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 noda

NOTE:

• If doing chemistry data assimilation, one needs to remove the no_da option and build as ./build.all
• If one want to do more chemistry species beyond smoke/dust, one needs to add the chem option and build as ./build.all chem noda, which will clone the cheMPAS-Fire/MPAS-Model to replace the default MPAS-Model

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.
cp config_resources/config.chemistry .
vi config.chemistry # double check whether chemistry related variables are set correctly
     # for realtime dev2 experiments, one only need to use the `exp.rt_jet_dev2` file and `config.chemistry` is NOT needed.
./setup_rocoto.py exp.conus12km

NOTE:

1. Lots of variables are modified in config.chemistry, such as CYC_INTERVAL, CYCLEDEF_IC_STEP_HRS, LBC_CYCS, COLDSTART_CYCS, FCST_LEN_HRS_CYCLES, LBC_LENGTH, 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 for retros.

Be aware that config.chemistry is NOT a must and one can always configure all chemistry-related settings in the exp file.

2. The default setting in config.chemistry 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.chemistry if available.
   So if one wants to do chemistry DA, one needs to change them back to true in config.chemistry or don't use 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

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

Usually, one mesh only needs one corresponding RAVE_dummy file. Once created, users need to copy it to under fix/chemistry/RAVE for local use temporarily and then request the FIX_RRFS2 management team to stage and sync it to all supported platforms.

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.chemistry or an exp file:
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