First version to changes answers from 3.1

Replaces the Icepack submodule in E3SM with Icepack version 1.5.3
and updates MPAS-seaice to accommodate the new code.

Additional 3.1 compsets and formation of maint-3.1

Add Polar CMIP7 based compsets,  add option to fix negative runoff.

Answer changing (other cases):

EAM:  Restrict nlmaps_atm2srf_conserve=.true. to v3HR coupled cases, not all ne120 cases

SCM:  fix init, updates the large-scale (LS) subsidence routine used in DPxx

RRM:  update RRM grids and configs for NA, EastAsia and Amazon (from maint-3.0)

ELM: Pass suplementation status before fineroot control (FATES), ensure that zenith angles
are passed to FATES (FATES), fix bug in carbon balance and litter loss in PhenologyMod.F90 (crops),

MALI: Update solid and liquid runoff spreading for Greenland 1-to-10km configurations,
Update runoff spreading files for Greenland 4to40km mesh

MPAS-ocean: move runoff removal to data runoff component.  answer changing for some G-cases

WW3: Add wave momentum coupling, add full Wave-Sea Ice coupling,

Other:

Add emulator infrastructure, stub inference backend, add atmosphere emulator,

Add AGENTS.md

Build: Remove SLIBS, flip cmake macro naming convention to match cases

coupled: Add CRYO2010 compset for repeat 2010 conditions

EAM: improve error messages in modal_aer_opt.F90, more ZM cleanup, add total water dycore tend output,
Adds new diagnostics for upwelling solar and longwave fluxes at surface,

ELM:  Add 1850-2023 to ELM sim_year_range for F20TR-CMIP7,    Replacing existing parameter
file in erosion test with file that classifies sugarcane as a perennial crop, add ocean
to land one-way coupling, clean up land units, add param for fine-scale topo radiation,
fix timers, allow irrigate=false and trasient_crops=true

MPAS-ocean: Add latitude-dependent function for background diffusivity south of a chosen latitude

MPAS-framework:   Fix undefined behavior in MPAS registry parser, initialize domain id to zero,
add syntax checks to MPAS stream element

MALI: update tests for Greenland ice sheets, improve performance for Greenland

GCAM:  Update submodule to skinny version

EAMxx:  Fix the grid for LINOZ and OXID files, start porting ZM, add CldFracNet emulator, allow lat,
lon output grid, add P3 property tests, improve wet deposition performance, implement prescribed trace gas,
cleanup horizontal remappers, update MAM4xx,   pass SHOC's eddy diffusivities to HOMME and apply
horizontal turbulent diffusion, fix implementation of mo_photo, add scale factor to dms surface,
emissions, adjust the SHOC configuration that disables SGS condensation, effectively reverting
the scheme to a 1.5-TKE closure when shoc_1p5tke=true, implement transposed outlook, passes HLM
biophysical landuse variables, refactors the microphysics interface, replace t0 ref time,
remove backtend diag, use different tag for pressure level layouts, Add testing support for
non-HPC machines and agents. skip accumulted fields in IC/restart, allow set/retrieve a mask field
directly from the Field class, replace arrays of views with multidim views in dropmixnuc,
add COSP dimension coordinate vars and bounds to EAMxx output.

driver-moab: re-implement spectral element mesh support, add SCM, remove separate import/export methods,
remove most of MCT scaffolding, add X-cases,

Utils:  Fix bug in toString

TPL/tools:  Update CIME, SCORPIO 1.9.2, Trilinos and Albiany paths, update PCD to 0.1.0

Merge branch 'brhillman:eamxx/add-cosp-dimension-bounds' (PR E3SM-Pro…

…ject#8273)

Add COSP dimension coordinate variables and bounds to EAMxx output.

Version used for v3.HR spinup

Make default the customized parameter values and input files used for v3HR.

Last change for 3.1 affecting most compsets

Climate changing: Increase precision of Stefan-Boltzmann constant.

Also:  Create CMIP7-based compsets, add coupling with GCAM

Answer changing:

Coupled:  Turn on CPL_ALBAV for CORE-II forcing cases, add 10 years to ERA5, update A-case resolutions,

ELM:  Add FATES fire capability (FATES), add summary variables that include carbon information,
soil BGC and wood decay (FATES), add sugarcane (Crop cases)

Other:

HOMME:   Finish C++/Kokkos for ETM; modify vertical discretization

GCAM:  fix PIO use

EAM:  Remove PAM and turn off MMF2 test, add tunable aerosol diameter thresholds for renaming
to strat coarse mode, implement a missing correction for the frontogenesis function,

ELM:  Add compset and test for 1km case, add ability to use MOAB-based domain decomposition,
Add an alternate way of defining soil layers and depth to bedrock.

