/kg & constant for converting per kg to per m^3 0440 :varlink:`surfSaltMinInit` & 4.0 & ppt & limits for carbon solver input at initialization 0441 :varlink:`surfSaltMaxInit` & 50.0 & ppt & ... 0442 :varlink:`surfTempMinInit` & -4.0 & C & 0443 :varlink:`surfTempMaxInit` & 39.0 & C & 0444 :varlink:`surfDICMinInit` & 10.0 & mmol C m\ :sup:`-3` & 0445 :varlink:`surfDICMaxInit` & 4000.0 & mmol C m\ :sup:`-3` & 0446 :varlink:`surfALKMinInit` & 10.0 & meq m\ :sup:`-3` & 0447 :varlink:`surfALKMaxInit` & 4000.0 & meq m\ :sup:`-3` & 0448 :varlink:`surfPO4MinInit` & 1D-10 & mmol P m\ :sup:`-3` & 0449 :varlink:`surfPO4MaxInit` & 10.0 & mmol P m\ :sup:`-3` & 0450 :varlink:`surfSiMinInit` & 1D-8 & mmol Si m\ :sup:`-3` & 0451 :varlink:`surfSiMaxInit` & 500.0 & mmol Si m\ :sup:`-3` & 0452 :varlink:`surfSaltMin` & 4.0 & ppt & limits for carbon solver input during run 0453 :varlink:`surfSaltMax` & 50.0 & ppt & ... 0454 :varlink:`surfTempMin` & -4.0 & C & 0455 :varlink:`surfTempMax` & 39.0 & C & 0456 :varlink:`surfDICMin` & 400.0 & mmol C m\ :sup:`-3` & 0457 :varlink:`surfDICMax` & 4000.0 & mmol C m\ :sup:`-3` & 0458 :varlink:`surfALKMin` & 400.0 & meq m\ :sup:`-3` & 0459 :varlink:`surfALKMax` & 4000.0 & meq m\ :sup:`-3` & 0460 :varlink:`surfPO4Min` & 1D-10 & mmol P m\ :sup:`-3` & 0461 :varlink:`surfPO4Max` & 10.0 & mmol P m\ :sup:`-3` & 0462 :varlink:`surfSiMin` & 1D-8 & mmol Si m\ :sup:`-3` & 0463 :varlink:`surfSiMax` & 500.0 & mmol Si m\ :sup:`-3` & 0464 :varlink:`diaz_ini_fac` & 1 & & reduce tracer concentrations by this factor on initialization 0465 :varlink:`O2crit` & 6.0 & mmol O\ :sub:`2` m\ :sup:`-3` & critical oxygen for O2/NO3 remineralization 0466 :varlink:`denit_NP` & 120.0 & mmol N / mmol P & ratio of n to p in denitrification process 0467 :varlink:`denit_NO3` & 104.0 & mmol N / mmol P & ratio of NO3 uptake to phos remineralization in denitrification 0468 :varlink:`NO3crit` & 1D-2 & mmol N m\ :sup:`-3` & critical nitrate below which no denit (or remin) happens** Warning **
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0469 :varlink:`PARmin` & 0.1 & μEin/m\ :sup:`2`/s & minimum light for photosynthesis; for non-Geider: 1.0 b3165fc3b9 Oliv*0470 :varlink:`aphy_chl_ave` & 0.02 & m\ :sup:`2`/mg Chl & Chl-specific absorption coefficient 1d947889e4 Oliv*0471 :varlink:`chl2nmax` & 3.00 & mg Chl / mmol N & max Chl:N ratio for Chl synthesis following Moore 2002 0472 :varlink:`synthcost` & 0.0 & mmol C / mmol N & cost of biosynthesis 0473 :varlink:`inhib_graz` & 1.0 & (mmol C m\ :sup:`-3`)\ :sup:`-1` & inverse decay scale for grazing inhibition 0474 :varlink:`inhib_graz_exp` & 0.0 & & exponent for grazing inhibition (0 to turn off inhibition) 0475 :varlink:`hillnumUptake` & 1.0 & & exponent for limiting quota uptake in nutrient uptake 0476 :varlink:`hillnumGraz` & 1.0 & & exponent for limiting quota uptake in grazing 0477 :varlink:`hollexp` & 1.0 & & grazing exponential 1= "Holling 2", 2= "Holling 3" 0478 :varlink:`phygrazmin` & 120D-10 & mmol C m\ :sup:`-3` & minimum total prey conc for grazing to occur 0479 :varlink:`pmaxDIN` & 20/day & 1/s & max DIN uptake rate for denitrifying bacteria 0480 :varlink:`pcoefO2` & 290.82/day & m\ :sup:`3`/mmol O\ :sub:`2`/s & max O2-specific O2 uptake rate for aerobic bacteria 0481 :varlink:`ksatDIN` & 0.01 & mmol N m\ :sup:`-3` & half-saturation conc of dissolved inorganic nitrogen 0482 :varlink:`alpha_hydrol` & 2.0 & & increase in POM needed due to hydrolysis 0483 :varlink:`yod` & 0.2 & & organic matter yield of aerobic bacteria 0484 :varlink:`yoe` & yod/467*4/(1-yod)*106 & & energy yield of aerobic bacteria 0485 :varlink:`ynd` & 0.16 & & organic matter yield of denitrifying bacteria 0486 :varlink:`yne` & ynd/467*5/(1-ynd)*106 & & energy yield of denitrifying bacteria 0487 0488 0489 .. csv-table:: Namelist DARWIN_CDOM_PARAMS 0490 :delim: & 0491 :widths: auto 0492 :header: Name, Default, Units, Description 0493 0494 :varlink:`fracCDOM` & 2 / 100 & & fraction of remineralized POP contributing to CDOM 0495 :varlink:`CDOMdegrd` & 1 / (200 days) & 1/s & CDOM degradation rate 0496 :varlink:`CDOMbleach` & 1 / (15 days) & 1/s & CDOM bleaching rate** Warning **
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0497 :varlink:`PARCDOM` & 20 & μEin/m\ :sup:`2`/s & PAR where CDOM bleaching becomes maximal faa67d1773 Oliv*0498 :varlink:`R_NP_CDOM` & 16 & mmol N / mmol P & CDOM N:P ratio (with #undef DARWIN_CDOM_UNITS_CARBON) 0499 :varlink:`R_FeP_CDOM` & 1D-3 & mmol Fe / mmol P & CDOM Fe:P ratio (with #undef DARWIN_CDOM_UNITS_CARBON) 0500 :varlink:`R_CP_CDOM` & 120 & mmol C / mmol P & CDOM C:P ratio (with #undef DARWIN_CDOM_UNITS_CARBON) 0501 :varlink:`R_NC_CDOM` & 16/120 & mmol N / mmol C & CDOM N:C ratio (with #define DARWIN_CDOM_UNITS_CARBON) 0502 :varlink:`R_PC_CDOM` & 1/120 & mmol P / mmol C & CDOM P:C ratio (with #define DARWIN_CDOM_UNITS_CARBON) 0503 :varlink:`R_FeC_CDOM` & 1D-3/120 & mmol Fe / mmol C & CDOM Fe:C ratio (with #define DARWIN_CDOM_UNITS_CARBON) 0504 :varlink:`CDOMcoeff` & 100.0 & m\ :sup:`2` / mmol P & P-specific absorption coefficient of CDOM at :math:`\lambda_{\op{CDOM}}` 0505 & 100/120 & m\ :sup:`2` / mmol C & - if #define DARWIN_CDOM_UNITS_CARBON 1d947889e4 Oliv*0506 0507 0508 .. tabularcolumns:: |\Y{.255}|\Y{.115}|\Y{.13}|\Y{.5}| 0509 0510 .. csv-table:: Namelist