Benchmark/GEOS-Chem 12.6.0

This page includes information about all benchmark simulations for GEOS-Chem 12.6.0.

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	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 Combined heterogeneous chemistry updates, includes N2O5, NO3, NO2 reactive uptake updates Subgrid cloud NOy chemistry Chris Holmes (FSU) Erin McDuffie (Dalhousie) Viral Shah (UW) Lyatt Jaegle (UW) HNO3 cold-temperature deposition Viral Shah (Harvard) Quick fix for aerosol pH calculation when dry Becky Alexander (UW) Xuan Wang (Harvard) Remove isoprene in VBS (leaving aqueous) Melissa Sulprizio (GCST) Updated aerosol hygroscopicity and optics Robyn Latimer (Dalhousie) Jun Meng (Dalhousie) Add EDGAR BCPI and BCPO emissions for remaining sectors to DICE-Africa Tomas Sherwen (York) Eloise Marais (Leicester) Updates that will NOT affect full-chemistry simulations Simple parameterization for CO2 dependence of stomatal resistance (off by default) Amos Tai (CUHK) Aerosol nitrate photolysis option (off by default) Tomas Sherwen (York) Prasad Kasibhatla (Duke) CMake in GEOS-Chem Classic (optional) Liam Bindle (Dalhousie) Enable GEOS-Chem "Classic" netCDF (History) diagnostics to be subsetted vertically and horizontally Bob Yantosca (GCST) BB4CMIP historical biomass burning emissions (1750-2014) NOTE: This is an optional emissions inventory. Pengfei Liu (Harvard) Surface diagnostic (O3, HNO3) with user-selected height Katie Travis (MIT) GCST APM update and integration with GEOS-Chem 12 Gan Luo (SUNY-Albany) Fangqun Yu (SUNY-Albany)
Version, resolution, met fields used:	GEOS-FP (72L), 4x5, July 2016
1-month benchmark finished on:	Sat Sep 14 03:12:29 EDT 2019
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: 07:10:48 CPU time / wall time: 21.4499 % of ideal performance: 89.37% Memory: 13.0503 GB
Compared to previous benchmark:	12.5.0
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_12/12.6.0/GCC/Plots/GC_12.6.0_Sep13.results.html
Metrics
Global mean OH from log file (% change):	11.7776515135847 x 105 molec/cm3 (-5.54%)
Methyl chloroform lifetime (% change):	5.3395 (4.07%)
Methane lifetime (% change):	8.9801 years (3.83%)
Overview
Comments on observed differences:	Below we summarize the notable changes caused by specific updates. Combined heterogeneous chemistry updates This update causes widespread changes in species concentrations. Global mean OH concentrations change by -4.14% due to this update alone. Notable changes at the surface include increases in NO3 and N2O5 over land and global decrease in HNO2. NOy decreases globally in the mid-to-upper troposphere. HNO3 cold-temperature deposition With this update, HNO3 concentrations decrease slightly at the surface and aloft while NOy increases slightly at all levels. Remove isoprene in VBS (leaving aqueous) The removal of ISOA/ISOG species manifests as widespread decreases in the complex SOA lumped species concentrations. Updated aerosol hygroscopicity and optics This update introduces slight decreases in NH4 and SO4 in the lower troposphere. Changes can also be seen in the AOD plots, where total AOD decreases. This is consistent with the changes reported by the developers. Scale DICE-Africa emissions to address errors in inventory This update contributes to changes in BC and OC concentrations over and just downwind of Africa. Slight differences can also be seen over Africa in the emission maps. The impact on the inventory emission totals are included below. ############################################################################### ### Inventory totals for DICEAfrica ### ### Ref = GC_12.5.0; Dev = GC_12.6.0 ### ############################################################################### Ref Dev Dev - Ref DICEAfrica BCPI  : 0.004153 0.006925 0.002772 Tg DICEAfrica BCPO  : 0.016612 0.027698 0.011087 Tg The following updates produced small changes: Quick fix for aerosol pH calculation when dry
Comments on additional differences in GCHP:	As of 19 Sep 2019, the GCHP 12.6.0 benchmark has issues (e.g. O3 is depleted). We are investigating this and will update the benchmark output once a fix is implemented.
Details
List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:	Oxidants: NOx Aerosols: NH4 NIT BCPI BCPO AERI BrSALA BrSALC ISALC NITs SO4s Complex_SOA Nitrogen: NOy NOx HNO3 HNO4 IPMN NIT NO NO2 NO3 N2O5 MPN PAN PPN NH3 NH4 ROy: RO2 Sulfur: DMS SO2 Iodine: IxOy I I2 ICl IO INO2 IONO2 CH2I2 OIO Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO Primary_Organics: ALK4 PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX RCHO Secondary_Organics: MVK ALD2 HPALD ISOPN IEPOX EOH Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOA3 ASOA1 ASOA2 ASOA3 TSOG0 TSOG1 TSOG2 TSOG3 ASOG1 ASOG2 ASOG3 INDIOL ISN1OA SOAIE SOAGX SOAME SOAMG J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Cl2 CH3CCl3 CH3Cl HCFC123 HCFC141b HCFC142b HCFC22 N2O O2 Column AOD: BCPI SO4 SOA_from_Aqueous_ISOP Total
List all 500 hPa species and J-Values that changed by 10% or more :	Oxidants: None Aerosols: NIT BCPI BCPO AERI BrSALA BrSALC Nitrogen: HNO3 IPMN NIT NO NO3 N2O5 NH3 ROy: RO2 Sulfur: DMS SO2 Iodine: IxOy I I2 ICl IO INO2 CH2I2 OIO Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO Primary_Organics: ALK4 BENZ PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX HCOOH MAP RCHO Secondary_Organics: MEK MVK ALD2 HPALD MP ISOPN IEPOX ACTA EOH Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOG0 TSOG1 ASOG1 INDIOL ISN1OA LVOCOA SOAIE SOAGX SOAME SOAMG
List all ZONAL MEAN species and J-Values that changed by 10% or more:	Oxidants: OH NOx Aerosols: NIT BCPO AERI BrSALA BrSALC SO4s Nitrogen: NOx HNO3 IPMN NIT NO NO2 NO3 N2O5 MPN PPN NH3 ROy: H2O2 H HO2 OH RO2 Sulfur: DMS SO2 Iodine: IxOy I I2 IBr ICl IO INO2 IONO2 CH2I2 CH2ICl CH2IBr OIO Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO Primary_Organics: BENZ PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX MAP RCHO Secondary_Organics: MEK MVK ALD2 HPALD MP ISOPN IEPOX ACTA EOH Secondary_Organic_Aerosols: TSOA1 TSOA3 ASOA3 TSOG0 TSOG1 TSOG2 TSOG3 ASOG1 ASOG2 ASOG3 INDIOL ISN1OA LVOCOA SOAIE SOAGX SOAME SOAMG J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Cl2 CH3CCl3 CH3Cl HCFC123 HCFC141b HCFC142b HCFC22 N2O O2
List all EMISSIONS that changed by 10% or more:	Anthro: BCPI BCPO Ship: NO O3 Total: BCPI BCPO NO
Approval
Requires further investigation:
Approved by:
Date of approval:

GCHP 1-month benchmark

The following sections contain validation plots for GCHP 12.6.0.

Comparison of GCHP versions

This table contains plots comparing GCHP 12.5.0 (Ref) and GCHP 12.6.0 (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 12.6.0 (Ref) against GCHP 12.6.0 (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

GCHP and GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 12.6.0 - GCHP 12.5.0] against the difference [GC Classic 12.6.0 - GC Classic 12.5.0], taken from 1-month benchmark simulations.

Category	Plots
	Level Map		Zonal Mean
Oxidants	sfc	500hPa	full column	stratosphere
Aerosols	sfc	500hPa	full column	stratosphere
Bromine	sfc	500hPa	full column	stratosphere
Chlorine	sfc	500hPa	full column	stratosphere
Iodine	sfc	500hPa	full column	stratosphere
Nitrogen	sfc	500hPa	full column	stratosphere
Primary Organics	sfc	500hPa	full column	stratosphere
Secondary Organics	sfc	500hPa	full column	stratosphere
Secondary Organic Aerosols	sfc	500hPa	full column	stratosphere
Sulfur	sfc	500hPa	full column	stratosphere
ROy	sfc	500hPa	full column	stratosphere

NOTE: At present, we have only created the diff-of-diffs plots for species concentration. This can be extended to other categories in the future.

GEOS-Chem Classic 1-year benchmark

1-year benchmark overview

In this 1-year benchmark, two GEOS-Chem model versions are compared to each other:

Color	Model Version	Met Type	Year	Updates affecting the benchmark simulation	Annual Mean OH [105 molec/cm3]	O3 STE [Tg a-1]
Black	Observations
Green	12.6.0	GEOS-FP, 72L, 4x5	2016	Updates introduced in 12.6.0: Combined heterogeneous chemistry updates HNO3 cold-temperature deposition Quick fix for aerosol pH calculation when dry Remove isoprene in VBS (leaving aqueous) Updated aerosol hygroscopicity and optics Add EDGAR BCPI and BCPO emissions for remaining sectors to DICE-Africa Updates introduced in 12.5.0: Retire obsolete emission inventories Updated offline biogenic emissions generated with GEOS-Chem 12.3.0 Updated volcano emissions to include eruptive emissions through April 2018 Scale DICE-Africa emissions to address errors in inventory Separate anthropogenic PM2.5 dust source from the DustDead extension Corrections for CFCs in the chemistry mechanism Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90 Bug fix: make sure stratospheric BrY concentrations are read properly each month	10.505	605.968
Red	12.4.0	GEOS-FP, 72L, 4x5	2016	Updates introduced in 12.4.0: Grid-independent lightning NOx emissions (3-hourly) Grid-independent biogenic emissions (hourly) Grid-independent sea salt emissions (hourly) Grid-independent soil NOx emissions (hourly) Updated volcano emissions (1978-2019) Updates introduced in 12.3.0: Update ISORROPIA from v2.0 to v2.2, in order to remove persistent noise in output Updated PFT file for MEGAN Read in and regrid existing MODIS LAI and OLSON data via HEMCO Updates introduced in 12.2.0: Retire BRAVO emissions and use CEDS for Mexico instead Update mask file applied to NEI2011 emissions Updates introduced in 12.1.0: Budget diagnostics Anthropogenic PM2.5 dust source GEOS-Chem restart file updates Add missing RCO sector to CEDS emissions entries Include CEDS ship emissions as default global ship emissions inventory Allow for SZA to 98 degrees when getting photolysis rates	11.302	607.121

1-year benchmark plots

These benchmarks plots were made using a combination of routines from GCPy and GAMAP. The 6-panel concentration, difference, and fractional difference plots were created with GCPy, while the model vs observation plots, the emissions plots and tables, and the aerosol tables were created with GAMAP because they have not been converted to Python yet.

Category1	Plots					Additional Information
	Level Map		Zonal Mean		Emissions
Primary	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	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	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	Surface Jan Apr Jul Oct	500 hPa Jan Apr Jul Oct	Full column Jan Apr Jul Oct	Stratosphere Jan Apr Jul Oct	-
Iodine	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	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	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	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	Surface Jan Apr Jul Oct	500 hPa Jan Apr Jul Oct	Full column Jan Apr Jul Oct	Stratosphere Jan Apr Jul Oct	-
Sulfur	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
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 Biofuel: Jan, Apr, Jul, Oct Biogenic: Jan, Apr, Jul, Oct Lightning: Jan, Apr, Jul, Oct Monoterpene: 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					Emissions tables
Plots still created by GAMAP
J-values	Maps Jan Apr Jul Oct	Differences Jan Apr Jul Oct	Ratios Jan Apr Jul Oct
Model vs observations	Aerosols: Seasonal plots, Scatter plots Aircraft: C2H6, C3H8, CO, H2O2, HNO3, NO, O3, PAN BrO: Seasonal plots 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

¹Benchmark category definitions: benchmark_categories.json
²Lumped species definitions: lumped_species.json

NOTES:

1. Category and lumped species definitions are simple to adjust. Updating them requires only editing the json files.
2. All 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.