diff --git a/data/dose_rates.json b/data/dose_rates.json index 1b71093e..f7f277b6 100644 --- a/data/dose_rates.json +++ b/data/dose_rates.json @@ -1,4 +1,7 @@ - "__description": "This file contains all the dose rates that can be calculated using data in this folder", + "__description": [ + "This file contains all the dose rates that can be calculated using data in this folder", + "The original TUV 5.4 source code and data sets can be found here: https://www2.acom.ucar.edu/modeling/tuv-download" + ], "dose rates": { "enable diagnostics": true, "rates": [ diff --git a/data/photolysis_rate_constants.json b/data/photolysis_rate_constants.json index 8cbb47f7..2f89aa75 100644 --- a/data/photolysis_rate_constants.json +++ b/data/photolysis_rate_constants.json @@ -1,4 +1,7 @@ - "__description": "This file contains configurations for each of the photolysis rate constants that can be calculated using data from this folder", + "__description": [ + "This file contains configurations for each of the TUV 5.4 photolysis rate constants that can be calculated using data from this folder", + "The original TUV 5.4 source code and data sets can be found here: https://www2.acom.ucar.edu/modeling/tuv-download" + ], "photolysis": { "enable diagnostics" : true, "reactions": [ diff --git a/examples/ts1_tsmlt.json b/examples/ts1_tsmlt.json new file mode 100644 index 00000000..b00663f3 --- /dev/null +++ b/examples/ts1_tsmlt.json @@ -0,0 +1,1592 @@ +{ + "__description": "TUV-x configuration for the MOZART-TS1 and MOZART-TSMLT chemical mechanisms", + "O2 absorption" : { + "cross section parameters file": "data/cross_sections/O2_parameters.txt" + }, + "grids": [ + { + "name": "height", + "type": "equal interval", + "units": "km", + "begins at" : 0.0, + "ends at" : 120.0, + "cell delta" : 1.0 + }, + { + "name": "wavelength", + "type": "from csv file", + "units": "nm", + "file path": "data/grids/wavelength/combined.grid" + }, + { + "name": "time", + "type": "from config file", + "units": "hours", + "values": [ 12.0, 14.0 ] + } + ], + "profiles": [ + { + "name": "O3", + "type": "O3", + "units": "molecule cm-3", + "file path": "data/profiles/atmosphere/ussa.ozone" + }, + { + "name": "air", + "type": "air", + "units": "molecule cm-3", + "file path": "data/profiles/atmosphere/ussa.dens" + }, + { + "name": "O2", + "type": "O2", + "units": "molecule cm-3", + "file path": "data/profiles/atmosphere/ussa.dens" + }, + { + "name": "temperature", + "type": "from csv file", + "units": "K", + "file path": "data/profiles/atmosphere/ussa.temp", + "grid": { + "name": "height", + "units": "km" + } + }, + { + "name": "solar zenith angle", + "type": "solar zenith angle", + "units": "degrees", + "year" : 2002, + "month": 3, + "day": 21, + "longitude": 0.0, + "latitude": 0.0 + }, + { + "name": "Earth-Sun distance", + "type": "Earth-Sun distance", + "units": "AU", + "year" : 2002, + "month": 3, + "day": 21 + }, + { + "name": "surface albedo", + "type": "from config file", + "units": "none", + "uniform value": 0.10, + "grid": { + "name": "wavelength", + "units": "nm" + } + }, + { + "name": "extraterrestrial flux", + "enable diagnostics" : true, + "type": "extraterrestrial flux", + "units": "photon cm-2 s-1", + "file path": ["data/profiles/solar/susim_hi.flx", + "data/profiles/solar/atlas3_1994_317_a.dat", + "data/profiles/solar/sao2010.solref.converted", + "data/profiles/solar/neckel.flx"], + "interpolator": ["","","","fractional target"] + } + ], + "radiative transfer": { + "__output": true, + "solver" : { + "type" : "delta eddington" + }, + "cross sections": [ + { + "name": "air", + "type": "air" + }, + { + "name": "O3", + "netcdf files": [ + { "file path": "data/cross_sections/O3_1.nc" }, + { "file path": "data/cross_sections/O3_2.nc" }, + { "file path": "data/cross_sections/O3_3.nc" }, + { "file path": "data/cross_sections/O3_4.nc" } + ], + "type": "O3" + }, + { + "name": "O2", + "netcdf files": [ + { + "file path": "data/cross_sections/O2_1.nc", + "lower extrapolation": { "type": "boundary" } + } + ], + "type": "base" + } + ], + "radiators": [ + { + "enable diagnostics" : true, + "name": "air", + "type": "base", + "treat as air": true, + "cross section": "air", + "vertical profile": "air", + "vertical profile units": "molecule cm-3" + }, + { + "enable diagnostics" : true, + "name": "O2", + "type": "base", + "cross section": "O2", + "vertical profile": "O2", + "vertical profile units": "molecule cm-3" + }, + { + "enable diagnostics" : true, + "name": "O3", + "type": "base", + "cross section": "O3", + "vertical profile": "O3", + "vertical profile units": "molecule cm-3" + }, + { + "enable diagnostics" : true, + "name": "aerosols", + "type": "aerosol", + "optical depths": [2.40e-01, 1.06e-01, 4.56e-02, 1.91e-02, 1.01e-02, 7.63e-03, + 5.38e-03, 5.00e-03, 5.15e-03, 4.94e-03, 4.82e-03, 4.51e-03, + 4.74e-03, 4.37e-03, 4.28e-03, 4.03e-03, 3.83e-03, 3.78e-03, + 3.88e-03, 3.08e-03, 2.26e-03, 1.64e-03, 1.23e-03, 9.45e-04, + 7.49e-04, 6.30e-04, 5.50e-04, 4.21e-04, 3.22e-04, 2.48e-04, + 1.90e-04, 1.45e-04, 1.11e-04, 8.51e-05, 6.52e-05, 5.00e-05, + 3.83e-05, 2.93e-05, 2.25e-05, 1.72e-05, 1.32e-05, 1.01e-05, + 7.72e-06, 5.91e-06, 4.53e-06, 3.46e-06, 2.66e-06, 2.04e-06, + 1.56e-06, 1.19e-06, 9.14e-07], + "single scattering albedo": 0.99, + "asymmetry factor": 0.61, + "550 nm optical depth": 0.235 + } + ] + }, + "photolysis": { + "reactions": [ + { + "name": "jo2_a", + "__reaction": "O2 + hv -> O + O1D", + "cross section": { + "netcdf files": [ + { + "file path": "data/cross_sections/O2_1.nc", + "lower extrapolation": { "type": "boundary" }, + "interpolator": { "type": "fractional target" } + } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 0, + "override bands": [ + { + "band": "lyman-alpha", + "value": 0.53 + }, + { + "band": "schumann-runge continuum", + "value": 1.0 + } + ] + } + }, + { + "name": "jo2_b", + "__reaction": "O2 + hv -> O + O", + "cross section": { + "netcdf files": [ + { + "file path": "data/cross_sections/O2_1.nc", + "lower extrapolation": { "type": "boundary" }, + "interpolator": { "type": "fractional target" } + } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0, + "override bands": [ + { + "band": "lyman-alpha", + "value": 0.47 + }, + { + "band": "schumann-runge continuum", + "value": 0.0 + } + ] + } + }, + { + "name": "jo3_a", + "__reaction": "O3 + hv -> O2 + O(1D)", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/O3_1.nc" }, + { "file path": "data/cross_sections/O3_2.nc" }, + { "file path": "data/cross_sections/O3_3.nc" }, + { "file path": "data/cross_sections/O3_4.nc" } + ], + "type": "O3" + }, + "quantum yield": { + "type": "O3+hv->O2+O(1D)" + } + }, + { + "name": "jo3_b", + "__reaction": "O3 + hv -> O2 + O(3P)", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/O3_1.nc" }, + { "file path": "data/cross_sections/O3_2.nc" }, + { "file path": "data/cross_sections/O3_3.nc" }, + { "file path": "data/cross_sections/O3_4.nc" } + ], + "type": "O3" + }, + "quantum yield": { + "type": "O3+hv->O2+O(3P)" + } + }, + { + "name": "jn2o", + "__reaction": "N2O + hv -> N2 + O(1D)", + "cross section": { + "type": "N2O+hv->N2+O(1D)" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jno2", + "__reaction": "NO2 + hv -> NO + O(3P)", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/NO2_1.nc" } + ], + "type": "NO2 tint" + }, + "quantum yield": { + "netcdf files": ["data/quantum_yields/NO2_1.nc"], + "type": "NO2 tint", + "lower extrapolation": { "type": "boundary" } + } + }, + { + "name": "jn2o5_a", + "__reaction": "N2O5 + hv -> NO2 + NO3", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/N2O5_1.nc" }, + { "file path": "data/cross_sections/N2O5_2.nc" } + ], + "type": "N2O5+hv->NO2+NO3" + }, + "quantum yield": { + "type": "base", + "netcdf files": [ "data/quantum_yields/N2O5_NO3_NO2.nc" ] + } + }, + { + "name": "jn2o5_b", + "__reaction": "N2O5 + hv -> NO + O + NO3", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/N2O5_1.nc" }, + { "file path": "data/cross_sections/N2O5_2.nc" } + ], + "type": "N2O5+hv->NO2+NO3" + }, + "quantum yield": { + "type": "base", + "netcdf files": [ "data/quantum_yields/N2O5_NO3_NO_O.nc" ] + } + }, + { + "name": "jhno3", + "__reaction": "HNO3 + hv -> OH + NO2", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/HNO3_1.nc" } + ], + "type": "HNO3+hv->OH+NO2" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jno3_a", + "__reaction": "NO3 + hv -> NO2 + O(3P)", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/NO3_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "netcdf files": [ + "data/quantum_yields/NO3-NO2+O(3P)_1.nc" + ], + "type": "tint", + "lower extrapolation": { + "type": "constant", + "value": 1.0 + } + } + }, + { + "name": "jno3_b", + "__reaction": "NO3 + hv -> NO + O2", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/NO3_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "netcdf files": [ + "data/quantum_yields/NO3-NO+O2_1.nc" + ], + "type": "tint" + } + }, + { + "name": "jch3ooh", + "__reaction": "CH3OOH + hv -> CH3O + OH", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CH3OOH_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jch2o_a", + "__reaction": "CH2O + hv -> H + HCO", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CH2O_1.nc" } + ], + "type": "CH2O" + }, + "quantum yield": { + "netcdf files": [ + "data/quantum_yields/CH2O_1.nc" + ], + "type": "base", + "lower extrapolation": { + "type": "boundary" + } + } + }, + { + "name": "jch2o_b", + "__reaction": "CH2O + hv -> H2 + CO", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CH2O_1.nc" } + ], + "type": "CH2O" + }, + "quantum yield": { + "netcdf files": [ + "data/quantum_yields/CH2O_1.nc" + ], + "type": "CH2O", + "lower extrapolation": { + "type": "boundary" + } + } + }, + { + "name": "jh2o2", + "__reaction": "H2O2 + hv -> OH + OH", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/H2O2_1.nc" } + ], + "type": "H2O2+hv->OH+OH" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jch3cho", + "__reaction": "CH3CHO + hv -> CH3 + HCO", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CH3CHO_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "netcdf files": [ + "data/quantum_yields/CH3CHO_1.nc" + ], + "type": "CH3CHO+hv->CH3+HCO" + } + }, + { + "name": "jpan", + "__reaction": "PAN + hv -> 0.6*CH3CO3 + 0.6*NO2 + 0.4*CH3O2 + 0.4*NO3 + 0.4*CO2", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/PAN_1.nc" } + ], + "type": "CH3ONO2+hv->CH3O+NO2" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jmvk", + "__reaction": "MVK + hv -> 0.7*C3H6 + 0.7*CO + 0.3*CH3O2 + 0.3*CH3CO3", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/MVK_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "MVK+hv->Products" + } + }, + { + "name": "jacet", + "__reaction": "CH3COCH3 + hv -> CH3CO + CH3", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CH3COCH3_1.nc" } + ], + "type": "CH3COCH3+hv->CH3CO+CH3" + }, + "quantum yield": { + "type": "CH3COCH3+hv->CH3CO+CH3" + } + }, + { + "name": "jmgly", + "__reaction": "CH3COCHO + hv -> CH3CO3 + CO + HO2", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CH3COCHO_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "CH3COCHO+hv->CH3CO+HCO" + } + }, + { + "name": "jglyald", + "__reaction": "GLYALD + hv -> 2*HO2 + CO + CH2O", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/HOCH2CHO_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 0.5 + } + }, + { + "name": "jglyoxal", + "__reaction": "GLYOXAL + hv -> 2*CO + 2*HO2", + "__comments": "TODO the products of this reaction don't exactly match", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CHOCHO_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "netcdf files": [ + "data/quantum_yields/CHOCHO-H2_CO_CO_1.nc" + ], + "type": "base", + "lower extrapolation": { + "type": "boundary" + } + } + }, + { + "name": "jbrcl", + "__reaction": "BrCl + hv -> Br + Cl", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/BrCl_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jbro", + "__reaction": "BrO + hv -> Br + O", + "cross section": { + "netcdf files": [ + { + "file path": "data/cross_sections/BrO_1.nc", + "interpolator": { + "type": "fractional target", + "fold in": true + } + } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jbrono2_a", + "__reaction": "BrONO2 + hv -> Br + NO3", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/BrONO2_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 0.85 + } + }, + { + "name": "jbrono2_b", + "__reaction": "BrONO2 + hv -> BrO + NO2", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/BrONO2_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 0.15 + } + }, + { + "name": "jccl4", + "__reaction": "CCl4 + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CCl4_1.nc" } + ], + "type": "CCl4+hv->Products" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jcf2clbr", + "__reaction": "CF2BrCl + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CF2BrCl_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jcf3br", + "__reaction": "CF3Br + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CF3Br_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jcfcl3", + "__reaction": "CCl3F + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CFC-11_1.nc" } + ], + "type": "CCl3F+hv->Products" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jcfc113", + "__reaction": "CFC-113 + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CFC-113_1.nc" } + ], + "type": "tint" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jcfc114", + "__reaction": "CFC-114 + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CFC-114_1.nc" } + ], + "type": "tint" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jcfc115", + "__reaction": "CFC-115 + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CFC-115_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jcf2cl2", + "__reaction": "CCl2F2 + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CFC-12_1.nc" } + ], + "type": "CCl3F+hv->Products" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jch2br2", + "__reaction": "CH2BR2 + hv -> 2*BR", + "cross section": { + "type": "temperature based", + "netcdf file": "data/cross_sections/CH2BR2_1.nc", + "parameterization": { + "AA": [ -70.211776, 1.940326e-1, 2.726152e-3, -1.695472e-5, 2.500066e-8 ], + "BB": [ 2.899280, -4.327724e-2, 2.391599e-4, -5.807506e-7, 5.244883e-10 ], + "lp": [ 0.0, 1.0, 2.0, 3.0, 4.0 ], + "minimum wavelength": 210.0, + "maximum wavelength": 290.0, + "temperature ranges": [ + { + "maximum": 209.999999999999, + "fixed value": 210.0 + }, + { + "minimum": 210, + "maximum": 300 + }, + { + "minimum": 300.00000000001, + "fixed value": 300.0 + } + ] + } + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jch3br", + "__reaction": "CH3Br + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CH3Br_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jch3ccl3", + "__reaction": "CH3CCl3+hv->Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CH3CCl3_1.nc" } + ], + "type": "tint" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jch3cl", + "__reaction": "CH3Cl + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CH3Cl_1.nc" } + ], + "type": "tint" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jchbr3", + "__reaction": "CHBr3 + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CHBr3_1.nc" } + ], + "type": "CHBr3+hv->Products", + "lower extrapolation": { + "type": "boundary" + } + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jcl2", + "__reaction": "Cl2 + hv -> Cl + Cl", + "cross section": { + "type": "Cl2+hv->Cl+Cl" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jcl2o2", + "__reaction": "ClOOCl + hv -> Cl + ClOO", + "__comments": "TODO - this doesn't exactly match the products in TS1", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/ClOOCl_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jclo", + "__reaction": "ClO + hv -> Cl + O(1D)", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/ClO_1.nc" } + ], + "type": "tint" + }, + "quantum yield": { + "type": "ClO+hv->Cl+O(1D)" + } + }, + { + "name": "jclono2_a", + "__reaction": "ClONO2 + hv -> Cl + NO3", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/ClONO2_1.nc" } + ], + "type": "ClONO2" + }, + "quantum yield": { + "type": "ClONO2+hv->Cl+NO3" + } + }, + { + "name": "jclono2_b", + "__reaction": "ClONO2 + hv -> ClO + NO2", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/ClONO2_1.nc" } + ], + "type": "ClONO2" + }, + "quantum yield": { + "type": "ClONO2+hv->ClO+NO2" + } + }, + { + "name": "jcof2", + "__reaction": "CF2O + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CF2O_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jcofcl", + "__reaction": "CClFO + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CClFO_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jh2402", + "__reaction": "H2402 + hv -> 2*BR + 2*COF2", + "__comments": "TUV data set name CF2BrCF2Br", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CF2BrCF2Br_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jhcfc141b", + "__reaction": "HCFC-141b + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CH3CFCl2_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jhcfc142b", + "__reaction": "HCFC-142b + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CH3CF2Cl_1.nc" } + ], + "type": "HCFC+hv->Products" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jhcfc22", + "__reaction": "HCFC-22 + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/CHClF2_1.nc" } + ], + "type": "tint" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jhcl", + "__reaction": "HCl + hv -> H + Cl", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/HCl_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jhobr", + "__reaction": "HOBr + hv -> OH + Br", + "cross section": { + "type": "HOBr+hv->OH+Br" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jhocl", + "__reaction": "HOCl + hv -> HO + Cl", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/HOCl_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "joclo", + "__reaction": "OClO + hv -> Products", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/OClO_1.nc" }, + { "file path": "data/cross_sections/OClO_2.nc" }, + { "file path": "data/cross_sections/OClO_3.nc" } + ], + "type": "OClO+hv->Products" + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jho2no2_a", + "__reaction": "HNO4 + hv -> OH + NO3", + "__comments": "TODO Doug's data sets have special temperature dependence - need new type?", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/HNO4_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 0.2 + } + }, + { + "name": "jho2no2_b", + "__reaction": "HNO4 + hv -> HO2 + NO2", + "__comments": "TODO Doug's data sets have special temperature dependence - need new type?", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/HNO4_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 0.8 + } + }, + { + "name": "jmacr_a", + "__reaction": "CH2=C(CH3)CHO->1.34HO2+0.66MCO3+1.34CH2O+CH3CO3", + "__comments": "Methacrolein photolysis channel 1", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/Methacrolein_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 0.005 + } + }, + { + "name": "jmacr_b", + "__reaction": "CH2=C(CH3)CHO->0.66OH+1.34CO", + "__comments": "Methacrolein photolysis channel 2", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/Methacrolein_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 0.005 + } + }, + { + "name": "jhyac", + "__reaction": "CH2(OH)COCH3->CH3CO3+HO2+CH2O", + "__comments": "hydroxy acetone TODO: the products of this reaction differ from standalone TUV-x", + "cross section": { + "netcdf files": [ + { "file path": "data/cross_sections/Hydroxyacetone_1.nc" } + ], + "type": "base" + }, + "quantum yield": { + "type": "base", + "constant value": 0.65 + } + }, + { + "name": "jh2o_a", + "__reaction": "H2O + hv -> OH + H", + "cross section": { + "type": "base", + "merge data": true, + "netcdf files": [ + { + "file path": "data/cross_sections/H2O_1.nc", + "zero above": 183.0 + }, + { + "file path": "data/cross_sections/H2O_2.nc", + "zero below": 183.00000000001, + "zero above": 190.0 + }, + { + "file path": "data/cross_sections/H2O_3.nc", + "zero below": 190.00000000001 + } + ] + }, + "quantum yield" : { + "type": "base", + "netcdf files": [ "data/quantum_yields/H2O_H_OH.nc" ] + } + }, + { + "name": "jh2o_b", + "__reaction": "H2O + hv -> H2 + O1D", + "cross section": { + "type": "base", + "merge data": true, + "netcdf files": [ + { + "file path": "data/cross_sections/H2O_1.nc", + "zero above": 183.0 + }, + { + "file path": "data/cross_sections/H2O_2.nc", + "zero below": 183.00000000001, + "zero above": 190.0 + }, + { + "file path": "data/cross_sections/H2O_3.nc", + "zero below": 190.00000000001 + } + ] + }, + "quantum yield" : { + "type": "base", + "netcdf files": [ "data/quantum_yields/H2O_H2_O1D.nc" ] + } + }, + { + "name": "jh2o_c", + "__reaction": "H2O + hv -> 2*H + O", + "cross section": { + "type": "base", + "merge data": true, + "netcdf files": [ + { + "file path": "data/cross_sections/H2O_1.nc", + "zero above": 183.0 + }, + { + "file path": "data/cross_sections/H2O_2.nc", + "zero below": 183.00000000001, + "zero above": 190.0 + }, + { + "file path": "data/cross_sections/H2O_3.nc", + "zero below": 190.00000000001 + } + ] + }, + "quantum yield" : { + "type": "base", + "netcdf files": [ "data/quantum_yields/H2O_2H_O3P.nc" ] + } + }, + { + "name": "jch4_a", + "__reaction": "CH4 + hv -> H + CH3O2", + "cross section": { + "type": "base", + "netcdf files": [ + { "file path": "data/cross_sections/CH4_1.nc" } + ] + }, + "quantum yield": { + "type": "base", + "constant value": 0.55 + } + }, + { + "name": "jch4_b", + "__reaction": "CH4 + hv -> 1.44*H2 + 0.18*CH2O + 0.18*O + 0.33*OH + 0.33*H + 0.44*CO2 + 0.38*CO + 0.05*H2O", + "cross section": { + "type": "base", + "netcdf files": [ + { "file path": "data/cross_sections/CH4_1.nc" } + ] + }, + "quantum yield": { + "type": "base", + "constant value": 0.45 + } + }, + { + "name": "jco2", + "__reaction": "CO2 + hv -> CO + O", + "cross section": { + "type": "base", + "netcdf files": [ + { "file path": "data/cross_sections/CO2_1.nc" } + ] + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jhbr", + "__reaction": "HBR + hv -> BR + H", + "cross section": { + "type": "base", + "netcdf files": [ + { "file path": "data/cross_sections/HBr_1.nc" } + ] + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jhf", + "__reaction": "HF + hv -> H + F", + "cross section": { + "type": "base", + "netcdf files": [ + { "file path": "data/cross_sections/HF_1.nc" } + ] + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jsf6", + "__reaction": "SF6 + hv -> sink", + "cross section": { + "type": "base", + "netcdf files": [ + { "file path": "data/cross_sections/SF6_1.nc" } + ] + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jh2so4", + "__reaction": "H2SO4 + hv -> SO3 + H2O", + "cross section": { + "type": "base", + "netcdf files": [ + { "file path": "data/cross_sections/H2SO4_1.nc" } + ] + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jocs", + "__reaction": "OCS + hv -> S + CO", + "cross section": { + "type": "base", + "netcdf files": [ + { "file path": "data/cross_sections/OCS_1.nc" } + ] + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jso", + "__reaction": "SO + hv -> S + O", + "cross section": { + "type": "base", + "netcdf files": [ + { "file