Difference between revisions of "Physical properties of GEOS-Chem species"

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<span style="color:red"><big><strong>This Guide has not been updated since [[GEOS-Chem 12#12.8.0|GEOS-Chem 12.8.0]].  [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/species-guide.html Species properties] for newer GEOS-Chem versions are now contained in the <tt>species_database.yml</tt> run-directory configuration file.</strong></big></span>
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__FORCETOC__
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'''''[[Species in GEOS-Chem|Previous]] | [[GEOS-Chem species database|Next]] | [[Guide to species in GEOS-Chem]]'''''
 +
 +
#[[Species in GEOS-Chem]]
 +
#<span style="color:blue">'''Physical properties of GEOS-Chem species'''</span>
 +
#[[GEOS-Chem species database]]
 +
#[[GEOS-Chem species units]]
 +
#[[Adding passive species to GEOS-Chem]]
 +
#[[Species indexing in GEOS-Chem]]
 +
<br>
 +
----
 +
<big><strong>For the most up-to-date information, please see the [https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/species-guide.html ''View GEOS-Chem Species Properties'' chapter of <tt>geos-chem.readthedocs.io</tt>]</strong></big>
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<br>
 
== Overview ==
 
== Overview ==
  
The [[GEOS-Chem Support Team]] is creating a [[GEOS-Chem species database|common data structure (aka the "GEOS-Chem species database")]] that will store all of the various physical properties for GEOS-Chem species.  Currently, these properties are defined (and sometimes redefined) in several locations in the code.
+
The [[GEOS-Chem Support Team]] has created a [[GEOS-Chem species database|common data structure (aka the "GEOS-Chem species database")]] that stores all of the various physical properties for GEOS-Chem species.  Formerly, these properties were defined (and sometimes redefined) in several locations in the code.
  
 
For example, the effective Henry's law value <tt>H<sub>eff</sub></tt> is calculated differently in the wet deposition module than in the dry deposition module.  The GEOS-Chem wet deposition module assumes a pH value of 4.5 for rainwater, and thus uses a set of Henry’s law constants that are appropriate for this pH.  On the other hand, the GEOS-Chem dry deposition module assumes a pH of 7 for water, and therefore uses a different set of Henry’s law constants.  Keeping two independent sets of Henry’s law constants can lead to confusion.
 
For example, the effective Henry's law value <tt>H<sub>eff</sub></tt> is calculated differently in the wet deposition module than in the dry deposition module.  The GEOS-Chem wet deposition module assumes a pH value of 4.5 for rainwater, and thus uses a set of Henry’s law constants that are appropriate for this pH.  On the other hand, the GEOS-Chem dry deposition module assumes a pH of 7 for water, and therefore uses a different set of Henry’s law constants.  Keeping two independent sets of Henry’s law constants can lead to confusion.
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In the [[GEOS-Chem v10-01]], Christoph Keller implemented a new GEOS-Chem module that can compute Heff for each species as a function of pH and the species-specific Henry’s law constants <tt>K0</tt>, <tt>CR</tt>, and <tt>pKA</tt>.  These Henry’s law constants can be obtained from the literature (cf. Sander, <u>Atmos. Chem. Phys</u>. '''15''', 4399-4381, 2015, [http://henrys-law.org download from this site], or similar references).  We would like to use Christoph’s new module to compute Heff in a consistent way everywhere in GEOS-Chem.
 
In the [[GEOS-Chem v10-01]], Christoph Keller implemented a new GEOS-Chem module that can compute Heff for each species as a function of pH and the species-specific Henry’s law constants <tt>K0</tt>, <tt>CR</tt>, and <tt>pKA</tt>.  These Henry’s law constants can be obtained from the literature (cf. Sander, <u>Atmos. Chem. Phys</u>. '''15''', 4399-4381, 2015, [http://henrys-law.org download from this site], or similar references).  We would like to use Christoph’s new module to compute Heff in a consistent way everywhere in GEOS-Chem.
  
We would also like to store these Henry's law constants together with other relevant physical parameters such as molecular weight, density, aerosol radius, reactivity factor for drydep (F0), etc. for each species.  Keeping all of these physical properties in a single data structure will streamline the code and help to reduce confusion.
+
We now store these Henry's law constants together with other relevant physical parameters such as molecular weight, density, aerosol radius, reactivity factor for drydep (F0), etc. for each species.  Keeping all of these physical properties in a single data structure will streamline the code and help to reduce confusion.
  
We have already started on this effort.  Phase 1 of the [[GEOS-Chem species database]] has already been incorporated into [[GEOS-Chem v11-01#v11-0d|GEOS-Chem v11-01d]].  Further phases (i.e. the adoption of different physical constants with respect to the previous code) will take place in [[GEOS-Chem v11-01e#v11-01e|GEOS-Chem v11-01e]] and later versions.  
+
Phase 1 of the [[GEOS-Chem species database]] was completed in [[GEOS-Chem v11-01#v11-0d|GEOS-Chem v11-01d]].  Phase 2 was completed in [[GEOS-Chem v11-01#v11-01e|GEOS-Chem v11-01e]].  Further work is slated for [[GEOS-Chem v11-02]].
  
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 21:51, 6 November 2015 (UTC)
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:33, 30 November 2016 (UTC)
  
 
== Henry's law ==
 
== Henry's law ==
  
=== Definition of Henry's law constants ===
+
Please see [[GEOS-Chem species: Henry's law metadata|our ''GEOS-Chem species: Henry's law metadata'' wiki page]] for the latest information about Henry's law constants in GEOS-Chem.
 
+
The table lists the Henry's law constants for each species as defined in the dry deposition and wet deposition modules in [[GEOS-Chem v11-01]] and prior versions.  These constants are:
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-bgcolor="#CCCCCC"
+
 
+
|-valign="top" bgcolor="#CCCCCC"
+
!width="100px"|Constant
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!width="75px"|Units
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!width="600px"|Description
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!width="200px"|Also known as
+
 
+
|-valign="top"
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|<tt>Hstar</tt>
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|M atm<sup>-1</sup>
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|This is the Henry's law solubility constant (for T = 298.15 K and pH = 7) that is used in the dry deposition module <tt>drydep_mod.F.</tt>
+
|
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*<tt>H<sup>cp</sup></tt>
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*<tt>Kstar298</tt>
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|-valign="top"
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|<tt>K0</tt>
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|M atm<sup>-1</sup>
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|This is the Henry's law solubility constant (for T = 298.15 K and pH = 4.5) that is currently used in the GEOS-Chem wet deposition module <tt>wetscav_mod.F</tt>.
+
|
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*<tt>H<sup>cp</sup></tt>
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*<tt>Kstar298</tt>
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+
|-valign="top"
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|<tt>CR</tt>
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|K
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|This is the Henry's law volatility constant that is currently used in the GEOS-Chem wet deposition module <tt>wetscav_mod.F</tt>.
+
|
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*<tt>H_298R</tt>
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*<tt>d(ln H<sup>cp</sup>) / d(1/T)</tt>
+
 
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|-valign="top"
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|<tt>pKa</tt>
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|1
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|Henry's law correction factor for pH.  This is used by the new <tt>CALC_KH</tt> and <tt>CALC_HEFF</tt> routines from <tt>henry_mod.F</tt>.
+
|
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 16:25, 6 October 2015 (UTC)
+
 
+
=== Henry's law constants used in GEOS-Chem ===
+
 
+
Note that because the GEOS-Chem dry deposition module (<tt>drydep_mod.F</tt>) and the wet deposition module (<tt>wetscav_mod.F</tt>) were developed (and modified) independently of each other, the Henry's law solubility constants often do not match.  This is mostly historical baggage.  We hope that this update to GEOS_Chem will ensure that dry deposition and wet deposition use the same Henry's law constants.
+
 
+
For dry deposition, we assume a pH value of 7.  For wet deposition, we assume a pH value of 4.5.
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-bgcolor="#CCCCCC"
+
!width="100px"|Species
+
!width="100px"|Hstar<br>[M atm<sup>-1</sup>]
+
!width="100px"|K0<br>[M atm<sup>-1</sup>]
+
!width="100px"|CR<br>[K]
+
!width="600px"|References
+
 
+
|-valign="top"
+
|ACET ||1.00e+05 ||2.70e+01 ||5300 ||
+
*HSTAR: Original value from drydep_mod.F
+
*NOTE: ACET now wet deposits in [[GEOS-Chem v11-01#v11-01d|GEOS-Chem v11-01d]]
+
 
+
|-valign="top"
+
|ALD2 ||1.10e+01 ||1.10e+01 ||6300 ||
+
*Bettermann & Hoffmann 1988
+
*NOTE: ALD2 now wet deposits in [[GEOS-Chem v11-01#v11-01d|GEOS-Chem v11-01d]]
+
 
+
|-valign="top"
+
|ASOG1<br>ASOG2<br>ASOG3 ||1.00e+5 ||1.00e+5 ||6039 ||
+
*Havala Pye
+
 
+
|-valign="top"
+
|Br2 ||7.6e-01 ||7.6e-01 ||3720 ||
+
*Yang et al 2005, Table 2 (assuming T = 298 K)
+
 
+
|-valign="top"
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|BrNO3 ||1.00e+20 || || ||
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*Assume an infinite value of HSTAR (cf. Sander)
+
 
+
|-valign="top"
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|CH2O ||6.00e+03 ||3.00e+03 ||7200 ||
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*[http://acmg.seas.harvard.edu/geos/wiki_docs/deposition/wetdep.jacob_etal_2000.pdf Jacob et al 2000], Table 1
+
 
+
|-valign="top"
+
|DMS || ||4.80e-01 ||3100 ||
+
 
+
|-valign="top"
+
|EOH ||1.90e+02 ||1.90e+02 ||6600 ||
+
*Snyder & Dawson (1985)
+
*NOTE: EOH added in [[GEOS-Chem v11-01#v11-01d]]
+
 
+
|-valign="top"
+
|GLYC ||4.10e+04 ||4.10e+04 ||4600 ||
+
*Betterton & Hoffman 1988
+
 
+
|-valign="top"
+
|GLYX ||3.6e+05 ||3.6e+05 ||7200 ||
+
*Betterton & Hoffman 1988
+
 
+
|-valign="top"
+
|H2O2 ||1.00e+05 ||8.30e+04 ||7400 ||
+
*HSTAR: This was the value that was originally in <tt>drydep_mod.F</tt>
+
*K0, CR: cf [http://acmg.seas.harvard.edu/geos/wiki_docs/deposition/wetdep.jacob_etal_2000.pdf Jacob et al 2000], Table 1
+
 
+
|-valign="top"
+
|HAC ||2.90e+03 ||2.93e+03 ||0 ||
+
*Spaulding et al 2002
+
 
+
|-valign="top"
+
|HBr ||7.10e+15 ||7.10e+13 ||10200 ||
+
*Set HSTAR to 7.1e+15, consistent with p-TOMCAT (cf. Dean 1992).  Assumes a pH of 7 for the plant stomata.
+
*K0 and CR are estimated by Yang et al 2005.
+
*HBr has a large effective Henry's Law Constant, similar to HCl and HNO3, which have retention fractions (RFs) of 1 for wet deposition. RFs have not been measured for HBr; however, Stuart and Jacobson [2003] suggest that species with large Hstar's should have RF's of about 1.
+
 
+
|-valign="top"
+
|HCl ||2.05e+06 ||7.10e+15 ||11000 ||
+
*HSTAR: Seb Eastham (17 Apr 2013)
+
*K0, CR: Yang et al 2005
+
 
+
|-valign="top"
+
|Hg2 ||1.00e+14 ||1.40e+06 ||8400 ||
+
*K0, CR: Lindqvist & Rhode 1985
+
*HSTAR: Set to 1e+14 by Helen Amos (23 Sep 2011)
+
 
+
|-valign="top"
+
|HNO3 ||1.0e+14 || || ||
+
*Original value from <tt>drydep_mod.F</tt>
+
 
+
|-valign="top"
+
|HOBr ||6.10e+03 ||6.10e+03 || 6014 ||
+
*Set HSTAR and H<sup>cp</sup> = 6.10e+3, which is consistent with p-TOMCAT (cf. Freznel et al 1998)
+
*McGrath and Rowland, 1994 says dH_sol for HOBr = - 50 kJ/mol (- 12 kcal/mol)
+
*Acid dissociation constant in Heff is small (1.5e-9), reported by Haag and Holne [1983]
+
 
+
|-valign="top"
+
|IEPOX ||1.e3+08 ||1.3e+08 ||0 ||
+
*F. Paulot??
+
 
+
|-valign="top"
+
|ISOG1<br>ISOG1<br>ISOG3 ||1.00e+05 ||1.00e+05 ||6039 ||
+
*Havala Pye
+
 
+
|-valign="top"
+
|ISOPN ||1.7e+04 ||1.7e+04 ||9200 ||
+
*NOTE: ISOPN dry deposits as ISOPND and ISOPNB
+
*HSTAR, K0, CR taken from Ito 2007
+
 
+
|-valign="top"
+
|LIMO ||7.00e-02 ||7.00e-02 ||0 ||
+
*??, maybe Havala Pye
+
 
+
|-valign="top"
+
|MACR ||6.50e+00 || || ||
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*R. Sander (year not specified, probably 1999)
+
 
+
|-valign="top"
+
|MAP ||8.4e+02 ||8.4e+02 ||5300 ||
+
*R. Sander (year not specified, probably 1999)
+
 
+
|-valign="top"
+
|MGLY ||8.4e+02 ||8.4e+02 ||5300 ||
+
*Betterton & Hoffmann 1988
+
 
+
|-valign="top"
+
|MOBA || ||2.30e+04 ||6300 ||
+
*Based on methacrylic acid with acetic acid T dependence (Fabien Paulot)
+
*pKa = 4.1, pH =5
+
 
+
|-valign="top"
+
|MMN ||1.7e+04 ||1.7e+04 ||9200 ||
+
*MMN dry deposits as MACRN + MVKN
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*Ito 2007
+
 
+
|-valign="top"
+
|MP<br>(aka CH3OOH) ||0.0e+00 || 3.10e+2 ||5200 ||
+
*[http://acmg.seas.harvard.edu/geos/wiki_docs/deposition/wetdep.jacob_etal_2000.pdf Jacob et al 2000], Table 1
+
 
+
|-valign="top"
+
|MTPA ||4.90e+02 ||4.90e+02 ||0 ||
+
*Use K0 = 0.049 for all pinene (Sander 1999)
+
 
+
|-valign="top"
+
|MTPO ||4.90e+02 ||4.90e+02 ||0 ||
+
*Use K0 = 0.049 for all pinene (Sander 1999)
+
 
+
|-valign="top"
+
|MVK ||4.40e+01 || || ||
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*R. Sander (year not specified, probably 1999)
+
 
+
|-valign="top"
+
|N2O5 ||0.0e+00 || || ||
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*N2O2 uses the same drydep velocity as HNO3, so set HSTAR = 0
+
 
+
|-valign="top"
+
|NH3 ||2.00e+04 ||3.30e+06 ||4100 ||
+
*?
+
+
|-valign="top"
+
|NO2 ||1.00e-02 || || ||
+
*? (original value from drydep_mod.F)
+
 
+
|-valign="top"
+
|O3  ||1.00e-02 || || ||
+
*? (original value from drydep_mod.F)
+
 
+
|-valign="top"
+
|OPOG1<br>OPOG2 ||1.00e+05 ||1.00e+05 ||6039 ||
+
*Havala Pye
+
 
+
|-valign="top"
+
|PAN ||3.60e+00 || || ||
+
*? (original value from drydep_mod.F)
+
 
+
|-valign="top"
+
|PMN ||0.00+00 || || ||
+
*PMN uses the same drydep velocity as PAN, so set HSTAR = 0
+
 
+
|-valign="top"
+
|POG1<br>POG2 ||9.5e+00 ||9.5e+00 ||4700 ||
+
*Based on phenanthrene (cf Sander 1999)
+
*NOTE: Make POG hydrophobic (cf Havala Pye)
+
 
+
|-valign="top"
+
|POPG (PHE) ||2.35e+01 ||2.35e+01 ||47 ||
+
*HSTAR and K0: Ma et al 2010 (<u>J. Chem Eng. Data</u>)
+
*CR: Scharzenbach 2003, p. 200
+
*NOTE: In the code HSTAR & K0 are computed as ( 1.0 / 1.74e-03 ) * 0.0409 = 23.505
+
 
+
|-valign="top"
+
|POPG (PYR) ||7.61e+01 ||7.61e+01 ||43 ||
+
*HSTAR and K0: Ma et al 2010 (<u>J. Chem Eng. Data</u>)
+
*CR: Scharzenbach 2003, p. 200
+
*NOTE: In the code HSTAR & K0 are computed as ( 1.0 / 5.37e-04 ) * 0.0409 = 76.163
+
 
+
|-valign="top"
+
|POPG (BaP) ||1.23e+03 ||1.23e+03 ||43 ||
+
*HSTAR and K0: Ma et al 2010 (<u>J. Chem Eng. Data</u>)
+
*CR: Scharzenbach 2003, p. 200
+
*NOTE: In the code HSTAR & K0 are computed as ( 1.0 / 3.10e-05 ) * 0.0409 = 1319.354
+
 
+
|-valign="top"
+
|PPN ||0.00+00 || || ||
+
*PPN uses the same drydep velocity as PAN, so set HSTAR = 0
+
 
+
|-valign="top"
+
|PROPNN ||1.0e+03 ||1.0e+03 || 0 ||
+
*Nitrooxyacetone in Sander 1999
+
 
+
|-valign="top"
+
|R4N2 ||0.00+00 || || ||R4N2
+
*Uses same dry deposition velocity as PAN, so set HSTAR = 0
+
 
+
|-valign="top"
+
|RIP  ||1.7e+06 ||1.7e+06 ||0 ||
+
*US EPA 2011
+
 
+
|-valign="top"
+
|SO2 ||1.00e+05 || || ||
+
*?
+
 
+
|-valign="top"
+
|TSOG0<br>TSOG1<br>TSOG2<br>TSOG3 ||1.00e+05 ||1.00e+05 ||6039 ||
+
*Havala Pye
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 18:52, 6 October 2015 (UTC)
+
 
+
=== Proposed list of Henry's law constants from the literature ===
+
 
+
[[User:Katherine Travis|Katie Travis]] has put together a proposed list of updates to the Henry's law constants for GEOS-Chem species.  As of this writing (August 28, 2015), these updates have not yet been implemented into GEOS-Chem, but will be soon (pending approval from the Oxidants and Chemistry Working Group).  The updated constants were mostly taken from the [http://www.atmos-chem-phys.net/15/4399/2015/acp-15-4399-2015.pdf Sander, 2015] compilation, and corresponding references.
+
 
+
:;Proposed <tt>K0</tt> [mol m<sup>-3</sup> Pa<sup>-1</sup>]: Proposed new value for the Henry's law solubility constant (for T = 298.15 K).
+
::*<span style="color:red">'''NOTE: Sander 2015 now lists K0 in units of mol m<sup>-3</sup> Pa<sup>-1</sup>.'''</span>
+
::*<span style="color:red">'''To compare this to the K0 values currently used in GEOS-Chem, you must use this conversion factor: 1 M atm<sup>-1</sup> = 9.86923 x 10<sup>-3</sup> mol m<sup>-3</sup> Pa<sup>-1</sup>'''</span>
+
:;Proposed CR [K]: Proposed new value for the Henry's law volatility constant.
+
:;Proposed pKa: Proposed new pH Correction factor.
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-bgcolor="#CCCCCC"
+
!width="100px"|Species
+
!width="100px"|Proposed K0<br>[mol m<sup>-3</sup> Pa<sup>-1</sup>]
+
!width="100px"|Proposed CR<br>[K]
+
!width="225px"|Reference
+
!width="175px"|Notes
+
!width="50px"|Proposed pKa<br>[1]
+
!width="225px"|Reference
+
 
+
|-valign="top"
+
|NO ||1.90E-05 ||1600 ||Warneck and Williams [2012] || || ||
+
 
+
|-valign="top"
+
|O3 ||1.10E-04 ||2800 ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|PAN ||2.90E+02 ||5700 ||Warneck and Williams [2012] || || ||
+
 
+
|-valign="top"
+
|CO ||9.70E-06 ||1300 ||Warneck and Williams [2012] || || ||
+
 
+
|-valign="top"
+
|ALK4 ||1.20E-05 ||3100 ||Sander et al [2011] ||As butane || ||
+
 
+
|-valign="top"
+
|ISOP ||3.40E-04 ||4400 ||Leng et al [2013] || || ||
+
 
+
|-valign="top"
+
|HNO3 ||2.10E+03 ||8700 ||Lelieveld and Crutzen [1991] || || ||
+
 
+
|-valign="top"
+
|H2O2 ||4.93E+05 ||6600 ||Nguyen et al [2014] (Table S4); Warneck and Williams [2012]  || ||11.6 ||Anglada et al [2015]
+
 
+
|-valign="top"
+
|ACET ||2.70E-01 ||5500 ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|MEK ||1.80E-01 ||5700 ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|ALD2 ||1.30E-01 ||5900 ||Sander et al [2011] || ||  ||
+
 
+
|-valign="top"
+
|RCHO || 9.50E-02 || 6200 ||Sander et al [2011] ||As butanal || ||
+
 
+
|-valign="top"
+
|MVK ||2.60E-01 ||4800 ||Ji and Evans [2007] || || ||
+
 
+
|-valign="top"
+
|MACR ||4.80E-02 ||4300 ||Ji and Evans [2007] || || ||
+
 
+
|-valign="top"
+
|PMN ||1.70E-02 || ||Kames and Schurath [1995] || || ||
+
 
+
|-valign="top"
+
|PPN ||2.90E-02 || ||Kames and Schurath [1995] || || ||
+
 
+
|-valign="top"
+
|R4N2 ||1.00E-02 ||5800 ||Sander et al [2011] ||as 1-butyl nitrate || ||
+
 
+
|-valign="top"
+
|PRPE ||7.30E-05 ||3400 ||Wilhelm et al [1997] ||as propene || ||
+
 
+
|-valign="top"
+
|C3H8 ||1.50E-05 ||2700 ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|CH2O ||3.20E+01 ||6800 ||Warneck and Williams [2012] || || ||
+
 
+
|-valign="top"
+
|C2H6 ||1.90E+05 ||2400 ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|N2O5 ||2.10E-02 ||3400 ||Fried et al [1994] || || ||
+
 
+
|-valign="top"
+
|HNO4 ||3.90E+01 ||8400 ||Leu and Zhang [1999] || || ||
+
     
+
|-valign="top"
+
|MP ||2.90E+00 ||5200 ||Warneck and Williams [2012] || || ||
+
 
+
|-valign="top"
+
|DMS ||4.80e-01 ||3100 ||De Bruyn et al [1995] || || ||
+
 
+
|-valign="top"
+
|SO2 ||1.30E-02 ||2900 ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|NH3 ||5.90E-01 ||4200 ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|Br2 ||7.20E-03 ||4400 ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|Br ||3.40E-04 ||1800 ||Berdnikov and Bashin [1970] || || ||
+
 
+
|-valign="top"
+
|BrO || || || || || ||
+
 
+
|-valign="top"
+
|HOBr ||1.30E+00 ||4000 ||Sander et al [2011]; Mozurkewich [1995] || || ||
+
 
+
|-valign="top"
+
|HBr ||2.40E-01 ||370 ||Dean [1992] || || ||
+
 
+
|-valign="top"
+
|BrNO2 ||3.00E-03 || || || || ||
+
 
+
|-valign="top"
+
|BrNO3  || || || || || ||
+
 
+
|-valign="top"
+
|CHBr3 ||1.70E-02 ||5200  ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|MPN || || || || || ||
+
 
+
|-valign="top"
+
|ISOPN ||1.97E+04 || ||Nguyen et al  2015 (Table S4) || || ||
+
 
+
|-valign="top"
+
|MOBA ||2.27E+02 ||-6.30E+03 || Need reference from <tt>wetscav_mod.F</tt> || || ||
+
 
+
|-valign="top"
+
|PROPNN ||4.93E+03 || ||Nguyen et al [2014] (Table S4) || || ||
+
 
+
|-valign="top"
+
|HAC ||7.70E+01 || ||Lee and Zhou [1993] || || ||
+
 
+
|-valign="top"
+
|GLYC ||4.10E+02 ||4600 ||Betterton and Hoffman [1988] || || ||
+
 
+
|-valign="top"
+
|MMN ||1.97E+04 || ||Nguyen et al [2014] (Table S4) || || ||
+
 
+
|-valign="top"
+
|RIP ||7.90E+05 ||0  ||Nguyen et al [2014] (Table S4) || || ||
+
 
+
|-valign="top"
+
|IEPOX ||7.60E+05 ||0  ||Nguyen et al [2014] (Table S4) || || ||
+
 
+
|-valign="top"
+
|MAP ||8.3 ||5300 ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|NO2 ||1.20E-04 ||2400 ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|NO3 ||3.80E-04 ||1900 ||Sander et al [2011]; Chameides (1986) || || ||
+
 
+
|-valign="top"
+
|HNO2 ||4.80E-01 ||4800 ||Schwartz and White [1981] || || ||
+
 
+
|-valign="top"
+
|ISN1 ||1.97E+04 || ||Set to MMN/ISOPN  || || ||
+
 
+
|-valign="top"
+
|ETHLN ||1.97E+04 || ||Set to MMN/ISOPN  || || ||
+
 
+
|-valign="top"
+
|MGLY ||3.20E+02 || || Zhou and Mopper [1990] || || ||
+
 
+
|-valign="top"
+
|GLYX ||4.10E+03 ||7500 ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|HCOOH ||8.80E+01 ||6100 ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|ACTA ||4.00E+01 ||6200 ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|DHDN ||1.97E+04 || ||Set to MMN/ISOPN || || ||
+
 
+
|-valign="top"
+
|LIM ||4.80E-04 ||4600 ||Leng et al [2013] || || ||
+
 
+
|-valign="top"
+
|API ||2.90E-04 ||1800 ||Leng et al [2013] || || ||
+
 
+
|-valign="top"
+
|MONIT ||1.68E+02 ||9200 ||Browne et al [2014] || || ||
+
 
+
|-valign="top"
+
|HONIT ||2.65E+11 ||5487 ||Browne et al [2014] || || ||
+
 
+
|-valign="top"
+
|HPALD ||3.95E+02 || ||Nguyen et al [2014] (Table S2) || || ||
+
 
+
|-valign="top"
+
|MNO3 ||2.00E-02 ||4700 ||Sander et al [2011] || || ||
+
 
+
|-valign="top"
+
|Hg2 ||1.40e+04 ||5300 || || || ||
+
 
+
|-valign="top"
+
|POPG (PHE) || || || || || ||
+
 
+
|-valign="top"
+
|POPG (PYR) || || || || || ||
+
 
+
|-valign="top"
+
|POPG (BaP) || || || || || ||
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 19:00, 6 October 2015 (UTC)
+
 
+
=== Computing the effective Henry's law constant ===
+
 
+
[[User:Christoph Keller|Christoph Keller]] has written a module (<tt>GeosUtil/henry_mod.F</tt>) to compute the effective Henry's law constant given the parameters listed above and the pH value.  This module is used in the [[HEMCO|HEMCO emissions component]] in [[GEOS-Chem v10-01]] and higher versions.
+
 
+
This computation requires three steps.
+
 
+
:1. If the value of <tt>K0</tt> for a given species [[#List of constants from the literature|from in the table above]] is in units of mol m<sup>-3</sup> Pa<sup>-1</sup>, then convert this to M atm<sup>-1</sup> by multiplying by 9.86923 x 10<sup>-3</sup>.  The formulae below require <tt>H<sup>cp</sup></tt> in M atm<sup>-1</sup>.
+
 
+
:2. Call routine <tt>CALC_KH</tt> in <tt>GeosUtil/henry_mod.F</tt> to compute the dimensionless liquid over gas Henry's law constant at a given temperature <tt>T</tt> .  This routine uses the following formula:
+
 
+
      KH = K0 * EXP( CR * ( 1/T - 1/298.15 ) ) * R * T / ATM
+
 
+
:where
+
 
+
:#<tt>K0</tt> is the Henry's law solubility constant, in M atm<sup>-1</sup>,
+
:#<tt>CR</tt> is the Henry's law volatility constant, in K,
+
:#<tt>T</tt> is the temperature in K,
+
:#<tt>R</tt> is the universal gas constant = 8.3144621 J K<sup>-1</sup> mol<sup>-1</sup>,
+
:#<tt>ATM</tt> is the reference pressure at STP = 101.325 mPa, and
+
:#<tt>298.15</tt> is the reference temperature (in K) at STP
+
 
+
:3. Call routine <tt>CALC_HEFF</tt> in <tt>GeosUtil/henry_mod.F</tt> to compute the effective Henry's law constant taking into account the pH value.  This applies a correction term to the <tt>KH</tt> value that we computed in Step 2.  This routine uses the formula:
+
 
+
      IF ( pH > 0 ) THEN
+
        HEFF = KH * 1 + 10**( pH - pKa )
+
      ELSE
+
        HEFF = KH
+
      ENDIF
+
 
+
:where
+
 
+
:#<tt>KH</tt> is the dimensionless liquid over gas Henry's constant we computed in Step 2,
+
:#<tt>pKa</tt> is the value of pKa listed in the table above,
+
:#<tt>pH</tt> is the desired pH value, and
+
:#<tt>HEFF</tt> is the dimensionless liquid over gas Henry's law constant, adjusted for pH
+
 
+
:NOTES:
+
:#It should be noted that the correction term calculated here is from a 'acid perspective', i.e. for compounds with the acid being in the gaseous phase. The correction term reads <tt>1 + 10**( -pH + pKa )</tt> for compounds with the base in the gas phase (e.g. ammonia).
+
:#The correction term becomes more complicated for compounds with more than two equilibrium compounds that are relevant under the current conditions (e.g. CO2)
+
:#We ignore any temperature dependencies of <tt>pKa</tt> for now.
+
 
+
'''''NOTE:''''' In [[GEOS-Chem v10-01]] and prior versions, the wet deposition module calls the older routine <tt>COMPUTE_L2G</tt>, which does the same computation, as <tt>CALC_KH</tt>, but is written in a slightly different way.  We will replace <tt>COMPUTE_L2G</tt> with the <tt>CALC_KH</tt> and <tt>CALC_HEFF</tt> so that GEOS-Chem uses the the same Henry's law routines everywhere.
+
 
+
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 19:12, 6 October 2015 (UTC)
+
  
 
== Dry deposition ==
 
== Dry deposition ==
Line 689: Line 173:
 
|-valign="top"
 
|-valign="top"
 
|MSA ||96 ||96 || - || - || - || - || - ||0.03 ||0.01 snow<br>0.01 land || - || -  
 
|MSA ||96 ||96 || - || - || - || - || - ||0.03 ||0.01 snow<br>0.01 land || - || -  
 +
 +
|-valign="top"
 +
|<span style="color:red">'''N2O5'''</span> ||<span style="color:red">'''63'''</span> ||<span style="color:red">'''63'''</span> || - || - || - || - || - || - || - ||<span style="color:red">'''0.0'''</span> || <span style="color:red">'''See Note 1 below'''</span>
  
 
|-valign="top"
 
|-valign="top"
Line 703: Line 190:
  
 
|-valign="top"
 
|-valign="top"
|NITs ||62 ||62 || - ||4.25e-6 ||2200 ||YES ||NO || - || - || - || -  
+
|NITs ||31.4 ||31.4 || - ||4.25e-6 ||2200 ||YES ||NO || - || - || - || -  
  
 
|-valign="top"
 
|-valign="top"
Line 722: Line 209:
 
|-valign="top"
 
|-valign="top"
 
|Pb210 ||210 ||210 || - || - || - || - || - ||0.03 || - || - || -  
 
|Pb210 ||210 ||210 || - || - || - || - || - ||0.03 || - || - || -  
 +
 +
|-valign="top"
 +
|<span style="color:green">'''PMN'''</span> ||<span style="color:green">'''121'''</span> ||<span style="color:green">'''121'''</span> || - || - || - || - || - || - || - ||<span style="color:green">'''1.0 '''</span> ||<span style="color:green">'''See Note 2 below'''</span>
  
 
|-valign="top"
 
|-valign="top"
Line 743: Line 233:
 
|-valign="top"
 
|-valign="top"
 
|POPG (BaP) ||252.31 ||252.31 || - || - || - || - || - || - || - ||0.0 ||
 
|POPG (BaP) ||252.31 ||252.31 || - || - || - || - || - || - || - ||0.0 ||
 +
 +
|-valign="top"
 +
|<span style="color:green">'''PPN'''</span> ||<span style="color:green">'''121'''</span> ||<span style="color:green">'''121'''</span> || - || - || - || - || - || - || - ||<span style="color:green">'''1.0 '''</span> ||<span style="color:green">'''See Note 2 below'''</span>
  
 
|-valign="top"
 
|-valign="top"
 
|PROPNN ||119 ||119 || - || - || - || - || - || - || - ||1.0 ||Karl et al [2010]
 
|PROPNN ||119 ||119 || - || - || - || - || - || - || - ||1.0 ||Karl et al [2010]
 +
 +
|-valign="top"
 +
|<span style="color:green">'''R4N2'''</span> ||<span style="color:green">'''121'''</span> ||<span style="color:green">'''121'''</span> || - || - || - || - || - || - || - ||<span style="color:green">'''1.0 '''</span> ||<span style="color:green">'''See Note 2 below'''</span>
  
 
|-valign="top"
 
|-valign="top"
Line 763: Line 259:
  
 
|-valign="top"
 
|-valign="top"
|SO4s ||96 ||96 || -  ||4.25e-6 ||2200 ||YES ||NO || - || - || - || -  
+
|SO4s ||31.4 ||31.4 || -  ||4.25e-6 ||2200 ||YES ||NO || - || - || - || -  
  
 
|-valign="top"
 
|-valign="top"
Line 782: Line 278:
  
 
NOTES:
 
NOTES:
*Dry deposition velocities for the following species are not computed:
+
#<span style="color:red">N2O5 uses the same dry deposition velocity (Vd) as HNO3.  In GEOS-Chem v11-01, we now compute Vd(N2O5) explicitly.  We therefore have to assign to N2O5 the same F0, Hstar_old, and MW_g values that HNO3 uses in order for the computation of Vd to be done correctly.</span>
**PMN, PPN, and R4N2 are assigned the same dry deposition velocity as PAN.
+
#<span style="color:green">PMN, PPN, and R4N2 all use the same dry deposition velocity (Vd) as PAN. In GEOS-Chem v11-01, we now compute Vd(PMN), Vd(PPN), and Vd(R4N2) explicitly.  We therefore have to assign to PMN, PPN, and R4N2 the same F0, Hstar_old, and MW_g values that PAN uses in order for the computations to be done correctly.</span>
**N2O5 is assigned the same dry deposition velocity as HNO3.
+
  
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 19:18, 23 October 2015 (UTC)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:55, 19 May 2016 (UTC)
  
 
=== Discrepancies found in the dry deposition module ===
 
=== Discrepancies found in the dry deposition module ===
Line 935: Line 430:
 
NOTE: ALK4 had been included in this table, but it is not a dry-deposited species.  We have therefore removed ALK4 from the above table.  Thanks to [[User:psk9|Prasad Kasibhatla]] for pointing out the error.
 
NOTE: ALK4 had been included in this table, but it is not a dry-deposited species.  We have therefore removed ALK4 from the above table.  Thanks to [[User:psk9|Prasad Kasibhatla]] for pointing out the error.
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:20, 3 February 2016 (UTC)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:13, 22 February 2016 (UTC)
  
 
== Wet deposition ==
 
== Wet deposition ==
Line 1,091: Line 586:
  
 
|-valign="top"
 
|-valign="top"
|NITs ||62 ||62 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
+
|NITs ||31.4 ||31.4 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
Line 1,097: Line 592:
  
 
|-valign="top"
 
|-valign="top"
|OCPO<br>POA2 ||12.01 ||12 ||1 ||NO ||1.0 ||0.5 ||0.5|| 0.5 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">1.0</span> || - || -
+
|OCPO<br>POA2 ||12.01 ||12 ||1 ||NO ||1.0 ||0.5 ||0.5|| 0.5 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|OPOA1<br>OPOA2 ||12.01 ||12 ||1 ||NO ||0.8 ||1.0 ||0.5 ||1.0 ||0.8<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||0.8<br><span style="color:red">0.8</span> || - || -
+
|OPOA1<br>OPOA2 ||12.01 ||12 ||1 ||NO ||0.8 ||1.0 ||0.5 ||1.0 ||0.8 ||0.0 ||0.8 || - || -
  
 
|-valign="top"
 
|-valign="top"
Line 1,106: Line 601:
  
 
|-valign="top"
 
|-valign="top"
|Pb210 ||210 ||210 ||- ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">1.0</span> || - || -
+
|Pb210 ||210 ||210 ||- ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
Line 1,112: Line 607:
  
 
|-valign="top"
 
|-valign="top"
|POPPBCPI<br>(PHE) ||178.23 ||178.23 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">1.0</span> || - || -
+
|POPPBCPI<br>(PHE) ||178.23 ||178.23 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|POPPBCPI<br>(PYR) ||202.25 ||202.25 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">1.0</span> || - || -
+
|POPPBCPI<br>(PYR) ||202.25 ||202.25 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|POPPBCPI<br>(BaP) ||252.31 ||252.31 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">1.0</span> || - || -
+
|POPPBCPI<br>(BaP) ||252.31 ||252.31 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|POPPBCPO<br>(PHE) ||178.23 ||178.23 || - ||NO ||1.0 ||1.0 ||1.0 ||0.5 ||1.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> || - || -
+
|POPPBCPO<br>(PHE) ||178.23 ||178.23 || - ||NO ||1.0 ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|POPPBCPO<br>(PYR) ||202.25 ||202.25 || - ||NO ||1.0 ||1.0 ||1.0 ||0.5 ||1.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> || - || -
+
|POPPBCPO<br>(PYR) ||202.25 ||202.25 || - ||NO ||1.0 ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|POPPBCPO<br>(BaP) ||252.31 ||252.31 || - ||NO ||1.0 ||1.0 ||1.0 ||0.5 ||1.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> || - || -
+
|POPPBCPO<br>(BaP) ||252.31 ||252.31 || - ||NO ||1.0 ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|POPPOCPI<br>(PHE) ||178.23 ||178.23 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">0.0</span> || - || -
+
|POPPOCPI<br>(PHE) ||178.23 ||178.23 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||1.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|POPPOCPI<br>(PHE) ||202.25 ||202.25 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">0.0</span> || - || -
+
|POPPOCPI<br>(PHE) ||202.25 ||202.25 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||1.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|POPPOCPI (PHE) ||252.31 ||252.31 || -  ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">0.0</span> || - || -
+
|POPPOCPI (PHE) ||252.31 ||252.31 || -  ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||1.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|POPOCPO<br>(PHE) ||178.23 ||178.23 || - ||NO ||1.0 ||1.0 ||1.0 ||0.5 ||1.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> || - || -
+
|POPOCPO<br>(PHE) ||178.23 ||178.23 || - ||NO ||1.0 ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|POPOCPO<br>(PYR) ||202.25 ||202.25 || - ||NO ||1.0 ||1.0 ||1.0 ||0.5 ||1.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> || - || -
+
|POPOCPO<br>(PYR) ||202.25 ||202.25 || - ||NO ||1.0 ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|POPOCPO<br>(BaP) ||252.31 ||252.31 || - ||NO ||1.0 ||1.0 ||1.0 ||0.5 ||1.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> || - || -
+
|POPOCPO<br>(BaP) ||252.31 ||252.31 || - ||NO ||1.0 ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
Line 1,163: Line 658:
  
 
|-valign="top"
 
|-valign="top"
|SALA ||31.4 ||31.4|| - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">1.0</span> || - || -
+
|SALA ||31.4 ||31.4|| - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|SALC ||31.4 ||31.4|| - ||YES ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">1.0</span> || - || -
+
|SALC ||31.4 ||31.4|| - ||YES ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
Line 1,172: Line 667:
  
 
|-valign="top"
 
|-valign="top"
|SO4 ||96 ||96 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">1.0</span> || - || -
+
|SO4 ||96 ||96 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|SO4s ||96 ||96 || - ||NO ||1.0 ||1.0 ||0.5|| 1.0 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">1.0</span> || - || -
+
|SO4s ||31.4 ||31.4 || - ||NO ||1.0 ||1.0 ||0.5|| 1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|TSOA0<br>TSOA1<br>TSOA2<br>TSOA3 ||150 ||150 || - ||NO ||0.8 ||1.0 ||0.5 ||1.0 ||0.8<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||0.8<br><span style="color:red">0.8</span> || - ||-
+
|TSOA0<br>TSOA1<br>TSOA2<br>TSOA3 ||150 ||150 || - ||NO ||0.8 ||1.0 ||0.5 ||1.0 ||0.8 ||0.0 ||0.8 || - ||-
  
 
|-valign="top"
 
|-valign="top"
Line 1,189: Line 684:
  
 
|-valign="top"
 
|-valign="top"
|DUST1-<br>DUST40 ||100 ||100 ||- ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">1.0</span> || - || -
+
|DUST1-<br>DUST40 ||100 ||100 ||- ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|ECIL1-<br>ECIL40 ||96 ||96 ||-  ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">1.0</span> || - || -
+
|ECIL1-<br>ECIL40 ||96 ||96 ||-  ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|NK1-NK40 ||1 ||1 ||- ||NO || 1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">1.0</span> || - || -
+
|NK1-NK40 ||1 ||1 ||- ||NO || 1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|OCIL1-<br>OCIL40 ||12 ||12 ||1 ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">1.0</span> || - || -
+
|OCIL1-<br>OCIL40 ||12 ||12 ||1 ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|SF1-<br>SF40 ||96 ||96 ||- ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">1.0</span> || - || -
+
|SF1-<br>SF40 ||96 ||96 ||- ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|-valign="top"
 
|-valign="top"
|SS1-<br>SS40 ||58.5 ||58.5 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0<br><span style="color:red">0.0</span> ||0.0<br><span style="color:red">0.0</span> ||1.0<br><span style="color:red">0.0</span> || - || -
+
|SS1-<br>SS40 ||58.5 ||58.5 || - ||NO ||1.0 ||1.0 ||0.5 ||1.0 ||1.0 ||0.0 ||1.0 || - || -
  
 
|}
 
|}
  
 
NOTES:
 
NOTES:
#For [[GEOS-5]] and [[MERRA]] met fields, we follow the algorithm of Qiaoqiao Wang et al (2014) for [[Wet_deposition#Add_scavenging_by_snow|scavenging by snow]] and [[Wet_deposition#Impaction_scavenging_for_hydrophobic_BC_and_homogeneous_IN_removal|impaction scavenging for BC and IN]], namely:
+
#We follow the algorithm of Qiaoqiao Wang et al (2014) for [[Wet_deposition#Add_scavenging_by_snow|scavenging by snow]] and [[Wet_deposition#Impaction_scavenging_for_hydrophobic_BC_and_homogeneous_IN_removal|impaction scavenging for BC and IN]], namely:
 
#*When 237 K <= T < 258 K:
 
#*When 237 K <= T < 258 K:
 
#**Multiply <tt>Kc</tt>&mdash;the rate at which cloud condensate changes into precipitation&mdash; by 0.5, and
 
#**Multiply <tt>Kc</tt>&mdash;the rate at which cloud condensate changes into precipitation&mdash; by 0.5, and
 
#**Allow black carbon, dust, HNO3, <sup>210</sup>Pb, and <sup>7</sup>Bethe following species, which are considered to be IN, to be rained out (aka "cold cloud scavenging").
 
#**Allow black carbon, dust, HNO3, <sup>210</sup>Pb, and <sup>7</sup>Bethe following species, which are considered to be IN, to be rained out (aka "cold cloud scavenging").
 
#**Do not allow any other soluble aerosol species to rain out (i.e. set the rainout fraction to zero).
 
#**Do not allow any other soluble aerosol species to rain out (i.e. set the rainout fraction to zero).
#For [[GEOS-FP]] and [[MERRA2]] met fields, we follow the algorithm of Qiaoqiao Wang et al (2014) mentioned above, but also apply [[Wet_deposition#Low_tropospheric_210Pb_lifetime_against_deposition_in_v11-01b|the fix submitted by Hongyu Liu and Bo Zhang]], namely:
 
#*When 237K <= T < 258K:
 
#**Multiply <tt>Kc</tt>&mdash;the rate at which cloud condensate changes into precipitation&mdash; by 0.5 (for most aerosols), following Qiaoqiao Wang et al 2014.
 
#*When T < 258K:
 
#**Do not allow ANY soluble aerosol species to rained out (i.e. set the rainout fraction to zero).
 
  
 
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 20:34, 23 October 2015 (UTC)
 
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 20:34, 23 October 2015 (UTC)
Line 1,247: Line 737:
 
|}
 
|}
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:36, 16 December 2015 (UTC)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:12, 22 February 2016 (UTC)
  
 
== POPs parameters ==
 
== POPs parameters ==
Line 1,271: Line 761:
  
 
|-valign="top"
 
|-valign="top"
|POPG (PYR) ||202 ||7.24e+08 ||1.0e+11 ||50.0e-12 ||0.0 ||3.0e+15 ||5.37e-04 || -8700 || 43
+
|POPG (PYR) ||202.25 ||7.24e+08 ||1.0e+11 ||50.0e-12 ||0.0 ||3.0e+15 ||5.37e-04 || -8700 || 43
  
 
|-valign="top"
 
|-valign="top"
|POPG (BaP) ||252 ||3.02e+11 ||7.94e+13 ||50.0e-12 ||0.0 ||2.8e+15 ||3.10e-05 ||-11000 ||43
+
|POPG (BaP) ||252.31 ||3.02e+11 ||7.94e+13 ||50.0e-12 ||0.0 ||2.8e+15 ||3.10e-05 ||-11000 ||43
  
 
|}
 
|}
 +
 +
== Previous issues that are now resolved ==
 +
 +
=== Fix Henry's law parameters for HCl ===
 +
 +
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02f|v11-02f]] (approved 17 May 2018).'''''</span>
 +
 +
'''''Xuan Wang wrote:'''''
 +
 +
:Heff at pH=7 is set to 2e6 for HCl, much lower than it should be.  H at pH=4.5 cannot be higher than at pH=7. Yang et al. (2005) is a Br paper without HCl Henry number shown. I suggest to change the HCl values to  Hstar=2.05e13 and K0=7e10, which are calculated from Sander 2015.
 +
 +
:Also in calc_heff in henry_mod.F (around bottom), we have
 +
 +
      IF ( thispKa > 0d0 ) THEN
 +
        HEFF = KH * ( 1d0 + 10d0**( pH - thispKa ) )
 +
 +
:It looks more reasonable to change to :
 +
 +
      IF ( pH >= 0d0 ) THEN
 +
 +
:Since pKa can be negative. Anyway, it may not matter much in the simulation, we could do it in the future.
 +
 +
'''''NOTE: The fix in henry_mod.F resulted in "Infinity in DO_CLOUD_CONVECTION" errors, so we will not include this suggested fix for now.'''''
 +
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:59, 17 May 2018 (UTC)
  
 
== References ==
 
== References ==
Line 1,299: Line 814:
  
 
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 16:13, 18 August 2015 (UTC)
 
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 16:13, 18 August 2015 (UTC)
 +
 +
 +
----
 +
'''''[[Species in GEOS-Chem|Previous]] | [[GEOS-Chem species database|Next]] | [[Guide to species in GEOS-Chem]]'''''

Latest revision as of 18:17, 16 September 2022


This Guide has not been updated since GEOS-Chem 12.8.0. Species properties for newer GEOS-Chem versions are now contained in the species_database.yml run-directory configuration file.



Previous | Next | Guide to species in GEOS-Chem

  1. Species in GEOS-Chem
  2. Physical properties of GEOS-Chem species
  3. GEOS-Chem species database
  4. GEOS-Chem species units
  5. Adding passive species to GEOS-Chem
  6. Species indexing in GEOS-Chem



For the most up-to-date information, please see the View GEOS-Chem Species Properties chapter of geos-chem.readthedocs.io



Overview

The GEOS-Chem Support Team has created a common data structure (aka the "GEOS-Chem species database") that stores all of the various physical properties for GEOS-Chem species. Formerly, these properties were defined (and sometimes redefined) in several locations in the code.

For example, the effective Henry's law value Heff is calculated differently in the wet deposition module than in the dry deposition module. The GEOS-Chem wet deposition module assumes a pH value of 4.5 for rainwater, and thus uses a set of Henry’s law constants that are appropriate for this pH. On the other hand, the GEOS-Chem dry deposition module assumes a pH of 7 for water, and therefore uses a different set of Henry’s law constants. Keeping two independent sets of Henry’s law constants can lead to confusion.

In the GEOS-Chem v10-01, Christoph Keller implemented a new GEOS-Chem module that can compute Heff for each species as a function of pH and the species-specific Henry’s law constants K0, CR, and pKA. These Henry’s law constants can be obtained from the literature (cf. Sander, Atmos. Chem. Phys. 15, 4399-4381, 2015, download from this site, or similar references). We would like to use Christoph’s new module to compute Heff in a consistent way everywhere in GEOS-Chem.

We now store these Henry's law constants together with other relevant physical parameters such as molecular weight, density, aerosol radius, reactivity factor for drydep (F0), etc. for each species. Keeping all of these physical properties in a single data structure will streamline the code and help to reduce confusion.

Phase 1 of the GEOS-Chem species database was completed in GEOS-Chem v11-01d. Phase 2 was completed in GEOS-Chem v11-01e. Further work is slated for GEOS-Chem v11-02.

--Bob Yantosca (talk) 19:33, 30 November 2016 (UTC)

Henry's law

Please see our GEOS-Chem species: Henry's law metadata wiki page for the latest information about Henry's law constants in GEOS-Chem.

Dry deposition

The table below shows the various dry-deposition parameters for both gas-phase and aerosol species. The quantities in each column correspond to fields of the Species derived type, as described on our GEOS-Chem species database wiki page.

Aerosol Species Parameters Gas-Phase Species Parameters
Species MW_g
[g mol-1]
EmMW_g
[g mol-1]
Molec
Ratio

[1]
Radius
[m]
Density
[kg m-3]
DD_Aero
Drydep

[1]
DD_Dust
Drydep

[1]
DD_Dvz
AerSnow

[cm s-1]
DD_Dvz
MinVal

[cm s-1]
DD_F0
[1]
References
ACET 58.08 12 3 - - - - - - 1.0 Karl et al [2010]
ALD2 44.05 12 2 - - - - - - 1.0 Karl et al [2010}??
ALK4 58.12 12 4 - - - - - - 1.0 From drydep_mod.F
ASOAN
ASOA1
ASOA2
ASOA3
150 150 - - - - - 0.03 - - -
ASOG1
ASOG2
ASOG3
150 150 - - - - - - - 0.0
BCPI
BCPO
12.01 12 1 - - - - 0.03 - - -
Be7 201 201 - - - - - 0.03 - - -
Br2 160 160 - - - - - - - 0.0 -
BrNO3 142 142 - - - - - - - 0.0 -
CH2O 30 30 - - - - - - - 1.0 Karl et al [2010]?
DST1
DSTAL1
NITD1
SO4D1
29 29 - 7.30e-07 2500 NO YES - - - -
DST2
DSTAL2
NITD2
SO4D2
29 29 - 1.40e-06 2650 NO YES - - - -
DST3
DSTAL3
NITD3
SO4D3
29 29 - 2.40e-06 2650 NO YES - - - -
DST4
DSTAL4
NITD4
SO4D4
29 29 - 4.5e-06 2650 NO YES - - - -
GLYC 60 60 - - - - - - - 1.0 Karl et al [2010]
GLYX 58 58 - - - - - - - 1.0 -
H2O2 34 34 - - - - - - - 1.0 From drydep_mod.F
H2SO4 98 98 - - - - - - - 0.0
HAC 74 74 - - - - - - - 1.0 Karl et al [2010]
HBr 81 81 - - - - - - - - -
HCl 36 36 - - - - - - - 0.0
Hg0 201 201 - - - - - - - 1.0e-5
HgP 201 201 - - - - - 0.03 - - -
Hg2 201 201 - - - - - - - 0.0
HNO3 63 63 - - - - - - - 0.0 From drydep_mod.F
HOBr 97 97 - - - - - - - 0.0 -
IEPOX 118 118 - - - - - - - 1.0 Karl et al [2010]
ISOPN 147 147 - - - - - - - 1.0 Karl et al [2010]
ISOA1
ISOA2
ISOA3
150 150 - - - - - 0.03 - 0.0 -
ISOG1
ISOG2
ISOG3
150 150 - - - - - - - 0.0 -
LIMO
MTPA
MTPO
136.23 136.23 - - - - - - - 0.0
MACR 70 70 - - - - - - - 1.0 Karl et al [2010]?
MAP 76 76 - - - - - - - 1.0 Karl et al [2010]
MMN 149 149 - - - - - - - 1.0 Karl et al [2010]
MOBA 114 114 - - - - - - - 1.0 Karl et al [2010]
MOPI 12.01 12 1 - - - - 0.03 - - -
MOPO 12.01 12 1 - - - - 0.03 - - -
MSA 96 96 - - - - - 0.03 0.01 snow
0.01 land
- -
N2O5 63 63 - - - - - - - 0.0 See Note 1 below
NH3 17 17 - 0.0 - - - 0.03 0.2 snow
0.3 land
- -
NH4 18 18 - - - - - 0.03 0.01 snow
0.01 land
- -
MVK 70 70 - - - - - - - 1.0 Karl et al [2010]?
NIT 62 62 - - - - - 0.03 0.01 snow
0.01 land
- -
NITs 31.4 31.4 - 4.25e-6 2200 YES NO - - - -
NO2 118 118 - - - - - - - 0.1 Karl et al [2010]
OCPI
OCPO
OPOA1
OPOA2
POA1
POA2
12.01 12 1 - - - - 0.03 - - -
O3 48 48 - - - - - - - 1.0 Karl et al [2010]
OPOG1
OPOG2
12.01 12 1 - - - - - - 0.0
PAN 121 121 - - - - - - - 1.0 Karl et al [2010]
Pb210 210 210 - - - - - 0.03 - - -
PMN 121 121 - - - - - - - 1.0 See Note 2 below
POG1
POG2
12.01 12 1 - - - - - - 0.0 Karl et al [2010]?
POPPBCPI
POPBCPO
POPPOCPI
POPOCPO
(PHE)
178.23 178.23 - - - - - 0.03 - - -
POPPBCPI
POPBCPO
POPPOCPI
POPOCPO
(PYR)
202.25 202.25 - - - - - 0.03 - - -
POPPBCPI
POPBCPO
POPPOCPI
POPOCPO
(BaP)
252.31 252.31 - - - - - 0.03 - - -
POPG (PHE) 178.23 178.23 - - - - - - - 0.0
POPG (PYR) 202.25 202.25 - - - - - - - 0.0
POPG (BaP) 252.31 252.31 - - - - - - - 0.0
PPN 121 121 - - - - - - - 1.0 See Note 2 below
PROPNN 119 119 - - - - - - - 1.0 Karl et al [2010]
R4N2 121 121 - - - - - - - 1.0 See Note 2 below
RIP 118 118 - - - - - - - 1.0 Karl et al [2010]
SALA 31.4 31.4 - 2.55e-7 2200 YES NO - - - -
SALC 31.4 31.4 - 4.25e-6 2200 YES NO - - - -
SO2 64 64 - - - - - 0.03 0.2 snow
0.3 land
0.0 -
SO4 96 96 - - - - - 0.03 0.01 snow
0.01 land
- -
SO4s 31.4 31.4 - 4.25e-6 2200 YES NO - - - -
TSOA0
TSOA1
TSOA2
TSOA3
150 150 - - - - - 0.03 - 0.0 -
TSOG0
TSOG1
TSOG2
TSOG3
150 150 - - - - - - - 0.0 -
TOMAS microphysics species Aerosol Species Parameters Gas-Phase Species Parameters
NK1-NK40 1 1 - - - - - 0.03 - - -

NOTES:

  1. N2O5 uses the same dry deposition velocity (Vd) as HNO3. In GEOS-Chem v11-01, we now compute Vd(N2O5) explicitly. We therefore have to assign to N2O5 the same F0, Hstar_old, and MW_g values that HNO3 uses in order for the computation of Vd to be done correctly.
  2. PMN, PPN, and R4N2 all use the same dry deposition velocity (Vd) as PAN. In GEOS-Chem v11-01, we now compute Vd(PMN), Vd(PPN), and Vd(R4N2) explicitly. We therefore have to assign to PMN, PPN, and R4N2 the same F0, Hstar_old, and MW_g values that PAN uses in order for the computations to be done correctly.

--Bob Yantosca (talk) 20:55, 19 May 2016 (UTC)

Discrepancies found in the dry deposition module

This update was validated with 1-month benchmark v11-01e (approved 04 Jan 2016).
Some of these issues had already been corrected in v11-01d (approved 12 Dec 2015).

During the implementation of the species database of physical properties into GEOS-Chem, we discovered several issues with how species were defined in the dry deposition module drydep_mod.F.

Species Issue Solution Status
ACET
  • Previously, drydep_mod.F used XMW = 0.058 kg/mol for the MW of ACET.
  • But the MW of ACET as defined in the GEOS-Chem species database = 58.08 g/mol = 0.05808 kg/mol.
  • Obtain the MW of ACET (= 58.08 g/mol = 0.05808 kg/mol) from the GEOS-Chem species database.
  • Assign this value to XMW in drydep_mod.F.
ALD2
  • Previously, drydep_mod.F used XMW = 0.044 kg/mol for the MW of ALD2.
  • But the MW of ALD2 as defined in the GEOS-Chem species database = 44.05 g/mol = 0.04405 kg/mol.
  • Obtain the MW of ALD2 (= 44.05 g/mol = 0.04405 kg/mol) from the GEOS-Chem species database.
  • Assign this value to XMW in drydep_mod.F.
MTPO
  • Previously, drydep_mod.F used XMW = 0.136 kg/mol for the MW of MTPO.
  • But the actual MW of MTPO as defined in the GEOS-Chem species database = 136.23 g/mol = 0.13623 kg/mol.
NITs
  • The dry deposition species name (i.e. stored in the DEPNAME array of drydep_mod.F was NITS (all caps).
  • But the given species name used throughout GEOS-Chem is NITs (lowercase "s").
  • Assign the name NITS to the DEPNAME array.
NITs
  • Previously, drydep_mod.F used XMW = 0.036 kg/mol for the MW of NITs.
    • This corresponded to the molecular weight of coarse sea-salt aerosol (SALC).
    • NOTE: Because NITs is internally mixed, it is appropriate to give NITs the MW of SALC.
  • But the MW of SALC was changed to 0.0314 kg/mol in GEOS-Chem v9-02.
POPG
POPPOCPI
POPPOCPO
POPPBCPI
POPPBCPO
  • The molecular weights as listed in the TRACER MENU section of input.geos often do not match the POP_MW setting in the POPS MENU.
  • For example:
    • PHE: MW = 178.23 but POP_MW = 178
    • PYR: MW = 202.25 but POP_MW = 202
    • BaP: MW = 252.31 but POP_MW = 252
  • Edit the input.geos files (i.e. in the GEOS-Chem Unit Tester) to ensure that the POP_MW value is the same as the molecular weight listed in the TRACER MENU section..
POPG
  • In routine INIT_DRYDEP, KOA is multiplied by 0.0409 but this may lead to a loss of precision.
  • Multiply KOA by 0.0409d0 to enforce REAL*8 precision.
  • In v11-01d and higher versions, this is now done in module Headers/species_database_mod.F90.
SALA
SALC
  • SALA and SALC have historically used MW's of 36 g/mol.
    • These values appear to have been used since at least v7-02-03 (Feb 2005).
  • In GEOS-Chem v9-02 (03 Mar 2015), the MW's of SALA and SALC were changed from 36 g/mol to 31.4 g/mol.
  • However, the new MW's of SALA and SALC were only added to the input.geos files, but not to the XMW variable of drydep_mod.F.
    • Therefore, since GEOS-Chem v9-02, dry deposition of SALA and SALC has been computed using the incorrect molecular weights.
  • Obtain the MW's of SALA and SALC (= 31.4 kg/mol = 0.0314 kg/mol) from the species database object.
  • Assign these values to XMW in drydep_mod.F.
SO4s
  • The dry deposition species name (i.e. stored in the DEPNAME array of drydep_mod.F was SO4S.
  • But the given species name used throughout GEOS-Chem is SO4s (lowercase "s").
  • Assign the name SO4S to the DEPNAME array.
SO4s
  • Previously, drydep_mod.F used XMW = 0.036 kg/mol for the MW of SO4s.
    • This corresponded to the molecular weight of coarse sea-salt aerosol (SALC).
    • NOTE: Because SO4s is internally mixed, it is appropriate to give SO4s the MW of SALC.
  • But the MW of SALC was changed to 0.0314 kg/mol in GEOS-Chem v9-02.


NOTE: ALK4 had been included in this table, but it is not a dry-deposited species. We have therefore removed ALK4 from the above table. Thanks to Prasad Kasibhatla for pointing out the error.

--Bob Yantosca (talk) 17:13, 22 February 2016 (UTC)

Wet deposition

The table below shows the various wet deposition parameters for both gas-phase and aerosol species. The quantities in each column correspond to fields of the Species derived type, as described on our GEOS-Chem species database wiki page.

Aerosol Species Parameters Gas-phase Species Parameters
Species MW_g
[g mol-1]
EmMW_g
[g mol-1]
Molec
Ratio

[1]
WD_Coarse
Aer

[?]
WD_Aer
ScavEff

[1]
WD_KcScaleFac
[1]
WD_RainoutEff
[1]
WD_Ret
Factor

[1]
References
T < 237 K 237 K <= T < 258 K T > 258 K T < 237 K 237 K <= T < 258 K T > 258 K
ACET 58.08 12 3 - - - - - - - - - -
ALD2 44.05 12 2 - - - - - - - - - -
ALK4 58.12 12 4 - - - - - - - - - -
ASOAN
ASOA1
ASOA2
ASOA3
150 150 - NO 0.8 1.0 0.5 1.0 0.8 0.0 0.8 - -
ASOG1
ASOG2
ASOG3
150 150 - - - - - - - - - 2.0e-2 -
Be7 201 201 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
Br2 160 160 - - - - - - - - - 0.0 -
BCPI 12.01 12 1 NO 1.0 1.0 1.0 0.5 1.0 0.0 1.0 - -
BCPO 12.01 12 1 NO 1.0 1.0 1.0 0.5 1.0 1.0 0.0 - -
CH2O 30 30 - - - - - - - - - 2.0e-2 Jacob et al [2000]
DST1
DSTAL1
NITD1
SO4D1
29 29 - NO 1.0 1.0 1.0 1.0 1.0 1.0 1.0 - -
DST2
DSTAL2
NITD2
SO4D2
29 29 - YES 1.0 1.0 1.0 1.0 1.0 1.0 1.0 - -
DST3
DSTAL3
NITD3
SO4D3
29 29 - YES 1.0 1.0 1.0 1.0 1.0 1.0 1.0 - -
DST4
DSTAL4
NITD4
SO4D4
29 29 - YES 1.0 1.0 1.0 1.0 1.0 1.0 1.0 - -
GLYC 60 60 - - - - - - - - - 2.0e-2 -
GLYX 58 58 - - - - - - - - - - -
H2O2 34 34 - - - - - - - - - 5.00e-2 Jacob et al [2000]
HAC 74 74 - - - - - - - - - - -
HBr 81 81 - - - - - - - - - 1.0 -
HCl 36 36 - - - - - - - - - 1.0 -
Hg2 201 201 - - - - - - - - - 0.0 -
HgP 201 201 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
HNO3 63 63 - - - - - - - - - - -
HOBr 97 97 - - - - - - - - - 0.0 -
IEPOX 118 118 - - - - - - - - - 2.0e-2 -
ISOA1
ISOA2
ISOA3
150 150 - NO 0.8 1.0 0.5 1.0 0.8 0.0 0.8 - -
ISOG1
ISOG2
ISOG3
150 150 - - - - - - - - - 2.0e-2 -
ISOPN 147 147 - - - - - - - - - 2.0e-2 -
LIMO
MTPA
MTPO
136.23 136.23 - - - - - - - - - 2.0e-2 -
MAP 76 76 - - - - - - - - - 2.0e-2 -
MMN 149 149 - - - - - - - - - 2.0e-2 -
MOBA 114 114 - - - - - - - - - 2.0e-2 -
MOPI 12.01 12 1 NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
MOPO 12.01 12 1 NO 0.0 1.0 1.0 1.0 0.0 0.0 0.0 - -
MSA 96 96 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
NH3 17 17 - - - - - - - - - 5.0e-2 Jacob et al [2000]?
NH4 18 18 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
NIT 62 62 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
NITs 31.4 31.4 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
OCPI
POA1
12.01 12 1 NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
OCPO
POA2
12.01 12 1 NO 1.0 0.5 0.5 0.5 1.0 0.0 1.0 - -
OPOA1
OPOA2
12.01 12 1 NO 0.8 1.0 0.5 1.0 0.8 0.0 0.8 - -
OPOG1
OPOG2
12.01 12 1 - - - - - - - - 2.0e-2 -
Pb210 210 210 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
POG1
POG2
12.01 12 1 - - - - - - - - 2.0e-2 -
POPPBCPI
(PHE)
178.23 178.23 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
POPPBCPI
(PYR)
202.25 202.25 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
POPPBCPI
(BaP)
252.31 252.31 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
POPPBCPO
(PHE)
178.23 178.23 - NO 1.0 1.0 1.0 0.5 1.0 1.0 0.0 - -
POPPBCPO
(PYR)
202.25 202.25 - NO 1.0 1.0 1.0 0.5 1.0 1.0 0.0 - -
POPPBCPO
(BaP)
252.31 252.31 - NO 1.0 1.0 1.0 0.5 1.0 1.0 0.0 - -
POPPOCPI
(PHE)
178.23 178.23 - NO 1.0 1.0 0.5 1.0 1.0 1.0 1.0 - -
POPPOCPI
(PHE)
202.25 202.25 - NO 1.0 1.0 0.5 1.0 1.0 1.0 1.0 - -
POPPOCPI (PHE) 252.31 252.31 - NO 1.0 1.0 0.5 1.0 1.0 1.0 1.0 - -
POPOCPO
(PHE)
178.23 178.23 - NO 1.0 1.0 1.0 0.5 1.0 1.0 0.0 - -
POPOCPO
(PYR)
202.25 202.25 - NO 1.0 1.0 1.0 0.5 1.0 1.0 0.0 - -
POPOCPO
(BaP)
252.31 252.31 - NO 1.0 1.0 1.0 0.5 1.0 1.0 0.0 - -
POPG (PHE) 178 178 - - - - - - - - - 0.0 -
POPG (PYR) 202 178 - - - - - - - - - 0.0 -
POPG (BaP) 252 178 - - - - - - - - - 0.0 -
PROPNN 119 119 - - - - - - - - - 2.0e-2 -
RIP 118 118 - - - - - - - - - 2.0e-2 -
SALA 31.4 31.4 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
SALC 31.4 31.4 - YES 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
SO2 64 64 - - - - - - - - - - -
SO4 96 96 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
SO4s 31.4 31.4 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
TSOA0
TSOA1
TSOA2
TSOA3
150 150 - NO 0.8 1.0 0.5 1.0 0.8 0.0 0.8 - -
TSOG0
TSOG1
TSOG2
TSOG3
150 150 - - - - - - - - - 2.0e-2 -
TOMAS microphysics species Aerosol Species Parameters Gas-phase Species Parameters
DUST1-
DUST40
100 100 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
ECIL1-
ECIL40
96 96 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
NK1-NK40 1 1 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
OCIL1-
OCIL40
12 12 1 NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
SF1-
SF40
96 96 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -
SS1-
SS40
58.5 58.5 - NO 1.0 1.0 0.5 1.0 1.0 0.0 1.0 - -

NOTES:

  1. We follow the algorithm of Qiaoqiao Wang et al (2014) for scavenging by snow and impaction scavenging for BC and IN, namely:
    • When 237 K <= T < 258 K:
      • Multiply Kc—the rate at which cloud condensate changes into precipitation— by 0.5, and
      • Allow black carbon, dust, HNO3, 210Pb, and 7Bethe following species, which are considered to be IN, to be rained out (aka "cold cloud scavenging").
      • Do not allow any other soluble aerosol species to rain out (i.e. set the rainout fraction to zero).

--Bob Y. (talk) 20:34, 23 October 2015 (UTC)

Discrepancies found in the wet deposition module

During the implementation of the species database of physical properties into GEOS-Chem, we discovered a few issues with how species were defined in the wet deposition module wetscav_mod.F. Some of these errors are typos, others (we think) are historical baggage.

Species Issue Solution Status
MOBA
  • Routines COMPUTE_F and RAINOUT use the Henry's law parameter K0 = 2.3e+4.
  • But routine WASHOUT uses the Henry's law parameter K0 = 2.6e+4.
  • This appears to be a typo.
  • Use the value K0 = 2.3e+4 for MOBA everywhere in GEOS-Chem.

--Bob Yantosca (talk) 17:12, 22 February 2016 (UTC)

POPs parameters

The persistent organic pollutants (POPs) species have special parameters:

Species Mol. Wt.
[g mol-1]
KOA KBC POPG_OH POPG_O3A POPG_O3B HSTAR DEL_H DEL_Hw
POPG (PHE) 178.23 4.37e+07 1.0e+10 2.7e-11 0.0 2.15e+15 1.74e-03 -7400 47
POPG (PYR) 202.25 7.24e+08 1.0e+11 50.0e-12 0.0 3.0e+15 5.37e-04 -8700 43
POPG (BaP) 252.31 3.02e+11 7.94e+13 50.0e-12 0.0 2.8e+15 3.10e-05 -11000 43

Previous issues that are now resolved

Fix Henry's law parameters for HCl

This update was included in v11-02f (approved 17 May 2018).

Xuan Wang wrote:

Heff at pH=7 is set to 2e6 for HCl, much lower than it should be. H at pH=4.5 cannot be higher than at pH=7. Yang et al. (2005) is a Br paper without HCl Henry number shown. I suggest to change the HCl values to Hstar=2.05e13 and K0=7e10, which are calculated from Sander 2015.
Also in calc_heff in henry_mod.F (around bottom), we have
     IF ( thispKa > 0d0 ) THEN
        HEFF = KH * ( 1d0 + 10d0**( pH - thispKa ) )
It looks more reasonable to change to :
     IF ( pH >= 0d0 ) THEN
Since pKa can be negative. Anyway, it may not matter much in the simulation, we could do it in the future.

NOTE: The fix in henry_mod.F resulted in "Infinity in DO_CLOUD_CONVECTION" errors, so we will not include this suggested fix for now.

--Bob Yantosca (talk) 15:59, 17 May 2018 (UTC)

References

  1. Berdnikov, V. M. and Bazhin, N. M.: Oxidation-reduction potentials of certain inorganic radicals in aqueous solutions, Russ. J. Phys. Chem., (Engl. Transl.), 44, 395–398, 1970.
  2. Betterton, E. A. and Hoffmann, M. R.: Henry’s law constants of some environmentally important aldehydes, Environ. Sci. Technol., 22, 1415–1418, 1988.
  3. Chameides, W. L.: Reply, J. Geophys. Res., 91D, 14571–14572, 1986.
  4. Dean, J. A.: Lange’s Handbook of Chemistry, McGraw-Hill, Inc., 1992.
  5. Fried, A., Henry, B. E., Calvert, J. G., and Mozurkewich, M.: The reaction probability of N2O5 with sulfuric acid aerosols at stratospheric temperatures and compositions, J. Geophys. Res., 99D, 3517–3532, 1994.
  6. Ji, C. and Evans, E. M.: Using an internal standard method to determine Henry’s law constants, Environ. Toxicol. Chem., 26, 231–236, 2007.
  7. Kames, J. and Schurath, U.: Henry’s law and hydrolysis-rate constants for peroxyacyl nitrates (PANs) using a homogeneous gasphase source, J. Atmos. Chem., 21, 151–164, 1995.
  8. Lee, Y.-N. and Zhou, X.: Method for the determination of some soluble atmospheric carbonyl compounds, Environ. Sci. Technol., 27, 749–756, 1993.
  9. Lelieveld, J. and Crutzen, P. J.: The role of clouds in tropospheric photochemistry, J. Atmos. Chem., 12, 229–267, 1991.
  10. Leng, C., Kish, J. D., Kelley, J., Mach, M., Hiltner, J., Zhang, Y., and Liu, Y.: Temperature-dependent Henry’s law constants of atmospheric organics of biogenic origin, J. Phys. Chem. A, 117, 10359–10367, 2013.
  11. Leu, M.-T. and Zhang, R.: Solubilities of CH3C(O)OO2NO2 and HO2NO2 in water and liquid H2SO4, Geophys. Res. Lett., 26, 1129–1132, 1999.
  12. Mozurkewich, M.: Mechanisms for the release of halogens from sea-salt particles by free radical reactions, J. Geophys. Res., 100D, 14 199–14 207, 1995.
  13. Sander, S. P., Abbatt, J., Barker, J. R., Burkholder, J. B., Friedl, R. R., Golden, D. M., Huie, R. E., Kolb, C. E., Kurylo, M. J., Moortgat, G. K., Orkin, V. L., and Wine, P. H.: Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 17, JPL Publication 10-6, Jet Propulsion Laboratory, Pasadena, available at: http://jpldataeval.jpl.nasa.gov (last access: 10 April 2015), 2011.
  14. Sander, R., Compilation of Henry's law constants (version 4.0) for water as solvent, Atmos. Chem. Phys, 15, 4399-4981, 2015. (Download from http://henrys-law.org]
  15. Schwartz, S. E. and White, W. H.: Solubility equilibria of the nitrogen oxides and oxyacids in dilute aqueous solution, in: Advances in Environmental Science and Engineering, edited by: Pfafflin, J. R. and Ziegler, E. N., Gordon and Breach Science Publishers, NY, vol. 4, 1–45, 1981.
  16. Warneck, P. and Williams, J.: The Atmospheric Chemist’s Companion: Numerical Data for Use in the Atmospheric Sciences, Springer Verlag, 2012.
  17. Zhou, X. and Mopper, K.: Apparent partition coefficients of 15 carbonyl compounds between air and seawater and between air and freshwater; Implications for air-sea exchange, Environ. Sci. Technol., 24, 1864–1869, 1990.

--Bob Y. (talk) 16:13, 18 August 2015 (UTC)



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