C++ DrudeForce类代码示例

void ReferenceCalcDrudeForceKernel::initialize(const System& system, const DrudeForce& force) {
    // Initialize particle parameters.
    
    int numParticles = force.getNumParticles();
    particle.resize(numParticles);
    particle1.resize(numParticles);
    particle2.resize(numParticles);
    particle3.resize(numParticles);
    particle4.resize(numParticles);
    charge.resize(numParticles);
    polarizability.resize(numParticles);
    aniso12.resize(numParticles);
    aniso34.resize(numParticles);
    for (int i = 0; i < numParticles; i++)
        force.getParticleParameters(i, particle[i], particle1[i], particle2[i], particle3[i], particle4[i], charge[i], polarizability[i], aniso12[i], aniso34[i]);
    
    // Initialize screened pair parameters.
    
    int numPairs = force.getNumScreenedPairs();
    pair1.resize(numPairs);
    pair2.resize(numPairs);
    pairThole.resize(numPairs);
    for (int i = 0; i < numPairs; i++)
        force.getScreenedPairParameters(i, pair1[i], pair2[i], pairThole[i]);
}

void testAnisotropicParticle() {
    const double k = ONE_4PI_EPS0*1.5;
    const double charge = 0.1;
    const double alpha = ONE_4PI_EPS0*charge*charge/k;
    const double a1 = 0.8;
    const double a2 = 1.1;
    const double k1 = k/a1;
    const double k2 = k/a2;
    const double k3 = k/(3-a1-a2);
    System system;
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(1.0);
    DrudeForce* drude = new DrudeForce();
    drude->addParticle(1, 0, 2, 3, 4, charge, alpha, a1, a2);
    system.addForce(drude);
    vector<Vec3> positions(5);
    positions[0] = Vec3(0, 0, 0);
    positions[1] = Vec3(0.1, -0.5, 0.8);
    positions[2] = Vec3(0, 2, 0);
    positions[3] = Vec3(1, 2, 0);
    positions[4] = Vec3(1, 2, 3);
    validateForce(system, positions, 0.5*k1*0.5*0.5 + 0.5*k2*0.8*0.8 + 0.5*k3*0.1*0.1);
}

void ReferenceIntegrateDrudeSCFStepKernel::initialize(const System& system, const DrudeSCFIntegrator& integrator, const DrudeForce& force) {
    // Identify Drude particles.
    
    for (int i = 0; i < force.getNumParticles(); i++) {
        int p, p1, p2, p3, p4;
        double charge, polarizability, aniso12, aniso34;
        force.getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
        drudeParticles.push_back(p);
    }

    // Record particle masses.

    vector<RealOpenMM> particleMass;
    for (int i = 0; i < system.getNumParticles(); i++) {
        double mass = system.getParticleMass(i);
        particleMass.push_back(mass);
        particleInvMass.push_back(mass == 0.0 ? 0.0 : 1.0/mass);
    }
    
    // Initialize the energy minimizer.
    
    minimizerPos = lbfgs_malloc(drudeParticles.size()*3);
    if (minimizerPos == NULL)
        throw OpenMMException("DrudeSCFIntegrator: Failed to allocate memory");
    lbfgs_parameter_init(&minimizerParams);
    minimizerParams.linesearch = LBFGS_LINESEARCH_BACKTRACKING_STRONG_WOLFE;
    if (sizeof(RealOpenMM) < 8)
        minimizerParams.xtol = 1e-7;
}

void testThole() {
    const double k = ONE_4PI_EPS0*1.5;
    const double charge = 0.1;
    const double alpha = ONE_4PI_EPS0*charge*charge/k;
    const double thole = 2.5;
    System system;
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(1.0);
    DrudeForce* drude = new DrudeForce();
    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
    drude->addParticle(3, 2, -1, -1, -1, charge, alpha, 1, 1);
    drude->addScreenedPair(0, 1, thole);
    system.addForce(drude);
    vector<Vec3> positions(4);
    positions[0] = Vec3(0, 0, 0);
    positions[1] = Vec3(0, -0.5, 0);
    positions[2] = Vec3(1, 0, 0);
    positions[3] = Vec3(1, 0, 0.3);
    double energySpring1 = 0.5*k*0.5*0.5;
    double energySpring2 = 0.5*k*0.3*0.3;
    double energyDipole = 0.0;
    double q[] = {-charge, charge, -charge, charge};
    for (int i = 0; i < 2; i++)
        for (int j = 2; j < 4; j++) {
            Vec3 delta = positions[i]-positions[j];
            double r = sqrt(delta.dot(delta));
            energyDipole += ONE_4PI_EPS0*q[i]*q[j]*computeScreening(r, thole, alpha, alpha)/r;
        }
    validateForce(system, positions, energySpring1+energySpring2+energyDipole);
}

void CudaIntegrateDrudeSCFStepKernel::initialize(const System& system, const DrudeSCFIntegrator& integrator, const DrudeForce& force) {
    cu.getPlatformData().initializeContexts(system);
    cu.setAsCurrent();

    // Identify Drude particles.
    
    for (int i = 0; i < force.getNumParticles(); i++) {
        int p, p1, p2, p3, p4;
        double charge, polarizability, aniso12, aniso34;
        force.getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
        drudeParticles.push_back(p);
    }
    
    // Initialize the energy minimizer.
    
    minimizerPos = lbfgs_malloc(drudeParticles.size()*3);
    if (minimizerPos == NULL)
        throw OpenMMException("DrudeSCFIntegrator: Failed to allocate memory");
    lbfgs_parameter_init(&minimizerParams);
    minimizerParams.linesearch = LBFGS_LINESEARCH_BACKTRACKING_STRONG_WOLFE;    

    // Create the kernels.
    
    map<string, string> defines;
    defines["NUM_ATOMS"] = cu.intToString(cu.getNumAtoms());
    defines["PADDED_NUM_ATOMS"] = cu.intToString(cu.getPaddedNumAtoms());
    CUmodule module = cu.createModule(CudaKernelSources::verlet, defines, "");
    kernel1 = cu.getKernel(module, "integrateVerletPart1");
    kernel2 = cu.getKernel(module, "integrateVerletPart2");
    prevStepSize = -1.0;
}

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 testSinglePair() {
    const double temperature = 300.0;
    const double temperatureDrude = 10.0;
    const double k = ONE_4PI_EPS0*1.5;
    const double charge = 0.1;
    const double alpha = ONE_4PI_EPS0*charge*charge/k;
    const double mass1 = 1.0;
    const double mass2 = 0.1;
    const double totalMass = mass1+mass2;
    const double reducedMass = (mass1*mass2)/(mass1+mass2);
    const double maxDistance = 0.05;
    System system;
    system.addParticle(mass1);
    system.addParticle(mass2);
    DrudeForce* drude = new DrudeForce();
    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
    system.addForce(drude);
    vector<Vec3> positions(2);
    positions[0] = Vec3(0, 0, 0);
    positions[1] = Vec3(0, 0, 0);
    DrudeLangevinIntegrator integ(temperature, 20.0, temperatureDrude, 20.0, 0.003);
    integ.setMaxDrudeDistance(maxDistance);
    Platform& platform = Platform::getPlatformByName("Reference");
    Context context(system, integ, platform);
    context.setPositions(positions);
    
    // Equilibrate.
    
    integ.step(1000);
    
    // Compute the internal and center of mass temperatures.
    
    double keCM = 0, keInternal = 0;
    int numSteps = 10000;
    for (int i = 0; i < numSteps; i++) {
        integ.step(10);
        State state = context.getState(State::Velocities | State::Positions);
        const vector<Vec3>& vel = state.getVelocities();
        Vec3 velCM = vel[0]*(mass1/totalMass) + vel[1]*(mass2/totalMass);
        keCM += 0.5*totalMass*velCM.dot(velCM);
        Vec3 velInternal = vel[0]-vel[1];
        keInternal += 0.5*reducedMass*velInternal.dot(velInternal);
        Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
        double distance = sqrt(delta.dot(delta));
        ASSERT(distance <= maxDistance*(1+1e-6));
    }
    ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperature, keCM/numSteps, 0.1);
    ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperatureDrude, keInternal/numSteps, 0.01);
}

void testSingleParticle() {
    const double k = ONE_4PI_EPS0*1.5;
    const double charge = 0.1;
    const double alpha = ONE_4PI_EPS0*charge*charge/k;
    System system;
    system.addParticle(1.0);
    system.addParticle(1.0);
    DrudeForce* drude = new DrudeForce();
    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
    system.addForce(drude);
    vector<Vec3> positions(2);
    positions[0] = Vec3(-1, 0, 0);
    positions[1] = Vec3(2, 0, 0);
    validateForce(system, positions, 0.5*k*3*3);
}

void CudaCalcDrudeForceKernel::copyParametersToContext(ContextImpl& context, const DrudeForce& force) {
    int numContexts = cu.getPlatformData().contexts.size();
    
    // Set the particle parameters.
    
    int startParticleIndex = cu.getContextIndex()*force.getNumParticles()/numContexts;
    int endParticleIndex = (cu.getContextIndex()+1)*force.getNumParticles()/numContexts;
    int numParticles = endParticleIndex-startParticleIndex;
    if (numParticles > 0) {
        if (particleParams == NULL || numParticles != particleParams->getSize())
            throw OpenMMException("updateParametersInContext: The number of Drude particles has changed");
        vector<float4> paramVector(numParticles);
        for (int i = 0; i < numParticles; i++) {
            int p, p1, p2, p3, p4;
            double charge, polarizability, aniso12, aniso34;
            force.getParticleParameters(startParticleIndex+i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
            double a1 = (p2 == -1 ? 1 : aniso12);
            double a2 = (p3 == -1 || p4 == -1 ? 1 : aniso34);
            double a3 = 3-a1-a2;
            double k3 = ONE_4PI_EPS0*charge*charge/(polarizability*a3);
            double k1 = ONE_4PI_EPS0*charge*charge/(polarizability*a1) - k3;
            double k2 = ONE_4PI_EPS0*charge*charge/(polarizability*a2) - k3;
            if (p2 == -1)
                k1 = 0;
            if (p3 == -1 || p4 == -1)
                k2 = 0;
            paramVector[i] = make_float4((float) k1, (float) k2, (float) k3, 0.0f);
        }
        particleParams->upload(paramVector);
    }
    
    // Set the pair parameters.
    
    int startPairIndex = cu.getContextIndex()*force.getNumScreenedPairs()/numContexts;
    int endPairIndex = (cu.getContextIndex()+1)*force.getNumScreenedPairs()/numContexts;
    int numPairs = endPairIndex-startPairIndex;
    if (numPairs > 0) {
        if (pairParams == NULL || numPairs != pairParams->getSize())
            throw OpenMMException("updateParametersInContext: The number of screened pairs has changed");
        vector<float2> paramVector(numPairs);
        for (int i = 0; i < numPairs; i++) {
            int drude1, drude2;
            double thole;
            force.getScreenedPairParameters(startPairIndex+i, drude1, drude2, thole);
            int p, p1, p2, p3, p4;
            double charge1, charge2, polarizability1, polarizability2, aniso12, aniso34;
            force.getParticleParameters(drude1, p, p1, p2, p3, p4, charge1, polarizability1, aniso12, aniso34);
            force.getParticleParameters(drude2, p, p1, p2, p3, p4, charge2, polarizability2, aniso12, aniso34);
            double screeningScale = thole/pow(polarizability1*polarizability2, 1.0/6.0);
            double energyScale = ONE_4PI_EPS0*charge1*charge2;
            paramVector[i] = make_float2((float) screeningScale, (float) energyScale);
        }
        pairParams->upload(paramVector);
    }
}

void testChangingParameters() {
    const double k = ONE_4PI_EPS0*1.5;
    const double charge = 0.1;
    const double alpha = ONE_4PI_EPS0*charge*charge/k;
    Platform& platform = Platform::getPlatformByName("OpenCL");
    
    // Create the system.
    
    System system;
    system.addParticle(1.0);
    system.addParticle(1.0);
    DrudeForce* drude = new DrudeForce();
    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
    system.addForce(drude);
    vector<Vec3> positions(2);
    positions[0] = Vec3(-1, 0, 0);
    positions[1] = Vec3(2, 0, 0);
    
    // Check the energy.
    
    VerletIntegrator integ(1.0);
    Context context(system, integ, platform);
    context.setPositions(positions);
    State state = context.getState(State::Energy);
    ASSERT_EQUAL_TOL(0.5*k*3*3, state.getPotentialEnergy(), 1e-5);
    
    // Modify the parameters.
    
    const double k2 = ONE_4PI_EPS0*2.2;
    const double charge2 = 0.3;
    const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
    drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
    drude->updateParametersInContext(context);
    state = context.getState(State::Energy);
    ASSERT_EQUAL_TOL(0.5*k2*3*3, state.getPotentialEnergy(), 1e-5);
}

void ReferenceCalcDrudeForceKernel::copyParametersToContext(ContextImpl& context, const DrudeForce& force) {
    if (force.getNumParticles() != particle.size())
        throw OpenMMException("updateParametersInContext: The number of Drude particles has changed");
    if (force.getNumScreenedPairs() != pair1.size())
        throw OpenMMException("updateParametersInContext: The number of screened pairs has changed");
    for (int i = 0; i < force.getNumParticles(); i++) {
        int p, p1, p2, p3, p4;
        force.getParticleParameters(i, p, p1, p2, p3, p4, charge[i], polarizability[i], aniso12[i], aniso34[i]);
        if (p != particle[i] || p1 != particle1[i] || p2 != particle2[i] || p3 != particle3[i] || p4 != particle4[i])
            throw OpenMMException("updateParametersInContext: A particle index has changed");
    }
    for (int i = 0; i < force.getNumScreenedPairs(); i++) {
        int p1, p2;
        force.getScreenedPairParameters(i, p1, p2, pairThole[i]);
        if (p1 != pair1[i] || p2 != pair2[i])
            throw OpenMMException("updateParametersInContext: A particle index for a screened pair has changed");
    }
}

void CudaCalcDrudeForceKernel::initialize(const System& system, const DrudeForce& force) {
    cu.setAsCurrent();
    int numContexts = cu.getPlatformData().contexts.size();
    int startParticleIndex = cu.getContextIndex()*force.getNumParticles()/numContexts;
    int endParticleIndex = (cu.getContextIndex()+1)*force.getNumParticles()/numContexts;
    int numParticles = endParticleIndex-startParticleIndex;
    if (numParticles > 0) {
        // Create the harmonic interaction .
        
        vector<vector<int> > atoms(numParticles, vector<int>(5));
        particleParams = CudaArray::create<float4>(cu, numParticles, "drudeParticleParams");
        vector<float4> paramVector(numParticles);
        for (int i = 0; i < numParticles; i++) {
            double charge, polarizability, aniso12, aniso34;
            force.getParticleParameters(startParticleIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], atoms[i][3], atoms[i][4], charge, polarizability, aniso12, aniso34);
            double a1 = (atoms[i][2] == -1 ? 1 : aniso12);
            double a2 = (atoms[i][3] == -1 || atoms[i][4] == -1 ? 1 : aniso34);
            double a3 = 3-a1-a2;
            double k3 = ONE_4PI_EPS0*charge*charge/(polarizability*a3);
            double k1 = ONE_4PI_EPS0*charge*charge/(polarizability*a1) - k3;
            double k2 = ONE_4PI_EPS0*charge*charge/(polarizability*a2) - k3;
            if (atoms[i][2] == -1) {
                atoms[i][2] = 0;
                k1 = 0;
            }
            if (atoms[i][3] == -1 || atoms[i][4] == -1) {
                atoms[i][3] = 0;
                atoms[i][4] = 0;
                k2 = 0;
            }
            paramVector[i] = make_float4((float) k1, (float) k2, (float) k3, 0.0f);
        }
        particleParams->upload(paramVector);
        map<string, string> replacements;
        replacements["PARAMS"] = cu.getBondedUtilities().addArgument(particleParams->getDevicePointer(), "float4");
        cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaDrudeKernelSources::drudeParticleForce, replacements), force.getForceGroup());
    }
    int startPairIndex = cu.getContextIndex()*force.getNumScreenedPairs()/numContexts;
    int endPairIndex = (cu.getContextIndex()+1)*force.getNumScreenedPairs()/numContexts;
    int numPairs = endPairIndex-startPairIndex;
    if (numPairs > 0) {
        // Create the screened interaction between dipole pairs.
        
        vector<vector<int> > atoms(numPairs, vector<int>(4));
        pairParams = CudaArray::create<float2>(cu, numPairs, "drudePairParams");
        vector<float2> paramVector(numPairs);
        for (int i = 0; i < numPairs; i++) {
            int drude1, drude2;
            double thole;
            force.getScreenedPairParameters(startPairIndex+i, drude1, drude2, thole);
            int p2, p3, p4;
            double charge1, charge2, polarizability1, polarizability2, aniso12, aniso34;
            force.getParticleParameters(drude1, atoms[i][0], atoms[i][1], p2, p3, p4, charge1, polarizability1, aniso12, aniso34);
            force.getParticleParameters(drude2, atoms[i][2], atoms[i][3], p2, p3, p4, charge2, polarizability2, aniso12, aniso34);
            double screeningScale = thole/pow(polarizability1*polarizability2, 1.0/6.0);
            double energyScale = ONE_4PI_EPS0*charge1*charge2;
            paramVector[i] = make_float2((float) screeningScale, (float) energyScale);
        }
        pairParams->upload(paramVector);
        map<string, string> replacements;
        replacements["PARAMS"] = cu.getBondedUtilities().addArgument(pairParams->getDevicePointer(), "float2");
        cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaDrudeKernelSources::drudePairForce, replacements), force.getForceGroup());
    }
    cu.addForce(new CudaDrudeForceInfo(force));
}

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);
}