Mercury

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  1. Simulations using KPP-built mechanisms
  2. Aerosol-only simulation
  3. Carbon simulation
  4. CH4 simulation
  5. CO2 simulation
  6. Hg simulation
  7. Metals simulation
  8. POPs simulation
  9. Tagged CO simulation
  10. Tagged O3 simulation
  11. TransportTracers simulation

The overall capabilities of the mercury simulation are described elsewhere in a Narrative description.

On this page we include information for users of the GEOS-Chem mercury simulations. Please also visit our Global Terrestrial Mercury Model page, which is an option that can be used with the GEOS-Chem mercury simulation.

For a list of current and on-going mercury projects, please visit the Hg and POPs Working Group page!

Mechanism

Please see the description of the current mercury (Hg) simulation at geos-chem.readthedocs.io.

Benchmarking

A script is now available to benchmark mercury simulations against existing observations. The script was created originally by Bess Corbitt, with contributions from Chris Holmes, Helen Amos, Jenny Fisher, Anne Soerensen, Noelle Selin, and others. The benchmark code is publicly available though you need a (free) account on github. If you'd like to make changes to the benchmark, email your username to Noelle Selin (selin at MIT dot edu) who will add you as a "collaborator".

[https://github.com/noelleselin/HgBenchmark] is the address. You can easily see any changes through this web system, but the access is similar to the geos-chem git server (i.e. you can use git commands through your own computer system same as downloading geos-chem from Harvard.) In this way, we hope to be able to track future versions of the Hg code more easily.

The benchmarking directory available on github includes all necessary IDL scripts, input files, tracerinfo and diaginfo files, sample bpch files that can be used as reference files, and a README. Please check the README for detailed information and instructions for setting up and running the benchmarking scripts.

Soil Emissions

Unless you are running GTMM, soil emissions are a function of soil mercury concentrations in a prespecified file. The soil concentrations distributed in the mercury_201007 data directory were calculated by Holmes et al. (2010) using a highly-modified version of v8-02-03 and the method of Selin et al. (2008). This method calculates steady-state soil concentration and emissions for the preindustrial period, then imposes a 15% enhancement according to anthropogenic Hg deposition.

In principle, the soil Hg concentrations should be recalculated after any changes to the model, meteorology, or resolution to ensure self-consistent treatment of deposition and emissions. In practice, the changes to soil emissions may be small for some model updates and recalculating soil Hg may be unnecessary. But it is the model users' responsibilities to determine when to update his or her soil Hg files.

Users who want to update their soil Hg files may use IDL code developed by Chris Holmes. Please contact him directly.


Helen Amos wrote:

Here are step-by-step instructions for making a new soil distribution if you are not using GTMM. You will need to use the following IDL scripts written by Chris Holmes: 

  soilhgdist_uniform.pro
  soilhgdist.pro

Step 1: Use soilhgdist_uniform.pro to create a uniform soil distribution. Save file as 'soilhg.uniform.bpch'.

Step 2: In mercury_mod.f SUBROUTINE MERCURY_READYR, specify that you want to run with 'soilhg.uniform.bpch'.

Step 3: Run three years (e.g. 2004-2006) of pre-industrial simulation with uniform soil distribution. Specify that it's a pre-industrial simulation in the input.geos file.

Step 4: Use soilhgdist.pro to create a new, scaled soil distribution (saved as a bpch file) and to calculate the ratio of deposition/emission.

Step 5: Adjust SOIL_EMIS_FAC in land_mercury_mod.f by multiplying SOIL_EMIS_FAC * (deposition/emission), where deposition/emission is the ratio from Step 4.

Step 6: In mercury_mod.f SUBROUTINE MERCURY_READYR, change input file to new soil distribution created in Step 4.

Step 7: Run three years (e.g. 2004-2006) of pre-industrial simulation. Start this run from where Step 3 left off by renaming the restart.totHg.* and ocean.totHg.* files (i.e. rename restart.totHg.2007010100 to restart.totHg.2004010100).

Step 8: Repeat Steps 4-7 until pre-industrial soil distribution converges. You can check for convergences with Gamap routine CTM_PLOTDIFF.

Step 9: Once the pre-industrial soil distribution has converged to with 5%, run three years (e.g. 2004-2006) of a present day simulation with ONLY direct anthropogenic emissions. Specify that it's a present day simulation by setting 'Is it a pre-industrial sim?' to 'F' in the input.geos file. Specifiy that you only want direct anthropogenic emissions by setting the logical LAnthroHgOnly to 'T' in mercury_mod.f SUBROUTINE INIT_MERCURY.

Step 10: Use soilhgdist.pro to create a present day soil distribution.


--Helen Amos 03:44, 13 Aug 2011 (EST)

Update for HEMCO

GCST and/or Team Hg to provide HEMCO-ready uniform soil distribution files - for now contact jennyf@uow.edu.au if you want one.

Step 1: In HEMCO_Config.rc change the name of the soil file to soilhg.uniform.$RES.nc

Step 2: Run three years (e.g. 2013-2015) of pre-industrial simulation with uniform soil distribution. Specify that it's a pre-industrial simulation in the input.geos file.

Step 3: Use soilhgdist_nc.pro to create a new, scaled soil distribution (saved as a netcdf file) and to calculate the ratio of deposition/emission.

Step 4: Make the new soil file HEMCO-ready by running the following nco commands:
ncrename -v HG_SRCE__Hg0_ln,HG0_DIST filename.nc
ncatted -a gamap_category,HG0_DIST,o,c,HG-SRCE filename.nc
ncatted -a units,HG0_DIST,o,c,1 filename.nc

Step 5: Adjust SOIL_EMIS_FAC in land_mercury_mod.f by multiplying SOIL_EMIS_FAC * (deposition/emission), where deposition/emission is the ratio from Step 4.

Step 6: In HEMCO_Config.rc, change soil file to new file created in Step 4.

Step 7: Run three years (e.g. 2013-2015) of pre-industrial simulation. Start this run from where Step 2 left off by renaming the trac_rst.* and ocean_rst.* and HEMCO_restart.* files (i.e. rename trac_rst.geosfp_4x5_Hg.201601010000 to trac_rst.geosfp_4x5_Hg.201301010000).

Step 8: Repeat Steps 2-7 until pre-industrial soil distribution converges to within 5%.

Step 9: Once the pre-industrial soil distribution has converged to with 5%, run three years (e.g. 2013-20015) of a present day simulation with ONLY direct anthropogenic emissions. Specify that it's a present day simulation by setting 'Is it a pre-industrial sim?' to 'F' in the input.geos file. Specifiy that you only want direct anthropogenic emissions by setting the logical LAnthroHgOnly to 'T' in mercury_mod.f SUBROUTINE INIT_MERCURY.

Step 10: Use soilhgdist_nc.pro to create a present day soil distribution.

