Difference between revisions of "GEOS-Chem 13.3.0"

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This page includes information about GEOS-Chem 13.3.0 which is currently in development.
 
This page includes information about GEOS-Chem 13.3.0 which is currently in development.
  
=== Version overview ===
+
== Version overview ==
  
 
The items listed below have been added to GEOS-Chem 13.3.0 since [[GEOS-Chem 13.2.0]]. See also the following Github pages:
 
The items listed below have been added to GEOS-Chem 13.3.0 since [[GEOS-Chem 13.2.0]]. See also the following Github pages:
*[https://github.com/geoschem/geos-chem/milestone/19 13.3.0 milestone for geoschem/geos-chem]
+
*[https://github.com/geoschem/geos-chem/milestone/19?closed=1 13.3.0 milestone for geoschem/geos-chem]
*[https://github.com/geoschem/GCHP/milestone/7 13.3.0 milestone for geoschem/GCHP]
+
*[https://github.com/geoschem/GCHP/milestone/7?closed=1 13.3.0 milestone for geoschem/GCHP]
*[https://github.com/geoschem/HEMCO/milestone/4 3.2.0 milestone for geoschem/HEMCO]
+
*[https://github.com/geoschem/HEMCO/milestone/4?closed=1 3.2.0 milestone for geoschem/HEMCO]
  
 
{| border=1 cellspacing=0 cellpadding=5  
 
{| border=1 cellspacing=0 cellpadding=5  
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|-valign="top"
 
|-valign="top"
|[https://doi.org/10.5194/acp-2021-441 Updates to IONO2 hydrolysis from Wang et al. (2021)]
+
!colspan="4" bgcolor="#CCFFFF"|Updates that will affect full-chemistry benchmark simulations
|Tomas Sherwen (York)
+
|Chemistry
+
|
+
*See [https://github.com/geoschem/geos-chem/pull/719 geoschem/geos-chem PR #719]
+
*See [https://github.com/geoschem/geos-chem/pull/923 geoschem/geos-chem PR #923]
+
  
 
|-valign="top"
 
|-valign="top"
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|-valign="top"
 
|-valign="top"
|[https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020JD032706 HMS chemistry]
+
|[https://doi.org/10.1525/elementa.2021.00109 C2H2 and C2H4 chemistry]
|Jonathan Moch (Harvard)<br>Mike Long (GCST)
+
|Chemistry
+
|
+
*See [https://github.com/geoschem/geos-chem/pull/905 geoschem/geos-chem PR #905]
+
 
+
|-valign="top"
+
|[https://doi.org/10.1525/elementa.2021.00109 C2H4 and C2H2 chemistry]
+
 
|Kelvin Bates (Harvard)<br>Ke Li (Harvard)<br>Mike Long (GCST)
 
|Kelvin Bates (Harvard)<br>Ke Li (Harvard)<br>Mike Long (GCST)
 
|Chemistry
 
|Chemistry
Line 54: Line 42:
  
 
|-valign="top"
 
|-valign="top"
|[https://github.com/geoschem/geos-chem/pull/897 Cleaning up heterogeneous chemistry reaction rate computations]
+
|[https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020JD032706 HMS chemistry (via sulfate_mod.F90)]
|Bob Yantosca (GCST)
+
|Jonathan Moch (Harvard)<br>Mike Long (GCST)
|Chemistry &<br>Structural
+
|Chemistry
 
|
 
|
*See [https://github.com/geoschem/geos-chem/pull/897 geoschem/geos-chem PR #897]
+
*See [https://github.com/geoschem/geos-chem/pull/905 geoschem/geos-chem PR #905]
 +
 
 +
|-valign="top"
 +
|[https://doi.org/10.5194/acp-2021-441 Updates to IONO2 hydrolysis from Wang et al. (2021)]
 +
|Tomas Sherwen (York)
 +
|Chemistry
 +
|
 +
*See [https://github.com/geoschem/geos-chem/pull/719 geoschem/geos-chem PR #719]
 +
*See [https://github.com/geoschem/geos-chem/pull/923 geoschem/geos-chem PR #923]
  
 
|-valign="top"
 
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/907 Revise gamma(N2O5) computation; cap Alpha at 3.2e-8]  
+
|[https://github.com/geoschem/geos-chem/issues/907 Revise gamma(N2O5) computation; cap A at 3.2e-8]  
 
|Viral Shah (Harvard)
 
|Viral Shah (Harvard)
 
|Chemistry
 
|Chemistry
Line 72: Line 68:
 
* [https://github.com/geoschem/geos-chem/issues/841 Fixed typos in ClNO2 hetchem reactions: HNO2 should be a product, not HNO3]
 
* [https://github.com/geoschem/geos-chem/issues/841 Fixed typos in ClNO2 hetchem reactions: HNO2 should be a product, not HNO3]
 
|Viral Shah (Harvard)<br>Chris Holmes(FSU)
 
|Viral Shah (Harvard)<br>Chris Holmes(FSU)
|Chemistry &<br>Bug fix
+
|Chemistry
 
|
 
|
 
*See [https://github.com/geoschem/geos-chem/issues/906 geoschem/geos-chem #906]
 
*See [https://github.com/geoschem/geos-chem/issues/906 geoschem/geos-chem #906]
Line 78: Line 74:
  
 
|-valign="top"
 
|-valign="top"
|The [http://wiki.seas.harvard.edu/geos-chem/index.php/ObsPack_diagnostic ObsPack diagnostic] can now use the <tt>?ADV?</tt> wildcard
+
|[https://github.com/geoschem/geos-chem/pull/897 Cleaning up heterogeneous chemistry reaction rate computations]
|Jessica Haskins (MIT)
+
|Bob Yantosca (GCST)
|Diagnostics
+
|Chemistry &<br>Structural
 
|
 
|
*See [https://github.com/geoschem/geos-chem/pull/922 geoschem/geos-chem PR #922]
+
*See [https://github.com/geoschem/geos-chem/pull/897 geoschem/geos-chem PR #897]
  
 
|-valign="top"
 
|-valign="top"
|[https://github.com/geoschem/geos-chem/issues/547 Update US emissions to NEI2016] (as option)
+
|[https://www.pnas.org/content/117/42/26076 Updated aerosol dry deposition]
|Barron Henderson (EPA)<br>Lyssa Freese (MIT)
+
|Jeff Pierce (CSU)
|Emissions
+
|Dry deposition
 
|
 
|
*See [https://github.com/geoschem/geos-chem/pull/920 geoschem/geos-chem PR #920]
+
*See [https://github.com/geoschem/geos-chem/issues/604 geoschem/geos-chem PR #604]
 
+
|-valign="top"
+
|[https://gmd.copernicus.org/articles/14/4249/2021/gmd-14-4249-2021.html Updated offline dust emissions from Meng et al. (2021)]
+
|Jun Meng (WUStL)<br>Yanshun Li (WUStL)
+
|Emissions
+
|
+
*See [https://github.com/geoschem/geos-chem/pull/816 geoschem/geos-chem PR #816]
+
  
 
|-valign="top"
 
|-valign="top"
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*See [https://github.com/geoschem/geos-chem/pull/921 geoschem/geos-chem PR #921]
 
*See [https://github.com/geoschem/geos-chem/pull/921 geoschem/geos-chem PR #921]
 
*See [https://github.com/geoschem/HEMCO/pull/110 geoschem/HEMCO PR #110]
 
*See [https://github.com/geoschem/HEMCO/pull/110 geoschem/HEMCO PR #110]
 +
 +
|-valign="top"
 +
!colspan="4" bgcolor="#CCFFFF"|Updates that will NOT affect full-chemistry benchmark simulations
 +
 +
|-valign="top"
 +
|[https://gmd.copernicus.org/articles/14/4249/2021/gmd-14-4249-2021.html Updated offline dust emissions from Meng et al. (2021)]
 +
|Jun Meng (WUStL)<br>Yanshun Li (WUStL)
 +
|Emissions
 +
|
 +
*See [https://github.com/geoschem/geos-chem/pull/816 geoschem/geos-chem PR #816]
 +
*Online dust emissions are used in benchmark simulations
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/547 Update US emissions to NEI2016] (as option)
 +
|Barron Henderson (EPA)<br>Lyssa Freese (MIT)<br>Melissa Sulprizio (GCST)
 +
|Emissions
 +
|
 +
*See [https://github.com/geoschem/geos-chem/pull/920 geoschem/geos-chem PR #920]
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/HEMCO/issues/29 Send all HEMCO error messages to GEOS-Chem log]
 +
|Lizzie Lundgren (GCST)
 +
|HEMCO
 +
|
 +
*See [https://github.com/geoschem/HEMCO/pull/111 geoschem/HEMCO PR #111]
 +
 +
|-valign="top"
 +
|The [http://wiki.seas.harvard.edu/geos-chem/index.php/ObsPack_diagnostic ObsPack diagnostic] can now use the <tt>?ADV?</tt> wildcard
 +
|Jessica Haskins (MIT)
 +
|Diagnostics
 +
|
 +
*See [https://github.com/geoschem/geos-chem/pull/922 geoschem/geos-chem PR #922]
 +
 +
|-
 +
!colspan="4" bgcolor="#CCFFFF"|Features only affecting GCHP:
 +
 +
|-valign="top"
 +
|Include thread number in GEOS-Chem and HEMCO error messages
 +
|Lizzie Lundgren (GCST)
 +
|GCHP/GEOS
 +
|
 +
*See [https://github.com/geoschem/geos-chem/pull/925 geoschem/geos-chem PR #925]
 +
*See [https://github.com/geoschem/HEMCO/pull/111 geoschem/HEMCO PR #111]
 +
 +
 +
|-valign="top"
 +
|GCHP Adjoint updates
 +
|Colin Lee (CU Boulder)
 +
|GCHP
 +
|
 +
*See [https://github.com/geoschem/GCHP/issues/146 geoschem/GCHP #146]
  
 
|}
 
|}
  
==== New data directories ====
+
=== New data directories ===
  
 
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.
 
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.
Line 129: Line 169:
 
|[[GEOS-Chem_restart_files|GEOS-Chem Restart Files]]
 
|[[GEOS-Chem_restart_files|GEOS-Chem Restart Files]]
 
|Default
 
|Default
|Updated full-chemistry and TOMAS restart files with new species added: C2H2, C2H4, HMS, ETHN, ETHP, ETO, ETOO.
+
|Updated full-chemistry and TOMAS restart files with new species for 13.3.0 added.
 
|<tt>ExtData/GEOSCHEM_RESTARTS/v2021-09/</tt>
 
|<tt>ExtData/GEOSCHEM_RESTARTS/v2021-09/</tt>
  
Line 135: Line 175:
 
|[[Setting_up_GEOS-Chem_nested_grid_simulations#Run_a_global_simulation_to_create_boundary_conditions|Boundary conditions]]
 
|[[Setting_up_GEOS-Chem_nested_grid_simulations#Run_a_global_simulation_to_create_boundary_conditions|Boundary conditions]]
 
|Default<br>(nested-grid simulations only)
 
|Default<br>(nested-grid simulations only)
|Updated sample nested-grid boundary conditions with new species added: C2H2, C2H4, HMS, ETHN, ETHP, ETO, ETOO.
+
|Updated sample nested-grid boundary conditions with new species for 13.3.0 added.
 
|<tt>ExtData/HEMCO/SAMPLE_BCs/v2021-09/</tt>
 
|<tt>ExtData/HEMCO/SAMPLE_BCs/v2021-09/</tt>
  
Line 148: Line 188:
 
|Default
 
|Default
 
|[https://github.com/geoschem/geos-chem/issues/833 Update offline dust emissions to May 2020 and add climatology]
 
|[https://github.com/geoschem/geos-chem/issues/833 Update offline dust emissions to May 2020 and add climatology]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/VOLCANO/v2021-09/README <tt>HEMCO/VOLCANO/v2021-09</tt>
+
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/VOLCANO/v2021-09/README <tt>HEMCO/VOLCANO/v2021-09</tt>]
  
 
|-valign="top"
 
|-valign="top"
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|Optional
 
|Optional
 
|[https://github.com/geoschem/geos-chem/issues/547 EPA NEI2016 emissions (2002-2020)]
 
|[https://github.com/geoschem/geos-chem/issues/547 EPA NEI2016 emissions (2002-2020)]
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/NEI2016/v2021-06/README.md <tt>HEMCO/NEI2016/v2021-06]
+
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/NEI2016/v2021-06/README.md <tt>HEMCO/NEI2016/v2021-06</tt>]
  
 
|}
 
|}
  
=== 1-month benchmarks ===
+
== 1-month benchmarks ==
  
TBD
+
=== 1-month fullchem: Model setup ===
 +
 
 +
The following table describes the GEOS-Chem setup for both GEOS-Chem Classic and GCHP 1-month benchmark simulations.
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
 
 +
|-valign="top"
 +
|width="250px"|Git tag(s):
 +
|width="400px"|
 +
*GEOS-Chem Classic: [https://github.com/geoschem/GCClassic/releases/tag/13.3.0-rc.0 13.3.0-rc.0]
 +
*GCHP: TBD
 +
 
 +
|-valign="top"
 +
|Compared to previous benchmark:
 +
|[[GEOS-Chem_13.2.0|13.2.0]]
 +
 
 +
|-valign="top"
 +
|Software environment:
 +
|gcc 10.2.0<br>OpenMPI 4.1.0<br>netcdf-fortran 4.5.3<br>CMake 3.17.3<br>ESMF 8.0.1
 +
 
 +
|-valign="top"
 +
|Model resolution:
 +
|
 +
*GEOS-Chem Classic: 4&deg; x 5&deg;
 +
*GCHP: c48
 +
 
 +
|-valign="top"
 +
|Meteorology fields:
 +
|[[MERRA-2]]
 +
*GEOS-Chem Classic: 4&deg; x 5&deg;
 +
*GCHP: 0.5&deg; x 0.625&deg;
 +
 
 +
|-valign="top"
 +
|Initial conditions:
 +
|[http://ftp.as.harvard.edu/gcgrid/data/ExtData/GEOSCHEM_RESTARTS/v2021-09/ July 1, 2019]
 +
*NOTE: GCHP c48 restart file regridded from GEOS-Chem Classic 4&deg; x 5&deg;
 +
 
 +
|-valign="top"
 +
|Benchmark month:
 +
|July 2019
 +
 
 +
|-valign="top"
 +
|Emissions setup:
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/HEMCO_Config.rc HEMCO_Config.rc]
 +
 
 +
|-valign="top"
 +
|Chemistry mechanism:
 +
|[https://github.com/geoschem/geos-chem/blob/release/KPP/fullchem/fullchem.eqn fullchem.eqn]
 +
 
 +
|-valign="top"
 +
|This version will impact:<br>(select all that apply with '''boldface''')
 +
|
 +
*Advection
 +
*BL Mixing
 +
*Convection
 +
*Meteorology Fields
 +
*'''Dry Deposition'''
 +
*Wet Deposition
 +
*'''Emissions'''
 +
*'''Photolysis'''
 +
*'''Chemistry'''
 +
*Other (please specify):
 +
 
 +
|}
 +
 
 +
=== Benchmark Plots and Tables ===
 +
 
 +
NOTES:
 +
*Enable PDF bookmarks in the file links to navigate between species.  If you do not see bookmarks in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.
 +
* See the [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/species_database.yml species database] for species definitions and details.
 +
* [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/benchmark_categories.yml Species categories] and [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/lumped_species.yml lumped species] are defined in YAML files within the GEOS-Chem post-processing software [https://github.com/geoschem/gcpy GCPy].
 +
 
 +
==== 1-month fullchem: GEOS-Chem Classic 13.3.0 vs 13.2.0 ====
 +
 
 +
Below are links to plots and tables comparing 1-month simulations for GEOS-Chem Classic 13.3.0 (Dev) and GEOS-Chem Classic 13.2.0 (Ref).
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
 
 +
|-
 +
!colspan="1" bgcolor="#CCFFFF" width="325px"|Species Category
 +
!colspan="5" bgcolor="#CCFFFF"|Plots
 +
!colspan="1" bgcolor="#CCFFFF"|Additional Information
 +
 
 +
|-
 +
!colspan="1"|
 +
!colspan="2"|Level Map
 +
!colspan="2"|Zonal Mean
 +
!colspan="1"|Emissions
 +
!colspan="1"|
 +
 
 +
|-valign="top"
 +
|'''Oxidants'''
 +
O3, CO, OH, NOx
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Oxidants/Oxidants_Surface.pdf sfc]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Oxidants/Oxidants_500hPa.pdf 500hPa]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Oxidants/Oxidants_FullColumn_ZonalMean.pdf full column]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Oxidants/Oxidants_Strat_ZonalMean.pdf stratosphere]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Oxidants/Oxidants_Emissions.pdf sfc]
 +
|
 +
 
 +
|-valign="top"
 +
|'''Aerosols'''
 +
DST1, DST2, DST3, DST4, NH4, NIT, SO4, HMS, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA, pFe
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Aerosols/Aerosols_Surface.pdf sfc]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Aerosols/Aerosols_500hPa.pdf 500hPa]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Aerosols/Aerosols_FullColumn_ZonalMean.pdf full column]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Aerosols/Aerosols_Strat_ZonalMean.pdf stratosphere]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Aerosols/Aerosols_Emissions.pdf column total]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Aerosols/Aerosols_ColumnOptDepth.pdf AOD]
 +
 
 +
|-valign="top"
 +
|'''Bromine'''
 +
Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Bromine/Bromine_Surface.pdf sfc]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Bromine/Bromine_500hPa.pdf 500hPa]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Bromine/Bromine_FullColumn_ZonalMean.pdf full column]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Bromine/Bromine_Strat_ZonalMean.pdf stratosphere]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Bromine/Bromine_Emissions.pdf column total]
 +
|
 +
 
 +
|-valign="top"
 +
|'''Chlorine'''
 +
Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, CHCl3, HOCl, HCl, Halons, HCFCs, OClO
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Chlorine/Chlorine_Surface.pdf sfc]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Chlorine/Chlorine_500hPa.pdf 500hPa]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Chlorine/Chlorine_FullColumn_ZonalMean.pdf full column]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Chlorine/Chlorine_Strat_ZonalMean.pdf stratosphere]
 +
| --
 +
|
 +
 
 +
|-valign="top"
 +
|'''Iodine'''
 +
Iy, IxOy, I, I2, IBr, ICl, IO, IONO, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Iodine/Iodine_Surface.pdf sfc]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Iodine/Iodine_500hPa.pdf 500hPa]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Iodine/Iodine_FullColumn_ZonalMean.pdf full column]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Iodine/Iodine_Strat_ZonalMean.pdf stratosphere]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Iodine/Iodine_Emissions.pdf column total]
 +
|
 +
 
 +
|-valign="top"
 +
|'''Nitrogen'''
 +
NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3, AONITA, ETHN, BZPAN, NPHEN
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Nitrogen/Nitrogen_Surface.pdf sfc]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Nitrogen/Nitrogen_500hPa.pdf 500hPa]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Nitrogen/Nitrogen_FullColumn_ZonalMean.pdf full column]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Nitrogen/Nitrogen_Strat_ZonalMean.pdf stratosphere]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Nitrogen/Nitrogen_Emissions.pdf column total]
 +
|
 +
 
 +
|-valign="top"
 +
|'''Primary Organics'''
 +
EOH, MOH, ISOP, MTPA, MTPO, LIMO,  ALK4, BENZ, CH4, C2H2, C2H4, C2H6, C3H8, PRPE, TOLU, XYLE
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Primary_Organics/Primary_Organics_Surface.pdf sfc]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Primary_Organics/Primary_Organics_500hPa.pdf 500hPa]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Primary_Organics/Primary_Organics_FullColumn_ZonalMean.pdf full column]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Primary_Organics/Primary_Organics_Strat_ZonalMean.pdf stratosphere]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Primary_Organics/Primary_Organics_Emissions.pdf column total]
 +
|
 +
 
 +
|-valign="top"
 +
|'''Secondary Organics'''
 +
ACTA, ALD2, BALD, CH2O, HPALDs, MACR, IEPOX, ACET, HAC, MEK, MVK, ISOPN, GLYC, GLYX, HCOOH, MAP, PHEN, RCHO, ETHP, MP
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Secondary_Organics/Secondary_Organics_Surface.pdf sfc]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Secondary_Organics/Secondary_Organics_500hPa.pdf 500hPa]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Secondary_Organics/Secondary_Organics_FullColumn_ZonalMean.pdf full column]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Secondary_Organics/Secondary_Organics_Strat_ZonalMean.pdf stratosphere]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Secondary_Organics/Secondary_Organics_Emissions.pdf column total]
 +
|
 +
 
 +
|-valign="top"
 +
|'''Secondary Organic Aerosols'''
 +
TSOA0, TSOA1, TSOA2, TSOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ASOG1, ASOG2, ASOG3, INDIOL, LVOCOA, SOAIE, SOAGX, SOAP, SOAS
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Secondary_Organic_Aerosols/Secondary_Organic_Aerosols_Surface.pdf sfc]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Secondary_Organic_Aerosols/Secondary_Organic_Aerosols_500hPa.pdf 500hPa]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Secondary_Organic_Aerosols/Secondary_Organic_Aerosols_FullColumn_ZonalMean.pdf full column]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Secondary_Organic_Aerosols/Secondary_Organic_Aerosols_Strat_ZonalMean.pdf stratosphere]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Secondary_Organic_Aerosols/Secondary_Organic_Aerosols_Emissions.pdf column total]
 +
|
 +
 
 +
|-valign="top"
 +
|'''Sulfur'''
 +
SOx, DMS, HMS, OCS, SO2, SO4
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Sulfur/Sulfur_Surface.pdf sfc]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Sulfur/Sulfur_500hPa.pdf 500hPa]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Sulfur/Sulfur_FullColumn_ZonalMean.pdf full column]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Sulfur/Sulfur_Strat_ZonalMean.pdf stratosphere]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Sulfur/Sulfur_Emissions.pdf column total]
 +
|
 +
 
 +
|-valign="top"
 +
|'''ROy'''
 +
H2O2, H, H2, H2O, HO2, O1D, OH, RO2
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/ROy/ROy_Surface.pdf sfc]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/ROy/ROy_500hPa.pdf 500hPa]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/ROy/ROy_FullColumn_ZonalMean.pdf full column]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/ROy/ROy_Strat_ZonalMean.pdf stratosphere]
 +
| --
 +
|
 +
 
 +
|-valign="top"
 +
|'''J-values'''
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/JValues/Jval_Surface.pdf sfc]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/JValues/Jval_500hPa.pdf 500hPa]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/JValues/Jval_FullColumn_ZonalMean.pdf full column]
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/JValues/Jval_Strat_ZonalMean.pdf stratosphere]
 +
| --
 +
| --
 +
 
 +
|-valign="top"
 +
!colspan="7" bgcolor="#CCCCCC"|&nbsp;
 +
 
 +
|-valign="top"
 +
|'''Emissions by HEMCO category'''
 +
|colspan="6"|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Emissions/Total_Emissions.pdf Total]
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Emissions/Aircraft_Emissions.pdf Aircraft],
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Emissions/Anthro_Emissions.pdf Anthropogenic],
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Emissions/BioBurn_Emissions.pdf Biomass Burning],
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Emissions/Biogenic_Emissions.pdf Biogenic],
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Emissions/Lightning_Emissions.pdf Lightning],
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Emissions/Natural_Emissions.pdf Natural],
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Emissions/Ocean_Emissions.pdf Ocean],
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Emissions/Seabirds_Emissions.pdf Seabirds],
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Emissions/PlantDecay_Emissions.pdf Decaying Plants],
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Emissions/Ship_Emissions.pdf Ship],
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Emissions/Soil_Emissions.pdf Soil],
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Emissions/VolcDegas_Emissions.pdf Degassing Volcanoes],
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Emissions/VolcErupt_Emissions.pdf Erupting Volcanoes]
 +
 
 +
|-valign="top"
 +
|'''Emission totals'''
 +
|colspan="6"|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Tables/Emission_totals.txt Tables by species]
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Tables/Inventory_totals.txt Tables by inventory]
 +
 
 +
|-valign="top"
 +
|'''Global mass'''
 +
|colspan="6"|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Tables/GlobalMass_TropStrat.txt Entire atmosphere]
 +
[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Tables/GlobalMass_Trop.txt Troposphere only]
 +
 
 +
|-valign="top"
 +
|'''Metrics'''
 +
|colspan="6"|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/Tables/OH_metrics.txt OH concentration, MCF lifetime, CH4 lifetime]
 +
 
 +
|}
 +
 
 +
=== Benchmark assessment form ===
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="325px"|Performance
 +
!width="250px"|GEOS-Chem Classic
 +
!width="250px"|GCHP
 +
 
 +
|-valign="top"
 +
|Grid resolution:
 +
|4&deg; x 5&deg;
 +
|C48
 +
 
 +
|-valign="top"
 +
|# CPUs, nodes:
 +
|48 CPUs<br>1 node (Intel Cascade Lake)
 +
|48 CPUs<br>2 nodes (Intel Cascade Lake)
 +
 
 +
|-valign="top"
 +
|Wall time:
 +
|03:30:53
 +
|TBD
 +
 
 +
|-valign="top"
 +
|[[Scalability|CPU time / wall time]]:
 +
|31.5510
 +
|TBD
 +
 
 +
|-valign="top"
 +
|% of ideal performance:
 +
|65.73%
 +
|TBD
 +
 
 +
|-valign="top"
 +
|Memory:
 +
|12.097 GB
 +
|TBD
 +
 
 +
|-valign="top"
 +
|Global mean OH:<br>(% change from previous version)
 +
|11.74989868895 x 10<sup>5</sup> molec/cm<sup>3</sup><br>(+4.68)
 +
|TBD
 +
 
 +
|-valign="top"
 +
|Methyl chloroform lifetime:<br>(% change from previous version)
 +
|5.263415 years<br>(-4.47%)
 +
|TBD
 +
 
 +
|-valign="top"
 +
|Methane lifetime:<br>(% change from previous version)
 +
|8.868914 years<br>(-4.34%)
 +
|TBD
 +
 
 +
|-valign="top" bgcolor="#cccccc"
 +
!colspan="3"|Details
 +
 
 +
|-valign="top"
 +
|Species, J-Values, and COLUMN AOD values that changed by 10% or more at the '''surface''':
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/SigDiffs_sfc.txt GEOS-Chem Classic 13.3.0 vs 13.2.0]
 +
|TBD
 +
 
 +
|-valign="top"
 +
|Species and J-Values that changed by 10% or more at '''500 hPa''':
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/SigDiffs_500hpa.txt GEOS-Chem Classic 13.3.0 vs 13.2.0]
 +
|TBD
 +
 
 +
|-valign="top"
 +
|Species and J-Values that changed by 10% or more in '''zonal mean''':
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/SigDiffs_zonalmean.txt GEOS-Chem Classic 13.3.0 vs 13.2.0]
 +
|TBD
 +
 
 +
|-valign="top"
 +
|'''Emissions''' that changed by 10% or more:
 +
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.3.0-rc.0/GCClassic/BenchmarkResults/SigDiffs_emissions.txt GEOS-Chem Classic 13.3.0 vs 13.2.0]
 +
|TBD
 +
 
 +
|-valign="top" bgcolor="#cccccc"
 +
!colspan="3"|Overview
 +
 
 +
|-valign="top"
 +
|colspan="3"|'''''Below we summarize the notable changes caused by specific updates. Supplementary plots may be viewed at http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/.'''''
 +
 
 +
'''1. [https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020JD032706 HMS chemistry (via sulfate_mod.F90)]'''
 +
 
 +
:This update introduces new advected species hydroxymethanesulfonate (HMS) in GEOS-Chem. This new chemistry has a relatively small impact on [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.2/Tables/GlobalMass_Trop.txt other species' concentrations] and on [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.2/Tables/OH_metrics.txt global mean OH]. Complete results from a 1-month benchmark evaluating the impact of this chemistry update may be viewed at [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.2/ this link].
 +
 
 +
'''2. [https://doi.org/10.1525/elementa.2021.00109 C2H2 and C2H4 chemistry]'''
 +
 
 +
:This update introduces new advected species C2H2, C2H4, ETHN, and ETHP and adds one photolysis reaction. The new chemistry has a large (>10% impact) on GLYC, GLYX, H2O2, HCOOH, HMHP, MO2, MOH, MP, SOAGX (see [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.3/Tables/GlobalMass_Trop.txt this table]). [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.3/Tables/OH_metrics.txt Global mean OH] is reduced by -1.49%. Complete results from a 1-month benchmark evaluating the impact of this chemistry update may be viewed at [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.3/ this link].
 +
 
 +
'''3. [https://github.com/geoschem/geos-chem/issues/906 Fixed typo in CloudHet]'''
 +
 
 +
:This fix has a large impact on [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.4/Tables/GlobalMass_Trop.txt many halogen species] and changed [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.4/Tables/OH_metrics.txt global mean OH] by +6.65%. These large changes are to be expected because the function in which this bug occurs (<tt>CloudHet</tt>) is used in the rate computations of many heterogeneous reactions.  See [https://github.com/geoschem/geos-chem/issues/906 this Github issue] for further discussion on the changes from this fix.
 +
 
 +
'''4. [https://github.com/geoschem/geos-chem/issues/907 Revise gamma(N2O5) computation; cap A at 3.2e-8]'''
 +
 
 +
:Prior to this fix, <tt>gamma(N2O5)</tt> (i.e. reaction probability) was too high over the oceans.  This update now prevents <tt>gamma(N2O5)</tt> from exceeding ~0.036, which is consistent with lab results.  We observe a relatively small (<10%) impact on [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.5/Tables/GlobalMass_Trop.txt most species], but ClNO2 shows a large decrease.  But as <tt>gamma(N2O5)</tt> decreases, the production of ClNO2 via the reaction <tt>N2O5 + HCl = ClNO2 + HNO3</tt> likewise decreases, so the results are to be expected.  See [https://github.com/geoschem/geos-chem/issues/907 this Github issue] for further discussion on the changes from this update.
 +
 
 +
'''5. [https://doi.org/10.5194/acp-2021-441 Updates to IONO2 hydrolysis from Wang et al. (2021)]'''
 +
 
