main_cpu_best.cpp

#include "Vector/vector_dist.hpp"
#include "Decomposition/CartDecomposition.hpp"
#include "data_type/aggregate.hpp"
#include "Plot/GoogleChart.hpp"
#include "Plot/util.hpp"
#include "timer.hpp"

#ifdef TEST_RUN
size_t nstep = 100;
#else
size_t nstep = 1000;
#endif

typedef float real_number;

constexpr int velocity = 0;
constexpr int force = 1;


template<typename VerletList>
void calc_forces(vector_dist<3,real_number, aggregate<real_number[3],real_number[3]> > & vd, VerletList & NN, real_number sigma12, real_number sigma6, real_number r_cut)
{
    // Reset force on the ghost

    auto itg = vd.getDomainAndGhostIterator();

    while (itg.isNext())
    {
        auto p = itg.get();

        // Reset force
        vd.getProp<force>(p)[0] = 0.0;
        vd.getProp<force>(p)[1] = 0.0;
        vd.getProp<force>(p)[2] = 0.0;

        ++itg;
    }


    // Get an iterator over particles
    auto it2 = vd.getParticleIteratorCRS(NN);


    // For each particle p ...
    while (it2.isNext())
    {
        // ... get the particle p
        auto p = it2.get();

        // Get the position xp of the particle
        Point<3,real_number> xp = vd.getPos(p);

        // Get an iterator over the neighborhood particles of p
        // Note that in case of symmetric
        auto Np = NN.template getNNIterator<NO_CHECK>(p);

        // For each neighborhood particle ...
        while (Np.isNext())
        {
            // ... q
            auto q = Np.get();

            // if (p == q) skip this particle
            if (q == p) {++Np; continue;};

            // Get the position of q
            Point<3,real_number> xq = vd.getPos(q);

            // Get the distance between p and q
            Point<3,real_number> r = xp - xq;

            // take the norm of this vector
            real_number rn = norm2(r);

            if (rn > r_cut * r_cut) {++Np;continue;}

            // Calculate the force, using pow is slower
            Point<3,real_number> f = 24.0*(2.0 *sigma12 / (rn*rn*rn*rn*rn*rn*rn) -  sigma6 / (rn*rn*rn*rn)) * r;

            // we sum the force produced by q on p
            vd.template getProp<force>(p)[0] += f.get(0);
            vd.template getProp<force>(p)[1] += f.get(1);
            vd.template getProp<force>(p)[2] += f.get(2);


            // we sum the force produced by p on q
            vd.template getProp<force>(q)[0] -= f.get(0);
            vd.template getProp<force>(q)[1] -= f.get(1);
            vd.template getProp<force>(q)[2] -= f.get(2);


            // Next neighborhood
            ++Np;
        }

        // Next particle
        ++it2;
    }

    // Sum the contribution to the real particles
    vd.ghost_put<add_,force>();
}


template<typename VerletList>
real_number calc_energy(vector_dist<3,real_number, aggregate<real_number[3],real_number[3]> > & vd, VerletList & NN, real_number sigma12, real_number sigma6, real_number r_cut)
{
    real_number E = 0.0;

    real_number rc = r_cut*r_cut;
    real_number shift = 4.0 * ( sigma12 / (rc*rc*rc*rc*rc*rc) - sigma6 / ( rc*rc*rc) );

    // Get an iterator over particles
    auto it2 = vd.getParticleIteratorCRS(NN);

    // For each particle ...
    while (it2.isNext())
    {
        // ... p
        auto p = it2.get();

        // Get the position of the particle p
        Point<3,real_number> xp = vd.getPos(p);

        // Get an iterator over the neighborhood particles of p
        auto Np = NN.template getNNIterator<NO_CHECK>(p);

        real_number Ep = E;

        // For each neighborhood of the particle p
        while (Np.isNext())
        {
            // Neighborhood particle q
            auto q = Np.get();

            // if p == q skip this particle
            if (q == p) {++Np; continue;};

            // Get position of the particle q
            Point<3,real_number> xq = vd.getPos(q);

            // take the normalized direction
            real_number rn = norm2(xp - xq);

            if (rn >= r_cut*r_cut)  {++Np;continue;}

            // potential energy (using pow is slower)
            E += 4.0 * ( sigma12 / (rn*rn*rn*rn*rn*rn) - sigma6 / ( rn*rn*rn) ) - shift;

            // Next neighborhood
            ++Np;
        }

        // To note that the crossing scheme go across the domain particles +
        // some ghost particles. This mean that we have to filter out the ghost
        // particles otherwise we count real_number energies
        //
        if (p < vd.size_local())
        {
            // Kinetic energy of the particle given by its actual speed
            E += (vd.template getProp<velocity>(p)[0]*vd.template getProp<velocity>(p)[0] +
                    vd.template getProp<velocity>(p)[1]*vd.template getProp<velocity>(p)[1] +
                    vd.template getProp<velocity>(p)[2]*vd.template getProp<velocity>(p)[2]) / 2;
        }

        // Next Particle
        ++it2;
    }

    // Calculated energy
    return E;
}

int main(int argc, char* argv[])
{
    real_number dt = 0.00005;
    real_number sigma = 0.01;
    real_number r_cut = 3.0*sigma;
    real_number r_gskin = 1.3*r_cut;
    real_number sigma12 = pow(sigma,12);
    real_number sigma6 = pow(sigma,6);

    openfpm::vector<real_number> x;
    openfpm::vector<openfpm::vector<real_number>> y;

    openfpm_init(&argc,&argv);
    Vcluster<> & v_cl = create_vcluster();

    // we will use it do place particles on a 10x10x10 Grid like
    size_t sz[3] = {100,100,100};

    // domain
    Box<3,float> box({0.0,0.0,0.0},{1.0,1.0,1.0});

    // Boundary conditions
    size_t bc[3]={PERIODIC,PERIODIC,PERIODIC};

    // ghost, big enough to contain the interaction radius
    Ghost<3,float> ghost(r_gskin);
    ghost.setLow(0,0.0);
    ghost.setLow(1,0.0);
    ghost.setLow(2,0.0);

    vector_dist<3,real_number, aggregate<real_number[3],real_number[3]> > vd(0,box,bc,ghost,BIND_DEC_TO_GHOST);

    size_t k = 0;
    size_t start = vd.accum();

    auto it = vd.getGridIterator(sz);

    while (it.isNext())
    {
        vd.add();

        auto key = it.get();

        vd.getLastPos()[0] = key.get(0) * it.getSpacing(0);
        vd.getLastPos()[1] = key.get(1) * it.getSpacing(1);
        vd.getLastPos()[2] = key.get(2) * it.getSpacing(2);

        vd.template getLastProp<velocity>()[0] = 0.0;
        vd.template getLastProp<velocity>()[1] = 0.0;
        vd.template getLastProp<velocity>()[2] = 0.0;

        vd.template getLastProp<force>()[0] = 0.0;
        vd.template getLastProp<force>()[1] = 0.0;
        vd.template getLastProp<force>()[2] = 0.0;

        k++;
        ++it;
    }

    vd.map();
    vd.ghost_get<>();

    timer tsim;
    tsim.start();

    // Get the Cell list structure
    auto NN = vd.getVerletCrs(r_gskin);;

    // calculate forces
    calc_forces(vd,NN,sigma12,sigma6,r_cut);
    unsigned long int f = 0;

    int cnt = 0;
    real_number max_disp = 0.0;

    // MD time stepping
    for (size_t i = 0; i < nstep ; i++)
    {
        // Get the iterator
        auto it3 = vd.getDomainIterator();

        real_number max_displ = 0.0;

        // integrate velicity and space based on the calculated forces (Step1)
        while (it3.isNext())
        {
            auto p = it3.get();

            // here we calculate v(tn + 0.5)
            vd.template getProp<velocity>(p)[0] += 0.5*dt*vd.template getProp<force>(p)[0];
            vd.template getProp<velocity>(p)[1] += 0.5*dt*vd.template getProp<force>(p)[1];
            vd.template getProp<velocity>(p)[2] += 0.5*dt*vd.template getProp<force>(p)[2];

            Point<3,real_number> disp({vd.template getProp<velocity>(p)[0]*dt,vd.template getProp<velocity>(p)[1]*dt,vd.template getProp<velocity>(p)[2]*dt});

            // here we calculate x(tn + 1)
            vd.getPos(p)[0] += disp.get(0);
            vd.getPos(p)[1] += disp.get(1);
            vd.getPos(p)[2] += disp.get(2);

            if (disp.norm() > max_displ)
                max_displ = disp.norm();

            ++it3;
        }

        if (max_disp < max_displ)
            max_disp = max_displ;

        // Because we moved the particles in space we have to map them and re-sync the ghost
        if (cnt % 10 == 0)
        {
            vd.map();
            vd.template ghost_get<>();
            // Get the Cell list structure
            vd.updateVerlet(NN,r_gskin,VL_CRS_SYMMETRIC);
        }
        else
        {
            vd.template ghost_get<>(SKIP_LABELLING);
        }

        cnt++;

        // calculate forces or a(tn + 1) Step 2
        calc_forces(vd,NN,sigma12,sigma6,r_cut);

        // Integrate the velocity Step 3
        auto it4 = vd.getDomainIterator();

        while (it4.isNext())
        {
            auto p = it4.get();

            // here we calculate v(tn + 1)
            vd.template getProp<velocity>(p)[0] += 0.5*dt*vd.template getProp<force>(p)[0];
            vd.template getProp<velocity>(p)[1] += 0.5*dt*vd.template getProp<force>(p)[1];
            vd.template getProp<velocity>(p)[2] += 0.5*dt*vd.template getProp<force>(p)[2];

            ++it4;
        }

        // After every iteration collect some statistic about the confoguration
        if (i % 100 == 0)
        {
            // We write the particle position for visualization (Without ghost)
            vd.deleteGhost();
            vd.write("particles_",f);

            // we resync the ghost
            vd.ghost_get<>();


            // We calculate the energy
            real_number energy = calc_energy(vd,NN,sigma12,sigma6,r_cut);
            auto & vcl = create_vcluster();
            vcl.sum(energy);
            vcl.max(max_disp);
            vcl.execute();

            // we save the energy calculated at time step i c contain the time-step y contain the energy
            x.add(i);
            y.add({energy});

            // We also print on terminal the value of the energy
            // only one processor (master) write on terminal
            if (vcl.getProcessUnitID() == 0)
                std::cout << "Energy: " << energy << "   " << max_disp << "   " << std::endl;

            max_disp = 0.0;

            f++;
        }
    }

    tsim.stop();
    std::cout << "Time: " << tsim.getwct()  << std::endl;

    // Google charts options, it store the options to draw the X Y graph
    GCoptions options;

    // Title of the graph
    options.title = std::string("Energy with time");

    // Y axis name
    options.yAxis = std::string("Energy");

    // X axis name
    options.xAxis = std::string("iteration");

    // width of the line
    options.lineWidth = 1.0;

    // Object that draw the X Y graph
    GoogleChart cg;

    // Add the graph
    // The graph that it produce is in svg format that can be opened on browser
    cg.AddLinesGraph(x,y,options);

    // Write into html format
    cg.write("gc_plot2_out.html");

    openfpm_finalize();
}