From ef48fd5f87544d250b3e3106054440a59700bbf3 Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Tue, 24 Mar 2020 13:34:03 +0000 Subject: [PATCH 01/31] Initial gh-pages setup, with skeleton layout and local build instructions --- .gitignore | 41 +++++ README.md | 24 +++ _static/theme_overrides.css | 13 ++ conf.py | 320 ++++++++++++++++++++++++++++++++++++ contents.rst | 9 + index.rst | 6 + make_www_local.bat | 8 + user/intro.rst | 26 +++ 8 files changed, 447 insertions(+) create mode 100644 .gitignore create mode 100644 _static/theme_overrides.css create mode 100644 conf.py create mode 100644 contents.rst create mode 100644 index.rst create mode 100644 make_www_local.bat create mode 100644 user/intro.rst diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..05d9664 --- /dev/null +++ b/.gitignore @@ -0,0 +1,41 @@ +# sphinx build folder +_build + +# Compiled source # +################### +*.com +*.class +*.dll +*.exe +*.o +*.so + +# Packages # +############ +# it's better to unpack these files and commit the raw source +# git has its own built in compression methods +*.7z +*.dmg +*.gz +*.iso +*.jar +*.rar +*.tar +*.zip + +# Logs and databases # +###################### +*.log +*.sql +*.sqlite + +# OS generated files # +###################### +.DS_Store? +ehthumbs.db +Icon? +Thumbs.db + +# Editor backup files # +####################### +*~ diff --git a/README.md b/README.md index 7775c9e..5dcc648 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,26 @@ # WecOptTool Documentation +## Compile Instructions + +### Setup Sphinx (One Time Only) + +Install [Anaconda Python](https://www.anaconda.com/distribution/) + +Create the Sphinx environment + +``` +> conda create -n _sphinx pip sphinx sphinx_rtd_theme +``` + +### Build Locally (Windows) + +``` +> cd path/to/WecOptTool +> make_www_local +``` + +Docs are built in the `_build` directory. + +## License + +[CC BY-NC-SA 4.0](https://creativecommons.org/licenses/by-nc-sa/4.0/) diff --git a/_static/theme_overrides.css b/_static/theme_overrides.css new file mode 100644 index 0000000..63ee6cc --- /dev/null +++ b/_static/theme_overrides.css @@ -0,0 +1,13 @@ +/* override table width restrictions */ +@media screen and (min-width: 767px) { + + .wy-table-responsive table td { + /* !important prevents the common CSS stylesheets from overriding + this as on RTD they are loaded after this stylesheet */ + white-space: normal !important; + } + + .wy-table-responsive { + overflow: visible !important; + } +} diff --git a/conf.py b/conf.py new file mode 100644 index 0000000..ceb332a --- /dev/null +++ b/conf.py @@ -0,0 +1,320 @@ +# -*- coding: utf-8 -*- +# +# WecOptTool documentation build configuration file, created by +# sphinx-quickstart on Wed Mar 09 15:08:01 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. + +import os +import sys +import datetime + +now = datetime.datetime.now() + +# 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('.')) + +# -- 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.mathjax', + 'sphinx.ext.napoleon' +] + +# Figure numbering +numfig = True + +# Napoleon settings +napoleon_google_docstring = True +napoleon_numpy_docstring = True +napoleon_include_private_with_doc = False +napoleon_include_special_with_doc = True +napoleon_use_admonition_for_examples = False +napoleon_use_admonition_for_notes = False +napoleon_use_admonition_for_references = False +napoleon_use_ivar = False +napoleon_use_param = True +napoleon_use_rtype = True + +# 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'WecOptTool' +copyright = u'2020-{} The WecOptTool Developers'.format(now.year) +author = u'unknown' + +# 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'0.1' +# The full version, including alpha/beta/rc tags. +release = u'0.1.0' + +# 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. +exclude_patterns = ['_build', + 'contents.rst'] + +# 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 = "sphinx_rtd_theme" + +# 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'] + +html_context = { + 'css_files': [ + '_static/theme_overrides.css', # override wide tables in RTD theme + ], + } + +# 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 '', 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 + +# 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' +#html_search_language = 'en' + +# A dictionary with options for the search language support, empty by default. +# Now only 'ja' uses this config value +#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 = 'WecOptTool Documentation' + +# -- Options for LaTeX output --------------------------------------------- + +ADDITIONAL_PREAMBLE = """ +\setcounter{tocdepth}{4} +\DeclareUnicodeCharacter{3003}{---"---} +""" + +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': ADDITIONAL_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 = [ + ('index', + 'wecopttool_docs.tex', + u'WecOptTool Documentation', + u'', + '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_toplevel_sectioning = "part" + +# 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 = [ + (master_doc, 'wecopttool-doc', u'WecOptTool 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, 'wecopttool-doc', u'WecOptTool Documentation', + author, 'wecopttool-doc', '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 diff --git a/contents.rst b/contents.rst new file mode 100644 index 0000000..8242c17 --- /dev/null +++ b/contents.rst @@ -0,0 +1,9 @@ +Contents +======== + +.. toctree:: + :maxdepth: 1 + :numbered: + :caption: User Guide + + user/intro diff --git a/index.rst b/index.rst new file mode 100644 index 0000000..92069bf --- /dev/null +++ b/index.rst @@ -0,0 +1,6 @@ +########## +WecOptTool +########## + +.. include:: contents.rst + diff --git a/make_www_local.bat b/make_www_local.bat new file mode 100644 index 0000000..e1bdf17 --- /dev/null +++ b/make_www_local.bat @@ -0,0 +1,8 @@ +@ECHO OFF + +REM Assumes sphinx, sphinx_rtd_theme are installed in the _sphinx conda +REM environment + +CALL activate _sphinx +sphinx-build -b html . _build +conda deactivate diff --git a/user/intro.rst b/user/intro.rst new file mode 100644 index 0000000..af63468 --- /dev/null +++ b/user/intro.rst @@ -0,0 +1,26 @@ +.. raw:: latex + + \part{User Guide} + +.. _introduction: + +************ +Introduction +************ + +An Overview of WecOptTool +========================= + +It's great + + +WecOptTool License +================== + + Copyright |copy| 2020-|year| The WecOptTool Developers + + Some license text here + + +.. |copy| unicode:: U+000A9 .. COPYRIGHT SIGN +.. |year| date:: %Y From b44d3e6afad887cef08d83c134b5549a112d0cff Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Wed, 25 Mar 2020 13:11:41 +0000 Subject: [PATCH 02/31] Update gitignore for leftovers from master branch --- .gitignore | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/.gitignore b/.gitignore index 05d9664..955c837 100644 --- a/.gitignore +++ b/.gitignore @@ -39,3 +39,12 @@ Thumbs.db # Editor backup files # ####################### *~ + +# NEMOH # +######### +~nemoh_runs/ + +# Tests # +######### +test_results/ +test_results.pdf From 38fe5fab6d986482b20e017099b28f3ce960b721 Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Wed, 25 Mar 2020 16:22:38 +0000 Subject: [PATCH 03/31] Add robust method to get source code and auto documentation --- README.md | 6 +++++- conf.py | 5 +++++ contents.rst | 1 + make_www_local.bat | 17 +++++++++++++++-- user/api.rst | 22 ++++++++++++++++++++++ 5 files changed, 48 insertions(+), 3 deletions(-) create mode 100644 user/api.rst diff --git a/README.md b/README.md index 5dcc648..57b9c7f 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,11 @@ Install [Anaconda Python](https://www.anaconda.com/distribution/) Create the Sphinx environment ``` -> conda create -n _sphinx pip sphinx sphinx_rtd_theme +> conda create -n _sphinx pip sphinx sphinx_rtd_theme colorama future +> activate _sphinx +(_sphinx) > pip install sphinxcontrib-matlabdomain +(_sphinx) > conda deactivate _sphinx +> ``` ### Build Locally (Windows) diff --git a/conf.py b/conf.py index ceb332a..9591871 100644 --- a/conf.py +++ b/conf.py @@ -34,6 +34,7 @@ extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.mathjax', + 'sphinxcontrib.matlab', 'sphinx.ext.napoleon' ] @@ -52,6 +53,10 @@ napoleon_use_param = True napoleon_use_rtype = True +# sphinxcontrib.matlab settings +matlab_src_dir = os.path.abspath("git_src/toolbox") +matlab_keep_package_prefix = False + # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] diff --git a/contents.rst b/contents.rst index 8242c17..80ff12e 100644 --- a/contents.rst +++ b/contents.rst @@ -7,3 +7,4 @@ Contents :caption: User Guide user/intro + user/api diff --git a/make_www_local.bat b/make_www_local.bat index e1bdf17..69ae239 100644 --- a/make_www_local.bat +++ b/make_www_local.bat @@ -1,7 +1,20 @@ @ECHO OFF +setlocal ENABLEDELAYEDEXPANSION -REM Assumes sphinx, sphinx_rtd_theme are installed in the _sphinx conda -REM environment +REM Assumes git is installed and that sphinx, sphinx_rtd_theme are installed in +REM the _sphinx conda environment + +SET "GETGIT=true" + +IF EXIST git_src ( + git --work-tree=git_src --git-dir=git_src/.git pull 2>&1 > NUL | findstr /C:"fatal" + IF !ERRORLEVEL! GTR 0 SET "GETGIT=" +) + +IF DEFINED GETGIT ( + RMDIR /Q /S git_src + git clone https://github.com/SNL-WaterPower/WecOptTool.git git_src +) CALL activate _sphinx sphinx-build -b html . _build diff --git a/user/api.rst b/user/api.rst new file mode 100644 index 0000000..f7ca1bf --- /dev/null +++ b/user/api.rst @@ -0,0 +1,22 @@ +*** +API +*** + +WecOptTool +========== + +.. mat:automodule:: +WecOptTool + :members: + +WecOptTool.geom +--------------- + +.. mat:automodule:: +WecOptTool.+geom + :members: + + +WecOptTool.control +------------------ + +.. mat:automodule:: +WecOptTool.+control + :members: From 28c92adf0344299a9596d5152aade4e961437237 Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Wed, 25 Mar 2020 17:14:20 +0000 Subject: [PATCH 04/31] Update front matter --- conf.py | 3 ++- contents.rst | 2 +- index.rst | 7 ++++++- user/intro.rst | 26 -------------------------- user/license.rst | 10 ++++++++++ 5 files changed, 19 insertions(+), 29 deletions(-) delete mode 100644 user/intro.rst create mode 100644 user/license.rst diff --git a/conf.py b/conf.py index 9591871..69356ca 100644 --- a/conf.py +++ b/conf.py @@ -73,7 +73,8 @@ # General information about the project. project = u'WecOptTool' -copyright = u'2020-{} The WecOptTool Developers'.format(now.year) +#copyright = u'2020-{} The WecOptTool Developers'.format(now.year) +copyright = u'2020 The WecOptTool Developers'.format(now.year) author = u'unknown' # The version info for the project you're documenting, acts as replacement for diff --git a/contents.rst b/contents.rst index 80ff12e..3a0e166 100644 --- a/contents.rst +++ b/contents.rst @@ -6,5 +6,5 @@ Contents :numbered: :caption: User Guide - user/intro user/api + user/license diff --git a/index.rst b/index.rst index 92069bf..1f5a426 100644 --- a/index.rst +++ b/index.rst @@ -2,5 +2,10 @@ WecOptTool ########## -.. include:: contents.rst +The WEC Design Optimization Toolbox (WecOptTool) allows users to perform wave +energy converter (WEC) device design optimization studies with constrained +optimal control. + +WecOptTool is developed by Sandia National Laboratories +.. include:: contents.rst diff --git a/user/intro.rst b/user/intro.rst deleted file mode 100644 index af63468..0000000 --- a/user/intro.rst +++ /dev/null @@ -1,26 +0,0 @@ -.. raw:: latex - - \part{User Guide} - -.. _introduction: - -************ -Introduction -************ - -An Overview of WecOptTool -========================= - -It's great - - -WecOptTool License -================== - - Copyright |copy| 2020-|year| The WecOptTool Developers - - Some license text here - - -.. |copy| unicode:: U+000A9 .. COPYRIGHT SIGN -.. |year| date:: %Y diff --git a/user/license.rst b/user/license.rst new file mode 100644 index 0000000..d196b4e --- /dev/null +++ b/user/license.rst @@ -0,0 +1,10 @@ +******* +License +******* + + Copyright |copy| 2020 The WecOptTool Developers + + Some license text here + +.. |copy| unicode:: U+000A9 .. COPYRIGHT SIGN +.. |year| date:: %Y From 6be94eb8cca7b104d4525de61811d7e9725435f7 Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Wed, 25 Mar 2020 17:14:38 +0000 Subject: [PATCH 05/31] Add installation guide --- contents.rst | 1 + user/install.rst | 148 +++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 149 insertions(+) create mode 100644 user/install.rst diff --git a/contents.rst b/contents.rst index 3a0e166..c3aabee 100644 --- a/contents.rst +++ b/contents.rst @@ -6,5 +6,6 @@ Contents :numbered: :caption: User Guide + user/install user/api user/license diff --git a/user/install.rst b/user/install.rst new file mode 100644 index 0000000..a21c99c --- /dev/null +++ b/user/install.rst @@ -0,0 +1,148 @@ +************ +Installation +************ + +Source Code +=========== + +The stable release versions or the latest development versions of the WecOptTool +source code are available for download. + +Stable +------ + +The latest stable version of the WecOptTool source code can be downloaded +from the `Releases `_ +section of the WecOptTool `Github repository +`_. + +Development +----------- + +The latest development version of the WecOptTool source code is available to +clone or download directly from the WecOptTool `Github repository +`_. + +Note that, although the developers endeavour to ensure that the development +code is not broken, bugs or unexpected behaviour may occur, so please beware. + + +Dependencies +============ + +The following table displays the required and optional dependencies for +WecOptTool. + +.. table:: + :widths: 40, 50, 10 + + +----------------------+------------------------------------------------------------+-----------+ + | Dependency | Website | Required? | + +======================+============================================================+===========+ + | MATLAB Optimization | https://www.mathworks.com/products/optimization.html | yes | + | Toolbox | | | + +----------------------+------------------------------------------------------------+-----------+ + | Nemoh | https://github.com/LHEEA/Nemoh | yes | + +----------------------+------------------------------------------------------------+-----------+ + | WAFO [#f1]_ | https://github.com/wafo-project/wafo | no | + +----------------------+------------------------------------------------------------+-----------+ + | MATLAB Parallel | https://www.mathworks.com/products/parallel-computing.html | no | + | Computing | | | + | Toolbox [#f2]_ | | | + +----------------------+------------------------------------------------------------+-----------+ + +Setup +===== + +1. **Add WecOptTool to your MATLAB path**: After downloading the + WecOptTool source code to a path of your choosing + (``/path/to/WecOptTool``), add the WecOptTool toolbox to your MATLAB + path using the MATLAB command prompt (alternatively the “Set Path” + tool can be used to add the toolbox): + + .. code:: matlab + + >> addpath(genpath('/path/to/WecOptTool/toolbox')); + >> savepath; + +2. **Prepare Nemoh:** + + a. **Windows:** Executables are provided in the ‘Release’ directory + of the NEMOH source code. These are installed into WecOptTool + using the ``installNemoh.m`` MATLAB script, run from the + WecOptTool root directory, as follows: + + .. code:: matlab + + >> cd /path/to/WecOptTool + >> installNemoh('/path/to/NEMOH/Release'); + + b. **Linux:** To set up NEMOH for linux, first, compile the + executables (you will need gfortran or the intel fortran + compiler): + + :: + + $ cd /path/to/NEMOH + $ make + + Executables will be created a new directory called ‘bin’, which must + then be installed into WecOptTool using the ``installNemoh.m`` MATLAB + script, run from the WecOptTool root directory: + + .. code:: matlab + + >> cd /path/to/WecOptTool + >> installNemoh('/path/to/NEMOH/bin'); + +3. **Verify dependencies installation:** You can verify that the + dependencies have been installed correctly by running the + ``dependencyCheck.m`` script provided in the root directory of the + WecOptTool source code. The script is called as follows: + + .. code:: matlab + + >> cd /path/to/WecOptTool + >> dependencyCheck + + and successful output may look like this: + + .. code:: matlab + + WecOptTool dependency checker + ------------------------------- + + Required + -------- + Optimization Toolbox: Found + NEMOH: Found + + Optional + -------- + Parallel Computing Toolbox: Not found + WAFO: Found + +4. **(optional) Run functionality tests:** A test suite is available to + verify that the code is operational. A script is provided in the root + directory of the WecOptTool source code and is run from the MATLAB command + window, as follows: + + .. code:: matlab + + >> cd /path/to/WecOptTool + >> runTests; + +5. **Begin use:** See the |example.m|_ file. + +.. |example.m| replace:: ``example.m`` +.. _example.m: https://github.com/SNL-WaterPower/WecOptTool/blob/master/example.m + +.. rubric:: Footnotes + +.. [#f1] WecOptTool requires an input wave spectra which is formatted to + match the output of the WAFO toolbox. These spectra can also be + produced 'by hand' and an example spectra is stored in the + ``example_data`` folder, to use if WAFO is not installed. + +.. [#f2] Optimisations can be conducted significantly more efficiently by + utilising parallel computation. From aa043a88e8d80875af1fd1a14a9f9c47bb98ec78 Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Wed, 25 Mar 2020 17:54:58 +0000 Subject: [PATCH 06/31] Start example documentation --- contents.rst | 1 + user/example.rst | 66 ++++++++++++++++++++++++++++++++++++++++++++++++ user/install.rst | 5 ---- 3 files changed, 67 insertions(+), 5 deletions(-) create mode 100644 user/example.rst diff --git a/contents.rst b/contents.rst index c3aabee..f8e1f4f 100644 --- a/contents.rst +++ b/contents.rst @@ -7,5 +7,6 @@ Contents :caption: User Guide user/install + user/example user/api user/license diff --git a/user/example.rst b/user/example.rst new file mode 100644 index 0000000..0ee7bb8 --- /dev/null +++ b/user/example.rst @@ -0,0 +1,66 @@ +******* +Example +******* + +This section explains and expands upon the |example.m|_ example file provided +in the root directory of the WecOptTool source code. + +.. raw:: html + +
See the entire example file
+ +.. literalinclude:: /git_src/example.m + :language: matlab + :linenos: + +.. raw:: html + +

+ +Create an RM3Study Object +========================= + +.. literalinclude:: /git_src/example.m + :language: matlab + :lines: 4-5 + :linenos: + :lineno-start: 4 + +The :mat:class:`~+WecOptTool.RM3Study` class allows the user to configure a +simulation to their specifications. Once instantiated, an RM3Study object can +be modified using other classes (as described below), and once prepared is +passed to the main functions of the toolbox. + +Define a Sea-State +================== + +.. literalinclude:: /git_src/example.m + :language: matlab + :lines: 7-17 + :linenos: + :lineno-start: 7 + +WecOptTool can simulate single or multiple spectra sea states, where weightings +can be provided to indicate the relative likelihood of each spectra. Spectra +are formatted following the convention of the WAFO_ matlab toolbox: + +.. code:: matlab + + S = + + 1×11 struct array with fields: + + S + w + tr + h + type + phi + norm + note + date + + +.. |example.m| replace:: ``example.m`` +.. _example.m: https://github.com/SNL-WaterPower/WecOptTool/blob/master/example.m +.. _WAFO: http://www.maths.lth.se/matstat/wafo/ diff --git a/user/install.rst b/user/install.rst index a21c99c..c06bf3c 100644 --- a/user/install.rst +++ b/user/install.rst @@ -132,11 +132,6 @@ Setup >> cd /path/to/WecOptTool >> runTests; -5. **Begin use:** See the |example.m|_ file. - -.. |example.m| replace:: ``example.m`` -.. _example.m: https://github.com/SNL-WaterPower/WecOptTool/blob/master/example.m - .. rubric:: Footnotes .. [#f1] WecOptTool requires an input wave spectra which is formatted to From 6fce53cb604835413f844abb12ef6a4416afb5d8 Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Wed, 25 Mar 2020 12:57:56 -0600 Subject: [PATCH 07/31] don't track internal copy of master --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index 955c837..ce561a3 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,9 @@ # sphinx build folder _build +# internal copy of master branch +git_src/ + # Compiled source # ################### *.com From a072128219de5e707d6eb1151f387edc177c4160 Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Wed, 25 Mar 2020 12:58:46 -0600 Subject: [PATCH 08/31] add makefile for OSX (UNIX too?) and update README instructions --- README.md | 15 +++++++++++++-- makefile | 16 ++++++++++++++++ 2 files changed, 29 insertions(+), 2 deletions(-) create mode 100644 makefile diff --git a/README.md b/README.md index 57b9c7f..ebd6d0e 100644 --- a/README.md +++ b/README.md @@ -16,14 +16,25 @@ Create the Sphinx environment > ``` -### Build Locally (Windows) +### Build Locally +The make process clones a copy of the master branch and then uses this to quote snippets of code. +Docs are built in the `_build` directory. + +#### Windows +This uses the instructions in `make_www_local.bat`. ``` > cd path/to/WecOptTool > make_www_local ``` -Docs are built in the `_build` directory. +#### OSX +This uses the instructions in `makefile`. + +```bash +> cd path/to/WecOptTool +> make html +``` ## License diff --git a/makefile b/makefile new file mode 100644 index 0000000..37a56ec --- /dev/null +++ b/makefile @@ -0,0 +1,16 @@ + +SPHINXBUILD = sphinx-build +BUILDDIR = _build +SPHINXOPTS = + +html: + if [ -d "git_src" ]; \ + then cd git_src; git pull; echo "updated git_src"; \ + else git clone https://github.com/SNL-WaterPower/WecOptTool.git git_src; echo "cloned git_src"; \ + fi + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) . $(BUILDDIR) + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)." + +clean: + rm -rf $(BUILDDIR)/* From b210a0a29e753b870f3a6beb13ca11b77d7df122 Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Wed, 25 Mar 2020 13:04:25 -0600 Subject: [PATCH 09/31] add funding statement --- index.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/index.rst b/index.rst index 1f5a426..cea76a9 100644 --- a/index.rst +++ b/index.rst @@ -9,3 +9,5 @@ optimal control. WecOptTool is developed by Sandia National Laboratories .. include:: contents.rst + +Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525. This paper describes objective technical results and analysis. Any subjective views or opinions that might be expressed in the paper do not necessarily represent the views of the U.S. Department of Energy or the United States Government. From 60bce25954be9d0592e6df8cb186a37fa5b26431 Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Wed, 25 Mar 2020 13:04:48 -0600 Subject: [PATCH 10/31] fix to previous commit --- index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.rst b/index.rst index cea76a9..7d022b4 100644 --- a/index.rst +++ b/index.rst @@ -10,4 +10,4 @@ WecOptTool is developed by Sandia National Laboratories .. include:: contents.rst -Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525. This paper describes objective technical results and analysis. Any subjective views or opinions that might be expressed in the paper do not necessarily represent the views of the U.S. Department of Energy or the United States Government. +Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525. From 5920b7a42dd9d36483799b2b4544909df3a2a29f Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Wed, 25 Mar 2020 13:46:51 -0600 Subject: [PATCH 11/31] complete draft of example page --- user/example.rst | 104 +++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 86 insertions(+), 18 deletions(-) diff --git a/user/example.rst b/user/example.rst index 0ee7bb8..6aea165 100644 --- a/user/example.rst +++ b/user/example.rst @@ -19,6 +19,10 @@ in the root directory of the WecOptTool source code. Create an RM3Study Object ========================= +The :mat:class:`~+WecOptTool.RM3Study` class allows the user to configure a +simulation to their specifications. Once instantiated, an RM3Study object can +be modified using other classes (as described below), and once prepared is +passed to the main functions of the toolbox. .. literalinclude:: /git_src/example.m :language: matlab @@ -26,13 +30,13 @@ Create an RM3Study Object :linenos: :lineno-start: 4 -The :mat:class:`~+WecOptTool.RM3Study` class allows the user to configure a -simulation to their specifications. Once instantiated, an RM3Study object can -be modified using other classes (as described below), and once prepared is -passed to the main functions of the toolbox. - Define a Sea-State ================== +WecOptTool can simulate single or multiple spectra sea states, where weightings +can be provided to indicate the relative likelihood of each spectra. The +following lines from |example.m|_ provide means of using the WAFO_ matlab +toolbox or preset spectra from WecOptTool. + .. literalinclude:: /git_src/example.m :language: matlab @@ -40,26 +44,90 @@ Define a Sea-State :linenos: :lineno-start: 7 -WecOptTool can simulate single or multiple spectra sea states, where weightings -can be provided to indicate the relative likelihood of each spectra. Spectra -are formatted following the convention of the WAFO_ matlab toolbox: +Spectra are formatted following the convention of the WAFO_ matlab toolbox, but +can be generated in via any means (e.g., from buoy measurements) as long as the +structure includes the ``S.S``, ``S.w``, and ``S.phi`` fields. .. code:: matlab S = - 1×11 struct array with fields: + struct with fields: + + S: [257×1 double] + w: [257×1 double] + tr: [] + h: Inf + type: 'freq' + phi: 0 + norm: 0 + note: 'Bretschneider, Hm0 = 4, Tp = 5' + date: '25-Mar-2020 13:08:28' + +The desired spectrum or spectra can then be added to the study object + +.. literalinclude:: /git_src/example.m + :language: matlab + :lines: 19-21 + :linenos: + :lineno-start: 19 + +Add a controller to the study +============================= +WecOptTool allows for three types of controllers: + + - **ProportionalDamping:** Resistive damping (i.e., a proportional feedback on velocity) + - **ComplexConjugate: ** Optimal power absorption + - **PseudoSpectral: ** Constrained optimal power absorption + +.. literalinclude:: /git_src/example.m + :language: matlab + :lines: 22-25 + :linenos: + :lineno-start: 22 - S - w - tr - h - type - phi - norm - note - date +Define design variables +======================= +The initial values, lower bounds, and upper bounds of the design variables can +be set as follows. For the RM3 study shown in |example.m|_, the design +variables are the radius of the surface float, r1, the radius of the heave +plate, r2, the draft of the surface float, d1, and the depth of the heave +plate, d2, such that ``x = [r1, r2, d1, d2]``. +.. literalinclude:: /git_src/example.m + :language: matlab + :lines: 26-33 + :linenos: + :lineno-start: 26 + +Alternatively, a simpler study with a single scalar design variable can be +employed. + +.. literalinclude:: /git_src/example.m + :language: matlab + :lines: 34-41 + :linenos: + :lineno-start: 34 + +Set optimization solver and options +=================================== +MATLAB's ``fmincon`` optimization solver is used in |example.m|_. + +.. literalinclude:: /git_src/example.m + :language: matlab + :lines: 42-46 + :linenos: + :lineno-start: 42 + +Run the study and view results +============================== +The study can be run and reviewed as follows: + +.. literalinclude:: /git_src/example.m + :language: matlab + :lines: 47-55 + :linenos: + :lineno-start: 47 .. |example.m| replace:: ``example.m`` .. _example.m: https://github.com/SNL-WaterPower/WecOptTool/blob/master/example.m From 9326e93415d4bbd8a75477c0db9f869d4101a0ce Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Wed, 25 Mar 2020 20:35:30 +0000 Subject: [PATCH 12/31] A little tidying and add links to the API for the geom and control sub packages and main functions --- user/api.rst | 13 ++++++------- user/example.rst | 24 +++++++++++++++++++----- 2 files changed, 25 insertions(+), 12 deletions(-) diff --git a/user/api.rst b/user/api.rst index f7ca1bf..a8b0fd2 100644 --- a/user/api.rst +++ b/user/api.rst @@ -8,15 +8,14 @@ WecOptTool .. mat:automodule:: +WecOptTool :members: -WecOptTool.geom ---------------- - -.. mat:automodule:: +WecOptTool.+geom - :members: - - WecOptTool.control ------------------ .. mat:automodule:: +WecOptTool.+control :members: + +WecOptTool.geom +--------------- + +.. mat:automodule:: +WecOptTool.+geom + :members: diff --git a/user/example.rst b/user/example.rst index 6aea165..5e70d03 100644 --- a/user/example.rst +++ b/user/example.rst @@ -19,6 +19,7 @@ in the root directory of the WecOptTool source code. Create an RM3Study Object ========================= + The :mat:class:`~+WecOptTool.RM3Study` class allows the user to configure a simulation to their specifications. Once instantiated, an RM3Study object can be modified using other classes (as described below), and once prepared is @@ -32,12 +33,12 @@ passed to the main functions of the toolbox. Define a Sea-State ================== + WecOptTool can simulate single or multiple spectra sea states, where weightings can be provided to indicate the relative likelihood of each spectra. The following lines from |example.m|_ provide means of using the WAFO_ matlab toolbox or preset spectra from WecOptTool. - .. literalinclude:: /git_src/example.m :language: matlab :lines: 7-17 @@ -74,11 +75,16 @@ The desired spectrum or spectra can then be added to the study object Add a controller to the study ============================= + WecOptTool allows for three types of controllers: - - **ProportionalDamping:** Resistive damping (i.e., a proportional feedback on velocity) - - **ComplexConjugate: ** Optimal power absorption - - **PseudoSpectral: ** Constrained optimal power absorption + - **ProportionalDamping:** Resistive damping (i.e., a proportional feedback on + velocity) + - **ComplexConjugate:** Optimal power absorption + - **PseudoSpectral:** Constrained optimal power absorption + +The controllers are defined as classes in the :mat:mod:`~+WecOptTool.+control` +sub-package. .. literalinclude:: /git_src/example.m :language: matlab @@ -88,6 +94,7 @@ WecOptTool allows for three types of controllers: Define design variables ======================= + The initial values, lower bounds, and upper bounds of the design variables can be set as follows. For the RM3 study shown in |example.m|_, the design variables are the radius of the surface float, r1, the radius of the heave @@ -109,8 +116,12 @@ employed. :linenos: :lineno-start: 34 +The options for design variables are defined as classes in the +:mat:mod:`~+WecOptTool.+geom` sub-package. + Set optimization solver and options =================================== + MATLAB's ``fmincon`` optimization solver is used in |example.m|_. .. literalinclude:: /git_src/example.m @@ -121,7 +132,10 @@ MATLAB's ``fmincon`` optimization solver is used in |example.m|_. Run the study and view results ============================== -The study can be run and reviewed as follows: + +The study can be :mat:func:`~+WecOptTool.run` and reviewed +(with :mat:func:`~+WecOptTool.result` and :mat:func:`~+WecOptTool.plot`) as +follows: .. literalinclude:: /git_src/example.m :language: matlab From 0d2faa22cdc413a174a6f453289304c4e0612155 Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Wed, 25 Mar 2020 15:26:11 -0600 Subject: [PATCH 13/31] add licensing and copyright information --- conf.py | 3 +- user/license.rst | 680 ++++++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 679 insertions(+), 4 deletions(-) diff --git a/conf.py b/conf.py index 69356ca..749d325 100644 --- a/conf.py +++ b/conf.py @@ -73,8 +73,7 @@ # General information about the project. project = u'WecOptTool' -#copyright = u'2020-{} The WecOptTool Developers'.format(now.year) -copyright = u'2020 The WecOptTool Developers'.format(now.year) +copyright = u'2020 Sandia National Labs'.format(now.year) author = u'unknown' # The version info for the project you're documenting, acts as replacement for diff --git a/user/license.rst b/user/license.rst index d196b4e..29210f5 100644 --- a/user/license.rst +++ b/user/license.rst @@ -2,9 +2,685 @@ License ******* - Copyright |copy| 2020 The WecOptTool Developers +MHKiT is copyrighted through Sandia National Laboratories. The software is +distributed under the GNU General Public License v3.0. - Some license text here +.. code-block:: none + + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for + software and other kinds of works. + + The licenses for most software and other practical works are designed + to take away your freedom to share and change the works. By contrast, + the GNU General Public License is intended to guarantee your freedom to + share and change all versions of a program--to make sure it remains free + software for all its users. We, the Free Software Foundation, use the + GNU General Public License for most of our software; it applies also to + any other work released this way by its authors. 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Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING + WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS + THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY + GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE + USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF + DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD + PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), + EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF + SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided + above cannot be given local legal effect according to their terms, + reviewing courts shall apply local law that most closely approximates + an absolute waiver of all civil liability in connection with the + Program, unless a warranty or assumption of liability accompanies a + copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest + possible use to the public, the best way to achieve this is to make it + free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest + to attach them to the start of each source file to most effectively + state the exclusion of warranty; and each file should have at least + the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + + Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short + notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + + The hypothetical commands `show w' and `show c' should show the appropriate + parts of the General Public License. Of course, your program's commands + might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, + if any, to sign a "copyright disclaimer" for the program, if necessary. + For more information on this, and how to apply and follow the GNU GPL, see + . + + The GNU General Public License does not permit incorporating your program + into proprietary programs. If your program is a subroutine library, you + may consider it more useful to permit linking proprietary applications with + the library. If this is what you want to do, use the GNU Lesser General + Public License instead of this License. But first, please read + . .. |copy| unicode:: U+000A9 .. COPYRIGHT SIGN .. |year| date:: %Y From 42c3952ec2bf1972b0883390d5d69bdfed590e84 Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Wed, 25 Mar 2020 16:37:25 -0600 Subject: [PATCH 14/31] fix error in what the code name is :) --- user/license.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/user/license.rst b/user/license.rst index 29210f5..bdce309 100644 --- a/user/license.rst +++ b/user/license.rst @@ -2,7 +2,7 @@ License ******* -MHKiT is copyrighted through Sandia National Laboratories. The software is +WecOptTool is copyrighted through Sandia National Laboratories. The software is distributed under the GNU General Public License v3.0. .. code-block:: none From 7711ada72d686ec0145de5928feedf35cacddf5c Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Thu, 26 Mar 2020 14:03:59 +0000 Subject: [PATCH 15/31] Tidying --- index.rst | 6 +- user/license.rst | 1348 +++++++++++++++++++++++----------------------- 2 files changed, 679 insertions(+), 675 deletions(-) diff --git a/index.rst b/index.rst index 7d022b4..7e82365 100644 --- a/index.rst +++ b/index.rst @@ -10,4 +10,8 @@ WecOptTool is developed by Sandia National Laboratories .. include:: contents.rst -Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525. +Sandia National Laboratories is a multi-mission laboratory managed and +operated by National Technology and Engineering Solutions of Sandia, +LLC., a wholly owned subsidiary of Honeywell International, Inc., for +the U.S. Department of Energy's National Nuclear Security Administration +under contract DE-NA0003525. diff --git a/user/license.rst b/user/license.rst index bdce309..16c52f7 100644 --- a/user/license.rst +++ b/user/license.rst @@ -7,680 +7,680 @@ distributed under the GNU General Public License v3.0. .. code-block:: none - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for - software and other kinds of works. - - The licenses for most software and other practical works are designed - to take away your freedom to share and change the works. By contrast, - the GNU General Public License is intended to guarantee your freedom to - share and change all versions of a program--to make sure it remains free - software for all its users. We, the Free Software Foundation, use the - GNU General Public License for most of our software; it applies also to - any other work released this way by its authors. You can apply it to - your programs, too. - - When we speak of free software, we are referring to freedom, not - price. Our General Public Licenses are designed to make sure that you - have the freedom to distribute copies of free software (and charge for - them if you wish), that you receive source code or can get it if you - want it, that you can change the software or use pieces of it in new - free programs, and that you know you can do these things. - - To protect your rights, we need to prevent others from denying you - these rights or asking you to surrender the rights. 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If your program is a subroutine library, you + may consider it more useful to permit linking proprietary applications with + the library. If this is what you want to do, use the GNU Lesser General + Public License instead of this License. But first, please read + . .. |copy| unicode:: U+000A9 .. COPYRIGHT SIGN .. |year| date:: %Y From d1bc70570d627fc0830e184acbfc2a1efe1db669 Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Thu, 26 Mar 2020 14:04:13 +0000 Subject: [PATCH 16/31] Fix conda deactivate command --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ebd6d0e..5c241c5 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ Create the Sphinx environment > conda create -n _sphinx pip sphinx sphinx_rtd_theme colorama future > activate _sphinx (_sphinx) > pip install sphinxcontrib-matlabdomain -(_sphinx) > conda deactivate _sphinx +(_sphinx) > conda deactivate > ``` From 0b355fbc05e4b1998882788cf33591ca23d8ff15 Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Thu, 26 Mar 2020 15:03:12 +0000 Subject: [PATCH 17/31] Fixes to the installation instructions --- user/install.rst | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/user/install.rst b/user/install.rst index c06bf3c..edac338 100644 --- a/user/install.rst +++ b/user/install.rst @@ -5,27 +5,27 @@ Installation Source Code =========== -The stable release