GEOS-Chem 12 benchmark history

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GEOS-Chem v11-02-final will also carry the designation GEOS-Chem 12.0.0. We are migrating to a purely numeric versioning system in order to adhere more closely to software development best practices. For a complete description of the new versioning system, please see our GEOS-Chem version numbering system wiki page.

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On this page we have posted complete information about all benchmark simulations (both 1-month and 1-year) for GEOS-Chem 12.

1-year full-chemistry benchmarks

12.0.0-Run0

Three GEOS-Chem model versions were 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	12.0.0-Run0	GEOS-FP, 72L, 4x5	2016	Updates introduced in this benchmark: 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
Blue	v11-02f-Run1	GEOS-FP, 72L, 4x5	2016	Updates introduced in this benchmark: Update HEMCO from v2.1.001 to v2.1.005 Use global 0.25x0.25 files for MEGAN input and MODIS LAI Update lightning BETA values and OTD/LIS files for consistency with latest met fields CEDS global anthropogenic emissions (1950-2014) EDGAR v4.3.1 emissions Historical Canadian emissions Global ethane emissions Inefficient combustion emissions in Africa (DICE-Africa inventory) Trash burning emissions Update GFED4 emission factors Retire GFED3 biomass burning emissions Ammonia emissions from Arctic seabirds Restore use of prod/loss rates from GMI in the mesosphere for UCX-based simulations Fix bug in units of UCX prod/loss rates Add fix for UCX mesospheric NOy routine Fix Henry's Law parameters for HCl Fix for N2O5 uptake Add fix for organic nitrate chemistry	11.532	593.857
Red	v11-02e-Run1	GEOS-FP, 72L, 4x5	2016	Updates introduced in this benchmark: Use GEOS-FP 4x5 met fields for 2016	11.541	603.246

The output plots for this run may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/GC_12/12.0.0/Run0/output
mget *

You may also view the PDF files online by pointing your browser to

http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/GC_12/12.0.0/Run0/output/

Please also view the following pages comparing this version to past 1-year benchmarks:

• Global Tropospheric Aerosol Burdens
• Global Tropospheric Mean Aerosol Optical Depth

--Melissa Sulprizio (talk) 11:44, 10 August 2018 (UTC)

1-year Rn-Pb-Be benchmarks

TBD

1-month benchmarks

12.0.0

This section includes the assessment form for the 1-month benchmark simulation of 12.0.0.

Description
New features added into GEOS-Chem	Feature Submitted by Features affecting the full-chemistry simulation: FlexGrid Stage 1: Use HEMCO to read met fields Jiawei Zhuang (Harvard) Jintai Lin (PKU) Anthropogenic PM2.5 dust source Sajeev Philip (Dalhousie) GEOS-Chem restart file updates Melissa Sulprizio (GCST) Updates and fixes for the CEDS anthropogenic emissions inventory: Add missing RCO sector to CEDS emissions entries Include CEDS ship emissions as default global ship emissions inventory Reduce file size for CEDS inventory Pengfei Liu (Harvard) Melissa Sulprizio (GCST) Jiawei Zhuang (Harvard) HEMCO fixes: HEMCO bug fix: prevent excessive attempts to read the HEMCO restart file when using GEOS-Chem "Classic" Add fix for collapsing model levels to reduced grid Fix unit conversion in HCO_UNIT_GetAreaScal GCST Fix mass conservation in non-local PBL mixing Jintai Lin (PKU) Allow for SZA to 98 degrees when getting photolysis rates Eric Palmer (GMAO) Features NOT affecting the full-chemistry simulation: Add fixes for seasonal scale factors in CH4 simulations Bram Maasakkers (SRON) Melissa Sulprizio (GCST) Convert input data for RRTMG from bpch to netCDF for input via HEMCO Bob Yantosca (GCST) Added netCDF diagnostics in the following areas: CH4 simulation CO2 simulation Persistent Organic Pollutants (POPS) simulation Mercury simulation netCDF diagnostics for mercury are partially implemented in 12.1.0; to be completed in 12.2.0 Bob Yantosca (GCST) Add support for continuous integration with TravisCI – automatically test each commit as soon as it is pushed to Github Jiawei Zhuang (Harvard) Bob Yantosca (GCST) Budget diagnostics Lizzie Lundgren (GCST) Chris Holmes (Florida State) Move Fast-JX .dat files from the geos-chem-unittest repository to gcgrid/ExtData Chris Holmes (Florida State) GCST Update HEMCO configuration file for the tagged CO simulation Bob Yantosca (GCST) Structural updates to facilitate interfacing GEOS-Chem into WRF Haipeng Lin (Peking U) GCST Structural updates to facilitate interfacing GEOS-Chem into GEOS-5 Christoph Keller (GMAO) Lizzie Lundgren (GCST) Features affecting GCHP only: Fix masking bug to correctly apply anthropogenic emissions Lizzie Lundgren (GCST) Remove erroneous 180 degree longitude shift in APEI regridding Lizzie Lundgren (GCST) Move GCHP run directory creation from GEOS-Chem Unit Tester to GCHP repository Lizzie Lundgren (GCST)
Version, resolution, met fields used:	GEOS-FP (72L), 4x5, July 2016
1-month benchmark finished on:	Wed Nov 7 04:20:45 EST 2018
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: 06:02:27 CPU time / wall time: 23.2894 % of ideal performance: 97.04% Memory: 8.9262 GB
Compared to previous benchmark:	12.0.0
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):
Unit test results may be viewed at:	http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.1.0/output/GC_12.1.0.results.html
Plots may be viewed at:	http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.1.0/output/
Metrics
Global mean OH from log file (% change):	TBD x 105 molec/cm3 (TBD%)
Methyl chloroform lifetime (% change):	TBD years (TBD%)
Methane lifetime (% change):	TBD years (TBD%)
O3 STE flux (% change):	TBD Tg O3/year (TBD%)
At the SURFACE, list all species that changed by 10% or more:
Comments on SURFACE differences:	Below we summarize the notable changes caused by specific updates. TBD The following updates impacted species concentrations slightly, but the changes did not amount to >10%.
At 500 hPa, list all species that changed by 10% or more:
Comments on 500 hPa differences:	See comments for surface differences
In the ZONAL MEAN differences, list all species that changed by 10% or more:
Comments on ZONAL MEAN differences:	See comments for surface differences
In the EMISSION RATIO maps, list all species that changed by 10% or more:
Comments on EMISSION RATIO differences:
Additional or summary comments:
Approval
Requires further investigation:
Approved by:
Date of approval:

--Melissa Sulprizio (talk) 19:52, 7 November 2018 (UTC)

12.0.0

This section includes the assessment form for the 1-month benchmark simulation of 12.0.0.

Description
New features added into GEOS-Chem	Feature Submitted by Features affecting the full-chemistry simulation: Turn off TRASH emissions by default to avoid double counting GCST Eloise Marais (U. Birmingham) Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory GCST Bug fix for liquid water content in gckpp_HetRates.F90 Jiayue Huang (U. Washington) Quanjie Chen (U. Washington) Bug fix for CH4 boundary conditions Lee Murray (Rochester) Fixed typo in call to GAMMA_HOBr_AER Xuan Wang GCST 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 Eloise Marais (U. Birmingham) GCST Add missing Criegee intermediate reaction Xin Chen (UMN) Bug fix for ARCTAS_SHIP in HEMCO_Config.rc files Barron Henderson (EPA) Avoid double counting CEDS and GEIA NH3 biofuel emissions Christoph Keller (NASA/GMAO) GCST Bug fix in FlexChem: do not zero out ACTA, EOH, HCOOH concentrations Katie Travis (MIT) Add GFED4.1 data for 2015 and 2016; Use GFED4.1 2016 in benchmarks Kate O'Dell (CSU) GCST Features NOT affecting the full-chemistry simulation: Minor fixes for mercury chemistry updates implemented in v11-02f Colin Thackray (Harvard) Restore default timestep for MERRA-2 nested grid simulations to 10/20 Ke Li (Harvard) Remove duplicate C3HI spectrum in FJX_spec.dat and FJX_j2j.dat Tomas Sherwen (York) Fixed typo that prevented PM2.5 from being archived to netCDF output Jonathan Moch (Harvard) GCST Bring two-way nested-grid code option up-to-date Yingying Yan (PKU) Jintai Lin (PKU) Do not force L=1 by default in planeflight_mod.F Katie Travis (MIT) GCST Add PH2O2 to the default list of prod/loss families in the KPP mechanisms GCST Update to HEMCO v2.1.007, which includes minor updates: Stop with error if multiple containers have the same name Bug fix for distributing emissions in the vertical dimension Add extra error checks in HEMCO standalone module Remove null string character from netCDF unit string Bug fix for HEMCO soil NOx error with ifort 17 GCST Christoph Keller Jenny Fisher Bug fix for reference time in netCDF diagnostic files GCST Updates for QFED biomass burning emissions: Update to QFED v2.5r1 Fix QFED v2.4r6 files for 2016/10/13 Christoph Keller (NASA GMAO) Fix issues in complexSOA and complexSOA_SVPOA restart files Eloise Marais (U. Birmingham) Bug fixes for v11-02 simulations using the RRTMG radiative transfer model Chris Holmes (U. Florida) Now always declare the netCDF time variable with an unlimited dimension Chris Holmes (U. Florida)
Version, resolution, met fields used:	GEOS-FP (72L), 4x5, July 2016
1-month benchmark finished on:	Mon Jul 30 21:05:43 EDT 2018
Performance statistics:	Compiled with ifort 11.1 Ran on 24 CPUs of holyjacob01.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz) Wall time: 06:38:04 CPU time / wall time: 21.9237 % of ideal performance: 91.35% Memory: 7.3247 GB
Compared to previous benchmark:	v11-02-rc
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):
Unit test results may be viewed at:	http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.0.0/output/GC_12.0.0.results.html
Plots may be viewed at:	http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.0.0/output/
Metrics
Global mean OH from log file (% change):	12.5734575378792 x 105 molec/cm3 (+1.80%)
Methyl chloroform lifetime (% change):	4.9162 years (-1.91%)
Methane lifetime (% change):	8.2830 years (-1.85%)
O3 STE flux (% change):	495.1870 Tg O3/year (-0.18%)
At the SURFACE, list all species that changed by 10% or more:	NO, O3, PAN, CO, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, NPMN, PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, NITs, BCPI, BCPO, OCPI, OCPO, 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, MTPO, TSOG*, TSOA*, ISOG*, ISOA*, ASOG*, ASOA*, SOAP, SOAS, EOH, MGLY, GLYX, ACTA, HPALD, DHDN, ETHLN, HCOOH, IEPOX*, ISN1, RIP*, IMAE, SOAIE, SOAME, SOAGX, SOAMG, LVOC, LVOCOA, ISN1OG, ISN1OA, MONITS, MONITU, HONIT, MONITA, INDIOL, 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, AERI, pFe, OH, HO2
Comments on SURFACE differences:	Below we summarize the notable changes caused by specific updates. Turn off TRASH emissions by default to avoid double counting This update resulted in slightly reduced concentrations over land for many species. Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory This fix caused increases in SOAP, SOAS, and pFe concentrations globally. Bug fix for CH4 boundary conditions This fix resulted in increased CH4 concentrations in the troposphere. Bug fix for liquid water content in gckpp_HetRates.F90 This fix reduced many Br and Cl species concentrations globally while increasing HBr, BrSALA, and BrSALC. Fix typo in call to GAMMA_HOBr_AER This fix caused slight changes in Br and Cl species concentrations, mainly over the oceans Fixes to DICE-Africa emissions These updates primarily caused increases in species concentrations near the surface over and downwind of Africa. This fix caused large increases in ACTA and HCOOH at all levels Add GFED4.1 data for 2016 and 2016 Updating the GFED4 year from 2014 to 2016 caused >10% increases and decreases in species concentrations over land globally. The following updates impacted species concentrations slightly, but the changes did not amount to >10%. Add missing Criegee intermediate reaction Bug fix for ARCTAS_SHIP in HEMCO_Config.rc files
At 500 hPa, list all species that changed by 10% or more:	NO, PAN, CO, ALK4, ISOP, HNO3, ACET, MEK, ALD2, RCHO, MVK, MACR, NPMN, PPN, R4N2, PRPE, C3H8, C2H6, N2O5, HNO4, MP, DMS, SO2, SO4, NH3, NH4, NIT, NITs, BCPI, BCPO, OCPI, OCPO, 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, MTPO, TSOG*, TSOA*, ISOG*, ISOA*, ASOG*, ASOA*, SOAP, SOAS, EOH, MGLY, GLYX, ACTA, HPALD, DHDN, ETHLN, HCOOH, IEPOX*, ISN1, RIP*, IMAE, SOAIE, SOAME, SOAGX, SOAMG, LVOC, LVOCOA, ISN1OG, ISN1OA, MONITS, MONITU, HONIT, MONITA, INDIOL, 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, pFe, OH
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, PAN, CO, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, NPMN, PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, NITs, BCPI, BCPO, OCPI, OCPO, 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, MTPO, TSOG*, TSOA*, ISOG*, ISOA*, ASOG*, ASOA*, SOAP, SOAS, EOH, MGLY, GLYX, ACTA, HPALD, DHDN, ETHLN, HCOOH, IEPOX*, ISN1, RIP*, IMAE, SOAIE, SOAME, SOAGX, SOAMG, LVOC, ISN1OG, ISN1OA, MONITS, MONITU, HONIT, IONITA, MONITA, INDIOL, IPMN, HC187, CH4, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, BrSALA, BrSALC, CH2I2, CH2IBr, HOI, I2, ICl, I, IO, HI, OIO, INO, IONO, IONO2, I2O2, I2O3, I2O4, pFe, 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:	Anthropogenic emissions: ACET, ALD2, ALK4, C3H8, CO, MEK, NH3, NO, OC, PRPE, SO2, SO4, XYLE Biomass burning emissions: ACET, ALD2, ALK4, BC, BENZ, C2H6, C3H8, CH2O, CO, EOH, MEK, MTPA, NH3, NO, OC, PRPE, SO2, TOLU, XYLE NO fertilizer & soil emissions SO2 ship emissions
Comments on EMISSION RATIO differences:	Anthropogenic emissions of many species increased over Africa. This is caused by the two fixes applied to DICE-Africa emissions. Biomass burning emissions for all species changed because of the update to GFED4.2 2016 emissions. NO fertilizer and soil emissions changed slightly because of changes in NOx concentrations. The change in ship SO2 emissions is caused by the bug fix in ARCTAS_SHIP SO2 scale factors.
Additional or summary comments:
Approval
Requires further investigation:	No
Approved by:	GCST
Date of approval:	02 Aug 2018

--Melissa Sulprizio (talk) 17:10, 31 July 2018 (UTC)

GCHP benchmarks

TBD