Benchmark/GEOS-Chem 12.4.0

GEOS-Chem Benchmarks

This page includes information about all benchmark simulations for GEOS-Chem 12.4.0.

GEOS-Chem Classic 1-month benchmark

1-month benchmark plots

These benchmarks were primarily made with GCPy. Some benchmark plots created by GAMAP still remain because they have not been recreated in GCPy yet.

Category1	Plots					Additional Information
	Level Map		Zonal Mean		Emissions
Primary	sfc	500hPa	full column	stratosphere	sfc
Aerosols	sfc	500hPa	full column	stratosphere	sfc	AOD
Bromine	sfc	500hPa	full column	stratosphere	sfc
Chlorine	sfc	500hPa	full column	stratosphere	--
Iodine	sfc	500hPa	full column	stratosphere	sfc
Nitrogen	sfc	500hPa	full column	stratosphere	sfc
Primary Organics	sfc	500hPa	full column	stratosphere	sfc
Secondary Organics	sfc	500hPa	full column	stratosphere	sfc
ROy	sfc	500hPa	full column	stratosphere	--
Sulfur	sfc	500hPa	full column	stratosphere	sfc
Emissions by HEMCO category	Total, Aircraft, Anthro, Bioburn, Biofuel, Biogenic, Lightning, Monoterp, Natural, Ocean, Seabirds, DecayingPlants, Ship, Soil, VolcDegas, VolcErupt,					Emissions tables
Plots still created by GAMAP
J-values	maps	differences	ratios	--	--
Budget	--	--	--	--	--	Ox and CO budgets

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.

Benchmark assessment form

Description
New features added into GEOS-Chem	Feature Submitted by Features affecting the full-chemistry simulation: Grid-independent dust emissions (hourly) David Ridley (CARB, formerly MIT) Jun Meng (Dalhousie) Grid-independent lightning NOx emissions (3-hourly) Lee Murray (Rochester) Grid-independent biogenic emissions (hourly) Jintai Lin (PKU) Hongjian Meng (PKU) Grid-independent sea salt emissions (hourly) Jintai Lin (PKU) Hongjian Meng (PKU) Grid-independent soil NOx emissions (hourly) Jintai Lin (PKU) Hongjian Meng (PKU) Updated volcano emissions (1978-2019) Christoph Keller (NASA/GMAO) Bug fix: Rebuild chemical mechanisms for FAST-JX fix added in 12.3.2 Katie Travis (NASA) Features affecting the full-chemistry simulation: FlexGrid Stage 2: Add capability to define custom grids Melissa Sulprizio (GCST) Jiawei Zhuang (Harvard) Add photolysis menu to input.geos for specifying FAST-JX directory Tomas Sherwen (York)
Version, resolution, met fields used:	GEOS-FP (72L), 4x5, July 2016
1-month benchmark finished on:	Fri May 24 06:51:03 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: 10:50:46 CPU time / wall time: 19.3517 % of ideal performance: 80.63% Memory: 13.8346 GB
Compared to previous benchmark:	12.3.0
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): Lightning NOx Emissions, Dust Emissions, Biogenic Emissions, Sea Salt Emissions, Soil NOx Emissions, Volcano Emissions
Unit test results may be viewed at:	http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.4.0/GCC/output/GC_12.4.0_May21.results.html
Metrics
Global mean OH from log file (% change):	12.6452510681687 x 105 molec/cm3 (0.91%)
Methyl chloroform lifetime (% change):	4.8037 years (-2.92%)
Methane lifetime (% change):	8.0807 years (-3.09%)
At the SURFACE, list all species that changed by 10% or more:	NO, O3, PAN, ISOP, HNO3, H2O2, ACET, ALD2, MVK, MACR, NPMN, PPN, R4N2, PRPE, CH2O, N2O5, HNO4, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, NITs, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, NO2, NO3, HNO2, XYLE, LIMO, TSOG1, TSOA1, ISOG1, ISOG2, ISOG3, ISOA1, ISOA3, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3, SOAP, EOH, MGLY, GLYX, HPALD, DHDN, ETHLN, HCOOH, IEPOXA, IEPOXB, IEPOXD, ISN1, RIPA, RIPB, RIPD, IMAE, SOAIE, SOAME, SOAGX, SOAMG, LVOC, LVOCOA, ISN1OG, ISN1OA, MONITS, MONITU, HONIT, IONITA, MONITA, INDIOL, IPMN, HC187, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, BrSALA, BrSALC, HOI, I2, IBr, ICl, I, IO, OIO, INO, IONO, IONO2, I2O2, I2O3, I2O4, ISALA, ISALC, OH, HO2
Comments on SURFACE differences:	Below we summarize the notable changes caused by specific updates. Grid-independent dust emissions ############################################################################### ### Emissions totals ### ### Ref = GC_12.3.0; Dev = GC_12.4.0 ### ############################################################################### Ref Dev Dev - Ref DST1 Natural  : 4.487948 11.225230 6.737282 Tg DST2 Natural  : 8.540177 23.995240 15.455063 Tg DST3 Natural  : 15.495716 43.538139 28.042424 Tg DST4 Natural  : 16.951628 47.628794 30.677167 Tg Overall, dust emissions and concentrations increased with the introduction of the grid-independent emissions. The offline dust emissions have been scaled to match 2x2.5 online dust emissions for 2016, so further validation with a 1-year benchmark is needed to ensure these changes make sense. Grid-independent lightning NOx emissions ############################################################################### ### Emissions totals ### ### Ref = GC_12.3.0; Dev = GC_12.4.0 ### ############################################################################### Ref Dev Dev - Ref NO Lightning  : 1.603119 1.700865 0.097746 Tg Lightning emissions increased slightly when using the grid-independent lightning NOx emissions. The pattern of the changes globally is consistent with the expected changes from caused by regridding. Some differences in the vertical distribution of NOx can be attributed to these changing emissions, with slightly lower emissions aloft and slightly higher emissions in the free troposphere. Grid-independent biogenic emissions ############################################################################### ### Emissions totals ### ### Ref = GC_12.3.0; Dev = GC_12.4.0 ### ############################################################################### Ref Dev Dev - Ref ACET Biogenic  : 3.199002 2.881931 -0.317071 Tg C ALD2 Biogenic  : 1.082313 0.877756 -0.204557 Tg C CO Monoterp  : 5.811675 5.504973 -0.306702 Tg EOH Biogenic  : 1.034973 0.839363 -0.195610 Tg C ISOP Biogenic  : 32.783415 23.495304 -9.288111 Tg C LIMO Biogenic  : 0.954841 1.022397 0.067556 Tg PRPE Biogenic  : 2.179011 1.971144 -0.207867 Tg C SOAP Biogenic  : 1.294232 0.086853 -1.207379 Tg SOAS Biogenic  : 1.294232 0.086853 -1.207379 Tg Biogenic emissions for all species except limonene decreased when using the grid-independent biogenic emissions. This caused decreases in many of the primary and secondary organic species over land. Grid-independent sea salt emissions ############################################################################### ### Emissions totals ### ### Ref = GC_12.3.0; Dev = GC_12.4.0 ### ############################################################################### Ref Dev Dev - Ref SALA Natural  : 4.653316 5.620708 0.967392 Tg SALC Natural  : 281.640070 340.191067 58.550997 Tg Sea salt emissions increased when using the grid-independent sea salt emissions, causing global increases in many of the sea-salt aerosol species (BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s) at the surface and aloft. Grid-independent soil NOx emissions ############################################################################### ### Emissions totals ### ### Ref = GC_12.3.0; Dev = GC_12.4.0 ### ############################################################################### Ref Dev Dev - Ref NO Soil  : 1.365916 1.580800 0.214884 Tg Soil NO emissions increased slightly when using the grid-independent soil NOx emissions. The pattern of the changes globally is consistent with the expected changes from caused by regridding. Updated volcano emissions (1978-2019) ############################################################################### ### Emissions totals ### ### Ref = GC_12.3.0; Dev = GC_12.4.0 ### ############################################################################### Ref Dev Dev - Ref SO2 VolcDegas  : 1.553769 1.509524 -0.044245 Tg SO2 VolcErupt  : 0.000000 0.000000 0.000000 Tg Updating to the newer volcano inventory reduced degassing volcano SO2 emissions by 0.044 Tg. This was expected because the last year of degassing emissions in the previous volcano dataset was 2009, which was a particularly active year. The eruptive volcano SO2 emissions remained at 0. NOTE: The bug fix to rebuild chemical mechanisms for FAST-JX fix did not impact this benchmark. The bug was introduced in 12.3.2, and would not show up in the comparisons here between 12.3.0 and 12.4.0.
At 500 hPa, list all species that changed by 10% or more:	NO, O3, ALK4, ISOP, HNO3, H2O2, RCHO, MVK, MACR, NPMN, R4N2, PRPE, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NIT, NITs, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, NO2, NO3, HNO2, TOLU, XYLE, LIMO, TSOG0, ASOG1, ASOG2, ASOG3, ASOA1, ASOA3, SOAP, GLYX, HPALD, DHDN, ETHLN, IEPOXA, IEPOXB, IEPOXD, ISN1, RIPA, RIPB, RIPD, IMAE, SOAME, LVOC, ISN1OG, ISN1OA, MONITS, HONIT, IONITA, IPMN, HC187, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, BrSALA, BrSALC, CH2I2, CH2ICl, CH2IBr, HOI, I2, IBr, ICl, I, IO, HI, OIO, INO, IONO, IONO2, I2O2, I2O3, I2O4, ISALA, ISALC, OH, HO2
Comments on 500 hPa differences:	See comments for surface differences
In the ZONAL MEAN differences, list all species that changed by 10% or more:	NO, O3, PAN, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, NPMN, PPN, R4N2, PRPE, C3H8, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, NITs, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, MAP, NO2, NO3, HNO2, BENZ, TOLU, XYLE, MTPA, LIMO, TSOG1, TSOA1, ISOG1, ISOG2, ISOG3, ISOA1, ISOA3, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3, SOAP, EOH, MGLY, GLYX, ACTA, HPALD, DHDN, ETHLN, HCOOH, IEPOXA, IEPOXB, IEPOXD, ISN1, RIPA, RIPB, RIPD, IMAE, SOAIE, SOAME, SOAGX, SOAMG, LVOC, LVOCOA, ISN1OG, ISN1OA, MONITS, MONITU, HONIT, IONITA, MONITA, INDIOL, IPMN, HC187, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, BrSALA, BrSALC, CH3I, CH2I2, CH2ICl, CH2IBr, HOI, I2, IBr, ICl, I, IO, HI, OIO, INO, IONO, IONO2, I2O2, I2O3, I2O4, ISALA, ISALC, OH, HO2
Comments on ZONAL MEAN differences:	See comments for surface differences
In the EMISSIONS maps, list all species that changed by 10% or more:	Volcano SO2 Lightning NO Soil NO Natural emissions: DST1, DST2, DST3, DST4, SALA, SALC Biogenic emissions for ACET, ALD2, CO, EOH, ISOP, LIMO, PRPE, SOAP, SOAS
Comments on EMISSIONS differences:	See comments for surface differences
Additional or summary comments:
Approval
Requires further investigation:	Will require a 1-year benchmark simulation
Approved by:
Date of approval:

GCHP 1-month benchmark

The following sections contain validation plots for GCHP 12.4.0.

Comparison of GCHP versions

This table contains plots comparing GCHP 12.3.2 (Ref) and GCHP 12.4.0 (Dev) for a 1-month simulation.

Category1	Plots2					Additional Information
	Level Map		Zonal Mean		Emissions
Primary	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
Sulfur	sfc	500hPa	full column	stratosphere	full column
Emissions by HEMCO category	Aircraft, Anthro, Bioburn, Biofuel, Biogenic, Lightning, Monoterp, Natural, Ocean, Seabirds, DecayingPlants, Ship, Soil, Total, VolcDegas, VolcErupt,					Emission totals

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

Comparison of GCHP and GEOS-Chem Classic

This table contains plots comparing GEOS-Chem Classic 12.4.0 (Ref) against GCHP 12.4.0 (Dev) for a 1-month simulation.

Category1	Plots2					Additional Information
	Level Map		Zonal Mean		Emissions
Primary	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
Sulfur	sfc	500hPa	full column	stratosphere	full column
Emissions by HEMCO category	Aircraft, Anthro, Bioburn, Biofuel, Biogenic, Lightning, Monoterp, Natural, Ocean, Seabirds, DecayingPlants, Ship, Soil, Total, VolcDegas, VolcErupt,					Emission totals

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

GCHP and GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 12.4.0 - GCHP 12.3.2] against the difference [GC Classic 12.4.0 - GC Classic 12.3.0], taken from 1-month benchmark simulations.

Category1	Plots2
	Level Map		Zonal Mean
Primary	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
Sulfur	sfc	500hPa	full column	stratosphere

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

NOTES:

1. 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	12.4.0	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
Red	12.0.0	GEOS-FP, 72L, 4x5	2016	Updates introduced in 12.0.0: Turn off TRASH emissions by default to avoid double counting Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory Bug fix for liquid water content in gckpp_HetRates.F90 Bug fix for CH4 boundary conditions Fixed typo in call to GAMMA_HOBr_AER Correct issues when specifying DICE-Africa emissions: Avoid double-counting between DICE-Africa and other inventories Use unique names for DICE-Africa entries in the HEMCO_Config.rc file Add missing Criegee intermediate reaction Bug fix for ARCTAS_SHIP in HEMCO_Config.rc files Bug fix in FlexChem: do not zero out ACTA, EOH, HCOOH concentrations Add GFED4.1 data for 2015 and 2016; Use GFED4.1 2016 in benchmarks	11.648	606.580

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.