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update for dev2 realtime run #1498

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98bae88
"update for chemistry"
haiqinli May 12, 2026
a46ffc1
"update to use GRA2PES anthropogenic emission"
haiqinli May 18, 2026
7bb7357
Merge branch 'rrfs-mpas-jedi' into rrfs-mpas-jedi-smoke
MatthewPyle-NOAA May 19, 2026
c633501
"update MPAS-Model and latest cheMPAS-fire configurations"
haiqinli Jun 1, 2026
53935fd
Merge branch 'rrfs-mpas-jedi' into rrfs-mpas-jedi-smoke
haiqinli Jun 4, 2026
e26668a
"sync from cheMPAS-Fire"
haiqinli Jun 4, 2026
916142c
"update the chemistry namelists"
haiqinli Jun 8, 2026
66d9e45
"update following reviewer's suggestions"
haiqinli Jun 8, 2026
215d540
Merge branch 'rrfs-mpas-jedi' into rrfs-mpas-jedi-smoke
MatthewPyle-NOAA Jun 9, 2026
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9 changes: 7 additions & 2 deletions .gitmodules
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@
ignore = all
[submodule "sorc/MPAS-Model"]
path = sorc/MPAS-Model
url = https://github.com/RRFSx/MPAS-Model
branch = gsl/develop
url = https://github.com/haiqinli/MPAS-Model
branch = gsl/develop-mp-emission

@guoqing-noaa guoqing-noaa May 26, 2026 •
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@haiqinli Could you merge the latest rrfs-mpas-jedi branch and then revert changes in lines 8-9? Thanks!

@haiqinli haiqinli Jun 8, 2026

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Updated as suggested. Thanks!

ignore = all
[submodule "sorc/RDASApp"]
path = sorc/RDASApp
Expand Down Expand Up @@ -43,3 +43,8 @@
path = workflow/sideload/pyDAmonitor
url = https://github.com/pyDAmonitor/pyDAmonitor.git
ignore = all
[submodule "sorc/regrid-wrapper"]
path = sorc/regrid-wrapper

@guoqing-noaa guoqing-noaa Jun 2, 2026

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sorc/chem-regrid-wrapper

url = https://github.com/jordanschnell/regrid-wrapper.git
branch = mpas_aero_v0
ignore = all
6 changes: 0 additions & 6 deletions fix/chemistry/mpassit/histlist_3d_anthro
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Original file line number Diff line number Diff line change
@@ -1,8 +1,2 @@
smoke_fine SMOKE_FINE
smoke_coarse SMOKE_COARSE
unspc_fine UNSPC_FINE
unspc_coarse UNSPC_COARSE
PM2_5 PM2_5
PM10 PM10
dust_fine DUST_FINE
dust_coarse DUST_COARSE
5 changes: 1 addition & 4 deletions fix/chemistry/mpassit/histlist_3d_chem
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@@ -1,5 +1,2 @@
smoke_fine SMOKE_FINE
PM2_5 PM2_5
PM10 PM10
dust_fine DUST_FINE
dust_coarse DUST_COARSE
vsb VSB
4 changes: 2 additions & 2 deletions fix/chemistry/mpassit/histlist_3d_pollen
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Expand Up @@ -5,5 +5,5 @@ polp_grass POLP_GRASS
polp_weed POLP_WEED
pols_all POLS_ALL
e_bio_out_polp_tree E_BIO_OUT_POLP_TREE
e_bio_out_polp_grass E_BIO_OUT_POLP_GRASS
e_bio_out_polp_weed E_BIO_OUT_POLP_WEED
e_bio_out_polp_grass E_BIO_OUT_POLP_GRASS
e_bio_out_polp_weed E_BIO_OUT_POLP_WEED
1 change: 0 additions & 1 deletion fix/chemistry/mpassit/histlist_3d_smoke
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@@ -1,4 +1,3 @@
smoke_fine SMOKE_FINE
PM2_5 PM2_5
PM10 PM10
e_bb_out_smoke_fine E_BB_OUT_SMOKE_FINE
19 changes: 19 additions & 0 deletions modulefiles/rrfs/gaeac6.regrid-wrapper-spack-stack.intel.lua
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@@ -0,0 +1,19 @@
prepend_path("MODULEPATH", "/gpfs/f6/bil-fire8/world-shared/Benjamin.Koziol/mpas-aerosols/spack-stack/envs/mpas-aerosols/modules/Core")

@guoqing-noaa guoqing-noaa May 18, 2026

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We usually don't do this way. Let's discuss this first.

prepend_path("MODULEPATH", "/gpfs/f6/bil-fire8/world-shared/Benjamin.Koziol/mpas-aerosols/spack-stack/envs/mpas-aerosols/modules/cray-mpich/8.1.32/intel-oneapi-compilers/2025.2.1")
prepend_path("MODULEPATH", "/gpfs/f6/bil-fire8/world-shared/Benjamin.Koziol/mpas-aerosols/spack-stack/envs/mpas-aerosols/modules/intel-oneapi-compilers/2025.2.1")

prepend_path("LD_LIBRARY_PATH", "/opt/intel/oneapi/mkl/2025.2/lib")

load("stack-intel-oneapi-compilers/2025.2.1")
load("stack-cray-mpich/8.1.32")

load("py-numpy/1.26.4")
load("esmf/8.9.1")
load("py-netcdf4/1.7.2")
load("py-pytest/8.2.1")
load("py-xarray/2024.7.0")
load("py-pydantic/2.10.1")
load("py-pydantic-settings/2.6.1")

load("Core/24.11")
load("nco/5.1.9")
16 changes: 16 additions & 0 deletions modulefiles/rrfs/ursa.regrid-wrapper-spack-stack.intel.lua
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@@ -0,0 +1,16 @@
prepend_path("MODULEPATH", "/scratch3/NCEPDEV/stmp/Benjamin.Koziol/sandbox/spack-stack/envs/mpas-aerosols/modules/Core")
prepend_path("MODULEPATH", "/scratch3/NCEPDEV/stmp/Benjamin.Koziol/sandbox/spack-stack/envs/mpas-aerosols/modules/intel-oneapi-mpi/2021.17/intel-oneapi-compilers/2025.3.1")
prepend_path("MODULEPATH", "/scratch3/NCEPDEV/stmp/Benjamin.Koziol/sandbox/spack-stack/envs/mpas-aerosols/modules/intel-oneapi-compilers/2025.3.1")

load("stack-intel-oneapi-compilers/2025.3.1")
load("stack-intel-oneapi-mpi/2021.17")

load("hdf5/1.14.3")
load("esmf/8.9.1")
load("py-netcdf4/1.7.2")
load("py-pytest/8.2.1")
load("py-xarray/2024.7.0")
load("py-pydantic/2.10.1")
load("py-pydantic-settings/2.6.1")

load("nco")
4 changes: 3 additions & 1 deletion parm/chemistry/namelist.atmosphere
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@@ -1,6 +1,7 @@
&chemistry
config_smoke_scheme = 'off'
config_dust_scheme = 'off'
config_anthro_scheme = 'off'
num_chem = 0
plume_wind_eff = 0
ebb_dcycle = 1
Expand All @@ -20,6 +21,7 @@
dust_moist_correction = 0.1
aero_dir_rad_fdb = false
config_mynn_enh_mix = false
kanthro = 20
config_mp_aero_emission = false
kanthro = 1
kwildfire = 1
/
10 changes: 8 additions & 2 deletions scripts/exrrfs_fcst.sh
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Expand Up @@ -63,6 +63,12 @@ if [[ "${FCST_CONVECTION_SCHEME^^}" == "TRUE" ]]; then
config_gfl_sub3d = 1/" namelist.atmosphere
fi

if [[ "${MESH_NAME^^}" == "FWX1.25km" ]]; then

@guoqing-noaa guoqing-noaa May 18, 2026

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We don't use if switches based on MESH_NAME inside j-jobs and ex-scripts.

