…ature/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>

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

…everal 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>

…fications (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

…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>

* 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.

…ity#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.

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

…ly.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>

…les 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).

…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.

…unity#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

*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.

…site and z0ice value change (ufs-community#996)

…nal 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.

…st 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

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

…r 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>

…hompson 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.

…ies that are no longer needed by other tests (ufs-community#1008)

* 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>

…-community#1011)

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

…mework 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.

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


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

* sync with ww3 develop branch

* 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

…ecision 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>

* 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

…(combined) (ufs-community#1037)

Co-authored-by: @SMoorthi-emc

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

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>

…community#1043)

…-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.

…V3 (ufs-community#982)

… 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

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.

* add new RT that uses NSSL MP; add new NSSL vars to default_vars.sh and rap.nml.IN; add new field table for using NSSL MP with hail on

updates all p8 tests to the p8b settings, which includes GOCART

Co-authored-by: Raffaele Montuoro <raffaele.montuoro@noaa.gov>

…ix CCPP's metadata2html.py (ufs-community#1061)

* Use WW3 CMake build

Co-authored-by: kgerheiser <kgerheiser@icloud.com>

* Require cmake version 3.19
* Update FV3:
   - Add 'valid time' variable using ISO string format to netcdf history files.
   - Use double precision variable to set value of 'time' attribute in wrt comp import state
   - Update ccpp/physics (setting surface-related interstitial variables for SCM prescribed-surface-flux mode)
   - Update inline_post_stub.F90 subroutine interfaces to match inline_post.F90

* Add hi-res regional test on small domain

…thern hemisphere (ufs-community#1087)

* Subroutine `lambert` in the FV3 write component has been fixed to do the mapping on the southern hemisphere correctly.
* CI fix
  - Docker container library updated. CI input data updated. Add chm_petlist_bounds.
  - Change gocart output file name for debug test
  - Changes for opnReqTest to also scan rt_gnu.conf
  - Change CI tests to noaero

Co-authored-by: Minsuk Ji <57227195+MinsukJi-NOAA@users.noreply.github.com>

…2S and S2SW (ufs-community#1118)

* Rectify total number of Thompson MP species
* Implement S2SWA/S2SA build app as the only one enabling prognostic aerosols in fully coupled model.
* Update output_fh documentation.

…y#1136)

Co-authored-by: jiandewang <jiande.wang@noaa.gov>
Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com>
Co-authored-by: DusanJovic-NOAA <dusan.jovic@noaa.gov>

* Update fms to 2021.04
* Add RT for ocean IAU
* Update documentation

Co-authored-by: Phil Pegion <38869668+pjpegion@users.noreply.github.com>
Co-authored-by: Jun Wang <37633869+junwang-noaa@users.noreply.github.com>

* reset the Noah-MP default options for those well tested

…community#1110)

* Update ESMF to version 8.3.0b09
* Increase wall clock limit for tests/regional_3km to 15 min
* Update AutoRT to use tfe01 ecflow node on Jet
* Updated Cheyenne baseline epicufsrt path
* Updated Cheyenne epicufsrt hpc-stack build

Co-authored-by: JONG KIM <jong.kim@noaa.gov>
Co-authored-by: Brian Curtis <brian.curtis@noaa.gov>

…list template

…ug fix for the Thompson scheme (issue ufs-community#881) (ufs-community#1120)

* release/p8c: it is related to ccpp-physics PBL and cumulus updates plus a bug fix to the Thompson scheme

* Add AQM submodule to integrate NOAA's Air Quality Model embedding
the U.S. EPA Community Multiscale Air Quality Model (CMAQ).

