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Adding new vertical levels and mpasout etc #565

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Adding new vertical levels and mpasout etc #565

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065de3a
Adding new vertical levels, L65.txt and L62.txt
chunhuazhou Dec 2, 2024
a4dec48
Update namelist.init_atmosphere
chunhuazhou Dec 2, 2024
5296297
Update namelist.init_atmosphere
chunhuazhou Dec 2, 2024
e91a36c
Update namelist.init_atmosphere
chunhuazhou Dec 2, 2024
125f01d
Merge branch 'rrfs-mpas-jedi' into updates_1202
MatthewPyle-NOAA Dec 3, 2024
c572697
Add optional file b if need to combine 2 GRIB-2 files, for UNGRIB tasks
chunhuazhou Dec 3, 2024
b95f5d0
Remove unnecessary items in namelist.init_atmosphere
chunhuazhou Dec 3, 2024
3ec4fcf
Merge remote-tracking branch 'zch/updates_1202' into updates_1202
chunhuazhou Dec 3, 2024
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62 changes: 62 additions & 0 deletions fix/meshes/L62.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,62 @@
0
19
39.89062
63.42188
90.3125
120.8438
155.25
194.0312
237.8125
287.25
343.0312
405.8125
476.2812
555.2812
643.8125
743
854.0312
978.0625
1116.25
1269.844
1440.219
1628.781
1836.812
2065.531
2316.281
2590.469
2889.344
3213.969
3565.25
3943.719
4349.281
4781.375
5239.5
5723.531
6233.5
6769.125
7329.281
7911.781
8513.812
9132.656
9766.062
10411.91
11068.19
11734.5
12412.91
13106.44
13817.19
14545.78
15291.84
16054.88
16835.16
17634.62
18458.14
19314.44
20214.39
21167.08
22179.47
23262.34
24436.02
25731.17
27190.78
28884.23
65 changes: 65 additions & 0 deletions fix/meshes/L65.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,65 @@
0
19
39.89062
63.42188
90.3125
120.8438
155.25
194.0312
237.8125
287.25
343.0312
405.8125
476.2812
555.2812
643.8125
743
854.0312
978.0625
1116.25
1269.844
1440.219
1628.781
1836.812
2065.531
2316.281
2590.469
2889.344
3213.969
3565.25
3943.719
4349.281
4781.375
5239.5
5723.531
6233.5
6769.125
7329.281
7911.781
8513.812
9132.656
9766.062
10411.91
11068.19
11734.5
12412.91
13106.44
13817.19
14545.78
15291.84
16054.88
16835.16
17634.62
18458.14
19314.44
20214.39
21167.08
22179.47
23262.34
24436.02
25731.17
27190.78
28884.23
30949.03
33656.09
37402.16
24 changes: 5 additions & 19 deletions parm/convection_permitting/namelist.atmosphere
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Expand Up @@ -53,28 +53,14 @@
config_radtlw_interval = '00:15:00'
config_radtsw_interval = '00:15:00'
config_bucket_update = 'none'
config_physics_suite = '${physics_suite}'
config_microp_scheme = 'mp_thompson'
config_thompson_hail_aware = true
config_convection_scheme = 'off'
! config_physics_suite = '${physics_suite}'
config_physics_suite = 'hrrrv5'
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  1. We need to use line 56 and define correct physics_suite in exrrfs_fcst.sh
  2. To confirm, do we have a hrrrv5 physics suite ready at this moment?

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This is the namelist that works for the current GSL MPAS model, consistent with the GSL real-time runs. My previous tests using "convection_permitting" would crash. For details we need inputs from the physics people.

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@chunhuazhou Thanks for the reply. We better NOT hardcode this to "hrrrv5", we can generate this on-the-fly in the exrrfs-fcst.sh script. So remove line 57, revert line 56, and specify "hrrrv5" in the script.

