C++ DrudeForce::addParticle方法代码示例

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 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 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 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 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);
}