Difference between revisions of "Mercury"

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On this page we include information relevant to 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.
+
__FORCETOC__
 +
'''''[[CO2 simulation|Previous]] | [[POPs simulation|Next]] | [[Guide to GEOS-Chem simulations]]'''''
 +
#[[GEOS-Chem chemistry mechanisms|Simulations using KPP-built mechanisms]]
 +
#[[Aerosol-only simulation]]
 +
#[[CH4 simulation]]
 +
#[[CO2 simulation]]
 +
#<span style="color:blue">'''Hg simulation'''</span>
 +
#[[POPs simulation]]
 +
#[[Tagged CO simulation]]
 +
#[[Tagged O3 simulation]]
 +
#[[TransportTracers simulation]]
 +
 
 +
The overall capabilities of the mercury simulation are described elsewhere in a [https://geos-chem.seas.harvard.edu/geos-chem-narrative#hg 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!
 
For a list of current and on-going mercury projects, please visit the [[Hg and POPs Working Group]] page!
  
== Code ==
+
== Benchmarking ==
  
=== Code.v9-01-01 ===
+
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".  
  
==== VEGEMIS/GCAP bug fix ====
+
[[https://github.com/noelleselin/HgBenchmark 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.
There was a bug introduced in v8-02-03 with the introduction of the logical LGCAPEMIS, which is designed to turn on or off scaling of GEIA emissions to Streets' 2006 regional GCAP emissions. This logical was then also used to turn off Hg emitted through transpiration, but this should be handled independently from the anthropogenic emissions. We have now introduced a new logical LVEGEMIS that allows you to turn these transpiration emissions on or off independently. This will be standard in [[GEOS-Chem v9-01-02]].
+
  
--Jenny Fisher & [[User:Bmy|Bob Y.]] 09:43, 13 April 2011 (EDT)
+
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.
  
==== Omitted code in Hg simulation ====
+
--[[User:Jaf|Jenny Fisher]] 9:45, 14 December 2011 (EDT)
Some of the updates to the Hg code from Holmes et al. (2010) didn't get properly implemented in v9-01-01.  We haven't looked *extensively* through the code, but a quick look through the obvious mercury routines showed a number of differences:
+
  
    (1) In LAND_MERCURY_FLUX (land_mercury_mod.f)
+
== Benchmark results for mercury-specific GEOS-Chem updates ==
+
        The first IF statement was
+
          IF ( (SNOW_HT > 1D0) .OR. (IS_ICE(I,J)) ) THEN
+
+
        But should have been
+
          IF ( (IS_ICE(I,J)) .OR. (IS_LAND(I,J) .AND. SNOW_HT>10d0) )THEN
+
+
    (2) In BIOMASSHG (land_mercury_mod.f)
+
+
        We currently have (with Bess's 50% reduction):
+
          BBRatio_Hg_CO=1.05D-7
+
+
        However, we should use this value from Holmes et al 2010:
+
          BBRatio_Hg_CO=1D-7
+
+
    (3) In SOILEMIS (land_mercury_mod.f):
+
+
        This IF statement was
+
          IF ( IS_LAND(I,J) .AND. (SNOW_HT < 1d0) ) THEN   
+
+
        But should have been
+
          IF ( IS_LAND(I,J) .AND. (SNOW_HT < 10d0) ) THEN
+
+
    (4) In SNOWPACK_MERCURY_FLUX (land_mercury_mod.f):
+
+
        Residence time when T > -3C was 7 days; i.e.
+
          K_EMIT = 1.6D-6
+
+
        Should have been 3 weeks; i.e.
+
          K_EMIT = 5D-7
+
+
    (5) In ADD_HG2_SNOWPACK (depo_mercury_mod.f):
+
+
        This IF statement was
+
          IF ( (SNOW_HT > 1d0) .OR. (IS_ICE(I,J)) ) THEN
+
+
        But should have been
+
          IF ( (IS_ICE(I,J)) .OR. (IS_LAND(I,J) .AND. SNOW_HT > 10d0) ) THEN
+
+
        We allowed 100% of deposited Hg available for emission; i.e.
+
          SNOW_HG(I,J,NN) = SNOW_HG(I,J,NN) + MAX( DEP_HG2, 0D0 )
+
+
        This Should have only been 60%; i.e.
+
          SNOW_HG(I,J,NN) = SNOW_HG(I,J,NN) + MAX( 0.6D0*DEP_HG2, 0D0 )
+
+
    (6) In OCEAN_MERCURY_FLUX (ocean_mercury_mod.f):
+
+
        We had the old definition
+
          IF ((ALBD(I,J) <= 0.4d0) .and. (FRAC_L < 0.8d0) .and. (MLDCM > 0.99d0)) THEN
+
+
        Holmes et al 2010 used consistent criteria for ocean/land/ice categories
+
          IF ( ( IS_WATER(I,J) ) .AND. ( MLDCM > 0.99d0 ) ) THEN
+
  
