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.e21.FCHIST.f09_f09_mg17.tutorial.test3 with the FCHIST compset; or
WACCM: f.e21.FWHIST.f09_f09_mg17.tutorial.test3 with the FWHIST compset.

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

Change the namelist variables to use daily fire emissions from QFED. This will also require a change of model STARTDATE. 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 location of qfed fire emissions on glade is described on the wiki: https://wiki.ucar.edu/display/camchem/Emission+Inventories

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 1995. 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.e21.FCHIST.f09_f09_mg17.tutorial.test3
set CASEDIR = /glade/u/home/$USER/cases/$CASENAME
set RUNDIR = /glade/scratch/$USER/$CASENAME/run
set COMPSET = FCHIST
set RESOLUTION = f09_f09_mg17

or for WACCM

set CASENAME = f.e21.FWHIST.f09_f09_mg17.tutorial.test3
set CASEDIR = /glade/u/home/$USER/cases/$CASENAME
set RUNDIR = /glade/scratch/$USER/$CASENAME/run
set COMPSET = FWHIST
set RESOLUTION = f09_f09_mg17

# Create a new case

Create a new case with the command create_newcase:

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

You may need to add --project "UESM0012" 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 regular and the project number UESM0012

cd $CASEDIR
./xmlchange JOB_QUEUE=regular,PROJECT=UESM0012

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

should return:

SSTICE_DATA_FILENAME: /glade/p/cesmdata/cseg/inputdata/atm/cam/sst/sst_HadOIBl_bc_0.9x1.25_1850_2017_c180507.nc

# 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','A','A','A','A','A','A','I'
 mfilt          = 1,30,365,240,240,480,365,73,30
 nhtfrq         = 0,-24,-24,-3,-1,1,-24,-120,-240
 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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/

&chem_inparm
 srf_emis_specifier		= 'BENZENE -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_BENZENE_0.9x1.25_mol_2000_2022.nc',
         'BIGALK -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_BIGALK_0.9x1.25_mol_2000_2022.nc',
         'BIGENE -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_BIGENE_0.9x1.25_mol_2000_2022.nc',
         'C2H2 -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_C2H2_0.9x1.25_mol_2000_2022.nc',
         'C2H4 -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_C2H4_0.9x1.25_mol_2000_2022.nc',
         'C2H4 -> /glade/p/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/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_C2H5OH_0.9x1.25_mol_2000_2022.nc',
         'C2H6 -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_C2H6_0.9x1.25_mol_2000_2022.nc',
         'C2H6 -> /glade/p/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/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_C3H6_0.9x1.25_mol_2000_2022.nc',
         'C3H6 -> /glade/p/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/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_C3H8_0.9x1.25_mol_2000_2022.nc',
         'C3H8 -> /glade/p/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/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_CH2O_0.9x1.25_mol_2000_2022.nc',
         'CH3CHO -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_CH3CHO_0.9x1.25_mol_2000_2022.nc',
         'CH3CN -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_CH3CN_0.9x1.25_mol_2000_2022.nc',
         'CH3COCH3 -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_CH3COCH3_0.9x1.25_mol_2000_2022.nc',
         'CH3COCHO -> /glade/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_CH3COCHO_0.9x1.25_mol_2000_2022.nc',
         'CH3COOH -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_CH3COOH_0.9x1.25_mol_2000_2022.nc',
         'CH3OH -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_CH3OH_0.9x1.25_mol_2000_2022.nc',
         'CO -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_CO_0.9x1.25_mol_2000_2022.nc',
         'CO -> /glade/p/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/p/cesmdata/cseg/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions_E90global_surface_1750-2100_0.9x1.25_c20170322.nc',
         'GLYALD -> /glade/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_GLYALD_0.9x1.25_mol_2000_2022.nc',
         'HCN -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_HCN_0.9x1.25_mol_2000_2022.nc',
         'HCOOH -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_HCOOH_0.9x1.25_mol_2000_2022.nc',
         'ISOP -> /glade/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_ISOP_0.9x1.25_mol_2000_2022.nc',
         'IVOC -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_IVOC_0.9x1.25_mol_2000_2022.nc',
         'MEK -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_MEK_0.9x1.25_mol_2000_2022.nc',
         'MTERP -> /glade/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_TERPENES_0.9x1.25_mol_2000_2022.nc ',
         'NH3 -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_NH3_0.9x1.25_mol_2000_2022.nc ',
         'NH3 -> /glade/p/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/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_NO_0.9x1.25_mol_2000_2022.nc ',
         'NO -> /glade/p/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/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_SVOC_0.9x1.25_mol_2000_2022.nc ',
         'TOLUENE -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_TOLUENE_0.9x1.25_mol_2000_2022.nc ',
         'XYLENES -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_XYLENES_0.9x1.25_mol_2000_2022.nc ',
         'bc_a4 -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_bc_a4_0.9x1.25_mol_2000_2022.nc ',
         'DMS -> /glade/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_DMS_0.9x1.25_mol_2000_2022.nc ',
         'DMS -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_num_so4_a1_0.9x1.25_mol_2000_2022.nc ',
         'num_a1 -> /glade/p/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/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_num_bc_a4_0.9x1.25_mol_2000_2022.nc ',
         'num_a4 -> /glade/p/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/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_num_pom_a4_0.9x1.25_mol_2000_2022.nc ',
         'pom_a4 -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_pom_a4_0.9x1.25_mol_2000_2022.nc ',
         'SO2 -> /glade/p/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/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_SO2_0.9x1.25_mol_2000_2022.nc',
         'so4_a1 -> /glade/p/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/p/acom/MUSICA/emissions/qfed2.5_finn/f09/qfed.emis_so4_a1_0.9x1.25_mol_2000_2022.nc ',
         'so4_a2 -> /glade/p/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'
/

# 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/p/cesmdata/cseg/inputdata/atm/waccm/lb/LBC_1750-2014_CMIP6_0p5degLat_c170126.nc'

# Initialization files for your new startdate

Note: Below are initialization files for 2010. For scientifically valid simulations you need to point to an initialization file for the start date you choose. If one is not available, you will need to spin up the model.

For CAM-chem: atmospheric initialization files are redefined in user_nl_cam

&cam_initfiles_nl
 ncdata         = '/glade/p/acom/acom-climate/tilmes/inputdata/init/camchem/FCnudged_MAM4_f09.carma_trop_strat09.aqchem.2001_2020.cam.i.2010-01-01-00000.nc'
/

For WACCM: atmospheric initialization files are redefined in user_nl_cam

&cam_initfiles_nl
 ncdata         = '/glade/p/acom/acom-climate/tilmes/inputdata/init/waccm/f.e21.FWHISTBgcCrop.f09_f09_mg17.CMIP6-AMIP-WACCM.001.cam.i.2010-01-01-00000.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/scratch/$USER/$CASENAME/run

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

cd /glade/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.e21.FCHIST.f09_f09_mg17.tutorial.test3.cam.h1.2010-01-01-00000.nc