[Yt-svn] yt-commit r456 - in trunk/doc/source: . extending modules/lagos
mturk at wrangler.dreamhost.com
mturk at wrangler.dreamhost.com
Fri May 9 14:11:42 PDT 2008
Author: mturk
Date: Fri May 9 14:11:40 2008
New Revision: 456
URL: http://yt.spacepope.org/changeset/456
Log:
Documentation modifications. Not much substantial.
Added:
trunk/doc/source/extending/analyzing_in_parallel.rst
trunk/doc/source/extending/creating_datatypes.rst
trunk/doc/source/extending/creating_derived_fields.rst
trunk/doc/source/extending/creating_derived_quantities.rst
trunk/doc/source/extending/plugin_file.rst
trunk/doc/source/extending/running_fortran_routines.rst
trunk/doc/source/extending/using_the_interpreter.rst
trunk/doc/source/extending/writing_scripts.rst
trunk/doc/source/modules/lagos/contours.rst
trunk/doc/source/modules/lagos/outputandhierarchy.rst
trunk/doc/source/modules/lagos/profiles.rst
Modified:
trunk/doc/source/conf.py
trunk/doc/source/extending/index.rst
trunk/doc/source/faq.rst
trunk/doc/source/modules/lagos/basedatatypes.rst
trunk/doc/source/modules/lagos/index.rst
Modified: trunk/doc/source/conf.py
==============================================================================
--- trunk/doc/source/conf.py (original)
+++ trunk/doc/source/conf.py Fri May 9 14:11:40 2008
@@ -24,6 +24,7 @@
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = ['sphinx.ext.autodoc']
+autoclass_content = 'both'
# Add any paths that contain templates here, relative to this directory.
templates_path = ['.templates']
Added: trunk/doc/source/extending/analyzing_in_parallel.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/extending/analyzing_in_parallel.rst Fri May 9 14:11:40 2008
@@ -0,0 +1,2 @@
+Analyzing in Parallel
+=====================
Added: trunk/doc/source/extending/creating_datatypes.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/extending/creating_datatypes.rst Fri May 9 14:11:40 2008
@@ -0,0 +1,2 @@
+Creating Datatypes
+==================
Added: trunk/doc/source/extending/creating_derived_fields.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/extending/creating_derived_fields.rst Fri May 9 14:11:40 2008
@@ -0,0 +1,2 @@
+Creating Derived Fields
+=======================
Added: trunk/doc/source/extending/creating_derived_quantities.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/extending/creating_derived_quantities.rst Fri May 9 14:11:40 2008
@@ -0,0 +1,2 @@
+Creating Derived Quantities
+===========================
Modified: trunk/doc/source/extending/index.rst
==============================================================================
--- trunk/doc/source/extending/index.rst (original)
+++ trunk/doc/source/extending/index.rst Fri May 9 14:11:40 2008
@@ -1,23 +1,16 @@
Extending yt
============
-Writing Scripts
----------------
+yt has been designed to be flexible, with several entry points.
-Dealing with the Interpreter
-----------------------------
+.. toctree::
+ :maxdepth: 2
-Creating Datatypes
-------------------
-
-Creating Derived Quantities
----------------------------
-
-Creating Derived Fields
------------------------
-
-Analyzing in Parallel
----------------------
-
-Running Fortran Routines
-------------------------
+ writing_scripts
+ using_the_interpreter
+ plugin_file
+ creating_datatypes
+ creating_derived_quantities
+ creating_derived_fields
+ analyzing_in_parallel
+ running_fortran_routines
Added: trunk/doc/source/extending/plugin_file.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/extending/plugin_file.rst Fri May 9 14:11:40 2008
@@ -0,0 +1,2 @@
+The Plugin File
+===============
Added: trunk/doc/source/extending/running_fortran_routines.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/extending/running_fortran_routines.rst Fri May 9 14:11:40 2008
@@ -0,0 +1,2 @@
+Running Fortran Routines
+========================
Added: trunk/doc/source/extending/using_the_interpreter.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/extending/using_the_interpreter.rst Fri May 9 14:11:40 2008
@@ -0,0 +1,2 @@
+Using the Interpreter
+=====================
Added: trunk/doc/source/extending/writing_scripts.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/extending/writing_scripts.rst Fri May 9 14:11:40 2008
@@ -0,0 +1,2 @@
+Writing Scripts
+===============
Modified: trunk/doc/source/faq.rst
==============================================================================
--- trunk/doc/source/faq.rst (original)
+++ trunk/doc/source/faq.rst Fri May 9 14:11:40 2008
@@ -44,6 +44,26 @@
Additionally, if you use yt in a paper, I'd love it if you'd drop me a line to
let me know.
+What are all these .yt files?