DARWIN_RADTRANS_PARAMS 0511 :delim: & 0512 :widths: auto 0513 :header: Name, Default, Units, Description 0514 0515 :varlink:`darwin_waterAbsorbFile` & ' ' & & filename for reading water absorption and scattering spectra 0516 :varlink:`darwin_phytoAbsorbFile` & ' ' & & filename for reading plankton absorption and scattering spectra 0517 :varlink:`darwin_particleAbsorbFile` & ' ' & & filename for reading particle absorption and scattering spectra 0518 :varlink:`darwin_part_size_P` & 1D-15 & mmol P/particle & conversion factor for particle absorption and scattering spectra 0519 :varlink:`darwin_bbmin` & 0.0002 & 1/m & minimum backscattering ratio 0520 :varlink:`darwin_bbw` & 0.5 & & backscattering ratio of water 0521 :varlink:`darwin_lambda_aCDOM` & 450.0 & nm & reference wavelength for CDOM absorption spectra 0522 :varlink:`darwin_Sdom` & 0.014 & 1/nm & coefficient for CDOM absorption spectra 0523 :varlink:`darwin_aCDOM_fac` & 0.2 & & factor for computing aCDOM from water+Chlorophyll absorption 0524 :varlink:`darwin_rCDOM` & 0.0 & mmol P/m\ :sup:`3` & recalcitrant CDOM concentration faa67d1773 Oliv*0525 & 0.0 & mmol C/m\ :sup:`3` & - if #define DARWIN_CDOM_UNITS_CARBON 1d947889e4 Oliv*0526 :varlink:`darwin_RPOC` & 0.0 & mmol C/m\ :sup:`3` & recalcitrant POC concentration 0527 :varlink:`darwin_allomSpectra` & .FALSE. & & enable/disable allometric scaling of plankton absorption and scattering spectra 0528 :varlink:`darwin_aCarCell` & 0.109D-9 & mg C/cell & coefficient coefficient for scaling plankton spectra 0529 :varlink:`darwin_bCarCell` & 0.991 & & coefficient coefficient for scaling plankton spectra 0530 :varlink:`darwin_absorpSlope` & -0.075 & & slope for scaled absorption spectra 0531 :varlink:`darwin_bbbSlope` & -1.458 & & slope for scaled backscattering ratio spectra** Warning **
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0532 :varlink:`darwin_scatSwitchSizeLog` & 0 & log(μm) & log of size for switching slopes 0533 :varlink:`darwin_scatSlopeSmall` & 1.5 & & slope for small plankton 0534 :varlink:`darwin_scatSlopeLarge` & 1.5 & & slope for large plankton 0535 0536 0537 0538 Traits 0539 '''''' 0540 0541 Traits are generated from the parameters in ``&DARWIN_TRAIT_PARAMS`` 0542 (see next section) but can be overridden in ``data.traits``: 0543 0544 .. tabularcolumns:: |\Y{.2}|\Y{.12}|\Y{.2}|\Y{.48}| 0545 0546 .. csv-table:: Namelist DARWIN_TRAITS 0547 :delim: & 0548 :widths: auto 0549 :class: longtable 0550 :header: Trait, Symbol, Units, Description 0551 0552 :varlink:`isPhoto` & isPhoto\ :math:`_j` & & 1: does photosynthesis, 0: not 0553 :varlink:`bactType` & bactType\ :math:`_j` & & 1: particle associated, 2: free living bacteria, 0: not bacteria 0554 :varlink:`isAerobic` & isAerobic\ :math:`_j` & & 1: is aerobic bacteria (also set bactType), 0: not 0555 :varlink:`isDenit` & isDenit\ :math:`_j` & & 1: is dentrifying bacteria (also set (bactType), 0: not 0556 :varlink:`hasSi` & hasSi\ :math:`_j` & & 1: uses silica (Diatom), 0: not 0557 :varlink:`hasPIC` & hasPIC\ :math:`_j` & & 1: calcifying, 0: set R_PICPOC to zero 0558 :varlink:`diazo` & diazo\ :math:`_j` & & 1: use molecular instead of mineral nitrogen, 0: not 0559 :varlink:`useNH4` & useNH4\ :math:`_j` & & 1: can use ammonia, 0: not 0560 :varlink:`useNO2` & useNO2\ :math:`_j` & & 1: can use nitrite, 0: not 0561 :varlink:`useNO3` & useNO3\ :math:`_j` & & 1: can use nitrate, 0: not 0562 :varlink:`combNO` & combNO\ :math:`_j` & & 1: combined nitrite/nitrate limitation, 0: not 0563 :varlink:`isPrey` & isPrey\ :math:`_j` & & 1: can be grazed, 0: not 0564 :varlink:`isPred` & isPred\ :math:`_j` & & 1: can graze, 0: not 0565 :varlink:`tempMort` & :math:`e^{\op{mort}}_j` & & 1: mortality is temperature dependent, 0: turn dependence off 0566 :varlink:`tempMort2` & :math:`e^{\op{mort2}}_j` & & 1: quadratic mortality is temperature dependent, 0: turn dependence off 0567 :varlink:`tempGraz` & :math:`e^{\op{graz}}_j` & & 1: grazing is temperature dependent, 0: turn dependence off 0568 :varlink:`Xmin` & :math:`c^{\min}_j` & mmol C m\ :sup:`-3` & minimum abundance for mortality, respiration and exudation 0569 :varlink:`amminhib` & :math:`\sigma_1` & (mmol N m\ :sup:`-3`)\ :sup:`-1` & coefficient for NH4 inhibition of NO uptake 0570 :varlink:`acclimtimescl` & :math:`\tau^{\op{acclim}}` & s\ :sup:`-1` & rate of chlorophyll acclimation 0571 :varlink:`mort` & :math:`m^{(1)}_j` & s\ :sup:`-1` & linear mortality rate 0572 :varlink:`mort2` & :math:`m^{(2)}_j` & (mmol C m\ :sup:`-3`)\ :sup:`-1` s\ :sup:`-1` & quadratic mortality coefficient 0573 :varlink:`ExportFracMort` & :math:`f^{\op{exp}\op{mort}}_j` & & fraction of linear mortality to POM 0574 :varlink:`ExportFracMort2` & :math:`f^{\op{exp}\op{mort2}}_j` & & fraction of quadratic mortality to POM 0575 :varlink:`ExportFracExude` & :math:`f^{\op{exp}\op{exude}}_j` & & fraction of exudation to POM c9bd7b3d4d Oliv*0576 :varlink:`phytoTempCoeff` & :math:`c_j` & & see :numref:`tab_phys_pkg_darwin_tempparams` 0577 :varlink:`phytoTempExp1` & :math:`e_{1j}` & exp(1/C) & see :numref:`tab_phys_pkg_darwin_tempparams` 0578 :varlink:`phytoTempAe` & :math:`A^{\op{phy}}_{\op{e}j}` & 1/C & see :numref:`tab_phys_pkg_darwin_tempparams` 0579 :varlink:`phytoTempExp2` & :math:`e_{2j}` & & see :numref:`tab_phys_pkg_darwin_tempparams` 