Created VariableVerletIntegrator

olla/include/openmm/kernels.h

@@ -32,6 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "openmm/VariableVerletIntegrator.h"
 #include "openmm/AndersenThermostat.h"
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMMotionRemover.h"
@@ -417,6 +418,32 @@ public:
     virtual void execute(OpenMMContextImpl& context, const BrownianIntegrator& integrator) = 0;
 };
 
+/**
+ * This kernel is invoked by VariableVerletIntegrator to take one time step.
+ */
+class IntegrateVariableVerletStepKernel : public KernelImpl {
+public:
+    static std::string Name() {
+        return "IntegrateVariableVerletStep";
+    }
+    IntegrateVariableVerletStepKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
+    }
+    /**
+     * Initialize the kernel.
+     *
+     * @param system     the System this kernel will be applied to
+     * @param integrator the VariableVerletIntegrator this kernel will be used for
+     */
+    virtual void initialize(const System& system, const VariableVerletIntegrator& integrator) = 0;
+    /**
+     * Execute the kernel.
+     *
+     * @param context    the context in which to execute this kernel
+     * @param integrator the VerletIntegrator this kernel is being used for
+     */
+    virtual void execute(OpenMMContextImpl& context, const VariableVerletIntegrator& integrator) = 0;
+};
+
 /**
  * This kernel is invoked by AndersenThermostat at the start of each time step to adjust the particle velocities.
  */

openmmapi/include/OpenMM.h

@@ -32,6 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "openmm/VariableVerletIntegrator.h"
 #include "openmm/AndersenThermostat.h"
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMMotionRemover.h"

openmmapi/include/openmm/VariableVerletIntegrator.h

+#ifndef OPENMM_VARIABLEVERLETINTEGRATOR_H_
+#define OPENMM_VARIABLEVERLETINTEGRATOR_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) 2008-2009 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 is an error contolled, variable time step Integrator that simulates a System using the
+ * velocity Verlet algorithm.  It compares the result of the Verlet integrator to that of an
+ * explicit Euler integrator, takes the difference between the two as a measure of the integration
+ * error in each time step, and continuously adjusts the step size to keep the error below a
+ * specified tolerance.  This allows it to take larger steps on average than a fixed step size
+ * integrator, while still maintaining comparable accuracy and stability.
+ *
+ * It is best not to think of the value of the accuracy parameter as having any absolute meaning.
+ * It is just an adjustable parameter that affects the step size and integration accuracy.  You
+ * should try different values to find the largest value that produces a trajectory sufficiently
+ * accurate for your purposes.  0.001 is often a good starting point.
+ *
+ * Unlike a fixed step size Verlet integrator, variable step size Verlet is not symplectic.  This
+ * means that at a given accuracy level, energy is not as precisely conserved over long time periods.
+ * This makes it most appropriate for constant temperate simulations.  In constant energy simulations
+ * where precise energy conservation over long time periods is important, a fixed step size Verlet
+ * integrator may be more appropriate.
+ */
+
+class OPENMM_EXPORT VariableVerletIntegrator : public Integrator {
+public:
+    /**
+     * Create a VariableVerletIntegrator.
+     *
+     * @param stepSize the initial step size to use (in picoseconds)
+     * @param accuracy the required accuracy
+     */
+    VariableVerletIntegrator(double stepSize, double accuracy);
+    /**
+     * Get the required accuracy.
+     */
+    double getAccuracy() const {
+        return accuracy;
+    }
+    /**
+     * Set the required accuracy.
+     */
+    void setAccuracy(double acc) {
+        accuracy = acc;
+    }
+   /**
+     * Advance a simulation through time by taking a series of time steps.
+     *
+     * @param steps   the number of time steps to take
+     */
+    void step(int steps);
+protected:
+    /**
+     * This will be called by the OpenMMContext 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 OpenMMContext.
+     */
+    void initialize(OpenMMContextImpl& context);
+    /**
+     * Get the names of all Kernels used by this Integrator.
+     */
+    std::vector<std::string> getKernelNames();
+private:
+    double accuracy;
+    OpenMMContextImpl* context;
+    Kernel kernel;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_VARIABLEVERLETINTEGRATOR_H_*/

openmmapi/src/BrownianIntegrator.cpp

@@ -65,6 +65,5 @@ void BrownianIntegrator::step(int steps) {
         context->updateContextState();
         context->calcForces();
         dynamic_cast<IntegrateBrownianStepKernel&>(kernel.getImpl()).execute(*context, *this);
-        context->setTime(context->getTime()+getStepSize());
     }
 }

