GEOS-Chem benchmarking

Overview

The following GEOS-Chem benchmarking procedure was adopted at the 5th International GEOS-Chem Meeting (May 2011).

1. Any change to the GEOS-Chem source code will require a dedicated 1-month benchmark with the standard chemistry mechanism and a version update code a, b, c, etc. (such as v10-01a, v10-01b, etc). These letter codes are for internal use only and do not represent a version release. The benchmark results will be posted publicly with an email sent to the GEOS-Chem Steering Committee.
2. The developer(s) will assess the benchmark results by filling out a form (created by Colette Heald and adapted to a wiki page) for all to see. If the developer has any concerns about the benchmark results they will contact the GEOS-Chem Support Team, the relevant GEOS-Chem Working Group Chairs, and/or Model Scientist Daniel Jacob. GEOS-Chem Steering Committee members are also encouraged to examine and comment on the benchmark results.
3. Once the developer is satisfied with the changes in the 1-month benchmark, GEOS-Chem Model Scientist Daniel Jacob will promptly review the results and approve the new internal version.
4. 1-year benchmarks for internal version updates will be conducted only if justifiably requested by the developer or by GEOS-Chem Steering Committee members.
5. Each new public version release (e.g. GEOS-Chem v10-01) will be subject to a 1-year benchmark to be inspected by the GEOS-Chem Steering Committee before approval. Changes will be bundled so that we will have new versions released every 9 months or so — this has been our rhythm in recent years.

List of GEOS-Chem benchmarks

Links to information about past 1-month and 1-year benchmark simulations can be found on GEOS-Chem versions under development wiki page. For an overview of version v8-03-01 and earlier, see this website.

1-month benchmark

Overview

Dates of run:	July 1, 2013 – August 1, 2013
Vertical Resolution:	GEOS-FP with 72 hybrid sigma-pressure levels
Horizontal Resolution:	4° latitude x 5° longitude
Advected species:	Gas-phase species: NO, O3, PAN, CO, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, PMN (isoprene and non-isoprene), PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, MP, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, MAP, NO2, NO3, HNO2, BENZ, TOLU, XYLE, MTPA, LIMO, MTPO, TSOG0-3, ISOG1-3, ASOG1-3, EOH, MGLY, GLYX, ACTA, HPALD, DHDN, ETHLN, HCOOH, IEPOXA, IEPOXB, IEPOXD, ISN1, RIPA, RIPB, RIPD, IMAE, LVOC, ISN1OG, MONITS, MONITU, HONIT, HC187 Aerosol species: DMS, SO2, SO4, MSA, NH3, NH4, NIT, BCPO, OCPI, BCPI, OCPI, DST1-4, SALA, SALC, SO4s, NITs, TSOA0-3, ISOA1-3, ASOAN, ASOA1-3, SOAIE, SOAME, SOAGX, SOAMG, LVOCOA, ISN1OA, IONITA, MONITA, INDIOL Bromine species: Br2, Br, BrO, HOBr, HBr, BrNO2 BrNO3, CHBr3, CH2Br2, CH3Br Stratospherically-important species: N2O, OCS, CH4, BrCl, HCl, CCl4, CH3Cl, CH3CCl3, CFCX, HCFCX, CFC11, CFC12, HCFC22, H1211, H2402, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl202, H2O
Chemical Mechanism:	FlexChem chemical solver using the standard chemistry mechanism (NOx-Ox-HC-Aer-Br + UCX + complex SOA) Chemistry is done in both the troposphere and the stratosphere.
Photolysis Mechanism:	FAST-JX v7.0 (Prather, 2012, Wild et al, 2000).
Operations:	Advection Aerosol thermodynamical equilibriium Boundary layer mixing Chemistry Cloud convection (with updraft scavenging) Dry deposition Emissions Photolysis Wet deposition
Diagnostic Output:	The following diagnostic outputs are archived as monthly means Sulfate production and loss quantities Dust aerosol sources Carbon aerosol sources Sea salt aerosol sources Acetone sources Sulfur sources Optical Depths Noontime J-values Biomass burning emission fluxes CO sources Surface Pressure NOx sources Biofuel emission fluxes Anthropogenic emission fluxes Scavenging loss from moist convection Scavenging loss from wet deposition Concentrations of chemically produced OH and HO2 Dry deposition fluxes and velocities Tracer concentrations Biogenic emission fluxes Tropopause height DAO 3-D met fields DAO 2-D met fields Air masses and grid box heights Surface area Lifetime of Methylchloroform (CH3CCl3)
Benchmark Plots and Summaries:	The following plots, budgets, and totals are created from the oxidant-aerosol simulation: Budget of Ox and CO Mean OH concentration Methyl Chloroform Lifetime (w/r/t loss by tropospheric OH) Aerosol optical depth maps (this benchmark) Aerosol optical depth differences (this benchmark - previous benchmark) Concentration maps (this benchmark) of tracers + OH + HO2 at the surface and at 500 hPa Difference maps (this benchmark - previous benchmark) of tracers + OH + HO2 at the surface and at 500 hPa Summary of emission totals (this benchmark vs. previous benchmark) Emissions maps (this benchmark) for all emitting tracers Emissions difference maps (this benchmark - previous benchmark) for all emitting tracers Emissions ratio maps (this benchmark / previous benchmark) for all emitting tracers Frequency distribution histogram of ratios (this benchmark vs previous benchmark) for tracers, OH, and optical depths J-value maps (this benchmark) J-value difference maps (this benchmark - previous benchmark) J-value ratio maps (this benchmark / previous benchmark) Ratio maps (this benchmark / previous benchmark) of tracers + OH + HO2 at the surface and at 500 hPa Zonal mean concentration maps (this benchmark) of tracers + OH + HO2 Zonal mean difference maps (this benchmark - previous benchmark) of tracers + OH + HO2

