Difference between revisions of "Mercury"

From Geos-chem
Jump to: navigation, search
(Code)
(Benchmark results for mercury-specific GEOS-Chem updates)
 
(171 intermediate revisions by 8 users not shown)
Line 1: Line 1:
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]]
  
For a list of current and on-going mercury projects, please visit the [[Hg and POPs Working Group]] page!
+
The overall capabilities of the mercury simulation are described elsewhere in a [https://geos-chem.seas.harvard.edu/geos-chem-narrative#hg Narrative description.]  
  
== Code ==
+
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.
  
In this section we describe the updates made to the mercury simulation in each recent GEOS-Chem model version.
+
For a list of current and on-going mercury projects, please visit the [[Hg and POPs Working Group]] page!
 
+
=== GEOS-Chem v11-01 ===
+
 
+
==== Remove in-plume reduction of Hg ====
+
 
+
'''''Yanxu Zhang wrote:'''''
+
 
+
:The in-plume reduction of divalent Hg (HgII) from coal-fired power plants was firstly introduced into the GEOS-Chem model by Zhang et al. (2012). This process was included into the 0.5x0.666 nested-grid model over North America to reconcile the observed relatively low wet deposition flux over Ohio River Valley (ORV) region. This is known to the mercury community as a "Mercury Dilemma": the ORV region has the highest HgII emissions from coal-fired power plants, and the largest acid deposition is indeed observed there, however, the highest wet deposition of HgII is observed at Florida, far south of ORV region. The in-plume reduction hypothesis assumes that the HgII emissions from these power plants are fast reduced back to elemental Hg (Hg0) in the power plant plumes, and Hg0 is a gas and not subject to wet deposition. Later this hypothesis was adopted by Amos et al. (2012) and generalized to a global model study.
+
 
+
:An alternative hypothesis for the in-plume reduction relies on the big uncertainties associated with our understanding of the initial speciation of Hg out of the stacks of these power plants. New data showed that the fraction of Hg emissions from the US coal-fired power plants as HgII is much lower than previous thought, due to the co-benefits of the installation of SO2 and NOx emission control instruments such as flue gas desulfurization and selective catalytic reactor (EPA 2011). Similar change was noted by Chinese studies (Zhang et al., 2014; Zhao et al., 2015 ). With these new information regarding emission speciation, plus new observational evidence supporting a weak in-plume reduction process (Landis et al., 2014), we decide to remove this process, or at least weaken it in the standard model.
+
 
+
'''Reference:'''
+
*Amos, H. M., et al. (2012), ''Gas-particle partitioning of atmospheric Hg(II) and its effect on global mercury deposition'', <u>Atmospheric Chemistry and Physics</u>, '''12'''(1), 591-603.
+
*EPA (2011), ''Air Quality Modeling Technical Support Document: EGU Mercury Analysis'', U.S. Environmental Protection Agency, Office of Air Quality Planning and Standards, Air Quality Assessment Division, Research Triangle Park, NC 27711
+
*Landis, M. S., J. V. Ryan, A. F. Ter Schure, and D. Laudal (2014), ''Behavior of Mercury Emissions from a Commercial Coal-Fired Power Plant: The Relationship between Stack Speciation and Near-Field Plume Measurements'', <u>Environ. Sci. Technol.</u>, '''48'''(22), 13540-13548.
+
*Zhang, Y., et al. (2012), ''Nested-grid simulation of mercury over North America'', <u>Atmospheric Chemistry and Physics Discussions</u>, '''12''', 2603-2646.
+
*Zhang, L., et al. (2015), ''Updated Emission Inventories for Speciated Atmospheric Mercury from Anthropogenic Sources in China'', <u>Environ Sci Technol.</u>
+
*Zhao, Y., H. Zhong, J. Zhang, and C. P. Nielsen (2014), ''Evaluating the effects of China's pollution control on inter-annual trends and uncertainties of atmospheric mercury emissions'', <u>Atmospheric Chemistry and Physics Discussions</u>, '''14'''(19), 26803-26855.
+
 
+
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:05, 26 May 2015 (UTC)
+
 
+
=== GEOS-Chem v10-01 ===
+
 
+
==== Bugs in MERRA wet deposition ====
+
 
+
Carey Friedman originally reported bugs in the calculation of <tt>WETLOSS</tt> in <tt>DO_MERRA_CONVECTION</tt> and <tt>DO_WASHOUT_ONLY</tt> that caused mass of scavenged tracer passed to <tt>depo_mercury_mod.F</tt> to differ from the mass that is archived in the wet deposition diagnostics (ND38 and ND39). Carey's fixes were implemented in [[GEOS-Chem v10-01#v10-01g|v10-01g]]. Viral Shah examined these bugs in more detail and proposed several additional bug fixes. Viral's fixes will be included in the [[GEOS-Chem v10-01#Fixes and updates added during the public comment period|GEOS-Chem v10-01 public release]]. For more information, please see [[Wet deposition#Bugs in MERRA wet deposition|this post on our ''Wet deposition'' wiki page]].
+
 
+
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 15:58, 21 May 2015 (UTC)
+
 
+
==== Remove array temporaries in routine READ_HG2_PARTITIONING ====
+
 
+
'''''These updates were validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''
+
 
