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Merge PR #2352 (Fixes for ALK4 and R4N2 chemistry from J. Brewer)
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This merge brings PR #2352 (Add fixes for ALK4 and R4N2 chemistry from
Brewer et al. (2023, JGR), by @msulprizio) into the GEOS-Chem 14.5.0
development stream.

R4N2 was a common product of alkane, isoprene, and monoterpene oxidation
and produced organonitrate SOA but we don’t want ALK4 to produce
organonitrate SOA as discusses in #1625. A fix from Jared Brewer is
included here.

Signed-off-by: Bob Yantosca <[email protected]>
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yantosca committed Aug 1, 2024
2 parents e29a4c9 + 6548a8b commit 0a392d4
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -8,6 +8,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
### Added
- Set `KPP_AbsTol` to 1e5 for dummy species in `species_database.yml` and `species_database_hg.yml`
- Vectors `State_Chm%KPP_AbsTol` and `State_Chm%KPP_RelTol`
- Four new species ALK4N1, ALK4N2, ALK4O2, and ALK4P to address issues in ALK4 and R4N2 chemistry following Brewer et al. (2023, JGR)
- ALK4N1 and ALK4N2 to Ox family in KPP

### Changed
- Copy values from `State_Chm%KPP_AbsTol` to `ATOL` and `State_Chm%KPP_RelTol` to `RTOL` for fullchem and Hg simulations
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52 changes: 45 additions & 7 deletions KPP/custom/custom.eqn
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Expand Up @@ -36,6 +36,7 @@ DEVELOPERS (initials and email/GitHub)
* HOTP : Havala Pye : [email protected]
* JAF : Jenny Fisher : @jennyfisher
* JAS : Johan Schmidt : [email protected]
* JFB : Jared Brewer : @JFBrewer
* JMAO : Jingqiu Mao : @jingqiumao
* JMM : Jonathan Moch : [email protected]
* JPP : Justin Parrella : [email protected]
Expand Down Expand Up @@ -64,6 +65,7 @@ REFERENCES (alphabetical order)
* Bates2019 : https://doi.org/10.5194/acp-19-9613-2019
* Bates2021a : https://doi.org/10.1029/2020JD033439
* Bates2021b : https://doi.org/10.5194/acp-2021-605
* Brewer2023 : https://doi.org/10.1029/2022JD037257
* Browne2011 : https://doi.org/10.5194/acp-11-4209-2011
* Browne2014 : https://doi.org/10.5194/acp-14-1225-2014
* Carter2022 : https://doi.org/10.5194/acp-22-12093-2022
Expand Down Expand Up @@ -123,6 +125,10 @@ ACTA = IGNORE; {CH3C(O)OH; Acetic acid}
AERI = IGNORE; {I; Dissolved iodine}
ALD2 = IGNORE; {CH3CHO; Acetaldehyde}
ALK4 = IGNORE; {>= C4 alkanes}
ALK4N1 = IGNORE; {RO2 from ALKN2}
ALK4N2 = IGNORE; {RO2NO; >= C4 alkylnitrates from ALK4}
ALK4O2 = IGNORE; {RO2 from ALK4}
ALK4P = IGNORE; {CH3CH2CH2CH2OOH; Peroxide from ALK4O2}
AONITA = IGNORE; {Aerosol-phase organic nitrate from aromatic precursors}
AROMRO2 = IGNORE; {generic peroxy radical from aromatic oxidation}
AROMP4 = IGNORE; {Generic C4 product from aromatic oxidation}
Expand Down Expand Up @@ -376,7 +382,7 @@ PRPN = IGNORE; {O2NOCH2CH(OOH)CH3; Peroxide from PRN1}
PYAC = IGNORE; {CH3COCOOH; Pyruvic acid}
R4N1 = IGNORE; {RO2 from R4N2}
R4N2 = IGNORE; {RO2NO; >= C4 alkylnitrates}
R4O2 = IGNORE; {RO2 from ALK4}
R4O2 = IGNORE; {RO2 from >= C4 biogenic organics}
R4P = IGNORE; {CH3CH2CH2CH2OOH; Peroxide from R4O2}
RA3P = IGNORE; {CH3CH2CH2OOH; Peroxide from A3O2}
RB3P = IGNORE; {CH3CH(OOH)CH3; Peroxide from B3O2}
Expand Down Expand Up @@ -521,7 +527,14 @@ C3H8 + OH = A3O2 : GCARR_abc(1.97d-12,1.23d0,-675.0d0)
A3O2 + NO = NO2 + HO2 + RCHO : GC_RO2NO_B2_aca(2.90d-12, 350.0d0, 3.0d0); {2019/05/10; Fisher2018; JAF}
A3O2 + NO = NPRNO3 : GC_RO2NO_A2_aca(2.90d-12, 350.0d0, 3.0d0); {2019/05/10; Fisher2018; JAF}
PO2 + NO = NO2 + HO2 + CH2O + ALD2 : GCARR_ac(2.70d-12, 350.0d0);
ALK4 + OH = R4O2 : GCARR_ac(9.10d-12, -405.0d0);
ALK4 + OH = ALK4O2 : GCARR_ac(9.10d-12, -405.0d0); {2023/05/14; Brewer2023; JFB}
ALK4O2 + NO = NO2 + 0.340ACET + 0.190MEK +
0.190MO2 + 0.270HO2 + 0.340ALD2 +
0.150RCHO + 0.050A3O2 + 0.190B3O2 +
0.340OTHRO2 : GC_RO2NO_B2_aca(2.70d-12, 350.0d0, 4.5d0); {2023/05/14; Brewer2023; JFB}
ALK4O2 + NO = ALK4N2 : GC_RO2NO_A2_aca(2.70d-12, 350.0d0, 4.5d0); {2023/05/14; Brewer2023; JFB}
ALK4N1 + NO = 2.000NO2 + 0.640RCHO +
0.970ALD2 + 0.640CH2O : GCARR_ac(2.70d-12, 350.0d0); {2023/05/14; Brewer2023; JFB}
R4O2 + NO = NO2 + 0.340ACET + 0.190MEK +
0.190MO2 + 0.270HO2 + 0.340ALD2 +
0.150RCHO + 0.050A3O2 + 0.190B3O2 +
Expand All @@ -531,12 +544,13 @@ R4N1 + NO = 2.000NO2 + 0.640RCHO +
0.970ALD2 + 0.640CH2O : GCARR_ac(2.70d-12, 350.0d0); {2023/04/18; Bates2023; KHB}
ATO2 + NO = NO2 + CH2O + MCO3 : GCARR_ac(2.90d-12, 300.0d0); {2023/04/18; JPL 19-5; KHB}
KO2 + NO = 0.928NO2 + 0.919ALD2 +
0.919MCO3 + 0.072R4N2 : GCARR_ac(2.70d-12, 350.0d0); {2023/04/18; Bates2023; KHB}
0.919MCO3 + 0.072ALK4N2 : GCARR_ac(2.70d-12, 350.0d0); {2023/04/18; Bates2023; KHB},{2023/05/14; Brewer2023; JFB}
B3O2 + NO = NO2 + HO2 + ACET : GC_RO2NO_B2_aca(2.70d-12, 360.0d0, 3.0d0); {2019/05/10; Fisher2018; JAF}
B3O2 + NO = IPRNO3 : GC_RO2NO_A2_aca(2.70d-12, 360.0d0, 3.0d0); {2019/05/10; Fisher2018; JAF}
PRN1 + NO = 2.000NO2 + CH2O + ALD2 : GCARR_ac(2.70d-12, 350.0d0);
ALK4 + NO3 = HNO3 + R4O2 : GCARR_ac(2.80d-12, -3280.0d0);
ALK4 + NO3 = HNO3 + ALK4O2 : GCARR_ac(2.80d-12, -3280.0d0); {2023/05/14; Brewer2023; JFB}
R4N2 + OH = R4N1 + H2O : 1.60d-12;
ALK4N2 + OH = ALK4N1 + H2O : 1.60d-12; {2023/05/14; Brewer2023; JFB}
ACTA + OH = MO2 + CO2 + H2O : GCARR_ac(3.15d-14, 920.0d0); {2013/02/12; JPL 10-6; BHH,JMAO,EAM}
OH + RCHO = RCO3 + H2O : GCARR_ac(6.00d-12, 410.0d0);
RCO3 + NO2 {+M} = PPN : GCJPLPR_abab(9.00d-28, 8.9d0, 7.7d-12, 0.2d0, 0.6d0); {JPL Eval 17}
Expand All @@ -552,6 +566,8 @@ PO2 + MO2 = HO2 + 0.500ALD2 + 1.250CH2O +
0.250ROH : 5.92d-13;
R4O2 + HO2 = R4P : GCARR_ac(7.40d-13, 700.0d0);
R4N1 + HO2 = R4N2 : GCARR_ac(7.40d-13, 700.0d0);
ALK4O2 + HO2 = ALK4P : GCARR_ac(7.40d-13, 700.0d0); {2023/05/14; Brewer2023; JFB}
ALK4N1 + HO2 = ALK4N2 : GCARR_ac(7.40d-13, 700.0d0); {2023/05/14; Brewer2023; JFB}
ATO2 + HO2 = 0.150MCO3 + 0.150OH +
0.150CH2O + 0.850ATOOH : GCARR_ac(8.60d-13, 700.0d0); {2013/03/22; Paulot2009; FP,EAM,JMAO,MJE}
KO2 + HO2 = 0.150OH + 0.150ALD2 +
Expand All @@ -572,6 +588,14 @@ R4O2 + MO2 = 0.160ACET + 0.100MEK +
R4N1 + MO2 = NO2 + 0.950CH2O + 0.380ALD2 +
0.580RCHO + 0.150R4O2 + 0.500HO2 +
0.250MOH + 0.375ROH : 8.37d-14; {2023/04/18; Bates2023; KHB}
ALK4O2 + MO2 = 0.160ACET + 0.100MEK +
0.090MO2 + 0.140HO2 + 0.160ALD2 +
0.130RCHO + 0.030A3O2 + 0.090B3O2 +
0.160OTHRO2 + 0.250MEK + 0.750CH2O +
0.250MOH + 0.380ROH + 0.500HO2 : 8.37d-14; {2023/05/14; Brewer2023; JFB}
ALK4N1 + MO2 = NO2 + 0.950CH2O + 0.380ALD2 +
0.580RCHO + 0.150R4O2 + 0.500HO2 +
0.250MOH + 0.375ROH : 8.37d-14; {2023/05/14; Brewer2023; JFB}
ATO2 + MO2 = 0.300HO2 + 0.500CH2O +
0.300MCO3 + 0.200HAC + 0.500MGLY +
0.500MOH + 0.300CO2 : GCARR_ac(7.50d-13, 500.0d0); {2023/04/18; Bates2023; KHB}
Expand Down Expand Up @@ -622,6 +646,8 @@ RA3P + OH = 0.640OH + 0.360A3O2 +
RB3P + OH = 0.791OH + 0.209B3O2 +
0.791ACET : GCARR_ac(8.78d-12, 200.0d0); {2013/03/22; Paulot2009; FP,EAM,JMAO,MJE}
R4P + OH = 0.790OH + 0.210R4O2 + 1.185RCHO : GCARR_ac(8.78d-12, 200.0d0); {2013/03/22; Paulot2009; FP,EAM,JMAO,MJE; 2023/04/18; Bates2023; KHB}
ALK4P + OH = 0.790OH + 0.210ALK4O2 +
1.185RCHO : GCARR_ac(8.78d-12, 200.0d0); {2023/05/14; Brewer2023; JFB}
RP + OH = RCO3 : GCARR_ac(6.13d-13, 200.0d0); {2013/03/22; Paulot2009; FP,EAM,JMAO,MJE}
PP + OH = 0.791OH + 0.209PO2 + 0.791HAC : GCARR_ac(8.78d-12, 200.0d0); {2013/03/22; Paulot2009; FP,EAM,JMAO,MJE}
LVOC + OH = OH : GCARR_ac(4.82d-11, -400.0d0); {2017/06/14; Marais2016; EAM}
Expand All @@ -635,6 +661,10 @@ R4O2 + MCO3 = 0.271MEK + 0.100ACTA +
0.900MO2 + 0.290ACET + 0.243HO2 +
0.290ALD2 + 0.290OTHRO2 + 0.255RCHO
+ 0.045A3O2 + 0.162B3O2 + 0.900CO2: GCARR_ac(1.87d-12, 500.0d0); {2023/04/18; Bates2023; KHB}
ALK4O2 + MCO3 = 0.271MEK + 0.100ACTA +
0.900MO2 + 0.290ACET + 0.243HO2 +
0.290ALD2 + 0.290OTHRO2 + 0.255RCHO
+ 0.045A3O2 + 0.162B3O2 + 0.900CO2: GCARR_ac(1.87d-12, 500.0d0); {2023/05/14; Brewer2023; JFB}
ATO2 + MCO3 = 0.900MO2 + 0.900MCO3 +
0.900CH2O + 0.100MGLY + 0.100ACTA +
0.900CO2 : GCARR_ac(1.87d-12, 500.0d0); {2023/04/18; Bates2023; KHB}
Expand All @@ -646,6 +676,9 @@ B3O2 + MCO3 = 0.900MO2 + 0.900HO2 +
R4N1 + MCO3 = 0.900MO2 + 0.100ACTA +
0.613RCHO + 0.351CH2O + 0.675ALD2 +
0.270R4O2 + 0.645CO2 + NO2 : GCARR_ac(1.87d-12, 500.0d0); {2023/04/18; Bates2023; KHB}
ALK4N1 + MCO3 = 0.900MO2 + 0.100ACTA +
0.613RCHO + 0.351CH2O + 0.675ALD2 +
0.270R4O2 + 0.645CO2 + NO2 : GCARR_ac(1.87d-12, 500.0d0); {2023/05/14; Brewer2023; JFB}
PRN1 + MCO3 = 0.900MO2 + 0.900CH2O +
0.900CO2 + 0.900ALD2 + 0.100RCHO +
0.100ACTA + NO2 : GCARR_ac(1.87d-12, 500.0d0); {2023/04/18; Bates2023; KHB}
Expand Down Expand Up @@ -818,7 +851,7 @@ Cl + C3H8 = HCl + B3O2 : GCARR_ac(6.54d-11, 60.0d0);
Cl + C3H8 = HCl + A3O2 : GCARR_ac(8.12d-11, -90.0d0); {2017/09/22; Sherwen2016b;TS,JAS,SDE}
Cl + ACET = HCl + ATO2 : GCARR_ac(1.63d-11, -610.0d0); {2017/09/22; Sherwen2016b;TS,JAS,SDE; 2023/04/18; JPL 19-5; KHB}
Cl + ISOP = HCl + 0.5IHOO1 + 0.5IHOO4 : GCARR_ac(7.60d-11, 500.0d0); {2019/11/06; Sherwen2016b;KHB,TS,JAS,SDE}
Cl + ALK4 = HCl + R4O2 : 2.05d-10; {2017/09/22; Sherwen2016b;TS,JAS,SDE}
Cl + ALK4 = HCl + ALK4O2 : 2.05d-10; {2023/05/14; Brewer2023; JFB}
Cl + PRPE {+M} = HCl + PO2 {+M} : GCJPLPR_aa(4.00d-28, 2.8d-10, 0.6d0); {2017/09/22; Sherwen2016b;TS,JAS,SDE}
Br + PRPE = HBr + PO2 : 3.60d-12; {2017/09/22; Sherwen2016b;TS,JAS,SDE}
I + NO {+M} = INO {+M} : GCJPLPR_aba(1.80d-32, 1.0d0, 1.70d-11, 0.6d0); {2017/09/22; Sherwen2016b;TS,JAS,SDE; 2023/04/18; JPL 19-5; KHB}
Expand Down Expand Up @@ -1396,8 +1429,8 @@ AROMP5 + OH = 0.6MGLY + 0.15ACTA +
0.33RCO3 + 0.25CO + 0.52RCOOH : 5.0d-11; {2021/09/29; Bates2021b; KHB,MSL}
AROMP5 + O3 = 0.6MGLY + 0.3ACTA + 0.2HCOOH +
0.5CO + 0.95GLYC + 0.1HO2 + 0.1OH : 8.0d-16; {2021/09/29; Bates2021b; KHB,MSL}
AROMP5 = 0.2HO2 + 0.2R4O2 +
0.2MGLY + 1.15RCHO + 0.05CO : 1.5d-3; {2021/09/29; Bates2021b; KHB,MSL; 2023/04/18; Bates2023; KHB}
AROMP5 = 0.2HO2 + 0.2ALK4O2 +
0.2MGLY + 1.15RCHO + 0.05CO : 1.5d-3; {2021/09/29; Bates2021b; KHB,MSL; 2023/04/18; Bates2023; KHB},{2023/05/14; Brewer2023; JFB}
//
// KHB -- "we still need to include the dummy species for aromatic oxidation
// to make the complex SOA code work. Hopefully this will be changed
Expand Down Expand Up @@ -1570,12 +1603,17 @@ ETP + hv = OH + HO2 + ALD2 : PHOTOL(80);
RA3P + hv = OH + HO2 + RCHO : PHOTOL(81);
RB3P + hv = OH + HO2 + ACET : PHOTOL(82);
R4P + hv = OH + HO2 + 1.500RCHO : PHOTOL(83); {2023/04/18; Bates2023; KHB}
ALK4P + hv = OH + HO2 + 1.500RCHO : PHOTOL(83); {2023/05/14; Brewer2023; JFB}
PP + hv = OH + HO2 + ALD2 + CH2O : PHOTOL(84);
RP + hv = OH + HO2 + ALD2 + MO2 : PHOTOL(85); {2023/04/18; Bates2023; KHB}
R4N2 + hv = NO2 + 0.340ACET + 0.190MEK +
0.190MO2 + 0.270HO2 + 0.340ALD2 +
0.150RCHO + 0.050A3O2 + 0.190B3O2 +
0.340OTHRO2 : PHOTOL(98); {2023/04/18; Bates2023; KHB}
ALK4N2 + hv = NO2 + 0.340ACET + 0.190MEK +
0.190MO2 + 0.270HO2 + 0.340ALD2 +
0.150RCHO + 0.050A3O2 + 0.190B3O2 +
0.340OTHRO2 : PHOTOL(98); {2023/05/14; Brewer2023; JFB}
MAP + hv = OH + MO2 + CO2 : PHOTOL(99); {2023/04/18; Bates2023; KHB}
Br2 + hv = 2.000Br : PHOTOL(23); {2012/06/07; Parrella2012; JPP}
BrO + hv = Br + O : PHOTOL(28); {2014/02/03; Eastham2014; SDE}
Expand Down
4 changes: 4 additions & 0 deletions KPP/fullchem/CHANGELOG_fullchem.md
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Expand Up @@ -4,6 +4,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),

# Mechanism history

## [14.5.0] - TBD
- Added four new species ALK4N1, ALK4N2, ALK4O2, and ALK4P to address issues in ALK4 and R4N2 chemistry following Brewer et al. (2023, JGR)
- Added ALK4N1 and ALK4N2 to Ox family in KPP

## [14.4.0] - 2024-05-30
- Bug fix: Change `3.4.e-31` to `3.4.d-31` in `NO2 + O = NO + O2` rxn
- Update rxns with zero Arrhenius `B` parameters to use function `GCARR_ac` instead of `GCARR_abc`
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