Updating AQM to CMAQv5.4

[drnimbusrain]

PR Checklist

• This PR has been tested on an RDHPCS machine and/or WCOSS2. Please select below:

  • [X ] RDHPCS.
  • [ X] WCOSS2. (Issues with output total PM2.5 fractions and calculation, equal to zero only on WCOSS2) Issue has been made on UWM by Jianping: The updated AQM with CMAQ5.4 in the UFS Weather Model predicts zero PM2.5 concentrations on WCOSS2 [AQMv8] ufs-community/ufs-weather-model#2378

• [X ] This PR has been tested with the ufs-srweather-app workflow [aqm_dev] and [develop] branch.

• [X ] New or updated input data is required by this PR.
  To test this PR with CMAQv5.4 in AQMv7, you will need the following:

• Updated aqm.rc template file that has updated mechanism (CB6r5AE7) and some other updates.

• Updated diag_table_aqm.FV3_GFS_v6 and field_table_aqm.FV3_GFS_v16 to accommodate CMAQv5.4 changes.

• [ X] Baselines are expected to change.

Description

This PR provides all necessary updates to AQM develop branch for ARL's work to update CMAQv5.4 submodule (from current CMAQv5.2.1) and all necessary AQM infrastructure to accommodate the CMAQv5.4 changes compared. Since our CMAQv5.4 changes were built upon our fork of the EMC develop branch, then it also contains some initial developments of our in-canopy photolysis infrastructure and code developments. The canopy option is turned off by default, and at this time, we recommend that the canopy option remains turned OFF (in aqm.rc) until further refined developments of the canopy codes in AQM (and later in UFS-SRW-App, UWM, FV3/CCPP, etc. via separate corresponding PRs to their authoritative repos to enable full functionality).

Issue(s) addressed

#100

Dependencies

Updates to UFS-SRW-App at non-default branches (e.g., production/AQM.v7) are needed to accommodate the CMAQv5.4 updates in AQM (see new or updated data section above). The question remains as to where and how to make these PRs. Our changes for CMAQv5.4 were built upon the previous [aqm_dev] branch of UFS-SRW-App, and do not correspond to the production/AQM.v7 branch. Please advise and we can update and make the correct PR to the correct UFS-SRW-App branch to accommodate testing the CMAQv5.4 updates to AQM.

@lwcugb @bbakernoaa @ytangnoaa

[JianpingHuang-NOAA]

@BrianCurtis-NOAA Can you merge this PR?

[BrianCurtis-NOAA]

@BrianCurtis-NOAA Can you merge this PR?

I think there is other work going on that will incorporate a bunch of things to get CMAQ 5.4 working. Let's get this figured out.

[ytangnoaa]

@BrianCurtis-NOAA Can you merge this PR?

Jianping. Please hold it. We may update it for some bugs.

[JianpingHuang-NOAA]

@ytangnoaa@lwcugb Do you have any preliminary results to share by using the latest code?

[BrianCurtis-NOAA]

This supersedes #98
Could you change line 23 of CMakeLists.txt to: set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -g -check all -check noarg_temp_created -fpe0 -fno-alias -ftrapuv -traceback")

[ytangnoaa]

This supersedes #98 Could you change line 23 of CMakeLists.txt to: set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -g -check all -check noarg_temp_created -fpe0 -fno-alias -ftrapuv -traceback")

Updated the compiler flag.

[BrianCurtis-NOAA]

If you could test a build it would save me some time later today, but there might be some tweaks to some of the code to conform to those options.