GEOS-Chem 13.0.0

Release date: 18 Mar 2021

This is a major version release featuring the following updates:

• GEOS-Chem is now a submodule in GCClassic and GCHP
• Separate HEMCO from GEOS-Chem to use as a git submodule in GCClassic and GCHP
• Retire the GEOS-Chem Unit Tester repository
• Retire the GNU Make and replace with CMake
• CEDS_GBD-MAPS emission inventory (1970 - 2017)
• Retire carbon-based units for VOCs
• Implement new tropchem simulation
• Update RRTMG (fix netCDF diagnostics; enable in GCHP)

See the GEOS-Chem 13.0.0 page for a complete list of updates

What's Changed

• [PULL REQUEST] Implement GEOS-Chem chemistry within CESM by @fritzt in #334
• Fix bug in RRTMG with stratospheric aerosol by @sdeastham in #347
• Enable GCHP to be compiled with RRTMG by @sdeastham in #348
• Remove Map_A2A Init and Cleanup. by @jimmielin in #338
• Allow RRTMG to be off even if compiled by @sdeastham in #429
• Feature/ewl/13.0.0+cesm pr by @lizziel in #405
• [CESM-GC] Minor changes required for CESM2 by @fritzt in #498
• Minor build system updates by @LiamBindle in #507
• Fix updaing SG parameters in input.nml by @LiamBindle in #532
• Revert switching to daily lightning files in GCHP by @LiamBindle in #562
• Expanded and restructured examples in runScriptSamples by @LiamBindle in #623
• added listInputDataFiles utility script to GCHP run directory by @LiamBindle in #622

Full Changelog: 12.9.3...13.0.0

GEOS-Chem 12.9.3

GEOS-Chem 12.9.3
06 Aug 2020

This release fixes some minor issues that were discovered after the release of 12.9.2.

1. Fix to make HEMCO properly read vertical coordinates for data on arbitrary vertical grids
2. Bug fix for planeflight diagnostic: Change parameter definition MAXAN=15 to MAXAN=20
3. Fix additional typos in GEOS-Chem species database

Read the GEOS-Chem online manual at:
http://manual.geos-chem.org

This release is compatible with GCHP. See the GCHP online manual for more information:
http://wiki.geos-chem.org/Getting_Started_With_GCHP

Learn how you can run GEOS-Chem on the Amazon Web Services cloud computing platform:
http://cloud.geos-chem.org

GEOS-Chem 12.9.2

GEOS-Chem 12.9.2
24 Jul 2020

This release adds fixes for several more bugs that were discovered during the 12.9.0 benchmarking phase.

1. Fix inconsistent tagged CO2 species names in the species_database.yml file
2. HEMCO Bug fix: Eliminate typos from HEMCO_Config.rc file that caused met field read issues for CO2 simulations
3. Dry run bug fix: Make sure FOUND gets set properly in HEMCO gets set properly before returning
4. Update incorrect PM2.5 definition for complexSOA_SVPOA simulations
5. PARANOX Bug fix: Make sure that NO and NO2 are nonzero before computing FNO_NOx

Read the GEOS-Chem online manual at:
http://manual.geos-chem.org

This release is compatible with GCHP. See the GCHP online manual for more information:
http://wiki.geos-chem.org/Getting_Started_With_GCHP

Learn how you can run GEOS-Chem on the Amazon Web Services cloud computing platform:
http://cloud.geos-chem.org

GEOS-Chem 12.9.1

GEOS-Chem 12.9.1
17 July 2020

This version includes the following updates:

1. Bug fix: Fixed a lingering issue that caused the GEOS-Chem dry-run not to recognize missing files
2. Fix run-time error when optional Luo wet deposition scheme is turned on
3. Fixes for interpolating RCP emissions data via HEMCO

Read the GEOS-Chem online manual at:
http://manual.geos-chem.org

This release is compatible with GCHP. See the GCHP online manual for more information:
http://wiki.geos-chem.org/Getting_Started_With_GCHP

Learn how you can run GEOS-Chem on the Amazon Web Services cloud computing platform:
http://cloud.geos-chem.org

GEOS-Chem 12.9.0

GEOS-Chem 12.9.0
17 July 2020

This version includes the following updates:

1. Updated halogen chemistry
2. Improved cloudwater pH
3. Update offline lightning data through Dec 2019
4. Convert GEOS-Chem species database to YAML format, includes:
   a. Defining all species properties in the species database, not just advected species
   b. Initializing the species database with values read from the YAML file
5. Update GEOS-Chem core to apply masking and scaling to HEMCO inputs
6. Bug fix: Restore missing photolysis reactions from 12.8.0 and add an extra error check
7. Bug fix: Remove inefficient code that was slowing down computation of heterogenous chemistry rates
8. Corrected issue in GEOS-Chem dry-run where some files were not being properly marked for download
9. Bug fixes for the ObsPack diagnostic:
   a. Change units of ObsPack specific humidity (Q) field to g/kg
   b. Restore missing code due to Git merge that caused the OBSPACK MENU of input.geos not to be read
10. Fixes for reading meteorology fields in HEMCO:
    a. Skip reading FLASH_DENS and CONV_DEPTH fields when lightning NOx extension is turned off
    b. Change time cycle flag for meteorology fields to use exact date
11. Restore missing metadata for satellite timeseries diagnostics
12. Fix bug where non-advected species not updated in restart file

Read the GEOS-Chem online manual at:
http://manual.geos-chem.org

This release is compatible with GCHP. See the GCHP online manual for more information:
http://wiki.geos-chem.org/Getting_Started_With_GCHP

Learn how you can run GEOS-Chem on the Amazon Web Services cloud computing platform:
http://cloud.geos-chem.org

GEOS-Chem 12.8.2

GEOS-Chem 12.8.2
27 May 2020

This version contains minor bug fixes, and structural changes to facilitate WRF-GC development.

1. Bug fix: Set version numbers to 12.8.2 in CMakeLists.txt and gc_classic_version.H
2. Updates to facilitate WRF-GC development:
   a. Ignore KPP integrate errors and send them to a log file instead
   b. Wrap OpenMP-specific code with #ifdef MODEL_CLASSIC and #ifndef NO_OMP blocks
   c. Move certain module variables into the State_Met and State_Chm objects
   d. Exit INIT_DRYDEP immediately if arrays have already been allocated

Read the GEOS-Chem online manual at:
http://manual.geos-chem.org

This release is compatible with GCHP. See the GCHP online manual for more information:
http://wiki.geos-chem.org/Getting_Started_With_GCHP

Learn how you can run GEOS-Chem on the Amazon Web Services cloud computing platform:
http://cloud.geos-chem.org

GEOS-Chem 12.8.1

GEOS-Chem 12.8.1
21 May 2020

This version fixes several issues that were identified during and after the benchmarking process for version 12.8.0:

1. Update the dry-run download data script to make files group-writeable
2. Add more timers for gas-phase chemistry
3. Reduce the amount of memory that GEOS-Chem dry-runs require
4. Add bounds-checking and floating point exceptions to CMake "Debug" target
5. Fix incorrect indexing for AOD diagnostics
6. Updates for GEOS-Chem "Classic" HISTORY diagnostics:
   • Fix for instantaneous timeseries diagnostics to avoid overwriting hour zero
   • Fix to allow diagnostics with frequency="End" to properly straddle year-end boundaries
7. Allow for missing species in boundary conditions
8. Disable FlexGrid checks to allow for running with any horizontal or vertical grid
9. Fixes for WRF-GC and CESM-GC, including:
   • Fix Init_Pressure error for NZ /= 47, 72
   • Only perform pole-averaging of regridded data if actually regridding to the poles
   • Add a State_Grid%ID field
10. Add fix for POPs emissions diagnostics
11. Avoid memory corruption bug in HEMCO when certain debug flags are on
12. Fix bug causing seg fault when ConcAboveSfc diagnostic collection is on
13. Fix bug causing crash if not starting on the first day and time of the month
14. Fix incorrect GCHP config file entry for surf_iodide source file in 12.8.0
15. Avoid unexpected behavior if dynamic timestep is changed to non-default values
16. Fix input data to avoid crashing in late Dec/early Jan if using offline biogenic VOCs
17. Add internal state met variables to benchmark and transport tracers simulations
18. Enable all budget diagnostics output in GCHP transport tracer simulation by default

Read the GEOS-Chem online manual at:
http://manual.geos-chem.org

This release is compatible with GCHP. See the GCHP online manual for more information:
http://wiki.geos-chem.org/Getting_Started_With_GCHP

Learn how you can run GEOS-Chem on the Amazon Web Services cloud computing platform:
http://cloud.geos-chem.org

GEOS-Chem 12.8.0

GEOS-Chem 12.8.0
04 May 2020

This version includes the following updates:

1. Isoprene chemistry
2. Wet deposition parameterization
3. Ozone deposition to the ocean
4. Use online DustDead, MEGAN, SeaSalt, and SoilNOx emissions for benchmark simulations
5. Shift CMIP6 time from middle to start of month to allow start in January
6. GFED 4.1s beta emissions for 2017-2019
7. Replace State_Chm%nAero with State_Chm%nAeroSpc and State_Chm%nAeroType
8. Convert all files in GeosCore, GeosUtil, and Headers to .F90
9. Change GEOS-Chem timers from a CPP switch to an option in input.geos
10. Remove potential for surface CH4 retrieval error in SET_CH4 due to reliance on HEMCO emissions year
11. Fix leap year handling bug in GCHP multi-run script
12. Fix SH surface ozone bias in GCHP

Read the GEOS-Chem online manual at:
http://manual.geos-chem.org

This release is compatible with GCHP. See the GCHP online manual for more information:
http://wiki.geos-chem.org/Getting_Started_With_GCHP

Learn how you can run GEOS-Chem on the Amazon Web Services cloud computing platform:
http://cloud.geos-chem.org

GEOS-Chem 12.7.2

GEOS-Chem 12.7.2
19 Feb 2020

This version introduces several bug fixes and minor updates.

Updates affecting GEOS-Chem "Classic" only:

• Restrict wet scavenging to troposphere in Luo et al 2019 wetdep scheme
  • NOTE: This is an option and is turned off by default
• Bug fix for reading 3-hourly boundary condition files after hour 21 (GEO- S-Chem "Classic" only)
• Remove unused routines in regrid_a2a_mod.F90

Updates affecting GCHP only:

• Fix pointer retrieval error in SET_CH4 introduced in 12.7.0 when running at c180+
  • NOTE: This also corrects a long-standing and previously unidentified issue when running with reduced timesteps
• Use new Ordonez files to avoid error in MAPL when running at c360

Read the GEOS-Chem online manual at:
http://manual.geos-chem.org

This release is compatible with GCHP. See the GCHP online manual for more information:
http://wiki.geos-chem.org/Getting_Started_With_GCHP

Learn how you can run GEOS-Chem on the Amazon Web Services cloud computing platform:
http://cloud.geos-chem.org

GEOS-Chem 12.7.1

GEOS-Chem 12.7.1
19 Feb 2020

1. Prevent excessive scavenging in Luo et al 2019 wet deposition scheme
   a. NOTE: Additional fixes will be added in 12.7.2
2. Bug fixes for the TOMAS microphysics simulation
3. Bug fix for ND51/ND51b satellite timeseries w/ nested-grid simulations
4. Bug fix in computation of AOD from isoprene SOA diagnostic
5. Bug fixes for ObsPack diagnostic re: instantaneous sampling
6. Fix for segmentation fault when dry deposition is turned off
7. Fix WRF-GC SetGridFromCtrEdges interface
8. Fix bug where GCHP 12.7.0 standard run failed if emissions turned off
9. Update MEGAN file used in GCHP 12.7.0 that caused run failure if using gfortran
10. Add MODEL_GCHP (and MODEL_CLASSIC) as CPP options in GEOS-Chem

Read the GEOS-Chem online manual at:
http://manual.geos-chem.org

This release is compatible with GCHP. See the GCHP online manual for more information:
http://wiki.geos-chem.org/Getting_Started_With_GCHP

Learn how you can run GEOS-Chem on the Amazon Web Services cloud computing platform:
http://cloud.geos-chem.org