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

void testWaterSystem() {
    ReferencePlatform platform;
    System system;
    static int numParticles = 648;
    const double boxSize = 1.86206;

    for (int i = 0 ; i < numParticles ; i++)
    {
       system.addParticle(1.0);
    }
    VerletIntegrator integrator(0.01);
    NonbondedForce* nonbonded = new NonbondedForce();
    for (int i = 0 ; i < numParticles/3 ; i++)
    {
      nonbonded->addParticle(-0.82, 1, 0);
      nonbonded->addParticle(0.41, 1, 0);
      nonbonded->addParticle(0.41, 1, 0);
    }
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    const double cutoff = 0.8;
    nonbonded->setCutoffDistance(cutoff);
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    nonbonded->setEwaldErrorTolerance(EWALD_TOL);
    system.addForce(nonbonded);
    Context context(system, integrator, platform);
    vector<Vec3> positions(numParticles);
    #include "water.dat"
    context.setPositions(positions);
    State state1 = context.getState(State::Forces | State::Energy);
    const vector<Vec3>& forces = state1.getForces();

// Take a small step in the direction of the energy gradient.
    
    double norm = 0.0;
    for (int i = 0; i < numParticles; ++i) {
        Vec3 f = state1.getForces()[i];
        norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
    }


    norm = std::sqrt(norm);
    const double delta = 1e-3;
    double step = delta/norm;
    for (int i = 0; i < numParticles; ++i) {
        Vec3 p = positions[i];
        Vec3 f = state1.getForces()[i];
        positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
    }
    context.setPositions(positions);
    
    // See whether the potential energy changed by the expected amount.
    
    nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
    State state2 = context.getState(State::Energy);
    ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state1.getPotentialEnergy())/delta, 0.01)


}

void testCutoffAndPeriodic() {
    ReferencePlatform platform;
    System system;
    system.addParticle(1.0);
    system.addParticle(1.0);
    LangevinIntegrator integrator(0, 0.1, 0.01);
    GBSAOBCForce* gbsa = new GBSAOBCForce();
    NonbondedForce* nonbonded = new NonbondedForce();
    gbsa->addParticle(-1, 0.15, 1);
    nonbonded->addParticle(-1, 1, 0);
    gbsa->addParticle(1, 0.15, 1);
    nonbonded->addParticle(1, 1, 0);
    const double cutoffDistance = 3.0;
    const double boxSize = 10.0;
    nonbonded->setCutoffDistance(cutoffDistance);
    gbsa->setCutoffDistance(cutoffDistance);
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    system.addForce(gbsa);
    system.addForce(nonbonded);
    vector<Vec3> positions(2);
    positions[0] = Vec3(0, 0, 0);
    positions[1] = Vec3(2, 0, 0);

    // Calculate the forces for both cutoff and periodic with two different atom positions.

    nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
    gbsa->setNonbondedMethod(GBSAOBCForce::CutoffNonPeriodic);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    State state1 = context.getState(State::Forces);
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    gbsa->setNonbondedMethod(GBSAOBCForce::CutoffPeriodic);
    context.reinitialize();
    context.setPositions(positions);
    State state2 = context.getState(State::Forces);
    positions[1][0]+= boxSize;
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
    gbsa->setNonbondedMethod(GBSAOBCForce::CutoffNonPeriodic);
    context.reinitialize();
    context.setPositions(positions);
    State state3 = context.getState(State::Forces);
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    gbsa->setNonbondedMethod(GBSAOBCForce::CutoffPeriodic);
    context.reinitialize();
    context.setPositions(positions);
    State state4 = context.getState(State::Forces);

    // All forces should be identical, exception state3 which should be zero.

    ASSERT_EQUAL_VEC(state1.getForces()[0], state2.getForces()[0], 0.01);
    ASSERT_EQUAL_VEC(state1.getForces()[1], state2.getForces()[1], 0.01);
    ASSERT_EQUAL_VEC(state1.getForces()[0], state4.getForces()[0], 0.01);
    ASSERT_EQUAL_VEC(state1.getForces()[1], state4.getForces()[1], 0.01);
    ASSERT_EQUAL_VEC(state3.getForces()[0], Vec3(0, 0, 0), 0.01);
    ASSERT_EQUAL_VEC(state3.getForces()[1], Vec3(0, 0, 0), 0.01);
}

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 testCutoff() {
    System system;
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(1.0);
    VerletIntegrator integrator(0.01);
    NonbondedForce* forceField = new NonbondedForce();
    forceField->addParticle(1.0, 1, 0);
    forceField->addParticle(1.0, 1, 0);
    forceField->addParticle(1.0, 1, 0);
    forceField->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
    const double cutoff = 2.9;
    forceField->setCutoffDistance(cutoff);
    const double eps = 50.0;
    forceField->setReactionFieldDielectric(eps);
    system.addForce(forceField);
    Context context(system, integrator, platform);
    vector<Vec3> positions(3);
    positions[0] = Vec3(0, 0, 0);
    positions[1] = Vec3(0, 2, 0);
    positions[2] = Vec3(0, 3, 0);
    context.setPositions(positions);
    State state = context.getState(State::Forces | State::Energy);
    const vector<Vec3>& forces = state.getForces();
    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 force1 = ONE_4PI_EPS0*(1.0)*(0.25-2.0*krf*2.0);
    const double force2 = ONE_4PI_EPS0*(1.0)*(1.0-2.0*krf*1.0);
    ASSERT_EQUAL_VEC(Vec3(0, -force1, 0), forces[0], TOL);
    ASSERT_EQUAL_VEC(Vec3(0, force1-force2, 0), forces[1], TOL);
    ASSERT_EQUAL_VEC(Vec3(0, force2, 0), forces[2], TOL);
    const double energy1 = ONE_4PI_EPS0*(1.0)*(0.5+krf*4.0-crf);
    const double energy2 = ONE_4PI_EPS0*(1.0)*(1.0+krf*1.0-crf);
    ASSERT_EQUAL_TOL(energy1+energy2, state.getPotentialEnergy(), TOL);
}

void testEwald2Ions() {
    System system;
    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->setNonbondedMethod(NonbondedForce::Ewald);
    const double cutoff = 2.0;
    nonbonded->setCutoffDistance(cutoff);
    nonbonded->setEwaldErrorTolerance(TOL);
    system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(0, 6, 0), Vec3(0, 0, 6));
    system.addForce(nonbonded);
    Context context(system, integrator, platform);
    vector<Vec3> positions(2);
    positions[0] = Vec3(3.048000,2.764000,3.156000);
    positions[1] = Vec3(2.809000,2.888000,2.571000);
    context.setPositions(positions);
    State state = context.getState(State::Forces | State::Energy);
    const vector<Vec3>& forces = state.getForces();

    ASSERT_EQUAL_VEC(Vec3(-123.711,  64.1877, -302.716), forces[0], 10*TOL);
    ASSERT_EQUAL_VEC(Vec3( 123.711, -64.1877,  302.716), forces[1], 10*TOL);
    ASSERT_EQUAL_TOL(-217.276, state.getPotentialEnergy(), 0.01/*10*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);
}

void testLargeSystem() {
    const int numMolecules = 50;
    const int numParticles = numMolecules*2;
    const double cutoff = 2.0;
    const double boxSize = 5.0;
    const double tolerance = 5;
    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    NonbondedForce* nonbonded = new NonbondedForce();
    nonbonded->setCutoffDistance(cutoff);
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    system.addForce(nonbonded);

    // 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(-1.0, 0.2, 0.2);
        nonbonded->addParticle(1.0, 0.2, 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);
    }

    // Minimize it and verify that the energy has decreased.
    
    ReferencePlatform platform;
    VerletIntegrator integrator(0.01);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    State initialState = context.getState(State::Forces | State::Energy);
    LocalEnergyMinimizer::minimize(context, tolerance);
    State finalState = context.getState(State::Forces | State::Energy | State::Positions);
    ASSERT(finalState.getPotentialEnergy() < initialState.getPotentialEnergy());

    // Compute the force magnitude, subtracting off any component parallel to a constraint, and
    // check that it satisfies the requested tolerance.

    double forceNorm = 0.0;
    for (int i = 0; i < numParticles; i += 2) {
        Vec3 dir = finalState.getPositions()[i+1]-finalState.getPositions()[i];
        double distance = sqrt(dir.dot(dir));
        dir *= 1.0/distance;
        Vec3 f = finalState.getForces()[i];
        f -= dir*dir.dot(f);
        forceNorm += f.dot(f);
        f = finalState.getForces()[i+1];
        f -= dir*dir.dot(f);
        forceNorm += f.dot(f);
    }
    forceNorm = sqrt(forceNorm/(4*numMolecules));
    ASSERT(forceNorm < 3*tolerance);
}

void testArgonBox() {
    const int gridSize = 8;
    const double mass = 40.0;            // Ar atomic mass
    const double temp = 120.0;           // K
    const double epsilon = BOLTZ * temp; // L-J well depth for Ar
    const double sigma = 0.34;           // L-J size for Ar in nm
    const double density = 0.8;          // atoms / sigma^3
    double cellSize = sigma / pow(density, 0.333);
    double boxSize = gridSize * cellSize;
    double cutoff = 2.0 * sigma;

    // Create a box of argon atoms.
    
    System system;
    NonbondedForce* nonbonded = new NonbondedForce();
    vector<Vec3> positions;
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    const Vec3 half(0.5, 0.5, 0.5);
    for (int i = 0; i < gridSize; i++) {
        for (int j = 0; j < gridSize; j++) {
            for (int k = 0; k < gridSize; k++) {
                system.addParticle(mass);
                nonbonded->addParticle(0, sigma, epsilon);
                positions.push_back((Vec3(i, j, k) + half + Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt))*0.1) * cellSize);
            }
        }
    }

    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    nonbonded->setCutoffDistance(cutoff);
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    system.addForce(nonbonded);

    VariableVerletIntegrator integrator(1e-5);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    context.setVelocitiesToTemperature(temp);

    // Equilibrate.
    
    integrator.stepTo(1.0);

    // Simulate it and see whether energy remains constant.
    
    State state0 = context.getState(State::Energy);
    double initialEnergy = state0.getKineticEnergy() + state0.getPotentialEnergy();
    for (int i = 0; i < 20; i++) {
        double t = 1.0 + 0.05*(i+1);
        integrator.stepTo(t);
        State state = context.getState(State::Energy);
        double energy = state.getKineticEnergy() + state.getPotentialEnergy();
        ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
    }
}

void testSwitchingFunction(NonbondedForce::NonbondedMethod method) {
    ReferencePlatform platform;
    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(0, 6, 0), Vec3(0, 0, 6));
    system.addParticle(1.0);
    system.addParticle(1.0);
    VerletIntegrator integrator(0.01);
    NonbondedForce* nonbonded = new NonbondedForce();
    nonbonded->addParticle(0, 1.2, 1);
    nonbonded->addParticle(0, 1.4, 2);
    nonbonded->setNonbondedMethod(method);
    nonbonded->setCutoffDistance(2.0);
    nonbonded->setUseSwitchingFunction(true);
    nonbonded->setSwitchingDistance(1.5);
    nonbonded->setUseDispersionCorrection(false);
    system.addForce(nonbonded);
    Context context(system, integrator, platform);
    vector<Vec3> positions(2);
    positions[0] = Vec3(0, 0, 0);
    double eps = SQRT_TWO;
    
    // Compute the interaction at various distances.
    
    for (double r = 1.0; r < 2.5; r += 0.1) {
        positions[1] = Vec3(r, 0, 0);
        context.setPositions(positions);
        State state = context.getState(State::Forces | State::Energy);
        
        // See if the energy is correct.
        
        double x = 1.3/r;
        double expectedEnergy = 4.0*eps*(std::pow(x, 12.0)-std::pow(x, 6.0));
        double switchValue;
        if (r <= 1.5)
            switchValue = 1;
        else if (r >= 2.0)
            switchValue = 0;
        else {
            double t = (r-1.5)/0.5;
            switchValue = 1+t*t*t*(-10+t*(15-t*6));
        }
        ASSERT_EQUAL_TOL(switchValue*expectedEnergy, state.getPotentialEnergy(), TOL);
        
        // See if the force is the gradient of the energy.
        
        double delta = 1e-3;
        positions[1] = Vec3(r-delta, 0, 0);
        context.setPositions(positions);
        double e1 = context.getState(State::Energy).getPotentialEnergy();
        positions[1] = Vec3(r+delta, 0, 0);
        context.setPositions(positions);
        double e2 = context.getState(State::Energy).getPotentialEnergy();
        ASSERT_EQUAL_TOL((e2-e1)/(2*delta), state.getForces()[0][0], 1e-3);
    }
}

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);
    }
}

/**
 * Test getting and setting per-DOF variables.
 */
void testPerDofVariables() {
    const int numParticles = 200;
    const double boxSize = 10;
    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    NonbondedForce* nb = new NonbondedForce();
    system.addForce(nb);
    nb->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
    vector<Vec3> positions(numParticles);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    for (int i = 0; i < numParticles; i++) {
        system.addParticle(1.5);
        nb->addParticle(i%2 == 0 ? 1 : -1, 0.1, 1);
        bool close = true;
        while (close) {
            positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
            close = false;
            for (int j = 0; j < i; ++j) {
                Vec3 delta = positions[i]-positions[j];
                if (delta.dot(delta) < 0.1)
                    close = true;
            }
        }
    }
    CustomIntegrator integrator(0.01);
    integrator.addPerDofVariable("temp", 0);
    integrator.addPerDofVariable("pos", 0);
    integrator.addComputePerDof("v", "v+dt*f/m");
    integrator.addComputePerDof("x", "x+dt*v");
    integrator.addComputePerDof("pos", "x");
    Context context(system, integrator, platform);
    context.setPositions(positions);
    vector<Vec3> initialValues(numParticles);
    for (int i = 0; i < numParticles; i++)
        initialValues[i] = Vec3(i+0.1, i+0.2, i+0.3);
    integrator.setPerDofVariable(0, initialValues);
    
    // Run a simulation, then query per-DOF values and see if they are correct.
    
    vector<Vec3> values;
    context.getState(State::Forces); // Cause atom reordering to happen before the first step
    for (int i = 0; i < 200; ++i) {
        integrator.step(1);
        State state = context.getState(State::Positions);
        integrator.getPerDofVariable(0, values);
        for (int j = 0; j < numParticles; j++)
            ASSERT_EQUAL_VEC(initialValues[j], values[j], 1e-5);
        integrator.getPerDofVariable(1, values);
        for (int j = 0; j < numParticles; j++)
            ASSERT_EQUAL_VEC(state.getPositions()[j], values[j], 1e-5);
    }
}

/**
 * Test a multiple time step r-RESPA integrator.
 */
void testRespa() {
    const int numParticles = 8;
    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
    CustomIntegrator integrator(0.002);
    integrator.addComputePerDof("v", "v+0.5*dt*f1/m");
    for (int i = 0; i < 2; i++) {
        integrator.addComputePerDof("v", "v+0.5*(dt/2)*f0/m");
        integrator.addComputePerDof("x", "x+(dt/2)*v");
        integrator.addComputePerDof("v", "v+0.5*(dt/2)*f0/m");
    }
    integrator.addComputePerDof("v", "v+0.5*dt*f1/m");
    HarmonicBondForce* bonds = new HarmonicBondForce();
    for (int i = 0; i < numParticles-2; i++)
        bonds->addBond(i, i+1, 1.0, 0.5);
    system.addForce(bonds);
    NonbondedForce* nb = new NonbondedForce();
    nb->setCutoffDistance(2.0);
    nb->setNonbondedMethod(NonbondedForce::Ewald);
    for (int i = 0; i < numParticles; ++i) {
        system.addParticle(i%2 == 0 ? 5.0 : 10.0);
        nb->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
    }
    nb->setForceGroup(1);
    nb->setReciprocalSpaceForceGroup(0);
    system.addForce(nb);
    Context context(system, integrator, platform);
    vector<Vec3> positions(numParticles);
    vector<Vec3> velocities(numParticles);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    for (int i = 0; i < numParticles; ++i) {
        positions[i] = Vec3(i/2, (i+1)/2, 0);
        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
    }
    context.setPositions(positions);
    context.setVelocities(velocities);
    
    // Simulate it and monitor energy conservations.
    
    double initialEnergy = 0.0;
    for (int i = 0; i < 1000; ++i) {
        State state = context.getState(State::Energy);
        double energy = state.getKineticEnergy()+state.getPotentialEnergy();
        if (i == 1)
            initialEnergy = energy;
        else if (i > 1)
            ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05);
        integrator.step(2);
    }
}

void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
    // Create a cloud of random point charges.

    const int numParticles = 51;
    const double boxWidth = 5.0;
    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
    NonbondedForce* force = new NonbondedForce();
    system.addForce(force);
    vector<Vec3> positions(numParticles);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);

    for (int i = 0; i < numParticles; i++) {
        system.addParticle(1.0);
        force->addParticle(-1.0+i*2.0/(numParticles-1), 1.0, 0.0);
        positions[i] = Vec3(boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt));
    }
    force->setNonbondedMethod(method);
    ReferencePlatform platform;

    // For various values of the cutoff and error tolerance, see if the actual error is reasonable.

    for (double cutoff = 1.0; cutoff < boxWidth/2; cutoff *= 1.2) {
        force->setCutoffDistance(cutoff);
        vector<Vec3> refForces;
        double norm = 0.0;
        for (double tol = 5e-5; tol < 1e-3; tol *= 2.0) {
            force->setEwaldErrorTolerance(tol);
            VerletIntegrator integrator(0.01);
            Context context(system, integrator, platform);
            context.setPositions(positions);
            State state = context.getState(State::Forces);
            if (refForces.size() == 0) {
                refForces = state.getForces();
                for (int i = 0; i < numParticles; i++)
                    norm += refForces[i].dot(refForces[i]);
                norm = sqrt(norm);
            }
            else {
                double diff = 0.0;
                for (int i = 0; i < numParticles; i++) {
                    Vec3 delta = refForces[i]-state.getForces()[i];
                    diff += delta.dot(delta);
                }
                diff = sqrt(diff)/norm;
                ASSERT(diff < 2*tol);
            }
        }
    }
}

void testTruncatedOctahedron() {
    const int numMolecules = 50;
    const int numParticles = numMolecules*2;
    const float cutoff = 2.0;
    Vec3 a(6.7929, 0, 0);
    Vec3 b(-2.264163559406279, 6.404455775962287, 0);
    Vec3 c(-2.264163559406279, -3.2019384603140684, 5.54658849047036);

    System system;
    system.setDefaultPeriodicBoxVectors(a, b, c);
    NonbondedForce* force = new NonbondedForce();
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    vector<Vec3> positions(numParticles);

    force->setCutoffDistance(cutoff);
    force->setNonbondedMethod(NonbondedForce::CutoffPeriodic);

    for (int i = 0; i < numMolecules; i++) {
        system.addParticle(1.0);
        system.addParticle(1.0);
        force->addParticle(-1, 0.2, 0.2);
        force->addParticle(1, 0.2, 0.2);
        positions[2*i] = a*(5*genrand_real2(sfmt)-2) + b*(5*genrand_real2(sfmt)-2) + c*(5*genrand_real2(sfmt)-2);
        positions[2*i+1] = positions[2*i] + Vec3(1.0, 0.0, 0.0);
        system.addConstraint(2*i, 2*i+1, 1.0);
    }
    system.addForce(force);

    VerletIntegrator integrator(0.01);
    Context context(system, integrator, Platform::getPlatformByName("Reference"));
    context.setPositions(positions);
    State initialState = context.getState(State::Positions | State::Energy, true);
    for (int i = 0; i < numMolecules; i++) {
        Vec3 center = (initialState.getPositions()[2*i]+initialState.getPositions()[2*i+1])*0.5;
        ASSERT(center[0] >= 0.0);
        ASSERT(center[1] >= 0.0);
        ASSERT(center[2] >= 0.0);
        ASSERT(center[0] <= a[0]);
        ASSERT(center[1] <= b[1]);
        ASSERT(center[2] <= c[2]);
    }
    double initialEnergy = initialState.getPotentialEnergy();

    context.setState(initialState);
    State finalState = context.getState(State::Positions | State::Energy, true);
    double finalEnergy = finalState.getPotentialEnergy();

    ASSERT_EQUAL_TOL(initialEnergy, finalEnergy, 1e-4);
}