Dry deposition: Difference between revisions

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<blockquote>where ''Ra'' is the aerodynamic resistance to transfer to the surface, ''Rb,i'' is the boundary resistance, and ''Rc,i'' is the canopy surface resistance.  ''Ra'' and ''Rb,i'' are calculated from the GCM meteorological variables [''Jacob et al 1993''].  Surface resistances Rc,i are based largely on the canopy model of ''Wesely'' [1989] with some improvements, including explicit dependence of canopy stomatal resistances on LAI [''Gao and Wesely'', 1995] and on direct and diffuse PAR within the canopy [''Baldocchi et al'', 1987].  The same radiative transfer model for direct and diffuse PAR in the canopy is used as in the formulation of isoprene emissions.  Surface resistances for deposition to tropical rain forest and tundra are taken from ''Jacob and Wofsy'' [1990] and ''Jacob et al'' [1992], respectively.  The surface resistance for deposition of NO2 is taken to be the same as that of ozone [''Erisman & Pul'', 1994; ''Kramm et al'', 1995; ''Eugster and Hesterberg'', 1996] and hence lower than specified by ''Wesely'' [1989].  Dry deposition of CO and hydrocarbons is negligibly small and not included in the model [''Mueller and Brasseur'', 1995].</blockquote>
<blockquote>where ''Ra'' is the aerodynamic resistance to transfer to the surface, ''Rb,i'' is the boundary resistance, and ''Rc,i'' is the canopy surface resistance.  ''Ra'' and ''Rb,i'' are calculated from the GCM meteorological variables [''Jacob et al 1993''].  Surface resistances Rc,i are based largely on the canopy model of ''Wesely'' [1989] with some improvements, including explicit dependence of canopy stomatal resistances on LAI [''Gao and Wesely'', 1995] and on direct and diffuse PAR within the canopy [''Baldocchi et al'', 1987].  The same radiative transfer model for direct and diffuse PAR in the canopy is used as in the formulation of isoprene emissions.  Surface resistances for deposition to tropical rain forest and tundra are taken from ''Jacob and Wofsy'' [1990] and ''Jacob et al'' [1992], respectively.  The surface resistance for deposition of NO2 is taken to be the same as that of ozone [''Erisman & Pul'', 1994; ''Kramm et al'', 1995; ''Eugster and Hesterberg'', 1996] and hence lower than specified by ''Wesely'' [1989].  Dry deposition of CO and hydrocarbons is negligibly small and not included in the model [''Mueller and Brasseur'', 1995].</blockquote>


== Validation ==
===Aerosol dry deposition===
Havala Pye reexamined the code, and she found that there are three routines basically using the Zhang et al.(2001) scheme:
# AERO_SFCRSII: Aerodynamic resistance for seasalt tracers. Hygroscopic growth is accounted for. Implemented by Rokjin Park ~ 2004? Used for: SALA, SALC, SO4S, NITS
# DUST_SFCRSII: Aerodynamic resistance of dust aerosol tracers. No hygroscopic growth. Implemented by bec ~2005? Used for: DST1, DST2, DST3, DST4
# ADUST_SFCRSII: Aerodynamic resistance of non-size resolved aersosols. No hygroscopic growth. Based on DUST_SRFCRSII and activated by Pye 2007. Assume particle diameter is 0.5 microns, density is 1.5 g/cm3 (1500 kg/m3). Used for all other aerosols that are not listed above (aerosols are indicated by a T/F flag in INIT_DRYDEP called AIROSOL).
This was briefly mentioned in Pye et al. (2009) paper.


Text to be added
===Reference===
#Pye, H. O. T., H. Liao, S. Wu, L. J. Mickley, D. J. Jacob, D. K. Henze, and J. H. Seinfeld (2009), Effect of changes in climate and emissions on future sulfate-nitrate-ammonium aerosol levels in the United States, Journal of Geophysical Research: Atmospheres, 114(D1), D01205, doi:10.1029/2008JD010701.
#Zhang, L. M., S. L. Gong, J. Padro, and L. Barrie (2001), A size-segregated particle dry deposition scheme for an atmospheric aerosol module, Atmos. Environ., 35(3), 549-560, doi:10.1016/s1352-2310(00)00326-5.


== Source code and data ==
== Source code and data ==


The source code of the various routines are located in <tt>drydep_mod.f</tt>.  Routine <tt>DO_DRYDEP</tt> is the main driver for the dry deposition.  It calls various setup routines before calling routine <tt>DEPVEL</tt>, which computes the dry deposition velocities in [m/s].  For the [[NOx-Ox-HC-aerosol]] "full-chemistry" simulation, the deposition velocities are then stored in an array and passed to the routine <tt>CALCRATE</tt> (in source file <tt>calcrate.f</tt>).  <tt>CALCRATE</tt> stores the deposition velocities in the proper rate arrays, which then get passed to either the SMVGEAR or the KPP solvers.  Dry deposition is thus treated as a loss reaction in the chemistry mechanism.
The source code of the various routines are located in <code>drydep_mod.f</code>.   


For more information about the data files required by the drydep scheme, please see the README file: [ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_1x1/drydep_200203/README GEOS_1x1/drydep_200203/README]
# Routine <code>DO_DRYDEP</code> is the main driver for the dry deposition. This calls various setup subroutines.
# Routine <code>DEPVEL</code> (which is called by <code>DO_DRYDEP</code>) computes dry deposition dry deposition velocities in [m/s]. 
# Dry deposition frequencies [1/s] for all species are computed in <code>DO_DRYDEP</code>, after the call to <code>DEPVEL</code>.


--[[User:Bmy|Bob Y.]] 10:46, 24 February 2010 (EST)
For more information about the input data files required by the drydep scheme, please see the README file: [ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_1x1/drydep_200203/README GEOS_1x1/drydep_200203/README]
 
=== In GEOS-Chem v10-01 and higher versions ===
 
<span style="color:green">'''''NOTE: This update was made to facilitate the implementation of both the [[HEMCO|HEMCO emissions component]] and FlexChem chemical solver.'''''</span>
 
In [[GEOS-Chem v10-01]] and higher versions, the following changes were made to how dry deposition is applied:
 
#Dry deposition is now applied to all tracers in module <code>GeosCore/mixing_mod.F90</code>.  Prior to this, dry deposition had been applied in several locations throughout the code, which was confusing and prone to error.
#Dry deposition fluxes (i.e. category DRYD-FLX) are now archived to the ND44 diagnostic in module <code>GeosCore/mixing_mod.F90</code>.  Furthermore, drydep fluxes are now archived with units of <code>molec/cm2/s</code> for all GEOS-Chem simulations.  In prior GEOS-Chem versions, some simulations (in particular Rn-Pb-Be) had archived drydep fluxes in units of <code>kg/s</code>.  <span style="color:red">Therefore, when analyzing output from GEOS-Chem v10-01 (or higher versions), please make sure to modify your plotting or budget programs to expect drydep fluxes in units of <code>molec/cm2/s</code>.</span>
#Routines <code>DRYFLX</code> and <code>DRYFLXRnPbBe</code> have now been removed from module <code>GeosCore/drydep_mod.F</code>.  The equivalent functionality is now provided by <code>GeosCore/mixing_mod.F90</code>.
 
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 21:34, 17 June 2015 (UTC)
 
== Input values for dry deposition ==
 
Here we list some of the various input values used by the dry deposition routines.  Full citations may be found in the [[#References|references section]] below.
 
=== Land cover parameters ===
 
The land cover input variables for the GEOS-Chem dry deposition module are listed in the table below:
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="100px"|Variable
!width="250px"|Read from
!width="300px"|Description
!width="300px"|Values
!width="200px"|Reference
 
|-valign="top"
|<tt>DRYCOEFF</tt>
|
*[[GEOS-Chem v9-01-03|v9-01-03]] and higher:<br><tt>Olson_1992_Drydep_inputs.nc</tt><br><br>
*Prior to v9-01-03:<br><tt>drydep.coef</tt>
|Local dependence of stomal resistance on the intensity I of light impinging the leaf; this is expressed as a mutliplicative factor I/(I+b) to the stomatal  resistance where b = 50 W m-2 (equation (7) of Baldocchi et al. [1987])
|<tt>-0.358, 3.02, 3.85, -0.0978, -3.66, 12, 0.252, -7.8, 0.226, 0.274, 1.14, -2.19, 0.261, -4.62, 0.685, -0.254, 4.37, -0.266, -0.159, -0.206</tt>
|
*Baldocchi et al, AE, 1987.
 
|-valign="top"
|<tt>IDRYDEP</tt>
|
*[[GEOS-Chem v9-01-03|v9-01-03]] and higher:<br><tt>Olson_1992_Drydep_inputs.nc</tt><br><br>
*Prior to v9-01-03:<br><tt>drydep.table</tt>
|Indices for the 11 dry deposition land types
|<tt>1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11</tt>
|
*Wesely, AE 1989;
*Jacob et al., JGR 1990, 1992.
 
|-valign="top"
|<tt>IOLSON</tt>
|
*[[GEOS-Chem v9-01-03|v9-01-03]] and higher:<br><tt>Olson_1992_Drydep_inputs.nc</tt><br><br>
*Prior to v9-01-03:<br><tt>drydep.table</tt>
|Indices for the 72 Olson land types
|<tt> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74</tt>
|
*Wesely, AE 1989;
*Jacob et al., JGR 1990, 1992.
 
|-valign="top"
|<tt>IDEP</tt>
|
*[[GEOS-Chem v9-01-03|v9-01-03]] and higher:<br><tt>Olson_1992_Drydep_inputs.nc</tt><br><br>
*Prior to v9-01-03:<br><tt>drydep.table</tt>
|Indices that map each of the 72 Olson land types to the corresponding dry deposition land type
|<tt>11, 10, 5, 1, 1, 1, 2, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 3, 3, 3, 3, 2, 2, 2, 3, 2, 2, 4, 4, 2, 6, 1, 1, 9, 4, 4, 4, 5, 5, 5, 5, 5, 9, 5, 5, 5, 5, 8, 8, 5, 7, 6, 2, 2, 2, 2, 2, 3, 3, 3, 5, 5, 11, 11, 11, 11, 8, 1, 8, 9, 11</tt>
|
*Wesely, AE 1989;
*Jacob et al., JGR 1990, 1992.
 
|-valign="top"
|<tt>IWATER</tt>
|
*[[GEOS-Chem v9-01-03|v9-01-03]] and higher:<br><tt>Olson_1992_Drydep_inputs.nc</tt><br><br>
*Prior to v9-01-03:<br><tt>drydep.table</tt>
|Indices of the Olson land types denoting water (i.e. ocean/lake/ice) surfaces
|<tt> 1, 66, 67, 68, 69, 74</tt>
|
*Wesely, AE 1989;
*Jacob et al., JGR 1990, 1992.
 
|-valign="top"
|<tt>IZO</tt>
|
*[[GEOS-Chem v9-01-03|v9-01-03]] and higher:<br><tt>Olson_1992_Drydep_inputs.nc</tt><br><br>
*Prior to v9-01-03:<br><tt>drydep.table</tt>
|Roughness heights (1e-4 m) for each of the 72 Olson land types
|<tt> 10, 25000, 100, 1000, 1000, 1000, 10000, 1000, 10, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1, 1000, 1000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 1000, 10000, 1000, 1000, 2000, 10000, 1000, 1000, 100, 1000, 1000, 1000, 100, 100, 100, 100, 100, 100, 1000, 1000, 1000, 1000, 10, 10, 100, 50, 10000, 2000, 2000, 2000, 2000, 2000, 10000, 10000, 10000, 2000, 50, 100, 100, 100, 100, 10, 1, 1, 500, 10</tt>
|
*Wesely, AE 1989;
*Jacob et al., JGR 1990, 1992.
 
|}
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:43, 21 July 2016 (UTC)
 
=== Aerodynamic resistances ===
 
The aerodynamic resistances (<tt>IRI, IRLU, IRAC, IRGSS, IRGSO, IRCLS, IRCLO</tt>) and maximum deposition velocity for aerosol (<tt>IVSMAX</tt>) for each of the 11 dry deposition land types are read from this file:
 
*[[GEOS-Chem v9-01-03|v9-01-03]] and higher: <tt>Olson_1992_Drydep_inputs.nc</tt>
*Prior to v9-01-03: <tt>drydep.table</tt>
 
and have the following values:
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC" valign="top"
!width="50px|DD type
!width="150px"|Description
!width="75px"|<tt>IRI</tt><br>[s m<sup>-1</sup>]
!width="75px"|<tt>IRLU</tt><br>[s m<sup>-1</sup>]
!width="75px"|<tt>IRAC</tt><br>[s m<sup>-1</sup>]
!width="75px"|<tt>IRGSS</tt><br>[s m<sup>-1</sup>]
!width="75px"|<tt>IRGSO</tt><br>[s m<sup>-1</sup>]
!width="75px"|<tt>IRCLS</tt><br>[s m<sup>-1</sup>]
!width="75px"|<tt>IRCLO</tt><br>[s m<sup>-1</sup>]
!width="100px"|<tt>IVSMAX</tt><br>[10<sup>-2</sup> cm s<sup>-1</sup>]
!width="200px"|Reference
 
|-valign="top"
|1  ||Snow/Ice          ||9999 ||9999 ||0    ||100  ||3500 ||9999 ||1000  ||100  ||Wesely, AE, 1989
 
|-valign="top"
|2  ||Deciduous forest  ||200  ||9000 ||2000 ||500  ||200  ||2000 ||1000  ||100  ||Wesely, AE, 1989
 
|-valign="top"
|3  ||Coniferous forest ||400  ||9000 ||2000 ||500  ||200  ||2000 ||1000  ||100  ||Wesely, AE, 1989
 
|-valign="top"
|4  ||Agricultural land ||200  ||9000 ||200  ||150  ||150  ||2000 ||1000  ||100  ||Wesely, AE, 1989
 
|-valign="top"
|5  ||Shrub/grassland  ||200  ||9000 ||100  ||350  ||200  ||2000 ||1000  ||100  ||Wesely, AE, 1989
 
|-valign="top"
|6  ||Amazon forest    ||200  ||1000 ||2000 ||200  ||200  ||9999 ||9999  ||100  ||Jacob & Wofsy, JGR 1990
 
|-valign="top"
|7  ||Tundra            ||200  ||4000 ||0    ||340  ||340  ||9999 ||9999  ||100  ||Jacob et al., JGR 1992
 
|-valign="top"
|8  ||Desert            ||9999 ||9999 ||0    ||1000 ||400  ||9999 ||9999  ||10  ||Wesely, AE, 1989
 
|-valign="top"
|9  ||Wetland          ||200  ||9000 ||300  ||0    ||1000 ||2500 ||1000  ||100  ||Wesely, AE, 1989
 
|-valign="top"
|10 ||Urban            ||9999 ||9999 ||100  ||400  ||300  ||9999 ||9999  ||100  ||Wesely, AE, 1989
 
|-valign="top"
|11 ||Water            ||9999 ||9999 ||0    ||0    ||2000 ||9999 ||9999  ||10  ||Wesely, AE, 1989
 
|}
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:43, 21 July 2016 (UTC)
 
== OVOCs dry deposition ==
 
These values were further changed as part of the new isoprene scheme. The most up-to-date values are on the [[New_isoprene_scheme#Henry.27s_law_constant|new isoprene scheme]] page.
 
--[[User:Jmao|Jmao]], [[User:Jaf|JAF]] 19 March 2014
 
<span style="color:green">'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03c|v9-01-03c]] and approved on 19 Dec 2011.'''''</span>
 
<span style="color:red">'''''In [[GEOS-Chem v11-01]] and higher versions, these parameters are now defined in the [[GEOS-Chem species database]], and are then copied into the local dry deposition arrays in routine <code>INIT_DRYDEP</code>.'''''</span>
 
According to Karl et al.(2010), I changed the reactivity factor(f0) for all OVOCs from 0 to 1.
 
Now dry dep is set up as:
{| border="1" bordercolor="#000000" cellpadding="5" cellspacing="0"
|-bgcolor="#cccccc"
!width="100pt" | Species
!width="100pt" | H*(moles L-1 atm-1 )
!width="200pt" | f0
!width="200pt" | Reference
|-
|NO2||0.01 ||0.1||
|-
|Ox ||0.01 ||1.0||
|-
|PAN ||3.6 ||0.1||
|-
|HNO3 ||1.0d+14 ||0.0||
|-
|H2O2 ||1.0d+5 ||1.0||
|-
|PMN || as PAN|| ||
|-
|PPN || as PAN|| ||
|-
|PYPAN || as PAN|| ||
|-
|ISN2 || as HNO3|| ||
|-
|R4N2 || as PAN|| ||
|-
|CH2O || 6.0e+3||change from 0 to 1.0||
|-
|GLYX ||3.6d+5 ||change from 0 to 1.0||
|-
|MGLY ||3.7d+3 ||change from 0 to 1.0||
|-
|GLYC ||4.1d+4 ||change from 0 to 1.0||
|-
|MPAN,GPAN, GLPAN ||as PAN || ||
|-
|N2O5 ||as HNO3 || ||
|-
|HCOOH ||1.67d+5 ||change from 0 to 1.0 ||
|-
|ACTA ||1.14d+4 ||change from 0 to 1.0||
|-
|ISOPND||1.7d+4 ||0.0||
|-
|ISOPNB||1.7d+4 ||0.0||
|-
|MVKN+MACRN||1.7d+4 ||0.0||
|-
|PROPNN||1.0d+3 ||0.0||NITROOXYACETONE IN SANDER TABLE
|-
|RIP ||as H2O2 || ||
|-
|IEPOX ||as H2O2 || ||
|-
|MAP ||8.4d+2 ||1.0 ||
|-
|MVK ||4.4d1 ||change from 0 to 1.0 || from R.Sander
|-
|MACR ||6.5d0 ||change from 0 to 1.0|| from R.Sander
|-
|SO2 ||1.0d+5 ||0.0||
|}
 
Karl, T., Harley, P., Emmons, L., Thornton, B., Guenther, A., Basu, C., Turnipseed, A., and Jardine, K.: Efficient Atmospheric Cleansing of Oxidized Organic Trace Gases by Vegetation, Science, 330, 816-819, 10.1126/science.1192534, 2010.
 
'''Notes: To run with non-local mixing, you don't need to modify globchem.dat with " MVK=DRYDEP+DRYMVK", because drydep here is done out of chemistry step.  But you need to modify that for full mixing scheme, which is using chemical solver to calculate drydep.'''
 
--[[User:Jmao|Jmao]] 15:06, 15 December 2011 (EST)
 
== Code updates ==
 
=== Cold-temperature dry deposition updates ===
 
<span style="color:green">'''''This update was included in [[GEOS-Chem 12#12.6.0|GEOS-Chem 12.6.0]], which was released on 18 Oct 2019.'''''</span>
 
Viral Shah implemented the following updates in drydep_mod.F:
   
* Set HNO3 bulk surface resistance to 1 s/m
* Limit increases in Rc at low temperature to a factor of 2
 
The reference for these updates is
:Jaeglé, L., Shah, V.,et al., ''Nitrogen oxides emissions, chemistry, deposition, and export over the Northeast United States during the WINTER aircraft campaign'', <u>J Geophys Res: Atmospheres</u>, '''123''', https://doi.org/10.1029/2018JD029133, 2018.
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:00, 27 June 2019 (UTC)
 
=== Simple parameterization for CO2 dependence of stomatal resistance ===
 
<span style="color:green">'''''This update was included in [[GEOS-Chem 12#12.6.0|GEOS-Chem 12.6.0]], which was released on 18 Oct 2019.'''''</span>
 
Anthony Wong and Amos Tai have developed code to apply CO2 effect on stomatal conductance according to Franks et a. (2013) equation. This feature is implemented as an option in the Deposition Menu of input.geos and is off by default:
 
------------------------+------------------------------------------------------
%%% DEPOSITION MENU %%% :
Turn on Dry Deposition? : T
Turn on Wet Deposition? : T
<span style="color:green">Turn on CO2 Effect?    : F
CO2 level              : 600.0
Reference CO2 level    : 380.0</span>
------------------------+------------------------------------------------------
 
'''References:'''
*Franks, Peter J., et al., ''Sensitivity of plants to changing atmospheric CO2 concentration: from the geological past to the next century'', <u>New Phytologist</u>, 197.4, 1077-1094, 2013.
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 17:40, 27 June 2019 (UTC)
 
=== Updates to dry deposition when using the Olson 2001 land map ===
 
<span style="color:green">'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01a|GEOS-Chem v10-01a]] and approved on 05 Feb 2014.'''''</span>
 
It was discovered that ozone in the eastern US in [[GEOS-Chem v9-02]] was too high when using the [[Olson land map#Olson 2001 land map|Olson 2001 land map]]. Patrick Kim implemented the following updates to correct this issue:
 
:1. Force the use of MODIS LAI from 2008 if the last year is beyond 2008. There is a large difference in the 2009 file that still needs to be investigated.
 
:In routine Init_Modis_Lai (modis_lai_mod.F90):
 
    IF ( USE_OLSON_2001 ) THEN
      I_MODIS    = 1440            ! For Olson 2001, use MODIS LAI
      J_MODIS    = 720              ! on the 0.25 x 0.25 native grid
      MODIS_START = 2005            ! First year of MODIS data 
      <b>MODIS_END  = 2008            ! Force to 2008 (skim, 1/29/14)</b>
 
:2. Change the internal resistance for coniferous forests to match the internal resistance for deciduous forests.
 
:In routine READ_DRYDEP_INPUTS (drydep_mod.F):
 
      !----------------------------------------
      ! VARIABLE: IRI
      !----------------------------------------
      ! Variable name
      v_name = "IRI"
      ! Read IRI from file
      st1d  = (/ 1        /)
      ct1d  = (/ NDRYDTYPE /)
      CALL NcRd( IRI, fId, TRIM(v_name), st1d, ct1d )
      ! Read the IRI:units attribute
      a_name = "units"
      CALL NcGet_Var_Attributes( fId,TRIM(v_name),TRIM(a_name),a_val )
      <b>! If using Olson 2001 land map, replace IRI for coniferous forests
      ! with IRI for deciduous forests (skim, mps, 2/3/14)
      IF ( USE_OLSON_2001 ) THEN
        IRI(3) = 200
      ENDIF</b>
      ! Echo info to stdout
      IF ( am_I_Root ) THEN
        WRITE( 6, 130 ) TRIM(v_name), TRIM(a_val)
      ENDIF
 
--[[User:Melissa Payer|Melissa Sulprizio]] 11:31, 3 February 2014 (EST)
 
=== Updates to facilitate grid-independent operation ===
 
<span style="color:green">'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03j|v9-01-03j]] and approved on 17 Apr 2012.'''''</span>
 
A number of structural updates were made to the dry deposition routines in order to remove bottlenecks that would have prevented [[Grid-independent GEOS-Chem|grid-independent functionality]].  These include:
 
# Introduction of [[Olson land map|a new module to read Olson land map data]] from native resolution and to regrid to the currently-selected model resolution.  The regridding is done in such a way so as to preserve backwards compatibility and to populate the existing arrays (<code>IREG</code>, <code>ILAND</code>, <code>IUSE</code>, <code>FRCLND</code>) in the same manner as before. 
# Introduction of [[Leaf area indices in GEOS-Chem|a new module to read MODIS LAI data]] from native resolution and regrid to the current resolution in a consistent manner.
# Removal of obsolete variables:
## From <code>Headers/CMN_VEL_mod.F</code>: <code>IJREG</code>, <code>IJUSE</code>, <code>IJLAND</code>
## From <code>GeosCore/drydep_mod.F</code>: <code>NNNTYPE</code>, <code>NNNVEGTYPE</code>
# Replacement of obsolete ASCII input files with netCDF files.
 
--[[User:Bmy|Bob Y.]] 15:35, 17 December 2012 (EST)
 
=== Update dry deposition to use local surface pressure ===
 
<span style="color:green">'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03d|v9-01-03d]] and approved on 12 Jan 2012.'''''</span>
 
'''''[mailto:jaegle@uw.edu Lyatt Jaegl&eacute;] wrote:'''''
 
:The only difference comes from the pressure value (<code>PRESS</code> variable) used  in the dry deposition code to calculate the diffusivity of a molecule in air. Pressure comes into play in the mean free path calculation in <code>DIFFG</code>. For some reason the pressure was set at a constant value of 1500hPa (I do not know why this value was chosen in the first place, any ideas?). When I was going over the dry deposition code for sea salt I had replaced this fixed value with local sea level pressure (SLP). I think that it makes sense to use the actual local pressure instead of this fixed value. The overall effect is small.
 
--[[User:Melissa Payer|Melissa Payer]] 11:19, 11 January 2012 (EST)
 
=== Aerosol dry deposition velocities over snow and ice surfaces ===
 
<span style="color:green">'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-02_benchmark_history#v9-01-02i|v9-01-02i]] and approved on 15 Aug 2011.'''''</span>
 
Modeled aerosol dry deposition velocities over snow and ice surfaces in the Arctic are much higher than estimated from measured values (e.g., ''Ibrahim et al.'' [1983]; ''Duan et al.'' [1988]; ''Nilsson and Rannik'' [2001]).  In [[GEOS-Chem v9-01-02]] we have imposed a dry deposition velocity of 0.03 cm/s for all aerosols over snow and ice surfaces.
 
This update affects the following aerosol tracers: SO4s, NITs, DST1, DST2, DST3, DST4, SALA, SALC.
 
--[[User:Jaf|Jenny Fisher]] 11:08, 20 January 2011 (EST)<br>
--[[User:Bmy|Bob Y.]] 10:26, 16 August 2011 (EDT)
 
=== Removal of CMN_DEP_mod.F ===
 
<span style="color:green">'''''This update was validated with 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02d|v9-02d]] and approved on 19 Dec 2012.'''''</span>
 
[[Grid-Independent GEOS-Chem: Chemistry Component#Activation of new pathways for data flow and other structural modifications|As described in this wiki post]], we have removed the module file <code>Headers/CMN_DEP_mod.F</code> from GEOS-Chem.  The dry deposition arrays that were contained in this module are now carried by the [[Derived type objects used by GEOS-Chem#The Meteorology State object|the Meteorology State object (aka <code>State_Met</code>)]].
 
--[[User:Bmy|Bob Y.]] 11:40, 4 March 2013 (EST)
 
=== Application of dry deposition with mixing_mod.F90 ===
 
This discussion has been [[#In GEOS-Chem v10-01 and higher versions|moved to a section above]].
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:42, 17 February 2016 (UTC)


== References ==
== References ==
#Alexander, B., R.J. Park, D.J. Jacob, Q.B. Li, R.M. Yantosca, J. Savarino, C.C.W. Lee, and M.H. Thiemens, ''Sulfate formation in sea-salt aerosols: Constraints from oxygen isotopes'', <u>J. Geophys. Res.</u>, '''110''', D10307, 2005. [http://acmg.seas.harvard.edu/publications/alexander2005.pdf PDF]
#Alexander, B., R.J. Park, D.J. Jacob, Q.B. Li, R.M. Yantosca, J. Savarino, C.C.W. Lee, and M.H. Thiemens, ''Sulfate formation in sea-salt aerosols: Constraints from oxygen isotopes'', <u>J. Geophys. Res.</u>, '''110''', D10307, 2005. [http://acmg.seas.harvard.edu/publications/2005/alexander2005.pdf PDF]
#Baldocchi, D.D., B.B. Hicks, and P. Camara, ''A canopy stomatal resistance model for gaseous deposition to vegetated surfaces'', <u>Atmos. Environ</u>. '''21''', 91-101, 1987.
#Baldocchi, D.D., B.B. Hicks, and P. Camara, ''A canopy stomatal resistance model for gaseous deposition to vegetated surfaces'', <u>Atmos. Environ</u>. '''21''', 91-101, 1987.
#Brutsaert, W., ''Evaporation into the Atmosphere'', <u>Reidel</u>, 1982.
#Brutsaert, W., ''Evaporation into the Atmosphere'', <u>Reidel</u>, 1982.
#Businger, J.A., et al., ''Flux-profile relationships in the atmospheric surface layer'', <u>J. Atmos. Sci.</u>, '''28''', 181-189, 1971.
#Businger, J.A., et al., ''Flux-profile relationships in the atmospheric surface layer'', <u>J. Atmos. Sci.</u>, '''28''', 181-189, 1971.
#Bey I., D. J. Jacob, R. M. Yantosca, J. A. Logan, B. Field, A. M. Fiore, Q. Li, H. Liu, L. J. Mickley, and M. Schultz, ''Global modeling of tropospheric chemistry with assimilated meteorology: Model description and evaluation'', <u>J. Geophys. Res.</u>, '''106''', 23,073-23,096, 2001. [http://acmg.seas.harvard.edu/publications/bey2001a.pdf PDF]
#Bey I., D. J. Jacob, R. M. Yantosca, J. A. Logan, B. Field, A. M. Fiore, Q. Li, H. Liu, L. J. Mickley, and M. Schultz, ''Global modeling of tropospheric chemistry with assimilated meteorology: Model description and evaluation'', <u>J. Geophys. Res.</u>, '''106''', 23,073-23,096, 2001. [http://acmg.seas.harvard.edu/publications/2001/bey2001a.pdf PDF]
#Corbitt, E. S., ''How does the current implementation of dry deposition work in GEOS-Chem?'', Graduate Student Forum Talk, 20 Oct 2011. [http://acmg.seas.harvard.edu/forum_files2/gsf_drydep_corbitt.pdf PDF]
#Duan, B., Fairall, C.W., and Thomson, D.W., ''Eddy correlation measurements of the dry deposition of particles in wintertime'', <u>J. Appl. Met.</u>, '''27''', 642-652, 1988.
#Duan, B., Fairall, C.W., and Thomson, D.W., ''Eddy correlation measurements of the dry deposition of particles in wintertime'', <u>J. Appl. Met.</u>, '''27''', 642-652, 1988.
#Dwight, H.B., ''Tables of integrals and other mathematical data'', <u>MacMillan</u>, 1957.
#Dwight, H.B., ''Tables of integrals and other mathematical data'', <u>MacMillan</u>, 1957.
Line 57: Line 442:
#Nilsson, E.D. and Rannik, U. ''Turbulent aerosol fluxes over the Arctic Ocean: 1. Dry deposition over sea and pack ice'', <u>J. Geophys. Res,</u> '''106''', 32,125-32,137, 2001.
#Nilsson, E.D. and Rannik, U. ''Turbulent aerosol fluxes over the Arctic Ocean: 1. Dry deposition over sea and pack ice'', <u>J. Geophys. Res,</u> '''106''', 32,125-32,137, 2001.
#Price, H., L. Jaegl&eacute;, A. Rice, P. Quay, P.C. Novelli, R. Gammon, ''Global Budget of Molecular Hydrogen and its Deuterium Content: Constraints from Ground Station, Cruise, and Aircraft Observations'', submitted to <u>J. Geophys. Res.</u>, 2007
#Price, H., L. Jaegl&eacute;, A. Rice, P. Quay, P.C. Novelli, R. Gammon, ''Global Budget of Molecular Hydrogen and its Deuterium Content: Constraints from Ground Station, Cruise, and Aircraft Observations'', submitted to <u>J. Geophys. Res.</u>, 2007
#Pye, H. O. T., H. Liao, S. Wu, L. J. Mickley, D. J. Jacob, D. K. Henze, and J. H. Seinfeld (2009), ''Effect of changes in climate and emissions on future sulfate-nitrate-ammonium aerosol levels in the United States'', <u>J. Geophys. Res.</u>, 114(D1), D01205, doi:10.1029/2008JD010701.
#Walcek, C.J., R.A. Brost, J.S. Chang, and M.L.Wesely, ''SO2, sulfate, and HNO3 deposition velocities computed using regional landuse and meteorological data'', <u>Atmos. Environ.</u>, '''20''', 949-964, 1986.
#Walcek, C.J., R.A. Brost, J.S. Chang, and M.L.Wesely, ''SO2, sulfate, and HNO3 deposition velocities computed using regional landuse and meteorological data'', <u>Atmos. Environ.</u>, '''20''', 949-964, 1986.
#Wang, Y., D.J. Jacob, and J.A. Logan, ''Global simulation of tropospheric O3-NOx-hydrocarbon chemistry, 1. Model formulation'', <u>J. Geophys. Res.</u>, '''103''', D9,10,713-10,726, 1998. [http://acmg.seas.harvard.edu/publications/wang1998a.pdf PDF]
#Wang, Y., D.J. Jacob, and J.A. Logan, ''Global simulation of tropospheric O3-NOx-hydrocarbon chemistry, 1. Model formulation'', <u>J. Geophys. Res.</u>, '''103''', D9,10,713-10,726, 1998. [http://acmg.seas.harvard.edu/publications/1998/wang1998a.pdf PDF]
#Wesely, M.L, ''Improved parameterizations for surface resistance to gaseous dry deposition in regional-scale numerical models'', <u>Environmental Protection Agency Report EPA/600/3-88/025</u>, Research Triangle Park (NC), 1988.
#Wesely, M.L, ''Improved parameterizations for surface resistance to gaseous dry deposition in regional-scale numerical models'', <u>Environmental Protection Agency Report EPA/600/3-88/025</u>, Research Triangle Park (NC), 1988.
#Wesely, M. L., ''Parameterization of surface resistance to gaseous dry deposition in regional-scale numerical models'', <u>Atmos. Environ.</u>, '''23''', 1293-1304, 1989.
#Wesely, M. L., ''Parameterization of surface resistance to gaseous dry deposition in regional-scale numerical models'', <u>Atmos. Environ.</u>, '''23''', 1293-1304, 1989.
#Wesely, M.L, and B.B. Hicks, ''Some factors that affect the deposition rates of sulfur dioxide and similar gases on vegetation'', <u>J. Air. Pollut. Control Assoc.</u>, '''27''', 1110-1116, 1977.
#Wesely, M.L, and B.B. Hicks, ''Some factors that affect the deposition rates of sulfur dioxide and similar gases on vegetation'', <u>J. Air. Pollut. Control Assoc.</u>, '''27''', 1110-1116, 1977.
#Zhang, L., S. Gong, J. Padro, and L. Barrie, ''A size-segregated particle dry deposition scheme for an atmospheric aerosol module'', <u>Atmos. Environ.,</u>, '''35''', 549–560, 2001.
#Zhang, L. M., S. L. Gong, J. Padro, and L. Barrie (2001), A size-segregated particle dry deposition scheme for an atmospheric aerosol module, Atmos. Environ., 35(3), 549-560, doi:10.1016/s1352-2310(00)00326-5.


--[[User:Bmy|Bob Y.]] 15:24, 19 February 2010 (EST)
--[[User:Bmy|Bob Y.]] 15:24, 19 February 2010 (EST)


== Known issues ==
== Previous issues that have now been resolved ==
 
=== Bug in computation of aerodynamic resistance RA ===
 
<span style="color:green">'''''This fix was included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span>
 
'''''Brian Boys wrote:'''''
 
<blockquote>In module <tt>GeosCore/drydep_mod.F</tt>, I discovered a bug in the subroutine <tt>DEPVEL</tt>. For the calculation of aerodynamic resistance RA under very stable atmospheric conditions (line 1811), the integration of the stability function phi_h (aka dimensionless vertical temperature gradient) from the roughness length to grid box center doesn't take into account the discontinuity occurring at z/L = 1 where phi_h switches from 1 + 5(z/L) to 5 + z/L  (Holtslag, 1993). The result is too high of a value for the integral of phi_h and subsequently RA.
 
A straightforward solution is to calculate RA under stable conditions (L>0) using an integral form of the stability function, such as equation (12) of Holtslag, 1988. I implemented these changes in drydep_mod.F (from GCv 10-01, public release). To see the effect of the bug, namely a discontinuity in RA, refer to '''Figure 1''', which plots RA as a function of stability (1/L).
 
[[Image:Depvel_figure_1.png]]
 
I've also attached two scatter plots comparing outputted RA  (GCv10-01, geosfp, 2x2.5, 2012/11/01) from the base model and an updated simulation employing the bug-fix as described above--please refer to '''Figure 2''' (linear comparison):


=== Aerosol dry deposition velocities over snow and ice surfaces ===
[[Image:Depvel_figure_2.png]]
 
and '''Figure 3''' (logarithmic comparison):


Modeled aerosol dry deposition velocities over snow and ice surfaces in the Arctic are much higher than estimated from measured values (e.g., ''Ibrahim et al.'' [1983]; ''Duan et al.'' [1988]; ''Nilsson and Rannik'' [2001]). A planned update to GEOS-Chem, to be included in [[GEOS-Chem v9-01-02|v9-01-02]], will impose a dry deposition velocity of 0.03 cm/s for all aerosols over snow and ice surfaces.
[[Image:Depvel_figure_3.png]]
</blockquote>


--[[User:Jaf|Jenny Fisher]] 11:08, 20 January 2011 (EST)
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:23, 17 February 2017 (UTC)


=== Dependency between dry deposition and soil NOx emissions ===
=== Dependency between dry deposition and soil NOx emissions ===
<span style="color:green">'''''This issue has been resolved in the new soil NOx algorithm that was added to [[GEOS-Chem v9-02]].  The new module <code>GeosCore/canopy_nox_mod.F</code> computes the NOx from the canopy independently of the dry deposition module.  We shall leave this post here for reference. '''''</span>
<span style="color:red">'''''The canopy reduction algorithm (originally done in <code>GeosCore/canopy_nox_mod.F</code>) has been moved to the [[HEMCO]] soil NOx extension module (<code>HEMCO/Extensions/hcox_soilnox_mod.F90</code>).  Module <code>GeosCore/canopy_nox_mod.F</code> was removed from [[GEOS-Chem v10-01]] and higher versions.'''''</span>


In GEOS-Chem there is a code dependency between the dry deposition routines [[Soil NOx emissions|soil NOx emissions routines]].  This is purely historical baggage that goes back to the days of the old 9-layer Harvard-GISS CTM (from which these routines were taken).
In GEOS-Chem there is a code dependency between the dry deposition routines [[Soil NOx emissions|soil NOx emissions routines]].  This is purely historical baggage that goes back to the days of the old 9-layer Harvard-GISS CTM (from which these routines were taken).


The dry deposition routine <tt>DEPVEL</tt> (in <tt>drydep_mod.f</tt>) computes a quantity called <tt>CANOPYNOX</tt>, which is the bulk surface resistance of the canopy to NOx deposition.  This is computed in the following lines of code:
The dry deposition routine <code>DEPVEL</code> (in <code>drydep_mod.f</code>) computes a quantity called <code>CANOPYNOX</code>, which is the bulk surface resistance of the canopy to NOx deposition.  This is computed in the following lines of code:


  C** Get the bulk surface resistance of the canopy, RSURFC, from the network
  C** Get the bulk surface resistance of the canopy, RSURFC, from the network
Line 94: Line 501:
                 ENDIF
                 ENDIF


However, the <tt>CANOPYNOX</tt> variable is not defined within <tt>drydep_mod.f</tt>, but is found instead within the soil NOx emissions code header file <tt>commsoil.h</tt>:
However, the <code>CANOPYNOX</code> variable is not defined within <code>drydep_mod.f</code>, but is found instead within the soil NOx emissions code header file <code>commsoil.h</code>:


       REAL*8 CANOPYNOX(MAXIJ,NTYPE) !track NOx within canopy dry dep.
       REAL*8 CANOPYNOX(MAXIJ,NTYPE) !track NOx within canopy dry dep.


and is then also used within the soil NOx emissions function <tt>SOILCRF</tt>, as follows:
and is then also used within the soil NOx emissions function <code>SOILCRF</code>, as follows:


       IF ((XLAI(IREF,JREF,K).GT.0.D0).AND.
       IF ((XLAI(IREF,JREF,K).GT.0.D0).AND.
Line 112: Line 519:
       END IF
       END IF


This is not necessarily a problem as long as dry deposition is always turned on whenever you are doing a full-chemistry simulation that requires soil NOx emissions.  In the driver routine <tt>main.f</tt>, dry deposition is always done before emissions.  However, this is bad coding style and a potential source of error.  (This also must be corrected for the [[GEOS-Chem column code]], in which all inputs must come thru the argument list.)
This is not necessarily a problem as long as dry deposition is always turned on whenever you are doing a full-chemistry simulation that requires soil NOx emissions.  In the driver routine <code>main.f</code>, dry deposition is always done before emissions.  However, this is bad coding style and a potential source of error.  (This also must be corrected for the [[GEOS-Chem column code]], in which all inputs must come thru the argument list.)


In the new soil NOx emissions code being developed by [mailto:hudman@berkeley.edu Rynda Hudman] (much of which is based on the GEOS-Chem column code being developed by Bob Yantosca and Philippe Le Sager), there is a new module called <tt>canopy_nox_mod.f</tt>.  This module computes the <tt>CANOPYNOX</tt> quantity independently of routine <tt>DEPVEL</tt> in <tt>drydep_mod.f</tt>, which allows for a totally clean separation between dry deposition routines and emissions routines.
In the new soil NOx emissions code being developed by [mailto:hudman@berkeley.edu Rynda Hudman] (much of which is based on the GEOS-Chem column code being developed by Bob Yantosca and Philippe Le Sager), there is a new module called <code>canopy_nox_mod.f</code>.  This module computes the <code>CANOPYNOX</code> quantity independently of routine <code>DEPVEL</code> in <code>drydep_mod.f</code>, which allows for a totally clean separation between dry deposition routines and emissions routines.


At present, the new <tt>canopy_nox_mod.f</tt> is not available in the [[GEOS-Chem versions under development|standard mainline GEOS-Chem code]].  It is slated to be incorporated with the soil NOx emissions update.
At present, the new <code>canopy_nox_mod.f</code> is not available in the [[GEOS-Chem versions under development|standard mainline GEOS-Chem code]].  It is slated to be incorporated with the soil NOx emissions update.


--[[User:Bmy|Bob Y.]] 13:51, 18 February 2010 (EST)
--[[User:Bmy|Bob Y.]] 13:51, 18 February 2010 (EST)
=== Add extra variables to PRIVATE declaration in parallel loop ===
<span style="color:green">'''''This fix was validated by 1-month benchmark simulation [[GEOS-Chem v9-02 benchmark history#v9-02p|GEOS-Chem v9-02p]] (approved 13 Sep 2013).'''''</span>
   
We have explicitly added variable <code>IW</code> to the <code>!$OMP+PRIVATE</code> list in routine <code>DEPVEL</code> in <code>GeosCore/drydep_mod.F</code>.  This should already be held private because it is a loop index, but it doesn't hurt to add it to the list.
   
We also have added <code>ZO</code> as a PRIVATE variable when compiling with GCAP meteorology.
Old code:
!$OMP+PRIVATE( DTMP1,  DTMP2,  DTMP3,  DTMP4,  VDS,    CZH    )
!$OMP+PRIVATE( CKUSTR, REYNO,  CORR1,  CORR2,  Z0OBK,  RA    )
!$OMP+PRIVATE( DUMMY1, DUMMY2, DUMMY3, DUMMY4, DAIR,  RB    )
!$OMP+PRIVATE( C1X,    VK,    I,      J                      )
New code:
!$OMP+PRIVATE( DTMP1,  DTMP2,  DTMP3,  DTMP4,  VDS,    CZH    )
!$OMP+PRIVATE( CKUSTR, REYNO,  CORR1,  CORR2,  Z0OBK,  RA    )
!$OMP+PRIVATE( DUMMY1, DUMMY2, DUMMY3, DUMMY4, DAIR,  RB    )
!$OMP+PRIVATE( C1X,    VK,    I,      J,      IW            )
#if defined( GCAP )
!$OMP+PRIVATE( ZO                                            )
#endif
--[[User:Bmy|Bob Y.]] 12:04, 12 September 2013 (EDT)
=== Parallelization error in routine METERO ===
<span style="color:green">'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem v9-02 benchmark history#1-month benchmark with GEOS-5 meteorology|v9-02r]] and approved on 14 Nov 2013.'''''
'''''This update is included in Adjoint [[GEOS-Chem_Adjoint_v35 | v35j]].'''''</span>
We discovered a minor bug in the parallel DO loop of routine <tt>METERO</tt> (in module <tt>GeosCore/drydep_mod.F</tt>):
      ! Loop over surface grid boxes
!$OMP PARALLEL DO
!$OMP+DEFAULT( SHARED )
!$OMP+PRIVATE( I, J, IJLOOP, THIK )
      DO J = 1, JJPAR
      DO I = 1, IIPAR
          ! 1-D grid box index
          IJLOOP        = ( (J-1) * IIPAR ) + I
          ! THIK = thickness of layer 1 [m]
          THIK          = State_Met%BXHEIGHT(I,J,1)
          ! Midpoint height of first model level [m]
          CZ1(IJLOOP)    = THIK / 2.0d0
          ! Local surface pressure [hPa] (mpayer, 1/10/12)
          SP            = GET_PEDGE(I,J,1)
          ! Convert from hPa to Pa for SFCPRESS
          PRESSU(IJLOOP) = SP * 1.d2
The <code>SP</code> variable (which is surface pressure) had not been held PRIVATE in the above parallel loop.  This caused slightly different surface pressure values to be saved into the <code>PRESSU</code> array.  Later on in the code, <code>PRESSU</code> is passed as an argument to function <code>DIFFG</code>, which computes the computes the molecular diffusivity of each drydep species.  This in turn affects the value of the drydep velocity of each species.  Therefore, as a result of this error, we would observe small numerical differences in the results of GEOS-Chem simulations when using OpenMP parallelization versus when OpenMP parallelization was turned off.
The fix is to add <code>SP</code> to the PRIVATE list:
        ! Loop over surface grid boxes
  !$OMP PARALLEL DO
  !$OMP+DEFAULT( SHARED )
  !$OMP+PRIVATE( I, J, IJLOOP, THIK, SP )
which then ensures that we obtain identical results whether or not OpenMP parallelization is turned on.
--[[User:Bmy|Bob Y.]] 15:25, 14 November 2013 (EST)
=== Remove obsolete ISN2 drydep species ===
<span style="color:green">'''''This update was validated with the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01i|v10-01i]] and approved on Approved 01 May 2015.'''''</span>
'''''[[User:Katherine_Travis|Katherine Travis]] wrote:'''''
<blockquote>In dry deposition, we still have a dry dep option for ISN2.  ISN2 was the nighttime isoprene nitrate in old versions of the chemistry, and ISN1 was the second generation product from this species.  But now, we call ISN1 the isoprene nitrate species.  So, we should replace IDTISN2 in dry dep and tracerid_mod with IDTISN1.  That fix is also in the above directory.</blockquote>
In <tt>GeosCore/drydep_mod.F</tt>, we replaced these lines of code:
        ! ISN2 (uses same dep vel as HNO3)
        ELSE IF ( N == IDTISN2 ) THEN
            . . .
            NTRAIND(NUMDEP) = IDTISN2
            . . .
            DEPNAME(NUMDEP) = 'ISN2'
with these:
        ! ISN1 (uses same dep vel as HNO3)
        ! This should be ISN1, krt (3/31/15)
        ELSE IF ( N == IDTISN1 ) THEN
            . . .
            NTRAIND(NUMDEP) = IDTISN1
            . . .
            DEPNAME(NUMDEP) = 'ISN1'
and in <tt>GeosCore/tracerid_mod.F</tt>, we replaced these lines of code:
      INTEGER            :: IDISN2,  IDR4N2,  IDCH2O,  IDC2H6,  IDMP
      . . .
      INTEGER            :: IDTPPN,  IDTISN1,  IDTR4N2, IDTPRPE, IDTC3H8
      . . .
      IF ( NAMEGAS(I) == 'ISN2'  ) IDISN2  = I
      . . .
      IDISN2    = 0
with:
      INTEGER            :: '''IDISN1''',  IDR4N2,  IDCH2O,  IDC2H6,  IDMP
      . . .
      INTEGER            :: IDTPPN,  '''IDTISN1''',  IDTR4N2, IDTPRPE, IDTC3H8   
      . . .
      IF ( NAMEGAS(I) == ''''ISN1''''  ) '''IDISN1'''  = I
      . . .
      '''IDISN1'''    = 0
--[[User:Bmy|Bob Y.]] 16:51, 1 April 2015 (EDT)
=== Fix for NO3 + ISOP product ===
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02c|v11-02c]] and approved on 21 Sep 2017.'''''</span>
'''''[[User:Katherine_Travis|Katie Travis]] wrote:'''''
:The nitrate isoprene nitrate is now called ISN1.  It must be added to GEOS-Chem as a transported tracer to undergo dry deposition. We can use the molecular weight given to other isoprene nitrates of 147 g/mol.  In addition, the references to ISN2 in drydep_mod.F and planeflight_mod.F (where the ANs are added up) should be changed to ISN1.
NOTE: We will add this fix after FlexChem is integrated into GEOS-Chem.  Because FlexChem will completly remove SMVGEAR from GEOS-Chem, we shall add this fix into the KPP master equation file (instead of the SMVGEAR <code>globchem.dat</code> file).
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:21, 17 June 2015 (UTC)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 22:17, 8 February 2016 (UTC)
== Unresolved issues ==
None that we are aware of at this time.

Latest revision as of 14:58, 18 October 2019

This page describes the current dry deposition scheme used in GEOS-Chem.

Overview

Here is a description of the GEOS-Chem dry deposition scheme from several journal articles:

From Section 4 of Alexander et al [2005]:

Dry deposition velocities for sea-salt aerosols (and sulfate formed in sea-salt aerosols) are computed with the size-dependent scheme of Zhang et al. [2001] integrated over each model size bin and accounting for hygroscopic growth as a function of relative humidity [Gerber, 1985]. Dry deposition velocities for all other species are computed with a standard resistance-in-series scheme based on Wesely [1989] as described by Wang et al. [1998].

From Section 2.4 of Bey et al [2001]:

Dry deposition of oxidants and water soluble species is computed using a resistance-in-series model based on the original formulation of Wesely [1989] with a number of modifications [Wang et al 1998]. The dry deposition velocities are calculated locally using GEOS data for surface values of momentum and sensible heat fluxes, temperature, and solar radiation.

From Section 6 of Wang et al [1998]:

We use a resistance-in-series model [Wesely and Hicks, 1977] to compute dry deposition velocities of O3, NO2, HNO3, PANs and H2O2. The deposition velocity Vi for species i is computed as:

     Vi = 1 / ( Ra + Rb,i + Rc,i )

where Ra is the aerodynamic resistance to transfer to the surface, Rb,i is the boundary resistance, and Rc,i is the canopy surface resistance. Ra and Rb,i are calculated from the GCM meteorological variables [Jacob et al 1993]. Surface resistances Rc,i are based largely on the canopy model of Wesely [1989] with some improvements, including explicit dependence of canopy stomatal resistances on LAI [Gao and Wesely, 1995] and on direct and diffuse PAR within the canopy [Baldocchi et al, 1987]. The same radiative transfer model for direct and diffuse PAR in the canopy is used as in the formulation of isoprene emissions. Surface resistances for deposition to tropical rain forest and tundra are taken from Jacob and Wofsy [1990] and Jacob et al [1992], respectively. The surface resistance for deposition of NO2 is taken to be the same as that of ozone [Erisman & Pul, 1994; Kramm et al, 1995; Eugster and Hesterberg, 1996] and hence lower than specified by Wesely [1989]. Dry deposition of CO and hydrocarbons is negligibly small and not included in the model [Mueller and Brasseur, 1995].

Aerosol dry deposition

Havala Pye reexamined the code, and she found that there are three routines basically using the Zhang et al.(2001) scheme:

  1. AERO_SFCRSII: Aerodynamic resistance for seasalt tracers. Hygroscopic growth is accounted for. Implemented by Rokjin Park ~ 2004? Used for: SALA, SALC, SO4S, NITS
  2. DUST_SFCRSII: Aerodynamic resistance of dust aerosol tracers. No hygroscopic growth. Implemented by bec ~2005? Used for: DST1, DST2, DST3, DST4
  3. ADUST_SFCRSII: Aerodynamic resistance of non-size resolved aersosols. No hygroscopic growth. Based on DUST_SRFCRSII and activated by Pye 2007. Assume particle diameter is 0.5 microns, density is 1.5 g/cm3 (1500 kg/m3). Used for all other aerosols that are not listed above (aerosols are indicated by a T/F flag in INIT_DRYDEP called AIROSOL).

This was briefly mentioned in Pye et al. (2009) paper.

Reference

  1. Pye, H. O. T., H. Liao, S. Wu, L. J. Mickley, D. J. Jacob, D. K. Henze, and J. H. Seinfeld (2009), Effect of changes in climate and emissions on future sulfate-nitrate-ammonium aerosol levels in the United States, Journal of Geophysical Research: Atmospheres, 114(D1), D01205, doi:10.1029/2008JD010701.
  2. Zhang, L. M., S. L. Gong, J. Padro, and L. Barrie (2001), A size-segregated particle dry deposition scheme for an atmospheric aerosol module, Atmos. Environ., 35(3), 549-560, doi:10.1016/s1352-2310(00)00326-5.

Source code and data

The source code of the various routines are located in drydep_mod.f.

  1. Routine DO_DRYDEP is the main driver for the dry deposition. This calls various setup subroutines.
  2. Routine DEPVEL (which is called by DO_DRYDEP) computes dry deposition dry deposition velocities in [m/s].
  3. Dry deposition frequencies [1/s] for all species are computed in DO_DRYDEP, after the call to DEPVEL.

For more information about the input data files required by the drydep scheme, please see the README file: GEOS_1x1/drydep_200203/README

In GEOS-Chem v10-01 and higher versions

NOTE: This update was made to facilitate the implementation of both the HEMCO emissions component and FlexChem chemical solver.

In GEOS-Chem v10-01 and higher versions, the following changes were made to how dry deposition is applied:

  1. Dry deposition is now applied to all tracers in module GeosCore/mixing_mod.F90. Prior to this, dry deposition had been applied in several locations throughout the code, which was confusing and prone to error.
  2. Dry deposition fluxes (i.e. category DRYD-FLX) are now archived to the ND44 diagnostic in module GeosCore/mixing_mod.F90. Furthermore, drydep fluxes are now archived with units of molec/cm2/s for all GEOS-Chem simulations. In prior GEOS-Chem versions, some simulations (in particular Rn-Pb-Be) had archived drydep fluxes in units of kg/s. Therefore, when analyzing output from GEOS-Chem v10-01 (or higher versions), please make sure to modify your plotting or budget programs to expect drydep fluxes in units of molec/cm2/s.
  3. Routines DRYFLX and DRYFLXRnPbBe have now been removed from module GeosCore/drydep_mod.F. The equivalent functionality is now provided by GeosCore/mixing_mod.F90.

--Bob Y. (talk) 21:34, 17 June 2015 (UTC)

Input values for dry deposition

Here we list some of the various input values used by the dry deposition routines. Full citations may be found in the references section below.

Land cover parameters

The land cover input variables for the GEOS-Chem dry deposition module are listed in the table below:

Variable Read from Description Values Reference
DRYCOEFF
  • v9-01-03 and higher:
    Olson_1992_Drydep_inputs.nc

  • Prior to v9-01-03:
    drydep.coef
Local dependence of stomal resistance on the intensity I of light impinging the leaf; this is expressed as a mutliplicative factor I/(I+b) to the stomatal resistance where b = 50 W m-2 (equation (7) of Baldocchi et al. [1987]) -0.358, 3.02, 3.85, -0.0978, -3.66, 12, 0.252, -7.8, 0.226, 0.274, 1.14, -2.19, 0.261, -4.62, 0.685, -0.254, 4.37, -0.266, -0.159, -0.206
  • Baldocchi et al, AE, 1987.
IDRYDEP
  • v9-01-03 and higher:
    Olson_1992_Drydep_inputs.nc

  • Prior to v9-01-03:
    drydep.table
Indices for the 11 dry deposition land types 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
  • Wesely, AE 1989;
  • Jacob et al., JGR 1990, 1992.
IOLSON
  • v9-01-03 and higher:
    Olson_1992_Drydep_inputs.nc

  • Prior to v9-01-03:
    drydep.table
Indices for the 72 Olson land types 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74
  • Wesely, AE 1989;
  • Jacob et al., JGR 1990, 1992.
IDEP
  • v9-01-03 and higher:
    Olson_1992_Drydep_inputs.nc

  • Prior to v9-01-03:
    drydep.table
Indices that map each of the 72 Olson land types to the corresponding dry deposition land type 11, 10, 5, 1, 1, 1, 2, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 3, 3, 3, 3, 2, 2, 2, 3, 2, 2, 4, 4, 2, 6, 1, 1, 9, 4, 4, 4, 5, 5, 5, 5, 5, 9, 5, 5, 5, 5, 8, 8, 5, 7, 6, 2, 2, 2, 2, 2, 3, 3, 3, 5, 5, 11, 11, 11, 11, 8, 1, 8, 9, 11
  • Wesely, AE 1989;
  • Jacob et al., JGR 1990, 1992.
IWATER
  • v9-01-03 and higher:
    Olson_1992_Drydep_inputs.nc

  • Prior to v9-01-03:
    drydep.table
Indices of the Olson land types denoting water (i.e. ocean/lake/ice) surfaces 1, 66, 67, 68, 69, 74
  • Wesely, AE 1989;
  • Jacob et al., JGR 1990, 1992.
IZO
  • v9-01-03 and higher:
    Olson_1992_Drydep_inputs.nc

  • Prior to v9-01-03:
    drydep.table
Roughness heights (1e-4 m) for each of the 72 Olson land types 10, 25000, 100, 1000, 1000, 1000, 10000, 1000, 10, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1, 1000, 1000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 1000, 10000, 1000, 1000, 2000, 10000, 1000, 1000, 100, 1000, 1000, 1000, 100, 100, 100, 100, 100, 100, 1000, 1000, 1000, 1000, 10, 10, 100, 50, 10000, 2000, 2000, 2000, 2000, 2000, 10000, 10000, 10000, 2000, 50, 100, 100, 100, 100, 10, 1, 1, 500, 10
  • Wesely, AE 1989;
  • Jacob et al., JGR 1990, 1992.

--Bob Yantosca (talk) 17:43, 21 July 2016 (UTC)

Aerodynamic resistances

The aerodynamic resistances (IRI, IRLU, IRAC, IRGSS, IRGSO, IRCLS, IRCLO) and maximum deposition velocity for aerosol (IVSMAX) for each of the 11 dry deposition land types are read from this file:

  • v9-01-03 and higher: Olson_1992_Drydep_inputs.nc
  • Prior to v9-01-03: drydep.table

and have the following values:

DD type Description IRI
[s m-1]
IRLU
[s m-1]
IRAC
[s m-1]
IRGSS
[s m-1]
IRGSO
[s m-1]
IRCLS
[s m-1]
IRCLO
[s m-1]
IVSMAX
[10-2 cm s-1]
Reference
1 Snow/Ice 9999 9999 0 100 3500 9999 1000 100 Wesely, AE, 1989
2 Deciduous forest 200 9000 2000 500 200 2000 1000 100 Wesely, AE, 1989
3 Coniferous forest 400 9000 2000 500 200 2000 1000 100 Wesely, AE, 1989
4 Agricultural land 200 9000 200 150 150 2000 1000 100 Wesely, AE, 1989
5 Shrub/grassland 200 9000 100 350 200 2000 1000 100 Wesely, AE, 1989
6 Amazon forest 200 1000 2000 200 200 9999 9999 100 Jacob & Wofsy, JGR 1990
7 Tundra 200 4000 0 340 340 9999 9999 100 Jacob et al., JGR 1992
8 Desert 9999 9999 0 1000 400 9999 9999 10 Wesely, AE, 1989
9 Wetland 200 9000 300 0 1000 2500 1000 100 Wesely, AE, 1989
10 Urban 9999 9999 100 400 300 9999 9999 100 Wesely, AE, 1989
11 Water 9999 9999 0 0 2000 9999 9999 10 Wesely, AE, 1989

--Bob Yantosca (talk) 17:43, 21 July 2016 (UTC)

OVOCs dry deposition

These values were further changed as part of the new isoprene scheme. The most up-to-date values are on the new isoprene scheme page.

--Jmao, JAF 19 March 2014

This update was tested in the 1-month benchmark simulation v9-01-03c and approved on 19 Dec 2011.

In GEOS-Chem v11-01 and higher versions, these parameters are now defined in the GEOS-Chem species database, and are then copied into the local dry deposition arrays in routine INIT_DRYDEP.

According to Karl et al.(2010), I changed the reactivity factor(f0) for all OVOCs from 0 to 1.

Now dry dep is set up as:

Species H*(moles L-1 atm-1 ) f0 Reference
NO2 0.01 0.1
Ox 0.01 1.0
PAN 3.6 0.1
HNO3 1.0d+14 0.0
H2O2 1.0d+5 1.0
PMN as PAN
PPN as PAN
PYPAN as PAN
ISN2 as HNO3
R4N2 as PAN
CH2O 6.0e+3 change from 0 to 1.0
GLYX 3.6d+5 change from 0 to 1.0
MGLY 3.7d+3 change from 0 to 1.0
GLYC 4.1d+4 change from 0 to 1.0
MPAN,GPAN, GLPAN as PAN
N2O5 as HNO3
HCOOH 1.67d+5 change from 0 to 1.0
ACTA 1.14d+4 change from 0 to 1.0
ISOPND 1.7d+4 0.0
ISOPNB 1.7d+4 0.0
MVKN+MACRN 1.7d+4 0.0
PROPNN 1.0d+3 0.0 NITROOXYACETONE IN SANDER TABLE
RIP as H2O2
IEPOX as H2O2
MAP 8.4d+2 1.0
MVK 4.4d1 change from 0 to 1.0 from R.Sander
MACR 6.5d0 change from 0 to 1.0 from R.Sander
SO2 1.0d+5 0.0

Karl, T., Harley, P., Emmons, L., Thornton, B., Guenther, A., Basu, C., Turnipseed, A., and Jardine, K.: Efficient Atmospheric Cleansing of Oxidized Organic Trace Gases by Vegetation, Science, 330, 816-819, 10.1126/science.1192534, 2010.

Notes: To run with non-local mixing, you don't need to modify globchem.dat with " MVK=DRYDEP+DRYMVK", because drydep here is done out of chemistry step. But you need to modify that for full mixing scheme, which is using chemical solver to calculate drydep.

--Jmao 15:06, 15 December 2011 (EST)

Code updates

Cold-temperature dry deposition updates

This update was included in GEOS-Chem 12.6.0, which was released on 18 Oct 2019.

Viral Shah implemented the following updates in drydep_mod.F:

  • Set HNO3 bulk surface resistance to 1 s/m
  • Limit increases in Rc at low temperature to a factor of 2

The reference for these updates is

Jaeglé, L., Shah, V.,et al., Nitrogen oxides emissions, chemistry, deposition, and export over the Northeast United States during the WINTER aircraft campaign, J Geophys Res: Atmospheres, 123, https://doi.org/10.1029/2018JD029133, 2018.

--Melissa Sulprizio (talk) 18:00, 27 June 2019 (UTC)

Simple parameterization for CO2 dependence of stomatal resistance

This update was included in GEOS-Chem 12.6.0, which was released on 18 Oct 2019.

Anthony Wong and Amos Tai have developed code to apply CO2 effect on stomatal conductance according to Franks et a. (2013) equation. This feature is implemented as an option in the Deposition Menu of input.geos and is off by default:

------------------------+------------------------------------------------------ 
%%% DEPOSITION MENU %%% :
Turn on Dry Deposition? : T
Turn on Wet Deposition? : T
Turn on CO2 Effect?     : F
CO2 level               : 600.0
Reference CO2 level     : 380.0
------------------------+------------------------------------------------------

References:

  • Franks, Peter J., et al., Sensitivity of plants to changing atmospheric CO2 concentration: from the geological past to the next century, New Phytologist, 197.4, 1077-1094, 2013.

--Melissa Sulprizio (talk) 17:40, 27 June 2019 (UTC)

Updates to dry deposition when using the Olson 2001 land map

This update was validated in the 1-month benchmark simulation GEOS-Chem v10-01a and approved on 05 Feb 2014.

It was discovered that ozone in the eastern US in GEOS-Chem v9-02 was too high when using the Olson 2001 land map. Patrick Kim implemented the following updates to correct this issue:

1. Force the use of MODIS LAI from 2008 if the last year is beyond 2008. There is a large difference in the 2009 file that still needs to be investigated.
In routine Init_Modis_Lai (modis_lai_mod.F90):
   IF ( USE_OLSON_2001 ) THEN
      I_MODIS     = 1440             ! For Olson 2001, use MODIS LAI
      J_MODIS     = 720              ! on the 0.25 x 0.25 native grid
      MODIS_START = 2005             ! First year of MODIS data  
      MODIS_END   = 2008             ! Force to 2008 (skim, 1/29/14)
2. Change the internal resistance for coniferous forests to match the internal resistance for deciduous forests.
In routine READ_DRYDEP_INPUTS (drydep_mod.F):
     !----------------------------------------
     ! VARIABLE: IRI
     !----------------------------------------

     ! Variable name
     v_name = "IRI"

     ! Read IRI from file
     st1d   = (/ 1         /)
     ct1d   = (/ NDRYDTYPE /)
     CALL NcRd( IRI, fId, TRIM(v_name), st1d, ct1d )

     ! Read the IRI:units attribute
     a_name = "units"
     CALL NcGet_Var_Attributes( fId,TRIM(v_name),TRIM(a_name),a_val )

     ! If using Olson 2001 land map, replace IRI for coniferous forests
     ! with IRI for deciduous forests (skim, mps, 2/3/14)
     IF ( USE_OLSON_2001 ) THEN
        IRI(3) = 200
     ENDIF

     ! Echo info to stdout
     IF ( am_I_Root ) THEN
        WRITE( 6, 130 ) TRIM(v_name), TRIM(a_val)
     ENDIF

--Melissa Sulprizio 11:31, 3 February 2014 (EST)

Updates to facilitate grid-independent operation

This update was tested in the 1-month benchmark simulation v9-01-03j and approved on 17 Apr 2012.

A number of structural updates were made to the dry deposition routines in order to remove bottlenecks that would have prevented grid-independent functionality. These include:

  1. Introduction of a new module to read Olson land map data from native resolution and to regrid to the currently-selected model resolution. The regridding is done in such a way so as to preserve backwards compatibility and to populate the existing arrays (IREG, ILAND, IUSE, FRCLND) in the same manner as before.
  2. Introduction of a new module to read MODIS LAI data from native resolution and regrid to the current resolution in a consistent manner.
  3. Removal of obsolete variables:
    1. From Headers/CMN_VEL_mod.F: IJREG, IJUSE, IJLAND
    2. From GeosCore/drydep_mod.F: NNNTYPE, NNNVEGTYPE
  4. Replacement of obsolete ASCII input files with netCDF files.

--Bob Y. 15:35, 17 December 2012 (EST)

Update dry deposition to use local surface pressure

This update was tested in the 1-month benchmark simulation v9-01-03d and approved on 12 Jan 2012.

Lyatt Jaeglé wrote:

The only difference comes from the pressure value (PRESS variable) used in the dry deposition code to calculate the diffusivity of a molecule in air. Pressure comes into play in the mean free path calculation in DIFFG. For some reason the pressure was set at a constant value of 1500hPa (I do not know why this value was chosen in the first place, any ideas?). When I was going over the dry deposition code for sea salt I had replaced this fixed value with local sea level pressure (SLP). I think that it makes sense to use the actual local pressure instead of this fixed value. The overall effect is small.

--Melissa Payer 11:19, 11 January 2012 (EST)

Aerosol dry deposition velocities over snow and ice surfaces

This update was tested in the 1-month benchmark simulation v9-01-02i and approved on 15 Aug 2011.

Modeled aerosol dry deposition velocities over snow and ice surfaces in the Arctic are much higher than estimated from measured values (e.g., Ibrahim et al. [1983]; Duan et al. [1988]; Nilsson and Rannik [2001]). In GEOS-Chem v9-01-02 we have imposed a dry deposition velocity of 0.03 cm/s for all aerosols over snow and ice surfaces.

This update affects the following aerosol tracers: SO4s, NITs, DST1, DST2, DST3, DST4, SALA, SALC.

--Jenny Fisher 11:08, 20 January 2011 (EST)
--Bob Y. 10:26, 16 August 2011 (EDT)

Removal of CMN_DEP_mod.F

This update was validated with 1-month benchmark simulation v9-02d and approved on 19 Dec 2012.

As described in this wiki post, we have removed the module file Headers/CMN_DEP_mod.F from GEOS-Chem. The dry deposition arrays that were contained in this module are now carried by the the Meteorology State object (aka State_Met).

--Bob Y. 11:40, 4 March 2013 (EST)

Application of dry deposition with mixing_mod.F90

This discussion has been moved to a section above.

--Bob Yantosca (talk) 18:42, 17 February 2016 (UTC)

References

  1. Alexander, B., R.J. Park, D.J. Jacob, Q.B. Li, R.M. Yantosca, J. Savarino, C.C.W. Lee, and M.H. Thiemens, Sulfate formation in sea-salt aerosols: Constraints from oxygen isotopes, J. Geophys. Res., 110, D10307, 2005. PDF
  2. Baldocchi, D.D., B.B. Hicks, and P. Camara, A canopy stomatal resistance model for gaseous deposition to vegetated surfaces, Atmos. Environ. 21, 91-101, 1987.
  3. Brutsaert, W., Evaporation into the Atmosphere, Reidel, 1982.
  4. Businger, J.A., et al., Flux-profile relationships in the atmospheric surface layer, J. Atmos. Sci., 28, 181-189, 1971.
  5. Bey I., D. J. Jacob, R. M. Yantosca, J. A. Logan, B. Field, A. M. Fiore, Q. Li, H. Liu, L. J. Mickley, and M. Schultz, Global modeling of tropospheric chemistry with assimilated meteorology: Model description and evaluation, J. Geophys. Res., 106, 23,073-23,096, 2001. PDF
  6. Corbitt, E. S., How does the current implementation of dry deposition work in GEOS-Chem?, Graduate Student Forum Talk, 20 Oct 2011. PDF
  7. Duan, B., Fairall, C.W., and Thomson, D.W., Eddy correlation measurements of the dry deposition of particles in wintertime, J. Appl. Met., 27, 642-652, 1988.
  8. Dwight, H.B., Tables of integrals and other mathematical data, MacMillan, 1957.
  9. Erisman, J.W, and A.V. Pul, Parameterization of surface resistance for the quantification of atmospheric deposition of acidifying pollutants and ozone, Atmos. Environ, 28, 2595-2607, 1994.
  10. Eugster, W. and R. Hesterberg, Transfer resistances of NO2 determined from eddy correlation flux measurements over a litter meadow at a rural site on the Swiss plateau, Atmos. Environ, 30, 1247-1254, 1996.
  11. Gao, W. and M.L. Wesely, Modeling gaseous dry deposition over regional scales with satellite observations, 1. Model development, Atmos. Environ, '29, 727-737, 1995.
  12. Gerber, H. E. (1985), Relative-humidity parameterization of the Navy aerosol model (NAM), NRL Rep. 8956, Natl. Res. Lab., Washington, D. C., 1985.
  13. Guenther, A., et al, A global model of natural volatile organic compound emissions, J. Geophys. Res., 100, 8873-8892, 1995.
  14. Hicks, B.B., and P.S. Liss, Transfer of SO2 and other reactive gases across the air-sea interface, Tellus, 28, 348-354, 1976.
  15. Ibrahim, M., Barrie, L.A., and Fanaki, F., An experimental and theoretical investigation of the dry deposition of particles to snow, pine trees, and artificial collectors, Atmos. Environ., 17, 781-788, 1983.
  16. Jacob, D.J., and S.C. Wofsy, Budgets of reactive nitrogen, hydrocarbons, and ozone over the Amazon forest during the wet season, J. Geophys. Res., 95, 16737-16754, 1990.
  17. Jacob, D.J., et al, Deposition of ozone to tundra, J. Geophys. Res., 97, 16473-16479, 1992.
  18. Jacob, D.J, et al, Summertime photochemistry of the troposphere at high northern latitudes, J. Geophys. Res., 98, 14,797-14,816, 1993.
  19. Kramm, G. R. Dlugi, G.J. Dollard, T. Foken, N. Moelders, H. Mueller, W. Seiler, and H. Sievering, On the dry deposition of ozone and reactive nitrogen species, Atmos. Environ, 29, 3208-3231, 1995.
  20. Levine, I.N., Physical Chemistry, 3rd ed., McGraw-Hill, New York, 1988.
  21. Mueller, J-F, and G. Brasseur, IMAGES, A three-dimensional chemical transport model of the global troposphere, J. Geophys. Res., 100, 16,445-16,490, 1995.
  22. Munger, J.W., et al, Atmospheric deposition of reactive nitrogen oxides and ozone in a temperate deciduous forest and a sub-arctic woodland, J. Geophys. Res., in press, 1996.
  23. Nilsson, E.D. and Rannik, U. Turbulent aerosol fluxes over the Arctic Ocean: 1. Dry deposition over sea and pack ice, J. Geophys. Res, 106, 32,125-32,137, 2001.
  24. Price, H., L. Jaeglé, A. Rice, P. Quay, P.C. Novelli, R. Gammon, Global Budget of Molecular Hydrogen and its Deuterium Content: Constraints from Ground Station, Cruise, and Aircraft Observations, submitted to J. Geophys. Res., 2007
  25. Pye, H. O. T., H. Liao, S. Wu, L. J. Mickley, D. J. Jacob, D. K. Henze, and J. H. Seinfeld (2009), Effect of changes in climate and emissions on future sulfate-nitrate-ammonium aerosol levels in the United States, J. Geophys. Res., 114(D1), D01205, doi:10.1029/2008JD010701.
  26. Walcek, C.J., R.A. Brost, J.S. Chang, and M.L.Wesely, SO2, sulfate, and HNO3 deposition velocities computed using regional landuse and meteorological data, Atmos. Environ., 20, 949-964, 1986.
  27. Wang, Y., D.J. Jacob, and J.A. Logan, Global simulation of tropospheric O3-NOx-hydrocarbon chemistry, 1. Model formulation, J. Geophys. Res., 103, D9,10,713-10,726, 1998. PDF
  28. Wesely, M.L, Improved parameterizations for surface resistance to gaseous dry deposition in regional-scale numerical models, Environmental Protection Agency Report EPA/600/3-88/025, Research Triangle Park (NC), 1988.
  29. Wesely, M. L., Parameterization of surface resistance to gaseous dry deposition in regional-scale numerical models, Atmos. Environ., 23, 1293-1304, 1989.
  30. Wesely, M.L, and B.B. Hicks, Some factors that affect the deposition rates of sulfur dioxide and similar gases on vegetation, J. Air. Pollut. Control Assoc., 27, 1110-1116, 1977.
  31. Zhang, L. M., S. L. Gong, J. Padro, and L. Barrie (2001), A size-segregated particle dry deposition scheme for an atmospheric aerosol module, Atmos. Environ., 35(3), 549-560, doi:10.1016/s1352-2310(00)00326-5.

--Bob Y. 15:24, 19 February 2010 (EST)

Previous issues that have now been resolved

Bug in computation of aerodynamic resistance RA

This fix was included in v11-02a and approved on 12 May 2017.

Brian Boys wrote:

In module GeosCore/drydep_mod.F, I discovered a bug in the subroutine DEPVEL. For the calculation of aerodynamic resistance RA under very stable atmospheric conditions (line 1811), the integration of the stability function phi_h (aka dimensionless vertical temperature gradient) from the roughness length to grid box center doesn't take into account the discontinuity occurring at z/L = 1 where phi_h switches from 1 + 5(z/L) to 5 + z/L (Holtslag, 1993). The result is too high of a value for the integral of phi_h and subsequently RA.

A straightforward solution is to calculate RA under stable conditions (L>0) using an integral form of the stability function, such as equation (12) of Holtslag, 1988. I implemented these changes in drydep_mod.F (from GCv 10-01, public release). To see the effect of the bug, namely a discontinuity in RA, refer to Figure 1, which plots RA as a function of stability (1/L).

Depvel figure 1.png

I've also attached two scatter plots comparing outputted RA (GCv10-01, geosfp, 2x2.5, 2012/11/01) from the base model and an updated simulation employing the bug-fix as described above--please refer to Figure 2 (linear comparison):

Depvel figure 2.png

and Figure 3 (logarithmic comparison):

Depvel figure 3.png

--Bob Yantosca (talk) 18:23, 17 February 2017 (UTC)

Dependency between dry deposition and soil NOx emissions

This issue has been resolved in the new soil NOx algorithm that was added to GEOS-Chem v9-02. The new module GeosCore/canopy_nox_mod.F computes the NOx from the canopy independently of the dry deposition module. We shall leave this post here for reference.

The canopy reduction algorithm (originally done in GeosCore/canopy_nox_mod.F) has been moved to the HEMCO soil NOx extension module (HEMCO/Extensions/hcox_soilnox_mod.F90). Module GeosCore/canopy_nox_mod.F was removed from GEOS-Chem v10-01 and higher versions.

In GEOS-Chem there is a code dependency between the dry deposition routines soil NOx emissions routines. This is purely historical baggage that goes back to the days of the old 9-layer Harvard-GISS CTM (from which these routines were taken).

The dry deposition routine DEPVEL (in drydep_mod.f) computes a quantity called CANOPYNOX, which is the bulk surface resistance of the canopy to NOx deposition. This is computed in the following lines of code:

C** Get the bulk surface resistance of the canopy, RSURFC, from the network
C** of resistances in parallel and in series (Fig. 1 of Wesely [1989])
               DTMP1=1.D0/RIXX
               DTMP2=1.D0/RLUXX
               DTMP3=1.D0/(RAC(LDT)+RGSX)
               DTMP4=1.D0/(RDC+RCLX)
               RSURFC(K,LDT) = 1.D0/(DTMP1 + DTMP2 + DTMP3 + DTMP4)
C  Save the within canopy depvel of NOx, used in calculating the 
C  canopy reduction factor for soil emissions.
               ! Remove hardwire for CANOPYNOX (bmy, 1/24/03)
               IF ( K == DRYDNO2 ) THEN
                  CANOPYNOX(IJLOOP,LDT)=DTMP1+DTMP2+DTMP3+DTMP4
               ENDIF

However, the CANOPYNOX variable is not defined within drydep_mod.f, but is found instead within the soil NOx emissions code header file commsoil.h:

     REAL*8 CANOPYNOX(MAXIJ,NTYPE) !track NOx within canopy dry dep.

and is then also used within the soil NOx emissions function SOILCRF, as follows:

     IF ((XLAI(IREF,JREF,K).GT.0.D0).AND.
    &    (CANOPYNOX(IJLOOP,K).GT.0.D0))THEN

        VFNEW=VFNEW*SQRT(WINDSQR/9.D0*7.D0/XLAI(IREF,JREF,K))*
    *        (SOILEXC(2)/SOILEXC(NN))
        SOILCRF=CANOPYNOX(IJLOOP,K)/(CANOPYNOX(IJLOOP,K)
    *        +VFNEW)
     ELSE
    
        SOILCRF=0.D0
     END IF

This is not necessarily a problem as long as dry deposition is always turned on whenever you are doing a full-chemistry simulation that requires soil NOx emissions. In the driver routine main.f, dry deposition is always done before emissions. However, this is bad coding style and a potential source of error. (This also must be corrected for the GEOS-Chem column code, in which all inputs must come thru the argument list.)

In the new soil NOx emissions code being developed by Rynda Hudman (much of which is based on the GEOS-Chem column code being developed by Bob Yantosca and Philippe Le Sager), there is a new module called canopy_nox_mod.f. This module computes the CANOPYNOX quantity independently of routine DEPVEL in drydep_mod.f, which allows for a totally clean separation between dry deposition routines and emissions routines.

At present, the new canopy_nox_mod.f is not available in the standard mainline GEOS-Chem code. It is slated to be incorporated with the soil NOx emissions update.

--Bob Y. 13:51, 18 February 2010 (EST)

Add extra variables to PRIVATE declaration in parallel loop

This fix was validated by 1-month benchmark simulation GEOS-Chem v9-02p (approved 13 Sep 2013).

We have explicitly added variable IW to the !$OMP+PRIVATE list in routine DEPVEL in GeosCore/drydep_mod.F. This should already be held private because it is a loop index, but it doesn't hurt to add it to the list.

We also have added ZO as a PRIVATE variable when compiling with GCAP meteorology.

Old code:
!$OMP+PRIVATE( DTMP1,  DTMP2,  DTMP3,  DTMP4,  VDS,    CZH    )
!$OMP+PRIVATE( CKUSTR, REYNO,  CORR1,  CORR2,  Z0OBK,  RA     )
!$OMP+PRIVATE( DUMMY1, DUMMY2, DUMMY3, DUMMY4, DAIR,   RB     )
!$OMP+PRIVATE( C1X,    VK,     I,      J                      )

New code:
!$OMP+PRIVATE( DTMP1,  DTMP2,  DTMP3,  DTMP4,  VDS,    CZH    )
!$OMP+PRIVATE( CKUSTR, REYNO,  CORR1,  CORR2,  Z0OBK,  RA     )
!$OMP+PRIVATE( DUMMY1, DUMMY2, DUMMY3, DUMMY4, DAIR,   RB     )
!$OMP+PRIVATE( C1X,    VK,     I,      J,      IW             )
#if defined( GCAP )
!$OMP+PRIVATE( ZO                                             )
#endif

--Bob Y. 12:04, 12 September 2013 (EDT)

Parallelization error in routine METERO

This update was tested in the 1-month benchmark simulation v9-02r and approved on 14 Nov 2013. This update is included in Adjoint v35j.

We discovered a minor bug in the parallel DO loop of routine METERO (in module GeosCore/drydep_mod.F):

      ! Loop over surface grid boxes
!$OMP PARALLEL DO
!$OMP+DEFAULT( SHARED )
!$OMP+PRIVATE( I, J, IJLOOP, THIK )
      DO J = 1, JJPAR
      DO I = 1, IIPAR

         ! 1-D grid box index
         IJLOOP         = ( (J-1) * IIPAR ) + I

         ! THIK = thickness of layer 1 [m]
         THIK           = State_Met%BXHEIGHT(I,J,1)

         ! Midpoint height of first model level [m]
         CZ1(IJLOOP)    = THIK / 2.0d0

         ! Local surface pressure [hPa] (mpayer, 1/10/12)
         SP             = GET_PEDGE(I,J,1)

         ! Convert from hPa to Pa for SFCPRESS
         PRESSU(IJLOOP) = SP * 1.d2

The SP variable (which is surface pressure) had not been held PRIVATE in the above parallel loop. This caused slightly different surface pressure values to be saved into the PRESSU array. Later on in the code, PRESSU is passed as an argument to function DIFFG, which computes the computes the molecular diffusivity of each drydep species. This in turn affects the value of the drydep velocity of each species. Therefore, as a result of this error, we would observe small numerical differences in the results of GEOS-Chem simulations when using OpenMP parallelization versus when OpenMP parallelization was turned off.

The fix is to add SP to the PRIVATE list:

       ! Loop over surface grid boxes
 !$OMP PARALLEL DO
 !$OMP+DEFAULT( SHARED )
 !$OMP+PRIVATE( I, J, IJLOOP, THIK, SP )

which then ensures that we obtain identical results whether or not OpenMP parallelization is turned on.

--Bob Y. 15:25, 14 November 2013 (EST)

Remove obsolete ISN2 drydep species

This update was validated with the 1-month benchmark simulation v10-01i and approved on Approved 01 May 2015.

Katherine Travis wrote:

In dry deposition, we still have a dry dep option for ISN2. ISN2 was the nighttime isoprene nitrate in old versions of the chemistry, and ISN1 was the second generation product from this species. But now, we call ISN1 the isoprene nitrate species. So, we should replace IDTISN2 in dry dep and tracerid_mod with IDTISN1. That fix is also in the above directory.

In GeosCore/drydep_mod.F, we replaced these lines of code:

        ! ISN2 (uses same dep vel as HNO3)
        ELSE IF ( N == IDTISN2 ) THEN
           . . .
           NTRAIND(NUMDEP) = IDTISN2
           . . .
           DEPNAME(NUMDEP) = 'ISN2'

with these:

        ! ISN1 (uses same dep vel as HNO3)
        ! This should be ISN1, krt (3/31/15)
        ELSE IF ( N == IDTISN1 ) THEN
           . . .
           NTRAIND(NUMDEP) = IDTISN1
           . . .
           DEPNAME(NUMDEP) = 'ISN1'

and in GeosCore/tracerid_mod.F, we replaced these lines of code:

     INTEGER            :: IDISN2,  IDR4N2,   IDCH2O,  IDC2H6,  IDMP
     . . .
     INTEGER            :: IDTPPN,  IDTISN1,  IDTR4N2, IDTPRPE, IDTC3H8
     . . .
     IF ( NAMEGAS(I) == 'ISN2'   ) IDISN2   = I
     . . .
     IDISN2    = 0

with:

     INTEGER            :: IDISN1,  IDR4N2,   IDCH2O,  IDC2H6,  IDMP
     . . .
     INTEGER            :: IDTPPN,  IDTISN1,  IDTR4N2, IDTPRPE, IDTC3H8     
     . . .
     IF ( NAMEGAS(I) == 'ISN1'   ) IDISN1   = I
     . . .
     IDISN1    = 0

--Bob Y. 16:51, 1 April 2015 (EDT)

Fix for NO3 + ISOP product

This update was included in v11-02c and approved on 21 Sep 2017.

Katie Travis wrote:

The nitrate isoprene nitrate is now called ISN1. It must be added to GEOS-Chem as a transported tracer to undergo dry deposition. We can use the molecular weight given to other isoprene nitrates of 147 g/mol. In addition, the references to ISN2 in drydep_mod.F and planeflight_mod.F (where the ANs are added up) should be changed to ISN1.

NOTE: We will add this fix after FlexChem is integrated into GEOS-Chem. Because FlexChem will completly remove SMVGEAR from GEOS-Chem, we shall add this fix into the KPP master equation file (instead of the SMVGEAR globchem.dat file).

--Melissa Sulprizio (talk) 18:21, 17 June 2015 (UTC)
--Bob Yantosca (talk) 22:17, 8 February 2016 (UTC)

Unresolved issues

None that we are aware of at this time.