 +
:This update replaced several heterogeneous reactions that converted gas-phase species HOI, IONO, and IONO2 to aerosol species ISALA and ISALC with the single hydrolysis reaction <tt>IONO2 + H2O = HOI + HNO3</tt>.  We observe a large (>10%) impact on IONO2 and HOI, but a relatively small impact on other species (see [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.9/Tables/GlobalMass_Trop.txt this table]). [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.9/Tables/OH_metrics.txt Global mean OH] changed by -0.11%. See the original [https://github.com/geoschem/geos-chem/pull/719 pull request on Github] for more details of this update and its impact on model output.
 +
 
 +
'''6. [https://acp.copernicus.org/preprints/acp-2021-605/ Aromatic VOC chemistry]'''
 +
 
 +
:This update added new advected species AONITA, AROMP4, AROMP5, BALD, BENZP, BZCO3H, BZPAN, CSL, MCT, NPHEN, PHEN, along with ~45 gas-phase reactions, 1 heterogeneous reaction, and 4 photolysis reactions. The impact on other species is summarized in [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.10/Tables/GlobalMass_Trop.txt this table], and [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.10/Tables/OH_metrics.txt global mean OH] changed by -0.36%. Complete results from a 1-month benchmark evaluating the impact of this chemistry update may be viewed at [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.10/ this link].
 +
 
 +
'''7. [https://www.pnas.org/content/117/42/26076 Updated aerosol dry deposition]'''
 +
 
 +
:This feature brings aerosol dry deposition in line with [https://www.pnas.org/content/117/42/26076 Emerson et al 2020], and several aerosol parameters within the dry deposition module were updated accordingly. Global mean OH [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.11/Tables/OH_metrics.txt increased by 0.024%].  Most gas-phase species show small changes in mass (except for Br2 and ClNO2, which decreased by more than 5%).  On the other hand, aerosol species such as AERI, ASOA1-4, DST1-4, show large decreases.  Also, the mass of MSA increased by 7.7%.  See [https://github.com/geoschem/geos-chem/issues/604 this Github feature request] for more information about this update. Complete results from a 1-month benchmark evaluating the impact of this chemistry update may be viewed at [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.11/ this link].
 +
 
 +
'''8. [https://github.com/geoschem/geos-chem/issues/833 Update volcano emissions to May 2020 and add climatology]'''
 +
 
 +
:The volcano emissions inventory from GMAO has been updated from v20180523 to v202005. Plots for a 1-month benchmark evaluating the impact of this fix may be viewed at [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.8/ this link]. The impact on SO2 emissions from volcanoes is:
 +
 
 +
    ###################################################################################
 +
    ### Emissions totals for inventory VOLCANOdegas [Tg]                            ###
 +
    ### Ref = GCC_13.3.0-alpha.7; Dev = GCC_13.3.0-alpha.8                          ###
 +
    ###################################################################################
 +
                                        Ref                Dev    Dev - Ref    % diff
 +
    VOLCANOdegas SO2  :          1.953161            1.826465    -0.126697    -6.487
 +
 
 +
    ###################################################################################
 +
    ### Emissions totals for inventory VOLCANOerupt [Tg]                            ###
 +
    ### Ref = GCC_13.3.0-alpha.7; Dev = GCC_13.3.0-alpha.8                          ###
 +
    ###################################################################################
 +
                                        Ref                Dev    Dev - Ref    % diff
 +
    VOLCANOerupt SO2  :          0.000000            0.101063      0.101063      nan
 +
   
 +
'''9. [https://github.com/geoschem/HEMCO/issues/92 Avoid double counting of acetone source from monoterpenes when using online MEGAN]'''
 +
 
 +
:This update reduced ACET emissions in the MEGAN extension. Plots for a 1-month benchmark evaluating the impact of this fix may be viewed at [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.0/ this link]. The impact on total ACET emissions from MEGAN is:
 +
 
 +
    ###################################################################################
 +
    ### Emissions totals for inventory MEGAN [Tg]                                  ###
 +
    ### Ref = GCC_13.2.1; Dev = GCC_13.3.0-alpha.0                                  ###
 +
    ###################################################################################
 +
                                        Ref                Dev    Dev - Ref    % diff
 +
    MEGAN ACET        :          4.967504            4.374804    -0.592700  -11.932
 +
 
 +
'''The following updates introduced differences on the order of numerical noise:'''
 +
*[https://github.com/geoschem/geos-chem/pull/897 Cleaning up heterogeneous chemistry reaction rate computations]
 +
*[https://github.com/geoschem/geos-chem/issues/841 Fixed typos in ClNO2 hetchem reactions: HNO2 should be a product, not HNO3]
 +
 
 +
|-bgcolor="#cccccc"
 +
!colspan="3"|Approval
 +
 
 +
|-valign="top"
 +
|Requires further investigation:
 +
|colspan="2"|
 +
 
 +
|-valign="top"
 +
|Approved by:
 +
|colspan="2"|
 +
 
 +
|-valign="top"
 +
|Date of approval:
 +
|colspan="2"|
 +
 
 +
|}
  
 
=== 1-year benchmarks ===  
 
=== 1-year benchmarks ===  
  
 
TBD
 
TBD

Revision as of 17:05, 15 October 2021

GEOS-Chem Versions Page

This page includes information about GEOS-Chem 13.3.0 which is currently in development.

