Created Cuda implementation of BrownianIntegrator

platforms/cuda/src/CudaKernelFactory.cpp

@@ -53,8 +53,8 @@ KernelImpl* CudaKernelFactory::createKernelImpl(std::string name, const Platform
 //        return new CudaIntegrateVerletStepKernel(name, platform);
     if (name == IntegrateLangevinStepKernel::Name())
         return new CudaIntegrateLangevinStepKernel(name, platform, data);
-//    if (name == IntegrateBrownianStepKernel::Name())
-//        return new CudaIntegrateBrownianStepKernel(name, platform);
+    if (name == IntegrateBrownianStepKernel::Name())
+        return new CudaIntegrateBrownianStepKernel(name, platform, data);
 //    if (name == ApplyAndersenThermostatKernel::Name())
 //        return new CudaApplyAndersenThermostatKernel(name, platform);
     if (name == CalcKineticEnergyKernel::Name())

platforms/cuda/src/CudaKernels.cpp

@@ -413,15 +413,96 @@ void CudaIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const
     kUpdatePart2(gpu);
     kApplySecondShake(gpu);
 }
-//
-//CudaIntegrateBrownianStepKernel::~CudaIntegrateBrownianStepKernel() {
-//}
-//
-//void CudaIntegrateBrownianStepKernel::initialize(const System& system, const BrownianIntegrator& integrator) {
-//}
-//
-//void CudaIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, const BrownianIntegrator& integrator) {
-//}
+
+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();
+    prevStepSize = -1.0;
+}
+
+void CudaIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, const BrownianIntegrator& integrator) {
+    _gpuContext* gpu = data.gpu;
+    double temperature = integrator.getTemperature();
+    double friction = integrator.getFriction();
+    double stepSize = integrator.getStepSize();
+    if (temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
+        // Initialize the GPU parameters.
+        
+        double tau = (friction == 0.0 ? 0.0 : 1.0/friction);
+        gpuSetBrownianIntegrationParameters(gpu, tau, stepSize, temperature);
+        gpuSetConstants(gpu);
+        kGenerateRandoms(gpu);
+        prevTemp = temperature;
+        prevFriction = friction;
+        prevStepSize = stepSize;
+    }
+    kBrownianUpdatePart1(gpu);
+    kApplyFirstShake(gpu);
+    if (data.removeCM) {
+        int step = context.getTime()/stepSize;
+        if (step%data.cmMotionFrequency == 0)
+            gpu->bCalculateCM = true;
+    }
+    kBrownianUpdatePart2(gpu);
+}
 //
 //CudaApplyAndersenThermostatKernel::~CudaApplyAndersenThermostatKernel() {
 //}

platforms/cuda/src/CudaKernels.h

@@ -310,39 +310,33 @@ private:
     CudaPlatform::PlatformData& data;
     double prevTemp, prevFriction, prevStepSize;
 };
-//
-///**
-// * This kernel is invoked by BrownianIntegrator to take one time step.
-// */
-//class CudaIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
-//public:
-//    CudaIntegrateBrownianStepKernel(std::string name, const Platform& platform) : IntegrateBrownianStepKernel(name, platform),
-//        dynamics(0), shake(0), masses(0), shakeParameters(0), constraintIndices(0) {
-//    }
-//    ~CudaIntegrateBrownianStepKernel();
-//    /**
-//     * Initialize the kernel.
-//     * 
-//     * @param system     the System this kernel will be applied to
-//     * @param integrator the BrownianIntegrator this kernel will be used for
-//     */
-//    void initialize(const System& system, const BrownianIntegrator& integrator);
-//    /**
-//     * Execute the kernel.
-//     * 
-//     * @param context    the context in which to execute this kernel
-//     * @param integrator the BrownianIntegrator this kernel is being used for
-//     */
-//    void execute(OpenMMContextImpl& context, const BrownianIntegrator& integrator);
-//private:
-//    CudaBrownianDynamics* dynamics;
-//    CudaShakeAlgorithm* shake;
-//    RealOpenMM* masses;
-//    RealOpenMM** shakeParameters;
-//    int** constraintIndices;
-//    int numConstraints;
-//    double prevTemp, prevFriction, prevStepSize;
-//};
+
+/**
+ * This kernel is invoked by BrownianIntegrator to take one time step.
+ */
+class CudaIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
+public:
+    CudaIntegrateBrownianStepKernel(std::string name, const Platform& platform, CudaPlatform::PlatformData& data) : IntegrateBrownianStepKernel(name, platform), data(data) {
+    }
+    ~CudaIntegrateBrownianStepKernel();
+    /**
+     * Initialize the kernel.
+     * 
+     * @param system     the System this kernel will be applied to
+     * @param integrator the BrownianIntegrator this kernel will be used for
+     */
+    void initialize(const System& system, const BrownianIntegrator& integrator);
+    /**
+     * Execute the kernel.
+     * 
+     * @param context    the context in which to execute this kernel
+     * @param integrator the BrownianIntegrator this kernel is being used for
+     */
+    void execute(OpenMMContextImpl& context, const BrownianIntegrator& integrator);
+private:
+    CudaPlatform::PlatformData& data;
+    double prevTemp, prevFriction, prevStepSize;
+};
 //
 ///**
 // * This kernel is invoked by AndersenThermostat at the start of each time step to adjust the particle velocities.

platforms/cuda/src/CudaPlatform.cpp

@@ -48,7 +48,7 @@ CudaPlatform::CudaPlatform() {
     registerKernelFactory(CalcGBSAOBCForceFieldKernel::Name(), factory);
 //    registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
     registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
-//    registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
+    registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
 //    registerKernelFactory(ApplyAndersenThermostatKernel::Name(), factory);
     registerKernelFactory(CalcKineticEnergyKernel::Name(), factory);
     registerKernelFactory(RemoveCMMotionKernel::Name(), factory);

platforms/cuda/tests/TestCudaBrownianIntegrator.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 "System.h"
+
+
+/**
+ * This tests the Cuda implementation of BrownianIntegrator.
+ */
+
+#include "../../../tests/AssertionUtilities.h"
+#include "OpenMMContext.h"
+#include "CudaPlatform.h"
+#include "HarmonicBondForce.h"
+#include "NonbondedForce.h"
+#include "System.h"
+#include "BrownianIntegrator.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);
+    double dt = 0.01;
+    BrownianIntegrator integrator(0, 0.1, dt);
+    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 an overdamped harmonic oscillator, so compare it to the analytical solution.
+    
+    double rate = 2*1.0/0.1;
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions | State::Velocities);
+        double time = state.getTime();
+        double expectedDist = 1.5+0.5*std::exp(-rate*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);
+        if (i > 0) {
+            double expectedSpeed = -0.5*rate*std::exp(-rate*(time-0.5*dt));
+            ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.11);
+            ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.11);
+        }
+        integrator.step(1);
+    }
+}
+
+void testTemperature() {
+    const int numParticles = 8;
+    const int numBonds = numParticles-1;
+    const double temp = 100.0;
+    CudaPlatform platform;
+    System system(numParticles, 0);
+    BrownianIntegrator integrator(temp, 2.0, 0.01);
+    HarmonicBondForce* forceField = new HarmonicBondForce(numBonds);
+    for (int i = 0; i < numParticles; ++i)
+        system.setParticleMass(i, 2.0);
+    for (int i = 0; i < numBonds; ++i)
+        forceField->setBondParameters(i, i, i+1, 1.0, i+1);
+    system.addForce(forceField);
+    OpenMMContext context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numParticles; ++i)
+        positions[i] = Vec3(i, 0, 0);
+    context.setPositions(positions);
+    
+    // Let it equilibrate.
+    
+    integrator.step(1000);
+    
+    // Now run it for a while and see if the temperature is correct.
+    
+    double pe = 0.0;
+    const int steps = 10000;
+    for (int i = 0; i < steps; ++i) {
+        State state = context.getState(State::Energy);
+        pe += state.getPotentialEnergy();
+        integrator.step(1);
+    }
+    pe /= steps;
+    double expected = 0.5*numBonds*BOLTZ*temp;
+    expected *= sqrt(2.0);
+    ASSERT_EQUAL_TOL(expected, pe, 4*expected/std::sqrt(steps));
+}
+
+void testConstraints() {
+    const int numParticles = 8;
+    const int numConstraints = numParticles/2;
+    const double temp = 20.0;
+    CudaPlatform platform;
+    System system(numParticles, numConstraints);
+    BrownianIntegrator integrator(temp, 2.0, 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, 0, 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.
+    
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions);
+        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);
+        }
+        integrator.step(1);
+    }
+}
+
+int main() {
+    try {
+        testSingleBond();
+        testTemperature();
+        testConstraints();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

platforms/cuda/tests/TestCudaRandom.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 random number generation.
+ */
+
+#include "../../../tests/AssertionUtilities.h"
+#include "../src/kernels/gpuTypes.h"
+#include "../src/kernels/cudaKernels.h"
+#include <iostream>
+
+using namespace OpenMM;
+using namespace std;
+
+static const float KILO                     =    1e3;                      // Thousand
+static const float BOLTZMANN                =    1.380658e-23f;            // (J/K)    
+static const float AVOGADRO                 =    6.0221367e23f;            // ()        
+static const float RGAS                     =    BOLTZMANN * AVOGADRO;     // (J/(mol K))
+static const float BOLTZ                    =    (RGAS / KILO);            // (kJ/(mol K)) 
+
+void testGaussian() {
+    _gpuContext* gpu = (_gpuContext*) gpuInit(1000);
+    gpu->sim.Yv = 1.0;
+    gpu->sim.Yx = 1.0;
+    gpu->sim.V = 1.0;
+    gpu->sim.X = 1.0;
+    gpuSetConstants(gpu);
+    kGenerateRandoms(gpu);
+    const int numValues = 4*gpu->psRandom4->_length;
+    gpu->psRandom4->Download();
+    float* data = reinterpret_cast<float*>(gpu->psRandom4->_pSysData);
+    double mean = 0.0;
+    double var = 0.0;
+    double skew = 0.0;
+    double kurtosis = 0.0;
+    for (int i = 0; i < numValues; i++) {
+        double value = data[i];
+        mean += value;
+        var += value*value;
+        skew += value*value*value;
+        kurtosis += value*value*value*value;
+    }
+    gpuShutDown(gpu);
+    mean /= numValues;
+    var /= numValues;
+    skew /= numValues;
+    kurtosis /= numValues;
+    double c2 = var-mean*mean;
+    double c3 = skew-3*var*mean+2*mean*mean*mean;
+    double c4 = kurtosis-4*skew*mean-3*var*var+12*var*mean*mean-6*mean*mean*mean*mean;
+    ASSERT_EQUAL_TOL(0.0, mean, 0.01);
+    ASSERT_EQUAL_TOL(1.0, c2, 0.01);
+    ASSERT_EQUAL_TOL(0.0, c3, 0.01);
+    ASSERT_EQUAL_TOL(0.0, c4, 0.01);
+}
+
+int main() {
+    try {
+        testGaussian();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

platforms/reference/tests/TestReferenceBrownianIntegrator.cpp

@@ -94,10 +94,9 @@ void testTemperature() {
     HarmonicBondForce* forceField = new HarmonicBondForce(numBonds);
     for (int i = 0; i < numParticles; ++i) {
         system.setParticleMass(i, 2.0);
-//        forceField->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     for (int i = 0; i < numBonds; ++i)
-        forceField->setBondParameters(i, i, i+1, 1.0, i);
+        forceField->setBondParameters(i, i, i+1, 1.0, i+1);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(numParticles);
@@ -112,14 +111,16 @@ void testTemperature() {
     // Now run it for a while and see if the temperature is correct.
     
     double pe = 0.0;
-    for (int i = 0; i < 1000; ++i) {
+    const int steps = 50000;
+    for (int i = 0; i < steps; ++i) {
         State state = context.getState(State::Energy);
         pe += state.getPotentialEnergy();
         integrator.step(1);
     }
-    pe /= 1000;
+    pe /= steps;
     double expected = 0.5*numBonds*BOLTZ*temp;
-    ASSERT_EQUAL_TOL(expected, pe, 3*expected/std::sqrt(1000.0));
+    expected *= sqrt(2.0);
+    ASSERT_EQUAL_TOL(expected, pe, 4*expected/std::sqrt(steps));
 }
 
 void testConstraints() {