* 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 <[email protected]>

…#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 <[email protected]>

…(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 <[email protected]>

…-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.

Supports CCPP with new NSSL microphysics scheme, which has separate hydrometeor categories for graupel and hail (Mansell et al. 2010, JAS). This PR allows fv3atm to compile correctly with CCPP+NSSL, but a further update to atmos_cubed_sphere is needed to run correctly. The NSSL scheme is used in NSSL's daily FV3 convection-allowing forecasts, and the scheme itself is aimed at this scale (dx <= 4km). Testing is underway also with a preliminary Warn-on-Forecast FV3 ensemble.

* add p8 suite files
* fix 2phases intermediate restart

Co-authored-by: Raffaele Montuoro <[email protected]>
Co-authored-by: Jun Wang <[email protected]>

…inor CCPP cleanup and documentation updates (NOAA-EMC#487)

* Minor cleanup and documentation updates for CCPP; split CCPP finalize into physics_finalize and (framework) finalize

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

Co-authored-by: Ted Mansell <[email protected]>
Co-authored-by: Grant Firl <[email protected]>

…thern hemisphere (NOAA-EMC#497)

Subroutine `lambert` in the write component has been fixed to do the mapping on the southern hemisphere correctly.

)

)

…us a bug fix to the Thompson scheme PR #882 (NOAA-EMC#503)

* change ccpp-physics branch to feature/p8c_pbl_cp branch

* change ccpp/physics in feature/p8c_pbl_cp branch

* revised GFS_typedefs.F90 for the paramters in the saSAS scheme

* sync upp

* Revert "sync upp"

This reverts commit 429d046.

* sync upp to 0185bb9

* Merge remote-tracking branch remote/main for ccpp-physics and update .gitmodules

* Reset to zero coupling arrays for accumulated snow,  large scale rain, and convective rain at the end of each coupling step if coupling with chemistry model.
* Properly set kind type of literal constants defining zero and one.
* Initialize to zero canopy resistance output variablein noah/osu land-surface model subdriver.
* Re-implement radiation diagnostic output involving spectral band layer cloud optical depths (0.55 and 10 mu channels)
to prevent floating invalid errors due to uninitialized optical depth arrays.
* Temporarily disable filling export fields during the NUOPC Realize phase since it breaks coupling with aerosol component.
* Increase maximum number of input aerosol scavenging factors to accommodate AQM/CMAQ 5.2.1 chemical tracers.
* Remove inst_pres_height_surface from chemistryFieldNames as its imported already elsewhere

Co-authored-by: Raffaele Montuoro <[email protected]>

* Add explict treatment of convective cloud to RRTMGP.
* Some cleanup and bug fixes from previous commit. working now with Thompson MP plus radiatively active convective cloud.
* Updated physics. New interstitials.
* Added explicit MYNN-EDMF cloud coupling to RRTMGP.
* Added switches for sgs clouds in GP.
* Replaced cld_mynn_ naming convention with cld_pbl_
* Fixed inconsistency between G/GP in Thompson MP.
* Some more cleanup of cloud-fraction...
* Pulled in Qingfu's changes to ccpp-physics
* Synced physics with main
* Updated physics.
* Revert change from previous commits (sampling of different cloud types). New SDFs for p8c
* Changed arguments to implied shape.
* Renamed scheme file in SDF. Now common to both RRTMG and RRTMGP SDFs
* Syntax error in ccpp-physics
* Revert changes to names
* Renamed p8_rrtmgp SDFs
* Added bounding to temperature at layer-interface used by RRTMGP.
* Reorder loop
* Combined gp sw and lw aerosol routines. Modest speedup (~4%)

…apabilities (NOAA-EMC#501)

* 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: Dom Heinzeller <[email protected]>
Co-authored-by: Dom Heinzeller <[email protected]>
Co-authored-by: Grant Firl <[email protected]>
Co-authored-by: Daniel Rosen <[email protected]>
Co-authored-by: man.zhang <[email protected]>
Co-authored-by: William Ramstrom <[email protected]>
Co-authored-by: Ufuk Turuncoglu <[email protected]>
Co-authored-by: Dusan Jovic <[email protected]>
Co-authored-by: A-Kyle <[email protected]>
Co-authored-by: Gerhard Theurich <[email protected]>
Co-authored-by: Dusan Jovic <[email protected]>

…ccpp_types (NOAA-EMC#508)

* Split GFS_typedefs.F90: move GFS_interstitial_type to CCPP_typedefs.F90; Rename CCPP_interstitial to GFDL_interstitial; Import ccpp_t from ccpp_types instead of ccpp_api
* Add bugfix in ccpp/data/GFS_typedefs.meta: mark input_nml_file as active only if the number of lines in the file is greater than zero

…AA-EMC#516)

* Pass SPP namelist entries outside of stochastic physics routines.

* Fixes to SPP metadata

* Add active attribute to spp_prt_list

* Add active metadata flag to spp_stddev_cutoff

* Add active metadata flag for spp_var_list

… moisture property calculation (NOAA-EMC#520)

…les (NOAA-EMC#519)

…ional veg (NOAA-EMC#513)

Updates to allow land perturbation scheme to be applied for Noah-MP.

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)

…EMC#524)

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.

* Unify global and regional inline posts and add bug fix for dx/dy computation.
* Update upp revision to dc8bc68
* Set up different configurations of read max/min 2m T for global and regional FV3.

* Change RRTMGP to RRTMG in suite_FV3_GFS_v17_p8 and suite_FV3_GFS_v17_coupled_p8
* deleted or modified some SDFs related to RRTMGP or Thompson schemes
* added a new SDF file for P8 with rrtmgp

…OAA-EMC#529)

Merge in GSL institutional fork

* Changes to ccpp to support 32-bit physics in NRL Neptune model

* update downstream submodules

* updating ccpp/physics submodule and coupling fields

* update ccpp/physics submodule, restart capability

* Update submodules and restart files

* updates submodule

* addressing some review comments

* update submodules fetch upstream

* update ccpp/physics submodule

* change conditional check to <= for saftey

* addressing some review comments

* removing wclosureflg

* Allow CA to run on non-uniform blocksizes

* cleaning and updating submodules

* updating submodules

* update atmos_cubed_sphere

* updating submodule atmos_cubed_sphere

* .gitmodules

* updating atmos_cubed_sphere

* updating submodules

* merge with develop

* merging with submodules

* updating ccpp/framework and upp submodules

* address some review comments, bug in active, correct initialization in ccpp/physics

* put back some diagnostic fields

* merge upstream cppp/physics

* resolving some conflicts

* remove check to allow CA to be used with non-divisible blocksize

* Add active flag for conditional variables in meta data, update ccpp/physics submodule

* merge submodule ccpp/physics upstream

* merge with ccpp/physics main

* revert .gitmodules and add the merged ccpp/physics code

The current logic in CCPP_driver does not allow for buckets to be emptied every time-step.
This one-line modification fixes that.

…A-EMC#517)

* 20220505 Jesse Meng create branch upp_unify_inline_2d from

* 20220610 Jesse Meng update upp url

… temperatures (NOAA-EMC#552)

* typo caused potential temperature calculation to use exponentiation instead of multiplication

* ccpp physics: Fix RAP (Grell Freitas) decomp b4b issues; moninshoc.meta missing mfpbl.f dependency
* dycore: Fixes failure of decomposition test for regional case with nrows_blend > 0. Also fixes a bug where nrows_blend=1 caused a crash.

Co-authored-by: Dom Heinzeller <[email protected]>
Co-authored-by: Jun.Wang <[email protected]>

…C#550)

* Add 'time_iso' variable to 6-tile history files
* Add '_Encoding' attribute to time_iso

Co-authored-by: jswhit2 <[email protected]>

…#556)

* Update atmos_model and FV3GFS_io read performance when io_layout=1,1 and allow one to override data integrity checks in FMS restart logic

Co-authored-by: Jun Wang <[email protected]>

NOAA-EMC#525)

* Added coupling of GOCART aerosols with radiation related to issue#899 in NCAR/ccpp-physics

* Updated ccpp/physics to include Barry Baker's updates for wet deposition in the Thompson scheme

* Updated physics/rte-rrtmgp with the latest commit in ccpp/physics

* Update ccpp/physics to include the updates of precipitation fluxes outputs in the Thompson microphysics scheme

* Updated ccpp/physics for fixing a bug in mp_thompson.F90

…NOAA-EMC#558)

* update upp revision to 8767929

* modify dx/dy calculation for RRFS with domain over north pole

This adds support for 32-bit physics to the FV3, based on prior work on the Neptune model.

Co-authored-by: Dusan Jovic <[email protected]>

* Switch to fms2 io
* Model should fail in post_namelist is missing or there's an error during read

* update submodule for ccpp/physics: Revert calculation of T2m in NOAH-MP

…ork to support IAP model (NOAA-EMC#564)

* fix for Aerosols (4d vars) causing PET log errors
* Update CCPP Framework to support IAP model

* Gerhard: Initialize wrttasks_per_group member in a way that automatically considers ESMF-managed threading when active.
* fix the fields on pv and sigma levels
* update upp to fix pressure level TCDC

* update upp, ccpp/physics and cmakelist to use w3emc 2.9.2

…leanup (NOAA-EMC#566)

* update submodule pointer to Man's ccpp-physics PR#944 branch: ccppv6 doc update

* 1)update upp revision to 8ed92cb; 2)read instant model top longwave;
3)output lat/lon of four corner point for rotated lat-lon grid.

* First attempt at allowing inline post to run on multiple domains

* Call subroutines from post_fv3 module directly. Skip inline_post module.
Fix compilation without inline post.

* Call post_getattr_fv3 from post_run_fv3 instead from wrt grid comp

* Append '.nestXX' suffix to nest grib file names.

* Set 'numx' in post_run_fv3 instead in the write component

…OAA-EMC#578)

* update ccpp-physics hash: update surface net heat fluxes for AQM coupling

* add new variables for NRL's host-provided random number seeds

* add lextop to GFS_typedefs and change units of ltp

…ase. (NOAA-EMC#581)

* moving nest inline post fix

…in branch to ufs-community/ccpp-physics ufs/dev branch (NOAA-EMC#584)

* Officially changed the ccpp-physics pointer from NCAR/ccpp-physics main branch to ufs-community/ccpp-physics ufs/dev branch

…th the Thompson microphysics scheme (NOAA-EMC#588)

* version worked for producing nifa and nwfa

* added mraerosol in typedef

* use ltaersol=.true. and merra2

* Add consistency check for Thompson aerosol options to GFS_typedefs.F90

* using field table instead of code change for mraerosol

* Updates and bug fixes for Thompson-Merra2

Co-authored-by: anning.cheng <[email protected]>
Co-authored-by: Dom Heinzeller <[email protected]>
Co-authored-by: AnningCheng-NOAA <[email protected]>

…re for the P8 physics suite) (NOAA-EMC#592)

* This is equivalent to PR66 in NCAR/fv3atm: NCAR/main PR NOAA-GSL#66 (Bugfix and optimization of prognostic closure for the P8 physics suite)

…EMC#587)

* fixes and workarounds for uninitialized memory in fv_regional_bc

* initialize kmaxfire in module_bl_mynn

* smoke bug fixes for restart

* remove smoke bug fixes

* remove workarounds and fix remaining known bugs in ps_reg

* a few more surface pressure bug fixes; now the test case runs in debug mode

* ccpp/physics: module_sf_ruclsm imprecision workaround for gfortran -DDEBUG=ON

* move sanity checks to lsm_ruc and add "snow on ice" check

* use i-1 & j-1 for two-point averages, when available

* Replace many changes with atmos_cubed_sphere PR NOAA-EMC#220

* update gitmodules and point to PR branch of ccpp/physics

* Small cloud tunings from Greg Thompson (NOAA-EMC#580)

Co-authored-by: Grant Firl <[email protected]>

* fixes for land coupling
* work to support external land component side-by-side config
* fix issue with ort dbg test

* Add a new SDF named FV3_WoFS_v0 for SRW_v2.1 release

* Minor bug fix to add variable nf_albd in the host model data structure (CCPP_typedefs.F90)

* Enable AOD diagnostics when coupled with AQM

Co-authored-by: Raffaele Montuoro <[email protected]>

…A-EMC#599)

* Improve radiative fluxes and cloud cover in ccpp/physics for HR1