AmoebaReferenceKernels.cpp 54.2 KB
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/* -------------------------------------------------------------------------- *
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 *                               OpenMMAmoeba                                 *
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 * -------------------------------------------------------------------------- *
 * 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:                                                                   *
 * Contributors:                                                              *
 *                                                                            *
 * This program is free software: you can redistribute it and/or modify       *
 * it under the terms of the GNU Lesser General Public License as published   *
 * by the Free Software Foundation, either version 3 of the License, or       *
 * (at your option) any later version.                                        *
 *                                                                            *
 * This program is distributed in the hope that it will be useful,            *
 * but WITHOUT ANY WARRANTY; without even the implied warranty of             *
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              *
 * GNU Lesser General Public License for more details.                        *
 *                                                                            *
 * You should have received a copy of the GNU Lesser General Public License   *
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
 * -------------------------------------------------------------------------- */

#include "AmoebaReferenceKernels.h"
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#include "AmoebaReferenceBondForce.h"
#include "AmoebaReferenceAngleForce.h"
#include "AmoebaReferenceInPlaneAngleForce.h"
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#include "AmoebaReferencePiTorsionForce.h"
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#include "AmoebaReferenceStretchBendForce.h"
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#include "AmoebaReferenceOutOfPlaneBendForce.h"
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#include "AmoebaReferenceTorsionTorsionForce.h"
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#include "AmoebaReferenceVdwForce.h"
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#include "AmoebaReferenceWcaDispersionForce.h"
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#include "AmoebaReferenceGeneralizedKirkwoodForce.h"
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#include "openmm/internal/AmoebaTorsionTorsionForceImpl.h"
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#include "openmm/internal/AmoebaWcaDispersionForceImpl.h"
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#include "ReferencePlatform.h"
#include "openmm/internal/ContextImpl.h"
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#include "openmm/AmoebaMultipoleForce.h"
#include "openmm/internal/AmoebaMultipoleForceImpl.h"
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#include "openmm/internal/AmoebaVdwForceImpl.h"
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#include "openmm/internal/AmoebaGeneralizedKirkwoodForceImpl.h"
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#include "openmm/NonbondedForce.h"
#include "openmm/internal/NonbondedForceImpl.h"
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#include <cmath>
#ifdef _MSC_VER
#include <windows.h>
#endif

using namespace OpenMM;
using namespace std;

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static vector<RealVec>& extractPositions(ContextImpl& context) {
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    ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
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    return *((vector<RealVec>*) data->positions);
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}
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static vector<RealVec>& extractVelocities(ContextImpl& context) {
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    ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
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    return *((vector<RealVec>*) data->velocities);
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}
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static vector<RealVec>& extractForces(ContextImpl& context) {
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    ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
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    return *((vector<RealVec>*) data->forces);
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}
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static RealVec& extractBoxSize(ContextImpl& context) {
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    ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
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    return *(RealVec*) data->periodicBoxSize;
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}

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static RealVec* extractBoxVectors(ContextImpl& context) {
    ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
    return (RealVec*) data->periodicBoxVectors;
}

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// ***************************************************************************

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ReferenceCalcAmoebaBondForceKernel::ReferenceCalcAmoebaBondForceKernel(std::string name, const Platform& platform, const System& system) : 
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                CalcAmoebaBondForceKernel(name, platform), system(system) {
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}

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ReferenceCalcAmoebaBondForceKernel::~ReferenceCalcAmoebaBondForceKernel() {
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}

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void ReferenceCalcAmoebaBondForceKernel::initialize(const System& system, const AmoebaBondForce& force) {
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    numBonds = force.getNumBonds();
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    for (int ii = 0; ii < numBonds; ii++) {
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        int particle1Index, particle2Index;
        double lengthValue, kValue;
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        force.getBondParameters(ii, particle1Index, particle2Index, lengthValue, kValue);
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        particle1.push_back(particle1Index); 
        particle2.push_back(particle2Index); 
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        length.push_back(static_cast<RealOpenMM>(lengthValue));
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        kQuadratic.push_back(static_cast<RealOpenMM>(kValue));
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    } 
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    globalBondCubic   = static_cast<RealOpenMM>(force.getAmoebaGlobalBondCubic());
    globalBondQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalBondQuartic());
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}

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double ReferenceCalcAmoebaBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    vector<RealVec>& posData   = extractPositions(context);
    vector<RealVec>& forceData = extractForces(context);
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    AmoebaReferenceBondForce amoebaReferenceBondForce;
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    RealOpenMM energy      = amoebaReferenceBondForce.calculateForceAndEnergy(numBonds, posData, particle1, particle2, length, kQuadratic,
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                                                                                       globalBondCubic, globalBondQuartic,
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                                                                                       forceData);
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    return static_cast<double>(energy);
}

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void ReferenceCalcAmoebaBondForceKernel::copyParametersToContext(ContextImpl& context, const AmoebaBondForce& force) {
    if (numBonds != force.getNumBonds())
        throw OpenMMException("updateParametersInContext: The number of bonds has changed");

    // Record the values.

    for (int i = 0; i < numBonds; ++i) {
        int particle1Index, particle2Index;
        double lengthValue, kValue;
        force.getBondParameters(i, particle1Index, particle2Index, lengthValue, kValue);
        if (particle1Index != particle1[i] || particle2Index != particle2[i])
            throw OpenMMException("updateParametersInContext: The set of particles in a bond has changed");
        length[i] = (RealOpenMM) lengthValue;
        kQuadratic[i] = (RealOpenMM) kValue;
    }
}

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// ***************************************************************************

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ReferenceCalcAmoebaAngleForceKernel::ReferenceCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, const System& system) :
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            CalcAmoebaAngleForceKernel(name, platform), system(system) {
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}

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ReferenceCalcAmoebaAngleForceKernel::~ReferenceCalcAmoebaAngleForceKernel() {
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}

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void ReferenceCalcAmoebaAngleForceKernel::initialize(const System& system, const AmoebaAngleForce& force) {
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    numAngles = force.getNumAngles();

    for (int ii = 0; ii < numAngles; ii++) {
        int particle1Index, particle2Index, particle3Index;
        double angleValue, k;
        force.getAngleParameters(ii, particle1Index, particle2Index, particle3Index, angleValue, k);
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        particle1.push_back(particle1Index); 
        particle2.push_back(particle2Index); 
        particle3.push_back(particle3Index); 
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        angle.push_back(static_cast<RealOpenMM>(angleValue));
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        kQuadratic.push_back(static_cast<RealOpenMM>(k));
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    }
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    globalAngleCubic    = static_cast<RealOpenMM>(force.getAmoebaGlobalAngleCubic());
    globalAngleQuartic  = static_cast<RealOpenMM>(force.getAmoebaGlobalAngleQuartic());
    globalAnglePentic   = static_cast<RealOpenMM>(force.getAmoebaGlobalAnglePentic());
    globalAngleSextic   = static_cast<RealOpenMM>(force.getAmoebaGlobalAngleSextic());
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}

