Add Chlorophyll Files to the Run

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

Caution

This method does not do a great job of resolving chlorophyll in estuaries and similar features. If possible, the generated chlorophyll file should be replaced with a better product (which can be done by replacing the file in CHL_FILE).

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_dir="<insert_dir>",
    output_file="get_seawifs_data.sh"
)

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Input In [1], in <cell line: 0>()
      1 from CrocoDash.raw_data_access.datasets import seawifs as sw
----> 2 sw.get_processed_global_seawifs_script_for_cli(
      3     output_dir="<insert_dir>",
      4     output_file="get_seawifs_data.sh"
      5 )

File ~/work/CrocoGallery/CrocoGallery/CrocoDash/CrocoDash/raw_data_access/datasets/seawifs.py:88, in get_processed_global_seawifs_script_for_cli(dates, lat_min, lat_max, lon_min, lon_max, output_dir, output_file)
     57 def get_processed_global_seawifs_script_for_cli(
     58     dates="UNUSED",
     59     lat_min="UNUSED",
   (...)
     64     output_file="processed_seawifs.nc",
     65 ):
     66     """
     67     Downloads chlor_a data from the CESM inputdata repository by generating a script users can run in their terminal.
     68     Parameters
   (...)
     85 
     86     """
---> 88     return utils.write_bash_curl_script(
     89         url="https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/ocn/mom/croc/chl/data/SeaWIFS.L3m.MC.CHL.chlor_a.0.25deg.nc",
     90         script_name="get_processed_seawifs.sh",
     91         output_dir=output_dir,
     92         output_filename=output_file,
     93     )

File ~/work/CrocoGallery/CrocoGallery/CrocoDash/CrocoDash/raw_data_access/datasets/utils.py:22, in write_bash_curl_script(url, script_name, output_dir, output_filename)
     13 full_path = os.path.join(output_dir, output_filename)
     14 script_lines = [
     15     "#!/bin/bash",
     16     "",
   (...)
     19     'echo "Download complete."',
     20 ]
---> 22 with open(full_script_path, "w") as f:
     23     f.write("\n".join(script_lines))
     24 os.chmod(full_script_path, 0o755)  # Make it executable

FileNotFoundError: [Errno 2] No such file or directory: '<insert_dir>/get_processed_seawifs.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>",
)
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