Version overview

The items listed below have been added to GEOS-Chem 13.3.0 since GEOS-Chem 13.2.0. See also the following Github pages:

Feature Contributor(s) Model scope Notes
Updates that will affect full-chemistry benchmark simulations
Aromatic VOC chemistry Kelvin Bates (Harvard)
Ke Li (Harvard)
Mike Long (Harvard)
Chemistry
C2H2 and C2H4 chemistry Kelvin Bates (Harvard)
Ke Li (Harvard)
Mike Long (GCST)
Chemistry
CH3O2 + OH reaction Kelvin Bates (Harvard) Chemistry
HMS chemistry (via sulfate_mod.F90) Jonathan Moch (Harvard)
Mike Long (GCST)
Chemistry
Updates to IONO2 hydrolysis from Wang et al. (2021) Tomas Sherwen (York) Chemistry
Revise gamma(N2O5) computation; cap A at 3.2e-8 Viral Shah (Harvard) Chemistry
Bug fixes in heterogeneous chemistry: Viral Shah (Harvard)
Chris Holmes(FSU)
Chemistry
Cleaning up heterogeneous chemistry reaction rate computations Bob Yantosca (GCST) Chemistry &
Structural
Updated aerosol dry deposition Jeff Pierce (CSU) Dry deposition
Avoid double counting of acetone source from monoterpenes when using online MEGAN Dylan Millet (UMN) Emissions
Update volcano emissions to May 2020 and add climatology Christoph Keller (NASA/GMAO) Emissions
Updates that will NOT affect full-chemistry benchmark simulations
Updated offline dust emissions from Meng et al. (2021) Jun Meng (WUStL)
Yanshun Li (WUStL)
Emissions
Update US emissions to NEI2016 (as option) Barron Henderson (EPA)
Lyssa Freese (MIT)
Melissa Sulprizio (GCST)
Emissions
Send all HEMCO error messages to GEOS-Chem log Lizzie Lundgren (GCST) HEMCO
The ObsPack diagnostic can now use the ?ADV? wildcard Jessica Haskins (MIT) Diagnostics
Features only affecting GCHP:
Include thread number in GEOS-Chem and HEMCO error messages Lizzie Lundgren (GCST) GCHP/GEOS


GCHP Adjoint updates Colin Lee (CU Boulder) GCHP

New data directories

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
GEOS-Chem Restart Files Default Updated full-chemistry and TOMAS restart files with new species for 13.3.0 added. ExtData/GEOSCHEM_RESTARTS/v2021-09/
Boundary conditions Default
(nested-grid simulations only)
Updated sample nested-grid boundary conditions with new species for 13.3.0 added. ExtData/HEMCO/SAMPLE_BCs/v2021-09/
OFFLINE_DUST Default Offline dust emissions from Meng et al. (2021) HEMCO/OFFLINE_DUST/v2021-08
VOLCANO Default Update offline dust emissions to May 2020 and add climatology HEMCO/VOLCANO/v2021-09
NEI2016 Optional EPA NEI2016 emissions (2002-2020) HEMCO/NEI2016/v2021-06

1-month benchmarks

1-month fullchem: Model setup

The following table describes the GEOS-Chem setup for both GEOS-Chem Classic and GCHP 1-month benchmark simulations.

Git tag(s):
Compared to previous benchmark: 13.2.0
Software environment: gcc 10.2.0
OpenMPI 4.1.0
netcdf-fortran 4.5.3
CMake 3.17.3
ESMF 8.0.1
Model resolution:
  • GEOS-Chem Classic: 4° x 5°
  • GCHP: c48
Meteorology fields: MERRA-2
  • GEOS-Chem Classic: 4° x 5°
  • GCHP: 0.5° x 0.625°
Initial conditions: July 1, 2019
  • NOTE: GCHP c48 restart file regridded from GEOS-Chem Classic 4° x 5°
Benchmark month: July 2019
Emissions setup: HEMCO_Config.rc
Chemistry mechanism: fullchem.eqn
This version will impact:
(select all that apply with boldface)
  • Advection
  • BL Mixing
  • Convection
  • Meteorology Fields
  • Dry Deposition
  • Wet Deposition
  • Emissions
  • Photolysis
  • Chemistry
  • Other (please specify):

Benchmark Plots and Tables

NOTES:

  • Enable PDF bookmarks in the file links to navigate between species. If you do not see bookmarks in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.
  • See the species database for species definitions and details.
  • Species categories and lumped species are defined in YAML files within the GEOS-Chem post-processing software GCPy.

1-month fullchem: GEOS-Chem Classic 13.3.0 vs 13.2.0

Below are links to plots and tables comparing 1-month simulations for GEOS-Chem Classic 13.3.0 (Dev) and GEOS-Chem Classic 13.2.0 (Ref).

Species Category Plots Additional Information
Level Map Zonal Mean Emissions
Oxidants

O3, CO, OH, NOx

sfc 500hPa full column stratosphere sfc
Aerosols

DST1, DST2, DST3, DST4, NH4, NIT, SO4, HMS, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA, pFe

sfc 500hPa full column stratosphere column total AOD
Bromine

Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr

sfc 500hPa full column stratosphere column total
Chlorine

Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, CHCl3, HOCl, HCl, Halons, HCFCs, OClO

sfc 500hPa full column stratosphere --
Iodine

Iy, IxOy, I, I2, IBr, ICl, IO, IONO, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO

sfc 500hPa full column stratosphere column total
Nitrogen

NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3, AONITA, ETHN, BZPAN, NPHEN

sfc 500hPa full column stratosphere column total
Primary Organics

EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H2, C2H4, C2H6, C3H8, PRPE, TOLU, XYLE

sfc 500hPa full column stratosphere column total
Secondary Organics

ACTA, ALD2, BALD, CH2O, HPALDs, MACR, IEPOX, ACET, HAC, MEK, MVK, ISOPN, GLYC, GLYX, HCOOH, MAP, PHEN, RCHO, ETHP, MP

sfc 500hPa full column stratosphere column total
Secondary Organic Aerosols

TSOA0, TSOA1, TSOA2, TSOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ASOG1, ASOG2, ASOG3, INDIOL, LVOCOA, SOAIE, SOAGX, SOAP, SOAS

sfc 500hPa full column stratosphere column total
Sulfur

SOx, DMS, HMS, OCS, SO2, SO4

sfc 500hPa full column stratosphere column total
ROy

H2O2, H, H2, H2O, HO2, O1D, OH, RO2

sfc 500hPa full column stratosphere --
J-values sfc 500hPa full column stratosphere -- --
 
Emissions by HEMCO category Total

Aircraft, Anthropogenic, Biomass Burning, Biogenic, Lightning, Natural, Ocean, Seabirds, Decaying Plants, Ship, Soil, Degassing Volcanoes, Erupting Volcanoes

Emission totals Tables by species

Tables by inventory

Global mass Entire atmosphere

Troposphere only

Metrics OH concentration, MCF lifetime, CH4 lifetime

Benchmark assessment form

Performance GEOS-Chem Classic GCHP
Grid resolution: 4° x 5° C48
# CPUs, nodes: 48 CPUs
1 node (Intel Cascade Lake)
48 CPUs
2 nodes (Intel Cascade Lake)
Wall time: 03:30:53 TBD
CPU time / wall time: 31.5510 TBD
% of ideal performance: 65.73% TBD
Memory: 12.097 GB TBD
Global mean OH:
(% change from previous version)
11.74989868895 x 105 molec/cm3
(+4.68)
TBD
Methyl chloroform lifetime:
(% change from previous version)
5.263415 years
(-4.47%)
TBD
Methane lifetime:
(% change from previous version)
8.868914 years
(-4.34%)
TBD
Details
Species, J-Values, and COLUMN AOD values that changed by 10% or more at the surface: GEOS-Chem Classic 13.3.0 vs 13.2.0 TBD
Species and J-Values that changed by 10% or more at 500 hPa: GEOS-Chem Classic 13.3.0 vs 13.2.0 TBD
Species and J-Values that changed by 10% or more in zonal mean: GEOS-Chem Classic 13.3.0 vs 13.2.0 TBD
Emissions that changed by 10% or more: GEOS-Chem Classic 13.3.0 vs 13.2.0 TBD
Overview
Below we summarize the notable changes caused by specific updates. Supplementary plots may be viewed at http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/.

1. HMS chemistry (via sulfate_mod.F90)

This update introduces new advected species hydroxymethanesulfonate (HMS) in GEOS-Chem. This new chemistry has a relatively small impact on other species' concentrations and on global mean OH. Complete results from a 1-month benchmark evaluating the impact of this chemistry update may be viewed at this link.

2. C2H2 and C2H4 chemistry

This update introduces new advected species C2H2, C2H4, ETHN, and ETHP and adds one photolysis reaction. The new chemistry has a large (>10% impact) on GLYC, GLYX, H2O2, HCOOH, HMHP, MO2, MOH, MP, SOAGX (see this table). Global mean OH is reduced by -1.49%. Complete results from a 1-month benchmark evaluating the impact of this chemistry update may be viewed at this link.

3. Fixed typo in CloudHet

This fix has a large impact on many halogen species and changed global mean OH by +6.65%. These large changes are to be expected because the function in which this bug occurs (CloudHet) is used in the rate computations of many heterogeneous reactions. See this Github issue for further discussion on the changes from this fix.

4. Revise gamma(N2O5) computation; cap A at 3.2e-8

Prior to this fix, gamma(N2O5) (i.e. reaction probability) was too high over the oceans. This update now prevents gamma(N2O5) from exceeding ~0.036, which is consistent with lab results. We observe a relatively small (<10%) impact on most species, but ClNO2 shows a large decrease. But as gamma(N2O5) decreases, the production of ClNO2 via the reaction N2O5 + HCl = ClNO2 + HNO3 likewise decreases, so the results are to be expected. See this Github issue for further discussion on the changes from this update.

5. Updates to IONO2 hydrolysis from Wang et al. (2021)

This update replaced several heterogeneous reactions that converted gas-phase species HOI, IONO, and IONO2 to aerosol species ISALA and ISALC with the single hydrolysis reaction IONO2 + H2O = HOI + HNO3. We observe a large (>10%) impact on IONO2 and HOI, but a relatively small impact on other species (see this table). Global mean OH changed by -0.11%. See the original pull request on Github for more details of this update and its impact on model output.

6. Aromatic VOC chemistry

This update added new advected species AONITA, AROMP4, AROMP5, BALD, BENZP, BZCO3H, BZPAN, CSL, MCT, NPHEN, PHEN, along with ~45 gas-phase reactions, 1 heterogeneous reaction, and 4 photolysis reactions. The impact on other species is summarized in this table, and global mean OH changed by -0.36%. Complete results from a 1-month benchmark evaluating the impact of this chemistry update may be viewed at this link.

7. Updated aerosol dry deposition

This feature brings aerosol dry deposition in line with Emerson et al 2020, and several aerosol parameters within the dry deposition module were updated accordingly. Global mean OH increased by 0.024%. Most gas-phase species show small changes in mass (except for Br2 and ClNO2, which decreased by more than 5%). On the other hand, aerosol species such as AERI, ASOA1-4, DST1-4, show large decreases. Also, the mass of MSA increased by 7.7%. See this Github feature request for more information about this update. Complete results from a 1-month benchmark evaluating the impact of this chemistry update may be viewed at this link.

8. Update volcano emissions to May 2020 and add climatology

The volcano emissions inventory from GMAO has been updated from v20180523 to v202005. Plots for a 1-month benchmark evaluating the impact of this fix may be viewed at this link. The impact on SO2 emissions from volcanoes is:
    ###################################################################################
    ### Emissions totals for inventory VOLCANOdegas [Tg]                            ###
    ### Ref = GCC_13.3.0-alpha.7; Dev = GCC_13.3.0-alpha.8                          ###
    ###################################################################################
                                        Ref                 Dev     Dev - Ref    % diff
    VOLCANOdegas SO2   :           1.953161            1.826465     -0.126697    -6.487
  
    ###################################################################################
    ### Emissions totals for inventory VOLCANOerupt [Tg]                            ###
    ### Ref = GCC_13.3.0-alpha.7; Dev = GCC_13.3.0-alpha.8                          ###
    ###################################################################################
                                        Ref                 Dev     Dev - Ref    % diff
    VOLCANOerupt SO2   :           0.000000            0.101063      0.101063       nan
    

9. Avoid double counting of acetone source from monoterpenes when using online MEGAN

This update reduced ACET emissions in the MEGAN extension. Plots for a 1-month benchmark evaluating the impact of this fix may be viewed at this link. The impact on total ACET emissions from MEGAN is:
    ###################################################################################
    ### Emissions totals for inventory MEGAN [Tg]                                   ###
    ### Ref = GCC_13.2.1; Dev = GCC_13.3.0-alpha.0                                  ###
    ###################################################################################
                                        Ref                 Dev     Dev - Ref    % diff
    MEGAN ACET         :           4.967504            4.374804     -0.592700   -11.932

The following updates introduced differences on the order of numerical noise:

Approval
Requires further investigation:
Approved by:
Date of approval:

1-year benchmarks

TBD