Difference between revisions of "GEOS-Chem 12"
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=== 12.2.0 === | === 12.2.0 === | ||
| − | + | '''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.2.0|new data directories for this version]]. | |
| + | |||
| + | Please see the following links for complete information about the validation of GEOS-Chem 12.2.0: | ||
| + | #[[GEOS-Chem_12_benchmark_history#12.2.0|''Approval form for 1-month benchmark simulation 12.2.0'']] | ||
| + | #1-year Rn-Pb-Be benchmark simulation | ||
| + | |||
| + | This version includes the updates listed below. | ||
{| border=1 cellspacing=0 cellpadding=5 | {| border=1 cellspacing=0 cellpadding=5 | ||
| Line 143: | Line 149: | ||
git clone https://github.com/geoschem/geos-chem Code.12.1.1 | git clone https://github.com/geoschem/geos-chem Code.12.1.1 | ||
cd Code.12.1.1 | cd Code.12.1.1 | ||
| − | git checkout | + | git checkout 12.1.1 |
cd .. | cd .. | ||
| Line 149: | Line 155: | ||
git clone https://github.com/geoschem/geos-chem-unittest UT | git clone https://github.com/geoschem/geos-chem-unittest UT | ||
cd UT | cd UT | ||
| − | git checkout | + | git checkout 12.1.1</nowiki> |
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.1.0|new data directories for 12.1.0 if you haven't already]]. | '''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.1.0|new data directories for 12.1.0 if you haven't already]]. | ||
| − | + | This version includes the updates listed below. | |
{| border=1 cellspacing=0 cellpadding=5 | {| border=1 cellspacing=0 cellpadding=5 | ||
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git clone https://github.com/geoschem/geos-chem Code.12.1.0 | git clone https://github.com/geoschem/geos-chem Code.12.1.0 | ||
cd Code.12.1.0 | cd Code.12.1.0 | ||
| − | git checkout | + | git checkout 12.1.0 |
cd .. | cd .. | ||
| Line 225: | Line 231: | ||
git clone https://github.com/geoschem/geos-chem-unittest UT | git clone https://github.com/geoschem/geos-chem-unittest UT | ||
cd UT | cd UT | ||
| − | git checkout | + | git checkout 12.1.0</nowiki> |
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.1.0|new data directories for this version]]. | '''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.1.0|new data directories for this version]]. | ||
| Line 232: | Line 238: | ||
#[[GEOS-Chem_12_benchmark_history#12.1.0|''Approval form for 1-month benchmark simulation 12.1.0'']] | #[[GEOS-Chem_12_benchmark_history#12.1.0|''Approval form for 1-month benchmark simulation 12.1.0'']] | ||
| − | This | + | This version includes the updates listed below. |
{| border=1 cellspacing=0 cellpadding=5 | {| border=1 cellspacing=0 cellpadding=5 | ||
| Line 456: | Line 462: | ||
git clone https://github.com/geoschem/geos-chem Code.12.0.3 | git clone https://github.com/geoschem/geos-chem Code.12.0.3 | ||
cd Code.12.0.3 | cd Code.12.0.3 | ||
| − | git checkout | + | git checkout 12.0.3 |
cd .. | cd .. | ||
| Line 462: | Line 468: | ||
git clone https://github.com/geoschem/geos-chem-unittest UT | git clone https://github.com/geoschem/geos-chem-unittest UT | ||
cd UT | cd UT | ||
| − | git checkout | + | git checkout 12.0.3</nowiki> |
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.0.0|new data directories for 12.0.0 if you haven't already]]. | '''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.0.0|new data directories for 12.0.0 if you haven't already]]. | ||
| Line 505: | Line 511: | ||
git clone https://github.com/geoschem/geos-chem Code.12.0.2 | git clone https://github.com/geoschem/geos-chem Code.12.0.2 | ||
cd Code.12.0.2 | cd Code.12.0.2 | ||
| − | git checkout | + | git checkout 12.0.2 |
cd .. | cd .. | ||
| Line 511: | Line 517: | ||
git clone https://github.com/geoschem/geos-chem-unittest UT | git clone https://github.com/geoschem/geos-chem-unittest UT | ||
cd UT | cd UT | ||
| − | git checkout | + | git checkout 12.0.2</nowiki> |
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.0.0|new data directories for 12.0.0 if you haven't already]]. | '''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.0.0|new data directories for 12.0.0 if you haven't already]]. | ||
| − | This version | + | This version includes the updates listed below. |
{| border=1 cellspacing=0 cellpadding=5 | {| border=1 cellspacing=0 cellpadding=5 | ||
| Line 560: | Line 566: | ||
git clone https://github.com/geoschem/geos-chem Code.12.0.1 | git clone https://github.com/geoschem/geos-chem Code.12.0.1 | ||
cd Code.12.0.1 | cd Code.12.0.1 | ||
| − | git checkout | + | git checkout 12.0.1 |
cd .. | cd .. | ||
| Line 566: | Line 572: | ||
git clone https://github.com/geoschem/geos-chem-unittest UT | git clone https://github.com/geoschem/geos-chem-unittest UT | ||
cd UT | cd UT | ||
| − | git checkout | + | git checkout 12.0.1</nowiki> |
'''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.0.0|new data directories for 12.0.0 if you haven't already]]. | '''<span style="color:red">Important:</span>''' Make sure you also download the [[#New data directories in 12.0.0|new data directories for 12.0.0 if you haven't already]]. | ||
| − | + | This version includes the updates listed below. | |
{| border=1 cellspacing=0 cellpadding=5 | {| border=1 cellspacing=0 cellpadding=5 | ||
Revision as of 13:42, 18 January 2019
Contents
- 1 Version history summary
- 2 Current version in development
- 3 Current bug fix patch version in development
- 4 Current stable version
- 5 Previously released stable versions
- 6 New data directories summary
- 7 Validation
- 8 Performance
- 9 Previous issues now resolved in GEOS-Chem 12
- 9.1 ESMF version update required for MAPL upgrade
- 9.2 Fix bug in stratosperic aerosol surface area netcdf diagnostics
- 9.3 GCHP Bug fix: use checkpoint output file as subsequent run restart
- 9.4 GCHP transport fix to prevent instant propagation from troposphere to stratosphere
- 9.5 Always enable BCPH_TPBC to allow saving out BC files in global simulations
- 9.6 Skip planeflight observations outside a nested domain
- 9.7 Allow for SZA to 98 degrees when getting photolysis rates
- 9.8 Fix bug in application of CFC surface mixing ratios in GCHP
- 9.9 Fix incorrect run configuration for offline sea salt emissions in GCHP
- 9.10 Update HEMCO configuration file for tagged CO simulation
- 9.11 Fix regional tile file used for APEI inventory in GCHP
- 9.12 Fix masked anthropogenic emissions bug in GCHP
- 9.13 Add support for continuous integration with TravisCI
- 9.14 Replace HEMCO built-in unit conversions with scale factors in config file
- 9.15 Fixed local-time averaging in ND51 and ND51b satellite timeseries diagnostics
- 9.16 Fix typo when registering the State_Chm%SSAlk field
- 9.17 Fixes for compilation issues
- 9.18 Fix mis-indexing in the ND05 diagnostic
- 9.19 Bug fix for HEMCO soil NOx error with ifort 17
- 9.20 FlexChem bug fix: do not zero ACTA, EOH, HCOOH
- 9.21 Avoid double counting CEDS and GEIA NH3 biofuel emissions
- 9.22 Fix bug in ARCTAS_SHIP_SO2 scale factors
- 9.23 Fix issues in complexSOA and complexSOA_SVPOA restart files
- 9.24 Bug fix for reference time in netCDF diagnostic files
- 9.25 Bug fix for CH4 boundary conditions
- 9.26 Fixed typo in call to GAMMA_HOBr_AER
- 9.27 Bug fix for liquid water content in gckpp_HetRates.F90
- 9.28 Add PH2O2 to the default list of prod/loss families in the KPP mechanisms
- 9.29 Fixed typo that prevented PM2.5 from being archived to netCDF output
- 9.30 Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory
- 9.31 Remove duplicate C3HI spectrum in FJX_spec.dat and FJX_j2j.dat
- 10 Outstanding issues not yet resolved in GEOS-Chem 12
- 10.1 GCHP silent bug when using gfortran compiler: Olson land map read as all zeros
- 10.2 Error reading restart file when using a fixed emissions year in HEMCO
- 10.3 Inconsistency in H2402 concentrations in GCHP vs GEOS-Chem Classic
- 10.4 RRTMG does not compile with GNU Fortran
- 10.5 TOMAS40 simulations exit with a floating-point exception
- 10.6 TOMAS simulations cannot use netCDF diagnostics
Version history summary
| Past releases | Current release: GEOS-Chem 12.1.0 | 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 version in development
The GEOS-Chem version listed below is currently under development.
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:
- Approval form for 1-month benchmark simulation 12.2.0
- 1-year Rn-Pb-Be benchmark simulation
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 | |
| Features NOT affecting the full-chemistry simulation: | |||
| 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 | |
| Features affecting GCHP only: | |||
| Update ESMF version 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/ |
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.
Current bug fix patch version in development
None at this time.
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.
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.
12.1.1
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 git checkout 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 git checkout 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)
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.
12.1.0
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 git checkout 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 git checkout 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.
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 git checkout 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 git checkout 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 git checkout 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 git checkout 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 Zheng (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 git checkout 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 git checkout 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 git checkout -b 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 git checkout -b 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)
New data directories summary
If you are upgrading from a prior version, please be sure to download these latest data directories (which are listed individually above, but linked here for convenience).
- New data directories in GEOS-Chem 12.2.0
- New data directories in GEOS-Chem 12.1.0
- New data directories in GEOS-Chem 12.0.0
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.
Unit tests for GEOS-Chem 12
We perform a full set of unit tests on GEOS-Chem on an almost daily basis. These tests ensure that each new feature being added does not break any existing functionality.
Here are the unit tests that we ran before submitting 1-month benchmark simulation for GEOS-Chem 12.0.0. Click on the links below to see the results from each set of unit tests:
| Unit test | Date |
|---|---|
| TBD |
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
The following bugs and/or technical issues have been resolved in GEOS-Chem 12.
ESMF version update required for MAPL upgrade
This fix will be included in 12.2.0.
GCHP versions 12.1.1 and prior use ESMF v5.2.0rp2 which was released in 2012. Besides this being a very old version that warrants updating, an update to a more recent version of ESMF is required for compatibility with new functionalities GMAO is incorporating into MAPL. Prior to implementing the MAPL update into GCHP we therefore must update ESMF and plan to use the last public release of ESMF, v7.1.0r. For more information see the ESMF documentation at www.earthsystemcog.org/projects/esmf.
--Lizzie Lundgren (talk) 18:36, 17 January 2019 (UTC)
Fix bug in stratosperic aerosol surface area netcdf diagnostics
This fix will be included in 12.2.0.
This update was submitted by Jonathan Moch who pointed out that "As written, the code is filling the stratospheric liquid aerosol surface area density and the polar strat cloud surface area with the stratospheric liquid aerosol surface area and then refilling the values with polar strat surface area. So if you aren't running the model inside GEOS-5 the AerSurfAreaPolarStratCloud and AerSurfAreaStratLiquid are identical, which shouldn't be the case."
A fix for this was implemented by Christoph Keller in the version of GEOS-Chem used in GEOS-5. To fix the issue in the offline model we use the same solution.
--Lizzie Lundgren (talk) 23:30, 4 January 2019 (UTC)
GCHP Bug fix: use checkpoint output file as subsequent run restart
This fix will be included in 12.2.0.
This bug fix applies only to the multi-run option of GCHP. It corrects a previous silent bug in which the initial restart file specified in runConfig.sh was used as the restart when doing multiple subsequent runs (i.e. in the presence of cap_restart). The proper behavior when using the multirun option (runScriptSamples/multirun.sh) is to use the checkpoint file (snapshot of end of last run) if the run is continuing from where the last run left off.
This is now corrected by automatically updating the entry for the initial restart file in GCHP.rc with the name of the checkpoint file if the file cap_restart is present just prior to execution. For simplicity the checkpoint file no longer contains the grid resolution in its name.
--Lizzie Lundgren (talk) 20:53, 4 January 2019 (UTC)
GCHP transport fix to prevent instant propagation from troposphere to stratosphere
This fix was included in 12.1.1, which was released on 13 Dec 2018 .
Sebastian Eastham describes this bug fix as follows:
GCHP uses a simple mass conservation kludge which rescales global tracer concentrations between transport steps. This is equivalent to the pressure fixer in GC-Classic, used to account for inconsistency between the surface pressure field (which sets the vertical grid spacing up to the upper troposphere) and the averaged wind speeds. Although the scaling factor is usually small, this can cause nonphysical redistribution of mass. This is especially problematic because mass can be transferred to, or from, the stratosphere, which should be impossible given that the stratosphere operates on fixed pressure levels. In a future update, this problem will be resolved by direct application of mass fluxes archived from GEOS in place of winds, but while that update is in development we have produced an interim fix
This patch forces mass redistribution to be constrained to the variable pressure levels in the troposphere. Although this slightly increases spurious mixing in the troposphere, it prevents changes in the troposphere from being instantly propagated to the stratosphere. This can have significant effects when inspecting (e.g.) the response to changes in surface emissions of NOx.
--Lizzie Lundgren (talk) 16:03, 6 December 2018 (UTC)
--Bob Yantosca (talk) 15:50, 13 December 2018 (UTC)
Always enable BCPH_TPBC to allow saving out BC files in global simulations
This fix was included in 12.1.1, which was released on 13 Dec 2018 .
Yanxu Zhang reported an issue in GEOS-Chem 12.1.0 where BC files would not save out, even when turned on in the Nested Grid Menu of input.geos. To resolve this issue, we will always add USER_DEFS += -DBPCH_TPBC in Makefile_header.mk. The switch to turn on saving out boundary condition files is still controlled by the options in input.geos, but this fix ensures the tpcore_bc_mod.F code is always compiled.
--Melissa Sulprizio (talk) 15:40, 30 November 2018 (UTC)
--Bob Yantosca (talk) 15:49, 13 December 2018 (UTC)
Skip planeflight observations outside a nested domain
This fix was included in 12.1.1, which was released on 13 Dec 2018 .
Lei Zhu provided a fix for planeflight_mod.F to skip flight observations outside the nested domains. With the fix, the code works for all 0.5 and 0.25 nested domains. For more information please see the pull request on Github.
--Melissa Sulprizio (talk) 13:29, 27 November 2018 (UTC)
--Bob Yantosca (talk) 15:48, 13 December 2018 (UTC)
Allow for SZA to 98 degrees when getting photolysis rates
This update was included in GEOS-Chem 12.1.0, which was released on 26 Nov 2018.
Eric Palmer (GMAO) wrote:
I see that the code that calls the photolysis rates (in flexchem_mod.F90), is only called when the solar zenith angle is < 90 degrees (COS(SZA) > 0.). However, Fast-Jx allows for SZA down to 98 degrees, which is important in the stratosphere-mesosphere where sunlight still illuminates at high altitudes if the sun is below the horizon at the surface. To allow for SZA down to 98 deg, I made the following one line change:
IF ( State_Met%SUNCOSmid(I,J) > 0.e+0_fp ) THEN
to:
IF ( State_Met%SUNCOSmid(I,J) > -0.13917e+0_fp ) THEN
where -0.13917e+0_fp = COS(98 degrees) This looks like it has the desired effect, as species with sharp gradients across the terminator (eg: Br, BrO), are now more "rounded" and look much more like GMI (which also allows SZA down to 98 degrees). This also eliminates the problem with the non-conservation of bromine family species in the mesosphere due to transport across the terminator (ie, the sharp edges of a square wave).
--Lizzie Lundgren (talk) 14:59, 16 October 2018 (UTC)
--Bob Yantosca (talk) 16:09, 26 November 2018 (UTC)
Fix bug in application of CFC surface mixing ratios in GCHP
This update was included in GEOS-Chem 12.0.3, which was released on 16 Oct 2018.
This fix is urgent, as any current users of the last several versions of GCHP will be see bad results for relevant species. We recommend that all GCHP users implement this update if not updating to the latest version.
Sebastian Eastham describes this bug as follows:
Basically, we specify a target year for CFC emissions to be read in in input.geos, so (eg) we can specify “2050” and all surface VMRs for CFCs will be set according to the expected value for 2050. Usually, though, we use a value of 0 – meaning “use the current year”. In GCC, the value Input_Opt%CFCYEAR is set to Get_Year () during initialization, and the offset is calculated in UCX_mod, meaning the right year gets used. However, in GCHP this isn’t possible because Get_Year doesn’t return the right value until after initialization. There was a workaround in UCX_mod already where we had a local variable “CFCYEAR” which was a copy of Input_Opt%CFCYEAR, and which got set to Get_Year() at runtime if it was still zero; however, this wasn’t being propagated in the case of an ESMF environment (where UCXNETCDF is .False.) because we only passed Input_Opt rather than the updated local variable. As a result, the CFC “emissions” were always for 1950 rather than for the true target year.
--Lizzie Lundgren (talk) 21:18, 15 October 2018 (UTC)
--Bob Yantosca (talk) 16:10, 26 November 2018 (UTC)
Fix incorrect run configuration for offline sea salt emissions in GCHP
This update was included in GEOS-Chem 12.0.3, which was released on 16 Oct 2018.
The offline sea salt emissions applied in GCHP starting in 12.0.0 contained a bug due to incorrect settings in HEMCO_Config.rc. SALA and SALC sea salt values read from file should be scaled and applied to BrSALA and BrSALC respectably. However, the HEMCO_Config.rc settings resulted in applying the scaled values to SALA and SALC instead. This bug was identified by Seb Eastham (MIT) and is corrected by updating the species column in HEMCO_Config.rc. No source code updates are necessary but you must create a new run directory or apply the fix in your existing run directories.
--Lizzie Lundgren (talk) 21:13, 15 October 2018 (UTC)
--Bob Yantosca (talk) 16:10, 26 November 2018 (UTC)
Update HEMCO configuration file for tagged CO simulation
This update was included in GEOS-Chem 12.1.0, which was released on 26 Nov 2018.
The tagged CO simulation was still using NEI2005 emissions over the US by default, while all other simulations had retired the NEI2005 option and were using NEI2011 instead. For consistency, we will use NEI2011 with the tagged CO simulation and remove NEI2005.
In addition, the CEDS and DICE_Africa inventories were omitted from tagged CO HEMCO configuration file. To maintain consistency with the full-chemistry simulations, these inventories are now added for tagged CO and are turned on by default.
--Melissa Sulprizio (talk) 17:37, 21 September 2018 (UTC)
--Bob Yantosca (talk) 16:10, 26 November 2018 (UTC)
Fix regional tile file used for APEI inventory in GCHP
This bug fix only requires downloading updated files from gcgrid/ExtData/GCHP/TileFiles
The regional tile file used by GCHP for regrigding the APEI inventory from native resolution to cubed sphere was incorrect at the time of the 12.0.0 release. The tile file erroneously caused the APEI inventory to be regridded at a 180 degree longitude offset. Corrected tile files now replace the erroneous ones at gcgrid/ExtData/GCHP/TileFiles. No changes are necessary to the model source code or the GCHP run directory.
--Lizzie Lundgren (talk) 17:30, 19 September 2018 (UTC)
Fix masked anthropogenic emissions bug in GCHP
This update was included in GEOS-Chem 12.1.0, which was released on 26 Nov 2018.
Integration of the DICE-Africa inventory in GCHP resulted in erroneously masking out total global anthropogenic emissions outside of Africa. Updating the Africa mask file from containing regional bounds to global bounds corrects the problem. GCHP users who are using the DICE-inventory prior to 12.1.0 can fix the issue by updating their Africa mask file to MASKS/v2014-07/AF_LANDMASK.geos.05x0666.global.nc which is now available on gcgrid.
--Lizzie Lundgren (talk) 16:50, 14 September 2018 (UTC)
--Bob Yantosca (talk) 16:11, 26 November 2018 (UTC)
Add support for continuous integration with TravisCI
This update was included in GEOS-Chem 12.1.0, which was released on 26 Nov 2018.
We have now linked the GEOS-Chem Github repository to the continuous integration tool TravisCI. Each time a commit is pushed to the repository, TravisCI will perform a test to ensure that the commit will not "break" GEOS_Chem. Right now, TravisCI only compiles GEOS-Chem, but we will eventually implement compile-and-run tests in the near future.
You can see the TravisCI status page for GEOS-Chem here: https://travis-ci.com/geoschem/geos-chem/builds
Also, if you navigate to the "commits" page of the GEOS-Chem Github repository, you will see a green checkmark next to each commit that was checked by TravisCI:
NOTE: As of this writing, only the dev/12.1.0 branch is being checked by TravisCI. When we merge this into the master branch, then all future branches will be checked.
--Bob Yantosca (talk) 16:11, 26 November 2018 (UTC)
Replace HEMCO built-in unit conversions with scale factors in config file
This update will be included in GEOS-Chem 12.2.0 or later.
HEMCO checks the unit string in HEMCO_Config.rc for each emission and converts to HEMCO standard units (kg/m2/s) upon file read if the input units are different. For VOCS, it further converts to kgC/m2/s. The code for the unit conversions is in HEMCO/Core/hco_unit_mod.F90.
Since the automatic unit conversion is performed during HEMCO file read it does not get executed in GCHP which uses MAPL/ESMF for I/O. GCHP users must instead manually include the conversion information as scale factors in HEMCO_Config.rc. To increase clarity and to make GCHP and GCC better match we plan on removing the HEMCO built-in unit conversions and replacing them with scale factors in HEMCO_Config.rc. This change may result in small number differences due to order of operations and precision of scale factors.
--Lizzie Lundgren (talk) 19:57, 23 August 2018 (UTC)
--Bob Yantosca (talk) 16:11, 26 November 2018 (UTC)
Fixed local-time averaging in ND51 and ND51b satellite timeseries diagnostics
This update was included in GEOS-Chem 12.0.2, which was released on 10 Oct 2018.
Bo Zhang wrote:
We encountered a potential issue in the satellite diagnostic ND51b in GEOS-Chem v11-01. We find some kind of discontinuity in total column AOD (a sum of all aerosol species) along the west-east direction. It feels like data are missing/reduced occasionally in every other pixels alone the W-E direction. We are running v11-01 with full chemistry + UCX driven by MERRA2. The same problem remains after switching to MERRA. We checked AOD maps in monthly output which looks normal.
Bob Yantosca replied:
In recent versions of GEOS-Chem, the number of advected species increased (to accommodate additional halogen and SOA species). So we had to increase the non-species tracer numbers to 500:
! ND51 tracer numbers:
! ============================================================================
! 1 - nAdvect : GEOS-CHEM advected species [v/v ]
! 501 : OH concentration [molec/cm3 ]
! 502 : NOy concentration [v/v ]
! 503 : Relative Humidity [% ]
! ... etc ...
Complicating matters further, some ND51/ND51b quantities, including the AOD’s, were only updated on every chemistry timestep (20 mins) instead of on every dynamic timestep (10 mins). There was a CASE statement in routine WRITE_DIAG51 to divide by the proper counting array to create the average quantity:
SELECT CASE( Input_Opt%ND51_TRACERS(W) )
CASE( 91, 92, 76, 77 )
... etc ...
CASE( 84:89, 115:121 )
... etc ...
CASE( 105:114 )
... etc ...
CASE DEFAULT
... etc ...
END SELECT
But we just realized that this CASE statement had the old ND51/ND51b tracer numbers ( < 500) and not the new ones.Therefore, we have made the following fixes, which should eliminate any striping or discontinuities
Also note: the ND51/ND51b diagnostics were developed in an ad-hoc fashion and were were never really thought out holistically. It is possible that there may be some issues with some of the other quantities in ND51/ND51b, but the GCST is not planning on investigating further. The bpch diagnostics will be eventually removed from GEOS-Chem once we have a satisfactory equivalent local-time averaging netCDF diagnostic.
- Archive most ND51/ND51b tracers (except for NOy, which has special handling) on every dynamic timestep. Remove the GOOD_CHEM, GOOD_CT_CHEM, GOOD_EMIS, GOOD_CT_EMIS arrays.
- Update the CASE statement shown above so that all tracers (except NOy) are divided by the number of dynamic timesteps when each grid box was within the proper local time range.
--Bob Yantosca (talk) 15:12, 10 October 2018 (UTC)
Fix typo when registering the State_Chm%SSAlk field
This update was included in GEOS-Chem 12.0.1, which was released on 24 Aug 2018.
Shuting Zhai wrote:
I found a typo in state_chm_mod.F90 where we register the State_Chm%SSAlk field. I believe this line:
CALL Register_ChmField( ... State_Chm%pHCloud, ... )
Should be:
CALL Register_ChmField( ... State_Chm%SSAlk, ... )
Upon fixing this issue, the GCST discovered that the State_Chm%SSAlk array cannot be registered as a single array because it is dimensioned as (IIPAR,JJPAR,LLPAR,2). When registering quantities, the 4th dimension is always interpreted as the number of chemical species. Therefore, registering State_Chm%SSAlk in this way caused an error.
The solution is to register the two dimensions of State_Chm%SSAlk separately:
- SSAlkAccum points to State_Chm%SSAlk(:,:,:,1)
- SSAlkCoarse points to State_Chm%SSAlk(:,:,:,2)
This update will require you to list Chem_SSAlkAccum and Chem_SSAlkCoarse as requested diagnostics instead of the single field Chem_SSAlk in the HISTORY.rc file ( which specifies input options for netCDF diagnostics).
--Bob Yantosca (talk) 15:33, 23 August 2018 (UTC)
Fixes for compilation issues
We have added several fixes for issues encountered during GEOS-Chem compilation:
- Add a more robust test for netCDF-Fortran in Makefile_header.mk
- Fixes for compilation issues encountered with GNU Fortran 8.2.0
- Fixes for compilation issues encountered with Intel Fortran 18
--Bob Yantosca (talk) 14:26, 22 August 2018 (UTC)
Fix mis-indexing in the ND05 diagnostic
This update was included in GEOS-Chem 12.0.1, which was released on 24 Aug 2018.
For a complete description of this issue, please see this post on our Sulfate aerosols wiki page.
--Bob Yantosca (talk) 14:18, 22 August 2018 (UTC)
Bug fix for HEMCO soil NOx error with ifort 17
This fix was included in GEOS-Chem 12.0.0.
For complete information about this issue and how it was resolved, please see this post on our Implementation of HEMCO in GEOS-Chem wiki page..
--Bob Yantosca (talk) 13:54, 27 June 2018 (UTC)
FlexChem bug fix: do not zero ACTA, EOH, HCOOH
This fix was included in GEOS-Chem 12.0.0.
For complete information about this bug and how it was fixed, please see this post on our FlexChem wiki page.
--Bob Yantosca (talk) 14:42, 27 June 2018 (UTC)
Avoid double counting CEDS and GEIA NH3 biofuel emissions
This fix was included in GEOS-Chem 12.0.0.
Eloise Marais wrote:
If CEDS includes NH3 emissions, then this will be double counting. I recommend using CEDS, as GEIA is very out of date (1998 according to the HEMCO configuration file I have).
Daniel Jacob replied:
We should use the GEIA NH3 natural emission inventory (1° x 1° file from Eleanor Morris) but not the GEIA NH3 biofuel inventory.
UPDATE 29 Jun 2018:
We discovered that HEMCO's default behavior is to ignore the GEIA NH3 anthro and biofuel emissions if CEDS is turned on. This is shown in the HEMCO.log file when VERBOSE = 3:
Register_Base: Checking GEIA_NH3_ANTH HEMCO: Entering Get_targetID (hco_config_mod.F90) ( 4) Skip container GEIA_NH3_ANTH because of CEDS_NH3_WST . . . Register_Base: Checking GEIA_NH3_BIOF HEMCO: Entering Get_targetID (hco_config_mod.F90) ( 4) Skip container GEIA_NH3_BIOF because of CEDS_NH3_WST_Cat00002
But for the sake of clarity, we will modify the HEMCO_Config.rc files to explicitly request this behavior:
(((.not.CEDS.or.EDGARv43 # GEIA NH3 anthro (skip if CEDS or EDGARv43 is on) 0 GEIA_NH3_ANTH $ROOT/NH3/v2014-07/NH3_geos.4x5.nc NH3_ANTH 1990/1-12/1/0 C xy kg/m2/s NH3 - 1 1 # GEIA NH3 biofuel (skip if CEDS or EDGARv43 is on) (((BIOFUEL 0 GEIA_NH3_BIOF $ROOT/NH3/v2014-07/NH3_biofuel.geos.1x1.nc NH3_BIOFUEL 1998/1-12/1/0 C xy kg/m2/s NH3 - 2 1 )))BIOFUEL ))).not.CEDS.or.EDGARv43
--Bob Yantosca (talk) 21:02, 29 June 2018 (UTC)
Fix bug in ARCTAS_SHIP_SO2 scale factors
This fix was included in GEOS-Chem 12.0.0.
For a complete description of this issue and how it was resolved, please see this post on our Ship Emissions wiki page.
--Bob Yantosca (talk) 15:54, 3 July 2018 (UTC)
Fix issues in complexSOA and complexSOA_SVPOA restart files
This fix was included in GEOS-Chem 12.0.0.
Eloise Marais wrote:
I just wanted to draw your attention to a few issues with the restart files provided on the ftp site (http://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/). The complexSOA and complexSOA_SVPOA restart files (4° x 5° and 2° x 2.5°) both have a species entry for IEPOX and also IEPOXD, IEPOXB, and IEPOXA, but should only have the latter 3. This is the same for RIP. The number of species in the 4° x 5° and 2° x 2.5° files for complexSOA is also different.
To fix these issues, we have generated new restart files for the complexSOA and complexSOA_SVPOA simulations. You can download these to your SPC_RESTARTS folder with the following commands:
wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.2x25_complexSOA.nc" wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.2x25_complexSOA_SVPOA.nc" wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.4x5_complexSOA.nc" wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.4x5_complexSOA_SVPOA.nc"
--Bob Yantosca (talk) 18:01, 5 July 2018 (UTC)
Bug fix for reference time in netCDF diagnostic files
This fix was included in GEOS-Chem 12.0.0.
Maria Zatko wrote:
For the sake of run time, we would like to run GEOS-Chem with the old (15/30 minute timesteps) instead of the recommended timesteps (10/20 minutes). I noticed that the output netcdf files have different timestamps depending on the timestep (e.g., 10/20 minutes, 15/30 minutes) used. For example, when 10/20 minute timesteps are used, the time units in the following netcdf output files range from 0 to 23 UTC:
GEOSChem3hrInst.SpeciesConcWithMet.20150701_0000z.nc4 (file size: 4.6 GB)
GEOSChem3hrInst.SpeciesConcWithMet.20150702_0000z.nc4 (file size: 5.3 GB)
time:units = "minutes since 2015-07-01 00:00:00 UTC"
When 15/30 minute timesteps are used, the time units in the following output files include hour 24:
GEOSChem3hrInst.SpeciesConcWithMet.20150701_0000z.nc4 (file size: 4.6 GB)
GEOSChem3hrInst.SpeciesConcWithMet.20150701_2400z.nc4 (file size: 5.3 GB)
GEOSChem3hrInst.SpeciesConcWithMet.20150702_2400z.nc4 (file size: 5.3 GB)
time:units = "minutes since 2015-07-01 24:00:00 UTC"
I wanted to check in to see if others have run into this issue as well.
Bob Yantosca replied:
This issue is caused by floating-point roundoff error in converting from the Julian date to the calendar date. I have created a more robust fix for this issue, which now computes the correct netCDF file reference time independent of the model "heartbeat" timestep.To apply the fix:
The fix will be standardized in the GEOS-Chem 12.0.0 release.
- Copy the patch file ftp://ftp.as.harvard.edu/pub/exchange/bmy/nc_ref_time_fix.txt to your computational server.
- Change to your GEOS-Chem v11-02 release candidate code directory and check out the "master" branch.
- Type: git am < nc_ref_time_fix.txt
--Bob Yantosca (talk) 15:10, 12 July 2018 (UTC)
Bug fix for CH4 boundary conditions
This fix was included in GEOS-Chem 12.0.0.
Lee Murray wrote:
I’ve been testing the release candidate, and believe that we need to change the default input.geos options for the Standard and Benchmark simulations in the unit tester to :
%%% EMISSIONS MENU %%% :
Turn on emissions? : T
HEMCO Input file : HEMCO_Config.rc
=> 1ppt MBL BRO Sim.? : F
Switches for UCX :---
=> Use CH4 emissions? : F
=> Turn on surface BCs :---
=> CH4? : F
=> OCS? : T
=> CFCs? : T
=> Cl species? : T
=> Br species? : F
=> N2O? : T
=> Set initial glob MRs:---
=> strat. H2O? : T
=> CFC emission year : 0
By default in the unit tester, => CH4 is still enabled. This appears to set up conflict between the older UCX surface layer and the newer HEMCO methane PBL boundary conditions, causing air to be a mix of preindustrial and present-day values (see below for Jul 1, 2013 surface methane in a benchmark run). Setting it to F and/or removing LCH4SBC causes the methane to behave as expected, i.e., being set by HEMCO in all simulations, with the expected spatial pattern. Also, we can slate Online CH4 chemistry? : T in the Chemistry Menu and Input_Opt%LCH4CHEM for future removal, as it no longer does anything.
--Melissa Sulprizio (talk) 18:16, 16 July 2018 (UTC)
Fixed typo in call to GAMMA_HOBr_AER
This fix was included in GEOS-Chem 12.0.0.
Xuan Wang wrote:
When looking back at the standard GC codes of v11-02d, I found a bug in the function HETHOBr_SS_JS (in module KPP/Standard/gckpp_HetRates.F90). When calling the gamma calculation, in v11-02d, around line 3514, we have:
CALL Gamma_HOBr_AER(rAer, denAir, 2, TK, clConc, brConc, &
hConc, GAM_HOBr, r_gp)
This will cause both HOBr+Cl- (X=1) and HOBr+Br- (X=2) on sea salt use the gamma of HOBr + Br- (X=2). It should be:
CALL Gamma_HOBr_AER(rAer, denAir, X, TK, clConc, brConc, &
hConc, GAM_HOBr, r_gp)
It looks like a typo which could lead to quite different result for halogen chemistry.
--Bob Yantosca (talk) 20:26, 17 July 2018 (UTC)
Bug fix for liquid water content in gckpp_HetRates.F90
This fix was included in GEOS-Chem 12.0.0.
Jiayue Huang wrote:
Qianjie Chen and I think that there is potential a bug in KPP/Standard/gckpp_HetRates.F90 for halogen chemistry in the model v11-02d/e/f.In the original code, we were using the grid-box average liquid water content, which likely underestimates the in-cloud Br- and Cl- concentration. So we think that we should change it to in-cloud liquid water content by dividing the cloud fraction. This results in increases the S(IV)+Br reaction in cloud, and thus reduces the BrO abundance, mainly in the 30-90N region.
This bug fix is to use cloud fraction when calculating liquid water content [cm3 H2O/cm3 air] in routine GET_HALIDE_CLDConc, which is used to calculate the in-cloud concentrations of Br- and Cl-.
--Bob Yantosca (talk) 15:48, 20 July 2018 (UTC)
Add PH2O2 to the default list of prod/loss families in the KPP mechanisms
This fix was included in GEOS-Chem 12.0.0.
The P(H2O2) field is required as input in the aerosol-only simulations. To simplify saving out new oxidant fields, we now include P(H2O2) by default in the prod/loss families so that it is saved out when users turn on the prod/loss diagnostic in either bpch or netCDF format.
--Bob Yantosca (talk) 16:16, 20 July 2018 (UTC)
Fixed typo that prevented PM2.5 from being archived to netCDF output
This fix was included in GEOS-Chem 12.0.0.
In routine Set_AerMass_Diagnostic of module GeosCore/diagnostics_mod.F90, there was a typo in the IF block where the PM2.5 diagnostic values get copied into State_Diag%PM25. The code in RED below:
IF ( Archive_BetaNO ) THEN
State_Diag%PM25(I,J,L) = ...etc...
needs to be replaced by the code in GREEN:
IF ( Archive_PM25 ) THEN
State_Diag%PM25(I,J,L) = ...etc...
--Bob Yantosca (talk) 20:33, 24 July 2018 (UTC)
Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory
This fix was included in GEOS-Chem 12.0.0.
The CEDS emissions entries in HEMCO_Config.rc were missing for species SOAP and pFe. To fix this, add the following lines in GREEN:
0 CEDS_CO_AGR $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc CO_agr 1950-2014/1-12/1/0 C xy kg/m2/s CO 26 1/2/12 5 0 CEDS_SOAP_AGR - - - - - - SOAP 26/280 1/2/12 5 0 CEDS_CO_ENE $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc CO_ene 1950-2014/1-12/1/0 C xy kg/m2/s CO 26 1/2/12 5 0 CEDS_SOAP_ENE - - - - - - SOAP 26/280 1/2/12 5 0 CEDS_CO_IND $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc CO_ind 1950-2014/1-12/1/0 C xy kg/m2/s CO 26 1/2/12 5 0 CEDS_SOAP_IND - - - - - - SOAP 26/280 1/2/12 5 0 CEDS_CO_TRA $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc CO_tra 1950-2014/1-12/1/0 C xy kg/m2/s CO 26 1/2/12 5 0 CEDS_SOAP_TRA - - - - - - SOAP 26/280 1/2/12 5 0 CEDS_CO_SLV $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc CO_slv 1950-2014/1-12/1/0 C xy kg/m2/s CO 26 1/2/12 5 0 CEDS_SOAP_SLV - - - - - - SOAP 26/280 1/2/12 5 0 CEDS_CO_WST $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc CO_wst 1950-2014/1-12/1/0 C xy kg/m2/s CO 26 1/2/12 5 0 CEDS_SOAP_WST - - - - - - SOAP 26/280 1/2/12 5 0 CEDS_SO2_AGR $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc SO2_agr 1950-2014/1-12/1/0 C xy kg/m2/s SO2 - 1/2/12 5 0 CEDS_SO4_AGR - - - - - - SO4 63 1/2/12 5 0 CEDS_pFe_AGR - - - - - - pFe 66 1/2/12 5 0 CEDS_SO2_ENE $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc SO2_ene 1950-2014/1-12/1/0 C xy kg/m2/s SO2 - 1/2/12 5 0 CEDS_SO4_ENE - - - - - - SO4 63 1/2/12 5 0 CEDS_pFe_ENE - - - - - - pFe 66 1/2/12 5 0 CEDS_SO2_IND $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc SO2_ind 1950-2014/1-12/1/0 C xy kg/m2/s SO2 - 1/2/12 5 0 CEDS_SO4_IND - - - - - - SO4 63 1/2/12 5 0 CEDS_pFe_IND - - - - - - pFe 66 1/2/12 5 0 CEDS_SO2_TRA $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc SO2_tra 1950-2014/1-12/1/0 C xy kg/m2/s SO2 - 1/2/12 5 0 CEDS_SO4_TRA - - - - - - SO4 63 1/2/12 5 0 CEDS_pFe_TRA - - - - - - pFe 66 1/2/12 5 0 CEDS_SO2_SLV $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc SO2_slv 1950-2014/1-12/1/0 C xy kg/m2/s SO2 - 1/2/12 5 0 CEDS_SO4_SLV - - - - - - SO4 63 1/2/12 5 0 CEDS_pFe_SLV - - - - - - pFe 66 1/2/12 5 0 CEDS_SO2_WST $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc SO2_wst 1950-2014/1-12/1/0 C xy kg/m2/s SO2 - 1/2/12 5 0 CEDS_SO4_WST - - - - - - SO4 63 1/2/12 5 0 CEDS_pFe_WST - - - - - - pFe 66 1/2/12 5
--Melissa Sulprizio (talk) 16:07, 27 July 2018 (UTC)
Remove duplicate C3HI spectrum in FJX_spec.dat and FJX_j2j.dat
This fix was included in GEOS-Chem 12.0.0.
Tomas Sherwen wrote:
- I've just found that both FJX_spec.dat the redundant CH3I spectrum and the new spectrum are both present in FJX_spec.dat and FJX_j2j.dat (in v12.0.0). This will have been due to the spectrum in my branch being under the species alias of "CH3IT" to preserve (and ignore) the use of "CH3I" in the namespace of the code for the existing methyl iodide simulation when the iodine simulation was developed. The "CH3IT" variables were replaced "CH3I" in the v11-1-Patches branches with halogen chemistry provided to GCST, but the existing methyl iodide simulation variable was not removed. There are no double ups in the KPP mechanism itself.
- Please remove lines 276-281 in FJX_spec.dat (copied below).
"
CH3I 243 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10
3.958E-20 4.769E-20 8.257E-19 2.154E-19 7.349E-20 3.351E-20
1.034E-20 4.435E-21 2.272E-21 4.393E-22 4.052E-24 0.000E+00
CH3I 300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10
3.958E-20 4.769E-20 8.376E-19 2.438E-19 9.355E-20 4.680E-20
1.529E-20 6.532E-21 3.328E-21 6.783E-22 1.038E-23 0.000E+00
"
- Please also remove the line 124 in FJX_j2j.dat (copied below).
"
123 CH3I PHOTON I PRODUCTS 1.000 /CH3I /
"
--Melissa Sulprizio (talk) 17:44, 27 July 2018 (UTC)
Outstanding issues not yet resolved in GEOS-Chem 12
GCHP silent bug when using gfortran compiler: Olson land map read as all zeros
This error is known to occur with GEOS-Chem 12.1.0 and previous versions. It is currently unresolved.
--Lizzie Lundgren (talk) 20:58, 4 January 2019 (UTC)
Error reading restart file when using a fixed emissions year in HEMCO
This error is known to occur with GEOS-Chem 12.1.0 and higher versions. It is currently unresolved.
Anthony Y.H. Wong wrote:
I use the v12.1.0 to run tropchem simulations that have to fix emission year. I used
Emission year: 2016
in my HEMCO_Config.rc file. The error message in HEMCO reads:
File:Hemco restart error fixed emission year gc12.png
Once I deleted the line in HEMCO_Config.rc that specifies emission year, the model runs normally. That "1713" is apparently the source of the problem. Perhaps when GC restart files is read from HEMCO, somehow the emission time confuses the real time steps. Is there any solution to this problem?
Melissa Sulprizio wrote:
I think I may have found the problem. As you indicated, you have set a fixed emissions year in your HEMCO configuration file. This will change the year for any file read in via HEMCO to the specified year. However, your restart file and the met fields that you want to use for your simulation are for July 2016.As a temporary fix, you can remove the $YYYY tokens from the GC_RESTART entries and the met field entries in HEMCO_Config.rc and manually set it to the year of your restart file (which is 2016).
We will need to think of a more elegant solution in HEMCO for this issue.
--Bob Yantosca (talk) 19:23, 20 December 2018 (UTC)
Inconsistency in H2402 concentrations in GCHP vs GEOS-Chem Classic
We have discovered an inconsistency with the concentrations of the halogen species H2402 (chemical formula: C2Br2F4) between GEOS-Chem "Classic" and GCHP. This inconsistency appears as the large fractional difference above ~50 km in the lower-right frame of the plot below.
We have traced this issue to the fact that surface boundary conditions for H2402 used by GCHP differ from those used by GEOS-Chem "Classic", and also that the boundary conditions in GEOS-Chem "Classic" are read in improperly. A fix will be made in an upcoming GEOS-Chem version.
--Bob Yantosca (talk) 20:10, 7 December 2018 (UTC)
RRTMG does not compile with GNU Fortran
For a complete description of this issue, please see this post on our Coupling GEOS-Chem with RRTMG wiki page.
--Bob Yantosca (talk) 18:55, 3 August 2018 (UTC)
TOMAS40 simulations exit with a floating-point exception
We were unit testing the TOMAS40 code in the GEOS-Chem v11-02-release-candidate (soon to be finalized as 12.0.0) with the debugging flags:
make –j8 DEBUG=y BOUNDS=y FPEX=y NO_ISO=y ut &
which revealed a a NaN error. This was thrown at line 903 of GeosCore/tomas_mod.F:
ERR_VAR = 'Gcout'
ERR_MSG = 'After COND_NUC'
! check for NaN and Inf (win, 10/4/08)
do jc = 1, icomp-1
ERR_IND(1) = I
ERR_IND(2) = J
ERR_IND(3) = L
ERR_IND(4) = 0
call check_value( Gcout(jc), ERR_IND, ERR_VAR, ERR_MSG )
! if( IT_IS_FINITE(Gcout(jc))) then
! print *,'xxxxxxxxx Found Inf in Gcout xxxxxxxxxxxxxx'
! print *,'Location ',I,J,L, 'comp',jc
! call debugprint( Nkout, Mkout, i,j,l,'After COND_NUC')
! stop
! endif
enddo
This error might be caused by the several chemistry and emissions updates that have been added to GEOS-Chem. The GEOS-Chem Support Team has referred the error to the TOMAS development team, who will be investigating further.
--Bob Yantosca (talk) 16:56, 6 August 2018 (UTC)
TOMAS simulations cannot use netCDF diagnostics
The TOMAS simulations depend on many of the "binary punch" (aka "bpch") diagnostics. As of this time, we have not yet been able to convert these to the new netCDF diagnostics. Therefore, as of GEOS-Chem 12.0.0, all TOMAS simulations must use the binary punch diagnostic option (which is turned ON by default at compile time). If you try to compile a TOMAS simulation with netCDF diagnostics (i.e. with makefile option NC_DIAG=y), then a compile-time error will be generated.
--Bob Yantosca (talk) 15:28, 9 August 2018 (UTC)
