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

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);
    }
}

void testLongRangeCorrection() {
    // Create a box of particles.

    int gridSize = 5;
    int numParticles = gridSize*gridSize*gridSize;
    double boxSize = gridSize*0.7;
    double cutoff = boxSize/3;
    System standardSystem;
    System customSystem;
    VerletIntegrator integrator1(0.01);
    VerletIntegrator integrator2(0.01);
    NonbondedForce* standardNonbonded = new NonbondedForce();
    CustomNonbondedForce* customNonbonded = new CustomNonbondedForce("4*eps*((sigma/r)^12-(sigma/r)^6); sigma=0.5*(sigma1+sigma2); eps=sqrt(eps1*eps2)");
    customNonbonded->addPerParticleParameter("sigma");
    customNonbonded->addPerParticleParameter("eps");
    vector<Vec3> positions(numParticles);
    int index = 0;
    vector<double> params1(2);
    params1[0] = 1.1;
    params1[1] = 0.5;
    vector<double> params2(2);
    params2[0] = 1;
    params2[1] = 1;
    for (int i = 0; i < gridSize; i++)
        for (int j = 0; j < gridSize; j++)
            for (int k = 0; k < gridSize; k++) {
                standardSystem.addParticle(1.0);
                customSystem.addParticle(1.0);
                if (index%2 == 0) {
                    standardNonbonded->addParticle(0, params1[0], params1[1]);
                    customNonbonded->addParticle(params1);
                }
                else {
                    standardNonbonded->addParticle(0, params2[0], params2[1]);
                    customNonbonded->addParticle(params2);
                }
                positions[index] = Vec3(i*boxSize/gridSize, j*boxSize/gridSize, k*boxSize/gridSize);
                index++;
            }
    standardNonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    customNonbonded->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
    standardNonbonded->setCutoffDistance(cutoff);
    customNonbonded->setCutoffDistance(cutoff);
    standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    customSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    standardNonbonded->setUseDispersionCorrection(true);
    customNonbonded->setUseLongRangeCorrection(true);
    standardNonbonded->setUseSwitchingFunction(true);
    customNonbonded->setUseSwitchingFunction(true);
    standardNonbonded->setSwitchingDistance(0.8*cutoff);
    customNonbonded->setSwitchingDistance(0.8*cutoff);
    standardSystem.addForce(standardNonbonded);
    customSystem.addForce(customNonbonded);

    // Compute the correction for the standard force.

    Context context1(standardSystem, integrator1, platform);
    context1.setPositions(positions);
    double standardEnergy1 = context1.getState(State::Energy).getPotentialEnergy();
    standardNonbonded->setUseDispersionCorrection(false);
    context1.reinitialize();
    context1.setPositions(positions);
    double standardEnergy2 = context1.getState(State::Energy).getPotentialEnergy();

    // Compute the correction for the custom force.

    Context context2(customSystem, integrator2, platform);
    context2.setPositions(positions);
    double customEnergy1 = context2.getState(State::Energy).getPotentialEnergy();
    customNonbonded->setUseLongRangeCorrection(false);
    context2.reinitialize();
    context2.setPositions(positions);
    double customEnergy2 = context2.getState(State::Energy).getPotentialEnergy();

    // See if they agree.

    ASSERT_EQUAL_TOL(standardEnergy1-standardEnergy2, customEnergy1-customEnergy2, 1e-4);
}

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 testDispersionCorrection() {
    // Create a box full of identical particles.

    int gridSize = 5;
    int numParticles = gridSize*gridSize*gridSize;
    double boxSize = gridSize*0.7;
    double cutoff = boxSize/3;
    System system;
    VerletIntegrator integrator(0.01);
    NonbondedForce* nonbonded = new NonbondedForce();
    vector<Vec3> positions(numParticles);
    int index = 0;
    for (int i = 0; i < gridSize; i++)
        for (int j = 0; j < gridSize; j++)
            for (int k = 0; k < gridSize; k++) {
                system.addParticle(1.0);
                nonbonded->addParticle(0, 1.1, 0.5);
                positions[index] = Vec3(i*boxSize/gridSize, j*boxSize/gridSize, k*boxSize/gridSize);
                index++;
            }
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    nonbonded->setCutoffDistance(cutoff);
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    system.addForce(nonbonded);

    // See if the correction has the correct value.

    Context context(system, integrator, platform);
    context.setPositions(positions);
    double energy1 = context.getState(State::Energy).getPotentialEnergy();
    nonbonded->setUseDispersionCorrection(false);
    context.reinitialize();
    context.setPositions(positions);
    double energy2 = context.getState(State::Energy).getPotentialEnergy();
    double term1 = (0.5*pow(1.1, 12)/pow(cutoff, 9))/9;
    double term2 = (0.5*pow(1.1, 6)/pow(cutoff, 3))/3;
    double expected = 8*M_PI*numParticles*numParticles*(term1-term2)/(boxSize*boxSize*boxSize);
    ASSERT_EQUAL_TOL(expected, energy1-energy2, 1e-4);

    // Now modify half the particles to be different, and see if it is still correct.

    int numType2 = 0;
    for (int i = 0; i < numParticles; i += 2) {
        nonbonded->setParticleParameters(i, 0, 1, 1);
        numType2++;
    }
    int numType1 = numParticles-numType2;
    nonbonded->updateParametersInContext(context);
    energy2 = context.getState(State::Energy).getPotentialEnergy();
    nonbonded->setUseDispersionCorrection(true);
    context.reinitialize();
    context.setPositions(positions);
    energy1 = context.getState(State::Energy).getPotentialEnergy();
    term1 = ((numType1*(numType1+1))/2)*(0.5*pow(1.1, 12)/pow(cutoff, 9))/9;
    term2 = ((numType1*(numType1+1))/2)*(0.5*pow(1.1, 6)/pow(cutoff, 3))/3;
    term1 += ((numType2*(numType2+1))/2)*(1*pow(1.0, 12)/pow(cutoff, 9))/9;
    term2 += ((numType2*(numType2+1))/2)*(1*pow(1.0, 6)/pow(cutoff, 3))/3;
    double combinedSigma = 0.5*(1+1.1);
    double combinedEpsilon = sqrt(1*0.5);
    term1 += (numType1*numType2)*(combinedEpsilon*pow(combinedSigma, 12)/pow(cutoff, 9))/9;
    term2 += (numType1*numType2)*(combinedEpsilon*pow(combinedSigma, 6)/pow(cutoff, 3))/3;
    term1 /= (numParticles*(numParticles+1))/2;
    term2 /= (numParticles*(numParticles+1))/2;
    expected = 8*M_PI*numParticles*numParticles*(term1-term2)/(boxSize*boxSize*boxSize);
    ASSERT_EQUAL_TOL(expected, energy1-energy2, 1e-4);
}