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Combining PRs #97 & 107: initialize ice fluxes and add "tiice" array #119

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merged 6 commits into from
May 27, 2020

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ShanSunNOAA
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Here is a combination of 2 PRs.

#97: When cplflx=T, initializing ice fluxes by PBL calculated values when fluxes from CICE are unavailable.

#107:
(1) Sfcprop%stc is currently used to store temperatures for both soil and internal ice. In the case of fractional grid, both surface types can exist at one grid point. Thus "tiice" is introduced to store internal ice temperature. "tiice" record will be added to phyf*nc output only when frac_grid=T.
(2) Controling frac_grid in the namelist and no longer modifying it inside FV3GFS_io.F90. frac_grid=F by default.

…ature. "tiice" will be added to phyf*nc output only when frac_grid=T.

(2) When cplflx=T, initializing ice fluxes by PBL calculated values when fluxes from CICE are unavailable.
(3) Adding frac_grid to namelist and no longer modifying it inside FV3GFS_io.F90. frac_grid=F by default.
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Where does Sfcprop%tiice get used? I see it is read in and written back to the restart files, but it should get used somewhere in sfc_sice.f/sfc_cice.f, or?

Also, is the corresponding CCPP PR NCAR/ccpp-physics#429?

Further, I thought we had agreed not to accept any further changes to IPD unless they are GFSv16 implementation bugfixes that are brought back to "develop". If we really want to follow this decision, then the changes to GFS_physics_driver.F90 should be reverted (all others are needed for CCPP as well).

@arunchawla-NOAA @junwang-noaa @DusanJovic-NOAA

ExtDiag(idx)%mod_name = 'gfs_sfc'
allocate (ExtDiag(idx)%data(nblks))
do nb = 1,nblks
ExtDiag(idx)%data(nb)%var2 => sfcprop(nb)%tiice(:,num)
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Use uppercase Sfcprop, please.

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Thanks!

@SMoorthi-emc
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SMoorthi-emc commented May 20, 2020 via email

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I am just communicating what was discussed between Arun, Vijay and DTC last week Friday. There was a concern raised that as long as people are able to make changes and develop IPD code, the development will not move over to CCPP entirely.

@junwang-noaa
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junwang-noaa commented May 20, 2020 via email

@ShanSunNOAA
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ShanSunNOAA commented May 20, 2020 via email

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Where does Sfcprop%tiice get used? I see it is read in and written back to the restart files, but it should get used somewhere in sfc_sice.f/sfc_cice.f, or?

Also, is the corresponding CCPP PR NCAR/ccpp-physics#429?

Further, I thought we had agreed not to accept any further changes to IPD unless they are GFSv16 implementation bugfixes that are brought back to "develop". If we really want to follow this decision, then the changes to GFS_physics_driver.F90 should be reverted (all others are needed for CCPP as well).

@arunchawla-NOAA @junwang-noaa @DusanJovic-NOAA

Most of my questions / concerns have been answered. It is still not clear to me what the exact policy is moving forward with accepting IPD changes. I will note that the changes on the IPD side are partial changes only, the ccpp-physics PR contains more changes (wrt using tiice).

Looking at the CCPP side of things, this PR looks good to me.

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ShanSunNOAA commented May 20, 2020 via email

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Hi Dom, Thanks for your prompt reply. Just to confirm, yes, you are right: (1) ice flux initialization was done earlier, where both IPD and CCPP were updated. (2) tiice change was done later and only under CCPP (GFS_surface_composites.F90 & sfc_sice.f). Therefore gfsphysics/physics/sfc_sice.f was not updated. I see your point of being consistent for these 2 PRs, and I have reverted any changes in GFS_physics_driver.F90. Let me know if you have any questions! Thanks, Shan

Thanks, Shan, consistency is always good.

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Approved from a CCPP perspective, contingent upon the results of the regression tests.

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Approved from a CCPP perspective, contingent upon the results of the regression tests.

