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

CHANGELOG

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

Full Changelog: 14.2.2...14.2.3

GEOS-Chem 14.2.2

Release date: 23 Oct 2023

What's Changed

• 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

---

What's Changed

• 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

CHANGELOG

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

GEOS-Chem 14.2.0

Release date: 05 Oct 2023

What's Changed

• Bug fix: restore consideration of sea salt alkalinity to heterogenerous acid-catalyzed reactions of halogens on sea salt aerosols by @yantosca in #1548
• Consolidate existing integration test scripts (slurm, lsf, interactive); Add LSF capability by @yantosca in #1565
• Integration/parallelization test scripts now place test scripts & artifacts into subdirectories of the root test folder by @yantosca in #1636
• Add reminders to compile with CMake options to createRunDir.sh scripts by @yantosca in #1638
• Convert log file prints to debug prints by @yantosca in #1549
• Fix bug where writing species metadata yaml file always attempted by @lizziel in #1644
• Remove NcdfUtil/perl folder by @yantosca in #1567
• Reset SPC_ time entry from EFYO to CYS for integration tests and fullchem_benchmark runs by @yantosca in #1647
• Remove LWI from carbon simulation run directories by @lizziel in #1643
• GEOS-only updates from Christoph Keller by @lizziel in #1653
• Update rundir configuration files to point to corrected NEI day-of-week scale factors (Closes #1608) by @yantosca in #1633
• Add entries for GFAS methanol to HEMCO_Config.rc templates by @yantosca in #1632
• Archive State_Chm%H2SO4_PRDR for production rate of H2SO4 (mol/mol) for CESM-GC by @jimmielin in #1624
• Apply work-around for GFAS pFe bug in GC-Classic and GCHP by @lizziel in #1621
• Simplify Github issue and pull request templates by @msulprizio in #1650
• Avoid compiler warning and compilation restart for KPP/fullchem/gckpp_Jacobian.F90 by @yantosca in #1657
• Change HEMCO time cycle flag in benchmark rundir & integration tests for 14.1.1 by @yantosca in #1656
• Removal of module variables from ucx_mod by @jimmielin in #1583
• Fix incorrect comparison in GET_IJ routine; Fix leftover issues from PR #1656 by @yantosca in #1663
• Fix bug in RRTMG optic diagnostics (AOD, SSA, Asym) by @lizziel in #1669
• Ask users for PI at registration; abstract user registration code into a single script by @yantosca in #1674
• Move GC-Classic run scripts to operational_examples directory by @lizziel in #1677
• Fix several issues with GitHub issue and PR templates by @yantosca in #1679
• Remove X-HRS printout from GEOS-Chem log file by @msulprizio in #1678
• Remove references to Compute Canada from data download scripts by @msulprizio in #1681
• Add lumped furans to chemistry and biomass burning emissions by @msulprizio in #1642
• Abstract fullchem mechanism history into CHANGELOG_fullchem.md - closes #1689 by @yantosca in #1690
• Fix typo in GCClassic/createRunDir.sh preventing benchmark run script from being copied to run directory by @msulprizio in #1694
• Prevent divide by zero in sulfur chemistry by @lizziel in #1698
• Turn on sea salt debromination for full-chemistry simulations by @msulprizio in #1703
• Now use consistent behavior when the first call to "Integrate" fails by @yantosca in #1609
• Reset "EFY" to "CYS" for nested boundary conditions in GCClassic integration & parallel tests by @yantosca in #1706
• Restore Iy sink reactions and rebuild fullchem mechanism with KPP 3.0.0 by @yantosca in #1620
• Restore consideration of sea salt alkalinity to heterogenerous acid-catalyzed reactions of halogens on sea salt aerosols by @msulprizio in #1702
• Add S(IV) + HOBr and S(IV) + HOCl to the fullchem mechanism (Closes #1627) by @yantosca in #1630
• Update entrainmment-limited kinetics in clouds by @cdholmes in #1292
• Include nitrate aerosol photolysis in the troposphere by @viral211 in #1623
• Update HEMCO_Config.rc and ExtData.rc template files to read GFED4 data thru 2022 by @yantosca in #1709
• Add lightning climatology option to HEMCO_Config.rc by @msulprizio in #1628
• Restore vertical emission distributions to CEDS energy and industry emissions by @msulprizio in #1712
• Add fix for CEDS energy and industry emissions to distribute vertically by @msulprizio in #1730
• GCHP bug fixes and run directory updates by @lizziel in #1724
• Add run configuration files for WRF-GC by @jimmielin in #1692
• Fix bug renaming midrun checkpoint files by @lizziel in #1737
• Fix computation of planeCount for Harvard Cannon GCHP run scripts and integration test scripts by @yantosca in #1686
• Restructure photolysis by @lizziel in #1733
• Update text displayed at user registration during rundir creation by @yantosca in #1732
• Remove array temporaries in carbon_mod.F90 and seasalt_mod.F90 by @yantosca in #1729
• Modify HEMCO_Config.rc templates to read HEMCO restart files from the rundir "Restarts/" subdirectory by @yantosca in #1718
• Prevent repeated printout of concs, rxn rates when KPP fails twice by @yantosca in #1749
• Fix bug in photolysis off option by @lizziel in #1750
• Fix bug in HOBr uptake rate calculation (closes #1746) by @yantosca in #1751
• Set CO2 concentration to 421 ppm in fullchem simulations -- fixes CO2 error norm for KPP by @yantosca in #1731
• Add GFED4 climatology emissions as an option in HEMCO_Config.rc by @msulprizio in #1758
• Update global_ch4_mod.F90 to correct bug that incorrectly selects troposphere-stratosphere boundary by @toddmooring in #1710
• Update global anthropogenic CH4 emissions to EDGARv7.0 by @msulprizio in #1773
• Remove operator splitting in CH4 simulation that biases diagnostics (closes #1738) by @yantosca in #1740
• Update CH4 simulation to use loss frequencies from GCClassic 14.0.0 10-year benchmark by @msulprizio in #1776
• Update README.md and AUTHORS.txt for 14.2.0 by @yantosca in #1774
• Update GCHP check for python and bc libs to prevent error checking fail by @lizziel in #1777
• Add modifications to sea salt chemistry in order to avoid KPP integration errors by @yantosca in #1779
• Add CH4 emissions from hydroelectric reservoirs by @msulprizio in #1784
• Add RxnConst diagnostic for archiving reaction rate constants by @jimmielin in #1728
• Fix GCHP time_mod start and elapsed times by @lizziel in #1781
• Update partitions and env files in Harvard Cannon operational examples by @yantosca in #1811
• Change relative tolerance back to 0.5e-2 to address model slowdown by @msulprizio in #1815
• Allow the use of OFFLINE_SEASALT for seasalt alkalinity, Cl, and Br in GEOS-Chem within CESM by @jimmielin in #1804
• Update transport tracer simulation for consistency with GMAO's tracer gridded component by @msulprizio in #1816
• Bug fixes for GEOS-only runs by @lizziel in #1842
• Add correct TransportTracers species names to GCHP HISTORY.rc.TransportTracers template by @yantosca in #1840
• Prevent run-time crash if using GEOS-IT meteorolology by @lizziel in #1846
• Fix GC-Classic run directory runScriptSamples symbolic link by @lizziel in #1852
• Fix bug in state_chm_mod that printed line of equals signs to log from every core by @lizziel in https://g...

GEOS-Chem 14.1.1

Release date: 03 Mar 2023

From CHANGELOG.md

Added

• New integration test functions in test/GCClassic/integration and test/GCHP/integration
• New parallelization test functions in test/GCClassic/parallel
• Added README.md files for integration and parallelization tests in the test folder structure
• Added GCHP integration test for the tagO3 simulation
• Added GCHP and GCClassic integration tests for the carbon simulation
• Integration and parallelization test folders have been separated into subdirectories to minimize clutter.
• GEOS-only updates
• Add about to GitHub issue templates (ensures they will be displayed)
• Added .github/ISSUE_TEMPLATE/config.yml file w/ Github issue options

Changed

• GCClassic integration tests now use a single set of scripts
• GCHP integration tests now use a single set of scripts
• Integration test run directories are created with the default names assigned by createRunDir.sh
• Several bash functions in test/shared/commonFunctionsForTests.sh have been combined so that they will work for both GCClassic and GCHP integration tests
• ./cleanRunDir.sh functions now take an argument for non-interactive execution (facilitates integration & parallelization tests)
• Moved several module variables from GeosCore/ucx_mod.F90 to Headers/state_chm_mod.F90. This facilitates using GEOS-Chem in CESM.
• Time cycle flags EFYO are changed to CYS for all GCClassic integration/parallel tests, and for GCClassic fullchem_benchmarksimulations.
• Ask users for the name of their research institution at registration
• Ask users for the name of their PI at registration
• Do not compile GCHP for tagO3 integration tests; use the default build instead
• Moved GC-Classic sample run scripts to operational_examples/harvard_cannon
• The GitHub PR template is now named ./github/PULL_REQUEST_TEMPLATE.md

Fixed

• Fixed bug in where writing species metadata yaml file write was always attempted
• Prevent a warning from being generated when compiling gckpp_Jacobian.F90
• Fixed a bug in routine GET_IJ where X and Y were swapped in an IF comparison.

Removed

• Removed intTest*_slurm.sh, intTest_*lsf.sh, and intTest*_interactive.sh integration test scripts
• Removed State_Met%LWI and input meteorology LWI from carbon simulation run config files
• Removed function CLEANUP_UCX; deallocations are now done in state_chm_mod.F90

Full Changelog: 14.1.0...14.1.1

GEOS-Chem 14.1.0

Release date: 01 Feb 2023

This is a release features the updates and fixes listed below.

From CHANGELOG.md

Added

• Added dry deposition updates to Hg0 from Feinberg22 ESPI publication + AMAP emissions
• Added MO2 + NO3 = NO2 + CH2O + HO2 reaction
• Added capability to write species metadata to YAML file
• Added satellite diagnostic (SatDiagn) collection, to archive several fields within a user-defined local-time interval. CAVEAT: For now, only one local-time interval is permitted.
• Added adaptive solver (rosenbrock_autoreduce) option for fullchem mechanism
• Added entries for BALD, BENZP, BZCO3H, NPHEN to JValues collection in HISTORY.rc for GCHP
• Added GCHP run script and environment files for MIT clusters Hex and Svante
• Added operational GCHP and GCClassic environment and run scripts for the University of York cluster, Viking
• Added tagO3 run directory for GCHP
• Added upwards mass flux diagnostic to GCHP History collection LevelEdgeDiags
• Added timestep menu to GCHP geoschem_config.yml template files
• Added HTAPv3 inventory as a global emissions option (off by default)
• Added carbon simulation and KPP mechanism for CO-CO2-CH4-OCS
• Added GCHP run script and environment file for UCI Australia cluster Gadi

Changed

• Moved in-module variables in global_ch4_mod.F90 to State_Chm
• Moved in-module variables in hco_interface_gc_mod.F90 to State_Met and State_Chm
• Modified SpeciesConc diagnostic to include option to output units in v/v or molec/cm3
• Rebuilt fullchem and Hg mechanisms with KPP 3.0.0
• Changed HEMCO timecycle flag for QFED and offline emissions from EF to EFY
• Updated the time refresh settings for O3_PROD and O3_LOSS in ExtData.rc.tagO3 to read data on the first of each month.

Fixed

• Fixed sign of Arrhenius "A" coefficient in reaction ETO = HO2 + 2CH2O
• Fixed products in HOBr + SO2 and HOCl + SO2 reactions
• Changed MW_g value of CH4 from 16.05 to 16.04
• Added "WD_CoarseAer:true" for SO4s and NITs in species_database.yml
• Fixed bug in computing State_Met surface type logicals (IsLand, IsWater, etc)
• Fixed bug where State_Met%FRSNO (fraction snow) was all zeros in GCHP
• Fixed HCFC141b and HCFC142b names in GCHP HISTORY.rc
• Fixed list of complex SOA species checked in input_mod.F90
• Now use a string array for reading the list of ObsPack diagnostic species (in GeosCore/input_mod.F90)
• Fixed bug in logic that caused restart files not to be linked to the Restarts/ folder of the GCHP tagO3 run directory
• Fixed timestamp for GCClassic History diagnostic so time-averaged collections match the reference time
• Fixed double-titration of seasalt alkalinity

Removed

• Removed LRED_JNO2 and AERO_HG2_PARTITON switches from HEMCO_Config.rc (and related code)

See the GEOS-Chem 14.1.0 page for a complete list of updates.

What's Changed

• Adding in dry deposition updates to Hg0 from Feinberg22 ESPI publication + AMAP emissions by @arifein in #1367
• Add MO2 + NO3 = NO2 + CH2O + HO2 reaction via KPP by @yantosca in #1444
• Bug fix: Change sign of Arrhenius "A" coefficient in rxn ETO = HO2 + 2CH2O by @yantosca in #1447
• Bug fix: HOBr + SO2 and HOCl +SO2 now produce SO4 instead of SO4s; Closes #1298 by @yantosca in #1448
• Update MW_g value of CH4 from 16.05 to 16.04 by @yantosca in #1445
• Add "WD_CoarseAer:true" for SO4s and NITs in species_database.yml by @yantosca in #1426
• Fix bug in computing State_Met fields IsLand, IsWater, IsOcean, IsIce by @lizziel in #1425
• Add capability to write metadata for defined species to a YAML file by @yantosca in #1316
• Move in-module variables in GLOBAL_CH4_MOD to State_Chm by @jimmielin in #1407
• GEOS-Chem Classic netCDF satellite diagnostics (supersedes PR #1134) by @yantosca in #1478
• Removes HCO_Interface_GC_Mod module variables SZAFACT, JNO2, JOH by @jimmielin in #1348
• Add MAPL ExtData format option required in MAPL 2.26.0 by @lizziel in #1489
• Add capability to save SpeciesConc diagnostic in units v/v or molec/cm3 by @msulprizio in #1572
• KPP 3.0.0 with auto-reduction solver by @yantosca in #1482
• Retire LWI met-field by @lizziel in #1435
• Fix GCHP bug where fraction snow all zeros by @lizziel in #1577
• Add missing J-value diagnostics to GCHP HISTORY.rc by @msulprizio in #1582
• Fix bug in GCHP HISTORY.rc names for HCFCs by @lizziel in #1590
• Fix list of Complex SOA species checked in input_mod.F90 by @jimmielin in #1546
• Add GCHP operational scripts for UoY by @kilicomu in #1570
• Add GCHP operational run scripts for MIT clusters by @lizziel in #1571
• Add GC-Classic operational scripts for York by @kilicomu in #1592
• Add tagged O3 run directory for GCHP by @Jourdan-He in #1380
• Fix parsing error for ObsPack diagnostic species in input_mod.F90 -- Closes #1542 by @yantosca in #1554
• Add GCHP upwards mass flux diagnostic to config files by @lizziel in #1584
• Remove LRED_JNO2 and AERO_HG2_PARTITION switches and related code by @yantosca in #1588
• Fix typos and add explanatory comments for Hg simulation emissions by @jennyfisher in #1591
• Add timestep menu back to GCHP geoschem_config.yml templates by @yantosca in #1589
• Fix timecycle flag for QFED and OFFLINE emissions in HEMCO_Config.rc by @msulprizio in #1595
• Add HTAPv3 inventory as a global emissions option by @yantosca in #1551
• Fix logic error in GCHP createRunDir.sh for tagO3 simulation by @yantosca in #1597
• Time-averaged file timestamp changed from averaging period mid-point to start by @yantosca in #1600
• Add fixes for minor issues in the GCHP tagO3 simulation by @yantosca in #1601
• Fix double-titration of seasalt alkalinity error -- Closes #1506 by @yantosca in #1521
• Add GCHP operational run files for NCI Australia cluster Gadi by @lizziel in #1615
• Add carbon simulation and KPP mechanism by @msulprizio in #1605
• Change Harvard Cannon "huce_cascade" partition name to "seas_compute" in sample run scripts by @yantosca in #1611
• Bug fix: Rename GCHP operational run script example directory for Australia's NCI Gadi cluster by @msulprizio in #1619

New Contributors

• @arifein made their first contribution in #1367
• @kilicomu made their first contribution in #1570
• @jennyfisher made their first contribution in #1591

Full Changelog: 14.0.2...14.1.0

GEOS-Chem 14.0.2

Release date: 29 Nov 2022

This is a bug fix release featuring the updates and fixes listed below.

From CHANGELOG.md

Fixed

• Added fix for writing dry-run header to log file
• Updated KPP diagnostics archive flags
• Rewrote code to avoid memory leaks (identified by the code sanitizer)
• Updated EDGAR v6 CH4 emission files to correct timestamp issue
• Updated CH4 Lakes emission files to correct time unit issue
• Added fix for CH4_RICE emissions from EDGAR v6
• Fixed indentation error in the legacy_bpch section ofgeoschem_config.yml template files
• Removed "dry air" from the metadata of fields State_Met%AIRVOL and State_Met%BXHEIGHT
• Applied fixes for CESM runs: Turned off sea salt emissions; Modified time cycle flag for YUAN_MODIS_LAI

Changed

• Updated CESM HISTORY.rc to work with new CESM-GC diagnostics interface
• Updated sample fullchem restart files copied to run directories to 14.0.0 10-year benchmark output

What's Changed

• Bug fix: Only write dry-run header to HEMCO.log if it has a unit number by @yantosca in #1476
• Update KPP diagnostics archive flags by @christophkeller in #1477
• Fix units of RxnRate diagnostic in Get_MetaData_State_Diag routine by @yantosca in #1483
• Fix memory leaks and other issues identified by the code sanitizer by @yantosca in #1353
• Fix indentation issue in geoschem_config.yml templates by @laestrada in #1505
• Add fix for EDGAR v6 CH4 emissions by @msulprizio in #1507
• Add fixes to restore the analytical inversion option for CH4 simulations by @msulprizio in #1512
• GEOS-Chem diagnostics in CESM by @lizziel in #1509
• Disallow wildcards in HISTORY.rc for CESM model by @jimmielin in #1513
• Close GEOS-Chem Classic restart files to disk immediately after writing -- Closes #1464 by @yantosca in #1515
• Replace HEMCO time slice selection from 'I' to 'C' in CESM by @lizziel in #1519
• Turn off GEOS-Chem seasalt emissions in CESM by @lizziel in #1520
• Update CH4 lake emission files to correct for wrong time units by @msulprizio in #1526
• Update sample fullchem restart files and specialty simulation oxidant fields to 14.0.0 10-year benchmark output by @msulprizio in #1530
• Restore CH4_RICE emissions in HEMCO_Config.rc.CH4 by @msulprizio in #1540

Full Changelog: 14.0.1...14.0.2