Merge pull request #773 from unoebauer/improved_docs

Update Documentation

docs/configuration/configuration_old.rst

@@ -249,14 +249,23 @@ The spectrum section defines the
 
     spectrum:
         start : 500 angstrom
-        end : 20000 angstrom
-        bins : 1000
-        sn_distance : lum_density
-        #sn_distance : 10 Mpc
-
-Start and end are given as Quantities with units. If they are given in frequency space they are switched around if
-necessary. The number of bins is just an integer. Finally the ``sn_distance`` can either be a distance or the special
-parameter ``lum_density`` which sets the distance to :math:`\sqrt{\frac{1}{4 \pi}}` to calculate the luminosity density.
+        stop : 20000 angstrom
+        num : 1000
+        method: virtual
+
+Start and end are given as Quantities with units. If they are given in
+frequency space they are switched around if necessary. The number of bins is
+just an integer. Finally, the method option selects the final spectral synthesis mode. Currently, there are three options:
+
+* real: construct spectrum from the real packet population alone
+* virtual: use the :doc:`virtual packet scheme <../montecarlo/virtualpackets>` for spectral synthesis
+* integrated: use the :doc:`formal integral method <../montecarlo/sourceintegration>` of Lucy 1999
+
+.. warning:: 
+
+  Currently, the "integrated" mode only works with the downbranching line
+  interaction mode. Note also the limitations listed at the bottom of the
+  dedicated page.
 
 
 Config Reader

docs/gui.rst

@@ -4,12 +4,6 @@
 Graphical User Interface
 ************************
 
-.. warning::
-    The GUI is currently not compatible with the latest development version of
-    TARDIS (see `TEP
-    <https://github.com/tardis-sn/tep/blob/master/TEP012_gui_overhaul.rst>`_
-    and `Issue #690 <https://github.com/tardis-sn/tardis/issues/690>`_)
-
 
 TARDIS uses the `PyQt4 framework <http://www.riverbankcomputing.com/software/pyqt/download>`_ for its cross-platform
 interface.

docs/index.rst

@@ -59,7 +59,7 @@ Developing Tardis
 References
 ==========
 
-* :doc:`TARDIS Papers and useful references <zreferences>`
+* :doc:`Studies using TARDIS and TARDIS references <zreferences>`
 
 ====
 News

docs/news.rst

@@ -1,3 +1,13 @@
+GSOC 2017
+---------
+
+.. image:: https://developers.google.com/open-source/gsoc/resources/downloads/GSoC-logo-horizontal.svg
+  :target: https://summerofcode.withgoogle.com/organizations/4793296782098432/
+  :width: 458 px
+
+TARDIS participates in the Google Summer of Code 2017 program as part of the Python Software Foundation!
+
+
 SOCIS 2016
 ----------
 

docs/running.rst

@@ -52,12 +52,6 @@ This model can then be used for inspecting the run as described
 Graphical User Interface
 ========================
 
-.. warning::
-    The GUI is currently not compatible with the latest development version of
-    TARDIS (see `TEP
-    <https://github.com/tardis-sn/tep/blob/master/TEP012_gui_overhaul.rst>`_
-    and `Issue #690 <https://github.com/tardis-sn/tardis/issues/690>`_)
-
 To get a detailed explanation on gui layout go to :ref:`gui_explanation` .
 
 **To setup and run the GUI(under development) follow these steps:**

docs/tardis.bib

@@ -1,4 +1,3 @@
-% This file was created with JabRef 2.10.
 % Encoding: UTF-8
 @Article{Abbott1985,
   Title                    = {{Multiline transfer and the dynamics of stellar winds}},
@@ -148,7 +147,6 @@ @Article{Magee2016
   Eid                      = {A89},
   Eprint                   = {1603.04728},
 }
-
 @Article{Mazzali1993,
   Title                    = {{The application of Monte Carlo methods to the synthesis of early-time supernovae spectra}},
   Author                   = {{Mazzali}, P.~A. and {Lucy}, L.~B.},
@@ -159,7 +157,6 @@ @Article{Mazzali1993
   Volume                   = {279},
   Adsurl                   = {http://adsabs.harvard.edu/abs/1993A%26A...279..447M},
 }
-
 @PhdThesis{Noebauer2014,
   Title                    = {A Monte Carlo Approach to Radiation Hydrodynamics in Stellar Outflows},
   Author                   = {{Noebauer}, U.~M.},
@@ -169,7 +166,6 @@ @PhdThesis{Noebauer2014
   Type                     = {Dissertation},
   Url                      = {http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:91-diss-20140731-1219398-0-8}
 }
-
 @Article{Sim2010,
   Title                    = {{Multidimensional modelling of X-ray spectra for AGN accretion disc outflows - III. Application to a hydrodynamical simulation}},
   Author                   = {{Sim}, S.~A. and {Proga}, D. and {Miller}, L. and {Long}, K.~S. and {Turner}, T.~J.},
@@ -183,4 +179,75 @@ @Article{Sim2010
   Doi                      = {10.1111/j.1365-2966.2010.17215.x},
   Eprint                   = {1006.3449},
 }
+@Article{Magee2017,
+  author        = {{Magee}, M. R. and {Kotak}, R. and {Sim}, S. A. and {Wright}, D. and {Smartt}, S. J. and {Berger}, E. and {Chornock}, R. and {Foley}, R. J. and {Howell}, D. A. and {Kaiser}, N. and {Magnier}, E. A. and {Wainscoat}, R. and {Waters}, C.},
+  title         = {Growing evidence that SNe Iax are not a one-parameter family. The case of PS1-12bwh},
+  journal       = {\aap},
+  year          = {2017},
+  volume        = {601},
+  pages         = {A62},
+  month         = may,
+  archiveprefix = {arXiv},
+  doi           = {10.1051/0004-6361/201629643},
+  eid           = {A62},
+  eprint        = {1701.05459},
+  keywords      = {supernovae: general, supernovae: individual: PS1-12bwh},
+  owner         = {ulrich},
+  primaryclass  = {astro-ph.HE},
+  timestamp     = {2017.07.27},
+}
+@Article{Inserra2016,
+  author        = {{Inserra}, C. and {Bulla}, M. and {Sim}, S. A. and {Smartt}, S. J.},
+  title         = {Spectropolarimetry of Superluminous Supernovae: Insight into Their Geometry},
+  journal       = {\apj},
+  year          = {2016},
+  volume        = {831},
+  pages         = {79},
+  month         = nov,
+  archiveprefix = {arXiv},
+  doi           = {10.3847/0004-637X/831/1/79},
+  eid           = {79},
+  eprint        = {1607.02353},
+  keywords      = {stars: jets, stars: magnetars, stars: mass-loss, supernovae: general, supernovae: individual: SN 2015bn},
+  owner         = {ulrich},
+  primaryclass  = {astro-ph.HE},
+  timestamp     = {2017.07.27},
+}
+@Article{Boyle2017,
+  author        = {{Boyle}, A. and {Sim}, S. A. and {Hachinger}, S. and {Kerzendorf}, W.},
+  title         = {Helium in double-detonation models of type Ia supernovae},
+  journal       = {Astronomy and Astrophysics},
+  year          = {2017},
+  volume        = {599},
+  pages         = {A46},
+  month         = mar,
+  archiveprefix = {arXiv},
+  doi           = {10.1051/0004-6361/201629712},
+  eid           = {A46},
+  eprint        = {1611.05938},
+}
+@Article{Barna2017,
+  author        = {{Barna}, B. and {Szalai}, T. and {Kromer}, M. and {Kerzendorf}, W. E. and {Vinko}, J. and {Silverman}, J. M. and {Marion}, G. H. and {Wheeler}, J. C.},
+  title         = {Abundance Tomography of Type Iax SN 2011ay with TARDIS},
+  journal       = {ArXiv e-prints},
+  year          = {2017},
+  month         = jul,
+  archiveprefix = {arXiv},
+  eprint        = {1707.07848},
+}
+
+@Article{Heringer2017,
+  author        = {{Heringer}, E. and {van Kerkwijk}, M.~H. and {Sim}, S.~A. and {Kerzendorf}, W.~E.},
+  title         = {{Spectral sequences of Type Ia supernovae. I. Connecting normal and sub-luminous SN Ia and the presence of unburned carbon}},
+  journal       = {ArXiv e-prints},
+  year          = {2017},
+  month         = jul,
+  adsnote       = {Provided by the SAO/NASA Astrophysics Data System},
+  adsurl        = {http://adsabs.harvard.edu/abs/2017arXiv170708572H},
+  archiveprefix = {arXiv},
+  eprint        = {1707.08572},
+  keywords      = {Astrophysics - High Energy Astrophysical Phenomena},
+}
+
 
+@Comment{jabref-meta: databaseType:bibtex;}

docs/zreferences.rst

@@ -11,9 +11,14 @@ TARDIS Code papers
 
 * :cite:`Kerzendorf2014`
 
-Works using TARDIS
+Studies using TARDIS
 ==================
 
+* :cite:`Barna2017`
+* :cite:`Heringer2017`
+* :cite:`Magee2017`
+* :cite:`Boyle2017`
+* :cite:`Inserra2016`
 * :cite:`Magee2016`
 
 Monte Carlo Radiative Transfer Works