/* -------------------------------------------------------------------------- *
 *                                   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) 2008-2016 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  *
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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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 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
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#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include <iostream>
#include <vector>

using namespace OpenMM;
using namespace std;

const double TOL = 1e-5;

void testBonds() {
    System system;
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(1.0);
    VerletIntegrator integrator(0.01);
    HarmonicBondForce* forceField = new HarmonicBondForce();
    forceField->addBond(0, 1, 1.5, 0.8);
    forceField->addBond(1, 2, 1.2, 0.7);
    system.addForce(forceField);
    Context context(system, integrator, platform);
    vector<Vec3> positions(3);
    positions[0] = Vec3(0, 2, 0);
    positions[1] = Vec3(0, 0, 0);
    positions[2] = Vec3(1, 0, 0);
    context.setPositions(positions);
    State state = context.getState(State::Forces | State::Energy);
    {
        const vector<Vec3>& forces = state.getForces();
        ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.5, 0), forces[0], TOL);
        ASSERT_EQUAL_VEC(Vec3(0.7*0.2, 0, 0), forces[2], TOL);
        ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
        ASSERT_EQUAL_TOL(0.5*0.8*0.5*0.5 + 0.5*0.7*0.2*0.2, state.getPotentialEnergy(), TOL);
    }
    
    // Try changing the bond parameters and make sure it's still correct.
    
    forceField->setBondParameters(0, 0, 1, 1.6, 0.9);
    forceField->setBondParameters(1, 1, 2, 1.3, 0.8);
    forceField->updateParametersInContext(context);
    state = context.getState(State::Forces | State::Energy);
    {
        const vector<Vec3>& forces = state.getForces();
        ASSERT_EQUAL_VEC(Vec3(0, -0.9*0.4, 0), forces[0], TOL);
        ASSERT_EQUAL_VEC(Vec3(0.8*0.3, 0, 0), forces[2], TOL);
        ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
        ASSERT_EQUAL_TOL(0.5*0.9*0.4*0.4 + 0.5*0.8*0.3*0.3, state.getPotentialEnergy(), TOL);
    }
}

void testPeriodic() {
    // Create a force that uses periodic boundary conditions.
    
    System system;
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
    VerletIntegrator integrator(0.01);
    HarmonicBondForce* bonds = new HarmonicBondForce();
    bonds->addBond(0, 1, 1.2, 0.8);
    bonds->setUsesPeriodicBoundaryConditions(true);
    system.addForce(bonds);
    Context context(system, integrator, platform);
    vector<Vec3> positions(2);
    positions[0] = Vec3(0, 2, 0);
    positions[1] = Vec3(0, 0, 0);
    context.setPositions(positions);
    State state = context.getState(State::Forces | State::Energy);
    const vector<Vec3>& forces = state.getForces();
    ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.2, 0), forces[0], TOL);
    ASSERT_EQUAL_VEC(Vec3(0, 0.8*0.2, 0), forces[1], TOL);
    ASSERT_EQUAL_TOL(0.5*0.8*0.2*0.2, state.getPotentialEnergy(), TOL);
}

void runPlatformTests();

int main(int argc, char* argv[]) {
    try {
        initializeTests(argc, argv);
        testBonds();
        testPeriodic();
        runPlatformTests();
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;
        return 1;
    }
    cout << "Done" << endl;
    return 0;
}