Plotting routines

NOTE: The 1-month benchmark plotting routines are currently written in IDL. We are planning on moving these routines to Python for the GEOS-Chem v11-02 release as part of the GCPy package.

The 1-month benchmark plotting routines are included with the GAMAP. For more information, see the this page in the GAMAP manual.

1-year benchmark

Overview

Spin-up:	January 1, 2013 – January 1, 2014
Dates of Run:	January 1, 2013 – January 1, 2014
Vertical Resolution:	GEOS-FP with 72 hybrid sigma-pressure levels
Horizontal Resolution:	4° latitude x 5° longitude
Advected species:	Gas-phase species: NO, O3, PAN, CO, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, PMN (isoprene and non-isoprene), PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, MP, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, MAP, NO2, NO3, HNO2, BENZ, TOLU, XYLE, MTPA, LIMO, MTPO, TSOG0-3, ISOG1-3, ASOG1-3, EOH, MGLY, GLYX, ACTA, HPALD, DHDN, ETHLN, HCOOH, IEPOXA, IEPOXB, IEPOXD, ISN1, RIPA, RIPB, RIPD, IMAE, LVOC, ISN1OG, MONITS, MONITU, HONIT, HC187 Aerosol species: DMS, SO2, SO4, MSA, NH3, NH4, NIT, BCPO, OCPI, BCPI, OCPI, DST1-4, SALA, SALC, SO4s, NITs, TSOA0-3, ISOA1-3, ASOAN, ASOA1-3, SOAIE, SOAME, SOAGX, SOAMG, LVOCOA, ISN1OA, IONITA, MONITA, INDIOL Bromine species: Br2, Br, BrO, HOBr, HBr, BrNO2 BrNO3, CHBr3, CH2Br2, CH3Br Stratospherically-important species: N2O, OCS, CH4, BrCl, HCl, CCl4, CH3Cl, CH3CCl3, CFCX, HCFCX, CFC11, CFC12, HCFC22, H1211, H2402, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl202, H2O
Chemical Mechanism:	FlexChem chemical solver using the standard chemistry mechanism (NOx-Ox-HC-Aer-Br + UCX + complex SOA) Chemistry is done in both the troposphere and the stratosphere.
Photolysis Mechanism:	FAST-JX v7.0 (Prather, 2012, Wild et al, 2000).
Operations:	Advection Aerosol thermodynamical equilibriium Boundary layer mixing Chemistry Cloud convection (with updraft scavenging) Dry deposition Emissions Photolysis Wet deposition
Diagnostic Output:	All diagnostics above are saved as monthly means. Sulfate production and loss quantities Dust aerosol sources Carbon aerosol sources Sea salt aerosol sources Acetone sources Sulfur sources Optical Depths Noontime J-values Transport fluxes (N/S, E/W, up/down) Biomass burning emission fluxes CO sources Surface Pressure NOx sources Biofuel emission fluxes Anthropogenic emission fluxes Scavenging loss from moist convection Scavenging loss from wet deposition Concentrations of chemically produced OH and HO2 Dry deposition fluxes and velocities Tracer concentrations Biogenic emission fluxes Tropopause height DAO 3-D met fields DAO 2-D met fields Air masses and grid box heights Surface area Lifetime of Methylchloroform (CH3CCl3) Satellite timeseries of BrO, cloud fraction, and cloud top height
Benchmark Plots:	The following plots compare advected species from 3 different benchmark simulations (versions 1-3, where version 3 is the current benchmark version). Plots are created for January, April, July, and October. Aerosol optical depth maps (version 1, version 2, and version 3) Emission maps (version 1, version 2, and version 3) Emisison difference maps (version 3 - version 1, version 3 - version 2) Emission ratio maps (version 3 / version 1, version 3 / version 2) J-value maps (version 1, version 2, and version 3) J-value difference maps (version 3 - version 1, version 3 - version 2) J-value ratio maps (version 3 / version 1, version 3 / version 2) Tracer difference maps at the surface and 500 hPa (version 3 - version 1, version 3 - version 2) Tracer ratio maps at the surface and 500 hPa (version 3 / version 1, version 3 / version 2) Tracer difference profiles along longitude slices (15S, 42N) (version 3 - version 1, version 3 - version 2) The following plots show data from 3 benchmark simulations side-by-side with observations. GEOS-Chem output is plotted in red for version 1, in green for version 2, and in blue for version 3 (current benchmark version) BrO seasonal columns vs. observations C2H6 vertical profiles vs. observations from various aircraft campaigns C3H8 vertical profiles vs. observations from various aircraft campaigns CO seasonal cycle at the surface vs. MOZAIC observations CO vertical profiles vs. MOZAIC observations CO vertical profiles vs. various sonde observations H2O2 vertical profiles vs. observations from various aircraft campaigns IMPROVE difference maps (benchmark simulation output vs. surface sites) IMPROVE scatter plots (benchmark simulation output vs. surface sites) HNO3 vertical profiles vs. observations from various aircraft campaigns NO vertical profiles vs. observations from various aircraft campaigns O3 seasonal cycle @ the surface vs. MOZAIC observations O3 seasonal cycle @ 300, 500, and 800 hPa vs. MOZAIC observations O3 seasonal cycle @ 300, 500, and 800 hPa vs. sonde observations O3 seasonal cycle @ 150, 300, 500,and 800 hPa vs. sonde observations O3 vertical profiles vs. observations from various aircraft campaigns O3 vertical profiles vs. observations from various aircraft campaigns O3 vertical profiles vs. various sonde observations O3 vertical profiles vs. MOZAIC observations PAN vertical profiles vs. observations from various aircraft campaigns PM2.5 difference maps (benchmark simulation output vs. surface sites) PM2.5 scatter plots (benchmark simulation output vs. surface sites)

