import pickle
from pathlib import Path

with open(Path("/tmp/ci_case.pkl"), "rb") as f:
    ci_data = pickle.load(f)
grid = ci_data["grid"]
topo = ci_data["topo"]
vgrid = ci_data["vgrid"]
caseroot = ci_data["caseroot"]
inputdir = ci_data["inputdir"]

Add Chlorophyll Files to the Run¶

MOM6 can take chlorophyll data as a file in the regional domain. It impacts shortwave penetration. MOM6 parameters that are impacted by it CHL_FROM_FILE, CHL_FILE, VAR_PEN_SW, and PEN_SW_NBANDS. In our workflow, we take raw data from SeaWIFS, process it globally, and subset to our regional domain.

Chlorophyll can be added into a CrocoDash case, using functions from mom6_bathy and called from configure_forcings. There is one parameter in configure forcings and three parameters in MOM6

CrocoDash Parameters¶

In case.configure_forcings(), the argument chl_processed_filepath takes in a processed global chlorophyll file. The global processed chlorophyll file is hosted on the CESM inputdata svn server under ocn/mom/croc/chl/data and can be accessed through the CrocoDash raw_data_access module like below:

from CrocoDash.raw_data_access.datasets import seawifs as sw
sw.get_processed_global_seawifs_script_for_cli(
    output_folder="<insert_dir>",
    output_filename="get_seawifs_data.sh"
)

The file path of the global file (after running the script from the code block) can be passed into configure forcings as shown in this demo

case.configure_forcings(
    date_range = ["2020-01-01 00:00:00", "2020-01-09 00:00:00"],
    chl_file = "<CHL_PROCESSED>",
)