main.cpp

 
#include "Vector/vector_dist.hpp"
#include "Plot/GoogleChart.hpp"
#include "Plot/util.hpp"
#include "timer.hpp"
 
 
constexpr int velocity = 0;
constexpr int force = 1;
 
 
 
template<typename CellList> void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList & NN, double sigma12, double sigma6, double r_cut2)
{
 
 
 
    vd.updateCellList(NN);
 
 
 
    // Get an iterator over particles
    auto it2 = vd.getDomainIterator();
 
    // For each particle p ...
    while (it2.isNext())
    {
        // ... get the particle p
        auto p = it2.get();
 
        // Get the position xp of the particle
        Point<3,double> xp = vd.getPos(p);
 
        // Reset the force counter
        vd.template getProp<force>(p)[0] = 0.0;
        vd.template getProp<force>(p)[1] = 0.0;
        vd.template getProp<force>(p)[2] = 0.0;
 
        // Get an iterator over the neighborhood particles of p
        auto Np = NN.getNNIteratorBox(NN.getCell(vd.getPos(p)));
 
        // For each neighborhood particle ...
        while (Np.isNext())
        {
            // ... q
            auto q = Np.get();
 
            // if (p == q) skip this particle
            if (q == p.getKey())    {++Np; continue;};
 
            // Get the position of p
            Point<3,double> xq = vd.getPos(q);
 
            // Get the distance between p and q
            Point<3,double> r = xp - xq;
 
            // take the norm of this vector
            double rn = norm2(r);
 
            if (rn > r_cut2)
            {++Np; continue;};
 
            // Calculate the force, using pow is slower
            Point<3,double> 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);
 
            // Next neighborhood
            ++Np;
        }
 
        // Next particle
        ++it2;
    }
 
 
 
}
 
 
 
template<typename CellList> double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList & NN, double sigma12, double sigma6, double r_cut2)
{
        double rc = r_cut2;
        double shift = 2.0 * ( sigma12 / (rc*rc*rc*rc*rc*rc) - sigma6 / ( rc*rc*rc) );
 
 
 
    double E = 0.0;
//  vd.updateCellList(NN);
 
 
 
    // Get the iterator
    auto it2 = vd.getDomainIterator();
 
    // For each particle ...
    while (it2.isNext())
    {
        // ... p
        auto p = it2.get();
 
        // Get the position of the particle p
        Point<3,double> xp = vd.getPos(p);
 
        // Get an iterator over the neighborhood of the particle p
        auto Np = NN.getNNIteratorBox(NN.getCell(vd.getPos(p)));
 
        // 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.getKey())    {++Np; continue;};
 
            // Get position of the particle q
            Point<3,double> xq = vd.getPos(q);
 
            // take the normalized direction
            double rn = norm2(xp - xq);
 
            if (rn > r_cut2)
            {++Np;continue;}
 
            // potential energy (using pow is slower)
            E += 2.0 * ( sigma12 / (rn*rn*rn*rn*rn*rn) - sigma6 / ( rn*rn*rn) ) - shift;
 
            // Next neighborhood
            ++Np;
        }
 
        // 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[])
{
 
    openfpm_init(&argc,&argv);
 
    auto & v_cl = create_vcluster();
    double sigma = 0.1;
    double r_cut = 3.0*sigma;
 
    // we will use it do place particles on a 10x10x10 Grid like
    size_t sz[3] = {50,50,50};
 
    // domain
    Box<3,double> 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,double> ghost(r_cut);
 
    double dt = 0.0005;
    double sigma12 = pow(sigma,12);
    double sigma6 = pow(sigma,6);
 
    openfpm::vector<double> x;
    openfpm::vector<openfpm::vector<double>> y;
 
 
 
    vector_dist<3,double, aggregate<double[3],double[3]> > vd(0,box,bc,ghost);
 
 
 
    // We create the grid iterator
    if (v_cl.rank() == 0) {
 
    auto it = vd.getGridIterator(sz);
 
    while (it.isNext())
    {
        // Create a new particle
        vd.add();
 
        // key contain (i,j,k) index of the grid
        auto key = it.get();
 
        // The index of the grid can be accessed with key.get(0) == i, key.get(1) == j ...
        // We use getLastPos to set the position of the last particle added
        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);
 
        // We use getLastProp to set the property value of the last particle we added
        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;
 
        ++it;
    }
 
    std::cerr << "size local 1 " << vd.size_local() << std::endl;
    }
    vd.addComputationCosts();
    vd.getDecomposition().decompose();
    vd.map();
    vd.ghost_get<>();
 
    std::cerr << "size local 2 " << vd.size_local() << std::endl;
 
    timer tsim;
    tsim.start();
 
 
    // Get the Cell list structure
    auto NN = vd.getCellList<CELL_MEMBAL<3,double>>(r_cut);
 
    // The standard
    // auto NN = vd.getCellList(r_cut);
 
    // calculate forces
    calc_forces(vd,NN,sigma12,sigma6,r_cut*r_cut);
    unsigned long int f = 0;
 
    // MD time stepping
    for (size_t i = 0; i < 10000 ; i++)
    {
        // Get the iterator
        auto it3 = vd.getDomainIterator();
 
        // 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];
 
            // here we calculate x(tn + 1)
            vd.getPos(p)[0] += vd.template getProp<velocity>(p)[0]*dt;
            vd.getPos(p)[1] += vd.template getProp<velocity>(p)[1]*dt;
            vd.getPos(p)[2] += vd.template getProp<velocity>(p)[2]*dt;
 
            ++it3;
        }
 
        // Because we moved the particles in space we have to map them and re-sync the ghost
        vd.map();
        vd.template ghost_get<>();
 
        // calculate forces or a(tn + 1) Step 2
        calc_forces(vd,NN,sigma12,sigma6,r_cut*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 configuration
                if (i % 100 == 0)
                {
                        // We write the particle position for visualization (Without ghost)
                        vd.deleteGhost();
                        vd.write_frame("particles_",f);
 
                        // we resync the ghost
                        vd.ghost_get<>();
 
                        // We calculate the energy
                        double energy = calc_energy(vd,NN,sigma12,sigma6,r_cut*r_cut);
                        auto & vcl = create_vcluster();
                        vcl.sum(energy);
                        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 << std::endl;
 
                        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;
 
    // Resolution in x
    options.width = 1280;
 
    // Resolution in y
    options.heigh = 720;
 
    // Add zoom capability
    options.more = GC_ZOOM;
 
    // 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();
 
 
}