CUG 6.17 CAM How do I use B compset history output to create SST ICE data files to drive an F compset

The following was contributed by Art Mirin and outlines the procedure you would use if you want to run an F-configuration case forced by monthly averages of SST and ice coverage from a B-configuration case. As an example, the following uses an f09_g16 CESM B-configuration simulation using CAM5 physics and with cosp enabled. The procedure to create the SST/ICE file is as follows:

1. Save monthly averaged 'aice' information from cice code (this is the default).
2. Save monthly averaged SST information from pop2. To do this, copy $CCSMROOT/models/ocn/pop2/input_templates/gx1v6_tavg_contents, to $CASEROOT/SourceMods/src.pop2 and change the 2 in front of SST to 1 for monthly frequency.
3. Extract (using ncrcat) SST from monthly pop2 history files and form a single netcdf file containing just SST; change SST to SST_cpl.

 > ncrcat -v SST case.pop.h.*.nc temp.nc
 > ncrename -v SST,SST_cpl temp.nc sst_cpl.nc

4. Extract aice from monthly cice history files and form a single netcdf file containing aice; change aice to ice_cov; divide values by 100 (to convert from percent to fraction).

 > ncrcat -v aice case.cice.h.*.nc temp.nc
 > ncrename -v aice,ice_cov temp.nc temp2.nc
 > ncap2 -s 'ice_cov=ice_cov/100.' temp2.nc ice_cov.nc

5. Modify fill values in the sst_cpl file (which are over land points) to have value -1.8 and remove fill and missing value designators; change coordinate lengths and names: to accomplish this, first run ncdump, then replace _ with -1.8 in SST_cpl, then remove lines with _FillValue and missing_value. (Note: although it might be possible to merely change the fill value to -1.8, this is conforming to other SST/ICE files, which have SST_cpl explicitly set to -1.8 over land.) To change coordinate lengths and names, replace nlon by lon, nlat by lat, TLONG by lon, TLAT by lat. The last step is to run ncgen. Note: when using ncdump followed by ncgen, precision will be lost; however, one can specify -d 9,17 to maximize precision - as in the following example:

 > ncdump -d 9,17 old.nc > old
 > ncgen -o new.nc new

6. Modify fill values in the ice_cov file (which are over land points) to have value 1 and remove fill and missing value designators; change coordinate lengths and names; patch longitude and latitude to replace missing values: to accomplish this, first run ncdump, then replace _ with 1 in ice_cov, then remove lines with _FillValue and missing_value. To change coordinate lengths and names, replace ni by lon, nj by lat, TLON by lon, TLAT by lat. To patch longitude and latitude arrays, replace values of those arrays with those in sst_cpl file. The last step is to run ncgen. (Note: the replacement of longitude and latitude missing values by actual values should not be necessary but is safer.)
7. Combine (using ncks) the two netcdf files.

 > ncks -v ice_cov ice_cov.nc sst_cpl.nc

Rename the file to ssticetemp.nc. The time variable will refer to the number of days at the end of each month, counting from year 0, whereas the actual simulation began at year 1 (CESM default); however, we want time values to be in the middle of each month, referenced to the first year of the simulation (first time value equals 15.5); extract (using ncks) time variable from existing amip sst file (for correct number of months - 132 in this example) into working netcdf file.

 > ncks -d time,0,131 -v time amipsst.nc ssticetemp.nc

Add date variable: ncdump date variable from existing amip sst file; modify first year to be year 0 instead of 1949 (do not including leading zeroes or it will interpret as octal) and use correct number of months; ncgen to new netcdf file; extract date (using ncks) and place in working netcdf file.

 > ncks -v date datefile.nc ssticetemp.nc

Add datesec variable: extract (using ncks) datesec (correct number of months) from existing amip sst file and place in working netcdf file.

 > ncks -d time,0,131 -v datesec amipsst.nc ssticetemp.nc

8. At this point, you have an SST/ICE file in the correct format. However, due to CAM's linear interpolation between mid-month values, you need to apply a procedure to assure that the computed monthly means are consistent with the input data. To do this, you can invoke the bcgen code in models/atm/cam/tools/icesst and following the following steps: a. Rename SST_cpl to SST, and ice_cov to ICEFRAC in the current SST/ICE file:

    > ncrename -v SST_cpl,SST -v ice_cov,ICEFRAC ssticetemp.nc

2. In driver.f90, sufficiently expand the lengths of variables prev_history and history (16384 should be sufficient); also comment out the test that the climate year be between 1982 and 2001 (lines 152-158).
3. In bcgen.f90 and setup_outfile.f90, change the dimensions of xlon and ???TODO xlat to (nlon,nlat); this is to accommodate use of non-cartesian ocean grid.
4. In setup_outfile.f90, modify the 4th and 5th ???TODO arguments in the calls to wrap_nf_def_var for lon and lat to be 2 and dimids; this is to accommodate use of non-cartesian ocean grid.
5. Adjust Makefile to have proper path for LIB_NETCDF and INC_NETCDF.
6. Modify namelist accordingly.
7. Make bcgen and execute per instructions. The resulting sstice_ts.nc file is the desired ICE/SST file.

9. Place new SST/ICE file in desired location. In the $CASEROOT for the F compset you create, modify env_run.xml to have :
   1. SSTICE_DATA_FILENAME point to the complete path of your SST/ICE file.
   2. SSTICE_GRID_FILENAME correspond to full path of (in this case) gx1v6 grid file.
   3. SSTICE_YEAR_START set to 0, and SSTICE_YEAR_END to one less than the total number of years; set SSTICE_YEAR_ALIGN to 1 (since CESM starts counting at year 1).