3: Test case: changing the emissions

3: Test case: changing the emissions#

Exercise 3: Using different emissions

Create, configure, build a new case as done in exercise 1 or 2, for one of these following configurations:

  • CAM-chem: f.e30.FHISTC_LTt1s.ne16pg3_mg17.tutorial.test3 with the FHISTC_LTt1s compset; or

  • WACCM: f.e30.FHISTC_WAt1ma.ne16pg3_mg17.tutorial.test3 with the FHISTC_WAt1ma compset.

Set up this simulation to run for 5 days, starting January 1st, 2010, with daily instantaneous output of the variables: ‘PS’,’Z3’,’T’,’U’,’V’,’O3’.

Change the namelist variables to use fire emissions from QFED. Once the simulation is complete, compare the 5th day output to the previous results.

Click here for hints

Pointing to new emission files

Point to new emission files in your user_nl_cam file. Note that you will also need to include pointers to emissions that you are not changing. The namelist variable for emissions is srf_emis_specifier. Copy the whole srf_emis_specifier entry from atm_in to user_nl_cam before editing. Emission files will add up in CESM.

The location of qfed fire emissions on glade is described on the wiki: https://wiki.ucar.edu/display/camchem/Emission+Inventories Search for files with bb in their name, which are fire / biomass burning emissions. Global one degree emissions are usually stored under an ‘f09’ folder.

Make sure your model start date is covered by the emissions files. For this model set up will also need to double check the following are available:

  • The SST file covers your selected dates (env_run.xml file)

  • Lower boundary condition file must include your selected dates (atm_in file)

  • Consider that the initialization file will be for the default startdate of 1979. If you don’t change your initialization file, you will need to run your own model spin up.

Click here for the solution

# Set environment variables Use the commands:

CAM-chem

set CASENAME = f.e30.FHISTC_LTt1s.ne16pg3_mg17.tutorial.test3
set CASEDIR = /glade/u/home/$USER/cases/$CASENAME
set RUNDIR = /glade/derecho/scratch/$USER/$CASENAME/run
set COMPSET = FHISTC_LTt1s
set RESOLUTION = ne16pg3_ne16pg3_mg17

or for WACCM

set CASENAME = f.e30.FHISTC_WAt1ma.ne16pg3_mg17.tutorial.test3
set CASEDIR = /glade/u/home/$USER/cases/$CASENAME
set RUNDIR = /glade/derecho/scratch/$USER/$CASENAME/run
set COMPSET = FHISTC_WAt1ma
set RESOLUTION = ne16pg3_ne16pg3_mg17

# Create a new case

Create a new case with the command create_newcase:

cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts/
./create_newcase --case $CASEDIR --res $RESOLUTION --compset $COMPSET

You may need to add --project "UESM0016" when creating a new case.

# Change the job queue and account number

If needed, change job queue and account number.
For instance, to run in the queue tutorial and the project number UESM0016

cd $CASEDIR
./xmlchange JOB_QUEUE=tutorial,PROJECT=UESM0016 --force

This step can be redone at anytime in the process.

# Setup

From within the case directory, invoke case.setup with the command:

cd $CASEDIR
./case.setup

Change the dates to cover emission files Here, we choose 2010

./xmlchange RUN_STARTDATE=2010-01-01

Make sure the sea surface temperature and ice (SSTICE) data file covers your dates of interest

./xmlquery SSTICE_DATA_FILENAME

# Build

Perform an initial build within the case directory

qcmd -- ./case.build

namelists (atm_in, ice_in, lnd_in, docn_in) will appear in the CaseDocs subdirectory, as well as in your $rundir

# Customize namelists

As before, edit the file user_nl_cam. First open the CaseDocs/atm_in and find the lines for avgflag_pertap, mfilt, nhtfrq and copy and paste them into user_nl_cam. Then make changes to those lines in user_nl_cam and add a line to write out a second history file, fincl2. The namelist lines should look something like:

&cam_history_nl
 avgflag_pertape = 'A','I'
 mfilt          = 1,30
 nhtfrq         = 0,-24
 interpolate_output  =  .true., .true.
 interpolate_nlat    =     91,     91
 interpolate_nlon    =     180,     180
 
 fincl2         = 'PS','Z3','T','U','V','O3'
/

You can do this with a text editor.

# Add in different emissions Also add in the namelist pointers to emission files, replacing the fire emissions (every file with ‘bb’ in the name) with qfed files found at /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/

&chem_inparm
 srf_emis_specifier		= 'BENZENE -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_BENZENE_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'BENZENE -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_BENZENE_0.9x1.25_mol_2000-present_c20230414.nc',
         'BIGALK -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_BIGALK_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'BIGALK -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_BIGALK_0.9x1.25_mol_2000-present_c20230414.nc',
         'BIGENE -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_BIGENE_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'BIGENE -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_BIGENE_0.9x1.25_mol_2000-present_c20230414.nc',
         'C2H2 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_C2H2_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'C2H2 -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_C2H2_0.9x1.25_mol_2000-present_c20230414.nc',
         'C2H4 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_C2H4_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'C2H4 -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_C2H4_0.9x1.25_mol_2000-present_c20230414.nc',
         'C2H4 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_C2H4_other_surface_1750-2015_0.9x1.25_c20170322.nc',
         'C2H5OH -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_C2H5OH_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'C2H5OH -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_C2H5OH_0.9x1.25_mol_2000-present_c20230414.nc',
         'C2H6 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_C2H6_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'C2H6 -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_C2H6_0.9x1.25_mol_2000-present_c20230414.nc',
         'C2H6 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_C2H6_other_surface_1750-2015_0.9x1.25_c20170322.nc',
         'C3H6 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_C3H6_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'C3H6 -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_C3H6_0.9x1.25_mol_2000-present_c20230414.nc',
         'C3H6 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_C3H6_other_surface_1750-2015_0.9x1.25_c20170322.nc',
         'C3H8 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_C3H8_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'C3H8 -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_C3H8_0.9x1.25_mol_2000-present_c20230414.nc',
         'C3H8 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_C3H8_other_surface_1750-2015_0.9x1.25_c20170322.nc',
         'CH2O -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_CH2O_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'CH2O -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_CH2O_0.9x1.25_mol_2000-present_c20230414.nc',
         'CH3CHO -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_CH3CHO_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'CH3CHO -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_CH3CHO_0.9x1.25_mol_2000-present_c20230414.nc',
         'CH3CN -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_CH3CN_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'CH3CN -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_CH3CN_0.9x1.25_mol_2000-present_c20230414.nc',
         'CH3COCH3 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_CH3COCH3_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'CH3COCH3 -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_CH3COCH3_0.9x1.25_mol_2000-present_c20230414.nc',
         'CH3COCHO -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_CH3COCHO_0.9x1.25_mol_2000-present_c20230414.nc',
         'CH3COOH -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_CH3COOH_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'CH3COOH -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_CH3COOH_0.9x1.25_mol_2000-present_c20230414.nc',
         'CH3OH -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_CH3OH_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'CH3OH -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_CH3OH_0.9x1.25_mol_2000-present_c20230414.nc',
         'CO -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_CO_anthro_surface_1750-2015_0.9x1.25_c20180504.nc',
         'CO -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_CO_0.9x1.25_mol_2000-present_c20230414.nc',
         'CO -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_CO_other_surface_1750-2015_0.9x1.25_c20170322.nc',
         'E90 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions_E90global_surface_1750-2100_0.9x1.25_c20170322.nc',
         'GLYALD -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_GLYALD_0.9x1.25_mol_2000-present_c20230414.nc',
         'HCN -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_HCN_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'HCN -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_HCN_0.9x1.25_mol_2000-present_c20230414.nc',
         'HCOOH -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_HCOOH_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'HCOOH -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_HCOOH_0.9x1.25_mol_2000-present_c20230414.nc',
         'ISOP -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_ISOP_0.9x1.25_mol_2000-present_c20230414.nc',
         'IVOC -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_IVOC_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'IVOC -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_IVOC_0.9x1.25_mol_2000-present_c20230414.nc',
         'MEK -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_MEK_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'MEK -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_MEK_0.9x1.25_mol_2000-present_c20230414.nc',
         'MTERP -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_TERPENES_0.9x1.25_mol_2000-present_c20230414.nc ',
         'NH3 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_NH3_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'NH3 -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_NH3_0.9x1.25_mol_2000-present_c20230414.nc ',
         'NH3 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_NH3_other_surface_1750-2015_0.9x1.25_c20170322.nc',
         'NO -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_NO_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'NO -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_NO_0.9x1.25_mol_2000-present_c20230414.nc ',
         'NO -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_NO_other_surface_1750-2015_0.9x1.25_c20170322.nc',
         'SVOC -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_SVOC_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'SVOC -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_SVOC_0.9x1.25_mol_2000-present_c20230414.nc ',
         'TOLUENE -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_TOLUENE_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'TOLUENE -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_TOLUENE_0.9x1.25_mol_2000-present_c20230414.nc ',
         'XYLENES -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_XYLENES_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'XYLENES -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_XYLENES_0.9x1.25_mol_2000-present_c20230414.nc ',
         'bc_a4 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_bc_a4_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'bc_a4 -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_bc_a4_0.9x1.25_mol_2000-present_c20230414.nc ',
         'DMS -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_DMS_0.9x1.25_mol_2000-present_c20230414.nc ',
         'DMS -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_DMS_other_surface_1750-2015_0.9x1.25_c20170322.nc',
         'num_a1 -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_num_so4_a1_0.9x1.25_mol_2000-present_c20230414.nc ',
         'num_a1 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_num_so4_a1_anthro-ag-ship_surface_1750-2015_0.9x1.25_c20170616.nc',
         'num_a2 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_num_so4_a2_anthro-res_surface_1750-2015_0.9x1.25_c20170616.nc',
         'num_a4 -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_num_bc_a4_0.9x1.25_mol_2000-present_c20230414.nc ',
         'num_a4 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_num_bc_a4_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'num_a4 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_num_pom_a4_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'num_a4 -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_num_pom_a4_0.9x1.25_mol_2000-present_c20230414.nc ',
         'pom_a4 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_pom_a4_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
         'pom_a4 -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_pom_a4_0.9x1.25_mol_2000-present_c20230414.nc ',
         'SO2 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_SO2_anthro-ag-ship-res_surface_1750-2015_0.9x1.25_c20170616.nc',
         'SO2 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_SO2_anthro-ene_surface_1750-2015_0.9x1.25_c20170616.nc',
         'SO2 -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_SO2_0.9x1.25_mol_2000-present_c20230414.nc',
         'so4_a1 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_so4_a1_anthro-ag-ship_surface_1750-2015_0.9x1.25_c20170616.nc',
         'so4_a1 -> /glade/campaign/acom/MUSICA/emis/qfed/qfed2.5_finn/f09/qfed.emis_so4_a1_0.9x1.25_mol_2000-present_c20230414.nc ',
         'so4_a2 -> /glade/campaign/cesm/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_so4_a2_anthro-res_surface_1750-2015_0.9x1.25_c20170616.nc'
/

*note: these emissions are at 1 degree resoution, but we are using a 2 degree model. Ideally, we would want emissions at the same resolution as the model, but for learning purposes in this tutorial, using higher resolution emissions is OK.

# Lower boundary condition file check

Make sure the LBC files cover your dates of interest. In CaseDocs/atm_in you should see:

 flbc_file              = '/glade/campaign/cesm/cesmdata/inputdata/atm/waccm/lb/LBC_17500116-25001216_CMIP6_SSP585_0p5degLat_c20200824.nc'

# Initialization files for your new startdate

Your model can run with the default 1979 initialization file, In CaseDocs/atm_in for CAM-chem you should see:

&cam_initfiles_nl
 ncdata         = '/glade/campaign/cesm/cesmdata/inputdata/atm/cam/inic/se/FHISTC_LTso_ne16pg3_ne16pg3_mg17.i.c260220.nc'
/

However, for scientifically valid simulations you need to point to an initialization file for the start date you choose, or spin up the model to create your own. If you would like to practice changin the initialization file you can add this to your user_nl_cam:

&cam_initfiles_nl
 ncdata         = '/glade/derecho/scratch/shawnh/FHISTC_LTso_ne16pg3_ne16pg3_mg17.i.2010-01-01.c260708.nc'
/

You build the namelists with the command:

./preview_namelists

This step is optional as the script preview_namelists is automatically called by case.build and case.submit. But it is nice to check that your changes made their way into:

$CASEDIR/CaseDocs/atm_in

# Set run length

If needed, change the run length. If you want to run 5 days, you don’t have to do this, as 5 days is the default.

./xmlchange STOP_N=5,STOP_OPTION=ndays

# Submit:

./case.submit

# Check your solution

When the run is completed, look at the run files and history files.

(1) Find your model output in your run directory ($run_dir) after finished:

ls /glade/derecho/scratch/$USER/$CASENAME/run

(2) Check that your archive directory on derecho (the path will be different on other machines):

cd /glade/derecho/scratch/$USER/archive/$CASENAME/atm/hist
ls

As your run is only 5-day, there should be no monthly file (h0)

(3) Look at the contents of the h1 files using ncdump.

ncdump –h f.e30.FHISTC_LTt1s.ne16pg3_mg17.tutorial.test3.cam.h1i.2010-01-02-00000.nc