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double ReferenceCalcAmoebaAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    vector<RealVec>& posData   = extractPositions(context);
    vector<RealVec>& forceData = extractForces(context);
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    AmoebaReferenceAngleForce amoebaReferenceAngleForce;
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    RealOpenMM energy      = amoebaReferenceAngleForce.calculateForceAndEnergy(numAngles, 
                                       posData, particle1, particle2, particle3, angle, kQuadratic, globalAngleCubic, globalAngleQuartic, globalAnglePentic, globalAngleSextic, forceData);
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    return static_cast<double>(energy);
}

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void ReferenceCalcAmoebaAngleForceKernel::copyParametersToContext(ContextImpl& context, const AmoebaAngleForce& force) {
    if (numAngles != force.getNumAngles())
        throw OpenMMException("updateParametersInContext: The number of angles has changed");

    // Record the values.

    for (int i = 0; i < numAngles; ++i) {
        int particle1Index, particle2Index, particle3Index;
        double angleValue, k;
        force.getAngleParameters(i, particle1Index, particle2Index, particle3Index, angleValue, k);
        if (particle1Index != particle1[i] || particle2Index != particle2[i] || particle3Index != particle3[i])
            throw OpenMMException("updateParametersInContext: The set of particles in an angle has changed");
        angle[i] = (RealOpenMM) angleValue;
        kQuadratic[i] = (RealOpenMM) k;
    }
}

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ReferenceCalcAmoebaInPlaneAngleForceKernel::ReferenceCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, const System& system) : 
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          CalcAmoebaInPlaneAngleForceKernel(name, platform), system(system) {
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}

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ReferenceCalcAmoebaInPlaneAngleForceKernel::~ReferenceCalcAmoebaInPlaneAngleForceKernel() {
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}

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void ReferenceCalcAmoebaInPlaneAngleForceKernel::initialize(const System& system, const AmoebaInPlaneAngleForce& force) {
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    numAngles = force.getNumAngles();
    for (int ii = 0; ii < numAngles; ii++) {
        int particle1Index, particle2Index, particle3Index, particle4Index;
        double angleValue, k;
        force.getAngleParameters(ii, particle1Index, particle2Index, particle3Index, particle4Index, angleValue, k);
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        particle1.push_back(particle1Index); 
        particle2.push_back(particle2Index); 
        particle3.push_back(particle3Index); 
        particle4.push_back(particle4Index); 
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        angle.push_back(static_cast<RealOpenMM>(angleValue));
        kQuadratic.push_back(static_cast<RealOpenMM>(k));
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    }
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    globalInPlaneAngleCubic    = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAngleCubic());
    globalInPlaneAngleQuartic  = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAngleQuartic());
    globalInPlaneAnglePentic   = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAnglePentic());
    globalInPlaneAngleSextic   = static_cast<RealOpenMM>(force.getAmoebaGlobalInPlaneAngleSextic());
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}

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double ReferenceCalcAmoebaInPlaneAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    vector<RealVec>& posData   = extractPositions(context);
    vector<RealVec>& forceData = extractForces(context);
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    AmoebaReferenceInPlaneAngleForce amoebaReferenceInPlaneAngleForce;
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    RealOpenMM energy      = amoebaReferenceInPlaneAngleForce.calculateForceAndEnergy(numAngles, posData, particle1, particle2, particle3, particle4, 
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                                                                                               angle, kQuadratic, globalInPlaneAngleCubic, globalInPlaneAngleQuartic,
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                                                                                               globalInPlaneAnglePentic, globalInPlaneAngleSextic, forceData);
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    return static_cast<double>(energy);
}

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void ReferenceCalcAmoebaInPlaneAngleForceKernel::copyParametersToContext(ContextImpl& context, const AmoebaInPlaneAngleForce& force) {
    if (numAngles != force.getNumAngles())
        throw OpenMMException("updateParametersInContext: The number of angles has changed");

    // Record the values.

    for (int i = 0; i < numAngles; ++i) {
        int particle1Index, particle2Index, particle3Index, particle4Index;
        double angleValue, k;
        force.getAngleParameters(i, particle1Index, particle2Index, particle3Index, particle4Index, angleValue, k);
        if (particle1Index != particle1[i] || particle2Index != particle2[i] || particle3Index != particle3[i] || particle4Index != particle4[i])
            throw OpenMMException("updateParametersInContext: The set of particles in an angle has changed");
        angle[i] = (RealOpenMM) angleValue;
        kQuadratic[i] = (RealOpenMM) k;
    }
}

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ReferenceCalcAmoebaPiTorsionForceKernel::ReferenceCalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform, const System& system) :
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         CalcAmoebaPiTorsionForceKernel(name, platform), system(system) {
}

ReferenceCalcAmoebaPiTorsionForceKernel::~ReferenceCalcAmoebaPiTorsionForceKernel() {
}

void ReferenceCalcAmoebaPiTorsionForceKernel::initialize(const System& system, const AmoebaPiTorsionForce& force) {

    numPiTorsions                     = force.getNumPiTorsions();
    for (int ii = 0; ii < numPiTorsions; ii++) {

        int particle1Index, particle2Index, particle3Index, particle4Index, particle5Index, particle6Index;
        double kTorsionParameter;
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        force.getPiTorsionParameters(ii, particle1Index, particle2Index, particle3Index, particle4Index, particle5Index, particle6Index, kTorsionParameter);
        particle1.push_back(particle1Index); 
        particle2.push_back(particle2Index); 
        particle3.push_back(particle3Index); 
        particle4.push_back(particle4Index); 
        particle5.push_back(particle5Index); 
        particle6.push_back(particle6Index); 
        kTorsion.push_back(static_cast<RealOpenMM>(kTorsionParameter));
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    }
}

double ReferenceCalcAmoebaPiTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    vector<RealVec>& posData   = extractPositions(context);
    vector<RealVec>& forceData = extractForces(context);
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    AmoebaReferencePiTorsionForce amoebaReferencePiTorsionForce;
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    RealOpenMM energy      = amoebaReferencePiTorsionForce.calculateForceAndEnergy(numPiTorsions, posData, particle1, particle2,
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                                                                                    particle3, particle4, particle5, particle6,
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                                                                                    kTorsion, forceData);
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    return static_cast<double>(energy);
}

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void ReferenceCalcAmoebaPiTorsionForceKernel::copyParametersToContext(ContextImpl& context, const AmoebaPiTorsionForce& force) {
    if (numPiTorsions != force.getNumPiTorsions())
        throw OpenMMException("updateParametersInContext: The number of torsions has changed");

    // Record the values.

    for (int i = 0; i < numPiTorsions; ++i) {
        int particle1Index, particle2Index, particle3Index, particle4Index, particle5Index, particle6Index;
        double kTorsionParameter;
        force.getPiTorsionParameters(i, particle1Index, particle2Index, particle3Index, particle4Index, particle5Index, particle6Index, kTorsionParameter);
        if (particle1Index != particle1[i] || particle2Index != particle2[i] || particle3Index != particle3[i] ||
            particle4Index != particle4[i] || particle5Index != particle5[i] || particle6Index != particle6[i])
            throw OpenMMException("updateParametersInContext: The set of particles in a torsion has changed");
        kTorsion[i] = (RealOpenMM) kTorsionParameter;
    }
}

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ReferenceCalcAmoebaStretchBendForceKernel::ReferenceCalcAmoebaStretchBendForceKernel(std::string name, const Platform& platform, const System& system) :
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                   CalcAmoebaStretchBendForceKernel(name, platform), system(system) {
}

ReferenceCalcAmoebaStretchBendForceKernel::~ReferenceCalcAmoebaStretchBendForceKernel() {
}

void ReferenceCalcAmoebaStretchBendForceKernel::initialize(const System& system, const AmoebaStretchBendForce& force) {

    numStretchBends = force.getNumStretchBends();
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    for (int ii = 0; ii < numStretchBends; ii++) {
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        int particle1Index, particle2Index, particle3Index;
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        double lengthAB, lengthCB, angle, k1, k2;
        force.getStretchBendParameters(ii, particle1Index, particle2Index, particle3Index, lengthAB, lengthCB, angle, k1, k2);
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        particle1.push_back(particle1Index); 
        particle2.push_back(particle2Index); 
        particle3.push_back(particle3Index); 
        lengthABParameters.push_back(static_cast<RealOpenMM>(lengthAB));
        lengthCBParameters.push_back(static_cast<RealOpenMM>(lengthCB));
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        angleParameters.push_back(static_cast<RealOpenMM>(angle));
        k1Parameters.push_back(static_cast<RealOpenMM>(k1));
        k2Parameters.push_back(static_cast<RealOpenMM>(k2));
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    }
}

double ReferenceCalcAmoebaStretchBendForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    vector<RealVec>& posData   = extractPositions(context);
    vector<RealVec>& forceData = extractForces(context);
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    AmoebaReferenceStretchBendForce amoebaReferenceStretchBendForce;
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    RealOpenMM energy      = amoebaReferenceStretchBendForce.calculateForceAndEnergy(numStretchBends, posData, particle1, particle2, particle3,
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                                                                                      lengthABParameters, lengthCBParameters, angleParameters, k1Parameters,
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                                                                                      k2Parameters, forceData);
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    return static_cast<double>(energy);
}

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void ReferenceCalcAmoebaStretchBendForceKernel::copyParametersToContext(ContextImpl& context, const AmoebaStretchBendForce& force) {
    if (numStretchBends != force.getNumStretchBends())
        throw OpenMMException("updateParametersInContext: The number of stretch-bends has changed");

    // Record the values.

    for (int i = 0; i < numStretchBends; ++i) {
        int particle1Index, particle2Index, particle3Index;
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        double lengthAB, lengthCB, angle, k1, k2;
        force.getStretchBendParameters(i, particle1Index, particle2Index, particle3Index, lengthAB, lengthCB, angle, k1, k2);
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        if (particle1Index != particle1[i] || particle2Index != particle2[i] || particle3Index != particle3[i])
            throw OpenMMException("updateParametersInContext: The set of particles in a stretch-bend has changed");
        lengthABParameters[i] = (RealOpenMM) lengthAB;
        lengthCBParameters[i] = (RealOpenMM) lengthCB;
        angleParameters[i] = (RealOpenMM) angle;
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        k1Parameters[i] = (RealOpenMM) k1;
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        k2Parameters[i] = (RealOpenMM) k2;
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    }
}

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ReferenceCalcAmoebaOutOfPlaneBendForceKernel::ReferenceCalcAmoebaOutOfPlaneBendForceKernel(std::string name, const Platform& platform, const System& system) :
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          CalcAmoebaOutOfPlaneBendForceKernel(name, platform), system(system) {
}

ReferenceCalcAmoebaOutOfPlaneBendForceKernel::~ReferenceCalcAmoebaOutOfPlaneBendForceKernel() {
}

void ReferenceCalcAmoebaOutOfPlaneBendForceKernel::initialize(const System& system, const AmoebaOutOfPlaneBendForce& force) {

    numOutOfPlaneBends = force.getNumOutOfPlaneBends();
    for (int ii = 0; ii < numOutOfPlaneBends; ii++) {

        int particle1Index, particle2Index, particle3Index, particle4Index;
        double k;

        force.getOutOfPlaneBendParameters(ii, particle1Index, particle2Index, particle3Index, particle4Index, k);
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        particle1.push_back(particle1Index); 
        particle2.push_back(particle2Index); 
        particle3.push_back(particle3Index); 
        particle4.push_back(particle4Index); 
        kParameters.push_back(static_cast<RealOpenMM>(k));
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    }
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    globalOutOfPlaneBendAngleCubic      = static_cast<RealOpenMM>(force.getAmoebaGlobalOutOfPlaneBendCubic());
    globalOutOfPlaneBendAngleQuartic    = static_cast<RealOpenMM>(force.getAmoebaGlobalOutOfPlaneBendQuartic());
    globalOutOfPlaneBendAnglePentic     = static_cast<RealOpenMM>(force.getAmoebaGlobalOutOfPlaneBendPentic());
    globalOutOfPlaneBendAngleSextic     = static_cast<RealOpenMM>(force.getAmoebaGlobalOutOfPlaneBendSextic());
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}

double ReferenceCalcAmoebaOutOfPlaneBendForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    vector<RealVec>& posData   = extractPositions(context);
    vector<RealVec>& forceData = extractForces(context);
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    AmoebaReferenceOutOfPlaneBendForce amoebaReferenceOutOfPlaneBendForce;
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    RealOpenMM energy      = amoebaReferenceOutOfPlaneBendForce.calculateForceAndEnergy(numOutOfPlaneBends, posData,
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                                                                                         particle1, particle2, particle3, particle4,
                                                                                         kParameters, 
                                                                                         globalOutOfPlaneBendAngleCubic,
                                                                                         globalOutOfPlaneBendAngleQuartic,
                                                                                         globalOutOfPlaneBendAnglePentic,
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                                                                                         globalOutOfPlaneBendAngleSextic, forceData); 
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    return static_cast<double>(energy);
}

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void ReferenceCalcAmoebaOutOfPlaneBendForceKernel::copyParametersToContext(ContextImpl& context, const AmoebaOutOfPlaneBendForce& force) {
    if (numOutOfPlaneBends != force.getNumOutOfPlaneBends())
        throw OpenMMException("updateParametersInContext: The number of out-of-plane bends has changed");

    // Record the values.

    for (int i = 0; i < numOutOfPlaneBends; ++i) {
        int particle1Index, particle2Index, particle3Index, particle4Index;
        double k;
        force.getOutOfPlaneBendParameters(i, particle1Index, particle2Index, particle3Index, particle4Index, k);
        if (particle1Index != particle1[i] || particle2Index != particle2[i] || particle3Index != particle3[i] || particle4Index != particle4[i])
            throw OpenMMException("updateParametersInContext: The set of particles in an out-of-plane bend has changed");
        kParameters[i] = (RealOpenMM) k;
    }
}

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ReferenceCalcAmoebaTorsionTorsionForceKernel::ReferenceCalcAmoebaTorsionTorsionForceKernel(std::string name, const Platform& platform, const System& system) :
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                CalcAmoebaTorsionTorsionForceKernel(name, platform), system(system) {
}

ReferenceCalcAmoebaTorsionTorsionForceKernel::~ReferenceCalcAmoebaTorsionTorsionForceKernel() {
}

void ReferenceCalcAmoebaTorsionTorsionForceKernel::initialize(const System& system, const AmoebaTorsionTorsionForce& force) {

    numTorsionTorsions = force.getNumTorsionTorsions();

    // torsion-torsion parameters

    for (int ii = 0; ii < numTorsionTorsions; ii++) {
        int particle1Index, particle2Index, particle3Index, particle4Index, particle5Index, chiralCheckAtomIndex, gridIndex;
        force.getTorsionTorsionParameters(ii, particle1Index, particle2Index, particle3Index,
                                          particle4Index, particle5Index, chiralCheckAtomIndex, gridIndex);
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        particle1.push_back(particle1Index); 
        particle2.push_back(particle2Index); 
        particle3.push_back(particle3Index); 
        particle4.push_back(particle4Index); 
        particle5.push_back(particle5Index); 
        chiralCheckAtom.push_back(chiralCheckAtomIndex); 
        gridIndices.push_back(gridIndex); 
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    }

    // torsion-torsion grids

    numTorsionTorsionGrids = force.getNumTorsionTorsionGrids();
    torsionTorsionGrids.resize(numTorsionTorsionGrids);
    for (int ii = 0; ii < numTorsionTorsionGrids; ii++) {

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        const TorsionTorsionGrid grid = force.getTorsionTorsionGrid(ii);
        torsionTorsionGrids[ii].resize(grid.size());
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        // check if grid needs to be reordered: x-angle should be 'slow' index

        TorsionTorsionGrid reorderedGrid;
        int reorder = 0; 
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        if (grid[0][0][0] != grid[0][1][0]) {
            AmoebaTorsionTorsionForceImpl::reorderGrid(grid, reorderedGrid);
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            reorder = 1; 
        }    

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        for (unsigned int kk = 0; kk < grid.size(); kk++) {

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            torsionTorsionGrids[ii][kk].resize(grid[kk].size());
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            for (unsigned int jj = 0; jj < grid[kk].size(); jj++) {

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                torsionTorsionGrids[ii][kk][jj].resize(grid[kk][jj].size());
                if (reorder) {
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                    for (unsigned int ll = 0; ll < grid[ll][jj].size(); ll++) {
                        torsionTorsionGrids[ii][kk][jj][ll] = static_cast<RealOpenMM>(reorderedGrid[kk][jj][ll]);
                    }
                } else {
                    for (unsigned int ll = 0; ll < grid[ll][jj].size(); ll++) {
                        torsionTorsionGrids[ii][kk][jj][ll] = static_cast<RealOpenMM>(grid[kk][jj][ll]);
                    }
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                }
            }
        }
    }
}

double ReferenceCalcAmoebaTorsionTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {

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    vector<RealVec>& posData   = extractPositions(context);
    vector<RealVec>& forceData = extractForces(context);
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    AmoebaReferenceTorsionTorsionForce amoebaReferenceTorsionTorsionForce;
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    RealOpenMM energy      = amoebaReferenceTorsionTorsionForce.calculateForceAndEnergy(numTorsionTorsions, posData,
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                                                                                         particle1, particle2, particle3, particle4, particle5,
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                                                                                         chiralCheckAtom, gridIndices, torsionTorsionGrids, forceData);
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    return static_cast<double>(energy);
}

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/* -------------------------------------------------------------------------- *
 *                             AmoebaMultipole                                *
 * -------------------------------------------------------------------------- */

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ReferenceCalcAmoebaMultipoleForceKernel::ReferenceCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, const System& system) : 
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         CalcAmoebaMultipoleForceKernel(name, platform), system(system), numMultipoles(0), mutualInducedMaxIterations(60), mutualInducedTargetEpsilon(1.0e-03),
                                                         usePme(false),alphaEwald(0.0), cutoffDistance(1.0) {  
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}

ReferenceCalcAmoebaMultipoleForceKernel::~ReferenceCalcAmoebaMultipoleForceKernel() {
}

void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, const AmoebaMultipoleForce& force) {

    numMultipoles   = force.getNumMultipoles();

    charges.resize(numMultipoles);
    dipoles.resize(3*numMultipoles);
    quadrupoles.resize(9*numMultipoles);
    tholes.resize(numMultipoles);
    dampingFactors.resize(numMultipoles);
    polarity.resize(numMultipoles);
    axisTypes.resize(numMultipoles);
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    multipoleAtomZs.resize(numMultipoles);
    multipoleAtomXs.resize(numMultipoles);
    multipoleAtomYs.resize(numMultipoles);
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    multipoleAtomCovalentInfo.resize(numMultipoles);

    int dipoleIndex      = 0;
    int quadrupoleIndex  = 0;
    int maxCovalentRange = 0;
    double totalCharge   = 0.0;
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    for (int ii = 0; ii < numMultipoles; ii++) {
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        // multipoles

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        int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
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        double charge, tholeD, dampingFactorD, polarityD;
        std::vector<double> dipolesD;
        std::vector<double> quadrupolesD;
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        force.getMultipoleParameters(ii, charge, dipolesD, quadrupolesD, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY,
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                                     tholeD, dampingFactorD, polarityD);
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        totalCharge                       += charge;
        axisTypes[ii]                      = axisType;
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        multipoleAtomZs[ii]                = multipoleAtomZ;
        multipoleAtomXs[ii]                = multipoleAtomX;
        multipoleAtomYs[ii]                = multipoleAtomY;
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        charges[ii]                        = static_cast<RealOpenMM>(charge);
        tholes[ii]                         = static_cast<RealOpenMM>(tholeD);
        dampingFactors[ii]                 = static_cast<RealOpenMM>(dampingFactorD);
        polarity[ii]                       = static_cast<RealOpenMM>(polarityD);

        dipoles[dipoleIndex++]             = static_cast<RealOpenMM>(dipolesD[0]);
        dipoles[dipoleIndex++]             = static_cast<RealOpenMM>(dipolesD[1]);
        dipoles[dipoleIndex++]             = static_cast<RealOpenMM>(dipolesD[2]);
        
        quadrupoles[quadrupoleIndex++]     = static_cast<RealOpenMM>(quadrupolesD[0]);
        quadrupoles[quadrupoleIndex++]     = static_cast<RealOpenMM>(quadrupolesD[1]);
        quadrupoles[quadrupoleIndex++]     = static_cast<RealOpenMM>(quadrupolesD[2]);
        quadrupoles[quadrupoleIndex++]     = static_cast<RealOpenMM>(quadrupolesD[3]);
        quadrupoles[quadrupoleIndex++]     = static_cast<RealOpenMM>(quadrupolesD[4]);
        quadrupoles[quadrupoleIndex++]     = static_cast<RealOpenMM>(quadrupolesD[5]);
        quadrupoles[quadrupoleIndex++]     = static_cast<RealOpenMM>(quadrupolesD[6]);
        quadrupoles[quadrupoleIndex++]     = static_cast<RealOpenMM>(quadrupolesD[7]);
        quadrupoles[quadrupoleIndex++]     = static_cast<RealOpenMM>(quadrupolesD[8]);

        // covalent info

        std::vector< std::vector<int> > covalentLists;
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        force.getCovalentMaps(ii, covalentLists);
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        multipoleAtomCovalentInfo[ii] = covalentLists;

    }

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    polarizationType = force.getPolarizationType();
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    if (polarizationType == AmoebaMultipoleForce::Mutual) {
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        mutualInducedMaxIterations = force.getMutualInducedMaxIterations();
        mutualInducedTargetEpsilon = force.getMutualInducedTargetEpsilon();
    }
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    // PME

    nonbondedMethod  = force.getNonbondedMethod();
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    if (nonbondedMethod == AmoebaMultipoleForce::PME) {
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        usePme     = true;
        alphaEwald = force.getAEwald();
        cutoffDistance = force.getCutoffDistance();
        force.getPmeGridDimensions(pmeGridDimension);
        if (pmeGridDimension[0] == 0 || alphaEwald == 0.0) {
            NonbondedForce nb;
            nb.setEwaldErrorTolerance(force.getEwaldErrorTolerance());
            nb.setCutoffDistance(force.getCutoffDistance());
            int gridSizeX, gridSizeY, gridSizeZ;
            NonbondedForceImpl::calcPMEParameters(system, nb, alphaEwald, gridSizeX, gridSizeY, gridSizeZ);
            pmeGridDimension[0] = gridSizeX;
            pmeGridDimension[1] = gridSizeY;
            pmeGridDimension[2] = gridSizeZ;
        }    
    } else {
        usePme = false;
    }
    return;
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}

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AmoebaReferenceMultipoleForce* ReferenceCalcAmoebaMultipoleForceKernel::setupAmoebaReferenceMultipoleForce(ContextImpl& context)
595
{
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    // amoebaReferenceMultipoleForce is set to AmoebaReferenceGeneralizedKirkwoodForce if AmoebaGeneralizedKirkwoodForce is present
    // amoebaReferenceMultipoleForce is set to AmoebaReferencePmeMultipoleForce if 'usePme' is set
    // amoebaReferenceMultipoleForce is set to AmoebaReferenceMultipoleForce otherwise

    // check if AmoebaGeneralizedKirkwoodForce is present 
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    ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel* gkKernel = NULL;
    for (unsigned int ii = 0; ii < context.getForceImpls().size() && gkKernel == NULL; ii++) {
        AmoebaGeneralizedKirkwoodForceImpl* gkImpl = dynamic_cast<AmoebaGeneralizedKirkwoodForceImpl*>(context.getForceImpls()[ii]);
        if (gkImpl != NULL) {
            gkKernel = dynamic_cast<ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel*>(&gkImpl->getKernel().getImpl());
        }
    }    

    AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = NULL;
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    if (gkKernel) {
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        // amoebaReferenceGeneralizedKirkwoodForce is deleted in AmoebaReferenceGeneralizedKirkwoodMultipoleForce
        // destructor

        AmoebaReferenceGeneralizedKirkwoodForce* amoebaReferenceGeneralizedKirkwoodForce = new AmoebaReferenceGeneralizedKirkwoodForce();
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        amoebaReferenceGeneralizedKirkwoodForce->setNumParticles(gkKernel->getNumParticles());
        amoebaReferenceGeneralizedKirkwoodForce->setSoluteDielectric(gkKernel->getSoluteDielectric());
        amoebaReferenceGeneralizedKirkwoodForce->setSolventDielectric(gkKernel->getSolventDielectric());
        amoebaReferenceGeneralizedKirkwoodForce->setDielectricOffset(gkKernel->getDielectricOffset());
        amoebaReferenceGeneralizedKirkwoodForce->setProbeRadius(gkKernel->getProbeRadius());
        amoebaReferenceGeneralizedKirkwoodForce->setSurfaceAreaFactor(gkKernel->getSurfaceAreaFactor());
        amoebaReferenceGeneralizedKirkwoodForce->setIncludeCavityTerm(gkKernel->getIncludeCavityTerm());
        amoebaReferenceGeneralizedKirkwoodForce->setDirectPolarization(gkKernel->getDirectPolarization());
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        vector<RealOpenMM> parameters; 
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        gkKernel->getAtomicRadii(parameters);
        amoebaReferenceGeneralizedKirkwoodForce->setAtomicRadii(parameters);
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        gkKernel->getScaleFactors(parameters);
        amoebaReferenceGeneralizedKirkwoodForce->setScaleFactors(parameters);
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        gkKernel->getCharges(parameters);
        amoebaReferenceGeneralizedKirkwoodForce->setCharges(parameters);
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        // calculate Grycuk Born radii

639
        vector<RealVec>& posData   = extractPositions(context);
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        amoebaReferenceGeneralizedKirkwoodForce->calculateGrycukBornRadii(posData);
641

642
        amoebaReferenceMultipoleForce = new AmoebaReferenceGeneralizedKirkwoodMultipoleForce(amoebaReferenceGeneralizedKirkwoodForce);
643

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    } else if (usePme) {
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        AmoebaReferencePmeMultipoleForce* amoebaReferencePmeMultipoleForce = new AmoebaReferencePmeMultipoleForce();
        amoebaReferencePmeMultipoleForce->setAlphaEwald(alphaEwald);
        amoebaReferencePmeMultipoleForce->setCutoffDistance(cutoffDistance);
        amoebaReferencePmeMultipoleForce->setPmeGridDimensions(pmeGridDimension);
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        RealVec* boxVectors = extractBoxVectors(context);
        double minAllowedSize = 1.999999*cutoffDistance;
652
        if (boxVectors[0][0] < minAllowedSize || boxVectors[1][1] < minAllowedSize || boxVectors[2][2] < minAllowedSize) {
653
            throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
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        }
        amoebaReferencePmeMultipoleForce->setPeriodicBoxSize(boxVectors);
        amoebaReferenceMultipoleForce = static_cast<AmoebaReferenceMultipoleForce*>(amoebaReferencePmeMultipoleForce);
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    } else {
659
         amoebaReferenceMultipoleForce = new AmoebaReferenceMultipoleForce(AmoebaReferenceMultipoleForce::NoCutoff);
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    }

