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[TEP006] Aggregate TARDIS restructure and configuration system cleanup #652

Merged
merged 127 commits into from
Dec 20, 2016
Merged

[TEP006] Aggregate TARDIS restructure and configuration system cleanup #652

merged 127 commits into from
Dec 20, 2016

Commits on Dec 8, 2016

  1. Upgrade the model module to a python package.

    @ftsamis
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  2. Introduce the basics of the new model/base.py.

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  3. Add a dynamic density property to the new model.

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  4. Add a volume and a no_of_shells property to the model.

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  5. Add a radius property to the Radial1DModel.

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  6. Make t_radiative optional and initialize it accordingly to the legacy… 

    … model if it's None.
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  7. Add properties for getting the indexes of the v_boundaries to the Rad… 

    …ial1DModel.
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  8. Add a model.density module and a model.base.from_config classmethod. 

    Organize the different density types in descriptor classes in the model.density
module. Add a way of creating the restructured Radial1DModel from
a Configuration object.
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  9. Convert the model's v_boundaries to properties.

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  10. Introduce Radial1DModel cutting to v_boundaries.

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  11. Revert 'Add a model.density module' back to HomologousDensity.

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  12. Change Radial1DModel.density to respect the v_boundaries.

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  13. Change Radial1DModel.abundance to respect the v_boundaries.

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  14. Allow model boundaries to be given as plain values.

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  15. New model.density module to hold HomologousDensity and density functi… 

    …ons.
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  16. Change MontecarloRunner so it doesn't depend on a Configuration object.

    @ftsamis
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  17. Add a plasma parameter to MontecarloRunner.run 

    The MontecarloRunner now needs a separate reference to the plasma since the restructured Radial1DModel doesn't have the plasma as an attribute anymore.
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  18. Move and adapt calculate_j_blues from the old Radial1DModel to Montec… 

    …arloRunner.
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  19. Add the time_of_simulation property to the MontecarloRunner.

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  20. Add the plasma as an argument to montecarlo.montecarlo_radial1d.

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  21. Remove every Configuration object usage from the montecarlo.pyx

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  22. Add a from_config classmethod to the MontecarloRunner.

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  23. montecarlo.pyx: Access atomic_data from the plasma, instead of model.

    @ftsamis
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  24. Remove the legacy Radial1DModel.

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  25. Replace LegacyPlasmaArray with a function.

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  26. assemble_plasma: prepare() the atom_data before passing it to the pla… 

    …sma.
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  27. Rename LTEJBlues to JBluesBlackBody

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  28. Add a JBluesDiluteBlackBody plasma property.

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  29. Add a JBlueEstimator input plasma property.

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  30. Remove JBlues as an Input plasma property.

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  31. Revert "Move and adapt calculate_j_blues from the old Radial1DModel t… 

    …o MontecarloRunner."

This reverts commit 9f4385e, because it
was decided that the j_blues will become plasma properties.
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  32. Add a calculate_time_of_simulation and a calculate_luminosity_inner t… 

    …o the MontecarloRunner.
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  33. Remove JBluesBlackBody from the nlte_properties collection.

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  34. Check the radiative_rates_type to add the appropriate JBlues plasma m… 

    …odule.
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  35. fixup! Add a JBluesDiluteBlackBody plasma property.

    @ftsamis
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  36. Change JBluesBlackBody's output name to j_blues from lte_j_blues.

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  37. Improve JBluesBlackBody's calculate method by using intensity_black_b… 

    …ody.
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  38. Implement the barebones of the restructured Simulation class.

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  39. Implement the Simulation.from_config classmethod.

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  40. Make Simulation take the Montecarlo runner as a parameter.

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  41. Simulation: Add the logic for the last iteration.

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  42. Move the sigma_thomson calculation from config_reader to montecarlo.

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  43. Move the spectrum frequency calculation from config_reader to monteca… 

    …rlo.
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  44. Remove supernova distance checking from config_dict

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  45. Don't rename virtual_spectrum_range's stop and num to end and samples.

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  46. Add a FIXME note for supporting initialization of plasma properties.

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  47. Fix and move the NLTE species conversions from config_reader to assem… 

    …ble_plasma.
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  48. model/density.py: Add support for all the specific density types.

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  49. Remove time_0 from a required property in specific densities. 

    Use time_explosion as time_0 if the latter was not provided in the configuration.
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  50. Add a time_0 property to the uniform density type.

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  51. Add support for density files in the restructured Model.

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  52. Move the t_radiative calculation from config_reader to Model.from_con… 

    …fig.
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  53. Properly pass the v_inner/outer_boundaries to the model, if proivded.

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  54. Move the abundance calculations from config_reader to Radial1DModel.f… 

    …rom_config
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  55. Move the t_inner calculation from config_reader to Radial1DModel

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  56. Remove unneeded model related code from config_reader.

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  57. Simulation: Log the plasma state when advancing the simulation.

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  58. Fix a bug when initializing the logger for montecarlo/base.py

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  59. Make sure all no_of_packets variables are passed as integers.

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  60. Fix accessing the abundance array from the config in assemble_plasma.

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  61. Remove unecessary imports from the config_reader.

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  62. Make sure velocity and time_explosion are passed in CGS to the Model.

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  63. Fix invalid access of the structure section of the configuration.

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  64. Remove atom_data from the init arguments of Simulation.

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  65. Move the luminosity_nu_[start|end] calculation from config_reader to … 

    …Simulation.from_config.
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  66. Move atom_data calculation from config_reader to assemble_plasma.

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  67. Don't duplicate information from the MontecarloRunner to the Simulation.

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  68. Add convergence checking and hold_iterations logic.

