.. include:: ../defs.hrst .. _sub_phys_pkg_darwin: DARWIN package -------------- The :filelink:`darwin package ` models the dynamics of a flexible number of phyto- and zooplankton and bacteria types, and the nutrient cycles of carbon, nitrogen, phosphorus, iron and silica. The description of the ecosystem model is split over a number of pages: .. toctree:: :maxdepth: 1 darwin_equations darwin_growth darwin_cstore darwin_light darwin_spectral darwin_uptake darwin_chl darwin_remin darwin_denit darwin_cdom darwin_airsea darwin_carbon darwin_iron darwin_resp darwin_mort darwin_exude darwin_grazing darwin_bacteria darwin_temperature darwin_sink darwin_cons darwin_changes Plankton and nutrients are represented by their concentration in the ocean, using the :ref:`sub_phys_pkg_ptracers`. The darwin package uses the following tracers (or a subset, depending on the configuration): .. table:: :widths: auto +---------------+--------------------------------+---------------------------------------------------------+ | Name | Units | Description | +===============+================================+=========================================================+ | DIC | mmol C m\ :sup:`--3` | concentration of dissolved inorganic carbon | +---------------+--------------------------------+---------------------------------------------------------+ | NO3 | mmol N m\ :sup:`--3` | concentration of nitrate | +---------------+--------------------------------+---------------------------------------------------------+ | NO2 | mmol N m\ :sup:`--3` | concentration of nitrite | +---------------+--------------------------------+---------------------------------------------------------+ | NH4 | mmol N m\ :sup:`--3` | concentration of ammonia | +---------------+--------------------------------+---------------------------------------------------------+ | PO4 | mmol P m\ :sup:`--3` | concentration of phosphate | +---------------+--------------------------------+---------------------------------------------------------+ | FeT | mmol Fe m\ :sup:`--3` | concentration of total dissolved iron | +---------------+--------------------------------+---------------------------------------------------------+ | SiO2 | mmol Si m\ :sup:`--3` | concentration of inorganic silica | +---------------+--------------------------------+---------------------------------------------------------+ | DOC | mmol C m\ :sup:`--3` | concentration of dissolved organic carbon | +---------------+--------------------------------+---------------------------------------------------------+ | DON | mmol N m\ :sup:`--3` | concentration of dissolved organic nitrogen | +---------------+--------------------------------+---------------------------------------------------------+ | DOP | mmol P m\ :sup:`--3` | concentration of dissolved organic phosphorus | +---------------+--------------------------------+---------------------------------------------------------+ | DOFe | mmol Fe m\ :sup:`--3` | concentration of dissolved organic iron | +---------------+--------------------------------+---------------------------------------------------------+ | POC | mmol C m\ :sup:`--3` | concentration of particulate organic carbon | +---------------+--------------------------------+---------------------------------------------------------+ | PON | mmol N m\ :sup:`--3` | concentration of particulate organic nitrogen | +---------------+--------------------------------+---------------------------------------------------------+ | POP | mmol P m\ :sup:`--3` | concentration of particulate organic phosphorus | +---------------+--------------------------------+---------------------------------------------------------+ | POFe | mmol Fe m\ :sup:`--3` | concentration of particulate organic iron | +---------------+--------------------------------+---------------------------------------------------------+ | POSi | mmol Si m\ :sup:`--3` | concentration of particulate organic silica | +---------------+--------------------------------+---------------------------------------------------------+ | PIC | mmol C m\ :sup:`--3` | concentration of particulate inorganic carbon | +---------------+--------------------------------+---------------------------------------------------------+ | ALK | meq m\ :sup:`--3` | alkalinity | +---------------+--------------------------------+---------------------------------------------------------+ | O2 | mmol O\ :sub:`2` m\ :sup:`--3` | concentration of oxygen | +---------------+--------------------------------+---------------------------------------------------------+ | CDOM | mmol C m\ :sup:`--3` | concentration of colored dissolved organic matter [#a]_ | | | | | | | (mmol P m\ :sup:`--3`) | | +---------------+--------------------------------+---------------------------------------------------------+ | c\ :sub:`j` | mmol C m\ :sup:`--3` | concentration of carbon in plankton type j | +---------------+--------------------------------+---------------------------------------------------------+ | n\ :sub:`j` | mmol N m\ :sup:`--3` | concentration of nitrogen in plankton type j | +---------------+--------------------------------+---------------------------------------------------------+ | p\ :sub:`j` | mmol P m\ :sup:`--3` | concentration of phosphorus in plankton type j | +---------------+--------------------------------+---------------------------------------------------------+ | fe\ :sub:`j` | mmol Fe m\ :sup:`--3` | concentration of iron in plankton type j | +---------------+--------------------------------+---------------------------------------------------------+ | si\ :sub:`j` | mmol Si m\ :sup:`--3` | concentration of silica in plankton type j | +---------------+--------------------------------+---------------------------------------------------------+ | Chl\ :sub:`j` | mg Chl a m\ :sup:`--3` | concentration of Chlorophyll-a in plankton type j | +---------------+--------------------------------+---------------------------------------------------------+ .. [#a] units of CDOM are mmol C m\ :sup:`--3` if #define DARWIN_CDOM_UNITS_CARBON (default), mmol P m\ :sup:`--3` otherwise Phyto- and zooplankton are not distinguished except that certain source terms will not be active, dependening on whether a plankton type can engage in photosynthesis, grazing, etc. This makes it very simple to include, for instance, mixotrophy in the model. Compiling and Running ~~~~~~~~~~~~~~~~~~~~~ Compiling ^^^^^^^^^ Include the word ``darwin`` in ``packages.conf`` in your code directory. This will automatically turn on gchem, ptracers and exf. Set compile-time options for darwin in file :filelink:`~pkg/darwin/DARWIN_OPTIONS.h` (see table below). Adjust the number of plankton types, functional groups, autotrophs, grazers, prey and optical types in :filelink:`~pkg/darwin/DARWIN_SIZE.h`. You will also have to adjust the number of passive tracers in :filelink:`~pkg/ptracers/PTRACERS_SIZE.h`. You can run :filelink:`tools/darwin/mkdarwintracers` in your code directory (after adjusting :filelink:`~pkg/darwin/DARWIN_OPTIONS.h` and :filelink:`~pkg/darwin/DARWIN_SIZE.h`) to find out how many ptracers you will need and what they are. In :filelink:`~pkg/gchem/GCHEM_OPTIONS.h` you need to define :varlink:`GCHEM_SEPARATE_FORCING`. In :filelink:`~pkg/exf/EXF_OPTIONS.h` you may want to undef :varlink:`ALLOW_CLIMSST_RELAXATION` and :varlink:`ALLOW_CLIMSSS_RELAXATION`. To use spectral