/* -------------------------------------------------------------------------- *
 *                                   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) 2012-2021 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
 * 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.                                     *
 * -------------------------------------------------------------------------- */

#ifdef WIN32
  #define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "ReferencePlatform.h"
#include "openmm/CustomCompoundBondForce.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/PeriodicTorsionForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>

using namespace OpenMM;
using namespace std;

const double TOL = 1e-5;

void testBond(bool byParticles) {
    // Create a system using a CustomCompoundBondForce.

    System customSystem;
    customSystem.addParticle(1.0);
    customSystem.addParticle(1.0);
    customSystem.addParticle(1.0);
    customSystem.addParticle(1.0);
    string expression;
    if (byParticles)
        expression = "0.5*kb*((distance(p1,p2)-b0)^2+(distance(p2,p3)-b0)^2)+0.5*ka*(angle(p2,p3,p4)-a0)^2+kt*(1+cos(dihedral(p1,p2,p3,p4)-t0))";
    else
        expression = "0.5*kb*((pointdistance(x1,y1,z1,x2,y2,z2)-b0)^2+(pointdistance(x2,y2,z2,x3,y3,z3)-b0)^2)+0.5*ka*(pointangle(x2,y2,z2,x3,y3,z3,x4,y4,z4)-a0)^2+kt*(1+cos(pointdihedral(x1,y1,z1,x2,y2,z2,x3,y3,z3,x4,y4,z4)-t0))";
    CustomCompoundBondForce* custom = new CustomCompoundBondForce(4, expression);
    custom->addPerBondParameter("kb");
    custom->addPerBondParameter("ka");
    custom->addPerBondParameter("kt");
    custom->addPerBondParameter("b0");
    custom->addPerBondParameter("a0");
    custom->addPerBondParameter("t0");
    vector<int> particles(4);
    particles[0] = 0;
    particles[1] = 1;
    particles[2] = 3;
    particles[3] = 2;
    vector<double> parameters(6);
    parameters[0] = 1.5;
    parameters[1] = 0.8;
    parameters[2] = 0.6;
    parameters[3] = 1.1;
    parameters[4] = 2.9;
    parameters[5] = 1.3;
    custom->addBond(particles, parameters);
    customSystem.addForce(custom);
    ASSERT(!custom->usesPeriodicBoundaryConditions());
    ASSERT(!customSystem.usesPeriodicBoundaryConditions());

    // Create an identical system using standard forces.

    System standardSystem;
    standardSystem.addParticle(1.0);
    standardSystem.addParticle(1.0);
    standardSystem.addParticle(1.0);
    standardSystem.addParticle(1.0);
    HarmonicBondForce* bonds = new HarmonicBondForce();
    bonds->addBond(0, 1, 1.1, 1.5);
    bonds->addBond(1, 3, 1.1, 1.5);
    standardSystem.addForce(bonds);
    HarmonicAngleForce* angles = new HarmonicAngleForce();
    angles->addAngle(1, 3, 2, 2.9, 0.8);
    standardSystem.addForce(angles);
    PeriodicTorsionForce* torsions = new PeriodicTorsionForce();
    torsions->addTorsion(0, 1, 3, 2, 1, 1.3, 0.6);
    standardSystem.addForce(torsions);

    // Set the atoms in various positions, and verify that both systems give identical forces and energy.

    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    VerletIntegrator integrator1(0.01);
    VerletIntegrator integrator2(0.01);
    Context c1(customSystem, integrator1, platform);
    Context c2(standardSystem, integrator2, platform);
    vector<Vec3> positions(4);
    for (int i = 0; i < 10; i++) {
        for (int j = 0; j < (int) positions.size(); j++)
            positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
        c1.setPositions(positions);
        c2.setPositions(positions);
        State s1 = c1.getState(State::Forces | State::Energy);
        State s2 = c2.getState(State::Forces | State::Energy);
        for (int i = 0; i < customSystem.getNumParticles(); i++)
            ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
        ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
    }
    
    // Try changing the bond parameters and make sure it's still correct.
    
