Bromine chemistry mechanism
- 1 Overview
- 2 Chemical Mechanism
- 3 Chemical Lifetimes
- 4 Source code and data files
- 5 References
- 6 Previous issues that are now resolved
In GEOS-Chem v9-01-03, we have added 10 additional bromine species to the standard GEOS-Chem chemistry mechanism. You can revert to the previous mechanism by turning off emissions for these species. This bromine simulation was updated in GEOS-Chem v11-02d as part of the updated halogen chemistry mechanism.
This update was tested in the 1-month benchmark simulation v9-01-03m and approved on 06 Jun 2012.
Justin Parrella added bromine chemistry as an extension to the standard model's full chemistry simulation in GEOS-Chem v8-03-01. We have now brought Justin's updates into GEOS-Chem v9-01-03. Important features include:
- Add 10 bromine tracers: Br2, Br, BrO, HOBr, HBr, BrNO2, BrONO2, CHBr3, CH2Br2, and CH3Br
- 4 source gases:
- CH3Br: PBL concentrations are set to average CMDL measured concentrations prior to each chemistry step.
- Very short lived (VSL) source gases:
- CH2Br2 and CHBr3. These account for > 80% of the VSL organic bromine through the troposphere (WMO, 2007).
- Emissions are taken from Q. Liang et al.  + a seasonal scaling for CHBr3 at lat > 30N described in J. Parrella et al. 
- 429 Gg CHBr3 / yr; 62 Gg CH2Br2 / yr
- Sea-salt debromination:
- Largely follows Yang et al. , treating the debromination as an emission of Br2, constrained to measured bromide depletion factors.
- 1.4 Tg Br2 / yr using the Monahan sea-salt production function and coarse aerosol bin range of 0.5 - 10 um.
- Stratospheric boundary conditions for Bry
- Bry concentrations are from the Liang et al.  stratospheric simulation with the GEOS-5 CCM.
- Monthly mean daytime and nighttime concentration data are applied for individual Bry species
- Wet and dry deposition for HBr, HOBr, and BrONO2.
Updates for GEOS-Chem v9-01-03o
Lee Muray and Justin Parrella modified the original implementation of the bromine chemistry. The mechanism now reverts to prescribing stratospheric bromine concentrations from the CCM_stratosphere_Bry fields, but from within the new stratospheric code.
Lee Murray wrote:
- In addition to the problems with bromine that Bob pointed out in his email from last week (e.g., won't work with nested simulations), the bromine code also would not work for GEOS-4 or GCAP as it used some GEOS-5-only met fields, or any type of other chemistry simulation (e.g., SOA) since the tracer numbers were hardwired. I made the following changes to the bromine code in this commit:
I made use of IDTBR, IDTBrO, etc., in the stratospheric code to generalize tracer number references for other simulation types
The Warwick VSL emission files are now a netCDF file always read in at 2x2.5, and re-gridded to whatever resolution the actual simulation is using REGRID_A2A
The bromine stratospheric input files have been re-gridded for the GEOS-4 and GCAP vertical resolutions
For nested simulations, the stratospheric bromine fields are interpolated from the native coarser resolution to the nested grid, as my new P & k files are
I have switched the use of FROCEAN and FRLAND (GEOS-5 met fields) to the helper functions IS_LAND, IS_WATER and IS_ICE to generalize the code to GEOS4/GCAP/other. I left in the old treatment for GEOS_5 for now with preprocessing statements, though the GEOS4/GCAP treatment should be identical and preferable as it is more universal.
Only GEOS-5 has cloud ice and liquid water content met fields, which is used by the bromine rate calculation in calcrate.F. Mimicking what we do in wetscav_mod.F, I parameterize those variables as a function of temperature for GEOS-4 and GCAP.
- I have extensively tested and validated the global simulations. I have tested the nested simulations, but not extensively.
