diff --git a/configs/miem/cams_finn_all_species_emissions_config.yaml b/configs/miem/cams_finn_all_species_emissions_config.yaml index f8337a5e5..36f265798 100644 --- a/configs/miem/cams_finn_all_species_emissions_config.yaml +++ b/configs/miem/cams_finn_all_species_emissions_config.yaml @@ -17,7 +17,7 @@ # individual sector variables -- "_sum" aggregates more sectors than just # those. # -# BC/OC have no gas-phase representation in ts1.json, so they get real miem +# BC/OC have no gas-phase representation in t1s2.json, so they get real miem # flux but no MICM Emission reaction (flux-only, no concentration curve). version: 1.0.0 species: [] diff --git a/configs/v1/miem_nox/mechanism.json b/configs/v1/miem_nox/mechanism.json index bea650cc5..524fe0722 100644 --- a/configs/v1/miem_nox/mechanism.json +++ b/configs/v1/miem_nox/mechanism.json @@ -1,7 +1,7 @@ { "name": "miem NOx box model", "version": "1.0.0", - "__description": "A small, purpose-built mechanism for the fortran/examples and python/musica/examples miem_nox_box_model* demos -- just enough chemistry to show a miem-driven EMISSION reaction feeding a real NOx/O3 photostationary-state signature, without splicing reactions into (or dragging in the other ~1400 reactions of) the real TS1 mechanism. The jno2 photolysis rate and the NO + O3 Arrhenius parameters are taken directly from configs/v1/ts1/ts1.json (real, validated values); the photolysis step lumps the real NO2 + hv -> NO + O(3P) followed by the fast O(3P) + O2 + M -> O3 into a single NO2 -> NO + O3 step, since O(3P)/O2/M aren't tracked here.", + "__description": "A small, purpose-built mechanism for the fortran/examples and python/musica/examples miem_nox_box_model* demos -- just enough chemistry to show a miem-driven EMISSION reaction feeding a real NOx/O3 photostationary-state signature, without splicing reactions into (or dragging in the other ~1400 reactions of) the real TS1 mechanism. The jno2 photolysis rate and the NO + O3 Arrhenius parameters are taken directly from configs/v1/ts1/t1s2.json (real, validated values); the photolysis step lumps the real NO2 + hv -> NO + O(3P) followed by the fast O(3P) + O2 + M -> O3 into a single NO2 -> NO + O3 step, since O(3P)/O2/M aren't tracked here.", "species": [ { "name": "NO" @@ -29,7 +29,7 @@ "type": "PHOTOLYSIS", "name": "jno2", "scaling factor": 1.0, - "__reaction": "NO2 + hv -> NO + O3 (lumped; real jno2 rate from ts1.json)", + "__reaction": "NO2 + hv -> NO + O3 (lumped; real jno2 rate from t1s2.json)", "reactants": [ { "species name": "NO2", "coefficient": 1.0 } ], @@ -41,7 +41,7 @@ }, { "type": "ARRHENIUS", - "__reaction": "NO + O3 -> NO2 (+ O2, untracked); rate constant from ts1.json", + "__reaction": "NO + O3 -> NO2 (+ O2, untracked); rate constant from t1s2.json", "A": 1806642.228, "B": 0.0, "C": -1500.0, diff --git a/configs/v1/ts1/initial_conditions.csv b/configs/v1/ts1/initial_conditions.csv index f767dbd75..0d8068fd7 100644 --- a/configs/v1/ts1/initial_conditions.csv +++ b/configs/v1/ts1/initial_conditions.csv @@ -329,23 +329,6 @@ PHOTO.jsoa4_a1,1.0e-20 PHOTO.jsoa4_a2,1.0e-20 PHOTO.jsoa5_a1,1.0e-20 PHOTO.jsoa5_a2,1.0e-20 -USER.het1,1.0E-20 -USER.het2,1.0E-20 -USER.het3,1.0E-20 -USER.het4,6.022140760000E-03 -USER.het5,6.022140760000E-03 -USER.het6,6.022140760000E-03 -USER.het7,1.0E-20 -USER.het8,1.0E-20 -USER.het9,6.022140760000E-03 -USER.het10,6.022140760000E-03 -USER.het11,1.0E-20 -USER.het12,1.0E-20 -USER.het13,1.0E-20 -USER.het14,1.0E-20 -USER.het15,6.022140760000E-03 -USER.het16,6.022140760000E-03 -USER.het17,6.022140760000E-03 SURF.usr_NO2_aer,2.820947917738780E-08,1.0e11 SURF.usr_HO2_aer,2.820947917738780E-08,1.0e11 SURF.usr_NO3_aer,2.820947917738780E-08,1.0e11 @@ -359,5 +342,14 @@ SURF.usr_NC4CHO_aer,2.820947917738780E-08,1.0e11 SURF.usr_TERPNIT_aer,2.820947917738780E-08,1.0e11 SURF.usr_NTERPOOH_aer,2.820947917738780E-08,1.0e11 SURF.usr_NC4CH2OH_aer,2.820947917738780E-08,1.0e11 +SURF.het7,1.0e-07,0.0 +SURF.het8,1.0e-07,0.0 +SURF.het11,1.0e-07,0.0 +SURF.het12,1.0e-07,0.0 +SURF.het13,1.0e-07,0.0 +SURF.het14,1.0e-07,0.0 +SURF.het1,1.0e-07,0.0 +SURF.het2,1.0e-07,0.0 +SURF.het3,1.0e-07,0.0 ENV.temperature,287.45 ENV.pressure,101319.9 \ No newline at end of file diff --git a/configs/v1/ts1/t1s2.json b/configs/v1/ts1/t1s2.json new file mode 100644 index 000000000..380f06d4b --- /dev/null +++ b/configs/v1/ts1/t1s2.json @@ -0,0 +1,18193 @@ +{ + "name": "MZ391_T1S2_20260129", + "reactions": [ + { + "type": "ARRHENIUS", + "A": 481771.2608, + "B": 0.0, + "C": 699.9997827108845, + "D": 300.0, + "E": 0.0, + "reactants": [ + { + "name": "HO2", + "coefficient": 1.0 + }, + { + "name": "XO2", + "coefficient": 1.0 + } + ], + "products": [ + { + "name": "XOOH", + "coefficient": 1.0 + } + ], + "gas phase": "gas" + }, + { + "type": "ARRHENIUS", + "A": 246907.77116, + "B": 0.0, + "C": 750.0023539654177, + "D": 300.0, + "E": 0.0, + 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8e-06 from Liu et al., Environ. Sci. & Tech, 53, 3517, 2019, doi:10.1021/acs.est.8b06367", + "gas phase": "gas", + "gas-phase species": "NO2", + "gas-phase products": [ + { + "species name": "OH", + "coefficient": 0.5 + }, + { + "species name": "NO", + "coefficient": 0.5 + }, + { + "species name": "HNO3", + "coefficient": 0.5 + } + ], + "reaction probability": 8e-06 + }, + { + "type": "SURFACE", + "name": "usr_HO2_aer", + "__description": "CAM mo_usrrxt.F90 hetrxtrate; reaction probability 0.1 from Gaubert et al. 2020, doi:10.5194/acp-20-14617-2020. Product is 0.5 H2O2 per mo_usrrxt.F90 comment 'ho2 -> 0.5 * h2o2' (line 2124); the camp_data export had this as H2O.", + "gas phase": "gas", + "gas-phase species": "HO2", + "gas-phase products": [ + { + "species name": "H2O2", + "coefficient": 0.5 + } + ], + "reaction probability": 0.1 + }, + { + "type": "SURFACE", + "name": "usr_GLYOXAL_aer", + "__description": "CAM mo_usrrxt.F90 hetrxtrate_gly; reaction probability 0.0002 from Washenfelder et al., JGR, 2011. Product is SOAG1 per mo_usrrxt.F90 comment 'glyoxal -> soag1' (line 2131); the camp_data export had this as SOAG0.", + "gas phase": "gas", + "gas-phase species": "GLYOXAL", + "gas-phase products": [ + { + "species name": "SOAG1", + "coefficient": 1.0 + } + ], + "reaction probability": 0.0002 + }, + { + "type": "SURFACE", + "name": "usr_ISOPNITA_aer", + "__description": "CAM mo_usrrxt.F90 hetrxtrate; reaction probability 0.005 from Fisher et al., ACP, 2016", + "gas phase": "gas", + "gas-phase species": "ISOPNITA", + "gas-phase products": [ + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "reaction probability": 0.005 + }, + { + "type": "SURFACE", + "name": "usr_ISOPNITB_aer", + "__description": "CAM mo_usrrxt.F90 hetrxtrate; reaction probability 0.005 from Fisher et al., ACP, 2016", + "gas phase": "gas", + "gas-phase species": "ISOPNITB", + "gas-phase products": [ + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "reaction probability": 0.005 + }, + { + "type": "SURFACE", + "name": "usr_ONITR_aer", + "__description": "CAM mo_usrrxt.F90 hetrxtrate; reaction probability 0.005 from mo_usrrxt.F90 (uncited in source)", + "gas phase": "gas", + "gas-phase species": "ONITR", + "gas-phase products": [ + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "reaction probability": 0.005 + }, + { + "type": "SURFACE", + "name": "usr_HONITR_aer", + "__description": "CAM mo_usrrxt.F90 hetrxtrate; reaction probability 0.005 from mo_usrrxt.F90 (uncited in source)", + "gas phase": "gas", + "gas-phase species": "HONITR", + "gas-phase products": [ + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "reaction probability": 0.005 + }, + { + "type": "SURFACE", + "name": "usr_TERPNIT_aer", + "__description": "CAM mo_usrrxt.F90 hetrxtrate; reaction probability 0.01 from mo_usrrxt.F90 (uncited in source)", + "gas phase": "gas", + "gas-phase species": "TERPNIT", + "gas-phase products": [ + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "reaction probability": 0.01 + }, + { + "type": "SURFACE", + "name": "usr_NTERPOOH_aer", + "__description": "CAM mo_usrrxt.F90 hetrxtrate; reaction probability 0.01 from mo_usrrxt.F90 (uncited in source)", + "gas phase": "gas", + "gas-phase species": "NTERPOOH", + "gas-phase products": [ + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "reaction probability": 0.01 + }, + { + "type": "SURFACE", + "name": "usr_NC4CHO_aer", + "__description": "CAM mo_usrrxt.F90 hetrxtrate; reaction probability 0.02 from mo_usrrxt.F90 (uncited in source)", + "gas phase": "gas", + "gas-phase species": "NC4CHO", + "gas-phase products": [ + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "reaction probability": 0.02 + }, + { + "type": "SURFACE", + "name": "usr_NC4CH2OH_aer", + "__description": "CAM mo_usrrxt.F90 hetrxtrate; reaction probability 0.005 from mo_usrrxt.F90 (uncited in source)", + "gas phase": "gas", + "gas-phase species": "NC4CH2OH", + "gas-phase products": [ + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "reaction probability": 0.005 + }, + { + "type": "SURFACE", + "name": "het1", + "__description": "CAM mo_strato_rates.F90 line 656-657, N2O5 hydrolysis on liquid sulfate aerosol (gprob_n2o5); reaction probability is composition/temperature-dependent in source (not a constant) and has not been implemented, so it is set to 0.0 here (no effect) rather than approximated", + "gas phase": "gas", + "gas-phase species": "N2O5", + "gas-phase products": [ + { + "species name": "HNO3", + "coefficient": 2.0 + } + ], + "reaction probability": 0.0 + }, + { + "type": "SURFACE", + "name": "het2", + "__description": "CAM mo_strato_rates.F90 line 707-708, ClONO2+H2O on liquid sulfate aerosol (gprob_cnt_h2o); reaction probability is composition/temperature-dependent in source (not a constant) and has not been implemented, so it is set to 0.0 here (no effect) rather than approximated", + "gas phase": "gas", + "gas-phase species": "CLONO2", + "gas-phase products": [ + { + "species name": "HOCL", + "coefficient": 1.0 + }, + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "reaction probability": 0.0 + }, + { + "type": "SURFACE", + "name": "het3", + "__description": "CAM mo_strato_rates.F90 line 727, BrONO2+H2O on liquid sulfate aerosol (gprob_bnt_h2o); reaction probability is composition/temperature-dependent in source (not a constant) and has not been implemented, so it is set to 0.0 here (no effect) rather than approximated", + "gas phase": "gas", + "gas-phase species": "BRONO2", + "gas-phase products": [ + { + "species name": "HOBR", + "coefficient": 1.0 + }, + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "reaction probability": 0.0 + }, + { + "type": "USER_DEFINED", + "name": "het4", + "__description": "CAM mo_strato_rates.F90, ClONO2+HCl on liquid sulfate aerosol; two gas-phase reactants, which MICM's SURFACE reaction type cannot represent (single reactant only), so this is a USER_DEFINED placeholder with scaling factor 0.0 (no effect) instead", + "scaling factor": 0.0, + "reactants": [ + { + "species name": "CLONO2", + "coefficient": 1.0 + }, + { + "species name": "HCL", + "coefficient": 1.0 + } + ], + "products": [ + { + "species name": "CL2", + "coefficient": 1.0 + }, + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "gas phase": "gas" + }, + { + "type": "USER_DEFINED", + "name": "het5", + "__description": "CAM mo_strato_rates.F90, HOCl+HCl on liquid sulfate aerosol; two gas-phase reactants, which MICM's SURFACE reaction type cannot represent (single reactant only), so this is a USER_DEFINED placeholder with scaling factor 0.0 (no effect) instead", + "scaling factor": 0.0, + "reactants": [ + { + "species name": "HCL", + "coefficient": 1.0 + }, + { + "species name": "HOCL", + "coefficient": 1.0 + } + ], + "products": [ + { + "species name": "CL2", + "coefficient": 1.0 + }, + { + "species name": "H2O", + "coefficient": 1.0 + } + ], + "gas phase": "gas" + }, + { + "type": "USER_DEFINED", + "name": "het6", + "__description": "CAM mo_strato_rates.F90, HOBr+HCl on liquid sulfate aerosol; two gas-phase reactants, which MICM's SURFACE reaction type cannot represent (single reactant only), so this is a USER_DEFINED placeholder with scaling factor 0.0 (no effect) instead", + "scaling factor": 0.0, + "reactants": [ + { + "species name": "HCL", + "coefficient": 1.0 + }, + { + "species name": "HOBR", + "coefficient": 1.0 + } + ], + "products": [ + { + "species name": "BRCL", + "coefficient": 1.0 + }, + { + "species name": "H2O", + "coefficient": 1.0 + } + ], + "gas phase": "gas" + }, + { + "type": "SURFACE", + "name": "het7", + "__description": "CAM mo_strato_rates.F90 line 949, N2O5 hydrolysis on NAT PSC; reaction probability 0.0004 (constant in source, not composition/temperature-dependent)", + "gas phase": "gas", + "gas-phase species": "N2O5", + "gas-phase products": [ + { + "species name": "HNO3", + "coefficient": 2.0 + } + ], + "reaction probability": 0.0004 + }, + { + "type": "SURFACE", + "name": "het8", + "__description": "CAM mo_strato_rates.F90 line 959, ClONO2+H2O on NAT PSC; reaction probability 0.004 (constant in source, not composition/temperature-dependent)", + "gas phase": "gas", + "gas-phase species": "CLONO2", + "gas-phase products": [ + { + "species name": "HOCL", + "coefficient": 1.0 + }, + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "reaction probability": 0.004 + }, + { + "type": "USER_DEFINED", + "name": "het9", + "__description": "CAM mo_strato_rates.F90, ClONO2+HCl on NAT PSC (reaction probability 0.2 in mo_strato_rates.F90, not usable here); two gas-phase reactants, which MICM's SURFACE reaction type cannot represent (single reactant only), so this is a USER_DEFINED placeholder with scaling factor 0.0 (no effect) instead", + "scaling factor": 0.0, + "reactants": [ + { + "species name": "CLONO2", + "coefficient": 1.0 + }, + { + "species name": "HCL", + "coefficient": 1.0 + } + ], + "products": [ + { + "species name": "CL2", + "coefficient": 1.0 + }, + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "gas phase": "gas" + }, + { + "type": "USER_DEFINED", + "name": "het10", + "__description": "CAM mo_strato_rates.F90, HOCl+HCl on NAT PSC (reaction probability 0.1 in mo_strato_rates.F90, not usable here); two gas-phase reactants, which MICM's SURFACE reaction type cannot represent (single reactant only), so this is a USER_DEFINED placeholder with scaling factor 0.0 (no effect) instead", + "scaling factor": 0.0, + "reactants": [ + { + "species name": "HCL", + "coefficient": 1.0 + }, + { + "species name": "HOCL", + "coefficient": 1.0 + } + ], + "products": [ + { + "species name": "CL2", + "coefficient": 1.0 + }, + { + "species name": "H2O", + "coefficient": 1.0 + } + ], + "gas phase": "gas" + }, + { + "type": "SURFACE", + "name": "het11", + "__description": "CAM mo_strato_rates.F90 line 1081, BrONO2+H2O on NAT PSC; reaction probability 0.006 (constant in source, not composition/temperature-dependent)", + "gas phase": "gas", + "gas-phase species": "BRONO2", + "gas-phase products": [ + { + "species name": "HOBR", + "coefficient": 1.0 + }, + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "reaction probability": 0.006 + }, + { + "type": "SURFACE", + "name": "het12", + "__description": "CAM mo_strato_rates.F90 line 1152, N2O5 hydrolysis on ice PSC; reaction probability 0.02 (constant in source, not composition/temperature-dependent)", + "gas phase": "gas", + "gas-phase species": "N2O5", + "gas-phase products": [ + { + "species name": "HNO3", + "coefficient": 2.0 + } + ], + "reaction probability": 0.02 + }, + { + "type": "SURFACE", + "name": "het13", + "__description": "CAM mo_strato_rates.F90 line 1162, ClONO2+H2O on ice PSC; reaction probability 0.3 (constant in source, not composition/temperature-dependent)", + "gas phase": "gas", + "gas-phase species": "CLONO2", + "gas-phase products": [ + { + "species name": "HOCL", + "coefficient": 1.0 + }, + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "reaction probability": 0.3 + }, + { + "type": "SURFACE", + "name": "het14", + "__description": "CAM mo_strato_rates.F90 line 1173, BrONO2+H2O on ice PSC; reaction probability 0.3 (constant in source, not composition/temperature-dependent)", + "gas phase": "gas", + "gas-phase species": "BRONO2", + "gas-phase products": [ + { + "species name": "HOBR", + "coefficient": 1.0 + }, + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "reaction probability": 0.3 + }, + { + "type": "USER_DEFINED", + "name": "het15", + "__description": "CAM mo_strato_rates.F90, ClONO2+HCl on ice PSC (reaction probability 0.3 in mo_strato_rates.F90, not usable here); two gas-phase reactants, which MICM's SURFACE reaction type cannot represent (single reactant only), so this is a USER_DEFINED placeholder with scaling factor 0.0 (no effect) instead", + "scaling factor": 0.0, + "reactants": [ + { + "species name": "CLONO2", + "coefficient": 1.0 + }, + { + "species name": "HCL", + "coefficient": 1.0 + } + ], + "products": [ + { + "species name": "CL2", + "coefficient": 1.0 + }, + { + "species name": "HNO3", + "coefficient": 1.0 + } + ], + "gas phase": "gas" + }, + { + "type": "USER_DEFINED", + "name": "het16", + "__description": "CAM mo_strato_rates.F90, HOCl+HCl on ice PSC (reaction probability 0.2 in mo_strato_rates.F90, not usable here); two gas-phase reactants, which MICM's SURFACE reaction type cannot represent (single reactant only), so this is a USER_DEFINED placeholder with scaling factor 0.0 (no effect) instead", + "scaling factor": 0.0, + "reactants": [ + { + "species name": "HCL", + "coefficient": 1.0 + }, + { + "species name": "HOCL", + "coefficient": 1.0 + } + ], + "products": [ + { + "species name": "CL2", + "coefficient": 1.0 + }, + { + "species name": "H2O", + "coefficient": 1.0 + } + ], + "gas phase": "gas" + }, + { + "type": "USER_DEFINED", + "name": "het17", + "__description": "CAM mo_strato_rates.F90, HOBr+HCl on ice PSC (reaction probability 0.3 in mo_strato_rates.F90, not usable here); two gas-phase reactants, which MICM's SURFACE reaction type cannot represent (single reactant only), so this is a USER_DEFINED placeholder with scaling factor 0.0 (no effect) instead", + "scaling factor": 0.0, + "reactants": [ + { + "species name": "HCL", + "coefficient": 1.0 + }, + { + "species name": "HOBR", + "coefficient": 1.0 + } + ], + "products": [ + { + "species name": "BRCL", + "coefficient": 1.0 + }, + { + "species name": "H2O", + "coefficient": 1.0 + } + ], + "gas phase": "gas" + }, + { + "type": "USER_DEFINED", + "name": "usr_CO_OH", + "__description": "CAM mo_usrrxt.F90 usr_CO_OH; JPL 19-5 Table 2-2 row K3, a chemical-activation reaction: k = k_f(T,[M]) + k_int(T)*(1 - k_f(T,[M])/k_inf(T)), k_f being a standard Troe association rate constant (k0_298=6.9e-33, n=2.1, k_inf_298=1.1e-12, m=-1.3, Fc=0.6, N=1) and k_int(T)=A*exp(-B/T) with A=1.85e-13, B=65. No MICM reaction type can represent this exactly (TROE and TERNARY_CHEMICAL_ACTIVATION were checked and ruled out; confirmed both algebraically and numerically). Needs a new CHEMICAL_ACTIVATION reaction type in MICM. Set to scaling factor 0.0 (no effect) until that is implemented.", + "scaling factor": 0.0, + "reactants": [ + { + "species name": "CO", + "coefficient": 1.0 + }, + { + "species name": "OH", + "coefficient": 1.0 + } + ], + "products": [ + { + "species name": "CO2", + "coefficient": 1.0 + }, + { + "species name": "HO2", + "coefficient": 1.0 + } + ], + "gas phase": "gas" + } + ], + "species": [ + { + "molecular weight [kg mol-1]": 0.133141, + "name": "ALKNIT", + "__description": "standard alkyl nitrate from BIGALK+OH chemistry" + }, + { + "molecular weight [kg mol-1]": 0.124135, + "name": "BZOOH", + "__description": "hydroperoxide from toluene oxidation" + }, + { + "molecular weight [kg mol-1]": 0.110109, + "name": "C6H5OOH", + "__description": "phenyl hydroperoxide" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "O2" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "O2_1S" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "O2_1D" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "COF2", + "__description": "carbonyl fluoride" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "COFCL", + "__description": "carbonyl chlorofluoride" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "F", + "__description": "fluorine atom" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "HF", + "__description": "hydrogen fluoride" + }, + { + "molecular weight [kg mol-1]": 0.159115, + "name": "BENZO2", + "__description": "bicyclic peroxy radical from OH + benzene" + }, + { + "molecular weight [kg mol-1]": 0.123128, + "name": "BZOO", + "__description": "peroxy radical from toluene oxidation" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "E90" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "NH_5", + "__description": "idealized tracer with 5 day loss rate" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "NH_50", + "__description": "idealized tracer with 50-day loss rate" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "ST80_25", + "__description": "Stratospheric loss tracer" + }, + { + "molecular weight [kg mol-1]": 0.121048, + "name": "PAN", + "__description": "peroxy acetyl nitrate" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "N2", + "__description": "nitrogen" + }, + { + "molecular weight [kg mol-1]": 0.0700878, + "name": "MVK", + "__description": "methyl vinyl ketone" + }, + { + "molecular weight [kg mol-1]": 0.120101, + "name": "MACROOH", + "__description": "peroxide from methacrolein" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "SOAG0", + "__description": "SOA gas-phase precursor VBS bin 0" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "SOAG1", + "__description": "SOA gas-phase precursor VBS bin 1" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "SOAG2", + "__description": "SOA gas-phase precursor VBS bin 2" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "SOAG3", + "__description": "SOA gas-phase precursor VBS bin 3" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "SOAG4", + "__description": "SOA gas-phase precursor VBS bin 4" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "soa4_a1", + "__description": "SOA bin 4, MAM accumulation mode" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "soa3_a1", + "__description": "SOA bin 3, MAM accumulation mode" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "soa2_a1", + "__description": "SOA bin 2, MAM accumulation mode" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "soa1_a1", + "__description": "SOA bin 1, MAM accumulation mode" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "soa1_a2", + "__description": "SOA bin 1, MAM Aitken mode" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "soa2_a2", + "__description": "SOA bin 2, MAM Aitken mode" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "soa3_a2", + "__description": "SOA bin 3, MAM Aitken mode" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "soa4_a2", + "__description": "SOA bin 4, MAM Aitken mode" + }, + { + "molecular weight [kg mol-1]": 0.147126, + "name": "ISOPNITB", + "__description": "1,4-hydroxynitrate from OH+isoprene chemistry" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "SO3", + "__description": "sulfur trioxide" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "OCS", + "__description": "carbonyl sulfide" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "SO", + "__description": "sulfur monoxide" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "S", + "__description": "atomic sulfur" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "BCARYO2VBS", + "__description": "BCARY oxidation proxy for NOx-dependent VBS-SOA" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "SF6", + "__description": "sulfur hexafluoride" + }, + { + "molecular weight [kg mol-1]": 0.0721026, + "name": "MEK", + "__description": "methyl ethyl ketone" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "MTERP", + "__description": "lumped monoterpenes" + }, + { + "molecular weight [kg mol-1]": 0.10801, + "name": "N2O5", + "__description": "dinitrogen pentoxide" + }, + { + "molecular weight [kg mol-1]": 0.0270251, + "name": "HCN", + "__description": "hydrogen cyanide" + }, + { + "molecular weight [kg mol-1]": 0.0010074, + "name": "H", + "__description": "hydrogen atom" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "NDEP", + "__description": "tracer for nitrogen deposition diagnostic" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "SVOC", + "__description": "semi-volatile organic precursor of VBS SOA" + }, + { + "molecular weight [kg mol-1]": 0.162118, + "name": "ISOPNO3", + "__description": "peroxy radical from isoprene NO3 oxidation" + }, + { + "molecular weight [kg mol-1]": 0.0890682, + "name": "RO2", + "__description": "peroxy radical from acetone" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "BENZO2VBS", + "__description": "benzene oxidation proxy for NOx-dependent VBS-SOA" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "IVOC", + "__description": "intermediate volatility organic precursor of VBS SOA" + }, + { + "molecular weight [kg mol-1]": 0.21524, + "name": "TERPNIT", + "__description": "mostly hydroxynitrates from OH+terpene chemistry" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "ISOPO2VBS", + "__description": "isoprene oxidation proxy for NOx-dependent VBS-SOA" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "IVOCO2VBS", + "__description": "IVOC oxidation proxy for NOx-dependent VBS-SOA" + }, + { + "molecular weight [kg mol-1]": 0.0630123, + "name": "HNO3", + "__description": "nitric acid" + }, + { + "molecular weight [kg mol-1]": 0.137112, + "name": "ACBZO2", + "__description": "acylperoxy radical from benzaldehyde" + }, + { + "molecular weight [kg mol-1]": 0.0760498, + "name": "CH3COOOH", + "__description": "peracetic acid" + }, + { + "molecular weight [kg mol-1]": 0.0640648, + "name": "SO2", + "__description": "sulfur dioxide" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "MTERPO2VBS", + "__description": "MTERP oxidation proxy for NOx-dependent VBS-SOA" + }, + { + "molecular weight [kg mol-1]": 0.0160406, + "name": "CH4", + "__description": "methane" + }, + { + "molecular weight [kg mol-1]": 0.0504859, + "name": "CH3CL", + "__description": "methyl chloride" + }, + { + "molecular weight [kg mol-1]": 0.0750424, + "name": "CH3CO3", + "__description": "acetylperoxy radical" + }, + { + "molecular weight [kg mol-1]": 0.109102, + "name": "C6H5O2", + "__description": "phenylperoxy radical" + }, + { + "molecular weight [kg mol-1]": 0.0740762, + "name": "HYAC", + "__description": "hydroxyacetone" + }, + { + "molecular weight [kg mol-1]": 0.116112, + "name": "HPALD", + "__description": "hydroperoxyaldehyde" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "TOLUO2VBS", + "__description": "toluene oxidation proxy for NOx-dependent VBS-SOA" + }, + { + "molecular weight [kg mol-1]": 0.103094, + "name": "MEKO2", + "__description": "peroxy radical formed from MEK oxidation" + }, + { + "molecular weight [kg mol-1]": 0.168227, + "name": "TERPROD1", + "__description": "lumped terpene oxidation product" + }, + { + "molecular weight [kg mol-1]": 0.0180142, + "name": "H2O" + }, + { + "molecular weight [kg mol-1]": 0.0460055, + "name": "NO2", + "__description": "nitrogen dioxide" + }, + { + "molecular weight [kg mol-1]": 0.0780646, + "name": "EOOH", + "__description": "hydroxyhydroperoxide from OH + ethene chemistry" + }, + { + "molecular weight [kg mol-1]": 0.23124, + "name": "NTERPOOH", + "__description": "nitrooxy-hydroperoxide from NO3+terpene chemistry" + }, + { + "molecular weight [kg mol-1]": 0.0, + "name": "XYLEO2VBS", + "__description": "xylenes oxidation proxy for NOx-dependent VBS-SOA" + }, + { + "molecular weight [kg mol-1]": 0.153822, + "name": "CCL4", + "__description": "carbon tetrachloride" + }, + { + "molecular weight [kg mol-1]": 0.165365, + "name": "CF2CLBR", + "__description": "bromochlorodifluoromethane (Halon 1211)" + }, + { + "molecular weight [kg mol-1]": 0.0300061, + "name": "NO", + "__description": "nitric oxide" + }, + { + "molecular weight [kg mol-1]": 0.14891, + "name": "CF3BR", + "__description": "bromotrifluoromethane (Halon 1301)" + }, + { + "molecular weight [kg mol-1]": 0.137368, + "name": "CFC11", + "__description": "trichlorofluoromethane" + }, + { + "molecular weight [kg mol-1]": 0.079904, + "name": "BR", + "__description": "bromine atom" + }, + { + "molecular weight [kg mol-1]": 0.115357, + "name": "BRCL", + "__description": "bromine chloride" + }, + { + "molecular weight [kg mol-1]": 0.0959034, + "name": "BRO", + "__description": "bromine monoxide" + }, + { + "molecular weight [kg mol-1]": 0.141909, + "name": "BRONO2", + "__description": "bromine nitrate" + }, + { + "molecular weight [kg mol-1]": 0.187375, + "name": "CFC113", + "__description": "1,1,2-trichlorotrifluoroethane" + }, + { + "molecular weight [kg mol-1]": 0.170921, + "name": "CFC114", + "__description": "1,2-dichloro-tetrafluoroethane" + }, + { + "molecular weight [kg mol-1]": 0.154467, + "name": "CFC115", + "__description": "chloropentafluoroethane" + }, + { + "molecular weight [kg mol-1]": 0.120913, + "name": "CFC12", + "__description": "dichlorodifluoromethane" + }, + { + "molecular weight [kg mol-1]": 0.173834, + "name": "CH2BR2", + "__description": "dibromomethane (methylene bromide)" + }, + { + "molecular weight [kg mol-1]": 0.0949372, + "name": "CH3BR", + "__description": "methyl bromide" + }, + { + "molecular weight [kg mol-1]": 0.133402, + "name": "CH3CCL3", + "__description": "mehtylchloroform" + }, + { + "molecular weight [kg mol-1]": 0.175114, + "name": "PHENO2", + "__description": "bicyclic peroxy radical from phenol" + }, + { + "molecular weight [kg mol-1]": 0.259824, + "name": "H2402", + "__description": "dibromotetrafluoroethane (Halon 2402)" + }, + { + "molecular weight [kg mol-1]": 0.0514521, + "name": "CLO", + "__description": "chlorine monoxide" + }, + { + "molecular weight [kg mol-1]": 0.0809114, + "name": "HBR", + "__description": "hydrogen bromide" + }, + { + "molecular weight [kg mol-1]": 0.25273, + "name": "CHBR3", + "__description": "bromoform" + }, + { + "molecular weight [kg mol-1]": 0.0460246, + "name": "HCOOH", + "__description": "formic acid" + }, + { + "molecular weight [kg mol-1]": 0.116948, + "name": "HCFC141B", + "__description": "1,1-dichoro-1-fluoroethane" + }, + { + "molecular weight [kg mol-1]": 0.0524595, + "name": "HOCL", + "__description": "hypochlorous acid" + }, + { + "molecular weight [kg mol-1]": 0.0140067, + "name": "N", + "__description": "nitrogen atom" + }, + { + "molecular weight [kg mol-1]": 0.199219, + "name": "TERP2O2", + "__description": "peroxy radical from lumped terpene product oxidation" + }, + { + "molecular weight [kg mol-1]": 0.0561032, + "name": "BIGENE", + "__description": "lumped alkenes C>3" + }, + { + "molecular weight [kg mol-1]": 0.0280516, + "name": "C2H4", + "__description": "ethene" + }, + { + "molecular weight [kg mol-1]": 0.0610578, + "name": "C2H5O2", + "__description": "ethylperoxy radical" + }, + { + "molecular weight [kg mol-1]": 0.0720614, + "name": "CH3COCHO", + "__description": "methyl glyoxal" + }, + { + "molecular weight [kg mol-1]": 0.0580768, + "name": "CH3COCH3", + "__description": "acetone" + }, + { + "molecular weight [kg mol-1]": 0.0159994, + "name": "O", + "__description": "ground state atomic oxygen" + }, + { + "molecular weight [kg mol-1]": 0.0674515, + "name": "OCLO" + }, + { + "molecular weight [kg mol-1]": 0.0159994, + "name": "O1D", + "__description": "excited state atomic oxygen" + }, + { + "molecular weight [kg mol-1]": 0.159115, + "name": "PHENO", + "__description": "phenoxy radical" + }, + { + "molecular weight [kg mol-1]": 0.100494, + "name": "HCFC142B", + "__description": "1-choro-1,1-difluoroethane" + }, + { + "molecular weight [kg mol-1]": 0.0864679, + "name": "HCFC22", + "__description": "chlorodifluoromethane" + }, + { + "molecular weight [kg mol-1]": 0.0364601, + "name": "HCL", + "__description": "hydrogen chloride" + }, + { + "molecular weight [kg mol-1]": 0.0621324, + "name": "DMS", + "__description": "dimethyl sulfide" + }, + { + "molecular weight [kg mol-1]": 0.0460658, + "name": "C2H5OH", + "__description": "ethanol" + }, + { + "molecular weight [kg mol-1]": 0.0969108, + "name": "HOBR", + "__description": "hypobromous acid" + }, + { + "molecular weight [kg mol-1]": 0.126109, + "name": "BEPOMUC", + "__description": "unsaturated dialdehydic epoxide from OH + benzene" + }, + { + "molecular weight [kg mol-1]": 0.102904, + "name": "CL2O2", + "__description": "chlorine monoxide dimer" + }, + { + "molecular weight [kg mol-1]": 0.0974576, + "name": "CLONO2", + "__description": "chlorine nitrate" + }, + { + "molecular weight [kg mol-1]": 0.0440098, + "name": "CO2", + "__description": "carbon dioxide" + }, + { + "molecular weight [kg mol-1]": 0.0354527, + "name": "CL", + "__description": "chlorine atom" + }, + { + "molecular weight [kg mol-1]": 0.0709054, + "name": "CL2", + "__description": "chlorine" + }, + { + "molecular weight [kg mol-1]": 0.106121, + "name": "BZALD", + "__description": "benzaldehyde" + }, + { + "molecular weight [kg mol-1]": 0.0781104, + "name": "BENZENE", + "__description": "benzene" + }, + { + "molecular weight [kg mol-1]": 0.0750836, + "name": "C3H7O2", + "__description": "propylperoxy radical" + }, + { + "molecular weight [kg mol-1]": 0.047032, + "name": "CH3O2", + "__description": "methylperoxy radical" + }, + { + "molecular weight [kg mol-1]": 0.204343, + "name": "BCARY", + "__description": "beta-caryophyllene" + }, + { + "molecular weight [kg mol-1]": 0.0980982, + "name": "BIGALD", + "__description": "lumped aldehyde from terpene ozonolysis" + }, + { + "molecular weight [kg mol-1]": 0.0980982, + "name": "BIGALD2", + "__description": "4-oxy-2-pentenal, a product of aromatic oxidation" + }, + { + "molecular weight [kg mol-1]": 0.0980982, + "name": "BIGALD3", + "__description": "2-methyl butenedial, a product of aromatic oxidation" + }, + { + "molecular weight [kg mol-1]": 0.112124, + "name": "BIGALD4", + "__description": "2-methyl-4-oxo-2-pentenal, a product of aromatic oxidation" + }, + { + "molecular weight [kg mol-1]": 0.0721438, + "name": "BIGALK", + "__description": "lumped alkanes C>3" + }, + { + "molecular weight [kg mol-1]": 0.0340136, + "name": "H2O2", + "__description": "hydrogen peroxide" + }, + { + "molecular weight [kg mol-1]": 0.0620652, + "name": "C2H5OOH", + "__description": "ethyl hydroperoxide" + }, + { + "molecular weight [kg mol-1]": 0.0300664, + "name": "C2H6", + "__description": "ethane" + }, + { + "molecular weight [kg mol-1]": 0.0440922, + "name": "C3H8", + "__description": "propane" + }, + { + "molecular weight [kg mol-1]": 0.0420774, + "name": "C3H6", + "__description": "propene" + }, + { + "molecular weight [kg mol-1]": 0.0300252, + "name": "CH2O", + "__description": "formaldehyde" + }, + { + "molecular weight [kg mol-1]": 0.0410509, + "name": "CH3CN", + "__description": "acetonitrile" + }, + { + "molecular weight [kg mol-1]": 0.0260368, + "name": "C2H2", + "__description": "ethyne" + }, + { + "molecular weight [kg mol-1]": 0.03204, + "name": "CH3OH", + "__description": "methanol" + }, + { + "molecular weight [kg mol-1]": 0.0480394, + "name": "CH3OOH", + "__description": "methyl hydroperoxide" + }, + { + "molecular weight [kg mol-1]": 0.108136, + "name": "CRESOL", + "__description": "lumped cresols (hydroxymethylbenzenes)" + }, + { + "molecular weight [kg mol-1]": 0.105109, + "name": "ENEO2", + "__description": "lumped hydroxyperoxy radical from OH + large alkenes" + }, + { + "molecular weight [kg mol-1]": 0.119093, + "name": "MACRO2", + "__description": "peroxy radical from methacrolein oxidation" + }, + { + "molecular weight [kg mol-1]": 0.11712, + "name": "ISOPAO2", + "__description": "1,2-isomer of isoprene peroxy radical" + }, + { + "molecular weight [kg mol-1]": 0.11712, + "name": "ISOPBO2", + "__description": "1,4-isomer of isoprene peroxy radical" + }, + { + "molecular weight [kg mol-1]": 0.101079, + "name": "MCO3", + "__description": "peroxy radical from OH abstraction reaction with MACR" + }, + { + "molecular weight [kg mol-1]": 0.0770572, + "name": "EO2", + "__description": "hydroxyperoxy radical from OH + ethene chemistry" + }, + { + "molecular weight [kg mol-1]": 0.0610578, + "name": "EO", + "__description": "hydroxyalkoxy radical from OH + ethene chemistry" + }, + { + "molecular weight [kg mol-1]": 0.0580356, + "name": "GLYOXAL", + "__description": "glyoxal" + }, + { + "molecular weight [kg mol-1]": 0.147085, + "name": "MPAN", + "__description": "methacrylol peroxynitrate" + }, + { + "molecular weight [kg mol-1]": 0.147126, + "name": "NC4CH2OH", + "__description": "nitrooxy-alcohol from NO3+isoprene chemistry" + }, + { + "molecular weight [kg mol-1]": 0.118127, + "name": "ISOPOOH", + "__description": "unsaturated hydroxyhydroperoxide" + }, + { + "molecular weight [kg mol-1]": 0.0600504, + "name": "GLYALD", + "__description": "glycolaldehyde" + }, + { + "molecular weight [kg mol-1]": 0.0330062, + "name": "HO2", + "__description": "hydroperoxyl radical" + }, + { + "molecular weight [kg mol-1]": 0.100113, + "name": "HYDRALD", + "__description": "lumped unsturated hydroxycarbonyl" + }, + { + "molecular weight [kg mol-1]": 0.0681142, + "name": "ISOP", + "__description": "isoprene" + }, + { + "molecular weight [kg mol-1]": 0.230232, + "name": "NTERPO2" + }, + { + "molecular weight [kg mol-1]": 0.106162, + "name": "XYLENES", + "__description": "lumped xylenes" + }, + { + "molecular weight [kg mol-1]": 0.091083, + "name": "PO2", + "__description": "propene peroxy radical" + }, + { + "molecular weight [kg mol-1]": 0.0921362, + "name": "TOLUENE", + "__description": "toluene" + }, + { + "molecular weight [kg mol-1]": 0.185234, + "name": "TERPO2", + "__description": "peroxy radical from terpenes+OH" + }, + { + "molecular weight [kg mol-1]": 0.183118, + "name": "PBZNIT", + "__description": "peroxy benzoyl nitrate" + }, + { + "molecular weight [kg mol-1]": 0.0700878, + "name": "MACR", + "__description": "methacrolein" + }, + { + "molecular weight [kg mol-1]": 0.1331, + "name": "HONITR", + "__description": "lumped hydroxynitrates from various compounds (formula updated 2017-04-06)" + }, + { + "molecular weight [kg mol-1]": 0.147126, + "name": "ISOPNITA", + "__description": "1,2-hydroxynitrate from OH+isoprene chemistry" + }, + { + "molecular weight [kg mol-1]": 0.163125, + "name": "ISOPNOOH", + "__description": "nitroxy-hydroperoxide from NO3+isoprene chemistry" + }, + { + "molecular weight [kg mol-1]": 0.118127, + "name": "IEPOX", + "__description": "isoprene epoxide" + }, + { + "molecular weight [kg mol-1]": 0.147126, + "name": "ONITR", + "__description": "lumped hydroxynitrates (formula updated 2017-04-06)" + }, + { + "molecular weight [kg mol-1]": 0.0980784, + "name": "H2SO4", + "__description": "sulfuric acid" + }, + { + "molecular weight [kg mol-1]": 0.0440129, + "name": "N2O", + "__description": "nitrous oxide" + }, + { + "molecular weight [kg mol-1]": 0.0020148, + "name": "H2", + "__description": "hydrogen" + }, + { + "molecular weight [kg mol-1]": 0.0630314, + "name": "HOCH2OO", + "__description": "formaldehyde / HO2 adduct" + }, + { + "molecular weight [kg mol-1]": 0.115064, + "name": "MALO2", + "__description": "acylperoxy radical from OH reaction with BIGALD1" + }, + { + "molecular weight [kg mol-1]": 0.117079, + "name": "MDIALO2", + "__description": "peroxy radical from OH addition to BIGALD1" + }, + { + "molecular weight [kg mol-1]": 0.104101, + "name": "MEKOOH", + "__description": "hydroperoxide from MEK oxidation" + }, + { + "molecular weight [kg mol-1]": 0.154201, + "name": "TERPROD2", + "__description": "lumped terpene oxidation product (2nd generation)" + }, + { + "molecular weight [kg mol-1]": 0.173141, + "name": "TOLO2", + "__description": "bicyclic peroxy radical from toluene" + }, + { + "molecular weight [kg mol-1]": 0.150126, + "name": "XOOH", + "__description": "lumped hydroperoxide from XO2 chemistry" + }, + { + "molecular weight [kg mol-1]": 0.187166, + "name": "XYLENO2", + "__description": "bicyclic peroxy radical from OH+xylenes chemistry" + }, + { + "molecular weight [kg mol-1]": 0.203166, + "name": "XYLOLO2", + "__description": "bicyclic peroxy radical from OH+XYLOL chemistry" + }, + { + "molecular weight [kg mol-1]": 0.0620049, + "name": "NO3", + "__description": "nitrate radical" + }, + { + "molecular weight [kg mol-1]": 0.0170068, + "name": "OH", + "__description": "hydroxyl radical" + }, + { + "molecular weight [kg mol-1]": 0.0941098, + "name": "PHENOL", + "__description": "phenol, product of benzene chemistry" + }, + { + "molecular weight [kg mol-1]": 0.0479982, + "name": "O3", + "__description": "ozone" + }, + { + "molecular weight [kg mol-1]": 0.186241, + "name": "TERPOOH", + "__description": "Hydroxy hydroperoxide from terpene 0 double bonds" + }, + { + "molecular weight [kg mol-1]": 0.0280104, + "name": "CO", + "__description": "carbon monoxide" + }, + { + "molecular weight [kg mol-1]": 0.0600504, + "name": "CH3COOH", + "__description": "acetic acid" + }, + { + "molecular weight [kg mol-1]": 0.044051, + "name": "CH3CHO", + "__description": "acetaldehyde" + }, + { + "molecular weight [kg mol-1]": 0.0840724, + "name": "BIGALD1", + "__description": "butenedial, a product of aromatic oxidation" + }, + { + "molecular weight [kg mol-1]": 0.104143, + "name": "ALKOOH", + "__description": "lumped alkane peroxide" + }, + { + "molecular weight [kg mol-1]": 0.12909, + "name": "DICARBO2", + "__description": "acylperoxy radical formed from aromatic oxidation, via unsaturated dicarbonyl chemistry" + }, + { + "molecular weight [kg mol-1]": 0.160122, + "name": "BENZOOH", + "__description": "bicyclic hydroperoxide from OH + benzene" + }, + { + "molecular weight [kg mol-1]": 0.103135, + "name": "ALKO2", + "__description": "lumped alkane peroxy radical from BIGALK" + }, + { + "molecular weight [kg mol-1]": 0.0790117, + "name": "HO2NO2", + "__description": "pernitric acid" + }, + { + "molecular weight [kg mol-1]": 0.076091, + "name": "C3H7OOH", + "__description": "propyl hydrogen peroxide" + }, + { + "molecular weight [kg mol-1]": 0.017031, + "name": "NH3", + "__description": "ammonia" + }, + { + "molecular weight [kg mol-1]": 0.200226, + "name": "TERP2OOH", + "__description": "2nd generation terpene hydroperoxide" + }, + { + "molecular weight [kg mol-1]": 0.188174, + "name": "XYLENOOH", + "__description": "bicyclic hydroperoxide from OH+xylenes chemistry" + }, + { + "molecular weight [kg mol-1]": 0.119074, + "name": "NOA", + "__description": "nitrooxyacetone, largely from NO3+propene chemistry" + }, + { + "molecular weight [kg mol-1]": 0.145111, + "name": "NC4CHO", + "__description": "nitrooxy-aldehyde from NO3+isoprene chemistry" + }, + { + "molecular weight [kg mol-1]": 0.140134, + "name": "TEPOMUC", + "__description": "toluene, xylenes product" + }, + { + "molecular weight [kg mol-1]": 0.176122, + "name": "PHENOOH", + "__description": "bicyclic hydroperoxide from phenol" + }, + { + "molecular weight [kg mol-1]": 0.0920904, + "name": "POOH", + "__description": "propene-derived hydroxy hydroperoxide" + }, + { + "molecular weight [kg mol-1]": 0.0900756, + "name": "ROOH", + "__description": "acetone hydroperoxide" + }, + { + "molecular weight [kg mol-1]": 0.174148, + "name": "TOLOOH", + "__description": "bicyclic hydroperoxide from toluene" + }, + { + "molecular weight [kg mol-1]": 0.149119, + "name": "XO2", + "__description": "peroxy radical from ISOPOOH, IEPOX, HPALD" + }, + { + "molecular weight [kg mol-1]": 0.122161, + "name": "XYLOL", + "__description": "dimethyl phenol from xylenes oxidation" + }, + { + "molecular weight [kg mol-1]": 0.204173, + "name": "XYLOLOOH", + "__description": "bicyclic hydroperoxide from OH+XYLOL chemistry" + }, + { + "name": "M", + "__description": "third-body species" + }, + { + "name": "sink", + "__description": "sink species" + }, + { + "name": "soa5_a1" + }, + { + "name": "soa5_a2" + }, + { + "molecular weight [kg mol-1]": 0.018039, + "name": "NH4" + } + ], + "phases": [ + { + "name": "gas", + "species": [ + { + "name": "ALKNIT" + }, + { + "name": "BZOOH" + }, + { + "name": "C6H5OOH" + }, + { + "name": "O2" + }, + { + "name": "O2_1S" + }, + { + "name": "O2_1D" + }, + { + "name": "COF2" + }, + { + "name": "COFCL" + }, + { + "name": "F" + }, + { + "name": "HF" + }, + { + "name": "BENZO2" + }, + { + "name": "BZOO" + }, + { + "name": "E90" + }, + { + "name": "NH_5" + }, + { + "name": "NH_50" + }, + { + "name": "ST80_25" + }, + { + "name": "PAN" + }, + { + "name": "N2" + }, + { + "name": "MVK" + }, + { + "name": "MACROOH" + }, + { + "name": "SOAG0" + }, + { + "name": "SOAG1" + }, + { + "name": "SOAG2" + }, + { + "name": "SOAG3" + }, + { + "name": "SOAG4" + }, + { + "name": "soa4_a1" + }, + { + "name": "soa3_a1" + }, + { + "name": "soa2_a1" + }, + { + "name": "soa1_a1" + }, + { + "name": "soa1_a2" + }, + { + "name": "soa2_a2" + }, + { + "name": "soa3_a2" + }, + { + "name": "soa4_a2" + }, + { + "name": "ISOPNITB", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "SO3" + }, + { + "name": "OCS" + }, + { + "name": "SO" + }, + { + "name": "S" + }, + { + "name": "BCARYO2VBS" + }, + { + "name": "SF6" + }, + { + "name": "MEK" + }, + { + "name": "MTERP" + }, + { + "name": "N2O5", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "HCN" + }, + { + "name": "H" + }, + { + "name": "NDEP" + }, + { + "name": "SVOC" + }, + { + "name": "ISOPNO3" + }, + { + "name": "RO2" + }, + { + "name": "BENZO2VBS" + }, + { + "name": "IVOC" + }, + { + "name": "TERPNIT", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "ISOPO2VBS" + }, + { + "name": "IVOCO2VBS" + }, + { + "name": "HNO3" + }, + { + "name": "ACBZO2" + }, + { + "name": "CH3COOOH" + }, + { + "name": "SO2" + }, + { + "name": "MTERPO2VBS" + }, + { + "name": "CH4" + }, + { + "name": "CH3CL" + }, + { + "name": "CH3CO3" + }, + { + "name": "C6H5O2" + }, + { + "name": "HYAC" + }, + { + "name": "HPALD" + }, + { + "name": "TOLUO2VBS" + }, + { + "name": "MEKO2" + }, + { + "name": "TERPROD1" + }, + { + "name": "H2O" + }, + { + "name": "NO2", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "EOOH" + }, + { + "name": "NTERPOOH", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "XYLEO2VBS" + }, + { + "name": "CCL4" + }, + { + "name": "CF2CLBR" + }, + { + "name": "NO" + }, + { + "name": "CF3BR" + }, + { + "name": "CFC11" + }, + { + "name": "BR" + }, + { + "name": "BRCL" + }, + { + "name": "BRO" + }, + { + "name": "BRONO2", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "CFC113" + }, + { + "name": "CFC114" + }, + { + "name": "CFC115" + }, + { + "name": "CFC12" + }, + { + "name": "CH2BR2" + }, + { + "name": "CH3BR" + }, + { + "name": "CH3CCL3" + }, + { + "name": "PHENO2" + }, + { + "name": "H2402" + }, + { + "name": "CLO" + }, + { + "name": "HBR" + }, + { + "name": "CHBR3" + }, + { + "name": "HCOOH" + }, + { + "name": "HCFC141B" + }, + { + "name": "HOCL" + }, + { + "name": "N" + }, + { + "name": "TERP2O2" + }, + { + "name": "BIGENE" + }, + { + "name": "C2H4" + }, + { + "name": "C2H5O2" + }, + { + "name": "CH3COCHO" + }, + { + "name": "CH3COCH3" + }, + { + "name": "O" + }, + { + "name": "OCLO" + }, + { + "name": "O1D" + }, + { + "name": "PHENO" + }, + { + "name": "HCFC142B" + }, + { + "name": "HCFC22" + }, + { + "name": "HCL" + }, + { + "name": "DMS" + }, + { + "name": "C2H5OH" + }, + { + "name": "HOBR" + }, + { + "name": "BEPOMUC" + }, + { + "name": "CL2O2" + }, + { + "name": "CLONO2", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "CO2" + }, + { + "name": "CL" + }, + { + "name": "CL2" + }, + { + "name": "BZALD" + }, + { + "name": "BENZENE" + }, + { + "name": "C3H7O2" + }, + { + "name": "CH3O2" + }, + { + "name": "BCARY" + }, + { + "name": "BIGALD" + }, + { + "name": "BIGALD2" + }, + { + "name": "BIGALD3" + }, + { + "name": "BIGALD4" + }, + { + "name": "BIGALK" + }, + { + "name": "H2O2" + }, + { + "name": "C2H5OOH" + }, + { + "name": "C2H6" + }, + { + "name": "C3H8" + }, + { + "name": "C3H6" + }, + { + "name": "CH2O" + }, + { + "name": "CH3CN" + }, + { + "name": "C2H2" + }, + { + "name": "CH3OH" + }, + { + "name": "CH3OOH" + }, + { + "name": "CRESOL" + }, + { + "name": "ENEO2" + }, + { + "name": "MACRO2" + }, + { + "name": "ISOPAO2" + }, + { + "name": "ISOPBO2" + }, + { + "name": "MCO3" + }, + { + "name": "EO2" + }, + { + "name": "EO" + }, + { + "name": "GLYOXAL", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "MPAN" + }, + { + "name": "NC4CH2OH", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "ISOPOOH" + }, + { + "name": "GLYALD" + }, + { + "name": "HO2", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "HYDRALD" + }, + { + "name": "ISOP" + }, + { + "name": "NTERPO2" + }, + { + "name": "XYLENES" + }, + { + "name": "PO2" + }, + { + "name": "TOLUENE" + }, + { + "name": "TERPO2" + }, + { + "name": "PBZNIT" + }, + { + "name": "MACR" + }, + { + "name": "HONITR", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "ISOPNITA", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "ISOPNOOH" + }, + { + "name": "IEPOX" + }, + { + "name": "ONITR", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "H2SO4" + }, + { + "name": "N2O" + }, + { + "name": "H2" + }, + { + "name": "HOCH2OO" + }, + { + "name": "MALO2" + }, + { + "name": "MDIALO2" + }, + { + "name": "MEKOOH" + }, + { + "name": "TERPROD2" + }, + { + "name": "TOLO2" + }, + { + "name": "XOOH" + }, + { + "name": "XYLENO2" + }, + { + "name": "XYLOLO2" + }, + { + "name": "NO3", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "OH" + }, + { + "name": "PHENOL" + }, + { + "name": "O3" + }, + { + "name": "TERPOOH" + }, + { + "name": "CO" + }, + { + "name": "CH3COOH" + }, + { + "name": "CH3CHO" + }, + { + "name": "BIGALD1" + }, + { + "name": "ALKOOH" + }, + { + "name": "DICARBO2" + }, + { + "name": "BENZOOH" + }, + { + "name": "ALKO2" + }, + { + "name": "HO2NO2" + }, + { + "name": "C3H7OOH" + }, + { + "name": "NH3" + }, + { + "name": "TERP2OOH" + }, + { + "name": "XYLENOOH" + }, + { + "name": "NOA" + }, + { + "name": "NC4CHO", + "diffusion coefficient [m2 s-1]": 1e-05 + }, + { + "name": "TEPOMUC" + }, + { + "name": "PHENOOH" + }, + { + "name": "POOH" + }, + { + "name": "ROOH" + }, + { + "name": "TOLOOH" + }, + { + "name": "XO2" + }, + { + "name": "XYLOL" + }, + { + "name": "XYLOLOOH" + }, + { + "name": "M" + }, + { + "name": "sink" + }, + { + "name": "soa5_a1" + }, + { + "name": "soa5_a2" + }, + { + "name": "NH4" + } + ] + } + ], + "version": "1.0.0" +} \ No newline at end of file diff --git a/fortran/examples/ts1_box_model.F90 b/fortran/examples/ts1_box_model.F90 index 4bb1a3193..0ed706fe4 100644 --- a/fortran/examples/ts1_box_model.F90 +++ b/fortran/examples/ts1_box_model.F90 @@ -91,7 +91,7 @@ program ts1_box_model ! --- Set up MICM for the TS1 mechanism --- write(*,*) "Setting up MICM (TS1)..." - micm => micm_t("../v1/ts1/ts1.json", RosenbrockStandardOrder, error) + micm => micm_t("../v1/ts1/t1s2.json", RosenbrockStandardOrder, error) call check(error, "creating MICM") state => micm%get_state(NUM_CELLS, error) diff --git a/julia/test/test_ts1_column_model.jl b/julia/test/test_ts1_column_model.jl index 5e4ec70aa..a877eb6fb 100644 --- a/julia/test/test_ts1_column_model.jl +++ b/julia/test/test_ts1_column_model.jl @@ -18,7 +18,7 @@ const _TS1_CONFIG_ROOT = joinpath(@__DIR__, "..", "..", "configs") const _TS1_TUVX_CONFIG = joinpath(_TS1_CONFIG_ROOT, "tuvx", "ts1_tsmlt.json") const _TS1_HOST_RADIATION_FIELD_CONFIG = joinpath(_TS1_CONFIG_ROOT, "tuvx", "ts1_tsmlt_host_radiation_field.json") -const _TS1_MICM_CONFIG = joinpath(_TS1_CONFIG_ROOT, "v1", "ts1", "ts1.json") +const _TS1_MICM_CONFIG = joinpath(_TS1_CONFIG_ROOT, "v1", "ts1", "t1s2.json") const _TS1_INITIAL_CONDITIONS = joinpath(_TS1_CONFIG_ROOT, "v1", "ts1", "initial_conditions.csv") diff --git a/pyproject.toml b/pyproject.toml index 6be3933e7..bc771365c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -161,7 +161,7 @@ test-command = [ '''python -c "import musica; print(f'musica v{musica.__version__}')"''', "musica-cli --help", "pytest {project}/python/test", - "musica-cli --convert configs/v0/TS1/config.json -o ts1.json", + "musica-cli --convert configs/v0/TS1/config.json -o t1s2.json", "musica-cli -e CARMA_Aluminum -o .", "musica-cli -e CARMA_Sulfate -o .", "musica-cli -e Lorenz_Attractor -o .", diff --git a/python/musica/examples/miem_cams_finn_box_model_real_fixture.py b/python/musica/examples/miem_cams_finn_box_model_real_fixture.py index 8cccc3dde..2c8e40a44 100644 --- a/python/musica/examples/miem_cams_finn_box_model_real_fixture.py +++ b/python/musica/examples/miem_cams_finn_box_model_real_fixture.py @@ -8,7 +8,7 @@ # 7 gas-phase species (NH3, CO, ISOP, MTERP, NO, NO2, SO2) get an `Emission` # reaction and a concentration+flux panel; NOx is split 9:1 NO:NO2, same as # elsewhere in this repo. BC/OC are aerosol mass with no gas-phase -# representation in ts1.json, so they get a flux-only panel instead. +# representation in t1s2.json, so they get a flux-only panel instead. # FINN's raw fixture is in molecules cm-2 s-1, not kg m-2 s-1 like CAMS; the # config's species-map scaling factors convert it before miem sums it with # CAMS. @@ -100,7 +100,7 @@ def main(plot=True): morning_local = datetime.combine(sim_date, time(9, 30), tzinfo=boulder_tz) sim_time = (morning_local - timedelta(hours=1)).astimezone(ZoneInfo("UTC")) - mechanism = parse(find_config_path("v1", "ts1", "ts1.json")) + mechanism = parse(find_config_path("v1", "ts1", "t1s2.json")) gas_phase = next(p for p in mechanism.phases if p.name == "gas") molecular_weights = {} diff --git a/python/musica/examples/miem_cams_finn_shared.py b/python/musica/examples/miem_cams_finn_shared.py index 00ce544ce..faaac170d 100644 --- a/python/musica/examples/miem_cams_finn_shared.py +++ b/python/musica/examples/miem_cams_finn_shared.py @@ -28,14 +28,14 @@ def resolve_inventory_directories(mechanism, config_dir): # 2024-11-01 00:00:00 UTC -- inside both CAMS's and FINN's valid data windows. SIM_EPOCH = 1730419200.0 -# Gas-phase species already in ts1.json; each gets a MICM `Emission` -# reaction and a concentration + flux plot panel. MTERP's ts1.json molecular +# Gas-phase species already in t1s2.json; each gets a MICM `Emission` +# reaction and a concentration + flux plot panel. MTERP's t1s2.json molecular # weight is a placeholder 0.0, so it uses the standard alpha-pinene # surrogate weight instead. GAS_PHASE_SPECIES = ("NH3", "CO", "ISOP", "MTERP", "NO", "NO2", "SO2") MTERP_MOLECULAR_WEIGHT_OVERRIDE = 0.13623 # kg mol-1, alpha-pinene surrogate -# Aerosol species: real mass, no gas-phase representation in ts1.json -- get +# Aerosol species: real mass, no gas-phase representation in t1s2.json -- get # real miem flux but no MICM Emission reaction (flux-only panel). AEROSOL_SPECIES = ("BC", "OC") diff --git a/python/musica/examples/miem_nox_box_model.py b/python/musica/examples/miem_nox_box_model.py index c3ab6346b..fc13385df 100644 --- a/python/musica/examples/miem_nox_box_model.py +++ b/python/musica/examples/miem_nox_box_model.py @@ -151,7 +151,7 @@ def main(plot=True): noon_local = datetime.combine(today_local, time(7, 30), tzinfo=boulder_tz) sim_time = (noon_local - timedelta(hours=1)).astimezone(ZoneInfo("UTC")) - mechanism = parse(find_config_path("v1", "ts1", "ts1.json")) + mechanism = parse(find_config_path("v1", "ts1", "t1s2.json")) gas_phase = next(p for p in mechanism.phases if p.name == "gas") no_species = next(s for s in mechanism.species if s.name == "NO") no_emission = Emission(name="NO", products=[no_species], gas_phase=gas_phase) diff --git a/python/musica/examples/miem_nox_box_model_real_fixture.py b/python/musica/examples/miem_nox_box_model_real_fixture.py index 31611ebc8..cebb0a7bd 100644 --- a/python/musica/examples/miem_nox_box_model_real_fixture.py +++ b/python/musica/examples/miem_nox_box_model_real_fixture.py @@ -156,7 +156,7 @@ def main(plot=True): noon_local = datetime.combine(sim_date, time(7, 30), tzinfo=boulder_tz) sim_time = (noon_local - timedelta(hours=1)).astimezone(ZoneInfo("UTC")) - mechanism = parse(find_config_path("v1", "ts1", "ts1.json")) + mechanism = parse(find_config_path("v1", "ts1", "t1s2.json")) gas_phase = next(p for p in mechanism.phases if p.name == "gas") nox_emissions = [ Emission(name=name, products=[next(s for s in mechanism.species if s.name == name)], gas_phase=gas_phase) diff --git a/python/musica/examples/ts1_box_model.py b/python/musica/examples/ts1_box_model.py index c291ae452..d8fa3095a 100644 --- a/python/musica/examples/ts1_box_model.py +++ b/python/musica/examples/ts1_box_model.py @@ -47,7 +47,7 @@ def main(plot=True): rate = tuv_rates.sel(reaction=tuv_label).photolysis_rate_constants.values * scale photolysis_rate_constants[f'PHOTO.{label}'] = rate[start:end] # skip the first grid cell which is at 0 km - mechanism = parse(find_config_path("v1", "ts1", "ts1.json")) + mechanism = parse(find_config_path("v1", "ts1", "t1s2.json")) solver = musica.MICM(mechanism=mechanism, solver_type=musica.SolverType.rosenbrock_standard_order) diff --git a/python/musica/examples/ts1_latin_hypercube.py b/python/musica/examples/ts1_latin_hypercube.py index 328b9cd35..760d01637 100644 --- a/python/musica/examples/ts1_latin_hypercube.py +++ b/python/musica/examples/ts1_latin_hypercube.py @@ -21,7 +21,7 @@ def main(plot=True): """ from scipy.stats import qmc - mechanism = parse(find_config_path("v1", "ts1", "ts1.json")) + mechanism = parse(find_config_path("v1", "ts1", "t1s2.json")) solver = musica.MICM(mechanism=mechanism, solver_type=musica.SolverType.rosenbrock_standard_order) @@ -88,13 +88,25 @@ def main(plot=True): lower_bounds.append(float(user) * (1 - user_defined_perturbation)) upper_bounds.append(float(user) * (1 + user_defined_perturbation)) + # A multiplicative perturbation collapses to a zero-width bound when the nominal + # value is exactly zero (e.g. particle number concentration for aerosol types that + # are not present in this scenario), so those get a small fixed-width bound instead. + zero_value_bound_width = 1e-10 + + def perturbed_bounds(value, perturbation): + if value == 0: + return 0.0, zero_value_bound_width + return value * (1 - perturbation), value * (1 + perturbation) + for _, row in surface_reactions.iterrows(): # effective radius - lower_bounds.append(float(row['value1']) * (1 - surface_perturbation)) - upper_bounds.append(float(row['value1']) * (1 + surface_perturbation)) + lower, upper = perturbed_bounds(float(row['value1']), surface_perturbation) + lower_bounds.append(lower) + upper_bounds.append(upper) # particle number concentration - lower_bounds.append(float(row['value2']) * (1 - surface_perturbation)) - upper_bounds.append(float(row['value2']) * (1 + surface_perturbation)) + lower, upper = perturbed_bounds(float(row['value2']), surface_perturbation) + lower_bounds.append(lower) + upper_bounds.append(upper) for environmental in environmental_conditions['value1']: lower_bounds.append(float(environmental) * diff --git a/tutorials/11. ts1_box_model.ipynb b/tutorials/11. ts1_box_model.ipynb index 12dd2858f..19a050bc9 100644 --- a/tutorials/11. ts1_box_model.ipynb +++ b/tutorials/11. ts1_box_model.ipynb @@ -171,37 +171,7 @@ "id": "c9d0e1f2", "metadata": {}, "outputs": [], - "source": [ - "start = 1\n", - "num_grid_cells = 9\n", - "\n", - "# Compute initial photolysis rates and grab the altitude edges for our grid cells\n", - "photolysis_rate_constants, tuv_rates = get_tuv_rates(sim_time, num_grid_cells, start)\n", - "vertical_edges = tuv_rates.vertical_edge[start:start + num_grid_cells].data\n", - "\n", - "print(f\"Altitude range: {vertical_edges.min():.1f} – {vertical_edges.max():.1f} km\")\n", - "\n", - "# US Standard Atmosphere T and P at those altitudes (km -> m)\n", - "atm = ussa1976.compute(z=vertical_edges * 1000, variables=[\"t\", \"p\"])\n", - "temperature = atm['t'].values\n", - "pressure = atm['p'].values\n", - "\n", - "print(f\"Temperature range: {temperature.min():.1f} – {temperature.max():.1f} K\")\n", - "print(f\"Pressure range: {pressure.min():.1f} – {pressure.max():.1f} Pa\")\n", - "\n", - "# Load mechanism and create solver\n", - "mechanism = parse(find_config_path(\"v1\", \"ts1\", \"ts1.json\"))\n", - "\n", - "solver = musica.MICM(\n", - " mechanism=mechanism,\n", - " solver_type=musica.SolverType.rosenbrock_standard_order\n", - ")\n", - "\n", - "state = solver.create_state(num_grid_cells)\n", - "\n", - "print(f\"Solver created with {num_grid_cells} grid cells\")\n", - "print(f\"Mechanism has {len(list(state.get_species_ordering()))} species\")" - ] + "source": "start = 1\nnum_grid_cells = 9\n\n# Compute initial photolysis rates and grab the altitude edges for our grid cells\nphotolysis_rate_constants, tuv_rates = get_tuv_rates(sim_time, num_grid_cells, start)\nvertical_edges = tuv_rates.vertical_edge[start:start + num_grid_cells].data\n\nprint(f\"Altitude range: {vertical_edges.min():.1f} – {vertical_edges.max():.1f} km\")\n\n# US Standard Atmosphere T and P at those altitudes (km -> m)\natm = ussa1976.compute(z=vertical_edges * 1000, variables=[\"t\", \"p\"])\ntemperature = atm['t'].values\npressure = atm['p'].values\n\nprint(f\"Temperature range: {temperature.min():.1f} – {temperature.max():.1f} K\")\nprint(f\"Pressure range: {pressure.min():.1f} – {pressure.max():.1f} Pa\")\n\n# Load mechanism and create solver\nmechanism = parse(find_config_path(\"v1\", \"ts1\", \"t1s2.json\"))\n\nsolver = musica.MICM(\n mechanism=mechanism,\n solver_type=musica.SolverType.rosenbrock_standard_order\n)\n\nstate = solver.create_state(num_grid_cells)\n\nprint(f\"Solver created with {num_grid_cells} grid cells\")\nprint(f\"Mechanism has {len(list(state.get_species_ordering()))} species\")" }, { "cell_type": "markdown", @@ -502,4 +472,4 @@ }, "nbformat": 4, "nbformat_minor": 5 -} +} \ No newline at end of file diff --git a/tutorials/19. miem_nox_box_model.ipynb b/tutorials/19. miem_nox_box_model.ipynb index ab2f2113d..7182fc088 100644 --- a/tutorials/19. miem_nox_box_model.ipynb +++ b/tutorials/19. miem_nox_box_model.ipynb @@ -129,19 +129,11 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "id": "a24cfce2", "metadata": {}, "outputs": [], - "source": [ - "mechanism = parse(find_config_path(\"v1\", \"ts1\", \"ts1.json\"))\n", - "gas_phase = next(p for p in mechanism.phases if p.name == \"gas\")\n", - "no_species = next(s for s in mechanism.species if s.name == \"NO\")\n", - "mechanism.reactions = list(mechanism.reactions) + [Emission(name=\"NO\", products=[no_species], gas_phase=gas_phase)]\n", - "\n", - "solver = musica.MICM(mechanism=mechanism, solver_type=musica.SolverType.rosenbrock_standard_order)\n", - "state = solver.create_state(num_grid_cells)" - ] + "source": "mechanism = parse(find_config_path(\"v1\", \"ts1\", \"t1s2.json\"))\ngas_phase = next(p for p in mechanism.phases if p.name == \"gas\")\nno_species = next(s for s in mechanism.species if s.name == \"NO\")\nmechanism.reactions = list(mechanism.reactions) + [Emission(name=\"NO\", products=[no_species], gas_phase=gas_phase)]\n\nsolver = musica.MICM(mechanism=mechanism, solver_type=musica.SolverType.rosenbrock_standard_order)\nstate = solver.create_state(num_grid_cells)" }, { "cell_type": "markdown", @@ -9505,4 +9497,4 @@ }, "nbformat": 4, "nbformat_minor": 5 -} +} \ No newline at end of file