\(\newcommand{\p}[1]{\frac{\partial }{\partial #1}}\) \(\newcommand{\pp}[2]{\frac{\partial #1}{\partial #2}}\) \(\newcommand{\dd}[2]{\frac{d #1}{d #2}}\) \(\newcommand{\h}{\frac{1}{2}}\) \(\newcommand{\op}[1]{\operatorname{#1}}\)

8.7.3. DARWIN package

The 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:

• 8.7.3.1. Model equations
• 8.7.3.2. Growth
• 8.7.3.3. Internal carbon store and exudation
• 8.7.3.4. Non-spectral Light
• 8.7.3.5. Spectral Light
• 8.7.3.6. Nutrient uptake and limitation
• 8.7.3.7. Chlorophyll synthesis
• 8.7.3.8. Remineralization and Nitrification
• 8.7.3.9. Denitrification
• 8.7.3.10. Dynamic CDOM
• 8.7.3.11. Air-sea exchanges
• 8.7.3.12. Carbon chemistry
• 8.7.3.13. Iron chemistry
• 8.7.3.14. Respiration
• 8.7.3.15. Mortality
• 8.7.3.16. Exudation
• 8.7.3.17. Grazing
• 8.7.3.18. Bacteria
• 8.7.3.19. Temperature dependence
• 8.7.3.20. Sinking and Swimming
• 8.7.3.21. Conservation of chemical elements
• 8.7.3.22. Change Log

Plankton and nutrients are represented by their concentration in the ocean, using the PTRACERS Package. The darwin package uses the following tracers (or a subset, depending on the configuration):

Name	Units	Description
DIC	mmol C m–3	concentration of dissolved inorganic carbon
NO3	mmol N m–3	concentration of nitrate
NO2	mmol N m–3	concentration of nitrite
NH4	mmol N m–3	concentration of ammonia
PO4	mmol P m–3	concentration of phosphate
FeT	mmol Fe m–3	concentration of total dissolved iron
SiO2	mmol Si m–3	concentration of inorganic silica
DOC	mmol C m–3	concentration of dissolved organic carbon
DON	mmol N m–3	concentration of dissolved organic nitrogen
DOP	mmol P m–3	concentration of dissolved organic phosphorus
DOFe	mmol Fe m–3	concentration of dissolved organic iron
POC	mmol C m–3	concentration of particulate organic carbon
PON	mmol N m–3	concentration of particulate organic nitrogen
POP	mmol P m–3	concentration of particulate organic phosphorus
POFe	mmol Fe m–3	concentration of particulate organic iron
POSi	mmol Si m–3	concentration of particulate organic silica
PIC	mmol C m–3	concentration of particulate inorganic carbon
ALK	meq m–3	alkalinity
O2	mmol O2 m–3	concentration of oxygen
CDOM	mmol C m–3 (mmol P m–3)	concentration of colored dissolved organic matter 1
cj	mmol C m–3	concentration of carbon in plankton type j
nj	mmol N m–3	concentration of nitrogen in plankton type j
pj	mmol P m–3	concentration of phosphorus in plankton type j
fej	mmol Fe m–3	concentration of iron in plankton type j
sij	mmol Si m–3	concentration of silica in plankton type j
Chlj	mg Chl a m–3	concentration of Chlorophyll-a in plankton type j

1

units of CDOM are mmol C m^–3 if #define DARWIN_CDOM_UNITS_CARBON (default), mmol P m^–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.

8.7.3.23. Compiling and Running

8.7.3.23.1. 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 DARWIN_OPTIONS.h (see table below).

Adjust the number of plankton types, functional groups, autotrophs, grazers, prey and optical types in DARWIN_SIZE.h.

You will also have to adjust the number of passive tracers in PTRACERS_SIZE.h. You can run tools/darwin/mkdarwintracers in your code directory (after adjusting DARWIN_OPTIONS.h and DARWIN_SIZE.h) to find out how many ptracers you will need and what they are.

In GCHEM_OPTIONS.h you need to define GCHEM_SEPARATE_FORCING.

In EXF_OPTIONS.h you may want to undef ALLOW_CLIMSST_RELAXATION and ALLOW_CLIMSSS_RELAXATION.

To use spectral light, compile the radtrans package, see Section 8.7.4.

Table 8.60 Darwin package CPP options

CPP option	description
DARWIN_ALLOW_NQUOTA	enable nitrogen quotas for all plankton
DARWIN_ALLOW_PQUOTA	enable phosphorus quotas for all plankton
DARWIN_ALLOW_FEQUOTA	enable iron quotas for all plankton
DARWIN_ALLOW_SIQUOTA	enable silica quotas for all plankton
DARWIN_ALLOW_CHLQUOTA	enable chlorophyll quotas for all phototrophs
DARWIN_ALLOW_CDOM	enable a dynamic CDOM tracer
DARWIN_CDOM_UNITS_CARBON	measure CDOM in units of mmol C/m3 and follow organic carbon instead of phosphorus
DARWIN_ALLOW_CSTORE	enable internal carbon store and exudation for all phototrophs
DARWIN_ALLOW_CSTORE_DIAGS	enable diagnostics for internal carbon store
DARWIN_ALLOW_CARBON	enable air-sea carbon exchange and ALK and O\(_2\) tracers
DARWIN_SOLVESAPHE	compile Munhoven “Solvesaphe” pH/pOC2 solver package
DARWIN_TOTALPHSCALE	consistently use the total pH scale for carbon chemistry coefficients
DARWIN_USE_PLOAD	take atmospheric pressure from coupled atmospheric model
DARWIN_ALLOW_RADI	enable RADI sediment model
DARWIN_ALLOW_DENIT	enable denitrification code
DARWIN_ALLOW_EXUDE	enable exudation of individual quotas
ALLOW_OLD_VIRTUALFLUX	enable old virtualflux code for DIC and ALK
DARWIN_NITRATE_FELIMIT	reduce nitrate uptake by iron limitation factor
DARWIN_BOTTOM_SINK	allow organic matter to sink into bottom (sedimentize)
DARWIN_NUTRIENT_RUNOFF	include code for reading nutrient runoff from files
DARWIN_AVPAR	compute average PAR in layer, assuming exponential decay (%)
DARWIN_ALLOW_GEIDER	enable GEIDER light code (required for radtrans)
DARWIN_GEIDER_RHO_SYNTH	use ρ instead of acclimated Chl:C for chlorophyll synthesis
DARWIN_CHL_INIT_LEGACY	initialize chlorophyll as in darwin2
DARWIN_SCATTER_CHL	scattering coefficients are per Chlorophyll
DARWIN_DIAG_IOP	make diagnostics for instrinsic optical properties available
DARWIN_GRAZING_SWITCH	enable quadratic grazing as in darwin2+quota
DARWIN_ALLOMETRIC_PALAT	compute palatability from size ratios
DARWIN_NOZOOTEMP	turn off grazing temperature dependence
DARWIN_NOTEMP	turn off all temperature dependence
DARWIN_TEMP_VERSION	select temperature version: 1, 2 or 3
DARWIN_TEMP_RANGE	restrict phytoplankton growth to a temperature range
DARWIN_MINFE	restrict maximum free iron (sic)
DARWIN_PART_SCAV	enable particle scavenging code
DARWIN_IRON_SED_SOURCE_VARIABLE	enable variable iron sediment source
DARWIN_ALLOW_HYDROTHERMAL_VENTS	include code for iron input from hydrothermal vents
DARWIN_DIAG_PERTYPE	enable per-type diagnostics PP####, GR####, GrGn####
DARWIN_DIAG_TENDENCIES	enable diagnostics for many tendency terms
DARWIN_DEBUG	turn on debugging output
DARWIN_ALLOW_CONS	compute and print global element totals
DARWIN_UNUSED	value for unused traits

