mirror of
https://github.com/wassname/simpeg.git
synced 2026-06-30 10:33:49 +08:00
Merge branch 'DCproblem' of https://github.com/simpeg/simpeg
This commit is contained in:
rowanc1
@@ -34,3 +34,7 @@ nosetests.xml
|
||||
.mr.developer.cfg
|
||||
.project
|
||||
.pydevproject
|
||||
|
||||
*.sublime-project
|
||||
*.sublime-workspace
|
||||
docs/_build/
|
||||
|
||||
+14
@@ -0,0 +1,14 @@
|
||||
language: python
|
||||
python:
|
||||
- "2.7"
|
||||
virtualenv:
|
||||
system_site_packages: true
|
||||
before_install:
|
||||
- sudo apt-get install -qq python-numpy python-scipy python-matplotlib
|
||||
- python SimPEG/setup.py
|
||||
- git clone https://github.com/simpeg/simpeg.git
|
||||
- ls
|
||||
# command to install dependencies
|
||||
install: "pip install -r requirements.txt --use-mirrors"
|
||||
# command to run tests
|
||||
script: nosetests -v
|
||||
@@ -1,6 +1,6 @@
|
||||
The MIT License (MIT)
|
||||
|
||||
Copyright (c) 2014 SimPEG
|
||||
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
|
||||
|
||||
+153
@@ -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 <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 " 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."
|
||||
@@ -0,0 +1,11 @@
|
||||
.. _api_DC:
|
||||
|
||||
|
||||
DC
|
||||
**
|
||||
|
||||
.. automodule:: simpegDC.DC
|
||||
:show-inheritance:
|
||||
:members:
|
||||
:undoc-members:
|
||||
:inherited-members:
|
||||
+244
@@ -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
|
||||
# "<project> v<release> 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 <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
|
||||
|
||||
# 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'
|
||||
@@ -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.
|
||||
|
||||
SimPEG-DC uses SimPEG as the framework for the forward and inverse
|
||||
direct current resistivity geophysical problem.
|
||||
|
||||
|
||||
DC
|
||||
==
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 2
|
||||
|
||||
api_DC
|
||||
|
||||
|
||||
Testing SimPEG
|
||||
==============
|
||||
|
||||
* Master Branch
|
||||
.. image:: https://travis-ci.org/simpeg/simpeg.png?branch=master
|
||||
:target: https://travis-ci.org/simpeg/simpeg
|
||||
:alt: Master Branch
|
||||
:align: center
|
||||
|
||||
* Develop Branch
|
||||
.. image:: https://travis-ci.org/simpeg/simpeg.png?branch=develop
|
||||
:target: https://travis-ci.org/simpeg/simpeg
|
||||
:alt: Develop Branch
|
||||
:align: center
|
||||
|
||||
|
||||
Project Index & Search
|
||||
======================
|
||||
|
||||
* :ref:`genindex`
|
||||
* :ref:`modindex`
|
||||
* :ref:`search`
|
||||
|
||||
+190
@@ -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 ^<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. 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
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 23 KiB |
@@ -0,0 +1,4 @@
|
||||
numpy
|
||||
scipy
|
||||
ipython
|
||||
matplotlib
|
||||
+248
@@ -0,0 +1,248 @@
|
||||
from SimPEG import *
|
||||
|
||||
|
||||
class DCData(Data.BaseData):
|
||||
"""
|
||||
**DCData**
|
||||
|
||||
Geophysical DC resistivity data.
|
||||
|
||||
"""
|
||||
|
||||
P = None #: projection
|
||||
|
||||
def __init__(self, **kwargs):
|
||||
Data.BaseData.__init__(self, **kwargs)
|
||||
Utils.setKwargs(self, **kwargs)
|
||||
|
||||
def reshapeFields(self, u):
|
||||
if len(u.shape) == 1:
|
||||
u = u.reshape([-1, self.RHS.shape[1]], order='F')
|
||||
return u
|
||||
|
||||
def projectField(self, u):
|
||||
"""
|
||||
Predicted data.
|
||||
|
||||
.. math::
|
||||
d_\\text{pred} = Pu(m)
|
||||
"""
|
||||
u = self.reshapeFields(u)
|
||||
return Utils.mkvc(self.P*u)
|
||||
|
||||
|
||||
|
||||
class DCProblem(Problem.BaseProblem):
|
||||
"""
|
||||
**DCProblem**
|
||||
|
||||
Geophysical DC resistivity problem.
|
||||
|
||||
"""
|
||||
|
||||
dataPair = DCData
|
||||
|
||||
def __init__(self, mesh, model, **kwargs):
|
||||
Problem.BaseProblem.__init__(self, mesh, model)
|
||||
self.mesh.setCellGradBC('neumann')
|
||||
Utils.setKwargs(self, **kwargs)
|
||||
|
||||
|
||||
def createMatrix(self, m):
|
||||
"""
|
||||
Makes the matrix A(m) for the DC resistivity problem.
|
||||
|
||||
:param numpy.array m: model
|
||||
:rtype: scipy.csc_matrix
|
||||
:return: A(m)
|
||||
|
||||
.. math::
|
||||
c(m,u) = A(m)u - q = G\\text{sdiag}(M(mT(m)))Du - q = 0
|
||||
|
||||
Where M() is the mass matrix and mT is the model transform.
|
||||
"""
|
||||
D = self.mesh.faceDiv
|
||||
G = self.mesh.cellGrad
|
||||
sigma = self.model.transform(m)
|
||||
Msig = self.mesh.getFaceMass(sigma)
|
||||
A = D*Msig*G
|
||||
return A.tocsc()
|
||||
|
||||
def field(self, m):
|
||||
A = self.createMatrix(m)
|
||||
solve = Solver(A)
|
||||
phi = solve.solve(self.data.RHS)
|
||||
return Utils.mkvc(phi)
|
||||
|
||||
def J(self, m, v, u=None):
|
||||
"""
|
||||
:param numpy.array m: model
|
||||
:param numpy.array v: vector to multiply
|
||||
:param numpy.array u: fields
|
||||
:rtype: numpy.array
|
||||
:return: Jv
|
||||
|
||||
.. math::
|
||||
c(m,u) = A(m)u - q = G\\text{sdiag}(M(mT(m)))Du - q = 0
|
||||
|
||||
\\nabla_u (A(m)u - q) = A(m)
|
||||
|
||||
\\nabla_m (A(m)u - q) = G\\text{sdiag}(Du)\\nabla_m(M(mT(m)))
|
||||
|
||||
Where M() is the mass matrix and mT is the model transform.
|
||||
|
||||
.. math::
|
||||
J = - P \left( \\nabla_u c(m, u) \\right)^{-1} \\nabla_m c(m, u)
|
||||
|
||||
J(v) = - P ( A(m)^{-1} ( G\\text{sdiag}(Du)\\nabla_m(M(mT(m))) v ) )
|
||||
"""
|
||||
if u is None:
|
||||
u = self.field(m)
|
||||
|
||||
u = self.data.reshapeFields(u)
|
||||
|
||||
P = self.data.P
|
||||
D = self.mesh.faceDiv
|
||||
G = self.mesh.cellGrad
|
||||
A = self.createMatrix(m)
|
||||
Av_dm = self.mesh.getFaceMassDeriv()
|
||||
mT_dm = self.model.transformDeriv(m)
|
||||
|
||||
dCdu = A
|
||||
|
||||
dCdm = np.empty_like(u)
|
||||
for i, ui in enumerate(u.T): # loop over each column
|
||||
dCdm[:, i] = D * ( Utils.sdiag( G * ui ) * ( Av_dm * ( mT_dm * v ) ) )
|
||||
|
||||
solve = Solver(dCdu)
|
||||
Jv = - P * solve.solve(dCdm)
|
||||
return Utils.mkvc(Jv)
|
||||
|
||||
def Jt(self, m, v, u=None):
|
||||
"""Takes data, turns it into a model..ish"""
|
||||
|
||||
if u is None:
|
||||
u = self.field(m)
|
||||
|
||||
u = self.data.reshapeFields(u)
|
||||
v = self.data.reshapeFields(v)
|
||||
|
||||
P = self.data.P
|
||||
D = self.mesh.faceDiv
|
||||
G = self.mesh.cellGrad
|
||||
A = self.createMatrix(m)
|
||||
Av_dm = self.mesh.getFaceMassDeriv()
|
||||
mT_dm = self.model.transformDeriv(m)
|
||||
|
||||
dCdu = A.T
|
||||
solve = Solver(dCdu)
|
||||
|
||||
w = solve.solve(P.T*v)
|
||||
|
||||
Jtv = 0
|
||||
for i, ui in enumerate(u.T): # loop over each column
|
||||
Jtv += Utils.sdiag( G * ui ) * ( D.T * w[:,i] )
|
||||
|
||||
Jtv = - mT_dm.T * ( Av_dm.T * Jtv )
|
||||
return Jtv
|
||||
|
||||
|
||||
|
||||
def genTxRxmat(nelec, spacelec, surfloc, elecini, mesh):
|
||||
""" Generate projection matrix (Q) and """
|
||||
elecend = 0.5+spacelec*(nelec-1)
|
||||
elecLocR = np.linspace(elecini, elecend, nelec)
|
||||
elecLocT = elecLocR+1
|
||||
nrx = nelec-1
|
||||
ntx = nelec-1
|
||||
q = np.zeros((mesh.nC, ntx))
|
||||
Q = np.zeros((mesh.nC, nrx))
|
||||
|
||||
for i in range(nrx):
|
||||
|
||||
rxind1 = np.argwhere((mesh.gridCC[:,0]==surfloc) & (mesh.gridCC[:,1]==elecLocR[i]))
|
||||
rxind2 = np.argwhere((mesh.gridCC[:,0]==surfloc) & (mesh.gridCC[:,1]==elecLocR[i+1]))
|
||||
|
||||
txind1 = np.argwhere((mesh.gridCC[:,0]==surfloc) & (mesh.gridCC[:,1]==elecLocT[i]))
|
||||
txind2 = np.argwhere((mesh.gridCC[:,0]==surfloc) & (mesh.gridCC[:,1]==elecLocT[i+1]))
|
||||
|
||||
q[txind1,i] = 1
|
||||
q[txind2,i] = -1
|
||||
Q[rxind1,i] = 1
|
||||
Q[rxind2,i] = -1
|
||||
|
||||
Q = sp.csr_matrix(Q)
|
||||
rxmidLoc = (elecLocR[0:nelec-1]+elecLocR[1:nelec])*0.5
|
||||
return q, Q, rxmidLoc
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
import matplotlib.pyplot as plt
|
||||
|
||||
# Create the mesh
|
||||
h1 = np.ones(20)
|
||||
h2 = np.ones(100)
|
||||
M = Mesh.TensorMesh([h1,h2])
|
||||
|
||||
# Create some parameters for the model
|
||||
sig1 = np.log(1)
|
||||
sig2 = np.log(0.01)
|
||||
|
||||
# Create a synthetic model from a block in a half-space
|
||||
p0 = [5, 10]
|
||||
p1 = [15, 50]
|
||||
condVals = [sig1, sig2]
|
||||
mSynth = Utils.ModelBuilder.defineBlockConductivity(M.gridCC,p0,p1,condVals)
|
||||
plt.colorbar(M.plotImage(mSynth))
|
||||
# plt.show()
|
||||
|
||||
# Set up the projection
|
||||
nelec = 50
|
||||
spacelec = 2
|
||||
surfloc = 0.5
|
||||
elecini = 0.5
|
||||
elecend = 0.5+spacelec*(nelec-1)
|
||||
elecLocR = np.linspace(elecini, elecend, nelec)
|
||||
rxmidLoc = (elecLocR[0:nelec-1]+elecLocR[1:nelec])*0.5
|
||||
q, Q, rxmidloc = genTxRxmat(nelec, spacelec, surfloc, elecini, M)
|
||||
P = Q.T
|
||||
|
||||
model = Model.LogModel(M)
|
||||
prob = DCProblem(M, model)
|
||||
|
||||
# Create some data
|
||||
data = prob.createSyntheticData(mSynth, std=0.05, P=P, RHS=q)
|
||||
|
||||
u = prob.field(mSynth)
|
||||
u = data.reshapeFields(u)
|
||||
M.plotImage(u[:,10])
|
||||
plt.show()
|
||||
|
||||
# Now set up the prob to do some minimization
|
||||
# prob.dobs = dobs
|
||||
# prob.std = dobs*0 + 0.05
|
||||
m0 = M.gridCC[:,0]*0+sig2
|
||||
|
||||
reg = Regularization.Tikhonov(model)
|
||||
objFunc = ObjFunction.BaseObjFunction(data, reg)
|
||||
opt = Optimization.InexactGaussNewton(maxIterLS=20, maxIter=3, tolF=1e-6, tolX=1e-6, tolG=1e-6, maxIterCG=6)
|
||||
inv = Inversion.BaseInversion(objFunc, opt)
|
||||
|
||||
# Check Derivative
|
||||
derChk = lambda m: [objFunc.dataObj(m), objFunc.dataObjDeriv(m)]
|
||||
# Tests.checkDerivative(derChk, mSynth)
|
||||
|
||||
print objFunc.dataObj(m0)
|
||||
print objFunc.dataObj(mSynth)
|
||||
|
||||
m = inv.run(m0)
|
||||
|
||||
plt.colorbar(M.plotImage(m))
|
||||
print m
|
||||
plt.show()
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -0,0 +1,14 @@
|
||||
from TestUtils import checkDerivative, Rosenbrock, OrderTest, getQuadratic
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
import os
|
||||
import glob
|
||||
import unittest
|
||||
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)
|
||||
@@ -0,0 +1,79 @@
|
||||
from SimPEG import *
|
||||
import unittest
|
||||
import simpegDC
|
||||
|
||||
|
||||
class DCProblemTests(unittest.TestCase):
|
||||
|
||||
def setUp(self):
|
||||
# Create the mesh
|
||||
h1 = np.ones(20)
|
||||
h2 = np.ones(20)
|
||||
mesh = Mesh.TensorMesh([h1,h2])
|
||||
|
||||
# Create some parameters for the model
|
||||
sig1 = 1
|
||||
sig2 = 0.01
|
||||
|
||||
# Create a synthetic model from a block in a half-space
|
||||
p0 = [2, 2]
|
||||
p1 = [5, 5]
|
||||
condVals = [sig1, sig2]
|
||||
mSynth = Utils.ModelBuilder.defineBlockConductivity(p0,p1,mesh.gridCC,condVals)
|
||||
|
||||
# Set up the projection
|
||||
nelec = 10
|
||||
spacelec = 2
|
||||
surfloc = 0.5
|
||||
elecini = 0.5
|
||||
elecend = 0.5+spacelec*(nelec-1)
|
||||
elecLocR = np.linspace(elecini, elecend, nelec)
|
||||
rxmidLoc = (elecLocR[0:nelec-1]+elecLocR[1:nelec])*0.5
|
||||
q, Q, rxmidloc = genTxRxmat(nelec, spacelec, surfloc, elecini, mesh)
|
||||
P = Q.T
|
||||
|
||||
# Create some data
|
||||
|
||||
problem = DCProblem(mesh)
|
||||
problem.P = P
|
||||
problem.RHS = q
|
||||
data = problem.createSyntheticData(mSynth, std=0.05)
|
||||
|
||||
# Now set up the problem to do some minimization
|
||||
opt = inverse.InexactGaussNewton(maxIterLS=20, maxIter=10, tolF=1e-6, tolX=1e-6, tolG=1e-6, maxIterCG=6)
|
||||
reg = inverse.Regularization(mesh)
|
||||
inv = inverse.Inversion(problem, reg, opt, data, beta0=1e4)
|
||||
|
||||
self.inv = inv
|
||||
self.reg = reg
|
||||
self.p = problem
|
||||
self.mesh = mesh
|
||||
self.m0 = mSynth
|
||||
self.data = data
|
||||
|
||||
def test_misfit(self):
|
||||
derChk = lambda m: [self.p.dpred(m), lambda mx: self.p.J(self.m0, mx)]
|
||||
passed = checkDerivative(derChk, self.m0, plotIt=False)
|
||||
self.assertTrue(passed)
|
||||
|
||||
def test_adjoint(self):
|
||||
# Adjoint Test
|
||||
u = np.random.rand(self.mesh.nC*self.p.RHS.shape[1])
|
||||
v = np.random.rand(self.mesh.nC)
|
||||
w = np.random.rand(self.data.dobs.shape[0])
|
||||
wtJv = w.dot(self.p.J(self.m0, v, u=u))
|
||||
vtJtw = v.dot(self.p.Jt(self.m0, w, u=u))
|
||||
passed = (wtJv - vtJtw) < 1e-10
|
||||
self.assertTrue(passed)
|
||||
|
||||
def test_dataObj(self):
|
||||
derChk = lambda m: [self.inv.dataObj(m), self.inv.dataObjDeriv(m)]
|
||||
checkDerivative(derChk, self.m0, plotIt=False)
|
||||
|
||||
def test_modelObj(self):
|
||||
derChk = lambda m: [self.reg.modelObj(m), self.reg.modelObjDeriv(m)]
|
||||
checkDerivative(derChk, self.m0, plotIt=False)
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
unittest.main()
|
||||
@@ -0,0 +1 @@
|
||||
from DC import *
|
||||
Reference in New Issue
Block a user