musica 0.12.2__cp39-cp39-win_arm64.whl → 0.13.0__cp39-cp39-win_arm64.whl

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Files changed (63) hide show
  1. musica/CMakeLists.txt +4 -0
  2. musica/_musica.cp39-win_amd64.pyd +0 -0
  3. musica/_version.py +1 -1
  4. musica/binding_common.cpp +6 -9
  5. musica/binding_common.hpp +17 -1
  6. musica/grid.cpp +206 -0
  7. musica/grid.py +98 -0
  8. musica/grid_map.cpp +117 -0
  9. musica/grid_map.py +167 -0
  10. musica/mechanism_configuration/__init__.py +18 -1
  11. musica/mechanism_configuration/ancillary.py +6 -0
  12. musica/mechanism_configuration/arrhenius.py +111 -269
  13. musica/mechanism_configuration/branched.py +116 -275
  14. musica/mechanism_configuration/emission.py +63 -52
  15. musica/mechanism_configuration/first_order_loss.py +73 -157
  16. musica/mechanism_configuration/mechanism.py +93 -0
  17. musica/mechanism_configuration/phase.py +44 -33
  18. musica/mechanism_configuration/phase_species.py +58 -0
  19. musica/mechanism_configuration/photolysis.py +77 -67
  20. musica/mechanism_configuration/reaction_component.py +54 -0
  21. musica/mechanism_configuration/reactions.py +17 -58
  22. musica/mechanism_configuration/species.py +45 -71
  23. musica/mechanism_configuration/surface.py +78 -74
  24. musica/mechanism_configuration/taylor_series.py +136 -0
  25. musica/mechanism_configuration/ternary_chemical_activation.py +138 -330
  26. musica/mechanism_configuration/troe.py +138 -330
  27. musica/mechanism_configuration/tunneling.py +105 -229
  28. musica/mechanism_configuration/user_defined.py +79 -68
  29. musica/mechanism_configuration.cpp +54 -162
  30. musica/musica.cpp +2 -5
  31. musica/profile.cpp +294 -0
  32. musica/profile.py +93 -0
  33. musica/profile_map.cpp +117 -0
  34. musica/profile_map.py +167 -0
  35. musica/test/examples/v1/full_configuration/full_configuration.json +91 -233
  36. musica/test/examples/v1/full_configuration/full_configuration.yaml +191 -290
  37. musica/test/integration/test_chapman.py +2 -2
  38. musica/test/integration/test_tuvx.py +72 -15
  39. musica/test/unit/test_grid.py +137 -0
  40. musica/test/unit/test_grid_map.py +126 -0
  41. musica/test/unit/test_parser.py +10 -10
  42. musica/test/unit/test_profile.py +169 -0
  43. musica/test/unit/test_profile_map.py +137 -0
  44. musica/test/unit/test_serializer.py +17 -16
  45. musica/test/unit/test_state.py +17 -4
  46. musica/test/unit/test_util_full_mechanism.py +78 -298
  47. musica/tuvx.cpp +94 -15
  48. musica/tuvx.py +92 -22
  49. musica/types.py +13 -5
  50. {musica-0.12.2.dist-info → musica-0.13.0.dist-info}/METADATA +14 -14
  51. musica-0.13.0.dist-info/RECORD +80 -0
  52. musica/mechanism_configuration/aqueous_equilibrium.py +0 -274
  53. musica/mechanism_configuration/condensed_phase_arrhenius.py +0 -309
  54. musica/mechanism_configuration/condensed_phase_photolysis.py +0 -88
  55. musica/mechanism_configuration/henrys_law.py +0 -44
  56. musica/mechanism_configuration/mechanism_configuration.py +0 -234
  57. musica/mechanism_configuration/simpol_phase_transfer.py +0 -217
  58. musica/mechanism_configuration/wet_deposition.py +0 -52
  59. musica-0.12.2.dist-info/RECORD +0 -70
  60. {musica-0.12.2.dist-info → musica-0.13.0.dist-info}/WHEEL +0 -0
  61. {musica-0.12.2.dist-info → musica-0.13.0.dist-info}/entry_points.txt +0 -0
  62. {musica-0.12.2.dist-info → musica-0.13.0.dist-info}/licenses/AUTHORS.md +0 -0
  63. {musica-0.12.2.dist-info → musica-0.13.0.dist-info}/licenses/LICENSE +0 -0
@@ -4,218 +4,60 @@
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  "species": [
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  {
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  "name": "A",
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+ "molecular weight [kg mol-1]": 0.02897,
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  "__absolute tolerance": 1.0e-30
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  },
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  {
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  "name": "B",
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- "tracer type": "AEROSOL"
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+ "constant concentration [mol m-3]": 1.0e19
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  },
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  {
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  "name": "C",
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- "tracer type": "THIRD_BODY"
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+ "constant mixing ratio [mol mol-1]": 1.0e-20
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  },
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  {
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- "name": "M"
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+ "name": "M",
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+ "is third body": true
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  },
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  {
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  "name": "H2O2",
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- "HLC(298K) [mol m-3 Pa-1]": 1.011596348,
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- "HLC exponential factor [K]": 6340,
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- "diffusion coefficient [m2 s-1]": 1.46E-05,
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- "N star": 1.74,
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  "molecular weight [kg mol-1]": 0.0340147,
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- "density [kg m-3]": 1000.0,
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  "__absolute tolerance": 1.0e-10
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  },
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  {
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  "name": "ethanol",
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- "diffusion coefficient [m2 s-1]": 0.95E-05,
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- "N star": 2.55,
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  "molecular weight [kg mol-1]": 0.04607,
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  "__absolute tolerance": 1.0e-20
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- },
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- {
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- "name": "ethanol_aq",
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- "molecular weight [kg mol-1]": 0.04607,
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- "density [kg m-3]": 1000.0,
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- "__absolute tolerance": 1.0e-20
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- },
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- {
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- "name": "H2O2_aq",
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- "molecular weight [kg mol-1]": 0.0340147,
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- "density [kg m-3]": 1000.0,
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- "__absolute tolerance": 1.0e-10
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- },
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- {
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- "name": "H2O_aq",
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- "density [kg m-3]": 1000.0,
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- "molecular weight [kg mol-1]": 0.01801
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- },
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- {
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- "name": "aerosol stuff",
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- "molecular weight [kg mol-1]": 0.5,
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- "density [kg m-3]": 1000.0,
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- "__absolute tolerance": 1.0e-20
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- },
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- {
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- "name": "more aerosol stuff",
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- "molecular weight [kg mol-1]": 0.2,
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- "density [kg m-3]": 1000.0,
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- "__absolute tolerance": 1.0e-20
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  }
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  ],
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  "phases": [
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  {
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  "name": "gas",
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  "species": [
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- "A",
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- "B",
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- "C",
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- "ethanol"
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- ]
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- },
