Benchmark/GEOS-Chem 12.8.0

This page includes information about all benchmark simulations for GEOS-Chem 12.8.0.

GEOS-Chem Classic 1-month benchmark

Benchmark plots

Enable PDF bookmarks¹ in the files linked below to navigate between species. See the Species in GEOS-Chem wiki page for species definitions and details.

Species Category2	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, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA	sfc	500hPa	full column	stratosphere	sfc	AOD
Bromine Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr	sfc	500hPa	full column	stratosphere	sfc
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	sfc
Nitrogen NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3	sfc	500hPa	full column	stratosphere	sfc
Primary Organics EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H6, C3H8, PRPE, TOLU, XYLE	sfc	500hPa	full column	stratosphere	sfc
Secondary Organics ACTA, ALD2, CH2O, HPALDs, MACR, IEPOX, ACET, MEK, MVK, ISOPN, GLYX, HCOOH, MAP, RCHO, MP	sfc	500hPa	full column	stratosphere	sfc
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	sfc
Sulfur SOx, DMS, OCS, SO2, SO4	sfc	500hPa	full column	stratosphere	sfc
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
OH metrics	OH concentration, MCF lifetime, CH4 lifetime

¹All plots created with GCPy have PDF bookmarks. If you do not see them in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.

²Species category and lumped species definitions are simple to adjust. Updating them requires only editing the YAML files.

