GEOS-Chem v10-01

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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:
TBD
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) " " " "
Online Radiative Transfer in GEOS-Chem Science David Ridley (MIT)
Colette Heald (MIT) 		v10-01f TBD
Correct ALD2 photolysis in FAST-JX v7.0 Bug fix 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) " " " "
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) " " " "
Two-way coupling between global and nested GEOS-Chem models Science Jintai Lin (Peking U.) v10-01g TBD
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)
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 11:26, 18 June 2014 (EDT)

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. 

GEOS_NATIVE/UCX_201403                    # Input files for the UCX mechanism

--Melissa Sulprizio 15:24, 24 February 2014 (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:

  1. Reduce memory footprint of the stratospheric chemistry module
  2. 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:

Simulation Status Updates
C2H6 simulation Needs attention
  • The C2H6 simulation is initialized with a call from routine GIGC_Init_Extra in module GeosCore/input_mod.F.
CH4 simulation Up-to-date
HCN/CH3CN simulation Needs attention
  • The HCN/CH3CN simulation is initialized with a call from routine GIGC_Init_Extra in module GeosCore/input_mod.F.
Tagged CO simulation Up-to-date
Hg + Global Terrestrial Mercury Model Up-to-date
POPs simulation Up-to-date
Tagged O3 simulation Up-to-date
TOMAS aerosol microphysics Up-to-date

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:
  • globchem.dat
  • FJX_spec.dat
 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 are being validated with the 1-month benchmark simulation v10-01e.

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 are being validated with the 1-month benchmark simulation v10-01e.

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:

  1. Incorrect carbonyl nitrate photolysis rate
  2. Incorrect acetaldehyde photolysis rate

These are currently open areas of research in GEOS-Chem.

--Bob Y. 15:50, 27 May 2014 (EDT)

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