openmmapi/src/LangevinIntegrator.cpp

@@ -65,6 +65,5 @@ void LangevinIntegrator::step(int steps) {
         context->updateContextState();
         context->calcForces();
         dynamic_cast<IntegrateLangevinStepKernel&>(kernel.getImpl()).execute(*context, *this);
-        context->setTime(context->getTime()+getStepSize());
     }
 }

openmmapi/src/VariableVerletIntegrator.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2008-2009 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 "openmm/VariableVerletIntegrator.h"
+#include "openmm/OpenMMContext.h"
+#include "openmm/internal/OpenMMContextImpl.h"
+#include "openmm/kernels.h"
+#include <string>
+
+using namespace OpenMM;
+using std::string;
+using std::vector;
+
+VariableVerletIntegrator::VariableVerletIntegrator(double stepSize, double accuracy) : accuracy(accuracy) {
+    setStepSize(stepSize);
+    setConstraintTolerance(1e-4);
+}
+
+void VariableVerletIntegrator::initialize(OpenMMContextImpl& contextRef) {
+    context = &contextRef;
+    kernel = context->getPlatform().createKernel(IntegrateVariableVerletStepKernel::Name(), contextRef);
+    dynamic_cast<IntegrateVariableVerletStepKernel&>(kernel.getImpl()).initialize(contextRef.getSystem(), *this);
+}
+
+vector<string> VariableVerletIntegrator::getKernelNames() {
+    std::vector<std::string> names;
+    names.push_back(IntegrateVariableVerletStepKernel::Name());
+    return names;
+}
+
+void VariableVerletIntegrator::step(int steps) {
+    for (int i = 0; i < steps; ++i) {
+        context->updateContextState();
+        context->calcForces();
+        dynamic_cast<IntegrateVariableVerletStepKernel&>(kernel.getImpl()).execute(*context, *this);
+    }
+}
+

openmmapi/src/VerletIntegrator.cpp

@@ -61,6 +61,5 @@ void VerletIntegrator::step(int steps) {
         context->updateContextState();
         context->calcForces();
         dynamic_cast<IntegrateVerletStepKernel&>(kernel.getImpl()).execute(*context, *this);
-        context->setTime(context->getTime()+getStepSize());
     }
 }

platforms/brook/src/BrookIntegrateLangevinStepKernel.cpp

@@ -250,5 +250,5 @@ void BrookIntegrateLangevinStepKernel::execute( OpenMMContextImpl& context, cons
 
    _brookLangevinDynamics->update( *(_openMMBrookInterface.getParticlePositions()), *(_openMMBrookInterface.getParticleVelocities()), 
                                    *(_openMMBrookInterface.getParticleForces()), *_brookShakeAlgorithm, *_brookRandomNumberGenerator );
-
+   _openMMBrookInterface->setTime(_openMMBrookInterface->getTime(integrator.getStepSize()));
 }

platforms/brook/src/BrookIntegrateVerletStepKernel.cpp

@@ -202,6 +202,5 @@ void BrookIntegrateVerletStepKernel::execute( OpenMMContextImpl& context, const
 
    _brookVerletDynamics->update( *(_openMMBrookInterface.getParticlePositions()), *(_openMMBrookInterface.getParticleVelocities()),
                                  *(_openMMBrookInterface.getParticleForces()), *_brookShakeAlgorithm );
-
-
+   _openMMBrookInterface->setTime(_openMMBrookInterface->getTime(stepSize));
 }

platforms/cuda/src/CudaKernels.cpp

@@ -458,6 +458,7 @@ void CudaIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, const Ve
             gpu->bCalculateCM = true;
     }
     kVerletUpdatePart2(gpu);
+    data.time += stepSize;
 }
 
 CudaIntegrateLangevinStepKernel::~CudaIntegrateLangevinStepKernel() {
@@ -500,6 +501,7 @@ void CudaIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const
     kApplySecondShake(gpu);
     kApplySecondSettle(gpu);
     kApplySecondCCMA(gpu);
+    data.time += stepSize;
 }
 
 CudaIntegrateBrownianStepKernel::~CudaIntegrateBrownianStepKernel() {
@@ -539,6 +541,7 @@ void CudaIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, const
             gpu->bCalculateCM = true;
     }
     kBrownianUpdatePart2(gpu);
+    data.time += stepSize;
 }
 
 CudaApplyAndersenThermostatKernel::~CudaApplyAndersenThermostatKernel() {

platforms/reference/src/ReferenceKernelFactory.cpp

@@ -59,11 +59,13 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla
     if (name == CalcGBVIForceKernel::Name())
         return new ReferenceCalcGBVIForceKernel(name, platform);
     if (name == IntegrateVerletStepKernel::Name())
-        return new ReferenceIntegrateVerletStepKernel(name, platform);
+        return new ReferenceIntegrateVerletStepKernel(name, platform, data);
     if (name == IntegrateLangevinStepKernel::Name())
-        return new ReferenceIntegrateLangevinStepKernel(name, platform);
+        return new ReferenceIntegrateLangevinStepKernel(name, platform, data);
     if (name == IntegrateBrownianStepKernel::Name())
-        return new ReferenceIntegrateBrownianStepKernel(name, platform);
+        return new ReferenceIntegrateBrownianStepKernel(name, platform, data);
+    if (name == IntegrateVariableVerletStepKernel::Name())
+        return new ReferenceIntegrateVariableVerletStepKernel(name, platform, data);
     if (name == ApplyAndersenThermostatKernel::Name())
         return new ReferenceApplyAndersenThermostatKernel(name, platform);
     if (name == CalcKineticEnergyKernel::Name())

platforms/reference/src/ReferenceKernels.cpp

@@ -33,6 +33,7 @@
 #include "ReferenceFloatStreamImpl.h"
 #include "gbsa/CpuObc.h"
 #include "gbsa/CpuGBVI.h"
+#include "SimTKReference/ReferenceVariableVerletDynamics.h"
 #include "SimTKReference/ReferenceAndersenThermostat.h"
 #include "SimTKReference/ReferenceAngleBondIxn.h"
 #include "SimTKReference/ReferenceBondForce.h"
@@ -639,6 +640,7 @@ void ReferenceIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, con
         prevStepSize = stepSize;
     }
     dynamics->update(context.getSystem().getNumParticles(), posData, velData, forceData, masses);
+    data.time += stepSize;
 }
 
 ReferenceIntegrateLangevinStepKernel::~ReferenceIntegrateLangevinStepKernel() {
@@ -702,6 +704,7 @@ void ReferenceIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, c
         prevStepSize = stepSize;
     }
     dynamics->update(context.getSystem().getNumParticles(), posData, velData, forceData, masses);
+    data.time += stepSize;
 }
 
 ReferenceIntegrateBrownianStepKernel::~ReferenceIntegrateBrownianStepKernel() {
@@ -764,6 +767,63 @@ void ReferenceIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, c
         prevStepSize = stepSize;
     }
     dynamics->update(context.getSystem().getNumParticles(), posData, velData, forceData, masses);
+    data.time += stepSize;
+}
+
+ReferenceIntegrateVariableVerletStepKernel::~ReferenceIntegrateVariableVerletStepKernel() {
+    if (dynamics)
+        delete dynamics;
+    if (constraints)
+        delete constraints;
+    if (masses)
+        delete[] masses;
+    if (constraintIndices)
+        disposeIntArray(constraintIndices, numConstraints);
+    if (constraintDistances)
+        delete[] constraintDistances;
+}
+
+void ReferenceIntegrateVariableVerletStepKernel::initialize(const System& system, const VariableVerletIntegrator& integrator) {
+    int numParticles = system.getNumParticles();
+    masses = new RealOpenMM[numParticles];
+    for (int i = 0; i < numParticles; ++i)
+        masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i));
+    numConstraints = system.getNumConstraints();
+    constraintIndices = allocateIntArray(numConstraints, 2);
+    constraintDistances = new RealOpenMM[numConstraints];
+    for (int i = 0; i < numConstraints; ++i) {
+        int particle1, particle2;
+        double distance;
+        system.getConstraintParameters(i, particle1, particle2, distance);
+        constraintIndices[i][0] = particle1;
+        constraintIndices[i][1] = particle2;
+        constraintDistances[i] = static_cast<RealOpenMM>(distance);
+    }
+}
+
+void ReferenceIntegrateVariableVerletStepKernel::execute(OpenMMContextImpl& context, const VariableVerletIntegrator& integrator) {
+    double stepSize = integrator.getStepSize();
+    double accuracy = integrator.getAccuracy();
+    RealOpenMM** posData = ((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData();
+    RealOpenMM** velData = ((ReferenceFloatStreamImpl&) context.getVelocities().getImpl()).getData();
+    RealOpenMM** forceData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData()); // Reference code needs to be made const correct
+    if (dynamics == 0 || stepSize != prevStepSize || accuracy != prevAccuracy) {
+        // Recreate the computation objects with the new parameters.
+
+        if (dynamics) {
+            delete dynamics;
+            delete constraints;
+        }
+        dynamics = new ReferenceVariableVerletDynamics(context.getSystem().getNumParticles(), static_cast<RealOpenMM>(stepSize), accuracy);
+        vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
+        findAnglesForCCMA(context.getSystem(), angles);
+        constraints = new ReferenceCCMAAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
+        dynamics->setReferenceConstraintAlgorithm(constraints);
+        prevStepSize = stepSize;
+        prevAccuracy = accuracy;
+    }
+    dynamics->update(context.getSystem().getNumParticles(), posData, velData, forceData, masses);
+    data.time += dynamics->getLastStepSize();
 }
 
 ReferenceApplyAndersenThermostatKernel::~ReferenceApplyAndersenThermostatKernel() {

platforms/reference/src/ReferenceKernels.h

@@ -43,6 +43,7 @@ class ReferenceAndersenThermostat;
 class ReferenceBrownianDynamics;
 class ReferenceStochasticDynamics;
 class ReferenceConstraintAlgorithm;
+class ReferenceVariableVerletDynamics;
 class ReferenceVerletDynamics;
 
 namespace OpenMM {
@@ -343,8 +344,8 @@ private:
  */
 class ReferenceIntegrateVerletStepKernel : public IntegrateVerletStepKernel {
 public:
-    ReferenceIntegrateVerletStepKernel(std::string name, const Platform& platform) : IntegrateVerletStepKernel(name, platform),
-        dynamics(0), constraints(0), masses(0), constraintDistances(0), constraintIndices(0) {
+    ReferenceIntegrateVerletStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVerletStepKernel(name, platform),
+        data(data), dynamics(0), constraints(0), masses(0), constraintDistances(0), constraintIndices(0) {
     }
     ~ReferenceIntegrateVerletStepKernel();
     /**
@@ -362,6 +363,7 @@ public:
      */
     void execute(OpenMMContextImpl& context, const VerletIntegrator& integrator);
 private:
+    ReferencePlatform::PlatformData& data;
     ReferenceVerletDynamics* dynamics;
     ReferenceConstraintAlgorithm* constraints;
     RealOpenMM* masses;
@@ -376,8 +378,8 @@ private:
  */
 class ReferenceIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel {
 public:
-    ReferenceIntegrateLangevinStepKernel(std::string name, const Platform& platform) : IntegrateLangevinStepKernel(name, platform),
-        dynamics(0), constraints(0), masses(0), constraintDistances(0), constraintIndices(0) {
+    ReferenceIntegrateLangevinStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateLangevinStepKernel(name, platform),
+        data(data), dynamics(0), constraints(0), masses(0), constraintDistances(0), constraintIndices(0) {
     }
     ~ReferenceIntegrateLangevinStepKernel();
     /**
@@ -395,6 +397,7 @@ public:
      */
     void execute(OpenMMContextImpl& context, const LangevinIntegrator& integrator);
 private:
+    ReferencePlatform::PlatformData& data;
     ReferenceStochasticDynamics* dynamics;
     ReferenceConstraintAlgorithm* constraints;
     RealOpenMM* masses;
@@ -409,8 +412,8 @@ private:
  */
 class ReferenceIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
 public:
-    ReferenceIntegrateBrownianStepKernel(std::string name, const Platform& platform) : IntegrateBrownianStepKernel(name, platform),
-        dynamics(0), constraints(0), masses(0), constraintDistances(0), constraintIndices(0) {
+    ReferenceIntegrateBrownianStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateBrownianStepKernel(name, platform),
+        data(data), dynamics(0), constraints(0), masses(0), constraintDistances(0), constraintIndices(0) {
     }
     ~ReferenceIntegrateBrownianStepKernel();
     /**
@@ -428,6 +431,7 @@ public:
      */
     void execute(OpenMMContextImpl& context, const BrownianIntegrator& integrator);
 private:
+    ReferencePlatform::PlatformData& data;
     ReferenceBrownianDynamics* dynamics;
     ReferenceConstraintAlgorithm* constraints;
     RealOpenMM* masses;
@@ -437,6 +441,40 @@ private:
     double prevTemp, prevFriction, prevStepSize;
 };
 
+/**
+ * This kernel is invoked by VariableVerletIntegrator to take one time step.
+ */
+class ReferenceIntegrateVariableVerletStepKernel : public IntegrateVariableVerletStepKernel {
+public:
+    ReferenceIntegrateVariableVerletStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateVariableVerletStepKernel(name, platform),
+        data(data), dynamics(0), constraints(0), masses(0), constraintDistances(0), constraintIndices(0) {
+    }
+    ~ReferenceIntegrateVariableVerletStepKernel();
+    /**
+     * Initialize the kernel.
+     *
+     * @param system     the System this kernel will be applied to
+     * @param integrator the VerletIntegrator this kernel will be used for
+     */
+    void initialize(const System& system, const VariableVerletIntegrator& integrator);
+    /**
+     * Execute the kernel.
+     *
+     * @param context    the context in which to execute this kernel
+     * @param integrator the VerletIntegrator this kernel is being used for
+     */
+    void execute(OpenMMContextImpl& context, const VariableVerletIntegrator& integrator);
+private:
+    ReferencePlatform::PlatformData& data;
+    ReferenceVariableVerletDynamics* dynamics;
+    ReferenceConstraintAlgorithm* constraints;
+    RealOpenMM* masses;
+    RealOpenMM* constraintDistances;
+    int** constraintIndices;
+    int numConstraints;
+    double prevStepSize, prevAccuracy;
+};
+
 /**
  * This kernel is invoked by AndersenThermostat at the start of each time step to adjust the particle velocities.
  */

platforms/reference/src/ReferencePlatform.cpp

@@ -51,6 +51,7 @@ ReferencePlatform::ReferencePlatform() {
     registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
     registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
     registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
+    registerKernelFactory(IntegrateVariableVerletStepKernel::Name(), factory);
     registerKernelFactory(ApplyAndersenThermostatKernel::Name(), factory);
     registerKernelFactory(CalcKineticEnergyKernel::Name(), factory);
     registerKernelFactory(RemoveCMMotionKernel::Name(), factory);

platforms/reference/src/SimTKReference/ReferenceDynamics.cpp

@@ -362,6 +362,23 @@ RealOpenMM ReferenceDynamics::getDeltaT( void ) const {
    return _deltaT;
 }
 
+/**---------------------------------------------------------------------------------------
+
+   Set delta t
+
+   --------------------------------------------------------------------------------------- */
+
+void ReferenceDynamics::setDeltaT( RealOpenMM deltaT ) {
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName  = "\nReferenceDynamics::setDeltaT";
+
+   // ---------------------------------------------------------------------------------------
+
+   _deltaT = deltaT;
+}
+
 /**---------------------------------------------------------------------------------------
 
    Get temperature

platforms/reference/src/SimTKReference/ReferenceDynamics.h

@@ -164,7 +164,7 @@ class ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceDynamics( );
+       virtual ~ReferenceDynamics( );
 
       /**---------------------------------------------------------------------------------------
       
@@ -206,6 +206,14 @@ class ReferenceDynamics {
       
       RealOpenMM getDeltaT( void ) const;
 
+      /**---------------------------------------------------------------------------------------
+
+         Set delta t
+
+         --------------------------------------------------------------------------------------- */
+
+      void setDeltaT( RealOpenMM deltaT );
+
       /**---------------------------------------------------------------------------------------
       
          Get temperature

platforms/reference/src/SimTKReference/ReferenceVariableVerletDynamics.cpp

+
+/* Portions copyright (c) 2006-2009 Stanford University and Simbios.
+ * Contributors: Peter Eastman, Pande Group
+ *
+ * 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 <string.h>
+#include <sstream>
+
+#include "../SimTKUtilities/SimTKOpenMMCommon.h"
+#include "../SimTKUtilities/SimTKOpenMMLog.h"
+#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "ReferenceVariableVerletDynamics.h"
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceVariableVerletDynamics constructor
+
+   @param numberOfAtoms  number of atoms
+   @param deltaT         initial delta t for dynamics
+   @param accuracy       required accuracy
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceVariableVerletDynamics::ReferenceVariableVerletDynamics( int numberOfAtoms,
+                                                          RealOpenMM deltaT, RealOpenMM accuracy ) :
+           ReferenceDynamics( numberOfAtoms, deltaT, 0.0 ), _accuracy(accuracy) {
+
+   // ---------------------------------------------------------------------------------------
+
+   static const char* methodName      = "\nReferenceVariableVerletDynamics::ReferenceVariableVerletDynamics";
+
+   static const RealOpenMM zero       =  0.0;
+   static const RealOpenMM one        =  1.0;
+
+   // ---------------------------------------------------------------------------------------
+
+   allocate2DArrays( numberOfAtoms, 3, Max2DArrays );
+   allocate1DArrays( numberOfAtoms, Max1DArrays );
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceVariableVerletDynamics destructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceVariableVerletDynamics::~ReferenceVariableVerletDynamics( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceVariableVerletDynamics::~ReferenceVariableVerletDynamics";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Get the required accuracy
+
+   @return accuracy
+
+ --------------------------------------------------------------------------------------- */
+
+RealOpenMM ReferenceVariableVerletDynamics::getAccuracy( void ) const {
+    return _accuracy;
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Set the required accuracy
+
+ --------------------------------------------------------------------------------------- */
+
+void ReferenceVariableVerletDynamics::setAccuracy( RealOpenMM accuracy ) {
+    _accuracy = accuracy;
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Get the actual size of the last step that was taken
+
+   @return step size
+
+   --------------------------------------------------------------------------------------- */
+
+RealOpenMM ReferenceVariableVerletDynamics::getLastStepSize( void ) const {
+    return _lastStepSize;
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Print parameters
+
+   @param message             message
+
+   @return ReferenceDynamics::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceVariableVerletDynamics::printParameters( std::stringstream& message ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   static const char* methodName  = "\nReferenceVariableVerletDynamics::printParameters";
+
+   // ---------------------------------------------------------------------------------------
+
+   // print parameters
+
+   ReferenceDynamics::printParameters( message );
+
+   return ReferenceDynamics::DefaultReturn;
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Update -- driver routine for performing Verlet dynamics update of coordinates
+   and velocities
+
+   @param numberOfAtoms       number of atoms
+   @param atomCoordinates     atom coordinates
+   @param velocities          velocities
+   @param forces              forces
+   @param masses              atom masses
+
+   @return ReferenceDynamics::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceVariableVerletDynamics::update( int numberOfAtoms, RealOpenMM** atomCoordinates,
+                                          RealOpenMM** velocities,
+                                          RealOpenMM** forces, RealOpenMM* masses ){
+
+    // ---------------------------------------------------------------------------------------
+
+    static const char* methodName      = "\nReferenceVariableVerletDynamics::update";
+
+    static const RealOpenMM zero       =  0.0;
+    static const RealOpenMM one        =  1.0;
+
+    static int debug                   =  0;
+
+    // ---------------------------------------------------------------------------------------
+
+    // get work arrays
+
+    RealOpenMM** xPrime = get2DArrayAtIndex( xPrime2D );
+    RealOpenMM** vPrime = get2DArrayAtIndex( vPrime2D );
+    RealOpenMM* inverseMasses = get1DArrayAtIndex( InverseMasses );
+
+    // first-time-through initialization
+
+    if( getTimeStep() == 0 ){
+
+       std::stringstream message;
+       message << methodName;
+       int errors = 0;
+
+       // invert masses
+
+       for( int ii = 0; ii < numberOfAtoms; ii++ ){
+          if( masses[ii] <= zero ){
+             message << "mass at atom index=" << ii << " (" << masses[ii] << ") is <= 0" << std::endl;
+             errors++;
+          } else {
+             inverseMasses[ii] = one/masses[ii];
+          }
+       }
+
+       // exit if errors
+
+       if( errors ){
+          SimTKOpenMMLog::printError( message );
+       }
+    }
+
+    // Try different step sizes until the accuracy is acceptable.
+
+    bool success = false;
+    RealOpenMM maxStepSize = 5.0f*getDeltaT();
+    while (!success) {
+        // Perform the integration and estimate the error.
+
+        _lastStepSize = getDeltaT();
+        RealOpenMM error = zero;
+        for (int i = 0; i < numberOfAtoms; ++i) {
+            for (int j = 0; j < 3; ++j) {
+                RealOpenMM xref = atomCoordinates[i][j] + velocities[i][j]*getDeltaT();
+                vPrime[i][j] = velocities[i][j] + inverseMasses[i]*forces[i][j]*getDeltaT();
+                xPrime[i][j] = atomCoordinates[i][j] + vPrime[i][j]*getDeltaT();
+                RealOpenMM xerror = xPrime[i][j]-xref;
+                error += xerror*xerror;
+            }
+        }
+        error = SQRT(error/(numberOfAtoms*3));
+
+        // Select a new step size.
+
+        const RealOpenMM Safety = 0.9f, MinShrink = 0.1f;
+        const RealOpenMM HysteresisLow = 0.9f, HysteresisHigh = 1.0f, ErrorOrder = 2.0f;
+
+        RealOpenMM newStepSize = Safety*getDeltaT()*POW(getAccuracy()/error, 1.0f/ErrorOrder);
+        if (newStepSize > getDeltaT()) {
+            if (newStepSize < HysteresisHigh*getDeltaT())
+                newStepSize = getDeltaT();
+        }
+        if (newStepSize < getDeltaT() && error <= getAccuracy())
+            newStepSize = getDeltaT();
+        newStepSize = std::min(newStepSize, maxStepSize);
+        newStepSize = std::max(newStepSize, MinShrink*getDeltaT());
+        if (newStepSize < getDeltaT())
+            newStepSize = std::min(newStepSize, HysteresisLow*getDeltaT());
+        success = (newStepSize >= getDeltaT());
+        if (success) {
+            ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
+            if (referenceConstraintAlgorithm)
+                success = (referenceConstraintAlgorithm->apply(numberOfAtoms, atomCoordinates, xPrime, inverseMasses) != ErrorReturn);
+            if (!success) {
+                newStepSize *= 0.5f;
+                maxStepSize = newStepSize;
+            }
+        }
+        setDeltaT(newStepSize);
+   }
+
+   // Update the positions and velocities.
+
+   RealOpenMM velocityScale = static_cast<RealOpenMM>( 1.0/_lastStepSize );
+   for (int i = 0; i < numberOfAtoms; ++i) {
+       for (int j = 0; j < 3; ++j) {
+           velocities[i][j] = velocityScale*(xPrime[i][j] - atomCoordinates[i][j]);
+           atomCoordinates[i][j] = xPrime[i][j];
+       }
+   }
+
+   incrementTimeStep();
+
+   return ReferenceDynamics::DefaultReturn;
+
+}
+
+

platforms/reference/src/SimTKReference/ReferenceVariableVerletDynamics.h

+
+/* Portions copyright (c) 2006-2009 Stanford University and Simbios.
+ * Contributors: Peter Eastman, Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __ReferenceVariableVerletDynamics_H__
+#define __ReferenceVariableVerletDynamics_H__
+
+#include "ReferenceDynamics.h"
+
+// ---------------------------------------------------------------------------------------
+
+class ReferenceVariableVerletDynamics : public ReferenceDynamics {
+
+   private:
+
+      enum TwoDArrayIndicies { xPrime2D, vPrime2D, Max2DArrays };
+      enum OneDArrayIndicies { InverseMasses, Max1DArrays };
+      RealOpenMM _accuracy, _lastStepSize;
+
+   public:
+
+      /**---------------------------------------------------------------------------------------
+
+         Constructor
+
+         @param numberOfAtoms  number of atoms
+         @param deltaT         initial delta t for dynamics
+         @param accuracy       required accuracy
+
+         --------------------------------------------------------------------------------------- */
+
+       ReferenceVariableVerletDynamics( int numberOfAtoms, RealOpenMM deltaT, RealOpenMM accuracy );
+
+      /**---------------------------------------------------------------------------------------
+
+         Destructor
+
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferenceVariableVerletDynamics( );
+
+      /**---------------------------------------------------------------------------------------
+
+         Get the required accuracy
+
+         @return accuracy
+
+         --------------------------------------------------------------------------------------- */
+
+      RealOpenMM getAccuracy( void ) const;
+
+      /**---------------------------------------------------------------------------------------
+
+         Set the required accuracy
+
+         --------------------------------------------------------------------------------------- */
+
+      void setAccuracy( RealOpenMM accuracy );
+
+      /**---------------------------------------------------------------------------------------
+
+         Get the actual size of the last step that was taken
+
+         @return step size
+
+         --------------------------------------------------------------------------------------- */
+
+      RealOpenMM getLastStepSize( void ) const;
+
+      /**---------------------------------------------------------------------------------------
+
+         Print parameters
+
+         @param message message
+
+         @return ReferenceDynamics::DefaultReturn
+
+         --------------------------------------------------------------------------------------- */
+
+      int printParameters( std::stringstream& message ) const;
+
+      /**---------------------------------------------------------------------------------------
+
+         Update
+
+         @param numberOfAtoms       number of atoms
+         @param atomCoordinates     atom coordinates
+         @param velocities          velocities
+         @param forces              forces
+         @param masses              atom masses
+
+         @return ReferenceDynamics::DefaultReturn
+
+         --------------------------------------------------------------------------------------- */
+
+      int update( int numberOfAtoms, RealOpenMM** atomCoordinates,
+                  RealOpenMM** velocities, RealOpenMM** forces, RealOpenMM* masses );
+
+};
+
+// ---------------------------------------------------------------------------------------
+
+#endif // __ReferenceVariableVerletDynamics_H__

platforms/reference/tests/TestReferenceVariableVerletIntegrator.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2008-2009 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests the reference implementation of VariableVerletIntegrator.
+ */
+
+#include "../../../tests/AssertionUtilities.h"
+#include "openmm/OpenMMContext.h"
+#include "ReferencePlatform.h"
+#include "openmm/HarmonicBondForce.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/System.h"
+#include "openmm/VariableVerletIntegrator.h"
+#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "../src/sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+const double TOL = 1e-5;
+
+void testSingleBond() {
+    ReferencePlatform platform;
+    System system;
+    system.addParticle(2.0);
+    system.addParticle(2.0);
+    VariableVerletIntegrator integrator(0.01, 1e-6);
+    HarmonicBondForce* forceField = new HarmonicBondForce();
+    forceField->addBond(0, 1, 1.5, 1);
+    system.addForce(forceField);
+    OpenMMContext context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    context.setPositions(positions);
+
+    // This is simply a harmonic oscillator, so compare it to the analytical solution.
+
+    const double freq = 1.0;
+    State state = context.getState(State::Energy);
+    const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
+    for (int i = 0; i < 1000; ++i) {
+        state = context.getState(State::Positions | State::Velocities | State::Energy);
+        double time = state.getTime();
+        double expectedDist = 1.5+0.5*std::cos(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
+        double expectedSpeed = -0.5*freq*std::sin(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
+        double energy = state.getKineticEnergy()+state.getPotentialEnergy();
+        ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05);
+        integrator.step(1);
+    }
+    ASSERT(state.getTime() > 1.0);
+}
+
+void testConstraints() {
+    const int numParticles = 8;
+    const double temp = 500.0;
+    ReferencePlatform platform;
+    System system;
+    VariableVerletIntegrator integrator(0.002, 1e-5);
+    integrator.setConstraintTolerance(1e-5);
+    NonbondedForce* forceField = new NonbondedForce();
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(i%2 == 0 ? 5.0 : 10.0);
+        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+    }
+    for (int i = 0; i < numParticles-1; ++i)
+        system.addConstraint(i, i+1, 1.0);
+    system.addForce(forceField);
+    OpenMMContext context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
+    init_gen_rand(0);
+    for (int i = 0; i < numParticles; ++i) {
+        positions[i] = Vec3(i/2, (i+1)/2, 0);
+        velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
+    }
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+
+    // Simulate it and see whether the constraints remain satisfied.
+
+    double initialEnergy = 0.0;
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions | State::Energy);
+        for (int j = 0; j < system.getNumConstraints(); ++j) {
+            int particle1, particle2;
+            double distance;
+            system.getConstraintParameters(j, particle1, particle2, distance);
+            Vec3 p1 = state.getPositions()[particle1];
+            Vec3 p2 = state.getPositions()[particle2];
+            double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
+            ASSERT_EQUAL_TOL(distance, dist, 2e-5);
+        }
+        double energy = state.getKineticEnergy()+state.getPotentialEnergy();
+        if (i == 1)
+            initialEnergy = energy;
+        else if (i > 1)
+            ASSERT_EQUAL_TOL(initialEnergy, energy, 0.1);
+        integrator.step(1);
+    }
+    ASSERT(context.getState(State::Positions).getTime() > 0.1);
+}
+
+void testConstrainedClusters() {
+    const int numParticles = 7;
+    const double temp = 500.0;
+    ReferencePlatform platform;
+    System system;
+    VariableVerletIntegrator integrator(0.002, 1e-5);
+    integrator.setConstraintTolerance(1e-5);
+    NonbondedForce* forceField = new NonbondedForce();
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(i > 1 ? 1.0 : 10.0);
+        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+    }
+    system.addConstraint(0, 1, 1.0);
+    system.addConstraint(0, 2, 1.0);
+    system.addConstraint(0, 3, 1.0);
+    system.addConstraint(0, 4, 1.0);
+    system.addConstraint(1, 5, 1.0);
+    system.addConstraint(1, 6, 1.0);
+    system.addConstraint(2, 3, sqrt(2.0));
+    system.addConstraint(2, 4, sqrt(2.0));
+    system.addConstraint(3, 4, sqrt(2.0));
+    system.addConstraint(5, 6, sqrt(2.0));
+    system.addForce(forceField);
+    OpenMMContext context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    positions[0] = Vec3(0, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    positions[2] = Vec3(-1, 0, 0);
+    positions[3] = Vec3(0, 1, 0);
+    positions[4] = Vec3(0, 0, 1);
+    positions[5] = Vec3(2, 0, 0);
+    positions[6] = Vec3(1, 1, 0);
+    vector<Vec3> velocities(numParticles);
+    init_gen_rand(0);
+    for (int i = 0; i < numParticles; ++i)
+        velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+
+    // Simulate it and see whether the constraints remain satisfied.
+
+    double initialEnergy = 0.0;
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions | State::Energy);
+        for (int j = 0; j < system.getNumConstraints(); ++j) {
+            int particle1, particle2;
+            double distance;
+            system.getConstraintParameters(j, particle1, particle2, distance);
+            Vec3 p1 = state.getPositions()[particle1];
+            Vec3 p2 = state.getPositions()[particle2];
+            double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
+            ASSERT_EQUAL_TOL(distance, dist, 2e-5);
+        }
+        double energy = state.getKineticEnergy()+state.getPotentialEnergy();
+        if (i == 1)
+            initialEnergy = energy;
+        else if (i > 1)
+            ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05);
+        integrator.step(1);
+    }
+    ASSERT(context.getState(State::Positions).getTime() > 0.1);
+}
+
+int main() {
+    try {
+        testSingleBond();
+        testConstraints();
+        testConstrainedClusters();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+