The following options are used for random trait generation (as in darwin2):

CPP option	description
DARWIN_RANDOM_TRAITS	assign traits based on random numbers as in darwin2
DARWIN_TWO_SPECIES_SETUP	set traits for darwin2 2-species setup (requires DARWIN_RANDOM_TRAITS)
DARWIN_NINE_SPECIES_SETUP	set traits for darwin2 9-species setup (requires DARWIN_RANDOM_TRAITS)
DARWIN_ALLOW_DIAZ	enable diazotrophy when using DARWIN_RANDOM_TRAITS

Random trait generation is supported mainly for backwards compatibility.

8.7.3.23.2. 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:

Namelist	Description
DARWIN_FORCING_PARAMS	parameters related to forcing and initialization
DARWIN_INTERP_PARAMS	parameters for interpolation of forcing fields (only used if USE_EXF_INTERPOLATION is defined)
DARWIN_PARAMS	general parameters (not per-plankton traits)
DARWIN_CDOM_PARAMS	parameters for dynamic CDOM
DARWIN_RADTRANS_PARAMS	parameters for radiative transer
DARWIN_RANDOM_PARAMS	parameters for randomly generated traits (deprecated)
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 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 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 DARWIN_FORCING_PARAMS in data.darwin. For light, ice area and wind speed, the following alternative sources can be given:

Table 8.61 Namelist DARWIN_FORCING_PARAMS

Name	Default	Description
darwin_useQsw	.FALSE.	whether to use model shortwave radiation for light
darwin_useSEAICE	.FALSE.	whether to use ice area from the seaice package
darwin_useEXFwind	.FALSE.	whether to use wind speed from the exf package

The forcing fields are:

Table 8.62 Darwin forcing fields

Name	Default	Units	Description
iron	0.0	mmol Fe m–2 s–1	iron input through sea surface, will be multiplied by solubility alpfe
PAR	0.0	μEin m–2 s–1	Photosynthetically active radiation below sea surface; not used with the radtrans package
ice	0.0	m2/m2	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 CO2; used for carbon and oxygen surface forcing
ventHe3	0.0	mmol 3He m–2 s–1	Helium-3 flux from hydrothermal vents; used for iron input
DOCrunoff	0.0	mmol C m–2 s–1	surface flux of DOC from runoff
DONrunoff	0.0	mmol N m–2 s–1	surface flux of DON from runoff
DOPrunoff	0.0	mmol P m–2 s–1	surface flux of DOP from runoff
DINrunoff	0.0	mmol N m–2 s–1	surface flux of DIN from runoff
IPrunoff	0.0	mmol P m–2 s–1	surface flux of IP from runoff
DSirunoff	0.0	mmol Si m–2 s–1	surface flux of DSi from runoff
POCrunoff	0.0	mmol C m–2 s–1	surface flux of POC from runoff
PONrunoff	0.0	mmol N m–2 s–1	surface flux of PON from runoff
POPrunoff	0.0	mmol P m–2 s–1	surface flux of POP from runoff
DICrunoff	0.0	mmol C m–2 s–1	surface flux of DIC from runoff

Each forcing field has a set of parameters in DARWIN_FORCING_PARAMS. These work as in the exf package, see Table 8.12. For instance, for PAR they are:

Table 8.63 Namelist DARWIN_FORCING_PARAMS, cont’d

Name	Default	Description
PARfile	‘ ‘	filename; if left empty no file will be read; PARconst will be used instead
PARconst	0.0	constant that will be used if no file is read
PARperiod	0.0	interval in seconds between two records
PARRepCycle	repeatPeriod	repeat cycle in seconds; only available if useExfYearlyFields is .FALSE.
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
PARstartdate1	0	date/time of first record when using the cal package; format: YYYYMMDD; start year (YYYY), month (MM), day (YY)
PARstartdate2	0	format: HHMMSS; start hour (HH), minute (MM), second(SS)
PAR_exfremo_intercept	0.0	can be used to remove global mean
PAR_exfremo_slope	0.0	can be used to remove global trend
PARmask	‘c’	grid point for masking: ‘ ‘ = no masking; ‘c’ = centered mask; ‘w’ = western mask; ‘s’ = southern
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 Table 8.64.

Table 8.64 Example unit conversions

Field	File units	Scaling factor
iron	mol Fe m–2 s–1	darwin_inscal_iron = 1000
	kg Fe m–2	darwin_inscal_iron = 17906.7
PAR	Ein m–2 day–1	darwin_inscal_PAR = 11.574074074074

Nutrient runoff has some extra parameters:

Table 8.65 Namelist DARWIN_FORCING_PARAMS, cont’d

Name	Default	Units	Description
R_ALK_DIC_runoff	1.0218	meq / mmol C	ALK:DIC ratio in runoff
R_NO3_DIN_runoff	0.6531	mmol N / mmol N	NO3 fraction of DIN in runoff
R_NO2_DIN_runoff	0.0158	mmol N / mmol N	NO2 fraction of DIN in runoff
R_NH4_DIN_runoff	0.3311	mmol N / mmol N	NH4 fraction of DIN in runoff
R_DIP_IP_runoff	0.333	mmol P / mmol P	ratio of dissolved to total inorganic P in runoff
R_DFe_DIP_runoff	0.0003	mmol Fe / mmol P	Fe:P ratio for inorganic P in runoff
R_DOFe_DOP_runoff	0.0003	mmol Fe / mmol P	Fe:P ratio for dissolved organic matter in runoff
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:

Table 8.66 Runoff forcing-tracer associations

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 DARWIN_INTERP_PARAMS. See the exf package for how to set them.

General parameters are set in namelist DARWIN_PARAMS:

Table 8.67 Namelist DARWIN_PARAMS

Name	Default	Units	Description
darwin_seed	0		seed for random number generator (for DARWIN_RANDOM_TRAITS)
darwin_strict_check	.FALSE.		stop instead of issuing warnings
iDEBUG	1		index in x dimension for debug prints
jDEBUG	1		index in y dimension for debug prints
kDEBUG	1		index in z dimension for debug prints
darwin_pickupSuff	pickupSuff		pickup suffix for darwin; set to ‘ ‘ to disable reading at PTRACERS_Iter0
darwin_linFSConserve	.FALSE.		correct non-conservation due to linear free surface (globally)
darwin_read_phos	.FALSE.		initial conditions for plankton biomass are in mmol P/m3
darwin_chlInitBalanced	.FALSE.		Initialize Chlorophyll to a balanced value following Geider
darwin_chlIter0	0		Iteration number when to initialize Chlorophyll
katten_w	4D-2	1/m	atten coefficient water
katten_chl	4D-2	m2/mg Chl	atten coefficient chl
parfrac	0.4		fraction Qsw that is PAR
parconv	1/0.2174	μEin/s/W	conversion from W/m2 to μEin/m2/s
tempnorm	0.3		set temperature function (was 1.0)
TempAeArr	-4000.0	K	slope for pseudo-Arrhenius (TEMP_VERSION 2)
TemprefArr	293.15	K	reference temp for pseudo-Arrhenius (TEMP_VERSION 2)
TempCoeffArr	0.5882		pre-factor for pseudo-Arrhenius (TEMP_VERSION 2)
reminTempAe	0.0438	1/K	temperature coefficient for remineralization (TEMP_VERSION 4)
mortTempAe	0.0438	1/K	temperature coefficient for linear mortality (TEMP_VERSION 4)
mort2TempAe	0.0438	1/K	temperature coefficient for quadr. mortality (TEMP_VERSION 4)
uptakeTempAe	0.0	1/K	temperature coefficient for uptake (TEMP_VERSION 4)
alpfe	0.04		solubility of Fe dust
scav	0.4/year	1/s	fixed iron scavenging rate
scav_tau	0.2		factor for converting Th scavenging rates to iron ones
scav_inter	0.079 / day	Le mg-e s-1	intercept of scavenging power law (e=escav)
scav_exp	0.58		exponent of scavenging power law
scav_POC_wgt	0.02173	g/mmol C	weight POC contributes to POM
scav_POSi_wgt	0.069	g/mmol Si	weight POSi contributes to POM
scav_PIC_wgt	0.100	g/mmol C	weight PIC contributes to POM
ligand_tot	1D-3	mol/m3	total ligand concentration
ligand_stab	2D5	m3/mol	ligand stability rate ratio
freefemax	0.4D-3	mol/m3	max concentration of free iron
depthfesed	-1.0	m	depth above which to add sediment source (was -1000)
fesedflux	1D-3 / day	mmol Fe /m2/s	fixed iron flux from sediment
fesedflux_pcm	0.68D-3	mmol Fe / mmol C	iron input per POC sinking into bottom for DARWIN_IRON_SED_SOURCE_VARIABLE
fesedflux_min	0.5D-3 / day	mmol Fe /s	min iron input rate subtracted from fesedflux_pcm*wc_sink*POC
R_CP_fesed	106	mmol C / mmol P	POC:POP conversion for DARWIN_IRON_SED_SOURCE_POP
depthFeVent	750	m	depth below which iron from hydrothermal vents is added
solFeVent	0.002		solubility of iron from hydrothermal vents
R_FeHe3_vent	4.5E8	mol Fe / mol 3He	Fe:3He ratio for hydrothermal vents
Knita	1/(0.5 days)	1/s	ammonia oxidation rate
Knitb	1/(10 days)	1/s	nitrite oxidation rate
PAR_oxi	10	μEin/m2/s	critical light level after which oxidation starts
Kdoc	1/(100 days)	1/s	DOC remineralization rate
Kdop	1/(100 days)	1/s	DON remineralization rate
Kdon	1/(100 days)	1/s	DOP remineralization rate
KdoFe	1/(100 days)	1/s	DOFe remineralization rate
KPOC	1/(50 days)	1/s	POC remineralization rate
KPOP	KPOC	1/s	POP remineralization rate
KPON	KPOC	1/s	PON remineralization rate
KPOFe	KPOC	1/s	POFe remineralization rate
KPOSi	1/(300 days)	1/s	POSi remineralization rate
wC_sink	10/day	m/s	sinking velocity for POC
wP_sink	wC_sink	m/s	sinking velocity for POP
wN_sink	wC_sink	m/s	sinking velocity for PON
wFe_sink	wC_sink	m/s	sinking velocity for POFe
wSi_sink	wC_sink	m/s	sinking velocity for POSi
wPIC_sink	15/day	m/s	sinking velocity for PIC
Kdissc	1/(300 days)	1/s	dissolution rate for PIC
R_OP	170	mmol O2 / mmol P	O:P ratio for respiration and consumption
R_OC	170/120.0	mmol O2 / mmol C	NOT USED
m3perkg	1 / 1024.5	m3/kg	constant for converting per kg to per m^3
surfSaltMinInit	4.0	ppt	limits for carbon solver input at initialization
surfSaltMaxInit	50.0	ppt	…
surfTempMinInit	-4.0	°C
surfTempMaxInit	39.0	°C
surfDICMinInit	10.0	mmol C m-3
surfDICMaxInit	4000.0	mmol C m-3
surfALKMinInit	10.0	meq m-3
surfALKMaxInit	4000.0	meq m-3
surfPO4MinInit	1D-10	mmol P m-3
surfPO4MaxInit	10.0	mmol P m-3
surfSiMinInit	1D-8	mmol Si m-3
surfSiMaxInit	500.0	mmol Si m-3
surfSaltMin	4.0	ppt	limits for carbon solver input during run
surfSaltMax	50.0	ppt	…
surfTempMin	-4.0	°C
surfTempMax	39.0	°C
surfDICMin	400.0	mmol C m-3
surfDICMax	4000.0	mmol C m-3
surfALKMin	400.0	meq m-3
surfALKMax	4000.0	meq m-3
surfPO4Min	1D-10	mmol P m-3
surfPO4Max	10.0	mmol P m-3
surfSiMin	1D-8	mmol Si m-3
surfSiMax	500.0	mmol Si m-3
diaz_ini_fac	1		reduce tracer concentrations by this factor on initialization
O2crit	6.0	mmol O2 m-3	critical oxygen for O2/NO3 remineralization
denit_NP	120.0	mmol N / mmol P	ratio of n to p in denitrification process
denit_NO3	104.0	mmol N / mmol P	ratio of NO3 uptake to phos remineralization in denitrification
NO3crit	1D-2	mmol N m-3	critical nitrate below which no denit (or remin) happens
PARmin	0.1	μEin/m2/s	minimum light for photosynthesis; for non-Geider: 1.0
aphy_chl_ave	0.02	m2/mg Chl	Chl-specific absorption coefficient
chl2nmax	3.00	mg Chl / mmol N	max Chl:N ratio for Chl synthesis following Moore 2002
synthcost	0.0	mmol C / mmol N	cost of biosynthesis
inhib_graz	1.0	(mmol C m-3)-1	inverse decay scale for grazing inhibition
inhib_graz_exp	0.0		exponent for grazing inhibition (0 to turn off inhibition)
hillnumUptake	1.0		exponent for limiting quota uptake in nutrient uptake
hillnumGraz	1.0		exponent for limiting quota uptake in grazing
hollexp	1.0		grazing exponential 1= “Holling 2”, 2= “Holling 3”
phygrazmin	120D-10	mmol C m-3	minimum total prey conc for grazing to occur
pmaxDIN	20/day	1/s	max DIN uptake rate for denitrifying bacteria
pcoefO2	290.82/day	m3/mmol O2/s	max O2-specific O2 uptake rate for aerobic bacteria
ksatDIN	0.01	mmol N m-3	half-saturation conc of dissolved inorganic nitrogen
alpha_hydrol	2.0		increase in POM needed due to hydrolysis
yod	0.2		organic matter yield of aerobic bacteria
yoe	yod/467*4/(1-yod)*106		energy yield of aerobic bacteria
ynd	0.16		organic matter yield of denitrifying bacteria
yne	ynd/467*5/(1-ynd)*106		energy yield of denitrifying bacteria

Table 8.68 Namelist DARWIN_CDOM_PARAMS

Name	Default	Units	Description
fracCDOM	2 / 100		fraction of remineralized POP contributing to CDOM
CDOMdegrd	1 / (200 days)	1/s	CDOM degradation rate
CDOMbleach	1 / (15 days)	1/s	CDOM bleaching rate
PARCDOM	20	μEin/m2/s	PAR where CDOM bleaching becomes maximal
R_NP_CDOM	16	mmol N / mmol P	CDOM N:P ratio (with #undef DARWIN_CDOM_UNITS_CARBON)
R_FeP_CDOM	1D-3	mmol Fe / mmol P	CDOM Fe:P ratio (with #undef DARWIN_CDOM_UNITS_CARBON)
R_CP_CDOM	120	mmol C / mmol P	CDOM C:P ratio (with #undef DARWIN_CDOM_UNITS_CARBON)
R_NC_CDOM	16/120	mmol N / mmol C	CDOM N:C ratio (with #define DARWIN_CDOM_UNITS_CARBON)
R_PC_CDOM	1/120	mmol P / mmol C	CDOM P:C ratio (with #define DARWIN_CDOM_UNITS_CARBON)
R_FeC_CDOM	1D-3/120	mmol Fe / mmol C	CDOM Fe:C ratio (with #define DARWIN_CDOM_UNITS_CARBON)
CDOMcoeff	100.0	m2 / mmol P	P-specific absorption coefficient of CDOM at \(\lambda_{\op{CDOM}}\)
	100/120	m2 / mmol C	if #define DARWIN_CDOM_UNITS_CARBON

Table 8.69 Namelist DARWIN_RADTRANS_PARAMS

Name	Default	Units	Description
darwin_waterAbsorbFile	‘ ‘		filename for reading water absorption and scattering spectra
darwin_phytoAbsorbFile	‘ ‘		filename for reading plankton absorption and scattering spectra
darwin_particleAbsorbFile	‘ ‘		filename for reading particle absorption and scattering spectra
darwin_part_size_P	1D-15	mmol P/particle	conversion factor for particle absorption and scattering spectra
darwin_bbmin	0.0002	1/m	minimum backscattering ratio
darwin_bbw	0.5		backscattering ratio of water
darwin_lambda_aCDOM	450.0	nm	reference wavelength for CDOM absorption spectra
darwin_Sdom	0.014	1/nm	coefficient for CDOM absorption spectra
darwin_aCDOM_fac	0.2		factor for computing aCDOM from water+Chlorophyll absorption
darwin_rCDOM	0.0	mmol P/m3	recalcitrant CDOM concentration
	0.0	mmol C/m3	if #define DARWIN_CDOM_UNITS_CARBON
darwin_RPOC	0.0	mmol C/m3	recalcitrant POC concentration
darwin_allomSpectra	.FALSE.		enable/disable allometric scaling of plankton absorption and scattering spectra
darwin_aCarCell	0.109D-9	mg C/cell	coefficient coefficient for scaling plankton spectra
darwin_bCarCell	0.991		coefficient coefficient for scaling plankton spectra
darwin_absorpSlope	-0.075		slope for scaled absorption spectra
darwin_bbbSlope	-1.458		slope for scaled backscattering ratio spectra
darwin_scatSwitchSizeLog	0	log(μm)	log of size for switching slopes
darwin_scatSlopeSmall	1.5		slope for small plankton
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:

Table 8.70 Namelist DARWIN_TRAITS

Trait	Symbol	Units	Description
isPhoto	isPhoto\(_j\)		1: does photosynthesis, 0: not
bactType	bactType\(_j\)		1: particle associated, 2: free living bacteria, 0: not bacteria
isAerobic	isAerobic\(_j\)		1: is aerobic bacteria (also set bactType), 0: not
isDenit	isDenit\(_j\)		1: is dentrifying bacteria (also set (bactType), 0: not
hasSi	hasSi\(_j\)		1: uses silica (Diatom), 0: not
hasPIC	hasPIC\(_j\)		1: calcifying, 0: set R_PICPOC to zero
diazo	diazo\(_j\)		1: use molecular instead of mineral nitrogen, 0: not
useNH4	useNH4\(_j\)		1: can use ammonia, 0: not
useNO2	useNO2\(_j\)		1: can use nitrite, 0: not
useNO3	useNO3\(_j\)		1: can use nitrate, 0: not
combNO	combNO\(_j\)		1: combined nitrite/nitrate limitation, 0: not
isPrey	isPrey\(_j\)		1: can be grazed, 0: not
isPred	isPred\(_j\)		1: can graze, 0: not
tempMort	\(e^{\op{mort}}_j\)		1: mortality is temperature dependent, 0: turn dependence off
tempMort2	\(e^{\op{mort2}}_j\)		1: quadratic mortality is temperature dependent, 0: turn dependence off
tempGraz	\(e^{\op{graz}}_j\)		1: grazing is temperature dependent, 0: turn dependence off
Xmin	\(c^{\min}_j\)	mmol C m-3	minimum abundance for mortality, respiration and exudation
amminhib	\(\sigma_1\)	(mmol N m-3)-1	coefficient for NH4 inhibition of NO uptake
acclimtimescl	\(\tau^{\op{acclim}}\)	s-1	rate of chlorophyll acclimation
mort	\(m^{(1)}_j\)	s-1	linear mortality rate
mort2	\(m^{(2)}_j\)	(mmol C m-3)-1 s-1	quadratic mortality coefficient
ExportFracMort	\(f^{\op{exp}\op{mort}}_j\)		fraction of linear mortality to POM
ExportFracMort2	\(f^{\op{exp}\op{mort2}}_j\)		fraction of quadratic mortality to POM
ExportFracExude	\(f^{\op{exp}\op{exude}}_j\)		fraction of exudation to POM
phytoTempCoeff	\(c_j\)		see Table 8.57
phytoTempExp1	\(e_{1j}\)	exp(1/°C)	see Table 8.57
phytoTempAe	\(A^{\op{phy}}_{\op{e}j}\)	1/°C	see Table 8.57
phytoTempExp2	\(e_{2j}\)		see Table 8.57
phytoTempOptimum	\(T^{\op{opt}}_j\)	°C	see Table 8.57
phytoDecayPower	\(p_j\)		see Table 8.57
hetTempAe	\(A^{\op{het}}_{\op{e}j}\)	1/°C	see Table 8.57
hetTempExp2	\(e^{\op{het}}_{2j}\)		see Table 8.57
hetTempOptimum	\(T^{\op{opt het}}_j\)	°C	see Table 8.57
hetDecayPower	\(p^{\op{het}}_j\)		see Table 8.57
grazTempAe	\(A^{\op{graz}}_{\op{e}j}\)	1/°C	see Table 8.57
grazTempExp2	\(e^{\op{graz}}_{2j}\)		see Table 8.57
grazTempOptimum	\(T^{\op{opt graz}}_j\)	°C	see Table 8.57
grazDecayPower	\(p^{\op{graz}}_j\)		see Table 8.57
R_NC	\(R^{\op{N}:\op{C}}_j\)	mmol N (mmol C)-1	nitrogen-carbon ratio (not used with DARWIN_ALLOW_NQUOTA)
R_PC	\(R^{\op{P}:\op{C}}_j\)	mmol P (mmol C)-1	phosphorus-carbon ratio (not used with DARWIN_ALLOW_PQUOTA)
R_SiC	\(R^{\op{Si}:\op{C}}_j\)	mmol Si (mmol C)-1	silica-carbon ratio (not used with DARWIN_ALLOW_SIQUOTA)
R_FeC	\(R^{\op{Fe}:\op{C}}_j\)	mmol Fe (mmol C)-1	iron-carbon ratio (not used with DARWIN_ALLOW_FEQUOTA)
R_ChlC	\(R^{\op{chl}c}_j\)	mg Chl (mmol C)-1	chlorophyll-carbon ratio (not used with DARWIN_ALLOW_CHLQUOTA)
R_PICPOC	\(R^{\op{PICPOC}}_j\)	mmol PIC (mmol POC)-1	inorganic-organic carbon ratio
biosink	\(w^{\op{sink}}_j\)	m s-1	sinking velocity (positive downwards)
bioswim	\(w^{\op{swim}}_j\)	m s-1	upward swimming velocity (positive upwards)
respRate	\(r^{\op{resp}}_j\)	s-1	respiration rate
PCmax	\(P^{\op{max}}_{\op{C},j}\)	s-1	maximum carbon-specific growth rate
Qnmax	\(Q^{\op{N}\op{max}}_j\)	mmol N (mmol C)-1	maximum nitrogen quota (only with DARWIN_ALLOW_NQUOTA)
Qnmin	\(Q^{\op{N}\min}_j\)	mmol N (mmol C)-1	minimum nitrogen quota (only with DARWIN_ALLOW_NQUOTA)
Qpmax	\(Q^{\op{P}\op{max}}_j\)	mmol P (mmol C)-1	maximum phosphorus quota (only with DARWIN_ALLOW_PQUOTA)
Qpmin	\(Q^{\op{P}\min}_j\)	mmol P (mmol C)-1	minimum phosphorus quota (only with DARWIN_ALLOW_PQUOTA)
Qsimax	\(Q^{\op{Si}\op{max}}_j\)	mmol Si (mmol C)-1	maximum silica quota (only with DARWIN_ALLOW_SIQUOTA)
Qsimin	\(Q^{\op{Si}\min}_j\)	mmol Si (mmol C)-1	minimum silica quota (only with DARWIN_ALLOW_SIQUOTA)
Qfemax	\(Q^{\op{Fe}\op{max}}_j\)	mmol Fe (mmol C)-1	maximum iron quota (only with DARWIN_ALLOW_FEQUOTA)
Qfemin	\(Q^{\op{Fe}\min}_j\)	mmol Fe (mmol C)-1	minimum iron quota (only with DARWIN_ALLOW_FEQUOTA)
VmaxNH4	\(V^{\op{NH4}\op{max}}_j\)	mmol N (mmol C)-1 s-1	maximum ammonia uptake rate (only with DARWIN_ALLOW_NQUOTA)
VmaxNO2	\(V^{\op{NO2}\op{max}}_j\)	mmol N (mmol C)-1 s-1	maximum nitrite uptake rate (only with DARWIN_ALLOW_NQUOTA)
VmaxNO3	\(V^{\op{NO3}\op{max}}_j\)	mmol N (mmol C)-1 s-1	maximum nitrate uptake rate (only with DARWIN_ALLOW_NQUOTA)
VmaxN	\(V^{\op{N}\op{max}}_j\)	mmol N (mmol C)-1 s-1	maximum nitrogen uptake rate for diazotrophs (only with DARWIN_ALLOW_NQUOTA)
VmaxPO4	\(V^{\op{PO4}\op{max}}_j\)	mmol P (mmol C)-1 s-1	maximum phosphate uptake rate (only with DARWIN_ALLOW_PQUOTA)
VmaxSiO2	\(V^{\op{SiO2}\op{max}}_j\)	mmol Si (mmol C)-1 s-1	maximum silica uptake rate (only with DARWIN_ALLOW_SIQUOTA)
VmaxFeT	\(V^{\op{Fe}\op{max}}_j\)	mmol Fe (mmol C)-1 s-1	maximum iron uptake rate (only with DARWIN_ALLOW_FEQUOTA)
ksatNH4	\(k^{\op{NH4}}_j\)	mmol N m-3	half-saturation conc. for ammonia uptake/limitation
ksatNO2	\(k^{\op{NO2}}_j\)	mmol N m-3	half-saturation conc. for nitrite uptake/limitation
ksatNO3	\(k^{\op{NO3}}_ji\)	mmol N m-3	half-saturation conc. for nitrate uptake/limitation
ksatPO4	\(k^{\op{PO4}}_j\)	mmol P m-3	half-saturation conc. for phosphate uptake/limitation
ksatSiO2	\(k^{\op{SiO2}}_j\)	mmol Si m-3	half-saturation conc. for silica uptake/limitation
ksatFeT	\(k^{\op{Fe}}_j\)	mmol Fe m-3	half-saturation conc. for iron uptake/limitation
kexcc	\(\kappa^{\op{exc}}_{\op{C} j}\)	s-1	exudation rate for carbon
kexcn	\(\kappa^{\op{exc}}_{\op{N} j}\)	s-1	exudation rate for nitrogen
kexcp	\(\kappa^{\op{exc}}_{\op{P} j}\)	s-1	exudation rate for phosphorus
kexcsi	\(\kappa^{\op{exc}}_{\op{Si} j}\)	s-1	exudation rate for silica
kexcfe	\(\kappa^{\op{exc}}_{\op{Fe} j}\)	s-1	exudation rate for iron
inhibGeider	\(c^{\op{inhib}}_j\)		photo-inhibition coefficient for Geider growth
ksatPAR	\(k^{\op{sat}}_{\op{PAR}}\)	(μEin m-2 s-1)-1	saturation coefficient for PAR (w/o GEIDER)
kinhPAR	\(k^{\op{inh}}_{\op{PAR}}\)	(μEin m-2 s-1)-1	inhibition coefficient for PAR (w/o GEIDER)
mQyield	\(\Phi_j\)	mmol C (μEin)-1	maximum quantum yield
chl2cmax	\(\op{Chl\text{:}C}^{\op{max}}_j\)	mg Chl (mmol C)-1	maximum Chlorophyll-carbon ratio
grazemax	\(g^{\op{max}}_z\)	s-1	maximum grazing rate
kgrazesat	\(k^{\op{graz}}_z\)	mmol C m-3	grazing half-saturation concentration
yield	\({Y_j}\)		bacterial growth yield for all organic matter
yieldO2	\({Y^{{\mathrm{O}}_2}_j}\)		bacterial growth yield for oxygen
yieldNO3	\({Y^{\op{NO}_3}_j}\)		bacterial growth yield for nitrate
ksatPON	\({k^{\op{PON}}}\)	mmol N m-3	half-saturation of PON for bacterial growth
ksatPOC	\({k^{\op{POC}}}\)	mmol C m-3	half-saturation of POC for bacterial growth
ksatPOP	\({k^{\op{POP}}}\)	mmol P m-3	half-saturation of POP for bacterial growth
ksatPOFe	\({k^{\op{POFe}}}\)	mmol Fe m-3	half-saturation of POFe for bacterial growth
ksatDON	\({k^{\op{DON}}}\)	mmol N m-3	half-saturation of DON for bacterial growth
ksatDOC	\({k^{\op{DOC}}}\)	mmol C m-3	half-saturation of DOC for bacterial growth
ksatDOP	\({k^{\op{DOP}}}\)	mmol P m-3	half-saturation of DOP for bacterial growth
ksatDOFe	\({k^{\op{DOFe}}}\)	mmol Fe m-3	half-saturation of DOFe for bacterial growth

