musica 0.12.0__cp39-cp39-macosx_11_0_arm64.whl → 0.12.1__cp39-cp39-macosx_11_0_arm64.whl

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Files changed (85) hide show
  1. musica/.dylibs/libaec.0.1.4.dylib +0 -0
  2. musica/.dylibs/libgcc_s.1.1.dylib +0 -0
  3. musica/.dylibs/libgfortran.5.dylib +0 -0
  4. musica/.dylibs/libhdf5.310.5.1.dylib +0 -0
  5. musica/.dylibs/libhdf5_hl.310.0.6.dylib +0 -0
  6. musica/.dylibs/libnetcdf.22.dylib +0 -0
  7. musica/.dylibs/libnetcdff.7.1.0.dylib +0 -0
  8. musica/.dylibs/libquadmath.0.dylib +0 -0
  9. musica/.dylibs/libsz.2.0.1.dylib +0 -0
  10. musica/.dylibs/libzstd.1.5.7.dylib +0 -0
  11. musica/CMakeLists.txt +28 -2
  12. musica/__init__.py +9 -49
  13. musica/_musica.cpython-39-darwin.so +0 -0
  14. musica/_version.py +1 -1
  15. musica/backend.py +41 -0
  16. musica/binding_common.cpp +23 -6
  17. musica/carma.cpp +911 -0
  18. musica/carma.py +1729 -0
  19. musica/constants.py +1 -1
  20. musica/cpu_binding.cpp +2 -1
  21. musica/cuda.py +4 -1
  22. musica/examples/__init__.py +1 -0
  23. musica/examples/carma_aluminum.py +123 -0
  24. musica/examples/carma_sulfate.py +245 -0
  25. musica/examples/examples.py +165 -0
  26. musica/examples/sulfate_box_model.py +439 -0
  27. musica/examples/ts1_latin_hypercube.py +245 -0
  28. musica/gpu_binding.cpp +2 -1
  29. musica/main.py +89 -0
  30. musica/mechanism_configuration/__init__.py +1 -1
  31. musica/mechanism_configuration/aqueous_equilibrium.py +227 -54
  32. musica/mechanism_configuration/arrhenius.py +228 -42
  33. musica/mechanism_configuration/branched.py +249 -66
  34. musica/mechanism_configuration/condensed_phase_arrhenius.py +243 -50
  35. musica/mechanism_configuration/condensed_phase_photolysis.py +16 -19
  36. musica/mechanism_configuration/emission.py +10 -6
  37. musica/mechanism_configuration/first_order_loss.py +133 -26
  38. musica/mechanism_configuration/henrys_law.py +7 -48
  39. musica/mechanism_configuration/mechanism_configuration.py +114 -41
  40. musica/mechanism_configuration/phase.py +6 -2
  41. musica/mechanism_configuration/photolysis.py +12 -7
  42. musica/mechanism_configuration/reactions.py +20 -8
  43. musica/mechanism_configuration/simpol_phase_transfer.py +180 -51
  44. musica/mechanism_configuration/species.py +23 -4
  45. musica/mechanism_configuration/surface.py +14 -9
  46. musica/mechanism_configuration/ternary_chemical_activation.py +352 -0
  47. musica/mechanism_configuration/troe.py +259 -44
  48. musica/mechanism_configuration/tunneling.py +196 -49
  49. musica/mechanism_configuration/user_defined.py +9 -4
  50. musica/mechanism_configuration/wet_deposition.py +11 -8
  51. musica/mechanism_configuration.cpp +184 -95
  52. musica/musica.cpp +48 -61
  53. musica/test/examples/v1/full_configuration/full_configuration.json +39 -22
  54. musica/test/examples/v1/full_configuration/full_configuration.yaml +29 -20
  55. musica/test/{test_analytical.py → integration/test_analytical.py} +0 -1
  56. musica/test/integration/test_carma.py +227 -0
  57. musica/test/integration/test_carma_aluminum.py +11 -0
  58. musica/test/integration/test_carma_sulfate.py +16 -0
  59. musica/test/integration/test_sulfate_box_model.py +34 -0
  60. musica/test/integration/test_tuvx.py +62 -0
  61. musica/test/unit/test_parser.py +64 -0
  62. musica/test/{test_serializer.py → unit/test_serializer.py} +2 -2
  63. musica/test/{test_util_full_mechanism.py → unit/test_util_full_mechanism.py} +152 -122
  64. musica/tools/prepare_build_environment_linux.sh +39 -32
  65. musica/tools/prepare_build_environment_macos.sh +1 -0
  66. musica/tuvx.cpp +93 -0
  67. musica/tuvx.py +199 -0
  68. musica/types.py +104 -60
  69. {musica-0.12.0.dist-info → musica-0.12.1.dist-info}/METADATA +40 -39
  70. musica-0.12.1.dist-info/RECORD +79 -0
  71. {musica-0.12.0.dist-info → musica-0.12.1.dist-info}/WHEEL +1 -1
  72. musica-0.12.1.dist-info/entry_points.txt +3 -0
  73. musica/test/examples/v0/config.json +0 -7
  74. musica/test/examples/v0/config.yaml +0 -3
  75. musica/test/examples/v0/reactions.json +0 -193
  76. musica/test/examples/v0/reactions.yaml +0 -142
  77. musica/test/examples/v0/species.json +0 -40
  78. musica/test/examples/v0/species.yaml +0 -19
  79. musica/test/test_parser.py +0 -57
  80. musica/test/tuvx.py +0 -10
  81. musica/tools/prepare_build_environment_windows.sh +0 -22
  82. musica-0.12.0.dist-info/RECORD +0 -57
  83. /musica/test/{test_chapman.py → integration/test_chapman.py} +0 -0
  84. {musica-0.12.0.dist-info → musica-0.12.1.dist-info}/licenses/AUTHORS.md +0 -0
  85. {musica-0.12.0.dist-info → musica-0.12.1.dist-info}/licenses/LICENSE +0 -0
@@ -1,57 +0,0 @@
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- import pytest
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- from musica.mechanism_configuration import *
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- from test_util_full_mechanism import get_fully_defined_mechanism, validate_full_v1_mechanism
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-
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-
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- def test_parsed_full_v1_configuration():
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- parser = Parser()
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- extensions = [".yaml", ".json"]
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- for extension in extensions:
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- path = f"musica/test/examples/v1/full_configuration/full_configuration{extension}"
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- mechanism = parser.parse(path)
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- validate_full_v1_mechanism(mechanism)
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-
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-
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- def test_parser_reports_bad_files():
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- parser = Parser()
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- extensions = [".yaml", ".json"]
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- for extension in extensions:
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- path = f"musica/test/examples/_missing_configuration{extension}"
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- with pytest.raises(Exception):
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- parser.parse(path)
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-
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-
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- def test_hard_coded_full_v1_configuration():
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- MECHANISM_FULLY_DEFINED = get_fully_defined_mechanism()
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- validate_full_v1_mechanism(MECHANISM_FULLY_DEFINED)
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-
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-
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- def test_hard_coded_default_constructed_types():
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- arrhenius = Arrhenius()
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- assert arrhenius.type == ReactionType.Arrhenius
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- condensed_phase_arrhenius = CondensedPhaseArrhenius()
