Aquaplanet-slab-ocean.md

@@ -173,19 +173,19 @@ Not yet there, but getting close...... Namelist parameters and input forcing fil
 While many input forcing files need to change, this is done by changing the link/pointing. However, to run with slab ocean, you'll need an extra file, the `heatflux` or `qflx` file. This is normally obtained by running a pure aquaplanet run first, and post-processing the output to get a climatological (maybe also zonally symmetric) flux file, that is then used as an input to the slab ocean part. Assume for the moment you have this file `T63_heatflux_test.nc`. There are also two other files that are not necessarily readily available, `T63GR15_surf_aqua_irad_noseason_final.nc` and `T63_ozone_historical_1850.nc`
 
 1. 3d initial file of atmosphere (spectral, no dependence on lsmask) 
-   ```
+   ```bash
    #get_file ${atmmod} input ${res_atm}L${vres_atm}_jan_spec.nc     unit.23
    aquadir=/pool/data/ECHAM6/T63/aqua
    get_file ${atmmod} input ${aquadir}/JW_balanced_init_spec_${res_atm}L${vres_atm}_ECHAM.nc    unit.23
    ``` 
 2. Surface boundary conditions (land/sea mask, albedo etc.), annual mean data; file depends on lsmask
-   ```
+   ```bash
    aquaindir=/work/mh1421/m300466/mpiesm-landveg/input/tra
    #get_file ${atmmod} input ${res_atm}${res_oce}_jan_surf.nc  unit.24
    get_file ${atmmod} input ${aquaindir}/echam6/T63GR15_surf_aqua_irad_noseason_final.nc  unit.24
    ```
 3. AMIP sst and sea ice concentration; files depend on lsmask
-   ```
+   ```bash
    if [ "${forcing}" = "amip" ]; then
      typeset -Z4 yr yp1 ym1
      yr=$(format_date -f4 -- ${startdate} | cut -f1 -d" ")
@@ -206,14 +206,14 @@ While many input forcing files need to change, this is done by changing the link
    fi
    ```
 4. Heat fluxes for mixed layer ocean (needed for slab ocean)
-   ```
+   ```yaml
    #
    # heat fluxes for mixed layer ocean
    #
    get_file ${atmmod} input ${aquaindir}/echam6/T63_heatflux_test.nc  unit.42
    ```
 5. Ozone
-   ```
+   ```bash
    #  # ozone
    #  if [[ ${io3} = 4 ]]; then   # read ozon climatology from file
    #    ozonedir=/pool/data/ECHAM6/input/${archive_rev_echam6}/${res_atm}/ozone
@@ -234,12 +234,12 @@ While many input forcing files need to change, this is done by changing the link
      get_file ${atmmod} input ${aquaindir}/echam6/T63_ozone_historical_1850.nc ozon${yrs}
    ```
 6. Soil layers
-   ```
+   ```bash
    #get_file ${srfmod} input jsbach_${grid}_${nsoil}layers_${refyear}_${dvtag}${surface_tag}.nc  jsbach.nc
    get_file ${srfmod} input ${aquadir}/jsbach_${res_atm}${res_oce}_11tiles_1976_aqua.nc   jsbach.nc
    ```
 7. Land use maps/ cover fraction
-   ```
+   ```bash
    #  [[ ${startyear} -le 1992 ]] && ludir=/pool/data/JSBACH/input/${archive_rev_jsbach}/${res_srf}/land_use_maps
    #  [[ ${startyear} -gt 1992 ]] && ludir=/pool/data/JSBACH/input/${archive_rev_jsbach}/${res_srf}/land_use_maps/A1B
      ludir=/pool/data/JSBACH/input/${archive_rev_jsbach}/${res_srf}/land_use_maps