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Changelog

All notable changes to this project will be documented in this file.

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

[3.9.3] - 2024-08-13

Fixed

  • Added brackets around exempt-issue-labels list in .github/workflows/stale.yml

[3.9.2] - 2024-07-24

Changed

  • RTD updates: Converted several :option: tags to subsections and updated references accordingly

Fixed

  • Typos in RTD doc file docs/source/hco_ref_guide/hemco-config.rst

Removed

  • Manual InvMEGAN diagnostics from src/Extensions/hcox_megan_mod.F90; Activate these with HEMCO_Diagn.rc instead

[3.9.1] - 2024-06-28

Fixed

  • Fixed formatting error in .github/workflows/stale.yml that caused the Mark Stale Issues action not to run

[3.9.0] - 2024-05-30

Added

  • GitHub Action config file .github/workflows/stale.yml, which replaces StaleBot

Removed

  • GitHub config files .github/stale.yml and .github/no-response.yml

Changed

  • Converted Github issue templates into issue forms using YAML definition files
  • Updated Python package versions for ReadTheDocs in docs/requirements.txt
  • Now request Python 3.12 for ReadTheDocs builds in .readthedocs.yaml

[3.8.1] - 2024-04-02

Changed

  • Now allow up to 10 nested brackets (((( )))) in the HEMCO_Config.rc file
  • Now use short submodule names (i.e. w/o path) in .gitmodules

Fixed

  • Limit volcano climatology file read message to root core
  • Updated hco_interp_mod.F90 to handle 3D NEI emissions.

[3.8.0] - 2024-02-07

Changed

  • Updated TOMAS_Jeagle sea salt extension

Fixed

  • Updated IsModelLevel check for CESM and WRF-GC
  • Interpolation error for 8-day MODIS LAI files (removed month loop in GetIndex2Interp)

[3.7.2] - 2023-12-01

Added

  • Script .release/changeVersionNumbers.sh to change version numbers before a new HEMCO release

Changed

  • Increased netCDF variable string length from 50 to 100

Fixed

  • Rename HEMCO_Config.rc.sample to HEMCO_Config.rc in createRunDir.sh if sample is used.
  • Added fix to turn off emissions extensions when EMISSIONS logical is false

[3.7.1] - 2023-10-10

Changed

  • Updated version numbers to 3.7.1
  • Make Hg0 emission factors in hcox_gfed_include_gfed4.H multipliers of the CO emission factor
  • Removed superfluous routine GetExtSpcVal_Dr in src/Core/hco_extlist_mod.F90
  • NetCDF routines in src/Shared/NcdfUtil now use the Fortran-90 API
  • Overhauled vertical regridding src/Core/hco_interp_mod.F90
    • Removed INFLATE (but retained its behavior only for 47L -> 72L vertical regridding, warning users that this isn't recommended)
    • ModelLev_Interpolate is only called when the input is 47/48, 72/73, or 102/103 levels (otherwise, MESSy is used).
    • A bug that averaged the wrong number of levels in COLLAPSE is fixed (and edges are now sampled instead of averaged).
    • Removed the now superfluous NC_ISMODELLEVEL and NC_SISIGMALEVEL from src/Shared/NcdfUtil/hco_ncdf_mod.F90
    • Removed old code and references to GEOS-4.

Fixed

  • Fixed incorrect XMIN, XMAX values in HEMCO_sa_Grid.025x03125.rc and HEMCO_sa_Grid.05x0625.rc
  • Fixed line length too long for the GC_72_EDGE_SIGMA variable in src/Core/hcoio_read_std_mod.F90

[3.7.0] - 2023-10-05

Added

  • HEMCO extensions now display a first-time message, whether Verbose is true or false.
  • Added 'src/Shared/NcdfUtil/README.md` file directing users to look for netCDF utility scripts at https://github.com/geoschem/netcdf-scripts
  • Added GFED4 biomass burning emissions for furans, PHEN, MVK, ISOP, ACTA, MGLY, MYLX, RCHO
  • Add GEOSIT as an allowable meteorology directory name in HEMCO_Config.rc
  • Added .readthedocs.yaml file to configure ReadTheDocs builds

