/* -----------------------------------------------------------------------------
 *              OpenMM(tm) HelloWaterBox example in C++ (June 2009)
 * -----------------------------------------------------------------------------
 * This is a complete, self-contained "hello world" example demonstrating 
 * GPU-accelerated simulation of a system with both bonded and nonbonded forces, 
 * using water (H-O-H) in a periodic box as an example. This is a constant-
 * temperature simulation using an Andersen thermostat. A multi-frame PDB file 
 * is written to stdout which can be read by VMD or other visualization tool to 
 * produce an animation of the resulting trajectory.
 *
 * Pay particular attention to the handling of units in this example. Incorrect
 * handling of units is a very common error; this example shows how you can
 * continue to work with Amber-style units of Angstroms and kCals while correctly
 * communicating with OpenMM in nanometers and kJoules.
 * -------------------------------------------------------------------------- */

#include <cstdio>
#include <string>
#include <vector>
#include <cstdlib>

// -----------------------------------------------------------------------------
//                                 MOCK MD CODE
// -----------------------------------------------------------------------------
// The code starting here and through main() below is meant to represent in 
// simplified form some pre-existing molecular dynamics code, which defines its 
// own data structures for force fields, the atoms in this simulation, and the 
// simulation parameters, and takes care of recording the trajectory. All this 
// has nothing to do with OpenMM; the OpenMM-dependent code comes later and is 
// clearly marked below.
// -----------------------------------------------------------------------------

//                     MODELING AND SIMULATION PARAMETERS
const int    NumWatersAlongEdge  = 10;     // Size of box is NxNxN waters.
const double Temperature         = 300;    // Kelvins
const double FrictionInPerPs     = 91.;    // collisions per picosecond
const double CutoffDistanceInAng = 10.;    // Angstroms

const bool   UseConstraints      = true;   // Should we constrain O-H bonds?
const double StepSizeInFs        = 2;      // integration step size (fs)
const double ReportIntervalInFs  = 100;    // how often to generate PDB frame (fs)
const double SimulationTimeInPs  = 10;     // total simulation time (ps)

//                              FORCE FIELD DATA
// For this example we're using a tiny subset of the Amber99 force field.
// We want to keep the data in the original unit system to avoid conversion
// bugs; this requires conversion on the way in and out of OpenMM.

// Amber reduces nonbonded forces between 1-4 bonded atoms. (These won't be
// used in our all-water simulation.)
const double Coulomb14Scale      = 0.5;
const double LennardJones14Scale = 0.5;

// We only need force field parameters for water here.
const double O_mass             = 15.9994;  // Daltons
const double O_charge           = -0.834;   // e
const double O_vdwRadInAng      = 1.7683;   // Angstroms
const double O_vdwEnergyInKcal  = 0.1520;   // kcal per mole

const double H_mass             = 1.00794;
const double H_charge           = 0.417;
const double H_vdwRadInAng      = 0.0001;
const double H_vdwEnergyInKcal  = 0.0000;

// Parameters for the O-H bonds.
const double OH_nominalLengthInAng      = 0.9572;
const double OH_stiffnessInKcalPerAng2  = 553.0; // that is, e=k(x-x0)^2

// Parameters for the H-O-H angle.
const double HOH_nominalAngleInDeg      = 104.52;
const double HOH_stiffnessInKcalPerRad2 = 100.; // that is e=k(a-a0)^2

//                               PDB FILE WRITER
// This is a PDB writer that only knows how to write out water molecules. It is
// just here for this example and has nothing to do with OpenMM!
static void
myWritePDBFrame(int frameNum, double timeInPs, const std::vector<double>& atomPosInAng) 
{
    const char* atomNames[] = {" O  ", " H1 ", " H2 "}; // cycle through these
    printf("MODEL     %d\n", frameNum);
    printf("REMARK 250 time=%.3f picoseconds\n", timeInPs);
    for (int atom=0; atom < (int)atomPosInAng.size()/3; ++atom) 
    {
        printf("HETATM%5d %4s HOH  %4d    ",        // start of pdb HETATM line
            atom+1, atomNames[atom%3], 1 + atom/3); // atom number, name, residue #
        printf("%8.3f%8.3f%8.3f",                   // middle of pdb HETATM line
            atomPosInAng[3*atom+0], atomPosInAng[3*atom+1], atomPosInAng[3*atom+2]);
        printf("  1.00  0.00            \n");       // end of pdb HETATM line
    }
    printf("ENDMDL\n"); // end of trajectory frame
}


