diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt index de72bc88..60ed39ea 100755 --- a/tests/CMakeLists.txt +++ b/tests/CMakeLists.txt @@ -22,6 +22,7 @@ ADD_LBPM_TEST( TestSphereCurvature ) ADD_LBPM_TEST( TestContactAngle ) ADD_LBPM_TEST_1_2_4( TestTwoPhase ) ADD_LBPM_TEST_PARALLEL( TestTwoPhase 8 ) +ADD_LBPM_TEST_PARALLEL( TestBlobAnalyze 8 ) ADD_LBPM_TEST_PARALLEL( TestSegDist 8 ) ADD_LBPM_TEST_1_2_4( testCommunication ) ADD_LBPM_TEST_1_2_4( testUtilities ) diff --git a/tests/TestBlobAnalyze.cpp b/tests/TestBlobAnalyze.cpp new file mode 100644 index 00000000..7db59531 --- /dev/null +++ b/tests/TestBlobAnalyze.cpp @@ -0,0 +1,399 @@ +// Sequential blob analysis +// Reads parallel simulation data and performs connectivity analysis +// and averaging on a blob-by-blob basis +// James E. McClure 2014 + +#include +#include +#include "common/Communication.h" +#include "analysis/analysis.h" +#ifdef PROFILE + #include "ProfilerApp.h" +#endif +#include "TwoPhase.h" + +//#include "Domain.h" + +using namespace std; + +void readRankData( int proc, int nx, int ny, int nz, DoubleArray& Phase, DoubleArray& SignDist ) +{ + Phase.resize(nx,ny,nz); + SignDist.resize(nx,ny,nz); + char file1[40], file2[40]; + sprintf(file1,"SignDist.%05d",proc); + sprintf(file2,"Phase.%05d",proc); + ReadBinaryFile(file1, Phase.get(), nx*ny*nz); + ReadBinaryFile(file2, SignDist.get(), nx*ny*nz); +} + +inline void WriteBlobStates(TwoPhase TCAT, double D, double porosity){ + int a; + double iVol=1.0/TCAT.Dm.Volume; + double PoreVolume; + double nwp_volume,vol_n,pan,pn,pw,pawn,pwn,awn,ans,aws,Jwn,Kwn,lwns,cwns,clwns; + double sw,awnD,awsD,ansD,lwnsDD,JwnD,pc; + nwp_volume=vol_n=pan=awn=ans=Jwn=Kwn=lwns=clwns=pawn=0.0; + sw = TCAT.sat_w; + pw = TCAT.paw_global; + aws = TCAT.aws; + // Compute the averages over the entire non-wetting phase + printf("Writing blobstates.tcat for %i components \n",TCAT.nblobs_global); + FILE *BLOBSTATES; + BLOBSTATES = fopen("./blobstates.tcat","w"); + if (BLOBSTATES==NULL) ERROR("Cannot open blobstates.tcat for writing"); + for (a=0; a0; a--){ + // Subtract the features one-by-one + vol_n -= TCAT.BlobAverages(0,a); + pan -= TCAT.BlobAverages(2,a)*TCAT.BlobAverages(0,a); + awn -= TCAT.BlobAverages(3,a); + ans -= TCAT.BlobAverages(4,a); + Jwn -= TCAT.BlobAverages(5,a)*TCAT.BlobAverages(3,a); + Kwn -= TCAT.BlobAverages(6,a)*TCAT.BlobAverages(3,a); + lwns -= TCAT.BlobAverages(7,a); + clwns -= TCAT.BlobAverages(8,a)*TCAT.BlobAverages(7,a); + nwp_volume -= TCAT.BlobAverages(1,a); + pawn -= TCAT.BlobAverages(2,a)*TCAT.BlobAverages(3,a); + + // Update wetting phase averages + aws += TCAT.BlobAverages(4,a); + if (vol_n > 64){ // Only consider systems with "large enough" blobs -- 4^3 + if (fabs(1.0 - nwp_volume/PoreVolume - sw) > 0.005 || a == 1){ + sw = 1.0 - nwp_volume/PoreVolume; + + JwnD = Jwn*D/awn; + //trJwnD = -trJwn*D/trawn; + cwns = clwns / lwns; + pwn = (pawn/awn-pw)*D/0.058; + pn = pan/vol_n; + awnD = awn*D*iVol; + awsD = aws*D*iVol; + ansD = ans*D*iVol; + lwnsDD = lwns*D*D*iVol; + pc = (pn-pw)*D/0.058; // hard-coded surface tension due to being lazy + + fprintf(BLOBSTATES,"%.5g %.5g %.5g ",sw,pn,pw); + fprintf(BLOBSTATES,"%.5g %.5g %.5g %.5g ",awnD,awsD,ansD,lwnsDD); + fprintf(BLOBSTATES,"%.5g %.5g %.5g %.5g %i\n",pc,pwn,JwnD,cwns,a); + } + } + } + fclose(BLOBSTATES); +} + +int main(int argc, char **argv) +{ + // Initialize MPI + int rank, nprocs; + MPI_Init(&argc,&argv); + MPI_Comm_rank(MPI_COMM_WORLD,&rank); + MPI_Comm_size(MPI_COMM_WORLD,&nprocs); + Utilities::setAbortBehavior( true, true, true ); + Utilities::setErrorHandlers(); + PROFILE_ENABLE(0); + PROFILE_DISABLE_TRACE(); + PROFILE_SYNCHRONIZE(); + PROFILE_START("main"); + + if ( rank==0 ) { + printf("-----------------------------------------------------------\n"); + printf("Labeling Blobs from Two-Phase Lattice Boltzmann Simulation \n"); + printf("-----------------------------------------------------------\n"); + } + + //....................................................................... + // Reading the domain information file + //....................................................................... + int nprocx, nprocy, nprocz, nx, ny, nz, nspheres; + double Lx, Ly, Lz; + + if (rank==0){ + ifstream domain("Domain.in"); + domain >> nprocx; + domain >> nprocy; + domain >> nprocz; + domain >> nx; + domain >> ny; + domain >> nz; + domain >> nspheres; + domain >> Lx; + domain >> Ly; + domain >> Lz; + } + MPI_Barrier(MPI_COMM_WORLD); + // Computational domain + MPI_Bcast(&nx,1,MPI_INT,0,MPI_COMM_WORLD); + MPI_Bcast(&ny,1,MPI_INT,0,MPI_COMM_WORLD); + MPI_Bcast(&nz,1,MPI_INT,0,MPI_COMM_WORLD); + MPI_Bcast(&nprocx,1,MPI_INT,0,MPI_COMM_WORLD); + MPI_Bcast(&nprocy,1,MPI_INT,0,MPI_COMM_WORLD); + MPI_Bcast(&nprocz,1,MPI_INT,0,MPI_COMM_WORLD); + MPI_Bcast(&nspheres,1,MPI_INT,0,MPI_COMM_WORLD); + MPI_Bcast(&Lx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + MPI_Bcast(&Ly,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + MPI_Bcast(&Lz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + //................................................. + MPI_Barrier(MPI_COMM_WORLD); + + // Check that the number of processors >= the number of ranks + if ( rank==0 ) { + printf("Number of MPI ranks required: %i \n", nprocx*nprocy*nprocz); + printf("Number of MPI ranks used: %i \n", nprocs); + printf("Full domain size: %i x %i x %i \n",nx*nprocx,ny*nprocy,nz*nprocz); + } + if ( nprocs < nprocx*nprocy*nprocz ) + ERROR("Insufficient number of processors"); + + // Set up the domain + int BC=0; + // Get the rank info + Domain Dm(nx,ny,nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BC); + // const RankInfoStruct rank_info(rank,nprocx,nprocy,nprocz); + TwoPhase Averages(Dm); + int N = (nx+2)*(ny+2)*(nz+2); + + // Read in sphere pack (initialize the non-wetting phase as inside of spheres) + if (rank==1) printf("nspheres =%i \n",nspheres); + //....................................................................... + double *cx,*cy,*cz,*rad; + cx = new double[nspheres]; + cy = new double[nspheres]; + cz = new double[nspheres]; + rad = new double[nspheres]; + //....................................................................... + if (rank == 0) printf("Reading the sphere packing \n"); + if (rank == 0) ReadSpherePacking(nspheres,cx,cy,cz,rad); + MPI_Barrier(MPI_COMM_WORLD); + // Broadcast the sphere packing to all processes + MPI_Bcast(cx,nspheres,MPI_DOUBLE,0,MPI_COMM_WORLD); + MPI_Bcast(cy,nspheres,MPI_DOUBLE,0,MPI_COMM_WORLD); + MPI_Bcast(cz,nspheres,MPI_DOUBLE,0,MPI_COMM_WORLD); + MPI_Bcast(rad,nspheres,MPI_DOUBLE,0,MPI_COMM_WORLD); + //........................................................................... + MPI_Barrier(MPI_COMM_WORLD); + if (rank == 0) cout << "Domain set." << endl; + //....................................................................... + DoubleArray Phase(Nx,Ny,Nz); + DoubleArray SignDist(Nx,Ny,Nz); + //....................................................................... + SignedDistance(Phase.get(),nspheres,cx,cy,cz,rad,Lx,Ly,Lz,Nx,Ny,Nz, + iproc,jproc,kproc,nprocx,nprocy,nprocz); + //....................................................................... + // Assign the phase ID field based on the signed distance + //....................................................................... + for ( k=1;k 0.0){ + id[n] = 2; + } + else{ + id[n] = 1; + } + } + } + } + //....................................................................... + Dm.CommInit(MPI_COMM_WORLD); // Initialize communications for domains + //....................................................................... + + MPI_Allreduce(&sum,&sum_global,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD); + porosity = sum_global/Dm.Volume; + if (rank==0) printf("Porosity = %f \n",porosity); + + double beta = 0.95; + Averages.SetupCubes(Dm); + Averages.UpdateSolid(); + Averages.Initialize(); + Averages.ComputeDelPhi(); + Averages.ColorToSignedDistance(beta,Averages.Phase.get(),Averages.SDn.get()); + Averages.UpdateMeshValues(); + Averages.ComputeLocalBlob(); + Averages.Reduce(); + + // Blobs.Set(Averages.BlobAverages.NBLOBS); + int dimx = (int)Averages.BlobAverages.size(0); + int dimy = (int)Averages.BlobAverages.size(1); + int TotalBlobInfoSize=dimx*dimy; + + // BlobContainer Blobs; + DoubleArray RecvBuffer(dimx); + // MPI_Allreduce(&Averages.BlobAverages.get(),&Blobs.get(),1,MPI_DOUBLE,MPI_SUM,Dm.Comm); + MPI_Barrier(MPI_COMM_WORLD); + if (rank==0) printf("Number of components is %i \n",dimy); + + for (int b=0; b 0.0){ + double Vn,pn,awn,ans,Jwn,Kwn,lwns,cwns,trawn,trJwn; + Vn = Averages.BlobAverages(1,b); + pn = Averages.BlobAverages(2,b)/Averages.BlobAverages(0,b); + awn = Averages.BlobAverages(3,b); + ans = Averages.BlobAverages(4,b); + if (awn != 0.0){ + Jwn = Averages.BlobAverages(5,b)/Averages.BlobAverages(3,b); + Kwn = Averages.BlobAverages(6,b)/Averages.BlobAverages(3,b); + } + else Jwn=Kwn=0.0; + + trawn = Averages.BlobAverages(12,b); + if (trawn != 0.0){ + trJwn = Averages.BlobAverages(13,b)/trawn; + } + else trJwn=0.0; + + lwns = Averages.BlobAverages(7,b); + if (lwns != 0.0) cwns = Averages.BlobAverages(8,b)/Averages.BlobAverages(7,b); + else cwns=0.0; + Averages.BlobAverages(2,b) = pn; + Averages.BlobAverages(5,b) = trJwn; + Averages.BlobAverages(6,b) = Kwn; + Averages.BlobAverages(8,b) = cwns; + // Averages.BlobAverages(13,b) = trJwn; + + } + } + + if (rank==0) printf("Sorting blobs by volume \n"); + Averages.SortBlobs(); + + FILE *BLOBLOG; + if (rank==0){ + printf("Writing the blob list \n"); + BLOBLOG=fopen("blobs.tcat","w"); + + // printf("Reduced blob %i \n",b); + fprintf(BLOBLOG,"%.5g %.5g %.5g\n",Averages.vol_w_global,Averages.paw_global,Averages.aws_global); + for (int b=0; b 0.0){ + double Vn,pn,awn,ans,Jwn,Kwn,lwns,cwns; + Vn = Averages.BlobAverages(1,b); + pn = Averages.BlobAverages(2,b); + awn = Averages.BlobAverages(3,b); + ans = Averages.BlobAverages(4,b); + Jwn = Averages.BlobAverages(5,b); + Kwn = Averages.BlobAverages(6,b); + lwns = Averages.BlobAverages(7,b); + cwns = Averages.BlobAverages(8,b); + + fprintf(BLOBLOG,"%.5g ", Vn); //Vn + fprintf(BLOBLOG,"%.5g ", pn); //pn + fprintf(BLOBLOG,"%.5g ", awn); //awn + fprintf(BLOBLOG,"%.5g ", ans); //ans + fprintf(BLOBLOG,"%.5g ", Jwn); //Jwn + fprintf(BLOBLOG,"%.5g ", Kwn); //Kwn + fprintf(BLOBLOG,"%.5g ", lwns); //lwns + fprintf(BLOBLOG,"%.5g\n",cwns); //cwns + } + } + fclose(BLOBLOG); + } + + if (rank==0) { + int a; + double D=1.0; + double iVol=1.0/Averages.Dm.Volume; + double PoreVolume; + double nwp_volume,vol_n,pan,pn,pw,pawn,pwn,awn,ans,aws,Jwn,Kwn,lwns,cwns,clwns; + double sw,awnD,awsD,ansD,lwnsDD,JwnD,pc; + nwp_volume=vol_n=pan=awn=ans=Jwn=Kwn=lwns=clwns=pawn=0.0; + sw = Averages.sat_w; + pw = Averages.paw_global; + aws = Averages.aws; + // Compute the averages over the entire non-wetting phase + printf("Writing blobstates.tcat for %i components \n",Averages.nblobs_global); + FILE *BLOBSTATES; + BLOBSTATES = fopen("./blobstates.tcat","w"); + if (BLOBSTATES==NULL) ERROR("Cannot open blobstates.tcat for writing"); + for (a=0; a0; a--){ + // Subtract the features one-by-one + vol_n -= Averages.BlobAverages(0,a); + pan -= Averages.BlobAverages(2,a)*Averages.BlobAverages(0,a); + awn -= Averages.BlobAverages(3,a); + ans -= Averages.BlobAverages(4,a); + Jwn -= Averages.BlobAverages(5,a)*Averages.BlobAverages(3,a); + Kwn -= Averages.BlobAverages(6,a)*Averages.BlobAverages(3,a); + lwns -= Averages.BlobAverages(7,a); + clwns -= Averages.BlobAverages(8,a)*Averages.BlobAverages(7,a); + nwp_volume -= Averages.BlobAverages(1,a); + pawn -= Averages.BlobAverages(2,a)*Averages.BlobAverages(3,a); + + // Update wetting phase averages + aws += Averages.BlobAverages(4,a); + if (vol_n > 64){ // Only consider systems with "large enough" blobs -- 4^3 + if (fabs(1.0 - nwp_volume/PoreVolume - sw) > 0.005 || a == 1){ + sw = 1.0 - nwp_volume/PoreVolume; + + JwnD = Jwn*D/awn; + //trJwnD = -trJwn*D/trawn; + cwns = clwns / lwns; + pwn = (pawn/awn-pw)*D/0.058; + pn = pan/vol_n; + awnD = awn*D*iVol; + awsD = aws*D*iVol; + ansD = ans*D*iVol; + lwnsDD = lwns*D*D*iVol; + pc = (pn-pw)*D/0.058; // hard-coded surface tension due to being lazy + + fprintf(BLOBSTATES,"%.5g %.5g %.5g ",sw,pn,pw); + fprintf(BLOBSTATES,"%.5g %.5g %.5g %.5g ",awnD,awsD,ansD,lwnsDD); + fprintf(BLOBSTATES,"%.5g %.5g %.5g %.5g %i\n",pc,pwn,JwnD,cwns,a); + } + } + } + fclose(BLOBSTATES); + + } + + //WriteBlobStates(Averages,Length,porosity); + + /*FILE *BLOBS = fopen("Blobs.dat","wb"); + fwrite(GlobalBlobID.get(),4,Nx*Ny*Nz,BLOBS); + fclose(BLOBS);*/ + PROFILE_STOP("main"); + PROFILE_SAVE("BlobIdentifyParallel",false); + MPI_Barrier(MPI_COMM_WORLD); + MPI_Finalize(); + return 0; +} +