For the physics suite, I did not run the new GSL version of MPAS, so we will need @hu5970's input on this.

config_tempo_aerosolaware = .true.
config_tempo_hailaware = .true.
config_gwdo_scheme = 'bl_ugwp_gwdo'
config_lsm_scheme = 'sf_ruc'
! config_sfclayer_scheme = 'sf_monin_obukhov'
! config_pbl_scheme = 'bl_ysu'
num_soil_layers = 9
config_mynn_cloudpdf = 2
config_mynn_mixlength= 1
config_mynn_edmf = 1
config_mynn_edmf_mom = 1
config_mynn_edmf_tke = 0
config_mynn_edmf_output = 0
config_mynn_closure = 2.6
config_mynn_mixscalars = 1
config_mynn_mixclouds = 1
config_mynn_mixqt = 0
config_mynn_tkeadvect = .false.
config_mynn_tkebudget = 0
config_radt_cld_scheme='cld_fraction_mynn'
config_pbl_scheme = 'bl_mynnedmf'
/
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so many model options are changed. But those are used by conus3km real-time runs. Need to figure out how to set conus 12km separately.

&soundings
config_sounding_interval = 'none'
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3 changes: 2 additions & 1 deletion parm/convection_permitting/namelist.init_atmosphere
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Expand Up @@ -29,7 +29,7 @@
config_soilcat_data = 'BNU'
/
&vertical_grid
config_ztop = 25878.712
config_ztop = ${ztop}
config_nsmterrain = 1
config_smooth_surfaces = true
config_dzmin = 0.3
Expand All @@ -44,6 +44,7 @@
&preproc_stages
config_static_interp = false
config_native_gwd_static = false
config_native_gwd_gsl_static = false
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Do we need to set up lines 46 and 47 on the fly?

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I think it is good to be like this, suggested by Mike Toy when I was having issues running the ic.

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If we don't use gsl_static, why do we bother to add this namelist option?

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The default value is true but it might be only used when generating static.nc
So for ic and lbc tasks, it is better to set it to false.

config_vertical_grid = true
config_met_interp = true
config_input_sst = false
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3 changes: 2 additions & 1 deletion parm/mesoscale_reference/namelist.atmosphere
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Expand Up @@ -33,7 +33,8 @@
/
&printout
config_print_global_minmax_vel = true
config_print_detailed_minmax_vel = false
config_print_detailed_minmax_vel = true
config_print_global_minmax_sca = true
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lines 36 and 37: Do we want to set them to true for all rrfs runs?

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These are useful printouts. I think it is good to add them.

/
&IAU
config_IAU_option = 'off'
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8 changes: 5 additions & 3 deletions parm/mesoscale_reference/namelist.init_atmosphere
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Expand Up @@ -13,11 +13,11 @@
config_nfgsoillevels = ${nfgsoillevels}
/
&data_sources
config_geog_data_path = ''
config_geog_data_path = '/mnt/lfs5/BMC/wrfruc/HRRRv5/geog/'
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config_geog_data_path can be empty in the rrfs-workflow

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I added this to be consistent with what is set for the "convection_permitting". Can't be removed if desired.

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Yes, let's keep it as an empty string.

Also, to be consistent, let's remove the hardwired PATH in convection_permitting as well. Thanks!

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Reverted. Thanks!

config_met_prefix = '${prefix}'
config_sfc_prefix = 'SST'
config_fg_interval = ${interval_seconds}
config_landuse_data = 'MODIFIED_IGBP_MODIS_NOAH'
config_landuse_data = 'MODIFIED_IGBP_MODIS_NOAH_15s'
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This file is under parm/mesoscal_reference. Do we have to modify line 20?

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I added this to be consistent with what is set for the "convection_permitting". Can't be reverted if desired.

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Let's keep the original version. We can revisit this if we have to make this change.

