Skip to content

Latest commit

 

History

History
172 lines (148 loc) · 9.27 KB

CHANGELOG.md

File metadata and controls

172 lines (148 loc) · 9.27 KB

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.

[Unreleased 14.2.0]

[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.

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

Fixed

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