// -----------------------------------------------------------------------------
//                           INTERFACE TO OpenMM
// -----------------------------------------------------------------------------
// These four functions and an opaque structure are used to interface our main
// program with OpenMM without the main program having any direct interaction
// with the OpenMM API. This is a clean approach for interfacing with any MD
// code, although the details of the interface routines will differ. This is
// still just "locally written" code and is not required by OpenMM. Normally 
// these would be in another compilation unit but they are defined later in
// this file.
struct MyOpenMMData;
static MyOpenMMData* myInitializeOpenMM(int    numWatersAlongEdge,
                                        double temperature,
                                        double frictionInPerPs,
                                        double stepSizeInFs, 
                                        std::string& platformName);
static void          myStepWithOpenMM(MyOpenMMData*, int numSteps);
static void          myGetOpenMMState(MyOpenMMData*, double& time,
                                      std::vector<double>& atomPosInAng);
static void          myTerminateOpenMM(MyOpenMMData*);


// -----------------------------------------------------------------------------
//                           WATER BOX MAIN PROGRAM
// -----------------------------------------------------------------------------
int main() {
    // ALWAYS enclose all OpenMM calls with a try/catch block to make sure that
    // usage and runtime errors are caught and reported.
    try {
        std::string   platformName;

        // Set up OpenMM data structures; return handle and OpenMM Platform name.
        MyOpenMMData* omm = myInitializeOpenMM(NumWatersAlongEdge, Temperature, 
                                               FrictionInPerPs, StepSizeInFs, 
                                               platformName); // output

        // Run the simulation:
        //  (1) Write the first line of the PDB file and the initial configuration.
        //  (2) Run silently entirely within OpenMM between reporting intervals.
        //  (3) Write a PDB frame when the time comes.
        printf("REMARK  Using OpenMM platform %s\n", platformName.c_str());

        std::vector<double> atomPositionsInAng; // x,y,z,x,y,z, ...
        const int NumSilentSteps = (int)(ReportIntervalInFs / StepSizeInFs + 0.5);
        for (int frame=1; ; ++frame) {
            double time;
            myGetOpenMMState(omm, time, atomPositionsInAng);
            myWritePDBFrame(frame, time, atomPositionsInAng);

            if (time >= SimulationTimeInPs)
                break;

            myStepWithOpenMM(omm, NumSilentSteps);
        } 
 
        // Clean up OpenMM data structures.
        myTerminateOpenMM(omm);

        return 0; // Normal return from main.
    }

    // Catch and report usage and runtime errors detected by OpenMM and fail.
    catch(const std::exception& e) {
        printf("EXCEPTION: %s\n", e.what());
        return 1;
    }
}


// -----------------------------------------------------------------------------
//                           OpenMM-USING CODE
// -----------------------------------------------------------------------------
// The OpenMM API is visible only at this point and below. Normally this would
// be in a separate compilation module; we're including it here for simplicity.
// -----------------------------------------------------------------------------

// Suppress irrelevant warnings from Microsoft's compiler.
#ifdef _MSC_VER
    #pragma warning(disable:4996)   // sprintf is unsafe 
#endif

#include "OpenMM.h"
using OpenMM::Vec3; // so we can just say "Vec3" below


// This is our opaque "handle" class containing all the OpenMM objects that
// must persist from call to call during a simulation. The main program gets 
// a pointer to one of these but sees it as essentially a void* since it 
// doesn't know the definition of this class.
struct MyOpenMMData {
    MyOpenMMData() : system(0), context(0), integrator(0) {}
    ~MyOpenMMData() {delete context; delete integrator; delete system;}
    OpenMM::System*         system;
    OpenMM::Integrator*     integrator;
    OpenMM::Context*  context;
};


// -----------------------------------------------------------------------------
//                      INITIALIZE OpenMM DATA STRUCTURES
// -----------------------------------------------------------------------------
// We take these actions here:
// (1) Load any available OpenMM plugins, e.g. Cuda and Brook.
// (2) Allocate a MyOpenMMData structure to hang on to OpenMM data structures
//     in a manner which is opaque to the caller.
// (3) Fill the OpenMM::System with the force field parameters we want to
//     use and the particular set of atoms to be simulated.
// (4) Create an Integrator and a Context associating the Integrator with
//     the System.
// (5) Select the OpenMM platform to be used.
// (6) Return the MyOpenMMData struct and the name of the Platform in use.
//
// Note that this function must understand the calling MD code's molecule and
// force field data structures so will need to be customized for each MD code.
static MyOpenMMData* 
myInitializeOpenMM( int                 numWatersAlongEdge,
                    double              temperature,
                    double              frictionInPerPs,
                    double              stepSizeInFs, 
                    std::string&        platformName) 
{
    // Load all available OpenMM plugins from their default location.
    OpenMM::Platform::loadPluginsFromDirectory
       (OpenMM::Platform::getDefaultPluginsDirectory());

    // Allocate space to hold OpenMM objects while we're using them.
    MyOpenMMData* omm = new MyOpenMMData();

    // Create a System and Force objects within the System. Retain a reference
    // to each force object so we can fill in the forces. Note: the System owns
    // the force objects and will take care of deleting them; don't do it yourself!
    OpenMM::System&                 system      = *(omm->system = new OpenMM::System());

    OpenMM::NonbondedForce&         nonbond     = *new OpenMM::NonbondedForce();
    system.addForce(&nonbond);

    OpenMM::HarmonicBondForce&      bondStretch = *new OpenMM::HarmonicBondForce();
    system.addForce(&bondStretch);

    OpenMM::HarmonicAngleForce&     bondBend    = *new OpenMM::HarmonicAngleForce();
    system.addForce(&bondBend);

    OpenMM::AndersenThermostat&     thermostat  = *new OpenMM::AndersenThermostat(
            temperature,      // kelvins
            frictionInPerPs); // collision frequency in 1/picoseconds
    system.addForce(&thermostat);
    
    // Volume of one water is 30 Angstroms cubed;
    // Thus length in one dimension is cube-root of 30,
    // or 3.107 Angstroms or 0.3107 nanometers
    const double WaterSizeInNm = 0.3107; // edge of cube containing one water, in nanometers
    // Place water molecules one at a time in an NxNxN rectilinear grid
    const double boxEdgeLengthInNm = WaterSizeInNm * numWatersAlongEdge;

    // Create periodic box
    nonbond.setNonbondedMethod(OpenMM::NonbondedForce::CutoffPeriodic);
    nonbond.setCutoffDistance(CutoffDistanceInAng * OpenMM::NmPerAngstrom);
    system.setDefaultPeriodicBoxVectors(Vec3(boxEdgeLengthInNm,0,0),
                                  Vec3(0,boxEdgeLengthInNm,0), 
                                  Vec3(0,0,boxEdgeLengthInNm));

    // Specify the atoms and their properties:
    //  (1) System needs to know the masses and constraints (if any).
    //  (2) NonbondedForce needs charges,van der Waals properties (in MD units!).
    //  (3) Collect starting positions for initializing the simulation later.

    // Create data structures to hold lists of initial positions and bonds
    std::vector<Vec3>                   initialPosInNm;
    std::vector< std::pair<int,int> >   bondPairs;
    
    // Add water molecules one at a time in the NxNxN cubic lattice
    for (int latticeX = 0; latticeX < numWatersAlongEdge; ++latticeX)
    for (int latticeY = 0; latticeY < numWatersAlongEdge; ++latticeY)
    for (int latticeZ = 0; latticeZ < numWatersAlongEdge; ++latticeZ)
    {
        // Add parameters for one water molecule
        
        // Add atom masses to system
        int  oIndex = system.addParticle(O_mass); // O
        int h1Index = system.addParticle(H_mass); // H1
        int h2Index = system.addParticle(H_mass); // H2
        
        // Add atom charge, sigma, and stiffness to nonbonded force
        nonbond.addParticle( // Oxygen
                O_charge,
                O_vdwRadInAng     * OpenMM::NmPerAngstrom * OpenMM::SigmaPerVdwRadius,
                O_vdwEnergyInKcal * OpenMM::KJPerKcal);
        nonbond.addParticle( // Hydrogen1
                H_charge,
                H_vdwRadInAng     * OpenMM::NmPerAngstrom * OpenMM::SigmaPerVdwRadius,
                H_vdwEnergyInKcal * OpenMM::KJPerKcal);
        nonbond.addParticle( // Hydrogen2
                H_charge,
                H_vdwRadInAng     * OpenMM::NmPerAngstrom * OpenMM::SigmaPerVdwRadius,
                H_vdwEnergyInKcal * OpenMM::KJPerKcal);
        