0580 :varlink:`phytoTempOptimum` & :math:`T^{\op{opt}}_j` & C & see :numref:`tab_phys_pkg_darwin_tempparams` 0581 :varlink:`phytoDecayPower` & :math:`p_j` & & see :numref:`tab_phys_pkg_darwin_tempparams` 0582 :varlink:`hetTempAe` & :math:`A^{\op{het}}_{\op{e}j}` & 1/C & see :numref:`tab_phys_pkg_darwin_tempparams` 0583 :varlink:`hetTempExp2` & :math:`e^{\op{het}}_{2j}` & & see :numref:`tab_phys_pkg_darwin_tempparams` 0584 :varlink:`hetTempOptimum` & :math:`T^{\op{opt het}}_j` & C & see :numref:`tab_phys_pkg_darwin_tempparams` 0585 :varlink:`hetDecayPower` & :math:`p^{\op{het}}_j` & & see :numref:`tab_phys_pkg_darwin_tempparams` 0586 :varlink:`grazTempAe` & :math:`A^{\op{graz}}_{\op{e}j}` & 1/C & see :numref:`tab_phys_pkg_darwin_tempparams` 0587 :varlink:`grazTempExp2` & :math:`e^{\op{graz}}_{2j}` & & see :numref:`tab_phys_pkg_darwin_tempparams` 0588 :varlink:`grazTempOptimum` & :math:`T^{\op{opt graz}}_j` & C & see :numref:`tab_phys_pkg_darwin_tempparams` 0589 :varlink:`grazDecayPower` & :math:`p^{\op{graz}}_j` & & see :numref:`tab_phys_pkg_darwin_tempparams` 1d947889e4 Oliv*0590 :varlink:`R_NC` & :math:`R^{\op{N}:\op{C}}_j` & mmol N (mmol C)\ :sup:`-1` & nitrogen-carbon ratio (not used with DARWIN_ALLOW_NQUOTA) 0591 :varlink:`R_PC` & :math:`R^{\op{P}:\op{C}}_j` & mmol P (mmol C)\ :sup:`-1` & phosphorus-carbon ratio (not used with DARWIN_ALLOW_PQUOTA) 0592 :varlink:`R_SiC` & :math:`R^{\op{Si}:\op{C}}_j` & mmol Si (mmol C)\ :sup:`-1` & silica-carbon ratio (not used with DARWIN_ALLOW_SIQUOTA) 0593 :varlink:`R_FeC` & :math:`R^{\op{Fe}:\op{C}}_j` & mmol Fe (mmol C)\ :sup:`-1` & iron-carbon ratio (not used with DARWIN_ALLOW_FEQUOTA) 0594 :varlink:`R_ChlC` & :math:`R^{\op{chl}c}_j` & mg Chl (mmol C)\ :sup:`-1` & chlorophyll-carbon ratio (not used with DARWIN_ALLOW_CHLQUOTA) 0595 :varlink:`R_PICPOC` & :math:`R^{\op{PICPOC}}_j` & mmol PIC (mmol POC)\ :sup:`-1` & inorganic-organic carbon ratio 0596 :varlink:`biosink` & :math:`w^{\op{sink}}_j` & m s\ :sup:`-1` & sinking velocity (positive downwards) 0597 :varlink:`bioswim` & :math:`w^{\op{swim}}_j` & m s\ :sup:`-1` & upward swimming velocity (positive upwards) 0598 :varlink:`respRate` & :math:`r^{\op{resp}}_j` & s\ :sup:`-1` & respiration rate 0599 :varlink:`PCmax` & :math:`P^{\op{max}}_{\op{C},j}` & s\ :sup:`-1` & maximum carbon-specific growth rate 0600 :varlink:`Qnmax` & :math:`Q^{\op{N}\op{max}}_j` & mmol N (mmol C)\ :sup:`-1` & maximum nitrogen quota (only with DARWIN_ALLOW_NQUOTA) 0601 :varlink:`Qnmin` & :math:`Q^{\op{N}\min}_j` & mmol N (mmol C)\ :sup:`-1` & minimum nitrogen quota (only with DARWIN_ALLOW_NQUOTA) 0602 :varlink:`Qpmax` & :math:`Q^{\op{P}\op{max}}_j` & mmol P (mmol C)\ :sup:`-1` & maximum phosphorus quota (only with DARWIN_ALLOW_PQUOTA) 0603 :varlink:`Qpmin` & :math:`Q^{\op{P}\min}_j` & mmol P (mmol C)\ :sup:`-1` & minimum phosphorus quota (only with DARWIN_ALLOW_PQUOTA) 0604 :varlink:`Qsimax` & :math:`Q^{\op{Si}\op{max}}_j` & mmol Si (mmol C)\ :sup:`-1` & maximum silica quota (only with DARWIN_ALLOW_SIQUOTA) 0605 :varlink:`Qsimin` & :math:`Q^{\op{Si}\min}_j` & mmol Si (mmol C)\ :sup:`-1` & minimum silica quota (only with DARWIN_ALLOW_SIQUOTA) 0606 :varlink:`Qfemax` & :math:`Q^{\op{Fe}\op{max}}_j` & mmol Fe (mmol C)\ :sup:`-1` & maximum iron quota (only with DARWIN_ALLOW_FEQUOTA) 0607 :varlink:`Qfemin` & :math:`Q^{\op{Fe}\min}_j` & mmol Fe (mmol C)\ :sup:`-1` & minimum iron quota (only with DARWIN_ALLOW_FEQUOTA) 0608 :varlink:`VmaxNH4` & :math:`V^{\op{NH4}\op{max}}_j` & mmol N (mmol C)\ :sup:`-1` s\ :sup:`-1` & maximum ammonia uptake rate (only with DARWIN_ALLOW_NQUOTA) 0609 :varlink:`VmaxNO2` & :math:`V^{\op{NO2}\op{max}}_j` & mmol N (mmol C)\ :sup:`-1` s\ :sup:`-1` & maximum nitrite uptake rate (only with DARWIN_ALLOW_NQUOTA) 0610 :varlink:`VmaxNO3` & :math:`V^{\op{NO3}\op{max}}_j` & mmol N (mmol C)\ :sup:`-1` s\ :sup:`-1` & maximum nitrate uptake rate (only with DARWIN_ALLOW_NQUOTA) 0611 :varlink:`VmaxN` & :math:`V^{\op{N}\op{max}}_j` & mmol N (mmol C)\ :sup:`-1` s\ :sup:`-1` & maximum nitrogen uptake rate for diazotrophs (only with DARWIN_ALLOW_NQUOTA) 0612 :varlink:`VmaxPO4` & :math:`V^{\op{PO4}\op{max}}_j` & mmol P (mmol C)\ :sup:`-1` s\ :sup:`-1` & maximum phosphate uptake rate (only with DARWIN_ALLOW_PQUOTA) 0613 :varlink:`VmaxSiO2` & :math:`V^{\op{SiO2}\op{max}}_j` & mmol Si (mmol C)\ :sup:`-1` s\ :sup:`-1` & maximum silica uptake rate (only with DARWIN_ALLOW_SIQUOTA) 0614 :varlink:`VmaxFeT` & :math:`V^{\op{Fe}\op{max}}_j` & mmol Fe (mmol C)\ :sup:`-1` s\ :sup:`-1` & maximum iron uptake rate (only with DARWIN_ALLOW_FEQUOTA) 0615 :varlink:`ksatNH4` & :math:`k^{\op{NH4}}_j` & mmol N m\ :sup:`-3` & half-saturation conc. for ammonia uptake/limitation 0616 :varlink:`ksatNO2` & :math:`k^{\op{NO2}}_j` & mmol N m\ :sup:`-3` & half-saturation conc. for nitrite uptake/limitation 0617 :varlink:`ksatNO3` & :math:`k^{\op{NO3}}_ji` & mmol N m\ :sup:`-3` & half-saturation conc. for nitrate uptake/limitation 0618 :varlink:`ksatPO4` & :math:`k^{\op{PO4}}_j` & mmol P m\ :sup:`-3` & half-saturation conc. for phosphate uptake/limitation 0619 :varlink:`ksatSiO2` & :math:`k^{\op{SiO2}}_j` & mmol Si m\ :sup:`-3` & half-saturation conc. for silica uptake/limitation 0620 :varlink:`ksatFeT` & :math:`k^{\op{Fe}}_j` & mmol Fe m\ :sup:`-3` & half-saturation conc. for iron uptake/limitation 0621 :varlink:`kexcc` & :math:`\kappa^{\op{exc}}_{\op{C} j}` & s\ :sup:`-1` & exudation rate for carbon 0622 :varlink:`kexcn` & :math:`\kappa^{\op{exc}}_{\op{N} j}` & s\ :sup:`-1` & exudation rate for nitrogen 0623 :varlink:`kexcp` & :math:`\kappa^{\op{exc}}_{\op{P} j}` & s\ :sup:`-1` & exudation rate for phosphorus 0624 :varlink:`kexcsi` & :math:`\kappa^{\op{exc}}_{\op{Si} j}` & s\ :sup:`-1` & exudation rate for silica 0625 :varlink:`kexcfe` & :math:`\kappa^{\op{exc}}_{\op{Fe} j}` & s\ :sup:`-1` & exudation rate for iron 0626 :varlink:`inhibGeider` & :math:`c^{\op{inhib}}_j` & & photo-inhibition coefficient for Geider growth** Warning **
