refactor morphdrain
This commit is contained in:
James E McClure
parent
facef798fd
commit
ad910a49a3
@ -326,6 +326,317 @@ double morph_open()
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}
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*/
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//***************************************************************************************
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double MorphDrain(DoubleArray &SignDist, char *id, std::shared_ptr<Domain> Dm, double VoidFraction){
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// SignDist is the distance to the object that you want to constaing the morphological opening
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// VoidFraction is the the empty space where the object inst
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// id is a labeled map
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// Dm contains information about the domain structure
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int nx = Dm->Nx;
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int ny = Dm->Ny;
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int nz = Dm->Nz;
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int iproc = Dm->iproc();
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int jproc = Dm->jproc();
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int kproc = Dm->kproc();
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int nprocx = Dm->nprocx();
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int nprocy = Dm->nprocy();
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int nprocz = Dm->nprocz();
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int rank = Dm->rank();
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DoubleArray phase(Nx,Ny,Nz);
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IntArray phase_label(Nx,Ny,Nz);
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int n;
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double final_void_fraction;
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double count,countGlobal,totalGlobal;
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count = 0.f;
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double maxdist=-200.f;
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double maxdistGlobal;
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for (int k=1; k<nz-1; k++){
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for (int j=1; j<ny-1; j++){
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for (int i=1; i<nx-1; i++){
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n = k*nx*ny+j*nx+i;
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// extract maximum distance for critical radius
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if ( SignDist(i,j,k) > maxdist) maxdist=SignDist(i,j,k);
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if ( SignDist(i,j,k) > 0.0 ){
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count += 1.0;
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id[n] = 2;
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}
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}
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}
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}
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MPI_Barrier(Dm->Comm);
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// total Global is the number of nodes in the pore-space
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MPI_Allreduce(&count,&totalGlobal,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
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MPI_Allreduce(&maxdist,&maxdistGlobal,1,MPI_DOUBLE,MPI_MAX,Dm->Comm);
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double volume=double(nprocx*nprocy*nprocz)*double(nx-2)*double(ny-2)*double(nz-2);
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double volume_fraction=totalGlobal/volume;
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if (rank==0) printf("Volume fraction for morphological opening: %f \n",volume_fraction);
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if (rank==0) printf("Maximum pore size: %f \n",maxdistGlobal);
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// Communication buffers
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char *sendID_x, *sendID_y, *sendID_z, *sendID_X, *sendID_Y, *sendID_Z;
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char *sendID_xy, *sendID_yz, *sendID_xz, *sendID_Xy, *sendID_Yz, *sendID_xZ;
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char *sendID_xY, *sendID_yZ, *sendID_Xz, *sendID_XY, *sendID_YZ, *sendID_XZ;
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char *recvID_x, *recvID_y, *recvID_z, *recvID_X, *recvID_Y, *recvID_Z;
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char *recvID_xy, *recvID_yz, *recvID_xz, *recvID_Xy, *recvID_Yz, *recvID_xZ;
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char *recvID_xY, *recvID_yZ, *recvID_Xz, *recvID_XY, *recvID_YZ, *recvID_XZ;
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// send buffers
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sendID_x = new char [Dm->sendCount_x];
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sendID_y = new char [Dm->sendCount_y];
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sendID_z = new char [Dm->sendCount_z];
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sendID_X = new char [Dm->sendCount_X];
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sendID_Y = new char [Dm->sendCount_Y];
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sendID_Z = new char [Dm->sendCount_Z];
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sendID_xy = new char [Dm->sendCount_xy];
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sendID_yz = new char [Dm->sendCount_yz];
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sendID_xz = new char [Dm->sendCount_xz];
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sendID_Xy = new char [Dm->sendCount_Xy];
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sendID_Yz = new char [Dm->sendCount_Yz];
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sendID_xZ = new char [Dm->sendCount_xZ];
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sendID_xY = new char [Dm->sendCount_xY];
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sendID_yZ = new char [Dm->sendCount_yZ];
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sendID_Xz = new char [Dm->sendCount_Xz];
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sendID_XY = new char [Dm->sendCount_XY];
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sendID_YZ = new char [Dm->sendCount_YZ];
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sendID_XZ = new char [Dm->sendCount_XZ];
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//......................................................................................
