[PULL REQUEST]Updates to IONO2 hydrolysis as described in Wang et al 2021

[tsherwen]

Hello GCST,

Please can I request that this minor commit be included in the timescales of the updated Cl+Br+I paper [Wang et al 2021]? the Wang et al [2021] paper is to be submitted to ACPD very very soon. This is a scientific change with small impacts. It includes IONO2 hydrolysis in a way that is more consistent with other XNOy species. A description of the changes will be included in Wang et al [2021].

I can write an accompanying issue for this pull request too.

Cheers,

Tomas

[msulprizio]

Hi @tsherwen. Thanks for this PR. We ask that science updates get approval by the working groups. Could you send an email to the Chemistry WG notifying them of these updates and asking them to prioritize this item at the next GCSC meeting for inclusion in GEOS-Chem?

[tsherwen]

Hello @msulprizio, thanks for the response. Yes, several members of the chemistry working group are aware of this update and I will be emailing the mailing list once the paper is subsmitted. I'll add a message here when I have an update on this. Thanks, Tomas

[yantosca]

@tsherwen : FYI, I am pulling out the heterogeneous chemistry reactions from gckpp_HetRates into gckpp.kpp, so that will likely result in more conflicts w/r/t my development branch.

[stale]

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[tsherwen]

Thanks for adding the #NeverStale tag @yantosca.

The manuscript is now in review in ACPD and once any reviewer comments are addressed I will raise inclusion in the core with the Chemistry working group.

Wang, X., Jacob, D. J., Downs, W., Zhai, S., Zhu, L., Shah, V., Holmes, C. D., Sherwen, T., Alexander, B., Evans, M. J., Eastham, S. D., Neuman, J. A., Veres, P., Koenig, T. K., Volkamer, R., Huey, L. G., Bannan, T. J., Percival, C. J., Lee, B. H., and Thornton, J. A.: Global tropospheric halogen (Cl, Br, I) chemistry and its impact on oxidants, Atmos. Chem. Phys. Discuss. [preprint], https://doi.org/10.5194/acp-2021-441, in review, 2021.

[tsherwen]

Hello @yantosca & @msulprizio,

As discussed on this thread, I have now contacted the Chemistry Working Group about this pull request (pasted below).

The manuscript including the code in this pull request [Wang et al 2021] has now been resubmitted and all reviewer comments addressed.

I will post any updates from the Chemistry Working Group here and I remain keen for this minor update to be included as soon as possible.

Thanks,

Tomás

Hello Lu, Barron, Jingqiu, Mat & Chemistry Working Group,

Please could I check if anyone has any comments about the below pull request below before it is merged into the main branch?

It is part of the code used for the updated "halogens (Cl, Br, I) in GEOS-Chem" paper [Wang et al 2021] linked below? If so, please could you add comments on GitHub (preferable) or respond to this email within 2 weeks (Aug 20th)?

The manuscript has been in review in ACPD and a final version was submitted today after all reviewer comments have been responded to. No issues about this specific part of the manuscript were raised. As well as the information on GitHub, I have also attached a screenshot detailing the minor change that this pull request covers. All other changes for the manuscript are already present within the v12.9.0 code used for the work. I am keen for this pull request to be part of the main code as soon as possible.

#719

Wang, X., Jacob, D. J., Downs, W., Zhai, S., Zhu, L., Shah, V., Holmes, C. D., Sherwen, T., Alexander, B., Evans, M. J., Eastham, S. D., Neuman, J. A., Veres, P., Koenig, T. K., Volkamer, R., Huey, L. G., Bannan, T. J., Percival, C. J., Lee, B. H., and Thornton, J. A.: Global tropospheric halogen (Cl, Br, I) chemistry and its impact on oxidants, Atmos. Chem. Phys. Discuss. [preprint], https://doi.org/10.5194/acp-2021-441, in review, 2021.

acp-2021-441-manuscript-version2.pdf

Thanks,

Tomás

--
Dr Tomás Sherwen
Research Scientist
National Centre for Atmospheric Science (NCAS)
Wolfson Atmospheric Chemistry Laboratories (WACL)
Department of Chemistry, University of York, York, YO10 5DD
tomas.sherwen@york.ac.uk

( Please note: I am temporarily working part-time and I may be slower to respond )

[msulprizio]

Thanks @tsherwen. I've added this item to our Model development priority page under "in the queue". These updates will need to be merged with the dev-kpp branch that will be going into 13.3.0. In that branch, @yantosca has greatly cleaned up gckpp_HetRates.F90 and @michael-s-long has moved sulfate chemistry to KPP and added HMS and C2H2/C2H4 chemistry, so there will likely be conflicts to resolve.

We recommend updating the base branch for this PR to dev once dev-kpp has been merged into dev and we will work with you to address the conflicts from there.

[barronh]

@tsherwen - I'm going to summarize the changes in my own words to make sure I understand this PR correctly. I'll use reaction numbers from your manuscript and reference code lines in the PR. Can you confirm my understanding?

R10, R11, and R12 are retained from the old chemistry.[1] The updates are the removal of persistent uptake reactions[2] and the addition of (R13) IONO2 hydrolysis[3].

The removal of uptake reactions have negligible affect on ISALA/ISALC burdens and small changes at the surface. For HOI, removing uptake increased burdens (11%) and surface concentrations (15%). IONO2, as expected, has the most substantial changes to burden (-25%) and surface concentrations (-47%), which are net changes both from removing persistent uptake (+) and adding photolysis (-).

If I understand the changes, they sound good to me.

[1] Standard.eqn PR new lines:

• 1348-1350 as R11 from the manuscript assuming rates include the branching ratio
• 1352-1355 as R10 from the manuscript assuming rates include the branching ratio
• 1356-1359 as R12 from the manuscript assuming rates include the branching ratio
  [2] Standard.eqn PR old lines 1339-1340, 1350-1353
  [3] Standard eqn PR new lines 1360

[yantosca]

Thanks @tsherwen & @barronh. I will take a look at this for 13.3.0. The only thing to note is that I will have to do a manual merge because the new hetchem rate law functions have been updated and are no longer stored in gckpp_HetRates.F90, so I can't do a direct merge.

[tsherwen]

Hello @barronh,

I've attached the text from the updated "halogens in GEOS-Chem" paper [Wang et al 2021] for reference, as it isn't showing in my copy-paste of the working group email on this thread.

OK. Your summary is correct.

Thanks for reviewing this!

Tomas

[yantosca]

This seems straightforward but I will make the modifications manually, as the hetrates have been updated.

[yantosca]

@tsherwen, I am looking at your code to try to bring this into 13.3.0. I have a question as to which gamma values you use to pass to CLOUDHET. If you look at the calling code in SET_HET, you have:

      !----------------------------------------------------------------------
      ! IONO2 hydrolysis
      !----------------------------------------------------------------------
      kITemp            = HETIONO2( XDenA, TempK, CldFr, SSAlk, H )
      kITemp = kITemp   + CloudHet( 'IONO2', CldFr, Aliq,  Aice,             &
                                     rLiq,   rIce,  TempK, XDenA, H         )

      HET(ind_IONO2, 7) = kIIR1Ltd( spcVec, H%IONO2%mId, H%H2O%mId,          &
                                    kITemp, HetMinLife                      )

And in routine CLOUDHET there is a CASE statement to pick gammaLiq and gammaIce:

      !------------------------------------------------------------------------
      ! Select Gamma and molar mass for this species
      !------------------------------------------------------------------------
      !%%% BMY NOTE: GET RID OF THIS CASE STATEMENT, IT IS INEFFICIENT
      !%%% TO DO A STRING TEST ON EVERY (I,J,L) GRID BOX (bmy, 6/16/20)
      select case (trim(speciesName))
      case ('HO2')
         gammaLiq = 0.10_fp
         gammaIce = 0.025_fp
         molmass  = H%HO2%MW_g
      case ('NO2')
         gammaLiq = 1e-8_fp
         gammaIce = 0.0_fp
         molmass  = H%NO2%MW_g
      case ('NO3')
         gammaLiq = 0.002_fp
         gammaIce = 0.001_fp
         molmass  = H%NO3%MW_g
      case ('N2O5')
         ! Reactive uptake coefficient for N2O5 on liquid water cloud
         ! Value is 0.03 at 298 K (JPL, Burkholder et al., 2015)
         ! For temperature dependence, JPL recommends the same as
         ! sulfuric acid aerosol at zero percent H2SO4, which is 0.019 at 298 K.
         ! Then apply constant scale factor (0.03/0.019)
         gammaLiq = ( 0.03_fp / 0.019_fp ) * &
              exp( -25.5265_fp + 9283.76_fp / T - 851801.0_fp / T**2 )
         ! Reactive uptake coefficient for N2O5 on water ice
         gammaIce = 0.02_fp
         molmass  = H%N2O5%MW_g
      case ('BrNO3')
         gammaLiq = MAX( 0.0021_fp*T - 0.561_fp, 1e-30_fp )
         gammaIce = 5.3e-4_fp * exp(1100.0_fp / T)
         molmass  = H%BrNO3%MW_g
      case ('ClNO3')
         if ( present(xliq) ) gammaLiq = xliq
         if ( present(xice) ) gammaIce = xice
         molmass = H%ClNO3%MW_g

      case ('IONO2')

         if ( present(xliq) ) gammaLiq = xliq
         if ( present(xice) ) gammaIce = xice
         molmass = H%IONO2%MW_g

But if you notice, for IONO2, it's expecting external optional variables XLIQ and XICE to be passed in. Yet in the calling sequence, XLIQ and XICE aren't passed. Is this a bug?

For hydrolysis I presume you'd want

XLIQ = gammaLiq = 1.0
XICE = gammaIce = 1.0

is that right?

[yantosca]

Or would you use the values for BrNO3:

         gammaLiq = MAX( 0.0021_fp*T - 0.561_fp, 1e-30_fp )
         gammaIce = 5.3e-4_fp * exp(1100.0_fp / T)

[yantosca]

Need clarification about the value of XLIQ and XICE for IONO2 to be passed into CloudHet. It seems that there is a bug but I cannot be sure.

[tsherwen]

Hello @yantosca,

Thanks for catching this. It seems to be a typo in the branch passed.

The values should be as below, as this what was used to make the uptake coefficient consistent with hydrolysis in aerosols.

case ('IONO2')
         gammaLiq = 0.01
         gammaIce = 0.01
         molmass = H%IONO2%MW_g

I know we have discussed this on various threads, but please @xuanw0316 can you just confirm that this is what was in the final runs for the ACP paper?

Thanks,

Tomas

[xuanw0316]

@tsherwen @yantosca
Yes those values are what I use in all my runs and the ACP paper.

gammaLiq = 0.01
gammaIce = 0.01

[tsherwen]

Thanks for the quick response @xuanw0316.

To be clear though, we do not have cloud hydrolysis of IONO2 switched on in the core runs in the ACP paper?

This was to be explored separately in the other work. Large impacts were found on including those additional updates.

[yantosca]

Thanks @tsherwen @xuanw0316! I can go forward with this. We'll definitely get it into 13.3.0.

[yantosca]

I am going to close out this PR, as it has now been superseded by PR #923. The modifications in this PR could not be merged because the base code no longer exists in the latest development branch. I have taken the algorithm described in this PR and applied it to the more recent development branch.