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0627 :varlink:`ksatPAR` & :math:`k^{\op{sat}}_{\op{PAR}}` & (μEin m\ :sup:`-2` s\ :sup:`-1`)\ :sup:`-1` & saturation coefficient for PAR (w/o GEIDER)** Warning **
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0628 :varlink:`kinhPAR` & :math:`k^{\op{inh}}_{\op{PAR}}` & (μEin m\ :sup:`-2` s\ :sup:`-1`)\ :sup:`-1` & inhibition coefficient for PAR (w/o GEIDER)** Warning **
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0629 :varlink:`mQyield` & :math:`\Phi_j` & mmol C (μEin)\ :sup:`-1` & maximum quantum yield 0630 :varlink:`chl2cmax` & :math:`\op{Chl\text{:}C}^{\op{max}}_j` & mg Chl (mmol C)\ :sup:`-1` & maximum Chlorophyll-carbon ratio 0631 :varlink:`grazemax` & :math:`g^{\op{max}}_z` & s\ :sup:`-1` & maximum grazing rate 0632 :varlink:`kgrazesat` & :math:`k^{\op{graz}}_z` & mmol C m\ :sup:`-3` & grazing half-saturation concentration 0633 :varlink:`yield` & :math:`{Y_j}` & & bacterial growth yield for all organic matter 0634 :varlink:`yieldO2` & :math:`{Y^{{\mathrm{O}}_2}_j}` & & bacterial growth yield for oxygen 0635 :varlink:`yieldNO3` & :math:`{Y^{\op{NO}_3}_j}` & & bacterial growth yield for nitrate 0636 :varlink:`ksatPON` & :math:`{k^{\op{PON}}}` & mmol N m\ :sup:`-3` & half-saturation of PON for bacterial growth 0637 :varlink:`ksatPOC` & :math:`{k^{\op{POC}}}` & mmol C m\ :sup:`-3` & half-saturation of POC for bacterial growth 0638 :varlink:`ksatPOP` & :math:`{k^{\op{POP}}}` & mmol P m\ :sup:`-3` & half-saturation of POP for bacterial growth 0639 :varlink:`ksatPOFe` & :math:`{k^{\op{POFe}}}` & mmol Fe m\ :sup:`-3` & half-saturation of POFe for bacterial growth 0640 :varlink:`ksatDON` & :math:`{k^{\op{DON}}}` & mmol N m\ :sup:`-3` & half-saturation of DON for bacterial growth 0641 :varlink:`ksatDOC` & :math:`{k^{\op{DOC}}}` & mmol C m\ :sup:`-3` & half-saturation of DOC for bacterial growth 0642 :varlink:`ksatDOP` & :math:`{k^{\op{DOP}}}` & mmol P m\ :sup:`-3` & half-saturation of DOP for bacterial growth 0643 :varlink:`ksatDOFe` & :math:`{k^{\op{DOFe}}}` & mmol Fe m\ :sup:`-3` & half-saturation of DOFe for bacterial growth 0644 0645 0646 .. csv-table:: Trait matrices for grazing; indices (prey, pred) 0647 :delim: & 0648 :widths: auto 0649 :class: longtable 0650 :header: Trait, Symbol, Units, Description 0651 0652 :varlink:`palat` & :math:`p_{j,z}` & & palatability matrix 0653 :varlink:`asseff` & :math:`a_{j,z}` & & assimilation efficiency matrix 0654 :varlink:`ExportFracPreyPred` & :math:`f^{\op{exp}\op{graz}}_{j,z}` & & fraction of unassimilated prey becoming particulate organic matter 0655 0656 0657 .. csv-table:: Namelist DARWIN_RADTRANS_TRAITS; indices (plankton, waveband) 0658 :delim: & 0659 :widths: auto 0660 :header: Trait, Symbol, Units, Description 0661 d37d18cf65 Oliv*0662 :varlink:`aphy_chl` & :math:`a^{\op{chl}}_{\op{phy}}` & m\ :sup:`2` (mg Chl)\ :sup:`-1` & phytoplankton Chl-specific absorption coefficient 0663 :varlink:`aphy_chl_ps` & :math:`a^{\op{chl}}_{\op{ps}}` & m\ :sup:`2` (mg Chl)\ :sup:`-1` & part of :varlink:`aphy_chl` that is used in photosynthesis 0664 :varlink:`aphy_mgC` & :math:`a^{\op{mgC}}_{\op{phy}}` & m\ :sup:`2` (mg C)\ :sup:`-1` & plankton carbon-specific absorption coefficient 0665 :varlink:`bphy_mgC` & :math:`b^{\op{mgC}}_{\op{phy}}` & m\ :sup:`2` (mg C)\ :sup:`-1` & carbon-specific total scattering coefficient 0666 :varlink:`bbphy_mgC` & :math:`b^{\op{mgC}}_{\op{b}\op{phy}}` & m\ :sup:`2` (mg C)\ :sup:`-1` & carbon-specific backscattering coefficient 1d947889e4 Oliv*0667 0668 0669 The dependent trait alphachl(plankton,waveband) is computed from the other traits 0670 (radtrans or not). 0671 0672 Allometric trait generation 0673 ''''''''''''''''''''''''''' 0674 0675 Plankton types are organized into functional groups. ``grp_nplank(g)`` 0676 sets the number of types in group ``g``. Traits may be set the same for 0677 all types in a group, e.g., ``grp_diazo(g)``, or based on allometric 0678 scaling relations, 0679 0680 .. math:: \mathrm{trait}_j = a_g \cdot V_j^{b_g} 0681 0682 with per-group scaling coefficients :math:`a_g` and :math:`b_g`. 0683 0684 The volumes :math:`V_j` of all types can be set in four ways (in order 0685 or decreasing precedence), 0686 0687 .. math:: 0688 0689 V_j = \begin{cases} 0690 \op{grp\_biovol(i,g)} & \\ b0bcc83b10 Oliv*0691 V_{\log}(\op{grp\_logvolind(i,g)}) \\ 1d947889e4 Oliv*0692 V_{\log}(\op{logvol0ind(g)}+i-1) \\ 0693 V_{0 g} f_g^{i-1} 0694 \end{cases} 0695 0696 where :math:`i` is the index of type :math:`j` within the functional 0697 group. :math:`V_{\log}` is a series of volumes, evenly spaced in log 0698 space and defined by parameters :math:`B=\op{logvolbase}` and 0699 :math:`I=\op{logvolinc}`, 0700 0701 .. math:: V_{\log} = 10^B, 10^{B+I}, 10^{B+2I}, \dots 0702 0703 and :math:`V_{0 g}=\op{biovol0(g)}` and 0704 :math:`f_g=\op{biovolfac(g)}`. 0705 0706 The scaling coefficients are read from namelist ``&darwin_trait_params`` 0707 in ``data.darwin``. The following table shows the correspondence between 0708 traits and trait parameters. Where :math:`b` is not given, it is set to faa67d1773 Oliv*0709 0, i.e., all types in the group share the same trait value. For some trait 0710 parameters *x*, a divisor may be specified in *x*\ _denom. This is** Warning **
