CTSM 5.2: New surface datasets and mksurfdata_esmf tool to create them

Summary

• All new surface datasets, with updated input datasets.
• New mksurfdata_esmf tool to make global surface datasets.
• New tools to create inputs for regional simulations.
• ne0np4 grid: New 1979 surface dataset and 1979-2026 land use.
• Transient urban and lake by default turned on for transient cases.
• Ocean is run as baresoil rather than wetland (for clm6_0).
• The urban streams file was also updated.
• Update the README files.
• New FATES parameter file: Tree PFT allometry, allometric mode options, leaf maintenance scaling coefficients.

New surface datasets

The new surface datasets are incompatible with previous versions (for example the ctsm5.1 series)—ctsm5.2.0 and following versions can NOT use the previous ctsm5.1 datasets, and vice versa.

See the section below about the new datasets used in their creation. Improvements in how landunits on coastal areas were also made.

Fields added to the surface datasets in ctsm5.2:

• ORGC, BULK, CFRAG, PHAQ (soil data) (currently NOT used by CTSM)
• mapunits (map units from the soil dataset)
• LANDFRAC_MKSURFDATA (for reference NOT used by CTSM)
• PCT_OCEAN (previously PCT_WETLAND was used)

Fields removed from the surface datasets in ctsm5.2:

• AREA
• PFTDATA_MASK

New input data used for making surface datasets

• New soil dataset: ISRIC/WISE dataset (Batjes, 2016; https://doi.org/10.1016/j.geoderma.2016.01.034)
• New PFT, soil-color, LAI datasets: Created by Peter J. Lawrence (2022)
• New Glacier datasets: Glacier outlines from RGI version 6 (Arendt et al., 2017).
  • vector data for GrIS and AIS retrieved from BedMachine version 4 and version 2 (Morlighem et al., 2017, 2020), respectively.
  • 30-arcsec topography/land mask retrieved GMTED2010 (Danielson and Gesch, 2011).
• New urban datasets: Gao and O'Neill (2021) and Gao and Pesaresi (2022), Oleson and Feddema (2020)
• New lake datasets: HydroLake: Messager et. al. (2016)

New mksurfdata_esmf Tool

mksurfdata_esmf is a parallel version of mksurfdata that uses ESMF regridding directly so that offline mapping files don't have to be created as a separate step. This allows surface datasets to be created at much higher resolutions.

The build for the tool is based on the CESM/CIME build system and uses cmake. This allows the build to be kept up with changes in CESM. Currently it's only setup and working on Derecho, but this design will enable it to be built and run on any CESM-supported machine (or a machine that a user ports to).

Any input grid from ccs_config can be used, or the user can supply their own mesh file to define the output grid. The user no longer has to add to the list of valid resolutions (as in the now-deprecated mksurfdata_map).

Creation of supported single point datasets. These datasets are created through the use of subset_data.

Test datasets for dynUrban, dynLake, and dynPFT is done with a simple NCO script.

All datasets can be easily made by running make all in the tools/mksurfdata_esmf/ directory.

For detailed instructions, see tools/mksurfdata_esmf/README.md.

release-clm5.0.37

Synopsis

Changes needed to run on Derecho. Flip the test list from Cheyenne to Derecho.
Add working PE layouts. Remove tools and tools testing. Update readme files.

What's Changed

• add smyle L83 compset and SSP3-7.0 extension by @jedwards4b in #1614
• Fix issues #1769, #1607, #1389 in release documentation by @olyson in #1781
• Fix issue #1864 in release documentation by @olyson in #1916

release-cesm2.2.04: Update PElayout and tests to work on Derecho

Get working PE-layouts for Derecho. Move test list over to Derecho from
Cheyenne.
Remove all of the CTSM tools, users should use the latest.
Some fixes to various tests to get them working.

NEON release: Some NEON updates fixing AG sites, update MOSART, small fixes

release tag for use with NEON:

Minor changes to python scripts and usermod_dirs for NEON cases. Also update the lightning mesh file so that it goes with the
smaller lightning file. Have NEON use new use-cases for 2018 and 2018-PD conditions for CLM. Have NEON
Agricultural sites run with prognostic crop. Simple fix for warning about NaN's in import/export data from/to coupler.

