/* -------------------------------------------------------------------------- *
 *                                   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) 2019-2025 Stanford University and the Authors.      *
 * Authors: Andreas Krämer and Andrew C. Simmonett                            *
 * Contributors: Peter Eastman                                                *
 *                                                                            *
 * 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/DrudeNoseHooverIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "openmm/Context.h"
#include "openmm/OpenMMException.h"
#include "openmm/DrudeKernels.h"
#include "openmm/DrudeForce.h"
#include "openmm/CMMotionRemover.h"
#include "openmm/kernels.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/DrudeHelpers.h"
#include <ctime>
#include <iostream>
#include <string>
#include <set>

using namespace OpenMM;
using std::string;
using std::vector;
using std::pair;

DrudeNoseHooverIntegrator::DrudeNoseHooverIntegrator(double temperature, double collisionFrequency, 
                                                     double drudeTemperature, double drudeCollisionFrequency,
                                                     double stepSize, int chainLength, int numMTS, int numYoshidaSuzuki) :
            NoseHooverIntegrator(stepSize), drudeTemperature(drudeTemperature) {
    setMaxDrudeDistance(0.02);
    hasSubsystemThermostats_ = false;
    addSubsystemThermostat(std::vector<int>(), std::vector<std::pair<int, int>>(), temperature,
                           collisionFrequency, drudeTemperature, drudeCollisionFrequency,
                           chainLength, numMTS, numYoshidaSuzuki);
}

DrudeNoseHooverIntegrator::~DrudeNoseHooverIntegrator() { }

double DrudeNoseHooverIntegrator::getMaxDrudeDistance() const {
    return maxPairDistance_;
}

void DrudeNoseHooverIntegrator::setMaxDrudeDistance(double distance) {
    if (distance < 0)
        throw OpenMMException("setMaxDrudeDistance: Distance cannot be negative");
    maxPairDistance_ = distance;
}

void DrudeNoseHooverIntegrator::initialize(ContextImpl& contextRef) {

    if (owner != NULL && &contextRef.getOwner() != owner)
        throw OpenMMException("This Integrator is already bound to a context");

    context = &contextRef;
    owner = &contextRef.getOwner();
    kernel = context->getPlatform().createKernel(IntegrateNoseHooverStepKernel::Name(), contextRef);
    kernel.getAs<IntegrateNoseHooverStepKernel>().initialize(contextRef.getSystem(), *this);
    forcesAreValid = false;

    // check for drude particles and build the Nose-Hoover Chains
    const System& system = context->getSystem();
    const DrudeForce* drudeForce = getDrudeForce(contextRef);

    if (drudeForce == NULL)
        throw OpenMMException("The System does not contain a DrudeForce");
    bool hasCMMotionRemover = false;
    for (int i = 0; i < system.getNumForces(); i++)
        if (dynamic_cast<const CMMotionRemover*>(&system.getForce(i)))
            hasCMMotionRemover = true;
    if (!hasCMMotionRemover) {
        std::cout << "Warning: Did not find a center-of-mass motion remover in the system. "
                     "This is problematic when using Drude." << std::endl;
    }
    for (auto& thermostat: noseHooverChains){
        if ( (thermostat.getThermostatedAtoms().size() == 0) && (thermostat.getThermostatedPairs().size() == 0) ){
            std::set<int> realParticlesSet;
            vector<int> realParticles, drudeParticles, drudeParents;
            vector<std::pair<int, int>> drudePairs;
            for (int i = 0; i < system.getNumParticles(); i++) {
                if (system.getParticleMass(i) > 0.0) realParticlesSet.insert(i);
            }
            for (int i = 0; i < drudeForce->getNumParticles(); i++) {
                int p, p1, p2, p3, p4;
                double charge, polarizability, aniso12, aniso34;
                drudeForce->getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
                realParticlesSet.erase(p);
                realParticlesSet.erase(p1);
                drudePairs.push_back({p,p1});
            }
            thermostat.setThermostatedPairs(drudePairs);
            thermostat.setThermostatedAtoms(std::vector<int>(realParticlesSet.begin(), realParticlesSet.end()));
        }
    }

    initializeThermostats(system);
}

double DrudeNoseHooverIntegrator::computeDrudeKineticEnergy() {
    double kE = 0.0;
    for (const auto &nhc: noseHooverChains){
        if (nhc.getThermostatedPairs().size() != 0) {
            kE += kernel.getAs<IntegrateNoseHooverStepKernel>().computeMaskedKineticEnergy(*context, nhc, true).second;
        }
    }
    return kE;
}

double DrudeNoseHooverIntegrator::computeTotalKineticEnergy() {
    return kernel.getAs<IntegrateNoseHooverStepKernel>().computeKineticEnergy(*context, *this);
}

double DrudeNoseHooverIntegrator::computeSystemTemperature() {
    if (context == NULL)
        throw OpenMMException("This Integrator is not bound to a context!");  
    context->calcForcesAndEnergy(true, false, getIntegrationForceGroups());
    vector<Vec3> velocities;
    context->computeShiftedVelocities(getVelocityTimeOffset(), velocities);
    return computeTemperaturesFromVelocities(*context, velocities).first;
}

double DrudeNoseHooverIntegrator::computeDrudeTemperature() {
    if (context == NULL)
        throw OpenMMException("This Integrator is not bound to a context!");  
    double kE = computeDrudeKineticEnergy();
    size_t num_dofs = 0;
    for (const auto &nhc: noseHooverChains){
       num_dofs += 3 * nhc.getThermostatedPairs().size();
    }
    return kE/(0.5 * num_dofs * BOLTZ);
}

std::vector<Vec3> DrudeNoseHooverIntegrator::getVelocitiesForTemperature(const System &system, double temperature,
                                                                         int randomSeedIn) const {
    return assignDrudeVelocities(*context, temperature, drudeTemperature, randomSeedIn);
}

