GEOS-Chem 13.0.0: Difference between revisions

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*Use [[MERRA-2]] meteorology instead of [[GEOS-FP]]
*Use [[MERRA-2]] meteorology instead of [[GEOS-FP]]
*Update benchmark year from 2016 to 2019
*Update benchmark year from 2016 to 2019
*Use restart file that has been spun up (July 2016 from GEOS-Chem 12.9.0 1-year benchmark)
*Use restart file that has been spun up (July 2016 restart file from GEOS-Chem 12.9.0 1-year benchmark)
|[[GCST]]
|[[GCST]]
|Structural
|Structural

Revision as of 05:26, 10 November 2020

GEOS-Chem Main Page | GCHP Main Page

This page includes information about 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
Changes to benchmark setup:
  • Use MERRA-2 meteorology instead of GEOS-FP
  • Update benchmark year from 2016 to 2019
  • Use restart file that has been spun up (July 2016 restart file from GEOS-Chem 12.9.0 1-year benchmark)
 GCST Structural
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 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
Create new GCClassic wrapper repository Lizzie Lundgren (GCST) Structural
Separate HEMCO from GEOS-Chem to use as a git submodule in GCClassic in GCHPctm Lizzie Lundgren (GCST) Structural
Retire the GEOS-Chem Unit Tester repository and move GEOS-Chem run directory creation to the GEOS-Chem 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: GCST Bug fix
Features only affecting GCHP:
Retire the existing GCHP repository and replace with a new wrapper repository (GCHPctm) 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
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.

Git tag(s): 13.0.0-rc.0
Compared to previous benchmark: 12.9.0
Software environment: ifort 18.0.5
openmpi 4.0.1
netcdf-fortran 4.5.2
cmake 3.16.1
Meteorology fields: MERRA-2
Benchmark month: July 2019
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

O3, CO, OH, NOx

sfc 500hPa full column stratosphere
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
Bromine

Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr

sfc 500hPa full column stratosphere
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
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
Primary Organics

EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H6, C3H8, PRPE, TOLU, XYLE

sfc 500hPa full column stratosphere
Secondary Organics

ACTA, ALD2, CH2O, HPALDs, MACR, IEPOX, ACET, MEK, MVK, ISOPN, GLYX, HCOOH, MAP, RCHO, MP

sfc 500hPa full column stratosphere
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
Sulfur

SOx, DMS, OCS, SO2, SO4

sfc 500hPa full column stratosphere
ROy

H2O2, H, H2, H2O, HO2, O1D, OH, RO2

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

Performance GCClassic GCHP
# CPUs, nodes: 24 CPUs
1 node (Intel Cascade Lake) 		48 CPUs
2 nodes (Intel Broadwell)
Wall time: 06:54:01 14:26:01
CPU time / wall time: 19.4750 47.0915
% of ideal performance: 81.15% 98.11%
Memory: 13.6795 GB 133.28 GB
Global mean OH:
(% change from previous version) 		11.22769648880 x 105 molec/cm3
(-8.60%) 		11.24518930757 x 105 molec/cm3
(N/A)
Methyl chloroform lifetime:
(% change from previous version) 		5.5460 years
(+8.20%) 		5.5318 years
(N/A)
Methane lifetime:
(% change from previous version) 		9.3297 years
(+8.09%) 		9.3064 years
(N/A)
Details
Species, J-Values, and COLUMN AOD values that changed by 10% or more at the surface: GCClassic version comparison GCHP version comparison

GCClassic vs GCHP

Species and J-Values that changed by 10% or more at 500 hPa: GCClassic version comparison GCHP version comparison

GCClassic vs GCHP

Species and J-Values that changed by 10% or more in zonal mean: GCClassic version comparison GCHP version comparison

GCClassic vs GCHP

Emissions that changed by 10% or more: GCClassic version comparison GCHP version comparison

GCClassic vs GCHP

Overview
Below we summarize the notable changes caused by specific updates.

Changes to benchmark setup

  • Use MERRA-2 meteorology instead of GEOS-FP
  • Update benchmark year from 2016 to 2019


CEDS_GBD-MAPS emission inventory (1970 - 2017)


Retire carbon-based units for VOCs


Heterogeneous chem fixes, performance improvements, and clarification


Fix handling of NOx coefficients in ucx_mod.F90

The following updates introduced differences on the order of numerical noise:


Approval
Requires further investigation:
Approved by:
Date of approval:

1-year full-chemistry benchmarks

Model setup

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

Git tag(s): TBD
Compared to previous benchmark: 12.9.0
Software environment: ifort 18.0.5
openmpi 4.0.1
netcdf-fortran 4.5.2
cmake 3.16.1
Meteorology fields: MERRA-2
Benchmark date: Spin-up run: Jan 2018 - Dec 2018
Production run: Jan 2019 - Dec 2019

Benchmark Plots and Tables

Coming soon

1-year transport tracers benchmarks

Model setup

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

Git tag(s): TBD
Compared to previous benchmark: 12.9.0
Software environment: ifort 18.0.5
openmpi 4.0.1
netcdf-fortran 4.5.2
cmake 3.16.1
Meteorology fields: MERRA-2
Benchmark date: Spinup run: Jan 2015 - Dec 2018
Production run: Jan 2019 - Dec 2019

Benchmark Plots and Tables

Coming soon

10-year stratospheric benchmarks

Model setup

The following table describes the GEOS-Chem setup for both GEOS-Chem Classic and GCHP 10-year benchmark simulations.

Git tag(s): TBD
Compared to previous benchmark: N/A
Software environment: ifort 18.0.5
openmpi 4.0.1
netcdf-fortran 4.5.2
cmake 3.16.1
Meteorology fields: MERRA-2
Benchmark date: Jan 2010 - Dec 2019

Benchmark Plots and Tables

Coming soon

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