Added unit test tests/TestBlobAnalyze
This commit is contained in:
James E McClure
parent
623fada1d2
commit
cb35d83bdf
@ -22,6 +22,7 @@ ADD_LBPM_TEST( TestSphereCurvature )
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ADD_LBPM_TEST( TestContactAngle )
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ADD_LBPM_TEST( TestContactAngle )
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ADD_LBPM_TEST_1_2_4( TestTwoPhase )
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ADD_LBPM_TEST_1_2_4( TestTwoPhase )
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ADD_LBPM_TEST_PARALLEL( TestTwoPhase 8 )
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ADD_LBPM_TEST_PARALLEL( TestTwoPhase 8 )
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ADD_LBPM_TEST_PARALLEL( TestBlobAnalyze 8 )
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ADD_LBPM_TEST_PARALLEL( TestSegDist 8 )
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ADD_LBPM_TEST_PARALLEL( TestSegDist 8 )
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ADD_LBPM_TEST_1_2_4( testCommunication )
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ADD_LBPM_TEST_1_2_4( testCommunication )
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ADD_LBPM_TEST_1_2_4( testUtilities )
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ADD_LBPM_TEST_1_2_4( testUtilities )
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399
tests/TestBlobAnalyze.cpp
Normal file
399
tests/TestBlobAnalyze.cpp
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@ -0,0 +1,399 @@
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// Sequential blob analysis
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// Reads parallel simulation data and performs connectivity analysis
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// and averaging on a blob-by-blob basis
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// James E. McClure 2014
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#include <iostream>
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#include <math.h>
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#include "common/Communication.h"
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#include "analysis/analysis.h"
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#ifdef PROFILE
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#include "ProfilerApp.h"
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#endif
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#include "TwoPhase.h"
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//#include "Domain.h"
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using namespace std;
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void readRankData( int proc, int nx, int ny, int nz, DoubleArray& Phase, DoubleArray& SignDist )
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{
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Phase.resize(nx,ny,nz);
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SignDist.resize(nx,ny,nz);
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char file1[40], file2[40];
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sprintf(file1,"SignDist.%05d",proc);
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sprintf(file2,"Phase.%05d",proc);
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ReadBinaryFile(file1, Phase.get(), nx*ny*nz);
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ReadBinaryFile(file2, SignDist.get(), nx*ny*nz);
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}
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inline void WriteBlobStates(TwoPhase TCAT, double D, double porosity){
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int a;
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double iVol=1.0/TCAT.Dm.Volume;
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double PoreVolume;
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double nwp_volume,vol_n,pan,pn,pw,pawn,pwn,awn,ans,aws,Jwn,Kwn,lwns,cwns,clwns;
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double sw,awnD,awsD,ansD,lwnsDD,JwnD,pc;
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nwp_volume=vol_n=pan=awn=ans=Jwn=Kwn=lwns=clwns=pawn=0.0;
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sw = TCAT.sat_w;
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pw = TCAT.paw_global;
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aws = TCAT.aws;
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// Compute the averages over the entire non-wetting phase
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printf("Writing blobstates.tcat for %i components \n",TCAT.nblobs_global);
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FILE *BLOBSTATES;
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BLOBSTATES = fopen("./blobstates.tcat","w");
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if (BLOBSTATES==NULL) ERROR("Cannot open blobstates.tcat for writing");
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for (a=0; a<TCAT.nblobs_global; a++){
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vol_n += TCAT.BlobAverages(0,a);
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pan += TCAT.BlobAverages(2,a)*TCAT.BlobAverages(0,a);
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awn += TCAT.BlobAverages(3,a);
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ans += TCAT.BlobAverages(4,a);
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Jwn += TCAT.BlobAverages(5,a)*TCAT.BlobAverages(3,a);
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Kwn += TCAT.BlobAverages(6,a)*TCAT.BlobAverages(3,a);
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lwns += TCAT.BlobAverages(7,a);
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clwns += TCAT.BlobAverages(8,a)*TCAT.BlobAverages(7,a);
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nwp_volume += TCAT.BlobAverages(1,a);
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pawn += TCAT.BlobAverages(2,a)*TCAT.BlobAverages(3,a);
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}
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// Compute the pore voume (sum of wetting an non-wetting phase volumes)
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PoreVolume=TCAT.wp_volume_global + nwp_volume;
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// Subtract off portions of non-wetting phase in order of size
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for (a=TCAT.nblobs_global-1; a>0; a--){
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// Subtract the features one-by-one
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vol_n -= TCAT.BlobAverages(0,a);
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pan -= TCAT.BlobAverages(2,a)*TCAT.BlobAverages(0,a);
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awn -= TCAT.BlobAverages(3,a);
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ans -= TCAT.BlobAverages(4,a);
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Jwn -= TCAT.BlobAverages(5,a)*TCAT.BlobAverages(3,a);
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Kwn -= TCAT.BlobAverages(6,a)*TCAT.BlobAverages(3,a);
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lwns -= TCAT.BlobAverages(7,a);
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clwns -= TCAT.BlobAverages(8,a)*TCAT.BlobAverages(7,a);
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nwp_volume -= TCAT.BlobAverages(1,a);
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pawn -= TCAT.BlobAverages(2,a)*TCAT.BlobAverages(3,a);
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// Update wetting phase averages
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aws += TCAT.BlobAverages(4,a);
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if (vol_n > 64){ // Only consider systems with "large enough" blobs -- 4^3
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if (fabs(1.0 - nwp_volume/PoreVolume - sw) > 0.005 || a == 1){
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sw = 1.0 - nwp_volume/PoreVolume;
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JwnD = Jwn*D/awn;
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//trJwnD = -trJwn*D/trawn;
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cwns = clwns / lwns;
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pwn = (pawn/awn-pw)*D/0.058;
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pn = pan/vol_n;
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awnD = awn*D*iVol;
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awsD = aws*D*iVol;
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ansD = ans*D*iVol;
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lwnsDD = lwns*D*D*iVol;
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pc = (pn-pw)*D/0.058; // hard-coded surface tension due to being lazy
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fprintf(BLOBSTATES,"%.5g %.5g %.5g ",sw,pn,pw);
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fprintf(BLOBSTATES,"%.5g %.5g %.5g %.5g ",awnD,awsD,ansD,lwnsDD);
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fprintf(BLOBSTATES,"%.5g %.5g %.5g %.5g %i\n",pc,pwn,JwnD,cwns,a);
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}
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}
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}
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fclose(BLOBSTATES);
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}
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int main(int argc, char **argv)
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{
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// Initialize MPI
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int rank, nprocs;
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MPI_Init(&argc,&argv);
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MPI_Comm_rank(MPI_COMM_WORLD,&rank);
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MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
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Utilities::setAbortBehavior( true, true, true );
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Utilities::setErrorHandlers();
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PROFILE_ENABLE(0);
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PROFILE_DISABLE_TRACE();
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PROFILE_SYNCHRONIZE();
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PROFILE_START("main");
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if ( rank==0 ) {
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printf("-----------------------------------------------------------\n");
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printf("Labeling Blobs from Two-Phase Lattice Boltzmann Simulation \n");
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printf("-----------------------------------------------------------\n");
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}
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//.......................................................................
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// Reading the domain information file
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//.......................................................................
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int nprocx, nprocy, nprocz, nx, ny, nz, nspheres;
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double Lx, Ly, Lz;
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if (rank==0){
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ifstream domain("Domain.in");
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domain >> nprocx;
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domain >> nprocy;
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domain >> nprocz;
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domain >> nx;
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domain >> ny;
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domain >> nz;
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domain >> nspheres;
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domain >> Lx;
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domain >> Ly;
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domain >> Lz;
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}
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MPI_Barrier(MPI_COMM_WORLD);
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// Computational domain
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MPI_Bcast(&nx,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&ny,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&nz,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&nprocx,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&nprocy,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&nprocz,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&nspheres,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&Lx,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
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MPI_Bcast(&Ly,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
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MPI_Bcast(&Lz,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
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//.................................................