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  69. Fix incorrect access of hold_iterations.

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  70. Remove all the unused code from config_reader.

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  71. Properly set Configuration.config_dirname.

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  72. Initialize model's raw_velocity earlier.

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  73. Reintroduce and adjust various to_hdf methods.

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  74. Implement a basic callback system for calling a custom function after… 

    … each iteration.
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  75. assemble_plasma now takes an atom_data parameter as well.

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  76. plasma conftest: Remove unused import.

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  77. Move test_quantity_linspace to test_util

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  78. Remove two redundant configuration_namespace tests from test_config_r… 

    …eader.
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  79. Allow overriding model,plasma,runner in Simulation.from_config.

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  80. Fix tests for simulation.

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  81. Remove unused fixture from test_complete_plasmas.

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  82. Remove commented out code from test_property_nlte.

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  83. Update test_plasmas_full to not use run_tardis.

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  84. Remove test_legacy_model_properties.

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  85. Update test_tardis_full to use the post-restructure call interface.

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  86. Add back the check for invalid volume in read_density_file.

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  87. Fix simulation trying to access hold_iterations value when convergenc… 

    …e type is not specific.
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  88. Make density array have the same length when read from a file as when… 

    … specific.
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  89. Update test_ascii_readers to test the restructured code.

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  90. Fix a parsing bug in read_simple_ascii_density

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  91. fixup! Update test_plasmas_full to not use run_tardis.

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  92. Adjust io/tests/test_model_reader to the changed model_reader.

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  93. Simplify test_config_reader, only testing the functions it provides.

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  94. Fix improperly accessing uniform density value in HomologousDensity f… 

    …rom_config.
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  95. Add a test module for model 

    Add a test module for Radial1DModel, containing the
tests that were part of config_reader before the restructure
and the config_reader cleanup. Therefore, these tests mostly
cover creating a Radial1DModel from various configuration
inputs and checking the correctness of the values read.
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  96. Allow initialization of modules in the BasePlasma.

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  97. fixup! Allow initialization of modules in the BasePlasma.

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  98. Remove the distinction of j_blues and lte_j_blues in the LevelBoltzma… 

    …nnFactorNLTE calculate methods.
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  99. Access nlte_species from nlte_data instead of plasma_parent. 

    Accessing attributes from the plasma_parent inside plasma modules should be avoided. In this case nlte_species could be accessed from nlte_data which is a ProcessingPlasmaProperty
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  100. Change references to Radial1DModel.t_rads to t_rad. 

    t_rads was renamed to t_radiative and t_rad.
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  101. Adjust the tardis script to the restructured code.

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  102. Adjust run_tardis helper function to the restructured code.

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  103. Move the j_blues properties from radiative_properties to a separate j… 

    …_blues module.
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  104. Reintroduce j_blues_detailed as a ProcessingPlasmaProperty instead of… 

    … just Input.
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  105. Store some more montecarlo properties in the to_hdf method.

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  106. Set the default path of Simulation.to_hdf to 'simulation'.

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  107. Adjust test_integration.py to the restructured code.

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  108. Skip test_plasma_simple.

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    ftsamis committed Dec 8, 2016
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  109. Fix plasma properties accessing the plasma_parent. Also fix assemble_… 

    …plasma.
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    ftsamis committed Dec 8, 2016
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  110. Bring back storing the previous_properties in NLTE runs.

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    ftsamis committed Dec 8, 2016
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  111. Fix JBluesDetailed.__init__ method not accepting plasma_parent.

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    ftsamis committed Dec 8, 2016
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  112. Fix not adding the detailed j_blues input properties to the plasma.

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    ftsamis committed Dec 8, 2016
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  113. Fix JBluesDetailed.calculate accessing t_rad.value instead of just t_… 

    …rad.
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  114. Return a numpy.array in the JBluesDetailed.calculate method instead o… 

    …f a DataFrame.
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  115. Use len(t_rad) instead of len(j_blues) in JBluesDetailed to represent… 

    … no_of_shells.
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  116. Fix typo on parameter name of Simulation.to_hdf call from test_integr… 

    …ation.
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    ftsamis committed Dec 8, 2016
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  117. Fix model.t_radiative not being cut to the specified v boundaries.

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  118. Fix slicing the t_radiative twice in the getter if it was initialized… 

    … inside the Radial1DModel.
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  119. Fix a wrong check in Radial1DModel.t_radiative setter regarding bound… 

    …ary slicing.
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  120. Fix the luminosity_inner hdf location in test_integration.

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    ftsamis committed Dec 8, 2016
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Commits on Dec 16, 2016

  1. Add docstrings for some classes and methods affected by the restructure.

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    ftsamis committed Dec 16, 2016
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  2. Fix a PEP8 violation in model_reader.

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    ftsamis committed Dec 16, 2016
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  3. Rename the after_time method of HomologousDensity to calculate_densit… 

    …y_at_time_of_simulation
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    ftsamis committed Dec 16, 2016
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  4. Use the return statement once in HomogolousDensity.from_config instea… 

    …d of in every 'if'.
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    ftsamis committed Dec 16, 2016
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  5. Remove an outdated TODO comment.

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    ftsamis committed Dec 16, 2016
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Commits on Dec 17, 2016

  1. Use sigma_T from astropy constants instead of hardcoding it, also fix… 

    …ing its unit.
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    ftsamis committed Dec 17, 2016
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Commits on Dec 20, 2016

  1. Revert "Use sigma_T from astropy constants instead of hardcoding it, … 

    …also fixing its unit."

This reverts commit 136f667.
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    ftsamis committed Dec 20, 2016
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