[Yt-svn] yt-commit r1021 - in branches/yt-1.0/doc: . source source/cookbook source/extending source/modules/lagos source/tour
mturk at wrangler.dreamhost.com
mturk at wrangler.dreamhost.com
Wed Dec 17 11:05:59 PST 2008
Author: mturk
Date: Wed Dec 17 11:05:58 2008
New Revision: 1021
URL: http://yt.spacepope.org/changeset/1021
Log:
Some minor reformatting of text, added cross-links for the documentation,
changed the "Getting Started" section to "Getting the Code", added note about
Kraken, and re-generated docs.
Removed:
branches/yt-1.0/doc/source/cookbook/grouping_data.rst
Modified:
branches/yt-1.0/doc/docs_html.zip
branches/yt-1.0/doc/source/cookbook/index.rst
branches/yt-1.0/doc/source/extending/creating_derived_fields.rst
branches/yt-1.0/doc/source/getting_started.rst
branches/yt-1.0/doc/source/modules/lagos/basedatatypes.rst
branches/yt-1.0/doc/source/tour/code_objects.rst
branches/yt-1.0/doc/source/tour/physical_objects.rst
branches/yt-1.0/doc/source/tour/plots.rst
branches/yt-1.0/doc/source/tour/reduced_objects.rst
Modified: branches/yt-1.0/doc/docs_html.zip
==============================================================================
Binary files. No diff available.
Modified: branches/yt-1.0/doc/source/cookbook/index.rst
==============================================================================
--- branches/yt-1.0/doc/source/cookbook/index.rst (original)
+++ branches/yt-1.0/doc/source/cookbook/index.rst Wed Dec 17 11:05:58 2008
@@ -33,7 +33,6 @@
analyzing_data
making_profiles
plotting_profiles
- grouping_data
making_movies
making_timeseries_plots
extracting_data
Modified: branches/yt-1.0/doc/source/extending/creating_derived_fields.rst
==============================================================================
--- branches/yt-1.0/doc/source/extending/creating_derived_fields.rst (original)
+++ branches/yt-1.0/doc/source/extending/creating_derived_fields.rst Wed Dec 17 11:05:58 2008
@@ -86,7 +86,13 @@
that we do not wish to display this field as logged, that we require both
``height_vector`` and ``center`` to be present in a given data object we wish
to calculate this for, and we say that it should not be displayed in a
-drop-down box of fields to display.
+drop-down box of fields to display. This is done through the parameter
+*validators*, which accepts a list of :class:`FieldValidator` objects. These
+objects define the way in which the field is generated, and when it is able to
+be created. In this case, we mandate that parameters *center* and
+*height_vector* are set before creating the field. These are set via
+:meth:`~yt.lagos.EnzoData.set_field_parameter`, which can be called on any
+object that has fields.
We can also define vector fields.
Modified: branches/yt-1.0/doc/source/getting_started.rst
==============================================================================
--- branches/yt-1.0/doc/source/getting_started.rst (original)
+++ branches/yt-1.0/doc/source/getting_started.rst Wed Dec 17 11:05:58 2008
@@ -1,6 +1,6 @@
-===============
-Getting Started
-===============
+================
+Getting the Code
+================
Maintained Installations
========================
@@ -40,15 +40,41 @@
where my_script.py is the script you wish to run.
+Kraken (NICS)
+-------------
+
+I do not currently have an installation on Kraken, but I have had success
+installing it with the :ref:`installation script <installation_script>`.
+However, if you are going to try to run ``yt`` on the compute nodes, be aware
+that -- while it does work -- it will take a bit of effort because the compute
+nodes run Compute Node Linux. As a result, all the libraries have to be
+compiled statically -- including all of Python and ``yt``!
+
+There are some resources to help you with this:
+
+* `<https://wiki.fysik.dtu.dk/gpaw/install/platforms_and_architectures.html#louhi-csc-fi>`_
+* `<http://code.google.com/p/pyprop/wiki/Installation_CrayXT4>`_
+
+It's non-trivial, but it does work. Be sure you have unloaded PrgEnv-pgi and
+loaded PrgEnv-gnu. The only other "gotcha" I ran into was the compilation of
+Matplotlib, which relies on C++ libraries, so you must either modify the Python
+makefile to compile libpython2.5.a with ``CC`` rather than ``cc`` or compile by
+hand. Additionally, ``MATPLOTLIBDIR`` has to be set to the local directory,
+because compute nodes do not have access to ``$HOME``.
+
Binary Packages
===============
Currently binary packages are only supplied for OSX. See the download page on
-the Wiki for up-to-date links.
+the Wiki for up-to-date links. Please note, these may be out of date.
+Building binary packages is non-trivial, and I often have trouble getting all
+of the included libraries to work properly.
Installing From Source
======================
+.. _installation_script:
+
Using the Installation Script
-----------------------------
Modified: branches/yt-1.0/doc/source/modules/lagos/basedatatypes.rst
==============================================================================
--- branches/yt-1.0/doc/source/modules/lagos/basedatatypes.rst (original)
+++ branches/yt-1.0/doc/source/modules/lagos/basedatatypes.rst Wed Dec 17 11:05:58 2008
@@ -14,9 +14,6 @@
>>> object["Density"]
>>> object["Density"].max()
-And so on. For more information, see the
-:ref:`the tutorial topic <basic_objects>` on basic objects.
