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Recent Releases of CTSM

CTSM - CTSM 5.3: New surface datasets, git-fleximod intro, Leung dust, explicit AC, Matrix-CN, FATES transient LU, time/history metadata changes

Purpose and description of changes since CTSM 5.2 (tag ctsm5.2.005)

New features

Answer changes

Changes to defaults for clm6_0 physics:

  • Urban explicit A/C turned on (links above).
  • Snow thermal conductivity method is now Sturm1997. (PR #2348; see also discussion #1960)
  • New initial conditions files for f09 ("1-degree" 1850, 2000), f19 (“2-degree” 1850), and ne30 (1850, 1979, 2000) resolutions.
  • New crop calendars. (PR #2664; informed by Rabin et al., 2023)
  • Dust emissions method is now Leung_2023 (links above).
  • Excess ice is turned on. (PR #1787)
  • Updates to MEGAN for BVOCs. (PR #2588)
  • New BGC fire method li2024crujra: Avoid crop fires during growing season; allow lightning ignitions in tropical closed forests; add effect of landscape fragmentation on ignitions and duration; recalibrate against GFED5 burned area and with CRU-JRA climate. (PR #2684, PR #2711, PR #2715)

Changes for all physics versions:

  • Parameters updated for CRU-JRA forcing: PPE-based modifications were made to the parameters leafcn, slatop, froot_leaf, medlynslope, and kmax. Lowers LAI and biomass in boreal and tropical forests, without reducing latent heat in the tropics. Affected PFTs: NET temperate, NET boreal, BET tropical, BDS boreal, C3 arctic grass. (PR #2500)
  • FATES parameter file updated (see section below).
  • Pass active glacier (CISM) runoff directly to river model (MOSART) (MOSART PR #94)
  • New surface datasets and landuse timeseries files (see section below).
  • CNMatrix is new default spinup method (links above).

Heads up

  • Small glacier changes mean that you can’t use a 5.3 surface dataset with pre-5.3 code and vice versa anymore. (Merged with PR #2500)
  • Updates the definition of history variable “time” from end of time_bounds to middle of time_bounds. (PR #2838; see section below)
  • Standardizes history variable attributes and a history dimension name. (PR #2052; see section below)

Additional detail

Changes related to time and history files

(Note that the same information in this section applies to MOSART and RTM.)

Startup and hybrid runs no longer run the 0th time step, consistent with the same change in CAM. (Branch and continue runs never had this 0th time step.) This means you will not get an extraneous initial history file anymore. In some circumstances this may also affect the names of history files.

In most cases, the history time variable is now defined as the middle of a history file’s time_bounds instead of the end, for consistency with the same change in CAM. The exception is if you specify hist_avgflag_pertape = 'I' for that file, in which case it will be treated as an “instantaneous” file. Instantaneous history files (a) have their time coordinate set to the end of the last timestep (as did all history files before this tag) and (b) do not include time_bounds.

The history dimension name hist_interval (of output variable time_bounds) is standardized to be nbnd. History variables time_bounds, mcdate, mcsec, mdcur, and mscur are standardized to include the calendar attribute.

New surface datasets and landuse timeseries files (PR #2500)

  • Transient landuse timeseries files going back to 1700 now possible (and made for f09).
  • Fix an important bug on soil fields that was there since ctsm5.2.0. This has the side effect of mksurfdata_esmf now giving identical answers with a change in number of processors, as it should. (Issue #2744)
  • Surface datasets now provided for the ne0np4.POLARCAP.ne30x4 grid. (PR #2716, issue #2720)
  • Surface datasets now have their version number embedded to prevent mismatch of surface dataset and CTSM version. (Issue #2723)
  • Remove outdated hydrology VIC (Variable Infiltration Capacity Hydrology model) fields from surface datasets.
  • Updates to input datasets:
    • PFT/LAI/soil-color raw datasets; now from the TRENDY2024 timeseries that ends in 2023. (Issues #2570 and #2452)
    • Two fire datasets: crop fire peak month and peatland fraction. (Issue #2618)
    • Glacier behavior dataset (related to how non-Greenland glaciers are handled). (Issue #423)

Changes to FATES parameter file

Changes to rpointer files

The rpointer files are simple text files that CESM uses to keep track of how far simulations have progressed, pointing to the filename of the latest restart file for that component. There is one such file for each component, so for CTSM I cases that's lnd, cpl, and atm (and rof if it's active). Normally, when the user is just extending the length of simulations, there’s no need to worry about these files.

However, if there was a problem when a simulation shut down, it's possible that different components will have mismatched restarts and rpointer files. In the past, this meant figuring out what restart file should be pointed to in each component rpointer file and correcting it by hand in an editor. There was only the final set of rpointer files that was kept for a case.

Now, with this update, the lnd, cpl, and atm rpointer files have the simulation date in the filenames, so it's easy to spot if the restarts are mismatched for one of the components. Also, since there are matching rpointer files for each time restarts are created, it's now easier to (a) make sure restarts and rpointer files are all correctly matched and (b) for a user to take a set of restarts and matching rpointer files to start up from for any part of an existing simulation. This means you don't have to hand-edit the rpointer files, making sure you don't make a mistake when you do.

Old rpointer filenames:

  • rpointer.atm
  • rpointer.cpl
  • rpointer.lnd

New names:

  • rpointer.atm.YYYY-MM-DD-SSSSS
  • rpointer.cpl.YYYY-MM-DD-SSSSS
  • rpointer.lnd.YYYY-MM-DD-SSSSS

Where YYYY-MM-DD-SSSSS is the year, month, day, and seconds into the day for the simulation timestamp. For example, rpointer.lnd.2000-01-01-00000 for a rpointer file for starting at midnight (beginning of the day) on January 1st, 2000.

Note that this is backwards-compatible, so for all the components you can use either the new or old format for the rpointer filenames. Thus, if you are restarting from an existing case before ctsm5.3.016, you CAN use the rpointer filenames that don't have the timestamps in the name.

Simulations supporting this release

Note: Dust emissions in CTSM 5.3 will be different from the above simulations because of a tuning update that came in after those.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek 3 months ago

CTSM - 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.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek 9 months ago

CTSM - ctsm5.2.005: Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems

Fix the clm6_0 defaults that were incorrect in ctsm5.2.0. The use-cases needed to be changed to handle clm6_0.
And clm6_0 wasn't handled in the merge of ctsm5.1.dev174 for the two new settings. Simplified the use-cases which
should help prevent these problems in the future. use_init_interp will be set for ctsm5.1 finidat files.

Fix some testing. mksurfdata_esmf and the MKSUIRFDATA test didn't work in a CESM checkout. build-namelist unit tests
weren't going over the use-cases. Also started adding some tests to go over finidat files, but didn't yet capture all of them.
Add some scripts to compare namelists in order to detect namelist issues for physics
version updates, and more easily see namelist changes in one place (bld/unit_testers/cmp_baseline_lnd_in_files,
bld/unit_testers/compare_namelists).

Add some tests to detect issues in CESM and CAM testing (add more tests for cam6.0 forcing, add new IHistClm60BgcCropG
compset). Add a NoAnthro compset to the ctsm_sci testing. Add I1850Clm60Sp test for f09 and f19 to ctsm_sci.

Change NoAnthro compsets to use RTM rather than MOSART. Add science support to some clm6_0 compsets, as was obvious.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek 9 months ago

CTSM - 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.

Climate Change - Earth and Climate Modeling - Fortran
Published by billsacks 12 months ago

CTSM - 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

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek 12 months ago

CTSM - 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

New Contributors

Full Changelog: https://github.com/ESCOMP/CTSM/compare/ctsm5.1.dev113...ctsm5.1.dev114

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek over 2 years ago

CTSM - 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.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 3 years ago

CTSM - 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.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek almost 5 years ago

CTSM - 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.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 5 years ago

CTSM - 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.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 5 years ago

CTSM - 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.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 5 years ago

CTSM - Update FATES to sci.1.30.0_api.8.0.0

Update FATES to sci.1.30.0_api.8.0.0, and point to the NGEET version, rather
than NCAR/fates-release version.

One change to soil-moisture (also check if gridcell weight is non-zero, before specifying prescribed soil moisture.
Also update mosart with cold start bug fix. Update rtm, cism, and cime to versions on cesm2.1.2 release tag.
Fix some issues with PTCLM.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 5 years ago

CTSM - Some answer changes needed for prescribed soil-moisture and clm4_5 defaults (1850-ndep, and urbantv settings)

Some answer changes needed for prescribed soil-moisture. And clm4_5 defaults for 1850 Nitrogen deposition and or urbantv
settings were made to be consistent with clm5_0.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 5 years ago

CTSM - Several bit-for-bit fixes especially around soil-moisture streams

A list of several bit-for-bit fixes. Some very minor and other's more extensive.

mksurfdata_map was extended so that when you specify vegetation types, you can let it use the natural and crop coverage
from the input datasets. This allows you to for example run a global simulation with all vegetation types in every grid cell.
This can be useful in seeing what types of vegetation grow in each grid cell. Also simplify some of the logic that allowed
for old format PFT datasets that didn't include crop information. Since, we don't have or need to work with such datasets
this complex logic could be removed. Also added some new unit tests for mksurfdata and the defining PFT values.

Add time interpolation alogrithm type to most of the stream files, so it can be changed via namelist. Add historical data to the
Nitrogen deposition future scenario datasets.

Add namelist control variables for soilm_offset, and tint_algo for most of the streams. tint_algo allows you to control the time
interpolation and change it to a simpler one (like upper) in order to show that the streams output agrees with the streams data
input. soilm_offset allows the user to change the time-stamp offset if the time-stamp isn't at the middle of averaging interval.
This is important for the soil moisture streams for a case where you want to use the output of a CTSM simulation for soil-moisture
as normally the time-stamp is the end of the interval (so you could use -1296000 to roughly compensate for the time-stamps to be
at the end of the month rather than mid-month). Add a namelist item to continue when soil moisture is prescribed and a gridpoint
is missing on the input streams file, but required for the simulation running. Also add an optional history field H2OSOI_PRESCRIBED_GRC
that corresponds to the input soil moisture streams, so you can ensure the prescribe soil moisture is working correctly and agrees
with the input dataset.

Fix the threading bug for soil-moisture and LAI streams. This is done by adding a new "advance" subroutine that does the streams
advance part of the calculation in a non-OpenMP area of the CLM driver, while the "interp" subroutine remains in the Open-MP
loop.

Include missing prescribed testmods directory. Allow branches with use_init_interp=T with a log message about it.
Move tests from hobart to izumi.

This is bit-for-bit

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 5 years ago

CTSM - Add prescribed soil moisture streams as an option, and a few fixes

Add new prescribed moisture streams feature from Sean Swenson. This allows the user
to specify a steams file for soil moisture and use it in place of the model prognostically
determining soil moisture. To turn it on set use_soil_moisture_streams=T. You can also
set the filename to use with stream_fldfilename_soilm, and there are other _soilm namelist
items to control the years to run over. The file MUST be on the same grid as the model resolution.

Update 0.125x0.125 mapping and surfdata data, and fix hirespft data issues. Update cime
with SSP1-2.6 presaero data. So now can run the SSP1-2.6 CMIP6 future scenario.
Update rtm release branch to rtm1_0_69, which brings in a fix for cold starts.

Move mksurfdata changes from ctsm1.0.dev053 over, which fixes a rare soil color bug.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 5 years ago

CTSM - Add CN prec. control call to fix problems related to small neg. values

Small negative values (roughly roundoff-level different from zero) in
frootc (and possibly other quantities) were occasionally creating
problems with carbon isotope fluxes and FPI in the first time step of
the year, at the time of transient landcover change. This tag fixes the
problem by introducing an extra call to SoilBiogeochemPrecisionControl
in between computing the patch-level transient landcover fluxes and
moving these to column-level. In particular, this truncates small
negative values of decomp_cpools_vr_col to zero, which prevents the
previous blow-ups.

For most of the problematic fields, the explanation seems to be: frootc
can sometimes be negative; this is intentional. Negative frootc causes
negative dwt_frootc_to_litter if the patch in question is shrinking. The
resulting negative fluxes cause problems in the ciso calculation. This
can be worked around by inserting an extra precision control call
between the calculation of the dwt fluxes and the ciso fluxes, so that
small negative dwt fluxes are set to 0.

This does not necessarily fully explain the issue with FPI, but the
insertion of the extra precision control call fixes that issue, too.

For more details, see the discussion in
https://github.com/ESCOMP/ctsm/issues/741

Resolves ESCOMP/ctsm#741

Climate Change - Earth and Climate Modeling - Fortran
Published by billsacks over 5 years ago

CTSM - Change two files from NetCDF-4 format to NetCDF-3 (because some machines have trouble with NetCDF-4 in pnetcdf)

There are two files in NetCDF-4 format that the model uses. Copy these files to NetCDF-3 classic format and point
to the new version in the CLM XML database (use nccopy -k classic). There are some machines that have trouble with
reading NetCDF-4 files in pnetcdf.

There are still some NetCDF-4 files for mksurfdata_map, but some of these are required to be in NetCDF-4 format. And we only
support mksurfdata_map and mkmapdata on cheyenne.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek almost 6 years ago

CTSM - Correct ndep end year for SSPs, 2-degree CMIP6WACCMDECK with C-isotopes off, fixes mksurfdata for high resolution

Fix a couple small issues. Correct end year for ndep for SSP's so can run to the end of 2100. Some fixes to mksurfdata_map for high
resolution surface datasets. Have 2-degree WACCM-CMIP6DECK match a user-mod directory without carbon isotopes on. Remove the
ne120np4 and conus_30_x8 surface dataset files, as they can't be used (see #673).
Remove 8x16, 32x64 resolutions as they are no longer needed and there are problems with them. Add in the mapping files needed for
94x192. Check that special landunit percent area's is not less than 0.0, and don't let PCT_WET be less than zero for areas with
ocean (see #673).

Change some of the longer single point tests to use Qian forcing (as faster, less memory, less problems). Add compsets for this.
This change was also done on master.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek almost 6 years ago

CTSM - Update cime to bring in CO2 transient files for the CMIP6 SSP's as well as presaero for three of them

the CMIP6 SSP scenarios (SSP3-7.0, SSP2-4.5, SSP5-8.5). Previously all SSP scenaros would run, and use the
closest SSP nitrogen deposition file, now only the ones that are available work (Tier I). Also CLM4.5 used
the old CMIP5 ndep files, and now they use the CMIP6 ones available.

Fix some small issues with some of the tools

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek almost 6 years ago

CTSM - Fix carbon isotope bug that caused wrong answers for isotopes under transient land-use change

We currently have a bug so that for transient land-use change cases answers are different starting in soil
carbon when Carbon isotopes (use_c13, or use_c14) are on versus off. Answers are identical if there is no
land-use change. The bug does cause bulk Carbon (C12) to be slightly different, but qualitatively the same.
There is a significant impact to the Carbon isotope simulation however. The bug was causing changes in isotopic
pools to be directed to the bulk Carbon. Because, isotopes are so much smaller than bulk Carbon, this doesn't
cause a marked difference in the bulk Carbon simulation. But, the lack of the change in the isotopic pool
does have a meaningful impact on the simulation of the Carbon isotopic fields.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek almost 6 years ago

CTSM - New ndep files, update fates, fix some issues

New nitrogen deposition files for future scenarios: SSP245 and SSP370. And now points
to the closest reasonable new CMIP6 SSP ndep file that we have (for clm50, clm45 points
to the old RCP files).

Update FATES to s1.21.0.a7.0.0. Which brings in a list of improvements and bug fixes. New
options include fates-hydro and fates-parteh

Point to all of the available CO2 files, so we can convert them for use by datm.

Bring in new high resolution PFT land-mask SCRIP grid file (MODISv2), as a start to get the -hirespft
option to work in mksrfdata.pl. Mapping files still need to be created.

Add a test that turning on Carbon isotopes does NOT change answers (currently triggered because of #667)

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek almost 6 years ago

CTSM - Update all fsurdat files and bring in files for future scenarios, remove CMIP5 rcp options, bring in some bug fixes

Update all surface datasets and add datasets needed for future scenarios. Remove CLM40-RCP options.

Also bring in change for reseeding so that reseeding happens for generic crop and
to increase the threshold from exactly zero to 1 (still very small). Fix QSNOEVAP history field.

