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/* -------------------------------------------------------------------------- *
 *                                   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 Stanford University and the Authors.           *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
 * Permission is hereby granted, free of charge, to any person obtaining a    *
 * 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,   *
 * and/or sell copies of the Software, and to permit persons to whom the      *
 * Software is furnished to do so, subject to the following conditions:       *
 *                                                                            *
 * The above copyright notice and this permission notice shall be included in *
 * all copies or substantial portions of the Software.                        *
 *                                                                            *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
 * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
 * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
 * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
 * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
 * -------------------------------------------------------------------------- */

#include "ReferenceKernels.h"

using namespace OpenMM;
using namespace std;

void ReferenceCalcStandardMMForcesKernel::initialize(const vector<vector<int> >& bondIndices, const vector<vector<double> >& bondParameters,
        const vector<vector<int> >& angleIndices, const vector<vector<double> >& angleParameters,
        const vector<vector<int> >& periodicTorsionIndices, const vector<vector<double> >& periodicTorsionParameters,
        const vector<vector<int> >& rbTorsionIndices, const vector<vector<double> >& rbTorsionParameters,
        const vector<vector<int> >& bonded14Indices, const vector<set<int> >& exclusions,
        const vector<vector<double> >& nonbondedParameters) {
    
}

void ReferenceCalcStandardMMForcesKernel::execute(const Stream& positions, Stream& forces) {
    
}

void ReferenceCalcStandardMMEnergyKernel::initialize(const vector<vector<int> >& bondIndices, const vector<vector<double> >& bondParameters,
        const vector<vector<int> >& angleIndices, const vector<vector<double> >& angleParameters,
        const vector<vector<int> >& periodicTorsionIndices, const vector<vector<double> >& periodicTorsionParameters,
        const vector<vector<int> >& rbTorsionIndices, const vector<vector<double> >& rbTorsionParameters,
        const vector<vector<int> >& bonded14Indices, const vector<set<int> >& exclusions,
        const vector<vector<double> >& nonbondedParameters) {
    
}

double ReferenceCalcStandardMMEnergyKernel::execute(const Stream& positions) {
    return 0.0; // TODO implement correctly
}

void ReferenceCalcGBSAOBCForcesKernel::initialize(const vector<double>& bornRadii, const vector<vector<double> >& atomParameters,
        double solventDielectric, double soluteDielectric) {
    
}

void ReferenceCalcGBSAOBCForcesKernel::execute(const Stream& positions, Stream& forces) {
    
}

void CalcGBSAOBCEnergyKernel::initialize(const vector<double>& bornRadii, const vector<vector<double> >& atomParameters,
        double solventDielectric, double soluteDielectric) {
    
}

double CalcGBSAOBCEnergyKernel::execute(const Stream& positions) {
    return 0.0; // TODO implement correctly
}

void ReferenceIntegrateVerletStepKernel::initialize(const vector<double>& masses, const vector<vector<int> >& constraintIndices,
        const vector<double>& constraintLengths) {
    
}

void ReferenceIntegrateVerletStepKernel::execute(Stream& positions, Stream& velocities, const Stream& forces, double stepSize) {
    
}

void ReferenceIntegrateLangevinStepKernel::initialize(const vector<double>& masses, const vector<vector<int> >& constraintIndices,
        const vector<double>& constraintLengths) {
    
}

void ReferenceIntegrateLangevinStepKernel::execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize) {
    
}

void ReferenceIntegrateBrownianStepKernel::initialize(const vector<double>& masses, const vector<vector<int> >& constraintIndices,
        const vector<double>& constraintLengths) {
    
}

void ReferenceIntegrateBrownianStepKernel::execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize) {
    
}

void ReferenceApplyAndersenThermostatKernel::initialize(const vector<double>& masses) {
    
}

void ReferenceApplyAndersenThermostatKernel::execute(Stream& velocities, double temperature, double collisionFrequency, double stepSize) {
    
}

void ReferenceCalcKineticEnergyKernel::initialize(const vector<double>& masses) {
    
}

double ReferenceCalcKineticEnergyKernel::execute(const Stream& positions) {
    return 0.0; // TODO implement correctly
}