1: Control case: running with chemistry#

Exercise 1: Run a present-day compset that includes chemistry

Create, configure, build and run a case for one of these following configurations:

  • CAM-chem: f.e21.FCHIST.f09_f09_mg17.tutorial.test1 with the FCHIST compset; or

  • WACCM: f.e21.FWHIST.f09_f09_mg17.tutorial.test1 with the FWHIST compset.

Run a simulation for 5 days, with daily instantaneous output of the variables: ‘PS’,’Z3’,’T’,’U’,’V’,’O3’. You are also welcome to output your own additional variables. Remember, F compsets have data ocean and data sea ice. Check your model output in your run directory.

Click here for hints

How do I output daily instantaneous variables?

  • Modify history stream 2 with namelist variable fincl2

  • Use namelist variables: nhtfrq, mfilt

  • For more information, look at the chapter:
    NAMELIST MODIFICATIONS -> Changing CAM namelist options

  • The default set up for these namelist variables can be found in CaseDocs/atm_in

What is the resolution for FCHIST and FWHIST?

  • Use resolution: f09_f09_mg17

Important! Check the newly generated namelist prior run

ls CaseDocs/*

atm_in atm_modelio.nml chem_mech.doc chem_mech.in cism.config cism_in cpl_modelio.nml docn_in ice_in docn.streams.txt.prescribed drv_flds_in drv_in esp_modelio.nml glc_modelio.nml ice_modelio.nml lnd_in lnd_modelio.nml mosart_in ocn_modelio.nml rof_modelio.nml seq_maps.rc wav_modelio.nml

  • atm_in: atmospheric namelist variables

  • chem_mech.in: chemical mechanism file

  • drv_flds_in: dry deposition variables, MEGAN variables (if used)

  • lnd_in: land namelist variables

  • …

Click here for the solution

# Set environment variables

Use the following commands
for CAM-chem:

set CASENAME = f.e21.FCHIST.f09_f09_mg17.tutorial.test1
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.test1
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 tutorial 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

# 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

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.

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

rundir example

(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.test1.cam.h1.1995-01-01-00000.nc