CTSM Master Tag This Corresponds To: ctsm1.0.dev025 (with many changes missing)

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 6 years ago

CTSM - Update cime version to one with updates for cheyenne after the Mar/5th/2019 downtime that resulting in mpt2.16 not being able to be used

Update cime version with changes needed to run on cheyenne after the Mar/5th/2019 downtime that resulted in the model
NOT being able to run

CIME important updates:
Update fv1.9x2.5,gx1v7 grids
Initial port to CGD machine izumi

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 6 years ago

CTSM - Add NoAnthro compset, reduce fields on fsurdat in mksurfdata_map, initial add of tools/contrib directory

New NoAnthro compsets: I1850Clm50BgcNoAnthro, I1850Clm50SpNoAnthro and tests for it.
More updates to surface dataset generation, to reduce the fields that are output, removing ones
that aren't used.

New tools/contrib directory with initial add of some useful scripts for users. Currently unsupported
and only expected to run on cheyenne. The following scripts are added:

run_clm_historical ---- does all the setup and submission required to do a 1850-2010 CLM historical
subset_surfdata ------- create regional domain, surface data, and rtm directional files by
extracting data from global datasets
singlept -------------- create single point domain, surface data, and datm forcing files by
extracting data from global datasets
SpinupStability.ncl --- This script assesses the equilibrium state of a spinup run
run_clmtowers --------- This script will run any number of flux tower sites.

Add new default f09 Potential Vegetation (PtVg) surface dataset. For mksurfdata new high resolution
PFT datasets (at 3x3min) for 2005. New rawdata PFT files from 0850-1849.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 6 years ago

CTSM - History fields for vertically-resolved sums of soil C and N, and minor fixes

Add history fields for vertically-resolved sums of SOIL1C, SOIL2C, and SOIL3C for C12, C13, C14, and similarly for N. New fields are SOILC_vr, C13_SOILC_vr, and C14_SOILC_vr, and SOILN_vr. For runs that use the output_bgc usermods, including cmip6 runs, we no longer output 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr'; instead we output 'SOILC_vr', 'SOILN_vr', and similarly for C isotopes.

Also minor fixes:

Climate Change - Earth and Climate Modeling - Fortran
Published by billsacks over 6 years ago

CTSM - PtVg and ssp_rcp future scenario options and Antarctica wetlands fix to mksurfdata, and option to dribble crop harvest XSMRPOOL flux to atmosphere

no-anthro changes on release branch. Update of mksurfdata for Antarctic.
Add in all SSP_RCP future datasets for mksurfdata_map.
Also add in new option for dribble_crophrv_xsmrpool_2atm.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek over 6 years ago

CTSM - Option for rain-to-snow to immediately run off in some regions

Up until now: When repartition_rain_snow is .true. (which is the default
for CLM5), rain that falls when the near-surface temperature is cold is
converted to snow. This repartitioning was put in place for two
reasons: (1) Downscaling to elevation classes: changing the balance
between rain and snow for different elevation classes; (2) Correcting
problems in CAM. However, members of the Land Ice Working Group would
like to change this behavior so that, when CAM produces cold-temperature
rain, this rain immediately runs off rather than being converted to
snow. The purpose of this is to reduce the too-high SMB over portions of
Greenland in CESM2 coupled runs (which results in part from CAM's
generation of liquid precipitation despite very cold temperatures).

This new behavior is implemented in a glacier region-specific manner,
based on a new namelist flag, glacier_region_rain_to_snow_behavior. It
is not at all ideal to make this aspect of the physics differ by region,
but this has been requested by members of the Land Ice Working Group in
order to address biases over Greenland while having minimal impact on
the climate (so that the climate can stay very similar to that of the
official CMIP6 runs). Note that, unlike other glacier region-specific
behaviors, this one applies to all landunits, not just glaciers. This
also seems a bit non-ideal, but we want the physics to be the same for
all landunit types in a given region, and we also want this behavior to
apply to vegetated columns because they are used for glacial
inception (and we want this alternate behavior to apply to glacial
inception, too, in order to decrease some instances of inception).

The justification for this new physics is: In the case of (1) above: If
CAM is generating rain at a given elevation / temperature, that doesn't
necessarily imply that an equal water equivalent of snow would be
generated at a higher elevation / lower temperature: indeed, in reality,
there might not be any precipitation falling at that higher elevation /
lower temperature. In the case of (2) above: There seem to be problems
with CAM's microphysics that cause it to produce too much rain when
temperatures are very cold; it seems (at least to some people) equally
justifiable to throw this cold rain away (by sending it to the ocean as
runoff) as it is to convert this cold rain to snow.