    parameters[0] = 1.6;
    parameters[3] = 1.3;
    custom->setBondParameters(0, particles, parameters);
    custom->updateParametersInContext(c1);
    bonds->setBondParameters(0, 0, 1, 1.3, 1.6);
    bonds->setBondParameters(1, 1, 3, 1.3, 1.6);
    bonds->updateParametersInContext(c2);
    {
        State s1 = c1.getState(State::Forces | State::Energy);
        State s2 = c2.getState(State::Forces | State::Energy);
        const vector<Vec3>& forces = s1.getForces();
        for (int i = 0; i < customSystem.getNumParticles(); i++)
            ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
        ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
    }
}

void testPositionDependence() {
    System customSystem;
    customSystem.addParticle(1.0);
    customSystem.addParticle(1.0);
    CustomCompoundBondForce* custom = new CustomCompoundBondForce(2, "scale1*distance(p1,p2)+scale2*x1+2*y2");
    custom->addGlobalParameter("scale1", 0.3);
    custom->addGlobalParameter("scale2", 0.2);
    vector<int> particles(2);
    particles[0] = 1;
    particles[1] = 0;
    vector<double> parameters;
    custom->addBond(particles, parameters);
    customSystem.addForce(custom);
    vector<Vec3> positions(2);
    positions[0] = Vec3(1.5, 1, 0);
    positions[1] = Vec3(0.5, 1, 0);
    VerletIntegrator integrator(0.01);
    Context context(customSystem, integrator, platform);
    context.setPositions(positions);
    State state = context.getState(State::Forces | State::Energy);
    ASSERT_EQUAL_TOL(0.3*1.0+0.2*0.5+2*1, state.getPotentialEnergy(), 1e-5);
    ASSERT_EQUAL_VEC(Vec3(-0.3, -2, 0), state.getForces()[0], 1e-5);
    ASSERT_EQUAL_VEC(Vec3(0.3-0.2, 0, 0), state.getForces()[1], 1e-5);
}

void testContinuous2DFunction() {
    const int xsize = 10;
    const int ysize = 11;
    const double xmin = 0.4;
    const double xmax = 1.1;
    const double ymin = 0.0;
    const double ymax = 0.95;
    System system;
    system.addParticle(1.0);
    VerletIntegrator integrator(0.01);
    CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1)+1");
    vector<int> particles(1, 0);
    forceField->addBond(particles, vector<double>());
    vector<double> table(xsize*ysize);
    for (int i = 0; i < xsize; i++) {
        for (int j = 0; j < ysize; j++) {
            double x = xmin + i*(xmax-xmin)/xsize;
            double y = ymin + j*(ymax-ymin)/ysize;
            table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
        }
    }
    forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
    system.addForce(forceField);
    Context context(system, integrator, platform);
    vector<Vec3> positions(1);
    for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
        for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
            positions[0] = Vec3(x, y, 1.5);
            context.setPositions(positions);
            State state = context.getState(State::Forces | State::Energy);
            const vector<Vec3>& forces = state.getForces();
            double energy = 1;
            Vec3 force(0, 0, 0);
            if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
                energy = sin(0.25*x)*cos(0.33*y)+1;
                force[0] = -0.25*cos(0.25*x)*cos(0.33*y);
                force[1] = 0.3*sin(0.25*x)*sin(0.33*y);
            }
            ASSERT_EQUAL_VEC(force, forces[0], 0.1);
            ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
        }
    }
}

void testContinuous3DFunction() {
    const int xsize = 10;
    const int ysize = 11;
    const int zsize = 12;
    const double xmin = 0.4;
    const double xmax = 1.1;
    const double ymin = 2.0;
    const double ymax = 2.9;
    const double zmin = 0.2;
    const double zmax = 1.35;
    System system;
    system.addParticle(1.0);
    VerletIntegrator integrator(0.01);
    CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1,z1)+1");
    vector<int> particles(1, 0);
    forceField->addBond(particles, vector<double>());
    vector<double> table(xsize*ysize*zsize);
    for (int i = 0; i < xsize; i++) {
        for (int j = 0; j < ysize; j++) {
            for (int k = 0; k < zsize; k++) {
                double x = xmin + i*(xmax-xmin)/xsize;
                double y = ymin + j*(ymax-ymin)/ysize;
                double z = zmin + k*(zmax-zmin)/zsize;
                table[i+xsize*j+xsize*ysize*k] = sin(0.25*x)*cos(0.33*y)*(1+z);
            }
        }
    }
    forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
    system.addForce(forceField);
    Context context(system, integrator, platform);
    vector<Vec3> positions(1);
    for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
        for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
            for (double z = zmin-0.15; z < zmax+0.2; z += 0.1) {
                positions[0] = Vec3(x, y, z);
                context.setPositions(positions);
                State state = context.getState(State::Forces | State::Energy);
                const vector<Vec3>& forces = state.getForces();
                double energy = 1;
                Vec3 force(0, 0, 0);
                if (x >= xmin && x <= xmax && y >= ymin && y <= ymax && z >= zmin && z <= zmax) {
                    energy = sin(0.25*x)*cos(0.33*y)*(1.0+z)+1;
                    force[0] = -0.25*cos(0.25*x)*cos(0.33*y)*(1.0+z);
                    force[1] = 0.3*sin(0.25*x)*sin(0.33*y)*(1.0+z);
                    force[2] = -sin(0.25*x)*cos(0.33*y);
                }
                ASSERT_EQUAL_VEC(force, forces[0], 0.1);
                ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
            }
        }
    }
}

