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
Budgets	Budgets after operations

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 reactions from 12.8.0 and add an extra error check	Melissa Sulprizio (GCST)
Bug fix: Remove inefficient code that was slowing down computation of heterogenous chemistry rates	Bob Yantosca (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)
Fixes for reading meteorology fields in HEMCO: Skip reading FLASH_DENS and CONV_DEPTH fields when lightning NOx extension is turned off Change time cycle flag for meteorology fields to use exact date	Melissa Sulprizio (GCST)
Restore missing metadata for satellite timeseries diagnostics	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.

Updated halogen chemistry

Four new species are introduced in this update: sea salt alkalinity (SALAAL, SALCAL) and sea salt chloride (SALACL, SALCCL). This update also includes updated Henry's law constants for several halogen species, update chemical reactions, and updated heterogeneous chemistry as described in Wang et al. (2019). It also includes improved cloudwater pH from Shah et al. (2020). This update causes large differences, most notably in the halogen species, and is responsible for a 3% increase in the global OH concentration.

Update offline lightning data through Dec 2019

This change causes differences in lightning NOx emissions due to updating the climatology:

###############################################################################
### Emissions totals for inventory LIGHTNOX                                 ###
### Ref = GC_12.8.0; Dev = GC_12.9.0                                        ###
###############################################################################
                                       Ref                 Dev      Dev - Ref
LIGHTNOX NO           :           1.700865            1.828790       0.127925 Tg

Convert GEOS-Chem species database to YAML format

This update introduces minor differences because all species properties are now defined in the species database, not just advected species. This means, chemical species are now defined with molecular weights and this introduces numerical differences when performing unit conversions to the species concentrations throughout the model. Overall differences attributed to these updates are small. This update changed the global mean OH concentration by -0.05%.

Update GEOS-Chem core to apply masking and scaling to HEMCO inputs

This updated introduced small changes because of the switch from Hco_GetPtr, which returns REAL*4 values, to Hco_EvalFld, which returns REAL*8 values. The global mean OH concentration changed by 0.01%.

Bug fix: Restore missing photolysis reactions from 12.8.0 and add an extra error check

This update introduces photolysis reactions that should have been included in 12.7.0 with updated isoprene chemistry from Bates et al. (2019), but were not because of a hardcoded maximum value in the number of photolysis reactions. The largest changes are to the species involved in those photolysis reactions (RIPA, RIPB, RIPC, RIPD, HPALDS1-4, IHN1-4, INPB, INPD, ICPDH, IDHDP, IDHPE, IDCHP, ITHN, ITCN).

Bug fix: Remove inefficient code that was slowing down computation of heterogenous chemistry rates

This update introduces small changes due to slight differences in molecular weight and Henry's law constants used in the heterogeneous chemistry module. Previously, many of these values were hardcoded, but they are now obtained from the species database for consistency with the rest of the source code. In addition, we have eliminated needless computations that were being done for every grid box but only needed to be done in the troposphere. These updates also vastly improve the wall clock time spent in the heterogeneous chemistry functions as shown below by the results from internal 1-month benchmark simulations (all completed on all 24 CPUs of holyjacob01.rc.fas.harvard.edu; Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz).

  Total seconds spent in heterogeneous chemistry code:

  Before halogen chemistry updates      4863
  After  halogen chemistry updates     26348
  After  this fix                        448

Details

List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:

Aerosols: NH4 NIT SO4 Complex_SOA AERI BrSALA BrSALC ISALA ISALC NITs 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 MPAN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4 MENO3 ETNO3
Oxidants: O3 OH NOx
Primary_Organics: EOH MOH ISOP MTPA MTPO LIMO TOLU XYLE
ROy: H2O2 H HO2 O1D OH RO2
Secondary_Organic_Aerosols: ASOA3 ASOAN ASOG3 INDIOL LVOCOA SOAIE SOAGX
Secondary_Organics: ACTA CH2O HPALDs MACR IEPOX MVK ISOPN GLYX MAP RCHO MP
Sulfur: SOx DMS SO2 SO4
J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Cl2 CH3CCl3 CH3Cl HCFC123 HCFC141b HCFC142b HCFC22 N2O O2
Column AOD: BCPI OCPI SALA SALC SO4 SOA_from_Aqueous_ISOP

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

Aerosols: NH4 NIT BrSALA BrSALC ISALA ISALC NITs 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 MPAN NIT NO NO2 NO3 N2O5 MPN PAN NHx NH3 NH4 MENO3
Oxidants: O3 OH NOx
Primary_Organics: EOH ISOP MTPA MTPO LIMO ALK4 C2H6 C3H8 TOLU
ROy: H2O2 H HO2 O1D OH RO2
Secondary_Organic_Aerosols: ASOA1 ASOA3 ASOG1 ASOG3 SOAGX
Secondary_Organics: CH2O HPALDs MACR IEPOX MVK ISOPN GLYX
Sulfur: DMS SO2

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

Aerosols: NH4 NIT SO4 BrSALA BrSALC ISALA ISALC NITs 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 CH2ICl CH2IBr HI HOI OIO
Nitrogen: NOx HNO2 HNO3 HNO4 MPAN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4 MENO3
Oxidants: O3 OH NOx
Primary_Organics: ISOP MTPA MTPO LIMO ALK4 C2H6 C3H8 PRPE TOLU XYLE
ROy: H2O2 H HO2 O1D OH RO2
Secondary_Organic_Aerosols: ASOA1 ASOA3 ASOG1 ASOG3 SOAGX
Secondary_Organics: ACTA ALD2 CH2O MACR IEPOX MEK MVK ISOPN GLYX HCOOH MAP RCHO MP
Sulfur: SOx DMS SO2 SO4

List all EMISSIONS that changed by 10% or more:

Lightning: NO
Ship: NO2 NO O3
Total: NO

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
Global mass	Entire atmosphere Troposphere only
Budgets	Budgets after operations

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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