* MOM6: An alternate fix to class(*) issues with FMS 2022-01

Co-authored-by: Raffaele Montuoro <raffaele.montuoro@noaa.gov>
Co-authored-by: jiandewang <jiande.wang@noaa.gov>

* New feature in RRTMGP enabled ccpp-physics.
* Updated physics. New FV3 interstitials.
* Cleanup of RRTMGP regression tests.
* Replaced cld_mynn_ naming convention with cld_pbl_
* Some more cleanup of cloud-fraction...
* Pulled in Qingfu's changes to ccpp-physics
* New RT's for RRTMGP p8. Revert change in ccpp-physics
* Changed arguments to implied shape. in ccpp-physics
* Updated RRTMGP regression tests
* Changes to FV3/ccpp-physics.
* RRTMGP RT cleanup, again. Bug-fix in FV3/ccpp-physics
* Revert changes to names in FV3/ccpp-physics
* Cleanup p8 tests.
* More RT cleanup for p8.
* Add GP setting to non-coupled p8 tests.
* Added bounding to temperature at layer-interface used by RRTMGP.
* Reorder loop
* Combined gp sw and lw aerosol routines. Modest speedup (~4%). Add GP setting to test setup.
* Add GP settings to cpld_control_c96_noaero_p8 test.
* update test resources default_vars.sh

* Add the storm-following or specified moving-nesting capability for both the regional and global configuration.
* Expand the UFS/HAFS FV3ATM-HYCOM ocean coupling to support the static and moving nesting configuration.
* Expand the write grid component to support outputting the moving nest domain properly.
* Five HAFS related moving-nesting regression tests are added to test these newly added features. The regional_hafs RT was removed.

Co-authored-by: Daniel Rosen <daniel.rosen@noaa.gov>
Co-authored-by: Ufuk Turuncoglu <ufuk.turuncoglu@noaa.gov>
Co-authored-by: uturuncoglu <turuncu@ucar.edu>
Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>
Co-authored-by: William Ramstrom <William.Ramstrom@noaa.gov>
Co-authored-by: A-Kyle <kyle.ahern@noaa.gov>

…_t from ccpp_types; contains bug fix for WW3 debug (ufs-community#1130)


Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov>

* update all tests using 1deg MOM6/CICE6
* pre-pend ufs to existing topo edits filename when
creating the new file
* update input-data directory

…s-community#1152)

* Updates to stochastic_physics and fv3 and CI

… moisture property calculation (ufs-community#1176)

…mmunity

…r intel licenses

…ent in sgscloud_radpre

…ional veg (ufs-community#1143)

Updates to allow land perturbation scheme to be applied for Noah-MP. Currently, for Noah-MP model parameters can perturb only vegetation fraction.

Main code changes:
-added lsm_noahmp model option to lndp_type==2 land perturbation scheme (fv3-atm, stochastic_physics)
-updated comments
-cleaned up the namelists to make the different options clearer. Removed misleading lndp_each_step variable from gfs_physics_nml, and replaced it with "lndp_model_type" in the nam_sfcperts namelist for the different forecast types (cycling DA, short forecasts, perturbing only initial conditions) (fv3-atm, stochastic_physics, ufs-weather-model)
NOTE: see note below, re: specification of smc perturbation for RAP/HRRR/etc (lndp_model_type==2)
-revised code in stochastic_physics_wrapper to only allocate arrays that will be used when passed into lndp_apply_perts (fv3-atm)
-deleted unused albedo arrays in stochastic_physics_wrapper and lndp_apply_perts (fv3-atm, stochastic_physics)
-fixed bug causing precision errors when calculating the soil moisture ice content (often ~0.0; stochastic_physics)
-fixed bug in which lndp_apply_perts wasn't called for nscyc = 0. (fv3-atm)
-increased max_nvar_lndp at Jeff Ator's request (fv3-atm)
-added a new test for the Noah-MP and lndp==2 combination (ufs-weather-model)

…nd reduce wall clock time used for the cpld_control_c192_p8 test on Jet (ufs-community#1156)

Co-authored-by: Yunheng Wang

…unity#1189)


* Update CMEPS submodule
* Add GOCART documentation

Co-authored-by: Li Pan <Li.Pan@noaa.gov>

…ommunity#1171)

Combined PROD and REPRO build modes into 'Release' build type. Now only 'Debug' and 'Release' build type are supported.
Both build types must produce bit-for-bit reproducible outputs using different number of threads, mpi tasks, different domain decomposition, have reproducible restarts etc.

* replace pwatclm to pwat in the all diag tables under tests/parm/diag_table.