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MPI_Barrier(MPI_COMM_WORLD);
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// Check that the number of processors >= the number of ranks
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if ( rank==0 ) {
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printf("Number of MPI ranks required: %i \n", nprocx*nprocy*nprocz);
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printf("Number of MPI ranks used: %i \n", nprocs);
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printf("Full domain size: %i x %i x %i \n",nx*nprocx,ny*nprocy,nz*nprocz);
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}
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if ( nprocs < nprocx*nprocy*nprocz )
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ERROR("Insufficient number of processors");
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// Set up the domain
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int BC=0;
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// Get the rank info
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Domain Dm(nx,ny,nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BC);
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// const RankInfoStruct rank_info(rank,nprocx,nprocy,nprocz);
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TwoPhase Averages(Dm);
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int N = (nx+2)*(ny+2)*(nz+2);
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// Read in sphere pack (initialize the non-wetting phase as inside of spheres)
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if (rank==1) printf("nspheres =%i \n",nspheres);
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//.......................................................................
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double *cx,*cy,*cz,*rad;
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cx = new double[nspheres];
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cy = new double[nspheres];
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cz = new double[nspheres];
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rad = new double[nspheres];
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//.......................................................................
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if (rank == 0) printf("Reading the sphere packing \n");
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if (rank == 0) ReadSpherePacking(nspheres,cx,cy,cz,rad);
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MPI_Barrier(MPI_COMM_WORLD);
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// Broadcast the sphere packing to all processes
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MPI_Bcast(cx,nspheres,MPI_DOUBLE,0,MPI_COMM_WORLD);
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MPI_Bcast(cy,nspheres,MPI_DOUBLE,0,MPI_COMM_WORLD);
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MPI_Bcast(cz,nspheres,MPI_DOUBLE,0,MPI_COMM_WORLD);
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MPI_Bcast(rad,nspheres,MPI_DOUBLE,0,MPI_COMM_WORLD);
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//...........................................................................
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MPI_Barrier(MPI_COMM_WORLD);
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if (rank == 0) cout << "Domain set." << endl;
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//.......................................................................
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DoubleArray Phase(Nx,Ny,Nz);
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DoubleArray SignDist(Nx,Ny,Nz);
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//.......................................................................
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SignedDistance(Phase.get(),nspheres,cx,cy,cz,rad,Lx,Ly,Lz,Nx,Ny,Nz,
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iproc,jproc,kproc,nprocx,nprocy,nprocz);
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//.......................................................................
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// Assign the phase ID field based on the signed distance
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//.......................................................................
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for ( k=1;k<Nz-1;k++){
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for ( j=1;j<Ny-1;j++){
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for ( i=1;i<Nx-1;i++){
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n = k*Nx*Ny+j*Nx+i;
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// Shrink the sphere sizes by two voxels to make sure they don't touch
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SignDist(i,j,k) = 100.0;
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Phase(i,j,k) += 2.0;
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if (Phase(i,j,k) > 0.0){
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id[n] = 2;
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}
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else{
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id[n] = 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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Dm.CommInit(MPI_COMM_WORLD); // Initialize communications for domains
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//.......................................................................
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MPI_Allreduce(&sum,&sum_global,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
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porosity = sum_global/Dm.Volume;
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if (rank==0) printf("Porosity = %f \n",porosity);
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double beta = 0.95;
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Averages.SetupCubes(Dm);
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Averages.UpdateSolid();
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Averages.Initialize();
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Averages.ComputeDelPhi();
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Averages.ColorToSignedDistance(beta,Averages.Phase.get(),Averages.SDn.get());
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Averages.UpdateMeshValues();
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Averages.ComputeLocalBlob();
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Averages.Reduce();
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// Blobs.Set(Averages.BlobAverages.NBLOBS);
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int dimx = (int)Averages.BlobAverages.size(0);
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int dimy = (int)Averages.BlobAverages.size(1);
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int TotalBlobInfoSize=dimx*dimy;
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// BlobContainer Blobs;
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DoubleArray RecvBuffer(dimx);
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// MPI_Allreduce(&Averages.BlobAverages.get(),&Blobs.get(),1,MPI_DOUBLE,MPI_SUM,Dm.Comm);
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MPI_Barrier(MPI_COMM_WORLD);
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if (rank==0) printf("Number of components is %i \n",dimy);
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for (int b=0; b<dimy; b++){
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MPI_Allreduce(&Averages.BlobAverages(0,b),&RecvBuffer(0),dimx,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
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for (int idx=0; idx<dimx-1; idx++) Averages.BlobAverages(idx,b)=RecvBuffer(idx);
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MPI_Barrier(MPI_COMM_WORLD);
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if (Averages.BlobAverages(0,b) > 0.0){
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double Vn,pn,awn,ans,Jwn,Kwn,lwns,cwns,trawn,trJwn;
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Vn = Averages.BlobAverages(1,b);
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pn = Averages.BlobAverages(2,b)/Averages.BlobAverages(0,b);
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awn = Averages.BlobAverages(3,b);
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ans = Averages.BlobAverages(4,b);
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if (awn != 0.0){
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Jwn = Averages.BlobAverages(5,b)/Averages.BlobAverages(3,b);
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Kwn = Averages.BlobAverages(6,b)/Averages.BlobAverages(3,b);
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}
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else Jwn=Kwn=0.0;
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trawn = Averages.BlobAverages(12,b);
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if (trawn != 0.0){
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trJwn = Averages.BlobAverages(13,b)/trawn;
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}
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else trJwn=0.0;
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lwns = Averages.BlobAverages(7,b);
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if (lwns != 0.0) cwns = Averages.BlobAverages(8,b)/Averages.BlobAverages(7,b);
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else cwns=0.0;
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Averages.BlobAverages(2,b) = pn;
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Averages.BlobAverages(5,b) = trJwn;
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Averages.BlobAverages(6,b) = Kwn;
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Averages.BlobAverages(8,b) = cwns;
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// Averages.BlobAverages(13,b) = trJwn;
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}
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}
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if (rank==0) printf("Sorting blobs by volume \n");
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Averages.SortBlobs();
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FILE *BLOBLOG;
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if (rank==0){
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printf("Writing the blob list \n");
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BLOBLOG=fopen("blobs.tcat","w");
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// printf("Reduced blob %i \n",b);
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fprintf(BLOBLOG,"%.5g %.5g %.5g\n",Averages.vol_w_global,Averages.paw_global,Averages.aws_global);
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for (int b=0; b<dimy; b++){
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if (Averages.BlobAverages(0,b) > 0.0){
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double Vn,pn,awn,ans,Jwn,Kwn,lwns,cwns;
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Vn = Averages.BlobAverages(1,b);
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pn = Averages.BlobAverages(2,b);
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awn = Averages.BlobAverages(3,b);
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ans = Averages.BlobAverages(4,b);
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Jwn = Averages.BlobAverages(5,b);
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Kwn = Averages.BlobAverages(6,b);
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lwns = Averages.BlobAverages(7,b);
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cwns = Averages.BlobAverages(8,b);
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fprintf(BLOBLOG,"%.5g ", Vn); //Vn
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fprintf(BLOBLOG,"%.5g ", pn); //pn
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fprintf(BLOBLOG,"%.5g ", awn); //awn
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|
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; a<Averages.nblobs_global; a++){
|
||||||
|
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);
|
||||||
|
}
|
||||||
|
|
||||||
|
// Compute the pore voume (sum of wetting an non-wetting phase volumes)
|
||||||
|
PoreVolume=Averages.wp_volume_global + nwp_volume;
|
||||||
|
// Subtract off portions of non-wetting phase in order of size
|
||||||
|
for (a=Averages.nblobs_global-1; a>0; 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;
|
||||||
|
}
|
||||||
|
|
||||||
Loading…
Reference in New Issue
Block a user