Began CUDA version of GayBerneForce

platforms/cuda/include/CudaKernels.h

@@ -1104,6 +1104,74 @@ private:
     CUevent event;
 };
 
+/**
+ * This kernel is invoked by GayBerneForce to calculate the forces acting on the system.
+ */
+class CudaCalcGayBerneForceKernel : public CalcGayBerneForceKernel {
+public:
+    CudaCalcGayBerneForceKernel(std::string name, const Platform& platform, CudaContext& cu) : CalcGayBerneForceKernel(name, platform), cu(cu),
+            hasInitializedKernels(false), sortedParticles(NULL), axisParticleIndices(NULL), sigParams(NULL), epsParams(NULL), scale(NULL), exceptionParticles(NULL),
+            exceptionParams(NULL), aMatrix(NULL),
+            bMatrix(NULL), gMatrix(NULL), exclusions(NULL), exclusionStartIndex(NULL), blockCenter(NULL), blockBoundingBox(NULL), neighbors(NULL),
+            neighborIndex(NULL), neighborBlockCount(NULL), sortedPos(NULL), torque(NULL) {
+    }
+    ~CudaCalcGayBerneForceKernel();
+    /**
+     * Initialize the kernel.
+     *
+     * @param system     the System this kernel will be applied to
+     * @param force      the GayBerneForce this kernel will be used for
+     */
+    void initialize(const System& system, const GayBerneForce& force);
+    /**
+     * Execute the kernel to calculate the forces and/or energy.
+     *
+     * @param context        the context in which to execute this kernel
+     * @param includeForces  true if forces should be calculated
+     * @return the potential energy due to the force
+     */
+    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the GayBerneForce to copy the parameters from
+     */
+    void copyParametersToContext(ContextImpl& context, const GayBerneForce& force);
+private:
+    class ReorderListener;
+    void sortAtoms();
+    CudaContext& cu;
+    bool hasInitializedKernels;
+    int numRealParticles, numExceptions, maxNeighborBlocks;
+    GayBerneForce::NonbondedMethod nonbondedMethod;
+    CudaArray* sortedParticles;
+    CudaArray* axisParticleIndices;
+    CudaArray* sigParams;
+    CudaArray* epsParams;
+    CudaArray* scale;
+    CudaArray* exceptionParticles;
+    CudaArray* exceptionParams;
+    CudaArray* aMatrix;
+    CudaArray* bMatrix;
+    CudaArray* gMatrix;
+    CudaArray* exclusions;
+    CudaArray* exclusionStartIndex;
+    CudaArray* blockCenter;
+    CudaArray* blockBoundingBox;
+    CudaArray* neighbors;
+    CudaArray* neighborIndex;
+    CudaArray* neighborBlockCount;
+    CudaArray* sortedPos;
+    CudaArray* torque;
+    std::vector<bool> isRealParticle;
+    std::vector<std::pair<int, int> > exceptionAtoms;
+    std::vector<std::pair<int, int> > excludedPairs;
+    std::vector<void*> framesArgs, blockBoundsArgs, neighborsArgs, forceArgs, torqueArgs;
+    CUfunction framesKernel, blockBoundsKernel, neighborsKernel, forceKernel, torqueKernel;
+    CUevent event;
+};
+
 /**
  * This kernel is invoked by VerletIntegrator to take one time step.
  */

platforms/cuda/src/CudaKernelFactory.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -110,6 +110,8 @@ KernelImpl* CudaKernelFactory::createKernelImpl(std::string name, const Platform
         return new CudaCalcCustomCompoundBondForceKernel(name, platform, cu, context.getSystem());
     if (name == CalcCustomManyParticleForceKernel::Name())
         return new CudaCalcCustomManyParticleForceKernel(name, platform, cu, context.getSystem());
+    if (name == CalcGayBerneForceKernel::Name())
+        return new CudaCalcGayBerneForceKernel(name, platform, cu);
     if (name == IntegrateVerletStepKernel::Name())
         return new CudaIntegrateVerletStepKernel(name, platform, cu);
     if (name == IntegrateLangevinStepKernel::Name())

platforms/cuda/src/CudaPlatform.cpp

@@ -92,6 +92,7 @@ CudaPlatform::CudaPlatform() {
     registerKernelFactory(CalcCustomCentroidBondForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomCompoundBondForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomManyParticleForceKernel::Name(), factory);
+    registerKernelFactory(CalcGayBerneForceKernel::Name(), factory);
     registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
     registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
     registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);

platforms/cuda/tests/TestCudaGayBerneForce.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) 2016 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 "TestGayBerneForce.h"
+
+void runPlatformTests() {
+}