-
.. currentmodule:: yt.lagos
Base Classes
Modified: branches/yt-1.0/doc/source/tour/code_objects.rst
==============================================================================
--- branches/yt-1.0/doc/source/tour/code_objects.rst (original)
+++ branches/yt-1.0/doc/source/tour/code_objects.rst Wed Dec 17 11:05:58 2008
@@ -24,7 +24,7 @@
from a simulation -- this is your entry point inside ``yt``. These particular
objects are meant to be very 'cheap' -- they're meant to be quick to
instantiate, so that you can, for instance, very rapidly identify which output
-you want to examine in a script. The class name is :class:`EnzoStaticOutput`.
+you want to examine in a script. The class name is :class:`~yt.lagos.EnzoStaticOutput`.
For example, here's a snippet from my own research. It uses a python module
called ``glob`` to do wildcard filename matching, and then it checks to see if
@@ -59,8 +59,8 @@
grids, this can take some time. (Efforts are under way to reduce this time,
but it's an unfortunate tradeoff between flexibility and speed. Typically it
doesn't feel sluggish unless you are instantiating more than 50,000 grid
-patches.) This class is :class:`EnzoHierarchyType`, but you will only need to
-access it as a property of an :class:`EnzoStaticOutput` called ``h``:
+patches.) This class is :class:`~yt.lagos.EnzoHierarchyType`, but you will only need to
+access it as a property of an :class:`~yt.lagos.EnzoStaticOutput` called ``h``:
.. code-block:: python
@@ -96,7 +96,7 @@
of a code objects rather than physical objects. However, despite that
categorization, the data returned to you when accessed through a grid is in cgs
units, as to allow better and more meaningful analysis. This class is the
-:class:`EnzoGridBase`.
+:class:`~yt.lagos.EnzoGridBase`.
You should not have to instantiate grid objects yourself -- they are
automatically created by the hierarchy, and stored in an array called
Modified: branches/yt-1.0/doc/source/tour/physical_objects.rst
==============================================================================
--- branches/yt-1.0/doc/source/tour/physical_objects.rst (original)
+++ branches/yt-1.0/doc/source/tour/physical_objects.rst Wed Dec 17 11:05:58 2008
@@ -12,8 +12,8 @@
----------------
These objects are all created from the hierarchy object; for instance, to
-obtain a sphere centered at ``(0.3, 0.5, 0.8)`` with a radius of one
-megaparsec, you could do:
+obtain a sphere (:class:`~yt.lagos.EnzoSphereBase`) centered at
+``(0.3, 0.5, 0.8)`` with a radius of one megaparsec, you could do:
.. code-block:: python
Modified: branches/yt-1.0/doc/source/tour/plots.rst
==============================================================================
--- branches/yt-1.0/doc/source/tour/plots.rst (original)
+++ branches/yt-1.0/doc/source/tour/plots.rst Wed Dec 17 11:05:58 2008
@@ -4,10 +4,10 @@
Through the plotting interface, you can have ``yt`` automatically generate many
of the analysis objects available to you!
-The primary plotting interface is through a :class:`PlotCollection`
+The primary plotting interface is through a :class:`~yt.raven.PlotCollection`
instantiated with a given parameter file and (optionally) a center. See
:ref:`quick_making_plots` for a brief example of how to generate a
-:class:`PlotCollection`.
+:class:`~yt.raven.PlotCollection`.
Two-Dimensional Images
----------------------
@@ -56,7 +56,7 @@
Thanks to the pylab interface in Matplotlib, we have an interactive plot
collection available for usage within ``IPython``. Instead of
-:class:`PlotCollection`, use :class:`PlotCollectionInteractive` -- this will
+:class:`~yt.raven.PlotCollection`, use :class:`~yt.raven.PlotCollectionInteractive` -- this will
generate automatically updating GUI windows with the plots inside them.
Callbacks
@@ -64,7 +64,7 @@
Callbacks are means of adding things on top of existing plots -- like vectors,
overplotted lines, and so on and so forth. They have to be added to the plot
-objects themselves, rather than the :class:`PlotCollection`. You can add them like so:
+objects themselves, rather than the :class:`~yt.raven.PlotCollection`. You can add them like so:
.. code-block:: python
Modified: branches/yt-1.0/doc/source/tour/reduced_objects.rst
==============================================================================
--- branches/yt-1.0/doc/source/tour/reduced_objects.rst (original)
+++ branches/yt-1.0/doc/source/tour/reduced_objects.rst Wed Dec 17 11:05:58 2008
@@ -43,7 +43,7 @@
can be displayed simultaneously.
You can generate these profiles yourself, but because their API is completely
-exposed by the :class:`PlotCollection` object, you rarely need to. But, if you
+exposed by the :class:`~yt.raven.PlotCollection` object, you rarely need to. But, if you
are determined to, see :ref:`making_profiles`. Otherwise, check out
:ref:`profiles_and_phase_plots`.
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