Documentation for GEOS GCM v10

This page lists pages with information on setting up and running GEOS GCM version 10. Earlier and later versions of GEOS may differ in details that, while minor, will require different steps for building and running, so caveat utilitor.

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Changelog

[10.3.5] - 2019-11-07

Restart Changes: NO

1. Enable reading netCDF increments during EXACT replay.
2. Fixed issues affecting the MOIST aerosol diagnostics:
   1. incorrect mapping of tracer names to diagnostics
   2. sign of the diagnostics by not allowing negative values.
3. New approach for increment diagnostics discussed in GEOSchem_GridComp v1.0.3.
4. OXIT and OXIM replaced with MTRI%PCHEM::OXIM and TRI%PCHEM::OXIT in most HISTORY files. OX increments due to moist and turblence are now computed using BundleIncrementMod.F90 and their names have been changed.
5. Implemented increments to land surface variables in the ADAS.
6. Fixed GUST for AMIP vs no-inc REPLAY difference in HISTORY.
7. Removed shallow.F90 which is no longer used.
8. Updated gcm_regress.j to be able to test both agcm and coupled models.
9. Remove references to gcm_stats.j in setup.

[10.3.4] - 2019-10-01

Restart Changes: NO

1. Fields out of the MTR bundle came in the “wrong” order and affected the Henry’s law constants. Hotfix to fetch field by name instead of by index.
2. Fixed triangular pdf option in SHUW.
3. Update chemistry to v1.0.2 to run GMI and Stratchem. Updated the StratChem and GMIchem setup scripts to better match gcm_setup.
4. Hotfix in fv_tracer2d.F90 to compare to ksplt instead of nsplt.
5. FVdycoreCubed_GridComp moved to separate repository.
6. FMS moved to separate repository and renamed GFDL_fms to fms
7. getco2.F90 moved to @GMAO_Shared.
8. Adapted GuestOcean_GridComp to select DATASEA, MOM5 or MOM6 at runtime.
9. Changes to enable LDAS to start using the develop branch:
   1. ensemble ID width for LDAS
   2. added co2 file for CatchCN support
   3. bug fix that only affects New Land when snow impurity model is active
10. Updates from S2S-3 CVS tag:
    1. Includes dual ocean code
    2. Update to precip correction and additional coupled diagnostics
11. MERRA2_EMISSIONS_DIRECTORY path bugfix for gcm_run.j and gcm_regress.j
12. Updates from CVS GEOSadas-5_25_2 tag.
13. Updated plots.
14. Enhancements to scm_setup script.

[10.3.3] - 2019-10-02

Restart Changes: NO

1. Move to GMAO_Shared 1.0.4 to merge more updates from CVS for plots
2. Updates for Travis CI

[10.3.2 / Jason-3_2] - 2019-08-02

Restart Changes: NO

1. Changes in FV3 related to Horizontal Advection choices. (from Bill: JU_20190722_WMP)
2. Changes in FV3 dddmp (from 0.1 to 0.2, to improve stability)
3. Changes in MOIST related to ICE-FALL. (from Bill: JU_20190722_WMP)
4. Updates to GEOS_OpenWaterGridComp.F90 and GEOS_DataSeaGridComp.F90 to modify the original Coupled/Merged System to include Santha’s reformulated ice/melt. (from Santha: sakella-GEOSadas-5_25_0_DV_in_MIZ_SSTunderIceFix)
5. Many updates related to CMAKE for upcoming GIT repository.
6. The addition of ERA5 to QUICKPLOT.
7. Modified STATS for NPO, SPO, and XPO regions. Modified Montage plots.

Restart Changes: None.

[10.3.1 / Jason-3_1] - 2019-06-13

Model Changes

1. Updates to GuestOcean_GridComp.F90 to re-sync OCEAN clock with ATMOS clock when running Regular REPLAY together with DataOcean. (non-zero diff)
2. Introduced code in MAPL_CFIO for HISTORY which corresponds to the “fix_undef” utility used in MERRA-2 post-processing. This creates consistency between horizontally transformed and vertically interpolated quantities and the target output level (i.e., values below surface are UNDEF).
3. MKIAU has been modified to allow for REPLAYing to different vertical resolution. Results are zero-diff to previous versions if vertical resolution is the same.
4. Updates to mk_restarts for Land/Catch. Zero-diff when regrid.pl points to standard (old-land) Icarus/Jason boundary area.

[10.3.0 / Jason-3_0] - 2019-05-03

Restart Changes: NO (with caveats)

Due to changes in import states and diagnostics, these restarts have changed but are passive to the prognostic restarts:

• irrad_internal_rst
• surf_import_rst
• tr_internal_rst
• turb_import_rst

Model Changes

1. Zero-Diff update to FV3 dynamics to allow FV3+ADV option
2. Updates from Mike Manyin to his tag: Jason-2_2_MEM_2
3. This tag primarily is a Merge between Jason-2_2 and Andrea Molod’s coupled tag. This produces a non-zero diff to Jason-2_2 due to a modified surface layer interface.

