GEOS-Chem 12: Difference between revisions

Latest revision as of 21:13, 21 June 2021

GEOS-Chem Main Page | GCHP Main Page

Version history summary

The sections below describe each GEOS-Chem feature version and GEOS-Chem bug fix patch version belonging to the GEOS-Chem 12 series. Each feature version carries the tag 12.Y.0, which indicates that the version will be (or has been) validated with a 1-month benchmark simulation (and one or more 1-year benchmark simulations if necessary). Each patch version carries the tag 12.Y.Z, which denotes that the version preserves backwards-compatibility with the prior feature version 12.Y.0. For more information, please see our GEOS-Chem version numbering system wiki page.

Several GEOS-Chem updates have been proposed by the relevant Working Groups, but have not yet been assigned to a specific GEOS-Chem version. For a complete list of these updates, please visit our GEOS-Chem model development priorities wiki page.

Previously released stable versions

We list below past releases of GEOS-Chem. But we recommend that you always download the current stable version listed above when starting a new research project. That version corresponds to the main branch of the GEOS-Chem source code repository on Github.

Each released version of GEOS-Chem will be assigned a unique Digital Object Identifier (DOI). This will allow you to cite each GEOS-Chem version in publications. We also have obtained a "Concept DOI", which will always point to the current stable version of GEOS-Chem: DOI 10.5281/zenodo.1343546. This can be convenient if you wish to cite GEOS-Chem without making reference to a particular version.

12.9.3

This version contains additional fixes for bugs and technical issues discovered after the release of 12.9.2.

This version was released on 06 Aug 2020.

DOI: 10.5281/zenodo.3959279

This version contains additional fixes for bugs and technical issues discovered during the 12.9.0 benchmarking process.

You can use the following Git commands to download the GEOS-Chem 12.9.2 source code and GEOS-Chem Unit Tester package.

NOTE: In GEOS-Chem 13.0.0 and later versions, run directory generation will be moved to the GEOS-Chem source code repository. The Unit Tester repository will be retired.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.9.3
 cd Code.12.9.3
 
 # Create and checkout a new branch "GC_12.9.3" at the tag "12.9.3"
 git checkout -b GC_12.9.3 12.9.3
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.9.3" at the tag "12.9.3"
 git checkout -b GC_12.9.3 12.9.3

Feature	Submitted by	Type	Notes and References
Updates that WILL NOT AFFECT the full-chemistry simulation
Fix to make HEMCO properly read vertical coordinates for data on arbitrary vertical grids	Lyssa Freese (MIT) Haipeng Lin (Harvard) Bob Yantosca (GCST)	Bug fix	This bug does not affect any data files used by the benchmark simulation.
Bug fix for planeflight diagnostic: Change parameter definition MAXAN=15 to MAXAN=20	Paolo Sebastianelli (Wollongong) Bob Yantosca (GCST)	Bug fix
Fix additional typos in GEOS-Chem species database	Thibaud Fritz (MIT) Bob Yantosca (GCST)	Bug fix	Typos were in species used by the specialty simulations or in the complexSOA_SVPOA simulation. None of the affected species were used by the standard or benchmark simulations.

12.9.2

This version was released on 24 Jul 2020.

DOI: 10.5281/zenodo.3959279

This version contains additional fixes for bugs and technical issues discovered during the 12.9.0 benchmarking process.

You can use the following Git commands to download the GEOS-Chem 12.9.2 source code and GEOS-Chem Unit Tester package.

NOTE: In GEOS-Chem 13.0.0 and later versions, run directory generation will be moved to the GEOS-Chem source code repository. The Unit Tester repository will be retired.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.9.2
 cd Code.12.9.2
 
 # Create and checkout a new branch "GC_12.9.2" at the tag "12.9.2"
 git checkout -b GC_12.9.2 12.9.2
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.9.2" at the tag "12.9.2"
 git checkout -b GC_12.9.2+GFAS_fix 12.9.2

Feature	Submitted by	Type	Notes and References
Updates that WILL NOT AFFECT the full-chemistry simulation
Bug fixes for the CO2 and tagged CO2 simulations: Fix for inconsistent tagged CO2 species names Fix for reading A3dyn met fields in the default HEMCO_Config.rc file for CO2 simulations	Monika Szelag (Finnish Met. Inst.) Xuyan Yue (U. New South Wales) Bob Yantosca (GCST)	Bug fix
Add OPOA to PM2.5 definition in complexSOA_SVPOA simulations	Maggie Marvin (Edinburgh) Aerosols Working Group Bob Yantosca (GCST)	Bug fix	This will not affect Standard or Benchmark simulations, only complexSOA with SVPOA.
Bug fix for dry-run issues in 12.9.0+	Lee Murray (Rochester) Bob Yantosca (GCST)	Bug fix
Prevent negative values in the computation of FNO_NOx in PARANOX	Tina Liu (Harvard) Eimy Bonilla (Harvard) Bob Yantosca (GCST)	Bug fix	NOTE: This issue seems to only arise at fine grid resolutions, such as the 0.5° x 0.625° nested grid simulations.

--Bob Yantosca (talk) 16:21, 24 July 2020 (UTC)

12.9.1

This version was released on 17 Jul 2020.

DOI: 10.5281/zenodo.3950473

You can use the following Git commands to download the GEOS-Chem 12.9.1 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.9.1
 cd Code.12.9.1
 
 # Create and checkout a new branch "GC_12.9.1" at the tag "12.9.1"
 git checkout -b GC_12.9.1 12.9.1
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.9.1" at the tag "12.9.1"
 git checkout -b GC_12.9.1 12.9.1

Important: Make sure you also download the new data directories for this version and for version 12.9.0.

This version contains fixes for bugs and technical issues discovered during the 12.9.0 benchmarking process.

Feature	Submitted by	Type	Notes and References
Updates that WILL NOT AFFECT the full-chemistry simulation
Bug fix: Fixed a lingering issue that caused the GEOS-Chem dry-run not to recognize missing files	Bob Yantosca (GCST)	Bug fix
Fix run-time error when optional Luo wet deposition scheme is turned on	Lizzie Lundgren (GCST)	Bug fix
Fixes for interpolating RCP emissions data via HEMCO	Jenny Fisher (Wollongong) Melissa Sulprizio (GCST) Bob Yantosca (GCST)	Bug fix	The RCP emissions are turned off by default in the full-chemistry simulations. This update will not affect benchmark results.

New data directories in 12.9.1

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
RCP	OPTIONAL	Fixes for interpolating RCP emissions data via HEMCO	`HEMCO/RCP/v2020-07/`

12.9.0

This version was released on 17 Jul 2020.

DOI: 10.5281/zenodo.3950327

You can use the following Git commands to download the GEOS-Chem 12.9.0 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.9.0
 cd Code.12.9.0
 
 # Create and checkout a new branch "GC_12.9.0" at the tag "12.9.0"
 git checkout -b GC_12.9.0 12.9.0
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.9.0" at the tag "12.9.0"
 git checkout -b GC_12.9.0 12.9.0

Important: Make sure you also download the new data directories for this version.

Please see the following links for complete information about the validation of GEOS-Chem 12.9.0:

Feature	Submitted by	Type	Notes and References
Updates that WILL AFFECT the full-chemistry simulation
Updated halogen chemistry	Xuan Wang (Harvard)	Science
Improved cloudwater pH	Viral Shah (Harvard) Jonathan Moch (Harvard)	Science
Update offline lightning data through Dec 2019	Lee Murray (Rochester)	Science
Convert GEOS-Chem species database to YAML format, includes: Defining all species properties in the species database, not just advected species Initializing the species database with values read from the YAML file	Melissa Sulprizio (GCST) Bob Yantosca (GCST)	Structural
Update GEOS-Chem core to apply masking and scaling to HEMCO inputs	Lizzie Lundgren (GCST)	Structural	Will introduce numerical noise differences due to precision change
Bug fix: Restore missing photolysis reactions from 12.8.0 and add an extra error check	Melissa Sulprizio (GCST)	Bug fix
Bug fix: remove inefficient code that was slowing down computation of heterogenous chemistry rates	Bob Yantosca (GCST)	Bug fix	Will introduce numerical differences due to removing inconsistently-defined parameters
Updates that WILL NOT AFFECT the full-chemistry simulation
Corrected issue in GEOS-Chem dry-run where some files were not being properly marked for download	Bob Yantosca (GCST)	Bug fix
Bug fixes for the ObsPack diagnostic: Change units of ObsPack specific humidity (Q) field to g/kg Restore missing code due to Git merge that caused the OBSPACK MENU of input.geos not to be read	Bob Yantosca (GCST)	Bug fix
Fixes for reading meteorology fields in HEMCO: Skip reading FLASH_DENS and CONV_DEPTH fields when lightning NOx extension is turned off Change time cycle flag for meteorology fields to use exact date	Melissa Sulprizio (GCST)	Bug fix
Restore missing metadata for satellite timeseries diagnostics	Melissa Sulprizio (GCST)	Bug fix
Fix bug compiling with Luo wet deposition scheme option	Lizzie Lundgren (GCST)	Bug fix
Updates that affect GCHP only
Fix bug where non-advected species not updated in restart file	Sebastian Eastham (MIT)	Bug fix

New data directories in 12.9.0

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
OFFLINE_LIGHTNING	DEFAULT (full-chemistry simulations)	Update offline lightning data through Dec 2019	`HEMCO/OFFLINE_LIGHTNING/v2020-03/`

12.8.2

This version was released on 27 May 2020.

DOI: 10.5281/zenodo.3860693

GEOS-Chem 12.8.2 contains minor fixes, as well as structural changes needed for WRF-GC development.

Feature	Submitted by	Type
Updates that WILL NOT AFFECT the full-chemistry simulation
Bug fix: Set version numbers to 12.8.2 in `CMakeLists.txt` and `gc_classic_version.H`	Bob Yantosca (GCST)	Bug fix
Updates to facilitate WRF-GC development: Ignore KPP integrate errors and send them to a log file instead Wrap OpenMP-specific code with `#ifdef MODEL_CLASSIC` and `#ifndef NO_OMP` blocks Move certain module variables into the `State_Met` and `State_Chm` objects Exit INIT_DRYDEP immediately if arrays have already been allocated	Haipeng Lin (Harvard)	Structural

12.8.1

This version was released on 21 May 2020.

DOI: 10.5281/zenodo.3837666

GEOS-Chem 12.8.1 fixes several issues that were discovered during and after the 12.8.0 benchmarking process.

You can use the following Git commands to download the GEOS-Chem 12.8.1 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.8.1
 cd Code.12.8.1
 
 # Create and checkout a new branch "GC_12.8.1" at the tag "12.8.1"
 git checkout -b GC_12.8.1 12.8.1
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.8.1" at the tag "12.8.1"
 git checkout -b GC_12.8.1 12.8.1

For GCHP users only: Make sure you also download the new data directories for this version.

Feature	Submitted by	Type	Notes
Features NOT affecting the full-chemistry simulation:
Update the dry-run download data script to make files group-writeable	Bob Yantosca (GCST)	Bug fix
Add more timers for gas-phase chemistry	Melissa Sulprizio (GCST)	Structural
Reduce the amount of memory that GEOS-Chem dry-runs require	Bob Yantosca (GCST)	Bug fix
Add bounds-checking and floating point exceptions to CMake "Debug" target	Melissa Sulprizio (GCST)	Structural
Fix incorrect indexing for AOD diagnostics	Melissa Sulprizio (GCST)	Bug fix
Updates for GEOS-Chem "Classic" HISTORY diagnostics: Fix for instantaneous timeseries diagnostics to avoid overwriting hour zero Fix to allow diagnostics with frequency="End" to properly straddle year-end boundaries	Bob Yantosca (GCST)	Bug fix
Allow for missing species in boundary conditions	Melissa Sulprizio (GCST)	Bug fix
Disable FlexGrid checks to allow for running with any horizontal or vertical grid	Melissa Sulprizio (GCST)	Bug fix
Fixes for WRF-GC and CESM-GC, including: Fix Init_Pressure error for NZ /= 47, 72 Only perform pole-averaging of regridded data if actually regridding to the poles Add a State_Grid%ID field	Haipeng Lin (Harvard)	Bug fix
Add fix for POPs emissions diagnostics	Melissa Sulprizio (GCST)	Bug fix
Avoid memory corruption bug in HEMCO when certain debug flags are on	Sebastian Eastham (MIT)	Bug fix
Fix bug causing seg fault when ConcAboveSfc diagnostic collection is on	Lizzie Lundgren (Harvard)	Bug fix
Fix bug causing crash if not starting on the first day and time of the month	Lizzie Lundgren (Harvard)	Bug fix
Features affecting GCHP only:
Fix incorrect GCHP config file entry for surf_iodide source file in 12.8.0	Lizzie Lundgren (Harvard)	Bug fix
Avoid unexpected behavior if dynamic timestep is changed to non-default values	Lizzie Lundgren (Harvard)	Bug fix
Fix input data to avoid crashing in late Dec/early Jan if using offline biogenic VOCs	Lizzie Lundgren (Harvard)	Bug fix	See updated data directories section below
Add internal state met variables to benchmark and transport tracers simulations	Lizzie Lundgren (Harvard)	Output data	For use in benchmarking
Enable all budget diagnostics output in GCHP transport tracer simulation by default	Lizzie Lundgren (Harvard)	Output data	For use in benchmarking

New or updated data directories in 12.8.1

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
OFFLINE_BIOVOC	Default	Update time dimension attribute to reflect current day in late December and early January for all GEOS-FP and MERRA2 years. This update impacts only GCHP.	`HEMCO/OFFLINE_BIOVOC/v2019-10`

12.8.0

This version was released on 04 May 2020.

DOI: 10.5281/zenodo.3784796

You can use the following Git commands to download the GEOS-Chem 12.8.0 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.8.0
 cd Code.12.8.0
 
 # Create and checkout a new branch "GC_12.8.0" at the tag "12.8.0"
 git checkout -b GC_12.8.0 12.8.0
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.8.0" at the tag "12.8.0"
 git checkout -b GC_12.8.0 12.8.0

Important: Make sure you also download the new data directories for this version.

Please see the following links for complete information about the validation of GEOS-Chem 12.8.0:

Feature	Submitted by	Type	Notes and References
Features affecting the full-chemistry simulation:
Isoprene chemistry	Kelvin Bates (Harvard)	Science	geoschem/geos-chem PR #142
Wet deposition parameterization	Kelvin Bates (Harvard) Sarah Safieddine (MIT)	Science	geoschem/geos-chem PR #142
Ozone deposition to the ocean	Ryan Pound (York) Mat Evans (York)	Science	geoschem/geos-chem PR #170
Use online DustDead, MEGAN, SeaSalt, and SoilNOx emissions for benchmark simulations	Melissa Sulprizio (GCST)	Science	Standard simulations still use high-resolution offline emissions by default
Shift CMIP6 time from middle to start of month to allow start in January	Lizzie Lundgren (GCST)	Bug fix
Features NOT affecting the full-chemistry simulation:
GFED 4.1s beta emissions for 2017-2019	Maggie Marvin (U. Edinburgh)	Science
Replace `State_Chm%nAero` with `State_Chm%nAeroSpc` and `State_Chm%nAeroType`	Seb Eastham (MIT) Bob Yantosca (GCST)	Structural
Convert all files in `GeosCore`, `GeosUtil`, and `Headers` to `.F90`	Melissa Sulprizio (GCST)	Structural
Change GEOS-Chem timers from a CPP switch to an option in input.geos	Melissa Sulprizio (GCST)	Structural
Remove potential for surface CH4 retrieval error in SET_CH4 due to reliance on HEMCO emissions year	Christoph Keller (GMAO)	Bug fix
Features affecting GCHP only:
Fix leap year handling bug in GCHP multi-run script	Lizzie Lundgren (Harvard)	Bug Fix
Fix SH surface ozone bias	Sebastian Eastham (MIT) Lizzie Lundgren (Harvard)	Bug Fix

New data directories in 12.8.0

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
CMIP6	DEFAULT (UCX-based simulations)	Shift time values from middle of month to start of month	`HEMCO/CMIP6/v2020-03`
OCEAN_O3_DRYDEP	DEFAULT	Ozone deposition to the ocean	`HEMCO/OCEAN_O3_DRYDEP/v2020-02`
GFED4	DEFAULT	GFED 4.1s beta emissions for 2017-2019 (previous years are unchanged from `GFED4/v2015-10`)	`HEMCO/GFED4/v2020-02`

12.7.2

This version was released on 09 Mar 2020.

DOI: 10.5281/zenodo.3701669

You can use the following Git commands to download the GEOS-Chem 12.7.2 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.7.2
 cd Code.12.7.2
 
 # Create and checkout a new branch "GC_12.7.2" at the tag "12.7.2"
 git checkout -b GC_12.7.2 12.7.2
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.7.2" at the tag "12.7.2"
 git checkout -b GC_12.7.2 12.7.2

Important: Make sure you also download the new data directories for this version.

This version fixed several minor issues identified during the 12.7.0 benchmarking process.

Feature	Submitted by	Type	Notes and References
Features affecting the full-chemistry simulation:
Restrict wet scavenging to troposphere in Luo et al 2019 wetdep scheme NOTE: The Luo et al 2019 wetdep scheme is turned OFF by default, but can be used for research purposes.	Gan Luo (Albany) Transport Working Group Bob Yantosca (GCST)	Bug fix
Bug fix for reading 3-hourly boundary condition files after hour 21	Melissa Sulprizio (GCST)	Bug fix
Remove unused routines in regrid_a2a_mod.F90	Haipeng Lin (Harvard)	Structural
Features affecting the GCHP only:
Fix pointer retrieval error in SET_CH4 introduced in 12.7.0 when running at c180+ NOTE: This also corrects a long-standing and previously unidentified issue when running with reduced timesteps	Lizzie Lundgren (GCST)	Bug fix	geoschem/gchp #62
Use new Ordonez files to avoid error in MAPL when running at c360	Lizzie Lundgren (GCST)	Bug fix

New data directories in 12.7.2

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
IODINE	Default (GCHP)	Shifted latitude range	`HEMCO/IODINE/v2020-02`

12.7.1

This version was released on 19 Feb 2020.

DOI: 10.5281/zenodo.3676008

You can use the following Git commands to download the GEOS-Chem 12.7.1 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.7.1
 cd Code.12.7.1
 
 # Create and checkout a new branch "GC_12.7.1" at the tag "12.7.1"
 git checkout -b GC_12.7.1 12.7.1
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.7.1" at the tag "12.7.1"
 git checkout -b GC_12.7.1 12.7.1

Important: Make sure you also download the new data directories for this version.

This version fixed several minor issues identified during the 12.7.0 benchmarking process.

Feature	Submitted by	Type
Features NOT affecting the full-chemistry simulation:
Prevent excessive scavenging in the stratosphere in the Luo et al 2019 wet deposition scheme The Luo wetdep scheme is turned off by default in the standard simulation. Further fixes will be applied in 12.7.2.	Gan Luo (Albany) Transport Working Group Bob Yantosca (GCST)	Bug fix
Bug fixes for the TOMAS microphysics simulation	Dana McGuffin (CMU) Bob Yantosca (GCST)	Bug fix
Bug fix for ND51/ND51b satellite timeseries w/ nested-grid simulations	Bob Yantosca (GCST)	Bug fix
Bug fix in computation of AOD from isoprene SOA diagnostic	Jun Meng (GCST) Bob Yantosca (GCST)	Bug fix
Bug fixes for ObsPack diagnostic re: instantaneous sampling	Charley Fite (FSU)	Bug fix
Fix for segmentation fault when dry deposition is turned off	Lizzie Lundgren (GCST)	Bug fix
Fix WRF-GC SetGridFromCtrEdges interface	Haipeng Lin (Harvard)	Bug fix
Features only affecting GCHP:
Fix bug where GCHP 12.7.0 standard run failed if emissions turned off	Lizzie Lundgren (GCST)	Bug fix
https://github.com/geoschem/geos-chem/issues/227 Update MEGAN file used in GCHP 12.7.0 that caused run failure if using gfortran]	Lizzie Lundgren (GCST)	Bug fix
Add MODEL_GCHP (and MODEL_CLASSIC) as CPP options in GEOS-Chem	Lizzie Lundgren (GCST)	Structural

New data directories in 12.7.1

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
MEGAN	Default (GCHP)	Changed seconds string in time dimension units attribute from '0.0' to '00'	`HEMCO/MEGAN/v2020-02`

12.7.0

This version was released on 03 Feb 2020.

DOI: 10.5281/zenodo.3634864

You can use the following Git commands to download the GEOS-Chem 12.7.0 source code and 12.7.0 GEOS-Chem Unit Tester package.