Changed

  • Verbose is now a true/false variable in run/HEMCO_sa_Config.rc and run/HEMCO_Config.rc.sample
  • HEMCO warnings are now only generated when Verbose: true is found in the HEMCO configuration file (no more numerical levels)
  • Updated GFED4 emission factors for VOCs to Andreae et al. (2019)
  • Refactored hco_calc_mod.F90 to avoid computational bottlenecks (PR #201)
  • Restart files are now written to the rundir Restarts/ subdirectory
  • Created a Restarts/ subdirectory in HEMCO standalone run directories
  • Added changes needed to build with NAG compiler
  • Renamed Be7Strat and Be10Strat to Be7s and Be10s for consistency with GMAO's TR_GridComp
  • Updated ReadTheDocs documentation about time cycle options RFY, RFY3
  • Updated ReadTheDocs documentation about the HEMCO_Diagn.rc file
  • Updated AUTHORS.txt for GEOS-Chem 14.2.0 and HEMCO 3.7.0
  • Updated formatting in README.md
  • Updated title and links to badges in README.md
  • Updated version number to 3.7.0

Fixed

  • Do not read masks if the filename is - (non-ESMF environments only)
  • Always assume partial coverage when reading masks in an ESMF environment (#163)
  • Increased the string length for reading lines from HEMCO grid file to fix error in global 0.25x0.3125 standalone simulations

Removed

  • Warnings is now removed from run/HEMCO_sa_Config.rc and run/HEMCO_Config.rc.sample
  • Removed the src/Shared/NcdfUtil/perl folder

[3.6.3] - 2023-09-15

Fixed

  • Fixed nvhpc compiler error in CESM by reducing line length of GC_72_EDGE_SIGMA assignment

[3.6.2] - 2023-03-02

Added

  • Added .github/config.yml with settings for the issue chooser page

Changed

  • Replace description: with about: in GitHub issue templates
  • The PR template is now .github/PULL_REQUEST_TEMPLATE.md

Fixed

  • Now point to proper commit of the geos-chem-shaed-docs submodule

[3.6.1] - 2023-03-01

Added

  • GEOS-only updates
  • Removed several memory leaks in HEMCO Core and Standalone routines

Changed

  • Simplified Github issue and pull request templates
  • Throw an error if input calendar is not supported

[3.6.0] - 2023-02-01

Added

  • Added MAPL_ESMF compiler option for use with GCHP and GEOS
  • New "Parallelize GEOS-Chem and HEMCO source code" guide on ReadTheDocs
  • Updated documentation describing a masking error that can happen when performing simulations with cropped horizontal grids

Changed

  • Set HCO_MISSVAL to MAPL missing value (1e15) if using GCHP or GEOS
  • Use fraction surface type inputs instead of ExtState%WLI
  • The version number in docs/source/conf.py is now 3.6.0
  • Updated compilation output splash screen in compiling.rst ReadTheDocs file

Fixed

  • Bug fix for inserting hard breaks in hemco-config.rst ReadTheDocs file

Removed

  • Removed old kludge for MAPL missing data if applying mask
  • Removed ExtState field for water-land-ice index (WLI)

[3.5.2] - 2022-11-29

Added

  • Added sanitizer option for detecting memory leaks in HEMCO standalone during build

Changed

  • Remove unused, commented-out code in src/Extensions/hcox_dustdead_mod.F
  • Replaced placeholder error messages in src/Core/hco_config_mod.F90 with more informational messages (often including the line of the HEMCO_Config.rc in the printout)
  • Added improved documentation for time cycle flag EFYO in ReadTheDocs

Fixed

  • Removed memory leaks that were identified by the code sanitizer

[3.5.1] - 2022-11-03

Fixed

  • Changed Inst%NP to Inst%NumP in HCOX_Seasalt_Mod for CESM compatibility

[3.5.0] - 2022-09-19

Added

  • Support for MAPL 2.16 (needed by GCHP and GEOS)
  • Bug fix for HEMCO standalone run directory creation
  • Bug fix: If HEMCO masks are specified as lon1/lat1/lon2/lat2, then don't try to read from disk
  • Documentation from the GEOS-Chem wiki (now on ReadTheDocs)
  • Badges for the ReadTheDocs front page
  • Bug fix for masking issues in MPI environment (for WRF, CESM)
  • Mapping of CAM-Chem species to GFED4 (for CESM)
  • New documentation for hemco.readthedocs.io, migrated from GC wiki
  • Updated documentation on vertical regridding behavior

Changed

  • Ignore non-printing characters (e.g. tabs) when reading HEMCO_Config.rc. This had caused a bug in GCHP.
  • Updated module names for MAPL 2.16 upgrade
  • "Diagnostic counter zero" warning is now printed at warning level 2 (instead of 1)
  • OFFLINE_BIOGENICVOC emissions in MEGAN now include species MOH

[3.4.0] - 2022-05-02

Added

  • Make sure each routine exits HEMCO with an error message (even if a placeholder message is used)
  • Fixed syntax error in hcox_tomas_dustdead_mod.F
  • GCHP bug fix: revert to all zeros in criteria for restart field not filled
  • Several fixes for OpenMP parallelization and numerical stability
  • Bug fix: Prevent out-of-bounds error in HEMCO vertical interpolation

Changed

  • Prevent undefined variable when calculating vertical scale factor
  • Set MEGAN biogenic annual emission factors to zero in before computing them
  • Updated ReadTheDocs documentation

Removed

  • Retired CH4 wetlands emissions extension

[3.3.0] - 2022-05-02

Changed

  • Updated Extensionss/hcox_gc_RnPbBe_mod.F90 to use Zhang et al 2021 emissions (now the default)` (cf doi:0.5194/acp-21-1861-2021)

[3.2.2] - 2021-12-01

Changed

  • Restore updating of manual HEMCO diagnostics, which had been clobbered due to a prior Git merge

[3.2.1] - 2021-11-15

Added

  • Add patch branches to continuous integration tests
  • Fix indexing of species in 'hcox_seasalt_mod.F90` when using marinePOA option

[3.2.0] - 2021-11-15

Added

  • GCHP adjoint updates
  • Add climatology input to volcano extension
  • Include PET number in error message if using ESMF
  • Send all HCO_ERROR messages to stderr and write from all threads

Changed

  • Modify volcano extension so that dry-run option also looks for climatology file
  • Modified HEMCO diagnostics and standalone config files for consistency with GEOS-Chem updates

[3.1.1] - 2021-09-10

Added

  • Fix to HEMCO lightning flash rate diagnostic units
  • Fix HEMCO's createRunDir.sh script to replace additional added tokens

[3.1.0] - 2021-09-07

Added

  • Blowing snow emissions of sea salt and sea salt bromide added to sea salt extension
  • Add HEMCO_INTERFACE cache variable to CMake build

[3.0.0] - 2021-01-08

Added

  • Updates to speed up HEMCO
  • Updates to calculate emissions sensitivities, apply emissions scaling factors, and output adjoint diagnostics
  • Support for GCAP 2.0
  • Several driver programs have been added to the src/Interfaces/ subdirectory for using HEMCO in other models
  • Unify HCOIO interfaces for standard and MAPL configurations
  • Updates for using HEMCO in CESM2-GC and WRF-GC
  • Fixed bug where met fields were only being read in once at the start of a simulation
  • Added stale bot and no-response bot to HEMCO GitHub repo
  • A script for creating HEMCO standalone rundirs is now included in the run/ folder
  • CEDS GDB-MAPS is now the default anthropogenic emissions inventory

Changed

  • HEMCO source code has been split off from the GEOS-Chem repository into https://github.com/geoschem/HEMCO repository
  • Source code has been reorganized
  • Set and update ExtState before computing emissions in HEMCO standalone
  • Use HcoState%NZ instead of NLEV in hco_interp_mod.F90
  • Make sure data containers with EFY time cycle flag are only updated once
  • CMake is now the default build system
  • Update isCoards script to account for files saved out by GCHP's History component

Removed

  • Support for GNU make
  • Carbon-based units for VOC species
  • Hard-coded scale factors in the DustDead extension
  • Duplicate Inst%FLUXSABI allocation in MEGAN HCO extension

[2.2.0] - 2020-02-03

Added

  • Implemented dry-run option
  • Now properly interpolate data with irregular timesteps
  • New logical switches for all inventories and datasets
  • New main switches for emissions, meteorology, and chemistry input
  • Fixed HEMCO's time shift capability to properly accommodate units of year, month, day, hour, minute, and second
  • New checks to adjust date and timestamps so they fall within physical ranges
  • Now avoid running HEMCO for the end timestep of a simulation
  • Now avoid running HEMCO twice on the first timestep of a simulation
  • New RFY3 time cycle option (3 hour input)

Changed

  • Now use semantic versioning (X.Y.Z)
  • Restore reading CHLR fields for marine POA simulations
  • Read met fields daily instead of hourly to improve file I/O

[2.1.012] - 2019-04-01

Added

  • Bug fixes for HEMCO interpolation
  • Updates from the NASA/GEOS development branch
  • New option to always use the simulation year for specified fields
  • Updates to the volcanic emissions extension

Changed

  • Bug fix: Prevent zero emissions for MEGAN_Mono extension

[2.1.010] - 2019-10-05

Added

  • Bug fix: Read data with the "E" cycle flag just once
  • Bug fix for collapsing model levels to reduced grid
  • New CS time cycle option

Changed

  • Fixed unit conversion in HCO_UNIT_GetAreaScal

[2.1.009] - 2018-09-13

Added

  • Wrap HEMCO extensions into instances

[2.1.008] - 2018-08-08

Added

  • Bug fix: respect range/exact flag for 1D values set in HEMCO_Config.rc

[2.1.007] - 2018-07-18

Added

  • Bug fix in E (exact) time cycling optiion
  • Now stop with error if multiple containers have the same
  • Bug fix for distributing emissions in the vertical dimension
  • New error checks in the HEMCO standalone module
  • Bug fix for ifort compiler in soil NOx extension

Removed

  • Null string character from netCDF unit string

[2.1.006] - 2018-06-10

Added

  • CH4 emissions from wetlands now uses category #1
  • CH4 emissions from rice now uses category #2
  • Unit mol/mol has beeeen added to the list of unitless quantities.

[2.1.005] - 2018-01-27

Added

  • Option to emit into the layer height read from netCDF file

[2.1.004] - 2017-12-30

Added

  • Updates to remove possible issues and excessive print statements when operating in GEOS environment
  • Fixed possible tracer ID mismatch in sea salt extension
  • New option to normalize MEGAN LAI, HEMCO diagnostics
  • Now write multiple time slices into one file
  • New error trap in hcox_dustginoux)mod.F90 to avoid seg faults
  • Bug fix in reference time code

[2.1.003] - 2017-07-19

Added

  • Now normalize MEGAN LAI by plant functional type.

[2.1.002] - 2017-07-17

Added

  • Enable tokens within math functions

[2.1.001] - 2017-05-16

Added

  • Now enable data compression in netCDF-4 output
  • Fixed bug in computation of local time in routine
  • HEMCO diagnostic and restart files now have an unlimited time dimension
  • All internal timestamp variables are now REAL*8
  • New option to define species-specific scale factors that are applied across all inventories, categories, hierarchies, and extensions
  • New option to use mathematical expressions in HEMCO_Config.rc
  • Regridding routines can now support non-global grids

[2.0.004] - 2017-01-26

Added

  • New passive tracer module
  • Improve write speed of netCDF output files

[2.0.003] - 2016-10-16

Added

  • New option DiagnRefTime (specfies reference time in created netCDF files)
  • Fix missing pointer in call to HCO_CalcVertRegrid
  • Bug fix: Prevent HEMCO from writing restart files more than once
  • Now uses updated timezones mask file.
  • Now accepts scale factors for extension fields.
  • New options to emit 2D fields across multiple vertical levels

Changed

  • In hcox_paranox_mod.F90: Archive deposition flux as a positive number to avoid negative values propagating.
  • The HEMCO state object (HcoState) now must be passed to each routine.
  • Updated the passive tracer code.

[1.1.016] - 2015-12-14

Added

  • New HEMCO standalone run directory

[1.1.015] - 2015-12-07

Added

  • Bug fix in GEOS5 -> GEOS-4 regridding
  • Bug fix in syncing the MEGAN LAI_PREVDAY variable

[1.1.014] - 2015-11-23

Added

  • Bug fix when interpolating/averaging between multiple files.

[1.1.013] - 2015-11-19

Added

  • Now allow mask grid points

[1.1.012] - 2015-11-06

Added

  • Now treat MEGAN restart variables as running averages
  • Bug fix: make sure that sea salt aerosol calculations work on curvilinear grids
  • New option DiagnTimeStamp to control diagnostics time stamp format
  • Bug fix: restrict day to last day of month when searching for file names.

Changed

  • The SeaFlux extension now uses HEMCO landtypes instead of land fraction

[1.1.011] - 2015-10-14

Added

  • Now allow horizontal coordinates longitude and latitude
  • New time flags EF and RF to force exit if field not found for current simulation datetime
  • Bug fix in Seaflux extension: pull variables out of parallel loop.

[1.1.010] - 2015-09-22

Added

  • HEMCO can now read any additional (arbitrary) dimension.

[1.1.009] - 2015-09-10

Added

  • Bug fixes to allow specifying flexible diagnostics output frequencies.

[1.1.008] - 2015-07-06

Added

  • Bug fix in hcoi_standalone_mod.F90: make sure current date and simulation end date are properly calculated
  • Make sure that negative emissions are correctly passed to hierarchy level diagnostics
  • Bug fix: When reading a data field, check if diagnostics container with the same name exist and write data into it.

