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Commit c4acc7d2 authored by peastman's avatar peastman
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Merge pull request #580 from peastman/docs 

Updates to documentation for 6.1
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docs/usersguide/Makefile deleted 100644 → 0
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# 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:
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@echo "Run \`make' in that directory to run these through (pdf)latex" \
"(use \`make latexpdf' here to do that automatically)."
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@echo "Running LaTeX files through pdflatex..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
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@echo "Running Texinfo files through makeinfo..."
make -C $(BUILDDIR)/texinfo info
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@echo
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@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/usersguide/application.rst deleted 100644 → 0
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docs/usersguide/conf.py deleted 100644 → 0
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# -*- 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/usersguide/header.rst deleted 100644 → 0
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.. role:: code
.. raw:: html
<style> .code {font-family:monospace;} </style>
<style> .caption {text-align:center;} </style>
.. |--| replace:: :option:`--`
docs/usersguide/index.rst deleted 100644 → 0
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.. 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/usersguide/introduction.rst deleted 100644 → 0
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.. 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.
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.. only:: html
Bibliography
############
.. bibliography:: references.bib
:style: unsrt
examples/simulateAmber.py
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......@@ -9,6 +9,8 @@ system = prmtop.createSystem(nonbondedMethod=PME, nonbondedCutoff=1*nanometer, c
integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
simulation = Simulation(prmtop.topology, system, integrator)
simulation.context.setPositions(inpcrd.positions)
if inpcrd.boxVectors is not None:
simulation.context.setPeriodicBoxVectors(*inpcrd.boxVectors)
simulation.minimizeEnergy()
simulation.reporters.append(PDBReporter('output.pdb', 1000))
simulation.reporters.append(StateDataReporter(stdout, 1000, step=True, potentialEnergy=True, temperature=True))
......
openmmapi/include/openmm/GBVIForce.h
View file @ c4acc7d2
......@@ -46,6 +46,8 @@ namespace OpenMM {
* be exactly equal to the number of particles in the System, or else an exception will be thrown when you
* try to create a Context. After a particle has been added, you can modify its force field parameters
* by calling setParticleParameters().
*
* @deprecated This class is not supported by most platforms, and will eventually be removed. You can implement the same force with CustomGBForce.
*/
class OPENMM_EXPORT GBVIForce : public Force {
......
openmmapi/include/openmm/NonbondedForce.h
View file @ c4acc7d2
......@@ -46,7 +46,7 @@ namespace OpenMM {
* This class implements nonbonded interactions between particles, including a Coulomb force to represent
* electrostatics and a Lennard-Jones force to represent van der Waals interactions. It optionally supports
* periodic boundary conditions and cutoffs for long range interactions. Lennard-Jones interactions are
* calculated with the Lorentz-Bertelot combining rule: it uses the arithmetic mean of the sigmas and the
* calculated with the Lorentz-Berthelot combining rule: it uses the arithmetic mean of the sigmas and the
* geometric mean of the epsilons for the two interacting particles.
*
* To use this class, create a NonbondedForce object, then call addParticle() once for each particle in the
......@@ -221,7 +221,7 @@ public:
* Add the nonbonded force parameters for a particle. This should be called once for each particle
* in the System. When it is called for the i'th time, it specifies the parameters for the i'th particle.
* For calculating the Lennard-Jones interaction between two particles, the arithmetic mean of the sigmas
* and the geometric mean of the epsilons for the two interacting particles is used (the Lorentz-Bertelot
* and the geometric mean of the epsilons for the two interacting particles is used (the Lorentz-Berthelot
* combining rule).
*
* @param charge the charge of the particle, measured in units of the proton charge
......@@ -242,7 +242,7 @@ public:
/**
* Set the nonbonded force parameters for a particle. When calculating the Lennard-Jones interaction between two particles,
* it uses the arithmetic mean of the sigmas and the geometric mean of the epsilons for the two interacting particles
* (the Lorentz-Bertelot combining rule).
* (the Lorentz-Berthelot combining rule).
*
* @param index the index of the particle for which to set parameters
* @param charge the charge of the particle, measured in units of the proton charge
......
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