* Add ufs driver. Remove NEMS submodule. Update CMEPS. Update CDEPS. Feature/ort addition.  (ufs-community#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 (ufs-community#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 (ufs-community#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 ufs-community#806, #807, ufs-community#813, and ort modifications (ufs-community#970)

- CCPP Physics changes: see Wrapper for ccpp-physics ufs-community#806, #807, ufs-community#813, NOAA-EMC/fv3atm#447.
- UFS weather model changes for ORT updates following changes in Fix Auto-RT on Gaea, Jet and Orion ufs-community#965

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

* update submodule pointer for regression testing for ccpp-physics ufs-community#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. (ufs-community#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 (ufs-community#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 (ufs-community#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) (ufs-community#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 (ufs-community#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 (ufs-community#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 (ufs-community#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 (ufs-community#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 (ufs-community#996)

* Radar-derived microphysics temperature tendencies similar to operational HRRR (ufs-community#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;  (ufs-community#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 (ufs-community#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 (ufs-community#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 (ufs-community#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 (ufs-community#1008)

* Add fhzero ort to coupled tests (ufs-community#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 (ufs-community#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 (ufs-community#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 (ufs-community#1018)

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


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

* sync-ww3 (ufs-community#1026)

* sync with ww3 develop branch

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

* This PR addresses part 2 of issue ufs-community#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 (ufs-community#1028)

- The 2D decomposition is enabled on write grid component.
- FV3atm PR NOAA-EMC/fv3atm#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 (ufs-community#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 (ufs-community#990)

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

Co-authored-by: @SMoorthi-emc

* Update esmf 821b04 (ufs-community#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 (ufs-community#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 (ufs-community#1043)

* Enable Thompson microphysics with UFS-Aerosols and update GOCART (ufs-community#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 (ufs-community#982)

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

* - Removes consistency check in GF, allows GF to run with different or no shallow scheme
- Add additional RAP based SDF

* - Add regression test logs

* jet intel test

* point to gsl/develop for FV3

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