MPAS-ocean: Fix ACC pragmas in ocn_surface_bulk_forcing_vel, fix branch hybrid runs.

EAMxx: refactor zonal average diagnostic, continue port of GW, reorg libraries, add water thermo fixer,
update the time interpolation for LINOZ and oxidants, refactor tendency calculation,
add data interpolation for MAM4 microphysics, replace MVK with RCS

TPL/Tools:  update CIME, EKAT

Climate changing: Change VIS/NIR radiation split in RRTMG

Answer changing:

ELM: correctly apply bendresist parameter (IM3 cases)

Other:

MPAS-ocean: Add Eddy energy correction for FOSI cases,

EAMxx:  Continue porting GW, continue porting ZM, increase user control of cloud and below cloud activation,

driver-moab:  compute fluxes and fractions with moab data, don't write mct restarts,

TPL/Tools:  Update CIME, EKAT, add Physical Constants Dictionary files

Climate changing: change default snow shape to plate hexagonal_plate

Answer changing:

MPAS-ocean:  add frazil tendencies for ocean ecosys tracers (BGC)

MALI: use depth-integrated velocity solver,  cleanup OCN/GLC TF-coupling, Fix sign of ice-shelf basal
melt flux MALI passes to rofi, update crevasse-depth calving and ocean extrapolation,
Allow retreat of ice-sheet calving front in MALI

Other:

EAM:  Add switch to split VIS/NIR to 55.5/44.5, fix bug in new oro drag scheme,

ELM: Remove the unnecessary TOP-related variables from the restart file, replacessthe local
error_tol with the common balance_check_tolerance for EcosystemBalanceCheckMod.F90,
add the minimum daily beta factor (BTRANMN), add SP to some I-compsets

Coupled:  Add ne256pg2 and RRSwISC6to18E3r5 coupling

MPAS-ocean:  add new spatially-variable horizontal upwind capability, Clarify registry descriptions
for avgSurface* variables, add new module to compute and apply a scaling factor on precipitation
fluxes, Restrict compsets that can use TL319 trigrids

MPAS-seaice:  Add new parameters for adjusting snow grain growth rate

MPAS framework: Set io_type in MPAS streams based on PIO_TYPENAME from the CIME settings

MALI: Adjust MALI SMB in G-cases and update hist fields, add regional stats history files

EAMxx: expose 3D diagnostic fields for aqueous SO4 and H2SO4 production and sink,  fill the rad output
fields with FillValue when rad not called, bring in ZM, change cld_frc_r settings, fix bugs in zonal mean,
add diagnostic output for more tendencies coming out of microphysics, enable on/off switch for linoz in mam4xx,
add prescribed Ozone option for MAM4x, add (dycore) energy fixer, add more of C++ gwd, add conditional
sampling diagnostic, change pgrad_correction and hv_ref_profiles for some resolutions, change MAM4xx
long runtime test cases to use MPASSI, add MVK test, C++20 updates, Update linoz and oxid files in XML,
implement online histograms,

driver-moab:  Refactor MOAB mapping infrastructure to support more map types and specific area reads,
makes area correction factors match MCT, makes history files match MCT for most cases, port to CICE.

Build: Avoid repeated configurations of sharedlibs

TPL/Tools:  SCORPIO 1.8.2, Set default value of fminval in python version of gen_domain to 1.0e-08,
refactor EKAT/Kokkos integration, update CIME

Climate changing: add isotropic surface stress to MPAS-ocean

Answer changing:

HR coupled:  Update domain files for ne120pg2_r025_RRSwISC6to18E3r5 resolution

EAM: Make L80 default for RRM grids, clean-up of ZM, refactor of GWD,
Fix a bug in coupling between zm microphys/hetfrz ice nucleation and mam aerosol

MPAS-ocean: Bugfix for frazil ice temperature tendency

MPAS-seaice:  bug fix for negative silicate in icepack

Other:

EAM:  add a dust emission cap option. Update zonal mean diagnostic calculations

ELM: Add option for transport of water within a gridcell from higher to lower elevation topounits,
fix errors for shallow snow with use_extrasnowlayers, Add winter wheat, make SNICAR-AD default, add option
for polygonal tundra landunits, with subsidence and variable surface hydrology, handle FAN and transient
land use, FATES to API 40, expand output vars,

MPAS-Ocean: Add support for ADIOS-compression, change IC for SOwISC12to30E3r3,
Add tracers for freshwater sources, allow coupling of ice and liquid runoff from glc,
Make landIceDraft diagnostic rather than a forcing variable

MPAS-Seaice:  add option for internal ocean frazil ice porosity, remove old column sea ice package,
fix bgc diags, radiative feedbacks for BGC, fix inconsistent iceberg melt temperature.

MALI:  Add data mode, add mpas.gis4to40km, add 3D thermal forcing with ocean.

MOSART:  Fix read of elevation profile

WW3:  conditionally add coupling fields based on compset, build with cmake

Coupled: Enable ne30pg2_r025_IcoswISC30E3r5 case, support northamericax4v1pg2_r05_IcoswISC30E3r5,
add SOwISC12to30E3r4, allow coupling of ne1024pg2 and RRSwISC6to18E3r5, support arcticx4v1pg2_r025_ARRM10to60E2r1

driver-mct:  Add nlmaps_atm2srf_conserve option, Adjust error detection for nlmaps test.

HOMME:  Fix negative weights in cube_to_target, refactor init code.

EAMxx:  Add IOP remapper, Add interface code for MAM4xx gas and aerosols dry deposition, update the aerosol optics interface.
Change RRTMGP to Kokkos, allow SPA to use data interpolation.  Add ne4 config, Add heterogeneous freezing calculations
from prognostic aerosols to P3 microphysics, de-scream some filenames, Add MVK, fix dry deposition of gases removal
from constituent flux, pass top_lev to ndrop, enforce name conventions, add gwd physics, add external forcings,
remove YAKL support for rrtmgp, allow SHOC without SGS, Fix preset MAM4xx optics, Output SO4 and H2SO4 deposition
flux diagnostics

Driver-moab: Make sure lat, lon, area, mask defined, allow and simplify reading maps, read aream

TPL/tools:  Update SCORPIO to 1.8.1, allow NCZaar, update CIME, generate_domain_files_E3SM.py for tri-grid, Kokkos 4.5

Fix bugs in Cmix/KPP interface; icepack 1.5

Climate changing:
MPAS-ocean:  fix bugs in Cmix/KPP interface.
MPAS-seaice: Update IcePack to v1.5

Answer changing:

ELM: Update fates to API37

MALI: Add MALI ocean extrapolation and fix to RK scheme

Other:

EAM and EAMxx: Increase accuracy of semi-Lagrangian tracer transport's trajectory calculations
and permit flexible trade-off between the trajectory accuracy and speed

EAM: Fix orodrag namelist reading.

MPAS-Ocean: Add ocean divergenceAtSurface to highFrequencyStats

MALI: Add new 4km mesh, support BGWCYCL20TR,

EAMxx: Add data-interpolation class, consistent extrapolation for SPA, allow source pressure profile,
flag for aerosol mixing, fix PSL output, fix non-BFB behavior for MAM4xx microphysics,

Data ocean: Add relaxed slab ocean option.

More mods for v3.1

Answer changes:   EAM: Fix a bug in VBS SOA gas-aerosol partition calculation.
ELM: Fix for seed initialization that caused C:N an C:P ratiios to diverge, limit stem:leaf allocation variable,
MOSART: prevent negative channel storage,  MALI:  modifies the conditions for river and ice runoff,
OCN to GLC thermal forcing coupling, OCN to GLC thermal forcing coupling

EAM:  Update gw_convect, avoid ice double counting in COSP CALIPSO,
Add new orographic drag parameterization scheme,  update PAM submodule to fix build error,

ELM:   Introduce land ice surface mass balance fields

MPAS-Ocean:  Add ocean relativeVorticityAtSurface to highFrequencyStats, disable land ice frazil
unless ISMF is on, add scaling of DIB and DISMF by running mean of removed Antarctic ice runoff,
Change SORRMv3 ice runoff mapping, Change range of solid ice runoff removal from 60S to 57S,

MALI:  separate logs from each processor, Fix alarm error for adaptive timestepper,
Fix total land-ice freshwater flux in data mode, Update glc coupler budgets for active Greenland ice sheet

EAMxx:  big downstream merge then start development in main repo after Nov 22.
Make VerticalRemapper more generic, make 0.08 for lambda_high default, remove the last f90 from P3,
fix the MAM4xx interface for wet scavenging

Wave: Add ICOS30 wave mesh

SCORPIO:  Support ADIOS compression.

Utils:  Add Pacer for C++ timing,

Testing:  upgrade container used in PR tests,

Machine updates:   update Frontier, change pe-layouts on anvil for testing, v3.NARRM PE-layouts on Chrysalis, update chicoma-gpu