light, compile the radtrans package, see :numref:`sub_phys_pkg_radtrans`. .. tabularcolumns:: |l|l| .. csv-table:: Darwin package CPP options :delim: & :widths: auto :class: longtable :header: CPP option, description :varlink:`DARWIN_ALLOW_NQUOTA` & enable nitrogen quotas for all plankton :varlink:`DARWIN_ALLOW_PQUOTA` & enable phosphorus quotas for all plankton :varlink:`DARWIN_ALLOW_FEQUOTA` & enable iron quotas for all plankton :varlink:`DARWIN_ALLOW_SIQUOTA` & enable silica quotas for all plankton :varlink:`DARWIN_ALLOW_CHLQUOTA` & enable chlorophyll quotas for all *phototrophs* :varlink:`DARWIN_ALLOW_CDOM` & enable a dynamic CDOM tracer :varlink:`DARWIN_CDOM_UNITS_CARBON` & measure CDOM in units of mmol C/m\ :sup:`3` and follow organic carbon instead of phosphorus :varlink:`DARWIN_ALLOW_CSTORE` & enable internal carbon store and exudation for all phototrophs :varlink:`DARWIN_ALLOW_CSTORE_DIAGS` & enable diagnostics for internal carbon store :varlink:`DARWIN_ALLOW_CARBON` & enable air-sea carbon exchange and ALK and O\ :math:`_2` tracers :varlink:`DARWIN_SOLVESAPHE` & compile Munhoven "Solvesaphe" pH/pOC2 solver package :varlink:`DARWIN_TOTALPHSCALE` & consistently use the total pH scale for carbon chemistry coefficients :varlink:`DARWIN_USE_PLOAD` & take atmospheric pressure from coupled atmospheric model :varlink:`DARWIN_ALLOW_RADI` & enable RADI sediment model :varlink:`DARWIN_ALLOW_DENIT` & enable denitrification code :varlink:`DARWIN_ALLOW_EXUDE` & enable exudation of individual quotas :varlink:`ALLOW_OLD_VIRTUALFLUX` & enable old virtualflux code for DIC and ALK :varlink:`DARWIN_NITRATE_FELIMIT` & reduce nitrate uptake by iron limitation factor :varlink:`DARWIN_BOTTOM_SINK` & allow organic matter to sink into bottom (sedimentize) :varlink:`DARWIN_NUTRIENT_RUNOFF` & include code for reading nutrient runoff from files :varlink:`DARWIN_AVPAR` & compute average PAR in layer, assuming exponential decay (%) :varlink:`DARWIN_ALLOW_GEIDER` & enable GEIDER light code (required for radtrans) :varlink:`DARWIN_GEIDER_RHO_SYNTH` & use ρ instead of acclimated Chl:C for chlorophyll synthesis :varlink:`DARWIN_CHL_INIT_LEGACY` & initialize chlorophyll as in darwin2 :varlink:`DARWIN_SCATTER_CHL` & scattering coefficients are per Chlorophyll :varlink:`DARWIN_DIAG_IOP` & make diagnostics for instrinsic optical properties available :varlink:`DARWIN_GRAZING_SWITCH` & enable quadratic grazing as in darwin2+quota :varlink:`DARWIN_ALLOMETRIC_PALAT` & compute palatability from size ratios :varlink:`DARWIN_NOZOOTEMP` & turn off grazing temperature dependence :varlink:`DARWIN_NOTEMP` & turn off all temperature dependence :varlink:`DARWIN_TEMP_VERSION` & select temperature version: 1, 2 or 3 :varlink:`DARWIN_TEMP_RANGE` & restrict phytoplankton growth to a temperature range :varlink:`DARWIN_MINFE` & restrict maximum free iron (sic) :varlink:`DARWIN_PART_SCAV` & enable particle scavenging code :varlink:`DARWIN_IRON_SED_SOURCE_VARIABLE` & enable variable iron sediment source :varlink:`DARWIN_ALLOW_HYDROTHERMAL_VENTS` & include code for iron input from hydrothermal vents :varlink:`DARWIN_DIAG_PERTYPE` & enable per-type diagnostics PP####, GR####, GrGn#### :varlink:`DARWIN_DIAG_TENDENCIES` & enable diagnostics for many tendency terms :varlink:`DARWIN_DEBUG` & turn on debugging output :varlink:`DARWIN_ALLOW_CONS` & compute and print global element totals :varlink:`DARWIN_UNUSED` & value for unused traits The following options are used for random trait generation (as in darwin2): .. tabularcolumns:: |l|L| .. csv-table:: :delim: & :widths: auto :header: CPP option, description :varlink:`DARWIN_RANDOM_TRAITS` & assign traits based on random numbers as in darwin2 :varlink:`DARWIN_TWO_SPECIES_SETUP` & set traits for darwin2 2-species setup (requires :varlink:`DARWIN_RANDOM_TRAITS`) :varlink:`DARWIN_NINE_SPECIES_SETUP` & set traits for darwin2 9-species setup (requires :varlink:`DARWIN_RANDOM_TRAITS`) :varlink:`DARWIN_ALLOW_DIAZ` & enable diazotrophy when using :varlink:`DARWIN_RANDOM_TRAITS` Random trait generation is supported mainly for backwards compatibility. Running ^^^^^^^ You will need to set ``useDARWIN=.TRUE.`` in ``data.gchem`` (and turn on gchem, ptracers, exf, etc. in ``data.pkg``). Runtime Parameters '''''''''''''''''' Runtime parameters are set in ``data.darwin`` in these namelists: .. csv-table:: :delim: & :widths: auto :header: Namelist, Description :varlink:`DARWIN_FORCING_PARAMS` & parameters related to forcing and initialization :varlink:`DARWIN_INTERP_PARAMS` & parameters for interpolation of forcing fields (only used if :varlink:`USE_EXF_INTERPOLATION` is defined) :varlink:`DARWIN_PARAMS` & general parameters (not per-plankton traits) :varlink:`DARWIN_CDOM_PARAMS` & parameters for dynamic CDOM :varlink:`DARWIN_RADTRANS_PARAMS` & parameters for radiative transer :varlink:`DARWIN_RANDOM_PARAMS` & parameters for randomly generated traits (deprecated) :varlink:`DARWIN_TRAIT_PARAMS` & parameters for trait generation (allometric and functional groups) Set initial values/files for the tracers in ``data.ptracers``. You can generate a template by running :filelink:`tools/darwin/mkdarwintracers` in your code directory (get help with the ‘-h’ option). You may generate a minimal file ``data.diagnostics`` with all the darwin tracers by running :filelink:`tools/darwin/mkdiagnosticsdata` in your input/run directory. Forcing fields are read in using the exf package. File names and forcing parameters are given in namelist :varlink:`DARWIN_FORCING_PARAMS` in ``data.darwin``. For light, ice area and wind speed, the following alternative sources can be given: .. csv-table:: Namelist DARWIN_FORCING_PARAMS :delim: & :widths: auto :header: Name, Default, Description :varlink:`darwin_useQsw` & .FALSE. & whether to use model shortwave radiation for light :varlink:`darwin_useSEAICE` & .FALSE. & whether to use ice area from the seaice package :varlink:`darwin_useEXFwind` & .FALSE. & whether to use wind speed from the exf package The forcing fields are: .. tabularcolumns:: |\Y{.09}|\Y{.09}|\Y{.17}|\Y{.65}| .. csv-table:: Darwin forcing fields :delim: & :widths: auto :class: longtable :header: Name, Default, Units, Description iron & 0.0 & mmol Fe m\ :sup:`--2` s\ :sup:`--1` & iron input through sea surface, will be multiplied by solubility :varlink:`alpfe` PAR & 0.0 & μEin m\ :sup:`--2` s\ :sup:`--1` & Photosynthetically active radiation below sea surface; not used with the radtrans package 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`` wind & 5.0 & m/s & wind speed; used for carbon and oxygen surface forcing pCO2 & 278E-6 & atm & partial pressure of atmospheric CO\ :sub:`2`; used for carbon and oxygen surface forcing ventHe3 & 0.0 & mmol |nbsp| :sup:`3`\ He m\ :sup:`--2` s\ :sup:`--1` & Helium-3 flux from hydrothermal vents; used for iron input DOCrunoff & 0.0 & mmol C m\ :sup:`--2` s\ :sup:`--1` & surface flux of DOC from runoff DONrunoff & 0.0 & mmol N m\ :sup:`--2` s\ :sup:`--1` & surface flux of DON from runoff DOPrunoff & 0.0 & mmol P m\ :sup:`--2` s\ :sup:`--1` & surface flux of DOP from runoff DINrunoff & 0.0 & mmol N m\ :sup:`--2` s\ :sup:`--1` & surface flux of DIN from runoff IPrunoff & 0.0 & mmol P m\ :sup:`--2` s\ :sup:`--1` & surface flux of IP from runoff DSirunoff & 0.0 & mmol Si m\ :sup:`--2` s\ :sup:`--1` & surface flux of DSi from runoff POCrunoff & 0.0 & mmol C m\ :sup:`--2` s\ :sup:`--1` & surface flux of POC from runoff PONrunoff & 0.0 & mmol N m\ :sup:`--2` s\ :sup:`--1` & surface flux of PON from runoff POPrunoff & 0.0 & mmol P m\ :sup:`--2` s\ :sup:`--1` & surface flux of POP from runoff DICrunoff & 0.0 & mmol C m\ :sup:`--2` s\ :sup:`--1` & surface flux of DIC from runoff Each forcing field has a set of parameters in :varlink:`DARWIN_FORCING_PARAMS`. These work as in the exf package, see :numref:`tab_phys_pkg_exf_runtime_attributes`. For instance, for PAR they are: .. csv-table:: Namelist DARWIN_FORCING_PARAMS, cont’d :delim: & :widths: auto :header: Name, Default, Description :varlink:`PARfile` & ' ' & filename; if left empty no file will be read; PARconst will be used instead :varlink:`PARconst` & 0.0 & constant that will be used if no file is read :varlink:`PARperiod` & 0.0 & interval in seconds between two records :varlink:`PARRepCycle` & :varlink:`repeatPeriod` & repeat cycle in seconds; only available if :varlink:`useExfYearlyFields` is .FALSE. :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 :varlink:`PARstartdate1` & 0 & date/time of first record when using the cal package; format: YYYYMMDD; start year (YYYY), month (MM), day (YY) :varlink:`PARstartdate2` & 0 & format: HHMMSS; start hour (HH), minute (MM), second(SS) :varlink:`PAR_exfremo_intercept` & 0.0 & can be used to remove global mean :varlink:`PAR_exfremo_slope` & 0.0 & can be used to remove global trend :varlink:`PARmask` & 'c' & grid point for masking: ' ' = no masking; 'c' = centered mask; 'w' = western mask; 's' = southern :varlink:`darwin_inscal_PAR` & 1.0 & optional rescaling of input fields to adjust units The parameters darwin_inscal\_«Name» can be used to convert units. Some examples are given in :numref:`tab_phys_pkgs_darwin_inscal`. .. csv-table:: Example unit conversions :delim: & :widths: auto :class: longtable :header: Field, File units, Scaling factor :name: tab_phys_pkgs_darwin_inscal iron & mol Fe m\ :sup:`--2` s\ :sup:`--1` & darwin_inscal_iron = 1000 & kg Fe m\ :sup:`--2` & darwin_inscal_iron = 17906.7 PAR & Ein m\ :sup:`--2` day\ :sup:`--1` & darwin_inscal_PAR = 11.574074074074 Nutrient runoff has some extra parameters: .. tabularcolumns:: |\Y{.25}|\Y{.12}|\Y{.14}|\Y{.49}| .. csv-table:: Namelist DARWIN_FORCING_PARAMS, cont’d :delim: & :widths: 25,12,14,49 :header: Name, Default, Units, Description :varlink:`R_ALK_DIC_runoff` & 1.0218 & meq / mmol C & ALK:DIC ratio in runoff :varlink:`R_NO3_DIN_runoff` & 0.6531 & mmol N / mmol N & NO3 fraction of DIN in runoff :varlink:`R_NO2_DIN_runoff` & 0.0158 & mmol N / mmol N & NO2 fraction of DIN in runoff :varlink:`R_NH4_DIN_runoff` & 0.3311 & mmol N / mmol N & NH4 fraction of DIN in runoff :varlink:`R_DIP_IP_runoff` & 0.333 & mmol P / mmol P & ratio of dissolved to total inorganic P in runoff :varlink:`R_DFe_DIP_runoff` & 0.0003 & mmol Fe / mmol P & Fe:P ratio for inorganic P in runoff :varlink:`R_DOFe_DOP_runoff` & 0.0003 & mmol Fe / mmol P & Fe:P ratio for dissolved organic matter in runoff :varlink:`R_POFe_POP_runoff` & 0.0003 & mmol Fe / mmol P & Fe:P ratio for particulate organic matter in runoff These govern how the various tracers receive contributions from the runoff files: .. csv-table:: Runoff forcing-tracer associations :delim: & :widths: auto :header: Tracer, Surface Forcing Field DOC & DOCrunoff DON & DONrunoff DOP & DOPrunoff NO3 & DINrunoff \* R_NO3_DIN_runoff NO2 & DINrunoff \* R_NO2_DIN_runoff NH4 & DINrunoff \* R_NH4_DIN_runoff PO4 & IPrunoff \* R_DIP_IP_runoff SiO2 & DSirunoff POC & POCrunoff PON & PONrunoff POP & POPrunoff DIC & DICrunoff ALK & DICrunoff \* R_ALK_DIC_runoff FeT & IPrunoff \* R_DIP_IP_runoff \* R_DFe_DIP_runoff DOFe & DOPrunoff \* R_DOFe_DOP_runoff POFe & POPrunoff \* R_POFe_POP_runoff Interpolation parameters for all forcing fields are set in namelist :varlink:`DARWIN_INTERP_PARAMS`. See the exf package for how to set them. General parameters are set in namelist :varlink:`DARWIN_PARAMS`: .. tabularcolumns:: |\Y{.235}|\Y{.135}|\Y{.14}|\Y{.49}| .. csv-table:: Namelist DARWIN_PARAMS :delim: & :widths: auto :class: longtable :header: Name, Default, Units, Description :varlink:`darwin_seed` & 0 & & seed for random number generator (for :varlink:`DARWIN_RANDOM_TRAITS`) :varlink:`darwin_strict_check` & .FALSE. & & stop instead of issuing warnings :varlink:`iDEBUG` & 1 & & index in x dimension for debug prints :varlink:`jDEBUG` & 1 & & index in y dimension for debug prints :varlink:`kDEBUG` & 1 & & index in z dimension for debug prints :varlink:`darwin_pickupSuff` & :varlink:`pickupSuff` & & pickup suffix for darwin; set to ' ' to disable reading at :varlink:`PTRACERS_Iter0` :varlink:`darwin_linFSConserve` & .FALSE. & & correct non-conservation due to linear free surface (globally) :varlink:`darwin_read_phos` & .FALSE. & & initial conditions for plankton biomass are in mmol P/m3 :varlink:`darwin_chlInitBalanced` & .FALSE. & & Initialize Chlorophyll to a balanced value following Geider :varlink:`darwin_chlIter0` & 0 & & Iteration number when to initialize Chlorophyll :varlink:`katten_w` & 4D-2 & 1/m & atten coefficient water :varlink:`katten_chl` & 4D-2 & m\ :sup:`2`/mg Chl & atten coefficient chl :varlink:`parfrac` & 0.4 & & fraction Qsw that is PAR :varlink:`parconv` & 1/0.2174 & μEin/s/W & conversion from W/m2 to μEin/m2/s :varlink:`tempnorm` & 0.3 & & set temperature function (was 1.0) :varlink:`TempAeArr` & -4000.0 & K & slope for pseudo-Arrhenius (TEMP_VERSION 2) :varlink:`TemprefArr` & 293.15 & K & reference temp for pseudo-Arrhenius (TEMP_VERSION 2) :varlink:`TempCoeffArr` & 0.5882 & & pre-factor for pseudo-Arrhenius (TEMP_VERSION 2) :varlink:`reminTempAe` & 0.0438 & 1/K & temperature coefficient for remineralization (TEMP_VERSION 4) :varlink:`mortTempAe` & 0.0438 & 1/K & temperature coefficient for linear mortality (TEMP_VERSION 4) :varlink:`mort2TempAe` & 0.0438 & 1/K & temperature coefficient for quadr. mortality (TEMP_VERSION 4) :varlink:`uptakeTempAe` & 0.0 & 1/K & temperature coefficient for uptake (TEMP_VERSION 4) :varlink:`alpfe` & 0.04 & & solubility of Fe dust :varlink:`scav` & 0.4/year & 1/s & fixed iron scavenging rate :varlink:`scav_tau` & 0.2 & & factor for converting Th scavenging rates to iron ones :varlink:`scav_inter` & 0.079 / day & L\ :sup:`e` mg\ :sup:`-e` s\ :sup:`-1` & intercept of scavenging power law (e=e\ :sub:`scav`) :varlink:`scav_exp` & 0.58 & & exponent of scavenging power law :varlink:`scav_POC_wgt` & 0.02173 & g/mmol |nbsp| C & weight POC contributes to POM :varlink:`scav_POSi_wgt` & 0.069 & g/mmol |nbsp| Si & weight POSi contributes to POM :varlink:`scav_PIC_wgt` & 0.100 & g/mmol |nbsp| C & weight PIC contributes to POM :varlink:`ligand_tot` & 1D-3 & mol/m\ :sup:`3` & total ligand concentration :varlink:`ligand_stab` & 2D5 & m\ :sup:`3`/mol & ligand stability rate ratio :varlink:`freefemax` & 0.4D-3 & mol/m\ :sup:`3` & max concentration of free iron :varlink:`depthfesed` & -1.0 & m & depth above which to add sediment source (was -1000) :varlink:`fesedflux` & 1D-3 / day & mmol Fe /m\ :sup:`2`/s & fixed iron flux from sediment :varlink:`fesedflux_pcm` & 0.68D-3 & mmol Fe / mmol C & iron input per POC sinking into bottom for :varlink:`DARWIN_IRON_SED_SOURCE_VARIABLE` :varlink:`fesedflux_min` & 0.5D-3 / day & mmol Fe /s & min iron input rate subtracted from fesedflux_pcm*wc_sink*POC :varlink:`R_CP_fesed` & 106 & mmol C / mmol