initial upload

PyLaGriT/README

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+PyLaGriT Class
+##############
+
+- The PyLaGriT class provides a python interface to the Los Alamos Grid Toolbox. 
+- The PyLaGrit class is derived class of the perplex packages spawn class, and its objects contains all of spawn's functionality. 
+- Commands can be sent using LaGriT syntax as string arguments to the sendline method. 
+- Direct access to the LaGriT shell is provided by the interact method. 
+- Subclasses of the PyLaGrit class include mesh object (MO), surface, and region and can be created using various methods to PyLaGriT objects. 
+- The mesh object subclass contains subclasses pset and eltset. 
+- Subclasses are contained in dictionaries in the parent class. 
+- The mesh object class contains gmv and paraview methods that dump the appropriate files and open them in viewer. 
+- PyLaGriT can be accessed in Julia using the Julia PyCall package (refer to PyLaGriT/examples/julia folder in the source code)
+
+See Documentation at https://lanl.github.io/LaGriT/pylagrit/original/index.html

PyLaGriT/documentation/Makefile

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+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: help
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  applehelp  to make an Apple Help Book"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  epub3      to make an epub3"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@echo "  coverage   to run coverage check of the documentation (if enabled)"
+	@echo "  dummy      to check syntax errors of document sources"
+
+.PHONY: clean
+clean:
+	rm -rf $(BUILDDIR)/*
+
+.PHONY: html
+html:
+	rm -rf $(BUILDDIR)/html
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	find $(BUILDDIR)/html -name "*.html" | xargs sed -i'.original' -e 's/_static/static/g'
+	find $(BUILDDIR)/html -name "*.html" | xargs sed -i'.original' -e 's/_image/image/g'
+	find $(BUILDDIR)/html -name "*.html" | xargs sed -i'.original' -e 's/_sources/sources/g'
+	mv $(BUILDDIR)/html/_static $(BUILDDIR)/html/static
+	mv $(BUILDDIR)/html/_images $(BUILDDIR)/html/images
+	mv $(BUILDDIR)/html/_sources $(BUILDDIR)/html/sources
+	rm -f $(BUILDDIR)/html/*.original
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: dirhtml
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+.PHONY: singlehtml
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+.PHONY: pickle
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+.PHONY: json
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+.PHONY: htmlhelp
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+.PHONY: qthelp
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/PyLaGriT.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/PyLaGriT.qhc"
+
+.PHONY: applehelp
+applehelp:
+	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
+	@echo
+	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
+	@echo "N.B. You won't be able to view it unless you put it in" \
+	      "~/Library/Documentation/Help or install it in your application" \
+	      "bundle."
+
+.PHONY: devhelp
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/PyLaGriT"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/PyLaGriT"
+	@echo "# devhelp"
+
+.PHONY: epub
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+.PHONY: epub3
+epub3:
+	$(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
+	@echo
+	@echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
+
+.PHONY: latex
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+.PHONY: latexpdf
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: latexpdfja
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: text
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+.PHONY: man
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+.PHONY: texinfo
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+.PHONY: info
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+.PHONY: gettext
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+.PHONY: changes
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+.PHONY: linkcheck
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+.PHONY: doctest
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+.PHONY: coverage
+coverage:
+	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+	@echo "Testing of coverage in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/coverage/python.txt."
+
+.PHONY: xml
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+.PHONY: pseudoxml
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+
+.PHONY: dummy
+dummy:
+	$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
+	@echo
+	@echo "Build finished. Dummy builder generates no files."

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

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+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

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+# -*- 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

@@ -0,0 +1,73 @@
+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

@@ -0,0 +1,42 @@
+.. 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

@@ -0,0 +1,11 @@
+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

PyLaGriT/examples/arctic_2D/bottom_peat2.avs

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PyLaGriT/examples/arctic_2D/mesh_pylagrit.py

@@ -0,0 +1,109 @@
+from pylagrit import PyLaGriT
+import numpy
+
+# Variables
+nx = 50 # Number of points in x direction
+dy = 0.25 # width of cells in y direction
+distance = 12.34364319 # distance in x direction
+
+l = PyLaGriT()
+
+# Create base layer
+layer = l.create_qua()
+layer.createpts_xyz((nx,2,1),[0.,0.,0.],[distance,dy,0.],rz_switch=[1,1,1],connect=True)
+layer.setatt('itetclr',1)
+layer.minmax_xyz()
+
+# Create top of mesh
+# Collapse y values
+layer.addatt('y_save',vtype='vdouble',rank='scalar')
+layer.copyatt('yic','y_save')
+layer.setatt('yic',0.)
+
+# Read in lidar top elevations
+peat_surf_pts = l.read('surface_coords2.avs')
+peat_surf_pts.addatt('z_save',vtype='vdouble',rank='scalar')
+peat_surf_pts.copyatt('zic','z_save')
+peat_surf_pts.setatt('zic',0.)
+
+# Interpolate surface elevations to layer mo
+layer.addatt('z_val',vtype='vdouble',rank='scalar')
+layer.interpolate_voronoi('z_val',peat_surf_pts,'z_save')
+layer.copyatt('y_save','yic')
+layer.copyatt('z_val','zic')
+
+# Save peat top
+layer.setatt('imt',1)
+layer.setatt('itetclr',1)
+layer.dump('tmp_lay_peat_top.inp')
+peat_surf_pts.delete()
+
+# Read in peat bottom elevations
+peat_bot_pts = l.read('bottom_peat2.avs')
+peat_bot_pts.addatt('z_save',vtype='vdouble',rank='scalar')
+peat_bot_pts.copyatt('zic','z_save')
+peat_bot_pts.setatt('zic',0.)
+
+# Interpolate peat bottom elevations to layer mo
+layer.setatt('yic',0.)
+layer.addatt('z_val',vtype='vdouble',rank='scalar')
+layer.interpolate_voronoi('z_val',peat_bot_pts,'z_save')
+layer.copyatt('y_save','yic')
+layer.delatt('y_save')
+layer.copyatt('z_val','zic')
+layer.delatt('z_val')
+
+# Save peat bot
+layer.dump('tmp_lay_peat_bot.inp')
+
+# Copy layer to peat_bot for use in generating additional layers
+peat_bot = layer.copy()
+
+stack_files = ['tmp_lay_peat_top.inp 1,5']
+stack_files.append('tmp_lay_peat_bot.inp 1,33')
+
+# Layer depths?
+#           1   2   3    4    5    6    7   8    9   10
+layers = [ 1.0, 0.16, 0.32, 0.64, 1.28, 3.2, 6.4, 8.0]
+addnum = [   3,    3,    3,    3,    4,   4,   3,   5]
+matnum = [2]*len(layers) 
+
+layer_interfaces = numpy.cumsum(layers)
+i = 1
+for li,m,a in zip(layer_interfaces,matnum,addnum):
+    layer.math('sub','zic',li,cmosrc=peat_bot)
+    stack_files.append('tmp_lay'+str(i)+'.inp '+str(int(m))+', '+str(a))
+    layer.dump('tmp_lay'+str(i)+'.inp')
+    i += 1
+
+layer.setatt('zic',-45.)
+layer.dump('tmp_lay_bot.inp')
+stack_files.append('tmp_lay_bot.inp 2')
+stack_files.reverse()
+
+# Create stacked layer mesh and fill
+stack = l.create()
+stack.stack_layers(stack_files,file_type='avs',flip_opt=True)
+stack_hex = stack.stack_fill()
+
+# Create boundary facesets, dictionary of PyLaGriT faceset objects is returned
+fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=True,reorder=True)
+
+# Should add this to PyLaGriT, but I'm feeling lazy ;-)
+stack_hex.sendline('quality volume itetclr')
+
+# Write exo file with boundary facesets
+stack_hex.dump_exo('arctic_siteb_2d.exo',facesets=fs.values())
+
+# Write region and faceset identifier file for ats_xml 
+matnames = {10000:'computational domain peat',
+            20000:'computational domain upper mineral'}
+facenames = {1:'bottom face',
+             2:'surface',
+             3:'front',
+             4:'right',
+             5:'back',
+             6:'left'}
+
+stack_hex.dump_ats_xml('arctic_siteb_2d_mesh.xml','/scratch/tundra/dharp/arctic/geophysics/mesh/from_lucia/arctic_siteb_2d.exo',matnames=matnames,facenames=facenames)
+stack_hex.dump_ats_xml('arctic_siteb_2d_par4_mesh.xml','/scratch/tundra/dharp/arctic/geophysics/mesh/from_lucia/arctic_siteb_2d.par',matnames=matnames,facenames=facenames)

PyLaGriT/examples/arctic_2D/surface_coords2.avs

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PyLaGriT/examples/arctic_2D_new/Topo_Profile_NS_ERT.csv

@@ -0,0 +1,142 @@
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PyLaGriT/examples/arctic_2D_new/transect.py

@@ -0,0 +1,118 @@
+from pylagrit import PyLaGriT
+import numpy as np
+
+lg = PyLaGriT()
+
+# Create base layer from x=10 to x=21 to match bert02 mesh
+x = np.linspace(10.,21,(21.-10.)/0.25+1)
+y = [0.,0.25]
+top = lg.gridder(x,y,elem_type='quad',connect=True)
+
+# Create top of mesh
+# Collapse y values
+top.addatt('y_save',vtype='vdouble',rank='scalar')
+top.copyatt('yic','y_save')
+top.setatt('yic',0.)
+
+# Read in top elevations
+d = np.genfromtxt("./Topo_Profile_NS_ERT.csv", delimiter=",", names=True)
+surf_pts = lg.points(x=d['Distance_m'],z=d['Z'],elem_type='quad')
+surf_pts.addatt('z_save',vtype='vdouble',rank='scalar')
+surf_pts.copyatt('zic','z_save')
+surf_pts.setatt('zic',0.)
+
+# Interpolate surface elevations to top
+top.addatt('z_val',vtype='vdouble',rank='scalar')
+top.interpolate_voronoi('z_val',surf_pts,'z_save')
+top.copyatt('y_save','yic')
+top.copyatt('z_val','zic')
+
+# Save top
+top.setatt('imt',1)
+top.setatt('itetclr',1)
+top.dump('tmp_lay_peat_top.inp')
+surf_pts.delete()
+
+# Copy top to create intermediate layers
+layer = top.copy()
+
+# Begin to construct stacked layer arrays
+# Names of layer files
+stack_files = ['tmp_lay_peat_top.inp']
+# Material id, should be same length as length of stack_files
+matids = [1]
+
+# Add (15) 2 cm thick layers
+layer.math('sub',0.02*15,'zic')
+layer.dump('tmp_lay1.inp')
+stack_files.append('tmp_lay1.inp')
+# Number of layers in between surfaces, should be length of stack_files - 1
+nlayers = [14]
+matids.append(1)
+
+# Add (15) 5 cm thick layers
+layer.math('sub',0.05*15,'zic')
+layer.dump('tmp_lay2.inp')
+stack_files.append('tmp_lay2.inp')
+# Number of layers in between surfaces, should be length of stack_files - 1
+nlayers.append(14)
+matids.append(2)
+
+# Add (15) 10 cm thick layers
+layer.math('sub',0.1*15,'zic')
+layer.dump('tmp_lay3.inp')
+stack_files.append('tmp_lay3.inp')
+# Number of layers in between surfaces, should be length of stack_files - 1
+nlayers.append(14)
+matids.append(2)
+
+# Add (15) 1 c thick layers
+layer.math('sub',1*15,'zic')
+layer.dump('tmp_lay3.inp')
+stack_files.append('tmp_lay3.inp')
+# Number of layers in between surfaces, should be length of stack_files - 1
+nlayers.append(14)
+matids.append(2)
+
+layer.math('sub',2.*15.,'zic')
+layer.dump('tmp_lay4.inp')
+stack_files.append('tmp_lay4.inp')
+nlayers.append(14)
+matids.append(2)
+ 
+layer.setatt('zic',-45.)
+layer.dump('tmp_lay_bot.inp')
+stack_files.append('tmp_lay_bot.inp 2')
+nlayers.append(1)
+matids.append(2)
+
+# Create stacked layer mesh and fill
+# Reverse arrays so that order is from bottom to top!!!
+stack_files.reverse()
+nlayers.reverse()
+matids.reverse()
+stack = lg.create()
+stack.stack_layers(stack_files,nlayers=nlayers,matids=matids,flip_opt=True)
+stack_hex = stack.stack_fill()
+
+# Create boundary facesets, dictionary of PyLaGriT faceset objects is returned
+fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=True,reorder=True)
+
+# Should add this to PyLaGriT, but I'm feeling lazy ;-)
+stack_hex.sendline('quality volume itetclr')
+
+# Write exo file with boundary facesets
+stack_hex.dump_exo('arctic_siteb_2d.exo',facesets=fs.values())
+
+# Write region and faceset identifier file for ats_xml 
+matnames = {10000:'computational domain peat',
+            20000:'computational domain upper mineral'}
+facenames = {1:'bottom face',
+             2:'surface',
+             3:'front',
+             4:'right',
+             5:'back',
+             6:'left'}
+
+stack_hex.dump_ats_xml('arctic_siteb_2d_mesh.xml','/scratch/tundra/dharp/arctic/geophysics/mesh/from_lucia/arctic_siteb_2d.exo',matnames=matnames,facenames=facenames)
+stack_hex.dump_ats_xml('arctic_siteb_2d_par4_mesh.xml','/scratch/tundra/dharp/arctic/geophysics/mesh/from_lucia/arctic_siteb_2d.par',matnames=matnames,facenames=facenames)

PyLaGriT/examples/arctic_w_ice_wedges/transectNWSE.PY

@@ -0,0 +1,160 @@
+from pylagrit import PyLaGriT
+import numpy as np
+
+lg = PyLaGriT()
+
+# Create base layer, with x matching s from the csv file 
+x = np.linspace(0.,29.75,(29.75-0.)/0.25+1)
+y = [0.,0.25]
+top = lg.gridder(x,y,elem_type='quad',connect=True)
+
+# Create top of mesh
+# Collapse y values
+top.addatt('y_save',vtype='vdouble',rank='scalar')
+top.copyatt('yic','y_save')
+top.setatt('yic',0.)
+
+# Read in top elevations
+d = np.genfromtxt("transectNWSE.csv", delimiter=",", names=True)
+coords = np.column_stack([d['s'],np.zeros_like(d['s']),d['z']])
+surf_pts = lg.points(coords,elem_type='quad')
+surf_pts.addatt('z_save',vtype='vdouble',rank='scalar')
+surf_pts.copyatt('zic','z_save')
+surf_pts.setatt('zic',0.)
+
+# Interpolate surface elevations to top
+top.addatt('z_val',vtype='vdouble',rank='scalar')
+top.interpolate_voronoi('z_val',surf_pts,'z_save')
+top.copyatt('y_save','yic')
+top.copyatt('z_val','zic')
+
+# Save top
+top.setatt('imt',1)
+top.setatt('itetclr',1)
+top.dump('tmp_lay_peat_top.inp')
+surf_pts.delete()
+
+# Copy top to create intermediate layers
+layer = top.copy()
+
+# Begin to construct stacked layer arrays
+# Names of layer files
+stack_files = ['tmp_lay_peat_top.inp']
+# Material id, should be same length as length of stack_files
+matids = [1]
+
+# Add (2) 1 cm thick layers
+layer.math('sub',0.01*2,'zic')
+layer.dump('tmp_lay1.inp')
+stack_files.append('tmp_lay1.inp')
+nlayers = [1]
+matids.append(1)
+
+# Add (6) 2 cm thick layers
+layer.math('sub',0.02*6,'zic')
+layer.dump('tmp_lay2.inp')
+stack_files.append('tmp_lay2.inp')
+nlayers.append(5)
+matids.append(2)
+
+# Add (8) 2 cm thick layers
+layer.math('sub',0.02*8,'zic')
+layer.dump('tmp_lay3.inp')
+stack_files.append('tmp_lay3.inp')
+nlayers.append(7)
+matids.append(3)
+
+# Add (15) 5 cm thick layers
+layer.math('sub',0.05*15,'zic')
+layer.dump('tmp_lay4.inp')
+stack_files.append('tmp_lay4.inp')
+nlayers.append(14)
+matids.append(3)
+
+# Add (15) 10 cm thick layers
+layer.math('sub',0.1*15,'zic')
+layer.dump('tmp_lay5.inp')
+stack_files.append('tmp_lay5.inp')
+nlayers.append(14)
+matids.append(3)
+
+# Add (15) 1 m thick layers
+layer.math('sub',1*15,'zic')
+layer.dump('tmp_lay6.inp')
+stack_files.append('tmp_lay6.inp')
+nlayers.append(14)
+matids.append(3)
+
+# Add (15) 2 m thick layers
+layer.math('sub',2.*15.,'zic')
+layer.dump('tmp_lay7.inp')
+stack_files.append('tmp_lay7.inp')
+nlayers.append(14)
+matids.append(3)
+
+# Add the bottom layer, and make the bottom boundary flat 
+layer.setatt('zic',29.)
+layer.dump('tmp_lay_bot.inp')
+stack_files.append('tmp_lay_bot.inp')
+nlayers.append(0)
+matids.append(3)
+
+# Create stacked layer mesh and fill
+# Reverse arrays so that order is from bottom to top!!!
+stack_files.reverse()
+nlayers.reverse()
+matids.reverse()
+stack = lg.create()
+stack.stack_layers(stack_files,nlayers=nlayers,matids=matids,flip_opt=True)
+stack_hex = stack.stack_fill()
+
+# Define ice wedges
+def iceWedgePoints( vtxL, vtxB, vtxR, dx, dz ):
+    xnodes = np.arange( vtxL[0], vtxR[0], dx )
+    znodes = np.arange( vtxB[1], vtxR[1], dz )
+    xg, zg = np.meshgrid(xnodes, znodes)
+    xg = xg.flatten(); zg = zg.flatten()
+    m1 = (vtxB[1] - vtxL[1])/(vtxB[0] - vtxL[0])
+    b1 = vtxL[1] - m1*vtxL[0]
+    m2 = (vtxR[1] - vtxB[1])/(vtxR[0] - vtxB[0])
+    b2 = vtxR[1] - m2*vtxR[0]
+    idx = [ (zg[i] > m1*xg[i]+b1) & (zg[i] > m2*xg[i]+b2)  for i in range(len(zg)) ]
+    iwx = xg[np.array(idx)]; iwz = zg[np.array(idx)]
+    iwy = np.concatenate( (np.ones(iwx.size)*0.05, np.ones(iwx.size)*0.2) )    
+    iwx = np.tile(iwx, 2); iwz = np.tile(iwz, 2)
+   
+    return iwx, iwy, iwz
+
+iw1x, iw1y, iw1z = iceWedgePoints( [3.25, 78.3], [3.875, 75.0], [4.5, 78.3], 0.125, 0.01 )
+iw1pts = lg.points(np.column_stack([iw1x, iw1y, iw1z]), connect=True)
+iw1 = stack_hex.eltset_object(iw1pts)
+iw1.setatt('itetclr', 4)
+
+iw2x, iw2y, iw2z = iceWedgePoints( [18.5, 78.4], [19.125, 75.1], [19.75,78.4], 0.125, 0.01 )
+iw2pts = lg.points(np.column_stack([iw2x, iw2y, iw2z]), connect=True)
+iw2 = stack_hex.eltset_object(iw2pts)
+iw2.setatt('itetclr', 4)
+
+# Create boundary facesets, dictionary of PyLaGriT faceset objects is returned
+fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=True,reorder=True)
+
+# Should add this to PyLaGriT, but I'm feeling lazy ;-)
+stack_hex.sendline('quality volume itetclr')
+
+# Write exo file with boundary facesets
+stack_hex.dump_exo('transectNWSE.exo',facesets=fs.values())
+
+# Write region and faceset identifier file for ats_xml 
+matnames = {10000:'computational domain moss',
+            20000:'computational domain peat',
+            30000:'computational domain mineral',
+            40000:'computational domain ice wedge'}
+facenames = {1:'bottom face',
+             2:'surface',
+             3:'front',
+             4:'right',
+             5:'back',
+             6:'left'}
+
+stack_hex.dump_ats_xml('transectNWSE_mesh.xml','../../mesh/transectNWSE.exo',matnames=matnames,facenames=facenames)
+stack_hex.dump_ats_xml('transectNWSE_parmesh.xml','../../mesh/4/transectNWSE.par',matnames=matnames,facenames=facenames)

PyLaGriT/examples/arctic_w_ice_wedges/transectNWSE.csv

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PyLaGriT/examples/basin_bnd_ply_rescale.inp

@@ -0,0 +1,315 @@
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PyLaGriT/examples/create_exo.py

@@ -0,0 +1,8 @@
+from pylagrit import PyLaGriT
+l = PyLaGriT()
+m = l.create()
+m.createpts_xyz((3,3,3),(0.,0.,0.),(1.,1.,1.),rz_switch=[1,1,1],connect=True)
+m.status ()
+m.status (brief=True)
+fs = m.create_boundary_facesets(base_name='faceset_bounds')
+m.dump_exo('cube.exo',facesets=fs.values())

PyLaGriT/examples/createpts_dxyz.py

@@ -0,0 +1,28 @@
+from pylagrit import PyLaGriT
+l = PyLaGriT()
+
+# Create 2x2x2 cell mesh
+m = l.create()
+m.createpts_dxyz((0.5,0.5,0.5),(0.,0.,0.),(1.,1.,1.),rz_switch=[1,1,1],connect=True)
+m.paraview()
+#m.gmv()
+
+# Create 2x2x2 mesh where maxs will be truncated to nearest value under given maxs
+m_under = l.create()
+m_under.createpts_dxyz((0.4,0.4,0.4),(0.,0.,0.),(1.,1.,1.),rz_switch=[1,1,1],connect=True)
+m_under.paraview()
+#m_under.gmv()
+
+# Create 3x3x3 mesh where maxs will be truncated to nearest value over given maxs
+m_over = l.create()
+m_over.createpts_dxyz((0.4,0.4,0.4),(0.,0.,0.),(1.,1.,1.),clip='over',rz_switch=[1,1,1],connect=True)
+m_over.paraview()
+#m_over.gmv()
+
+# Create 3x3x3 mesh where x and y maxs will be truncated to nearest value over given maxs
+# and z min will be truncated  to nearest value 
+m_mixed = l.create()
+m_mixed.createpts_dxyz((0.4,0.4,0.4),(0.,0.,-1.),(1.,1.,0.),hard_bound=('min','min','max'),clip=('under','under','over'),rz_switch=[1,1,1],connect=True)
+m_mixed.paraview()
+#m_over.gmv()
+

PyLaGriT/examples/ex_convert_files.py

@@ -0,0 +1,17 @@
+#To use pylagrit, import the module.
+import pylagrit
+
+#Create your pylagrit session.
+lg = pylagrit.PyLaGriT()
+
+#Create a mesh object and dump it to a gmv file 'test.gmv'.
+mo = lg.create(name='test')
+mo.createpts_brick_xyz((5,5,5), (0,0,0), (5,5,5,))
+mo.dump('gmv', 'test.gmv')
+
+#Convert test.gmv to exoduce and contour files.
+lg.convert('test.gmv', 'exo')
+lg.convert('test.gmv', 'avs')
+
+
+

PyLaGriT/examples/ex_gridder.py

@@ -0,0 +1,13 @@
+from pylagrit import PyLaGriT
+import numpy
+
+lg = PyLaGriT()
+
+x0 = -numpy.logspace(1,2,15,endpoint=True)
+x1 = numpy.arange(-10,10,1)
+x2 = -x0
+x = numpy.concatenate([x0,x1,x2])
+y = x
+mqua = lg.gridder(x,y,elem_type='quad',connect=True)
+
+mqua.paraview()

PyLaGriT/examples/ex_merge_mesh_objects.py

@@ -0,0 +1,30 @@
+################################################################################
+# This example shows how to merge multiple mesh objects together.              #
+################################################################################
+
+#To use pylagrit, import the module.
+import pylagrit
+import numpy
+
+#Instantiate the lagrit object.
+lg = pylagrit.PyLaGriT()
+
+# Create list with mesh object as first element
+dxyz = numpy.array([0.25]*3)
+mins = numpy.array([0.]*3)
+maxs = numpy.array([1.]*3)
+ms = [lg.createpts_dxyz(dxyz,mins,maxs,'tet',connect=True)]
+
+# Create three new mesh objects, each one directly above the other
+for i in range(3):
+    ms.append(ms[-1].copy())
+    ms[-1].trans(ms[-1].mins,ms[-1].mins+numpy.array([0.,0.,1.]))
+
+# Merge list of mesh objects and clean up
+mo_merge = lg.merge(ms)
+for mo in ms: mo.delete()
+mo_merge.rmpoint_compress(filter_bool=True,resetpts_itp=True)
+
+mo_merge.paraview(filename='mo_merge.inp')
+
+

PyLaGriT/examples/ex_read_lagrit_binary_mos.py

@@ -0,0 +1,28 @@
+#To use pylagrit, import the module.
+import pylagrit
+import numpy
+
+#Instantiate the lagrit object.
+lg = pylagrit.PyLaGriT()
+
+# Create list with mesh object as first element
+dxyz = numpy.array([0.25]*3)
+mins = numpy.array([0.]*3)
+maxs = numpy.array([1.]*3)
+ms = [lg.createpts_dxyz(dxyz,mins,maxs,'tet',connect=True,name='testmo')]
+
+# Create three new mesh objects, each one directly above the other
+for i in range(3):
+    ms.append(ms[-1].copy())
+    ms[-1].trans(ms[-1].mins,ms[-1].mins+numpy.array([0.,0.,1.]))
+
+lg.dump('lagrit_binary.lg')
+lg.close()
+
+lg = pylagrit.PyLaGriT()
+ms_read = lg.read('lagrit_binary.lg')
+
+print('Name of mesh object read in should be testmo, is: ', ms_read.name)
+
+
+

PyLaGriT/examples/ex_read_mesh.py

@@ -0,0 +1,18 @@
+#To use pylagrit, import the module.
+import pylagrit
+
+#Create your pylagrit session.
+lg = pylagrit.PyLaGriT()
+
+#Create a mesh object and dump it to a gmv file 'test.gmv'.
+mo = lg.create(name='test')
+mo.createpts_brick_xyz((5,5,5), (0,0,0), (5,5,5,))
+mo.dump('test.gmv')
+mo.dump('test.avs')
+mo.dump('test.lg')
+
+mo1 = lg.read('test.gmv')
+mo2 = lg.read('test.avs')
+mo3 = lg.read('test.lg',name='test')
+
+

PyLaGriT/examples/ex_refine_edge.py

@@ -0,0 +1,42 @@
+from pylagrit import PyLaGriT
+import numpy
+import sys
+
+df = 0.0005 # Fault half aperture
+lr = 7 # Levels of refinement
+nx = 4 # Number of base mesh blocks in x direction
+nz = 20 # Number of base mesh blocks in z direction
+d_base = df*2**(lr+1) # Calculated dimension of base block
+w = d_base*nx # Calculated width of model
+d = d_base*nz # Calculated depth of model
+
+lg = PyLaGriT()
+
+# Create discrete fracture mesh
+dxyz = numpy.array([d_base,d_base,0.])
+mins = numpy.array([0.,-d,0.])
+maxs = numpy.array([w,0,0])
+mqua = lg.createpts_dxyz(dxyz,mins,maxs,'quad',hard_bound=('min','max','min'),connect=True)
+
+for i in range(lr):
+    prefine = mqua.pset_geom_xyz(mins-0.1,(0.0001,0.1,0))
+    erefine = prefine.eltset()
+    erefine.refine()
+    prefine.delete()
+    erefine.delete()
+
+mtri = mqua.copypts('triplane')
+mtri.connect()
+# Make sure that not nodes are lost during connect
+if 'The mesh is complete but could not include all points.' in str(lg.before):
+    print("Error: Lost some points during connect, not completing mesh and exiting workflow!\n")
+    sys.exit()
+mtri.tri_mesh_output_prep()
+mtri.reorder_nodes(cycle='xic yic zic')
+pfault = mtri.pset_geom_xyz(mins-0.1,(0.0001,0.1,0))
+psource = mtri.pset_geom_xyz(mins-0.1,mins+0.0001)
+mtri.setatt('imt',1)
+pfault.setatt('imt',10)
+psource.setatt('imt',20)
+
+mtri.paraview(filename='discrete_fracture.inp')

PyLaGriT/examples/ex_rotate.py

@@ -0,0 +1,16 @@
+from pylagrit import PyLaGriT
+import numpy
+
+x = numpy.arange(0,10.1,1)
+y = x
+z = [0,1]
+
+lg = PyLaGriT()
+mqua = lg.gridder(x,y,z,elem_type='hex',connect=True)
+
+mqua.rotateln([mqua.xmin-0.1,0,0],[mqua.xmax+0.1,0,0],25)
+
+mqua.dump_exo('rotated.exo')
+mqua.dump_ats_xml('rotated.xml','rotated.exo')
+
+mqua.paraview()

PyLaGriT/examples/ex_rotate_stack.py

@@ -0,0 +1,47 @@
+from pylagrit import PyLaGriT
+import numpy
+
+x = numpy.arange(0,10.1,1)
+y = [0,1]
+#z = [0,1]
+
+lg = PyLaGriT()
+layer = lg.gridder(x=x,y=y,elem_type='quad',connect=True)
+layer.rotateln([0,layer.ymin-0.10,0],[0,layer.ymax+0.1,0],25)
+layer.dump('tmp_lay_top.inp')
+
+# Layer depths?
+#           1   2   3    4    5    6    7   8    9   10
+layers = [ .1, 1.]
+addnum = [  4, 2]
+#matnum = [2]*len(layers)
+matnum = [2, 1]
+layer_interfaces = numpy.cumsum(layers)
+
+mtop = layer.copy()
+stack_files = ['tmp_lay_top.inp 1,9']
+#stack_files.append('tmp_lay_peat_bot.inp 1,33')
+
+i = 1
+for li,m,a in zip(layer_interfaces,matnum,addnum):
+    layer.math('sub','zic',value=li,cmosrc=mtop)
+    stack_files.append('tmp_lay'+str(i)+'.inp '+str(int(m))+', '+str(a))
+    layer.dump('tmp_lay'+str(i)+'.inp')
+    i += 1
+
+layer.math('sub','zic',2,cmosrc=mtop)
+#layer.setatt('zic',-2.)
+layer.dump('tmp_lay_bot.inp')
+stack_files.append('tmp_lay_bot.inp 2')
+stack_files.reverse()
+
+# Create stacked layer mesh and fill
+stack = lg.create()
+stack.stack_layers(stack_files,file_type='avs',flip_opt=True)
+stack_hex = stack.stack_fill()
+
+
+stack_hex.dump_exo('rotated.exo')
+stack_hex.dump_ats_xml('rotated.xml','rotated.exo')
+
+stack_hex.paraview()

PyLaGriT/examples/ex_select_subset.py

@@ -0,0 +1,15 @@
+#To use pylagrit, import the module.
+import pylagrit
+
+#Start the lagrit session.
+lg = pylagrit.PyLaGriT()
+
+#Create a mesh object.
+mo = lg.create()
+mo.createpts_brick_xyz((5,5,5), (0,0,0), (5,5,5))
+
+#Take the subset from (3,3,3)
+mo.subset((3,3,3),(5,5,5))
+
+
+

PyLaGriT/examples/ex_triangulate.py

@@ -0,0 +1,41 @@
+from pylagrit import PyLaGriT
+
+# Create pylagrit object
+lg = PyLaGriT()
+
+# Define polygon points in clockwise direction
+# and create tri mesh object
+coords = [[0.0, 0.0, 0.0], 
+          [0.0, 1000.0, 0.0], 
+          [2200.0, 200.0, 0.0], 
+          [2200.0, 0.0, 0.0]]
+motri = lg.tri_mo_from_polyline(coords)
+
+# Triangulate polygon
+motri.triangulate()
+motri.setatt('imt',1)
+motri.setatt('itetclr',1)
+
+# refine mesh with successively smaller edge length constraints
+edge_length = [1000,500,250,125,75,40,20,15]
+for i,l in enumerate(edge_length):
+    motri.resetpts_itp()
+    motri.refine(refine_option='rivara',refine_type='edge',values=[l],inclusive_flag='inclusive')
+    motri.smooth()
+    motri.recon(0)
+
+# provide additional smoothing after the last refine
+for i in range(5):
+    motri.smooth()
+    motri.recon(0)
+
+# create delaunay mesh and clean up
+motri.tri_mesh_output_prep()
+
+# dump fehm files
+motri.dump_fehm('nk_mesh00')
+
+# view results
+motri.paraview()
+
+

PyLaGriT/examples/ideas_mesh/dem0.5m.dat

@@ -0,0 +1,38 @@
+ ncols         160
+ nrows          32
+ xllcorner 0.0
+ yllcorner 0.0
+ cellsize 0.5
+ NODATA_value -9999
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       3.67578006       3.68144989       3.68711996       3.69248009       3.70193005       3.71139002       3.72045994       3.72463012       3.72571993       3.72680998       3.72736001       3.72216010       3.71445990       3.70704007       3.69990993       3.69770002       3.69538999       3.69307995       3.69259000       3.69402003       3.69736004       3.70071006       3.70419002       3.70565009       3.71426010       3.72584009       3.73499990       3.73781991       3.73324990       3.72867990       3.72610998       3.71973991       3.70866990       3.69759011       3.68889999       3.67723989       3.67195010       3.66666007       3.66304994       3.66676998       3.67002010       3.67326999       3.67732000       3.68808007      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       3.80152011       3.81911993       3.83673000       3.83797002       3.81517005       3.79237008       3.76943994       3.74967003       3.73159003       3.71310997       3.69426990       3.69110990       3.70169997       3.70654011       3.71008992       3.71265006       3.71826005       3.72740006       3.73315001       3.73889995       3.74063993       3.74092007       3.74107003       3.73696995       3.72748995       3.71965003       3.71497989       3.71276999       3.71054006       3.71019006       3.71073008       3.71127009       3.71427011       3.71776009       3.72124004       3.72307992       3.72341990       3.73109007       3.73631001       3.73947001       3.74030995       3.73793006       3.73568010       3.73297000       3.72312999       3.71462989       3.70613003       3.69215012       3.67993999       3.67463994       3.67669010       3.68144989       3.68470001       3.69039011       3.69951010       3.70972991       3.72053003       3.72772002       3.73278999       3.73739004       3.73105001       3.72470999       3.71394992       3.70319009       3.69095993       3.67872000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       3.75475001       3.74907994       3.74724007       3.75851989       3.76999998       3.78148007       3.80120993       3.81920004       3.83546996       3.83880997       3.83655000       3.83053994       3.80749989       3.78425002       3.76565003       3.74860001       3.73019004       3.71093988       3.70831990       3.71953011       3.72837996       3.73249006       3.73286009       3.73133993       3.73551989       3.74054003       3.74421000       3.73726010       3.73628998       3.73530006       3.73233008       3.72877002       3.72726011       3.72456002       3.71945000       3.71072006       3.70832992       3.70797992       3.70799994       3.70991993       3.71309996       3.71493006       3.71777010       3.72303009       3.72380996       3.72325993       3.72297001       3.71752000       3.71604991       3.71501994       3.72231007       3.71914005       3.71275997       3.70576000       3.69827008       3.69089007       3.68551993       3.68823004       3.68945003       3.69720006       3.71041989       3.72168994       3.73023009       3.73304009       3.73585010       3.74305010       3.75445008       3.74754000       3.73182988       3.72687006       3.72262001       3.71024990       3.69779992       3.68760991       3.68583989       3.68603992       3.68623996       3.68857002       3.70222998       3.71672010       3.73120999       3.74965000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       3.84483004       3.82737994       3.80970001       3.79201007       3.77605009       3.76996994       3.76430988       3.75865006       3.76278996       3.76799989       3.77947998       3.79763007       3.81759000       3.83240008       3.83574009       3.83877993       3.83465004       3.82170010       3.80574012       3.78974009       3.76957011       3.74766994       3.73929000       3.72761011       3.72497010       3.73044991       3.73018003       3.72920990       3.72807002       3.73006010       3.73337007       3.73451996       3.72147989       3.71216989       3.71082997       3.70819998       3.70526004       3.70721006       3.72006989       3.72303009       3.71444011       3.70405006       3.69823003       3.69833994       3.69854999       3.69981003       3.70095992       3.70166993       3.70431995       3.70296001       3.70022988       3.69894004       3.69344997       3.68783998       3.68524003       3.69456005       3.70389009       3.70372009       3.69616008       3.68835998       3.68086004       3.66948009       3.65727997       3.65849996       3.66400003       3.67234993       3.68558002       3.70854998       3.72836995       3.73825002       3.74397993       3.75030994       3.75149012       3.75268006       3.74242997       3.74024010       3.73833990       3.72913003       3.71856999       3.70839000       3.70251012       3.70272994       3.70296001       3.70512009       3.71431994       3.72881007       3.74329996       3.75938010       3.78412008       3.81211996       3.83978009       3.84027004       3.81645012       3.79262996      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
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+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       4.63767004       4.55955982       4.48145008       4.40333986       4.32523012       4.29421997       4.26513004       4.23603010       4.20696020       4.18704987       4.16715002       4.14724016       4.12802982       4.12390995       4.11978006       4.11566019       4.11306000       4.12680006       4.14053011       4.15427017       4.16422987       4.14826012       4.13229990       4.11633015       4.10558987       4.12061977       4.13565016       4.15067005       4.16071987       4.15205002       4.14337015       4.13468981       4.12848997       4.12966013       4.13082981       4.13199997       4.13345003       4.13556004       4.13767004       4.13978004       4.13732004       4.12576008       4.11420012       4.10263014       4.09898996       4.10848999       4.11798000       4.12748003       4.13206005       4.12978983       4.12751007       4.12523985       4.12190008       4.11729002       4.11267996       4.10806990       4.11207008       4.12468004       4.13729000       4.14989996       4.14412022       4.12278986       4.10145998       4.08013010       4.06821012       4.06302023       4.05781984       4.05262995       4.03741980       4.01620007       3.99497008       3.97375011       3.96543002       3.96358991       3.96174002       3.95989990       3.95745993       3.95477009       3.95209002       3.94940996       3.91546988       3.87106991       3.82666993       3.78226995      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    

PyLaGriT/examples/ideas_mesh/dem1m.dat

@@ -0,0 +1,22 @@
+ ncols          80
+ nrows          16
+ xllcorner 0.0
+ yllcorner 0.0
+ cellsize 1.0
+ NODATA_value -9999
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+  -9999.00000      -9999.00000       4.08056021       4.03021002       3.97554994       3.96744990       3.96454000       3.96043992       3.93502998       3.88625002       3.80773997       3.75567007       3.71145010       3.68425012       3.62757993       3.54643989       3.47901011       3.43943000       3.39190006       3.33290005       3.27805996       3.24868989       3.23566008       3.20618010       3.16253996       3.11444998       3.09419990       3.07409000       3.05212998       3.02804995       3.00203991       2.98604012       2.98108006       2.98636007       2.98809004       2.98990989       2.99160004       2.99549007       3.01216006       3.01435995       3.00728011       3.00518990       3.00177002       3.01401997       3.01781988       3.00535011       3.00322008       3.00254011       3.00037003       2.99166989       2.98130989       3.01029992       3.06195998       3.07175994       3.07405996       3.11138010       3.16626000       3.20573997       3.21698999       3.24619007       3.31199002       3.36210990       3.40650010       3.44888997       3.49475002       3.52310991       3.56508994       3.60157990       3.64304996       3.68530989       3.70687008       3.72404003       3.72502995       3.72311997       3.70644999       3.69006991       3.67417002       3.66610003      -9999.00000      -9999.00000    
+  -9999.00000       4.17643976       4.10390997       3.97607994       3.89861989       3.85435009       3.81108999       3.78051996       3.75936007       3.75047994       3.64608002       3.54189992       3.46359992       3.44306993       3.39913011       3.31353998       3.23955011       3.20812011       3.18319011       3.14372993       3.09769011       3.05991006       3.03835011       3.00462008       2.98114991       2.98615003       2.98948002       2.99089003       2.99953008       3.00716996       3.01724005       3.00921011       3.01032996       3.02570009       3.03816009       3.03851008       3.04104996       3.06101990       3.08590007       3.09742999       3.09222007       3.07147002       3.08153009       3.10124993       3.10500002       3.08592010       3.07090998       3.07936001       3.09131002       3.07593989       3.04626989       3.03160000       3.01507998       3.00090003       2.98080993       3.00290990       3.03574991       3.06944990       3.08284998       3.10534000       3.15187001       3.20514011       3.24820995       3.29709005       3.35172009       3.40943003       3.45816994       3.50570989       3.56209993       3.59572005       3.62329006       3.67304993       3.69532990       3.69238997       3.70085001       3.70246005       3.69505000       3.68829012      -9999.00000      -9999.00000    
+  -9999.00000       4.24236012       4.09855986       3.91252995       3.76834989       3.70830011       3.59031010       3.51260996       3.49142003       3.51143003       3.42268991       3.23323011       3.17428994       3.17407990       3.12173009       3.05750990       3.01828003       2.99637008       2.98281002       2.99205995       2.99881005       2.99673009       3.00162005       3.01030993       3.02418995       3.03158998       3.03176999       3.03296995       3.04728007       3.06346011       3.07817006       3.07838011       3.09077001       3.12357998       3.15052009       3.16090012       3.16596007       3.18351007       3.21501994       3.23701000       3.24569988       3.22339010       3.23500991       3.25476003       3.25937009       3.23691010       3.20707989       3.21790004       3.21984005       3.20320010       3.16915011       3.13944006       3.12245989       3.09775996       3.06613994       3.03109002       3.01264000       2.99286008       2.98671007       3.01121998       3.04731989       3.09072995       3.11647010       3.16470003       3.22282004       3.28312993       3.32658005       3.36889005       3.41938996       3.45702004       3.49959993       3.55202007       3.60661006       3.63202000       3.66960001       3.69051003      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000       4.29971981       4.10629988       3.83737993       3.59399009       3.47365999       3.30367994       3.20103002       3.15771008       3.10987997       3.06352997       2.99652004       2.98945999       3.00626993       3.03315997       3.03697991       3.02785993       3.02589989       3.03076005       3.03990006       3.04690003       3.04946995       3.05135989       3.05876994       3.07023001       3.08350992       3.09370995       3.10203004       3.13198996       3.15823007       3.18322992       3.19155002       3.21530008       3.29510999       3.33300996       3.35775995       3.40023994       3.40590000       3.41758990       3.44348001       3.45841002       3.46871996       3.45460010       3.45779991       3.45900989       3.45091009       3.43195009       3.42033005       3.38880992       3.36106992       3.32400990       3.28205991       3.25758004       3.22212005       3.18089008       3.13333011       3.10859990       3.08309007       3.04491997       3.01049995       2.99011993       2.99732995       3.02582002       3.05786991       3.11262012       3.15846992       3.18129992       3.22334003       3.26321006       3.30721998       3.35206008       3.40335989       3.46203995       3.54347992       3.58182001      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000       4.43861008       4.17054987       3.86994004       3.53736997       3.25597000       3.20038009       3.08452010       3.03712010       3.10261011       3.12493992       3.10684991       3.07525992       3.07524991       3.09787011       3.10535002       3.11404991       3.11512995       3.10285997       3.12579989       3.15029001       3.16046000       3.16025996       3.17108989       3.19092989       3.20595002       3.21574998       3.22956991       3.27025008       3.31076002       3.37841010       3.39192009       3.45056009       3.51063991       3.55185008       3.59440994       3.64246011       3.64417005       3.62995005       3.64646006       3.66740990       3.68558002       3.66199994       3.64866996       3.63913012       3.64798999       3.64030004       3.60897994       3.56533003       3.52887988       3.48669004       3.44168997       3.40675998       3.36542010       3.33564997       3.28865004       3.25092006       3.21391010       3.15182996       3.08898997       3.06352997       3.03574991       2.99936008       2.98095012       3.01904011       3.05187011       3.07034993       3.08738995       3.12649989       3.16768003       3.20777988       3.26090002       3.31991005      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000       4.57731009       4.33658981       4.07664013       3.77132010       3.55111003       3.41736007       3.32752991       3.26822996       3.28042006       3.27336001       3.25344992       3.22819996       3.21158004       3.23557997       3.26879001       3.29426003       3.29137993       3.29047990       3.31513000       3.34335995       3.35736990       3.35695004       3.36314011       3.38662004       3.40035009       3.40897012       3.42754006       3.45870996       3.50495005       3.57962990       3.63894010       3.69623995       3.73137999       3.76063991       3.79294991       3.83254004       3.82194996       3.80666995       3.81192994       3.82526994       3.83078003       3.80167007       3.78429008       3.77467990       3.78880000       3.77147007       3.74549007       3.70541000       3.66699004       3.62378001       3.57565999       3.52970004       3.50422001       3.49130988       3.46569991       3.43094993       3.38494992       3.30970001       3.23032999       3.17314005       3.13644004       3.09240007       3.06037998       3.04159999       3.00019002       2.99084997       3.00775003       3.02535009       3.05351996       3.10082006      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000       4.57560015       4.37607002       4.20177984       4.01429987       3.87034988       3.77456999       3.71565008       3.64509010       3.57018995       3.50861001       3.47612000       3.46308994       3.48081994       3.51987004       3.54540992       3.54459000       3.55202007       3.56594992       3.58985996       3.59822989       3.60551000       3.61189008       3.62537003       3.63271999       3.63729000       3.64698005       3.66808009       3.71257997       3.76557994       3.81666994       3.87055993       3.89491010       3.91667008       3.93983006       3.94470000       3.94535995       3.93807006       3.93723011       3.93302011       3.92212009       3.90139008       3.88089991       3.87199998       3.86624002       3.85402012       3.83102989       3.79874992       3.75980997       3.71024990       3.65822005       3.62374997       3.61437988       3.62491989       3.62020993       3.60022998       3.56051993       3.48305011       3.40926003       3.33383012       3.27803993       3.21555996       3.16777992       3.14651990       3.11034989       3.05351996       3.00648999       2.98060989       3.00207996      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000       4.51867008       4.35922003       4.26718998       4.18594980       4.07220984       3.97362995       3.88965988       3.82112002       3.77624011       3.75555992       3.77010012       3.78081989       3.79038000       3.79234004       3.79977012       3.80716991       3.81455994       3.82194996       3.83102989       3.83831000       3.83976007       3.83709002       3.83874011       3.85103011       3.86532998       3.89446998       3.92010999       3.95538998       3.99272990       4.02166986       4.03460979       4.04231977       4.04194021       4.04672003       4.03694010       4.03138018       4.01698017       4.00165987       3.97779989       3.95024991       3.93858004       3.92491007       3.91535997       3.89463997       3.86547995       3.81423998       3.75416994       3.70116997       3.67047000       3.66912007       3.69726992       3.71468997       3.71936989       3.69407010       3.65030003       3.58697009       3.49704003       3.43596005       3.38104010       3.33449006       3.29909992       3.24625993       3.17236996       3.10206008      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       4.58134985       4.48944998       4.39742994       4.28569984       4.18388987       4.09923983       4.03039980       4.00988007       3.99761009       3.97807002       3.98390007       3.99950004       4.01413012       3.99914002       3.99207997       3.99616003       4.02147007       4.02345991       4.02088022       4.01127005       4.01202011       4.01789999       4.04221010       4.03633022       4.03916979       4.06193018       4.08783007       4.10255003       4.11400986       4.10411978       4.10311985       4.11502981       4.11170006       4.08641005       4.06730986       4.05387020       4.03119993       3.99847007       3.96706009       3.95353007       3.95288992       3.94675994       3.90494990       3.83586001       3.76796007       3.71741009       3.68933010       3.68394995       3.71424007       3.75681996       3.78045988       3.77634001       3.74535990       3.69663000       3.62673998       3.58439994       3.55714011       3.53695989       3.51200008       3.42859006      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    
+  -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000       4.55066013       4.39344978       4.29017019       4.23160982       4.18378019       4.14372015       4.12312984       4.11482000       4.12974977       4.15740013       4.14442015       4.11228991       4.12460995       4.15486002       4.14951992       4.13205004       4.13003016       4.13239002       4.13628006       4.14053011       4.12151003       4.09823990       4.11220980       4.13132000       4.12883997       4.12425995       4.11524010       4.10596991       4.13058996       4.15518999       4.11225986       4.07076979       4.06031990       4.04735994       4.00464010       3.96624994       3.96253991       3.95858002       3.95318007       3.93288994       3.84352994      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000      -9999.00000    

PyLaGriT/examples/ideas_mesh/ideas_mesh.py

@@ -0,0 +1,194 @@
+import optparse
+import shutil, distutils.dir_util, os, sys, glob
+
+import numpy
+import math
+import matplotlib.pyplot as plt
+from pylagrit import PyLaGriT
+
+#
+#  Create parser and options
+#
+p = optparse.OptionParser()
+p.add_option('--dem-file', help='DEM data file name including path', type='string', dest='dem_filename' )
+p.add_option('--exo-file', help='Exodus II mesh output including path', type='string', dest='exo_filename')
+p.add_option('--dry-run', help='Show commands and diagnostics but no execution', default=False, dest='dry_run', action='store_true')
+p.add_option('--plot', help='Show commands and diagnostics but no execution', default=False, dest='plot', action='store_true')
+#
+(opts,args) = p.parse_args()
+
+print(opts.dem_filename)
+print(opts.dry_run)
+
+# Input: DEM data
+dem_file_fullname=opts.dem_filename
+dem_file_noext, dem_file_ext=os.path.splitext(opts.dem_filename)
+dem_file_base=os.path.basename(opts.dem_filename).rstrip(dem_file_ext)
+dem_file_path=os.path.dirname(opts.dem_filename)
+
+# Output: Exodus II mesh
+exo_file_fullname=opts.exo_filename
+exo_file_noext, exo_file_ext=os.path.splitext(opts.exo_filename)
+exo_file_base=os.path.basename(opts.exo_filename).rstrip(exo_file_ext)
+exo_file_path=os.path.dirname(opts.exo_filename)
+
+# Output: XML region specifications for the new mesh
+xml_file_fullname=exo_file_path+exo_file_base+'.xml'
+
+# DEM parsing
+# 
+with open(dem_file_fullname) as dem_header:
+    for line in dem_header:
+        if ("ncols" in line):
+            nx=int(line.split()[1])
+        elif ("nrows" in line):
+            ny=int(line.split()[1])
+        elif ("xllcorner" in line):
+            xll_corner=float(line.split()[1])
+        elif ("yllcorner" in line):
+            yll_corner=float(line.split()[1])
+        elif ("cellsize" in line):
+            dx=float(line.split()[1])
+            dy=dx
+        elif ("NODATA_value" in line):
+            no_data_value=int(line.split()[1])
+            break
+
+print(nx, ny, xll_corner, yll_corner, dx, dy, no_data_value)
+dem_header.close()
+
+d = numpy.flipud(numpy.genfromtxt(dem_file_fullname,skip_header=6))
+#plt.matshow(d)
+
+# Create mesh based on ncols and nrows in file, could automatically read
+x = numpy.linspace(xll_corner,dx*(nx-1),nx)
+y = numpy.linspace(yll_corner,dy*(ny-1),ny)
+
+x=numpy.arange(xll_corner,dx*nx,dx)
+y=numpy.arange(yll_corner,dy*ny,dy)
+
+xx, yy = numpy.meshgrid(x,y)
+
+# Write avs file
+fh = open(dem_file_base+'.avs','w')
+# Find number of data values and write avs header
+N = numpy.where(numpy.isnan(d)==False)[0].shape[0]
+fh.write(str(N)+' 0 0 0 0\n')
+# Collect data into avs format
+# JDM:  Not sure if this should be nx*ny? 
+davs = numpy.zeros([nx*ny,4])
+ind = 0
+for i,row in enumerate(d):
+    for j,v in enumerate(row):
+        davs[ind,:] = [ind + 1, xx[i,j], yy[i,j], v]
+        ind += 1
+# Write data to avs file 
+numpy.savetxt(fh,davs,fmt=['%4d','%.1lf','%.1lf','%.8lf'])   
+fh.close()
+
+# Crank up pylagrit
+lg = PyLaGriT()
+# Read in elevations in avs fromat
+m = lg.read(dem_file_base+'.avs')
+# Take a look, change paraview exe
+# Will need to use glyph filter to view points
+#m.paraview(exe='paraview')
+
+# Copy z values over to attribute
+m.addatt('z_save',vtype='vdouble',rank='scalar')
+m.copyatt('zic','z_save')
+# Not sure why this has to be done, but not data elements don't get removed otherwise
+m.setatt('zic',0.)
+
+# Create connected quad mesh surface
+m2 = lg.create()
+#m2.createpts_xyz((nx,ny,1),[xx.min(),yy.min(),0.],[xx.max(),yy.max(),0],rz_switch=[1,1,1],connect=True)
+m2.createpts_xyz((nx,ny,1),[xx.min(),yy.min(),0.],[xx.max(),yy.max(),0],rz_switch=[1,1,1])
+# Create temporary z value attribute
+m2.addatt('z_save',vtype='vdouble',rank='scalar')
+# Interpolate elevations to z_save
+m2.interpolate_voronoi('z_save',m,'z_save')
+# Find nodes associated with nodata
+pdel = m2.pset_attribute('z_save',-9999)
+# Create element set from these nodes and remove elements
+edel = pdel.eltset()
+m2.rmpoint_eltset(edel)
+# Copy temp z values over to actual a values
+#m2.copyatt('z_save','zic')
+# Take a look to make sure everything is ok
+#m2.paraview(exe='paraview')
+
+
+
+m3 = m2.copypts(elem_type='triplane')
+m3.connect()
+# To lazy to add to pylagrit now, and don't know how to make it intuitive
+# Creates edge_max element attribute containing max edge length
+m3.sendline('quality/edge_max/y')
+# Query created attribute
+#m3.printatt('edgemax')
+m3.minmax('edgemax')
+# Figure out max desired edge length
+max_edge = numpy.sqrt(dx**2+dy**2)
+# Identify elements with longer edges
+edel = m3.eltset_attribute('edgemax',max_edge*2.05,'gt')
+m3.rmpoint_eltset(edel)
+
+#m3 = m2.grid2grid_quadtotri2()
+#m3=m2
+# Create temporary z value attribute
+m3.addatt('z_save',vtype='vdouble',rank='scalar')
+# Interpolate elevations to z_save
+m3.interpolate_voronoi('z_save',m,'z_save')
+
+# Find nodes associated with nodata
+pdel = m3.pset_attribute('z_save',-9999)
+# Create element set from these nodes and remove elements
+edel = pdel.eltset()
+m3.rmpoint_eltset(edel)
+# Copy temp z values over to actual a values
+m3.copyatt('z_save','zic')
+# Take a look to make sure everything is ok
+#m2.paraview(exe='paraview')
+
+# Create top surface avs
+m3.dump('top.inp')
+## Subtract 1 from z values of top and dump into bottom surface avs
+m3.math('sub',1,'zic',cmosrc=m3)
+m3.dump('mid.inp')
+m3.setatt('zic',0.0)
+m3.dump('bot.inp')
+
+# Stack the layers in a new mesh object
+stack = lg.create()
+stack.stack_layers('avs',['bot.inp 1','mid.inp 1,3','top.inp 1,0'],flip_opt=True)
+stack_hex = stack.stack_fill()
+# Automatically create face sets based on normal vectors and layer id
+#fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=True)
+#fs = stack_hex.create_boundary_facesets(base_name='faceset_bounds',stacked_layers=False)
+# Diagnostic
+#stack_hex.sendline('quality volume itetclr')
+
+# Write exo file with boundary facesets
+#stack_hex.dump_exo(exo_file_fullname,facesets=fs.values())
+stack_hex.dump_exo(exo_file_fullname)
+
+# Write region and faceset identifier file for ats_xml
+matnames = {10000:'computational domain peat'}
+facenames = {1:'bottom face',
+             2:'surface',
+             3:'front',
+             4:'right',
+             5:'back',
+             6:'left'}
+
+# Dump ats style xml for mesh, can provide options for other schemas easily also
+#stack_hex.dump_ats_xml(xml_file_fullname,exo_file_fullname,matnames=matnames,facenames=facenames)
+stack_hex.dump_ats_xml(xml_file_fullname,exo_file_fullname,matnames=matnames,facenames=facenames)
+
+# Take a look
+if opts.plot: 
+    stack_hex.paraview(exe='/Applications/paraview.app/Contents/MacOS/paraview')
+
+
+

