Difference between revisions of "GEOS-Chem 13.4.0"
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'''''3. [https://github.com/geoschem/geos-chem/pull/1067 Fix scale factors applied to VOC aircraft emissions in AEIC inventory]''''' | '''''3. [https://github.com/geoschem/geos-chem/pull/1067 Fix scale factors applied to VOC aircraft emissions in AEIC inventory]''''' | ||
− | <blockquote>The updated scale factors, which corrected the conversion from atoms C to kg species, resulted in significant decreases in emissions for VOC species. This was observed mostly in the northern | + | <blockquote>The updated scale factors, which corrected the conversion from atoms C to kg species, resulted in significant decreases in emissions for VOC species. This was observed mostly in the northern hemisphere and up to the lower stratosphere (where most aircraft emissions occur).</blockquote> |
################################################################################### | ################################################################################### | ||
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AEIC RCHO : 0.001384 0.003358 0.001974 142.621 | AEIC RCHO : 0.001384 0.003358 0.001974 142.621 | ||
− | <blockquote>However, this update resulted in minimal changes to global quantities, as VOC aircraft emissions are typically less than 1Gg for the simulation month. | + | <blockquote>However, this update resulted in minimal changes to global quantities, as VOC aircraft emissions are typically less than 1Gg for the simulation month. |
+ | |||
+ | Other changes in benchmark output related to this update are: | ||
* Very small changes in oxidants (too small to show up in ratio plots). | * Very small changes in oxidants (too small to show up in ratio plots). | ||
* Slight change in most primary organics, but % differences are of order 1e-4 or 1e-5. | * Slight change in most primary organics, but % differences are of order 1e-4 or 1e-5. | ||
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'''''4. [https://github.com/geoschem/geos-chem/issues/1034 Bug fix: Remove double-counting of HCl uptake on acidic sea salt]''''' | '''''4. [https://github.com/geoschem/geos-chem/issues/1034 Bug fix: Remove double-counting of HCl uptake on acidic sea salt]''''' | ||
− | <blockquote> | + | <blockquote>Changes in benchmark output related to this update are: |
− | + | ||
− | + | ||
*As expected, chlorine species concentrations decrease in the southern latitudes (esp. at about 40S), where there is more sea salt (and now less removal of HCl due to the bug fix). | *As expected, chlorine species concentrations decrease in the southern latitudes (esp. at about 40S), where there is more sea salt (and now less removal of HCl due to the bug fix). | ||
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<blockquote>Barten et.al 2021 (https://doi.org/10.5194/acp-21-10229-2021) increased the surface resistance of ozone dry deposition to snow and ice to 1E4 s m−1, this results in a reduction of ozone deposition velocity to ice of <= 0.01 cm s−1 (~ 66% reduction) which has better agreement with observations and results in improved comparison between Ozone observations in the arctic. | <blockquote>Barten et.al 2021 (https://doi.org/10.5194/acp-21-10229-2021) increased the surface resistance of ozone dry deposition to snow and ice to 1E4 s m−1, this results in a reduction of ozone deposition velocity to ice of <= 0.01 cm s−1 (~ 66% reduction) which has better agreement with observations and results in improved comparison between Ozone observations in the arctic. | ||
− | + | Changes in benchmark output related to this update are: | |
*Increase in O3 concentration at the summer polar latitudes (i.e. deposition to ice/snow is suppressed); | *Increase in O3 concentration at the summer polar latitudes (i.e. deposition to ice/snow is suppressed); | ||
*Minor change in other oxidants; | *Minor change in other oxidants; | ||
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<span style="color:red">SO2 Total : 9.325534 9.224471 -0.101063 -1.084</span> | <span style="color:red">SO2 Total : 9.325534 9.224471 -0.101063 -1.084</span> | ||
+ | <blockquote>Other changes in benchmark output related to this update are: | ||
+ | *OH metrics show very small change; | ||
+ | *SO2 mass changes by -9%, SO4 by -4.6%, NIT by +4.3%, NH3 by +1.5%, NH4 by -1.1%. | ||