P & POC:POP conversion for :varlink:`DARWIN_IRON_SED_SOURCE_POP` :varlink:`depthFeVent` & 750 & m & depth below which iron from hydrothermal vents is added :varlink:`solFeVent` & 0.002 & & solubility of iron from hydrothermal vents :varlink:`R_FeHe3_vent` & 4.5E8 & mol Fe / mol :sup:`3`\ He & Fe:\ :sup:`3`\ He ratio for hydrothermal vents :varlink:`Knita` & 1/(0.5 days) & 1/s & ammonia oxidation rate :varlink:`Knitb` & 1/(10 days) & 1/s & nitrite oxidation rate :varlink:`PAR_oxi` & 10 & μEin/m\ :sup:`2`/s & critical light level after which oxidation starts :varlink:`Kdoc` & 1/(100 days) & 1/s & DOC remineralization rate :varlink:`Kdop` & 1/(100 days) & 1/s & DON remineralization rate :varlink:`Kdon` & 1/(100 days) & 1/s & DOP remineralization rate :varlink:`KdoFe` & 1/(100 days) & 1/s & DOFe remineralization rate :varlink:`KPOC` & 1/(50 days) & 1/s & POC remineralization rate :varlink:`KPOP` & :varlink:`KPOC` & 1/s & POP remineralization rate :varlink:`KPON` & :varlink:`KPOC` & 1/s & PON remineralization rate :varlink:`KPOFe` & :varlink:`KPOC` & 1/s & POFe remineralization rate :varlink:`KPOSi` & 1/(300 days) & 1/s & POSi remineralization rate :varlink:`wC_sink` & 10/day & m/s & sinking velocity for POC :varlink:`wP_sink` & :varlink:`wC_sink` & m/s & sinking velocity for POP :varlink:`wN_sink` & :varlink:`wC_sink` & m/s & sinking velocity for PON :varlink:`wFe_sink` & :varlink:`wC_sink` & m/s & sinking velocity for POFe :varlink:`wSi_sink` & :varlink:`wC_sink` & m/s & sinking velocity for POSi :varlink:`wPIC_sink` & 15/day & m/s & sinking velocity for PIC :varlink:`Kdissc` & 1/(300 days) & 1/s & dissolution rate for PIC :varlink:`R_OP` & 170 & mmol O\ :sub:`2` / mmol P & O:P ratio for respiration and consumption :varlink:`R_OC` & 170/120.0 & mmol O\ :sub:`2` / mmol C & NOT USED :varlink:`m3perkg` & 1 / 1024.5 & m\ :sup:`3`/kg & constant for converting per kg to per m^3 :varlink:`surfSaltMinInit` & 4.0 & ppt & limits for carbon solver input at initialization :varlink:`surfSaltMaxInit` & 50.0 & ppt & ... :varlink:`surfTempMinInit` & -4.0 & °C & :varlink:`surfTempMaxInit` & 39.0 & °C & :varlink:`surfDICMinInit` & 10.0 & mmol C m\ :sup:`-3` & :varlink:`surfDICMaxInit` & 4000.0 & mmol C m\ :sup:`-3` & :varlink:`surfALKMinInit` & 10.0 & meq m\ :sup:`-3` & :varlink:`surfALKMaxInit` & 4000.0 & meq m\ :sup:`-3` & :varlink:`surfPO4MinInit` & 1D-10 & mmol P m\ :sup:`-3` & :varlink:`surfPO4MaxInit` & 10.0 & mmol P m\ :sup:`-3` & :varlink:`surfSiMinInit` & 1D-8 & mmol Si m\ :sup:`-3` & :varlink:`surfSiMaxInit` & 500.0 & mmol Si m\ :sup:`-3` & :varlink:`surfSaltMin` & 4.0 & ppt & limits for carbon solver input during run :varlink:`surfSaltMax` & 50.0 & ppt & ... :varlink:`surfTempMin` & -4.0 & °C & :varlink:`surfTempMax` & 39.0 & °C & :varlink:`surfDICMin` & 400.0 & mmol C m\ :sup:`-3` & :varlink:`surfDICMax` & 4000.0 & mmol C m\ :sup:`-3` & :varlink:`surfALKMin` & 400.0 & meq m\ :sup:`-3` & :varlink:`surfALKMax` & 4000.0 & meq m\ :sup:`-3` & :varlink:`surfPO4Min` & 1D-10 & mmol P m\ :sup:`-3` & :varlink:`surfPO4Max` & 10.0 & mmol P m\ :sup:`-3` & :varlink:`surfSiMin` & 1D-8 & mmol Si m\ :sup:`-3` & :varlink:`surfSiMax` & 500.0 & mmol Si m\ :sup:`-3` & :varlink:`diaz_ini_fac` & 1 & & reduce tracer concentrations by this factor on initialization :varlink:`O2crit` & 6.0 & mmol O\ :sub:`2` m\ :sup:`-3` & critical oxygen for O2/NO3 remineralization :varlink:`denit_NP` & 120.0 & mmol N / mmol P & ratio of n to p in denitrification process :varlink:`denit_NO3` & 104.0 & mmol N / mmol P & ratio of NO3 uptake to phos remineralization in denitrification :varlink:`NO3crit` & 1D-2 & mmol N m\ :sup:`-3` & critical nitrate below which no denit (or remin) happens :varlink:`PARmin` & 0.1 & μEin/m\ :sup:`2`/s & minimum light for photosynthesis; for non-Geider: 1.0 :varlink:`aphy_chl_ave` & 0.02 & m\ :sup:`2`/mg Chl & Chl-specific absorption coefficient :varlink:`chl2nmax` & 3.00 & mg Chl / mmol N & max Chl:N ratio for Chl synthesis following Moore 2002 :varlink:`synthcost` & 0.0 & mmol C / mmol N & cost of biosynthesis :varlink:`inhib_graz` & 1.0 & (mmol C m\ :sup:`-3`)\ :sup:`-1` & inverse decay scale for grazing inhibition :varlink:`inhib_graz_exp` & 0.0 & & exponent for grazing inhibition (0 to turn off inhibition) :varlink:`hillnumUptake` & 1.0 & & exponent for limiting quota uptake in nutrient uptake :varlink:`hillnumGraz` & 1.0 & & exponent for limiting quota uptake in grazing :varlink:`hollexp` & 1.0 & & grazing exponential 1= "Holling 2", 2= "Holling 3" :varlink:`phygrazmin` & 120D-10 & mmol C m\ :sup:`-3` & minimum total prey conc for grazing to occur :varlink:`pmaxDIN` & 20/day & 1/s & max DIN uptake rate for denitrifying bacteria :varlink:`pcoefO2` & 290.82/day & m\ :sup:`3`/mmol O\ :sub:`2`/s & max O2-specific O2 uptake rate for aerobic bacteria :varlink:`ksatDIN` & 0.01 & mmol N m\ :sup:`-3` & half-saturation conc of dissolved inorganic nitrogen :varlink:`alpha_hydrol` & 2.0 & & increase in POM needed due to hydrolysis :varlink:`yod` & 0.2 & & organic matter yield of aerobic bacteria :varlink:`yoe` & yod/467*4/(1-yod)*106 & & energy yield of aerobic bacteria :varlink:`ynd` & 0.16 & & organic matter yield of denitrifying bacteria :varlink:`yne` & ynd/467*5/(1-ynd)*106 & & energy yield of denitrifying bacteria .. csv-table:: Namelist DARWIN_CDOM_PARAMS :delim: & :widths: auto :header: Name, Default, Units, Description :varlink:`fracCDOM` & 2 / 100 & & fraction of remineralized POP contributing to CDOM :varlink:`CDOMdegrd` & 1 / (200 days) & 1/s & CDOM degradation rate :varlink:`CDOMbleach` & 1 / (15 days) & 1/s & CDOM bleaching rate :varlink:`PARCDOM` & 20 & μEin/m\ :sup:`2`/s & PAR where CDOM bleaching becomes maximal :varlink:`R_NP_CDOM` & 16 & mmol N / mmol P & CDOM N:P ratio (with #undef DARWIN_CDOM_UNITS_CARBON) :varlink:`R_FeP_CDOM` & 1D-3 & mmol Fe / mmol P & CDOM Fe:P ratio (with #undef DARWIN_CDOM_UNITS_CARBON) :varlink:`R_CP_CDOM` & 120 & mmol C / mmol P & CDOM C:P ratio (with #undef DARWIN_CDOM_UNITS_CARBON) :varlink:`R_NC_CDOM` & 16/120 & mmol N / mmol C & CDOM N:C ratio (with #define DARWIN_CDOM_UNITS_CARBON) :varlink:`R_PC_CDOM` & 1/120 & mmol P / mmol C & CDOM P:C ratio (with #define DARWIN_CDOM_UNITS_CARBON) :varlink:`R_FeC_CDOM` & 1D-3/120 & mmol Fe / mmol C & CDOM Fe:C ratio (with #define DARWIN_CDOM_UNITS_CARBON) :varlink:`CDOMcoeff` & 100.0 & m\ :sup:`2` / mmol P & P-specific absorption coefficient of CDOM at :math:`\lambda_{\op{CDOM}}` & 100/120 & m\ :sup:`2` / mmol C & - if #define DARWIN_CDOM_UNITS_CARBON .. tabularcolumns:: |\Y{.255}|\Y{.115}|\Y{.13}|\Y{.5}| .. csv-table:: Namelist DARWIN_RADTRANS_PARAMS :delim: & :widths: auto :header: Name, Default, Units, Description :varlink:`darwin_waterAbsorbFile` & ' ' & & filename for reading water absorption and scattering spectra :varlink:`darwin_phytoAbsorbFile` & ' ' & & filename for reading plankton absorption and scattering spectra :varlink:`darwin_particleAbsorbFile` & ' ' & & filename for reading particle absorption and scattering spectra :varlink:`darwin_part_size_P` & 1D-15 & mmol P/particle & conversion factor for particle absorption and scattering spectra :varlink:`darwin_bbmin` & 0.0002 & 1/m & minimum backscattering ratio :varlink:`darwin_bbw` & 0.5 & & backscattering ratio of water :varlink:`darwin_lambda_aCDOM` & 450.0 & nm & reference wavelength for CDOM absorption spectra :varlink:`darwin_Sdom` & 0.014 & 1/nm & coefficient for CDOM absorption spectra :varlink:`darwin_aCDOM_fac` & 0.2 & & factor for computing aCDOM from water+Chlorophyll absorption :varlink:`darwin_rCDOM` & 0.0 & mmol P/m\ :sup:`3` & recalcitrant CDOM concentration & 0.0 & mmol C/m\ :sup:`3` & - if #define DARWIN_CDOM_UNITS_CARBON :varlink:`darwin_RPOC` & 0.0 & mmol C/m\ :sup:`3` & recalcitrant POC concentration :varlink:`darwin_allomSpectra` & .FALSE. & & enable/disable allometric scaling of plankton absorption and scattering spectra :varlink:`darwin_aCarCell` & 0.109D-9 & mg C/cell & coefficient coefficient for scaling plankton spectra :varlink:`darwin_bCarCell` & 0.991 & & coefficient coefficient for scaling plankton spectra :varlink:`darwin_absorpSlope` & -0.075 & & slope for scaled absorption spectra :varlink:`darwin_bbbSlope` & -1.458 & & slope for scaled backscattering ratio spectra :varlink:`darwin_scatSwitchSizeLog` & 0 & log(μm) & log of size for switching slopes :varlink:`darwin_scatSlopeSmall` & 1.5 & & slope for small plankton :varlink:`darwin_scatSlopeLarge` & 1.5 & & slope for large plankton Traits '''''' Traits are generated from the parameters in ``&DARWIN_TRAIT_PARAMS`` (see next section) but can be overridden in ``data.traits``: .. tabularcolumns:: |\Y{.2}|\Y{.12}|\Y{.2}|\Y{.48}| .. csv-table:: Namelist DARWIN_TRAITS :delim: & :widths: auto :class: longtable :header: Trait, Symbol, Units, Description :varlink:`isPhoto` & isPhoto\ :math:`_j` & & 1: does photosynthesis, 0: not :varlink:`bactType` & bactType\ :math:`_j` & & 1: particle associated, 2: free living bacteria, 0: not bacteria :varlink:`isAerobic` & isAerobic\ :math:`_j` & & 1: is aerobic bacteria (also set bactType), 0: not :varlink:`isDenit` & isDenit\ :math:`_j` & & 1: is dentrifying bacteria (also set (bactType), 0: not :varlink:`hasSi` & hasSi\ :math:`_j` & & 1: uses silica (Diatom), 0: not :varlink:`hasPIC` & hasPIC\ :math:`_j` & & 1: calcifying, 0: set R_PICPOC to zero :varlink:`diazo` & diazo\ :math:`_j` & & 1: use molecular instead of mineral nitrogen, 0: not :varlink:`useNH4` & useNH4\ :math:`_j` & & 1: can use ammonia, 0: not :varlink:`useNO2` & useNO2\ :math:`_j` & & 1: can use nitrite, 0: not :varlink:`useNO3` & useNO3\ :math:`_j` & & 1: can use nitrate, 0: not :varlink:`combNO` & combNO\ :math:`_j` & & 1: combined nitrite/nitrate limitation, 0: not :varlink:`isPrey` & isPrey\ :math:`_j` & & 1: can be grazed, 0: not :varlink:`isPred` & isPred\ :math:`_j` & & 1: can graze, 0: not :varlink:`tempMort` & :math:`e^{\op{mort}}_j` & & 1: mortality is temperature dependent, 0: turn dependence off :varlink:`tempMort2` & :math:`e^{\op{mort2}}_j` & & 1: quadratic mortality is temperature dependent, 0: turn dependence off :varlink:`tempGraz` & :math:`e^{\op{graz}}_j` & & 1: grazing is temperature dependent, 0: turn dependence off :varlink:`Xmin` & :math:`c^{\min}_j` & mmol C m\ :sup:`-3` & minimum abundance for mortality, respiration and exudation :varlink:`amminhib` & :math:`\sigma_1` & (mmol N m\ :sup:`-3`)\ :sup:`-1` & coefficient for NH4 inhibition of NO uptake :varlink:`acclimtimescl` & :math:`\tau^{\op{acclim}}` & s\ :sup:`-1` & rate of chlorophyll acclimation :varlink:`mort` & :math:`m^{(1)}_j` & s\ :sup:`-1` & linear mortality rate :varlink:`mort2` & :math:`m^{(2)}_j` & (mmol C m\ :sup:`-3`)\ :sup:`-1` s\ :sup:`-1` & quadratic mortality coefficient :varlink:`ExportFracMort` & :math:`f^{\op{exp}\op{mort}}_j` & & fraction of linear mortality to POM :varlink:`ExportFracMort2` & :math:`f^{\op{exp}\op{mort2}}_j` & & fraction of quadratic mortality to POM :varlink:`ExportFracExude` & :math:`f^{\op{exp}\op{exude}}_j` & & fraction of exudation to POM :varlink:`phytoTempCoeff` & :math:`c_j` & & see :numref:`tab_phys_pkg_darwin_tempparams` :varlink:`phytoTempExp1` & :math:`e_{1j}` & exp(1/°C) & see :numref:`tab_phys_pkg_darwin_tempparams` :varlink:`phytoTempAe` & :math:`A^{\op{phy}}_{\op{e}j}` & 1/°C & see :numref:`tab_phys_pkg_darwin_tempparams` :varlink:`phytoTempExp2` & :math:`e_{2j}` & & see :numref:`tab_phys_pkg_darwin_tempparams` :varlink:`phytoTempOptimum` & :math:`T^{\op{opt}}_j` & °C & see :numref:`tab_phys_pkg_darwin_tempparams` :varlink:`phytoDecayPower` & :math:`p_j` & & see :numref:`tab_phys_pkg_darwin_tempparams` :varlink:`hetTempAe` & :math:`A^{\op{het}}_{\op{e}j}` & 1/°C & see :numref:`tab_phys_pkg_darwin_tempparams` :varlink:`hetTempExp2` & :math:`e^{\op{het}}_{2j}` & & see :numref:`tab_phys_pkg_darwin_tempparams` :varlink:`hetTempOptimum` & :math:`T^{\op{opt het}}_j` & °C & see :numref:`tab_phys_pkg_darwin_tempparams` :varlink:`hetDecayPower` & :math:`p^{\op{het}}_j` & & see :numref:`tab_phys_pkg_darwin_tempparams` :varlink:`grazTempAe` & :math:`A^{\op{graz}}_{\op{e}j}` & 1/°C & see :numref:`tab_phys_pkg_darwin_tempparams` :varlink:`grazTempExp2` & :math:`e^{\op{graz}}_{2j}` & & see :numref:`tab_phys_pkg_darwin_tempparams` :varlink:`grazTempOptimum` & :math:`T^{\op{opt graz}}_j` & °C & see :numref:`tab_phys_pkg_darwin_tempparams` :varlink:`grazDecayPower` & :math:`p^{\op{graz}}_j` & & see :numref:`tab_phys_pkg_darwin_tempparams` :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) :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) :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) :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) :varlink:`R_ChlC` & :math:`R^{\op{chl}c}_j` & mg Chl (mmol C)\ :sup:`-1` & chlorophyll-carbon ratio (not used with DARWIN_ALLOW_CHLQUOTA) :varlink:`R_PICPOC` & :math:`R^{\op{PICPOC}}_j` & mmol PIC (mmol POC)\ :sup:`-1` & inorganic-organic carbon ratio :varlink:`biosink` & :math:`w^{\op{sink}}_j` & m s\ :sup:`-1` & sinking velocity (positive downwards) :varlink:`bioswim` & :math:`w^{\op{swim}}_j` & m s\ :sup:`-1` & upward swimming velocity (positive upwards) :varlink:`respRate` & :math:`r^{\op{resp}}_j` & s\ :sup:`-1` & respiration rate :varlink:`PCmax` & :math:`P^{\op{max}}_{\op{C},j}` & s\ :sup:`-1` & maximum carbon-specific growth rate :varlink:`Qnmax` & :math:`Q^{\op{N}\op{max}}_j` & mmol N (mmol C)\ :sup:`-1` & maximum nitrogen quota (only with DARWIN_ALLOW_NQUOTA) :varlink:`Qnmin` & :math:`Q^{\op{N}\min}_j` & mmol N (mmol C)\ :sup:`-1` & minimum nitrogen quota (only with DARWIN_ALLOW_NQUOTA) :varlink:`Qpmax` & :math:`Q^{\op{P}\op{max}}_j` & mmol P (mmol C)\ :sup:`-1` & maximum phosphorus quota (only with DARWIN_ALLOW_PQUOTA) :varlink:`Qpmin` & :math:`Q^{\op{P}\min}_j` & mmol P (mmol C)\ :sup:`-1` & minimum phosphorus quota (only with DARWIN_ALLOW_PQUOTA) :varlink:`Qsimax` & :math:`Q^{\op{Si}\op{max}}_j` & mmol Si (mmol C)\ :sup:`-1` & maximum silica quota (only with DARWIN_ALLOW_SIQUOTA) :varlink:`Qsimin` & :math:`Q^{\op{Si}\min}_j` & mmol Si (mmol C)\ :sup:`-1` & minimum silica quota (only with DARWIN_ALLOW_SIQUOTA) :varlink:`Qfemax` & :math:`Q^{\op{Fe}\op{max}}_j` & mmol Fe (mmol C)\ :sup:`-1` & maximum iron quota (only with DARWIN_ALLOW_FEQUOTA) :varlink:`Qfemin` & :math:`Q^{\op{Fe}\min}_j` & mmol Fe (mmol C)\ :sup:`-1` & minimum iron quota (only with DARWIN_ALLOW_FEQUOTA) :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) :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) :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) :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) :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) :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) :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) :varlink:`ksatNH4` & :math:`k^{\op{NH4}}_j` & mmol N m\ :sup:`-3` & half-saturation conc. for ammonia uptake/limitation :varlink:`ksatNO2` & :math:`k^{\op{NO2}}_j` & mmol N m\ :sup:`-3` & half-saturation conc. for nitrite uptake/limitation :varlink:`ksatNO3` & :math:`k^{\op{NO3}}_ji` & mmol N m\ :sup:`-3` & half-saturation conc. for nitrate uptake/limitation :varlink:`ksatPO4` & :math:`k^{\op{PO4}}_j` & mmol P m\ :sup:`-3` & half-saturation conc. for phosphate uptake/limitation :varlink:`ksatSiO2` & :math:`k^{\op{SiO2}}_j` & mmol Si m\ :sup:`-3` & half-saturation conc. for silica uptake/limitation :varlink:`ksatFeT` & :math:`k^{\op{Fe}}_j` & mmol Fe m\ :sup:`-3` & half-saturation conc. for iron uptake/limitation :varlink:`kexcc` & :math:`\kappa^{\op{exc}}_{\op{C} j}` & s\ :sup:`-1` & exudation rate for carbon :varlink:`kexcn` & :math:`\kappa^{\op{exc}}_{\op{N} j}` & s\ :sup:`-1` & exudation rate for nitrogen :varlink:`kexcp` & :math:`\kappa^{\op{exc}}_{\op{P} j}` & s\ :sup:`-1` & exudation rate for phosphorus :varlink:`kexcsi` & :math:`\kappa^{\op{exc}}_{\op{Si} j}` & s\ :sup:`-1` & exudation rate for silica :varlink:`kexcfe` & :math:`\kappa^{\op{exc}}_{\op{Fe} j}` & s\ :sup:`-1` & exudation rate for iron :varlink:`inhibGeider` & :math:`c^{\op{inhib}}_j` & & photo-inhibition coefficient for Geider growth :varlink:`ksatPAR` & :math:`k^{\op{sat}}_{\op{PAR}}` & (μEin m\ :sup:`-2` s\ :sup:`-1`)\ :sup:`-1` & saturation coefficient for PAR (w/o GEIDER) :varlink:`kinhPAR` & :math:`k^{\op{inh}}_{\op{PAR}}` & (μEin m\ :sup:`-2` s\ :sup:`-1`)\ :sup:`-1` & inhibition coefficient for PAR (w/o GEIDER) :varlink:`mQyield` & :math:`\Phi_j` & mmol C (μEin)\ :sup:`-1` & maximum quantum yield :varlink:`chl2cmax` & :math:`\op{Chl\text{:}C}^{\op{max}}_j` & mg Chl (mmol C)\ :sup:`-1` & maximum Chlorophyll-carbon ratio :varlink:`grazemax` & :math:`g^{\op{max}}_z` & s\ :sup:`-1` & maximum grazing rate :varlink:`kgrazesat` & :math:`k^{\op{graz}}_z` & mmol C m\ :sup:`-3` & grazing half-saturation concentration :varlink:`yield` & :math:`{Y_j}` & & bacterial growth yield for all organic matter :varlink:`yieldO2` & :math:`{Y^{{\mathrm{O}}_2}_j}` & & bacterial growth yield for oxygen :varlink:`yieldNO3` & :math:`{Y^{\op{NO}_3}_j}` & & bacterial growth yield for nitrate :varlink:`ksatPON` & :math:`{k^{\op{PON}}}` & mmol N m\ :sup:`-3` & half-saturation of PON for bacterial growth :varlink:`ksatPOC` & :math:`{k^{\op{POC}}}` & mmol C m\ :sup:`-3` & half-saturation of POC for bacterial growth :varlink:`ksatPOP` & :math:`{k^{\op{POP}}}` & mmol P m\ :sup:`-3` & half-saturation of POP for bacterial growth :varlink:`ksatPOFe` & :math:`{k^{\op{POFe}}}` & mmol Fe m\ :sup:`-3` & half-saturation of POFe for bacterial growth :varlink:`ksatDON` & :math:`{k^{\op{DON}}}` & mmol N m\ :sup:`-3` & half-saturation of DON for bacterial growth :varlink:`ksatDOC` & :math:`{k^{\op{DOC}}}` & mmol C m\ :sup:`-3` & half-saturation of DOC for bacterial growth :varlink:`ksatDOP` & :math:`{k^{\op{DOP}}}` & mmol P m\ :sup:`-3` & half-saturation of DOP for bacterial growth :varlink:`ksatDOFe` & :math:`{k^{\op{DOFe}}}` & mmol Fe m\ :sup:`-3` & half-saturation of DOFe for bacterial growth .. csv-table:: Trait matrices for grazing; indices (prey, pred) :delim: & :widths: auto :class: longtable :header: Trait, Symbol, Units, Description :varlink:`palat` & :math:`p_{j,z}` & & palatability matrix :varlink:`asseff` & :math:`a_{j,z}` & & assimilation efficiency matrix :varlink:`ExportFracPreyPred` & :math:`f^{\op{exp}\op{graz}}_{j,z}` & & fraction of unassimilated prey becoming particulate organic matter .. csv-table:: Namelist DARWIN_RADTRANS_TRAITS; indices (plankton, waveband) :delim: & :widths: auto :header: Trait, Symbol, Units, Description :varlink:`aphy_chl` & :math:`a^{\op{chl}}_{\op{phy}}` & m\ :sup:`2` (mg Chl)\ :sup:`-1` & phytoplankton Chl-specific absorption coefficient :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 :varlink:`aphy_mgC` & :math:`a^{\op{mgC}}_{\op{phy}}` & m\ :sup:`2` (mg C)\ :sup:`-1` & plankton carbon-specific absorption coefficient :varlink:`bphy_mgC` & :math:`b^{\op{mgC}}_{\op{phy}}` & m\ :sup:`2` (mg C)\ :sup:`-1` & carbon-specific total scattering coefficient :varlink:`bbphy_mgC` & :math:`b^{\op{mgC}}_{\op{b}\op{phy}}` & m\ :sup:`2` (mg C)\ :sup:`-1` & carbon-specific backscattering coefficient The dependent trait alphachl(plankton,waveband) is computed from the other traits (radtrans or not). Allometric trait generation ''''''''''''''''''''''''''' Plankton types are organized into functional groups. ``grp_nplank(g)`` sets the number of types in group ``g``. Traits may be set the same for all types in a group, e.g., ``grp_diazo(g)``, or based on allometric scaling relations, .. math:: \mathrm{trait}_j = a_g \cdot V_j^{b_g} with per-group scaling coefficients :math:`a_g` and :math:`b_g`. The volumes :math:`V_j` of all types can be set in four ways (in order or decreasing precedence), .. math:: V_j = \begin{cases} \op{grp\_biovol(i,g)} & \\ V_{\log}(\op{grp\_biovolind(i,g)}) \\ V_{\log}(\op{logvol0ind(g)}+i-1) \\ V_{0 g} f_g^{i-1} \end{cases} where :math:`i` is the index of type :math:`j` within the functional group. :math:`V_{\log}` is a series of volumes, evenly spaced in log space and defined by parameters :math:`B=\op{logvolbase}` and :math:`I=\op{logvolinc}`, .. math:: V_{\log} = 10^B, 10^{B+I}, 10^{B+2I}, \dots and :math:`V_{0 g}=\op{biovol0(g)}` and :math:`f_g=\op{biovolfac(g)}`. The scaling coefficients are read from namelist ``&darwin_trait_params`` in ``data.darwin``. The following table shows the correspondence between traits and trait parameters. Where :math:`b` is not given, it is set to 0, i.e., all types in the group share the same trait value. For some trait parameters *x*, a divisor may be specified in *x*\ _denom. This is particularly useful for specifying a rate in ‘per-day’ units, i.e., *x*\ _denom=86400. .. csv-table:: Namelist DARWIN_TRAIT_PARAMS :delim: & :widths: auto :header: Trait, a, Default, b, Default :varlink:`isPhoto` & :varlink:`grp_photo` & 1 & & :varlink:`bactType` & :varlink:`grp_bacttype` & 0 & & :varlink:`isAerobic` & :varlink:`grp_aerobic` & 0 & & :varlink:`isDenit` & :varlink:`grp_denit` & 0 & & :varlink:`isPred` & :varlink:`grp_pred` & 0 & & :varlink:`isPrey` & :varlink:`grp_prey` & 1 & & :varlink:`hasSi` & :varlink:`grp_hasSi` & 0 & & :varlink:`hasPIC` & :varlink:`grp_hasPIC` & 0 & & :varlink:`diazo` & :varlink:`grp_diazo` & 0 & & :varlink:`useNH4` & :varlink:`grp_useNH4` & 1 & & :varlink:`useNO2` & :varlink:`grp_useNO2` & 1 & & :varlink:`useNO3` & :varlink:`grp_useNO3` & 1 & & :varlink:`combNO` & :varlink:`grp_combNO` & 1 & & :varlink:`aptype` & :varlink:`grp_aptype` & 0 & & :varlink:`tempMort` & :varlink:`grp_tempMort` & 1 & & :varlink:`tempMort2` & :varlink:`grp_tempMort2` & 1 & & :varlink:`tempGraz` & :varlink:`grp_tempGraz` & 1 & & :varlink:`Xmin` & :varlink:`a_Xmin` & 0 & & :varlink:`R_NC` & :varlink:`a_R_NC` & 16/120 & & :varlink:`R_PC` & :varlink:`a_R_PC` & 1/120 & & :varlink:`R_SiC` & :varlink:`a_R_SiC` & 0 & & :varlink:`R_FeC` & :varlink:`a_R_FeC` & 1D-3/120 & & :varlink:`R_ChlC` & :varlink:`a_R_ChlC` & 16/120 & & :varlink:`R_PICPOC` & :varlink:`a_R_PICPOC` & 0.8 & & :varlink:`ExportFracMort` & :varlink:`a_ExportFracMort` & 0.5 & & :varlink:`ExportFracMort2` & :varlink:`a_ExportFracMort2` & 0.5 & & :varlink:`ExportFracExude` & :varlink:`a_ExportFracExude` & UNINIT & & :varlink:`mort` & :varlink:`a_mort` & 0.02 / day & & :varlink:`mort2` & :varlink:`a_mort2` & 0 & & :varlink:`phytoTempCoeff` & :varlink:`a_phytoTempCoeff` & 1/3 & & :varlink:`phytoTempExp1` & :varlink:`a_phytoTempExp1` & 1.04 & & :varlink:`phytoTempAe` & :varlink:`a_phytoTempAe` & 0.0438 & & :varlink:`phytoTempExp2` & :varlink:`a_phytoTempExp2` & 0.001 & & :varlink:`phytoTempOptimum` & :varlink:`a_phytoTempOptimum` & 2 & & :varlink:`phytoDecayPower` & :varlink:`a_phytoDecayPower` & 4 & & :varlink:`hetTempAe` & :varlink:`a_hetTempAe` & 0.0438 & & :varlink:`hetTempExp2` & :varlink:`a_hetTempExp2` & 0.001 & & :varlink:`hetTempOptimum` & :varlink:`a_hetTempOptimum` & 2 & & :varlink:`hetDecayPower` & :varlink:`a_hetDecayPower` & 4 & & :varlink:`grazTempAe` & :varlink:`a_grazTempAe` & 0.0438 & & :varlink:`grazTempExp2` & :varlink:`a_grazTempExp2` & 0.001 & & :varlink:`grazTempOptimum` & :varlink:`a_grazTempOptimum` & 2 & & :varlink:`grazDecayPower` & :varlink:`a_grazDecayPower` & 4 & & :varlink:`mQyield` & :varlink:`a_mQyield` & 75D-6 & & :varlink:`chl2cmax` & :varlink:`a_chl2cmax` & .3 & & :varlink:`inhibGeider` & :varlink:`a_inhibGeider` & 0 & & :varlink:`ksatPAR` & :varlink:`a_ksatPAR` & 0.012 & & :varlink:`kinhPAR` & :varlink:`a_kinhPAR` & 6D-3 & & :varlink:`amminhib` & :varlink:`a_amminhib` & 4.6 & & :varlink:`acclimtimescl` & :varlink:`a_acclimtimescl` & 1/(20 days) & & & :varlink:`a_acclimtimescl_denom` & 1 & & :varlink:`ksatPON` & :varlink:`a_ksatPON` & 1 & & :varlink:`ksatDON` & :varlink:`a_ksatDON` & 1 & & :varlink:`grazemax` & :varlink:`a_grazemax` & 21.9 / day & :varlink:`b_grazemax` & -0.16 & :varlink:`a_grazemax_denom` & 1 & & :varlink:`kgrazesat` & :varlink:`a_kgrazesat` & 1.00 & :varlink:`b_kgrazesat` & 0.00 :varlink:`biosink` & :varlink:`a_biosink` & 0.28D-1 / day & :varlink:`b_biosink` & 0.39 & :varlink:`a_biosink_denom` & 1 & & :varlink:`bioswim` & :varlink:`a_bioswim` & 0.00 / day & :varlink:`b_bioswim` & 0.18 & :varlink:`a_bioswim_denom` & 1 & & :varlink:`palat` & :varlink:`a_ppSig` & 1 & *see note* [#palat]_ :varlink:`palat` & :varlink:`a_ppOpt` & 1024 & :varlink:`b_ppOpt` & 0.00 :varlink:`palat` & :varlink:`palat_min` & 0 & & :varlink:`PCmax` & :varlink:`a_PCmax` & 1.00 / day & :varlink:`b_PCmax` & -0.15 & :varlink:`a_PCmax_denom` & 1 & & :varlink:`qcarbon` & :varlink:`a_qcarbon` & 1.80D-11 & :varlink:`b_qcarbon` & 0.94 :varlink:`respRate` & :varlink:`a_respRate_c` & 0.00 & :varlink:`b_respRate_c` & 0.93 & :varlink:`a_respRate_c_denom` & 1 & *see note* [#resprate]_ :varlink:`kexcc` & :varlink:`a_kexcC` & 0.00 & :varlink:`b_kexcC` & -0.33 :varlink:`vmaxNO3` & :varlink:`a_vmaxNO3` & 0.51 / day & :varlink:`b_vmaxNO3` & -0.27 & :varlink:`a_vmaxNO3_denom` & 1 & & :varlink:`ksatNO3` & :varlink:`a_ksatNO3` & 0.17 & :varlink:`b_ksatNO3` & 0.27 :varlink:`Qnmin` & :varlink:`a_Qnmin` & 0.07 & :varlink:`b_Qnmin` & -0.17 :varlink:`Qnmax` & :varlink:`a_Qnmax` & 0.25 & :varlink:`b_Qnmax` & -0.13 :varlink:`kexcn` & :varlink:`a_kexcN` & 0.00 & :varlink:`b_kexcN` & -0.33 :varlink:`vmaxNO2` & :varlink:`a_vmaxNO2` & 0.51 / day & :varlink:`b_vmaxNO2` & -0.27 & :varlink:`a_vmaxNO2_denom` & 1 & & :varlink:`ksatNO2` & :varlink:`a_ksatNO2` & 0.17 & :varlink:`b_ksatNO2` & 0.27 & :varlink:`a_ksatNO2fac` & 1 & *used for eff.ksat* :varlink:`vmaxNH4` & :varlink:`a_vmaxNH4` & 0.26 / day & :varlink:`b_vmaxNH4` & -0.27 & :varlink:`a_vmaxNH4_denom` & 1 & & :varlink:`ksatNH4` & :varlink:`a_ksatNH4` & 0.85D-1 & :varlink:`b_ksatNH4` & 0.27 & :varlink:`a_ksatNH4fac` & 0.5 & *used for eff.ksat* :varlink:`vmaxN` & :varlink:`a_vmaxN` & 1.28 / day & :varlink:`b_vmaxN` & -0.27 & :varlink:`a_vmaxN_denom` & 1 & & :varlink:`vmaxPO4` & :varlink:`a_vmaxPO4` & 0.77D-1 / day & :varlink:`b_vmaxPO4` & -0.27 & :varlink:`a_vmaxPO4_denom` & 1 & & :varlink:`ksatPO4` & :varlink:`a_ksatPO4` & 0.26D-1 & :varlink:`b_ksatPO4` & 0.27 :varlink:`Qpmin` & :varlink:`a_Qpmin` & 2.00D-3 & :varlink:`b_Qpmin` & 0.00 :varlink:`Qpmax` & :varlink:`a_Qpmax` & 0.01 & :varlink:`b_Qpmax` & 0.00 :varlink:`kexcp` & :varlink:`a_kexcP` & 0.24D-1 / day & :varlink:`b_kexcP` & -0.33 :varlink:`vmaxSiO2` & :varlink:`a_vmaxSiO2` & 0.77D-1 / day & :varlink:`b_vmaxSiO2` & -0.27 & :varlink:`a_vmaxSiO2_denom` & 1 & & :varlink:`ksatSiO2` & :varlink:`a_ksatSiO2` & 0.24D-1 & :varlink:`b_ksatSiO2` & 0.27 :varlink:`Qsimin` & :varlink:`a_Qsimin` & 2.00D-3 & :varlink:`b_Qsimin` & 0.00 :varlink:`Qsimax` & :varlink:`a_Qsimax` & 4.00D-3 & :varlink:`b_Qsimax` & 0.00 :varlink:`kexcsi` & :varlink:`a_kexcSi` & 0.00 / day & :varlink:`b_kexcSi` & 0.00 :varlink:`vmaxFeT` & :varlink:`a_vmaxFeT` & 14D-6 / day & :varlink:`b_vmaxFeT` & -0.27 & :varlink:`a_vmaxFeT_denom` & 1 & & :varlink:`ksatFeT` & :varlink:`a_ksatFeT` & 80D-6 & :varlink:`b_ksatFeT` & 0.27 :varlink:`Qfemin` & :varlink:`a_Qfemin` & 1.50D-6 & :varlink:`b_Qfemin` & 0.00 :varlink:`Qfemax` & :varlink:`a_Qfemax` & 80D-6 & :varlink:`b_Qfemax` & 0.00 :varlink:`kexcfe` & :varlink:`a_kexcFe` & 0.00 / day & :varlink:`b_kexcFe` & 0.00 :varlink:`ExportFracPreyPred` & :varlink:`grp_ExportFracPreyPred` & 0.5 & *(nGroup* :math:`\times` *nGroup)* :varlink:`asseff` & :varlink:`grp_ass_eff` & 0.7 & *(nGroup* :math:`\times` *nGroup)* :varlink:`aphy_chl` & :varlink:`aphy_chl_type` & *read* & *via* :varlink:`grp_aptype` :varlink:`aphy_chl_ps` & :varlink:`aphy_chl_ps_type` & *read* & *via* :varlink:`grp_aptype` :varlink:`aphy_mgC` & :varlink:`aphy_mgC_type` & *read* & *via* :varlink:`grp_aptype` :varlink:`bphy_mgC` & :varlink:`bphy_mgC_type` & *read* & *via* :varlink:`grp_aptype` :varlink:`bbphy_mgC` & :varlink:`bbphy_mgC_type` & *read* & *via* :varlink:`grp_aptype` .. [#palat] Palatabilities are initialized to zero and have to be set in ``data.traits`` unless :varlink:`DARWIN_ALLOMETRIC_PALAT` is defined in which case they are computed from pp_opt, pp_sig and palat_min based on predator and prey sizes, see :numref:`Grazing`. .. [#resprate] The respiration rate follows a different scaling law from other traits. It scales in terms of cellular carbon content, see :numref:`Respiration`. Diagnostics ~~~~~~~~~~~ .. tabularcolumns:: |\Y{.16}|\Y{.16}|\Y{.18}|\Y{.5}| .. csv-table:: Darwin package diagnostic fields :delim: & :widths: auto :class: longtable :header: Name, Code, Units, Description plankC & ``SMR_____MR`` & mmol C /m\ :sup:`3` & Total plankton carbon biomass Chl & ``SMR_____MR`` & mg Chl a /m\ :sup:`3` & Total Chlorophyll a PP & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Primary Production Nfix & ``SMRP____MR`` & mmol N /m\ :sup:`3`/s & N fixation Denit & ``SMRP____MR`` & mmol N /m\ :sup:`3`/s & Denitrification DenitN & ``SMRP____MR`` & mmol N /m\ :sup:`3`/s & Nitrogen loss due to denitrification EXU & ``SM_P____MR`` & mmol C /m\ :sup:`3`/s & Carbon exudation BioSyn & ``SM_P____MR`` & mmol C /m\ :sup:`3`/s & Biosynthesis rate DmdN & ``SM_P____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from N limit DmdP & ``SM_P____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from P limit DmdFe & ``SM_P____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from Fe limit DmdSi & ``SM_P____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from Si limit Dmdmin & ``SM_P____MR`` & mmol C /m\ :sup:`3`/s & Minimum carbon demand PAR### & ``SMRP____MR`` & µEin/m\ :sup:`2`/s & PAR waveband ### PARF### & ``SM_P____LR`` & µEin/m\ :sup:`2`/s & PAR at W point, waveband ### a### & ``SMRP____MR`` & 1/m & total absorption for waveband ### bt### & ``SMRP____MR`` & 1/m & total scattering for waveband ### bb### & ``SMRP____MR`` & 1/m & total backscattering for waveband ### aplk### & ``SMRP____MR`` & 1/m & absorption by plankton for waveband ### btplk### & ``SMRP____MR`` & 1/m & scattering by plankton for waveband ### bbplk### & ``SMRP____MR`` & 1/m & backscattering by plankton for waveband ### aprt### & ``SMRP____MR`` & 1/m & absorption by particles for waveband ### btprt### & ``SMRP____MR`` & 1/m & scattering by particles for waveband ### bbprt### & ``SMRP____MR`` & 1/m & backscattering by particles for waveband ### aCDOM### & ``SMRP____MR`` & 1/m & absorption by CDOM for waveband ### atten & ``SMRP____MR`` & 1 & attenuation in layer PARF & ``SM_P____LR`` & µEin/m\ :sup:`2`/s & PAR at top of layer PAR & ``SMRP____MR`` & µEin/m\ :sup:`2`/s & total PAR at layer center 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)` C_NO3 & ``SMRP____MR`` & mmol N /m\ :sup:`3`/s & consumption of NO3: :math:`\sum_j U^{\op{NO3}}_j` C_NO2 & ``SMRP____MR`` & mmol N /m\ :sup:`3`/s & consumption of NO2: :math:`\sum_j U^{\op{NO2}}_j` C_NH4 & ``SMRP____MR`` & mmol N /m\ :sup:`3`/s & consumption of NH4: :math:`\sum_j U^{\op{NH4}}_j` C_PO4 & ``SMRP____MR`` & mmol P /m\ :sup:`3`/s & consumption of PO4: :math:`\sum_j U^{\op{PO4}}_j` C_Si & ``SMRP____MR`` & mmol Si /m\ :sup:`3`/s & consumption of Si: :math:`\sum _j U^{\op{SiO2}}_j` C_Fe & ``SMRP____MR`` & mmol Fe /m\ :sup:`3`/s & consumption of Fe: :math:`\sum_j U^{\op{Fe}}_j` 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}}` S_NO3 & ``SMR_____MR`` & mmol N /m\ :sup:`3`/s & non-transport source of NO3 S_NO2 & ``SMR_____MR`` & mmol N /m\ :sup:`3`/s & non-transport source of NO2 S_NH4 & ``SMR_____MR`` & mmol N /m\ :sup:`3`/s & non-transport source of NH4 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}]` S_Si & ``SMR_____MR`` & mmol Si /m\ :sup:`3`/s & non-transport source of Si: :math:`r_{\op{POSi}}\op{POSi}` 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}}` gDAR## & ``SMR_____MR`` & [TRAC##]/s & ptracer ## tendency from DARWIN [#b]_ gECO## & ``SMR_____MR`` & [TRAC##]/s & ptracer ## tendency from DARWIN w/o sink/swim [#b]_ PP#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Primary Production plankton #### PC#### & ``SMRP____MR`` & 1/s & Carbon-specific phototrophic growth rate plankton #### HP#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Heterotrophic production plankton #### HC#### & ``SMRP____MR`` & 1/s & Carbon-specific heterotrophic growth rate plankton #### GR#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Grazing loss of plankton #### GrGn#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Grazing gain of plankton #### GrGC#### & ``SMRP____MR`` & 1/s & Carbon-specific grazing rate plankton #### EXU#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Exudation plankton #### BS#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Biosynthesis rate plankton #### DN#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from N limit plankton #### DP#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from P limit plankton #### DFe#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from Fe limit plankton #### DSi#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Carbon demand from Si limit plankton #### Dmin#### & ``SMRP____MR`` & mmol C /m\ :sup:`3`/s & Minimum carbon demand plankton #### sfcSolFe & ``SM_P____L1`` & mmol Fe /m\ :sup:`2`/s & Soluble iron input at sea surface scvLosFe & ``SMRP____MR`` & mmol Fe /m\ :sup:`3`/s & Iron loss from scavenging scavRate & ``SMRP____MR`` & 1/s & Iron scavenging rate sedFe & ``SMRP____MR`` & mmol Fe /m\ :sup:`3`/s & Iron input from sediment freeFeLs & ``SMRP____MR`` & mmol Fe /m\ :sup:`3`/s & Iron loss due to free iron limit sedFlxFe & ``SM_P____U1`` & mmol Fe /m\ :sup:`2`/s & Iron sediment flux gDICEpr & ``SM______L1`` & mmol C /m\ :sup:`3`/s & Tendency of DIC due to E/P/runoff gNO3Epr & ``SM______L1`` & mmol N /m\ :sup:`3`/s & Tendency of DIC due to E/P/runoff gNO2Epr & ``SM______L1`` & mmol N /m\ :sup:`3`/s & Tendency of DIC due to E/P/runoff gNH4Epr & ``SM______L1`` & mmol N /m\ :sup:`3`/s & Tendency of DIC due to E/P/runoff gPO4Epr & ``SM______L1`` & mmol P /m\ :sup:`3`/s & Tendency of PO4 due to E/P/runoff gFeTEpr & ``SM______L1`` & mmol Fe /m\ :sup:`3`/s & Tendency of FeT due to E/P/runoff gSiO2Epr & ``SM______L1`` & mmol Si /m\ :sup:`3`/s & Tendency of SiO2 due to E/P/runoff gALKEpr & ``SM______L1`` & meq/m\ :sup:`3`/s & Tendency of ALK due to E/P/runoff gO2Epr & ``SM______L1`` & mmol O2 /m\ :sup:`3`/s & Tendency of O2 due to E/P/runoff surfPAR & ``SM_P____L1`` & µEin/m\ :sup:`2`/s & PAR forcing at surface surfiron & ``SM_P____L1`` & mmol Fe /m\ :sup:`2`/s & iron forcing at surface DARice & ``SM_P____L1`` & m\ :sup:`2`/m\ :sup:`2` & ice area fraction DARwind & ``SM_P____L1`` & m/s & wind speed used for carbon exchange surfpCO2 & ``SM_P____L1`` & mol/mol & atmospheric surface pCO2 .. [#b] does not include free iron adjustment for FeT tracer Diagnostics related to carbon chemistry are listed in :numref:`CarbonChemistryDiagnostics`. Also of interest are the following diagnostics from the ptracers and gchem packages: .. csv-table:: :delim: & :widths: auto :class: longtable :header: Name, Code, Units, Description Tp_g## & ``SMR_____MR`` & [TRAC##]/s & ptracer ## total transport tendency (before gchem_forcing_sep) TRAC## & ``SMR_____MR`` & [TRAC##] & ptracer ## concentration before transport GC_Tr## & ``SMR_____MR`` & [TRAC##] & ptracer ## concentration before GCHEM The ptracer number ## here and in gDAR## is the one defined in the ptracers package, see :numref:`ptracers_diagnostics` for value larger than 99. Call Tree ~~~~~~~~~ .. parsed-literal:: the_model_main initialise_fixed packages_readparms gchem_readparms **darwin_readparms** darwin_exf_readparms darwin_read_params darwin_read_traitparams gchem_tr_register **darwin_tr_register** packages_init_fixed gchem_init_fixed **darwin_init_fixed** darwin_exf_init_fixed darwin_diagnostics_init darwin_random_init darwin_generate_random darwin_random darwin_random_normal darwin_generate_allometric darwin_read_traits packages_check gchem_check **darwin_check** the_main_loop initialise_varia packages_init_variables gchem_init_vari **darwin_init_varia** darwin_exf_init_varia darwin_read_pickup darwin_init_chl darwin_light darwin_insol darwin_light_radtrans darwin_surfforcing_init darwin_coeffs_surf darwin_coeffs_deep darwin_carbon_coeffs ahini_for_at calc_pco2_solvesaphe solve_at_general anw_infsup equation_at solve_at_general_sec anw_infsup equation_at solve_at_fast equation_at darwin_calc_pco2_approx do_the_model_io gchem_output **darwin_diags** main_do_loop forward_step load_fields_driver gchem_fields_load **darwin_fields_load** darwin_exf_load darwin_monitor gchem_cons **darwin_cons** gchem_forcing_sep **darwin_conserve_surface** **darwin_cons** **darwin_cons_reset** **darwin_nut_supply** **darwin_forcing** darwin_light_radtrans darwin_light... darwin_surfforcing darwin_coeffs_surf darwin_coeffs_deep darwin_carbon_coeffs calc_pco2_solvesaphe... darwin_calc_pco2_approx darwin_add_surfforc darwin_fe_chem darwin_tempfunc darwin_plankton darwin_sinking **darwin_atmos** do_the_model_io... do_write_pickup packages_write_pickup gchem_write_pickup **darwin_write_pickup**