Table 8.71 Trait matrices for grazing; indices (prey, pred)

Trait	Symbol	Units	Description
palat	\(p_{j,z}\)		palatability matrix
asseff	\(a_{j,z}\)		assimilation efficiency matrix
ExportFracPreyPred	\(f^{\op{exp}\op{graz}}_{j,z}\)		fraction of unassimilated prey becoming particulate organic matter

Table 8.72 Namelist DARWIN_RADTRANS_TRAITS; indices (plankton, waveband)

Trait	Symbol	Units	Description
aphy_chl	\(a^{\op{chl}}_{\op{phy}}\)	m2 (mg Chl)-1	phytoplankton Chl-specific absorption coefficient
aphy_chl_ps	\(a^{\op{chl}}_{\op{ps}}\)	m2 (mg Chl)-1	part of aphy_chl that is used in photosynthesis
aphy_mgC	\(a^{\op{mgC}}_{\op{phy}}\)	m2 (mg C)-1	plankton carbon-specific absorption coefficient
bphy_mgC	\(b^{\op{mgC}}_{\op{phy}}\)	m2 (mg C)-1	carbon-specific total scattering coefficient
bbphy_mgC	\(b^{\op{mgC}}_{\op{b}\op{phy}}\)	m2 (mg C)-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,

\[\mathrm{trait}_j = a_g \cdot V_j^{b_g}\]

with per-group scaling coefficients \(a_g\) and \(b_g\).

The volumes \(V_j\) of all types can be set in four ways (in order or decreasing precedence),

\[\begin{split}V_j = \begin{cases} \op{grp\_biovol(i,g)} & \\ V_{\log}(\op{grp\_biovolind(i,g)}) \\ V_{\log}(\op{logvol0ind(g)}+i-1) \\ V_{0 g} f_g^{i-1} \end{cases}\end{split}\]

where \(i\) is the index of type \(j\) within the functional group. \(V_{\log}\) is a series of volumes, evenly spaced in log space and defined by parameters \(B=\op{logvolbase}\) and \(I=\op{logvolinc}\),

\[V_{\log} = 10^B, 10^{B+I}, 10^{B+2I}, \dots\]

and \(V_{0 g}=\op{biovol0(g)}\) and \(f_g=\op{biovolfac(g)}\).

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 \(b\) 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.

