Benchmark/GEOS-Chem 12.3.0

This page includes information about all benchmark simulations for GEOS-Chem 12.3.0.

1-month benchmark

Benchmark plots

This is the first GEOS-Chem benchmark to utilize GCPy. Some benchmark plots created by GAMAP still remain because they have not been recreated in GCPy yet. To view the entirety of the old version of benchmark plots created by GAMAP, visit http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.3.0/output/.

Category1	Plots				Additional Information
	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
ROy	sfc	500hPa	full column	stratosphere
Sulfur	sfc	500hPa	full column	stratosphere
Emissions	sfc	--	--	--	Emissions totals
Plots still created by GAMAP
AOD	maps	differences	--	--
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.

--Melissa Sulprizio (talk) 16:41, 15 March 2019 (UTC)

Benchmark assessment form

Description
New features added into GEOS-Chem	Feature Submitted by Features affecting the full-chemistry simulation: Update ISORROPIA from v2.0 to v2.2, in order to remove persistent noise in output Seb Eastham (Harvard) Updated PFT file for MEGAN Jenny Fisher (Wollongong) Dylan Millet (UMN) Bug fix for eruptive volcanic emissions Barron Henderson (EPA) Read in and regrid existing MODIS LAI and OLSON data via HEMCO Bob Yantosca (GCST) Update from HEMCO version 2.1.011 to 2.1.012 Bug fixes for the HEMCO interpolation algorithm Updates from the NASA GEOS development branch Add option to always use simulation year for specified fields Prevent zero emissions for MEGAN_Mono extension species Updates to the HEMCO volcanic emissions extension Christoph Keller (NASA/GMAO) GCST Features NOT affecting the full-chemistry simulation: Update to Yuan processed MODIS LAI product (covering years 2005-2016) Off while we investigate an issue in the HEMCO interpolation Jenny Fisher (Wollongong) Barron Henderson (US EPA) OMI-based Volcanic emissions 2005-2012 (off by default) Cui Ge (U. Iowa) Jun Wang (U. Iowa) GCST Further bug fix for netCDF diagnostics spanning leap years Bob Yantosca (GCST) Fix GFAS_SOAP entry in HEMCO_Config.rc Killian Murphy (York) Tagged CO bug fixes: Fix CO units and write secondary production into a netcdf file Beata Bukosa (Wollongong) Features affecting GCHP only: Enable running time backwards in GCHP (off by default) Atanas Trayanov (GMAO), Lizzie Lundgren (GCST)
Version, resolution, met fields used:	GEOS-FP (72L), 4x5, July 2016
1-month benchmark finished on:	Thu Mar 28 08:33:50 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: 10:04:56 CPU time / wall time: 20.1441 % of ideal performance: 83.93% Memory: 13.5919 GB
Compared to previous benchmark:	12.2.0
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): Volcano emissions
Unit test results may be viewed at:	http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.3.0/output/GC_12.3.0_Mar27.results.html
Metrics
Global mean OH from log file (% change):	12.5308895343096 x 105 molec/cm3 (0.04%)
Methyl chloroform lifetime (% change):	4.9406 years (-0.05%)
Methane lifetime (% change):	8.3253 years (-0.05%)
At the SURFACE, list all species that changed by 10% or more:	ISOP, H2O2, RCHO, MVK, MACR, NPMN, PPN, R4N2, PRPE, N2O5, SO2, SO4s, NH3, NH4, NIT, NITs, Br, BrO, HOBr, HBr, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, NO3, MTPA, LIMO, MTPO, ISOG1, ISOG3, ISOA1, ISOA3, 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, IPMN, HC187, BrCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, HI, I2O3, I2O4, ISALA, ISALC, OH