+-----------------------------
+
+By default, yt attempts to serialize a couple pieces of data that help speed it
+up in future invocations. Specifically, the entire contents of the hierarchy,
+the parent-child relationships between the grids, and any projections of the
+entire volume that are made.
+
+The numbers that make up the filenames are taken from one of two places. If
+your Enzo outputs the "CurrentTimeIdentifier" parameter, that is the number that it
+uses. (This is a string of digits representing the number of seconds since the
+epoch.) If that is unavailable, the creation time of the file as reported by
+the file system is used.
+
+This can cause problems. Ticket #91 on the bug tracker records some of these.
+If you are creating multiple parameter files per second, this can lead to
+incorrect hierarchies, and thus incorrect behavior, inside your analysis. In
+such cases, it is recommended that the parameter 'serialize' in the section
+'lagos' of your configuration file is set to 'False'.
+
How can I help?
---------------
@@ -62,6 +82,15 @@
files, and either send an email to the ``yt-users`` mailing list (subscribe
first!) or attach them to a ticket at `<http://yt.spacepope.org/>`_.
+.. _axis-specification:
+
+How do I specify an axis?
+-------------------------
+
+For now, axes are specified by integers -- 0,1,2 for x,y,z. In the next
+version, this will probably change, and allow for string-identification as
+well.
+
Where can I go for support?
---------------------------
Modified: trunk/doc/source/modules/lagos/basedatatypes.rst
==============================================================================
--- trunk/doc/source/modules/lagos/basedatatypes.rst (original)
+++ trunk/doc/source/modules/lagos/basedatatypes.rst Fri May 9 14:11:40 2008
@@ -1,15 +1,66 @@
-:mod:`lagos.BaseDataTypes` -- Data Types
+:mod:`yt.lagos.BaseDataTypes` -- Data Types
===========================================
-.. module:: lagos.BaseDataTypes
+.. module:: yt.lagos.BaseDataTypes
:synopsis: Generate containers to hold AMR data
.. moduleauthor:: Matthew Turk <mturk at stanford.edu>
+.. toctree::
+
+Base Containers
+---------------
+
+.. autoclass:: yt.lagos.FakeGridForParticles
+ :members:
+
.. autoclass:: yt.lagos.EnzoData
:members:
+.. autoclass:: yt.lagos.Enzo1DData
+ :members:
+
+.. autoclass:: yt.lagos.Enzo2DData
+ :members:
+
.. autoclass:: yt.lagos.Enzo3DData
:members:
+1D Data Containers
+------------------
+
+.. autoclass:: yt.lagos.EnzoOrthoRayBase
+ :members:
+
+2D Data Containers
+------------------
+
+.. autoclass:: yt.lagos.EnzoSliceBase
+ :members:
+
+.. autoclass:: yt.lagos.EnzoCuttingPlaneBase
+ :members:
+
+.. autoclass:: yt.lagos.EnzoProjBase
+ :members:
+
+3D Data Containers
+------------------
+
.. autoclass:: yt.lagos.EnzoSphereBase
:members:
+
+.. autoclass:: yt.lagos.EnzoRegionBase
+ :members:
+
+.. autoclass:: yt.lagos.EnzoCylinderBase
+ :members:
+
+.. autoclass:: yt.lagos.EnzoGridCollection
+ :members:
+
+.. autoclass:: yt.lagos.EnzoCoveringGrid
+ :members:
+
+.. autoclass:: yt.lagos.ExtractedRegionBase
+ :members:
+
Added: trunk/doc/source/modules/lagos/contours.rst
==============================================================================
Modified: trunk/doc/source/modules/lagos/index.rst
==============================================================================
--- trunk/doc/source/modules/lagos/index.rst (original)
+++ trunk/doc/source/modules/lagos/index.rst Fri May 9 14:11:40 2008
@@ -6,4 +6,7 @@
.. toctree::
:maxdepth: 2
+ outputandhierarchy
basedatatypes
+ contours
+ profiles
Added: trunk/doc/source/modules/lagos/outputandhierarchy.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/modules/lagos/outputandhierarchy.rst Fri May 9 14:11:40 2008
@@ -0,0 +1,17 @@
+:mod:`yt.lagos` -- Grid Type
+=========================================
+
+.. module:: yt.lagos.HierarchyType
+ :synopsis: The various types of outputs from a simulation
+.. moduleauthor:: Matthew Turk <mturk at stanford.edu>
+
+.. autoclass:: yt.lagos.HierarchyType
+ :members:
+
+.. autoclass:: yt.lagos.EnzoStaticOutput
+ :members:
+
+.. autoclass:: yt.lagos.BaseGridType
+ :members:
+
+
Added: trunk/doc/source/modules/lagos/profiles.rst
==============================================================================
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