Version 2 of implicit surface flux modifications.

Version 2 of implicit surface flux modifications with CLUBB running a…

…fter coupling.

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