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    // set polarization type

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    if (polarizationType == AmoebaMultipoleForce::Mutual) {
        amoebaReferenceMultipoleForce->setPolarizationType(AmoebaReferenceMultipoleForce::Mutual);
        amoebaReferenceMultipoleForce->setMutualInducedDipoleTargetEpsilon(mutualInducedTargetEpsilon);
        amoebaReferenceMultipoleForce->setMaximumMutualInducedDipoleIterations(mutualInducedMaxIterations);
    } else if (polarizationType == AmoebaMultipoleForce::Direct) {
        amoebaReferenceMultipoleForce->setPolarizationType(AmoebaReferenceMultipoleForce::Direct);
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    } else {
671
        throw OpenMMException("Polarization type not recognzied.");
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    }

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    return amoebaReferenceMultipoleForce;

}

double ReferenceCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {

680
    AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce(context);
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    vector<RealVec>& posData   = extractPositions(context);
    vector<RealVec>& forceData = extractForces(context);
684
    RealOpenMM energy          = amoebaReferenceMultipoleForce->calculateForceAndEnergy(posData, charges, dipoles, quadrupoles, tholes,
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                                                                                         dampingFactors, polarity, axisTypes, 
                                                                                         multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
                                                                                         multipoleAtomCovalentInfo, forceData);
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689
    delete amoebaReferenceMultipoleForce;
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    return static_cast<double>(energy);
}

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void ReferenceCalcAmoebaMultipoleForceKernel::getInducedDipoles(ContextImpl& context, vector<Vec3>& outputDipoles) {
    int numParticles = context.getSystem().getNumParticles();
    outputDipoles.resize(numParticles);

    // Create an AmoebaReferenceMultipoleForce to do the calculation.
    
700
    AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce(context);
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    vector<RealVec>& posData = extractPositions(context);
    
    // Retrieve the induced dipoles.
    
    vector<RealVec> inducedDipoles;
    amoebaReferenceMultipoleForce->calculateInducedDipoles(posData, charges, dipoles, quadrupoles, tholes,
            dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs, multipoleAtomCovalentInfo, inducedDipoles);
    for (int i = 0; i < numParticles; i++)
        outputDipoles[i] = inducedDipoles[i];
    delete amoebaReferenceMultipoleForce;
}

713
void ReferenceCalcAmoebaMultipoleForceKernel::getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
714
                                                                        std::vector< double >& outputElectrostaticPotential) {
715

716
    AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce(context);
717
    vector<RealVec>& posData                                     = extractPositions(context);
718
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720
    vector<RealVec> grid(inputGrid.size());
    vector<RealOpenMM> potential(inputGrid.size());
    for (unsigned int ii = 0; ii < inputGrid.size(); ii++) {
721
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        grid[ii] = inputGrid[ii];
    }
723
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    amoebaReferenceMultipoleForce->calculateElectrostaticPotential(posData, charges, dipoles, quadrupoles, tholes,
                                                                   dampingFactors, polarity, axisTypes, 
                                                                   multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
                                                                   multipoleAtomCovalentInfo, grid, potential);
727

728
729
    outputElectrostaticPotential.resize(inputGrid.size());
    for (unsigned int ii = 0; ii < inputGrid.size(); ii++) {
730
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733
        outputElectrostaticPotential[ii] = potential[ii];
    }

    delete amoebaReferenceMultipoleForce;
734
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}

736
void ReferenceCalcAmoebaMultipoleForceKernel::getSystemMultipoleMoments(ContextImpl& context, std::vector< double >& outputMultipoleMoments) {
737
738
739

    // retrieve masses

740
    const System& system             = context.getSystem();
741
742
    vector<RealOpenMM> masses;
    for (int i = 0; i <  system.getNumParticles(); ++i) {
743
        masses.push_back(static_cast<RealOpenMM>(system.getParticleMass(i)));
744
745
    }    

746
    AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce(context);
747
    vector<RealVec>& posData                                     = extractPositions(context);
748
749
750
751
    amoebaReferenceMultipoleForce->calculateAmoebaSystemMultipoleMoments(masses, posData, charges, dipoles, quadrupoles, tholes,
                                                                         dampingFactors, polarity, axisTypes, 
                                                                         multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
                                                                         multipoleAtomCovalentInfo, outputMultipoleMoments);
752
753

    delete amoebaReferenceMultipoleForce;
754
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}

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void ReferenceCalcAmoebaMultipoleForceKernel::copyParametersToContext(ContextImpl& context, const AmoebaMultipoleForce& force) {
    if (numMultipoles != force.getNumMultipoles())
        throw OpenMMException("updateParametersInContext: The number of multipoles has changed");

    // Record the values.

    int dipoleIndex = 0;
    int quadrupoleIndex = 0;
    for (int i = 0; i < numMultipoles; ++i) {
        int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
        double charge, tholeD, dampingFactorD, polarityD;
        std::vector<double> dipolesD;
        std::vector<double> quadrupolesD;
        force.getMultipoleParameters(i, charge, dipolesD, quadrupolesD, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, tholeD, dampingFactorD, polarityD);
        axisTypes[i] = axisType;
        multipoleAtomZs[i] = multipoleAtomZ;
        multipoleAtomXs[i] = multipoleAtomX;
        multipoleAtomYs[i] = multipoleAtomY;
        charges[i] = (RealOpenMM) charge;
        tholes[i] = (RealOpenMM) tholeD;
        dampingFactors[i] = (RealOpenMM) dampingFactorD;
        polarity[i] = (RealOpenMM) polarityD;
        dipoles[dipoleIndex++] = (RealOpenMM) dipolesD[0];
        dipoles[dipoleIndex++] = (RealOpenMM) dipolesD[1];
        dipoles[dipoleIndex++] = (RealOpenMM) dipolesD[2];
        quadrupoles[quadrupoleIndex++] = (RealOpenMM) quadrupolesD[0];
        quadrupoles[quadrupoleIndex++] = (RealOpenMM) quadrupolesD[1];
        quadrupoles[quadrupoleIndex++] = (RealOpenMM) quadrupolesD[2];
        quadrupoles[quadrupoleIndex++] = (RealOpenMM) quadrupolesD[3];
        quadrupoles[quadrupoleIndex++] = (RealOpenMM) quadrupolesD[4];
        quadrupoles[quadrupoleIndex++] = (RealOpenMM) quadrupolesD[5];
        quadrupoles[quadrupoleIndex++] = (RealOpenMM) quadrupolesD[6];
        quadrupoles[quadrupoleIndex++] = (RealOpenMM) quadrupolesD[7];
        quadrupoles[quadrupoleIndex++] = (RealOpenMM) quadrupolesD[8];
    }
}