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Reverted. Thanks!

config_topo_data = 'GMTED2010'
config_vegfrac_data = 'MODIS'
config_albedo_data = 'MODIS'
Expand All @@ -26,20 +26,22 @@
config_use_spechumd = false
/
&vertical_grid
config_ztop = 30000.0
config_ztop = ${ztop}
config_nsmterrain = 1
config_smooth_surfaces = true
config_dzmin = 0.3
config_nsm = 30
config_tc_vertical_grid = true
config_blend_bdy_terrain = true
config_specified_zeta_levels = '${zeta_levels}'
/
&interpolation_control
config_extrap_airtemp = 'lapse-rate'
/
&preproc_stages
config_static_interp = false
config_native_gwd_static = false
config_native_gwd_gsl_static = false
config_vertical_grid = true
config_met_interp = true
config_input_sst = false
Expand Down
24 changes: 22 additions & 2 deletions parm/streams.atmosphere_fcst
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@@ -1,10 +1,29 @@
<streams>
<immutable_stream name="invariant"
type="input"
precision="single"
filename_template="invariant.nc"
io_type="pnetcdf,cdf5"
input_interval="initial_only" />

<immutable_stream name="input"
type="input"
filename_template="init.nc"
io_type="pnetcdf,cdf5"
input_interval="initial_only" />

<immutable_stream name="da_state"
type="output"
precision="single"
clobber_mode="truncate"
filename_template="mpasout.$Y-$M-$D_$h.$m.$s.nc"
packages="jedi_da"
io_type="pnetcdf,cdf5"
output_interval="1:00:00" />
<var name="pressure" />
<var name="uReconstructZonal" />
<var name="uReconstructMeridional" />

<immutable_stream name="restart"
type="input;output"
filename_template="restart.$Y-$M-$D_$h.$m.$s.nc"
Expand All @@ -17,6 +36,7 @@
type="output"
filename_template="history.$Y-$M-$D_$h.$m.$s.nc"
io_type="pnetcdf,cdf5"
clobber_mode="replace_files"
output_interval="@history_interval@:00:00" >
<file name="stream_list/stream_list.atmosphere.output"/>
</stream>
Expand All @@ -40,7 +60,7 @@

<immutable_stream name="iau"
type="input"
filename_template="conus12km.AmB.$Y-$M-$D_$h.$m.$s.nc"
filename_template="AmB.$Y-$M-$D_$h.$m.$s.nc"
filename_interval="none"
packages="iau"
input_interval="initial_only" />
Expand All @@ -55,6 +75,6 @@

<immutable_stream name="ugwp_oro_data_in"
type="input"
filename_template="3km_conus.ugwp_oro_data.nc"
filename_template="ugwp_oro_data.nc"
input_interval="initial_only" />
</streams>
5 changes: 3 additions & 2 deletions scripts/exrrfs_fcst.sh
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Expand Up @@ -38,7 +38,8 @@ fi
ln -snf ${UMBRELLA_DATA}/cycbdys/lbc*.nc .

ln -snf ${FIXrrfs}/physics/${PHYSICS_SUITE}/* .
ln -snf ${FIXrrfs}/meshes/3km_conus.ugwp_oro_data.nc .
ln -snf ${FIXrrfs}/meshes/3km_conus.ugwp_oro_data.nc ./ugwp_oro_data.nc
ln -snf ${FIXrrfs}/meshes/${MESH_NAME}.invariant.nc_L65 ./invariant.nc
mkdir -p graphinfo stream_list
ln -snf ${FIXrrfs}/graphinfo/* graphinfo/
ln -snf ${FIXrrfs}/stream_list/${PHYSICS_SUITE}/* stream_list/
Expand All @@ -48,7 +49,7 @@ ln -snf ${FIXrrfs}/stream_list/${PHYSICS_SUITE}/* stream_list/
start_time=$(date -d "${CDATE:0:8} ${CDATE:8:2}" +%Y-%m-%d_%H:%M:%S)
run_duration=${fcst_len_hrs_thiscyc:-1}:00:00
physics_suite=${PHYSICS_SUITE:-'mesoscale_reference'}
jedi_da="false" #true
jedi_da="true" #true