Plotting routines

NOTE: The 1-month benchmark plotting routines are currently written in IDL. We are planning on moving these routines to Python for the GEOS-Chem v11-02 release as part of the GCPy package.

The 1-year benchmark plotting routines can be downloaded from Bitbucket via Git using:

 git clone https://bitbucket.org/gcst/gc_1yr_benchmark

The data files needed for the plots are included in the repository and are discussed in more detail below.

Observations

Here we provide an overview of the data used in the 1-year benchmark plots.

Directory	Data source	Data year	Species	Provided by
BrO/	GOME-2	2007-2008	BrO	Justin Parrella Used to reproduce Figure 5 of Parrella et al. (2012)
cmdl/	GMD (formerly CMDL)	2005, 2009	CO	Jennifer Logan and Inna Megretskaia
PAN/	ARCTAS-A, ARCTAS-B, ARCPAC, INTEX-B, ITCT-2K2		PAN	Emily Fischer Used to reproduce Figure S1 of Fischer et al. (2014) Supplement

Update 2005/2009 CMDL CO data to 2013/2014 GMD CO data

This update is slated for inclusion into v11-02c.

Jenny Fisher wrote:

Attached is a zip file containing routines to process the GMD (previously CMDL) CO data for use in the benchmarking scripts, as well as the 2013 and 2014 data. I added the 2014 data because there was no ships data for 2013 (or 2012), so this seemed like the best approximation.

To replace the existing benchmark data with these, you will want to do the following in the 1-year benchmark code:

1. Put the 2013data/ and 2014data/ in the data/cmdl/ directory of the 1-year benchmark code
2. Change newdata/ to 2013data/ in plot_cmdl_3_models_4_months.pro
3. Change Feb09/ to 2013data/ in plot_surface_co_geos_3_models.pro
4. Change newdata/ to 2014data/ in plot_ships_3_models_4_months.pro and plot_ships_3_models_co.pro
5. Change the line file=pre+name_sta(kk)+'.mn' to file=pre+name_sta(kk)+’.mn.2013' in plot_cmdl_3_models_4_months.pro
6. Change the line file=pre+name_sta(kk)+’.mn.2005' to file=pre+name_sta(kk)+’.mn.2013' in plot_surface_co_geos_3_models.pro
7. Change the line file=pre+name_sta(kk)+'.mn' to file=pre+name_sta(kk)+’.mn.2014' in plot_ships_3_models_4_months.pro and plot_ships_3_models_co.pro

As I said before, I think this would be a useful improvement to our benchmarks, rather than using data >10 years old!

--Melissa Sulprizio (talk) 22:10, 15 August 2017 (UTC)