489 lines
16 KiB
C++
489 lines
16 KiB
C++
// 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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Utilities::startup( argc, argv );
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Utilities::MPI comm( MPI_COMM_WORLD );
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int rank = comm.getRank();
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int nprocs = comm.getSize();
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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(comm);
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// Computational domain
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MPI_Bcast(&nx,1,MPI_INT,0,comm);
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MPI_Bcast(&ny,1,MPI_INT,0,comm);
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MPI_Bcast(&nz,1,MPI_INT,0,comm);
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MPI_Bcast(&nprocx,1,MPI_INT,0,comm);
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MPI_Bcast(&nprocy,1,MPI_INT,0,comm);
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MPI_Bcast(&nprocz,1,MPI_INT,0,comm);
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MPI_Bcast(&nspheres,1,MPI_INT,0,comm);
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MPI_Bcast(&Lx,1,MPI_DOUBLE,0,comm);
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MPI_Bcast(&Ly,1,MPI_DOUBLE,0,comm);
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MPI_Bcast(&Lz,1,MPI_DOUBLE,0,comm);
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//.................................................
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MPI_Barrier(comm);
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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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// Filenames used
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char LocalRankString[8];
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char LocalRankFilename[40];
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char LocalRestartFile[40];
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char tmpstr[10];
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sprintf(LocalRankString,"%05d",rank);
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// sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
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sprintf(LocalRestartFile,"%s%s","Restart.",LocalRankString);
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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 the local file
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DoubleArray Phase;
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DoubleArray SignDist;
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readRankData( rank, nx+2, ny+2, nz+2, Phase, SignDist );
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// Communication the halos
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const RankInfoStruct rank_info(rank,nprocx,nprocy,nprocz);
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fillHalo<double> fillData(rank_info,nx,ny,nz,1,1,1,0,1);
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fillData.fill(Phase);
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fillData.fill(SignDist);
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// Find blob domains
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if ( rank==0 ) { printf("Finding blob domains\n"); }
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double vF=0.0;
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double vS=0.0;
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IntArray GlobalBlobID;
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int nblobs = ComputeGlobalBlobIDs(nx,ny,nz,Dm.rank_info,
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Phase,SignDist,vF,vS,GlobalBlobID);
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if ( rank==0 ) { printf("Identified %i blobs\n",nblobs); }
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// Write the local blob ids
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sprintf(LocalRankFilename,"BlobLabel.%05i",rank);
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FILE *BLOBLOCAL = fopen(LocalRankFilename,"wb");
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fwrite(GlobalBlobID.get(),4,GlobalBlobID.length(),BLOBLOCAL);
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fclose(BLOBLOCAL);
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printf("Wrote BlobLabel.%05i \n",rank);
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sprintf(LocalRankString,"%05d",rank);
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// sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
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// WriteLocalSolidID(LocalRankFilename, id, N);
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sprintf(LocalRankFilename,"%s%s","SignDist.",LocalRankString);
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ReadBinaryFile(LocalRankFilename, Averages.SDs.get(), N);
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MPI_Barrier(comm);
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if (rank == 0) cout << "Domain set." << endl;
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//.......................................................................
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//copies of data needed to perform checkpointing from cpu
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double *Den, *DistEven, *DistOdd;
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Den = new double[2*N];
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DistEven = new double[10*N];
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DistOdd = new double[9*N];
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//.........................................................................
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if (rank==0) printf("Reading restart file! \n");
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// Read in the restart file to CPU buffers
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ReadCheckpoint(LocalRestartFile, Den, DistEven, DistOdd, N);
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MPI_Barrier(comm);
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//.........................................................................
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// Populate the arrays needed to perform averaging
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if (rank==0) printf("Populate arrays \n");
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for (int k=0; k<nz+2; k++){
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for (int j=0; j<ny+2; j++){
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for (int i=0; i<nx+2; i++){
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double phi,da,db,press,vx,vy,vz;
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int n = k*(nx+2)*(ny+2)+j*(nx+2)+i;
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double f0,f1,f2,f3,f4,f5,f6,f7,f8,f9,f10,f11,f12,f13,f14,f15,f16,f17,f18;
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da = Den[n];
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db = Den[N+n];
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f0 = DistEven[n];
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f2 = DistEven[N+n];
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f4 = DistEven[2*N+n];
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f6 = DistEven[3*N+n];
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f8 = DistEven[4*N+n];
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f10 = DistEven[5*N+n];
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f12 = DistEven[6*N+n];
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f14 = DistEven[7*N+n];
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f16 = DistEven[8*N+n];
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f18 = DistEven[9*N+n];
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//........................................................................
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f1 = DistOdd[n];
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f3 = DistOdd[1*N+n];
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f5 = DistOdd[2*N+n];
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f7 = DistOdd[3*N+n];
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f9 = DistOdd[4*N+n];
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f11 = DistOdd[5*N+n];
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f13 = DistOdd[6*N+n];
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f15 = DistOdd[7*N+n];
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f17 = DistOdd[8*N+n];
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//.................Compute the velocity...................................
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press = 0.3333333333333333*(f0+f2+f1+f4+f3+f6+f5+f8+f7+f10+
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f9+f12+f11+f14+f13+f16+f15+f18+f17);
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vx = f1-f2+f7-f8+f9-f10+f11-f12+f13-f14;
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vy = f3-f4+f7-f8-f9+f10+f15-f16+f17-f18;
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vz = f5-f6+f11-f12-f13+f14+f15-f16-f17+f18;
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// Assign array components needed for averaging
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//Averages.SDs(i,j,k)=SignDist(i,j,k);
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Averages.Phase(i,j,k)=Phase(i,j,k);//(da-db)/(da+db);
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Averages.Phase_tplus(i,j,k)=Phase(i,j,k);//(da-db)/(da+db);
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Averages.Phase_tminus(i,j,k)=Phase(i,j,k);//(da-db)/(da+db);
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Averages.Press(i,j,k)=press;
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Averages.Vel_x(i,j,k)=vx;
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Averages.Vel_y(i,j,k)=vy;
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Averages.Vel_z(i,j,k)=vz;
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}
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}
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}
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delete [] DistEven;
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delete [] DistOdd;
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// Compute porosity
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double porosity,sum,sum_global;
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sum=0.0;
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for (int k=1; k<Dm.Nz-1; k++){
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for (int j=1; j<Dm.Ny-1; j++){
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for (int i=1; i<Dm.Nx-1; i++){
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int n = k*Dm.Nx*Dm.Ny+j*Dm.Nx+i;
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if (Averages.SDs(i,j,k) > 0.0){
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Dm.id[n]=1;
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sum += 1.0;
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}
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else Dm.id[n]=0;
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}
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}
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}
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Dm.CommInit(); // Initialize communications for domains
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MPI_Allreduce(&sum,&sum_global,1,MPI_DOUBLE,MPI_SUM,comm);
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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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// nblobs = ComputeGlobalBlobIDs(nx,ny,nz,rank_info,
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// Averages.Phase,Averages.SDs,vF,vS,Averages.BlobLabel);
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// if ( rank==0 ) { printf("Identified %i blobs\n",nblobs); }
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for (int k=0; k<nz+2; k++){
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for (int j=0; j<ny+2; j++){
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for (int i=0; i<nx+2; i++){
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Averages.SDs(i,j,k) -= 1.0; // map the distance
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}
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}
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}
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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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Dm.CommunicateMeshHalo(Averages.Phase);
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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(comm);
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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,comm);
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for (int idx=0; idx<dimx-1; idx++) Averages.BlobAverages(idx,b)=RecvBuffer(idx);
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MPI_Barrier(comm);
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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
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fprintf(BLOBLOG,"%.5g ", Jwn); //Jwn
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fprintf(BLOBLOG,"%.5g ", Kwn); //Kwn
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fprintf(BLOBLOG,"%.5g ", lwns); //lwns
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fprintf(BLOBLOG,"%.5g\n",cwns); //cwns
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}
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}
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fclose(BLOBLOG);
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}
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if (rank==0) {
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int a;
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double D=1.0;
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double iVol=1.0/Averages.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 = Averages.sat_w;
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pw = Averages.paw_global;
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aws = Averages.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",Averages.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<Averages.nblobs_global; a++){
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vol_n += Averages.BlobAverages(0,a);
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pan += Averages.BlobAverages(2,a)*Averages.BlobAverages(0,a);
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awn += Averages.BlobAverages(3,a);
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ans += Averages.BlobAverages(4,a);
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Jwn += Averages.BlobAverages(5,a)*Averages.BlobAverages(3,a);
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Kwn += Averages.BlobAverages(6,a)*Averages.BlobAverages(3,a);
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lwns += Averages.BlobAverages(7,a);
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clwns += Averages.BlobAverages(8,a)*Averages.BlobAverages(7,a);
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nwp_volume += Averages.BlobAverages(1,a);
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pawn += Averages.BlobAverages(2,a)*Averages.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=Averages.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=Averages.nblobs_global-1; a>0; a--){
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// Subtract the features one-by-one
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vol_n -= Averages.BlobAverages(0,a);
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pan -= Averages.BlobAverages(2,a)*Averages.BlobAverages(0,a);
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awn -= Averages.BlobAverages(3,a);
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ans -= Averages.BlobAverages(4,a);
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Jwn -= Averages.BlobAverages(5,a)*Averages.BlobAverages(3,a);
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Kwn -= Averages.BlobAverages(6,a)*Averages.BlobAverages(3,a);
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lwns -= Averages.BlobAverages(7,a);
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clwns -= Averages.BlobAverages(8,a)*Averages.BlobAverages(7,a);
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nwp_volume -= Averages.BlobAverages(1,a);
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pawn -= Averages.BlobAverages(2,a)*Averages.BlobAverages(3,a);
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// Update wetting phase averages
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aws += Averages.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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//WriteBlobStates(Averages,Length,porosity);
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/*FILE *BLOBS = fopen("Blobs.dat","wb");
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fwrite(GlobalBlobID.get(),4,Nx*Ny*Nz,BLOBS);
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fclose(BLOBS);*/
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PROFILE_STOP("main");
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PROFILE_SAVE("BlobIdentifyParallel",false);
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comm.barrier();
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Utilities::shutdown();
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return 0;
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}
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