versions or the latest development versions of the WecOptTool -source code are available for download. +The WecOptTool source code is downloaded from the `WecOptTool Github repository +`_. Stable or development versions +are available. -Stable ------- +Stable Version +-------------- -The latest stable version of the WecOptTool source code can be downloaded -from the `Releases `_ -section of the WecOptTool `Github repository -`_. +The latest stable version of WecOptTool can be downloaded from the `Releases +`_ section of the +Github repository. -Development ------------ +Development Version +------------------- -The latest development version of the WecOptTool source code is available to -clone or download directly from the WecOptTool `Github repository -`_. +To get the latest development version of WecOptTool, clone or download directly +from the WecOptTool Github repository using the '`Clone or download +`_' +button. Note that, although the developers endeavour to ensure that the development -code is not broken, bugs or unexpected behaviour may occur, so please beware. - +version is not broken, bugs or unexpected behaviour may occur, so please beware. Dependencies ============ @@ -107,7 +107,7 @@ Setup and successful output may look like this: - .. code:: matlab + .. code:: WecOptTool dependency checker ------------------------------- @@ -139,5 +139,5 @@ Setup produced 'by hand' and an example spectra is stored in the ``example_data`` folder, to use if WAFO is not installed. -.. [#f2] Optimisations can be conducted significantly more efficiently by +.. [#f2] Optimizations can be conducted significantly more efficiently by utilising parallel computation. From 4e58b76988876f827563c55d1e5f01e58c314560 Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Thu, 26 Mar 2020 09:34:59 -0600 Subject: [PATCH 18/31] add citations for controllers --- user/example.rst | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/user/example.rst b/user/example.rst index 5e70d03..bbf8d0c 100644 --- a/user/example.rst +++ b/user/example.rst @@ -79,9 +79,9 @@ Add a controller to the study WecOptTool allows for three types of controllers: - **ProportionalDamping:** Resistive damping (i.e., a proportional feedback on - velocity) - - **ComplexConjugate:** Optimal power absorption - - **PseudoSpectral:** Constrained optimal power absorption + velocity) (see, e.g., [1]_) + - **ComplexConjugate:** Optimal power absorption (see, e.g., [1]_) + - **PseudoSpectral:** Constrained optimal power absorption [2]_ The controllers are defined as classes in the :mat:mod:`~+WecOptTool.+control` sub-package. @@ -143,6 +143,14 @@ follows: :linenos: :lineno-start: 47 +.. [1] Falnes, Johannes. Ocean waves and oscillating systems: linear + interactions including wave-energy extraction. Cambridge University + Press, 2002. + +.. [2] Bacelli, Giorgio, and John V. Ringwood. "Numerical optimal control of + wave energy converters." IEEE Transactions on Sustainable Energy 6.2 + (2014): 294-302. + .. |example.m| replace:: ``example.m`` .. _example.m: https://github.com/SNL-WaterPower/WecOptTool/blob/master/example.m .. _WAFO: http://www.maths.lth.se/matstat/wafo/ From 2c6f2700ba5271a34d96e9bcb78417c1b42add4e Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Thu, 26 Mar 2020 09:38:09 -0600 Subject: [PATCH 19/31] add link for RM3 --- user/example.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/user/example.rst b/user/example.rst index bbf8d0c..fa810df 100644 --- a/user/example.rst +++ b/user/example.rst @@ -3,7 +3,8 @@ Example ******* This section explains and expands upon the |example.m|_ example file provided -in the root directory of the WecOptTool source code. +in the root directory of the WecOptTool source code. This example considers the +DOE Reference Model 3 (RM3_) device. .. raw:: html @@ -154,3 +155,4 @@ follows: .. |example.m| replace:: ``example.m`` .. _example.m: https://github.com/SNL-WaterPower/WecOptTool/blob/master/example.m .. _WAFO: http://www.maths.lth.se/matstat/wafo/ +.. _RM3: https://energy.sandia.gov/programs/renewable-energy/water-power/technology-development/reference-model-project-rmp/ From 7d19869966a9962274ca7d729369309111ee9ef4 Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Thu, 26 Mar 2020 09:42:21 -0600 Subject: [PATCH 20/31] expand on design variable bounds and x0 --- user/example.rst | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/user/example.rst b/user/example.rst index fa810df..9021e5a 100644 --- a/user/example.rst +++ b/user/example.rst @@ -96,11 +96,12 @@ sub-package. Define design variables ======================= -The initial values, lower bounds, and upper bounds of the design variables can -be set as follows. For the RM3 study shown in |example.m|_, the design -variables are the radius of the surface float, r1, the radius of the heave -plate, r2, the draft of the surface float, d1, and the depth of the heave -plate, d2, such that ``x = [r1, r2, d1, d2]``. +The initial values, lower bounds ``lb``, and upper bounds ``ub`` of the design +variables can be set as follows. For the RM3 study shown in |example.m|_, the +design variables are the radius of the surface float, ``r1``, the radius of the +heave plate, ``r2``, the draft of the surface float, ``d1``, and the depth of +the heave plate, ``d2``, such that ``x = [r1, r2, d1, d2]``. In addition to +bounding the design variables, we must provide an initial guess, ``x0``. .. literalinclude:: /git_src/example.m :language: matlab From d7376f8ed67f0c4b771fe495765da470b7e8f3d9 Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Thu, 26 Mar 2020 09:44:19 -0600 Subject: [PATCH 21/31] explain single scalar design variable more fully --- user/example.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/user/example.rst b/user/example.rst index 9021e5a..4c530f2 100644 --- a/user/example.rst +++ b/user/example.rst @@ -110,7 +110,8 @@ bounding the design variables, we must provide an initial guess, ``x0``. :lineno-start: 26 Alternatively, a simpler study with a single scalar design variable can be -employed. +employed. In this case, instead of scaling various dimensions of the device +individually, the entire device is scaled based on a single design variable. .. literalinclude:: /git_src/example.m :language: matlab From 7f50b08652e914f6958dc7ced38cc94ed92c413b Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Thu, 26 Mar 2020 17:10:20 +0000 Subject: [PATCH 22/31] Basic citations can't be numeric --- user/example.rst | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/user/example.rst b/user/example.rst index 4c530f2..d3813bd 100644 --- a/user/example.rst +++ b/user/example.rst @@ -80,9 +80,9 @@ Add a controller to the study WecOptTool allows for three types of controllers: - **ProportionalDamping:** Resistive damping (i.e., a proportional feedback on - velocity) (see, e.g., [1]_) - - **ComplexConjugate:** Optimal power absorption (see, e.g., [1]_) - - **PseudoSpectral:** Constrained optimal power absorption [2]_ + velocity) (see, e.g., [Falnes]_) + - **ComplexConjugate:** Optimal power absorption (see, e.g., [Falnes]_) + - **PseudoSpectral:** Constrained optimal power absorption [Bacelli]_ The controllers are defined as classes in the :mat:mod:`~+WecOptTool.+control` sub-package. @@ -146,12 +146,12 @@ follows: :linenos: :lineno-start: 47 -.. [1] Falnes, Johannes. Ocean waves and oscillating systems: linear +.. [Falnes] Falnes, Johannes. Ocean waves and oscillating systems: linear interactions including wave-energy extraction. Cambridge University Press, 2002. -.. [2] Bacelli, Giorgio, and John V. Ringwood. "Numerical optimal control of - wave energy converters." IEEE Transactions on Sustainable Energy 6.2 +.. [Bacelli] Bacelli, Giorgio, and John V. Ringwood. "Numerical optimal control + of wave energy converters." IEEE Transactions on Sustainable Energy 6.2 (2014): 294-302. .. |example.m| replace:: ``example.m`` From 7966e2847e2c749f9c6d0285a417b4541ca0dc5c Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Thu, 26 Mar 2020 12:50:22 -0600 Subject: [PATCH 23/31] add image of RM3 dimensions to example docs --- _static/example_rm3Parametric.svg | 100 ++++++++++++++++++++++++++++++ user/example.rst | 4 ++ 2 files changed, 104 insertions(+) create mode 100644 _static/example_rm3Parametric.svg diff --git a/_static/example_rm3Parametric.svg b/_static/example_rm3Parametric.svg new file mode 100644 index 0000000..787ac89 --- /dev/null +++ b/_static/example_rm3Parametric.svg @@ -0,0 +1,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/user/example.rst b/user/example.rst index 4c530f2..bbfc8f8 100644 --- a/user/example.rst +++ b/user/example.rst @@ -103,6 +103,10 @@ heave plate, ``r2``, the draft of the surface float, ``d1``, and the depth of the heave plate, ``d2``, such that ``x = [r1, r2, d1, d2]``. In addition to bounding the design variables, we must provide an initial guess, ``x0``. +.. image:: /_static/example_rm3Parametric.svg + :width: 400pt + :alt: RM3 device parametric dimensions + .. literalinclude:: /git_src/example.m :language: matlab :lines: 26-33 From 2ab244a856b5c093767e93d3836eac6d01db3780 Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Thu, 26 Mar 2020 13:26:26 -0600 Subject: [PATCH 24/31] credit developers --- index.rst | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/index.rst b/index.rst index 7e82365..2c73b1c 100644 --- a/index.rst +++ b/index.rst @@ -6,7 +6,11 @@ The WEC Design Optimization Toolbox (WecOptTool) allows users to perform wave energy converter (WEC) device design optimization studies with constrained optimal control. -WecOptTool is developed by Sandia National Laboratories +Delevopers +========== +WecOptTool is developed by |Sandia National Laboratories|_, with support from +|Data Only Greater|_. The developers would also like to acknowledge benefit from +past collaborations with the |Oregon State University Design Engineering Lab|_. .. include:: contents.rst @@ -14,4 +18,14 @@ Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration -under contract DE-NA0003525. +under contract DE-NA0003525. + + +.. |Oregon State University Design Engineering Lab| replace:: Oregon State University Design Engineering Lab +.. _Oregon State University Design Engineering Lab: https://design.engr.oregonstate.edu + +.. |Sandia National Laboratories| replace:: Sandia National Laboratories +.. _Sandia National Laboratories: https://www.sandia.gov + +.. |Data Only Greater| replace:: Data Only Greater +.. _Data Only Greater: https://www.dataonlygreater.com From c7f4515053d0b432ee1764bc2ecd3da113d163f6 Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Thu, 26 Mar 2020 14:01:56 -0600 Subject: [PATCH 25/31] add workflow diagram and description --- _static/WecOptTool_algorithmDiagram.svg | 228 ++++++++++++++++++++++++ user/example.rst | 19 ++ 2 files changed, 247 insertions(+) create mode 100644 _static/WecOptTool_algorithmDiagram.svg diff --git a/_static/WecOptTool_algorithmDiagram.svg b/_static/WecOptTool_algorithmDiagram.svg new file mode 100644 index 0000000..06bd277 --- /dev/null +++ b/_static/WecOptTool_algorithmDiagram.svg @@ -0,0 +1,228 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Produced by OmniGraffle 7.13 + 2020-03-26 19:33:51 +0000 + + + Canvas 1 + + + Layer 1 + + + + + + + + + Dynamics + from BEM + (NEMOH) + + + + + + + Controller + ProportionalDamping + ComplexConjugate + PseudoSpectral + + + + + + + Optimal dynamics + + + + + + + Power + absorbed + + + + + + + Loading + + + + + + + Cost + proxy + + + + + + + Optimization algorithm + + + + + + + + + + + + + + + + + + + + + + + + + + + + Deployment + site wave + resource + + + + + + + + + + + + + Design variables (e.g., for RM3): + • Geometry ( + r + 1 + , r + 2 + , d + 1 + , d + 2 + ) + • PTO ( + F + max + , Δx + max + ) + • Operational limits (H + s,max + ) + + + + + + + + geometry design vars. + + + + + + + + PTO and operational design vars. + + + + + + + + + + CAPEX + estimation + + + + + + + + Freq. resp. funs. + + + + + + + finite set of + sea states + + + + + + + + + + + + + … + + + + + + + + + + + + + + diff --git a/user/example.rst b/user/example.rst index bd59a55..7d8eb00 100644 --- a/user/example.rst +++ b/user/example.rst @@ -18,6 +18,24 @@ DOE Reference Model 3 (RM3_) device.
+The general concept of WecOptTool is illustrated in the diagram below. In the +upper left-hand corner, an optimization algorithm controls the selection of a +set of design variables. In this diagram, some geometric design variables, +:math:`a^2`r_1, r_2, d_1, d_2`, are considered along with constraints on the power +take-off (PTO) max force, :math:`F_{max}`, and max stroke :math:`\Delta x_{max}` +and an operational constraint, :math:`H_{s,max}`. The device defined by these +design variables is passed to the grey *evaluation* block. Here, Nemoh_ is used +to compute the linear wave-body interaction properties using the boundary +element method (BEM). Next, using these properties and some set of sea states, +one of three controllers (``ProportionalDamping``, ``ComplexConjugat``, ``PseudoSpectral``) +are used to compute the resulting dynamics. From on these dynamics and some +model for cost (e.g., based on the size dimensions and the capabilities of the +PTO) can be combine to produce an objective function, which is returned to the +optimization solver. + +.. image:: /_static/WecOptTool_algorithmDiagram.svg + :alt: Conceptual illustration of WecOptTool functionality + Create an RM3Study Object ========================= @@ -162,3 +180,4 @@ follows: .. _example.m: https://github.com/SNL-WaterPower/WecOptTool/blob/master/example.m .. _WAFO: http://www.maths.lth.se/matstat/wafo/ .. _RM3: https://energy.sandia.gov/programs/renewable-energy/water-power/technology-development/reference-model-project-rmp/ +.. _Nemoh: https://github.com/LHEEA/Nemoh From e6e40cda992adc90f254d4ae17e09151f4b214b5 Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Thu, 26 Mar 2020 14:02:25 -0600 Subject: [PATCH 26/31] justified section text --- _static/theme_overrides.css | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/_static/theme_overrides.css b/_static/theme_overrides.css index 63ee6cc..ddd202b 100644 --- a/_static/theme_overrides.css +++ b/_static/theme_overrides.css @@ -11,3 +11,7 @@ overflow: visible !important; } } + +.section { + text-align:justify; +} From d10036a9cb8eaf3c494eca71b13d6dea3d14fb77 Mon Sep 17 00:00:00 2001 From: Ryan Coe Date: Thu, 26 Mar 2020 14:24:40 -0600 Subject: [PATCH 27/31] add plot of spectra to example docs --- _static/example_spectra.svg | 619 ++++++++++++++++++++++++++++++++++++ user/example.rst | 21 +- 2 files changed, 639 insertions(+), 1 deletion(-) create mode 100644 _static/example_spectra.svg diff --git a/_static/example_spectra.svg b/_static/example_spectra.svg new file mode 100644 index 0000000..286dc2d --- /dev/null +++ b/_static/example_spectra.svg @@ -0,0 +1,619 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/user/example.rst b/user/example.rst index 7d8eb00..8e9fc53 100644 --- a/user/example.rst +++ b/user/example.rst @@ -84,7 +84,24 @@ structure includes the ``S.S``, ``S.w``, and ``S.phi`` fields. note: 'Bretschneider, Hm0 = 4, Tp = 5' date: '25-Mar-2020 13:08:28' -The desired spectrum or spectra can then be added to the study object +In the active code above from |example.m|_, there are eight spectra loaded into +a |struct array|_. These can be plotted using standard MATLAB commands. + +.. code:: matlab + + figure + hold on + grid on + arrayfun(@(x) plot(x.w,x.S,'DisplayName',x.note), S) + legend() + xlim([0,3]) + xlabel('Freq. [rad/s]') + ylabel('Spect. density [m^2 rad/s]') + +.. image:: /_static/example_spectra.svg + :alt: Eight spectra consider in example.m + +The desired spectrum or spectra can then be added to the study object. .. literalinclude:: /git_src/example.m :language: matlab @@ -181,3 +198,5 @@ follows: .. _WAFO: http://www.maths.lth.se/matstat/wafo/ .. _RM3: https://energy.sandia.gov/programs/renewable-energy/water-power/technology-development/reference-model-project-rmp/ .. _Nemoh: https://github.com/LHEEA/Nemoh +.. |struct array| replace:: ``struct array`` +.. _struct array: https://www.mathworks.com/help/matlab/matlab_prog/create-a-structure-array.html From e3c4bf394e6329826d81212ac456961367070c8d Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Fri, 27 Mar 2020 14:08:49 +0000 Subject: [PATCH 28/31] Downgrade Sphinx and add note about docstring formatting to README --- README.md | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 5c241c5..70273cf 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ Install [Anaconda Python](https://www.anaconda.com/distribution/) Create the Sphinx environment ``` -> conda create -n _sphinx pip sphinx sphinx_rtd_theme colorama future +> conda create -n _sphinx pip "sphinx=1.8.5" sphinx_rtd_theme colorama future > activate _sphinx (_sphinx) > pip install sphinxcontrib-matlabdomain (_sphinx) > conda deactivate @@ -17,10 +17,12 @@ Create the Sphinx environment ``` ### Build Locally -The make process clones a copy of the master branch and then uses this to quote snippets of code. -Docs are built in the `_build` directory. + +The make process clones a copy of the master branch and then uses this to quote +snippets of code. Docs are built in the `_build` directory. #### Windows + This uses the instructions in `make_www_local.bat`. ``` @@ -29,6 +31,7 @@ This uses the instructions in `make_www_local.bat`. ``` #### OSX + This uses the instructions in `makefile`. ```bash @@ -39,3 +42,12 @@ This uses the instructions in `makefile`. ## License [CC BY-NC-SA 4.0](https://creativecommons.org/licenses/by-nc-sa/4.0/) + +## Docstring Formatting + +Docstring formatting should be [Google style] for auto documentation with +[sphinx.ext.napoleon]. See the docstrings in the WecOptTool package for +examples. + +[Google style]: https://www.sphinx-doc.org/en/master/usage/extensions/example_google.html#example-google) +[sphinx.ext.napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html From 5e24ea1627e2474a9c0a66538b65d40da9783dbc Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Fri, 27 Mar 2020 14:11:49 +0000 Subject: [PATCH 29/31] Add unistallation instructions --- user/install.rst | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/user/install.rst b/user/install.rst index edac338..47cd0a5 100644 --- a/user/install.rst +++ b/user/install.rst @@ -54,7 +54,17 @@ WecOptTool. Setup ===== -1. **Add WecOptTool to your MATLAB path**: After downloading the +#. **(optional) Remove existing WecOptTool installation**: If you have a + previous version of WecOptTool installed (at path ``/path/to/WecOptTool``), + it should be removed to avoid conflicts. This can be achieved using the + MATLAB command prompt (alternatively the "Set Path" tool can be used to + remove the toolbox): + + .. code:: matlab + + >> rmpath('/path/to/WecOptTool/toolbox'); + +#. **Add WecOptTool to your MATLAB path**: After downloading the WecOptTool source code to a path of your choosing (``/path/to/WecOptTool``), add the WecOptTool toolbox to your MATLAB path using the MATLAB command prompt (alternatively the “Set Path” @@ -62,10 +72,10 @@ Setup .. code:: matlab - >> addpath(genpath('/path/to/WecOptTool/toolbox')); + >> addpath('/path/to/WecOptTool/toolbox'); >> savepath; -2. **Prepare Nemoh:** +#. **Prepare Nemoh:** a. **Windows:** Executables are provided in the ‘Release’ directory of the NEMOH source code. These are installed into WecOptTool @@ -95,7 +105,7 @@ Setup >> cd /path/to/WecOptTool >> installNemoh('/path/to/NEMOH/bin'); -3. **Verify dependencies installation:** You can verify that the +#. **Verify dependencies installation:** You can verify that the dependencies have been installed correctly by running the ``dependencyCheck.m`` script provided in the root directory of the WecOptTool source code. The script is called as follows: @@ -122,7 +132,7 @@ Setup Parallel Computing Toolbox: Not found WAFO: Found -4. **(optional) Run functionality tests:** A test suite is available to +#. **(optional) Run functionality tests:** A test suite is available to verify that the code is operational. A script is provided in the root directory of the WecOptTool source code and is run from the MATLAB command window, as follows: From 42addc29353e63543f9f364963b935b28e3a9d86 Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Fri, 27 Mar 2020 14:12:06 +0000 Subject: [PATCH 30/31] Fix line numbering in example --- user/example.rst | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/user/example.rst b/user/example.rst index 8e9fc53..ea3ae52 100644 --- a/user/example.rst +++ b/user/example.rst @@ -46,9 +46,9 @@ passed to the main functions of the toolbox. .. literalinclude:: /git_src/example.m :language: matlab - :lines: 4-5 + :lines: 22-23 :linenos: - :lineno-start: 4 + :lineno-start: 22 Define a Sea-State ================== @@ -60,9 +60,9 @@ toolbox or preset spectra from WecOptTool. .. literalinclude:: /git_src/example.m :language: matlab - :lines: 7-17 + :lines: 25-32 :linenos: - :lineno-start: 7 + :lineno-start: 25 Spectra are formatted following the convention of the WAFO_ matlab toolbox, but can be generated in via any means (e.g., from buoy measurements) as long as the @@ -105,9 +105,9 @@ The desired spectrum or spectra can then be added to the study object. .. literalinclude:: /git_src/example.m :language: matlab - :lines: 19-21 + :lines: 34-35 :linenos: - :lineno-start: 19 + :lineno-start: 34 Add a controller to the study ============================= @@ -124,9 +124,9 @@ sub-package. .. literalinclude:: /git_src/example.m :language: matlab - :lines: 22-25 + :lines: 37-39 :linenos: - :lineno-start: 22 + :lineno-start: 37 Define design variables ======================= @@ -144,9 +144,9 @@ bounding the design variables, we must provide an initial guess, ``x0``. .. literalinclude:: /git_src/example.m :language: matlab - :lines: 26-33 + :lines: 41-47 :linenos: - :lineno-start: 26 + :lineno-start: 41 Alternatively, a simpler study with a single scalar design variable can be employed. In this case, instead of scaling various dimensions of the device @@ -154,9 +154,9 @@ individually, the entire device is scaled based on a single design variable. .. literalinclude:: /git_src/example.m :language: matlab - :lines: 34-41 + :lines: 49-55 :linenos: - :lineno-start: 34 + :lineno-start: 49 The options for design variables are defined as classes in the :mat:mod:`~+WecOptTool.+geom` sub-package. @@ -168,9 +168,9 @@ MATLAB's ``fmincon`` optimization solver is used in |example.m|_. .. literalinclude:: /git_src/example.m :language: matlab - :lines: 42-46 + :lines: 57-60 :linenos: - :lineno-start: 42 + :lineno-start: 57 Run the study and view results ============================== @@ -181,9 +181,9 @@ follows: .. literalinclude:: /git_src/example.m :language: matlab - :lines: 47-55 + :lines: 62-69 :linenos: - :lineno-start: 47 + :lineno-start: 62 .. [Falnes] Falnes, Johannes. Ocean waves and oscillating systems: linear interactions including wave-energy extraction. Cambridge University From e29591b1f7c0ee55ce010d1670966ebf64ca499a Mon Sep 17 00:00:00 2001 From: Mathew Topper Date: Fri, 27 Mar 2020 14:12:24 +0000 Subject: [PATCH 31/31] Add short descriptions to API --- user/api.rst | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/user/api.rst b/user/api.rst index a8b0fd2..d3b87f7 100644 --- a/user/api.rst +++ b/user/api.rst @@ -5,17 +5,23 @@ API WecOptTool ========== +The WecOptTool package provides the main interface for the toolbox. + .. mat:automodule:: +WecOptTool :members: WecOptTool.control ------------------ +The control subpackage provides options for device control. + .. mat:automodule:: +WecOptTool.+control :members: WecOptTool.geom --------------- +The geom subpackage provides options for device geometry variation. + .. mat:automodule:: +WecOptTool.+geom :members: