From CHANGELOG.md
Added
- Added entries for FINNv25 biomass burning emissions to template HEMCO configuration files
- Added comments to
HEMCO_Diagn.rctemplate files instructing users on which ExtNr/Cat/Hier to use for online vs. offline biomass burning emissions - Added subroutine
Print_Species_Global_Massto print_mod for use by GC-Classic - Added log print of species global mass at start of each timestep if verbose is true
- Added print of global mass computed from restart file values if delta pressure present in restart file
- Added the capability for GCHP simulations to use CH4 restarts for Jacobian Tracers
- Added operational run scripts for WashU Compute2
- Added the option for LPJ_MERRA2 wetland CH4 emissions in CH4 and carbon simulations
- Added GC-Classic config file option to read restart file as
REAL*8via GEOS-Chem rather than HEMCO - Added new GCHP run-time option in GCHP.rc to print species mass proxy (Species 1 only) to log file from FV3
- Added GEOS-Chem export in GCHP to send restart file (internal state) delta pressures to FV3 for mixing ratio scaling upon start-up
- Added chemistry budget diagnostics to GCHP carbon HISTORY.rc
- Added IUPAC names for Hg species in
run/shared/species_database.yml - Added
gc_4x5_merra2_carbon_ch4_straddle_00utcintegraton test which runs across a UTC date boundary - Added statement to zero the
State_Diag%DryDepChmarray in routineZero_Diagnostics_StartOfTimestep - Added clarifying comments in
flexgrid_read_met_mod.F90forTSandT2Mmet fields - Added
&DSTbinpropertiesand&METALSpropertiesYAML anchors inrun/shared/species_database.yml - Added
DustL23Mas HEMCO extension 125 inHEMCO_Config.rc.aerosolandHEMCO_Config.rc.fullchemtemplates
Changed
- Replaced comments in template HEMCO configuration files directing users to obsolete wiki documentation with comments directing users to
hemco.readthedocs.io - Updated
EmisOCS_BioburntoEmisOCS_BiomassBurnin both GCHPHEMCO_Diagn.rc.carbonandHISTORY.rc.carbontemplate files - Updated the ESMF version from 8.4.2 to 8.6.1 in sample environment file
gchp.gcc12_openmpi4_cannon_rocky.env - Changed call to
Accept_External_Date_Timeto also pass the seconds value, in order to prevent a WRF-GC bug - Removed convective washout for default scheme but keep it for LUO_WETDEP
- Adapted Luo2023 WetDep for GF convection
- Updated timestep scaling for convective precipitation areal fraction
- Wrapped tests for infinity/NaN in
#ifdef DEBUGblocks inDO_GF_CLOUD_CONVECTION - Changed optional argument
Update_Mixing_Ratioin subroutineAirqntto False by default - Change GC-Classic call to
Airqntto only update mixing ratios if advection is turned off - Updated mass flux and courant number import scaling in GCHP for compatibility with horizontal flux regridding in MAPL 2.59
- Updated operational run script sample for WashU Compute1
- Update GCHP AWS EFA operational run script examples to avoid crashes over large core counts
- Updated GFEIv3 files to correct issue in original version
- Updated
download_data.pyfor compatibility with 0.125 x 0.15625 grids plus all pre-defined nested-grids - Restructured
download_data.pyto avoid several instances of repeated code - Changed
read_restart_as_real8fromfalsetotrueingeoschem_config.ymlfor GC-Classic benchmark simulations - Changed the default setting of
read_restart_as_real8fromfalsetotruein template filegeoschem_config.yml.TransportTracers - Disable PARANOX extension when using GEOS-Chem Classic 0.25x0.3125 or 0.125x0.15625 grids
- Commented out met-fields
PEDGEDRY,PFICU,PFILSAN,PFLCU, andPFLLSANby default in GC-Classic and GCHP carbon HISTORY.rc, and GC-Classic CH4 HISTORY.rc - Turned on Carbon collection in
HISTORY.rcfor carbon simulations by default - Consolidated Hg species metdata from
run/shared/species_database_hg.ymlintorun/shared/species_database.yml - Updated
run/shared/download_data.ymlso that aerosol and fullchem simulations will get the restart file fromGEOSCHEM_RESTARTS/GC_14.7.0 - Updated