This fix will be standardized in [[GEOS-Chem v9-01-02]].  In the meantime, we have released a post-release patch for v9-01-01.  Use the "Git Pull" command to apply the patch into your v9-01-01 code directory:
+
{| border=1 cellspacing=0 cellpadding=5
 +
|- bgcolor="#CCCCCC"
 +
!width="400px"|Feature(s)
 +
!width="75px"|Type
 +
!width="200px"|Submitted by
 +
!width="75px"|Version
 +
!width="600px"|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 [[GEOS-Chem_v9-02_benchmark_history#v9-02c|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 [[GEOS-Chem_v9-02_benchmark_history#v9-02k|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.
  
git pull git://git.as.harvard.edu/bmy/GEOS-Chem  master
+
|-
 +
|
 +
'''Updates introduced in [[GEOS-Chem v11-01#v11-01c|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 [[GEOS-Chem v11-01#v11-01e|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/
  
The patch contains 3 commits named:
+
|}
  
Fixed minor error in depo_mercury_mod.f
+
== Benchmark results for the nested NA grid ==
Add comments to denote updates to Holmes 2010 Hg
+
Update to Holmes et al. 2010 version
+
  
and is tagged as <tt>v9-01-01-Patch-Hg</tt>.
+
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 https://github.com/yanxuz/HgBenchmark_nested_NA].  
  
--Jenny Fisher & [[User:Bmy|Bob Y.]] 09:43, 13 April 2011 (EDT)
+
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.
  
==== Division by zero error ====
+
{| border=1 cellspacing=0 cellpadding=5
 +
|- bgcolor="#CCCCCC"
 +
!Feature
 +
!Type
 +
!Submitted by
 +
!Version
 +
!Notes
 +
|-
 +
|
 +
'''Updates introduced in [[GEOS-Chem_v9-02_benchmark_history#v9-02c|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).
 +
|}
  
There is a div by 0 error in mercury_mod.f <tt>FUNCTION GET_BR</tt> that affects [[GEOS-Chem v8-03-02|v8-03-02]] and [[GEOS-Chem v9-01-01|v9-01-01]]. It's a quick fix.
+
== GTMM ==
  
  Replace:
+
<span style="color:red">'''''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]].'''''</span>
  BR_FAC = ( 1440d0 / TTDAY(I,J) )
+
  with:
+
  BR_FAC = SAFE_DIV( 1440d0, TTDAY(I,J), 0d0)
+
+
  Replace:
+
  BR_FAC = BR_FAC / ( 4D-4 * TTDAY(I,J) )
+
  with:
+
  BR_FAC = SAFE_DIV( BR_FAC, 4D-4* TTDAY(I,J), 0d0)
+
+
  And add:
+
  !Refernces to F90 modules
+
  USE ERROR_MOD, ONLY: SAFE_DIV
+
  
Sometimes TTDAY is 0, so BR_FAC becomes Inf and C_BR becomes Inf. The problem trickles down and shows up as 'PL-HG2-$' diagnostics Hg2_OH, Hg2_O3, Hg2_BR, and Br diagnostics having NaNs in their arrays. Adding the SAFE_DIV fixes the problem. (H Amos, 9 Mar 2011)
+
[[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.
  