+
The [[GEOS-Chem Unit Tester]] revealed the presence of [[Passing array arguments efficiently in GEOS-Chem|array temporaries]] in routine <tt>READ_HG2_PARTITIONING</tt>, located in module <tt>GeosCore/ocean_mercury_mod.F</tt>.  We made the following modifications in order to eliminate these array temporaries.
+
 
+
(1) Declare array <tt>ARRAYtemp</tt> in the local variables section:
+
 
+
      ! Arrays to hold aerosol concentrations 
+
      REAL*4              :: ARRAYso4(  IGLOB, JGLOB, LGLOB )  ! so4
+
      ... etc ...
+
      REAL*4              :: ARRAYtemp( IGLOB, JGLOB, LGLOB )  ! temporary
+
 
+
(2) Sum arrays into <tt>ARRAYtemp</tt> before passing to routine <tt>TRANSFER_3D_TROP</tt>, as follows:
+
 
+
      ! convert REAL*4 to REAL*8
+
!-----------------------------------------------------------------------------
+
! Prior to 4/15/14:
+
! Remove an array temporary (bmy, 4/15/14)
+
!      CALL TRANSFER_3D_TROP( ARRAYbcpi + ARRAYbcpo , BC_CONC )
+
!-----------------------------------------------------------------------------
+
      ARRAYtemp = ARRAYbcpi + ARRAYbcpo
+
      CALL TRANSFER_3D_TROP( ARRAYtemp, BC_CONC )
+
+
      ... etc ...
+
+
      ! convert REAL*4 to REAL*8
+
!-----------------------------------------------------------------------------
+
! Prior to 4/15/14:
+
! Remove an array temporary (bmy, 4/15/14)
+
!      CALL TRANSFER_3D_TROP( ARRAYocpi + ARRAYocpo , OC_CONC )
+
!-----------------------------------------------------------------------------
+
      ARRAYtemp = ARRAYocpi + ARRAYocpo
+
      CALL TRANSFER_3D_TROP( ARRAYtemp, OC_CONC )
+
 
+
--[[User:Bmy|Bob Y.]] 17:08, 30 May 2014 (EDT)
+
 
+
=== GEOS-Chem v9-02 ===
+
 
+
==== Nested-grid Hg simulation over North America ====
+
 
+
This update was implemented in 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02c|v9-02c]] and contains the following items:
+
 
+
'''''[mailto:yanxuz@atmos.washington.edu Yanxu Zhang] wrote:'''''
+
 
+
:1. Nested Hg simulation over North America
+
::The GEOS-Chem simulation now can be run in nested-grid mode within North American domain, with lateral boundary conditions provided by a 4x5 global run. The nested model can be run with GEOS-5 meteorological data.
+
 
+
:2. NEI 2005 and NPRI 2005 emission inventory
+
::The emisison inventories for US and Canada are updated according to the NEI2005 and NPRI2005 emission inventories. A triger <tt>LNEI2005</tt> is added to control this. If enabled, the emission inventory will be overrided by the NEI2005 and NPRI2005 emission inventories in US and Canada, respectively.
+
 
+
:3. In-plume reduction (CFPP and other sectors)
+
::A triger <tt>LInPlume</tt> is added to controlled the in-plume reduction. If enabled, the coal fired power plants emission speciation is modified as 86.5:9.9:3.6. In the US and Canada, the location and emission rate from coal fired power plants are available in the NEi2005 and NPRI2005 emission inventories, respectively.
+
 
+
:4. Updated reduction according to cloud fraction
+
::Adjust the liquid water content (<tt>LWC</tt>) by dividing it by cloud cover:
+
            LWC    = SAFE_DIV( LWC, FC, 0d0 )
+
::After calculating the fraction of HgII in aqueous phase (<tt>FA</tt>), the <tt>FA</tt> is multiplied by cloud cover:
+
        IF ( LGEOSLWC ) FA =  FA * FC
+
::This implementation was firstly introduced by lzh, jaf and bmy.
+
::The <tt>K_RED_JNO2</tt> is also tuned:
+
      REAL*8, PARAMETER    :: K_RED_JNO2 = 6.4d-3
+
 
+
:5. Reading data in different spatial resolutions
+
::The code is modified to handle files in different resolutions, including <tt>global_o3_mod.F, mercury_mod.F</tt> and <tt>ocean_mercury_mod.F</tt>.
+
 
+
:6. Sensitivity run to turn off North American anthropogenic emissions
+
::Modify the definition of North American anthropogenic emissions:
+
!            IF ( GET_XMID(I) > -125 .AND. GET_XMID(I) < -65 .AND.
+
!    &          GET_YMID(J) >  25  .AND. GET_YMID(J) < 50 ) THEN
+
            IF ( GET_XMID(I) > -140 .AND. GET_XMID(I) < -40 .AND.
+
      &          GET_YMID(J) >  10  .AND. GET_YMID(J) < 70 ) THEN
+
 
+
--[[User:Melissa Payer|Melissa Payer]] 11:27, 13 December 2011 (EST)
+
 
+
==== Streets future Hg emissions ====
+
 
+
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02c|v9-02c]] and approved on 29 Nov 2012.'''''
+
 
+
Bess Corbitt has  implemented Streets future Hg emissions into the Hg simulation based on the 1x1 gridded GEIA 2005 anthropogenic emissions inventory. Within major world regions (e.g. United States, Eastern Europe, etc.) the spatial pattern of the GEIA inventory is maintained, but a scaling factor is applied so that regional total emissions equal that of Streets et al. 2009.
+
 
+
Emissions are available for the present-day (2006) or future (2050) scenarios. Future emissions are based on the four IPCC SRES scenarios: A1B, A2, B1, or B2. Additional options have been added to the Mercury Menu in input.geos to allow the user to select an emissions scenario.
+
 
+
For more information, see [http://acmg.seas.harvard.edu/publications/corbitt2011.pdf Corbitt et al. 2011].
+
 
+
--[[User:Melissa Payer|Melissa Payer]] 16:33, 27 November 2012 (EST)
+
 
+
==== Updated Hg(0) oxidation kinetics ====
+
 
+
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02c|v9-02c]] and approved on 29 Nov 2012.'''''
+
 
+
Hg(0) + Br rate constants have been updated to use the Goodsite et al. 2012 corrected values. The new rates are denoted as <tt>GoodsiteUpdate</tt> in subroutine GET_HGBR_RATE (mercury_mod.F).
+
 
+
--[[User:Melissa Payer|Melissa Payer]] 16:33, 27 November 2012 (EST)
+
 
+
==== Capability to use GEOS-Chem Br/BrO fields in Hg simulation ====
+
 
+
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02c|v9-02c]] and approved on 29 Nov 2012.'''''
+
 
+
The mercury simulation has been updated to use Br and BrO mixing ratios from GEOS-Chem using the [[Bromine_chemistry_mechanism|tropospheric bromine chemistry mechanism]] described in Parrella et al. 2012. Users can choose between using the GEOS-Chem tropospheric bromine fields or the older TOMCAT fields by setting the <tt>LGCBROMINE</tt> switch in subroutine INIT_MERCURY (mercury_mod.F).
+
 
+
--[[User:Melissa Payer|Melissa Payer]] 16:33, 27 November 2012 (EST)
+
 
+
==== Bug fixes for nested Hg simulation ====
+
 
+
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02f|v9-02f]] and approved on 07 Feb 2013.'''''
+
 
+
'''''[mailto:yanxuz@atmos.washington.edu Yanxu Zhang] wrote:'''''
+
 
+
:Several bugs in the code:
+
:1. <tt>input_mod.F</tt>: change the number of diagnostics.
+
 
+
      !--------------------------
+
      ! ND03: Hg diagnostics
+
      !--------------------------
+
      CALL SPLIT_ONE_LINE( SUBSTRS, N, -1, 'read_diagnostic_menu:5' )
+
      READ( SUBSTRS(1), * ) ND03
+
      IF ( .not. ITS_A_MERCURY_SIM() ) ND03 = 0
+
      !CALL SET_TINDEX( am_I_Root, 03, ND03, SUBSTRS(2:N), N-1, PD03_PL ) !eds 9/9/10
+
      CALL SET_TINDEX( am_I_Root, 03, ND03, SUBSTRS(2:N), N-1, PD03 ) !yzh 12/15/12
+
 
+
:2. <tt>land_mercury_mod.F</tt>: value for SOIL_EMIS_FAC in 0.5x0.666 nested-grid, now we can use the same value for 4x5 grid. Further tuning may slightly change the value.
+
 
+
#elif defined(GRID05x0666)
+
      !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
      ! lhu, 1/5/2012, add pre-defined SOIL_EMIS_FAC for 05x0667 simulation
+
      ! This is a non-physical value and would need to be changed for an
+
      ! actual mercury simulation
+
      REAL*8, PARAMETER :: SOIL_EMIS_FAC = 2.4D-2*0.71d0  !yzh
+
      !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 
+
:3. <tt>mercury_mod.F</tt>: GC Br filed for nested-grid. I have interpolate the Br filed from GC Br simulation for the nested-grid run. So now the nested-grid model and global model are consistent. We can choose use either GC or TOMCAT Br filed for the nest and global models. However, I suggest always choose the same Br field for the nested and global models.
+
 
+
!#if defined( GRID05x0666 ) && defined( NESTED_NA )
+
      !LGCBROMINE = .FALSE.
+
!#else
+
    LGCBROMINE = .TRUE.
+
!#endif
+
 
+
:4. <tt>ocean_mercury_mod.F</tt>: unit transfer for aerosol concentrations in nested-grid model:
+
 
+
#if defined( GRID4x5 )
+
        BULK_CONC(I,J,L) = 1d9 * ( BULK_CONC(I,J,L) * AIRDEN(L,I,J)  )
+
#elif defined( GRID2x25 )
+
        BULK_CONC(I,J,L) = ( BULK_CONC(I,J,L) * AIRDEN(L,I,J)  )
+
#elif defined( GRID05x0666 ) && defined( NESTED_NA )
+
        BULK_CONC(I,J,L) = 1d9 * ( BULK_CONC(I,J,L) * AIRDEN(L,I,J)  )  !yzh, 12/15/2012
+
#endif
+
 
+
--[[User:Melissa Payer|Melissa Payer]] 09:29, 1 February 2013 (EST)
+
 
+
==== Bug in tagged Hg emissions in v9-02 ====
+
 
+
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''<p>This issue will be resolved when the [[HEMCO|HEMCO emissions component]] is implemented into [[GEOS-Chem v10-01]].  HEMCO will render the current emissions routines obsolete.</p><p>&mdash; Melissa Sulprizio, 16 September 2014</p>'''</div>
+
 
