Continuing to implement ReferencePlatform

olla/include/KernelFactory.h

@@ -49,7 +49,7 @@ public:
      * 
      * @param name the name of the kernel to create
      */
-    virtual KernelImpl* createKernelImpl(std::string name) const = 0;
+    virtual KernelImpl* createKernelImpl(std::string name, const Platform& platform) const = 0;
     virtual ~KernelFactory() {
     }
 };

olla/include/KernelImpl.h

@@ -32,6 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "Platform.h"
 #include <string>
 
 namespace OpenMM {
@@ -47,9 +48,10 @@ public:
     /**
      * Create a KernelImpl.
      * 
-     * @param name the name of the kernel to create
+     * @param name      the name of the kernel to create
+     * @param platform  the Platform that created this kernel
      */
-    KernelImpl(std::string name);
+    KernelImpl(std::string name, const Platform& platform);
     virtual ~KernelImpl() {
         assert(referenceCount == 0);
     }
@@ -57,9 +59,14 @@ public:
      * Get the name of this kernel.
      */
     std::string getName() const;
+    /**
+     * Get the Platform that created this KernelImpl.
+     */
+    const Platform& getPlatform();
 private:
     friend class Kernel;
     std::string name;
+    const Platform* platform;
     int referenceCount;
 };
 

olla/include/StreamFactory.h

@@ -51,7 +51,7 @@ public:
      * @param size the number of elements in the stream
      * @param type the data type of each element in the stream
      */
-    virtual StreamImpl* createStreamImpl(std::string name, int size, Stream::DataType type) const = 0;
+    virtual StreamImpl* createStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform) const = 0;
     virtual ~StreamFactory() {
     }
 };

olla/include/StreamImpl.h

@@ -32,6 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "Platform.h"
 #include "Stream.h"
 #include <string>
 
@@ -46,11 +47,12 @@ public:
     /**
      * Create a StreamImpl.
      * 
-     * @param name the name of the stream to create
-     * @param size the number of elements in the stream
-     * @param type the data type of each element in the stream
+     * @param name     the name of the stream to create
+     * @param size     the number of elements in the stream
+     * @param type     the data type of each element in the stream
+     * @param platform the Platform that created this kernel
      */
-    StreamImpl(std::string name, int size, Stream::DataType type);
+    StreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform);
     virtual ~StreamImpl() {
         assert(referenceCount == 0);
     }
@@ -66,6 +68,10 @@ public:
      * Get the data type of each element in the stream.
      */
     Stream::DataType getDataType() const;
+    /**
+     * Get the Platform that created this KernelImpl.
+     */
+    const Platform& getPlatform();
     /**
      * Copy the contents of an array into this stream.
      * 
@@ -95,6 +101,7 @@ private:
     std::string name;
     int size;
     Stream::DataType type;
+    const Platform* platform;
     int referenceCount;
 };
 

olla/include/kernels.h

@@ -48,7 +48,7 @@ public:
     static std::string Name() {
         return "CalcStandardMMForces";
     }
-    CalcStandardMMForcesKernel(std::string name) : KernelImpl(name) {
+    CalcStandardMMForcesKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
     /**
      * Initialize the kernel, setting up the values of all the force field parameters.
@@ -92,7 +92,7 @@ public:
     static std::string Name() {
         return "CalcStandardMMEnergy";
     }
-    CalcStandardMMEnergyKernel(std::string name) : KernelImpl(name) {
+    CalcStandardMMEnergyKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
     /**
      * Initialize the kernel, setting up the values of all the force field parameters.
@@ -135,7 +135,7 @@ public:
     static std::string Name() {
         return "CalcGBSAOBCForces";
     }
-    CalcGBSAOBCForcesKernel(std::string name) : KernelImpl(name) {
+    CalcGBSAOBCForcesKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
     /**
      * Initialize the kernel, setting up the values of all the force field parameters.
@@ -165,7 +165,7 @@ public:
     static std::string Name() {
         return "CalcGBSAOBCEnergy";
     }
-    CalcGBSAOBCEnergyKernel(std::string name) : KernelImpl(name) {
+    CalcGBSAOBCEnergyKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
     /**
      * Initialize the kernel, setting up the values of all the force field parameters.
@@ -194,7 +194,7 @@ public:
     static std::string Name() {
         return "IntegrateVerletStep";
     }
-    IntegrateVerletStepKernel(std::string name) : KernelImpl(name) {
+    IntegrateVerletStepKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
     /**
      * Initialize the kernel, setting up all parameters related to integrator.
@@ -224,7 +224,7 @@ public:
     static std::string Name() {
         return "IntegrateLangevinStep";
     }
-    IntegrateLangevinStepKernel(std::string name) : KernelImpl(name) {
+    IntegrateLangevinStepKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
     /**
      * Initialize the kernel, setting up all parameters related to integrator.
@@ -256,7 +256,7 @@ public:
     static std::string Name() {
         return "IntegrateBrownianStep";
     }
-    IntegrateBrownianStepKernel(std::string name) : KernelImpl(name) {
+    IntegrateBrownianStepKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
     /**
      * Initialize the kernel, setting up all parameters related to integrator.
@@ -288,7 +288,7 @@ public:
     static std::string Name() {
         return "ApplyAndersenThermostat";
     }
-    ApplyAndersenThermostatKernel(std::string name) : KernelImpl(name) {
+    ApplyAndersenThermostatKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
     /**
      * Initialize the kernel, setting up the values of unchanging parameters.
@@ -315,7 +315,7 @@ public:
     static std::string Name() {
         return "CalcKineticEnergy";
     }
-    CalcKineticEnergyKernel(std::string name) : KernelImpl(name) {
+    CalcKineticEnergyKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
     }
     /**
      * Initialize the kernel, setting up the atomic masses.

olla/src/KernelImpl.cpp

@@ -34,9 +34,14 @@
 using namespace OpenMM;
 using namespace std;
 
-KernelImpl::KernelImpl(string name) : name(name), referenceCount(1) {
+KernelImpl::KernelImpl(string name, const Platform& platform) : name(name), platform(&platform), referenceCount(1) {
 }
 
 std::string KernelImpl::getName() const {
     return name;
 }
+
+const Platform& KernelImpl::getPlatform() {
+    return *platform;
+}
+

olla/src/Platform.cpp

@@ -73,13 +73,13 @@ bool Platform::supportsKernels(std::vector<std::string> kernelNames) const {
 Kernel Platform::createKernel(std::string name) const {
     if (kernelFactories.find(name) == kernelFactories.end())
         throw PlatformException("Called createKernel() on a Platform which does not support the requested kernel");
-    return Kernel(kernelFactories.find(name)->second->createKernelImpl(name));
+    return Kernel(kernelFactories.find(name)->second->createKernelImpl(name, *this));
 }
 
 Stream Platform::createStream(std::string name, int size, Stream::DataType type) const {
     if (streamFactories.find(name) == streamFactories.end())
-        return Stream(getDefaultStreamFactory().createStreamImpl(name, size, type));
-    return Stream(streamFactories.find(name)->second->createStreamImpl(name, size, type));
+        return Stream(getDefaultStreamFactory().createStreamImpl(name, size, type, *this));
+    return Stream(streamFactories.find(name)->second->createStreamImpl(name, size, type, *this));
 }
 
 void Platform::registerPlatform(Platform* platform) {

olla/src/StreamImpl.cpp

@@ -34,7 +34,7 @@
 using namespace OpenMM;
 using namespace std;
 
-StreamImpl::StreamImpl(string name, int size, Stream::DataType type) : name(name), size(size), type(type), referenceCount(1) {
+StreamImpl::StreamImpl(string name, int size, Stream::DataType type, const Platform& platform) : name(name), size(size), type(type), platform(&platform), referenceCount(1) {
 }
 
 std::string StreamImpl::getName() const {
@@ -49,3 +49,6 @@ Stream::DataType StreamImpl::getDataType() const {
     return  type;
 }
 
+const Platform& StreamImpl::getPlatform() {
+    return *platform;
+}

platforms/reference/include/ReferenceKernelFactory.h

@@ -42,7 +42,7 @@ namespace OpenMM {
 
 class ReferenceKernelFactory : public KernelFactory {
 public:
-    KernelImpl* createKernelImpl(std::string name) const;
+    KernelImpl* createKernelImpl(std::string name, const Platform& platform) const;
 };
 
 } // namespace OpenMM

platforms/reference/include/ReferenceStreamFactory.h

@@ -42,7 +42,7 @@ namespace OpenMM {
 
 class ReferenceStreamFactory : public StreamFactory {
 public:
-    StreamImpl* createStreamImpl(std::string name, int size, Stream::DataType type) const;
+    StreamImpl* createStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform) const;
 };
 
 } // namespace OpenMM

platforms/reference/src/ReferenceFloatStreamImpl.cpp

@@ -33,7 +33,7 @@
 
 using namespace OpenMM;
 
-ReferenceFloatStreamImpl::ReferenceFloatStreamImpl(std::string name, int size, Stream::DataType type) : StreamImpl(name, size, type) {
+ReferenceFloatStreamImpl::ReferenceFloatStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform) : StreamImpl(name, size, type, platform) {
     switch (type) {
     case Stream::Float:
     case Stream::Float2:

platforms/reference/src/ReferenceFloatStreamImpl.h

@@ -43,7 +43,7 @@ namespace OpenMM {
 
 class ReferenceFloatStreamImpl : public StreamImpl {
 public:
-    ReferenceFloatStreamImpl(std::string name, int size, Stream::DataType type);
+    ReferenceFloatStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform);
     ~ReferenceFloatStreamImpl();
     void loadFromArray(const void* array);
     void saveToArray(void* array);

platforms/reference/src/ReferenceIntStreamImpl.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 "ReferenceIntStreamImpl.h"
+
+using namespace OpenMM;
+
+ReferenceIntStreamImpl::ReferenceIntStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform) : StreamImpl(name, size, type, platform) {
+    switch (type) {
+    case Stream::Integer:
+        width = 1;
+        break;
+    case Stream::Integer2:
+        width = 2;
+        break;
+    case Stream::Integer3:
+        width = 3;
+        break;
+    case Stream::Integer4:
+        width = 4;
+        break;
+    }
+    data = new int*[size];
+    for (int i = 0; i < size; ++i)
+        data[i] = new int[width];
+}
+
+ReferenceIntStreamImpl::~ReferenceIntStreamImpl() {
+    delete data;
+}
+
+void ReferenceIntStreamImpl::loadFromArray(const void* array) {
+    int* arrayData = (int*) array;
+    for (int i = 0; i < getSize(); ++i)
+        for (int j = 0; j < width; ++j)
+            data[i][j] = arrayData[i*width+j];
+}
+
+void ReferenceIntStreamImpl::saveToArray(void* array) {
+    int* arrayData = (int*) array;
+    for (int i = 0; i < getSize(); ++i)
+        for (int j = 0; j < width; ++j)
+            arrayData[i*width+j] = data[i][j];
+}
+
+void ReferenceIntStreamImpl::fillWithValue(void* value) {
+    int valueData = *((int*) value);
+    for (int i = 0; i < getSize(); ++i)
+        for (int j = 0; j < width; ++j)
+            data[i][j] = valueData;
+}
+
+int** ReferenceIntStreamImpl::getData() {
+    return data;
+}
+

platforms/reference/src/ReferenceIntStreamImpl.h

+#ifndef OPENMM_REFERENCEINTSTREAMIMPL_H_
+#define OPENMM_REFERENCEINTSTREAMIMPL_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 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 "StreamImpl.h"
+
+namespace OpenMM {
+
+/**
+ * This is the implementation of Float and Double streams in the reference Platform.
+ */
+
+class ReferenceIntStreamImpl : public StreamImpl {
+public:
+    ReferenceIntStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform);
+    ~ReferenceIntStreamImpl();
+    void loadFromArray(const void* array);
+    void saveToArray(void* array);
+    void fillWithValue(void* value);
+    int** getData();
+private:
+    int width;
+    Stream::DataType baseType;
+    int** data;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_REFERENCEINTSTREAMIMPL_H_*/

platforms/reference/src/ReferenceKernelFactory.cpp

@@ -30,26 +30,27 @@
  * -------------------------------------------------------------------------- */
 
 #include "ReferenceKernelFactory.h"
+#include "ReferenceKernels.h"
 
 using namespace OpenMM;
 
-KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name) const {
+KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Platform& platform) const {
     if (name == CalcStandardMMForcesKernel::Name())
-        return new ReferenceCalcStandardMMForcesKernel(name);
+        return new ReferenceCalcStandardMMForcesKernel(name, platform);
     if (name == CalcStandardMMEnergyKernel::Name())
-        return new ReferenceCalcStandardMMEnergyKernel(name);
+        return new ReferenceCalcStandardMMEnergyKernel(name, platform);
     if (name == CalcGBSAOBCForcesKernel::Name())
-        return new ReferenceCalcGBSAOBCForcesKernel(name);
+        return new ReferenceCalcGBSAOBCForcesKernel(name, platform);
     if (name == CalcGBSAOBCEnergyKernel::Name())
-        return new ReferenceCalcGBSAOBCEnergyKernel(name);
+        return new ReferenceCalcGBSAOBCEnergyKernel(name, platform);
     if (name == IntegrateVerletStepKernel::Name())
-        return new ReferenceIntegrateVerletStepKernel(name);
+        return new ReferenceIntegrateVerletStepKernel(name, platform);
     if (name == IntegrateLangevinStepKernel::Name())
-        return new ReferenceIntegrateLangevinStepKernel(name);
+        return new ReferenceIntegrateLangevinStepKernel(name, platform);
     if (name == IntegrateBrownianStepKernel::Name())
-        return new ReferenceIntegrateBrownianStepKernel(name);
+        return new ReferenceIntegrateBrownianStepKernel(name, platform);
     if (name == ApplyAndersenThermostatKernel::Name())
-        return new ReferenceApplyAndersenThermostatKernel(name);
+        return new ReferenceApplyAndersenThermostatKernel(name, platform);
     if (name == CalcKineticEnergyKernel::Name())
-        return new ReferenceCalcKineticEnergyKernel(name);
+        return new ReferenceCalcKineticEnergyKernel(name, platform);
 }

platforms/reference/src/ReferenceKernels.cpp

@@ -34,13 +34,85 @@
 using namespace OpenMM;
 using namespace std;
 
+int** allocateIntArray(int length, int width) {
+    int** array = new int*[length];
+    for (int i = 0; i < length; ++i)
+        array[i] = new int[width];
+    return array;
+}
+
+RealOpenMM** allocateRealArray(int length, int width) {
+    RealOpenMM** array = new RealOpenMM*[length];
+    for (int i = 0; i < length; ++i)
+        array[i] = new RealOpenMM[width];
+    return array;
+}
+
+int** copyToArray(const vector<vector<int> > vec) {
+    if (vec.size() == 0)
+        return new int*[0];
+    int** array = allocateIntArray(vec.size(), vec[0].size());
+    for (int i = 0; i < vec.size(); ++i)
+        for (int j = 0; j < vec[i].size(); ++j)
+            array[i][j] = vec[i][j];
+    return array;
+}
+
+RealOpenMM** copyToArray(const vector<vector<double> > vec) {
+    if (vec.size() == 0)
+        return new RealOpenMM*[0];
+    RealOpenMM** array = allocateRealArray(vec.size(), vec[0].size());
+    for (int i = 0; i < vec.size(); ++i)
+        for (int j = 0; j < vec[i].size(); ++j)
+            array[i][j] = vec[i][j];
+    return array;
+}
+
+void disposeIntArray(int** array, int size) {
+    if (array) {
+        for (int i = 0; i < size; ++i)
+            delete[] array[i];
+        delete[] array;
+    }
+}
+
+void disposeRealArray(RealOpenMM** array, int size) {
+    if (array) {
+        for (int i = 0; i < size; ++i)
+            delete[] array[i];
+        delete[] array;
+    }
+}
+
+ReferenceCalcStandardMMForcesKernel::~ReferenceCalcStandardMMForcesKernel() {
+    disposeIntArray(bondIndexArray, numBonds);
+    disposeRealArray(bondParamArray, numBonds);
+    disposeIntArray(angleIndexArray, numAngles);
+    disposeRealArray(angleParamArray, numAngles);
+    disposeIntArray(periodicTorsionIndexArray, numPeriodicTorsions);
+    disposeRealArray(periodicTorsionParamArray, numPeriodicTorsions);
+    disposeIntArray(rbTorsionIndexArray, numRBTorsions);
+    disposeRealArray(rbTorsionParamArray, numRBTorsions);
+}
+
 void ReferenceCalcStandardMMForcesKernel::initialize(const vector<vector<int> >& bondIndices, const vector<vector<double> >& bondParameters,
         const vector<vector<int> >& angleIndices, const vector<vector<double> >& angleParameters,
         const vector<vector<int> >& periodicTorsionIndices, const vector<vector<double> >& periodicTorsionParameters,
         const vector<vector<int> >& rbTorsionIndices, const vector<vector<double> >& rbTorsionParameters,
         const vector<vector<int> >& bonded14Indices, const vector<set<int> >& exclusions,
         const vector<vector<double> >& nonbondedParameters) {
-    
+    numBonds = bondIndices.size();
+    numAngles = angleIndices.size();
+    numPeriodicTorsions = periodicTorsionIndices.size();
+    numRBTorsions = rbTorsionIndices.size();
+    bondIndexArray = copyToArray(bondIndices);
+    bondParamArray = copyToArray(bondParameters);
+    angleIndexArray = copyToArray(angleIndices);
+    angleParamArray = copyToArray(angleParameters);
+    periodicTorsionIndexArray = copyToArray(periodicTorsionIndices);
+    periodicTorsionParamArray = copyToArray(periodicTorsionParameters);
+    rbTorsionIndexArray = copyToArray(rbTorsionIndices);
+    rbTorsionParamArray = copyToArray(rbTorsionParameters);
 }
 
 void ReferenceCalcStandardMMForcesKernel::execute(const Stream& positions, Stream& forces) {
@@ -69,12 +141,12 @@ void ReferenceCalcGBSAOBCForcesKernel::execute(const Stream& positions, Stream&
     
 }
 
-void CalcGBSAOBCEnergyKernel::initialize(const vector<double>& bornRadii, const vector<vector<double> >& atomParameters,
+void ReferenceCalcGBSAOBCEnergyKernel::initialize(const vector<double>& bornRadii, const vector<vector<double> >& atomParameters,
         double solventDielectric, double soluteDielectric) {
     
 }
 
-double CalcGBSAOBCEnergyKernel::execute(const Stream& positions) {
+double ReferenceCalcGBSAOBCEnergyKernel::execute(const Stream& positions) {
     return 0.0; // TODO implement correctly
 }
 

platforms/reference/src/ReferenceKernels.h

@@ -33,6 +33,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "kernels.h"
+#include "SimTKUtilities/SimTKOpenMMRealType.h"
 
 namespace OpenMM {
 
@@ -41,8 +42,9 @@ namespace OpenMM {
  */
 class ReferenceCalcStandardMMForcesKernel : public CalcStandardMMForcesKernel {
 public:
-    ReferenceCalcStandardMMForcesKernel(std::string name) : CalcStandardMMForcesKernel(name) {
+    ReferenceCalcStandardMMForcesKernel(std::string name, const Platform& platform) : CalcStandardMMForcesKernel(name, platform) {
     }
+    ~ReferenceCalcStandardMMForcesKernel();
     /**
      * Initialize the kernel, setting up the values of all the force field parameters.
      * 
@@ -75,6 +77,10 @@ public:
      *                    have been calculated so far.  The kernel should add its own forces to the values already in the stream.
      */
     void execute(const Stream& positions, Stream& forces);
+private:
+    int numAtoms, numBonds, numAngles, numPeriodicTorsions, numRBTorsions;
+    int **bondIndexArray, **angleIndexArray, **periodicTorsionIndexArray, **rbTorsionIndexArray;
+    RealOpenMM **bondParamArray, **angleParamArray, **periodicTorsionParamArray, **rbTorsionParamArray;
 };
 
 /**
@@ -82,7 +88,7 @@ public:
  */
 class ReferenceCalcStandardMMEnergyKernel : public CalcStandardMMEnergyKernel {
 public:
-    ReferenceCalcStandardMMEnergyKernel(std::string name) : CalcStandardMMEnergyKernel(name) {
+    ReferenceCalcStandardMMEnergyKernel(std::string name, const Platform& platform) : CalcStandardMMEnergyKernel(name, platform) {
     }
     /**
      * Initialize the kernel, setting up the values of all the force field parameters.
@@ -122,7 +128,7 @@ public:
  */
 class ReferenceCalcGBSAOBCForcesKernel : public CalcGBSAOBCForcesKernel {
 public:
-    ReferenceCalcGBSAOBCForcesKernel(std::string name) : CalcGBSAOBCForcesKernel(name) {
+    ReferenceCalcGBSAOBCForcesKernel(std::string name, const Platform& platform) : CalcGBSAOBCForcesKernel(name, platform) {
     }
     /**
      * Initialize the kernel, setting up the values of all the force field parameters.
@@ -149,7 +155,7 @@ public:
  */
 class ReferenceCalcGBSAOBCEnergyKernel : public CalcGBSAOBCEnergyKernel {
 public:
-    ReferenceCalcGBSAOBCEnergyKernel(std::string name) : CalcGBSAOBCEnergyKernel(name) {
+    ReferenceCalcGBSAOBCEnergyKernel(std::string name, const Platform& platform) : CalcGBSAOBCEnergyKernel(name, platform) {
     }
     /**
      * Initialize the kernel, setting up the values of all the force field parameters.
@@ -175,7 +181,7 @@ public:
  */
 class ReferenceIntegrateVerletStepKernel : public IntegrateVerletStepKernel {
 public:
-    ReferenceIntegrateVerletStepKernel(std::string name) : IntegrateVerletStepKernel(name) {
+    ReferenceIntegrateVerletStepKernel(std::string name, const Platform& platform) : IntegrateVerletStepKernel(name, platform) {
     }
     /**
      * Initialize the kernel, setting up all parameters related to integrator.
@@ -202,7 +208,7 @@ public:
  */
 class ReferenceIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel {
 public:
-    ReferenceIntegrateLangevinStepKernel(std::string name) : IntegrateLangevinStepKernel(name) {
+    ReferenceIntegrateLangevinStepKernel(std::string name, const Platform& platform) : IntegrateLangevinStepKernel(name, platform) {
     }
     /**
      * Initialize the kernel, setting up all parameters related to integrator.
@@ -231,7 +237,7 @@ public:
  */
 class ReferenceIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
 public:
-    ReferenceIntegrateBrownianStepKernel(std::string name) : IntegrateBrownianStepKernel(name) {
+    ReferenceIntegrateBrownianStepKernel(std::string name, const Platform& platform) : IntegrateBrownianStepKernel(name, platform) {
     }
     /**
      * Initialize the kernel, setting up all parameters related to integrator.
@@ -260,7 +266,7 @@ public:
  */
 class ReferenceApplyAndersenThermostatKernel : public ApplyAndersenThermostatKernel {
 public:
-    ReferenceApplyAndersenThermostatKernel(std::string name) : ApplyAndersenThermostatKernel(name) {
+    ReferenceApplyAndersenThermostatKernel(std::string name, const Platform& platform) : ApplyAndersenThermostatKernel(name, platform) {
     }
     /**
      * Initialize the kernel, setting up the values of unchanging parameters.
@@ -284,7 +290,7 @@ public:
  */
 class ReferenceCalcKineticEnergyKernel : public CalcKineticEnergyKernel {
 public:
-    ReferenceCalcKineticEnergyKernel(std::string name) : CalcKineticEnergyKernel(name) {
+    ReferenceCalcKineticEnergyKernel(std::string name, const Platform& platform) : CalcKineticEnergyKernel(name, platform) {
     }
     /**
      * Initialize the kernel, setting up the atomic masses.

platforms/reference/src/ReferencePlatform.cpp

@@ -32,6 +32,7 @@
 #include "ReferencePlatform.h"
 #include "ReferenceKernelFactory.h"
 #include "ReferenceKernels.h"
+#include "SimTKUtilities/SimTKOpenMMRealType.h"
 
 using namespace OpenMM;
 
@@ -54,3 +55,11 @@ ReferencePlatform::ReferencePlatform() {
     registerKernelFactory(ApplyAndersenThermostatKernel::Name(), factory);
     registerKernelFactory(CalcKineticEnergyKernel::Name(), factory);
 }
+
+bool ReferencePlatform::supportsDoublePrecision() const {
+    return (sizeof(RealOpenMM) >= sizeof(double));
+}
+
+const StreamFactory& ReferencePlatform::getDefaultStreamFactory() const {
+    return defaultStreamFactory;
+}

platforms/reference/src/ReferenceStreamFactory.cpp

@@ -29,12 +29,14 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "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 {
+StreamImpl* ReferenceStreamFactory::createStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform) const {
     switch (type) {
     case Stream::Float:
     case Stream::Float2:
@@ -44,9 +46,12 @@ StreamImpl* ReferenceStreamFactory::createStreamImpl(std::string name, int size,
     case Stream::Double2:
     case Stream::Double3:
     case Stream::Double4:
-        return new ReferenceFloatStreamImpl(name, size, type);
-    default:
-        // TODO implement integer streams
-        return 0;
+        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.");
 }

platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "SimTKOpenMMCommon.h"
-#include "SimTKOpenMMLog.h"
-#include "SimTKOpenMMUtilities.h"
+#include "../SimTKUtilities/SimTKOpenMMCommon.h"
+#include "../SimTKUtilities/SimTKOpenMMLog.h"
+#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
 #include "ReferenceAngleBondIxn.h"
 #include "ReferenceForce.h"