Comments
     "Changed to Chem-UCI-MAM5 by Ziming Ke"
     "last touch 20200326 - QT"
     "Modified by Juno Hsu and Qi Tang - 4/9/2020"
     "chemUCI + MAM4 for E3SM"
     "last touch 20200331 - MJP"
End Comments

SPECIES

 Solution
* UCI Chem species
  O3
  OH
  HO2
  H2O2
  CH2O
  CH3O2
  CH3OOH -> CH4O2
  HCL -> HCl
  NH3
  NO
  NO2
  NO3
  N2O5
  HNO3
  HO2NO2
  PAN -> CH3CO3NO2
  CO
  C2H6
  C3H8
  C2H4
  ROHO2 -> C2H5O3
  CH3COCH3
  C2H5O2
  C2H5OOH
  CH3CHO
  CH3CO3
  ISOP -> C5H8
  ISOPO2 -> HOCH2COOCH3CHCH2
  C10H16
  MVKMACR -> C4H6O
* MVKMACR = sum of MVK -> CH2CHCOCH3 + MACR -> CH2CCH3CHO
  MVKO2 -> C4H7O4
  E90 -> O3
  N2OLNZ -> N2
  NOYLNZ -> N
  CH4LNZ -> CH4
  H2OLNZ -> H2O
* MAM4 species
  DMS -> C2H6S
  SO2 -> O2S
  H2SO4
  SOAG0 -> C15H38O2
  SOAG15 ->  C15H38O2
  SOAG24 ->  C15H38O2
  SOAG31 ->  C15H38O2
  SOAG32 ->  C15H38O2
  SOAG33 ->  C15H38O2
  SOAG34 ->  C15H38O2
  SOAG35 ->  C15H38O2
  so4_a1 -> SO4
  so4_a2 -> SO4
  so4_a3 -> SO4
  so4_a5 -> SO4
  nh4_a1 -> NH4
  nh4_a2 -> NH4
  nh4_a3 -> NH4
  no3_a1 -> NO3
  no3_a2 -> NO3
  no3_a3 -> NO3
  pom_a1 -> C
* pom_a2 does not exist
  pom_a3 -> C
  pom_a4 -> C
  soa_a1 -> C15H38O2
  soa_a2 -> C15H38O2
  soa_a3 -> C15H38O2
  bc_a1 -> C
* bc_a2 does not exist
  bc_a3 -> C
  bc_a4 -> C
  dst_a1 -> AlSiO5
* dst_a2 does not exist
  dst_a3 -> AlSiO5
* dst_a4 does not exist
  ca_a1 -> Ca
  ca_a3 -> Ca
  co3_a1 -> CO3
  co3_a3 -> CO3
  ncl_a1 -> Na
  ncl_a2 -> Na
  ncl_a3 -> Na
  cl_a1 -> Cl
  cl_a2 -> Cl
  cl_a3 -> Cl
  mom_a1 -> C8520H11360O8520
  mom_a2 -> C8520H11360O8520
  mom_a3 -> C8520H11360O8520
  mom_a4 -> C8520H11360O8520
  num_a1 -> H
  num_a2 -> H
  num_a3 -> H
  num_a4 -> H
  num_a5 -> H
 End Solution

 Fixed
   M, N2, O2, H2O, H2, CH4, cnst_NO3, cnst_OH
 End Fixed

 Col-int
   O3 = 0.
   O2 = 0.
 End Col-int

End SPECIES


Solution Classes

 Explicit
   E90, N2OLNZ, NOYLNZ, CH4LNZ, H2OLNZ
 End Explicit

 Implicit
   CO, C2H6, C3H8, CH3COCH3
   O3, OH, HO2, H2O2, CH2O, CH3O2, CH3OOH
   NO, NO2, NO3, N2O5, HNO3, HO2NO2, PAN
   C2H5O2, C2H5OOH, CH3CHO, CH3CO3, C2H4, ROHO2
   ISOP, ISOPO2, C10H16, MVKMACR, MVKO2, NH3, HCL
   DMS, SO2, H2SO4 
   SOAG0, SOAG15, SOAG24, SOAG31 
   SOAG32, SOAG33, SOAG34, SOAG35
   so4_a1,  so4_a2,  so4_a3,  so4_a5
   nh4_a1,  nh4_a2,  nh4_a3
   no3_a1,  no3_a2,  no3_a3
   pom_a1,           pom_a3,  pom_a4
   soa_a1,  soa_a2,  soa_a3
   bc_a1,            bc_a3,   bc_a4
   dst_a1,           dst_a3
   ca_a1,            ca_a3
   co3_a1,           co3_a3
   ncl_a1,  ncl_a2,  ncl_a3
   cl_a1,   cl_a2,   cl_a3
   mom_a1,  mom_a2,  mom_a3,  mom_a4
   num_a1,  num_a2,  num_a3,  num_a4, num_a5
 End Implicit

End Solution Classes


CHEMISTRY

 Photolysis
  [jo1dU->,jo3_a]   O3 + hv -> O3
* Production rate of O(1D), this rate is null so as to not lose O3.
  [jo2_b=userdefined,]    O2 + hv -> 2*O3
*  [jo2]       O2 + hv -> 2*O3
  [jh2o2]     H2O2 + hv -> 2*OH
  [jch2o_a]   CH2O + hv -> CO + 2*HO2
  [jch2o_b]   CH2O + hv -> CO + H2
  [jch3ooh]   CH3OOH + hv -> CH2O + HO2 + OH
  [jc2h5ooh->,jch3ooh]   C2H5OOH + hv -> CH3CHO + HO2 + OH
*  [jc2h5ooh]  C2H5OOH + hv -> CH3CHO + HO2 + OH
  [jno2]      NO2 + hv -> NO + O3
  [jno3_a]    NO3 + hv -> NO2 + O3
  [jno3_b]    NO3 + hv -> NO
*  [jno3]      NO3 + hv -> 0.114*NO + 0.886*NO2 + 0.886*O3
  [jn2o5_a]   N2O5 + hv -> NO2 + NO3
  [jn2o5_b]   N2O5 + hv -> NO + O3 + NO3
*  [jn2o5]     N2O5 + hv -> NO2 + NO3
  [jhno3]     HNO3 + hv -> NO2 + OH
  [jho2no2_a] HO2NO2 + hv -> OH + NO3
  [jho2no2_b] HO2NO2 + hv -> NO2 + HO2
*  [jho2no2]   HO2NO2 + hv -> 0.67*NO2 + 0.67*HO2 + 0.33*OH + 0.33*NO3
  [jch3cho]   CH3CHO + hv -> CH3O2 + HO2 + CO
  [jpan]      PAN + hv -> CH3CO3 + NO2
  [jacet]     CH3COCH3 + hv -> 0.67*CH3CO3 + 1.33*CH3O2 + 0.33*CO
*        with Fast-J update to include [jacet_b]= 1/2[jacet_a]  CH3COCH3 + hv -> 2*CH3O2 + CO
*            = 2/3[CH3CO3 + CH3O2] + 1/3[2*CH3O2 + CO]
  [jmvk]      MVKMACR + hv -> 2.0*CH2O + 1.5*CO + 0.5*CH3O2 + 0.5*HO2
*        with Fast-J update to merge values w/[jmacr] = 1/3[jmvk] ?
*             MACR +hv -> CH2O + 2.0*CO + CH3O2 + HO2
*             MVK + hv -> 3*CH2O + CO    **final products estimated
 [jsoa_a1->,.0004*jno2]  soa_a1 + hv ->
 [jsoa_a2->,.0004*jno2]  soa_a2 + hv ->
 [jsoa_a3->,.0004*jno2]  soa_a3 + hv ->
 End Photolysis

 Reactions
[uci1] O3 + H2O -> 2*OH                           ; 1.630E-10, 60
*   fix typo, exp(-B/T), B=60 (JPL15)
[uci2] O3 + H2 -> OH + HO2                        ; 1.200E-10,  0
[uci3] O3 + CH4LNZ -> OH + CH3OO                     ; 1.750E-10,  0
*  These 3 rates for O(1D) rxt w/ H2O, H2, CH4 are scaled with jo1d and divided
*     by the key quenching rates are: N2 = 3.30e-11 exp(55/T), O2 = 2.15e-11 exp(110/T)
*     and H2O = 1.63e-10 exp(60/T), and then multiplied by the rates above.
*  effectively k[uci1] = J(jo1d)*1.63e-10*exp(60/T) /
*     (1.63e-10*exp(60/T)*[H2O] + 3.30e-11*exp(55/T)*[N2] + 2.15e-11*exp(110/T)*[O2])
*  and rxt[uci1] = k[uci1]*[O3]*[H2O]
[lco_h]      CO + OH -> H                                   ; 1.500E-13,  0
[lco_ho2]    CO + OH + M -> HO2 + M                         ; 5.90e-33, 1.0, 1.10E-12, -1.3, 0.6
[lh2_ho2]    H2 + OH -> HO2 + H2O                           ; 2.800E-12, -1800
[lch4]       CH4LNZ + OH -> CH3O2 + H2O                     ; 2.450E-12, -1775
[lc2h6]      C2H6 + OH -> C2H5O2                            ; 7.660E-12, -1020
[lc3h8]      C3H8 + OH -> HO2 + 0.80*CH3COCH3 + 0.20*CH3CHO ; 8.700E-12, -615
[lc2h4_oh]   C2H4 + OH + M -> ROHO2                         ; 1.10E-28, 3.5, 8.40E-12, 1.75, 0.6
[lc2h4_o3]   C2H4 + O3 -> CH2O + CO + 0.5*CH3CHO            ; 1.200E-14, -2630
[lisop_o3]   ISOP + O3 -> MVKMACR + CH2O + OH               ; 1.100e-14, -2000
[lisop_oh]   ISOP + OH -> ISOPO2                            ; 3.000E-11, 360
[lch2o]      CH2O + OH -> CO + H2O + HO2                    ; 5.500E-12, 125
[lo3_oh]     OH + O3 -> HO2 + O2                            ; 1.700E-12, -940
[po3_oh]     OH + OH -> O3 + H2O                            ; 1.800E-12, 0
[lo3_ho2]    HO2 + O3 -> 2*O2 + OH                          ; 1.000E-14, -490
[lho2_oh]    HO2 + OH -> H2O + O2                           ; 4.800E-11, 250
[uci4]  HO2 + HO2 + M -> H2O2 + M                 ; 2.100E-33, 920
*     k[uci4] -> k[uci4] * (1 + 1.4e-21*exp(2200/T)*[H2O])
[uci5]  HO2 + HO2 -> H2O2                         ; 3.000E-13, 460
*     k[uci5] -> k[uci5] * (1 + 1.4e-21*exp(2200/T)*[H2O])
[ph2o2]     OH + OH + M -> H2O2 + M                        ; 6.90e-31, 1.0,  2.60e-11, 0.0, 0.6
[lh2o2]     H2O2 + OH -> H2O + HO2                         ; 1.800E-12, 0
[lo3_no]    NO + O3 -> NO2 + O2                            ; 3.000E-12, -1500
[lno_ho2]   NO + HO2 -> NO2 + OH                           ; 3.300E-12, 270
[lo3_no2]   NO2 + O3 -> NO3 + O2                           ; 1.200E-13, -2450
[lno3_oh]   OH + NO3 -> HO2 + NO2                          ; 2.200e-11, 0
[lno3_no]   NO + NO3 -> 2.*NO2                             ; 1.500e-11, 170
[lhno4]     HO2NO2 + OH -> NO2 + H2O + O2                  ; 1.300E-12, 380
[lhno3]     HNO3 + OH -> NO3 + H2O                         ; 2.400E-14, 460
*   fix needed to add this bimolec rate, missing from the one below
[uci6] HNO3 + OH -> NO3 + H2O
*    k[uci6] = (k2*k3*[M])/(k2 + k3*[M])  k2=2.7e-17*exp(2199/T)  k3=6.5e-34*exp(1335/T)*[M]
[lno2_oh]   NO2 + OH + M -> HNO3 + M              ; 1.80e-30, 3.0,  2.80e-11, 0.0, 0.6
[HO2NO2f]  NO2 + HO2 + M -> HO2NO2 + M            ; 1.90e-31, 3.4,  4.00e-12, 0.3, 0.6
[N2O5f]  NO2 + NO3 + M -> N2O5 + M                ; 2.40E-30, 3.0,  1.60E-12,-0.1, 0.6
[PANf]   CH3CO3 + NO2 + M -> PAN + M              ; 9.70E-29, 5.6,  9.30E-12, 1.5, 0.6
[uci7]   HO2NO2 + M -> HO2 + NO2 + M              ; 2.10E-27, 10900
*     k[uci7] -> k[HO2NO2] / k[uci7]
[uci8]   N2O5 + M -> NO2 + NO3 + M                ; 5.80E-27, 10840
*     k[uci8] -> k[N2O5] / k[uci8]
[uci9]   PAN + M -> CH3CO3 + NO2 + M              ; 9.00E-29, 14000
*     k[uci9] -> k[PAN] / k[uci9]
[lch3o2_ho2]   CH3O2 + HO2 -> CH3OOH + O2                     ; 4.100E-13, 750
[lch3o2_no]    CH3O2 + NO -> CH2O + HO2 + NO2                 ; 2.800E-12, 300
[lch3o2]       CH3O2 + CH3O2 -> 2*CH2O +  2*HO2               ; 9.500E-14, 390
[lch3ooh]      CH3OOH + OH -> 0.7*CH3O2 + 0.3*CH2O + 0.3*OH   ; 3.800E-12, 200
[lc2h5o2_no]   C2H5O2 + NO -> CH3CHO + HO2 + NO2              ; 2.600E-12, 365
[lc2h5o2]      C2H5O2 + C2H5O2 -> 2*CH3CHO + 2*HO2            ; 6.800E-14, 0
[lc2h5o2_ch3]  C2H5O2 + CH3O2 -> CH3CHO + CH2O + 2*HO2        ; 2.500E-14, 0
[lc2h5o2_ho2]  C2H5O2 + HO2 -> C2H5OOH                        ; 7.500E-13, 700
[lc2h5ooh_a]   C2H5OOH + OH -> C2H5O2                         ; 1.900E-12, 190
[lc2h5ooh_b]   C2H5OOH + OH -> CH3CHO + OH                    ; 8.010E-12, 0
[lch3cho_oh]   CH3CHO + OH -> 0.5*CH3CO3 + 0.5*CH3O2 + 0.5*CO ; 4.630E-12, 350
[lch3cho_no3]  CH3CHO + NO3 -> CH3CO3 + HNO3                  ; 1.400E-12, -1900
[lch3co3_no]   CH3CO3 + NO -> CH3O2 + NO2                     ; 8.100E-12, 270
[lch3co3_ch3]  CH3CO3 + CH3O2 -> CH2O + CH3O2 + HO2           ; 2.000E-12, 500
[lch3co3]      CH3CO3 + CH3CO3 -> 2*CH3O2                     ; 2.900E-12, 500
[lch3coch3_a]  CH3COCH3 + OH ->  CH3CO3 + CH2O                ; 1.330e-13, 0
[lch3coch3_b]  CH3COCH3 + OH ->  CH3CO3 + CH2O                ; 3.820e-11, -2000
[lroho2_no]    ROHO2 + NO -> CH3CHO + CH2O + NO2              ; 2.700E-12, 360
[lroho2_ho2]   ROHO2 + HO2 -> CH3CHO + CH2O + OH              ; 1.500E-13, 1300
[lroho2_ch3o2] ROHO2 + CH3O2 -> CH3CO + 2*CH2O + HO2          ; 1.000E-13, 0
[lisopo2_no]   ISOPO2 + NO -> MVKMACR + CH2O + NO2            ; 2.700E-12, 360
[lisopo2_ho2]  ISOPO2 + HO2 -> C2H5OOH + 2*CO                 ; 2.050E-13, 1300
[lisopo2_ch3]  ISOPO2 + CH3O2 -> MVKMACR + 2*CH2O + 2*HO2     ; 1.000E-13, 0
[lmvkmacr_o3]  MVKMACR + O3 -> 0.5*CH3CO3 + CH2O + CH3O2      ; 8.500E-16, -1520
[lmvkmacr_oh]  MVKMACR + OH -> MVKO2                          ; 2.600E-12, 610
[lmvko2_no]    MVKO2 + NO -> 0.5*CH3CO3 + CH2O + NO2          ; 2.700E-12, 360
[lmvko2_ho2]   MVKO2 + HO2 -> C2H5OOH + CO                    ; 1.820E-13, 1300

* UCI heterogeneous reactions has problems with E3SM MAM4 aerosols
* comment out for now. To be fixed with the aerosol team.
*[ucih1]  N2O5  -> 2*HNO3                          ; 0.05E+00
*[ucih2]  NO3   -> HNO3                            ; 0.03E+00
*[ucih3]  HO2   ->                                 ; 0.10E+00

[usr_e90]  E90 ->                                 ; 1.286E-7, 0.

* MAM4 chemistry below
[ldms_oh]     DMS + OH -> SO2                    ; 9.600E-12, -234
[usr_DMS_OH]  DMS + OH ->  .5 * SO2 + .5 * HO2
[usr_SO2_OH]  SO2 + OH -> H2SO4
[ldms_no3]    DMS + NO3 -> SO2 + HNO3            ; 1.9e-13,  520.
[NH3_OH]      NH3 + OH -> H2O                    ; 1.70e-12,    -710.

* VBS SOAG reactions
              SOAG0 + OH -> 1.15*SOAG15                                       ; 2e-11
              SOAG15 + OH -> 1.15*SOAG24                                      ; 2e-11
              SOAG24 + OH -> 0.46*SOAG33 + 0.5*SOAG35                         ; 2e-11

              ISOP + OH ->   0.00272*SOAG32 + 0.00981*SOAG33 + 0.00218*SOAG34       ; 2.54e-11, 410
              C10H16 + OH -> 0.14986*SOAG32 + 0.05450*SOAG33 + 0.09264*SOAG34     ; 1.2e-11, 444
              ISOP + O3 -> 0.00327*SOAG33                                         ; 1.05e-14, -2000
              C10H16 + O3 -> 0.04360*SOAG31 + 0.01035*SOAG32 + 0.09809*SOAG33 + 0.01635*SOAG34     ; 1.e-15, -732
              ISOP + NO3 -> 0.00027*SOAG32 + 0.04060*SOAG33 + 0.06458*SOAG34      ; 3.03e-12,-446
              C10H16 + NO3 -> 0.17493*SOAG33 + 0.59019*SOAG34                     ; 1.2e-12, 490

              SOAG35 + OH -> 0.46*SOAG34  + 0.5*SOAG35      ; 2e-11
              SOAG34 + OH -> 0.46*SOAG33  + 0.5*SOAG35      ; 2e-11
              SOAG33 + OH -> 0.46*SOAG32  + 0.5*SOAG35      ; 2e-11
              SOAG32 + OH -> 0.46*SOAG31  + 0.5*SOAG35      ; 2e-11
 End Reactions

 Ext Forcing
      NO2 <- dataset
      SO2 <- dataset
      so4_a1 <- dataset
      so4_a2 <- dataset
      pom_a4 <- dataset
      bc_a4 <- dataset
      num_a1 <- dataset
      num_a2 <- dataset
      num_a4 <- dataset
      SOAG0 <- dataset
 End Ext Forcing

END CHEMISTRY

SIMULATION PARAMETERS

     Version Options
        model   = cam
        machine = intel
        architecture = hybrid
        vec_ftns  = on
        multitask = on
        namemod = on
        modules = on
     End Version Options

   END SIMULATION PARAMETERS

ENDSIM