Dom/Shan,
In CCPP PR #454, for those variables with name changed from "_ocn" to "_wat", can you change the associated comments or the meta data explanation from "open ocean" to "open water" or"over_ocean" to "over_water" in the future commit so that the names and comments/meta data are consistent? Thanks

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ShanSunNOAA commented May 26, 2020 via email

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Approved from a CCPP perspective, contingent upon the results of the regression tests.

Dom/Shan,
In CCPP PR #454, for those variables with name changed from "_ocn" to "_wat", can you change the associated comments or the meta data explanation from "open ocean" to "open water" or"over_ocean" to "over_water" in the future commit so that the names and comments/meta data are consistent? Thanks

See NCAR/ccpp-physics#455.

@DusanJovic-NOAA DusanJovic-NOAA merged commit 9868550 into NOAA-EMC:develop May 27, 2020
tsupinie pushed a commit to tsupinie/fv3atm that referenced this pull request Jul 20, 2020
(1) Introducing a separate array "tiice" to store internal ice temperature. "tiice" will be added to phyf*nc output only when frac_grid=T.
(2) When cplflx=T, initializing ice fluxes by PBL calculated values when fluxes from CICE are unavailable.
(3) Adding frac_grid to namelist and no longer modifying it inside FV3GFS_io.F90. frac_grid=F by default.
christinaholtNOAA referenced this pull request in NOAA-GSL/fv3atm Jun 15, 2021
* Add NSSL 2-Moment Microphysics

* Update data structures to handle the additional tracer species in NSSL microphysics
* Add the code files for NSSL microphysics to the CCPP prebuild config

* Add suite for NSSL microphysics

* Add a CCPP suite to test NSSL microphysics

* Initialize ice fluxes and add "tiice" array (#119)

(1) Introducing a separate array "tiice" to store internal ice temperature. "tiice" will be added to phyf*nc output only when frac_grid=T.
(2) When cplflx=T, initializing ice fluxes by PBL calculated values when fluxes from CICE are unavailable.
(3) Adding frac_grid to namelist and no longer modifying it inside FV3GFS_io.F90. frac_grid=F by default.

* Remove cheyenne.pgi from CCPP config (#117)

remove cheyenne.pgi from CCPP config (ccpp/set_compilers.sh, ccpp/build_ccpp.sh)

* develop: merge HWRF version of saSAS with GFS version (#93)

* Merge branch 'man_hafs_sas_without_updates_of_dtc_develop_49b73a8f4149ca88f071dbaae81f1769b120f1e0' into HEAD
* gfsphysics/physics/GFS_debug.F90: add capability to debug 1-d logical arrays
* Clean up error messages in gfsphysics/GFS_layer/GFS_typedefs.F90

Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>

* Merge GFDL FV3 dynamic core new (201912) version (#65)

* Change 'mytile' to 'mygrid' corresponding to the change in atmos_cubed_sphere

* GFS.v16.0.4 physics update (#128)

* physics update from GFS.v16.0.4
* GFS.v16.0.4 physics udpate
* remove whitespaces in sfc_diff.f
* keep z0 unchanged in coupled mode in sfc_diff.f
* fix IPD run
* point to NCAR ccpp-physics branch

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>

* Update for GFDL_atmos_cubed_sphere (dycore GNU bugfix) (#131)

* Bugfix for regional runs when dycore is compiled in double precision (#133)

* Update .gitmodules and submodule pointer for fv3atm for code review and testing

* Revert change to .gitmodules and update submodule pointer for GFDL_atmos_cubed_sphere

* Update develop from gsd/develop 2020/06/30 (#134)

- output of auxiliary arrays (2d, 3d) from CCPP to assist developers debugging their physics
- correctly output 3-dim tendencies for t, u, v, qv, ozone from CCPP physics
- mandatory changes for the CCPP framework updates to handle blocked data structures correctly: fix inconsistent use of `horizontal_dimension` (ix) versus `horizontal_loop_extent` (im) and other metadata corrections
- remove old pset logic from `ccpp_prebuild_config.py` (was required for CCPP dynamic build)
- updates to all suite definition files: change the order of interstitial schemes get_phi_fv3+GFS_suite_interstitial_3 and GFS_DCNV_generic_pre to match the logical flow (does not change the answer)
- move CCPP physics initialization calls in `atmos_model.F90` so that the physics can see the data from the restart files at initialization time
- add capability to read large-scale and small-scale orographic data when using GSL drag suite
- add additional fields to restart files as required for GSL physics updates
- new suite definition files for RAP and HRRR configurations
- capability to call radiation for the first `nhfrad` physics time steps for cold starts, afterwards on the cycle defined by the radiation time step

