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

/**
 * 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 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);
}

/**
 * Test evaluating force groups separately.
 */
void testForceGroups() {
    System system;
    system.addParticle(2.0);
    system.addParticle(2.0);
    CustomIntegrator integrator(0.01);
    integrator.addPerDofVariable("outf", 0);
    integrator.addPerDofVariable("outf1", 0);
    integrator.addPerDofVariable("outf2", 0);
    integrator.addGlobalVariable("oute", 0);
    integrator.addGlobalVariable("oute1", 0);
    integrator.addGlobalVariable("oute2", 0);
    integrator.addComputePerDof("outf", "f");
    integrator.addComputePerDof("outf1", "f1");
    integrator.addComputePerDof("outf2", "f2");
    integrator.addComputeGlobal("oute", "energy");
    integrator.addComputeGlobal("oute1", "energy1");
    integrator.addComputeGlobal("oute2", "energy2");
    HarmonicBondForce* bonds = new HarmonicBondForce();
    bonds->addBond(0, 1, 1.5, 1.1);
    bonds->setForceGroup(1);
    system.addForce(bonds);
    NonbondedForce* nb = new NonbondedForce();
    nb->addParticle(0.2, 1, 0);
    nb->addParticle(0.2, 1, 0);
    nb->setForceGroup(2);
    system.addForce(nb);
    Context context(system, integrator, platform);
    vector<Vec3> positions(2);
    positions[0] = Vec3(-1, 0, 0);
    positions[1] = Vec3(1, 0, 0);
    context.setPositions(positions);
    
    // See if the various forces are computed correctly.
    
    integrator.step(1);
    vector<Vec3> f, f1, f2;
    double e1 = 0.5*1.1*0.5*0.5;
    double e2 = 138.935456*0.2*0.2/2.0;
    integrator.getPerDofVariable(0, f);
    integrator.getPerDofVariable(1, f1);
    integrator.getPerDofVariable(2, f2);
    ASSERT_EQUAL_VEC(Vec3(1.1*0.5, 0, 0), f1[0], 1e-5);
    ASSERT_EQUAL_VEC(Vec3(-1.1*0.5, 0, 0), f1[1], 1e-5);
    ASSERT_EQUAL_VEC(Vec3(-138.935456*0.2*0.2/4.0, 0, 0), f2[0], 1e-5);
    ASSERT_EQUAL_VEC(Vec3(138.935456*0.2*0.2/4.0, 0, 0), f2[1], 1e-5);
    ASSERT_EQUAL_VEC(f1[0]+f2[0], f[0], 1e-5);
    ASSERT_EQUAL_VEC(f1[1]+f2[1], f[1], 1e-5);
    ASSERT_EQUAL_TOL(e1, integrator.getGlobalVariable(1), 1e-5);
    ASSERT_EQUAL_TOL(e2, integrator.getGlobalVariable(2), 1e-5);
    ASSERT_EQUAL_TOL(e1+e2, integrator.getGlobalVariable(0), 1e-5);
    
    // Make sure they also match the values returned by the Context.
    
    State s = context.getState(State::Forces | State::Energy, false);
    State s1 = context.getState(State::Forces | State::Energy, false, 2);
    State s2 = context.getState(State::Forces | State::Energy, false, 4);
    vector<Vec3> c, c1, c2;
    c = context.getState(State::Forces, false).getForces();
    c1 = context.getState(State::Forces, false, 2).getForces();
    c2 = context.getState(State::Forces, false, 4).getForces();
    ASSERT_EQUAL_VEC(f[0], c[0], 1e-5);
    ASSERT_EQUAL_VEC(f[1], c[1], 1e-5);
    ASSERT_EQUAL_VEC(f1[0], c1[0], 1e-5);
    ASSERT_EQUAL_VEC(f1[1], c1[1], 1e-5);
    ASSERT_EQUAL_VEC(f2[0], c2[0], 1e-5);
    ASSERT_EQUAL_VEC(f2[1], c2[1], 1e-5);
    ASSERT_EQUAL_TOL(s.getPotentialEnergy(), integrator.getGlobalVariable(0), 1e-5);
    ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), integrator.getGlobalVariable(1), 1e-5);
    ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), integrator.getGlobalVariable(2), 1e-5);
}

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.........