DrudeLangevinIntegrator.cpp

/* -------------------------------------------------------------------------- *
 *                                   OpenMM                                   *
 * -------------------------------------------------------------------------- *
 * This is part of the OpenMM molecular simulation toolkit originating from   *
 * Simbios, the NIH National Center for Physics-Based Simulation of           *
 * Biological Structures at Stanford, funded under the NIH Roadmap for        *
 * Medical Research, grant U54 GM072970. See https://simtk.org.               *
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 * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
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#include "sfmt/SFMT.h"
#include "SimTKOpenMMRealType.h"
#include "openmm/DrudeLangevinIntegrator.h"
#include "openmm/Context.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/DrudeKernels.h"
#include <cmath>
#include <ctime>
#include <set>
#include <string>

using namespace OpenMM;
using std::string;
using std::vector;

DrudeLangevinIntegrator::DrudeLangevinIntegrator(double temperature, double frictionCoeff, double drudeTemperature, double drudeFrictionCoeff, double stepSize) {
    setTemperature(temperature);
    setFriction(frictionCoeff);
    setDrudeTemperature(drudeTemperature);
    setDrudeFriction(drudeFrictionCoeff);
    setMaxDrudeDistance(0);
    setStepSize(stepSize);
    setConstraintTolerance(1e-5);
    setRandomNumberSeed(0);
}

double DrudeLangevinIntegrator::getMaxDrudeDistance() const {
    return maxDrudeDistance;
}

void DrudeLangevinIntegrator::setMaxDrudeDistance(double distance) {
    if (distance < 0)
        throw OpenMMException("setMaxDrudeDistance: Distance cannot be negative");
    maxDrudeDistance = distance;
}

void DrudeLangevinIntegrator::initialize(ContextImpl& contextRef) {
    if (owner != NULL && &contextRef.getOwner() != owner)
        throw OpenMMException("This Integrator is already bound to a context");
    const DrudeForce* force = NULL;
    const System& system = contextRef.getSystem();
    for (int i = 0; i < system.getNumForces(); i++)
        if (dynamic_cast<const DrudeForce*>(&system.getForce(i)) != NULL) {
            if (force == NULL)
                force = dynamic_cast<const DrudeForce*>(&system.getForce(i));
            else
                throw OpenMMException("The System contains multiple DrudeForces");
        }
    if (force == NULL)
        throw OpenMMException("The System does not contain a DrudeForce");
    context = &contextRef;
    owner = &contextRef.getOwner();
    kernel = context->getPlatform().createKernel(IntegrateDrudeLangevinStepKernel::Name(), contextRef);
    kernel.getAs<IntegrateDrudeLangevinStepKernel>().initialize(contextRef.getSystem(), *this, *force);
}

void DrudeLangevinIntegrator::cleanup() {
    kernel = Kernel();
}

void DrudeLangevinIntegrator::stateChanged(State::DataType changed) {
}

vector<string> DrudeLangevinIntegrator::getKernelNames() {
    std::vector<std::string> names;
    names.push_back(IntegrateDrudeLangevinStepKernel::Name());
    return names;
}

double DrudeLangevinIntegrator::computeKineticEnergy() {
    return kernel.getAs<IntegrateDrudeLangevinStepKernel>().computeKineticEnergy(*context, *this);
}

std::vector<Vec3> DrudeLangevinIntegrator::getVelocitiesForTemperature(const System &system, double temperature, int randomSeed) const {
    // Find the underlying Drude force object
    const DrudeForce* drudeForce = NULL;
    for (int i = 0; i < system.getNumForces(); i++)
        if (dynamic_cast<const DrudeForce*>(&system.getForce(i)) != NULL) {
            if (drudeForce == NULL)
                drudeForce = dynamic_cast<const DrudeForce*>(&system.getForce(i));
            else
                throw OpenMMException("The System contains multiple DrudeForces");
        }
    if (drudeForce == NULL)
        throw OpenMMException("The System does not contain a DrudeForce");

    // Figure out which particles are individual and which are Drude pairs
    std::set<int> particles;
    std::vector<std::pair<int, int>> pairParticles;
    for (int i = 0; i < system.getNumParticles(); i++) {
        particles.insert(i);
    }
    for (int i = 0; i < drudeForce->getNumParticles(); i++) {
        int p, p1, p2, p3, p4;
        double charge, polarizability, aniso12, aniso34;
        drudeForce->getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
        particles.erase(p);
        particles.erase(p1);
        pairParticles.emplace_back(p, p1);
    }
    std::vector<int> normalParticles(particles.begin(), particles.end());

    // Generate the list of Gaussian random numbers.
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(randomSeed, sfmt);
    std::vector<double> randoms;
    while (randoms.size() < system.getNumParticles()*3) {
        double x, y, r2;
        do {
            x = 2.0*genrand_real2(sfmt)-1.0;
            y = 2.0*genrand_real2(sfmt)-1.0;
            r2 = x*x + y*y;
        } while (r2 >= 1.0 || r2 == 0.0);
        double multiplier = sqrt((-2.0*std::log(r2))/r2);
        randoms.push_back(x*multiplier);
        randoms.push_back(y*multiplier);
    }

    // Assign the velocities.
    std::vector<Vec3> velocities(system.getNumParticles(), Vec3());
    int nextRandom = 0;
    // First the indivitual atoms
    for (const auto &atom : normalParticles ) {
        double mass = system.getParticleMass(atom);
        if (mass != 0) {
            double velocityScale = sqrt(BOLTZ*temperature/mass);
            velocities[atom] = Vec3(randoms[nextRandom++], randoms[nextRandom++], randoms[nextRandom++])*velocityScale;
        }
    }
    // Now the particle-Drude pairs
    for (const auto &pair : pairParticles ) {
        const auto atom1 = pair.first;
        const auto atom2 = pair.second;
        double mass1 = system.getParticleMass(atom1);
        double mass2 = system.getParticleMass(atom2);
        if (mass1 != 0 && mass2 != 0) {
            double invMass = 1.0 / (mass1 + mass2);
            double redMass = mass1 * mass2 * invMass;
            double fracM1 = mass1 * invMass;
            double fracM2 = mass2 * invMass;
            Vec3 comVelocity = Vec3(randoms[nextRandom++], randoms[nextRandom++], randoms[nextRandom++])*sqrt(BOLTZ*temperature*invMass);
            Vec3 relVelocity = Vec3(randoms[nextRandom++], randoms[nextRandom++], randoms[nextRandom++])*sqrt(BOLTZ*drudeTemperature/redMass);
            velocities[atom1] = comVelocity - fracM2 * relVelocity;
            velocities[atom2] = comVelocity + fracM1 * relVelocity;
        }
    }
    return velocities;
}

void DrudeLangevinIntegrator::step(int steps) {
    if (context == NULL)
        throw OpenMMException("This Integrator is not bound to a context!");    
    for (int i = 0; i < steps; ++i) {
        context->updateContextState();
        context->calcForcesAndEnergy(true, false);
        kernel.getAs<IntegrateDrudeLangevinStepKernel>().execute(*context, *this);
    }
}