GEOS-Chem 12: Difference between revisions
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Revision as of 21:45, 4 August 2020
GEOS-Chem Main Page | GCHP Main Page
Version history summary
| Past releases | Current release: GEOS-Chem 12.9.2 | Future releases |
The sections below describe each GEOS-Chem feature version and GEOS-Chem bug fix patch version belonging to the GEOS-Chem 12 series. Each feature version carries the tag 12.Y.0, which indicates that the version will be (or has been) validated with a 1-month benchmark simulation (and one or more 1-year benchmark simulations if necessary). Each patch version carries the tag 12.Y.Z, which denotes that the version preserves backwards-compatibility with the prior feature version 12.Y.0. For more information, please see our GEOS-Chem version numbering system wiki page.
Several GEOS-Chem updates have been proposed by the relevant Working Groups, but have not yet been assigned to a specific GEOS-Chem version. For a complete list of these updates, please visit our GEOS-Chem model development priorities wiki page.
Current versions in development
The GEOS-Chem versions listed below are currently under development.
12.9.3
This version contains additional fixes for bugs and technical issues discovered after the release of 12.9.2.
| Feature | Submitted by | Type | Notes and References |
|---|---|---|---|
| Updates that WILL NOT AFFECT the full-chemistry simulation | |||
| Fix to make HEMCO properly read vertical coordinates for data on arbitrary vertical grids | Lyssa Freese (MIT) Haipeng Lin (Harvard) Bob Yantosca (GCST) |
Bug fix |
|
| Bug fix for planeflight diagnostic: Change parameter definition MAXAN=15 to MAXAN=20 | Jenny Fisher (Wollongong) Bob Yantosca (GCST) |
Bug fix | |
| Fix additional typos in GEOS-Chem species database | Thibaud Fritz (MIT) Bob Yantosca (GCST) |
Bug fix |
|
13.0.0
Please see our GEOS-Chem 13 wiki page.
Current stable version
The GEOS-Chem version listed below is considered stable and can be used to start a new research project. This version corresponds to the master branch of the GEOS-Chem source code repository on Github.
NOTE: In GEOS-Chem 13.0.0 and later versions, the master branch will be renamed to main.
Each released version of GEOS-Chem will be assigned a unique Digital Object Identifier (DOI). This will allow you to cite each GEOS-Chem version in publications. We also have obtained a "Concept DOI", which will always point to the current stable version of GEOS-Chem: DOI 10.5281/zenodo.1343546. This can be convenient if you wish to cite GEOS-Chem without making reference to a particular version.
12.9.2
This version was released on 24 Jul 2020.
This version contains additional fixes for bugs and technical issues discovered during the 12.9.0 benchmarking process.
You can use the following Git commands to download the GEOS-Chem 12.9.2 source code and GEOS-Chem Unit Tester package.
NOTE: In GEOS-Chem 13.0.0 and later versions, run directory generation will be moved to the GEOS-Chem source code repository. The Unit Tester repository will be retired.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.9.2 cd Code.12.9.2 # Create and checkout a new branch "GC_12.9.2" at the tag "12.9.2" git checkout -b GC_12.9.2 12.9.2 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.9.2" at the tag "12.9.2" git checkout -b GC_12.9.2+GFAS_fix 12.9.2
| Feature | Submitted by | Type | Notes and References |
|---|---|---|---|
| Updates that WILL NOT AFFECT the full-chemistry simulation | |||
| Bug fixes for the CO2 and tagged CO2 simulations: | Monika Szelag (Finnish Met. Inst.) Xuyan Yue (U. New South Wales) Bob Yantosca (GCST) |
Bug fix | |
| Add OPOA to PM2.5 definition in complexSOA_SVPOA simulations | Maggie Marvin (Edinburgh) Aerosols Working Group Bob Yantosca (GCST) |
Bug fix |
|
| Bug fix for dry-run issues in 12.9.0+ | Lee Murray (Rochester) Bob Yantosca (GCST) |
Bug fix | |
| Prevent negative values in the computation of FNO_NOx in PARANOX | Tina Liu (Harvard) Eimy Bonilla (Harvard) Bob Yantosca (GCST) |
Bug fix |
|
--Bob Yantosca (talk) 16:21, 24 July 2020 (UTC)
Previously released stable versions
We list below past releases of GEOS-Chem. But we recommend that you always download the current stable version listed above when starting a new research project.
12.9.1
This version was released on 17 Jul 2020.
You can use the following Git commands to download the GEOS-Chem 12.9.1 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.9.1 cd Code.12.9.1 # Create and checkout a new branch "GC_12.9.1" at the tag "12.9.1" git checkout -b GC_12.9.1 12.9.1 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.9.1" at the tag "12.9.1" git checkout -b GC_12.9.1 12.9.1
Important: Make sure you also download the new data directories for this version and for version 12.9.0.
This version contains fixes for bugs and technical issues discovered during the 12.9.0 benchmarking process.
| Feature | Submitted by | Type | Notes and References |
|---|---|---|---|
| Updates that WILL NOT AFFECT the full-chemistry simulation | |||
| Bug fix: Fixed a lingering issue that caused the GEOS-Chem dry-run not to recognize missing files | Bob Yantosca (GCST) | Bug fix | |
| Fix run-time error when optional Luo wet deposition scheme is turned on | Lizzie Lundgren (GCST) | Bug fix | |
| Fixes for interpolating RCP emissions data via HEMCO | Jenny Fisher (Wollongong) Melissa Sulprizio (GCST) Bob Yantosca (GCST) |
Bug fix |
|
New data directories in 12.9.1
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 |
|---|---|---|---|
| RCP | OPTIONAL | Fixes for interpolating RCP emissions data via HEMCO | HEMCO/RCP/v2020-07/ |
12.9.0
This version was released on 17 Jul 2020.
You can use the following Git commands to download the GEOS-Chem 12.9.0 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.9.0 cd Code.12.9.0 # Create and checkout a new branch "GC_12.9.0" at the tag "12.9.0" git checkout -b GC_12.9.0 12.9.0 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.9.0" at the tag "12.9.0" git checkout -b GC_12.9.0 12.9.0
Important: Make sure you also download the new data directories for this version.
Please see the following links for complete information about the validation of GEOS-Chem 12.9.0:
- 1-month benchmark for GEOS-Chem Classic
- 1-month benchmark for GCHP
- 1-year full-chemistry benchmark for GEOS-Chem Classic
| Feature | Submitted by | Type | Notes and References |
|---|---|---|---|
| Updates that WILL AFFECT the full-chemistry simulation | |||
| Updated halogen chemistry | Xuan Wang (Harvard) | Science | |
| Improved cloudwater pH | Viral Shah (Harvard) Jonathan Moch (Harvard) |
Science | |
| Update offline lightning data through Dec 2019 | Lee Murray (Rochester) | Science | |
| Convert GEOS-Chem species database to YAML format, includes: | Melissa Sulprizio (GCST) Bob Yantosca (GCST) |
Structural | |
| Update GEOS-Chem core to apply masking and scaling to HEMCO inputs | Lizzie Lundgren (GCST) | Structural |
|
| Bug fix: Restore missing photolysis reactions from 12.8.0 and add an extra error check | Melissa Sulprizio (GCST) | Bug fix | |
| Bug fix: remove inefficient code that was slowing down computation of heterogenous chemistry rates | Bob Yantosca (GCST) | Bug fix |
|
| Updates that WILL NOT AFFECT the full-chemistry simulation | |||
| Corrected issue in GEOS-Chem dry-run where some files were not being properly marked for download | Bob Yantosca (GCST) | Bug fix | |
| Bug fixes for the ObsPack diagnostic: | Bob Yantosca (GCST) | Bug fix | |
| Fixes for reading meteorology fields in HEMCO: | Melissa Sulprizio (GCST) | Bug fix | |
| Restore missing metadata for satellite timeseries diagnostics | Melissa Sulprizio (GCST) | Bug fix | |
| Fix bug compiling with Luo wet deposition scheme option | Lizzie Lundgren (GCST) | Bug fix | |
| Updates that affect GCHP only | |||
| Fix bug where non-advected species not updated in restart file | Sebastian Eastham (MIT) | Bug fix | |
New data directories in 12.9.0
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 |
|---|---|---|---|
| OFFLINE_LIGHTNING | DEFAULT (full-chemistry simulations) |
Update offline lightning data through Dec 2019 | HEMCO/OFFLINE_LIGHTNING/v2020-03/ |
12.8.2
This version was released on 27 May 2020.
