initial upload

PyLaGriT/documentation/source/autodoc.rst

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+.. _class_docs:
+
+Class Documentation
+-------------------
+
+.. toctree::
+
+    PyLaGriT Class <autodoc_pylagrit.rst>
+
+    Mesh Class <autodoc_mo.rst>
+
+    Point Set Class <autodoc_pset.rst>
+
+    Element Set Class <autodoc_eltset.rst>
+
+    Face Set Class <autodoc_faceset.rst>
+
+    Region Class <autodoc_region.rst>
+
+    
+

PyLaGriT/documentation/source/autodoc_eltset.rst

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+Element Set Object
+------------------
+.. automodule:: pylagrit
+
+.. autoclass:: EltSet
+   :members:
+   :undoc-members:
+

PyLaGriT/documentation/source/autodoc_faceset.rst

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+Face Set Object
+---------------
+.. automodule:: pylagrit
+
+.. autoclass:: FaceSet
+   :members:
+   :undoc-members:
+

PyLaGriT/documentation/source/autodoc_mo.rst

@@ -0,0 +1,8 @@
+Mesh Object
+-----------
+.. automodule:: pylagrit
+
+.. autoclass:: MO
+   :members:
+   :undoc-members:
+

PyLaGriT/documentation/source/autodoc_pset.rst

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+Point Set Object
+----------------
+.. automodule:: pylagrit
+
+.. autoclass:: PSet
+   :members:
+   :undoc-members:
+

PyLaGriT/documentation/source/autodoc_pylagrit.rst

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+PyLaGriT
+--------
+.. automodule:: pylagrit
+
+.. autoclass:: PyLaGriT
+   :members:
+   :undoc-members:
+

PyLaGriT/documentation/source/autodoc_region.rst

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+Region Object
+-------------
+.. automodule:: pylagrit
+
+.. autoclass:: Region
+   :members:
+   :undoc-members:
+

PyLaGriT/documentation/source/conf.py

@@ -0,0 +1,343 @@
+# -*- coding: utf-8 -*-
+#
+# PyLaGriT documentation build configuration file, created by
+# sphinx-quickstart on Tue Oct  4 10:10:46 2016.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# 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',
+    'sphinx.ext.doctest',
+    'sphinx.ext.mathjax',
+    #'sphinx.ext.githubpages',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The encoding of source files.
+#
+# source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'PyLaGriT'
+copyright = u'2016, Dylan R. Harp'
+author = u'Dylan R. Harp'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = u'0'
+# The full version, including alpha/beta/rc tags.
+release = u'0.0.0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#
+# today = ''
+#
+# Else, today_fmt is used as the format for a strftime call.
+#
+# today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#
+# default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#
+# add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#
+# add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#
+# show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+# modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+# keep_warnings = False
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+# html_theme_path = []
+
+# The name for this set of Sphinx documents.
+# "<project> v<release> documentation" by default.
+#
+# html_title = u'PyLaGriT v0.0.0'
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#
+# html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#
+# html_logo = None
+
+# The name of an image file (relative to this directory) to use as a favicon of
+# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#
+# html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['static']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#
+# html_extra_path = []
+
+# If not None, a 'Last updated on:' timestamp is inserted at every page
+# bottom, using the given strftime format.
+# The empty string is equivalent to '%b %d, %Y'.
+#
+# html_last_updated_fmt = None
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#
+# html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#
+# html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#
+# html_additional_pages = {}
+
+# If false, no module index is generated.
+#
+# html_domain_indices = True
+
+# If false, no index is generated.
+#
+# html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#
+# html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#
+# html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#
+# html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#
+# html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#
+# html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+# html_file_suffix = None
+
+# Language to be used for generating the HTML full-text search index.
+# Sphinx supports the following languages:
+#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
+#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh'
+#
+# html_search_language = 'en'
+
+# A dictionary with options for the search language support, empty by default.
+# 'ja' uses this config value.
+# 'zh' user can custom change `jieba` dictionary path.
+#
+# html_search_options = {'type': 'default'}
+
+# The name of a javascript file (relative to the configuration directory) that
+# implements a search results scorer. If empty, the default will be used.
+#
+# html_search_scorer = 'scorer.js'
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'PyLaGriTdoc'
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+     # The paper size ('letterpaper' or 'a4paper').
+     #
+     # 'papersize': 'letterpaper',
+
+     # The font size ('10pt', '11pt' or '12pt').
+     #
+     # 'pointsize': '10pt',
+
+     # Additional stuff for the LaTeX preamble.
+     #
+     # 'preamble': '',
+
+     # Latex figure (float) alignment
+     #
+     # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'PyLaGriT.tex', u'PyLaGriT Documentation',
+     u'Dylan R. Harp', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#
+# latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#
+# latex_use_parts = False
+
+# If true, show page references after internal links.
+#
+# latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#
+# latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#
+# latex_appendices = []
+
+# It false, will not define \strong, \code, 	itleref, \crossref ... but only
+# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
+# packages.
+#
+# latex_keep_old_macro_names = True
+
+# If false, no module index is generated.
+#
+# latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'pylagrit', u'PyLaGriT Documentation',
+     [author], 1)
+]
+
+# If true, show URL addresses after external links.
+#
+# man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'PyLaGriT', u'PyLaGriT Documentation',
+     author, 'PyLaGriT', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#
+# texinfo_appendices = []
+
+# If false, no module index is generated.
+#
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#
+# texinfo_no_detailmenu = False