Also config_lbc_w = 'zero' should be a standard option now, right?

sed -i -e "s/ config_apply_lbcs = true/\
config_apply_lbcs = true\n\
config_lbc_w = 'zero'/" namelist.atmosphere
fi

# generate the streams file on the fly using sed as this file contains "filename_template='lbc.$Y-$M-$D_$h.$m.$s.nc'"
lbc_interval=${LBC_INTERVAL:-3}
restart_interval=${RESTART_INTERVAL:-none}
Expand All @@ -82,9 +88,9 @@ sed -e "s/@restart_interval@/${restart_interval}/" -e "s/@history_interval@/${hi
-e "s/@diag_interval@/${diag_interval}/" -e "s/@lbc_interval@/${lbc_interval}/" \
-e "${mpasout_replacement}" "${PARMrrfs}"/streams.atmosphere > streams.atmosphere
#
if [[ "${mpasout_interval,,}" == "none" ]]; then # remove the da_state stream for coldstart only forecasts
#if [[ "${mpasout_interval,,}" == "none" ]]; then # remove the da_state stream for coldstart only forecasts

@guoqing-noaa guoqing-noaa May 18, 2026

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We cannot comment out this part. Let us talk about a better way to address the Chem needs.

@haiqinli haiqinli May 19, 2026

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I agree. When I run with rrfsx/MPAS-Model, we don't need to comment out this part. However, we have to comment out this when run with ufs-community/MPAS-Model

@haiqinli haiqinli Jun 8, 2026

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Fixed as suggested. Thanks!

sed -i '/<stream name="da_state"/,/<\/stream>/d' streams.atmosphere
fi
#fi
#
# chemistry related processing
if [[ "${DO_CHEMISTRY^^}" == "TRUE" ]]; then
Expand Down
46 changes: 33 additions & 13 deletions scripts/exrrfs_prep_chem.sh
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Expand Up @@ -14,7 +14,8 @@
# 1. CHEM_GROUP -- which chem emission group is this task performing? (anthro, pollen, dust)
# 2. ANTHRO_EMISINV -- undecided, may merge for custom dataset, or leave option to combine
# 3. CHEM_INPUT -- location of interpolated files, ready to be used
# 4. MESH_NAME -- name of the MPAS domain, required to know if we have weights or data intepolated to the domain
# 4. MESH_NAME -- name of the MPAS domain, required to know if we have weights or data intepolated to the domain
# TEST COMMIT

@guoqing-noaa guoqing-noaa May 18, 2026

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Line 18 can be removed

@haiqinli haiqinli May 19, 2026

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Will remove line 18. Thanks!

@haiqinli haiqinli Jun 8, 2026

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Removed as suggested.

#
# shellcheck disable=SC1091,SC2153,SC2154,SC2034
# rrfslint: file-disable=all
Expand All @@ -28,11 +29,13 @@
#
fcst_len_hrs_cycles=${FCST_LEN_HRS_CYCLES:-"01 01"}
my_fcst_length=$("${USHrrfs}/find_fcst_length.sh" "${fcst_len_hrs_cycles}" "${cyc}" )
export FCST_LENGTH="${my_fcst_length}"
echo "forecast length for this cycle is ${my_fcst_length}"
#
# ... Set some date variables
#
timestr=$(date -d "${CDATE:0:8} ${CDATE:8:2}" +%Y-%m-%d_%H.%M.%S)
JJJ=$(date -d "${CDATE:0:8} ${CDATE:8:2}" +%j)
YYYY=$(date -d "${CDATE:0:8} ${CDATE:8:2}" +%Y)
MM=$(date -d "${CDATE:0:8} ${CDATE:8:2}" +%m)
DD=$(date -d "${CDATE:0:8} ${CDATE:8:2}" +%d)
Expand All @@ -50,12 +53,12 @@
DDp=$(date -d "${CDATE:0:8} ${CDATE:8:2} - 1 day" +%d)
HHp=$(date -d "${CDATE:0:8} ${CDATE:8:2}- 1 day" +%H)
#
current_day=$(date -d "${YYYY}${MM}${DD}")
current_hh=$(date -d "${HH}" +"%H")
current_day="${YYYY}${MM}${DD}" #$(date -d "${YYYY}${MM}${DD}")
current_hh="${HH}" #$(date -d "${HH}" +"%H")
#
prev_hh=$(date -d "$current_hh -24 hour" +"%H")
#prev_hh=$(date -d "$current_hh -24 hour" +"%H")
previous_day=$(date '+%C%y%m%d' -d "$current_day-1 days")
previous_day="${previous_day} ${prev_hh}"
previous_day="${previous_day} ${HH}"
#
if [[ ${DOW} -le 5 ]]; then
DOW_STRING=weekdy
Expand Down Expand Up @@ -85,25 +88,38 @@
DOY_END=$(date -d "${CDATE:0:8} ${CDATE:8:2} + ${my_fcst_length} hours" +%j) # Julian day
#
# Set the init/mesh file name and link here:\
if [[ -r "${UMBRELLA_PREP_IC_DATA}"/init.nc ]]; then
if [[ -r "${FIXrrfs}/${MESH_NAME}/${MESH_NAME}.static.nc" ]]; then
ln -sf "${FIXrrfs}/${MESH_NAME}/${MESH_NAME}.static.nc" init.nc
INIT_FILE=./init.nc
elif [[ -r "${UMBRELLA_PREP_IC_DATA}"/init.nc ]]; then
ln -sf "${UMBRELLA_PREP_IC_DATA}"/init.nc init.nc
INIT_FILE=./${MESH_NAME}.init.nc
INIT_FILE=./init.nc
elif [[ -r "${UMBRELLA_PREP_IC_DATA}"/mpasout.nc ]]; then
ln -sf "${UMBRELLA_PREP_IC_DATA}"/mpasout.nc init.nc
INIT_FILE=./init.nc
else
echo "WARNING: NO Init File available, cannot reinterpolate if files are missing, did you run the task out of order?"
echo "FATAL: NO Init File available, cannot reinterpolate if files are missing, did you run the task out of order?"
err_exit
fi

#
SCRIPT=${USHrrfs}/chem_regrid.py
VINTERP_SCRIPT=${USHrrfs}/chem_vinterp.py
INTERP_WEIGHTS_DIR=${CHEM_INPUT}/grids/interpolation_weights/
SCRIP_FILES_DIR=${CHEM_INPUT}/grids/scrip_files/
# Now set the same for the scrip file:
if [[ "${SCRIP_FILES_DIR}/mpas_${MESH_NAME}_scrip.nc" ]]; then