+ | *Some gas phase species show corresponding mass changes (e.g.ITCN & ITHN, +1.3%, KO2, -0.49%, MCHRN ; 5 S+0.8; *Other species mass change typically by +/- 0.5%; | ||
+ | *Minor decreases in SOx concentration at surface observed over SA, Africa, Indonesia, Australia. | ||
+ | </blockquote> | ||
'''''8. [https://github.com/geoschem/geos-chem/pull/945 Add option for driving GEOS-Chem & GCHP with native GEOS meteorological files]''''' | '''''8. [https://github.com/geoschem/geos-chem/pull/945 Add option for driving GEOS-Chem & GCHP with native GEOS meteorological files]''''' |
Revision as of 21:31, 25 January 2022
This page includes information about GEOS-Chem 13.4.0 (currently under development)
Contents
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:
- 13.4.0 milestone for geoschem/geos-chem
- 13.4.0 milestone for geoschem/GCHP
- 3.4.0 milestone for geoschem/HEMCO
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: |
|
Meteorology fields: | MERRA-2
|
Initial conditions: | July 1, 2019
|
Benchmark month: | July 2019 |
Emissions setup: | TBD |
Chemistry mechanism: | TBD |
This version will impact: (select all that apply with boldface) |
|
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: | GEOS-Chem Classic 13.4.0-rc.1 vs. 13.3.0-rc.0 |
TBD | ||
Species and J-Values that changed by 10% or more at 500 hPa: | GEOS-Chem Classic 13.4.0-rc.1 vs. 13.3.0-rc.0 |
TBD | ||
Species and J-Values that changed by 10% or more in zonal mean: | GEOS-Chem Classic 13.4.0-rc.1 vs. 13.3.0-rc.0 |
TBD | ||
Emissions that changed by 10% or more: | GEOS-Chem Classic 13.4.0-rc.1 vs. 13.3.0-rc.0 |
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 The updated scale factors, which corrected the conversion from atoms C to kg species, resulted in significant decreases in emissions for VOC species. This was observed mostly in the northern hemisphere and up to the lower stratosphere (where most aircraft emissions occur). ################################################################################### ### Emissions totals for inventory AEIC [Tg] ### ### Ref = GCC_13.3.0-rc.1; Dev = GCC_13.4.0-rc.0 ### ################################################################################### Ref Dev Dev - Ref % diff AEIC ACET : 0.000139 0.000086 -0.000053 -38.027 AEIC ALD2 : 0.001829 0.000996 -0.000833 -45.529 AEIC ALK4 : 0.005617 0.004274 -0.001343 -23.912 AEIC C2H6 : 0.000152 0.000122 -0.000031 -20.213 AEIC C3H8 : 0.000022 0.000018 -0.000004 -18.386 AEIC MACR : 0.001827 0.000100 -0.001727 -94.522 AEIC PRPE : 0.004855 0.003779 -0.001076 -22.168 AEIC RCHO : 0.001384 0.003358 0.001974 142.621 However, this update resulted in minimal changes to global quantities, as VOC aircraft emissions are typically less than 1Gg for the simulation month. 4. Bug fix: Remove double-counting of HCl uptake on acidic sea salt Changes in benchmark output related to this update are: 5. Update surface resistance for ozone deposition to ice/snow Barten et.al 2021 (https://doi.org/10.5194/acp-21-10229-2021) increased the surface resistance of ozone dry deposition to snow and ice to 1E4 s m−1, this results in a reduction of ozone deposition velocity to ice of <= 0.01 cm s−1 (~ 66% reduction) which has better agreement with observations and results in improved comparison between Ozone observations in the arctic. This update causes the fer 7. Use degassing-only volcano emissions in GEOS-Chem benchmark simulations This update causes a -1% reduction in the amount of SO2 that is emitted to the atmosphere: ################################################################################### ### Emissions totals for species SO2 [Tg] ### ### Ref = GCC_13.3.0-rc.1; Dev = GCC_13.4.0-rc.0 ### ################################################################################### Ref Dev Dev - Ref % diff SO2 Aircraft : 0.019036 0.019036 0.000000 0.000 SO2 Anthro : 5.872509 5.872509 0.000000 0.000 SO2 BioBurn : 0.555350 0.555350 0.000000 0.000 SO2 Ship : 0.951114 0.951114 0.000000 0.000 SO2 VolcDegas : 1.826465 1.826465 0.000000 0.000 SO2 VolcErupt : 0.101063 0.000000 -0.101063 -100.000 ----------------------------------------------------------------------------------- SO2 Total : 9.325534 9.224471 -0.101063 -1.084 Other changes in benchmark output related to this update are: 8. 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:
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Approval | ||||
Requires further investigation: | ||||
Approved by: | ||||
Date of approval: |