if [[ "${MESH_NAME}" == "conus12km" ]]; then
pio_num_iotasks=6
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11 changes: 8 additions & 3 deletions scripts/exrrfs_ic.sh
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Expand Up @@ -32,11 +32,9 @@ start_time=$(date -d "${CDATE:0:8} ${CDATE:8:2}" +%Y-%m-%d_%H:%M:%S)
end_time=${start_time}
case ${MESH_NAME} in
conus12km)
nvertlevels=55
nsoillevels=4
;;
conus3km)
nvertlevels=59
nsoillevels=9
;;
*)
Expand All @@ -45,9 +43,12 @@ case ${MESH_NAME} in
;;
esac

zeta_levels=${FIXrrfs}/meshes/L65.txt

if [[ "${prefix}" == "RAP" || "${prefix}" == "HRRR" ]]; then
nfglevels=51
nfgsoillevels=9
zeta_levels=${FIXrrfs}/meshes/L62.txt
elif [[ "${prefix}" == "RRFS" ]]; then
nfglevels=66
nfgsoillevels=9
Expand All @@ -58,8 +59,12 @@ elif [[ "${prefix}" == "GEFS" ]]; then
nfglevels=32
nfgsoillevels=4
fi

echo ${zeta_levels}
ztop=$(tail -1 ${zeta_levels})
nvertlevels=$(( $(wc -l < ${zeta_levels}) - 1 ))

interval_seconds=3600 # just a place holder as we use metatask to run lbc hour by hour
zeta_levels=${FIXrrfs}/meshes/L60.txt
decomp_file_prefix="${MESH_NAME}.graph.info.part."
#
physics_suite=${PHYSICS_SUITE:-'PHYSICS_SUITE_not_defined'}
Expand Down
26 changes: 23 additions & 3 deletions scripts/exrrfs_lbc.sh
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Expand Up @@ -46,11 +46,26 @@ EDATE=$($NDATE ${fhr_begin} ${CDATEin})
start_time=$(date -d "${EDATE:0:8} ${EDATE:8:2}" +%Y-%m-%d_%H:%M:%S)
EDATE=$($NDATE ${fhr_end} ${CDATEin})
end_time=$(date -d "${EDATE:0:8} ${EDATE:8:2}" +%Y-%m-%d_%H:%M:%S)
nvertlevels=55
nsoillevels=4

case ${MESH_NAME} in
conus12km)
nsoillevels=4
;;
conus3km)
nsoillevels=9
;;
*)
echo "unknow MESH_NAME=${MESH_NAME}"
export err=99; err_chk
;;
esac
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Soil levels are not related to the mesh. It is decided by the outside model.
If we use GFS to initialize the CONUS3km, the soil level should be 4 also.


zeta_levels=${FIXrrfs}/meshes/L65.txt

if [[ "${prefix}" == "RAP" || "${prefix}" == "HRRR" ]]; then
nfglevels=51
nfgsoillevels=9
zeta_levels=${FIXrrfs}/meshes/L62.txt
elif [[ "${prefix}" == "RRFS" ]]; then
nfglevels=66
nfgsoillevels=9
Expand All @@ -61,8 +76,13 @@ elif [[ "${prefix}" == "GEFS" ]]; then
nfglevels=32
nfgsoillevels=4
fi


echo ${zeta_levels}
ztop=$(tail -1 ${zeta_levels})
nvertlevels=$(( $(wc -l < ${zeta_levels}) - 1 ))

interval_seconds=$((10#${INTERVAL}*3600)) # just a place holder as we use metatask to run lbc hour by hour
zeta_levels=${FIXrrfs}/meshes/L60.txt
decomp_file_prefix="${MESH_NAME}.graph.info.part."
#
physics_suite=${PHYSICS_SUITE:-'PHYSICS_SUITE_not_defined'}
Expand Down