void testMultipleBonds() {
    // Two compound bonds using Urey-Bradley example from API doc
    System customSystem;
    customSystem.addParticle(1.0);
    customSystem.addParticle(1.0);
    customSystem.addParticle(1.0);
    customSystem.addParticle(1.0);
    CustomCompoundBondForce* custom = new CustomCompoundBondForce(3,
            "0.5*(kangle*(angle(p1,p2,p3)-theta0)^2+kbond*(distance(p1,p3)-r0)^2)");
    custom->addPerBondParameter("kangle");
    custom->addPerBondParameter("kbond");
    custom->addPerBondParameter("theta0");
    custom->addPerBondParameter("r0");
    vector<double> parameters(4);
    parameters[0] = 1.0;
    parameters[1] = 1.0;
    parameters[2] = 2 * M_PI / 3;
    parameters[3] = sqrt(3.0) / 2;
    vector<int> particles0(3);
    particles0[0] = 0;
    particles0[1] = 1;
    particles0[2] = 2;
    vector<int> particles1(3);
    particles1[0] = 1;
    particles1[1] = 2;
    particles1[2] = 3;
    custom->addBond(particles0, parameters);
    custom->addBond(particles1, parameters);
    customSystem.addForce(custom);

    vector<Vec3> positions(4);
    positions[0] = Vec3(0, 0.5, 0);
    positions[1] = Vec3(0, 0, 0);
    positions[2] = Vec3(0.5, 0, 0);
    positions[3] = Vec3(0.6, 0, 0.4);
    VerletIntegrator integrator(0.01);
    Context context(customSystem, integrator, platform);
    context.setPositions(positions);
    State state = context.getState(State::Forces | State::Energy);
    ASSERT_EQUAL_TOL(0.199, state.getPotentialEnergy(), 1e-3);
    vector<Vec3> forces(state.getForces());
    ASSERT_EQUAL_VEC(Vec3(-1.160, 0.112, 0.0), forces[0], 1e-3);
    ASSERT_EQUAL_VEC(Vec3(0.927, 1.047, -0.638), forces[1], 1e-3);
    ASSERT_EQUAL_VEC(Vec3(-0.543, -1.160, 0.721), forces[2], 1e-3);
    ASSERT_EQUAL_VEC(Vec3(0.776, 0.0, -0.084), forces[3], 1e-3);
}

void testIllegalVariable() {
    System system;
    system.addParticle(1.0);
    system.addParticle(1.0);
    CustomCompoundBondForce* force = new CustomCompoundBondForce(2, "1+none");
    vector<int> particles;
    particles.push_back(0);
    particles.push_back(1);
    force->addBond(particles);
    system.addForce(force);
    VerletIntegrator integrator(0.001);
    bool threwException = false;
    try {
        Context(system, integrator, platform);
    }
    catch (const exception& e) {
        threwException = true;
    }
    ASSERT(threwException);
}

void testPeriodic(bool byParticles) {
    // Create a force that uses periodic boundary conditions.

    System customSystem;
    customSystem.addParticle(1.0);
    customSystem.addParticle(1.0);
    customSystem.addParticle(1.0);
    customSystem.addParticle(1.0);
    customSystem.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
    string expression;
    if (byParticles)
        expression = "0.5*kb*((distance(p1,p2)-b0)^2+(distance(p2,p3)-b0)^2)+0.5*ka*(angle(p2,p3,p4)-a0)^2+kt*(1+cos(dihedral(p1,p2,p3,p4)-t0))";
    else
        expression = "0.5*kb*((pointdistance(x1,y1,z1,x2,y2,z2)-b0)^2+(pointdistance(x2,y2,z2,x3,y3,z3)-b0)^2)+0.5*ka*(pointangle(x2,y2,z2,x3,y3,z3,x4,y4,z4)-a0)^2+kt*(1+cos(pointdihedral(x1,y1,z1,x2,y2,z2,x3,y3,z3,x4,y4,z4)-t0))";
    CustomCompoundBondForce* custom = new CustomCompoundBondForce(4, expression);
    custom->addPerBondParameter("kb");
    custom->addPerBondParameter("ka");
    custom->addPerBondParameter("kt");
    custom->addPerBondParameter("b0");
    custom->addPerBondParameter("a0");
    custom->addPerBondParameter("t0");
    vector<int> particles(4);
    particles[0] = 0;
    particles[1] = 1;
    particles[2] = 3;
    particles[3] = 2;
    vector<double> parameters(6);
    parameters[0] = 1.5;
    parameters[1] = 0.8;
    parameters[2] = 0.6;
    parameters[3] = 1.1;
    parameters[4] = 2.9;
    parameters[5] = 1.3;
    custom->addBond(particles, parameters);
    custom->setUsesPeriodicBoundaryConditions(true);
    customSystem.addForce(custom);

    // Create an identical system using standard forces.

    System standardSystem;
    standardSystem.addParticle(1.0);
    standardSystem.addParticle(1.0);
    standardSystem.addParticle(1.0);
    standardSystem.addParticle(1.0);
    standardSystem.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
    HarmonicBondForce* bonds = new HarmonicBondForce();
    bonds->addBond(0, 1, 1.1, 1.5);
    bonds->addBond(1, 3, 1.1, 1.5);
    bonds->setUsesPeriodicBoundaryConditions(true);
    standardSystem.addForce(bonds);
    HarmonicAngleForce* angles = new HarmonicAngleForce();
    angles->addAngle(1, 3, 2, 2.9, 0.8);
    angles->setUsesPeriodicBoundaryConditions(true);
    standardSystem.addForce(angles);
    PeriodicTorsionForce* torsions = new PeriodicTorsionForce();
    torsions->addTorsion(0, 1, 3, 2, 1, 1.3, 0.6);
    torsions->setUsesPeriodicBoundaryConditions(true);
    standardSystem.addForce(torsions);

    // Set the atoms in various positions, and verify that both systems give identical forces and energy.

    OpenMM_SFMT::SFMT sfmt;
    init_gen_rand(0, sfmt);
    VerletIntegrator integrator1(0.01);
    VerletIntegrator integrator2(0.01);
    Context c1(customSystem, integrator1, platform);
    Context c2(standardSystem, integrator2, platform);
    vector<Vec3> positions(4);
    for (int i = 0; i < 10; i++) {
        for (int j = 0; j < (int) positions.size(); j++)
            positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
        c1.setPositions(positions);
        c2.setPositions(positions);
        State s1 = c1.getState(State::Forces | State::Energy);
        State s2 = c2.getState(State::Forces | State::Energy);
        for (int i = 0; i < customSystem.getNumParticles(); i++)
            ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
        ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
    }
}

void testEnergyParameterDerivatives() {
    System system;
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(1.0);
    system.addParticle(1.0);
    VerletIntegrator integrator(0.01);
    CustomCompoundBondForce* custom = new CustomCompoundBondForce(4, "k*(dihedral(p1,p2,p3,p4)-theta0)^2");
    custom->addGlobalParameter("theta0", 0.0);
    custom->addGlobalParameter("k", 0.0);
    custom->addEnergyParameterDerivative("theta0");
    custom->addEnergyParameterDerivative("k");
    vector<int> particles(4);
    particles[0] = 0;
    particles[1] = 1;
    particles[2] = 2;
    particles[3] = 3;
    vector<double> parameters;
    custom->addBond(particles, parameters);
    system.addForce(custom);
    Context context(system, integrator, platform);
    vector<Vec3> positions(4);
    positions[0] = Vec3(0, 2, 0);
    positions[1] = Vec3(0, 0, 0);
    positions[2] = Vec3(1, 0, 0);
    positions[3] = Vec3(1, 1, 1);
    context.setPositions(positions);
    double theta = M_PI/4;
    for (int i = 0; i < 10; i++) {
        double theta0 = 0.1*i;
        double k = 10-i;
        context.setParameter("theta0", theta0);
        context.setParameter("k", k);
        State state = context.getState(State::ParameterDerivatives);
        map<string, double> derivs = state.getEnergyParameterDerivatives();
        double dEdtheta0 = -2*k*(theta-theta0);
        double dEdk = (theta-theta0)*(theta-theta0);
        ASSERT_EQUAL_TOL(dEdtheta0, derivs["theta0"], 1e-5);
        ASSERT_EQUAL_TOL(dEdk, derivs["k"], 1e-5);
    }
}

void runPlatformTests();

int main(int argc, char* argv[]) {
    try {
        initializeTests(argc, argv);
        testBond(true);
        testBond(false);
        testPositionDependence();
        testContinuous2DFunction();
        testContinuous3DFunction();
        testMultipleBonds();
        testIllegalVariable();
        testPeriodic(true);
        testPeriodic(false);
        testEnergyParameterDerivatives();
        runPlatformTests();
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;
        return 1;
    }
    cout << "Done" << endl;
    return 0;
}