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// recv buffers
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recvID_x = new char [Dm->recvCount_x];
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recvID_y = new char [Dm->recvCount_y];
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recvID_z = new char [Dm->recvCount_z];
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recvID_X = new char [Dm->recvCount_X];
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recvID_Y = new char [Dm->recvCount_Y];
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recvID_Z = new char [Dm->recvCount_Z];
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recvID_xy = new char [Dm->recvCount_xy];
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recvID_yz = new char [Dm->recvCount_yz];
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recvID_xz = new char [Dm->recvCount_xz];
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recvID_Xy = new char [Dm->recvCount_Xy];
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recvID_xZ = new char [Dm->recvCount_xZ];
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recvID_xY = new char [Dm->recvCount_xY];
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recvID_yZ = new char [Dm->recvCount_yZ];
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recvID_Yz = new char [Dm->recvCount_Yz];
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recvID_Xz = new char [Dm->recvCount_Xz];
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recvID_XY = new char [Dm->recvCount_XY];
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recvID_YZ = new char [Dm->recvCount_YZ];
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recvID_XZ = new char [Dm->recvCount_XZ];
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//......................................................................................
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int sendtag,recvtag;
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sendtag = recvtag = 7;
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int x,y,z;
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int ii,jj,kk;
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int Nx = nx;
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int Ny = ny;
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int Nz = nz;
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double void_fraction_old=1.0;
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double void_fraction_new=1.0;
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double void_fraction_diff_old = 1.0;
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double void_fraction_diff_new = 1.0;
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// Increase the critical radius until the target saturation is met
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double deltaR=0.05; // amount to change the radius in voxel units
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double Rcrit_old;
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double GlobalNumber = 1.f;
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int imin,jmin,kmin,imax,jmax,kmax;
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double Rcrit_new = maxdistGlobal;
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//if (argc>2){
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// Rcrit_new = strtod(argv[2],NULL);
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// if (rank==0) printf("Max. distance =%f, Initial critical radius = %f \n",maxdistGlobal,Rcrit_new);
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//}
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while (void_fraction_new > VoidFraction)
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{
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void_fraction_diff_old = void_fraction_diff_new;
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void_fraction_old = void_fraction_new;
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Rcrit_old = Rcrit_new;
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Rcrit_new -= deltaR*Rcrit_old;
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int Window=round(Rcrit_new);
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if (Window == 0) Window = 1; // If Window = 0 at the begining, after the following process will have sw=1.0
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// and sw<Sw will be immediately broken
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double LocalNumber=0.f;
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for(int k=0; k<Nz; k++){
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for(int j=0; j<Ny; j++){
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for(int i=0; i<Nx; i++){
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n = k*nx*ny + j*nx+i;
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if (SignDist(i,j,k) > Rcrit_new){
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// loop over the window and update
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imin=max(1,i-Window);
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jmin=max(1,j-Window);
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kmin=max(1,k-Window);
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imax=min(Nx-1,i+Window);
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jmax=min(Ny-1,j+Window);
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kmax=min(Nz-1,k+Window);
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for (kk=kmin; kk<kmax; kk++){
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for (jj=jmin; jj<jmax; jj++){
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for (ii=imin; ii<imax; ii++){
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int nn = kk*nx*ny+jj*nx+ii;
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double dsq = double((ii-i)*(ii-i)+(jj-j)*(jj-j)+(kk-k)*(kk-k));
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if (id[nn] == 2 && dsq <= Rcrit_new*Rcrit_new){
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LocalNumber+=1.0;
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id[nn]=1;
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}
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}
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}
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}
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}
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// move on
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}
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}
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}
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// Pack and send the updated ID values
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PackID(Dm->sendList_x, Dm->sendCount_x ,sendID_x, id);
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PackID(Dm->sendList_X, Dm->sendCount_X ,sendID_X, id);
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PackID(Dm->sendList_y, Dm->sendCount_y ,sendID_y, id);
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PackID(Dm->sendList_Y, Dm->sendCount_Y ,sendID_Y, id);
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PackID(Dm->sendList_z, Dm->sendCount_z ,sendID_z, id);
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PackID(Dm->sendList_Z, Dm->sendCount_Z ,sendID_Z, id);
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PackID(Dm->sendList_xy, Dm->sendCount_xy ,sendID_xy, id);
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PackID(Dm->sendList_Xy, Dm->sendCount_Xy ,sendID_Xy, id);
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PackID(Dm->sendList_xY, Dm->sendCount_xY ,sendID_xY, id);
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PackID(Dm->sendList_XY, Dm->sendCount_XY ,sendID_XY, id);
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PackID(Dm->sendList_xz, Dm->sendCount_xz ,sendID_xz, id);
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PackID(Dm->sendList_Xz, Dm->sendCount_Xz ,sendID_Xz, id);
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PackID(Dm->sendList_xZ, Dm->sendCount_xZ ,sendID_xZ, id);
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PackID(Dm->sendList_XZ, Dm->sendCount_XZ ,sendID_XZ, id);
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PackID(Dm->sendList_yz, Dm->sendCount_yz ,sendID_yz, id);
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PackID(Dm->sendList_Yz, Dm->sendCount_Yz ,sendID_Yz, id);
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PackID(Dm->sendList_yZ, Dm->sendCount_yZ ,sendID_yZ, id);
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PackID(Dm->sendList_YZ, Dm->sendCount_YZ ,sendID_YZ, id);
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//......................................................................................
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MPI_Sendrecv(sendID_x,Dm->sendCount_x,MPI_CHAR,Dm->rank_x(),sendtag,
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recvID_X,Dm->recvCount_X,MPI_CHAR,Dm->rank_X(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_X,Dm->sendCount_X,MPI_CHAR,Dm->rank_X(),sendtag,
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recvID_x,Dm->recvCount_x,MPI_CHAR,Dm->rank_x(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_y,Dm->sendCount_y,MPI_CHAR,Dm->rank_y(),sendtag,
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recvID_Y,Dm->recvCount_Y,MPI_CHAR,Dm->rank_Y(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Y,Dm->sendCount_Y,MPI_CHAR,Dm->rank_Y(),sendtag,
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recvID_y,Dm->recvCount_y,MPI_CHAR,Dm->rank_y(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_z,Dm->sendCount_z,MPI_CHAR,Dm->rank_z(),sendtag,
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recvID_Z,Dm->recvCount_Z,MPI_CHAR,Dm->rank_Z(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Z,Dm->sendCount_Z,MPI_CHAR,Dm->rank_Z(),sendtag,
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recvID_z,Dm->recvCount_z,MPI_CHAR,Dm->rank_z(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_xy,Dm->sendCount_xy,MPI_CHAR,Dm->rank_xy(),sendtag,
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recvID_XY,Dm->recvCount_XY,MPI_CHAR,Dm->rank_XY(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_XY,Dm->sendCount_XY,MPI_CHAR,Dm->rank_XY(),sendtag,
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recvID_xy,Dm->recvCount_xy,MPI_CHAR,Dm->rank_xy(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Xy,Dm->sendCount_Xy,MPI_CHAR,Dm->rank_Xy(),sendtag,
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recvID_xY,Dm->recvCount_xY,MPI_CHAR,Dm->rank_xY(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_xY,Dm->sendCount_xY,MPI_CHAR,Dm->rank_xY(),sendtag,
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recvID_Xy,Dm->recvCount_Xy,MPI_CHAR,Dm->rank_Xy(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_xz,Dm->sendCount_xz,MPI_CHAR,Dm->rank_xz(),sendtag,
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recvID_XZ,Dm->recvCount_XZ,MPI_CHAR,Dm->rank_XZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_XZ,Dm->sendCount_XZ,MPI_CHAR,Dm->rank_XZ(),sendtag,
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recvID_xz,Dm->recvCount_xz,MPI_CHAR,Dm->rank_xz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Xz,Dm->sendCount_Xz,MPI_CHAR,Dm->rank_Xz(),sendtag,
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recvID_xZ,Dm->recvCount_xZ,MPI_CHAR,Dm->rank_xZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_xZ,Dm->sendCount_xZ,MPI_CHAR,Dm->rank_xZ(),sendtag,
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recvID_Xz,Dm->recvCount_Xz,MPI_CHAR,Dm->rank_Xz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_yz,Dm->sendCount_yz,MPI_CHAR,Dm->rank_yz(),sendtag,
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recvID_YZ,Dm->recvCount_YZ,MPI_CHAR,Dm->rank_YZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_YZ,Dm->sendCount_YZ,MPI_CHAR,Dm->rank_YZ(),sendtag,
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recvID_yz,Dm->recvCount_yz,MPI_CHAR,Dm->rank_yz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Yz,Dm->sendCount_Yz,MPI_CHAR,Dm->rank_Yz(),sendtag,
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recvID_yZ,Dm->recvCount_yZ,MPI_CHAR,Dm->rank_yZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_yZ,Dm->sendCount_yZ,MPI_CHAR,Dm->rank_yZ(),sendtag,
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recvID_Yz,Dm->recvCount_Yz,MPI_CHAR,Dm->rank_Yz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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//......................................................................................
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UnpackID(Dm->recvList_x, Dm->recvCount_x ,recvID_x, id);
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UnpackID(Dm->recvList_X, Dm->recvCount_X ,recvID_X, id);
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UnpackID(Dm->recvList_y, Dm->recvCount_y ,recvID_y, id);
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UnpackID(Dm->recvList_Y, Dm->recvCount_Y ,recvID_Y, id);
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UnpackID(Dm->recvList_z, Dm->recvCount_z ,recvID_z, id);
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UnpackID(Dm->recvList_Z, Dm->recvCount_Z ,recvID_Z, id);
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UnpackID(Dm->recvList_xy, Dm->recvCount_xy ,recvID_xy, id);
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UnpackID(Dm->recvList_Xy, Dm->recvCount_Xy ,recvID_Xy, id);
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UnpackID(Dm->recvList_xY, Dm->recvCount_xY ,recvID_xY, id);
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UnpackID(Dm->recvList_XY, Dm->recvCount_XY ,recvID_XY, id);
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UnpackID(Dm->recvList_xz, Dm->recvCount_xz ,recvID_xz, id);
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UnpackID(Dm->recvList_Xz, Dm->recvCount_Xz ,recvID_Xz, id);
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UnpackID(Dm->recvList_xZ, Dm->recvCount_xZ ,recvID_xZ, id);
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UnpackID(Dm->recvList_XZ, Dm->recvCount_XZ ,recvID_XZ, id);
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UnpackID(Dm->recvList_yz, Dm->recvCount_yz ,recvID_yz, id);
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UnpackID(Dm->recvList_Yz, Dm->recvCount_Yz ,recvID_Yz, id);
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UnpackID(Dm->recvList_yZ, Dm->recvCount_yZ ,recvID_yZ, id);
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UnpackID(Dm->recvList_YZ, Dm->recvCount_YZ ,recvID_YZ, id);
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//......................................................................................
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MPI_Allreduce(&LocalNumber,&GlobalNumber,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
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for (int k=0;k<Nz;k++){
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for (int j=0;j<Ny;j++){
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for (int i=0;i<Nx;i++){
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int n = k*Nx*Ny+j*Nx+i;
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if (id[n] == 1){
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phase(i,j,k) = 1.0;
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}
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else
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phase(i,j,k) = -1.0;
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}
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}
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}
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// Extract only the connected part
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BlobIDstruct new_index;
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double vF=0.0; double vS=0.0;
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ComputeGlobalBlobIDs(Nx-2,Ny-2,Nz-2,Dm->rank_info,phase,SignDist,vF,vS,phase_label,Dm->Comm);
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MPI_Barrier(comm);
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for (int k=0;k<Nz;k++){
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for (int j=0;j<Ny;j++){
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for (int i=0;i<Nx;i++){
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int n = k*Nx*Ny+j*Nx+i;
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if (id[n] == 1 && phase_label(i,j,k) > 1){
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id[n] = 2;
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}
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}
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}
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}
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count = 0.f;
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for (int k=1; k<Nz-1; k++){
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for (int j=1; j<Ny-1; j++){
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for (int i=1; i<Nx-1; i++){
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n=k*Nx*Ny+j*Nx+i;
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if (id[n] == 2){
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count+=1.0;
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}
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}
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}
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}
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MPI_Allreduce(&count,&countGlobal,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
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void_fraction_new = countGlobal/totalGlobal;
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void_fraction_diff_new = abs(void_fraction_new-VoidFraction);
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if (rank==0){
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printf(" %f ",void_fraction_new);
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printf(" %f\n",Rcrit_new);
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}
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}
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if (void_fraction_diff_new<void_fraction_diff_old){
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final_void_fraction=void_fraction_new;
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if (rank==0){
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printf("Final void fraction =%f\n",void_fraction_new);
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printf("Final critical radius=%f\n",Rcrit_new);
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}
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}
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else{
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final_void_fraction=void_fraction_old;
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if (rank==0){
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printf("Final void fraction=%f\n",void_fraction_old);
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printf("Final critical radius=%f\n",Rcrit_old);
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}
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}
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return final_void_fraction;
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}
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double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id, std::shared_ptr<Domain> Dm, double TargetGrowth){
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int Nx = Dm->Nx;
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@ -1,6 +1,8 @@
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// Morphological opening routine
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#include "common/Array.h"
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#include "common/Domain.h"
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#include "analysis/runAnalysis.h"
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double MorphOpen(DoubleArray &SignDist, char *id, std::shared_ptr<Domain> Dm, double VoidFraction);
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double MorphDrain(DoubleArray &SignDist, char *id, std::shared_ptr<Domain> Dm, double VoidFraction);
|
||||
double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id, std::shared_ptr<Domain> Dm, double TargetVol);
|
||||
@ -98,8 +98,6 @@ int main(int argc, char **argv)
|
||||
// Initialize the domain and communication
|
||||
Array<char> id_solid(nx,ny,nz);
|
||||
DoubleArray SignDist(nx,ny,nz);
|
||||
DoubleArray phase(nx,ny,nz);
|
||||
IntArray phase_label(nx,ny,nz);
|
||||
|
||||
// Solve for the position of the solid phase
|
||||
for (int k=0;k<nz;k++){
|
||||
@ -129,39 +127,8 @@ int main(int argc, char **argv)
|
||||
MPI_Barrier(comm);
|
||||
|
||||
// Run the morphological opening
|
||||
MorphOpen(SignDist, id, Dm, SW);
|
||||
|
||||
for (int k=0;k<nz;k++){
|
||||
for (int j=0;j<ny;j++){
|
||||
for (int i=0;i<nx;i++){
|
||||
int n = k*nx*ny+j*nx+i;
|
||||
if (id[n] == 1){
|
||||
phase(i,j,k) = 1.0;
|
||||
}
|
||||
else
|
||||
phase(i,j,k) = -1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Extract only the connected part
|
||||
BlobIDstruct new_index;
|
||||
double vF=0.0; double vS=0.0;
|
||||
ComputeGlobalBlobIDs(nx-2,ny-2,nz-2,Dm->rank_info,phase,SignDist,vF,vS,phase_label,Dm->Comm);
|
||||
MPI_Barrier(comm);
|
||||
|
||||
for (int k=0;k<nz;k++){
|
||||
for (int j=0;j<ny;j++){
|
||||
for (int i=0;i<nx;i++){
|
||||
int n = k*nx*ny+j*nx+i;
|
||||
if (id[n] == 1 && phase_label(i,j,k) > 1){
|
||||
id[n] = 2;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
MorphDrain(SignDist, id, Dm, SW);
|
||||
|
||||
// calculate distance to non-wetting fluid
|
||||
if (domain_db->keyExists( "HistoryLabels" )){
|
||||
if (rank==0) printf("Relabel solid components that touch fluid 1 \n");
|
||||
|
||||
Loading…
Reference in New Issue
Block a user