Difference between revisions of "GEOS-Chem 13.4.0"

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(Version overview)
(Benchmark assessment form)
Line 352: Line 352:
 
|Memory:
 
|Memory:
 
|11.4128 GB
 
|11.4128 GB
| 0.0145 GB ????
+
|108.5 GB
  
 
|-valign="top"
 
|-valign="top"
 
|Global mean OH:<br>(% change from previous version)
 
|Global mean OH:<br>(% change from previous version)
|TBD
+
|11.70790814279 x 10<sup>5</sup> molec/cm3 <br>(-0.329%)
 
|TBD
 
|TBD
  
 
|-valign="top"
 
|-valign="top"
 
|Methyl chloroform lifetime:<br>(% change from previous version)
 
|Methyl chloroform lifetime:<br>(% change from previous version)
|TBD
+
|5.294530 years<br>(+0.557%)
 
|TBD
 
|TBD
  
 
|-valign="top"
 
|-valign="top"
 
|Methane lifetime:<br>(% change from previous version)
 
|Methane lifetime:<br>(% change from previous version)
|TBD
+
|8.923431 years<br>(+0.581%)
 
|TBD
 
|TBD
  
Line 374: Line 374:
 
|-valign="top"
 
|-valign="top"
 
|Species, J-Values, and COLUMN AOD values that changed by 10% or more at the '''surface''':
 
|Species, J-Values, and COLUMN AOD values that changed by 10% or more at the '''surface''':
|TBD
+
|
 +
* Aerosols: NH4 NIT SO4 HMS BCPI BCPO OCPI OCPO Complex_SOA Simple_SOA AERI BrSALA BrSALC ISALA ISALC NITs SALAAL SALACL SALCAL SO4s
 +
* Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
 +
* Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
 +
* Iodine: Iy IxOy I I2 IBr ICl IO IONO IONO2 CH2I2 HI HOI OIO
 +
* Nitrogen: NOy HNO2 HNO3 MPAN NIT NO NO3 N2O5 MPN NHx NH3 NH4 MENO3 ETNO3 AONITA ETHN NPHEN
 +
* Oxidants: O3 OH
 +
* Primary_Organics: ISOP MTPA MTPO LIMO C2H4 PRPE XYLE
 +
* ROy: O1D OH RO2
 +
* Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOA3 ASOA1 ASOA2 ASOA3 ASOAN TSOG1 TSOG2 TSOG3 ASOG1 ASOG2 ASOG3 INDIOL LVOCOA SOAIE SOAGX SOAS
 +
* Secondary_Organics: ACTA ALD2 HPALDs MACR ACET HAC MVK ISOPN PHEN RCHO ETHP MP
 +
* Sulfur: SOx DMS HMS MSA SO2 SO4
 +
* J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Br2 CH2Cl2 CH3Br CH3CCl3 CH3Cl H1301 HCFC123 HCFC141b HCFC142b HCFC22 N2O NO O2 OCS
 +
* Column AOD: OCPI SO4 SOA_from_Aqueous_ISOP Total
 
|TBD
 
|TBD
  
 
|-valign="top"
 
|-valign="top"
 
|Species and J-Values that changed by 10% or more at '''500 hPa''':
 
|Species and J-Values that changed by 10% or more at '''500 hPa''':
|TBD
+
|
 +
* Aerosols: DST4 NIT SO4 HMS BCPO OCPO BrSALA BrSALC SALAAL SALACL SALC SALCAL SALCCL SO4s
 +
* Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
 +
* Chlorine: ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl OClO
 +
* Iodine: IxOy I I2 IBr ICl CH2I2 HI OIO
 +
* Nitrogen: MPAN NIT NO NO3 NH3
 +
* Oxidants: OH
 +
* Primary_Organics: ISOP MTPA MTPO LIMO C2H4 TOLU XYLE
 +
* ROy: OH RO2
 +
* Secondary_Organic_Aerosols: SOAIE SOAGX
 +
* Secondary_Organics: ALD2 BALD HPALDs MACR IEPOX MVK ISOPN GLYC GLYX PHEN RCHO ETHP
 +
* Sulfur: DMS HMS SO4
 
|TBD
 
|TBD
  
 
|-valign="top"
 
|-valign="top"
 
|Species and J-Values that changed by 10% or more in '''zonal mean''':
 