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- {
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- "name": "aqueous aerosol",
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- "species": [
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- "H2O2_aq",
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- "H2O_aq",
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- "ethanol_aq",
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- "A",
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- "B",
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- "C"
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- ]
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- },
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- {
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- "name": "surface reacting phase",
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- "species": [
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- "aerosol stuff",
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- "more aerosol stuff"
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- ]
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- },
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- {
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- "name": "cloud",
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- "species": [
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- "B",
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- "C"
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- ]
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- }
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- ],
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- "reactions": [
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- {
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- "type": "SIMPOL_PHASE_TRANSFER",
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- "gas phase": "gas",
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- "gas-phase species": "ethanol",
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- "condensed phase": "aqueous aerosol",
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- "condensed-phase species": "ethanol_aq",
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- "B": [
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- -1.97E+03,
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- 2.91E+00,
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- 1.96E-03,
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- -4.96E-01
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- ],
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- "name": "my simpol",
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- "__irrelevant": "2"
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- },
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- {
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- "type": "AQUEOUS_EQUILIBRIUM",
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- "condensed phase": "aqueous aerosol",
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- "condensed-phase water": "H2O_aq",
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- "A": 1.14e-2,
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- "C": 2300.0,
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- "k_reverse": 0.32,
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- "reactants": [
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  {
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- "species name": "A",
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- "coefficient": 2
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- }
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- ],
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- "products": [
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- {
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- "species name": "B",
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- "coefficient": 1
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+ "name": "A",
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+ "diffusion coefficient [m2 s-1]": 1.0
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  },
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  {
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- "species name": "C",
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- "coefficient": 1
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- }
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- ],
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- "name": "my aqueous eq",
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- "__irrelevant": "2"
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- },
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- {
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- "type": "CONDENSED_PHASE_ARRHENIUS",
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- "condensed phase": "aqueous aerosol",
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- "A": 123.45,
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- "Ea": 123.45,
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- "B": 1.3,
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- "D": 300.0,
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- "E": 0.6E-5,
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- "reactants": [
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- {
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- "species name": "H2O2_aq",
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- "coefficient": 1
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+ "name": "B"
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  },
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  {
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- "species name": "H2O_aq",
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- "coefficient": 1
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- }
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- ],
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- "products": [
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- {
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- "species name": "ethanol_aq",
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- "coefficient": 1
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- }
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- ],
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- "name": "my condensed arrhenius",
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- "__irrelevant": "2"
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- },
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- {
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- "type": "CONDENSED_PHASE_ARRHENIUS",
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- "condensed phase": "aqueous aerosol",
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- "A": 123.45,
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- "C": 123.45,
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- "B": 1.3,
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- "D": 300.0,
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- "E": 0.6E-5,
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- "reactants": [
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- {
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- "species name": "H2O2_aq",
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- "coefficient": 1
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+ "name": "C"
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  },
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  {
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- "species name": "H2O_aq",
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- "coefficient": 1
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- }
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- ],
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- "products": [
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- {
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- "species name": "ethanol_aq",
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- "coefficient": 1
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- }
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- ],
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- "name": "my other condensed arrhenius"
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- },
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- {
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- "type": "CONDENSED_PHASE_PHOTOLYSIS",
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- "condensed phase": "aqueous aerosol",
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- "reactants": [
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- {
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- "species name": "H2O2_aq",
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- "coefficient": 1
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- }
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- ],
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- "products": [
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+ "name": "ethanol"
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+ },
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  {
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- "species name": "ethanol_aq",
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- "coefficient": 1
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+ "name": "H2O2"
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  }
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- ],
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- "scaling factor": 12.3,
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- "name": "condensed photo B",
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- "__irrelevant": "2"
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- },
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+ ]
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+ }
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+ ],
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+ "reactions": [
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  {
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  "type": "EMISSION",
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+ "name": "my emission",
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+ "scaling factor": 12.3,
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  "gas phase": "gas",
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  "products": [
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  {
@@ -223,12 +65,12 @@
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  "coefficient": 1
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  }
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  ],
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- "name": "my emission",
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- "scaling factor": 12.3,
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  "__irrelevant": "2"
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  },
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  {
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  "type": "FIRST_ORDER_LOSS",
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+ "name": "my first order loss",
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+ "scaling factor": 12.3,
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  "gas phase": "gas",
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  "reactants": [
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  {
@@ -236,12 +78,12 @@
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  "coefficient": 1
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  }
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  ],
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- "name": "my first order loss",
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- "scaling factor": 12.3,
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  "__irrelevant": "2"
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  },
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  {
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  "type": "PHOTOLYSIS",
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+ "name": "photo B",
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+ "scaling factor": 12.3,
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  "gas phase": "gas",
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  "reactants": [
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  {
@@ -255,15 +97,14 @@
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  "coefficient": 1
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  }
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  ],
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- "name": "photo B",
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- "scaling factor": 12.3,
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  "__irrelevant": "2"
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  },
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  {
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  "type": "SURFACE",
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+ "name": "my surface",
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+ "reaction probability": 2.0e-2,
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  "gas phase": "gas",
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  "gas-phase species": "A",
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- "reaction probability": 2.0e-2,
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  "gas-phase products": [
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  {
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  "species name": "B",
@@ -274,12 +115,19 @@
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  "coefficient": 1
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  }
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  ],
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- "condensed phase": "surface reacting phase",
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- "name": "my surface",
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  "__irrelevant": "2"
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  },
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  {
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  "type": "TROE",
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+ "name": "my troe",
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+ "k0_A": 1.2e-12,
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+ "k0_B": 167,
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+ "k0_C": 3,
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+ "kinf_A": 136,
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+ "kinf_B": 5,
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+ "kinf_C": 24,
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+ "Fc": 0.9,
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+ "N": 0.8,
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  "gas phase": "gas",
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  "reactants": [
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  {
@@ -297,21 +145,20 @@
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  "coefficient": 1
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  }
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  ],
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- "k0_A": 1.2e-12,
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- "k0_B": 167,
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- "k0_C": 3,
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- "kinf_A": 136,
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- "kinf_B": 5,
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- "kinf_C": 24,
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- "Fc": 0.9,
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- "N": 0.8,
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- "name": "my troe",
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  "__irrelevant": "2"
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  },
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  {
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  "type": "TERNARY_CHEMICAL_ACTIVATION",
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- "gas phase": "gas",
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  "name": "my ternary chemical activation",
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+ "gas phase": "gas",
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+ "k0_A": 32.1,
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+ "k0_B": -2.3,
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+ "k0_C": 102.3,
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+ "kinf_A": 63.4,
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+ "kinf_B": -1.3,
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+ "kinf_C": 908.5,
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+ "Fc": 1.3,
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+ "N": 32.1,
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  "reactants": [
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  {
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  "species name": "B",
@@ -325,21 +172,17 @@
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  "products": [
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  {
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  "species name": "C",
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- "coefficient": 1
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  }
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  ],
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- "k0_A": 32.1,
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- "k0_B": -2.3,
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- "k0_C": 102.3,
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- "kinf_A": 63.4,
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- "kinf_B": -1.3,
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- "kinf_C": 908.5,
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- "Fc": 1.3,
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- "N": 32.1,
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  "__irrelevant": "2"
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  },
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  {
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  "type": "BRANCHED_NO_RO2",
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+ "name": "my branched",
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+ "X": 1.2e-4,
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+ "Y": 167,
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+ "a0": 0.15,
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+ "n": 9,
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  "gas phase": "gas",
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  "reactants": [
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  {
@@ -359,20 +202,15 @@
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  "coefficient": 1
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  }
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  ],
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- "X": 1.2e-4,
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- "Y": 167,
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- "a0": 0.15,
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- "n": 9,
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- "name": "my branched",
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  "__irrelevant": "2"
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  },
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  {
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- "gas phase": "gas",
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- "name": "my tunneling",
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  "type": "TUNNELING",
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+ "name": "my tunneling",
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  "A": 123.45,
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  "B": 1200.0,
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  "C": 1.0e8,
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+ "gas phase": "gas",
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  "reactants": [
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  {
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  "species name": "B",
@@ -387,16 +225,15 @@
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  ],
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  "__irrelevant": "2"
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  },
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- {
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- "type": "WET_DEPOSITION",
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- "condensed phase": "cloud",
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- "name": "rxn cloud",
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- "scaling factor": 12.3,
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- "__irrelevant": "2"
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- },
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  {
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  "type": "ARRHENIUS",
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+ "name": "my arrhenius",
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  "gas phase": "gas",
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+ "A": 32.1,
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+ "B": -2.3,
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+ "C": 102.3,
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+ "D": 63.4,
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+ "E": -1.3,
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  "reactants": [
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  {
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  "species name": "B",
@@ -409,16 +246,16 @@
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  "coefficient": 1
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  }
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  ],
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- "A": 32.1,
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- "B": -2.3,
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- "C": 102.3,
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- "D": 63.4,
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- "E": -1.3,
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- "name": "my arrhenius",
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  "__irrelevant": "2"
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  },
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  {
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  "type": "ARRHENIUS",
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+ "name": "my other arrhenius",
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+ "A": 29.3,
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+ "B": -1.5,
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+ "Ea": 101.2,
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+ "D": 82.6,
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+ "E": -0.98,
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  "gas phase": "gas",
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  "reactants": [
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  {
@@ -431,16 +268,12 @@
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  "species name": "B",
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  "coefficient": 1.2
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  }
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- ],
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- "A": 29.3,
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- "B": -1.5,
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- "Ea": 101.2,
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- "D": 82.6,
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- "E": -0.98,
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- "name": "my other arrhenius"
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+ ]
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  },
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  {
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  "type": "USER_DEFINED",
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+ "name": "my user defined",
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+ "scaling factor": 12.3,
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  "gas phase": "gas",
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  "reactants": [
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  {
@@ -458,9 +291,34 @@
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  "coefficient": 1.3
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  }
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  ],
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- "name": "my user defined",
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- "scaling factor": 12.3,
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  "__irrelevant": "2"
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+ },
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+ {
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+ "type": "TAYLOR_SERIES",
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+ "name": "my taylor series",
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+ "A": 12.3,
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+ "B": -1.5,
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+ "C": 1.0e-6,
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+ "D": 340.0,
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+ "E": 0.00032,
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+ "taylor coefficients": [
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+ 1.0,
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+ 0.1,
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+ -0.01
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+ ],
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+ "gas phase": "gas",
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+ "reactants": [
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+ {
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+ "species name": "B",
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+ "coefficient": 1
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+ }
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+ ],
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+ "products": [
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+ {
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+ "species name": "C",
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+ "coefficient": 1
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+ }
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+ ]
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  }
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  ]
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  }