\(\newcommand{\p}[1]{\frac{\partial }{\partial #1}}\) \(\newcommand{\pp}[2]{\frac{\partial #1}{\partial #2}}\) \(\newcommand{\dd}[2]{\frac{d #1}{d #2}}\) \(\newcommand{\h}{\frac{1}{2}}\) \(\newcommand{\op}[1]{\operatorname{#1}}\)
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. Non-spectral Light
- 8.7.3.4. Spectral Light
- 8.7.3.5. Nutrient uptake and limitation
- 8.7.3.6. Chlorophyll synthesis
- 8.7.3.7. Remineralization and Nitrification
- 8.7.3.8. Denitrification
- 8.7.3.9. Dynamic CDOM
- 8.7.3.10. Carbon chemistry
- 8.7.3.11. Iron chemistry
- 8.7.3.12. Mortality and Respiration
- 8.7.3.13. Exudation
- 8.7.3.14. Grazing
- 8.7.3.15. Bacteria
- 8.7.3.16. Temperature dependence
- 8.7.3.17. Sinking and Swimming
- 8.7.3.18. Conservation of chemical elements
- 8.7.3.19. 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 P m–3
mmol C m–3
|
concentration of colored dissolved organic matter
- if #define DARWIN_CDOM_UNITS_CARBON
|
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 |
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.
8.7.3.20. Compiling and Running¶
8.7.3.20.1. 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.
CPP option |
description |
---|---|
enable nitrogen quotas for all plankton |
|
enable phosphorus quotas for all plankton |
|
enable iron quotas for all plankton |
|
enable silica quotas for all plankton |
|
enable chlorophyll quotas for all phototrophs |
|
enable a dynamic CDOM tracer |
|
measure CDOM in units of mmol C/m3 and follow organic carbon instead of phosphorus |
|
enable air-sea carbon exchange and ALK and O\(_2\) tracers |
|
consistently use the total pH scale for carbon chemistry coefficients |
|
enable denitrification code |
|
enable exudation of individual quotas |
|
enable old virtualflux code for DIC and ALK |
|
reduce nitrate uptake by iron limitation factor |
|
allow organic matter to sink into bottom (sedimentize) |
|
compute average PAR in layer, assuming exponential decay (%) |
|
enable GEIDER light code (required for radtrans) |
|
use ρ instead of acclimated Chl:C for chlorophyll synthesis |
|
initialize chlorophyll as in darwin2 |
|
scattering coefficients are per Chlorophyll |
|
make diagnostics for instrinsic optical properties available |
|
enable quadratic grazing as in darwin2+quota |
|
compute palatability from size ratios |
|
turn off grazing temperature dependence |
|
turn off all temperature dependence |
|
select temperature version: 1, 2 or 3 |
|
restrict phytoplankton growth to a temperature range |
|
restrict maximum free iron (sic) |
|
enable particle scavenging code |
|
enable variable iron sediment source |
|
enable per-type diagnostics PP####, GR####, GrGn#### |
|
turn on debugging output |
|
compute and print global element totals |
|
value for unused traits |
The following options are used for random trait generation (as in darwin2):
CPP option |
description |
---|---|
assign traits based on random numbers as in darwin2 |
|
set traits for darwin2 2-species setup (requires DARWIN_RANDOM_TRAITS) |
|
set traits for darwin2 9-species setup (requires DARWIN_RANDOM_TRAITS) |
|
enable diazotrophy when using DARWIN_RANDOM_TRAITS |
Random trait generation is supported mainly for backwards compatibility.
8.7.3.20.2. 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 |
---|---|
parameters related to forcing and initialization |
|
parameters for interpolation of forcing fields (only used if USE_EXF_INTERPOLATION is defined) |
|
general parameters (not per-plankton traits) |
|
parameters for dynamic CDOM |
|
parameters for radiative transer |
|
parameters for randomly generated traits (deprecated) |
|
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:
Name |
Default |
Description |
---|---|---|
.FALSE. |
whether to use model shortwave radiation for light |
|
.FALSE. |
whether to use ice area from the seaice package |
|
.FALSE. |
whether to use wind speed from the exf package |
The forcing fields are:
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 |
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 |
The parameters darwin_inscal_«Name» can be used to convert units. Some examples are given in Table 8.53.
