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Reorganizing files in docs (1/2) #1371

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Reorganizing files in docs (1/2) #1371

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4c534c2
deleting unused files
isaacgsmith Dec 1, 2020
82f171e
reorganizing docs/running
isaacgsmith Dec 3, 2020
b9a5ef6
clarifying which file to use in toctree, as there is a to_hdf.rst and…
isaacgsmith Dec 3, 2020
74d1c1f
fixing new_plasma toc
isaacgsmith Dec 4, 2020
5f3edbc
fixing headers on outdated sections
isaacgsmith Dec 4, 2020
3ff6efa
adding custom_source and physical_quantities to additional interactiv…
isaacgsmith Dec 4, 2020
84d0e1c
removing physical_quantities from old_physics
isaacgsmith Dec 4, 2020
3d29959
fixing heading on CONTRIBUTING.md
isaacgsmith Dec 6, 2020
ac98ba8
adding using_formal_integral
isaacgsmith Dec 6, 2020
28e161a
doing Jaladh's suggestions
isaacgsmith Dec 8, 2020
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2 changes: 1 addition & 1 deletion CONTRIBUTING.md
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@@ -1,4 +1,4 @@
# Contributing to TARDIS
# Contribution Guidelines

So you are wondering how can you contribute to TARDIS? Congrats, you've landed on the right page!

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40 changes: 0 additions & 40 deletions docs/governance.rst
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44 changes: 0 additions & 44 deletions docs/physics/index.rst
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7 changes: 3 additions & 4 deletions docs/physics/old_physics.rst
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*********************
Old Physics Section of the TARDIS Docu (Outdated)
*********************
******************************
Old Physics Section (Outdated)
******************************

.. note::
The following entries reflects the physics section of the old TARDIS
Expand All @@ -10,6 +10,5 @@ Old Physics Section of the TARDIS Docu (Outdated)


.. toctree::
physical_quantities
montecarlo_old
plasma/index
13 changes: 9 additions & 4 deletions docs/physics/new_plasma.rst → docs/physics/plasma.rst
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Expand Up @@ -2,6 +2,7 @@
Plasma
******


The role of the plasma module is to determine the ionisation and excitation states of the elements of the
supernova ejecta, given the basic structure, including the elemental abundances, densities and radiation temperature.
After the calculation of the plasma state, the :math:`\tau_{\textrm{sobolev}}` values can be calculated.
Expand Down Expand Up @@ -40,9 +41,13 @@ Updating the Plasma
-------------------
During each iteration of the main code, TARDIS updates the plasma using the `update_radiationfield` function. This requires, at minimum, new values for `t_rad` (the radiation temperature), `w` (the dilution factor) and `j_blues` (the intensity in the blue part of each line).



Plasma Calculations
-------------------
.. toctree::
:maxdepth: 2

plasma/index

plasma/lte_plasma
plasma/nebular_plasma
plasma/macroatom
plasma/nlte
plasma/helium_nlte
6 changes: 3 additions & 3 deletions docs/physics/plasma/plasma.rst → docs/physics/plasma/old_plasma.rst
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.. _plasmas:

******
Plasma
******
*****************
Plasma (Outdated)
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Good call!

*****************

.. currentmodule:: tardis.plasma_array

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35 changes: 0 additions & 35 deletions docs/running/index.rst
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2 changes: 1 addition & 1 deletion docs/running/interaction/Custom_TARDIS_Model_Tutorial.ipynb
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Expand Up @@ -788,7 +788,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.7"
"version": "3.7.8"
}
},
"nbformat": 4,
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0 docs/running/commandline.rst → docs/running/interaction/commandline.rst
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0 docs/running/converters/cmfgen.rst → ...running/interaction/converters/cmfgen.rst
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0 docs/running/converters/index.rst → .../running/interaction/converters/index.rst
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0 docs/running/converters/mesa.stella.dat → ...ng/interaction/converters/mesa.stella.dat
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0 ...running/converters/stella_to_tardis.ipynb → ...raction/converters/stella_to_tardis.ipynb
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0 docs/running/custom_source.ipynb → docs/running/interaction/custom_source.ipynb
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11 changes: 7 additions & 4 deletions docs/running/interaction/index.rst
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Expand Up @@ -8,17 +8,20 @@ have full access to the model properties (as described in :ref:`physical_quantit
:maxdepth: 1


../commandline
commandline
callback_example
../converters/index
converters/index
Custom_TARDIS_Model_Tutorial
../gui
custom_source
old_gui
access
init_trad_bug
integrator
isotope_pd_subclass
to_hdf
to_hdf.rst
hdf_writer
physical_quantities
using_formal_integral

.. examples/run_simple_example.ipynb

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62 changes: 31 additions & 31 deletions docs/running/interaction/integrator.ipynb
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Expand Up @@ -60,19 +60,19 @@
"name": "stderr",
"output_type": "stream",
"text": [
"[\u001B[1mtardis.plasma.standard_plasmas\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5 (\u001B[1mstandard_plasmas.py\u001B[0m:72)\n",
"tardis.plasma.standard_plasmas - \u001B[1;37mINFO\u001B[0m - Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5\n",
"[\u001b[1mtardis.plasma.standard_plasmas\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5 (\u001b[1mstandard_plasmas.py\u001b[0m:72)\n",
"tardis.plasma.standard_plasmas - \u001b[1;37mINFO\u001b[0m - Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5\n",
"tardis.atomic - INFO - Read Atom Data with UUID=5ca3035ca8b311e3bb684437e69d75d7 and MD5=21095dd25faa1683f4c90c911a00c3f8\n",
"[\u001B[1mtardis.plasma.base \u001B[0m][\u001B[1;34mDEBUG\u001B[0m ] Updating modules in the following order: (\u001B[1mbase.py\u001B[0m:195)\n",
"tardis.plasma.base - \u001B[1;34mDEBUG\u001B[0m - Updating modules in the following order:\n",
"[\u001B[1mtardis.montecarlo.base\u001B[0m][\u001B[1;34mDEBUG\u001B[0m ] Electron scattering switched on (\u001B[1mbase.py\u001B[0m:411)\n",
"tardis.montecarlo.base - \u001B[1;34mDEBUG\u001B[0m - Electron scattering switched on\n",
"[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Starting iteration 1/1 (\u001B[1mbase.py\u001B[0m:194)\n",
"tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Starting iteration 1/1\n",
"[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001B[1mbase.py\u001B[0m:271)\n",
"tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s\n",
"[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Simulation finished in 1 iterations and took 0.90 s (\u001B[1mbase.py\u001B[0m:221)\n",
"tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Simulation finished in 1 iterations and took 0.90 s\n"
"[\u001b[1mtardis.plasma.base \u001b[0m][\u001b[1;34mDEBUG\u001b[0m ] Updating modules in the following order: (\u001b[1mbase.py\u001b[0m:195)\n",
"tardis.plasma.base - \u001b[1;34mDEBUG\u001b[0m - Updating modules in the following order:\n",
"[\u001b[1mtardis.montecarlo.base\u001b[0m][\u001b[1;34mDEBUG\u001b[0m ] Electron scattering switched on (\u001b[1mbase.py\u001b[0m:411)\n",
"tardis.montecarlo.base - \u001b[1;34mDEBUG\u001b[0m - Electron scattering switched on\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 1/1 (\u001b[1mbase.py\u001b[0m:194)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Starting iteration 1/1\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:271)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Simulation finished in 1 iterations and took 0.90 s (\u001b[1mbase.py\u001b[0m:221)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Simulation finished in 1 iterations and took 0.90 s\n"
]
}
],
Expand Down Expand Up @@ -919,21 +919,21 @@
"name": "stdout",
"output_type": "stream",
"text": [
"[\u001B[1mtardis.plasma.standard_plasmas\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5 (\u001B[1mstandard_plasmas.py\u001B[0m:72)\n",
"tardis.plasma.standard_plasmas - \u001B[1;37mINFO\u001B[0m - Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5\n",
"[\u001b[1mtardis.plasma.standard_plasmas\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5 (\u001b[1mstandard_plasmas.py\u001b[0m:72)\n",
"tardis.plasma.standard_plasmas - \u001b[1;37mINFO\u001b[0m - Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5\n",
"tardis.atomic - INFO - Read Atom Data with UUID=5ca3035ca8b311e3bb684437e69d75d7 and MD5=21095dd25faa1683f4c90c911a00c3f8\n",
"[\u001B[1mtardis.plasma.base \u001B[0m][\u001B[1;34mDEBUG\u001B[0m ] Updating modules in the following order: (\u001B[1mbase.py\u001B[0m:195)\n",
"tardis.plasma.base - \u001B[1;34mDEBUG\u001B[0m - Updating modules in the following order:\n",
"[\u001B[1mtardis.montecarlo.base\u001B[0m][\u001B[1;34mDEBUG\u001B[0m ] Electron scattering switched on (\u001B[1mbase.py\u001B[0m:411)\n",
"tardis.montecarlo.base - \u001B[1;34mDEBUG\u001B[0m - Electron scattering switched on\n",
"[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Starting iteration 1/1 (\u001B[1mbase.py\u001B[0m:194)\n",
"tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Starting iteration 1/1\n",
"[\u001b[1mtardis.plasma.base \u001b[0m][\u001b[1;34mDEBUG\u001b[0m ] Updating modules in the following order: (\u001b[1mbase.py\u001b[0m:195)\n",
"tardis.plasma.base - \u001b[1;34mDEBUG\u001b[0m - Updating modules in the following order:\n",
"[\u001b[1mtardis.montecarlo.base\u001b[0m][\u001b[1;34mDEBUG\u001b[0m ] Electron scattering switched on (\u001b[1mbase.py\u001b[0m:411)\n",
"tardis.montecarlo.base - \u001b[1;34mDEBUG\u001b[0m - Electron scattering switched on\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 1/1 (\u001b[1mbase.py\u001b[0m:194)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Starting iteration 1/1\n",
"Running with OpenMP - 4 threads\n",
"\u001B[2K\t[100%] Packets(finished/total): 10000/10000\n",
"[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001B[1mbase.py\u001B[0m:271)\n",
"tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s\n",
"[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Simulation finished in 1 iterations and took 1.05 s (\u001B[1mbase.py\u001B[0m:221)\n",
"tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Simulation finished in 1 iterations and took 1.05 s\n",
"\u001b[2K\t[100%] Packets(finished/total): 10000/10000\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:271)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Simulation finished in 1 iterations and took 1.05 s (\u001b[1mbase.py\u001b[0m:221)\n",
"tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Simulation finished in 1 iterations and took 1.05 s\n",
"Saving the integrated spectrum.\n",
"Doing the formal integral with 4 threads\n",
"\n",
Expand Down Expand Up @@ -1720,23 +1720,23 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"display_name": "Python 3",
"language": "python",
"name": "python2"
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.12"
"pygments_lexer": "ipython3",
"version": "3.7.8"
}
},
"nbformat": 4,
"nbformat_minor": 1
}
}
2 changes: 1 addition & 1 deletion docs/running/interaction/isotope_pd_subclass.ipynb
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Expand Up @@ -217,7 +217,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.7"
"version": "3.7.8"
}
},
"nbformat": 4,
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6 changes: 3 additions & 3 deletions docs/running/gui.rst → docs/running/interaction/old_gui.rst
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*************************************
Old Graphical User Interface Section
*************************************
***************************************
Old Graphical User Interface (Outdated)
***************************************

TARDIS uses the `PyQt5 framework <http://www.riverbankcomputing.com/software/pyqt/download5>`_ for its cross-platform
interface.
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0 docs/running/to_hdf.rst → docs/running/interaction/to_hdf.rst
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0 docs/running/using_formal_integral.rst → ...ing/interaction/using_formal_integral.rst
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