DST1/DST1/DST3/DST4toTDST/DSTbin1/DSTbin2/.../DSTbin7ingeoschem_config.yml,HEMCO_Config.rc, andHEMCO_Diagn.rctemplate files for aerosol & fullchem simulations - Updated routine
ExtState_SetFieldsinhco_interface_gc_mod.F90for readability and clarity - Assigned
ExtState%TSKINfromState_Met%TSandExtState%T2MfromState_Met%T2Min routineExtState_SetFields - Updated dust mass tuning factors for the
DustL23Mextension inrun/GCClassic/createRunDir.shandrun/GCHP/setCommonRunSettings.sh.template - Replaced
id_DST{1..4}withid_DSTbin{1..7}in theAPMidtypederived type andAPMIDSobject - Replace hardwired values with constant parameters in routine
Aerosol_Conc(inGeosCore/aerosol_mod.F90 - Updated species database so that dust species use the anchor
&DSTbin propertiesand metals species use&METALSproperties - Updated call to
ExtData_Setinhco_gc_interface_mod.F90to acceptExtState%SNOMAS - Upated sample carbon simulation restart file to output generated from 10-year simulation
Fixed
- Restored entries for TMB emissions in
HEMCO_Config.rc.fullchemtemplate files for GCClassic and GCHP - Moved
EmisOCS_Totalto the head of theEmisOCSdiagnostic entries in the GCHPHISTORY.rc.carbontemplate file - Fixed OM/OC ratio for OCPO in SimpleSOA to be 1.4 instead of 2.1
- Fixed precipitation formation rate unit in Luo2023 convective washout
- Fixed bug where species mass in restart file was not conserved in first timestep if run-time meteorology different from restart file meteorology
- Fixed parallel errors in
convection_mod.F90by settingAER = . TRUE.andKIN = .TRUE.before callingWASHOUT - Fixed Hg directional ocean flux diagnostics in the Hg simulation so that they equal net flux
- Fixed error where
//were not being changed to/indownload_data.py - Change precision of area import from GCHP advection from
REAL*4to nativeREAL*8 - Fixed time-range and units for CH4 emission inventories to be consistent with the corresponding netCDF files in ExtData directory for
HEMCO_Config.rcandExtData.rc - Updated scaling factor ID at 3000 to avoid conflicts with CEDS_01x01 scaling factor enabled in carbon simulation for IMI analytical inversion
- Fixed typos in
ind_variable names inKPP/carbon/carbon_Funcs.F90 - Fixed typo in GCHP operational run script for Harvard Cannon to properly retrieve the run duration string
- Fixed bug in ObsPack to include instantaneously-sampled data whose timestamps are within 1/2 of a model timestep of the end of the day
- Fixed out-of-bounds error in
carbon_gases_mod.F90that is caused by refernencingOHdiurnalFacarray when it is not defined - Updated routines
Init_State_Chm,Init_Mapping_Vectors, andMapProdLossSpeciesto acceptTaggedDiag_Listas an argument - Updated routine
MapProdLossSpeciesto test if prod/loss family species or wildcards are scheduled for diagnostic archival before populating mapping arrays - Fixed indexing error in routine
Grav_Settling(in moduleGeosCore/sulfate_mod.F90), which caused incorrect dry deposition diagnostics for some species - Fixed incorrect met vertical flipping in GCHP for cases where advection and non-advection met are from different sources, e.g. raw versus processed
- Fixed several inconsistencies in
species_database.yml - Fixed typo in GEOS-FP settings file used in GCClassic run directory creation
Removed
- Removed entries for FINN v1.5 biomass burning emissions from template HEMCO configuration files
- Removed
Is_Advectedtags fromrun/shared/species_database*.ymltemplate files - Removed GCHP initialization of
State_MetfieldsTropLev,BxHeight, andDELP_DRYfrom restart file values since over-written with values of current meteorology - Removed
OH_PosteriorSFentry in carbon and CH4 HEMCO_Config.rc since never used - Retired the CO2, CH4, and tagCO simulations. These are now replaced by the carbon simulation, which can be used in joint or single-species mode.