Comments on SURFACE differences:	Below we summarize the notable changes caused by specific updates. Update ISORROPIA from v2.0 to v2.2 This update caused changes in NH3 and NIT at all levels. These differences are small number differences where concentrations are low. Updated PFT file for MEGAN This update caused changes in the primary and secondary organic species. Percent differences are largest over the oceans, where concentrations are low. Bug fix for eruptive volcanic emissions This bug fix caused decreases in SO2 and SO4 over Southeast Asia. Barron Henderson wrote: The problem is with the eruptions being treated as cycling. The VOLCANO emissions use hemco's cycling option for both degassing and for eruptions. The last year in our dataset is 2009, which had a particularly active June. For example, 2009 June SO2 eruption mass is 4 times the average of the 2000-2009 June. The cycling option takes 2009 and applies it to *all* future years. The following updates impacted species concentrations slightly, but the changes did not amount to >10%. Read in and regrid existing MODIS LAI and OLSON data via HEMCO Update from HEMCO version 2.1.011 to 2.1.012: Bug fix for HEMCO interpolation algorithm
At 500 hPa, list all species that changed by 10% or more:	ISOP, H2O2, MVK, MACR, NPMN, R4N2, N2O5, SO2, NH3, NIT, NITs, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, ISOPND, ISOPNB, MOBA, PROPNN, GLYC, MVKN, MACRN, NO3, MTPA, LIMO, MTPO, EOH, MGLY, GLYX, HPALD, DHDN, ETHLN, IEPOXA, IEPOXB, IEPOXD, ISN1, RIPA, RIPB, RIPD, IMAE, SOAIE, LVOC, ISN1OG, MONITS, MONITU, HONIT, IPMN, HC187, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, BrSALA, BrSALC, CH2I2, HOI, ICl, I, HI, OIO, IONO, I2O2, I2O3, I2O4, ISALA
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, ISOP, HNO3, H2O2, MEK, RCHO, MVK, MACR, NPMN, PPN, R4N2, PRPE, N2O5, HNO4, SO2, SO4, SO4s, NH3, NH4, NIT, NITs, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, NO2, NO3, HNO2, MTPA, LIMO, MTPO, TSOG3, TSOA2, TSOA3, ISOG1, ISOG3, ISOA1, ISOA3, 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, IPMN, HC187, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, BrSALA, BrSALC, CH2I2, 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 EMISSION RATIO maps, list all species that changed by 10% or more:	Biogenic emissions: ACET, ALD2, APIN, BCAR, BPIN, CARE, CO, EOH, FARN, ISOP, LIMO, MBOX, MONX, MYRC, OMON, OSQT, PRPE, SABI SO2 volcano emissions
Comments on EMISSION RATIO differences:	The differences in biogenic emissions are caused by updating to a new plant functional type (PFT) file created from higher resolution data.
Additional or summary comments:	The original 1-month benchmark for this version included OMI-based Volcanic emissions for 1979-2018, however this option has since been turned off and we reverted to the AEROCOM-based volcanic emissions instead. This update caused large decreases in SO2 over and downwind of volcanic regions. This also impacted SO4, SO4s, NH3, NH4, NIT, NITs, HNO3, several bromine species near those regions. Cui Ge wrote: I saw the non-eruptive volcano emission in July of 2016 seems 0 everywhere. If the NASA online data shows this, I think it is OK to be consistent with that. Thanks for confirming this data includes both explosive and effusive eruptions. By my understanding, because volcano emission has big uncertainty (from literature also from our volcano paper), NASA team did some adjustment (the amount of volcano emission, the duration of each volcano, etc) after we published our paper. I think this updated volcano data would be the best volcano data we have for now, also we may want to keep our data to be consistent with this online source data. The AEROCOM volcano data (used in GEOS-Chem) has much bigger uncertainties. To summarize this, I think the code, the process and the data what you are using is all right. As long as we have consistent volcano data with this online source, it would be great. Bob Yantosca has confirmed that volcanic emissions in the 12.3.0 benchmark for July 2016 for is much smaller the emissions from the volcano dataset in the 12.2.0 benchmark. For more information, please follow this link.
Approval
Requires further investigation:
Approved by:
Date of approval:

--Melissa Sulprizio (talk) 15:59, 14 March 2019 (UTC)