* Per-file CODEOWNERS in ccpp/physics to set up automatic review requests

…OAA-EMC#440)

* Remove ESMF Alarm and TimeInterval variables from module_fv3_config.
* Variables nfhmax, nfhmax_hf are unused outside InitializeAdvertise. Declared them as local variables.
* There is no need to keep duplicates of all time related variables in atm_int_state when we can easily access them from atm_int_state%Atm.
* Remove redundant call to fms_init
* Add few missing ESMF_LogFoundError checks in module_fcst_grid_comp.F90
* Delete time_utils.F90. Unused.
* print only actual errors to stderr, everything else to stdout
* Move realizeConnectedCplFields to module_cplfields from module_cap_cpl
* Declare Atmos as module variable, and remove atmos_internalstate_wrapper
* Move code from clock_cplIntval to InitializeAdvertise
* Removed INTERNAL_FILE_NML from atmos_model.F90

…OAA-EMC#443)

* Remove old comments from GFS_typedefs.F90.
* Update logic that sets Model%cnvcld = .false.

…AA-EMC#447)

* CCPP physics updates from PR NOAA-EMC#806(only diagnostic changes for RRTMGP - small diag-only RT impact for tests involving RRTMGP),NOAA-EMC#807 (only aborting model if sfc emis file not present when needed) ,NOAA-EMC#813(only SCM-specific physics changes)

…ice and NoahMP tsurf bugfix) (NOAA-EMC#452)

This PR contains the ccpp physics PR NOAA-EMC#808 and NOAA-EMC#816. 808 addresses an error in the momentum roughness length over tiles with ice. 816 fixes an occasional segfault bug related to the tsurf variable in NoahMP and updates to "improve snow simulation in NoahMP for P8".

* Add 'SetRunClock' specialization routine to FV3 NUOPC cap, which sets fv3 model clock. FV3 cap does not keep local copy of clock (clock_fv3) as saved module variable anymore.
* Minor code cleanup.

…-EMC#445)

Clean up the exponential cloud overlapping method in RRTMG, which reflects the practice of the pre-2018 operational HWRF model.

…rtran code and CCPP metadata (NOAA-EMC#431)

* Add additional diagnostic arrays for radiation-microphysics development
* Bug fixes for WAM model runs with levr < levs

* Update UPP revision
* Add foundation temperaure in GFS read interface for inline post.

* update submodule pointer for regression testing of ccpp-physics#812

…files (NOAA-EMC#455)

* Fix uninitialized variable zmtnblck in ccpp/data/GFS_typedefs.F90
* Fix typo in CCPP standard name for ncnvwind in ccpp/data/GFS_typedefs.meta
* Add ten 2d variables required for MYNNSFC restart reproducibility to ccpp/driver/GFS_restart.F90
* create initial p8 suites, P8 initial SDFs as copies of FV3_GFS_v16_coupled_nsstNoahmpUGWPv1
and FV3_GFS_v16_nsstNoahmpUGWPv1

Co-authored-by: Denise Worthen <denise.worthen@noaa.gov>

…#461)

* modify FV3GFS_io.F90 by fixing errors associated with initializing snow depth over ice in the case where both land and water coexist (i.e. fractional grid case)
* z0ice is changed to 1.0 cm from 1.1cm in atmos_model.F90

…nal HRRR (NOAA-EMC#457)

- 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.
* HRRR-like radar-derived temperature tendencies
* Give a warning when convection is enabled with radar tten
* Fix uninitialized variable zmtnblck in ccpp/data/GFS_typedefs.F90
* Add ten 2d variables required for MYNNSFC restart reproducibility to ccpp/driver/GFS_restart.F90

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

* Added a new suite definition file: suite_FV3_HAFS_v0_thompson_tedmf_gfdlsf.xml. This SDF is a legacy hwrf SDF but only the GFDL surface layer scheme and the Thompson scheme are kept.

…hompson MP (NOAA-EMC#462)

* This PR updates the submodule pointer for ccpp-physics for the changes described in NCAR/ccpp-physics#786 (Update consistency checks and effective radii calculation for Thompson MP)

…A-EMC#466)

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

…mework and physics (NOAA-EMC#467)

*Change standard name and unit of CCPP error flag variable in CCPP framework and physics.

* Implement ESMF-managed-threading for fcstComp and wrtComp's.

*This PR addresses part 2 of CCPP issue NOAA-EMC#748 to activate the exponential-random cloud overlap method (iovr=5) in RRTMG.

* update write grid comp to have 2D decomposition on output grid.
* combine PR#468: Bug fix in FV3GFS_io.F90 for allocation of temp2d

Co-authored-by: Ted Mansell <ted.mansell@noaa.gov>

…(combined) (NOAA-EMC#475)

* add lsm_cold_start variable in GFS_typedefs.F90/meta and update ccpp/physics for testing
* includes @SMoorthi-emc 's bugfix for gwdps.f.

Update fv3 cap and write grid component to enable outputting multiple domains.
This is done be creating an array of fcstGrids, and array of rout handles where each element of these arrays correspond to one atm domain.
In the write grid component updates were made to allow grid spec parameters for each output grid to be specified separately.

Co-authored-by: Gerhard Theurich <theurich@sourcespring.net>

…-EMC#479)

…V3 and add the FV3_RRFS_v1alpha SDF. (NOAA-EMC#454)

Adds the necessary code in fv3atm to allow for Stochastically Perturbed Parameterizations (SPP) in a set of RAP/HRRR-based physics parameterizations. Specific to the fv3atm repository, code in this PR defines the necessary variables associated with various SPP-related fields (e.g., logical to activate SPP, parameterization-specific SPP variables, etc.) that are then passed to ccpp-physics.