Merge 14.5.1 into the dev/14.6.0 branch

This merge brings updates from GEOS-Chem 14.5.1 into the
dev/14.6.0 branch.  This will be tagged as 14.5.0-alpha.1.

Signed-off-by: Bob Yantosca <[email protected]>

.gitmodules

@@ -1,4 +1,3 @@
 [submodule "KPP/standalone"]
 	path = KPP/standalone
 	url = https://github.com/geoschem/KPP-Standalone
-	branch = geoschem-dev

CHANGELOG.md

@@ -4,16 +4,65 @@ This file documents all notable changes to the GEOS-Chem repository starting in
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased] - TBD
+## [14.5.1] - 2025-01-10
 ### Added
+- Added Australian Hg emissions for 2000-2019 from MacFarlane et. al. [2022], plus corresponding mask file
+- Added comments in GEOS-Chem Classic `HISTORY.rc` template files advising users not to change the `BoundaryConditions.frequency` setting
+
+### Fixed
+- Reverted CH4 livestock emissions to EDGAR v7 to avoid hotspots and to apply seasonality
+
+## [14.5.1] - 2025-01-10
+### Added
+- Added allocate guards for arrays in `pressure_mod`
+- Added `State_Diag%SatDiagnEdgeCount` counter for the `SatDiagnEdge` collection
+- Added `State_Diag%Archive_SatDiagnEdgeCount` field
+- Added `State_Diag%Archive_SatDiagnEdge` field
+- Added routine `SatDiagn_or_SatDiagnEdge` in `History/history_utils_mod.F90`
+- Added error trap in `History/history_mod.F90` to ensure that collection duration is always shorter than frequency
 - Added KPP standalone interface (archives model state to selected locations)
-- Added `https://github/geoschem/KPP-Standalone` as a Git submodule (`geoschem-dev` branch)
+- Added `https://github/geoschem/KPP-Standalone` as a Git submodule
+- Added comments in `./run/sharedcleanRunDir.sh` describing the `--force` option (i.e. remove files w/o user confirmation)
+- Specified meteorology source in GCHP geoschem_config.yml
+- Added Input_Opt logical for whether to reconstruct convective precipitation fluxes rather than use met-fields
+- Added to run directory creation a warning about convection discontinuity and bug if GEOS-FP meteorology is chosen
+- Added surface precipitation flux fields as inputs to GCHP
 
 ### Changed
-- Moved PINO3H to be in alphabetical order in `species_database.yml`
+- Renamed `Emiss_Carbon_Gases` to `CO2_Production` in `carbon_gases_mod.F90`
+- Updated start date and restart file for CO2 and tagCO simulations for consistency with carbon simulations
+- Allocated `State_Diag%SatDiagnPEDGE` ffield with vertical dimension `State_Grid%NZ+1`
+- Modified `run/GCClassic/cleanRunDir.sh` to skip removing bpch files, as well as now removing `fort.*` and `OutputDir/*.txt` files
+- Edited `run/shared/kpp_standalone_interface.yml` to include additional entries under `active cells` and `locations`
+- Changed doing Linoz and Linearized chemistry messages to print only if verbose
+- Updated HEMCO subroutine calls for error and log handling changes in HEMCO 3.9.1
+- Updated configuration files for using GEOS-Chem 14.5 in CESM
+- Modified tagCO simulation to use GFED4 biomass burning emissions and GEOS-Chem v5 OH fields for consistency with carbon simulation
+- Changed integration tests to use Harvard Cannon GNU 12 environment files by default
 
 ### Fixed
-- Fixed CEDS HEMCO_Config.rc entries to emit TMB into the TMB species (and not HCOOH)
+- Added a fix to skip the call to KPP when only CO2 is defined in the carbon simulation
+- Added fix to turn on ship emissions for CO2 in the carbon simulation
+- Updated `HEMCO_Config.rc` for carbon simulation to read data based on carbon species used
+- Fixed entries for CO2 emissions in `ExtData.rc.carbon`
+- Fixed metals simulation name in config file template comments
+- Fixed bug in `download_data.py` which caused script to fail if log filename contained uppercase characters.
+- Fixed the satellite diagnostics counters from being inadvertently being reset
+- Fixed segmentation fault in qfyaml when running with certain compilers without debug flags on
+- Fixed errors in adjoint-only code preventing successful adjoint build
+- Fixed zero convective precipitation and high cloud base in runs using GEOS-FP (>=01Jun2020) or GEOS-IT
+- Updated GEOS-only code and configuration files for compatibility with GEOS-Chem 14.5
+- Fixed missing Is_Advected for TMB in species_database.yml
+- Fixed typos in `HEMCO_Config.rc` for CH4 simulations causing mobile combustion emissions to be double counted
+- Fixed handling of FIRST flag in carbon_gases_mod.F to limit log prints to first timestep only
+- Removed extraneous pressure correction in GCHP carbon simulations by adding 'activate: true' to geoschem_config.yml
+- Fixed bug in GC-Classic OCS emissions where unit conversion of km2 to m2 occurred twice
+- Changed dimension of EmisOCS_Total from 3D to 2D since all emissions for all sectors are 2D
+- Added fixes to only apply archived PCO_CH4 field for carbon simulations with CO only
+
+### Removed
+- Removed duplicate `WD_RetFactor` tag for HgClHO2 in `species_database.yml`
+- Removed error messages in HEMCO interface pointing users to HEMCO log
 
 ## [14.5.0] - 2024-11-07
 ### Added
@@ -42,6 +91,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - 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`
+- Excluded HEMCO interface and ExtState fields from `MODEL_CESM` in `hco_interface_gc_mod.F90` for compatibility with CESM, which runs HEMCO separately
 
 ### Fixed
 - Simplified SOA representations and fixed related AOD and TotalOA/OC calculations in benchmark