GEOS-Chem 14.4.3

Release date: 13 Aug 2024

From CHANGELOG.md

Added

• Added ModelE2.1(GCAP 2.0) simulation to integration tests for GCClassic
• Added simulation with all diagnostics on in HISTORY.rc to integration tests for GCClassic (including Planeflight + ObsPack) and GCHP
• Added descriptive error message in Interfaces/GCHP/gchp_historyexportsmod.F90
• Auto-update GCHP HEMCO_Diagn.rc settings at run-time to ensure seasalt, dust, soil NOx, and biogenic emissions match settings in HEMCO_Config.rc

Fixed

• Added brackets around exempt-issue-labels list in .github/workflows/stale.yml

Removed

• Removed XNUMOL_H2O2 / CM3PERM3 in routine Chem_H2O2, which removes an unnecessary unit conversion for the aerosol-only simulation

Pull Requests Included

• Add ModelE2.1 (GCAP 2.0) simulation to GCClassic integration tests by @msulprizio in #2394
• Add simulation with all diagnostics turned to integration testing by @msulprizio in #2399
• Add tropopause pressure to the GEOS-Chem Classic "SatDiagn" collection by @yantosca in #2410
• Add GC-Classic transport tracer global half-degree run option with GEOS-IT by @lizziel in #2397
• Fix incorrect unit conversion for H2O2 in the aerosol-only simulation by @yantosca in #2413
• Fixes for HEMCO diagnostic config file HEMCO_Diagn.rc by @lizziel in #2402

Full Changelog: 14.4.2...14.4.3

GEOS-Chem 14.4.2

Release date: 2024-07-24

From CHANGELOG.md

Added

• Added number of levels with clouds for photolysis to geoschem_config.yml and Input_Opt to pass to Cloud-J
• Added State_Grid%CPU_Subdomain_ID and State_Grid%CPU_Subdomain_FirstID as "identifier numbers" for multiple instances of GEOS-Chem on one core in WRF and CESM

Changed

• Now reset State_Diag%SatDiagnCount to zero in routineHistory_Write (instead of in History_Netcdf_Write)
• Update rundir creation scripts to turn off the MEGAN extension for "standard" fullchem simulations
• Updated emissions used in CESM to match standard emissions used in the 14.4 offline model
• Disable support For FAST-JX for all simulations except Hg
• Only read photolysis data in Init_Photolysis in first instance of GEOS-Chem on each PET in CESM as PIO requires it

Fixed

• Typo in setCommonRunSettings.sh that made GCHP always choose mass fluxes for meteorology
• Fixed bug in # levels with cloud used in photolysis when using GCAP met or CESM
• Fixed typos for SatDiagnEdge collection in HISTORY.rc templates
• The SatDiagnOH diagnostic now works for the carbon simulation

Removed

• Entry SatDiagnPEDGE from the SatDiagn collection; This needs to go into the SatDiagnEdge collection.

Pull Requests Included

• Read number of levels with clouds used in photolysis from config file by @lizziel in #2342
• Cloud-J error handling by @lizziel in #2353
• Changes for coupling GEOS-Chem to CESM in Spectral-element Dynamical Core (CAM-SE) by @jimmielin in #2366
• Fix several issues with the GEOS-Chem Classic satellite diagnostics (SatDiagn and SatDiagnEdge collections) by @yantosca in #2369
• Turn off the MEGAN extension for fullchem "non-benchmark" simulations by @yantosca in #2372
• Update standard emissions in CESM to match standard model by @lizziel in #2375

Full Changelog: 14.4.1...14.4.2

GEOS-Chem 14.4.1

Release date: 28 Jun 2024

From CHANGELOG.md

Added

• Added initialization of PHOTDELTA in ucx_h2so4phot to avoid run-time error in CESM

Changed

• Alphabetically sort Complex SOA species into geoschem_config.yml in run directory creation
• Use hard-coded years for met fields and BC files in HEMCO_Config.rc so they are not read hourly
• Updated run/CESM with alphabetical sorting of species in geoschem_config.yml
• Added clarifying comments in GCHP configuration files for several settings, particularly related to domain decomposition, mass fluxes, and stretched grid
• Added pre-run GCHP configuration checks to setCommonRunSettings.sh related to domain decomposition, mass fluxes, and stretched grid.
• Changed search criteria for GCHP auto-update of met-field refresh frequency to not rely on presence of MetDir symlink in ExtData.rc file path

Fixed

• Fixed formatting error in .github/workflows/stale.yml that caused the Mark Stale Issues action not to run
• Fixed typo $GCAPVERTRESL -> $GCAPVERTRES in HEMCO_Config.rc.fullchem template file
• Fixed GCHP ExtData.rc entry for lightning climatology files

Removed

• Removed BudgetWetDep* entries from simulations with no soluble species in HISTORY.rc templates
• Disabled run/CESM ParaNOx extension by default in HEMCO_Config.rc
• Removed MPI broadcasts in CESM-only UCX code; MPI broadcast done at coupler level
• Remove enabling O-server in GCHP for high core counts

Pull Requests Included

• Now use comma-separated list for exempt-issue-labels YAML tag in stale.yml by @yantosca in #2308
• Remove BudgetWetDep* entries from HISTORY.rc files for simulations where wetdep is turned off by @yantosca in #2313
• Fix filename for CMIP6 aircraft emissions in HEMCO_Config.rc.template by @ltmurray in #2317
• Correct alphabetical order of complex SOA species in geoschem_config.yml by @jimmielin in #2346
• Initialization fix to avoid run-time error in UCX in CESM by @lizziel in #2349
• Changes for GEOS-Chem v14.4 within CESM compatibility by @jimmielin in #2348
• GCHP run directory fixes and improvements by @lizziel in #2326

Full Changelog: 14.4.0...14.4.1

GEOS-Chem 14.4.0

Release Date: 30 May 2024

From CHANGELOG.md

Added

• Added SpcConc%Units for species-specific unit conversion
• Diel and day-of-week scale factors for CEDS global base emissions
• Input_Opt%Satellite_CH4_Columns logical flag; Set this to true if any of AIRS, GOSAT, TCCON observational operators are selected
• Add explicit handling of gravitational settling and hygroscopic growth in dry deposition
• Added CO2, CO, and OCS single-tracer carbon simulations to the integration tests
• Added missing entry in HEMCO_Config.rc for natural gas postmeter CH4 emissions in GHGIv2 Express Extension
• Added tagged species capability and PM25nit and PM25nh4 diagnostics for GEOS runs
• Added real*4 diagnostics for State_Met logical masks IsWater, IsLand, IsIce, and IsSnow
• New parameterization for effective radius of SNA/OM aersols (see PR #2236)
• New CHEM_INPUTS/FAST_JX/v2024-05 and CHEM_INPUTS/FAST_JX/v2024-05-Hg folders with updated org.dat and so4.dat files
• Added global continental chlorine (pCl and HCl) emissions
• Extended GFED4 emissions through the end of 2023
• Added a parameterization for dry aerosol size (Rg) for SNA and OM aerosols. Updated AOD calculation reflecting varying aerosol size.

Changed

• Updated routines in GeosUtil/unitconv_mod.F90 for species-specific unit conversion
• Halt timers during calls to Convert_Spc_Units so as to time unit conversions separately
• Streamline IF statements for CH4 observational operators in Interfaces/GCClassic/main.F90
• Disable parallel loop in Do_Convection when using TOMAS; it causes unit conversion issues. Revisit later.
• Add explicit handling of gravitational settling and hygroscopic growth in dry deposition
• Added CO2, CO, and OCS single-tracer carbon simulations to the integration tests
• GitHub Action config file .github/workflows/stale.yml, which replaces StaleBot
• Switch from fixed to monthly timezones, which account for daylight savings time more accurately when computing emissions
• Updated NOAA GMD surface CH4 boundary conditions through 2022
• Rename NITs_Jscale_JHNO3 to NITs_Jscale and NIT_Jscale_JHNO2 to NIT_Jscale in geoschem_config.yml templates
• Updated volcano emissions from GMAO v202005 product to v202401 which extends to the end of 2024
• Use local scale height and level thickness to determine the PBL to determine the PBL top level and PBL pressure thickness
• Update drydep mean diameters of aerosols to account for size distribution
• Corrected the formula for 1st order heterogeneous chemical loss on stratospheric aerosol for NO2, NO3, and VOC.
• Fixed incorrect time refresh entries and other errors in run/GCHP/ExtData.rc.templates/ExtData.rc.carbon
• Changed time range entries in HEMCO_Config.rc for met, restart, and BC files to use year, month, and day tokens instead of hardcoded range
• Renamed State_Met%FRSNO and State_Met%FRLANDIC to State_Met%FRSNOW and State_Met%FRLANDICE
• Renamed isorropiaII_mod.F90 to aerosol_thermodynamics_mod.F90
• Changed aerosol thermodynamics scheme from ISORROPIA II to HETP for fullchem and APM
• Changed input data paths in run/GEOS directory to match location change on NASA discover cluster
• Use new mask files at 0.1 x 0.1 degree resoluiton for CH4/tagCH4/carbon simulations to avoid I/O bottlenecks
• Update config files for CH4/carbon simulations to avoid reading the same variable multiple times
• Converted Github issue templates to issue forms using YAML definition files

Fixed

• Corrected the formula for 1st order heterogeneous chemical loss on stratospheric aerosol for NO2, NO3, and VOC.
• Use rate-law function GCARR_ac for rxns that have Arrhenius B parameters that are zero
• Now use correct index WEAEROSOL(I,J,L,2+NDUST) in routine Settle_Strat_Aer of GeosCore/ucx_mod.F90
• Now get density of BCPI species from the species database in ucx_mod.F90
• Fix issues that prevented single-species carbon simulations from running in GCHP
• Update HEMCO_Config.rc.carbon and ExtData.rc.carbon templates for consistency
• Updated several emissions files for CO and CH4 for COARDS and MAPL compliance
• Fixed several issues in GCHP single-species carbon simulation setup scripts
• Corrected the formula for 1st order heterogeneous chemical loss on stratospheric aerosol for NO2, NO3, and VOC.
• Change restart file time cycle flag from EFYO to CYS for TOMAS simulations to avoid missing species error.
• Now define REEVAPSO2 in wetscav_mod when units are kg species; this avoids floating-point errors.
• Fixed State_Met%FRSNO to be fraction of grid box with snow rather than fraction of land with snow
• Fixed variable definitions in the DryDep collection of run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem

Removed

• Legacy binary punch diagnostic code contained within #ifdef BPCH_DIAG blocks
• IU_BPCH logical file unit (in GeosUtil/file_mod.F90)
• Removed tagged CH4 and CO species handling from carbon_gases_mod.F90
• GitHub config files .github/stale.yml and .github/no-response.yml
• Unused CO2 and carbon simulation options from geoschem_config.yml (and from related code in co2_mod.F90).
• Removed ISORROPIA
• Removed Begin array in do_fullchem (declared but not used)
• Removed tagCH4 simulation as option
• Removed --request-payer requester from run/shared/download_data.py; the s3://gcgrid data is open-source

Pull Requests Included

• Replace "huce_intel" with "huce_cascade" in Harvard Cannon sample run scripts by @yantosca in #2100
• Run scripts and environment for the Imperial College London HPC by @sdeastham in #2138
• Add budget diagnostic option for fixed level vertical region by @lizziel in #2127
• Fixes to run GEOS-Chem 14.3 in GEOS by @lizziel in #2155
• Run directory updates related to GEOS-IT by @lizziel in #2153
• Implement updated timezones file for HEMCO, that better accounts for daylight savings time worldwide by @yantosca in #2145
• Update NOAA GMD surface CH4 boundary conditions through 2022 by @msulprizio in #1979
• Rename tags in geoschem_config.yml for nitrate aerosol photolysis as per GCSC suggestion by @yantosca in #1998
• Remove remaining binary punch diagnostics code by @yantosca in #2166
• UCX bug fixes : (1) Use proper 4th index for WERADIUS array; (2) Get density of black carbon from the species database by @yantosca in #2176
• Add #SBATCH -c 1 to Harvard Cannon GCHP run scripts and integration tests; Also allow scheduler none in integration tests by @yantosca in #2182
• Rename "native" to "raw" in GCHP run directory creation scripts & templates by @yantosca in #2178
• Update volcano emissions through the end of 2022 by @msulprizio in #2198
• Updates for GEOS-Chem 14.3 in CESM by @lizziel in #2154
• Fix uptake coefficients on stratospheric aerosol by @cdholmes in #2205
• Fix bug for SLP and TROPP scaling by @lizziel in #2207
• Fix PBL level calculations by @cdholmes in #2078
• Update integration & parallel test scripts to input the test type and reduce the number of input arguments by @yantosca in #2187
• Initialize PBL variables by @cdholmes in #2211
• Change NEI 2D emissions to xy dimension by @nicholasbalasus in #2213
• Update integration tests to pass quick option to compile scripts by @msulprizio in #2222
• Fix geopotential height units in netCDF file by @cdholmes in #2224
• Add GCHP diagnostics for GCHPctmEnv and FV3 gridded components by @lizziel in #2199
• Add updates for CH4 analytical inversion by @msulprizio in #2218
• Fix bug in transport tracer pressure mask criteria affecting tracer st80_25 by @lizziel in #2226
• Remove requirement for photolysis data directories to end with slash by @lizziel in #2225
• Update CH4 emissions from EDGARv7 to EDGARv8 by @nicholasbalasus in #2228
• Merge 14.3.1 into the 14.4.0 development branch by @msulprizio in #2232
• Fixes for the carbon simulation by @yantosca in #1992
• Add CO2, CO, and OCS single-tracer carbon simulations to the integration tests by @msulprizio in #2236
• Replace stalebot with "stale" GitHub action by @yantosca in #2260
• Only convert units for species that require it by @yantosca in #2072
• Remove hardcoded year range for met fields, restart, and BC files in HEMCO_Config.rc by @msulprizio in #2263
• Add missing gas postmeter CH4 emissions for the GHGI express extension inventory by @msulprizio in #22...

GEOS-Chem 14.3.1

Release date: 02 Apr 2024

From CHANGELOG.md

• Added operational run scripts for the Imperial College London (ICL) cluster
• Added new vertical region option to budget diagnostic for fixed bottom and top levels
• Added GEOS-IT processed lat-lon fields as a valid option when creating GCHP run directories
• Functions charArr2str and str2CharArr in Headers/charpak_mod.F90
• Field State_Diag%Obspack_CharArray as a 2-D character array
• Added util folder in run/CESM to include .cdl file used to generate CESM NetCDF input file for deposition
• Add GCClassic operational example environment files for Harvard Cannon
• Added new GCHP history collections for advection diagnostics
• Added slash in front of names of LUT files read into photolysis_mod.F90 to avoid needing it in path

Changed

• Updated Harvard Cannon operational run scripts to use huce_cascade instead of huce_intel; also added sapphire
• Changed exponent 'e' to 'd' for one entry in KPP to prevent precision error in external models
• Changed GCHP sample run scripts to not print script execution commands to log
• Changed offline emissions grid resolution templates in config files to be more descriptive
• Read obspack_id from netCDF files into a character array, then convert to string
• Add #SBATCH -c 1 to GCHP integration test scripts and sample run scripts for Harvard Cannon
• In GCC/GCHP integration tests, passing -s none will run compile-only tests. Query user to proceed or to exit.
• GCC/GCHP integration tests will exit immediately if scheduler is omitted.
• Now use raw instead of native in GCHP run directory scripts & templates
• Rename env var RUNDIR_METLIGHTNING_DIR_NATIVE to RUNDIR_METLIGHTNING_DIR
• Rename env var RUNDIR_METLIGHTNING_NATIVE_RES to RUNDIR_METLIGHTNING_RES
• Updated config files used in CESM from GEOS-Chem 14.1 to 14.3
• Don't create run directories for integration/parallel tests if invoked with -t compile
• Refactor integration and parallel test scripts to reduce the number of input arguments
• Copy utility scripts that allow you to resubmit failed to integration and parallel test root directories
• Update GCHP operational example environment files for Harvard Cannon
• Do not run GCClassic integration test compile jobs in the background
• Updated integration tests to pass quick option to compile scripts
• Removed emissions handling from global_ch4_mod.F90 and carbon_gases_mod.F90 and instead apply scale factors to emissions directly in HEMCO_Config.rc
• Loop over advected species CH4 chemistry routines to allow for multiple CH4 tracers within analytical inversion framework
• Updated CH4 global anthropogenic emission inventory from EDGARv7 to EDGARv8

Fixed

• Fixed unit conversions in GEOS-only code
• Fixed GEOS-IT native lat-lon filenames used for clusters other than discover
• Fixed offline emission paths set when using GEOS-IT meteorology
• Fixed format issue in input_mod RRTMG print statement caught by some compilers
• Fixed GEOS-IT SLP and TROPP scaling in pre-processed files used in GCHP
• Fixed reading of NEI emissions through HEMCO
• Fixed incorrect units metadata for State_Met%PHIS
• Fixed bug in transport tracer ST80 mask criteria which prevented mask from ever being zero

Removed

• Removed MPI broadcasts in CESM-only photolysis code; will read on all cores
• Removed State_Chm%CH4_EMIS

Pull requests included

• Replace "huce_intel" with "huce_cascade" in Harvard Cannon sample run scripts by @yantosca in #2100
• Run scripts and environment for the Imperial College London HPC by @sdeastham in #2138
• Add budget diagnostic option for fixed level vertical region by @lizziel in #2127
• Fixes to run GEOS-Chem 14.3 in GEOS by @lizziel in #2155
• Run directory updates related to GEOS-IT by @lizziel in #2153
• Add #SBATCH -c 1 to Harvard Cannon GCHP run scripts and integration tests; Also allow scheduler none in integration tests by @yantosca in #2182
• Rename "native" to "raw" in GCHP run directory creation scripts & templates by @yantosca in #2178
• Updates for GEOS-Chem 14.3 in CESM by @lizziel in #2154
• Fix bug for SLP and TROPP scaling by @lizziel in #2207
• Update integration & parallel test scripts to input the test type and reduce the number of input arguments by @yantosca in #2187
• Change NEI 2D emissions to xy dimension by @nicholasbalasus in #2213
• Update integration tests to pass quick option to compile scripts by @msulprizio in #2222
• Fix geopotential height units in netCDF file by @cdholmes in #2224
• Add GCHP diagnostics for GCHPctmEnv and FV3 gridded components by @lizziel in #2199
• Add updates for CH4 analytical inversion by @msulprizio in #2218
• Fix bug in transport tracer pressure mask criteria affecting tracer st80_25 by @lizziel in #2226
• Remove requirement for photolysis data directories to end with slash by @lizziel in #2225
• Update CH4 emissions from EDGARv7 to EDGARv8 by @nicholasbalasus in #2228

Full Changelog: 14.3.0...14.3.1

GEOS-Chem 14.3.0

Release date: 09 Feb 2024

From CHANGELOG.md

Added

• Added capability for TOMAS simulations in GCHP
• Added State_Chm%nTomasBins to replace hardcoded bins in TOMAS diagnostics
• Added interface to Cloud-J package for computing photolysis rates
• Added compile-time option FASTJX to use legacy Fast-JX photolysis instead of Cloud-J
• Added new diagnostics OD600 and TCOD600 for 600 nm optical depths (per-level and total column) used for computing J-values in either Fast-JX or Cloud-J
• Added GEOS-IT as meteorology option and labeled as beta during run directory creation until full inventory and offline emissions are available.
• Added support for running GEOS-Chem on the NASA discover cluster
• Added inclusion of c30 restart file in GCHP run directories since c24 and c48 not supported when using GEOS-IT meteorology
• Added automatic updating of GCHP lightning climatology in ExtData.rc based on settings in HEMCO_Config.rc
• Added two new diagnostics to track number of negative concentrations after first and last KPP integration
• Added capability of running GEOS-Chem transport tracer simulation within the GEOS model
• Added radiative forcing contributions due to trop-only ozone, CFCs, water vapor, N2O, CO2 and changes in stratosphere to RRTMG
• Added computation of radiative forcing at the tropopause to RRTMG
• Added option to compute stratospherically-adjusted radiative forcing at the tropopause using RK4 time marching integration with fixed dynamical heating approximation (FDH)
• Added experimental option to apply seasonally-evolving fixed dyanmical heating approximation in RRTMG

Changed

• Updated fullchem mechanism following JPL/IUPAC. See KPP/fullchem/CHANGELOG_fullchem.md for details.
• Reorganized GCHP run directory creation prompts for GEOS-FP native meteorology input
• Converted TOMAS bpch diagnostics to netCDF
• Now read the Hg restart file from ExtData/GEOSCHEM_RESTARTS/v2023-12
• Increse requested time limits in GCHP integration tests (compile 2h30m, run 5h)
• Changed CO2 concentration used in RRTMG to be modifiable in geoschem_config.yml
• Changed water vapor used in RRTMG to match to tracer field at all altitudes
• Updated restart file path for GCHP TOMAS simulations
• Look for fullchem restarts in the GEOSCHEM_RESTARTS/GC_14.3.0 folder
• Look for fullchem/aerosol boundary conditions in the HEMCO/SAMPLE_BCs/GC_14.3.0/fullchem folder

Fixed

• Fixed bug in stratospheric aerosols optical depths passed to Fast-JX
• Restored consideration of both isSnow and isIce in dry deposition
• Fixed calculation of FRLAND_NOSNO_NOICE in calc_met_mod.F90
• Added missing units in comments of KPP/fullchem/commonIncludeVars.H
• Use run directory (not absolute path) to determine the executable file name in integration & parallel tests.
• Fixed memory leaks in State_Chm%AerMass and State_Chm%Phot containers
• Fixed incorrect time-avaging in RRTMG diagnostics wheres zeros included prior to first RRTMG call

Removed

• Removed references to unused met-fields RADLWG and LWGNT
• Removed inclusion of c360 restart file in GCHP run directories
• Reduced timers saved out to essential list used for benchmarking model performance

See the GEOS-Chem 14.3.0 page for a complete list of updates.

Pull Requests Included

• Bug fix for TOMAS sulfate production rates by @BettyCroft in #1569
• Fix to address GCClassic failure to integrate with TOMAS when using dev/tomas branch by @BettyCroft in #1959
• Fix to address GCHP failure to integrate with TOMAS when using dev/tomas branch by @BettyCroft in #1960
• JPL/IUPAC updates by @kelvinhb in #1765
• Interim fix for runaway HMS chemistry by @sdeastham in #2006
• Fix bugs setting strat aerosol OD passed to Fast-JX by @lizziel in #2018
• Dry deposition to snow and ice by @r-pound in #2045
• Application of FRSNO in land cover arrays by @r-pound in #2046
• Move aerosol_mod.F90 arrays to State_Chm%AerMass object by @lizziel in #2015
• TOMAS updates: Capability to run in GCHP, NetCDF diagnostics, and other fixes by @msulprizio in #2060
• Add missing units in comments of KPP/fullchem/commonIncludeVars.sh by @yantosca in #2061
• Fix unit conversion code for TOMAS following merge with 14.2.3 by @msulprizio in #2063
• Now read the Hg restart file from GEOSCHEM_RESTARTS/v2023-12 by @yantosca in #2059
• Reduce timers to essential list only by @msulprizio in #2069
• Add Cloud-J as new default photolysis option by @lizziel in #1522
• GEOS-Chem Transport Tracers simulation GEOS by @lizziel in #2058
• Use rundir (not absolute path) to select the executable file for integration and parallel tests by @yantosca in #2084
• Increase time limits for GCHP integration tests by @yantosca in #2095
• Updates to run GEOS-Chem with GEOS-IT by @lizziel in #1848
• Updates from GMAO for GEOS by @lizziel in #2062
• Fix errors in GCClassic dry-run simulations when Cloud-J photolysis is activated by @yantosca in #2082
• Merge no-diff-to-benchmark updates into the 14.3.0 development stream by @yantosca in #2106
• Fix additional memory leaks in GEOS-Chem by @yantosca in #2104
• Limit Cloud-J initialization prints to single core by @lizziel in #2109
• Add fix to cldj_interface_mod.F90 to avoid floating-point exception in GCHP integration tests by @msulprizio in #2111
• Add nitrate aerosol to Ox family definition in gckpp.kpp by @msulprizio in #2071
• Stratospheric adjustment and additional output fields for RRTMG in GCHP by @sdeastham in #2010
• Add fixes for TOMAS simulations in GCHP by @msulprizio in #2136
• Update run directory scripts to get certain restarts from 14.3.0 1-year benchmark output and boundary condition output by @yantosca in #2134
• [WIP] Change units of Loss_Ox diagnostic from molec/cm3/s to unitless (to fix an issue in tagO3 simulations) by @yantosca in #2096

New Contributors

• @BettyCroft made their first contribution in #1569
• @kelvinhb made their first contribution in #1765
• @r-pound made their first contribution in #2045

Full Changelog: 14.2.3...14.3.0

GEOS-Chem 14.2.3

Release date 01 Dec 2023

From CHANGELOG.md

Added

• GEOS-Chem Classic rundir script run/GCClassic/setupForRestarts.sh

Changed

• Added the -n aka --no-bootstrap option to integration tests to disable bootstrapping missing species in restart files
• Use integer parameters for species units instead of strings (for computational efficiency)
• Update error message for missing surface CH4 emissions with instructions on how to resolve the problem
• Change GCHP grid resolution threshold for lowering timesteps from C180 inclusive to C180 exclusive
• Read GEOS-Chem Classic restart file paths from the relevant download_data.yml file

Fixed

• Prevent POAEMISS from being assigned a value if not allocated (in carbon_mod.F90)
• Changed incorrect comment about static H2O option in GeosCore/input_mod.F90
• Fixed typos (GCClassic -> GCHP) written to GCHP integration test log files
• Add fix to properly read GHGI v2 express extension emissions in CH4 and carbon simulations
• Move OH perturbation scale factor to outside EMISSIONS logical bracket in HEMCO_Config.rc files for CH4 and carbon simulations

Removed

• Remove definition of METDIR from primary HEMCO_Config.rc files to ensure use of the definition in the HEMCO_Config.rc.*_metfields files

Pull Requests Included

• Updates for GEOS-Chem within CESM2 - convective scavenging correction and MPI fixes by @jimmielin in #1993
• Fix titles for 14.2.0 and 14.2.2 in CHANGELOG.md by @msulprizio in #2011
• Prevent POAEMISS variable from being assigned if not allocated by @yantosca in #1987
• Use integer flags to denote species units instead of strings by @yantosca in #1796
• Fix incorrect comment on static H2O option by @sdeastham in #2013
• Add a --no-bootstrap option to integration tests to prevent switching EFYO -> CYS in HEMCO_Config.rc by @yantosca in #1990
• Improve missing ch4 emissions error message by @lizziel in #2039
• Add fixes to HEMCO_Config.rc for CH4 and carbon simulations by @msulprizio in #2042
• Fix typos written to GCHP integration test log files by @yantosca in #2043
• Update GEOS-Chem Classic rundir scripts to read restart file paths from download_data.yml by @yantosca in #2050

Full Changelog: 14.2.2...14.2.3

GEOS-Chem 14.2.2

Release date: 23 Oct 2023

From CHANGELOG.md

Changed

• Updated sample restart files for fullchem and TransportTracers simulations to files saved out from the 14.2.0 1-year benchmarks

Pull Requests Included

• Update sample restart files for fullchem and TransportTracers to 14.2.0 benchmark files by @msulprizio in #1989
• Fix broken links to CONTRIBUTING.html and SUPPORT.html in GitHub templates by @yantosca in #2009

Full Changelog: 14.2.1...14.2.2

GEOS-Chem 14.1.2

Release date: 10 Oct 2023

This release contains updates for GEOS-Chem in CESM only. It is zero diff for GEOS-Chem in all other applications.

From CHANGELOG.md

Added

• CESM-only update: Added option for correctConvUTLS for correcting buildup of soluble tracers in the UT/LS to match CAM-chem behavior

Changed

• CESM-only update: extend existing KppError, KppStop to CESM for model stability
• CESM-only update: Removed mpi_bcast in ucx_mod NOXCOEFF_INIT to be handled at coupler level to support spectral-element dynamical core

Pull Requests Included

• Updates for GEOS-Chem within CESM2 - convective scavenging correction and MPI fixes by @jimmielin in #1993

Full Changelog: 14.1.1...14.1.2

GEOS-Chem 14.2.1

Release date: 10 Oct 2023

From CHANGELOG.md

Added

• Script test/difference/diffTest.sh, checks 2 different integration tests for differences
• Added GCHP environment file and export/unset env variables in run script for NASA Pleiades cluster
  SatDiagnEdge collection to all GEOS-Chem Classic HISTORY.rc templates
• Added new GCHP config file ESMF.rc for configuring ESMF logging
• Added several new run directory files for use with GEOS-Chem in GEOS
• GCClassic integration tests now display proper commit info in results.compile.log
• Stopped OCEAN_CONC from needlessly being pushed through vertical regridding for Hg simulations
• Added warning in GCHP HISTORY.rc about outputting area-dependent variables on custom grids
• Added option to use a single advected species in the carbon simulation
• Added option to perturb CH4 boundary conditions in CH4 simulation
• Added option to perturb OH in CH4 simulation using scale factor in HEMCO_Config.rc

Changed

• Update DiagnFreq in GCClassic integration tests to ensure HEMCO diagnostic output
• Rename restart files in GCHP integration tests (as we do in non-test runs)
• Request 6 hours of execution time for GEOS-Chem Classic integration tests
• Invert directory structure where integration and parallel test scripts are stored
• Error check to stop run if any MW_g values are undefined
• Explicitly define tagCH4 simulations in Input_Opt rather than basing off of number of advected species
• The fullchem mechanism must now be built with KPP 3.0.0 or later
• Changed the AEIC 2019 monthly climatology specification format in ExtData.rc to match standard convention for climatology
• Changed default ESMF logging in GCHP to be ESMF_LOGKIND_NONE (no log)
• NetCDF utilities in NcdfUtil folder now use the netCDF-F90 API
• GEOS-only updates for running GEOS-Chem in GEOS
• Boundary conditions for nested-grid simulations are now imposed at every time step instead of 3-hourly
• Update GeosCore/carbon_gases_mod.F90 for consistency with config file updates in PR #1916
• Update MPI usage in CESM-only code to match new conventions in CAM
• Updated GEPA inventory to GHGI v2 for CH4 and carbon simulations
• Updated integration tests scripts to run on the WashU Compute1 cluster

Fixed

• Add missing mol wt for HgBrO in run/shared/species_database_hg.yml
• Moved the EDGAR REF_TRF CH4 emissions to the Oil emissions category so it is superseded by GFEIv2 for carbon simulations.
• Prevent State_Diag%SatDiagnCount from not being allocated
• For satellite diagnostics, do not test for id_OH if OH is not a species
• Fixed parallelization in Luo wetdep simulations caused by uninitialized variable
• Fixed parallelization for Hg0 species in GeosCore/drydep_mod.F90
• Fixed incorrect time-slice when reading nested-grid boundary conditions
• Fixed initialization of advected species missing in GCHP restart file
• Fixed comments in GeosUtil/unitconv_mod.F90 to reflect code implementation
• Fixed compilation issues for KPP/custom; updated equations in custom.eqn
• Prevent users from creating GCClassic rundirs at 0.25 x 0.3125 resolution for MERRA-2 met
• Added fix to set RUNDIR_GRID_HALF_POLAR option for global grids at 0.25x0.3125 or 0.5x0.625 resolutions
• Moved OCEAN_MASK out of ExtData.rc.TransportTracers and into the
  meteorology template files
• Update ExtData.rc.CO2 to get meteorology entries from template files
• Added fix for CH4 analytical inversions to convert the state vector value read from file to the nearest integer before comparing to the Input_Opt%StateVectorElement read from geoschem_config.yml

Removed

• Remove references to the obsolete tagged Hg simulation

New Contributors

• @nicholasbalasus made their first contribution in #1856

Full Changelog: 14.2.0...14.2.1