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- assert condensed_phase_arrhenius.type == ReactionType.CondensedPhaseArrhenius
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- condensed_phase_photolysis = CondensedPhasePhotolysis()
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- assert condensed_phase_photolysis.type == ReactionType.CondensedPhasePhotolysis
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- emission = Emission()
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- assert emission.type == ReactionType.Emission
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- first_order_loss = FirstOrderLoss()
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- assert first_order_loss.type == ReactionType.FirstOrderLoss
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- henrys_law = HenrysLaw()
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- assert henrys_law.type == ReactionType.HenrysLaw
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- photolysis = Photolysis()
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- assert photolysis.type == ReactionType.Photolysis
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- simpol_phase_transfer = SimpolPhaseTransfer()
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- assert simpol_phase_transfer.type == ReactionType.SimpolPhaseTransfer
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- surface = Surface()
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- assert surface.type == ReactionType.Surface
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- troe = Troe()
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- assert troe.type == ReactionType.Troe
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- tunneling = Tunneling()
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- assert tunneling.type == ReactionType.Tunneling
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- wet_deposition = WetDeposition()
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- assert wet_deposition.type == ReactionType.WetDeposition
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- branched = Branched()
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- assert branched.type == ReactionType.Branched
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- user_defined = UserDefined()
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- assert user_defined.type == ReactionType.UserDefined
musica/test/tuvx.py DELETED
@@ -1,10 +0,0 @@
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- import pytest
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- import musica
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-
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-
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- def test_tuvx_run():
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- assert 1 != 0
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-
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-
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- if __name__ == '__main__':
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- pytest.main()
@@ -1,22 +0,0 @@
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- #! /bin/bash
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-
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- set -e
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- set -x
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-
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- CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.8"
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- # curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.2.2/local_installers/cuda_12.2.2_537.13_windows.exe
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- curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.8.1/local_installers/cuda_12.8.1_572.61_windows.exe
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- ./cuda.exe -s nvcc_12.8 cudart_12.8 cublas_dev_12.8 curand_dev_12.8
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- rm cuda.exe
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-
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- export CUDA_PATH="/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.8"
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- export PATH="$CUDA_PATH/bin:$PATH"
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-
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- ls "c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.8/extras/visual_studio_integration/MSBuildExtensions"
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- ls "c/Program Files (x86)/Microsoft Visual Studio/"
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-
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- # choco install cuda
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-
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- ls "$CUDA_PATH"
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- ls "$CUDA_PATH/bin"
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- which nvcc.exe
@@ -1,57 +0,0 @@
1
- musica-0.12.0.dist-info/RECORD,,
2
- musica-0.12.0.dist-info/WHEEL,sha256=gUcXopd-K2IKuDoaEe4uBUYaf2fjHRiHplXdACpNr9A,112
3
- musica-0.12.0.dist-info/METADATA,sha256=ecoVy_lRUnvTA_JTGQRg8SB3EtlnFMr2Lq_8Ke8X1gs,25995
4
- musica-0.12.0.dist-info/licenses/AUTHORS.md,sha256=CYIlKZmXT9ngFk6d0MiD0A_Pt8BFoID4n-29OMrKkbM,2632
5
- musica-0.12.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
6
- musica/CMakeLists.txt,sha256=E5Z8tLfxUc0RAma1vKtN2-2s3CqHog2njYje9qHehQc,1050
7
- musica/_version.py,sha256=0d_eblF-LMXh1_mZw-q2DqmmX_vZj5tYDy8MONmqkNU,19
8
- musica/constants.py,sha256=BlRH2m12F7NXGZd5slV0qIgYa-qt1yfjKBbMpTQQd1c,122
9
- musica/binding_common.cpp,sha256=40rvAVZQkOloAKXNhUngkiZNaD7LfHE8jnCcoOOXAak,560
10
- musica/__init__.py,sha256=TXWCmKd4hBa09jf9917-cM5_DQ0Qcio__a1ZkfysT5k,1748
11
- musica/cpu_binding.cpp,sha256=nOLBGDWvvtxeAyIbeP3bXIeB_xzZoU_ALduHanHjR0Q,224
12
- musica/types.py,sha256=F4Gq2kXi3NTnj3_t7H-zN3E51n81kidThVYIJaNA-PM,14788
13
- musica/gpu_binding.cpp,sha256=wWkM_J_2Ky0OawxEXkdvPCzctfSsiH7THs2cVkr0S2s,228
14
- musica/_musica.cpython-39-darwin.so,sha256=HoeWT1LnrggQvYy4Paicv_ibzaqDE3JzdUAem4g4ukI,1559840
15
- musica/cuda.py,sha256=A0U0plsFuQgezWrwN8217kkC5URxjlsKI0ymYJCSdDE,224
16
- musica/cuda.cpp,sha256=qQOLKTUOB83gE-963rT579Me-NrqMUWnXDKmpTPMVFg,346
17
- musica/binding_common.hpp,sha256=YVG7TS1JeVC4W_yisV4kL61qo3N6Dt6JdAh9bdr6z2w,102
18
- musica/mechanism_configuration.cpp,sha256=OSYEoF6GeDntcyPRajKUdiU7b6r-6SFv4UsG8hySH0A,27034
19
- musica/musica.cpp,sha256=cMi5OfncDV_ROlhjCSvvGtUHWBl_oYcUwTu4KFLTBjg,8400
20
- musica/tools/prepare_build_environment_windows.sh,sha256=zMY_RIerqfMC1VlfpZ2KjjDWfBUOvvx8oRNk_jJhmII,826
21
- musica/tools/prepare_build_environment_linux.sh,sha256=yKjBD_eFMMvqth_PSF1qzmr7VLSMWiPufBh1inhuIRs,1457
22
- musica/tools/repair_wheel_gpu.sh,sha256=GJcKUJ2n9KMsj3QC5Shxt_ks9uFu2f9Than-4vVhG9U,1485
23
- musica/test/test_parser.py,sha256=6G2RIR6u8V_EtDBJqjWJPkdSwa7ZXNDD9pkDqezm8fI,2259
24
- musica/test/test_chapman.py,sha256=gOISpApVIMLCEv6W0Hq1yNGF0xu2MlZMHQQhOGPmoQI,3512
25
- musica/test/test_serializer.py,sha256=8WnFme_CpJBMlACG_YePCjxdm6qAZxYhqFw-ZgnWPNA,2466
26
- musica/test/tuvx.py,sha256=rWvBcG6cgLJylqkf8M0MFMKT2AkyoaZlGdaKjVSbCR8,116
27
- musica/test/test_util_full_mechanism.py,sha256=rTxHljAJSODDYAcDbstneT0NlVGZxEIuXLU9o1qFi7k,24063
28
- musica/test/test_analytical.py,sha256=U35zRGMjOQ_lRtFoKHn-MtA78oYagm7XzhiR96jPgE4,13806
29
- musica/test/examples/v1/full_configuration/full_configuration.yaml,sha256=bY9JWnmnio03kUDX58aAzsPC5R2-lfLKavMFD_NtO3k,5535
30
- musica/test/examples/v1/full_configuration/full_configuration.json,sha256=L_QdufMp4M1YqPMpHvI_g1jWjIWfVzEHfskilUFg3uo,9212
31
- musica/test/examples/v0/species.json,sha256=xKTcwh9QV9sRjLPK9GvGEnatBrRPbP857NmPG0bCXqU,565
32
- musica/test/examples/v0/species.yaml,sha256=vUYTs7bp2AYVWHDgXBFxnCkmqdO6ysJ_ulOQTAoKa1M,283
33
- musica/test/examples/v0/config.json,sha256=7s6g5jxH2GiEiRcZmO13IJ5k4walg1C9t-dQr9o45U4,79
34
- musica/test/examples/v0/config.yaml,sha256=GgA18mP8ZCzOdY-AlAePK48M05PJFPeWCk-IfrPN_VE,44
35
- musica/test/examples/v0/reactions.json,sha256=7WJhItBPtGu89vLcPMK6izW8BvwUAIjfzqwjtDmfPPg,4188
36
- musica/test/examples/v0/reactions.yaml,sha256=uEuQOz5i7vGyn0G7KsmdWv23V2Gn0QUmexrK030CFlo,2266
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- musica/mechanism_configuration/phase.py,sha256=1bT9iAn8Ah0txW9SkjRhViFlry027aZD95fKBrJOVkc,1539
38
- musica/mechanism_configuration/species.py,sha256=S1jU9j4Pf6MjiepqM1jwaz6r5tiIanHS4_naduJxbl8,3923
39
- musica/mechanism_configuration/henrys_law.py,sha256=ue5e_M0U37gbJeOq_kelv0kgXptEjbpMLSPWG5ByqxA,4181
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- musica/mechanism_configuration/tunneling.py,sha256=CtzNq7VyLsdI0_W9NdLOC89N99tSSbfRZMn5j1g-0as,4305
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- musica/mechanism_configuration/mechanism_configuration.py,sha256=A6JhB1VbNcMjsPhPuuihYI190rlzXqRsm-K_-uAdXmU,6867
42
- musica/mechanism_configuration/branched.py,sha256=Ei0mFGUaxg8_nIfIi5UkFuye74KRyK5_bNuoertI7U8,5215
43
- musica/mechanism_configuration/reactions.py,sha256=UXVRjWGY-n4RFF4xp4kGeFhdTr3J1z6dyLxIAQ5Zg6I,1674
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- musica/mechanism_configuration/__init__.py,sha256=WVIbDCgpAd-jH9TBPou-5tyrdxb5Vbm9Zl2h7xmNiQ8,38
45
- musica/mechanism_configuration/user_defined.py,sha256=r2QwOkmRVeVJvJKXxnyxxjXkX4xmMQZ_AlOzO4s2UAg,3752
46
- musica/mechanism_configuration/aqueous_equilibrium.py,sha256=NvuIlbMap4vJbHXBgLhrRku-uuWiN1Y_cDp3pMtwQzc,4760
47
- musica/mechanism_configuration/condensed_phase_arrhenius.py,sha256=1HOWYXPL40koeCJOZKxUwJbt8sZybugP7Qa-Yh6e3Ok,5361
48
- musica/mechanism_configuration/first_order_loss.py,sha256=blRz-RKUZICA5nd2SciQNXbxoLVF5iEV4_aITuKCHPo,3048
49
- musica/mechanism_configuration/utils.py,sha256=nR-ukwYsplFfnsjXtKQsXnryMPvtjkZkFQv7TjcSrnE,346
50
- musica/mechanism_configuration/wet_deposition.py,sha256=k6MV7vGWsxmR7FWbH2YPALFAwtZB37rNdoeyWICOleU,2183
51
- musica/mechanism_configuration/condensed_phase_photolysis.py,sha256=nlWWKCKenPDHfQR-cyq6RNLoOpS0wW5-1Zw_BH4XiZo,4392
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- musica/mechanism_configuration/arrhenius.py,sha256=Q7ncI08AxN1yXvhslhe6oCFea43-44l2BYcy2HEaKWA,5147
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- musica/mechanism_configuration/troe.py,sha256=SX9REl-6ts1BEbEhIDtUBDbEZPpLjhZPWIgFv10-qpM,6576
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- musica/mechanism_configuration/simpol_phase_transfer.py,sha256=pPy1laAO9F4cmBcMM1NJ-RHuWjirfRZUF4zAWMVGF60,4247
55
- musica/mechanism_configuration/photolysis.py,sha256=HXkOn_bU67Qe5VyPrAcyh1KPzIS19GyCXpDCVmU1yzs,3744
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- musica/mechanism_configuration/emission.py,sha256=uTVCN9M1XXsooiGyXDK9eOX3uBsSKnwxXMjVIAMU424,2946
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- musica/mechanism_configuration/surface.py,sha256=XdCWeIZ1OojjOfFO_Tw2MEhnyWGzncc64qOw6XHXZUI,4185