Climate Change - Earth and Climate Modeling - Fortran
Published by billsacks over 6 years ago

CTSM - Update cime and fix surface dataset for f05 1850 non-crop case

Update cime to next version being used in cesm2.1.0 release. And fix the XML for f05
surface dataset for 1850 and non-crop. Test that all six f05 cases work (1850/2000/Hist,crop/non-crop).

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek over 6 years ago

CTSM - Update externals with new CO2/presearo/rtm/mosart, add science_support, change testing

Update externals with new CO2 and prescribed aerosols. As well as rtm and mosart that now
properly does history output in double precision. Add science support to three new transient
compsets for clm4_0/clm4_5/clm5_0. Do some changes to testing.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek over 6 years ago

CTSM - New IC files for clm45/clm50 coupled cases, add 2010 compset

Improve logic for picking initial condition files (finidat). Add new finidat files
for when coupled to CAM (LND_TUNING_MODE=clm*_cam6.0) for both 1850 (from CMIP6 B1850 case)
and 2000/2010 (from CMIP6 BHIST case).

Logic for picking finidat files now will pick a finidat file that it interpolates from
provided the default settings allow use_init_interp to be true. This makes it more likely
to pick a file to startup from if at all possible, rather than dying with an error that
a finidat couldn't be found (which the user could override to get the new behavior by adding
use_init_interp=T to their user_nl_clm).

In namelist settings for finding finidat files for sim_yr=2000, be explict on which tuning mode
is being matched and duplicate the clm4_5/clm5_0 GSWP3v1/CRUv7 matches. This gets it to match
the correct ones and allows them to be distinquished in the future.

Added CLM_NML_USE_CASE=2010_control, and settings for sim_yr=2010, which is needed for some new CAM compsets.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek over 6 years ago

CTSM - Bring in CMIP6 compset modifiers, output usermods and bit-for-bit fixes from dev014 and dev015

Bring in all changes from ctsm1.0.dev014 and ctsm1.0.dev015:

From ctsm1.0.dev015:

(1) Support %BGC-CROP-CMIP6DECK and %BGC-CROP-CMIP6WACCMDECK compset
modifiers, so that we can turn on the necessary options
(output-related and others) via new CMIP6-specific compsets.

(2) Turn on carbon isotopes in CMIP6 runs (from Erik Kluzek)

(3) Remove setting of CCSM_BGC=CO2A in the cmip6 usermods

(4) Add usermods directories for getting typical extra output that's
wanted in many cases: output_crop, output_crop_highfreq, output_bgc,
output_bgc_highfreq, output_sp, and output_sp_highfreq. These can be
enabled by adding something like '--user-mods-dir output_crop' on
the create_newcase line (that short-hand works for an I compset; for
F or B compsets, you need to provide the full path to the usermod
directory).

(4) Allow holes in the number of history tapes. Holes are cases where,
for example, we have h0, h1 and h3 tapes, but no h2 tape (because
there are no fields on the h2 tape). (This is needed for (3).)

(5) Fix reading and writing of 1-d logical global arrays. This fixes
ESCOMP/ctsm#24 for real (rather than just preventing an attempt to
read/write 1-d logical arrays, as was done in the previous 'fix').

(6) Add C13_NBP and C14_NBP diagnostic fields (from Keith Oleson)

(7) Make a bunch of carbon isotope diagnostic fields inactive by default

(8) Don't allow interpolation (use_init_interp) from a case without
carbon isotopes to a case with carbon isotopes: Due to
https://github.com/ESCOMP/ctsm/issues/67, interpolation from a case
without carbon isotopes to a case with carbon isotopes yields
incorrect initialization values for the carbon isotopes. Now that
we're turning carbon isotopes on via some semi-out-of-the-box
usermods (for cmip6), it is becoming more important to check to make
sure someone doesn't shoot themselves in the foot this way.

