CHANGELOG.md

Changelog

This file documents all notable changes to the GEOS-Chem repository starting in version 14.0.0, including all GEOS-Chem Classic and GCHP run directory updates.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[14.2.1] - 2023-10-10

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

[Unreleased 14.2.0] - TBD

Added

• Added a printout of GEOS-Chem species and indices
• Added NcdfUtil/README.md file directing users to look for netCDF utility scripts at https://github.com/geoschem/netcdf-scripts
• Restored sink reactions for HOI, IONO, IONO2 (fullchem, custom mechanisms)
• S(IV) + HOBr and S(IV) + HOCl reactions to KPP/fullchem/fullchem.eqn
• Added setting in GCHP setCommonRunSettings.sh to require species in restarts
• Added setting in GCHP HISTORY.rc to control whether output can be overwritten
• Activated nitrate photolysis
• Added LightingClimatology option to HEMCO_Config.rc
• Added run configuration files for WRF-GC
• Added new files photolysis_mod.F90, phot_container_mod.F90, and fjx_interface_mod.F90
• Added photolysis toggle in geoschem_config.yml and Input_Opt variable Do_Photolysis
• Added speed of light and Planck's constant to PhysConstants module
• Added GFED4_CLIMATOLOGY option to HEMCO_Config.rc
• Added CH4 emissions from hydroelectric reservoirs to CH4, Carbon, and tagCH4 simulations
• Added RxnConst diagnostic for archiving reaction rate constants
• Added GCHP run-time option in GCHP.rc to choose dry or total pressure in GCHP advection
• Added GCHP run-time option in GCHP.rc to correct native mass fluxes for humidity
• Added new tracer_mod.F90 containing subroutines for applying sources and sinks for the TransportTracer simulation
• Added new species to the TransportTracer simulation: aoa (replaces CLOCK), aoa_bl, aoa_nh, st80_25
• Added GEOS-IT and GEOSIT as allowable meteorology source options in geoschem_config.yml

Changed

• Most printout has been converted to debug printout (toggled by debug_printout: true in geoschem_config.yml
• HEMCO_Config.rc template files now use Verbose: true to toggle debug printout
• Turn on sea salt debromination via switches in HEMCO_config.rc
• If KPP integration fails, reset to prior concentrations and set RSTATE(3) = 0 before retrying
• Suppress integration errors after 20 errors have been printed to stdout
• Simplified and added comments for bimolecular reactions in clouds in function CloudHet2R
• HEMCO_Config.rc and ExtData.rc templates now point HEMCO/GFED4/v2023-03
• Updated GCHP carbon simulation Global Cl and P(CO) inputs to use 14.0.0 files
• Write GCHP restart files directory to Restarts subdirectory
• Rename GCHP mid-run checkpoint files to standard GEOS-Chem restart format
• Rules for species in restarts files are now the same in GCHP as in GC-Classic
• Moved parts of CMN_FJX_Mod.F90 not used in original Fast-JX to new container State_Chm%Phot
• Restructured photolysis to create generic photolysis module, interface with Fast-JX, and module containing original Fast-JX analogous to Cloud-J
• Moved UVFlux diagnostics out of JValues collection and into new collection called UVFlux
• In the user registration process:
  • Now ask for both first and last names of the user
  • Now state that user registration is needed for GEOS-Chem support
• Updated HEMCO_Config.rc templates to read HEMCO restarts from the Restarts rundir folder
• In fullchem simulations, set CO2 to 421 ppm (avg global conc in 2022) everywhere
• Updated CH4 simulation to use CH4 loss frequencies from GCClassic 14.0.0 10-year benchmarks instead of GMI
• Updated CH4 global anthropogenic emission inventory from EDGARv6 to EDGARv7
• Updated AUTHORS.txt for version 14.2.0
• Updated links in README.md to point to http://geos-chem.org
• Changed GCHP default settings to use dry pressure rather than total pressure in advection and correct native mass fluxes for humidity
• Updated partitions requested in Harvard run script examples
• Change RTOL value from 0.5e-3 back to 0.5e-2 to address model slowdown
• Allow the use of OFFLINE_SEASALT for seasalt alkalinity, Cl, and Br in GEOS-Chem within CESM
• Renamed TransportTracer species for consistency with GMAO's TR_GridComp
• See KPP/fullchem/CHANGELOG_fullchem.md for fullchem-mechanism changes
• Update template HEMCO_Config.rc.carbon files to allow running the carbon simulation with only a single species.

Fixed

• Fixed typo in GCClassic/createRunDir.sh preventing benchmark run script from being copied to the run directory
• Fixed divide by zero bug in sulfur chemistry introduced in 14.1.0
• Updates for 0.5 x 0.625 degree GCClassic integration & parallel tests
  • Use CYS in HEMCO_Config.rc so that missing species in GC_BCs will not stop simulations
  • Tests now run for 20 model minutes instead of an hour
• Fixed divide by zero bug in sulfur chemistry introduced in 14.1.0
• Fixed GCHP HISTORY.rc issue preventing running with over 3000 cores
• Fixed GCHP ExtData.rc error in tagged ozone simulation
• Fixed GCHP HISTORY.rc issue preventing diagnostic file overwrite
• Update GCHP interactive run script to fix error handling silent bugs
• Rewrote subroutine calls in carbon_mod.F90 and seasalt_mod.F90 to prevent array temporaries.
• Prevent repeated printing of KPP integrate errors to the stdout stream.
• Fixed selection of troposphere-stratosphere boundary in global_ch4_mod.F90
• Removed operator splitting in CH4 simulation that was biasing diagnostics
• Fixed GCHP start and elapsed times in time_mod.F90 to use cap_restart value
• Disabled SpeciesConcMND output for benchmark simulations
• Exit Init_Photolysis before calling Calc_AOD when doing dry-run simulations
• Make sure State_Het%f_Alk_SSA and State_Het%f_Alk_SSC are in the range 0..1
• Restore seasalt alkalinity to heterogeneous acid-catalyzed reactions of halogens on seasalt aerosols

Removed

• Warnings: 1 is now removed from HEMCO_Config.rc.* template files
• Removed the NcdfUtil/perl folder
• Removed X-HRS output from log file
• IONO2 recycling (fullchem, custom mechanisms)
• Deleted unused file set_prof_o3.F90

Fixed

• Fixed entries for CH4 emissions in HEMCO_Config.rc.carbon

[14.1.1] - 2023-03-03

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.
• Fixed bug in GFAS pFe by applying work-around in config files

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

[14.1.0] - 2023-02-01

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
• Added GFAS entries in GCHP config file ExtData.rc

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
• Fixed bug in GFAS pFe by applying work-around in config files

Removed

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

[14.0.2] - 2022-11-29

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 of geoschem_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

Changed

• Use met-field surface type fractions instead of input land-water-ice (LWI) index

Removed

• Removed State_Met%LWI and LWI as a met-field input

[14.0.1] - 2022-10-31

Fixed

• Corrected units in metadata for State_Met%AirNumDen and State_Met%PHIS
• Fixed file path for AEIC2019_DAILY emissions for aerosol-only simulations
• Fixed GCHP bug to populate non-species data in mid-run restart files
• Fixed typo preventing ND51 satellite diagnostic from turning on

Changed

• Documented and cleaned up GCHP run script operational examples
• Updated README.md and AUTHORS.txt
• Set species concentration arrays as pointers to internal state in GCHP
• Updated Restart collection in HISTORY.rc to save out BXHEIGHT and TROPLEV for all simulations

[14.0.0] - 2022-10-25

Added

• Added user registration with dynamodb database during run directory creation
• Added Hg simulation with KPP
• Added yaml-format config file geoschem_config.yml which replaces input.geos
• Added native GEOS-FP and mass fluxes options to GCHP run directory creation
• Added cap_restart file to GCHP run directories to set simulation start time
• Added updates for compatibility with CESM, GEOS, and WRF-GC

Fixed

• Fixed missing output boundary conditions on first timestep of run
• Added missing entries for POG1, POG2, and pFe to HEMCO_Config.rc
• Reverted GC-Classic pressure fixer to v13.3 to fix bug in v13.4
• Fixed dry deposition of methanol over oceans
• Fixed issues in creating run directory for GCAP2
• Removed duplicate species for SO4 in aciduptake.eqn
• Fixed CEDS_CO2_SHP emissions in HEMCO_Config.rc file for CO2 simulation
• Fixed Volcano_Table entry in HEMCO config template for GCHP
• Fixed transport tracers simulation in GCHP
• Applied fix to avoid divide-by-zero in routine MMR_Compute_FLux
• Fixed HEMCO diagnostic counter zero warnings in full chemistry simulation
• Fixed bug in totalOC diagnostic
• Fixed bugs causing differences when splitting up GC-Classic and GCHP simulations in time
• Fixed bug setting GEOS-FP meteorology in GCHP run directories

Changed

• Updated KPP to version 2.5.0
• Updated GCHP run scripts to easily segment runs in time
• Changed GCHP restart filename convention to exclude seconds
• Updated offline biogenic VOC and soil NOx emissions
• Reduced root logging level for MAPL from INFO to WARNING
• Changed 4D State_Chm%Species array to vector of 3D concentration arrays
• Renamed GCHP config file runConfig.sh to setCommonRunSettings.sh
• Moved restart file location in run directory to Restarts subdirectory
• Updated sample restart files copied to run directories to 14.0.0 1-year benchmark output

Removed

• Removed TMPU1, SPHU1, PS1_WET, and PS1_DRY from GC-Classic restart file
• Removed input.geos; replaced with geoschem_config.yml
• Removed HEMCO.log output file; HEMCO log info now sent to main GEOS-Chem log