C++ NonbondedForce::addException方法代码示例

void testSerialization() {
    // Create a Force.

    NonbondedForce force;
    force.setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    force.setCutoffDistance(2.0);
    force.setEwaldErrorTolerance(1e-3);
    force.setReactionFieldDielectric(50.0);
    force.setUseDispersionCorrection(false);
    force.addParticle(1, 0.1, 0.01);
    force.addParticle(0.5, 0.2, 0.02);
    force.addParticle(-0.5, 0.3, 0.03);
    force.addException(0, 1, 2, 0.5, 0.1);
    force.addException(1, 2, 0.2, 0.4, 0.2);

    // Serialize and then deserialize it.

    stringstream buffer;
    XmlSerializer::serialize<NonbondedForce>(&force, "Force", buffer);
    NonbondedForce* copy = XmlSerializer::deserialize<NonbondedForce>(buffer);

    // Compare the two forces to see if they are identical.

    NonbondedForce& force2 = *copy;
    ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
    ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
    ASSERT_EQUAL(force.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
    ASSERT_EQUAL(force.getReactionFieldDielectric(), force2.getReactionFieldDielectric());
    ASSERT_EQUAL(force.getUseDispersionCorrection(), force2.getUseDispersionCorrection());
    ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
    for (int i = 0; i < force.getNumParticles(); i++) {
        double charge1, sigma1, epsilon1;
        double charge2, sigma2, epsilon2;
        force.getParticleParameters(i, charge1, sigma1, epsilon1);
        force2.getParticleParameters(i, charge2, sigma2, epsilon2);
        ASSERT_EQUAL(charge1, charge2);
        ASSERT_EQUAL(sigma1, sigma2);
        ASSERT_EQUAL(epsilon1, epsilon2);
    }
    ASSERT_EQUAL(force.getNumExceptions(), force2.getNumExceptions());
    for (int i = 0; i < force.getNumExceptions(); i++) {
        int a1, a2, b1, b2;
        double charge1, sigma1, epsilon1;
        double charge2, sigma2, epsilon2;
        force.getExceptionParameters(i, a1, b1, charge1, sigma1, epsilon1);
        force2.getExceptionParameters(i, a2, b2, charge2, sigma2, epsilon2);
        ASSERT_EQUAL(a1, a2);
        ASSERT_EQUAL(b1, b2);
        ASSERT_EQUAL(charge1, charge2);
        ASSERT_EQUAL(sigma1, sigma2);
        ASSERT_EQUAL(epsilon1, epsilon2);
    }
}

void testPeriodic() {
    System system;
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(1.0);
    VerletIntegrator integrator(0.01);
    NonbondedForce* nonbonded = new NonbondedForce();
    nonbonded->addParticle(1.0, 1, 0);
    nonbonded->addParticle(1.0, 1, 0);
    nonbonded->addParticle(1.0, 1, 0);
    nonbonded->addException(0, 1, 0.0, 1.0, 0.0);
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    const double cutoff = 2.0;
    nonbonded->setCutoffDistance(cutoff);
    system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
    system.addForce(nonbonded);
    Context context(system, integrator, platform);
    vector<Vec3> positions(3);
    positions[0] = Vec3(0, 0, 0);
    positions[1] = Vec3(2, 0, 0);
    positions[2] = Vec3(3, 0, 0);
    context.setPositions(positions);
    State state = context.getState(State::Forces | State::Energy);
    const vector<Vec3>& forces = state.getForces();
    const double eps = 78.3;
    const double krf = (1.0/(cutoff*cutoff*cutoff))*(eps-1.0)/(2.0*eps+1.0);
    const double crf = (1.0/cutoff)*(3.0*eps)/(2.0*eps+1.0);
    const double force = ONE_4PI_EPS0*(1.0)*(1.0-2.0*krf*1.0);
    ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[0], TOL);
    ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[1], TOL);
    ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[2], TOL);
    ASSERT_EQUAL_TOL(2*ONE_4PI_EPS0*(1.0)*(1.0+krf*1.0-crf), state.getPotentialEnergy(), TOL);
}

void testForceEnergyConsistency() {
    // Create a box of polarizable particles.
    
    const int gridSize = 3;
    const int numAtoms = gridSize*gridSize*gridSize;
    const double spacing = 0.6;
    const double boxSize = spacing*(gridSize+1);
    const double temperature = 300.0;
    const double temperatureDrude = 10.0;
    System system;
    vector<Vec3> positions;
    NonbondedForce* nonbonded = new NonbondedForce();
    DrudeForce* drude = new DrudeForce();
    system.addForce(nonbonded);
    system.addForce(drude);
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    nonbonded->setNonbondedMethod(NonbondedForce::PME);
    nonbonded->setCutoffDistance(1.0);
    nonbonded->setUseSwitchingFunction(true);
    nonbonded->setSwitchingDistance(0.9);
    nonbonded->setEwaldErrorTolerance(5e-5);
    for (int i = 0; i < numAtoms; i++) {
        int startIndex = system.getNumParticles();
        system.addParticle(1.0);
        system.addParticle(1.0);
        nonbonded->addParticle(1.0, 0.3, 1.0);
        nonbonded->addParticle(-1.0, 0.3, 1.0);
        nonbonded->addException(startIndex, startIndex+1, 0, 1, 0);
        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.0, 0.001, 1, 1);
    }
    for (int i = 0; i < gridSize; i++)
        for (int j = 0; j < gridSize; j++)
            for (int k = 0; k < gridSize; k++) {
                Vec3 pos(i*spacing, j*spacing, k*spacing);
                positions.push_back(pos);
                positions.push_back(pos);
            }
    
    // Simulate it and check that force and energy remain consistent.
    
    DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.001);
    Platform& platform = Platform::getPlatformByName("Reference");
    Context context(system, integ, platform);
    context.setPositions(positions);
    State prevState;
    for (int i = 0; i < 100; i++) {
        State state = context.getState(State::Energy | State::Forces | State::Positions);
        if (i > 0) {
            double expectedEnergyChange = 0;
            for (int j = 0; j < system.getNumParticles(); j++) {
                Vec3 delta = state.getPositions()[j]-prevState.getPositions()[j];
                expectedEnergyChange -= 0.5*(state.getForces()[j]+prevState.getForces()[j]).dot(delta);
            }
            ASSERT_EQUAL_TOL(expectedEnergyChange, state.getPotentialEnergy()-prevState.getPotentialEnergy(), 0.05);
        }
        prevState = state;
        integ.step(1);
    }
}

void testParallelComputation(NonbondedForce::NonbondedMethod method) {
    System system;
    const int numParticles = 200;
    for (int i = 0; i < numParticles; i++)
        system.addParticle(1.0);
    NonbondedForce* force = new NonbondedForce();
    for (int i = 0; i < numParticles; i++)
        force->addParticle(i%2-0.5, 0.5, 1.0);
    force->setNonbondedMethod(method);
    system.addForce(force);
    system.setDefaultPeriodicBoxVectors(Vec3(5,0,0), Vec3(0,5,0), Vec3(0,0,5));
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    vector<Vec3> positions(numParticles);
    for (int i = 0; i < numParticles; i++)
        positions[i] = Vec3(5*genrand_real2(sfmt), 5*genrand_real2(sfmt), 5*genrand_real2(sfmt));
    for (int i = 0; i < numParticles; ++i)
        for (int j = 0; j < i; ++j) {
            Vec3 delta = positions[i]-positions[j];
            if (delta.dot(delta) < 0.1)
                force->addException(i, j, 0, 1, 0);
        }
    
    // Create two contexts, one with a single device and one with two devices.
    
    VerletIntegrator integrator1(0.01);
    Context context1(system, integrator1, platform);
    context1.setPositions(positions);
    State state1 = context1.getState(State::Forces | State::Energy);
    VerletIntegrator integrator2(0.01);
    string deviceIndex = platform.getPropertyValue(context1, CudaPlatform::CudaDeviceIndex());
    map<string, string> props;
    props[CudaPlatform::CudaDeviceIndex()] = deviceIndex+","+deviceIndex;
    Context context2(system, integrator2, platform, props);
    context2.setPositions(positions);
    State state2 = context2.getState(State::Forces | State::Energy);
    
    // See if they agree.
    
    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
    for (int i = 0; i < numParticles; i++)
        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
    
    // Modify some particle parameters and see if they still agree.

    for (int i = 0; i < numParticles; i += 5) {
        double charge, sigma, epsilon;
        force->getParticleParameters(i, charge, sigma, epsilon);
        force->setParticleParameters(i, 0.9*charge, sigma, epsilon);
    }
    force->updateParametersInContext(context1);
    force->updateParametersInContext(context2);
    state1 = context1.getState(State::Forces | State::Energy);
    state2 = context2.getState(State::Forces | State::Energy);
    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
    for (int i = 0; i < numParticles; i++)
        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}

/**
 * Make sure that atom reordering respects virtual sites.
 */
void testReordering() {
    const double cutoff = 2.0;
    const double boxSize = 20.0;
    System system;
    NonbondedForce* nonbonded = new NonbondedForce();
    system.addForce(nonbonded);
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
    nonbonded->setCutoffDistance(cutoff);
    vector<Vec3> positions;
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    
    // Create linear molecules with TwoParticleAverage virtual sites.
    
    for (int i = 0; i < 50; i++) {
        int start = system.getNumParticles();
        system.addParticle(1.0);
        system.addParticle(1.0);
        system.addParticle(0.0);
        system.setVirtualSite(start+2, new TwoParticleAverageSite(start, start+1, 0.4, 0.6));
        system.addConstraint(start, start+1, 2.0);
        for (int i = 0; i < 3; i++) {
            nonbonded->addParticle(0, 0.2, 1);
            for (int j = 0; j < i; j++)
                nonbonded->addException(start+i, start+j, 0, 1, 0);
        }
        Vec3 pos(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
        positions.push_back(pos);
        positions.push_back(pos+Vec3(2, 0, 0));
        positions.push_back(Vec3());
    }
    
    // Create planar molecules with ThreeParticleAverage virtual sites.
    
    for (int i = 0; i < 50; i++) {
        int start = system.getNumParticles();
        system.addParticle(1.0);
        system.addParticle(1.0);
        system.addParticle(1.0);
        system.addParticle(0.0);
        system.setVirtualSite(start+3, new ThreeParticleAverageSite(start, start+1, start+2, 0.3, 0.5, 0.2));
        system.addConstraint(start, start+1, 1.0);
        system.addConstraint(start, start+2, 1.0);
        system.addConstraint(start+1, start+2, sqrt(2.0));
        for (int i = 0; i < 4; i++) {
            nonbonded->addParticle(0, 0.2, 1);
            for (int j = 0; j < i; j++)
                nonbonded->addException(start+i, start+j, 0, 1, 0);
        }
        Vec3 pos(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
        positions.push_back(pos);
        positions.push_back(pos+Vec3(1, 0, 0));
        positions.push_back(pos+Vec3(0, 1, 0));
        positions.push_back(Vec3());
    }
    
    // Create tetrahedral molecules with OutOfPlane virtual sites.
    