- In my comparisons of v9-01-03n and my most recent commit, I found a few small differences in the in the bromine species in stratosphere (e.g., pages 44-47 of this PDF). Stratospheric bromine fields in GEOS-Chem are a weighted average of the monthly mean day and night concentrations in CCM_stratosphere_Bry/, depending on relative amount of daylight and nighttime in the grid box. In July, the South Pole is entirely night and North Pole is entirely day. We should expect them to match the CCM_stratosphere_Bry/ exactly there, but v9-01-03n does not (v9-01-03n benchmark file is used in this plot). That being said, I do not see anything wrong with the original implementation in SCHEM.F. Regardless, my implementation in strat_chem_mod.F90 does match the input fields exactly as expected, and I am confident it is correct.
--Bob Y. 12:42, 10 July 2012 (EDT)
Size-dependent sea salt bromine depletion factors
For the release of GEOS-Chem v9-01-03, sea salt debromination has been updated to include size-dependent depletion factors based on Table 1 from Yang et al. . We now use SSA dry diameter bin range of 0.2 - 10 um. For SSA dry diameters <0.8 um, depletion factors are negative, indicating bromine uptake by SSA. The size-dependent depletion factors result in reduced flux of bromine into the atmosphere.
--Melissa Payer 10:21, 28 August 2012 (EDT)
Source code and data files
In GEOS-Chem v10-01 and newer versions
In GEOS-Chem v10-01 and newer versions, bromine emissions and concentrations are read from disk with the HEMCO emissions component. We have created HEMCO-compatible data files (in COARDS-compliant netCDF format) for the following species:
- Very-short-lived (VSL) species (cf. Qing Liang)
- Stratospheric Bry data from the CCM model (cf. Qing Liang)
These new data files are contained in the HEMCO data directory tree. For detailed instructions on how to download these data files to your disk server, please see our Downloading the HEMCO data directories wiki post.
--Bob Y. 13:24, 3 March 2015 (EST)
In GEOS-Chem versions prior to v10-01
The new bromine chemistry mechanism uses the following data files:
Emissions of VSLs (very short-lived) species (cf. Qing Liang):
# For GEOS-Chem global 2 x 2.5 grid (and all nested grids) ftp://ftp.as.harvard.edu/gcgrid/geos-chem/data/GEOS_NATIVE/bromine_201205/VSL_emissions/ # For GEOS-Chem global 4 x 5 grid ftp://ftp.as.harvard.edu/gcgrid/geos-chem/data/GEOS_4x5/bromine_201205/VSL_emissions/ # For GCAP global 4 x 5 grid ftp://ftp.as.harvard.edu/gcgrid/geos-chem/data/GEOS_4x5/bromine_201205/VSL_emissions/
Stratospheric Bry data from the CCM model (cf. Qing Liang):
# For GEOS-Chem global 2 x 2.5 grid (and all nested grids) ftp://ftp.as.harvard.edu/gcgrid/geos-chem/data/GEOS_NATIVE/bromine_201205/CCM_stratosphere_Bry/ # For GEOS-Chem global 4 x 5 grid ftp://ftp.as.harvard.edu/gcgrid/geos-chem/data/GEOS_4x5/bromine_201205/CCM_stratosphere_Bry/ # For GCAP global 4 x 5 grid ftp://ftp.as.harvard.edu/gcgrid/geos-chem/data/GEOS_4x5/bromine_201205/CCM_stratosphere_Bry/
--Bob Y. 12:56, 10 July 2012 (EDT)
- Liang, Q., Stolarski, R. S., Kawa, S. R., Nielsen, J. E., Douglass, A. R., Rodriguez, J. M., Blake, D. R., Atlas, E. L., and Ott, L. E., Finding the missing stratospheric Bry: a global modeling study of CHBr3 and CH2Br2, Atmos. Chem. Phys., 10, 2269-2286, 2010.
- Parrella, J.P., D.J. Jacob, Q. Liang, Y. Zhang, L.J. Mickley, B. Miller, M.J. Evans, X. Yang, J.A. Pyle, N. Theys, and M. Van Roozendael, Tropospheric bromine chemistry: implications for present and pre-industrial ozone and mercury, Atmos. Chem. Phys., 12, 6723-6740, 2012. PDF
- Warwick, N. J., Pyle, J. A., Carver, G. D., Yang, X., Savage, N. H., O'Connor, F. M., and Cox, R. A., Global modeling of biogenic bromocarbons, J. Geophys. Res., 111, 2006.
- Yang, X., Cox, R. A., Warwick, N. J., Pyle, J. A., Carver, G. D., O’Connor, F. M., and Savage, N. H.: Tropospheric bromine chemistry and its impacts on ozone: A model study, J. Geophys. Res., 110, D23311, doi:10.1029/2005JD006244, 2005.
- Yang, X., Pyle, J. A., and Cox, R. A.: Sea salt aerosol production and bromine release: Role of snow on sea ice, Geophys. Res. Lett., 35, L16815, doi:10.1029/2008GL034536, 2008.
--Melissa Payer 10:55, 28 August 2012 (EDT)
Previous issues that are now resolved
Bugs in data files used to prescribe stratospheric Bry
These updates were validated with the 1-month benchmark simulation v10-01f and approved on Approved 13 Jan 2015.
Johan Schmidt wrote:
- There are two bugs:
- 1) Serious: Bry fields used for 4x5 GEOS-4 runs is too high by a factor of 4. The problem can be removed by copying corrected data /home/jschmidt/Strat-Bry/Bry_Stratosphere_*.bpch.geos4.4x5 in the /as/data/geos/GEOS_4x5/bromine_201205/CCM_stratosphere_Bry/ folder.
- 2) Less serious: Night Bry data is equal to day Bry data. This bug is found in the GEOS-5 2x2.5, GEOS-5 1x1 and all GEOS-4 Strat Bry fields. The problem is not present GEOS-5 4x5 Strat Bry fields. The correct daytime and night time Strat Bry fields from Qing Liang are located in /home/jschmidt/Strat-Bry/qliang_data/ as netCDF files in 2x2.5 and G-5 vertical resolution.
The corrected daytime and nighttime stratospheric Bry netCDF files are now read in by HEMCO. For more information, please see this post on our HEMCO wiki page.
--Melissa Sulprizio 10:12, 12 December 2014 (EST)
Add more robust error check in cldice_HBrHOBr_rxn.F
NOTE: This fix was included in GEOS-Chem v9-02p.
We changed the error check criterion for variable IWC in routine GeosCore/cldice_HBr_HOBr_rxn.F. The former error check was:
Old code: !%%% ERROR CHECK! Do not let IWC=0 because it will cause the !%%% LOG10 statement in the upcoming section (bmy, 10/23/12) IF ( ( .not. ( ABS( IWC ) > 0d0 ) ) ) THEN gamma = 0.d0 k_hbr = 0.d0 k_hobr = 0.d0 RETURN ENDIF
But because IWC is the argument to the LOG10 (logarithm, base 10) function, a value of IWC = 0 will cause a floating-point error. We therefore modified the error check to return out of the subroutine UNLESS IWC > 0.
New code: !%%% ERROR CHECK! Do not let IWC<=0 because it will cause the !%%% LOG10 statement in the upcoming section (bmy, 10/23/12) IF ( .not. ( IWC > 0d0 ) ) THEN gamma = 0.d0 k_hbr = 0.d0 k_hobr = 0.d0 RETURN ENDIF
This error condition was caught by the GEOS-Chem unit tester when compiling with option FPE=yes.
--Bob Y. 15:42, 12 September 2013 (EDT) GeosCore/cldice_HBrHObr_rxn.F: Now exit unless IWC is > 0, or else this can cause the log10 call to choke.
Bug fix for Br2 emissions
This update was tested in the 1-month benchmark simulation v9-02d and approved on 19 Dec 2012.
Module ssa_bromine_mod.F was removed from GEOS-Chem v10-01 and newer versions. Bromine emissions are now implemented via HEMCO.
In subroutine EMIT_BR2 (ssa_bromine_mod.F), we need to replace loop limits NLAT and NLONG with JJPAR and IIPAR, respectively. Otherwise, the loop indices will be incorrect and Br2 will not be emitted. The following lines have been changed from:
DO J = 1, NLAT DO I = 1, NLONG
DO J = 1, JJPAR DO I = 1, IIPAR
--Melissa Payer 17:29, 18 December 2012 (EST)