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Make thompson_mynn_lam3km ccpp suite available #644

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merged 8 commits into from
Dec 13, 2021
Merged

Make thompson_mynn_lam3km ccpp suite available #644

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e599897
Add FV3_GFS_v15_thompson_mynn_lam3km
chan-hoo Dec 2, 2021
816297b
Add a we2e test for thompson_mynn_lam3km
chan-hoo Dec 2, 2021
7a99882
Update namelist files
chan-hoo Dec 2, 2021
bf092f0
Add MERRA2 data
chan-hoo Dec 3, 2021
19ae300
Merge branch 'feature/merra2' into feature/thompson_mynn
chan-hoo Dec 3, 2021
425a8de
Fix typos
chan-hoo Dec 6, 2021
75e0b36
Move the SDF line in scripts
chan-hoo Dec 6, 2021
71dda91
remove change of nstf_name
chan-hoo Dec 13, 2021
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1 change: 1 addition & 0 deletions scripts/exregional_make_ics.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -187,6 +187,7 @@ case "${CCPP_PHYS_SUITE}" in
"FV3_GSD_SAR" | \
"FV3_RRFS_v1alpha" | \
"FV3_RRFS_v1beta" | \
"FV3_GFS_v15_thompson_mynn_lam3km" | \
"FV3_HRRR" )
if [ "${EXTRN_MDL_NAME_ICS}" = "RAP" ] || \
[ "${EXTRN_MDL_NAME_ICS}" = "HRRR" ]; then
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1 change: 1 addition & 0 deletions scripts/exregional_make_lbcs.sh
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Expand Up @@ -186,6 +186,7 @@ case "${CCPP_PHYS_SUITE}" in
"FV3_GSD_SAR" | \
"FV3_RRFS_v1alpha" | \
"FV3_RRFS_v1beta" | \
"FV3_GFS_v15_thompson_mynn_lam3km" | \
"FV3_HRRR" )
if [ "${EXTRN_MDL_NAME_LBCS}" = "RAP" ] || \
[ "${EXTRN_MDL_NAME_LBCS}" = "HRRR" ]; then
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22 changes: 22 additions & 0 deletions scripts/exregional_run_fcst.sh
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Expand Up @@ -405,6 +405,28 @@ done
#
#-----------------------------------------------------------------------
#
# Create links in the current run directory to the MERRA2 aerosol
# climatology data files and lookup table for optics properties.
#
#-----------------------------------------------------------------------
#
for f_nm_path in ${FIXclim}/*; do
f_nm=$( basename "${f_nm_path}" )
pre_f="${f_nm%%.*}"

if [ "${pre_f}" = "merra2" ]; then
mnth=$( printf "%s\n" "${f_nm}" | grep -o -P '(?<=2014.m).*(?=.nc)' )
symlink="${run_dir}/aeroclim.m${mnth}.nc"
else
symlink="${run_dir}/${pre_f}.dat"
fi
target="${f_nm_path}"
create_symlink_to_file target="$target" symlink="$symlink" \
relative="${relative_link_flag}"
done
#
#-----------------------------------------------------------------------
#
# If running this cycle/ensemble member combination more than once (e.g.
# using rocotoboot), remove any time stamp file that may exist from the
# previous attempt.
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25 changes: 25 additions & 0 deletions ...y/config.grid_RRFS_CONUS_3km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v15_thompson_mynn_lam3km.sh
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@@ -0,0 +1,25 @@
#
# TEST PURPOSE/DESCRIPTION:
# ------------------------
#
# This test is to ensure that the workflow running in community mode
# completes successfully on the RRFS_CONUS_3km grid using the GFS_v15_
# thompson_mynn_lam3km physics suite with ICs and LBCs derived from FV3GFS.
#

RUN_ENVIR="community"
PREEXISTING_DIR_METHOD="rename"

PREDEF_GRID_NAME="RRFS_CONUS_3km"
CCPP_PHYS_SUITE="FV3_GFS_v15_thompson_mynn_lam3km"

