GEOS-Chem 12: Difference between revisions

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'''''[[Main_Page|GEOS-Chem Main Page]] | [[GCHP_Main_Page|GCHP Main Page]]'''''
== Version history summary ==
== Version history summary ==


Line 4: Line 6:


|width="225px" align="center"|<font size="+2">[[GEOS-Chem versions|Past releases]]</font>
|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#12.1.0|'''Current release: GEOS-Chem 12.1.0''']]</font>
|width="225px" align="center"|<font size="+2">[[GEOS-Chem model development_priorities|Future releases]]</font>
|width="225px" align="center"|<font size="+2">[[GEOS-Chem model development_priorities|Future releases]]</font>


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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]].
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 version 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.


The GEOS-Chem version listed below is currently under development.
<span style="color:green">'''''This version was released on 06 Aug 2020.'''''</span>


=== 12.2.0 ===
[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.


The items listed below are slated to be included in GEOS-Chem 12.2.0.  This is a feature release which will be benchmarked with a 1-month benchmark simulation and a 1-year Rn-Pb-Be benchmark simulation.
<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  
{| border=1 cellspacing=0 cellpadding=5  
Line 26: Line 54:
!width="200px"|Submitted by
!width="200px"|Submitted by
!width="100px"|Type
!width="100px"|Type
!width="300px"|Status
!width="300px"|Notes and References


|-
|-valign="top"
!colspan="4" bgcolor="#CCFFFF"|Features affecting the full-chemistry simulation:
!colspan="4" bgcolor="#CCFFFF"|Updates that WILL NOT AFFECT the full-chemistry simulation


|-valign="top"
|-valign="top"
|[[Anthropogenic_emissions#BRAVO|Retire BRAVO emissions and use CEDS for Mexico instead]]
|[https://github.com/geoschem/geos-chem/issues/391 Fix to make HEMCO properly read vertical coordinates for data on arbitrary vertical grids]
|[[GCST]]
|Lyssa Freese (MIT)<br>Haipeng Lin (Harvard)<br>Bob Yantosca (GCST)
|Science
|Bug fix
|
|
*Now in dev/12.2.0
*This bug does not affect any data files used by the benchmark simulation.
*This update introduces the following changes in a 1-month benchmark:
**&Delta; Mean OH: 0.0019%
**&Delta; MCF lifetime: -0.0040%
**&Delta; CH4 lifetime: -.00036%
**&Delta;NO emissions: 0.000433 Tg N
**&Delta;CO emissions: -0.013199 Tg
**&Delta;SO2 emissions: 0.001560 Tg S
**&Delta;SO4 emissions: 0.000041 Tg S
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:


|-valign="top"
|-valign="top"
|[[Transport_Working_Group#Common_set_of_tracers_in_GEOS-Chem_and_GEOS|Common set of tracers in GEOS-Chem and GEOS]]
|[https://github.com/geoschem/geos-chem/issues/397 Bug fix for planeflight diagnostic: Change parameter definition MAXAN=15 to MAXAN=20]
|Transport WG<br>[[GCST]]
|Paolo Sebastianelli (Wollongong)<br>Bob Yantosca (GCST)
|Benchmarking
|Bug fix
|
|
*[[Transport_Working_Group#List_of_tracers_in_GEOS|A set of passive species]] will be added to the GEOS-Chem Rn-Pb-Be benchmark simulation.  This will facilitate comparisons between GEOS-Chem "Classic" and/or GCHP vs. the NASA GEOS-DAS system.


|-valign="top"
|-valign="top"
|[https://www.esrl.noaa.gov/gmd/ccgg/obspack/ ObsPack diagnostic]
|[https://github.com/geoschem/geos-chem/issues/400 Fix additional typos in GEOS-Chem species database]
|Andy Jacobson (NOAA/ESRL)
|Thibaud Fritz (MIT)<br>Bob Yantosca (GCST)
|Structural
|Bug fix
|
|
*Delivered to GCST (May 2017)
*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.


|-valign="top"
|}
|[[GEOS-Chem_12#Replace_HEMCO_built-in_unit_conversions_with_scale_factors_in_config_file|Replace HEMCO built-in unit conversions with scale factors in config file]]
|[[GCST]]
|Structural
|
*Differences in precision and order of operations may result in small number differences


|-valign="top"
=== 12.9.2 ===
|[[GFAS biomass burning emissions]] (as an option)
|Mat Evans (York)<br>Killian Murphy (York)
|Science
|
*Now in dev/12.2.0 branch


|-
<span style="color:green">'''''This version was released on 24 Jul 2020.'''''</span>
!colspan="4" bgcolor="#CCFFFF"|Features affecting GCHP only:


|-valign="top"
[https://doi.org/10.5281/zenodo.3959279 '''DOI: 10.5281/zenodo.3959279''']
|[[GEOS-Chem_Output_Files#New_fields_in_GEOS-Chem_restart_file|New fields in GCHP output restart file]]
|[[GCST]]
|Bug Fix &<br>Structural
|
*Adds additional variables to GCHP internal state for carrying across multi-segmented runs
*Equivalent to GEOS-Chem Classic update in [[GEOS-Chem_12#12.1.0|12.1.0]]


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


== Current bug fix patch version in development ==
You can use the following Git commands to download the GEOS-Chem 12.9.2 source code and [[GEOS-Chem Unit Tester]] package.


=== 12.1.1 ===
<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>


GEOS-Chem 12.1.1 contains fixes and updates that do not impact the GEOS-Chem Classic full-chemistry benchmark simulation.
  <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 ..  


{| border=1 cellspacing=0 cellpadding=5  
# 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  
|-bgcolor="#CCCCCC"
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="500px"|Feature
!width="200px"|Submitted by
!width="200px"|Submitted by
!width="100px"|Type
!width="100px"|Type
!width="300px"|Notes
!width="300px"|Notes and References
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry (benchmark) simulation:


|-valign="top"
|-valign="top"
|[[Tagged CO simulation#Do not multiply emission timestep by 60|Bug fix for tagged CO: don't multiply emissions timestep by 60]]
!colspan="4" bgcolor="#CCFFFF"|Updates that WILL NOT AFFECT the full-chemistry simulation
|Dylan Jones (U. Toronto)
|Bug fix
|
*Now in dev/12.1.1. branch


|-valign="top"
|-valign="top"
|[[GEOS-Chem_12#Skip_planeflight_observations_outside_a_nested_domain|Skip planeflight observations outside a nested domain]]
|Bug fixes for the CO2 and tagged CO2 simulations:
|Lei Zhu (Harvard)
#[https://github.com/geoschem/geos-chem/issues/381 Fix for inconsistent tagged CO2 species names]
#[https://github.com/geoschem/geos-chem/issues/258 Fix for reading A3dyn met fields in the default HEMCO_Config.rc file for CO2 simulations]
|Monika Szelag (Finnish Met. Inst.)<br>Xuyan Yue (U. New South Wales)<br>Bob Yantosca (GCST)
|Bug fix
|Bug fix
|
|
*Now in dev/12.1.1. branch


|-valign="top"
|-valign="top"
|[[GEOS-Chem_12#Always_enable_BCPH_TPBC_to_allow_saving_out_BC_files_in_global_simulations|Always enable BCPH_TPBC to allow saving out BC files in global simulations]]
|[https://github.com/geoschem/geos-chem/issues/384 Add OPOA to PM2.5 definition in complexSOA_SVPOA simulations]
|Yanxu Zhang (Nanjing)
|Maggie Marvin (Edinburgh)<br>Aerosols Working Group<br>Bob Yantosca (GCST)
|Bug fix
|Bug fix
|
|
*Now in dev/12.1.1. branch
*This will not affect Standard or Benchmark simulations, only complexSOA with SVPOA.


|-valign="top"
|-valign="top"
|Fix compilation issues:
|[https://github.com/geoschem/geos-chem/issues/369 Bug fix for dry-run issues in 12.9.0+]
*[https://github.com/geoschem/geos-chem/commit/096ad29d02afbdba64a5dd138df0c976ddee3140 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"]
|Lee Murray (Rochester)<br>Bob Yantosca (GCST)
*[https://github.com/geoschem/geos-chem/commit/f9b2f19593afeaa396ff3ee3d315148d5a6f8600 Add flexgrid_read_mod.o to list of dependencies for hcoi_gc_main_mod.o]
|<br>Bob Yantosca ([[GCST]])<br>Haipeng Lin (PKU)
|Bug fix
|Bug fix
|
|
*Now in dev/12.1.1 branch
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting GCHP only:


|-valign="top"
|-valign="top"
|[[GEOS-Chem_12#GCHP_transport_fix_to_prevent_instant_propagation_from_troposphere_to_stratosphere|GCHP transport fix to prevent instant propagation from troposphere to stratosphere]]
|[https://github.com/geoschem/geos-chem/issues/380 Prevent negative values in the computation of FNO_NOx in PARANOX]
|Seb Eastham (MIT)
|Tina Liu (Harvard)<br>Eimy Bonilla (Harvard)<br>Bob Yantosca (GCST)
|Bug fix
|Bug fix
|
|
*In development
*NOTE: This issue seems to only arise at fine grid resolutions, such as the 0.5&deg; x 0.625&deg; nested grid simulations.


|}
|}


--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 16:05, 6 December 2018 (UTC)
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:21, 24 July 2020 (UTC)


== Current stable version ==
=== 12.9.1 ===


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].
<span style="color:green">'''''This version was released on 17 Jul 2020.'''''</span>


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.
[https://doi.org/10.5281/zenodo.3950473 '''DOI: 10.5281/zenodo.3950473''']


=== 12.1.0 ===
You can use the following Git commands to download the GEOS-Chem 12.9.1 source code and [[GEOS-Chem Unit Tester]] package.


<span style="color:green">'''''This version was released on 26 Nov 2018.'''''</span>
   <nowiki># Download the GEOS-Chem source code
 
  git clone https://github.com/geoschem/geos-chem Code.12.9.1
'''[https://doi.org/10.5281/zenodo.1553349 DOI: 10.5281/zenodo.1553349]'''
  cd Code.12.9.1
 
You can use the following Git commands to download the GEOS-Chem 12.1.0 source code and [[GEOS-Chem Unit Tester]] package.
# 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
   <nowiki># Download the GEOS-Chem source code
  git clone https://github.com/geoschem/geos-chem Code.12.1.0
  cd Code.12.1.0
  git checkout master
  cd ..  
  cd ..  


Line 172: Line 169:
  git clone https://github.com/geoschem/geos-chem-unittest UT
  git clone https://github.com/geoschem/geos-chem-unittest UT
  cd UT
  cd UT
  git checkout master</nowiki>
# 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</nowiki>


Please see the following links for complete information about the validation of GEOS-Chem 12.1.0:
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.9.1|new data directories for this version]] and [[#New data directories in 12.9.0|for version 12.9.0]].
#[[GEOS-Chem_12_benchmark_history#12.1.0|''Approval form for 1-month benchmark simulation 12.1.0'']]


This release contains several new features as well as fixes for issues discovered after the GEOS-Chem 12.0.3 release
This version contains fixes for bugs and technical issues discovered during the 12.9.0 benchmarking process.


{| border=1 cellspacing=0 cellpadding=5  
{| border=1 cellspacing=0 cellpadding=5  
Line 184: Line 182:
!width="200px"|Submitted by
!width="200px"|Submitted by
!width="100px"|Type
!width="100px"|Type
!width="300px"|Notes
!width="300px"|Notes and References


|-
|-valign="top"
!colspan="4" bgcolor="#CCFFFF"|Features affecting the full-chemistry simulation:
!colspan="4" bgcolor="#CCFFFF"|Updates that WILL NOT AFFECT the full-chemistry simulation


|-valign="top"
|-valign="top"
|[[List_of_diagnostics_archived_to_netCDF_format#The_Budget_collection|Budget diagnostics]]
|[https://github.com/geoschem/geos-chem/issues/355 Bug fix: Fixed a lingering issue that caused the GEOS-Chem dry-run not to recognize missing files]
|Lizzie Lundgren ([[GCST]])<br>Chris Holmes (Florida State)
|Bob Yantosca (GCST)
|Diagnostics
|Bug fix
|
|
*This update introduces differences on the level of numerical noise due to unit conversions


|-valign="top"
|-valign="top"
|[[Mineral_dust_aerosols#Anthropogenic_PM2.5_dust_source_in_GEOS-Chem|Anthropogenic PM2.5 dust source]]
|[https://github.com/geoschem/geos-chem/issues/372 Fix run-time error when optional Luo wet deposition scheme is turned on]
|Sajeev Philip (Dalhousie)
|Lizzie Lundgren (GCST)
|Science
|Bug fix
|
|
*This update introduces the following changes:
 
**DST1 emissions increased by 1.09 Tg/mon (13.1 Tg/yr)
**&Delta; Mean OH: -0.000066%
**&Delta; MCF lifetime: 0.0020%
**&Delta; CH4 lifetime: 0.0012%
 
|-valign="top"
|-valign="top"
|[[GEOS-Chem restart files#Restart files in GEOS-Chem 12|GEOS-Chem restart file updates]]  
|[https://github.com/geoschem/geos-chem/issues/369 Fixes for interpolating RCP emissions data via HEMCO]
|Melissa Sulprizio ([[GCST]])
|Jenny Fisher (Wollongong)<br>Melissa Sulprizio (GCST)<br>Bob Yantosca (GCST)
|Bug Fix &<br>Structural
|Bug fix
|
|
*GEOS-Chem Classic only update
*The RCP emissions are turned off by default in the full-chemistry simulations.  This update will not affect benchmark results.
*This update introduces the following changes:
 
**&Delta; Mean OH: -0.016%
|}
**&Delta; MCF lifetime: 0.022%
 
**&Delta; CH4 lifetime: 0.024%
==== New data directories in 12.9.1 ====
 
The following data directories have been added or updated in this version.  You will have to [[Downloading_GEOS-Chem_data_directories|download the directories]] relevant to your simulation.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="200px"|Inventory
!width="100px"|Type
!width="400px"|What was added?
!width="300px"|Directory


|-valign="top"
|-valign="top"
|Updates and fixes for the CEDS anthropogenic emissions inventory:
|RCP
*[[CEDS_anthropogenic_emissions#Add_missing_RCO_sector_to_CEDS_emissions_entries|Add missing RCO sector to CEDS emissions entries]]
|OPTIONAL
*[[CEDS_anthropogenic_emissions#Include_CEDS_ship_emissions|Include CEDS ship emissions as default global ship emissions inventory]]
|[https://github.com/geoschem/geos-chem/issues/369 Fixes for interpolating RCP emissions data via HEMCO]
*[[CEDS_anthropogenic_emissions#Reduce_file_size_for_CEDS_inventory|Reduce file size for CEDS inventory]]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/RCP/v2020-07/MERRA2/README <tt>HEMCO/RCP/v2020-07/</tt>]
|<br>Pengfei Liu (Harvard)<br>Melissa Sulprizio ([[GCST]])<br>Jiawei Zhuang (Harvard)
 
|Bug fix
|}
|
 
*This update introduces the following changes:
 
**&Delta; Mean OH: 0.17%
=== 12.9.0 ===
**&Delta; MCF lifetime: -0.37%
 
**&Delta; CH4 lifetime: -0.40%
<span style="color:green">'''''This version was released on 17 Jul 2020.'''''</span>


|-valign="top"
[https://doi.org/10.5281/zenodo.3950327 '''DOI: 10.5281/zenodo.3950327''']
|HEMCO fixes:
*[[Implementation_of_HEMCO_in_GEOS-Chem#Bug_fix:_Read_data_with_the_.22E.22_cycle_flag_just_once|HEMCO bug fix: prevent excessive attempts to read the HEMCO restart file when using GEOS-Chem "Classic"]]
*[[Implementation_of_HEMCO_in_GEOS-Chem#Add_fix_for_collapsing_model_levels_to_reduced_grid|Add fix for collapsing model levels to reduced grid]]
*[[Implementation_of_HEMCO_in_GEOS-Chem#Fix_unit_conversion_in_HCO_UNIT_GetAreaScal|Fix unit conversion in HCO_UNIT_GetAreaScal]]
|<br>Bob Yantosca ([[GCST]])<br>Melissa Sulprizio ([[GCST]])<br>Erin McDuffie (Dalhousie)
|Bug fix
|
*This update introduces very small changes:
**&Delta; Mean OH: -0.952%
**&Delta; MCF lifetime: 1.454%
**&Delta; CH4 lifetime: 1.502%


|-valign="top"
You can use the following Git commands to download the GEOS-Chem 12.9.0 source code and [[GEOS-Chem Unit Tester]] package.
|[[Boundary_layer_mixing#Mass_is_not_conserved_when_using_non-local_PBL_mixing|Fix mass conservation in non-local PBL mixing]]
 
|Jintai Lin (PKU)
  <nowiki># Download the GEOS-Chem source code
|Bug fix
git clone https://github.com/geoschem/geos-chem Code.12.9.0
|
cd Code.12.9.0
*This update introduces very small changes:
**&Delta; Mean OH: 0.0057%
# Create and checkout a new branch "GC_12.9.0" at the tag "12.9.0"
**&Delta; MCF lifetime: -0.0061%
git checkout -b GC_12.9.0 12.9.0
**&Delta; CH4 lifetime: -0.0073%
cd ..  


|-valign="top"
# Download the GEOS-Chem Unit Tester, from which run directories can be generated
|[[#Allow_for_SZA_to_98_degrees_when_getting_photolysis_rates|Allow for SZA to 98 degrees when getting photolysis rates]]
git clone https://github.com/geoschem/geos-chem-unittest UT
|Eric Fleming (GMAO)
cd UT
|Bug fix
|
# Create and checkout a new branch "GC_12.9.0" at the tag "12.9.0"
*This update introduces the following changes:
git checkout -b GC_12.9.0 12.9.0</nowiki>
**&Delta; Mean OH: 0.3982%
**&Delta; MCF lifetime: -0.3665%
**&Delta; CH4 lifetime: -0.3680%


|-
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.9.0|new data directories for this version]].
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:


|-valign="top"
Please see the following links for complete information about the validation of GEOS-Chem 12.9.0:
|[[FlexGrid|FlexGrid Stage 1: Use HEMCO to read met fields]]
#[[Benchmark/GEOS-Chem_12.9.0#GEOS-Chem_Classic_1-month_benchmark|''1-month benchmark for GEOS-Chem Classic'']]
|Jiawei Zhuang (Harvard)<br>Jintai Lin (PKU)
#[[Benchmark/GEOS-Chem_12.9.0#GCHP_1-month_benchmark|''1-month benchmark for GCHP'']]
|Structural
#[[Benchmark/GEOS-Chem_12.9.0#GEOS-Chem_Classic_1-year_benchmark|''1-year full-chemistry benchmark for GEOS-Chem Classic'']]
|
 
{| 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 AFFECT the full-chemistry simulation


|-valign="top"
|-valign="top"
|[[GEOS-Chem 12#Add support for continuous integration with TravisCI|Add support for continuous integration with TravisCI &ndash; automatically test each commit as soon as it is pushed to Github]]
|[https://www.atmos-chem-phys.net/19/3981/2019/ Updated halogen chemistry]
|Jiawei Zhuang (Harvard)<br>Bob Yantosca ([[GCST]])
|Xuan Wang (Harvard)
|Structural
|Science
|
|
*[https://travis-ci.com/geoschem/geos-chem/builds See build status page here]


|-valign="top"
|-valign="top"
|Added [[List of diagnostics archived to netCDF format|netCDF diagnostics]] in the following areas:
|[http://acmg.seas.harvard.edu/publications/2020/Shah_2020.pdf Improved cloudwater pH]
*[[CH4 simulation]]
|Viral Shah (Harvard)<br>Jonathan Moch (Harvard)
*[[CO2 simulation]]
|Science
*[[POPs simulation|Persistent Organic Pollutants (POPS) simulation]]
*[[Mercury|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.


|-valign="top"
|-valign="top"
|[[Coupling_GEOS-Chem_with_RRTMG#netCDF_inputs_via_HEMCO|Convert input data for RRTMG from bpch to netCDF for input via HEMCO]]
|[https://github.com/geoschem/geos-chem-unittest/pull/20 Update offline lightning data through Dec 2019]
|Bob Yantosca ([[GCST]])
|Lee Murray (Rochester)
|Structural
|Science
|
|


|-valign="top"
|-valign="top"
|[[CH4_simulation#Add_fixes_for_seasonal_scale_factors_in_CH4_simulations|Add fixes for seasonal scale factors in CH4 simulations]]
|Convert GEOS-Chem species database to YAML format, includes:
|Bram Maasakkers (SRON)<br>Melissa Sulprizio ([[GCST]])
*[https://github.com/geoschem/geos-chem/issues/110 Defining all species properties in the species database, not just advected species]
|Bug fix
*[https://github.com/geoschem/geos-chem/issues/216 Initializing the species database with values read from the YAML file]
|Melissa Sulprizio (GCST)<br>Bob Yantosca (GCST)
|Structural
|
|


|-valign="top"
|-valign="top"
|[[GEOS-Chem_v11-02#Code_cleanup_suggestions|Move Fast-JX .dat files from the <tt>geos-chem-unittest</tt> repository to <tt>gcgrid/ExtData</tt>]]
|[https://github.com/geoschem/geos-chem/issues/232 Update GEOS-Chem core to apply masking and scaling to HEMCO inputs]
|Chris Holmes (Florida State)<br>[[GCST]]
|Lizzie Lundgren (GCST)
|Structural
|Structural
|
|
*Will introduce numerical noise differences due to precision change


|-valign="top"
|-valign="top"
|[[GEOS-Chem_12#Update_HEMCO_configuration_file_for_tagged_CO_simulation|Update HEMCO configuration file for the tagged CO simulation]]
|[https://github.com/geoschem/geos-chem/issues/324 Bug fix: Restore missing photolysis reactions from 12.8.0 and add an extra error check]
|Bob Yantosca ([[GCST]])
|Melissa Sulprizio (GCST)
|Bug fix
|Bug fix
|
|


|-valign="top"
|-valign="top"
|Structural updates to facilitate interfacing GEOS-Chem into WRF
|[https://github.com/geoschem/geos-chem/issues/362 Bug fix: remove inefficient code that was slowing down computation of heterogenous chemistry rates]
|Haipeng Lin (Peking U)<br>[[GCST]]
|Bob Yantosca (GCST)
|Structural
|Bug fix
|
|
*This process will be ongoing throughout the GEOS-Chem 12 series of releases.
*Will introduce numerical differences due to removing inconsistently-defined parameters


|-valign="top"
|-valign="top"
|Structural updates to facilitate interfacing GEOS-Chem into GEOS-5
!colspan="4" bgcolor="#CCFFFF"|Updates that WILL NOT AFFECT the full-chemistry simulation
|Christoph Keller (GMAO)<br>Lizzie Lundgren (GCST)
|Structural
|
*This process will be ongoing throughout the GEOS-Chem 12 series of releases.


|-
|-valign="top"
!colspan="4" bgcolor="#CCFFFF"|Features affecting GCHP only:
|[https://github.com/geoschem/geos-chem/issues/312 Corrected issue in GEOS-Chem dry-run where some files were not being properly marked for download]
|Bob Yantosca (GCST)
|Bug fix
|


|-valign="top"
|-valign="top"
|[[GEOS-Chem_12#Fix_masked_anthropogenic_emissions_bug_in_GCHP|Fix masking bug to correctly apply anthropogenic emissions]]
|Bug fixes for the ObsPack diagnostic:
|Lizzie Lundgren ([[GCST]])
*[https://github.com/geoschem/geos-chem/issues/333 Change units of ObsPack specific humidity (Q) field to g/kg]
*[https://github.com/geoschem/geos-chem/issues/337 Restore missing code due to Git merge that caused the OBSPACK MENU of input.geos not to be read]
|Bob Yantosca (GCST)
|Bug fix
|Bug fix
|
|


|-valign="top"
|-valign="top"
|[[GEOS-Chem_12#Fix_regional_tile_file_used_for_APEI_inventory_in_GCHP|Remove erroneous 180 degree longitude shift in APEI regridding]]
|Fixes for reading meteorology fields in HEMCO:
|Lizzie Lundgren ([[GCST]])
*[https://github.com/geoschem/geos-chem/issues/279 Skip reading FLASH_DENS and CONV_DEPTH fields when lightning NOx extension is turned off]
*[https://github.com/geoschem/geos-chem/issues/357 Change time cycle flag for meteorology fields to use exact date]
|Melissa Sulprizio (GCST)
|Bug fix
|Bug fix
|
|


|-valign="top"
|-valign="top"
|Move GCHP run directory creation from GEOS-Chem Unit Tester to GCHP repository
|[https://github.com/geoschem/geos-chem/issues/353 Restore missing metadata for satellite timeseries diagnostics]
|Lizzie Lundgren ([[GCST]])
|Melissa Sulprizio (GCST)
|Structural
|Bug fix
|
 
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/371 Fix bug compiling with Luo wet deposition scheme option]
|Lizzie Lundgren (GCST)
|Bug fix
|
 
|-valign="top"
!colspan="4" bgcolor="#CCFFFF"|Updates that affect GCHP only
 
|-valign="top"
|[https://github.com/geoschem/gchp/issues/70 Fix bug where non-advected species not updated in restart file]
|Sebastian Eastham (MIT)
|Bug fix
|
|


|}
|}


--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 15:21, 26 November 2018 (UTC)
==== New data directories in 12.9.0 ====
 
The following data directories have been added or updated in this version.  You will have to [[Downloading_GEOS-Chem_data_directories|download the directories]] relevant to your simulation.


== Previously released stable versions ==
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="200px"|Inventory
!width="100px"|Type
!width="400px"|What was added?
!width="300px"|Directory


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.
|-valign="top"
|OFFLINE_LIGHTNING
|DEFAULT<br>(full-chemistry simulations)
|[https://github.com/geoschem/geos-chem-unittest/pull/20 Update offline lightning data through Dec 2019]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/OFFLINE_LIGHTNING/v2020-03/MERRA2/README <tt>HEMCO/OFFLINE_LIGHTNING/v2020-03/</tt>]


=== 12.0.3 ===
|}


<span style="color:green">'''''This version was released on 16 Oct 2018.'''''</span>
=== 12.8.2 ===


'''[https://doi.org/10.5281/zenodo.1464210 DOI: 10.5281/zenodo.1464210]'''
<span style="color:green">'''''This version was released on 27 May 2020.'''''</span>


You can use the following Git commands to download the GEOS-Chem 12.0.3 source code and [[GEOS-Chem Unit Tester]] package.
[https://doi.org/10.5281/zenodo.3860693 '''DOI: 10.5281/zenodo.3860693''']


  <nowiki># Download the GEOS-Chem source code
GEOS-Chem 12.8.2 contains minor fixes, as well as structural changes needed for WRF-GC development.
git clone https://github.com/geoschem/geos-chem Code.12.0.3
cd Code.12.0.3
git checkout master
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
git checkout master</nowiki>


{| border=1 cellspacing=0 cellpadding=5  
{| border=1 cellspacing=0 cellpadding=5  
Line 383: Line 394:
!width="200px"|Submitted by
!width="200px"|Submitted by
!width="100px"|Type
!width="100px"|Type
!width="300px"|Notes
!width="300px"|Notes and References


|-
|-valign="top"
!colspan="4" bgcolor="#CCFFFF"|Features affecting GCHP only:
!colspan="4" bgcolor="#CCFFFF"|Updates that WILL NOT AFFECT the full-chemistry simulation


|-valign="top"
|-valign="top"
|[[#Fix_incorrect_run_configuration_for_offline_sea_salt_emissions_in_GCHP|Fix incorrect run configuration for offline sea salt emissions in GCHP]]
|[https://github.com/geoschem/geos-chem/commit/2770922e7b6254a0a77f62ec695e2560e74cedb7 Bug fix: Set version numbers to 12.8.2 in <tt>CMakeLists.txt</tt> and <tt>gc_classic_version.H</tt>]
|Sebastian Eastham (MIT)
|Bob Yantosca (GCST)
|Bug fix
|Bug fix
|
|


|-valign="top"
|-valign="top"
|[[#Fix_bug_in_application_of_CFC_surface_mixing_ratios_in_GCHP|Fix bug in application of CFC surface mixing ratios in GCHP]]
|Updates to facilitate WRF-GC development:
|Sebastian Eastham (MIT)
*[https://github.com/geoschem/geos-chem/pull/319 Ignore KPP integrate errors and send them to a log file instead]
|Bug fix
*[https://github.com/geoschem/geos-chem/pull/323 Wrap OpenMP-specific code with <tt>#ifdef MODEL_CLASSIC</tt> and <tt>#ifndef NO_OMP</tt> blocks]
*[https://github.com/geoschem/geos-chem/pull/325 Move certain module variables into the <tt>State_Met</tt> and <tt>State_Chm</tt> objects]
*[https://github.com/geoschem/geos-chem/pull/326 Exit INIT_DRYDEP immediately if arrays have already been allocated]
|Haipeng Lin (Harvard)  
|Structural
|
|


|}
|}


--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 18:21, 16 October 2018 (UTC)
=== 12.8.1 ===


=== 12.0.2 ===
<span style="color:green">'''''This version was released on 21 May 2020.'''''</span>


<span style="color:green">'''''This version was released on 10 Oct 2018.'''''</span>
[https://doi.org/10.5281/zenodo.3837666 '''DOI: 10.5281/zenodo.3837666''']


[https://doi.org/10.5281/zenodo.1455215 '''DOI: 10.5281/zenodo.1455215''']
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 12.0.2 source code and [[GEOS-Chem Unit Tester]] package.
You can use the following Git commands to download the GEOS-Chem 12.8.1 source code and [[GEOS-Chem Unit Tester]] package.


   <nowiki># Download the GEOS-Chem source code
   <nowiki># Download the GEOS-Chem source code
  git clone https://github.com/geoschem/geos-chem Code.12.0.2
  git clone https://github.com/geoschem/geos-chem Code.12.8.1
  cd Code.12.0.2
  cd Code.12.8.1
  git checkout master
# 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 ..  
  cd ..  


Line 421: Line 438:
  git clone https://github.com/geoschem/geos-chem-unittest UT
  git clone https://github.com/geoschem/geos-chem-unittest UT
  cd UT
  cd UT
  git checkout master</nowiki>
# 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</nowiki>


This version contains fixes for specialty simulations that were identified after the release of [[GEOS-Chem 12#12.0.1|GEOS-Chem 12.0.1]].
'''<span style="color:red">For GCHP users only:</span> ''' Make sure you also download the [[#New data directories in 12.8.1|new data directories for this version]].


{| border=1 cellspacing=0 cellpadding=5  
{| border=1 cellspacing=0 cellpadding=5  
Line 433: Line 452:


|-
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry (benchmark) simulation:
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:


|-valign="top"
|-valign="top"
|[[#Fixed_local-time_averaging_in_ND51_and_ND51b_satellite_timeseries_diagnostics|Fixed local-time averaging in ND51 and ND51b satellite timeseries diagnostics]]
|[https://github.com/geoschem/geos-chem/issues/318 Update the dry-run download data script to make files group-writeable]
|Bo Zheng (NIA)
|Bob Yantosca (GCST)
|Bug fix
|Bug fix
|Implemented 04 Oct 2018
|


|-valign="top"
|-valign="top"
|[[TOMAS_aerosol_microphysics#Fixes_for_missing_biomass_emissions_and_incorrect_aerosol_dry_deposition|Fixes to correct missing BC/OC biomass emissions and incorrect aerosol drydep in TOMAS simulations]]
|[https://github.com/geoschem/geos-chem/issues/240 Add more timers for gas-phase chemistry]
|Pengfei Liu (Harvard)
|Melissa Sulprizio (GCST)
|Bug fix
|Structural
|Implemented 25 Sep 2018
|


|-valign="top"
|-valign="top"
|[[CO2_simulation#CO2_emissions_are_double_counted|Avoid double-counting of emissions in the CO2 simulation]]
|[https://github.com/geoschem/geos-chem/issues/306 Reduce the amount of memory that GEOS-Chem dry-runs require]
|Beata Bukosa (U. Wollongong)<br>Christoph Keller (GMAO)
|Bob Yantosca (GCST)
|Bug fix
|Bug fix
|Implemented 24 Sep 2018.
|


|}
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/303 Add bounds-checking and floating point exceptions to CMake "Debug" target]
|Melissa Sulprizio (GCST)
|Structural
|


--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 18:21, 16 October 2018 (UTC)
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/293 Fix incorrect indexing for AOD diagnostics]
|Melissa Sulprizio (GCST)
|Bug fix
|


=== 12.0.1 ===
|-valign="top"
|Updates for GEOS-Chem "Classic" HISTORY diagnostics:
*[https://github.com/geoschem/geos-chem/issues/269 Fix for instantaneous timeseries diagnostics to avoid overwriting hour zero]
*[https://github.com/geoschem/geos-chem/issues/305 Fix to allow diagnostics with frequency="End" to properly straddle year-end boundaries]
|Bob Yantosca (GCST)
|Bug fix
|


<span style="color:green">'''''This version was released on 24 Aug 2018.'''''</span>
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/268  Allow for missing species in boundary conditions]
|Melissa Sulprizio (GCST)
|Bug fix
|


'''[https://doi.org/10.5281/zenodo.1403144 DOI: 10.5281/zenodo.1403144]'''
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/251 Disable FlexGrid checks to allow for running with any horizontal or vertical grid]
|Melissa Sulprizio (GCST)
|Bug fix
|


You can use the following Git commands to download the GEOS-Chem 12.0.1 source code and [[GEOS-Chem Unit Tester]] package.
|-valign="top"
 
|Fixes for WRF-GC and CESM-GC, including:
  <nowiki># Download the GEOS-Chem source code
*[https://github.com/geoschem/geos-chem/pull/257 Fix Init_Pressure error for NZ /= 47, 72]
git clone https://github.com/geoschem/geos-chem Code.12.0.1
*[https://github.com/geoschem/geos-chem/pull/274 Only perform pole-averaging of regridded data if actually regridding to the poles]
cd Code.12.0.1
*[https://github.com/geoschem/geos-chem/pull/282 Add a State_Grid%ID field]
git checkout master
|Haipeng Lin (Harvard)
cd ..
|Bug fix
 
|
# 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
git checkout master</nowiki>
 
GEOS-Chem 12.0.1 contains fixes for minor issues discovered after the GEOS-Chem 12.0.0 release.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry (benchmark) simulation:


|-valign="top"
|-valign="top"
|[[#Fix typo when registering the State_Chm%SSAlk field|Fix typo when registering the <tt>State_Chm%SSAlk</tt> field]]
|[https://github.com/geoschem/geos-chem/issues/292 Add fix for POPs emissions diagnostics]
|Shuting Zhai (U. Washington)<br>[[GCST]]
|Melissa Sulprizio (GCST)
|Bug fix
|Bug fix
|
|


|-valign="top"
|-valign="top"
|Add fixes for several compilation issues:
|[https://github.com/geoschem/HEMCO/issues/30  Avoid memory corruption bug in HEMCO when certain debug flags are on]
#Nullify rather than deallocate 3D met arrays for compatibility with gfortran 6+ when using GCHP
|Sebastian Eastham (MIT)
#[[GEOS-Chem_Makefile_Structure#Add a more robust test for netCDF-Fortran in Makefile_header.mk|Add a more robust test for netCDF-Fortran in Makefile_header.mk]]
|Bug fix
#[[GNU_Fortran_compiler#Compiliation_issues_with_GNU_Fortran_8.2.0|Fix compilation issues encountered with GNU Fortran 8.2.0]]
|
#[[Intel_Fortran_Compiler#Compilation_issues_with_Intel_Fortran_18|Fix compilation issues encountered with Intel Fortran 18]]


|[[GCST]]
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/297  Fix bug causing seg fault when ConcAboveSfc diagnostic collection is on]
|Lizzie Lundgren (Harvard)
|Bug fix
|Bug fix
|
|


|-valign="top"
|-valign="top"
|[[Mercury#Restore_biomass_emissions_and_do_not_double_count_anthropogenic_emissions|Fixes for the Hg specialty simualtion: Restore biomass emissions and do not double-count anthropogenic emissions]]
|[https://github.com/geoschem/geos-chem/issues/304  Fix bug causing crash if not starting on the first day and time of the month]
|Colin Thackray (Harvard)
|Lizzie Lundgren (Harvard)
|Bug fix
|Bug fix
|
|
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting GCHP only:


|-valign="top"
|-valign="top"
|[[Sulfate aerosols#Fix mis-indexing in the ND05 diagnostic|Fix mis-indexing in the ND05 diagnostic]]
|[https://github.com/geoschem/geos-chem/issues/313 Fix incorrect GCHP config file entry for surf_iodide source file in 12.8.0]
|[[GCST]]
|Lizzie Lundgren (Harvard)
|Bug fix
|Bug fix
|
|


|-valign="top"
|-valign="top"
|Minor updates to facilitate interfacing GEOS-Chem into GEOS-5
|[https://github.com/GEOS-ESM/MAPL/issues/279 Avoid unexpected behavior if dynamic timestep is changed to non-default values]
|Lizzie Lundgren (GCST)
|Lizzie Lundgren (Harvard)
|Structural
|Bug fix
|
|


|}
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/271 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


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:31, 10 October 2018 (UTC)
|-valign="top"
|[https://github.com/geoschem/gcpy/issues/67 Add internal state met variables to benchmark and transport tracers simulations]
|Lizzie Lundgren (Harvard)
|Output data
|
*For use in benchmarking


=== 12.0.0 ===
|-valign="top"
|[https://github.com/geoschem/gcpy/issues/40 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 [[Downloading_GEOS-Chem_data_directories|download the directories]] relevant to your simulation.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="200px"|Inventory
!width="100px"|Type
!width="400px"|What was added?
!width="300px"|Directory
 
|-valign="top"
|[[Grid-independent_emissions#Biogenic_VOC_emissions|OFFLINE_BIOVOC]]
|Default
|[https://github.com/geoschem/geos-chem/issues/271 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.]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/OFFLINE_BIOVOC/v2019-10/ <tt>HEMCO/OFFLINE_BIOVOC/v2019-10</tt>]
 
 
|}
 
=== 12.8.0 ===


<span style="color:green">'''''This version was released on 10 Aug 2018'''''</span>
<span style="color:green">'''''This version was released on 04 May 2020.'''''</span>


[https://doi.org/10.5281/zenodo.1343547 '''DOI 10.5281/zenodo.1343547''']
'''[https://doi.org/10.5281/zenodo.3784796 DOI: 10.5281/zenodo.3784796]'''


You can use the following Git commands to download the GEOS-Chem 12.0.0 source code and [[GEOS-Chem Unit Tester]] package.
You can use the following Git commands to download the GEOS-Chem 12.8.0 source code and [[GEOS-Chem Unit Tester]] package.


   <nowiki># Download the GEOS-Chem source code
   <nowiki># Download the GEOS-Chem source code
  git clone https://github.com/geoschem/geos-chem Code.12.0.0
  git clone https://github.com/geoschem/geos-chem Code.12.8.0
  cd Code.12.0.0
  cd Code.12.8.0
  git checkout -b 12.0.0
# 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 ..  
  cd ..  


Line 544: Line 614:
  git clone https://github.com/geoschem/geos-chem-unittest UT
  git clone https://github.com/geoschem/geos-chem-unittest UT
  cd UT
  cd UT
  git checkout -b 12.0.0</nowiki>
# 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</nowiki>


For more information about getting set up with GEOS-Chem, please see the [http://manual.geos-chem.org GEOS-Chem Online User's Guide].
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.8.0|new data directories for this version]].


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#v11-02 GEOS-Chem v11-02 release candidate|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 12.8.0:
#[[Benchmark/GEOS-Chem_12.8.0#GEOS-Chem_Classic_1-month_benchmark|''1-month benchmark for GEOS-Chem Classic'']]
#[[Benchmark/GEOS-Chem_12.8.0#GCHP_1-month_benchmark|''1-month benchmark for GCHP'']]
#[[Benchmark/GEOS-Chem_12.8.0#1-year_Transport_Tracers_benchmarks|''1-year transport tracer benchmark for GEOS-Chem Classic'']]
#[[Benchmark/GEOS-Chem_12.8.0#GEOS-Chem_Classic_1-year_benchmark|''1-year full-chemistry benchmark for GEOS-Chem Classic'']]


Please see the following links for complete information about the validation of GEOS-Chem 12.0.0:
{| border=1 cellspacing=0 cellpadding=5  
#[[GEOS-Chem_12_benchmark_history#12.0.0|''Approval form for 1-month benchmark simulation 12.0.0'']]
#[[GEOS-Chem_12_benchmark_history#12.0.0-Run0|''Results for 1-year benchmark simulation 12.0.0-Run0'']]
 
{| border=1 cellspacing=0 cellpadding=5  
|-bgcolor="#CCCCCC"
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="500px"|Feature
!width="200px"|Submitted by
!width="200px"|Submitted by
!width="100px"|Type
!width="100px"|Type
!width="300px"|Notes
!width="300px"|Notes and References


|-
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting the full-chemistry (benchmark) simulation:
!colspan="4" bgcolor="#CCFFFF"|Features affecting the full-chemistry simulation:


|-valign="top"
|-valign="top"
|[[Trash_burning_emissions#Avoid_double_counting_trash_emissions|Turn off TRASH emissions by default to avoid double counting]]
|[https://www.atmos-chem-phys.net/19/9613/2019/ Isoprene chemistry]
|[[GCST]]<br>Eloise Marais (U. Birmingham)
|Kelvin Bates (Harvard)
|Bug fix
|Science
|
|
*This update introduces relatively small changes:
*[https://github.com/geoschem/geos-chem/pull/142 geoschem/geos-chem PR #142]
**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%


|-valign="top"
|-valign="top"
|[[GEOS-Chem 12#Add_entries_to_HEMCO_Config.rc_for_SOAP_and_pFe_in_CEDS_inventory|Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory]]
|[https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2017GL075270 Wet deposition parameterization]
|[[GCST]]
|Kelvin Bates (Harvard)<br>Sarah Safieddine (MIT)
|Bug fix
|Science
|
|
*This update introduces relatively small changes:
*[https://github.com/geoschem/geos-chem/pull/142 geoschem/geos-chem PR #142]
**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%


|-valign="top"
|-valign="top"
|[[#Bug fix for liquid water content in gckpp_HetRates.F90|Bug fix for liquid water content in gckpp_HetRates.F90]]
|[https://www.atmos-chem-phys.net/20/4227/2020/ Ozone deposition to the ocean]
|Jiayue Huang (U. Washington)<br>Quanjie Chen (U. Washington)
|Ryan Pound (York)<br>Mat Evans (York)
|Bug fix
|Science
|
|
*This update introduces relatively small changes:
*[https://github.com/geoschem/geos-chem/pull/170 geoschem/geos-chem PR #170]
**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%


|-valign="top"
|-valign="top"
|[[GEOS-Chem 12#Bug_fix_for_CH4_boundary_conditions|Bug fix for CH4 boundary conditions]]
|Use online [[Mineral_dust_aerosols|DustDead]], [[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions|MEGAN]], [[Sea_salt_aerosols|SeaSalt]], and [[Hudman_et_al_2012_soil_NOx_emissions_algorithm|SoilNOx]] emissions for benchmark simulations
|Lee Murray (Rochester)
|Melissa Sulprizio (GCST)
|Bug fix
|Science
|
|
*Results approved by Lee Murray
*Standard simulations still use [[Grid-independent_emissions|high-resolution offline emissions]] by default
*This update introduces small changes:
**Mean OH decreased by 0.48%
**MCF lifetime increased by 0.82%
**O3 STE decreased by: 0.022%


|-valign="top"
|-valign="top"
|[[GEOS-Chem 12#Fixed typo in call to GAMMA_HOBr_AER|Fixed typo in call to GAMMA_HOBr_AER]]
|[https://github.com/geoschem/geos-chem/issues/233 Shift CMIP6 time from middle to start of month to allow start in January]
|Xuan Wang<br>[[GCST]]
|Lizzie Lundgren (GCST)
|Bug fix
|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%
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:
**CH4 lifetime increased by 0.084%
**O3 STE flux decreased by 0.005%


|-valign="top"
|-valign="top"
|Correct issues when specifying [[DICE-Africa anthropogenic emissions inventory|DICE-Africa emissions]]:
|[[GFED4_biomass_burning_emissions|GFED 4.1s beta emissions for 2017-2019]]
*[[DICE-Africa_anthropogenic_emissions_inventory#Avoid_double-counting_between_DICE-Africa_and_other_inventories|Avoid double-counting between DICE-Africa and other inventories]]
|Maggie Marvin (U. Edinburgh)
*[[DICE-Africa_anthropogenic_emissions_inventory#Use_unique_names_for_DICE-Africa_entries_in_HEMCO_Config.rc|Use unique names for DICE-Africa entries in the <tt>HEMCO_Config.rc</tt> file]]
|Science
|Eloise Marais (U. Birmingham)<br>[[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%


|-valign="top"
|-valign="top"
|[[Organics_Working_Group#Add_missing_Criegee_intermediate_reaction|Add missing Criegee intermediate reaction]]
|[https://github.com/geoschem/geos-chem/issues/137 Replace <tt>State_Chm%nAero</tt> with <tt>State_Chm%nAeroSpc</tt> and <tt>State_Chm%nAeroType</tt>]
|Xin Chen (UMN)
|Seb Eastham (MIT)<br>Bob Yantosca (GCST)
|Bug fix
|Structural
|
|
*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%


|-valign="top"
|-valign="top"
|[[Ship_emissions#Fix_bug_in_ARCTAS_SHIP_SO2_scale_factors|Bug fix for ARCTAS_SHIP in <tt>HEMCO_Config.rc</tt> files]]
|[https://github.com/geoschem/geos-chem/issues/92 Convert all files in <tt>GeosCore</tt>, <tt>GeosUtil</tt>, and <tt>Headers</tt> to <tt>.F90</tt>]
|Barron Henderson (EPA)
|Melissa Sulprizio (GCST)
|Bug Fix
|Structural
|
|
*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


|-valign="top"
|-valign="top"
|[[FlexChem#FlexChem bug fix: do not zero ACTA, EOH, HCOOH|Bug fix in FlexChem: do not zero out ACTA, EOH, HCOOH concentrations]]
|[https://github.com/geoschem/geos-chem/issues/247 Change GEOS-Chem timers from a CPP switch to an option in input.geos]
|Katie Travis (MIT)
|Melissa Sulprizio (GCST)
|Bug Fix
|Structural
|
|
*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%


|-valign="top"
|-valign="top"
|[[GFED4_biomass_burning_emissions#Years_2015_and_2016_have_been_added|Add GFED4.1 data for 2015 and 2016; Use GFED4.1 2016 in benchmarks]]
|[https://github.com/geoschem/geos-chem/issues/250 Remove potential for surface CH4 retrieval error in SET_CH4 due to reliance on HEMCO emissions year]
|Kate O'Dell (CSU)<br>[[GCST]]
|Christoph Keller (GMAO)
|Science
|Bug fix
|
|
*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%


|-
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:
!colspan="4" bgcolor="#CCFFFF"|Features affecting GCHP only:


|-valign="top"
|-valign="top"
|Bug fixes for stratospheric chemistry:
|[https://github.com/geoschem/gchp/issues/64 Fix leap year handling bug in GCHP multi-run script]
*[[Stratospheric_chemistry#Disable_STE_calculation_printed_to_log_file|Disable STE calculation printed to log file]]
|Lizzie Lundgren (Harvard)
*[[Linoz_stratospheric_ozone_chemistry#Turn_on_Synoz_when_Linoz_is_set_to_false_in_input.geos|Turn on Synoz when Linoz is set to false in input.geos]]
|Bug Fix
|[[GCST]]
|Bug fix
|
|


|-valign="top"
|-valign="top"
|[[Lightning_NOx_emissions#Limit_flash_rate_density_in_hcox_lightnox_mod.F90|Limit flash rate density in hcox_lightnox_mod.F90]]
|[https://github.com/geoschem/gchp/issues/34 Fix SH surface ozone bias]
|Lee Murray (Rochester)
|Sebastian Eastham (MIT)<br>Lizzie Lundgren (Harvard)
|Bug fix
|Bug Fix
|
|
 
|}
 
==== New data directories in 12.8.0 ====


|-valign="top"
The following data directories have been added or updated in this version.  You will have to [[Downloading_GEOS-Chem_data_directories|download the directories]] relevant to your simulation.
|[[Coupling_GEOS-Chem_with_NCAR_models#WRF|Initial structural modifications for interfacing GEOS-Chem into WRF]]
|Haipeng Lin (Peking U.)
|Structural
|
*This process is ongoing in GEOS-Chem 12


|-
{| border=1 cellspacing=0 cellpadding=5
|[[Mercury#Added_chemistry_and_ocean_from_Horowitz_et_al._2017|Minor fixes for mercury chemistry updates implemented in v11-02f]]
|-bgcolor="#CCCCCC"
|Colin Thackray (Harvard)
!width="200px"|Inventory
|Bug fix
!width="100px"|Type
|
!width="400px"|What was added?
!width="300px"|Directory


|-valign="top"
|-valign="top"
|[[MERRA-2_implementation_details#Default_timestep_for_MERRA-2_nested_grid_simulations|Restore default timestep for MERRA-2 nested grid simulations to 10/20]]
|CMIP6
|Ke Li (Harvard)
|DEFAULT<br>(UCX-based simulations)
|Bug fix
|[https://github.com/geoschem/geos-chem/issues/233 Shift time values from middle of month to start of month]
|
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/CMIP6/v2020-03/README <tt>HEMCO/CMIP6/v2020-03</tt>]
 
|-valign-"top"
|OCEAN_O3_DRYDEP
|DEFAULT
|[https://www.atmos-chem-phys-discuss.net/acp-2019-1043/ Ozone deposition to the ocean]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/OCEAN_O3_DRYDEP/v2020-02/README <tt>HEMCO/OCEAN_O3_DRYDEP/v2020-02</tt>]


|-valign="top"
|-valign="top"
|[[GEOS-Chem 12#Remove_duplicate_C3HI_spectrum_in_FJX_spec.dat_and_FJX_j2j.dat|Remove duplicate C3HI spectrum in FJX_spec.dat and FJX_j2j.dat]]
|[[GFED4_biomass_burning_emissions|GFED4]]
|Tomas Sherwen (York)
|DEFAULT
|Bug fix
|GFED 4.1s beta emissions for 2017-2019 (previous years are unchanged from <tt>GFED4/v2015-10</tt>)
|
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/GFED4/v2020-02README <tt>HEMCO/GFED4/v2020-02</tt>]
*A difference test w/r/t the previous commit yielded identical results
 
|}
 
=== 12.7.2 ===


|-valign="top"
<span style="color:green">'''''This version was released on 09 Mar 2020.'''''</span>
|[[GEOS-Chem 12#Fixed typo that prevented PM2.5 from being archived to netCDF output|Fixed typo that prevented PM2.5 from being archived to netCDF output]]
|Jonathan Moch (Harvard)<br>[[GCST]]
|Bug fix
|


|-valign="top"
'''[https://doi.org/10.5281/zenodo.3701669 DOI: 10.5281/zenodo.3701669]'''
|[[Two-way_coupling_between_global_and_nested_GEOS-Chem_models|Bring two-way nested-grid code option up-to-date]]
|Yingying Yan (PKU)<br>Jintai Lin (PKU)
|Structural
|
*This option is invoked by compiling with <tt>EXCHANGE=y</tt>
*A difference test w/r/t the previous commit yielded identical results.


|-valign="top"
You can use the following Git commands to download the GEOS-Chem 12.7.2 source code and [[GEOS-Chem Unit Tester]] package.
|[[Planeflight_diagnostic#Do_not_force_L.3D1_by_default_in_planeflight_mod.F|Do not force L=1 by default in planeflight_mod.F]]
|Katie Travis (MIT)<br>[[GCST]]
|Bug fix
|


|-valign="top"
  <nowiki># Download the GEOS-Chem source code
|[[#Add PH2O2 to the default list of prod/loss families in the KPP mechanisms|Add PH2O2 to the default list of prod/loss families in the KPP mechanisms]]
git clone https://github.com/geoschem/geos-chem Code.12.7.2
|[[GCST]]
cd Code.12.7.2
|Structural
# 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</nowiki>
 
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.7.2|new data directories for this version]].
 