This fix will be standardized in [[GEOS-Chem v9-01-02]].
+
#[[Global Terrestrial Mercury Model]] wiki page
 +
#[http://acmg.seas.harvard.edu/geos/doc/GTMM/GTMM_manual_20100811.pdf GTMM User's Manual] (PDF)
  
--[[User:hamos|hamos]] 10:46, 9 March 2011 (EST)<br>
+
== Soil Emissions ==
--[[User:Bmy|Bob Y.]] 10:46, 9 March 2011 (EST)
+
  
=== Code.v8-03-02 ===
+
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.
Diagnostics fix for Hg simulation (Helen Amos, 30 September 2010):
+
  
If the WETDLS-$ and WETDCV-$ diagnostics are only showing up for Hg2 (and not for HgP) in your ctm.bpch file, make the following change to the 'Diagnostics Menu' in input.geos:
+
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.
  
  ND38: Cld Conv scav loss: 47  all
+
Users who want to update their soil Hg files may use IDL code developed by Chris Holmes. Please contact him directly.
  ND39: Wetdep scav loss  : 47  all
+
  
  ND38: Cld Conv scav loss: 47  2 3
 
  ND39: Wetdep scav loss  : 47  2 3
 
  
Recommendations for running code versions 8-03-02 and later (eds):
+
'''''[mailto:amos@fas.harvard.edu Helen Amos] wrote:'''
<ol><li>Reduce geogenic emissions by 50%
+
* ref. Soerensen et al. 2010
+
* mercury_mod.f line 3470:
+
&nbsp;'''EHg0_nt = EHg0_nt / SEC_PER_YR''' <br>
+
&nbsp;'''EHg0_nt = EHg0_nt * 0.5D0''' <br></li>
+
<li>Reduce biomass burning emissions by 50%
+
* ref. Soerensen et al. 2010
+
* land_mercury_mod.f line 225:
+
&nbsp;'''!REAL*8,  PARAMETER  :: BBRatio_Hg_CO = 2.1D-7'''<br>
+
&nbsp;'''REAL*8,  PARAMETER  :: BBRatio_Hg_CO = 1.05D-7'''</li>
+
<li>Reduce intermediate water mercury concentration in Southern Ocean to 0.9pM total
+
* ref. low end of uncertainty range Sunderland and Mason 2007
+
* ocean_mercury_mod.f line 2950:
+
&nbsp;'''!CDEEPSAT = (/ 1.0d-10, 5.0d-10, 5.0d-10 /)'''<br>
+
&nbsp;'''CDEEPSAT = (/ 0.8d-10, 4.1d-10, 4.1d-10 /)'''</li>
+
<li>Reduce concentration of BrO in Arctic during depletion events to 5pptv
+
* ref. low end of uncertainty range in Holmes et al. 2010
+
* ref. low [BrO] observed Neuman et al. 2010
+
* mercury_mod.f line 3805:
+
&nbsp;'''!REAL*8, PARAMETER  :: BRO_POLAR=10D0'''<br>
+
&nbsp;'''REAL*8, PARAMETER  :: BRO_POLAR=5D0'''</li>
+
<li>Adopt Qiaoqiao Wang's modification to rainout & washout (this is standard in [[GEOS-Chem v9-01-01]] and later)
+
* uncomment wetscav_mod.f line 4101:
+
&nbsp;'''IF ( PDOWN(L,I,J) > 0d0 ) THEN'''<br>
+
&emsp;&emsp;'''F_RAINOUT = F_PRIME'''<br>
+
&emsp;&emsp;'''! Washout occurs where there is no rainout'''<br>
+
&emsp;&emsp;'''F_WASHOUT = MAX( FTOP - F_RAINOUT, 0d0 )'''<br>
+
&nbsp;'''ELSE'''<br>
+
&emsp;&emsp;'''F_RAINOUT = 0d0'''<br>
+
&emsp;&emsp;'''F_WASHOUT = 0d0'''<br>
+
&nbsp;'''ENDIF'''<br>
+
* comment out wetscav_mod.f line 4121:
+
&nbsp;'''!F_RAINOUT = 0d0'''<br>
+
&nbsp;'''!F_WASHOUT = 0d0'''<br>
+
&nbsp;'''!IF ( PDOWN(L,I,J) > 0d0 ) THEN'''<br>
+
&nbsp;'''!&emsp;&emsp;IF (QQ(L,I,J) > 0d0) THEN'''<br>
+
&nbsp;'''!&emsp;&emsp;&emsp;F_RAINOUT = MAX( FTOP, F_PRIME )'''<br>
+
&nbsp;'''!&emsp;&emsp;ENDIF'''<br>
+
&nbsp;'''!&emsp;&emsp;F_WASHOUT = MAX( FTOP - F_RAINOUT, 0d0 )'''<br>
+
&nbsp;'''!ENDIF'''<br></li>
+
</ol>
+
  
<br>
+
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
  
=== Previous discussions (6/2008) ===
+
'''Step 1:''' Use soilhgdist_uniform.pro to create a uniform soil distribution. Save file as 'soilhg.uniform.bpch'.
  
#Standardize the solver.  Everyone should use the solver Chris developed for the Hg chemistry <br>(located at ~cdh/GC/RevisedChem.v7-04-06/mercury_mod.f)
+
'''Step 2:''' In mercury_mod.f SUBROUTINE MERCURY_READYR, specify that you want to run with 'soilhg.uniform.bpch'.
#*outstanding issue - dry dep of Hg0*  <- currently working on this (eds)
+
#*''See [[GEOS-Chem v8-03-02]] and later for Holmes et al. 2010 Hg+Br simulation.''
+
#Catalog all emissions options and develop clear flagging system to choose your own adventure.  This will include:<ul><li> different anthropogenic emissions scenarios/corrections (i.e Jaffe vs. Streets) <- going to work on the anthro emissions soon (eds), <br><li>different land emissions. <- nvd will work on this</ul>
+
#*''Logicals implemented to select anthropogenic emissions from GEIA 2000, GEIA 2005, or GEIA scaled to Streets et al. 2006 regional totals.''
+
#Diagnostics. See separate section below. 
+
#*''Diagnostics have been updated.''
+
#''Comment everything'' in the code.  Remove old bits of code that are hanging around & commented out.
+
#*''Ongoing.''
+
#GEOS-5
+
#*''This is the standard meteorology to use at present.  [[MERRA]] is in development.''
+
#Get the land stuff out of ocean_mercury_mod.f and into it's own module <- nvd will work on this
+
#*''Implemented by ccarouge v8-03-02.''
+
  
== Chemistry 'issues' ==
+
'''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.
  
=== Dry deposition of HgP over snow/ice ===
+
'''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.
  
The HgP dry deposition velocity over snow/ice is now set to a constant value to better match observational constraints. HgP is treated the same as all other fine aerosols in this respect. This update will be standard in [[GEOS-Chem v9-01-02|v9-01-02]]. For more information see the [[Dry deposition#Aerosol dry deposition velocities over snow and ice surfaces|dry deposition]] page. (Jenny Fisher, Harvard).
+
'''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.  
  
=== Previous discussions ===
+
'''Step 6:''' In mercury_mod.f SUBROUTINE MERCURY_READYR, change input file to new soil distribution created in Step 4.
  
#Oxidant.  
+
'''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).
#*Chris has a simulation with Hg-Br chemistry and SS aerosol deposition; the global budget is ok, but the Br concentrations in the BL are too low to generate diurnal cycles. (cdh working on it)
+
#Snow/ice scavenging of HgII
+
#*Cold-temperature wet scavenging of HgII is now included in the standard code.
+
#Dry deposition of "aqueous HgII.  
+
#*(Explanation from Chris: We calculate the fraction of HgII, Fg, which is gas phase. But we're currently applying the dry deposition velocity to both gas and aqueous fractions. I think it would be better to deposit the aqueous fraction at the velocity of HgP; this would be slower dep, but I don't know how much. This is definitely up for discussion.)
+
#*''See Holmes et al. 2010 for discussion of chemistry in standard version.''
+
  
== Diagnostics ==
+
'''Step 8:''' Repeat Steps 4-7 until pre-industrial soil distribution converges. You can check for convergences with Gamap routine CTM_PLOTDIFF. 
  
=== Notes ===
+
'''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.  
#Helen Amos is developing diagnostics for reactive gaseous mercury and reactive particulate mercury.
+
#Bess Corbitt is developing diagnostics for a tagged-tracer simulation with 17 world regions. For example, when running with this option, for prompt recycling of deposited mercury, instead of HG-SRCE category and Hg0_ln tracer name for the total tracer, I would have category HG0-RECY and tracername Hg0_usa, Hg0_can, etc.
+
  
=== Previous discussions ===
+
'''Step 10:''' Use soilhgdist.pro to create a present day soil distribution.
  
Here are some suggested changes:
 
# Emissions should have units 'kg/m2/s' or something of the form 'mass/area/time' (they are currently 'kg'). The HG-SRCE diagnostic currently has all of the Ocean tracers and fluxes; these should go elsewhere.
 
# The Ocean Hg0, Hg2, HgC should have concentration units not kg. Is 'molar' the best choice? Fluxes of these should be in concentration/time, not kg.
 
# The ocean restart files should have concentration units not kg. They currently use the category 'OCEAN-HG' which would make sense for the ND03 ocean Hg0, Hg2, HgC output too.
 
# 'PL-HG2-$' doesn't really describe all of the fluxes in our model. There are a lot of diagnostic quantities which are either chemical P/L fluxes or rate constants. I think these should all be in one diagnostic called something like 'PL-HG-$' (or maybe 'PL-HG-A', 'PL-HG-O' to separate the atmosphere and ocean). The fluxes in this diagnostic would include redox in air and water, colloidal sinking, ocean-atmosphere piston velocity, ...
 
  
Here are the current GEOS-Chem Hg outputs
+
--[[User:hamos|Helen Amos]] 03:44, 13 Aug 2011 (EST)<br>
  
      CATEGORY ILUN TRCNAME  TRC        UNIT      TAU0(DATE)      DIMENSIONS
+
=== Update for HEMCO ===
  1 : IJ-AVG-$  23    Hg0    1        pptv 157776.00(2003010100)  72 46 30
+
  2 : IJ-AVG-$  23    Hg2    2        pptv 157776.00(2003010100)  72 46 30
+
  3 : IJ-AVG-$  23    HgP    3        pptv 157776.00(2003010100)  72 46 30
+
  4 : WETDCV-$  23    Hg2  3002        kg/s 157776.00(2003010100)  72 46 30
+
  5 : WETDCV-$  23    HgP  3003        kg/s 157776.00(2003010100)  72 46 30
+
  6 : WETDLS-$  23    Hg2  3002        kg/s 157776.00(2003010100)  72 46 30
+
  7 : WETDLS-$  23    HgP  3003        kg/s 157776.00(2003010100)  72 46 30
+
  8 :  HG-SRCE  23  Hg0_an 34001          kg 157776.00(2003010100)  72 46  1
+
  9 :  HG-SRCE  23  Hg0_aq 34002          kg 157776.00(2003010100)  72 46  1
+
  10 :  HG-SRCE  23  Hg0_oc 34003          kg 157776.00(2003010100)  72 46  1
+
  11 :  HG-SRCE  23  Hg0_ln 34004          kg 157776.00(2003010100)  72 46  1
+
  12 :  HG-SRCE  23  Hg0_na 34005          kg 157776.00(2003010100)  72 46  1
+
  13 :  HG-SRCE  23  Hg2_an 34006          kg 157776.00(2003010100)  72 46  1
+
  14 :  HG-SRCE  23  Hg2_aq 34007          kg 157776.00(2003010100)  72 46  1
+
  15 :  HG-SRCE  23  Hg2_sk 34008          kg 157776.00(2003010100)  72 46  1
+
  16 :  HG-SRCE  23  HgP_an 34009          kg 157776.00(2003010100)  72 46  1
+
  17 :  HG-SRCE  23    KwHg 34010        cm/h 157776.00(2003010100)  72 46  1
+
  18 :  HG-SRCE  23    HgC 34011          kg 157776.00(2003010100)  72 46  1
+
  19 :  HG-SRCE  23 Hg_to_C 34012          kg 157776.00(2003010100)  72 46  1
+
  20 : PL-HG2-$  23 Hg2_Hg0 35001          kg 157776.00(2003010100)  72 46 30
+
  21 : PL-HG2-$  23  Hg2_OH 35002          kg 157776.00(2003010100)  72 46 30
+
  22 : PL-HG2-$  23  Hg2_O3 35003          kg 157776.00(2003010100)  72 46 30
+
  23 : PL-HG2-$  23  Hg2_SS 35004          kg 157776.00(2003010100)  72 46  1
+
  24 : PL-HG2-$  23 Hg2_SSR 35005          /s 157776.00(2003010100)  72 46  1
+
  25 : DRYD-FLX  23  Hg0df 36001  molec/cm2/s 157776.00(2003010100)  72 46  1
+
  26 : DRYD-FLX  23  Hg2df 36002  molec/cm2/s 157776.00(2003010100)  72 46  1
+
  27 : DRYD-FLX  23  HgPdf 36003  molec/cm2/s 157776.00(2003010100)  72 46  1
+
  28 : DRYD-VEL  23  Hg2dv 37002        cm/s 157776.00(2003010100)  72 46  1
+
  29 : DRYD-VEL  23  HgPdv 37003        cm/s 157776.00(2003010100)  72 46  1
+
  
I think we should change lines 8-24 (I've kept the same line numbers and TRCNAME, but changed CATEGORY, TRC, or UNIT):
+
GCST and/or Team Hg to provide HEMCO-ready uniform soil distribution files - for now contact jennyf@uow.edu.au if you want one.
  
      CATEGORY  TRCNAME    TRC        UNIT
+
'''Step 1:''' In HEMCO_Config.rc change the name of the soil file to soilhg.uniform.$RES.nc
  8 : HG-SRCE  Hg0_an  34001      kg/m2/s
+
  10 :  HG-SRCE  Hg0_oc  34002      kg/m2/s
+
  11 :  HG-SRCE  Hg0_ln  34003      kg/m2/s
+
  12 :  HG-SRCE  Hg0_na  34004      kg/m2/s
+
  13 :  HG-SRCE  Hg2_an  34005      kg/m2/s
+
  16 :  HG-SRCE  HgP_an  34006      kg/m2/s
+
  9 : OCEAN-HG  Hg0_aq  xxxx1        mol/L
+
  14 : OCEAN-HG  Hg2_aq  xxxx2        mol/L
+
  18 : OCEAN-HG  HgC    xxxx3        mol/L
+
  20 :  PL-HG-A  Hg2_Hg0 35001      kg/m3/s
+
  21 :  PL-HG-A  Hg2_OH  35002      kg/m3/s
+
  22 :  PL-HG-A  Hg2_O3  35003      kg/m3/s
+
  23 :  PL-HG-A  Hg2_SS  35004      kg/m3/s
+
  24 :  PL-HG-A  Hg2_SSR 35005          /s
+
  15 :  PL-HG-O  Hg2_sk  xxxx1      kg/m3/s
+
  19 :  PL-HG-O  Hg_to_C xxxx2      kg/m3/s
+
  17 :  PL-HG-O  KwHg    xxxx3        cm/h
+
  
 +
'''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.
  
The only thing I have to add is that at first I didn't realize that wet deposition of Hg(II) was composed of both WETDCV and WETDLS. Is it important to save those components out as 2 separate parts? (nvd)
+
'''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.
To answer Nicole, it is useful to have the large scale and convective wet scavenging written out separately for comparison to wet deposition observations. They are different processes in the model and can tell us different things about where the model is performing well and where it needs improvement (for example, convective scavenging over the Gulf Coast region).  (eds)
+
  
== GTMM ==
+
'''Step 4:''' Make the new soil file HEMCO-ready by running the following nco commands:<br>
 +
ncrename -v HG_SRCE__Hg0_ln,HG0_DIST filename.nc<br>
 +
ncatted -a gamap_category,HG0_DIST,o,c,HG-SRCE filename.nc<br>
 +
ncatted -a units,HG0_DIST,o,c,1 filename.nc<br>
  
[[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.
+
'''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.  
  
#[[Global Terrestrial Mercury Model]] wiki page
+
'''Step 6:''' In HEMCO_Config.rc, change soil file to new file created in Step 4.  
#[http://www.geos-chem.org/doc/man/files/GTMM_manual_20100811.pdf GTMM User's Manual] (PDF)
+
  
 +
'''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).
  
== Soil Emissions ==
+
'''Step 8:''' Repeat Steps 2-7 until pre-industrial soil distribution converges to within 5%.
  
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.
+
'''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.  
  
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.
+
'''Step 10:''' Use soilhgdist_nc.pro to create a present day soil distribution.
  
Users who want to update their soil Hg files may use IDL code developed by Chris Holmes. Please contact him directly.
+
-- Jenny Fisher, 19 Mar 2016
  
 
== References ==
 
== References ==
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, Atmospheric Chemistry and Physics, 10, 12,037-12,057, 2010
+
#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", <u> Environ. Sci. Technol.</u>, DOI.10.1021/es502134t, 2014.
 
+
#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'', <u>Atm. Chem. Phys.</u>, '''12''', 591-603, 2012.
 
+
#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'', <u>Environ. Sci. Technol.</u>, '''45''', 10477-10484, 2011.
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
+
#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'', <u>Environ. Sci. Technol.</u>, 46, 5262−5262, 2012.
 
+
#Holmes, C. D., D. J. Jacob, and X. Yang, ''Global lifetime of elemental mercury against oxidation by atomic bromine in the free troposphere'', <u>Geophys. Res. Lett.</u>, '''33''', L20808, 2006.
 
+
#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'', <u>Atm. Chem. Phys.</u>, '''10''', 12,037-12,057, 2010
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
+
#Holmes, C.D., D.J. Jacob, R.P. Mason, D.A. Jaffe, ''Sources and deposition of reactive gaseous mercury in the marine atmosphere'', <u>Atm. Environ.</u>, '''43''', 2278-2285, 2009.
 
+
#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'', <u>Atmos. Chem. Phys.</u>, '''12''', 723-6,740, 2012.
 
+
#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'', <u>J. Geophys. Res</u>, '''112''', DO2308, doi:10.1029/2006JD007450, 2007.
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
+
#Selin, N.E. and D.J. Jacob. ''Seasonal and spatial patterns of mercury wet deposition in the United States: North American vs. intercontinental sources'', <u>Atm. Environ</u>, '''42''', 5193-5204, 2008.
 
+
#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'', <u>Glob. Biogeochem. Cycles</u>, '''22''', GB2011, 2008.
 
+
#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'', <u>J. Geophys. Res.</u>, '''115''', G03008, 2010.
Holmes, C.D., D.J. Jacob, R.P. Mason, D.A. Jaffe, Sources and deposition of reactive gaseous mercury in the marine atmosphere,Atmospheric Environment,43, 2278-2285, 2009
+
#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'', <u>Environ. Sci. Technol.</u>, '''44''', 8574-8580, 2010.
 
+
#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'', <u>Glob. Biogeochem. Cycles</u>, '''21''', GB1017, 2006.
 
+
#S. Strode, L. Jaeglé, D. A. Jaffe, P. C. Swartzendruber, N. E. Selin, C. Holmes, and R. M. Yantosca, ''Trans-Pacific Transport of Mercury'', <u>J. Geophys. Res.</u>, '''112''', D02308, 2008
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
+
#S. Strode, L. Jaeglé, and N. E. Selin, ''Impact of mercury emissions from historic gold and silver mining: Global modeling'', <u>Atmos. Environ.</u>, '''43''', 2012-2017,2009
 
+
#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'', <u>Atm. Chem. Phys. Discuss.</u>, '''11''', 19395-19442, 2011.
 
+
#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'', <u>Atmos. Chem. Physics</u>, 12, 6095-6011, 2012.
Selin, N.E. and D.J. Jacob. Seasonal and spatial patterns of mercury wet deposition in the United States: North American vs. intercontinental sources , Atmospheric Environment, 42, 5193-5204, 2008
+
 
+
 
+
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", Global Biogeochemical Cycles , 22, GB2011, 2008
+
 
+
 
+
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
+
 
+
 
+
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, Global Biogeochemical Cycles, 21, GB1017, 2006
+
 
+
  
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
+
----
 +
'''''[[CO2 simulation|Previous]] | [[POPs simulation|Next]] | [[Guide to GEOS-Chem simulations]]'''''

Latest revision as of 14:52, 18 October 2023

Previous | Next | Guide to GEOS-Chem simulations

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