You can also use our GEOS-Chem 12.7.0 tutorial AMI to initialize your Amazon Web Services cloud instance with a pre-compiled GEOS-Chem 12.7.0 executable and all required software libraries. For more details, see our Quick Start Guide at cloud.geos-chem.org.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.7.0
 cd Code.12.7.0
 
 # Create and checkout a new branch "GC_12.7.0" at the tag "12.7.0"
 git checkout -b GC_12.7.0
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.7.0" at the tag "12.7.0"
 git checkout -b GC_12.7.0 12.7.0

Please see the following links for complete information about the validation of GEOS-Chem 12.7.0:

Feature	Submitted by	Type	Notes and References
Features affecting the full-chemistry simulation:
Small alkyl nitrate chemistry	Jenny Fisher (Wollongong)	Science
Methanol as part of standard chemical mechanism	Xin Chen (UMN) Dylan Millet (UMN) Katie Travis (NASA)	Science
Update to Yuan processed MODIS LAI product (covering years 2005-2016)	GCST	Science
Latitudinally and monthly resolved fixed surface concentrations for long-lived organohalogen species (1750-2014) and methane (prior to 1979)	Tomás Sherwen (York) Lee Murray (Rochester)	Science
Bug fix: Prevent differences in chemistry caused by toggling the ND65 bpch diagnostics off or on	Bob Yantosca (GCST)	Bug fix
Fix incorrect uptake coefficient for N2O5 in heterogeneous chemistry	Hyeonmin Kim (Seoul Nat'l U.) Chris Holmes (FSU)	Bug fix	geoschem/geos-chem PR #124
Fix offline dust scale factors	Jun Meng (GCST)	Bug fix
Features NOT affecting the full-chemistry simulation:
Add GEOS-Chem "dry-run" option to obtain a list of required input files	Haipeng Lin (Harvard) Jiawei Zhuang (Harvard) Bob Yantosca (GCST)	Structural	geoschem/geos-chem PR #122 Tutorial at youtube.geos-chem.org
HEMCO 2.2.0: Updates and fixes to improve file I/O	Melissa Sulprizio (GCST)	Structural	Needed for Yuan processed MODIS LAI
Implement Gan Luo et al wetdep (GMD-12-3439-2019) as an option	Gan Luo (SUNY-Albany) Fangqun Yu (SUNY-Albany) Bob Yantosca (GCST)	Science (optional)	This scheme is turned OFF by default. To activate, compile with LUO_WETDEP=y. Further updates are expected for GEOS-Chem 12.8.0. Code: geoschem/geos-chem PR #95 Paper: GMD-12-3439-2019
CH4 soil absorption from MeMo model	Melissa Sulprizio (Harvard)	Science	geoschem/geos-chem commits 9b2e87ce, 2714b8c8
Removal of most binary punch (aka "bpch") diagnostics NOTE: The following bpch diagnostics will be preserved for the time being: For RRTMG: ND72 For TOMAS: ND06, ND44, ND59, ND60, ND61 For Hg: ND03 For POPS: ND53 For Satellite timeseries: ND51, ND51b	GCST	Structural
Add netCDF diagnostic for UV fluxes from FAST-JX	Jonathan Moch (Harvard) Bob Yantosca (GCST)	Structural
KPP equation reactivity rate and OH reactivity diagnostics	Christoph Keller (GMAO)	Structural
Bug fix for HEMCO standalone using high-resolution input grids	Chris Holmes (FSU)	Bug fix
Incorrect units returned from GET_OH in sulfate_mod.F	Rong Tian (NUIST)	Bug fix
Use common build_mechanism.sh script for all KPP mechanisms	Lizzie Lundgren (GCST)	Structural	geoschem/geos-chem Commit 0a19e43d
Features only affecting GCHP:
Preserve mass conservation when advection is off by adding delta pressure to internal state for mixing ratio scaling during initialization	Lizzie Lundgren (GCST)	Bug fix
Use same CEDS anthropogenic emissions inventory as GC Classic, including 1750-1949 and additional VOC species	Lizzie Lundgren (GCST)	Structural	Enables GC Classic 12.3.2 update in GCHP
Assorted GCHP structural changes to facilitate GEOS-Chem in GEOS Move high-level GCHP files to GEOS-Chem repository Move GCHP run directory creation to GEOS-Chem repository	Lizzie Lundgren (GCST)	Structural
Use same precision in non-species Internal state variables and the equivalent GEOS-Chem states (REAL8)	Lizzie Lundgren (GCST)	Bug fix
Update ESMF to v8.0.0 public release	Lizzie Lundgren (GCST)	Structural

New data directories in 12.7.0

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

NOTE: In GEOS-Chem 12.7.0 and later versions, you can use the GEOS-Chem dry-run option to simplify the data download process!

Inventory	Type	What was added?	Directory
OFFLINE_BIOVOC	Default	Offline biogenic VOC emissions generated using GEOS-Chem 12.3.0 and the Yuan-processed MODIS-LAI product	`HEMCO/OFFLINE_BIOVOC/v2019-10`
XUAN_XLAI	DEFAULT	Yuan-processed MODIS LAI product (covering years 2005-2016)	`HEMCO/Yuan_XLAI/v2019-03`
RONO2	DEFAULT	Monthly seawater concentrations of methyl nitrate (MENO3) and ethyl nitrate (ETNO3) needed for small alkyl nitrate chemistry	`HEMCO/RONO2/v2019-05`
MOH	DEFAULT	Methanol emissions as described in Chen et al. (2019)	`HEMCO/MOH/v2019-12`
CMIP6	DEFAULT (UCX-based simulations)	Latitudinally and monthly resolved fixed surface concentrations for long-lived organohalogen species (1750-2014) and methane (prior to 1979)	`HEMCO/CMIP6/v2019-12`
SfcFix	DEFAULT (UCX-based simulations)	Latitudinally and monthly resolved fixed surface concentrations for long-lived organohalogen species from GMI and UCX (1959-2099)	`HEMCO/SfcFix/v2019-12`
MODIS_CHLR	OPTIONAL	MODIS-Aqua Chlorophyll-A data for use in the marinePOA simulation	`HEMCO/MODIS_CHLR/v2019-11`

12.6.3

This version was released on 25 Nov 2019.

DOI: 10.5281/zenodo.3552959

You can use the following Git commands to download the GEOS-Chem 12.6.3 source code and 12.6.0 GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.6.3
 cd Code.12.6.3
 
 # Create and checkout a new branch "GC_12.6.3" at the tag "12.6.3"
 git checkout -b GC_12.6.3 12.6.3
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.6.0" at the tag "12.6.0"
 # NOTE: You can use 12.6.0 rundirs, as GC 12.6.3 does not change rundirs.
 git checkout -b GC_12.6.0 12.6.0

Important: Make sure you also download the new data directories for this version.

Feature	Submitted by	Type	Notes and References
Features only affecting GCHP:
Fix bug preventing successful transport tracer simulation runs	Lizzie Lundgren (GCST)	Bug fix

12.6.2

This version was released on 15 Nov 2019.

DOI: 10.5281/zenodo.3543702

You can use the following Git commands to download the GEOS-Chem 12.6.2 source code and 12.6.0 GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.6.12
 cd Code.12.6.2
 
 # Create and checkout a new branch "GC_12.6.2" at the tag "12.6.2"
 git checkout -b GC_12.6.2 12.6.2
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.6.0" at the tag "12.6.0"
 # NOTE: You can use 12.6.0 rundirs, as GC 12.6.2 does not change rundirs.
 git checkout -b GC_12.6.0 12.6.0

Important: Make sure you also download the new data directories for this version.

Feature	Submitted by	Type	Notes and References
Features NOT affecting the full-chemistry simulation:
geoschem/geos-chem Now make sure the HEMCO standalone gets the proper met field name and grid resolution	Jun Meng (GCST) Bob Yantosca (GCST)	Bug Fix	geoschem/HEMCO #5
Prevent overwriting restart variables H2O2AfterChem and SO2AfterChem if present	Lizzie Lundgren (GCST)	Bug Fix
Features only affecting GCHP:
Fix incorrect vertical flipping of MAPL 3D imports impacting mesospheric chemistry	Lizzie Lundgren (GCST) Sebastian Eastham (MIT)	Bug fix	Fixes issue introduced in 12.5.0
Fix incorrect mapping between internal state H2O2AfterChem and the equivalent State_Chm field	Lizzie Lundgren (GCST)	Bug fix
Fix two timestep delay in update time for LAI upon day change	Lizzie Lundgren (GCST)	Bug fix

12.6.1

This version was released on 28 Oct 2019.

DOI: 10.5281/zenodo.3520966

You can use the following Git commands to download the GEOS-Chem 12.6.1 source code and 12.6.0 GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.6.1
 cd Code.12.6.1
 
 # Create and checkout a new branch "GC_12.6.1" at the tag "12.6.1"
 git checkout -b GC_12.6.1 12.6.1
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.6.0" at the tag "12.6.0"
 # NOTE: You can use 12.6.0 rundirs, as GC 12.6.1 does not change rundirs.
 git checkout -b GC_12.6.0 12.6.0

Important: Make sure you also download the new data directories for this version.

Feature	Submitted by	Type	Notes and References
Updates that will NOT affect full-chemistry simulations
Fix CMake error message for when NetCDF is not found	Liam Bindle (Dalhousie)	Bug fix
Fix units for PRECANV, PRECCON, PRECLSC, PRECTOT in state_met_mod.F90	Tomas Sherwen (York)	Bug fix
Various minor structural updates: ObsPack now defaults to hourly sampling if a sampling interval is not found in data files GEOS-Chem now prints the full path of each file that is read GNU Fortran 9.2.1 can now compile GEOS-Chem Use Microsoft Azure DevOps instead of TravisCI for continuous integration	Bob Yantosca (GCST) Liam Bindle (GCST)	Structural
Features only affecting GCHP:
Fix regridding bug at poles	Lizzie Lundgren (GCST)	Bug fix	Corrects problem running with MERRA2

12.6.0

This version was released on 18 Oct 2019.

DOI: 10.5281/zenodo.3507501

You can use the following Git commands to download the GEOS-Chem 12.6.0 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.6.0
 cd Code.12.6.0
 
 # Create and checkout a new branch "GC_12.6.0" at the tag "12.6.0"
 git checkout -b GC_12.6.0 12.6.0
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.6.0" at the tag "12.6.0"
 git checkout -b GC_12.6.0 12.6.0

Important: Make sure you also download the new data directories for this version.

Please see the following links for complete information about the validation of GEOS-Chem 12.6.0:

Feature	Submitted by	Type	Notes and References
Updates that will affect full-chemistry simulations
Combined heterogeneous chemistry updates, includes N2O5, NO3, NO2 reactive uptake updates Subgrid cloud NOy chemistry	Chris Holmes (FSU) Erin McDuffie (Dalhousie) Viral Shah (UW) Lyatt Jaegle (UW)	Science
HNO3 cold-temperature deposition	Viral Shah (Harvard)	Science
Quick fix for aerosol pH calculation when dry	Becky Alexander (UW) Xuan Wang (Harvard)	Science
Remove isoprene in VBS (leaving aqueous)	Melissa Sulprizio (GCST)	Science
Updated aerosol hygroscopicity and optics	Robyn Latimer (Dalhousie) Jun Meng (Dalhousie)	Science	See New data directories in 12.6.0
Add EDGAR BCPI and BCPO emissions for remaining sectors to DICE-Africa	Tomas Sherwen (York) Eloise Marais (Leicester)	Bug fix	geoschem/geos-chem-unittest PR #9
Updates that will NOT affect full-chemistry simulations
Simple parameterization for CO2 dependence of stomatal resistance (off by default)	Amos Tai (CUHK)	Science	geoschem/geos-chem PR #41
Aerosol nitrate photolysis option (off by default)	Tomas Sherwen (York) Prasad Kasibhatla (Duke)	Science	geoschem/geos-chem PR #32
CMake in GEOS-Chem Classic (optional)	Liam Bindle (Dalhousie)	Structural	geoschem/geos-chem PR #35
Enable GEOS-Chem "Classic" netCDF (History) diagnostics to be subsetted vertically and horizontally	Bob Yantosca (GCST)	Structural
BB4CMIP historical biomass burning emissions (1750-2014) NOTE: This is an optional emissions inventory.	Pengfei Liu (Harvard)	Science	See New data directories in 12.6.0
Surface diagnostic (O3, HNO3) with user-selected height	Katie Travis (MIT) GCST	Science
APM update and integration with GEOS-Chem 12	Gan Luo (SUNY-Albany) Fangqun Yu (SUNY-Albany)	Science	geoschem/geos-chem PR #40 More work (e.g. converting RF diagnostics to netCDF) will be done in a later version

New data directories in 12.6.0

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
FAST_JX	DEFAULT	The `FJX_j2j.dat` file (which lists the photolyzing species for FAST-JX) was updated to include the aerosol nitrate photolysis option The `so4.dat` and `org.dat` files have been updated following Latimer et al. (2019)	`CHEM_INPUTS/FAST_JX/v2019-06`
BB4CMIP6	OPTIONAL	Historical biomass burning emissions (1750-2015, BB4CMIP)	`HEMCO/BB4CMIP6/v2019-06`

12.5.0

This version was released on 09 Sep 2019.

DOI: 10.5281/zenodo.3403111

You can use the following Git commands to download the GEOS-Chem 12.5.0 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.5.0
 cd Code.12.5.0
 
 # Create and checkout a new branch "GC_12.5.0" at the tag "12.5.0"
 git checkout -b GC_12.5.0 12.5.0
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.5.0" at the tag "12.5.0"
 git checkout -b GC_12.5.0 12.5.0

Important: Make sure you also download the new data directories for this version.

Please see the following links for complete information about the validation of GEOS-Chem 12.5.0:

This version includes the updates listed below.

Feature	Submitted by	Type	Notes and References
Updates that will affect full-chemistry simulations
Retire obsolete emission inventories	Eloise Marais (Leicester) Emissions and Deposition Working Group	Science
Updated offline biogenic emissions generated with GEOS-Chem 12.3.0 Includes fixes for biogenic SOAP, SOAS, and CO emissions	Hongjian Weng (PKU)	Science
Updated volcano emissions to include eruptive emissions through April 2018	Christoph Keller (NASA/GMAO)	Science
Remove CO from MEGAN HEMCO extension to avoid double counting	Jenny Fisher (Wollongong)	Bug fix
Fixes for GFED4 emissions, including: Change the HEMCO cycling flag so that the model crashes if it doesn't find the right GFED year Remove the 27% scaling of POG to POA and emit 1:1 instead	Sidhant Pai (MIT)	Bug fix
Scale DICE-Africa emissions to address errors in inventory	Eloise Marais (Leicester)	Bug fix
Bug fix for C3H8 anthropogenic emissions	Melissa Sulprizio (GCST)	Bug fix
Separate anthropogenic PM2.5 dust source from the DustDead extension	Melissa Sulprizio (GCST)	Bug fix
Corrections for CFCs in the chemistry mechanism	Xuan Wang (Harvard)	Bug fix
Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90	Stephen Steenrod (NASA GMAO)	Bug fix
Bug fix: make sure stratospheric BrY concentrations are read properly each month	Lyatt Jaeglé (U. Washington)	Bug fix
Updates that will NOT affect full-chemistry simulations
Enable accurate cloud pH diagnostic calculation via post-processing	Jonathan Moch (Harvard)	Structural	geoschem/geos-chem PR #37 Applies to NetCDF diagnostic only
Bug fix for proposed Henry's law constants	Jenny Fisher (Wollongong)	Bug fix
Updates that will only affect GCHP
Update GCHP to use MAPL v1.0.0 and ESMF v8.0.0 beta snapshot 28	Lizzie Lundgren (GCST)	Structural	Replaces external tile files with online ESMF regridding weights Includes parallel file I/O module Enables use of GNU fortran compiler
Replace 4x5 input files in GCHP with higher resolution equivalents to avoid ESMF domain decomposition issue at high core counts	Lizzie Lundgren (GCST)	Emissions

New data directories in 12.5.0

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
OFFLINE_BIOVOC	Default	Offline biogenic VOC emissions generated using GEOS-Chem 12.3.0 and: GEOS-FP meteorology (0.25°x0.3125°, 2014-2017) MERRA-2 meteorlogy (0.5°x0.625°, 1980-2017)	`HEMCO/OFFLINE_BIOVOC/v2019-08`
Volcano	Default	Updated volcanic SO2 emissions (1978-2019), with eruptive emissions through 28 April 2018	`HEMCO/VOLCANO/v2019-08`
AFCID	Default	Separate anthropogenic PM2.5 dust emissions from the DustDead extension	`HEMCO/AFCID/v2018-04`
C2H6_2010	Default	Removed unused lev dimension and include 2x2.5 files regridded from 4x5	`HEMCO/C2H6_2010/v2019-06`
DUST_DEAD	Optional	Changed longitude dimension format from integer to float and time units seconds string from '0.0' to '00'	`HEMCO/DUST_DEAD/v2019-06`
UVALBEDO	Default	Changed seconds string in time dimension units attribute from '0.0' to '00'	`HEMCO/UVALBEDO/v2019-06`
TOMS/SBUV	Default	Changed seconds string in time dimension units attribute from '0.0' to '00'	`HEMCO/TOMS_SBUV/v2019-06`
India mask	Default	Removed unused attribute 'valid_range'	`HEMCO/MASKS/v2019-05`
BIOFUEL	Default	Regridded from 4x5 to 2x2.5	`HEMCO/BIOFUEL/v2019-08`

12.4.0

This version was released on 05 Aug 2019.

DOI 10.5281/zenodo.3360635

NOTE: We recommend users update to GEOS-Chem 12.5.0, which contains some bug fixes and updates for the offline biogenic VOC and volcano emissions.

Please see the following links for complete information about the validation of GEOS-Chem 12.4.0:

This version includes the updates listed below.

Feature	Submitted by	Type	Notes and References
Features affecting the full-chemistry simulation:
Grid-independent dust emissions (hourly)	David Ridley (CARB, formerly MIT) Jun Meng (Dalhousie)	Science	See New data directories in 12.4.0
Grid-independent lightning NOx emissions (3-hourly)	Lee Murray (Rochester)	Science	See New data directories in 12.4.0
Grid-independent biogenic emissions (hourly)	Jintai Lin (PKU) Hongjian Meng (PKU)	Science	See New data directories in 12.4.0
Grid-independent sea salt emissions (hourly)	Jintai Lin (PKU) Hongjian Meng (PKU)	Science	See New data directories in 12.4.0
Grid-independent soil NOx emissions (hourly)	Jintai Lin (PKU) Hongjian Meng (PKU)	Science	See New data directories in 12.4.0
Updated volcano emissions (1978-2019)	Christoph Keller (NASA/GMAO)	Science	See New data directories in 12.4.0
Bug fix: Rebuild chemical mechanisms for FAST-JX fix added in 12.3.2	Katie Travis (NASA)	Bug fix
Features NOT affecting the full-chemistry simulation:
FlexGrid Stage 2: Add capability to define custom grids	Melissa Sulprizio (GCST) Jiawei Zhuang (Harvard)	Structural
Add photolysis menu to input.geos for specifying FAST-JX directory	Tomas Sherwen (York)	Structural	geoschem/geos-chem PR #34

New data directories in 12.4.0

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
OFFLINE_DUST	Default	Offline dust emissions generated with: GEOS-FP meteorology (0.25°x0.3125°, 2014-present) MERRA-2 meteorlogy (0.5°x0.625°, 1980-present)	`HEMCO/OFFLINE_DUST/v2019-01`
OFFLINE_LIGHTNING	Default	Offline lightning flash densities and convective-cloud depths generated with: GEOS-FP meteorology (0.25x0.3125, 2014-2018) MERRA-2 meteorology (0.5x0.625, 1980-2018).	`HEMCO/OFFLINE_LIGHTNING/v2019-01`
OFFLINE_BIOVOC	Default	Offline biogenic VOC emissions generated using GEOS-Chem v11-02 and: GEOS-FP meteorology (0.25°x0.3125°, 2014-2017) MERRA-2 meteorlogy (0.5°x0.625°, 1980-2017)	`HEMCO/OFFLINE_BIOVOC/v2019-01`
OFFLINE_SEASALT	Default	Offline sea salt emissions generated with: GEOS-FP meteorology (0.25°x0.3125°, 2014-2017) MERRA-2 meteorlogy (0.5°x0.625°, 1980-2017)	`HEMCO/OFFLINE_SEASALT/v2019-01`
OFFLINE_SOILNOX	Default	Offline soil NOx emissions generated with: GEOS-FP meteorology (0.25°x0.3125°, 2014-2017) MERRA-2 meteorlogy (0.5°x0.625°, 1980-2017)	`HEMCO/OFFLINE_SOILNOX/v2019-01`
Volcano	Default	Updated volcanic SO2 emissions (1978-2019), with eruptive emissions through 3 Dec 2015	`HEMCO/VOLCANO/v2019-04/`

12.3.2

This version was released on 02 May 2019.

DOI 10.5281/zenodo.2658178

You can use the following Git commands to download the GEOS-Chem 12.3.1 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone -b 12.3.2 https://github.com/geoschem/geos-chem Code.12.3.2
 cd Code.12.3.2
 git checkout 12.3.2
 cd ..

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone -b 12.3.2 https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 git checkout 12.3.2
 cd ..

Please see the following links for complete information about the validation of GEOS-Chem 12.3.2:

1-month benchmark simulation 12.3.2 for GCC and GCHP (unofficial)

This version includes the updates listed below.

Feature	Submitted by	Type	Notes
Features affecting the full-chemistry simulation:
Fix inconsistency for species H2402 between GCHP and GEOS-Chem "Classic"	Sebastian Eastham (MIT) GCST	Bug fix	This update results in very minor changes w/r/t the prior 1-month benchmark (Bug fixes for the FAST-JX mechanism): Mean OH changed by -0.0002% MCF lifetime was unchanged CH4 lifetime changed by +0.0012%
Bug fixes for the FAST-JX photolysis mechanism: Remove duplicate entry for species ClNO2 in the FJX_j2j.dat file Species DHDC was not listed as photolyzing in the GEOS-Chem species database	Bob Yantosca (GCST)	Bug fix	This update results in very minor changes w/r/t the 12.3.0 1-month benchmark: Mean OH changed by +0.2782% MCF lifetime changed by -0.3597% CH4 lifetime changed by -0.3936%
Updates and fixes for HEMCO diagnostics, including: Enable saving out fertilizer NOx emissions Lightning NOx emissions are 3D not, 2D HNO3 ship emissions are 2D, not 3D Update and fill in missing inventory diagnostics (currently used in only in benchmark simulations)	Melissa Sulprizio (GCST)	Bug fix	These fixes impact both GEOS-Chem "Classic" and GCHP
Features NOT affecting the full-chemistry simulation:
Extending the CEDS anthropogenic emissions inventory to include 1750-1949 and additional VOC species	Melissa Sulprizio (GCST)	Science
Features only affecting GCHP:
Disable Br2 offline seasalt emissions to match GEOS-Chem Classic default	Sebastian Eastham (MIT)	Bug fix
Assorted GCHP run directory feature updates Rename Makefile clean and build options Remove deprecated Makefile/build.sh clean and build options Remove aliases from sample run scripts Remove output file runConfig.log; send to gchp.log instead Update benchmark run directory to match GEOS-Chem Classic settings	Lizzie Lundgren (GCST)	Structural	Users should use 'make' or 'make help' at the command prompt to view all clean and compile options
Embed GEOS code within select GCHP files	Lizzie Lundgren (GCST)	Structural	All GEOS-only code is within if defined MODEL_GEOS blocks and will not impact GCHP simulations

New data directories in 12.3.2

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
FAST_JX	DEFAULT	The `FJX_j2j.dat` file (which lists the photolyzing species for FAST-JX) was edited to remove a duplicate entry for ClNO2. This was causing the J-values of ClNO2 to be passed to the solver twice. The new `FJX_j2j.dat` file corrects this issue.	`CHEM_INPUTS/FAST_JX/v2019-04`
UCX chemistry mechanism	DEFAULT	A new file (`Montreal_fix.nc`) was created to fix an inconsistency in H2402 concentrations between GCHP and GEOS-Chem "Classic".	`CHEM_INPUTS/UCX_201904`
CEDS	OPTIONAL	CEDS anthropogenic emissions for 1750-1949. Data now encompasses the entire CEDS record of 1750-2014. New files for additional NMVOCs	`HEMCO/CEDS/v2018-08`

12.3.1

This version was released on 08 Apr 2019.

