spectra-config: Generate configuration files for MARBL-SPECTRA

MARBL-SPECTRA is an extension of the base marine ecosystem in the Marine Biogeochemistry Library (MARBL) to include 15 plankton: 9 phytoplankton and 6 zooplankton with broad size and trait diversity. These codes generate the runtime-configurable namelist settings for the SPECTRA model, but are written so that one could generate a starting set of parameters for any number of plankton greater than 4 phytoplankton and 2 zooplankton. The codes here also generate initial conditions for the model.

To generate the initial conditions:

cd initial_conditions
./gen_input_dataset.py

This generates a netcdf file that will need to be called in user_nl_pop:

init_ecosys_init_file = 'YOUR_PATH/ecosys_jan_IC_gx1v6_9p6z_20180124_3impCalc.nc'

To generate the namelist settings:

./gen_input_data.R
./gen_marbl_input_data.R

This then generates a namelist file called user_nl_marbl, which needs to be placed in your CASEROOT in order for these settings to take effect.

You can modify parameters in input_parms.R, and generate plots that visualizes the parameters by running analyze_model_setup.R.

The size_structured_ecosystem.R script is a wrapper script that takes one input, a casename, and creates a new copy of the four main R scripts in a new case folder and runs the scripts. This can assist in setting up new parameter cases.

To replicate the settings in Negrete-García et al.:

Add the following to the user_nl_marbl file:

lo2_consumption_scalef = .false.
parm_SiO2_diss =   7.7000000000000000e+04
parm_FeLig_scavenge_rate0 = 1.4
parm_Fe_scavenge_rate0 = 18.0
parm_scalelen_vals(2) = 3.0
parm_scalelen_vals(3) = 4.5
parm_scalelen_vals(4) = 5.5

NB: make sure that the CORE2_IAF datm stream is using coszen for the time interpolation for SWDN, or else the results will be incorrect.

Run configuration: We also recommend changing NTASKS_OCN=324 to optimize the PE layout for the additional ecosystem tracers.

Reference:

Gabriela Negrete-García, Jessica Y. Luo, Matthew C. Long, Keith Lindsay, Michael Levy, Andrew D. Barton. Plankton energy flows using a global size-structured and trait-based model. Preprint. doi: https://doi.org/10.1101/2022.02.01.478546

Contact:

Jessica Luo: jessica.luo [at] noaa.gov
Gaby Negrete-García: g1negret [at] ucsd.edu