Merge master

.travis.yml

@@ -73,6 +73,7 @@ matrix:
            CUDA=false
            CC=clang
            CXX=clang++
+           DOCS_DEPLOY=true
            CMAKE_FLAGS=""
 
     - sudo: false
@@ -98,11 +99,11 @@ before_install:
   # but this is a fast way to get an apparently functional precompiled
   # build of swig that's more modern than what's in apt.
   - if [[ "$OPENCL" == "false" && "$CUDA" == "false" && "$TRAVIS_OS_NAME" == "linux" ]]; then
-      wget https://anaconda.org/anaconda/swig/3.0.2/download/linux-64/swig-3.0.2-0.tar.bz2;
+      wget https://anaconda.org/omnia/swig/3.0.7/download/linux-64/swig-3.0.7-0.tar.bz2;
       mkdir $HOME/swig;
-      tar -xjvf swig-3.0.2-0.tar.bz2 -C $HOME/swig;
+      tar -xjvf swig-3.0.7-0.tar.bz2 -C $HOME/swig;
       export PATH=$HOME/swig/bin:$PATH;
-      export SWIG_LIB=$HOME/swig/share/swig/3.0.2;
+      export SWIG_LIB=$HOME/swig/share/swig/3.0.7;
     fi
 
   - if [[ "$CUDA" == "true" ]]; then
@@ -140,3 +141,25 @@ script:
   - if [ -s Testing/Temporary/LastTestsFailed.log ]; then
       ctest -I FailedTests.log;
     fi
+  - if [[ ! -z "${DOCS_DEPLOY}" && "${DOCS_DEPLOY}" = "true" ]]; then
+      pip install sphinx numpydoc;
+      make DoxygenApiDocs PythonApiDocs;
+      mkdir -p api-docs;
+      mv api-python api-docs;
+      mv api-c++ api-docs;
+    fi
+
+deploy:
+  - provider: s3
+    access_key_id:
+      secure: "AjE3nuj6kVuf21mOf0aZydW/3S/uCWsaoXC/huRxkxrmsNlnHBNGHZ9N48san1IxZAQM5pyaf7Yo9gkHur9obgq+e3lNgGvPp2mfkNXtLYcLJ46JF4kYliAtutjLWskrLg25Gu3xzF4EQkqSe0Le/oWldWWbTgvvH+KRq/vTHzI="
+    secret_access_key:
+      secure: "ISDQNSG2t0666PULtffo4wsKLFdu622EzuZxmiTxvLkjQGQlqm5+qn1Gd5UMLk7Ts2E0psdnmSrf6LVVCfrrQO/hcZHiJw3ZslMPDBBlRr8Epwdldn98ULhVoyQKtjXjCPzroa2UZCl1RFs4Nwb/VdDlI490XV0Lp4Woj1AT8tY="
+    bucket: "docs.openmm.org"
+    skip_cleanup: true
+    region: us-west-1
+    local_dir: api-docs/
+    upload_dir: development
+    on:
+      branch: master
+      condition: '! -z "${DOCS_DEPLOY}" && "${DOCS_DEPLOY}" = "true"'

CMakeLists.txt

@@ -65,6 +65,11 @@ ELSE(WIN32)
     ENDIF(NOT OPENMM_INSTALL_PREFIX)
 ENDIF(WIN32)
 
+IF(WIN32)
+    ADD_DEFINITIONS(-DWIN32)
+ENDIF(WIN32)
+
+
 # Include CPU-Features for Android
 IF (ANDROID)
     INCLUDE_DIRECTORIES(${ANDROID_NDK}/sources/cpufeatures)
@@ -119,7 +124,7 @@ IF (APPLE AND (NOT PNACL))
         SET (CMAKE_OSX_ARCHITECTURES "x86_64" CACHE STRING "The processor architectures to build for" FORCE)
     ENDIF (NOT CMAKE_OSX_ARCHITECTURES)
     IF (NOT CMAKE_OSX_SYSROOT)
-        EXECUTE_PROCESS(COMMAND "xcrun" "--show-sdk-path" OUTPUT_VARIABLE XCRUN_OSX_SYSROOT RESULT_VARIABLE XCRUN_OSX_SYSROOT_STATUS)
+        EXECUTE_PROCESS(COMMAND "xcrun" "--show-sdk-path" OUTPUT_VARIABLE XCRUN_OSX_SYSROOT RESULT_VARIABLE XCRUN_OSX_SYSROOT_STATUS OUTPUT_STRIP_TRAILING_WHITESPACE)
         IF (XCRUN_OSX_SYSROOT_STATUS EQUAL 0)
             SET (CMAKE_OSX_SYSROOT "${XCRUN_OSX_SYSROOT}" CACHE STRING "SDK Path" FORCE)
         ENDIF (XCRUN_OSX_SYSROOT_STATUS EQUAL 0)