        // Constrain O-H bond lengths or use harmonic forces.
        if (UseConstraints) {
            system.addConstraint(oIndex, h1Index,
                             OH_nominalLengthInAng * OpenMM::NmPerAngstrom);
            system.addConstraint(oIndex, h2Index,
                             OH_nominalLengthInAng * OpenMM::NmPerAngstrom);
        } else {
            // Add stretch parameters for two covalent bonds
            // Note factor of 2 for stiffness below because Amber specifies the constant
            // as it is used in the harmonic energy term kx^2 with force 2kx; OpenMM wants 
            // it as used in the force term kx, with energy kx^2/2.
            bondStretch.addBond(oIndex, h1Index,
                    OH_nominalLengthInAng     * OpenMM::NmPerAngstrom,
                    OH_stiffnessInKcalPerAng2 * 2 * OpenMM::KJPerKcal 
                        * OpenMM::AngstromsPerNm * OpenMM::AngstromsPerNm);
            bondStretch.addBond(oIndex, h2Index,
                    OH_nominalLengthInAng     * OpenMM::NmPerAngstrom,
                    OH_stiffnessInKcalPerAng2 * 2 * OpenMM::KJPerKcal 
                        * OpenMM::AngstromsPerNm * OpenMM::AngstromsPerNm);
        }

        // Store bonds for exclusion list
        bondPairs.push_back(std::make_pair(oIndex, h1Index));
        bondPairs.push_back(std::make_pair(oIndex, h2Index));
                    
        // Add bond bend parameters for one angle.
        // See note under bond stretch above regarding the factor of 2 here.
        bondBend.addAngle(h1Index, oIndex, h2Index,
                HOH_nominalAngleInDeg      * OpenMM::RadiansPerDegree,
                HOH_stiffnessInKcalPerRad2 * 2 * OpenMM::KJPerKcal);
               
        // Location of this molecule in the lattice
        Vec3 latticeVec(WaterSizeInNm * latticeX, 
                        WaterSizeInNm * latticeY, 
                        WaterSizeInNm * latticeZ);

        // flip half the waters to prevent giant dipole
        int flip = (rand() % 100) > 49 ? 1 : -1;

        // place this water
        initialPosInNm.push_back(Vec3(0,0,0) + latticeVec); // O
        initialPosInNm.push_back(Vec3(0.09572*flip,0,0) + latticeVec); // H1
        initialPosInNm.push_back(Vec3(-0.02397*flip,0.09267*flip,0) + latticeVec); // H2
    }
    
    // Populate nonbonded exclusions
    nonbond.createExceptionsFromBonds(bondPairs, Coulomb14Scale, LennardJones14Scale);    
            
    // Choose an Integrator for advancing time, and a Context connecting the
    // System with the Integrator for simulation. Let the Context choose the
    // best available Platform. Initialize the configuration from the default
    // positions we collected above. Initial velocities will be zero.
    omm->integrator = new OpenMM::VerletIntegrator(StepSizeInFs * OpenMM::PsPerFs);
    omm->context    = new OpenMM::Context(*omm->system, *omm->integrator);
    omm->context->setPositions(initialPosInNm);

    platformName = omm->context->getPlatform().getName();
    return omm;
}


// -----------------------------------------------------------------------------
//                     COPY STATE BACK TO CPU FROM OPENMM
// -----------------------------------------------------------------------------
static void
myGetOpenMMState(MyOpenMMData* omm, double& timeInPs,
                 std::vector<double>& atomPositionsInAng)
{
    // We don't calculate energy in this example because it would take most of the time
    const OpenMM::State state = omm->context->getState(OpenMM::State::Positions);
    timeInPs = state.getTime(); // OpenMM time is in ps already

    // Copy OpenMM positions into output array and change units from nm to Angstroms.
    const std::vector<Vec3>& positionsInNm = state.getPositions();
    atomPositionsInAng.resize(3*positionsInNm.size());
    for (int i=0; i < (int)positionsInNm.size(); ++i)
        for (int j=0; j < 3; ++j)
            atomPositionsInAng[3*i+j] = positionsInNm[i][j] * OpenMM::AngstromsPerNm;
}


// -----------------------------------------------------------------------------
//                     TAKE MULTIPLE STEPS USING OpenMM 
// -----------------------------------------------------------------------------
static void 
myStepWithOpenMM(MyOpenMMData* omm, int numSteps) {
    omm->integrator->step(numSteps);
}

// -----------------------------------------------------------------------------
//                     DEALLOCATE OpenMM OBJECTS
// -----------------------------------------------------------------------------
static void 
myTerminateOpenMM(MyOpenMMData* omm) {
    delete omm;
}

