GEOS-Chem benchmarking

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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.

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:
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:
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