-- Jenny Fisher, 19 Mar 2016

References

  1. H. M. Amos, D. J. Jacob, D. Kocman, H. M. Horrowitz, Y. Zhang, S. Dutkiewicz, M. Horvat, E. S. Corbitt, D. P. Krabbenhoft, E. M. Sunderland, "Global Biogeochemical Implications of Mercury Discharges from Rivers and Sediment Burial", Environ. Sci. Technol., DOI.10.1021/es502134t, 2014.
  2. H. M. Amos, D. J. Jacob, C. D. Holmes, J. A. Fisher, Q. Wang, R. M. Yantosca, E. S. Corbitt, E. Galarneau, A. P. Rutter, M. S. Gustin, A. Steffen, J. J. Schauer, J. A. Graydon, V. L. St. Louis, R. W. Talbot, E. S. Edgerton, Y. Zhang, and E. M. Sunderland, Gas-particle partitioning of atmospheric Hg(II) and its effect on global mercury deposition, Atm. Chem. Phys., 12, 591-603, 2012.
  3. Corbitt, E.S., D.J. Jacob, C.D. Holmes, D.G. Streets, and E.M. Sunderland, Global source-receptor relationships for mercury deposition under present-day and 2050 emissions scenarios, Environ. Sci. Technol., 45, 10477-10484, 2011.
  4. Goodsite, M.E., J.M.C. Plane, and H. Skov, Correction to A Theoretical Study of the Oxidation of Hg0 to HgBr2 in the Troposphere, Environ. Sci. Technol., 46, 5262−5262, 2012.
  5. Holmes, C. D., D. J. Jacob, and X. Yang, Global lifetime of elemental mercury against oxidation by atomic bromine in the free troposphere, Geophys. Res. Lett., 33, L20808, 2006.
  6. Holmes, C.D., D.J. Jacob, E.S. Corbitt, J. Mao, X. Yang, R. Talbot, and F. Slemr, Global atmospheric model for mercury including oxidation by bromine atoms, Atm. Chem. Phys., 10, 12,037-12,057, 2010
  7. Holmes, C.D., D.J. Jacob, R.P. Mason, D.A. Jaffe, Sources and deposition of reactive gaseous mercury in the marine atmosphere, Atm. Environ., 43, 2278-2285, 2009.
  8. 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, 723-6,740, 2012.
  9. Selin, N.E., D.J. Jacob, R.J. Park, R.M. Yantosca, S. Strode, L. Jaegle, and D. Jaffe, Chemical cycling and deposition of atmospheric mercury: Global constraints from observations, J. Geophys. Res, 112, DO2308, doi:10.1029/2006JD007450, 2007.
  10. Selin, N.E. and D.J. Jacob. Seasonal and spatial patterns of mercury wet deposition in the United States: North American vs. intercontinental sources, Atm. Environ, 42, 5193-5204, 2008.
  11. Selin, N.E., D.J. Jacob, R.M. Yantosca, S. Strode, L. Jaegle, and E.M. Sunderland, Global 3-D land-ocean-atmosphere model for mercury: present-day vs. pre-industrial cycles and anthropogenic enrichment factors for deposition, Glob. Biogeochem. Cycles, 22, GB2011, 2008.
  12. Smith-Downey, N.V., Sunderland, E.M., and Jacob, D.J., Anthropogenic impacts on global storage and emissions of mercury from terrestrial soils: insights from a new global model, J. Geophys. Res., 115, G03008, 2010.
  13. Soerensen, A.L., E.M. Sunderland, C.D. Holmes, D.J. Jacob, R.M. Yantosca, H. Skov, J.H. Christensen, and R.P. Mason, An improved global model for air-sea exchange of mercury: High concentrations over the North Atlantic, Environ. Sci. Technol., 44, 8574-8580, 2010.
  14. Strode, S.A., L. Jaegle, N.E. Selin, D.J. Jacob, R.J. Park, R.M. Yantosca, R.P. Mason, and F. Slemr, Air-sea exchange in the global mercury cycle, Glob. Biogeochem. Cycles, 21, GB1017, 2006.
  15. S. Strode, L. Jaeglé, D. A. Jaffe, P. C. Swartzendruber, N. E. Selin, C. Holmes, and R. M. Yantosca, Trans-Pacific Transport of Mercury, J. Geophys. Res., 112, D02308, 2008
  16. S. Strode, L. Jaeglé, and N. E. Selin, Impact of mercury emissions from historic gold and silver mining: Global modeling, Atmos. Environ., 43, 2012-2017,2009
  17. Wang, Q., D.J. Jacob, J.A. Fisher, J. Mao, E.M. Leibensperger, C.C. Carouge, P. Le Sager, Y. Kondo, J.L. Jimenez, M.J. Cubison, and S.J. Doherty, Sources of carbonaceous aerosols and deposited black carbon in the Arctic in winter-spring: implications for radiative forcing, Atm. Chem. Phys. Discuss., 11, 19395-19442, 2011.
  18. Zhang, Y., L. Jaegle, A. van Donkelaar, R.V. Martin, C.D. Holmes, H.M. Amos, Q. Wang, R. Talbot, R. Artz, S. Brooks, W. Luke, T.M. Holsen, D. Felton, E.K. Miller, K.D. Perry, D. Schmeltz, A. Steffen, R. Torden, P. Weiss-Penzias, R. Zsolway, Nested-grid modeling of mercury over North America, Atmos. Chem. Physics, 12, 6095-6011, 2012.

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