Mercury: Difference between revisions

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--[[User:Melissa Payer|Melissa Payer]] 12:31, 4 February 2013 (EST)


== Chemistry 'issues' ==
== Chemistry 'issues' ==

Revision as of 17:31, 4 February 2013

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.

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

Code

GEOS-Chem v9-02

Nested-grid Hg simulation over North America

This update was implemented in 1-month benchmark simulation v9-02c and contains the following items:

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 LNEI2005 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 LInPlume 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 (LWC) by dividing it by cloud cover:
           LWC     = SAFE_DIV( LWC, FC, 0d0 )
After calculating the fraction of HgII in aqueous phase (FA), the FA is multiplied by cloud cover:
        IF ( LGEOSLWC ) FA =  FA * FC
This implementation was firstly introduced by lzh, jaf and bmy.
The K_RED_JNO2 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 global_o3_mod.F, mercury_mod.F and ocean_mercury_mod.F.
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

--Melissa Payer 11:27, 13 December 2011 (EST)

Streets future Hg emissions

This update was tested in the 1-month benchmark simulation 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 Corbitt et al. 2011.

--Melissa Payer 16:33, 27 November 2012 (EST)

Updated Hg(0) oxidation kinetics

This update was tested in the 1-month benchmark simulation 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 GoodsiteUpdate in subroutine GET_HGBR_RATE (mercury_mod.F).

--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 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 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 LGCBROMINE switch in subroutine INIT_MERCURY (mercury_mod.F).

--Melissa Payer 16:33, 27 November 2012 (EST)

Bug fixes for nested Hg simulation

Yanxu Zhang wrote:

Several bugs in the code:
1. input_mod.F: 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. land_mercury_mod.F: 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. mercury_mod.F: 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. ocean_mercury_mod.F: 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

--Melissa Payer 09:29, 1 February 2013 (EST)

GEOS-Chem v9-01-03

Hg(II) gas-particle partitioning

This update was tested in the 1-month benchmark simulation v9-01-03h and approved on 09 Mar 2012.

This update will be included in 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).

-- Helen Amos 18:11 25 January 2012 (EST)

Bug fix for reading Hg emissions

This update was tested in the 1-month benchmark simulation v9-01-03g and approved on 27 Feb 2012.

Jenny Fisher discovered that anthropogenic mercury emission files on the generic 1°x1° grid (360x180) were being read as GEOS 1°x1° (360x181) files.

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.

--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.

--Bob Y. 14:49, 29 November 2011 (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)

   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

   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)

   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 v9-01-02e and approved on 01 Aug 2011.

A typo was discovered in the source code file global_br_mod.f.

Chris Holmes wrote:

The variable BR_DIR 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 DATA_DIR variable (in directory_mod.f), analogous to the way most other directories are found. This should make the code run more easily on systems outside Harvard.

--Bob Y. 11:35, 25 July 2011 (EDT)

Negative aquatic mercury concentrations

This update was tested in the 1-month benchmark simulation v9-01-02e and approved on 01 Aug 2011.

There was a bug in ocean_mercury_mod.f 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 v9-01-02p and approved on 29 Sep 2011.

There is a div by 0 error in mercury_mod.f FUNCTION GET_BR that affects v8-03-02 and 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 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)

This fix will be standardized in GEOS-Chem v9-01-02.

--hamos 10:46, 9 March 2011 (EST)
--Bob Y. 11:35, 25 July 2011 (EDT)

Bug fixes for ND03 mercury diagnostics

This update was tested in the 1-month benchmark simulation v9-01-02p and approved on 29 Sep 2011.

Chris Holmes found and fixed several issues with the ND03 diagnostic (which only affects the offline Hg simulation).

Chris Holmes wrote:

I found a bug in ND03 diagnostics in GEOS-Chem v9-01-01 (last updated 2011-5-27). The PL-HG2-$ diagnostics were not in the ctm.bpch file and the tracer names for these diagnostics were not in tracerinfo.dat. 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 diag03_mod.f to hopefully make it easier to maintain as diagnostics are added or changed in the future.
I confirmed that my changes to diag03_mod.f do not alter the diagnostic outputs, within expected REAL*4 precision.
At the same time I was fixing the diagnostics, I found and corrected (with SAFE_DIV) a floating point overflow error in mercury_mod.f and removed legacy comments in mercury_mod.f that were left over from my personal debugging. I also corrected a diagnostic tracer name in gamap_mod.f, 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.

--Bob Y. 11:35, 25 July 2011 (EDT)

VEGEMIS/GCAP bug fix

This update was tested in the 1-month benchmark simulation 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)
--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

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)
--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):

  1. Reduce geogenic emissions by 50%
    • ref. Soerensen et al. 2010
    • mercury_mod.f line 3470:
     EHg0_nt = EHg0_nt / SEC_PER_YR
     EHg0_nt = EHg0_nt * 0.5D0
  2. Reduce biomass burning emissions by 50%
    • ref. Soerensen et al. 2010
    • land_mercury_mod.f line 225:
     !REAL*8, PARAMETER  :: BBRatio_Hg_CO = 2.1D-7
     REAL*8, PARAMETER  :: BBRatio_Hg_CO = 1.05D-7
  3. 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:
     !CDEEPSAT = (/ 1.0d-10, 5.0d-10, 5.0d-10 /)
     CDEEPSAT = (/ 0.8d-10, 4.1d-10, 4.1d-10 /)
  4. 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:
     !REAL*8, PARAMETER  :: BRO_POLAR=10D0
     REAL*8, PARAMETER  :: BRO_POLAR=5D0
  5. 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:
     IF ( PDOWN(L,I,J) > 0d0 ) THEN
      F_RAINOUT = F_PRIME
      ! Washout occurs where there is no rainout
      F_WASHOUT = MAX( FTOP - F_RAINOUT, 0d0 )
     ELSE
      F_RAINOUT = 0d0
      F_WASHOUT = 0d0
     ENDIF
    • comment out wetscav_mod.f line 4121:
     !F_RAINOUT = 0d0
     !F_WASHOUT = 0d0
     !IF ( PDOWN(L,I,J) > 0d0 ) THEN
     !  IF (QQ(L,I,J) > 0d0) THEN
     !   F_RAINOUT = MAX( FTOP, F_PRIME )
     !  ENDIF
     !  F_WASHOUT = MAX( FTOP - F_RAINOUT, 0d0 )
     !ENDIF


Previous discussions (6/2008)

  1. Standardize the solver. Everyone should use the solver Chris developed for the Hg chemistry
    (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.
  2. Catalog all emissions options and develop clear flagging system to choose your own adventure. This will include:
    • different anthropogenic emissions scenarios/corrections (i.e Jaffe vs. Streets) <- going to work on the anthro emissions soon (eds),
    • different land emissions. <- nvd will work on this
    • Logicals implemented to select anthropogenic emissions from GEIA 2000, GEIA 2005, or GEIA scaled to Streets et al. 2006 regional totals.
  3. Diagnostics. See separate section below.
    • Diagnostics have been updated.
  4. Comment everything in the code. Remove old bits of code that are hanging around & commented out.
    • Ongoing.
  5. GEOS-5
    • This is the standard meteorology to use at present. MERRA is in development.
  6. 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

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 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
get Hg_benchmark_v9-01-03h.tar.gz

For details on Hg(II) partitioning, please see Amos et al. (2012, ACP).

Nested grid simulation over North America Science Yanxu Zhang (UW) v9-02c A 1-year benchmark (2009, 4x5) was performed for v9-02c against v9-01-03h by Yanxu Wang. A complete set of benchmark plots are available at: 
ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/Hg_benchmarks
get Hg_benchmark_v9-02c.tar.gz

For more information on the nested grid Hg simulation, please see Zhang et al. (2012, ACP).

EPA/NEI05 North American Hg emissions Science Yanxu Zhang (UW) " " " "
Updated Hg(0) oxidation kinetics Science Bess Corbitt (Harvard) " " " "
Capability to use GEOS-Chem Br/BrO fields in Hg simulation Science Bess Corbitt (Harvard) " " " "
Streets future Hg emissions Science Bess Corbitt (Harvard) " " " "

--Melissa Payer 11:46, 11 January 2013 (EST)

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
Nested grid simulation over North America 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
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).

EPA/NEI05 North American Hg emissions Science Yanxu Zhang (UW) " " " "
Updated Hg(0) oxidation kinetics Science Bess Corbitt (Harvard) " " " "
Capability to use GEOS-Chem Br/BrO fields in Hg simulation Science Bess Corbitt (Harvard) " " " "
Streets future Hg emissions Science Bess Corbitt (Harvard) " " " "

--Melissa Payer 12:31, 4 February 2013 (EST)

Chemistry 'issues'

Dry deposition of HgP over snow/ice

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 v9-01-02. For more information see the dry deposition page. (Jenny Fisher, Harvard).

Previous discussions

  1. 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)
  2. Snow/ice scavenging of HgII
    • Cold-temperature wet scavenging of HgII is now included in the standard code.
  3. 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

  1. Helen Amos is developing diagnostics for reactive gaseous mercury and reactive particulate mercury.
  2. 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:

  1. 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.
  2. 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.
  3. 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.
  4. '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.

  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)

Anthropogenic Emissions

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: 

  ftp ftp.as.harvard.edu
  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.

Note that the GEIA 2005 emissions DO include artisanal mining and the GEIA 2000 do NOT include artisanal mining.

--Helen Amos 12:06, 06 Oct 2011 (EST)
--Bob Y. 16:53, 24 October 2011 (EDT)

References

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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
  15. 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
  16. 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.
  17. 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.

--Melissa Payer 11:41, 11 January 2013 (EST)

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