EXTRN_MDL_NAME_ICS="FV3GFS"
EXTRN_MDL_NAME_LBCS="FV3GFS"
USE_USER_STAGED_EXTRN_FILES="TRUE"

DATE_FIRST_CYCL="20190701"
DATE_LAST_CYCL="20190701"
CYCL_HRS=( "00" )

FCST_LEN_HRS="6"
LBC_SPEC_INTVL_HRS="3"
8 changes: 8 additions & 0 deletions ush/config_defaults.sh
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Expand Up @@ -1330,6 +1330,12 @@ SFC_CLIMO_FIELDS=( \
# System directory in which the majority of fixed (i.e. time-independent)
# files that are needed to run the FV3-LAM model are located
#
# FIXaer:
# System directory where MERRA2 aerosol climatology files are located
#
# FIXlut:
# System directory where the lookup tables for optics properties are located
#
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# TOPO_DIR:
# The location on disk of the static input files used by the make_orog
# task (orog.x and shave.x). Can be the same as FIXgsm.
Expand Down Expand Up @@ -1389,6 +1395,8 @@ SFC_CLIMO_FIELDS=( \
# to a null string which will then be overwritten in setup.sh unless the
# user has specified a different value in config.sh
FIXgsm=""
FIXaer=""
FIXlut=""
TOPO_DIR=""
SFC_CLIMO_INPUT_DIR=""

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22 changes: 20 additions & 2 deletions ush/generate_FV3LAM_wflow.sh
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Expand Up @@ -593,6 +593,25 @@ fi
#
#-----------------------------------------------------------------------
#
# Copy MERRA2 aerosol climatology data.
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@chan-hoo @JeffBeck-NOAA Question: Do these directories need to always be copied or only when using the thompson_mynn_lam3km suite? If the latter, can we wrap them in an if-statement that checks for the suite (i.e. in a new PR, or I can throw it in my current PR)? Just want to reduce the time it takes to generate a new experiment... Thanks.

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@gsketefian, Jili answered this question above: "the MERRA2 aero clim dataset is for the independent aerosol module/scheme and not particular for Thompson scheme."

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@chan-hoo, is the MERRA2 aero clim dataset only used when running RRFS-CMAQ? If so, then, we may want something like DO_CMAQ="true" in the config.sh file to avoid copying these files unless it's being used.

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@JeffBeck-NOAA, No. Since RRFS-CMAQ is coupled with GFS v15, CCPP is not available. MERR2 is used in SRW App (FV3-LAM).

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@chan-hoo, right, so CMAQ isn't in the picture. So what component of the SRW App uses the MERRA2 dataset?

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@JeffBeck-NOAA, if I understand correctly, it is used in thompson_mynn_lam3km now but it can be selected by other CCPP suites. @JiliDong-NOAA, is this correct? Can we turn it on/off in the fv3 namelist?

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@gsketefian @JeffBeck-NOAA , I'll put a flag to turn on/off MERRA2 like 'DO_MERRA' into the regional workflow soon.

#
#-----------------------------------------------------------------------
#
print_info_msg "$VERBOSE" "
Copying MERRA2 aerosol climatology data files from system directory
(FIXaer/FIXlut) to a subdirectory (FIXclim) in the experiment directory:
FIXaer = \"${FIXaer}\"
FIXlut = \"${FIXlut}\"
FIXclim = \"${FIXclim}\""

check_for_preexist_dir_file "${FIXclim}" "delete"
mkdir_vrfy -p "${FIXclim}"

cp_vrfy "${FIXaer}/merra2.aerclim"*".nc" "${FIXclim}/"
cp_vrfy "${FIXlut}/optics"*".dat" "${FIXclim}/"
#
#-----------------------------------------------------------------------
#
# Copy templates of various input files to the experiment directory.
#
#-----------------------------------------------------------------------
Expand All @@ -609,8 +628,7 @@ print_info_msg "$VERBOSE" "
cp_vrfy "${FIELD_TABLE_TMPL_FP}" "${FIELD_TABLE_FP}"

print_info_msg "$VERBOSE" "
Copying the template NEMS configuration file to the experiment direct-
ory..."
Copying the template NEMS configuration file to the experiment directory..."
cp_vrfy "${NEMS_CONFIG_TMPL_FP}" "${NEMS_CONFIG_FP}"
#
# Copy the CCPP physics suite definition file from its location in the
Expand Down
28 changes: 27 additions & 1 deletion ush/setup.sh
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Expand Up @@ -940,66 +940,84 @@ case "$MACHINE" in

"WCOSS_CRAY")
FIXgsm=${FIXgsm:-"/gpfs/hps3/emc/global/noscrub/emc.glopara/git/fv3gfs/fix/fix_am"}
FIXaer=${FIXaer:-"/gpfs/hps3/emc/global/noscrub/emc.glopara/git/fv3gfs/fix/fix_aer"}
FIXlut=${FIXlut:-"/gpfs/hps3/emc/global/noscrub/emc.glopara/git/fv3gfs/fix/fix_lut"}
TOPO_DIR=${TOPO_DIR:-"/gpfs/hps3/emc/global/noscrub/emc.glopara/git/fv3gfs/fix/fix_orog"}
SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/gpfs/hps3/emc/global/noscrub/emc.glopara/git/fv3gfs/fix/fix_sfc_climo"}
FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/needs/to/be/specified"}
;;

"WCOSS_DELL_P3")
FIXgsm=${FIXgsm:-"/gpfs/dell2/emc/modeling/noscrub/emc.glopara/git/fv3gfs/fix/fix_am"}
FIXaer=${FIXaer:-"/gpfs/dell2/emc/modeling/noscrub/emc.glopara/git/fv3gfs/fix/fix_aer"}
FIXlut=${FIXlut:-"/gpfs/dell2/emc/modeling/noscrub/emc.glopara/git/fv3gfs/fix/fix_lut"}
TOPO_DIR=${TOPO_DIR:-"/gpfs/dell2/emc/modeling/noscrub/emc.glopara/git/fv3gfs/fix/fix_orog"}
SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/gpfs/dell2/emc/modeling/noscrub/emc.glopara/git/fv3gfs/fix/fix_sfc_climo"}
FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/needs/to/be/specified"}
;;

"HERA")
FIXgsm=${FIXgsm:-"/scratch1/NCEPDEV/global/glopara/fix/fix_am"}
FIXaer=${FIXaer:-"/scratch1/NCEPDEV/global/glopara/fix/fix_aer"}
FIXlut=${FIXlut:-"/scratch1/NCEPDEV/global/glopara/fix/fix_lut"}
TOPO_DIR=${TOPO_DIR:-"/scratch1/NCEPDEV/global/glopara/fix/fix_orog"}
SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/scratch1/NCEPDEV/global/glopara/fix/fix_sfc_climo"}
FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/scratch2/BMC/det/FV3LAM_pregen"}
;;

"ORION")
FIXgsm=${FIXgsm:-"/work/noaa/global/glopara/fix/fix_am"}
FIXaer=${FIXaer:-"/work/noaa/global/glopara/fix/fix_aer"}
FIXlut=${FIXlut:-"/work/noaa/global/glopara/fix/fix_lut"}
TOPO_DIR=${TOPO_DIR:-"/work/noaa/global/glopara/fix/fix_orog"}
SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/work/noaa/global/glopara/fix/fix_sfc_climo"}
FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/needs/to/be/specified"}
;;

"JET")
FIXgsm=${FIXgsm:-"/lfs4/HFIP/hfv3gfs/glopara/git/fv3gfs/fix/fix_am"}
FIXaer=${FIXaer:-"/lfs4/HFIP/hfv3gfs/glopara/git/fv3gfs/fix/fix_aer"}
FIXlut=${FIXlut:-"/lfs4/HFIP/hfv3gfs/glopara/git/fv3gfs/fix/fix_lut"}
TOPO_DIR=${TOPO_DIR:-"/lfs4/HFIP/hfv3gfs/glopara/git/fv3gfs/fix/fix_orog"}
SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/lfs4/HFIP/hfv3gfs/glopara/git/fv3gfs/fix/fix_sfc_climo"}
FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/needs/to/be/specified"}
;;

