Updated dry deposition velocities for aerosols over ice and snow

Modeled aerosol dry deposition velocities over snow and ice surfaces in the Arctic were much higher than estimated from measured values (e.g., Ibrahim et al. [1983]; Duan et al. [1988]; Nilsson and Rannik [2001]). In v9–01–02, a dry deposition velocity of 0.03 cm/s is imposed for all aerosols over snow and ice surfaces.

Imposed seasonality on the NH3 emissions from David Streets 2000 inventory

The Streets 2000 inventory for anthropogenic ammonia (NH3) does not include any seasonal cycle. This has been corrected by using the annual total from Streets 2000 superimposed with monthly scale factors from a global inventory compiled by Marcel Meinders and Lex Bouwman.

RETRO anthropogenic VOC emissions

Monthly RETRO anthropogenic VOC emissions have been added as an optional inventory.

For more information, please see this document:

• W. Reinhart and D. Millet, Implementation of the RETRO Anthropogenic Emission Inventory into the GEOS–Chem model, May 2011.

APM aerosol microphysics

Fangqun Yu and Gan Luo developed the Advanced Particle Microphysics (APM) package for implementation into GEOS–Chem. APM is now one of two microphysics packages in GEOS–Chem, the other being TOMAS.

GFED3 biomass burning emissions

Monthly mean GFED3 biomass burning emissions have been added to v9-01-02. The GFED3 emissions inventory will eventually replace GFED2.

GEIA 2005 Hg emissions

Bess Corbit prepared the GEIA 2005 emission inventory for anthropogenic Hg.

Modifications for compatability with ESMF

Modifications were made to GEOS–Chem source code to enable compatability with the Earth System Model Framework (ESMF). These changes were were aimed at cleaning up legacy code and making specific portions of the code FORTRAN 90/95 compliant. For more information, please see the following links:

1. Source code cleanup and initial ESMF prep
2. Elimination of COMMON blocks

MERRA SEAICExx fields added to the planeflight diagnostic

The MERRA SEAICExx fields are now saved to the plane flight diagnostic.

Overhaul of AOD diagnostics

Patrick Kim discovered some inconsistencies in the way aerosol optical depth diagnostics were being computed in v9–01–01 and prior versions. See this wiki page for more information.

Archive MERRA SWGDN field in the ND67 diagnostic

MERRA "incident shortwave radiation at the ground" (SWGDN) is now archived to ND67, not "net longwave radiation at the ground" (LWGNT).

Centralized chemistry time step

The time at which chemistry, emissions, photolysis, and drydep operations are performed has been moved to the midpoint of the chemistry time step. See this wiki page for more information.

Bug fixes for the offline Hg simulation

The following issues were discovered in the offline Hg simulation shortly after the release of v9-01-01 and have been fixed in v9-01-02:

• De-hardwire file path BR_DIR in global_br_mod.F
• Negative concentrations of aquatic mercury
• VEGEMIS bug fix for GCAP simulation
• Division by zero error
• Bug fixes for ND03 mercury diagnostics

Various other bug fixes

The following updates were made to fix several bugs:

• Corrected mis-indexing error in partition.F caused by the dynamic tropopause
• Corrected out-of-bounds error in readchem.F
• Fix for mis-indexing issue in CSPEC restart file
• Bug fixes for leap years when using GCAP met fields
• Minor bug fixes for emissions routines affecting offline simulations
• Fixes for minor issues affecting nested-grid simulations
• Bug fixes for compatibility with the PGI compiler
• Washout fix for non-aerosol species
• Fix for GEIA emissions scaling factor over Botswana
• Fixed minor issues in MERRA cloud convection routine
• Fix for vertical regridding of offline OH for offline simulations
• Further fixes for nested-grid simulations
• Fix for partitioning chemical species
• Bug fix for Streets biofuel emissions
• Bug fix in EDGAR ship emissions code
• Bug fix in ship NOx emissions

Capability to run with GMAO MERRA meteorological fields

GEOS–Chem v9–01–01 is the first version to be compatible with the MERRA met data product from GMAO. MERRA is a 30-year reanalysis data set which spans the years 1979-2010.

Bug fix for lightning NOx emissions

In GEOS–Chem v9–01–01, the following updates were made that impact the emissions of lightning NOx:

1. Bug fix for incorrect cloud-top-height determination
2. Addition of updated vertical release profiles (cf. Ott et al 2010)
3. Removal of obsolete options from the source code (lightning_nox_mod.f)

For detailed information about these updates, please see this document:

• L.T. Murray, Changes affecting lightning NOx emissions in GEOS–Chem v9-01-01, January 2011

Improvements to the wet deposition and convective updraft scavenging algorithms

Helen Amos and Bess Corbitt have updated the wet deposition and convective updraft scavenging algorithms, particularly for the new MERRA met fields. Also, following upon the work of Qiaoqiao Wang, we now allow both rainout and washout to happen simultaneously in a grid box where new precipitation is forming.

Updated volcanic SO2 emissions from Aerocom

The latest volcanic SO2 emissions update from Thomas Diehl have been applied to GEOS–Chem v9–01–01.

Important bug fixes for ship emissions

Geert Vinken has submitted a couple of important fixes for ship emissions. These have been added to v9-01-01. For more information, please see the following links:

• Bug fix for ship emissions in emfossil.f
• Updated mask for EMEP ship emissions

A bug in the EPA/NEI05 emissions code was found prior to the release of GEOS–Chem v9–01–01. Long story short: when the EPA/NEI05 option is selected, the wrong biofuel emissions inventory is used over the continental USA.

For a complete description of this bug, please see this post on our EPA/NEI05 wiki page.

Various technical improvements

The following updates were made to fix several technical issues:

• All bug fix patches from v8–03–02 have now been standardized in v9–01–01
• Simulations may be started at times other than 0h GMT
• Modifications were made to the non-local PBL mixing scheme to improve efficiency
• The main loop in the LINOZ stratospheric chemistry scheme was parallelized
• Duplicate printout of certain diagnostics was corrected
• A fix was added to prevent div-by-zero in sulfate_mod.f
• Erroneous ND15 diagnostic behavior in the non-local PBL scheme was corrected
• The PEDGE-$ diagnostic category is archived to timeseries diagnostics
• Offline simulations can now run on the GEOS-5/MERRA full-vertical grid

Caltech isoprene chemistry mechanism

A new isoprene chemistry was introduced as an option to solve an over-estimation in isoprene in previous GEOSChem versions.

LINOZ stratospheric ozone chemistry

Implementation of LINOZ which provides a linear chemistry for ozone in the stratosphere.

ISORROPIA II

ISORROPIA II is now used to calculate the aerosol thermodynamic equilibrium instead of RPMARES.

Updated aerosol optical properties for FAST-J photolysis

The GEOS–Chem Aerosols Working Group has created an updated list of aerosol optical properties (i.e. quantum yields, cross-sections) for input into the FAST–J photolysis mechanism.

Option to use chemical solver from KPP software

The KPP chemical solver now contains 3 mechanisms to choose from:

• Standard simulation without secondary organic aerosols
• Standard simulation with secondary organic aerosols
• Simulation with new isoprene chemistry scheme

Emissions modifications

Various modifications to existing emissions inventories, including:

• Extension of annual anthropogenic scale factors to 2006
• EMEP emissions extended to 2007 and Seasonality extended to SOx, CO, and NH3
• BOND inventory for BC and OC with monthly variations
• Implementation of MEGAN v2.1 biogenic emissions
• Implementation of ICOADS ship emissions
• Volcanic SO2 emissions from AeroCom
• EPA/NEI 2005 inventory for North America

New non-local planetary boundary layer scheme

Jintai Lin has implemented a new boundary layer mixing scheme option into GEOS–Chem. It is a non-local scheme formulated by Holtslag and Boville (1993).

Modifications to SOA formation

Several modifications were applied to the secondary organic aerosol scheme:

• SOA no longer depends on inorganic concentrations
• SOA formation now includes formation by aromatics
• We now use the speciated emissions from MEGAN v2.1

Updates for sea salt aerosols

Lyatt Jaeglé and Becky Alexander have updated the sea salt emissions scheme in GEOS–Chem.

TOMAS aerosol microphysics option

The Carnegie-Mellon group has interfaced the TOMAS aerosol microphysics scheme into GEOS–Chem.

Lok Lamsal from Dalhousie University has added the capability to run GEOS–Chem at the GEOS–4 native resolution of 1° x 1.25°.

Several modifications were made to GEOS–Chem's nested grid simulation capability, including:

• Standardization of North America 0.5° x 0.667° nested grid (GEOS–5)
• Introduction of Europe 0.5° x 0.667° nested grid (GEOS–5)
• Ability to keep boundary conditions for different grids in different directories
• HDF5 output has been added to selected timeseries diagnostics.

Christopher Pickett-Heaps and Kevin Wecht have updated the CH4 simulation in GEOS–Chem, following earlier work by Jerome Drevet.

Terrestrial and deep ocean mercury

The Global Terrestrial Mercury Model (cf. Nicole Smith-Downey) can now be selected as an option in the standard mercury simulation. Many features of the mercury simulation have also been improved (cf. E. Sunderland, C. Holmes).

Updated CO2 simulation

Ray Nassar has updated the CO2 simulation with new inventories and fluxes. For a full description, see our CO2 simulation wiki page.

Obtain liquid water content from GEOS–5 met fields

Jenny Fisher modified the existing SO2 chemistry scheme such that it will obtain the cloud fraction and liquid water content directly from the GEOS–5 meteorlogy.

Updated chemical reactions

Chemical relations and relation rates are updated mainly from JPL06 and IUPAC06. Photolysis quantum yields are updated from FAST–JX version 6.4 data. See HERE for detailed changes compared to v8–01–04. The pressure-dependency sheme for acetone photolysis is now updated to FAST–JX version 6.4.

The format of jv_spec.dat file has slightly changed. The new format is explained in Chapter 5: GEOS–Chem run directories.

Updated dust scattering

Updated emissions

Several emission inventories are updated or newly implemented. All details concerning emissions are in Chapter 4: GEOS–Chem data directories.

Improved stratospheric exchange

GEOS–Chem uses now the transport routine and pressure fixer from GMI. This ensures to have a reasonable troposphere-stratosphere exchange.

Compatibility with GEOS–5 meteorological fields

GEOS–Chem v8–01–01 is now fully compatible with the GMAO GEOS–5 operational data product (e.g. GEOS-5.0.1 and GEOS-5.1.0). You must upgrade to GEOS–Chem v8–01–01 if you wish to drive GEOS–Chem with the GEOS–5 meteorology.

Please see the GEOS–Chem wiki for a more complete account of some of the issues that were encountered during GEOS–5 implementation.

GEOS–1 and GEOS–STRAT meteorology is no longer supported

With the availability of several years of GMAO's GEOS–4 and GEOS–5 meteorological data products, it is no longer necessary to use the older GEOS–1 and GEOS–STRAT products. Therefore, GEOS–Chem v8–01–01 no longer supports these data sets.

NOTE: GMAO's GEOS–3 meteorological data product is still supported in GEOS–Chem v8–01–01, and will continue to be supported indefinitely.

Dynamic tropopause

GEOS–Chem now has the capability to perform chemistry with SMVGEAR up to the location of the actual tropopause, as diagnosed by the tropopause pressure (TROPP) meteorological field. This results in a more accurate representation of the tropopause, and causes more grid boxes in the tropics to be sent to the SMVGEAR solver. In prior versions, SMVGEAR chemistry was only done up to the location of the annual mean tropopause.

Updated lightning with OTD/LIS local redistribution

The lightning NOx emissions algorithm in GEOS–Chem v8–01–01 has been substantially rewritten to try to better match the observational distribution of lightning flashes. The location of lightning flashes now follows the patterns observed by the OTD/LIS satellite instruments.

Updated global and regional anthropogenic emissions

In GEOS–Chem v8–01–01, the default GEIA/Piccot anthropogenic emissions can now be overwritten with a combination of global and regional anthropogenic emissions inventories, including:

• EDGAR (global)
• EMEP (Europe)
• BRAVO (Mexico)
• Updated EPA-NEI99 (USA)
• David Streets (SE Asia)

Click HERE to view a table with more detailed information about each of these inventories.

NOTE: In afuture version of GEOS–Chem, we will be introducing an improved algorithm to scale fossil fuel emissions from the baseline year of 2000 to the present year (cf. Aaron van Donkelaar).

GFED2 biomass burning emissions

In GEOS–Chem v8–01–01, you may select either the default Duncan et al (2001) biomass burning emissions, or the GFED2 biomass burning emissions.

NOTE: At present only the GFED2 monthly mean emissions have been implemented. The 8-day-averaged GFED2 emissions will be introduced into a future version of GEOS–Chem (cf. Ray Nassar).

Safer floating-point operations

GEOS–Chem v8–01–01 includes some extra floating point error traps (e.g. safe division, avoiding division by zero, etc.) in order to prevent NaN and infinity values from propagating throughout the code. Also, a bug fix was implemented into SMVGEAR in order to better screen out negative values.

Aerosol Thermodynamic Equilibrium with RPMARES

It was recently discovered that the version of ISORROPIA that ships with GEOS–Chem can give bad values when computing the aerosol thermodynamical equilibrium for grid boxes where relative humidity is below 30%. Therefore, until further notice we have reverted back to the RPMARES code for computing aerosol thermodynamical equilibrium until further notice.

Compatibility with SunStudio 11/12 and Intel Fortran Compiler 10

GEOS–Chem v8–01–01 now ships with Makefiles for compiling with the newest Sun or Intel Fortran compilers. Options for using the TotalView Debugger are also now included in the makefiles.