[Jason-2_2] - 2019-04-25

Restart Changes: NO (with caveats)

There was a long_name change in TR restart

Model Changes

1. StratChem updated to tag: Jason-2_0_MEM_2, as well as updates to GEOS-Chem and HEMCO from Mike Manyin
2. CARMA updated to tag: prc+asd-AeroChem-Icarus-3_3_p2+a1-v7 from Pete Colarco (with minor mods in DustEmissionMod.F90 because of an interface differences)
3. GIT related updates.

[Jason-2_1] - 2019-04-17

Restart Changes: YES

• turb_import_rst: Simply Bootstrap.
• surf_import_rst: Simply Bootstrap.
• irrad_internal_rst (passive, for clear-sky diagnostics only): Simply Bootstrap

Model Changes

1. Retuning when using NewLand.
2. Addition of Optional RRTMPG (off by Default).
3. Modifications for New RRTMG diagnostics.
4. Updates for regrid.pl and related code.
5. StratChem updated to tag: Jason-2_0_MEM_1
6. GIT related updates.

[Jason-2_0] - 2019-03-04

Restart Changes: YES

• solar_internal_rst (for RRTMG). Simply Bootstrap.

Model Changes

1. This is a MAJOR update to include updated moist processes based on the tag: merge_JDB7p1_retuned

• It uses RRTMG for BOTH Shortwave and Longwave radiation.
• It uses the GF Convection Scheme, as well as the UW Shallow Cumulus scheme.
• It uses dynamics tunings based on the DYAMOND experiments.

2. Option included for running Stochastic Physics.
3. 2nd-Moment Cloud MicroPhysics updated to tag: b_Jason_2_0_donifan

[Jason-1_1] - 2019-01-23

Restart Changes: YES

• GOCART IMPORT was modified by adding LWI and FRACI to be non-skip
• TR IMPORT was modified by removing ALL but CLDTT (from RAD), since TR is run after SURF RUN(1,2)
• Note: When TR adopts a 2-phase approach, additional IMPORT variables from SURF will need to be included.

Model Changes

1. An error was found related to GOCART and TR regarding the TR and GOCART IMPORT restarts. This error was introduced going from Icarus-1_0_p1 to Icarus-2_0 with the splitting of GOCART into RUN1 and RUN2 methods. Essentially, the ordering in PHYSICS is: SURF,CHEM,TURB RUN1, followd by SURF,TURB,CHEM RUN2. Emissions are computed in CHEM RUN1 based on LWI locations. However, LWI is not computed until SURF RUN2. Therefore, LWI is required on the GOCART IMPORT. But this variable was labeled as RESTART_SKIP. The TR IMPORT did contain LWI, thus when TR was Enabled, GOCART saw the proper LWI. But when TR was Disabled, LWI was no longer available for GOCART, and resulted in non-zero differences. The quick solution was to label LWI as non-skip on the GOCART IMPORT restart.
2. An error was found related to the TH_for_CHEM within the SYNC-TQ sequence. The error was fixed, but experiments showed negligible impact due to its second-order influence.
3. Modifications to the STATS plotting package to include Mean-Square-Error decompostion.

[Jason-1_0_BETA] – 2018-09-17

Restart Changes: YES

• saltwater_internal ==> openwater_internal & seaicethermo_internal

Model Changes

1. Saltwater split => openwater and seaicethermo. This means saltwater_internal is now two files: openwater_internal and seaicethermo_internal. saltwater_import remains. Regridding utility (regrid.pl) will always produce the split ocean with this tag. You can, however, provide the single saltwater_internal as input.
2. Sponge Layer fix in FV3 to include damping between top model layer and bottom of sponge.
3. Regridding in MAPL now done in a new abstract/OO paradigm. This leads to the new grid definitions in AGCM.rc
4. New HISTORY.rc grid_label definitions. This HISTORY is designated as VERSION: 1. Older HISTORY files (using resolution attribute) will still work provided VERSION = 0.
5. QUICKPLOT updates to produce automated “closeness” plots.

Previous Versions

For previous changes please see ChangeLog-PreJason.txt

Running GEOS GCM

• GEOS GCM Quick Start: This page describes the minimum steps required to build and run GEOS GCM v10 on NCCS discover and NAS pleiades. You should successfully complete the steps in these instructions before doing anything more complicated.

• GEOS GCM User's Guide

• Regridding Restarts for GEOS GCM

• Using the ExtData component

• Running a Suite of Forecasts

• Setting up to create an experiment page on GMAO Intranet

• Using the SatSim Gridded Component in Jason

• GEOS GCM Single Column Model

GEOS GCM Documentation

• GEOS 5 Developer's Guide (pdf)
• List of Export/Import/Internal states, generated with src/GMAO_Shared/MAPL_Base/mapl_vlist.py
  • Sorted by short name
  • Sorted by component name

• GEOS-5 Run-Time Characteristics

• Hierarchical structure: Below is a (partially folded) view of the Jason 3.0 hierarchy where each node is a GridComp. Some of the nodes are folded (marked with a circle at the end) for clarity - clicking the composite node reveals the sub-nodes.

File:J30 tree.mm

flash|500px|parameters startCollapsedToLevel=4

<mm>flash|500px|parameters startCollapsedToLevel=4</mm>

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