Table 8.73 Namelist DARWIN_TRAIT_PARAMS

Trait	a	Default	b	Default
isPhoto	grp_photo	1
bactType	grp_bacttype	0
isAerobic	grp_aerobic	0
isDenit	grp_denit	0
isPred	grp_pred	0
isPrey	grp_prey	1
hasSi	grp_hasSi	0
hasPIC	grp_hasPIC	0
diazo	grp_diazo	0
useNH4	grp_useNH4	1
useNO2	grp_useNO2	1
useNO3	grp_useNO3	1
combNO	grp_combNO	1
aptype	grp_aptype	0
tempMort	grp_tempMort	1
tempMort2	grp_tempMort2	1
tempGraz	grp_tempGraz	1
Xmin	a_Xmin	0
R_NC	a_R_NC	16/120
R_PC	a_R_PC	1/120
R_SiC	a_R_SiC	0
R_FeC	a_R_FeC	1D-3/120
R_ChlC	a_R_ChlC	16/120
R_PICPOC	a_R_PICPOC	0.8
ExportFracMort	a_ExportFracMort	0.5
ExportFracMort2	a_ExportFracMort2	0.5
ExportFracExude	a_ExportFracExude	UNINIT
mort	a_mort	0.02 / day
mort2	a_mort2	0
phytoTempCoeff	a_phytoTempCoeff	1/3
phytoTempExp1	a_phytoTempExp1	1.04
phytoTempAe	a_phytoTempAe	0.0438
phytoTempExp2	a_phytoTempExp2	0.001
phytoTempOptimum	a_phytoTempOptimum	2
phytoDecayPower	a_phytoDecayPower	4
hetTempAe	a_hetTempAe	0.0438
hetTempExp2	a_hetTempExp2	0.001
hetTempOptimum	a_hetTempOptimum	2
hetDecayPower	a_hetDecayPower	4
grazTempAe	a_grazTempAe	0.0438
grazTempExp2	a_grazTempExp2	0.001
grazTempOptimum	a_grazTempOptimum	2
grazDecayPower	a_grazDecayPower	4
mQyield	a_mQyield	75D-6
chl2cmax	a_chl2cmax	.3
inhibGeider	a_inhibGeider	0
ksatPAR	a_ksatPAR	0.012
kinhPAR	a_kinhPAR	6D-3
amminhib	a_amminhib	4.6
acclimtimescl	a_acclimtimescl	1/(20 days)
	a_acclimtimescl_denom	1
ksatPON	a_ksatPON	1
ksatDON	a_ksatDON	1
grazemax	a_grazemax	21.9 / day	b_grazemax	-0.16
	a_grazemax_denom	1
kgrazesat	a_kgrazesat	1.00	b_kgrazesat	0.00
biosink	a_biosink	0.28D-1 / day	b_biosink	0.39
	a_biosink_denom	1
bioswim	a_bioswim	0.00 / day	b_bioswim	0.18
	a_bioswim_denom	1
palat	a_ppSig	1	see note 2
palat	a_ppOpt	1024	b_ppOpt	0.00
palat	palat_min	0
PCmax	a_PCmax	1.00 / day	b_PCmax	-0.15
	a_PCmax_denom	1
qcarbon	a_qcarbon	1.80D-11	b_qcarbon	0.94
respRate	a_respRate_c	0.00	b_respRate_c	0.93
	a_respRate_c_denom	1	see note 3
kexcc	a_kexcC	0.00	b_kexcC	-0.33
vmaxNO3	a_vmaxNO3	0.51 / day	b_vmaxNO3	-0.27
	a_vmaxNO3_denom	1
ksatNO3	a_ksatNO3	0.17	b_ksatNO3	0.27
Qnmin	a_Qnmin	0.07	b_Qnmin	-0.17
Qnmax	a_Qnmax	0.25	b_Qnmax	-0.13
kexcn	a_kexcN	0.00	b_kexcN	-0.33
vmaxNO2	a_vmaxNO2	0.51 / day	b_vmaxNO2	-0.27
	a_vmaxNO2_denom	1
ksatNO2	a_ksatNO2	0.17	b_ksatNO2	0.27
	a_ksatNO2fac	1	used for eff.ksat
vmaxNH4	a_vmaxNH4	0.26 / day	b_vmaxNH4	-0.27
	a_vmaxNH4_denom	1
ksatNH4	a_ksatNH4	0.85D-1	b_ksatNH4	0.27
	a_ksatNH4fac	0.5	used for eff.ksat
vmaxN	a_vmaxN	1.28 / day	b_vmaxN	-0.27
	a_vmaxN_denom	1
vmaxPO4	a_vmaxPO4	0.77D-1 / day	b_vmaxPO4	-0.27
	a_vmaxPO4_denom	1
ksatPO4	a_ksatPO4	0.26D-1	b_ksatPO4	0.27
Qpmin	a_Qpmin	2.00D-3	b_Qpmin	0.00
Qpmax	a_Qpmax	0.01	b_Qpmax	0.00
kexcp	a_kexcP	0.24D-1 / day	b_kexcP	-0.33
vmaxSiO2	a_vmaxSiO2	0.77D-1 / day	b_vmaxSiO2	-0.27
	a_vmaxSiO2_denom	1
ksatSiO2	a_ksatSiO2	0.24D-1	b_ksatSiO2	0.27
Qsimin	a_Qsimin	2.00D-3	b_Qsimin	0.00
Qsimax	a_Qsimax	4.00D-3	b_Qsimax	0.00
kexcsi	a_kexcSi	0.00 / day	b_kexcSi	0.00
vmaxFeT	a_vmaxFeT	14D-6 / day	b_vmaxFeT	-0.27
	a_vmaxFeT_denom	1
ksatFeT	a_ksatFeT	80D-6	b_ksatFeT	0.27
Qfemin	a_Qfemin	1.50D-6	b_Qfemin	0.00
Qfemax	a_Qfemax	80D-6	b_Qfemax	0.00
kexcfe	a_kexcFe	0.00 / day	b_kexcFe	0.00
ExportFracPreyPred	grp_ExportFracPreyPred	0.5	(nGroup \(\times\) nGroup)
asseff	grp_ass_eff	0.7	(nGroup \(\times\) nGroup)
aphy_chl	aphy_chl_type	read	via grp_aptype
aphy_chl_ps	aphy_chl_ps_type	read	via grp_aptype
aphy_mgC	aphy_mgC_type	read	via grp_aptype
bphy_mgC	bphy_mgC_type	read	via grp_aptype
bbphy_mgC	bbphy_mgC_type	read	via grp_aptype

2

Palatabilities are initialized to zero and have to be set in data.traits unless 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 Section 8.7.3.17.

3

The respiration rate follows a different scaling law from other traits. It scales in terms of cellular carbon content, see Section 8.7.3.14.