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0711 particularly useful for specifying a rate in ‘per-day’ units, i.e., 0712 *x*\ _denom=86400. 1d947889e4 Oliv*0713 0714 .. csv-table:: Namelist DARWIN_TRAIT_PARAMS 0715 :delim: & 0716 :widths: auto 0717 :header: Trait, a, Default, b, Default 0718 0719 :varlink:`isPhoto` & :varlink:`grp_photo` & 1 & & 0720 :varlink:`bactType` & :varlink:`grp_bacttype` & 0 & & 0721 :varlink:`isAerobic` & :varlink:`grp_aerobic` & 0 & & 0722 :varlink:`isDenit` & :varlink:`grp_denit` & 0 & & 0723 :varlink:`isPred` & :varlink:`grp_pred` & 0 & & 0724 :varlink:`isPrey` & :varlink:`grp_prey` & 1 & & 0725 :varlink:`hasSi` & :varlink:`grp_hasSi` & 0 & & 0726 :varlink:`hasPIC` & :varlink:`grp_hasPIC` & 0 & & 0727 :varlink:`diazo` & :varlink:`grp_diazo` & 0 & & 0728 :varlink:`useNH4` & :varlink:`grp_useNH4` & 1 & & 0729 :varlink:`useNO2` & :varlink:`grp_useNO2` & 1 & & 0730 :varlink:`useNO3` & :varlink:`grp_useNO3` & 1 & & 0731 :varlink:`combNO` & :varlink:`grp_combNO` & 1 & & 0732 :varlink:`aptype` & :varlink:`grp_aptype` & 0 & & 0733 :varlink:`tempMort` & :varlink:`grp_tempMort` & 1 & & 0734 :varlink:`tempMort2` & :varlink:`grp_tempMort2` & 1 & & 0735 :varlink:`tempGraz` & :varlink:`grp_tempGraz` & 1 & & 0736 :varlink:`Xmin` & :varlink:`a_Xmin` & 0 & & 0737 :varlink:`R_NC` & :varlink:`a_R_NC` & 16/120 & & 0738 :varlink:`R_PC` & :varlink:`a_R_PC` & 1/120 & & 0739 :varlink:`R_SiC` & :varlink:`a_R_SiC` & 0 & & 0740 :varlink:`R_FeC` & :varlink:`a_R_FeC` & 1D-3/120 & & 0741 :varlink:`R_ChlC` & :varlink:`a_R_ChlC` & 16/120 & & 0742 :varlink:`R_PICPOC` & :varlink:`a_R_PICPOC` & 0.8 & & 0743 :varlink:`ExportFracMort` & :varlink:`a_ExportFracMort` & 0.5 & & 0744 :varlink:`ExportFracMort2` & :varlink:`a_ExportFracMort2` & 0.5 & & 0745 :varlink:`ExportFracExude` & :varlink:`a_ExportFracExude` & UNINIT & & 0746 :varlink:`mort` & :varlink:`a_mort` & 0.02 / day & & 0747 :varlink:`mort2` & :varlink:`a_mort2` & 0 & & 0748 :varlink:`phytoTempCoeff` & :varlink:`a_phytoTempCoeff` & 1/3 & & 0749 :varlink:`phytoTempExp1` & :varlink:`a_phytoTempExp1` & 1.04 & & 09b16dd232 Oliv*0750 :varlink:`phytoTempAe` & :varlink:`a_phytoTempAe` & 0.0438 & & 0751 :varlink:`phytoTempExp2` & :varlink:`a_phytoTempExp2` & 0.001 & & 1d947889e4 Oliv*0752 :varlink:`phytoTempOptimum` & :varlink:`a_phytoTempOptimum` & 2 & & 0753 :varlink:`phytoDecayPower` & :varlink:`a_phytoDecayPower` & 4 & & 09b16dd232 Oliv*0754 :varlink:`hetTempAe` & :varlink:`a_hetTempAe` & 0.0438 & & 0755 :varlink:`hetTempExp2` & :varlink:`a_hetTempExp2` & 0.001 & & 0756 :varlink:`hetTempOptimum` & :varlink:`a_hetTempOptimum` & 2 & & 0757 :varlink:`hetDecayPower` & :varlink:`a_hetDecayPower` & 4 & & 0758 :varlink:`grazTempAe` & :varlink:`a_grazTempAe` & 0.0438 & & 0759 :varlink:`grazTempExp2` & :varlink:`a_grazTempExp2` & 0.001 & & 0760 :varlink:`grazTempOptimum` & :varlink:`a_grazTempOptimum` & 2 & & 0761 :varlink:`grazDecayPower` & :varlink:`a_grazDecayPower` & 4 & & 1d947889e4 Oliv*0762 :varlink:`mQyield` & :varlink:`a_mQyield` & 75D-6 & & 0763 :varlink:`chl2cmax` & :varlink:`a_chl2cmax` & .3 & & 0764 :varlink:`inhibGeider` & :varlink:`a_inhibGeider` & 0 & & 0765 :varlink:`ksatPAR` & :varlink:`a_ksatPAR` & 0.012 & & 0766 :varlink:`kinhPAR` & :varlink:`a_kinhPAR` & 6D-3 & & 0767 :varlink:`amminhib` & :varlink:`a_amminhib` & 4.6 & & 0768 :varlink:`acclimtimescl` & :varlink:`a_acclimtimescl` & 1/(20 days) & & 0769 & :varlink:`a_acclimtimescl_denom` & 1 & & 0770 :varlink:`ksatPON` & :varlink:`a_ksatPON` & 1 & & 0771 :varlink:`ksatDON` & :varlink:`a_ksatDON` & 1 & & 0772 :varlink:`grazemax` & :varlink:`a_grazemax` & 21.9 / day & :varlink:`b_grazemax` & -0.16 0773 & :varlink:`a_grazemax_denom` & 1 & & 0774 :varlink:`kgrazesat` & :varlink:`a_kgrazesat` & 1.00 & :varlink:`b_kgrazesat` & 0.00 0775 :varlink:`biosink` & :varlink:`a_biosink` & 0.28D-1 / day & :varlink:`b_biosink` & 0.39 0776 & :varlink:`a_biosink_denom` & 1 & & 0777 :varlink:`bioswim` & :varlink:`a_bioswim` & 0.00 / day & :varlink:`b_bioswim` & 0.18 0778 & :varlink:`a_bioswim_denom` & 1 & & faa67d1773 Oliv*0779 :varlink:`palat` & :varlink:`a_ppSig` & 1 & *see note* [#palat]_ 1d947889e4 Oliv*0780 :varlink:`palat` & :varlink:`a_ppOpt` & 1024 & :varlink:`b_ppOpt` & 0.00 faa67d1773 Oliv*0781 :varlink:`palat` & :varlink:`palat_min` & 0 & & 1d947889e4 Oliv*0782 :varlink:`PCmax` & :varlink:`a_PCmax` & 1.00 / day & :varlink:`b_PCmax` & -0.15 0783 & :varlink:`a_PCmax_denom` & 1 & & 0784 :varlink:`qcarbon` & :varlink:`a_qcarbon` & 1.80D-11 & :varlink:`b_qcarbon` & 0.94 0785 :varlink:`respRate` & :varlink:`a_respRate_c` & 0.00 & :varlink:`b_respRate_c` & 0.93 faa67d1773 Oliv*0786 & :varlink:`a_respRate_c_denom` & 1 & *see note* [#resprate]_ 1d947889e4 Oliv*0787 :varlink:`kexcc` & :varlink:`a_kexcC` & 0.00 & :varlink:`b_kexcC` & -0.33 0788 :varlink:`vmaxNO3` & :varlink:`a_vmaxNO3` & 0.51 / day & :varlink:`b_vmaxNO3` & -0.27 0789 & :varlink:`a_vmaxNO3_denom` & 1 & & 0790 :varlink:`ksatNO3` & :varlink:`a_ksatNO3` & 0.17 & :varlink:`b_ksatNO3` & 0.27 0791 :varlink:`Qnmin` & :varlink:`a_Qnmin` & 0.07 & :varlink:`b_Qnmin` & -0.17 0792 :varlink:`Qnmax` & :varlink:`a_Qnmax` & 0.25 & :varlink:`b_Qnmax` & -0.13 0793 :varlink:`kexcn` & :varlink:`a_kexcN` & 0.00 & :varlink:`b_kexcN` & -0.33 0794 :varlink:`vmaxNO2` & :varlink:`a_vmaxNO2` & 0.51 / day & :varlink:`b_vmaxNO2` & -0.27 0795 & :varlink:`a_vmaxNO2_denom` & 1 & & 0796 :varlink:`ksatNO2` & :varlink:`a_ksatNO2` & 0.17 & :varlink:`b_ksatNO2` & 0.27 0797 & :varlink:`a_ksatNO2fac` & 1 & *used for eff.ksat* 0798 :varlink:`vmaxNH4` & :varlink:`a_vmaxNH4` & 0.26 / day & :varlink:`b_vmaxNH4` & -0.27 0799 & :varlink:`a_vmaxNH4_denom` & 1 & & 0800 :varlink:`ksatNH4` & :varlink:`a_ksatNH4` & 0.85D-1 & :varlink:`b_ksatNH4` & 0.27 0801 & :varlink:`a_ksatNH4fac` & 0.5 & *used for eff.ksat* 0802 :varlink:`vmaxN` & :varlink:`a_vmaxN` & 1.28 / day & :varlink:`b_vmaxN` & -0.27 0803 & :varlink:`a_vmaxN_denom` & 1 & & 0804 :varlink:`vmaxPO4` & :varlink:`a_vmaxPO4` & 0.77D-1 / day & :varlink:`b_vmaxPO4` & -0.27 0805 & :varlink:`a_vmaxPO4_denom` & 1 & & 0806 :varlink:`ksatPO4` & :varlink:`a_ksatPO4` & 0.26D-1 & :varlink:`b_ksatPO4` & 0.27 0807 :varlink:`Qpmin` & :varlink:`a_Qpmin` & 2.00D-3 & :varlink:`b_Qpmin` & 0.00 0808 :varlink:`Qpmax` & :varlink:`a_Qpmax` & 0.01 & :varlink:`b_Qpmax` & 0.00 0809 :varlink:`kexcp` & :varlink:`a_kexcP` & 0.24D-1 / day & :varlink:`b_kexcP` & -0.33 0810 :varlink:`vmaxSiO2` & :varlink:`a_vmaxSiO2` & 0.77D-1 / day & :varlink:`b_vmaxSiO2` & -0.27 0811 & :varlink:`a_vmaxSiO2_denom` & 1 & & 0812 :varlink:`ksatSiO2` & :varlink:`a_ksatSiO2` & 0.24D-1 & :varlink:`b_ksatSiO2` & 0.27 0813 :varlink:`Qsimin` & :varlink:`a_Qsimin` & 2.00D-3 & :varlink:`b_Qsimin` & 0.00 0814 :varlink:`Qsimax` & :varlink:`a_Qsimax` & 4.00D-3 & :varlink:`b_Qsimax` & 0.00 0815 :varlink:`kexcsi` & :varlink:`a_kexcSi` & 0.00 / day & :varlink:`b_kexcSi` & 0.00 0816 :varlink:`vmaxFeT` & :varlink:`a_vmaxFeT` & 14D-6 / day & :varlink:`b_vmaxFeT` & -0.27 0817 & :varlink:`a_vmaxFeT_denom` & 1 & & 0818 :varlink:`ksatFeT` & :varlink:`a_ksatFeT` & 80D-6 & :varlink:`b_ksatFeT` & 0.27 0819 :varlink:`Qfemin` & :varlink:`a_Qfemin` & 1.50D-6 & :varlink:`b_Qfemin` & 0.00 0820 :varlink:`Qfemax` & :varlink:`a_Qfemax` & 80D-6 & :varlink:`b_Qfemax` & 0.00 0821 :varlink:`kexcfe` & :varlink:`a_kexcFe` & 0.00 / day & :varlink:`b_kexcFe` & 0.00 0822 :varlink:`ExportFracPreyPred` & :varlink:`grp_ExportFracPreyPred` & 0.5 & *(nGroup* :math:`\times` *nGroup)* 0823 :varlink:`asseff` & :varlink:`grp_ass_eff` & 0.7 & *(nGroup* :math:`\times` *nGroup)* 0824 :varlink:`aphy_chl` & :varlink:`aphy_chl_type` & *read* & *via* :varlink:`grp_aptype` 0825 :varlink:`aphy_chl_ps` & :varlink:`aphy_chl_ps_type` & *read* & *via* :varlink:`grp_aptype` f61b1017e2 Oliv*0826 :varlink:`aphy_mgC` & :varlink:`aphy_mgC_type` & *read* & *via* :varlink:`grp_aptype` 1d947889e4 Oliv*0827 :varlink:`bphy_mgC` & :varlink:`bphy_mgC_type` & *read* & *via* :varlink:`grp_aptype` 0828 :varlink:`bbphy_mgC` & :varlink:`bbphy_mgC_type` & *read* & *via* :varlink:`grp_aptype` 0829 faa67d1773 Oliv*0830 .. [#palat] Palatabilities are initialized to zero and have to be set in 0831 ``data.traits`` unless :varlink:`DARWIN_ALLOMETRIC_PALAT` is defined in 0832 which case they are computed from pp_opt, pp_sig and palat_min based on 0833 predator and prey sizes, see :numref:`Grazing`. 1d947889e4 Oliv*0834 faa67d1773 Oliv*0835 .. [#resprate] The respiration rate follows a different scaling law from other 0836 traits. It scales in terms of cellular carbon content, see 65f39704e7 Oliv*0837 :numref:`Respiration`. 1d947889e4 Oliv*0838 0839 0840 Diagnostics 0841 ~~~~~~~~~~~ 0842 4c914c90da Oliv*0843 .. tabularcolumns:: |\Y{.16}|\Y{.16}|\Y{.18}|\Y{.5}| 0844 141d0e903d Oliv*0845 .. csv-table:: Darwin package diagnostic fields faa67d1773 Oliv*0846 :delim: & 0847 :widths: auto 0848 :class: longtable 0849 :header: Name, Code, Units, Description 0850 0851 plankC & ``SMR_____MR`` & mmol C /m\ :sup:`3` & Total plankton carbon biomass 0852 Chl & ``SMR_____MR`` & mg Chl a /m\ :sup:`3` & Total Chlorophyll a 0853 PP & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Primary Production 0854 Nfix & ``SMRP____MR`` & mmol N /m\ :sup:`3`/s & N fixation 0855 Denit & ``SMRP____MR`` & mmol N /m\ :sup:`3`/s & Denitrification 0856 DenitN & ``SMRP____MR`` & mmol N /m\ :sup:`3`/s & Nitrogen loss due to denitrification 141d0e903d Oliv*0857 EXU & ``SM_P____MR`` & mmol C /m\ :sup:`3`/s & Carbon exudation 0858 BioSyn & ``SM_P____MR`` & mmol C /m\ :sup:`3`/s & Biosynthesis rate 0859 DmdN & ``SM_P____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from N limit 0860 DmdP & ``SM_P____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from P limit 0861 DmdFe & ``SM_P____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from Fe limit 0862 DmdSi & ``SM_P____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from Si limit 0863 Dmdmin & ``SM_P____MR`` & mmol C /m\ :sup:`3`/s & Minimum carbon demand faa67d1773 Oliv*0864 PAR### & ``SMRP____MR`` & Ein/m\ :sup:`2`/s & PAR waveband ### 141d0e903d Oliv*0865 PARF### & ``SM_P____LR`` & Ein/m\ :sup:`2`/s & PAR at W point, waveband ### faa67d1773 Oliv*0866 a### & ``SMRP____MR`` & 1/m & total absorption for waveband ### 0867 bt### & ``SMRP____MR`` & 1/m & total scattering for waveband ### 0868 bb### & ``SMRP____MR`` & 1/m & total backscattering for waveband ### 0869 aplk### & ``SMRP____MR`` & 1/m & absorption by plankton for waveband ### 0870 btplk### & ``SMRP____MR`` & 1/m & scattering by plankton for waveband ### 0871 bbplk### & ``SMRP____MR`` & 1/m & backscattering by plankton for waveband ### 0872 aprt### & ``SMRP____MR`` & 1/m & absorption by particles for waveband ### 0873 btprt### & ``SMRP____MR`` & 1/m & scattering by particles for waveband ### 0874 bbprt### & ``SMRP____MR`` & 1/m & backscattering by particles for waveband ### 0875 aCDOM### & ``SMRP____MR`` & 1/m & absorption by CDOM for waveband ### 0876 atten & ``SMRP____MR`` & 1 & attenuation in layer 141d0e903d Oliv*0877 PARF & ``SM_P____LR`` & Ein/m\ :sup:`2`/s & PAR at top of layer faa67d1773 Oliv*0878 PAR & ``SMRP____MR`` & Ein/m\ :sup:`2`/s & total PAR at layer center 0879 C_DIN & ``SMRP____MR`` & mmol N /m\ :sup:`3`/s & consumption of DIN: :math:`\sum_j(U^{\op{NO3}}_j+U^{\op{NO2}}_j+U^{\op{NH4}}_j)` 0880 C_NO3 & ``SMRP____MR`` & mmol N /m\ :sup:`3`/s & consumption of NO3: :math:`\sum_j U^{\op{NO3}}_j` 0881 C_NO2 & ``SMRP____MR`` & mmol N /m\ :sup:`3`/s & consumption of NO2: :math:`\sum_j U^{\op{NO2}}_j` 0882 C_NH4 & ``SMRP____MR`` & mmol N /m\ :sup:`3`/s & consumption of NH4: :math:`\sum_j U^{\op{NH4}}_j` 0883 C_PO4 & ``SMRP____MR`` & mmol P /m\ :sup:`3`/s & consumption of PO4: :math:`\sum_j U^{\op{PO4}}_j` 0884 C_Si & ``SMRP____MR`` & mmol Si /m\ :sup:`3`/s & consumption of Si: :math:`\sum _j U^{\op{SiO2}}_j` 0885 C_Fe & ``SMRP____MR`` & mmol Fe /m\ :sup:`3`/s & consumption of Fe: :math:`\sum_j U^{\op{Fe}}_j` 0886 S_DIN & ``SMR_____MR`` & mmol N /m\ :sup:`3`/s & non-transport source of DIN: :math:`r_{\op{DON}}\op{DON}+[r_{\op{PON}}\op{PON}]-D_{\op{NH4}}-D_{\op{NO3}}` 0887 S_NO3 & ``SMR_____MR`` & mmol N /m\ :sup:`3`/s & non-transport source of NO3 0888 S_NO2 & ``SMR_____MR`` & mmol N /m\ :sup:`3`/s & non-transport source of NO2 0889 S_NH4 & ``SMR_____MR`` & mmol N /m\ :sup:`3`/s & non-transport source of NH4 0890 S_PO4 & ``SMR_____MR`` & mmol P /m\ :sup:`3`/s & non-transport source of PO4: :math:`r_{\op{DOP}}\op{DOP}+[r_{\op{POP}}\op{POP}]` 0891 S_Si & ``SMR_____MR`` & mmol Si /m\ :sup:`3`/s & non-transport source of Si: :math:`r_{\op{POSi}}\op{POSi}` 0892 S_Fe & ``SMR_____MR`` & mmol Fe /m\ :sup:`3`/s & non-transport source of Fe: :math:`r_{\op{DOFe}}\op{DOFe}+[r_{\op{POFe}}\op{POFe}]+S_{\op{Fe}}` 3ded9f825b Oliv*0893 gDAR## & ``SMR_____MR`` & [TRAC##]/s & ptracer ## tendency from DARWIN [#b]_ 0894 gECO## & ``SMR_____MR`` & [TRAC##]/s & ptracer ## tendency from DARWIN w/o sink/swim [#b]_ faa67d1773 Oliv*0895 PP#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Primary Production plankton #### d1275a52cd Oliv*0896 PC#### & ``SMRP____MR`` & 1/s & Carbon-specific phototrophic growth rate plankton #### 0897 HP#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Heterotrophic production plankton #### 0898 HC#### & ``SMRP____MR`` & 1/s & Carbon-specific heterotrophic growth rate plankton #### faa67d1773 Oliv*0899 GR#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Grazing loss of plankton #### 0900 GrGn#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Grazing gain of plankton #### d1275a52cd Oliv*0901 GrGC#### & ``SMRP____MR`` & 1/s & Carbon-specific grazing rate plankton #### fd20fa810c Oliv*0902 Mort#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Mortality loss plankton #### 0903 Resp#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Respiration loss plankton #### 0904 limN#### & ``SMRP____MR`` & [0/1] & N growth limitation plankton #### 0905 limP#### & ``SMRP____MR`` & [0/1] & P growth limitation plankton #### 0906 limF#### & ``SMRP____MR`` & [0/1] & Fe growth limitation plankton #### 0907 limS#### & ``SMRP____MR`` & [0/1] & Si growth limitation plankton #### 0908 fnut#### & ``SMRP____MR`` & [0/1] & Nutrient growth factor plankton #### 0909 fIph#### & ``SMRP____MR`` & [0/1] & Light growth factor plankton #### 0910 fTph#### & ``SMRP____MR`` & [0/1] & Temperature growth factor plankton #### 141d0e903d Oliv*0911 EXU#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Exudation plankton #### 0912 BS#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Biosynthesis rate plankton #### 0913 DN#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from N limit plankton #### 0914 DP#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from P limit plankton #### 0915 DFe#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from Fe limit plankton #### 0916 DSi#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from Si limit plankton #### 0917 Dmin#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Minimum carbon demand plankton #### faa67d1773 Oliv*0918 sfcSolFe & ``SM_P____L1`` & mmol Fe /m\ :sup:`2`/s & Soluble iron input at sea surface 141d0e903d Oliv*0919 scvLosFe & ``SMRP____MR`` & mmol Fe /m\ :sup:`3`/s & Iron