/* -------------------------------------------------------------------------- *
 *                                   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.               *
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 * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
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#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/VariableLangevinIntegrator.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>

using namespace OpenMM;
using namespace std;

const double TOL = 1e-5;

void testSingleBond() {
    System system;
    system.addParticle(2.0);
    system.addParticle(2.0);
    VariableLangevinIntegrator integrator(0, 0.1, 1e-6);
    HarmonicBondForce* forceField = new HarmonicBondForce();
    forceField->addBond(0, 1, 1.5, 1);
    system.addForce(forceField);
    Context context(system, integrator, platform);
    vector<Vec3> positions(2);
    positions[0] = Vec3(-1, 0, 0);
    positions[1] = Vec3(1, 0, 0);
    context.setPositions(positions);

    // This is simply a damped harmonic oscillator, so compare it to the analytical solution.

    double freq = std::sqrt(1-0.05*0.05);
    for (int i = 0; i < 1000; ++i) {
        State state = context.getState(State::Positions | State::Velocities);
        double time = state.getTime();
        double expectedDist = 1.5+0.5*std::exp(-0.05*time)*std::cos(freq*time);
        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
        double expectedSpeed = -0.5*std::exp(-0.05*time)*(0.05*std::cos(freq*time)+freq*std::sin(freq*time));
        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
        ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
        integrator.step(1);
    }

    // Now set the friction to 0 and see if it conserves energy.

    integrator.setFriction(0.0);
    context.setPositions(positions);
    State state = context.getState(State::Energy);
    double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
    for (int i = 0; i < 1000; ++i) {
        state = context.getState(State::Energy);
        double energy = state.getKineticEnergy()+state.getPotentialEnergy();
        ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05);
        integrator.step(1);
    }
}

void testTemperature() {
    const int numParticles = 8;
    const double temp = 100.0;
    System system;
    VariableLangevinIntegrator integrator(temp, 5.0, 5e-5);
    NonbondedForce* forceField = new NonbondedForce();
    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);
    for (int i = 0; i < numParticles; ++i)
        positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
    context.setPositions(positions);
    context.setVelocitiesToTemperature(temp);

    // Let it equilibrate.

    integrator.step(5000);

    // Now run it for a while and see if the temperature is correct.

    double ke = 0.0;
    for (int i = 0; i < 5000; ++i) {
        State state = context.getState(State::Energy);
        ke += state.getKineticEnergy();
        integrator.step(5);
    }
    ke /= 5000;
    double expected = 0.5*numParticles*3*BOLTZ*temp;
    ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.1);
}

void testConstraints() {
    const int numParticles = 8;
    const double temp = 100.0;
    System system;
    VariableLangevinIntegrator integrator(temp, 2.0, 1e-5);
    integrator.setConstraintTolerance(1e-5);
    integrator.setRandomNumberSeed(0);
    NonbondedForce* forceField = new NonbondedForce();
    for (int i = 0; i < numParticles; ++i) {
        system.addParticle(10.0);
        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
    }
    for (int i = 0; i < numParticles-1; ++i)
        system.addConstraint(i, i+1, 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 < numParticles-1; ++j) {
            Vec3 p1 = state.getPositions()[j];
            Vec3 p2 = state.getPositions()[j+1];
            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(1.0, dist, 2e-5);
        }
        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);
    VariableLangevinIntegrator integrator(300.0, 2.0, 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;
    VariableLangevinIntegrator integrator(temp, 2.0, 1e-5);
    NonbondedForce* forceField = new NonbondedForce();
    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(state1.getPositions()[i][j] == state2.getPositions()[i][j]);
            ASSERT(state3.getPositions()[i][j] == state4.getPositions()[i][j]);
            ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
        }
    }
}

void testArgonBox() {
    const int gridSize = 8;
    const double mass = 40.0;            // Ar atomic mass
    const double temp = 120.0;           // K
    const double epsilon = BOLTZ * temp; // L-J well depth for Ar
    const double sigma = 0.34;           // L-J size for Ar in nm
    const double density = 0.8;          // atoms / sigma^3
    double cellSize = sigma / pow(density, 0.333);
    double boxSize = gridSize * cellSize;
    double cutoff = 2.0 * sigma;

    // Create a box of argon atoms.
    
    System system;
    NonbondedForce* nonbonded = new NonbondedForce();
    vector<Vec3> positions;
    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    const Vec3 half(0.5, 0.5, 0.5);
    int numParticles = 0;
    for (int i = 0; i < gridSize; i++) {
        for (int j = 0; j < gridSize; j++) {
            for (int k = 0; k < gridSize; k++) {
                system.addParticle(mass);
                nonbonded->addParticle(0, sigma, epsilon);
                positions.push_back((Vec3(i, j, k) + half + Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt))*0.1) * cellSize);
                ++numParticles;
            }
        }
    }

    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    nonbonded->setCutoffDistance(cutoff);
    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
    system.addForce(nonbonded);

    VariableLangevinIntegrator integrator(temp, 6.0, 1e-4);
    Context context(system, integrator, platform);
    context.setPositions(positions);
    context.setVelocitiesToTemperature(temp);

    // Equilibrate.

    integrator.stepTo(2.0);

    // Make sure the temperature is correct.
    
    double ke = 0.0;
    for (int i = 0; i < 1000; ++i) {
        double t = 2.0 + 0.02 * (i + 1);
        integrator.stepTo(t);
        State state = context.getState(State::Energy);
        ke += state.getKineticEnergy();
    }
    ke /= 1000;
    double expected = 1.5 * numParticles * BOLTZ * temp;
    ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.01);
}

void runPlatformTests();

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