refactor morphopen
This commit is contained in:
James E McClure
parent
3398b90285
commit
ab46862a5f
@ -53,6 +53,7 @@ int main(int argc, char **argv)
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MPI_Comm comm = MPI_COMM_WORLD;
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MPI_Comm_rank(comm,&rank);
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MPI_Comm_size(comm,&nprocs);
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{
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//double Rcrit_new=1.f; // Hard-coded 'Rcrit' to avoid any calculations under resolutions.
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double Rcrit_new=0.f;
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@ -62,9 +63,6 @@ int main(int argc, char **argv)
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printf("Target saturation %f \n",SW);
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}
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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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@ -72,66 +70,45 @@ int main(int argc, char **argv)
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double Lx, Ly, Lz;
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int i,j,k,n;
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int BC=0;
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// char fluidValue,solidValue;
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int MAXTIME=1000;
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int READ_FROM_BLOCK=0;
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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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}
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char LocalRankString[8];
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char LocalRankFilename[40];
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int BoundaryCondition=1;
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Domain Dm(nx,ny,nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BoundaryCondition);
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string filename;
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double Rcrit_new, SW;
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if (argc > 2){
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filename=argv[1];
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Rcrit_new=0.f;
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SW=strtod(argv[2],NULL);
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}
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else ERROR("No input database provided\n");
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// read the input database
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auto db = std::make_shared<Database>( filename );
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auto domain_db = db->getDatabase( "Domain" );
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nx+=2; ny+=2; nz+=2;
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int N = nx*ny*nz;
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char *id;
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id = new char[N];
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// Read domain parameters
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auto L = domain_db->getVector<double>( "L" );
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auto size = domain_db->getVector<int>( "n" );
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auto nproc = domain_db->getVector<int>( "nproc" );
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auto ReadValues = domain_db->getVector<char>( "ReadValues" );
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auto WriteValues = domain_db->getVector<char>( "WriteValues" );
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// Define communication sub-domain -- everywhere
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for (int k=0; k<nz; k++){
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for (int j=0; j<ny; j++){
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for (int i=0; i<nx; i++){
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n = k*nx*ny+j*nx+i;
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Dm.id[n] = 1;
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}
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}
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}
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Dm.CommInit();
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nx = size[0];
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ny = size[1];
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nz = size[2];
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nprocx = nproc[0];
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nprocy = nproc[1];
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nprocz = nproc[2];
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int N = (nx+2)*(ny+2)*(nz+2);
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std::shared_ptr<Domain> Dm (new Domain(domain_db,comm));
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// std::shared_ptr<Domain> Dm (new Domain(nx,ny,nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BC));
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for (n=0; n<N; n++) Dm->id[n]=1;
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Dm->CommInit();
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DoubleArray SignDist(nx,ny,nz);
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// Read the signed distance from file
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@ -169,106 +146,6 @@ int main(int argc, char **argv)
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if (rank==0) printf("Media Porosity: %f \n",porosity);
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if (rank==0) printf("Maximum pore size: %f \n",maxdistGlobal);\
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/* // Generate a histogram of pore size distribution
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// Get all local pore sizes (local maxima)
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if (rank==0) printf("Generating a histogram of pore sizes \n");
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int NumBins=100;
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int *BinCounts;
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BinCounts = new int [NumBins];
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int *GlobalHistogram;
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GlobalHistogram = new int [NumBins];
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double GlobalValue;
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double BinWidth,MinPoreSize,MaxPoreSize;
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std::vector<double> PoreSize;
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for (int k=1; k<nz-1; k++){
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for (int j=1; j<ny-1; j++){
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for (int i=1; i<nx-1; i++){
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n = k*nx*ny+j*nx+i;
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if (SignDist(i,j,k) > 0.0){
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// Generate a list of all local maxima (each processor -- aggregate these later)
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if ( SignDist(i,j,k) > SignDist(i+1,j,k) && SignDist(i,j,k) > SignDist(i-1,j,k) &&
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SignDist(i,j,k) > SignDist(i,j+1,k) && SignDist(i,j,k) > SignDist(i,j-1,k) &&
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SignDist(i,j,k) > SignDist(i,j,k+1) && SignDist(i,j,k) > SignDist(i,j,k-1) &&
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SignDist(i,j,k) > SignDist(i+1,j+1,k) && SignDist(i,j,k) > SignDist(i-1,j+1,k) &&
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SignDist(i,j,k) > SignDist(i+1,j-1,k) && SignDist(i,j,k) > SignDist(i-1,j-1,k) &&
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SignDist(i,j,k) > SignDist(i+1,j,k+1) && SignDist(i,j,k) > SignDist(i-1,j,k+1) &&
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SignDist(i,j,k) > SignDist(i+1,j,k-1) && SignDist(i,j,k) > SignDist(i-1,j,k-1) &&
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SignDist(i,j,k) > SignDist(i,j+1,k+1) && SignDist(i,j,k) > SignDist(i,j-1,k+1) &&
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SignDist(i,j,k) > SignDist(i,j+1,k-1) && SignDist(i,j,k) > SignDist(i,j-1,k-1) &&
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SignDist(i,j,k) > SignDist(i+1,j+1,k+1) && SignDist(i,j,k) > SignDist(i-1,j-1,k-1) &&
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SignDist(i,j,k) > SignDist(i+1,j-1,k+1) && SignDist(i,j,k) > SignDist(i-1,j+1,k-1) &&
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SignDist(i,j,k) > SignDist(i-1,j+1,k+1) && SignDist(i,j,k) > SignDist(i+1,j-1,k-1) &&
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SignDist(i,j,k) > SignDist(i+1,j+1,k-1) && SignDist(i,j,k) > SignDist(i-1,j-1,k+1)){
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// save the size of each pore
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PoreSize.push_back(SignDist(i,j,k));
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}
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}
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}
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}
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}
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// Compute min and max poresize
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if (rank==0) printf(" computing local minimum and maximum... \n");
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MinPoreSize=MaxPoreSize=PoreSize[0];
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for (size_t idx=0; idx<PoreSize.size(); idx++){
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if (PoreSize[idx] < MinPoreSize) MinPoreSize=PoreSize[idx];
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if (PoreSize[idx] > MaxPoreSize) MaxPoreSize=PoreSize[idx];
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}
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// reduce to get global minimum and maximum
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MPI_Allreduce(&MinPoreSize,&GlobalValue,1,MPI_DOUBLE,MPI_MIN,comm);
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MinPoreSize=GlobalValue;
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MPI_Allreduce(&MaxPoreSize,&GlobalValue,1,MPI_DOUBLE,MPI_MAX,comm);
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MaxPoreSize=GlobalValue;
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//if (rank==0) printf(" MaxPoreSize %f\n", MaxPoreSize);
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//if (rank==0) printf(" MinPoreSize %f\n", MinPoreSize);
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// Generate histogram counts
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if (rank==0) printf(" generating local bin counts... \n");
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BinWidth=(MaxPoreSize-MinPoreSize)/double(NumBins);
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for (size_t idx=0; idx<PoreSize.size(); idx++){
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double value = PoreSize[idx];
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int myBin = 0;
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while (MinPoreSize+myBin*BinWidth < value) myBin++;
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//int((value-MinPoreSize)/double(BinWidth));
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BinCounts[myBin]+=1;
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}
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if (rank==0) printf(" summing global bin counts... \n");
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// Reduce the counts to generate the fhistogram at rank=0
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MPI_Reduce(BinCounts,GlobalHistogram,NumBins,MPI_INT,MPI_SUM,0,comm);
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FILE *PORESIZE;
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if (rank==0){
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PORESIZE=fopen("PoreSize.hist","w");
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printf(" writing PoreSize.hist \n");
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int PoreCount=0;
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int Count;
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for (int idx=0; idx<NumBins; idx++){
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double BinCenter=MinPoreSize+idx*BinWidth;
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Count=GlobalHistogram[idx];
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PoreCount+=Count;
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fprintf(PORESIZE,"%i %f\n",Count,BinCenter);
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}
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fclose(PORESIZE);
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// Compute quartiles
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double Q1,Q2,Q3,Q4;
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int Qval=PoreCount/4;
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Q1=Q2=Q3=MinPoreSize;
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Q4=MaxPoreSize;
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Count=0;
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for (int idx=0; idx<NumBins; idx++){
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double BinCenter=MinPoreSize+idx*BinWidth;
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Count+=GlobalHistogram[idx];
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if (Count<Qval) Q1+=BinWidth;
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if (Count<2*Qval) Q2+=BinWidth;
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if (Count<3*Qval) Q3+=BinWidth;
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}
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printf("Quartiles for pore size distribution \n");
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printf("Q1 %f\n",Q1);
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printf("Q2 %f\n",Q2);
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printf("Q3 %f\n",Q3);
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printf("Q4 %f\n",Q4);
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}
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MPI_Barrier(comm);
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*/
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Dm.CommInit();
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int iproc = Dm.iproc();
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@ -517,6 +394,7 @@ int main(int argc, char **argv)
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FILE *ID = fopen(LocalRankFilename,"wb");
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fwrite(id,1,N,ID);
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fclose(ID);
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}
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MPI_Barrier(comm);
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MPI_Finalize();
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