loss from scavenging 0920 scavRate & ``SMRP____MR`` & 1/s & Iron scavenging rate 0921 sedFe & ``SMRP____MR`` & mmol Fe /m\ :sup:`3`/s & Iron input from sediment faa67d1773 Oliv*0922 freeFeLs & ``SMRP____MR`` & mmol Fe /m\ :sup:`3`/s & Iron loss due to free iron limit 141d0e903d Oliv*0923 sedFlxFe & ``SM_P____U1`` & mmol Fe /m\ :sup:`2`/s & Iron sediment flux faa67d1773 Oliv*0924 gDICEpr & ``SM______L1`` & mmol C /m\ :sup:`3`/s & Tendency of DIC due to E/P/runoff 0925 gNO3Epr & ``SM______L1`` & mmol N /m\ :sup:`3`/s & Tendency of DIC due to E/P/runoff 0926 gNO2Epr & ``SM______L1`` & mmol N /m\ :sup:`3`/s & Tendency of DIC due to E/P/runoff 0927 gNH4Epr & ``SM______L1`` & mmol N /m\ :sup:`3`/s & Tendency of DIC due to E/P/runoff 0928 gPO4Epr & ``SM______L1`` & mmol P /m\ :sup:`3`/s & Tendency of PO4 due to E/P/runoff 3c930300af Oliv*0929 gFeTEpr & ``SM______L1`` & mmol Fe /m\ :sup:`3`/s & Tendency of FeT due to E/P/runoff faa67d1773 Oliv*0930 gSiO2Epr & ``SM______L1`` & mmol Si /m\ :sup:`3`/s & Tendency of SiO2 due to E/P/runoff 3c930300af Oliv*0931 gALKEpr & ``SM______L1`` & meq/m\ :sup:`3`/s & Tendency of ALK due to E/P/runoff 0932 gO2Epr & ``SM______L1`` & mmol O2 /m\ :sup:`3`/s & Tendency of O2 due to E/P/runoff faa67d1773 Oliv*0933 surfPAR & ``SM_P____L1`` & Ein/m\ :sup:`2`/s & PAR forcing at surface 0934 surfiron & ``SM_P____L1`` & mmol Fe /m\ :sup:`2`/s & iron forcing at surface 0935 DARice & ``SM_P____L1`` & m\ :sup:`2`/m\ :sup:`2` & ice area fraction 0936 DARwind & ``SM_P____L1`` & m/s & wind speed used for carbon exchange 0937 surfpCO2 & ``SM_P____L1`` & mol/mol & atmospheric surface pCO2 4c914c90da Oliv*0938 3ded9f825b Oliv*0939 .. [#b] does not include free iron adjustment for FeT tracer 1d947889e4 Oliv*0940 3c930300af Oliv*0941 Diagnostics related to carbon chemistry are listed in 0942 :numref:`CarbonChemistryDiagnostics`. 167fbde97e Oliv*0943 faa67d1773 Oliv*0944 Also of interest are the following diagnostics from the ptracers and gchem packages: 0945 0946 .. csv-table:: 0947 :delim: & 0948 :widths: auto 0949 :class: longtable 0950 :header: Name, Code, Units, Description 0951 0952 Tp_g## & ``SMR_____MR`` & [TRAC##]/s & ptracer ## total transport tendency (before gchem_forcing_sep) 0953 TRAC## & ``SMR_____MR`` & [TRAC##] & ptracer ## concentration before transport 0954 GC_Tr## & ``SMR_____MR`` & [TRAC##] & ptracer ## concentration before GCHEM 0955 0956 The ptracer number ## here and in gDAR## is the one defined in the ptracers 0957 package, see :numref:`ptracers_diagnostics` for value larger than 99. 0958 1d947889e4 Oliv*0959 0960 Call Tree 0961 ~~~~~~~~~ 0962 3ded9f825b Oliv*0963 .. parsed-literal:: 1d947889e4 Oliv*0964 0965 the_model_main 0966 initialise_fixed 0967 packages_readparms 0968 gchem_readparms 3ded9f825b Oliv*0969 **darwin_readparms** 1d947889e4 Oliv*0970 darwin_exf_readparms 0971 darwin_read_params 0972 darwin_read_traitparams 0973 gchem_tr_register 3ded9f825b Oliv*0974 **darwin_tr_register** 1d947889e4 Oliv*0975 packages_init_fixed 0976 gchem_init_fixed 3ded9f825b Oliv*0977 **darwin_init_fixed** 1d947889e4 Oliv*0978 darwin_exf_init_fixed 0979 darwin_diagnostics_init 0980 darwin_random_init 0981 darwin_generate_random 0982 darwin_random 0983 darwin_random_normal 0984 darwin_generate_allometric 0985 darwin_read_traits 0986 packages_check 0987 gchem_check 3ded9f825b Oliv*0988 **darwin_check** 1d947889e4 Oliv*0989 the_main_loop 0990 initialise_varia 0991 packages_init_variables 0992 gchem_init_vari 3ded9f825b Oliv*0993 **darwin_init_varia** 1d947889e4 Oliv*0994 darwin_exf_init_varia 0995 darwin_read_pickup 0996 darwin_init_chl 0997 darwin_light 0998 darwin_insol 3c930300af Oliv*0999 darwin_light_radtrans 1d947889e4 Oliv*1000 darwin_surfforcing_init 3c930300af Oliv*1001 darwin_coeffs_surf 1002 darwin_coeffs_deep 1d947889e4 Oliv*1003 darwin_carbon_coeffs 3c930300af Oliv*1004 ahini_for_at 1005 calc_pco2_solvesaphe 1006 solve_at_general 1007 anw_infsup 1008 equation_at 1009 solve_at_general_sec 1010 anw_infsup 1011 equation_at 1012 solve_at_fast 1013 equation_at 1d947889e4 Oliv*1014 darwin_calc_pco2_approx 1015 do_the_model_io 1016 gchem_output 3ded9f825b Oliv*1017 **darwin_diags** 1d947889e4 Oliv*1018 main_do_loop 1019 forward_step 1020 load_fields_driver 1021 gchem_fields_load 3ded9f825b Oliv*1022 **darwin_fields_load** 1d947889e4 Oliv*1023 darwin_exf_load 1024 darwin_monitor 3c930300af Oliv*1025 gchem_cons 3ded9f825b Oliv*1026 **darwin_cons** 1d947889e4 Oliv*1027 gchem_forcing_sep 3ded9f825b Oliv*1028 **darwin_conserve_surface** 1029 **darwin_cons** 1030 **darwin_cons_reset** 1031 **darwin_nut_supply** 1032 **darwin_forcing** 1d947889e4 Oliv*1033 darwin_light_radtrans 1034 darwin_light... 1035 darwin_surfforcing 3c930300af Oliv*1036 darwin_coeffs_surf 1037 darwin_coeffs_deep 1d947889e4 Oliv*1038 darwin_carbon_coeffs 3c930300af Oliv*1039 calc_pco2_solvesaphe... 1d947889e4 Oliv*1040 darwin_calc_pco2_approx 3c930300af Oliv*1041 darwin_add_surfforc 1d947889e4 Oliv*1042 darwin_fe_chem 1043 darwin_tempfunc 1044 darwin_plankton 1045 darwin_sinking 3ded9f825b Oliv*1046 **darwin_atmos** 1d947889e4 Oliv*1047 do_the_model_io... 1048 do_write_pickup 1049 packages_write_pickup 1050 gchem_write_pickup 3ded9f825b Oliv*1051 **darwin_write_pickup**
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