From ad910a49a31971cc39a5c2e17cd8166d51391ec9 Mon Sep 17 00:00:00 2001 From: James E McClure Date: Thu, 21 Feb 2019 10:06:29 -0500 Subject: [PATCH] refactor morphdrain --- analysis/morphology.cpp | 311 +++++++++++++++++++++++++++++++++++ analysis/morphology.h | 2 + tests/lbpm_morphdrain_pp.cpp | 37 +---- 3 files changed, 315 insertions(+), 35 deletions(-) diff --git a/analysis/morphology.cpp b/analysis/morphology.cpp index c15620c2..64d6ff62 100644 --- a/analysis/morphology.cpp +++ b/analysis/morphology.cpp @@ -326,6 +326,317 @@ double morph_open() } */ +//*************************************************************************************** +double MorphDrain(DoubleArray &SignDist, char *id, std::shared_ptr Dm, double VoidFraction){ + // SignDist is the distance to the object that you want to constaing the morphological opening + // VoidFraction is the the empty space where the object inst + // id is a labeled map + // Dm contains information about the domain structure + + int nx = Dm->Nx; + int ny = Dm->Ny; + int nz = Dm->Nz; + int iproc = Dm->iproc(); + int jproc = Dm->jproc(); + int kproc = Dm->kproc(); + int nprocx = Dm->nprocx(); + int nprocy = Dm->nprocy(); + int nprocz = Dm->nprocz(); + int rank = Dm->rank(); + + DoubleArray phase(Nx,Ny,Nz); + IntArray phase_label(Nx,Ny,Nz); + + int n; + double final_void_fraction; + double count,countGlobal,totalGlobal; + count = 0.f; + double maxdist=-200.f; + double maxdistGlobal; + for (int k=1; k maxdist) maxdist=SignDist(i,j,k); + if ( SignDist(i,j,k) > 0.0 ){ + count += 1.0; + id[n] = 2; + } + } + } + } + + MPI_Barrier(Dm->Comm); + + // total Global is the number of nodes in the pore-space + MPI_Allreduce(&count,&totalGlobal,1,MPI_DOUBLE,MPI_SUM,Dm->Comm); + MPI_Allreduce(&maxdist,&maxdistGlobal,1,MPI_DOUBLE,MPI_MAX,Dm->Comm); + double volume=double(nprocx*nprocy*nprocz)*double(nx-2)*double(ny-2)*double(nz-2); + double volume_fraction=totalGlobal/volume; + if (rank==0) printf("Volume fraction for morphological opening: %f \n",volume_fraction); + if (rank==0) printf("Maximum pore size: %f \n",maxdistGlobal); + + // Communication buffers + char *sendID_x, *sendID_y, *sendID_z, *sendID_X, *sendID_Y, *sendID_Z; + char *sendID_xy, *sendID_yz, *sendID_xz, *sendID_Xy, *sendID_Yz, *sendID_xZ; + char *sendID_xY, *sendID_yZ, *sendID_Xz, *sendID_XY, *sendID_YZ, *sendID_XZ; + char *recvID_x, *recvID_y, *recvID_z, *recvID_X, *recvID_Y, *recvID_Z; + char *recvID_xy, *recvID_yz, *recvID_xz, *recvID_Xy, *recvID_Yz, *recvID_xZ; + char *recvID_xY, *recvID_yZ, *recvID_Xz, *recvID_XY, *recvID_YZ, *recvID_XZ; + // send buffers + sendID_x = new char [Dm->sendCount_x]; + sendID_y = new char [Dm->sendCount_y]; + sendID_z = new char [Dm->sendCount_z]; + sendID_X = new char [Dm->sendCount_X]; + sendID_Y = new char [Dm->sendCount_Y]; + sendID_Z = new char [Dm->sendCount_Z]; + sendID_xy = new char [Dm->sendCount_xy]; + sendID_yz = new char [Dm->sendCount_yz]; + sendID_xz = new char [Dm->sendCount_xz]; + sendID_Xy = new char [Dm->sendCount_Xy]; + sendID_Yz = new char [Dm->sendCount_Yz]; + sendID_xZ = new char [Dm->sendCount_xZ]; + sendID_xY = new char [Dm->sendCount_xY]; + sendID_yZ = new char [Dm->sendCount_yZ]; + sendID_Xz = new char [Dm->sendCount_Xz]; + sendID_XY = new char [Dm->sendCount_XY]; + sendID_YZ = new char [Dm->sendCount_YZ]; + sendID_XZ = new char [Dm->sendCount_XZ]; + //...................................................................................... + // recv buffers + recvID_x = new char [Dm->recvCount_x]; + recvID_y = new char [Dm->recvCount_y]; + recvID_z = new char [Dm->recvCount_z]; + recvID_X = new char [Dm->recvCount_X]; + recvID_Y = new char [Dm->recvCount_Y]; + recvID_Z = new char [Dm->recvCount_Z]; + recvID_xy = new char [Dm->recvCount_xy]; + recvID_yz = new char [Dm->recvCount_yz]; + recvID_xz = new char [Dm->recvCount_xz]; + recvID_Xy = new char [Dm->recvCount_Xy]; + recvID_xZ = new char [Dm->recvCount_xZ]; + recvID_xY = new char [Dm->recvCount_xY]; + recvID_yZ = new char [Dm->recvCount_yZ]; + recvID_Yz = new char [Dm->recvCount_Yz]; + recvID_Xz = new char [Dm->recvCount_Xz]; + recvID_XY = new char [Dm->recvCount_XY]; + recvID_YZ = new char [Dm->recvCount_YZ]; + recvID_XZ = new char [Dm->recvCount_XZ]; + //...................................................................................... + int sendtag,recvtag; + sendtag = recvtag = 7; + + int x,y,z; + int ii,jj,kk; + int Nx = nx; + int Ny = ny; + int Nz = nz; + + double void_fraction_old=1.0; + double void_fraction_new=1.0; + double void_fraction_diff_old = 1.0; + double void_fraction_diff_new = 1.0; + + // Increase the critical radius until the target saturation is met + double deltaR=0.05; // amount to change the radius in voxel units + double Rcrit_old; + + double GlobalNumber = 1.f; + int imin,jmin,kmin,imax,jmax,kmax; + + double Rcrit_new = maxdistGlobal; + //if (argc>2){ + // Rcrit_new = strtod(argv[2],NULL); + // if (rank==0) printf("Max. distance =%f, Initial critical radius = %f \n",maxdistGlobal,Rcrit_new); + //} + + while (void_fraction_new > VoidFraction) + { + void_fraction_diff_old = void_fraction_diff_new; + void_fraction_old = void_fraction_new; + Rcrit_old = Rcrit_new; + Rcrit_new -= deltaR*Rcrit_old; + int Window=round(Rcrit_new); + if (Window == 0) Window = 1; // If Window = 0 at the begining, after the following process will have sw=1.0 + // and sw Rcrit_new){ + // loop over the window and update + imin=max(1,i-Window); + jmin=max(1,j-Window); + kmin=max(1,k-Window); + imax=min(Nx-1,i+Window); + jmax=min(Ny-1,j+Window); + kmax=min(Nz-1,k+Window); + for (kk=kmin; kksendList_x, Dm->sendCount_x ,sendID_x, id); + PackID(Dm->sendList_X, Dm->sendCount_X ,sendID_X, id); + PackID(Dm->sendList_y, Dm->sendCount_y ,sendID_y, id); + PackID(Dm->sendList_Y, Dm->sendCount_Y ,sendID_Y, id); + PackID(Dm->sendList_z, Dm->sendCount_z ,sendID_z, id); + PackID(Dm->sendList_Z, Dm->sendCount_Z ,sendID_Z, id); + PackID(Dm->sendList_xy, Dm->sendCount_xy ,sendID_xy, id); + PackID(Dm->sendList_Xy, Dm->sendCount_Xy ,sendID_Xy, id); + PackID(Dm->sendList_xY, Dm->sendCount_xY ,sendID_xY, id); + PackID(Dm->sendList_XY, Dm->sendCount_XY ,sendID_XY, id); + PackID(Dm->sendList_xz, Dm->sendCount_xz ,sendID_xz, id); + PackID(Dm->sendList_Xz, Dm->sendCount_Xz ,sendID_Xz, id); + PackID(Dm->sendList_xZ, Dm->sendCount_xZ ,sendID_xZ, id); + PackID(Dm->sendList_XZ, Dm->sendCount_XZ ,sendID_XZ, id); + PackID(Dm->sendList_yz, Dm->sendCount_yz ,sendID_yz, id); + PackID(Dm->sendList_Yz, Dm->sendCount_Yz ,sendID_Yz, id); + PackID(Dm->sendList_yZ, Dm->sendCount_yZ ,sendID_yZ, id); + PackID(Dm->sendList_YZ, Dm->sendCount_YZ ,sendID_YZ, id); + //...................................................................................... + MPI_Sendrecv(sendID_x,Dm->sendCount_x,MPI_CHAR,Dm->rank_x(),sendtag, + recvID_X,Dm->recvCount_X,MPI_CHAR,Dm->rank_X(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_X,Dm->sendCount_X,MPI_CHAR,Dm->rank_X(),sendtag, + recvID_x,Dm->recvCount_x,MPI_CHAR,Dm->rank_x(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_y,Dm->sendCount_y,MPI_CHAR,Dm->rank_y(),sendtag, + recvID_Y,Dm->recvCount_Y,MPI_CHAR,Dm->rank_Y(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_Y,Dm->sendCount_Y,MPI_CHAR,Dm->rank_Y(),sendtag, + recvID_y,Dm->recvCount_y,MPI_CHAR,Dm->rank_y(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_z,Dm->sendCount_z,MPI_CHAR,Dm->rank_z(),sendtag, + recvID_Z,Dm->recvCount_Z,MPI_CHAR,Dm->rank_Z(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_Z,Dm->sendCount_Z,MPI_CHAR,Dm->rank_Z(),sendtag, + recvID_z,Dm->recvCount_z,MPI_CHAR,Dm->rank_z(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_xy,Dm->sendCount_xy,MPI_CHAR,Dm->rank_xy(),sendtag, + recvID_XY,Dm->recvCount_XY,MPI_CHAR,Dm->rank_XY(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_XY,Dm->sendCount_XY,MPI_CHAR,Dm->rank_XY(),sendtag, + recvID_xy,Dm->recvCount_xy,MPI_CHAR,Dm->rank_xy(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_Xy,Dm->sendCount_Xy,MPI_CHAR,Dm->rank_Xy(),sendtag, + recvID_xY,Dm->recvCount_xY,MPI_CHAR,Dm->rank_xY(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_xY,Dm->sendCount_xY,MPI_CHAR,Dm->rank_xY(),sendtag, + recvID_Xy,Dm->recvCount_Xy,MPI_CHAR,Dm->rank_Xy(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_xz,Dm->sendCount_xz,MPI_CHAR,Dm->rank_xz(),sendtag, + recvID_XZ,Dm->recvCount_XZ,MPI_CHAR,Dm->rank_XZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_XZ,Dm->sendCount_XZ,MPI_CHAR,Dm->rank_XZ(),sendtag, + recvID_xz,Dm->recvCount_xz,MPI_CHAR,Dm->rank_xz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_Xz,Dm->sendCount_Xz,MPI_CHAR,Dm->rank_Xz(),sendtag, + recvID_xZ,Dm->recvCount_xZ,MPI_CHAR,Dm->rank_xZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_xZ,Dm->sendCount_xZ,MPI_CHAR,Dm->rank_xZ(),sendtag, + recvID_Xz,Dm->recvCount_Xz,MPI_CHAR,Dm->rank_Xz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_yz,Dm->sendCount_yz,MPI_CHAR,Dm->rank_yz(),sendtag, + recvID_YZ,Dm->recvCount_YZ,MPI_CHAR,Dm->rank_YZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_YZ,Dm->sendCount_YZ,MPI_CHAR,Dm->rank_YZ(),sendtag, + recvID_yz,Dm->recvCount_yz,MPI_CHAR,Dm->rank_yz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_Yz,Dm->sendCount_Yz,MPI_CHAR,Dm->rank_Yz(),sendtag, + recvID_yZ,Dm->recvCount_yZ,MPI_CHAR,Dm->rank_yZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + MPI_Sendrecv(sendID_yZ,Dm->sendCount_yZ,MPI_CHAR,Dm->rank_yZ(),sendtag, + recvID_Yz,Dm->recvCount_Yz,MPI_CHAR,Dm->rank_Yz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE); + //...................................................................................... + UnpackID(Dm->recvList_x, Dm->recvCount_x ,recvID_x, id); + UnpackID(Dm->recvList_X, Dm->recvCount_X ,recvID_X, id); + UnpackID(Dm->recvList_y, Dm->recvCount_y ,recvID_y, id); + UnpackID(Dm->recvList_Y, Dm->recvCount_Y ,recvID_Y, id); + UnpackID(Dm->recvList_z, Dm->recvCount_z ,recvID_z, id); + UnpackID(Dm->recvList_Z, Dm->recvCount_Z ,recvID_Z, id); + UnpackID(Dm->recvList_xy, Dm->recvCount_xy ,recvID_xy, id); + UnpackID(Dm->recvList_Xy, Dm->recvCount_Xy ,recvID_Xy, id); + UnpackID(Dm->recvList_xY, Dm->recvCount_xY ,recvID_xY, id); + UnpackID(Dm->recvList_XY, Dm->recvCount_XY ,recvID_XY, id); + UnpackID(Dm->recvList_xz, Dm->recvCount_xz ,recvID_xz, id); + UnpackID(Dm->recvList_Xz, Dm->recvCount_Xz ,recvID_Xz, id); + UnpackID(Dm->recvList_xZ, Dm->recvCount_xZ ,recvID_xZ, id); + UnpackID(Dm->recvList_XZ, Dm->recvCount_XZ ,recvID_XZ, id); + UnpackID(Dm->recvList_yz, Dm->recvCount_yz ,recvID_yz, id); + UnpackID(Dm->recvList_Yz, Dm->recvCount_Yz ,recvID_Yz, id); + UnpackID(Dm->recvList_yZ, Dm->recvCount_yZ ,recvID_yZ, id); + UnpackID(Dm->recvList_YZ, Dm->recvCount_YZ ,recvID_YZ, id); + //...................................................................................... + MPI_Allreduce(&LocalNumber,&GlobalNumber,1,MPI_DOUBLE,MPI_SUM,Dm->Comm); + + + for (int k=0;krank_info,phase,SignDist,vF,vS,phase_label,Dm->Comm); + MPI_Barrier(comm); + + for (int k=0;k 1){ + id[n] = 2; + } + } + } + } + + count = 0.f; + for (int k=1; kComm); + void_fraction_new = countGlobal/totalGlobal; + void_fraction_diff_new = abs(void_fraction_new-VoidFraction); + if (rank==0){ + printf(" %f ",void_fraction_new); + printf(" %f\n",Rcrit_new); + } + } + + if (void_fraction_diff_new &id, std::shared_ptr Dm, double TargetGrowth){ int Nx = Dm->Nx; diff --git a/analysis/morphology.h b/analysis/morphology.h index a543d6e3..4692475d 100644 --- a/analysis/morphology.h +++ b/analysis/morphology.h @@ -1,6 +1,8 @@ // Morphological opening routine #include "common/Array.h" #include "common/Domain.h" +#include "analysis/runAnalysis.h" double MorphOpen(DoubleArray &SignDist, char *id, std::shared_ptr Dm, double VoidFraction); +double MorphDrain(DoubleArray &SignDist, char *id, std::shared_ptr Dm, double VoidFraction); double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array &id, std::shared_ptr Dm, double TargetVol); \ No newline at end of file diff --git a/tests/lbpm_morphdrain_pp.cpp b/tests/lbpm_morphdrain_pp.cpp index 4184e4ba..9f655f37 100644 --- a/tests/lbpm_morphdrain_pp.cpp +++ b/tests/lbpm_morphdrain_pp.cpp @@ -98,8 +98,6 @@ int main(int argc, char **argv) // Initialize the domain and communication Array 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;krank_info,phase,SignDist,vF,vS,phase_label,Dm->Comm); - MPI_Barrier(comm); - - for (int k=0;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");