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…leanup (#1355) * point to Man's ccpp-physics PR#944 branch: ccppv6 doc update
* Point FV3 to my branch upp_update_aug: Update inline post for RRFS and HAFS
* Update CDEPS
* * add 2 new MOM6 files in cmake * switch to use infra/FMS2 code in cmake * using MOM6 testing branch
* Run inline post in two hafs tests * Update two hafs tests that run inline post
* acorn and common .lua changes, hera.intel (not hera.gnu) .lua changes * CMake_Platform --> CMAKE_Platform * jet and wcoss2 .lua changes, cheyenne.gnu/intel lua updates, orion lua updates, typo in jet.lua files, Orion fixes for .lua files * Set proper number of non-advected tracers in regional_atmaq regression test. * Add proper convective scavenging coefficients to the regional_ataqm regression test. * Update ufs_s4.intel.lua, Update ufs_s4.intel_debug.lua
* update .gitmodules and FV3 submodule pointer for RTs: Misc NRL bugfixes
…include s2swa tests (#1401) * update GNU to include s2swa tests * switch to MOM6 testing branch: update MOM6 to its main branch 20220902 commit
…itch three HPC's to epic's HPC Stack (#1405) * Bring in barry's AQM changes for fengsha * Update to PIO 2.5.7 and add EPIC Stack locations for Orion, Gaea and Jet Co-authored-by: jkbk2004 <[email protected]>
* update/condense Ch2 Code Overview, Ch2 links, formatting, add Glossary terms, etc.
* point to WW3 feature branch * update submodule and branch used for WW3 * update WW3 to latest meshcap_stripped commit Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>
* Moving nest inline post fix * Enable hafs_regional_specified_moving_1nest_atm test on orion and wcoss2. Update BL_DATE Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>
…sics ufs/dev branch for fv3atm (#1429) * Officially changed the ccpp-physics pointer from NCAR/ccpp-physics main branch to ufs-community/ccpp-physics ufs/dev branch for fv3atm
* update crtm-2.4.0 library and remove yaFyaml * update GOCART Co-authored-by: Jun Wang <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>
…th the Thompson microphysics scheme (#1438) * added test case merra2_thompson * version worked for producing nifa and nwfa * added mraerosol for testing * use ltaersol=.true. and merra2 * using field table instead of code change for mraerosol * DNATS value was traced to merra2_thompson.nml.IN * added field and diag tables for regression tests * gocart aerosol coupled with thompson microphysics * Made CmakeModules and GOCART point to the correct hash * Updated FV3 for modifying the Thompson scheme Co-authored-by: anning.cheng <[email protected]> Co-authored-by: Dom Heinzeller <[email protected]> Co-authored-by: AnningCheng-NOAA <[email protected]> Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>
* update FV3: Use saved routehandles in fv3 cap init phase Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>
* Add RRFS-A to weekly tests
* Update input-data and hpc-stack containers * Update Dockerfile and opnReqTest * Update Jenkinsfile to handle PRs properly Co-authored-by: JONG KIM <[email protected]>
* .gitmodules updates and hash to rmontuoro/bugfix/aqm-build-system for AQM Co-authored-by: jkbk2004 <[email protected]>
…he P8 physics suite) (#1451) * This is equivalent to PR66 in NCAR/ufs-weather-model: Bugfix and optimization of prognostic closure for the P8 physics suite Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>
#1437) * fixes for rrfs debug tests (uninitialized memory in fv_regional_bc and module_bl_mynn) * rrfs 13km debug tests * smoke bug fixes for restart * RRFS tests, but smoke takes too long due to 2hr wallclock limit, needed for restart test * remove smoke test variants * 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 * update conus13km test list * workarounds and bug fixes from gnu compiler testing * atmos_cubed_sphere fixes&tweaks; ccpp/physics fix for precision issue that fails gfortran -DDEBUG=ON * 120s timestep for conus13km tests * atmos_cubed_sphere: simplify comments and explain snan * move task calculations to compute_petbounds_and_tasks in rt_utils.sh; call it from rt.sh * disable conus13km decomp and restart tests that are known to not match the control * hera.gnu tests pass, except conus13km decomp and restart which are expected to fail * move sanity checks to lsm_ruc and add "snow on ice" check * use i-1 & j-1 for two-point averages, when available * hera.gnu tests pass against new baseline after atmos_cubed_sphere i-j change * Replace many changes with atmos_cubed_sphere PR #220 * update stochastic_physics url Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>
* update FV3 submodule pointer and .gitmodules for RTs * small cloud tuning from Greg Thompson (#1410) * Simplify Jenkins pipeline Co-authored-by: Grant Firl <[email protected]> Co-authored-by: Jesse McFarland <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: JONG KIM <[email protected]>
* Sync WW3 develop with dev/ufs-weather-model, Oct 12th 2022 * fix needed for cheyenne lmod update * Update fv3_qsub.IN_cheyenne * acorn intel lua cray-mpich update * acorn intel debug lua cray mpich update Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: jkbk2004 <[email protected]>
* update components and add external land component support * use cubed_sphere_grid as output grid * point updated CMEPS fork * switch to another fix for inconsistent land sea mask issue * make grid file configurable for external land Co-authored-by: Ufuk Turuncoglu <[email protected]> Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>
* Add a new RT for SDF FV3_WoFS_v0 * Update delta_srw210 branch in ccpp/physics and minor bug fix in CCPP_typedefs Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>
…clouds, ESMF 8.4 support for AQM, Update WW3. (#1456) * Bring in AQM PR #24 changes * Update WW3 hash to DeniseWorthen/feature/updatewm * Update AQM hash, bringing in EXMF 8.4 support for AQM * remove bio from aqm.rc Co-authored-by: jkbk2004 <[email protected]>
* Improve radiative fluxes and cloud cover in FV3 for HR1 Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>
* Replace low resolution regression tests with high resolution. * Rename ICs and result directory * Remove "calendar" variable from namelists. * Remove unused scripts: gfdlmp_run.IN & gsd_run.IN * Add '--cpus-per-task=@[THRD]' to fv3_conf/fv3_slurm.IN_jet * add omplace to cheyenne qsub script Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]> Co-authored-by: Dusan Jovic <[email protected]>
… 550nm (#1475) * Adjust GFS diagnostic ADO output to the exact 550nm in ccpp/physics * Modify a few lines of code in FV3/ccpp/physics/physics/radiation_aerosols.f to make them properly indented Co-authored-by: JONG KIM <[email protected]> Co-authored-by: Brian Curtis <[email protected]>
…2273) * MERRA2 climatology upgraded to 2014 to 2024 mean
…+ develop]: Minor documentation bug fixes #2296 (#2281) * UFSWM - Add new capability to allow diagnostic accumulation bucket to change in fv3atm integration * FV3 - Add new capability to allow diagnostic accumulation bucket to change in fv3atm integration * UFSWM - Update requirements.txt; fix EMC broken link in Glossary; fix sample rt.sh run command for single RT run (add compiler)
) * UFSWM - A few miscellaneous minor fixes to regression test scripts - Bring in changes for WCOSS2 to match the spack-stack 1.6.0 setup - Bring in updated pnetcdf/pio for CICE - Print 'ECFLOW Tasks Remaining' message only when the number of tasks changes - Remove explicit 'set -e'. Use -v command line option for verbose mode - Remove 'Computing PET bounds and tasks' message - Fix bugs with log generation script (from @BrianCurtis-NOAA) - Uncomment new_compile=true in rocoto_create_compile_task - Removed unneeded colonifnco
*UFSWM:
*Updates modulefiles to spack-stack version 1.6.0
*Updates Hera GNU version to 13.3
…nts (ATM_DS2S and ATM_DS2S-PCICE) and regression tests (atm_ds2s_docn_dice and atm_ds2s_docn_pcice) (#2186) * UFSWM - Add ATM_DS2S and ATM_DS2S-PCICE applications by adding CDEPS dice and enabling prescribed ice CICE. Add corresponding atm_ds2s_docn_dice and atm_ds2s_docn_dice-pcice regression tests. New gnv1_nested regression test with Water in the West domain at C96 resolution using templates compatible with global-workflow * CDEPS - Add dice cplhist datamode * CICE - Enable ice prescribed CICE mode
*UFSWM - update WAM RT compatible with v17 *UFSWM - fix derecho modulefile path for Spack Stackv1.6
…s_cubed_sphere to fix a typo when printing out the nest grid corner locations #2323+Bump urllib3 from 2.2.1 to 2.2.2 in /doc/UsersGuide #2329 + Orion changes for switch to new OS - Rocky-9 #2336 (#2324) * CICE - Adds restart write capability at the end of a run for CICE * FV3 - * atmos_cubed_sphere - Update submodule FV3/atmos_cubed_sphere to fix a typo when printing out the nest grid corner locations * doc/UsersGuide/requirements.txt: Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.2.1 to 2.2.2. * Orion Spack stack modulefile update: Rocky-9 * update detect_machine.sh: hercules
… similar to hydrostatic method (#2327) * atmos_cubed_sphere - A new parameter, pass_full_omega_to_physics_in_non_hydrostatic_mode, has been added in dycore. When set to true, the omega calculation will match that of hydrostatic runs, using the formula omega = dp/dt. The default value is false, where the calculation remains omega = w * dp/dz as before.
* HR4 GWD update for FV3 * point to PR#549 of ccpp-framework * Update default_vars.sh: GWD parameters * Update global_control.nml.IN * update cpld case GWD parameters: gfsv17 * Update Jenkinsfile.combined fix multi-label removal * Update Jenkinsfile for ORT Pipeline * update input oro files for control_run.IN: gsfv17 --------- Co-authored-by: Grant Firl <[email protected]> Co-authored-by: Jong Kim <[email protected]> Co-authored-by: Dustin Swales <[email protected]> Co-authored-by: zach1221 <[email protected]>
* UFSWM -
* FV3 -
* atmos_cubed_sphere - bug fix to address debug mode crashes caused by floating-point exception in subroutine a2b_ord2 in model/a2b_edge.F90
…nd PR#2265) (#2335) * UFSWM - restore error checking to regression test system and add a self-test suite - Detect_machine.sh identifies Frontera --------- Co-authored-by: Sam Trahan <[email protected]> Co-authored-by: Benjamin Cash <[email protected]>
… in the GFS physics suite (#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.
* 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
* 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.
…omponents (#2370) * UFSWM - * CICE - initialize scalar field when created * MOM6 - initialize scalar field when created * WW3 - initialize scalar field when created
…s arrays (#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 #2277 + SKEB fix with d_con = zero #2374 (#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
* 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
* 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) (#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.
…3/SAS/MYNN fix) (#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
*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
* 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.
…#2430) * UFSWM - Use EMC/CICE:develop branch from CICE-Consortium:main * CICE - Use EMC/CICE:develop branch from CICE-Consortium:main
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