Benchmark/GEOS-Chem 12.3.2

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This page includes information about benchmark simulations for GEOS-Chem 12.3.2.

1-month benchmark

NOTE: The GEOS-Chem "Classic" benchmark for 12.3.2 is an unofficial benchmark. GEOS-Chem "Classic" 12.4.0 will be compared against GEOS-Chem "Classic" 12.3.0. We ran this 12.3.2 benchmark so as to facilitate comparison with GCHP and also to test the new GCPy benchmark plotting package.

Benchmark plots

This table contains plots comparing GEOS-Chem Classic 12.3.0 (Ref) vs. GEOS-Chem Classic 12.3.2 (Dev).

Category1 Plots 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
ROy sfc 500hPa full column stratosphere --
Sulfur sfc 500hPa full column stratosphere full column
Emissions by HEMCO category

Total, Aircraft, Anthro, Bioburn, Biofuel, Biogenic,
Lightning, Monoterp, Natural, Ocean, Seabirds, SenescingPlants,
Ship, Soil, VolcDegas, VolcErupt,

Emissions tables
J-values sfc 500hPa full column stratosphere --
Plots/tables still created by GAMAP
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.

--Bob Yantosca (talk) 18:32, 30 April 2019 (UTC)

Benchmark assessment form

Description
New features added into GEOS-Chem
Feature Submitted by
Features affecting the full-chemistry simulation:
Fix inconsistency for species H2402 between GCHP and GEOS-Chem "Classic" Sebastian Eastham (MIT)
GCST
Bug fixes for the FAST-JX photolysis mechanism: Bob Yantosca (GCST)
Updates and fixes for HEMCO diagnostics, including:
  • Enable saving out fertilizer NOx emissions
  • Lightning NOx emissions are 3D not, 2D
  • HNO3 ship emissions are 2D, not 3D
  • Update and fill in missing inventory diagnostics (currently used in only in benchmark simulations)
Melissa Sulprizio (GCST)
Features NOT affecting the full-chemistry simulation:
Extending the CEDS anthropogenic emissions inventory to include 1750-1949 and additional VOC species Melissa Sulprizio (GCST)
Features only affecting GCHP:
Disable Br2 offline seasalt emissions to match GEOS-Chem Classic default Sebastian Eastham (MIT)
Assorted GCHP run directory feature updates
  • Rename Makefile clean and build options
  • Remove deprecated Makefile/build.sh clean and build options
  • Remove aliases from sample run scripts
  • Remove output file runConfig.log; send to gchp.log instead
  • Update benchmark run directory to match GEOS-Chem Classic settings
Lizzie Lundgren (GCST)
Embed GEOS code within select GCHP files Lizzie Lundgren (GCST)
Version, resolution, met fields used: GEOS-FP (72L), 4x5, July 2016
1-month benchmark finished on:
Performance statistics:
  • Compiled with ifort 17.0.4
  • Ran on 24 CPUs of holy2c12205.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2683 v4 @ 2.10GHz)
  • Wall time: 09:14
  • CPU time / wall time: 20.0261
  • % of ideal performance: 83.44%
  • Memory: TBD 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, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): HEMCO diagnostic output
Unit test results may be viewed at:
Metrics
Global mean OH from log file (% change): 12.5657321664519 x 105 molec/cm3 (0.27%)
Methyl chloroform lifetime (% change): 4.9303 years (-0.36%)
Methane lifetime (% change): 8.3059 years (-0.39%)
At the SURFACE, list all species that changed by 10% or more:
  • Primary: O3 OH NOx
  • Aerosols: NH4 NIT SO4 AERI BrSALA BrSALC ISALA ISALC NITS SO4s SOA_Complex SOA_Simple
  • Bromine: All Br species EXCEPT ChBr CH2Br2 CHBr3
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl
  • Iodine: All species
  • Nitrogen: NOx NOy HNO2 HNO3 HNO4 IPMN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH4
  • Primary Organics: PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX MAP RCHO
  • Secondary Organics: MEK MVK CH2O HPALD MP ISOPN IEPOX ACTA
  • ROy: H2O2 H HO2 O1D OH RO2
  • Sulfur: SOx SO2 SO4
Comments on SURFACE differences:
  • As emissions did not change between versions, we can likely attribute these to the updates to FAST-JX.
  • Many species showed larger percent differences in areas where concentrations were very small.
At 500hPA, list all species that changed by 10% or more: Same as for surface
Comments on 500 hPa differences: See comments for surface differences
In ZONAL MEANS, list all species that changed by 10% or more: Same as for surface
Comments on ZONAL MEAN differences: See comments for surface differences
In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences: Emissions in 12.3.2 are 100% identical to 12.3.0
Additional or summary comments: The bug fixes for FAST-JX resulted in very small changes w/r/t the 12.3.0 1-month benchmark:
  • Mean OH changed by +0.2782%
  • MCF lifetime changed by -0.3597%
  • CH4 lifetime changed by -0.3936%

The fix to make species H2402 consistent between GCHP and GC "Classic" resulted in very minor additional changes on top of the FAST-JX fixes:

  • Mean OH changed by -0.0002%
  • MCF lifetime was unchanged
  • CH4 lifetime changed by +0.0012%

So it appears that most of the changes between 12.3.0 and 12.3.2 are being driven by the bug fixes to FAST-JX.

Comments on additional differences in GCHP:
  1. Additional differences exist for dust (and to a lesser extent other natural sources with resolution dependence) that are driven by emission differences.
    • GCST NOTE: We expect these to be resolved by the grid-independent dust emissions in version 12.4.0.
  2. Differences in stratospheric aerosol OD have been noted due to resolution sensitivities in UCX.
  3. The polar chlorine differences are likely due to the (lack of) polar averaging in GCHP and differences in “true” resolution.
  4. Concentrations of marine bromine species improved but remain elevated in GCHP relative to GCC
Approval
Requires further investigation:
Approved by:
Date of approval:

--Bob Yantosca (talk) 19:04, 30 April 2019 (UTC)

GCHP 1-month benchmark

The following sections contain validation plots for GCHP 12.3.2.

Comparison of GCHP versions

This table contains plots comparing GCHP 12.3.0 (Ref) and GCHP 12.3.2 (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, SenescingPlants,
Ship, Soil, Total, VolcDegas, VolcErupt,

Emission totals

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

--Bob Yantosca (talk) 17:02, 30 April 2019 (UTC)

Comparison of GCHP and GEOS-Chem Classic

This table contains plots comparing GEOS-Chem Classic 12.3.2 (Ref) against GCHP 12.3.2 (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, SenescingPlants,
Ship, Soil, Total, VolcDegas, VolcErupt,

Emission totals

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

--Bob Yantosca (talk) 17:16, 30 April 2019 (UTC)

GCHP and GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 12.3.2 - GCHP 12.3.0] against the difference [GC Classic 12.3.2 - 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.

--Bob Yantosca (talk) 19:00, 1 May 2019 (UTC)