Do Chemistry

Most steps follow the same instructions as regular rrfs-workflow with some special options or configurations at some steps.

1. Build

which git-lfs 2>/dev/null ||  module load git-lfs
GIT_LFS_SKIP_SMUDGE=1 git clone -b rrfs-mpas-jedi --recursive https://github.com/NOAA-EMC/rrfs-workflow
cd rrfs-workflow/sorc
./build.all chem noda

NOTE: If doing chemistry data assimilation, one needs to build as ./build.all chem

2. Setup and run experiments:

Example:

cd workflow
cp exp/exp.conus12km exp.conus12km
vi exp.conus12km # set DO_CHEMISTRY=true; modify EXP_NAME, OPSROOT, RETRO_PERIOD and others as needed.
vi config_resources/config.chemistry # double check chemistry related variables are set correctly
./setup_rocoto.py exp.conus12km

NOTE:

1. Lots of variables should be modified in config_resources/config.chemistry, such as CYC_INTERVAL, CYCLEDEF_IC_STEP_HRS, LBC_CYCS, COLDSTART_CYCS, FCST_LEN_HRS_CYCLES, LBC_LENGTH, ACCOUNT, etc. The settings in config.chemistry will override the corresponding settings in the exp file.
   We adopt this strategy so that one can run the chemistry workflow out-of-the-box with minimum changes.

2. The default setting does NOT do data assimilation.
   Although DO_IODA,DO_JEDI,DO_CYC are set to true by default in exp files, they are overrode to false in config_resources/config.chemistry. So if one wants to chemistry DA, one needs to change them back to true in config.chemistry.

3. In the testing/debugging stage, one can add export RETRO_CYCLETHROTTLE=1, export KEEPDATA=YES in the exp file to help with the process.

The other procedures/steps are the same as running regular RRFS experiments in this documentation link

3. Under the hood

3.1 The RAVE_dummy file

When RAVE emission file is not available, rrfs-workflow will try to find a RAVE_dummy file from ${COMINrrfs}/RAVE_dummy.nc; if the dummy file is not available, the workflow will stop with an error.

setup_rocoto.py will try to find a RAVE_dummy file from ${CHEM_INPUT} and link it to ${COMINrrfs}/RAVE_dummy.nc. One can create/replace this link with an appropriate RAVE_dummy file after the exp setup.

One can create a new dummy file from an RAVE emission file under the prep_chem run directory using the utility workflow/ush/chem_create_rave_dummy.sh.

Usually, one mesh only needs one corresponding RAVE_dummy file and most times it may be found at ${CHME_INPUT}/emissions/RAVE/processed/RAVE.dummy.${MESH_NAME}.nc.

3.2 Specify chemistry emission groups

One can set what groups to be included in the workflow by configuring the CHME_GROUPS variable in config_resources/config.chemistry:
Examples:

CHEM_GROUPS="smoke" 
CHEM_GROUPS="smoke, dust"
CHEM_GROUPS="smoke, anthro, pollen, dust, rwc"

3.3 Staged Chemistry input data

Hera/Ursa: /scratch4/BMC/acomp/cheMPAS-Fire/input
Jet: /lfs6/BMC/rtwbl/cheMPAS-Fire/input
   and realtime raw RAVE data: /public/data/grids/nesdis/3km_fire_emissions
Gaea: /gpfs/f6/drsa-fire3/world-shared/cheMPAS-Fire/input