GEOS-Chem 12.8.2 contains minor fixes, as well as structural changes needed for WRF-GC development.
| Feature | Submitted by | Type | Notes and References |
|---|---|---|---|
| Updates that WILL NOT AFFECT the full-chemistry simulation | |||
| Bug fix: Set version numbers to 12.8.2 in CMakeLists.txt and gc_classic_version.H | Bob Yantosca (GCST) | Bug fix | |
| Updates to facilitate WRF-GC development: | Haipeng Lin (Harvard) | Structural | |
12.8.1
This version was released on 21 May 2020.
GEOS-Chem 12.8.1 fixes several issues that were discovered during and after the 12.8.0 benchmarking process.
You can use the following Git commands to download the GEOS-Chem 12.8.1 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.8.1 cd Code.12.8.1 # Create and checkout a new branch "GC_12.8.1" at the tag "12.8.1" git checkout -b GC_12.8.1 12.8.1 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.8.1" at the tag "12.8.1" git checkout -b GC_12.8.1 12.8.1
For GCHP users only: Make sure you also download the new data directories for this version.
New or updated data directories in 12.8.1
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 |
|---|---|---|---|
| OFFLINE_BIOVOC | Default | Update time dimension attribute to reflect current day in late December and early January for all GEOS-FP and MERRA2 years. This update impacts only GCHP. | HEMCO/OFFLINE_BIOVOC/v2019-10
|
12.8.0
This version was released on 04 May 2020.
You can use the following Git commands to download the GEOS-Chem 12.8.0 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.8.0 cd Code.12.8.0 # Create and checkout a new branch "GC_12.8.0" at the tag "12.8.0" git checkout -b GC_12.8.0 12.8.0 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.8.0" at the tag "12.8.0" git checkout -b GC_12.8.0 12.8.0
Important: Make sure you also download the new data directories for this version.
Please see the following links for complete information about the validation of GEOS-Chem 12.8.0:
- 1-month benchmark for GEOS-Chem Classic
- 1-month benchmark for GCHP
- 1-year transport tracer benchmark for GEOS-Chem Classic
- 1-year full-chemistry benchmark for GEOS-Chem Classic
| Feature | Submitted by | Type | Notes and References |
|---|---|---|---|
| Features affecting the full-chemistry simulation: | |||
| Isoprene chemistry | Kelvin Bates (Harvard) | Science | |
| Wet deposition parameterization | Kelvin Bates (Harvard) Sarah Safieddine (MIT) |
Science | |
| Ozone deposition to the ocean | Ryan Pound (York) Mat Evans (York) |
Science | |
| Use online DustDead, MEGAN, SeaSalt, and SoilNOx emissions for benchmark simulations | Melissa Sulprizio (GCST) | Science |
|
| Shift CMIP6 time from middle to start of month to allow start in January | Lizzie Lundgren (GCST) | Bug fix | |
| Features NOT affecting the full-chemistry simulation: | |||
| GFED 4.1s beta emissions for 2017-2019 | Maggie Marvin (U. Edinburgh) | Science | |
| Replace State_Chm%nAero with State_Chm%nAeroSpc and State_Chm%nAeroType | Seb Eastham (MIT) Bob Yantosca (GCST) |
Structural | |
| Convert all files in GeosCore, GeosUtil, and Headers to .F90 | Melissa Sulprizio (GCST) | Structural | |
| Change GEOS-Chem timers from a CPP switch to an option in input.geos | Melissa Sulprizio (GCST) | Structural | |
| Remove potential for surface CH4 retrieval error in SET_CH4 due to reliance on HEMCO emissions year | Christoph Keller (GMAO) | Bug fix | |
| Features affecting GCHP only: | |||
| Fix leap year handling bug in GCHP multi-run script | Lizzie Lundgren (Harvard) | Bug Fix | |
| Fix SH surface ozone bias | Sebastian Eastham (MIT) Lizzie Lundgren (Harvard) |
Bug Fix | |
New data directories in 12.8.0
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 |
|---|---|---|---|
| CMIP6 | DEFAULT (UCX-based simulations) |
Shift time values from middle of month to start of month | HEMCO/CMIP6/v2020-03 |
| OCEAN_O3_DRYDEP | DEFAULT | Ozone deposition to the ocean | HEMCO/OCEAN_O3_DRYDEP/v2020-02 |
| GFED4 | DEFAULT | GFED 4.1s beta emissions for 2017-2019 (previous years are unchanged from GFED4/v2015-10) | HEMCO/GFED4/v2020-02 |
12.7.2
This version was released on 09 Mar 2020.
You can use the following Git commands to download the GEOS-Chem 12.7.2 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.7.2 cd Code.12.7.2 # Create and checkout a new branch "GC_12.7.2" at the tag "12.7.2" git checkout -b GC_12.7.2 12.7.2 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.7.2" at the tag "12.7.2" git checkout -b GC_12.7.2 12.7.2
Important: Make sure you also download the new data directories for this version.
This version fixed several minor issues identified during the 12.7.0 benchmarking process.
| Feature | Submitted by | Type | Notes and References |
|---|---|---|---|
| Features affecting the full-chemistry simulation: | |||
Restrict wet scavenging to troposphere in Luo et al 2019 wetdep scheme
|
Gan Luo (Albany) Transport Working Group Bob Yantosca (GCST) |
Bug fix | |
| Bug fix for reading 3-hourly boundary condition files after hour 21 | Melissa Sulprizio (GCST) | Bug fix | |
| Remove unused routines in regrid_a2a_mod.F90 | Haipeng Lin (Harvard) | Structural | |
| Features affecting the GCHP only: | |||
Fix pointer retrieval error in SET_CH4 introduced in 12.7.0 when running at c180+
|
Lizzie Lundgren (GCST) | Bug fix | |
| Use new Ordonez files to avoid error in MAPL when running at c360 | Lizzie Lundgren (GCST) | Bug fix | |
New data directories in 12.7.2
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 |
|---|---|---|---|
| IODINE | Default (GCHP) | Shifted latitude range | HEMCO/IODINE/v2020-02 |
12.7.1
This version was released on 19 Feb 2020.
You can use the following Git commands to download the GEOS-Chem 12.7.1 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.7.1 cd Code.12.7.1 # Create and checkout a new branch "GC_12.7.1" at the tag "12.7.1" git checkout -b GC_12.7.1 12.7.1 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.7.1" at the tag "12.7.1" git checkout -b GC_12.7.1 12.7.1
Important: Make sure you also download the new data directories for this version.
This version fixed several minor issues identified during the 12.7.0 benchmarking process.
New data directories in 12.7.1
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 |
|---|---|---|---|
| MEGAN | Default (GCHP) | Changed seconds string in time dimension units attribute from '0.0' to '00' | HEMCO/MEGAN/v2020-02 |
12.7.0
This version was released on 03 Feb 2020.
You can use the following Git commands to download the GEOS-Chem 12.7.0 source code and 12.7.0 GEOS-Chem Unit Tester package.
You can also use our GEOS-Chem 12.7.0 tutorial AMI to initialize your Amazon Web Services cloud instance with a pre-compiled GEOS-Chem 12.7.0 executable and all required software libraries. For more details, see our Quick Start Guide at cloud.geos-chem.org.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.7.0 cd Code.12.7.0 # Create and checkout a new branch "GC_12.7.0" at the tag "12.7.0" git checkout -b GC_12.7.0 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.7.0" at the tag "12.7.0" git checkout -b GC_12.7.0 12.7.0
Please see the following links for complete information about the validation of GEOS-Chem 12.7.0:
- 1-month benchmark for GEOS-Chem Classic
- 1-month benchmark for GCHP
- 1-year transport tracer benchmark for GEOS-Chem Classic
| Feature | Submitted by | Type | Notes and References |
|---|---|---|---|
| Features affecting the full-chemistry simulation: | |||
| Small alkyl nitrate chemistry | Jenny Fisher (Wollongong) | Science | |
| Methanol as part of standard chemical mechanism | Xin Chen (UMN) Dylan Millet (UMN) Katie Travis (NASA) |
Science | |
| Update to Yuan processed MODIS LAI product (covering years 2005-2016) | GCST | Science | |
| Latitudinally and monthly resolved fixed surface concentrations for long-lived organohalogen species (1750-2014) and methane (prior to 1979) | Tomás Sherwen (York) Lee Murray (Rochester) |
Science | |
| Bug fix: Prevent differences in chemistry caused by toggling the ND65 bpch diagnostics off or on | Bob Yantosca (GCST) | Bug fix | |
| Fix incorrect uptake coefficient for N2O5 in heterogeneous chemistry | Hyeonmin Kim (Seoul Nat'l U.) Chris Holmes (FSU) |
Bug fix | |
| Fix offline dust scale factors | Jun Meng (GCST) | Bug fix | |
| Features NOT affecting the full-chemistry simulation: | |||
| Add GEOS-Chem "dry-run" option to obtain a list of required input files | Haipeng Lin (Harvard) Jiawei Zhuang (Harvard) Bob Yantosca (GCST) |
Structural | |
| HEMCO 2.2.0: Updates and fixes to improve file I/O | Melissa Sulprizio (GCST) | Structural |
|
| Implement Gan Luo et al wetdep (GMD-12-3439-2019) as an option | Gan Luo (SUNY-Albany) Fangqun Yu (SUNY-Albany) Bob Yantosca (GCST) |
Science (optional) |
|
| CH4 soil absorption from MeMo model | Melissa Sulprizio (Harvard) | Science | |
| Removal of most binary punch (aka "bpch") diagnostics
NOTE: The following bpch diagnostics will be preserved for the time being:
|
GCST | Structural | |
| Add netCDF diagnostic for UV fluxes from FAST-JX | Jonathan Moch (Harvard) Bob Yantosca (GCST) |
Structural | |
| KPP equation reactivity rate and OH reactivity diagnostics | Christoph Keller (GMAO) | Structural | |
| Bug fix for HEMCO standalone using high-resolution input grids | Chris Holmes (FSU) | Bug fix | |
| Incorrect units returned from GET_OH in sulfate_mod.F | Rong Tian (NUIST) | Bug fix | |
| Use common build_mechanism.sh script for all KPP mechanisms | Lizzie Lundgren (GCST) | Structural | |
| Features only affecting GCHP: | |||
| Preserve mass conservation when advection is off by adding delta pressure to internal state for mixing ratio scaling during initialization | Lizzie Lundgren (GCST) | Bug fix | |
| Use same CEDS anthropogenic emissions inventory as GC Classic, including 1750-1949 and additional VOC species | Lizzie Lundgren (GCST) | Structural |
|
| Assorted GCHP structural changes to facilitate GEOS-Chem in GEOS | Lizzie Lundgren (GCST) | Structural | |
| Use same precision in non-species Internal state variables and the equivalent GEOS-Chem states (REAL8) | Lizzie Lundgren (GCST) | Bug fix | |
| Update ESMF to v8.0.0 public release | Lizzie Lundgren (GCST) | Structural | |
New data directories in 12.7.0
The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.
NOTE: In GEOS-Chem 12.7.0 and later versions, you can use the GEOS-Chem dry-run option to simplify the data download process!
| Inventory | Type | What was added? | Directory |
|---|---|---|---|
| OFFLINE_BIOVOC | Default | Offline biogenic VOC emissions generated using GEOS-Chem 12.3.0 and the Yuan-processed MODIS-LAI product | HEMCO/OFFLINE_BIOVOC/v2019-10 |
| XUAN_XLAI | DEFAULT | Yuan-processed MODIS LAI product (covering years 2005-2016) | HEMCO/Yuan_XLAI/v2019-03 |
| RONO2 | DEFAULT | Monthly seawater concentrations of methyl nitrate (MENO3) and ethyl nitrate (ETNO3) needed for small alkyl nitrate chemistry | HEMCO/RONO2/v2019-05 |
| MOH | DEFAULT | Methanol emissions as described in Chen et al. (2019) | HEMCO/MOH/v2019-12 |
| CMIP6 | DEFAULT (UCX-based simulations) |
Latitudinally and monthly resolved fixed surface concentrations for long-lived organohalogen species (1750-2014) and methane (prior to 1979) | HEMCO/CMIP6/v2019-12 |
| SfcFix | DEFAULT (UCX-based simulations) |
Latitudinally and monthly resolved fixed surface concentrations for long-lived organohalogen species from GMI and UCX (1959-2099) | HEMCO/SfcFix/v2019-12 |
| MODIS_CHLR | OPTIONAL | MODIS-Aqua Chlorophyll-A data for use in the marinePOA simulation | HEMCO/MODIS_CHLR/v2019-11 |
12.6.3
This version was released on 25 Nov 2019.
You can use the following Git commands to download the GEOS-Chem 12.6.3 source code and 12.6.0 GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.6.3 cd Code.12.6.3 # Create and checkout a new branch "GC_12.6.3" at the tag "12.6.3" git checkout -b GC_12.6.3 12.6.3 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.6.0" at the tag "12.6.0" # NOTE: You can use 12.6.0 rundirs, as GC 12.6.3 does not change rundirs. git checkout -b GC_12.6.0 12.6.0
Important: Make sure you also download the new data directories for this version.
| Feature | Submitted by | Type | Notes and References |
|---|---|---|---|
| Features only affecting GCHP: | |||
| Fix bug preventing successful transport tracer simulation runs | Lizzie Lundgren (GCST) | Bug fix | |
12.6.2
This version was released on 15 Nov 2019.
You can use the following Git commands to download the GEOS-Chem 12.6.2 source code and 12.6.0 GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.6.12 cd Code.12.6.2 # Create and checkout a new branch "GC_12.6.2" at the tag "12.6.2" git checkout -b GC_12.6.2 12.6.2 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.6.0" at the tag "12.6.0" # NOTE: You can use 12.6.0 rundirs, as GC 12.6.2 does not change rundirs. git checkout -b GC_12.6.0 12.6.0
Important: Make sure you also download the new data directories for this version.
| Feature | Submitted by | Type | Notes and References |
|---|---|---|---|
| Features NOT affecting the full-chemistry simulation: | |||
| geoschem/geos-chem Now make sure the HEMCO standalone gets the proper met field name and grid resolution | Jun Meng (GCST) Bob Yantosca (GCST) |
Bug Fix | |
| Prevent overwriting restart variables H2O2AfterChem and SO2AfterChem if present | Lizzie Lundgren (GCST) | Bug Fix | |
| Features only affecting GCHP: | |||
| Fix incorrect vertical flipping of MAPL 3D imports impacting mesospheric chemistry | Lizzie Lundgren (GCST) Sebastian Eastham (MIT) |
Bug fix |
|
| Fix incorrect mapping between internal state H2O2AfterChem and the equivalent State_Chm field | Lizzie Lundgren (GCST) | Bug fix | |
| Fix two timestep delay in update time for LAI upon day change | Lizzie Lundgren (GCST) | Bug fix | |
12.6.1
This version was released on 28 Oct 2019.
