…-physics for gsl/develop branch

Implementation of RUC LSM ice model in CCPP

* Squash-merge climbfuji:rucice_gfsv16dzmin into gsl/develop

* Fix bug in gfsphysics/GFS_layer/GFS_typedefs.F90 from merge

* Remove lsm_ruc_sfc_sice from suite FV3_GSD_v0_unified_ugwp_suite and update submodule pointer for ccpp-physics

* Remove sfc_sice from ccpp/suites/suite_FV3_GSD_v0_unified_ugwp_suite.xml

* Update submodule pointer for ccpp-physics

* Revert change to .gitmodules and update submodule pointer for ccpp-physics

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

* Fix for updating stochastic physics on separate time-step. (NOAA-EMC#199)

This bug fix allows the random patterns in the stochastic physics persist the for a period of time (defined as SKEBINT,SPPTINT, etc.) before calculating new patterns.
The fix is to move the allocation of the saved variables into the init section of stochastic_physics_wrapper, and remove the deallocates in the run section.

* Bug fixes in (1) running with frac_grid=T and GFDL MP and (2) restarting with frac_grid=T (NOAA-EMC#204)

* -- Pointing to Moorthi's modifications in ccpp/physics, which fixed the crash when running GFDL MP with frac_grid=T;
-- Not setting fice to zero in order to leave lake ice untouched;
-- Restart in the coupled model with the default physics is reproducible, if bad water temperature is only filtered at initial time;
Co-authored-with: Shrinivas Moorthi <[email protected]>
Co-authored-with: Denise Worthen <[email protected]>

* Revert change to .gitmodules and update submodule pointer for ccpp-physics

Co-authored-by: Phil Pegion <[email protected]>
Co-authored-by: shansun6 <[email protected]>

…s and bugfixes (NCAR#63)

* Move initialization of stochastic physics after the physics
initialization in CCPP.
* Add albedo variables to land perturbations with lndp_type=2 option. Change to accommodate soil perturbations with RUC LSM.

* Max/min soil moisture variables are introduced via GFS_Control_type
variables instead of through the use of namelist_soilveg*. This is a
more flexible way for different LSMs.

* Added pores and resid variables for max/min soil moisture to GFS_typedefs.f90.

* Remove tracer_sanitizer from all suites and from CCPP prebuild config

* Add namelist option to apply land surface perturbations at every time step, clean up stochastic_physics/stochastic_physics_wrapper.F90

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

…perturbed variables (NCAR#70)

* Added roughness length over land to the perturbed variables.
* Bugfix in gfsphysics/GFS_layer/GFS_typedefs.F90: remove Diag%cldcov, in particular the reset call because the variable is not allocated

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

* Fix for updating stochastic physics on separate time-step. (NOAA-EMC#199)

This bug fix allows the random patterns in the stochastic physics persist the for a period of time (defined as SKEBINT,SPPTINT, etc.) before calculating new patterns.
The fix is to move the allocation of the saved variables into the init section of stochastic_physics_wrapper, and remove the deallocates in the run section.

* Bug fixes in (1) running with frac_grid=T and GFDL MP and (2) restarting with frac_grid=T (NOAA-EMC#204)

* -- Pointing to Moorthi's modifications in ccpp/physics, which fixed the crash when running GFDL MP with frac_grid=T;
-- Not setting fice to zero in order to leave lake ice untouched;
-- Restart in the coupled model with the default physics is reproducible, if bad water temperature is only filtered at initial time;
Co-authored-with: Shrinivas Moorthi <[email protected]>
Co-authored-with: Denise Worthen <[email protected]>

* jedi-ufs with ccpp-physics submodule update (contains NOAA-EMC#201) (NOAA-EMC#211)

* updated CMakeLists.txt
* Changes for JEDI linking/control
* Update .gitmodules and submodule pointer for ccpp-physics for code review and testing
* Revert change to .gitmodules and update submodule pointer for ccpp-physics

Co-authored-by: Mark Potts <[email protected]>

* Final-final GFS v16 updates / restart reproducibility bugfixes (NOAA-EMC#212)

* updates the submodule pointer for ccpp-physics for the final-final (!) GFS v16 physics updates
* fixes a bug in io/FV3GFS_io.F90 to obtain restart reproducibility for uncoupled and coupled runs - contributed by @SMoorthi-emc

Co-authored-by: Shrinivas.Moorthi <[email protected]>

* RRTMGP coupling to Thompson MP in ccpp-physics (NOAA-EMC#208)

* Updated physics. Added infrastructure to FV3 to handle new GP capabilities. Thompson MP, LW scattering, Use of LW-jacobian to update surface tendencies.
* Some small changes to work with physics improvements to RRTMGP.
* RRTMGP working with Thompson MP.
* Updated .gitmodules.
* Updated physics. New interstitials.
* Synced with NCAR/master
* Updated ccpp-physics
* Updated physics submodule.
* Cleanup
* Update physics
* Updated physics submodule pointer.
* Updated physics submodule hash.

