From 281b700dfc8fca5c3c906bb2646ffc55718b70bf Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Mon, 10 Apr 2023 17:35:32 -0500 Subject: [PATCH 01/24] parsing henry and aqua stuff --- capram_convert/capram24_red.txt | 748 ++++++++++++++++++++++++++++++++ capram_convert/convert.py | 79 ++++ 2 files changed, 827 insertions(+) create mode 100644 capram_convert/capram24_red.txt create mode 100644 capram_convert/convert.py diff --git a/capram_convert/capram24_red.txt b/capram_convert/capram24_red.txt new file mode 100644 index 00000000..ed643766 --- /dev/null +++ b/capram_convert/capram24_red.txt @@ -0,0 +1,748 @@ +COMMENT All the names of non-ionic aqueous phase species begin with a, cations end +COMMENT with p and anions end with m, respectively. + +COMMENT CLASS: HENRY, TYPE: TEMP3 +COMMENT Phase transfer +COMMENT Kh = A exp(B (1/T - 1/298)) +COMMENT B = dH/R [K] +COMMENT Further uptake parameters according to Schwartz's approach (alpha, Dg) +COMMENT are read elsewhere in the program + +CLASS: HENRY +CO2 = aCO2 +TEMP3: A: 3.1e-2 B: 2423.0 + +CLASS: HENRY +O3 = aO3 +TEMP3: A: 1.14e-2 B: 2300.0 + +CLASS: HENRY +HO2 = aHO2 +TEMP3: A: 9.0e3 B: 0.0 + +CLASS: HENRY +HO = aHO +TEMP3: A: 25.0 B: 5280.0 + +CLASS: HENRY +H2O2 = aH2O2 +TEMP3: A: 1.02e5 B: 6340.0 + +CLASS: HENRY +NO2 = aNO2 +TEMP3: A: 1.2e-2 B: 1263.0 + +CLASS: HENRY +HONO = aHONO +TEMP3: A: 49.0 B: 4880.0 + +CLASS: HENRY +HNO3 = aHNO3 +TEMP3: A: 2.1e5 B: 8700.0 + +CLASS: HENRY +NO3 = aNO3 +TEMP3: A: 6.0e-1 B: 0.0 + +CLASS: HENRY +N2O5 = aN2O5 +TEMP3: A: 1.4e0 B: 0.0 + +CLASS: HENRY +NH3 = aNH3 +TEMP3: A: 60.7 B: 3920.0 + +CLASS: HENRY +HCL = aHCL +TEMP3: A: 1.1 B: 2020.0 + +CLASS: HENRY +HCHO = aHCHO +TEMP3: A: 2.5 B: 7216.0 + +CLASS: HENRY +ORA1 = aORA1 +TEMP3: A: 5.53e3 B: 5630.0 + +CLASS: HENRY +SO2 = aSO2 +TEMP3: A: 1.24 B: 3247.0 + +CLASS: HENRY +OP1 = aOP1 +TEMP3: A: 310.0 B: 5607.0 + +CLASS: HENRY +ORA2 = aORA2 +TEMP3: A: 5.5e3 B: 5890.0 + +CLASS: HENRY +MO2 = aMO2 +TEMP3: A: 310.0 B: 5607.0 + +CLASS: HENRY +ETHPX = aETHPX +TEMP3: A: 340.0 B: 87.0 + +CLASS: HENRY +ETOH = aETOH +TEMP3: A: 1.9e2 B: 6290.0 + +CLASS: HENRY +CH3OH = aCH3OH +TEMP3: A: 2.2e2 B: 5390.0 + +CLASS: HENRY +ALD = aALD +TEMP3: A: 4.8 B: 6254.0 + +CLASS: HENRY +BR2 = aBR2 +TEMP3: A: 7.58e-1 B: 3800.0 + +CLASS: HENRY +CL2 = aCL2 +TEMP3: A: 9.15e-2 B: 2490.0 + +CLASS: HENRY +SULF = aSULF +TEMP3: A: 8.7e11 B: 0.0 + +CLASS: HENRY +HNO4 = aHNO4 +TEMP3: A: 3e4 B: 0.0 + +CLASS: HENRY +ACO3 = aACO3 +TEMP3: A: 6.69e2 B: 5893.0 + +CLASS: HENRY +GLY = aGLY +TEMP3: A: 1.4 B: 0.0 + +CLASS: HENRY +[O2] = aO2 +TEMP3: A: 1.3e-3 B: 1700.0 + +CLASS: HENRY +CLNO2 = aCLNO2 +TEMP3: A: 0.024 B: 0.0 + +CLASS: HENRY +BRNO2 = aBRNO2 +TEMP3: A: 0.3 B: 0.0 + +CLASS: HENRY +BRCL = aBRCL +TEMP3: A: 0.94 B: 0.0 + +CLASS: HENRY +NO = aNO +TEMP3: A: 1.9e-3 B: 0.0 + +COMMENT CLASS: AQUA, TYPE: PHOTABC photolysis reactions according to +COMMENT j = A * exp (B *(1 - 1 /(cos (C * chi)); A = jmax; chi = zenith angle + +CLASS: AQUA +FEOHpp = FEpp + aHO +PHOTABC: A: 4.76e-03 B: 2.19894e+00 C: 0.76087e+00 + +CLASS: AQUA +NO3m = aNO2 + aHO + OHm +PHOTABC: A: 4.57e-7 B: 2.59408e+00 C: 0.77213e+00 + +CLASS: AQUA +aH2O2 = aHO + aHO +PHOTABC: A: 7.64e-06 B: 2.46425e+00 C: 0.76355e+00 + +CLASS: AQUA +FEC2O42m = FEpp + C2O4mm + aCO2 + CO2m +PHOTABC: A: 2.47e-2 B: 1.95825e+00 C: 0.76782e+00 + +COMMENT CLASS: AQUA; TYPE: TEMP3 +COMMENT TEmperature dependent reation +COMMENT k(T)=A*exp(B*(1/T-1/298)) +COMMENT A=k(298 K) +COMMENT B=-Ea/R + +CLASS: AQUA +aH2O2 + FEpp = FEppp + aHO + OHm +TEMP3: A: 50.0 B: 0.0 + +CLASS: AQUA +aH2O2 + CUp = CUpp + aHO + OHm +TEMP3: A: 7.0e3 B: 0.0 + +CLASS: AQUA +O2m + FEppp = FEpp + aO2 +TEMP3: A: 1.5e8 B: 0.0 + +CLASS: AQUA +aHO2 + FEOHpp = FEpp + aO2 + [aH2O] +TEMP3: A: 1.3e5 B: 0.0 + +CLASS: AQUA +O2m + FEOHpp = FEpp + aO2 + OHm +TEMP3: A: 1.5e8 B: 0.0 + +CLASS: AQUA +O2m + FEpp = FEppp + aH2O2 -2.0 Hp +TEMP3: A: 1.0e7 B: 0.0 + +CLASS: AQUA +aHO2 + FEpp = FEppp + aH2O2 -1.0 Hp +TEMP3: A: 1.2e6 B: -5050.0 + +CLASS: AQUA +aHO + FEpp = FEOHpp +TEMP3: A: 4.3e8 B: -1100.0 + +CLASS: AQUA +O2m + CUp = CUpp + aH2O2 -2.0 Hp +TEMP3: A: 1e10 B: 0.0 + +CLASS: AQUA +aHO2 + CUp = CUpp + aH2O2 -1.0 Hp +TEMP3: A: 2.3e9 B: 0.0 + +CLASS: AQUA +aHO2 + CUpp = CUp + aO2 + Hp +TEMP3: A: 1.0e8 B: 0.0 + +CLASS: AQUA +O2m + CUpp = CUp + aO2 +TEMP3: A: 8.0e9 B: 0.0 + +CLASS: AQUA +FEppp + CUp = FEpp + CUpp +TEMP3: A: 1.3e7 B: 0.0 + +CLASS: AQUA +FEOHpp + CUp = FEpp + CUpp + OHm +TEMP3: A: 1.3e7 B: 0.0 + +CLASS: AQUA +aO3 + O2m = O3m + aO2 +TEMP3: A: 1.5e9 B: -2200.0 + +CLASS: AQUA +aHO3 = aHO + aO2 +TEMP3: A: 330.0 B: -4500.0 + +CLASS: AQUA +aH2O2 + aHO = aHO2 + [aH2O] +TEMP3: A: 3.0e7 B: -1680.0 + +CLASS: AQUA +HSO3m + aHO = SO3m + [aH2O] +TEMP3: A: 2.7e9 B: 0.0 + +CLASS: AQUA +CUp + aO2 = CUpp + O2m +TEMP3: A: 4.6e5 B: 0.0 + +CLASS: AQUA +FEpp + aO3 = FEOpp + aO2 +TEMP3: A: 8.2e5 B: -4690.0 + +CLASS: AQUA +FEOpp + CLm = FEppp + CLOHm -1.0 Hp +TEMP3: A: 100.0 B: 0.0 + +CLASS: AQUA +FEOpp + FEpp = 2 FEppp + 2 OHm +TEMP3: A: 7.2e4 B: -842.0 + +CLASS: AQUA +aN2O5 = NO2p + NO3m +TEMP3: A: 1e9 B: 0.0 + +CLASS: AQUA +NO2p + [aH2O] = NO3m + Hp + Hp +TEMP3: A: 8.9e7 B: 0.0 + +CLASS: AQUA +aNO3 + HSO3m = NO3m + Hp + SO3m +TEMP3: A: 1.3e9 B: -2000 + +CLASS: AQUA +aNO3 + SO4mm = NO3m + SO4m +TEMP3: A: 1e5 B: 0.0 + +CLASS: AQUA +NO4m = NO2m + aO2 +TEMP3: A: 1.0 B: 0.0 + +CLASS: AQUA +aHNO4 + HSO3m = HSO4m + Hp + NO3m +TEMP3: A: 3.3e5 B: 0.0 + +CLASS: AQUA +NO2p + CLm = aCLNO2 +TEMP3: A: 1e10 B: 0.0 + +CLASS: AQUA +NO2p + BRm = aBRNO2 +TEMP3: A: 1e10 B: 0.0 + +CLASS: AQUA +aCLNO2 + BRm = NO2m + aBRCL +TEMP3: A: 5e6 B: 0.0 + +CLASS: AQUA +aBRNO2 + BRm = aBR2 + NO2m +TEMP3: A: 2.55e4 B: 0.0 + +CLASS: AQUA +aBRNO2 + CLm = NO2m + aBRCL +TEMP3: A: 10.0 B: 0.0 + +CLASS: AQUA +HMSm + aHO = CHOHSO3m + [aH2O] +TEMP3: A: 3.0e8 B: 0.0 + +CLASS: AQUA +CHOHSO3m + aO2 = O2CHOHSO3m +TEMP3: A: 2.6e9 B: 0.0 + +CLASS: AQUA +O2CHOHSO3m = aHO2 + CHOSO3m +TEMP3: A: 1.7e4 B: 0.0 + +CLASS: AQUA +O2CHOHSO3m = aO2CHO + HSO3m +TEMP3: A: 7.0e3 B: 0.0 + +CLASS: AQUA +CHOSO3m + [aH2O] = HSO3m + aORA1 +TEMP3: A: 1.26e-2 B: 0.0 + +CLASS: AQUA +aO2CHO + [aH2O] = aORA1 + aHO2 +TEMP3: A: 44.32 B: 0.0 + +CLASS: AQUA +HSO3m + aH2O2 + Hp = SO4mm + [aH2O] + 2 Hp +TEMP3: A: 7.2e7 B: -4000.0 + +CLASS: AQUA +HSO3m + aO3 = SO4mm + Hp + aO2 +TEMP3: A: 3.7e5 B: -5530.0 + +CLASS: AQUA +SO3mm + aO3 = SO4mm + aO2 +TEMP3: A: 1.5e9 B: -5280.0 + +CLASS: AQUA +SO5m + FEpp = HSO5m + FEOHpp +TEMP3: A: 2.65e7 B: -5809.0 + +CLASS: AQUA +HSO5m + FEpp = SO4m + FEOHpp +TEMP3: A: 3.0e4 B: 0.0 + +CLASS: AQUA +FEpp + SO4m = FEOHpp + SO4mm + Hp +TEMP3: A: 4.6e9 B: 2165.0 + +CLASS: AQUA +SO5m + SO5m = SO4m + SO4m + aO2 +TEMP3: A: 2.2e8 B: -2600.0 + +CLASS: AQUA +SO5m + aHO2 = SO5O2Hm +TEMP3: A: 1.7e9 B: 0.0 + +CLASS: AQUA +SO5O2mm = HSO5m + aO2 -1.0 Hp +TEMP3: A: 1.2e3 B: 0.0 + +CLASS: AQUA +SO3m + aO2 = SO5m +TEMP3: A: 2.5e9 B: 0.0 + +CLASS: AQUA +SO4m + [aH2O] = SO4mm + aHO + Hp +TEMP3: A: 11.0 B: -1110.0 + +CLASS: AQUA +HSO5m + HSO3m + Hp = 2 SO4mm + 3 Hp +TEMP3: A: 7.14e6 B: 0.0 + +CLASS: AQUA +aCH3OH + aHO = [aH2O] + aCH2OH +TEMP3: A: 1.0e9 B: -580.0 + +CLASS: AQUA +aCH2OH + aO2 = aO2CH2OH +TEMP3: A: 2e9 B: 0.0 + +CLASS: AQUA +aO2CH2OH + aO2CH2OH = aCH3OH + aO2 + aHCHO +TEMP3: A: 1.05e9 B: 0.0 + +CLASS: AQUA +aETOH + aHO = [aH2O] + aCH3CHOH +TEMP3: A: 1.9e9 B: 0.0 + +CLASS: AQUA +aCH3CHOH + aO2 = aO2CH3CHOH +TEMP3: A: 2e9 B: 0.0 + +CLASS: AQUA +aO2CH3CHOH = aALD + aHO2 +TEMP3: A: 52.0 B: -7217.0 + +CLASS: AQUA +aCH2OH2 + aHO = aCHOH2 + [aH2O] +TEMP3: A: 1.0e9 B: -1020.0 + +CLASS: AQUA +aCHOH2 + aO2 = aHO2 + aORA1 +TEMP3: A: 2e9 B: 0.0 + +CLASS: AQUA +aCH3CHOH2 + aHO = [aH2O] + aCH3COH2 +TEMP3: A: 1.2e9 B: 0.0 + +CLASS: AQUA +aALD + aHO = [aH2O] + aCH3CO +TEMP3: A: 3.6e9 B: 0.0 + +CLASS: AQUA +aORA1 + aHO = aCO2H + [aH2O] +TEMP3: A: 1.3e8 B: -1000.0 + +CLASS: AQUA +HCOOm + aHO = aCO2H + OHm +TEMP3: A: 3.2e9 B: -1000.0 + +CLASS: AQUA +aORA2 + aHO = [aH2O] + aCH2COOH +TEMP3: A: 1.5e7 B: -1330.0 + +CLASS: AQUA +MCOOm + aHO = [aH2O] + CH2COOm +TEMP3: A: 1.0e8 B: -1800.0 + +CLASS: AQUA +aCH2COOH + aO2 = aACO3 +TEMP3: A: 1.7e9 B: 0.0 + +CLASS: AQUA +aMO2 + aMO2 = aCH3OH + aHCHO + aO2 +TEMP3: A: 7.4e7 B: -2200.0 + +CLASS: AQUA +aMO2 + aMO2 = aCH3O + aCH3O + aO2 +TEMP3: A: 3.6e7 B: -2200.0 + +CLASS: AQUA +aACO3 + aACO3 = aMO2 + aMO2 + aCO2 + aCO2 + aO2 +TEMP3: A: 1.5e8 B: 0.0 + +CLASS: AQUA +aMO2 + HSO3m = aOP1 + SO3m +TEMP3: A: 5.0e5 B: 0.0 + +CLASS: AQUA +aETHPX + aETHPX = aCH3CH2O + aCH3CH2O + aO2 +TEMP3: A: 1.0e8 B: 750.0 + +CLASS: AQUA +aCH3CH2O = aCH3CHOH +TEMP3: A: 1e6 B: 0.0 + +CLASS: AQUA +aHO + HC2O4m = [aH2O] + C2O4m +TEMP3: A: 3.2e7 B: 0.0 + +CLASS: AQUA +aHO + C2O4mm = OHm + C2O4m +TEMP3: A: 5.3e6 B: 0.0 + +CLASS: AQUA +C2O4m + aO2 = aCO2 + O2m + aCO2 +TEMP3: A: 2e9 B: 0.0 + +CLASS: AQUA +aHO + aCHOH2CHOH2 = [aH2O] + aCOH2CHOH2 +TEMP3: A: 1.1e9 B: -1516.0 + +CLASS: AQUA +aCOH2CHOH2 + aO2 = aO2COH2CHOH2 +TEMP3: A: 1.38e9 B: 0.0 + +CLASS: AQUA +aO2COH2CHOH2 = aHO2 + aCHOH2COOH +TEMP3: A: 2e9 B: 0.0 + +CLASS: AQUA +aHO + aCHOH2COOH = [aH2O] + aCOH2COOH +TEMP3: A: 1.1e9 B: -1516.0 + +CLASS: AQUA +aCOH2COOH + aO2 = aO2COH2COOH +TEMP3: A: 2e9 B: 0.0 + +CLASS: AQUA +aO2COH2COOH = aHO2 + aH2C2O4 +TEMP3: A: 2e9 B: 0.0 + +CLASS: AQUA +aCH3COH2 + aO2 = aCH3COH2OO +TEMP3: A: 2e9 B: 0.0 + +CLASS: AQUA +aCH3COH2OO = Hp + Hp + MCOOm + O2m +TEMP3: A: 1e5 B: 0.0 + +CLASS: AQUA +aCH3O = aCH2OH +TEMP3: A: 1e6 B: 0.0 + +CLASS: AQUA +CH2COOm + aO2 = O2CH2COOm +TEMP3: A: 2e9 B: 0.0 + +CLASS: AQUA +O2CH2COOm + O2CH2COOm = 2 CHOH2COOm + aH2O2 +TEMP3: A: 2e7 B: 0.0 + +CLASS: AQUA +CO2m + aO2 = aCO2 + O2m +TEMP3: A: 4e9 B: 0.0 + +CLASS: AQUA +CL2m + FEpp = 2 CLm + FEppp +TEMP3: A: 1.0e7 B: -3030.0 + +CLASS: AQUA +CL2m + aHO2 = 2 CLm + Hp + aO2 +TEMP3: A: 1.3e10 B: 0.0 + +CLASS: AQUA +CL2m + HSO3m = 2 CLm + Hp + SO3m +TEMP3: A: 1.7e8 B: -400.0 + +CLASS: AQUA +aCL2 + [aH2O] = Hp + CLm + aHOCL +TEMP3: A: 0.4 B: -7900.0 + +CLASS: AQUA +CL2m + [aH2O] = Hp + CLm + CLm + aHO +TEMP3: A: 6.0 B: 0.0 + +CLASS: AQUA +BRm + SO4m = SO4mm + aBR +TEMP3: A: 2.1e9 B: 0.0 + +CLASS: AQUA +BRm + aNO3 = NO3m + aBR +TEMP3: A: 3.8e9 B: 0.0 + +CLASS: AQUA +BR2m + BR2m = aBR2 + 2 BRm +TEMP3: A: 1.7e9 B: 0.0 + +CLASS: AQUA +BR2m + FEpp = 2 BRm + FEppp +TEMP3: A: 3.6e6 B: -3330.0 + +CLASS: AQUA +BR2m + aH2O2 = 2 BRm + Hp + aHO2 +TEMP3: A: 1.0e5 B: 0.0 + +CLASS: AQUA +BR2m + aHO2 = 2 BRm + aO2 + Hp +TEMP3: A: 6.5e9 B: 0.0 + +CLASS: AQUA +BR2m + HSO3m = 2 BRm + Hp + SO3m +TEMP3: A: 5.0e7 B: -780.0 + +CLASS: AQUA +aBR2 + [aH2O] = Hp + BRm + aHOBR +TEMP3: A: 0.031 B: -7500.0 + +CLASS: AQUA +BROHm = aBR + OHm +TEMP3: A: 4.2e6 B: 0.0 + +COMMENT CLASS: DISS, TYPE: DCONST +COMMENT Temperature dependent dissociation +COMMENT Ke = A exp(B*(1/T - 1/298)); +COMMENT B=-Ea/R +COMMENT C = k(back reaction) + + +COMMENT CLASS: DISS, TYPE: DCONST +COMMENT Dissociation +COMMENT Ke = A +COMMENT B= k(back reaction) + +CLASS: DISS +[aH2O] = OHm + Hp +DTEMP: A: 1.8e-16 B: -6800.0 C: 1.3e11 + +CLASS: AQUA +aCO2 + [aH2O] = aH2CO3 +TEMP3: A: 4.3e-2 B: -9250.0 + +CLASS: AQUA +aH2CO3 = aCO2 + [aH2O] +TEMP3: A: 5.6e4 B: -8500.0 + +CLASS: DISS +aH2CO3 = HCO3m + Hp +DCONST: A: 2.0e-04 B: 5.0e10 + +CLASS: DISS +aHCL = CLm + Hp +DTEMP: A: 1.72e+6 B: 6890.0 C: 2.9e5 + +CLASS: DISS +aNH3 + [aH2O] = NH4p + OHm +DTEMP: A: 3.17e-7 B: -560.0 C: 3.4e10 + +CLASS: DISS +aHO2 = O2m + Hp +DCONST: A: 1.6e-5 B: 5.0e10 + +CLASS: DISS +aHNO3 = NO3m + Hp +DTEMP: A: 22.0 B: 1800.0 C: 5.0e10 + +CLASS: DISS +aHONO = NO2m + Hp +DTEMP: A: 5.3e-4 B: -1760.0 C: 5.0e10 + +CLASS: DISS +aHNO4 = NO4m + Hp +DCONST: A: 1.0e-5 B: 5.0e10 + +CLASS: DISS +aNO2 + aHO2 = aHNO4 +DCONST: A: 2.2e9 B: 4.6e-3 + +CLASS: DISS +aSO2 + [aH2O] = HSO3m + Hp +DTEMP: A: 3.13e-4 B: 1940.0 C: 2.0e8 + +CLASS: DISS +HSO3m = SO3mm + Hp +DTEMP: A: 6.22e-8 B: 1960.0 C: 5.0e10 + +CLASS: DISS +aSULF = HSO4m + Hp +DCONST: A: 1000.0 B: 5e10 + +CLASS: DISS +HSO4m = Hp + SO4mm +DTEMP: A: 1.02e-2 B: 2700.0 C: 1e11 + +CLASS: DISS +aORA1 = Hp + HCOOm +DTEMP: A: 1.77e-4 B: 12 C: 5e10 + +CLASS: DISS +aORA2 = Hp + MCOOm +DTEMP: A: 1.75e-5 B: 46.0 C: 5e10 + +CLASS: DISS +FEppp + [aH2O] = FEOHpp + Hp +DCONST: A: 1.1e-4 B: 4.3e8 + +CLASS: DISS +aHCHO + [aH2O] = aCH2OH2 +DTEMP: A: 36.0 B: 4030.0 C: 5.1e-3 + +CLASS: DISS +aALD + [aH2O] = aCH3CHOH2 +DTEMP: A: 2.46e-2 B: 2500.0 C: 5.69e-3 + +CLASS: DISS +HSO3m + aCH2OH2 = HMSm + [aH2O] +DTEMP: A: 2e8 B: -2500.0 C: 2.2e-9 + +CLASS: AQUA +SO3mm + aCH2OH2 = HMSm + OHm +TEMP3: A: 1.36e5 B: -2450.0 + +CLASS: AQUA +HMSm + OHm = SO3mm + aCH2OH2 +TEMP3: A: 4.15e3 B: -5530.0 + +CLASS: DISS +aCL + CLm = CL2m +DCONST: A: 1.4e5 B: 6e4 + +CLASS: DISS +aBR + BRm = BR2m +DCONST: A: 6.32e5 B: 1.9e4 + +CLASS: DISS +CLm + aHO = CLOHm +DCONST: A: 0.7 B: 6.1e9 + +CLASS: DISS +CLOHm + Hp = aCL + [aH2O] +DCONST: A: 5.1e6 B: 4100.0 + +CLASS: DISS +BRm + aHO = BROHm +DCONST: A: 333.0 B: 3.3e7 + +CLASS: DISS +BROHm + Hp = aBR + [aH2O] +DCONST: A: 1.8e12 B: 2.45e-2 + +CLASS: DISS +aHO3 = Hp + O3m +DCONST: A: 6.3e-9 B: 5.2e+10 + +CLASS: DISS +CHOHSO3m = CHOSO3mm + Hp +DCONST: A: 1.34e-6 B: 4.4e10 + +CLASS: DISS +SO5O2Hm = Hp + SO5O2mm +DCONST: A: 1.5e-5 B: 5e10 + +CLASS: DISS +HC2O4m = C2O4mm + Hp +DCONST: A: 6.25e-5 B: 5.0e10 + +CLASS: DISS +aCHOH2COOH = Hp + CHOH2COOm +DCONST: A: 3.16e-4 B: 2e10 + +CLASS: DISS +aGLY + [aH2O] = aCHOH2CHOH2 +DCONST: A: 3900.0 B: 5.5e-3 + +CLASS: DISS +FEppp + C2O4mm = FEC2O4p +DCONST: A: 2.9e9 B: 3e-3 + +CLASS: DISS +FEC2O4p + C2O4mm = FEC2O42m +DCONST: A: 6.3e6 B: 3e-3 + +CLASS: DISS +SO4m + CLm = SO4mm + aCL +DCONST: A: 1.2 B: 2.1e8 + +CLASS: DISS +aNO3 + CLm = NO3m + aCL +DTEMP: A: 3.4 B: -4300.0 C: 1e8 + +CLASS: DISS +aCH3CO + [aH2O] = aCH3COH2 +DTEMP: A: 367.0 B: 0.0 C: 3e4 + +CLASS: DISS +aACO3 = Hp + O2CH2COOm +DTEMP: A: 1.75e-5 B: 46.0 C: 5e10 + + diff --git a/capram_convert/convert.py b/capram_convert/convert.py new file mode 100644 index 00000000..d63f47b3 --- /dev/null +++ b/capram_convert/convert.py @@ -0,0 +1,79 @@ +import re + +# file from https://capram.tropos.de/capram_24.html +with open("capram24_red.txt") as f: + content = f.readlines() + +## +# comments here taken from the capram file +## + +# for example molecules_to_identifier['CO2'] = 'aCO2' +# for example molecules_to_identifier['aCO2'] = 'CO2' +molecules_identifier_mapping = {} + +# CLASS: HENRY, TYPE: TEMP3 +# Phase transfer +# Kh = A exp(B (1/T - 1/298)) +# B = dH/R [K] +# Further uptake parameters according to Schwartz's approach (alpha, Dg) +# are read elsewhere in the program +# for example, henry['CO2'] = {A: '3.1e-2', B: '2423.0'} +henry = {} + +# CLASS: AQUA, TYPE: PHOTABC photolysis reactions according to +# j = A * exp (B *(1 - 1 /(cos (C * chi)); A = jmax; chi = zenith angle +aqua_photo = [] + +# CLASS: AQUA; TYPE: TEMP3 +# TEmperature dependent reation +# k(T)=A*exp(B*(1/T-1/298)) +# A=k(298 K) +# B=-Ea/R +aqua_temp = [] + +# CLASS: DISS, TYPE: DCONST +# Dissociation +# Ke = A +# B= k(back reaction) +diss = [] + +line_index = 0 +while line_index < len(content): + line = content[line_index].strip() + if line.startswith('CLASS'): + type = line.split(':')[1].strip() + if type == 'HENRY': + mol = content[line_index + 1].strip().split(' = ') + ident = mol[1].strip() + mol = mol[0].strip() + + temp = content[line_index + 2].strip().split('TEMP3:') + a = temp[1].split('B:')[0].strip().split('A:')[1].strip() + b = temp[1].split('B:')[1].strip() + + molecules_identifier_mapping[mol] = ident + molecules_identifier_mapping[ident] = mol + henry[mol] = { 'A': a, 'B': b } + + line_index += 2 + elif type == 'AQUA': + reaction = content[line_index + 1].strip().split('=') + reactants = [i.strip() for i in reaction[0].strip().split('+')] + products = [i.strip() for i in reaction[1].strip().split('+')] + # thanks chatgpt + pattern = re.compile(r"(?:PHOTABC|TEMP3):\s+A:\s+([\d\.e+-]+)\s+B:\s+([\d\.e+-]+)(?:\s+C:\s+([\d\.e+-]+))?") + match = pattern.search(content[line_index + 2]) + if content[line_index + 2].startswith('PHOTABC'): + A, B, C = match.group(1), match.group(2), match.group(3) + aqua_photo.append(dict(reactants = reactants, products=products, A=A, B=B, C=C)) + elif content[line_index + 2].startswith('TEMP3'): + A, B = match.group(1), match.group(2) + aqua_temp.append(dict(reactants = reactants, products=products, A=A, B=B, C=C)) + else: + print(f"Unknown aqua type: {content[line_index + 2]}") + elif type == 'DISS': + pass + else: + print(f'Unknown type: {type}') + line_index += 1 From e52f5e20b89ddcbc2433e8cdc74f5418bc35d187 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Tue, 11 Apr 2023 14:50:57 -0500 Subject: [PATCH 02/24] parsing dissociation reactions --- capram_convert/convert.py | 26 ++++++++++++++++++++------ 1 file changed, 20 insertions(+), 6 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index d63f47b3..25f433f0 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -38,6 +38,12 @@ # B= k(back reaction) diss = [] + +# pattern that matches A, B, and optionall C constants for PHOTABC and TEMP3 reactions +# thanks chatgpt +pattern = re.compile(r"(PHOTABC|TEMP3|DCONST|DTEMP):\s+A:\s+([\d\.e+-]+)\s+B:\s+([\d\.e+-]+)(?:\s+C:\s+([\d\.e+-]+))?") + + line_index = 0 while line_index < len(content): line = content[line_index].strip() @@ -62,18 +68,26 @@ reactants = [i.strip() for i in reaction[0].strip().split('+')] products = [i.strip() for i in reaction[1].strip().split('+')] # thanks chatgpt - pattern = re.compile(r"(?:PHOTABC|TEMP3):\s+A:\s+([\d\.e+-]+)\s+B:\s+([\d\.e+-]+)(?:\s+C:\s+([\d\.e+-]+))?") match = pattern.search(content[line_index + 2]) if content[line_index + 2].startswith('PHOTABC'): - A, B, C = match.group(1), match.group(2), match.group(3) + A, B, C = match.group(2), match.group(3), match.group(4) aqua_photo.append(dict(reactants = reactants, products=products, A=A, B=B, C=C)) elif content[line_index + 2].startswith('TEMP3'): - A, B = match.group(1), match.group(2) - aqua_temp.append(dict(reactants = reactants, products=products, A=A, B=B, C=C)) + A, B = match.group(2), match.group(3) + aqua_temp.append(dict(reactants = reactants, products=products, A=A, B=B)) else: print(f"Unknown aqua type: {content[line_index + 2]}") + line_index += 2 elif type == 'DISS': - pass + reaction = content[line_index + 1].strip().split('=') + reactants = [i.strip() for i in reaction[0].strip().split('+')] + products = [i.strip() for i in reaction[1].strip().split('+')] + match = pattern.search(content[line_index + 2]) + type, A, B, C = match.group(1), match.group(2), match.group(3), match.group(4) + if C is None: + diss.append(dict(reactants = reactants, products=products, A=A, B=B)) + else: + diss.append(dict(reactants = reactants, products=products, A=A, B=B, C=C)) else: print(f'Unknown type: {type}') - line_index += 1 + line_index += 1 \ No newline at end of file From 2eace18bac3e3c36ba75ac4d00d803156717e01f Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Tue, 11 Apr 2023 17:45:44 -0500 Subject: [PATCH 03/24] preserving the hyrdogen? ions --- capram_convert/convert.py | 47 ++++++++++++++++++++++++++++----------- 1 file changed, 34 insertions(+), 13 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index 25f433f0..c4c1349d 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -41,8 +41,28 @@ # pattern that matches A, B, and optionall C constants for PHOTABC and TEMP3 reactions # thanks chatgpt -pattern = re.compile(r"(PHOTABC|TEMP3|DCONST|DTEMP):\s+A:\s+([\d\.e+-]+)\s+B:\s+([\d\.e+-]+)(?:\s+C:\s+([\d\.e+-]+))?") +constants_pattern = re.compile(r"(PHOTABC|TEMP3|DCONST|DTEMP):\s+A:\s+([\d\.e+-]+)\s+B:\s+([\d\.e+-]+)(?:\s+C:\s+([\d\.e+-]+))?") +reaction_pattern = r"^([^=]*)=([^=]*)$" +def parse_reactants_products(line): + match = re.search(reaction_pattern, line.replace(" ", "")) + if match: + reactants = combine_stoichiometric_coeffs(match.group(1).strip()) + products = combine_stoichiometric_coeffs(match.group(2).strip()) + return reactants, products + +def combine_stoichiometric_coeffs(species): + # given this: O2m + FEpp = FEppp + aH2O2 -2.0 Hp + # output this for the products: ['FEppp', 'aH2O2', '-2.0Hp'] + groups = [i for i in re.split(r'([+-])', species) if i != '+'] + result = [] + for i, group in enumerate(groups): + if (i > 0) and (groups[i-1] == '-'): + result.append(groups[i-1] + group) + elif group != '-': + result.append(group) + + return result line_index = 0 while line_index < len(content): @@ -64,25 +84,21 @@ line_index += 2 elif type == 'AQUA': - reaction = content[line_index + 1].strip().split('=') - reactants = [i.strip() for i in reaction[0].strip().split('+')] - products = [i.strip() for i in reaction[1].strip().split('+')] - # thanks chatgpt - match = pattern.search(content[line_index + 2]) - if content[line_index + 2].startswith('PHOTABC'): - A, B, C = match.group(2), match.group(3), match.group(4) + reactants, products = parse_reactants_products(content[line_index + 1]) + match = constants_pattern.search(content[line_index + 2]) + type, A, B, C = match.group(1), match.group(2), match.group(3), match.group(4) + if type == 'PHOTABC': aqua_photo.append(dict(reactants = reactants, products=products, A=A, B=B, C=C)) - elif content[line_index + 2].startswith('TEMP3'): - A, B = match.group(2), match.group(3) + elif type == 'TEMP3': aqua_temp.append(dict(reactants = reactants, products=products, A=A, B=B)) else: - print(f"Unknown aqua type: {content[line_index + 2]}") + print(f"Unknown aqua type: {type}") line_index += 2 elif type == 'DISS': reaction = content[line_index + 1].strip().split('=') reactants = [i.strip() for i in reaction[0].strip().split('+')] products = [i.strip() for i in reaction[1].strip().split('+')] - match = pattern.search(content[line_index + 2]) + match = constants_pattern.search(content[line_index + 2]) type, A, B, C = match.group(1), match.group(2), match.group(3), match.group(4) if C is None: diss.append(dict(reactants = reactants, products=products, A=A, B=B)) @@ -90,4 +106,9 @@ diss.append(dict(reactants = reactants, products=products, A=A, B=B, C=C)) else: print(f'Unknown type: {type}') - line_index += 1 \ No newline at end of file + line_index += 1 + + +print(aqua_photo) +print() +print(aqua_temp) \ No newline at end of file From 1caa8847580c564ed21674c9153044f7bf4de3cc Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Tue, 11 Apr 2023 17:52:13 -0500 Subject: [PATCH 04/24] putting aqua reactions in the dissociations section in the correct array --- capram_convert/convert.py | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index c4c1349d..fcc2d815 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -65,8 +65,17 @@ def combine_stoichiometric_coeffs(species): return result line_index = 0 +# there are a few AQUA type reactions in the dissociation reactions, +# when those exist, add them to the appropriate array +is_diss = False while line_index < len(content): line = content[line_index].strip() + if line.startswith('COMMENT CLASS: AQUA, TYPE: PHOTABC'): + pass + if line.startswith('COMMENT CLASS: AQUA; TYPE: TEMP3'): + pass + if line.startswith('COMMENT CLASS: DISS, TYPE: DCONST'): + is_diss = True if line.startswith('CLASS'): type = line.split(':')[1].strip() if type == 'HENRY': @@ -90,7 +99,10 @@ def combine_stoichiometric_coeffs(species): if type == 'PHOTABC': aqua_photo.append(dict(reactants = reactants, products=products, A=A, B=B, C=C)) elif type == 'TEMP3': - aqua_temp.append(dict(reactants = reactants, products=products, A=A, B=B)) + if is_diss: + diss.append(dict(reactants = reactants, products=products, A=A, B=B)) + else: + aqua_temp.append(dict(reactants = reactants, products=products, A=A, B=B)) else: print(f"Unknown aqua type: {type}") line_index += 2 @@ -107,8 +119,3 @@ def combine_stoichiometric_coeffs(species): else: print(f'Unknown type: {type}') line_index += 1 - - -print(aqua_photo) -print() -print(aqua_temp) \ No newline at end of file From 8c78422c126d2b9287f5bed5dc45bdbec2efcb69 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Wed, 12 Apr 2023 12:09:05 -0500 Subject: [PATCH 05/24] creating species file --- capram_convert/convert.py | 13 ++++ capram_convert/species.json | 136 ++++++++++++++++++++++++++++++++++++ 2 files changed, 149 insertions(+) create mode 100644 capram_convert/species.json diff --git a/capram_convert/convert.py b/capram_convert/convert.py index fcc2d815..77ea2941 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -1,4 +1,5 @@ import re +import json # file from https://capram.tropos.de/capram_24.html with open("capram24_red.txt") as f: @@ -119,3 +120,15 @@ def combine_stoichiometric_coeffs(species): else: print(f'Unknown type: {type}') line_index += 1 + + +# for k,v in molecules_identifier_mapping.items(): +# print(f"{k} -> {v}") + +species = {} +species["camp-data"] = [ + dict(name=name, type="CHEM_SPEC") for name,_ in molecules_identifier_mapping.items() if not name.startswith("a") +] + +with open('species.json', 'w') as f: + json.dump(species, f, indent=2) \ No newline at end of file diff --git a/capram_convert/species.json b/capram_convert/species.json new file mode 100644 index 00000000..20d33aef --- /dev/null +++ b/capram_convert/species.json @@ -0,0 +1,136 @@ +{ + "camp-data": [ + { + "name": "CO2", + "type": "CHEM_SPEC" + }, + { + "name": "O3", + "type": "CHEM_SPEC" + }, + { + "name": "HO2", + "type": "CHEM_SPEC" + }, + { + "name": "HO", + "type": "CHEM_SPEC" + }, + { + "name": "H2O2", + "type": "CHEM_SPEC" + }, + { + "name": "NO2", + "type": "CHEM_SPEC" + }, + { + "name": "HONO", + "type": "CHEM_SPEC" + }, + { + "name": "HNO3", + "type": "CHEM_SPEC" + }, + { + "name": "NO3", + "type": "CHEM_SPEC" + }, + { + "name": "N2O5", + "type": "CHEM_SPEC" + }, + { + "name": "NH3", + "type": "CHEM_SPEC" + }, + { + "name": "HCL", + "type": "CHEM_SPEC" + }, + { + "name": "HCHO", + "type": "CHEM_SPEC" + }, + { + "name": "ORA1", + "type": "CHEM_SPEC" + }, + { + "name": "SO2", + "type": "CHEM_SPEC" + }, + { + "name": "OP1", + "type": "CHEM_SPEC" + }, + { + "name": "ORA2", + "type": "CHEM_SPEC" + }, + { + "name": "MO2", + "type": "CHEM_SPEC" + }, + { + "name": "ETHPX", + "type": "CHEM_SPEC" + }, + { + "name": "ETOH", + "type": "CHEM_SPEC" + }, + { + "name": "CH3OH", + "type": "CHEM_SPEC" + }, + { + "name": "ALD", + "type": "CHEM_SPEC" + }, + { + "name": "BR2", + "type": "CHEM_SPEC" + }, + { + "name": "CL2", + "type": "CHEM_SPEC" + }, + { + "name": "SULF", + "type": "CHEM_SPEC" + }, + { + "name": "HNO4", + "type": "CHEM_SPEC" + }, + { + "name": "ACO3", + "type": "CHEM_SPEC" + }, + { + "name": "GLY", + "type": "CHEM_SPEC" + }, + { + "name": "[O2]", + "type": "CHEM_SPEC" + }, + { + "name": "CLNO2", + "type": "CHEM_SPEC" + }, + { + "name": "BRNO2", + "type": "CHEM_SPEC" + }, + { + "name": "BRCL", + "type": "CHEM_SPEC" + }, + { + "name": "NO", + "type": "CHEM_SPEC" + } + ] +} \ No newline at end of file From 00eb2ce62e26bb53338bed65199f427f07fb82c2 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Wed, 12 Apr 2023 12:42:23 -0500 Subject: [PATCH 06/24] adding all species from all reactions --- capram_convert/convert.py | 20 +- capram_convert/species.json | 526 ++++++++++++++++++++++++++++++++++-- 2 files changed, 516 insertions(+), 30 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index 77ea2941..06a62fee 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -125,10 +125,20 @@ def combine_stoichiometric_coeffs(species): # for k,v in molecules_identifier_mapping.items(): # print(f"{k} -> {v}") -species = {} -species["camp-data"] = [ - dict(name=name, type="CHEM_SPEC") for name,_ in molecules_identifier_mapping.items() if not name.startswith("a") -] +species = set( + name for name,_ in molecules_identifier_mapping.items() if not name.startswith("a") +) + +for list in [aqua_photo, aqua_temp, diss]: + for item in list: + for spec in item['reactants']: + species.add(spec) + for spec in item['products']: + species.add(spec) with open('species.json', 'w') as f: - json.dump(species, f, indent=2) \ No newline at end of file + json.dump( + { + "camp-data" : [dict(name=name, type="CHEM_SPEC") for name in species] + }, f, indent=2 + ) \ No newline at end of file diff --git a/capram_convert/species.json b/capram_convert/species.json index 20d33aef..aa093b5f 100644 --- a/capram_convert/species.json +++ b/capram_convert/species.json @@ -1,19 +1,87 @@ { "camp-data": [ { - "name": "CO2", + "name": "aCHOH2", "type": "CHEM_SPEC" }, { - "name": "O3", + "name": "aO2CHO", "type": "CHEM_SPEC" }, { - "name": "HO2", + "name": "HONO", "type": "CHEM_SPEC" }, { - "name": "HO", + "name": "HCL", + "type": "CHEM_SPEC" + }, + { + "name": "2OHm", + "type": "CHEM_SPEC" + }, + { + "name": "aCH2OH2", + "type": "CHEM_SPEC" + }, + { + "name": "HCHO", + "type": "CHEM_SPEC" + }, + { + "name": "CL2", + "type": "CHEM_SPEC" + }, + { + "name": "aACO3", + "type": "CHEM_SPEC" + }, + { + "name": "2BRm", + "type": "CHEM_SPEC" + }, + { + "name": "NO2m", + "type": "CHEM_SPEC" + }, + { + "name": "aBR", + "type": "CHEM_SPEC" + }, + { + "name": "aHONO", + "type": "CHEM_SPEC" + }, + { + "name": "CHOH2COOm", + "type": "CHEM_SPEC" + }, + { + "name": "CLm", + "type": "CHEM_SPEC" + }, + { + "name": "ETHPX", + "type": "CHEM_SPEC" + }, + { + "name": "SO4mm", + "type": "CHEM_SPEC" + }, + { + "name": "BR2m", + "type": "CHEM_SPEC" + }, + { + "name": "NO4m", + "type": "CHEM_SPEC" + }, + { + "name": "aO2", + "type": "CHEM_SPEC" + }, + { + "name": "Hp", "type": "CHEM_SPEC" }, { @@ -21,23 +89,63 @@ "type": "CHEM_SPEC" }, { - "name": "NO2", + "name": "SO5O2mm", "type": "CHEM_SPEC" }, { - "name": "HONO", + "name": "2CHOH2COOm", "type": "CHEM_SPEC" }, { - "name": "HNO3", + "name": "HSO3m", "type": "CHEM_SPEC" }, { - "name": "NO3", + "name": "aO3", "type": "CHEM_SPEC" }, { - "name": "N2O5", + "name": "ACO3", + "type": "CHEM_SPEC" + }, + { + "name": "OP1", + "type": "CHEM_SPEC" + }, + { + "name": "O2CHOHSO3m", + "type": "CHEM_SPEC" + }, + { + "name": "aCH3OH", + "type": "CHEM_SPEC" + }, + { + "name": "CH2COOm", + "type": "CHEM_SPEC" + }, + { + "name": "CH3OH", + "type": "CHEM_SPEC" + }, + { + "name": "aCL", + "type": "CHEM_SPEC" + }, + { + "name": "aNO2", + "type": "CHEM_SPEC" + }, + { + "name": "-1.0Hp", + "type": "CHEM_SPEC" + }, + { + "name": "HCO3m", + "type": "CHEM_SPEC" + }, + { + "name": "aH2CO3", "type": "CHEM_SPEC" }, { @@ -45,15 +153,23 @@ "type": "CHEM_SPEC" }, { - "name": "HCL", + "name": "aCH3CHOH2", "type": "CHEM_SPEC" }, { - "name": "HCHO", + "name": "FEpp", "type": "CHEM_SPEC" }, { - "name": "ORA1", + "name": "FEOHpp", + "type": "CHEM_SPEC" + }, + { + "name": "GLY", + "type": "CHEM_SPEC" + }, + { + "name": "aALD", "type": "CHEM_SPEC" }, { @@ -61,76 +177,436 @@ "type": "CHEM_SPEC" }, { - "name": "OP1", + "name": "CLOHm", "type": "CHEM_SPEC" }, { - "name": "ORA2", + "name": "HMSm", "type": "CHEM_SPEC" }, { - "name": "MO2", + "name": "aHO", "type": "CHEM_SPEC" }, { - "name": "ETHPX", + "name": "N2O5", "type": "CHEM_SPEC" }, { - "name": "ETOH", + "name": "aN2O5", "type": "CHEM_SPEC" }, { - "name": "CH3OH", + "name": "C2O4m", "type": "CHEM_SPEC" }, { - "name": "ALD", + "name": "aMO2", "type": "CHEM_SPEC" }, { - "name": "BR2", + "name": "aCH3O", "type": "CHEM_SPEC" }, { - "name": "CL2", + "name": "NO2", + "type": "CHEM_SPEC" + }, + { + "name": "HNO3", + "type": "CHEM_SPEC" + }, + { + "name": "aHNO3", + "type": "CHEM_SPEC" + }, + { + "name": "CHOHSO3m", + "type": "CHEM_SPEC" + }, + { + "name": "aORA2", + "type": "CHEM_SPEC" + }, + { + "name": "FEppp", + "type": "CHEM_SPEC" + }, + { + "name": "aCH3CO", + "type": "CHEM_SPEC" + }, + { + "name": "ORA1", + "type": "CHEM_SPEC" + }, + { + "name": "FEC2O42m", + "type": "CHEM_SPEC" + }, + { + "name": "FEC2O4p", + "type": "CHEM_SPEC" + }, + { + "name": "NH4p", + "type": "CHEM_SPEC" + }, + { + "name": "aHO2", + "type": "CHEM_SPEC" + }, + { + "name": "-2.0Hp", + "type": "CHEM_SPEC" + }, + { + "name": "aO2CH2OH", + "type": "CHEM_SPEC" + }, + { + "name": "HCOOm", + "type": "CHEM_SPEC" + }, + { + "name": "SO5O2Hm", + "type": "CHEM_SPEC" + }, + { + "name": "aCOH2CHOH2", + "type": "CHEM_SPEC" + }, + { + "name": "aHOCL", + "type": "CHEM_SPEC" + }, + { + "name": "aCL2", + "type": "CHEM_SPEC" + }, + { + "name": "aCOH2COOH", + "type": "CHEM_SPEC" + }, + { + "name": "aCH3COH2OO", + "type": "CHEM_SPEC" + }, + { + "name": "OHm", + "type": "CHEM_SPEC" + }, + { + "name": "aHNO4", "type": "CHEM_SPEC" }, { "name": "SULF", "type": "CHEM_SPEC" }, + { + "name": "HSO4m", + "type": "CHEM_SPEC" + }, + { + "name": "BRNO2", + "type": "CHEM_SPEC" + }, + { + "name": "aH2C2O4", + "type": "CHEM_SPEC" + }, + { + "name": "aNO3", + "type": "CHEM_SPEC" + }, + { + "name": "HSO5m", + "type": "CHEM_SPEC" + }, + { + "name": "O2CH2COOm", + "type": "CHEM_SPEC" + }, + { + "name": "aBRNO2", + "type": "CHEM_SPEC" + }, + { + "name": "aORA1", + "type": "CHEM_SPEC" + }, + { + "name": "NO2p", + "type": "CHEM_SPEC" + }, + { + "name": "HC2O4m", + "type": "CHEM_SPEC" + }, + { + "name": "CUpp", + "type": "CHEM_SPEC" + }, + { + "name": "aBR2", + "type": "CHEM_SPEC" + }, + { + "name": "NO3", + "type": "CHEM_SPEC" + }, + { + "name": "aO2COH2COOH", + "type": "CHEM_SPEC" + }, + { + "name": "SO3mm", + "type": "CHEM_SPEC" + }, + { + "name": "O3m", + "type": "CHEM_SPEC" + }, + { + "name": "2FEppp", + "type": "CHEM_SPEC" + }, + { + "name": "SO4m", + "type": "CHEM_SPEC" + }, + { + "name": "aHO3", + "type": "CHEM_SPEC" + }, + { + "name": "2CLm", + "type": "CHEM_SPEC" + }, + { + "name": "BR2", + "type": "CHEM_SPEC" + }, + { + "name": "FEOpp", + "type": "CHEM_SPEC" + }, + { + "name": "aO2CH3CHOH", + "type": "CHEM_SPEC" + }, + { + "name": "2SO4mm", + "type": "CHEM_SPEC" + }, + { + "name": "aCO2H", + "type": "CHEM_SPEC" + }, { "name": "HNO4", "type": "CHEM_SPEC" }, { - "name": "ACO3", + "name": "aBRCL", "type": "CHEM_SPEC" }, { - "name": "GLY", + "name": "aNH3", + "type": "CHEM_SPEC" + }, + { + "name": "aHCHO", + "type": "CHEM_SPEC" + }, + { + "name": "ORA2", + "type": "CHEM_SPEC" + }, + { + "name": "aETHPX", + "type": "CHEM_SPEC" + }, + { + "name": "[aH2O]", + "type": "CHEM_SPEC" + }, + { + "name": "CHOSO3m", + "type": "CHEM_SPEC" + }, + { + "name": "aO2COH2CHOH2", + "type": "CHEM_SPEC" + }, + { + "name": "MCOOm", + "type": "CHEM_SPEC" + }, + { + "name": "aETOH", + "type": "CHEM_SPEC" + }, + { + "name": "BRCL", "type": "CHEM_SPEC" }, { "name": "[O2]", "type": "CHEM_SPEC" }, + { + "name": "aCLNO2", + "type": "CHEM_SPEC" + }, + { + "name": "aHOBR", + "type": "CHEM_SPEC" + }, + { + "name": "aCHOH2COOH", + "type": "CHEM_SPEC" + }, + { + "name": "aCH2OH", + "type": "CHEM_SPEC" + }, + { + "name": "HO", + "type": "CHEM_SPEC" + }, + { + "name": "O2m", + "type": "CHEM_SPEC" + }, + { + "name": "aCH3CH2O", + "type": "CHEM_SPEC" + }, + { + "name": "SO3m", + "type": "CHEM_SPEC" + }, + { + "name": "BRm", + "type": "CHEM_SPEC" + }, + { + "name": "ALD", + "type": "CHEM_SPEC" + }, + { + "name": "3Hp", + "type": "CHEM_SPEC" + }, + { + "name": "aCO2", + "type": "CHEM_SPEC" + }, + { + "name": "aCHOH2CHOH2", + "type": "CHEM_SPEC" + }, + { + "name": "ETOH", + "type": "CHEM_SPEC" + }, + { + "name": "CL2m", + "type": "CHEM_SPEC" + }, { "name": "CLNO2", "type": "CHEM_SPEC" }, { - "name": "BRNO2", + "name": "SO5m", "type": "CHEM_SPEC" }, { - "name": "BRCL", + "name": "aCH2COOH", "type": "CHEM_SPEC" }, { "name": "NO", "type": "CHEM_SPEC" + }, + { + "name": "CHOSO3mm", + "type": "CHEM_SPEC" + }, + { + "name": "CO2", + "type": "CHEM_SPEC" + }, + { + "name": "aSO2", + "type": "CHEM_SPEC" + }, + { + "name": "aSULF", + "type": "CHEM_SPEC" + }, + { + "name": "HO2", + "type": "CHEM_SPEC" + }, + { + "name": "C2O4mm", + "type": "CHEM_SPEC" + }, + { + "name": "O3", + "type": "CHEM_SPEC" + }, + { + "name": "NO3m", + "type": "CHEM_SPEC" + }, + { + "name": "aCH3COH2", + "type": "CHEM_SPEC" + }, + { + "name": "aGLY", + "type": "CHEM_SPEC" + }, + { + "name": "aCH3CHOH", + "type": "CHEM_SPEC" + }, + { + "name": "BROHm", + "type": "CHEM_SPEC" + }, + { + "name": "CO2m", + "type": "CHEM_SPEC" + }, + { + "name": "CUp", + "type": "CHEM_SPEC" + }, + { + "name": "aHCL", + "type": "CHEM_SPEC" + }, + { + "name": "aH2O2", + "type": "CHEM_SPEC" + }, + { + "name": "MO2", + "type": "CHEM_SPEC" + }, + { + "name": "aOP1", + "type": "CHEM_SPEC" + }, + { + "name": "2Hp", + "type": "CHEM_SPEC" } ] } \ No newline at end of file From de1ea2a09fc574d273537dca3a73fb989815fd79 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Wed, 12 Apr 2023 16:19:49 -0500 Subject: [PATCH 07/24] converting equilibrium reactions --- capram_convert/capram24_red.txt | 2 +- capram_convert/config.json | 6 + capram_convert/convert.py | 138 ++- capram_convert/mechanism.json | 1900 +++++++++++++++++++++++++++++++ capram_convert/species.json | 300 ++--- 5 files changed, 2177 insertions(+), 169 deletions(-) create mode 100644 capram_convert/config.json create mode 100644 capram_convert/mechanism.json diff --git a/capram_convert/capram24_red.txt b/capram_convert/capram24_red.txt index ed643766..93ca7299 100644 --- a/capram_convert/capram24_red.txt +++ b/capram_convert/capram24_red.txt @@ -569,7 +569,7 @@ CLASS: AQUA BROHm = aBR + OHm TEMP3: A: 4.2e6 B: 0.0 -COMMENT CLASS: DISS, TYPE: DCONST +COMMENT CLASS: DISS, TYPE: DTEMP COMMENT Temperature dependent dissociation COMMENT Ke = A exp(B*(1/T - 1/298)); COMMENT B=-Ea/R diff --git a/capram_convert/config.json b/capram_convert/config.json new file mode 100644 index 00000000..4629149f --- /dev/null +++ b/capram_convert/config.json @@ -0,0 +1,6 @@ +{ + "camp-files" : [ + "camp_data/species.json", + "camp_data/mechanism.json" + ] +} diff --git a/capram_convert/convert.py b/capram_convert/convert.py index 06a62fee..699ea148 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -1,5 +1,6 @@ import re import json +import numpy as np # file from https://capram.tropos.de/capram_24.html with open("capram24_red.txt") as f: @@ -33,12 +34,17 @@ # B=-Ea/R aqua_temp = [] +# CLASS: DISS, TYPE: DTEMP +# Temperature dependent dissociation +# Ke = A exp(B*(1/T - 1/298)); +# B=-Ea/R +# C = k(back reaction) +diss_with_c = [] # CLASS: DISS, TYPE: DCONST # Dissociation # Ke = A # B= k(back reaction) -diss = [] - +diss_without_c = [] # pattern that matches A, B, and optionall C constants for PHOTABC and TEMP3 reactions # thanks chatgpt @@ -68,7 +74,6 @@ def combine_stoichiometric_coeffs(species): line_index = 0 # there are a few AQUA type reactions in the dissociation reactions, # when those exist, add them to the appropriate array -is_diss = False while line_index < len(content): line = content[line_index].strip() if line.startswith('COMMENT CLASS: AQUA, TYPE: PHOTABC'): @@ -76,7 +81,7 @@ def combine_stoichiometric_coeffs(species): if line.startswith('COMMENT CLASS: AQUA; TYPE: TEMP3'): pass if line.startswith('COMMENT CLASS: DISS, TYPE: DCONST'): - is_diss = True + pass if line.startswith('CLASS'): type = line.split(':')[1].strip() if type == 'HENRY': @@ -96,14 +101,11 @@ def combine_stoichiometric_coeffs(species): elif type == 'AQUA': reactants, products = parse_reactants_products(content[line_index + 1]) match = constants_pattern.search(content[line_index + 2]) - type, A, B, C = match.group(1), match.group(2), match.group(3), match.group(4) + type, A, B, C = match.group(1), float(match.group(2)), float(match.group(3)), match.group(4) if type == 'PHOTABC': - aqua_photo.append(dict(reactants = reactants, products=products, A=A, B=B, C=C)) + aqua_photo.append(dict(reactants = reactants, products=products, A=A, B=B, C=float(C))) elif type == 'TEMP3': - if is_diss: - diss.append(dict(reactants = reactants, products=products, A=A, B=B)) - else: - aqua_temp.append(dict(reactants = reactants, products=products, A=A, B=B)) + aqua_temp.append(dict(reactants = reactants, products=products, A=A, B=B)) else: print(f"Unknown aqua type: {type}") line_index += 2 @@ -112,24 +114,21 @@ def combine_stoichiometric_coeffs(species): reactants = [i.strip() for i in reaction[0].strip().split('+')] products = [i.strip() for i in reaction[1].strip().split('+')] match = constants_pattern.search(content[line_index + 2]) - type, A, B, C = match.group(1), match.group(2), match.group(3), match.group(4) + type, A, B, C = match.group(1), float(match.group(2)), float(match.group(3)), match.group(4) if C is None: - diss.append(dict(reactants = reactants, products=products, A=A, B=B)) + diss_without_c.append(dict(reactants = reactants, products=products, A=A, B=B)) else: - diss.append(dict(reactants = reactants, products=products, A=A, B=B, C=C)) + diss_with_c.append(dict(reactants = reactants, products=products, A=A, B=B, C=float(C))) else: print(f'Unknown type: {type}') line_index += 1 -# for k,v in molecules_identifier_mapping.items(): -# print(f"{k} -> {v}") - species = set( name for name,_ in molecules_identifier_mapping.items() if not name.startswith("a") ) -for list in [aqua_photo, aqua_temp, diss]: +for list in [aqua_photo, aqua_temp, diss_with_c, diss_without_c]: for item in list: for spec in item['reactants']: species.add(spec) @@ -141,4 +140,107 @@ def combine_stoichiometric_coeffs(species): { "camp-data" : [dict(name=name, type="CHEM_SPEC") for name in species] }, f, indent=2 - ) \ No newline at end of file + ) + +henrys_law = [ + +] + +photolysis_reactions = [ + { + "type": "PHOTOLYSIS", + "reactants": { + reactant: {} for reactant in reaction["reactants"] + }, + "products": { + product: {} for product in reaction["products"] + } + } + for reaction in aqua_photo +] + +# CAMP uses this formula: A * exp(-Ea/Kb * (1/T)) * (T/D) ** B * (1 + E*P) +# CAPRAM uses A*exp(B * (1/T - 1/298)) +# +# The A in CAPRAM is not equal to A in CAMP. A in CAPRAM is the rate constant at 298 K (A=k(298K)) +# +# To convert CAPRAM's A into CAMP's A, +# A * exp(B*(1/T - 1/298)) +# = A * exp(B/T) * exp(-B/298) +# = (A * exp(-B/298)) * exp(B/T) +# = A_ * exp(-B/298) +# with A_ = A * exp(-B/298) +# Then specify the "C" option of the the CAMP configuaration +# by setting it equal to -B of CAPRAM. +# +# CAMP's B, D, and E are all left as the default values +# For example +# CAPRAM A = 50, B=0 -> CAMP A = A(capram)*exp(-1 * B(capram) / 298), C(camp) = B(capram) +# +# + +arrhenius_reactions = [ + { + "type": "ARRHENIUS", + "reactants": { + reactant: {} for reactant in reaction["reactants"] + }, + "products": { + product: {} for product in reaction["products"] + }, + "A" : reaction['A'] * np.exp(-1 * reaction['B'] / 298), + "C" : reaction['B'] + } + for reaction in aqua_temp +] + +aqueous_equilibrium = [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + reactant: {} for reactant in reaction["reactants"] + }, + "products": { + product: {} for product in reaction["products"] + }, + "A" : reaction['A'], + "C" : reaction['B'], + "k_reverse" : reaction['C'] + } + for reaction in diss_with_c +] + +aqueous_equilibrium.extend( + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + reactant: {} for reactant in reaction["reactants"] + }, + "products": { + product: {} for product in reaction["products"] + }, + "A" : reaction['A'], + "C" : 0, + "k_reverse" : reaction['B'] + } + for reaction in diss_without_c + ] +) + +mechanisms = { + "camp-data" : [ + { + "name": "CAPRAM2.4 reduced", + "url": "https://capram.tropos.de/capram_24.html", + "reactions": [ + *henrys_law, + *photolysis_reactions, + *arrhenius_reactions, + *aqueous_equilibrium, + ] + } + ] +} +with open('mechanism.json', 'w') as f: + json.dump(mechanisms, f, indent=2) \ No newline at end of file diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json new file mode 100644 index 00000000..8acb6ea4 --- /dev/null +++ b/capram_convert/mechanism.json @@ -0,0 +1,1900 @@ +{ + "camp-data": [ + { + "name": "CAPRAM2.4 reduced", + "url": "https://capram.tropos.de/capram_24.html", + "reactions": [ + { + "type": "PHOTOLYSIS", + "reactants": { + "FEOHpp": {} + }, + "products": { + "FEpp": {}, + "aHO": {} + } + }, + { + "type": "PHOTOLYSIS", + "reactants": { + "NO3m": {} + }, + "products": { + "aNO2": {}, + "aHO": {}, + "OHm": {} + } + }, + { + "type": "PHOTOLYSIS", + "reactants": { + "aH2O2": {} + }, + "products": { + "aHO": {} + } + }, + { + "type": "PHOTOLYSIS", + "reactants": { + "FEC2O42m": {} + }, + "products": { + "FEpp": {}, + "C2O4mm": {}, + "aCO2": {}, + "CO2m": {} + } + }, + { + "type": "ARRHENIUS", + "reactants": { + "aH2O2": {}, + "FEpp": {} + }, + "products": { + "FEppp": {}, + "aHO": {}, + "OHm": {} + }, + "A": 50.0, + "C": 0.0 + }, + { + "type": "ARRHENIUS", + "reactants": { + "aH2O2": {}, + "CUp": {} + }, + "products": { + "CUpp": {}, + "aHO": {}, + "OHm": {} + }, + "A": 7000.0, + "C": 0.0 + }, + { + "type": "ARRHENIUS", + "reactants": { + "O2m": {}, + "FEppp": {} + }, + "products": { + "FEpp": {}, + "aO2": {} + }, + "A": 150000000.0, + "C": 0.0 + }, + { + "type": "ARRHENIUS", + "reactants": { + "aHO2": {}, + "FEOHpp": {} + }, + "products": { + "FEpp": {}, + "aO2": {}, + "[aH2O]": {} + }, + "A": 130000.0, + "C": 0.0 + }, + { + "type": "ARRHENIUS", + "reactants": { + "O2m": {}, + "FEOHpp": {} + }, + "products": { + "FEpp": {}, + "aO2": {}, + "OHm": {} + }, + "A": 150000000.0, + "C": 0.0 + }, + { + "type": "ARRHENIUS", + "reactants": { + "O2m": {}, + "FEpp": {} + }, + "products": { + "FEppp": {}, + "aH2O2": {}, + "-2.0Hp": {} + }, + "A": 10000000.0, + "C": 0.0 + }, + { + "type": "ARRHENIUS", + "reactants": { + "aHO2": {}, + "FEpp": {} + }, + "products": { + "FEppp": {}, + "aH2O2": {}, + "-1.0Hp": {} + }, + "A": 27470692899786.598, + "C": -5050.0 + }, + { + "type": "ARRHENIUS", + "reactants": { + "aHO": {}, + "FEpp": {} + }, + "products": { + "FEOHpp": {} + }, + "A": 17241255673.805157, + "C": -1100.0 + }, + { + "type": "ARRHENIUS", + "reactants": { + "O2m": {}, + "CUp": {} + }, + "products": { + "CUpp": {}, + "aH2O2": {}, + "-2.0Hp": {} + }, + "A": 10000000000.0, + "C": 0.0 + }, + { + "type": "ARRHENIUS", + "reactants": { + "aHO2": {}, + "CUp": {} + }, + "products": { + "CUpp": {}, + "aH2O2": {}, + "-1.0Hp": {} + }, + "A": 2300000000.0, + "C": 0.0 + }, + { + "type": "ARRHENIUS", + "reactants": { + "aHO2": {}, + "CUpp": {} + }, + "products": { + "CUp": {}, + "aO2": {}, + "Hp": {} + }, + "A": 100000000.0, + "C": 0.0 + }, + { + "type": "ARRHENIUS", + "reactants": { + "O2m": {}, + "CUpp": {} + }, + "products": { + "CUp": {}, + "aO2": {} + }, + "A": 8000000000.0, + "C": 0.0 + }, + { + "type": "ARRHENIUS", + "reactants": { + "FEppp": {}, + "CUp": {} + }, + "products": { + "FEpp": {}, + "CUpp": {} + }, + "A": 13000000.0, + "C": 0.0 + }, + { + "type": "ARRHENIUS", + "reactants": { + "FEOHpp": {}, + "CUp": {} + }, + "products": { + "FEpp": {}, + "CUpp": {}, + "OHm": {} + }, + "A": 13000000.0, + 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"products": { + "Hp": {}, + "CHOH2COOm": {} + }, + "A": 0.000316, + "C": 0, + "k_reverse": 20000000000.0 + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aGLY": {}, + "[aH2O]": {} + }, + "products": { + "aCHOH2CHOH2": {} + }, + "A": 3900.0, + "C": 0, + "k_reverse": 0.0055 + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "FEppp": {}, + "C2O4mm": {} + }, + "products": { + "FEC2O4p": {} + }, + "A": 2900000000.0, + "C": 0, + "k_reverse": 0.003 + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "FEC2O4p": {}, + "C2O4mm": {} + }, + "products": { + "FEC2O42m": {} + }, + "A": 6300000.0, + "C": 0, + "k_reverse": 0.003 + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "SO4m": {}, + "CLm": {} + }, + "products": { + "SO4mm": {}, + "aCL": {} + }, + "A": 1.2, + "C": 0, + "k_reverse": 210000000.0 + } + ] + } + ] +} \ No newline at end of file diff --git a/capram_convert/species.json b/capram_convert/species.json index aa093b5f..2dcda70c 100644 --- a/capram_convert/species.json +++ b/capram_convert/species.json @@ -1,483 +1,483 @@ { "camp-data": [ { - "name": "aCHOH2", + "name": "HCL", "type": "CHEM_SPEC" }, { - "name": "aO2CHO", + "name": "aCH3CHOH2", "type": "CHEM_SPEC" }, { - "name": "HONO", + "name": "SO2", "type": "CHEM_SPEC" }, { - "name": "HCL", + "name": "3Hp", "type": "CHEM_SPEC" }, { - "name": "2OHm", + "name": "CH2COOm", "type": "CHEM_SPEC" }, { - "name": "aCH2OH2", + "name": "aSULF", "type": "CHEM_SPEC" }, { - "name": "HCHO", + "name": "NO", "type": "CHEM_SPEC" }, { - "name": "CL2", + "name": "BRNO2", "type": "CHEM_SPEC" }, { - "name": "aACO3", + "name": "NO2p", "type": "CHEM_SPEC" }, { - "name": "2BRm", + "name": "aCH3O", "type": "CHEM_SPEC" }, { - "name": "NO2m", + "name": "HNO4", "type": "CHEM_SPEC" }, { - "name": "aBR", + "name": "BRm", "type": "CHEM_SPEC" }, { - "name": "aHONO", + "name": "aO2CH2OH", "type": "CHEM_SPEC" }, { - "name": "CHOH2COOm", + "name": "aSO2", "type": "CHEM_SPEC" }, { - "name": "CLm", + "name": "aCH2OH", "type": "CHEM_SPEC" }, { - "name": "ETHPX", + "name": "aO2COH2CHOH2", "type": "CHEM_SPEC" }, { - "name": "SO4mm", + "name": "aH2C2O4", "type": "CHEM_SPEC" }, { - "name": "BR2m", + "name": "CHOSO3m", "type": "CHEM_SPEC" }, { - "name": "NO4m", + "name": "aHNO3", "type": "CHEM_SPEC" }, { - "name": "aO2", + "name": "aN2O5", "type": "CHEM_SPEC" }, { - "name": "Hp", + "name": "aO2COH2COOH", "type": "CHEM_SPEC" }, { - "name": "H2O2", + "name": "NH4p", "type": "CHEM_SPEC" }, { - "name": "SO5O2mm", + "name": "C2O4m", "type": "CHEM_SPEC" }, { - "name": "2CHOH2COOm", + "name": "aHONO", "type": "CHEM_SPEC" }, { - "name": "HSO3m", + "name": "aBR", "type": "CHEM_SPEC" }, { - "name": "aO3", + "name": "-1.0Hp", "type": "CHEM_SPEC" }, { - "name": "ACO3", + "name": "CLm", "type": "CHEM_SPEC" }, { - "name": "OP1", + "name": "NO4m", "type": "CHEM_SPEC" }, { - "name": "O2CHOHSO3m", + "name": "aO2CH3CHOH", "type": "CHEM_SPEC" }, { - "name": "aCH3OH", + "name": "aO2CHO", "type": "CHEM_SPEC" }, { - "name": "CH2COOm", + "name": "CLNO2", "type": "CHEM_SPEC" }, { - "name": "CH3OH", + "name": "aCOH2CHOH2", "type": "CHEM_SPEC" }, { - "name": "aCL", + "name": "ACO3", "type": "CHEM_SPEC" }, { - "name": "aNO2", + "name": "aCHOH2COOH", "type": "CHEM_SPEC" }, { - "name": "-1.0Hp", + "name": "HCHO", "type": "CHEM_SPEC" }, { - "name": "HCO3m", + "name": "aCH3COH2", "type": "CHEM_SPEC" }, { - "name": "aH2CO3", + "name": "aCHOH2CHOH2", "type": "CHEM_SPEC" }, { - "name": "NH3", + "name": "CLOHm", "type": "CHEM_SPEC" }, { - "name": "aCH3CHOH2", + "name": "HSO4m", "type": "CHEM_SPEC" }, { - "name": "FEpp", + "name": "H2O2", "type": "CHEM_SPEC" }, { - "name": "FEOHpp", + "name": "ORA2", "type": "CHEM_SPEC" }, { - "name": "GLY", + "name": "HSO5m", "type": "CHEM_SPEC" }, { - "name": "aALD", + "name": "HCOOm", "type": "CHEM_SPEC" }, { - "name": "SO2", + "name": "CL2", "type": "CHEM_SPEC" }, { - "name": "CLOHm", + "name": "aCH3CO", "type": "CHEM_SPEC" }, { - "name": "HMSm", + "name": "NO2", "type": "CHEM_SPEC" }, { - "name": "aHO", + "name": "aHOCL", "type": "CHEM_SPEC" }, { - "name": "N2O5", + "name": "SULF", "type": "CHEM_SPEC" }, { - "name": "aN2O5", + "name": "aHNO4", "type": "CHEM_SPEC" }, { - "name": "C2O4m", + "name": "O3m", "type": "CHEM_SPEC" }, { - "name": "aMO2", + "name": "aNH3", "type": "CHEM_SPEC" }, { - "name": "aCH3O", + "name": "aETHPX", "type": "CHEM_SPEC" }, { - "name": "NO2", + "name": "aCH3OH", "type": "CHEM_SPEC" }, { - "name": "HNO3", + "name": "FEOpp", "type": "CHEM_SPEC" }, { - "name": "aHNO3", + "name": "N2O5", "type": "CHEM_SPEC" }, { - "name": "CHOHSO3m", + "name": "aHCHO", "type": "CHEM_SPEC" }, { - "name": "aORA2", + "name": "aOP1", "type": "CHEM_SPEC" }, { - "name": "FEppp", + "name": "aCH3COH2OO", "type": "CHEM_SPEC" }, { - "name": "aCH3CO", + "name": "aORA1", "type": "CHEM_SPEC" }, { - "name": "ORA1", + "name": "aHO", "type": "CHEM_SPEC" }, { - "name": "FEC2O42m", + "name": "HONO", "type": "CHEM_SPEC" }, { - "name": "FEC2O4p", + "name": "HMSm", "type": "CHEM_SPEC" }, { - "name": "NH4p", + "name": "aCL2", "type": "CHEM_SPEC" }, { - "name": "aHO2", + "name": "GLY", "type": "CHEM_SPEC" }, { - "name": "-2.0Hp", + "name": "CHOHSO3m", "type": "CHEM_SPEC" }, { - "name": "aO2CH2OH", + "name": "O2CHOHSO3m", "type": "CHEM_SPEC" }, { - "name": "HCOOm", + "name": "SO4mm", "type": "CHEM_SPEC" }, { - "name": "SO5O2Hm", + "name": "2FEppp", "type": "CHEM_SPEC" }, { - "name": "aCOH2CHOH2", + "name": "aORA2", "type": "CHEM_SPEC" }, { - "name": "aHOCL", + "name": "OP1", "type": "CHEM_SPEC" }, { - "name": "aCL2", + "name": "aCL", "type": "CHEM_SPEC" }, { - "name": "aCOH2COOH", + "name": "[aH2O]", "type": "CHEM_SPEC" }, { - "name": "aCH3COH2OO", + "name": "aO3", "type": "CHEM_SPEC" }, { - "name": "OHm", + "name": "aCHOH2", "type": "CHEM_SPEC" }, { - "name": "aHNO4", + "name": "aHO3", "type": "CHEM_SPEC" }, { - "name": "SULF", + "name": "2OHm", "type": "CHEM_SPEC" }, { - "name": "HSO4m", + "name": "CUp", "type": "CHEM_SPEC" }, { - "name": "BRNO2", + "name": "ETHPX", "type": "CHEM_SPEC" }, { - "name": "aH2C2O4", + "name": "HO", "type": "CHEM_SPEC" }, { - "name": "aNO3", + "name": "aCLNO2", "type": "CHEM_SPEC" }, { - "name": "HSO5m", + "name": "aCH2COOH", "type": "CHEM_SPEC" }, { - "name": "O2CH2COOm", + "name": "FEC2O4p", "type": "CHEM_SPEC" }, { - "name": "aBRNO2", + "name": "NO2m", "type": "CHEM_SPEC" }, { - "name": "aORA1", + "name": "NO3m", "type": "CHEM_SPEC" }, { - "name": "NO2p", + "name": "aCH3CHOH", "type": "CHEM_SPEC" }, { - "name": "HC2O4m", + "name": "aALD", "type": "CHEM_SPEC" }, { - "name": "CUpp", + "name": "CL2m", "type": "CHEM_SPEC" }, { - "name": "aBR2", + "name": "CHOH2COOm", "type": "CHEM_SPEC" }, { - "name": "NO3", + "name": "SO3m", "type": "CHEM_SPEC" }, { - "name": "aO2COH2COOH", + "name": "BR2", "type": "CHEM_SPEC" }, { - "name": "SO3mm", + "name": "SO5O2mm", "type": "CHEM_SPEC" }, { - "name": "O3m", + "name": "ETOH", "type": "CHEM_SPEC" }, { - "name": "2FEppp", + "name": "NO3", "type": "CHEM_SPEC" }, { - "name": "SO4m", + "name": "HO2", "type": "CHEM_SPEC" }, { - "name": "aHO3", + "name": "aMO2", "type": "CHEM_SPEC" }, { - "name": "2CLm", + "name": "aGLY", "type": "CHEM_SPEC" }, { - "name": "BR2", + "name": "O2m", "type": "CHEM_SPEC" }, { - "name": "FEOpp", + "name": "aH2O2", "type": "CHEM_SPEC" }, { - "name": "aO2CH3CHOH", + "name": "2SO4mm", "type": "CHEM_SPEC" }, { - "name": "2SO4mm", + "name": "-2.0Hp", "type": "CHEM_SPEC" }, { - "name": "aCO2H", + "name": "O2CH2COOm", "type": "CHEM_SPEC" }, { - "name": "HNO4", + "name": "MCOOm", "type": "CHEM_SPEC" }, { - "name": "aBRCL", + "name": "aHOBR", "type": "CHEM_SPEC" }, { - "name": "aNH3", + "name": "Hp", "type": "CHEM_SPEC" }, { - "name": "aHCHO", + "name": "CO2", "type": "CHEM_SPEC" }, { - "name": "ORA2", + "name": "BR2m", "type": "CHEM_SPEC" }, { - "name": "aETHPX", + "name": "[O2]", "type": "CHEM_SPEC" }, { - "name": "[aH2O]", + "name": "SO5O2Hm", "type": "CHEM_SPEC" }, { - "name": "CHOSO3m", + "name": "aH2CO3", "type": "CHEM_SPEC" }, { - "name": "aO2COH2CHOH2", + "name": "ALD", "type": "CHEM_SPEC" }, { - "name": "MCOOm", + "name": "aBR2", "type": "CHEM_SPEC" }, { - "name": "aETOH", + "name": "2CLm", "type": "CHEM_SPEC" }, { - "name": "BRCL", + "name": "aACO3", "type": "CHEM_SPEC" }, { - "name": "[O2]", + "name": "aO2", "type": "CHEM_SPEC" }, { - "name": "aCLNO2", + "name": "HSO3m", "type": "CHEM_SPEC" }, { - "name": "aHOBR", + "name": "FEpp", "type": "CHEM_SPEC" }, { - "name": "aCHOH2COOH", + "name": "HNO3", "type": "CHEM_SPEC" }, { - "name": "aCH2OH", + "name": "aNO2", "type": "CHEM_SPEC" }, { - "name": "HO", + "name": "FEOHpp", "type": "CHEM_SPEC" }, { - "name": "O2m", + "name": "aBRCL", "type": "CHEM_SPEC" }, { @@ -485,75 +485,75 @@ "type": "CHEM_SPEC" }, { - "name": "SO3m", + "name": "aCH2OH2", "type": "CHEM_SPEC" }, { - "name": "BRm", + "name": "FEppp", "type": "CHEM_SPEC" }, { - "name": "ALD", + "name": "CHOSO3mm", "type": "CHEM_SPEC" }, { - "name": "3Hp", + "name": "BROHm", "type": "CHEM_SPEC" }, { - "name": "aCO2", + "name": "2BRm", "type": "CHEM_SPEC" }, { - "name": "aCHOH2CHOH2", + "name": "aCO2H", "type": "CHEM_SPEC" }, { - "name": "ETOH", + "name": "MO2", "type": "CHEM_SPEC" }, { - "name": "CL2m", + "name": "CO2m", "type": "CHEM_SPEC" }, { - "name": "CLNO2", + "name": "HC2O4m", "type": "CHEM_SPEC" }, { - "name": "SO5m", + "name": "C2O4mm", "type": "CHEM_SPEC" }, { - "name": "aCH2COOH", + "name": "aETOH", "type": "CHEM_SPEC" }, { - "name": "NO", + "name": "2CHOH2COOm", "type": "CHEM_SPEC" }, { - "name": "CHOSO3mm", + "name": "NH3", "type": "CHEM_SPEC" }, { - "name": "CO2", + "name": "CH3OH", "type": "CHEM_SPEC" }, { - "name": "aSO2", + "name": "OHm", "type": "CHEM_SPEC" }, { - "name": "aSULF", + "name": "SO3mm", "type": "CHEM_SPEC" }, { - "name": "HO2", + "name": "aNO3", "type": "CHEM_SPEC" }, { - "name": "C2O4mm", + "name": "ORA1", "type": "CHEM_SPEC" }, { @@ -561,51 +561,51 @@ "type": "CHEM_SPEC" }, { - "name": "NO3m", + "name": "FEC2O42m", "type": "CHEM_SPEC" }, { - "name": "aCH3COH2", + "name": "SO4m", "type": "CHEM_SPEC" }, { - "name": "aGLY", + "name": "aHO2", "type": "CHEM_SPEC" }, { - "name": "aCH3CHOH", + "name": "aHCL", "type": "CHEM_SPEC" }, { - "name": "BROHm", + "name": "SO5m", "type": "CHEM_SPEC" }, { - "name": "CO2m", + "name": "2Hp", "type": "CHEM_SPEC" }, { - "name": "CUp", + "name": "CUpp", "type": "CHEM_SPEC" }, { - "name": "aHCL", + "name": "HCO3m", "type": "CHEM_SPEC" }, { - "name": "aH2O2", + "name": "aCO2", "type": "CHEM_SPEC" }, { - "name": "MO2", + "name": "aBRNO2", "type": "CHEM_SPEC" }, { - "name": "aOP1", + "name": "BRCL", "type": "CHEM_SPEC" }, { - "name": "2Hp", + "name": "aCOH2COOH", "type": "CHEM_SPEC" } ] From a94366c2ce0c9665479644012507842bec7d2f5d Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 10:26:37 -0500 Subject: [PATCH 08/24] writing out henry's law stuff for speciees --- capram_convert/convert.py | 79 +++--- capram_convert/mechanism.json | 231 ++++++++++++++++ capram_convert/species.json | 500 +++++++++++++++++++++------------- 3 files changed, 590 insertions(+), 220 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index 699ea148..a6de0598 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -10,10 +10,6 @@ # comments here taken from the capram file ## -# for example molecules_to_identifier['CO2'] = 'aCO2' -# for example molecules_to_identifier['aCO2'] = 'CO2' -molecules_identifier_mapping = {} - # CLASS: HENRY, TYPE: TEMP3 # Phase transfer # Kh = A exp(B (1/T - 1/298)) @@ -21,7 +17,7 @@ # Further uptake parameters according to Schwartz's approach (alpha, Dg) # are read elsewhere in the program # for example, henry['CO2'] = {A: '3.1e-2', B: '2423.0'} -henry = {} +henry = [] # CLASS: AQUA, TYPE: PHOTABC photolysis reactions according to # j = A * exp (B *(1 - 1 /(cos (C * chi)); A = jmax; chi = zenith angle @@ -76,27 +72,13 @@ def combine_stoichiometric_coeffs(species): # when those exist, add them to the appropriate array while line_index < len(content): line = content[line_index].strip() - if line.startswith('COMMENT CLASS: AQUA, TYPE: PHOTABC'): - pass - if line.startswith('COMMENT CLASS: AQUA; TYPE: TEMP3'): - pass - if line.startswith('COMMENT CLASS: DISS, TYPE: DCONST'): - pass if line.startswith('CLASS'): type = line.split(':')[1].strip() if type == 'HENRY': - mol = content[line_index + 1].strip().split(' = ') - ident = mol[1].strip() - mol = mol[0].strip() - - temp = content[line_index + 2].strip().split('TEMP3:') - a = temp[1].split('B:')[0].strip().split('A:')[1].strip() - b = temp[1].split('B:')[1].strip() - - molecules_identifier_mapping[mol] = ident - molecules_identifier_mapping[ident] = mol - henry[mol] = { 'A': a, 'B': b } - + reactants, products = parse_reactants_products(content[line_index + 1]) + match = constants_pattern.search(content[line_index + 2]) + type, A, B, C = match.group(1), float(match.group(2)), float(match.group(3)), match.group(4) + henry.append(dict(reactants = reactants, products=products, A=A, B=B)) line_index += 2 elif type == 'AQUA': reactants, products = parse_reactants_products(content[line_index + 1]) @@ -110,9 +92,7 @@ def combine_stoichiometric_coeffs(species): print(f"Unknown aqua type: {type}") line_index += 2 elif type == 'DISS': - reaction = content[line_index + 1].strip().split('=') - reactants = [i.strip() for i in reaction[0].strip().split('+')] - products = [i.strip() for i in reaction[1].strip().split('+')] + reactants, products = parse_reactants_products(content[line_index + 1]) match = constants_pattern.search(content[line_index + 2]) type, A, B, C = match.group(1), float(match.group(2)), float(match.group(3)), match.group(4) if C is None: @@ -124,26 +104,49 @@ def combine_stoichiometric_coeffs(species): line_index += 1 -species = set( - name for name,_ in molecules_identifier_mapping.items() if not name.startswith("a") -) - -for list in [aqua_photo, aqua_temp, diss_with_c, diss_without_c]: - for item in list: - for spec in item['reactants']: - species.add(spec) - for spec in item['products']: - species.add(spec) +species = {} + +for item in henry: + for name in item['reactants']: + spec = dict(name=name, type="CHEM_SPEC") + spec["HLC(298K) [M Pa-1]"] = item['A'] + spec["HLC exp factor [K]"] = item['B'] + spec["diffusion coeff [m2 s-1]"] = 1.00 # TODO: replace + spec["N star"] = 1.00 # TODO: replace + species[name] = spec + for name in item['products']: + spec = dict(name=name, type="CHEM_SPEC") + species[name] = spec + +for collection in [aqua_photo, aqua_temp, diss_with_c, diss_without_c]: + for item in collection: + for name in item['reactants']: + if name not in species: + spec = dict(name=name, type="CHEM_SPEC") + species[name] = spec + for name in item['products']: + if name not in species: + spec = dict(name=name, type="CHEM_SPEC") + species[name] = spec + +print(list(species.values())) with open('species.json', 'w') as f: json.dump( { - "camp-data" : [dict(name=name, type="CHEM_SPEC") for name in species] + "camp-data" : list(species.values()) }, f, indent=2 ) henrys_law = [ - + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : "my gas spec", + "aerosol-phase species" : "my aero spec", + "areosol phase" : "my aqueous phase", + "aerosol-phase water" : "H2O_aq", + } + for reaction in henry ] photolysis_reactions = [ diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json index 8acb6ea4..ea871ec1 100644 --- a/capram_convert/mechanism.json +++ b/capram_convert/mechanism.json @@ -4,6 +4,237 @@ "name": "CAPRAM2.4 reduced", "url": "https://capram.tropos.de/capram_24.html", "reactions": [ + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "my gas spec", + "aerosol-phase species": "my aero spec", + "areosol phase": "my aqueous phase", + "aerosol-phase water": "H2O_aq" + }, { "type": "PHOTOLYSIS", "reactants": { diff --git a/capram_convert/species.json b/capram_convert/species.json index 2dcda70c..634bbbe8 100644 --- a/capram_convert/species.json +++ b/capram_convert/species.json @@ -1,611 +1,747 @@ { "camp-data": [ { - "name": "HCL", - "type": "CHEM_SPEC" + "name": "CO2", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 0.031, + "HLC exp factor [K]": 2423.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aCH3CHOH2", + "name": "aCO2", "type": "CHEM_SPEC" }, { - "name": "SO2", - "type": "CHEM_SPEC" + "name": "O3", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 0.0114, + "HLC exp factor [K]": 2300.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "3Hp", + "name": "aO3", "type": "CHEM_SPEC" }, { - "name": "CH2COOm", - "type": "CHEM_SPEC" + "name": "HO2", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 9000.0, + "HLC exp factor [K]": 0.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aSULF", + "name": "aHO2", "type": "CHEM_SPEC" }, { - "name": "NO", - "type": "CHEM_SPEC" + "name": "HO", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 25.0, + "HLC exp factor [K]": 5280.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "BRNO2", + "name": "aHO", "type": "CHEM_SPEC" }, { - "name": "NO2p", - "type": "CHEM_SPEC" + "name": "H2O2", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 102000.0, + "HLC exp factor [K]": 6340.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aCH3O", + "name": "aH2O2", "type": "CHEM_SPEC" }, { - "name": "HNO4", - "type": "CHEM_SPEC" + "name": "NO2", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 0.012, + "HLC exp factor [K]": 1263.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "BRm", + "name": "aNO2", "type": "CHEM_SPEC" }, { - "name": "aO2CH2OH", - "type": "CHEM_SPEC" + "name": "HONO", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 49.0, + "HLC exp factor [K]": 4880.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aSO2", + "name": "aHONO", "type": "CHEM_SPEC" }, { - "name": "aCH2OH", - "type": "CHEM_SPEC" + "name": "HNO3", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 210000.0, + "HLC exp factor [K]": 8700.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aO2COH2CHOH2", + "name": "aHNO3", "type": "CHEM_SPEC" }, { - "name": "aH2C2O4", - "type": "CHEM_SPEC" + "name": "NO3", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 0.6, + "HLC exp factor [K]": 0.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "CHOSO3m", + "name": "aNO3", "type": "CHEM_SPEC" }, { - "name": "aHNO3", - "type": "CHEM_SPEC" + "name": "N2O5", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 1.4, + "HLC exp factor [K]": 0.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { "name": "aN2O5", "type": "CHEM_SPEC" }, { - "name": "aO2COH2COOH", - "type": "CHEM_SPEC" + "name": "NH3", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 60.7, + "HLC exp factor [K]": 3920.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "NH4p", + "name": "aNH3", "type": "CHEM_SPEC" }, { - "name": "C2O4m", - "type": "CHEM_SPEC" + "name": "HCL", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 1.1, + "HLC exp factor [K]": 2020.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aHONO", + "name": "aHCL", "type": "CHEM_SPEC" }, { - "name": "aBR", - "type": "CHEM_SPEC" + "name": "HCHO", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 2.5, + "HLC exp factor [K]": 7216.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "-1.0Hp", + "name": "aHCHO", "type": "CHEM_SPEC" }, { - "name": "CLm", - "type": "CHEM_SPEC" + "name": "ORA1", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 5530.0, + "HLC exp factor [K]": 5630.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "NO4m", + "name": "aORA1", "type": "CHEM_SPEC" }, { - "name": "aO2CH3CHOH", - "type": "CHEM_SPEC" + "name": "SO2", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 1.24, + "HLC exp factor [K]": 3247.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aO2CHO", + "name": "aSO2", "type": "CHEM_SPEC" }, { - "name": "CLNO2", - "type": "CHEM_SPEC" + "name": "OP1", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 310.0, + "HLC exp factor [K]": 5607.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aCOH2CHOH2", + "name": "aOP1", "type": "CHEM_SPEC" }, { - "name": "ACO3", - "type": "CHEM_SPEC" + "name": "ORA2", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 5500.0, + "HLC exp factor [K]": 5890.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aCHOH2COOH", + "name": "aORA2", "type": "CHEM_SPEC" }, { - "name": "HCHO", - "type": "CHEM_SPEC" + "name": "MO2", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 310.0, + "HLC exp factor [K]": 5607.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aCH3COH2", + "name": "aMO2", "type": "CHEM_SPEC" }, { - "name": "aCHOH2CHOH2", - "type": "CHEM_SPEC" + "name": "ETHPX", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 340.0, + "HLC exp factor [K]": 87.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "CLOHm", + "name": "aETHPX", "type": "CHEM_SPEC" }, { - "name": "HSO4m", - "type": "CHEM_SPEC" + "name": "ETOH", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 190.0, + "HLC exp factor [K]": 6290.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "H2O2", + "name": "aETOH", "type": "CHEM_SPEC" }, { - "name": "ORA2", - "type": "CHEM_SPEC" + "name": "CH3OH", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 220.0, + "HLC exp factor [K]": 5390.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "HSO5m", + "name": "aCH3OH", "type": "CHEM_SPEC" }, { - "name": "HCOOm", - "type": "CHEM_SPEC" + "name": "ALD", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 4.8, + "HLC exp factor [K]": 6254.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "CL2", + "name": "aALD", "type": "CHEM_SPEC" }, { - "name": "aCH3CO", - "type": "CHEM_SPEC" + "name": "BR2", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 0.758, + "HLC exp factor [K]": 3800.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "NO2", + "name": "aBR2", "type": "CHEM_SPEC" }, { - "name": "aHOCL", + "name": "CL2", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 0.0915, + "HLC exp factor [K]": 2490.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 + }, + { + "name": "aCL2", "type": "CHEM_SPEC" }, { "name": "SULF", - "type": "CHEM_SPEC" + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 870000000000.0, + "HLC exp factor [K]": 0.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aHNO4", + "name": "aSULF", "type": "CHEM_SPEC" }, { - "name": "O3m", - "type": "CHEM_SPEC" + "name": "HNO4", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 30000.0, + "HLC exp factor [K]": 0.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aNH3", + "name": "aHNO4", "type": "CHEM_SPEC" }, { - "name": "aETHPX", - "type": "CHEM_SPEC" + "name": "ACO3", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 669.0, + "HLC exp factor [K]": 5893.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aCH3OH", + "name": "aACO3", "type": "CHEM_SPEC" }, { - "name": "FEOpp", - "type": "CHEM_SPEC" + "name": "GLY", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 1.4, + "HLC exp factor [K]": 0.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "N2O5", + "name": "aGLY", "type": "CHEM_SPEC" }, { - "name": "aHCHO", - "type": "CHEM_SPEC" + "name": "[O2]", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 0.0013, + "HLC exp factor [K]": 1700.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aOP1", + "name": "aO2", "type": "CHEM_SPEC" }, { - "name": "aCH3COH2OO", - "type": "CHEM_SPEC" + "name": "CLNO2", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 0.024, + "HLC exp factor [K]": 0.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aORA1", + "name": "aCLNO2", "type": "CHEM_SPEC" }, { - "name": "aHO", - "type": "CHEM_SPEC" + "name": "BRNO2", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 0.3, + "HLC exp factor [K]": 0.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "HONO", + "name": "aBRNO2", "type": "CHEM_SPEC" }, { - "name": "HMSm", - "type": "CHEM_SPEC" + "name": "BRCL", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 0.94, + "HLC exp factor [K]": 0.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "aCL2", + "name": "aBRCL", "type": "CHEM_SPEC" }, { - "name": "GLY", - "type": "CHEM_SPEC" + "name": "NO", + "type": "CHEM_SPEC", + "HLC(298K) [M Pa-1]": 0.0019, + "HLC exp factor [K]": 0.0, + "diffusion coeff [m2 s-1]": 1.0, + "N star": 1.0 }, { - "name": "CHOHSO3m", + "name": "aNO", "type": "CHEM_SPEC" }, { - "name": "O2CHOHSO3m", + "name": "FEOHpp", "type": "CHEM_SPEC" }, { - "name": "SO4mm", + "name": "FEpp", "type": "CHEM_SPEC" }, { - "name": "2FEppp", + "name": "NO3m", "type": "CHEM_SPEC" }, { - "name": "aORA2", + "name": "OHm", "type": "CHEM_SPEC" }, { - "name": "OP1", + "name": "FEC2O42m", "type": "CHEM_SPEC" }, { - "name": "aCL", + "name": "C2O4mm", "type": "CHEM_SPEC" }, { - "name": "[aH2O]", + "name": "CO2m", "type": "CHEM_SPEC" }, { - "name": "aO3", + "name": "FEppp", "type": "CHEM_SPEC" }, { - "name": "aCHOH2", + "name": "CUp", "type": "CHEM_SPEC" }, { - "name": "aHO3", + "name": "CUpp", "type": "CHEM_SPEC" }, { - "name": "2OHm", + "name": "O2m", "type": "CHEM_SPEC" }, { - "name": "CUp", + "name": "[aH2O]", "type": "CHEM_SPEC" }, { - "name": "ETHPX", + "name": "-2.0Hp", "type": "CHEM_SPEC" }, { - "name": "HO", + "name": "-1.0Hp", "type": "CHEM_SPEC" }, { - "name": "aCLNO2", + "name": "Hp", "type": "CHEM_SPEC" }, { - "name": "aCH2COOH", + "name": "O3m", "type": "CHEM_SPEC" }, { - "name": "FEC2O4p", + "name": "aHO3", "type": "CHEM_SPEC" }, { - "name": "NO2m", + "name": "HSO3m", "type": "CHEM_SPEC" }, { - "name": "NO3m", + "name": "SO3m", "type": "CHEM_SPEC" }, { - "name": "aCH3CHOH", + "name": "FEOpp", "type": "CHEM_SPEC" }, { - "name": "aALD", + "name": "CLm", "type": "CHEM_SPEC" }, { - "name": "CL2m", + "name": "CLOHm", "type": "CHEM_SPEC" }, { - "name": "CHOH2COOm", + "name": "2FEppp", "type": "CHEM_SPEC" }, { - "name": "SO3m", + "name": "2OHm", "type": "CHEM_SPEC" }, { - "name": "BR2", + "name": "NO2p", "type": "CHEM_SPEC" }, { - "name": "SO5O2mm", + "name": "SO4mm", "type": "CHEM_SPEC" }, { - "name": "ETOH", + "name": "SO4m", "type": "CHEM_SPEC" }, { - "name": "NO3", + "name": "NO4m", "type": "CHEM_SPEC" }, { - "name": "HO2", + "name": "NO2m", "type": "CHEM_SPEC" }, { - "name": "aMO2", + "name": "HSO4m", "type": "CHEM_SPEC" }, { - "name": "aGLY", + "name": "BRm", "type": "CHEM_SPEC" }, { - "name": "O2m", + "name": "HMSm", "type": "CHEM_SPEC" }, { - "name": "aH2O2", + "name": "CHOHSO3m", "type": "CHEM_SPEC" }, { - "name": "2SO4mm", + "name": "O2CHOHSO3m", "type": "CHEM_SPEC" }, { - "name": "-2.0Hp", + "name": "CHOSO3m", "type": "CHEM_SPEC" }, { - "name": "O2CH2COOm", + "name": "aO2CHO", "type": "CHEM_SPEC" }, { - "name": "MCOOm", + "name": "2Hp", "type": "CHEM_SPEC" }, { - "name": "aHOBR", + "name": "SO3mm", "type": "CHEM_SPEC" }, { - "name": "Hp", + "name": "SO5m", "type": "CHEM_SPEC" }, { - "name": "CO2", + "name": "HSO5m", "type": "CHEM_SPEC" }, { - "name": "BR2m", + "name": "SO5O2Hm", "type": "CHEM_SPEC" }, { - "name": "[O2]", + "name": "SO5O2mm", "type": "CHEM_SPEC" }, { - "name": "SO5O2Hm", + "name": "2SO4mm", "type": "CHEM_SPEC" }, { - "name": "aH2CO3", + "name": "3Hp", "type": "CHEM_SPEC" }, { - "name": "ALD", + "name": "aCH2OH", "type": "CHEM_SPEC" }, { - "name": "aBR2", + "name": "aO2CH2OH", "type": "CHEM_SPEC" }, { - "name": "2CLm", + "name": "aCH3CHOH", "type": "CHEM_SPEC" }, { - "name": "aACO3", + "name": "aO2CH3CHOH", "type": "CHEM_SPEC" }, { - "name": "aO2", + "name": "aCH2OH2", "type": "CHEM_SPEC" }, { - "name": "HSO3m", + "name": "aCHOH2", "type": "CHEM_SPEC" }, { - "name": "FEpp", + "name": "aCH3CHOH2", "type": "CHEM_SPEC" }, { - "name": "HNO3", + "name": "aCH3COH2", "type": "CHEM_SPEC" }, { - "name": "aNO2", + "name": "aCH3CO", "type": "CHEM_SPEC" }, { - "name": "FEOHpp", + "name": "aCO2H", "type": "CHEM_SPEC" }, { - "name": "aBRCL", + "name": "HCOOm", "type": "CHEM_SPEC" }, { - "name": "aCH3CH2O", + "name": "aCH2COOH", "type": "CHEM_SPEC" }, { - "name": "aCH2OH2", + "name": "MCOOm", "type": "CHEM_SPEC" }, { - "name": "FEppp", + "name": "CH2COOm", "type": "CHEM_SPEC" }, { - "name": "CHOSO3mm", + "name": "aCH3O", "type": "CHEM_SPEC" }, { - "name": "BROHm", + "name": "aCH3CH2O", "type": "CHEM_SPEC" }, { - "name": "2BRm", + "name": "HC2O4m", "type": "CHEM_SPEC" }, { - "name": "aCO2H", + "name": "C2O4m", "type": "CHEM_SPEC" }, { - "name": "MO2", + "name": "aCHOH2CHOH2", "type": "CHEM_SPEC" }, { - "name": "CO2m", + "name": "aCOH2CHOH2", "type": "CHEM_SPEC" }, { - "name": "HC2O4m", + "name": "aO2COH2CHOH2", "type": "CHEM_SPEC" }, { - "name": "C2O4mm", + "name": "aCHOH2COOH", "type": "CHEM_SPEC" }, { - "name": "aETOH", + "name": "aCOH2COOH", "type": "CHEM_SPEC" }, { - "name": "2CHOH2COOm", + "name": "aO2COH2COOH", "type": "CHEM_SPEC" }, { - "name": "NH3", + "name": "aH2C2O4", "type": "CHEM_SPEC" }, { - "name": "CH3OH", + "name": "aCH3COH2OO", "type": "CHEM_SPEC" }, { - "name": "OHm", + "name": "O2CH2COOm", "type": "CHEM_SPEC" }, { - "name": "SO3mm", + "name": "2CHOH2COOm", "type": "CHEM_SPEC" }, { - "name": "aNO3", + "name": "CL2m", "type": "CHEM_SPEC" }, { - "name": "ORA1", + "name": "2CLm", "type": "CHEM_SPEC" }, { - "name": "O3", + "name": "aHOCL", "type": "CHEM_SPEC" }, { - "name": "FEC2O42m", + "name": "aBR", "type": "CHEM_SPEC" }, { - "name": "SO4m", + "name": "BR2m", "type": "CHEM_SPEC" }, { - "name": "aHO2", + "name": "2BRm", "type": "CHEM_SPEC" }, { - "name": "aHCL", + "name": "aHOBR", "type": "CHEM_SPEC" }, { - "name": "SO5m", + "name": "BROHm", "type": "CHEM_SPEC" }, { - "name": "2Hp", + "name": "aH2CO3", "type": "CHEM_SPEC" }, { - "name": "CUpp", + "name": "NH4p", "type": "CHEM_SPEC" }, { - "name": "HCO3m", + "name": "aCL", "type": "CHEM_SPEC" }, { - "name": "aCO2", + "name": "HCO3m", "type": "CHEM_SPEC" }, { - "name": "aBRNO2", + "name": "CHOSO3mm", "type": "CHEM_SPEC" }, { - "name": "BRCL", + "name": "CHOH2COOm", "type": "CHEM_SPEC" }, { - "name": "aCOH2COOH", + "name": "FEC2O4p", "type": "CHEM_SPEC" } ] From 4a76f0333e44242eaa369870192db80f2009b661 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 10:45:44 -0500 Subject: [PATCH 09/24] adding henry's law stuff? --- capram_convert/convert.py | 79 ++++-- capram_convert/mechanism.json | 508 ++++++++++++++++++---------------- 2 files changed, 326 insertions(+), 261 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index a6de0598..5c26ef36 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -17,30 +17,30 @@ # Further uptake parameters according to Schwartz's approach (alpha, Dg) # are read elsewhere in the program # for example, henry['CO2'] = {A: '3.1e-2', B: '2423.0'} -henry = [] +henry = list() # CLASS: AQUA, TYPE: PHOTABC photolysis reactions according to # j = A * exp (B *(1 - 1 /(cos (C * chi)); A = jmax; chi = zenith angle -aqua_photo = [] +aqua_photo = list() # CLASS: AQUA; TYPE: TEMP3 # TEmperature dependent reation # k(T)=A*exp(B*(1/T-1/298)) # A=k(298 K) # B=-Ea/R -aqua_temp = [] +aqua_temp = list() # CLASS: DISS, TYPE: DTEMP # Temperature dependent dissociation # Ke = A exp(B*(1/T - 1/298)); # B=-Ea/R # C = k(back reaction) -diss_with_c = [] +diss_with_c = list() # CLASS: DISS, TYPE: DCONST # Dissociation # Ke = A # B= k(back reaction) -diss_without_c = [] +diss_without_c = list() # pattern that matches A, B, and optionall C constants for PHOTABC and TEMP3 reactions # thanks chatgpt @@ -104,19 +104,44 @@ def combine_stoichiometric_coeffs(species): line_index += 1 -species = {} +species = dict() + +henrys_law_reactions = list() +henrys_species = list() + for item in henry: - for name in item['reactants']: - spec = dict(name=name, type="CHEM_SPEC") - spec["HLC(298K) [M Pa-1]"] = item['A'] - spec["HLC exp factor [K]"] = item['B'] - spec["diffusion coeff [m2 s-1]"] = 1.00 # TODO: replace - spec["N star"] = 1.00 # TODO: replace - species[name] = spec - for name in item['products']: - spec = dict(name=name, type="CHEM_SPEC") - species[name] = spec + gas_phase = item['reactants'][0] + aero_phase = item['products'][0] + + henrys_species.append(gas_phase) + + spec = dict(name=gas_phase, type="CHEM_SPEC") + spec["HLC(298K) [M Pa-1]"] = item['A'] + spec["HLC exp factor [K]"] = item['B'] + spec["diffusion coeff [m2 s-1]"] = 1.00 # TODO: replace + spec["N star"] = 1.00 # TODO: replace + species[gas_phase] = spec + + species[aero_phase] = dict(name=aero_phase, type="CHEM_SPEC") + + henrys_law_reactions.append( + { + "type" : "HL_PHASE_TRANSFER", + "gas-phase species" : gas_phase, + "aerosol phase" : "aqueous aerosol", + "aerosol-phase species" : aero_phase, + "aerosol-phase water" : "aH2O" #TODO: verify this + } + ) + +henrys_law_aero_phase = [ + { + "name" : "aqueous aerosol", + "type" : "AERO_PHASE", + "species" : henrys_species + } +] for collection in [aqua_photo, aqua_temp, diss_with_c, diss_without_c]: for item in collection: @@ -129,8 +154,6 @@ def combine_stoichiometric_coeffs(species): spec = dict(name=name, type="CHEM_SPEC") species[name] = spec -print(list(species.values())) - with open('species.json', 'w') as f: json.dump( { @@ -138,17 +161,6 @@ def combine_stoichiometric_coeffs(species): }, f, indent=2 ) -henrys_law = [ - { - "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : "my gas spec", - "aerosol-phase species" : "my aero spec", - "areosol phase" : "my aqueous phase", - "aerosol-phase water" : "H2O_aq", - } - for reaction in henry -] - photolysis_reactions = [ { "type": "PHOTOLYSIS", @@ -235,15 +247,22 @@ def combine_stoichiometric_coeffs(species): "camp-data" : [ { "name": "CAPRAM2.4 reduced", + "type" : "MECHANISM", "url": "https://capram.tropos.de/capram_24.html", "reactions": [ - *henrys_law, *photolysis_reactions, *arrhenius_reactions, *aqueous_equilibrium, ] + }, + *henrys_law_aero_phase, + { + "name" : "Henry's Law phase transfer", + "type" : "MECHANISM", + "reactions" : henrys_law_reactions } ] } + with open('mechanism.json', 'w') as f: json.dump(mechanisms, f, indent=2) \ No newline at end of file diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json index ea871ec1..32de188a 100644 --- a/capram_convert/mechanism.json +++ b/capram_convert/mechanism.json @@ -2,239 +2,9 @@ "camp-data": [ { "name": "CAPRAM2.4 reduced", + "type": "MECHANISM", "url": "https://capram.tropos.de/capram_24.html", "reactions": [ - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "my gas spec", - "aerosol-phase species": "my aero spec", - "areosol phase": "my aqueous phase", - "aerosol-phase water": "H2O_aq" - }, { "type": "PHOTOLYSIS", "reactants": { @@ -2126,6 +1896,282 @@ "k_reverse": 210000000.0 } ] + }, + { + "name": "aqueous aerosol", + "type": "AERO_PHASE", + "species": [ + "CO2", + "O3", + "HO2", + "HO", + "H2O2", + "NO2", + "HONO", + "HNO3", + "NO3", + "N2O5", + "NH3", + "HCL", + "HCHO", + "ORA1", + "SO2", + "OP1", + "ORA2", + "MO2", + "ETHPX", + "ETOH", + "CH3OH", + "ALD", + "BR2", + "CL2", + "SULF", + "HNO4", + "ACO3", + "GLY", + "[O2]", + "CLNO2", + "BRNO2", + "BRCL", + "NO" + ] + }, + { + "name": "Henry's Law phase transfer", + "type": "MECHANISM", + "reactions": [ + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "CO2", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aCO2", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "O3", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aO3", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "HO2", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aHO2", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "HO", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aHO", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "H2O2", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aH2O2", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "NO2", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aNO2", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "HONO", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aHONO", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "HNO3", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aHNO3", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "NO3", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aNO3", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "N2O5", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aN2O5", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "NH3", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aNH3", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "HCL", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aHCL", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "HCHO", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aHCHO", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "ORA1", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aORA1", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "SO2", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aSO2", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "OP1", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aOP1", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "ORA2", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aORA2", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "MO2", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aMO2", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "ETHPX", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aETHPX", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "ETOH", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aETOH", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "CH3OH", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aCH3OH", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "ALD", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aALD", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "BR2", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aBR2", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "CL2", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aCL2", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "SULF", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aSULF", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "HNO4", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aHNO4", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "ACO3", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aACO3", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "GLY", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aGLY", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "[O2]", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aO2", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "CLNO2", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aCLNO2", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "BRNO2", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aBRNO2", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "BRCL", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aBRCL", + "aerosol-phase water": "aH2O" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "NO", + "aerosol phase": "aqueous aerosol", + "aerosol-phase species": "aNO", + "aerosol-phase water": "aH2O" + } + ] } ] } \ No newline at end of file From 91978266af4fcb860ed56d8aae6e609b26ba7db6 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 10:49:51 -0500 Subject: [PATCH 10/24] adding binned thing for henry's law --- capram_convert/convert.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index 5c26ef36..1e372583 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -256,6 +256,19 @@ def combine_stoichiometric_coeffs(species): ] }, *henrys_law_aero_phase, + { + "type" : "AERO_REP_MODAL_BINNED_MASS", + "name" : "my aero rep 2", + "modes/bins" : + { + "the mode" : + { + "type" : "MODAL", + "phases" : ["aqueous aerosol"], + "shape" : "LOG_NORMAL" + } + } + }, { "name" : "Henry's Law phase transfer", "type" : "MECHANISM", From 1d1b2a7d0cf516b01bcc04fb59a3b212a5fc0ba6 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 11:01:00 -0500 Subject: [PATCH 11/24] adding binned mass --- capram_convert/mechanism.json | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json index 32de188a..9d041b19 100644 --- a/capram_convert/mechanism.json +++ b/capram_convert/mechanism.json @@ -1936,6 +1936,19 @@ "NO" ] }, + { + "type": "AERO_REP_MODAL_BINNED_MASS", + "name": "my aero rep 2", + "modes/bins": { + "the mode": { + "type": "MODAL", + "phases": [ + "aqueous aerosol" + ], + "shape": "LOG_NORMAL" + } + } + }, { "name": "Henry's Law phase transfer", "type": "MECHANISM", From 923fbbabbeefe71cb6da033a256b56bc7261eb84 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 11:19:33 -0500 Subject: [PATCH 12/24] phase name, henrys law correction --- capram_convert/convert.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index 1e372583..4b0d0d1b 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -109,12 +109,13 @@ def combine_stoichiometric_coeffs(species): henrys_law_reactions = list() henrys_species = list() +aerosol_phase_name = "cloud aerosols" for item in henry: gas_phase = item['reactants'][0] aero_phase = item['products'][0] - henrys_species.append(gas_phase) + henrys_species.append(aero_phase) spec = dict(name=gas_phase, type="CHEM_SPEC") spec["HLC(298K) [M Pa-1]"] = item['A'] @@ -129,7 +130,7 @@ def combine_stoichiometric_coeffs(species): { "type" : "HL_PHASE_TRANSFER", "gas-phase species" : gas_phase, - "aerosol phase" : "aqueous aerosol", + "aerosol phase" : aerosol_phase_name, "aerosol-phase species" : aero_phase, "aerosol-phase water" : "aH2O" #TODO: verify this } @@ -137,7 +138,7 @@ def combine_stoichiometric_coeffs(species): henrys_law_aero_phase = [ { - "name" : "aqueous aerosol", + "name" : aerosol_phase_name, "type" : "AERO_PHASE", "species" : henrys_species } @@ -237,7 +238,8 @@ def combine_stoichiometric_coeffs(species): }, "A" : reaction['A'], "C" : 0, - "k_reverse" : reaction['B'] + "k_reverse" : reaction['B'], + "phase": aerosol_phase_name } for reaction in diss_without_c ] @@ -264,7 +266,7 @@ def combine_stoichiometric_coeffs(species): "the mode" : { "type" : "MODAL", - "phases" : ["aqueous aerosol"], + "phases" : [aerosol_phase_name], "shape" : "LOG_NORMAL" } } From 9d7b3e3177f74b4a751f54290f2f6b8abb502ee1 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 11:21:27 -0500 Subject: [PATCH 13/24] putting henry's law into overall mechanism --- capram_convert/convert.py | 6 +- capram_convert/mechanism.json | 241 ++++++++++++++++++---------------- 2 files changed, 129 insertions(+), 118 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index 4b0d0d1b..feff9520 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -255,6 +255,7 @@ def combine_stoichiometric_coeffs(species): *photolysis_reactions, *arrhenius_reactions, *aqueous_equilibrium, + *henrys_law_reactions ] }, *henrys_law_aero_phase, @@ -270,11 +271,6 @@ def combine_stoichiometric_coeffs(species): "shape" : "LOG_NORMAL" } } - }, - { - "name" : "Henry's Law phase transfer", - "type" : "MECHANISM", - "reactions" : henrys_law_reactions } ] } diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json index 9d041b19..8a8d3054 100644 --- a/capram_convert/mechanism.json +++ b/capram_convert/mechanism.json @@ -1629,7 +1629,8 @@ }, "A": 0.0002, "C": 0, - "k_reverse": 50000000000.0 + "k_reverse": 50000000000.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1642,7 +1643,8 @@ }, "A": 1.6e-05, "C": 0, - "k_reverse": 50000000000.0 + "k_reverse": 50000000000.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1655,7 +1657,8 @@ }, "A": 1e-05, "C": 0, - "k_reverse": 50000000000.0 + "k_reverse": 50000000000.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1668,7 +1671,8 @@ }, "A": 2200000000.0, "C": 0, - "k_reverse": 0.0046 + "k_reverse": 0.0046, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1681,7 +1685,8 @@ }, "A": 1000.0, "C": 0, - "k_reverse": 50000000000.0 + "k_reverse": 50000000000.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1695,7 +1700,8 @@ }, "A": 0.00011, "C": 0, - "k_reverse": 430000000.0 + "k_reverse": 430000000.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1708,7 +1714,8 @@ }, "A": 140000.0, "C": 0, - "k_reverse": 60000.0 + "k_reverse": 60000.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1721,7 +1728,8 @@ }, "A": 632000.0, "C": 0, - "k_reverse": 19000.0 + "k_reverse": 19000.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1734,7 +1742,8 @@ }, "A": 0.7, "C": 0, - "k_reverse": 6100000000.0 + "k_reverse": 6100000000.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1748,7 +1757,8 @@ }, "A": 5100000.0, "C": 0, - "k_reverse": 4100.0 + "k_reverse": 4100.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1761,7 +1771,8 @@ }, "A": 333.0, "C": 0, - "k_reverse": 33000000.0 + "k_reverse": 33000000.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1775,7 +1786,8 @@ }, "A": 1800000000000.0, "C": 0, - "k_reverse": 0.0245 + "k_reverse": 0.0245, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1788,7 +1800,8 @@ }, "A": 6.3e-09, "C": 0, - "k_reverse": 52000000000.0 + "k_reverse": 52000000000.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1801,7 +1814,8 @@ }, "A": 1.34e-06, "C": 0, - "k_reverse": 44000000000.0 + "k_reverse": 44000000000.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1814,7 +1828,8 @@ }, "A": 1.5e-05, "C": 0, - "k_reverse": 50000000000.0 + "k_reverse": 50000000000.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1827,7 +1842,8 @@ }, "A": 6.25e-05, "C": 0, - "k_reverse": 50000000000.0 + "k_reverse": 50000000000.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1840,7 +1856,8 @@ }, "A": 0.000316, "C": 0, - "k_reverse": 20000000000.0 + "k_reverse": 20000000000.0, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1853,7 +1870,8 @@ }, "A": 3900.0, "C": 0, - "k_reverse": 0.0055 + "k_reverse": 0.0055, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1866,7 +1884,8 @@ }, "A": 2900000000.0, "C": 0, - "k_reverse": 0.003 + "k_reverse": 0.003, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1879,7 +1898,8 @@ }, "A": 6300000.0, "C": 0, - "k_reverse": 0.003 + "k_reverse": 0.003, + "phase": "cloud aerosols" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1893,298 +1913,293 @@ }, "A": 1.2, "C": 0, - "k_reverse": 210000000.0 - } - ] - }, - { - "name": "aqueous aerosol", - "type": "AERO_PHASE", - "species": [ - "CO2", - "O3", - "HO2", - "HO", - "H2O2", - "NO2", - "HONO", - "HNO3", - "NO3", - "N2O5", - "NH3", - "HCL", - "HCHO", - "ORA1", - "SO2", - "OP1", - "ORA2", - "MO2", - "ETHPX", - "ETOH", - "CH3OH", - "ALD", - "BR2", - "CL2", - "SULF", - "HNO4", - "ACO3", - "GLY", - "[O2]", - "CLNO2", - "BRNO2", - "BRCL", - "NO" - ] - }, - { - "type": "AERO_REP_MODAL_BINNED_MASS", - "name": "my aero rep 2", - "modes/bins": { - "the mode": { - "type": "MODAL", - "phases": [ - "aqueous aerosol" - ], - "shape": "LOG_NORMAL" - } - } - }, - { - "name": "Henry's Law phase transfer", - "type": "MECHANISM", - "reactions": [ + "k_reverse": 210000000.0, + "phase": "cloud aerosols" + }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CO2", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aCO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "O3", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aO3", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HO2", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aHO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HO", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aHO", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "H2O2", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aH2O2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NO2", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aNO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HONO", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aHONO", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HNO3", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aHNO3", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NO3", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aNO3", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "N2O5", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aN2O5", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NH3", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aNH3", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HCL", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aHCL", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HCHO", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aHCHO", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ORA1", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aORA1", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "SO2", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aSO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "OP1", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aOP1", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ORA2", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aORA2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "MO2", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aMO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ETHPX", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aETHPX", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ETOH", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aETOH", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CH3OH", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aCH3OH", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ALD", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aALD", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "BR2", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aBR2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CL2", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aCL2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "SULF", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aSULF", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HNO4", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aHNO4", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ACO3", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aACO3", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "GLY", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aGLY", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "[O2]", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CLNO2", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aCLNO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "BRNO2", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aBRNO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "BRCL", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aBRCL", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NO", - "aerosol phase": "aqueous aerosol", + "aerosol phase": "cloud aerosols", "aerosol-phase species": "aNO", "aerosol-phase water": "aH2O" } ] + }, + { + "name": "cloud aerosols", + "type": "AERO_PHASE", + "species": [ + "aCO2", + "aO3", + "aHO2", + "aHO", + "aH2O2", + "aNO2", + "aHONO", + "aHNO3", + "aNO3", + "aN2O5", + "aNH3", + "aHCL", + "aHCHO", + "aORA1", + "aSO2", + "aOP1", + "aORA2", + "aMO2", + "aETHPX", + "aETOH", + "aCH3OH", + "aALD", + "aBR2", + "aCL2", + "aSULF", + "aHNO4", + "aACO3", + "aGLY", + "aO2", + "aCLNO2", + "aBRNO2", + "aBRCL", + "aNO" + ] + }, + { + "type": "AERO_REP_MODAL_BINNED_MASS", + "name": "my aero rep 2", + "modes/bins": { + "the mode": { + "type": "MODAL", + "phases": [ + "cloud aerosols" + ], + "shape": "LOG_NORMAL" + } + } } ] } \ No newline at end of file From 9f618993b22292bdcffc2141e3b63d224bf3466d Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 11:26:02 -0500 Subject: [PATCH 14/24] correcting arrhenius and aqueous equilibrium --- capram_convert/convert.py | 13 +- capram_convert/mechanism.json | 617 ++++++++++++++++++++++++---------- 2 files changed, 449 insertions(+), 181 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index feff9520..ec2c1ed2 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -109,7 +109,7 @@ def combine_stoichiometric_coeffs(species): henrys_law_reactions = list() henrys_species = list() -aerosol_phase_name = "cloud aerosols" +aerosol_phase_name = "cloud water" for item in henry: gas_phase = item['reactants'][0] @@ -205,7 +205,9 @@ def combine_stoichiometric_coeffs(species): product: {} for product in reaction["products"] }, "A" : reaction['A'] * np.exp(-1 * reaction['B'] / 298), - "C" : reaction['B'] + "C" : reaction['B'], + "aerosol phase" : aerosol_phase_name, + "aerosol-phase water" : "H2O_aq" } for reaction in aqua_temp ] @@ -221,7 +223,9 @@ def combine_stoichiometric_coeffs(species): }, "A" : reaction['A'], "C" : reaction['B'], - "k_reverse" : reaction['C'] + "k_reverse" : reaction['C'], + "phase": aerosol_phase_name, + "aerosol-phase water" : "H2O_aq" } for reaction in diss_with_c ] @@ -239,7 +243,8 @@ def combine_stoichiometric_coeffs(species): "A" : reaction['A'], "C" : 0, "k_reverse" : reaction['B'], - "phase": aerosol_phase_name + "phase": aerosol_phase_name, + "aerosol-phase water" : "H2O_aq" } for reaction in diss_without_c ] diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json index 8a8d3054..4381505d 100644 --- a/capram_convert/mechanism.json +++ b/capram_convert/mechanism.json @@ -59,7 +59,9 @@ "OHm": {} }, "A": 50.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -73,7 +75,9 @@ "OHm": {} }, "A": 7000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -86,7 +90,9 @@ "aO2": {} }, "A": 150000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -100,7 +106,9 @@ "[aH2O]": {} }, "A": 130000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -114,7 +122,9 @@ "OHm": {} }, "A": 150000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -128,7 +138,9 @@ "-2.0Hp": {} }, "A": 10000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -142,7 +154,9 @@ "-1.0Hp": {} }, "A": 27470692899786.598, - "C": -5050.0 + "C": -5050.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -154,7 +168,9 @@ "FEOHpp": {} }, "A": 17241255673.805157, - "C": -1100.0 + "C": -1100.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -168,7 +184,9 @@ "-2.0Hp": {} }, "A": 10000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -182,7 +200,9 @@ "-1.0Hp": {} }, "A": 2300000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -196,7 +216,9 @@ "Hp": {} }, "A": 100000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -209,7 +231,9 @@ "aO2": {} }, "A": 8000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -222,7 +246,9 @@ "CUpp": {} }, "A": 13000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -236,7 +262,9 @@ "OHm": {} }, "A": 13000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -249,7 +277,9 @@ "aO2": {} }, "A": 2411527019006.37, - "C": -2200.0 + "C": -2200.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -261,7 +291,9 @@ "aO2": {} }, "A": 1193031991.1270792, - "C": -4500.0 + "C": -4500.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -274,7 +306,9 @@ "[aH2O]": {} }, "A": 8423504855.756161, - "C": -1680.0 + "C": -1680.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -287,7 +321,9 @@ "[aH2O]": {} }, "A": 2700000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -300,7 +336,9 @@ "O2m": {} }, "A": 460000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -313,7 +351,9 @@ "aO2": {} }, "A": 5608557390760.588, - "C": -4690.0 + "C": -4690.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -327,7 +367,9 @@ "-1.0Hp": {} }, "A": 100.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -340,7 +382,9 @@ "2OHm": {} }, "A": 1214599.2606213153, - "C": -842.0 + "C": -842.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -352,7 +396,9 @@ "NO3m": {} }, "A": 1000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -365,7 +411,9 @@ "Hp": {} }, "A": 89000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -379,7 +427,9 @@ "SO3m": {} }, "A": 1068246352911.5388, - "C": -2000.0 + "C": -2000.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -392,7 +442,9 @@ "SO4m": {} }, "A": 100000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -404,7 +456,9 @@ "aO2": {} }, "A": 1.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -418,7 +472,9 @@ "NO3m": {} }, "A": 330000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -430,7 +486,9 @@ "aCLNO2": {} }, "A": 10000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -442,7 +500,9 @@ "aBRNO2": {} }, "A": 10000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -455,7 +515,9 @@ "aBRCL": {} }, "A": 5000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -468,7 +530,9 @@ "NO2m": {} }, "A": 25500.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -481,7 +545,9 @@ "aBRCL": {} }, "A": 10.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -494,7 +560,9 @@ "[aH2O]": {} }, "A": 300000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -506,7 +574,9 @@ "O2CHOHSO3m": {} }, "A": 2600000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -518,7 +588,9 @@ "CHOSO3m": {} }, "A": 17000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -530,7 +602,9 @@ "HSO3m": {} }, "A": 7000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -543,7 +617,9 @@ "aORA1": {} }, "A": 0.0126, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -556,7 +632,9 @@ "aHO2": {} }, "A": 44.32, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -571,7 +649,9 @@ "2Hp": {} }, "A": 48617052944753.77, - "C": -4000.0 + "C": -4000.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -585,7 +665,9 @@ "aO2": {} }, "A": 42405757730857.71, - "C": -5530.0 + "C": -5530.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -598,7 +680,9 @@ "aO2": {} }, "A": 7.429735524861723e+16, - "C": -5280.0 + "C": -5280.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -611,7 +695,9 @@ "FEOHpp": {} }, "A": 7745929554766653.0, - "C": -5809.0 + "C": -5809.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -624,7 +710,9 @@ "FEOHpp": {} }, "A": 30000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -638,7 +726,9 @@ "Hp": {} }, "A": 3217841.880265981, - "C": 2165.0 + "C": 2165.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -650,7 +740,9 @@ "aO2": {} }, "A": 1353845691603.3787, - "C": -2600.0 + "C": -2600.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -662,7 +754,9 @@ "SO5O2Hm": {} }, "A": 1700000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -675,7 +769,9 @@ "-1.0Hp": {} }, "A": 1200.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -687,7 +783,9 @@ "SO5m": {} }, "A": 2500000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -701,7 +799,9 @@ "Hp": {} }, "A": 456.10702574818845, - "C": -1110.0 + "C": -1110.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -715,7 +815,9 @@ "3Hp": {} }, "A": 7140000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -728,7 +830,9 @@ "aCH2OH": {} }, "A": 7002790586.531466, - "C": -580.0 + "C": -580.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -740,7 +844,9 @@ "aO2CH2OH": {} }, "A": 2000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -753,7 +859,9 @@ "aHCHO": {} }, "A": 1050000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -766,7 +874,9 @@ "aCH3CHOH": {} }, "A": 1900000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -778,7 +888,9 @@ "aO2CH3CHOH": {} }, "A": 2000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -790,7 +902,9 @@ "aHO2": {} }, "A": 1713166492299.335, - "C": -7217.0 + "C": -7217.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -803,7 +917,9 @@ "[aH2O]": {} }, "A": 30655705402.09484, - "C": -1020.0 + "C": -1020.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -816,7 +932,9 @@ "aORA1": {} }, "A": 2000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -829,7 +947,9 @@ "aCH3COH2": {} }, "A": 1200000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -842,7 +962,9 @@ "aCH3CO": {} }, "A": 3600000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -855,7 +977,9 @@ "[aH2O]": {} }, "A": 3726553714.606836, - "C": -1000.0 + "C": -1000.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -868,7 +992,9 @@ "OHm": {} }, "A": 91730552974.9375, - "C": -1000.0 + "C": -1000.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -881,7 +1007,9 @@ "aCH2COOH": {} }, "A": 1301323951.4818943, - "C": -1330.0 + "C": -1330.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -894,7 +1022,9 @@ "CH2COOm": {} }, "A": 42000577298.10133, - "C": -1800.0 + "C": -1800.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -906,7 +1036,9 @@ "aACO3": {} }, "A": 1700000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -919,7 +1051,9 @@ "aO2": {} }, "A": 118968666270.98093, - "C": -2200.0 + "C": -2200.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -931,7 +1065,9 @@ "aO2": {} }, "A": 57876648456.152885, - "C": -2200.0 + "C": -2200.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -944,7 +1080,9 @@ "aO2": {} }, "A": 150000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -957,7 +1095,9 @@ "SO3m": {} }, "A": 500000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -969,7 +1109,9 @@ "aO2": {} }, "A": 8071922.343268531, - "C": 750.0 + "C": 750.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -980,7 +1122,9 @@ "aCH3CHOH": {} }, "A": 1000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -993,7 +1137,9 @@ "C2O4m": {} }, "A": 32000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1006,7 +1152,9 @@ "C2O4m": {} }, "A": 5300000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1019,7 +1167,9 @@ "O2m": {} }, "A": 2000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1032,7 +1182,9 @@ "aCOH2CHOH2": {} }, "A": 178137994858.22678, - "C": -1516.0 + "C": -1516.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1044,7 +1196,9 @@ "aO2COH2CHOH2": {} }, "A": 1380000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1056,7 +1210,9 @@ "aCHOH2COOH": {} }, "A": 2000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1069,7 +1225,9 @@ "aCOH2COOH": {} }, "A": 178137994858.22678, - "C": -1516.0 + "C": -1516.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1081,7 +1239,9 @@ "aO2COH2COOH": {} }, "A": 2000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1093,7 +1253,9 @@ "aH2C2O4": {} }, "A": 2000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1105,7 +1267,9 @@ "aCH3COH2OO": {} }, "A": 2000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1118,7 +1282,9 @@ "O2m": {} }, "A": 100000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1129,7 +1295,9 @@ "aCH2OH": {} }, "A": 1000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1141,7 +1309,9 @@ "O2CH2COOm": {} }, "A": 2000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1153,7 +1323,9 @@ "aH2O2": {} }, "A": 20000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1166,7 +1338,9 @@ "O2m": {} }, "A": 4000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1179,7 +1353,9 @@ "FEppp": {} }, "A": 260503174919.8385, - "C": -3030.0 + "C": -3030.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1193,7 +1369,9 @@ "aO2": {} }, "A": 13000000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1207,7 +1385,9 @@ "SO3m": {} }, "A": 650720568.7854763, - "C": -400.0 + "C": -400.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1221,7 +1401,9 @@ "aHOCL": {} }, "A": 130387468611.99103, - "C": -7900.0 + "C": -7900.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1235,7 +1417,9 @@ "aHO": {} }, "A": 6.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1248,7 +1432,9 @@ "aBR": {} }, "A": 2100000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1261,7 +1447,9 @@ "aBR": {} }, "A": 3800000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1273,7 +1461,9 @@ "2BRm": {} }, "A": 1700000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1286,7 +1476,9 @@ "FEppp": {} }, "A": 256640227408.05545, - "C": -3330.0 + "C": -3330.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1300,7 +1492,9 @@ "aHO2": {} }, "A": 100000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1314,7 +1508,9 @@ "Hp": {} }, "A": 6500000000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1328,7 +1524,9 @@ "SO3m": {} }, "A": 685036875.6354121, - "C": -780.0 + "C": -780.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1342,7 +1540,9 @@ "aHOBR": {} }, "A": 2639927153.6309934, - "C": -7500.0 + "C": -7500.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1354,7 +1554,9 @@ "OHm": {} }, "A": 4200000.0, - "C": 0.0 + "C": 0.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1366,7 +1568,9 @@ "aH2CO3": {} }, "A": 1300426356398.6077, - "C": -9250.0 + "C": -9250.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1378,7 +1582,9 @@ "[aH2O]": {} }, "A": 1.3670434220265014e+17, - "C": -8500.0 + "C": -8500.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1391,7 +1597,9 @@ "OHm": {} }, "A": 505918766.97323936, - "C": -2450.0 + "C": -2450.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "ARRHENIUS", @@ -1404,7 +1612,9 @@ "aCH2OH2": {} }, "A": 475632147521.7825, - "C": -5530.0 + "C": -5530.0, + "aerosol phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1417,7 +1627,9 @@ }, "A": 1.8e-16, "C": -6800.0, - "k_reverse": 130000000000.0 + "k_reverse": 130000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1430,7 +1642,9 @@ }, "A": 1720000.0, "C": 6890.0, - "k_reverse": 290000.0 + "k_reverse": 290000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1444,7 +1658,9 @@ }, "A": 3.17e-07, "C": -560.0, - "k_reverse": 34000000000.0 + "k_reverse": 34000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1457,7 +1673,9 @@ }, "A": 22.0, "C": 1800.0, - "k_reverse": 50000000000.0 + "k_reverse": 50000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1470,7 +1688,9 @@ }, "A": 0.00053, "C": -1760.0, - "k_reverse": 50000000000.0 + "k_reverse": 50000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1484,7 +1704,9 @@ }, "A": 0.000313, "C": 1940.0, - "k_reverse": 200000000.0 + "k_reverse": 200000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1497,7 +1719,9 @@ }, "A": 6.22e-08, "C": 1960.0, - "k_reverse": 50000000000.0 + "k_reverse": 50000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1510,7 +1734,9 @@ }, "A": 0.0102, "C": 2700.0, - "k_reverse": 100000000000.0 + "k_reverse": 100000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1523,7 +1749,9 @@ }, "A": 0.000177, "C": 12.0, - "k_reverse": 50000000000.0 + "k_reverse": 50000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1536,7 +1764,9 @@ }, "A": 1.75e-05, "C": 46.0, - "k_reverse": 50000000000.0 + "k_reverse": 50000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1549,7 +1779,9 @@ }, "A": 36.0, "C": 4030.0, - "k_reverse": 0.0051 + "k_reverse": 0.0051, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1562,7 +1794,9 @@ }, "A": 0.0246, "C": 2500.0, - "k_reverse": 0.00569 + "k_reverse": 0.00569, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1576,7 +1810,9 @@ }, "A": 200000000.0, "C": -2500.0, - "k_reverse": 2.2e-09 + "k_reverse": 2.2e-09, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1590,7 +1826,9 @@ }, "A": 3.4, "C": -4300.0, - "k_reverse": 100000000.0 + "k_reverse": 100000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1603,7 +1841,9 @@ }, "A": 367.0, "C": 0.0, - "k_reverse": 30000.0 + "k_reverse": 30000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1616,7 +1856,9 @@ }, "A": 1.75e-05, "C": 46.0, - "k_reverse": 50000000000.0 + "k_reverse": 50000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1630,7 +1872,8 @@ "A": 0.0002, "C": 0, "k_reverse": 50000000000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1644,7 +1887,8 @@ "A": 1.6e-05, "C": 0, "k_reverse": 50000000000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1658,7 +1902,8 @@ "A": 1e-05, "C": 0, "k_reverse": 50000000000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1672,7 +1917,8 @@ "A": 2200000000.0, "C": 0, "k_reverse": 0.0046, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1686,7 +1932,8 @@ "A": 1000.0, "C": 0, "k_reverse": 50000000000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1701,7 +1948,8 @@ "A": 0.00011, "C": 0, "k_reverse": 430000000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1715,7 +1963,8 @@ "A": 140000.0, "C": 0, "k_reverse": 60000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1729,7 +1978,8 @@ "A": 632000.0, "C": 0, "k_reverse": 19000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1743,7 +1993,8 @@ "A": 0.7, "C": 0, "k_reverse": 6100000000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1758,7 +2009,8 @@ "A": 5100000.0, "C": 0, "k_reverse": 4100.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1772,7 +2024,8 @@ "A": 333.0, "C": 0, "k_reverse": 33000000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1787,7 +2040,8 @@ "A": 1800000000000.0, "C": 0, "k_reverse": 0.0245, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1801,7 +2055,8 @@ "A": 6.3e-09, "C": 0, "k_reverse": 52000000000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1815,7 +2070,8 @@ "A": 1.34e-06, "C": 0, "k_reverse": 44000000000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1829,7 +2085,8 @@ "A": 1.5e-05, "C": 0, "k_reverse": 50000000000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1843,7 +2100,8 @@ "A": 6.25e-05, "C": 0, "k_reverse": 50000000000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1857,7 +2115,8 @@ "A": 0.000316, "C": 0, "k_reverse": 20000000000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1871,7 +2130,8 @@ "A": 3900.0, "C": 0, "k_reverse": 0.0055, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1885,7 +2145,8 @@ "A": 2900000000.0, "C": 0, "k_reverse": 0.003, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1899,7 +2160,8 @@ "A": 6300000.0, "C": 0, "k_reverse": 0.003, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -1914,243 +2176,244 @@ "A": 1.2, "C": 0, "k_reverse": 210000000.0, - "phase": "cloud aerosols" + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CO2", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aCO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "O3", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aO3", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HO2", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aHO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HO", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aHO", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "H2O2", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aH2O2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NO2", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aNO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HONO", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aHONO", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HNO3", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aHNO3", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NO3", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aNO3", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "N2O5", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aN2O5", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NH3", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aNH3", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HCL", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aHCL", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HCHO", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aHCHO", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ORA1", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aORA1", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "SO2", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aSO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "OP1", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aOP1", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ORA2", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aORA2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "MO2", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aMO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ETHPX", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aETHPX", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ETOH", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aETOH", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CH3OH", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aCH3OH", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ALD", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aALD", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "BR2", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aBR2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CL2", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aCL2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "SULF", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aSULF", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HNO4", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aHNO4", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ACO3", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aACO3", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "GLY", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aGLY", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "[O2]", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CLNO2", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aCLNO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "BRNO2", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aBRNO2", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "BRCL", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aBRCL", "aerosol-phase water": "aH2O" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NO", - "aerosol phase": "cloud aerosols", + "aerosol phase": "cloud water", "aerosol-phase species": "aNO", "aerosol-phase water": "aH2O" } ] }, { - "name": "cloud aerosols", + "name": "cloud water", "type": "AERO_PHASE", "species": [ "aCO2", @@ -2195,7 +2458,7 @@ "the mode": { "type": "MODAL", "phases": [ - "cloud aerosols" + "cloud water" ], "shape": "LOG_NORMAL" } From bb819c7df0faee4f0c6eb97236011c8cec8ed395 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 12:00:34 -0500 Subject: [PATCH 15/24] adding all species to the aerosol phase that need to be there --- capram_convert/convert.py | 109 ++--- capram_convert/mechanism.json | 819 ++++++++++++++++++++-------------- 2 files changed, 533 insertions(+), 395 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index ec2c1ed2..f7c3a500 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -55,6 +55,7 @@ def parse_reactants_products(line): return reactants, products def combine_stoichiometric_coeffs(species): + #TODO: for the ceofficients, make sure they get put into the products with a yield # given this: O2m + FEpp = FEppp + aH2O2 -2.0 Hp # output this for the products: ['FEppp', 'aH2O2', '-2.0Hp'] groups = [i for i in re.split(r'([+-])', species) if i != '+'] @@ -107,7 +108,7 @@ def combine_stoichiometric_coeffs(species): species = dict() henrys_law_reactions = list() -henrys_species = list() +aerosol_phase_species = set() aerosol_phase_name = "cloud water" @@ -115,7 +116,7 @@ def combine_stoichiometric_coeffs(species): gas_phase = item['reactants'][0] aero_phase = item['products'][0] - henrys_species.append(aero_phase) + aerosol_phase_species.add(aero_phase) spec = dict(name=gas_phase, type="CHEM_SPEC") spec["HLC(298K) [M Pa-1]"] = item['A'] @@ -136,12 +137,7 @@ def combine_stoichiometric_coeffs(species): } ) -henrys_law_aero_phase = [ - { - "name" : aerosol_phase_name, - "type" : "AERO_PHASE", - "species" : henrys_species - } +aero_phase_species = [ ] for collection in [aqua_photo, aqua_temp, diss_with_c, diss_without_c]: @@ -195,43 +191,30 @@ def combine_stoichiometric_coeffs(species): # # -arrhenius_reactions = [ - { - "type": "ARRHENIUS", - "reactants": { - reactant: {} for reactant in reaction["reactants"] - }, - "products": { - product: {} for product in reaction["products"] - }, - "A" : reaction['A'] * np.exp(-1 * reaction['B'] / 298), - "C" : reaction['B'], - "aerosol phase" : aerosol_phase_name, - "aerosol-phase water" : "H2O_aq" - } - for reaction in aqua_temp -] - -aqueous_equilibrium = [ - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - reactant: {} for reactant in reaction["reactants"] - }, - "products": { - product: {} for product in reaction["products"] - }, - "A" : reaction['A'], - "C" : reaction['B'], - "k_reverse" : reaction['C'], - "phase": aerosol_phase_name, - "aerosol-phase water" : "H2O_aq" - } - for reaction in diss_with_c -] +arrhenius_reactions = list() +for reaction in aqua_temp: + arrhenius_reactions.append( + { + "type": "ARRHENIUS", + "reactants": { + reactant: {} for reactant in reaction["reactants"] + }, + "products": { + product: {} for product in reaction["products"] + }, + "A" : reaction['A'] * np.exp(-1 * reaction['B'] / 298), + "C" : reaction['B'], + "aerosol phase" : aerosol_phase_name, + "aerosol-phase water" : "H2O_aq" + } + ) + aerosol_phase_species.update(reaction["reactants"]) + aerosol_phase_species.update(reaction["products"]) + -aqueous_equilibrium.extend( - [ +aqueous_equilibrium = list() +for reaction in diss_with_c: + aqueous_equilibrium.append( { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { @@ -241,14 +224,36 @@ def combine_stoichiometric_coeffs(species): product: {} for product in reaction["products"] }, "A" : reaction['A'], - "C" : 0, - "k_reverse" : reaction['B'], + "C" : reaction['B'], + "k_reverse" : reaction['C'], "phase": aerosol_phase_name, "aerosol-phase water" : "H2O_aq" } - for reaction in diss_without_c - ] -) + ) + aerosol_phase_species.update(reaction["reactants"]) + aerosol_phase_species.update(reaction["products"]) + +for reaction in diss_without_c: + aqueous_equilibrium.append( + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + reactant: {} for reactant in reaction["reactants"] + }, + "products": { + product: {} for product in reaction["products"] + }, + "A" : reaction['A'], + "C" : 0, + "k_reverse" : reaction['B'], + "phase": aerosol_phase_name, + "aerosol-phase water" : "H2O_aq" + } + ] + ) + aerosol_phase_species.update(reaction["reactants"]) + aerosol_phase_species.update(reaction["products"]) mechanisms = { "camp-data" : [ @@ -263,7 +268,11 @@ def combine_stoichiometric_coeffs(species): *henrys_law_reactions ] }, - *henrys_law_aero_phase, + { + "name" : aerosol_phase_name, + "type" : "AERO_PHASE", + "species" : list(aerosol_phase_species) + }, { "type" : "AERO_REP_MODAL_BINNED_MASS", "name" : "my aero rep 2", diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json index 4381505d..46d76eab 100644 --- a/capram_convert/mechanism.json +++ b/capram_convert/mechanism.json @@ -1860,325 +1860,367 @@ "phase": "cloud water", "aerosol-phase water": "H2O_aq" }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "aH2CO3": {} - }, - "products": { - "HCO3m": {}, - "Hp": {} - }, - "A": 0.0002, - "C": 0, - "k_reverse": 50000000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "aHO2": {} - }, - "products": { - "O2m": {}, - "Hp": {} - }, - "A": 1.6e-05, - "C": 0, - "k_reverse": 50000000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "aHNO4": {} - }, - "products": { - "NO4m": {}, - "Hp": {} - }, - "A": 1e-05, - "C": 0, - "k_reverse": 50000000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "aNO2": {}, - "aHO2": {} - }, - "products": { - "aHNO4": {} - }, - "A": 2200000000.0, - "C": 0, - "k_reverse": 0.0046, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "aSULF": {} - }, - "products": { - "HSO4m": {}, - "Hp": {} - }, - "A": 1000.0, - "C": 0, - "k_reverse": 50000000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "FEppp": {}, - "[aH2O]": {} - }, - "products": { - "FEOHpp": {}, - "Hp": {} - }, - "A": 0.00011, - "C": 0, - "k_reverse": 430000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "aCL": {}, - "CLm": {} - }, - "products": { - "CL2m": {} - }, - "A": 140000.0, - "C": 0, - "k_reverse": 60000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "aBR": {}, - "BRm": {} - }, - "products": { - "BR2m": {} - }, - "A": 632000.0, - "C": 0, - "k_reverse": 19000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "CLm": {}, - "aHO": {} - }, - "products": { - "CLOHm": {} - }, - "A": 0.7, - "C": 0, - "k_reverse": 6100000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "CLOHm": {}, - "Hp": {} - }, - "products": { - "aCL": {}, - "[aH2O]": {} - }, - "A": 5100000.0, - "C": 0, - "k_reverse": 4100.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "BRm": {}, - "aHO": {} - }, - "products": { - "BROHm": {} - }, - "A": 333.0, - "C": 0, - "k_reverse": 33000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "BROHm": {}, - "Hp": {} - }, - "products": { - "aBR": {}, - "[aH2O]": {} - }, - "A": 1800000000000.0, - "C": 0, - "k_reverse": 0.0245, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "aHO3": {} - }, - "products": { - "Hp": {}, - "O3m": {} - }, - "A": 6.3e-09, - "C": 0, - "k_reverse": 52000000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "CHOHSO3m": {} - }, - "products": { - "CHOSO3mm": {}, - "Hp": {} - }, - "A": 1.34e-06, - "C": 0, - "k_reverse": 44000000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "SO5O2Hm": {} - }, - "products": { - "Hp": {}, - "SO5O2mm": {} - }, - "A": 1.5e-05, - "C": 0, - "k_reverse": 50000000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "HC2O4m": {} - }, - "products": { - "C2O4mm": {}, - "Hp": {} - }, - "A": 6.25e-05, - "C": 0, - "k_reverse": 50000000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "aCHOH2COOH": {} - }, - "products": { - "Hp": {}, - "CHOH2COOm": {} - }, - "A": 0.000316, - "C": 0, - "k_reverse": 20000000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "aGLY": {}, - "[aH2O]": {} - }, - "products": { - "aCHOH2CHOH2": {} - }, - "A": 3900.0, - "C": 0, - "k_reverse": 0.0055, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "FEppp": {}, - "C2O4mm": {} - }, - "products": { - "FEC2O4p": {} - }, - "A": 2900000000.0, - "C": 0, - "k_reverse": 0.003, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "FEC2O4p": {}, - "C2O4mm": {} - }, - "products": { - "FEC2O42m": {} - }, - "A": 6300000.0, - "C": 0, - "k_reverse": 0.003, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "SO4m": {}, - "CLm": {} - }, - "products": { - "SO4mm": {}, - "aCL": {} - }, - "A": 1.2, - "C": 0, - "k_reverse": 210000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aH2CO3": {} + }, + "products": { + "HCO3m": {}, + "Hp": {} + }, + "A": 0.0002, + "C": 0, + "k_reverse": 50000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aHO2": {} + }, + "products": { + "O2m": {}, + "Hp": {} + }, + "A": 1.6e-05, + "C": 0, + "k_reverse": 50000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aHNO4": {} + }, + "products": { + "NO4m": {}, + "Hp": {} + }, + "A": 1e-05, + "C": 0, + "k_reverse": 50000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aNO2": {}, + "aHO2": {} + }, + "products": { + "aHNO4": {} + }, + "A": 2200000000.0, + "C": 0, + "k_reverse": 0.0046, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aSULF": {} + }, + "products": { + "HSO4m": {}, + "Hp": {} + }, + "A": 1000.0, + "C": 0, + "k_reverse": 50000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "FEppp": {}, + "[aH2O]": {} + }, + "products": { + "FEOHpp": {}, + "Hp": {} + }, + "A": 0.00011, + "C": 0, + "k_reverse": 430000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aCL": {}, + "CLm": {} + }, + "products": { + "CL2m": {} + }, + "A": 140000.0, + "C": 0, + "k_reverse": 60000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aBR": {}, + "BRm": {} + }, + "products": { + "BR2m": {} + }, + "A": 632000.0, + "C": 0, + "k_reverse": 19000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "CLm": {}, + "aHO": {} + }, + "products": { + "CLOHm": {} + }, + "A": 0.7, + "C": 0, + "k_reverse": 6100000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "CLOHm": {}, + "Hp": {} + }, + "products": { + "aCL": {}, + "[aH2O]": {} + }, + "A": 5100000.0, + "C": 0, + "k_reverse": 4100.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "BRm": {}, + "aHO": {} + }, + "products": { + "BROHm": {} + }, + "A": 333.0, + "C": 0, + "k_reverse": 33000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "BROHm": {}, + "Hp": {} + }, + "products": { + "aBR": {}, + "[aH2O]": {} + }, + "A": 1800000000000.0, + "C": 0, + "k_reverse": 0.0245, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aHO3": {} + }, + "products": { + "Hp": {}, + "O3m": {} + }, + "A": 6.3e-09, + "C": 0, + "k_reverse": 52000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "CHOHSO3m": {} + }, + "products": { + "CHOSO3mm": {}, + "Hp": {} + }, + "A": 1.34e-06, + "C": 0, + "k_reverse": 44000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "SO5O2Hm": {} + }, + "products": { + "Hp": {}, + "SO5O2mm": {} + }, + "A": 1.5e-05, + "C": 0, + "k_reverse": 50000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "HC2O4m": {} + }, + "products": { + "C2O4mm": {}, + "Hp": {} + }, + "A": 6.25e-05, + "C": 0, + "k_reverse": 50000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aCHOH2COOH": {} + }, + "products": { + "Hp": {}, + "CHOH2COOm": {} + }, + "A": 0.000316, + "C": 0, + "k_reverse": 20000000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aGLY": {}, + "[aH2O]": {} + }, + "products": { + "aCHOH2CHOH2": {} + }, + "A": 3900.0, + "C": 0, + "k_reverse": 0.0055, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "FEppp": {}, + "C2O4mm": {} + }, + "products": { + "FEC2O4p": {} + }, + "A": 2900000000.0, + "C": 0, + "k_reverse": 0.003, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "FEC2O4p": {}, + "C2O4mm": {} + }, + "products": { + "FEC2O42m": {} + }, + "A": 6300000.0, + "C": 0, + "k_reverse": 0.003, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], + [ + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "SO4m": {}, + "CLm": {} + }, + "products": { + "SO4mm": {}, + "aCL": {} + }, + "A": 1.2, + "C": 0, + "k_reverse": 210000000.0, + "phase": "cloud water", + "aerosol-phase water": "H2O_aq" + } + ], { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CO2", @@ -2416,39 +2458,126 @@ "name": "cloud water", "type": "AERO_PHASE", "species": [ - "aCO2", - "aO3", - "aHO2", - "aHO", - "aH2O2", - "aNO2", - "aHONO", - "aHNO3", - "aNO3", - "aN2O5", + "CUpp", + "HMSm", + "aH2C2O4", "aNH3", - "aHCL", - "aHCHO", - "aORA1", - "aSO2", + "BROHm", + "-1.0Hp", + "HC2O4m", + "C2O4mm", + "2SO4mm", + "CHOH2COOm", + "aNO3", + "SO5m", + "CLm", + "aCH3OH", + "aMO2", + "CL2m", + "OHm", + "aBRNO2", + "aHNO4", + "aCH3O", + "CUp", + "aBRCL", + "aO2CH2OH", + "aH2O2", + "aCH3CH2O", + "aCOH2COOH", + "aCH3COH2OO", + "aHO2", "aOP1", + "FEpp", + "SO5O2mm", + "aO3", + "aO2CHO", + "CHOSO3m", + "HSO5m", + "FEppp", + "aACO3", + "aO2", + "2CLm", + "aH2CO3", + "aHOCL", + "aGLY", + "aCH3CHOH2", + "aBR", + "NH4p", "aORA2", - "aMO2", + "FEOpp", + "aNO", + "[aH2O]", + "aNO2", + "aCHOH2COOH", + "aCH2COOH", + "FEC2O4p", + "aCH2OH2", + "HSO4m", + "CO2m", "aETHPX", - "aETOH", - "aCH3OH", + "aCL2", + "aORA1", + "O2m", + "aHCL", + "aCLNO2", "aALD", + "SO4mm", "aBR2", - "aCL2", + "2OHm", + "O3m", + "aN2O5", + "Hp", + "aO2COH2COOH", + "aO2COH2CHOH2", + "SO3mm", + "HCO3m", + "SO3m", + "BRm", + "NO2m", + "CLOHm", + "aHONO", + "aCHOH2", + "HCOOm", + "aHCHO", + "FEOHpp", + "3Hp", + "aSO2", + "2FEppp", + "CHOHSO3m", + "aHNO3", + "aCH2OH", + "aCOH2CHOH2", + "MCOOm", + "O2CH2COOm", + "-2.0Hp", + "2BRm", + "aCH3CHOH", + "SO4m", + "CH2COOm", + "aO2CH3CHOH", + "NO4m", + "aCO2H", + "BR2m", + "aHOBR", + "NO3m", + "FEC2O42m", + "aCH3CO", + "aHO", + "aETOH", + "HSO3m", "aSULF", - "aHNO4", - "aACO3", - "aGLY", - "aO2", - "aCLNO2", - "aBRNO2", - "aBRCL", - "aNO" + "NO2p", + "aCL", + "2Hp", + "aCHOH2CHOH2", + "aCO2", + "2CHOH2COOm", + "aCH3COH2", + "SO5O2Hm", + "O2CHOHSO3m", + "aHO3", + "C2O4m", + "CHOSO3mm" ] }, { From d6e8816376a4c39f4f6dd5acf4ce0f68494921d5 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 12:13:43 -0500 Subject: [PATCH 16/24] stubbing out thing to produce yields, fixing water aerosol water name --- capram_convert/convert.py | 11 +- capram_convert/mechanism.json | 274 +++++++++++++++++----------------- 2 files changed, 145 insertions(+), 140 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index f7c3a500..ab77d915 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -52,10 +52,12 @@ def parse_reactants_products(line): if match: reactants = combine_stoichiometric_coeffs(match.group(1).strip()) products = combine_stoichiometric_coeffs(match.group(2).strip()) - return reactants, products + #TODO: now, convert the products into a species with a yield + # also, sometimes the list of producdts is like CL2m + [aH2O] = Hp + CLm + CLm + aHO + # this should end up being represented as if it were written like CL2m + [aH2O] = Hp + 2CLm + aHO + return reactants, convert_products_to_yield(products) def combine_stoichiometric_coeffs(species): - #TODO: for the ceofficients, make sure they get put into the products with a yield # given this: O2m + FEpp = FEppp + aH2O2 -2.0 Hp # output this for the products: ['FEppp', 'aH2O2', '-2.0Hp'] groups = [i for i in re.split(r'([+-])', species) if i != '+'] @@ -68,6 +70,9 @@ def combine_stoichiometric_coeffs(species): return result +def convert_products_to_yield(products): + return products + line_index = 0 # there are a few AQUA type reactions in the dissociation reactions, # when those exist, add them to the appropriate array @@ -133,7 +138,7 @@ def combine_stoichiometric_coeffs(species): "gas-phase species" : gas_phase, "aerosol phase" : aerosol_phase_name, "aerosol-phase species" : aero_phase, - "aerosol-phase water" : "aH2O" #TODO: verify this + "aerosol-phase water" : "[aH2O]" } ) diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json index 46d76eab..95b26d70 100644 --- a/capram_convert/mechanism.json +++ b/capram_convert/mechanism.json @@ -2226,231 +2226,231 @@ "gas-phase species": "CO2", "aerosol phase": "cloud water", "aerosol-phase species": "aCO2", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "O3", "aerosol phase": "cloud water", "aerosol-phase species": "aO3", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HO2", "aerosol phase": "cloud water", "aerosol-phase species": "aHO2", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HO", "aerosol phase": "cloud water", "aerosol-phase species": "aHO", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "H2O2", "aerosol phase": "cloud water", "aerosol-phase species": "aH2O2", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NO2", "aerosol phase": "cloud water", "aerosol-phase species": "aNO2", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HONO", "aerosol phase": "cloud water", "aerosol-phase species": "aHONO", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HNO3", "aerosol phase": "cloud water", "aerosol-phase species": "aHNO3", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NO3", "aerosol phase": "cloud water", "aerosol-phase species": "aNO3", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "N2O5", "aerosol phase": "cloud water", "aerosol-phase species": "aN2O5", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NH3", "aerosol phase": "cloud water", "aerosol-phase species": "aNH3", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HCL", "aerosol phase": "cloud water", "aerosol-phase species": "aHCL", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HCHO", "aerosol phase": "cloud water", "aerosol-phase species": "aHCHO", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ORA1", "aerosol phase": "cloud water", "aerosol-phase species": "aORA1", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "SO2", "aerosol phase": "cloud water", "aerosol-phase species": "aSO2", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "OP1", "aerosol phase": "cloud water", "aerosol-phase species": "aOP1", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ORA2", "aerosol phase": "cloud water", "aerosol-phase species": "aORA2", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "MO2", "aerosol phase": "cloud water", "aerosol-phase species": "aMO2", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ETHPX", "aerosol phase": "cloud water", "aerosol-phase species": "aETHPX", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ETOH", "aerosol phase": "cloud water", "aerosol-phase species": "aETOH", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CH3OH", "aerosol phase": "cloud water", "aerosol-phase species": "aCH3OH", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ALD", "aerosol phase": "cloud water", "aerosol-phase species": "aALD", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "BR2", "aerosol phase": "cloud water", "aerosol-phase species": "aBR2", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CL2", "aerosol phase": "cloud water", "aerosol-phase species": "aCL2", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "SULF", "aerosol phase": "cloud water", "aerosol-phase species": "aSULF", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HNO4", "aerosol phase": "cloud water", "aerosol-phase species": "aHNO4", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ACO3", "aerosol phase": "cloud water", "aerosol-phase species": "aACO3", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "GLY", "aerosol phase": "cloud water", "aerosol-phase species": "aGLY", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "[O2]", "aerosol phase": "cloud water", "aerosol-phase species": "aO2", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CLNO2", "aerosol phase": "cloud water", "aerosol-phase species": "aCLNO2", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "BRNO2", "aerosol phase": "cloud water", "aerosol-phase species": "aBRNO2", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "BRCL", "aerosol phase": "cloud water", "aerosol-phase species": "aBRCL", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NO", "aerosol phase": "cloud water", "aerosol-phase species": "aNO", - "aerosol-phase water": "aH2O" + "aerosol-phase water": "[aH2O]" } ] }, @@ -2458,126 +2458,126 @@ "name": "cloud water", "type": "AERO_PHASE", "species": [ - "CUpp", - "HMSm", - "aH2C2O4", + "HCOOm", + "aCH3CO", + "aALD", + "CUp", + "aACO3", + "HSO4m", + "aHO", + "HCO3m", + "aCHOH2COOH", + "HSO5m", + "2FEppp", + "aCOH2COOH", + "O2CHOHSO3m", + "aCH3CH2O", + "HSO3m", + "aCL2", + "BRm", "aNH3", - "BROHm", - "-1.0Hp", - "HC2O4m", - "C2O4mm", - "2SO4mm", + "aO2COH2COOH", "CHOH2COOm", - "aNO3", - "SO5m", - "CLm", - "aCH3OH", - "aMO2", - "CL2m", - "OHm", - "aBRNO2", - "aHNO4", - "aCH3O", - "CUp", + "aGLY", + "Hp", + "C2O4m", + "aCO2", + "aETHPX", + "NO3m", + "aO2", "aBRCL", - "aO2CH2OH", - "aH2O2", - "aCH3CH2O", - "aCOH2COOH", - "aCH3COH2OO", - "aHO2", - "aOP1", - "FEpp", - "SO5O2mm", - "aO3", - "aO2CHO", - "CHOSO3m", - "HSO5m", + "CHOSO3mm", + "aCO2H", + "aN2O5", + "aCH3OH", + "NO4m", + "CHOHSO3m", + "aSO2", "FEppp", - "aACO3", - "aO2", - "2CLm", - "aH2CO3", + "CO2m", + "HC2O4m", + "aHO3", + "SO3m", + "O2CH2COOm", + "aHOBR", "aHOCL", - "aGLY", - "aCH3CHOH2", - "aBR", - "NH4p", + "aCL", + "SO5m", + "aO3", + "CL2m", + "CLOHm", + "SO5O2Hm", + "C2O4mm", + "NO2p", + "BROHm", + "3Hp", + "aCH3O", "aORA2", - "FEOpp", - "aNO", - "[aH2O]", - "aNO2", - "aCHOH2COOH", - "aCH2COOH", - "FEC2O4p", - "aCH2OH2", - "HSO4m", - "CO2m", - "aETHPX", - "aCL2", - "aORA1", - "O2m", - "aHCL", "aCLNO2", - "aALD", - "SO4mm", + "CLm", + "aCH2COOH", + "aO2CH3CHOH", "aBR2", - "2OHm", - "O3m", - "aN2O5", - "Hp", - "aO2COH2COOH", "aO2COH2CHOH2", - "SO3mm", - "HCO3m", - "SO3m", - "BRm", + "FEC2O4p", + "aHO2", + "2BRm", + "O3m", + "aNO2", "NO2m", - "CLOHm", "aHONO", - "aCHOH2", - "HCOOm", - "aHCHO", - "FEOHpp", - "3Hp", - "aSO2", - "2FEppp", - "CHOHSO3m", - "aHNO3", "aCH2OH", - "aCOH2CHOH2", - "MCOOm", - "O2CH2COOm", - "-2.0Hp", - "2BRm", - "aCH3CHOH", - "SO4m", - "CH2COOm", - "aO2CH3CHOH", - "NO4m", - "aCO2H", - "BR2m", - "aHOBR", - "NO3m", - "FEC2O42m", - "aCH3CO", - "aHO", + "FEOHpp", + "aH2CO3", + "-1.0Hp", "aETOH", - "HSO3m", + "aO2CHO", + "[aH2O]", + "aCH3COH2OO", + "aCH3CHOH2", + "aHCL", + "HMSm", + "NH4p", + "O2m", + "aORA1", "aSULF", - "NO2p", - "aCL", - "2Hp", + "SO5O2mm", + "2CLm", + "SO3mm", + "aH2O2", + "aBRNO2", "aCHOH2CHOH2", - "aCO2", - "2CHOH2COOm", + "2SO4mm", "aCH3COH2", - "SO5O2Hm", - "O2CHOHSO3m", - "aHO3", - "C2O4m", - "CHOSO3mm" + "aMO2", + "CHOSO3m", + "-2.0Hp", + "MCOOm", + "aNO", + "aBR", + "CUpp", + "BR2m", + "SO4m", + "aHNO3", + "FEC2O42m", + "aCOH2CHOH2", + "aHNO4", + "aHCHO", + "aNO3", + "SO4mm", + "CH2COOm", + "2OHm", + "2CHOH2COOm", + "aCHOH2", + "aH2C2O4", + "aOP1", + "aCH2OH2", + "FEOpp", + "aCH3CHOH", + "2Hp", + "OHm", + "aO2CH2OH", + "FEpp" ] }, { From ea419e0f85a984917a01ad5722739c4633246995 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 12:30:27 -0500 Subject: [PATCH 17/24] combining some yields --- capram_convert/convert.py | 45 +- capram_convert/mechanism.json | 1392 +++++++++++++++++++++++---------- 2 files changed, 1023 insertions(+), 414 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index ab77d915..01bc5715 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -52,7 +52,7 @@ def parse_reactants_products(line): if match: reactants = combine_stoichiometric_coeffs(match.group(1).strip()) products = combine_stoichiometric_coeffs(match.group(2).strip()) - #TODO: now, convert the products into a species with a yield + #TODO: now, go through the lists of products and reactants and combine like species # also, sometimes the list of producdts is like CL2m + [aH2O] = Hp + CLm + CLm + aHO # this should end up being represented as if it were written like CL2m + [aH2O] = Hp + 2CLm + aHO return reactants, convert_products_to_yield(products) @@ -71,6 +71,21 @@ def combine_stoichiometric_coeffs(species): return result def convert_products_to_yield(products): + # first, combine duplicated products + prods = {} + for product in products: + existing = prods.get(product, 0.0) + prods[product] = existing + 1.0 + + products = [] + for name, _yield in prods.items(): + spec = dict(name=name, type="CHEM_SPEC", ) + spec["yield"] = _yield + products.append(spec) + + # now, go through each product and, when there's a + print(products) + print() return products line_index = 0 @@ -121,7 +136,7 @@ def convert_products_to_yield(products): gas_phase = item['reactants'][0] aero_phase = item['products'][0] - aerosol_phase_species.add(aero_phase) + aerosol_phase_species.add(aero_phase['name']) spec = dict(name=gas_phase, type="CHEM_SPEC") spec["HLC(298K) [M Pa-1]"] = item['A'] @@ -130,14 +145,14 @@ def convert_products_to_yield(products): spec["N star"] = 1.00 # TODO: replace species[gas_phase] = spec - species[aero_phase] = dict(name=aero_phase, type="CHEM_SPEC") + species[aero_phase['name']] = dict(name=aero_phase['name'], type="CHEM_SPEC") henrys_law_reactions.append( { "type" : "HL_PHASE_TRANSFER", "gas-phase species" : gas_phase, "aerosol phase" : aerosol_phase_name, - "aerosol-phase species" : aero_phase, + "aerosol-phase species" : aero_phase['name'], "aerosol-phase water" : "[aH2O]" } ) @@ -151,10 +166,10 @@ def convert_products_to_yield(products): if name not in species: spec = dict(name=name, type="CHEM_SPEC") species[name] = spec - for name in item['products']: - if name not in species: - spec = dict(name=name, type="CHEM_SPEC") - species[name] = spec + for product in item['products']: + if product['name'] not in species: + spec = dict(name=product['name'], type="CHEM_SPEC") + species[product['name']] = spec with open('species.json', 'w') as f: json.dump( @@ -170,7 +185,7 @@ def convert_products_to_yield(products): reactant: {} for reactant in reaction["reactants"] }, "products": { - product: {} for product in reaction["products"] + product['name']: { 'yield': product['yield'] } for product in reaction["products"] } } for reaction in aqua_photo @@ -205,7 +220,7 @@ def convert_products_to_yield(products): reactant: {} for reactant in reaction["reactants"] }, "products": { - product: {} for product in reaction["products"] + product['name']: { 'yield': product['yield'] } for product in reaction["products"] }, "A" : reaction['A'] * np.exp(-1 * reaction['B'] / 298), "C" : reaction['B'], @@ -214,7 +229,7 @@ def convert_products_to_yield(products): } ) aerosol_phase_species.update(reaction["reactants"]) - aerosol_phase_species.update(reaction["products"]) + aerosol_phase_species.update([ product['name'] for product in reaction['products']]) aqueous_equilibrium = list() @@ -226,7 +241,7 @@ def convert_products_to_yield(products): reactant: {} for reactant in reaction["reactants"] }, "products": { - product: {} for product in reaction["products"] + product['name']: { 'yield': product['yield'] } for product in reaction["products"] }, "A" : reaction['A'], "C" : reaction['B'], @@ -236,7 +251,7 @@ def convert_products_to_yield(products): } ) aerosol_phase_species.update(reaction["reactants"]) - aerosol_phase_species.update(reaction["products"]) + aerosol_phase_species.update([ product['name'] for product in reaction['products']]) for reaction in diss_without_c: aqueous_equilibrium.append( @@ -247,7 +262,7 @@ def convert_products_to_yield(products): reactant: {} for reactant in reaction["reactants"] }, "products": { - product: {} for product in reaction["products"] + product['name']: { 'yield': product['yield'] } for product in reaction["products"] }, "A" : reaction['A'], "C" : 0, @@ -258,7 +273,7 @@ def convert_products_to_yield(products): ] ) aerosol_phase_species.update(reaction["reactants"]) - aerosol_phase_species.update(reaction["products"]) + aerosol_phase_species.update([ product['name'] for product in reaction['products']]) mechanisms = { "camp-data" : [ diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json index 95b26d70..f482e54f 100644 --- a/capram_convert/mechanism.json +++ b/capram_convert/mechanism.json @@ -11,8 +11,12 @@ "FEOHpp": {} }, "products": { - "FEpp": {}, - "aHO": {} + "FEpp": { + "yield": 1.0 + }, + "aHO": { + "yield": 1.0 + } } }, { @@ -21,9 +25,15 @@ "NO3m": {} }, "products": { - "aNO2": {}, - "aHO": {}, - "OHm": {} + "aNO2": { + "yield": 1.0 + }, + "aHO": { + "yield": 1.0 + }, + "OHm": { + "yield": 1.0 + } } }, { @@ -32,7 +42,9 @@ "aH2O2": {} }, "products": { - "aHO": {} + "aHO": { + "yield": 2.0 + } } }, { @@ -41,10 +53,18 @@ "FEC2O42m": {} }, "products": { - "FEpp": {}, - "C2O4mm": {}, - "aCO2": {}, - "CO2m": {} + "FEpp": { + "yield": 1.0 + }, + "C2O4mm": { + "yield": 1.0 + }, + "aCO2": { + "yield": 1.0 + }, + "CO2m": { + "yield": 1.0 + } } }, { @@ -54,9 +74,15 @@ "FEpp": {} }, "products": { - "FEppp": {}, - "aHO": {}, - "OHm": {} + "FEppp": { + "yield": 1.0 + }, + "aHO": { + "yield": 1.0 + }, + "OHm": { + "yield": 1.0 + } }, "A": 50.0, "C": 0.0, @@ -70,9 +96,15 @@ "CUp": {} }, "products": { - "CUpp": {}, - "aHO": {}, - "OHm": {} + "CUpp": { + "yield": 1.0 + }, + "aHO": { + "yield": 1.0 + }, + "OHm": { + "yield": 1.0 + } }, "A": 7000.0, "C": 0.0, @@ -86,8 +118,12 @@ "FEppp": {} }, "products": { - "FEpp": {}, - "aO2": {} + "FEpp": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + } }, "A": 150000000.0, "C": 0.0, @@ -101,9 +137,15 @@ "FEOHpp": {} }, "products": { - "FEpp": {}, - "aO2": {}, - "[aH2O]": {} + "FEpp": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + }, + "[aH2O]": { + "yield": 1.0 + } }, "A": 130000.0, "C": 0.0, @@ -117,9 +159,15 @@ "FEOHpp": {} }, "products": { - "FEpp": {}, - "aO2": {}, - "OHm": {} + "FEpp": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + }, + "OHm": { + "yield": 1.0 + } }, "A": 150000000.0, "C": 0.0, @@ -133,9 +181,15 @@ "FEpp": {} }, "products": { - "FEppp": {}, - "aH2O2": {}, - "-2.0Hp": {} + "FEppp": { + "yield": 1.0 + }, + "aH2O2": { + "yield": 1.0 + }, + "-2.0Hp": { + "yield": 1.0 + } }, "A": 10000000.0, "C": 0.0, @@ -149,9 +203,15 @@ "FEpp": {} }, "products": { - "FEppp": {}, - "aH2O2": {}, - "-1.0Hp": {} + "FEppp": { + "yield": 1.0 + }, + "aH2O2": { + "yield": 1.0 + }, + "-1.0Hp": { + "yield": 1.0 + } }, "A": 27470692899786.598, "C": -5050.0, @@ -165,7 +225,9 @@ "FEpp": {} }, "products": { - "FEOHpp": {} + "FEOHpp": { + "yield": 1.0 + } }, "A": 17241255673.805157, "C": -1100.0, @@ -179,9 +241,15 @@ "CUp": {} }, "products": { - "CUpp": {}, - "aH2O2": {}, - "-2.0Hp": {} + "CUpp": { + "yield": 1.0 + }, + "aH2O2": { + "yield": 1.0 + }, + "-2.0Hp": { + "yield": 1.0 + } }, "A": 10000000000.0, "C": 0.0, @@ -195,9 +263,15 @@ "CUp": {} }, "products": { - "CUpp": {}, - "aH2O2": {}, - "-1.0Hp": {} + "CUpp": { + "yield": 1.0 + }, + "aH2O2": { + "yield": 1.0 + }, + "-1.0Hp": { + "yield": 1.0 + } }, "A": 2300000000.0, "C": 0.0, @@ -211,9 +285,15 @@ "CUpp": {} }, "products": { - "CUp": {}, - "aO2": {}, - "Hp": {} + "CUp": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 100000000.0, "C": 0.0, @@ -227,8 +307,12 @@ "CUpp": {} }, "products": { - "CUp": {}, - "aO2": {} + "CUp": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + } }, "A": 8000000000.0, "C": 0.0, @@ -242,8 +326,12 @@ "CUp": {} }, "products": { - "FEpp": {}, - "CUpp": {} + "FEpp": { + "yield": 1.0 + }, + "CUpp": { + "yield": 1.0 + } }, "A": 13000000.0, "C": 0.0, @@ -257,9 +345,15 @@ "CUp": {} }, "products": { - "FEpp": {}, - "CUpp": {}, - "OHm": {} + "FEpp": { + "yield": 1.0 + }, + "CUpp": { + "yield": 1.0 + }, + "OHm": { + "yield": 1.0 + } }, "A": 13000000.0, "C": 0.0, @@ -273,8 +367,12 @@ "O2m": {} }, "products": { - "O3m": {}, - "aO2": {} + "O3m": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + } }, "A": 2411527019006.37, "C": -2200.0, @@ -287,8 +385,12 @@ "aHO3": {} }, "products": { - "aHO": {}, - "aO2": {} + "aHO": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + } }, "A": 1193031991.1270792, "C": -4500.0, @@ -302,8 +404,12 @@ "aHO": {} }, "products": { - "aHO2": {}, - "[aH2O]": {} + "aHO2": { + "yield": 1.0 + }, + "[aH2O]": { + "yield": 1.0 + } }, "A": 8423504855.756161, "C": -1680.0, @@ -317,8 +423,12 @@ "aHO": {} }, "products": { - "SO3m": {}, - "[aH2O]": {} + "SO3m": { + "yield": 1.0 + }, + "[aH2O]": { + "yield": 1.0 + } }, "A": 2700000000.0, "C": 0.0, @@ -332,8 +442,12 @@ "aO2": {} }, "products": { - "CUpp": {}, - "O2m": {} + "CUpp": { + "yield": 1.0 + }, + "O2m": { + "yield": 1.0 + } }, "A": 460000.0, "C": 0.0, @@ -347,8 +461,12 @@ "aO3": {} }, "products": { - "FEOpp": {}, - "aO2": {} + "FEOpp": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + } }, "A": 5608557390760.588, "C": -4690.0, @@ -362,9 +480,15 @@ "CLm": {} }, "products": { - "FEppp": {}, - "CLOHm": {}, - "-1.0Hp": {} + "FEppp": { + "yield": 1.0 + }, + "CLOHm": { + "yield": 1.0 + }, + "-1.0Hp": { + "yield": 1.0 + } }, "A": 100.0, "C": 0.0, @@ -378,8 +502,12 @@ "FEpp": {} }, "products": { - "2FEppp": {}, - "2OHm": {} + "2FEppp": { + "yield": 1.0 + }, + "2OHm": { + "yield": 1.0 + } }, "A": 1214599.2606213153, "C": -842.0, @@ -392,8 +520,12 @@ "aN2O5": {} }, "products": { - "NO2p": {}, - "NO3m": {} + "NO2p": { + "yield": 1.0 + }, + "NO3m": { + "yield": 1.0 + } }, "A": 1000000000.0, "C": 0.0, @@ -407,8 +539,12 @@ "[aH2O]": {} }, "products": { - "NO3m": {}, - "Hp": {} + "NO3m": { + "yield": 1.0 + }, + "Hp": { + "yield": 2.0 + } }, "A": 89000000.0, "C": 0.0, @@ -422,9 +558,15 @@ "HSO3m": {} }, "products": { - "NO3m": {}, - "Hp": {}, - "SO3m": {} + "NO3m": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + }, + "SO3m": { + "yield": 1.0 + } }, "A": 1068246352911.5388, "C": -2000.0, @@ -438,8 +580,12 @@ "SO4mm": {} }, "products": { - "NO3m": {}, - "SO4m": {} + "NO3m": { + "yield": 1.0 + }, + "SO4m": { + "yield": 1.0 + } }, "A": 100000.0, "C": 0.0, @@ -452,8 +598,12 @@ "NO4m": {} }, "products": { - "NO2m": {}, - "aO2": {} + "NO2m": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + } }, "A": 1.0, "C": 0.0, @@ -467,9 +617,15 @@ "HSO3m": {} }, "products": { - "HSO4m": {}, - "Hp": {}, - "NO3m": {} + "HSO4m": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + }, + "NO3m": { + "yield": 1.0 + } }, "A": 330000.0, "C": 0.0, @@ -483,7 +639,9 @@ "CLm": {} }, "products": { - "aCLNO2": {} + "aCLNO2": { + "yield": 1.0 + } }, "A": 10000000000.0, "C": 0.0, @@ -497,7 +655,9 @@ "BRm": {} }, "products": { - "aBRNO2": {} + "aBRNO2": { + "yield": 1.0 + } }, "A": 10000000000.0, "C": 0.0, @@ -511,8 +671,12 @@ "BRm": {} }, "products": { - "NO2m": {}, - "aBRCL": {} + "NO2m": { + "yield": 1.0 + }, + "aBRCL": { + "yield": 1.0 + } }, "A": 5000000.0, "C": 0.0, @@ -526,8 +690,12 @@ "BRm": {} }, "products": { - "aBR2": {}, - "NO2m": {} + "aBR2": { + "yield": 1.0 + }, + "NO2m": { + "yield": 1.0 + } }, "A": 25500.0, "C": 0.0, @@ -541,8 +709,12 @@ "CLm": {} }, "products": { - "NO2m": {}, - "aBRCL": {} + "NO2m": { + "yield": 1.0 + }, + "aBRCL": { + "yield": 1.0 + } }, "A": 10.0, "C": 0.0, @@ -556,8 +728,12 @@ "aHO": {} }, "products": { - "CHOHSO3m": {}, - "[aH2O]": {} + "CHOHSO3m": { + "yield": 1.0 + }, + "[aH2O]": { + "yield": 1.0 + } }, "A": 300000000.0, "C": 0.0, @@ -571,7 +747,9 @@ "aO2": {} }, "products": { - "O2CHOHSO3m": {} + "O2CHOHSO3m": { + "yield": 1.0 + } }, "A": 2600000000.0, "C": 0.0, @@ -584,8 +762,12 @@ "O2CHOHSO3m": {} }, "products": { - "aHO2": {}, - "CHOSO3m": {} + "aHO2": { + "yield": 1.0 + }, + "CHOSO3m": { + "yield": 1.0 + } }, "A": 17000.0, "C": 0.0, @@ -598,8 +780,12 @@ "O2CHOHSO3m": {} }, "products": { - "aO2CHO": {}, - "HSO3m": {} + "aO2CHO": { + "yield": 1.0 + }, + "HSO3m": { + "yield": 1.0 + } }, "A": 7000.0, "C": 0.0, @@ -613,8 +799,12 @@ "[aH2O]": {} }, "products": { - "HSO3m": {}, - "aORA1": {} + "HSO3m": { + "yield": 1.0 + }, + "aORA1": { + "yield": 1.0 + } }, "A": 0.0126, "C": 0.0, @@ -628,8 +818,12 @@ "[aH2O]": {} }, "products": { - "aORA1": {}, - "aHO2": {} + "aORA1": { + "yield": 1.0 + }, + "aHO2": { + "yield": 1.0 + } }, "A": 44.32, "C": 0.0, @@ -644,9 +838,15 @@ "Hp": {} }, "products": { - "SO4mm": {}, - "[aH2O]": {}, - "2Hp": {} + "SO4mm": { + "yield": 1.0 + }, + "[aH2O]": { + "yield": 1.0 + }, + "2Hp": { + "yield": 1.0 + } }, "A": 48617052944753.77, "C": -4000.0, @@ -660,9 +860,15 @@ "aO3": {} }, "products": { - "SO4mm": {}, - "Hp": {}, - "aO2": {} + "SO4mm": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + } }, "A": 42405757730857.71, "C": -5530.0, @@ -676,8 +882,12 @@ "aO3": {} }, "products": { - "SO4mm": {}, - "aO2": {} + "SO4mm": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + } }, "A": 7.429735524861723e+16, "C": -5280.0, @@ -691,8 +901,12 @@ "FEpp": {} }, "products": { - "HSO5m": {}, - "FEOHpp": {} + "HSO5m": { + "yield": 1.0 + }, + "FEOHpp": { + "yield": 1.0 + } }, "A": 7745929554766653.0, "C": -5809.0, @@ -706,8 +920,12 @@ "FEpp": {} }, "products": { - "SO4m": {}, - "FEOHpp": {} + "SO4m": { + "yield": 1.0 + }, + "FEOHpp": { + "yield": 1.0 + } }, "A": 30000.0, "C": 0.0, @@ -721,9 +939,15 @@ "SO4m": {} }, "products": { - "FEOHpp": {}, - "SO4mm": {}, - "Hp": {} + "FEOHpp": { + "yield": 1.0 + }, + "SO4mm": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 3217841.880265981, "C": 2165.0, @@ -736,8 +960,12 @@ "SO5m": {} }, "products": { - "SO4m": {}, - "aO2": {} + "SO4m": { + "yield": 2.0 + }, + "aO2": { + "yield": 1.0 + } }, "A": 1353845691603.3787, "C": -2600.0, @@ -751,7 +979,9 @@ "aHO2": {} }, "products": { - "SO5O2Hm": {} + "SO5O2Hm": { + "yield": 1.0 + } }, "A": 1700000000.0, "C": 0.0, @@ -764,9 +994,15 @@ "SO5O2mm": {} }, "products": { - "HSO5m": {}, - "aO2": {}, - "-1.0Hp": {} + "HSO5m": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + }, + "-1.0Hp": { + "yield": 1.0 + } }, "A": 1200.0, "C": 0.0, @@ -780,7 +1016,9 @@ "aO2": {} }, "products": { - "SO5m": {} + "SO5m": { + "yield": 1.0 + } }, "A": 2500000000.0, "C": 0.0, @@ -794,9 +1032,15 @@ "[aH2O]": {} }, "products": { - "SO4mm": {}, - "aHO": {}, - "Hp": {} + "SO4mm": { + "yield": 1.0 + }, + "aHO": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 456.10702574818845, "C": -1110.0, @@ -811,8 +1055,12 @@ "Hp": {} }, "products": { - "2SO4mm": {}, - "3Hp": {} + "2SO4mm": { + "yield": 1.0 + }, + "3Hp": { + "yield": 1.0 + } }, "A": 7140000.0, "C": 0.0, @@ -826,8 +1074,12 @@ "aHO": {} }, "products": { - "[aH2O]": {}, - "aCH2OH": {} + "[aH2O]": { + "yield": 1.0 + }, + "aCH2OH": { + "yield": 1.0 + } }, "A": 7002790586.531466, "C": -580.0, @@ -841,7 +1093,9 @@ "aO2": {} }, "products": { - "aO2CH2OH": {} + "aO2CH2OH": { + "yield": 1.0 + } }, "A": 2000000000.0, "C": 0.0, @@ -854,9 +1108,15 @@ "aO2CH2OH": {} }, "products": { - "aCH3OH": {}, - "aO2": {}, - "aHCHO": {} + "aCH3OH": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + }, + "aHCHO": { + "yield": 1.0 + } }, "A": 1050000000.0, "C": 0.0, @@ -870,8 +1130,12 @@ "aHO": {} }, "products": { - "[aH2O]": {}, - "aCH3CHOH": {} + "[aH2O]": { + "yield": 1.0 + }, + "aCH3CHOH": { + "yield": 1.0 + } }, "A": 1900000000.0, "C": 0.0, @@ -885,7 +1149,9 @@ "aO2": {} }, "products": { - "aO2CH3CHOH": {} + "aO2CH3CHOH": { + "yield": 1.0 + } }, "A": 2000000000.0, "C": 0.0, @@ -898,8 +1164,12 @@ "aO2CH3CHOH": {} }, "products": { - "aALD": {}, - "aHO2": {} + "aALD": { + "yield": 1.0 + }, + "aHO2": { + "yield": 1.0 + } }, "A": 1713166492299.335, "C": -7217.0, @@ -913,8 +1183,12 @@ "aHO": {} }, "products": { - "aCHOH2": {}, - "[aH2O]": {} + "aCHOH2": { + "yield": 1.0 + }, + "[aH2O]": { + "yield": 1.0 + } }, "A": 30655705402.09484, "C": -1020.0, @@ -928,8 +1202,12 @@ "aO2": {} }, "products": { - "aHO2": {}, - "aORA1": {} + "aHO2": { + "yield": 1.0 + }, + "aORA1": { + "yield": 1.0 + } }, "A": 2000000000.0, "C": 0.0, @@ -943,8 +1221,12 @@ "aHO": {} }, "products": { - "[aH2O]": {}, - "aCH3COH2": {} + "[aH2O]": { + "yield": 1.0 + }, + "aCH3COH2": { + "yield": 1.0 + } }, "A": 1200000000.0, "C": 0.0, @@ -958,8 +1240,12 @@ "aHO": {} }, "products": { - "[aH2O]": {}, - "aCH3CO": {} + "[aH2O]": { + "yield": 1.0 + }, + "aCH3CO": { + "yield": 1.0 + } }, "A": 3600000000.0, "C": 0.0, @@ -973,8 +1259,12 @@ "aHO": {} }, "products": { - "aCO2H": {}, - "[aH2O]": {} + "aCO2H": { + "yield": 1.0 + }, + "[aH2O]": { + "yield": 1.0 + } }, "A": 3726553714.606836, "C": -1000.0, @@ -988,8 +1278,12 @@ "aHO": {} }, "products": { - "aCO2H": {}, - "OHm": {} + "aCO2H": { + "yield": 1.0 + }, + "OHm": { + "yield": 1.0 + } }, "A": 91730552974.9375, "C": -1000.0, @@ -1003,8 +1297,12 @@ "aHO": {} }, "products": { - "[aH2O]": {}, - "aCH2COOH": {} + "[aH2O]": { + "yield": 1.0 + }, + "aCH2COOH": { + "yield": 1.0 + } }, "A": 1301323951.4818943, "C": -1330.0, @@ -1018,8 +1316,12 @@ "aHO": {} }, "products": { - "[aH2O]": {}, - "CH2COOm": {} + "[aH2O]": { + "yield": 1.0 + }, + "CH2COOm": { + "yield": 1.0 + } }, "A": 42000577298.10133, "C": -1800.0, @@ -1033,7 +1335,9 @@ "aO2": {} }, "products": { - "aACO3": {} + "aACO3": { + "yield": 1.0 + } }, "A": 1700000000.0, "C": 0.0, @@ -1046,9 +1350,15 @@ "aMO2": {} }, "products": { - "aCH3OH": {}, - "aHCHO": {}, - "aO2": {} + "aCH3OH": { + "yield": 1.0 + }, + "aHCHO": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + } }, "A": 118968666270.98093, "C": -2200.0, @@ -1061,8 +1371,12 @@ "aMO2": {} }, "products": { - "aCH3O": {}, - "aO2": {} + "aCH3O": { + "yield": 2.0 + }, + "aO2": { + "yield": 1.0 + } }, "A": 57876648456.152885, "C": -2200.0, @@ -1075,9 +1389,15 @@ "aACO3": {} }, "products": { - "aMO2": {}, - "aCO2": {}, - "aO2": {} + "aMO2": { + "yield": 2.0 + }, + "aCO2": { + "yield": 2.0 + }, + "aO2": { + "yield": 1.0 + } }, "A": 150000000.0, "C": 0.0, @@ -1091,8 +1411,12 @@ "HSO3m": {} }, "products": { - "aOP1": {}, - "SO3m": {} + "aOP1": { + "yield": 1.0 + }, + "SO3m": { + "yield": 1.0 + } }, "A": 500000.0, "C": 0.0, @@ -1105,8 +1429,12 @@ "aETHPX": {} }, "products": { - "aCH3CH2O": {}, - "aO2": {} + "aCH3CH2O": { + "yield": 2.0 + }, + "aO2": { + "yield": 1.0 + } }, "A": 8071922.343268531, "C": 750.0, @@ -1119,7 +1447,9 @@ "aCH3CH2O": {} }, "products": { - "aCH3CHOH": {} + "aCH3CHOH": { + "yield": 1.0 + } }, "A": 1000000.0, "C": 0.0, @@ -1133,8 +1463,12 @@ "HC2O4m": {} }, "products": { - "[aH2O]": {}, - "C2O4m": {} + "[aH2O]": { + "yield": 1.0 + }, + "C2O4m": { + "yield": 1.0 + } }, "A": 32000000.0, "C": 0.0, @@ -1148,8 +1482,12 @@ "C2O4mm": {} }, "products": { - "OHm": {}, - "C2O4m": {} + "OHm": { + "yield": 1.0 + }, + "C2O4m": { + "yield": 1.0 + } }, "A": 5300000.0, "C": 0.0, @@ -1163,8 +1501,12 @@ "aO2": {} }, "products": { - "aCO2": {}, - "O2m": {} + "aCO2": { + "yield": 2.0 + }, + "O2m": { + "yield": 1.0 + } }, "A": 2000000000.0, "C": 0.0, @@ -1178,8 +1520,12 @@ "aCHOH2CHOH2": {} }, "products": { - "[aH2O]": {}, - "aCOH2CHOH2": {} + "[aH2O]": { + "yield": 1.0 + }, + "aCOH2CHOH2": { + "yield": 1.0 + } }, "A": 178137994858.22678, "C": -1516.0, @@ -1193,7 +1539,9 @@ "aO2": {} }, "products": { - "aO2COH2CHOH2": {} + "aO2COH2CHOH2": { + "yield": 1.0 + } }, "A": 1380000000.0, "C": 0.0, @@ -1206,8 +1554,12 @@ "aO2COH2CHOH2": {} }, "products": { - "aHO2": {}, - "aCHOH2COOH": {} + "aHO2": { + "yield": 1.0 + }, + "aCHOH2COOH": { + "yield": 1.0 + } }, "A": 2000000000.0, "C": 0.0, @@ -1221,8 +1573,12 @@ "aCHOH2COOH": {} }, "products": { - "[aH2O]": {}, - "aCOH2COOH": {} + "[aH2O]": { + "yield": 1.0 + }, + "aCOH2COOH": { + "yield": 1.0 + } }, "A": 178137994858.22678, "C": -1516.0, @@ -1236,7 +1592,9 @@ "aO2": {} }, "products": { - "aO2COH2COOH": {} + "aO2COH2COOH": { + "yield": 1.0 + } }, "A": 2000000000.0, "C": 0.0, @@ -1249,8 +1607,12 @@ "aO2COH2COOH": {} }, "products": { - "aHO2": {}, - "aH2C2O4": {} + "aHO2": { + "yield": 1.0 + }, + "aH2C2O4": { + "yield": 1.0 + } }, "A": 2000000000.0, "C": 0.0, @@ -1264,7 +1626,9 @@ "aO2": {} }, "products": { - "aCH3COH2OO": {} + "aCH3COH2OO": { + "yield": 1.0 + } }, "A": 2000000000.0, "C": 0.0, @@ -1277,9 +1641,15 @@ "aCH3COH2OO": {} }, "products": { - "Hp": {}, - "MCOOm": {}, - "O2m": {} + "Hp": { + "yield": 2.0 + }, + "MCOOm": { + "yield": 1.0 + }, + "O2m": { + "yield": 1.0 + } }, "A": 100000.0, "C": 0.0, @@ -1292,7 +1662,9 @@ "aCH3O": {} }, "products": { - "aCH2OH": {} + "aCH2OH": { + "yield": 1.0 + } }, "A": 1000000.0, "C": 0.0, @@ -1306,7 +1678,9 @@ "aO2": {} }, "products": { - "O2CH2COOm": {} + "O2CH2COOm": { + "yield": 1.0 + } }, "A": 2000000000.0, "C": 0.0, @@ -1319,8 +1693,12 @@ "O2CH2COOm": {} }, "products": { - "2CHOH2COOm": {}, - "aH2O2": {} + "2CHOH2COOm": { + "yield": 1.0 + }, + "aH2O2": { + "yield": 1.0 + } }, "A": 20000000.0, "C": 0.0, @@ -1334,8 +1712,12 @@ "aO2": {} }, "products": { - "aCO2": {}, - "O2m": {} + "aCO2": { + "yield": 1.0 + }, + "O2m": { + "yield": 1.0 + } }, "A": 4000000000.0, "C": 0.0, @@ -1349,8 +1731,12 @@ "FEpp": {} }, "products": { - "2CLm": {}, - "FEppp": {} + "2CLm": { + "yield": 1.0 + }, + "FEppp": { + "yield": 1.0 + } }, "A": 260503174919.8385, "C": -3030.0, @@ -1364,9 +1750,15 @@ "aHO2": {} }, "products": { - "2CLm": {}, - "Hp": {}, - "aO2": {} + "2CLm": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + } }, "A": 13000000000.0, "C": 0.0, @@ -1380,9 +1772,15 @@ "HSO3m": {} }, "products": { - "2CLm": {}, - "Hp": {}, - "SO3m": {} + "2CLm": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + }, + "SO3m": { + "yield": 1.0 + } }, "A": 650720568.7854763, "C": -400.0, @@ -1396,9 +1794,15 @@ "[aH2O]": {} }, "products": { - "Hp": {}, - "CLm": {}, - "aHOCL": {} + "Hp": { + "yield": 1.0 + }, + "CLm": { + "yield": 1.0 + }, + "aHOCL": { + "yield": 1.0 + } }, "A": 130387468611.99103, "C": -7900.0, @@ -1412,9 +1816,15 @@ "[aH2O]": {} }, "products": { - "Hp": {}, - "CLm": {}, - "aHO": {} + "Hp": { + "yield": 1.0 + }, + "CLm": { + "yield": 2.0 + }, + "aHO": { + "yield": 1.0 + } }, "A": 6.0, "C": 0.0, @@ -1428,8 +1838,12 @@ "SO4m": {} }, "products": { - "SO4mm": {}, - "aBR": {} + "SO4mm": { + "yield": 1.0 + }, + "aBR": { + "yield": 1.0 + } }, "A": 2100000000.0, "C": 0.0, @@ -1443,8 +1857,12 @@ "aNO3": {} }, "products": { - "NO3m": {}, - "aBR": {} + "NO3m": { + "yield": 1.0 + }, + "aBR": { + "yield": 1.0 + } }, "A": 3800000000.0, "C": 0.0, @@ -1457,8 +1875,12 @@ "BR2m": {} }, "products": { - "aBR2": {}, - "2BRm": {} + "aBR2": { + "yield": 1.0 + }, + "2BRm": { + "yield": 1.0 + } }, "A": 1700000000.0, "C": 0.0, @@ -1472,8 +1894,12 @@ "FEpp": {} }, "products": { - "2BRm": {}, - "FEppp": {} + "2BRm": { + "yield": 1.0 + }, + "FEppp": { + "yield": 1.0 + } }, "A": 256640227408.05545, "C": -3330.0, @@ -1487,9 +1913,15 @@ "aH2O2": {} }, "products": { - "2BRm": {}, - "Hp": {}, - "aHO2": {} + "2BRm": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + }, + "aHO2": { + "yield": 1.0 + } }, "A": 100000.0, "C": 0.0, @@ -1503,9 +1935,15 @@ "aHO2": {} }, "products": { - "2BRm": {}, - "aO2": {}, - "Hp": {} + "2BRm": { + "yield": 1.0 + }, + "aO2": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 6500000000.0, "C": 0.0, @@ -1519,9 +1957,15 @@ "HSO3m": {} }, "products": { - "2BRm": {}, - "Hp": {}, - "SO3m": {} + "2BRm": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + }, + "SO3m": { + "yield": 1.0 + } }, "A": 685036875.6354121, "C": -780.0, @@ -1535,9 +1979,15 @@ "[aH2O]": {} }, "products": { - "Hp": {}, - "BRm": {}, - "aHOBR": {} + "Hp": { + "yield": 1.0 + }, + "BRm": { + "yield": 1.0 + }, + "aHOBR": { + "yield": 1.0 + } }, "A": 2639927153.6309934, "C": -7500.0, @@ -1550,8 +2000,12 @@ "BROHm": {} }, "products": { - "aBR": {}, - "OHm": {} + "aBR": { + "yield": 1.0 + }, + "OHm": { + "yield": 1.0 + } }, "A": 4200000.0, "C": 0.0, @@ -1565,7 +2019,9 @@ "[aH2O]": {} }, "products": { - "aH2CO3": {} + "aH2CO3": { + "yield": 1.0 + } }, "A": 1300426356398.6077, "C": -9250.0, @@ -1578,8 +2034,12 @@ "aH2CO3": {} }, "products": { - "aCO2": {}, - "[aH2O]": {} + "aCO2": { + "yield": 1.0 + }, + "[aH2O]": { + "yield": 1.0 + } }, "A": 1.3670434220265014e+17, "C": -8500.0, @@ -1593,8 +2053,12 @@ "aCH2OH2": {} }, "products": { - "HMSm": {}, - "OHm": {} + "HMSm": { + "yield": 1.0 + }, + "OHm": { + "yield": 1.0 + } }, "A": 505918766.97323936, "C": -2450.0, @@ -1608,8 +2072,12 @@ "OHm": {} }, "products": { - "SO3mm": {}, - "aCH2OH2": {} + "SO3mm": { + "yield": 1.0 + }, + "aCH2OH2": { + "yield": 1.0 + } }, "A": 475632147521.7825, "C": -5530.0, @@ -1622,8 +2090,12 @@ "[aH2O]": {} }, "products": { - "OHm": {}, - "Hp": {} + "OHm": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 1.8e-16, "C": -6800.0, @@ -1637,8 +2109,12 @@ "aHCL": {} }, "products": { - "CLm": {}, - "Hp": {} + "CLm": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 1720000.0, "C": 6890.0, @@ -1653,8 +2129,12 @@ "[aH2O]": {} }, "products": { - "NH4p": {}, - "OHm": {} + "NH4p": { + "yield": 1.0 + }, + "OHm": { + "yield": 1.0 + } }, "A": 3.17e-07, "C": -560.0, @@ -1668,8 +2148,12 @@ "aHNO3": {} }, "products": { - "NO3m": {}, - "Hp": {} + "NO3m": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 22.0, "C": 1800.0, @@ -1683,8 +2167,12 @@ "aHONO": {} }, "products": { - "NO2m": {}, - "Hp": {} + "NO2m": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 0.00053, "C": -1760.0, @@ -1699,8 +2187,12 @@ "[aH2O]": {} }, "products": { - "HSO3m": {}, - "Hp": {} + "HSO3m": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 0.000313, "C": 1940.0, @@ -1714,8 +2206,12 @@ "HSO3m": {} }, "products": { - "SO3mm": {}, - "Hp": {} + "SO3mm": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 6.22e-08, "C": 1960.0, @@ -1729,8 +2225,12 @@ "HSO4m": {} }, "products": { - "Hp": {}, - "SO4mm": {} + "Hp": { + "yield": 1.0 + }, + "SO4mm": { + "yield": 1.0 + } }, "A": 0.0102, "C": 2700.0, @@ -1744,8 +2244,12 @@ "aORA1": {} }, "products": { - "Hp": {}, - "HCOOm": {} + "Hp": { + "yield": 1.0 + }, + "HCOOm": { + "yield": 1.0 + } }, "A": 0.000177, "C": 12.0, @@ -1759,8 +2263,12 @@ "aORA2": {} }, "products": { - "Hp": {}, - "MCOOm": {} + "Hp": { + "yield": 1.0 + }, + "MCOOm": { + "yield": 1.0 + } }, "A": 1.75e-05, "C": 46.0, @@ -1775,7 +2283,9 @@ "[aH2O]": {} }, "products": { - "aCH2OH2": {} + "aCH2OH2": { + "yield": 1.0 + } }, "A": 36.0, "C": 4030.0, @@ -1790,7 +2300,9 @@ "[aH2O]": {} }, "products": { - "aCH3CHOH2": {} + "aCH3CHOH2": { + "yield": 1.0 + } }, "A": 0.0246, "C": 2500.0, @@ -1805,8 +2317,12 @@ "aCH2OH2": {} }, "products": { - "HMSm": {}, - "[aH2O]": {} + "HMSm": { + "yield": 1.0 + }, + "[aH2O]": { + "yield": 1.0 + } }, "A": 200000000.0, "C": -2500.0, @@ -1821,8 +2337,12 @@ "CLm": {} }, "products": { - "NO3m": {}, - "aCL": {} + "NO3m": { + "yield": 1.0 + }, + "aCL": { + "yield": 1.0 + } }, "A": 3.4, "C": -4300.0, @@ -1837,7 +2357,9 @@ "[aH2O]": {} }, "products": { - "aCH3COH2": {} + "aCH3COH2": { + "yield": 1.0 + } }, "A": 367.0, "C": 0.0, @@ -1851,8 +2373,12 @@ "aACO3": {} }, "products": { - "Hp": {}, - "O2CH2COOm": {} + "Hp": { + "yield": 1.0 + }, + "O2CH2COOm": { + "yield": 1.0 + } }, "A": 1.75e-05, "C": 46.0, @@ -1867,8 +2393,12 @@ "aH2CO3": {} }, "products": { - "HCO3m": {}, - "Hp": {} + "HCO3m": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 0.0002, "C": 0, @@ -1884,8 +2414,12 @@ "aHO2": {} }, "products": { - "O2m": {}, - "Hp": {} + "O2m": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 1.6e-05, "C": 0, @@ -1901,8 +2435,12 @@ "aHNO4": {} }, "products": { - "NO4m": {}, - "Hp": {} + "NO4m": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 1e-05, "C": 0, @@ -1919,7 +2457,9 @@ "aHO2": {} }, "products": { - "aHNO4": {} + "aHNO4": { + "yield": 1.0 + } }, "A": 2200000000.0, "C": 0, @@ -1935,8 +2475,12 @@ "aSULF": {} }, "products": { - "HSO4m": {}, - "Hp": {} + "HSO4m": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 1000.0, "C": 0, @@ -1953,8 +2497,12 @@ "[aH2O]": {} }, "products": { - "FEOHpp": {}, - "Hp": {} + "FEOHpp": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 0.00011, "C": 0, @@ -1971,7 +2519,9 @@ "CLm": {} }, "products": { - "CL2m": {} + "CL2m": { + "yield": 1.0 + } }, "A": 140000.0, "C": 0, @@ -1988,7 +2538,9 @@ "BRm": {} }, "products": { - "BR2m": {} + "BR2m": { + "yield": 1.0 + } }, "A": 632000.0, "C": 0, @@ -2005,7 +2557,9 @@ "aHO": {} }, "products": { - "CLOHm": {} + "CLOHm": { + "yield": 1.0 + } }, "A": 0.7, "C": 0, @@ -2022,8 +2576,12 @@ "Hp": {} }, "products": { - "aCL": {}, - "[aH2O]": {} + "aCL": { + "yield": 1.0 + }, + "[aH2O]": { + "yield": 1.0 + } }, "A": 5100000.0, "C": 0, @@ -2040,7 +2598,9 @@ "aHO": {} }, "products": { - "BROHm": {} + "BROHm": { + "yield": 1.0 + } }, "A": 333.0, "C": 0, @@ -2057,8 +2617,12 @@ "Hp": {} }, "products": { - "aBR": {}, - "[aH2O]": {} + "aBR": { + "yield": 1.0 + }, + "[aH2O]": { + "yield": 1.0 + } }, "A": 1800000000000.0, "C": 0, @@ -2074,8 +2638,12 @@ "aHO3": {} }, "products": { - "Hp": {}, - "O3m": {} + "Hp": { + "yield": 1.0 + }, + "O3m": { + "yield": 1.0 + } }, "A": 6.3e-09, "C": 0, @@ -2091,8 +2659,12 @@ "CHOHSO3m": {} }, "products": { - "CHOSO3mm": {}, - "Hp": {} + "CHOSO3mm": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 1.34e-06, "C": 0, @@ -2108,8 +2680,12 @@ "SO5O2Hm": {} }, "products": { - "Hp": {}, - "SO5O2mm": {} + "Hp": { + "yield": 1.0 + }, + "SO5O2mm": { + "yield": 1.0 + } }, "A": 1.5e-05, "C": 0, @@ -2125,8 +2701,12 @@ "HC2O4m": {} }, "products": { - "C2O4mm": {}, - "Hp": {} + "C2O4mm": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } }, "A": 6.25e-05, "C": 0, @@ -2142,8 +2722,12 @@ "aCHOH2COOH": {} }, "products": { - "Hp": {}, - "CHOH2COOm": {} + "Hp": { + "yield": 1.0 + }, + "CHOH2COOm": { + "yield": 1.0 + } }, "A": 0.000316, "C": 0, @@ -2160,7 +2744,9 @@ "[aH2O]": {} }, "products": { - "aCHOH2CHOH2": {} + "aCHOH2CHOH2": { + "yield": 1.0 + } }, "A": 3900.0, "C": 0, @@ -2177,7 +2763,9 @@ "C2O4mm": {} }, "products": { - "FEC2O4p": {} + "FEC2O4p": { + "yield": 1.0 + } }, "A": 2900000000.0, "C": 0, @@ -2194,7 +2782,9 @@ "C2O4mm": {} }, "products": { - "FEC2O42m": {} + "FEC2O42m": { + "yield": 1.0 + } }, "A": 6300000.0, "C": 0, @@ -2211,8 +2801,12 @@ "CLm": {} }, "products": { - "SO4mm": {}, - "aCL": {} + "SO4mm": { + "yield": 1.0 + }, + "aCL": { + "yield": 1.0 + } }, "A": 1.2, "C": 0, @@ -2458,126 +3052,126 @@ "name": "cloud water", "type": "AERO_PHASE", "species": [ - "HCOOm", - "aCH3CO", - "aALD", - "CUp", - "aACO3", - "HSO4m", + "aO3", + "CL2m", + "aHOCL", + "O2m", + "aCOH2CHOH2", + "aNO", + "aCH3CH2O", "aHO", - "HCO3m", - "aCHOH2COOH", - "HSO5m", + "aO2", + "aHNO4", "2FEppp", + "aCH3CHOH", + "BR2m", + "aCL", "aCOH2COOH", - "O2CHOHSO3m", - "aCH3CH2O", - "HSO3m", - "aCL2", + "HC2O4m", + "CLOHm", + "aORA1", + "aH2C2O4", + "aSULF", + "aCH3COH2", + "aCH3O", "BRm", - "aNH3", - "aO2COH2COOH", - "CHOH2COOm", - "aGLY", + "aCH3OH", + "aO2CH3CHOH", + "CUp", + "-1.0Hp", + "NO2m", + "3Hp", + "CO2m", + "aMO2", + "aHCL", "Hp", - "C2O4m", - "aCO2", - "aETHPX", - "NO3m", - "aO2", + "O2CH2COOm", + "MCOOm", + "aCH2OH", "aBRCL", - "CHOSO3mm", - "aCO2H", - "aN2O5", - "aCH3OH", - "NO4m", - "CHOHSO3m", - "aSO2", + "2Hp", + "aH2CO3", + "2SO4mm", + "SO3mm", + "aCL2", "FEppp", - "CO2m", - "HC2O4m", - "aHO3", "SO3m", - "O2CH2COOm", - "aHOBR", - "aHOCL", - "aCL", "SO5m", - "aO3", - "CL2m", - "CLOHm", - "SO5O2Hm", - "C2O4mm", - "NO2p", - "BROHm", - "3Hp", - "aCH3O", - "aORA2", - "aCLNO2", - "CLm", - "aCH2COOH", - "aO2CH3CHOH", - "aBR2", - "aO2COH2CHOH2", - "FEC2O4p", - "aHO2", "2BRm", - "O3m", - "aNO2", - "NO2m", - "aHONO", - "aCH2OH", + "aALD", + "HMSm", + "aHNO3", + "aCO2H", + "2CHOH2COOm", "FEOHpp", - "aH2CO3", - "-1.0Hp", - "aETOH", - "aO2CHO", + "aCHOH2", + "O2CHOHSO3m", + "FEC2O42m", + "FEOpp", + "CH2COOm", + "FEC2O4p", + "O3m", + "NO2p", + "SO4mm", + "aNO3", + "aSO2", + "-2.0Hp", + "C2O4mm", + "aCHOH2COOH", + "aBR", "[aH2O]", - "aCH3COH2OO", + "aCH2COOH", + "CHOSO3mm", + "aHONO", + "HCO3m", + "aCLNO2", + "HSO3m", + "NO3m", + "CHOH2COOm", + "SO4m", + "aCHOH2CHOH2", + "CUpp", + "aO2COH2COOH", + "OHm", + "aCH2OH2", "aCH3CHOH2", - "aHCL", - "HMSm", + "aACO3", "NH4p", - "O2m", - "aORA1", - "aSULF", - "SO5O2mm", - "2CLm", - "SO3mm", + "aHOBR", + "HCOOm", + "aNH3", + "aETHPX", + "aHO3", + "2OHm", + "aN2O5", + "aHCHO", + "aO2COH2CHOH2", + "CHOHSO3m", + "aHO2", + "aCH3CO", + "aORA2", "aH2O2", - "aBRNO2", - "aCHOH2CHOH2", - "2SO4mm", - "aCH3COH2", - "aMO2", + "FEpp", + "aCH3COH2OO", "CHOSO3m", - "-2.0Hp", - "MCOOm", - "aNO", - "aBR", - "CUpp", - "BR2m", - "SO4m", - "aHNO3", - "FEC2O42m", - "aCOH2CHOH2", - "aHNO4", - "aHCHO", - "aNO3", - "SO4mm", - "CH2COOm", - "2OHm", - "2CHOH2COOm", - "aCHOH2", - "aH2C2O4", "aOP1", - "aCH2OH2", - "FEOpp", - "aCH3CHOH", - "2Hp", - "OHm", + "SO5O2mm", + "aNO2", + "HSO5m", + "aGLY", + "aBR2", + "C2O4m", + "CLm", + "aETOH", + "aBRNO2", + "SO5O2Hm", + "2CLm", "aO2CH2OH", - "FEpp" + "HSO4m", + "aCO2", + "aO2CHO", + "BROHm", + "NO4m" ] }, { From a5f7c6273d5d35f03543fd0cf0baadd4db43d943 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 12:42:41 -0500 Subject: [PATCH 18/24] combining products and writing out yields --- capram_convert/convert.py | 17 +- capram_convert/mechanism.json | 982 +++++++++++++++++----------------- capram_convert/species.json | 228 ++++---- 3 files changed, 599 insertions(+), 628 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index 01bc5715..320d481e 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -45,10 +45,11 @@ # pattern that matches A, B, and optionall C constants for PHOTABC and TEMP3 reactions # thanks chatgpt constants_pattern = re.compile(r"(PHOTABC|TEMP3|DCONST|DTEMP):\s+A:\s+([\d\.e+-]+)\s+B:\s+([\d\.e+-]+)(?:\s+C:\s+([\d\.e+-]+))?") -reaction_pattern = r"^([^=]*)=([^=]*)$" +reaction_pattern = re.compile(r"^([^=]*)=([^=]*)$") +stoichiemetric_coefficient_pattern = re.compile(r"(-?\d+(?:\.\d+)?)([A-Za-z]*)") def parse_reactants_products(line): - match = re.search(reaction_pattern, line.replace(" ", "")) + match = reaction_pattern.search(line.replace(" ", "")) if match: reactants = combine_stoichiometric_coeffs(match.group(1).strip()) products = combine_stoichiometric_coeffs(match.group(2).strip()) @@ -74,8 +75,16 @@ def convert_products_to_yield(products): # first, combine duplicated products prods = {} for product in products: + # check if this has a coefficient + match = stoichiemetric_coefficient_pattern.search(product) existing = prods.get(product, 0.0) - prods[product] = existing + 1.0 + _yield = 1.0 + if match: + # it does! add that coefficient as the yeidl + _yield = float(match.group(1)) + # also, use the matched text as the species name so that the species name doesn't include the yield + product = match.group(2) + prods[product] = existing + _yield products = [] for name, _yield in prods.items(): @@ -84,8 +93,6 @@ def convert_products_to_yield(products): products.append(spec) # now, go through each product and, when there's a - print(products) - print() return products line_index = 0 diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json index f482e54f..ba83a8f4 100644 --- a/capram_convert/mechanism.json +++ b/capram_convert/mechanism.json @@ -25,8 +25,8 @@ "NO3m": {} }, "products": { - "aNO2": { - "yield": 1.0 + "": { + "yield": 2.0 }, "aHO": { "yield": 1.0 @@ -56,14 +56,14 @@ "FEpp": { "yield": 1.0 }, - "C2O4mm": { - "yield": 1.0 + "O": { + "yield": 2.0 }, - "aCO2": { - "yield": 1.0 + "": { + "yield": 2.0 }, - "CO2m": { - "yield": 1.0 + "m": { + "yield": 2.0 } } }, @@ -121,8 +121,8 @@ "FEpp": { "yield": 1.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 150000000.0, @@ -140,11 +140,11 @@ "FEpp": { "yield": 1.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 }, - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 130000.0, @@ -162,8 +162,8 @@ "FEpp": { "yield": 1.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 }, "OHm": { "yield": 1.0 @@ -184,11 +184,11 @@ "FEppp": { "yield": 1.0 }, - "aH2O2": { - "yield": 1.0 + "O": { + "yield": 2.0 }, - "-2.0Hp": { - "yield": 1.0 + "Hp": { + "yield": -2.0 } }, "A": 10000000.0, @@ -206,11 +206,11 @@ "FEppp": { "yield": 1.0 }, - "aH2O2": { - "yield": 1.0 + "O": { + "yield": 2.0 }, - "-1.0Hp": { - "yield": 1.0 + "Hp": { + "yield": -1.0 } }, "A": 27470692899786.598, @@ -244,11 +244,11 @@ "CUpp": { "yield": 1.0 }, - "aH2O2": { - "yield": 1.0 + "O": { + "yield": 2.0 }, - "-2.0Hp": { - "yield": 1.0 + "Hp": { + "yield": -2.0 } }, "A": 10000000000.0, @@ -266,11 +266,11 @@ "CUpp": { "yield": 1.0 }, - "aH2O2": { - "yield": 1.0 + "O": { + "yield": 2.0 }, - "-1.0Hp": { - "yield": 1.0 + "Hp": { + "yield": -1.0 } }, "A": 2300000000.0, @@ -288,8 +288,8 @@ "CUp": { "yield": 1.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 }, "Hp": { "yield": 1.0 @@ -310,8 +310,8 @@ "CUp": { "yield": 1.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 8000000000.0, @@ -367,11 +367,11 @@ "O2m": {} }, "products": { - "O3m": { - "yield": 1.0 + "m": { + "yield": 3.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 2411527019006.37, @@ -388,8 +388,8 @@ "aHO": { "yield": 1.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 1193031991.1270792, @@ -404,11 +404,11 @@ "aHO": {} }, "products": { - "aHO2": { - "yield": 1.0 + "": { + "yield": 2.0 }, - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 8423504855.756161, @@ -423,11 +423,11 @@ "aHO": {} }, "products": { - "SO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 }, - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 2700000000.0, @@ -445,8 +445,8 @@ "CUpp": { "yield": 1.0 }, - "O2m": { - "yield": 1.0 + "m": { + "yield": 2.0 } }, "A": 460000.0, @@ -464,8 +464,8 @@ "FEOpp": { "yield": 1.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 5608557390760.588, @@ -486,8 +486,8 @@ "CLOHm": { "yield": 1.0 }, - "-1.0Hp": { - "yield": 1.0 + "Hp": { + "yield": -1.0 } }, "A": 100.0, @@ -502,11 +502,11 @@ "FEpp": {} }, "products": { - "2FEppp": { - "yield": 1.0 + "FEppp": { + "yield": 2.0 }, - "2OHm": { - "yield": 1.0 + "OHm": { + "yield": 2.0 } }, "A": 1214599.2606213153, @@ -520,11 +520,11 @@ "aN2O5": {} }, "products": { - "NO2p": { - "yield": 1.0 + "p": { + "yield": 2.0 }, - "NO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 } }, "A": 1000000000.0, @@ -539,8 +539,8 @@ "[aH2O]": {} }, "products": { - "NO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 }, "Hp": { "yield": 2.0 @@ -558,14 +558,11 @@ "HSO3m": {} }, "products": { - "NO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 }, "Hp": { "yield": 1.0 - }, - "SO3m": { - "yield": 1.0 } }, "A": 1068246352911.5388, @@ -580,11 +577,8 @@ "SO4mm": {} }, "products": { - "NO3m": { - "yield": 1.0 - }, - "SO4m": { - "yield": 1.0 + "m": { + "yield": 4.0 } }, "A": 100000.0, @@ -598,11 +592,11 @@ "NO4m": {} }, "products": { - "NO2m": { - "yield": 1.0 + "m": { + "yield": 2.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 1.0, @@ -617,14 +611,11 @@ "HSO3m": {} }, "products": { - "HSO4m": { - "yield": 1.0 + "m": { + "yield": 3.0 }, "Hp": { "yield": 1.0 - }, - "NO3m": { - "yield": 1.0 } }, "A": 330000.0, @@ -639,8 +630,8 @@ "CLm": {} }, "products": { - "aCLNO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 10000000000.0, @@ -655,8 +646,8 @@ "BRm": {} }, "products": { - "aBRNO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 10000000000.0, @@ -671,8 +662,8 @@ "BRm": {} }, "products": { - "NO2m": { - "yield": 1.0 + "m": { + "yield": 2.0 }, "aBRCL": { "yield": 1.0 @@ -690,11 +681,11 @@ "BRm": {} }, "products": { - "aBR2": { - "yield": 1.0 + "": { + "yield": 2.0 }, - "NO2m": { - "yield": 1.0 + "m": { + "yield": 2.0 } }, "A": 25500.0, @@ -709,8 +700,8 @@ "CLm": {} }, "products": { - "NO2m": { - "yield": 1.0 + "m": { + "yield": 2.0 }, "aBRCL": { "yield": 1.0 @@ -728,11 +719,11 @@ "aHO": {} }, "products": { - "CHOHSO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 }, - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 300000000.0, @@ -747,8 +738,8 @@ "aO2": {} }, "products": { - "O2CHOHSO3m": { - "yield": 1.0 + "CHOHSO": { + "yield": 2.0 } }, "A": 2600000000.0, @@ -762,11 +753,11 @@ "O2CHOHSO3m": {} }, "products": { - "aHO2": { - "yield": 1.0 + "": { + "yield": 2.0 }, - "CHOSO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 } }, "A": 17000.0, @@ -780,11 +771,11 @@ "O2CHOHSO3m": {} }, "products": { - "aO2CHO": { - "yield": 1.0 + "CHO": { + "yield": 2.0 }, - "HSO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 } }, "A": 7000.0, @@ -799,10 +790,10 @@ "[aH2O]": {} }, "products": { - "HSO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 }, - "aORA1": { + "": { "yield": 1.0 } }, @@ -818,11 +809,8 @@ "[aH2O]": {} }, "products": { - "aORA1": { - "yield": 1.0 - }, - "aHO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 44.32, @@ -838,14 +826,14 @@ "Hp": {} }, "products": { - "SO4mm": { - "yield": 1.0 + "mm": { + "yield": 4.0 }, - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 }, - "2Hp": { - "yield": 1.0 + "Hp": { + "yield": 2.0 } }, "A": 48617052944753.77, @@ -860,14 +848,14 @@ "aO3": {} }, "products": { - "SO4mm": { - "yield": 1.0 + "mm": { + "yield": 4.0 }, "Hp": { "yield": 1.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 42405757730857.71, @@ -882,11 +870,11 @@ "aO3": {} }, "products": { - "SO4mm": { - "yield": 1.0 + "mm": { + "yield": 4.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 7.429735524861723e+16, @@ -901,8 +889,8 @@ "FEpp": {} }, "products": { - "HSO5m": { - "yield": 1.0 + "m": { + "yield": 5.0 }, "FEOHpp": { "yield": 1.0 @@ -920,8 +908,8 @@ "FEpp": {} }, "products": { - "SO4m": { - "yield": 1.0 + "m": { + "yield": 4.0 }, "FEOHpp": { "yield": 1.0 @@ -942,8 +930,8 @@ "FEOHpp": { "yield": 1.0 }, - "SO4mm": { - "yield": 1.0 + "mm": { + "yield": 4.0 }, "Hp": { "yield": 1.0 @@ -960,11 +948,11 @@ "SO5m": {} }, "products": { - "SO4m": { - "yield": 2.0 + "m": { + "yield": 4.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 1353845691603.3787, @@ -979,8 +967,8 @@ "aHO2": {} }, "products": { - "SO5O2Hm": { - "yield": 1.0 + "O": { + "yield": 5.0 } }, "A": 1700000000.0, @@ -994,14 +982,14 @@ "SO5O2mm": {} }, "products": { - "HSO5m": { - "yield": 1.0 + "m": { + "yield": 5.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 }, - "-1.0Hp": { - "yield": 1.0 + "Hp": { + "yield": -1.0 } }, "A": 1200.0, @@ -1016,8 +1004,8 @@ "aO2": {} }, "products": { - "SO5m": { - "yield": 1.0 + "m": { + "yield": 5.0 } }, "A": 2500000000.0, @@ -1032,8 +1020,8 @@ "[aH2O]": {} }, "products": { - "SO4mm": { - "yield": 1.0 + "mm": { + "yield": 4.0 }, "aHO": { "yield": 1.0 @@ -1055,11 +1043,11 @@ "Hp": {} }, "products": { - "2SO4mm": { - "yield": 1.0 + "SO": { + "yield": 2.0 }, - "3Hp": { - "yield": 1.0 + "Hp": { + "yield": 3.0 } }, "A": 7140000.0, @@ -1074,11 +1062,11 @@ "aHO": {} }, "products": { - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 }, - "aCH2OH": { - "yield": 1.0 + "OH": { + "yield": 2.0 } }, "A": 7002790586.531466, @@ -1093,8 +1081,8 @@ "aO2": {} }, "products": { - "aO2CH2OH": { - "yield": 1.0 + "CH": { + "yield": 2.0 } }, "A": 2000000000.0, @@ -1108,11 +1096,11 @@ "aO2CH2OH": {} }, "products": { - "aCH3OH": { - "yield": 1.0 + "OH": { + "yield": 3.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 }, "aHCHO": { "yield": 1.0 @@ -1130,11 +1118,11 @@ "aHO": {} }, "products": { - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 }, - "aCH3CHOH": { - "yield": 1.0 + "CHOH": { + "yield": 3.0 } }, "A": 1900000000.0, @@ -1149,8 +1137,8 @@ "aO2": {} }, "products": { - "aO2CH3CHOH": { - "yield": 1.0 + "CH": { + "yield": 2.0 } }, "A": 2000000000.0, @@ -1167,8 +1155,8 @@ "aALD": { "yield": 1.0 }, - "aHO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 1713166492299.335, @@ -1183,11 +1171,11 @@ "aHO": {} }, "products": { - "aCHOH2": { - "yield": 1.0 + "": { + "yield": 2.0 }, - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 30655705402.09484, @@ -1202,10 +1190,7 @@ "aO2": {} }, "products": { - "aHO2": { - "yield": 1.0 - }, - "aORA1": { + "": { "yield": 1.0 } }, @@ -1221,11 +1206,11 @@ "aHO": {} }, "products": { - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 }, - "aCH3COH2": { - "yield": 1.0 + "COH": { + "yield": 3.0 } }, "A": 1200000000.0, @@ -1240,11 +1225,11 @@ "aHO": {} }, "products": { - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 }, - "aCH3CO": { - "yield": 1.0 + "CO": { + "yield": 3.0 } }, "A": 3600000000.0, @@ -1259,11 +1244,11 @@ "aHO": {} }, "products": { - "aCO2H": { - "yield": 1.0 + "H": { + "yield": 2.0 }, - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 3726553714.606836, @@ -1278,8 +1263,8 @@ "aHO": {} }, "products": { - "aCO2H": { - "yield": 1.0 + "H": { + "yield": 2.0 }, "OHm": { "yield": 1.0 @@ -1297,11 +1282,11 @@ "aHO": {} }, "products": { - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 }, - "aCH2COOH": { - "yield": 1.0 + "COOH": { + "yield": 2.0 } }, "A": 1301323951.4818943, @@ -1316,11 +1301,11 @@ "aHO": {} }, "products": { - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 }, - "CH2COOm": { - "yield": 1.0 + "COOm": { + "yield": 2.0 } }, "A": 42000577298.10133, @@ -1335,8 +1320,8 @@ "aO2": {} }, "products": { - "aACO3": { - "yield": 1.0 + "": { + "yield": 3.0 } }, "A": 1700000000.0, @@ -1350,14 +1335,14 @@ "aMO2": {} }, "products": { - "aCH3OH": { - "yield": 1.0 + "OH": { + "yield": 3.0 }, "aHCHO": { "yield": 1.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 118968666270.98093, @@ -1371,11 +1356,11 @@ "aMO2": {} }, "products": { - "aCH3O": { - "yield": 2.0 + "O": { + "yield": 3.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 57876648456.152885, @@ -1389,14 +1374,8 @@ "aACO3": {} }, "products": { - "aMO2": { - "yield": 2.0 - }, - "aCO2": { + "": { "yield": 2.0 - }, - "aO2": { - "yield": 1.0 } }, "A": 150000000.0, @@ -1411,11 +1390,11 @@ "HSO3m": {} }, "products": { - "aOP1": { + "": { "yield": 1.0 }, - "SO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 } }, "A": 500000.0, @@ -1429,11 +1408,11 @@ "aETHPX": {} }, "products": { - "aCH3CH2O": { - "yield": 2.0 + "CH": { + "yield": 3.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 8071922.343268531, @@ -1447,8 +1426,8 @@ "aCH3CH2O": {} }, "products": { - "aCH3CHOH": { - "yield": 1.0 + "CHOH": { + "yield": 3.0 } }, "A": 1000000.0, @@ -1463,11 +1442,8 @@ "HC2O4m": {} }, "products": { - "[aH2O]": { - "yield": 1.0 - }, - "C2O4m": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 32000000.0, @@ -1485,8 +1461,8 @@ "OHm": { "yield": 1.0 }, - "C2O4m": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 5300000.0, @@ -1501,11 +1477,11 @@ "aO2": {} }, "products": { - "aCO2": { + "": { "yield": 2.0 }, - "O2m": { - "yield": 1.0 + "m": { + "yield": 2.0 } }, "A": 2000000000.0, @@ -1520,11 +1496,11 @@ "aCHOH2CHOH2": {} }, "products": { - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 }, - "aCOH2CHOH2": { - "yield": 1.0 + "CHOH": { + "yield": 2.0 } }, "A": 178137994858.22678, @@ -1539,8 +1515,8 @@ "aO2": {} }, "products": { - "aO2COH2CHOH2": { - "yield": 1.0 + "COH": { + "yield": 2.0 } }, "A": 1380000000.0, @@ -1554,11 +1530,11 @@ "aO2COH2CHOH2": {} }, "products": { - "aHO2": { - "yield": 1.0 + "": { + "yield": 2.0 }, - "aCHOH2COOH": { - "yield": 1.0 + "COOH": { + "yield": 2.0 } }, "A": 2000000000.0, @@ -1573,11 +1549,11 @@ "aCHOH2COOH": {} }, "products": { - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 }, - "aCOH2COOH": { - "yield": 1.0 + "COOH": { + "yield": 2.0 } }, "A": 178137994858.22678, @@ -1592,8 +1568,8 @@ "aO2": {} }, "products": { - "aO2COH2COOH": { - "yield": 1.0 + "COH": { + "yield": 2.0 } }, "A": 2000000000.0, @@ -1607,11 +1583,11 @@ "aO2COH2COOH": {} }, "products": { - "aHO2": { - "yield": 1.0 + "": { + "yield": 2.0 }, - "aH2C2O4": { - "yield": 1.0 + "C": { + "yield": 2.0 } }, "A": 2000000000.0, @@ -1626,8 +1602,8 @@ "aO2": {} }, "products": { - "aCH3COH2OO": { - "yield": 1.0 + "COH": { + "yield": 3.0 } }, "A": 2000000000.0, @@ -1647,8 +1623,8 @@ "MCOOm": { "yield": 1.0 }, - "O2m": { - "yield": 1.0 + "m": { + "yield": 2.0 } }, "A": 100000.0, @@ -1662,8 +1638,8 @@ "aCH3O": {} }, "products": { - "aCH2OH": { - "yield": 1.0 + "OH": { + "yield": 2.0 } }, "A": 1000000.0, @@ -1678,8 +1654,8 @@ "aO2": {} }, "products": { - "O2CH2COOm": { - "yield": 1.0 + "CH": { + "yield": 2.0 } }, "A": 2000000000.0, @@ -1693,11 +1669,11 @@ "O2CH2COOm": {} }, "products": { - "2CHOH2COOm": { - "yield": 1.0 + "CHOH": { + "yield": 2.0 }, - "aH2O2": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 20000000.0, @@ -1712,11 +1688,11 @@ "aO2": {} }, "products": { - "aCO2": { - "yield": 1.0 + "": { + "yield": 2.0 }, - "O2m": { - "yield": 1.0 + "m": { + "yield": 2.0 } }, "A": 4000000000.0, @@ -1731,8 +1707,8 @@ "FEpp": {} }, "products": { - "2CLm": { - "yield": 1.0 + "CLm": { + "yield": 2.0 }, "FEppp": { "yield": 1.0 @@ -1750,14 +1726,14 @@ "aHO2": {} }, "products": { - "2CLm": { - "yield": 1.0 + "CLm": { + "yield": 2.0 }, "Hp": { "yield": 1.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 13000000000.0, @@ -1772,14 +1748,14 @@ "HSO3m": {} }, "products": { - "2CLm": { - "yield": 1.0 + "CLm": { + "yield": 2.0 }, "Hp": { "yield": 1.0 }, - "SO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 } }, "A": 650720568.7854763, @@ -1838,8 +1814,8 @@ "SO4m": {} }, "products": { - "SO4mm": { - "yield": 1.0 + "mm": { + "yield": 4.0 }, "aBR": { "yield": 1.0 @@ -1857,8 +1833,8 @@ "aNO3": {} }, "products": { - "NO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 }, "aBR": { "yield": 1.0 @@ -1875,11 +1851,11 @@ "BR2m": {} }, "products": { - "aBR2": { - "yield": 1.0 + "": { + "yield": 2.0 }, - "2BRm": { - "yield": 1.0 + "BRm": { + "yield": 2.0 } }, "A": 1700000000.0, @@ -1894,8 +1870,8 @@ "FEpp": {} }, "products": { - "2BRm": { - "yield": 1.0 + "BRm": { + "yield": 2.0 }, "FEppp": { "yield": 1.0 @@ -1913,14 +1889,14 @@ "aH2O2": {} }, "products": { - "2BRm": { - "yield": 1.0 + "BRm": { + "yield": 2.0 }, "Hp": { "yield": 1.0 }, - "aHO2": { - "yield": 1.0 + "": { + "yield": 2.0 } }, "A": 100000.0, @@ -1935,11 +1911,11 @@ "aHO2": {} }, "products": { - "2BRm": { - "yield": 1.0 + "BRm": { + "yield": 2.0 }, - "aO2": { - "yield": 1.0 + "": { + "yield": 2.0 }, "Hp": { "yield": 1.0 @@ -1957,14 +1933,14 @@ "HSO3m": {} }, "products": { - "2BRm": { - "yield": 1.0 + "BRm": { + "yield": 2.0 }, "Hp": { "yield": 1.0 }, - "SO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 } }, "A": 685036875.6354121, @@ -2019,8 +1995,8 @@ "[aH2O]": {} }, "products": { - "aH2CO3": { - "yield": 1.0 + "CO": { + "yield": 2.0 } }, "A": 1300426356398.6077, @@ -2034,11 +2010,11 @@ "aH2CO3": {} }, "products": { - "aCO2": { - "yield": 1.0 + "": { + "yield": 2.0 }, - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 1.3670434220265014e+17, @@ -2072,11 +2048,11 @@ "OHm": {} }, "products": { - "SO3mm": { - "yield": 1.0 + "mm": { + "yield": 3.0 }, - "aCH2OH2": { - "yield": 1.0 + "OH": { + "yield": 2.0 } }, "A": 475632147521.7825, @@ -2129,8 +2105,8 @@ "[aH2O]": {} }, "products": { - "NH4p": { - "yield": 1.0 + "p": { + "yield": 4.0 }, "OHm": { "yield": 1.0 @@ -2148,8 +2124,8 @@ "aHNO3": {} }, "products": { - "NO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 }, "Hp": { "yield": 1.0 @@ -2167,8 +2143,8 @@ "aHONO": {} }, "products": { - "NO2m": { - "yield": 1.0 + "m": { + "yield": 2.0 }, "Hp": { "yield": 1.0 @@ -2187,8 +2163,8 @@ "[aH2O]": {} }, "products": { - "HSO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 }, "Hp": { "yield": 1.0 @@ -2206,8 +2182,8 @@ "HSO3m": {} }, "products": { - "SO3mm": { - "yield": 1.0 + "mm": { + "yield": 3.0 }, "Hp": { "yield": 1.0 @@ -2228,8 +2204,8 @@ "Hp": { "yield": 1.0 }, - "SO4mm": { - "yield": 1.0 + "mm": { + "yield": 4.0 } }, "A": 0.0102, @@ -2283,8 +2259,8 @@ "[aH2O]": {} }, "products": { - "aCH2OH2": { - "yield": 1.0 + "OH": { + "yield": 2.0 } }, "A": 36.0, @@ -2300,8 +2276,8 @@ "[aH2O]": {} }, "products": { - "aCH3CHOH2": { - "yield": 1.0 + "CHOH": { + "yield": 3.0 } }, "A": 0.0246, @@ -2320,8 +2296,8 @@ "HMSm": { "yield": 1.0 }, - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 200000000.0, @@ -2337,8 +2313,8 @@ "CLm": {} }, "products": { - "NO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 }, "aCL": { "yield": 1.0 @@ -2357,8 +2333,8 @@ "[aH2O]": {} }, "products": { - "aCH3COH2": { - "yield": 1.0 + "COH": { + "yield": 3.0 } }, "A": 367.0, @@ -2376,8 +2352,8 @@ "Hp": { "yield": 1.0 }, - "O2CH2COOm": { - "yield": 1.0 + "CH": { + "yield": 2.0 } }, "A": 1.75e-05, @@ -2393,8 +2369,8 @@ "aH2CO3": {} }, "products": { - "HCO3m": { - "yield": 1.0 + "m": { + "yield": 3.0 }, "Hp": { "yield": 1.0 @@ -2414,8 +2390,8 @@ "aHO2": {} }, "products": { - "O2m": { - "yield": 1.0 + "m": { + "yield": 2.0 }, "Hp": { "yield": 1.0 @@ -2435,8 +2411,8 @@ "aHNO4": {} }, "products": { - "NO4m": { - "yield": 1.0 + "m": { + "yield": 4.0 }, "Hp": { "yield": 1.0 @@ -2457,8 +2433,8 @@ "aHO2": {} }, "products": { - "aHNO4": { - "yield": 1.0 + "": { + "yield": 4.0 } }, "A": 2200000000.0, @@ -2475,8 +2451,8 @@ "aSULF": {} }, "products": { - "HSO4m": { - "yield": 1.0 + "m": { + "yield": 4.0 }, "Hp": { "yield": 1.0 @@ -2519,8 +2495,8 @@ "CLm": {} }, "products": { - "CL2m": { - "yield": 1.0 + "m": { + "yield": 2.0 } }, "A": 140000.0, @@ -2538,8 +2514,8 @@ "BRm": {} }, "products": { - "BR2m": { - "yield": 1.0 + "m": { + "yield": 2.0 } }, "A": 632000.0, @@ -2579,8 +2555,8 @@ "aCL": { "yield": 1.0 }, - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 5100000.0, @@ -2620,8 +2596,8 @@ "aBR": { "yield": 1.0 }, - "[aH2O]": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 1800000000000.0, @@ -2641,8 +2617,8 @@ "Hp": { "yield": 1.0 }, - "O3m": { - "yield": 1.0 + "m": { + "yield": 3.0 } }, "A": 6.3e-09, @@ -2659,8 +2635,8 @@ "CHOHSO3m": {} }, "products": { - "CHOSO3mm": { - "yield": 1.0 + "mm": { + "yield": 3.0 }, "Hp": { "yield": 1.0 @@ -2683,8 +2659,8 @@ "Hp": { "yield": 1.0 }, - "SO5O2mm": { - "yield": 1.0 + "O": { + "yield": 5.0 } }, "A": 1.5e-05, @@ -2701,8 +2677,8 @@ "HC2O4m": {} }, "products": { - "C2O4mm": { - "yield": 1.0 + "O": { + "yield": 2.0 }, "Hp": { "yield": 1.0 @@ -2725,8 +2701,8 @@ "Hp": { "yield": 1.0 }, - "CHOH2COOm": { - "yield": 1.0 + "COOm": { + "yield": 2.0 } }, "A": 0.000316, @@ -2744,8 +2720,8 @@ "[aH2O]": {} }, "products": { - "aCHOH2CHOH2": { - "yield": 1.0 + "CHOH": { + "yield": 2.0 } }, "A": 3900.0, @@ -2763,8 +2739,8 @@ "C2O4mm": {} }, "products": { - "FEC2O4p": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 2900000000.0, @@ -2782,8 +2758,8 @@ "C2O4mm": {} }, "products": { - "FEC2O42m": { - "yield": 1.0 + "O": { + "yield": 2.0 } }, "A": 6300000.0, @@ -2801,8 +2777,8 @@ "CLm": {} }, "products": { - "SO4mm": { - "yield": 1.0 + "mm": { + "yield": 4.0 }, "aCL": { "yield": 1.0 @@ -2819,21 +2795,21 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "CO2", "aerosol phase": "cloud water", - "aerosol-phase species": "aCO2", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "O3", "aerosol phase": "cloud water", - "aerosol-phase species": "aO3", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HO2", "aerosol phase": "cloud water", - "aerosol-phase species": "aHO2", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { @@ -2847,14 +2823,14 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "H2O2", "aerosol phase": "cloud water", - "aerosol-phase species": "aH2O2", + "aerosol-phase species": "O", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NO2", "aerosol phase": "cloud water", - "aerosol-phase species": "aNO2", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { @@ -2868,28 +2844,28 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "HNO3", "aerosol phase": "cloud water", - "aerosol-phase species": "aHNO3", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NO3", "aerosol phase": "cloud water", - "aerosol-phase species": "aNO3", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "N2O5", "aerosol phase": "cloud water", - "aerosol-phase species": "aN2O5", + "aerosol-phase species": "O", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NH3", "aerosol phase": "cloud water", - "aerosol-phase species": "aNH3", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { @@ -2910,35 +2886,35 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "ORA1", "aerosol phase": "cloud water", - "aerosol-phase species": "aORA1", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "SO2", "aerosol phase": "cloud water", - "aerosol-phase species": "aSO2", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "OP1", "aerosol phase": "cloud water", - "aerosol-phase species": "aOP1", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ORA2", "aerosol phase": "cloud water", - "aerosol-phase species": "aORA2", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "MO2", "aerosol phase": "cloud water", - "aerosol-phase species": "aMO2", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { @@ -2959,7 +2935,7 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "CH3OH", "aerosol phase": "cloud water", - "aerosol-phase species": "aCH3OH", + "aerosol-phase species": "OH", "aerosol-phase water": "[aH2O]" }, { @@ -2973,14 +2949,14 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "BR2", "aerosol phase": "cloud water", - "aerosol-phase species": "aBR2", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CL2", "aerosol phase": "cloud water", - "aerosol-phase species": "aCL2", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { @@ -2994,14 +2970,14 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "HNO4", "aerosol phase": "cloud water", - "aerosol-phase species": "aHNO4", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ACO3", "aerosol phase": "cloud water", - "aerosol-phase species": "aACO3", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { @@ -3015,21 +2991,21 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "[O2]", "aerosol phase": "cloud water", - "aerosol-phase species": "aO2", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CLNO2", "aerosol phase": "cloud water", - "aerosol-phase species": "aCLNO2", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "BRNO2", "aerosol phase": "cloud water", - "aerosol-phase species": "aBRNO2", + "aerosol-phase species": "", "aerosol-phase water": "[aH2O]" }, { @@ -3052,126 +3028,122 @@ "name": "cloud water", "type": "AERO_PHASE", "species": [ - "aO3", - "CL2m", - "aHOCL", + "", + "FEpp", + "CH", + "aSO2", + "CHOHSO", + "HCOOm", + "HC2O4m", + "FEppp", + "CLm", + "FEOpp", + "aMO2", + "aO2CH2OH", "O2m", - "aCOH2CHOH2", - "aNO", + "aCH2OH2", + "HSO4m", + "aH2O2", + "COOH", + "aHOBR", + "SO4mm", "aCH3CH2O", + "p", + "O2CHOHSO3m", + "H", + "aSULF", + "CHO", + "NO4m", + "SO5O2mm", + "CLOHm", + "aHO3", + "aCH3COH2OO", + "aHNO3", + "SO", + "aORA2", "aHO", - "aO2", - "aHNO4", - "2FEppp", - "aCH3CHOH", - "BR2m", + "aBRCL", "aCL", - "aCOH2COOH", - "HC2O4m", - "CLOHm", - "aORA1", - "aH2C2O4", - "aSULF", - "aCH3COH2", + "aO2COH2CHOH2", + "aCHOH2COOH", + "aNH3", + "HMSm", + "SO3mm", + "CHOSO3m", + "mm", + "OHm", + "aHNO4", + "aETHPX", "aCH3O", - "BRm", - "aCH3OH", - "aO2CH3CHOH", - "CUp", - "-1.0Hp", - "NO2m", - "3Hp", - "CO2m", - "aMO2", - "aHCL", - "Hp", - "O2CH2COOm", + "aCH3CO", + "aO2", + "aO2CHO", "MCOOm", + "aCLNO2", + "FEC2O4p", + "aBR2", "aCH2OH", - "aBRCL", - "2Hp", + "aCO2", + "C2O4mm", + "O2CH2COOm", "aH2CO3", - "2SO4mm", - "SO3mm", + "CUp", + "CHOHSO3m", "aCL2", - "FEppp", - "SO3m", - "SO5m", - "2BRm", + "CO", + "aETOH", "aALD", - "HMSm", - "aHNO3", - "aCO2H", - "2CHOH2COOm", - "FEOHpp", - "aCHOH2", - "O2CHOHSO3m", - "FEC2O42m", - "FEOpp", - "CH2COOm", - "FEC2O4p", - "O3m", - "NO2p", - "SO4mm", "aNO3", - "aSO2", - "-2.0Hp", - "C2O4mm", - "aCHOH2COOH", + "NO2p", + "aCOH2CHOH2", + "HSO3m", + "Hp", + "aBRNO2", + "BRm", + "aCH2COOH", + "aN2O5", "aBR", + "aACO3", + "CL2m", + "C", + "aHOCL", "[aH2O]", - "aCH2COOH", - "CHOSO3mm", + "CH2COOm", + "aO2CH3CHOH", + "HSO5m", + "aGLY", + "aHCL", "aHONO", - "HCO3m", - "aCLNO2", - "HSO3m", - "NO3m", - "CHOH2COOm", - "SO4m", + "SO5O2Hm", + "aO3", + "aHO2", + "O", + "aCH3OH", + "OH", + "aHCHO", + "CHOH", + "BR2m", + "aORA1", + "aCOH2COOH", + "BROHm", + "aCHOH2", + "COOm", + "aCH3COH2", + "m", + "aCH3CHOH", + "aCH3CHOH2", + "aO2COH2COOH", + "aNO", "aCHOH2CHOH2", "CUpp", - "aO2COH2COOH", - "OHm", - "aCH2OH2", - "aCH3CHOH2", - "aACO3", - "NH4p", - "aHOBR", - "HCOOm", - "aNH3", - "aETHPX", - "aHO3", - "2OHm", - "aN2O5", - "aHCHO", - "aO2COH2CHOH2", - "CHOHSO3m", - "aHO2", - "aCH3CO", - "aORA2", - "aH2O2", - "FEpp", - "aCH3COH2OO", - "CHOSO3m", - "aOP1", - "SO5O2mm", + "SO5m", + "COH", + "CO2m", "aNO2", - "HSO5m", - "aGLY", - "aBR2", "C2O4m", - "CLm", - "aETOH", - "aBRNO2", - "SO5O2Hm", - "2CLm", - "aO2CH2OH", - "HSO4m", - "aCO2", - "aO2CHO", - "BROHm", - "NO4m" + "FEOHpp", + "SO3m", + "SO4m" ] }, { diff --git a/capram_convert/species.json b/capram_convert/species.json index 634bbbe8..99f5515b 100644 --- a/capram_convert/species.json +++ b/capram_convert/species.json @@ -9,7 +9,7 @@ "N star": 1.0 }, { - "name": "aCO2", + "name": "", "type": "CHEM_SPEC" }, { @@ -20,10 +20,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aO3", - "type": "CHEM_SPEC" - }, { "name": "HO2", "type": "CHEM_SPEC", @@ -32,10 +28,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aHO2", - "type": "CHEM_SPEC" - }, { "name": "HO", "type": "CHEM_SPEC", @@ -57,7 +49,7 @@ "N star": 1.0 }, { - "name": "aH2O2", + "name": "O", "type": "CHEM_SPEC" }, { @@ -68,10 +60,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aNO2", - "type": "CHEM_SPEC" - }, { "name": "HONO", "type": "CHEM_SPEC", @@ -92,10 +80,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aHNO3", - "type": "CHEM_SPEC" - }, { "name": "NO3", "type": "CHEM_SPEC", @@ -104,10 +88,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aNO3", - "type": "CHEM_SPEC" - }, { "name": "N2O5", "type": "CHEM_SPEC", @@ -116,10 +96,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aN2O5", - "type": "CHEM_SPEC" - }, { "name": "NH3", "type": "CHEM_SPEC", @@ -128,10 +104,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aNH3", - "type": "CHEM_SPEC" - }, { "name": "HCL", "type": "CHEM_SPEC", @@ -164,10 +136,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aORA1", - "type": "CHEM_SPEC" - }, { "name": "SO2", "type": "CHEM_SPEC", @@ -176,10 +144,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aSO2", - "type": "CHEM_SPEC" - }, { "name": "OP1", "type": "CHEM_SPEC", @@ -188,10 +152,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aOP1", - "type": "CHEM_SPEC" - }, { "name": "ORA2", "type": "CHEM_SPEC", @@ -200,10 +160,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aORA2", - "type": "CHEM_SPEC" - }, { "name": "MO2", "type": "CHEM_SPEC", @@ -212,10 +168,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aMO2", - "type": "CHEM_SPEC" - }, { "name": "ETHPX", "type": "CHEM_SPEC", @@ -249,7 +201,7 @@ "N star": 1.0 }, { - "name": "aCH3OH", + "name": "OH", "type": "CHEM_SPEC" }, { @@ -272,10 +224,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aBR2", - "type": "CHEM_SPEC" - }, { "name": "CL2", "type": "CHEM_SPEC", @@ -284,10 +232,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aCL2", - "type": "CHEM_SPEC" - }, { "name": "SULF", "type": "CHEM_SPEC", @@ -308,10 +252,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aHNO4", - "type": "CHEM_SPEC" - }, { "name": "ACO3", "type": "CHEM_SPEC", @@ -320,10 +260,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aACO3", - "type": "CHEM_SPEC" - }, { "name": "GLY", "type": "CHEM_SPEC", @@ -344,10 +280,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aO2", - "type": "CHEM_SPEC" - }, { "name": "CLNO2", "type": "CHEM_SPEC", @@ -356,10 +288,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aCLNO2", - "type": "CHEM_SPEC" - }, { "name": "BRNO2", "type": "CHEM_SPEC", @@ -368,10 +296,6 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, - { - "name": "aBRNO2", - "type": "CHEM_SPEC" - }, { "name": "BRCL", "type": "CHEM_SPEC", @@ -413,15 +337,15 @@ "type": "CHEM_SPEC" }, { - "name": "FEC2O42m", + "name": "aH2O2", "type": "CHEM_SPEC" }, { - "name": "C2O4mm", + "name": "FEC2O42m", "type": "CHEM_SPEC" }, { - "name": "CO2m", + "name": "m", "type": "CHEM_SPEC" }, { @@ -441,15 +365,7 @@ "type": "CHEM_SPEC" }, { - "name": "[aH2O]", - "type": "CHEM_SPEC" - }, - { - "name": "-2.0Hp", - "type": "CHEM_SPEC" - }, - { - "name": "-1.0Hp", + "name": "aHO2", "type": "CHEM_SPEC" }, { @@ -457,7 +373,7 @@ "type": "CHEM_SPEC" }, { - "name": "O3m", + "name": "aO3", "type": "CHEM_SPEC" }, { @@ -469,7 +385,7 @@ "type": "CHEM_SPEC" }, { - "name": "SO3m", + "name": "aO2", "type": "CHEM_SPEC" }, { @@ -485,11 +401,11 @@ "type": "CHEM_SPEC" }, { - "name": "2FEppp", + "name": "aN2O5", "type": "CHEM_SPEC" }, { - "name": "2OHm", + "name": "p", "type": "CHEM_SPEC" }, { @@ -497,29 +413,37 @@ "type": "CHEM_SPEC" }, { - "name": "SO4mm", + "name": "[aH2O]", "type": "CHEM_SPEC" }, { - "name": "SO4m", + "name": "aNO3", "type": "CHEM_SPEC" }, { - "name": "NO4m", + "name": "SO4mm", "type": "CHEM_SPEC" }, { - "name": "NO2m", + "name": "NO4m", "type": "CHEM_SPEC" }, { - "name": "HSO4m", + "name": "aHNO4", "type": "CHEM_SPEC" }, { "name": "BRm", "type": "CHEM_SPEC" }, + { + "name": "aCLNO2", + "type": "CHEM_SPEC" + }, + { + "name": "aBRNO2", + "type": "CHEM_SPEC" + }, { "name": "HMSm", "type": "CHEM_SPEC" @@ -528,10 +452,18 @@ "name": "CHOHSO3m", "type": "CHEM_SPEC" }, + { + "name": "CHOHSO", + "type": "CHEM_SPEC" + }, { "name": "O2CHOHSO3m", "type": "CHEM_SPEC" }, + { + "name": "CHO", + "type": "CHEM_SPEC" + }, { "name": "CHOSO3m", "type": "CHEM_SPEC" @@ -541,7 +473,7 @@ "type": "CHEM_SPEC" }, { - "name": "2Hp", + "name": "mm", "type": "CHEM_SPEC" }, { @@ -557,7 +489,7 @@ "type": "CHEM_SPEC" }, { - "name": "SO5O2Hm", + "name": "SO4m", "type": "CHEM_SPEC" }, { @@ -565,21 +497,33 @@ "type": "CHEM_SPEC" }, { - "name": "2SO4mm", + "name": "SO3m", + "type": "CHEM_SPEC" + }, + { + "name": "SO", "type": "CHEM_SPEC" }, { - "name": "3Hp", + "name": "aCH3OH", "type": "CHEM_SPEC" }, { "name": "aCH2OH", "type": "CHEM_SPEC" }, + { + "name": "CH", + "type": "CHEM_SPEC" + }, { "name": "aO2CH2OH", "type": "CHEM_SPEC" }, + { + "name": "CHOH", + "type": "CHEM_SPEC" + }, { "name": "aCH3CHOH", "type": "CHEM_SPEC" @@ -601,15 +545,19 @@ "type": "CHEM_SPEC" }, { - "name": "aCH3COH2", + "name": "COH", "type": "CHEM_SPEC" }, { - "name": "aCH3CO", + "name": "CO", + "type": "CHEM_SPEC" + }, + { + "name": "aORA1", "type": "CHEM_SPEC" }, { - "name": "aCO2H", + "name": "H", "type": "CHEM_SPEC" }, { @@ -617,7 +565,11 @@ "type": "CHEM_SPEC" }, { - "name": "aCH2COOH", + "name": "aORA2", + "type": "CHEM_SPEC" + }, + { + "name": "COOH", "type": "CHEM_SPEC" }, { @@ -625,11 +577,19 @@ "type": "CHEM_SPEC" }, { - "name": "CH2COOm", + "name": "COOm", "type": "CHEM_SPEC" }, { - "name": "aCH3O", + "name": "aCH2COOH", + "type": "CHEM_SPEC" + }, + { + "name": "aMO2", + "type": "CHEM_SPEC" + }, + { + "name": "aACO3", "type": "CHEM_SPEC" }, { @@ -640,6 +600,10 @@ "name": "HC2O4m", "type": "CHEM_SPEC" }, + { + "name": "C2O4mm", + "type": "CHEM_SPEC" + }, { "name": "C2O4m", "type": "CHEM_SPEC" @@ -669,19 +633,31 @@ "type": "CHEM_SPEC" }, { - "name": "aH2C2O4", + "name": "C", + "type": "CHEM_SPEC" + }, + { + "name": "aCH3COH2", "type": "CHEM_SPEC" }, { "name": "aCH3COH2OO", "type": "CHEM_SPEC" }, + { + "name": "aCH3O", + "type": "CHEM_SPEC" + }, + { + "name": "CH2COOm", + "type": "CHEM_SPEC" + }, { "name": "O2CH2COOm", "type": "CHEM_SPEC" }, { - "name": "2CHOH2COOm", + "name": "CO2m", "type": "CHEM_SPEC" }, { @@ -689,7 +665,7 @@ "type": "CHEM_SPEC" }, { - "name": "2CLm", + "name": "aCL2", "type": "CHEM_SPEC" }, { @@ -705,7 +681,7 @@ "type": "CHEM_SPEC" }, { - "name": "2BRm", + "name": "aBR2", "type": "CHEM_SPEC" }, { @@ -716,12 +692,28 @@ "name": "BROHm", "type": "CHEM_SPEC" }, + { + "name": "aCO2", + "type": "CHEM_SPEC" + }, { "name": "aH2CO3", "type": "CHEM_SPEC" }, { - "name": "NH4p", + "name": "aNH3", + "type": "CHEM_SPEC" + }, + { + "name": "aHNO3", + "type": "CHEM_SPEC" + }, + { + "name": "aSO2", + "type": "CHEM_SPEC" + }, + { + "name": "HSO4m", "type": "CHEM_SPEC" }, { @@ -729,15 +721,15 @@ "type": "CHEM_SPEC" }, { - "name": "HCO3m", + "name": "aCH3CO", "type": "CHEM_SPEC" }, { - "name": "CHOSO3mm", + "name": "aNO2", "type": "CHEM_SPEC" }, { - "name": "CHOH2COOm", + "name": "SO5O2Hm", "type": "CHEM_SPEC" }, { From 3eeb1b2b4c4df5ecbde4e8539c9170fe225772d6 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 13:55:35 -0500 Subject: [PATCH 19/24] correctly placing the coefficent and recovering the name --- capram_convert/convert.py | 8 +- capram_convert/mechanism.json | 904 +++++++++++++++++----------------- capram_convert/species.json | 230 ++++----- 3 files changed, 570 insertions(+), 572 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index 320d481e..778c6d89 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -46,7 +46,7 @@ # thanks chatgpt constants_pattern = re.compile(r"(PHOTABC|TEMP3|DCONST|DTEMP):\s+A:\s+([\d\.e+-]+)\s+B:\s+([\d\.e+-]+)(?:\s+C:\s+([\d\.e+-]+))?") reaction_pattern = re.compile(r"^([^=]*)=([^=]*)$") -stoichiemetric_coefficient_pattern = re.compile(r"(-?\d+(?:\.\d+)?)([A-Za-z]*)") +stoichiemetric_coefficient_pattern = re.compile(r"^(-?\d+(?:\.\d+)?)([A-Za-z]*)") def parse_reactants_products(line): match = reaction_pattern.search(line.replace(" ", "")) @@ -75,13 +75,15 @@ def convert_products_to_yield(products): # first, combine duplicated products prods = {} for product in products: - # check if this has a coefficient - match = stoichiemetric_coefficient_pattern.search(product) existing = prods.get(product, 0.0) _yield = 1.0 + + # check if this has a coefficient + match = stoichiemetric_coefficient_pattern.search(product) if match: # it does! add that coefficient as the yeidl _yield = float(match.group(1)) + print(product, match.groups()) # also, use the matched text as the species name so that the species name doesn't include the yield product = match.group(2) prods[product] = existing + _yield diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json index ba83a8f4..0f7dabe4 100644 --- a/capram_convert/mechanism.json +++ b/capram_convert/mechanism.json @@ -25,8 +25,8 @@ "NO3m": {} }, "products": { - "": { - "yield": 2.0 + "aNO2": { + "yield": 1.0 }, "aHO": { "yield": 1.0 @@ -56,14 +56,14 @@ "FEpp": { "yield": 1.0 }, - "O": { - "yield": 2.0 + "C2O4mm": { + "yield": 1.0 }, - "": { - "yield": 2.0 + "aCO2": { + "yield": 1.0 }, - "m": { - "yield": 2.0 + "CO2m": { + "yield": 1.0 } } }, @@ -121,8 +121,8 @@ "FEpp": { "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 } }, "A": 150000000.0, @@ -140,11 +140,11 @@ "FEpp": { "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 }, - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 } }, "A": 130000.0, @@ -162,8 +162,8 @@ "FEpp": { "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 }, "OHm": { "yield": 1.0 @@ -184,8 +184,8 @@ "FEppp": { "yield": 1.0 }, - "O": { - "yield": 2.0 + "aH2O2": { + "yield": 1.0 }, "Hp": { "yield": -2.0 @@ -206,8 +206,8 @@ "FEppp": { "yield": 1.0 }, - "O": { - "yield": 2.0 + "aH2O2": { + "yield": 1.0 }, "Hp": { "yield": -1.0 @@ -244,8 +244,8 @@ "CUpp": { "yield": 1.0 }, - "O": { - "yield": 2.0 + "aH2O2": { + "yield": 1.0 }, "Hp": { "yield": -2.0 @@ -266,8 +266,8 @@ "CUpp": { "yield": 1.0 }, - "O": { - "yield": 2.0 + "aH2O2": { + "yield": 1.0 }, "Hp": { "yield": -1.0 @@ -288,8 +288,8 @@ "CUp": { "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 }, "Hp": { "yield": 1.0 @@ -310,8 +310,8 @@ "CUp": { "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 } }, "A": 8000000000.0, @@ -367,11 +367,11 @@ "O2m": {} }, "products": { - "m": { - "yield": 3.0 + "O3m": { + "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 } }, "A": 2411527019006.37, @@ -388,8 +388,8 @@ "aHO": { "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 } }, "A": 1193031991.1270792, @@ -404,11 +404,11 @@ "aHO": {} }, "products": { - "": { - "yield": 2.0 + "aHO2": { + "yield": 1.0 }, - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 } }, "A": 8423504855.756161, @@ -423,11 +423,11 @@ "aHO": {} }, "products": { - "m": { - "yield": 3.0 + "SO3m": { + "yield": 1.0 }, - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 } }, "A": 2700000000.0, @@ -445,8 +445,8 @@ "CUpp": { "yield": 1.0 }, - "m": { - "yield": 2.0 + "O2m": { + "yield": 1.0 } }, "A": 460000.0, @@ -464,8 +464,8 @@ "FEOpp": { "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 } }, "A": 5608557390760.588, @@ -520,11 +520,11 @@ "aN2O5": {} }, "products": { - "p": { - "yield": 2.0 + "NO2p": { + "yield": 1.0 }, - "m": { - "yield": 3.0 + "NO3m": { + "yield": 1.0 } }, "A": 1000000000.0, @@ -539,8 +539,8 @@ "[aH2O]": {} }, "products": { - "m": { - "yield": 3.0 + "NO3m": { + "yield": 1.0 }, "Hp": { "yield": 2.0 @@ -558,11 +558,14 @@ "HSO3m": {} }, "products": { - "m": { - "yield": 3.0 + "NO3m": { + "yield": 1.0 }, "Hp": { "yield": 1.0 + }, + "SO3m": { + "yield": 1.0 } }, "A": 1068246352911.5388, @@ -577,8 +580,11 @@ "SO4mm": {} }, "products": { - "m": { - "yield": 4.0 + "NO3m": { + "yield": 1.0 + }, + "SO4m": { + "yield": 1.0 } }, "A": 100000.0, @@ -592,11 +598,11 @@ "NO4m": {} }, "products": { - "m": { - "yield": 2.0 + "NO2m": { + "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 } }, "A": 1.0, @@ -611,11 +617,14 @@ "HSO3m": {} }, "products": { - "m": { - "yield": 3.0 + "HSO4m": { + "yield": 1.0 }, "Hp": { "yield": 1.0 + }, + "NO3m": { + "yield": 1.0 } }, "A": 330000.0, @@ -630,8 +639,8 @@ "CLm": {} }, "products": { - "": { - "yield": 2.0 + "aCLNO2": { + "yield": 1.0 } }, "A": 10000000000.0, @@ -646,8 +655,8 @@ "BRm": {} }, "products": { - "": { - "yield": 2.0 + "aBRNO2": { + "yield": 1.0 } }, "A": 10000000000.0, @@ -662,8 +671,8 @@ "BRm": {} }, "products": { - "m": { - "yield": 2.0 + "NO2m": { + "yield": 1.0 }, "aBRCL": { "yield": 1.0 @@ -681,11 +690,11 @@ "BRm": {} }, "products": { - "": { - "yield": 2.0 + "aBR2": { + "yield": 1.0 }, - "m": { - "yield": 2.0 + "NO2m": { + "yield": 1.0 } }, "A": 25500.0, @@ -700,8 +709,8 @@ "CLm": {} }, "products": { - "m": { - "yield": 2.0 + "NO2m": { + "yield": 1.0 }, "aBRCL": { "yield": 1.0 @@ -719,11 +728,11 @@ "aHO": {} }, "products": { - "m": { - "yield": 3.0 + "CHOHSO3m": { + "yield": 1.0 }, - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 } }, "A": 300000000.0, @@ -738,8 +747,8 @@ "aO2": {} }, "products": { - "CHOHSO": { - "yield": 2.0 + "O2CHOHSO3m": { + "yield": 1.0 } }, "A": 2600000000.0, @@ -753,11 +762,11 @@ "O2CHOHSO3m": {} }, "products": { - "": { - "yield": 2.0 + "aHO2": { + "yield": 1.0 }, - "m": { - "yield": 3.0 + "CHOSO3m": { + "yield": 1.0 } }, "A": 17000.0, @@ -771,11 +780,11 @@ "O2CHOHSO3m": {} }, "products": { - "CHO": { - "yield": 2.0 + "aO2CHO": { + "yield": 1.0 }, - "m": { - "yield": 3.0 + "HSO3m": { + "yield": 1.0 } }, "A": 7000.0, @@ -790,10 +799,10 @@ "[aH2O]": {} }, "products": { - "m": { - "yield": 3.0 + "HSO3m": { + "yield": 1.0 }, - "": { + "aORA1": { "yield": 1.0 } }, @@ -809,8 +818,11 @@ "[aH2O]": {} }, "products": { - "": { - "yield": 2.0 + "aORA1": { + "yield": 1.0 + }, + "aHO2": { + "yield": 1.0 } }, "A": 44.32, @@ -826,11 +838,11 @@ "Hp": {} }, "products": { - "mm": { - "yield": 4.0 + "SO4mm": { + "yield": 1.0 }, - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 }, "Hp": { "yield": 2.0 @@ -848,14 +860,14 @@ "aO3": {} }, "products": { - "mm": { - "yield": 4.0 + "SO4mm": { + "yield": 1.0 }, "Hp": { "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 } }, "A": 42405757730857.71, @@ -870,11 +882,11 @@ "aO3": {} }, "products": { - "mm": { - "yield": 4.0 + "SO4mm": { + "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 } }, "A": 7.429735524861723e+16, @@ -889,8 +901,8 @@ "FEpp": {} }, "products": { - "m": { - "yield": 5.0 + "HSO5m": { + "yield": 1.0 }, "FEOHpp": { "yield": 1.0 @@ -908,8 +920,8 @@ "FEpp": {} }, "products": { - "m": { - "yield": 4.0 + "SO4m": { + "yield": 1.0 }, "FEOHpp": { "yield": 1.0 @@ -930,8 +942,8 @@ "FEOHpp": { "yield": 1.0 }, - "mm": { - "yield": 4.0 + "SO4mm": { + "yield": 1.0 }, "Hp": { "yield": 1.0 @@ -948,11 +960,11 @@ "SO5m": {} }, "products": { - "m": { - "yield": 4.0 - }, - "": { + "SO4m": { "yield": 2.0 + }, + "aO2": { + "yield": 1.0 } }, "A": 1353845691603.3787, @@ -967,8 +979,8 @@ "aHO2": {} }, "products": { - "O": { - "yield": 5.0 + "SO5O2Hm": { + "yield": 1.0 } }, "A": 1700000000.0, @@ -982,11 +994,11 @@ "SO5O2mm": {} }, "products": { - "m": { - "yield": 5.0 + "HSO5m": { + "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 }, "Hp": { "yield": -1.0 @@ -1004,8 +1016,8 @@ "aO2": {} }, "products": { - "m": { - "yield": 5.0 + "SO5m": { + "yield": 1.0 } }, "A": 2500000000.0, @@ -1020,8 +1032,8 @@ "[aH2O]": {} }, "products": { - "mm": { - "yield": 4.0 + "SO4mm": { + "yield": 1.0 }, "aHO": { "yield": 1.0 @@ -1062,11 +1074,11 @@ "aHO": {} }, "products": { - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 }, - "OH": { - "yield": 2.0 + "aCH2OH": { + "yield": 1.0 } }, "A": 7002790586.531466, @@ -1081,8 +1093,8 @@ "aO2": {} }, "products": { - "CH": { - "yield": 2.0 + "aO2CH2OH": { + "yield": 1.0 } }, "A": 2000000000.0, @@ -1096,11 +1108,11 @@ "aO2CH2OH": {} }, "products": { - "OH": { - "yield": 3.0 + "aCH3OH": { + "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 }, "aHCHO": { "yield": 1.0 @@ -1118,11 +1130,11 @@ "aHO": {} }, "products": { - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 }, - "CHOH": { - "yield": 3.0 + "aCH3CHOH": { + "yield": 1.0 } }, "A": 1900000000.0, @@ -1137,8 +1149,8 @@ "aO2": {} }, "products": { - "CH": { - "yield": 2.0 + "aO2CH3CHOH": { + "yield": 1.0 } }, "A": 2000000000.0, @@ -1155,8 +1167,8 @@ "aALD": { "yield": 1.0 }, - "": { - "yield": 2.0 + "aHO2": { + "yield": 1.0 } }, "A": 1713166492299.335, @@ -1171,11 +1183,11 @@ "aHO": {} }, "products": { - "": { - "yield": 2.0 + "aCHOH2": { + "yield": 1.0 }, - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 } }, "A": 30655705402.09484, @@ -1190,7 +1202,10 @@ "aO2": {} }, "products": { - "": { + "aHO2": { + "yield": 1.0 + }, + "aORA1": { "yield": 1.0 } }, @@ -1206,11 +1221,11 @@ "aHO": {} }, "products": { - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 }, - "COH": { - "yield": 3.0 + "aCH3COH2": { + "yield": 1.0 } }, "A": 1200000000.0, @@ -1225,11 +1240,11 @@ "aHO": {} }, "products": { - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 }, - "CO": { - "yield": 3.0 + "aCH3CO": { + "yield": 1.0 } }, "A": 3600000000.0, @@ -1244,11 +1259,11 @@ "aHO": {} }, "products": { - "H": { - "yield": 2.0 + "aCO2H": { + "yield": 1.0 }, - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 } }, "A": 3726553714.606836, @@ -1263,8 +1278,8 @@ "aHO": {} }, "products": { - "H": { - "yield": 2.0 + "aCO2H": { + "yield": 1.0 }, "OHm": { "yield": 1.0 @@ -1282,11 +1297,11 @@ "aHO": {} }, "products": { - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 }, - "COOH": { - "yield": 2.0 + "aCH2COOH": { + "yield": 1.0 } }, "A": 1301323951.4818943, @@ -1301,11 +1316,11 @@ "aHO": {} }, "products": { - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 }, - "COOm": { - "yield": 2.0 + "CH2COOm": { + "yield": 1.0 } }, "A": 42000577298.10133, @@ -1320,8 +1335,8 @@ "aO2": {} }, "products": { - "": { - "yield": 3.0 + "aACO3": { + "yield": 1.0 } }, "A": 1700000000.0, @@ -1335,14 +1350,14 @@ "aMO2": {} }, "products": { - "OH": { - "yield": 3.0 + "aCH3OH": { + "yield": 1.0 }, "aHCHO": { "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 } }, "A": 118968666270.98093, @@ -1356,11 +1371,11 @@ "aMO2": {} }, "products": { - "O": { - "yield": 3.0 - }, - "": { + "aCH3O": { "yield": 2.0 + }, + "aO2": { + "yield": 1.0 } }, "A": 57876648456.152885, @@ -1374,8 +1389,14 @@ "aACO3": {} }, "products": { - "": { + "aMO2": { "yield": 2.0 + }, + "aCO2": { + "yield": 2.0 + }, + "aO2": { + "yield": 1.0 } }, "A": 150000000.0, @@ -1390,11 +1411,11 @@ "HSO3m": {} }, "products": { - "": { + "aOP1": { "yield": 1.0 }, - "m": { - "yield": 3.0 + "SO3m": { + "yield": 1.0 } }, "A": 500000.0, @@ -1408,11 +1429,11 @@ "aETHPX": {} }, "products": { - "CH": { - "yield": 3.0 - }, - "": { + "aCH3CH2O": { "yield": 2.0 + }, + "aO2": { + "yield": 1.0 } }, "A": 8071922.343268531, @@ -1426,8 +1447,8 @@ "aCH3CH2O": {} }, "products": { - "CHOH": { - "yield": 3.0 + "aCH3CHOH": { + "yield": 1.0 } }, "A": 1000000.0, @@ -1442,8 +1463,11 @@ "HC2O4m": {} }, "products": { - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 + }, + "C2O4m": { + "yield": 1.0 } }, "A": 32000000.0, @@ -1461,8 +1485,8 @@ "OHm": { "yield": 1.0 }, - "O": { - "yield": 2.0 + "C2O4m": { + "yield": 1.0 } }, "A": 5300000.0, @@ -1477,11 +1501,11 @@ "aO2": {} }, "products": { - "": { + "aCO2": { "yield": 2.0 }, - "m": { - "yield": 2.0 + "O2m": { + "yield": 1.0 } }, "A": 2000000000.0, @@ -1496,11 +1520,11 @@ "aCHOH2CHOH2": {} }, "products": { - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 }, - "CHOH": { - "yield": 2.0 + "aCOH2CHOH2": { + "yield": 1.0 } }, "A": 178137994858.22678, @@ -1515,8 +1539,8 @@ "aO2": {} }, "products": { - "COH": { - "yield": 2.0 + "aO2COH2CHOH2": { + "yield": 1.0 } }, "A": 1380000000.0, @@ -1530,11 +1554,11 @@ "aO2COH2CHOH2": {} }, "products": { - "": { - "yield": 2.0 + "aHO2": { + "yield": 1.0 }, - "COOH": { - "yield": 2.0 + "aCHOH2COOH": { + "yield": 1.0 } }, "A": 2000000000.0, @@ -1549,11 +1573,11 @@ "aCHOH2COOH": {} }, "products": { - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 }, - "COOH": { - "yield": 2.0 + "aCOH2COOH": { + "yield": 1.0 } }, "A": 178137994858.22678, @@ -1568,8 +1592,8 @@ "aO2": {} }, "products": { - "COH": { - "yield": 2.0 + "aO2COH2COOH": { + "yield": 1.0 } }, "A": 2000000000.0, @@ -1583,11 +1607,11 @@ "aO2COH2COOH": {} }, "products": { - "": { - "yield": 2.0 + "aHO2": { + "yield": 1.0 }, - "C": { - "yield": 2.0 + "aH2C2O4": { + "yield": 1.0 } }, "A": 2000000000.0, @@ -1602,8 +1626,8 @@ "aO2": {} }, "products": { - "COH": { - "yield": 3.0 + "aCH3COH2OO": { + "yield": 1.0 } }, "A": 2000000000.0, @@ -1623,8 +1647,8 @@ "MCOOm": { "yield": 1.0 }, - "m": { - "yield": 2.0 + "O2m": { + "yield": 1.0 } }, "A": 100000.0, @@ -1638,8 +1662,8 @@ "aCH3O": {} }, "products": { - "OH": { - "yield": 2.0 + "aCH2OH": { + "yield": 1.0 } }, "A": 1000000.0, @@ -1654,8 +1678,8 @@ "aO2": {} }, "products": { - "CH": { - "yield": 2.0 + "O2CH2COOm": { + "yield": 1.0 } }, "A": 2000000000.0, @@ -1672,8 +1696,8 @@ "CHOH": { "yield": 2.0 }, - "O": { - "yield": 2.0 + "aH2O2": { + "yield": 1.0 } }, "A": 20000000.0, @@ -1688,11 +1712,11 @@ "aO2": {} }, "products": { - "": { - "yield": 2.0 + "aCO2": { + "yield": 1.0 }, - "m": { - "yield": 2.0 + "O2m": { + "yield": 1.0 } }, "A": 4000000000.0, @@ -1732,8 +1756,8 @@ "Hp": { "yield": 1.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 } }, "A": 13000000000.0, @@ -1754,8 +1778,8 @@ "Hp": { "yield": 1.0 }, - "m": { - "yield": 3.0 + "SO3m": { + "yield": 1.0 } }, "A": 650720568.7854763, @@ -1814,8 +1838,8 @@ "SO4m": {} }, "products": { - "mm": { - "yield": 4.0 + "SO4mm": { + "yield": 1.0 }, "aBR": { "yield": 1.0 @@ -1833,8 +1857,8 @@ "aNO3": {} }, "products": { - "m": { - "yield": 3.0 + "NO3m": { + "yield": 1.0 }, "aBR": { "yield": 1.0 @@ -1851,8 +1875,8 @@ "BR2m": {} }, "products": { - "": { - "yield": 2.0 + "aBR2": { + "yield": 1.0 }, "BRm": { "yield": 2.0 @@ -1895,8 +1919,8 @@ "Hp": { "yield": 1.0 }, - "": { - "yield": 2.0 + "aHO2": { + "yield": 1.0 } }, "A": 100000.0, @@ -1914,8 +1938,8 @@ "BRm": { "yield": 2.0 }, - "": { - "yield": 2.0 + "aO2": { + "yield": 1.0 }, "Hp": { "yield": 1.0 @@ -1939,8 +1963,8 @@ "Hp": { "yield": 1.0 }, - "m": { - "yield": 3.0 + "SO3m": { + "yield": 1.0 } }, "A": 685036875.6354121, @@ -1995,8 +2019,8 @@ "[aH2O]": {} }, "products": { - "CO": { - "yield": 2.0 + "aH2CO3": { + "yield": 1.0 } }, "A": 1300426356398.6077, @@ -2010,11 +2034,11 @@ "aH2CO3": {} }, "products": { - "": { - "yield": 2.0 + "aCO2": { + "yield": 1.0 }, - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 } }, "A": 1.3670434220265014e+17, @@ -2048,11 +2072,11 @@ "OHm": {} }, "products": { - "mm": { - "yield": 3.0 + "SO3mm": { + "yield": 1.0 }, - "OH": { - "yield": 2.0 + "aCH2OH2": { + "yield": 1.0 } }, "A": 475632147521.7825, @@ -2105,8 +2129,8 @@ "[aH2O]": {} }, "products": { - "p": { - "yield": 4.0 + "NH4p": { + "yield": 1.0 }, "OHm": { "yield": 1.0 @@ -2124,8 +2148,8 @@ "aHNO3": {} }, "products": { - "m": { - "yield": 3.0 + "NO3m": { + "yield": 1.0 }, "Hp": { "yield": 1.0 @@ -2143,8 +2167,8 @@ "aHONO": {} }, "products": { - "m": { - "yield": 2.0 + "NO2m": { + "yield": 1.0 }, "Hp": { "yield": 1.0 @@ -2163,8 +2187,8 @@ "[aH2O]": {} }, "products": { - "m": { - "yield": 3.0 + "HSO3m": { + "yield": 1.0 }, "Hp": { "yield": 1.0 @@ -2182,8 +2206,8 @@ "HSO3m": {} }, "products": { - "mm": { - "yield": 3.0 + "SO3mm": { + "yield": 1.0 }, "Hp": { "yield": 1.0 @@ -2204,8 +2228,8 @@ "Hp": { "yield": 1.0 }, - "mm": { - "yield": 4.0 + "SO4mm": { + "yield": 1.0 } }, "A": 0.0102, @@ -2259,8 +2283,8 @@ "[aH2O]": {} }, "products": { - "OH": { - "yield": 2.0 + "aCH2OH2": { + "yield": 1.0 } }, "A": 36.0, @@ -2276,8 +2300,8 @@ "[aH2O]": {} }, "products": { - "CHOH": { - "yield": 3.0 + "aCH3CHOH2": { + "yield": 1.0 } }, "A": 0.0246, @@ -2296,8 +2320,8 @@ "HMSm": { "yield": 1.0 }, - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 } }, "A": 200000000.0, @@ -2313,8 +2337,8 @@ "CLm": {} }, "products": { - "m": { - "yield": 3.0 + "NO3m": { + "yield": 1.0 }, "aCL": { "yield": 1.0 @@ -2333,8 +2357,8 @@ "[aH2O]": {} }, "products": { - "COH": { - "yield": 3.0 + "aCH3COH2": { + "yield": 1.0 } }, "A": 367.0, @@ -2352,8 +2376,8 @@ "Hp": { "yield": 1.0 }, - "CH": { - "yield": 2.0 + "O2CH2COOm": { + "yield": 1.0 } }, "A": 1.75e-05, @@ -2369,8 +2393,8 @@ "aH2CO3": {} }, "products": { - "m": { - "yield": 3.0 + "HCO3m": { + "yield": 1.0 }, "Hp": { "yield": 1.0 @@ -2390,8 +2414,8 @@ "aHO2": {} }, "products": { - "m": { - "yield": 2.0 + "O2m": { + "yield": 1.0 }, "Hp": { "yield": 1.0 @@ -2411,8 +2435,8 @@ "aHNO4": {} }, "products": { - "m": { - "yield": 4.0 + "NO4m": { + "yield": 1.0 }, "Hp": { "yield": 1.0 @@ -2433,8 +2457,8 @@ "aHO2": {} }, "products": { - "": { - "yield": 4.0 + "aHNO4": { + "yield": 1.0 } }, "A": 2200000000.0, @@ -2451,8 +2475,8 @@ "aSULF": {} }, "products": { - "m": { - "yield": 4.0 + "HSO4m": { + "yield": 1.0 }, "Hp": { "yield": 1.0 @@ -2495,8 +2519,8 @@ "CLm": {} }, "products": { - "m": { - "yield": 2.0 + "CL2m": { + "yield": 1.0 } }, "A": 140000.0, @@ -2514,8 +2538,8 @@ "BRm": {} }, "products": { - "m": { - "yield": 2.0 + "BR2m": { + "yield": 1.0 } }, "A": 632000.0, @@ -2555,8 +2579,8 @@ "aCL": { "yield": 1.0 }, - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 } }, "A": 5100000.0, @@ -2596,8 +2620,8 @@ "aBR": { "yield": 1.0 }, - "O": { - "yield": 2.0 + "[aH2O]": { + "yield": 1.0 } }, "A": 1800000000000.0, @@ -2617,8 +2641,8 @@ "Hp": { "yield": 1.0 }, - "m": { - "yield": 3.0 + "O3m": { + "yield": 1.0 } }, "A": 6.3e-09, @@ -2635,8 +2659,8 @@ "CHOHSO3m": {} }, "products": { - "mm": { - "yield": 3.0 + "CHOSO3mm": { + "yield": 1.0 }, "Hp": { "yield": 1.0 @@ -2659,8 +2683,8 @@ "Hp": { "yield": 1.0 }, - "O": { - "yield": 5.0 + "SO5O2mm": { + "yield": 1.0 } }, "A": 1.5e-05, @@ -2677,8 +2701,8 @@ "HC2O4m": {} }, "products": { - "O": { - "yield": 2.0 + "C2O4mm": { + "yield": 1.0 }, "Hp": { "yield": 1.0 @@ -2701,8 +2725,8 @@ "Hp": { "yield": 1.0 }, - "COOm": { - "yield": 2.0 + "CHOH2COOm": { + "yield": 1.0 } }, "A": 0.000316, @@ -2720,8 +2744,8 @@ "[aH2O]": {} }, "products": { - "CHOH": { - "yield": 2.0 + "aCHOH2CHOH2": { + "yield": 1.0 } }, "A": 3900.0, @@ -2739,8 +2763,8 @@ "C2O4mm": {} }, "products": { - "O": { - "yield": 2.0 + "FEC2O4p": { + "yield": 1.0 } }, "A": 2900000000.0, @@ -2758,8 +2782,8 @@ "C2O4mm": {} }, "products": { - "O": { - "yield": 2.0 + "FEC2O42m": { + "yield": 1.0 } }, "A": 6300000.0, @@ -2777,8 +2801,8 @@ "CLm": {} }, "products": { - "mm": { - "yield": 4.0 + "SO4mm": { + "yield": 1.0 }, "aCL": { "yield": 1.0 @@ -2795,21 +2819,21 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "CO2", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aCO2", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "O3", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aO3", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "HO2", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aHO2", "aerosol-phase water": "[aH2O]" }, { @@ -2823,14 +2847,14 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "H2O2", "aerosol phase": "cloud water", - "aerosol-phase species": "O", + "aerosol-phase species": "aH2O2", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NO2", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aNO2", "aerosol-phase water": "[aH2O]" }, { @@ -2844,28 +2868,28 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "HNO3", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aHNO3", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NO3", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aNO3", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "N2O5", "aerosol phase": "cloud water", - "aerosol-phase species": "O", + "aerosol-phase species": "aN2O5", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NH3", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aNH3", "aerosol-phase water": "[aH2O]" }, { @@ -2886,35 +2910,35 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "ORA1", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aORA1", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "SO2", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aSO2", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "OP1", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aOP1", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ORA2", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aORA2", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "MO2", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aMO2", "aerosol-phase water": "[aH2O]" }, { @@ -2935,7 +2959,7 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "CH3OH", "aerosol phase": "cloud water", - "aerosol-phase species": "OH", + "aerosol-phase species": "aCH3OH", "aerosol-phase water": "[aH2O]" }, { @@ -2949,14 +2973,14 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "BR2", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aBR2", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CL2", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aCL2", "aerosol-phase water": "[aH2O]" }, { @@ -2970,14 +2994,14 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "HNO4", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aHNO4", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "ACO3", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aACO3", "aerosol-phase water": "[aH2O]" }, { @@ -2991,21 +3015,21 @@ "type": "HL_PHASE_TRANSFER", "gas-phase species": "[O2]", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aO2", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "CLNO2", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aCLNO2", "aerosol-phase water": "[aH2O]" }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "BRNO2", "aerosol phase": "cloud water", - "aerosol-phase species": "", + "aerosol-phase species": "aBRNO2", "aerosol-phase water": "[aH2O]" }, { @@ -3028,122 +3052,118 @@ "name": "cloud water", "type": "AERO_PHASE", "species": [ - "", - "FEpp", - "CH", - "aSO2", - "CHOHSO", - "HCOOm", + "aHNO3", + "SO5O2Hm", + "SO", + "SO3mm", + "aH2O2", + "aCO2H", + "aBR2", + "FEOHpp", + "SO5m", + "aNO2", + "HSO3m", + "SO3m", + "NH4p", + "CL2m", + "NO3m", + "aHNO4", + "CO2m", + "aGLY", + "aCOH2COOH", + "aCH3COH2OO", + "aCHOH2", + "aHOCL", + "FEC2O42m", + "aALD", + "CHOSO3m", + "aCL2", + "aBRNO2", + "[aH2O]", + "MCOOm", "HC2O4m", - "FEppp", - "CLm", + "O2CHOHSO3m", "FEOpp", - "aMO2", - "aO2CH2OH", - "O2m", - "aCH2OH2", - "HSO4m", - "aH2O2", - "COOH", - "aHOBR", + "O2CH2COOm", + "CLm", + "SO4m", + "aH2C2O4", + "aO2", + "CUpp", + "NO2m", + "aBR", "SO4mm", + "BROHm", + "aN2O5", + "aO2COH2CHOH2", + "CHOSO3mm", + "aHOBR", "aCH3CH2O", - "p", - "O2CHOHSO3m", - "H", - "aSULF", - "CHO", + "aCH3OH", + "FEppp", "NO4m", - "SO5O2mm", - "CLOHm", + "aCH2OH", + "C2O4m", + "aNO3", + "aOP1", + "CHOHSO3m", "aHO3", - "aCH3COH2OO", - "aHNO3", - "SO", - "aORA2", + "aCH3CHOH2", + "aHONO", + "CHOH2COOm", + "SO5O2mm", + "aETOH", + "CH2COOm", + "aO2COH2COOH", + "aCH2COOH", + "aCLNO2", + "BRm", + "O2m", + "aCHOH2CHOH2", + "aORA1", + "aO2CHO", + "aCH3CHOH", + "NO2p", + "BR2m", + "aHCHO", + "FEpp", + "aNO", + "aH2CO3", + "aCH2OH2", + "aHCL", + "C2O4mm", + "HSO4m", "aHO", - "aBRCL", "aCL", - "aO2COH2CHOH2", - "aCHOH2COOH", - "aNH3", - "HMSm", - "SO3mm", - "CHOSO3m", - "mm", - "OHm", - "aHNO4", - "aETHPX", + "aCO2", + "HCO3m", "aCH3O", - "aCH3CO", - "aO2", - "aO2CHO", - "MCOOm", - "aCLNO2", "FEC2O4p", - "aBR2", - "aCH2OH", - "aCO2", - "C2O4mm", - "O2CH2COOm", - "aH2CO3", - "CUp", - "CHOHSO3m", - "aCL2", - "CO", - "aETOH", - "aALD", - "aNO3", - "NO2p", - "aCOH2CHOH2", - "HSO3m", - "Hp", - "aBRNO2", - "BRm", - "aCH2COOH", - "aN2O5", - "aBR", - "aACO3", - "CL2m", - "C", - "aHOCL", - "[aH2O]", - "CH2COOm", "aO2CH3CHOH", - "HSO5m", - "aGLY", - "aHCL", - "aHONO", - "SO5O2Hm", - "aO3", - "aHO2", - "O", - "aCH3OH", - "OH", - "aHCHO", + "aBRCL", + "aACO3", "CHOH", - "BR2m", - "aORA1", - "aCOH2COOH", - "BROHm", - "aCHOH2", - "COOm", "aCH3COH2", - "m", - "aCH3CHOH", - "aCH3CHOH2", - "aO2COH2COOH", - "aNO", - "aCHOH2CHOH2", - "CUpp", - "SO5m", - "COH", - "CO2m", - "aNO2", - "C2O4m", - "FEOHpp", - "SO3m", - "SO4m" + "CUp", + "aHO2", + "aCHOH2COOH", + "aMO2", + "aETHPX", + "Hp", + "aSULF", + "aCOH2CHOH2", + "aO3", + "O3m", + "aSO2", + "HSO5m", + "HCOOm", + "aORA2", + "aCH3CO", + "CLOHm", + "OHm", + "aNH3", + "HMSm", + "aO2CH2OH" ] }, { diff --git a/capram_convert/species.json b/capram_convert/species.json index 99f5515b..a852c9e7 100644 --- a/capram_convert/species.json +++ b/capram_convert/species.json @@ -9,7 +9,7 @@ "N star": 1.0 }, { - "name": "", + "name": "aCO2", "type": "CHEM_SPEC" }, { @@ -20,6 +20,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aO3", + "type": "CHEM_SPEC" + }, { "name": "HO2", "type": "CHEM_SPEC", @@ -28,6 +32,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aHO2", + "type": "CHEM_SPEC" + }, { "name": "HO", "type": "CHEM_SPEC", @@ -49,7 +57,7 @@ "N star": 1.0 }, { - "name": "O", + "name": "aH2O2", "type": "CHEM_SPEC" }, { @@ -60,6 +68,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aNO2", + "type": "CHEM_SPEC" + }, { "name": "HONO", "type": "CHEM_SPEC", @@ -80,6 +92,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aHNO3", + "type": "CHEM_SPEC" + }, { "name": "NO3", "type": "CHEM_SPEC", @@ -88,6 +104,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aNO3", + "type": "CHEM_SPEC" + }, { "name": "N2O5", "type": "CHEM_SPEC", @@ -96,6 +116,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aN2O5", + "type": "CHEM_SPEC" + }, { "name": "NH3", "type": "CHEM_SPEC", @@ -104,6 +128,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aNH3", + "type": "CHEM_SPEC" + }, { "name": "HCL", "type": "CHEM_SPEC", @@ -136,6 +164,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aORA1", + "type": "CHEM_SPEC" + }, { "name": "SO2", "type": "CHEM_SPEC", @@ -144,6 +176,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aSO2", + "type": "CHEM_SPEC" + }, { "name": "OP1", "type": "CHEM_SPEC", @@ -152,6 +188,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aOP1", + "type": "CHEM_SPEC" + }, { "name": "ORA2", "type": "CHEM_SPEC", @@ -160,6 +200,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aORA2", + "type": "CHEM_SPEC" + }, { "name": "MO2", "type": "CHEM_SPEC", @@ -168,6 +212,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aMO2", + "type": "CHEM_SPEC" + }, { "name": "ETHPX", "type": "CHEM_SPEC", @@ -201,7 +249,7 @@ "N star": 1.0 }, { - "name": "OH", + "name": "aCH3OH", "type": "CHEM_SPEC" }, { @@ -224,6 +272,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aBR2", + "type": "CHEM_SPEC" + }, { "name": "CL2", "type": "CHEM_SPEC", @@ -232,6 +284,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aCL2", + "type": "CHEM_SPEC" + }, { "name": "SULF", "type": "CHEM_SPEC", @@ -252,6 +308,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aHNO4", + "type": "CHEM_SPEC" + }, { "name": "ACO3", "type": "CHEM_SPEC", @@ -260,6 +320,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aACO3", + "type": "CHEM_SPEC" + }, { "name": "GLY", "type": "CHEM_SPEC", @@ -280,6 +344,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aO2", + "type": "CHEM_SPEC" + }, { "name": "CLNO2", "type": "CHEM_SPEC", @@ -288,6 +356,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aCLNO2", + "type": "CHEM_SPEC" + }, { "name": "BRNO2", "type": "CHEM_SPEC", @@ -296,6 +368,10 @@ "diffusion coeff [m2 s-1]": 1.0, "N star": 1.0 }, + { + "name": "aBRNO2", + "type": "CHEM_SPEC" + }, { "name": "BRCL", "type": "CHEM_SPEC", @@ -337,15 +413,15 @@ "type": "CHEM_SPEC" }, { - "name": "aH2O2", + "name": "FEC2O42m", "type": "CHEM_SPEC" }, { - "name": "FEC2O42m", + "name": "C2O4mm", "type": "CHEM_SPEC" }, { - "name": "m", + "name": "CO2m", "type": "CHEM_SPEC" }, { @@ -365,7 +441,7 @@ "type": "CHEM_SPEC" }, { - "name": "aHO2", + "name": "[aH2O]", "type": "CHEM_SPEC" }, { @@ -373,7 +449,7 @@ "type": "CHEM_SPEC" }, { - "name": "aO3", + "name": "O3m", "type": "CHEM_SPEC" }, { @@ -385,7 +461,7 @@ "type": "CHEM_SPEC" }, { - "name": "aO2", + "name": "SO3m", "type": "CHEM_SPEC" }, { @@ -400,48 +476,32 @@ "name": "CLOHm", "type": "CHEM_SPEC" }, - { - "name": "aN2O5", - "type": "CHEM_SPEC" - }, - { - "name": "p", - "type": "CHEM_SPEC" - }, { "name": "NO2p", "type": "CHEM_SPEC" }, - { - "name": "[aH2O]", - "type": "CHEM_SPEC" - }, - { - "name": "aNO3", - "type": "CHEM_SPEC" - }, { "name": "SO4mm", "type": "CHEM_SPEC" }, { - "name": "NO4m", + "name": "SO4m", "type": "CHEM_SPEC" }, { - "name": "aHNO4", + "name": "NO4m", "type": "CHEM_SPEC" }, { - "name": "BRm", + "name": "NO2m", "type": "CHEM_SPEC" }, { - "name": "aCLNO2", + "name": "HSO4m", "type": "CHEM_SPEC" }, { - "name": "aBRNO2", + "name": "BRm", "type": "CHEM_SPEC" }, { @@ -452,18 +512,10 @@ "name": "CHOHSO3m", "type": "CHEM_SPEC" }, - { - "name": "CHOHSO", - "type": "CHEM_SPEC" - }, { "name": "O2CHOHSO3m", "type": "CHEM_SPEC" }, - { - "name": "CHO", - "type": "CHEM_SPEC" - }, { "name": "CHOSO3m", "type": "CHEM_SPEC" @@ -472,10 +524,6 @@ "name": "aO2CHO", "type": "CHEM_SPEC" }, - { - "name": "mm", - "type": "CHEM_SPEC" - }, { "name": "SO3mm", "type": "CHEM_SPEC" @@ -489,41 +537,25 @@ "type": "CHEM_SPEC" }, { - "name": "SO4m", + "name": "SO5O2Hm", "type": "CHEM_SPEC" }, { "name": "SO5O2mm", "type": "CHEM_SPEC" }, - { - "name": "SO3m", - "type": "CHEM_SPEC" - }, { "name": "SO", "type": "CHEM_SPEC" }, - { - "name": "aCH3OH", - "type": "CHEM_SPEC" - }, { "name": "aCH2OH", "type": "CHEM_SPEC" }, - { - "name": "CH", - "type": "CHEM_SPEC" - }, { "name": "aO2CH2OH", "type": "CHEM_SPEC" }, - { - "name": "CHOH", - "type": "CHEM_SPEC" - }, { "name": "aCH3CHOH", "type": "CHEM_SPEC" @@ -545,19 +577,15 @@ "type": "CHEM_SPEC" }, { - "name": "COH", - "type": "CHEM_SPEC" - }, - { - "name": "CO", + "name": "aCH3COH2", "type": "CHEM_SPEC" }, { - "name": "aORA1", + "name": "aCH3CO", "type": "CHEM_SPEC" }, { - "name": "H", + "name": "aCO2H", "type": "CHEM_SPEC" }, { @@ -565,11 +593,7 @@ "type": "CHEM_SPEC" }, { - "name": "aORA2", - "type": "CHEM_SPEC" - }, - { - "name": "COOH", + "name": "aCH2COOH", "type": "CHEM_SPEC" }, { @@ -577,19 +601,11 @@ "type": "CHEM_SPEC" }, { - "name": "COOm", - "type": "CHEM_SPEC" - }, - { - "name": "aCH2COOH", - "type": "CHEM_SPEC" - }, - { - "name": "aMO2", + "name": "CH2COOm", "type": "CHEM_SPEC" }, { - "name": "aACO3", + "name": "aCH3O", "type": "CHEM_SPEC" }, { @@ -600,10 +616,6 @@ "name": "HC2O4m", "type": "CHEM_SPEC" }, - { - "name": "C2O4mm", - "type": "CHEM_SPEC" - }, { "name": "C2O4m", "type": "CHEM_SPEC" @@ -633,41 +645,25 @@ "type": "CHEM_SPEC" }, { - "name": "C", - "type": "CHEM_SPEC" - }, - { - "name": "aCH3COH2", + "name": "aH2C2O4", "type": "CHEM_SPEC" }, { "name": "aCH3COH2OO", "type": "CHEM_SPEC" }, - { - "name": "aCH3O", - "type": "CHEM_SPEC" - }, - { - "name": "CH2COOm", - "type": "CHEM_SPEC" - }, { "name": "O2CH2COOm", "type": "CHEM_SPEC" }, { - "name": "CO2m", + "name": "CHOH", "type": "CHEM_SPEC" }, { "name": "CL2m", "type": "CHEM_SPEC" }, - { - "name": "aCL2", - "type": "CHEM_SPEC" - }, { "name": "aHOCL", "type": "CHEM_SPEC" @@ -680,10 +676,6 @@ "name": "BR2m", "type": "CHEM_SPEC" }, - { - "name": "aBR2", - "type": "CHEM_SPEC" - }, { "name": "aHOBR", "type": "CHEM_SPEC" @@ -692,28 +684,12 @@ "name": "BROHm", "type": "CHEM_SPEC" }, - { - "name": "aCO2", - "type": "CHEM_SPEC" - }, { "name": "aH2CO3", "type": "CHEM_SPEC" }, { - "name": "aNH3", - "type": "CHEM_SPEC" - }, - { - "name": "aHNO3", - "type": "CHEM_SPEC" - }, - { - "name": "aSO2", - "type": "CHEM_SPEC" - }, - { - "name": "HSO4m", + "name": "NH4p", "type": "CHEM_SPEC" }, { @@ -721,15 +697,15 @@ "type": "CHEM_SPEC" }, { - "name": "aCH3CO", + "name": "HCO3m", "type": "CHEM_SPEC" }, { - "name": "aNO2", + "name": "CHOSO3mm", "type": "CHEM_SPEC" }, { - "name": "SO5O2Hm", + "name": "CHOH2COOm", "type": "CHEM_SPEC" }, { From c3a8b60bb3737e533093db4c126b3e1f068307cf Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 14:07:52 -0500 Subject: [PATCH 20/24] combining reactants --- capram_convert/convert.py | 57 +- capram_convert/mechanism.json | 1188 +++++++++++++++++++++++---------- 2 files changed, 885 insertions(+), 360 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index 778c6d89..0c22930f 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -56,7 +56,7 @@ def parse_reactants_products(line): #TODO: now, go through the lists of products and reactants and combine like species # also, sometimes the list of producdts is like CL2m + [aH2O] = Hp + CLm + CLm + aHO # this should end up being represented as if it were written like CL2m + [aH2O] = Hp + 2CLm + aHO - return reactants, convert_products_to_yield(products) + return convert_reactants_to_quantity(reactants), convert_products_to_yield(products) def combine_stoichiometric_coeffs(species): # given this: O2m + FEpp = FEppp + aH2O2 -2.0 Hp @@ -71,6 +71,32 @@ def combine_stoichiometric_coeffs(species): return result +def convert_reactants_to_quantity(reactants): + # first, combine duplicated products + react = {} + for reactant in reactants: + existing = react.get(reactant, 0.0) + quantity = 1.0 + + # check if this has a coefficient + match = stoichiemetric_coefficient_pattern.search(reactant) + if match: + # it does! add that coefficient as the yeidl + quantity = float(match.group(1)) + print(reactant, match.groups()) + # also, use the matched text as the species name so that the species name doesn't include the yield + reactant = match.group(2) + react[reactant] = existing + quantity + + reactants = [] + for name, quantity in react.items(): + spec = dict(name=name, type="CHEM_SPEC", ) + spec["qty"] = quantity + reactants.append(spec) + + # now, go through each product and, when there's a + return reactants + def convert_products_to_yield(products): # first, combine duplicated products prods = {} @@ -83,7 +109,6 @@ def convert_products_to_yield(products): if match: # it does! add that coefficient as the yeidl _yield = float(match.group(1)) - print(product, match.groups()) # also, use the matched text as the species name so that the species name doesn't include the yield product = match.group(2) prods[product] = existing + _yield @@ -147,19 +172,19 @@ def convert_products_to_yield(products): aerosol_phase_species.add(aero_phase['name']) - spec = dict(name=gas_phase, type="CHEM_SPEC") + spec = dict(name=gas_phase['name'], type="CHEM_SPEC") spec["HLC(298K) [M Pa-1]"] = item['A'] spec["HLC exp factor [K]"] = item['B'] spec["diffusion coeff [m2 s-1]"] = 1.00 # TODO: replace spec["N star"] = 1.00 # TODO: replace - species[gas_phase] = spec + species[gas_phase['name']] = spec species[aero_phase['name']] = dict(name=aero_phase['name'], type="CHEM_SPEC") henrys_law_reactions.append( { "type" : "HL_PHASE_TRANSFER", - "gas-phase species" : gas_phase, + "gas-phase species" : gas_phase['name'], "aerosol phase" : aerosol_phase_name, "aerosol-phase species" : aero_phase['name'], "aerosol-phase water" : "[aH2O]" @@ -171,10 +196,10 @@ def convert_products_to_yield(products): for collection in [aqua_photo, aqua_temp, diss_with_c, diss_without_c]: for item in collection: - for name in item['reactants']: - if name not in species: - spec = dict(name=name, type="CHEM_SPEC") - species[name] = spec + for reactant in item['reactants']: + if reactant['name'] not in species: + spec = dict(name=reactant['name'], type="CHEM_SPEC") + species[reactant['name']] = spec for product in item['products']: if product['name'] not in species: spec = dict(name=product['name'], type="CHEM_SPEC") @@ -191,7 +216,7 @@ def convert_products_to_yield(products): { "type": "PHOTOLYSIS", "reactants": { - reactant: {} for reactant in reaction["reactants"] + reactant['name']: { 'qty': reactant['qty'] } for reactant in reaction["reactants"] }, "products": { product['name']: { 'yield': product['yield'] } for product in reaction["products"] @@ -226,7 +251,7 @@ def convert_products_to_yield(products): { "type": "ARRHENIUS", "reactants": { - reactant: {} for reactant in reaction["reactants"] + reactant['name']: { 'qty': reactant['qty'] } for reactant in reaction["reactants"] }, "products": { product['name']: { 'yield': product['yield'] } for product in reaction["products"] @@ -237,7 +262,7 @@ def convert_products_to_yield(products): "aerosol-phase water" : "H2O_aq" } ) - aerosol_phase_species.update(reaction["reactants"]) + aerosol_phase_species.update([ reactant['name'] for reactant in reaction['reactants']]) aerosol_phase_species.update([ product['name'] for product in reaction['products']]) @@ -247,7 +272,7 @@ def convert_products_to_yield(products): { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - reactant: {} for reactant in reaction["reactants"] + reactant['name']: { 'qty': reactant['qty'] } for reactant in reaction["reactants"] }, "products": { product['name']: { 'yield': product['yield'] } for product in reaction["products"] @@ -259,7 +284,7 @@ def convert_products_to_yield(products): "aerosol-phase water" : "H2O_aq" } ) - aerosol_phase_species.update(reaction["reactants"]) + aerosol_phase_species.update([ reactant['name'] for reactant in reaction['reactants']]) aerosol_phase_species.update([ product['name'] for product in reaction['products']]) for reaction in diss_without_c: @@ -268,7 +293,7 @@ def convert_products_to_yield(products): { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - reactant: {} for reactant in reaction["reactants"] + reactant['name']: { 'qty': reactant['qty'] } for reactant in reaction["reactants"] }, "products": { product['name']: { 'yield': product['yield'] } for product in reaction["products"] @@ -281,7 +306,7 @@ def convert_products_to_yield(products): } ] ) - aerosol_phase_species.update(reaction["reactants"]) + aerosol_phase_species.update([ reactant['name'] for reactant in reaction['reactants']]) aerosol_phase_species.update([ product['name'] for product in reaction['products']]) mechanisms = { diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json index 0f7dabe4..95afc8d3 100644 --- a/capram_convert/mechanism.json +++ b/capram_convert/mechanism.json @@ -8,7 +8,9 @@ { "type": "PHOTOLYSIS", "reactants": { - "FEOHpp": {} + "FEOHpp": { + "qty": 1.0 + } }, "products": { "FEpp": { @@ -22,7 +24,9 @@ { "type": "PHOTOLYSIS", "reactants": { - "NO3m": {} + "NO3m": { + "qty": 1.0 + } }, "products": { "aNO2": { @@ -39,7 +43,9 @@ { "type": "PHOTOLYSIS", "reactants": { - "aH2O2": {} + "aH2O2": { + "qty": 1.0 + } }, "products": { "aHO": { @@ -50,7 +56,9 @@ { "type": "PHOTOLYSIS", "reactants": { - "FEC2O42m": {} + "FEC2O42m": { + "qty": 1.0 + } }, "products": { "FEpp": { @@ -70,8 +78,12 @@ { "type": "ARRHENIUS", "reactants": { - "aH2O2": {}, - "FEpp": {} + "aH2O2": { + "qty": 1.0 + }, + "FEpp": { + "qty": 1.0 + } }, "products": { "FEppp": { @@ -92,8 +104,12 @@ { "type": "ARRHENIUS", "reactants": { - "aH2O2": {}, - "CUp": {} + "aH2O2": { + "qty": 1.0 + }, + "CUp": { + "qty": 1.0 + } }, "products": { "CUpp": { @@ -114,8 +130,12 @@ { "type": "ARRHENIUS", "reactants": { - "O2m": {}, - "FEppp": {} + "O2m": { + "qty": 1.0 + }, + "FEppp": { + "qty": 1.0 + } }, "products": { "FEpp": { @@ -133,8 +153,12 @@ { "type": "ARRHENIUS", "reactants": { - "aHO2": {}, - "FEOHpp": {} + "aHO2": { + "qty": 1.0 + }, + "FEOHpp": { + "qty": 1.0 + } }, "products": { "FEpp": { @@ -155,8 +179,12 @@ { "type": "ARRHENIUS", "reactants": { - "O2m": {}, - "FEOHpp": {} + "O2m": { + "qty": 1.0 + }, + "FEOHpp": { + "qty": 1.0 + } }, "products": { "FEpp": { @@ -177,8 +205,12 @@ { "type": "ARRHENIUS", "reactants": { - "O2m": {}, - "FEpp": {} + "O2m": { + "qty": 1.0 + }, + "FEpp": { + "qty": 1.0 + } }, "products": { "FEppp": { @@ -199,8 +231,12 @@ { "type": "ARRHENIUS", "reactants": { - "aHO2": {}, - "FEpp": {} + "aHO2": { + "qty": 1.0 + }, + "FEpp": { + "qty": 1.0 + } }, "products": { "FEppp": { @@ -221,8 +257,12 @@ { "type": "ARRHENIUS", "reactants": { - "aHO": {}, - "FEpp": {} + "aHO": { + "qty": 1.0 + }, + "FEpp": { + "qty": 1.0 + } }, "products": { "FEOHpp": { @@ -237,8 +277,12 @@ { "type": "ARRHENIUS", "reactants": { - "O2m": {}, - "CUp": {} + "O2m": { + "qty": 1.0 + }, + "CUp": { + "qty": 1.0 + } }, "products": { "CUpp": { @@ -259,8 +303,12 @@ { "type": "ARRHENIUS", "reactants": { - "aHO2": {}, - "CUp": {} + "aHO2": { + "qty": 1.0 + }, + "CUp": { + "qty": 1.0 + } }, "products": { "CUpp": { @@ -281,8 +329,12 @@ { "type": "ARRHENIUS", "reactants": { - "aHO2": {}, - "CUpp": {} + "aHO2": { + "qty": 1.0 + }, + "CUpp": { + "qty": 1.0 + } }, "products": { "CUp": { @@ -303,8 +355,12 @@ { "type": "ARRHENIUS", "reactants": { - "O2m": {}, - "CUpp": {} + "O2m": { + "qty": 1.0 + }, + "CUpp": { + "qty": 1.0 + } }, "products": { "CUp": { @@ -322,8 +378,12 @@ { "type": "ARRHENIUS", "reactants": { - "FEppp": {}, - "CUp": {} + "FEppp": { + "qty": 1.0 + }, + "CUp": { + "qty": 1.0 + } }, "products": { "FEpp": { @@ -341,8 +401,12 @@ { "type": "ARRHENIUS", "reactants": { - "FEOHpp": {}, - "CUp": {} + "FEOHpp": { + "qty": 1.0 + }, + "CUp": { + "qty": 1.0 + } }, "products": { "FEpp": { @@ -363,8 +427,12 @@ { "type": "ARRHENIUS", "reactants": { - "aO3": {}, - "O2m": {} + "aO3": { + "qty": 1.0 + }, + "O2m": { + "qty": 1.0 + } }, "products": { "O3m": { @@ -382,7 +450,9 @@ { "type": "ARRHENIUS", "reactants": { - "aHO3": {} + "aHO3": { + "qty": 1.0 + } }, "products": { "aHO": { @@ -400,8 +470,12 @@ { "type": "ARRHENIUS", "reactants": { - "aH2O2": {}, - "aHO": {} + "aH2O2": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } }, "products": { "aHO2": { @@ -419,8 +493,12 @@ { "type": "ARRHENIUS", "reactants": { - "HSO3m": {}, - "aHO": {} + "HSO3m": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } }, "products": { "SO3m": { @@ -438,8 +516,12 @@ { "type": "ARRHENIUS", "reactants": { - "CUp": {}, - "aO2": {} + "CUp": { + "qty": 1.0 + }, + "aO2": { + "qty": 1.0 + } }, "products": { "CUpp": { @@ -457,8 +539,12 @@ { "type": "ARRHENIUS", "reactants": { - "FEpp": {}, - "aO3": {} + "FEpp": { + "qty": 1.0 + }, + "aO3": { + "qty": 1.0 + } }, "products": { "FEOpp": { @@ -476,8 +562,12 @@ { "type": "ARRHENIUS", "reactants": { - "FEOpp": {}, - "CLm": {} + "FEOpp": { + "qty": 1.0 + }, + "CLm": { + "qty": 1.0 + } }, "products": { "FEppp": { @@ -498,8 +588,12 @@ { "type": "ARRHENIUS", "reactants": { - "FEOpp": {}, - "FEpp": {} + "FEOpp": { + "qty": 1.0 + }, + "FEpp": { + "qty": 1.0 + } }, "products": { "FEppp": { @@ -517,7 +611,9 @@ { "type": "ARRHENIUS", "reactants": { - "aN2O5": {} + "aN2O5": { + "qty": 1.0 + } }, "products": { "NO2p": { @@ -535,8 +631,12 @@ { "type": "ARRHENIUS", "reactants": { - "NO2p": {}, - "[aH2O]": {} + "NO2p": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "NO3m": { @@ -554,8 +654,12 @@ { "type": "ARRHENIUS", "reactants": { - "aNO3": {}, - "HSO3m": {} + "aNO3": { + "qty": 1.0 + }, + "HSO3m": { + "qty": 1.0 + } }, "products": { "NO3m": { @@ -576,8 +680,12 @@ { "type": "ARRHENIUS", "reactants": { - "aNO3": {}, - "SO4mm": {} + "aNO3": { + "qty": 1.0 + }, + "SO4mm": { + "qty": 1.0 + } }, "products": { "NO3m": { @@ -595,7 +703,9 @@ { "type": "ARRHENIUS", "reactants": { - "NO4m": {} + "NO4m": { + "qty": 1.0 + } }, "products": { "NO2m": { @@ -613,8 +723,12 @@ { "type": "ARRHENIUS", "reactants": { - "aHNO4": {}, - "HSO3m": {} + "aHNO4": { + "qty": 1.0 + }, + "HSO3m": { + "qty": 1.0 + } }, "products": { "HSO4m": { @@ -635,8 +749,12 @@ { "type": "ARRHENIUS", "reactants": { - "NO2p": {}, - "CLm": {} + "NO2p": { + "qty": 1.0 + }, + "CLm": { + "qty": 1.0 + } }, "products": { "aCLNO2": { @@ -651,8 +769,12 @@ { "type": "ARRHENIUS", "reactants": { - "NO2p": {}, - "BRm": {} + "NO2p": { + "qty": 1.0 + }, + "BRm": { + "qty": 1.0 + } }, "products": { "aBRNO2": { @@ -667,8 +789,12 @@ { "type": "ARRHENIUS", "reactants": { - "aCLNO2": {}, - "BRm": {} + "aCLNO2": { + "qty": 1.0 + }, + "BRm": { + "qty": 1.0 + } }, "products": { "NO2m": { @@ -686,8 +812,12 @@ { "type": "ARRHENIUS", "reactants": { - "aBRNO2": {}, - "BRm": {} + "aBRNO2": { + "qty": 1.0 + }, + "BRm": { + "qty": 1.0 + } }, "products": { "aBR2": { @@ -705,8 +835,12 @@ { "type": "ARRHENIUS", "reactants": { - "aBRNO2": {}, - "CLm": {} + "aBRNO2": { + "qty": 1.0 + }, + "CLm": { + "qty": 1.0 + } }, "products": { "NO2m": { @@ -724,8 +858,12 @@ { "type": "ARRHENIUS", "reactants": { - "HMSm": {}, - "aHO": {} + "HMSm": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } }, "products": { "CHOHSO3m": { @@ -743,8 +881,12 @@ { "type": "ARRHENIUS", "reactants": { - "CHOHSO3m": {}, - "aO2": {} + "CHOHSO3m": { + "qty": 1.0 + }, + "aO2": { + "qty": 1.0 + } }, "products": { "O2CHOHSO3m": { @@ -759,7 +901,9 @@ { "type": "ARRHENIUS", "reactants": { - "O2CHOHSO3m": {} + "O2CHOHSO3m": { + "qty": 1.0 + } }, "products": { "aHO2": { @@ -777,7 +921,9 @@ { "type": "ARRHENIUS", "reactants": { - "O2CHOHSO3m": {} + "O2CHOHSO3m": { + "qty": 1.0 + } }, "products": { "aO2CHO": { @@ -795,8 +941,12 @@ { "type": "ARRHENIUS", "reactants": { - "CHOSO3m": {}, - "[aH2O]": {} + "CHOSO3m": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "HSO3m": { @@ -814,8 +964,12 @@ { "type": "ARRHENIUS", "reactants": { - "aO2CHO": {}, - "[aH2O]": {} + "aO2CHO": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "aORA1": { @@ -833,9 +987,15 @@ { "type": "ARRHENIUS", "reactants": { - "HSO3m": {}, - "aH2O2": {}, - "Hp": {} + "HSO3m": { + "qty": 1.0 + }, + "aH2O2": { + "qty": 1.0 + }, + "Hp": { + "qty": 1.0 + } }, "products": { "SO4mm": { @@ -856,8 +1016,12 @@ { "type": "ARRHENIUS", "reactants": { - "HSO3m": {}, - "aO3": {} + "HSO3m": { + "qty": 1.0 + }, + "aO3": { + "qty": 1.0 + } }, "products": { "SO4mm": { @@ -878,8 +1042,12 @@ { "type": "ARRHENIUS", "reactants": { - "SO3mm": {}, - "aO3": {} + "SO3mm": { + "qty": 1.0 + }, + "aO3": { + "qty": 1.0 + } }, "products": { "SO4mm": { @@ -897,8 +1065,12 @@ { "type": "ARRHENIUS", "reactants": { - "SO5m": {}, - "FEpp": {} + "SO5m": { + "qty": 1.0 + }, + "FEpp": { + "qty": 1.0 + } }, "products": { "HSO5m": { @@ -916,8 +1088,12 @@ { "type": "ARRHENIUS", "reactants": { - "HSO5m": {}, - "FEpp": {} + "HSO5m": { + "qty": 1.0 + }, + "FEpp": { + "qty": 1.0 + } }, "products": { "SO4m": { @@ -935,8 +1111,12 @@ { "type": "ARRHENIUS", "reactants": { - "FEpp": {}, - "SO4m": {} + "FEpp": { + "qty": 1.0 + }, + "SO4m": { + "qty": 1.0 + } }, "products": { "FEOHpp": { @@ -957,7 +1137,9 @@ { "type": "ARRHENIUS", "reactants": { - "SO5m": {} + "SO5m": { + "qty": 2.0 + } }, "products": { "SO4m": { @@ -975,8 +1157,12 @@ { "type": "ARRHENIUS", "reactants": { - "SO5m": {}, - "aHO2": {} + "SO5m": { + "qty": 1.0 + }, + "aHO2": { + "qty": 1.0 + } }, "products": { "SO5O2Hm": { @@ -991,7 +1177,9 @@ { "type": "ARRHENIUS", "reactants": { - "SO5O2mm": {} + "SO5O2mm": { + "qty": 1.0 + } }, "products": { "HSO5m": { @@ -1012,8 +1200,12 @@ { "type": "ARRHENIUS", "reactants": { - "SO3m": {}, - "aO2": {} + "SO3m": { + "qty": 1.0 + }, + "aO2": { + "qty": 1.0 + } }, "products": { "SO5m": { @@ -1028,8 +1220,12 @@ { "type": "ARRHENIUS", "reactants": { - "SO4m": {}, - "[aH2O]": {} + "SO4m": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "SO4mm": { @@ -1050,9 +1246,15 @@ { "type": "ARRHENIUS", "reactants": { - "HSO5m": {}, - "HSO3m": {}, - "Hp": {} + "HSO5m": { + "qty": 1.0 + }, + "HSO3m": { + "qty": 1.0 + }, + "Hp": { + "qty": 1.0 + } }, "products": { "SO": { @@ -1070,8 +1272,12 @@ { "type": "ARRHENIUS", "reactants": { - "aCH3OH": {}, - "aHO": {} + "aCH3OH": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } }, "products": { "[aH2O]": { @@ -1089,8 +1295,12 @@ { "type": "ARRHENIUS", "reactants": { - "aCH2OH": {}, - "aO2": {} + "aCH2OH": { + "qty": 1.0 + }, + "aO2": { + "qty": 1.0 + } }, "products": { "aO2CH2OH": { @@ -1105,7 +1315,9 @@ { "type": "ARRHENIUS", "reactants": { - "aO2CH2OH": {} + "aO2CH2OH": { + "qty": 2.0 + } }, "products": { "aCH3OH": { @@ -1126,8 +1338,12 @@ { "type": "ARRHENIUS", "reactants": { - "aETOH": {}, - "aHO": {} + "aETOH": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } }, "products": { "[aH2O]": { @@ -1145,8 +1361,12 @@ { "type": "ARRHENIUS", "reactants": { - "aCH3CHOH": {}, - "aO2": {} + "aCH3CHOH": { + "qty": 1.0 + }, + "aO2": { + "qty": 1.0 + } }, "products": { "aO2CH3CHOH": { @@ -1161,7 +1381,9 @@ { "type": "ARRHENIUS", "reactants": { - "aO2CH3CHOH": {} + "aO2CH3CHOH": { + "qty": 1.0 + } }, "products": { "aALD": { @@ -1179,8 +1401,12 @@ { "type": "ARRHENIUS", "reactants": { - "aCH2OH2": {}, - "aHO": {} + "aCH2OH2": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } }, "products": { "aCHOH2": { @@ -1198,8 +1424,12 @@ { "type": "ARRHENIUS", "reactants": { - "aCHOH2": {}, - "aO2": {} + "aCHOH2": { + "qty": 1.0 + }, + "aO2": { + "qty": 1.0 + } }, "products": { "aHO2": { @@ -1217,8 +1447,12 @@ { "type": "ARRHENIUS", "reactants": { - "aCH3CHOH2": {}, - "aHO": {} + "aCH3CHOH2": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } }, "products": { "[aH2O]": { @@ -1236,8 +1470,12 @@ { "type": "ARRHENIUS", "reactants": { - "aALD": {}, - "aHO": {} + "aALD": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } }, "products": { "[aH2O]": { @@ -1255,8 +1493,12 @@ { "type": "ARRHENIUS", "reactants": { - "aORA1": {}, - "aHO": {} + "aORA1": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } }, "products": { "aCO2H": { @@ -1274,8 +1516,12 @@ { "type": "ARRHENIUS", "reactants": { - "HCOOm": {}, - "aHO": {} + "HCOOm": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } }, "products": { "aCO2H": { @@ -1293,8 +1539,12 @@ { "type": "ARRHENIUS", "reactants": { - "aORA2": {}, - "aHO": {} + "aORA2": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } }, "products": { "[aH2O]": { @@ -1312,8 +1562,12 @@ { "type": "ARRHENIUS", "reactants": { - "MCOOm": {}, - "aHO": {} + "MCOOm": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } }, "products": { "[aH2O]": { @@ -1331,8 +1585,12 @@ { "type": "ARRHENIUS", "reactants": { - "aCH2COOH": {}, - "aO2": {} + "aCH2COOH": { + "qty": 1.0 + }, + "aO2": { + "qty": 1.0 + } }, "products": { "aACO3": { @@ -1347,7 +1605,9 @@ { "type": "ARRHENIUS", "reactants": { - "aMO2": {} + "aMO2": { + "qty": 2.0 + } }, "products": { "aCH3OH": { @@ -1368,7 +1628,9 @@ { "type": "ARRHENIUS", "reactants": { - "aMO2": {} + "aMO2": { + "qty": 2.0 + } }, "products": { "aCH3O": { @@ -1386,7 +1648,9 @@ { "type": "ARRHENIUS", "reactants": { - "aACO3": {} + "aACO3": { + "qty": 2.0 + } }, "products": { "aMO2": { @@ -1407,8 +1671,12 @@ { "type": "ARRHENIUS", "reactants": { - "aMO2": {}, - "HSO3m": {} + "aMO2": { + "qty": 1.0 + }, + "HSO3m": { + "qty": 1.0 + } }, "products": { "aOP1": { @@ -1426,7 +1694,9 @@ { "type": "ARRHENIUS", "reactants": { - "aETHPX": {} + "aETHPX": { + "qty": 2.0 + } }, "products": { "aCH3CH2O": { @@ -1444,8 +1714,10 @@ { "type": "ARRHENIUS", "reactants": { - "aCH3CH2O": {} - }, + "aCH3CH2O": { + "qty": 1.0 + } + }, "products": { "aCH3CHOH": { "yield": 1.0 @@ -1459,8 +1731,12 @@ { "type": "ARRHENIUS", "reactants": { - "aHO": {}, - "HC2O4m": {} + "aHO": { + "qty": 1.0 + }, + "HC2O4m": { + "qty": 1.0 + } }, "products": { "[aH2O]": { @@ -1478,8 +1754,12 @@ { "type": "ARRHENIUS", "reactants": { - "aHO": {}, - "C2O4mm": {} + "aHO": { + "qty": 1.0 + }, + "C2O4mm": { + "qty": 1.0 + } }, "products": { "OHm": { @@ -1497,8 +1777,12 @@ { "type": "ARRHENIUS", "reactants": { - "C2O4m": {}, - "aO2": {} + "C2O4m": { + "qty": 1.0 + }, + "aO2": { + "qty": 1.0 + } }, "products": { "aCO2": { @@ -1516,8 +1800,12 @@ { "type": "ARRHENIUS", "reactants": { - "aHO": {}, - "aCHOH2CHOH2": {} + "aHO": { + "qty": 1.0 + }, + "aCHOH2CHOH2": { + "qty": 1.0 + } }, "products": { "[aH2O]": { @@ -1535,8 +1823,12 @@ { "type": "ARRHENIUS", "reactants": { - "aCOH2CHOH2": {}, - "aO2": {} + "aCOH2CHOH2": { + "qty": 1.0 + }, + "aO2": { + "qty": 1.0 + } }, "products": { "aO2COH2CHOH2": { @@ -1551,7 +1843,9 @@ { "type": "ARRHENIUS", "reactants": { - "aO2COH2CHOH2": {} + "aO2COH2CHOH2": { + "qty": 1.0 + } }, "products": { "aHO2": { @@ -1569,8 +1863,12 @@ { "type": "ARRHENIUS", "reactants": { - "aHO": {}, - "aCHOH2COOH": {} + "aHO": { + "qty": 1.0 + }, + "aCHOH2COOH": { + "qty": 1.0 + } }, "products": { "[aH2O]": { @@ -1588,8 +1886,12 @@ { "type": "ARRHENIUS", "reactants": { - "aCOH2COOH": {}, - "aO2": {} + "aCOH2COOH": { + "qty": 1.0 + }, + "aO2": { + "qty": 1.0 + } }, "products": { "aO2COH2COOH": { @@ -1604,7 +1906,9 @@ { "type": "ARRHENIUS", "reactants": { - "aO2COH2COOH": {} + "aO2COH2COOH": { + "qty": 1.0 + } }, "products": { "aHO2": { @@ -1622,8 +1926,12 @@ { "type": "ARRHENIUS", "reactants": { - "aCH3COH2": {}, - "aO2": {} + "aCH3COH2": { + "qty": 1.0 + }, + "aO2": { + "qty": 1.0 + } }, "products": { "aCH3COH2OO": { @@ -1638,7 +1946,9 @@ { "type": "ARRHENIUS", "reactants": { - "aCH3COH2OO": {} + "aCH3COH2OO": { + "qty": 1.0 + } }, "products": { "Hp": { @@ -1659,7 +1969,9 @@ { "type": "ARRHENIUS", "reactants": { - "aCH3O": {} + "aCH3O": { + "qty": 1.0 + } }, "products": { "aCH2OH": { @@ -1674,8 +1986,12 @@ { "type": "ARRHENIUS", "reactants": { - "CH2COOm": {}, - "aO2": {} + "CH2COOm": { + "qty": 1.0 + }, + "aO2": { + "qty": 1.0 + } }, "products": { "O2CH2COOm": { @@ -1690,7 +2006,9 @@ { "type": "ARRHENIUS", "reactants": { - "O2CH2COOm": {} + "O2CH2COOm": { + "qty": 2.0 + } }, "products": { "CHOH": { @@ -1708,8 +2026,12 @@ { "type": "ARRHENIUS", "reactants": { - "CO2m": {}, - "aO2": {} + "CO2m": { + "qty": 1.0 + }, + "aO2": { + "qty": 1.0 + } }, "products": { "aCO2": { @@ -1727,8 +2049,12 @@ { "type": "ARRHENIUS", "reactants": { - "CL2m": {}, - "FEpp": {} + "CL2m": { + "qty": 1.0 + }, + "FEpp": { + "qty": 1.0 + } }, "products": { "CLm": { @@ -1746,8 +2072,12 @@ { "type": "ARRHENIUS", "reactants": { - "CL2m": {}, - "aHO2": {} + "CL2m": { + "qty": 1.0 + }, + "aHO2": { + "qty": 1.0 + } }, "products": { "CLm": { @@ -1768,8 +2098,12 @@ { "type": "ARRHENIUS", "reactants": { - "CL2m": {}, - "HSO3m": {} + "CL2m": { + "qty": 1.0 + }, + "HSO3m": { + "qty": 1.0 + } }, "products": { "CLm": { @@ -1790,8 +2124,12 @@ { "type": "ARRHENIUS", "reactants": { - "aCL2": {}, - "[aH2O]": {} + "aCL2": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "Hp": { @@ -1812,8 +2150,12 @@ { "type": "ARRHENIUS", "reactants": { - "CL2m": {}, - "[aH2O]": {} + "CL2m": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "Hp": { @@ -1834,8 +2176,12 @@ { "type": "ARRHENIUS", "reactants": { - "BRm": {}, - "SO4m": {} + "BRm": { + "qty": 1.0 + }, + "SO4m": { + "qty": 1.0 + } }, "products": { "SO4mm": { @@ -1853,8 +2199,12 @@ { "type": "ARRHENIUS", "reactants": { - "BRm": {}, - "aNO3": {} + "BRm": { + "qty": 1.0 + }, + "aNO3": { + "qty": 1.0 + } }, "products": { "NO3m": { @@ -1872,7 +2222,9 @@ { "type": "ARRHENIUS", "reactants": { - "BR2m": {} + "BR2m": { + "qty": 2.0 + } }, "products": { "aBR2": { @@ -1890,8 +2242,12 @@ { "type": "ARRHENIUS", "reactants": { - "BR2m": {}, - "FEpp": {} + "BR2m": { + "qty": 1.0 + }, + "FEpp": { + "qty": 1.0 + } }, "products": { "BRm": { @@ -1909,8 +2265,12 @@ { "type": "ARRHENIUS", "reactants": { - "BR2m": {}, - "aH2O2": {} + "BR2m": { + "qty": 1.0 + }, + "aH2O2": { + "qty": 1.0 + } }, "products": { "BRm": { @@ -1931,8 +2291,12 @@ { "type": "ARRHENIUS", "reactants": { - "BR2m": {}, - "aHO2": {} + "BR2m": { + "qty": 1.0 + }, + "aHO2": { + "qty": 1.0 + } }, "products": { "BRm": { @@ -1953,8 +2317,12 @@ { "type": "ARRHENIUS", "reactants": { - "BR2m": {}, - "HSO3m": {} + "BR2m": { + "qty": 1.0 + }, + "HSO3m": { + "qty": 1.0 + } }, "products": { "BRm": { @@ -1975,8 +2343,12 @@ { "type": "ARRHENIUS", "reactants": { - "aBR2": {}, - "[aH2O]": {} + "aBR2": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "Hp": { @@ -1997,7 +2369,9 @@ { "type": "ARRHENIUS", "reactants": { - "BROHm": {} + "BROHm": { + "qty": 1.0 + } }, "products": { "aBR": { @@ -2015,8 +2389,12 @@ { "type": "ARRHENIUS", "reactants": { - "aCO2": {}, - "[aH2O]": {} + "aCO2": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "aH2CO3": { @@ -2031,7 +2409,9 @@ { "type": "ARRHENIUS", "reactants": { - "aH2CO3": {} + "aH2CO3": { + "qty": 1.0 + } }, "products": { "aCO2": { @@ -2049,8 +2429,12 @@ { "type": "ARRHENIUS", "reactants": { - "SO3mm": {}, - "aCH2OH2": {} + "SO3mm": { + "qty": 1.0 + }, + "aCH2OH2": { + "qty": 1.0 + } }, "products": { "HMSm": { @@ -2068,8 +2452,12 @@ { "type": "ARRHENIUS", "reactants": { - "HMSm": {}, - "OHm": {} + "HMSm": { + "qty": 1.0 + }, + "OHm": { + "qty": 1.0 + } }, "products": { "SO3mm": { @@ -2087,7 +2475,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "[aH2O]": {} + "[aH2O]": { + "qty": 1.0 + } }, "products": { "OHm": { @@ -2106,7 +2496,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aHCL": {} + "aHCL": { + "qty": 1.0 + } }, "products": { "CLm": { @@ -2125,8 +2517,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aNH3": {}, - "[aH2O]": {} + "aNH3": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "NH4p": { @@ -2145,7 +2541,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aHNO3": {} + "aHNO3": { + "qty": 1.0 + } }, "products": { "NO3m": { @@ -2164,7 +2562,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aHONO": {} + "aHONO": { + "qty": 1.0 + } }, "products": { "NO2m": { @@ -2183,8 +2583,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aSO2": {}, - "[aH2O]": {} + "aSO2": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "HSO3m": { @@ -2203,7 +2607,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "HSO3m": {} + "HSO3m": { + "qty": 1.0 + } }, "products": { "SO3mm": { @@ -2222,7 +2628,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "HSO4m": {} + "HSO4m": { + "qty": 1.0 + } }, "products": { "Hp": { @@ -2241,7 +2649,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aORA1": {} + "aORA1": { + "qty": 1.0 + } }, "products": { "Hp": { @@ -2260,7 +2670,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aORA2": {} + "aORA2": { + "qty": 1.0 + } }, "products": { "Hp": { @@ -2279,8 +2691,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aHCHO": {}, - "[aH2O]": {} + "aHCHO": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "aCH2OH2": { @@ -2296,8 +2712,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aALD": {}, - "[aH2O]": {} + "aALD": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "aCH3CHOH2": { @@ -2313,8 +2733,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "HSO3m": {}, - "aCH2OH2": {} + "HSO3m": { + "qty": 1.0 + }, + "aCH2OH2": { + "qty": 1.0 + } }, "products": { "HMSm": { @@ -2333,8 +2757,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aNO3": {}, - "CLm": {} + "aNO3": { + "qty": 1.0 + }, + "CLm": { + "qty": 1.0 + } }, "products": { "NO3m": { @@ -2353,8 +2781,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aCH3CO": {}, - "[aH2O]": {} + "aCH3CO": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "aCH3COH2": { @@ -2370,7 +2802,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aACO3": {} + "aACO3": { + "qty": 1.0 + } }, "products": { "Hp": { @@ -2390,7 +2824,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aH2CO3": {} + "aH2CO3": { + "qty": 1.0 + } }, "products": { "HCO3m": { @@ -2411,7 +2847,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aHO2": {} + "aHO2": { + "qty": 1.0 + } }, "products": { "O2m": { @@ -2432,7 +2870,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aHNO4": {} + "aHNO4": { + "qty": 1.0 + } }, "products": { "NO4m": { @@ -2453,8 +2893,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aNO2": {}, - "aHO2": {} + "aNO2": { + "qty": 1.0 + }, + "aHO2": { + "qty": 1.0 + } }, "products": { "aHNO4": { @@ -2472,7 +2916,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aSULF": {} + "aSULF": { + "qty": 1.0 + } }, "products": { "HSO4m": { @@ -2493,8 +2939,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "FEppp": {}, - "[aH2O]": {} + "FEppp": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "FEOHpp": { @@ -2515,8 +2965,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aCL": {}, - "CLm": {} + "aCL": { + "qty": 1.0 + }, + "CLm": { + "qty": 1.0 + } }, "products": { "CL2m": { @@ -2534,8 +2988,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aBR": {}, - "BRm": {} + "aBR": { + "qty": 1.0 + }, + "BRm": { + "qty": 1.0 + } }, "products": { "BR2m": { @@ -2553,8 +3011,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "CLm": {}, - "aHO": {} + "CLm": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } }, "products": { "CLOHm": { @@ -2572,8 +3034,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "CLOHm": {}, - "Hp": {} + "CLOHm": { + "qty": 1.0 + }, + "Hp": { + "qty": 1.0 + } }, "products": { "aCL": { @@ -2594,8 +3060,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "BRm": {}, - "aHO": {} + "BRm": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } }, "products": { "BROHm": { @@ -2613,8 +3083,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "BROHm": {}, - "Hp": {} + "BROHm": { + "qty": 1.0 + }, + "Hp": { + "qty": 1.0 + } }, "products": { "aBR": { @@ -2635,7 +3109,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aHO3": {} + "aHO3": { + "qty": 1.0 + } }, "products": { "Hp": { @@ -2656,7 +3132,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "CHOHSO3m": {} + "CHOHSO3m": { + "qty": 1.0 + } }, "products": { "CHOSO3mm": { @@ -2677,7 +3155,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "SO5O2Hm": {} + "SO5O2Hm": { + "qty": 1.0 + } }, "products": { "Hp": { @@ -2698,7 +3178,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "HC2O4m": {} + "HC2O4m": { + "qty": 1.0 + } }, "products": { "C2O4mm": { @@ -2719,7 +3201,9 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aCHOH2COOH": {} + "aCHOH2COOH": { + "qty": 1.0 + } }, "products": { "Hp": { @@ -2740,8 +3224,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "aGLY": {}, - "[aH2O]": {} + "aGLY": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } }, "products": { "aCHOH2CHOH2": { @@ -2759,8 +3247,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "FEppp": {}, - "C2O4mm": {} + "FEppp": { + "qty": 1.0 + }, + "C2O4mm": { + "qty": 1.0 + } }, "products": { "FEC2O4p": { @@ -2778,8 +3270,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "FEC2O4p": {}, - "C2O4mm": {} + "FEC2O4p": { + "qty": 1.0 + }, + "C2O4mm": { + "qty": 1.0 + } }, "products": { "FEC2O42m": { @@ -2797,8 +3293,12 @@ { "type": "AQUEOUS_EQUILIBRIUM", "reactants": { - "SO4m": {}, - "CLm": {} + "SO4m": { + "qty": 1.0 + }, + "CLm": { + "qty": 1.0 + } }, "products": { "SO4mm": { @@ -3052,118 +3552,118 @@ "name": "cloud water", "type": "AERO_PHASE", "species": [ - "aHNO3", - "SO5O2Hm", - "SO", - "SO3mm", - "aH2O2", - "aCO2H", - "aBR2", - "FEOHpp", - "SO5m", - "aNO2", - "HSO3m", - "SO3m", - "NH4p", - "CL2m", - "NO3m", + "HSO5m", "aHNO4", - "CO2m", - "aGLY", + "NO4m", + "SO5O2mm", "aCOH2COOH", - "aCH3COH2OO", + "NO2p", + "aN2O5", + "BR2m", + "aHCL", + "O2CH2COOm", + "FEOHpp", + "CLOHm", + "aHNO3", + "aCH3CHOH", + "aSO2", "aCHOH2", + "CHOHSO3m", + "SO4m", + "aCH3CO", "aHOCL", - "FEC2O42m", - "aALD", - "CHOSO3m", - "aCL2", - "aBRNO2", - "[aH2O]", - "MCOOm", - "HC2O4m", + "CH2COOm", "O2CHOHSO3m", + "aO3", + "aCH3CHOH2", + "aCH2COOH", + "aOP1", + "CHOH2COOm", + "aH2O2", + "aETHPX", + "NO2m", + "aCOH2CHOH2", + "aCHOH2CHOH2", + "aNO", + "NO3m", + "aCH3OH", + "aCH2OH", + "aACO3", "FEOpp", - "O2CH2COOm", - "CLm", - "SO4m", + "aCH3CH2O", + "aBR", + "SO3mm", + "aCH3O", "aH2C2O4", - "aO2", + "aHO2", + "aORA2", + "SO", + "FEppp", + "FEC2O42m", + "CUp", + "aMO2", + "aBR2", + "O3m", "CUpp", - "NO2m", - "aBR", "SO4mm", - "BROHm", - "aN2O5", - "aO2COH2CHOH2", - "CHOSO3mm", - "aHOBR", - "aCH3CH2O", - "aCH3OH", - "FEppp", - "NO4m", - "aCH2OH", - "C2O4m", - "aNO3", - "aOP1", - "CHOHSO3m", - "aHO3", - "aCH3CHOH2", - "aHONO", - "CHOH2COOm", - "SO5O2mm", - "aETOH", - "CH2COOm", - "aO2COH2COOH", - "aCH2COOH", - "aCLNO2", - "BRm", - "O2m", - "aCHOH2CHOH2", - "aORA1", - "aO2CHO", - "aCH3CHOH", - "NO2p", - "BR2m", - "aHCHO", + "aO2CH3CHOH", "FEpp", - "aNO", - "aH2CO3", - "aCH2OH2", - "aHCL", - "C2O4mm", + "aCH3COH2", + "OHm", "HSO4m", + "aO2CHO", + "CHOSO3m", + "aALD", + "aCH3COH2OO", + "NH4p", + "aO2CH2OH", + "aCO2H", "aHO", + "aCL2", + "aHONO", "aCL", + "aBRCL", + "aHCHO", + "CL2m", + "HCOOm", "aCO2", + "CLm", + "CO2m", + "BRm", + "C2O4m", "HCO3m", - "aCH3O", + "HMSm", + "HSO3m", + "SO5m", + "aO2COH2COOH", + "aGLY", + "aHOBR", + "aETOH", + "C2O4mm", + "aO2COH2CHOH2", + "aCLNO2", + "Hp", "FEC2O4p", - "aO2CH3CHOH", - "aBRCL", - "aACO3", - "CHOH", - "aCH3COH2", - "CUp", - "aHO2", + "SO3m", "aCHOH2COOH", - "aMO2", - "aETHPX", - "Hp", + "aORA1", + "SO5O2Hm", + "aCH2OH2", "aSULF", - "aCOH2CHOH2", - "aO3", - "O3m", - "aSO2", - "HSO5m", - "HCOOm", - "aORA2", - "aCH3CO", - "CLOHm", - "OHm", + "aHO3", + "MCOOm", + "aNO2", + "[aH2O]", + "aNO3", + "HC2O4m", + "aO2", + "CHOSO3mm", + "CHOH", + "BROHm", + "aBRNO2", + "aH2CO3", "aNH3", - "HMSm", - "aO2CH2OH" + "O2m" ] }, { From 73d81d1fb62f62b24ced824cd0c0bd4a35ac57f7 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 14:09:06 -0500 Subject: [PATCH 21/24] comments --- capram_convert/convert.py | 5 +- capram_convert/mechanism.json | 190 +++++++++++++++++----------------- 2 files changed, 98 insertions(+), 97 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index 0c22930f..3d48f5e5 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -53,9 +53,10 @@ def parse_reactants_products(line): if match: reactants = combine_stoichiometric_coeffs(match.group(1).strip()) products = combine_stoichiometric_coeffs(match.group(2).strip()) - #TODO: now, go through the lists of products and reactants and combine like species - # also, sometimes the list of producdts is like CL2m + [aH2O] = Hp + CLm + CLm + aHO + # now, go through the lists of products and reactants and combine like species + # e.g., sometimes the list of products is like CL2m + [aH2O] = Hp + CLm + CLm + aHO # this should end up being represented as if it were written like CL2m + [aH2O] = Hp + 2CLm + aHO + # same thing, but for reactants return convert_reactants_to_quantity(reactants), convert_products_to_yield(products) def combine_stoichiometric_coeffs(species): diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json index 95afc8d3..e3893e36 100644 --- a/capram_convert/mechanism.json +++ b/capram_convert/mechanism.json @@ -3552,118 +3552,118 @@ "name": "cloud water", "type": "AERO_PHASE", "species": [ - "HSO5m", - "aHNO4", - "NO4m", "SO5O2mm", - "aCOH2COOH", + "aCHOH2COOH", + "aALD", + "NO2m", + "aCH3COH2", + "CHOSO3mm", + "FEC2O4p", "NO2p", - "aN2O5", - "BR2m", - "aHCL", - "O2CH2COOm", - "FEOHpp", - "CLOHm", - "aHNO3", - "aCH3CHOH", - "aSO2", - "aCHOH2", - "CHOHSO3m", - "SO4m", - "aCH3CO", - "aHOCL", - "CH2COOm", - "O2CHOHSO3m", - "aO3", - "aCH3CHOH2", - "aCH2COOH", + "aO2CH2OH", + "aGLY", + "SO4mm", + "aNH3", "aOP1", - "CHOH2COOm", - "aH2O2", - "aETHPX", - "NO2m", - "aCOH2CHOH2", - "aCHOH2CHOH2", - "aNO", - "NO3m", - "aCH3OH", - "aCH2OH", - "aACO3", - "FEOpp", - "aCH3CH2O", "aBR", - "SO3mm", - "aCH3O", - "aH2C2O4", - "aHO2", - "aORA2", - "SO", - "FEppp", - "FEC2O42m", - "CUp", - "aMO2", - "aBR2", + "SO5O2Hm", + "aCH3CH2O", + "aSO2", "O3m", - "CUpp", - "SO4mm", - "aO2CH3CHOH", - "FEpp", - "aCH3COH2", - "OHm", - "HSO4m", - "aO2CHO", - "CHOSO3m", - "aALD", - "aCH3COH2OO", - "NH4p", - "aO2CH2OH", + "FEppp", + "Hp", + "HCOOm", + "CLm", + "C2O4m", + "aHNO3", + "CLOHm", + "aO3", "aCO2H", - "aHO", - "aCL2", + "SO", "aHONO", + "FEpp", + "aCOH2COOH", + "aCLNO2", + "FEOpp", + "aCH3CHOH2", + "aHO2", + "aH2C2O4", + "aBR2", + "aETHPX", "aCL", + "HSO5m", + "SO3mm", + "aO2COH2COOH", + "aNO2", "aBRCL", - "aHCHO", - "CL2m", - "HCOOm", - "aCO2", - "CLm", - "CO2m", - "BRm", - "C2O4m", - "HCO3m", + "aHCL", + "CHOHSO3m", + "aO2CHO", + "FEC2O42m", "HMSm", - "HSO3m", - "SO5m", - "aO2COH2COOH", - "aGLY", - "aHOBR", - "aETOH", - "C2O4mm", - "aO2COH2CHOH2", - "aCLNO2", - "Hp", - "FEC2O4p", - "SO3m", - "aCHOH2COOH", + "HC2O4m", "aORA1", - "SO5O2Hm", - "aCH2OH2", + "aO2COH2CHOH2", + "aNO3", + "aACO3", + "NO4m", + "aO2CH3CHOH", + "aCO2", + "NH4p", "aSULF", - "aHO3", "MCOOm", - "aNO2", - "[aH2O]", - "aNO3", - "HC2O4m", + "aCH3CHOH", "aO2", - "CHOSO3mm", + "SO3m", + "CHOSO3m", + "aHOBR", + "aH2CO3", + "[aH2O]", + "aHOCL", + "aCH3OH", + "aCH2COOH", + "aCH3COH2OO", + "aHCHO", + "aNO", + "HSO4m", + "O2CHOHSO3m", "CHOH", + "CUpp", + "CL2m", + "SO5m", + "HSO3m", + "OHm", + "O2m", + "FEOHpp", + "CUp", + "aCHOH2CHOH2", + "aORA2", + "SO4m", + "aCH2OH", + "BRm", + "aHO3", + "aHO", "BROHm", + "O2CH2COOm", + "aCH2OH2", + "aH2O2", + "NO3m", + "HCO3m", + "aCOH2CHOH2", + "aMO2", "aBRNO2", - "aH2CO3", - "aNH3", - "O2m" + "aCL2", + "aN2O5", + "CO2m", + "CH2COOm", + "aETOH", + "aCH3O", + "aCHOH2", + "CHOH2COOm", + "BR2m", + "aHNO4", + "C2O4mm", + "aCH3CO" ] }, { From 9251ba78a5670cf437f6bab190e4d7fdc92610ba Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 14:16:18 -0500 Subject: [PATCH 22/24] correctly outputting aqeuous_equilibrium without back constant --- capram_convert/convert.py | 34 +- capram_convert/mechanism.json | 1462 ++++++++++++++++----------------- 2 files changed, 726 insertions(+), 770 deletions(-) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index 3d48f5e5..70b812ad 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -260,7 +260,7 @@ def convert_products_to_yield(products): "A" : reaction['A'] * np.exp(-1 * reaction['B'] / 298), "C" : reaction['B'], "aerosol phase" : aerosol_phase_name, - "aerosol-phase water" : "H2O_aq" + "aerosol-phase water" : "[aH2O]" } ) aerosol_phase_species.update([ reactant['name'] for reactant in reaction['reactants']]) @@ -282,7 +282,7 @@ def convert_products_to_yield(products): "C" : reaction['B'], "k_reverse" : reaction['C'], "phase": aerosol_phase_name, - "aerosol-phase water" : "H2O_aq" + "aerosol-phase water" : "[aH2O]" } ) aerosol_phase_species.update([ reactant['name'] for reactant in reaction['reactants']]) @@ -290,22 +290,20 @@ def convert_products_to_yield(products): for reaction in diss_without_c: aqueous_equilibrium.append( - [ - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - reactant['name']: { 'qty': reactant['qty'] } for reactant in reaction["reactants"] - }, - "products": { - product['name']: { 'yield': product['yield'] } for product in reaction["products"] - }, - "A" : reaction['A'], - "C" : 0, - "k_reverse" : reaction['B'], - "phase": aerosol_phase_name, - "aerosol-phase water" : "H2O_aq" - } - ] + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + reactant['name']: { 'qty': reactant['qty'] } for reactant in reaction["reactants"] + }, + "products": { + product['name']: { 'yield': product['yield'] } for product in reaction["products"] + }, + "A" : reaction['A'], + "C" : 0, + "k_reverse" : reaction['B'], + "phase": aerosol_phase_name, + "aerosol-phase water" : "[aH2O]" + } ) aerosol_phase_species.update([ reactant['name'] for reactant in reaction['reactants']]) aerosol_phase_species.update([ product['name'] for product in reaction['products']]) diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json index e3893e36..0fd8fb19 100644 --- a/capram_convert/mechanism.json +++ b/capram_convert/mechanism.json @@ -99,7 +99,7 @@ "A": 50.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -125,7 +125,7 @@ "A": 7000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -148,7 +148,7 @@ "A": 150000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -174,7 +174,7 @@ "A": 130000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -200,7 +200,7 @@ "A": 150000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -226,7 +226,7 @@ "A": 10000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -252,7 +252,7 @@ "A": 27470692899786.598, "C": -5050.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -272,7 +272,7 @@ "A": 17241255673.805157, "C": -1100.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -298,7 +298,7 @@ "A": 10000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -324,7 +324,7 @@ "A": 2300000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -350,7 +350,7 @@ "A": 100000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -373,7 +373,7 @@ "A": 8000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -396,7 +396,7 @@ "A": 13000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -422,7 +422,7 @@ "A": 13000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -445,7 +445,7 @@ "A": 2411527019006.37, "C": -2200.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -465,7 +465,7 @@ "A": 1193031991.1270792, "C": -4500.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -488,7 +488,7 @@ "A": 8423504855.756161, "C": -1680.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -511,7 +511,7 @@ "A": 2700000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -534,7 +534,7 @@ "A": 460000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -557,7 +557,7 @@ "A": 5608557390760.588, "C": -4690.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -583,7 +583,7 @@ "A": 100.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -606,7 +606,7 @@ "A": 1214599.2606213153, "C": -842.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -626,7 +626,7 @@ "A": 1000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -649,7 +649,7 @@ "A": 89000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -675,7 +675,7 @@ "A": 1068246352911.5388, "C": -2000.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -698,7 +698,7 @@ "A": 100000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -718,7 +718,7 @@ "A": 1.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -744,7 +744,7 @@ "A": 330000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -764,7 +764,7 @@ "A": 10000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -784,7 +784,7 @@ "A": 10000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -807,7 +807,7 @@ "A": 5000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -830,7 +830,7 @@ "A": 25500.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -853,7 +853,7 @@ "A": 10.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -876,7 +876,7 @@ "A": 300000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -896,7 +896,7 @@ "A": 2600000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -916,7 +916,7 @@ "A": 17000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -936,7 +936,7 @@ "A": 7000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -959,7 +959,7 @@ "A": 0.0126, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -982,7 +982,7 @@ "A": 44.32, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1011,7 +1011,7 @@ "A": 48617052944753.77, "C": -4000.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1037,7 +1037,7 @@ "A": 42405757730857.71, "C": -5530.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1060,7 +1060,7 @@ "A": 7.429735524861723e+16, "C": -5280.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1083,7 +1083,7 @@ "A": 7745929554766653.0, "C": -5809.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1106,7 +1106,7 @@ "A": 30000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1132,7 +1132,7 @@ "A": 3217841.880265981, "C": 2165.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1152,7 +1152,7 @@ "A": 1353845691603.3787, "C": -2600.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1172,7 +1172,7 @@ "A": 1700000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1195,7 +1195,7 @@ "A": 1200.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1215,7 +1215,7 @@ "A": 2500000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1241,7 +1241,7 @@ "A": 456.10702574818845, "C": -1110.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1267,7 +1267,7 @@ "A": 7140000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1290,7 +1290,7 @@ "A": 7002790586.531466, "C": -580.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1310,7 +1310,7 @@ "A": 2000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1333,7 +1333,7 @@ "A": 1050000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1356,7 +1356,7 @@ "A": 1900000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1376,7 +1376,7 @@ "A": 2000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1396,7 +1396,7 @@ "A": 1713166492299.335, "C": -7217.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1419,7 +1419,7 @@ "A": 30655705402.09484, "C": -1020.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1442,7 +1442,7 @@ "A": 2000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1465,7 +1465,7 @@ "A": 1200000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1488,7 +1488,7 @@ "A": 3600000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1511,7 +1511,7 @@ "A": 3726553714.606836, "C": -1000.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1534,7 +1534,7 @@ "A": 91730552974.9375, "C": -1000.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1557,7 +1557,7 @@ "A": 1301323951.4818943, "C": -1330.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1580,7 +1580,7 @@ "A": 42000577298.10133, "C": -1800.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1600,7 +1600,7 @@ "A": 1700000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1623,7 +1623,7 @@ "A": 118968666270.98093, "C": -2200.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1643,7 +1643,7 @@ "A": 57876648456.152885, "C": -2200.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1666,7 +1666,7 @@ "A": 150000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1689,7 +1689,7 @@ "A": 500000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1709,7 +1709,7 @@ "A": 8071922.343268531, "C": 750.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1726,7 +1726,7 @@ "A": 1000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1749,7 +1749,7 @@ "A": 32000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1772,7 +1772,7 @@ "A": 5300000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1795,7 +1795,7 @@ "A": 2000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1818,7 +1818,7 @@ "A": 178137994858.22678, "C": -1516.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1838,7 +1838,7 @@ "A": 1380000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1858,7 +1858,7 @@ "A": 2000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1881,7 +1881,7 @@ "A": 178137994858.22678, "C": -1516.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1901,7 +1901,7 @@ "A": 2000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1921,7 +1921,7 @@ "A": 2000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1941,7 +1941,7 @@ "A": 2000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1964,7 +1964,7 @@ "A": 100000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -1981,7 +1981,7 @@ "A": 1000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2001,7 +2001,7 @@ "A": 2000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2021,7 +2021,7 @@ "A": 20000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2044,7 +2044,7 @@ "A": 4000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2067,7 +2067,7 @@ "A": 260503174919.8385, "C": -3030.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2093,7 +2093,7 @@ "A": 13000000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2119,7 +2119,7 @@ "A": 650720568.7854763, "C": -400.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2145,7 +2145,7 @@ "A": 130387468611.99103, "C": -7900.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2171,7 +2171,7 @@ "A": 6.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2194,7 +2194,7 @@ "A": 2100000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2217,7 +2217,7 @@ "A": 3800000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2237,7 +2237,7 @@ "A": 1700000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2260,7 +2260,7 @@ "A": 256640227408.05545, "C": -3330.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2286,7 +2286,7 @@ "A": 100000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2312,7 +2312,7 @@ "A": 6500000000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2338,7 +2338,7 @@ "A": 685036875.6354121, "C": -780.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2364,7 +2364,7 @@ "A": 2639927153.6309934, "C": -7500.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2384,7 +2384,7 @@ "A": 4200000.0, "C": 0.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2404,7 +2404,7 @@ "A": 1300426356398.6077, "C": -9250.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2424,7 +2424,7 @@ "A": 1.3670434220265014e+17, "C": -8500.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2447,7 +2447,7 @@ "A": 505918766.97323936, "C": -2450.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "ARRHENIUS", @@ -2470,7 +2470,7 @@ "A": 475632147521.7825, "C": -5530.0, "aerosol phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2491,7 +2491,7 @@ "C": -6800.0, "k_reverse": 130000000000.0, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2512,7 +2512,7 @@ "C": 6890.0, "k_reverse": 290000.0, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2536,7 +2536,7 @@ "C": -560.0, "k_reverse": 34000000000.0, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2557,7 +2557,7 @@ "C": 1800.0, "k_reverse": 50000000000.0, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2578,7 +2578,7 @@ "C": -1760.0, "k_reverse": 50000000000.0, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2602,7 +2602,7 @@ "C": 1940.0, "k_reverse": 200000000.0, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2623,7 +2623,7 @@ "C": 1960.0, "k_reverse": 50000000000.0, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2644,7 +2644,7 @@ "C": 2700.0, "k_reverse": 100000000000.0, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2665,7 +2665,7 @@ "C": 12.0, "k_reverse": 50000000000.0, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2686,7 +2686,7 @@ "C": 46.0, "k_reverse": 50000000000.0, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2707,7 +2707,7 @@ "C": 4030.0, "k_reverse": 0.0051, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2728,7 +2728,7 @@ "C": 2500.0, "k_reverse": 0.00569, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2752,7 +2752,7 @@ "C": -2500.0, "k_reverse": 2.2e-09, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2776,7 +2776,7 @@ "C": -4300.0, "k_reverse": 100000000.0, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2797,7 +2797,7 @@ "C": 0.0, "k_reverse": 30000.0, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" + "aerosol-phase water": "[aH2O]" }, { "type": "AQUEOUS_EQUILIBRIUM", @@ -2818,559 +2818,517 @@ "C": 46.0, "k_reverse": 50000000000.0, "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - }, - [ - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "aH2CO3": { - "qty": 1.0 - } - }, - "products": { - "HCO3m": { - "yield": 1.0 - }, - "Hp": { - "yield": 1.0 - } - }, - "A": 0.0002, - "C": 0, - "k_reverse": 50000000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - } - ], - [ - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "aHO2": { - "qty": 1.0 - } - }, - "products": { - "O2m": { - "yield": 1.0 - }, - "Hp": { - "yield": 1.0 - } - }, - "A": 1.6e-05, - "C": 0, - "k_reverse": 50000000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - } - ], - [ - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "aHNO4": { - "qty": 1.0 - } - }, - "products": { - "NO4m": { - "yield": 1.0 - }, - "Hp": { - "yield": 1.0 - } - }, - "A": 1e-05, - "C": 0, - "k_reverse": 50000000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - } - ], - [ - { - 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- }, - "A": 5100000.0, - "C": 0, - "k_reverse": 4100.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - } - ], - [ - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "BRm": { - "qty": 1.0 - }, - "aHO": { - "qty": 1.0 - } - }, - "products": { - "BROHm": { - "yield": 1.0 - } - }, - "A": 333.0, - "C": 0, - "k_reverse": 33000000.0, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - } - ], - [ - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "BROHm": { - "qty": 1.0 - }, - "Hp": { - "qty": 1.0 - } - }, - "products": { - "aBR": { - "yield": 1.0 - }, - "[aH2O]": { - "yield": 1.0 - } - }, - "A": 1800000000000.0, - "C": 0, - "k_reverse": 0.0245, - "phase": "cloud water", - "aerosol-phase water": "H2O_aq" - } - ], - [ - { - "type": "AQUEOUS_EQUILIBRIUM", - "reactants": { - "aHO3": { - "qty": 1.0 - } - }, - "products": { - "Hp": { - "yield": 1.0 - }, - "O3m": { - "yield": 1.0 - } - }, - "A": 6.3e-09, - "C": 0, - "k_reverse": 52000000000.0, - "phase": "cloud 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"type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aH2CO3": { + "qty": 1.0 + } + }, + "products": { + "HCO3m": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } + }, + "A": 0.0002, + "C": 0, + "k_reverse": 50000000000.0, + "phase": "cloud water", "aerosol-phase water": "[aH2O]" }, { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "HO", - "aerosol phase": "cloud water", - "aerosol-phase species": "aHO", + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aHO2": { + "qty": 1.0 + } + }, + "products": { + "O2m": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } + }, + "A": 1.6e-05, + "C": 0, + "k_reverse": 50000000000.0, + "phase": "cloud water", "aerosol-phase water": "[aH2O]" }, { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "H2O2", - "aerosol phase": "cloud water", - "aerosol-phase species": "aH2O2", + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aHNO4": { + "qty": 1.0 + } + }, + "products": { + "NO4m": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } + }, + "A": 1e-05, + "C": 0, + "k_reverse": 50000000000.0, + "phase": "cloud water", "aerosol-phase water": "[aH2O]" }, { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "NO2", - "aerosol phase": "cloud water", - "aerosol-phase species": "aNO2", + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aNO2": { + "qty": 1.0 + }, + "aHO2": { + "qty": 1.0 + } + }, + "products": { + "aHNO4": { + "yield": 1.0 + } + }, + "A": 2200000000.0, + "C": 0, + "k_reverse": 0.0046, + "phase": "cloud water", "aerosol-phase water": "[aH2O]" }, { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "HONO", - "aerosol phase": "cloud water", - "aerosol-phase species": "aHONO", + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aSULF": { + "qty": 1.0 + } + }, + "products": { + "HSO4m": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } + }, + "A": 1000.0, + "C": 0, + "k_reverse": 50000000000.0, + "phase": "cloud water", "aerosol-phase water": "[aH2O]" }, { - "type": "HL_PHASE_TRANSFER", - "gas-phase species": "HNO3", - "aerosol phase": "cloud water", - "aerosol-phase species": "aHNO3", - "aerosol-phase water": "[aH2O]" - }, + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "FEppp": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } + }, + "products": { + "FEOHpp": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } + }, + "A": 0.00011, + "C": 0, + "k_reverse": 430000000.0, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aCL": { + "qty": 1.0 + }, + "CLm": { + "qty": 1.0 + } + }, + "products": { + "CL2m": { + "yield": 1.0 + } + }, + "A": 140000.0, + "C": 0, + "k_reverse": 60000.0, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aBR": { + "qty": 1.0 + }, + "BRm": { + "qty": 1.0 + } + }, + "products": { + "BR2m": { + "yield": 1.0 + } + }, + "A": 632000.0, + "C": 0, + "k_reverse": 19000.0, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "CLm": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } + }, + "products": { + "CLOHm": { + "yield": 1.0 + } + }, + "A": 0.7, + "C": 0, + "k_reverse": 6100000000.0, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "CLOHm": { + "qty": 1.0 + }, + "Hp": { + "qty": 1.0 + } + }, + "products": { + "aCL": { + "yield": 1.0 + }, + "[aH2O]": { + "yield": 1.0 + } + }, + "A": 5100000.0, + "C": 0, + "k_reverse": 4100.0, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "BRm": { + "qty": 1.0 + }, + "aHO": { + "qty": 1.0 + } + }, + "products": { + "BROHm": { + "yield": 1.0 + } + }, + "A": 333.0, + "C": 0, + "k_reverse": 33000000.0, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "BROHm": { + "qty": 1.0 + }, + "Hp": { + "qty": 1.0 + } + }, + "products": { + "aBR": { + "yield": 1.0 + }, + "[aH2O]": { + "yield": 1.0 + } + }, + "A": 1800000000000.0, + "C": 0, + "k_reverse": 0.0245, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aHO3": { + "qty": 1.0 + } + }, + "products": { + "Hp": { + "yield": 1.0 + }, + "O3m": { + "yield": 1.0 + } + }, + "A": 6.3e-09, + "C": 0, + "k_reverse": 52000000000.0, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "CHOHSO3m": { + "qty": 1.0 + } + }, + "products": { + "CHOSO3mm": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } + }, + "A": 1.34e-06, + "C": 0, + "k_reverse": 44000000000.0, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "SO5O2Hm": { + "qty": 1.0 + } + }, + "products": { + "Hp": { + "yield": 1.0 + }, + "SO5O2mm": { + "yield": 1.0 + } + }, + "A": 1.5e-05, + "C": 0, + "k_reverse": 50000000000.0, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "HC2O4m": { + "qty": 1.0 + } + }, + "products": { + "C2O4mm": { + "yield": 1.0 + }, + "Hp": { + "yield": 1.0 + } + }, + "A": 6.25e-05, + "C": 0, + "k_reverse": 50000000000.0, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aCHOH2COOH": { + "qty": 1.0 + } + }, + "products": { + "Hp": { + "yield": 1.0 + }, + "CHOH2COOm": { + "yield": 1.0 + } + }, + "A": 0.000316, + "C": 0, + "k_reverse": 20000000000.0, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "aGLY": { + "qty": 1.0 + }, + "[aH2O]": { + "qty": 1.0 + } + }, + "products": { + "aCHOH2CHOH2": { + "yield": 1.0 + } + }, + "A": 3900.0, + "C": 0, + "k_reverse": 0.0055, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "FEppp": { + "qty": 1.0 + }, + "C2O4mm": { + "qty": 1.0 + } + }, + "products": { + "FEC2O4p": { + "yield": 1.0 + } + }, + "A": 2900000000.0, + "C": 0, + "k_reverse": 0.003, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "FEC2O4p": { + "qty": 1.0 + }, + "C2O4mm": { + "qty": 1.0 + } + }, + "products": { + "FEC2O42m": { + "yield": 1.0 + } + }, + "A": 6300000.0, + "C": 0, + "k_reverse": 0.003, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "AQUEOUS_EQUILIBRIUM", + "reactants": { + "SO4m": { + "qty": 1.0 + }, + "CLm": { + "qty": 1.0 + } + }, + "products": { + "SO4mm": { + "yield": 1.0 + }, + "aCL": { + "yield": 1.0 + } + }, + "A": 1.2, + "C": 0, + "k_reverse": 210000000.0, + "phase": "cloud water", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "CO2", + "aerosol phase": "cloud water", + "aerosol-phase species": "aCO2", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "O3", + "aerosol phase": "cloud water", + "aerosol-phase species": "aO3", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "HO2", + "aerosol phase": "cloud water", + "aerosol-phase species": "aHO2", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "HO", + "aerosol phase": "cloud water", + "aerosol-phase species": "aHO", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "H2O2", + "aerosol phase": "cloud water", + "aerosol-phase species": "aH2O2", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "NO2", + "aerosol phase": "cloud water", + "aerosol-phase species": "aNO2", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "HONO", + "aerosol phase": "cloud water", + "aerosol-phase species": "aHONO", + "aerosol-phase water": "[aH2O]" + }, + { + "type": "HL_PHASE_TRANSFER", + "gas-phase species": "HNO3", + "aerosol phase": "cloud water", + "aerosol-phase species": "aHNO3", + "aerosol-phase water": "[aH2O]" + }, { "type": "HL_PHASE_TRANSFER", "gas-phase species": "NO3", @@ -3552,118 +3510,118 @@ "name": "cloud water", "type": "AERO_PHASE", "species": [ - "SO5O2mm", - "aCHOH2COOH", - "aALD", - "NO2m", - "aCH3COH2", - "CHOSO3mm", - "FEC2O4p", - "NO2p", - "aO2CH2OH", - "aGLY", - "SO4mm", - "aNH3", - "aOP1", - "aBR", - "SO5O2Hm", - "aCH3CH2O", - "aSO2", - "O3m", - "FEppp", - "Hp", - "HCOOm", - "CLm", - "C2O4m", - "aHNO3", - "CLOHm", - "aO3", - "aCO2H", - "SO", - "aHONO", - "FEpp", - "aCOH2COOH", - "aCLNO2", - "FEOpp", "aCH3CHOH2", - "aHO2", - "aH2C2O4", + "aO3", + "aN2O5", + "HCO3m", + "SO4m", + "SO3m", + "CO2m", "aBR2", - "aETHPX", - "aCL", - "HSO5m", - "SO3mm", - "aO2COH2COOH", - "aNO2", - "aBRCL", + "aH2CO3", + "O3m", + "aHO", + "CLm", + "FEC2O42m", + "aOP1", + "aCH2OH", + "SO5m", "aHCL", + "C2O4mm", + "OHm", + "O2CHOHSO3m", + "aCL", + "MCOOm", + "[aH2O]", + "aHONO", + "aCH3O", "CHOHSO3m", - "aO2CHO", - "FEC2O42m", + "CUp", + "aHO3", + "aETHPX", + "CHOSO3m", + "aO2CH2OH", + "Hp", + "FEC2O4p", + "aHOBR", + "O2CH2COOm", + "aMO2", + "aCH3COH2OO", + "BROHm", + "aO2CH3CHOH", + "aCHOH2COOH", + "aHOCL", + "aNH3", "HMSm", + "O2m", + "CHOH", + "FEOHpp", + "aGLY", + "SO", + "HSO5m", + "aCH2COOH", + "NO3m", + "aSULF", "HC2O4m", + "aCHOH2", + "aCH3OH", + "aACO3", + "NH4p", + "aALD", + "aNO2", + "FEpp", + "aCH3COH2", + "aHO2", + "HCOOm", + "NO2p", + "aSO2", + "CUpp", "aORA1", - "aO2COH2CHOH2", + "aBRCL", + "SO4mm", + "BRm", + "aCOH2CHOH2", + "CLOHm", + "aH2O2", + "aHNO3", + "SO5O2mm", + "CHOH2COOm", + "aCHOH2CHOH2", "aNO3", - "aACO3", - "NO4m", - "aO2CH3CHOH", + "BR2m", + "SO3mm", "aCO2", - "NH4p", - "aSULF", - "MCOOm", + "aBR", "aCH3CHOH", - "aO2", - "SO3m", - "CHOSO3m", - "aHOBR", - "aH2CO3", - "[aH2O]", - "aHOCL", - "aCH3OH", - "aCH2COOH", - "aCH3COH2OO", - "aHCHO", - "aNO", + "aORA2", "HSO4m", - "O2CHOHSO3m", - "CHOH", - "CUpp", - "CL2m", - "SO5m", + "aH2C2O4", + "aETOH", + "C2O4m", + "aO2", + "aCOH2COOH", "HSO3m", - "OHm", - "O2m", - "FEOHpp", - "CUp", - "aCHOH2CHOH2", - "aORA2", - "SO4m", - "aCH2OH", - "BRm", - "aHO3", - "aHO", - "BROHm", - "O2CH2COOm", - "aCH2OH2", - "aH2O2", - "NO3m", - "HCO3m", - "aCOH2CHOH2", - "aMO2", - "aBRNO2", + "aHCHO", "aCL2", - "aN2O5", - "CO2m", + "CL2m", + "aCO2H", + "NO2m", + "FEOpp", "CH2COOm", - "aETOH", - "aCH3O", - "aCHOH2", - "CHOH2COOm", - "BR2m", + "aO2COH2CHOH2", + "CHOSO3mm", + "aCH3CO", "aHNO4", - "C2O4mm", - "aCH3CO" + "aCH3CH2O", + "aNO", + "aCH2OH2", + "aO2CHO", + "aBRNO2", + "FEppp", + "aCLNO2", + "SO5O2Hm", + "aO2COH2COOH", + "NO4m" ] }, { From 324fd6d8ca134c95ff6cf0d22b665f345647cb16 Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Thu, 13 Apr 2023 14:26:25 -0500 Subject: [PATCH 23/24] added todo comment --- capram_convert/convert.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/capram_convert/convert.py b/capram_convert/convert.py index 70b812ad..56ebfeae 100644 --- a/capram_convert/convert.py +++ b/capram_convert/convert.py @@ -213,6 +213,10 @@ def convert_products_to_yield(products): }, f, indent=2 ) +# TODO: aqueous phase photolysis reactions are calculated like this in capram2.4 +# j = A * exp (B *(1 - 1 /(cos (C * chi)); A = jmax; chi = zenith angle +# +# We recoded the A, B, and C values but have not done anything with them. Figure out what to do photolysis_reactions = [ { "type": "PHOTOLYSIS", From bfd9662869c28841a5ade6f907da4ec2e415ee2c Mon Sep 17 00:00:00 2001 From: Kyle Shores Date: Wed, 31 May 2023 09:40:53 -0500 Subject: [PATCH 24/24] latest config --- capram_convert/mechanism.json | 186 +++++++++++++++++----------------- 1 file changed, 93 insertions(+), 93 deletions(-) diff --git a/capram_convert/mechanism.json b/capram_convert/mechanism.json index 0fd8fb19..08028bc1 100644 --- a/capram_convert/mechanism.json +++ b/capram_convert/mechanism.json @@ -3510,118 +3510,118 @@ "name": "cloud water", "type": "AERO_PHASE", "species": [ - "aCH3CHOH2", - "aO3", - "aN2O5", + "aCH3CH2O", + "SO4mm", + "aHCL", + "BROHm", + "aETHPX", + "aSO2", "HCO3m", - "SO4m", - "SO3m", - "CO2m", - "aBR2", + "BR2m", + "aHOBR", + "aALD", "aH2CO3", - "O3m", - "aHO", - "CLm", - "FEC2O42m", - "aOP1", - "aCH2OH", - "SO5m", - "aHCL", + "aNO3", + "aCO2H", + "aMO2", + "aHCHO", + "FEOpp", + "aBR", "C2O4mm", - "OHm", - "O2CHOHSO3m", - "aCL", + "aO2COH2CHOH2", + "SO5O2Hm", + "aCHOH2CHOH2", + "aCL2", + "aACO3", + "aCH2OH", "MCOOm", - "[aH2O]", + "CL2m", + "SO3m", + "aCH3COH2", + "aHNO4", + "NH4p", + "HSO3m", + "aCO2", + "HSO4m", + "FEppp", + "OHm", + "aCHOH2COOH", + "CLOHm", + "NO3m", + "BRm", + "aNO", + "aBR2", + "O3m", + "aH2C2O4", + "aORA1", + "aCH3CHOH", + "HSO5m", + "aCH3COH2OO", "aHONO", "aCH3O", + "aNO2", + "aBRCL", + "aGLY", + "aCLNO2", "CHOHSO3m", - "CUp", - "aHO3", - "aETHPX", - "CHOSO3m", - "aO2CH2OH", - "Hp", + "aSULF", + "CHOH", + "aORA2", + "aCH3OH", "FEC2O4p", - "aHOBR", - "O2CH2COOm", - "aMO2", - "aCH3COH2OO", - "BROHm", + "C2O4m", + "SO3mm", + "Hp", + "O2m", + "aH2O2", + "aO2CHO", + "HMSm", + "aOP1", + "CO2m", + "aCHOH2", + "O2CHOHSO3m", + "FEC2O42m", "aO2CH3CHOH", - "aCHOH2COOH", + "HC2O4m", "aHOCL", + "SO5m", + "aCH3CO", + "aN2O5", + "NO4m", + "CH2COOm", + "CHOSO3mm", + "aCOH2CHOH2", + "CHOSO3m", + "O2CH2COOm", "aNH3", - "HMSm", - "O2m", - "CHOH", - "FEOHpp", - "aGLY", - "SO", - "HSO5m", + "aHO3", "aCH2COOH", - "NO3m", - "aSULF", - "HC2O4m", - "aCHOH2", - "aCH3OH", - "aACO3", - "NH4p", - "aALD", - "aNO2", - "FEpp", - "aCH3COH2", - "aHO2", + "CLm", "HCOOm", + "aO3", + "NO2m", + "aCL", + "SO", + "aCH3CHOH2", "NO2p", - "aSO2", - "CUpp", - "aORA1", - "aBRCL", - "SO4mm", - "BRm", - "aCOH2CHOH2", - "CLOHm", - "aH2O2", - "aHNO3", - "SO5O2mm", + "CUp", "CHOH2COOm", - "aCHOH2CHOH2", - "aNO3", - "BR2m", - "SO3mm", - "aCO2", - "aBR", - "aCH3CHOH", - "aORA2", - "HSO4m", - "aH2C2O4", + "CUpp", "aETOH", - "C2O4m", - "aO2", + "aBRNO2", "aCOH2COOH", - "HSO3m", - "aHCHO", - "aCL2", - "CL2m", - "aCO2H", - "NO2m", - "FEOpp", - "CH2COOm", - "aO2COH2CHOH2", - "CHOSO3mm", - "aCH3CO", - "aHNO4", - "aCH3CH2O", - "aNO", + "aO2CH2OH", + "SO4m", + "FEpp", "aCH2OH2", - "aO2CHO", - "aBRNO2", - "FEppp", - "aCLNO2", - "SO5O2Hm", "aO2COH2COOH", - "NO4m" + "aO2", + "aHO2", + "[aH2O]", + "aHO", + "aHNO3", + "SO5O2mm", + "FEOHpp" ] }, {