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 |
Each forcing field has a set of parameters in DARWIN_FORCING_PARAMS. These work as in the exf package, see Table 8.10. For instance, for PAR they are:
Name |
Default |
Description |
---|---|---|
‘ ‘ |
filename; if left empty no file will be read; PARconst will be used instead |
|
0.0 |
constant that will be used if no file is read |
|
0.0 |
interval in seconds between two records |
|
repeat cycle in seconds; only available if useExfYearlyFields is .FALSE. |
||
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 |
|
0 |
date/time of first record when using the cal package; format: YYYYMMDD; start year (YYYY), month (MM), day (YY) |
|
0 |
format: HHMMSS; start hour (HH), minute (MM), second(SS) |
|
0.0 |
can be used to remove global mean |
|
0.0 |
can be used to remove global trend |
|
‘c’ |
grid point for masking: ‘ ‘ = no masking; ‘c’ = centered mask; ‘w’ = western mask; ‘s’ = southern |
|
1.0 |
optional rescaling of input fields to adjust units |
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:
Name |
Default |
Units |
Description |
---|---|---|---|
0 |
seed for random number generator (for DARWIN_RANDOM_TRAITS) |
||
.FALSE. |
stop instead of issuing warnings |
||
1 |
index in x dimension for debug prints |
||
1 |
index in y dimension for debug prints |
||
1 |
index in z dimension for debug prints |
||
pickup suffix for darwin; set to ‘ ‘ to disable reading at PTRACERS_Iter0 |
|||
.FALSE. |
correct non-conservation due to linear free surface (globally) |
||
.FALSE. |
initial conditions for plankton biomass are in mmol P/m3 |
||
.FALSE. |
Initialize Chlorophyll to a balanced value following Geider |
||
0 |
Iteration number when to initialize Chlorophyll |
||
4D-2 |
1/m |
atten coefficient water |
|
4D-2 |
m2/mg Chl |
atten coefficient chl |
|
0.4 |
fraction Qsw that is PAR |
||
1/0.2174 |
μEin/s/W |
conversion from W/m2 to μEin/m2/s |
|
0.3 |
set temperature function (was 1.0) |
||
-4000.0 |
K |
slope for pseudo-Arrhenius (TEMP_VERSION 2) |
|
293.15 |
K |
reference temp for pseudo-Arrhenius (TEMP_VERSION 2) |
|
0.5882 |
pre-factor for pseudo-Arrhenius (TEMP_VERSION 2) |
||
0.0438 |
1/K |
temperature coefficient for remineralization (TEMP_VERSION 4) |
|
0.0438 |
1/K |
temperature coefficient for linear mortality (TEMP_VERSION 4) |
|
0.0438 |
1/K |
temperature coefficient for quadr. mortality (TEMP_VERSION 4) |
|
0.0 |
1/K |
temperature coefficient for uptake (TEMP_VERSION 4) |
|
0.04 |
solubility of Fe dust |
||
0.4/year |
1/s |
fixed iron scavenging rate |
|
1D-3 |
mol/m3 |
total ligand concentration |
|
2D5 |
m3/mol |
ligand stability rate ratio |
|
0.4D-3 |
mol/m3 |
max concentration of free iron |
|
0.005 / day |
1/s |
rate of POM-based iron scavenging |
|
0.079 |
intercept of scavenging power law |
||
0.58 |
exponent of scavenging power law |
||
1.1321D-4 |
mmol P / mmol C |
POP:POC ratio for DARWIN_PART_SCAV_POP |
|
-1.0 |
m |
depth above which to add sediment source (was -1000) |
|
1D-3 / day |
mmol Fe /m2/s |
fixed iron flux from sediment |
|
0.68D-3 |
mmol Fe / mmol C |
iron input per POC sinking into bottom for DARWIN_IRON_SED_SOURCE_VARIABLE |
|
0.5D-3 / day |
mmol Fe /s |
min iron input rate subtracted from fesedflux_pcm*wc_sink*POC |
|
106 |
mmol C / mmol P |
POC:POP conversion for DARWIN_IRON_SED_SOURCE_POP |
|
1/(0.5 days) |
1/s |
ammonia oxidation rate |
|
1/(10 days) |
1/s |
nitrite oxidation rate |
|
10 |
μEin/m2/s |
critical light level after which oxidation starts |
|
1/(100 days) |
1/s |
DOC remineralization rate |
|
1/(100 days) |
1/s |
DON remineralization rate |
|
1/(100 days) |
1/s |
DOP remineralization rate |
|
1/(100 days) |
1/s |
DOFe remineralization rate |
|
1/(50 days) |
1/s |
POC remineralization rate |
|
1/s |
