Renamed docs to docs-source

docs-source/licenses/LGPL.txt

+		   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

docs-source/licenses/Licenses.txt

+OpenMM was developed by Simbios, the NIH National Center for Physics-Based
+Simulation of Biological Structures at Stanford, funded under the NIH Roadmap
+for Medical Research, grant U54 GM072970. See https://simtk.org.
+
+Portions copyright © 2008-2009 Stanford University and the Authors.
+
+There are several licenses which cover different parts of OpenMM as described
+below.
+
+
+1. API and Reference Platform
+
+The OpenMM API and the Reference Platform may be used under the terms of the
+MIT License:
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject
+to the following conditions:
+
+The above copyright notice and this permission notice shall be included
+in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+
+2. CUDA and OpenCL Platforms
+
+The CUDA Platform and OpenCL Platform may be used under the terms of the GNU
+Lesser General Public License.  A copy of this license may be found in the
+accompanying file "LGPL.txt".  It in turn incorporates the terms of the GNU
+General Public License, which may be found in the accompanying file "GPL.txt".
+
+
+3. SIMD-oriented Fast Mersenne Twister (SFMT)
+
+OpenMM uses the SFMT library which is copyright 2006-2007 Mutsuo Saito, Makoto
+Matsumoto and Hiroshima University.  It may be used under the following terms:
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above
+      copyright notice, this list of conditions and the following
+      disclaimer in the documentation and/or other materials provided
+      with the distribution.
+    * Neither the name of the Hiroshima University nor the names of
+      its contributors may be used to endorse or promote products
+      derived from this software without specific prior written
+      permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+4. Hilbert Curve
+
+OpenMM uses an implementation of Hilbert curves which is copyright 1998-2000
+Rice University.  It may be used under the following terms:
+
+This software is copyrighted by Rice University.  It may be freely copied,
+modified, and redistributed, provided that the copyright notice is
+preserved on all copies.
+
+There is no warranty or other guarantee of fitness for this software,
+it is provided solely "as is".  Bug reports or fixes may be sent
+to the author, who may or may not act on them as he desires.
+
+You may include this software in a program or other software product,
+but must display the notice:
+
+Hilbert Curve implementation copyright 1998, Rice University
+
+in any place where the end-user would see your own copyright.
+
+If you modify this software, you should include a notice giving the
+name of the person performing the modification, the date of modification,
+and the reason for such modification.
+
+
+5. GPU-BBSort
+
+The CUDA platform uses the GPU-BBSort library written by Chen Shifu.  It
+includes the following license statement:
+
+The code is distributed under BSD license, you are allowed to use, modify
+or sell this code, but a statement is required if you used this code any where.
\ No newline at end of file

docs-source/sphinx/autonumber.py

+from docutils.parsers.rst import roles
+from docutils.nodes import Text, reference, section
+from sphinx.roles import XRefRole
+    
+class autonumber(Text):
+    pass
+    
+class autonumber_ref(reference):
+    pass
+
+def autonumber_role(name, rawtext, text, lineno, inliner, options={}, content=[]):
+    return ([autonumber(text)], [])
+
+def doctree_resolved(app, doctree, docname):
+    index = {};
+    refTable = {}
+    if app.config.autonumber_by_chapter:
+        # Record the number of each chapter
+        
+        env = app.builder.env
+        sectionNumbers = {}
+        for doc in env.toc_secnumbers:
+            sections = env.toc_secnumbers[doc]
+            for sectionId in sections:
+                sectionNumbers[sectionId[1:]] = sections[sectionId]
+        lastChapter = -1
+    
+    # Assign numbers to all the autonumbered objects.
+    
+    for node in doctree.traverse(autonumber):
+        category = node.astext().split(',')[0]
+        if category in index:
+            nextNumber = index[category]+1
+        else:
+            nextNumber = 1
+        if app.config.autonumber_by_chapter:
+            parent = node.parent
+            chapter = None
+            while chapter is None:
+                if isinstance(parent, section):
+                    chapter = parent
+                parent = parent.parent
+            chapter = sectionNumbers[chapter.attributes['ids'][0]][0]
+            if chapter != lastChapter:
+                index = {}
+            newNode = Text('%s %d-%d' % (category, chapter, nextNumber))
+            lastChapter = chapter
+        else:
+            newNode = Text('%s %d' % (category, nextNumber))            
+        index[category] = nextNumber
+        refTable[node.astext()] = newNode
+        node.parent.replace(node, newNode)
+    
+    # Replace references with the name of the referenced object
+    
+    for ref_info in doctree.traverse(autonumber_ref):
+        target = ref_info['reftarget']
+        if target not in refTable:
+            raise ValueError('Unknown target for autonumber reference: '+target)
+        ref_info.replace_self(Text(refTable[target].astext()))
+
+def setup(app):
+    app.add_config_value('autonumber_by_chapter', True, False)
+    roles.register_local_role('autonumber', autonumber_role)
+    app.add_node(autonumber)
+    app.add_node(autonumber_ref)
+    app.add_role('numref', XRefRole(nodeclass=autonumber_ref))
+    app.connect('doctree-resolved', doctree_resolved)
+
+

docs-source/sphinx/caption.py

+from docutils.parsers.rst import Directive
+from docutils.nodes import compound, raw
+
+class CaptionDirective(Directive):
+    
+    has_content = True
+
+    def run(self):
+        latexPrefix = raw('', '{\\centering', format='latex')
+        latexSuffix = raw('', '\\par}\\bigskip', format='latex')
+        text = '\n'.join(self.content)
+        content_node = compound(rawsource=text)
+        self.state.nested_parse(self.content, self.content_offset, content_node)
+        content_node.attributes['classes'].append('caption')
+        return [latexPrefix, content_node, latexSuffix]
+
+def setup(app):
+    app.add_directive('caption', CaptionDirective)

docs-source/sphinx/numsec.py

+"""
+Changes section references to be the section number
+instead of the title of the section.
+"""
+
+from docutils import nodes
+import sphinx.domains.std
+
+class CustomStandardDomain(sphinx.domains.std.StandardDomain):
+
+    def __init__(self, env):
+        env.settings['footnote_references'] = 'superscript'
+        sphinx.domains.std.StandardDomain.__init__(self, env)
+
+    def resolve_xref(self, env, fromdocname, builder,
+                     typ, target, node, contnode):
+        res = super(CustomStandardDomain, self).resolve_xref(env, fromdocname, builder,
+                                                            typ, target, node, contnode)
+        
+        if res is None:
+            return res
+        
+        if typ == 'ref' and not node['refexplicit']:
+            docname, labelid, sectname = self.data['labels'].get(target, ('','',''))
+            res['refdocname'] = docname
+        
+        return res
+
+def doctree_resolved(app, doctree, docname):
+    secnums = app.builder.env.toc_secnumbers
+    for node in doctree.traverse(nodes.reference):
+        if 'refdocname' in node:
+            refdocname = node['refdocname']
+            if refdocname in secnums:
+                secnum = secnums[refdocname]
+                emphnode = node.children[0]
+                textnode = emphnode.children[0]
+                
+                toclist = app.builder.env.tocs[refdocname]
+                anchorname = None
+                for refnode in toclist.traverse(nodes.reference):
+                    if refnode.astext() == textnode.astext():
+                        anchorname = refnode['anchorname']
+                if anchorname is None:
+                    continue
+                linktext = '.'.join(map(str, secnum[anchorname]))
+                node.replace(emphnode, nodes.Text(linktext))
+
+def setup(app):
+    app.override_domain(CustomStandardDomain)
+    app.connect('doctree-resolved', doctree_resolved)
+

docs-source/sphinx/samepage.py

+from docutils.parsers.rst import Directive
+from docutils.nodes import compound, raw
+
+class SamepageDirective(Directive):
+    
+    has_content = True
+
+    def run(self):
+        prefix = raw('', '\\par\\begin{samepage}', format='latex')
+        suffix = raw('', '\\end{samepage}\\par', format='latex')
+        text = '\n'.join(self.content)
+        content_node = compound(rawsource=text)
+        self.state.nested_parse(self.content, self.content_offset, content_node)
+        return [prefix, content_node, suffix]
+
+def setup(app):
+    app.add_directive('samepage', SamepageDirective)

docs-source/usersguide/Makefile

+# 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/OpenMMDeveloperGuide.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/OpenMMDeveloperGuide.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/OpenMMDeveloperGuide"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/OpenMMDeveloperGuide"
+	@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."

docs-source/usersguide/conf.py

+# -*- coding: utf-8 -*-
+#
+# OpenMM Developer Guide documentation build configuration file, created by
+# sphinx-quickstart on Fri Feb  7 12:42:06 2014.
+#
+# 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(os.path.abspath('../sphinx'))
+
+# -- 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.pngmath', 'sphinx.ext.mathjax', 'sphinxcontrib.bibtex', 'autonumber', 'samepage', 'caption', 'numsec']
+
+# 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'OpenMM Users Guide'
+copyright = u'2008-2014, Stanford University'
+
+# 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 = os.getenv('OPENMM_VERSION')
+# The full version, including alpha/beta/rc tags.
+release = os.getenv('OPENMM_VERSION')
+
+# 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 = 'agogo'
+
+# 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 = 'OpenMMUsersGuidedoc'
+
+
+# -- 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': """
+    \\usepackage[none]{hyphenat}
+    \\usepackage{xstring}
+    \\usepackage{color}
+    \\usepackage{caption}
+    \\setcounter{tocdepth}{3}
+    \\captionsetup[figure]{labelformat=empty}
+    \\renewcommand{\DUspan}[2]{%
+        \\IfEqCase{#1}{%
+            {code}{\\small{}\\texttt{#2}\\normalsize{}}%
+        }[\\PackageError{DUspan}{Unrecognized option passed to DUspan: #1}{}]%
+    }%""",
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+  ('index', 'OpenMMUsersGuide.tex', u'OpenMM Users Guide',
+   u'Peter Eastman', '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', 'openmmusersguide', u'OpenMM Users Guide',
+     [u'Peter Eastman'], 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', 'OpenMMUsersGuide', u'OpenMM Users Guide',
+   u'Peter Eastman', 'OpenMMUsersGuide', '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'

docs-source/usersguide/header.rst

+.. role:: code
+.. raw:: html
+
+    <style> .code {font-family:monospace;} </style>
+    <style> .caption {text-align:center;} </style>
+
+.. |--| replace:: :option:`--`

docs-source/usersguide/index.rst

+.. include:: header.rst
+
+####################################
+OpenMM Users Manual and Theory Guide
+####################################
+
+
+Portions copyright (c) 2008-2014 Stanford University and the Authors
+
+Contributors:  Kyle Beauchamp, Christopher Bruns, Peter Eastman, Mark
+Friedrichs, Joy P. Ku, Vijay Pande, Randy Radmer, Michael Sherman, Tom Markland
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this document (the "Document"), to deal in the Document without restriction,
+including without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Document, and to permit
+persons to whom the Document is furnished to do so, subject to the following
+conditions:
+
+This copyright and permission notice shall be included in all copies or
+substantial portions of the Document.
+
+THE DOCUMENT IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE AUTHORS,
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE DOCUMENT OR THE USE OR OTHER DEALINGS IN THE
+DOCUMENT.
+
+
+.. toctree::
+   :numbered:
+   :maxdepth: 3
+
+   introduction   
+   application
+   library
+   theory
+   zbibliography
+

docs-source/usersguide/introduction.rst

+.. include:: header.rst
+
+Introduction
+############
+
+OpenMM consists of two parts:
+
+#. A set of libraries that lets programmers easily add molecular simulation
+   features to their programs
+#. An “application layer” that exposes those features to end users who just want
+   to run simulations
+
+
+This guide is divided into three sections:
+
+* Part I (Chapters :ref:`the-openmm-application-layer-introduction`\ -\ :ref:`creating-force-fields`\ )
+  describes the application layer.  It is relevant to all users, but especially relevant to people
+  who want to use OpenMM as a stand-alone application for running simulations.
+* Part II (Chapters :ref:`the-openmm-library-introduction`\ -\ :ref:`drude-plugin`\ )
+  describes how to use the OpenMM libraries within your own applications.  It is primarily
+  relevant to programmers who want to write simulation applications.
+* Part III (Chapters :ref:`the-theory-behind-openmm-introduction`\ -\ :ref:`other-features`\ )
+  describes the mathematical theory behind the features found in OpenMM.  It is relevant to all users.
+
+
+Online Resources
+****************
+
+You can find more documentation and other material at our website
+http://simtk.org/home/openmm.   Among other things there is a discussion forum,
+a wiki, and videos of lectures on using OpenMM.
+
+
+Referencing OpenMM
+******************
+
+Any work that uses OpenMM should cite the following publication:
+
+P. Eastman, M. S. Friedrichs, J. D. Chodera, R. J. Radmer, C. M. Bruns, J. P.
+Ku, K. A. Beauchamp, T. J. Lane, L.-P. Wang, D. Shukla, T. Tye, M. Houston, T.
+Stich, C. Klein, M. R. Shirts, and V. S. Pande. "OpenMM 4: A Reusable,
+Extensible, Hardware Independent Library for High Performance Molecular
+Simulation." J. Chem. Theor. Comput. 9(1): 461-469. (2013).
+
+We depend on academic research grants to fund the OpenMM development efforts;
+citations of our publication will help demonstrate the value of OpenMM.
+
+
+Acknowledgments
+***************
+
+OpenMM software and all related activities, such as this manual, are funded by
+the Simbios National Center for Biomedical Computing through the National
+Institutes of Health Roadmap for Medical Research, Grant U54 GM072970.
+Information on the National Centers can be found at
+http://nihroadmap.nih.gov/bioinformatics.
+