NonbondedForceImpl.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.               *
 *                                                                            *
 * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
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 * copy of this software and associated documentation files (the "Software"), *
 * to deal in the Software without restriction, including without limitation  *
 * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
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 * Software is furnished to do so, subject to the following conditions:       *
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 * The above copyright notice and this permission notice shall be included in *
 * all copies or substantial portions of the Software.                        *
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 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
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#include "openmm/OpenMMException.h"
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/internal/NonbondedForceImpl.h"
#include "openmm/kernels.h"
#include <sstream>

using namespace OpenMM;
using std::pair;
using std::vector;
using std::set;
using std::stringstream;

NonbondedForceImpl::NonbondedForceImpl(NonbondedForce& owner) : owner(owner) {
}

NonbondedForceImpl::~NonbondedForceImpl() {
}

void NonbondedForceImpl::initialize(OpenMMContextImpl& context) {
    kernel = context.getPlatform().createKernel(CalcNonbondedForceKernel::Name(), context);

    // Check for errors in the specification of exceptions.

    System& system = context.getSystem();
    if (owner.getNumParticles() != system.getNumParticles())
        throw OpenMMException("NonbondedForce must have exactly as many particles as the System it belongs to.");
    vector<set<int> > exceptions(owner.getNumParticles());
    for (int i = 0; i < owner.getNumExceptions(); i++) {
        int particle1, particle2;
        double chargeProd, sigma, epsilon;
        owner.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
        if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
            stringstream msg;
            msg << "NonbondedForce: Illegal particle index for an exception: ";
            msg << particle1;
            throw OpenMMException(msg.str());
        }
        if (particle2 < 0 || particle2 >= owner.getNumParticles()) {
            stringstream msg;
            msg << "NonbondedForce: Illegal particle index for an exception: ";
            msg << particle2;
            throw OpenMMException(msg.str());
        }
        if (exceptions[particle1].count(particle2) > 0 || exceptions[particle2].count(particle1) > 0) {
            stringstream msg;
            msg << "NonbondedForce: Multiple exceptions are specified for particles ";
            msg << particle1;
            msg << " and ";
            msg << particle2;
            throw OpenMMException(msg.str());
        }
        exceptions[particle1].insert(particle2);
        exceptions[particle2].insert(particle1);
    }
    dynamic_cast<CalcNonbondedForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
}

void NonbondedForceImpl::calcForces(OpenMMContextImpl& context, Stream& forces) {
    dynamic_cast<CalcNonbondedForceKernel&>(kernel.getImpl()).executeForces(context);
}

double NonbondedForceImpl::calcEnergy(OpenMMContextImpl& context) {
    return dynamic_cast<CalcNonbondedForceKernel&>(kernel.getImpl()).executeEnergy(context);
}

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