Recent mods from MPAS-JEDI

[snyderdad]

Here's a consolidated list of modifications from JCSDA-internal/MPAS-Model that we hope to merge with MPAS-Dev/MPAS-Model. All except cmake build are specific to core_atmosphere or core_init_atmosphere.

• Enable core_init_atmosphere to use mpas_new_unit and mpas_release_unit instead of fixed file unit numbers. See Make the handling of file units consistent for all unformatted files JCSDA-internal/MPAS-Model#12. Handled by PR Eliminate the use of hard-coded Fortran unit numbers in atmosphere code #988 .
• Add optional parameters to the mpas_init signature, allowing the caller to pass in a namelist and/or streams filename, identical to the functionality already present when using the -n and -s command-line parameters. See Add namelist and streams filename parameters to mpas_init JCSDA-internal/MPAS-Model#10. @svahl991 Handled by PR Add optional arguments for namelist and streams files to mpas_init #990 .
• Cloud fraction and cloud height diagnostics. See Add cloud fraction and cloud height diagnostics #733 from @jamiebresch.
• "2-stream I/O". This splits input streams into static and time-varying variables, as in an earlier branch from Ha, Skamarock. Also reduces the number of variables for I/O relative to a restart file and includes logic to manage the I/O, both similarly (but not identical) to Ha, Skamarock branch. See Reduce file size via 2-stream model initialization and DA cycling JCSDA-internal/MPAS-Model#5. @junmeiban, @liujake
• adjoint of halo exchange. See JCSDA-internal@b22c340. @byoung-joo Handled by PR Merge the halo adjoint exchange code for real_2d fields #1138
• bug fixes in core_init_atmosphere for initializing rho_zz and xice. @liujake (Bugfix for calculating moist air density in init_atm_core #829 addresses part)
• optional cmake build process and dependence on the jedi-cmake repository. See https://github.com/JCSDA-internal/mpas-bundle/pull/64. @svahl991
• Modify cmake build procedure to disable OpenMP. See Add cmake option to not build OpenMP by default. JCSDA-internal/MPAS-Model#11.

PR for 2nd through 5th changes on list into JCSDA-internal/MPAS-model is JCSDA-internal#8. @jjguerrette (Edit: @mgduda changed the order, so 2nd through 5th may not correspond anymore...)

Aim is to merge these into MPAS-Dev.

[mgduda]

As PRs are created to handle the modifications listed in this issue, it might be helpful to reference this issue in the description of the PR.

[svahl991]

Here's a consolidated list of modifications from JCSDA-internal/MPAS-Model that we hope to merge with MPAS-Dev/MPAS-Model.

An addition to the list:
Add optional parameters to the mpas_init signature, allowing the caller to pass in a namelist and/or streams filename, identical to the functionality already present when using the -n and -s command-line parameters. See JCSDA-internal#10.

[jjguerrette]

The cmake build procedure is modified to disable OpenMP in JCSDA-internal#11.

[jjguerrette]

JCSDA-internal#12 enables core_init_atmosphere to use mpas_new_unit and mpas_release_unit instead of fixed file unit numbers

[jjguerrette]

Additional JCSDA-internal PR's since the list was last updated are as follows...

• Three bug fix PR's for IAU (can be merged into one commit) @syha

  • Release stable iaufix JCSDA-internal/MPAS-Model#31
  • Add a missing term for (-qv*d(rho_zz)/dt) in updating theta_m tendency JCSDA-internal/MPAS-Model#32
  • A missing parenthesis is now added back in MPAS IAU. JCSDA-internal/MPAS-Model#33

• Very small change to cmake build to allow for single-precision in mpas-bundle @metdyn: enable single precision build for JCSDA-internal/MPAS-Model JCSDA-internal/MPAS-Model#27

• Adding the 1D adjoint halo communications JCSDA-internal/MPAS-Model#25 can be combined with @byoung-joo's previous 2D adjoint of halo exchanges in a single commit

• Another fix for cmake for Pnetcdf: Properly link pnetcdf library JCSDA-internal/MPAS-Model#23

• Bug fixes to cmake for ecbuild 3.5: Bugfix/ecbuild35 support JCSDA-internal/MPAS-Model#21

• Update to 2-stream I/O to avoid error/warning messages: Remove warnings JCSDA-internal/MPAS-Model#19

• Add cmake HIDE_MPI flag to esmf_time_f90 build to prevent double mpi_finalize JCSDA-internal/MPAS-Model#13