Difference between revisions of "GEOS-Chem v10-01"
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Revision as of 20:09, 12 January 2015
Contents
- 1 Overview
- 2 Previous issues now resolved in GEOS-Chem v10-01
- 2.1 Now use correct value of molecular weight for the PROPNN tracer in input.geos
- 2.2 Now use MAP_A2A to regrid 1x1 TOMS O3 to model resolution
- 2.3 Bug fix for determining when to use TOMS O3 columns
- 2.4 Fixes for the stratospheric chemistry module
- 2.5 Various updates for GEOS-Chem specialty simulations
- 2.6 Updates to speed up GEOS-Chem execution
- 2.7 Bug fixes and and updates for v10-01d
- 2.8 Reactivating dust tracers in TOMAS simulations
- 2.9 Fix for ND61 diagnostic in TOMAS simulations
- 3 Outstanding issues not yet resolved in GEOS-Chem v10-01
Overview
History
The table below shows the previous, current, and successive versions of GEOS-Chem:
Previous version | This version | Next version |
---|---|---|
GEOS-Chem v9-02 | GEOS-Chem v10-01 | TBD |
PUBLIC RELEASE 03 Mar 2014 | TBD | TBD |
View v9-02 benchmark history | View v10-01 benchmark history | TBD |
--Bob Y. 13:17, 16 January 2014 (EST)
What's new in this version
GEOS-Chem v10-01 will be released after a fixed interval of time (approxmiately 9 months after the release of the prior version, GEOS-Chem v9-02). The GEOS-Chem Steering Committee has prioritized the following updates and improvements for inclusion into GEOS-Chem v10-01. (This list is subject to change.) Updates that do not get included into GEOS-Chem v10-01 will be held over for the next version.
NOTE: v10-01a, v10-02b, etc. denote 1-month benchmark simulations, which are designed to evaluate GEOS-Chem's performance at intermediate stages of development.
Alternating stripes of color (white & cyan) in the table below group together features that were evaluated in the same 1-month benchmark.
Feature | Type | Submitted by | Benchmark(s) | Status | |||||
---|---|---|---|---|---|---|---|---|---|
Updates to dry deposition when using the Olson 2001 land map | Science | Patrick Kim (Harvard) | v10-01a | Approved 05 Feb 2014 | |||||
Now use correct molecular weight for the PROPNN tracer in input.geos | Bug fix | Jenny Fisher (U. Wollongong) | v10-01b | Approved 06 Mar 2014 | |||||
Use MAP_A2A to regrid 1x1 TOMS O3 to model resolution | Structural | Jintai Lin (Peking U.) | " " | " " | |||||
UCX strat chem mechanism, includes: | Science | UCX: Sebastian Eastham (MIT) Fast-JX: Sebastian Eastham (MIT), Jingqiu Mao (Princeton) |
v10-01c | 1-month benchmark: Approved 29 May 2014 1-year benchmark: Approved 26 Jun 2014 | |||||
Bug fix for determining when to use TOMS O3 columns | Bug fix | GEOS-Chem Support Team | " " | " " | |||||
Add support for TAU performance profiler | Structural | John Linford (ParaTools, Inc.) GEOS-Chem Support Team |
" " | " " | |||||
Fixes for timeseries diagnostics to allow for more transported tracers | Bug fix | GEOS-Chem Support Team | " " | " " | |||||
Fixes for the stratospheric chemistry module | Structural | GEOS-Chem Support Team | " " | " " | |||||
Various updates for GEOS-Chem specialty simulations | Bug fix & Structural |
Jeff Pierce (CSU) Kevin Wecht (Harvard) Matthew Johnson (NASA) GEOS-Chem Support Team |
" " | " " | |||||
Updates to speed up GEOS-Chem execution | Structural | GEOS-Chem Support Team | " " | " " | |||||
Fix error in ISOPO2 isomerization reaction in globchem.dat | Bug fix | Ploy Achakulwisut (Harvard) | v10-01d | Approved 03 Jun 2014 | |||||
Modify NcdfUtil code to allow re-opening of netCDF "define mode" | Structural | GEOS-Chem Support Team | " " | " " | |||||
Fix parallelization error in nested grid simulations | Bug fix | Jintai Lin (Peking U.) | " " | " " | |||||
Fixed bug in ND44 drydep diagnostic for sea salt aerosols | Bug fix | Kateryna Lapina (CU Boulder) | " " | " " | |||||
Implement final recommendation for J(HAC) and J(PAN) in FAST-JX v7.0 | Science | Sebastian Eastham (MIT), Jingqiu Mao (Princeton) | " " | " " | |||||
HEMCO emissions component | Structural | Christoph Keller (Harvard) GEOS-Chem Support Team GMAO |
v10-01e | 1-month benchmark: Approved 07 Nov 2014 1-year benchmark: Approved 01 Dec 2014 | |||||
Removing references to modules made obsolete by GIGC and HEMCO | Structural | GEOS-Chem Support Team | " " | " " | |||||
Reactivating dust tracers in TOMAS simulations | Bug fix | Jeff Pierce (CSU) David Ridley (MIT) |
" " | " " | |||||
Fix for ND61 diagnostic in TOMAS simulations | Bug fix | Betty Croft (Dalhousie) | " " | " " | |||||
Two-way coupling between global and nested GEOS-Chem models | Science | Jintai Lin (Peking U.) Yingying Yan (Peking U.) |
v10-01f | TBD | |||||
Update ALD2 photolysis in FAST-JX v7.0 | Science | Jingqiu Mao (Princeton), Sebastian Eastham (MIT) | " " | " " | |||||
Read 2D data for individual NOx species in ucx_mod.F | Bug fix | Sebastian Eastham (MIT) | " " | " " | |||||
Bug fixes and updates for tagged CO simulation | Bug fix | Jenny Fisher (U. Wollongong) | " " | " " | |||||
Bug fixes for scavenging by co-condensation | Bug fix | Duncan Fairlie (NASA LaRC) | " " | " " | |||||
Correct bugs in stratospheric Bry data | Bug fix | Johan Schmidt (Harvard) | " " | " " | |||||
Introduction of flexible precision into GEOS-Chem | Structural | GEOS-Chem Support Team | " " | " " | |||||
Updates for 0.25° x 0.3125° China nested grid with GEOS-FP meteorology | Structural | Yuxuan Wang (Tsinghua/Galveston) | " " | " " | |||||
Additional minor updates to HEMCO | Structural | Christoph Keller (Harvard) | " " | " " | |||||
Online Radiative Transfer in GEOS-Chem | Science | David Ridley (MIT), Colette Heald (MIT) |
v10-01g | TBD | Add fix to prevent a segmentation fault in HEMCO when emissions are turned off | Bug fix | Christoph Keller (Harvard) | " " | " " |
FINN biomass burning emissions | Science | Jenny Fisher (U. Wollongong) Min Huang (JPL) |
v10-01h | Will be added via HEMCO (order TBD) | |||||
Updates to ship NOx chemistry, includes: | Science & Bug fix | Chris Holmes (UC Irvine) Geert Vinken (Eindhoven) |
TBD | Will be added via HEMCO (order TBD) | |||||
Update EMEP emissions for 2008-2010 | Science | Aaron van Donkelaar (Dalhousie) | TBD | Will be added via HEMCO (order TBD) | |||||
MASAGE NH3 inventory | Science | Fabien Paulot (Harvard) | TBD | Will be added via HEMCO (order TBD) | |||||
HTAP and hi-res Asian emissions | Science | Qiang Zhang (Tsinghua U.) | TBD | Will be added via HEMCO (order TBD) | |||||
Improve temporal resolution of anthropogenic CO2 sources | Science | Ray Nassar (Environment Canada) | TBD | Will be added via HEMCO (order TBD) | |||||
Replace CASA CO2 biosphere climatology with year-specific fluxes | Science | Ray Nassar (Environment Canada) Dylan Jones (U. Toronto) |
TBD | Will be added via HEMCO (order TBD) | |||||
UNEP 2010 anthropogenic Hg emissions | Science | Shaojie Song (MIT) | TBD | Will be added via HEMCO (order TBD) | |||||
Historical anthropogenic atmospheric emissions of Hg | Science | Bess Corbitt (Harvard) | TBD | Will be added via HEMCO (order TBD) | |||||
NEI 2008 emissions with hourly resolution | Science | Katie Travis (Harvard) | TBD | Will be added via HEMCO (order TBD) | |||||
Update to MEGAN2.1 | Science | Dylan Millet (U. Minnesota) | TBD | Will be added via HEMCO (order TBD) | |||||
Update to EDGAR 4.2 anthropogenic emissions | Science | Meng Li and Qiang Zhang (Tsinghua) Sajeev Philip (Dalhousie) |
TBD | Will be added via HEMCO (order TBD) | |||||
NEI 2008 Hg emission inventory | Science | Yanxu Zhang (Harvard) | TBD | Will be added via HEMCO (order TBD) | |||||
Update OTD/LIS factors for GEOS-FP through October 2014 | Science | Lee Murray (Columbia) | TBD | Will be added via HEMCO (order TBD) | |||||
PAN / Organics | Science | Emily Fischer (CSU) | TBD | TBD | |||||