appveyor.yml

@@ -20,7 +20,7 @@ install:
   - "set PATH=C:\\fftw;%PATH%"
 
 # Download and install some OpenMM build dependencies (doxygen, swig)
-  - choco install -y doxygen.portable swig
+  - choco install -y doxygen.portable swig > null
 
 # Set CMake options
   - ps: $env:CMAKE_FLAGS='-DOPENMM_BUILD_PME_PLUGIN=ON -DFFTW_LIBRARY=C:/fftw/libfftw3f-3.lib -DFFTW_INCLUDES=C:/fftw -DCMAKE_BUILD_TYPE=Release -DOPENMM_BUILD_EXAMPLES=OFF -DCMAKE_CXX_FLAGS_RELEASE="/MD /Od /Ob0 /D NDEBUG"'

docs-source/usersguide/application.rst

@@ -1125,6 +1125,13 @@ perform integration on a modified potential energy surface to allow much faster
 sampling of conformations.  For details on how to use them, consult the API
 documentation.
 
+Compound Integrator
+-------------------
+
+The :class:`CompoundIntegrator` class is useful for cases where you want to use
+multiple integration algorithms within a single simulation.  It allows you to
+create multiple integrators, then switch back and forth between them.  For
+details on how to use it, consult the API documentation.
 
 Temperature Coupling
 ====================

libraries/pthreads/include/pthread.h

@@ -121,6 +121,9 @@
 #endif
 
 
+#if _MSC_VER >= 1900
+#include <ctime>
+#else
 /* Windows doesn't have this, so declare it ourselves. */
 struct timespec
 {
@@ -128,6 +131,7 @@ struct timespec
 	long long tv_sec;
 	long long tv_nsec;
 };
+#endif
 
 typedef struct _pthread_cleanup _pthread_cleanup;
 struct _pthread_cleanup

openmmapi/include/OpenMM.h

@@ -36,6 +36,7 @@
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMAPTorsionForce.h"
 #include "openmm/CMMotionRemover.h"
+#include "openmm/CompoundIntegrator.h"
 #include "openmm/CustomBondForce.h"
 #include "openmm/CustomCentroidBondForce.h"
 #include "openmm/CustomCompoundBondForce.h"

openmmapi/include/openmm/CMAPTorsionForce.h

@@ -85,8 +85,8 @@ public:
      * Get the energy values of a map.
      *
      * @param index        the index of the map for which to get energy values
-     * @param size    the size of the map along each dimension
-     * @param energy  the energy values for the map.  This must be of length size*size.
+     * @param[out] size    the size of the map along each dimension
+     * @param[out] energy  the energy values for the map.  This must be of length size*size.
      *                     The element energy[i+size*j] contains the energy when the first
      *                     torsion angle equals i*2*PI/size and the second torsion angle
      *                     equals j*2*PI/size.
@@ -122,15 +122,15 @@ public:
      * Get the force field parameters for a CMAP torsion term.
      *
      * @param index      the index of the torsion for which to get parameters
-     * @param map   the index of the map to use for this term
-     * @param a1    the index of the first particle forming the first torsion
-     * @param a2    the index of the second particle forming the first torsion
-     * @param a3    the index of the third particle forming the first torsion
-     * @param a4    the index of the fourth particle forming the first torsion
-     * @param b1    the index of the first particle forming the second torsion
-     * @param b2    the index of the second particle forming the second torsion
-     * @param b3    the index of the third particle forming the second torsion
-     * @param b4    the index of the fourth particle forming the second torsion
+     * @param[out] map   the index of the map to use for this term
+     * @param[out] a1    the index of the first particle forming the first torsion
+     * @param[out] a2    the index of the second particle forming the first torsion
+     * @param[out] a3    the index of the third particle forming the first torsion
+     * @param[out] a4    the index of the fourth particle forming the first torsion
+     * @param[out] b1    the index of the first particle forming the second torsion
+     * @param[out] b2    the index of the second particle forming the second torsion
+     * @param[out] b3    the index of the third particle forming the second torsion
+     * @param[out] b4    the index of the fourth particle forming the second torsion
      */
     void getTorsionParameters(int index, int& map, int& a1, int& a2, int& a3, int& a4, int& b1, int& b2, int& b3, int& b4) const;
     /**

