Code

General bugfixing#39

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wkerzendorf merged 120 commits intomastertardis-sn/tardis:masterfrom general_bugfixingtardis-sn/tardis:general_bugfixingCopy head branch name to clipboardJun 25, 2013

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Commits

Commits on Mar 17, 2013

• updated test cases in test_lte_plasma.py

  maryampatel

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Commits on Mar 26, 2013

• got rid of sigma_thomson in montecarlo_multizone

  wkerzendorf

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• added logging for nlte

  wkerzendorf

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• added new setup.py from package templates

  wkerzendorf

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Commits on Apr 1, 2013

• added logger warnings when overflowing macroatom

  wkerzendorf

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• added default values for last_no_of_packets and virtual_packets (in config_reader)

  wkerzendorf

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• fixes

  wkerzendorf

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Commits on Apr 2, 2013

• added w_epsilon to the config_file

  wkerzendorf

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• fixed j_blues = 0 using w_epsilon

  wkerzendorf

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• logger for atom data uuid and md5

  wkerzendorf

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• cleanup of various files - included new atom_data.h5 with new tardisatomic

  wkerzendorf

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• CRITICAL error in the NLTE calculation - merge as soon as possible

  wkerzendorf

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• removed pdb.set_trace debugging statement

  wkerzendorf

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• changed np.empty.. to np.zeros

  wkerzendorf

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Commits on Apr 3, 2013

• Merge pull request #29 from wkerzendorf/general_bugfixing

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Commits on Apr 4, 2013

• fixed problems with the collision data. It should work now.

  wkerzendorf

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Commits on Apr 5, 2013

• CRITICAL Error prevented NLTE level populations making it in the tau_sobolev calculations (they were overwritten beforehand).

  wkerzendorf

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Commits on Apr 7, 2013

• updated test cases

  maryampatel

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Commits on Apr 8, 2013

• added electron density to history

  wkerzendorf

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• debugging problems - with debug statements in there DO NOT USE

  wkerzendorf

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• minor changes to model_history

  wkerzendorf

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• first construction of the collision_matrix

  wkerzendorf

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Commits on Apr 9, 2013

• implemented new_matrix

  wkerzendorf

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• bug fixing new rates matrix

  wkerzendorf

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• fixed up rates_matrix just changing nlte container class. speedup of 3000

  wkerzendorf

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• changed to NLTE data

  wkerzendorf

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• restructure complete ready for merge

  wkerzendorf

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Commits on Apr 10, 2013

• Merge pull request #32 from maryampatel/plasma/testing2

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  wkerzendorf

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Commits on Apr 13, 2013

• added classical nebular and coronal approximations.

  wkerzendorf

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Commits on Apr 14, 2013

• changed the BasePlasma class initializer. Added a classmethod to read from an abundance dictionary

  wkerzendorf

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• changed the BasePlasma class initializer. Added a classmethod to read from an abundance dictionary

  wkerzendorf

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• finished class method for baseplasma

  wkerzendorf

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Commits on Apr 15, 2013

• restructured plasma

  wkerzendorf

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Commits on Apr 16, 2013

• mainly fixed the synpp writer

  wkerzendorf

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• saha treatment was set to lte for nebular plasma

  wkerzendorf

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• small fix in the plasma calculation

  wkerzendorf

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Commits on Apr 18, 2013

• Merge pull request #34 from wkerzendorf/general_bugfixing

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• small fix to plasma, to raise an exception when electron density goes to nan or when the iterations go over 100

  wkerzendorf

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Commits on Apr 21, 2013

• fixed a number of bugs

  wkerzendorf

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• finished the HDF5 modification

  wkerzendorf

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Commits on May 24, 2013

• some changes for convergence pattern

  wkerzendorf

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• Merge branch 'general_bugfixing' of github.com:wkerzendorf/tardis into general_bugfixing

  nathanielatom

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Commits on May 29, 2013

• added last line interaction id in montecarlo

  wkerzendorf

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• read last_line interaction into model

  wkerzendorf

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• added analysis tool

  wkerzendorf

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• added analysis class. In addition added last_line_interaction_shell and last_interaction_line

  wkerzendorf

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• added interactive plotting to line interaction analysis class.

  wkerzendorf

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Commits on May 30, 2013

• fixed issue with iterations=1 not working in new while True scheme.

  wkerzendorf

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Commits on Jun 3, 2013

• several fixes to analysis

  wkerzendorf

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• fixed documentation for plasma

  wkerzendorf

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• removed the tests for now.

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  wkerzendorf

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Commits on Jun 4, 2013

• added 'specific' convergence option

  wkerzendorf

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• specific convergence implemented and tested

  wkerzendorf

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• finished convergence structure. Currently only undamped and specific is implemented

  wkerzendorf

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• moved the convergence parsing to the config_reader.

  wkerzendorf

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• fixed quantity issues.

  wkerzendorf

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• finsihed move of convergence parsing to config_reader

  wkerzendorf

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• finished writing all the plasma information to the HDF5File.

  wkerzendorf

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• implemented writing the HDF5 files from the radial1d_mdl - will continue to add attrbutes to the writer.

  wkerzendorf

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Commits on Jun 5, 2013

• added some more attributes for hdf5 storer

  wkerzendorf

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• deleted the testing documentation

  wkerzendorf

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• fixed the doc plot generating scripts and am on the hunt for the wrong ionization equation

  wkerzendorf

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• fixed saha treatment in plasma for classmethod initialization (everything else should have worked).

  wkerzendorf

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  8abf70e

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• finished updating the LTE and nebular ionization example calculations.

  wkerzendorf

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Commits on Jun 6, 2013

• finished putting in the configuration page for TARDIS docs

  wkerzendorf

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• added stimulated emission to macroatom and tau_sobolevs.

  wkerzendorf

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• changed the population inversion to a critical warning. Issues with Si2 (e.g. level 39) are apparent with nebular approximation.

  wkerzendorf

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• finished adding stimulated emission. including update of documentation

  wkerzendorf

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  5b48545

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• changed automodapi

  wkerzendorf

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• several cleanup actions. also added a simple explanation to running.rst

  wkerzendorf

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Commits on Jun 7, 2013

• changed tardis.bib to link with the paper tardis.bib. some changes in conf.py

  wkerzendorf

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• cghanged the critical population inversion warning to only apply if none of the levels are metastable.

  wkerzendorf

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• updated the bib file

  wkerzendorf

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• Merge branch 'general_bugfixing' of github.com:wkerzendorf/tardis into general_bugfixing

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• "added requirements"

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• "added "

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• "added "

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• "Flipped columns and rows"

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• "Flipped columns and rows - fixed"

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• "Flipped columns and rows - fixed"

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• "Can now display numpy.float64 by converting them to float"

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• "Added adjustable headerdata"

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• "Dynamic data - fixed"

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• "Dynamic data - fixed"

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• "Embedded matplotlib figure showing 20 shells"

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• "Shell Picker added"

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• "Shell Picker added - now highlights row"

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• "Colourbar added and updatable, shells use inner and outer radiuses"

  nathanielatom

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• Merge pull request #40 from nathanielatom/gui/matplotlib_figure

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Commits on Jun 12, 2013

• fixed convergence type default setting

  wkerzendorf

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• added several docstrings

  nathanielatom

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• "New layout, and dialog plot"

  nathanielatom

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• Merge pull request #41 from nathanielatom/gui/docs

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  wkerzendorf

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• added adam's gui to the running of tardis

  wkerzendorf

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Commits on Jun 13, 2013

• added spectrum plotting

  wkerzendorf

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Commits on Jun 14, 2013

• added several docstrings

  nathanielatom

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• "New layout, and dialog plot"

  nathanielatom

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• added adam's gui to the running of tardis

  

  wkerzendorf

  authored and

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• added spectrum plotting

  

  wkerzendorf

  authored and

  nathanielatom

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• updated comment on how to start up ipython

  nathanielatom

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• updated comment on how to start up ipython

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• "changed comment regarding how to initialize IPython"

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• "Added spectrum plot"

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• "changed comment regarding how to initialize IPython"

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Commits on Jun 15, 2013

• "changed comment regarding how to initialize IPython"

  nathanielatom

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• changed intialization description

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Commits on Jun 17, 2013

• "added t_rads subplot, and ability to change between displaying spec_flux_angstrom and spec_virtual_flux_angstrom"

  nathanielatom

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Commits on Jun 18, 2013

• fixed some problems in the docs

  wkerzendorf

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Commits on Jun 21, 2013

• removed tracked files

  nathanielatom

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• removed tracked files

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• removed tracked files

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Commits on Jun 24, 2013

• fixed W > 1 in excitation formula

  wkerzendorf

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• fixed stupid numpy error

  wkerzendorf

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Commits on Jun 25, 2013

• Merge branch 'general_bugfixing' of github.com:wkerzendorf/tardis

  nathanielatom

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• added switchable shell viewer (t_rads or Ws)

  nathanielatom

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• started on shell info dialogue

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• started on shell info dialog

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• "deleted some files"

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• deleted orig file

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• Merge pull request #46 from nathanielatom/gui/dialogue

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