A comprehensive reference table of parameters used in the Simstrat-AED2 configuration, including their default (template) values, units, and a brief description of each parameter's role.
Format
A data frame with columns:
- module
The model module the parameter belongs to.
- group
A functional grouping of the parameter within the module.
- parameter
The parameter's name as it appears in the configuration file (
simstrat.paroraed2.nml).- label
A short human-readable label for the parameter.
- symbol
A mathematical symbol for the parameter, where applicable.
- description
A description of the parameter's role in the model.
- units
The units of the parameter.
- default
The default (template) value of the parameter.
- source
A URL for further information about the parameter.
The physical (hydrodynamic) parameters configure Simstrat's seiche
(internal wave) energy, wind drag, bottom drag, surface heat fluxes,
light absorption, and ice/snow dynamics – described in Table 1 of the
Simstrat User Manual. Default values are those in AEME's bundled
inst/extdata/simstrat_aed2/simstrat.par template.
The AED2 (Aquatic EcoDynamics) parameters configure the biogeochemical
modules coupled to Simstrat: oxygen, carbon (dissolved inorganic carbon,
pH, methane), silica, inorganic nitrogen, inorganic phosphorus, organic
matter, phytoplankton, and zooplankton. Simstrat-AED2 and GLM-AED couple
to the same underlying AED2 library, so most module/parameter
descriptions here are shared with glm_aed_parameter_library
(only the module name prefix differs: "aed2_" here vs.
"aed_" there, matching each model's actual configuration file).
The carbon module has no AED (v1) analogue and is documented directly from
AEME's bundled aed2.nml template.
As with glm_aed_parameter_library, aed2_phytoplankton and
aed2_zooplankton parameters listed under groups such as
"growth", "light", "nitrogen", "phosphorus",
and "silica" are per-group parameters specified in the separate
aed2_phyto_pars.nml/aed2_zoop_pars.nml files rather than
directly in aed2.nml.
Source
Simstrat User Manual and source code: https://github.com/Eawag-AppliedSystemAnalysis/Simstrat
AED Science Manual: https://aquaticecodynamics.github.io/aed-science/
Goudsmit, G-H., Burchard, H., Peeters, F., and Wuest, A. (2002). Application of k-epsilon turbulence models to enclosed basins: The role of internal seiches. Journal of Geophysical Research: Oceans, 107(C12), 23-1–23-13.
Examples
# Load the parameter library
data(simstrat_aed2_parameter_library)
# View the structure
str(simstrat_aed2_parameter_library)
#> tibble [286 × 9] (S3: tbl_df/tbl/data.frame)
#> $ module : chr [1:286] "simstrat" "simstrat" "simstrat" "simstrat" ...
#> $ group : chr [1:286] "site" "site" "seiche" "seiche" ...
#> $ parameter : chr [1:286] "lat" "p_air" "a_seiche" "a_seiche_w" ...
#> $ label : chr [1:286] "Latitude" "Air pressure" "Seiche parameter" "Seiche parameter (winter)" ...
#> $ symbol : chr [1:286] "lat" "p_air" "a_seiche" "a_seiche^w" ...
#> $ description: chr [1:286] "Latitude of the site (used for Coriolis force and albedo calculation)" "Long-term average air pressure at the site" "Fraction of wind energy transferred to seiche (internal wave) energy" "Fraction of wind energy transferred to seiche energy in winter (used instead of a_seiche when N2 < strat_sumr, "| __truncated__ ...
#> $ units : chr [1:286] "deg" "mbar" "-" "-" ...
#> $ default : chr [1:286] "45" "965" "0.00424" "0" ...
#> $ source : chr [1:286] "https://github.com/Eawag-AppliedSystemAnalysis/Simstrat" "https://github.com/Eawag-AppliedSystemAnalysis/Simstrat" "https://github.com/Eawag-AppliedSystemAnalysis/Simstrat" "https://github.com/Eawag-AppliedSystemAnalysis/Simstrat" ...
# List all unique modules
unique(simstrat_aed2_parameter_library$module)
#> [1] "simstrat" "aed2_carbon" "aed2_oxygen"
#> [4] "aed2_nitrogen" "aed2_phosphorus" "aed2_silica"
#> [7] "aed2_phytoplankton" "aed2_organic_matter" "aed2_zooplankton"
# Filter to the physical (hydrodynamic) parameters
simstrat_aed2_parameter_library[simstrat_aed2_parameter_library$module ==
"simstrat", ]
#> # A tibble: 23 × 9
#> module group parameter label symbol description units default source
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 simstrat site lat Latitude lat Latitude o… deg 45 https…
#> 2 simstrat site p_air Air press… p_air Long-term … mbar 965 https…
#> 3 simstrat seiche a_seiche Seiche pa… a_sei… Fraction o… - 0.00424 https…
#> 4 simstrat seiche a_seiche_w Seiche pa… a_sei… Fraction o… - 0 https…
#> 5 simstrat seiche strat_sumr Stratific… N2_th… Brunt-Vais… 1/s2 0 https…
#> 6 simstrat seiche q_nn Seiche en… q_NN Fit parame… - 1.1 https…
#> 7 simstrat seiche seiche_ini Initial s… E_sei… Initial to… J 0 https…
#> 8 simstrat wind f_wind Filtered … f_wind Fit parame… - 1.2193 https…
#> 9 simstrat wind c10 Wind drag… C_10 Wind drag … - 1 https…
#> 10 simstrat mixing cd Bottom dr… C_D Bottom dra… - 0.002 https…
#> # ℹ 13 more rows
# Count parameters per module
table(simstrat_aed2_parameter_library$module)
#>
#> aed2_carbon aed2_nitrogen aed2_organic_matter aed2_oxygen
#> 19 27 60 9
#> aed2_phosphorus aed2_phytoplankton aed2_silica aed2_zooplankton
#> 15 95 7 31
#> simstrat
#> 23