resolved conflict

README.md

@@ -18,7 +18,7 @@ Need Help? Check out the [documentation](http://docs.openmm.org/) and [discussio
 Badges
 ------
 * Travis CI `linux` and `osx` integration tests:
-  * GitHub master [![Build Status](https://travis-ci.org/pandegroup/openmm.png?branch=master)](https://travis-ci.org/pandegroup/openmm)
+  * GitHub master [![Build Status](https://travis-ci.org/pandegroup/openmm.svg?branch=master)](https://travis-ci.org/pandegroup/openmm)
   * `openmm-dev` recipe [![Build Status](https://travis-ci.org/omnia-md/conda-dev-recipes.svg?branch=master)](https://travis-ci.org/omnia-md/conda-dev-recipes)
 * Anaconda Cloud `openmm` conda release: [![Binstar `openmm` conda release](https://anaconda.org/omnia/openmm/badges/version.svg)](https://anaconda.org/omnia/openmm)
 * Anaconda Cloud `openmm-dev` conda package: [![Binstar `openmm-dev` conda package](https://anaconda.org/omnia/openmm-dev/badges/version.svg)](https://anaconda.org/omnia/openmm-dev)

docs-source/CMakeLists.txt

@@ -27,16 +27,23 @@ FILE(MAKE_DIRECTORY "${SPHINX_BUILD_DIR}")
 
 FILE(GLOB_RECURSE USER_GUIDE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/usersguide/*)
 FILE(GLOB_RECURSE DEVELOPER_GUIDE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/developerguide/*)
+IF(WIN32)
+    SET(SPHINX_MAKE_USERGUIDE_COMMAND "${CMAKE_COMMAND}" -E env "OPENMM_VERSION=${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" "BUILDDIR=${SPHINX_BUILD_DIR}/userguide" make.bat)
+    SET(SPHINX_MAKE_DEVELOPERGUIDE_COMMAND "${CMAKE_COMMAND}" -E env "OPENMM_VERSION=${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" "BUILDDIR=${SPHINX_BUILD_DIR}/developerguide" make.bat)
+ELSE(WIN32)
+    SET(SPHINX_MAKE_USERGUIDE_COMMAND "${CMAKE_MAKE_PROGRAM}" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" BUILDDIR="${SPHINX_BUILD_DIR}/userguide")
+    SET(SPHINX_MAKE_DEVELOPERGUIDE_COMMAND "${CMAKE_MAKE_PROGRAM}" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" BUILDDIR="${SPHINX_BUILD_DIR}/developerguide")
+ENDIF(WIN32)
 ADD_CUSTOM_COMMAND(
     OUTPUT "${SPHINX_BUILD_DIR}/userguide/latex/OpenMMUsersGuide.pdf"
-    COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/userguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" latexpdf
+    COMMAND ${SPHINX_MAKE_USERGUIDE_COMMAND} latexpdf
     DEPENDS ${USER_GUIDE_FILES}
     WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/usersguide"
     COMMENT "Generating PDF user guide"
 )
 ADD_CUSTOM_COMMAND(
     OUTPUT "${SPHINX_BUILD_DIR}/developerguide/latex/OpenMMDeveloperGuide.pdf"
-    COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/developerguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" latexpdf
+    COMMAND ${SPHINX_MAKE_DEVELOPERGUIDE_COMMAND} latexpdf
     DEPENDS ${DEVELOPER_GUIDE_FILES}
     WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/developerguide"
     COMMENT "Generating PDF developer guide"
@@ -47,14 +54,14 @@ ADD_CUSTOM_TARGET(sphinxpdf
 
 ADD_CUSTOM_COMMAND(
     OUTPUT "${SPHINX_BUILD_DIR}/userguide/html/index.html"
-    COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/userguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" html
+    COMMAND ${SPHINX_MAKE_USERGUIDE_COMMAND} html
     DEPENDS ${USER_GUIDE_FILES}
     WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/usersguide"
     COMMENT "Generating HTML user guide"
 )
 ADD_CUSTOM_COMMAND(
     OUTPUT "${SPHINX_BUILD_DIR}/developerguide/html/index.html"
-    COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/developerguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" html
+    COMMAND ${SPHINX_MAKE_DEVELOPERGUIDE_COMMAND} html
     DEPENDS ${DEVELOPER_GUIDE_FILES}
     WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/developerguide"
     COMMENT "Generating HTML developer guide"

docs-source/developerguide/license.rst

-Portions copyright (c) 2011-2015 Stanford University and the Authors
+Portions copyright (c) 2011-2016 Stanford University and the Authors
 
 Contributors: Peter Eastman
 

docs-source/developerguide/make.bat

+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+REM set BUILDDIR=_build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+set I18NSPHINXOPTS=%SPHINXOPTS% .
+if NOT "%PAPER%" == "" (
+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+	:help
+	echo.Please use `make ^<target^>` where ^<target^> is one of
+	echo.  html       to make standalone HTML files
+	echo.  dirhtml    to make HTML files named index.html in directories
+	echo.  singlehtml to make a single large HTML file
+	echo.  pickle     to make pickle files
+	echo.  json       to make JSON files
+	echo.  htmlhelp   to make HTML files and a HTML help project
+	echo.  qthelp     to make HTML files and a qthelp project
+	echo.  devhelp    to make HTML files and a Devhelp project
+	echo.  epub       to make an epub
+	echo.  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+	echo.  text       to make text files
+	echo.  man        to make manual pages
+	echo.  texinfo    to make Texinfo files
+	echo.  gettext    to make PO message catalogs
+	echo.  changes    to make an overview over all changed/added/deprecated items
+	echo.  xml        to make Docutils-native XML files
+	echo.  pseudoxml  to make pseudoxml-XML files for display purposes
+	echo.  linkcheck  to check all external links for integrity
+	echo.  doctest    to run all doctests embedded in the documentation if enabled
+	echo.  coverage   to run coverage check of the documentation if enabled
+	goto end
+)
+
+if "%1" == "clean" (
+	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+	del /q /s %BUILDDIR%\*
+	goto end
+)
+
+
+REM Check if sphinx-build is available and fallback to Python version if any
+%SPHINXBUILD% 2> nul
+if errorlevel 9009 goto sphinx_python
+goto sphinx_ok
+
+:sphinx_python
+
+set SPHINXBUILD=python -m sphinx.__init__
+%SPHINXBUILD% 2> nul
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+:sphinx_ok
+
+
+if "%1" == "html" (
+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+	goto end
+)
+
+if "%1" == "dirhtml" (
+	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+	goto end
+)
+
+if "%1" == "singlehtml" (
+	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+	goto end
+)
+
+if "%1" == "pickle" (
+	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the pickle files.
+	goto end
+)
+
+if "%1" == "json" (
+	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the JSON files.
+	goto end
+)
+
+if "%1" == "htmlhelp" (
+	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+	goto end
+)
+
+if "%1" == "qthelp" (
+	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\OpenMM.qhcp
+	echo.To view the help file:
+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\OpenMM.ghc
+	goto end
+)
+
+if "%1" == "devhelp" (
+	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished.
+	goto end
+)
+
+if "%1" == "epub" (
+	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The epub file is in %BUILDDIR%/epub.
+	goto end
+)
+
+if "%1" == "latex" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "latexpdf" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	cd %BUILDDIR%/latex
+	make all-pdf
+	cd %~dp0
+	echo.
+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "latexpdfja" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	cd %BUILDDIR%/latex
+	make all-pdf-ja
+	cd %~dp0
+	echo.
+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "text" (
+	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The text files are in %BUILDDIR%/text.
+	goto end
+)
+
+if "%1" == "man" (
+	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The manual pages are in %BUILDDIR%/man.
+	goto end
+)
+
+if "%1" == "texinfo" (
+	%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
+	goto end
+)
+
+if "%1" == "gettext" (
+	%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
+	goto end
+)
+
+if "%1" == "changes" (
+	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.The overview file is in %BUILDDIR%/changes.
+	goto end
+)
+
+if "%1" == "linkcheck" (
+	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+	goto end
+)
+
+if "%1" == "doctest" (
+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+	goto end
+)
+
+if "%1" == "coverage" (
+	%SPHINXBUILD% -b coverage %ALLSPHINXOPTS% %BUILDDIR%/coverage
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Testing of coverage in the sources finished, look at the ^
+results in %BUILDDIR%/coverage/python.txt.
+	goto end
+)
+
+if "%1" == "xml" (
+	%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The XML files are in %BUILDDIR%/xml.
+	goto end
+)
+
+if "%1" == "pseudoxml" (
+	%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
+	goto end
+)
+
+:end

docs-source/usersguide/application.rst

@@ -395,7 +395,7 @@ files in the newer PDBx/mmCIF format: just change :class:`PDBFile` to :class:`PD
 This line specifies the force field to use for the simulation.  Force fields are
 defined by XML files.  OpenMM includes XML files defining lots of standard force fields (see Section :ref:`force-fields`).
 If you find you need to extend the repertoire of force fields available,
-you can find more information on how to create these XML files in Section :ref:`creating-force-fields`.
+you can find more information on how to create these XML files in Chapter :ref:`creating-force-fields`.
 In this case we load two of those files: :file:`amber99sb.xml`, which contains the
 Amber99SB force field, and :file:`tip3p.xml`, which contains the TIP3P water model.  The
 :class:`ForceField` object is assigned to a variable called :code:`forcefield`\ .
@@ -417,10 +417,8 @@ Note the way we specified the cutoff distance 1 nm using :code:`1*nanometer`:
 This is an example of the powerful units tracking and automatic conversion facility
 built into the OpenMM Python API that makes specifying unit-bearing quantities
 convenient and less error-prone.  We could have equivalently specified
-:code:`10*angstrom` instead of :code:`1*nanometer` and achieved the same result,
-but had we specified the wrong dimensions, such as :code:`1*(nanometer**2)` or
-:code:`1*picoseconds`, OpenMM would have thrown an exception. The units system
-will be described in more detail later, in Section :ref:`units-and-dimensional-analysis`.
+:code:`10*angstrom` instead of :code:`1*nanometer` and achieved the same result.
+The units system will be described in more detail later, in Section :ref:`units-and-dimensional-analysis`.
 ::
 
     integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
@@ -748,7 +746,7 @@ double precision:
 ::
 
     platform = Platform.getPlatformByName('CUDA')
-    properties = {'CudaDeviceIndex': '0,1', 'CudaPrecision': 'double'}
+    properties = {'DeviceIndex': '0,1', 'Precision': 'double'}
     simulation = Simulation(prmtop.topology, system, integrator, platform, properties)
 
 .. _force-fields:
@@ -1322,11 +1320,12 @@ Writing Trajectories
 ====================
 
 
-OpenMM can save simulation trajectories to disk in two formats: PDB_ and DCD_.
-Both of these are widely supported formats, so you should be able to read them
-into most analysis and visualization programs.
+OpenMM can save simulation trajectories to disk in three formats: PDB_,
+`PDBx/mmCIF`_, and DCD_.  All of these are widely supported formats, so you
+should be able to read them into most analysis and visualization programs.
 
 .. _PDB: http://www.wwpdb.org/documentation/format33/v3.3.html
+.. _PDBx/mmCIF: http://mmcif.wwpdb.org
 .. _DCD: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html
 
 To save a trajectory, just add a “reporter” to the simulation, as shown in the
@@ -1336,9 +1335,9 @@ example scripts above:
     simulation.reporters.append(PDBReporter('output.pdb', 1000))
 
 The two parameters of the :class:`PDBReporter` are the output filename and how often (in
-number of time steps) output structures should be written.  To use DCD format,
-just replace :class:`PDBReporter` with :class:`DCDReporter`.  The parameters represent the
-same values:
+number of time steps) output structures should be written.  To use PDBx/mmCIF or
+DCD format, just replace :class:`PDBReporter` with :class:`PDBxReporter` or
+:class:`DCDReporter`.  The parameters represent the same values:
 ::
 
     simulation.reporters.append(DCDReporter('output.dcd', 1000))
@@ -1771,8 +1770,8 @@ not an arbitrary choice.
 Extracting and Reporting Forces (and other data)
 ************************************************
 
-OpenMM provides reporters for two output formats: PDB_ and DCD_.  Both of those
-formats store only positions, not velocities, forces, or other data.  In this
+OpenMM provides reporters for three output formats: PDB_, `PDBx/mmCIF`_ and DCD_.
+All of those formats store only positions, not velocities, forces, or other data.  In this
 section, we create a new reporter that outputs forces.  This illustrates two
 important things: how to write a reporter, and how to query the simulation for
 forces or other data.
@@ -1862,7 +1861,7 @@ the potential energy of each one.  Assume we have already created our :class:`Sy
             pdb = PDBFile(os.path.join('structures', file))
             simulation.context.setPositions(pdb.positions)
             state = simulation.context.getState(getEnergy=True)
-            print file, state.getPotentialEnergy()
+            print(file, state.getPotentialEnergy())
 
     .. caption::
 
@@ -2068,7 +2067,7 @@ Missing residue templates
 =========================
 
 .. CAUTION::
-   These features are experimental, and its API is subject to change.
+   These features are experimental, and their API is subject to change.
 
 You can use the :meth:`getUnmatchedResidues()` method to get a list of residues
 in the provided :code:`topology` object that do not currently have a matching
@@ -2106,7 +2105,7 @@ are being matched:
     forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
     templates = forcefield.getMatchingTemplates(topology)
     for (residue, template) in zip(pdb.topology.residues(), templates):
-        print "Residue %d %s matched template %s" % (residue.id, residue.name, template.name)
+        print("Residue %d %s matched template %s" % (residue.id, residue.name, template.name))
 
 <HarmonicBondForce>
 ===================
@@ -2916,17 +2915,19 @@ This :code:`generator` function must conform to the following API:
         -------
         success : bool
             If the generator is able to successfully parameterize the residue, `True` is returned.
-            If the generator cannot parameterize the residue, it should return `False` and not modify `forcefield`.
+            If the generator cannot parameterize the residue, it should return `False` and not
+            modify `forcefield`.
 
-        The generator should either register a residue template directly with `forcefield.registerResidueTemplate(template)`
-        or it should call `forcefield.loadFile(file)` to load residue definitions from an ffxml file.
+        The generator should either register a residue template directly with
+        `forcefield.registerResidueTemplate(template)` or it should call `forcefield.loadFile(file)`
+        to load residue definitions from an ffxml file.
 
-        It can also use the `ForceField` programmatic API to add additional atom types (via `forcefield.registerAtomType(parameters)`)
-        or additional parameters.
+        It can also use the `ForceField` programmatic API to add additional atom types (via
+        `forcefield.registerAtomType(parameters)`) or additional parameters.
 
         """
 
-The :code:`ForceField` object will be modified by the residue template generator as residues without previously
-defined templates are encountered.  Because these templates are added to `ForceField` as new residue
+The :class:`ForceField` object will be modified by the residue template generator as residues without previously
+defined templates are encountered.  Because these templates are added to the :class:`ForceField` as new residue
 types are encountered, subsequent residues will be parameterized using the same residue templates without
 calling the :code:`generator` again.

docs-source/usersguide/library.rst

@@ -347,11 +347,6 @@ The choice of which platform to use for a simulation depends on various factors:
    OpenCL platform running on the CPU.
 #. The CUDA platform can only be used with NVIDIA GPUs.  For using an AMD or
    Intel GPU, use the OpenCL platform.
-#. When running on recent NVIDIA GPUs (Fermi and Kepler generations), the CUDA
-   platform is usually faster and should be used.  On older GPUs, the OpenCL
-   platform is likely to be faster.  Also, some very old GPUs (GeForce 8000 and
-   9000 series) are only supported by the OpenCL platform, not by the CUDA
-   platform.
 #. The AMOEBA force field only works with the CUDA platform, not with the OpenCL
    platform.  It also works with the Reference and CPU platforms, but the performance
    is usually too slow to be useful on those platforms.
@@ -393,14 +388,9 @@ Mac and Linux: clang or gcc
 
 Use clang or gcc on Mac/Linux.  OpenMM should compile correctly with all recent
 versions of these compilers.  We recommend clang since it produces faster code,
-especially when using the CPU platform.
-
-If you do not already have a compiler installed, you will need to download and
-install it.  On Mac OS X, this means downloading the Xcode Tools from the App
-Store. (With Xcode 4.3, you must then launch Xcode, open the Preferences window,
-go to the Downloads tab, and tell it to install the command line tools.  With
-Xcode 4.2 and earlier, the command line tools are automatically installed when
-you install Xcode.)
+especially when using the CPU platform.  If you do not already have a compiler
+installed, you will need to download and install it.  On Mac OS X, this means
+downloading the Xcode Tools from the App Store.
 
 Windows: Visual Studio
 ----------------------
@@ -545,6 +535,8 @@ There are several variables that can be adjusted in the CMake interface:
   and documentation.
 * Set the variable CMAKE_INSTALL_PREFIX to the location where you want to
   install OpenMM.
+* Set the variable PYTHON_EXECUTABLE to the Python interpreter you plan to use
+  OpenMM with.
 
 
 Configure (press “c”) again.  Adjust any variables that cause an
@@ -1844,7 +1836,7 @@ Context constructor:
 
     Platform& platform = Platform::getPlatformByName("OpenCL");
     map<string, string> properties;
-    properties["OpenCLDeviceIndex"] = "1";
+    properties["DeviceIndex"] = "1";
     Context context(system, integrator, platform, properties);
 
 After a Context is created, you can use the Platform’s \
@@ -1855,7 +1847,7 @@ OpenCL Platform
 
 The OpenCL Platform recognizes the following Platform-specific properties:
 
-* OpenCLPrecision: This selects what numeric precision to use for calculations.
+* Precision: This selects what numeric precision to use for calculations.
   The allowed values are “single”, “mixed”, and “double”.  If it is set to
   “single”, nearly all calculations are done in single precision.  This is the
   fastest option but also the least accurate.  If it is set to “mixed”, forces are
@@ -1863,7 +1855,7 @@ The OpenCL Platform recognizes the following Platform-specific properties:
   gives much better energy conservation with only a slight decrease in speed.
   If it is set to “double”, all calculations are done in double precision.  This
   is the most accurate option, but is usually much slower than the others.
-* OpenCLUseCpuPme: This selects whether to use the CPU-based PME
+* UseCpuPme: This selects whether to use the CPU-based PME
   implementation.  The allowed values are “true” or “false”.  Depending on your
   hardware, this might (or might not) improve performance.  To use this option,
   you must have FFTW (single precision, multithreaded) installed, and your CPU
@@ -1873,19 +1865,19 @@ The OpenCL Platform recognizes the following Platform-specific properties:
   zero-based index of the platform (in the OpenCL sense, not the OpenMM sense) to use,
   in the order they are returned by the OpenCL platform API.  This is useful, for
   example, in selecting whether to use a GPU or CPU based OpenCL implementation.
-* OpenCLDeviceIndex: When multiple OpenCL devices are available on your
+* DeviceIndex: When multiple OpenCL devices are available on your
   computer, this is used to select which one to use.  The value is the zero-based
   index of the device to use, in the order they are returned by the OpenCL device
   API.
 
 
 The OpenCL Platform also supports parallelizing a simulation across multiple
-GPUs.  To do that, set the OpenCLDeviceIndex property to a comma separated list
+GPUs.  To do that, set the DeviceIndex property to a comma separated list
 of values.  For example,
 
 .. code-block:: c
 
-    properties["OpenCLDeviceIndex"] = "0,1";
+    properties["DeviceIndex"] = "0,1";
 
 This tells it to use both devices 0 and 1, splitting the work between them.
 
@@ -1894,7 +1886,7 @@ CUDA Platform
 
 The CUDA Platform recognizes the following Platform-specific properties:
 
-* CudaPrecision: This selects what numeric precision to use for calculations.
+* Precision: This selects what numeric precision to use for calculations.
   The allowed values are “single”, “mixed”, and “double”.  If it is set to
   “single”, nearly all calculations are done in single precision.  This is the
   fastest option but also the least accurate.  If it is set to “mixed”, forces are
@@ -1902,7 +1894,7 @@ The CUDA Platform recognizes the following Platform-specific properties:
   gives much better energy conservation with only a slight decrease in speed.
   If it is set to “double”, all calculations are done in double precision.  This
   is the most accurate option, but is usually much slower than the others.
-* CudaUseCpuPme: This selects whether to use the CPU-based PME implementation.
+* UseCpuPme: This selects whether to use the CPU-based PME implementation.
   The allowed values are “true” or “false”.  Depending on your hardware, this
   might (or might not) improve performance.  To use this option, you must have
   FFTW (single precision, multithreaded) installed, and your CPU must support SSE
@@ -1920,28 +1912,36 @@ The CUDA Platform recognizes the following Platform-specific properties:
     appends \nvcc.exe to it.  That environment variable is set by the CUDA
     installer, so it usually is present.
 
-* CudaTempDirectory: This specifies a directory where temporary files can be
+* TempDirectory: This specifies a directory where temporary files can be
   written while compiling kernels.  OpenMM usually can locate your operating
   system’s temp directory automatically (for example, by looking for the TEMP
   environment variable), so you rarely need to specify this.
-* CudaDeviceIndex: When multiple CUDA devices are available on your computer,
+* DeviceIndex: When multiple CUDA devices are available on your computer,
   this is used to select which one to use.  The value is the zero-based index of
   the device to use, in the order they are returned by the CUDA API.
-* CudaUseBlockingSync: This is used to control how the CUDA runtime
+* UseBlockingSync: This is used to control how the CUDA runtime
   synchronizes between the CPU and GPU.  If this is set to “true” (the default),
   CUDA will allow the calling thread to sleep while the GPU is performing a
   computation, allowing the CPU to do other work.  If it is set to “false”, CUDA
   will spin-lock while the GPU is working.  Setting it to "false" can improve performance slightly,
   but also prevents the CPU from doing anything else while the GPU is working.
-
+* DeterministicForces: In some cases, the CUDA platform may compute forces
+  in ways that are not fully deterministic (typically differing in what order a
+  set of numbers get added together).  This means that if you compute the forces
+  twice for the same particle positions, there may be tiny differences in the
+  results.  In most cases this is not a problem, but certain algorithms depend
+  on forces being exactly reproducible to the last bit.  If you set this
+  property to "true", it will instead do these calculations in a way that
+  produces fully deterministic results, at the cost of a small decrease in
+  performance.
 
 The CUDA Platform also supports parallelizing a simulation across multiple GPUs.
-To do that, set the CudaDeviceIndex property to a comma separated list of
+To do that, set the DeviceIndex property to a comma separated list of
 values.  For example,
 
 .. code-block:: c
 
-    properties["CudaDeviceIndex"] = "0,1";
+    properties["DeviceIndex"] = "0,1";
 
 This tells it to use both devices 0 and 1, splitting the work between them.
 
@@ -1950,7 +1950,7 @@ CPU Platform
 
 The CPU Platform recognizes the following Platform-specific properties:
 
-* CpuThreads: This specifies the number of CPU threads to use.  If you do not
+* Threads: This specifies the number of CPU threads to use.  If you do not
   specify this, OpenMM will select a default number of threads as follows:
 
   * If an environment variable called OPENMM_CPU_THREADS is set, its value is

docs-source/usersguide/license.rst

-Portions copyright (c) 2008-2015 Stanford University and the Authors
+Portions copyright (c) 2008-2016 Stanford University and the Authors
 
 Contributors:  Kyle Beauchamp, Christopher Bruns, John Chodera, Peter Eastman, Mark
 Friedrichs, Joy P. Ku, Tom Markland, Vijay Pande, Randy Radmer, Michael Sherman,

docs-source/usersguide/make.bat

+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+REM set BUILDDIR=_build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+set I18NSPHINXOPTS=%SPHINXOPTS% .
+if NOT "%PAPER%" == "" (
+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+	:help
+	echo.Please use `make ^<target^>` where ^<target^> is one of
+	echo.  html       to make standalone HTML files
+	echo.  dirhtml    to make HTML files named index.html in directories
+	echo.  singlehtml to make a single large HTML file
+	echo.  pickle     to make pickle files
+	echo.  json       to make JSON files
+	echo.  htmlhelp   to make HTML files and a HTML help project
+	echo.  qthelp     to make HTML files and a qthelp project
+	echo.  devhelp    to make HTML files and a Devhelp project
+	echo.  epub       to make an epub
+	echo.  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+	echo.  text       to make text files
+	echo.  man        to make manual pages
+	echo.  texinfo    to make Texinfo files
+	echo.  gettext    to make PO message catalogs
+	echo.  changes    to make an overview over all changed/added/deprecated items
+	echo.  xml        to make Docutils-native XML files
+	echo.  pseudoxml  to make pseudoxml-XML files for display purposes
+	echo.  linkcheck  to check all external links for integrity
+	echo.  doctest    to run all doctests embedded in the documentation if enabled
+	echo.  coverage   to run coverage check of the documentation if enabled
+	goto end
+)
+
+if "%1" == "clean" (
+	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+	del /q /s %BUILDDIR%\*
+	goto end
+)
+
+
+REM Check if sphinx-build is available and fallback to Python version if any
+%SPHINXBUILD% 2> nul
+if errorlevel 9009 goto sphinx_python
+goto sphinx_ok
+
+:sphinx_python
+
+set SPHINXBUILD=python -m sphinx.__init__
+%SPHINXBUILD% 2> nul
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+:sphinx_ok
+
+
+if "%1" == "html" (
+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+	goto end
+)
+
+if "%1" == "dirhtml" (
+	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+	goto end
+)
+
+if "%1" == "singlehtml" (
+	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+	goto end
+)
+
+if "%1" == "pickle" (
+	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the pickle files.
+	goto end
+)
+
+if "%1" == "json" (
+	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the JSON files.
+	goto end
+)
+
+if "%1" == "htmlhelp" (
+	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+	goto end
+)
+
+if "%1" == "qthelp" (
+	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\OpenMM.qhcp
+	echo.To view the help file:
+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\OpenMM.ghc
+	goto end
+)
+
+if "%1" == "devhelp" (
+	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished.
+	goto end
+)
+
+if "%1" == "epub" (
+	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The epub file is in %BUILDDIR%/epub.
+	goto end
+)
+
+if "%1" == "latex" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "latexpdf" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	cd %BUILDDIR%/latex
+	make all-pdf
+	cd %~dp0
+	echo.
+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "latexpdfja" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	cd %BUILDDIR%/latex
+	make all-pdf-ja
+	cd %~dp0
+	echo.
+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "text" (
+	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The text files are in %BUILDDIR%/text.
+	goto end
+)
+
+if "%1" == "man" (
+	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The manual pages are in %BUILDDIR%/man.
+	goto end
+)
+
+if "%1" == "texinfo" (
+	%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
+	goto end
+)
+
+if "%1" == "gettext" (
+	%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
+	goto end
+)
+
+if "%1" == "changes" (
+	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.The overview file is in %BUILDDIR%/changes.
+	goto end
+)
+
+if "%1" == "linkcheck" (
+	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+	goto end
+)
+
+if "%1" == "doctest" (
+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+	goto end
+)
+
+if "%1" == "coverage" (
+	%SPHINXBUILD% -b coverage %ALLSPHINXOPTS% %BUILDDIR%/coverage
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Testing of coverage in the sources finished, look at the ^
+results in %BUILDDIR%/coverage/python.txt.
+	goto end
+)
+
+if "%1" == "xml" (
+	%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The XML files are in %BUILDDIR%/xml.
+	goto end
+)
+
+if "%1" == "pseudoxml" (
+	%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
+	goto end
+)
+
+:end

examples/benchmark.py

@@ -81,18 +81,12 @@ def runOneTest(testName, options):
     print('Step Size: %g fs' % dt.value_in_unit(unit.femtoseconds))
     properties = {}
     initialSteps = 5
-    if options.device is not None:
-        if platform.getName() == 'CUDA':
-            properties['CudaDeviceIndex'] = options.device
-        elif platform.getName() == 'OpenCL':
-            properties['OpenCLDeviceIndex'] = options.device
+    if options.device is not None and platform.getName() in ('CUDA', 'OpenCL'):
+        properties['DeviceIndex'] = options.device
         if ',' in options.device or ' ' in options.device:
             initialSteps = 250
-    if options.precision is not None:
-        if platform.getName() == 'CUDA':
-            properties['CudaPrecision'] = options.precision
-        elif platform.getName() == 'OpenCL':
-            properties['OpenCLPrecision'] = options.precision
+    if options.precision is not None and platform.getName() in ('CUDA', 'OpenCL'):
+        properties['Precision'] = options.precision
     
     # Run the simulation.
     

libraries/lepton/src/CompiledExpression.cpp

@@ -78,6 +78,7 @@ CompiledExpression& CompiledExpression::operator=(const CompiledExpression& expr
     for (int i = 0; i < (int) operation.size(); i++)
         operation[i] = expression.operation[i]->clone();
 #ifdef LEPTON_USE_JIT
+    if (workspace.size() > 0)
         generateJitCode();
 #endif
     return *this;

olla/include/openmm/Platform.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -236,7 +236,9 @@ protected:
      */
     const ContextImpl& getContextImpl(const Context& context) const;
     std::vector<std::string> platformProperties;
+    std::map<std::string, std::string> deprecatedPropertyReplacements;
 private:
+    friend class ContextImpl;
     std::map<std::string, KernelFactory*> kernelFactories;
     std::map<std::string, std::string> defaultProperties;
     static std::vector<Platform*>& getPlatforms();

olla/include/openmm/kernels.h

@@ -187,7 +187,7 @@ public:
      * @param b      the vector defining the second edge of the periodic box
      * @param c      the vector defining the third edge of the periodic box
      */
-    virtual void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const = 0;
+    virtual void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) = 0;
     /**
      * Create a checkpoint recording the current state of the Context.
      * 

olla/src/Platform.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -89,15 +89,21 @@ void Platform::setPropertyValue(Context& context, const string& property, const
 }
 
 const string& Platform::getPropertyDefaultValue(const string& property) const {
-    map<string, string>::const_iterator value = defaultProperties.find(property);
+    string propertyName = property;
+    if (deprecatedPropertyReplacements.find(property) != deprecatedPropertyReplacements.end())
+        propertyName = deprecatedPropertyReplacements.find(property)->second;
+    map<string, string>::const_iterator value = defaultProperties.find(propertyName);
     if (value == defaultProperties.end())
         throw OpenMMException("getPropertyDefaultValue: Illegal property name");
     return value->second;
 }
 
 void Platform::setPropertyDefaultValue(const string& property, const string& value) {
+    string propertyName = property;
+    if (deprecatedPropertyReplacements.find(property) != deprecatedPropertyReplacements.end())
+        propertyName = deprecatedPropertyReplacements.find(property)->second;
     for (int i = 0; i < (int) platformProperties.size(); i++)
-        if (platformProperties[i] == property) {
+        if (platformProperties[i] == propertyName) {
             defaultProperties[property] = value;
             return;
         }
@@ -314,7 +320,11 @@ const string& Platform::getDefaultPluginsDirectory() {
 #define STRING(x) STRING1(x)
 
 const string& Platform::getOpenMMVersion() {
+#if OPENMM_BUILD_VERSION == 0
     static const string version = STRING(OPENMM_MAJOR_VERSION) "." STRING(OPENMM_MINOR_VERSION);
+#else
+    static const string version = STRING(OPENMM_MAJOR_VERSION) "." STRING(OPENMM_MINOR_VERSION) "." STRING(OPENMM_BUILD_VERSION);
+#endif
     return version;
 }
 

openmmapi/include/openmm/CMAPTorsionForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -159,15 +159,18 @@ public:
      * new bonds and torsions cannot be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns false
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
@@ -175,6 +178,7 @@ private:
     class CMAPTorsionInfo;
     std::vector<MapInfo> maps;
     std::vector<CMAPTorsionInfo> torsions;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/CustomAngleForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -203,15 +203,18 @@ public:
      * the Context.  The set of particles involved in a angle cannot be changed, nor can new angles be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns false
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
@@ -222,6 +225,7 @@ private:
     std::vector<AngleParameterInfo> parameters;
     std::vector<GlobalParameterInfo> globalParameters;
     std::vector<AngleInfo> angles;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/CustomBondForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -200,15 +200,18 @@ public:
      * the Context.  The set of particles involved in a bond cannot be changed, nor can new bonds be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns false
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
@@ -219,6 +222,7 @@ private:
     std::vector<BondParameterInfo> parameters;
     std::vector<GlobalParameterInfo> globalParameters;
     std::vector<BondInfo> bonds;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/CustomCentroidBondForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -324,15 +324,18 @@ public:
      * bonds be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns false
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
@@ -348,6 +351,7 @@ private:
     std::vector<GroupInfo> groups;
     std::vector<BondInfo> bonds;
     std::vector<FunctionInfo> functions;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/CustomCompoundBondForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -298,15 +298,18 @@ public:
      * the Context.  The set of particles involved in a bond cannot be changed, nor can new bonds be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns false
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
@@ -320,6 +323,7 @@ private:
     std::vector<GlobalParameterInfo> globalParameters;
     std::vector<BondInfo> bonds;
     std::vector<FunctionInfo> functions;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/CustomIntegrator.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2011-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2011-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -266,15 +266,15 @@ public:
         /**
          * Begin an "if" block.
          */
-        BeginIfBlock = 6,
+        IfBlockStart = 6,
         /**
          * Begin a while" block.
          */
-        BeginWhileBlock = 7,
+        WhileBlockStart = 7,
         /**
          * End an "if" or "while" block.
          */
-        EndBlock = 8
+        BlockEnd = 8
     };
     /**
      * Create a CustomIntegrator.

openmmapi/include/openmm/CustomTorsionForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -206,15 +206,18 @@ public:
      * the Context.  The set of particles involved in a torsion cannot be changed, nor can new torsions be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
      * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
@@ -225,6 +228,7 @@ private:
     std::vector<TorsionParameterInfo> parameters;
     std::vector<GlobalParameterInfo> globalParameters;
     std::vector<TorsionInfo> torsions;
+    bool usePeriodic;
 };
 
 /**