/* -------------------------------------------------------------------------- *
 *                      SimTK Core: SimTK Simbody(tm)                         *
 * -------------------------------------------------------------------------- *
 * This is part of the SimTK Core biosimulation 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) 2006-7 Stanford University and the Authors.         *
 * Authors: Christopher Bruns                                                 *
 * 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 "SimTKmolmodel.h"

#include <iostream>
#include <fstream>

using namespace SimTK;
using namespace std;

#define ASSERT(x, msg) SimTK_ASSERT_ALWAYS(x, msg)

int main(int argc, char **argv) {
    ASSERT(argc == 2, "Invalid number of arguments");

    try {
        CompoundSystem system; // molecule-specialized simbody System
        SimbodyMatterSubsystem matter(system);
        DuMMForceFieldSubsystem dumm(system); // molecular force field

        dumm.loadAmber99Parameters();

        // dumm.setGbsaGlobalScaleFactor(0.97);

        std::ifstream is(argv[1]);
        ASSERT(is.good(), "Cannot open SantaLucia parameters file");
        dumm.populateFromTinkerParameterFile(is);

        RNA rna ("AA");
        // rna.writeDefaultPdb(cout);
        NaPhosphodiesterLinkage po2("", "", 'X');

        // MagnesiumIon mg1, mg2;
        MagnesiumIon::setAmberLikeParameters(dumm);
        MagnesiumIon mg1, mg2;
        ZincIon::setAmberLikeParameters(dumm);

        // system.adoptCompound(p2, Vec3( 0.5, 0, 0));
        system.adoptCompound(mg1, Vec3(-0.5, 0.6, 0.6));
        // system.adoptCompound(mg2, Vec3(-0.5, -1, 0));
        system.adoptCompound(rna, Vec3(-0.5, 0, 0));
        // system.adoptCompound(po2, Vec3(-0.5, 0, 0));

        std::ofstream of("test.pdb");
        system.addEventReporter(new PeriodicPdbWriter(system, of, 0.020));
        system.addEventHandler(new VelocityRescalingThermostat(system, 293.15, 0.050));

        // rna.setBondMobility(BondMobility::Free , "0/O3'" ,"1/P");

        // rna.writeDefaultPdb(cout);

        system.modelCompounds();

        cerr << "O3' mobilized body index = " << rna.getAtomMobilizedBodyIndex(rna.getAtomIndex("0/O3'")) << endl;

        system.realizeTopology();

        system.realize(system.updDefaultState(), Stage::Dynamics);
        Vec3 mg1Force = system.getRigidBodyForces(system.updDefaultState(), Stage::Dynamics)[mg1.getAtomMobilizedBodyIndex(Compound::AtomIndex(0))][1];
        cout << "Force on first magnesium = " << mg1Force << endl;

        cout << "Mobilized body Id " << mg1.getAtomMobilizedBodyIndex(Compound::AtomIndex(0)) << endl;

        // LocalEnergyMinimizer::minimizeEnergy(system, system.updDefaultState(), 15.0);

        VerletIntegrator integrator(system);
        TimeStepper timeStepper(system, integrator);
        timeStepper.initialize(system.updDefaultState());

        double endTime = 0.0100;

        // while ( timeStepper.getTime() < endTime )
        timeStepper.stepTo(endTime);

        return 0;
    } catch (const std::exception& e) {
        cerr << "EXCEPTION THROWN: " << e.what() << std::endl;
        return 1;
    } catch (...) {
        cerr << "UNKNOWN EXCEPTION THROWN" << std::endl;
        return 1;
    }
}