POP remineralization rate |
||
1/s |
PON remineralization rate |
||
1/s |
POFe remineralization rate |
||
1/(300 days) |
1/s |
POSi remineralization rate |
|
10/day |
m/s |
sinking velocity for POC |
|
m/s |
sinking velocity for POP |
||
m/s |
sinking velocity for PON |
||
m/s |
sinking velocity for POFe |
||
m/s |
sinking velocity for POSi |
||
15/day |
m/s |
sinking velocity for PIC |
|
1/(300 days) |
1/s |
dissolution rate for PIC |
|
170 |
mmol O2 / mmol P |
O:P ratio for respiration and consumption |
|
170/120.0 |
mmol O2 / mmol C |
NOT USED |
|
1 / 1024.5 |
m3/kg |
constant for converting per kg to per m^3 |
|
4.0 |
ppt |
limits for carbon solver input at initialization |
|
50.0 |
ppt |
… |
|
-4.0 |
°C |
||
39.0 |
°C |
||
10.0 |
mmol C m-3 |
||
4000.0 |
mmol C m-3 |
||
10.0 |
meq m-3 |
||
4000.0 |
meq m-3 |
||
1D-10 |
mmol P m-3 |
||
10.0 |
mmol P m-3 |
||
1D-8 |
mmol Si m-3 |
||
500.0 |
mmol Si m-3 |
||
4.0 |
ppt |
limits for carbon solver input during run |
|
50.0 |
ppt |
… |
|
-4.0 |
°C |
||
39.0 |
°C |
||
400.0 |
mmol C m-3 |
||
4000.0 |
mmol C m-3 |
||
400.0 |
meq m-3 |
||
4000.0 |
meq m-3 |
||
1D-10 |
mmol P m-3 |
||
10.0 |
mmol P m-3 |
||
1D-8 |
mmol Si m-3 |
||
500.0 |
mmol Si m-3 |
||
1 |
reduce tracer concentrations by this factor on initialization |
||
6.0 |
mmol O2 m-3 |
critical oxygen for O2/NO3 remineralization |
|
120.0 |
mmol N / mmol P |
ratio of n to p in denitrification process |
|
104.0 |
mmol N / mmol P |
ratio of NO3 uptake to phos remineralization in denitrification |
|
1D-2 |
mmol N m-3 |
critical nitrate below which no denit (or remin) happens |
|
0.1 |
μEin/m2/s |
minimum light for photosynthesis; for non-Geider: 1.0 |
|
0.02 |
m2/mg Chl |
Chl-specific absorption coefficient |
|
3.00 |
mg Chl / mmol N |
max Chl:N ratio for Chl synthesis following Moore 2002 |
|
0.0 |
mmol C / mmol N |
cost of biosynthesis |
|
1.0 |
(mmol C m-3)-1 |
inverse decay scale for grazing inhibition |
|
0.0 |
exponent for grazing inhibition (0 to turn off inhibition) |
||
1.0 |
exponent for limiting quota uptake in nutrient uptake |
||
1.0 |
exponent for limiting quota uptake in grazing |
||
1.0 |
grazing exponential 1= “Holling 2”, 2= “Holling 3” |
||
120D-10 |
mmol C m-3 |
minimum total prey conc for grazing to occur |
|
20/day |
1/s |
max DIN uptake rate for denitrifying bacteria |
|
290.82/day |
m3/mmol O2/s |
max O2-specific O2 uptake rate for aerobic bacteria |
|
0.01 |
mmol N m-3 |
half-saturation conc of dissolved inorganic nitrogen |
|
2.0 |
increase in POM needed due to hydrolysis |
||
0.2 |
organic matter yield of aerobic bacteria |
||
yod/467*4/(1-yod)*106 |
energy yield of aerobic bacteria |
||
0.16 |
organic matter yield of denitrifying bacteria |
||
ynd/467*5/(1-ynd)*106 |
energy yield of denitrifying bacteria |
Name |
Default |
Units |
Description |
---|---|---|---|
2 / 100 |
fraction of remineralized POP contributing to CDOM |
||
1 / (200 days) |
1/s |
CDOM degradation rate |
|
1 / (15 days) |
1/s |
CDOM bleaching rate |
|
20 |
μEin/m2/s |
PAR where CDOM bleaching becomes maximal |
|
16 |
mmol N / mmol P |
CDOM N:P ratio (with #undef DARWIN_CDOM_UNITS_CARBON) |
|
1D-3 |
mmol Fe / mmol P |
CDOM Fe:P ratio (with #undef DARWIN_CDOM_UNITS_CARBON) |
|
120 |
mmol C / mmol P |
CDOM C:P ratio (with #undef DARWIN_CDOM_UNITS_CARBON) |
|
16/120 |
mmol N / mmol C |
CDOM N:C ratio (with #define DARWIN_CDOM_UNITS_CARBON) |
|
1/120 |
mmol P / mmol C |
CDOM P:C ratio (with #define DARWIN_CDOM_UNITS_CARBON) |
|
1D-3/120 |
mmol Fe / mmol C |
CDOM Fe:C ratio (with #define DARWIN_CDOM_UNITS_CARBON) |
|
100.0 |
m2 / mmol P |
P-specific absorption coefficient of CDOM at \(\lambda_{\op{CDOM}}\) |
|
100/120 |
m2 / mmol C |
|
Name |
Default |
Units |
Description |
---|---|---|---|
‘ ‘ |
filename for reading water absorption and scattering spectra |
||
‘ ‘ |
filename for reading plankton absorption and scattering spectra |
||
‘ ‘ |
filename for reading particle absorption and scattering spectra |
||
1D-15 |
mmol P/particle |
conversion factor for particle absorption and scattering spectra |
|
0.0002 |
1/m |
minimum backscattering ratio |
|
0.5 |
backscattering ratio of water |
||
450.0 |
nm |
reference wavelength for CDOM absorption spectra |
|
0.014 |
1/nm |
coefficient for CDOM absorption spectra |
|
0.2 |
factor for computing aCDOM from water+Chlorophyll absorption |
||
0.0 |
mmol P/m3 |
recalcitrant CDOM concentration |
|
0.0 |
mmol C/m3 |
|
|
0.0 |
mmol C/m3 |
recalcitrant POC concentration |
|
.FALSE. |
enable/disable allometric scaling of plankton absorption and scattering spectra |
||
0.109D-9 |
mg C/cell |
coefficient coefficient for scaling plankton spectra |
|
0.991 |
coefficient coefficient for scaling plankton spectra |
||
-0.075 |
slope for scaled absorption spectra |
||
-1.458 |
slope for scaled backscattering ratio spectra |
||
0 |
log(μm) |
log of size for switching slopes |
|
1.5 |
slope for small plankton |
||
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
:
Trait |
Symbol |
Units |
Description |
---|---|---|---|
isPhoto\(_j\) |
1: does photosynthesis, 0: not |
||
bactType\(_j\) |
1: particle associated, 2: free living bacteria, 0: not bacteria |
||
isAerobic\(_j\) |
1: is aerobic bacteria (also set bactType), 0: not |
||
isDenit\(_j\) |
1: is dentrifying bacteria (also set (bactType), 0: not |
||
hasSi\(_j\) |
1: uses silica (Diatom), 0: not |
||
hasPIC\(_j\) |
1: calcifying, 0: set R_PICPOC to zero |
||
diazo\(_j\) |
1: use molecular instead of mineral nitrogen, 0: not |
||
useNH4\(_j\) |
1: can use ammonia, 0: not |
||
useNO2\(_j\) |
1: can use nitrite, 0: not |
||
useNO3\(_j\) |
1: can use nitrate, 0: not |
||
combNO\(_j\) |
1: combined nitrite/nitrate limitation, 0: not |
||
isPrey\(_j\) |
1: can be grazed, 0: not |
||
isPred\(_j\) |
1: can graze, 0: not |
||
\(e^{\op{mort}}_j\) |
1: mortality is temperature dependent, 0: turn dependence off |
||
\(e^{\op{mort2}}_j\) |
1: quadratic mortality is temperature dependent, 0: turn dependence off |
||
\(e^{\op{graz}}_j\) |
1: grazing is temperature dependent, 0: turn dependence off |
||
\(c^{\min}_j\) |
mmol C m-3 |
minimum abundance for mortality, respiration and exudation |
|
\(\sigma_1\) |
(mmol N m-3)-1 |
coefficient for NH4 inhibition of NO uptake |
|
\(\tau^{\op{acclim}}\) |
s-1 |
rate of chlorophyll acclimation |
|
\(m^{(1)}_j\) |
s-1 |
linear mortality rate |
|
\(m^{(2)}_j\) |
(mmol C m-3)-1 s-1 |
quadratic mortality coefficient |
|
\(f^{\op{exp}\op{mort}}_j\) |
fraction of linear mortality to POM |
||
\(f^{\op{exp}\op{mort2}}_j\) |
fraction of quadratic mortality to POM |
||
\(f^{\op{exp}\op{exude}}_j\) |
fraction of exudation to POM |
||
\(c_j\) |
see Table 8.47 |
||
\(e_{1j}\) |
exp(1/°C) |
see Table 8.47 |
|
\(A^{\op{phy}}_{\op{e}j}\) |
1/°C |
see Table 8.47 |
|
\(e_{2j}\) |
see Table 8.47 |
||
\(T^{\op{opt}}_j\) |
°C |
see Table 8.47 |
|
\(p_j\) |
see Table 8.47 |
||
\(A^{\op{het}}_{\op{e}j}\) |
1/°C |
see Table 8.47 |
|
\(e^{\op{het}}_{2j}\) |
see Table 8.47 |
||
\(T^{\op{opt het}}_j\) |
°C |
see Table 8.47 |
|
\(p^{\op{het}}_j\) |
see Table 8.47 |
||
\(A^{\op{graz}}_{\op{e}j}\) |
1/°C |
see Table 8.47 |
|
\(e^{\op{graz}}_{2j}\) |
see Table 8.47 |
||
\(T^{\op{opt graz}}_j\) |
°C |
see Table 8.47 |
|
\(p^{\op{graz}}_j\) |
see Table 8.47 |
||
\(R^{\op{N}:\op{C}}_j\) |
mmol N (mmol C)-1 |
nitrogen-carbon ratio (not used with DARWIN_ALLOW_NQUOTA) |
|
\(R^{\op{P}:\op{C}}_j\) |
mmol P (mmol C)-1 |
phosphorus-carbon ratio (not used with DARWIN_ALLOW_PQUOTA) |
|
\(R^{\op{Si}:\op{C}}_j\) |
mmol Si (mmol C)-1 |
silica-carbon ratio (not used with DARWIN_ALLOW_SIQUOTA) |