"ODIN")
FIXgsm=${FIXgsm:-"/scratch/ywang/fix/theia_fix/fix_am"}
FIXaer=${FIXaer:-"/scratch/ywang/fix/theia_fix/fix_aer"}
FIXlut=${FIXlut:-"/scratch/ywang/fix/theia_fix/fix_lut"}
TOPO_DIR=${TOPO_DIR:-"/scratch/ywang/fix/theia_fix/fix_orog"}
SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/scratch/ywang/fix/climo_fields_netcdf"}
FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/needs/to/be/specified"}
;;

"CHEYENNE")
FIXgsm=${FIXgsm:-"/glade/p/ral/jntp/UFS_CAM/fix/fix_am"}
FIXaer=${FIXaer:-"/glade/p/ral/jntp/UFS_CAM/fix/fix_aer"}
FIXlut=${FIXlut:-"/glade/p/ral/jntp/UFS_CAM/fix/fix_lut"}
TOPO_DIR=${TOPO_DIR:-"/glade/p/ral/jntp/UFS_CAM/fix/fix_orog"}
SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/glade/p/ral/jntp/UFS_CAM/fix/climo_fields_netcdf"}
FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/needs/to/be/specified"}
;;

"STAMPEDE")
FIXgsm=${FIXgsm:-"/work/00315/tg455890/stampede2/regional_fv3/fix_am"}
FIXaer=${FIXaer:-"/work/00315/tg455890/stampede2/regional_fv3/fix_aer"}
FIXlut=${FIXlut:-"/work/00315/tg455890/stampede2/regional_fv3/fix_lut"}
TOPO_DIR=${TOPO_DIR:-"/work/00315/tg455890/stampede2/regional_fv3/fix_orog"}
SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/work/00315/tg455890/stampede2/regional_fv3/climo_fields_netcdf"}
FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/needs/to/be/specified"}
;;

*)
if [ -z "$FIXgsm" -o -z "$TOPO_DIR" -o -z "$SFC_CLIMO_INPUT_DIR" ]; then
if [ -z "$FIXgsm" -o -z "$FIXaer" -o -z "$FIXlut" -o -z "$TOPO_DIR" -o -z "$SFC_CLIMO_INPUT_DIR" ]; then
print_err_msg_exit "\
One or more fix file directories have not been specified for this machine:
MACHINE = \"$MACHINE\"
FIXgsm = \"${FIXgsm:-\"\"}
FIXaer = \"${FIXaer:-\"\"}
FIXlut = \"${FIXlut:-\"\"}
TOPO_DIR = \"${TOPO_DIR:-\"\"}
SFC_CLIMO_INPUT_DIR = \"${SFC_CLIMO_INPUT_DIR:-\"\"}
FIXLAM_NCO_BASEDIR = \"${FIXLAM_NCO_BASEDIR:-\"\"}
Expand Down Expand Up @@ -1400,6 +1418,10 @@ check_for_preexist_dir_file "$EXPTDIR" "${PREEXISTING_DIR_METHOD}"
# the fixed files containing various fields on global grids (which are
# usually much coarser than the native FV3-LAM grid).
#
# FIXclim:
# This is the directory that will contain the MERRA2 aerosol climatology
# data file and lookup tables for optics properties
#
# FIXLAM:
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# This is the directory that will contain the fixed files or symlinks to
# the fixed files containing the grid, orography, and surface climatology
Expand Down Expand Up @@ -1434,6 +1456,7 @@ check_for_preexist_dir_file "$EXPTDIR" "${PREEXISTING_DIR_METHOD}"
LOGDIR="${EXPTDIR}/log"

