GEOS-Chem 13.3.0

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:

• 13.3.0 milestone for geoschem/geos-chem
• 13.3.0 milestone for geoschem/GCHP
• 3.2.0 milestone for geoschem/HEMCO

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	See geoschem/geos-chem PR #919
C2H2 and C2H4 chemistry	Kelvin Bates (Harvard) Ke Li (Harvard) Mike Long (GCST)	Chemistry	See geoschem/geos-chem PR #904
CH3O2 + OH reaction	Kelvin Bates (Harvard)	Chemistry	See geoschem/geos-chem PR #904
HMS chemistry (via sulfate_mod.F90)	Jonathan Moch (Harvard) Mike Long (GCST)	Chemistry	See geoschem/geos-chem PR #905
Updates to IONO2 hydrolysis from Wang et al. (2021)	Tomas Sherwen (York)	Chemistry	See geoschem/geos-chem PR #719 See geoschem/geos-chem PR #923
Revise gamma(N2O5) computation; cap A at 3.2e-8	Viral Shah (Harvard)	Chemistry	See geoschem/geos-chem #907
Bug fixes in heterogeneous chemistry: Fixed typo in CloudHet Fixed typos in ClNO2 hetchem reactions: HNO2 should be a product, not HNO3	Viral Shah (Harvard) Chris Holmes(FSU)	Chemistry	See geoschem/geos-chem #906 See geoschem/geos-chem #841
Cleaning up heterogeneous chemistry reaction rate computations	Bob Yantosca (GCST)	Chemistry & Structural	See geoschem/geos-chem PR #897
Updated aerosol dry deposition	Jeff Pierce (CSU)	Dry deposition	See geoschem/geos-chem PR #604
Avoid double counting of acetone source from monoterpenes when using online MEGAN	Dylan Millet (UMN)	Emissions	See also geoschem/HEMCO PR #93
Update volcano emissions to May 2020 and add climatology	Christoph Keller (NASA/GMAO)	Emissions	See geoschem/geos-chem PR #921 See geoschem/HEMCO PR #110
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	See geoschem/geos-chem PR #816 Online dust emissions are used in benchmark simulations
Update US emissions to NEI2016 (as option)	Barron Henderson (EPA) Lyssa Freese (MIT) Melissa Sulprizio (GCST)	Emissions	See geoschem/geos-chem PR #920
Send all HEMCO error messages to GEOS-Chem log	Lizzie Lundgren (GCST)	HEMCO	See geoschem/HEMCO PR #111
The ObsPack diagnostic can now use the ?ADV? wildcard	Jessica Haskins (MIT)	Diagnostics	See geoschem/geos-chem PR #922
Features only affecting GCHP:
Include thread number in GEOS-Chem and HEMCO error messages	Lizzie Lundgren (GCST)	GCHP/GEOS	See geoschem/geos-chem PR #925 See geoschem/HEMCO PR #111
GCHP Adjoint updates	Colin Lee (CU Boulder)	GCHP	See geoschem/GCHP #146

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):	GEOS-Chem Classic: 13.3.0-rc.0 GCHP: TBD
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: Cleaning up heterogeneous chemistry reaction rate computations Fixed typos in ClNO2 hetchem reactions: HNO2 should be a product, not HNO3
Approval
Requires further investigation:
Approved by:
Date of approval:

1-year full-chemistry benchmarks

Model setup

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

Git tag(s):	[1]
Compared to previous benchmark:	GEOS-Chem 13.0.0
Software environment:	ifort 18.0.5 OpenMPI 4.0.1 netcdf-fortran 4.5.2 CMake 3.16.1 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°
Spin-up initial conditions:	January 1, 2017 from 12.9.0 1-year benchmark NOTE: GCHP c48 regridded from GEOS-Chem Classic 4° x 5°
Benchmark date:	Spin-up run: Jan 2018 - Dec 2018 Production run: Jan 2019 - Dec 2019

Benchmark Plots and Tables

NOTES:

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

GEOS-Chem Classic 13.3.0 vs 13.0.0

Below are links to plots and tables comparing 1-year full-chemistry simulations for GEOS-Chem Classic 13.3.0 (Dev) and GEOS-Chem Classic 13.0.0 (Ref).

Category1	Plots					Additional Information
	Level Map		Zonal Mean		Emissions
Oxidants O3, CO, OH, NOx	Surface Jan Apr Jul Oct	500 hPa Jan Apr Jul Oct	Full column Jan Apr Jul Oct	Stratosphere Jan Apr Jul Oct	Full column Jan Apr Jul Oct
Aerosols DST1, DST2, DST3, DST4, NH4, NIT, SO4, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA	Surface Jan Apr Jul Oct	500 hPa Jan Apr Jul Oct	Full column Jan Apr Jul Oct	Stratosphere Jan Apr Jul Oct	Full column Jan Apr Jul Oct	AOD Jan Apr Jul Oct Aerosol profiles Aerosol burdens Global mean AOD
Bromine Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH4Br, CH2Br2, CH2Br2, CH3Br3, HOBr, HBr	Surface Jan Apr Jul Oct	500 hPa Jan Apr Jul Oct	Full column Jan Apr Jul Oct	Stratosphere Jan Apr Jul Oct	Full column Jan Apr Jul Oct
Chlorine Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH4CCl3, HOCl, HCl, Halons, HCFCs, OClO	Surface Jan Apr Jul Oct	500 hPa Jan Apr Jul Oct	Full column Jan Apr Jul Oct	Stratosphere Jan Apr Jul Oct	-
Iodine Iy, IxOy, I, I2, IBr, ICl, IO, INO2, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO	Surface Jan Apr Jul Oct	500 hPa Jan Apr Jul Oct	Full column Jan Apr Jul Oct	Stratosphere Jan Apr Jul Oct	Full column Jan Apr Jul Oct
Nitrogen NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3	Surface Jan Apr Jul Oct	500 hPa Jan Apr Jul Oct	Full column Jan Apr Jul Oct	Stratosphere Jan Apr Jul Oct	Full column Jan Apr Jul Oct
Primary Organics EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H6, C3H8, PRPE, TOLU, XYLE	Surface Jan Apr Jul Oct	500 hPa Jan Apr Jul Oct	Full column Jan Apr Jul Oct	Stratosphere Jan Apr Jul Oct	Full column Jan Apr Jul Oct
Secondary Organics ACTA, ALD2, CH2O, HPALDs, MACR, IEPOX, ACET, MEK, MVK, ISOPN, GLYX, HCOOH, MAP, RCHO, MP	Surface Jan Apr Jul Oct	500 hPa Jan Apr Jul Oct	Full column Jan Apr Jul Oct	Stratosphere Jan Apr Jul Oct	Full column Jan Apr Jul Oct
Secondary Organic Aerosols TSOA0, TSOA1, TSOA2, TSOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ASOG1, ASOG2, ASOG3, INDIOL, LVOCOA, SOAIE, SOAGX, SOAP, SOAS	Surface Jan Apr Jul Oct	500 hPa Jan Apr Jul Oct	Full column Jan Apr Jul Oct	Stratosphere Jan Apr Jul Oct	Full column Jan Apr Jul Oct
Sulfur SOx, DMS, OCS, SO2, SO4	Surface Jan Apr Jul Oct	500 hPa Jan Apr Jul Oct	Full column Jan Apr Jul Oct	Stratosphere Jan Apr Jul Oct	Full column Jan Apr Jul Oct
ROy H2O2, H, H2, H2O, HO2, O1D, OH, RO2	Surface Jan Apr Jul Oct	500 hPa Jan Apr Jul Oct	Full column Jan Apr Jul Oct	Stratosphere Jan Apr Jul Oct	-
J-values	Surface Jan Apr Jul Oct	500 hPa Jan Apr Jul Oct	Full column Jan Apr Jul Oct	Stratosphere Jan Apr Jul Oct	-
Emissions by HEMCO category	Total: Jan, Apr, Jul, Oct Aircraft: Jan, Apr, Jul, Oct Anthropogenic: Jan, Apr, Jul, Oct Biomass burning: Jan, Apr, Jul, Oct Biogenic: Jan, Apr, Jul, Oct Lightning: Jan, Apr, Jul, Oct Natural: Jan, Apr, Jul, Oct Ocean: Jan, Apr, Jul, Oct Plant decay:Jan, Apr, Jul, Oct Sea birds: Jan, Apr, Jul, Oct Ship: Jan, Apr, Jul, Oct Soil: Jan, Apr, Jul, Oct Volcano degassing: Jan, Apr, Jul, Oct Volcano erupting: Jan, Apr, Jul, Oct
Emission totals	Tables by species Tables by inventory
Global mass	Entire atmosphere: Jan, Apr, Jul, Oct Troposphere only: Jan, Apr, Jul, Oct
Metrics	OH concentration, MCF lifetime, CH4 lifetime
Budgets	Budgets after operations: Jan, Apr, Jul, Oct
Strat-trop exchange	Monthly and annual mean values
Model vs Observations	Aerosols: Seasonal plots, Scatter plots Aircraft: C2H6, C3H8, CO, H2O2, HNO3, NO, O3, PAN CO: Profiles, Latitudal distribution, Ships, Seasonal plots (Surface, MOZAIC 4 levels) O3: Profiles (GMI, MOZAIC), Seasonal plots (Surface, GMI 3 levels, GMI 4 levels, MOZAIC 3 levels, MOZAIC 4 levels) PAN: Profiles PM2.5 with simple SOA: Maps, Scatter plots PM2.5 with complex SOA: Maps, Scatter plots

GCHP 13.3.0 vs GEOS-Chem Classic 13.3.0

TBD