Periodic box dimensions can be changed in the middle of a simulation

examples/HelloWaterBox.cpp

@@ -248,7 +248,7 @@ myInitializeOpenMM( int                 numWatersAlongEdge,
     // Create periodic box
     nonbond.setNonbondedMethod(OpenMM::NonbondedForce::CutoffPeriodic);
     nonbond.setCutoffDistance(CutoffDistanceInAng * OpenMM::NmPerAngstrom);
-    system.setPeriodicBoxVectors(Vec3(boxEdgeLengthInNm,0,0),
+    system.setDefaultPeriodicBoxVectors(Vec3(boxEdgeLengthInNm,0,0),
                                   Vec3(0,boxEdgeLengthInNm,0), 
                                   Vec3(0,0,boxEdgeLengthInNm));
 

libraries/validate/src/ValidateOpenMM.cpp

@@ -387,8 +387,8 @@ System* ValidateOpenMM::copySystemExcludingForces( const System& systemToCopy )
     }   
 
     Vec3 a, b, c;
-    systemToCopy.getPeriodicBoxVectors( a, b, c ); 
-    system->setPeriodicBoxVectors( a, b, c );
+    systemToCopy.getDefaultPeriodicBoxVectors( a, b, c );
+    system->setDefaultPeriodicBoxVectors( a, b, c );
 
     copyConstraints( systemToCopy, system );
 
@@ -490,7 +490,7 @@ void ValidateOpenMM::writeMasses( FILE* filePtr, const System& system ) const {
     }
 
     Vec3 a, b, c;
-    system.getPeriodicBoxVectors( a, b, c);
+    system.getDefaultPeriodicBoxVectors( a, b, c);
     (void) fprintf( filePtr, "Box %14.6f %14.6f %14.6f  %14.6f %14.6f %14.6f   %14.6f %14.6f %14.6f\n",
                     a[0], a[1], a[2], b[0], b[1], b[2], c[0], c[1], c[2] );
 }

openmmapi/include/openmm/Context.h

@@ -153,6 +153,30 @@ public:
      * @param value the value of the parameter
      */
     void setParameter(const std::string& name, double value);
+    /**
+     * Get the vectors defining the axes of the periodic box (measured in nm).  They will affect
+     * any Force that uses periodic boundary conditions.
+     *
+     * Currently, only rectangular boxes are supported.  This means that a, b, and c must be aligned with the
+     * x, y, and z axes respectively.  Future releases may support arbitrary triclinic boxes.
+     *
+     * @param a      on exit, this contains the vector defining the first edge of the periodic box
+     * @param b      on exit, this contains the vector defining the second edge of the periodic box
+     * @param c      on exit, this contains the vector defining the third edge of the periodic box
+     */
+    void getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const;
+    /**
+     * Set the vectors defining the axes of the periodic box (measured in nm).  They will affect
+     * any Force that uses periodic boundary conditions.
+     *
+     * Currently, only rectangular boxes are supported.  This means that a, b, and c must be aligned with the
+     * x, y, and z axes respectively.  Future releases may support arbitrary triclinic boxes.
+     *
+     * @param a      the vector defining the first edge of the periodic box
+     * @param b      the vector defining the second edge of the periodic box
+     * @param c      the vector defining the third edge of the periodic box
+     */
+    void setPeriodicBoxVectors(Vec3 a, Vec3 b, Vec3 c);
     /**
      * When a Context is created, it may cache information about the System being simulated
      * and the Force objects contained in it.  This means that, if the System or Forces are then
@@ -167,6 +191,7 @@ private:
     friend class Platform;
     ContextImpl* impl;
     std::map<std::string, std::string> properties;
+    Vec3 periodicBoxVectors[3];
 };
 
 } // namespace OpenMM

openmmapi/include/openmm/System.h

@@ -165,7 +165,8 @@ public:
         return *forces[index];
     }
     /**
-     * Get the vectors which define the axes of the periodic box (measured in nm).  These will affect
+     * Get the default values of the vectors defining the axes of the periodic box (measured in nm).  Any newly
+     * created Context will have its box vectors set to these.  They will affect
      * any Force added to the System that uses periodic boundary conditions.
      *
      * Currently, only rectangular boxes are supported.  This means that a, b, and c must be aligned with the
@@ -175,9 +176,10 @@ public:
      * @param b      on exit, this contains the vector defining the second edge of the periodic box
      * @param c      on exit, this contains the vector defining the third edge of the periodic box
      */
-    void getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const;
+    void getDefaultPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const;
     /**
-     * Set the vectors which define the axes of the periodic box (measured in nm).  These will affect
+     * Set the default values of the vectors defining the axes of the periodic box (measured in nm).  Any newly
+     * created Context will have its box vectors set to these.  They will affect
      * any Force added to the System that uses periodic boundary conditions.
      *
      * Currently, only rectangular boxes are supported.  This means that a, b, and c must be aligned with the
@@ -187,7 +189,7 @@ 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
      */
-    void setPeriodicBoxVectors(Vec3 a, Vec3 b, Vec3 c);
+    void setDefaultPeriodicBoxVectors(Vec3 a, Vec3 b, Vec3 c);
 private:
     class ConstraintInfo;
     Vec3 periodicBoxVectors[3];

openmmapi/src/Context.cpp

@@ -38,14 +38,17 @@ using namespace std;
 
 Context::Context(System& system, Integrator& integrator) : properties(map<string, string>()) {
     impl = new ContextImpl(*this, system, integrator, 0, properties);
+    system.getDefaultPeriodicBoxVectors(periodicBoxVectors[0], periodicBoxVectors[1], periodicBoxVectors[2]);
 }
 
 Context::Context(System& system, Integrator& integrator, Platform& platform) : properties(map<string, string>()) {
     impl = new ContextImpl(*this, system, integrator, &platform, properties);
+    system.getDefaultPeriodicBoxVectors(periodicBoxVectors[0], periodicBoxVectors[1], periodicBoxVectors[2]);
 }
 
 Context::Context(System& system, Integrator& integrator, Platform& platform, const map<string, string>& properties) : properties(properties) {
     impl = new ContextImpl(*this, system, integrator, &platform, properties);
+    system.getDefaultPeriodicBoxVectors(periodicBoxVectors[0], periodicBoxVectors[1], periodicBoxVectors[2]);
 }
 
 Context::~Context() {
@@ -120,10 +123,29 @@ void Context::setParameter(const string& name, double value) {
     impl->setParameter(name, value);
 }
 
+void Context::getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const {
+    a = periodicBoxVectors[0];
+    b = periodicBoxVectors[1];
+    c = periodicBoxVectors[2];
+}
+
+void Context::setPeriodicBoxVectors(Vec3 a, Vec3 b, Vec3 c) {
+    if (a[1] != 0.0 || a[2] != 0.0)
+        throw OpenMMException("First periodic box vector must be parallel to x.");
+    if (b[0] != 0.0 || b[2] != 0.0)
+        throw OpenMMException("Second periodic box vector must be parallel to y.");
+    if (c[0] != 0.0 || c[1] != 0.0)
+        throw OpenMMException("Third periodic box vector must be parallel to z.");
+    periodicBoxVectors[0] = a;
+    periodicBoxVectors[1] = b;
+    periodicBoxVectors[2] = c;
+}
+
 void Context::reinitialize() {
     System& system = impl->getSystem();
     Integrator& integrator = impl->getIntegrator();
     Platform& platform = impl->getPlatform();
+    system.getDefaultPeriodicBoxVectors(periodicBoxVectors[0], periodicBoxVectors[1], periodicBoxVectors[2]);
     delete impl;
     impl = new ContextImpl(*this, system, integrator, &platform, properties);
 }

openmmapi/src/CustomGBForceImpl.cpp

@@ -97,7 +97,7 @@ void CustomGBForceImpl::initialize(ContextImpl& context) {
     }
     if (owner.getNonbondedMethod() == CustomGBForce::CutoffPeriodic) {
         Vec3 boxVectors[3];
-        system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+        system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
         double cutoff = owner.getCutoffDistance();
         if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
             throw OpenMMException("CustomGBForce: The cutoff distance cannot be greater than half the periodic box size.");

openmmapi/src/CustomHbondForceImpl.cpp

@@ -170,7 +170,7 @@ void CustomHbondForceImpl::initialize(ContextImpl& context) {
     }
     if (owner.getNonbondedMethod() == CustomHbondForce::CutoffPeriodic) {
         Vec3 boxVectors[3];
-        system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+        system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
         double cutoff = owner.getCutoffDistance();
         if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
             throw OpenMMException("CustomHbondForce: The cutoff distance cannot be greater than half the periodic box size.");

openmmapi/src/CustomNonbondedForceImpl.cpp

@@ -97,7 +97,7 @@ void CustomNonbondedForceImpl::initialize(ContextImpl& context) {
     }
     if (owner.getNonbondedMethod() == CustomNonbondedForce::CutoffPeriodic) {
         Vec3 boxVectors[3];
-        system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+        system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
         double cutoff = owner.getCutoffDistance();
         if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
             throw OpenMMException("CustomNonbondedForce: The cutoff distance cannot be greater than half the periodic box size.");

openmmapi/src/GBSAOBCForceImpl.cpp

@@ -47,7 +47,7 @@ void GBSAOBCForceImpl::initialize(ContextImpl& context) {
         throw OpenMMException("GBSAOBCForce must have exactly as many particles as the System it belongs to.");
     if (owner.getNonbondedMethod() == GBSAOBCForce::CutoffPeriodic) {
         Vec3 boxVectors[3];
-        context.getSystem().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+        context.getSystem().getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
         double cutoff = owner.getCutoffDistance();
         if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
             throw OpenMMException("GBSAOBCForce: The cutoff distance cannot be greater than half the periodic box size.");

openmmapi/src/GBVIForceImpl.cpp

@@ -96,7 +96,7 @@ void GBVIForceImpl::initialize(ContextImpl& context) {
     }   
     if (owner.getNonbondedMethod() == GBVIForce::CutoffPeriodic) {
         Vec3 boxVectors[3];
-        system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+        system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
         double cutoff = owner.getCutoffDistance();
         if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
             throw OpenMMException("GBVIForce: The cutoff distance cannot be greater than half the periodic box size.");

openmmapi/src/NonbondedForceImpl.cpp

@@ -89,7 +89,7 @@ void NonbondedForceImpl::initialize(ContextImpl& context) {
             owner.getNonbondedMethod() == NonbondedForce::Ewald ||
             owner.getNonbondedMethod() == NonbondedForce::PME) {
         Vec3 boxVectors[3];
-        system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+        system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
         double cutoff = owner.getCutoffDistance();
         if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
             throw OpenMMException("NonbondedForce: The cutoff distance cannot be greater than half the periodic box size.");
@@ -130,7 +130,7 @@ private:
 
 void NonbondedForceImpl::calcEwaldParameters(const System& system, const NonbondedForce& force, double& alpha, int& kmaxx, int& kmaxy, int& kmaxz) {
     Vec3 boxVectors[3];
-    system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+    system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
     double tol = force.getEwaldErrorTolerance();
     alpha = (1.0/force.getCutoffDistance())*std::sqrt(-log(2.0*tol));
     kmaxx = findZero(EwaldErrorFunction(boxVectors[0][0], alpha, tol), 10);
@@ -146,7 +146,7 @@ void NonbondedForceImpl::calcEwaldParameters(const System& system, const Nonbond
 
 void NonbondedForceImpl::calcPMEParameters(const System& system, const NonbondedForce& force, double& alpha, int& xsize, int& ysize, int& zsize) {
     Vec3 boxVectors[3];
-    system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+    system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
     double tol = force.getEwaldErrorTolerance();
     alpha = (1.0/force.getCutoffDistance())*std::sqrt(-log(2.0*tol));
     xsize = (int) ceil(alpha*boxVectors[0][0]/pow(0.5*tol, 0.2));

openmmapi/src/System.cpp

@@ -63,13 +63,13 @@ void System::setConstraintParameters(int index, int particle1, int particle2, do
     constraints[index].distance = distance;
 }
 
-void System::getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const {
+void System::getDefaultPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const {
     a = periodicBoxVectors[0];
     b = periodicBoxVectors[1];
     c = periodicBoxVectors[2];
 }
 
-void System::setPeriodicBoxVectors(Vec3 a, Vec3 b, Vec3 c) {
+void System::setDefaultPeriodicBoxVectors(Vec3 a, Vec3 b, Vec3 c) {
     if (a[1] != 0.0 || a[2] != 0.0)
         throw OpenMMException("First periodic box vector must be parallel to x.");
     if (b[0] != 0.0 || b[2] != 0.0)

platforms/cuda/src/CudaKernels.cpp

@@ -45,6 +45,13 @@ void CudaCalcForcesAndEnergyKernel::initialize(const System& system) {
 
 void CudaCalcForcesAndEnergyKernel::beginForceComputation(ContextImpl& context) {
     _gpuContext* gpu = data.gpu;
+    Vec3 boxVectors[3];
+    context.getOwner().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+    float boxx = boxVectors[0][0], boxy = boxVectors[1][1], boxz = boxVectors[2][2];
+    if (boxx != gpu->sim.periodicBoxSizeX || boxy != gpu->sim.periodicBoxSizeY || boxz != gpu->sim.periodicBoxSizeZ) {
+        gpuSetPeriodicBoxSize(gpu, boxx, boxy, boxz);
+        gpuSetConstants(gpu);
+    }
     if (data.nonbondedMethod != NO_CUTOFF && data.computeForceCount%100 == 0)
         gpuReorderAtoms(gpu);
     data.computeForceCount++;
@@ -77,6 +84,13 @@ void CudaCalcForcesAndEnergyKernel::finishForceComputation(ContextImpl& context)
 
 void CudaCalcForcesAndEnergyKernel::beginEnergyComputation(ContextImpl& context) {
     _gpuContext* gpu = data.gpu;
+    Vec3 boxVectors[3];
+    context.getOwner().getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+    float boxx = boxVectors[0][0], boxy = boxVectors[1][1], boxz = boxVectors[2][2];
+    if (boxx != gpu->sim.periodicBoxSizeX || boxy != gpu->sim.periodicBoxSizeY || boxz != gpu->sim.periodicBoxSizeZ) {
+        gpuSetPeriodicBoxSize(gpu, boxx, boxy, boxz);
+        gpuSetConstants(gpu);
+    }
     if (data.nonbondedMethod != NO_CUTOFF && data.stepCount%100 == 0)
         gpuReorderAtoms(gpu);
     data.stepCount++;
@@ -490,9 +504,6 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
             exclusionList[exclusions[i].first].push_back(exclusions[i].second);
             exclusionList[exclusions[i].second].push_back(exclusions[i].first);
         }
-        Vec3 boxVectors[3];
-        system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
-        gpuSetPeriodicBoxSize(gpu, (float)boxVectors[0][0], (float)boxVectors[1][1], (float)boxVectors[2][2]);
         CudaNonbondedMethod method = NO_CUTOFF;
         if (force.getNonbondedMethod() != NonbondedForce::NoCutoff) {
             gpuSetNonbondedCutoff(gpu, (float) force.getCutoffDistance(), (float) force.getReactionFieldDielectric());
@@ -583,9 +594,6 @@ void CudaCalcCustomNonbondedForceKernel::initialize(const System& system, const
         exclusionList[particle1].push_back(particle2);
         exclusionList[particle2].push_back(particle1);
     }
-    Vec3 boxVectors[3];
-    system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
-    gpuSetPeriodicBoxSize(gpu, (float)boxVectors[0][0], (float)boxVectors[1][1], (float)boxVectors[2][2]);
     CudaNonbondedMethod method = NO_CUTOFF;
     if (force.getNonbondedMethod() != CustomNonbondedForce::NoCutoff)
         method = CUTOFF;

platforms/cuda/tests/TestCudaCustomNonbondedForce.cpp

@@ -187,7 +187,7 @@ void testPeriodic() {
     forceField->addParticle(vector<double>());
     forceField->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
     forceField->setCutoffDistance(2.0);
-    system.setPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
+    system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
     system.addForce(forceField);
     Context context(system, integrator, platform);
     vector<Vec3> positions(3);

platforms/cuda/tests/TestCudaEwald.cpp

@@ -79,7 +79,7 @@ void testEwaldPME(bool includeExceptions) {
         nonbonded->addParticle(1.0, 1.0,0.0);
     for (int i = 0; i < numParticles/2; i++)
         nonbonded->addParticle(-1.0, 1.0,0.0);
-    system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
     system.addForce(nonbonded);
 
     vector<Vec3> positions(numParticles);
@@ -184,7 +184,7 @@ void testEwald2Ions() {
     const double cutoff = 2.0;
     nonbonded->setCutoffDistance(cutoff);
     nonbonded->setEwaldErrorTolerance(TOL);
-    system.setPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(0, 6, 0), Vec3(0, 0, 6));
+    system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(0, 6, 0), Vec3(0, 0, 6));
     system.addForce(nonbonded);
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);
@@ -205,7 +205,7 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
     const int numParticles = 51;
     const double boxWidth = 5.0;
     System system;
-    system.setPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
+    system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
     NonbondedForce* force = new NonbondedForce();
     system.addForce(force);
     vector<Vec3> positions(numParticles);

platforms/cuda/tests/TestCudaGBSAOBCForce.cpp

@@ -91,7 +91,7 @@ void testCutoffAndPeriodic() {
     const double boxSize = 10.0;
     nonbonded->setCutoffDistance(cutoffDistance);
     gbsa->setCutoffDistance(cutoffDistance);
-    system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
     system.addForce(gbsa);
     system.addForce(nonbonded);
     vector<Vec3> positions(2);
@@ -152,7 +152,7 @@ void testForce(int numParticles, NonbondedForce::NonbondedMethod method, GBSAOBC
     int grid = (int) floor(0.5+pow(numParticles, 1.0/3.0));
     if (method == NonbondedForce::CutoffPeriodic) {
         double boxSize = (grid+1)*1.1;
-        system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+        system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
     }
     system.addForce(gbsa);
     system.addForce(nonbonded);

platforms/cuda/tests/TestCudaNonbondedForce.cpp

@@ -343,7 +343,7 @@ void testPeriodic() {
     nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
     const double cutoff = 2.0;
     nonbonded->setCutoffDistance(cutoff);
-    system.setPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
+    system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
     system.addForce(nonbonded);
     Context context(system, integrator, platform);
     vector<Vec3> positions(3);
@@ -423,7 +423,7 @@ void testLargeSystem() {
     // Now do the same thing with periodic boundary conditions.
 
     nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
     cudaContext.reinitialize();
     referenceContext.reinitialize();
     cudaContext.setPositions(positions);
@@ -461,7 +461,7 @@ void testBlockInteractions(bool periodic) {
     }
     nonbonded->setNonbondedMethod(periodic ? NonbondedForce::CutoffPeriodic : NonbondedForce::CutoffNonPeriodic);
     nonbonded->setCutoffDistance(cutoff);
-    system.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
     system.addForce(nonbonded);
     Context context(system, integrator, cuda);
     context.setPositions(positions);

platforms/cuda/tests/TstCudaUsingParameterFile.cpp

@@ -3848,9 +3848,9 @@ Integrator* readParameterFile( const std::string& inputParameterFile, MapStringI
                   boxIndex++;
                }
             }
-            system.setPeriodicBoxVectors( box[0], box[1], box[2] );
+            system.setDefaultPeriodicBoxVectors( box[0], box[1], box[2] );
             Vec3 a, b, c;
-            system.getPeriodicBoxVectors( a, b, c);
+            system.getDefaultPeriodicBoxVectors( a, b, c);
             if( log ){
                (void) fprintf( log, "Box [%14.7f %14.7f %14.7f]\n    [%14.7f %14.7f %14.7f]\n    [%14.7f %14.7f %14.7f]\n",
                                a[0], a[1], a[2], b[0], b[1], b[2], c[0], c[1], c[2] );

platforms/opencl/src/OpenCLContext.cpp

@@ -408,7 +408,6 @@ void OpenCLContext::reorderAtoms() {
 
     posq->download();
     velm->download();
-    mm_float4 periodicBoxSize = nonbonded->getPeriodicBoxSize();
     float minx = posq->get(0).x, maxx = posq->get(0).x;
     float miny = posq->get(0).y, maxy = posq->get(0).y;
     float minz = posq->get(0).z, maxz = posq->get(0).z;

platforms/opencl/src/OpenCLContext.h

@@ -315,6 +315,25 @@ public:
     int getSIMDWidth() const {
         return simdWidth;
     }
+    /**
+     * Get the size of the periodic box.
+     */
+    mm_float4 getPeriodicBoxSize() const {
+        return periodicBoxSize;
+    }
+    /**
+     * Set the size of the periodic box.
+     */
+    void setPeriodicBoxSize(double xsize, double ysize, double zsize) {
+        periodicBoxSize = mm_float4((float) xsize, (float) ysize, (float) zsize, 0);
+        invPeriodicBoxSize = mm_float4((float) (1.0/xsize), (float) (1.0/ysize), (float) (1.0/zsize), 0);
+    }
+    /**
+     * Get the inverse of the size of the periodic box.
+     */
+    mm_float4 getInvPeriodicBoxSize() const {
+        return invPeriodicBoxSize;
+    }
     /**
      * Get the OpenCLIntegrationUtilities for this context.
      */
@@ -347,6 +366,8 @@ private:
     int numThreadBlocks;
     int numForceBuffers;
     int simdWidth;
+    mm_float4 periodicBoxSize;
+    mm_float4 invPeriodicBoxSize;
     std::string compilationOptions;
     cl::Context context;
     cl::Device device;