GEOS-Chem v9-02

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NOTE: In light of our new benchmarking procedure instituted at IGC5, every GEOS-Chem version released to the user community is now a public release, in the sense that we run a 1-year benchmark before making the code available. The 1-month benchmarks now replace what we used to call "beta releases". This allows us to retire the last two numbers in the version name. We shall henceforth denote GEOS-Chem versions as GEOS-Chem v9-02, etc. instead of using the previous nomenclature (e.g. GEOS-Chem v9-01-03).

Overview

What's new in this version

GEOS-Chem v9-02 shall contain the following major updates and improvements. The order has been determined by the GEOS-Chem Steering Committee. We will also continue to add source code updates for the Grid-independent GEOS-Chem project at regular intervals.

NOTE: v9-02a, v9-02b, etc. denote 1-month benchmark simulations.

Feature Type Submitted by Benchmark(s) Status
Correction for GEOS-5 PBL heights Bug Fix Sajeev Philip (Dalhousie) v9-02a Approved 16 Oct 2012
New soil NOx emission module Science Rynda Hudman Kay (EPA)
Neil Moore (formerly of Dalhousie)
Bram Maasakkers (Eindhoven)
v9-02b Approved 29 Oct 2012
Bug fix in hdf_mod.F Bug Fix Sajeev Philip (Dalhousie) " " " "
Bug fixes for tagged CO simulation Bug Fix Jenny Fisher (Wollongong)
GEOS-Chem Support Team
" " " "
Bug fix for nested simulation in nei_anthro_mod.F Bug Fix Sajeev Philip (Dalhousie) " " " "
EPA/NEI05 North American Hg emissions Science Yanxu Zhang (U. Washington)
Lyatt Jaeglé (U. Washington)
v9-02c
+ Hg benchmark (by Hg and POPs Working Group)
Approved 29 Nov 2012
Nested-grid Hg simulation Science Yanxu Zhang (U. Washington)
Lyatt Jaeglé (U. Washington)
" " " "
Streets future Hg emissions Science Bess Corbitt (Harvard) " " " "
Correct Hg simulation to use updated Hg(0) oxidation kinetics Science Bess Corbitt(Harvard)
Justin Parrella (Harvard)
" " " "
Capability to use GEOS-Chem Br/BrO fields in Hg simulation Science Bess Corbitt(Harvard)
Justin Parrella (Harvard)
" " " "
POPs simulation: Polycyclic aromatic hydrocarbons Science Carey Friedman (MIT)
Noelle Selin (MIT)
" " " "
Bug fix for updated CAC emissions Bug Fix Aaron van Donkelaar (Dalhousie) " " " "
Grid-independent GEOS-Chem updates: Activation of new data pathways and other structural modifications Structural GEOS-Chem Support Team v9-02d Approved 19 Dec 2012
Bug fix for Br2 emissions Bug Fix GEOS-Chem Support Team " " " "
Bug fix in regridding of anthropogenic emissions (NEI2005, Streets) Bug Fix GEOS-Chem Support Team v9-02e Approved 09 Jan 2013
Additional bug fixes for MAP_A2A regridding Bug Fix GEOS-Chem Support Team " " " "
Bug fix for MEGAN emissions when using MERRA or GEOS-5.7.2 Bug Fix Tzung-May Fu (Peking University) " " " "
Inorganic chemistry updates Science Mat Evans (York) v9-02f
+ 1-year benchmark
1-mon benchmark: Approved 07 Feb 2013
1-year benchmark: Approved 20 Mar 2013
Methyl peroxy nitrate (MPN) chemistry Science Ellie Browne (UC Berkeley) " " " "
Bug fixes for nested Hg simulation Bug fix Yanxu Zhang (U. Washington) " " " "
Prevent bad drydep flux values from being passed to the soil NOx emissions module Bug fix Patrick Kim (Harvard)
GEOS-Chem Support Team
" " " "
Adopt Paulot isoprene scheme as standard Science Fabien Paulot (Harvard)
Eloise Marais (Harvard)
Jingqiu Mao (NOAA/GFDL)
Mat Evans (York)
v9-02g
+1-year benchmark
1-mon benchmark: Approved 24 Mar 2013
1-year benchmark: Approved 01 Apr 2013
Fix RO2+HO2 rate constant Science Fabien Paulot (Harvard) " " " "