PyLaGriT/documentation/source/gettingstarted.rst

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+Getting Started
+===============
+
+Installation
+------------
+
+The Python module PyLaGriT allows LaGriT to be accessed interactively and in batch mode from Python. 
+To install PyLaGriT on your system, change to the PyLaGriT directory and run ``python setup.py install``. 
+Alternatively, the PyLaGriT folder can be added to your **PYTHONPATH** environment variable. 
+Due to the use of the pexpect Python module, PyLaGriT does not work on Windows. 
+It has been tested on Mac and Linux operating systems. 
+
+Since PyLaGriT is simply a frontend for LaGriT, you will need a lagrit executable to use PyLaGriT.
+To use the paraview and gmv methods, you will need ParaView (http://www.paraview.org) and GMV (http://www.generalmeshviewer.com) installed, respectively.
+
+To avoid specifying the LaGriT, ParaView, and GMV executable locations, copy the **pylagritrc_example** file:
+
+.. literalinclude:: ../../pylagritrc_example
+
+in the PyLaGriT folder to your home directory or working directory changing its name to either **pylagritrc** or **.pylagritrc** and uncomment and change the path locations.
+
+Simple example
+--------------
+
+The following is a PyLaGriT script for creating a simple cube shaped mesh using the :func:`gridder <pylagrit.PyLaGriT.gridder>` and `connect <pylagrit.PyLaGriT.connect>` methods:
+
+.. code-block:: python
+
+    # Import PyLaGriT class from pylagrit module
+    from pylagrit import PyLaGriT
+    
+    # Create PyLaGriT object
+    # This assumes that pylagritrc is being used so that lagrit_exe option does not need to be specified
+    l = PyLaGriT()
+
+    # Create x,y,z arrays for location of points
+    x = range(1,5)
+    y = range(1,5)
+    z = range(1,5)
+
+    # Create mesh object using x,y,z arrays
+    m = l.gridder(x,y,z)
+
+    # Connect points
+    m.connect()
+
+    # Visualize connected mesh using ParaView
+    # This assumes that pylagritrc is being used so that exe option does not need to be specified
+    m.paraview()
+
+The script can be pasted line by line into a Python or IPython terminal, or saved in a file (e.g., ``script.py``) and run on the command line as ``python script.py``.
+
+This will open up ParaView with the mesh loaded:
+
+.. image:: cube.png
+
+Next steps
+----------
+
+Additional example PyLaGriT scripts are provided in the PyLaGriT/examples folder and in the :ref:`class_docs`. 
+
+Combining LaGriT and Python functionality
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+An example of using PyLaGriT to facilitate looping over LaGriT functionality is described in the :func:`merge method <pylagrit.PyLaGriT.merge>` documentation, where a mesh is successively copied, translated and merged into a larger mesh.
+Other examples of usage are provided for other methods and more will be added in the future.
+
+User defined error checking
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Since PyLaGriT stores the LaGriT terminal output from each command in the PyLaGriT object attribute ``before``, user-defined error checking can be easily implemented.
+The example provided with the :func:`refine method <pylagrit.EltSet.refine>` demonstrates this by checking for the string `The mesh is complete but could not include all points.` in the LaGriT output using ``lg.before``. 
+In this example, an error message is printed to the screen and the script is aborted.

PyLaGriT/documentation/source/index.rst

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+.. PyLaGriT documentation master file, created by
+   sphinx-quickstart on Tue Oct  4 10:10:46 2016.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+PyLaGriT, Python interface for LaGriT
+=====================================
+
+.. include:: ../../README
+
+.. toctree::
+   :maxdepth: 2
+
+   Getting Started <gettingstarted.rst>    
+
+   Stratigraphic Hex Mesh Tutorial <stratigraphic.rst>
+
+   Class Documentation <autodoc.rst>
+
+PyLaGriT source code is packaged with LaGriT source code `here <https://github.com/lanl/LaGriT>`_.
+
+Example scripts can be found `here <https://github.com/lanl/LaGriT/tree/master/PyLaGriT/examples>`_.
+
+Development team
+################
+* Dylan Harp <dharp@lanl.gov>
+
+* Daniel Livingston <livingston@lanl.gov>
+
+* James (Joe) Beisman <jjbeisman@gmail.com>
+
+* Terry Miller <tamiller@lanl.gov>
+
+* Carl Gable <gable@lanl.gov>
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

PyLaGriT/documentation/source/stratigraphic.rst

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+Stratigraphic Hex Mesh Tutorial
+===============================
+Written by Guoyan Jiang (gyjiang@whu.edu.cn) with technical support from Dylan Harp (dharp@lanl.gov) and Terry Miller (tamiller@lanl.gov). 
+The associated LaGriT tutorial is `here <https://lanl.github.io/LaGriT/pages/tutorial/stratigraphy/index.html>`_.
+This example script can be downloaded `here <https://github.com/lanl/LaGriT/blob/master/PyLaGriT/examples/stratigraphic_hex_mesh_tutorial.py>`_.
+
+.. literalinclude:: ../../examples/stratigraphic_hex_mesh_tutorial.py
+
+The final result:
+
+.. image:: stratigraphy.png