|Species and J-Values that changed by 10% or more in '''zonal mean''':
|TBD
+
|
 +
* Aerosols: DST3 NH4 NIT SO4 HMS BCPI BCPO OCPI OCPO Complex_SOA Simple_SOA AERI BrSALA BrSALC NITs SALAAL SALACL SALCAL SALCCL SO4s
 +
* Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
 +
* Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
 +
* Iodine: IxOy I IBr ICl IONO CH2I2 CH2IBr OIO
 +
* Nitrogen: HNO3 MPAN NIT NO NO3 N2O5 NHx NH3 NH4 ETHN BZPAN NPHEN
 +
* Oxidants: O3
 +
* Primary_Organics: ISOP MTPA MTPO LIMO C2H4 PRPE TOLU XYLE
 +
* ROy: O1D RO2
 +
* Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOA3 ASOA1 ASOA2 ASOA3 ASOAN INDIOL LVOCOA SOAIE SOAGX SOAS
 +
* Secondary_Organics: BALD HPALDs MACR IEPOX ACET MEK MVK ISOPN GLYC RCHO ETHP MP
 +
* Sulfur: SOx HMS MSA SO2 SO4
 +
* J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Cl2 CH3Br CH3CCl3 CH3Cl HCFC123 HCFC141b HCFC142b HCFC22 N2O O2 OCS
 
|TBD
 
|TBD
  
 
|-valign="top"
 
|-valign="top"
 
|'''Emissions''' that changed by 10% or more:
 
|'''Emissions''' that changed by 10% or more:
|TBD
+
|
 +
* Aircraft: ALK4 C2H6 C3H8 MACR PRPE RCHO
 +
* Fert: NO
 +
* Ocean: ACET ALD2 DMS ETNO3 MENO3 MOH
 +
* Ship: NO2 NO O3
 +
* Soil: NO
 +
* Total: ACET ALD2 BENZ C2H2 C2H4 MACR MOH NO RCHO TOLU XYLE
 +
* VolcErupt: SO2
 
|TBD
 
|TBD
  

Revision as of 20:40, 25 January 2022

GEOS-Chem Versions Page

This page includes information about GEOS-Chem 13.4.0 (currently under development)

Version overview

The following items have been added to GEOS-Chem 13.4.0 since the last GEOS-Chem version GEOS-Chem 13.3.4. Also see the following Github pages:

Feature Contributor(s) Model scope Notes and references
Updates that will affect full-chemistry benchmark simulations
Migrating sulfate chemistry into KPP Mike Long (GCST)
Viral Shah (Harvard)
Bob Yantosca (GCST)
Chemistry &
Structural
Fix bug in Henry law CALC_HEFF routine in hetchem computations Viral Shah (Harvard) Chemistry
Bug fix: Remove double-counting of HCl uptake on acidic sea salt Viral Shah (Harvard) Chemistry
Update surface resistance for ozone deposition to ice/snow Ryan Pound (York)
Shuting Zhai (UW)
Drydep
Use updated definition of PM2.5; Add PM10 diagnostic Bob Yantosca (GCST) Diagnostics &
Benchmarking
Fix scale factors applied to VOC aircraft emissions in AEIC inventory Flavio Quadros (TU Delft)
Seb Eastham (GCST)
Emissions &
Bug Fix
HEMCO bug fix: restore archiving via manual diagnostics (which had been inadvertently disabled in a prior update) Melissa Sulprizio (GCST)
Bob Yantosca (GCST)
Emissions
Use degassing-only volcano emissions in GEOS-Chem benchmark simulations Christoph Keller (GMAO)
Daniel Jacob (Harvard)
Emissions &
Benchmarking
Add option for driving GEOS-Chem with native GEOS meteorological files Liam Bindle (GCST) Structural
Updates that will NOT affect full-chemistry benchmark simulations
Updated Hg chemistry in KPP Viral Shah (Harvard)
Colin Thackray (Harvard)
Mike Long (GCST)
Bob Yantosca (GCST)
Chemistry
Bug fix: Use REAL*8 precision in for CH3O2 + OH reaction definition in fullchem.eqn Bob Yantosca (GCST) Chemistry
Updated Global Inventory of Methane Emissions from Oil/Gas/Coal (GFEI v2) Tia Scarpelli (U. Edinburgh) Emissions
Anthropogenic Methane Emission Inventory for Canada Tia Scarpelli (U. Edinburgh) Emissions
Use EDGARv6 global anthro emissions for CH4 simulation Melissa Sulprizio (GCST) Emissions
Updated Rn-222 emissions for TransportTracers simulations Bo Zhang (NIA) Emissions
Retire HEMCO extension for CH4 wetland emissions Melissa Sulprizio (GCST) Emissions
Updates to enable automated run directory creation Liam Bindle (GCST)
Melissa Sulprizio (GCST)
Run directory
Bug fix: Allow GEOS-Chem Classic History to archive irregular intervals (e.g. a month and a day) Bob Yantosca (GCST) Diagnostics
Updates for running GEOS-Chem within GEOS Christoph Keller (GMAO)
Lizzie Lundgren (GCST)
GEOS
Updates that will only affect GCHP
Add capability to use mass fluxes in advection Sebastian Eastham (MIT)
Liam Bindle (GCST)
Advection
Define a GCHP "Default" diagnostic collection that will archive a small number of commonly-requested diagnostic fields Liam Bindle (GCST) Structural
Add capability to read native meteorological data files Liam Bindle (GCST)
Bob Yantosca (GCST)
Structural

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 Needed for What was added? Directory
ZHANG_Rn222 TransportTracers simulations only Updated Rn222 emissions for TransportTracers simulations. See Bo Zhang et al (2021) HEMCO/ZHANG_Rn222/v2021-11
Updated Hg simulation restart file Hg simulations only Sample restart file for the updated Hg mechanism. See Viral Shah et al (2021) ExtData/GEOSCHEM_RESTARTS/v2021-12
Updated TOMAS simulation restart files TOMAS simulations only Added HSO3m and SO3mm species to TOMAS restart files ExtData/GEOSCHEM_RESTARTS/v2021-12

1-month benchmarks

Model setup for 1-month benchmarks

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

Git tag(s):
Compared to previous benchmark: 13.3.0
Software environment: gcc 10.2.0
OpenMPI 4.1.0
netcdf-fortran 4.5.3
CMake 3.17.3
ESMF 8.0.1
Model resolution:
  • GEOS-Chem Classic: 4° x 5°
  • GCHP: c48
Meteorology fields: MERRA-2
  • GEOS-Chem Classic: 4° x 5°
  • GCHP: 0.5° x 0.625°
Initial conditions: July 1, 2019
  • NOTE: GCHP c48 restart file regridded from GEOS-Chem Classic 4° x 5°
Benchmark month: July 2019
Emissions setup: TBD
Chemistry mechanism: TBD
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):
    • Diagnostics
    • CH4 simulation
    • TransportTracers simulation
    • Run directory creation scripts

1-month fullchem: GEOS-Chem Classic 13.4.0-rc.0 vs 13.3.0

NOTES:

  • Enable PDF bookmarks in the file links to navigate between species. If you do not see bookmarks in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.
  • See the species database for species definitions and details.
  • Species categories and lumped species are defined in YAML files within the GEOS-Chem post-processing software GCPy.

TBD

Benchmark assessment form

Performance GEOS-Chem Classic (rc.0) GCHP (rc.0)
Grid resolution: 4° x 5° C48
# CPUs, nodes: 48 CPUs
1 node (Intel Cascade Lake)
48 CPUs
2 nodes (Intel Cascade Lake)
Wall time: 03:37:13 06:20:26
CPU time / wall time: 31.79 95.0732
% of ideal performance: 66.23% 99.03%
Memory: 11.4128 GB 108.5 GB
Global mean OH:
(% change from previous version)
11.70790814279 x 105 molec/cm3
(-0.329%)
TBD
Methyl chloroform lifetime:
(% change from previous version)
5.294530 years
(+0.557%)
TBD
Methane lifetime:
(% change from previous version)
8.923431 years
(+0.581%)
TBD
Details
Species, J-Values, and COLUMN AOD values that changed by 10% or more at the surface:
  • Aerosols: NH4 NIT SO4 HMS BCPI BCPO OCPI OCPO Complex_SOA Simple_SOA AERI BrSALA BrSALC ISALA ISALC NITs SALAAL SALACL SALCAL SO4s
  • Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
  • Iodine: Iy IxOy I I2 IBr ICl IO IONO IONO2 CH2I2 HI HOI OIO
  • Nitrogen: NOy HNO2 HNO3 MPAN NIT NO NO3 N2O5 MPN NHx NH3 NH4 MENO3 ETNO3 AONITA ETHN NPHEN
  • Oxidants: O3 OH
  • Primary_Organics: ISOP MTPA MTPO LIMO C2H4 PRPE XYLE
  • ROy: O1D OH RO2
  • Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOA3 ASOA1 ASOA2 ASOA3 ASOAN TSOG1 TSOG2 TSOG3 ASOG1 ASOG2 ASOG3 INDIOL LVOCOA SOAIE SOAGX SOAS
  • Secondary_Organics: ACTA ALD2 HPALDs MACR ACET HAC MVK ISOPN PHEN RCHO ETHP MP
  • Sulfur: SOx DMS HMS MSA SO2 SO4
  • J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Br2 CH2Cl2 CH3Br CH3CCl3 CH3Cl H1301 HCFC123 HCFC141b HCFC142b HCFC22 N2O NO O2 OCS
  • Column AOD: OCPI SO4 SOA_from_Aqueous_ISOP Total
TBD
Species and J-Values that changed by 10% or more at 500 hPa:
  • Aerosols: DST4 NIT SO4 HMS BCPO OCPO BrSALA BrSALC SALAAL SALACL SALC SALCAL SALCCL SO4s
  • Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
  • Chlorine: ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl OClO
  • Iodine: IxOy I I2 IBr ICl CH2I2 HI OIO
  • Nitrogen: MPAN NIT NO NO3 NH3
  • Oxidants: OH
  • Primary_Organics: ISOP MTPA MTPO LIMO C2H4 TOLU XYLE
  • ROy: OH RO2
  • Secondary_Organic_Aerosols: SOAIE SOAGX
  • Secondary_Organics: ALD2 BALD HPALDs MACR IEPOX MVK ISOPN GLYC GLYX PHEN RCHO ETHP
  • Sulfur: DMS HMS SO4
TBD
Species and J-Values that changed by 10% or more in zonal mean:
  • Aerosols: DST3 NH4 NIT SO4 HMS BCPI BCPO OCPI OCPO Complex_SOA Simple_SOA AERI BrSALA BrSALC NITs SALAAL SALACL SALCAL SALCCL SO4s
  • Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
  • Iodine: IxOy I IBr ICl IONO CH2I2 CH2IBr OIO
  • Nitrogen: HNO3 MPAN NIT NO NO3 N2O5 NHx NH3 NH4 ETHN BZPAN NPHEN
  • Oxidants: O3
  • Primary_Organics: ISOP MTPA MTPO LIMO C2H4 PRPE TOLU XYLE
  • ROy: O1D RO2
  • Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOA3 ASOA1 ASOA2 ASOA3 ASOAN INDIOL LVOCOA SOAIE SOAGX SOAS
  • Secondary_Organics: BALD HPALDs MACR IEPOX ACET MEK MVK ISOPN GLYC RCHO ETHP MP
  • Sulfur: SOx HMS MSA SO2 SO4
  • J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Cl2 CH3Br CH3CCl3 CH3Cl HCFC123 HCFC141b HCFC142b HCFC22 N2O O2 OCS
TBD
Emissions that changed by 10% or more:
  • Aircraft: ALK4 C2H6 C3H8 MACR PRPE RCHO
  • Fert: NO
  • Ocean: ACET ALD2 DMS ETNO3 MENO3 MOH
  • Ship: NO2 NO O3
  • Soil: NO
  • Total: ACET ALD2 BENZ C2H2 C2H4 MACR MOH NO RCHO TOLU XYLE
  • VolcErupt: SO2
TBD
Overview
Below we summarize the notable changes caused by specific updates. Supplementary plots may be viewed at http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/13.4.0/.

1. Migrating sulfate chemistry into KPP

TBD

2. Fix bug in Henry law CALC_HEFF routine in hetchem computations

TBD

3. Fix scale factors applied to VOC aircraft emissions in AEIC inventory

TBD

4. Bug fix: Remove double-counting of HCl uptake on acidic sea salt

TBD

5. Update surface resistance for ozone deposition to ice/snow

TBD

6. Use updated definition of PM2.5; Add PM10 diagnostic

TBD

7. HEMCO bug fix: restore archiving via manual diagnostics (which had been inadvertently disabled in a prior update)

TBD

8. Use degassing-only volcano emissions in GEOS-Chem benchmark simulations

TBD

9. Add option for driving GEOS-Chem & GCHP with native GEOS meteorological files

TBD

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

TBD


The following were zero-difference updates:

  1. GCHP-specific updates:
  2. CH4 simulation updates:
  3. Hg simulation updates:
  4. TransportTracers simulation updates:
  5. Other updates:
Approval
Requires further investigation:
Approved by:
Date of approval: