Halogen chemistry mechanism
- 1 Overview
- 1.1 Chlorine
- 1.2 Bromine
- 1.3 Iodine
- 1.4 Key differences from publication
- 1.5 Changes in heterogeneous chemistry
- 1.6 Inclusion of sulfur-halogen chemistry from Chen et al 
- 1.7 Key differences in Simulation
- 1.8 Source code and data files
- 1.9 Known issues
- 2 Configuring simulations
- 3 On-going development
- 4 Previous issues that are now resolved
- 5 References
The halogen simulation present in GEOS-Chem v11-02d (approved 12 Feb 2018) was build atop of GEOS-Chem v10-01 and brought into the main code branch at v11-01g. This code brings together published halogen developments in GEOS-Chem as described in detail by Sherwen et al [2016b], including the methyl iodide simulation [Bell et al 2002], the iodine simulation from Sherwen et al [2016a], the original bromine simulation in GEOS-Chem [Parrella et al 2012] (as described on the wiki), the UCX simulation including stratospheric halogens [Eastham et al 2014], and updates to bromine mechanism [Schmidt et al 2016]. Further updates were made to use NASA JPL15-10 halogen cross-sections and rates [Sherwen et al. 2017].
The gas-phase chemistry follows Sherwen et al [2016b], with updates made to the heterogenous code to work with structural changes from v10-01 to v11-01.
- Key additions vs. "out of the box" v10-01:
- Addition of 21 new tracers (for further details on these tracers, please see the GEOS-Chem species wiki page). All halogen tracers are shown below, with new ones in bold. This includes five aerosol tracers for bromine (BrSALA, BrSALC) and iodine (ISALA, ISALC, AERI).
- Emissions of iodocarbons (CH3I, CH2I2, CH2ICl, CH2IBr) have been included following Ordonez et al . Emissions of inorganic iodine (HOI, I2) has been using the parameterisation from Carpenter et al  and Macdonald et al .
- Wet deposition of 10 species (HOCl, ClNO3, HI, HOI, INOy, I2OX, AERI) and dry deposition of 8 species (HI, HOI, INOy, I2OX, AERI).
Stratospheric chlorine chemistry is from UCX [Eastham et al 2014]. Tropospheric chlorine chemistry follows that described in Eastham et al  and Schmidt et al , with additions described in Sherwen et al [2016b]. These additions include tropospherically relevant reactions based on the JPL 10-6 compilation [Sander et al., 2011] and IUPAC [Atkinson et al., 2006]. The heterogenous reaction of N2O5 on aerosols was updated to yield products of ClNO2 and HNO3 [Bertram and Thornton, 2009; Roberts et al., 2009] on sea salt and 2HNO3 on other aerosol types. Reaction probabilities are unchanged [Evans and Jacob, 2005].
The bromine simulation incorporates the work of Parrella et al  (See wiki article here on incorporation in earlier versions), with updates (especially to heterogenous process) as described in detail by Schmidt et al . Minor updates to Schmidt et al  are described in Sherwen et al [2016b].
The iodine simulation is described in Sherwen et al [2016a], with updates to coupling with bromine and chlorine described in Sherwen et al [2016b]. Notably, the cycling of iodine on aerosol now results in production of ICl and IBr, instead of I2 as in Sherwen et al [2016a].
Key differences from publication
Certain changes were made during implementation of the halogens code in v10-01 into v11-02 that are not described in Sherwen et al (2016b). These include:
- In combination with UCX [Eastham et al 2014], halogen chemistry is calculated online for both troposphere and stratosphere. In Sherwen et al [2016a, 2016b, 2107] the troposphere was calculated offline.
- Updates to heterogeneous chemistry (see separate section with detail below).
- Minor deposition routes included in previous publications were removed for simplicity (Br2, ICl, IBr, I2).
- Rates were updated following the JPL15-10 complication [Sherwen et al 2017]. Rates were also updated to more consistently use JPL over alternative options (e.g. vs IUPAC).
- Updates to VOCs (inc. oceanic acetaldehyde source) in the simulation (see “PAN updates”) will decrease Bry mixing ratios and therefore halogen impacts.
- Uptake of HOBr by Br-/Cl-/S(IV) in aerosols and cloud droplets now treated as a "one-bulk" process following Chen et al , rather than "multiple" uptake of HOBr by Br-/Cl-/S(IV) in aerosol and cloud droplets.
Changes in heterogeneous chemistry
Due to updates structuctural changes in GEOS-Chem (aka Flexchem making the smvgear mechanism obsolete), the heterogenous chemistry routines have been updated to allow for use of more complex heterogenous chemistry previously calculated in Calcrate.F [Eastham et al 2014, Schmidt et al. 2016, Sherwen et al 2016b].
This work required a revamp of the heterogeneous chemistry. As a result, all heterogeneous reactions except for direct uptake (e.g. HO2) and those involving sea salt Cl- (which is not explicitly tracked) are now calculated using a second-order rate constant. This should help to make the het-chem easier to extend, as new functions have been implemented which will automatically convert a pseudo-first-order rate constant into a second order constant while performing safety checks and imposing (if requested) limits on depletion rates to avoid instability.
These changes are implemented using the helper function "kIIrILtd" in gckpp_HetRates.F90. It’s a helper function which converts an pseudo-1st-order reaction to a 2nd-order one, by dividing the reaction rate by the concentration of the other reactant (kII from kI). If provided, a minimum reactant lifetime can also be provided, which has been important in the past for some chlorine activation chemistry (hence Ltd). For example, the reaction rate for ClONO2 + HCl –aerosol--> Cl2 + HNO3 is calculated as the first order rate kI, but if we write the reaction as ClONO2 = Cl2 + HNO3 then we will get an artificial source of chlorine (while also failing to account for possible chemical depletion of HCl). The answer is to use kIIrILtd to convert kI to kII, where kII = kI / [HCl]. The overall reaction rate will be unaffected, but we can now write the “correct” reaction rate in the KPP reaction file, and will not run into the problems described above in terms of balancing Cl atoms and capturing HCl loss.
Inclusion of sulfur-halogen chemistry from Chen et al 
Sulfur oxidation by reactive halogens, as described by Chen et al , was included in the same development branch (v11-2d) of the GEOS-Chem code as the updates to the halogen simulation detailed here.
From Chen et al :
Sulfur and reactive bromine (Bry) play important roles in tropospheric chemistry and the global radiation budget. The oxidation of dissolved SO2 (S(IV)) by HOBr increases sulfate aerosol abundance and may also impact the Bry budget, but is generally not included in global climate and chemistry models. In this study, we implement HOBr + S(IV) reactions into the GEOS-Chem global chemical transport model and evaluate the global impacts on both sulfur and Bry budgets. Modeled HOBr mixing ratios on the order of 0.1–1.0 parts per trillion (ppt) lead to HOBr + S(IV) contributing to 8% of global sulfate production and up to 45% over some tropical ocean regions with high HOBr mixing ratios (0.6–0.9 ppt). Inclusion of HOBr + S(IV) in the model leads to a global Bry decrease of 50%, initiated by the decrease in bromide recycling in cloud droplets. Observations of HOBr are necessary to better understand the role of HOBr + S(IV) in tropospheric sulfur and Bry cycles.
Text S2 in the supporting document for Chen et al  describes the parameterisation of HOBr + S(IV) reactions now included in GEOS-Chem.
Key differences in Simulation
In addition to changes seen on implementation of halogen chemistry in v10-01 detailed in publications [Eastham et al 2014, Schmidt et al. 2016, Sherwen et al 2016b]. Please find some details on changes to the standard simulation seen (full 1yr benchmark plots are found inked here).
Differences in simulation to publications
Once v11-2 is released, detail will be added here on how different configurations of v11-2 compare to published versions.
Source code and data files
A monthly inventory of Iodocarbon emissions are included from Ordonez et al. . These files were the result of a project lead by Alfonso Saiz-Lopez and he has kindly allowed for them to be distributed with the main GEOS-Chem code.
These new data files are contained in the HEMCO data directory tree. For detailed instructions on how to download these data files to your disk server, please see our Downloading the HEMCO data directories wiki post.
- CH3I is not currently calculated on-line. Instead the emissions of Bell et al  are currently read in from an offline NetCDF.
- For consistency with published work. Certain reactions that are included in the stratosphere (e.g. ClNO3+HCl, BrNO3+HCl, HOCl+HCl and HOCl+HBr) remain unconsidered in the troposphere.
- ClNO2 production on sulfate following condensation of HCl is not considered (HCl+N2O5=(sulfate aerosol)>ClNO2) for consistency with Sherwen et al 2016b.
- The “uptake” reaction of HCl results in destruction of Cl, as there is no aerosol-phase Cl tracer.
- There are only aerosol-phase bromine tracers for sea-salt, so Bry uptake cannot occur on sulfate.
- Release of IX by heterogenous iodine cycling (HOI, INOy) leads to net production of Cly and Bry as no aqueous phase Cl/Br is considered in the reaction (e.g. excess Cl-/Br- is assumed).
Switching on sea-salt bromide emission
Sea-salt debromination was "switched on" in Chen et al. , but not in the updated heterogenous Br simulation [Schmidt et al. 2016] and subsequent papers that included this scheme [Sherwen et al 2016a,b,c,2017]. To turn on "sea-salt debromination" in v11-2, bromide is emitted with sea-salt. This is done in v11-2d by updating the HEMCO extension settings in HEMCO_Config.rc as below:
--> Emit Br2 : false --> Br2 scaling : 1.0 --> Model sea salt Br- : false --> Br- mass ratio : 2.11e-3
--> Emit Br2 : false --> Br2 scaling : 1.0 --> Model sea salt Br- : true --> Br- mass ratio : 2.11e-3
Switching off HOBr + S(IV) chemistry
Chen et al  describes "HOBr + S(IV)" chemistry, which is included in the standard simulation from v11-2d. Other recent GEOS-Chem halogen papers do not include this chemistry [Eastham et al 2014, Schmidt et al. 2016, Sherwen et al 2016a,b,c,2017]. To switch off this chemistry you just update in gckpp_HetRates.F90 (in KPP/Standard/, at line ~650) as shown below.
!-------------------------------------------------------------------- ! Get parameters for HOBr + S(IV) !-------------------------------------------------------------------- ! Cloud bisulfite (HSO3-) concentration [mol/l] from sulfate_mod.F HSO3conc_Cld = State_Chm%HSO3_AQ(I,J,L) ! Cloud sulfite (SO3--) concentration [mol/l] from sulfate_mod.F SO3conc_Cld = State_Chm%SO3_AQ(I,J,L)
!-------------------------------------------------------------------- ! Get parameters for HOBr + S(IV) !-------------------------------------------------------------------- ! Cloud bisulfite (HSO3-) concentration [mol/l] from sulfate_mod.F HSO3conc_Cld = TINY(1e+0_fp) ! Cloud sulfite (SO3--) concentration [mol/l] from sulfate_mod.F SO3conc_Cld = TINY(1e+0_fp)
The halogen simulation will developed further in the future. Please see the GEOS-Chem model development priorities for more details.
Previous issues that are now resolved
Fix for N2O5 uptake
This update was included in v11-02f (approved 17 May 2018).
Xuan Wang wrote:
- In KPP directory, gckpp_HetRates.F90, around line 700:
HET(ind_N2O5, 1) = kIIR1Ltd( spcVec, Ind_('N2O5'), Ind_('H2O'), & HETN2O5(1.08E2_fp, 1E-1_fp))
- This changes the N2O5 uptake rate calculation from 1st order to 2nd order, but no corresponding changes in equation file are found. To fix it, change the equation file from:
N2O5 = 2.000HNO3 : HET(ind_N2O5,1);
N2O5 + H2O = 2.000HNO3 : HET(ind_N2O5,1);
This bug decreases the HNO3 budget and increase N2O5.
Fixes in gckpp_HetRates.F90 following implementation in v11-02d
This update was included in v11-02e (approved 24 Mar 2018).
NOTE: The bugs listed below are only present in the v11-02d development code and not in any of the halogen chemistry papers referred to above.
Lei Zhu wrote:
- There are still a few bugs in gckpp_HetRates.F90 to be fixed in v11-02d. Here is my list.
- 1. Around line 6163 and 6171, signs of Henry’s volatility constant, CR, should be positive. This bug and its fix have been submitted to GCST by Seb.
- 2. Around line 4382, 4489, and 4646, the sign of H_HOBr_E is also wrong. It should be defined as:
REAL(fp), PARAMETER :: H_HOBr_E = -6014.0
- As suggested by Tomas and Seb, we may want to retrieve Henry’s law parameters in gckpp_HetRates.F90 directly from the species database. This would prevent this kind (both 1 and 2) of bug in future.
- 3. Cloud fraction (CLDF) should not be used in calculating the cloud volume (Vliq and VIce) in CLD_PARAMS function around line 6074-6075. Cloud water mixing ratio (QL and QI), by definition, is kg of cloud water per kg of dry air mass in the grid. So QL and QI contain cloud fraction information already. To fix it, change
VLiq = CLDF(I,J,L) * QL * AD(I,J,L) / dens_h2o VIce = CLDF(I,J,L) * QI * AD(I,J,L) / dens_h2o
VLiq = QL * AD(I,J,L) / dens_h2o VIce = QI * AD(I,J,L) / dens_h2o
- 4. Lastly, we may want to reevaluate the impact of bromide from sea salt aerosol given recent updates. Now the model has additional sinks of Bry via oceanic Br+ALD2 and HOBr+S(IV). I will do some sensitivity tests on this topic.
- Bell, N., L. Hsu, D. J. Jacob, M. G. Schultz, D. R. Blake, J. H. Butler, D. B. King, J. M. Lobert, and E. Maier-Reimer (2002), Methyl iodide: Atmospheric budget and use as a tracer of marine convection in global models, J. Geophys. Res-Atmos., 107(D17), ACH 8-1–ACH 8-12, doi:http://dx.doi.org/10.1029/2001jd001151
- Eastham, S. D., D. K. Weisenstein, and S. R. H. Barrett (2014), Development and evaluation of the unified tropospheric–stratospheric chemistry extension (UCX) for the global chemistry-transport model GEOS-Chem, Atmos. Environ., 89, 52–63, doi:http://dx.doi.org/10.1016/j.atmosenv.2014.02.001
- Parrella, J. P. et al. (2012), Tropospheric bromine chemistry: implications for present and pre-industrial ozone and mercury, Atmos. Chem. Phys., 12(15), 6723–6740, doi:http://dx.doi.org/10.5194/acp-12-6723-2012
- Schmidt, J. A. et al. (2016), Modeling the observed tropospheric BrO background: Importance of multiphase chemistry and implications for ozone, OH, and mercury, J Geophys. Res-Atmos., doi:http://dx.doi.org/10.1002/2015JD024229
- Sherwen, T. et al. (2016a), Iodine’s impact on tropospheric oxidants: a global model study in GEOS-Chem, Atmos. Chem. Phys., 16(2), 1161–1186, doi:http://dx.doi.org/10.5194/acp-16-1161-2016
- Sherwen, T. et al. (2016b), Global impacts of tropospheric halogens (Cl, Br, I) on oxidants and composition in GEOS-Chem, Atmos. Chem. Phys., 16(18), 12239–12271, doi:http://dx.doi.org/10.5194/acp-16-12239-2016
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- Carpenter, L. J., S. M. MacDonald, M. D. Shaw, R. Kumar, R. W. Saunders, R. Parthipan, J. Wilson, and J. M. C. Plane (2013), Atmospheric iodine levels influenced by sea surface emissions of inorganic iodine, Nat. Geosci., 6(2), 108–111, doi:http://dx.doi.org/10.1038/ngeo1687
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- Tomás Sherwen, Mathew John J Evans, Roberto Sommariva, Lloyd D. J. Hollis, Stephen Ball, Paul Monks, Christopher Reed, Lucy Carpenter, James D Lee, Grant Forster, Brian Bandy, Claire Reeves and William Bloss, Effects of halogens on European air-quality, Faraday Discussions, 200, 2017, DOI:http://dx.doi.org/10.1039/c7fd00026j
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- Bertram, T. H. and Thornton, J. A.: Toward a general parameterization of N2O5 reactivity on aqueous particles: the competing effects of particle liquid water, nitrate and chloride, Atmos. Chem. Phys., 9, 8351-8363, https://doi.org/10.5194/acp-9-8351-2009, 2009
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