You can use the following Git commands to download the GEOS-Chem 12.6.1 source code and 12.6.0 GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.6.1 cd Code.12.6.1 # Create and checkout a new branch "GC_12.6.1" at the tag "12.6.1" git checkout -b GC_12.6.1 12.6.1 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.6.0" at the tag "12.6.0" # NOTE: You can use 12.6.0 rundirs, as GC 12.6.1 does not change rundirs. git checkout -b GC_12.6.0 12.6.0
Important: Make sure you also download the new data directories for this version.
| Feature | Submitted by | Type | Notes and References |
|---|---|---|---|
| Updates that will NOT affect full-chemistry simulations | |||
| Fix CMake error message for when NetCDF is not found | Liam Bindle (Dalhousie) | Bug fix | |
| Fix units for PRECANV, PRECCON, PRECLSC, PRECTOT in state_met_mod.F90 | Tomas Sherwen (York) | Bug fix | |
| Various minor structural updates: | Bob Yantosca (GCST) Liam Bindle (GCST) |
Structural | |
| Features only affecting GCHP: | |||
| Fix regridding bug at poles | Lizzie Lundgren (GCST) | Bug fix |
|
12.6.0
This version was released on 18 Oct 2019.
You can use the following Git commands to download the GEOS-Chem 12.6.0 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.6.0 cd Code.12.6.0 # Create and checkout a new branch "GC_12.6.0" at the tag "12.6.0" git checkout -b GC_12.6.0 12.6.0 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.6.0" at the tag "12.6.0" git checkout -b GC_12.6.0 12.6.0
Important: Make sure you also download the new data directories for this version.
Please see the following links for complete information about the validation of GEOS-Chem 12.6.0:
- 1-month benchmark for GEOS-Chem Classic
- 1-month benchmark for GCHP
- 1-year benchmark for GEOS-Chem Classic
| Feature | Submitted by | Type | Notes and References |
|---|---|---|---|
| Updates that will affect full-chemistry simulations | |||
Combined heterogeneous chemistry updates, includes
|
Chris Holmes (FSU) Erin McDuffie (Dalhousie) Viral Shah (UW) Lyatt Jaegle (UW) |
Science | |
| HNO3 cold-temperature deposition | Viral Shah (Harvard) | Science |
|
| Quick fix for aerosol pH calculation when dry | Becky Alexander (UW) Xuan Wang (Harvard) |
Science | |
| Remove isoprene in VBS (leaving aqueous) | Melissa Sulprizio (GCST) | Science | |
| Updated aerosol hygroscopicity and optics | Robyn Latimer (Dalhousie) Jun Meng (Dalhousie) |
Science | See New data directories in 12.6.0 |
| Add EDGAR BCPI and BCPO emissions for remaining sectors to DICE-Africa | Tomas Sherwen (York) Eloise Marais (Leicester) |
Bug fix | geoschem/geos-chem-unittest PR #9 |
| Updates that will NOT affect full-chemistry simulations | |||
| Simple parameterization for CO2 dependence of stomatal resistance (off by default) | Amos Tai (CUHK) | Science | geoschem/geos-chem PR #41 |
| Aerosol nitrate photolysis option (off by default) | Tomas Sherwen (York) Prasad Kasibhatla (Duke) |
Science | geoschem/geos-chem PR #32 |
| CMake in GEOS-Chem Classic (optional) | Liam Bindle (Dalhousie) | Structural | geoschem/geos-chem PR #35 |
| Enable GEOS-Chem "Classic" netCDF (History) diagnostics to be subsetted vertically and horizontally | Bob Yantosca (GCST) | Structural | |
BB4CMIP historical biomass burning emissions (1750-2014)
|
Pengfei Liu (Harvard) | Science | See New data directories in 12.6.0 |
| Surface diagnostic (O3, HNO3) with user-selected height | Katie Travis (MIT) GCST |
Science | |
| APM update and integration with GEOS-Chem 12 | Gan Luo (SUNY-Albany) Fangqun Yu (SUNY-Albany) |
Science | geoschem/geos-chem PR #40
|
New data directories in 12.6.0
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 |
|---|---|---|---|
| FAST_JX | DEFAULT |
|
CHEM_INPUTS/FAST_JX/v2019-06 |
| BB4CMIP6 | OPTIONAL | Historical biomass burning emissions (1750-2015, BB4CMIP) | HEMCO/BB4CMIP6/v2019-06 |
12.5.0
This version was released on 09 Sep 2019.
You can use the following Git commands to download the GEOS-Chem 12.5.0 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.5.0 cd Code.12.5.0 # Create and checkout a new branch "GC_12.5.0" at the tag "12.5.0" git checkout -b GC_12.5.0 12.5.0 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.5.0" at the tag "12.5.0" git checkout -b GC_12.5.0 12.5.0
Important: Make sure you also download the new data directories for this version.
Please see the following links for complete information about the validation of GEOS-Chem 12.5.0:
This version includes the updates listed below.
| Feature | Submitted by | Type | Notes and References |
|---|---|---|---|
| Updates that will affect full-chemistry simulations | |||
| Retire obsolete emission inventories | Eloise Marais (Leicester) Emissions and Deposition Working Group |
Science | |
| Updated offline biogenic emissions generated with GEOS-Chem 12.3.0 | Hongjian Weng (PKU) | Science | |
| Updated volcano emissions to include eruptive emissions through April 2018 | Christoph Keller (NASA/GMAO) | Science | |
| Remove CO from MEGAN HEMCO extension to avoid double counting | Jenny Fisher (Wollongong) | Bug fix | |
Fixes for GFED4 emissions, including:
|
Sidhant Pai (MIT) | Bug fix | |
| Scale DICE-Africa emissions to address errors in inventory | Eloise Marais (Leicester) | Bug fix | |
| Bug fix for C3H8 anthropogenic emissions | Melissa Sulprizio (GCST) | Bug fix | |
| Separate anthropogenic PM2.5 dust source from the DustDead extension | Melissa Sulprizio (GCST) | Bug fix | |
| Corrections for CFCs in the chemistry mechanism | Xuan Wang (Harvard) | Bug fix | |
| Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90 | Stephen Steenrod (NASA GMAO) | Bug fix | |
| Bug fix: make sure stratospheric BrY concentrations are read properly each month | Lyatt Jaeglé (U. Washington) | Bug fix | |
| Updates that will NOT affect full-chemistry simulations | |||
| Enable accurate cloud pH diagnostic calculation via post-processing | Jonathan Moch (Harvard) | Structural | geoschem/geos-chem PR #37
|
| Bug fix for proposed Henry's law constants | Jenny Fisher (Wollongong) | Bug fix | |
| Updates that will only affect GCHP | |||
| Update GCHP to use MAPL v1.0.0 and ESMF v8.0.0 beta snapshot 28 | Lizzie Lundgren (GCST) | Structural |
|
| Replace 4x5 input files in GCHP with higher resolution equivalents to avoid ESMF domain decomposition issue at high core counts | Lizzie Lundgren (GCST) | Emissions | |
New data directories in 12.5.0
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 |
|---|---|---|---|
| OFFLINE_BIOVOC | Default | Offline biogenic VOC emissions generated using GEOS-Chem 12.3.0 and:
|
HEMCO/OFFLINE_BIOVOC/v2019-08 |
| Volcano | Default | Updated volcanic SO2 emissions (1978-2019), with eruptive emissions through 28 April 2018 | HEMCO/VOLCANO/v2019-08 |
| AFCID | Default | Separate anthropogenic PM2.5 dust emissions from the DustDead extension | HEMCO/AFCID/v2018-04 |
| C2H6_2010 | Default | Removed unused lev dimension and include 2x2.5 files regridded from 4x5 | HEMCO/C2H6_2010/v2019-06 |
| DUST_DEAD | Optional | Changed longitude dimension format from integer to float and time units seconds string from '0.0' to '00' | HEMCO/DUST_DEAD/v2019-06 |
| UVALBEDO | Default | Changed seconds string in time dimension units attribute from '0.0' to '00' | HEMCO/UVALBEDO/v2019-06 |
| TOMS/SBUV | Default | Changed seconds string in time dimension units attribute from '0.0' to '00' | HEMCO/TOMS_SBUV/v2019-06 |
| India mask | Default | Removed unused attribute 'valid_range' | HEMCO/MASKS/v2019-05 |
| BIOFUEL | Default | Regridded from 4x5 to 2x2.5 | HEMCO/BIOFUEL/v2019-08 |
12.4.0
This version was released on 05 Aug 2019.
