update to NOAA-EMC fork #3
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* fv3atm issue #37: fix the real(8) lat/lon in netcdf file * fv3atm #35: Reducing background vertical diffusivities in the inversion layers * fv3atm #24: bug in gfsphysics/physics/moninedmf_hafs.f * fv3atm #18: Optimize netcdf write component and bugfix for post and samfdeepcnv.f * set (0-1) bounds for ficein_cpl * remove cache_size due to lower netcdf verion 4.5.1 on mars * Change ice falling to 0.9 in gfsphysics/physics/gfdl_cloud_microphys.F90
* netcdf parallel writing and lon/lat in netcdf file * some changes to get it to (almost) run on hera * lat should be in degrees - remove conversion to radians. * import updates from jswhit/fv3atm * more bug fixes - now works on hera * specify collective access if compression turned on. * use classic model * bug fixes for parallel IO with compression * fix calculation of max compression error * turn off shuffle filter * code simplification * remove debug print * don't use parallel IO for 2d file (since it seems to increase run time) * allow multiple values of output_file, as long as they all start with 'netcdf' * use default chunksize for 2d vars * delete commented out macro ESMF_ERR_ABORT * delete rad2dg * add module_write_netcdf_parallel.F90 * add option to build without parallel netcdf (-DNO_PARALLEL_NETCDF) * fix typo * stub file for building without parallel netcdf lib * allow chunksizes for 2d arrays to be set in model_configure (ichunk2d,jchunk2d) Default is size of array on each write task. * add ichunk3d,jchunk3d,kchunk3d to specify 3d chunksizes. Default is now ichunk3d,jchunk3d same as array size on each PE, kchunk3d=nlevs This results in the fastest writes on hera. * fix typo * put ifdefs in module_write_netcdf_parallel.F90 so no stub file needed * don't need this file anymore * remove module_write_netcdf_parallel_stub.o target * use specified chunksizes for serial IO. If chunksize parameter negative, let netcdf library choose defaults. * update comments * get output_file without esmf call error * syntax fix * fix stub interface in module_write_netcdf_parallel.F90 for cmake build Co-authored-by: junwang-noaa <37633869+junwang-noaa@users.noreply.github.com>
* add namelist variable iau_drymassfixer and use consistent coupled fields * dump out coupled fields in native grid for fv3 * add default(none) for openmp in post_gfs.F90 * update fv3 dycore with reproduce option in g_sum * change fv3 dycore to point to the NOAA-EMC dev/emc branch
* github version of latest branch * some fixes to physics driver * adding import field of z0 surface roughness length and cplwav2atm flag for coupling wave to atm * removing 271.2 near line 1884 * minor update of atmos_model.F90 * updating GFS_typedef for includeing ras in ccpp, plus minor mod in physics driver * after merging with Jessica's wave update in fv3 * coupling with ww3 * after merging with fv3atm develop branch and updating for ras * FV3 updates for RAS MG3 SHOC so that IPD and CCPP reproduce in REPRO mode * updating mg driver, physics driver and typedef * updating gcm_shoc.f90 to turn on commented code in assumed pdf * constraing imported ice fraction in atmos_model.F90 * after merging with NOAA-EMC/fv3atm/develop * minor fix to atmos_model.F90 and IPD physics driver * updating .gitmodules * adding two couplrd suites * a bug fix in atmos_model.F90, added a logical frac_grid_off to enable reading fractional grid orography file and run as no fractional grid, and minor bug fix in physics driver related to the fractional grid - FV3GFS_io.F90 is modified to use lake fraction if it exists to distinguish lake from ocean * adding con_csol to GFS_typedefs.F90 and GFS_typedefs.meta for CCPP * Update long names of hydrometeors to match the ccpp-physics change * reverting white space changes in .gitmodules * adding ignore_lake flag to GFS_typedefs.F90 andFV3GFS_io.F90 to preserve the option used in current s2s benchmarks * settng the momentum, sensible and latent heat fluxes over land exported to the mediator set to large values and over 100% sea ice set to values imported from icemodel. The mask identifying the ocean points to the mediator is correted based on ocean fraction. Updates also include name changes for the ice fields as changed by Denise Worthen. Also added an ignore_lake option to the namelist * changing variable puny to epsln in atmos_model.F90 on Denise's recommendation * added a new namelist parameter, min_lake_height, with default value of 250m, changeable by user to give more generality * update gcycle * point atmos_cubed_sphere to NOAA-EMC repo and ccpp/physics to SMoorthi-EMC SM_Jan102020 branch * reverting definition of do_cnvgwd in GFS_typedefs.F90 * removed 3 lines from gcycle.F90, which I previously forgot to delete * fixing a bug in gcycle update * removing updating tsfco in gcycle when nsstr is on * updating .gitmodules to point to NCAR/ccpp-physics master branch 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>
* fix omp error in dycore and atmos_model.F90 * Update atmos_cubed_sphere submodule
fv3atm:
fractional landmask changes (from @shansun6)
ccpp-framework:
bugfixes for handling optional arguments (no impact on current setup)
bugfix for debug messages (no impact on current setup)
ccpp-physics:
GFSv16 physics updates
add moninedmf_hafs
scientific documentation for NoahMP and satmedmfvdifq
bugfix for threading (avoid dead lock) when calculating Thompson MP lookup tables
addition of radar reflectivity reset switch for Thompson MP, bugfix for non-aerosol Thompson runs (from @ericaligo-NOAA)
fractional landmask changes (from @shansun6)
CCPP version of RAS, updates to shoc and MG (from @SMoorthi-emc)
bugfixes when levr < levs (from @SMoorthi-emc)
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