Bug fix for declaration of GEOS-5.7.2 PFICU, PFLCU, PFILSAN, PFLLSAN fields Bug fix GEOS-Chem Support Team " " " "
Bug in EMIS_STREETS_ANTHRO_05x0666 Bug fix Jenny Fisher (U. Wollongong) " " " "
Removal of NOx-Ox partitioning Science GEOS-Chem Support Team v9-02h Approved 15 May 2013
Inhibition of N2O5 uptake by nitrate aerosol Science Lin Zhang (Beijing University) v9-02i Approved 17 May 2013
Improved HO2 uptake by aerosol Science Jingqiu Mao (NOAA/GFDL) v9-02j
+1-year benchmark
1-mon benchmark: Approved 28 May 2013
1-year benchmark: Approved 03 Jun 2013
Inline the latest source code modifications updates for the TOMAS microphysics package into GEOS-Chem Structural Sal Farina (CSU)
GEOS-Chem Support Team
v9-02k
+ Hg benchmark
Approved 07 Jun 2013
Hg benchmark pending approval
Additional modifications to enable GEOS-Chem to run within the GEOS-5 GCM Structural GEOS-Chem Support Team " " " "
Streamlining of the code in GeosCore/mercury_mod.F Structural Chris Holmes (UC Irvine) " " " "
Rewriting inefficient subroutine calls to avoid wasting memory and CPU cycles Structural GEOS-Chem Support Team " " " "
Updated NH3 seasonal scaling factors over the US Science Lin Zhang (Peking University) v9-02l
+ 1-year benchmark
In progress
Updated Canadian NH3 inventory Science Wai-Ho Lo (Dalhousie) " " " "
Bug in wet deposition Henry's constant Bug fix Fabien Paulot " " " "
Add DRYACET to globchem.dat Bug fix Emily Fischer (Harvard) " " " "
Fix diurnal NOx scale factors and fix double counting of biofuels over Mexico and Canada Bug Fix Christoph Keller (Harvard) " " " "
Bug fix for 3-hourly GFED3 emissions Bug fix Christoph Keller (Harvard) " " " "
Bug fix in grid_mod.F90 Bug Fix Christoph Keller (Harvard) " " " "
Bug fix for anthropogenic scaling factors for years 2006 and later Bug fix Jenny Fisher (U. Wollongong) " " " "
Correct additional bugs in ship emissions w/ non-local PBL mixing Bug Fix Chris Holmes (UC Irvine)
Geert Vinken (Eindhoven)
" " " "
Bug fix for ship CO emissions Bug Fix Chris Holmes (UC Irvine) " " " "
Fix typo in VOLCPRESS definition Bug fix Thibaud Thonat (U. Edinburgh) " " " "
Eliminate several more array temporaries Structural GEOS-Chem Support Team " " " "
Bug fixes in day-of-week computation Bug fix GEOS-Chem Support Team " " " "
Bug fix in diag48_mod.F Bug fix Jenny Fischer (U. Wollongong) " " " "
RCP emission scenarios Science Chris Holmes (UC Irvine) v9-02m
+ CO2/CH4 benchmarks (by Carbon Gases & Organics WG)
TBD
EDGAR v4.2 emissions for CH4 simulation Science Kevin Wecht (Harvard) " " " "
Update anthropogenic scale factors through 2010 Science Aaron van Donkelaar (Dalhousie) " " " "
Improve temporal resolution of anthropogenic CO2 sources Science Ray Nassar (Environment Canada) " " " "
Replace CASA CO2 biosphere climatology with year-specific fluxes Science Ray Nassar (Environment Canada)
Dylan Jones (U. Toronto)
" " " "
Update GFED3 emissions to 2011 Science Prasad Kasibhatla (Duke) " " " "
Update to EDGAR 4 anthropogenic emissions Science Qiang Zhang (Tsinghua)
Sajeev Philip (Dalhousie)
" " " "
Update jv_spec.dat with better representation
of OC growth with RH and correction to sulfate optics
Science David Ridley (MIT) " " " "
AEIC aircraft emissions inventory Science Steven Barrett (MIT) v9-02n TBD
SOA simulation with semi-volatile POA Science Havala Pye (EPA)
GEOS-Chem Support Team
v9-02o TBD
Acid uptake on dust aerosols Science T. Duncan Fairlie (NASA/LARC) v9-02p TBD
Cloudwater pH for sulfate formation Science Becky Alexander (U. Washington) v9-02q
+ 1-year benchmark
TBD


Nested-grid model at 0.25° x 0.3125° resolution using GEOS-5 "FP" met data product from GMAO Structural Yuxuan Wang (Tsinghua)
GEOS-Chem Support Team
v9-02r
+ Rn-Pb-Be benchmark
+ Nested-grid benchmark (by Nested Model WG)
TBD
High-resolution emissions for above nested-grid model Science Yuxuan Wang (Tsinghua)
GEOS-Chem Support Team
" " " "
Global simulations with GEOS-5 "FP" data product from GMAO
(Needed for the 0.25° x 0.3125° nested-grid simulations)
Structural GEOS-Chem Support Team " " " "
Add unit tester capability (i.e. to automatically compile GEOS-Chem for all met fields/grid combinations in order to spot common errors) Structural GEOS-Chem Support Team pre-release of v9-02 TBD

--Melissa Payer 15:15, 18 June 2013 (EDT)

New data directories

The following new data directories have been added for GEOS-Chem v9-02. 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_0.5x0.666_NA/RETRO_201103     # RETRO anthropogenic VOC emissions
GEOS_0.5x0.666_EU/RETRO_201103     # RETRO anthropogenic VOC emissions
GEOS_0.5x0.666_CH/RETRO_201103     # RETRO anthropogenic VOC emissions

GEOS_NATIVE/soil_NOx_201208        # Files for updated soil NOx emission scheme

--Melissa Payer 11:44, 30 October 2012 (EDT)

Previous issues now resolved in GEOS-Chem v9-02

Correction for GEOS-5 PBL heights

This update was tested in the 1-month benchmark simulation v9-02a and approved on 16 Oct 2012.

Please see this post on our Boundary layer mixing wiki page for a full description of this issue.

--Bob Y. 11:01, 5 October 2012 (EDT)

Bug fixes for tagged CO simulation

This update was tested in the 1-month benchmark simulation v9-02b and approved on 29 Oct 2012.

Please see this post on our Tagged CO simulation wiki page for more a complete description of the issue.

--Bob Y. 10:59, 20 December 2012 (EST)

Bug fix in nei2005_anthro_mod.F

This update was tested in the 1-month benchmark simulation v9-02b and approved on 29 Oct 2012.

We corrected incorrect subroutine calls to the regridding subroutine DO_REGRID_A2A from routines GET_NEI99_SEASON_05x0666 and GET_VISTAS_SEASON_05x0666 of GeosCore/nei2005_anthro_mod.F. Please see this wiki post on our EPA/NEI05 North American emissions wiki page for further information.

--Bob Y. 11:13, 20 December 2012 (EST)

Bug fix for updated CAC emissions

This update was tested in the 1-month benchmark simulation v9-02c and approved on 29 Nov 2012.

Aaron van Donkelaar wrote:

The code as implemented in v9-01-03 contains only few of the changes I submitted to update CAC to 2008. My guess is that somehow two versions of this file were being worked on simultaneously.
As a result of the mix-up, simulations using CAC emissions and running 2006 or 2007 will crash. Other than that it shouldn't have had any major ramifications.

--Melissa Payer 15:51, 27 November 2012 (EST)

Bug fix for Br2 emissions

This update was tested in the 1-month benchmark simulation v9-02d and approved on 19 Dec 2012.

Please see this wiki post on our Bromine Chemistry Mechanism wiki page for a full description of this issue.

--Bob Y. 15:38, 20 December 2012 (EST)

Bug in regridding of anthropogenic emissions

NOTE: This issue was tested in the 1-month benchmark simulation in v9-02e, which was approved on 09 Jan 2013.

We corrected an issue in the regridding of the anthropogenic Streets and NEI2005 emissions. Please see the discussion on our Regridding in GEOS-Chem wiki page for more information.

--Bob Y. 10:21, 10 January 2013 (EST)

Bug in MEGAN emissions when running with MERRA or GEOS-5.7.2

NOTE: This issue was tested in the 1-month benchmark simulation in v9-02e, which was approved on 09 Jan 2013.

Please see the discussion on our MEGAN biogenic emissions wiki page for a complete description of this issue.

--Bob Y. 10:34, 10 January 2013 (EST)

Additional bug fixes for MAP_A2A regridding algorithm

NOTE: This issue was tested in the 1-month benchmark simulation v9-02e, which was approved on 09 Jan 2013.

Please see the discussion on our Regridding in GEOS-Chem wiki page for a complete description of this issue.

--Bob Y. 10:25, 10 January 2013 (EST)

Prevent bad drydep flux values from being passed to the soil NOx emissions module

This issue was tested in the 1-year benchmark simulation v9-02f and approved on 20 Mar 2013.

It was discovered that junk values in the drydep fluxes were being passed to the soil NOx emissions module (via routine SOIL_DRYDEP) when the ND44 dry deposition diagnostic was switched off. We have now corrected this issue. Please see this post on our Soil NOx emissions wiki page for more information.

--Bob Y. 09:29, 14 March 2013 (EDT)

Bug fix for declaration of GEOS-5.7.2 PFICU, PFLCU, PFILSAN, PFLLSAN fields

This update was tested in the 1-month benchmark simulation v9-02g and approved on 24 Mar 2013.

Please see this wiki post on our GEOS-5.7.2 implementation details wiki page for a full description of this issue.

--Bob Y. 11:42, 18 March 2013 (EDT)

Outstanding issues not yet resolved in GEOS-Chem v9-02

Bug in wet deposition Henry's constant

Fabien Paulot found a small bug in Henry's constant used in the wet deposition routine. Please see this post on our Wet deposition wiki page for a full description of this issue.

--Melissa Payer 17:58, 15 May 2013 (EDT)

Bug fix for anthropogenic scaling factors for years 2006 and later

Please see this post on our Scale factors for anthropogenic emissions wiki page for a full description of this issue. We plan to include this fix in GEOS-Chem v9-02n. --Melissa Payer 12:25, 22 March 2013 (EDT)

Bug in ship CO emissions

Please see this post on our Ship Emissions wiki page for a full description of the issue. We plan to include this fix in GEOS-Chem v9-02m.

--Bob Y. 15:47, 8 April 2013 (EDT)

Bug fixes in biofuel_mod.F and emfossil.F

We plan to include this fix in GEOS-Chem v9-02l. (Included in Adjoint v34j )

Christoph Keller wrote:

I found two bugs in the emissions code which I think we should fix.
Firstly, the diurnal NOx scale factors should be based on UTC instead of local time. The fix is easy, we just have to use the local time for a given grid box instead of taking the UTC hour when calculating the emissions in emfossil.F
Secondly, I think that we currently double count biofuel emissions over Canada and Mexico if the respective local inventories (CAC and BRAVO) are used. Again, this is an easy fix, we just have to set the biofuel emissions for the given tracers and regions to zero if CAC and/or BRAVO are used.

--Melissa Payer 10:31, 16 November 2012 (EST)

Bug fixes in day-of-week computation

We corrected a couple of issues regarding how the day of the week is computed in GEOS-Chem. We made this fix primarily to ensure EPA/NEI weekday or weekend emissions were being selected properly. The EPA/NEI emissions are defined over the United States, where the local solar time can be 5-8 hours behind Greenwich Mean Time. Therefore, when deciding if EPA/NEI weekday or weekend emissions should be applied, we should use the day of the week w/r/t the local time at each grid box location over the United States. But in all GEOS-Chem versions prior to v9-02, the day of the week was always computed w/r/t Greenwich Mean Time.

In order to correct this discrepancy, we made the following modifications in GEOS-Chem v9-02l:

(1) We have now moved the location of where the day of the week (w/r/t the GMT date) is computed:
  • Subroutine SET_CURRENT_TIME (in GeosUtil/time_mod.F) computes the day of the week and stores it in module variable DAY_OF_WEEK.
  • Function GET_DAY_OF_WEEK (also in GeosUtil/time_mod.F) now just returns the value of module variable DAY_OF_WEEK to the calling program.
(2) We fixed a couple of numerical issues in the computation of the day of the week (w/r/t the GMT date), namely:
(a) In subroutine SET_CURRENT_TIME (in module GeosUtil/time_mod.F), we need to round off the B term to 4 decimal places in order to avoid roundoff errors. We added this line:
          ! NOTE: This is not in the Duffett-Smith book, but when using
          ! REAL*8, we have to round B to 4 decimal places in order
          ! to avoid floating-point errors. (bmy, 6/13/13)
          B           = INT( NINT( B*1d5 + SIGN( 5d0, B ) ) / 10d0 ) / 1d4
(b) Also in SET_CURRENT_TIME, we changed the line:
          DAY_NUM = INT( B + 0.5d0 )
to
          DAY_NUM = INT( B )
The extra 0.5 was causing the day of week to increment 12 hours ahead of time. (The 0.5 is present in the algorithm upon which the function is based. But since this algorithm was developed for hand-held calculators, it may not take into account the roundoff that may exist in floating point numerical computations.)
(3) Note that as written, subroutine SET_CURRENT_TIME returns the day of the week with respect to the Greenwich Mean Time (GMT). But when deciding to apply either weekday or weekend emissions at a particular location on the globe, we really want to get the day of the week with respect to the local solar time at that location. The local solar time may differ from GMT by several hours depending on distance from the prime meridian. Therefore, we have introduced a new function named GET_DAY_OF_WEEK_LT, which computes the day of the week with respect to the local time at a given location. Emissions routines that need to know the day of the week shall now use GET_DAY_OF_WEEK_LT instead of GET_DAY_OF_WEEK.
(a) In the following emissions modules:
  • GeosCore/biofuel_mod.F
  • GeosCore/emfossil.F
  • GeosCore/epa_nei_mod.F
  • GeosCore/nei2005_anthro_mod.F
  • GeosCore/sulfate_mod.F
  • GeosCore/vistas_anthro_mod.F
we have added code to call the new function GET_DAY_OF_WEEK_LT, in order to obtain the day of the week w/r/t the local solar time at GEOS-Chem grid box (I,J,L). The typical pattern that we use is as follows:
               REAL*8  :: DOW_LT
               LOGICAL :: WEEKDAY

               . . .

               DO J = 1, JJPAR
               DO I = 1, IIPAR

                  ! Determine if we should use weekday or weekend NEI
                  ! emissions at grid box (I,J,L).  Since NEI is over
                  ! the US, then weekend is Sat/Sun.
                  DOW_LT       = GET_DAY_OF_WEEK_LT( I, J, 1 )
                  WEEKDAY      = ( DOW_LT > 0 .and. DOW_LT < 6 )
 
                  ! Call emissions routines (in this example, EPA/NEI99)
                  AN           = GET_EPA_ANTHRO(  I, J, IDTSO2, WEEKDAY )
                  BF           = GET_EPA_BIOFUEL( I, J, ITDSO2, WEEKDAY )

                  ... etc ...

               ENDDO
               ENDDO
Important notes:
  • Sunday is denoted when DOW_LT == 0, and Saturday is denoted when DOW_LT == 6. For the purposes of the EPA/NEI emissions (over the United States), a "weekend" is Saturday/Sunday. (NOTE: in some locations of the world, particularly in the Middle East, weekends are defined as Friday/Saturday.)
  • We now need to call GET_DAY_OF_WEEK_LT from the same DO loop where the call to the emissions routines (in this example, for EPA/NEI99) are located. This is because GET_DAY_OF_WEEK_LT now needs to know the I, J, (and for multi-level data, L) indices of the grid box.
  • If the DO loop is parallelized, then the variables DOW_LT and WEEKDAY need to be added to the !$OMP PRIVATE declaration.

--Bob Y. 14:27, 18 June 2013 (EDT)

Bug fix in diag48_mod.F

Jenny Fisher wrote:

A couple of bugs in diag48_mod.F:
1. GET_LOCALTIME is called with LT = GET_LOCALTIME( I, J, L )
But L hasn't been defined. This should either be K or 1, but not L.
2.
          DO L = 1, K
             Q(L) = GET_PEDGE( I, J, K )
          ENDDO
The K in GET_PEDGE should be L.

--Melissa Payer 14:36, 18 June 2013 (EDT)