commit beb87d1f368eeeab675b65e5b6efc64a3a506507 Author: rowanc1 Date: Tue Feb 25 11:20:27 2014 -0800 initial commit diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 00000000..1272ce31 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,25 @@ +language: python +python: + - "2.7" +virtualenv: + system_site_packages: true +before_install: + - sudo apt-get install -qq gcc gfortran libblas-dev liblapack-dev python-numpy python-scipy python-matplotlib python-pip + - sudo pip install scipy --upgrade + - sudo pip install numpy --upgrade + - cd ../ + - git clone https://github.com/simpeg/simpeg.git + - cd simpeg/SimPEG/ + - python setup.py + - cd ../../ + - echo export PYTHONPATH=$PYTHONPATH:/home/travis/build/simpeg/simpeg >> .bashrc + - source .bashrc + - cd simpegflow +# command to install dependencies +install: "pip install -r requirements.txt --use-mirrors" +# command to run tests +script: nosetests -v + +notifications: + email: + - rowanc1@gmail.com diff --git a/LICENSE b/LICENSE new file mode 100644 index 00000000..f94a23fd --- /dev/null +++ b/LICENSE @@ -0,0 +1,20 @@ +The MIT License (MIT) + +Copyright (c) 2013-2014 SimPEG Developers + +Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the "Software"), to deal in +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of +the Software, and to permit persons to whom the Software is furnished to do so, +subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS +FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR +COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER +IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN +CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/README.md b/README.md new file mode 100644 index 00000000..947fadb6 --- /dev/null +++ b/README.md @@ -0,0 +1,21 @@ +simpegflow +********** + +A groundwater forward modelling and inversion package for SimPEG. + + + +Documentation: +[http://simpegflow.readthedocs.org/en/latest/](http://simpegflow.readthedocs.org/en/latest/) + +Code: +[https://github.com/simpeg/simpegflow](https://github.com/simpeg/simpegflow) + +Tests: +[https://travis-ci.org/simpeg/simpegflow](https://travis-ci.org/simpeg/simpegflow) + +Build Status: +[![Build Status](https://travis-ci.org/simpeg/simpegflow.png)](https://travis-ci.org/simpeg/simpegflow) + +Bugs & Issues: +[https://github.com/simpeg/simpegflow/issues](https://github.com/simpeg/simpegflow/issues) diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 00000000..bee80244 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,153 @@ +# 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) . +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make ' where 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 " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @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 " 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 " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + -rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +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." + +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/SimPEG.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/SimPEG.qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/SimPEG" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/SimPEG" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +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)." + +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." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +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)." + +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." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +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." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." diff --git a/docs/api_Richards.rst b/docs/api_Richards.rst new file mode 100644 index 00000000..084ae86e --- /dev/null +++ b/docs/api_Richards.rst @@ -0,0 +1,38 @@ +.. _api_Richards: + +There are two different forms of Richards equation that differ +on how they deal with the non-linearity in the time-stepping term. + +The most fundamental form, referred to as the +'mixed'-form of Richards Equation [Celia et al., 1990] + +.. math:: + + \\frac{\partial \\theta(\psi)}{\partial t} - \\nabla \cdot k(\psi) \\nabla \psi - \\frac{\partial k(\psi)}{\partial z} = 0 + \quad \psi \in \Omega + +where theta is water content, and psi is pressure head. +This formulation of Richards equation is called the +'mixed'-form because the equation is parameterized in psi +but the time-stepping is in terms of theta. + +As noted in [Celia et al., 1990] the 'head'-based form of Richards +equation can be written in the continuous form as: + +.. math:: + + \\frac{\partial \\theta}{\partial \psi}\\frac{\partial \psi}{\partial t} - \\nabla \cdot k(\psi) \\nabla \psi - \\frac{\partial k(\psi)}{\partial z} = 0 + \quad \psi \in \Omega + +However, it can be shown that this does not conserve mass in the discrete formulation. + + + +Richards +======== + +.. automodule:: simpegFLOW.Richards + :show-inheritance: + :members: + :undoc-members: + :inherited-members: diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 00000000..86aacce4 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,244 @@ +# -*- coding: utf-8 -*- +# +# SimPEG documentation build configuration file, created by +# sphinx-quickstart on Fri Aug 30 18:42:44 2013. +# +# 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. + +import sys, os + +# 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. +#sys.path.insert(0, os.path.abspath('.')) + +sys.path.append('../') + +# -- 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.todo', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', 'sphinx.ext.autodoc', 'matplotlib.sphinxext.plot_directive'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +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'SimPEG' +copyright = u'2013, SimPEG Developers' + +# 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 = '0.0.1' +# The full version, including alpha/beta/rc tags. +release = '0.0.1' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#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. +exclude_patterns = ['_build'] + +# 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 = [] + + +# -- 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 = 'default' + +# 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. If None, it defaults to +# " v documentation". +#html_title = None + +# 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 (within the static path) to use as 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'] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# 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 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 + +# Output file base name for HTML help builder. +htmlhelp_basename = 'SimPEGdoc' + + +# -- 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': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, author, documentclass [howto/manual]). +latex_documents = [ + ('index', 'SimPEG.tex', u'SimPEG Documentation', + u'Rowan Cockett', '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 = [] + +# 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 = [ + ('index', 'simpeg', u'SimPEG Documentation', + [u'Rowan Cockett'], 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 = [ + ('index', 'SimPEG', u'SimPEG Documentation', + u'Rowan Cockett', 'SimPEG', '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' diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 00000000..b2966f24 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,45 @@ +.. image:: simpeg-logo.png + :width: 300 px + :alt: SimPEG + :align: center + +SimPEG (Simulation and Parameter Estimation in Geophysics) is a python +package for simulation and gradient based parameter estimation in the +context of geoscience applications. + +simpegFLOW uses SimPEG as the framework for the forward and inverse +problems in groundwater flow. + + +Richards +******** + +.. toctree:: + :maxdepth: 2 + + api_Richards + + +Testing SimPEG +============== + +* Master Branch + .. image:: https://travis-ci.org/simpeg/simpegflow.png?branch=master + :target: https://travis-ci.org/simpeg/simpegflow + :alt: Master Branch + :align: center + +* Develop Branch + .. image:: https://travis-ci.org/simpeg/simpegflow.png?branch=develop + :target: https://travis-ci.org/simpeg/simpegflow + :alt: Develop Branch + :align: center + + +Project Index & Search +====================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 00000000..2ac3df69 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,190 @@ +@ECHO OFF + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set BUILDDIR=_build +set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . +set I18NSPHINXOPTS=%SPHINXOPTS% . +if NOT "%PAPER%" == "" ( + set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% + set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% +) + +if "%1" == "" goto help + +if "%1" == "help" ( + :help + echo.Please use `make ^` where ^ 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. devhelp to make HTML files and a Devhelp project + echo. epub to make an epub + echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter + echo. text to make text files + echo. man to make manual pages + echo. texinfo to make Texinfo files + echo. gettext to make PO message catalogs + echo. changes to make an overview over all changed/added/deprecated items + echo. linkcheck to check all external links for integrity + echo. doctest to run all doctests embedded in the documentation if enabled + goto end +) + +if "%1" == "clean" ( + for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i + del /q /s %BUILDDIR%\* + goto end +) + +if "%1" == "html" ( + %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/html. + goto end +) + +if "%1" == "dirhtml" ( + %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. + goto end +) + +if "%1" == "singlehtml" ( + %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. + goto end +) + +if "%1" == "pickle" ( + %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the pickle files. + goto end +) + +if "%1" == "json" ( + %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the JSON files. + goto end +) + +if "%1" == "htmlhelp" ( + %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run HTML Help Workshop with the ^ +.hhp project file in %BUILDDIR%/htmlhelp. + goto end +) + +if "%1" == "qthelp" ( + %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run "qcollectiongenerator" with the ^ +.qhcp project file in %BUILDDIR%/qthelp, like this: + echo.^> qcollectiongenerator %BUILDDIR%\qthelp\SimPEG.qhcp + echo.To view the help file: + echo.^> assistant -collectionFile %BUILDDIR%\qthelp\SimPEG.ghc + goto end +) + +if "%1" == "devhelp" ( + %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. + goto end +) + +if "%1" == "epub" ( + %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The epub file is in %BUILDDIR%/epub. + goto end +) + +if "%1" == "latex" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "text" ( + %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The text files are in %BUILDDIR%/text. + goto end +) + +if "%1" == "man" ( + %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The manual pages are in %BUILDDIR%/man. + goto end +) + +if "%1" == "texinfo" ( + %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. + goto end +) + +if "%1" == "gettext" ( + %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The message catalogs are in %BUILDDIR%/locale. + goto end +) + +if "%1" == "changes" ( + %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes + if errorlevel 1 exit /b 1 + echo. + echo.The overview file is in %BUILDDIR%/changes. + goto end +) + +if "%1" == "linkcheck" ( + %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck + if errorlevel 1 exit /b 1 + echo. + echo.Link check complete; look for any errors in the above output ^ +or in %BUILDDIR%/linkcheck/output.txt. + goto end +) + +if "%1" == "doctest" ( + %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest + if errorlevel 1 exit /b 1 + echo. + echo.Testing of doctests in the sources finished, look at the ^ +results in %BUILDDIR%/doctest/output.txt. + goto end +) + +:end diff --git a/docs/simpeg-logo.png b/docs/simpeg-logo.png new file mode 100644 index 00000000..a0ec740f Binary files /dev/null and b/docs/simpeg-logo.png differ diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 00000000..6b7df820 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,4 @@ +numpy +scipy +ipython +matplotlib diff --git a/setup.py b/setup.py new file mode 100644 index 00000000..95fb3b72 --- /dev/null +++ b/setup.py @@ -0,0 +1,8 @@ +import os +try: + import SimPEG +except ImportError, e: + os.system('git clone https://github.com/simpeg/simpeg.git') + os.system('mv simpeg/SimPEG temp') + os.system('rm -rf simpeg') + os.system('mv temp SimPEG') diff --git a/simpegFLOW/Richards/__init__.py b/simpegFLOW/Richards/__init__.py new file mode 100644 index 00000000..85657732 --- /dev/null +++ b/simpegFLOW/Richards/__init__.py @@ -0,0 +1 @@ +#blank! diff --git a/simpegFLOW/Tests/__init__.py b/simpegFLOW/Tests/__init__.py new file mode 100644 index 00000000..420388ef --- /dev/null +++ b/simpegFLOW/Tests/__init__.py @@ -0,0 +1,12 @@ +import os +import glob +import unittest + +if __name__ == '__main__': + test_file_strings = glob.glob('test_*.py') + module_strings = [str[0:len(str)-3] for str in test_file_strings] + suites = [unittest.defaultTestLoader.loadTestsFromName(str) for str + in module_strings] + testSuite = unittest.TestSuite(suites) + + unittest.TextTestRunner(verbosity=2).run(testSuite) diff --git a/simpegFLOW/Tests/test_Richards.py b/simpegFLOW/Tests/test_Richards.py new file mode 100644 index 00000000..72c1cbf5 --- /dev/null +++ b/simpegFLOW/Tests/test_Richards.py @@ -0,0 +1,56 @@ +import unittest +from SimPEG import * +from SimPEG.Tests.TestUtils import OrderTest, checkDerivative +from scipy.sparse.linalg import dsolve +import simpegFLOW.Richards + +TOL = 1E-8 + +class EmpiricalRelations(unittest.TestCase): + + + def test_BaseHaverkamp_Theta(self): + mesh = Mesh.TensorMesh([50]) + hav = Richards.BaseHaverkamp_theta(mesh) + m = np.random.randn(50) + def wrapper(u): + return hav.transform(u, m), hav.transformDerivU(u, m) + passed = checkDerivative(wrapper, np.random.randn(50), plotIt=False) + self.assertTrue(passed,True) + + + def test_BaseHaverkamp_k(self): + mesh = Mesh.TensorMesh([50]) + hav = Richards.BaseHaverkamp_k(mesh) + m = np.random.randn(50) + def wrapper(u): + return hav.transform(u, m), hav.transformDerivU(u, m) + passed = checkDerivative(wrapper, np.random.randn(50), plotIt=False) + self.assertTrue(passed,True) + + hav = Richards.BaseHaverkamp_k(mesh) + u = np.random.randn(50) + def wrapper(m): + return hav.transform(u, m), hav.transformDerivM(u, m) + passed = checkDerivative(wrapper, np.random.randn(50), plotIt=False) + self.assertTrue(passed,True) + + # def test_Haverkamp_hydraulicConductivity(self): + # print 'Haverkamp_hydraulicConductivity' + # hav = Richards.Haverkamp() + # def wrapper(x): + # return hav.hydraulicConductivity(x), hav.hydraulicConductivityDeriv(x) + # passed = checkDerivative(wrapper, np.random.randn(50), plotIt=False) + # self.assertTrue(passed,True) + + # def test_Haverkamp_hydraulicConductivity_FullKs(self): + # print 'Haverkamp_hydraulicConductivity_FullKs' + # n = 50 + # hav = Richards.Haverkamp(Ks=np.random.rand(n)) + # def wrapper(x): + # return hav.hydraulicConductivity(x), hav.hydraulicConductivityDeriv(x) + # passed = checkDerivative(wrapper, np.random.randn(n), plotIt=False) + # self.assertTrue(passed,True) + +if __name__ == '__main__': + unittest.main() diff --git a/simpegFLOW/__init__.py b/simpegFLOW/__init__.py new file mode 100644 index 00000000..622d2f2f --- /dev/null +++ b/simpegFLOW/__init__.py @@ -0,0 +1 @@ +import Richards