Eliminated Stream and related classes, replacing their functionality with UpdateStateDataKernel.

platforms/reference/src/ReferenceKernels.h

@@ -99,11 +99,12 @@ public:
 };
 
 /**
- * This kernel is invoked to get or set the current time.
+ * This kernel provides methods for setting and retrieving various state data: time, positions,
+ * velocities, and forces.
  */
-class ReferenceUpdateTimeKernel : public UpdateTimeKernel {
+class ReferenceUpdateStateDataKernel : public UpdateStateDataKernel {
 public:
-    ReferenceUpdateTimeKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : UpdateTimeKernel(name, platform), data(data) {
+    ReferenceUpdateStateDataKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : UpdateStateDataKernel(name, platform), data(data) {
     }
     /**
      * Initialize the kernel.
@@ -123,6 +124,36 @@ public:
      * @param context    the context in which to execute this kernel
      */
     void setTime(ContextImpl& context, double time);
+    /**
+     * Get the positions of all particles.
+     *
+     * @param positions  on exit, this contains the particle positions
+     */
+    void getPositions(ContextImpl& context, std::vector<Vec3>& positions);
+    /**
+     * Set the positions of all particles.
+     *
+     * @param positions  a vector containg the particle positions
+     */
+    void setPositions(ContextImpl& context, const std::vector<Vec3>& positions);
+    /**
+     * Get the velocities of all particles.
+     *
+     * @param velocities  on exit, this contains the particle velocities
+     */
+    void getVelocities(ContextImpl& context, std::vector<Vec3>& velocities);
+    /**
+     * Set the velocities of all particles.
+     *
+     * @param velocities  a vector containg the particle velocities
+     */
+    void setVelocities(ContextImpl& context, const std::vector<Vec3>& velocities);
+    /**
+     * Get the current forces on all particles.
+     *
+     * @param forces  on exit, this contains the forces
+     */
+    void getForces(ContextImpl& context, std::vector<Vec3>& forces);
 private:
     ReferencePlatform::PlatformData& data;
 };

platforms/reference/src/ReferencePlatform.cpp

@@ -40,7 +40,7 @@ using namespace OpenMM;
 ReferencePlatform::ReferencePlatform() {
     ReferenceKernelFactory* factory = new ReferenceKernelFactory();
     registerKernelFactory(CalcForcesAndEnergyKernel::Name(), factory);
-    registerKernelFactory(UpdateTimeKernel::Name(), factory);
+    registerKernelFactory(UpdateStateDataKernel::Name(), factory);
     registerKernelFactory(CalcHarmonicBondForceKernel::Name(), factory);
     registerKernelFactory(CalcHarmonicAngleForceKernel::Name(), factory);
     registerKernelFactory(CalcPeriodicTorsionForceKernel::Name(), factory);
@@ -63,15 +63,39 @@ bool ReferencePlatform::supportsDoublePrecision() const {
     return (sizeof(RealOpenMM) >= sizeof(double));
 }
 
-const StreamFactory& ReferencePlatform::getDefaultStreamFactory() const {
-    return defaultStreamFactory;
-}
-
 void ReferencePlatform::contextCreated(ContextImpl& context) const {
-    context.setPlatformData(new PlatformData());
+    context.setPlatformData(new PlatformData(context.getSystem().getNumParticles()));
 }
 
 void ReferencePlatform::contextDestroyed(ContextImpl& context) const {
     PlatformData* data = reinterpret_cast<PlatformData*>(context.getPlatformData());
     delete data;
 }
+
+ReferencePlatform::PlatformData::PlatformData(int numParticles) : time(0.0), stepCount(0), numParticles(numParticles) {
+    RealOpenMM** positions = new RealOpenMM*[numParticles];
+    RealOpenMM** velocities = new RealOpenMM*[numParticles];
+    RealOpenMM** forces = new RealOpenMM*[numParticles];
+    for (int i = 0; i < numParticles; ++i) {
+        positions[i] = new RealOpenMM[3];
+        velocities[i] = new RealOpenMM[3];
+        forces[i] = new RealOpenMM[3];
+    }
+    this->positions = positions;
+    this->velocities = velocities;
+    this->forces = forces;
+}
+
+ReferencePlatform::PlatformData::~PlatformData() {
+    RealOpenMM** positions = (RealOpenMM**) this->positions;
+    RealOpenMM** velocities = (RealOpenMM**) this->velocities;
+    RealOpenMM** forces = (RealOpenMM**) this->forces;
+    for (int i = 0; i < numParticles; ++i) {
+        delete[] positions[i];
+        delete[] velocities[i];
+        delete[] forces[i];
+    }
+    delete[] positions;
+    delete[] velocities;
+    delete[] forces;
+}

platforms/reference/src/ReferenceStreamFactory.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 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/OpenMMException.h"
-#include "ReferenceStreamFactory.h"
-#include "ReferenceFloatStreamImpl.h"
-#include "ReferenceIntStreamImpl.h"
-
-using namespace OpenMM;
-
-StreamImpl* ReferenceStreamFactory::createStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, ContextImpl& context) const {
-    switch (type) {
-    case Stream::Float:
-    case Stream::Float2:
-    case Stream::Float3:
-    case Stream::Float4:
-    case Stream::Double:
-    case Stream::Double2:
-    case Stream::Double3:
-    case Stream::Double4:
-        return new ReferenceFloatStreamImpl(name, size, type, platform);
-    case Stream::Integer:
-    case Stream::Integer2:
-    case Stream::Integer3:
-    case Stream::Integer4:
-        return new ReferenceIntStreamImpl(name, size, type, platform);
-    }
-    throw OpenMMException("Tried to create a Stream with an illegal DataType.");
-}