PyLaGriT/examples/julia/calc_volume/calc_volume.jl

@@ -0,0 +1,47 @@
+using PyCall
+@pyimport pylagrit
+
+l = pylagrit.PyLaGriT(lagrit_exe="lagrit")
+
+# Create mesh object 'm'
+m = l[:create](elem_type="triplane")
+m[:read]("data.inp")
+
+# Set imt to 1 for all points
+m[:setatt]("imt",1)
+m[:minmax_xyz]()
+
+# Connect mesh
+m[:connect]()
+
+# Lift the triangulation by assigning the Z coordinate to the data value (value)
+m[:copyatt]("value","zic")
+m[:minmax_xyz]()
+
+# Dump surface to vis file
+m[:dump]("tmp_tri_surf.inp")
+
+# Extrude mesh to 0
+mprism = m[:extrude](0.1,offset_type="min",return_type="volume", direction=[0.,0.,-1.])
+
+# Diagnostic
+l[:sendline]("quality / volume")
+
+# Add e_volume attribute of type "volume"
+mprism[:addatt]("e_volume", keyword="volume")
+
+# Calculate volume
+mprism[:math]("sum","volume_sum",attsrc="e_volume")
+
+# Dump surface to vis file
+mprism[:dump]("tmp_prism.inp")
+
+# Just to check the math do this again and assign all the 'values' to 1.0 and see if we get the expected result.
+mprism[:delete]()
+m[:setatt]("value", 1.0)
+m[:copyatt]("value","zic")
+mprism = m[:extrude](0.1,offset_type="min",return_type="volume", direction=[0.,0.,-1.])
+l[:sendline]("quality / volume")
+mprism[:addatt]("e_volume", keyword="volume")
+mprism[:math]("sum","volume_sum",attsrc="e_volume")
+

PyLaGriT/examples/julia/calc_volume/data.inp

@@ -0,0 +1,13 @@
+5 0 1 0 0
+1 0. 0. 0.
+2 1. 0. 0.
+3 1. 1. 0.
+4 0. 1. 0.
+5 .3 .7 0.
+1 1
+value, real
+1 0.1
+2 0.2
+3 0.4
+4 0.4
+5 0.5

PyLaGriT/examples/julia/polygon_map/2d_mesh.avs

@@ -0,0 +1,112 @@
+        36         34          4          0          0
+001   6.013520000000E+01  7.815840000000E+01  0.000000000000E+00
+002   6.225470000000E+01  7.304140000000E+01  0.000000000000E+00
+003   6.636100000000E+01  7.733150000000E+01  0.000000000000E+00
+004   6.743270000000E+01  7.545220000000E+01  0.000000000000E+00
+005   6.859450000000E+01  7.817220000000E+01  0.000000000000E+00
+006   6.951440000000E+01  7.399160000000E+01  0.000000000000E+00
+007   7.084420000000E+01  7.675250000000E+01  0.000000000000E+00
+008   7.160620000000E+01  7.163580000000E+01  0.000000000000E+00
+009   7.446970000000E+01  7.667770000000E+01  0.000000000000E+00
+010   7.634490000000E+01  6.771360000000E+01  0.000000000000E+00
+011   7.675880000000E+01  6.338200000000E+01  0.000000000000E+00
+012   7.897770000000E+01  6.857050000000E+01  0.000000000000E+00
+013   7.901310000000E+01  6.423670000000E+01  0.000000000000E+00
+014   8.278350000000E+01  6.370140000000E+01  0.000000000000E+00
+015   8.581780000000E+01  6.354890000000E+01  0.000000000000E+00
+016   8.837110000000E+01  6.236630000000E+01  0.000000000000E+00
+017   9.139940000000E+01  5.620000000000E+01  0.000000000000E+00
+018   9.220260000000E+01  5.174260000000E+01  0.000000000000E+00
+019   9.029090000000E+01  5.127020000000E+01  0.000000000000E+00
+020   8.814240000000E+01  4.745050000000E+01  0.000000000000E+00
+021   8.651860000000E+01  4.605400000000E+01  0.000000000000E+00
+022   8.447390000000E+01  4.624540000000E+01  0.000000000000E+00
+023   8.032490000000E+01  4.764650000000E+01  0.000000000000E+00
+024   7.972940000000E+01  5.571550000000E+01  0.000000000000E+00
+025   7.884580000000E+01  5.498510000000E+01  0.000000000000E+00
+026   7.671340000000E+01  5.763060000000E+01  0.000000000000E+00
+027   7.543020000000E+01  5.673740000000E+01  0.000000000000E+00
+028   7.536320000000E+01  5.840850000000E+01  0.000000000000E+00
+029   7.325510000000E+01  6.345750000000E+01  0.000000000000E+00
+030   7.111320000000E+01  6.315590000000E+01  0.000000000000E+00
+031   7.113480000000E+01  6.613580000000E+01  0.000000000000E+00
+032   7.012260000000E+01  6.643770000000E+01  0.000000000000E+00
+033   6.865560000000E+01  6.764970000000E+01  0.000000000000E+00
+034   6.784250000000E+01  6.752880000000E+01  0.000000000000E+00
+035   6.589600000000E+01  6.792520000000E+01  0.000000000000E+00
+036   6.262800000000E+01  6.655140000000E+01  0.000000000000E+00
+001        0   tri  1  2  3
+002        0   tri  3  4  5
+003        0   tri  5  6  7
+004        0   tri  9 10 11
+005        0   tri 13 14 15
+006        0   tri 15 16 17
+007        0   tri 17 18 19
+008        0   tri 19 20 21
+009        0   tri 21 22 23
+010        0   tri 23 24 25
+011        0   tri 25 26 27
+012        0   tri 28 29 30
+013        0   tri 34 35 36
+014        0   tri  1  3  5
+015        0   tri  5  7  8
+016        0   tri  8  9 11
+017        0   tri 13 15 17
+018        0   tri 17 19 21
+019        0   tri 21 23 25
+020        0   tri 25 27 28
+021        0   tri 28 30 31
+022        0   tri  1  5  8
+023        0   tri  8 11 12
+024        0   tri 13 17 21
+025        0   tri 21 25 28
+026        0   tri 28 31 32
+027        0   tri  1  8 12
+028        0   tri 12 13 21
+029        0   tri 21 28 32
+030        0   tri 12 21 32
+031        0   tri 12 32 33
+032        0   tri  1 12 33
+033        0   tri  1 33 34
+034        0   tri  1 34 36
+00004  1  1  1  1
+imt1, integer 
+itp1, integer 
+icr1, integer 
+isn1, integer 
+0000000001  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000002  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000003  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000004  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000005  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000006  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000007  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000008  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000009  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000010  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000011  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000012  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000013  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000014  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000015  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000016  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000017  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000018  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000019  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000020  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000021  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000022  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000023  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000024  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000025  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000026  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000027  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000028  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000029  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000030  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000031  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000032  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000033  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000034  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000035  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00
+0000000036  0.000000000000E+00  1.000000000000E+01  0.000000000000E+00  0.000000000000E+00

PyLaGriT/examples/julia/polygon_map/README

@@ -0,0 +1 @@
+This example demonstrates how PyLaGriT can be used within a Julia script. The julia script "polygon_map.jl" and the python script "polygon_map.py" perform the same LaGriT operations. The two scripts can be compared to see how the syntax is modified for the Julia languange.

PyLaGriT/examples/julia/polygon_map/polygon_map.jl

@@ -0,0 +1,43 @@
+using PyCall
+@pyimport pylagrit 
+@pyimport numpy as np
+
+# User parameters #######################
+# Discretization
+nx = 61; ny = 61
+# Polygon delineation filename
+polygon_file = "2d_mesh.avs"
+# User parameters #######################
+
+l = pylagrit.PyLaGriT()
+
+# Read in polygon delineation mesh
+mopoly = l[:read](polygon_file)
+
+# Create quad using polygon min and max coordinates
+xs = linspace(mopoly[:xmin],mopoly[:xmax],nx)
+ys = linspace(mopoly[:ymin],mopoly[:ymax],ny)
+#xs = np.linspace(mopoly.xmin,mopoly.xmax,nx)
+#ys = np.linspace(mopoly.ymin,mopoly.ymax,ny)
+moquad = l[:gridder](xs,ys,elem_type="quad",connect=true)
+mopoly[:setatt]("itetclr",1)
+
+# Create extruded quad to tet and center at z=0
+moprism = mopoly[:extrude](1.0)
+moprism[:trans]((0.,0.,0.),(0.,0.,0.5))
+motet = moprism[:grid2grid_prismtotet3]()
+
+# Clean up a little
+mopoly[:delete]()
+moprism[:delete]()
+
+# Add attribute to moquad to store if in polygon or not
+moquad[:addatt]("if_in_poly",vtype="vint")
+moquad[:setatt]("if_in_poly", 0) # Make sure attr starts as zero
+
+# Interpolate motet's itetclr into moquad's if_in_poly
+moquad[:interpolate_map]("if_in_poly",motet,"itetclr")
+moquad[:intersect_elements](motet,attr_name="if_inter")
+
+# Write out file, mapping is stored as cell attribute in if_inter
+moquad[:dump]("polygon_map_julia.inp")

PyLaGriT/examples/julia/polygon_map/polygon_map.py

@@ -0,0 +1,40 @@
+from pylagrit import PyLaGriT
+import numpy as np
+
+# User parameters #######################
+# Discretization
+nx = 61; ny = 61
+# Polygon delineation filename
+polygon_file = '2d_mesh.avs'
+# User parameters #######################
+
+l = PyLaGriT()
+
+# Read in polygon delineation mesh
+mopoly = l.read(polygon_file)
+
+# Create quad using polygon min and max coordinates
+xs = np.linspace(mopoly.xmin,mopoly.xmax,nx)
+ys = np.linspace(mopoly.ymin,mopoly.ymax,ny)
+moquad = l.gridder(xs,ys,elem_type='quad',connect=True)
+mopoly.setatt('itetclr',1)
+
+# Create extruded quad to tet and center at z=0
+mopoly.extrude(1.0)
+moprism = mopoly.extrude(1.0)
+moprism.trans((0.,0.,0.),(0.,0.,0.5))
+motet = moprism.grid2grid_prismtotet3()
+
+# Clean up a little
+mopoly.delete()
+moprism.delete()
+
+# Add attribute to moquad to store if in polygon or not
+moquad.addatt('if_in_poly',vtype='vint')
+moquad.setatt('if_in_poly', 0) # Make sure attr starts as zero
+
+# Interpolate motet's itetclr into moquad's if_in_poly
+moquad.interpolate_map('if_in_poly',motet,'itetclr')
+moquad.intersect_elements(motet,attr_name='if_inter')
+
+moquad.dump('polygon_map_python.inp')

PyLaGriT/examples/read_fehm_mesh/read_fehm_mesh.py

@@ -0,0 +1,11 @@
+from pylagrit import PyLaGriT
+l = PyLaGriT()
+mhex = l.read_fehm('fehm.grid')
+#mhex.paraview()
+
+mtet = l.create(elem_type='tet')
+mtet = mhex.copypts()
+mtet.connect()
+mtet.paraview()
+
+

PyLaGriT/examples/refine_to_object.py

@@ -0,0 +1,96 @@
+# Set up a five spot co2 injection and brine production problem
+import os,sys
+#from fdata import*
+#from fpost import*
+import zipfile
+import time
+from glob import glob
+import pylagrit
+import numpy as np
+
+batch = False
+dip = 90. # Degrees, dip of fault, angle is measured from horizontal
+pars = {'k_cap':-18,
+    'k_res':-12.,
+    'k_aq':-14,
+    'k_leak':-12,
+    'zcap1':100.,
+    'zcap2':100.,       
+    'fx':3000.,
+    'fw':380,
+    'fl':1.e3,
+    'injection_rate':10.,
+    'specific_storage':1.e-4,
+    'failure_pressure':3.,
+    }
+
+# dimensions
+xmin, xmax = -2000., 6000.
+zmin, zmax = -1000.,0.
+print('zmin = '+str(zmin)+' zmax '+str(zmax))
+zmid = -1.e3        # 1 km depth
+
+fx = pars['fx']         # distance between fault and injector
+fw = pars['fw']
+fl = pars['fl']
+
+############################################## generate grid
+
+# ndivisions
+nxbase = 11
+nzbase = int((zmax-zmin)/25.)
+
+xmm = np.linspace(xmin,xmax,nxbase)
+ymm = [0.,25.]
+zmm = np.linspace(zmin,zmax,nzbase+1)
+
+#N = len(xmm)*len(ymm)*len(zmm)
+#print('Grid will contain '+str(N) +' nodes')
+#print(str(len(zmm))+' in the z direction')
+#
+## assemble parameters and root names
+#dat = fdata()
+#dat.work_dir='.'
+#
+#dat.grid.make(dat.work_dir+os.sep+'GRID.inp',x=xmm,y=ymm,z=zmm)
+#dat.grid.write('AVS.inp', format='avs')
+l = pylagrit.PyLaGriT(batch=batch)
+mtemp = l.gridder(xmm,ymm,zmm,connect=True)
+mtemp.dump("AVS.inp")
+m = l.read('AVS.inp')
+#z_inj = dat.grid.node_nearest_point((0,0,zmid)).position[2]
+#m_l = l.create_line(2, (0.1,0.1,zmin), (0.1,0.1,zmax))
+#m_l.connect_delaunay()
+#m.refine_to_object(m_l,level=3)
+#m_l.delete()
+
+#for i in range(4):
+#    prefine = m.pset_geom( (-.1,-.1,zmin), (.1,.1,zmax))
+#    prefine.refine('constant','element',inclusive_flag='inclusive',prd_choice=12)
+#    prefine.delete()
+
+m_l = l.create_line(2, [fx+fw/2.,-fl/2.,zmax+.1], [fx+fw/2.,fl/2.,zmax+.1])
+m_h = m_l.extrude(fw, direction=[1,0,0])
+m_l.delete()
+m_c = m_h.extrude((zmax-zmin)*2, direction=[np.tan(np.radians(90.-dip)),0.,-1])
+m_h.delete()
+m_c.connect_delaunay()
+for i in range(4): m.refine_to_object(m_c,prd_choice=1)
+
+m2 = m.grid2grid_tree_to_fe()
+#m2.gmv()
+m2.connect_delaunay()
+
+# Set imt at injector
+#p_inj = m.pset_geom( (-.1,-.1,z_inj-0.1), (.1,.1,z_inj+0.1))
+#p_inj.setatt('imt',10)
+ 
+# set imt of fault
+attr_name = m2.intersect_elements(m_c)
+e_fault = m2.eltset_attribute(attr_name,0,boolstr='gt')
+p_fault = e_fault.pset()
+p_fault.setatt('imt',20)
+
+if batch: l.run_batch()
+else: m2.paraview()
+

PyLaGriT/examples/region_example.py

@@ -0,0 +1,21 @@
+from pylagrit import PyLaGriT
+lg = PyLaGriT()
+mesh = lg.create()
+mins = (0,0,0)
+maxs = (5,5,5)
+eighth = mesh.surface_box(mins,maxs)
+boolstr1 = 'le '+eighth.name
+boolstr2 = 'gt '+eighth.name
+reg1 = mesh.region(boolstr1)
+reg2 = mesh.region(boolstr2)
+mreg1 = mesh.mregion(boolstr1)
+mreg2 = mesh.mregion(boolstr2)
+mesh.createpts_brick_xyz((10,10,10), (0,0,0), (10,10,10))
+mesh.rmregion(reg1)
+mesh.dump('reg_test.gmv')
+
+
+
+
+
+

