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!

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.

--Jenny Fisher 9:45, 14 December 2011 (EDT)

Benchmark results for mercury-specific GEOS-Chem updates

Feature(s)	Type	Submitted by	Version	Notes
Hg(II) gas-particle partitioning	Science	Helen Amos (Harvard)	v9-01-03h	A 1-yr benchmark (2009, 4x5) was performed for v9-01-03h against v9-01-02 by Helen Amos. A complete set of benchmark plots are available on Harvard's ftp server: ftp ftp.as.harvard.edu cd gcgrid/geos-chem/Hg_benchmarks/v9-01-03 get Hg_benchmark_v9-01-03h.tar.gz For details on Hg(II) partitioning, please see Amos et al. (2012, ACP).
Updates introduced in v9-02c: Nested grid simulation over North America EPA/NEI05 North American Hg emissions Updated Hg(0) oxidation kinetics Capability to use GEOS-Chem Br/BrO fields in Hg simulation Streets future Hg emissions	Science	Yanxu Zhang (UW)	v9-02c	A 1-year benchmark (2009, 4x5) was performed for v9-02c against v9-01-03h by Yanxu Zhang. A complete set of benchmark plots are available at: ftp ftp.as.harvard.edu cd gcgrid/geos-chem/Hg_benchmarks/v9-02 get Hg_benchmark_v9-02c.tar.gz For more information on the nested grid Hg simulation, please see Zhang et al. (2012, ACP).
None	N/A	Chris Holmes (UC Irvine)	v9-02g	A 1-year benchmark (2009, 4x5) was performed by Chris Holmes for v9-02g against v9-01-03h (and against v9-02c, not discussed). A complete set of benchmark plots are available at: ftp ftp.as.harvard.edu cd gcgrid/geos-chem/Hg_benchmarks/v9-02 get Hg_benchmark_v9-02g.tar.gz The Hg0 chemical lifetime increased from 0.51 to 0.69 yr and the total atm. lifetime increased from 0.69 to 0.81 yr. Major changes in emissions worldwide, overall decreasing Hg(0) emission while increasing Hg(II) emission. Surface TGM increased ~0.1-0.15 ng/m3 over N. America and Europe, but decreased ~0.3ng/m3 over E. Asia. Surface Hg(II) doubled over Europe, E. Asia and ice-covered oceans, but decreased over ice-free oceans. Wet and dry deposition change 50-100% over many regions, with the same sign as Hg(II).
Updates introduced in v9-02k: Streamlining of the code in GeosCore/mercury_mod.F, includes: Replace Hg2 and HgP with Hg2g and Hg2p Update mercury chemistry to Runge-Kutta method Remove PBM uptake by sea salt aerosol	Science	Chris Holmes (UC Irvine)	v9-02k	A 1-year benchmark (2009, 4x5) was performed by Chris Holmes for v9-02k against v9-02g (and against v9-01-03h, v9-01-03-release, and v9-02c, not discussed). A complete set of benchmark plots are available at: ftp ftp.as.harvard.edu cd gcgrid/geos-chem/Hg_benchmarks/v9-02 get Hg_benchmark_v9-02k.tar.gz The difference between v9-02g and v9-02k is negligible, as expected. Sea-salt uptake decreases 50% in continental outflow regions because SSA uptake is applied only to Hg2g, not Hg2p. In response, wet and dry deposition increase in these regions.
Updates introduced in v11-01c: Hg Ocean MLD bug fixes Hg Arctic process updates Hg emission updates (NEI2011, NPRI2011, UNEP2010 with adjustments for and emission controls) Updates introduced in v11-01e: Bug fixes to v11-01c Hg updates	Science	Jenny Fisher (Wollongong)	v11-01e	A 1-year benchmark (2009, 4x5) was performed by Jenny Fisher for v11-01e against v9-02. A complete set of benchmark plots are available at: ftp ftp.as.harvard.edu cd gcgrid/geos-chem/Hg_benchmarks/Hg_benchmark_v11-01c/

Benchmark results for the nested NA grid

Yanxu Zhang has developed a script to benchmark nested-grid mercury simulations over North America. The benchmark code is publicly available at https://github.com/yanxuz/HgBenchmark_nested_NA.

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.

Feature	Type	Submitted by	Version	Notes
Updates introduced in v9-02c: Nested grid simulation over North America EPA/NEI05 North American Hg emissions Updated Hg(0) oxidation kinetics Capability to use GEOS-Chem Br/BrO fields in Hg simulation Streets future Hg emissions	Science	Yanxu Zhang (UW)	v9-02c	A 1-year benchmark (2009, 4x5) was performed for v9-02c by Yanxu Wang. A complete set of benchmark plots are available at: ftp ftp.as.harvard.edu cd gcgrid/geos-chem/Hg_benchmarks/v9-02 get Hg_benchmark_v9-02c.05x0666_NA.tar.gz For more information on the nested grid Hg simulation, please see Zhang et al. (2012, ACP).

GTMM

GTMM has not been supported since GEOS-Chem v10-01. If you are interested in using this simulation, please contact the Hg and POPs Working Group.

GEOS-Chem v8-03-02 and higher versions provide the option to use the Global Terrestrial Mercury Model, which is a detailed land-surface model for use with the Hg simulations. Please see the following references for more information.

1. Global Terrestrial Mercury Model wiki page
2. GTMM User's Manual (PDF)

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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