This version fixed several minor issues identified during the [[#12.7.0|12.7.0]] benchmarking process.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes and References
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting the full-chemistry simulation:
 
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/211 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)<br>[[Transport Working Group]]<br>Bob Yantosca (GCST)
|Bug fix
|
|
*This update facilitates saving out oxidant fields from a full-chemistry simulation that can be used to drive an aerosol-only simulation.


|-valign="top"
|-valign="top"
|Update to HEMCO v2.1.008, which includes minor updates:
|[https://github.com/geoschem/geos-chem/issues/226 Bug fix for reading 3-hourly boundary condition files after hour 21]
#[[Implementation of HEMCO in GEOS-Chem#Fixed_error_in_HEMCO_.22exact.22_time_option|Fixed error in HEMCO "exact" cycling option]]
|Melissa Sulprizio (GCST)
#*NOTE: This update introduced an unforeseen side-effect which will be fixed in [[#12.1.0|GEOS-Chem 12.1.0]].
|Bug fix
Update to HEMCO v2.1.007, which includes minor updates:
|
#[[Implementation of HEMCO in GEOS-Chem#Stop with error if multiple containers have the same name|Stop with error if multiple containers have the same name]]
#[[Implementation of HEMCO in GEOS-Chem#Bug fix for distributing emissions in the vertical dimension|Bug fix for distributing emissions in the vertical dimension]]
#[[Implementation of HEMCO in GEOS-Chem#Add extra error checks in HEMCO standalone module|Add extra error checks in HEMCO standalone module]]
#[[Implementation of HEMCO in GEOS-Chem#Remove null string character from netCDF unit string|Remove null string character from netCDF unit string]]
#[[Implementation_of_HEMCO_in_GEOS-Chem#Bug fix for HEMCO soil NOx error with ifort 17|Bug fix for HEMCO soil NOx error with ifort 17]]
|[[GCST]]<br>Christoph Keller<br>Jenny Fisher
|Structural &<br>Bug fix
|


|-valign="top"
|-valign="top"
|[[GEOS-Chem 12#Bug fix for reference time in netCDF diagnostic files|Bug fix for reference time in netCDF diagnostic files]]
|[https://github.com/geoschem/geos-chem/pull/225 Remove unused routines in regrid_a2a_mod.F90]
|[[GCST]]
|Haipeng Lin (Harvard)
|Bug fix
|Structural
|
|


|-valign="top"
|-
|Updates for [[QFED biomass burning emissions]]:
!colspan="4" bgcolor="#CCFFFF"|Features affecting the GCHP only:
#[[QFED biomass burning emissions#Update to QFED v2.5r1|Update to QFED v2.5r1]]
#[[QFED_biomass_burning_emissions#Fix_QFED_files_for_2016.2F10.2F13|Fix QFED v2.4r6 files for 2016/10/13]]
|Christoph Keller (NASA GMAO)
|Bug fix
|


|-valign="top"
|-valign="top"
|[[GEOS-Chem_12#Fix_issues_in_complexSOA_and_complexSOA_SVPOA_restart_files|Fix issues in complexSOA and complexSOA_SVPOA restart files]]
|[https://github.com/geoschem/geos-chem/issues/219 Fix pointer retrieval error in SET_CH4 introduced in 12.7.0 when running at c180+]
|Eloise Marais (U. Birmingham)
*NOTE: This also corrects a long-standing and previously unidentified issue when running with reduced timesteps
|Lizzie Lundgren (GCST)
|Bug fix
|Bug fix
|
|
*[https://github.com/geoschem/gchp/issues/62 geoschem/gchp #62]


|-valign="top"
|-valign="top"
|[[GEOS-Chem 12#Avoid double counting CEDS and GEIA NH3 biofuel emissions|Avoid double counting CEDS and GEIA NH3 biofuel emissions]]
|[https://github.com/geoschem/gchp/issues/59 Use new Ordonez files to avoid error in MAPL when running at c360]
|Christoph Keller (NASA/GMAO)<br>[[GCST]]
|Lizzie Lundgren (GCST)
|Bug fix
|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 <tt>HEMCO_Config.rc</tt> files that ship with the [[GEOS-Chem Unit Tester]].


|-valign="top"
|}
|[[Coupling_GEOS-Chem_with_RRTMG#Bug_fixes_for_RRTMG_in_v11-02|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.


|-valign="top"
==== New data directories in 12.7.2 ====
|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.


|}
The following data directories have been added or updated in this version.  You will have to [[Downloading_GEOS-Chem_data_directories|download the directories]] relevant to your simulation.
 
== New data directories ==
 
The following [[HEMCO data directories]] have been added or updated for GEOS-Chem 12.  You will have to [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|download the directories]] relevant to your simulation.


{| border=1 cellspacing=0 cellpadding=5
{| border=1 cellspacing=0 cellpadding=5
Line 813: Line 835:
!width="100px"|Type
!width="100px"|Type
!width="400px"|What was added?
!width="400px"|What was added?
!width="100px"|Version added
!width="300px"|Directory
!width="300px"|Directory


|-valign="top"
|-valign="top"
|[[Coupling GEOS-Chem with RRTMG|RRTMG input data]]
|[[Halogen_chemistry_mechanism#Source_code_and_data_files|IODINE]]
|OPTIONAL
|Default (GCHP)
|[[Coupling_GEOS-Chem_with_RRTMG#netCDF_inputs_via_HEMCO|netCDF input data files for the RRTMG specialty simulation (converted from the old "binary punch" format files)]]
|[https://github.com/geoschem/gchp/issues/59 Shifted latitude range]
|[[#12.1.0|12.1.0]]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/IODINE/v2020-02/ <tt>HEMCO/IODINE/v2020-02</tt>]
|<tt>HEMCO/RRTMG/v2018-11/</tt>


|-valign="top"
|}
|[[CEDS anthropogenic emissions]]
|DEFAULT
|[[CEDS_anthropogenic_emissions#Reduce_file_size_for_CEDS_inventory|Reduce file size for CEDS inventory]]
|[[#12.1.0|12.1.0]]
|<tt>HEMCO/CEDS/v2018-08/YYYY</tt>


|-valign="top"
=== 12.7.1 ===
|[[QFED biomass burning emissions]]
|OPTIONAL
|New data files for QFED v2.5r1
|[[#12.0.0|12.0.0]]
|<tt>HEMCO/QFED/v2018-07</tt>


|-valign="top"
<span style="color:green">'''''This version was released on 19 Feb 2020.'''''</span>
|[[GFED4 biomass burning emissions]]
|DEFAULT
|[[GFED4 biomass_burning_emissions#Years_2015_and_2016_have_been_added|GFED4.1 data files for 2015 and 2016 have been added]]
|[[#12.0.0|12.0.0]]
|<tt>HEMCO/GFED4/v2015-10/2015</tt><br><tt>HEMCO/GFED4/v2015-10/2016</tt>


|-valign="top"
'''[https://doi.org/10.5281/zenodo.3676008 DOI: 10.5281/zenodo.3676008]'''
|[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions|MEGAN]]
|DEFAULT
|[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Global_0.25x0.25_MEGAN_input_and_MODIS_LAI|Global 0.25x0.3125 CLM4 PFT and emission factor input files for MEGAN]]
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|<tt>HEMCO/MEGAN/v2017-07/</tt>


|-valign="top"
You can use the following Git commands to download the GEOS-Chem 12.7.1 source code and [[GEOS-Chem Unit Tester]] package.
|[[MODIS_leaf_area_indices|MODIS LAI]]
|DEFAULT
|[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Global_0.25x0.25_MEGAN_input_and_MODIS_LAI|Updated 0.25 x 0.25 MODIS LAI files (2005-2011)]]
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|<tt>CHEM_INPUTS/MODIS_LAI_201707/</tt>


|-valign="top"
  <nowiki># Download the GEOS-Chem source code
|[[Lightning_NOx_emissions|Lightning NOx]]
git clone https://github.com/geoschem/geos-chem Code.12.7.1
|DEFAULT
cd Code.12.7.1
|GEOS-FP OTD-LIS redistribution factors for Apr 2012 - Jul 2017 and MERRA-2 OTD-LIS redistribution factors for any date
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
# Create and checkout a new branch "GC_12.7.1" at the tag "12.7.1"
|<tt>HEMCO/LIGHTNOX/v2017-09/</tt>
git checkout -b GC_12.7.1 12.7.1
cd ..


|-valign="top"
# Download the GEOS-Chem Unit Tester, from which run directories can be generated
|[[Volcanic_SO2_emissions_from_Aerocom|Volcanic SO2 emissions]]
git clone https://github.com/geoschem/geos-chem-unittest UT
|DEFAULT
cd UT
|[[Volcanic_SO2_emissions_from_Aerocom#OMI-based_volcanic_emissions|OMI-based volcanic emissions for 2005-2012]]
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
# Create and checkout a new branch "GC_12.7.1" at the tag "12.7.1"
|<tt>HEMCO/VOLCANO/v2018-03/</tt>
git checkout -b GC_12.7.1 12.7.1</nowiki>
 
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.7.0|new data directories for this version]].
 
This version fixed several minor issues identified during the [[#12.7.0|12.7.0]] benchmarking process.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes and References
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:


|-valign="top"
|-valign="top"
|APEI
|[https://github.com/geoschem/geos-chem/issues/211 Prevent excessive scavenging in the stratosphere in the Luo et al 2019 wet deposition scheme]
|DEFAULT
*The Luo wetdep scheme is turned off by default in the standard simulation.
|[[CAC_anthropogenic_emissions#Historical_Canadian_emissions|Historical Canadian emissions]]
*Further fixes will be applied in [[#12.7.2|12.7.2]].
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|Gan Luo (Albany)<br>[[Transport Working Group]]<br>Bob Yantosca ([[GCST]])
|<tt>HEMCO/APEI/v2016-11/</tt>
|Bug fix
|


|-valign="top"
|-valign="top"
|[[EDGAR_v4.3_anthropogenic_emissions|EDGAR v4.3]]
|[https://github.com/geoschem/geos-chem/issues/218 Bug fixes for the TOMAS microphysics simulation]
|OPTIONAL
|Dana McGuffin (CMU)<br>Bob Yantosca ([[GCST]])
|Annual global anthropogenic emissions for 1970-2010 at 0.1x0.1 resolution
|Bug fix
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|
|<tt>HEMCO/EDGARv43/v2016-11/</tt>


|-valign="top"
|-valign="top"
|C2H6_2010
|[https://github.com/geoschem/geos-chem/issues/206 Bug fix for ND51/ND51b satellite timeseries w/ nested-grid simulations]
|DEFAULT
|Bob Yantosca ([[GCST]])
|[[Anthropogenic_emissions#C2H6|Global fossil fuel and biofuel emissions of C2H6 for 2010]]
|Bug fix
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|
|<tt>HEMCO/C2H6_2010/v2017-05/</tt>


|-valign="top"
|-valign="top"
|[[DICE-Africa_anthropogenic_emissions_inventory|DICE-Africa]]
|[https://github.com/geoschem/geos-chem/issues/208 Bug fix in computation of AOD from isoprene SOA diagnostic]
|DEFAULT
|Jun Meng ([[GCST]])<br>Bob Yantosca ([[GCST]])
|Biofuel and diffuse anthropogenic emissions for Africa
|Bug fix
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|
|<tt>HEMCO/DICE_Africa/v2016-10/</tt>


|-valign="top"
|-valign="top"
|[[Trash burning emissions]]
|[https://github.com/geoschem/geos-chem/pull/204 Bug fixes for ObsPack diagnostic re: instantaneous sampling]
|OPTIONAL
|Charley Fite (FSU)
|Global trash burning emissions from Wiedinmyer et al. (2014)
|Bug fix
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|
|<tt>HEMCO/TrashEmis/v2015-03/</tt>


|-valign="top"
|-valign="top"
|SEABIRD NH3
|[https://github.com/geoschem/geos-chem/issues/205 Fix for segmentation fault when dry deposition is turned off]
|DEFAULT
|Lizzie Lundgren ([[GCST]])
|[[NH3_emissions#NH3_emissions_from_arctic_seabirds|NH3 emissions from arctic sea birds]]
|Bug fix
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|
|<tt>HEMCO/NH3/v2018-04</tt>


|-valign="top"
|-valign="top"
|OMOC
|[https://github.com/geoschem/geos-chem/pull/184 Fix WRF-GC SetGridFromCtrEdges interface]
|OPTIONAL
|Haipeng Lin (Harvard)
|[[Particulate_matter_in_GEOS-Chem#Option_to_include_spatially_and_seasonally_varying_OM.2FOC|Spatially varying OM/OC ratio]]
|Bug fix
|[[GEOS-Chem v11-02#v11-02e|v11-02e]]
|
|<tt>HEMCO/OMOC/v2018-01</tt>
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features only affecting GCHP:


|-valign="top"
|-valign="top"
|NOAA GMD CH4
|[https://github.com/geoschem/geos-chem/issues/207 Fix bug where GCHP 12.7.0 standard run failed if emissions turned off]
|DEFAULT
|Lizzie Lundgren ([[GCST]])
|[[NOx-Ox-HC-aerosol#Monthly_mean_surface_distributions|Monthly mean surface methane distributions]]
|Bug fix
|[[GEOS-Chem v11-02#v11-02e|v11-02e]]
|
|<tt>HEMCO/NOAA_GMD/v2018-01</tt>


|-valign="top"
|-valign="top"
|UCX
|https://github.com/geoschem/geos-chem/issues/227 Update MEGAN file used in GCHP 12.7.0 that caused run failure if using gfortran]
|Tropchem only
|Lizzie Lundgren ([[GCST]])
|[[Stratospheric_chemistry#Prod.2Floss_rates_from_UCX|Input files for applying linearized stratospheric chemistry production and loss rates saved out from a UCX simulation using GEOS-Chem v11-02d]]
|Bug fix
|[[GEOS-Chem v11-02#v11-02e|v11-02e]]
|
|<tt>HEMCO/UCX/v2018-02/</tt>


|-valign="top"
|-valign="top"
|IODINE
|[https://github.com/geoschem/geos-chem/issues/168 Add MODEL_GCHP (and MODEL_CLASSIC) as CPP options in GEOS-Chem]
|DEFAULT
|Lizzie Lundgren ([[GCST]])
|[[Halogen_chemistry_mechanism#Source_code_and_data_files|Monthly emission fluxes of organic iodine compounds (CH3I, CH2I2, CH2ICl, CH2IBr) from Carlos Ordonez.]]
|Structural
|[[GEOS-Chem v11-02#v11-02d|v11-02d]]
|
|<tt>HEMCO/IODINE/v2017-03/</tt>


|-valign="top"
|}
|GMI
 
|DEFAULT
==== New data directories in 12.7.1 ====
|New symbolic links:
*<tt>gmi.clim.RIPA.geos5.2x25.nc -> gmi.clim.RIP.geos5.2x25</tt>
*<tt>gmi.clim.RIPB.geos5.2x25.nc -> gmi.clim.RIP.geos5.2x25</tt>
*<tt>gmi.clim.RIPD.geos5.2x25.nc -> gmi.clim.RIP.geos5.2x25</tt>
*<tt>gmi.clim.IPMN.geos5.2x25.nc -> gmi.clim.PMN.geos5.2x25</tt>
*<tt>gmi.clim.NPMN.geos5.2x25.nc -> gmi.clim.PMN.geos5.2x25</tt>
|[[GEOS-Chem v11-02#v11-02c|v11-02c]]
|<tt>HEMCO/GMI/v2015-02/</tt>


|-valign="top"
The following data directories have been added or updated in this version.  You will have to [[Downloading_GEOS-Chem_data_directories|download the directories]] relevant to your simulation.
|[[EPA/NEI11_North_American_emissions|NEI2011 North American emissions]]
|DEFAULT (global)<br>OPTIONAL (nested NA)
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/NEI2011/v2017-02-MM/README Monthly mean data files] (created from the existing hourly data in <tt>HEMCO/NEI2011/v2015-03</tt>)
|[[GEOS-Chem v11-02#v11-02a|v11-02a]]
|<tt>HEMCO/NEI2011/v2017-02-MM/</tt>


|-valign="top"
{| border=1 cellspacing=0 cellpadding=5
|ALD2
|-bgcolor="#CCCCCC"
|DEFAULT
!width="200px"|Inventory
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/ALD2/v2017-03/README Fields for ALD2 emissions], including:
!width="100px"|Type
*Seawater concentration of acetaldehyde
!width="400px"|What was added?
*Heterotrophic respiration rates, used to compute biogenic emissions of ALD2 and EOH
!width="300px"|Directory
(added with the [[PAN#Updates_to_Emissions|PAN updates]])
|[[GEOS-Chem v11-02#v11-02a|v11-02a]]
|<tt>HEMCO/ALD2/v2017-03/</tt>


|-valign="top"
|-valign="top"
|POET
|[[MEGAN_biogenic_emissions|MEGAN]]
|DEFAULT
|Default (GCHP)
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/POET/v2017-03/README Anthropogenic emissions of ethanol from the POET inventory]<br>(added with the [[PAN#Updates_to_Emissions|PAN updates]])
|Changed seconds string in time dimension units attribute from '0.0' to '00'
|[[GEOS-Chem v11-02#v11-02a|v11-02a]]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2020-02/ <tt>HEMCO/MEGAN/v2020-02</tt>]
|<tt>HEMCO/POET/v2017-03/</tt>
 
|-valign="top"
|[[Hudman_et_al_2012_soil_NOx_emissions_algorithm|Soil NOx]]
|DEFAULT
|New file: <tt>DepReservoirDefault.nc</tt><br>[[Implementation_of_HEMCO_in_GEOS-Chem#Read_default_DEP_RESERVOIR_fields_from_file_when_not_found_in_HEMCO_restart_file|Read default DEP_RESERVOIR fields from file when not found in HEMCO restart file]]
|[[GEOS-Chem v11-02#v11-02a|v11-02a]]
|<tt>HEMCO/SOILNOX/v2014-07/</tt>


|}
|}


NOTES:
=== 12.7.0 ===
#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.


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:02, 29 June 2018 (UTC)
<span style="color:green">'''''This version was released on 03 Feb 2020.'''''</span>


== Validation ==
'''[https://doi.org/10.5281/zenodo.3634864 DOI: 10.5281/zenodo.3634864]'''


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


=== 1-month and 1-year benchmarks ===
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 [https://cloud-gc.readthedocs.io/en/latest/chapter02_beginner-tutorial/quick-start.html our ''Quick Start Guide'' at cloud.geos-chem.org].


For complete information about the benchmark simulations used to validate GEOS-Chem v11-03, please see [[GEOS-Chem v11-03 benchmark history|our ''GEOS-Chem 12 benchmark history'' wiki page]].
  <nowiki># 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 ..  


=== Unit tests for GEOS-Chem 12 ===
# Download the GEOS-Chem Unit Tester, from which run directories can be generated
 
git clone https://github.com/geoschem/geos-chem-unittest UT
We perform a full set of unit tests on GEOS-Chem on an almost daily basis. These tests ensure that each new feature being added does not break any existing functionality.
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</nowiki>


Here are the unit tests that we ran before submitting 1-month benchmark simulation for GEOS-Chem 12.0.0. Click on the links below to see the results from each set of unit tests:
Please see the following links for complete information about the validation of GEOS-Chem 12.7.0:
#[[Benchmark/GEOS-Chem_12.7.0#GEOS-Chem_Classic_1-month_benchmark|''1-month benchmark for GEOS-Chem Classic'']]
#[[Benchmark/GEOS-Chem_12.7.0#GCHP_1-month_benchmark|''1-month benchmark for GCHP'']]
#[[Benchmark/GEOS-Chem_12.7.0#1-year_Transport_Tracers_benchmarks|''1-year transport tracer benchmark for GEOS-Chem Classic'']]


{| border=1 cellspacing=0 cellpadding=5  
{| border=1 cellspacing=0 cellpadding=5  
|-bgcolor="#CCCCCC"
|-bgcolor="#CCCCCC"
!width="100px"|Unit test
!width="500px"|Feature
!width="100px"|Date
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes and References
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting the full-chemistry simulation:


|-valign="top"
|-valign="top"
|TBD
|[https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2018JD029046 Small alkyl nitrate chemistry]
|Jenny Fisher (Wollongong)
|Science
|
|


|}
|-valign="top"
|[https://www.atmos-chem-phys.net/19/9097/2019/acp-19-9097-2019.html Methanol as part of standard chemical mechanism]
|Xin Chen (UMN)<br>Dylan Millet (UMN)<br>Katie Travis (NASA)
|Science
|


== Performance ==
|-valign="top"
|[[Leaf_area_indices_in_GEOS-Chem#Yuan_processed_MODIS_LAI|Update to Yuan processed MODIS LAI product (covering years 2005-2016)]]
|GCST
|Science
|


Please see the following resources below for more information about the performance of GEOS-Chem 12.0.0.
|-valign="top"
|[https://github.com/geoschem/geos-chem/pull/78 Latitudinally and monthly resolved fixed surface concentrations for long-lived organohalogen species (1750-2014) and methane (prior to 1979)]
|Tomás Sherwen (York)<br>Lee Murray (Rochester)
|Science
|


=== GEOS-Chem "Classic" performance ===
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/84 Bug fix: Prevent differences in chemistry caused by toggling the ND65 bpch diagnostics off or on]
|Bob Yantosca (GCST)
|Bug fix
|


We have performed several timing tests with GEOS-Chem "Classic" 12.0.0 and have posted our results on the wiki:
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/123 Fix incorrect uptake coefficient for N2O5 in heterogeneous chemistry]
|Hyeonmin Kim (Seoul Nat'l U.)<br>Chris Holmes (FSU)
|Bug fix
|
*[https://github.com/geoschem/geos-chem/pull/124 geoschem/geos-chem PR #124]


*[[Timing_tests_with_GEOS-Chem_12.0.0#Table_of_7-model-day_run_times|Table of 7-day timing test results with GEOS-Chem 12.0.0]]
|-valign="top"
*[[Timing_tests_with_GEOS-Chem_12.0.0#Graphs_of_7-model-day_run_times|Graphs of 7-day timing test results with GEOS-Chem 12.0.0]]
|[https://github.com/geoschem/geos-chem/issues/121 Fix offline dust scale factors]
*[[Media:GEOS-Chem_12.0.0_timing_results.pdf|''GEOS-Chem 12.0.0 "Classic" timing results'' by Bob Yantosca (PDF)]]
|Jun Meng (GCST)
|Bug fix
|


We invite you to add your own time test results to the wiki.
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:06, 17 August 2018 (UTC)
|-valign="top"
|[[Downloading data with the GEOS-Chem dry-run option|Add GEOS-Chem "dry-run" option to obtain a list of required input files]]
|Haipeng Lin (Harvard)<br>Jiawei Zhuang (Harvard)<br>Bob Yantosca (GCST)
|Structural
|
*[https://github.com/geoschem/geos-chem/pull/122 geoschem/geos-chem PR #122]
*[https://www.youtube.com/watch?v=L7T5QtWehLs Tutorial at youtube.geos-chem.org]


=== GCHP performance ===
|-valign="top"
|[[HEMCO_versions#HEMCO_development_history|HEMCO 2.2.0: Updates and fixes to improve file I/O]]
|Melissa Sulprizio ([[GCST]])
|Structural
|
*Needed for Yuan processed MODIS LAI


Help us pool performance information across systems by contributing your GCHP run information on [[GCHP_Timing_Tests|our ''GCHP Timing Tests'' page]].
|-valign="top"
|[https://github.com/geoschem/geos-chem/pull/95 Implement Gan Luo et al wetdep (GMD-12-3439-2019) as an option]
|Gan Luo (SUNY-Albany)<br>Fangqun Yu (SUNY-Albany)<br>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: [https://github.com/geoschem/geos-chem/pull/95 geoschem/geos-chem PR #95]
*Paper: [https://www.geosci-model-dev.net/12/3439/2019/ GMD-12-3439-2019]


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:06, 17 August 2018 (UTC)
|-valign="top"
|[https://www.geosci-model-dev.net/11/2009/2018/ CH4 soil absorption from MeMo model]
|Melissa Sulprizio (Harvard)
|Science
|
*geoschem/geos-chem commits [https://github.com/geoschem/geos-chem-unittest/commit/9b2e87ceca329272ba234680042b6a736bb56656 9b2e87ce], [https://github.com/geoschem/geos-chem-unittest/commit/2714b8c8bf8809f029c0079ee35bcb6a70e59135 2714b8c8]


== Previous issues now resolved in GEOS-Chem 12 ==
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/82 Removal of most binary punch (aka "bpch") diagnostics]


The following bugs and/or technical issues have been resolved in GEOS-Chem 12.
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
|


=== GCHP transport fix to prevent instant propagation from troposphere to stratosphere ===
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/69 Add netCDF diagnostic for UV fluxes from FAST-JX]
|Jonathan Moch (Harvard)<br>Bob Yantosca ([[GCST]])
|Structural
|


<span style="color:darkorange">'''''This fix will be included in [[GEOS-Chem 12#12.1.1|GEOS-Chem 12.1.1]].'''''</span>
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/134 KPP equation reactivity rate and OH reactivity diagnostics]
|Christoph Keller (GMAO)
|Structural
|


'''Sebastian Eastham describes this bug fix as follows:'''
|-valign="top"
 
|[https://github.com/geoschem/geos-chem/pull/157 Bug fix for HEMCO standalone using high-resolution input grids]
GCHP uses a simple mass conservation kludge which rescales global tracer concentrations between transport steps. This is equivalent to the pressure fixer in GC-Classic, used to account for inconsistency between the surface pressure field (which sets the vertical grid spacing up to the upper troposphere) and the averaged wind speeds. Although the scaling factor is usually small, this can cause nonphysical redistribution of mass. This is especially problematic because mass can be transferred to, or from, the stratosphere, which should be impossible given that the stratosphere operates on fixed pressure levels. In a future update, this problem will be resolved by direct application of mass fluxes archived from GEOS in place of winds, but while that update is in development we have produced an interim fix
|Chris Holmes (FSU)
|Bug fix
This patch forces mass redistribution to be constrained to the variable pressure levels in the troposphere. Although this slightly increases spurious mixing in the troposphere, it prevents changes in the troposphere from being instantly propagated to the stratosphere. This can have significant effects when inspecting (e.g.) the response to changes in surface emissions of NOx.
|


--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 16:03, 6 December 2018 (UTC)
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/166 Incorrect units returned from GET_OH in sulfate_mod.F]
|Rong Tian (NUIST)
|Bug fix
|


=== Always enable BCPH_TPBC to allow saving out BC files in global simulations ===
|-valign="top"
|[[FlexChem#Building_a_custom_chemical_mechanism|Use common build_mechanism.sh script for all KPP mechanisms]]
|Lizzie Lundgren (GCST)
|Structural
|
*[https://github.com/geoschem/geos-chem/commit/0a19e43dc7e5afb9bb5091eafb74a8ea3c9c06e1 geoschem/geos-chem Commit 0a19e43d]


<span style="color:darkorange">'''''This fix will be included in [[GEOS-Chem 12#12.1.1|GEOS-Chem 12.1.1]].'''''</span>
|-
!colspan="4" bgcolor="#CCFFFF"|Features only affecting GCHP:


Yanxu Zhang reported an issue in [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]] where BC files would not save out, even when turned on in the Nested Grid Menu of input.geos. To resolve this issue, we will always add <tt>USER_DEFS += -DBPCH_TPBC</tt> in Makefile_header.mk. The switch to turn on saving out boundary condition files is still controlled by the options in input.geos, but this fix ensures the tpcore_bc_mod.F code is always compiled.
|-valign="top"
|[https://github.com/geoschem/gchp/issues/49 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
|


--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 15:40, 30 November 2018 (UTC)
|-valign="top"
|[https://github.com/geoschem/gchp/issues/3 Use same CEDS anthropogenic emissions inventory as GC Classic, including 1750-1949 and additional VOC species]
|Lizzie Lundgren (GCST)
|Structural
|
*Enables [[CEDS_anthropogenic_emissions#Updates_introduces_in_GEOS-Chem_12.3.2|GC Classic 12.3.2 update]] in GCHP


=== Skip planeflight observations outside a nested domain ===
|-valign="top"
|Assorted GCHP structural changes to facilitate GEOS-Chem in GEOS
*[https://github.com/geoschem/gchp/issues/46 Move high-level GCHP files to GEOS-Chem repository]
*[https://github.com/geoschem/gchp/issues/47 Move GCHP run directory creation to GEOS-Chem repository]
|Lizzie Lundgren (GCST)
|Structural
|


<span style="color:darkorange">'''''This fix will be included in [[GEOS-Chem 12#12.1.1|GEOS-Chem 12.1.1]].'''''</span>
|-valign="top"
|[https://github.com/geoschem/gchp/issues/48 Use same precision in non-species Internal state variables and the equivalent GEOS-Chem states (REAL8)]
|Lizzie Lundgren (GCST)
|Bug fix
|


Lei Zhu provided a fix for planeflight_mod.F to skip flight observations outside the nested domains. With the fix, the code works for all 0.5 and 0.25 nested domains. For more information please see the [https://github.com/geoschem/geos-chem/pull/21 pull request on Github].
|-valign="top"
 
|[https://github.com/geoschem/gchp/issues/58 Update ESMF to v8.0.0 public release]
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 13:29, 27 November 2018 (UTC)
|Lizzie Lundgren (GCST)
|Structural
|


=== Allow for SZA to 98 degrees when getting photolysis rates ===
|}


<span style="color:green">'''''This update was included in [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]], which was released on 26 Nov 2018.'''''</span>
==== New data directories in 12.7.0 ====


'''''Eric Palmer (GMAO) wrote:'''''
The following data directories have been added or updated in this version. You will have to [[Downloading_GEOS-Chem_data_directories|download the directories]] relevant to your simulation.
<blockquote>I see that the code that calls the photolysis rates (in flexchem_mod.F90), is only called when the solar zenith angle is < 90 degrees (COS(SZA) > 0.). However, Fast-Jx allows for SZA down to 98 degrees, which is important in the stratosphere-mesosphere where sunlight still illuminates at high altitudes if the sun is below the horizon at the surface.
   
To allow for SZA down to 98 deg, I made the following one line change:</blockquote>
   
      IF ( State_Met%SUNCOSmid(I,J) > <span style="color:red">0.e+0_fp</span> ) THEN


<blockquote>to:</blockquote>
''NOTE: In GEOS-Chem 12.7.0 and later versions, you can use the '''[[Downloading_data_with_the_GEOS-Chem_dry-run_option|GEOS-Chem dry-run option]]''' to simplify the data download process!''
 
      IF ( State_Met%SUNCOSmid(I,J) > <span style="color:green">-0.13917e+0_fp</span> ) THEN


<blockquote>where -0.13917e+0_fp = COS(98 degrees)   
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="200px"|Inventory
!width="100px"|Type
!width="400px"|What was added?
!width="300px"|Directory


This looks like it has the desired effect, as species with sharp gradients across the terminator (eg: Br, BrO), are now more "rounded" and look much more like GMI (which also allows SZA down to 98 degrees). This also eliminates the problem with the non-conservation of bromine family species in the mesosphere due to transport across the terminator (ie, the sharp edges of a square wave).</blockquote>
|-valign="top"
|[[Grid-independent_emissions#Biogenic_VOC_emissions|OFFLINE_BIOVOC]]
|Default
|Offline biogenic VOC emissions generated using GEOS-Chem 12.3.0 and the Yuan-processed MODIS-LAI product
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/OFFLINE_BIOVOC/v2019-10/ <tt>HEMCO/OFFLINE_BIOVOC/v2019-10</tt>]


--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 14:59, 16 October 2018 (UTC)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:09, 26 November 2018 (UTC)
|-valign="top"
|XUAN_XLAI
|DEFAULT
|[[Leaf_area_indices_in_GEOS-Chem#Yuan_processed_MODIS_LAI|Yuan-processed MODIS LAI product (covering years 2005-2016)]]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/Yuan_XLAI/v2019-03/README <tt>HEMCO/Yuan_XLAI/v2019-03</tt>]


=== Fix bug in application of CFC surface mixing ratios in GCHP ===
|-valign="top"
|RONO2
|DEFAULT
|Monthly seawater concentrations of methyl nitrate (MENO3) and ethyl nitrate (ETNO3) needed for [https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2018JD029046 small alkyl nitrate chemistry]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/RONO2/v2019-05/README <tt>HEMCO/RONO2/v2019-05</tt>]


<span style="color:green">'''''This update was included in [[GEOS-Chem 12#12.0.3|GEOS-Chem 12.0.3]], which was released on 16 Oct 2018.'''''</span>
|-valign="top"
|MOH
|DEFAULT
|Methanol emissions as described in [https://www.atmos-chem-phys.net/19/9097/2019/acp-19-9097-2019.html Chen et al. (2019)]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MOH/v2019-12/README <tt>HEMCO/MOH/v2019-12</tt>]


This fix is urgent, as any current users of the last several versions of GCHP will be see bad results for relevant species. We recommend that all GCHP users implement this update if not updating to the latest version.
|-valign="top"
|CMIP6
|DEFAULT<br>(UCX-based simulations)
|[https://github.com/geoschem/geos-chem/pull/78 Latitudinally and monthly resolved fixed surface concentrations for long-lived organohalogen species (1750-2014) and methane (prior to 1979)]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/CMIP6/v2019-12/README <tt>HEMCO/CMIP6/v2019-12</tt>]


'''Sebastian Eastham describes this bug as follows:'''
|-valign="top"
|SfcFix
|DEFAULT<br>(UCX-based simulations)
|Latitudinally and monthly resolved fixed surface concentrations for long-lived organohalogen species from GMI and UCX (1959-2099)
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/SfcFix/v2019-12/README <tt>HEMCO/SfcFix/v2019-12</tt>]


<blockquote>Basically, we specify a target year for CFC emissions to be read in in input.geos, so (eg) we can specify “2050” and all surface VMRs for CFCs will be set according to the expected value for 2050. Usually, though, we use a value of 0 – meaning “use the current year”. In GCC, the value Input_Opt%CFCYEAR is set to Get_Year () during initialization, and the offset is calculated in UCX_mod, meaning the right year gets used. However, in GCHP this isn’t possible because Get_Year doesn’t return the right value until after initialization. There was a workaround in UCX_mod already where we had a local variable “CFCYEAR” which was a copy of Input_Opt%CFCYEAR, and which got set to Get_Year() at runtime if it was still zero; however, this wasn’t being propagated in the case of an ESMF environment (where UCXNETCDF is .False.) because we only passed Input_Opt rather than the updated local variable. As a result, the CFC “emissions” were always for 1950 rather than for the true target year.</blockquote>
|-valign="top"
|MODIS_CHLR
|OPTIONAL
|MODIS-Aqua Chlorophyll-A data for use in the [[Aerosol_emissions#Online_emission_of_marine_primary_organic_aerosol_.28POA.29|marinePOA simulation]]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MODIS_CHLR/v2019-11/README <tt>HEMCO/MODIS_CHLR/v2019-11</tt>]


--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 21:18, 15 October 2018 (UTC)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:10, 26 November 2018 (UTC)
|}


=== Fix incorrect run configuration for offline sea salt emissions in GCHP ===
=== 12.6.3 ===


<span style="color:green">'''''This update was included in [[GEOS-Chem 12#12.0.3|GEOS-Chem 12.0.3]], which was released on 16 Oct 2018.'''''</span>
<span style="color:green">'''''This version was released on 25 Nov 2019.'''''</span>


The offline sea salt emissions applied in GCHP starting in 12.0.0 contained a bug due to incorrect settings in HEMCO_Config.rc. SALA and SALC sea salt values read from file should be scaled and applied to BrSALA and BrSALC respectably. However, the HEMCO_Config.rc settings resulted in applying the scaled values to SALA and SALC instead. This bug was identified by Seb Eastham (MIT) and is corrected by updating the species column in HEMCO_Config.rc. No source code updates are necessary but you must create a new run directory or apply the fix in your existing run directories.
'''[https://doi.org/10.5281/zenodo.3552959 DOI: 10.5281/zenodo.3552959]'''


--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 21:13, 15 October 2018 (UTC)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:10, 26 November 2018 (UTC)
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.


=== Update HEMCO configuration file for tagged CO simulation ===
  <nowiki># 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 ..


<span style="color:green">'''''This update was included in [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]], which was released on 26 Nov 2018.'''''</span>
# 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</nowiki>


The tagged CO simulation was still using NEI2005 emissions over the US by default, while all other simulations had retired the NEI2005 option and were using NEI2011 instead. For consistency, we will use NEI2011 with the tagged CO simulation and remove NEI2005.  
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.6.0|new data directories for this version]].


In addition, the CEDS and DICE_Africa inventories were omitted from tagged CO HEMCO configuration file. To maintain consistency with the full-chemistry simulations, these inventories are now added for tagged CO and are turned on by default.
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes and References


--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 17:37, 21 September 2018 (UTC)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:10, 26 November 2018 (UTC)
|-
!colspan="4" bgcolor="#CCFFFF"|Features only affecting GCHP:


=== Fix regional tile file used for APEI inventory in GCHP ===
|-valign="top"
|[https://github.com/geoschem/gchp/issues/57 Fix bug preventing successful transport tracer simulation runs]
|Lizzie Lundgren (GCST)
|Bug fix
|


<span style="color:green">'''''This bug fix only requires downloading updated files from <tt>gcgrid/ExtData/GCHP/TileFiles</tt>'''''</span>
|}


The regional tile file used by GCHP for regrigding the APEI inventory from native resolution to cubed sphere was incorrect at the time of the 12.0.0 release. The tile file erroneously caused the APEI inventory to be regridded at a 180 degree longitude offset. Corrected tile files now replace the erroneous ones at <tt>gcgrid/ExtData/GCHP/TileFiles</tt>. No changes are necessary to the model source code or the GCHP run directory.
=== 12.6.2 ===


--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 17:30, 19 September 2018 (UTC)
<span style="color:green">'''''This version was released on 15 Nov 2019.'''''</span>


=== Fix masked anthropogenic emissions bug in GCHP ===
'''[https://doi.org/10.5281/zenodo.3543702 DOI: 10.5281/zenodo.3543702]'''


<span style="color:green">'''''This update was included in [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]], which was released on 26 Nov 2018.'''''</span>
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.


Integration of the DICE-Africa inventory in GCHP resulted in erroneously masking out total global anthropogenic emissions outside of Africa. Updating the Africa mask file from containing regional bounds to global bounds corrects the problem. GCHP users who are using the DICE-inventory prior to 12.1.0 can fix the issue by updating their Africa mask file to <tt>MASKS/v2014-07/AF_LANDMASK.geos.05x0666.global.nc</tt> which is now available on <tt>gcgrid</tt>.  
  <nowiki># 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 ..  


--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 16:50, 14 September 2018 (UTC)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:11, 26 November 2018 (UTC)
# 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</nowiki>


=== Add support for continuous integration with TravisCI ===
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.6.0|new data directories for this version]].


<span style="color:green">'''''This update was included in [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]], which was released on 26 Nov 2018.'''''</span>
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes and References


We have now linked the [https://github.com/geoschem/geos-chem GEOS-Chem Github repository] to the continuous integration tool TravisCI.  Each time a commit is pushed to the repository, TravisCI will perform a test to ensure that the commit will not "break" GEOS_Chem.  Right now, TravisCI only compiles GEOS-Chem, but we will eventually implement compile-and-run tests in the near future.
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:


You can see the TravisCI status page for GEOS-Chem here: https://travis-ci.com/geoschem/geos-chem/builds
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/126 geoschem/geos-chem Now make sure the HEMCO standalone gets the proper met field name and grid resolution]
|Jun Meng (GCST)<br>Bob Yantosca (GCST)
|Bug Fix
|
*[https://github.com/geoschem/HEMCO/issues/5 geoschem/HEMCO #5]


Also, if you navigate to the [https://github.com/geoschem/geos-chem/commits "commits" page of the GEOS-Chem Github repository], you will see a green checkmark next to each commit that was checked by TravisCI:
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/135 Prevent overwriting restart variables H2O2AfterChem and SO2AfterChem if present]
|Lizzie Lundgren (GCST)
|Bug Fix
|


[[Image:travis_ci.png]]
|-
!colspan="4" bgcolor="#CCFFFF"|Features only affecting GCHP:


NOTE: As of this writing, only the '''dev/12.1.0''' branch is being checked by TravisCI.  When we merge this into the '''master''' branch, then all future branches will be checked.
|-valign="top"
|[https://github.com/geoschem/gchp/issues/53 Fix incorrect vertical flipping of MAPL 3D imports impacting mesospheric chemistry]
|Lizzie Lundgren (GCST)<br>Sebastian Eastham (MIT)
|Bug fix
|
*Fixes issue introduced in 12.5.0


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:11, 26 November 2018 (UTC)
|-valign="top"
|[https://github.com/geoschem/gchp/issues/54 Fix incorrect mapping between internal state H2O2AfterChem and the equivalent State_Chm field]
|Lizzie Lundgren (GCST)
|Bug fix
|


=== Replace HEMCO built-in unit conversions with scale factors in config file ===
|-valign="top"
|[https://github.com/geoschem/gchp/issues/55  Fix two timestep delay in update time for LAI upon day change]
|Lizzie Lundgren (GCST)
|Bug fix
|


<span style="color:darkorange">'''''This update will be included in [[GEOS-Chem 12#12.2.0|GEOS-Chem 12.2.0]] or later.'''''</span>
|}


HEMCO checks the unit string in HEMCO_Config.rc for each emission and converts to HEMCO standard units (kg/m2/s) upon file read if the input units are different. For VOCS, it further converts to kgC/m2/s. The code for the unit conversions is in HEMCO/Core/hco_unit_mod.F90.  
=== 12.6.1 ===


Since the automatic unit conversion is performed during HEMCO file read it does not get executed in GCHP which uses MAPL/ESMF for I/O. GCHP users must instead manually include the conversion information as scale factors in HEMCO_Config.rc. To increase clarity and to make GCHP and GCC better match we plan on removing the HEMCO built-in unit conversions and replacing them with scale factors in HEMCO_Config.rc. This change may result in small number differences due to order of operations and precision of scale factors.
<span style="color:green">'''''This version was released on 28 Oct 2019.'''''</span>


--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 19:57, 23 August 2018 (UTC)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:11, 26 November 2018 (UTC)
'''[https://doi.org/10.5281/zenodo.3520966 DOI: 10.5281/zenodo.3520966]'''


=== Fixed local-time averaging in ND51 and ND51b satellite timeseries diagnostics ===
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.


<span style="color:green">'''''This update was included in [[GEOS-Chem 12#12.0.2|GEOS-Chem 12.0.2]], which was released on 10 Oct 2018.'''''</span>
  <nowiki># 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 ..  


'''''Bo Zhang wrote:'''''
# 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</nowiki>


<blockquote>We encountered a potential issue in the satellite diagnostic ND51b in [[GEOS-Chem v11-01]].  We find some kind of discontinuity in total column AOD (a sum of all aerosol species) along the west-east direction. It feels like data are missing/reduced occasionally in every other pixels alone the W-E direction. We are running v11-01 with full chemistry + UCX driven by MERRA2. The same problem remains after switching to MERRA. We checked AOD maps in monthly output which looks normal.</blockquote>
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.6.0|new data directories for this version]].


'''''[[User:bmy|Bob Yantosca]] replied:'''''
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes and References


<blockquote>In recent versions of GEOS-Chem, the number of advected species increased (to accommodate additional halogen and SOA species).  So we had to increase the non-species tracer numbers to 500:</blockquote>
|-valign="top"
!colspan="4" bgcolor="#CCFFFF"|Updates that will NOT affect full-chemistry simulations


      !  ND51 tracer numbers:
|-valign="top"
      !  ============================================================================
|[https://github.com/geoschem/geos-chem/pull/94 Fix CMake error message for when NetCDF is not found]
      !  1 - nAdvect  : GEOS-CHEM advected species              [v/v        ]
|Liam Bindle (Dalhousie)
      !  501          : OH concentration                        [molec/cm3  ]
|Bug fix
      !  502          : NOy concentration                        [v/v        ]
|
      !  503          : Relative Humidity                        [%          ]
      !  ... etc ...


<blockquote>Complicating matters further, some ND51/ND51b quantities, including the AOD’s, were only updated on every chemistry timestep (20 mins) instead of on every dynamic timestep (10 mins).  There was a CASE statement in routine WRITE_DIAG51 to divide by the proper counting array to create the average quantity:</blockquote>
|-valign="top"
|[https://github.com/geoschem/geos-chem/commit/ab0e743f2b19ff46abb87dfa608f1c1bba0cd089 Fix units for PRECANV, PRECCON, PRECLSC, PRECTOT in state_met_mod.F90]
        SELECT CASE( Input_Opt%ND51_TRACERS(W) )
|Tomas Sherwen (York)
|Bug fix
            <span style="color:red">CASE( 91, 92, 76, 77 )</span>               
|
            ... etc ...
            <span style="color:red">CASE( 84:89, 115:121 )</span>               
            ... etc ...
            <span style="color:red">CASE( 105:114 )</span>               
            ... etc ...
 
            CASE DEFAULT
            ... etc ...
        END SELECT


<blockquote>But we just realized that this CASE statement had the <span style="color:red">old ND51/ND51b tracer numbers ( < 500)</span> and not the new ones.
|-valign="top"
|Various minor structural updates:
#[https://github.com/geoschem/geos-chem/issues/105 ObsPack now defaults to hourly sampling if a sampling interval is not found in data files]
#[https://github.com/geoschem/geos-chem/issues/106 GEOS-Chem now prints the full path of each file that is read]
#[https://github.com/geoschem/geos-chem/issues/113 GNU Fortran 9.2.1 can now compile GEOS-Chem]
#[https://github.com/geoschem/geos-chem/pull/112 Use Microsoft Azure DevOps instead of TravisCI for continuous integration]
|Bob Yantosca (GCST)<br>Liam Bindle (GCST)
|Structural
|


Therefore, we have made the following fixes, which should eliminate any striping or discontinuities
|-
!colspan="4" bgcolor="#CCFFFF"|Features only affecting GCHP:


#Archive most ND51/ND51b tracers (except for NOy, which has special handling) on every dynamic timestep.  Remove the GOOD_CHEM, GOOD_CT_CHEM, GOOD_EMIS, GOOD_CT_EMIS arrays.
|-valign="top"
#Update the CASE statement shown above so that all tracers (except NOy) are divided by the number of dynamic timesteps when each grid box was within the proper local time range.
|[https://github.com/geoschem/gchp/issues/50 Fix regridding bug at poles]
|Lizzie Lundgren (GCST)
|Bug fix
|
*Corrects problem running with MERRA2


''Also note: the ND51/ND51b diagnostics were developed in an ad-hoc fashion and were were never really thought out holistically.  It is possible that there may be some issues with some of the other quantities in ND51/ND51b, but the GCST is not planning on investigating further.  The bpch diagnostics will be eventually removed from GEOS-Chem once we have a satisfactory equivalent local-time averaging netCDF diagnostic.''</blockquote>
|}


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:12, 10 October 2018 (UTC)
=== 12.6.0 ===


=== Fix typo when registering the State_Chm%SSAlk field ===
<span style="color:green">'''''This version was released on 18 Oct 2019.'''''</span>


<span style="color:green">'''''This update was included in [[GEOS-Chem 12#12.0.1|GEOS-Chem 12.0.1]], which was released on 24 Aug 2018.'''''</span>
[https://doi.org/10.5281/zenodo.3507501 '''DOI: 10.5281/zenodo.3507501''']


'''Shuting Zhai wrote:'''
You can use the following Git commands to download the GEOS-Chem 12.6.0 source code and [[GEOS-Chem Unit Tester]] package.
   
<blockquote>I found a typo in state_chm_mod.F90 where we register the State_Chm%SSAlk field.   I believe this line:</blockquote>


      CALL Register_ChmField( ... State_Chm%<span style="color:red">pHCloud</span>, ...  )
  <nowiki># 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 ..


<blockquote>Should be:</blockquote>
# 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</nowiki>


      CALL Register_ChmField( ... State_Chm%<span style="color:green">SSAlk</span>, ... )
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.6.0|new data directories for this version]].


Upon fixing this issue, the [[GCST]] discovered that the <tt>State_Chm%SSAlk</tt> array cannot be registered as a single array because it is dimensioned as <tt>(IIPAR,JJPAR,LLPAR,2)</tt>. When registering quantities, the 4th dimension is always interpreted as the number of chemical species. Therefore, registering <tt>State_Chm%SSAlk</tt> in this way caused an error.
Please see the following links for complete information about the validation of GEOS-Chem 12.6.0:
#[[Benchmark/GEOS-Chem_12.6.0#GEOS-Chem_Classic_1-month_benchmark|''1-month benchmark for GEOS-Chem Classic'']]
#[[Benchmark/GEOS-Chem_12.6.0#GCHP_1-month_benchmark|''1-month benchmark for GCHP'']]
#[[Benchmark/GEOS-Chem_12.6.0#GEOS-Chem_Classic_1-year_benchmark|''1-year benchmark for GEOS-Chem Classic'']]


The solution is to register the two dimensions of <tt>State_Chm%SSAlk</tt> separately:
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes and References


#<tt>SSAlkAccum</tt> points to <tt>State_Chm%SSAlk(:,:,:,1)</tt>
|-valign="top"
#<tt>SSAlkCoarse</tt> points to <tt>State_Chm%SSAlk(:,:,:,2)</tt>
!colspan="4" bgcolor="#CCFFFF"|Updates that will affect full-chemistry simulations


This update will require you to list <tt>Chem_SSAlkAccum</tt> and <tt>Chem_SSAlkCoarse</tt> as requested diagnostics instead of the single field <tt>Chem_SSAlk</tt> in the <tt>HISTORY.rc</tt> file ( which specifies input options for netCDF diagnostics).
|-valign="top"
|[[GEOS-Chem_chemistry_mechanisms#Updates_to_heterogeneous_and_cloud_chemistry|Combined heterogeneous chemistry updates]], includes
*N2O5, NO3, NO2 reactive uptake updates
*Subgrid cloud NOy chemistry
|Chris Holmes (FSU)<br>Erin McDuffie (Dalhousie)<br>Viral Shah (UW)<br>Lyatt Jaegle (UW)
|Science
|


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:33, 23 August 2018 (UTC)
|-valign="top"
|[[Dry_deposition#Cold-temperature_dry_deposition_updates|HNO3 cold-temperature deposition]]
|Viral Shah (Harvard)
|Science
|


=== Fixes for compilation issues ===


We have added several fixes for issues encountered during GEOS-Chem compilation:
|-valign="top"
|[[GEOS-Chem_12#Quick_fix_for_aerosol_pH_calculation_when_dry|Quick fix for aerosol pH calculation when dry]]
|Becky Alexander (UW)<br>Xuan Wang (Harvard)
|Science
|


#[[GEOS-Chem_Makefile_Structure#Add a more robust test for netCDF-Fortran in Makefile_header.mk|Add a more robust test for netCDF-Fortran in Makefile_header.mk]]
|-valign="top"
#[[GNU_Fortran_compiler#Compiliation_issues_with_GNU_Fortran_8.2.0|Fixes for compilation issues encountered with GNU Fortran 8.2.0]]
|[[Secondary_organic_aerosols#Removal_of_VBS_isoprene_SOA|Remove isoprene in VBS]] (leaving aqueous)
#[[Intel_Fortran_Compiler#Compilation_issues_with_Intel_Fortran_18|Fixes for compilation issues encountered with Intel Fortran 18]]
|Melissa Sulprizio (GCST)
|Science
|


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:26, 22 August 2018 (UTC)
|-valign="top"
|[[FAST-JX_v7.0_photolysis_mechanism#Updated_aerosol_hygroscopicity_and_optics|Updated aerosol hygroscopicity and optics]]
|Robyn Latimer (Dalhousie)<br>Jun Meng (Dalhousie)
|Science
|[[#New data directories in 12.6.0|See ''New data directories in 12.6.0'']]


=== Fix mis-indexing in the ND05 diagnostic ===
|-valign="top"
|[[DICE-Africa_anthropogenic_emissions_inventory#Add_EDGAR_BCPI_and_BCPO_emissions_for_remaining_sectors_to_DICE-Africa|Add EDGAR BCPI and BCPO emissions for remaining sectors to DICE-Africa]]
|Tomas Sherwen (York)<br>Eloise Marais (Leicester)
|Bug fix
|[https://github.com/geoschem/geos-chem-unittest/pull/9 geoschem/geos-chem-unittest PR #9]


<span style="color:green">'''''This update was included in [[GEOS-Chem 12#12.0.1|GEOS-Chem 12.0.1]], which was released on 24 Aug 2018.'''''</span>
|-valign="top"
!colspan="4" bgcolor="#CCFFFF"|Updates that will NOT affect full-chemistry simulations


For a complete description of this issue, please see [[Sulfate aerosols#Fix mis-indexing in the ND05 diagnostic|this post on our ''Sulfate aerosols'' wiki page]].
|-valign="top"
|[[Dry_deposition#Simple_parameterization_for_CO2_dependence_of_stomatal_resistance|Simple parameterization for CO2 dependence of stomatal resistance]] (off by default)
|Amos Tai (CUHK)
|Science
|[https://github.com/geoschem/geos-chem/pull/41 geoschem/geos-chem PR #41]


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:18, 22 August 2018 (UTC)
|-valign="top"
|[[GEOS-Chem_chemistry_mechanisms#Aerosol_nitrate_photolysis_option|Aerosol nitrate photolysis option]] (off by default)
|Tomas Sherwen (York)<br>Prasad Kasibhatla (Duke)
|Science
|[https://github.com/geoschem/geos-chem/pull/32 geoschem/geos-chem PR #32]


=== Bug fix for HEMCO soil NOx error with ifort 17 ===
|-valign="top"
|[[Building_GEOS-Chem_with_CMake|CMake in GEOS-Chem Classic]] (optional)
|Liam Bindle (Dalhousie)
|Structural
|[https://github.com/geoschem/geos-chem/pull/35 geoschem/geos-chem PR #35]


<span style="color:green">'''''This fix was included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span>
|-valign="top"
|[[Overview_of_History_diagnostics#Sample_HISTORY.rc_diagnostic_input_file|Enable GEOS-Chem "Classic" netCDF (History) diagnostics to be subsetted vertically and horizontally]]
|Bob Yantosca (GCST)
|Structural
|


For complete information about this issue and how it was resolved, please see [[Implementation_of_HEMCO_in_GEOS-Chem#Bug_fix_for_HEMCO_soil_NOx_error_with_ifort_17|this post on our ''Implementation of HEMCO in GEOS-Chem'' wiki page.]].
|-valign="top"
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/BB4CMIP6/v2019-07/README BB4CMIP historical biomass burning emissions (1750-2014)]
*NOTE: This is an optional emissions inventory.
|Pengfei Liu (Harvard)
|Science
|[[#New data directories in 12.6.0|See ''New data directories in 12.6.0'']]


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 13:54, 27 June 2018 (UTC)
|-valign="top"
|[[GEOS-Chem chemistry mechanisms#Correcting ozone from the height of the lowest model level to 10m|Surface diagnostic (O3, HNO3) with user-selected height]]
|Katie Travis (MIT)<br>GCST
|Science
|


=== FlexChem bug fix: do not zero ACTA, EOH, HCOOH ===
|-valign="top"
|[[APM aerosol microphysics|APM update and integration with GEOS-Chem 12]]
|Gan Luo (SUNY-Albany)<br>Fangqun Yu (SUNY-Albany)
|Science
|[https://github.com/geoschem/geos-chem/pull/40 geoschem/geos-chem PR #40]
*More work (e.g. converting RF diagnostics to netCDF) will be done in a later version


<span style="color:green">'''''This fix was included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span>
|}


For complete information about this bug and how it was fixed, please see [[FlexChem#FlexChem_bug_fix:_do_not_zero_ACTA.2C_EOH.2C_HCOOH|this post on our ''FlexChem'' wiki page]].
==== New data directories in 12.6.0 ====


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:42, 27 June 2018 (UTC)
The following data directories have been added or updated in this version.  You will have to [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|download the directories]] relevant to your simulation.


=== Avoid double counting CEDS and GEIA NH3 biofuel emissions ===
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="200px"|Inventory
!width="100px"|Type
!width="400px"|What was added?
!width="300px"|Directory


<span style="color:green">'''''This fix was included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span>
|-valign="top"
|[[FAST-JX_v7.0_photolysis_mechanism|FAST_JX]]
|DEFAULT
|
*The <tt>FJX_j2j.dat</tt> file (which lists the photolyzing species for FAST-JX) was updated to include the [[GEOS-Chem_chemistry_mechanisms#Aerosol_nitrate_photolysis_option|aerosol nitrate photolysis option]]
*The <tt>so4.dat</tt> and <tt>org.dat</tt> files have been updated [[FAST-JX_v7.0_photolysis_mechanism#Updated_aerosol_hygroscopicity_and_optics|following Latimer et al. (2019)]]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/CHEM_INPUTS/FAST_JX/v2019-06/README <tt>CHEM_INPUTS/FAST_JX/v2019-06</tt>]


'''''[[User:emarais|Eloise Marais]] wrote:'''''
|-valign="top"
|BB4CMIP6
|OPTIONAL
|Historical biomass burning emissions (1750-2015, BB4CMIP)
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/BB4CMIP6/v2019-07/README <tt>HEMCO/BB4CMIP6/v2019-06</tt>]


<blockquote>If CEDS includes NH3 emissions, then this will be double counting. I recommend using CEDS, as GEIA is very out of date (1998 according to the HEMCO configuration file I have).</blockquote>
|}


'''''Daniel Jacob replied:'''''
=== 12.5.0 ===


<blockquote>We should use the GEIA NH3 natural emission inventory (1&deg; x 1&deg; file from Eleanor Morris) but not the GEIA NH3 biofuel inventory.</blockquote>
<span style="color:green">'''''This version was released on 09 Sep 2019.'''''</span>


'''''UPDATE 29 Jun 2018:'''''
'''[https://doi.org/10.5281/zenodo.3403111 DOI: 10.5281/zenodo.3403111]'''


We discovered that HEMCO's default behavior is to ignore the GEIA NH3 anthro and biofuel emissions if CEDS is turned on.  This is shown in the <tt>HEMCO.log</tt> file when <tt>VERBOSE = 3</tt>:
You can use the following Git commands to download the GEOS-Chem 12.5.0 source code and [[GEOS-Chem Unit Tester]] package.


   Register_Base: Checking GEIA_NH3_ANTH
   <nowiki># Download the GEOS-Chem source code
  HEMCO: Entering Get_targetID (hco_config_mod.F90) ( 4)
git clone https://github.com/geoschem/geos-chem Code.12.5.0
  Skip container GEIA_NH3_ANTH because of CEDS_NH3_WST
  cd Code.12.5.0
  . . .
  Register_Base: Checking GEIA_NH3_BIOF
  # Create and checkout a new branch "GC_12.5.0" at the tag "12.5.0"
  HEMCO: Entering Get_targetID (hco_config_mod.F90) ( 4)
git checkout -b GC_12.5.0 12.5.0
  Skip container GEIA_NH3_BIOF because of CEDS_NH3_WST_Cat00002
  cd ..  


But for the sake of clarity, we will modify the <tt>HEMCO_Config.rc</tt> files to explicitly request this behavior:
# Download the GEOS-Chem Unit Tester, from which run directories can be generated
 
  git clone https://github.com/geoschem/geos-chem-unittest UT
  <span style="color:green">(((.not.CEDS.or.EDGARv43</span>
  cd UT
# GEIA NH3 anthro (skip if CEDS or EDGARv43 is on)
0 GEIA_NH3_ANTH $ROOT/NH3/v2014-07/NH3_geos.4x5.nc        NH3_ANTH    1990/1-12/1/0 C xy  kg/m2/s NH3 - 1 1
# GEIA NH3 biofuel (skip if CEDS or EDGARv43 is on)
(((BIOFUEL
0 GEIA_NH3_BIOF $ROOT/NH3/v2014-07/NH3_biofuel.geos.1x1.nc NH3_BIOFUEL  1998/1-12/1/0 C xy  kg/m2/s NH3 - 2 1
  )))BIOFUEL
   
   
  <span style="color:green">))).not.CEDS.or.EDGARv43</span>
  # 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</nowiki>


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:02, 29 June 2018 (UTC)
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.5.0|new data directories for this version]].


=== Fix bug in ARCTAS_SHIP_SO2 scale factors ===
Please see the following links for complete information about the validation of GEOS-Chem 12.5.0:
#[[Benchmark/GEOS-Chem_12.5.0#GEOS-Chem_Classic_1-month_benchmark|''1-month benchmark for GEOS-Chem Classic'']]
<span style="color:green">'''''This fix was included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span>
#[[Benchmark/GEOS-Chem_12.5.0#GCHP_1-month_benchmark|''1-month benchmark for GCHP'']]


For a complete description of this issue and how it was resolved, please see [[Ship_emissions#Fix_bug_in_ARCTAS_SHIP_SO2_scale_factors|this post on our ''Ship Emissions'' wiki page]].
This version includes the updates listed below.


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:54, 3 July 2018 (UTC)
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes and References


=== Fix issues in complexSOA and complexSOA_SVPOA restart files ===
|-valign="top"
!colspan="4" bgcolor="#CCFFFF"|Updates that will affect full-chemistry simulations


<span style="color:green">'''''This fix was included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span>
|-valign="top"
|[[Issues_now_resolved_in_GEOS-Chem_12#Retire_obsolete_emission_inventories|Retire obsolete emission inventories]]
|Eloise Marais (Leicester)<br>[[Emissions and Deposition Working Group]]
|Science
|


'''''[[User:emarais|Eloise Marais]] wrote:'''''
|-valign="top"
|[[Grid-independent_emissions#Biogenic_VOC_emissions|Updated offline biogenic emissions generated with GEOS-Chem 12.3.0]]
*Includes [[Grid-independent_emissions#Fixes_for_biogenic_SOAP.2C_SOAS.2C_and_CO_emissions|fixes for biogenic SOAP, SOAS, and CO emissions]]
|Hongjian Weng (PKU)
|Science
|


<blockquote>I just wanted to draw your attention to a few issues with the restart files provided on the ftp site (http://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/). The complexSOA and complexSOA_SVPOA restart files (4&deg; x 5&deg; and 2&deg; x 2.5&deg;) both have a species entry for IEPOX and also IEPOXD, IEPOXB, and IEPOXA, but should only have the latter 3. This is the same for RIP. The number of species in the 4&deg; x 5&deg; and 2&deg; x 2.5&deg; files for complexSOA is also different.</blockquote>
|-valign="top"
|[[Volcanic_SO2_emissions|Updated volcano emissions to include eruptive emissions through April 2018]]
|Christoph Keller (NASA/GMAO)
|Science
|


To fix these issues, we have generated new restart files for the complexSOA and complexSOA_SVPOA simulations. You can download these to your <tt>SPC_RESTARTS</tt> folder with the following commands:
|-valign="top"
|[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Remove_biogenic_CO_emissions_to_avoid_double_counting|Remove CO from MEGAN HEMCO extension to avoid double counting]]
|Jenny Fisher (Wollongong)
|Bug fix
|


<nowiki> wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.2x25_complexSOA.nc"
|-valign="top"
wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.2x25_complexSOA_SVPOA.nc"
|Fixes for GFED4 emissions, including:
wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.4x5_complexSOA.nc"
*Change the HEMCO cycling flag so that the model crashes if it doesn't find the right GFED year
wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.4x5_complexSOA_SVPOA.nc"</nowiki>
*Remove the 27% scaling of POG to POA and emit 1:1 instead
|Sidhant Pai (MIT)
|Bug fix
|


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:01, 5 July 2018 (UTC)
|-valign="top"
 
|[[DICE-Africa_anthropogenic_emissions_inventory#Scale_DICE-Africa_emissions_to_address_errors_in_inventory|Scale DICE-Africa emissions to address errors in inventory]]
=== Bug fix for reference time in netCDF diagnostic files ===
|Eloise Marais (Leicester)
|Bug fix
|


<span style="color:green">'''''This fix was included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span>
|-valign="top"
|[[Issues_now_resolved_in_GEOS-Chem_12#Bug_fix_for_C3H8_anthropogenic_emissions|Bug fix for C3H8 anthropogenic emissions]]
|Melissa Sulprizio ([[GCST]])
|Bug fix
|


'''''Maria Zatko wrote:'''''
|-valign="top"
|[[Mineral_dust_aerosols#Separate_AFCID_from_DustDead_extension|Separate anthropogenic PM2.5 dust source from the DustDead extension]]
|Melissa Sulprizio ([[GCST]])
|Bug fix
|


<blockquote>For the sake of run time, we would like to run GEOS-Chem with the old (15/30 minute timesteps) instead of the recommended timesteps (10/20 minutes). I noticed that the output netcdf files have different timestamps depending on the timestep (e.g., 10/20 minutes, 15/30 minutes) used.
|-valign="top"
|[[Issues_now_resolved_in_GEOS-Chem_12#Corrections_for_CFCs_in_the_chemistry_mechanism|Corrections for CFCs in the chemistry mechanism]]
|Xuan Wang (Harvard)
|Bug fix
|


For example, when 10/20 minute timesteps are used, the time units in the following netcdf output files range from 0 to 23 UTC:</blockquote>
|-valign="top"
|[[Issues_now_resolved_in_GEOS-Chem_12#Fix_typo_in_CLD_PARAMS_routine_in_gckpp_HetRates.F90|Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90]]
|Stephen Steenrod (NASA GMAO)
|Bug fix
|


      GEOSChem3hrInst.SpeciesConcWithMet.20150701_0000z.nc4 (file size: 4.6 GB)
|-valign="top"
      GEOSChem3hrInst.SpeciesConcWithMet.20150702_0000z.nc4 (file size: 5.3 GB)
|[[Stratospheric_chemistry#Bug_fix:_make_sure_stratospheric_BrY_concentrations_are_read_properly_each_month|Bug fix: make sure stratospheric BrY concentrations are read properly each month]]
      time:units = "minutes since 2015-07-01 00:00:00 UTC"
|Lyatt Jaegl&eacute; (U. Washington)
|Bug fix
|


<blockquote>When 15/30 minute timesteps are used, the time units in the following output files include hour 24:</blockquote>
|-valign="top"
!colspan="4" bgcolor="#CCFFFF"|Updates that will NOT affect full-chemistry simulations


      GEOSChem3hrInst.SpeciesConcWithMet.20150701_0000z.nc4 (file size: 4.6 GB)
|-valign="top"
      GEOSChem3hrInst.SpeciesConcWithMet.20150701_2400z.nc4 (file size: 5.3 GB)
|[[Issues_now_resolved_in_GEOS-Chem_12#Enable_accurate_cloud_pH_diagnostic_calculation|Enable accurate cloud pH diagnostic calculation via post-processing]]
      GEOSChem3hrInst.SpeciesConcWithMet.20150702_2400z.nc4 (file size: 5.3 GB)
|Jonathan Moch (Harvard)
      time:units = "minutes since 2015-07-01 24:00:00 UTC"
|Structural
|[https://github.com/geoschem/geos-chem/pull/37 geoschem/geos-chem PR #37]
*Applies to NetCDF diagnostic only


I wanted to check in to see if others have run into this issue as well.  
|-valign="top"
|[[Physical_properties_of_GEOS-Chem_species#Proposed_list_of_Henry.27s_law_constants_from_the_literature|Bug fix for proposed Henry's law constants]]
|Jenny Fisher (Wollongong)
|Bug fix
|


'''''[[User:Bmy|Bob Yantosca]] replied:'''''
|-valign="top"
!colspan="4" bgcolor="#CCFFFF"|Updates that will only affect GCHP


<blockquote>This issue is caused by floating-point roundoff error in converting from the Julian date to the calendar date. I have created a more robust fix for this issue, which now computes the correct netCDF file reference time independent of the model "heartbeat" timestep.
|-valign="top"
 
|[[Getting_Started_with_GCHP#New_in_12.5.0|Update GCHP to use MAPL v1.0.0 and ESMF v8.0.0 beta snapshot 28]]
To apply the fix:
|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


#Copy the patch file <tt>ftp://ftp.as.harvard.edu/pub/exchange/bmy/nc_ref_time_fix.txt</tt> to your computational server.
|-valign="top"
#Change to your [[GEOS-Chem v11-02#GEOS-Chem v11-02 release candidate|GEOS-Chem v11-02 release candidate]] code directory and check out the "master" branch.
|[[Getting_Started_with_GCHP#New_in_12.5.0|Replace 4x5 input files in GCHP with higher resolution equivalents to avoid ESMF domain decomposition issue at high core counts]]
#Type: <tt>git am < nc_ref_time_fix.txt</tt>
|Lizzie Lundgren (GCST)
|Emissions
|
|}


The fix will be standardized in the GEOS-Chem 12.0.0 release.</blockquote>
==== New data directories in 12.5.0 ====


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:10, 12 July 2018 (UTC)
The following data directories have been added or updated in this version.  You will have to [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|download the directories]] relevant to your simulation.


=== Bug fix for CH4 boundary conditions ===
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="200px"|Inventory
!width="100px"|Type
!width="400px"|What was added?
!width="300px"|Directory


<span style="color:green">'''''This fix was included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span>
|-valign="top"
|[[Grid-independent_emissions#Biogenic_VOC_emissions|OFFLINE_BIOVOC]]
|Default
|Offline biogenic VOC emissions generated using GEOS-Chem 12.3.0 and:
*GEOS-FP meteorology (0.25&deg;x0.3125&deg;, 2014-2017)
*MERRA-2 meteorlogy (0.5&deg;x0.625&deg;, 1980-2017)
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/OFFLINE_BIOVOC/v2019-08/ <tt>HEMCO/OFFLINE_BIOVOC/v2019-08</tt>]


'''''Lee Murray wrote:'''''
|-valign="top"
|[[Volcanic_SO2_emissions|Volcano]]
|Default
|[[Volcanic_SO2_emissions#OMI-based_volcanic_emissions|Updated volcanic SO2 emissions (1978-2019), with eruptive emissions through 28 April 2018]]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/VOLCANO/v2019-08/ <tt>HEMCO/VOLCANO/v2019-08</tt>]


<blockquote>I’ve been testing the release candidate, and believe that we need to change the default input.geos options for the Standard and Benchmark simulations in the unit tester to :</blockquote>
|-valign="top"
|[[Mineral_dust_aerosols|AFCID]]
    %%% EMISSIONS MENU %%%  :
|Default
    Turn on emissions?      : T 
|Separate [[Mineral_dust_aerosols#Anthropogenic_PM2.5_dust_source_in_GEOS-Chem|anthropogenic PM2.5 dust emissions]] from the DustDead extension
    HEMCO Input file        : HEMCO_Config.rc
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/AFCID/v2018-04/ <tt>HEMCO/AFCID/v2018-04</tt>]
      => 1ppt MBL BRO Sim.?  : F
    Switches for UCX        :---
      => Use CH4 emissions?  : F
      => Turn on surface BCs :---
        <span style="color:red">'''=> CH4?            : F'''</span>
        => OCS?            : T
        => CFCs?            : T
        => Cl species?      : T
        => Br species?      : F
        => N2O?            : T
      => Set initial glob MRs:---
        => strat. H2O?      : T
      => CFC emission year  : 0


<blockquote>By default in the unit tester, => CH4 is still enabled. This appears to set up conflict between the older UCX surface layer and the newer HEMCO methane PBL boundary conditions, causing air to be a mix of preindustrial and present-day values (see below for Jul 1, 2013 surface methane in a benchmark run). Setting it to F and/or removing LCH4SBC causes the methane to behave as expected, i.e., being set by HEMCO in all simulations, with the expected spatial pattern.
|-valign="top"
 
|[https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2016JD025767 C2H6_2010]
Also, we can slate <tt>Online CH4 chemistry?  : T</tt> in the Chemistry Menu and <tt>Input_Opt%LCH4CHEM</tt> for future removal, as it no longer does anything.</blockquote>
|Default
|Removed unused lev dimension and include 2x2.5 files regridded from 4x5
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:16, 16 July 2018 (UTC)
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/C2H6_2010/v2019-06/ <tt>HEMCO/C2H6_2010/v2019-06</tt>]


=== Fixed typo in call to GAMMA_HOBr_AER ===
|-valign="top"
|[[Mineral_dust_aerosols|DUST_DEAD]]
|Optional
|Changed longitude dimension format from integer to float and time units seconds string from '0.0' to '00'
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/DUST_DEAD/v2019-06/ <tt>HEMCO/DUST_DEAD/v2019-06</tt>]


<span style="color:green">'''''This fix was included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span>
|-valign="top"
|UVALBEDO
|Default
|Changed seconds string in time dimension units attribute from '0.0' to '00'
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/UVALBEDO/v2019-06/ <tt>HEMCO/UVALBEDO/v2019-06</tt>]


'''''Xuan Wang wrote:'''''
|-valign="top"
|TOMS/SBUV
|Default
|Changed seconds string in time dimension units attribute from '0.0' to '00'
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/TOMS_SBUV/v2019-06/ <tt>HEMCO/TOMS_SBUV/v2019-06</tt>]


<blockquote>When looking back at the standard GC codes of v11-02d, I found a bug in the function <tt>HETHOBr_SS_JS</tt> (in module <tt>KPP/Standard/gckpp_HetRates.F90</tt>).  When calling the gamma calculation, in v11-02d, around line 3514, we have:</blockquote>
|-valign="top"
|India mask
|Default
|Removed unused attribute 'valid_range'
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MASKS/v2019-05/ <tt>HEMCO/MASKS/v2019-05</tt>]


      CALL Gamma_HOBr_AER(rAer, denAir, <span style="color:red">2</span>, TK, clConc, brConc, &
|-valign="top"
                          hConc, GAM_HOBr, r_gp)
|BIOFUEL
|Default
|Regridded from 4x5 to 2x2.5
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/BIOFUEL/v2019-08/ <tt>HEMCO/BIOFUEL/v2019-08</tt>]


<blockquote>This will cause both HOBr+Cl- (<tt>X=1</tt>) and HOBr+Br- (<tt>X=2</tt>) on sea salt use the gamma of HOBr + Br- (<tt>X=2</tt>).
|}


It should be:</blockquote>
=== 12.4.0 ===


      CALL Gamma_HOBr_AER(rAer, denAir, <span style="color:green">X</span>, TK, clConc, brConc, &
<span style="color:green">'''''This version was released on 05 Aug 2019.'''''</span>
                          hConc, GAM_HOBr, r_gp)


<blockquote>It looks like a typo which could lead to quite different result for halogen chemistry.</blockquote>
'''[https://doi.org/10.5281/zenodo.3360635 DOI 10.5281/zenodo.3360635]'''


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:26, 17 July 2018 (UTC)
<span style="color:red">'''''NOTE: We recommend users update to [[#12.5.0|GEOS-Chem 12.5.0]], which contains some bug fixes and updates for the offline biogenic VOC and volcano emissions.'''''</span>


=== Bug fix for liquid water content in gckpp_HetRates.F90 ===
Please see the following links for complete information about the validation of GEOS-Chem 12.4.0:
#[[Benchmark/GEOS-Chem_12.4.0#GEOS-Chem_Classic_1-month_benchmark|''1-month benchmark for GEOS-Chem Classic'']]
#[[Benchmark/GEOS-Chem_12.4.0#GCHP_1-month_benchmark|''1-month benchmark for GCHP'']]
#[[Benchmark/GEOS-Chem_12.4.0#GEOS-Chem_Classic_1-year_benchmark|''1-year benchmark for GEOS-Chem Classic'']]


<span style="color:green">'''''This fix was included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span>
This version includes the updates listed below.


'''''Jiayue Huang wrote:'''''
{| border=1 cellspacing=0 cellpadding=5
 
|-bgcolor="#CCCCCC"
<blockquote>Qianjie Chen and I think that there is potential a bug in <tt>KPP/Standard/gckpp_HetRates.F90</tt> for halogen chemistry in the model v11-02d/e/f.
!width="500px"|Feature
 
!width="200px"|Submitted by
In the original code, we were using the grid-box average liquid water content, which likely underestimates the in-cloud Br- and Cl- concentration. So we think that we should change it to in-cloud liquid water content by dividing the cloud fraction. This results in increases the S(IV)+Br reaction in cloud, and thus reduces the BrO abundance, mainly in the 30-90N region.
!width="100px"|Type
!width="300px"|Notes and References


This bug fix is to use cloud fraction when calculating liquid water content [cm3 H2O/cm3 air] in routine <tt>GET_HALIDE_CLDConc</tt>, which is used to calculate the in-cloud concentrations of Br- and Cl-.</blockquote>
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting the full-chemistry simulation:


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:48, 20 July 2018 (UTC)
|-valign="top"
|[[Mineral_dust_aerosols#Offline_Dust_Emissions|Grid-independent dust emissions]] (hourly)
|David Ridley (CARB, formerly MIT)<br>Jun Meng (Dalhousie)
|Science
|[[#New data directories in 12.4.0|See ''New data directories in 12.4.0'']]


=== Add PH2O2 to the default list of prod/loss families in the KPP mechanisms ===
|-valign="top"
|[[Grid-independent_emissions#Lightning_NOx_emissions|Grid-independent lightning NOx emissions]] (3-hourly)
|Lee Murray (Rochester)
|Science
|[[#New data directories in 12.4.0|See ''New data directories in 12.4.0'']]


<span style="color:green">'''''This fix was included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span>
|-valign="top"
|[[Grid-independent_emissions#Biogenic_VOC_emissions|Grid-independent biogenic emissions]] (hourly)
|Jintai Lin (PKU)<br>Hongjian Meng (PKU)
|Science
|[[#New data directories in 12.4.0|See ''New data directories in 12.4.0'']]


The P(H2O2) field is required as input in the aerosol-only simulations. To simplify saving out new oxidant fields, we now include P(H2O2) by default in the prod/loss families so that it is saved out when users turn on the prod/loss diagnostic in either bpch or netCDF format.
|-valign="top"
|[[Grid-independent_emissions#Sea_salt_emissions|Grid-independent sea salt emissions]] (hourly)
|Jintai Lin (PKU)<br>Hongjian Meng (PKU)
|Science
|[[#New data directories in 12.4.0|See ''New data directories in 12.4.0'']]


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:16, 20 July 2018 (UTC)
|-valign="top"
|[[Grid-independent_emissions#Soil_NOx_emissions|Grid-independent soil NOx emissions]] (hourly)
|Jintai Lin (PKU)<br>Hongjian Meng (PKU)
|Science
|[[#New data directories in 12.4.0|See ''New data directories in 12.4.0'']]


=== Fixed typo that prevented PM2.5 from being archived to netCDF output ===
|-valign="top"
|[[Volcanic_SO2_emissions#OMI-based_volcanic_emissions|Updated volcano emissions (1978-2019)]]
|Christoph Keller (NASA/GMAO)
|Science
|[[#New data directories in 12.4.0|See ''New data directories in 12.4.0'']]


<span style="color:green">'''''This fix was included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span>
|-
|[[FAST-JX_v7.0_photolysis_mechanism#Further_fix_added_in_12.4.0|Bug fix: Rebuild chemical mechanisms for FAST-JX fix added in 12.3.2]]
|Katie Travis (NASA)
|Bug fix
|


In routine <tt>Set_AerMass_Diagnostic</tt> of module <tt>GeosCore/diagnostics_mod.F90</tt>, there was a typo in the IF block where the PM2.5 diagnostic values get copied into <tt>State_Diag%PM25</tt>.  The code in <span style="color:red">RED</span> below:
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:


        IF ( <span style="color:red">Archive_BetaNO</span> ) THEN
|-valign="top"
          State_Diag%PM25(I,J,L)            = ...etc...
|[[FlexGrid|FlexGrid Stage 2: Add capability to define custom grids]]
|Melissa Sulprizio ([[GCST]])<br>Jiawei Zhuang (Harvard)
|Structural
|


needs to be replaced by the code in <span style="color:green">GREEN</span>:
|-valign="top"
|[[FAST-JX_v7.0_photolysis_mechanism#FAST-JX_directory|Add photolysis menu to input.geos for specifying FAST-JX directory]]
|Tomas Sherwen (York)
|Structural
|[https://github.com/geoschem/geos-chem/pull/34 geoschem/geos-chem PR #34]


        IF ( <span style="color:green">Archive_PM25</span> ) THEN
|}
          State_Diag%PM25(I,J,L)            = ...etc...
 
==== New data directories in 12.4.0 ====
 
The following data directories have been added or updated in this version. You will have to [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|download the directories]] relevant to your simulation.


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:33, 24 July 2018 (UTC)
{| border=1 cellspacing=0 cellpadding=5
 
|-bgcolor="#CCCCCC"
=== Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory ===
!width="200px"|Inventory
 
!width="100px"|Type
<span style="color:green">'''''This fix was included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span>
!width="400px"|What was added?
 
!width="300px"|Directory
The CEDS emissions entries in HEMCO_Config.rc were missing for species SOAP and pFe. To fix this, add the following lines in <span style="color:green">GREEN</span>:
 
 
|-valign="top"
0 CEDS_CO_AGR    $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc            CO_agr            1950-2014/1-12/1/0 C xy kg/m2/s CO    26    1/2/12 5
|[[Mineral_dust_aerosols#Offline_Dust_Emissions|OFFLINE_DUST]]
<span style="color:green">0 CEDS_SOAP_AGR  -                                                                     -                 -                 - - -       SOAP  26/280 1/2/12 5</span>
|Default
0 CEDS_CO_ENE    $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc            CO_ene            1950-2014/1-12/1/0 C xy kg/m2/s CO    26    1/2/12 5
|Offline dust emissions generated with:
<span style="color:green">0 CEDS_SOAP_ENE  -                                                                     -                 -                 - - -      SOAP  26/280 1/2/12 5</span>
*GEOS-FP meteorology (0.25&deg;x0.3125&deg;, 2014-present)
0 CEDS_CO_IND    $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc            CO_ind            1950-2014/1-12/1/0 C xy kg/m2/s CO    26    1/2/12 5
*MERRA-2 meteorlogy (0.5&deg;x0.625&deg;, 1980-present)
<span style="color:green">0 CEDS_SOAP_IND  -                                                                     -                 -                 - - -      SOAP  26/280 1/2/12 5</span>
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/OFFLINE_DUST/v2019-01/ <tt>HEMCO/OFFLINE_DUST/v2019-01</tt>]
0 CEDS_CO_TRA    $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc            CO_tra            1950-2014/1-12/1/0 C xy kg/m2/s CO    26    1/2/12 5
 
<span style="color:green">0 CEDS_SOAP_TRA  -                                                                     -                 -                  - -  -      SOAP  26/280 1/2/12 5</span>
|-valign="top"
0 CEDS_CO_SLV    $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc            CO_slv            1950-2014/1-12/1/0 C xy kg/m2/s CO    26    1/2/12 5
|[[Grid-independent_emissions#Lightning_NOx_emissions|OFFLINE_LIGHTNING]]
<span style="color:green">0 CEDS_SOAP_SLV  -                                                                      -                -                  - -  -      SOAP  26/280 1/2/12 5</span>
|Default
0 CEDS_CO_WST    $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc            CO_wst            1950-2014/1-12/1/0 C xy kg/m2/s CO    26    1/2/12 5
|Offline lightning flash densities and convective-cloud depths generated with:
  <span style="color:green">0 CEDS_SOAP_WST  -                                                                      -                -                  - -  -       SOAP  26/280 1/2/12 5</span>
*GEOS-FP meteorology (0.25x0.3125, 2014-2018)
0 CEDS_SO2_AGR    $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc          SO2_agr          1950-2014/1-12/1/0 C xy kg/m2/s SO2  -      1/2/12 5
*MERRA-2 meteorology (0.5x0.625, 1980-2018).
  0 CEDS_SO4_AGR    -                                                                     -                 -                  - -  -      SO4  63    1/2/12 5
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/OFFLINE_LIGHTNING/v2019-01/ <tt>HEMCO/OFFLINE_LIGHTNING/v2019-01</tt>]
  <span style="color:green">0 CEDS_pFe_AGR    -                                                                     -                -                  - -  -      pFe  66    1/2/12 5</span>
 
0 CEDS_SO2_ENE    $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc          SO2_ene          1950-2014/1-12/1/0 C xy kg/m2/s SO2  -      1/2/12 5
|-valign="top"
0 CEDS_SO4_ENE    -                                                                     -                -                  - -  -       SO4  63    1/2/12 5
|[[Grid-independent_emissions#Biogenic_VOC_emissions|OFFLINE_BIOVOC]]
<span style="color:green">0 CEDS_pFe_ENE    -                                                                     -                -                  - - -       pFe  66    1/2/12 5</span>
|Default
0 CEDS_SO2_IND    $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc          SO2_ind          1950-2014/1-12/1/0 C xy kg/m2/s SO2  -     1/2/12 5
|Offline biogenic VOC emissions generated using GEOS-Chem v11-02 and:
0 CEDS_SO4_IND    -                                                                     -                -                  - - -       SO4  63    1/2/12 5
*GEOS-FP meteorology (0.25&deg;x0.3125&deg;, 2014-2017)
<span style="color:green">0 CEDS_pFe_IND    -                                                                     -                -                  - -  -      pFe  66    1/2/12 5</span>
*MERRA-2 meteorlogy (0.5&deg;x0.625&deg;, 1980-2017)
0 CEDS_SO2_TRA    $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc          SO2_tra          1950-2014/1-12/1/0 C xy kg/m2/s SO2  -      1/2/12 5
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/OFFLINE_BIOVOC/v2019-01/ <tt>HEMCO/OFFLINE_BIOVOC/v2019-01</tt>]
0 CEDS_SO4_TRA    -                                                                      -                -                  - -  -      SO4  63    1/2/12 5
 
<span style="color:green">0 CEDS_pFe_TRA    -                                                                     -                 -                 - -  -      pFe  66    1/2/12 5</span>
|-valign="top"
0 CEDS_SO2_SLV    $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc          SO2_slv          1950-2014/1-12/1/0 C xy kg/m2/s SO2  -      1/2/12 5
|[[Grid-independent_emissions#Sea_salt_emissions|OFFLINE_SEASALT]]
0 CEDS_SO4_SLV    -                                                                     -                -                  - -  -      SO4  63    1/2/12 5
|Default
<span style="color:green">0 CEDS_pFe_SLV    -                                                                     -                 -                 - -  -      pFe  66    1/2/12 5</span>
|Offline sea salt emissions generated with:
0 CEDS_SO2_WST    $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc          SO2_wst          1950-2014/1-12/1/0 C xy kg/m2/s SO2  -      1/2/12 5
*GEOS-FP meteorology (0.25&deg;x0.3125&deg;, 2014-2017)
0 CEDS_SO4_WST    -                                                                     -                -                  - -  -      SO4  63    1/2/12 5
*MERRA-2 meteorlogy (0.5&deg;x0.625&deg;, 1980-2017)
<span style="color:green">0 CEDS_pFe_WST    -                                                                      -                 -                  - -  -      pFe  66    1/2/12 5</span>
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/OFFLINE_SEASALT/v2019-01/ <tt>HEMCO/OFFLINE_SEASALT/v2019-01</tt>]
 
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 16:07, 27 July 2018 (UTC)
|-valign="top"
 
|[[Grid-independent_emissions#Soil_NOx_emissions|OFFLINE_SOILNOX]]
=== Remove duplicate C3HI spectrum in FJX_spec.dat and FJX_j2j.dat ===
|Default
 
|Offline soil NOx emissions generated with:
<span style="color:green">'''''This fix was included in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]].'''''</span>
*GEOS-FP meteorology (0.25&deg;x0.3125&deg;, 2014-2017)
*MERRA-2 meteorlogy (0.5&deg;x0.625&deg;, 1980-2017)
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/OFFLINE_SOILNOX/v2019-01/ <tt>HEMCO/OFFLINE_SOILNOX/v2019-01</tt>]
 
|-valign="top"
|[[Volcanic_SO2_emissions|Volcano]]
|Default
|[[Volcanic_SO2_emissions#OMI-based_volcanic_emissions|Updated volcanic SO2 emissions (1978-2019), with eruptive emissions through 3 Dec 2015]]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/VOLCANO/v2019-04/ <tt>HEMCO/VOLCANO/v2019-04/</tt>]
 
|}
 
=== 12.3.2 ===
 
<span style="color:green">'''''This version was released on 02 May 2019.'''''</span>
 
'''[https://doi.org/10.5281/zenodo.2658178 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.
 
  <nowiki> # 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 ..</nowiki>
 
Please see the following links for complete information about the validation of GEOS-Chem 12.3.2:
 
#[[Benchmark/GEOS-Chem_12.3.2|1-month benchmark simulation 12.3.2 for GCC and GCHP (unofficial)]]
 
This version includes the updates listed below.
 
{| border=1 cellspacing=0 cellpadding=5  
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting the full-chemistry simulation:
 
|-valign="top"
|[[#Inconsistency in H2402 concentrations in GCHP vs GEOS-Chem Classic|Fix inconsistency for species H2402 between GCHP and GEOS-Chem "Classic"]]
|Sebastian Eastham (MIT)<br>[[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%
 
|-valign="top"
|Bug fixes for the FAST-JX photolysis mechanism:
*[[FAST-JX_v7.0_photolysis_mechanism#Duplicate_entries_for_species_ClNO2_in_FJX_j2j.dat_file|Remove duplicate entry for species ClNO2 in the FJX_j2j.dat file]]
*[[FAST-JX_v7.0_photolysis_mechanism#Species_DHDC_was_not_listed_as_photolyzing_in_the_species_database|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%
 
|-valign="top"
|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
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:
 
|-valign="top"
|[[CEDS_anthropogenic_emissions#Updates_introduces_in_GEOS-Chem_12.3.2|Extending the CEDS anthropogenic emissions inventory to include 1750-1949 and additional VOC species]]
|Melissa Sulprizio (GCST)
|Science
|
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features only affecting GCHP:
 
|-valign="top"
|[[#Disable Br2 offline seasalt emissions to match GEOS-Chem Classic default|Disable Br2 offline seasalt emissions to match GEOS-Chem Classic default]]
|Sebastian Eastham (MIT)
|Bug fix
|
 
|-valign="top"
|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
 
|-valign="top"
|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 [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|download the directories]] relevant to your simulation.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="200px"|Inventory
!width="100px"|Type
!width="400px"|What was added?
!width="300px"|Directory
 
|-valign="top"
|[[FAST-JX_v7.0_photolysis_mechanism|FAST_JX]]
|DEFAULT
|
*The <tt>FJX_j2j.dat</tt> file (which lists the photolyzing species for FAST-JX) was edited to [[FAST-JX_v7.0_photolysis_mechanism#Duplicate_entries_for_species_ClNO2_in_FJX_j2j.dat_file|remove a duplicate entry for ClNO2]]. This was causing the J-values of ClNO2 to be passed to the solver twice.  The new <tt>FJX_j2j.dat</tt> file corrects this issue.
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/CHEM_INPUTS/FAST_JX/v2019-04/README <tt>CHEM_INPUTS/FAST_JX/v2019-04</tt>]
 
|-valign="top"
|[[UCX chemistry mechanism]]
|DEFAULT
|
*A new file (<tt>Montreal_fix.nc</tt>) was created to fix an [[#Inconsistency in H2402 concentrations in GCHP vs GEOS-Chem Classic|inconsistency in H2402 concentrations between GCHP and GEOS-Chem "Classic"]].
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/CHEM_INPUTS/UCX_201904/README <tt>CHEM_INPUTS/UCX_201904</tt>]
 
|-valign="top"
|[[CEDS_anthropogenic_emissions|CEDS]]
|OPTIONAL
|
*CEDS anthropogenic emissions for 1750-1949. Data now encompasses the entire CEDS record of 1750-2014.
*New files for additional NMVOCs
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/CEDS/v2018-08/ <tt>HEMCO/CEDS/v2018-08</tt>]
 
|}
 
=== 12.3.1 ===
 
<span style="color:green">'''''This version was released on 08 Apr 2019.'''''</span>
 
'''[https://doi.org/10.5281/zenodo.2633278 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.
 
<nowiki> # 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</nowiki>
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:
 
|-valign="top"
|[[List_of_diagnostics_archived_to_netCDF_format#The_JValuesLocalNoon_collection|Fix the netCDF diagnostic for noontime J-values]]
|[[GCST]]
|Bug fix
|
 
|-valign="top"
|[[Planeflight_diagnostic#Planeflight_diagnostic_now_writes_out_data_for_the_last_timestep_of_the_day|Planeflight diagnostic now writes out data for the last timestep of the day]]
|Luke Schiferl (LDEO/Columbia)<br>[[GCST]]
|Bug fix
|
 
|-valign="top"
|[[Stratospheric_chemistry#Do not allocate memory to array MINIT in strat_chem_mod.F90|Reduce memory footprint: Do not allocate memory to array MINIT in <tt>strat_chem_mod.F90</tt>]]
|Bob Yantosca ([[GCST]])
|Bug fix
|
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features only affecting GCHP:
 
|-valign="top"
|[[#Declare State_Met%AREA_M2 as 2-dimensional, not 3-dimensional|Declare <tt>State_Met%AREA_M2</tt> as 2-dimensional, not 3-dimensional]]
|[[GCST]]
|Bug fix
|
 
|}
 
=== 12.3.0 ===
 
<span style="color:green">'''''This version was released on 01 Apr 2019.'''''</span>
 
'''[https://doi.org/10.5281/zenodo.2620535 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.
 
  <nowiki># 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</nowiki>
 
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.3.0|new data directories for this version]].
 
Please see the following links for complete information about the validation of GEOS-Chem 12.3.0:
#[[Benchmark/GEOS-Chem 12.3.0|''Approval form for 1-month benchmark simulation 12.3.0]]
This version includes the updates listed below.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting the full-chemistry simulation:
 
|-valign="top"
|[[ISORROPIA_II#Investigating_persistent_noise_observed_in_ISORROPIA_output|Update ISORROPIA from v2.0 to v2.2, in order to remove persistent noise in output]]
|Seb Eastham (Harvard)
|Science
|
 
|-valign="top"
|[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Updated_PFT_file|Updated PFT file for MEGAN]]
|Jenny Fisher (Wollongong)<br>Dylan Millet (UMN)
|Science
|
 
|-valign="top"
|[[Volcanic_SO2_emissions#Bug_fix_for_eruptive_volcanic_emissions|Bug fix for eruptive volcanic emissions]]
|Barron Henderson (EPA)
|Bug fix
|
 
|-valign="top"
|Read in and regrid existing MODIS LAI and OLSON data via HEMCO
|Bob Yantosca ([[GCST]])
|Structural
|
 
|-valign="top"
|Update from [[HEMCO_versions#HEMCO_development_history|HEMCO version]] 2.1.011 to 2.1.012
*[[HEMCO_versions#Bug_fixes_for_HEMCO_interpolation_algorithm|Bug fixes for the HEMCO interpolation algorithm]]
*[[HEMCO_versions#Updates from the NASA GEOS development branch|Updates from the NASA GEOS development branch]]
*[[HEMCO_versions#Add_option_to_always_use_simulation_year_for_specified_fields|Add option to always use simulation year for specified fields]]
*[[HEMCO_versions#Prevent zero emissions for MEGAN_Mono extension species|Prevent zero emissions for MEGAN_Mono extension species]]
*[[HEMCO_versions#Updates_to_the_volcanic_emissions_extension|Updates to the HEMCO volcanic emissions extension]]
|Christoph Keller (NASA/GMAO)<br>[[GCST]]
|Bug fix &<br>Structural
|
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:
 
|-valign="top"
|[[Leaf_area_indices_in_GEOS-Chem#Yuan_processed_MODIS_LAI|Update to Yuan processed MODIS LAI product (covering years 2005-2016)]]
*'''Off while we investigate an issue in the HEMCO interpolation'''
|Jenny Fisher (Wollongong) <br>Barron Henderson (US EPA)
|Science
|
 
|-valign="top"
|[[Volcanic_SO2_emissions#OMI-based_volcanic_emissions|OMI-based Volcanic emissions 2005-2012]] (off by default)
|Cui Ge (U. Iowa)<br>Jun Wang (U. Iowa)<br>[[GCST]]
|Science
|
 
|-valign="top"
|[[#Further_bug_fix_to_prevent_incorrect_restart_file_output_when_spanning_leap_year_days|Further bug fix for netCDF diagnostics spanning leap years]]
|Bob Yantosca ([[GCST]])
|Bug fix
|
 
|-valign="top"
|[[GFAS_biomass_burning_emissions#Fix_GFAS_SOAP_entry_in_HEMCO_Config.rc|Fix GFAS_SOAP entry in HEMCO_Config.rc]]
|Killian Murphy (York)
|Bug fix
|
 
|-valign="top"
|[[GEOS-Chem_12#Tagged_CO_bug_fixes:_Fix_CO_units_and_write_secondary_production_into_a_netcdf_file|Tagged CO bug fixes: Fix CO units and write secondary production into a netcdf file]]
|Beata Bukosa (Wollongong)
|Bug fix
|
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting GCHP only:
 
|-valign="top"
|[[#GCHP_adjoint_development_requires_time_to_run_backwards_in_GCHP|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 [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|download the directories]] relevant to your simulation.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="200px"|Inventory
!width="100px"|Type
!width="400px"|What was added?
!width="300px"|Directory
 
|-valign="top"
|OLSON_MAP
|DEFAULT
|Olson 2001 land map masks, separated into 73 netCDF variables (one per land type).  This format facilitates regridding by HEMCO.
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/OLSON_MAP/v2019-02/ <tt>HEMCO/OLSON_MAP/v2019-02</tt>]
 
|-valign="top"
|MODIS_XLAI
|DEFAULT
|MODIS LAI data (corresponding to <tt>ExtData/CHEM_INPUTS/MODIS_LAI_201707</tt>)
 
This data has been processed into 73 netCDF variables (one corresponding to each Olson land type), which facilitates regridding by HEMCO.
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MODIS_XLAI/v2017-07/ <tt>HEMCO/MODIS_XLAI/v2017-07</tt>]
 
|-valign="top"
|MEGAN
|DEFAULT
|[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Updated_PFT_file|Updated PFT file for MEGAN]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2018-05/ <tt>HEMCO/MEGAN/v2018-05/</tt>]
 
|}
 
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 ===
 
<span style="color:green">'''''This version was released on 28 Feb 2019.'''''</span>
 
[https://doi.org/10.5281/zenodo.2580198 '''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.
 
  <nowiki># 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</nowiki>
 
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.2.1|new data directories for this version]].
 
This version includes the updates listed below.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:
 
|-valign="top"
|[[#Bug fix: netCDF diagnostic collections with frequency "End" now properly span leap year days|Bug fix: netCDF diagnostic collections with frequency "End" now properly span leap year days]]
|Amos Tai (CUHK)<br>[[GCST]]
|Structural
|
 
|-valign="top"
|[https://github.com/geoschem/geos-chem/pull/27 Move module-level variables from Linoz and MODIS LAI]
|Haipeng Lin (PKU)
|Structural
|
 
|-valign="top"
|[[Mercury#Polar_bromine_explosion_default_option|Make polar bromine explosion the default option in Hg simulation]]
|Colin Thackray (Harvard)<br>Jenny Fisher (Wollongong)
|Science
|
 
|-valign="top"
|TOMAS updates
*[[TOMAS_aerosol_microphysics#Biomass_burning_subgrid_coagulation_switch|Add biomass burning subgrid coagulation option]]
*[[TOMAS_aerosol_microphysics#Restore_DST1.2C_DST2.2C_DST3.2C_and_DST4_in_TOMAS_simulations|Restore DST1, DST2, DST3, and DST4 in TOMAS simulations]]
|Emily Ramnarine (Colorado State)<br>Jeff Pierce (Colorado State)<br>Betty Croft (Dalhousie)
|Science
|
 
|-valign="top"
|[[GEOS-Chem_12#Fix_Henry.27s_Law_coefficient_for_C2H6|Fix Henry's Law coefficient for C2H6]]
|Chris Holmes (FSU)
|Bug fix
|
 
|-valign="top"
|Add routine to save the GC species database to JSON format (commented out)
|Bob Yantosca ([[GCST]])
|Structural
|
 
|-valign="top"
|[[List_of_diagnostics_archived_to_netCDF_format|Add RRTMG fluxes to netCDF diagnostics]]
|Bob Yantosca ([[GCST]])
|Structural
|
*Still needs to be validated
 
|-valign="top"
|[[CO2_simulation#Prevent_double-counting_in_CO2_chemical_source|Fix for CO2 simulation chemical source]]
|Beata Bukosa (U. Wollongong)
|Bug fix
|
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting GCHP only:
 
|-valign="top"
|[[GEOS-Chem_12#GCHP_uses_outdated_MODIS_files_missing_projection_error_fix|Update MODIS LAI source directory to match GEOS-Chem Classic]]
|GCST
|Bug fix
|
 
|-valign="top"
|[[GEOS-Chem_12#Missing_scaling_factors_for_MERRA-2_simulations_with_GCHP|Missing scaling factors for MERRA-2 simulations with GCHP]]
|Sebastian Eastham (MIT)
|Bug fix
|
 
|-valign="top"
|[[GEOS-Chem_12#Use_online_sea_flux_emissions_by_default_in_GCHP|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 [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|download the directories]] relevant to your simulation.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="200px"|Inventory
!width="100px"|Type
!width="400px"|What was added?
!width="300px"|Directory
 
|-valign="top"
|[[CO2_simulation#Prevent_double-counting_in_CO2_chemical_source|Updated chemical source for CO2 simulation]]
|OPTIONAL
|Reprocessed the chemical source file for the [[CO2 simulation]], because the existing file was somehow corrupted.
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/CO2/v2019-02/CHEM <tt>HEMCO/CO2/v2019-02/CHEM/</tt>]
 
|-valign="top"
|[[FINNv1_biomass_burning_emissions|FINN]]
|OPTIONAL
|[[TOMAS_aerosol_microphysics#Biomass_burning_subgrid_coagulation_switch|Files containing the number of fires per grid box for use with the biomass burning subgrid coagulation option in TOMAS simulations]].
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/FINN/v2015-02/ <tt>HEMCO/FINN/v2015-02/</tt>]
 
|}
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:34, 13 February 2019 (UTC)
 
=== 12.2.0 ===
 
<span style="color:green">'''''This version was released on 19 Feb 2019.'''''</span>
 
[https://doi.org/10.5281/zenodo.2572887 '''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.
 
  <nowiki># 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</nowiki>
 
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.2.0|new data directories for this version]].
 
Please see the following links for complete information about the validation of GEOS-Chem 12.2.0:
#[[GEOS-Chem_12_benchmark_history#12.2.0|''Approval form for 1-month benchmark simulation 12.2.0'']]
#[[GEOS-Chem_12_benchmark_history#12.2.0-TransportTracers|''1-year transport benchmark simulation'']]
 
This version includes the updates listed below.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting the full-chemistry simulation:
 
|-valign="top"
|[[Anthropogenic_emissions#BRAVO|Retire BRAVO emissions and use CEDS for Mexico instead]]
|Melissa Sulprizio ([[GCST]])
|Science
|
 
|-valign="top"
|[[EPA/NEI11_North_American_emissions#Update_mask_file_applied_to_NEI2011_emissions|Update mask file applied to NEI2011 emissions]]
|Melissa Sulprizio ([[GCST]])
|Bug fix
|
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:
 
|-valign="top"
|[[Transport_Working_Group#Transport_Tracers_simulation|Transport Tracers simulation: a common set of tracers in GEOS-Chem and GEOS]]
|Transport WG<br>Melissa Sulprizio ([[GCST]])
|Benchmarking
|
*Added to the GEOS-Chem Rn-Pb-Be simulation, but may be added to any simulation by following [[Transport_Working_Group#Implementation_in_GEOS-Chem|these steps]].
*This will facilitate comparisons of transport between GEOS-Chem "Classic" and/or GCHP vs. the NASA GEOS-DAS system.
 
|-valign="top"
|[[ObsPack diagnostic]]
|Andy Jacobson (NOAA/ESRL)<br>Bob Yantosca ([[GCST]])
|Structural
|
 
|-valign="top"
|[[GFAS biomass burning emissions]] (as an option)
|Mat Evans (York)<br>Killian Murphy (York)
|Science
|
 
|-valign="top"
|[[GEOS-Chem_12#Fix_bug_in_stratosperic_aerosol_surface_area_netcdf_diagnostics|Fix bug in stratosperic aerosol surface area netcdf diagnostics]]
|Jonathan Moch (Harvard)<br>Christoph Keller (GMAO)
|Bug fix
|
 
|-valign="top"
|Update from HEMCO 2.1.010 to HEMCO 2.1.011:
*[[HEMCO versions#Wrap remaining HEMCO extensions in instances|Now wrap the remaining HEMCO extensions in instances (to facilitate running in HPC environments)]]
*[[HEMCO_versions#Update_HEMCO_standalone_for_compatibility_with_FlexGrid|Update HEMCO standalone for compatibility with FlexGrid met field names]]
*[[HEMCO_versions#HEMCO_standalone_now_calls_HCO_RUN_in_two_phases|HEMCO standalone now calls HCO_RUN in two phases]]
|[[GCST]]
|Structural
|
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting GCHP only:
 
|-valign="top"
|[[GEOS-Chem_12#ESMF_version_update_required_for_MAPL_upgrade|Update ESMF version in GCHP from v5.2.0rp2 to v7.1.0r]]
|Lizzie Lundgren ([[GCST]])
|Structural
|
*Currently compatible with Intel compilers only
 
|-valign="top"
|[[GEOS-Chem_restart_files#New_fields_added_to_the_GEOS-Chem_restart_file|New fields in GCHP output restart file]]
|Lizzie Lundgren ([[GCST]])
|Bug Fix &<br>Structural
|
*Adds additional variables to GCHP internal state for carrying across multi-segmented runs
*Equivalent to GEOS-Chem Classic update in [[GEOS-Chem_12#12.1.0|12.1.0]]
 
|-valign="top"
|[[GEOS-Chem_12#GCHP_Bug_fix:_use_checkpoint_output_file_as_subsequent_run_restart|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 [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|download the directories]] relevant to your simulation.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="200px"|Inventory
!width="100px"|Type
!width="400px"|What was added?
!width="300px"|Directory
 
|-valign="top"
|[[GFAS biomass burning emissions]]
|OPTIONAL
|GFAS biomass burning emissions for 2003-present (updated monthly)
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/GFAS/v2018-09/ <tt>HEMCO/GFAS/v2018-09/</tt>]
 
|-valign="top"
|[[EDGAR_v4.2_anthropogenic_emissions|EDGAR v4.2 emissions of SF6]]
|DEFAULT
|EDGAR v4.2 emissions of SF6 for 1970-2008
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/SF6/v2019-01/ <tt>HEMCO/SF6/v2019-01/</tt>]
 
|-valign="top"
|MASKS
|DEFAULT
|[[EPA/NEI11_North_American_emissions#Update_mask_file_applied_to_NEI2011_emissions|Update mask file applied to NEI2011 emissions]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MASKS/v2018-09/ <tt>HEMCO/MASKS/v2018-09/</tt>]
 
|-valign="top"
|TileFiles
|DEFAULT<br>(in GCHP)
|New tile files for 0.1x0.1 CONUS, Canada, and Mexico mask files
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/GCHP/TileFiles/ <tt>GCHP/TileFiles</tt>]
 
|}
 
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 ===
 
<span style="color:green">'''''This version was released on 13 Dec 2018.'''''</span>
 
[https://doi.org/10.5281/zenodo.2249246 '''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.
 
  <nowiki># 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</nowiki>
 
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.1.0|new data directories for 12.1.0 if you haven't already]].
 
This version includes the updates listed below.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes
 
|-valign="top"
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry (benchmark) simulation:
 
|-valign="top"
|[[Tagged CO simulation#Do not multiply emission timestep by 60|Bug fix for tagged CO: don't multiply emissions timestep by 60]]
|Dylan Jones (U. Toronto)
|Bug fix
|
 
|-valign="top"
|[[GEOS-Chem_12#Skip_planeflight_observations_outside_a_nested_domain|Skip planeflight observations outside a nested domain]]
|Lei Zhu (Harvard)
|Bug fix
|
 
|-valign="top"
|[[GEOS-Chem_12#Always_enable_BCPH_TPBC_to_allow_saving_out_BC_files_in_global_simulations|Always enable BCPH_TPBC to allow saving out BC files in global simulations]]
|Yanxu Zhang (Nanjing)
|Bug fix
|
 
|-valign="top"
|Fix compilation issues:
*[https://github.com/geoschem/geos-chem/commit/096ad29d02afbdba64a5dd138df0c976ddee3140 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"]
*[https://github.com/geoschem/geos-chem/commit/f9b2f19593afeaa396ff3ee3d315148d5a6f8600 Add flexgrid_read_mod.o to list of dependencies for hcoi_gc_main_mod.o]
|<br>Bob Yantosca ([[GCST]])<br>Haipeng Lin (PKU)
|Bug fix
|
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting GCHP only:
 
|-valign="top"
|[[GEOS-Chem_12#GCHP_transport_fix_to_prevent_instant_propagation_from_troposphere_to_stratosphere|GCHP transport fix to prevent instant propagation from troposphere to stratosphere]]
|Seb Eastham (MIT)
|Bug fix
|
 
|}
 
--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 16:05, 6 December 2018 (UTC)
 
=== 12.1.0 ===
 
<span style="color:green">'''''This version was released on 26 Nov 2018.'''''</span>
 
'''[https://doi.org/10.5281/zenodo.1553349 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.
 
  <nowiki># 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</nowiki>
 
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.1.0|new data directories for this version]].
 
Please see the following links for complete information about the validation of GEOS-Chem 12.1.0:
#[[GEOS-Chem_12_benchmark_history#12.1.0|''Approval form for 1-month benchmark simulation 12.1.0'']]
 
This version includes the updates listed below.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting the full-chemistry simulation:
 
|-valign="top"
|[[List_of_diagnostics_archived_to_netCDF_format#The_Budget_collection|Budget diagnostics]]
|Lizzie Lundgren ([[GCST]])<br>Chris Holmes (Florida State)
|Diagnostics
|
*This update introduces differences on the level of numerical noise due to unit conversions
 
|-valign="top"
|[[Mineral_dust_aerosols#Anthropogenic_PM2.5_dust_source_in_GEOS-Chem|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)
**&Delta; Mean OH: -0.000066%
**&Delta; MCF lifetime: 0.0020%
**&Delta; CH4 lifetime: 0.0012%
 
|-valign="top"
|[[GEOS-Chem restart files#Restart files in GEOS-Chem 12|GEOS-Chem restart file updates]]
|Melissa Sulprizio ([[GCST]])
|Bug Fix &<br>Structural
|
*GEOS-Chem Classic only update
*This update introduces the following changes:
**&Delta; Mean OH: -0.016%
**&Delta; MCF lifetime: 0.022%
**&Delta; CH4 lifetime: 0.024%
 
|-valign="top"
|Updates and fixes for the CEDS anthropogenic emissions inventory:
*[[CEDS_anthropogenic_emissions#Add_missing_RCO_sector_to_CEDS_emissions_entries|Add missing RCO sector to CEDS emissions entries]]
*[[CEDS_anthropogenic_emissions#Include_CEDS_ship_emissions|Include CEDS ship emissions as default global ship emissions inventory]]
*[[CEDS_anthropogenic_emissions#Reduce_file_size_for_CEDS_inventory|Reduce file size for CEDS inventory]]
|<br>Pengfei Liu (Harvard)<br>Melissa Sulprizio ([[GCST]])<br>Jiawei Zhuang (Harvard)
|Bug fix
|
*This update introduces the following changes:
**&Delta; Mean OH: 0.17%
**&Delta; MCF lifetime: -0.37%
**&Delta; CH4 lifetime: -0.40%
 
|-valign="top"
|HEMCO fixes:
*[[Implementation_of_HEMCO_in_GEOS-Chem#Bug_fix:_Read_data_with_the_.22E.22_cycle_flag_just_once|HEMCO bug fix: prevent excessive attempts to read the HEMCO restart file when using GEOS-Chem "Classic"]]
*[[Implementation_of_HEMCO_in_GEOS-Chem#Add_fix_for_collapsing_model_levels_to_reduced_grid|Add fix for collapsing model levels to reduced grid]]
*[[Implementation_of_HEMCO_in_GEOS-Chem#Fix_unit_conversion_in_HCO_UNIT_GetAreaScal|Fix unit conversion in HCO_UNIT_GetAreaScal]]
|<br>Bob Yantosca ([[GCST]])<br>Melissa Sulprizio ([[GCST]])<br>Erin McDuffie (Dalhousie)
|Bug fix
|
*This update introduces very small changes:
**&Delta; Mean OH: -0.952%
**&Delta; MCF lifetime: 1.454%
**&Delta; CH4 lifetime: 1.502%
 
|-valign="top"
|[[Boundary_layer_mixing#Mass_is_not_conserved_when_using_non-local_PBL_mixing|Fix mass conservation in non-local PBL mixing]]
|Jintai Lin (PKU)
|Bug fix
|
*This update introduces very small changes:
**&Delta; Mean OH: 0.0057%
**&Delta; MCF lifetime: -0.0061%
**&Delta; CH4 lifetime: -0.0073%
 
|-valign="top"
|[[#Allow_for_SZA_to_98_degrees_when_getting_photolysis_rates|Allow for SZA to 98 degrees when getting photolysis rates]]
|Eric Fleming (GMAO)
|Bug fix
|
*This update introduces the following changes:
**&Delta; Mean OH: 0.3982%
**&Delta; MCF lifetime: -0.3665%
**&Delta; CH4 lifetime: -0.3680%
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:
 
|-valign="top"
|[[FlexGrid|FlexGrid Stage 1: Use HEMCO to read met fields]]
|Jiawei Zhuang (Harvard)<br>Jintai Lin (PKU)
|Structural
|
 
|-valign="top"
|[[GEOS-Chem 12#Add support for continuous integration with TravisCI|Add support for continuous integration with TravisCI &ndash; automatically test each commit as soon as it is pushed to Github]]
|Jiawei Zhuang (Harvard)<br>Bob Yantosca ([[GCST]])
|Structural
|
*[https://travis-ci.com/geoschem/geos-chem/builds See build status page here]
 
|-valign="top"
|Added [[List of diagnostics archived to netCDF format|netCDF diagnostics]] in the following areas:
*[[CH4 simulation]]
*[[CO2 simulation]]
*[[POPs simulation|Persistent Organic Pollutants (POPS) simulation]]
*[[Mercury|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.
 
|-valign="top"
|[[Coupling_GEOS-Chem_with_RRTMG#netCDF_inputs_via_HEMCO|Convert input data for RRTMG from bpch to netCDF for input via HEMCO]]
|Bob Yantosca ([[GCST]])
|Structural
|
 
|-valign="top"
|[[CH4_simulation#Add_fixes_for_seasonal_scale_factors_in_CH4_simulations|Add fixes for seasonal scale factors in CH4 simulations]]
|Bram Maasakkers (SRON)<br>Melissa Sulprizio ([[GCST]])
|Bug fix
|
 
|-valign="top"
|[[GEOS-Chem_v11-02#Code_cleanup_suggestions|Move Fast-JX .dat files from the <tt>geos-chem-unittest</tt> repository to <tt>gcgrid/ExtData</tt>]]
|Chris Holmes (Florida State)<br>[[GCST]]
|Structural
|
 
|-valign="top"
|[[GEOS-Chem_12#Update_HEMCO_configuration_file_for_tagged_CO_simulation|Update HEMCO configuration file for the tagged CO simulation]]
|Bob Yantosca ([[GCST]])
|Bug fix
|
 
|-valign="top"
|Structural updates to facilitate interfacing GEOS-Chem into WRF
|Haipeng Lin (Peking U)<br>[[GCST]]
|Structural
|
*This process will be ongoing throughout the GEOS-Chem 12 series of releases.
 
|-valign="top"
|Structural updates to facilitate interfacing GEOS-Chem into GEOS-5
|Christoph Keller (GMAO)<br>Lizzie Lundgren (GCST)
|Structural
|
*This process will be ongoing throughout the GEOS-Chem 12 series of releases.
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting GCHP only:
 
|-valign="top"
|[[GEOS-Chem_12#Fix_masked_anthropogenic_emissions_bug_in_GCHP|Fix masking bug to correctly apply anthropogenic emissions]]
|Lizzie Lundgren ([[GCST]])
|Bug fix
|
 
|-valign="top"
|[[GEOS-Chem_12#Fix_regional_tile_file_used_for_APEI_inventory_in_GCHP|Remove erroneous 180 degree longitude shift in APEI regridding]]
|Lizzie Lundgren ([[GCST]])
|Bug fix
|
 
|-valign="top"
|Move GCHP run directory creation from GEOS-Chem Unit Tester to GCHP repository
|Lizzie Lundgren ([[GCST]])
|Structural
|
 
|}
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|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 [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|download the directories]] relevant to your simulation.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="200px"|Inventory
!width="100px"|Type
!width="400px"|What was added?
!width="300px"|Directory
 
|-valign="top"
|[[Mineral_dust_aerosols|DUST DEAD]]
|DEFAULT
|[[Mineral_dust_aerosols#Anthropogenic_PM2.5_dust_source_in_GEOS-Chem|Anthropogenic PM2.5 dust source]]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/DUST_DEAD/v2018-04/ <tt>HEMCO/DUST_DEAD/v2018-04/</tt>]
 
|-valign="top"
|[[GEOS-Chem restart files]]
|DEFAULT
|[[GEOS-Chem_restart_files#New_fields_added_to_the_GEOS-Chem_restart_file|GEOS-Chem restart file updates: New variables, new variable names, new file names]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/GEOSCHEM_RESTARTS/v2018-11/ <tt>GEOSCHEM_RESTARTS/v2018-11/</tt>]
 
|-valign="top"
|[[FAST-JX_v7.0_photolysis_mechanism#Input_files_for_FAST-JX_v7.0|Input files for FAST-JX]]
|DEFAULT
|[[GEOS-Chem_v11-02#Code_cleanup_suggestions|Move Fast-JX .dat files from the <tt>geos-chem-unittest</tt> repository to <tt>gcgrid/ExtData</tt>]]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/CHEM_INPUTS/FAST_JX/v2018-09/ <tt>CHEM_INPUTS/FAST_JX/v2018-09/</tt>]
 
|-valign="top"
|[[Coupling GEOS-Chem with RRTMG|RRTMG input data]]
|OPTIONAL
|[[Coupling_GEOS-Chem_with_RRTMG#netCDF_inputs_via_HEMCO|netCDF input data files for the RRTMG specialty simulation (converted from the old "binary punch" format files)]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/RRTMG/v2018-11/ <tt>HEMCO/RRTMG/v2018-11/</tt>]
 
|-valign="top"
|[[CEDS anthropogenic emissions]]
|DEFAULT
|[[CEDS_anthropogenic_emissions#Reduce_file_size_for_CEDS_inventory|Reduce file size for CEDS inventory]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/CEDS/v2018-08/ <tt>HEMCO/CEDS/v2018-08/YYYY</tt>]
 
|-valign="top"
|MASKS
|DEFAULT
|Clean up mask file directory to remove obsolete files
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MASKS/v2018-09/ <tt>HEMCO/MASKS/v2018-09/</tt>]
 
|}
 
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 ===
 
<span style="color:green">'''''This version was released on 16 Oct 2018.'''''</span>
 
'''[https://doi.org/10.5281/zenodo.1464210 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.
 
<nowiki># 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</nowiki>
 
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.0.0|new data directories for 12.0.0 if you haven't already]].
 
This version contains fixes that will only impact [[GCHP]].
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting GCHP only:
 
|-valign="top"
|[[#Fix_incorrect_run_configuration_for_offline_sea_salt_emissions_in_GCHP|Fix incorrect run configuration for offline sea salt emissions in GCHP]]
|Sebastian Eastham (MIT)
|Bug fix
|
 
|-valign="top"
|[[#Fix_bug_in_application_of_CFC_surface_mixing_ratios_in_GCHP|Fix bug in application of CFC surface mixing ratios in GCHP]]
|Sebastian Eastham (MIT)
|Bug fix
|
 
|}
 
--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 18:21, 16 October 2018 (UTC)
 
=== 12.0.2 ===
 
<span style="color:green">'''''This version was released on 10 Oct 2018.'''''</span>
 
[https://doi.org/10.5281/zenodo.1455215 '''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.
 
  <nowiki># 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</nowiki>
 
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.0.0|new data directories for 12.0.0 if you haven't already]].
 
This version includes the updates listed below.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry (benchmark) simulation:
 
|-valign="top"
|[[#Fixed_local-time_averaging_in_ND51_and_ND51b_satellite_timeseries_diagnostics|Fixed local-time averaging in ND51 and ND51b satellite timeseries diagnostics]]
|Bo Zhang (NIA)
|Bug fix
|Implemented 04 Oct 2018
 
|-valign="top"
|[[TOMAS_aerosol_microphysics#Fixes_for_missing_biomass_emissions_and_incorrect_aerosol_dry_deposition|Fixes to correct missing BC/OC biomass emissions and incorrect aerosol drydep in TOMAS simulations]]
|Pengfei Liu (Harvard)
|Bug fix
|Implemented 25 Sep 2018
 
|-valign="top"
|[[CO2_simulation#CO2_emissions_are_double_counted|Avoid double-counting of emissions in the CO2 simulation]]
|Beata Bukosa (U. Wollongong)<br>Christoph Keller (GMAO)
|Bug fix
|Implemented 24 Sep 2018.
 
|}
 
--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 18:21, 16 October 2018 (UTC)
 
=== 12.0.1 ===
 
<span style="color:green">'''''This version was released on 24 Aug 2018.'''''</span>
 
'''[https://doi.org/10.5281/zenodo.1403144 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.
 
  <nowiki># 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</nowiki>
 
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.0.0|new data directories for 12.0.0 if you haven't already]].
 
This version includes the updates listed below.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry (benchmark) simulation:
 
|-valign="top"
|[[#Fix typo when registering the State_Chm%SSAlk field|Fix typo when registering the <tt>State_Chm%SSAlk</tt> field]]
|Shuting Zhai (U. Washington)<br>[[GCST]]
|Bug fix
|
 
|-valign="top"
|Add fixes for several compilation issues:
#Nullify rather than deallocate 3D met arrays for compatibility with gfortran 6+ when using GCHP
#[[GEOS-Chem_Makefile_Structure#Add a more robust test for netCDF-Fortran in Makefile_header.mk|Add a more robust test for netCDF-Fortran in Makefile_header.mk]]
#[[GNU_Fortran_compiler#Compiliation_issues_with_GNU_Fortran_8.2.0|Fix compilation issues encountered with GNU Fortran 8.2.0]]
#[[Intel_Fortran_Compiler#Compilation_issues_with_Intel_Fortran_18|Fix compilation issues encountered with Intel Fortran 18]]
 
|[[GCST]]
|Bug fix
|
 
|-valign="top"
|[[Mercury#Restore_biomass_emissions_and_do_not_double_count_anthropogenic_emissions|Fixes for the Hg specialty simualtion: Restore biomass emissions and do not double-count anthropogenic emissions]]
|Colin Thackray (Harvard)
|Bug fix
|
 
|-valign="top"
|[[Sulfate aerosols#Fix mis-indexing in the ND05 diagnostic|Fix mis-indexing in the ND05 diagnostic]]
|[[GCST]]
|Bug fix
|
 
|-valign="top"
|Minor updates to facilitate interfacing GEOS-Chem into GEOS-5
|Lizzie Lundgren (GCST)
|Structural
|
 
|}
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:31, 10 October 2018 (UTC)
 
=== 12.0.0 ===
 
<span style="color:green">'''''This version was released on 10 Aug 2018'''''</span>
 
[https://doi.org/10.5281/zenodo.1343547 '''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.
 
  <nowiki># 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</nowiki>
 
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.0.0|new data directories for this version]].
 
