/* -------------------------------------------------------------------------- *
 *                                   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) 2025 Stanford University and the Authors.           *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
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#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/CustomExternalForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/DPDIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>

using namespace OpenMM;
using namespace std;

double computeEnergy(Context& context) {
    const System& system = context.getSystem();
    double dt = context.getIntegrator().getStepSize();
    State state = context.getState(State::Energy | State::Velocities | State::Forces);
    double energy = state.getPotentialEnergy();
    for (int i = 0; i < system.getNumParticles(); i++) {
        double m = system.getParticleMass(i);
        Vec3 v = state.getVelocities()[i];
        v += (0.5*dt/m)*state.getForces()[i];
        energy += 0.5*m*v.dot(v);
    }
    return energy;
}

void testConservationLaws() {
    const int numParticles = 8;
    const double temp = 100.0;
    const double boxSize = 5.0;
    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    DPDIntegrator integrator(temp, 3.0, 2.5, 0.002);
    NonbondedForce* forceField = new NonbondedForce();
    forceField->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    forceField->setCutoffDistance(2.5);
    for (int i = 0; i < numParticles; ++i) {
        system.addParticle(2.0);
        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
    }
    system.addForce(forceField);
    Context context(system, integrator, platform);
    vector<Vec3> positions(numParticles);
    vector<Vec3> velocities(numParticles);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    for (int i = 0; i < numParticles; ++i)
        positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
    velocities[0][0] = 2.0;

    // The integrator should conserve momentum.

    Vec3 initialMomentum = system.getParticleMass(0)*velocities[0];
    context.setPositions(positions);
    context.setVelocities(velocities);
    for (int i = 0; i < 100; i++) {
        integrator.step(1);
        State state = context.getState(State::Velocities);
        Vec3 momentum;
        for (int j = 0; j < numParticles; j++)
            momentum += system.getParticleMass(j)*state.getVelocities()[j];
        ASSERT_EQUAL_VEC(initialMomentum, momentum, 1e-5);
    }

    // If we set the friction to 0, it should also conserve energy.

    integrator.setDefaultFriction(0.0);
    context.reinitialize();
    context.setPositions(positions);
    context.setVelocities(velocities);
    double energy = computeEnergy(context);
    for (int i = 0; i < 100; i++) {
        integrator.step(1);
        State state = context.getState(State::Velocities | State::Energy);
        Vec3 momentum;
        for (int j = 0; j < numParticles; j++)
            momentum += system.getParticleMass(j)*state.getVelocities()[j];
        ASSERT_EQUAL_VEC(initialMomentum, momentum, 1e-5);
        ASSERT_EQUAL_TOL(energy, computeEnergy(context), 0.02);
    }
}

void testDiffusion() {
    const int gridWidth = 10;
    const int numParticles = gridWidth*gridWidth*gridWidth;
    const double density = 3.0;
    const double boxSize = pow(numParticles/density, 1.0/3.0);
    const double cutoff = 1.0;
    const double friction = 6.75;
    const double dt = 0.04;
    const double temp = 1.0/BOLTZ; // So kT = 1.0 kJ/mol
    
    // Create a periodic box of particles.
    
    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    HarmonicBondForce* force = new HarmonicBondForce();
    force->setUsesPeriodicBoundaryConditions(true);
    for (int i = 0; i < numParticles; i++)
        system.addParticle(1.0);
    system.addForce(force);
    vector<Vec3> positions(numParticles);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    double scale = boxSize/gridWidth;
    for (int i = 0; i < gridWidth; i++)
        for (int j = 0; j < gridWidth; j++)
            for (int k = 0; k < gridWidth; k++)
                positions[i*gridWidth*gridWidth + j*gridWidth + k] = scale*Vec3(i+0.1*genrand_real2(sfmt), j+0.1*genrand_real2(sfmt), k+0.1*genrand_real2(sfmt));
    DPDIntegrator integrator(temp, friction, cutoff, dt);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    context.setVelocitiesToTemperature(temp, 0);
    
    // Simulate it and compute the diffusion coefficient.
    
    integrator.step(100);
    State state1 = context.getState(State::Positions);
    integrator.step(1000);
    State state2 = context.getState(State::Positions);
    double r2 = 0.0;
    for (int i = 0; i < numParticles; i++) {
        Vec3 delta = state1.getPositions()[i]-state2.getPositions()[i];
        r2 += delta.dot(delta);
    }
    r2 /= numParticles;
    double diffusion = r2/6.0/(state2.getTime()-state1.getTime());

    // Compare to a value computed with LAMMPS.

    ASSERT_USUALLY_EQUAL_TOL(0.5203, diffusion, 0.05);
}

void testTemperature() {
    const int numParticles = 100;
    const double temp = 100.0;
    const double boxSize = 8.0;
    System system;
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    DPDIntegrator integrator(temp, 20.0, 2.5, 0.002);
    NonbondedForce* force = new NonbondedForce();
    force->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    force->setCutoffDistance(2.5);
    vector<Vec3> positions(numParticles);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    for (int i = 0; i < numParticles; ++i) {
        system.addParticle(2.0);
        force->addParticle((i%2 == 0 ? 0.1 : -0.1), 0.2, 1.0);
        bool close = true;
        while (close) {
            positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
            close = false;
            for (int j = 0; j < i; ++j) {
                Vec3 delta = positions[i]-positions[j];
                if (delta.dot(delta) < 0.1)
                    close = true;
            }
        }
    }
    force->addException(0, numParticles-1, 0.0, 0.0, 0.0); // So there will be an off-diagonal tile with exclusions
    system.addForce(force);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    context.setVelocitiesToTemperature(temp, 0);
    
    // Let it equilibrate.
    
    integrator.step(1000);
    
    // Now run it for a while and see if the temperature is correct.
    
    double ke = 0.0;
    int steps = 5000;
    for (int i = 0; i < steps; ++i) {
        State state = context.getState(State::Energy);
        ke += state.getKineticEnergy();
        integrator.step(1);
    }
    ke /= steps;
    double expected = 0.5*numParticles*3*BOLTZ*temp;
    ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.08);
}

void testTypePairs() {
    const int numParticles = 8;
    const double temp = 100.0;
    System system;
    DPDIntegrator integrator(temp, 1.0, 2.0, 0.01);
    vector<Vec3> positions(numParticles);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    for (int i = 0; i < numParticles; ++i) {
        system.addParticle(2.0);
        positions[i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
        if (i > 3) {
            positions[i][0] += 5.0;
            integrator.setParticleType(i, 1);
        }
    }
    integrator.addTypePair(1, 1, 0.0, 2.0);
    Context context(system, integrator, platform);
    context.setPositions(positions);

    // The integrator should not affect the second cluster of particles.  The friction
    // for their mutual interactions is 0, and they're outside the cutoff distance from
    // the first cluster.
    
    integrator.step(10);
    State state = context.getState(State::Positions);
    for (int i = 0; i < 4; i++)
        for (int j = 0; j < 3; j++)
            ASSERT(positions[i][j] != state.getPositions()[i][j]);
    for (int i = 4; i < numParticles; i++)
        for (int j = 0; j < 3; j++)
            ASSERT_EQUAL_TOL(positions[i][j], state.getPositions()[i][j], 1e-6);
}

void testConstraints() {
    const int numParticles = 8;
    const int numConstraints = 5;
    const double temp = 100.0;
    System system;
    DPDIntegrator integrator(temp, 2.0, 1.5, 0.01);
    integrator.setConstraintTolerance(1e-5);
    NonbondedForce* forceField = new NonbondedForce();
    forceField->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
    forceField->setCutoffDistance(10.0);
    for (int i = 0; i < numParticles; ++i) {
        system.addParticle(10.0);
        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
    }
    system.addConstraint(0, 1, 1.0);
    system.addConstraint(1, 2, 1.0);
    system.addConstraint(2, 3, 1.0);
    system.addConstraint(4, 5, 1.0);
    system.addConstraint(6, 7, 1.0);
    system.addForce(forceField);
    Context context(system, integrator, platform);
    vector<Vec3> positions(numParticles);
    vector<Vec3> velocities(numParticles);
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);

    for (int i = 0; i < numParticles; ++i) {
        positions[i] = Vec3(i/2, (i+1)/2, 0);
        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
    }
    context.setPositions(positions);
    context.setVelocities(velocities);

    // Simulate it and see whether the constraints remain satisfied.

    for (int i = 0; i < 1000; ++i) {
        State state = context.getState(State::Positions);
        for (int j = 0; j < numConstraints; ++j) {
            int particle1, particle2;
            double distance;
            system.getConstraintParameters(j, particle1, particle2, distance);
            Vec3 p1 = state.getPositions()[particle1];
            Vec3 p2 = state.getPositions()[particle2];
            double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
            ASSERT_EQUAL_TOL(distance, dist, 1e-4);
        }
        integrator.step(1);
    }
}

void testConstrainedMasslessParticles() {
    System system;
    system.addParticle(0.0);
    system.addParticle(1.0);
    system.addConstraint(0, 1, 1.5);
    vector<Vec3> positions(2);
    positions[0] = Vec3(-1, 0, 0);
    positions[1] = Vec3(1, 0, 0);
    DPDIntegrator integrator(300.0, 2.0, 3.0, 0.01);
    bool failed = false;
    try {
        // This should throw an exception.
        
        Context context(system, integrator, platform);
    }
    catch (exception& ex) {
        failed = true;
    }
    ASSERT(failed);
    
    // Now make both particles massless, which should work.
    
    system.setParticleMass(1, 0.0);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    context.setVelocitiesToTemperature(300.0);
    integrator.step(1);
    State state = context.getState(State::Velocities);
    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}

void testRandomSeed() {
    const int numParticles = 8;
    const double temp = 100.0;
    System system;
    DPDIntegrator integrator(temp, 2.0, 5.0, 0.01);
    NonbondedForce* forceField = new NonbondedForce();
    forceField->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
    forceField->setCutoffDistance(10.0);
    for (int i = 0; i < numParticles; ++i) {
        system.addParticle(2.0);
        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
    }
    system.addForce(forceField);
    vector<Vec3> positions(numParticles);
    vector<Vec3> velocities(numParticles);
    for (int i = 0; i < numParticles; ++i) {
        positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
        velocities[i] = Vec3(0, 0, 0);
    }

    // Try twice with the same random seed.

    integrator.setRandomNumberSeed(5);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    context.setVelocities(velocities);
    integrator.step(10);
    State state1 = context.getState(State::Positions);
    context.reinitialize();
    context.setPositions(positions);
    context.setVelocities(velocities);
    integrator.step(10);
    State state2 = context.getState(State::Positions);

    // Try twice with a different random seed.

    integrator.setRandomNumberSeed(10);
    context.reinitialize();
    context.setPositions(positions);
    context.setVelocities(velocities);
    integrator.step(10);
    State state3 = context.getState(State::Positions);
    context.reinitialize();
    context.setPositions(positions);
    context.setVelocities(velocities);
    integrator.step(10);
    State state4 = context.getState(State::Positions);

    // Compare the results.

    for (int i = 0; i < numParticles; i++) {
        for (int j = 0; j < 3; j++) {
            ASSERT_EQUAL_TOL(state1.getPositions()[i][j], state2.getPositions()[i][j], 1e-7);
            ASSERT_EQUAL_TOL(state3.getPositions()[i][j], state4.getPositions()[i][j], 1e-7);
            ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
        }
    }
}

void testInitialTemperature() {
    // Check temperature initialization for a collection of randomly placed particles
    const int numParticles = 50000;
    const int nDoF = 3 * numParticles;
    const double targetTemperature = 300;
    System system;
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    std::vector<Vec3> positions(numParticles);

    for (int i = 0; i < numParticles; i++) {
        system.addParticle(1.0);
        positions[i][0] = genrand_real2(sfmt);
        positions[i][1] = genrand_real2(sfmt);
        positions[i][2] = genrand_real2(sfmt);
    }

    DPDIntegrator integrator(300, 25, 0.5, 0.001);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    context.setVelocitiesToTemperature(targetTemperature);
    auto velocities = context.getState(State::Velocities).getVelocities();
    double kineticEnergy = 0;
    for(const auto &v : velocities) kineticEnergy += 0.5 * v.dot(v);
    double temperature = (2*kineticEnergy / (nDoF*BOLTZ));
    ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
}

void testForceGroups() {
    System system;
    system.addParticle(1.0);
    DPDIntegrator integrator(0.0, 1.0, 1.0, 0.01);
    integrator.setIntegrationForceGroups(1<<1);
    CustomExternalForce* f1 = new CustomExternalForce("x");
    f1->addParticle(0);
    f1->setForceGroup(1);
    CustomExternalForce* f2 = new CustomExternalForce("y");
    f2->addParticle(0);
    f2->setForceGroup(2);
    system.addForce(f1);
    system.addForce(f2);
    Context context(system, integrator, platform);
    context.setPositions(vector<Vec3>(1));

    // Take one step and verify that the position was updated based only on f1.

    integrator.step(1);
    Vec3 pos = context.getState(State::Positions).getPositions()[0];
    ASSERT(pos[0] < 0);
    ASSERT(pos[1] == 0);
    ASSERT(pos[2] == 0);
}

void runPlatformTests();

int main(int argc, char* argv[]) {
    try {
        initializeTests(argc, argv);
        testConservationLaws();
        testDiffusion();
        testTemperature();
        testTypePairs();
        testConstraints();
        testConstrainedMasslessParticles();
        testRandomSeed();
        testInitialTemperature();
        testForceGroups();
        runPlatformTests();
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;
        return 1;
    }
    cout << "Done" << endl;
    return 0;
}