Benchmark/GEOS-Chem 12.7.0

This page includes information about all benchmark simulations for GEOS-Chem 12.7.0.

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 NH4, NIT, SO4, DST1, DST2, DST3, DST4, BC, OC, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, SOA_Simple, SOA_Complex	sfc	500hPa	full column	stratosphere	sfc	AOD
Bromine Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH4Br, CH2Br2, CH2Br2, CH3Br3, HOBr, HBr	sfc	500hPa	full column	stratosphere	sfc
Chlorine Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH4CCl3, HOCl, HCl, Halons, HCFCs, OClO	sfc	500hPa	full column	stratosphere	--
Iodine Iy, IxOy, I, I2, IBr, ICl, IO, INO2, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO	sfc	500hPa	full column	stratosphere	sfc
Nitrogen NOy, NOx, HNO2, HNO3, HNO4, IMPN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3	sfc	500hPa	full column	stratosphere	sfc
Primary Organics ALK4, BENZ, CH4, C2H6, C2H4, C3H8, PRPE, TOLU, XYLE, ISOP, MTPA, MTPO, LIMO, GLYX, HCOOH, MAP, MBO, MOH, RCHO	sfc	500hPa	full column	stratosphere	sfc
Secondary Organics ACET, MEK, MVK, ALD2, CH2O, HPALD, MP, ISOPN, IEPOX, ACTA, EOH, MOH	sfc	500hPa	full column	stratosphere	sfc
Secondary Organic Aerosols SOAP, SOAS, TSOA0, TSOA1, TSOA2, TSOA3, ISOA1, ISOA2, ISOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ISOG1, ISOG2, ISOG3, ASOG1, ASOG2, ASOG3, INDIOL, ISN1OA, LVOCOA, SOAIE, SOAGX, SOAME, SOAMG	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 json files.

Benchmark assessment form

Description
New features added into GEOS-Chem	Feature Submitted by Updates that will affect full-chemistry simulations Small alkyl nitrate chemistry Jenny Fisher (Wollongong) Methanol as part of standard chemical mechanism Xin Chen (UMN) Dylan Millet (UMN) Katie Travis (NASA) Update to Yuan processed MODIS LAI product (covering years 2005-2016) GCST 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) Bug fix: Prevent differences in chemistry caused by toggling the ND65 bpch diagnostics off or on Bob Yantosca (GCST) Fix incorrect uptake coefficient for N2O5 in heterogeneous chemistry Hyeonmin Kim (Seoul Nat'l U.) Chris Holmes (FSU) Fix offline dust scale factors Jun Meng (GCST) 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) HEMCO 2.2.0: Updates and fixes to improve file I/O Melissa Sulprizio (GCST) Implement Gan Luo et al wetdep (GMD-12-3439-2019) as an option Gan Luo (SUNY-Albany) Fangqun Yu (SUNY-Albany) Bob Yantosca (GCST) CH4 soil absorption from MeMo model Melissa Sulprizio (Harvard) Removal of most binary punch (aka "bpch") diagnostics GCST Add netCDF diagnostic for UV fluxes from FAST-JX Jonathan Moch (Harvard) Bob Yantosca (GCST) KPP equation reactivity rate and OH reactivity diagnostics Christoph Keller (GMAO) Bug fix for HEMCO standalone using high-resolution input grids Chris Holmes (FSU) Incorrect units returned from GET_OH in sulfate_mod.F Rong Tian (NUIST) Use common build_mechanism.sh script for all KPP mechanisms Lizzie Lundgren (GCST) 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) Use same CEDS anthropogenic emissions inventory as GC Classic, including 1750-1949 and additional VOC species Lizzie Lundgren (GCST) Assorted GCHP structural changes to facilitate GEOS-Chem in GEOS Move high-level GCHP files to GEOS-Chem repository Move GCHP run directory creation to GEOS-Chem repository Lizzie Lundgren (GCST) Use same precision in non-species Internal state variables and the equivalent GEOS-Chem states (REAL8) Lizzie Lundgren (GCST) Update ESMF to v8.0.0 public release Lizzie Lundgren (GCST)
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: 08:40:40 CPU time / wall time: 21.1277 % of ideal performance: 88.03% Memory: 12.1784 GB
Git tag	12.7.0-rc.0
Compared to previous benchmark:	12.6.0
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_12/12.7.0/GCC/Plots/GC_12.7.0_Jan02.results.html
Metrics
Global mean OH from log file (% change):	11.7991194063953 x 105 molec/cm3 (+0.33%)
Methyl chloroform lifetime (% change):	5.3039 years (-0.67%)
Methane lifetime (% change):	8.9168 years (-0.70%)
Overview
Comments on observed differences:	Below we summarize the notable changes caused by specific updates. Small alkyl nitrate chemistry This update introduced four new advected species: MENO3, ETNO3, IPRNO3, and NPRNO3. These species have been added to the Nitrogen benchmark category. The global mean OH concentrations increase of +0.17% as a result of this chemistry update. Methanol as part of standard chemical mechanism With this update, methanol is now a chemically active species as well as a transported species. The overall impact of this update is small, contributing to a global mean OH change of +0.0083%. Update to Yuan processed MODIS LAI product (covering years 2005-2016) This update contributed to a global mean OH change of +0.21% and primarily impacts the biogenic emissions. The Yuan-processed MODIS LAI product is used as input in the MEGAN extension (off by default) and in this version we have switched to the updated offline biogenic VOC files generated with that MODIS LAI product. The impact on biogenic emissions is summarized below: ############################################################################### ### Emissions totals ### ### Ref = GC_12.7.0_Ref; Dev = GC_12.7.0_YuanXLAI ### ############################################################################### Ref Dev Dev - Ref ACET Biogenic  : 2.982478 2.734815 -0.247663 Tg C ALD2 Biogenic  : 1.037183 0.971226 -0.065957 Tg C EOH Biogenic  : 0.991817 0.928745 -0.063072 Tg C ISOP Biogenic  : 33.723910 33.565337 -0.158573 Tg C LIMO Biogenic  : 0.976173 0.930596 -0.045576 Tg MTPA Biogenic  : 8.644930 8.089232 -0.555698 Tg MTPO Biogenic  : 4.000710 3.756286 -0.244424 Tg PRPE Biogenic  : 2.030293 1.855930 -0.174363 Tg C SOAP Biogenic  : 1.467334 1.405632 -0.061702 Tg SOAS Biogenic  : 1.467334 1.405632 -0.061702 Tg Latitudinally and monthly resolved fixed surface concentrations for long-lived organohalogen species (1750-2014) and methane (prior to 1979) This update changes surface concentrations of CH3Br, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, Halons, HCFCs, and as a result it also impacts concentrations of several other halogen species. Global mean OH changes by -0.12%. Fix incorrect uptake coefficient for N2O5 in heterogeneous chemistry This fix causes small changes in N2O5 and in some halogen species. The impact on global mean OH is -0.015%. Fix offline dust scale factors This update corrects the scale factor used for offline emissions of DST1 so that the species uses the same factor used for DST2, DST3, and DST4. The impact on emissions is summarized below: ############################################################################### ### Emissions totals for species DST1 ### ### Ref = GC_12.7.0_YuanXLAI; Dev = GC_12.7.0_DustSF ### ############################################################################### Ref Dev Dev - Ref DST1 Natural  : 11.225230 9.550223 -1.675007 Tg
Details
List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:	Oxidants: OH NOx Aerosols: NIT BrSALA BrSALC Complex_SOA Simple_SOA Nitrogen: NOy NOx HNO2 HNO3 HNO4 IPMN NIT NO NO2 NO3 N2O5 MPN PAN PPN NH3 ROy: H2O2 OH RO2 Sulfur: DMS Iodine: I I2 ICl INO2 IONO2 HI OIO Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 CCl4 CH2Cl2 CH3CCl3 HOCl HCl HCFCs OClO Primary_Organics: PRPE XYLE ISOP MTPA MTPO LIMO EOH MOH Secondary_Organics: ACET MEK MVK HPALD MACR ISOPN IEPOX GLYX HCOOH RCHO Secondary_Organic_Aerosols: SOAP TSOA0 TSOA1 TSOA2 TSOA3 TSOG0 TSOG1 TSOG2 TSOG3 ASOG1 ASOG2 ASOG3 INDIOL ISN1OA LVOCOA SOAIE SOAGX SOAME SOAMG J-Values: Column AOD: SOA_from_Aqueous_ISOP Total
List all 500 hPa species and J-Values that changed by 10% or more :	Oxidants: NOx Aerosols: NIT BrSALA BrSALC Nitrogen: NOy NOx HNO2 HNO4 IPMN NIT NO NO2 NO3 N2O5 MPN PPN NH3 ROy: RO2 Sulfur: DMS SO2 Iodine: ICl INO2 IONO2 CH2I2 OIO Bromine: BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 CCl4 CH2Cl2 CH3CCl3 HOCl HCl HCFCs OClO Primary_Organics: PRPE TOLU XYLE ISOP MTPA MTPO LIMO EOH MOH Secondary_Organics: ACET MEK MVK HPALD MACR ISOPN IEPOX GLYX HCOOH RCHO Secondary_Organic_Aerosols: LVOCOA SOAIE SOAME
List all ZONAL MEAN species and J-Values that changed by 10% or more:	Aerosols: NIT BrSALA Nitrogen: NOy NOx HNO4 IPMN NIT NO NO3 N2O5 MPN PPN NH3 ROy: None Sulfur: DMS Iodine: I ICl INO2 CH2I2 OIO Bromine: BrOx Br BrCl BrO HBr Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 CCl4 CH2Cl2 HOCl HCl HCFCs OClO Primary_Organics: ALK4 C3H8 PRPE TOLU XYLE ISOP MTPA MTPO LIMO MOH Secondary_Organics: ACET MEK MVK ALD2 HPALD MACR ISOPN IEPOX GLYX HCOOH RCHO Secondary_Organic_Aerosols: None 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 Ship: O3 Total: ACET ALD2 EOH ISOP MTPA PRPE SOAP
Approval
Requires further investigation:	A second 1-month benchmark (Git tag 12.7.0-rc.1) was performed to address the following issues identified in this benchmark: Bug fix in AODfromISOPSOA diagnostic to remove double use of BXHEIGHT In SfcFix/v2019-12/ directory, rename "GMI" to "WMO_2018" and remove unused "UCX" files Add WMO-2018 surface VMR for H2402 Plots for this final 12.7.0 1-month benchmark may be viewed at: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.7.0-rc.1
Approved by:	Daniel Jacob
Date of approval:	27 Jan 2020

GCHP 1-month benchmark

The following sections contain validation plots for GCHP 12.7.0.

Comparison of GCHP versions

This table contains plots comparing GCHP 12.6.0 (Ref) and GCHP 12.7.0 (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

Comparison of GCHP and GEOS-Chem Classic

This table contains plots comparing GEOS-Chem Classic 12.7.0 (Ref) against GCHP 12.7.0 (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 12.7.0:

• 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.