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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.

[14.5.0] - 2024-11-07

Added

  • Added vectors State_Chm%KPP_AbsTol and State_Chm%KPP_RelTol
  • Added setting KPP_AbsTol to 1e5 for dummy species in species_database.yml and species_database_hg.yml
  • Implemented PPN photolysis from Horner et al (2024)
  • Added four new species ALK4N1, ALK4N2, ALK4O2, and ALK4P to address issues in ALK4 and R4N2 chemistry following Brewer et al. (2023, JGR)
  • Added new species ALK4N1 and ALK4N2 to Ox family in KPP
  • Added Cloud-J input parameters to geoschem_config.yml in new photolysis sub-menu called cloud-j
  • Added computation of water concentration to use in photolysis for application of UV absorption by water in Cloud-J v8
  • Added ACO3, ACR, ACRO2, ALK4N{1,2,O}2, ALK4P, ALK6, APAN, APINN, APINO2, APINP, AROCMCHO, AROMCO3, AROMPN, BPINN, BPINO2, BPINON, BPINOO2, BPINOOH, BPINP, BUTN, BUTO2, C4H6, C96N, C96O2, C9602H, EBZ, GCO3, HACTA, LIMAL, LIMKB, LIMKET, LIMKO2, LIMN, LIMNB, LIMO2H, LIMO3, LIMO3H, LIMPAN, MEKCO3, MEKPN, MYRCO, PHAN, PIN, PINAL, PINO3, PINONIC, PINPAN, R7N{1,2}, R7O2, R7P, RNO3, STYR, TLFUO2, TLFUONE, TMB, ZRO2 to species_database.yml following Travis et al. 2024
  • Added TSOIL1 field to State_Met for use in HEMCO soil NOx extension. This should only be read in when the UseSoilTemperature option is true in HEMCO config

Changed

  • Copied values from State_Chm%KPP_AbsTol to ATOL and State_Chm%KPP_RelTol to RTOL for fullchem and Hg simulations
  • Introduced seasalt Ca, K, Mg back to aerosol thermodynamics via HETP.
  • Updated HEMCO_Config.rc.fullchem (GCClassic + GCHP) and ExtData.rc to add emissons of new species from Travis et al 2023
  • Activated the DryDep collection for GCClassic & GCHP fullchem benchmarks
  • Reduced the GCHP DryDep collection to only the necessary species for benchmarks
  • Removed unused VDIFFAR routine from vdiff_mod.F90
  • Updated MW for CH4 and OH in global_ch4_mod.F90
  • Added fix to not convert from kg/kg to mol/mol before passing State_Chm to PBL mixing in vdiff_mod.F90
  • Updated GC-Classic and GCHP run scripts and environment files for NASA discover cluster
  • Updated GFED4_Climatology entries to point to the climatology file for 2010-2023
  • Moved aerosol optical properties files to a new data directory specified in geoschem_config.yml rather than specifying in photolysis input files
  • Moved calls to RD_AOD and CALC_AOD from Init_Aerosol rather than Init_Photolysis
  • Updated ResME CH4 reservoir emissions to apply seasonality via mask file
  • Changed fullchem restart file folder from GC_14.3.0 to GC_14.5.0

Fixed

  • Simplified SOA representations and fixed related AOD and TotalOA/OC calculations in benchmark
  • Changed mass conservation adjustment in vdiff_mod.F90 to use a mass tendency with units of kg species/kg dry air
  • Converted the top pressure edge from hPa to Pa in vdiff_mod.F90
  • Updated Jval_ entries in run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem
  • Updated species database Is_Photolysis entries to remove J-value diagnostics with all zeros in full chemistry simulation
  • Removed EDGAR8_CH4_AWB emissions from CH4 and carbon simulations to avoid double counting with GFED
  • Fixed formatting error in .github/workflows/stale.yml that caused the Mark Stale Issues action not to run
  • Fixed emissions in GCHP carbon ExtData.rc so that data in molecules/cm2/s are converted to kg/m2/s

Removed

  • Removed dry-run checks for files that are no longer needed for Cloud-J v8 from cldj_interface_mod.F90

[14.4.3] - 2024-08-13

Added

  • Added tropopause pressure field in the satellite diagnostic (by @eamarais)
  • Added ModelEe.2 (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

[14.4.2] - 2024-07-24

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
  • Added transport tracer run directory option for global half-degree GC-Classic run with GEOS-IT 0.5x0.625 fields

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
  • Replace calls to GEOS_CHEM_STOP with calls to GC_Error in planeflight_mod.F90
  • Script test/integration/GCHP/integrationTestExecute.sh now resets cap_restart time to 000000, to facilitate manual restart

Fixed

  • In Headers/roundoff_mod.F90, first cast and then only round off if places > 0
  • 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
  • Restored missing fields for UVFlux collection in run/GCClassic/HISTORY.rc.templates/HISTORY.rc.fullchem
  • Comment out UVFlux diagnostic in the "alldiags" integration test, there is a floating point error. Look at this later.
  • Now use SO4 instead of O3 in the GCHP fullchem budget diagnostic (SO4 is soluble, O3 is not)
  • Convert UVFlux_Tag_Names to uppercase in the comparison in Get_UVFlux_Bin(located inHeaders/state_diag_mod.F90)
  • Fixed typo (missing _ character) in GCHP DryDep collection diagnostic entries
  • Commented out with ### emissions diagnostics in the GCHP HISTORY.rc.fullchem template that are not present in the corresponding HEMCO_DIAGN.rc template

Removed

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

[14.4.1] - 2024-06-28

Added

  • Added initialization of PHOTDELTA in ucx_h2so4phot to avoid run-time error in CESM
  • Added Cloud-J status output and error handling for it

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

Fixed

  • In Headers/roundoff_mod.F90, first cast and then only round off if places > 0

[14.4.0] - 2024-05-30

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.
  • 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

[14.3.1] - 2024-04-02

Added

  • 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

[14.3.0] - 2024-02-07

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
  • Added fix for runaway HMS chemistry. See KPP/fullchem/CHANGELOG_fullchem.md for details.

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
  • Removed State_Chm%Spc_Units; this is now superseded by State_Chm%Species(:)%Units

[14.2.3] - 2023-12-01

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
  • Moved aerosol_mod module variables to new State_Chm container called AerMass

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
  • Removed State_Chm%Spc_Units

[14.2.2] - 2023-10-23

Changed

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

[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

[14.2.0] - 2023-10-05

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

[14.1.2] - 2023-10-20

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

[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