Benchmark assessment form

Description
New features added into GEOS-Chem	Feature Submitted by Isoprene chemistry Kelvin Bates (Harvard) Wet deposition parameterization Kelvin Bates (Harvard) Sarah Safieddine (MIT) Ozone deposition to the ocean Ryan Pound (York) Mat Evans (York) Use online MEGAN, DustDead, SeaSalt, and SoilNOx emissions for benchmark simulations Melissa Sulprizio (GCST) Shift CMIP6 time from middle to start of month to allow start in January Lizzie Lundgren (GCST) Features NOT affecting the full-chemistry simulation: GFED 4.1s beta emissions for 2017-2019 Maggie Marvin (U. Edinburgh) Replace State_Chm%nAero with State_Chm%nAeroSpc and State_Chm%nAeroType Seb Eastham (MIT) GCST Convert all files in GeosCore, GeosUtil, and Headers to .F90 Melissa Sulprizio (GCST) Change GEOS-Chem timers from a CPP switch to an option in input.geos Melissa Sulprizio (GCST) Remove potential for surface CH4 retrieval error in SET_CH4 due to reliance on HEMCO emissions year Christoph Keller (GMAO) Features affecting GCHP only: Fix leap year handling bug in GCHP multi-run script Lizzie Lundgren (Harvard)
Version, resolution, met fields used:	GEOS-FP (72L), 4x5, July 2016
1-month benchmark finished on:	Mon Jan 6 06:18:07 EST 2020
Performance statistics:	Compiled with ifort 17.0.4 Ran on 24 CPUs of holyjacob01.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz) Wall time: 09:28:36 CPU time / wall time: 21.4657 % of ideal performance: 89.44% Memory: 13.2477 GB
Git tag	12.8.0-rc.0
Compared to previous benchmark:	12.7.0
This update will impact: (select all that apply with boldface)	Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Emissions, Photolysis, Chemistry, Other (please specify):
Unit test results may be viewed at:	http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.8.0/GCC/Plots/GC_12.8.0_Mar19.results.html
Metrics
Global mean OH from log file (% change):	11.8937088091687 x 105 molec/cm3 (+0.96%)
Methyl chloroform lifetime (% change):	5.2374 years (-1.25%)
Methane lifetime (% change):	8.8001years (-1.30%)
Overview
Comments on observed differences:	Below we summarize the notable changes caused by specific updates. Isoprene chemistry This update introduced several new advected species: HMHP, ETP, HPETHNL, HCOOH, PYAC, ATOOH, ETHLN, MCRHN, MCRHNB, R4P, RP, RA3P, RB3P, PIP, PP, RIPA, RIPB, RIPC, RIPD, IEPOXA, IEPOXB, IEPOXD, ICHE, HC5A, HMML, HPALD1, HPALD2, HPALD3, HPALD4, IDC, IHN1, IHN2, IHN3, IHN4, INPB, INPD, IDN, ICN, ITCN, ITHN, ICPDH, IDCHP, IDHDP, IDHPE, MVKDH, MVKHC, MVKHCB, MVKHP, MVKPC, MCRDH, MCRENOL, MCRHP, MACR1OOH and removed several species: NPMN, ISOPND, ISOPNB, MOBA, MACRN, IMAE, SOAME, SOAMG, ISN1OG, ISN1OA, IPMN, HC187 The benchmark categories have been updated to account for these changes, following recommendations from Kelvin Bates. For remarks on impacts caused by these changes, please see this discussion on Github. NOTE: There are large decreases observed in AOD from isoprene SOA in this version. These changes are partially due to removing some species that were included in the isoprene SOA calculation in aerosol_mod.F, but are mainly due to the bug fix for the AOD from isoprene SOA diagnostic that went into GEOS-Chem 12.7.1. Ozone deposition to the ocean This update increases O3 concentrations over the ocean at the surface by up to 5 ppb, primarily at high latitudes. Global mean OH is increased by 0.15% with these changes. Use online DustDead, MEGAN, SeaSalt, and SoilNOx emissions for benchmark simulations The entries below from the emissions tables by species show differences caused by turning the DustDead, MEGAN, SeaSalt, and SoilNOx extensions back on in benchmark simulations. These changes are similar, but of the opposite sign, to the changes observed in the GEOS-Chem 12.4.0 benchmark when offline emissions were implemented. ############################################################################### ### Emissions totals ### ### Ref = GC_12.7.0; Dev = GC_12.8.0 ### ############################################################################### Ref Dev Dev - Ref DST1 Natural  : 9.550223 3.400091 -6.150131 Tg DST2 Natural  : 23.987765 8.540177 -15.447588 Tg DST3 Natural  : 43.524575 15.495716 -28.028860 Tg DST4 Natural  : 47.613968 16.951628 -30.662340 Tg ... ACET Biogenic  : 2.734815 2.936038 0.201222 Tg C ALD2 Biogenic  : 0.971226 0.993718 0.022492 Tg C EOH Biogenic  : 0.928745 0.950253 0.021508 Tg C ISOP Biogenic  : 33.565337 30.881374 -2.683962 Tg C LIMO Biogenic  : 0.930596 0.903745 -0.026852 Tg MTPA Biogenic  : 8.089232 8.345941 0.256708 Tg MTPO Biogenic  : 3.756286 3.860389 0.104104 Tg PRPE Biogenic  : 1.855930 1.997076 0.141146 Tg C SOAP Biogenic  : 1.405632 1.206619 -0.199013 Tg SOAS Biogenic  : 1.405632 1.206619 -0.199013 Tg .. SALA Natural  : 5.620708 4.653316 -0.967392 Tg SALC Natural  : 340.191067 281.640070 -58.550997 Tg ... NO Soil  : 1.580800 1.376302 -0.204498 Tg
Details
List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:	Aerosols: DST1 DST2 DST3 DST4 NH4 NIT SO4 Complex_SOA Simple_SOA AERI BrSALA BrSALC ISALA ISALC NITs SALC SO4s Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO Iodine: Iy IxOy I I2 IBr ICl IO IONO IONO2 CH2I2 HI HOI OIO Nitrogen: NOy NOx HNO2 HNO3 HNO4 NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4 MENO3 ETNO3 IPRNO3 NPRNO3 Oxidants: O3 OH NOx Primary_Organics: EOH ISOP MTPA MTPO LIMO PRPE TOLU ROy: H2O2 H HO2 O1D OH RO2 Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOA3 ASOA1 ASOA2 ASOA3 ASOAN TSOG0 TSOG1 TSOG2 TSOG3 ASOG1 ASOG2 ASOG3 INDIOL LVOCOA SOAIE SOAP SOAS Secondary_Organics: ACTA ALD2 CH2O MACR IEPOX ACET MEK MVK ISOPN GLYX HCOOH MAP RCHO MP Sulfur: SOx DMS SO2 SO4 Aerosols: DST1 DST2 DST3 DST4 NH4 NIT SO4 Complex_SOA Simple_SOA AERI BrSALA BrSALC ISALA ISALC NITs SALC SO4s Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO Iodine: Iy IxOy I I2 IBr ICl IO IONO IONO2 CH2I2 HI HOI OIO Nitrogen: NOy NOx HNO2 HNO3 HNO4 NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4 MENO3 ETNO3 IPRNO3 NPRNO3 Oxidants: O3 OH NOx Primary_Organics: EOH ISOP MTPA MTPO LIMO PRPE TOLU ROy: H2O2 H HO2 O1D OH RO2 Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOA3 ASOA1 ASOA2 ASOA3 ASOAN TSOG0 TSOG1 TSOG2 TSOG3 ASOG1 ASOG2 ASOG3 INDIOL LVOCOA SOAIE SOAP SOAS Secondary_Organics: ACTA ALD2 CH2O HPALDs MACR IEPOX ACET MEK MVK ISOPN GLYX HCOOH MAP RCHO MP Sulfur: SOx DMS SO2 SO4 J-Values: None Column AOD: None
List all 500 hPa species and J-Values that changed by 10% or more :	Aerosols: DST2 DST3 DST4 NIT Complex_SOA BrSALA BrSALC NITs Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO Iodine: I2 IBr ICl IO IONO IONO2 CH2I2 HI OIO Nitrogen: NOx HNO2 HNO3 HNO4 NIT NO NO2 N2O5 MPN PPN NH3 Oxidants: OH NOx Primary_Organics: EOH ISOP MTPA MTPO LIMO PRPE XYLE ROy: H2O2 H HO2 OH RO2 Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOA3 TSOG0 TSOG1 TSOG2 TSOG3 INDIOL SOAP Secondary_Organics: ACTA ALD2 CH2O MACR IEPOX ACET MVK ISOPN GLYX HCOOH MAP RCHO Sulfur: DMS SO2 Aerosols: DST2 DST3 DST4 NIT Complex_SOA BrSALA BrSALC NITs Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO Iodine: I2 IBr ICl IO IONO IONO2 CH2I2 HI OIO Nitrogen: NOx HNO2 HNO3 HNO4 NIT NO NO2 N2O5 MPN PPN NH3 Oxidants: OH NOx Primary_Organics: EOH ISOP MTPA MTPO LIMO PRPE XYLE ROy: H2O2 H HO2 OH RO2 Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOA3 TSOG0 TSOG1 TSOG2 TSOG3 INDIOL SOAP Secondary_Organics: ACTA ALD2 CH2O HPALDs MACR IEPOX ACET MVK ISOPN GLYX HCOOH MAP RCHO Sulfur: DMS SO2
List all ZONAL MEAN species and J-Values that changed by 10% or more:	Aerosols: NH4 NIT Complex_SOA AERI BrSALC Bromine: BrOx Br BrCl BrNO3 BrO HOBr HBr Chlorine: ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO3 HOCl HCl OClO Iodine: I I2 IBr ICl IO IONO2 CH2I2 CH2ICl CH2IBr HI HOI OIO Nitrogen: HNO3 NIT NO3 N2O5 MPN PAN PPN NH3 NH4 NPRNO3 Oxidants: O3 OH Primary_Organics: ISOP MTPA MTPO LIMO C3H8 PRPE ROy: H HO2 O1D OH RO2 Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOG0 TSOG1 TSOG2 TSOG3 INDIOL LVOCOA Secondary_Organics: ACTA ALD2 CH2O MACR IEPOX MVK ISOPN GLYX HCOOH MAP RCHO Sulfur: DMS SO2 Aerosols: NH4 NIT Complex_SOA AERI BrSALC Bromine: BrOx Br BrCl BrNO3 BrO HOBr HBr Chlorine: ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO3 HOCl HCl OClO Iodine: I I2 IBr ICl IO IONO2 CH2I2 CH2ICl CH2IBr HI HOI OIO Nitrogen: HNO3 NIT NO3 N2O5 MPN PAN PPN NH3 NH4 NPRNO3 Oxidants: O3 OH Primary_Organics: ISOP MTPA MTPO LIMO C3H8 PRPE ROy: H HO2 O1D OH RO2 Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOG0 TSOG1 TSOG2 TSOG3 INDIOL LVOCOA Secondary_Organics: ACTA ALD2 CH2O HPALDs MACR IEPOX MVK ISOPN GLYX HCOOH MAP RCHO Sulfur: DMS SO2 J-Values: None
List all EMISSIONS that changed by 10% or more:	Biogenic: ACET ALD2 EOH ISOP LIMO MTPA MTPO PRPE SESQ SOAP SOAS Natural: DST1 DST2 DST3 DST4 SALA SALC Ship: HNO3 NO2 NO O3 Soil: NO Total: ACET ALD2 DST1 EOH ISOP MTPA NO PRPE SOAP
Approval
Requires further investigation:
Approved by:
Date of approval:

GCHP 1-month benchmark

The following sections contain validation plots for GCHP 12.80.

Comparison of GCHP versions

This table contains plots comparing GCHP 12.7.0 (Ref) and GCHP 12.80 (Dev) for a 1-month simulation.

Category	Plots					Additional Information
	Level Map		Zonal Mean		Emissions
Oxidants	sfc	500hPa	full column	stratosphere	full column
Aerosols	sfc	500hPa	full column	stratosphere	full column	Column AOD
Bromine	sfc	500hPa	full column	stratosphere	full column
Chlorine	sfc	500hPa	full column	stratosphere	--
Iodine	sfc	500hPa	full column	stratosphere	full column
Nitrogen	sfc	500hPa	full column	stratosphere	full column
Primary Organics	sfc	500hPa	full column	stratosphere	full column
Secondary Organics	sfc	500hPa	full column	stratosphere	full column
Secondary Organic Aerosols	sfc	500hPa	full column	stratosphere	full column
Sulfur	sfc	500hPa	full column	stratosphere	full column
ROy	sfc	500hPa	full column	stratosphere	--
J-values	sfc	500hPa	full column	stratosphere	--
Emissions by HEMCO category	Aircraft, Anthro, Bioburn, Biogenic, Lightning, Monoterp, Natural, Ocean, Seabirds, DecayingPlants, [http:/ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.8.0/GCHP/plots/GCHP_version_comparison/Emissions/Ship_Emissions.pdf Ship], Soil, Total, VolcDegas, VolcErupt,					Emission totals

Comparison of GCHP and GEOS-Chem Classic

This table contains plots comparing GEOS-Chem Classic 12.8.0 (Ref) against GCHP 12.8.0 (Dev) for a 1-month simulation.

Category	Plots					Additional Information
	Level Map		Zonal Mean		Emissions
Oxidants	sfc	500hPa	full column	stratosphere	full column
Aerosols	sfc	500hPa	full column	stratosphere	full column	Column AOD
Bromine	sfc	500hPa	full column	stratosphere	full column
Chlorine	sfc	500hPa	full column	stratosphere	--
Iodine	sfc	500hPa	full column	stratosphere	full column
Nitrogen	sfc	500hPa	full column	stratosphere	full column
Primary Organics	sfc	500hPa	full column	stratosphere	full column
Secondary Organics	sfc	500hPa	full column	stratosphere	full column
Secondary Organic Aerosols	sfc	500hPa	full column	stratosphere	full column
Sulfur	sfc	500hPa	full column	stratosphere	full column
ROy	sfc	500hPa	full column	stratosphere	--
J-values	sfc	500hPa	full column	stratosphere	--
Emissions by HEMCO category	Aircraft, Anthro, Bioburn, Biogenic, Lightning, Monoterp, Natural, Ocean, Seabirds, DecayingPlants, Ship, Soil, Total, VolcDegas, VolcErupt,					Emission totals

1-year Transport Tracers benchmarks

Two 1-year Transport Tracers benchmark simulation were performed using GEOS-Chem 12.8.0:

• Run0-StdWetDep
• Run1-LuoWetDep

Both simulations utilized 4° x 5° GEOS-FP met fields for the year 2016, with a 10-year spinup. These simulations can be used to validate the Luo wet dep scheme which is offered as an option starting in this version.

Month	Plots
	Level Map		Zonal Mean
January	sfc	500hPa	full column	stratosphere
April	sfc	500hPa	full column	stratosphere
July	sfc	500hPa	full column	stratosphere
October	sfc	500hPa	full column	stratosphere
Emissions	Total Emissions

NOTE: At present, we have only created the 6-panel difference plots for species concentrations and total emissions, but this can be expanded to other benchmark output in the future.