8.7.3.24. Diagnostics

Table 8.74 Darwin package diagnostic fields

Name	Code	Units	Description
plankC	SMR_____MR	mmol C /m3	Total plankton carbon biomass
Chl	SMR_____MR	mg Chl a /m3	Total Chlorophyll a
PP	SMRP____MR	mmol C /m3/s	Primary Production
Nfix	SMRP____MR	mmol N /m3/s	N fixation
Denit	SMRP____MR	mmol N /m3/s	Denitrification
DenitN	SMRP____MR	mmol N /m3/s	Nitrogen loss due to denitrification
EXU	SM_P____MR	mmol C /m3/s	Carbon exudation
BioSyn	SM_P____MR	mmol C /m3/s	Biosynthesis rate
DmdN	SM_P____MR	mmol C /m3/s	Carbon demand from N limit
DmdP	SM_P____MR	mmol C /m3/s	Carbon demand from P limit
DmdFe	SM_P____MR	mmol C /m3/s	Carbon demand from Fe limit
DmdSi	SM_P____MR	mmol C /m3/s	Carbon demand from Si limit
Dmdmin	SM_P____MR	mmol C /m3/s	Minimum carbon demand
PAR###	SMRP____MR	µEin/m2/s	PAR waveband ###
PARF###	SM_P____LR	µEin/m2/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/m2/s	PAR at top of layer
PAR	SMRP____MR	µEin/m2/s	total PAR at layer center
C_DIN	SMRP____MR	mmol N /m3/s	consumption of DIN: \(\sum_j(U^{\op{NO3}}_j+U^{\op{NO2}}_j+U^{\op{NH4}}_j)\)
C_NO3	SMRP____MR	mmol N /m3/s	consumption of NO3: \(\sum_j U^{\op{NO3}}_j\)
C_NO2	SMRP____MR	mmol N /m3/s	consumption of NO2: \(\sum_j U^{\op{NO2}}_j\)
C_NH4	SMRP____MR	mmol N /m3/s	consumption of NH4: \(\sum_j U^{\op{NH4}}_j\)
C_PO4	SMRP____MR	mmol P /m3/s	consumption of PO4: \(\sum_j U^{\op{PO4}}_j\)
C_Si	SMRP____MR	mmol Si /m3/s	consumption of Si: \(\sum _j U^{\op{SiO2}}_j\)
C_Fe	SMRP____MR	mmol Fe /m3/s	consumption of Fe: \(\sum_j U^{\op{Fe}}_j\)
S_DIN	SMR_____MR	mmol N /m3/s	non-transport source of DIN: \(r_{\op{DON}}\op{DON}+[r_{\op{PON}}\op{PON}]-D_{\op{NH4}}-D_{\op{NO3}}\)
S_NO3	SMR_____MR	mmol N /m3/s	non-transport source of NO3
S_NO2	SMR_____MR	mmol N /m3/s	non-transport source of NO2
S_NH4	SMR_____MR	mmol N /m3/s	non-transport source of NH4
S_PO4	SMR_____MR	mmol P /m3/s	non-transport source of PO4: \(r_{\op{DOP}}\op{DOP}+[r_{\op{POP}}\op{POP}]\)
S_Si	SMR_____MR	mmol Si /m3/s	non-transport source of Si: \(r_{\op{POSi}}\op{POSi}\)
S_Fe	SMR_____MR	mmol Fe /m3/s	non-transport source of Fe: \(r_{\op{DOFe}}\op{DOFe}+[r_{\op{POFe}}\op{POFe}]+S_{\op{Fe}}\)
gDAR##	SMR_____MR	[TRAC##]/s	ptracer ## tendency from DARWIN 4
gECO##	SMR_____MR	[TRAC##]/s	ptracer ## tendency from DARWIN w/o sink/swim 4
PP####	SMRP____MR	mmol C /m3/s	Primary Production plankton ####
PC####	SMRP____MR	1/s	Carbon-specific phototrophic growth rate plankton ####
HP####	SMRP____MR	mmol C /m3/s	Heterotrophic production plankton ####
HC####	SMRP____MR	1/s	Carbon-specific heterotrophic growth rate plankton ####
GR####	SMRP____MR	mmol C /m3/s	Grazing loss of plankton ####
GrGn####	SMRP____MR	mmol C /m3/s	Grazing gain of plankton ####
GrGC####	SMRP____MR	1/s	Carbon-specific grazing rate plankton ####
EXU####	SMRP____MR	mmol C /m3/s	Exudation plankton ####
BS####	SMRP____MR	mmol C /m3/s	Biosynthesis rate plankton ####
DN####	SMRP____MR	mmol C /m3/s	Carbon demand from N limit plankton ####
DP####	SMRP____MR	mmol C /m3/s	Carbon demand from P limit plankton ####
DFe####	SMRP____MR	mmol C /m3/s	Carbon demand from Fe limit plankton ####
DSi####	SMRP____MR	mmol C /m3/s	Carbon demand from Si limit plankton ####
Dmin####	SMRP____MR	mmol C /m3/s	Minimum carbon demand plankton ####
sfcSolFe	SM_P____L1	mmol Fe /m2/s	Soluble iron input at sea surface
scvLosFe	SMRP____MR	mmol Fe /m3/s	Iron loss from scavenging
scavRate	SMRP____MR	1/s	Iron scavenging rate
sedFe	SMRP____MR	mmol Fe /m3/s	Iron input from sediment
freeFeLs	SMRP____MR	mmol Fe /m3/s	Iron loss due to free iron limit
sedFlxFe	SM_P____U1	mmol Fe /m2/s	Iron sediment flux
gDICEpr	SM______L1	mmol C /m3/s	Tendency of DIC due to E/P/runoff
gNO3Epr	SM______L1	mmol N /m3/s	Tendency of DIC due to E/P/runoff
gNO2Epr	SM______L1	mmol N /m3/s	Tendency of DIC due to E/P/runoff
gNH4Epr	SM______L1	mmol N /m3/s	Tendency of DIC due to E/P/runoff
gPO4Epr	SM______L1	mmol P /m3/s	Tendency of PO4 due to E/P/runoff
gFeTEpr	SM______L1	mmol Fe /m3/s	Tendency of FeT due to E/P/runoff
gSiO2Epr	SM______L1	mmol Si /m3/s	Tendency of SiO2 due to E/P/runoff
gALKEpr	SM______L1	meq/m3/s	Tendency of ALK due to E/P/runoff
gO2Epr	SM______L1	mmol O2 /m3/s	Tendency of O2 due to E/P/runoff
surfPAR	SM_P____L1	µEin/m2/s	PAR forcing at surface
surfiron	SM_P____L1	mmol Fe /m2/s	iron forcing at surface
DARice	SM_P____L1	m2/m2	ice area fraction
DARwind	SM_P____L1	m/s	wind speed used for carbon exchange
surfpCO2	SM_P____L1	mol/mol	atmospheric surface pCO2

4(1,2)

does not include free iron adjustment for FeT tracer

Diagnostics related to carbon chemistry are listed in Section 8.7.3.12.3.

Also of interest are the following diagnostics from the ptracers and gchem packages:

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 Section 8.3.3.4 for value larger than 99.

8.7.3.25. Call Tree

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