PyLaGriT/examples/stratigraphic_hex_mesh_tutorial.py

@@ -0,0 +1,479 @@
+# -*- coding: utf-8
+# This script is the PyLaGriT version of LaGriT tutorial example at
+# https://lanl.github.io/LaGriT/pages/tutorial/stratigraphy/index.html.
+# Written by Guoyan Jiang (gyjiang@whu.edu.cn) with technical support
+# from Dylan Harp (dharp@lanl.gov) and Terry Miller (tamiller@lanl.gov). 
+
+# Import PyLaGriT class from pylagrit module
+from pylagrit import PyLaGriT
+import numpy
+
+# Variables
+maxX  = 4000              # Max value in x direction
+maxY  = 4000              # Max value in y direction
+maxZ  = 3000              # Max value in z direction
+numX = 51                 # Number of points in x direction
+numY = 51                 # Number of points in y direction
+numZ = 26                 # Number of points in z direction
+
+# Create PyLaGriT object
+# This assumes that pylagritrc is being used so that lagrit_exe option does not need to be specified
+lg = PyLaGriT()
+
+#********************************************
+# 01 Built HEX Mesh
+#********************************************
+# Create mesh object 
+mo = lg.create_hex()
+mo.createpts_brick_xyz((numX, numY, numZ), (0,0,0), (maxX, maxY, maxZ))
+
+# Save the mesh object
+mo.dump('tmp_hex_01.inp')
+
+# Set vertices (imt) and cells (itetlcr) to 1
+mo.setatt('imt', 1)
+mo.setatt('itetclr', 1)
+
+# Set node type from connectivity of mesh
+mo.resetpts_itp()
+
+#********************************************
+# 02 Use pset’s to identify (for setting boundary conditions, 
+# initial conditions, etc.) a set of vertices on the top 
+# surface of the mesh
+#********************************************
+# Create a pset named p_top, which contains all nodes (stride = 1 0 0) 
+# where the node’s Z value (zic) is greater than or equal to (ge) the top of the mesh (maxZ) 
+pset0 = mo.pset_attribute('zic', maxZ, 'ge', (1,0,0), 'p_top')
+
+# Define three cylindrical objects
+pset1 = mo.pset_geom((0,0,-1), (1100,360,10000), (1500,1500,0), 'rtz', (1,0,0), 'p_circle1')
+pset2 = mo.pset_geom((0,0,-1), (1100,360,10000), (2500,2500,0), 'rtz', (1,0,0), 'p_circle2')
+pset3 = mo.pset_geom((0,0,-1), (1100,360,10000), (2500,1500,0), 'rtz', (1,0,0), 'p_circle3')
+
+# Intersect four psets, points belonging to the union of all given sets are preserved into the pset p_region
+pset4 = mo.pset_inter([pset0, pset1, pset2, pset3], 'p_region')
+
+# Map psets to an attribute
+mo.addatt('id_top_region', vtype='vint', rank='scalar')     # Creat a node-based attribute id_top_region within the mesh object
+mo.setatt('id_top_region', 1)              #Fill the entire attribute with 1
+pset1.setatt('id_top_region', 2)           #Color all nodes in the pset p_circle1 with the value 2
+pset2.setatt('id_top_region', 3)
+pset3.setatt('id_top_region', 4)
+pset4.setatt('id_top_region', 5)
+
+# Release the psets from memory
+pset0.delete()
+pset1.delete()
+pset2.delete()
+pset3.delete()
+pset4.delete()
+
+#********************************************
+# 03 Build some surfaces to define stratigraphy.
+# In a real model, the surfaces would come from some geologic framework model
+# and would define geologic or hydro-geologic horizons and topography.
+#********************************************
+mosurf1 = lg.create_qua()       # Create the top surface
+p1 = (-20, -20, 1000)
+p2 = (4020, -20, 1500)
+p3 = (4020, 4020, 2500)
+p4 = (-20, 4020, 500)
+pts = [p1, p2, p3, p4]
+nnodes = (numX, numY, 1)
+mosurf1.quadxy(nnodes, pts)
+#mosurf1.paraview()
+mosurf1.minmax_xyz()
+mosurf1.dump('tmp_surf1_quad.inp')
+
+mosurf2 = lg.create_qua()       # Create the bottom surface
+p1 = (-20, -20, 1800)
+p2 = (4020, -20, 2100)
+p3 = (4020, 4020, 2800)
+p4 = (-20, 4020, 800)
+pts = [p1, p2, p3, p4]
+nnodes = (numX, numY, 1)
+mosurf2.quadxy(nnodes, pts)
+#mosurf2.paraview()
+mosurf2.minmax_xyz()
+mosurf2.dump('tmp_surf2_quad.inp')
+
+#********************************************
+# 04 Use the surfaces to define regions and set
+# vertex and cell ids
+#********************************************
+# Define Regions
+sf1 = mosurf1.surface('sf1')
+sf2 = mosurf2.surface('sf2')
+
+r1 = mo.region('le ' + str(sf1))
+r2 = mo.region('gt ' + str(sf1) + ' and ' + 'le ' + str(sf2))
+r3 = mo.region('gt ' + str(sf2))
+
+mosurf1.delete()
+mosurf2.delete()
+
+# Create Eltsets and PSets from Regions
+pset1 = mo.pset_region(r1)
+pset2 = mo.pset_region(r2)
+pset3 = mo.pset_region(r3)
+
+eltset1 = mo.eltset_region(r1)
+eltset2 = mo.eltset_region(r2)
+eltset3 = mo.eltset_region(r3)
+
+#Set Attributes from Eltsets and PSets
+pset1.setatt('imt', 1)
+pset2.setatt('imt', 2)
+pset3.setatt('imt', 3)
+
+eltset1.setatt('itetclr', 1)
+eltset2.setatt('itetclr', 2)
+eltset3.setatt('itetclr', 3)
+
+#********************************************
+# 05 Build a fault surface and define stratigraphy 
+# on each side of the fault
+#********************************************
+# Create fault surface and surfaces to either side of fault
+mosurf1_fminus = lg.create_qua()       
+p1 = (-20, -20, 1000)
+p2 = (4020, -20, 1500)
+p3 = (4020, 4020, 2500)
+p4 = (-20, 4020, 500)
+pts = [p1, p2, p3, p4]
+nnodes = (numX, numY, 1)
+mosurf1_fminus .quadxy(nnodes, pts)
+#mosurf1_fminus .paraview()
+mosurf1_fminus .minmax_xyz()
+mosurf1_fminus .dump('tmp_s1_fm.inp')
+
+mosurf2_fminus = lg.create_qua()      
+p1 = (-20, -20, 1800)
+p2 = (4020, -20, 2100)
+p3 = (4020, 4020, 2800)
+p4 = (-20, 4020, 800)
+pts = [p1, p2, p3, p4]
+nnodes = (numX, numY, 1)
+mosurf2_fminus.quadxy(nnodes, pts)
+#mosurf2_fminus.paraview()
+mosurf2_fminus.minmax_xyz()
+mosurf2_fminus.dump('tmp_s2_fm.inp')
+
+mosurf1_fplus = lg.create_qua()      
+p1 = (-20, -20, 1400)
+p2 = (4020, -20, 1900)
+p3 = (4020, 4020, 2900)
+p4 = (-20, 4020, 900)
+pts = [p1, p2, p3, p4]
+nnodes = (numX, numY, 1)
+mosurf1_fplus.quadxy(nnodes, pts)
+#mosurf1_fplus.paraview()
+mosurf1_fplus.minmax_xyz()
+mosurf1_fplus.dump('mosurf1_fplus.inp')
+
+mosurf2_fplus = lg.create_qua()      
+p1 = (-20, -20, 2200)
+p2 = (4020, -20, 2500)
+p3 = (4020, 4020, 3200)
+p4 = (-20, 4020, 1200)
+pts = [p1, p2, p3, p4]
+nnodes = (numX, numY, 1)
+mosurf2_fplus.quadxy(nnodes, pts)
+#mosurf2_fplus.paraview()
+mosurf2_fplus.minmax_xyz()
+mosurf2_fplus.dump('mosurf2_fplus.inp')
+
+mosurf_fault = lg.create_qua()      
+p1 = (-20, -20, -1.e4)
+p2 = (4020, -20, -1.e4)
+p3 = (4020, 4020, 1.e4)
+p4 = (-20, 4020, 1.e4)
+pts = [p1, p2, p3, p4]
+nnodes = (numX, numY, 1)
+mosurf_fault.quadxy(nnodes, pts)
+#mosurf_fault.paraview()
+mosurf_fault.minmax_xyz()
+mosurf_fault.dump('mosurf_fault.inp')
+
+# Define geometry of hydrostratigraphic model
+sf1_fm = mosurf1_fminus.surface('sf1_fm')
+sf2_fm = mosurf2_fminus.surface('sf2_fm')
+sf1_fp = mosurf1_fplus.surface('sf1_fp')
+sf2_fp = mosurf2_fplus.surface('sf2_fp')
+sf_f = mosurf_fault.surface('sf_f')
+
+r1_fm = mo.region('le ' + str(sf1_fm) + ' and ' + 'le ' + str(sf_f))
+r2_fm = mo.region('gt ' + str(sf1_fm) + ' and ' + 'le ' + str(sf2_fm) + ' and ' + 'le ' + str(sf_f))
+r3_fm = mo.region('gt ' + str(sf2_fm) + ' and ' + 'le ' + str(sf_f))
+r1_fp = mo.region('le ' + str(sf1_fp) + ' and ' + 'gt ' + str(sf_f))
+r2_fp = mo.region('gt ' + str(sf1_fp) + ' and ' + 'le ' + str(sf2_fp) + ' and ' + 'gt ' + str(sf_f))
+r3_fp = mo.region('gt ' + str(sf2_fp) + ' and ' + 'gt ' + str(sf_f))
+
+mosurf1_fminus.delete()
+mosurf2_fminus.delete()
+mosurf1_fplus.delete()
+mosurf2_fplus.delete()
+mosurf_fault.delete()
+
+# Set fault node and element materials
+pset1_fm = mo.pset_region(r1_fm)
+pset2_fm = mo.pset_region(r2_fm)
+pset3_fm = mo.pset_region(r3_fm)
+pset1_fp = mo.pset_region(r1_fp)
+pset2_fp = mo.pset_region(r2_fp)
+pset3_fp = mo.pset_region(r3_fp)
+
+eltset1_fm = mo.eltset_region(r1_fm)
+eltset2_fm = mo.eltset_region(r2_fm)
+eltset3_fm = mo.eltset_region(r3_fm)
+eltset1_fp = mo.eltset_region(r1_fp)
+eltset2_fp = mo.eltset_region(r2_fp)
+eltset3_fp = mo.eltset_region(r3_fp)
+
+#Set Attributes from Eltsets and PSets
+mo.setatt('imt', 7)
+mo.setatt('itetclr', 7)
+
+pset1_fm.setatt('imt', 1)
+pset2_fm.setatt('imt', 2)
+pset3_fm.setatt('imt', 3)
+pset1_fp.setatt('imt', 4)
+pset2_fp.setatt('imt', 5)
+pset3_fp.setatt('imt', 6)
+
+eltset1_fm.setatt('itetclr', 1)
+eltset2_fm.setatt('itetclr', 2)
+eltset3_fm.setatt('itetclr', 3)
+eltset1_fp.setatt('itetclr', 4)
+eltset2_fp.setatt('itetclr', 5)
+eltset3_fp.setatt('itetclr', 6)
+
+#********************************************
+# 06 Define a polyline and truncate the exterior boundary of the mesh with the polyline
+#********************************************
+# Read boundary polygon file
+mobndry = lg.read('basin_bnd_ply_rescale.inp')
+
+# Extrude the polyline into a vertical surface
+mofence = mobndry.extrude(3200, 'const', 'volume', [0, 0, -1])
+
+mobndry.minmax_xyz()
+mofence.minmax_xyz()
+
+# Translate the extrusion to make it cover the vertical extent of the hex mesh
+mofence.trans((0, 0, -3100), (0, 0 ,0))
+
+mofence.minmax_xyz()
+#mofence.paraview()
+#mofence.dump('3D_vertical_surface.inp')
+#mo.dump('cube.inp')
+
+# Truncate mesh
+sf_bndry = mofence.surface('sf_bndry')
+r_bndry = mo.region('ge ' + str(sf_bndry))
+pset_bndry = mo.pset_region(r_bndry)
+
+mobndry.delete()
+mofence.delete()
+
+# Method 1: Only remove a cell if ALL vertices are outside
+e_delete1 = pset_bndry.eltset('exclusive')
+
+# Method 2: Remove a cell if the centroid (average of all vertices) is outside
+e_delete2 = mo.eltset_region(r_bndry)
+
+# Method 3: Remove a cell if one or more vertices are outside
+e_delete3 = pset_bndry.eltset('inclusive')
+
+#mo.addatt('id_in_out_bndry', vtype='vint', rank='scalar', length='nelements')
+mo.add_element_attribute('id_in_out_bndry', vtype='vint')
+mo.setatt('id_in_out_bndry', 4)              #Fill the entire attribute with 4
+e_delete3.setatt('id_in_out_bndry', 3)          
+e_delete2.setatt('id_in_out_bndry', 2)
+e_delete1.setatt('id_in_out_bndry', 1)
+
+eltset4 = mo.eltset_attribute('id_in_out_bndry', 4, 'eq')
+eltset3 = mo.eltset_attribute('id_in_out_bndry', 3, 'eq')
+#eltset2 = mo.eltset_attribute('id_in_out_bndry', 2, 'eq')
+#eltset1 = mo.eltset_attribute('id_in_out_bndry', 1, 'eq')
+
+mo.rmpoint_eltset(eltset4, False, False)
+mo.rmpoint_eltset(eltset3, True, True)
+
+#********************************************
+# 07 Refine the mesh around the fault
+#********************************************
+f_zone = mo.intersect_elements(sf_f, 'f_zone')
+fz_i = mo.eltset_attribute('f_zone', 0, 'gt')     #Non-zero indicates intersection
+fz_i.refine()
+
+mo.delatt('f_zone')
+
+mo.status (brief=True)
+
+#sf_f.delete()
+#sf1_fm.delete()
+#sf2_fm.delete()
+#sf1_fp.delete()
+#sf1_fp.delete()
+#sf_bndry.delete()
+
+#********************************************
+# 08 Insert a couple of 'wells' by refining the mesh and identifying a line of nodes
+# that will be the well source/sink for boundary conditions.
+#********************************************
+Well1X = 1234.56
+Well1Y = 1987.65
+Well2X = 2243.21
+Well2Y = 1212.34
+Radius = 25
+NRadius = 2
+
+#Well 1
+mowell1 = lg.create_tet()
+mowell1.createpts_rtz((NRadius, 9, numZ), (0, 0, 3100), (Radius, 360, 1500))   #Create a cylindrical point cloud 
+
+mowell1.filter()              # Filter (delete) points that are too close ( default distance <=1.e-16) or duplicate points
+mowell1.rmpoint_compress()    # Remove all marked nodes and correct the itet array
+mowell1.setatt('imt', 1)
+
+mowell1.connect()             # Connect the point cloud
+mowell1.resetpts_itp()
+mowell1.minmax_xyz()
+
+mowell1.trans((0, 0, 0), (Well1X, Well1Y, 0))
+mowell1.minmax_xyz()
+#mowell1.paraview()
+mowell1.dump('tmp_well1.inp')
+
+#Well 2
+mowell2 = lg.create_tet()
+mowell2.createpts_rtz((NRadius, 9, numZ), (0, 0, 3100), (Radius, 360, 2200))   
+
+mowell2.filter()              
+mowell2.rmpoint_compress()    
+mowell2.setatt('imt', 1)
+
+mowell2.connect()             
+mowell2.resetpts_itp()
+mowell2.minmax_xyz()
+
+mowell2.trans((0, 0, 0), (Well2X, Well2Y, 0))
+mowell2.minmax_xyz()
+#mowell2.paraview()
+mowell2.dump('tmp_well2.inp')
+
+# Join the two distinct wells into a single mesh object 
+mowells = lg.merge([mowell1, mowell2])
+mowells.dump('tmp_wells.inp') 
+#mowells.paraview()
+
+# Refine the mo around the wells
+# First pass refinement
+w_zone = mo.intersect_elements(mowells, 'w_zone')
+wz_i = mo.eltset_attribute('w_zone', 0, 'gt')     #Non-zero indicates intersection
+wz_i.refine()
+mo.setatt('w_zone', 0)
+#wz_i.delete()
+
+# Second pass refinement
+w_zone = mo.intersect_elements(mowells, 'w_zone')
+wz_i = mo.eltset_attribute('w_zone', 0, 'gt')     #Non-zero indicates intersection
+wz_i.refine()
+mo.setatt('w_zone', 0)
+#wz_i.delete()
+
+mohex = mo.grid2grid_tree_to_fe()                         #Quadtree or octree grid to grid
+
+#mo.status (brief=True)
+
+# Identify the column of vertices closest to the well center.
+#Well1
+mo_pts1 = lg.create()
+mo_pts1.createpts_rtz((2, 2, 1000), (0, 0, 3100), (Radius, 360, 2200))   
+mo_pts1.trans((0, 0, 0), (Well1X, Well1Y, 0))
+
+#Well2
+mo_pts2 = lg.create()
+mo_pts2.createpts_rtz((2, 2, 1000), (0, 0, 3100), (Radius, 360, 2200))   
+mo_pts2.trans((0, 0, 0), (Well2X, Well2Y, 0))
+
+mo_pts = lg.merge([mo_pts1, mo_pts2])
+mo_pts.filter()              
+mo_pts.rmpoint_compress()   
+
+# Compute a distance field attribute
+mo.compute_distance(mo_pts, option='distance_field', attname='dfield_well')
+
+mo_pts1.delete()
+mo_pts2.delete()
+mo_pts.delete()
+mowell1.delete()
+mowell2.delete()
+mowells.delete()
+
+# Describe all nodes within 32, 16, 8, 4, 2 and 1 meters of the wells.
+pwell = mo.pset_attribute('dfield_well', 1.0, 'le', (1,0,0), 'pwell1')
+pwell.dump('zone_radius_01.0.zone')
+
+pwell = mo.pset_attribute('dfield_well', 2.0, 'le', (1,0,0), 'pwell2')
+pwell.dump('zone_radius_02.0.zone')
+
+pwell = mo.pset_attribute('dfield_well', 4.0, 'le', (1,0,0), 'pwell4')
+pwell.dump('zone_radius_04.0.zone')
+
+pwell = mo.pset_attribute('dfield_well', 8.0, 'le', (1,0,0), 'pwell8')
+pwell.dump('zone_radius_08.0.zone')
+
+pwell = mo.pset_attribute('dfield_well', 16.0, 'le', (1,0,0), 'pwell16')
+pwell.dump('zone_radius_16.0.zone')
+
+pwell = mo.pset_attribute('dfield_well', 32.0, 'le', (1,0,0), 'pwell32')
+pwell.dump('zone_radius_32.0.zone')
+
+mo.dump('Hex_mesh.inp') 
+
+#********************************************
+# 09 Convert hex mesh to tet mesh
+#********************************************
+motet = mohex.copypts()
+motet.setatt('imt', 1)
+motet.setatt('itp', 0)
+motet.connect(option1='check_interface')
+motet.resetpts_itp()
+
+motet.interpolate_voronoi('imt', mohex, 'imt')
+motet.interpolate_map('itetclr', mohex, 'itetclr')
+
+#Remove all nodes and elements with imt and itetclr values of 7
+motet.rmmat(7)
+#pset7 = motet.pset_attribute('imt', 7, 'eq', (1,0,0), 'pset7')
+#motet.rmpoint_pset(pset7)
+#eltset7 = motet.eltset_attribute('itetclr', 7, 'eq')
+#motet.rmpoint_eltset(eltset7, True, True)
+
+motet.rmpoint_compress() 
+motet.resetpts_itp()
+
+# Visualize connected mesh using ParaView
+# This assumes that pylagritrc is being used so that exe option does not need to be specified
+#motet.paraview()
+
+motet.dump('Tet_mesh.inp')
+
+#********************************************
+# 10 Write tet mesh files for FEHM
+# FEHM uses node based materials and properties
+#********************************************
+#motet.resetpts_parent()
+motet.filter() 
+motet.rmpoint_compress() 
+motet.resetpts_itp()
+motet.minmax('imt')
+motet.setatt('itetclr', 1)
+#motet. tri_mesh_output_prep()
+motet.dump_fehm('Example3')
+
+
+

PyLaGriT/pylagrit/__init__.py

@@ -0,0 +1,3 @@
+from pylagrit.pylagrit import *
+
+__xall__ = ["PyLaGriT"]

PyLaGriT/pylagrit/utilities.py

@@ -0,0 +1,231 @@
+import os
+import numpy as np
+from datetime import datetime
+
+
+def zone_to_zonn(zonefile):
+    zonnfile = os.path.splitext(zonefile)[0] + ".zonn"
+    with open(zonefile, "r") as fh:
+        fh.readline()
+        lns = fh.readlines()
+    with open(zonnfile, "w") as fout:
+        fout.write("zonn\n")
+        for l in lns:
+            fout.write(l)
+
+
+def spherical_writeFEHM(node_locations, filename_base, title="default"):
+    """
+    Create FEHM .stor and .fehmn input files for 1d spherical simulations.
+    Assumes logical 1D structure.
+    :arg node_locations: radial location of nodes
+    :type node_locations: array(float)
+    :arg filename_base: base name for the .stor and .fehmn files
+    :type filename_base: str
+    :arg title: optional title for simulation
+    :type title: str
+
+    Example:
+    from pylagrit import utilities as util
+    import numpy as np
+    nodes = np.linspace(0.0,200.0)
+    filename_base = "test"
+    title = "test sim"
+    # write .stor and .fehmn files
+    util.spherical_writeFEHM(nodes,filename_base,title)
+    """
+    # stor file header
+    now = datetime.now()
+    print_datetime = now.strftime("%m/%d/%Y  %H:%M:%S")
+    header = (
+        "FEHM .stor file generated by PyLaGriT  "
+        + print_datetime
+        + "\n"
+        + "title:  "
+        + title
+        + "\n"
+    )
+
+    # calculate dx, face locations, face areas, volumes, and geometric coefficients
+    dx = spherical_dx(node_locations)
+    faces = spherical_faces(node_locations)
+    area = spherical_areas(faces)
+    volumes = spherical_volumes(node_locations)
+    coeffs = area / dx
+
+    # matrix metadata header info
+    neq = np.size(node_locations)
+    num_coeffs = neq - 1
+    FEHM_mem = (neq - 2) * 3 + 4 + neq + 1
+    num_area_coeff = 1
+    max_connect = 3
+    matrix_params = (num_coeffs, neq, FEHM_mem, num_area_coeff, max_connect)
+    params_header = "        " + "        ".join(str(s) for s in matrix_params) + "\n"
+
+    # row count
+    row_count = np.empty([neq + 1])
+    start = neq + 1
+    row_count[0] = start
+    row_count[1] = row_count[0] + 2
+    for i in range(2, neq):
+        row_count[i] = row_count[i - 1] + 3
+    row_count[neq] = row_count[neq - 1] + 2
+
+    # row entries
+    row_entries = []
+    row_entries.append(1)
+    row_entries.append(2)
+    for i in range(1, neq - 1):
+        row_entries.append(i)
+        row_entries.append(i + 1)
+        row_entries.append(i + 2)
+    row_entries.append(neq - 1)
+    row_entries.append(neq)
+
+    # index into geometric coefficient matrix
+    coeff_indices = []
+    coeff_indices.append(0)
+    coeff_indices.append(1)
+    for i in range(1, neq - 1):
+        coeff_indices.append(i)
+        coeff_indices.append(0)
+        coeff_indices.append(i + 1)
+    coeff_indices.append(neq - 1)
+    coeff_indices.append(0)
+    # neq + 1 extra 0s for padding
+    for i in range(0, neq + 1):
+        coeff_indices.append(0)
+
+    # index of diagonal entries
+    diagonal_indices = np.empty([neq])
+    diagonal_indices[0] = neq + 2
+    for i in range(1, neq):
+        diagonal_indices[i] = diagonal_indices[i - 1] + 3
+
+    # open stor file, write header and matrix parameters
+    storfile = filename_base + ".stor"
+    sfile = open(storfile, "w")
+    _ = sfile.write(header)
+    _ = sfile.write(params_header)
+
+    # write Voronoi volumes
+    count = 1
+    for vol in volumes:
+        print("  %1.12e" % vol, end="" if count % 5 else "\n", file=sfile)
+        count += 1
+    if (count - 1) % 5:
+        _ = sfile.write("\n")
+
+    # write row counts
+    count = 1
+    for row in row_count:
+        print(" %9d" % row, end="" if count % 5 else "\n", file=sfile)
+        count += 1
+    if (count - 1) % 5:
+        _ = sfile.write("\n")
+
+    # write row entries
+    count = 1
+    for row in row_entries:
+        print(" %9d" % row, end="" if count % 5 else "\n", file=sfile)
+        count += 1
+    if (count - 1) % 5:
+        _ = sfile.write("\n")
+
+    # write geometric coefficient indices
+    count = 1
+    for idx in coeff_indices:
+        print(" %9d" % idx, end="" if count % 5 else "\n", file=sfile)
+        count += 1
+    if (count - 1) % 5:
+        _ = sfile.write("\n")
+
+    # write diagonal indices
+    count = 1
+    for idx in diagonal_indices:
+        print(" %9d" % idx, end="" if count % 5 else "\n", file=sfile)
+        count += 1
+    if (count - 1) % 5:
+        _ = sfile.write("\n")
+
+    # write geometric coefficients
+    count = 1
+    for coef in coeffs:
+        print("  %1.12e" % coef, end="" if count % 5 else "\n", file=sfile)
+        count += 1
+
+    # close stor file
+    if (count - 1) % 5:
+        _ = sfile.write("\n")
+    _ = sfile.close()
+
+    # open fehmn file
+    fehmnfile = filename_base + ".fehmn"
+    ifile = open(fehmnfile, "w")
+    # write header and neq
+    _ = ifile.write("coor\n%d\n" % neq)
+    # write node number and radial location
+    for i in range(1, neq + 1):
+        print(
+            "        %3d        %12f        0        0" % (i, node_locations[i - 1]),
+            file=ifile,
+        )
+    # write connectivity
+    _ = ifile.write("\nelem\n")
+    _ = ifile.write("%d %d\n" % (2, neq - 1))
+    for i in range(1, neq):
+        print("%3d   %3d   %3d" % (i, i, i + 1), file=ifile)
+    # close fehmn file
+    _ = ifile.write("\nstop\n")
+    _ = ifile.close()
+
+
+def spherical_faces(node_locations):
+    """
+    Calculate radial interface locations given radial node locations.
+    Assumes 1st and last nodes lie on domain boundary.
+    :arg node_locations: radial location of nodes
+    :type node_locations: array_like(float)
+    Returns: array of radial interface locations of size node_locations - 1
+    """
+    interface_locations = node_locations[:-1] + np.diff(node_locations) / 2.0
+    return interface_locations
+
+
+def spherical_areas(interface_locations):
+    """
+    Calculate spherical area of each interface given radial interface locations.
+    :arg interface_locations: radial location of interfaces
+    :type interface_locations: array_like(float)
+    Returns: array of spherical interface areas of size interface_locations
+    """
+    areas = 4.0 * np.pi * interface_locations ** 2
+    return areas
+
+
+def spherical_dx(node_locations):
+    """
+    Calculate Delaunay edge lengths given radial node locations.
+    :arg node_locations: radial location of nodes
+    :type node_locations: array_like(float)
+    Returns: array of Delaunay edge lengths of size node_locations - 1
+    """
+    delaunay = np.diff(node_locations)
+    return delaunay
+
+
+def spherical_volumes(node_locations):
+    """
+    Calculate Voronoi volume associated with each node given radial node locations.
+    :arg node_locations: radial location of nodes
+    :type node_locations: array_like(float)
+    Returns: array of Voronoi volumes of size node_locations
+    """
+    coeff = np.pi * 4.0 / 3.0
+    edges = spherical_faces(node_locations)
+    edges = np.insert(edges, 0, node_locations[0])
+    edges = np.append(edges, node_locations[np.size(node_locations) - 1])
+    spheres = coeff * edges ** 3
+    volumes = np.diff(spheres)
+    assert np.all(volumes > 0), "ERROR: Negative volumes are not good."
+    return volumes

PyLaGriT/pylagritrc_example

@@ -0,0 +1,7 @@
+# This is an example pylagritrc file. 
+# To use, change its name to pylagritrc or .pylagritrc, uncomment and modify attributes and move to your working directory or your home directory. 
+# The rc file in the working directory will take precedence over the one in your home directory. 
+
+#lagrit_exe : '/lagrit/executable/location/lagrit' 
+#gmv_exe : '/gmv/executable/location/gmv' 
+#paraview_exe : '/paraview/executable/location/paraview' 

PyLaGriT/setup.py

@@ -0,0 +1,27 @@
+"""
+Build script for PyLaGriT
+"""
+
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+import os
+
+setup(
+    name="pylagrit",
+    version="1.0.1",
+    description="Python interface for LaGriT",
+    author="Dylan R. Harp",
+    author_email="dharp@lanl.gov",
+    url="lagrit.lanl.gov",
+    license="LGPL",
+    install_requires=[
+        "pexpect>=4.6.0",
+        "numpy",
+    ],
+    packages=[
+        "pylagrit",
+    ],
+)

PyLaGriT/tests/.directory

@@ -0,0 +1,3 @@
+[Dolphin]
+Timestamp=2014,7,24,15,5,28
+ViewMode=1

PyLaGriT/tests/test_pylagrit.py

@@ -0,0 +1,204 @@
+import unittest
+import pylagrit
+import glob
+import sys
+import os
+from contextlib import contextmanager
+import itertools
+
+class TestPyLaGriT(unittest.TestCase):
+    '''
+    A PyLagriT Test
+    
+    Represents a test of PyLaGriT functionality.
+    '''
+
+    def setUp(self):
+        #Sets upt a lagrit object to be used during tests.
+        with suppress_stdout():
+            self.lg = pylagrit.PyLaGriT('../../build/lagrit')
+
+    def test_read_script(self):
+        '''
+        Test the Read Script Function
+        
+        Tests that pylagrit can read a lagrit script. 
+        '''
+        
+        lg = self.lg
+        for f in glob.glob('/test_scripts/*.lg'):
+            with suppress_stdout():
+                lg.read_script(f)
+                
+    def test_convert(self):
+        '''
+        Test the Conversion Function
+        
+        Tests that pylagrit can convert files from one format to a new one.
+        '''
+        
+        lg = self.lg      
+        
+        old_formats = ['avs', 'gmv']
+        new_formats = ['avs', 'gmv', 'exo']
+        
+        for old_ft, new_ft in itertools.product(old_formats, new_formats):
+            #Convert all avs files to gmv with pylagrit
+            with suppress_stdout():
+                lg.convert('test_convert/*.%s'%old_ft, new_ft)
+            
+            #If the file did not get generated, assume fail.
+            if not os.path.isfile('test.%s'%new_ft): 
+                raise OSError('Failed Conversion.')         
+            os.remove('test.%s'%new_ft)
+            
+    def test_merge(self):
+        '''
+        Tests the Merge Function
+        
+        Tests that pylagrit can merge 3 mesh objects and return a single mesh
+        object.
+        '''
+        
+        lg = self.lg
+        with suppress_stdout():
+            mo1 = lg.read('avs', 'contour_file.avs')
+            mo2 = lg.read('avs', 'contour_file.avs')
+            mo3 = lg.read('avs', 'contour_file.avs')
+            new_mo = lg.merge([mo1, mo2, mo3]) 
+        #Test that the merge created a new mesh object.
+        if type(new_mo) is type(None):
+            raise ValueError('An expected mesh object was not created.')
+                    
+    def test_create(self):
+        '''
+        Tests the Create Function
+        
+        Tests that the create function returns a mesh object.
+        '''
+        
+        lg = self.lg
+        with suppress_stdout():
+            mo1 = lg.create() 
+            mo2 = lg.create_hex() 
+            mo3 = lg.create(elem_type='pri') 
+        if any([type(x) is type(None) for x in [mo1, mo2, mo3]]):
+            raise ValueError('An expected mesh object was not created.')
+            
+    def test_createpts_brick(self):
+        '''
+        Test the Create Points Function
+        
+        Tests that a mesh object can run the createpts method with fail.
+        '''
+        
+        lg = self.lg
+        with suppress_stdout():
+            mo = lg.create()
+            npts = (4, 4, 4)
+            mins = (0, 0, 0)
+            maxs = (4, 4, 4)
+            mo.createpts_brick('xyz', npts, mins, maxs)    
+            
+    def test_pset_geom(self):
+        '''
+        Test the MO Geometry Function
+        
+        Tests that each geom method returns a PSet.
+        '''
+        
+        lg = self.lg
+        mins = (1, 1, 1)
+        maxs = (2, 2, 2)
+        with suppress_stdout():
+            mo = lg.create()
+            ps = []
+            ps.append(mo.pset_geom(mins, maxs))
+            ps.append(mo.pset_geom_xyz(mins, maxs))
+            ps.append(mo.pset_geom_rtz(mins, maxs))
+            ps.append(mo.pset_geom_rtp(mins, maxs))
+             
+        if any([not isinstance(x, pylagrit.PSet) for x in ps]):
+            raise ValueError('PSet not returned.')
+            
+    def test_copy(self):
+        '''
+        Test the Copy Function
+        
+        Tests that the copy function returns a mesh object.
+        '''
+        
+        lg = self.lg
+        with suppress_stdout():
+            mo = lg.create()
+            mo_clone = lg.copy(mo)
+        if not isinstance(mo_clone, pylagrit.MO):
+            raise ValueError('MO not returned.')
+            
+    def test_pset_not(self):
+        '''
+        Test the Mesh Object Not Function
+        
+        Tests that a mesh object can return a PSet using the pset_not function.
+        '''
+        
+        lg = self.lg
+        mins = (1, 1, 1)
+        maxs = (2, 2, 2)
+        with suppress_stdout():
+            mo = lg.create()
+            ps1 = mo.pset_geom(mins, maxs)
+            ps2 = mo.pset_not(ps1)
+        if not isinstance(ps2, pylagrit.PSet):
+            raise ValueError('PSet not returned.')
+            
+    def test_subset(self):
+        '''
+        Test the MO Subset Function
+        
+        Tests that a mesh object can return another mesh object with the subset
+        methods.
+        '''
+        
+        lg = self.lg
+        mins = (1,1,1)
+        maxs = (2,2,2)
+        with suppress_stdout():
+            mo = lg.create()
+            mo_subs = []
+            mo_subs = mo_subs + [mo.subset(mins, maxs)]
+            mo_subs = mo_subs + [mo.subset(mins, maxs, geom='rtz')]
+            mo_subs = mo_subs + [mo.subset(mins, maxs, geom='rtp')]
+            mo_subs = mo_subs + [mo.subset_rtp(mins, maxs)]
+            mo_subs = mo_subs + [mo.subset_rtz(mins, maxs)]
+            
+        if any([not isinstance(x, pylagrit.MO) for x in mo_subs]):
+            raise ValueError('MO not returned.')
+                     
+@contextmanager
+def suppress_stdout():
+    #Utility to supress standard output.
+    with open(os.devnull, 'w') as devnull:
+        old_stdout = sys.stdout
+        sys.stdout = devnull
+        try:
+            yield
+        finally:
+            sys.stdout = old_stdout
+                               
+if __name__ == '__main__':    
+    runner = unittest.TextTestRunner(verbosity=2)    
+    suite = unittest.TestSuite()
+    suite.addTest(TestPyLaGriT('test_read_script'))
+    suite.addTest(TestPyLaGriT('test_convert'))
+    suite.addTest(TestPyLaGriT('test_merge'))
+    suite.addTest(TestPyLaGriT('test_create'))
+    suite.addTest(TestPyLaGriT('test_createpts_brick'))
+    suite.addTest(TestPyLaGriT('test_pset_geom'))
+    suite.addTest(TestPyLaGriT('test_copy'))
+    suite.addTest(TestPyLaGriT('test_pset_not'))
+    suite.addTest(TestPyLaGriT('test_subset'))
+    runner.run(suite)
+    
+    
+    

PyLaGriT/tests/test_scripts/test_script1.lg

@@ -0,0 +1 @@
+cmo / create / cmotri / / / tri

PyLaGriT/tests/test_scripts/test_script2.lg

@@ -0,0 +1,6 @@
+*Example Comment
+cmo / create / cmotri / / / tri
+read / avs / input.inp / cmotri
+*
+
+finish

PyLaGriT/tests/test_scripts/test_script3.lg

@@ -0,0 +1,8 @@
+* Example of Some Comments
+* More Comments
+* 
+define/nx/20
+define/ny/20
+define/nz/20
+   
+finish