Merge pull request enzo-project#112 from fearmayo/quickstart

[JOSS] Fixing the quickstart JOSS issue with the Collapse Test

Author: bwoshea

doc/manual/source/user_guide/bootcamp.rst

@@ -1,7 +1,7 @@
 Quickstart Guide to Enzo
 ========================
 
-This is an unofficial quickstart guide to using Enzo, starting from
+This is the quickstart guide to using Enzo, starting from
 checking out the Enzo and YT sources, through to building them, then
 to running an example problem and looking at its output.
 
@@ -10,7 +10,7 @@ useful information or useful tools:
 
 * `github.com/enzo-project/enzo-dev <http://github.com/enzo-project/enzo-dev>`_
 * `yt-project.org <http://yt-project.org>`_
-* `jacques.enzotools.org <http://jacques.enzotools.org>`_
+
 
 If you ever get stuck, please email `enzo-users
 <https://groups.google.com/forum/#!forum/enzo-users>`_. This is not
@@ -21,7 +21,15 @@ interlocking modules, unusual combinations of parameters may require
 some care, and the individual developers that have created those
 modules will be able to discuss them with you.
 
-
+Getting YT
+------------
+YT was initially developed to allow fast and easy analysis of Enzo output. Since it's
+original inception YT has grown to be a powerful tool capable of analysing
+many different astrophysical simulation code outputs and also non-astro
+simulation outputs too.
+To get your hands on YT (which you will need to complete this quickstart tutorial)
+then go to the `YT installation page <https://yt-project.org/doc/installing.html>`_
+and install YT locally.
 
 Getting Enzo
 ------------
@@ -240,20 +248,55 @@ script, you should be able to execute this command:
 
 This will take three slices through the center of the domain along
 each axis, as sliced through the very first output. The images will be
-saved to the subdirectory frames .
+saved to the subdirectory frames. Here is a plot of the outputs that can be
+expected from the DD0000 snapshots:
 
-Now let's take a look at DD0010 :
+.. image:: ../../../../run/Hydro/Hydro-3D/CollapseTestNonCosmological/frames/DD0000_Slice_x_density.png
+    :width: 30%
+ 
 
+.. image:: ../../../../run/Hydro/Hydro-3D/CollapseTestNonCosmological/frames/DD0000_Slice_y_density.png
+    :width: 30%
 
+.. image:: ../../../../run/Hydro/Hydro-3D/CollapseTestNonCosmological/frames/DD0000_Slice_z_density.png
+    :width: 30%
+
+
+
+
+Now let's take a look at DD0010 :
+   
 ::
 
     $ yt plot DD0010/DD0010
 
 
+.. image:: ../../../../run/Hydro/Hydro-3D/CollapseTestNonCosmological/frames/DD0010_Slice_x_density.png
+    :width: 30%
+ 
+
+.. image:: ../../../../run/Hydro/Hydro-3D/CollapseTestNonCosmological/frames/DD0010_Slice_y_density.png
+    :width: 30%
+
+.. image:: ../../../../run/Hydro/Hydro-3D/CollapseTestNonCosmological/frames/DD0010_Slice_z_density.png
+    :width: 30%
+
+
 By this point the simulation has not collapsed very far. Feel free to
-check later outputs.
+check later outputs (e.g. the yt output from DD0070 shown below)
+
+.. image:: ../../../../run/Hydro/Hydro-3D/CollapseTestNonCosmological/frames/DD0070_Slice_x_density.png
+    :width: 30%
+ 
+
+.. image:: ../../../../run/Hydro/Hydro-3D/CollapseTestNonCosmological/frames/DD0070_Slice_y_density.png
+    :width: 30%
+
+.. image:: ../../../../run/Hydro/Hydro-3D/CollapseTestNonCosmological/frames/DD0070_Slice_z_density.png
+    :width: 30%
+
 
-Another handy command is yt stats , which will describe the current
+Another handy command is yt stats, which will describe the current
 state of the simulation in a couple metrics.