main.cpp

#include "Grid/grid_dist_id.hpp"
#include "data_type/aggregate.hpp"
#include "timer.hpp"
 
 
constexpr int U = 0;
constexpr int V = 1;
 
constexpr int x = 0;
constexpr int y = 1;
constexpr int z = 2;
 
 
void init(grid_dist_id<3,double,aggregate<double,double> > & Old, grid_dist_id<3,double,aggregate<double,double> > & New, Box<3,double> & domain)
{
    auto it = Old.getDomainIterator();
 
    while (it.isNext())
    {
        // Get the local grid key
        auto key = it.get();
 
        // Old values U and V
        Old.template get<U>(key) = 1.0;
        Old.template get<V>(key) = 0.0;
 
        // Old values U and V
        New.template get<U>(key) = 0.0;
        New.template get<V>(key) = 0.0;
 
        ++it;
    }
 
    long int x_start = Old.size(0)*1.55f/domain.getHigh(0);
    long int y_start = Old.size(1)*1.55f/domain.getHigh(1);
    long int z_start = Old.size(1)*1.55f/domain.getHigh(2);
 
    long int x_stop = Old.size(0)*1.85f/domain.getHigh(0);
    long int y_stop = Old.size(1)*1.85f/domain.getHigh(1);
    long int z_stop = Old.size(1)*1.85f/domain.getHigh(2);
 
    grid_key_dx<3> start({x_start,y_start,z_start});
    grid_key_dx<3> stop ({x_stop,y_stop,z_stop});
    auto it_init = Old.getSubDomainIterator(start,stop);
 
    while (it_init.isNext())
    {
        auto key = it_init.get();
 
                Old.template get<U>(key) = 0.5 + (((double)std::rand())/RAND_MAX -0.5)/10.0;
                Old.template get<V>(key) = 0.25 + (((double)std::rand())/RAND_MAX -0.5)/20.0;
 
        ++it_init;
    }
}
 
 
int main(int argc, char* argv[])
{
    openfpm_init(&argc,&argv);
 
    // domain
    Box<3,double> domain({0.0,0.0,0.0},{2.5,2.5,2.5});
    
    // grid size
        size_t sz[3] = {128,128,128};
 
    // Define periodicity of the grid
    periodicity<3> bc = {PERIODIC,PERIODIC,PERIODIC};
    
    // Ghost in grid unit
    Ghost<3,long int> g(1);
    
    // deltaT
    double deltaT = 1;
 
    // Diffusion constant for specie U
    double du = 2*1e-5;
 
    // Diffusion constant for specie V
    double dv = 1*1e-5;
 
    // Number of timesteps
        size_t timeSteps = 5000;
 
    // K and F (Physical constant in the equation)
        double K = 0.053;
        double F = 0.014;
 
    grid_dist_id<3, double, aggregate<double,double>> Old(sz,domain,g,bc);
 
    // New grid with the decomposition of the old grid
    grid_dist_id<3, double, aggregate<double,double>> New(Old.getDecomposition(),sz,g);
 
    
    // spacing of the grid on x and y
    double spacing[3] = {Old.spacing(0),Old.spacing(1),Old.spacing(2)};
 
    init(Old,New,domain);
 
    // sync the ghost
    size_t count = 0;
    Old.template ghost_get<U,V>();
 
    // because we assume that spacing[x] == spacing[y] we use formula 2
    // and we calculate the prefactor of Eq 2
    double uFactor = deltaT * du/(spacing[x]*spacing[x]);
    double vFactor = deltaT * dv/(spacing[x]*spacing[x]);
 
    timer tot_sim;
    tot_sim.start();
 
 
    static grid_key_dx<3> star_stencil_3D[7] = {{0,0,0},
                                                {0,0,-1},
                                                {0,0,1},
                                                {0,-1,0},
                                                {0,1,0},
                                                {-1,0,0},
                                                {1,0,0}};
 
 
    for (size_t i = 0; i < timeSteps; ++i)
    {
        if (i % 300 == 0)
        {std::cout << "STEP: " << i << std::endl;}
 
 
        auto it = Old.getDomainIteratorStencil(star_stencil_3D);
 
        while (it.isNext())
        {
            // center point
            auto Cp = it.getStencil<0>();
 
            // plus,minus X,Y,Z
            auto mx = it.getStencil<1>();
            auto px = it.getStencil<2>();
            auto my = it.getStencil<3>();
            auto py = it.getStencil<4>();
            auto mz = it.getStencil<5>();
            auto pz = it.getStencil<6>();
 
            // update based on Eq 2
            New.get<U>(Cp) = Old.get<U>(Cp) + uFactor * (
                                        Old.get<U>(mz) +
                                        Old.get<U>(pz) +
                                        Old.get<U>(my) +
                                        Old.get<U>(py) +
                                        Old.get<U>(mx) +
                                        Old.get<U>(px) -
                                        6.0*Old.get<U>(Cp)) +
                                        - deltaT * Old.get<U>(Cp) * Old.get<V>(Cp) * Old.get<V>(Cp) +
                                        - deltaT * F * (Old.get<U>(Cp) - 1.0);
 
 
            // update based on Eq 2
            New.get<V>(Cp) = Old.get<V>(Cp) + vFactor * (
                                        Old.get<V>(mz) +
                                        Old.get<V>(pz) +
                                        Old.get<V>(my) +
                                        Old.get<V>(py) +
                                        Old.get<V>(mx) +
                                        Old.get<V>(px) -
                                        6*Old.get<V>(Cp)) +
                                        deltaT * Old.get<U>(Cp) * Old.get<V>(Cp) * Old.get<V>(Cp) +
                                        - deltaT * (F+K) * Old.get<V>(Cp);
 
            // Next point in the grid
            ++it;
        }
 
 
        // Here we copy New into the old grid in preparation of the new step
        // It would be better to alternate, but using this we can show the usage
        // of the function copy. To note that copy work only on two grid of the same
        // decomposition. If you want to copy also the decomposition, or force to be
        // exactly the same, use Old = New
        Old.copy(New);
 
        // After copy we synchronize again the ghost part U and V
        Old.ghost_get<U,V>();
 
        // Every 500 time step we output the configuration for
        // visualization
        if (i % 500 == 0)
        {
//          Old.save("output_" + std::to_string(count));
            count++;
        }
    }
    
    tot_sim.stop();
    std::cout << "Total simulation: " << tot_sim.getwct() << std::endl;
 
 
 
    openfpm_finalize();
 
 
}