GEOS-Chem 12: Difference between revisions
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Revision as of 22:21, 12 September 2018
GEOS-Chem v11-02-final will also carry the designation GEOS-Chem 12.0.0. We are migrating to a purely numeric versioning system in order to adhere more closely to software development best practices. For a complete description of the new versioning system, please see our GEOS-Chem version numbering system wiki page.
Version history summary
| Previous major release | Current stable version | Version in development |
|---|---|---|
| GEOS-Chem v11-01-public | GEOS-Chem 12.0.1 DOI: 10.5281/zenodo.1403144 |
GEOS-Chem 12.1.0 |
| Released01 Feb 2017 | Released 24 Aug 2018 | Release TBD |
| GC v11-01 online manual | GC 12 online manual | GC 12 benchmark history |
The sections below describe each GEOS-Chem feature version and GEOS-Chem 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.
12.1.0
The items listed below are slated to be included in GEOS-Chem 12.1.0. This is a feature release which will be validated with a 1-month benchmark simulation.
| Feature | Submitted by | Type | Notes |
|---|---|---|---|
| Features affecting the full-chemistry simulation: | |||
| FlexGrid Stage 1: Use HEMCO to read met fields | Jiawei Zhuang (Harvard) Jintai Lin (PKU) |
Structural |
|
| Anthropogenic PM2.5 dust source | Sajeev Philip (Dalhousie) | Science |
|
| NetCDF Output Phase 3b: Updates to eliminate differences between single and multi-segmented GEOS-Chem runs | GCST Christoph Keller (GMAO) |
Bug Fix & Structural |
|
| Updates and fixes for the CEDS anthropogenic emissions inventory: | Pengfei Liu (Harvard) Melissa Sulprizio (GCST) Jiawei Zhuang (Harvard) |
Bug fix | Now in dev/12.1.0 branch
|
| Replace HEMCO built-in unit conversions with scale factors in config file | GCST | Structural |
|
| Fix mass conservation in non-local PBL mixing | Jintai Lin (PKU) | Bug fix | |
| Features NOT affecting the full-chemistry simulation: | |||
| Add support for continuous integration with TravisCI – automatically test each commit as soon as it is pushed to Github | Jiawei Zhuang (Harvard) GCST |
Structural | |
| Budget diagnostics | Chris Holmes (Florida State) Lizzie Lundgren (GCST) |
Diagnostics | |
| 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 |
|
Current bug fix patch version in development
This version adds fixes for bugs or technical issues that were discovered after the current stable version listed below was released.
- At this time there are no bug fix patch versions in development.
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 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.
12.0.1
This version was released on 24 Aug 2018.
GEOS-Chem 12.0.1 contains fixes for minor issues discovered after the GEOS-Chem 12.0.0 release.
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 master 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 master
| 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 | |
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.
12.0.0
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
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 v2.1.007, 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
The following HEMCO data directories have been added or updated for GEOS-Chem 12. You will have to download the directories relevant to your simulation.
| Inventory | Type | What was added? | Version added | Directory |
|---|---|---|---|---|
| QFED biomass burning emissions | OPTIONAL | New data files for QFED v2.5r1 | 12.0.0 | HEMCO/QFED/v2018-07 |
| GFED4 biomass burning emissions | DEFAULT | GFED4.1 data files for 2015 and 2016 have been added | 12.0.0 | HEMCO/GFED4/v2015-10/2015 HEMCO/GFED4/v2015-10/2016 |
| CEDS anthropogenic emissions | DEFAULT | Reduce file size for CEDS inventory | 12.1.0 | HEMCO/CEDS/v2018-08/YYYY |
| DICE Africa emissions | DEFAULT | New regional emission inventory for Africa | 12.0.0 | HEMCO/DICE_Africa
|
| MEGAN 2.1 biogenic emissions | DEFAULT | Update for MEGAN biogenic emissions | 12.0.0? | HEMCO/MEGAN/v2018-05, v2017-07
|
| OMOC | DEFAULT | OMOC | 12.0.0? | HEMCO/OMOC |
| APEI | DEFAULT | APEI | 12.0.0? | HEMCO/APEI |
| EDGAR v4.3 | DEFAULT | Update for EDGAR global anthropogenic emissions | 12.0.0? | HEMCO/EDGARv43 |
| NH3 emissions from sea birds | DEFAULT | New NH3 emissions from sea birds | 12.0.0? | HEMCO/NH3/v2018-04 |
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.
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.
Add support for continuous integration with TravisCI
This update will be included in GEOS-Chem 12.1.0.
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) 16:23, 27 August 2018 (UTC)
Replace HEMCO built-in unit conversions with scale factors in config file
This update will be included in GEOS-Chem 12.1.0.
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)
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:
- 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
The fix will be standardized in the GEOS-Chem 12.0.0 release.
--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
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)