CO2 direct effect on isoprene emissions | Science | Amos Tai (The Chinese University of Hong Kong) | TBD | TBD | |||||
Arctic Hg cycling | Science | Jenny Fisher (U. Wollongong) | TBD | TBD | |||||
Criegee intermediate | Science | Dylan Millet (U. Minnesota) | TBD | TBD | |||||
Impaction scavenging for hydrophobic BC | Science | Qiaoqiao Wang (formerly Harvard, now Max-Planck Institute) | TBD | TBD | |||||
Homogeneous IN removal | Science | Qiaoqiao Wang (formerly Harvard, now Max-Planck Institute) | TBD | TBD | |||||
Acid uptake on dust aerosols | Science | T. Duncan Fairlie (NASA/LARC) | TBD | TBD | |||||
Subsurface ocean Hg concentration update | Science | Anne Soerensen (Harvard) | TBD | TBD | |||||
RRTMG radiative transfer code in APM aerosol microphysics | Science | Fangqun Yu (SUNY Albany) | TBD | TBD | |||||
Interannual lightning | Science | Lee Murray (Harvard) | TBD | TBD | |||||
Updates to PAH code | Science | Carey Friedman (MIT) Helen Amos (Harvard) |
TBD | TBD | |||||
Improved dust size distribution scheme | Science | Li Zhang (Colorado U.) Daven Henze (Colorado U.) |
TBD | TBD |
--Melissa Sulprizio 17:31, 6 January 2015 (EST)
New data directories
The following new data directories have been added for GEOS-Chem v10-01. You will have to download the directories relevant to your simulation.
You can download these directories with anonymous FTP or the Wget utility. For instructions, please see Chapter 2.4, Downloading the GEOS-Chem shared data directories in the GEOS-Chem Online User's Guide.
ExtData/HEMCO # Emission files for HEMCO (netCDF format) GEOS_NATIVE/UCX_201403 # Input files for the UCX mechanism
--Melissa Sulprizio 12:52, 12 January 2015 (EST)
Previous issues now resolved in GEOS-Chem v10-01
The following bugs and/or technical issues have now been resolved in GEOS-Chem v10-01.
Now use correct value of molecular weight for the PROPNN tracer in input.geos
This update was validated in the 1-month benchmark simulation v10-01b and approved on 06 Mar 2014.
This unresolved issue from GEOS-Chem v9-02 has now been corrected.
--Bob Y. 15:45, 12 March 2014 (EDT)
Now use MAP_A2A to regrid 1x1 TOMS O3 to model resolution
This update was validated in the 1-month benchmark simulation v10-01b and approved on 06 Mar 2014.
For complete information about this issue, please see this post on our FAST-J photolysis mechanism wiki page.
--Bob Y. 15:47, 12 March 2014 (EDT)
Bug fix for determining when to use TOMS O3 columns
This update was validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.
For complete information about this issue, please see this post on our FAST-J photolysis mechanism wiki page.
--Bob Y. 16:58, 30 May 2014 (EDT)
Fixes for the stratospheric chemistry module
These updates were validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.
We have introduced the following fixes to the stratospheric chemistry module. Please see the following posts for more information:
- Reduce memory footprint of the stratospheric chemistry module
- Bug fix in routine GET_RATES_INTERP. affecting nested-grid simulations
--Bob Y. 16:58, 30 May 2014 (EDT)
Various updates for GEOS-Chem specialty simulations
These updates were validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.
We have added several updates (both structural updates and minor bug fixes) to the GEOS-Chem specialty simulations. Please view the following posts for more information:
NOTE: Initializing the various specialty simulations from routine GIGC_Init_Extra is necessaary for compatibility with our Grid-Independent GEOS-Chem (aka GIGC) development. We need to initialize all GEOS-Chem simulations at the start of the simulation, and not on the first chemistry or emissiosn timestep after the simulation has already started. This is a requirement of the Earth System Model Framework (ESMF) software upon which our GIGC code relies.
--Bob Y. 16:58, 30 May 2014 (EDT)
Updates to speed up GEOS-Chem execution
These updates were validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.
We used the GEOS-Chem Unit Tester and the Tuning and Analysis Utilities (TAU) to locate and fix the following inefficiencies in GEOS-Chem:
Location | Problem | Solution |
---|---|---|
Olson land map module | Performance bottleneck | Speed up computations in subroutine COMPUTE_OLSON_LANDMAP |
GEOS-4 convection module | Array temporary | Removed array temporaries in the call to the GEOS-4 convection routine |
GCAP convection module | Array temporary | Removed array temporaries in the call to the GCAP convection routine |
Ocean mercury module | Array temporary | Removed array temporaries in subroutine READ_HG2_PARTITIONING |
GEOS-5 / GEOS-FP / MERRA advection module | Passing a pointer to an explicit-shape array (inefficiency) | Reduce time spent in advection driver routine TPCORE_FVDAS |
GEOS-FP / MERRA convection module | Inefficient load balancing | Reduce time spent in routine DO_CONVECTION when using GEOS-FP or MERRA |
--Bob Y. 16:59, 30 May 2014 (EDT)
Bug fixes and and updates for v10-01d
These updates were validated in the 1-month benchmark simulation v10-01d and approved on 03 Jun 2014.
GEOS-Chem v10-01d contains fixes for the following minor issues:
Location | Problem | Solution |
---|---|---|
globchem.dat input file | Typo in RIO2 reaction | Remove duplicate GLYX product from RIO2 reaction |
NcdfUtil/m_netcdf_io_define.F90 | Need to re-open netCDF define mode to facilitate HEMCO I/O | Added routine NcBegin_Def to open or re-open the netCDF define mode. Turning on define mode lets you to define a netCDF variable and all its attributes. But before you can write the actual data to the netCDF file, you first have to switch to data mode. Being able to switch between define mode and data mode frees you from the restriction of having to define all netCDF variables and attributes in a single step. |
GeosCore/tpcore_geos5_window_mod.F90 GeosCore/tpcore_geosfp_window_mod.F90 |
Parallelization bug in nested grid simulations | Fix parallelization error in nested grid simulations |
GeosCore/seasalt_mod.F | The ND44 dry dep diagnostic was not being archived properly when the non-local PBL mixing option was turned off (i.e. when using TURBDAY full PBL mixing). | Fixed bug in ND44 drydep diagnostic for sea salt aerosols |
Full-chemistry input files:
|
Implement the final recommendation for J(HAC) and J(PAN). We were not able to include this in the 1-month benchmarks for v10-01c. But these were included in the 1-year benchmarks for v10-01c. | Final recommendation for J(HAC) and J(PAN) |
--Bob Y. 17:20, 3 June 2014 (EDT)
Reactivating dust tracers in TOMAS simulations
These updates were validated with the 1-month benchmark simulation v10-01e and approved on Approved 07 Nov 2014.
The TOMAS team has submitted a fix that allows you to use the online dust tracers in TOMAS simulations. Due to a bug in input_mod.F, this capability had been omitted. For more information, please see this post on our TOMAS aerosol microphysics wiki page.
--Bob Y. 16:15, 13 June 2014 (EDT)
Fix for ND61 diagnostic in TOMAS simulations
These updates were validated with the 1-month benchmark simulation v10-01e and approved on Approved 07 Nov 2014.
Betty Croft submitted a fix for the ND61 diagnostic (TOMAS nucleation rates). For more information, please see this post on our TOMAS aerosol microphysics wiki page.
--Melissa Sulprizio 10:28, 17 September 2014 (EDT)
Outstanding issues not yet resolved in GEOS-Chem v10-01
The following issues have not yet been resolved in GEOS-Chem v10-01. Some of these issues represent questions of open research rather than bugs in the source code.
Incorrect photolysis rates in FAST-JX v7.0
Jingqiu Mao (Princeton) and Chris Chan Miller (Harvard) discovered that some FAST-JX v7.0 photolysis rates are incorrect:
These are currently open areas of research in GEOS-Chem.
--Bob Y. 15:50, 27 May 2014 (EDT)