Updates for Moist/MG3, GAAS, and Bug Fixes

Zero-diff to previous release: YES (v10.12.0)

Restart Changes: NO - except moist_internal restart now has an additional 3 fields: NGRAUPEL, NRAIN, NSNOW

Major changes are:

1. Broader support for various computing environments including SLES12. Adds a new question to gcm_setup (and other setup scripts) that asks a user what type of processor to run on. It then uses the "default" number of cores per those processors to better figure out how to handle the IOserver nodes.
2. Changes that enable MAPL2 GEOS to work with MPT at NCCS.
3. Changed REPLAY_Shutoff alarm from NON-STICKY to STICKY, and used it in GAAS to stop updates in forecasts during REPLAY mode.
4. Updates to moist and GOCART using 2MOMENT microphysics and MG3. These are 0-diff when running the default 1MOMENT microphysics.
5. Modified gcmpost.script to only operate on pressure-level collections.
6. Fixes issues where systems do not have either ImageMagick or F2Py. If F2Py is not found, then F2Py targets are not built.
7. Changes to GMAO_hermes:
   • Split off the independent sections of module m_topo_remap used by FV core into shared_topo_remap
   • write_eta.F90 added to prepare for a config file which eventually will replace m_set_eta module
   • Add option to build HERMES_LIGHT

GF fix

An important non zero-diff update. The major changes are:

1. Fixed "zero-diff" issue related to GF evaporation vs total rain, fixed GF cloud-mass-flux scaling issue.
2. Move ShallowCu contribution to mass flux and add scale-dependent stochastics to convection.

Upgrade to RRTMG_SW v4.10

Zero-diff to previous release: NO

Restart Changes: NO

Major changes are:

1. RRTMG_SW:
   Updates RRTMG_SW in GEOS to be equivalent to RRTMG_SW v4.10. This fix increases the heating rates near the stratopause region and is a non zero-diff change.

2. RAS_NO_NEG:
   Provides an optional flag that ensures RAS results are non-negative. This is an important fix for chemical species that was extremely useful in the Icarus but did not make it into Jason. The fix is "off" by default and therefore zero-diff.

3. Plots:

• Enable additional upper levels for forecast stats plots.
• Add QITOT & QLTOT to horizontal plots.
• Add aerosols to time series plots.

Other updates:

• Remove #PBS pragmas at NCCS to use #SBATCH.
• Brought the chem setup scripts in line with gcm_setup.
• Bug fixes for gcm_run and gcm_forecast scripts.

Upgrade to FMS Release 2019.01.01

Zero-diff to previous release: NO

Restart Changes: NO

This release is equivalent to the NOAA 2019.01.01 Release but with the addition of GEOS constants controlled by -DMAPL_MODE. Additional changes allow building with CMake.

Upgrade to MAPL-2.0

Zero-diff to previous release: NO

Restart Changes: NO

This release is equivalent in physics to v10.8.0 but now uses MAPL
2.0. The release
is non-zero-diff due to the use of ESMF regridding for History and
ExtData.

Also, this version of GEOSgcm now uses the new PFIO IO server to handle
History and ExtData file access and writing. By default, these IO
servers run on the same resources (i.e., nodes) as the application.
However, gcm_setup and gcm_run.j have been altered so that, by
default, at high-resolution (C180+) the IO servers are on separate nodes
for performance and memory reasons.

Recoded AOIL

Zero-diff to previous release: NO

Zero-diff to CVS tag Jason-3_6_aoil

Restart Changes: NO (only if AOIL_COMP_SWITCH=ON)

Recoded atmosphere-ocean interface layer (AOIL). Provides an option to exercise old/new versions of the AOIL.

1. Old version (AOIL_COMP_SWITCH = ON):
   Default. Using the old interface is still non-zero diff to x0039, however, shown to be statistically insignificant in terms of forecast skill scores. Restarts with old interface can be used as is.

2. New version (AOIL_COMP_SWITCH = OFF):
   If the new interface is turned on, then additional fields in the openwater internal state are needed. They can be bootstrapped or contact Santha Akella for a utility to create them.

