Finished implementing CompoundIntegrator

openmmapi/include/openmm/CompoundIntegrator.h

@@ -94,6 +94,12 @@ public:
      * @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.
      */

openmmapi/src/CompoundIntegrator.cpp

@@ -64,6 +64,11 @@ Integrator& CompoundIntegrator::getIntegrator(int index) {
     return *integrators[index];
 }
 
+const Integrator& CompoundIntegrator::getIntegrator(int index) const {
+    ASSERT_VALID_INDEX(index, integrators);
+    return *integrators[index];
+}
+
 int CompoundIntegrator::getCurrentIntegrator() const {
     return currentIntegrator;
 }
@@ -95,6 +100,8 @@ void CompoundIntegrator::step(int steps) {
 }
 
 void CompoundIntegrator::initialize(ContextImpl& context) {
+    if (integrators.size() == 0)
+        throw OpenMMException("CompoundIntegrator must contain at least one Integrator");
     for (int i = 0; i < integrators.size(); i++)
         integrators[i]->initialize(context);
 }

platforms/cpu/tests/TestCpuCompoundIntegrator.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) 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 "CpuTests.h"
+#include "TestCompoundIntegrator.h"
+
+void runPlatformTests() {
+}

platforms/cuda/include/CudaIntegrationUtilities.h

@@ -62,6 +62,14 @@ public:
     CudaArray& getStepSize() {
         return *stepSize;
     }
+    /**
+     * Set the size to use for the next step.
+     */
+    void setNextStepSize(double size);
+    /**
+     * Get the size that was used for the last step.
+     */
+    double getLastStepSize();
     /**
      * Apply constraints to the atom positions.
      *
@@ -154,6 +162,7 @@ private:
     CudaArray* vsiteLocalCoordsParams;
     int randomPos;
     int lastSeed, numVsites;
+    double2 lastStepSize;
     struct ShakeCluster;
     struct ConstraintOrderer;
 };

platforms/cuda/include/CudaKernels.h

@@ -1123,7 +1123,6 @@ public:
     double computeKineticEnergy(ContextImpl& context, const VerletIntegrator& integrator);
 private:
     CudaContext& cu;
-    double prevStepSize;
     CUfunction kernel1, kernel2;
 };
 
@@ -1354,7 +1353,7 @@ private:
     void recordChangedParameters(ContextImpl& context);
     bool evaluateCondition(int step);
     CudaContext& cu;
-    double prevStepSize, energy;
+    double energy;
     float energyFloat;
     int numGlobalVariables;
     bool hasInitializedKernels, deviceValuesAreCurrent, deviceGlobalsAreCurrent, modifiesParameters, keNeedsForce, hasAnyConstraints;

platforms/cuda/include/CudaPlatform.h

@@ -121,7 +121,7 @@ public:
     ContextImpl* context;
     std::vector<CudaContext*> contexts;
     std::vector<double> contextEnergy;
-    bool removeCM, peerAccessSupported, useCpuPme;
+    bool hasInitializedContexts, removeCM, peerAccessSupported, useCpuPme;
     int cmMotionFrequency;
     int stepCount, computeForceCount;
     double time;

platforms/cuda/src/CudaIntegrationUtilities.cpp

@@ -106,21 +106,21 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S
         vsiteOutOfPlaneAtoms(NULL), vsiteOutOfPlaneWeights(NULL), vsiteLocalCoordsAtoms(NULL), vsiteLocalCoordsParams(NULL) {
     // Create workspace arrays.
 
+    lastStepSize = make_double2(0.0, 0.0);
     if (context.getUseDoublePrecision() || context.getUseMixedPrecision()) {
         posDelta = CudaArray::create<double4>(context, context.getPaddedNumAtoms(), "posDelta");
         vector<double4> deltas(posDelta->getSize(), make_double4(0.0, 0.0, 0.0, 0.0));
         posDelta->upload(deltas);
         stepSize = CudaArray::create<double2>(context, 1, "stepSize");
-        vector<double2> step(1, make_double2(0.0, 0.0));
-        stepSize->upload(step);
+        stepSize->upload(&lastStepSize);
     }
     else {
         posDelta = CudaArray::create<float4>(context, context.getPaddedNumAtoms(), "posDelta");
         vector<float4> deltas(posDelta->getSize(), make_float4(0.0f, 0.0f, 0.0f, 0.0f));
         posDelta->upload(deltas);
         stepSize = CudaArray::create<float2>(context, 1, "stepSize");
-        vector<float2> step(1, make_float2(0.0f, 0.0f));
-        stepSize->upload(step);
+        float2 lastStepSizeFloat = make_float2(0.0f, 0.0f);
+        stepSize->upload(&lastStepSizeFloat);
     }
 
     // Record the set of constraints and how many constraints each atom is involved in.
@@ -650,6 +650,29 @@ CudaIntegrationUtilities::~CudaIntegrationUtilities() {
         delete vsiteLocalCoordsParams;
 }
 
+void CudaIntegrationUtilities::setNextStepSize(double size) {
+    if (size != lastStepSize.x || size != lastStepSize.y) {
+        lastStepSize = make_double2(size, size);
+        if (context.getUseDoublePrecision() || context.getUseMixedPrecision())
+            stepSize->upload(&lastStepSize);
+        else {
+            float2 lastStepSizeFloat = make_float2((float) size, (float) size);
+            stepSize->upload(&lastStepSizeFloat);
+        }
+    }
+}
+
+double CudaIntegrationUtilities::getLastStepSize() {
+    if (context.getUseDoublePrecision() || context.getUseMixedPrecision())
+        stepSize->download(&lastStepSize);
+    else {
+        float2 lastStepSizeFloat;
+        stepSize->download(&lastStepSizeFloat);
+        lastStepSize = make_double2(lastStepSizeFloat.x, lastStepSizeFloat.y);
+    }
+    return lastStepSize.y;
+}
+
 void CudaIntegrationUtilities::applyConstraints(double tol) {
     applyConstraints(false, tol);
 }

platforms/cuda/src/CudaKernels.cpp

@@ -5674,7 +5674,6 @@ void CudaIntegrateVerletStepKernel::initialize(const System& system, const Verle
     CUmodule module = cu.createModule(CudaKernelSources::verlet, defines, "");
     kernel1 = cu.getKernel(module, "integrateVerletPart1");
     kernel2 = cu.getKernel(module, "integrateVerletPart2");
-    prevStepSize = -1.0;
 }
 
 void CudaIntegrateVerletStepKernel::execute(ContextImpl& context, const VerletIntegrator& integrator) {
@@ -5683,19 +5682,7 @@ void CudaIntegrateVerletStepKernel::execute(ContextImpl& context, const VerletIn
     int numAtoms = cu.getNumAtoms();
     int paddedNumAtoms = cu.getPaddedNumAtoms();
     double dt = integrator.getStepSize();
-    if (dt != prevStepSize) {
-        if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
-            vector<double2> stepSizeVec(1);
-            stepSizeVec[0] = make_double2(dt, dt);
-            cu.getIntegrationUtilities().getStepSize().upload(stepSizeVec);
-        }
-        else {
-            vector<float2> stepSizeVec(1);
-            stepSizeVec[0] = make_float2((float) dt, (float) dt);
-            cu.getIntegrationUtilities().getStepSize().upload(stepSizeVec);
-        }
-        prevStepSize = dt;
-    }
+    cu.getIntegrationUtilities().setNextStepSize(dt);
 
     // Call the first integration kernel.
 
@@ -5752,6 +5739,7 @@ void CudaIntegrateLangevinStepKernel::execute(ContextImpl& context, const Langev
     double temperature = integrator.getTemperature();
     double friction = integrator.getFriction();
     double stepSize = integrator.getStepSize();
+    cu.getIntegrationUtilities().setNextStepSize(stepSize);
     if (temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
         // Calculate the integration parameters.
 
@@ -5766,8 +5754,6 @@ void CudaIntegrateLangevinStepKernel::execute(ContextImpl& context, const Langev
             p[1] = fscale;
             p[2] = noisescale;
             params->upload(p);
-            double2 ss = make_double2(0, stepSize);
-            integration.getStepSize().upload(&ss);
         }
         else {
             vector<float> p(params->getSize());
@@ -5775,8 +5761,6 @@ void CudaIntegrateLangevinStepKernel::execute(ContextImpl& context, const Langev
             p[1] = (float) fscale;
             p[2] = (float) noisescale;
             params->upload(p);
-            float2 ss = make_float2(0, (float) stepSize);
-            integration.getStepSize().upload(&ss);
         }
         prevTemp = temperature;
         prevFriction = friction;
@@ -5929,20 +5913,13 @@ double CudaIntegrateVariableVerletStepKernel::execute(ContextImpl& context, cons
 
     // Update the time and step count.
 
-    double dt, time;
+    double dt = cu.getIntegrationUtilities().getLastStepSize();
+    double time = cu.getTime()+dt;
     if (useDouble) {
-        double2 stepSize;
-        cu.getIntegrationUtilities().getStepSize().download(&stepSize);
-        dt = stepSize.y;
-        time = cu.getTime()+dt;
         if (dt == maxStepSize)
             time = maxTime; // Avoid round-off error
     }
     else {
-        float2 stepSize;
-        cu.getIntegrationUtilities().getStepSize().download(&stepSize);
-        dt = stepSize.y;
-        time = cu.getTime()+dt;
         if (dt == maxStepSizeFloat)
             time = maxTime; // Avoid round-off error
     }
@@ -6023,20 +6000,13 @@ double CudaIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, co
 
     // Update the time and step count.
 
-    double dt, time;
+    double dt = cu.getIntegrationUtilities().getLastStepSize();
+    double time = cu.getTime()+dt;
     if (useDouble) {
-        double2 stepSize;
-        cu.getIntegrationUtilities().getStepSize().download(&stepSize);
-        dt = stepSize.y;
-        time = cu.getTime()+dt;
         if (dt == maxStepSize)
             time = maxTime; // Avoid round-off error
     }
     else {
-        float2 stepSize;
-        cu.getIntegrationUtilities().getStepSize().download(&stepSize);
-        dt = stepSize.y;
-        time = cu.getTime()+dt;
         if (dt == maxStepSizeFloat)
             time = maxTime; // Avoid round-off error
     }
@@ -6139,7 +6109,6 @@ void CudaIntegrateCustomStepKernel::initialize(const System& system, const Custo
     summedValue = new CudaArray(cu, 1, elementSize, "summedValue");
     perDofValues = new CudaParameterSet(cu, integrator.getNumPerDofVariables(), 3*system.getNumParticles(), "perDofVariables", false, cu.getUseDoublePrecision() || cu.getUseMixedPrecision());
     cu.addReorderListener(new ReorderListener(cu, *perDofValues, localPerDofValuesFloat, localPerDofValuesDouble, deviceValuesAreCurrent));
-    prevStepSize = -1.0;
     SimTKOpenMMUtilities::setRandomNumberSeed(integrator.getRandomNumberSeed());
 }
 
@@ -6553,9 +6522,7 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
     }
     localValuesAreCurrent = false;
     double stepSize = integrator.getStepSize();
-    if (stepSize != prevStepSize) {
-        recordGlobalValue(stepSize, GlobalTarget(DT, dtVariableIndex));
-    }
+    recordGlobalValue(stepSize, GlobalTarget(DT, dtVariableIndex));
     for (int i = 0; i < (int) parameterNames.size(); i++) {
         double value = context.getParameter(parameterNames[i]);
         if (value != globalValuesDouble[parameterVariableIndex[i]]) {
@@ -6760,17 +6727,10 @@ double CudaIntegrateCustomStepKernel::computeKineticEnergy(ContextImpl& context,
 void CudaIntegrateCustomStepKernel::recordGlobalValue(double value, GlobalTarget target) {
     switch (target.type) {
         case DT:
+            if (value != globalValuesDouble[dtVariableIndex])
+                deviceGlobalsAreCurrent = false;
             globalValuesDouble[dtVariableIndex] = value;
-            deviceGlobalsAreCurrent = false;
-            if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
-                double size[] = {0, value};
-                cu.getIntegrationUtilities().getStepSize().upload(size);
-            }
-            else {
-                float size[] = {0, (float) value};
-                cu.getIntegrationUtilities().getStepSize().upload(size);
-            }
-            prevStepSize = value;
+            cu.getIntegrationUtilities().setNextStepSize(value);
             break;
         case VARIABLE:
         case PARAMETER:

platforms/cuda/src/CudaPlatform.cpp

@@ -179,7 +179,7 @@ void CudaPlatform::contextDestroyed(ContextImpl& context) const {
 }
 
 CudaPlatform::PlatformData::PlatformData(ContextImpl* context, const System& system, const string& deviceIndexProperty, const string& blockingProperty, const string& precisionProperty,
-            const string& cpuPmeProperty, const string& compilerProperty, const string& tempProperty, const string& hostCompilerProperty) : context(context), removeCM(false), stepCount(0), computeForceCount(0), time(0.0) {
+            const string& cpuPmeProperty, const string& compilerProperty, const string& tempProperty, const string& hostCompilerProperty) : context(context), removeCM(false), stepCount(0), computeForceCount(0), time(0.0), hasInitializedContexts(false) {
     bool blocking = (blockingProperty == "true");
     vector<string> devices;
     size_t searchPos = 0, nextPos;
@@ -247,8 +247,11 @@ CudaPlatform::PlatformData::~PlatformData() {
 }
 
 void CudaPlatform::PlatformData::initializeContexts(const System& system) {
+    if (hasInitializedContexts)
+        return;
     for (int i = 0; i < (int) contexts.size(); i++)
         contexts[i]->initialize();
+    hasInitializedContexts = true;
 }
 
 void CudaPlatform::PlatformData::syncContexts() {

platforms/cuda/tests/TestCudaCompoundIntegrator.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) 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 "CudaTests.h"
+#include "TestCompoundIntegrator.h"
+
+void runPlatformTests() {
+}

platforms/opencl/include/OpenCLIntegrationUtilities.h

@@ -62,6 +62,14 @@ public:
     OpenCLArray& getStepSize() {
         return *stepSize;
     }
+    /**
+     * Set the size to use for the next step.
+     */
+    void setNextStepSize(double size);
+    /**
+     * Get the size that was used for the last step.
+     */
+    double getLastStepSize();
     /**
      * Apply constraints to the atom positions.
      *
@@ -153,6 +161,7 @@ private:
     int randomPos;
     int lastSeed, numVsites;
     bool hasInitializedPosConstraintKernels, hasInitializedVelConstraintKernels, ccmaUseDirectBuffer, hasOverlappingVsites;
+    mm_double2 lastStepSize;
     struct ShakeCluster;
     struct ConstraintOrderer;
 };

platforms/opencl/include/OpenCLKernels.h

@@ -1103,7 +1103,6 @@ public:
     double computeKineticEnergy(ContextImpl& context, const VerletIntegrator& integrator);
 private:
     OpenCLContext& cl;
-    double prevStepSize;
     bool hasInitializedKernels;
     cl::Kernel kernel1, kernel2;
 };
@@ -1342,7 +1341,7 @@ private:
     void recordChangedParameters(ContextImpl& context);
     bool evaluateCondition(int step);
     OpenCLContext& cl;
-    double prevStepSize, energy;
+    double energy;
     float energyFloat;
     int numGlobalVariables;
     bool hasInitializedKernels, deviceValuesAreCurrent, deviceGlobalsAreCurrent, modifiesParameters, keNeedsForce, hasAnyConstraints;

platforms/opencl/include/OpenCLPlatform.h

@@ -106,7 +106,7 @@ public:
     ContextImpl* context;
     std::vector<OpenCLContext*> contexts;
     std::vector<double> contextEnergy;
-    bool removeCM, useCpuPme;
+    bool hasInitializedContexts, removeCM, useCpuPme;
     int cmMotionFrequency;
     int stepCount, computeForceCount;
     double time;

platforms/opencl/src/OpenCLIntegrationUtilities.cpp

@@ -106,21 +106,21 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
         hasInitializedPosConstraintKernels(false), hasInitializedVelConstraintKernels(false), hasOverlappingVsites(false) {
     // Create workspace arrays.
 
+    lastStepSize = mm_double2(0.0, 0.0);
     if (context.getUseDoublePrecision() || context.getUseMixedPrecision()) {
         posDelta = OpenCLArray::create<mm_double4>(context, context.getPaddedNumAtoms(), "posDelta");
         vector<mm_double4> deltas(posDelta->getSize(), mm_double4(0.0, 0.0, 0.0, 0.0));
         posDelta->upload(deltas);
         stepSize = OpenCLArray::create<mm_double2>(context, 1, "stepSize");
-        vector<mm_double2> step(1, mm_double2(0.0, 0.0));
-        stepSize->upload(step);
+        stepSize->upload(&lastStepSize);
     }
     else {
         posDelta = OpenCLArray::create<mm_float4>(context, context.getPaddedNumAtoms(), "posDelta");
         vector<mm_float4> deltas(posDelta->getSize(), mm_float4(0.0f, 0.0f, 0.0f, 0.0f));
         posDelta->upload(deltas);
         stepSize = OpenCLArray::create<mm_float2>(context, 1, "stepSize");
-        vector<mm_float2> step(1, mm_float2(0.0f, 0.0f));
-        stepSize->upload(step);
+        mm_float2 lastStepSizeFloat = mm_float2(0.0f, 0.0f);
+        stepSize->upload(&lastStepSizeFloat);
     }
     
     // Create the time shift kernel for calculating kinetic energy.
@@ -724,6 +724,29 @@ OpenCLIntegrationUtilities::~OpenCLIntegrationUtilities() {
         delete vsiteLocalCoordsParams;
 }
 
+void OpenCLIntegrationUtilities::setNextStepSize(double size) {
+    if (size != lastStepSize.x || size != lastStepSize.y) {
+        lastStepSize = mm_double2(size, size);
+        if (context.getUseDoublePrecision() || context.getUseMixedPrecision())
+            stepSize->upload(&lastStepSize);
+        else {
+            mm_float2 lastStepSizeFloat = mm_float2((float) size, (float) size);
+            stepSize->upload(&lastStepSizeFloat);
+        }
+    }
+}
+
+double OpenCLIntegrationUtilities::getLastStepSize() {
+    if (context.getUseDoublePrecision() || context.getUseMixedPrecision())
+        stepSize->download(&lastStepSize);
+    else {
+        mm_float2 lastStepSizeFloat;
+        stepSize->download(&lastStepSizeFloat);
+        lastStepSize = mm_double2(lastStepSizeFloat.x, lastStepSizeFloat.y);
+    }
+    return lastStepSize.y;
+}
+
 void OpenCLIntegrationUtilities::applyConstraints(double tol) {
     applyConstraints(false, tol);
 }

platforms/opencl/src/OpenCLKernels.cpp

@@ -5866,7 +5866,6 @@ void OpenCLIntegrateVerletStepKernel::initialize(const System& system, const Ver
     cl::Program program = cl.createProgram(OpenCLKernelSources::verlet, "");
     kernel1 = cl::Kernel(program, "integrateVerletPart1");
     kernel2 = cl::Kernel(program, "integrateVerletPart2");
-    prevStepSize = -1.0;
 }
 
 void OpenCLIntegrateVerletStepKernel::execute(ContextImpl& context, const VerletIntegrator& integrator) {
@@ -5889,19 +5888,7 @@ void OpenCLIntegrateVerletStepKernel::execute(ContextImpl& context, const Verlet
         kernel2.setArg<cl::Buffer>(4, cl.getVelm().getDeviceBuffer());
         kernel2.setArg<cl::Buffer>(5, integration.getPosDelta().getDeviceBuffer());
     }
-    if (dt != prevStepSize) {
-        if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
-            vector<mm_double2> stepSizeVec(1);
-            stepSizeVec[0] = mm_double2(dt, dt);
-            cl.getIntegrationUtilities().getStepSize().upload(stepSizeVec);
-        }
-        else {
-            vector<mm_float2> stepSizeVec(1);
-            stepSizeVec[0] = mm_float2((cl_float) dt, (cl_float) dt);
-            cl.getIntegrationUtilities().getStepSize().upload(stepSizeVec);
-        }
-        prevStepSize = dt;
-    }
+    cl.getIntegrationUtilities().setNextStepSize(dt);
 
     // Call the first integration kernel.
 
@@ -5971,6 +5958,7 @@ void OpenCLIntegrateLangevinStepKernel::execute(ContextImpl& context, const Lang
     double temperature = integrator.getTemperature();
     double friction = integrator.getFriction();
     double stepSize = integrator.getStepSize();
+    cl.getIntegrationUtilities().setNextStepSize(stepSize);
     if (temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
         // Calculate the integration parameters.
 
@@ -5985,8 +5973,6 @@ void OpenCLIntegrateLangevinStepKernel::execute(ContextImpl& context, const Lang
             p[1] = fscale;
             p[2] = noisescale;
             params->upload(p);
-            mm_double2 ss = mm_double2(0, stepSize);
-            integration.getStepSize().upload(&ss);
         }
         else {
             vector<cl_float> p(params->getSize());
@@ -5994,8 +5980,6 @@ void OpenCLIntegrateLangevinStepKernel::execute(ContextImpl& context, const Lang
             p[1] = (cl_float) fscale;
             p[2] = (cl_float) noisescale;
             params->upload(p);
-            mm_float2 ss = mm_float2(0, (float) stepSize);
-            integration.getStepSize().upload(&ss);
         }
         prevTemp = temperature;
         prevFriction = friction;
@@ -6186,20 +6170,13 @@ double OpenCLIntegrateVariableVerletStepKernel::execute(ContextImpl& context, co
 
     // Update the time and step count.
 
-    double dt, time;
+    double dt = cl.getIntegrationUtilities().getLastStepSize();
+    double time = cl.getTime()+dt;
     if (useDouble) {
-        mm_double2 stepSize;
-        cl.getIntegrationUtilities().getStepSize().download(&stepSize);
-        dt = stepSize.y;
-        time = cl.getTime()+dt;
         if (dt == maxStepSize)
             time = maxTime; // Avoid round-off error
     }
     else {
-        mm_float2 stepSize;
-        cl.getIntegrationUtilities().getStepSize().download(&stepSize);
-        dt = stepSize.y;
-        time = cl.getTime()+dt;
         if (dt == maxStepSizeFloat)
             time = maxTime; // Avoid round-off error
     }
@@ -6300,20 +6277,13 @@ double OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context,
 
     // Update the time and step count.
 
-    double dt, time;
+    double dt = cl.getIntegrationUtilities().getLastStepSize();
+    double time = cl.getTime()+dt;
     if (useDouble) {
-        mm_double2 stepSize;
-        cl.getIntegrationUtilities().getStepSize().download(&stepSize);
-        dt = stepSize.y;
-        time = cl.getTime()+dt;
         if (dt == maxStepSize)
             time = maxTime; // Avoid round-off error
     }
     else {
-        mm_float2 stepSize;
-        cl.getIntegrationUtilities().getStepSize().download(&stepSize);
-        dt = stepSize.y;
-        time = cl.getTime()+dt;
         if (dt == maxStepSizeFloat)
             time = maxTime; // Avoid round-off error
     }
@@ -6414,7 +6384,6 @@ void OpenCLIntegrateCustomStepKernel::initialize(const System& system, const Cus
     summedValue = new OpenCLArray(cl, 1, elementSize, "summedValue");
     perDofValues = new OpenCLParameterSet(cl, integrator.getNumPerDofVariables(), 3*system.getNumParticles(), "perDofVariables", false, cl.getUseDoublePrecision() || cl.getUseMixedPrecision());
     cl.addReorderListener(new ReorderListener(cl, *perDofValues, localPerDofValuesFloat, localPerDofValuesDouble, deviceValuesAreCurrent));
-    prevStepSize = -1.0;
     SimTKOpenMMUtilities::setRandomNumberSeed(integrator.getRandomNumberSeed());
 }
 
@@ -6825,9 +6794,7 @@ void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
     }
     localValuesAreCurrent = false;
     double stepSize = integrator.getStepSize();
-    if (stepSize != prevStepSize) {
-        recordGlobalValue(stepSize, GlobalTarget(DT, dtVariableIndex));
-    }
+    recordGlobalValue(stepSize, GlobalTarget(DT, dtVariableIndex));
     for (int i = 0; i < (int) parameterNames.size(); i++) {
         double value = context.getParameter(parameterNames[i]);
         if (value != globalValuesDouble[parameterVariableIndex[i]]) {
@@ -7032,17 +6999,10 @@ double OpenCLIntegrateCustomStepKernel::computeKineticEnergy(ContextImpl& contex
 void OpenCLIntegrateCustomStepKernel::recordGlobalValue(double value, GlobalTarget target) {
     switch (target.type) {
         case DT:
+            if (value != globalValuesDouble[dtVariableIndex])
+                deviceGlobalsAreCurrent = false;
             globalValuesDouble[dtVariableIndex] = value;
-            deviceGlobalsAreCurrent = false;
-            if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
-                double size[] = {0, value};
-                cl.getIntegrationUtilities().getStepSize().upload(size);
-            }
-            else {
-                float size[] = {0, (float) value};
-                cl.getIntegrationUtilities().getStepSize().upload(size);
-            }
-            prevStepSize = value;
+            cl.getIntegrationUtilities().setNextStepSize(value);
             break;
         case VARIABLE:
         case PARAMETER:

platforms/opencl/src/OpenCLPlatform.cpp

@@ -169,7 +169,7 @@ void OpenCLPlatform::contextDestroyed(ContextImpl& context) const {
 }
 
 OpenCLPlatform::PlatformData::PlatformData(const System& system, const string& platformPropValue, const string& deviceIndexProperty,
-        const string& precisionProperty, const string& cpuPmeProperty) : removeCM(false), stepCount(0), computeForceCount(0), time(0.0)  {
+        const string& precisionProperty, const string& cpuPmeProperty) : removeCM(false), stepCount(0), computeForceCount(0), time(0.0), hasInitializedContexts(false)  {
     int platformIndex = -1;
     if (platformPropValue.length() > 0)
         stringstream(platformPropValue) >> platformIndex;
@@ -227,8 +227,11 @@ OpenCLPlatform::PlatformData::~PlatformData() {
 }
 
 void OpenCLPlatform::PlatformData::initializeContexts(const System& system) {
+    if (hasInitializedContexts)
+        return;
     for (int i = 0; i < (int) contexts.size(); i++)
         contexts[i]->initialize();
+    hasInitializedContexts = true;
 }
 
 void OpenCLPlatform::PlatformData::syncContexts() {

platforms/opencl/tests/TestOpenCLCompoundIntegrator.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) 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 "OpenCLTests.h"
+#include "TestCompoundIntegrator.h"
+
+void runPlatformTests() {
+}

serialization/include/openmm/serialization/CompoundIntegratorProxy.h

+#ifndef OPENMM_COMPOUND_INTEGRATOR_PROXY_H_
+#define OPENMM_COMPOUND_INTEGRATOR_PROXY_H_
+
+#include "openmm/serialization/XmlSerializer.h"
+
+namespace OpenMM {
+
+class CompoundIntegratorProxy : public SerializationProxy {
+public:
+    CompoundIntegratorProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+}
+
+#endif /*OPENMM_COMPOUND_INTEGRATOR_PROXY_H_*/
\ No newline at end of file

serialization/src/CompoundIntegratorProxy.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) 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 "openmm/serialization/CompoundIntegratorProxy.h"
+#include <OpenMM.h>
+
+using namespace std;
+using namespace OpenMM;
+
+CompoundIntegratorProxy::CompoundIntegratorProxy() : SerializationProxy("CompoundIntegrator") {
+}
+
+void CompoundIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const CompoundIntegrator& integrator = *reinterpret_cast<const CompoundIntegrator*>(object);
+    node.setIntProperty("currentIntegrator", integrator.getCurrentIntegrator());
+    for (int i = 0; i < integrator.getNumIntegrators(); i++)
+        node.createChildNode("Integrator", &integrator.getIntegrator(i));
+}
+
+void* CompoundIntegratorProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    CompoundIntegrator *integrator = new CompoundIntegrator();
+    for (int i = 0; i < node.getChildren().size(); i++)
+        integrator->addIntegrator(node.getChildren()[i].decodeObject<Integrator>());
+    integrator->setCurrentIntegrator(node.getIntProperty("currentIntegrator"));
+    return integrator;
+}
\ No newline at end of file

serialization/src/SerializationProxyRegistration.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -33,6 +33,7 @@
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMAPTorsionForce.h"
 #include "openmm/CMMotionRemover.h"
+#include "openmm/CompoundIntegrator.h"
 #include "openmm/CustomAngleForce.h"
 #include "openmm/CustomBondForce.h"
 #include "openmm/CustomCompoundBondForce.h"
@@ -65,6 +66,7 @@
 #include "openmm/serialization/AndersenThermostatProxy.h"
 #include "openmm/serialization/CMAPTorsionForceProxy.h"
 #include "openmm/serialization/CMMotionRemoverProxy.h"
+#include "openmm/serialization/CompoundIntegratorProxy.h"
 #include "openmm/serialization/CustomAngleForceProxy.h"
 #include "openmm/serialization/CustomBondForceProxy.h"
 #include "openmm/serialization/CustomCompoundBondForceProxy.h"
@@ -112,6 +114,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(BrownianIntegrator), new BrownianIntegratorProxy());
     SerializationProxy::registerProxy(typeid(CMAPTorsionForce), new CMAPTorsionForceProxy());
     SerializationProxy::registerProxy(typeid(CMMotionRemover), new CMMotionRemoverProxy());
+    SerializationProxy::registerProxy(typeid(CompoundIntegrator), new CompoundIntegratorProxy());
     SerializationProxy::registerProxy(typeid(Continuous1DFunction), new Continuous1DFunctionProxy());
     SerializationProxy::registerProxy(typeid(Continuous2DFunction), new Continuous2DFunctionProxy());
     SerializationProxy::registerProxy(typeid(Continuous3DFunction), new Continuous3DFunctionProxy());