HarmonicBondForceImpl.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) 2008-2021 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
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#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/HarmonicBondForceImpl.h"
#include "openmm/kernels.h"
#include <sstream>

using namespace OpenMM;
using namespace std;

HarmonicBondForceImpl::HarmonicBondForceImpl(const HarmonicBondForce& owner) : owner(owner) {
}

HarmonicBondForceImpl::~HarmonicBondForceImpl() {
}

void HarmonicBondForceImpl::initialize(ContextImpl& context) {
    const System& system = context.getSystem();
    for (int i = 0; i < owner.getNumBonds(); i++) {
        int particle[2];
        double length, k;
        owner.getBondParameters(i, particle[0], particle[1], length, k);
        for (int j = 0; j < 2; j++) {
            if (particle[j] < 0 || particle[j] >= system.getNumParticles()) {
                stringstream msg;
                msg << "HarmonicBondForce: Illegal particle index for a bond: ";
                msg << particle[j];
                throw OpenMMException(msg.str());
            }
        }
        if (length < 0)
            throw OpenMMException("HarmonicBondForce: bond length cannot be negative");
        if (k < 0)
            throw OpenMMException("HarmonicBondForce: force constant cannot be negative");
    }
    kernel = context.getPlatform().createKernel(CalcHarmonicBondForceKernel::Name(), context);
    kernel.getAs<CalcHarmonicBondForceKernel>().initialize(context.getSystem(), owner);
}

double HarmonicBondForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
    if ((groups&(1<<owner.getForceGroup())) != 0)
        return kernel.getAs<CalcHarmonicBondForceKernel>().execute(context, includeForces, includeEnergy);
    return 0.0;
}

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

vector<pair<int, int> > HarmonicBondForceImpl::getBondedParticles() const {
    int numBonds = owner.getNumBonds();
    vector<pair<int, int> > bonds(numBonds);
    for (int i = 0; i < numBonds; i++) {
        double length, k;
        owner.getBondParameters(i, bonds[i].first, bonds[i].second, length, k);
    }
    return bonds;
}

void HarmonicBondForceImpl::updateParametersInContext(ContextImpl& context) {
    kernel.getAs<CalcHarmonicBondForceKernel>().copyParametersToContext(context, owner);
    context.systemChanged();
}