Adjustment for RRTMG SW Cold Bias

Zero-diff to previous release: NO

Zero-diff to CVS tag Jason-3_5_aoil

Restart Changes: NO

1. Correction to RRTMG Shortwave 'layreffr' variable to reduce stratospheric cold bias.
2. Stats plots updates to produce stratospheric forecast statistics up to 1mb.
3. Correction to gcm_run.j & gcm_forecast.tmpl related to REPLAY with GAAS aod files.

Updates Consistent with f525land_fpp

Zero-diff to previous release: NO

Zero-diff to CVS tag Jason-3_4_aoil

Restart Changes: NO

1. Atmospheric constituents (aersols, co, co2, etc) are now transported through moist (GF deep/congestus convection and UW shallow convection). This is equivalent to the way transport is handled in f525land_fpp/f525_fp.
2. Added exports for nitrate tendency and other fluxes related to GF convection.
3. Added nitrate tendency to history templates.
4. Upgraded to GEOSchem_GridComp to v1.1.0.
5. Set the default k_split = 2.
6. Fixed gcm_convert.j to work consistent with how gcm_setup and gcm_run.j interact.

New 4DIAU Methodology

Zero-diff to previous release: YES (but user must setup experiment differently)

Restart Changes: NO

1. Hotfixed a bug to enable regridding of catchement restarts from MERRA2

2. REPLAY updates:

   The REPLAY algorithm within the GEOSagcm has been modified to enable a 4DIAU methodology consistent with that used in DAS mode. Prior to this release, REPLAY could only incorporate one analysis increment within the CORRECTOR_DURATION window (nominally 6-hours). The 4DIAU update allows for multiple analysis increments to be used within the CORRECTOR window. The number of increments that wiil be used is determined by the settings of the REPLAY_FILE_FREQUENCY (in nnnnnn seconds format) and the REPLAY_FILE_REFERENCE_TIME (in HHMMSS format). Based on these two settings, the code will determine how many analysis increments will properly fit within the CORRECTOR window. Note: the previous setting of PREDICTOR_DURATION is no longer needed since the code computes the required length automatically.

   The updated algorthm allows for 2 types of REPLAY:

   1. Exact (Uses Archived Increment Files)

      Exact REPLAYs identically reproduce (bit-for-bit) a previous GEOS DAS experiment by simply using the archived IAU forcing from the DAS experiment. For these cases, only the CORRECTOR step is employed and is, therefore, as efficient as a stand-alone model run.

   2. Regular (Uses Archived Analysis/Assimilation Files)

      Regular REPLAYs are used to mimic the original IAU methodology, i.e., both the PREDICTOR and the CORRECTOR steps are employed. The key difference being that the Analysis is based on archived datasets. These Analyses may be from the GEOS DAS system, or from any other source that is written using the appropriate GEOS DAS ana.eta data format.

   For more detailed information, please see the comments within the AGCM.rc.tmpl file.

0-diff Updates Running the Default Jason-3_2 Configuration

Zero-diff to previous release: YES (with defaults and without regridding)

Restart Changes: YES (land regridding)

• Non-zero-diff updates for:
  1. Regridding land restarts
  2. Running Chou-Suarez longwave radiation.

1. Update FV3 to latest version v1.0.9 which fixed UH25 diagnostic to build in both R4 and R8.
2. Land Updates:
   1. Clarified LONG_NAME of "snow depth" variable.
   2. Added wemin wemout options.
   3. Add PEATMAP data processing (disabled by default).
   4. GEOSsurface_GridComp changed values of pi to MAPL_PI.
   5. Added 8 more climatological (fPAR, VISDF, NIRDF stats for CATCHCN) data files and new clsm/country_and _state_code.data file.
   6. Extra column on soil_param.* files.
3. Non-zero-diif bug fix in Chou-Suarez for erroneous cloud contamination in OLR-OLRNA (aerosol forcing).
4. Fixed MAPL bug with vector regridding of winds in CTM.
5. Workaround fix building FMS on macOS.

** Due to issues do not use v10.4.0