Benchmark/GEOS-Chem 12.9.0

This page includes information about all benchmark simulations for GEOS-Chem 12.9.0.

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
Metrics	OH concentration, MCF lifetime, CH4 lifetime
Budget tables	GEOS-Chem 12.7.0 (Ref) Budget totals by vertical region PBL Troposphere Full atmosphere			GEOS-Chem 12.9.0 (Dev) Budget totals by vertical region PBL Troposphere Full atmosphere Comparison of stratosphere and troposphere budgets

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
Updates that WILL AFFECT the full-chemistry simulation
Updated halogen chemistry	Xuan Wang (Harvard)
Improved cloudwater pH	Viral Shah (Harvard) Jonathan Moch (Harvard)
Update offline lightning data through Dec 2019	Lee Murray (Rochester)
Convert GEOS-Chem species database to YAML format, includes: Defining all species properties in the species database, not just advected species Initializing the species database with values read from the YAML file	Melissa Sulprizio (GCST) Bob Yantosca (GCST)
Update GEOS-Chem core to apply masking and scaling to HEMCO inputs	Lizzie Lundgren (GCST)
Bug fix: Restore missing photolysis reatctions from 12.8.0 and add an extra error check	Melissa Sulprizio (GCST)
Updates that WILL NOT AFFECT the full-chemistry simulation
Corrected issue in GEOS-Chem dry-run where some files were not being properly marked for download	Bob Yantosca (GCST)
Bug fixes for the ObsPack diagnostic: Change units of ObsPack specific humidity (Q) field to g/kg Restore missing code due to Git merge that caused the OBSPACK MENU of input.geos not to be read	Bob Yantosca (GCST)
Skip reading FLASH_DENS and CONV_DEPTH fields when lightning NOx extension is turned off	Melissa Sulprizio (GCST)
Updates that affect GCHP only
Fix bug where non-advected species not updated in restart file	Sebastian Eastham (MIT)

Version, resolution, met fields used:

GEOS-FP (72L), 4x5, July 2016

1-month benchmark finished on:

Tue Jun 30 04:27:21 EDT 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: 08:27:00
CPU time / wall time: 20.8684
% of ideal performance: 86.95%
Memory: 13.5412 GB

Git tag

12.9.0-rc.0

Compared to previous benchmark:

12.8.0

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_12/12.9.0/GCC/Plots/GC_12.9.0_Jun26.results.html

Metrics

Global mean OH from log file (% change):

12.2836928383580 x 10⁵ molec/cm³ (+3.55%)

Methyl chloroform lifetime (% change):

5.1257 years (-1.91%)

Methane lifetime (% change):

8.6311 years (-1.69%)

Overview

Comments on observed differences:

Below we summarize the notable changes caused by specific updates.

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 BCPI BCPO OCPI OCPO Complex_SOA Simple_SOA AER

I BrSALA BrSALC ISALA ISALC NITs SALA SALC SO4s

Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO CH2Br2 CHBr3 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 CH3I CH2I2 CH2ICl CH2IBr HI HOI OIO
Nitrogen: NOy NOx HNO2 HNO3 HNO4 MPAN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4 MENO3 ETNO3 IPRNO3 NPRNO3
Oxidants: O3 CO OH NOx
Primary_Organics: EOH MOH ISOP MTPA MTPO LIMO ALK4 BENZ C2H6 C3H8 PRPE TOLU XYLE
ROy: H2O2 H H2O 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 SOAGX 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: ACET ALD2 ATOOH Br2 BrCl BrNO2 BrNO3 BrO CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Br2 CH2Cl2 CH2I2 CH2IBr CH2ICl CH2O CH3Br CH3CCl3 CH3Cl CH3I CHBr3 Cl2 Cl2O2 ClNO2 ClNO3 ClO ClOO ETHLN ETNO3 ETP GLYC GLYX H1211 H1301 H2402 H2O2 HAC HCFC123 HCFC141b HCFC142b HCFC22 HMHP HNO2 HNO3 HNO4 HOBr HOCl HOI HONIT HPETHNL I2 I2O2 I2O3 I2O4 IBr ICN ICl IDN INO IO IONO IONO2 IPRNO3 MACR MACR1OOH MAP MCRENOL MCRHN MCRHNB MCRHP MEK MENO3 MGLY MONITS MONITU MP MPN MVK MVKHC MVKHCB MVKHP MVKN MVKPC N2O N2O5 NO NO2 NO3 NPRNO3 O2 O3O1D O3O3P OCS OClO OIO PAN PIP PP PROPNN PRPN PYAC R4N2 R4P RA3P RB3P RCHO RP
Column AOD: Dust BCPI OCPI SALA SALC SO4 Polar_Strat_Cloud SOA_from_Aqueous_ISOP Strat_Liquid_Aerosol Total

List all 500 hPa species and J-Values that changed by 10% or more :

Aerosols: DST1 DST2 DST3 DST4 NH4 NIT SO4 BCPI BCPO OCPI OCPO Complex_SOA Simple_SOA AERI BrSALA BrSALC ISALA ISALC NITs SALA SALC SO4s
Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO CH2Br2 CHBr3 HOBr HBr
Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 CH2Cl2 CH3CCl3 CHCl3 HOCl HCl OClO
Iodine: Iy IxOy I I2 IBr ICl IO IONO IONO2 CH3I CH2I2 CH2ICl CH2IBr HI HOI OIO
Nitrogen: NOy NOx HNO2 HNO3 HNO4 MPAN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4 MENO3 ETNO3 IPRNO3 NPRNO3
Oxidants: O3 CO OH NOx
Primary_Organics: EOH MOH ISOP MTPA MTPO LIMO ALK4 BENZ C2H6 C3H8 PRPE TOLU XYLE
ROy: H2O2 H H2O 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 SOAGX SOAP SOAS
Secondary_Organics: ACTA ALD2 CH2O HPALDs MACR IEPOX ACET MEK MVK ISOPN GLYX HCOOH MAP RCHO MP
Sulfur: SOx DMS SO2 SO4

List all ZONAL MEAN species and J-Values that changed by 10% or more:

Aerosols: DST1 DST2 DST3 DST4 NH4 NIT SO4 BCPI BCPO OCPI OCPO Complex_SOA Simple_SOA AERI BrSALA BrSALC ISALA ISALC NITs SALA SALC SO4s
Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO CH3Br CH2Br2 CHBr3 HOBr HBr
Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 CCl4 CFCs CH3Cl CH2Cl2 CH3CCl3 CHCl3 HOCl HCl Halons HCFCs OClO
Iodine: Iy IxOy I I2 IBr ICl IO IONO IONO2 CH3I CH2I2 CH2ICl CH2IBr HI HOI OIO
Nitrogen: NOy NOx HNO2 HNO3 HNO4 MPAN NIT NO NO2 NO3 N2O5 MPN PAN PPN N2O NHx NH3 NH4 MENO3 ETNO3 IPRNO3 NPRNO3
Oxidants: O3 CO OH NOx
Primary_Organics: EOH MOH ISOP MTPA MTPO LIMO ALK4 BENZ CH4 C2H6 C3H8 PRPE TOLU XYLE
ROy: H2O2 H H2O 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 SOAGX SOAP SOAS
Secondary_Organics: ACTA ALD2 CH2O HPALDs MACR IEPOX ACET MEK MVK ISOPN GLYX HCOOH MAP RCHO MP
Sulfur: SOx DMS OCS SO2 SO4
J-Values: ACET ALD2 ATOOH Br2 BrCl BrNO2 BrNO3 BrO CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Br2 CH2Cl2 CH2I2 CH2IBr CH2ICl CH2O CH3Br CH3CCl3 CH3Cl CH3I CHBr3 Cl2 Cl2O2 ClNO2 ClNO3 ClO ClOO ETHLN ETNO3 ETP GLYC GLYX H1211 H1301 H2402 H2O2 HAC HCFC123 HCFC141b HCFC142b HCFC22 HMHP HNO2 HNO3 HNO4 HOBr HOCl HOI HONIT HPETHNL I2 I2O2 I2O3 I2O4 IBr ICN ICl IDN INO IO IONO IONO2 IPRNO3 MACR MACR1OOH MAP MCRENOL MCRHN MCRHNB MCRHP MEK MENO3 MGLY MONITS MONITU MP MPN MVK MVKHC MVKHCB MVKHP MVKN MVKPC N2O N2O5 NO NO2 NO3 NPRNO3 O2 O3O1D O3O3P OCS OClO OIO PAN PIP PP PROPNN PRPN PYAC R4N2 R4P RA3P RB3P RCHO RP SO4

List all EMISSIONS that changed by 10% or more:

Biogenic: ACET ALD2 EOH ISOP LIMO MOH MTPA MTPO PRPE SOAP SOAS
Lightning: NO
Natural: DST1 DST2 DST3 DST4 SALA SALC
Ocean: ACET ALD2 DMS ETNO3 MENO3 MOH
Ship: HNO3 NO2 NO O3
Soil: NO
Total: ACET ALD2 DST1 EOH ISOP MOH 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 12.9.0.

Comparison of GCHP versions

This table contains plots comparing GCHP 12.8.0 (Ref) and GCHP 12.9.0 (Dev) for a 1-month simulation.

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

Comparison of GCHP and GEOS-Chem Classic

This table contains plots comparing GEOS-Chem Classic 12.9.0 (Ref) against GCHP 12.9.0 (Dev) for a 1-month simulation.

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

GCHP and GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 12.9.0 - GCHP 12.8.0] against the difference [GC Classic 12.9.0 - GC Classic 12.8.0], 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.

Benchmark/GEOS-Chem 12.9.0

Contents

GEOS-Chem Classic 1-month benchmark

Benchmark plots

Benchmark assessment form

GCHP 1-month benchmark

Comparison of GCHP versions

Comparison of GCHP and GEOS-Chem Classic

GCHP and GEOS-Chem Classic difference of differences

Navigation menu

Benchmark/GEOS-Chem 12.9.0

GEOS-Chem Classic 1-month benchmark

Benchmark plots

Benchmark assessment form

GCHP 1-month benchmark

Comparison of GCHP versions

Comparison of GCHP and GEOS-Chem Classic

GCHP and GEOS-Chem Classic difference of differences

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