Created Cuda implementation of VerletIntegrator

platforms/cuda/src/CudaKernelFactory.cpp

@@ -49,8 +49,8 @@ KernelImpl* CudaKernelFactory::createKernelImpl(std::string name, const Platform
         return new CudaCalcNonbondedForceKernel(name, platform, data, context.getSystem());
     if (name == CalcGBSAOBCForceFieldKernel::Name())
         return new CudaCalcGBSAOBCForceFieldKernel(name, platform, data);
-//    if (name == IntegrateVerletStepKernel::Name())
-//        return new CudaIntegrateVerletStepKernel(name, platform);
+    if (name == IntegrateVerletStepKernel::Name())
+        return new CudaIntegrateVerletStepKernel(name, platform, data);
     if (name == IntegrateLangevinStepKernel::Name())
         return new CudaIntegrateLangevinStepKernel(name, platform, data);
     if (name == IntegrateBrownianStepKernel::Name())

platforms/cuda/src/CudaKernels.cpp

@@ -311,22 +311,7 @@ void CudaCalcGBSAOBCForceFieldKernel::initialize(const System& system, const GBS
 void CudaCalcGBSAOBCForceFieldKernel::executeForces(OpenMMContextImpl& context) {
 }
 
-double CudaCalcGBSAOBCForceFieldKernel::executeEnergy(OpenMMContextImpl& context) {
-}
-
-//CudaIntegrateVerletStepKernel::~CudaIntegrateVerletStepKernel() {
-//}
-//
-//void CudaIntegrateVerletStepKernel::initialize(const System& system, const VerletIntegrator& integrator) {
-//}
-//
-//void CudaIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, const VerletIntegrator& integrator) {
-//}
-
-CudaIntegrateLangevinStepKernel::~CudaIntegrateLangevinStepKernel() {
-}
-
-void CudaIntegrateLangevinStepKernel::initialize(const System& system, const LangevinIntegrator& integrator) {
+static void initializeIntegration(const System& system, CudaPlatform::PlatformData& data) {
     
     // Set masses.
     
@@ -384,6 +369,45 @@ void CudaIntegrateLangevinStepKernel::initialize(const System& system, const Lan
     kClearBornForces(gpu);
     kClearForces(gpu);
     cudaThreadSynchronize();
+}
+
+double CudaCalcGBSAOBCForceFieldKernel::executeEnergy(OpenMMContextImpl& context) {
+}
+
+CudaIntegrateVerletStepKernel::~CudaIntegrateVerletStepKernel() {
+}
+
+void CudaIntegrateVerletStepKernel::initialize(const System& system, const VerletIntegrator& integrator) {
+    initializeIntegration(system, data);
+    prevStepSize = -1.0;
+}
+
+void CudaIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, const VerletIntegrator& integrator) {
+    _gpuContext* gpu = data.gpu;
+    double stepSize = integrator.getStepSize();
+    if (stepSize != prevStepSize) {
+        // Initialize the GPU parameters.
+        
+        gpuSetVerletIntegrationParameters(gpu, stepSize);
+        gpuSetConstants(gpu);
+        kGenerateRandoms(gpu);
+        prevStepSize = stepSize;
+    }
+    kVerletUpdatePart1(gpu);
+    kApplyFirstShake(gpu);
+    if (data.removeCM) {
+        int step = context.getTime()/stepSize;
+        if (step%data.cmMotionFrequency == 0)
+            gpu->bCalculateCM = true;
+    }
+    kVerletUpdatePart2(gpu);
+}
+
+CudaIntegrateLangevinStepKernel::~CudaIntegrateLangevinStepKernel() {
+}
+
+void CudaIntegrateLangevinStepKernel::initialize(const System& system, const LangevinIntegrator& integrator) {
+    initializeIntegration(system, data);
     prevStepSize = -1.0;
 }
 
@@ -418,63 +442,7 @@ CudaIntegrateBrownianStepKernel::~CudaIntegrateBrownianStepKernel() {
 }
 
 void CudaIntegrateBrownianStepKernel::initialize(const System& system, const BrownianIntegrator& integrator) {
-    
-    // Set masses.
-    
-    _gpuContext* gpu = data.gpu;
-    int numParticles = system.getNumParticles();
-    vector<float> mass(numParticles);
-    for (int i = 0; i < numParticles; i++)
-        mass[i] = (float) system.getParticleMass(i);
-    gpuSetMass(gpu, mass);
-    
-    // Set constraints.
-    
-    int numConstraints = system.getNumConstraints();
-    vector<int> particle1(numConstraints);
-    vector<int> particle2(numConstraints);
-    vector<float> distance(numConstraints);
-    vector<float> invMass1(numConstraints);
-    vector<float> invMass2(numConstraints);
-    for (int i = 0; i < numConstraints; i++) {
-        int particle1Index, particle2Index;
-        double constraintDistance;
-        system.getConstraintParameters(i, particle1Index, particle2Index, constraintDistance);
-        particle1[i] = particle1Index;
-        particle2[i] = particle2Index;
-        distance[i] = (float) constraintDistance;
-        invMass1[i] = 1.0f/mass[particle1Index];
-        invMass2[i] = 1.0f/mass[particle2Index];
-    }
-    gpuSetShakeParameters(gpu, particle1, particle2, distance, invMass1, invMass2);
-    
-    // Initialize any terms that haven't already been handled by a Force.
-    
-    if (!data.hasBonds)
-        gpuSetBondParameters(gpu, vector<int>(), vector<int>(), vector<float>(), vector<float>());
-    if (!data.hasAngles)
-        gpuSetBondAngleParameters(gpu, vector<int>(), vector<int>(), vector<int>(), vector<float>(), vector<float>());
-    if (!data.hasPeriodicTorsions)
-        gpuSetDihedralParameters(gpu, vector<int>(), vector<int>(), vector<int>(), vector<int>(), vector<float>(), vector<float>(), vector<int>());
-    if (!data.hasRB)
-        gpuSetRbDihedralParameters(gpu, vector<int>(), vector<int>(), vector<int>(), vector<int>(), vector<float>(), vector<float>(),
-                vector<float>(), vector<float>(), vector<float>(), vector<float>());
-    if (!data.hasNonbonded) {
-        gpuSetCoulombParameters(gpu, 138.935485f, vector<int>(), vector<float>(), vector<float>(), vector<float>(), vector<char>(), vector<vector<int> >());
-        gpuSetLJ14Parameters(gpu, 138.935485f, 1.0f, vector<int>(), vector<int>(), vector<float>(), vector<float>(), vector<float>(), vector<float>());
-    }
-    
-    // Finish initialization.
-    
-    gpuBuildThreadBlockWorkList(gpu);
-    gpuBuildExclusionList(gpu);
-    gpuBuildOutputBuffers(gpu);
-    gpuSetConstants(gpu);
-    kCalculateObcGbsaBornSum(gpu);
-    kReduceObcGbsaBornSum(gpu);
-    kClearBornForces(gpu);
-    kClearForces(gpu);
-    cudaThreadSynchronize();
+    initializeIntegration(system, data);
     prevStepSize = -1.0;
 }
 

platforms/cuda/src/CudaKernels.h

@@ -250,39 +250,33 @@ public:
 private:
     CudaPlatform::PlatformData& data;
 };
-//
-///**
-// * This kernel is invoked by VerletIntegrator to take one time step.
-// */
-//class CudaIntegrateVerletStepKernel : public IntegrateVerletStepKernel {
-//public:
-//    CudaIntegrateVerletStepKernel(std::string name, const Platform& platform) : IntegrateVerletStepKernel(name, platform),
-//        dynamics(0), shake(0), masses(0), shakeParameters(0), constraintIndices(0) {
-//    }
-//    ~CudaIntegrateVerletStepKernel();
-//    /**
-//     * Initialize the kernel.
-//     * 
-//     * @param system     the System this kernel will be applied to
-//     * @param integrator the VerletIntegrator this kernel will be used for
-//     */
-//    void initialize(const System& system, const VerletIntegrator& integrator);
-//    /**
-//     * Execute the kernel.
-//     * 
-//     * @param context    the context in which to execute this kernel
-//     * @param integrator the VerletIntegrator this kernel is being used for
-//     */
-//    void execute(OpenMMContextImpl& context, const VerletIntegrator& integrator);
-//private:
-//    CudaVerletDynamics* dynamics;
-//    CudaShakeAlgorithm* shake;
-//    RealOpenMM* masses;
-//    RealOpenMM** shakeParameters;
-//    int** constraintIndices;
-//    int numConstraints;
-//    double prevStepSize;
-//};
+
+/**
+ * This kernel is invoked by VerletIntegrator to take one time step.
+ */
+class CudaIntegrateVerletStepKernel : public IntegrateVerletStepKernel {
+public:
+    CudaIntegrateVerletStepKernel(std::string name, const Platform& platform, CudaPlatform::PlatformData& data) : IntegrateVerletStepKernel(name, platform), data(data) {
+    }
+    ~CudaIntegrateVerletStepKernel();
+    /**
+     * Initialize the kernel.
+     * 
+     * @param system     the System this kernel will be applied to
+     * @param integrator the VerletIntegrator this kernel will be used for
+     */
+    void initialize(const System& system, const VerletIntegrator& integrator);
+    /**
+     * Execute the kernel.
+     * 
+     * @param context    the context in which to execute this kernel
+     * @param integrator the VerletIntegrator this kernel is being used for
+     */
+    void execute(OpenMMContextImpl& context, const VerletIntegrator& integrator);
+private:
+    CudaPlatform::PlatformData& data;
+    double prevStepSize;
+};
 
 /**
  * This kernel is invoked by LangevinIntegrator to take one time step.

platforms/cuda/src/CudaPlatform.cpp

@@ -46,7 +46,7 @@ CudaPlatform::CudaPlatform() {
     registerKernelFactory(CalcRBTorsionForceKernel::Name(), factory);
     registerKernelFactory(CalcNonbondedForceKernel::Name(), factory);
     registerKernelFactory(CalcGBSAOBCForceFieldKernel::Name(), factory);
-//    registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
+    registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
     registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
     registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
 //    registerKernelFactory(ApplyAndersenThermostatKernel::Name(), factory);

platforms/cuda/tests/TestCudaCMMotionRemover.cpp

@@ -41,6 +41,7 @@
 #include "NonbondedForce.h"
 #include "System.h"
 #include "LangevinIntegrator.h"
+#include "VerletIntegrator.h"
 #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
 #include "../src/sfmt/SFMT.h"
 #include <iostream>
@@ -59,11 +60,10 @@ Vec3 calcCM(const vector<Vec3>& values, System& system) {
     return cm;
 }
 
-void testMotionRemoval() {
+void testMotionRemoval(Integrator& integrator) {
     const int numParticles = 8;
     CudaPlatform platform;
     System system(numParticles, 0);
-    LangevinIntegrator integrator(0.0, 1e-5, 0.01);
     HarmonicBondForce* bonds = new HarmonicBondForce(1);
     bonds->setBondParameters(0, 2, 3, 2.0, 0.5);
     system.addForce(bonds);
@@ -103,7 +103,10 @@ void testMotionRemoval() {
 
 int main() {
     try {
-        testMotionRemoval();
+        LangevinIntegrator langevin(0.0, 1e-5, 0.01);
+        testMotionRemoval(langevin);
+        VerletIntegrator verlet(0.01);
+        testMotionRemoval(verlet);
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

platforms/cuda/tests/TestCudaVerletIntegrator.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.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests the Cuda implementation of VerletIntegrator.
+ */
+
+#include "../../../tests/AssertionUtilities.h"
+#include "OpenMMContext.h"
+#include "CudaPlatform.h"
+#include "HarmonicBondForce.h"
+#include "NonbondedForce.h"
+#include "System.h"
+#include "VerletIntegrator.h"
+#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "../src/sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+const double TOL = 1e-5;
+
+void testSingleBond() {
+    CudaPlatform platform;
+    System system(2, 0);
+    system.setParticleMass(0, 2.0);
+    system.setParticleMass(1, 2.0);
+    VerletIntegrator integrator(0.01);
+    HarmonicBondForce* forceField = new HarmonicBondForce(1);
+    forceField->setBondParameters(0, 0, 1, 1.5, 1);
+    system.addForce(forceField);
+    OpenMMContext context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    context.setPositions(positions);
+    
+    // This is simply a harmonic oscillator, so compare it to the analytical solution.
+    
+    const double freq = 1.0;;
+    State state = context.getState(State::Energy);
+    const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
+    for (int i = 0; i < 1000; ++i) {
+        state = context.getState(State::Positions | State::Velocities | State::Energy);
+        double time = state.getTime();
+        double expectedDist = 1.5+0.5*std::cos(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
+        double expectedSpeed = -0.5*freq*std::sin(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
+        double energy = state.getKineticEnergy()+state.getPotentialEnergy();
+        ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
+        integrator.step(1);
+    }
+}
+
+void testConstraints() {
+    const int numParticles = 8;
+    const int numConstraints = numParticles/2;
+    const double temp = 100.0;
+    CudaPlatform platform;
+    System system(numParticles, numConstraints);
+    VerletIntegrator integrator(0.001);
+    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
+    for (int i = 0; i < numParticles; ++i) {
+        system.setParticleMass(i, 10.0);
+        forceField->setParticleParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+    }
+    for (int i = 0; i < numConstraints; ++i)
+        system.setConstraintParameters(i, 2*i, 2*i+1, 1.0);
+    system.addForce(forceField);
+    OpenMMContext context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
+    init_gen_rand(0);
+    for (int i = 0; i < numParticles; ++i) {
+        positions[i] = Vec3(i/2, (i+1)/2, 0);
+        velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
+    }
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    
+    // Simulate it and see whether the constraints remain satisfied.
+    
+    double initialEnergy = 0.0;
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions | State::Energy);
+        for (int j = 0; j < numConstraints; ++j) {
+            int particle1, particle2;
+            double distance;
+            system.getConstraintParameters(j, particle1, particle2, distance);
+            Vec3 p1 = state.getPositions()[particle1];
+            Vec3 p2 = state.getPositions()[particle2];
+            double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
+            ASSERT_EQUAL_TOL(distance, dist, 2e-4);
+        }
+        double energy = state.getKineticEnergy()+state.getPotentialEnergy();
+        if (i == 1)
+            initialEnergy = energy;
+        else if (i > 1)
+            ASSERT_EQUAL_TOL(initialEnergy, energy, 0.02);
+        integrator.step(1);
+    }
+}
+
+int main() {
+    try {
+        testSingleBond();
+        testConstraints();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}