Set up ACCESS-ESM1.5 for Miocene land-sea mask

Earth System Paleoclimate
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This is a work-in-progress guide to setting up ACCESS-ESM1.5 for the Mid-Miocene climate optimum (15 Ma). There are several aspects that are unfinished, but posting here now as it may be useful as a starting point. The scripts referred to here in this github repository and the accompanying files will be added to lg87 on Gadi in the near future. Some of the following is a clone of the README from the github repo, but some additional steps will be added for starting the experiments.

Temporary location is:
/g/data/y99/dkh157/access_esm/bdy_setup/access_esm_miocene

Part 1: Creating the new restart files

1.1 Create the ocean input files

Go into the directory make_ocean. Run the following:

  • make_topog.py : This interpolates the original Miocene topography (0.5 deg resolution) onto the model grid.
  • adjust_topo_mio.py : This gets rid of the isolated ocean grid cells (lakes and narrow straits), and makes a few manual adjustments. The output is topog_mio_v3.nc which is the new ocean bathymetry file.
  • fill_restart_gaps_mio.py : This extrapolates the pre-industrial temperature/salinity restart file onto the new land-seak mask.
  • basin_mask_mio.py : Adjusts basin_mask.nc for the new land-sea mask
  • bgc_restart_mio.py : Adjusts csiro_bgc.res.nc for the new land-sea mask
  • bgc_sediment_mio.py : Adjusts csiro_bgc_sediment.res.nc for the new land-sea mask
  • fix_kmt.py : Adjusts kmt.nc for the new land-sea mask
  • ssw_mio.py : Adjusts ssw_atten_depth.nc for the new land-sea mask

1.2 Create the coupler grids

Go into the directory make_coupler_grids. Run the following:

  • regrid_um_mask.py : Updates the masks.nc for the new land-sea mask (using topog_mio_v3.nc). This also generates landfrac_um1t.nc, which is the fractional land-sea mask for the Miocene.
  • make_scrip_files.ncl : An NCL script to convert the grids and masks into SCRIP files for ESMF
  • run_esmf_regrid.sh : Generates the remapping files using ESMF_RegridWeightGen
  • run_rename_oasis.sh : Renames the remapping files using OASIS conventions for the model

1.3 Create the atmos restart files

Go into the directory make_atmos. Run the following:

  • make_lsm.py : Generates a netcdf file of the new binary land-sea mask called lsm_mio_v3.nc, using the landfrac_um1t.nc fractional land mask.
  • interp_fields_mio.py : Uses nearest neighbour interpolation to create a new atmos restart file on the updated land-sea mask. The new restart file is called restart.mio. This script relies on utility scripts located in:
    /g/data/access/projects/access/apps/pythonlib/umfile_utils/
  • interp_fields_mio_arg.py : This is a command-line script (using argparse) requiring an input and output file of ancillary files. This should be done as in the following:
  • ./interp_fields_mio_arg.py cable_vegfunc_N96.anc cable_vegfunc_N96.anc.mio
  • ./interp_fields_mio_arg.py qrclim.slt qrclim.slt.mio
  • ./interp_fields_mio_arg.py qrclim.smow qrclim.smow.mio
  • ./interp_fields_mio_arg.py qrparm.mask qrparm.mask.mio
  • ./interp_fields_mio_arg.py qrparm.soil_igbp_vg qrparm.soil_igbp_vg.mio

In each case above, the “input” is the pre-industrial ancillary file, and the “output” is the Miocene one.

1.4 Make coupler restart files

Go to directory coupler_inputs. Run the following:

  • fix_a2i_mio.py : Adjusts a2i.nc flux file for the new mask.
  • fix_i2a_mio.py : Adjusts i2a.nc flux file for the new mask.
  • fix_o2i_mio.py : Adjusts o2i.nc flux file for the new mask.

1.5 Make ocean common files

Go to directory oc_common. Run the following:

  • dust_mio.py : Adjusts dust.nc file for new mask.
  • fice_mio.py : Adjusts ocmip2_fice_monthly_om1p5_bc.nc file for the new mask.
  • press_mio.py : Adjusts ocmip2_press_monthly_om1p5_bc.nc file for the new mask.
  • xkw_mio.py : Adjusts ocmip2_xkw_monthly_om1p5_bc.nc file for the new mask.

Part 2 Set up experiment on Gadi

2.1 Clone pre-industrial configuration

First, clone the pre-industrial configuration of ACCESS-ESM1.5.

git clone https://github.com/coecms/esm-pre-industrial.git

You should first test that you can run this, by adapting it to your own project in config.yaml, and then run using
payu run -n 1

2.2 Make a new set of input and restart folders

Create a new set of input and restart folders that you can edit, that mirrors the original structure of inputs. (See config.yaml in the pre-industrial case for a list of input folders that needs to be emulated.)

In my case, I create the input folder:
/g/data/y99/dkh157/access_esm/input/mio_v3
with subfolders
atmosphere, coupler, ice, ocean, start_dump.

And
/g/data/y99/dkh157/access_esm/restart/mio_v3
with subfolders
atmosphere, coupler, ice, ocean

In these folders, you can either copy or soft-link all of the original restart and input files from the pre-industrial configuration, which are at:
/g/data/access/payu/access-esm/input/pre-industrial
and
/g/data/access/payu/access-esm/restart/pre-industrial

In my case, my new experiment has the name mio_v3 instead of pre-industrial. I will use that from here on.

2.3 Replace atmosphere input files

In your your new input/mio_v3/atmosphere folder on gdata, replace the following files:
cable_vegfunc_N96.anc
qrclim.slt
qrclim.smow
qrparm.mask
qrparm.soil_igbp_vg

with the equivalent files with the extension *.mio added to them from Step 1.3.

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