FIXam="${EXPTDIR}/fix_am"
FIXclim="${EXPTDIR}/fix_clim"
FIXLAM="${EXPTDIR}/fix_lam"

if [ "${RUN_ENVIR}" = "nco" ]; then
Expand Down Expand Up @@ -2776,8 +2799,11 @@ PARMDIR="$PARMDIR"
MODULES_DIR="${MODULES_DIR}"
EXECDIR="$EXECDIR"
FIXam="$FIXam"
FIXclim="$FIXclim"
FIXLAM="$FIXLAM"
FIXgsm="$FIXgsm"
FIXaer="$FIXaer"
FIXlut="$FIXlut"
COMROOT="$COMROOT"
COMOUT_BASEDIR="${COMOUT_BASEDIR}"
TEMPLATE_DIR="${TEMPLATE_DIR}"
Expand Down
48 changes: 46 additions & 2 deletions ush/templates/FV3.input.yml
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Expand Up @@ -62,8 +62,6 @@ FV3_HRRR:
kord_wz: 9
nord_tr: 2
nrows_blend: 10
regional_bcs_from_gsi: False
write_restart_with_bcs: False
gfs_physics_nml:
<<: *gsd_sar_phys
cdmbgwd: [3.5, 1.0]
Expand Down Expand Up @@ -287,6 +285,52 @@ FV3_GFS_v15p2:
ldebug: False
surf_map_nml:

FV3_GFS_v15_thompson_mynn_lam3km:
atmos_model_nml:
avg_max_length: 3600.0
fv_core_nml:
agrid_vel_rst: true
full_zs_filter: !!python/none
n_sponge: 9
npz_type: ''
rf_fast: false
sg_cutoff: 10000.0
vtdm4: 0.02
gfs_physics_nml:
avg_max_length: 3600.0
cdmbgwd: [0.88, 0.04]
do_deep: false
do_mynnsfclay: true
do_ugwp: false
fhswr: 900.0
fhlwr: 900.0
iaer: 1011
iccn: 2
icliq_sw: 2
imfdeepcnv: 2
imfshalcnv: 2
iopt_alb: 2
iopt_btr: 1
iopt_crs: 1
iopt_dveg: 2
iopt_frz: 1
iopt_inf: 1
iopt_rad: 1
iopt_run: 1
iopt_sfc: 1
iopt_snf: 4
iopt_stc: 1
iopt_tbot: 2
iovr: 3
ldiag_ugwp: false
lgfdlmprad: false
lsm: 1
lsoil_lsm: !!python/none
ltaerosol: false
xkzminv: 0.3
xkzm_m: 1.0
xkzm_h: 1.0

FV3_GFS_v16:
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@JeffBeck-NOAA JeffBeck-NOAA Dec 13, 2021 •
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@chan-hoo, This SDF won't work with RAP/HRRR-based ICs unless "nstf_name" is 2, 1, 0, 0, 0. Does it need to be 2, 0, 0, 0, 0, or can we change it?

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I believe that switching the second flag in nstf_name from 0 to 1 means that the NSST data from the surface data file will not be read into the model. If this is not desired/needed, I don't see an issue with changing nstf_name to 2,1,0,0,0

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@BenjaminBlake-NOAA, do you have an answer to Jeff's comment? I'll test [2,1,0,0,0] with both FV3GFS and RAP/HRRR.

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@chan-hoo I think we added comments at the same time :)

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Thanks, @BenjaminBlake-NOAA, @chan-hoo, it looks like we need a switch in the workflow to change the values of nstf_name based on the external model data being used for ICs. Since we don't have that at the moment, the easiest solution is to set all suites to 2,1,0,0,0, in which case, I believe FV3 will spin up its own NSST values.

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Thanks, @BenjaminBlake-NOAA. I'll test them.

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@JeffBeck-NOAA Yes I think that's right about FV3 spinning up its own NSST values

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@JeffBeck-NOAA, @BenjaminBlake-NOAA, both FV3GFS and RAP/HRRR works well with 2,1,0,0,0.

cires_ugwp_nml:
launch_level: 27
Expand Down
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