Skip to content

GitLab

Commit 67004571 authored by peastman's avatar peastman
Browse files

Merge branch 'master' of https://github.com/SimTk/openmm

parents 37457b25 25f1080a
Expand all Show whitespace changes
Inline Side-by-side
Showing with 9462 additions and 0 deletions
docs-source/licenses/GPL.txt 0 → 100644
View file @ 67004571
This diff is collapsed.
docs-source/licenses/LGPL.txt 0 → 100644
View file @ 67004571
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 0 → 100644
View file @ 67004571
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 0 → 100644
View file @ 67004571
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 0 → 100644
View file @ 67004571
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/samepage.py 0 → 100644
View file @ 67004571
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 0 → 100644
View file @ 67004571
# 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/application.rst 0 → 100644
View file @ 67004571
This diff is collapsed.
docs-source/usersguide/conf.py 0 → 100644
View file @ 67004571
# -*- 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 0 → 100644
View file @ 67004571
.. role:: code
.. raw:: html
<style> .code {font-family:monospace;} </style>
<style> .caption {text-align:center;} </style>
.. |--| replace:: :option:`--`
docs-source/usersguide/index.rst 0 → 100644
View file @ 67004571
.. 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 0 → 100644
View file @ 67004571
.. 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.
docs-source/usersguide/library.rst 0 → 100644
View file @ 67004571
This diff is collapsed.
docs-source/usersguide/references.bib 0 → 100644
View file @ 67004571
@article{Andersen1980
author = {Andersen, Hans C.},
title = {Molecular dynamics simulations at constant pressure and/or temperature},
journal = {Journal of Chemical Physics},
volume = {72},
number = {4},
pages = {2384-2393},
year = {1980},
type = {Journal Article}
}
@article{Aqvist2004
author = {Åqvist, Johan and Wennerström, Petra and Nervall, Martin and Bjelic, Sinisa and Brandsdal, Bjørn O.},
title = {Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm},
journal = {Chemical Physics Letters},
volume = {384},
pages = {288-294},
year = {2004},
type = {Journal Article}
}
@article{Berendsen1987
author = {Berendsen, H. J. C. and Grigera, J. R. and Straatsma, T. P.},
title = {The missing term in effective pair potentials},
journal = {Journal of Physical Chemistry},
volume = {91},
pages = {6269-6271},
year = {1987},
type = {Journal Article}
}
@article{Ceriotti2010
author = {Ceriotti, M. and Parrinello, M. and Markland, Thomas E. and Manolopoulos, David E.},
title = {Efficient stochastic thermostatting of path integral molecular dynamics},
journal = {Journal of Chemical Physics},
volume = {133},
number = {12},
year = {2010},
type = {Journal Article}
}
@article{Chow1995
author = {Chow, Kim-Hung and Ferguson, David M.},
title = {Isothermal-isobaric molecular dynamics simulations with Monte Carlo volume sampling},
journal = {Computer Physics Communications},
volume = {91},
pages = {283-289},
year = {1995},
type = {Journal Article}
}
@article{Craig2004
author = {Craig, I. R. and Manolopoulos, David E.},
title = {Quantum statistics and classical mechanics: Real time correlation functions from ring polymer molecular dynamics},
journal = {Journal of Chemical Physics},
volume = {121},
pages = {3368-3373},
year = {2004},
type = {Journal Article}
}
@article{Duan2003
author = {Duan, Y.; Wu, C. and Chowdhury, S. and Lee, M.C. and Xiong, G. and Zhang, W. and Yang, R. and Cieplak, P. and Luo, R. and Lee, T.},
title = {A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations},
journal = {Journal of Computational Chemistry},
volume = {24},
pages = {1999-2012},
year = {2003},
type = {Journal Article}
}
@article{Essmann1995
author = {Essmann, Ulrich and Perera, Lalith and Berkowitz, Max L. and Darden, Tom and Lee, Hsing and Pedersen, Lee G.},
title = {A smooth particle mesh Ewald method},
journal = {Journal of Chemical Physics},
volume = {103},
number = {19},
pages = {8577-8593},
year = {1995},
type = {Journal Article}
}
@article{Hall1984
author = {Hall, Randall W. and Berne, B. J.},
title = {Nonergodicity in path integral molecular dynamics},
journal = {Journal of Chemical Physics},
volume = {81},
number = {8},
year = {1984},
type = {Journal Article}
}
@article{Hawkins1995
author = {Hawkins, Gregory D. and Cramer, Christopher J. and Truhlar, Donald G.},
title = {Pairwise solute descreening of solute charges from a dielectric medium},
journal = {Chemical Physics Letters},
volume = {246},
number = {1-2},
pages = {122-129},
year = {1995},
type = {Journal Article}
}
@article{Horn2004
author = {Horn, Hans W. and Swope, William C. and Pitera, Jed W. and Madura, Jeffry D. and Dick, Thomas J. and Hura, Greg L. and Head-Gordon, Teresa},
title = {Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew},
journal = {Journal of Chemical Physics},
volume = {120},
pages = {9665-9678},
year = {2004},
type = {Journal Article}
}
@article{Hornak2006
author = {Hornak, V. and Abel, R. and Okur, A. and Strockbine, B. and Roitberg, A. and Simmerling, C.},
title = {Comparison of multiple Amber force fields and development of improved protein backbone parameters},
journal = {Proteins},
volume = {65},
pages = {712-725},
year = {2006},
type = {Journal Article}
}
@article{Izaguirre2010
author = {Izaguirre, Jesús A. and Sweet, Chris R. and Pande, Vijay S.},
title = {Multiscale dynamics of macromolecules using Normal Mode Langevin},
journal = {Pacific Symposium on Biocomputing},
volume = {15},
pages = {240-251},
year = {2010},
type = {Journal Article}
}
@article{Jorgensen1983
author = {Jorgensen, William L. and Chandrasekhar, Jayaraman and Madura, Jeffry D. and Impey, Roger W. and Klein, Michael L.},
title = {Comparison of simple potential functions for simulating liquid water},
journal = {Journal of Chemical Physics},
volume = {79},
pages = {926-935},
year = {1983},
type = {Journal Article}
}
@inbook{Kollman1997
author = {Kollman, P.A. and Dixon, R. and Cornell, W. and Fox, T. and Chipot, C. and Pohorille, A.},
title = {Computer Simulation of Biomolecular Systems},
editor = {Wilkinson, A. and Weiner, P. and van Gunsteren, Wilfred F.},
publisher = {Elsevier},
volume = {3},
pages = {83-96},
year = {1997},
type = {Book Section}
}
@article{Labute2008
author = {Labute, Paul},
title = {The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area},
journal = {Journal of Computational Chemistry},
volume = {29},
number = {10},
pages = {1693-1698},
year = {2008},
type = {Journal Article}
}
@article{Lamoureux2006
author = {Lamoureux, Guillaume and Harder, Edward and Vorobyov, Igor V. and Roux, Benoit and MacKerell Jr., Alexander D.},
title = {A polarizable model of water for molecular dynamics simulations of biomolecules},
journal = {Chemical Physics Letters},
volume = {418},
number = {1-3},
pages = {245-249},
year = {2006},
type = {Journal Article}
}
@article{Lamoureux2003
author = {Lamoureux, Guillaume and Roux, Benoit},
title = {Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm},
journal = {Journal of Chemical Physics},
volume = {119},
number = {6},
pages = {3025-3039},
year = {2003},
type = {Journal Article}
}
@article{Li2010
author = {Li, D.W. and Br{\"u}schweiler, R.},
title = {NMR-based protein potentials},
journal = {Angewandte Chemie International Edition},
volume = {49},
pages = {6778-6780},
year = {2010},
type = {Journal Article}
}
@article{Lindorff-Larsen2010
author = {Lindorff-Larsen, K. and Piana, S. and Palmo, K. and Maragakis, P. and Klepeis, J. and Dror, R.O. and Shaw, D.E.},
title = {Improved side-chain torsion potentials for the Amber ff99SB protein force field},
journal = {Proteins},
volume = {78},
pages = {1950-1958},
year = {2010},
type = {Journal Article}
}
@article{Liu1989
author = {Liu, Dong C. and Nocedal, Jorge},
title = {On the Limited Memory BFGS Method For Large Scale Optimization},
journal = {Mathematical Programming},
volume = {45},
pages = {503-528},
year = {1989},
type = {Journal Article}
}
@article{Lopes2013,
author = {Lopes, Pedro E. M. and Huang, Jing and Shim, Jihyun and Luo, Yun and Li, Hui and Roux, Benoît and MacKerell, Alexander D.},
title = {Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator},
journal = {Journal of Chemical Theory and Computation},
volume = {9},
number = {12},
pages = {5430-5449},
year = {2013},
type = {Journal Article}
}
@article{Mahoney2000
author = {Mahoney, Michael W. and Jorgensen, William L.},
title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
journal = {Journal of Chemical Physics},
volume = {112},
pages = {8910-8922},
year = {2000},
type = {Journal Article}
}
@article{Markland2008
author = {Markland, Thomas E. and Manolopoulos, David E.},
title = {An efficient ring polymer contraction scheme for imaginary time path integral simulations},
journal = {Journal of Chemical Physics},
volume = {129},
number = {2},
year = {2008},
type = {Journal Article}
}
@article{Mongan2007
author = {Mongan, John and Simmerling, Carlos and McCammon, J. Andrew and Case, David A. and Onufriev, Alexey},
title = {Generalized Born model with a simple, robust molecular volume correction},
journal = {Journal of Chemical Theory and Computation},
volume = {3},
number = {1},
pages = {156-169},
year = {2007},
type = {Journal Article}
}
@article{Nguyen2013
author = {Nguyen, Hai and Roe, Daniel R. and Simmerling, Carlos},
title = {Improved Generalized Born Solvent Model Parameters for Protein Simulations},
journal = {Journal of Chemical Theory and Computation},
volume = {9},
number = {4},
pages = {2020-2034},
year = {2013},
type = {Journal Article}
}
@article{Onufriev2004
author = {Onufriev, Alexey and Bashford, Donald and Case, David A.},
title = {Exploring protein native states and large-scale conformational changes with a modified generalized born model},
journal = {Proteins},
volume = {55},
number = {22},
pages = {383-394},
year = {2004},
type = {Journal Article}
}
@article{Parrinello1984
author = {Parrinello, M. and Rahman, A.},
title = {Study of an F center in molten KCl},
journal = {Journal of Chemical Physics},
volume = {80},
number = {2},
pages = {860-867},
year = {1984},
type = {Journal Article}
}
@misc{Ponder
author = {Ponder, Jay W.},
title = {Personal communication},
type = {Personal Communication}
}
@article{Ren2002
author = {Ren, P. and Ponder, Jay W.},
title = {A Consistent Treatment of Inter- and Intramolecular Polarization in Molecular Mechanics Calculations},
journal = {Journal of Computational Chemistry},
volume = {23},
pages = {1497-1506},
year = {2002},
type = {Journal Article}
}
@article{Ren2003
author = {Ren, P. and Ponder, Jay W.},
title = {Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation},
journal = {Journal of Physical Chemistry B},
volume = {107},
pages = {5933-5947},
year = {2003},
type = {Journal Article}
}
@article{Schaefer1998
author = {Schaefer, Michael and Bartels, Christian and Karplus, Martin},
title = {Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model},
journal = {Journal of Molecular Biology},
volume = {284},
number = {3},
pages = {835-848},
year = {1998},
type = {Journal Article}
}
@article{Schnieders2007
author = {Schnieders, Michael J. and Ponder, Jay W.},
title = {Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum},
journal = {Journal of Chemical Theory and Computation},
volume = {3},
pages = {2083-2097},
year = {2007},
type = {Journal Article}
}
@article{Shirts2008
author = {Shirts, Michael R. and Chodera, John D.},
title = {Statistically optimal analysis of samples from multiple equilibrium states},
journal = {Journal of Chemical Physics},
volume = {129},
pages = {124105},
year = {2008},
type = {Journal Article}
}
@article{Shi2013
author = {Shi, Yue and Xia, Zhen and Zhang, Jiajing and Best, Robert and Wu, Chuanjie and Ponder, Jay W. and Ren, Pengyu},
title = {Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins},
journal = {Journal of Chemical Theory and Computation},
volume = {9},
number = {9},
pages = {4046-4063},
year = {2013},
type = {Journal Article}
}
@article{Shirts2007
author = {Shirts, Michael R. and Mobley, David L. and Chodera, John D. and Pande, Vijay S.},
title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations},
journal = {Journal of Physical Chemistry B},
volume = {111},
pages = {13052-13063},
year = {2007},
type = {Journal Article}
}
@article{Shirts2005
author = {Shirts, Michael R. and Pande, Vijay S.},
title = {Solvation free energies of amino acid side chain analogs for common molecular mechanics water models},
journal = {Journal of Chemical Physics},
volume = {132},
pages = {134508},
year = {2005},
type = {Journal Article}
}
@article{Thole1981
author = {Thole, B. T.},
title = {Molecular polarizabilities calculated with a modified dipole interaction},
journal = {Chemical Physics},
volume = {59},
number = {3},
pages = {341-350},
year = {1981},
type = {Journal Article}
}
@article{Tironi1995
author = {Tironi, Ilario G. and Sperb, René and Smith, Paul E. and van Gunsteren, Wilfred F.},
title = {A generalized reaction field method for molecular dynamics simulations},
journal = {Journal of Chemical Physics},
volume = {102},
number = {13},
pages = {5451-5459},
year = {1995},
type = {Journal Article}
}
@article{Toukmaji1996
author = {Toukmaji, Abdulnour Y. and Board Jr, John A.},
title = {Ewald summation techniques in perspective: a survey},
journal = {Computer Physics Communications},
volume = {95},
pages = {73-92},
year = {1996},
type = {Journal Article}
}
@article{Wang2000
author = {Wang, J. and Cieplak, P. and Kollman, P.A.},
title = {How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?},
journal = {Journal of Computational Chemistry},
volume = {21},
pages = {1049-1074},
year = {2000},
type = {Journal Article}
}
@article{Wang2014
author = {Wang, Lee-Ping and Martinez, Todd J. and Pande, Vijay S.},
title = {Building force fields: an automatic, systematic, and reproducible approach},
journal = {Journal of Physical Chemistry Letters},
volume = {5},
pages = {1885-1891},
year = {2014},
type = {Journal Article}
}
docs-source/usersguide/theory.rst 0 → 100644
View file @ 67004571
This diff is collapsed.
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment