… in the GFS physics suite (ufs-community#2340)

* ccpp-physics - update convection and PBL schemes to improve cloud/convection interaction

* Output updraft value of convective cloud condensate in FV3 and CCPP

* update xkinv1 to 0.15

* add check if progsigma is true

* HR4 land surface upgrades to address surface cold biases

* update noahmp table

  * CMEPS - Sync CMEPS with ESCOMP/main.

…ity#2355)

* UFSWM - Fix dumpfields=true option in FV3 by using ESMF_FieldBundleWrite
  * FV3 - Fix dumpfields=true option by using ESMF_FieldBundleWrite

* Update rt_utils.sh. Set ECF_HOST on wcoss2 explicitly

…y#2373)

* UFSWM - Adds pass_full_omega_to_physics_in_non_hydrostatic_model parameter in the global_control.nml.IN namelist and
          sets it to true for non-hydrostatic runs. An additional field (omga) has been added to the diag_tables.

…ture for CCPP. More CMake modifications

…omponents (ufs-community#2370)

* UFSWM - 
  * CICE - initialize scalar field when created
  * MOM6 - initialize scalar field when created
  * WW3 - initialize scalar field when created

…s arrays (ufs-community#2183)

* UFSWM - In fv3atm and submodules, convert internal GFS DDTs from blocked data structures to contiguous arrays. This excludes the (external) `GFS_extdiag` and `GFS_restart` DDTs.
  * AQM - 
  * CDEPS - 
  * CICE - 
  * CMEPS - 
  * CMakeModules - 
  * FV3 - Convert GFS DDTs from blocked data structures to contiguous arrays (not including GFS_restart and GFS_extdiag DDTs)
    * ccpp-physics - Convert GFS DDTs from blocked data structures to contiguous arrays (affects `GFS_debug.{F90,meta} only`)
    * atmos_cubed_sphere - Convert GFS DDTs from blocked data structures to contiguous arrays and remove IPD_Data super DDT
  * GOCART - 
  * HYCOM - 
  * MOM6 - 
  * NOAHMP - 
  * WW3 - 
  * stochastic_physics -

… FV3 diag table documentation ufs-community#2277 + SKEB fix with d_con = zero ufs-community#2374 (ufs-community#2278)

* UFSWM - python scripts for yaml and rocoto-xml conversion, experiment setup, and test log output  
* Add python superlint option
* Documentation update: doc/UsersGuide/source/tables/fv3_diag_table.rst
    * FV3 - 
    * atmos_cubed_sphere - bugfix: allocates heat_source when skeb is True and d_con is zero

…mmunity#2381)

* using MOM6 test branch
      add MOM_dynamics_split_RK2b.F90 and MOM_EOS_base_type.F90 in cmake list
      add extra 8PE for cpld_debug_pdlib job
      set DEFAULT_ANSWER_DATE=20231231 in 5x5 case
      add USE_HUYNH_STENCIL_BUG = True in MOM_input
      using MOM6 restart file as BL for sfs and hafs_mom jobs

* remove USE_HUYNH_STENCIL_BUG = True in MOM_input
  switch FIX_USTAR_GUSTLESS_BUG=F to USTAR_GUSTLESS_BUG=T

* switch FIX_USTAR_GUSTLESS_BUG to USTAR_GUSTLESS_BUG for MOM_input_hafs

* set USE_HUYNH_STENCIL_BUG = True

…s-community#2375)

* UFSWM - Update the MOM_input templates and RT scripts to allow use of downscaled MOM6 and CICE6 warmstarts.

* update script variables and sfs test

* UFSWM - update g2tmpl library, g2 library, UPP hash. Sync parm files with new UPP version.
  * FV3 - update inline post for UPP, point UPP submodule to head of develop, revise spack.yaml

…ng in rt.sh (2388) + Add ability to read increment files on native cubed sphere grid (2304) (ufs-community#2389)

* UFSWM -  Unify CDEPS gfs, cfsr, and gefs datm datamodes. Add ability to read increment files on native cubed sphere grid.  Update rt scripts to fix checking the job exit status from Slurm and PBS schedulers.
  * FV3 - Add namelist parameter for cubed sphere increment read and update atmos_cubed_sphere hash for GFDL 
    Atmospheric Cubed Sphere PR #[342](NOAA-GFDL/GFDL_atmos_cubed_sphere#342)
     * atmos_cubed_sphere - Add ability to read increments from files on native cubed sphere grid
  * CDEPS - Unify CDEPS gfs, cfsr, and gefs datm datamodes. Rename CDEPS-related FILENAME_BASE to FILEBASE_DATM in 
     tests. Sunset gfs_hafs datamode.

…(H2O scheme refactor and C3/SAS/MYNN fix) (ufs-community#2408)

* UFSWM - Refactor NRL h2o photochemical scheme; add "tendency_of_vertically_diffused_tracer_concentration" as output 
     from the MYNN PBL scheme
  * FV3 - Refactor NRL h2o photochemical scheme; add "tendency_of_vertically_diffused_tracer_concentration" as output from 
     the MYNN PBL scheme
      * ccpp-physics - Refactor NRL h2o photochemical scheme; add "tendency_of_vertically_diffused_tracer_concentration" as 
         output from the MYNN PBL scheme

…Switch to using Aux history files in atm_ds2s_docn_dice test; Remove IFI tests (was ufs-community#2417) (ufs-community#2395)

* UFSWM - 
  * CMEPS - fix aux history functionality; sync with ESCOMP
  * UFSWM - use auxiliary history files as input for atm_ds2s_docn_dice; remove the IFI tests

 *MOM6 - update MOM6 to its main repo. 20240824 updating (GFDL's FMA PR)

* UFSWM - Update default parameter values for damping based off of work done for GW

…#2220)

* UFSWM - The fire_behavior component has been added and a new application created 'ATMF'. This work also includes a new regression test 'cpld_regional_atm_fbh' for testing two-way coupling of the atm component (fv3atm) and fbh component (fire_behavior)
  * CMEPS - CMEPS required modifications to be aligned with the changes to the ccpp physics package
  * FV3 - the fv3 cap has been modified to export atmosphere forcing data to the fire component when 'cpl_fire' is set to true. It will also import new fields for physics.
    * ccpp-physics - the ccpp physics package has been modified to add heat fluxes, upward specific humidity flux, and a smoke tracer from the fire component.

…ufs-community#2430)

* UFSWM - Use EMC/CICE:develop branch from CICE-Consortium:main
  * CICE - Use EMC/CICE:develop branch from CICE-Consortium:main

…to fms/2024.01 (ufs-community#2431)

* UFSWM - Bump libraries on WCOSS2 to ip/4.0.0 w3emc/2.12.0 and fms/2024.01

* Adjust FMS location and bump ufs_common.lua

* Acorn lua update for fms bump, remove ifi library load

* UFSWM -  Add support for Intel LLVM compiler
  * CICE -  Add support for Intel LLVM compiler
  * FV3 -  Add support for Intel LLVM compiler
    * ccpp-physics -  Add support for Intel LLVM compiler
    * atmos_cubed_sphere -  Add support for Intel LLVM compiler 
    * upp -  Add support for Intel LLVM compiler 
  * WW3 - Add support for Intel LLVM compiler

…r-model into feature/mpas-dycore-reorg