GEOS-Chem 13.0.0

This page includes information about all benchmark simulations for GEOS-Chem 13.0.0.

Version overview

The following items have been added to GEOS-Chem 13.0.0 since the last benchmark for GEOS-Chem 12.9.0.

Feature	Submitted by	Type
Updates that will affect full-chemistry simulations
CEDS_GBD-MAPS emission inventory (1970 - 2017)	Erin McDuffie (Dalhousie)	Science
Retire carbon-based units for VOCs	Melissa Sulprizio (GCST)	Science
Removal of HEMCO code from within the non-local PBL mixing modules	Bob Yantosca (GCST)	Structural
Heterogeneous chem fixes, performance improvements, and clarification	Chris Holmes (FSU)	Bug fix
Fix handling of NOx coefficients in ucx_mod.F90	Sebastian Eastham (MIT)	Bug fix
Prevent divide-by-zero errors in UCX routine UCX_NOX	Bob Yantosca (GCST)	Bug fix
Updates that will NOT affect full-chemistry simulations
Use GEOS-FP 5.22 data for Jan - May 2020 and store GEOS-FP 5.25 for April - May 2020 as option	Jun Meng (GCST) Melissa Sulprizio (GCST)	Data
Update QFED emissions through July 2020	Christoph Keller (NASA GMAO)	Science
ODIAC fossil fuel emissions for CO2 simulations	Jenny Fisher (UOW) Yi Cao (UOW)	Science
Global Hg emissions from Streets et al. (2019) (as option)	Colin Thackray (Harvard)	Science
Global Hg emissions from EDGARv4.tox2 (as option)	Amanda Giang (UBC)	Science
Global Inventory of Methane Emissions from Fuel Exploitation	Tia Scarpelli (Harvard)	Science
Retire tropchem mechanism; implement new tropchem simulation using Standard mechanism below the tropopause and archived P/L rates above	Melissa Sulprizio (GCST)	Science
RRTMG fixes and updates Fix bug with stratospheric aerosol Shift RRTMG call time sequence to begin first timestep Fix bugs in GEOS-Chem 12 implementation of netCDF diagnostics Complete remaining implementation of netCDF diagnostics to match binary Fix seg fault when building RRTMG with Intel compilers Allow turning RRTMG off when using RRTMG-enabled executable	Sebastian Eastham (MIT) Lizzie Lundgren (GCST)	Bug fix
Add global mean OH and CH4 lifetime diagnostics	Bob Yantosca (GCST)	Structural
Retire the GNU Make build system in both GEOS-Chem Classic and GCHP and replace with CMake	Liam Bindle (WashU) GCST	Structural
Retire the GEOS-Chem Unit Tester repository and move GEOS-Chem run directory creation to the GEOS-Chem source code repository	Melissa Sulprizio (GCST)	Structural
Updates to GEOS-Chem and HEMCO interface for compatibility with CESM	Haipeng Lin (Harvard) Thibaud Fritz (MIT) Lizzie Lundgren (GCST)	Structural
Dynamically allocate diagnostic arrays based on HISTORY.rc content to minimize memory footprint	Bob Yantosca (GCST)	Structural
Fixes for typos: Incorrect density value used to calculate cloud ice volume Fix stratospheric loss in CH4 simulation using 12.9.0 Update format statements in fast_jx_mod.F90 for 3 integers Fix typo in mercury_mod.F for saving EmisHg0land Fix for reading archived OH and Cl in CH4 simulations Fix species name typo in Init_HetInfo subroutine	GCST	Bug fix
Features only affecting GCHP:
Retire the existing GCHP repository and replace with a new wrapper repository that uses ESMF as an external library and integrates GEOS-Chem and NASA/GMAO GEOS-ESM git repositories as git submodules	Lizzie Lundgren (GCST)	Structural
Separate HEMCO from GEOS-Chem to use as an ESMF gridded component in GCHP	Lizzie Lundgren (GCST)	Structural
Enable a stretched grid capability in GCHP to run global simulations at regional high resolution	Liam Bindle (WashU)	Structural
Update MAPL (v2.2.7) and GMAO library dependencies	Lizzie Lundgren (GCST)	Structural
Enable GCHP to be compiled with RRTMG	Sebastian Eastham (MIT) Lizzie Lundgren (GCST)	Science

New data directories

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory	Type	What was added?	Directory
CEDS	DEFAULT (full-chemistry simulations)	CEDS_GBD-MAPS emission inventory (1970 - 2017)	HEMCO/CEDS/v2020-08/
QFED	OPTIONAL	Update QFED emissions through July 2020	HEMCO/QFED/v2018-07/
ODIAC CO2	DEFAULT (CO2 simulations)	ODIAC fossil fuel emissions for CO2 simulations	HEMCO/CO2/v2019-12/
MERCURY	OPTIONAL (Hg simulations)	Updated Streets Hg emissions Updated EDGAR 4.3 Hg emissions	HEMCO/MERCURY/v2020-07/
CH4	DEFAULT (CH4 simulations)	Global Inventory of Methane Emissions from Fuel Exploitation Updated wetland and seep CH4 emissions	HEMCO/CH4/v2020-02/ HEMCO/CH4/v2020-04/

1-month benchmarks

Model setup

The following table describes the GEOS-Chem setup for both GEOS-Chem Classic and GCHP 1-month benchmark simulations.

Meteorology fields:	MERRA-2
Benchmark month:	July 2019
Git tag(s):	13.0.0-rc.0
Compared to previous benchmark:	12.9.0
This version will impact: (select all that apply with boldface)	Advection BL Mixing Convection Meteorology Fields Dry Deposition* Wet Deposition Emissions Photolysis Chemistry Other (please specify):

Benchmark Plots and Tables

NOTES:

• Enable PDF bookmarks in the files linked above to navigate between species. See the Species in GEOS-Chem wiki page for species definitions and details. If you do not see bookmarks in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.
• Species categories and lumped species definitions are simple to adjust. Updating them requires only editing the YAML files.

GCClassic version comparison

Below are links to plots and tables comparing 1-month simulations for GEOS-Chem Classic 12.9.0 (Ref) and GEOS-Chem Classic 13.0.0 (Dev).

Species Category	Plots					Additional Information
	Level Map		Zonal Mean		Emissions
Oxidants O3, CO, OH, NOx	sfc	500hPa	full column	stratosphere	sfc
Aerosols DST1, DST2, DST3, DST4, NH4, NIT, SO4, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA	sfc	500hPa	full column	stratosphere	sfc	AOD
Bromine Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr	sfc	500hPa	full column	stratosphere	sfc
Chlorine Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, CHCl3, HOCl, HCl, Halons, HCFCs, OClO	sfc	500hPa	full column	stratosphere	--
Iodine Iy, IxOy, I, I2, IBr, ICl, IO, IONO, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO	sfc	500hPa	full column	stratosphere	sfc
Nitrogen NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3	sfc	500hPa	full column	stratosphere	sfc
Primary Organics EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H6, C3H8, PRPE, TOLU, XYLE	sfc	500hPa	full column	stratosphere	sfc
Secondary Organics ACTA, ALD2, CH2O, HPALDs, MACR, IEPOX, ACET, MEK, MVK, ISOPN, GLYX, HCOOH, MAP, RCHO, MP	sfc	500hPa	full column	stratosphere	sfc
Secondary Organic Aerosols TSOA0, TSOA1, TSOA2, TSOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ASOG1, ASOG2, ASOG3, INDIOL, LVOCOA, SOAIE, SOAGX, SOAP, SOAS	sfc	500hPa	full column	stratosphere	sfc
Sulfur SOx, DMS, OCS, SO2, SO4	sfc	500hPa	full column	stratosphere	sfc
ROy H2O2, H, H2, H2O, HO2, O1D, OH, RO2	sfc	500hPa	full column	stratosphere	--
J-values	sfc	500hPa	full column	stratosphere	--	--
Emissions by HEMCO category	Total Aircraft, Anthropogenic, Biomass Burning, Biogenic, Lightning, Natural, Ocean, Seabirds, Decaying Plants, Ship, Soil, Degassing Volcanoes, Erupting Volcanoes
Emission totals	Tables by species Tables by inventory
Global mass	Entire atmosphere Troposphere only
Metrics	OH concentration, MCF lifetime, CH4 lifetime
Budgets	Budgets after operations

GCHP version comparison

Below are links to plots and tables comparing 1-month simulations for GCHP 12.9.0 (Ref) and GCHP 13.0.0 (Dev).

Species Category2	Plots					Additional Information
	Level Map		Zonal Mean		Emissions
Oxidants O3, CO, OH, NOx	sfc	500hPa	full column	stratosphere	sfc
Aerosols DST1, DST2, DST3, DST4, NH4, NIT, SO4, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA	sfc	500hPa	full column	stratosphere	sfc	AOD
Bromine Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr	sfc	500hPa	full column	stratosphere	sfc
Chlorine Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, CHCl3, HOCl, HCl, Halons, HCFCs, OClO	sfc	500hPa	full column	stratosphere	--
Iodine Iy, IxOy, I, I2, IBr, ICl, IO, IONO, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO	sfc	500hPa	full column	stratosphere	sfc
Nitrogen NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3	sfc	500hPa	full column	stratosphere	sfc
Primary Organics EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H6, C3H8, PRPE, TOLU, XYLE	sfc	500hPa	full column	stratosphere	sfc
Secondary Organics ACTA, ALD2, CH2O, HPALDs, MACR, IEPOX, ACET, MEK, MVK, ISOPN, GLYX, HCOOH, MAP, RCHO, MP	sfc	500hPa	full column	stratosphere	sfc
Secondary Organic Aerosols TSOA0, TSOA1, TSOA2, TSOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ASOG1, ASOG2, ASOG3, INDIOL, LVOCOA, SOAIE, SOAGX, SOAP, SOAS	sfc	500hPa	full column	stratosphere	sfc
Sulfur SOx, DMS, OCS, SO2, SO4	sfc	500hPa	full column	stratosphere	sfc
ROy H2O2, H, H2, H2O, HO2, O1D, OH, RO2	sfc	500hPa	full column	stratosphere	--
J-values	sfc	500hPa	full column	stratosphere	--	--
Emissions by HEMCO category	Total Aircraft, Anthropogenic, Biomass Burning, Biogenic, Lightning, Natural, Ocean, Seabirds, Decaying Plants, Ship, Soil, Degassing Volcanoes, Erupting Volcanoes
Emission totals	Tables by species Tables by inventory
Global mass	Entire atmosphere Troposphere only
Budgets	Budgets after operations

GCHP and GEOS-Chem Classic comparison

Below are links to plots and tables comparing 1-month simulations for GEOS-Chem Classic 13.0.0 (Ref) and GCHP 13.0.0 (Dev).

Species Category2	Plots					Additional Information
	Level Map		Zonal Mean		Emissions
Oxidants O3, CO, OH, NOx	sfc	500hPa	full column	stratosphere	sfc
Aerosols DST1, DST2, DST3, DST4, NH4, NIT, SO4, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA	sfc	500hPa	full column	stratosphere	sfc	AOD
Bromine Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr	sfc	500hPa	full column	stratosphere	sfc
Chlorine Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, CHCl3, HOCl, HCl, Halons, HCFCs, OClO	sfc	500hPa	full column	stratosphere	--
Iodine Iy, IxOy, I, I2, IBr, ICl, IO, IONO, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO	sfc	500hPa	full column	stratosphere	sfc
Nitrogen NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3	sfc	500hPa	full column	stratosphere	sfc
Primary Organics EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H6, C3H8, PRPE, TOLU, XYLE	sfc	500hPa	full column	stratosphere	sfc
Secondary Organics ACTA, ALD2, CH2O, HPALDs, MACR, IEPOX, ACET, MEK, MVK, ISOPN, GLYX, HCOOH, MAP, RCHO, MP	sfc	500hPa	full column	stratosphere	sfc
Secondary Organic Aerosols TSOA0, TSOA1, TSOA2, TSOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ASOG1, ASOG2, ASOG3, INDIOL, LVOCOA, SOAIE, SOAGX, SOAP, SOAS	sfc	500hPa	full column	stratosphere	sfc
Sulfur SOx, DMS, OCS, SO2, SO4	sfc	500hPa	full column	stratosphere	sfc
ROy H2O2, H, H2, H2O, HO2, O1D, OH, RO2	sfc	500hPa	full column	stratosphere	--
J-values	sfc	500hPa	full column	stratosphere	--	--
Emissions by HEMCO category	Total Aircraft, Anthropogenic, Biomass Burning, Biogenic, Lightning, Natural, Ocean, Seabirds, Decaying Plants, Ship, Soil, Degassing Volcanoes, Erupting Volcanoes
Emission totals	Tables by species Tables by inventory
Global mass	Entire atmosphere Troposphere only
Budgets	Budgets after operations

GCHP and GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 13.0.0 - GCHP 12.9.0] against the difference [GC Classic 13.0.0 - GC Classic 12.9.0], taken from 1-month benchmark simulations.

Category	Plots
	Level Map		Zonal Mean
Oxidants	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
Secondary Organic Aerosols	sfc	500hPa	full column	stratosphere
Sulfur	sfc	500hPa	full column	stratosphere
ROy	sfc	500hPa	full column	stratosphere

NOTE: At present, we have only created the diff-of-diffs plots for species concentration. This can be extended to other categories in the future.

Benchmark assessment form

Description
1-month benchmark finished on:	Mon Nov 2 03:24:27 EST 2020
Performance statistics:	Compiled with ifort 18.0.5 Ran on 24 CPUs of holy7c20304.rc.fas.harvard.edu (Intel(R) Xeon(R) Platinum 8268 CPU @ 2.90GHz) Wall time: 06:54:01 CPU time / wall time: 19.4750 % of ideal performance: 81.15% Memory: 13.6795 GB
Metrics
Global mean OH from log file (% change):	11.22769648880 x 105 molec/cm3 (-8.60)
Methyl chloroform lifetime (% change):	5.5460 years (+8.20%)
Methane lifetime (% change):	9.3297 years (+8.09%)
Overview
Comments on observed differences:	Below we summarize the notable changes caused by specific updates.
Details
List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:
List all 500 hPa species and J-Values that changed by 10% or more :
List all ZONAL MEAN species and J-Values that changed by 10% or more:
List all EMISSIONS that changed by 10% or more:
Approval
Requires further investigation:
Approved by:
Date of approval: