GEOS-Chem v9-01-02

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Contents

Overview

History

The table below shows the previous, current, and successive versions of GEOS-Chem:

Previous version This version Next version
GEOS-Chem v9-01-01 GEOS-Chem v9-01-02 GEOS-Chem v9-01-03
PUBLIC RELEASE Feb 10 2011
RE-RELEASED ON 07 Jun 2011
PUBLIC RELEASE 28 Nov 2011 PUBLIC RELEASE 14 Sep 2012
View v9-01-01 benchmark history View v9-01-02 benchmark history View v9-01-03 benchmark history

--Bob Y. 10:21, 16 January 2014 (EST)

What's new in this version

GEOS-Chem v9-01-02 contains the following new features:

v9-01-02a, v9-01-02b, 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
(1 Month)
Status
Corrected mis-indexing error in partition.f caused by the dynamic tropopause Bug Fix Daven Henze (Colorado U)
Jamin Koo (MIT)
v9-01-02a Approved 28 Jun 2011
Corrected out-of-bounds error in readchem.f Bug Fix GEOS-Chem Support Team " " " "
Fix for mis-indexing issue in CSPEC restart file Bug Fix Jingqiu Mao (NOAA/GFDL)
GEOS-Chem Support Team
v9-01-02c Approved 21 Jul 2011
Initial source code modifications for compatibility with Earth System Model Framework Structural GEOS-Chem Support Team v9-01-02d Approved 26 Jul 2011
Various bug fixes for the offline Hg simulation Bug Fix Jenny Fisher (Harvard)
Helen Amos (Harvard)
Chris Holmes (UC Irvine)
v9-01-02e Approved 01 Aug 2011
Bug fixes for leap years when using GCAP met fields Bug Fix GEOS-Chem Support Team " " " "
Minor bug fixes for emissions routines affecting offline simulations Bug Fix GEOS-Chem Support Team " " " "
Fixes for minor issues affecting nested-grid simulations Bug Fix Luke Schiferl (Colorado State)
Lin Zhang (Harvard)
" " " "
Fixes for better compatibility with the PGI compiler Bug Fix Gan Luo (SUNY Albany)
GEOS-Chem Support Team
" " " "
Add MERRA SEAICExx fields to the planeflight diagnostic Structural Jenny Fisher (Harvard)
GEOS-Chem Support Team
" " " "
Washout fix for non-aerosol species Bug Fix Helen Amos (Harvard) v9-01-02f Approved 02 Aug 2011
Overhaul of AOD diagnostics Structural Sungshik Patrick Kim (Harvard)
GEOS-Chem Support Team
v9-01-02g Approved 10 Aug 2011
Fix for GEIA emissions scaling factor over Botswana Bug Fix Dylan Millet (U. Minnesota) v9-01-02h Approved 12 Aug 2011
Updated dry deposition velocities for aerosols over ice and snow Science Jenny Fisher (Harvard) v9-01-02i Approved 15 Aug 2011
Archive the MERRA SWGDN (incident radiation @ sfc) field in the ND67 diagnostic Structural Jenny Fisher (Harvard) " " " "
Imposed seasonality on NH3 emissions from David Streets 2000 inventory Science Jenny Fisher (Harvard) v9-01-02j Approved 16 Aug 2011
Fixed minor issues in MERRA cloud convection routine Bug Fix Jenny Fisher (Harvard) " " " "
Implementation of RETRO Anthropogenic Emissions Science Wes Reinhart (U. Minnesota)
Dylan Millet (U. Minnesota)
v9-01-02k Approved 17 Aug 2011
APM aerosol microphysics Science Fangqun Yu (SUNY Albany)
Gan Luo (SUNY Albany)
v9-01-02l Approved 23 Aug 2011
Attempt to eliminate numerical noise in ISORROPIA II (ifort compiler only) Structural Shannon Capps (Georgia Tech) " " " "
Eliminate common block header files + Other source-code updates for ESMF compatibility Structural GEOS-Chem Support Team v9-01-02m Approved 07 Sep 2011
GFED3 biomass burning emissions Science Prasad Kasibhatla (Duke) v9-01-02n Approved 22 Sep 2011
Minor fixes in APM microphysics Structural Gan Luo (SUNY Albany) " " " "
Eliminate double-counting of residential biofuel when using RETRO anthro VOC emissions Bug Fix Dylan Millet (U. Minnesota) v9-01-02o Approved 27 Sep 2011
Fix for vertical regridding of offline OH for offline simulations Bug Fix Chris Holmes (UC Irvine) v9-01-02p Approved 29 Sep 2011
Further bug fixes for the offline Hg simulation Bug Fix Chris Holmes (UC Irvine) " " " "
Further fixes for nested-grid simulations Bug Fix Luke Schiferl (Colo. State U.)
Aaron van Donkelaar (Dalhousie)
" " " "
Further fixes for APM microphysics Bug Fix Gan Luo (SUNY Albany) " " " "
Centralizing chemistry time step Structural Mauricio Santillana (Harvard)
Jingqiu Mao (NOAA/GFDL)
Lin Zhang (Harvard)
GEOS-Chem Support Team
v9-01-02q Approved 18 Oct 2011
Fix for partitioning chemical species Bug Fix Daven Henze (Colorado U)
Prasad Kasibhatla (Duke)
v9-01-02r Approved 20 Oct 2011
Bug fixes for biofuel emissions Bug Fix Chris Holmes (UC Irvine)
Dylan Millet (U. Minnesota)
Chris Miller (Harvard)
v9-01-02s Approved 5 Nov 2011
Fix bug in EDGAR ship emissions code Bug Fix GEOS-Chem Support Team
Chris Holmes (UC Irvine)
" " " "
Bug fix for ship NOx emissions Bug fix Chris Holmes (UC Irvine) " " " "
GEIA 2005 Hg emissions Science Bess Corbitt (Harvard)
Noelle Selin (MIT)
" " " "
Prevent out-of-bounds errors in ND01 and ND02 diagnostics for Rn-Pb-Be simulation Bug fix GEOS-Chem Support Team last-minute fix 08 Nov 2011
Do not use erroneous MEGAN AEF data for nested-grid simulations Bug fix Lin Zhang last-minute fix 22 Nov 2011
Modify constant used for in-plume reduction in Hg simulation Science Helen Amos(Harvard)
Noelle Selin (MIT)
Yanxu Zhang (U. Washington
last-minute fix 28 Nov 2011