|
\(R^{\op{Fe}:\op{C}}_j\) |
mmol Fe (mmol C)-1 |
iron-carbon ratio (not used with DARWIN_ALLOW_FEQUOTA) |
|
\(R^{\op{chl}c}_j\) |
mg Chl (mmol C)-1 |
chlorophyll-carbon ratio (not used with DARWIN_ALLOW_CHLQUOTA) |
|
\(R^{\op{PICPOC}}_j\) |
mmol PIC (mmol POC)-1 |
inorganic-organic carbon ratio |
|
\(w^{\op{sink}}_j\) |
m s-1 |
sinking velocity (positive downwards) |
|
\(w^{\op{swim}}_j\) |
m s-1 |
upward swimming velocity (positive upwards) |
|
\(r^{\op{resp}}_j\) |
s-1 |
respiration rate |
|
\(P^{\op{max}}_{\op{C},j}\) |
s-1 |
maximum carbon-specific growth rate |
|
\(Q^{\op{N}\op{max}}_j\) |
mmol N (mmol C)-1 |
maximum nitrogen quota (only with DARWIN_ALLOW_NQUOTA) |
|
\(Q^{\op{N}\min}_j\) |
mmol N (mmol C)-1 |
minimum nitrogen quota (only with DARWIN_ALLOW_NQUOTA) |
|
\(Q^{\op{P}\op{max}}_j\) |
mmol P (mmol C)-1 |
maximum phosphorus quota (only with DARWIN_ALLOW_PQUOTA) |
|
\(Q^{\op{P}\min}_j\) |
mmol P (mmol C)-1 |
minimum phosphorus quota (only with DARWIN_ALLOW_PQUOTA) |
|
\(Q^{\op{Si}\op{max}}_j\) |
mmol Si (mmol C)-1 |
maximum silica quota (only with DARWIN_ALLOW_SIQUOTA) |
|
\(Q^{\op{Si}\min}_j\) |
mmol Si (mmol C)-1 |
minimum silica quota (only with DARWIN_ALLOW_SIQUOTA) |
|
\(Q^{\op{Fe}\op{max}}_j\) |
mmol Fe (mmol C)-1 |
maximum iron quota (only with DARWIN_ALLOW_FEQUOTA) |
|
\(Q^{\op{Fe}\min}_j\) |
mmol Fe (mmol C)-1 |
minimum iron quota (only with DARWIN_ALLOW_FEQUOTA) |
|
\(V^{\op{NH4}\op{max}}_j\) |
mmol N (mmol C)-1 s-1 |
maximum ammonia uptake rate (only with DARWIN_ALLOW_NQUOTA) |
|
\(V^{\op{NO2}\op{max}}_j\) |
mmol N (mmol C)-1 s-1 |
maximum nitrite uptake rate (only with DARWIN_ALLOW_NQUOTA) |
|
\(V^{\op{NO3}\op{max}}_j\) |
mmol N (mmol C)-1 s-1 |
maximum nitrate uptake rate (only with DARWIN_ALLOW_NQUOTA) |
|
\(V^{\op{N}\op{max}}_j\) |
mmol N (mmol C)-1 s-1 |
maximum nitrogen uptake rate for diazotrophs (only with DARWIN_ALLOW_NQUOTA) |
|
\(V^{\op{PO4}\op{max}}_j\) |
mmol P (mmol C)-1 s-1 |
maximum phosphate uptake rate (only with DARWIN_ALLOW_PQUOTA) |
|
\(V^{\op{SiO2}\op{max}}_j\) |
mmol Si (mmol C)-1 s-1 |
maximum silica uptake rate (only with DARWIN_ALLOW_SIQUOTA) |
|
\(V^{\op{Fe}\op{max}}_j\) |
mmol Fe (mmol C)-1 s-1 |
maximum iron uptake rate (only with DARWIN_ALLOW_FEQUOTA) |
|
\(k^{\op{NH4}}_j\) |
mmol N m-3 |
half-saturation conc. for ammonia uptake/limitation |
|
\(k^{\op{NO2}}_j\) |
mmol N m-3 |
half-saturation conc. for nitrite uptake/limitation |
|
\(k^{\op{NO3}}_ji\) |
mmol N m-3 |
half-saturation conc. for nitrate uptake/limitation |
|
\(k^{\op{PO4}}_j\) |
mmol P m-3 |
half-saturation conc. for phosphate uptake/limitation |
|
\(k^{\op{SiO2}}_j\) |
mmol Si m-3 |
half-saturation conc. for silica uptake/limitation |
|
\(k^{\op{Fe}}_j\) |
mmol Fe m-3 |
half-saturation conc. for iron uptake/limitation |
|
\(\kappa^{\op{exc}}_{\op{C} j}\) |
s-1 |
exudation rate for carbon |
|
\(\kappa^{\op{exc}}_{\op{N} j}\) |
s-1 |
exudation rate for nitrogen |
|
\(\kappa^{\op{exc}}_{\op{P} j}\) |
s-1 |
exudation rate for phosphorus |
|
\(\kappa^{\op{exc}}_{\op{Si} j}\) |
s-1 |
exudation rate for silica |
|
\(\kappa^{\op{exc}}_{\op{Fe} j}\) |
s-1 |
exudation rate for iron |
|
\(c^{\op{inhib}}_j\) |
photo-inhibition coefficient for Geider growth |
||
\(k^{\op{sat}}_{\op{PAR}}\) |
(μEin m-2 s-1)-1 |
saturation coefficient for PAR (w/o GEIDER) |
|
\(k^{\op{inh}}_{\op{PAR}}\) |
(μEin m-2 s-1)-1 |
inhibition coefficient for PAR (w/o GEIDER) |
|
\(\Phi_j\) |
mmol C (μEin)-1 |
maximum quantum yield |
|
\(\op{Chl\text{:}C}^{\op{max}}_j\) |
mg Chl (mmol C)-1 |
maximum Chlorophyll-carbon ratio |
|
\(g^{\op{max}}_z\) |
s-1 |
maximum grazing rate |
|
\(k^{\op{graz}}_z\) |
mmol C m-3 |
grazing half-saturation concentration |
|
\({Y_j}\) |
bacterial growth yield for all organic matter |
||
\({Y^{{\mathrm{O}}_2}_j}\) |
bacterial growth yield for oxygen |
||
\({Y^{\op{NO}_3}_j}\) |
bacterial growth yield for nitrate |
||
\({k^{\op{PON}}}\) |
mmol N m-3 |
half-saturation of PON for bacterial growth |
|
\({k^{\op{POC}}}\) |
mmol C m-3 |
half-saturation of POC for bacterial growth |
|
\({k^{\op{POP}}}\) |
mmol P m-3 |
half-saturation of POP for bacterial growth |
|
\({k^{\op{POFe}}}\) |
mmol Fe m-3 |
half-saturation of POFe for bacterial growth |
|
\({k^{\op{DON}}}\) |
mmol N m-3 |
half-saturation of DON for bacterial growth |
|
\({k^{\op{DOC}}}\) |
mmol C m-3 |
half-saturation of DOC for bacterial growth |
|
\({k^{\op{DOP}}}\) |
mmol P m-3 |
half-saturation of DOP for bacterial growth |
|
\({k^{\op{DOFe}}}\) |
mmol Fe m-3 |
half-saturation of DOFe for bacterial growth |
Trait |
Symbol |
Units |
Description |
---|---|---|---|
\(p_{j,z}\) |
palatability matrix |
||
\(a_{j,z}\) |
assimilation efficiency matrix |
||
\(f^{\op{exp}\op{graz}}_{j,z}\) |
fraction of unassimilated prey becoming particulate organic matter |
Trait |
Symbol |
Units |
Description |
---|---|---|---|
\(a^{\op{chl}}_{\op{phy}}\) |
m2 (mg Chl)-1 |
phytoplankton Chl-specific absorption coefficient |
|
\(a^{\op{chl}}_{\op{ps}}\) |
m2 (mg Chl)-1 |
part of aphy_chl that is used in photosynthesis |
|
\(a^{\op{mgC}}_{\op{phy}}\) |
m2 (mg C)-1 |
plankton carbon-specific absorption coefficient |
|
\(b^{\op{mgC}}_{\op{phy}}\) |
m2 (mg C)-1 |
carbon-specific total scattering coefficient |
|
\(b^{\op{mgC}}_{\op{b}\op{phy}}\) |
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,
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),
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 \(I=\op{logvolinc}\),
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.
Trait |
a |
Default |
b |
Default |
---|---|---|---|---|
1 |
||||
0 |
||||
0 |
||||
0 |
||||
0 |
||||
1 |
||||
0 |
||||
0 |
||||
0 |
||||
1 |
||||
1 |
||||
1 |
||||
1 |
||||
0 |
||||
1 |
||||
1 |
||||
1 |
||||
0 |
||||
16/120 |
||||
1/120 |
||||
0 |
||||
1D-3/120 |
||||
16/120 |
||||
0.8 |
||||
0.5 |
||||
0.5 |
||||
UNINIT |
||||
0.02 / day |
||||
0 |
||||
1/3 |
||||
1.04 |
||||
0.0438 |
||||
0.001 |
||||
2 |
||||
4 |
||||
0.0438 |
||||
0.001 |
||||
2 |
||||
4 |
||||
0.0438 |
||||
0.001 |
||||
2 |
||||
4 |
||||
75D-6 |
||||
.3 |
||||
0 |
||||
0.012 |
||||
6D-3 |
||||
4.6 |
||||
1/(20 days) |
||||
1 |
||||
1 |
||||
1 |
||||
21.9 / day |
-0.16 |
|||
1 |
||||
1.00 |
0.00 |
|||
0.28D-1 / day |
0.39 |
|||
1 |
||||
0.00 / day |
0.18 |
|||
1 |
||||
1 |
see note 1 |
|||
1024 |
0.00 |
|||
0 |
||||
1.00 / day |
-0.15 |
|||
1 |
||||
1.80D-11 |
0.94 |
|||
0.00 |
0.93 |
|||
1 |
see note 2 |
|||
0.00 |
-0.33 |
|||
0.51 / day |
-0.27 |
|||
1 |
||||
0.17 |
0.27 |
|||
0.07 |
-0.17 |
|||
0.25 |
-0.13 |
|||
0.00 |
-0.33 |
|||
0.51 / day |
-0.27 |
|||
1 |
||||
0.17 |
0.27 |
|||
1 |
used for eff.ksat |
|||
0.26 / day |
-0.27 |
|||
1 |
||||
0.85D-1 |
0.27 |
|||
0.5 |
used for eff.ksat |
|||
1.28 / day |
-0.27 |
|||
1 |
||||
0.77D-1 / day |
-0.27 |
|||
1 |
||||
0.26D-1 |
0.27 |
|||
2.00D-3 |
0.00 |
|||
0.01 |
0.00 |
|||
0.24D-1 / day |
-0.33 |
|||
0.77D-1 / day |
-0.27 |
|||
1 |
||||
0.24D-1 |
0.27 |
|||
2.00D-3 |
0.00 |
|||
4.00D-3 |
0.00 |
|||
0.00 / day |
0.00 |
|||
14D-6 / day |
-0.27 |
|||
1 |
||||
80D-6 |
0.27 |
|||
1.50D-6 |
0.00 |
|||
80D-6 |
0.00 |
|||
0.00 / day |
0.00 |
|||
0.5 |
(nGroup \(\times\) nGroup) |
|||
0.7 |
(nGroup \(\times\) nGroup) |
|||
read |
via grp_aptype |
|||
read |
via grp_aptype |
|||
read |
via grp_aptype |
|||
read |
via grp_aptype |
|||
read |
via grp_aptype |
- 1
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 8.7.3.14.- 2
The respiration rate follows a different scaling law from other traits. It scales in terms of cellular carbon content, see Section 8.7.3.12.
8.7.3.21. Diagnostics¶
Name |
Code |
Units |
Description |
---|---|---|---|
plankC |
|
mmol C /m3 |
Total plankton carbon biomass |
Chl |
|
mg Chl a /m3 |
Total Chlorophyll a |
PP |
|
mmol C /m3/s |
Primary Production |
Nfix |
|
mmol N /m3/s |
N fixation |
Denit |
|
mmol N /m3/s |
Denitrification |
DenitN |
|
mmol N /m3/s |
Nitrogen loss due to denitrification |
PAR### |
|
µEin/m2/s |
PAR waveband ### |
PARF### |
|
µEin/m2/s |
PAR at W point, waveband ### |
a### |
|
1/m |
total absorption for waveband ### |
bt### |
|
1/m |
total scattering for waveband ### |
bb### |
|
1/m |
total backscattering for waveband ### |
aplk### |
|
1/m |
absorption by plankton for waveband ### |
btplk### |
|
1/m |
scattering by plankton for waveband ### |
bbplk### |
|
1/m |
backscattering by plankton for waveband ### |
aprt### |
|
1/m |
absorption by particles for waveband ### |
btprt### |
|
1/m |
scattering by particles for waveband ### |
bbprt### |
|
1/m |
backscattering by particles for waveband ### |
aCDOM### |
|
1/m |
absorption by CDOM for waveband ### |
atten |
|
1 |
attenuation in layer |
PARF |
|
µEin/m2/s |
PAR at top of layer |
PAR |
|
µEin/m2/s |
total PAR at layer center |
C_DIN |
|
mmol N /m3/s |
consumption of DIN: \(\sum_j(U^{\op{NO3}}_j+U^{\op{NO2}}_j+U^{\op{NH4}}_j)\) |
C_NO3 |
|
mmol N /m3/s |
consumption of NO3: \(\sum_j U^{\op{NO3}}_j\) |
C_NO2 |
|
mmol N /m3/s |
consumption of NO2: \(\sum_j U^{\op{NO2}}_j\) |
C_NH4 |
|
mmol N /m3/s |
consumption of NH4: \(\sum_j U^{\op{NH4}}_j\) |
C_PO4 |
|
mmol P /m3/s |
consumption of PO4: \(\sum_j U^{\op{PO4}}_j\) |
C_Si |
|
mmol Si /m3/s |
consumption of Si: \(\sum _j U^{\op{SiO2}}_j\) |
C_Fe |
|
mmol Fe /m3/s |
consumption of Fe: \(\sum_j U^{\op{Fe}}_j\) |
S_DIN |
|
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 |
|
mmol N /m3/s |
non-transport source of NO3 |
S_NO2 |
|
mmol N /m3/s |
non-transport source of NO2 |
S_NH4 |
|
mmol N /m3/s |
non-transport source of NH4 |
S_PO4 |
|
mmol P /m3/s |
non-transport source of PO4: \(r_{\op{DOP}}\op{DOP}+[r_{\op{POP}}\op{POP}]\) |
S_Si |
|
mmol Si /m3/s |
non-transport source of Si: \(r_{\op{POSi}}\op{POSi}\) |
S_Fe |
|
mmol Fe /m3/s |
non-transport source of Fe: \(r_{\op{DOFe}}\op{DOFe}+[r_{\op{POFe}}\op{POFe}]+S_{\op{Fe}}\) |
gDAR## |
|
[TRAC##]/s |
ptracer ## tendency from DARWIN 3 |
gECO## |
|
[TRAC##]/s |
ptracer ## tendency from DARWIN w/o sink/swim 3 |
PP#### |
|
mmol C /m3/s |
Primary Production plankton #### |
PC#### |
|
1/s |
Carbon-specific phototrophic growth rate plankton #### |
HP#### |
|
mmol C /m3/s |
Heterotrophic production plankton #### |
HC#### |
|
1/s |
Carbon-specific heterotrophic growth rate plankton #### |
GR#### |
|
mmol C /m3/s |
Grazing loss of plankton #### |
GrGn#### |
|
mmol C /m3/s |
Grazing gain of plankton #### |
GrGC#### |
|
1/s |
Carbon-specific grazing rate plankton #### |
sfcSolFe |
|
mmol Fe /m2/s |
Soluble iron input at sea surface |
sedFe |
|
mmol Fe /m2/s |
Iron input from sediment |
freeFeLs |
|
mmol Fe /m3/s |
Iron loss due to free iron limit |
pH |
|
1 |
pH |
pCO2 |
|
atm |
Partial Pressure of CO2 |
fugfCO2 |
|
1 |
Fugacity factor of CO2 at surface |
fCO2 |
|
atm |
Fugacity of CO2 (atm) |
fluxCO2 |
|
mmol C /m2/s |
Flux of CO2 - air-sea exch |
fluxO2 |
|
mmol O2 /m2/s |
Flux of O2 - air-sea exch |
VfluxCO2 |
|
mmol C /m2/s |
Virtual flux of CO2 |
VfluxAlk |
|
meq/m2/s |
Virtual flux of alkalinity |
gDICsurf |
|
mmol C /m3/s |
Tendency of DIC due to air-sea exch + oldvirt.flux |
gDICEpr |
|
mmol C /m3/s |
Tendency of DIC due to E/P/runoff |
gALKEpr |
|
mmol eq./m3/s |
Tendency of ALK due to E/P/runoff |
gO2Epr |
|
mmol eq./m3/s |
Tendency of O2 due to E/P/runoff |
gNO3Epr |
|
mmol N /m3/s |
Tendency of DIC due to E/P/runoff |
gNO2Epr |
|
mmol N /m3/s |
Tendency of DIC due to E/P/runoff |
gNH4Epr |
|
mmol N /m3/s |
Tendency of DIC due to E/P/runoff |
gPO4Epr |
|
mmol P /m3/s |
Tendency of PO4 due to E/P/runoff |
gFeTEpr |
|
mmol C /m3/s |
Tendency of FeT due to E/P/runoff |
gSiO2Epr |
|
mmol Si /m3/s |
Tendency of SiO2 due to E/P/runoff |
gALKsurf |
|
meq/m3/s |
Tendency of ALK due to oldvirt.flux |
gO2surf |
|
mmol O2 /m3/s |
Tendency of O2 due to air-sea exch |
C_DIC |
|
mmol C /m3/s |
Consumption of DIC |
C_DICPIC |
|
mmol C /m3/s |
Consumption of DIC due to PIC |
respDIC |
|
mmol C /m3/s |
DIC due to respiration |
rDIC_DOC |
|
mmol C /m3/s |
DIC due to remineralization of DOC |
rDIC_POC |
|
mmol C /m3/s |
DIC due to remineralization of POC |
dDIC_PIC |
|
mmol C /m3/s |
DIC due to dissolution of PIC |
C_ALK |
|
mmol eq./m3/s |
Consumption of alkalinity |
S_ALK |
|
mmol eq./m3/s |
Non-transport source of alkalinity |
C_O2 |
|
mmol O /m3/s |
Consumption of oxygen |
S_O2 |
|
mmol O /m3/s |
Non-transport source of oxygen |
surfPAR |
|
µEin/m2/s |
PAR forcing at surface |
surfiron |
|
mmol Fe /m2/s |
iron forcing at surface |
DARice |
|
m2/m2 |
ice area fraction |
DARwind |
|
m/s |
wind speed used for carbon exchange |
surfpCO2 |
|
mol/mol |
atmospheric surface pCO2 |
apCO2 |
|
atm |
atmospheric pCO2 |
apCO2sat |
|
atm |
atmospheric pCO2 sat |
The sign convention for the fluxCO2, gDICsurf, gALKsurf and gO2surf diagnostics is such that positive values increase the concentration in the ocean. Note that the units vary: gDICsurf, gALKsurf and gO2surf are tracer tendencies, i.e., change rates of concentration, while fluxCO2 is a flux per area of sea surface.
Also of interest are the following diagnostics from the ptracers and gchem packages:
Name |
Code |
Units |
Description |
---|---|---|---|
Tp_g## |
|
[TRAC##]/s |
ptracer ## total transport tendency (before gchem_forcing_sep) |
TRAC## |
|
[TRAC##] |
ptracer ## concentration before transport |
GC_Tr## |
|
[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.
8.7.3.22. 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_radtrans
darwin_light
darwin_insol
darwin_surfforcing_init
darwin_carbon_coeffs
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_forcing_sep
darwin_conserve_surface
darwin_cons
darwin_nut_supply
darwin_forcing
darwin_light_radtrans
darwin_light...
darwin_surfforcing
darwin_carbon_coeffs
darwin_calc_pco2_approx
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
8.7.3.22.1. Differences to darwin2¶
Not up-to-date!
Particulate/dissolved split of plankton mortality products is not allometric or element-dependent as it was in quota.
grazing and mortality temperature dependent with TEMP_VERSION 2.
chl2cmin affects acclim.
Bug fixes:
1e-3 replaced by 1 _d -3 in conversion of tracers for pH solver.