Aquaplanet-slab-ocean.md

@@ -116,11 +116,12 @@ Create_TASKS.frm -F setup_mpiesm-as_aqua --id aqua0101 mpiesm-as
 
 ### Edits to run script
 Not yet there, but getting close...... Namelist parameters and input forcing files must be specified in accordance to aquaplanet slab ocean requirements. 
-Namelist settings you'll need to add:
-1. Under **runctl** \
+
+**Modifications to namelist settings** 
+1. Under **runctl**, please add \
    `echo   "    l_orbvsop87 = .false."                           >>  namelist.echam` \
    `echo   "    lmlo = .true."                                   >>  namelist.echam` 
-2. Under **radctl** \
+2. Under **radctl**, please add \
    `echo   "    ldiur = false"                                   >>  namelist.echam` \
    `echo   "    cecc = 0.0"                                      >>  namelist.echam` \
    Please also comment out as follows:
@@ -143,9 +144,80 @@ Namelist settings you'll need to add:
    #  echo "    yr_perp = 1850"                                  >>  namelist.echam
    #fi
    ```
+3. Under **greenhouse gases** \
+   Please comment out and add 3 lines like this:
+   ```bash
+   #if [[ ${co2_transport} = true ]]; then
+   #  ico2=1   # prognostic CO2 mass mixing ratio
+   #  lco2_scenario=false
+   #elif [[ ${read_ghg} == true ]]; then
+   #  lco2_scenario=true # use CO2 scenario in jsbach
+   #  ico2=4             # use CO2 scenario in echam radiation
+   #else
+   #  ico2=2   # uniform CO2 volume mixing ratio
+   #fi
+   lco2_scenario=false
+   ico2=2
+   #if [[ ${n2o_transport} = true ]]; then
+   #  in2o=1   # prognostic N2O mass mixing ratio
+   #elif [[ ${read_ghg} == true ]]; then
+   #  in2o=4   # use N2O scenario in echam radiation
+   #else
+   #  in2o=3   # uniform N2O volume mixing ratio
+   #fi
+   in2o=3
+   ```
+
+**Modifications to linking input files**
+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`
+
+1. 3d initial file of atmosphere (spectral, no dependence on lsmask) 
+   ```
+   #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
+   ```
+   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 ${aquaindir}/echam6/T63GR15_surf_aqua_irad_noseason_final.nc  unit.24
+   ```
+3. AMIP sst and sea ice concentration; files depend on lsmask
+   ```
+   if [ "${forcing}" = "amip" ]; then
+     typeset -Z4 yr yp1 ym1
+     yr=$(format_date -f4 -- ${startdate} | cut -f1 -d" ")
+     (( yp1 = yr + 1 ))
+     (( ym1 = yr - 1 ))
+     for yrs in ${yr} ${yp1} ${ym1}; do
+       amipdir=/pool/data/ECHAM6/input/${archive_rev_echam6}/${res_atm}/amip
+       #get_file ${atmmod} input  ${amipdir}/${res_atm}_amipsst_${yrs}.nc  sst${yrs}
+       #get_file ${atmmod} input  ${amipdir}/${res_atm}_amipsic_${yrs}.nc  ice${yrs}
+       get_file ${atmmod} input ${aquadir}/${res_atm}_sst_aqua_Qobs.nc       sst${yrs}
+       get_file ${atmmod} input ${aquadir}/${res_atm}_sic_aqua.nc            ice${yrs}
+     done
+   else
+     #get_file ${atmmod} input ${res_atm}_amipsst_clim.nc       unit.20
+     #get_file ${atmmod} input ${res_atm}_amipsic_clim.nc       unit.96
+     get_file ${atmmod} input ${aquadir}/${res_atm}_sst_aqua_Qobs.nc       unit.20
+     get_file ${atmmod} input ${aquadir}/${res_atm}_sic_aqua.nc            unit.96
+   fi
+   ```
+4. Heat fluxes for mixed layer ocean (needed for slab ocean)
+   ```
+   #
+   # heat fluxes for mixed layer ocean
+   #
+   get_file ${atmmod} input ${aquaindir}/echam6/T63_heatflux_test.nc  unit.42
+   ```
+
+
+
+
+
 
 
-In fact, to run with slab ocean, you'll need a `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 and its called `T63_heatflux_test.nc`