Port of stress correction code from Thomas Toniazzo.

First clean version of implicit land flux code.

v2beta3

EAM: Fix nudging, change default value of vtheta_thresh
MPAS-ocean:  Add a better shallow shortwave fixer

v2beta2.5

EAM: Fix aero_model after name change, Fix radiation diags, Fix issue for dcape
without ZM, Read aircraft and surface CO2 emissions, Update CF compliance,
remove unused compsets, grids.

HOMME: Fix remap state memory bug, update topo tool

MMF: Add ESMT to SAM++

ELM: Update CF compliance

MOSART: Add r2 grid, Update CF compliance

MPAS-ocean: Fix cmake build, Fix and then remove fix for shallow shortwave absorption,
Add Wright EOS, Remove shortwave energy conservation fix, fix redi_term2, fix BGC init logic

MPAS-seaice: Improve error messages, fix regional stats bug, fix BGC init logic

coupler: fix tri-grid budgets (fracr_lfrin)

All: update CIME to 2b49cf54f1

config: Fix ocean/ice params and IC for EC30to60 and WC14to60 ocn/ice meshes,Remove _ICG grids,
updateWC14 and EC30to60 IC for WCv2

v2beta2

EAM: Add doubly-periodic planar HOMME, Fix SCM large scale bug, Init mixing ratios
when reading restarts, Set defaults for v2 compsets, Add SL error messages,
Fix nbfb issues with gust-param CLUBB settings, Add v2 case files and compsets,
Fix dcape_ull trigger bug, Remove UNICON, Fixes to reprosum, consolidate v2 param
settings, fix CLUBB restart problem whenclubb_ipdf_call_placement=2

MMF: add variance transport

ELM: Fix mksurfdata, fix units bug, Fix for neg nitro fixation, update FATES API to 14.2 and conform to BGC pipeline,

MPAS-ocean: Widen Redi hmix halo, Add semi-implicit baro solver, Add cosine-bell test case,
Add GPU baro vel, Update core, framework, Finish ocean diags module, move sfc pressure and zmid before EOS

MPAS-seaice: Fix algal grazing, fix threading bug.

config: make ocean/ice configs be v2 out-of-box, add bi-grid coupled NA RRM

all: disable travis and add CircleCI, update SCORPIO to 1.1.6, update CIME to 6335dd8b8

v2beta1

ELM: add surface files forne30np4pg2 for 1850 and 2000

MPAS-seaice: Fix freezing temp, Fix bug in high-frequency coupling, update blackbody emissivity

all: Chrysalis layouts and intel compiler

v2beta0

Make theta-l default

EAM: OMP race fix, Fix COSP snow backscattering, Init rad to fillvalue,
Allow SCM to use theta-l, Make theta-l default dycore

ELM: Change variables,files from clm to elm.

MMF: Fix momentum feedback, SAM++ bugfixes

MPAS-ocean: GPU diags

MPAS-seaice: Align atmosphere coupling, Fix sea-ice freezing, switch to high-frequency coupling

all: update SCORPIO to 1.1.4, Add Chrysalis config

v2alpha5

Code used for "5_59 fallback" run

EAM: Fix small bugs in SL, remap, remove some output fields,  rename cam to eam,
add diags for SSW, fix print_cost, Fix bug in dry size calculations, increase
tolerance on CO2_FF mass test

HOMME: Add kokkos version of theta-l, optimizations for SCREAM

MMF: fix output variable names

ELM: update LUT, turn on snow morphology, rename clm to elm, Allow crops on
separate land units, All restarts w/o plant hydraulics, Allow transient crops
w/o prog crop model,  fix input data for usrdat tests

MOSART:  Add dam construction, fix inconsistency with domain file

MPAS-ocean:  Fix limiting on Redi, fix surf buoy forcing, revert GM buoyancy to v1,
Fix OMP directives, alter stage 1 vertical transport, fix and update CVmix, Make
freezing match sea-ice,  update monthly fields, update ICG initial conditions,
add and modify E&G length scale, save GM-induced MOC, COMPASS updates, speed up diagnostics

MPAS-seaice: Add GPU offload, Add more output, turn on snicar-on-sea ice, switch output to SP,
add prescribed sea-ice mode, change snowlayers in BGC tests

config:  support EC30to60E2r2 and WC14to60E2r3, add WC14to60E2r3, add thetal-SL-pg2 for
Antarctica RRM, update mapping and domain for EC30to60E2r2

all:  update SCORPIO to v1.1.3, allow Travis CI, update kokkos, Remove support for Makefile-based builds

v2alpha4

EAM: Allow runtime pcols, Add trigrid drydep files, Improve chunk load-balancing,
init phys_proc_cost, Clean up ARKODE-HOMME interface, Remove CARMA, Fix RRTMPG
delta-scaling calc and band indices, Remove poor NH IMEX options, Lower print_cost_p
cost, Add flag for limiter warnings in RRTMGP, Change DYN_PS output, Allow H and NH
cases with type=9, Allow DCAPE or ULL trigger to be used, Make CLUBBv2 params
namelist vars, cleanup min droplet number conc.,

MMF:  Add CRM friction, Add 1-mom MMF case, Calculate aerosol optical properties
less often, Add C++ version of CRM along with YAKL and CUB code.

ELM:  Change source for h2osno, frac_sno, Update to FATES API 13, Fix fsurfdat
for 2000, r0125. Fix crop allocation bug, Fix inline interpolation of land IC,
Update LUT for iESM and ELM consistency

MOSART:  Add new USRDAT resolutions, Redo CLMMOSARTTEST support, Allow ugrid format on output,

MPAS-ocean:  Turn on ocean Redi mixing, Fix CVMix surface layer averaging, Improve GM drhodx,
Change GM kappa computation, Reduce pointer retrievals, Change OpenMP Threading, add coastal
modeling updates, add activeTracerHorMixTendency, build updates, compute heatbudget once and
hour, Fix landIceMask diag, fix 3rd-order advection coeffs, add coupling frequencies for new
grids, COMPASS updates, ocean-only updates

MPAS-seaice:  Fix carbon conservation, Add warnings for snow,ice layers, Fix bug in snow
melt calculation,

MPAS-landice:  Allow coupling of 1 year, Add JRA1.4, JRA55v1.4, support gis1to10km config,
update Albany version in MALI

Data models:  new data runoff funtionality,

mct-driver:  Update dry-deposition data, support MOSART stratification.

config: Add ne30_r0125_oRRS18to6v3 and ne120_r0125_oRRS18to6v3 and pg2 versions,
Add support for ne4pg2-r05-oQU480 and ne16pg2-r05-oQU240, Lower some compy opt,
Add singularity, Add ne45pg2 and ne45pg2_r05_oECv3, script support for ECwISC30to60E1r2,
EC30to60E2r2 mesh

all:  Move cime config dir, Update SCORPIO to 1.1.2, Make CIME a submodule,
Add gpu tests, Fix modpes reproducibility on haswell, Update cime submodule to e0dcc590.

v2alpha3

v2alpha3

EAM: Reduce ne4 remap dt, Add MMF, Cleanup physgrid and SL, Fix ftype1 for NH theta-l, Prevent nans in theta-l init
Modify chem_pp pgi optimization, Implement superfast chemistry, Fix uninit elem MPI error, Add wsubmin param
for gustiness, Revised nudging code, Improve vectorization and threading in SL transport, Make PSC T threshold
namelist, allow pcols runtime option, Fix trop_strat/mam3/mam7 bugs, Add total column ozone output, Update dust
shortwave optics for RRTMGP, Fix moisture when init theta-l Tv, Add limiters on RRTMGP cloud optics, Antarctica
RRM support for F2010, Fix swband/lwband for history, Add co2 mass conservation test, Reinstate CLUBBv2 as default.

MMF: Fix COSP, Fix RRTMGP bug, Fix MMF radiation_tend, Summit runs, enable ESMT, add RCE compset

ELM: support SSP585, add v1.1. diags, Update FATES API to v10, Add fsurfdat for r05, 2010

MOSART: don't assume all fluxes are from land, replace latent heat formula for water vaporization

MPAS-ocean: FIx Redi mixing, Add ocean mesh structure for GPUs, Add analysis members, Fix cvmix driver area weighting,
Move daysSinceStartofSim calc, Remove RediKapp from gm, fix bad array sizes, fix tracer_adv bugs, Add mixed layer AM,
del2 ref. cell width, Add horizontal variable GM bolus

MPAS-seaice: qchange runoff interp for cryosphere compsets

config: add many v1.1 BGCEXP compsets, add ne0np4_northmaerica Initial Intel ifx support, use r0125 for ne120np4

all: Switch to SCORPIO, Update CIME to 5.8.23, full support for oARRM60to10 tri-grid