Zero-diff Updates with Lightning Module

A Zero-diff update. The major changes are:

1. Added connectivity from MOIST to CHEM for 2 fields (RI and RL).
2. Updates to the obio component which was in the CVS Icarus-2.0 tag.
3. Bugfix for coupled mode renaming TSKINI to TSKINICE.
4. Bugfix for DTDT_moist which was initially set to temperature but never updated to provide tendency.
5. Compute the lightning flash rate (LFR) online following the approach used by GEOSCHEMchem_GridComp. The LFR is calculated in MOIST and then made available to other components as a new export field (LFR_GCC).
6. Modified the mk_Restarts script to run on SLES-12.
7. Update RRTMGP to Pincus 2020-Feb-12.
8. New Surface parameter resource file (GEOSsurface_GridComp/Shared/GEOS_SurfaceGridComp.rc) to avoid having to add new parameters into AGCM.rc.tmpl and prepare for further science development.
9. Correcting the following issues with the single column model: (1) GF imports from DYN were not filled; (2) scm_setup incompletely adjusted for L132; (3) SST file for cfmip_s11 case was incorrect.

Updates for Moist/MG3, GAAS, and Bug Fixes

A zero-diff update when running the default configuration, except moist_internal restart now includes 3 additional fields: NGRAUPEL,NRAIN,NSNOW. The major changes in this release are:

1. Changed REPLAY_Shutoff alarm from NON-STICKY to STICKY, and used it in GAAS to stop updates in forecasts during REPLAY mode.
2. Updates to moist and GOCART using 2MOMENT microphysics and MG3. These are 0-diff when running the default 1MOMENT microphysics.
3. A bug fix that solved ESMF log errors resulting from calling ESMF_AlarmIsRinging on an alarm that wasn't created.
4. Upticked GEOSchem_GridComp to v1.3.2 which includes new CCNtuning for 2MOMENT microphysics.

Land Updates

A zero-diff update. The major changes are:

1. In re-gridding/tiling, "getids" subroutines were placed into a module so it is now accessible to GEOSldas. Also contains some clean-up and renaming.
2. Fixed a bug to properly read catch analysis increments into Catch GridComp.

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.

RRTMG_SW v4.10 Update

An important non zero-diff update. The 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 stratospause 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.

Minor changes also included CircleCi and mepo updates.

Upgrade to MAPL-2.0

A big non zero-diff PR to merge the dev/MAPL-2.0 branch into master. The major changes are:

1. Syntax:
   • use MAPL_Mod => use MAPL
   • MAPL_Base in CMake => MAPL
   • Use ESMF upper and lowercase utilities and not MPEU
   • ASSERT_(X) becomes _ASSERT(X,'message')
2. ESMF regridding

Recoded AOIL

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 the user must provide additional fields in the internal state. Contact Santha Akella for a utility to do that.

Adjustment for RRTMG SW Cold Bias

Correction to RRTMG Shortwave to reduce stratospheric cold bias.

Updates Consistent with f525land_fpp

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. Upgraded to GEOSchem_GridComp to v1.1.0.

New 4DIAU Methodology

The REPLAY algorithm within the GEOSagcm has been modified to enable a 4DIAU methodology consistent with that used in DAS mode. The updated algorthm allows for 2 types of REPLAY:

1. Exact (Uses Archived Increment Files)
2. Regular (Uses Archived Analysis/Assimilation Files)