DOI 10.5281/zenodo.2633278

You can use the following Git commands to download the GEOS-Chem 12.3.1 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone -b 12.3.1 https://github.com/geoschem/geos-chem Code.12.3.1

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone -b 12.3.1 https://github.com/geoschem/geos-chem-unittest UT

Feature	Submitted by	Type
Features NOT affecting the full-chemistry simulation:
Fix the netCDF diagnostic for noontime J-values	GCST	Bug fix
Planeflight diagnostic now writes out data for the last timestep of the day	Luke Schiferl (LDEO/Columbia) GCST	Bug fix
Reduce memory footprint: Do not allocate memory to array MINIT in `strat_chem_mod.F90`	Bob Yantosca (GCST)	Bug fix
Features only affecting GCHP:
Declare `State_Met%AREA_M2` as 2-dimensional, not 3-dimensional	GCST	Bug fix

12.3.0

This version was released on 01 Apr 2019.

DOI: 10.5281/zenodo.2620535

You can use the following Git commands to download the GEOS-Chem 12.3.0 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.3.0
 cd Code.12.3.0
 
 # Create and checkout a new branch "GC_12.3.0" at the tag "12.3.0"
 git checkout -b GC_12.3.0 12.3.0
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.3.0" at the tag "12.3.0"
 git checkout -b GC_12.3.0 12.3.0

Important: Make sure you also download the new data directories for this version.

Please see the following links for complete information about the validation of GEOS-Chem 12.3.0:

Approval form for 1-month benchmark simulation 12.3.0

This version includes the updates listed below.

Feature	Submitted by	Type	Notes
Features affecting the full-chemistry simulation:
Update ISORROPIA from v2.0 to v2.2, in order to remove persistent noise in output	Seb Eastham (Harvard)	Science
Updated PFT file for MEGAN	Jenny Fisher (Wollongong) Dylan Millet (UMN)	Science
Bug fix for eruptive volcanic emissions	Barron Henderson (EPA)	Bug fix
Read in and regrid existing MODIS LAI and OLSON data via HEMCO	Bob Yantosca (GCST)	Structural
Update from HEMCO version 2.1.011 to 2.1.012 Bug fixes for the HEMCO interpolation algorithm Updates from the NASA GEOS development branch Add option to always use simulation year for specified fields Prevent zero emissions for MEGAN_Mono extension species Updates to the HEMCO volcanic emissions extension	Christoph Keller (NASA/GMAO) GCST	Bug fix & Structural
Features NOT affecting the full-chemistry simulation:
Update to Yuan processed MODIS LAI product (covering years 2005-2016) Off while we investigate an issue in the HEMCO interpolation	Jenny Fisher (Wollongong) Barron Henderson (US EPA)	Science
OMI-based Volcanic emissions 2005-2012 (off by default)	Cui Ge (U. Iowa) Jun Wang (U. Iowa) GCST	Science
Further bug fix for netCDF diagnostics spanning leap years	Bob Yantosca (GCST)	Bug fix
Fix GFAS_SOAP entry in HEMCO_Config.rc	Killian Murphy (York)	Bug fix
Tagged CO bug fixes: Fix CO units and write secondary production into a netcdf file	Beata Bukosa (Wollongong)	Bug fix
Features affecting GCHP only:
Enable running time backwards in GCHP	Atanas Trayanov (GMAO), Lizzie Lundgren (GCST)	Structural	Off by default

New data directories in 12.3.0

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
OLSON_MAP	DEFAULT	Olson 2001 land map masks, separated into 73 netCDF variables (one per land type). This format facilitates regridding by HEMCO.	`HEMCO/OLSON_MAP/v2019-02`
MODIS_XLAI	DEFAULT	MODIS LAI data (corresponding to `ExtData/CHEM_INPUTS/MODIS_LAI_201707`) This data has been processed into 73 netCDF variables (one corresponding to each Olson land type), which facilitates regridding by HEMCO.	`HEMCO/MODIS_XLAI/v2017-07`
MEGAN	DEFAULT	Updated PFT file for MEGAN	`HEMCO/MEGAN/v2018-05/`

NOTES:

DEFAULT denotes that the inventory is part of the default HEMCO emissions configuration that you get when you run GEOS-Chem "out-of-the-box".
OPTIONAL denotes optional inventories that you may use (or not) according to your research needs.

12.2.1

This version was released on 28 Feb 2019.

DOI: 10.5281/zenodo.2580198

You can use the following Git commands to download the GEOS-Chem 12.2.1 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.2.1
 cd Code.12.2.1
 
 # Create and checkout a new branch "GC_12.2.1" at the tag "12.2.1"
 git checkout -b GC_12.2.1 12.2.1
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.2.1" at the tag "12.2.1"
 git checkout -b GC_12.2.1 12.2.1

Important: Make sure you also download the new data directories for this version.

This version includes the updates listed below.

Feature	Submitted by	Type	Notes
Features NOT affecting the full-chemistry simulation:
Bug fix: netCDF diagnostic collections with frequency "End" now properly span leap year days	Amos Tai (CUHK) GCST	Structural
Move module-level variables from Linoz and MODIS LAI	Haipeng Lin (PKU)	Structural
Make polar bromine explosion the default option in Hg simulation	Colin Thackray (Harvard) Jenny Fisher (Wollongong)	Science
TOMAS updates Add biomass burning subgrid coagulation option Restore DST1, DST2, DST3, and DST4 in TOMAS simulations	Emily Ramnarine (Colorado State) Jeff Pierce (Colorado State) Betty Croft (Dalhousie)	Science
Fix Henry's Law coefficient for C2H6	Chris Holmes (FSU)	Bug fix
Add routine to save the GC species database to JSON format (commented out)	Bob Yantosca (GCST)	Structural
Add RRTMG fluxes to netCDF diagnostics	Bob Yantosca (GCST)	Structural	Still needs to be validated
Fix for CO2 simulation chemical source	Beata Bukosa (U. Wollongong)	Bug fix
Features affecting GCHP only:
Update MODIS LAI source directory to match GEOS-Chem Classic	GCST	Bug fix
Missing scaling factors for MERRA-2 simulations with GCHP	Sebastian Eastham (MIT)	Bug fix
Use online sea flux emissions by default in GCHP	GCST	Emissions

New data directories in 12.2.1

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
Updated chemical source for CO2 simulation	OPTIONAL	Reprocessed the chemical source file for the CO2 simulation, because the existing file was somehow corrupted.	`HEMCO/CO2/v2019-02/CHEM/`
FINN	OPTIONAL	Files containing the number of fires per grid box for use with the biomass burning subgrid coagulation option in TOMAS simulations.	`HEMCO/FINN/v2015-02/`

--Bob Yantosca (talk) 16:34, 13 February 2019 (UTC)

12.2.0

This version was released on 19 Feb 2019.

10.5281/zenodo.2572887

You can use the following Git commands to download the GEOS-Chem 12.2.0 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.2.0
 cd Code.12.2.0
 
 # Create and checkout a new branch "GC_12.2.0" at the tag "12.2.0"
 git checkout -b GC_12.2.0 12.2.0
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.2.0" at the tag "12.2.0"
 git checkout -b GC_12.2.0 12.2.0

Important: Make sure you also download the new data directories for this version.

Please see the following links for complete information about the validation of GEOS-Chem 12.2.0:

This version includes the updates listed below.

Feature	Submitted by	Type	Notes
Features affecting the full-chemistry simulation:
Retire BRAVO emissions and use CEDS for Mexico instead	Melissa Sulprizio (GCST)	Science
Update mask file applied to NEI2011 emissions	Melissa Sulprizio (GCST)	Bug fix
Features NOT affecting the full-chemistry simulation:
Transport Tracers simulation: a common set of tracers in GEOS-Chem and GEOS	Transport WG Melissa Sulprizio (GCST)	Benchmarking	Added to the GEOS-Chem Rn-Pb-Be simulation, but may be added to any simulation by following these steps. This will facilitate comparisons of transport between GEOS-Chem "Classic" and/or GCHP vs. the NASA GEOS-DAS system.
ObsPack diagnostic	Andy Jacobson (NOAA/ESRL) Bob Yantosca (GCST)	Structural
GFAS biomass burning emissions (as an option)	Mat Evans (York) Killian Murphy (York)	Science
Fix bug in stratosperic aerosol surface area netcdf diagnostics	Jonathan Moch (Harvard) Christoph Keller (GMAO)	Bug fix
Update from HEMCO 2.1.010 to HEMCO 2.1.011: Now wrap the remaining HEMCO extensions in instances (to facilitate running in HPC environments) Update HEMCO standalone for compatibility with FlexGrid met field names HEMCO standalone now calls HCO_RUN in two phases	GCST	Structural
Features affecting GCHP only:
Update ESMF version in GCHP from v5.2.0rp2 to v7.1.0r	Lizzie Lundgren (GCST)	Structural	Currently compatible with Intel compilers only
New fields in GCHP output restart file	Lizzie Lundgren (GCST)	Bug Fix & Structural	Adds additional variables to GCHP internal state for carrying across multi-segmented runs Equivalent to GEOS-Chem Classic update in 12.1.0
Bug fix: use checkpoint output file as subsequent run restart	Lizzie Lundgren (GCST)	Bug Fix	Does not impact single duration runs

New data directories in 12.2.0

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
GFAS biomass burning emissions	OPTIONAL	GFAS biomass burning emissions for 2003-present (updated monthly)	`HEMCO/GFAS/v2018-09/`
EDGAR v4.2 emissions of SF6	DEFAULT	EDGAR v4.2 emissions of SF6 for 1970-2008	`HEMCO/SF6/v2019-01/`
MASKS	DEFAULT	Update mask file applied to NEI2011 emissions	`HEMCO/MASKS/v2018-09/`
TileFiles	DEFAULT (in GCHP)	New tile files for 0.1x0.1 CONUS, Canada, and Mexico mask files	`GCHP/TileFiles`

NOTES:

DEFAULT denotes that the inventory is part of the default HEMCO emissions configuration that you get when you run GEOS-Chem "out-of-the-box".
OPTIONAL denotes optional inventories that you may use (or not) according to your research needs.

12.1.1

This version was released on 13 Dec 2018.

DOI: 10.5281/zenodo.2249246

You can use the following Git commands to download the GEOS-Chem 12.1.1 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.1.1
 cd Code.12.1.1
 
 # Create and checkout a new branch "GC_12.1.1" at the tag "12.1.1"
 git checkout -b GC_12.1.1 12.1.1
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.1.1" at the tag "12.1.1"
 git checkout -b GC_12.1.1 12.1.1

Important: Make sure you also download the new data directories for 12.1.0 if you haven't already.

This version includes the updates listed below.