NOTE: We recommend users update to GEOS-Chem 12.5.0, which contains some bug fixes and updates for the offline biogenic VOC and volcano emissions.
Please see the following links for complete information about the validation of GEOS-Chem 12.4.0:
- 1-month benchmark for GEOS-Chem Classic
- 1-month benchmark for GCHP
- 1-year benchmark for GEOS-Chem Classic
This version includes the updates listed below.
New data directories in 12.4.0
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 |
|---|---|---|---|
| OFFLINE_DUST | Default | Offline dust emissions generated with:
|
HEMCO/OFFLINE_DUST/v2019-01 |
| OFFLINE_LIGHTNING | Default | Offline lightning flash densities and convective-cloud depths generated with:
|
HEMCO/OFFLINE_LIGHTNING/v2019-01 |
| OFFLINE_BIOVOC | Default | Offline biogenic VOC emissions generated using GEOS-Chem v11-02 and:
|
HEMCO/OFFLINE_BIOVOC/v2019-01 |
| OFFLINE_SEASALT | Default | Offline sea salt emissions generated with:
|
HEMCO/OFFLINE_SEASALT/v2019-01 |
| OFFLINE_SOILNOX | Default | Offline soil NOx emissions generated with:
|
HEMCO/OFFLINE_SOILNOX/v2019-01 |
| Volcano | Default | Updated volcanic SO2 emissions (1978-2019), with eruptive emissions through 3 Dec 2015 | HEMCO/VOLCANO/v2019-04/ |
12.3.2
This version was released on 02 May 2019.
You can use the following Git commands to download the GEOS-Chem 12.3.1 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone -b 12.3.2 https://github.com/geoschem/geos-chem Code.12.3.2 cd Code.12.3.2 git checkout 12.3.2 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone -b 12.3.2 https://github.com/geoschem/geos-chem-unittest UT cd UT git checkout 12.3.2 cd ..
Please see the following links for complete information about the validation of GEOS-Chem 12.3.2:
This version includes the updates listed below.
| Feature | Submitted by | Type | Notes |
|---|---|---|---|
| Features affecting the full-chemistry simulation: | |||
| Fix inconsistency for species H2402 between GCHP and GEOS-Chem "Classic" | Sebastian Eastham (MIT) GCST |
Bug fix |
|
| Bug fixes for the FAST-JX photolysis mechanism: | Bob Yantosca (GCST) | Bug fix |
|
Updates and fixes for HEMCO diagnostics, including:
|
Melissa Sulprizio (GCST) | Bug fix |
|
| Features NOT affecting the full-chemistry simulation: | |||
| Extending the CEDS anthropogenic emissions inventory to include 1750-1949 and additional VOC species | Melissa Sulprizio (GCST) | Science | |
| Features only affecting GCHP: | |||
| Disable Br2 offline seasalt emissions to match GEOS-Chem Classic default | Sebastian Eastham (MIT) | Bug fix | |
Assorted GCHP run directory feature updates
|
Lizzie Lundgren (GCST) | Structural |
|
| Embed GEOS code within select GCHP files | Lizzie Lundgren (GCST) | Structural |
|
New data directories in 12.3.2
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 |
|---|---|---|---|
| FAST_JX | DEFAULT |
|
CHEM_INPUTS/FAST_JX/v2019-04 |
| UCX chemistry mechanism | DEFAULT |
|
CHEM_INPUTS/UCX_201904 |
| CEDS | OPTIONAL |
|
HEMCO/CEDS/v2018-08 |
12.3.1
This version was released on 08 Apr 2019.
You can use the following Git commands to download the GEOS-Chem 12.3.1 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone -b 12.3.1 https://github.com/geoschem/geos-chem Code.12.3.1 # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone -b 12.3.1 https://github.com/geoschem/geos-chem-unittest UT
| Feature | Submitted by | Type | Notes |
|---|---|---|---|
| Features NOT affecting the full-chemistry simulation: | |||
| Fix the netCDF diagnostic for noontime J-values | GCST | Bug fix | |
| Planeflight diagnostic now writes out data for the last timestep of the day | Luke Schiferl (LDEO/Columbia) GCST |
Bug fix | |
| Reduce memory footprint: Do not allocate memory to array MINIT in strat_chem_mod.F90 | Bob Yantosca (GCST) | Bug fix | |
| Features only affecting GCHP: | |||
| Declare State_Met%AREA_M2 as 2-dimensional, not 3-dimensional | GCST | Bug fix | |
12.3.0
This version was released on 01 Apr 2019.
You can use the following Git commands to download the GEOS-Chem 12.3.0 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.3.0 cd Code.12.3.0 # Create and checkout a new branch "GC_12.3.0" at the tag "12.3.0" git checkout -b GC_12.3.0 12.3.0 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.3.0" at the tag "12.3.0" git checkout -b GC_12.3.0 12.3.0
Important: Make sure you also download the new data directories for this version.
Please see the following links for complete information about the validation of GEOS-Chem 12.3.0:
This version includes the updates listed below.
| Feature | Submitted by | Type | Notes |
|---|---|---|---|
| Features affecting the full-chemistry simulation: | |||
| Update ISORROPIA from v2.0 to v2.2, in order to remove persistent noise in output | Seb Eastham (Harvard) | Science | |
| Updated PFT file for MEGAN | Jenny Fisher (Wollongong) Dylan Millet (UMN) |
Science | |
| Bug fix for eruptive volcanic emissions | Barron Henderson (EPA) | Bug fix | |
| Read in and regrid existing MODIS LAI and OLSON data via HEMCO | Bob Yantosca (GCST) | Structural | |
| Update from HEMCO version 2.1.011 to 2.1.012 | Christoph Keller (NASA/GMAO) GCST |
Bug fix & Structural |
|
| Features NOT affecting the full-chemistry simulation: | |||
Update to Yuan processed MODIS LAI product (covering years 2005-2016)
|
Jenny Fisher (Wollongong) Barron Henderson (US EPA) |
Science | |
| OMI-based Volcanic emissions 2005-2012 (off by default) | Cui Ge (U. Iowa) Jun Wang (U. Iowa) GCST |
Science | |
| Further bug fix for netCDF diagnostics spanning leap years | Bob Yantosca (GCST) | Bug fix | |
| Fix GFAS_SOAP entry in HEMCO_Config.rc | Killian Murphy (York) | Bug fix | |
| Tagged CO bug fixes: Fix CO units and write secondary production into a netcdf file | Beata Bukosa (Wollongong) | Bug fix | |
| Features affecting GCHP only: | |||
| Enable running time backwards in GCHP | Atanas Trayanov (GMAO), Lizzie Lundgren (GCST) | Structural |
|
New data directories in 12.3.0
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 |
|---|---|---|---|
| OLSON_MAP | DEFAULT | Olson 2001 land map masks, separated into 73 netCDF variables (one per land type). This format facilitates regridding by HEMCO. | HEMCO/OLSON_MAP/v2019-02 |
| MODIS_XLAI | DEFAULT | MODIS LAI data (corresponding to ExtData/CHEM_INPUTS/MODIS_LAI_201707)
This data has been processed into 73 netCDF variables (one corresponding to each Olson land type), which facilitates regridding by HEMCO. |
HEMCO/MODIS_XLAI/v2017-07 |
| MEGAN | DEFAULT | Updated PFT file for MEGAN | HEMCO/MEGAN/v2018-05/ |
NOTES:
- DEFAULT denotes that the inventory is part of the default HEMCO emissions configuration that you get when you run GEOS-Chem "out-of-the-box".
- OPTIONAL denotes optional inventories that you may use (or not) according to your research needs.
12.2.1
This version was released on 28 Feb 2019.
You can use the following Git commands to download the GEOS-Chem 12.2.1 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.2.1 cd Code.12.2.1 # Create and checkout a new branch "GC_12.2.1" at the tag "12.2.1" git checkout -b GC_12.2.1 12.2.1 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.2.1" at the tag "12.2.1" git checkout -b GC_12.2.1 12.2.1
Important: Make sure you also download the new data directories for this version.
This version includes the updates listed below.
| Feature | Submitted by | Type | Notes |
|---|---|---|---|
| Features NOT affecting the full-chemistry simulation: | |||
| Bug fix: netCDF diagnostic collections with frequency "End" now properly span leap year days | Amos Tai (CUHK) GCST |
Structural | |
| Move module-level variables from Linoz and MODIS LAI | Haipeng Lin (PKU) | Structural | |
| Make polar bromine explosion the default option in Hg simulation | Colin Thackray (Harvard) Jenny Fisher (Wollongong) |
Science | |
| TOMAS updates | Emily Ramnarine (Colorado State) Jeff Pierce (Colorado State) Betty Croft (Dalhousie) |
Science | |
| Fix Henry's Law coefficient for C2H6 | Chris Holmes (FSU) | Bug fix | |
| Add routine to save the GC species database to JSON format (commented out) | Bob Yantosca (GCST) | Structural | |
| Add RRTMG fluxes to netCDF diagnostics | Bob Yantosca (GCST) | Structural |
|
| Fix for CO2 simulation chemical source | Beata Bukosa (U. Wollongong) | Bug fix | |
| Features affecting GCHP only: | |||
| Update MODIS LAI source directory to match GEOS-Chem Classic | GCST | Bug fix | |
| Missing scaling factors for MERRA-2 simulations with GCHP | Sebastian Eastham (MIT) | Bug fix | |
| Use online sea flux emissions by default in GCHP | GCST | Emissions | |
New data directories in 12.2.1
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 |
|---|---|---|---|
| Updated chemical source for CO2 simulation | OPTIONAL | Reprocessed the chemical source file for the CO2 simulation, because the existing file was somehow corrupted. | HEMCO/CO2/v2019-02/CHEM/ |
| FINN | OPTIONAL | Files containing the number of fires per grid box for use with the biomass burning subgrid coagulation option in TOMAS simulations. | HEMCO/FINN/v2015-02/ |
--Bob Yantosca (talk) 16:34, 13 February 2019 (UTC)
12.2.0
This version was released on 19 Feb 2019.
You can use the following Git commands to download the GEOS-Chem 12.2.0 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.2.0 cd Code.12.2.0 # Create and checkout a new branch "GC_12.2.0" at the tag "12.2.0" git checkout -b GC_12.2.0 12.2.0 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.2.0" at the tag "12.2.0" git checkout -b GC_12.2.0 12.2.0
Important: Make sure you also download the new data directories for this version.
Please see the following links for complete information about the validation of GEOS-Chem 12.2.0:
This version includes the updates listed below.
| Feature | Submitted by | Type | Notes |
|---|---|---|---|
| Features affecting the full-chemistry simulation: | |||
| Retire BRAVO emissions and use CEDS for Mexico instead | Melissa Sulprizio (GCST) | Science | |
| Update mask file applied to NEI2011 emissions | Melissa Sulprizio (GCST) | Bug fix | |
| Features NOT affecting the full-chemistry simulation: | |||
| Transport Tracers simulation: a common set of tracers in GEOS-Chem and GEOS | Transport WG Melissa Sulprizio (GCST) |
Benchmarking |
|
| ObsPack diagnostic | Andy Jacobson (NOAA/ESRL) Bob Yantosca (GCST) |
Structural | |
| GFAS biomass burning emissions (as an option) | Mat Evans (York) Killian Murphy (York) |
Science | |
| Fix bug in stratosperic aerosol surface area netcdf diagnostics | Jonathan Moch (Harvard) Christoph Keller (GMAO) |
Bug fix | |
| Update from HEMCO 2.1.010 to HEMCO 2.1.011: | GCST | Structural | |
| Features affecting GCHP only: | |||
| Update ESMF version in GCHP from v5.2.0rp2 to v7.1.0r | Lizzie Lundgren (GCST) | Structural |
|
| New fields in GCHP output restart file | Lizzie Lundgren (GCST) | Bug Fix & Structural |
|
| Bug fix: use checkpoint output file as subsequent run restart | Lizzie Lundgren (GCST) | Bug Fix |
|
New data directories in 12.2.0
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 |
|---|---|---|---|
| GFAS biomass burning emissions | OPTIONAL | GFAS biomass burning emissions for 2003-present (updated monthly) | HEMCO/GFAS/v2018-09/ |
| EDGAR v4.2 emissions of SF6 | DEFAULT | EDGAR v4.2 emissions of SF6 for 1970-2008 | HEMCO/SF6/v2019-01/ |
| MASKS | DEFAULT | Update mask file applied to NEI2011 emissions | HEMCO/MASKS/v2018-09/ |
| TileFiles | DEFAULT (in GCHP) |
New tile files for 0.1x0.1 CONUS, Canada, and Mexico mask files | GCHP/TileFiles |
NOTES:
- DEFAULT denotes that the inventory is part of the default HEMCO emissions configuration that you get when you run GEOS-Chem "out-of-the-box".
- OPTIONAL denotes optional inventories that you may use (or not) according to your research needs.
12.1.1
This version was released on 13 Dec 2018.
You can use the following Git commands to download the GEOS-Chem 12.1.1 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.1.1 cd Code.12.1.1 # Create and checkout a new branch "GC_12.1.1" at the tag "12.1.1" git checkout -b GC_12.1.1 12.1.1 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.1.1" at the tag "12.1.1" git checkout -b GC_12.1.1 12.1.1
Important: Make sure you also download the new data directories for 12.1.0 if you haven't already.
This version includes the updates listed below.
| Feature | Submitted by | Type | Notes |
|---|---|---|---|
| Features NOT affecting the full-chemistry (benchmark) simulation: | |||
| Bug fix for tagged CO: don't multiply emissions timestep by 60 | Dylan Jones (U. Toronto) | Bug fix | |
| Skip planeflight observations outside a nested domain | Lei Zhu (Harvard) | Bug fix | |
| Always enable BCPH_TPBC to allow saving out BC files in global simulations | Yanxu Zhang (Nanjing) | Bug fix | |
| Fix compilation issues: | Bob Yantosca (GCST) Haipeng Lin (PKU) |
Bug fix | |
| Features affecting GCHP only: | |||
| GCHP transport fix to prevent instant propagation from troposphere to stratosphere | Seb Eastham (MIT) | Bug fix | |
--Lizzie Lundgren (talk) 16:05, 6 December 2018 (UTC)
12.1.0
This version was released on 26 Nov 2018.
You can use the following Git commands to download the GEOS-Chem 12.1.0 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.1.0 cd Code.12.1.0 # Create and checkout a new branch "GC_12.1.0" at the tag "12.1.0" git checkout -b GC_12.1.0 12.1.0 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.1.0" at the tag "12.1.0" git checkout -b GC_12.1.0 12.1.0
Important: Make sure you also download the new data directories for this version.
Please see the following links for complete information about the validation of GEOS-Chem 12.1.0:
This version includes the updates listed below.
| Feature | Submitted by | Type | Notes |
|---|---|---|---|
| Features affecting the full-chemistry simulation: | |||
| Budget diagnostics | Lizzie Lundgren (GCST) Chris Holmes (Florida State) |
Diagnostics |
|
| Anthropogenic PM2.5 dust source | Sajeev Philip (Dalhousie) | Science |
|
| GEOS-Chem restart file updates | Melissa Sulprizio (GCST) | Bug Fix & Structural |
|
| Updates and fixes for the CEDS anthropogenic emissions inventory: | Pengfei Liu (Harvard) Melissa Sulprizio (GCST) Jiawei Zhuang (Harvard) |
Bug fix |
|
| HEMCO fixes: | Bob Yantosca (GCST) Melissa Sulprizio (GCST) Erin McDuffie (Dalhousie) |
Bug fix |
|
| Fix mass conservation in non-local PBL mixing | Jintai Lin (PKU) | Bug fix |
|
| Allow for SZA to 98 degrees when getting photolysis rates | Eric Fleming (GMAO) | Bug fix |
|
| Features NOT affecting the full-chemistry simulation: | |||
| FlexGrid Stage 1: Use HEMCO to read met fields | Jiawei Zhuang (Harvard) Jintai Lin (PKU) |
Structural | |
| 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) |
Structural | |
Added netCDF diagnostics in the following areas:
|
Bob Yantosca (GCST) | Diagnostics |
|
| Convert input data for RRTMG from bpch to netCDF for input via HEMCO | Bob Yantosca (GCST) | Structural | |
| Add fixes for seasonal scale factors in CH4 simulations | Bram Maasakkers (SRON) Melissa Sulprizio (GCST) |
Bug fix | |
| Move Fast-JX .dat files from the geos-chem-unittest repository to gcgrid/ExtData | Chris Holmes (Florida State) GCST |
Structural | |
| Update HEMCO configuration file for the tagged CO simulation | Bob Yantosca (GCST) | Bug fix | |
| Structural updates to facilitate interfacing GEOS-Chem into WRF | Haipeng Lin (Peking U) GCST |
Structural |
|
| Structural updates to facilitate interfacing GEOS-Chem into GEOS-5 | Christoph Keller (GMAO) Lizzie Lundgren (GCST) |
Structural |
|
| Features affecting GCHP only: | |||
| Fix masking bug to correctly apply anthropogenic emissions | Lizzie Lundgren (GCST) | Bug fix | |
| Remove erroneous 180 degree longitude shift in APEI regridding | Lizzie Lundgren (GCST) | Bug fix | |
| Move GCHP run directory creation from GEOS-Chem Unit Tester to GCHP repository | Lizzie Lundgren (GCST) | Structural | |
--Melissa Sulprizio (talk) 15:21, 26 November 2018 (UTC)
New data directories in 12.1.0
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 |
|---|---|---|---|
| DUST DEAD | DEFAULT | Anthropogenic PM2.5 dust source | HEMCO/DUST_DEAD/v2018-04/ |
| GEOS-Chem restart files | DEFAULT | GEOS-Chem restart file updates: New variables, new variable names, new file names | GEOSCHEM_RESTARTS/v2018-11/ |
| Input files for FAST-JX | DEFAULT | Move Fast-JX .dat files from the geos-chem-unittest repository to gcgrid/ExtData | CHEM_INPUTS/FAST_JX/v2018-09/ |
| RRTMG input data | OPTIONAL | netCDF input data files for the RRTMG specialty simulation (converted from the old "binary punch" format files) | HEMCO/RRTMG/v2018-11/ |
| CEDS anthropogenic emissions | DEFAULT | Reduce file size for CEDS inventory | HEMCO/CEDS/v2018-08/YYYY |
| MASKS | DEFAULT | Clean up mask file directory to remove obsolete files | HEMCO/MASKS/v2018-09/ |
NOTES:
- DEFAULT denotes that the inventory is part of the default HEMCO emissions configuration that you get when you run GEOS-Chem "out-of-the-box".
- OPTIONAL denotes optional inventories that you may use (or not) according to your research needs.
12.0.3
This version was released on 16 Oct 2018.
You can use the following Git commands to download the GEOS-Chem 12.0.3 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.0.3 cd Code.12.0.3 # Create and checkout a new branch "GC_12.0.3" at the tag "12.0.3" git checkout -b GC_12.0.3 12.0.3 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.0.3" at the tag "12.0.3" git checkout -b GC_12.0.3 12.0.3
Important: Make sure you also download the new data directories for 12.0.0 if you haven't already.
This version contains fixes that will only impact GCHP.
| Feature | Submitted by | Type | Notes |
|---|---|---|---|
| Features affecting GCHP only: | |||
| Fix incorrect run configuration for offline sea salt emissions in GCHP | Sebastian Eastham (MIT) | Bug fix | |
| Fix bug in application of CFC surface mixing ratios in GCHP | Sebastian Eastham (MIT) | Bug fix | |
--Lizzie Lundgren (talk) 18:21, 16 October 2018 (UTC)
12.0.2
This version was released on 10 Oct 2018.
You can use the following Git commands to download the GEOS-Chem 12.0.2 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.0.2 cd Code.12.0.2 # Create and checkout a new branch "GC_12.0.2" at the tag "12.0.2" git checkout -b GC_12.0.2 12.0.2 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.0.2" at the tag "12.0.2" git checkout -b GC_12.0.2 12.0.2
Important: Make sure you also download the new data directories for 12.0.0 if you haven't already.
This version includes the updates listed below.
| Feature | Submitted by | Type | Notes |
|---|---|---|---|
| Features NOT affecting the full-chemistry (benchmark) simulation: | |||
| Fixed local-time averaging in ND51 and ND51b satellite timeseries diagnostics | Bo Zhang (NIA) | Bug fix | Implemented 04 Oct 2018 |
| Fixes to correct missing BC/OC biomass emissions and incorrect aerosol drydep in TOMAS simulations | Pengfei Liu (Harvard) | Bug fix | Implemented 25 Sep 2018 |
| Avoid double-counting of emissions in the CO2 simulation | Beata Bukosa (U. Wollongong) Christoph Keller (GMAO) |
Bug fix | Implemented 24 Sep 2018. |
--Lizzie Lundgren (talk) 18:21, 16 October 2018 (UTC)
12.0.1
This version was released on 24 Aug 2018.
You can use the following Git commands to download the GEOS-Chem 12.0.1 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.0.1 cd Code.12.0.1 # Create and checkout a new branch "GC_12.0.1" at the tag "12.0.1" git checkout -b GC_12.0.1 12.0.1 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.0.1" at the tag "12.0.1" git checkout -b GC_12.0.1 12.0.1
Important: Make sure you also download the new data directories for 12.0.0 if you haven't already.