--Bob Y. 14:51, 29 November 2011 (EST)

New data directories

The following new data directories have been added for GEOS-Chem v9-01-02. 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_1x1/APM_201011                                             # For APM microphysics only
GEOS_1x1/Streets_200607/NH3-Streets-SeasonalScalar.generic.1x1  # For NH3 seasonality in Streets 2000
GEOS_1x1/GFED3_201110                                           # GFED3 biomass burning emissions

GEOS_2x2.5/CO_201003/fossilfuel_andres/annual_v2010             # CO2 annual emissions from CDIAC
GEOS_2x2.5/CO_201003/fossilfuel_andres/monthly_v2010            # CO2 monthly emissions from CDIAC
GEOS_2x2.5/mercury_201007                                       # Renamed from mercury_201002
GEOS_2x2.5/mercury_201110                                       # Soil conc's of Hg (present + pre-ind)
GEOS_2x2.5/RETRO_201103                                         # RETRO anthropogenic VOC emissions
 
GEOS_4x5/CO_201003/fossilfuel_andres/annual_v2010               # CO2 annual emissions from CDIAC
GEOS_4x5/CO_201003/fossilfuel_andres/monthly_v2010              # CO2 monthly emissions from CDIAC
GEOS_4x5/mercury_201110                                         # Soil conc's of Hg (present + pre-ind)
GEOS_4x5/RETRO_201103                                           # RETRO anthropogenic VOC emissions

--Bob Y. 16:58, 15 November 2011 (EST)

1-year benchmarks

For a complete description of the 1-year benchmark simulations that were used to validate GEOS-Chem v9-01-02, please see the 1-year benchmark simulations section of our GEOS-Chem v9-01-02 benchmark history wiki page.