Feature	Submitted by	Type
Features NOT affecting the full-chemistry (benchmark) simulation:
Bug fix for tagged CO: don't multiply emissions timestep by 60	Dylan Jones (U. Toronto)	Bug fix
Skip planeflight observations outside a nested domain	Lei Zhu (Harvard)	Bug fix
Always enable BCPH_TPBC to allow saving out BC files in global simulations	Yanxu Zhang (Nanjing)	Bug fix
Fix compilation issues: Add hco_interface_mod.o to list of dependencies for get_met_mod.o and only compile get_met_mod.F90 and flexgrid_mod.F90 for GEOS-Chem "Classic" Add flexgrid_read_mod.o to list of dependencies for hcoi_gc_main_mod.o	Bob Yantosca (GCST) Haipeng Lin (PKU)	Bug fix
Features affecting GCHP only:
GCHP transport fix to prevent instant propagation from troposphere to stratosphere	Seb Eastham (MIT)	Bug fix

--Lizzie Lundgren (talk) 16:05, 6 December 2018 (UTC)

12.1.0

This version was released on 26 Nov 2018.

DOI: 10.5281/zenodo.1553349

You can use the following Git commands to download the GEOS-Chem 12.1.0 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.1.0
 cd Code.12.1.0
 
 # Create and checkout a new branch "GC_12.1.0" at the tag "12.1.0"
 git checkout -b GC_12.1.0 12.1.0
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.1.0" at the tag "12.1.0"
 git checkout -b GC_12.1.0 12.1.0

Important: Make sure you also download the new data directories for this version.

Please see the following links for complete information about the validation of GEOS-Chem 12.1.0:

Approval form for 1-month benchmark simulation 12.1.0

This version includes the updates listed below.

Feature	Submitted by	Type	Notes
Features affecting the full-chemistry simulation:
Budget diagnostics	Lizzie Lundgren (GCST) Chris Holmes (Florida State)	Diagnostics	This update introduces differences on the level of numerical noise due to unit conversions
Anthropogenic PM2.5 dust source	Sajeev Philip (Dalhousie)	Science	This update introduces the following changes: DST1 emissions increased by 1.09 Tg/mon (13.1 Tg/yr) Δ Mean OH: -0.000066% Δ MCF lifetime: 0.0020% Δ CH4 lifetime: 0.0012%
GEOS-Chem restart file updates	Melissa Sulprizio (GCST)	Bug Fix & Structural	GEOS-Chem Classic only update This update introduces the following changes: Δ Mean OH: -0.016% Δ MCF lifetime: 0.022% Δ CH4 lifetime: 0.024%
Updates and fixes for the CEDS anthropogenic emissions inventory: Add missing RCO sector to CEDS emissions entries Include CEDS ship emissions as default global ship emissions inventory Reduce file size for CEDS inventory	Pengfei Liu (Harvard) Melissa Sulprizio (GCST) Jiawei Zhuang (Harvard)	Bug fix	This update introduces the following changes: Δ Mean OH: 0.17% Δ MCF lifetime: -0.37% Δ CH4 lifetime: -0.40%
HEMCO fixes: HEMCO bug fix: prevent excessive attempts to read the HEMCO restart file when using GEOS-Chem "Classic" Add fix for collapsing model levels to reduced grid Fix unit conversion in HCO_UNIT_GetAreaScal	Bob Yantosca (GCST) Melissa Sulprizio (GCST) Erin McDuffie (Dalhousie)	Bug fix	This update introduces very small changes: Δ Mean OH: -0.952% Δ MCF lifetime: 1.454% Δ CH4 lifetime: 1.502%
Fix mass conservation in non-local PBL mixing	Jintai Lin (PKU)	Bug fix	This update introduces very small changes: Δ Mean OH: 0.0057% Δ MCF lifetime: -0.0061% Δ CH4 lifetime: -0.0073%
Allow for SZA to 98 degrees when getting photolysis rates	Eric Fleming (GMAO)	Bug fix	This update introduces the following changes: Δ Mean OH: 0.3982% Δ MCF lifetime: -0.3665% Δ CH4 lifetime: -0.3680%
Features NOT affecting the full-chemistry simulation:
FlexGrid Stage 1: Use HEMCO to read met fields	Jiawei Zhuang (Harvard) Jintai Lin (PKU)	Structural
Add support for continuous integration with TravisCI – automatically test each commit as soon as it is pushed to Github	Jiawei Zhuang (Harvard) Bob Yantosca (GCST)	Structural	See build status page here
Added netCDF diagnostics in the following areas: CH4 simulation CO2 simulation Persistent Organic Pollutants (POPS) simulation Mercury simulation netCDF diagnostics for mercury are partially implemented in 12.1.0; to be completed in 12.2.0	Bob Yantosca (GCST)	Diagnostics	NOTE: The remaining netCDF diagnostics will be implemented into 12.2.0 and later versions, as time allows.
Convert input data for RRTMG from bpch to netCDF for input via HEMCO	Bob Yantosca (GCST)	Structural
Add fixes for seasonal scale factors in CH4 simulations	Bram Maasakkers (SRON) Melissa Sulprizio (GCST)	Bug fix
Move Fast-JX .dat files from the `geos-chem-unittest` repository to `gcgrid/ExtData`	Chris Holmes (Florida State) GCST	Structural
Update HEMCO configuration file for the tagged CO simulation	Bob Yantosca (GCST)	Bug fix
Structural updates to facilitate interfacing GEOS-Chem into WRF	Haipeng Lin (Peking U) GCST	Structural	This process will be ongoing throughout the GEOS-Chem 12 series of releases.
Structural updates to facilitate interfacing GEOS-Chem into GEOS-5	Christoph Keller (GMAO) Lizzie Lundgren (GCST)	Structural	This process will be ongoing throughout the GEOS-Chem 12 series of releases.
Features affecting GCHP only:
Fix masking bug to correctly apply anthropogenic emissions	Lizzie Lundgren (GCST)	Bug fix
Remove erroneous 180 degree longitude shift in APEI regridding	Lizzie Lundgren (GCST)	Bug fix
Move GCHP run directory creation from GEOS-Chem Unit Tester to GCHP repository	Lizzie Lundgren (GCST)	Structural

--Melissa Sulprizio (talk) 15:21, 26 November 2018 (UTC)

New data directories in 12.1.0

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
DUST DEAD	DEFAULT	Anthropogenic PM2.5 dust source	`HEMCO/DUST_DEAD/v2018-04/`
GEOS-Chem restart files	DEFAULT	GEOS-Chem restart file updates: New variables, new variable names, new file names	`GEOSCHEM_RESTARTS/v2018-11/`
Input files for FAST-JX	DEFAULT	Move Fast-JX .dat files from the `geos-chem-unittest` repository to `gcgrid/ExtData`	`CHEM_INPUTS/FAST_JX/v2018-09/`
RRTMG input data	OPTIONAL	netCDF input data files for the RRTMG specialty simulation (converted from the old "binary punch" format files)	`HEMCO/RRTMG/v2018-11/`
CEDS anthropogenic emissions	DEFAULT	Reduce file size for CEDS inventory	`HEMCO/CEDS/v2018-08/YYYY`
MASKS	DEFAULT	Clean up mask file directory to remove obsolete files	`HEMCO/MASKS/v2018-09/`

NOTES:

DEFAULT denotes that the inventory is part of the default HEMCO emissions configuration that you get when you run GEOS-Chem "out-of-the-box".
OPTIONAL denotes optional inventories that you may use (or not) according to your research needs.

12.0.3

This version was released on 16 Oct 2018.

DOI: 10.5281/zenodo.1464210

You can use the following Git commands to download the GEOS-Chem 12.0.3 source code and GEOS-Chem Unit Tester package.

# Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.0.3
 cd Code.12.0.3
 
 # Create and checkout a new branch "GC_12.0.3" at the tag "12.0.3"
 git checkout -b GC_12.0.3 12.0.3
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
  
 # Create and checkout a new branch "GC_12.0.3" at the tag "12.0.3"
 git checkout -b GC_12.0.3 12.0.3

Important: Make sure you also download the new data directories for 12.0.0 if you haven't already.

This version contains fixes that will only impact GCHP.

Feature	Submitted by	Type
Features affecting GCHP only:
Fix incorrect run configuration for offline sea salt emissions in GCHP	Sebastian Eastham (MIT)	Bug fix
Fix bug in application of CFC surface mixing ratios in GCHP	Sebastian Eastham (MIT)	Bug fix

--Lizzie Lundgren (talk) 18:21, 16 October 2018 (UTC)

12.0.2

This version was released on 10 Oct 2018.

DOI: 10.5281/zenodo.1455215

You can use the following Git commands to download the GEOS-Chem 12.0.2 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.0.2
 cd Code.12.0.2
 
 # Create and checkout a new branch "GC_12.0.2" at the tag "12.0.2"
 git checkout -b GC_12.0.2 12.0.2
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.0.2" at the tag "12.0.2"
 git checkout -b GC_12.0.2 12.0.2

Important: Make sure you also download the new data directories for 12.0.0 if you haven't already.

This version includes the updates listed below.

Feature	Submitted by	Type	Notes
Features NOT affecting the full-chemistry (benchmark) simulation:
Fixed local-time averaging in ND51 and ND51b satellite timeseries diagnostics	Bo Zhang (NIA)	Bug fix	Implemented 04 Oct 2018
Fixes to correct missing BC/OC biomass emissions and incorrect aerosol drydep in TOMAS simulations	Pengfei Liu (Harvard)	Bug fix	Implemented 25 Sep 2018
Avoid double-counting of emissions in the CO2 simulation	Beata Bukosa (U. Wollongong) Christoph Keller (GMAO)	Bug fix	Implemented 24 Sep 2018.

--Lizzie Lundgren (talk) 18:21, 16 October 2018 (UTC)

12.0.1

This version was released on 24 Aug 2018.

DOI: 10.5281/zenodo.1403144

You can use the following Git commands to download the GEOS-Chem 12.0.1 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.0.1
 cd Code.12.0.1
 
 # Create and checkout a new branch "GC_12.0.1" at the tag "12.0.1"
 git checkout -b GC_12.0.1 12.0.1
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.0.1" at the tag "12.0.1"
 git checkout -b GC_12.0.1 12.0.1

Important: Make sure you also download the new data directories for 12.0.0 if you haven't already.

This version includes the updates listed below.

Feature	Submitted by	Type
Features NOT affecting the full-chemistry (benchmark) simulation:
Fix typo when registering the `State_Chm%SSAlk` field	Shuting Zhai (U. Washington) GCST	Bug fix
Add fixes for several compilation issues: Nullify rather than deallocate 3D met arrays for compatibility with gfortran 6+ when using GCHP Add a more robust test for netCDF-Fortran in Makefile_header.mk Fix compilation issues encountered with GNU Fortran 8.2.0 Fix compilation issues encountered with Intel Fortran 18	GCST	Bug fix
Fixes for the Hg specialty simualtion: Restore biomass emissions and do not double-count anthropogenic emissions	Colin Thackray (Harvard)	Bug fix
Fix mis-indexing in the ND05 diagnostic	GCST	Bug fix
Minor updates to facilitate interfacing GEOS-Chem into GEOS-5	Lizzie Lundgren (GCST)	Structural

--Bob Yantosca (talk) 14:31, 10 October 2018 (UTC)

12.0.0

This version was released on 10 Aug 2018

DOI 10.5281/zenodo.1343547

You can use the following Git commands to download the GEOS-Chem 12.0.0 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.0.0
 cd Code.12.0.0
 
 # Create and checkout a new branch "GC_12.0.0" at the tag "12.0.0"
 git checkout -b GC_12.0.0 12.0.0
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 
 # Create and checkout a new branch "GC_12.0.0" at the tag "12.0.0"
 git checkout -b GC_12.0.0 12.0.0

Important: Make sure you also download the new data directories for this version.