(9) Add tests of the new output usermods as well as of the CMIP6 compset
modifiers

From ctsm1.0.dev014: Four miscellaneous minor, bit-for-bit bug fixes:

(1) Py3 pylint check and address cime issue ESMCI/cime#2822 (from Jim
Edwards: ESCOMP/ctsm#526)

(2) Change uppercase DEBUG variables to lowercase debug (requested by
Jim Edwards to avoid conflicting with the DEBUG CPP token)
(Fixes ESCOMP/ctsm#534)

(3) Remove unnecessary line of code in LunaMod.F90 that was causing
problems with some compilers due to an uninitialized variable
(Fixes ESCOMP/ctsm#322)

(4) Add r8 to 0 constant to fix build issue with XLF compiler (from Jim
Edwards: ESCOMP/ctsm#531)

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek over 6 years ago

CTSM - Bring fix for transient Bgc/Sp to release branch (from ctsm1.0.dev013)

Fix transient non-crop cases that had constant crop area so that crop area will change in time
(and hence natural veg area will also change corresponding to it).

Also bring in changes to update mksurfdata_map to handle SSP-RCP future scenarios. Right now
it can handle SSP5-8.5 out of the box. Also add a new test for that.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek over 6 years ago

CTSM - Bring in bit-for-bit changes from master up to ctsm1.0.dev012: AnnEt init, snowmip fields

Bring in new diagnostic fields added by Justin Perket, Sean Swenson and Mark Flanner
for Snow-MIP. Most of those are fields that represent "Snow Free" data.

Also bring in fixes for a list of issues. Add handling of the new CO2 which includes
both latitude-band and global average versions. Add some changes to make it easier
for input data processing including NOT doing the slow 1km map file creation. Have
the number of steps that are skipped at startup dependent on the time-step size. Add
a test for some requirements of WACCMX (time-step and use of ESMF). Calculations of
local time are now done in a global subroutine, that can handle negative longitudes.
Fix how FFIX_TO_SMINN is handled for history output. The namelist logical "calc_human_stress_indices"
changed from logical to a character string of three values: FAST, NONE, ALL. FAST
is the default so the less expensive ones are output, NONE turns them all off, and ]
ALL does all of them including the expensive ones.

InitAccVars was mistakenly setting qflx_evap_tot_col rather than
AnnET. This fix allows us to remove now-redundant cold start and restart
code for AnnET.

CTSM Master Tag This Corresponds To: ctsm1.0.dev012

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek over 6 years ago

CTSM - Updated CMIP6 ndep file for historical transient Bgc cases, 1850_control same as before

Update the ndep file for transient cases for CLM50 to the CMIP6 version that has identical
data for 1849-1850 to the previous CMIP6 1850_control (with different mid-month times however), and
new 3-member ensemble average/5-year smoothing from the WACCM case: b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.00[123].
The new data is monthly rather than yearly, which means there will be a seasonal cycle to nitrogen deposition
for transient cases now. The midmonth times/dates are different for the multi-year file from
the previous file, so answers change when using it for 1850_control cases even though the data is exactly the same.
Because, of that we are still pointing to the previous 1850 CMIP6 ndep file.

CLM4.5 is still using the previous CMIP5 ndep dataset.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek over 6 years ago

CTSM - Bring in some simple fixes from ctsm1.0.dev006 and avoid glacier adjustment at startup from ctsm1.0.dev007

Bring in a list of simple fixes that came to CTSM master. Also change so glacier initialization is ALWAYS done
at startup (time step zero) even if it isn't cold or interpolated initial conditions. Also synchronize some of the
files in the doc directory with the files in ctsm/master.

This is a duplicate of the release-clm5.0.06 tag, but properly on the release-clm5.0 branch. The previous tag was stand-alone.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek over 6 years ago

CTSM - Bring in some simple fixes from ctsm1.0.dev006 and avoid glacier adjustment at startup from ctsm1.0.dev007

Bring in a list of simple fixes that came to CTSM master. Also change so glacier initialization is ALWAYS done
at startup (time step zero) even if it isn't cold or interpolated initial conditions. Also synchronize some of the
files in the doc directory with the files in ctsm/master.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek over 6 years ago

CTSM - Update 1850 ndep file, and last year for transient streams

Update to latest Nitrogen Deposition file from simulations with WACCM for 1850.
Also fix an issue with the last year for historical transient cases.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek over 6 years ago

CTSM - Fix some NFIX variables, update cime/cism for upgraded hobart new glade, new diagnostic fields, update cmip6 output

Add some new diagnostic fields. Some needed for CMIP6. Update the CMIP6 user-mods output.
Fix a couple issues. Get full list of history tapes working correctly. Check for valid range
of CO2. New IC file interpolated from the previous one for f19_g17_gl4 for 2000 Clm50BgcCrop

Update cime and cism so can work on upgraded hobart. Also fix an issue that the Nag6.2 compiler found
in CTSM. Also get working with glade changes that happened on cheyenne, DIN_LOC_ROOT_CLMFORC was
changed to a new directory.

Nitrogen Fixation flux arrays were being set to missing value over non-vegetated landunits. This sets them to zero everywhere
and averages in the zero's at the gridcell level for history output. It also reads in restarts with missing values and converts
them to zero's.

There are also some tools updates, getting the tools working on the new upgraded hobart.cgd.ucar.edu.

And mksurfdata_map is updated to add some *_MAX files on the landuse.timeseries files that will allow us to conserve memory
for transient cases.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek almost 7 years ago

CTSM - Second release branch tag for CESM2.0 release, fixing DA and tools and README files, identical to clm5.0.dev013

Update cime and cism to newer versions used in release. These bring in some answer
changes. The cime version updates the orbit for 2000 compsets. The cism version
changes answers for two fields with NO_EVOLVE and more fields for EVOLVE.

Fixes an important bug needed for use with Data Assimulation. Several changes
to testing. Adding wallclock as needed, changing a few compsets so science
supported compsets are used, added tput_tolerance to some tests known to be
variable.

Many changes to the clm tools for creating input files. Added the version by
querying "git describe" and adding it as an attribute to NetCDF files. Changes
to get tools working, and tested. Also changed so that tools can be run in either
a CTSM checkout or a CESM checkout.

Updated README files so they are accurate.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek almost 7 years ago

CTSM - Mistake tag identical to previous version

Mistake that was intended to point to clm5.0.dev013, but really points to clm5.0.dev012.

CTSM Master Tag This Corresponds To: clm5.0.dev012

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek almost 7 years ago

CTSM - First release branch tag for CESM2.0 release, identical to clm5.0.dev012

This is the first release branch tag for the CESM2.0 release for CTSM. There are many changes
to software mostly to fix a list of issues. There are some changes to the science that change
answers to fix some small problems, but don't have a large effect on simulations. Externals are
updated to new versions, fixing issues, and

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek almost 7 years ago

CTSM - Initial version of CLM5.0

This is the initial science version of CLM5.0.

Developments for CLM5.0 build on the progress made in CLM4.5. Most major components of the model have been updated with particularly notable changes made to soil and plant hydrology, snow density, river modeling, carbon and nitrogen cycling and coupling, and crop modeling.
The updates to CLM science are documented here:

https://escomp.github.io/ctsm-docs/doc/build/html/tech_note/Introduction/CLM50_Tech_Note_Introduction.html#clm5-0

This version has production versions of CLM5.0 CMIP6 land-use change files for 1850, historical, and 2000. It has preliminary versions of CMIP6 forcing files for Nitrogen deposition and population density. Further updates are needed for prescribed aerosols, and future scenarios.

Spunup initial conditions are provided for several CLM physics and forcing combinations from simulations run at 1-degree resolution (fv 0.9x1.25 with g1xv6 ocean mask).

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 7 years ago

CTSM - Update initial condition files, update fates, new CMIP6 pop-dens, more lnd_tuning_mod options, updated ndep for fully coupled

Update the initial condition files for clm4_0, clm4_5, clm5_0 at f09_g16 for both CRUNCEpv7
forcing and GSWP3v1 forcing. Update FATES with science change to science-1.4.1_api-3.0.0.
New CMIP6 population density file that has years beyond 1850 (the old one just had 1850, so
was incorrect for historical or present-day). clm4_0 compsets now use CRUNCEPv7 forcing rather than
the CRUNCEPv4 forcing. LND_TUNING_MODE is now used for initial conditions
for different forcing. For fully coupled 1850 cases the ndep file is updated to a preliminary CMIP6
version. Fix the tools testing and build-namelist testing to work in the git checkout.

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 7 years ago

CTSM -

Last version working only in subversion. This version does not work in a git checkout!

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 7 years ago

CTSM -

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 7 years ago

CTSM -

Climate Change - Earth and Climate Modeling - Fortran
Published by ekluzek about 7 years ago