--Bob Y. 11:24, 28 November 2011 (EST)

Previous issues now resolved in v9-01-02

Patches from v9-01-01

The following patches that were issued after the initial release of GEOS-Chem v9-01-01 are now standardized in v9-01-02:

  1. Double counting of biofuel emissions over Asia
  2. Updated annual and monthly CO2 emissions from CDIAC
  3. Typos in vdiff_mod.f90
  4. Negative tracer caused by DO_MERRA_CONVECTION
  5. Omitted code in Hg simulation
  6. Bug fixes for drydep (ND44) and wetdep (ND17,ND18,ND37,ND38,ND39) diagnostic archival
  7. Bug fix for time-in-tropopause (ND54) diagnostic
  8. Only apply wetdep error trap when using MERRA met fields
  9. Apply washout to the proper fraction of the grid box
  10. Better representation of aqueous SO2 chemistry

--Bob Y. 11:51, 24 June 2011 (EDT)

Mis-indexing error in partition.f

This update was tested in the 1-month benchmark simulation v9-01-02a and approved on 28 Jun 2011.

NOTE: Routine partition.F will be removed (along with the other SMVGEAR routines) once FlexChem is implemented into GEOS-Chem.

The implementation of the Dynamic tropopause was causing a mis-indexing error in subroutine partition.f. On every timestep, partition.f uses the concentrations of grid boxes at the previous timestep to partition family tracers (e.g. NOx, Ox) into individual species (e.g. NO2, NO, O3, etc.). The way in which this was done did not take into account the fact that some boxes near the tropopause could be in the troposphere at one timestep and in the stratosphere at the next timestep (or vice-versa). Thus, the concentrations that partition.f was sending to the chemistry solver was incorrect.

This problem affected both the forward and adjoint models.

--Bob Y. 10:14, 6 July 2011 (EDT)
--Bob Yantosca (talk) 14:47, 14 April 2016 (UTC)

Out-of-bounds error in readchem.f

This update was tested in the 1-month benchmark simulation v9-01-02a and approved on 28 Jun 2011.

SMVGEAR will be completely removed from GEOS-Chem v11-01. It will be replaced by the FlexChem solver package.

It was discovered that this code near the end of subroutine readchem.f:

                 ELSEIF ( J == MAPPL(ILBRO2H,NCS) .or.
    &                     J == MAPPL(ILBRO2N,NCS) .or.
    &                     J == MAPPL(ILTRO2H,NCS) .or.
    &                     J == MAPPL(ILTRO2N,NCS) .or.
    &                     J == MAPPL(ILXRO2H,NCS) .or.
    &                     J == MAPPL(ILXRO2N,NCS) ) THEN
                    ITS_NOT_A_ND65_FAMILY(J) = .FALSE.
                    EXIT

will cause an out-of-bounds error if any of the IL* indices are zero. This error manifested itself in a standard 43-tracer simulation.

We have corrected this error by first making sure that each IL* index is nonzero before doing the corresponding IF ( J = ... ) test:

                 ! Avoid out-of-bounds-errors by making sure that each
                 ! IL* index is nonzero before doing the IF test for J. 
                 ! (bmy, 3/1/11)
                 IF ( ILBRO2H > 0 ) THEN 
                    IF ( J == MAPPL(ILBRO2H,NCS) ) THEN
                       ITS_NOT_A_ND65_FAMILY(J) = .FALSE.
                       EXIT
                    ENDIF
                 ENDIF

                 ... etc ...

--Bob Y. 10:42, 24 June 2011 (EDT)

Mis-indexing when reading restart.cspec file

This update was tested in the 1-month benchmark simulation v9-01-02c and approved on 21 Jul 2011.

Please see this post on the "Restart files" wiki page for more information about an indexing problem when reading the restart.cspec.YYYYMMDDhh file.

--Bob Y. 15:22, 21 July 2011 (EDT)

Various bug fixes for the offline Hg simulation

This update was tested in the 1-month benchmark simulation v9-01-02e and approved on 01 Aug 2011.

The following issues were discovered in the offline Hg simulation shortly after the release of v9-01-01. These have all been fixed in v9-01-02. Please follow the links below for more information:

  1. De-hardwire file path BR_DIR in global_br_mod.f
  2. Negative concentrations of aquatic mercury
  3. VEGEMIS bug fix for GCAP simulation

--Bob Y. 10:41, 1 August 2011 (EDT)

Bug fix for leap years with GCAP

This update was tested in the 1-month benchmark simulation v9-01-02e and approved on 01 Aug 2011.

Recall that the GCAP met fields are climatological GCM output, and do not have any leap years (i.e. there are no Feb 29ths). In GEOS-Chem v9-01-01 and prior versions, the code did not robustly skip over leap year days.

This issue has now been fixed in GEOS-Chem v9-01-02. We have posted the the implementation details on the GCAP wiki page.

--Bob Y. 10:25, 31 October 2011 (EDT)

Minor bug fixes for emissions routines affecting offline simulations

We have now corrected some bugs that caused errors when running the offline aerosol-only simulation and tagged CO simulation. (NOTE: These errors do NOT occur when running the full-chemistry simulation, only the offline simulations.)

Fixes in biomass_mod.f

This update was tested in the 1-month benchmark simulation v9-01-02e and approved on 01 Aug 2011.

Module biomass_mod.F was removed from GEOS-Chem v10-01 and higher versions. Emissions in these versions are now handled by HEMCO.

In biomass_mod.f, there are some IF blocks such as:

           IF ( ITS_A_FULLCHEM_SIM() ) THEN              
              BIOMASS(:,:,IDBCO) = BIOMASS(:,:,IDBCO) * 1.05d0
           ELSE IF ( ITS_A_TAGCO_SIM() ) THEN
              BIOMASS(:,:,IDBCO) = BIOMASS(:,:,IDBCO) * 1.11d0
           ENDIF

However, if your simulation does not use CO (e.g. offline aerosols), then the ID flags IDTCO and IDBCO will both equal zero. If IDBCO = 0, this will cause an out-of-bounds error.

The solution is to add an outer IF block to prevent the code from being executed if IDBCO = 0.

           IF ( IDBCO > 0 ) THEN
              IF ( ITS_A_FULLCHEM_SIM() ) THEN              
                 BIOMASS(:,:,IDBCO) = BIOMASS(:,:,IDBCO) * 1.05d0
              ELSE IF ( ITS_A_TAGCO_SIM() ) THEN
                 BIOMASS(:,:,IDBCO) = BIOMASS(:,:,IDBCO) * 1.11d0
              ENDIF
           ENDIF

--Bob Y. 10:44, 1 August 2011 (EDT)

Fixes for minor issues affecting nested-grid simulations

The following typographical errors affect nested-grid simulations:

Wrong directory specified in nei2005_anthro_mod.f

This update was tested in the 1-month benchmark simulation v9-01-02e and approved on 01 Aug 2011.

Module nei2005_anthro_mod.F was removed from GEOS-Chem v10-01 and higher versions. Emissions in these versions are now handled by HEMCO.

Luke Schiferl wrote:

I have been working with the nested NA simulation and ran into a bug in the code. In GEOS-Chem v9-01-01, line 779 of nei2005_anthro_mod.f should point to the NEI2005_201007 directory rather than NEI2005_200710. There is a comment in line 709 that confirms this.

--Bob Y. 13:34, 27 July 2011 (EDT)

CAC, BRAVO emissions inadvertently turned off in NA nested grid runs

This update was tested in the 1-month benchmark simulation v9-01-02e and approved on 01 Aug 2011.

In GEOS-Chem v10-01 and higher versions, all emissions options are read in via the HEMCO configuration file.

Lin Zhang wrote:

I found a small bug in recent GEOS-Chem v9-01-01 when running nested NA. The error is in routine READ_EMISSIONS_MENU of module input_mod.f, around line 1700. The line:
   #if defined( GRID05x0666 ) || defined( NESTED_CH ) 
should be
   #if defined( GRID05x0666 ) && defined( NESTED_CH ) 
or just simply
   #if defined( NESTED_CH )
Otherwise, it will turn off CAC, BRAVO emissions when running nested NA.

--Bob Y. 10:44, 1 August 2011 (EDT)

Bug fixes for compatibility with the PGI compiler

This update was tested in the 1-month benchmark simulation v9-01-02e and approved on 01 Aug 2011.

Include file define.h was removed from GEOS-Chem v9-02 and higher versions.


Gan Luo from SUNY/Albany pointed out several minor typos that cause the PGI compiler to choke when building the GEOS-Chem executable. These will all be fixed in v9-01-02.

(1) Line 303 of GeosCore/depo_mercury_mod.f:

Change this:
 #include 'define.h'

to this:
 #include "define.h"

(2) Line 169 of GeosCore/ocean_mercury_mod.f:

Change this:
 REAL*8, PARAMETER     :: Kd_part   = 10**(5.5)

to this:
 REAL*8, PARAMETER     :: Kd_part   = 10d0**(5.5d0)

(3) Line 1281 of GeosCore/ocean_mercury_mod.f:

Change this:
 HgPaq(I,J)   = MAX ( HgPaq(I,J) , 0.0 )

to this:
 HgPaq(I,J)   = MAX ( HgPaq(I,J) , 0d0 )

(4) In subroutine DO_MERRA_CONVECTION of convection_mod.f

Change this:
 REAL*8            :: ALPHA,       ALPHA2,   CLDBASE, CMFMC_BELOW

to this:
 INTEGER           :: CLDBASE
 REAL*8            :: CMFMC_BELOW, ALPHA,    ALPHA2

(5) In module vdiff_mod.f90: Several numerical constants had to be rewritten so that explicitly use "D" exponents. In other words:

Change numbers like these:
 1.
 1.e-12

to these:
 1.d0
 1.d-12

In short, the PGI compiler expects constants to agree strictly with the type of the variable that they are being assigned to (i.e. if A is a REAL*8, then you must use A = 1.0d0 instead of A = 1.0). IFORT will correct for this situation during compilation, but PGI will throw an error.

--Bob Y. 10:44, 1 August 2011 (EDT)

Planeflight diagnostic update

This update was tested in the 1-month benchmark simulation v9-01-02e and approved on 01 Aug 2011.

The MERRA SEAICExx fields are now saved to the plane flight diagnostic, per request of Jenny Fisher.

--Bob Y. 10:45, 1 August 2011 (EDT)

Washout fix for non-aerosol species

This update was tested in the 1-month benchmark simulation v9-01-02f and approved on 02 Aug 2011.

The current Wet deposition algorithm was underestimating washout of non-aerosol species. Please see this wiki post for more information about how we corrected this situation.

--Bob Y. 14:34, 2 August 2011 (EDT)

Overhaul of aerosol optical depth diagnostics

This update was tested in the 1-month benchmark simulation v9-01-02g and approved on 10 Aug 2011.

Patrick Kim discovered some inconsistencies in the way aerosol optical depth diagnostics were being computed in GEOS-Chem v9-01-01 and prior versions. We have now corrected these inconsistencies.

Sungshik Patrick Kim wrote:

Here is an example of a daily (first page) and monthly (second page) average AOD for January 2008 from the public release of v9-01-01 and a newer version that addresses the changes we discussed earlier vs. the corresponding average AERONET data, a difference plot, and a histogram of the differences by grid box. [T]he largest differences appear to be due to the change in met field rather than changing the timing of the AOD calculation and it may be largest in the Arctic due to uncertainties in the previous calculation of RH.

--Bob Y. 15:15, 10 August 2011 (EDT)

Fix for GEIA emissions scaling factor over Botswana

This update was tested in the 1-month benchmark simulation v9-01-02h and approved on 12 Aug 2011.

In GEOS-Chem v10-01 and higher versions, all emissions and scale factors are handled by the HEMCO emissions component.

Please see this wiki post about a problem in the scale factors for GEIA emissions over Botswana and southern Africa.

--Bob Y. 11:16, 15 August 2011 (EDT)

Archive the MERRA SWGDN field in the ND67 diagnostic

This update was tested in the 1-month benchmark simulation v9-01-02i and approved on 15 Aug 2011.

Jenny Fisher pointed out that we were saving the MERRA "longwave radiation at the ground" (LWGNT) field into the ND67 diagnostic instead of the MERRA "shortwave radiation at the ground" (SWGDN) field. We have fixed this by archiving SWGDN to ND67 instead of LWGNT. This is done in the module merra_a1_mod.F.

--Bob Y. 10:24, 16 August 2011 (EDT)

Fixed minor issues in MERRA cloud convection routine

Jenny Fisher discovered two minor issues in the MERRA convection routine DO_MERRA_CONVECTION (in module convection_mod.f). Please see this post on our Cloud convection wiki page for a full description of the issue.

--Bob Y. 15:54, 20 December 2012 (EST)

Minor fixes in APM microphysics

This update was tested in the 1-month benchmark simulation v9-01-02n and approved on 22 Sep 2011.

Gan Luo wrote:

I have finished the checking of the updated V9-01-02 version copied from you last week. The updates from us are listed as follows:
1. Current version does not include updated code for pbl_mix_mod.F in GeosApm. The tracers need to be extended to all APM tracers.
2. In GeosApm/wetscav_mod.F:
a) Please add the missing codes after Line2066
        ELSE IF ( (N >= IDTCTSEA .and. N<(IDTCTSEA+NCTSEA)) .or.
       &          (N >= IDTSEABIN1 .and. N<(IDTSEABIN1+NSEA)) ) THEN
           CALL F_AEROSOL( KC, F )
b) Lines 5628-5632 need to be moved to the line after Line 5646
3. In GeosCore/vdiff_mod.F: Line884 [ustar(i) = max( ustr,.01 )] need to be changed to [ustar(i) = max( ustr,.01d0 )]
We have finished one year benchmark run with 4x5 horizontal resolution, and we also analyzed the results. They look reasonable.

--Bob Y. 15:39, 7 September 2011 (EDT)

Fix for vertical regridding of offline OH for offline simulations

This update was tested in the 1-month benchmark simulation v9-01-02p and approved on 29 Sep 2011.

This code was removed from GEOS-Chem v10-01 and higher versions. The HEMCO emissions component now reads in 3D oxidant fields from netCDF data files.

Chris Holmes wrote:

I have a bug fix for offline simulations that use offline OH fields. The way the code previously lumped layers in the stratosphere was incorrect for OH. Other offline fields (e.g. O3, Br, BrO) are OK, as long as they are in mixing ratio units.
Unlumped layers are unaffected. OH number densities in the lumped layers increase up to 7%. I tested for Hg only and found that they Hg changes were correspondingly modest.
Here are my comments from the commit:
Offline OH fields are stored as number concentrations (molec/cm3) on a 3D grid with unreduced vertical coordinate (e.g. in the file OH_3Dglobal.geos5.4x5). The model lumps layers in the stratosphere into a reduced vertical grid within global_oh_mod.f. The regridding routine (subroutine transfer_3d) requires input as a mixing ratio, but this assumption was violated for OH fields. To correct this problem, we convert OH number concentration to a mixing ratio, then regrid, then convert back to number concentration.
OH concentrations in unlumped layers are unaffected, while increases up to 7% occur in lumped layers in the stratosphere.

--Bob Y. 15:15, 10 August 2011 (EDT)

Further bug fixes for the offline Hg simulation

This update was tested in the 1-month benchmark simulation v9-01-02p and approved on 29 Sep 2011.

The following bugs were discovered after the release of v9-01-01 and have been fixed in v9-01-02. Please follow the links below for more information:

  1. Division by zero error
  2. Bug fixes for ND03 mercury diagnostics

--Melissa Payer 14:51, 19 September 2011 (EDT)

Further fixes for nested-grid simulations

The following fixes were submitted in September 2011 from the nested-grid user community:

Bug fix in planeflight diagnostic for nested-grid simulation

This update was tested in the 1-month benchmark simulation v9-01-02p and approved on 29 Sep 2011.

Luke Schiferl wrote:

While running the planeflight diagnostic with the NA nested grid in v9-01-01, I discovered an issue with the formulas that assign the grid box index from which to pull the concentration values. The formulas remained valid for the global grid regardless if running either a global or nested simulation, thus improperly assigning the grid box index for a nested run. I've made the necessary modifications which now take into account the offsets assigned in input.geos. These offsets are required when running a nested simulation, so the indices will now be properly calculated. I successfully tested the modification with global 2x2.5 and NA nested 0.5x0.667.

--Bob Y. 14:00, 6 September 2011 (EDT)

NH3 emissions set to zero in China nested-grid simulations

This update was tested in the 1-month benchmark simulation v9-01-02p and approved on 29 Sep 2011.

In GEOS-Chem v10-01 and higher versions, the HEMCO emissions component now processes all emissions.

Aaron van Donkelaar wrote:

We've recently found that CH Nested NH3 emissions were being set to zero when using the 2006 inventory in v9-0-01. This bug had already been addressed for the global simulation, but had not been applied to the CH nested one. Attached please find a patch file that corrects the problem.

--Bob Y. 11:47, 8 September 2011 (EDT)

Further fixes for APM microphysics

This update was tested in the 1-month benchmark simulation v9-01-02p and approved on 29 Sep 2011.

Gan Luo wrote:

The column concentrations of the original tracers of BC, OC and dust in GEOS-Chem (59 tracers for full chemistry simulation) simulated by v9-01-02n at remote oceans are much lower than those simulated by v9-01-02l. And we believe that the low values over remote oceans in v9-01-02n may be not reasonable.
The bug leading to the differences between v9-01-02n and v9-01-02l over remote regions is located at wetscav_mod.F. In v9-01-02n, GEOS_5 is undefined in module WETSCAV_MOD. After added # include "define.h" into wetscav_mod.F, the differences between v9-01-02n and v9-01-02l disappeared.
The summary of v9-01-02n debugging for APM is here:
1. In GeosApm/Makefile, the rules to make GFED3 related codes need to be added
2. Please add # include "define.h" at GeosApm/wetscav_mod.F line 19 and GeosApm/apm_wets_mod.F line 130

--Melissa Payer 13:57, 27 September 2011 (EDT)

Fix for partitioning chemical species

This update was tested in the 1-month benchmark simulation v9-01-02r and approved on 20 Oct 2011.

NOTE: The CSPEC array will be removed (along with all other SMVGEAR arrays) once the FlexChem solver is implemented into GEOS-Chem.

Prasad Kasibhatla wrote:

It seems to me that CSPEC has the latest (post-transport) concentrations coming into PARTITION - but the index JLOOP_P refers to the previous time-step. So the effect of the statement CSAVE(JLOOP,N) = CSPEC(JLOOP_P,CSAVEID_JJ(N)) would be to populate CSAVE with the latest CSPEC array but with an index from the previous time step - which may mean it is from a different grid box since the same first index of CSPEC does not necessarily refer to the same box in each time step as it is recalculated in subroutine RURALBOX before each chem step.

Daven Henze wrote:

The problem is that CSPEC gets overwritten by CSPEC_FULL prior to partitioning. I believe the only thing required to make this fix work is to change:
     IF ( LVARTROP .or. FIRSTCHEM .or. READ_CSPEC ) CALL COPY_FULL_TROP
to
     IF ( FIRSTCHEM .or. READ_CSPEC ) CALL COPY_FULL_TROP
in gasconc.f.
The problem with the existing code is that it uses JLOOP_P but references a current CSPEC array which is ordered by JLOOP.
The corrected version uses JLOOP_P and the CSPEC array from the previous step. New tropospheric grid cells inherit concentrations below them, rather than values held over since the last time the cell was in the trop. The only issue I see now with the version of CSPEC_FULL that gets written to a restart file would still contain some of these hold-over values.

--Melissa Payer 15:15, 18 October 2011 (EDT)

Bug fixes for biofuel emissions

This update was tested in the 1-month benchmark simulation v9-01-02s and approved on 5 Nov 2011. (Included in Adjoint v34e )

This code was removed from GEOS-Chem v10-01 and higher versions. The HEMCO emissions component now processes all emissions data in these versions.

The following issues were discovered in biofuel_mod.F. Please follow the links below for more information:

  1. Further fix for double-counting of residential biofuel when using RETRO
  2. Bug fix in biofuel emissions using Streets inventory

--Melissa Payer 13:27, 21 October 2011 (EDT)

Prevent out-of-bounds errors in ND01 and ND02 diagnostics for Rn-Pb-Be simulation

This bug fix was added to GEOS-Chem v9-01-02 just prior to release. It does not affect the full-chemistry simulation, only the Rn-Pb-Be simulations.

For more information about this issue, please see this post on our Rn-Pb-Be simulation wiki page.

--Bob Y. 11:13, 28 November 2011 (EST)

Do not use erroneous MEGAN AEF's for nested grid simulations

This bug fix was added to GEOS-Chem v9-01-02 just prior to release. It does not affect the full-chemistry simulation, only nested-grid simulations.

For more information about this issue, please see this post on our MEGAN biogenic emissions wiki page.

--Bob Y. 10:18, 28 November 2011 (EST)

Under further investigation

The following updates (which should ideally not yield any differences) seem to cause slight numerical discrepancies when added to the standard code. We shall postpone including these into the standard code, pending investigation.

Minor bug fixes in ISORROPIA II

Please see this post on our ISORROPIA II wiki page for a description of two proposed bug fixes that should go into source code file ISOROPIA/isorropiaIIcode.f. This bug should not affect the current GEOS-Chem ISORROPIA configuration, but may affect future development.

Update 7/28/11: Implementing this change causes the 1-month standard benchmark simulation to have divergent results than the previous version. Therefore, we should understand the source of these differences before we add this update into the standard repository.

--Bob Y. 14:40, 28 July 2011 (EDT)

Fixes in emep_mod.f

NOTE: This issue was ultimately resolved in GEOS-Chem v9-01-03g.

Module emep_mod.F was removed from GEOS-Chem v10-01 and higher versions. Emissions in these versions are now handled by HEMCO.

Please see this post on our EMEP European anthropogenic emissions wiki page for a full description of this issue.

--Bob Y. 12:43, 20 December 2012 (EST)

Fix for offline simulations in nei2005_anthro_mod.f

NOTE: This issue was ultimately resolved in GEOS-Chem v9-01-03g.

Module nei2005_anthro_mod.F was removed from GEOS-Chem v10-01 and higher versions. Emissions in these versions are now handled by HEMCO.

Please see this post on our EPA/NEI05 North American Emissions wiki page for a full description of the issue.

--Bob Y. 12:46, 20 December 2012 (EST)

Outstanding issues not yet resolved in v9-01-02

Please also see our Currently unresolved issues in GEOS-Chem wiki page for more information about as-yet unresolved issues first identified in prior versions.

RETRO anthropogenic ethane emissions are too low

NOTE: All emissions are handled by HEMCO in GEOS-Chem v10-01 and higher versions.

Please see this wiki post on the RETRO emissions wiki page for a full description of this issue. We expect to fix this issue in GEOS-Chem v9-01-03.

--Bob Y. 11:17, 28 November 2011 (EST)

Apparent bug in LINOZ

Prasad Kasibhatla wrote:

There is a bug in LINOZ related to calculation of column ozone associated with very tiny negative O3 mixing ratios in strat, that can cause the model to crash. This is compiler dependent because sometimes the tiny concentrations appear as tiny positive numbers and the model does not crash. Dylan Jones. is looking into this - a quick fix is possible to prevent the model from crashing, but a bigger issue is the non-physical tiny O3 concentrations that occassionally occur in stratosphere - I suspect this has something to do with handling of STT and CSPEC arrays when a box goes [from the troposphere to the stratosphere] in a time-step.

--Bob Y. 10:52, 1 August 2011 (EDT)

Incompatibility with GNU Make v3.80

This is a minor technical issue caused by some leftover test code in the GeosApm/Makefile and GeosTomas/Makefile. This will be corrected in GEOS-Chem v9-01-03.

May Fu wrote:

In testing v912, I found that gnu make version 3.81 or later is required, because the ‘else ifeq’ syntax is used in the Makefiles. I would imagine most people have at least v3.81, unless they are using a really old Linux distribution like I do, where the default gnu make is 3.80. The danger is that the user will not be able to do a proper ‘make realclean’, but might still be able to ‘make’, resulting in a bad build.

Michael Long wrote:

The instance of else ifeq is not meant to be operational in v9-01-02. I will revise the Makefiles to undo this.

--Bob Y. 15:54, 6 December 2011 (EST)