[1.1.007] - 2015-07-06

Added

  • Grid edges can now be explicitly given in HEMCO standalone model

[1.1.006] - 2015-07-01

Added

  • Aerocom, CH4, FINN, GFED, and soil NOx extensions now accept scale fields
  • Bug fix: diagnostics update can now span multiple diagnostics levels

[1.1.005] - 2015-06-09

Added

  • Now also build HEMCO standalone executable
  • New extension module hcox_aerocom_mod.F90
  • Capability to emit 2D data into levels other than the surface
  • Bug fix: Avoid out of bounds errors in MEGAN_Mono extension
  • Bug fix: Restore archiving biogenic CO emissions form monoterpenes

Changed

  • Now ensure that longitudes fall within the range -180 to 180, for COARDS compliance.
  • Unit strings % and percent are now treated as unitless.

[1.1.004] - 2015-05-20

Added

  • New capability to apply scale factors to meteorological fields.
  • Bug fix: Now allow FINN biomass emission diagnostics to be archived.
  • Extra flexibility to the definition of the vertical dimension used in HEMCO_Config.rc (i.e. attribute SrcDim).

Changed

  • Base emissions can now have a dynamic number of scale factors (used to be limited to a fixed number).
  • Now compute SUNCOS and SUNCOS - 5 in the PARANOX extension instead of reading these as restarrt fields.

[1.1] - 2015-04-16

Added

  • Various updates to PARANOX:
    • Bug fix in calculation of H2O ambient air concentration'
    • Bug fix in computation of solar zenith angle for the current date calculation of the current date SZA;
    • Loss fluxes of O3 and HNO3 are now passed in kg/m2/s via the HEMCO diagnostics instead of converting them to a deposition velocity (and then recalculating a flux from this value);
    • The SUNCOS values for the previous 5 hours are now saved out to the HEMCO restart file.
  • Diagnostic collections are now organized in a linked list.
  • Masks can now be treated as fractions (instead of binary values).
  • Various updates to the HEMCO standalone code
  • Modifications to on/off switches in HEMCO_Config.rc:
    • Extension names can be used as switches
    • Multiple switches can be combined with .or

Changed

  • HEMCO has now two run phases:
  • Phase 1 reads the HEMCO list
  • Phase 2 calculates emissions.
  • Environmental fields used by HEMCO (stored in the ExtState object) can now be read directly from disk.
  • Various updates to the HEMCO standalone code
  • Modifications to on/off switches in the HEMCO configuration file

[1.0] - 2014-11-07

Initial HEMCO release

Added

  • Bug fix: Prevent seg fault when emissions are turned off
  • Bug fixes for the BIOGENIC_OCPI diagnostic
  • Bug fixes in the computation of alkalinity
  • PARANOx updates:
  • Can now read the lookup table from netCDF or ASCII format
  • Wind speed is now accounted for in the parameterization
  • Dry deposition of N is included va loss of HNO3.
  • Total tropospheric column mass is used to calculate dry deposition frequencies.
  • Local times can now be calculated based on a time zone map (at 1x1 degree resolution).
  • Non-emissions data may now be specified in HEMCO_Config.rc by setting the extension number to the wildcard (*) character.
  • New MAP_A2A horizontal regridding algorithm
  • The R time cycling option will cause HEMCO only to read data that is within the specified time range
  • Entries in the HEMCO_Config.rc file may now be grouped into collections
  • Minor updates in the HEMCO-to-GEOS-Chem interface
  • UV albedo data is now read by HEMCO as a non-emissions data set.
  • Included GFED4 biomass burning as an extension.
  • Nested configuration files are now allowed
  • Added the capability to exclude collections with .not.
  • Added hco_restart_mod.F90 to define and obtain HEMCO restart variables
  • Vertical mapping between 72 and 47 level GEOS-Chem grids
  • The MEGAN extension can now read initial data from a HEMCO restart file
  • Index-sorted data can now be read from an ASCII file and mapped onto the simulation grid

Changed

  • Treat OCPI, OCPO, BCPI, and BCPO separately
  • Stratospheric production and loss are read as non-emissions data
  • Multiple emissions categories can now be assigned to each emissions field
  • Extension switches has been moved to the beginning of HEMCO_Config.rc
  • Verbose is no longer a logical switch but a number between 0 and 3
  • Masks can now be applied to scale factors

Removed

  • Extension data has been removed from HEMCO_Config.rc. This is now a subsection of Base Emissions.