    for (int i = 0; i < 50; i++) {
        int start = system.getNumParticles();
        system.addParticle(1.0);
        system.addParticle(1.0);
        system.addParticle(1.0);
        system.addParticle(0.0);
        system.setVirtualSite(start+3, new OutOfPlaneSite(start, start+1, start+2, 0.3, 0.5, 0.2));
        system.addConstraint(start, start+1, 1.0);
        system.addConstraint(start, start+2, 1.0);
        system.addConstraint(start+1, start+2, sqrt(2.0));
        for (int i = 0; i < 4; i++) {
            nonbonded->addParticle(0, 0.2, 1);
            for (int j = 0; j < i; j++)
                nonbonded->addException(start+i, start+j, 0, 1, 0);
        }
        Vec3 pos(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
        positions.push_back(pos);
        positions.push_back(pos+Vec3(1, 0, 0));
        positions.push_back(pos+Vec3(0, 1, 0));
        positions.push_back(Vec3());
    }

    // Simulate it and check conservation laws.
    
    LangevinIntegrator integrator(300.0, 0.1, 0.002);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    context.applyConstraints(0.0001);
    for (int i = 0; i < 1000; i++) {
        State state = context.getState(State::Positions);
        const vector<Vec3>& pos = state.getPositions();
        for (int j = 0; j < 150; j += 3)
            ASSERT_EQUAL_VEC(pos[j]*0.4+pos[j+1]*0.6, pos[j+2], 1e-5);
        for (int j = 150; j < 350; j += 4)
            ASSERT_EQUAL_VEC(pos[j]*0.3+pos[j+1]*0.5+pos[j+2]*0.2, pos[j+3], 1e-5);
        for (int j = 350; j < 550; j += 4) {
            Vec3 v12 = pos[j+1]-pos[j];
            Vec3 v13 = pos[j+2]-pos[j];
            Vec3 cross = v12.cross(v13);
//.........这里部分代码省略.........

/**
 * Make sure that energy, linear momentum, and angular momentum are all conserved
 * when using virtual sites.
 */
void testConservationLaws() {
    System system;
    NonbondedForce* forceField = new NonbondedForce();
    system.addForce(forceField);
    vector<Vec3> positions;
    
    // Create a linear molecule with a TwoParticleAverage virtual site.
    
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(0.0);
    system.setVirtualSite(2, new TwoParticleAverageSite(0, 1, 0.4, 0.6));
    system.addConstraint(0, 1, 2.0);
    for (int i = 0; i < 3; i++) {
        forceField->addParticle(0, 1, 10);
        for (int j = 0; j < i; j++)
            forceField->addException(i, j, 0, 1, 0);
    }
    positions.push_back(Vec3(0, 0, 0));
    positions.push_back(Vec3(2, 0, 0));
    positions.push_back(Vec3());
    
    // Create a planar molecule with a ThreeParticleAverage virtual site.
    
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(0.0);
    system.setVirtualSite(6, new ThreeParticleAverageSite(3, 4, 5, 0.3, 0.5, 0.2));
    system.addConstraint(3, 4, 1.0);
    system.addConstraint(3, 5, 1.0);
    system.addConstraint(4, 5, sqrt(2.0));
    for (int i = 0; i < 4; i++) {
        forceField->addParticle(0, 1, 10);
        for (int j = 0; j < i; j++)
            forceField->addException(i+3, j+3, 0, 1, 0);
    }
    positions.push_back(Vec3(0, 0, 1));
    positions.push_back(Vec3(1, 0, 1));
    positions.push_back(Vec3(0, 1, 1));
    positions.push_back(Vec3());
    
    // Create a tetrahedral molecule with an OutOfPlane virtual site.
    
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(0.0);
    system.setVirtualSite(10, new OutOfPlaneSite(7, 8, 9, 0.3, 0.5, 0.2));
    system.addConstraint(7, 8, 1.0);
    system.addConstraint(7, 9, 1.0);
    system.addConstraint(8, 9, sqrt(2.0));
    for (int i = 0; i < 4; i++) {
        forceField->addParticle(0, 1, 10);
        for (int j = 0; j < i; j++)
            forceField->addException(i+7, j+7, 0, 1, 0);
    }
    positions.push_back(Vec3(1, 0, -1));
    positions.push_back(Vec3(2, 0, -1));
    positions.push_back(Vec3(1, 1, -1));
    positions.push_back(Vec3());
    
    // Create a molecule with a LocalCoordinatesSite virtual site.
    
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(0.0);
    system.setVirtualSite(14, new LocalCoordinatesSite(11, 12, 13, Vec3(0.3, 0.3, 0.4), Vec3(1.0, -0.5, -0.5), Vec3(0, -1.0, 1.0), Vec3(0.2, 0.2, 1.0)));
    system.addConstraint(11, 12, 1.0);
    system.addConstraint(11, 13, 1.0);
    system.addConstraint(12, 13, sqrt(2.0));
    for (int i = 0; i < 4; i++) {
        forceField->addParticle(0, 1, 10);
        for (int j = 0; j < i; j++)
            forceField->addException(i+11, j+11, 0, 1, 0);
    }
    positions.push_back(Vec3(1, 2, 0));
    positions.push_back(Vec3(2, 2, 0));
    positions.push_back(Vec3(1, 3, 0));
    positions.push_back(Vec3());

    // Simulate it and check conservation laws.
    
    VerletIntegrator integrator(0.002);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    context.applyConstraints(0.0001);
    int numParticles = system.getNumParticles();
    double initialEnergy;
    Vec3 initialMomentum, initialAngularMomentum;
    for (int i = 0; i < 1000; i++) {
        State state = context.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
        const vector<Vec3>& pos = state.getPositions();
        const vector<Vec3>& vel = state.getVelocities();
        const vector<Vec3>& f = state.getForces();
//.........这里部分代码省略.........

void testWithBarostat() {
    const int gridSize = 3;
    const int numMolecules = gridSize*gridSize*gridSize;
    const int numParticles = numMolecules*2;
    const int numCopies = 5;
    const double spacing = 2.0;
    const double cutoff = 3.0;
    const double boxSize = spacing*(gridSize+1);
    const double temperature = 300.0;
    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    HarmonicBondForce* bonds = new HarmonicBondForce();
    system.addForce(bonds);
    NonbondedForce* nonbonded = new NonbondedForce();
    nonbonded->setCutoffDistance(cutoff);
    nonbonded->setNonbondedMethod(NonbondedForce::PME);
    nonbonded->setForceGroup(1);
    nonbonded->setReciprocalSpaceForceGroup(2);
    system.addForce(nonbonded);
    system.addForce(new MonteCarloBarostat(0.5, temperature));

    // Create a cloud of molecules.

    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    vector<Vec3> positions(numParticles);
    for (int i = 0; i < numMolecules; i++) {
        system.addParticle(1.0);
        system.addParticle(1.0);
        nonbonded->addParticle(-0.2, 0.2, 0.2);
        nonbonded->addParticle(0.2, 0.2, 0.2);
        nonbonded->addException(2*i, 2*i+1, 0, 1, 0);
        bonds->addBond(2*i, 2*i+1, 1.0, 10000.0);
    }
    RPMDIntegrator integ(numCopies, temperature, 50.0, 0.001);
    Platform& platform = Platform::getPlatformByName("Reference");
    Context context(system, integ, platform);
    for (int copy = 0; copy < numCopies; copy++) {
        for (int i = 0; i < gridSize; i++)
            for (int j = 0; j < gridSize; j++)
                for (int k = 0; k < gridSize; k++) {
                    Vec3 pos = Vec3(spacing*(i+0.02*genrand_real2(sfmt)), spacing*(j+0.02*genrand_real2(sfmt)), spacing*(k+0.02*genrand_real2(sfmt)));
                    int index = k+gridSize*(j+gridSize*i);
                    positions[2*index] = pos;
                    positions[2*index+1] = Vec3(pos[0]+1.0, pos[1], pos[2]);
                }
        integ.setPositions(copy, positions);
    }

    // Check the temperature.
    
    const int numSteps = 500;
    integ.step(100);
    vector<double> ke(numCopies, 0.0);
    for (int i = 0; i < numSteps; i++) {
        integ.step(1);
        vector<State> state(numCopies);
        for (int j = 0; j < numCopies; j++)
            state[j] = integ.getState(j, State::Velocities, true);
        for (int j = 0; j < numParticles; j++) {
            for (int k = 0; k < numCopies; k++) {
                Vec3 v = state[k].getVelocities()[j];
                ke[k] += 0.5*system.getParticleMass(j)*v.dot(v);
            }
        }
    }
    double meanKE = 0.0;
    for (int i = 0; i < numCopies; i++)
        meanKE += ke[i];
    meanKE /= numSteps*numCopies;
    double expectedKE = 0.5*numCopies*numParticles*3*BOLTZ*temperature;
    ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
}

void testCoulombLennardJones() {
    const int numMolecules = 300;
    const int numParticles = numMolecules*2;
    const double boxSize = 20.0;

    // Create two systems: one with a NonbondedForce, and one using a CustomNonbondedForce to implement the same interaction.

    System standardSystem;
    System customSystem;
    for (int i = 0; i < numParticles; i++) {
        standardSystem.addParticle(1.0);
        customSystem.addParticle(1.0);
    }
    NonbondedForce* standardNonbonded = new NonbondedForce();
    CustomNonbondedForce* customNonbonded = new CustomNonbondedForce("4*eps*((sigma/r)^12-(sigma/r)^6)+138.935456*q/r; q=q1*q2; sigma=0.5*(sigma1+sigma2); eps=sqrt(eps1*eps2)");
    customNonbonded->addPerParticleParameter("q");
    customNonbonded->addPerParticleParameter("sigma");
    customNonbonded->addPerParticleParameter("eps");
    vector<Vec3> positions(numParticles);
    vector<Vec3> velocities(numParticles);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);

    vector<double> params(3);
    for (int i = 0; i < numMolecules; i++) {
        if (i < numMolecules/2) {
            standardNonbonded->addParticle(1.0, 0.2, 0.1);
            params[0] = 1.0;
            params[1] = 0.2;
            params[2] = 0.1;
            customNonbonded->addParticle(params);
            standardNonbonded->addParticle(-1.0, 0.1, 0.1);
            params[0] = -1.0;
            params[1] = 0.1;
            customNonbonded->addParticle(params);
        }
        else {
            standardNonbonded->addParticle(1.0, 0.2, 0.2);
            params[0] = 1.0;
            params[1] = 0.2;
            params[2] = 0.2;
            customNonbonded->addParticle(params);
            standardNonbonded->addParticle(-1.0, 0.1, 0.2);
            params[0] = -1.0;
            params[1] = 0.1;
            customNonbonded->addParticle(params);
        }
        positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
        positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
        velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
        velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
        standardNonbonded->addException(2*i, 2*i+1, 0.0, 1.0, 0.0);
        customNonbonded->addExclusion(2*i, 2*i+1);
    }
    standardNonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
    customNonbonded->setNonbondedMethod(CustomNonbondedForce::NoCutoff);
    standardSystem.addForce(standardNonbonded);
    customSystem.addForce(customNonbonded);
    VerletIntegrator integrator1(0.01);
    VerletIntegrator integrator2(0.01);
    Context context1(standardSystem, integrator1, platform);
    Context context2(customSystem, integrator2, platform);
    context1.setPositions(positions);
    context2.setPositions(positions);
    context1.setVelocities(velocities);
    context2.setVelocities(velocities);
    State state1 = context1.getState(State::Forces | State::Energy);
    State state2 = context2.getState(State::Forces | State::Energy);
    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
    for (int i = 0; i < numParticles; i++) {
        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
    }
}

void testWater() {
    // Create a box of SWM4-NDP water molecules.  This involves constraints, virtual sites,
    // and Drude particles.
    
    const int gridSize = 3;
    const int numMolecules = gridSize*gridSize*gridSize;
    const double spacing = 0.6;
    const double boxSize = spacing*(gridSize+1);
    System system;
    NonbondedForce* nonbonded = new NonbondedForce();
    DrudeForce* drude = new DrudeForce();
    system.addForce(nonbonded);
    system.addForce(drude);
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    nonbonded->setCutoffDistance(1.0);
    for (int i = 0; i < numMolecules; i++) {
        int startIndex = system.getNumParticles();
        system.addParticle(15.6); // O
        system.addParticle(0.4);  // D
        system.addParticle(1.0);  // H1
        system.addParticle(1.0);  // H2
        system.addParticle(0.0);  // M
        nonbonded->addParticle(1.71636, 0.318395, 0.21094*4.184);
        nonbonded->addParticle(-1.71636, 1, 0);
        nonbonded->addParticle(0.55733, 1, 0);
        nonbonded->addParticle(0.55733, 1, 0);
        nonbonded->addParticle(-1.11466, 1, 0);
        for (int j = 0; j < 5; j++)
            for (int k = 0; k < j; k++)
                nonbonded->addException(startIndex+j, startIndex+k, 0, 1, 0);
        system.addConstraint(startIndex, startIndex+2, 0.09572);
        system.addConstraint(startIndex, startIndex+3, 0.09572);
        system.addConstraint(startIndex+2, startIndex+3, 0.15139);
        system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
    }
    vector<Vec3> positions;
    for (int i = 0; i < gridSize; i++)
        for (int j = 0; j < gridSize; j++)
            for (int k = 0; k < gridSize; k++) {
                Vec3 pos(i*spacing, j*spacing, k*spacing);
                positions.push_back(pos);
                positions.push_back(pos);
                positions.push_back(pos+Vec3(0.09572, 0, 0));
                positions.push_back(pos+Vec3(-0.023999, 0.092663, 0));
                positions.push_back(pos);
            }
    
    // Simulate it and check energy conservation and the total force on the Drude particles.
    
    DrudeSCFIntegrator integ(0.0005);
    Platform& platform = Platform::getPlatformByName("Reference");
    Context context(system, integ, platform);
    context.setPositions(positions);
    context.applyConstraints(1e-5);
    context.setVelocitiesToTemperature(300.0);
    State state = context.getState(State::Energy);
    double initialEnergy;
    int numSteps = 1000;
    for (int i = 0; i < numSteps; i++) {
        integ.step(1);
        state = context.getState(State::Energy | State::Forces);
        if (i == 0)
            initialEnergy = state.getPotentialEnergy()+state.getKineticEnergy();
        else
            ASSERT_EQUAL_TOL(initialEnergy, state.getPotentialEnergy()+state.getKineticEnergy(), 0.01);
        const vector<Vec3>& force = state.getForces();
        double norm = 0.0;
        for (int j = 1; j < (int) force.size(); j += 5)
            norm += sqrt(force[j].dot(force[j]));
        norm = (norm/numMolecules);
        ASSERT(norm < 1.0);
    }
}

void testWater() {
    // Create a box of SWM4-NDP water molecules.  This involves constraints, virtual sites,
    // and Drude particles.
    
    const int gridSize = 3;
    const int numMolecules = gridSize*gridSize*gridSize;
    const double spacing = 0.6;
    const double boxSize = spacing*(gridSize+1);
    const double temperature = 300.0;
    const double temperatureDrude = 10.0;
    System system;
    NonbondedForce* nonbonded = new NonbondedForce();
    DrudeForce* drude = new DrudeForce();
    system.addForce(nonbonded);
    system.addForce(drude);
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    nonbonded->setCutoffDistance(1.0);
    for (int i = 0; i < numMolecules; i++) {
        int startIndex = system.getNumParticles();
        system.addParticle(15.6); // O
        system.addParticle(0.4);  // D
        system.addParticle(1.0);  // H1
        system.addParticle(1.0);  // H2
        system.addParticle(0.0);  // M
        nonbonded->addParticle(1.71636, 0.318395, 0.21094*4.184);
        nonbonded->addParticle(-1.71636, 1, 0);
        nonbonded->addParticle(0.55733, 1, 0);
        nonbonded->addParticle(0.55733, 1, 0);
        nonbonded->addParticle(-1.11466, 1, 0);
        for (int j = 0; j < 5; j++)
            for (int k = 0; k < j; k++)
                nonbonded->addException(startIndex+j, startIndex+k, 0, 1, 0);
        system.addConstraint(startIndex, startIndex+2, 0.09572);
        system.addConstraint(startIndex, startIndex+3, 0.09572);
        system.addConstraint(startIndex+2, startIndex+3, 0.15139);
        system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
    }
    vector<Vec3> positions;
    for (int i = 0; i < gridSize; i++)
        for (int j = 0; j < gridSize; j++)
            for (int k = 0; k < gridSize; k++) {
                Vec3 pos(i*spacing, j*spacing, k*spacing);
                positions.push_back(pos);
                positions.push_back(pos);
                positions.push_back(pos+Vec3(0.09572, 0, 0));
                positions.push_back(pos+Vec3(-0.023999, 0.092663, 0));
                positions.push_back(pos);
            }
    
    // Simulate it and check the temperature.
    
    DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.0005);
    Platform& platform = Platform::getPlatformByName("Reference");
    Context context(system, integ, platform);
    context.setPositions(positions);
    context.applyConstraints(1e-5);
    
    // Equilibrate.
    
    integ.step(500);
    
    // Compute the internal and center of mass temperatures.
    
    double ke = 0;
    int numSteps = 4000;
    for (int i = 0; i < numSteps; i++) {
        integ.step(1);
        ke += context.getState(State::Energy).getKineticEnergy();
    }
    ke /= numSteps;
    int numStandardDof = 3*3*numMolecules-system.getNumConstraints();
    int numDrudeDof = 3*numMolecules;
    int numDof = numStandardDof+numDrudeDof;
    double expectedTemp = (numStandardDof*temperature+numDrudeDof*temperatureDrude)/numDof;
    ASSERT_USUALLY_EQUAL_TOL(expectedTemp, ke/(0.5*numDof*BOLTZ), 0.03);
}

void testEwaldPME(bool includeExceptions) {

//      Use amorphous NaCl system for the tests

    const int numParticles = 894;
    const double cutoff = 1.2;
    const double boxSize = 3.00646;
    double tol = 1e-5;

    ReferencePlatform reference;
    System system;
    NonbondedForce* nonbonded = new NonbondedForce();
    nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
    nonbonded->setCutoffDistance(cutoff);
    nonbonded->setEwaldErrorTolerance(tol);

    for (int i = 0; i < numParticles/2; i++)
        system.addParticle(22.99);
    for (int i = 0; i < numParticles/2; i++)
        system.addParticle(35.45);
    for (int i = 0; i < numParticles/2; i++)
        nonbonded->addParticle(1.0, 1.0,0.0);
    for (int i = 0; i < numParticles/2; i++)
        nonbonded->addParticle(-1.0, 1.0,0.0);
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    system.addForce(nonbonded);

    vector<Vec3> positions(numParticles);
#include "nacl_amorph.dat"
    if (includeExceptions) {
        // Add some exclusions.

        for (int i = 0; i < numParticles-1; i++) {
            Vec3 delta = positions[i]-positions[i+1];
            if (sqrt(delta.dot(delta)) < 0.5*cutoff)
                nonbonded->addException(i, i+1, i%2 == 0 ? 0.0 : 0.5, 1.0, 0.0);
        }
    }

//    (1)  Check whether the Reference and CPU platforms agree when using Ewald Method

    VerletIntegrator integrator1(0.01);
    VerletIntegrator integrator2(0.01);
    Context cpuContext(system, integrator1, platform);
    Context referenceContext(system, integrator2, reference);
    cpuContext.setPositions(positions);
    referenceContext.setPositions(positions);
    State cpuState = cpuContext.getState(State::Forces | State::Energy);
    State referenceState = referenceContext.getState(State::Forces | State::Energy);
    tol = 1e-2;
    for (int i = 0; i < numParticles; i++) {
        ASSERT_EQUAL_VEC(referenceState.getForces()[i], cpuState.getForces()[i], tol);
    }
    tol = 1e-5;
    ASSERT_EQUAL_TOL(referenceState.getPotentialEnergy(), cpuState.getPotentialEnergy(), tol);

//    (2) Check whether Ewald method in CPU is self-consistent

    double norm = 0.0;
    for (int i = 0; i < numParticles; ++i) {
        Vec3 f = cpuState.getForces()[i];
        norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
    }

    norm = std::sqrt(norm);
    const double delta = 5e-3;
    double step = delta/norm;
    for (int i = 0; i < numParticles; ++i) {
        Vec3 p = positions[i];
        Vec3 f = cpuState.getForces()[i];
        positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
    }
    VerletIntegrator integrator3(0.01);
    Context cpuContext2(system, integrator3, platform);
    cpuContext2.setPositions(positions);

    tol = 1e-2;
    State cpuState2 = cpuContext2.getState(State::Energy);
    ASSERT_EQUAL_TOL(norm, (cpuState2.getPotentialEnergy()-cpuState.getPotentialEnergy())/delta, tol)

//    (3)  Check whether the Reference and CPU platforms agree when using PME

    nonbonded->setNonbondedMethod(NonbondedForce::PME);
    cpuContext.reinitialize();
    referenceContext.reinitialize();
    cpuContext.setPositions(positions);
    referenceContext.setPositions(positions);
    cpuState = cpuContext.getState(State::Forces | State::Energy);
    referenceState = referenceContext.getState(State::Forces | State::Energy);
    tol = 1e-2;
    for (int i = 0; i < numParticles; i++) {
        ASSERT_EQUAL_VEC(referenceState.getForces()[i], cpuState.getForces()[i], tol);
    }
    tol = 1e-5;
    ASSERT_EQUAL_TOL(referenceState.getPotentialEnergy(), cpuState.getPotentialEnergy(), tol);

//    (4) Check whether PME method in CPU is self-consistent

    norm = 0.0;
    for (int i = 0; i < numParticles; ++i) {
//.........这里部分代码省略.........

void testSerialization() {
    // Create a Force.

    NonbondedForce force;
    force.setForceGroup(3);
    force.setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    force.setSwitchingDistance(1.5);
    force.setUseSwitchingFunction(true);
    force.setCutoffDistance(2.0);
    force.setEwaldErrorTolerance(1e-3);
    force.setReactionFieldDielectric(50.0);
    force.setUseDispersionCorrection(false);
    double alpha = 0.5;
    int nx = 3, ny = 5, nz = 7;
    force.setPMEParameters(alpha, nx, ny, nz);
    double dalpha = 0.8;
    int dnx = 4, dny = 6, dnz = 7;
    force.setLJPMEParameters(dalpha, dnx, dny, dnz);
    force.addParticle(1, 0.1, 0.01);
    force.addParticle(0.5, 0.2, 0.02);
    force.addParticle(-0.5, 0.3, 0.03);
    force.addException(0, 1, 2, 0.5, 0.1);
    force.addException(1, 2, 0.2, 0.4, 0.2);
    force.addGlobalParameter("scale1", 1.0);
    force.addGlobalParameter("scale2", 2.0);
    force.addParticleParameterOffset("scale1", 2, 1.5, 2.0, 2.5);
    force.addExceptionParameterOffset("scale2", 1, -0.1, -0.2, -0.3);

    // Serialize and then deserialize it.

    stringstream buffer;
    XmlSerializer::serialize<NonbondedForce>(&force, "Force", buffer);
    NonbondedForce* copy = XmlSerializer::deserialize<NonbondedForce>(buffer);

    // Compare the two forces to see if they are identical.

    NonbondedForce& force2 = *copy;
    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
    ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
    ASSERT_EQUAL(force.getSwitchingDistance(), force2.getSwitchingDistance());
    ASSERT_EQUAL(force.getUseSwitchingFunction(), force2.getUseSwitchingFunction());
    ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
    ASSERT_EQUAL(force.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
    ASSERT_EQUAL(force.getReactionFieldDielectric(), force2.getReactionFieldDielectric());
    ASSERT_EQUAL(force.getUseDispersionCorrection(), force2.getUseDispersionCorrection());
    ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
    ASSERT_EQUAL(force.getNumExceptions(), force2.getNumExceptions());
    ASSERT_EQUAL(force.getNumGlobalParameters(), force2.getNumGlobalParameters());
    ASSERT_EQUAL(force.getNumParticleParameterOffsets(), force2.getNumParticleParameterOffsets());
    ASSERT_EQUAL(force.getNumExceptionParameterOffsets(), force2.getNumExceptionParameterOffsets());
    double alpha2;
    int nx2, ny2, nz2;
    force2.getPMEParameters(alpha2, nx2, ny2, nz2);
    ASSERT_EQUAL(alpha, alpha2);
    ASSERT_EQUAL(nx, nx2);
    ASSERT_EQUAL(ny, ny2);
    ASSERT_EQUAL(nz, nz2);    
    double dalpha2;
    int dnx2, dny2, dnz2;
    force2.getLJPMEParameters(dalpha2, dnx2, dny2, dnz2);
    ASSERT_EQUAL(dalpha, dalpha2);
    ASSERT_EQUAL(dnx, dnx2);
    ASSERT_EQUAL(dny, dny2);
    ASSERT_EQUAL(dnz, dnz2);
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
        ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
    }
    for (int i = 0; i < force.getNumParticleParameterOffsets(); i++) {
        int index1, index2;
        string param1, param2;
        double charge1, sigma1, epsilon1;
        double charge2, sigma2, epsilon2;
        force.getParticleParameterOffset(i, param1, index1, charge1, sigma1, epsilon1);
        force2.getParticleParameterOffset(i, param2, index2, charge2, sigma2, epsilon2);
        ASSERT_EQUAL(index1, index1);
        ASSERT_EQUAL(param1, param2);
        ASSERT_EQUAL(charge1, charge2);
        ASSERT_EQUAL(sigma1, sigma2);
        ASSERT_EQUAL(epsilon1, epsilon2);
    }
    for (int i = 0; i < force.getNumExceptionParameterOffsets(); i++) {
        int index1, index2;
        string param1, param2;
        double charge1, sigma1, epsilon1;
        double charge2, sigma2, epsilon2;
        force.getExceptionParameterOffset(i, param1, index1, charge1, sigma1, epsilon1);
        force2.getExceptionParameterOffset(i, param2, index2, charge2, sigma2, epsilon2);
        ASSERT_EQUAL(index1, index1);
        ASSERT_EQUAL(param1, param2);
        ASSERT_EQUAL(charge1, charge2);
        ASSERT_EQUAL(sigma1, sigma2);
        ASSERT_EQUAL(epsilon1, epsilon2);
    }
    for (int i = 0; i < force.getNumParticles(); i++) {
        double charge1, sigma1, epsilon1;
        double charge2, sigma2, epsilon2;
        force.getParticleParameters(i, charge1, sigma1, epsilon1);
        force2.getParticleParameters(i, charge2, sigma2, epsilon2);
        ASSERT_EQUAL(charge1, charge2);
//.........这里部分代码省略.........

void testChangingParameters() {
    const int numMolecules = 600;
    const int numParticles = numMolecules*2;
    const double cutoff = 2.0;
    const double boxSize = 20.0;
    const double tol = 2e-3;
    ReferencePlatform reference;
    System system;
    for (int i = 0; i < numParticles; i++)
        system.addParticle(1.0);
    NonbondedForce* nonbonded = new NonbondedForce();
    vector<Vec3> positions(numParticles);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);

    for (int i = 0; i < numMolecules; i++) {
        if (i < numMolecules/2) {
            nonbonded->addParticle(-1.0, 0.2, 0.1);
            nonbonded->addParticle(1.0, 0.1, 0.1);
        }
        else {
            nonbonded->addParticle(-1.0, 0.2, 0.2);
            nonbonded->addParticle(1.0, 0.1, 0.2);
        }
        positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
        positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
        system.addConstraint(2*i, 2*i+1, 1.0);
        nonbonded->addException(2*i, 2*i+1, 0.0, 0.15, 0.0);
    }
    nonbonded->setNonbondedMethod(NonbondedForce::PME);
    nonbonded->setCutoffDistance(cutoff);
    system.addForce(nonbonded);
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    
    // See if Reference and Cuda give the same forces and energies.
    
    VerletIntegrator integrator1(0.01);
    VerletIntegrator integrator2(0.01);
    Context cuContext(system, integrator1, platform);
    Context referenceContext(system, integrator2, reference);
    cuContext.setPositions(positions);
    referenceContext.setPositions(positions);
    State cuState = cuContext.getState(State::Forces | State::Energy);
    State referenceState = referenceContext.getState(State::Forces | State::Energy);
    for (int i = 0; i < numParticles; i++)
        ASSERT_EQUAL_VEC(cuState.getForces()[i], referenceState.getForces()[i], tol);
    ASSERT_EQUAL_TOL(cuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
    
    // Now modify parameters and see if they still agree.

    for (int i = 0; i < numParticles; i += 5) {
        double charge, sigma, epsilon;
        nonbonded->getParticleParameters(i, charge, sigma, epsilon);
        nonbonded->setParticleParameters(i, 1.5*charge, 1.1*sigma, 1.7*epsilon);
    }
    nonbonded->updateParametersInContext(cuContext);
    nonbonded->updateParametersInContext(referenceContext);
    cuState = cuContext.getState(State::Forces | State::Energy);
    referenceState = referenceContext.getState(State::Forces | State::Energy);
    for (int i = 0; i < numParticles; i++)
        ASSERT_EQUAL_VEC(cuState.getForces()[i], referenceState.getForces()[i], tol);
    ASSERT_EQUAL_TOL(cuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
}

void testLargeSystem() {
    const int numMolecules = 600;
    const int numParticles = numMolecules*2;
    const double cutoff = 2.0;
    const double boxSize = 20.0;
    const double tol = 2e-3;
    ReferencePlatform reference;
    System system;
    for (int i = 0; i < numParticles; i++)
        system.addParticle(1.0);
    NonbondedForce* nonbonded = new NonbondedForce();
    HarmonicBondForce* bonds = new HarmonicBondForce();
    vector<Vec3> positions(numParticles);
    vector<Vec3> velocities(numParticles);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);

    for (int i = 0; i < numMolecules; i++) {
        if (i < numMolecules/2) {
            nonbonded->addParticle(-1.0, 0.2, 0.1);
            nonbonded->addParticle(1.0, 0.1, 0.1);
        }
        else {
            nonbonded->addParticle(-1.0, 0.2, 0.2);
            nonbonded->addParticle(1.0, 0.1, 0.2);
        }
        positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
        positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
        velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
        velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
        bonds->addBond(2*i, 2*i+1, 1.0, 0.1);
        nonbonded->addException(2*i, 2*i+1, 0.0, 0.15, 0.0);
    }

    // Try with cutoffs but not periodic boundary conditions, and make sure the cl and Reference
    // platforms agree.

    nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
    nonbonded->setCutoffDistance(cutoff);
    system.addForce(nonbonded);
    system.addForce(bonds);
    VerletIntegrator integrator1(0.01);
    VerletIntegrator integrator2(0.01);
    Context cuContext(system, integrator1, platform);
    Context referenceContext(system, integrator2, reference);
    cuContext.setPositions(positions);
    cuContext.setVelocities(velocities);
    referenceContext.setPositions(positions);
    referenceContext.setVelocities(velocities);
    State cuState = cuContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
    State referenceState = referenceContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
    for (int i = 0; i < numParticles; i++) {
        ASSERT_EQUAL_VEC(cuState.getPositions()[i], referenceState.getPositions()[i], tol);
        ASSERT_EQUAL_VEC(cuState.getVelocities()[i], referenceState.getVelocities()[i], tol);
        ASSERT_EQUAL_VEC(cuState.getForces()[i], referenceState.getForces()[i], tol);
    }
    ASSERT_EQUAL_TOL(cuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);

    // Now do the same thing with periodic boundary conditions.

    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    cuContext.reinitialize();
    referenceContext.reinitialize();
    cuContext.setPositions(positions);
    cuContext.setVelocities(velocities);
    referenceContext.setPositions(positions);
    referenceContext.setVelocities(velocities);
    cuState = cuContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
    referenceState = referenceContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
    for (int i = 0; i < numParticles; i++) {
        double dx = cuState.getPositions()[i][0]-referenceState.getPositions()[i][0];
        double dy = cuState.getPositions()[i][1]-referenceState.getPositions()[i][1];
        double dz = cuState.getPositions()[i][2]-referenceState.getPositions()[i][2];
        ASSERT_EQUAL_TOL(fmod(cuState.getPositions()[i][0]-referenceState.getPositions()[i][0], boxSize), 0, tol);
        ASSERT_EQUAL_TOL(fmod(cuState.getPositions()[i][1]-referenceState.getPositions()[i][1], boxSize), 0, tol);
        ASSERT_EQUAL_TOL(fmod(cuState.getPositions()[i][2]-referenceState.getPositions()[i][2], boxSize), 0, tol);
        ASSERT_EQUAL_VEC(cuState.getVelocities()[i], referenceState.getVelocities()[i], tol);
        ASSERT_EQUAL_VEC(cuState.getForces()[i], referenceState.getForces()[i], tol);
    }
    ASSERT_EQUAL_TOL(cuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
}