3D dynamic adaptive mesh refinement (AMR) using PABLO
3D dynamic adaptive mesh refinement (AMR) using PABLOThis example creates a 3D Octree mesh on the cube domain [0,1]x[0,1]x[0,1]. The domain is adapted to track a set of moving bubbles with random initialization.
To run: ./PABLO_bubbles_3D
To see the result visit: PABLO website
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#include "bitpit_PABLO.hpp"
 
#if BITPIT_ENABLE_MPI==1
#include "PABLO_userDataComm.hpp"
#include "PABLO_userDataLB.hpp"
#include <mpi.h>
#endif
 
using namespace std;
using namespace bitpit;
 
// =================================================================================== //
class bubble{
public:
    double c[3];
    double r;
};
 
void run()
{
    int iter = 0;
 
    PabloUniform pabloBB(3);
 
    pabloBB.setBalanceCodimension(1);
    int idx = 0;
    pabloBB.setBalance(idx,true);
 
    for (iter=1; iter<4; iter++){
        pabloBB.adaptGlobalRefine();
    }
 
#if BITPIT_ENABLE_MPI==1
    pabloBB.loadBalance();
#endif
 
    uint32_t nocts = pabloBB.getNumOctants();
 
    srand(0);
 
#if BITPIT_ENABLE_MPI==1
    int nb = 50;
#else
    int nb = 10;
#endif
    vector<bubble> BB;
    vector<bubble> BB0;
    vector<double> DZ;
    vector<double> OM;
    vector<double> AA;
 
    for (int i=0; i<nb; i++){
        double randc[3];
        randc[0] = 0.8 * (double) (rand()) /  RAND_MAX + 0.1;
        randc[1] = 0.8 * (double) (rand()) /  RAND_MAX + 0.1;
        randc[2] = (double) (rand()) /  RAND_MAX - 0.5;
        double randr = (0.05 * (double) (rand()) / RAND_MAX + 0.04);
        double dz = 0.005 + 0.05 * (double) (rand()) / RAND_MAX;
        double omega = 0.5 * (double) (rand()) / RAND_MAX;
        double aa = 0.15 * (double) (rand()) / RAND_MAX;
        bubble bb;
        bb.c[0] = randc[0];
        bb.c[1] = randc[1];
        bb.c[2] = randc[2];
        bb.r = randr;
        BB.push_back(bb);
        BB0.push_back(bb);
        DZ.push_back(dz);
        OM.push_back(omega);
        AA.push_back(aa);
    }
    double t0 = 0;
    double t = t0;
    double Dt = 0.5;
 
    vector<double> oct_data(nocts, 0.0),oct_data_ghost;
    vector<double> oct_data_new(nocts, 0.0);
 
    int itstart = 1;
    int itend = 200;
 
    for (iter=itstart; iter<itend; iter++){
        if(pabloBB.getRank()==0) cout << "iter " << iter << endl;
        t += Dt;
 
        for (int i=0; i<nb; i++){
            BB[i].c[0] = BB0[i].c[0];// + AA[i]*cos(OM[i]*t);
            BB[i].c[1] = BB0[i].c[1];// + AA[i]*cos(OM[i]*t);
            BB[i].c[2] = BB[i].c[2]+ Dt*DZ[i];
        }
 
        bool adapt = true;
        while (adapt){
 
            for (unsigned int i=0; i<nocts; i++){
                bool inside = false;
                vector<array<double,3> > nodes = pabloBB.getNodes(i);
                array<double,3> center = pabloBB.getCenter(i);
                int ib = 0;
                while (!inside && ib<nb){
                    double xc = BB[ib].c[0];
                    double yc = BB[ib].c[1];
                    double zc = BB[ib].c[2];
                    double radius = BB[ib].r;
                    if (((!inside))){
                        if (((pow((center[0]-xc),2.0)+pow((center[1]-yc),2.0)+pow((center[2]-zc),2.0) <= 1.25*pow(radius,2.0) &&
                                        pow((center[0]-xc),2.0)+pow((center[1]-yc),2.0)+pow((center[2]-zc),2.0) >= 0.75*pow(radius,2.0)))){
                            if (pabloBB.getLevel(i) < 7){
                                pabloBB.setMarker(i,1);
                                oct_data[i] = 1.0;
                            }
                            else{
                                pabloBB.setMarker(i,0);
                                oct_data[i] = 1.0;
                            }
                            inside = true;
                        }
                    }
                    for (int j=0; j<8; j++){
                        double x = nodes[j][0];
                        double y = nodes[j][1];
                        double z = nodes[j][2];
                        if (((!inside))){
                            if (((pow((x-xc),2.0)+pow((y-yc),2.0)+pow((z-zc),2.0) <= 1.25*pow(radius,2.0) &&
                                    pow((x-xc),2.0)+pow((y-yc),2.0)+pow((z-zc),2.0) >= 0.75*pow(radius,2.0)))){
                                if (pabloBB.getLevel(i) < 7){
                                    pabloBB.setMarker(i,1);
                                    oct_data[i] = 1.0;
                                }
                                else{
                                    pabloBB.setMarker(i,0);
                                    oct_data[i] = 1.0;
                                }
                                inside = true;
                            }
                        }
                    }
                    ib++;
                }
                if (!inside){
                    oct_data[i] = 0.0;
                    if (pabloBB.getLevel(i) > 3){
                        pabloBB.setMarker(i,3-pabloBB.getLevel(i));
                    }
                }
            }
 
            vector<uint32_t> mapidx;
            vector<bool> isghost;
            adapt = pabloBB.adapt(true);
 
            nocts = pabloBB.getNumOctants();
 
            oct_data_new.resize(nocts, 0);
            for (uint32_t i=0; i<nocts; i++){
                pabloBB.getMapping(i, mapidx, isghost);
                oct_data_new[i] = oct_data[mapidx[0]];
            }
            oct_data = oct_data_new;
            vector<double>().swap(oct_data_new);
 
        }
 
#if BITPIT_ENABLE_MPI==1
        UserDataLB<vector<double> > data_lb(oct_data,oct_data_ghost);
        pabloBB.loadBalance(data_lb);
        nocts = pabloBB.getNumOctants();
#endif
 
        pabloBB.updateConnectivity();
        pabloBB.writeTest("PabloBubble3D_iter"+to_string(static_cast<unsigned long long>(iter)), oct_data);
    }
}
 
int main(int argc, char *argv[])
{
#if BITPIT_ENABLE_MPI==1
    MPI_Init(&argc,&argv);
#else
    BITPIT_UNUSED(argc);
    BITPIT_UNUSED(argv);
#endif
 
    int nProcs;
    int rank;
#if BITPIT_ENABLE_MPI==1
    MPI_Comm_size(MPI_COMM_WORLD, &nProcs);
    MPI_Comm_rank(MPI_COMM_WORLD, &rank);
#else
    nProcs = 1;
    rank   = 0;
#endif
 
    // Initialize the logger
    log::manager().initialize(log::MODE_SEPARATE, false, nProcs, rank);
    log::cout() << log::fileVerbosity(log::LEVEL_INFO);
    log::cout() << log::disableConsole();
 
    // Run the example
    try {
        run();
    } catch (const std::exception &exception) {
        log::cout() << exception.what();
        exit(1);
    }
 
#if BITPIT_ENABLE_MPI==1
    MPI_Finalize();
#endif
}