* Add regression tests with MULTI_GASES (#108)

* Update suite_FV3_GFS_2017_fv3wam.xml

* Remove unnecessary file from the CCPP prebuild configuration

* Add TACC frontera configuration

* Update to RAS in CCPP, update submodule pointer for ccpp-framework (CI tests) (NOAA-EMC#252)

* Reactivate mass flux arrays
* fix the argument list in inline_post_getattr and remove prints and post_gfs_stub.F90
* ccpp/data/GFS_typedefs.F90: correct initialization of Model%fscav
* Add FV3_GFS_v16_ras

* Cld perts (NOAA-EMC#233)

Addition of stochastic physics restarts in netCDF format that will be written at the restart interval, and at end of run.  
Also, addition of stochastic cloud perturbation and microphyiscs perturbations for SPPT.

* upgrade OPAC aerosol with more advanced MERRA2 aerosol (NOAA-EMC#254)

* changed .gitmodules to point to merra2 ccpp/physics
* revert .gitmodule

* update to Larissa version

* add atmos_cube_sphere and ccpp/physics as submodules

* add submodules of emc-2021-cloud

* update ccpp/physics: remove CAPS version mp_nssl_2mom

* ccpp/physics update: fix nssl mp reproducibility issue

* Updating pointer to ccpp/physics.

* Pointing to Christin's branch

* Adding new suite for NSSL physics.

* Updating suites to match HWT.

* Updating gitmodules

* Updating pointer to atmos_cubed_sphere.

Co-authored-by: Tim Supinie <tsupinie@ou.edu>
Co-authored-by: shansun6 <48043606+shansun6@users.noreply.github.com>
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>
Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>
Co-authored-by: XiaqiongZhou-NOAA <48254930+XiaqiongZhou-NOAA@users.noreply.github.com>
Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com>
Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: Phil Pegion <38869668+pjpegion@users.noreply.github.com>
Co-authored-by: AnningCheng-NOAA <48297505+AnningCheng-NOAA@users.noreply.github.com>
Co-authored-by: Jili Dong <jili.dong@noaa.gov>
SamuelTrahanNOAA referenced this pull request in SamuelTrahanNOAA/fv3atm Jun 13, 2022
* Remove unused and unsupported code (See NCAR#21)
* Remove APPBUILD step from rt.conf
SamuelTrahanNOAA referenced this pull request in SamuelTrahanNOAA/fv3atm Jun 13, 2022
* Add ufs driver. Remove NEMS submodule. Update CMEPS. Update CDEPS. Feature/ort addition.  (NOAA-EMC#931)

* Add UFS driver, a copy of two fortran files from the NEMS repository. Remove NEMS submodule.

* Update CMEPS for current escomp/master. Implement the ability to write mediator history files for ATM on tiles rather than mesh

* Update CDEPS component. The updated CDEPS includes code updates for GFS v16 data mode.

* Operation requirement test (ORT) for:
  - cpld_control_p7 thread and decomposition tests
  - cpld_bmark_p7 thread and decomposition tests
  - Due to the wave component in these tests, restart and debug do not work

Co-authored-by: Minsuk Ji <57227195+MinsukJi-NOAA@users.noreply.github.com>
Co-authored-by: Denise Worthen <denise.worthen@noaa.gov>
Co-authored-by: BinLi-NOAA <bin.li@noaa.gov>

* fv3atm cap cleanup (#954)

FV3 nuopc cap code cleanup. Remove used code/variables. Fix minor inconsistencies.

* CCPP cloud cover change for Thompson MP associated with Xu Randall, several bug fixes for regression testing scripts (#962)

This PR contains code changes 1) to remove old comments in GFS_typedefs.F90, increase cloud cover for Thompson MP by passing convective cloud water mixing ratio to progcld6. 2) Updates for auto fixes

Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>

* ccpp-physics NOAA-EMC#806, NOAA-EMC#807, NOAA-EMC#813, and ort modifications (#970)

- CCPP Physics changes: see Wrapper for ccpp-physics NOAA-EMC#806, NOAA-EMC#807, NOAA-EMC#813, NOAA-EMC#447.
- UFS weather model changes for ORT updates following changes in Fix Auto-RT on Gaea, Jet and Orion #965

* Wrapper for ccpp-physics NOAA-EMC#808 and 816 (roughness length over ice and NoahMP tsurf bugfix) (#971)

* update submodule pointer for regression testing for ccpp-physics NOAA-EMC#808,816: roughness length over ice and NoahMP tsurf bugfix
* Reduce time step from 600s to 450s for tests control_csawmg and control_csawmg_debug

Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>
Co-authored-by: climbfuji <dom.heinzeller@icloud.com>

* Use 'model set run clock' routine in FV3 NUOPC cap. (#967)

* Update FV3 cap by adding 'model set run clock' specialization routine. Because FV3 cap does not modify 'Earth clock' anymore in case of a restarted run, that adjustment is now done in the UFS driver.
* Fix model_configure file for two tests to define `fhrot` parameter.

* Revert iovr=4 (exponential cloud overlap method) in RRTMG (#963)

Revert/cleanup iovr=4 in RRTMG per developer's request. The current exponential cloud overlapping method used in RRTMG represents the method used in the pre-2018 operational HWRF model.

* Add fhzero ort test (#977)

* Fhzero ORT applies to the two tests `control` and `control_p7`
* Test can be run by invoking, for example, `./opnReqTest -n control -c fhz`

* Add a new CDEPS test to use GSFv16 data mode in CDEPS ,update rt_weekly.conf and update MOM6 to main branch (20211220) (#976)

* add a new cdeps test using GFS data mode
* update rt_weekly.conf to include cpld_bmark_p7_35d tests
* update MOM6

Co-authored-by: jiandewang <jiande.wang@noaa.gov>

* Bug fixes for WAM physics and regression tests, remove duplicate modules from ccpp-physics CMakeLists.txt (#947)

*adds a new regression test control_wam_debug and fixes problems with the existing control_wam test (e.g. IAER was not set as intended).

* Update global inline post for outputting foundation temperature (#968)

Update upp submodule in fv3atm with latest UPP version for outputting foundation temperature and fixing land-sea mask issue in global inline post.

* Regression test bug fixes for running on Jet or with Rocoto (#981)

* Bug fixes for running on jet or with rocoto
1. Correctly detect Jet when deciding build job runtimes
2. Do not delete out and err files in compile & test jobs
3. Correct dependencies for WW3 in Rocoto
4. Do not hard-code ACCNR to h-nems
This PR also contains fv3/ccpp physics (CCPP PR#812) updates that implements a vertically-integrated formula to properly compute tracer column mass and ensure mass conservation for all tracers except TKE. See issue NCAR/ccpp-physics#811 for details

* MYNN sfclay (RAP suite) restart reproducibility (#984)

*This PR turns on the rap_restart tests. Bit-for-bit reproducibility is achieved with the bug fixes for MYNN sfclay in the associated fv3atm and ccpp-physics PRs.

* fixes on initializing snow over fractional ice and GFS_surface_composite and z0ice value change (#996)

* Radar-derived microphysics temperature tendencies similar to operational HRRR (#986)

This PR implements a feature of the operational HRRR, radar-derived microphysics temperature tendencies applied in the first N minutes of the forecast to improve clouds in the first few hours. Two regression tests are added.

* Turn on CICE albedo use by ATM for coupled model; update Prototype test suite to initial P8 configuration;  (#944)

* add updates for suites, tests for initial P8 configuration
* add IOPT_SFC=3 as default; set IOPT_SFC=1 in p7 tests
* change min_seaice to 1e-6; set to 1e-11 in p7 tests
* set dddmp=0.1 in both P7 and P8. This matches the final
P7 configuration. It will change P7 baselines.
* set cdmbwd in both P7 and P8 to the final P7 configuration.
(1.0,2.2,1.0,1.0) for all resolutions. It will change P7 baselines.
* add dusan's ecflow fix for wcoss2
* update FV3 with Moorthis' snod fix
* update rt_weekly to use p8 tests
* change integration length to 5 days

* Thompson MP cloud tuning (#1005)

* improves cloud fraction when using Thompson MP. See NCAR/ccpp-physics#809 for more details.

* Add a new HAFS regression test with Thompson MP and GFDL surface layer schemes and Corrected S4 template regression testing job card (#995)

* Added a new regression test for HAFS. 
* Fixed the S4 RT template job card.

Co-authored-by: David Huber <david.huber@noaa.gov>
Co-authored-by: Bin Liu <Bin.Liu@noaa.gov>

* CCPP: Update consistency checks and effective radii calculation for Thompson MP (#1000)

This PR contains changes in ccpp-physics (Update consistency checks and effective radii calculation for Thompson MP) and adds two new regression tests for both Intel and GNU that use the new prognostic cloud scheme progcld_thompson with GFS v16 and with RAP. The new cloud scheme is activated by setting icloud == 3 in input.nml.

* Rremove nems_datm related code, update CDEPS, and remove run directories that are no longer needed by other tests (#1008)

* Add fhzero ort to coupled tests (#1009)

* Add fhz ort to cpld tests
* Set ACCNR in rt.sh, not detect_machine.sh. Add some comments explaining where the variable should not be set or used.

Co-authored-by: Samuel Trahan <Samuel.Trahan@noaa.gov>

* Unified write_netcdf, add single file 'cubed_sphere_grid' output (#1011)

* Unify write_netcdf and write_netcdf_parallel modules.
* Add support for writing 'cubed_sphere_grid' history files in a single netcdf file.

* Change standard name and unit of CCPP error flag variable in CCPP framework and physics (#1013)

* updates the submodule pointers for fv3atm, ccpp-framework and ccpp-physics for:  Change standard name and unit of CCPP error flag variable in CCPP framework and physics.

* ESMF managed threading (#1018)

Add code updates to enable the ESMF managed threading in UFS.


Co-authored-by: Gerhard Theurich <gerhard.j.theurich@noaa.gov >

* sync-ww3 (#1026)

* sync with ww3 develop branch

* Revisions to repair iovr=5 cloud overlap option (#1025)

* This PR addresses part 2 of issue NOAA-EMC#748 to activate the exponential-random cloud overlap method (iovr=5) in RRTMG. RT tests were added for  iovr=4 and iovr=5 options
* change iovr to use the environment variable in control.nml.IN; modify all tests that use control.nml.IN to set env. var. iovr=3 (except for new tests); remove restart files from new tests

* 2D decomposition on write grid, bug fix in FV3GFS_IO.F90, and quad precision in stochastic physics (#1028)

- The 2D decomposition is enabled on write grid component.
- FV3atm PR NOAA-EMC#468 from @MicroTed 
- stochastic physics PR NOAA-PSL/stochastic_physics#53 from Dom.

Co-authored-by: Ted Mansell <ted.mansell@noaa.gov>
Co-authored-by: Dom Heinzeller <heinzell@ucar.edu>

* Update CMEPS for wave coupling (#1034)


* add run phases to allow waves to run in the slow loop
* re-order hafs wave test
* update aliases in fd_nems.yaml
* update CMEPS to prevent advertise conflicts when s2sw is
still using connectors
* add correct masking variables to hafs nems.configure files

* 4DIAU bug fix when iau_filter_increments=T (#990)

* Add lsm_cold_start variable for RUC LSM SCM support and gwdps bugfix (combined) (#1037)

Co-authored-by: @SMoorthi-emc

* Update esmf 821b04 (#1041)

* Update the version of ESMF library to 8.2.1b04
* Add the write group lon info for upp 2d decomposition test.

* Multiple output (nested) grids from fv3atm (#1044)

Update fv3atm to support writing multiple history files for parent and nested domains.
Nested HAFS regression tests were updated to write out history files from all nested domains.

Co-authored-by: Bin Liu <bin.liu@noaa.gov>

* GPU-enabled version of Grell-Freitas convection in ccpp-physics (#1043)

* Enable Thompson microphysics with UFS-Aerosols and update GOCART (#1049)

This update allows the Thompson microphysics scheme to be used with prognostic aerosols (UFS-Aerosols) and updates GOCART to version 2.0.2.

* Add support for Stochastically Perturbed Parameterizations (SPP) in FV3 (#982)

* Update CICE; add support for restart test when running single RT (was PR 1058); update MOM6 (was PR 1060) (#1045)


* update cice
* (1) pointing MOM6 to testing branch (MOM6 main repo PR: mom-ocean/MOM6#1556 (comment))
    (2) add three new files in mom_cmake file
            core/MOM_porous_barriers.F90
            external/drifters/MOM_particles.F90
            external/drifters/MOM_particles_types.F90
    (3) explicitly set in MOM_input for all resolutions to reflect the default value changes in code to retain answer
        EPBL_MLD_BISECTION = True (default changed from T to F in this MOM6 PR)
        INTERNAL_WAVE_SPEED_BETTER_EST = False (default changed from F to T in this MOM6 PR)
        note BBL_USE_EOS now set to use the value of USE_EOS in this MOM6 PR,
        but we set BBL_USE_EOS explicit so it has no impact

* remove duplicated CHL input setting in MOM_input_template_050
* add support for restart tests while running single RT

* lateral boundary fix for regional runs (#1050)

This PR fixes a transient increase in noise caused by incorrect processing of winds along the lateral boundary on the final acoustic time step before fresh boundary information is ingested into the model.

* Update pointer to FV3

* Point to Christina's branches.

* Update RT log for Hera Intel.

* Adding RT log for Hera GNU tests.

* Updating RT log for Jet Intel tests.

* Latest regression tests on Jet.

* Adding regression logs.

* Updating regression test date stamp.

* Point to GSL repositories for FV3 and FV3/ccpp/physics

Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com>
Co-authored-by: Minsuk Ji <57227195+MinsukJi-NOAA@users.noreply.github.com>
Co-authored-by: Denise Worthen <denise.worthen@noaa.gov>
Co-authored-by: BinLi-NOAA <bin.li@noaa.gov>
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>
Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>
Co-authored-by: Grant Firl <grant.firl@noaa.gov>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>
Co-authored-by: mzhangw <mzhangw@gmail.com>
Co-authored-by: jiandewang <jiande.wang@noaa.gov>
Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com>
Co-authored-by: Samuel Trahan (NOAA contractor) <39415369+SamuelTrahanNOAA@users.noreply.github.com>
Co-authored-by: SMoorthi-emc <47667426+SMoorthi-emc@users.noreply.github.com>
Co-authored-by: ChunxiZhang-NOAA <49283036+ChunxiZhang-NOAA@users.noreply.github.com>
Co-authored-by: David Huber <david.huber@noaa.gov>
Co-authored-by: Bin Liu <Bin.Liu@noaa.gov>
Co-authored-by: Samuel Trahan <Samuel.Trahan@noaa.gov>
Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com>
Co-authored-by: Gerhard Theurich <gerhard.j.theurich@noaa.gov >
Co-authored-by: Ali.Abdolali <37336972+aliabdolali@users.noreply.github.com>
Co-authored-by: Ted Mansell <ted.mansell@noaa.gov>
Co-authored-by: Dom Heinzeller <heinzell@ucar.edu>
Co-authored-by: Jeff Whitaker <jswhit@fastmail.fm>
Co-authored-by: DomHeinzeller <58610420+DomHeinzeller@users.noreply.github.com>
Co-authored-by: Raffaele Montuoro <raffaele.montuoro@noaa.gov>
Co-authored-by: JeffBeck-NOAA <55201531+JeffBeck-NOAA@users.noreply.github.com>
Co-authored-by: MatthewPyle-NOAA <48285220+MatthewPyle-NOAA@users.noreply.github.com>
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