openmmapi/include/openmm/CompoundIntegrator.h

+#ifndef OPENMM_COMPOUNDINTEGRATOR_H_
+#define OPENMM_COMPOUNDINTEGRATOR_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * 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 (c) 2015 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "Integrator.h"
+#include "openmm/Kernel.h"
+#include "internal/windowsExport.h"
+
+namespace OpenMM {
+
+/**
+ * This class allows you to use multiple integration algorithms within a single simulation,
+ * switching back and forth between them.  To use it, create whatever other Integrators
+ * you need, then add all of them to a CustomIntegrator:
+ * 
+ * <tt><pre>
+ * CompoundIntegrator compoundIntegrator;
+ * compoundIntegrator.addIntegrator(new VerletIntegrator(0.001));
+ * compoundIntegrator.addIntegrator(new LangevinIntegrator(300.0, 1.0, 0.001));
+ * </pre></tt>
+ * 
+ * Next create a Context, specifying the CompoundIntegrator as the Integrator to use for
+ * the Context:
+ * 
+ * <tt><pre>
+ * Context context(system, compoundIntegrator);
+ * </pre></tt>
+ * 
+ * Finally, call setCurrentIntegrator() to set which Integrator is active.  That one will
+ * be used for all calls to step() until the next time you change it.
+ * 
+ * <tt><pre>
+ * compoundIntegrator.setCurrentIntegrator(0);
+ * compoundIntegrator.step(1000); // Take 1000 steps of Verlet dynamics
+ * compoundIntegrator.setCurrentIntegrator(1);
+ * compoundIntegrator.step(1000); // Take 1000 steps of Langevin dynamics
+ * </pre></tt>
+ * 
+ * When switching between integrators, it is important to make sure they are compatible with
+ * each other, and that they will interpret the positions and velocities in the same way.
+ * Remember that leapfrog style integrators assume the positions and velocities are offset
+ * from each other by half a time step.  When switching between a leapfrog and non-leapfrog
+ * integrator, you must first adjust the velocities to avoid introducing error.  This is also
+ * true when switching between two leapfrog integrators that use different step sizes,
+ * since they will interpret the velocities as corresponding to different times.
+ */
+
+class OPENMM_EXPORT CompoundIntegrator : public Integrator {
+public:
+    /**
+     * Create a CompoundIntegrator.
+     */
+    explicit CompoundIntegrator();
+    ~CompoundIntegrator();
+    /**
+     * Get the number of Integrators that have been added to this CompoundIntegrator.
+     */
+    int getNumIntegrators() const;
+    /**
+     * Add an Integrator to this CompoundIntegrator.  The Integrator object should have
+     * been created on the heap with the "new" operator.  The CompoundIntegrator takes over
+     * ownership of it, and deletes it when the CompoundIntegrator itself is deleted.
+     * All Integrators must be added before the Context is created.
+     * 
+     * @param integrator    the Integrator to add
+     * @return the index of the Integrator that was added
+     */
+    int addIntegrator(Integrator* integrator);
+    /**
+     * Get a reference to one of the Integrators that have been added to this CompoundIntegrator.
+     * 
+     * @param index     the index of the Integrator to get
+     */
+    Integrator& getIntegrator(int index);
+    /**
+     * Get a const reference to one of the Integrators that have been added to this CompoundIntegrator.
+     * 
+     * @param index     the index of the Integrator to get
+     */
+    const Integrator& getIntegrator(int index) const;
+    /**
+     * Get the index of the current Integrator.
+     */
+    int getCurrentIntegrator() const;
+    /**
+     * Set the current Integrator.
+     * 
+     * @param index    the index of the Integrator to use
+     */
+    void setCurrentIntegrator(int index);
+    /**
+     * Get the size of each time step, in picoseconds.  This method calls getStepSize() on
+     * whichever Integrator has been set as current.
+     * 
+     * @return the step size, measured in ps
+     */
+    double getStepSize() const;
+    /**
+     * Set the size of each time step, in picoseconds.  This method calls setStepSize() on
+     * whichever Integrator has been set as current.
+     * 
+     * @param size    the step size, measured in ps
+     */
+    void setStepSize(double size);
+    /**
+     * Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
+     * This method calls getConstraintTolerance() on whichever Integrator has been set as current.
+     */
+    double getConstraintTolerance() const;
+    /**
+     * Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
+     * This method calls setConstraintTolerance() on whichever Integrator has been set as current.
+     */
+    void setConstraintTolerance(double tol);
+   /**
+     * Advance a simulation through time by taking a series of time steps.  This method
+     * calls step() on whichever Integrator has been set as current.
+     * 
+     * @param steps   the number of time steps to take
+     */
+    void step(int steps);
+protected:
+    /**
+     * This will be called by the Context when it is created.  It informs the Integrator
+     * of what context it will be integrating, and gives it a chance to do any necessary initialization.
+     * It will also get called again if the application calls reinitialize() on the Context.
+     * 
+     * The implementation calls initialize() on each Integrator that has been added to this CompoundIntegrator.
+     */
+    void initialize(ContextImpl& context);
+    /**
+     * This will be called by the Context when it is destroyed to let the Integrator do any necessary
+     * cleanup.  It will also get called again if the application calls reinitialize() on the Context.
+     * 
+     * The implementation calls cleanup() on each Integrator that has been added to this CompoundIntegrator.
+     */
+    void cleanup();
+    /**
+     * Get the names of all Kernels used by this Integrator.
+     * 
+     * The implementation returns the union of all kernel names required by all Integrators that have been added.
+     */
+    std::vector<std::string> getKernelNames();
+    /**
+     * Compute the kinetic energy of the system at the current time.
+     * 
+     * The implementation calls computeKineticEnergy() on whichever Integrator has been set as current.
+     */
+    double computeKineticEnergy();
+private:
+    int currentIntegrator;
+    std::vector<Integrator*> integrators;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_COMPOUNDINTEGRATOR_H_*/

openmmapi/include/openmm/Context.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) 2008-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -165,6 +165,11 @@ public:
      * @param randomSeed     the random number seed to use when selecting velocities
      */
     void setVelocitiesToTemperature(double temperature, int randomSeed=osrngseed());
+    /**
+     * Get all adjustable parameters that have been defined by Force objects in the System, along
+     * with their current values.
+     */
+    const std::map<std::string, double>& getParameters() const;
     /**
      * Get the value of an adjustable parameter defined by a Force object in the System.
      * 

openmmapi/include/openmm/CustomAngleForce.h

@@ -159,7 +159,7 @@ public:
      * Set the default value of a global parameter.
      *
      * @param index          the index of the parameter for which to set the default value
-     * @param name           the default value of the parameter
+     * @param defaultValue   the default value of the parameter
      */
     void setGlobalParameterDefaultValue(int index, double defaultValue);
     /**
@@ -176,10 +176,10 @@ public:
      * Get the force field parameters for an angle term.
      *
      * @param index              the index of the angle for which to get parameters
-     * @param particle1     the index of the first particle connected by the angle
-     * @param particle2     the index of the second particle connected by the angle
-     * @param particle3     the index of the third particle connected by the angle
-     * @param parameters    the list of parameters for the angle
+     * @param[out] particle1     the index of the first particle connected by the angle
+     * @param[out] particle2     the index of the second particle connected by the angle
+     * @param[out] particle3     the index of the third particle connected by the angle
+     * @param[out] parameters    the list of parameters for the angle
      */
     void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, std::vector<double>& parameters) const;
     /**

openmmapi/include/openmm/CustomBondForce.h

@@ -159,7 +159,7 @@ public:
      * Set the default value of a global parameter.
      *
      * @param index          the index of the parameter for which to set the default value
-     * @param name           the default value of the parameter
+     * @param defaultValue   the default value of the parameter
      */
     void setGlobalParameterDefaultValue(int index, double defaultValue);
     /**
@@ -175,9 +175,9 @@ public:
      * Get the force field parameters for a bond term.
      *
      * @param      index         the index of the bond for which to get parameters
-     * @param particle1     the index of the first particle connected by the bond
-     * @param particle2     the index of the second particle connected by the bond
-     * @param parameters    the list of parameters for the bond
+     * @param[out] particle1     the index of the first particle connected by the bond
+     * @param[out] particle2     the index of the second particle connected by the bond
+     * @param[out] parameters    the list of parameters for the bond
      */
     void getBondParameters(int index, int& particle1, int& particle2, std::vector<double>& parameters) const;
     /**

openmmapi/include/openmm/CustomCentroidBondForce.h

@@ -226,7 +226,7 @@ public:
      * Set the default value of a global parameter.
      *
      * @param index          the index of the parameter for which to set the default value
-     * @param name           the default value of the parameter
+     * @param defaultValue   the default value of the parameter
      */
     void setGlobalParameterDefaultValue(int index, double defaultValue);
     /**
@@ -242,8 +242,8 @@ public:
      * Get the properties of a group.
      *
      * @param index            the index of the group to get
-     * @param particles   the indices of the particles in the group
-     * @param weights     the weight used for each particle when computing the center position.
+     * @param[out] particles   the indices of the particles in the group
+     * @param[out] weights     the weight used for each particle when computing the center position.
      *                         If no weights were specified, this vector will be empty indicating that particle
      *                         masses should be used as weights.
      */
@@ -269,8 +269,8 @@ public:
      * Get the properties of a bond.
      *
      * @param      index       the index of the bond to get
-     * @param groups      the indices of the groups in the bond
-     * @param parameters  the list of per-bond parameter values for the bond
+     * @param[out] groups      the indices of the groups in the bond
+     * @param[out] parameters  the list of per-bond parameter values for the bond
      */
     void getBondParameters(int index, std::vector<int>& groups, std::vector<double>& parameters) const;
     /**

openmmapi/include/openmm/CustomCompoundBondForce.h

@@ -209,7 +209,7 @@ public:
      * Set the default value of a global parameter.
      *
      * @param index          the index of the parameter for which to set the default value
-     * @param name           the default value of the parameter
+     * @param defaultValue   the default value of the parameter
      */
     void setGlobalParameterDefaultValue(int index, double defaultValue);
     /**
@@ -224,8 +224,8 @@ public:
      * Get the properties of a bond.
      *
      * @param index            the index of the bond to get
-     * @param particles   the indices of the particles in the bond
-     * @param parameters  the list of per-bond parameter values for the bond
+     * @param[out] particles   the indices of the particles in the bond
+     * @param[out] parameters  the list of per-bond parameter values for the bond
      */
     void getBondParameters(int index, std::vector<int>& particles, std::vector<double>& parameters) const;
     /**

openmmapi/include/openmm/CustomExternalForce.h

@@ -170,7 +170,7 @@ public:
      * Set the default value of a global parameter.
      *
      * @param index          the index of the parameter for which to set the default value
-     * @param name           the default value of the parameter
+     * @param defaultValue   the default value of the parameter
      */
     void setGlobalParameterDefaultValue(int index, double defaultValue);
     /**
@@ -185,8 +185,8 @@ public:
      * Get the force field parameters for a force field term.
      *
      * @param index              the index of the particle term for which to get parameters
-     * @param particle      the index of the particle this term is applied to
-     * @param parameters    the list of parameters for the force field term
+     * @param[out] particle      the index of the particle this term is applied to
+     * @param[out] parameters    the list of parameters for the force field term
      */
     void getParticleParameters(int index, int& particle, std::vector<double>& parameters) const;
     /**

openmmapi/include/openmm/CustomGBForce.h

@@ -309,7 +309,7 @@ public:
      * Set the default value of a global parameter.
      *
      * @param index         the index of the parameter for which to set the default value
-     * @param name           the default value of the parameter
+     * @param defaultValue  the default value of the parameter
      */
     void setGlobalParameterDefaultValue(int index, double defaultValue);
     /**
@@ -324,7 +324,7 @@ public:
      * Get the nonbonded force parameters for a particle.
      *
      * @param index            the index of the particle for which to get parameters
-     * @param parameters  the list of parameters for the specified particle
+     * @param[out] parameters  the list of parameters for the specified particle
      */
     void getParticleParameters(int index, std::vector<double>& parameters) const;
     /**
@@ -355,8 +355,8 @@ public:
      * Get the properties of a computed value.
      *
      * @param index            the index of the computed value for which to get parameters
-     * @param name        the name of the value
-     * @param expression  an algebraic expression to evaluate when calculating the computed value.  If the
+     * @param[out] name        the name of the value
+     * @param[out] expression  an algebraic expression to evaluate when calculating the computed value.  If the
      *                         ComputationType is SingleParticle, the expression is evaluated independently
      *                         for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle
      *                         parameters and previous computed values for that particle.  If the ComputationType is ParticlePair
@@ -366,7 +366,7 @@ public:
      *                         the per-particle parameters and previous computed values for each of them.
      *                         Append "1" to a variable name to indicate the parameter for the particle whose
      *                         value is being calculated, and "2" to indicate the particle it is interacting with.
-     * @param type        the method to use for computing this value
+     * @param[out] type        the method to use for computing this value
      */
     void getComputedValueParameters(int index, std::string& name, std::string& expression, ComputationType& type) const;
     /**
@@ -407,7 +407,7 @@ public:
      * Get the properties of a term to the energy computation.
      *
      * @param index            the index of the term for which to get parameters
-     * @param expression  an algebraic expression to evaluate when calculating the energy.  If the
+     * @param[out] expression  an algebraic expression to evaluate when calculating the energy.  If the
      *                         ComputationType is SingleParticle, the expression is evaluated once
      *                         for each particle, and may depend on its x, y, and z coordinates, as well as the per-particle
      *                         parameters and computed values for that particle.  If the ComputationType is ParticlePair or
@@ -417,7 +417,7 @@ public:
      *                         the per-particle parameters and computed values for each of them.
      *                         Append "1" to a variable name to indicate the parameter for the first particle
      *                         in the pair and "2" to indicate the second particle in the pair.
-     * @param type        the method to use for computing this value
+     * @param[out] type        the method to use for computing this value
      */
     void getEnergyTermParameters(int index, std::string& expression, ComputationType& type) const;
     /**
@@ -449,8 +449,8 @@ public:
      * Get the particles in a pair whose interaction should be excluded.
      *
      * @param index           the index of the exclusion for which to get particle indices
-     * @param particle1  the index of the first particle in the pair
-     * @param particle2  the index of the second particle in the pair
+     * @param[out] particle1  the index of the first particle in the pair
+     * @param[out] particle2  the index of the second particle in the pair
      */
     void getExclusionParticles(int index, int& particle1, int& particle2) const;
     /**

openmmapi/include/openmm/CustomHbondForce.h

@@ -282,7 +282,7 @@ public:
      * Set the default value of a global parameter.
      *
      * @param index          the index of the parameter for which to set the default value
-     * @param name           the default value of the parameter
+     * @param defaultValue   the default value of the parameter
      */
     void setGlobalParameterDefaultValue(int index, double defaultValue);
     /**
@@ -301,12 +301,12 @@ public:
      * Get the properties of a donor group.
      *
      * @param index            the index of the donor group to get
-     * @param d1          the index of the first particle for this donor group
-     * @param d2          the index of the second particle for this donor group.  If the group only
+     * @param[out] d1          the index of the first particle for this donor group
+     * @param[out] d2          the index of the second particle for this donor group.  If the group only
      *                         includes one particle, this will be -1.
-     * @param d3          the index of the third particle for this donor group.  If the group includes
+     * @param[out] d3          the index of the third particle for this donor group.  If the group includes
      *                         less than three particles, this will be -1.
-     * @param parameters  the list of per-donor parameter values for the donor
+     * @param[out] parameters  the list of per-donor parameter values for the donor
      */
     void getDonorParameters(int index, int& d1, int& d2, int& d3, std::vector<double>& parameters) const;
     /**
@@ -337,12 +337,12 @@ public:
      * Get the properties of an acceptor group.
      *
      * @param index            the index of the acceptor group to get
-     * @param a1          the index of the first particle for this acceptor group
-     * @param a2          the index of the second particle for this acceptor group.  If the group only
+     * @param[out] a1          the index of the first particle for this acceptor group
+     * @param[out] a2          the index of the second particle for this acceptor group.  If the group only
      *                         includes one particle, this will be -1.
-     * @param a3          the index of the third particle for this acceptor group.  If the group includes
+     * @param[out] a3          the index of the third particle for this acceptor group.  If the group includes
      *                         less than three particles, this will be -1.
-     * @param parameters  the list of per-acceptor parameter values for the acceptor
+     * @param[out] parameters  the list of per-acceptor parameter values for the acceptor
      */
     void getAcceptorParameters(int index, int& a1, int& a2, int& a3, std::vector<double>& parameters) const;
     /**
@@ -369,16 +369,16 @@ public:
      * Get the donor and acceptor in a pair whose interaction should be excluded.
      *
      * @param index           the index of the exclusion for which to get donor and acceptor indices
-     * @param particle1  the index of the donor
-     * @param particle2  the index of the acceptor
+     * @param[out] particle1  the index of the donor
+     * @param[out] particle2  the index of the acceptor
      */
     void getExclusionParticles(int index, int& donor, int& acceptor) const;
     /**
      * Get the donor and acceptor in a pair whose interaction should be excluded.
      *
      * @param index      the index of the exclusion for which to get donor and acceptor indices
-     * @param particle1  the index of the donor
-     * @param particle2  the index of the acceptor
+     * @param donor      the index of the donor
+     * @param acceptor   the index of the acceptor
      */
     void setExclusionParticles(int index, int donor, int acceptor);
     /**

openmmapi/include/openmm/CustomIntegrator.h

@@ -371,7 +371,7 @@ public:
      * Get the value of a per-DOF variable, specified by name.
      *
      * @param name         the name of the variable to get
-     * @param values  the values of the variable for all degrees of freedom
+     * @param[out] values  the values of the variable for all degrees of freedom
      *                     are stored into this
      */
     void getPerDofVariableByName(const std::string& name, std::vector<Vec3>& values) const;
@@ -446,7 +446,7 @@ public:
     /**
      * Add a step which begins a new "if" block.
      *
-     * @param expression  a mathematical expression involving a comparison operator
+     * @param condition   a mathematical expression involving a comparison operator
      *                    and global variables.  All steps between this one and
      *                    the end of the block are executed only if the condition
      *                    is true.
@@ -457,7 +457,7 @@ public:
     /**
      * Add a step which begins a new "while" block.
      *
-     * @param expression  a mathematical expression involving a comparison operator
+     * @param condition   a mathematical expression involving a comparison operator
      *                    and global variables.  All steps between this one and
      *                    the end of the block are executed repeatedly as long as
      *                    the condition remains true.
@@ -476,12 +476,13 @@ public:
      * Get the details of a computation step that has been added to the integration algorithm.
      *
      * @param      index       the index of the computation step to get
-     * @param type       on exit, the type of computation this step performs
-     * @param variable   on exit, the variable into which this step stores its result.  If this
-     *                   step does not store a result in a variable, this will be an
-     *                   empty string.
-     * @param expression on exit, the expression this step evaluates.  If this step does not
-     *                   evaluate an expression, this will be an empty string.
+     * @param[out] type        the type of computation this step performs
+     * @param[out] variable    the variable into which this step stores its
+     *                         result.  If this step does not store a result in
+     *                         a variable, this will be an empty string.
+     * @param[out] expression  the expression this step evaluates.  If
+     *                         this step does not evaluate an expression, this
+     *                         will be an empty string.
      */
     void getComputationStep(int index, ComputationType& type, std::string& variable, std::string& expression) const;
     /**

openmmapi/include/openmm/CustomManyParticleForce.h

@@ -337,7 +337,7 @@ public:
      * Set the default value of a global parameter.
      *
      * @param index          the index of the parameter for which to set the default value
-     * @param name           the default value of the parameter
+     * @param defaultValue   the default value of the parameter
      */
     void setGlobalParameterDefaultValue(int index, double defaultValue);
     /**
@@ -353,8 +353,8 @@ public:
      * Get the nonbonded force parameters for a particle.
      *
      * @param index            the index of the particle for which to get parameters
-     * @param parameters  the list of parameters for the specified particle
-     * @param type        the type of the specified particle
+     * @param[out] parameters  the list of parameters for the specified particle
+     * @param[out] type        the type of the specified particle
      */
     void getParticleParameters(int index, std::vector<double>& parameters, int& type) const;
     /**
@@ -379,8 +379,8 @@ public:
      * Get the particles in a pair whose interaction should be excluded.
      *
      * @param index           the index of the exclusion for which to get particle indices
-     * @param particle1  the index of the first particle in the pair
-     * @param particle2  the index of the second particle in the pair
+     * @param[out] particle1  the index of the first particle in the pair
+     * @param[out] particle2  the index of the second particle in the pair
      */
     void getExclusionParticles(int index, int& particle1, int& particle2) const;
     /**
@@ -406,7 +406,7 @@ public:
      * regardless of the type of the specified particle.
      *
      * @param index         the index of the particle within the interaction (between 0 and getNumParticlesPerSet())
-     * @param types    the allowed types for the specified particle
+     * @param[out] types    the allowed types for the specified particle
      */
     void getTypeFilter(int index, std::set<int>& types) const;
     /**

openmmapi/include/openmm/CustomNonbondedForce.h

@@ -318,7 +318,7 @@ public:
      * Set the default value of a global parameter.
      *
      * @param index          the index of the parameter for which to set the default value
-     * @param name           the default value of the parameter
+     * @param defaultValue   the default value of the parameter
      */
     void setGlobalParameterDefaultValue(int index, double defaultValue);
     /**
@@ -333,7 +333,7 @@ public:
      * Get the nonbonded force parameters for a particle.
      *
      * @param index            the index of the particle for which to get parameters
-     * @param parameters  the list of parameters for the specified particle
+     * @param[out] parameters  the list of parameters for the specified particle
      */
     void getParticleParameters(int index, std::vector<double>& parameters) const;
     /**
@@ -357,8 +357,8 @@ public:
      * Get the particles in a pair whose interaction should be excluded.
      *
      * @param index           the index of the exclusion for which to get particle indices
-     * @param particle1  the index of the first particle in the pair
-     * @param particle2  the index of the second particle in the pair
+     * @param[out] particle1  the index of the first particle in the pair
+     * @param[out] particle2  the index of the second particle in the pair
      */
     void getExclusionParticles(int index, int& particle1, int& particle2) const;
     /**
@@ -441,8 +441,8 @@ public:
      * Get the parameters for an interaction group.
      *
      * @param index        the index of the interaction group for which to get parameters
-     * @param set1    the first set of particles forming the interaction group
-     * @param set2    the second set of particles forming the interaction group
+     * @param[out] set1    the first set of particles forming the interaction group
+     * @param[out] set2    the second set of particles forming the interaction group
      */
     void getInteractionGroupParameters(int index, std::set<int>& set1, std::set<int>& set2) const;
     /**

openmmapi/include/openmm/CustomTorsionForce.h

@@ -159,7 +159,7 @@ public:
      * Set the default value of a global parameter.
      *
      * @param index          the index of the parameter for which to set the default value
-     * @param name           the default value of the parameter
+     * @param defaultValue   the default value of the parameter
      */
     void setGlobalParameterDefaultValue(int index, double defaultValue);
     /**
@@ -177,11 +177,11 @@ public:
      * Get the force field parameters for a torsion term.
      *
      * @param index              the index of the torsion for which to get parameters
-     * @param particle1     the index of the first particle connected by the torsion
-     * @param particle2     the index of the second particle connected by the torsion
-     * @param particle3     the index of the third particle connected by the torsion
-     * @param particle4     the index of the fourth particle connected by the torsion
-     * @param parameters    the list of parameters for the torsion
+     * @param[out] particle1     the index of the first particle connected by the torsion
+     * @param[out] particle2     the index of the second particle connected by the torsion
+     * @param[out] particle3     the index of the third particle connected by the torsion
+     * @param[out] particle4     the index of the fourth particle connected by the torsion
+     * @param[out] parameters    the list of parameters for the torsion
      */
     void getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, std::vector<double>& parameters) const;
     /**