* Minor bug fixes to CCPP UGWP (update submodule pointer for ccpp-physics) (NOAA-EMC#216)

Update the submodule pointer for ccpp-physics for minor bugfixes in CCPP's Unified Gravity Wave Drag parameterization.

* Remove IPD (step 1) (NOAA-EMC#215)

Remove all IPD source files that are not needed to compile with CCPP. Update gfsphysics/CMakeLists.txt and gfsphysics/GFS_layer/GFS_driver.F90 so that the code compiles after removing IPD sources.

Also: update submodule pointer for GFDL_atmos_cubed_sphere to include PR NOAA-EMC/GFDL_atmos_cubed_sphere#48 ("Removed use of mpp_node for use with FMS 2020.04").

* Update submodule pointers for ccpp-framework (ccpp_prebuild bugfix) and ccpp-physics (RRTMGP GFDL-MP bugfix) (NOAA-EMC#218)

Update the submodule pointers for ccpp-framework and ccpp-physics for the changes described in
NCAR/ccpp-framework#343 and NCAR/ccpp-physics#536.

* Remove unnecessary SIMD instruction sets from ccpp/CMakeLists.txt (NOAA-EMC#220)

* Remove additional/unnecessary SIMD instruction sets from ccpp/CMakeLists.txt

* Implementation of CCPP timestep_init and timestep_final phases (NOAA-EMC#217)

- replace calls to CCPP step `time_vary` with `timestep_init` in `atmos_model.F90`, add call to CCPP step `timestep_final` 
- update `ccpp/driver/CCPP_driver.F90` with calls to CCPP `timestep_init` and `timestep_final`
- add `h2o_def.f` and `ozne_def.` to `ccpp_prebuild_config.py`
- update of `gfsphysics/GFS_layer/GFS_typedefs.F90`: cleanup work for o3 and h2o physics (required by the updates to the CCPP time vary physics)
- update metadata in `gfsphysics/GFS_layer/GFS_typedefs.meta` for the above changes, and clean up the index used for the surface wind enhancement due to convection in the `phy_f2d` array (use proper index, not just the last entry in the array)

* add radiation_clouds_thompson_dependency in ccpp physics  (NOAA-EMC#225)

* using radiation_clouds_thompson_dependency ccpp physics branch
* point to ccpp master branch

* Remove IPD steps 3 and 5 (NOAA-EMC#224)

* Implementation of CCPP timestep_init and timestep_final phases in fv3atm; cleanup work in GFS_typedefs for o3 and h2o physics as a result of the changes to the time vary physics in CCPP
* Use proper index variable for surface wind enhancement due to convection in phy_f2d array in GFS_typedefs.{F90,meta}, move code to clear diagnostic buckets using GFS DDT bound procedures from atmos_model.F90 to CCPP_driver.F90
* First step of cleanup process: remove CCPP preprocessor directives, remove parts of unused IPD code, update cmake build system, Delete IPD source code, Replace IPD DDTs with GFS DDTs, Bugfix in atmos_model.F90; add missing call to GFS_externaldiag_populate, Move contents of gfsphysics/{CCPP_layer,GFS_layer} to ccpp/{data,driver}, entirely deleted IPD typedefs, Rename module GFS_driver to GFS_init
* Fix indentation in ccpp/data/CMakeLists.txt and ccpp/driver/CMakeLists.txt
* Add logic to set DYN32 depending on 32BIT setting
* Pass preprocessor directive GFS_TYPES to dycore to enable use of GFS data types
* Compile GFS_diagnostics.F90 without optimization, this leads to out of memory errors on wcoss_dell_p3

* Add CCPP rrtmgp fix (NOAA-EMC#237)

* ccpp physics merged with top of master
* point back to ccpp master branch

* Update develop from NOAA-GSL: RUC ice, MYNN sfclay, stochastic land perturbations (NOAA-EMC#239)

* Update .gitmodules and submodule pointers for ccpp-framework and ccpp-physics for gsl/develop branch
* RUC ice for gsl/develop (replaces NCAR#54 and NCAR#56) (NCAR#60) Implementation of RUC LSM ice model in CCPP
* Fix bug in gfsphysics/GFS_layer/GFS_typedefs.F90 from merge
* Remove lsm_ruc_sfc_sice from suite FV3_GSD_v0_unified_ugwp_suite and update submodule pointer for ccpp-physics
* Remove sfc_sice from ccpp/suites/suite_FV3_GSD_v0_unified_ugwp_suite.xml
* Update gsl/develop from develop 2020/12/08 (NCAR#61)
* Fix for updating stochastic physics on separate time-step. (NOAA-EMC#199)
This bug fix allows the random patterns in the stochastic physics persist the for a period of time (defined as SKEBINT,SPPTINT, etc.) before calculating new patterns.
The fix is to move the allocation of the saved variables into the init section of stochastic_physics_wrapper, and remove the deallocates in the run section.
* Bug fixes in (1) running with frac_grid=T and GFDL MP and (2) restarting with frac_grid=T (NOAA-EMC#204)
* -- Pointing to Moorthi's modifications in ccpp/physics, which fixed the crash when running GFDL MP with frac_grid=T;
-- Not setting fice to zero in order to leave lake ice untouched;
-- Restart in the coupled model with the default physics is reproducible, if bad water temperature is only filtered at initial time;
Co-authored-with: Shrinivas Moorthi <[email protected]>
Co-authored-with: Denise Worthen <[email protected]>
* Revert change to .gitmodules and update submodule pointer for ccpp-physics
* Update submodule pointer for ccpp-physics - MYNN surface layer updates and bugfixes (NCAR#63)
* Land stochastic perturbations (wrapper PR for NCAR#65) (NCAR#68)
* Move initialization of stochastic physics after the physics
initialization in CCPP.
* Add albedo variables to land perturbations with lndp_type=2 option. Change to accommodate soil perturbations with RUC LSM.
* Max/min soil moisture variables are introduced via GFS_Control_type
variables instead of through the use of namelist_soilveg*. This is a
more flexible way for different LSMs.
* Added pores and resid variables for max/min soil moisture to GFS_typedefs.f90.
* Remove tracer_sanitizer from all suites and from CCPP prebuild config
* Add namelist option to apply land surface perturbations at every time step, clean up stochastic_physics/stochastic_physics_wrapper.F90
* Stochastic land perturbations: add roughness length over land to the perturbed variables (NCAR#70)
* Added roughness length over land to the perturbed variables.
* Bugfix in gfsphysics/GFS_layer/GFS_typedefs.F90: remove Diag%cldcov, in particular the reset call because the variable is not allocated
* Update .gitmodules and submodule pointer for GFDL_atmos_cubed_sphere for code review and testing
* Revert change to .gitmodules for ccpp-physics, update submodule pointer for ccpp-physics
* Revert change to .gitmodules and update submodule pointer for GFDL_atmos_cubed_sphere
Co-authored-by: DomHeinzeller <[email protected]>
Co-authored-by: Phil Pegion <[email protected]>
Co-authored-by: shansun6 <[email protected]>
Co-authored-by: tanyasmirnova <[email protected]>

* Dycore change to add an option to zero-gradient BC for height advection and change dz_min as a namelist input (NOAA-EMC#232)

* Point dycore to a personal branch
* Point to new version of dycore
* Update the dycore version
* Update the dycore version
* Point to NOAA-EMC dev/emc dycore branch

* Remove gnumake build remnants, change v16beta to v16 (NOAA-EMC#234)

* Remove gnumake files
* Replace v16beta with v16 for all CCPP suites
* Remove unused CCPP_INCLUDE_DIRS/CCPP_LIB_DIRS from ccpp/CMakeLists.txt

* Move LSM vegetation lookup tables into CCPP, clean up RUC snow cover on ice initialization  (remove IPD step 2) (NOAA-EMC#244)

* Move LSM vegetation lookup tables into CCPP, clean up RUC snow cover on ice initialization
* Revert change to .gitmodules and update submodule pointer for ccpp-physics

* UGWP v0 v1 combined (NOAA-EMC#241)

* .gitmodules/gsl atmos-cubed cccp-fram cccp/physics
* update fv3atm from NOAA-EMC Jan 9
* new suite_FV3_GFS_v16b_ugwpv1.xml and modifications Jan 11/2021
* Added new logical flag do_ugwp_v0_nst_only which allows non-stationary drag from ugwp_v0 to be run with GSL drag suite
* Fix formatting in ccpp/data/GFS_typedefs.*
* Clean up allocation of arrays in ccpp/data/GFS_typedefs.F90, add active attribute (pass 1) to ccpp/data/GFS_typedefs.meta, strip trailing whitespaces from both
* Update and cleanup of metadata for UGWPv0, UGWPv1, drag suite
* Reorganize UGWP diagnostic variables in data/GFS_typedefs.{F90,meta}
* Bugfix for uninitialized data in ccpp/data/GFS_typedefs.F90
* Update submodule pointer for ccpp-physics
* Allocate 3d diagnostic arrays as dummy arrays if not used

Co-authored-by: valery.yudin <[email protected]>
Co-authored-by: Michael Toy <[email protected]>

* SDF for GFSv16 with Thompson (NOAA-EMC#238)

* SDF for GFSv16 with Thompson
* Delete suite_FV3_GFS_v16beta_thompson.xml
* update to new commit of Thompson MP in ccpp physics

Co-authored-by: Phil Pegion <[email protected]>
Co-authored-by: shansun6 <[email protected]>
Co-authored-by: Mark Potts <[email protected]>
Co-authored-by: Shrinivas.Moorthi <[email protected]>
Co-authored-by: dustinswales <[email protected]>
Co-authored-by: Jun Wang <[email protected]>
Co-authored-by: XiaqiongZhou-NOAA <[email protected]>
Co-authored-by: valery.yudin <[email protected]>
Co-authored-by: Michael Toy <[email protected]>
Co-authored-by: XiaSun-NOAA <[email protected]>

…NCAR#74)

* Update .gitmodules and submodule pointer for ccpp-physics for code review and testing

* Revert change to .gitmodules and update submodule pointer for ccpp-physics

* Add logical convert_dry_rho for Thompson MP, hardcoded to false
* Initialize all variables to NaN in ccpp-physics in DEBUG mode
* Update submodule pointer for ccpp-physics

… HEAD

…amework and ccpp-physics

…ter_20210316

Update gsl/develop from develop 20210316

…ange stats

…hanges.

…-physics for code review and testing

…ate_gsl_develop_from_develop_20210331

…ramework and ccpp-physics

…elop_20210331

Update gsl/develop from develop 2021/03/31

…tep-pgr-like-wrf

…-pgr-like-wrf

per-timestep diagnostic output: FV3 version of WRF noise parameter

Add diagnostic tendencies for all tracers. Move all d*3dt variables into a 4D sparse array stored as `dtend(i,k,dtidx(tracer,process))` to reduce memory usage.

* Fix incorrect units in dtend metadata

* Make the tracer tendency units mandatory.

…-physics

…ate_gsl_develop_from_develop

…amework and ccpp-physics

…elop

Update gsl/develop from develop 2021/05/21

…CAR#92)

* Fix incorrect units in dtend metadata

* Point to corresponding ccpp/physics branch

* fixes to dtend support:

1. Store rtg (AKA clw AKA qtr) instead of gq0 in DCNV and SCNV
pre/post for schemes that use convective transport. Tracers handled
solely by convective transport (ones not in rtg) are reported as
convective transport tendencies. Tendencies for variables in rtg are
reported as dcnv and scnv tendencies.

2. Report TKE tendencies from gfs v16 PBL.

3. Add diagnostic tendencies to drag_suite

4. Only report rayleigh damping tendencies if rayleigh damping is enabled

5. List all possible diagnostic tendencies, even if they are not
enabled. In the output, label them "selected" or "disabled."

6. Add phys_tend to the fv3_rap suite.

* Merge gsl/develop into ccpp/physics

* Add phys_tend to suite_FV3_GSD_SAR and remove some debug prints

* Remove some debug prints and commented-out code.

* Correct error in dtend variable availability list print.

* Enable convtrans diagnostic tendencies for number concentrations and qrimef.

* Disable cnvtrans diagnostic tendencies for schemes that do their own diagnostic tendency reporting.

* Point to gsl repositories

…ate_gsl_develop_from_develop_20210531

…f ccpp/physics and ccpp/framework

…view and testing

…into gsl_develop_hannah_and_joe_changes_combined_20210712

Minor code cleanup

…into gsl_develop_hannah_and_joe_changes_combined_20210712

…ysics

…_changes_combined_20210712

Wrapper for PR NCAR#100 (GF aerosols updates and tunings)

….F90

…ramework and ccpp-physics

…velop_20210721

Update gsl/develop from develop 20210721

…view and testing

…view and testing

…ysics

MYNN-EDMF updates and bug fixes

horizontal_dimension to horizontal_loop_extent

… GF_RadiationUpdate_RevertAerosols

…view and testing

Update .gitmodules and submodule pointer for ccpp-physics for code review and testing

…ysics

…pdate

Revert change to .gitmodules and update submodule pointer for ccpp-physics

Testing Flake model with HRRR and GSD_v0 suites.

…ysics

… GF_RadiationUpdate_RevertAerosols

…erosols

Gf radiation update revert aerosols

… update_gsl_develop_from_main_20210819

…hysics and ccpp-framework

…in_20210819

Update gsl develop from develop 2021/08/24

…ramework and ccpp-physics

…velop_20210921

Update gsl/develop from develop 2021/09/21

Tune clwdet (cloud water detrainment)
Make evfact (evaporation factor) and radiation factor scale-aware

…-physics for code review and testing

…ate_gsl_develop_from_develop_20211019

…3atm into hannah_gf_dom