Check failure

Code scanning / shellcheck

Argument to implicit -n is always true due to literal strings. Error

Argument to implicit -n is always true due to literal strings.
ln -s "${SCRIP_FILES_DIR}/mpas_${MESH_NAME}_scrip.nc" ./
else
echo "WARNING: NO SCRIP file available for this domain in ${SCRIP_FILES_DIR}, you will need to supply it as an argument to ${SCRIPT}"
fi
#
#
# Set a few things for the CONDA environment
export REGRID_WRAPPER_LOG_DIR=${DATA}
regrid_wrapper_dir=${REGRID_WRAPPER_DIR} #/lfs5/BMC/rtwbl/rap-chem/mpas_rt/working/ben_interp/regrid-wrapper/
PYTHONDIR=${regrid_wrapper_dir}/src
regrid_conda_env=${REGRID_CONDA_ENV} #CONDAENV=/lfs5/BMC/rtwbl/rap-chem/miniconda/envs/regrid-wrapper
export PATH=${regrid_conda_env}/bin:${PATH}
export ESMFMKFILE=${regrid_conda_env}/lib/esmf.mk
#regrid_conda_env=${REGRID_CONDA_ENV} #CONDAENV=/lfs5/BMC/rtwbl/rap-chem/miniconda/envs/regrid-wrapper
#export PATH=${regrid_conda_env}/bin:${PATH}
#export ESMFMKFILE=${regrid_conda_env}/lib/esmf.mk
export PYTHONPATH=${PYTHONDIR}:${PYTHONPATH}
#
#==================================================================================================#
Expand All @@ -123,6 +139,10 @@
source "${USHrrfs}"/chem_prep_pollen.sh
fi # bio/pollen

if [[ "${CHEM_GROUP}" == "GOES_AOD" ]] ; then
source "${USHrrfs}"/chem_prep_goes_aod.sh
fi

if [[ "${CHEM_GROUP}" == "dust" ]]; then

@jordanschnell jordanschnell May 20, 2026

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we will need to update the FIX files for dust based on the name changes in MPAS-Model

if [[ ! -s "${FIXrrfs}/chemistry/dust/fengsha_dust_inputs.${MESH_NAME}.nc" ]]; then
source "${HOMErrfs}/workflow/tools/chem_prep_dust.sh"
Expand Down
2 changes: 1 addition & 1 deletion sorc/MPAS-Model
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@guoqing-noaa guoqing-noaa May 18, 2026

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We cannot use the ufs-community/MPAS-Model directly as it misses the output_timelevels and output_done_marker

@haiqinli haiqinli May 19, 2026

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I have a pending PR (ufs-community/MPAS-Model#240). Should I update the PR with output_timelevels and output_done_marker? Thanks!

@guoqing-noaa guoqing-noaa May 19, 2026

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We have two routes:
(1) We get ufs-community/MPAS-Model#240 merged first; then merge the changes to rrfsx/MPAS-Model which already has output_timelevels and output_done_marker
(2) If you need the above PR #240 change earlier, you can create a PR to rrfsx/MPAS-Model.

@haiqinli haiqinli May 21, 2026

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I just submitted a PR (RRFSx/MPAS-Model#25) to rrfsx/MPAS-Model. Thanks!

Submodule MPAS-Model updated 13 files
+3 −4 .github/PULL_REQUEST_TEMPLATE.md
+1 −1 README.md
+1 −0 src/core_atmosphere/CMakeLists.txt
+1 −1 src/core_atmosphere/Registry.xml
+59 −24 src/core_atmosphere/physics/mpas_atmphys_driver_smoke.F
+5 −10 src/core_atmosphere/physics/mpas_atmphys_update_surface.F
+2 −4 src/core_atmosphere/physics/mpas_atmphys_vars.F
+1 −1 src/core_atmosphere/physics/physics_noaa/SMOKE
+10 −14 src/core_atmosphere/physics/registry.chemistry.xml
+0 −15 src/framework/mpas_stream_list_types.inc
+166 −1,048 src/framework/mpas_stream_manager.F
+1 −3 src/framework/mpas_stream_manager_types.inc
+19 −84 src/framework/xml_stream_parser.c
1 change: 1 addition & 0 deletions sorc/regrid-wrapper
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Submodule regrid-wrapper added at 769e48
54 changes: 35 additions & 19 deletions ush/chem_fcst.sh
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Expand Up @@ -12,10 +12,10 @@ cat "${FIXrrfs}/chemistry/stream_list/stream_list.atmosphere.output" >> ./stream
# Biogenic/Pollen
if [[ "${CHEM_GROUPS,,}" == *pollen* ]]; then
if [[ -s "${UMBRELLA_PREP_CHEM_DATA}/bio.init.nc" ]]; then
sed -i "\${e} cat ${PARMrrfs}/chemistry/streams.atmosphere.pollen" streams.atmosphere # append before the last line (i.e. </stream>)
sed -i "\$e cat ${PARMrrfs}/chemistry/streams.atmosphere.pollen" streams.atmosphere # append before the last line (i.e. </stream>)

@guoqing-noaa guoqing-noaa May 18, 2026

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why change ${e} to $e?