This version includes the updates listed below.
| Feature | Submitted by | Type | Notes |
|---|---|---|---|
| Features NOT affecting the full-chemistry (benchmark) simulation: | |||
| Fix typo when registering the State_Chm%SSAlk field | Shuting Zhai (U. Washington) GCST |
Bug fix | |
Add fixes for several compilation issues:
|
GCST | Bug fix | |
| Fixes for the Hg specialty simualtion: Restore biomass emissions and do not double-count anthropogenic emissions | Colin Thackray (Harvard) | Bug fix | |
| Fix mis-indexing in the ND05 diagnostic | GCST | Bug fix | |
| Minor updates to facilitate interfacing GEOS-Chem into GEOS-5 | Lizzie Lundgren (GCST) | Structural | |
--Bob Yantosca (talk) 14:31, 10 October 2018 (UTC)
12.0.0
This version was released on 10 Aug 2018
You can use the following Git commands to download the GEOS-Chem 12.0.0 source code and GEOS-Chem Unit Tester package.
# Download the GEOS-Chem source code git clone https://github.com/geoschem/geos-chem Code.12.0.0 cd Code.12.0.0 # Create and checkout a new branch "GC_12.0.0" at the tag "12.0.0" git checkout -b GC_12.0.0 12.0.0 cd .. # Download the GEOS-Chem Unit Tester, from which run directories can be generated git clone https://github.com/geoschem/geos-chem-unittest UT cd UT # Create and checkout a new branch "GC_12.0.0" at the tag "12.0.0" git checkout -b GC_12.0.0 12.0.0
Important: Make sure you also download the new data directories for this version.
For more information about getting set up with GEOS-Chem, please see the GEOS-Chem Online User's Guide.
The table below shows the updates that were added to GEOS-Chem 12.0.0. Most of these fix issues that were reported by users during the GEOS-Chem v11-02 release candidate testing period (June 22 thru August 10 2018).
Please see the following links for complete information about the validation of GEOS-Chem 12.0.0:
- Approval form for 1-month benchmark simulation 12.0.0
- Results for 1-year benchmark simulation 12.0.0-Run0
| Feature | Submitted by | Type | Notes |
|---|---|---|---|
| Features affecting the full-chemistry (benchmark) simulation: | |||
| Turn off TRASH emissions by default to avoid double counting | GCST Eloise Marais (U. Birmingham) |
Bug fix |
|
| Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory | GCST | Bug fix |
|
| Bug fix for liquid water content in gckpp_HetRates.F90 | Jiayue Huang (U. Washington) Quanjie Chen (U. Washington) |
Bug fix |
|
| Bug fix for CH4 boundary conditions | Lee Murray (Rochester) | Bug fix |
|
| Fixed typo in call to GAMMA_HOBr_AER | Xuan Wang GCST |
Bug fix |
|
| Correct issues when specifying DICE-Africa emissions: | Eloise Marais (U. Birmingham) GCST |
Bug Fix |
|
| Add missing Criegee intermediate reaction | Xin Chen (UMN) | Bug fix |
|
| Bug fix for ARCTAS_SHIP in HEMCO_Config.rc files | Barron Henderson (EPA) | Bug Fix |
|
| Bug fix in FlexChem: do not zero out ACTA, EOH, HCOOH concentrations | Katie Travis (MIT) | Bug Fix |
|
| Add GFED4.1 data for 2015 and 2016; Use GFED4.1 2016 in benchmarks | Kate O'Dell (CSU) GCST |
Science |
|
| Features NOT affecting the full-chemistry simulation: | |||
| Bug fixes for stratospheric chemistry: | GCST | Bug fix | |
| Limit flash rate density in hcox_lightnox_mod.F90 | Lee Murray (Rochester) | Bug fix | |
| Initial structural modifications for interfacing GEOS-Chem into WRF | Haipeng Lin (Peking U.) | Structural |
|
| Minor fixes for mercury chemistry updates implemented in v11-02f | Colin Thackray (Harvard) | Bug fix | |
| Restore default timestep for MERRA-2 nested grid simulations to 10/20 | Ke Li (Harvard) | Bug fix | |
| Remove duplicate C3HI spectrum in FJX_spec.dat and FJX_j2j.dat | Tomas Sherwen (York) | Bug fix |
|
| Fixed typo that prevented PM2.5 from being archived to netCDF output | Jonathan Moch (Harvard) GCST |
Bug fix | |
| Bring two-way nested-grid code option up-to-date | Yingying Yan (PKU) Jintai Lin (PKU) |
Structural |
|
| Do not force L=1 by default in planeflight_mod.F | Katie Travis (MIT) GCST |
Bug fix | |
| Add PH2O2 to the default list of prod/loss families in the KPP mechanisms | GCST | Structural |
|
Update to HEMCO v2.1.008, which includes minor updates:
Update to HEMCO v2.1.007, which includes minor updates: |
GCST Christoph Keller Jenny Fisher |
Structural & Bug fix |
|
| Bug fix for reference time in netCDF diagnostic files | GCST | Bug fix | |
| Updates for QFED biomass burning emissions: | Christoph Keller (NASA GMAO) | Bug fix | |
| Fix issues in complexSOA and complexSOA_SVPOA restart files | Eloise Marais (U. Birmingham) | Bug fix | |
| Avoid double counting CEDS and GEIA NH3 biofuel emissions | Christoph Keller (NASA/GMAO) GCST |
Bug fix |
|
| Bug fixes for v11-02 simulations using the RRTMG radiative transfer model | Chris Holmes (U. Florida) | Bug Fix |
|
| Now always declare the netCDF time variable with an unlimited dimension | Chris Holmes (U. Florida) | Structural |
|
New data directories in 12.0.0
The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.
NOTES:
- DEFAULT denotes that the inventory is part of the default HEMCO emissions configuration that you get when you run GEOS-Chem "out-of-the-box".
- OPTIONAL denotes optional inventories that you may use (or not) according to your research needs.
--Bob Yantosca (talk) 20:02, 29 June 2018 (UTC)
Validation
In this section we provide information about the benchmarks and tests that we have done to validate GEOS-Chem v11-03.
1-month and 1-year benchmarks
For complete information about the benchmark simulations used to validate GEOS-Chem v11-03, please see our GEOS-Chem 12 benchmark history wiki page.
Performance
Please see the following resources below for more information about the performance of GEOS-Chem 12.0.0.
GEOS-Chem "Classic" performance
We have performed several timing tests with GEOS-Chem "Classic" 12.0.0 and have posted our results on the wiki:
- Table of 7-day timing test results with GEOS-Chem 12.0.0
- Graphs of 7-day timing test results with GEOS-Chem 12.0.0
- GEOS-Chem 12.0.0 "Classic" timing results by Bob Yantosca (PDF)
We invite you to add your own time test results to the wiki.
--Bob Yantosca (talk) 18:06, 17 August 2018 (UTC)
GCHP performance
Help us pool performance information across systems by contributing your GCHP run information on our GCHP Timing Tests page.
--Bob Yantosca (talk) 18:06, 17 August 2018 (UTC)
Previous issues now resolved in GEOS-Chem 12
Please see Issues now resolved in GEOS-Chem 12 for a list of bugs and/or technical issues have been resolved in GEOS-Chem 12.0.0 through GEOS-Chem 12.5.0. Issues resolved after GEOS-Chem 12.5.0 can be found on the following Github pages:
Outstanding issues not yet resolved in GEOS-Chem 12
Unresolved issues are listed on the following Github pages: