C++ DrudeForce::getParticleParameters方法代码示例

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 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 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 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 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");
    }
}