@haiqinli haiqinli May 19, 2026 •
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Will change $e back to ${e}. Thanks!

@jordanschnell jordanschnell May 20, 2026

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for some reason the brackets cause this command to fail

@guoqing-noaa guoqing-noaa May 20, 2026

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I cannot remember exactly, but I think I manually tested ${e} in this command and it worked.
I will double check this. If it fails, we are fine to use $e. Thanks!

cat "${FIXrrfs}/chemistry/stream_list/stream_list.atmosphere.output.pollen" >> ./stream_list/stream_list.atmosphere.output
ln -snf "${UMBRELLA_PREP_CHEM_DATA}"/bio.init.nc bio.init.nc
sed -i "s/config_pollen_scheme\s*=\s*'off'/config_pollen_scheme = 'speciated_pollen_primary'/g" namelist.atmosphere
sed -i "s/config_pollen_scheme\s*=\s*'off'/config_pollen_scheme = 'speciated_primary'/g" namelist.atmosphere
num_chem=$(( num_chem + 4 ))
else
echo "WARNING: No pollen emission file exists"
Expand All @@ -26,7 +26,7 @@ if [[ "${CHEM_GROUPS,,}" == *dust* ]]; then
if [[ -s "${FIXrrfs}/chemistry/dust/fengsha_dust_inputs.${MESH_NAME}.nc" ]]; then
ln -snf "${FIXrrfs}/chemistry/dust/fengsha_dust_inputs.${MESH_NAME}.nc" dust.init.nc
cat "${FIXrrfs}/chemistry/stream_list/stream_list.atmosphere.output.dust" >> ./stream_list/stream_list.atmosphere.output
sed -i "\${e} cat ${PARMrrfs}/chemistry/streams.atmosphere.dust" streams.atmosphere
sed -i "\$e cat ${PARMrrfs}/chemistry/streams.atmosphere.dust" streams.atmosphere
sed -i "s/config_dust_scheme\s*=\s*'off'/config_dust_scheme = 'on'/g" namelist.atmosphere
num_chem=$(( num_chem + 2 ))
# Append the xtime variable if it is missing
Expand All @@ -44,32 +44,39 @@ save_nullglob=$(shopt -p nullglob)
shopt -s nullglob

# Anthropogenic
if [[ "${CHEM_GROUPS,,}" == *anthro* ]]; then
files=("${UMBRELLA_PREP_CHEM_DATA}"/anthro.init*)
if (( ${#files[@]} )); then # at least one file exists
sed -i "\${e} cat ${PARMrrfs}/chemistry/streams.atmosphere.anthro" streams.atmosphere
sed -i "\$e cat ${PARMrrfs}/chemistry/streams.atmosphere.anthro" streams.atmosphere
ln -snf "${UMBRELLA_PREP_CHEM_DATA}"/anthro.init* ./
ptfiles=("${UMBRELLA_PREP_CHEM_DATA}"/anthro_pt.*)
if (( ${#ptfiles[@]} )); then
sed -i "\$e cat ${PARMrrfs}/chemistry/streams.atmosphere.anthro_pt" streams.atmosphere
sed -i "s/config_anthro_pt_scheme\s*=\s*'off'/config_anthro_pt_scheme = 'on'/g" namelist.atmosphere
ln -snf "${UMBRELLA_PREP_CHEM_DATA}"/anthro_pt.* ./
fi
for ifl in anthro*.nc
do
ncks -O -6 "${ifl}" "${ifl}"
done
#
if [[ "${CHEM_GROUPS,,}" == *anthro* ]]; then
sed -i "s/config_anthro_scheme\s*=\s*'off'/config_anthro_scheme = 'on'/g" namelist.atmosphere
num_chem=$(( num_chem + 6 ))
if [[ "${CHEM_GROUPS,,}" == *dust* ]]; then
num_chem=$(( num_chem - 2 ))
fi
if [[ "${CHEM_GROUPS,,}" == *smoke* ]]; then
num_chem=$(( num_chem - 2 ))
fi
sed -i "s/config_anthro_scheme\s*=\s*'off'/config_anthro_scheme = 'simple_aero'/g" namelist.atmosphere
num_chem=$(( num_chem + 1 ))
if [[ "${CONFIG_COARSE}" == "TRUE" ]]; then
num_chem=$(( num_chem + 1 ))
fi
fi
fi