+
'''''[[User:Carey_Friedman|Carey Friedman]] wrote:'''''
+
 
+
:In the <tt>mercury_mod.F</tt> file, in the <tt>MERCURY_READYR</tt> routine, for tagged tracer emissions of Hg2 and HgP, I think the routine from Hg0 was copied and revised but the emissions array variable in <tt>DO_REGRID_A2A</tt> wasn't updated. So for both Hg2 and HgP, the emissions are regridded into, for example, an EHg0_usa array, overwriting whatever was there before. It looks like this is the case for all source regions for both Hg2 and HgP (at least in v902).
+
 
+
To fix this bug, change the <tt>OUTGRID</tt> argument in all calls to <tt>DO_REGRID_A2A</tt> for the Hg2 and HgP tagged tracers. For example, change the bold lines below from:
+
 
+
              !===========================
+
              ! Anthro United States Hg2
+
              !===========================
+
              FILENAME = TRIM( Input_Opt%DATA_DIR_1x1 ) //
+
    &              'mercury_201205/' //
+
    &                    'GEIA_Streets_'      // TRIM( SCENARIO )  //
+
    &                    '_Hg2_USA.geos.1x1.YYYY'
+
           
+
              ! Add year to the filename
+
              CALL EXPAND_DATE( FILENAME, NYMD, 000000 )
+
           
+
              ! Echo info
+
              WRITE( 6, 119 ) TRIM( FILENAME )
+
119          FORMAT( '    - MERCURY_READYR: Reading ', a )
+
           
+
              ! Read data in [kg/yr]
+
              CALL READ_BPCH2( FILENAME, 'HG-SRCE', 6,
+
    &                          XTAU,      I1x1,    J1x1-1,
+
    &                          1,        ARRAY1,  QUIET=.TRUE. )
+
           
+
              ! Cast to REAL*8 before regridding
+
              GEN_1x1(:,:) = ARRAY1(:,:,1)
+
+
              ! Regrid from GENERIC 1x1 to the current grid
+
              INGRID  => GEN_1x1(:,:)
+
              <b>CALL DO_REGRID_A2A( LLFILENAME, I1x1,    J1x1-1,
+
    &                            INGRID,    EHg0_usa, IS_MASS=1,
+
    &                            netCDF=.TRUE.                  )</b>
+
           
+
              ! Convert from [kg/yr] to [kg/s]
+
              EHg2_usa = EHg2_usa / SEC_PER_YR
+
+
              ! Free pointer
+
              NULLIFY( INGRID )
+
 
+
to:
+
 
+
              CALL DO_REGRID_A2A( LLFILENAME, I1x1,    J1x1-1,
+
    &                            INGRID,    EHg2_usa, IS_MASS=1,
+
    &                            netCDF=.TRUE.                  )
+
 
+
--[[User:Melissa Payer|Melissa Sulprizio]] 16:40, 16 September 2014 (EDT)
+
 
+
=== GEOS-Chem v9-01-03 ===
+
 
+
==== GAMAP can't read v9-01-03 output for Hg ====
+
 
+
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02k|v9-02k]] and approved on 07 Jun 2013.'''''
+
 
+
The ctm.bpch and restart files created by the GEOS-Chem v9-01-03 mercury simulation cannot be read by GAMAP, due to a bug in gamap_mod.F causing missing lines in tracerinfo.dat. In addition, the ctm.bpch file does not contain dry deposition velocities for PBM.
+
 
+
Although this bug will be fixed in v9-02, users of v9-01-03 should apply this patch with git: [[Media:Patch_GC-Hg.v9-01-03.txt‎]]. The patch should apply after the commit "Bug fix: Add inquireMod.o to dependency listing for bpch2_mod.o" on 2012-09-14 12:52:51. For instructions on applying patches, see [[Using_Git_with_GEOS-Chem#Checking_the_validity_of_a_patch_file|this wiki page]].
+
 
+
The patch also makes several other changes to the model:
+
 
+
:1. The 3 Hg tracers in restart and ctm.bpch files should be interpreted as Hg(0), RGM and PBM, where RGM and PBM are both reactive and semi-volatile (as described by Amos et al., 2012). The ND03 PL-HG2-$ diagnostics for RGM and PBM are thus redundant with the ND45 IJ-AVG-$ diagnostic. In new code, I suggest replacing the legacy terms Hg2 and HgP with  Hg2g and Hg2p (i.e. gaseous and particle-bound Hg(II)).
+
 
+
:2. Mercury chemistry is solved with a 4th-order Runge-Kutta method. This simplifies and shortens (by 800 lines!) the source code without loss of speed or accuracy. Maximum differences with the prior code are of order 0.001% for Hg(II) and 100 times smaller for Hg(0).
+
 
+
:3. PBM is not taken up by sea-salt aerosol. The parameterization for Hg(II) uptake (Holmes et al., 2010) is appropriate only for gaseous Hg(II).
+
 
+
--[[User:Chris Holmes|Chris Holmes]] 16:14, 9 April 2013 (EDT)
+
 
+
==== Hg(II) gas-particle partitioning ====
+
 
+
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03h|v9-01-03h]] and approved on 09 Mar 2012.'''''
+
 
+
This update will be included in [[GEOS-Chem v9-01-03|v9-01-03]] and contains the following items:
+
 
+
:1. Hg(II) gas-particle partitioning from Amos ''et al''. (2012)
+
::Hg(II) now partitions between the gas and particle phases as a function of the local air temperature and aerosol burden. Hg(II) phase partitioning affects both wet and dry deposition. This will be the new default for Hg(II) gas-particle partitioning, but partitioning Hg(II) 50/50 to the gas and particle phases is still an option (see mercury_mod.F).
+
 
+
:2. Primary anthropogenic Hg(p) is emitted as Hg(II)
+
:: Due to the lack of experimental evidence that primary anthropogenic Hg(p) is chemically inert, we no longer treat this species as refractory. Hg(p) is now emitted as Hg(II) and is thus part of the Hg(II) pool available for gas-particle partitioning. More details on this can be found in Amos et al. (2012).
+
 
+
-- [[User:Helen Amos|Helen Amos]] 18:11 25 January 2012 (EST)
+
 
+
==== Bug fix for reading Hg emissions ====
+
 
+
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03g|v9-01-03g]] and approved on 27 Feb 2012.'''''
+
 
+
Jenny Fisher discovered that anthropogenic mercury emission files on the generic 1&deg;x1&deg; grid (360x180) were being read as GEOS 1&deg;x1&deg; (360x181) files.
+
 
+
'''''[mailto:jafisher@fas.harvard.edu Jenny Fisher] wrote:'''''
+
 
+
: If that's the case, then we were reading generic files but assuming they were GEOS files. Also reading real*4 but not recasting into real*8. I've fixed both problems (code based on how we read emissions in full chem). The differences are minimal and mainly over source regions.
+
 
+
This issue will be fixed in [[GEOS-Chem v9-01-03]].
+
 
+
--[[User:Melissa Payer|Melissa Payer]] 16:55, 17 February 2012 (EST)
+
 
+
=== GEOS-Chem v9-01-02 ===
+
 
+
==== In-plume reduction ====
+
 
+
Change the speciation of fossil fuel anthro emissions (46%) of total emissions from 50:40:10 to 86.5:9.9:3.6. This is now standard in v9-01-02. The speciation comes from Yanxu Zhang at UW and is more consistent with observations (Edgerton et al. 2006). Speciation factors were calculated by Helen Amos at Harvard.
+
 
+
--[[User:Bmy|Bob Y.]] 14:49, 29 November 2011 (EST)
+
 
+
Yanxu Zhang, Helen Amos, and Bess Corbitt have prepared a description of in-plume reduction and its implementation in the GEOS-Chem Hg simulation. [http://wiki.seas.harvard.edu/geos-chem/index.php/Image:IPR_20130513.pdf Download the IPR document here.] (PDF)
+
 
+
--[[User:Helen Amos|Helen Amos.]] 17:35, 14 May 2013  (EST)
+
 
+
==== Bug fix for gross Hg0 air-sea exchange diagnostics ====
+
The gross fluxes of Hg0 across the air-sea interphase (diagnostics 34016 and 34017) are incorrectly described in the model (including v9-01-02).  The equation for the evasion flux (Flux = Kw (Hg0aq – Hg0air / H) was split into an upward and a downward component (Fup = Kw * Hg0aq and Fdown = Kw * Hg0air/H). This way of splitting the equation has no physical meaning. With this fix the flux is only considered to be downwards (from air to sea) if the sea-water is undersaturated compared to the air (Flux is negative). This does not happen often (downwards flux can be expected to be around 2% of the upwards evasion flux) as sea-water is mostly supersaturated with Hg0.
+
This will lbe changed in the next version of the model.
+
 
+
In ocean_mercury_mod.f
+
 
+
    Change:
+
    FUP(I,J,NN) = (Kw * CHg0aq)
+
    FDOWN(I,J,NN) = (Kw * CHg0 / H)
+
    With:
+
    ! FUP(I,J,NN) = (Kw * CHg0aq)
+
    ! FDOWN(I,J,NN) = (Kw * CHg0 / H)
+
 
+
and
+
 
+
    Change:
+
    FUP(I,J,NN) = FUP(I,J,NN) * TO_KGM2S * A_M2 * FRAC_O
+
    FDOWN(I,J,NN) = FDOWN(I,J,NN) * TO_KGM2S * A_M2 * FRAC_O
+
    With:
+
    ! FUP(I,J,NN) = FUP(I,J,NN) * TO_KGM2S * A_M2 * FRAC_O
+
    ! FDOWN(I,J,NN) = FDOWN(I,J,NN) * TO_KGM2S * A_M2 * FRAC_O
+
 
+
and
+
+
    Change:
+
    FUP(I,J,NN) = FLUX(I,J,NN)-FDOWN(I,J,NN)
+
    With:
+
    ! FUP(I,J,NN) = FLUX(I,J,NN)-FDOWN(I,J,NN)
+
+
and
+
 
+
    Change:
+
    AD03(I,J,16) = AD03(I,J,16) + FUP(I,J,ID_Hg_tot) * DTSRCE
+
    AD03(I,J,17) = AD03(I,J,17) + FDOWN(I,J,ID_Hg_tot) * DTSRCE
+
    With:
+
    ! AD03(I,J,16) = AD03(I,J,16) + FUP(I,J,ID_Hg_tot) * DTSRCE
+
    ! AD03(I,J,17) = AD03(I,J,17) + FDOWN(I,J,ID_Hg_tot) * DTSRCE
+
    IF (FLUX(I,J,ID_Hg_tot) > 0d0) THEN
+
    AD03(I,J,16) = AD03(I,J,16)
+
    + FLUX(I,J,ID_Hg_tot) * DTSRCE
+
    ELSE IF (FLUX(I,J,ID_Hg_tot) < 0d0) THEN
+
    AD03(I,J,17) = AD03(I,J,17)
+
    + ( abs (FLUX(I,J,ID_Hg_tot) * DTSRCE ) )
+
    ENDIF
+
 
+
- Anne Laerke Soerensen 02:00, 9 Sept 2011 (EDT)
+
 
+
==== De-hardwire file path BR_DIR in global_br_mod.f ====
+
 
+
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-02_benchmark_history#v9-01-02e|v9-01-02e]] and approved on 01 Aug 2011.'''''
+
 
+
A typo was discovered in the source code file <tt>global_br_mod.f</tt>.
+
 
+
'''''[mailto:cdholmes@uci.edu Chris Holmes] wrote:'''''
+
 
+
:The variable <tt>BR_DIR</tt> was previously hard-coded with an absolute file path that would only work on the Harvard AS servers.  With [my submitted fix], the directory with Br data is constructed from the <tt>DATA_DIR</tt> variable (in <tt>directory_mod.f</tt>), analogous to the way most other directories are found.  This should make the code run more easily on systems outside Harvard.
+
 
+
--[[User:Bmy|Bob Y.]] 11:35, 25 July 2011 (EDT)
+
 
+
==== Negative aquatic mercury concentrations ====
+
 
+
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-02_benchmark_history#v9-01-02e|v9-01-02e]] and approved on 01 Aug 2011.'''''
+
 
+
There was a bug in <tt>ocean_mercury_mod.f</tt> that occasionally allowed the concentrations of aqueous mercury in the ocean to be negative. This has been fixed by changing the way the rate of change of ocean mixed layer depths is calculated and adding error traps to set negative mixed layer depths and negative oceanic mercury concentrations to zero. This will be standard in [[GEOS-Chem v9-01-02]].
+
 
+
--Jenny Fisher 17:46, 8 July 2011 (EDT)
+
 
+
==== Division by zero error ====
+
 
+
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-02_benchmark_history#v9-01-02p|v9-01-02p]] and approved on 29 Sep 2011.'''''
+
 
+
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.
+
 
+
  Replace:
+
  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 <tt>TTDAY</tt> is 0, so <tt>BR_FAC</tt> becomes <tt>Inf</tt> and <tt>C_BR</tt> becomes <tt>Inf</tt>. The problem trickles down and shows up as <tt>PL-HG2-$</tt> diagnostics <tt>Hg2_OH</tt>, <tt>Hg2_O3</tt>, <tt>Hg2_BR</tt>, and <tt>Br</tt> diagnostics having <tt>NaNs</tt> in their arrays. Adding the SAFE_DIV fixes the problem. (H Amos, 9 Mar 2011)
+
 
+
This fix will be standardized in [[GEOS-Chem v9-01-02]].
+
 
+
--[[User:hamos|hamos]] 10:46, 9 March 2011 (EST)<br>
+
--[[User:Bmy|Bob Y.]] 11:35, 25 July 2011 (EDT)
+
 
+
==== Bug fixes for ND03 mercury diagnostics ====
+
 
+
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-02_benchmark_history#v9-01-02p|v9-01-02p]] and approved on 29 Sep 2011.'''''
+
 
+
Chris Holmes found and fixed several issues with the ND03 diagnostic (which only affects the [[Mercury|offline Hg simulation]]). 
+
 
+
'''''[mailto:cdholmes@uci.edu Chris Holmes] wrote:'''''
+
 
+
:I found a bug in ND03 diagnostics in [[GEOS-Chem v9-01-01]] (last updated 2011-5-27). The <tt>PL-HG2-$</tt> diagnostics were not in the <tt>ctm.bpch</tt> file and the tracer names for these diagnostics were not in <tt>tracerinfo.dat</tt>. The reason is because there are more ND03 diagnostics than the number given in PD03. This has been a confusing and muddled part of the code for a long time.  I fixed the bug with the attached patch and also simplified <tt>diag03_mod.f</tt> to hopefully make it easier to maintain as diagnostics are added or changed in the future.
+
 
+
:I confirmed that my changes to <tt>diag03_mod.f</tt> do not alter the diagnostic outputs, within expected <tt>REAL*4</tt> precision.
+
 
+
:At the same time I was fixing the diagnostics, I found and corrected (with <tt>SAFE_DIV</tt>) a floating point overflow error in <tt>mercury_mod.f</tt> and removed legacy comments in <tt>mercury_mod.f</tt> that were left over from my personal debugging. I also corrected a diagnostic tracer name in <tt>gamap_mod.f</tt>, which was introduced when Anne Soerensen's ocean was added.
+
 
+
We also have restored printing of the soil Hg emissions to the standard output (aka the GEOS-Chem log file).  This error was probably a relic of someone debugging.
+
 
+
--[[User:Bmy|Bob Y.]] 11:35, 25 July 2011 (EDT)
+
 
+
==== VEGEMIS/GCAP bug fix ====
+
 
+
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-02_benchmark_history#v9-01-02e|v9-01-02e]] and approved on 01 Aug 2011.'''''
+
 
+
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 09:43, 13 April 2011 (EDT)<br>
+
--[[User:Bmy|Bob Y.]] 11:35, 25 July 2011 (EDT)
+
 
+
=== GEOS-Chem v9-01-01 ===
+
 
+
The following issues were fixed in the re-release of [[GEOS-Chem v9-01-01]] (07 Jun 2011).
+
 
+
==== Omitted code in Hg simulation ====
+
 
+
We created a patch to fix this issue.  This update was standardized in the re-release of v9-01-01.
+
 
+
*Designated as: '''v9-01-01-Patch-Hg'''
+
*Applied: 2011-04-13
+
*Authors: Chris Holmes, Jenny Fisher
+
*Signed off by: Bob Yantosca
+
 
+
'''''[mailto:jafisher@fas.harvard.edu Jenny Fisher] wrote:'''''
+
 
+
:After some discussion between Chris Holmes and I, we realized that some of his updates to the Hg code (i.e. the version published in his paper) didn't get properly implemented in v9-01-01.  I haven't looked *extensively* through his code, but I have done a quick look through the obvious mercury routines and found a number of differences:
+
 
+
    (1) In LAND_MERCURY_FLUX (land_mercury_mod.f)
+
+
        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
+
 
+
The patch, which is present in the re-release of v9-01-01 (07 Jun 2011) contains 3 individual commits named:
+
 
+
Fixed minor error in depo_mercury_mod.f
+
Add comments to denote updates to Holmes 2010 Hg
+
Update to Holmes et al. 2010 version
+
 
+
--Jenny Fisher 09:43, 13 April 2011 (EDT)<br>
+
--[[User:Bmy|Bob Y.]] 11:35, 25 July 2011 (EDT)
+
 
+
=== GEOS-Chem v8-03-02 ===
+
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:
+
 
+
  ND38: Cld Conv scav loss: 47  all
+
  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):
+
<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)
+
* ref. Wang et al. 2011
+
* 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>
+
 
+
=== Previous discussions (6/2008) ===
+
 
+
#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)
+
#*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.''
+
  
 
== Benchmarking ==
 
== Benchmarking ==
Line 587: Line 31:
 
{| border=1 cellspacing=0 cellpadding=5  
 
{| border=1 cellspacing=0 cellpadding=5  
 
|- bgcolor="#CCCCCC"
 
|- bgcolor="#CCCCCC"
!width="400px"|Feature
+
!width="400px"|Feature(s)
 
!width="75px"|Type
 
!width="75px"|Type
 
!width="200px"|Submitted by
 
!width="200px"|Submitted by
Line 593: Line 37:
 
!width="600px"|Notes
 
!width="600px"|Notes
 
|-
 
|-
|[[Mercury#Hg.28II.29_gas-particle_partitioning|Hg(II) gas-particle partitioning]]
+
|Hg(II) gas-particle partitioning
 
|Science
 
|Science
 
|Helen Amos (Harvard)
 
|Helen Amos (Harvard)
Line 603: Line 47:
 
For details on Hg(II) partitioning, please see Amos et al. (2012, ACP).  
 
For details on Hg(II) partitioning, please see Amos et al. (2012, ACP).  
 
|-
 
|-
|[[Mercury#Nested-grid_Hg_simulation_over_North_America|Nested grid simulation over North America]]
+
|
 +
'''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
 
|Science
 
|Yanxu Zhang (UW)
 
|Yanxu Zhang (UW)
Line 612: Line 62:
 
  get Hg_benchmark_v9-02c.tar.gz
 
  get Hg_benchmark_v9-02c.tar.gz
 
For more information on the nested grid Hg simulation, please see Zhang et al. (2012, ACP).
 
For more information on the nested grid Hg simulation, please see Zhang et al. (2012, ACP).
|-
 
|[[EPA/NEI05_North_American_emissions|EPA/NEI05 North American Hg emissions]]
 
|Science
 
|Yanxu Zhang (UW)
 
|" "
 
|" "
 
|-
 
|[[Mercury#Updated_Hg.280.29_oxidation_kinetics|Updated Hg(0) oxidation kinetics]]
 
|Science
 
|Bess Corbitt (Harvard)
 
|" "
 
|" "
 
|-
 
|[[Mercury#Capability_to_use_GEOS-Chem_Br.2FBrO_fields_in_Hg_simulation|Capability to use GEOS-Chem Br/BrO fields in Hg simulation]]
 
|Science
 
|Bess Corbitt (Harvard)
 
|" "
 
|" "
 
|-
 
|[[Mercury#Streets_future_Hg_emissions|Streets future Hg emissions]]
 
|Science
 
|Bess Corbitt (Harvard)
 
|" "
 
|" "
 
 
|-
 
|-
 
|None
 
|None
Line 647: Line 73:
 
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).
 
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).
 
|-
 
|-
|[[Mercury#GAMAP_can.27t_read_v9-01-03_output_for_Hg|Replace Hg2 and HgP with Hg2g and Hg2p;<br>Update mercury chemistry to Runge-Kutta method;<br>Remove PBM uptake by sea salt aerosol]]
+
|
 +
'''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
 
|Science
 
|Chris Holmes (UC Irvine)
 
|Chris Holmes (UC Irvine)
Line 656: Line 87:
 
  get Hg_benchmark_v9-02k.tar.gz
 
  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.  
 
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.  
|}
 
  
--[[User:Melissa Payer|Melissa Payer]] 12:04, 1 July 2013 (EDT)
+
|-
 +
|
 +
'''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/
 +
 
 +
|}
  
 
== Benchmark results for the nested NA grid ==
 
== Benchmark results for the nested NA grid ==
Line 674: Line 119:
 
!Notes
 
!Notes
 
|-
 
|-
|[[Mercury#Nested-grid_Hg_simulation_over_North_America|Nested grid simulation over North America]]
+
|
 +
'''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
 
|Science
 
|Yanxu Zhang (UW)
 
|Yanxu Zhang (UW)
Line 683: Line 134:
 
  get Hg_benchmark_v9-02c.05x0666_NA.tar.gz
 
  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).
 
For more information on the nested grid Hg simulation, please see Zhang et al. (2012, ACP).
|-
 
|[[EPA/NEI05_North_American_emissions|EPA/NEI05 North American Hg emissions]]
 
|Science
 
|Yanxu Zhang (UW)
 
|" "
 
|" "
 
|-
 
|[[Mercury#Updated_Hg.280.29_oxidation_kinetics|Updated Hg(0) oxidation kinetics]]
 
|Science
 
|Bess Corbitt (Harvard)
 
|" "
 
|" "
 
|-
 
|[[Mercury#Capability_to_use_GEOS-Chem_Br.2FBrO_fields_in_Hg_simulation|Capability to use GEOS-Chem Br/BrO fields in Hg simulation]]
 
|Science
 
|Bess Corbitt (Harvard)
 
|" "
 
|" "
 
|-
 
|[[Mercury#Streets_future_Hg_emissions|Streets future Hg emissions]]
 
|Science
 
|Bess Corbitt (Harvard)
 
|" "
 
|" "
 
|-
 
 
|}
 
|}
--[[User:Melissa Payer|Melissa Payer]] 12:31, 4 February 2013 (EST)
 
  
== Chemistry 'issues' ==
+
== GTMM ==
  
=== Dry deposition of HgP over snow/ice ===
+
<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>
 
+
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).
+
 
+
=== Previous discussions ===
+
 
+
#Oxidant.
+
#*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 ==
+
 
+
=== Notes ===
+
#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 ===
+
 
+
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
+
 
+
      CATEGORY ILUN TRCNAME  TRC        UNIT      TAU0(DATE)      DIMENSIONS
+
  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):
+
 
+
      CATEGORY  TRCNAME    TRC        UNIT
+
  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
+
 
+
 
+
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) 
+
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 ==
+
  
 
[[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.
 
[[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.
  
 
#[[Global Terrestrial Mercury Model]] wiki page
 
#[[Global Terrestrial Mercury Model]] wiki page
#[http://www.geos-chem.org/doc/man/files/GTMM_manual_20100811.pdf GTMM User's Manual] (PDF)
+
#[http://acmg.seas.harvard.edu/geos/doc/GTMM/GTMM_manual_20100811.pdf GTMM User's Manual] (PDF)
  
 
== Soil Emissions ==
 
== Soil Emissions ==
Line 844: Line 183:
 
--[[User:hamos|Helen Amos]] 03:44, 13 Aug 2011 (EST)<br>
 
--[[User:hamos|Helen Amos]] 03:44, 13 Aug 2011 (EST)<br>
  
== Anthropogenic Emissions ==
+
=== Update for HEMCO ===
The GEIA 2005 emission inventory for anthropogenic Hg (Pacyna ''et al''., 2010) is now available on the ftp server for public use. The bpch files were prepared by Bess Corbitt at Harvard and are available at:
+
 
 +
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:<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>
 +
 
 +
'''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).
  
  ftp ftp.as.harvard.edu
+
'''Step 8:''' Repeat Steps 2-7 until pre-industrial soil distribution converges to within 5%.  
  cd gcgrid/geos-chem/data/GEOS_1x1/mercury_201002/
+
+
  get GEIA_Hg0.geos.1x1.2005
+
  get GEIA_Hg2.geos.1x1.2005
+
  get GEIA_HgP.geos.1x1.2005
+
  
Previous options for anthropogenic Hg emissions have included GEIA 2000 (Pacyna ''et al''., 2006) and GCAP (GEIA 2000 scaled to David Streets' 2006 inventory; Streets ''et al''., 2009). The GCAP inventory was also prepared by Bess Corbitt.  
+
'''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.  
  
Note that the GEIA 2005 emissions DO include artisanal mining and the GEIA 2000 do NOT include artisanal mining.  
+
'''Step 10:''' Use soilhgdist_nc.pro to create a present day soil distribution.
  
--[[User:hamos|Helen Amos]] 12:06, 06 Oct 2011 (EST)<br>
+
-- Jenny Fisher, 19 Mar 2016
--[[User:Bmy|Bob Y.]] 16:53, 24 October 2011 (EDT)
+
  
 
== References ==
 
== References ==
 +
#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.
 
#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.
 
#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.
Line 880: Line 232:
 
#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.
 
#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.
  
--[[User:Melissa Payer|Melissa Payer]] 11:41, 11 January 2013 (EST)
+
----
 +
'''''[[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.

Previous | Next | Guide to GEOS-Chem simulations