path": "data/cross_sections/SO_1.nc" } + ] + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jso2", + "__reaction": "SO2 + hv -> SO + O", + "cross section": { + "type": "base", + "netcdf files": [ + { "file path": "data/cross_sections/SO2_1.nc" } + ] + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + }, + { + "name": "jso3", + "__reaction": "SO3 + hv -> SO2 + O", + "cross section": { + "type": "base", + "netcdf files": [ + { "file path": "data/cross_sections/SO3_1.nc" } + ] + }, + "quantum yield": { + "type": "base", + "constant value": 1.0 + } + } + ] + }, + "__CAM options": { + "aliasing": { + "default matching": "backup", + "pairs": [ + { + "to": "jalknit", + "__reaction": "ALKNIT + hv -> NO2 + 0.4*CH3CHO + 0.1*CH2O + 0.25*CH3COCH3 + HO2 + 0.8*MEK", + "from": "jch3ooh" + }, + { + "to": "jpooh", + "__reaction": "POOH (C3H6OHOOH) + hv -> CH3CHO + CH2O + HO2 + OH", + "from": "jch3ooh" + }, + { + "to": "jch3co3h", + "__reaction": "CH3COOOH + hv -> CH3O2 + OH + CO2", + "from": "jh2o2", + "scale by": 0.28 + }, + { + "to": "jmpan", + "__reaction": "MPAN + hv -> MCO3 + NO2", + "from": "jpan" + }, + { + "to": "jc2h5ooh", + "__reaction": "C2H5OOH + hv -> CH3CHO + HO2 + OH", + "from": "jch3ooh" + }, + { + "to": "jc3h7ooh", + "__reaction": "C3H7OOH + hv -> 0.82*CH3COCH3 + OH + HO2", + "from": "jch3ooh" + }, + { + "to": "jc6h5ooh", + "__reaction": "C6H5OOH + hv -> PHENO + OH", + "from": "jch3ooh" + }, + { + "to": "jeooh", + "__reaction": "EOOH + hv -> EO + OH", + "from": "jch3ooh" + }, + { + "to": "jrooh", + "__reaction": "ROOH + hv -> CH3CO3 + CH2O + OH", + "from": "jch3ooh" + }, + { + "to": "jxooh", + "__reaction": "XOOH + hv -> OH", + "from": "jch3ooh" + }, + { + "to": "jonitr", + "__reaction": "ONITR + hv -> NO2", + "from": "jch3cho" + }, + { + "to": "jisopooh", + "__reaction": "ISOPOOH + hv -> 0.402*MVK + 0.288*MACR + 0.69*CH2O + HO2", + "from": "jch3ooh" + }, + { + "to": "jmek", + "__reaction": "MEK + hv -> CH3CO3 + C2H5O2", + "from": "jacet" + }, + { + "to": "jalkooh", + "__reaction": "ALKOOH + hv -> .4*CH3CHO + .1*CH2O + .25*CH3COCH3 + .9*HO2 + .8*MEK + OH", + "from": "jch3ooh" + }, + { + "to": "jbenzooh", + "__reaction": "BENZOOH + hv -> OH + GLYOXAL + 0.5*BIGALD1 + HO2", + "from": "jch3ooh" + }, + { + "to": "jbepomuc", + "__reaction": "BEPOMUC + hv -> BIGALD1 + 1.5*HO2 + 1.5*CO", + "from": "jno2", + "scale by": 0.1 + }, + { + "to": "jbigald", + "__reaction": "BIGALD + hv -> 0.45*CO + 0.13*GLYOXAL + 0.56*HO2 + 0.13*CH3CO3 + 0.18*CH3COCHO", + "from": "jno2", + "scale by": 0.2 + }, + { + "to": "jbigald1", + "__reaction": "BIGALD1 + hv -> 0.6*MALO2 + HO2", + "from": "jno2", + "scale by": 0.14 + }, + { + "to": "jbigald2", + "__reaction": "BIGALD2 + hv -> 0.6*HO2 + 0.6*DICARBO2", + "from": "jno2", + "scale by": 0.2 + }, + { + "to": "jbigald3", + "__reaction": "BIGALD3 + hv -> 0.6*HO2 + 0.6*CO + 0.6*MDIALO2", + "from": "jno2", + "scale by": 0.2 + }, + { + "to": "jbigald4", + "__reaction": "BIGALD4 + hv -> HO2 + CO + CH3COCHO + CH3CO3", + "from": "jno2", + "scale by": 0.006 + }, + { + "to": "jbzooh", + "__reaction": "BZOOH + hv -> BZALD + OH + HO2", + "from": "jch3ooh" + }, + { + "to": "jmekooh", + "__reaction": "MEKOOH + hv -> OH + CH3CO3 + CH3CHO", + "from": "jch3ooh" + }, + { + "to": "jtolooh", + "__reaction": "TOLOOH + hv -> OH + .45*GLYOXAL + .45*CH3COCHO + .9*BIGALD", + "from": "jch3ooh" + }, + { + "to": "jterpooh", + "__reaction": "TERPOOH + hv -> OH + .1*CH3COCH3 + HO2 + MVK + MACR", + "from": "jch3ooh" + }, + { + "to": "jhonitr", + "__reaction": "HONITR + hv -> NO2 + 0.67*HO2 + 0.33*CH3CHO + 0.33*CH2O + 0.33*CO + 0.33*GLYALD + 0.33*CH3CO3 + 0.17*HYAC + 0.17*CH3COCH3", + "from": "jch2o_a" + }, + { + "to": "jhpald", + "__reaction": "HPALD + hv -> BIGALD3 + OH + HO2", + "from": "jno2", + "scale by": 0.006 + }, + { + "to": "jisopnooh", + "__reaction": "ISOPNOOH + hv -> NO2 + HO2 + ISOPOOH", + "from": "jch3ooh" + }, + { + "to": "jnc4cho", + "__reaction": "NC4CHO + hv -> BIGALD3 + NO2 + HO2", + "from": "jch2o_a" + }, + { + "to": "jnoa", + "__reaction": "NOA + hv -> NO2 + CH2O + CH3CO3", + "from": "jch2o_a" + }, + { + "to": "jnterpooh", + "__reaction": "NTERPOOH + hv -> TERPROD1 + NO2 + OH", + "from": "jch3ooh" + }, + { + "to": "jphenooh", + "__reaction": "PHENOOH + hv -> OH + HO2 + 0.7*GLYOXAL", + "from": "jch3ooh" + }, + { + "to": "jtepomuc", + "__reaction": "TEPOMUC + hv -> 0.5*CH3CO3 + HO2 + 1.5*CO", + "from": "jno2", + "scale by": 0.1 + }, + { + "to": "jterp2ooh", + "__reaction": "TERP2OOH + hv -> OH + 0.375*CH2O + 0.3*CH3COCH3 + 0.25*CO + CO2 + TERPROD2 + HO2 + 0.25*GLYALD", + "from": "jch3ooh" + }, + { + "to": "jterpnit", + "__reaction": "TERPNIT + hv -> TERPROD1 + NO2 + HO2", + "from": "jch3ooh" + }, + { + "to": "jterprd1", + "__reaction": "TERPROD1 + hv -> HO2 + CO + TERPROD2", + "from": "jch3cho" + }, + { + "to": "jterprd2", + "__reaction": "TERPROD2 + hv -> 0.15*RO2 + 0.68*CH2O + 0.8*CO2 + 0.5*CH3COCH3 + 0.65*CH3CO3 + 1.2*HO2 + 1.7*CO", + "from": "jch3cho" + }, + { + "to": "jxylenooh", + "__reaction": "XYLENOOH + hv -> OH + HO2 + 0.34*GLYOXAL + 0.54*CH3COCHO + 0.06*BIGALD1 + 0.2*BIGALD2 + 0.15*BIGALD3 + 0.21*BIGALD4", + "from": "jch3ooh" + }, + { + "to": "jxylolooh", + "__reaction": "XYLOLOOH + hv -> OH + 0.17*GLYOXAL + 0.51*CH3COCHO + HO2", + "from": "jch3ooh" + }, + { + "to": "jsoa1_a1", + "__reaction": "soa1_a1 + hv -> Products", + "from": "jno2", + "scale by": 0.0004 + }, + { + "to": "jsoa1_a2", + "__reaction": "soa1_a2 + hv -> Products", + "from": "jno2", + "scale by": 0.0004 + }, + { + "to": "jsoa2_a1", + "__reaction": "soa2_a1 + hv -> Products", + "from": "jno2", + "scale by": 0.0004 + }, + { + "to": "jsoa2_a2", + "__reaction": "soa2_a2 + hv -> Products", + "from": "jno2", + "scale by": 0.0004 + }, + { + "to": "jsoa3_a1", + "__reaction": "soa3_a1 + hv -> Products", + "from": "jno2", + "scale by": 0.0004 + }, + { + "to": "jsoa3_a2", + "__reaction": "soa3_a2 + hv -> Products", + "from": "jno2", + "scale by": 0.0004 + }, + { + "to": "jsoa4_a1", + "__reaction": "soa4_a1 + hv -> Products", + "from": "jno2", + "scale by": 0.0004 + }, + { + "to": "jsoa4_a2", + "__reaction": "soa4_a2 + hv -> Products", + "from": "jno2", + "scale by": 0.0004 + }, + { + "to": "jsoa5_a1", + "__reaction": "soa5_a1 + hv -> Products", + "from": "jno2", + "scale by": 0.0004 + }, + { + "to": "jsoa5_a2", + "__reaction": "soa5_a2 + hv -> Products", + "from": "jno2", + "scale by": 0.0004 + } + ] + } + } +} diff --git a/examples/full_config.json b/examples/tuv_5_4.json similarity index 99% rename from examples/full_config.json rename to examples/tuv_5_4.json index d79d2628..861236cf 100644 --- a/examples/full_config.json +++ b/examples/tuv_5_4.json @@ -1,4 +1,8 @@ { + "__description": [ + "TUV-x configuration that reporoduces photolysis rate constants of the TUV 5.4 calculator", + "The original TUV 5.4 source code and data sets can be found here: https://www2.acom.ucar.edu/modeling/tuv-download" + ], "O2 absorption" : { "cross section parameters file": "data/cross_sections/O2_parameters.txt" }, @@ -169,7 +173,6 @@ } ] }, - "__description": "This file contains configurations for each of the photolysis rate constants that can be calculated using data from this folder", "photolysis": { "enable diagnostics" : true, "reactions": [ diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index ef24ac8f..01cfa50a 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -34,7 +34,9 @@ endif() ################################################################################ # Run examples as tests -add_test(NAME full_example COMMAND tuv-x examples/full_config.json +add_test(NAME TUV_5_4 COMMAND tuv-x examples/tuv_5_4.json + WORKING_DIRECTORY ${CMAKE_BINARY_DIR}) +add_test(NAME TS1_TSMLT COMMAND tuv-x examples/ts1_tsmlt.json WORKING_DIRECTORY ${CMAKE_BINARY_DIR}) ################################################################################