# Smoke/Wildfire
files=("${UMBRELLA_PREP_CHEM_DATA}"/smoke.init*)
if (( ${#files[@]} )); then # at least one file exists
cat "${FIXrrfs}/chemistry/stream_list/stream_list.atmosphere.output.smoke" >> ./stream_list/stream_list.atmosphere.output
#
if (( EBB_DCYCLE == 1 )); then # Diurnal cycle for EBB (Emissions from Biomass Burning)
sed -i "\${e} cat ${PARMrrfs}/chemistry/streams.atmosphere.smoke_retro" streams.atmosphere
if (( EBB_DCYCLE == 1 )) || (( EBB_DCYCLE == -1 )); then # Diurnal cycle for EBB (Emissions from Biomass Burning)
sed -i "\$e cat ${PARMrrfs}/chemistry/streams.atmosphere.smoke_retro" streams.atmosphere
elif (( EBB_DCYCLE == 2 )); then
sed -i "\${e} cat ${PARMrrfs}/chemistry/streams.atmosphere.smoke_forecast" streams.atmosphere
sed -i "\$e cat ${PARMrrfs}/chemistry/streams.atmosphere.smoke_forecast" streams.atmosphere
else
echo "Not appending any smoke stream"
fi
Expand All @@ -78,18 +85,27 @@ if (( ${#files[@]} )); then # at least one file exists
#
if [[ "${CHEM_GROUPS,,}" == *smoke* ]]; then
sed -i "s/config_smoke_scheme\s*=\s*'off'/config_smoke_scheme = 'on'/g" namelist.atmosphere
num_chem=$(( num_chem + 2 ))
num_chem=$(( num_chem + 1 ))
added_smoke="TRUE"
fi
if [[ "${CONFIG_COARSE}" == "TRUE" ]]; then
num_chem=$(( num_chem + 1 ))
fi
# Set EBB_DCYCLE
sed -i -e "s/@ebb_dcycle@/${EBB_DCYCLE}/" namelist.atmosphere
fi

# RWC - Residual Wood Combustion
if [[ -s "${UMBRELLA_PREP_CHEM_DATA}/rwc.init.nc" ]]; then
sed -i "\${e} cat ${PARMrrfs}/chemistry/streams.atmosphere.rwc" streams.atmosphere
sed -i "\$e cat ${PARMrrfs}/chemistry/streams.atmosphere.rwc" streams.atmosphere
ln -snf "${UMBRELLA_PREP_CHEM_DATA}"/rwc.init.nc rwc.init.nc
# Set namelist
#sed -e "s/@online_rwc_emis@/1/" "${PARMrrfs}"/namelist.atmosphere > namelist.atmosphere
sed -i "s/config_rwc_scheme\s*=\s*'off'/config_rwc_scheme = 'on'/g" namelist.atmosphere
if [[ "${added_smoke}" == "TRUE" ]]; then
echo "Smoke already added and num_chem adjusted"
else
num_chem=$(( num_chem + 1 ))
fi
fi
#
# Replace the num_chem value with the correct number
Expand Down
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