/* -------------------------------------------------------------------------- *
 *                                   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) 2013 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 "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/Platform.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include <iostream>
#include <vector>

using namespace OpenMM;
using namespace std;

void testFindMolecules() {
    const int numMolecules = 5;
    const int moleculeSize[] = {1, 10, 100, 1000, 10000};
    vector<int> particleMolecule;
    System system;
    HarmonicBondForce* bonds = new HarmonicBondForce();
    system.addForce(bonds);
    for (int i = 0; i < numMolecules; i++)
        for (int j = 0; j < moleculeSize[i]; j++) {
            int index = system.addParticle(1.0);
            particleMolecule.push_back(i);
            if (j > 0)
                bonds->addBond(index, index-1, 1.0, 1.0);
        }
    VerletIntegrator integrator(1.0);
    Context context(system, integrator, Platform::getPlatformByName("Reference"));
    ContextImpl* contextImpl = *reinterpret_cast<ContextImpl**>(&context);
    const vector<vector<int> >& molecules = contextImpl->getMolecules();
    ASSERT_EQUAL(numMolecules, molecules.size());
    for (int i = 0; i < numMolecules; i++) {
        ASSERT_EQUAL(moleculeSize[i], molecules[i].size());
        for (int j = 0; j < moleculeSize[i]; j++)
            ASSERT_EQUAL(particleMolecule[molecules[i][j]], i);
    }
}

int main() {
    try {
        testFindMolecules();
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;
        return 1;
    }
    cout << "Done" << endl;
    return 0;
}