For more information about getting set up with GEOS-Chem, please see the [http://manual.geos-chem.org 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#v11-02 GEOS-Chem v11-02 release candidate|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:
#[[GEOS-Chem_12_benchmark_history#12.0.0|''Approval form for 1-month benchmark simulation 12.0.0'']]
#[[GEOS-Chem_12_benchmark_history#12.0.0-Run0|''Results for 1-year benchmark simulation 12.0.0-Run0'']]
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="500px"|Feature
!width="200px"|Submitted by
!width="100px"|Type
!width="300px"|Notes
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features affecting the full-chemistry (benchmark) simulation:
 
|-valign="top"
|[[Trash_burning_emissions#Avoid_double_counting_trash_emissions|Turn off TRASH emissions by default to avoid double counting]]
|[[GCST]]<br>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%
 
|-valign="top"
|[[GEOS-Chem 12#Add_entries_to_HEMCO_Config.rc_for_SOAP_and_pFe_in_CEDS_inventory|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%
 
|-valign="top"
|[[#Bug fix for liquid water content in gckpp_HetRates.F90|Bug fix for liquid water content in gckpp_HetRates.F90]]
|Jiayue Huang (U. Washington)<br>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%
 
|-valign="top"
|[[GEOS-Chem 12#Bug_fix_for_CH4_boundary_conditions|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%
 
|-valign="top"
|[[GEOS-Chem 12#Fixed typo in call to GAMMA_HOBr_AER|Fixed typo in call to GAMMA_HOBr_AER]]
|Xuan Wang<br>[[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%
 
|-valign="top"
|Correct issues when specifying [[DICE-Africa anthropogenic emissions inventory|DICE-Africa emissions]]:
*[[DICE-Africa_anthropogenic_emissions_inventory#Avoid_double-counting_between_DICE-Africa_and_other_inventories|Avoid double-counting between DICE-Africa and other inventories]]
*[[DICE-Africa_anthropogenic_emissions_inventory#Use_unique_names_for_DICE-Africa_entries_in_HEMCO_Config.rc|Use unique names for DICE-Africa entries in the <tt>HEMCO_Config.rc</tt> file]]
|Eloise Marais (U. Birmingham)<br>[[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%
 
|-valign="top"
|[[Organics_Working_Group#Add_missing_Criegee_intermediate_reaction|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%
 
|-valign="top"
|[[Ship_emissions#Fix_bug_in_ARCTAS_SHIP_SO2_scale_factors|Bug fix for ARCTAS_SHIP in <tt>HEMCO_Config.rc</tt> 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
 
|-valign="top"
|[[FlexChem#FlexChem bug fix: do not zero ACTA, EOH, HCOOH|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%
 
|-valign="top"
|[[GFED4_biomass_burning_emissions#Years_2015_and_2016_have_been_added|Add GFED4.1 data for 2015 and 2016; Use GFED4.1 2016 in benchmarks]]
|Kate O'Dell (CSU)<br>[[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%
 
|-
!colspan="4" bgcolor="#CCFFFF"|Features NOT affecting the full-chemistry simulation:
 
|-valign="top"
|Bug fixes for stratospheric chemistry:
*[[Stratospheric_chemistry#Disable_STE_calculation_printed_to_log_file|Disable STE calculation printed to log file]]
*[[Linoz_stratospheric_ozone_chemistry#Turn_on_Synoz_when_Linoz_is_set_to_false_in_input.geos|Turn on Synoz when Linoz is set to false in input.geos]]
|[[GCST]]
|Bug fix
|
 
|-valign="top"
|[[Lightning_NOx_emissions#Limit_flash_rate_density_in_hcox_lightnox_mod.F90|Limit flash rate density in hcox_lightnox_mod.F90]]
|Lee Murray (Rochester)
|Bug fix
|
 
|-valign="top"
|[[Coupling_GEOS-Chem_with_NCAR_models#WRF|Initial structural modifications for interfacing GEOS-Chem into WRF]]
|Haipeng Lin (Peking U.)
|Structural
|
*This process is ongoing in GEOS-Chem 12
 
|-
|[[Mercury#Added_chemistry_and_ocean_from_Horowitz_et_al._2017|Minor fixes for mercury chemistry updates implemented in v11-02f]]
|Colin Thackray (Harvard)
|Bug fix
|
 
|-valign="top"
|[[MERRA-2_implementation_details#Default_timestep_for_MERRA-2_nested_grid_simulations|Restore default timestep for MERRA-2 nested grid simulations to 10/20]]
|Ke Li (Harvard)
|Bug fix
|
 
|-valign="top"
|[[GEOS-Chem 12#Remove_duplicate_C3HI_spectrum_in_FJX_spec.dat_and_FJX_j2j.dat|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
 
|-valign="top"
|[[GEOS-Chem 12#Fixed typo that prevented PM2.5 from being archived to netCDF output|Fixed typo that prevented PM2.5 from being archived to netCDF output]]
|Jonathan Moch (Harvard)<br>[[GCST]]
|Bug fix
|
 
|-valign="top"
|[[Two-way_coupling_between_global_and_nested_GEOS-Chem_models|Bring two-way nested-grid code option up-to-date]]
|Yingying Yan (PKU)<br>Jintai Lin (PKU)
|Structural
|
*This option is invoked by compiling with <tt>EXCHANGE=y</tt>
*A difference test w/r/t the previous commit yielded identical results.
 
|-valign="top"
|[[Planeflight_diagnostic#Do_not_force_L.3D1_by_default_in_planeflight_mod.F|Do not force L=1 by default in planeflight_mod.F]]
|Katie Travis (MIT)<br>[[GCST]]
|Bug fix
|
 
|-valign="top"
|[[#Add PH2O2 to the default list of prod/loss families in the KPP mechanisms|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.
 
|-valign="top"
|Update to HEMCO v2.1.008, which includes minor updates:
#[[Implementation of HEMCO in GEOS-Chem#Fixed_error_in_HEMCO_.22exact.22_time_option|Fixed error in HEMCO "exact" cycling option]]
#*NOTE: This update introduced an unforeseen side-effect which will be fixed in [[#12.1.0|GEOS-Chem 12.1.0]].
Update to HEMCO v2.1.007, which includes minor updates:
#[[Implementation of HEMCO in GEOS-Chem#Stop with error if multiple containers have the same name|Stop with error if multiple containers have the same name]]
#[[Implementation of HEMCO in GEOS-Chem#Bug fix for distributing emissions in the vertical dimension|Bug fix for distributing emissions in the vertical dimension]]
#[[Implementation of HEMCO in GEOS-Chem#Add extra error checks in HEMCO standalone module|Add extra error checks in HEMCO standalone module]]
#[[Implementation of HEMCO in GEOS-Chem#Remove null string character from netCDF unit string|Remove null string character from netCDF unit string]]
#[[Implementation_of_HEMCO_in_GEOS-Chem#Bug fix for HEMCO soil NOx error with ifort 17|Bug fix for HEMCO soil NOx error with ifort 17]]
|[[GCST]]<br>Christoph Keller<br>Jenny Fisher
|Structural &<br>Bug fix
|
 
|-valign="top"
|[[GEOS-Chem 12#Bug fix for reference time in netCDF diagnostic files|Bug fix for reference time in netCDF diagnostic files]]
|[[GCST]]
|Bug fix
|
 
|-valign="top"
|Updates for [[QFED biomass burning emissions]]:
#[[QFED biomass burning emissions#Update to QFED v2.5r1|Update to QFED v2.5r1]]
#[[QFED_biomass_burning_emissions#Fix_QFED_files_for_2016.2F10.2F13|Fix QFED v2.4r6 files for 2016/10/13]]
|Christoph Keller (NASA GMAO)
|Bug fix
|
 
|-valign="top"
|[[GEOS-Chem_12#Fix_issues_in_complexSOA_and_complexSOA_SVPOA_restart_files|Fix issues in complexSOA and complexSOA_SVPOA restart files]]
|Eloise Marais (U. Birmingham)
|Bug fix
|
 
|-valign="top"
|[[GEOS-Chem 12#Avoid double counting CEDS and GEIA NH3 biofuel emissions|Avoid double counting CEDS and GEIA NH3 biofuel emissions]]
|Christoph Keller (NASA/GMAO)<br>[[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 <tt>HEMCO_Config.rc</tt> files that ship with the [[GEOS-Chem Unit Tester]].
 
|-valign="top"
|[[Coupling_GEOS-Chem_with_RRTMG#Bug_fixes_for_RRTMG_in_v11-02|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.
 
|-valign="top"
|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 [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|download the directories]] relevant to your simulation.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="200px"|Inventory
!width="100px"|Type
!width="400px"|What was added?
!width="100px"|Version added
!width="300px"|Directory
 
|-valign="top"
|[[QFED biomass burning emissions]]
|OPTIONAL
|New data files for QFED v2.5r1
|[[#12.0.0|12.0.0]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/QFED/v2018-07/ <tt>HEMCO/QFED/v2018-07</tt>]
 
|-valign="top"
|[[GFED4 biomass burning emissions]]
|DEFAULT
|[[GFED4 biomass_burning_emissions#Years_2015_and_2016_have_been_added|GFED4.1 data files for 2015 and 2016 have been added]]
|[[#12.0.0|12.0.0]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/GFED4/v2015-10/ <tt>HEMCO/GFED4/v2015-10/</tt>]
 
|-valign="top"
|[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions|MEGAN]]
|DEFAULT
|[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Global_0.25x0.25_MEGAN_input_and_MODIS_LAI|Global 0.25x0.3125 CLM4 PFT and emission factor input files for MEGAN]]
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2017-07/ <tt>HEMCO/MEGAN/v2017-07/</tt>]
 
|-valign="top"
|[[MODIS_leaf_area_indices|MODIS LAI]]
|DEFAULT
|[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Global_0.25x0.25_MEGAN_input_and_MODIS_LAI|Updated 0.25 x 0.25 MODIS LAI files (2005-2011)]]
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/CHEM_INPUTS/MODIS_LAI_201707/ <tt>CHEM_INPUTS/MODIS_LAI_201707/</tt>]
 
|-valign="top"
|[[Lightning_NOx_emissions|Lightning NOx]]
|DEFAULT
|GEOS-FP OTD-LIS redistribution factors for Apr 2012 - Jul 2017 and MERRA-2 OTD-LIS redistribution factors for any date
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/LIGHTNOX/v2017-09/ <tt>HEMCO/LIGHTNOX/v2017-09/</tt>]
 
|-valign="top"
|[[Volcanic_SO2_emissions_from_Aerocom|Volcanic SO2 emissions]]
|DEFAULT
|[[Volcanic_SO2_emissions_from_Aerocom#OMI-based_volcanic_emissions|OMI-based volcanic emissions for 2005-2012]]
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/VOLCANO/v2018-03/ <tt>HEMCO/VOLCANO/v2018-03/</tt>]
 
|-valign="top"
|APEI
|DEFAULT
|[[CAC_anthropogenic_emissions#Historical_Canadian_emissions|Historical Canadian emissions]]
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/APEI/v2016-11/ <tt>HEMCO/APEI/v2016-11/</tt>]
 
|-valign="top"
|[[EDGAR_v4.3_anthropogenic_emissions|EDGAR v4.3]]
|OPTIONAL
|Annual global anthropogenic emissions for 1970-2010 at 0.1x0.1 resolution
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/EDGARv43/v2016-11/ <tt>HEMCO/EDGARv43/v2016-11/</tt>]
 
|-valign="top"
|C2H6_2010
|DEFAULT
|[[Anthropogenic_emissions#C2H6|Global fossil fuel and biofuel emissions of C2H6 for 2010]]
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/C2H6_2010/v2017-05/ <tt>HEMCO/C2H6_2010/v2017-05/</tt>]
 
|-valign="top"
|[[DICE-Africa_anthropogenic_emissions_inventory|DICE-Africa]]
|DEFAULT
|Biofuel and diffuse anthropogenic emissions for Africa
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/DICE_Africa/v2016-10/ <tt>HEMCO/DICE_Africa/v2016-10/</tt>]
 
|-valign="top"
|[[Trash burning emissions]]
|OPTIONAL
|Global trash burning emissions from Wiedinmyer et al. (2014)
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/TrashEmis/v2015-03/ <tt>HEMCO/TrashEmis/v2015-03/</tt>]
 
|-valign="top"
|SEABIRD NH3
|DEFAULT
|[[NH3_emissions#NH3_emissions_from_arctic_seabirds|NH3 emissions from arctic sea birds]]
|[[GEOS-Chem v11-02#v11-02f|v11-02f]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/NH3/v2018-04/ <tt>HEMCO/NH3/v2018-04</tt>]
 
|-valign="top"
|OMOC
|OPTIONAL
|[[Particulate_matter_in_GEOS-Chem#Option_to_include_spatially_and_seasonally_varying_OM.2FOC|Spatially varying OM/OC ratio]]
|[[GEOS-Chem v11-02#v11-02e|v11-02e]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/OMOC/v2018-01/ <tt>HEMCO/OMOC/v2018-01</tt>]
 
|-valign="top"
|NOAA GMD CH4
|DEFAULT
|[[NOx-Ox-HC-aerosol#Monthly_mean_surface_distributions|Monthly mean surface methane distributions]]
|[[GEOS-Chem v11-02#v11-02e|v11-02e]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/NOAA_GMD/v2018-01/ <tt>HEMCO/NOAA_GMD/v2018-01</tt>]
 
|-valign="top"
|UCX
|Tropchem only
|[[Stratospheric_chemistry#Prod.2Floss_rates_from_UCX|Input files for applying linearized stratospheric chemistry production and loss rates saved out from a UCX simulation using GEOS-Chem v11-02d]]
|[[GEOS-Chem v11-02#v11-02e|v11-02e]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/UCX/v2018-02/ <tt>HEMCO/UCX/v2018-02/</tt>]
 
|-valign="top"
|IODINE
|DEFAULT
|[[Halogen_chemistry_mechanism#Source_code_and_data_files|Monthly emission fluxes of organic iodine compounds (CH3I, CH2I2, CH2ICl, CH2IBr) from Carlos Ordonez.]]
|[[GEOS-Chem v11-02#v11-02d|v11-02d]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/IODINE/v2017-09/ <tt>HEMCO/IODINE/v2017-09/</tt>]
 
|-valign="top"
|GMI
|DEFAULT
|New symbolic links:
*<tt>gmi.clim.RIPA.geos5.2x25.nc -> gmi.clim.RIP.geos5.2x25</tt>
*<tt>gmi.clim.RIPB.geos5.2x25.nc -> gmi.clim.RIP.geos5.2x25</tt>
*<tt>gmi.clim.RIPD.geos5.2x25.nc -> gmi.clim.RIP.geos5.2x25</tt>
*<tt>gmi.clim.IPMN.geos5.2x25.nc -> gmi.clim.PMN.geos5.2x25</tt>
*<tt>gmi.clim.NPMN.geos5.2x25.nc -> gmi.clim.PMN.geos5.2x25</tt>
|[[GEOS-Chem v11-02#v11-02c|v11-02c]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/GMI/v2015-02/ <tt>HEMCO/GMI/v2015-02/</tt>]
 
|-valign="top"
|[[EPA/NEI11_North_American_emissions|NEI2011 North American emissions]]
|DEFAULT (global)<br>OPTIONAL (nested NA)
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/NEI2011/v2017-02-MM/README Monthly mean data files] (created from the existing hourly data in <tt>HEMCO/NEI2011/v2015-03</tt>)
|[[GEOS-Chem v11-02#v11-02a|v11-02a]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/NEI2011/v2017-02-MM/ <tt>HEMCO/NEI2011/v2017-02-MM/</tt>]
 
|-valign="top"
|ALD2
|DEFAULT
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/ALD2/v2017-03/README 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_to_Emissions|PAN updates]])
|[[GEOS-Chem v11-02#v11-02a|v11-02a]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/ALD2/v2017-03/ <tt>HEMCO/ALD2/v2017-03/</tt>]
 
|-valign="top"
|POET
|DEFAULT
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/POET/v2017-03/README Anthropogenic emissions of ethanol from the POET inventory]<br>(added with the [[PAN#Updates_to_Emissions|PAN updates]])
|[[GEOS-Chem v11-02#v11-02a|v11-02a]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/POET/v2017-03/ <tt>HEMCO/POET/v2017-03/</tt>]
 
|-valign="top"
|[[Hudman_et_al_2012_soil_NOx_emissions_algorithm|Soil NOx]]
|DEFAULT
|New file: <tt>DepReservoirDefault.nc</tt><br>[[Implementation_of_HEMCO_in_GEOS-Chem#Read_default_DEP_RESERVOIR_fields_from_file_when_not_found_in_HEMCO_restart_file|Read default DEP_RESERVOIR fields from file when not found in HEMCO restart file]]
|[[GEOS-Chem v11-02#v11-02a|v11-02a]]
|[ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/SOILNOX/v2014-07/ <tt>HEMCO/SOILNOX/v2014-07/</tt>]
 
|}
 
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.
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 [[GEOS-Chem v11-03 benchmark history|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:
 
*[[Timing_tests_with_GEOS-Chem_12.0.0#Table_of_7-model-day_run_times|Table of 7-day timing test results with GEOS-Chem 12.0.0]]
*[[Timing_tests_with_GEOS-Chem_12.0.0#Graphs_of_7-model-day_run_times|Graphs of 7-day timing test results with GEOS-Chem 12.0.0]]
*[[Media:GEOS-Chem_12.0.0_timing_results.pdf|''GEOS-Chem 12.0.0 "Classic" timing results'' by Bob Yantosca (PDF)]]
 
We invite you to add your own time test results to the wiki.
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:06, 17 August 2018 (UTC)
 
=== GCHP performance ===
 
Help us pool performance information across systems by contributing your GCHP run information on [[GCHP_Timing_Tests|our ''GCHP Timing Tests'' page]].
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:06, 17 August 2018 (UTC)
 
== Previous issues now resolved in GEOS-Chem 12 ==


'''''Tomas Sherwen wrote:'''''
Please see [[Issues now resolved in GEOS-Chem 12]] for a list of bugs and/or technical issues have been resolved in [[#12.0.0|GEOS-Chem 12.0.0]] through [[#12.5.0|GEOS-Chem 12.5.0]]. Issues resolved after GEOS-Chem 12.5.0 can be found on the following Github pages:
 
*[https://github.com/geoschem/geos-chem/issues?q=is%3Aissue+is%3Aclosed GEOS-Chem closed issues]
:I've just found that both FJX_spec.dat the redundant CH3I spectrum and the new spectrum are both present in FJX_spec.dat and FJX_j2j.dat (in v12.0.0). This will have been due to the spectrum in my branch being under the species alias of "CH3IT" to preserve (and ignore) the use of "CH3I" in the namespace of the code for the existing methyl iodide simulation when the iodine simulation was developed. The "CH3IT" variables were replaced "CH3I" in the v11-1-Patches branches with halogen chemistry provided to GCST, but the existing methyl iodide simulation variable was not removed. There are no double ups in the KPP mechanism itself.
*[https://github.com/geoschem/gchp/issues?q=is%3Aissue+is%3Aclosed GCHP closed issues]
 
:Please remove lines 276-281 in FJX_spec.dat (copied below).
 
    "
    CH3I 243 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10
              3.958E-20 4.769E-20 8.257E-19 2.154E-19 7.349E-20 3.351E-20
              1.034E-20 4.435E-21 2.272E-21 4.393E-22 4.052E-24 0.000E+00
    CH3I 300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10
              3.958E-20 4.769E-20 8.376E-19 2.438E-19 9.355E-20 4.680E-20
              1.529E-20 6.532E-21 3.328E-21 6.783E-22 1.038E-23 0.000E+00
    "
 
:Please also remove the line 124 in FJX_j2j.dat (copied below).
 
    "
      123 CH3I PHOTON I PRODUCTS 1.000 /CH3I /
    "
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 17:44, 27 July 2018 (UTC)


== Outstanding issues not yet resolved in GEOS-Chem 12 ==
== Outstanding issues not yet resolved in GEOS-Chem 12 ==


=== Inconsistency in H2402 concentrations in GCHP vs GEOS-Chem Classic ===
Unresolved issues are listed on the following Github pages:
 
*[https://github.com/geoschem/geos-chem/issues GEOS-Chem open issues]
We have discovered an inconsistency with the concentrations of the halogen species H2402 (chemical formula: C<sub>2</sub>Br<sub>2</sub>F<sub>4</sub>) between GEOS-Chem "Classic" and [[GCHP]].  This inconsistency appears as the large fractional difference above ~50 km in the lower-right frame of the plot below.
*[https://github.com/geoschem/gchp GCHP open issues]
 
[[Image:H2402_issue.png]]
 
We have traced this issue to the fact that surface boundary conditions for H2402 used by GCHP differ from those used by GEOS-Chem "Classic", and also that the boundary conditions in GEOS-Chem "Classic" are read in improperly.  A fix will be made in an upcoming GEOS-Chem version.
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:10, 7 December 2018 (UTC)
 
=== RRTMG does not compile with GNU Fortran ===
 
For a complete description of this issue, please see [[Coupling_GEOS-Chem_with_RRTMG#RRTMG_does_not_compile_with_GNU_Fortran|this post on our ''Coupling GEOS-Chem with RRTMG'' wiki page]].
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:55, 3 August 2018 (UTC)
 
=== TOMAS40 simulations exit with a floating-point exception ===
 
We were unit testing the TOMAS40 code in the [[GEOS-Chem v11-02#GEOS-Chem v11-02-release-candidate|GEOS-Chem v11-02-release-candidate]] (soon to be finalized as 12.0.0) with the debugging flags:
 
make –j8 DEBUG=y BOUNDS=y FPEX=y NO_ISO=y ut &
 
which revealed a a NaN error. This was thrown at <span style="color:red">line 903</span> of <tt>GeosCore/tomas_mod.F</tt>:
 
            ERR_VAR = 'Gcout'
            ERR_MSG = 'After COND_NUC'
            ! check for NaN and Inf (win, 10/4/08)
            do jc = 1, icomp-1
                ERR_IND(1) = I
                ERR_IND(2) = J
                ERR_IND(3) = L
                ERR_IND(4) = 0
                <span style="color:red">call check_value( Gcout(jc), ERR_IND, ERR_VAR, ERR_MSG )</span>
!              if( IT_IS_FINITE(Gcout(jc))) then
!                  print *,'xxxxxxxxx Found Inf in Gcout xxxxxxxxxxxxxx'
!                  print *,'Location ',I,J,L, 'comp',jc
!                  call debugprint( Nkout, Mkout, i,j,l,'After COND_NUC')
!                  stop
!              endif
            enddo
 
This error might be caused by the several chemistry and emissions updates that have been added to GEOS-Chem.  The GEOS-Chem Support Team has referred the error to the TOMAS development team, who will be investigating further.
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:56, 6 August 2018 (UTC)
 
=== TOMAS simulations cannot use netCDF diagnostics ===


The TOMAS simulations depend on many of the [[List of diagnostics archived to bpch format|"binary punch" (aka "bpch") diagnostics]].  As of this time, we have not yet been able to convert these to the new [[List of diagnostics archived to netCDF format|netCDF diagnostics]].  Therefore, as of GEOS-Chem 12.0.0, all TOMAS simulations must use the binary punch diagnostic option (which is turned ON by default at compile time).  If you try to compile a TOMAS simulation with netCDF diagnostics (i.e. with makefile option <tt>NC_DIAG=y</tt>), then a compile-time error will be generated.
------------------------


--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:28, 9 August 2018 (UTC)
'''''[[Main_Page|GEOS-Chem Main Page]] | [[GCHP_Main_Page|GCHP Main Page]]'''''

Latest revision as of 21:13, 21 June 2021

GEOS-Chem Main Page | GCHP Main Page

Version history summary

Past releases Future releases

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:
  1. Fix for inconsistent tagged CO2 species names
  2. 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:

  1. 1-month benchmark for GEOS-Chem Classic
  2. 1-month benchmark for GCHP
  3. 1-year full-chemistry benchmark for GEOS-Chem Classic
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: 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: Bob Yantosca (GCST) Bug fix
Fixes for reading meteorology fields in HEMCO: 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 Notes and References
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: 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: 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: 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:

  1. 1-month benchmark for GEOS-Chem Classic
  2. 1-month benchmark for GCHP
  3. 1-year transport tracer benchmark for GEOS-Chem Classic
  4. 1-year full-chemistry benchmark for GEOS-Chem Classic
Feature Submitted by Type Notes and References
Features affecting the full-chemistry simulation:
Isoprene chemistry Kelvin Bates (Harvard) Science
Wet deposition parameterization Kelvin Bates (Harvard)
Sarah Safieddine (MIT) 		Science
Ozone deposition to the ocean Ryan Pound (York)
Mat Evans (York) 		Science
Use online DustDead, MEGAN, SeaSalt, and SoilNOx emissions for benchmark simulations Melissa Sulprizio (GCST) Science
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
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 Notes and References
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:

  1. 1-month benchmark for GEOS-Chem Classic
  2. 1-month benchmark for GCHP
  3. 1-year transport tracer benchmark for GEOS-Chem Classic
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
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
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)
CH4 soil absorption from MeMo model Melissa Sulprizio (Harvard) Science
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
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
Assorted GCHP structural changes to facilitate GEOS-Chem in GEOS 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
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:
  1. ObsPack now defaults to hourly sampling if a sampling interval is not found in data files
  2. GEOS-Chem now prints the full path of each file that is read
  3. GNU Fortran 9.2.1 can now compile GEOS-Chem
  4. 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:

  1. 1-month benchmark for GEOS-Chem Classic
  2. 1-month benchmark for GCHP
  3. 1-year benchmark for GEOS-Chem Classic
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 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:

  1. 1-month benchmark for GEOS-Chem Classic
  2. 1-month benchmark for GCHP

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 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:

  1. 1-month benchmark for GEOS-Chem Classic
  2. 1-month benchmark for GCHP
  3. 1-year benchmark for GEOS-Chem Classic

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. 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: 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 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 Notes
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:

  1. 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 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:

  1. 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".
  2. 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 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:

  1. Approval form for 1-month benchmark simulation 12.2.0
  2. 1-year transport benchmark simulation

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: 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:

  1. 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".
  2. 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 Notes
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:
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:

  1. 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:
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:
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
Added netCDF diagnostics in the following areas: 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:

  1. 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".
  2. 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 Notes
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 Notes
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:
  1. Nullify rather than deallocate 3D met arrays for compatibility with gfortran 6+ when using GCHP
  2. Add a more robust test for netCDF-Fortran in Makefile_header.mk
  3. Fix compilation issues encountered with GNU Fortran 8.2.0
  4. 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:

  1. Approval form for 1-month benchmark simulation 12.0.0
  2. Results for 1-year benchmark simulation 12.0.0-Run0
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: 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: 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:
  1. 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:

  1. Stop with error if multiple containers have the same name
  2. Bug fix for distributing emissions in the vertical dimension
  3. Add extra error checks in HEMCO standalone module
  4. Remove null string character from netCDF unit string
  5. 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:
  1. Update to QFED v2.5r1
  2. 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:

  1. 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".
  2. 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

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