* See #43 #34 #31

…c-v4 back to master (#113)

* Update CCPP version number from 3 to 4
* gfsphysics/GFS_layer/GFS_physics_driver.F90: update comment on location of code in CCPP
* Add no_nsst CCPP suites from public release
* Bugfixes for CCPP: check for and correct syntax of \htmlinclude lines

…s.F90, ... (#115)

* atmos_model.F90: bugfix for GNU compiler
* Update CCPP suite definition files suite_FV3_GFS_2017_gfdlmp_regional.xml and suite_FV3_GFS_2017_gfdlmp_regional_c768.xml
* gfsphysics/CCPP_layer/CCPP_typedefs.F90: set pointers to hydrometeors only if valid
* Remove non-existent include directory namphysics

(1) Introducing a separate array "tiice" to store internal ice temperature. "tiice" will be added to phyf*nc output only when frac_grid=T.
(2) When cplflx=T, initializing ice fluxes by PBL calculated values when fluxes from CICE are unavailable.
(3) Adding frac_grid to namelist and no longer modifying it inside FV3GFS_io.F90. frac_grid=F by default.

remove cheyenne.pgi from CCPP config (ccpp/set_compilers.sh, ccpp/build_ccpp.sh)

* Merge branch 'man_hafs_sas_without_updates_of_dtc_develop_49b73a8f4149ca88f071dbaae81f1769b120f1e0' into HEAD
* gfsphysics/physics/GFS_debug.F90: add capability to debug 1-d logical arrays
* Clean up error messages in gfsphysics/GFS_layer/GFS_typedefs.F90

Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>

* Change 'mytile' to 'mygrid' corresponding to the change in atmos_cubed_sphere

* physics update from GFS.v16.0.4
* GFS.v16.0.4 physics udpate
* remove whitespaces in sfc_diff.f
* keep z0 unchanged in coupled mode in sfc_diff.f
* fix IPD run
* point to NCAR ccpp-physics branch

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>

…133)

* Update .gitmodules and submodule pointer for fv3atm for code review and testing

* Revert change to .gitmodules and update submodule pointer for GFDL_atmos_cubed_sphere

- output of auxiliary arrays (2d, 3d) from CCPP to assist developers debugging their physics
- correctly output 3-dim tendencies for t, u, v, qv, ozone from CCPP physics
- mandatory changes for the CCPP framework updates to handle blocked data structures correctly: fix inconsistent use of `horizontal_dimension` (ix) versus `horizontal_loop_extent` (im) and other metadata corrections
- remove old pset logic from `ccpp_prebuild_config.py` (was required for CCPP dynamic build)
- updates to all suite definition files: change the order of interstitial schemes get_phi_fv3+GFS_suite_interstitial_3 and GFS_DCNV_generic_pre to match the logical flow (does not change the answer)
- move CCPP physics initialization calls in `atmos_model.F90` so that the physics can see the data from the restart files at initialization time
- add capability to read large-scale and small-scale orographic data when using GSL drag suite
- add additional fields to restart files as required for GSL physics updates
- new suite definition files for RAP and HRRR configurations
- capability to call radiation for the first `nhfrad` physics time steps for cold starts, afterwards on the cycle defined by the radiation time step

* Update suite_FV3_GFS_2017_fv3wam.xml

* point to the dycore branch with Toms fix
* update Toms regional DA fix
* merge to fv3 develop branch
* add Dans Changes for when INTERNAL_FILE_NML is not used and update ccpp framework/physics
* remove hardcoded levp=65 for source_FV3GFS
* point back to EMC dycore repo

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>

This PR contains cleanup work to address wrong units and some issues raised in recently merged PRs:
- correct units for latitude, longitude, and pi
- correct standard name air_temperature_save_from_cumulus_paramterization to air_temperature_save_from_convective_parameterization
- remove unused variables in two routines in `GFS_typedefs.F90`
- remove recently introduced variable `cycling` (part of GFS_control DDT), now a local variable in `physics/module_MYNNPBL_wrapper.F90`
- change order of interstitial schemes in `ccpp/suites/suite_FV3_GFS_2017_fv3wam.xml` to match other SDFs

Fixes #138 and parts of #137.

* This is EMC flake model
* Updated .gitmodules file under FV3
* Removed the reset of lake fraction and lake depth statements
* point to ccpp physics branch flake
* Reset lkm to 0
* Swapped the order of calls in the suite file
* update to the latest ccpp/physics branch
* Revert change to .gitmodules and update submodule pointer for ccpp-physics

…0/07/21) (#147)

- remove `include ./depend` from several GNU makefiles (from @DusanJovic-NOAA)
- correct CCPP version number in several suite definition files
- GFS_typedefs.F90: allow using `iopt_snf == 4` for other microphysics schemes than GFDL MP (required for RRFS, needs NoahMP and Thompson)

)

As the title says. Note that the affected files are for the gnumake build - if we had transitioned entirely to cmake, we wouldn't need to maintain these files any longer.

* atmos_model.F90: remove dependency of stochastic physics on IPD_Control
* Add mpi_wrapper to stochastic_physics to substitute calls to fv_mp_mod routines
* Make cellular automata code independent of fv_mp_mod
* Make cellular automata code independent of atmosphere_mod
* Add halo exchange routine to stochastic_physics code
* Remove dependency on GFS_coupling_type from stochastic_physics.F90
* Remove dependency on GFS_grid_type in stochastic_physics and stochastic_physics_sfc
* Cleanup work, avoid unnecessary data copies
* Move stochastic physics code into its own wrapper/driver
* Remove dependency on Statein, Coupling and Intdiag DDT from cellular_automata_sgs.F90
* Compile kinddef module, cleanup stochastic_physics_wrapper.F90
* Update cmake build system
* Fix a bug in atmos_model.F90, inadvertetly removed a closing parenthesis
* Update to build system for stochastic_physics_wrapper following cmake updates
* Update gnumake build to include stochastic_physics wrapper
* Remove commented out lines from stochastic_physics/makefile

Co-authored-by: Jun Wang <jun.wang@noaa.gov>

* Add infrastructure to FV3 for recent RRTMGP improvements in ccpp-physics
* Move allocate statements
* Updated ccpp-physics
* Updated physics. Some changes on FV3 side to handle physics changes.
* Updated .gitmodules
* Revert change to .gitmodules and update submodule pointer for ccpp-physics
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

#155)

Fixes several bugs in several physics schemes. 
Adds update to the two-way WW3 atmosphere coupling.
Save surface roughness over water, ice and land in three separate variables so that restarts can be reproducible, even for the fractional grid case.
Makes uncoupled standalone GFS work with fractional grid.

Co-authored-by: Jessica.Meixner <Jessica.Meixner@noaa.gov>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>
Co-authored-by: Jun.Wang <Jun.Wang@noaa.gov>

* Diagnostic 3D instantaneous cloud fractions added.
* Bug fix for reflectivity in restart files.
* Update to GFS_restart.F90 to include if block to test for reflectivity flag.

* add esmf810 VMEpoch change and iau restart timing change

* update to pre-existing land perts scheme, ready for addition of the new scheme
* updates to land perts scheme, so that namelist input and control_type variables are in generic (i.e., variable agnostic) arrays
* minor bug fix GFS_typedefs.meta
* Phil's ccpp changes
* minor bug fix
* Lndp updates, including moving around the calling structure.
* lndp clean-up
* lndp submodule clean-up
* Updated submodules for merge.
* Fixed typo in vegfrac name
* deleted GFS_land_perts.F90 (moved to stochastic_physics)
* Removing FV3 dependency from stochastic_physics, and into wrapper
* Fix linker problem in gfsphysics/CMakeLists.txt by removing physics/physparam.f from IPD sources
* edits to compile with gnumake
* Revert change to .gitmodules for ccpp-physics and update submodule pointer for ccpp-physics

Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>

This PR removes dependency information from the CCPP prebuild config. See NCAR/ccpp-framework#308 and NCAR/ccpp-framework#317 for details on the motivation for this change and the actual implementation. It also removes some legacy code used by the dynamic CCPP build in the past.

This PR also contains the changes in #156, i.e. the completion of adding the active attribute to GFS_typedefs.F90. On top of this PR, the missing active attribute for phy_fctd is added.

Additionally, gfortran-10 compiler flags are added to CCPP's CMakeLists.txt.

* set up dycore_data at atmos_init
* fix syntax error in atmos_model.F90
* put in initial fields in fv3 export fields at init
* add state_diagnose from Denise
* fix state diagnose on write tasks


Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: Denise.Worthen <denise.worthen@noaa.gov>

Add two new interstitial variables to GFS_typedefs.{F90,meta} that are required for the RRTMG cloud overlap additions by @mjiacono (see NCAR/ccpp-physics#487). Other changes:

* fix wrong metadata in GFS_typedefs.meta (optional and intent are not valid for host model variable tables)
* note that RRTMG and RRTMGP use different interstitial variables for the decorrelation parameter alpha; this is because RRTMGP only works when the number of model levels is the same for radiation (levr) and other physics (levs), while RRTMG works with different numbers of levels; only the one in use gets allocated
* replace GSL drag suite with CIRES UGWP/GFS GWD in ccpp/suites/suite_FV3_RRFS_v1beta.xml (cherry-picked from PR #173 for release/public-v2)

…ry update in dycore (#178)

* contributions from @SMoorthi-emc to fix the global restart reproducibility and to keep compiling without CCPP
* updates the submodule pointers for GFDL_atmos_cubed_sphere and ccpp-physics
* bugfix in ccpp/CMakeLists.txt to correctly set AVX2 flags or not (discovered by Yunheng)
* changes mod_name of non-phys tendencies in GFS_diagnostics.F90 to gfs_dyn from gfs_phys (from @grantfirl)

* replace #ifdef OPENMP with #ifdef _OPENMP
* OpenMP link libraries
* fix typos and missing stuff
* clean up compile defs
* move CCPP code generator call to FV3, where it belongs
* install targets are updated
* minor cleanups

…ep 1) to develop (#186)

- update the syntax in the XML suite definition files, replace `lib="ccppphys" ver="N"` with `version=1` which indicates the suite definition file format version (i.e. the XML schema version) rather than the release version of ccpp-physics ; update the XML schema for the CCPP suite definition files (`suite.xsd`)
- add variables in `GFS_typedefs.{f90,meta}` that are require to support the removal of the GFS DDT dependency in the radiation physics (mainly additional indices; see NCAR/ccpp-physics#508)

* update dynamic core submodule with hord=-5
* update ccpp/framework submodule

* add parallel netcdf call in wrt grid comp
* output restart files at non-integer forecast time
* bug fix for fcstField index and add error message for lossy compression for regional grids

HWRF physics implementation in CCPP
- addition of new CCPP schemes to ccpp_prebuild_config.py
- update of suite definition files related to HWRF physics
- update of GFS_typdefs.{F90,meta} with new/modified variables for HWRF physics
- additional logic in FV3GFS_io.F90 for HWRF Noah LSM

Co-authored-by: Jun.Wang <Jun.Wang@noaa.gov>
Co-authored-by: Jili Dong <Jili.Dong@noaa.gov>
Co-authored-by: Bin Liu <Bin.Liu@noaa.gov>
Co-authored-by: Chunxi.Zhang-NOAA <Chunxi.Zhang@noaa.gov>
Co-authored-by: andrew.hazelton <andrew.hazelton@noaa.gov>
Co-authored-by: Jili.Dong@noaa.gov <Jili.Dong@v72a1.ncep.noaa.gov>
Co-authored-by: ZhanZhang-NOAA <zhan.zhang@noaa.gov>
Co-authored-by: Grant Firl <grantf@ucar.edu>
Co-authored-by: Man.Zhang <Man.Zhang@noaa.gov>
Co-authored-by: Dom Heinzeller <dom.heinzeller@noaa.gov>

* New metadata for GP scheme.
* Removed redundant importing of kind_phys
* add units to index_for_diagnostic_printout metadata
* Bugfix in GP sampling routines.

* update post lib to upp lib and add dzmin change in fv3 dycore
* add dycore change #35
* merge with top of dev/emc dycore branch
* remove duplicate read_data in fms_mod in external_ic.F90

* Fix to allow quilting with non-factors for layout (#244)
* Remove the inline comments

…, updates to other GSL physics (#202)

This PR updates the GSL physics and does a few other things:

*add --debug to ccpp_prebuild.py call when model is compiled in DEBUG mode, and pretty print the output in the build log (fixes #187 and ufs-community/ufs-weather-model#135)
*add unified gravity wave drag (called unified ugwp) that combines the UGWP v1 with the GSL drag suite
*add suite definition file for GFS v16beta for coupled model
*move static array zs (depth of soil layer), dimensioned as 1:lsoil_lsm from Sfcprop to Model (since this is a model configuration and only needs to be stored once, not for each block)

Co-authored-by: DomHeinzeller <58610420+DomHeinzeller@users.noreply.github.com>
Co-authored-by: samuel.trahan <Samuel.Trahan@noaa.gov>
Co-authored-by: hannah barnes <hannah.barnes@noaa.gov>
Co-authored-by: tanyasmirnova <tanya.smirnova@noaa.gov>
Co-authored-by: Joseph Olson <Joseph.B.Olson@noaa.gov>
Co-authored-by: Michael Toy <michael.toy@noaa.gov>

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.