- Deleted
co2_mod.F90,global_ch4_mod.F90, andtagged_co_mod.F90 - Removed commented-out code for tagged Hg species in
state_diag_mod.F90 - Removed extraneous division by
TS_EMISin routineChem_H2O2(located inGeosCore/sulfate_mod.F90) - Removed
run/shared/species_database_hg.yml - Removed obsolete metadata for tagged Hg species from
run/shared/species_database.yml - Removed code to zero
State_DiagDryDepMixinCompute_SFlx_For_Vdiff; these are zeroed previously inZero_Diagnostics_StartOfTimestep - Removed entries for
DustGinouxandDustDeadextensions fromHEMCO_Config.rc.aerosolandHEMCO_Config.rc.fullchemtemplates - Removed
&DST{1,2,3,4}propertiesinrun/shared/species_database.yml - Removed references to
DustDeadandDustGinouxHEMCO extensios in template configuration files
Pull requests included
- Add FINN v2.5 biomass burning as an optional inventory by @yantosca in #2900
- Update ESMF to 8.6.1 in the sample GCHP environment file for Harvard Cannon by @yantosca in #2916
- Improving fine mineral dust simulation in GEOS-Chem 14.4.1 by @1Dandan in #2753
- Merge updates from 14.6.3 into the dev/14.7.0 branch by @yantosca in #2978
- Fix ocean flux diagnostics in Hg simulation by @agriff86 in #2974
- Fix GCHP restart for Jacobian tracers by @1Dandan in #2984
- Update operational run script sample for WashU compute1 by @yuanjianz in #2988
- Add operational run scripts for WashU Compute2 by @yuanjianz in #2989
- Update GCHP AWS EFA operational run script examples to avoid crashes by @yuanjianz in #2990
- Update for MAPL 2.59 compatibility by @lizziel in #2885
- Update GFEIv3 files to correct for issue found during peer review by @msulprizio in #2996
- Pass in second when calling Accept_External_Date_Time by @jimmielin in #2997
- Fixed OM/OC ratio for OCPO in SimpleSOA by @yuanjianz in #3000
- Update convective washout for Grell-Freitas and Luo wetdeposition by @yuanjianz in #3001
- Conserve initial restart file mass in GC-Classic runs by @lizziel in #3014
- Update mass flux and Courant number scalings for changes to MAPL by @lizziel in #3016
- Fixed parallelization error in PR #3014 by @yantosca in #3019
- Add LPJ_MERRA2 wetland CH4 emissions as an option in CH4 and carbon simulations by @msulprizio in #3010
- Fix parallel error in convection_mod.F90 by @yantosca in #3029
- Merge updates from dev/no-diff-to-benchmark into dev/14.7.0 in advance of 14.7.0 release by @yantosca in #3021
- Remove Is_Advected tags from species database template files by @yantosca in #3027
- Unhide feature to bypass HEMCO to read GC-Classic restart file by @lizziel in #3020
- Fixed several issues in download_data.py script by @yantosca in #3055
- Fix precision of GCHP import of area from advection by @lizziel in #3050
- Updates for GCHP conservation of restart file species mass by @lizziel in #3062
- Toggle "read_restart_as_real8" from false to true for fullchem benchmark simulations by @yantosca in #3066
- Turn off PARANOx for GEOS-Chem Classic 0.25 x 0.3125 and 0.125 x 0.15625 grids by @yantosca in #3011
- Fix for emission configurations for carbon simulations by @1Dandan in #2893
- Fix typos causing carbon simulations with the Carbon collection enabled to crash by @msulprizio in #3074
- Fix typo in GCHP operational run script for Harvard Cannon to properly retrieve the run duration string by @msulprizio in #3073
- Bug fix: Include instantaneous ObsPack data lying within 1/2 model timestep of the end of the model date in the sampling by @yantosca in #3087
- Fix LPJ wetland path in GCHP carbon ExtData.rc to use HEMCO directory by @lizziel in #3086
- Do not reference OHdiurnalFac in carbon_gases_mod.F90 for carbon simulations where OH is not used by @yantosca in #3095
- Retire CO2, CH4, and tagged CO simulations by @msulprizio in #2685
- Make sure prod/loss species or wildcards are requested for diagnostic output before updating mapping vectors in State_Chm by @yantosca in #3115
- Do not divide PH2O2m by TS_EMIS in routine CHEM_H2O2 (aerosol-only bugfix) by @yantosca in #3104
- Consolidate all Hg species metadata into run/shared/species_database.yml by @yantosca in #3113
- Add GC-Classic integration test straddling the 00 UTC date boundary by @yantosca in #3121
- Fix out-of-bounds errors in State_Diag%DryDepChm diagnostics by @yantosca in #3118
- Fix vertical flipping of C720 met fields when using with GEOS-FP processed lat-lon data by @lizziel in #3131
- Merge PR #2753 (7 dust bins in GEOS-Chem) up to 14.7.0 and add necessary fixes/updates by @yantosca in #2946
- Fix typo in GEOS-FP settings file used in GCClassic run directory creation by @msulprizio in #3187
- Update sample restart file for the carbon simulation by @msulprizio in #3147
- GEOS-Chem (science codebase) 14.7.0 release by @yantosca in #3193
New Contributors
Full Changelog: 14.6.3...14.7.0
See the GEOS-Chem 14.7.0 page for a complete list of updates.”