Get NEON tests working on izumi, add --inputdata-dir to subset_data and modify_singlept_site_neon.py so they aren't tied
to only running on cheyenne.

Also update MOSART with fixed for direct_to_outlet option.

Add error checking in ParitionWoodFluxes. Fix value of albgrd_col in SurfaceAlbefdoType.F90.
Previously, the wrong value (albgri_col) was being set in InitHistory.

What's Changed

• Neon updates by @wwieder in #1872
• Fix albgrd_col value in SurfaceAlbedoType by @ka7eh in #1810
• Add error checking in ParitionWoodFluxes by @ka7eh in #1814

New Contributors

• @ka7eh made their first contribution in #1810

Full Changelog: ctsm5.1.dev113...ctsm5.1.dev114

Add SSP3-7.0 extension, and SMYLE 1850 and transient, compsets and use-cases

Update externals for cism and cime to cesm2.1.4-rc-10. cime update was needed to run on izumi.
iAdds a compset for the smyle L83 model (both 1850 and transient). BWsc1850smyle (jedwards4b)
Add SSP3-7.0 extension compset and use-case, that runs for fixed 2100 conditions with 2100 landuse
and 2100 harvest and fertilizer.

Update Nitrogen-deposition datasets with files created from WACCM simulations for SSP scenarios (SSP3-7.0,
SSP5-3.4, and SSP5-8.5).

Fix several issues.

Add LILAC

Add LILAC: The Lightweight Infrastructure for Land-Atmosphere Coupling. This
infrastructure consists of two major pieces:

(1) A lightweight coupling infrastructure built on top of ESMF that makes it easier for
atmosphere models to call CTSM directly, rather than using the hub-and-spoke architecture
that is used by CESM.

(2) A set of python-based tools for building CTSM and creating its runtime inputs when
running in an atmosphere model via LILAC. Although these tools are built on top of cime,
details of the create_newcase / case.setup / case.build process are hidden from the user,
because many of the aspects of this workflow don't make sense in the LILAC context.

So far we have used LILAC to couple CTSM to WRF. There are plans to use the same
infrastructure to couple CTSM to other regional atmosphere models.

Documentation of LILAC is provided in
https://escomp.github.io/ctsm-docs/versions/master/html/lilac/index.html (though there are
still some missing sections), as well as in various presentations on the wiki
(https://github.com/ESCOMP/CTSM/wiki/Presentations).

There have been many contributors to the development, testing and documentation of LILAC;
chief among them being Mariana Vertenstein, Negin Sobhani, Bill Sacks, Joe Hamman, Sam
Levis, Mike Barlage and Dave Lawrence.

Update documentation for release-clm5.0 branch, and fix issues with no-anthro surface dataset creation

Fix the issues with the no-anthro surface dataset creation (the PtVg simulation year). This
makes sure GDP and urban is set to zero and abm to missing for this case. Also bring in the python3
fix that was intended for the last release tag.

Turn irrigation on for 2300 SSP extensions

Irrigation was turned off for the 2300 extensions. This turns it on. Also add SSP2-4.5 to the
anomaly forcing script.

Extensions to 2300 for SSP5-8.5,SSP5-3.4, and SSP1-2.6

Add 2100 surface datasets, landuse.timeseries files for 2100-2300 for SSP5-3.4, SSP5-8.5, and SSP1-2.6.
Also add compsets to run them and the build-namelist use-cases for them. Only for f09 resolution with crop on.

Updates cime as a cime update was needed to run the extensions in I compsets (for presaero and CO2).
Add a test for it. Add -ignore_warnings to cmip6_waccm_deck user-mod which is required for the
fully coupled compset for BWSSP534osext as the ndep file doesn't exist for it, but WACCM is
providing ndep. Get more of the build-namelist unit tester tests working, which previously weren't running.

Bring in raw datasets for 2100-2300 extension for SSP5-8.5/3.5 and SSP1-2.6, some other misc. changes

New Raw datasets to 2300 for SSP1-2.6, SSP5-3.4 and SSP5-8.5.
Fix the pgi build on izumi. Bring in anomaly forcing script to create af forcing that can be used by datm
to run anomoly forcing to get SSP like forcing. Update manage_externals that fixes the python 3.8 bug.

Update cime and cism-wrapper.