For more information about getting set up with GEOS-Chem, please see the GEOS-Chem Online User's Guide.

The table below shows the updates that were added to GEOS-Chem 12.0.0. Most of these fix issues that were reported by users during the GEOS-Chem v11-02 release candidate testing period (June 22 thru August 10 2018).

Please see the following links for complete information about the validation of GEOS-Chem 12.0.0:

Feature	Submitted by	Type	Notes
Features affecting the full-chemistry (benchmark) simulation:
Turn off TRASH emissions by default to avoid double counting	GCST Eloise Marais (U. Birmingham)	Bug fix	This update introduces relatively small changes: Mean OH decreased by 0.12% MCF lifetime increased by 0.23% CH4 lifetime increased by 0.24% O3 STE flux increased by 0.042%
Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory	GCST	Bug fix	This update introduces relatively small changes: Mean OH decreased by 0.15% MCF lifetime increased by 0.28% CH4 lifetime increased by 0.29% O3 STE flux increased by 0.043%
Bug fix for liquid water content in gckpp_HetRates.F90	Jiayue Huang (U. Washington) Quanjie Chen (U. Washington)	Bug fix	This update introduces relatively small changes: Mean OH increased by 1.91% MCF lifetime decreased by 2.41% CH4 lifetime decreased by 2.41% O3 STE flux decreased by 0.18%
Bug fix for CH4 boundary conditions	Lee Murray (Rochester)	Bug fix	Results approved by Lee Murray This update introduces small changes: Mean OH decreased by 0.48% MCF lifetime increased by 0.82% O3 STE decreased by: 0.022%
Fixed typo in call to GAMMA_HOBr_AER	Xuan Wang GCST	Bug fix	This update produced only very small differences w/r/t internal run v11-02-rc-DICEnewrc Mean OH decreased by -0.058% MCF lifetime increased by 0.082% CH4 lifetime increased by 0.084% O3 STE flux decreased by 0.005%
Correct issues when specifying DICE-Africa emissions: Avoid double-counting between DICE-Africa and other inventories Use unique names for DICE-Africa entries in the `HEMCO_Config.rc` file	Eloise Marais (U. Birmingham) GCST	Bug Fix	Results approved by Eloise Marais. This update produced only very small differences w/r/t internal run v11-02-rc-arctasship: Mean OH increased by 0.07% MCF lifetime decreased by 0.12% CH4 lifetime decreased by 0.13% O3 STE flux decreased by -0.0023%
Add missing Criegee intermediate reaction	Xin Chen (UMN)	Bug fix	This update produced only very small differences w/r/t internal run v11-02-rc-arctasship: Mean OH decreased by 0.00002% MCF lifetime was unchanged CH4 lifetime increased by 0.001% O3 STE flux increased by 0.0001%
Bug fix for ARCTAS_SHIP in `HEMCO_Config.rc` files	Barron Henderson (EPA)	Bug Fix	This update only produced very small differences w/r/t internal run v11-02-rc-gfed2016: Mean OH decreased by 0.0004% O3 STE flux decreased by 0.0007% MCF and CH4 lifetimes were unchanged
Bug fix in FlexChem: do not zero out ACTA, EOH, HCOOH concentrations	Katie Travis (MIT)	Bug Fix	This update only produced very small differences w/r/t v11-02-rc: Mean OH decreased by 0.083% MCF lifefime increased by 0.112% CH4 lifetime increased by 0.112% O3 STE flux decreased by 0.011%
Add GFED4.1 data for 2015 and 2016; Use GFED4.1 2016 in benchmarks	Kate O'Dell (CSU) GCST	Science	Data files downloaded 27 Jun 2018 This update only produced small differences: Mean OH increased by 0.60% MCF lifefime decreased by 0.65% CH4 lifetime decreased by 0.64% O3 STE flux decreased by 0.0093%
Features NOT affecting the full-chemistry simulation:
Bug fixes for stratospheric chemistry: Disable STE calculation printed to log file Turn on Synoz when Linoz is set to false in input.geos	GCST	Bug fix
Limit flash rate density in hcox_lightnox_mod.F90	Lee Murray (Rochester)	Bug fix
Initial structural modifications for interfacing GEOS-Chem into WRF	Haipeng Lin (Peking U.)	Structural	This process is ongoing in GEOS-Chem 12
Minor fixes for mercury chemistry updates implemented in v11-02f	Colin Thackray (Harvard)	Bug fix
Restore default timestep for MERRA-2 nested grid simulations to 10/20	Ke Li (Harvard)	Bug fix
Remove duplicate C3HI spectrum in FJX_spec.dat and FJX_j2j.dat	Tomas Sherwen (York)	Bug fix	A difference test w/r/t the previous commit yielded identical results
Fixed typo that prevented PM2.5 from being archived to netCDF output	Jonathan Moch (Harvard) GCST	Bug fix
Bring two-way nested-grid code option up-to-date	Yingying Yan (PKU) Jintai Lin (PKU)	Structural	This option is invoked by compiling with `EXCHANGE=y` A difference test w/r/t the previous commit yielded identical results.
Do not force L=1 by default in planeflight_mod.F	Katie Travis (MIT) GCST	Bug fix
Add PH2O2 to the default list of prod/loss families in the KPP mechanisms	GCST	Structural	This update facilitates saving out oxidant fields from a full-chemistry simulation that can be used to drive an aerosol-only simulation.
Update to HEMCO v2.1.008, which includes minor updates: Fixed error in HEMCO "exact" cycling option NOTE: This update introduced an unforeseen side-effect which will be fixed in GEOS-Chem 12.1.0. Update to HEMCO v2.1.007, which includes minor updates: Stop with error if multiple containers have the same name Bug fix for distributing emissions in the vertical dimension Add extra error checks in HEMCO standalone module Remove null string character from netCDF unit string Bug fix for HEMCO soil NOx error with ifort 17	GCST Christoph Keller Jenny Fisher	Structural & Bug fix
Bug fix for reference time in netCDF diagnostic files	GCST	Bug fix
Updates for QFED biomass burning emissions: Update to QFED v2.5r1 Fix QFED v2.4r6 files for 2016/10/13	Christoph Keller (NASA GMAO)	Bug fix
Fix issues in complexSOA and complexSOA_SVPOA restart files	Eloise Marais (U. Birmingham)	Bug fix
Avoid double counting CEDS and GEIA NH3 biofuel emissions	Christoph Keller (NASA/GMAO) GCST	Bug fix	The default HEMCO behavior is to prioritize CEDS over GEIA NH3 anthro and biofuel emissions. But to avoid confusion, we will explicitly request this behavior in the `HEMCO_Config.rc` files that ship with the GEOS-Chem Unit Tester.
Bug fixes for v11-02 simulations using the RRTMG radiative transfer model	Chris Holmes (U. Florida)	Bug Fix	This only affects the RRTMG simulations. Full-chemistry difference-tests yielded identical results w/r/t v11-02-rc.
Now always declare the netCDF time variable with an unlimited dimension	Chris Holmes (U. Florida)	Structural	Full-chemistry difference-tests yielded identical results w/r/t v11-02-rc.

New data directories in 12.0.0

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Version added	Directory
QFED biomass burning emissions	OPTIONAL	New data files for QFED v2.5r1	12.0.0	`HEMCO/QFED/v2018-07`
GFED4 biomass burning emissions	DEFAULT	GFED4.1 data files for 2015 and 2016 have been added	12.0.0	`HEMCO/GFED4/v2015-10/`
MEGAN	DEFAULT	Global 0.25x0.3125 CLM4 PFT and emission factor input files for MEGAN	v11-02f	`HEMCO/MEGAN/v2017-07/`
MODIS LAI	DEFAULT	Updated 0.25 x 0.25 MODIS LAI files (2005-2011)	v11-02f	`CHEM_INPUTS/MODIS_LAI_201707/`
Lightning NOx	DEFAULT	GEOS-FP OTD-LIS redistribution factors for Apr 2012 - Jul 2017 and MERRA-2 OTD-LIS redistribution factors for any date	v11-02f	`HEMCO/LIGHTNOX/v2017-09/`
Volcanic SO2 emissions	DEFAULT	OMI-based volcanic emissions for 2005-2012	v11-02f	`HEMCO/VOLCANO/v2018-03/`
APEI	DEFAULT	Historical Canadian emissions	v11-02f	`HEMCO/APEI/v2016-11/`
EDGAR v4.3	OPTIONAL	Annual global anthropogenic emissions for 1970-2010 at 0.1x0.1 resolution	v11-02f	`HEMCO/EDGARv43/v2016-11/`
C2H6_2010	DEFAULT	Global fossil fuel and biofuel emissions of C2H6 for 2010	v11-02f	`HEMCO/C2H6_2010/v2017-05/`
DICE-Africa	DEFAULT	Biofuel and diffuse anthropogenic emissions for Africa	v11-02f	`HEMCO/DICE_Africa/v2016-10/`
Trash burning emissions	OPTIONAL	Global trash burning emissions from Wiedinmyer et al. (2014)	v11-02f	`HEMCO/TrashEmis/v2015-03/`
SEABIRD NH3	DEFAULT	NH3 emissions from arctic sea birds	v11-02f	`HEMCO/NH3/v2018-04`
OMOC	OPTIONAL	Spatially varying OM/OC ratio	v11-02e	`HEMCO/OMOC/v2018-01`
NOAA GMD CH4	DEFAULT	Monthly mean surface methane distributions	v11-02e	`HEMCO/NOAA_GMD/v2018-01`
UCX	Tropchem only	Input files for applying linearized stratospheric chemistry production and loss rates saved out from a UCX simulation using GEOS-Chem v11-02d	v11-02e	`HEMCO/UCX/v2018-02/`
IODINE	DEFAULT	Monthly emission fluxes of organic iodine compounds (CH3I, CH2I2, CH2ICl, CH2IBr) from Carlos Ordonez.	v11-02d	`HEMCO/IODINE/v2017-09/`
GMI	DEFAULT	New symbolic links: `gmi.clim.RIPA.geos5.2x25.nc -> gmi.clim.RIP.geos5.2x25` `gmi.clim.RIPB.geos5.2x25.nc -> gmi.clim.RIP.geos5.2x25` `gmi.clim.RIPD.geos5.2x25.nc -> gmi.clim.RIP.geos5.2x25` `gmi.clim.IPMN.geos5.2x25.nc -> gmi.clim.PMN.geos5.2x25` `gmi.clim.NPMN.geos5.2x25.nc -> gmi.clim.PMN.geos5.2x25`	v11-02c	`HEMCO/GMI/v2015-02/`
NEI2011 North American emissions	DEFAULT (global) OPTIONAL (nested NA)	Monthly mean data files (created from the existing hourly data in `HEMCO/NEI2011/v2015-03`)	v11-02a	`HEMCO/NEI2011/v2017-02-MM/`
ALD2	DEFAULT	Fields for ALD2 emissions, including: Seawater concentration of acetaldehyde Heterotrophic respiration rates, used to compute biogenic emissions of ALD2 and EOH (added with the PAN updates)	v11-02a	`HEMCO/ALD2/v2017-03/`
POET	DEFAULT	Anthropogenic emissions of ethanol from the POET inventory (added with the PAN updates)	v11-02a	`HEMCO/POET/v2017-03/`
Soil NOx	DEFAULT	New file: `DepReservoirDefault.nc` Read default DEP_RESERVOIR fields from file when not found in HEMCO restart file	v11-02a	`HEMCO/SOILNOX/v2014-07/`

NOTES:

DEFAULT denotes that the inventory is part of the default HEMCO emissions configuration that you get when you run GEOS-Chem "out-of-the-box".
OPTIONAL denotes optional inventories that you may use (or not) according to your research needs.

--Bob Yantosca (talk) 20:02, 29 June 2018 (UTC)

Validation

In this section we provide information about the benchmarks and tests that we have done to validate GEOS-Chem v11-03.

1-month and 1-year benchmarks

For complete information about the benchmark simulations used to validate GEOS-Chem v11-03, please see our GEOS-Chem 12 benchmark history wiki page.

Performance

Please see the following resources below for more information about the performance of GEOS-Chem 12.0.0.

GEOS-Chem "Classic" performance

We have performed several timing tests with GEOS-Chem "Classic" 12.0.0 and have posted our results on the wiki:

We invite you to add your own time test results to the wiki.

--Bob Yantosca (talk) 18:06, 17 August 2018 (UTC)

GCHP performance

Help us pool performance information across systems by contributing your GCHP run information on our GCHP Timing Tests page.

--Bob Yantosca (talk) 18:06, 17 August 2018 (UTC)

Previous issues now resolved in GEOS-Chem 12

Please see Issues now resolved in GEOS-Chem 12 for a list of bugs and/or technical issues have been resolved in GEOS-Chem 12.0.0 through GEOS-Chem 12.5.0. Issues resolved after GEOS-Chem 12.5.0 can be found on the following Github pages:

Outstanding issues not yet resolved in GEOS-Chem 12

Unresolved issues are listed on the following Github pages:

GEOS-Chem Main Page | GCHP Main Page

@@ Line 6: / Line 6: @@
 |width="225px" align="center"|<font size="+2">[[GEOS-Chem versions|Past releases]]</font>
-|width="450px" align="center" bgcolor="#CCFFFF"|<font size="+2">[[GEOS-Chem 12#12.9.1|'''Current release: GEOS-Chem 12.9.1''']]</font>'''''
 |width="225px" align="center"|<font size="+2">[[GEOS-Chem model development_priorities|Future releases]]</font>
@@ Line 15: / Line 14: @@
 Several GEOS-Chem updates have been proposed by the relevant Working Groups, but have not yet been assigned to a specific GEOS-Chem version.  For a complete list of these updates, please visit [[GEOS-Chem model development priorities|our ''GEOS-Chem model development priorities'' wiki page]].
-== Current versions in development ==
+== Previously released stable versions ==
+We list below past releases of GEOS-Chem.  But we recommend that you always download the current stable version listed above when starting a new research project. That version corresponds to the '''main''' branch of the [https://github.com/geoschem/geos-chem GEOS-Chem source code repository on Github].
+Each released version of GEOS-Chem will be assigned a unique Digital Object Identifier (DOI).  This will allow you to cite each GEOS-Chem version in publications. We also have obtained a "Concept DOI", which will always point to the current stable version of GEOS-Chem: [https://doi.org/10.5281/zenodo.1343546 '''DOI 10.5281/zenodo.1343546'''].  This can be convenient if you wish to cite GEOS-Chem without making reference to a particular version.
+=== 12.9.3 ===
+This version contains additional fixes for bugs and technical issues discovered after the release of 12.9.2.
+<span style="color:green">'''''This version was released on 06 Aug 2020.'''''</span>
+[https://doi.org/10.5281/zenodo.3959279 '''DOI: 10.5281/zenodo.3959279''']
+This version contains additional fixes for bugs and technical issues discovered during the 12.9.0 benchmarking process.
+You can use the following Git commands to download the GEOS-Chem 12.9.2 source code and [[GEOS-Chem Unit Tester]] package.
+<blockquote>''NOTE: In GEOS-Chem 13.0.0 and later versions, run directory generation will be moved to the GEOS-Chem source code repository.  The Unit Tester repository will be retired.''</blockquote>
+  <nowiki># Download the GEOS-Chem source code
+ git clone https://github.com/geoschem/geos-chem Code.12.9.3
+ cd Code.12.9.3
+ # Create and checkout a new branch "GC_12.9.3" at the tag "12.9.3"
+ git checkout -b GC_12.9.3 12.9.3
+ cd ..
+ # Download the GEOS-Chem Unit Tester, from which run directories can be generated
+ git clone https://github.com/geoschem/geos-chem-unittest UT
+ cd UT
+ # Create and checkout a new branch "GC_12.9.3" at the tag "12.9.3"
+ git checkout -b GC_12.9.3 12.9.3</nowiki>
+{| border=1 cellspacing=0 cellpadding=5
+|-bgcolor="#CCCCCC"
+!width="500px"|Feature
+!width="200px"|Submitted by
+!width="100px"|Type
+!width="300px"|Notes and References
+|-valign="top"
+!colspan="4" bgcolor="#CCFFFF"|Updates that WILL NOT AFFECT the full-chemistry simulation
+|-valign="top"
+|[https://github.com/geoschem/geos-chem/issues/391 Fix to make HEMCO properly read vertical coordinates for data on arbitrary vertical grids]
+|Lyssa Freese (MIT)<br>Haipeng Lin (Harvard)<br>Bob Yantosca (GCST)
+|Bug fix
+|
+*This bug does not affect any data files used by the benchmark simulation.
+|-valign="top"
+|[https://github.com/geoschem/geos-chem/issues/397 Bug fix for planeflight diagnostic: Change parameter definition MAXAN=15 to MAXAN=20]
+|Paolo Sebastianelli (Wollongong)<br>Bob Yantosca (GCST)
+|Bug fix
+|
+|-valign="top"
+|[https://github.com/geoschem/geos-chem/issues/400 Fix additional typos in GEOS-Chem species database]
+|Thibaud Fritz (MIT)<br>Bob Yantosca (GCST)
+|Bug fix
+|
+*Typos were in species used by the specialty simulations or in the complexSOA_SVPOA simulation.  None of the affected species were used by the standard or benchmark simulations.
-The GEOS-Chem versions listed below are currently under development.
+|}
 === 12.9.2 ===
-This version contains fixes for bugs and technical issues discovered during the 12.9.0 benchmarking process.
+<span style="color:green">'''''This version was released on 24 Jul 2020.'''''</span>
+[https://doi.org/10.5281/zenodo.3959279 '''DOI: 10.5281/zenodo.3959279''']
+This version contains additional fixes for bugs and technical issues discovered during the 12.9.0 benchmarking process.
+You can use the following Git commands to download the GEOS-Chem 12.9.2 source code and [[GEOS-Chem Unit Tester]] package.
+<blockquote>''NOTE: In GEOS-Chem 13.0.0 and later versions, run directory generation will be moved to the GEOS-Chem source code repository.  The Unit Tester repository will be retired.''</blockquote>
+  <nowiki># Download the GEOS-Chem source code
+ git clone https://github.com/geoschem/geos-chem Code.12.9.2
+ cd Code.12.9.2
+ # Create and checkout a new branch "GC_12.9.2" at the tag "12.9.2"
+ git checkout -b GC_12.9.2 12.9.2
+ cd ..
+ # Download the GEOS-Chem Unit Tester, from which run directories can be generated
+ git clone https://github.com/geoschem/geos-chem-unittest UT
+ cd UT
+ # Create and checkout a new branch "GC_12.9.2" at the tag "12.9.2"
+ git checkout -b GC_12.9.2+GFAS_fix 12.9.2</nowiki>
 {| border=1 cellspacing=0 cellpadding=5
@@ Line 42: / Line 127: @@
 |-valign="top"
-|[https://github.com/geoschem/geos-chem/issues/384 Add OPOA to PM2.5 definition in complex SOA simulations]
+|[https://github.com/geoschem/geos-chem/issues/384 Add OPOA to PM2.5 definition in complexSOA_SVPOA simulations]
 |Maggie Marvin (Edinburgh)<br>Aerosols Working Group<br>Bob Yantosca (GCST)
 |Bug fix
 |
-*This will not affect Standard or Benchmark simulations, only complex SOA.
+*This will not affect Standard or Benchmark simulations, only complexSOA with SVPOA.
 |-valign="top"
@@ Line 63: / Line 148: @@
 |}
-=== 13.0.0 ===
+--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:21, 24 July 2020 (UTC)
-<span style="color:darkorange">'''''Please see our [[GEOS-Chem 13]] wiki page.'''''</span>
-== Current stable version ==
-The GEOS-Chem version listed below is considered stable and can be used to start a new research project.  This version corresponds to the '''master''' branch of the [https://github.com/geoschem/geos-chem GEOS-Chem source code repository on Github].
-Each released version of GEOS-Chem will be assigned a unique Digital Object Identifier (DOI).  This will allow you to cite each GEOS-Chem version in publications. We also have obtained a "Concept DOI", which will always point to the current stable version of GEOS-Chem: [https://doi.org/10.5281/zenodo.1343546 '''DOI 10.5281/zenodo.1343546'''].  This can be convenient if you wish to cite GEOS-Chem without making reference to a particular version.
 === 12.9.1 ===
@@ Line 150: / Line 227: @@
 |}
-== Previously released stable versions ==
-We list below past releases of GEOS-Chem.  But we recommend that you always download the [[#Current stable version|current stable version]] listed above when starting a new research project.
 === 12.9.0 ===

GEOS-Chem 12: Difference between revisions

Latest revision as of 21:13, 21 June 2021

Version history summary

Previously released stable versions

12.9.3

12.9.2

12.9.1

New data directories in 12.9.1

12.9.0

New data directories in 12.9.0

12.8.2

12.8.1

New or updated data directories in 12.8.1

12.8.0

New data directories in 12.8.0

12.7.2

New data directories in 12.7.2

12.7.1

New data directories in 12.7.1

12.7.0

New data directories in 12.7.0

12.6.3

12.6.2

12.6.1

12.6.0

New data directories in 12.6.0

12.5.0

New data directories in 12.5.0

12.4.0

New data directories in 12.4.0

12.3.2

New data directories in 12.3.2

12.3.1

12.3.0

New data directories in 12.3.0

12.2.1

New data directories in 12.2.1

12.2.0

New data directories in 12.2.0

12.1.1

12.1.0

New data directories in 12.1.0

12.0.3

12.0.2

12.0.1

12.0.0

New data directories in 12.0.0

Validation

1-month and 1-year benchmarks

Performance

GEOS-Chem "Classic" performance

GCHP performance

Previous issues now resolved in GEOS-Chem 12

Outstanding issues not yet resolved in GEOS-Chem 12

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