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801
void ReferenceCalcAmoebaMultipoleForceKernel::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
    if (!usePme)
        throw OpenMMException("getPMEParametersInContext: This Context is not using PME");
    alpha = alphaEwald;
    nx = pmeGridDimension[0];
    ny = pmeGridDimension[1];
    nz = pmeGridDimension[2];
}

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/* -------------------------------------------------------------------------- *
 *                       AmoebaGeneralizedKirkwood                            *
 * -------------------------------------------------------------------------- */

806
ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform, const System& system) : 
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812
           CalcAmoebaGeneralizedKirkwoodForceKernel(name, platform), system(system) {
}

ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::~ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel() {
}

813
int ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getNumParticles() const {
814
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816
    return numParticles;
}

817
int ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getIncludeCavityTerm() const {
818
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    return includeCavityTerm;
}

821
int ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getDirectPolarization() const {
822
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824
    return directPolarization;
}

825
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getSoluteDielectric() const {
826
827
828
    return soluteDielectric;
}

829
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getSolventDielectric() const {
830
831
832
    return solventDielectric;
}

833
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getDielectricOffset() const {
834
835
836
    return dielectricOffset;
}

837
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getProbeRadius() const {
838
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840
    return probeRadius;
}

841
RealOpenMM ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getSurfaceAreaFactor() const {
842
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844
    return surfaceAreaFactor;
}

845
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847
void ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getAtomicRadii(vector<RealOpenMM>& outputAtomicRadii) const {
    outputAtomicRadii.resize(atomicRadii.size());
    copy(atomicRadii.begin(), atomicRadii.end(), outputAtomicRadii.begin());
848
849
}

850
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void ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getScaleFactors(vector<RealOpenMM>& outputScaleFactors) const {
    outputScaleFactors.resize(scaleFactors.size());
    copy(scaleFactors.begin(), scaleFactors.end(), outputScaleFactors.begin());
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}

855
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857
void ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::getCharges(vector<RealOpenMM>& outputCharges) const {
    outputCharges.resize(charges.size());
    copy(charges.begin(), charges.end(), outputCharges.begin());
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}

void ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::initialize(const System& system, const AmoebaGeneralizedKirkwoodForce& force) {

    // check that AmoebaMultipoleForce is present

    const AmoebaMultipoleForce* amoebaMultipoleForce = NULL;
    for (int ii = 0; ii < system.getNumForces() && amoebaMultipoleForce == NULL; ii++) {
        amoebaMultipoleForce = dynamic_cast<const AmoebaMultipoleForce*>(&system.getForce(ii));
    }

    if (amoebaMultipoleForce == NULL) {
        throw OpenMMException("AmoebaGeneralizedKirkwoodForce requires the System to also contain an AmoebaMultipoleForce.");
    }

873
    if (amoebaMultipoleForce->getNonbondedMethod() != AmoebaMultipoleForce::NoCutoff) {
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878
        throw OpenMMException("AmoebaGeneralizedKirkwoodForce requires the AmoebaMultipoleForce use the NoCutoff nonbonded method.");
    }

    numParticles = system.getNumParticles();

879
    for (int ii = 0; ii < numParticles; ii++) {
880
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882

        double particleCharge, particleRadius, scalingFactor;
        force.getParticleParameters(ii, particleCharge, particleRadius, scalingFactor);
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885
        atomicRadii.push_back(static_cast<RealOpenMM>(particleRadius));
        scaleFactors.push_back(static_cast<RealOpenMM>(scalingFactor));
        charges.push_back(static_cast<RealOpenMM>(particleCharge));
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891

        // Make sure the charge matches the one specified by the AmoebaMultipoleForce.

        double charge2, thole, damping, polarity;
        int axisType, atomX, atomY, atomZ;
        vector<double> dipole, quadrupole;
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        amoebaMultipoleForce->getMultipoleParameters(ii, charge2, dipole, quadrupole, axisType, atomZ, atomX, atomY, thole, damping, polarity);
        if (particleCharge != charge2) {
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            throw OpenMMException("AmoebaGeneralizedKirkwoodForce and AmoebaMultipoleForce must specify the same charge for every atom.");
        }

    }   
    includeCavityTerm  = force.getIncludeCavityTerm();
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    soluteDielectric   = static_cast<RealOpenMM>(force.getSoluteDielectric());
    solventDielectric  = static_cast<RealOpenMM>(force.getSolventDielectric());
    dielectricOffset   = static_cast<RealOpenMM>(0.009);
    probeRadius        = static_cast<RealOpenMM>(force.getProbeRadius()), 
    surfaceAreaFactor  = static_cast<RealOpenMM>(force.getSurfaceAreaFactor()); 
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    directPolarization = amoebaMultipoleForce->getPolarizationType() == AmoebaMultipoleForce::Direct ? 1 : 0;
}

double ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
    // handled in AmoebaReferenceGeneralizedKirkwoodMultipoleForce, a derived class of the class AmoebaReferenceMultipoleForce
    return 0.0;
}
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void ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel::copyParametersToContext(ContextImpl& context, const AmoebaGeneralizedKirkwoodForce& force) {
    if (numParticles != force.getNumParticles())
        throw OpenMMException("updateParametersInContext: The number of particles has changed");

    // Record the values.

    for (int i = 0; i < numParticles; ++i) {
        double particleCharge, particleRadius, scalingFactor;
        force.getParticleParameters(i, particleCharge, particleRadius, scalingFactor);
        atomicRadii[i] = particleRadius;
        scaleFactors[i] = scalingFactor;
        charges[i] = particleCharge;
    }
}

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ReferenceCalcAmoebaVdwForceKernel::ReferenceCalcAmoebaVdwForceKernel(std::string name, const Platform& platform, const System& system) :
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       CalcAmoebaVdwForceKernel(name, platform), system(system) {
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    useCutoff = 0;
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    usePBC = 0;
    cutoff = 1.0e+10;
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    neighborList = NULL;
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}

ReferenceCalcAmoebaVdwForceKernel::~ReferenceCalcAmoebaVdwForceKernel() {
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    if (neighborList) {
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        delete neighborList;
    } 
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}

void ReferenceCalcAmoebaVdwForceKernel::initialize(const System& system, const AmoebaVdwForce& force) {

    // per-particle parameters

    numParticles = system.getNumParticles();

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    indexIVs.resize(numParticles);
    allExclusions.resize(numParticles);
    sigmas.resize(numParticles);
    epsilons.resize(numParticles);
    reductions.resize(numParticles);
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    for (int ii = 0; ii < numParticles; ii++) {
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        int indexIV;
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        double sigma, epsilon, reduction;
        std::vector<int> exclusions;

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        force.getParticleParameters(ii, indexIV, sigma, epsilon, reduction);
        force.getParticleExclusions(ii, exclusions);
        for (unsigned int jj = 0; jj < exclusions.size(); jj++) {
           allExclusions[ii].insert(exclusions[jj]);
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        }

        indexIVs[ii]      = indexIV;
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        sigmas[ii]        = static_cast<RealOpenMM>(sigma);
        epsilons[ii]      = static_cast<RealOpenMM>(epsilon);
        reductions[ii]    = static_cast<RealOpenMM>(reduction);
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    }   
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    sigmaCombiningRule     = force.getSigmaCombiningRule();
    epsilonCombiningRule   = force.getEpsilonCombiningRule();
    useCutoff              = (force.getNonbondedMethod() != AmoebaVdwForce::NoCutoff);
    usePBC                 = (force.getNonbondedMethod() == AmoebaVdwForce::CutoffPeriodic);
    cutoff                 = force.getCutoff();
    neighborList           = useCutoff ? new NeighborList() : NULL;
    dispersionCoefficient  = force.getUseDispersionCorrection() ?  AmoebaVdwForceImpl::calcDispersionCorrection(system, force) : 0.0;

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}

double ReferenceCalcAmoebaVdwForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {

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    vector<RealVec>& posData   = extractPositions(context);
    vector<RealVec>& forceData = extractForces(context);
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    AmoebaReferenceVdwForce vdwForce(sigmaCombiningRule, epsilonCombiningRule);
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    RealOpenMM energy;
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    if (useCutoff) {
        vdwForce.setCutoff(cutoff);
        computeNeighborListVoxelHash(*neighborList, numParticles, posData, allExclusions, extractBoxVectors(context), usePBC, cutoff, 0.0);
        if (usePBC) {
            vdwForce.setNonbondedMethod(AmoebaReferenceVdwForce::CutoffPeriodic);
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            RealVec* boxVectors = extractBoxVectors(context);
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            double minAllowedSize = 1.999999*cutoff;
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            if (boxVectors[0][0] < minAllowedSize || boxVectors[1][1] < minAllowedSize || boxVectors[2][2] < minAllowedSize) {
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                throw OpenMMException("The periodic box size has decreased to less than twice the cutoff.");
            }
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            vdwForce.setPeriodicBox(boxVectors);
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            energy  = vdwForce.calculateForceAndEnergy(numParticles, posData, indexIVs, sigmas, epsilons, reductions, *neighborList, forceData);
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            energy += dispersionCoefficient/(boxVectors[0][0]*boxVectors[1][1]*boxVectors[2][2]);
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        } else {
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            vdwForce.setNonbondedMethod(AmoebaReferenceVdwForce::CutoffNonPeriodic);
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        }
    } else {
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        vdwForce.setNonbondedMethod(AmoebaReferenceVdwForce::NoCutoff);
        energy = vdwForce.calculateForceAndEnergy(numParticles, posData, indexIVs, sigmas, epsilons, reductions, allExclusions, forceData);
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    }
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    return static_cast<double>(energy);
}

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void ReferenceCalcAmoebaVdwForceKernel::copyParametersToContext(ContextImpl& context, const AmoebaVdwForce& force) {
    if (numParticles != force.getNumParticles())
        throw OpenMMException("updateParametersInContext: The number of particles has changed");

    // Record the values.

    for (int i = 0; i < numParticles; ++i) {
        int indexIV;
        double sigma, epsilon, reduction;
        force.getParticleParameters(i, indexIV, sigma, epsilon, reduction);
        indexIVs[i] = indexIV;
        sigmas[i] = (RealOpenMM) sigma;
        epsilons[i] = (RealOpenMM) epsilon;
        reductions[i]= (RealOpenMM) reduction;
    }
}

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/* -------------------------------------------------------------------------- *
 *                           AmoebaWcaDispersion                              *
 * -------------------------------------------------------------------------- */

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ReferenceCalcAmoebaWcaDispersionForceKernel::ReferenceCalcAmoebaWcaDispersionForceKernel(std::string name, const Platform& platform, const System& system) : 
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           CalcAmoebaWcaDispersionForceKernel(name, platform), system(system) {
}

ReferenceCalcAmoebaWcaDispersionForceKernel::~ReferenceCalcAmoebaWcaDispersionForceKernel() {
}

void ReferenceCalcAmoebaWcaDispersionForceKernel::initialize(const System& system, const AmoebaWcaDispersionForce& force) {

    // per-particle parameters

    numParticles = system.getNumParticles();
    radii.resize(numParticles);
    epsilons.resize(numParticles);
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    for (int ii = 0; ii < numParticles; ii++) {
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        double radius, epsilon;
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        force.getParticleParameters(ii, radius, epsilon);
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        radii[ii]         = static_cast<RealOpenMM>(radius);
        epsilons[ii]      = static_cast<RealOpenMM>(epsilon);
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    }   

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    totalMaximumDispersionEnergy = static_cast<RealOpenMM>(AmoebaWcaDispersionForceImpl::getTotalMaximumDispersionEnergy(force));
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    epso                         = static_cast<RealOpenMM>(force.getEpso());
    epsh                         = static_cast<RealOpenMM>(force.getEpsh());
    rmino                        = static_cast<RealOpenMM>(force.getRmino());
    rminh                        = static_cast<RealOpenMM>(force.getRminh());
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    awater                       = static_cast<RealOpenMM>(force.getAwater());
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    shctd                        = static_cast<RealOpenMM>(force.getShctd());
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    dispoff                      = static_cast<RealOpenMM>(force.getDispoff());
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    slevy                        = static_cast<RealOpenMM>(force.getSlevy());
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}

double ReferenceCalcAmoebaWcaDispersionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    vector<RealVec>& posData   = extractPositions(context);
    vector<RealVec>& forceData = extractForces(context);
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    AmoebaReferenceWcaDispersionForce amoebaReferenceWcaDispersionForce(epso, epsh, rmino, rminh, awater, shctd, dispoff, slevy);
    RealOpenMM energy      = amoebaReferenceWcaDispersionForce.calculateForceAndEnergy(numParticles, posData, radii, epsilons, totalMaximumDispersionEnergy, forceData);
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    return static_cast<double>(energy);
}
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void ReferenceCalcAmoebaWcaDispersionForceKernel::copyParametersToContext(ContextImpl& context, const AmoebaWcaDispersionForce& force) {
    if (numParticles != force.getNumParticles())
        throw OpenMMException("updateParametersInContext: The number of particles has changed");

    // Record the values.

    for (int i = 0; i < numParticles; ++i) {
        double radius, epsilon;
        force.getParticleParameters(i, radius, epsilon);
        radii[i] = (RealOpenMM) radius;
        epsilons[i] = (RealOpenMM) epsilon;
    }
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    totalMaximumDispersionEnergy = (RealOpenMM) AmoebaWcaDispersionForceImpl::getTotalMaximumDispersionEnergy(force);
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}