383 lines
12 KiB
C++
383 lines
12 KiB
C++
/*
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* Pre-processor to refine signed distance mesh
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* this is a good way to increase the resolution
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*/
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#include <stdio.h>
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#include <stdlib.h>
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#include <math.h>
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#include <iostream>
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#include <fstream>
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#include <sstream>
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#include "common/Array.h"
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#include "common/Communication.h"
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#include "common/Domain.h"
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#include "analysis/pmmc.h"
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#include "analysis/distance.h"
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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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{
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//.......................................................................
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// Reading the domain information file
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//.......................................................................
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double Lx, Ly, Lz;
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Lx = Ly = Lz = 1.0;
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int i,j,k,n;
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string filename;
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if (argc > 1){
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filename=argv[1];
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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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// Read domain parameters
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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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int nx = size[0];
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int ny = size[1];
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int nz = size[2];
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int nprocx = nproc[0];
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int nprocy = nproc[1];
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int nprocz = nproc[2];
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int BoundaryCondition=0;
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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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//Domain Mask(nx,ny,nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BoundaryCondition);
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Domain Mask(domain_db,MPI_COMM_WORLD);
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if (domain_db->keyExists( "Filename" )){
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auto Filename = domain_db->getScalar<std::string>( "Filename" );
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if (rank==0) printf("Reading domain from %s \n",Filename.c_str());
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Mask.Decomp(Filename);
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if (rank==0) printf("Complete. \n");
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}
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else{
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Mask.ReadIDs();
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}
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Mask.CommInit();
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char LocalRankFilename[40];
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int rnx=2*nx;
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int rny=2*ny;
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int rnz=2*nz;
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if (rank==0) printf("Refining mesh to %i x %i x %i \n",rnx,rny,rnz);
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Domain Dm(rnx,rny,rnz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BoundaryCondition);
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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(comm,rank_info,{rnx,rny,rnz},{1,1,1},0,1);
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nx+=2; ny+=2; nz+=2;
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rnx+=2; rny+=2; rnz+=2;
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int N = nx*ny*nz;
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// Define communication sub-domain -- everywhere
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if (rank==0) printf("Initialize refined domain \n");
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for (int k=0; k<rnz; k++){
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for (int j=0; j<rny; j++){
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for (int i=0; i<rnx; i++){
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n = k*rnx*rny+j*rnx+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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// Generate the signed distance map
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// Initialize the domain and communication
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Array<char> Labels(nx,ny,nz);
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DoubleArray SignDist(nx,ny,nz);
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// Solve for the position of the solid phase
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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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int n = k*nx*ny+j*nx+i;
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// Initialize the solid phase
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signed char label = Mask.id[n];
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if (label > 0) Labels(i,j,k) = 1;
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else Labels(i,j,k) = 0;
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}
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}
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}
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// Initialize the signed distance function
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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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// Initialize distance to +/- 1
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SignDist(i,j,k) = 2.0*double(Labels(i,j,k))-1.0;
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}
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}
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}
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// MeanFilter(Averages->SDs);
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if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
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CalcDist(SignDist,Labels,Mask);
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/* // Read the signed distance from file
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sprintf(LocalRankFilename,"SignDist.%05i",rank);
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FILE *DIST = fopen(LocalRankFilename,"rb");
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size_t ReadSignDist;
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ReadSignDist=fread(SignDist.data(),8,N,DIST);
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if (ReadSignDist != size_t(N)) printf("lbpm_refine_pp: Error reading signed distance function (rank=%i)\n",rank);
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fclose(DIST);
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char *Labels;
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Labels = new char[N];
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sprintf(LocalRankFilename,"ID.%05i",rank);
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FILE *LABELS = fopen(LocalRankFilename,"rb");
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size_t ReadLabels;
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ReadLabels=fread(Labels,1,N,LABELS);
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if (ReadLabels != size_t(N)) printf("lbpm_refine_pp: Error reading ID (rank=%i)\n",rank);
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fclose(LABELS);
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*/
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if ( rank==0 ) printf("Set up Domain, read input distance \n");
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DoubleArray RefinedSignDist(rnx,rny,rnz);
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TriLinPoly LocalApprox;
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Point pt;
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// double the distance value (since it is evaluated in pixels)
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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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SignDist(i,j,k) = 2.f*SignDist(i,j,k);
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}
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}
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}
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//char *RefineLabel;
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//RefineLabel = new char [rnx*rny*rnz];
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Array <char> RefineLabel(rnx,rny,rnz);
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for (int rk=1; rk<rnz-1; rk++){
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for (int rj=1; rj<rny-1; rj++){
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for (int ri=1; ri<rnx-1; ri++){
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n = rk*rnx*rny+rj*rnx+ri;
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// starting node for each processor matches exactly
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i = (ri-1)/2+1;
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j = (rj-1)/2+1;
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k = (rk-1)/2+1;
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//printf("(%i,%i,%i -> %i,%i,%i) \n",ri,rj,rk,i,j,k);
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// Assign local tri-linear polynomial
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LocalApprox.assign(SignDist,i,j,k);
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pt.x=0.5*(ri-1)+1.f;
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pt.y=0.5*(rj-1)+1.f;
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pt.z=0.5*(rk-1)+1.f;
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RefinedSignDist(ri,rj,rk) = LocalApprox.eval(pt);
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RefineLabel(ri,rj,rk) = Labels(i,j,k);
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Dm.id[n] = Labels(i,j,k);
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}
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}
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}
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fillData.fill(RefinedSignDist);
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if (domain_db->keyExists( "Filename" )){
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auto Filename = domain_db->getScalar<std::string>( "Filename" );
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if ( rank==0 ) printf("Write output \n");
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Dm.AggregateLabels("id_2x.raw");
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Mask.AggregateLabels("id.raw");
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//FILE *WRITEID = fopen("refine.raw","wb");
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//fwrite(RefineLabel.data(),1,rnx*rny*rnz,WRITEID);
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//fclose(WRITEID);
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}
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else{
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DoubleArray BlockDist(nx,ny,nz);
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FILE *WRITEID, *REFINEDIST;
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char * id;
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id = new char [N];
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int writerank;
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// Write output blocks with the same sub-domain size as origina
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// refinement increases the size of the process grid
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writerank = 8*Dm.kproc()*nprocx*nprocy + 4*Dm.jproc()*nprocx + 2*Dm.iproc();
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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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BlockDist(i,j,k) = RefinedSignDist(i,j,k);
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if (BlockDist(i,j,k) > 0) id[k*nx*ny + j*nx + i]=2;
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else id[k*nx*ny + j*nx + i] = RefineLabel(i,j,k);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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sprintf(LocalRankFilename,"RefineID.%05i",writerank);
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WRITEID = fopen(LocalRankFilename,"wb");
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fwrite(id,1,nx*ny*nz,WRITEID);
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fclose(WRITEID);
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writerank = 8*Dm.kproc()*nprocx*nprocy + 4*Dm.jproc()*nprocx + 2*Dm.iproc()+1;
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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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BlockDist(i,j,k) = RefinedSignDist(i+nx-2,j,k);
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if (BlockDist(i,j,k) > 0) id[k*nx*ny + j*nx + i]=2;
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else id[k*nx*ny + j*nx + i] = RefineLabel(i+nx-2,j,k);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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sprintf(LocalRankFilename,"RefineID.%05i",writerank);
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WRITEID = fopen(LocalRankFilename,"wb");
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fwrite(id,1,nx*ny*nz,WRITEID);
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fclose(WRITEID);
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writerank = (2*Dm.kproc())*4*nprocx*nprocy + (2*Dm.jproc()+1)*2*nprocx + 2*Dm.iproc()+1;
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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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BlockDist(i,j,k) = RefinedSignDist(i+nx-2,j+ny-2,k);
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if (BlockDist(i,j,k) > 0) id[k*nx*ny + j*nx + i]=2;
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else id[k*nx*ny + j*nx + i] = RefineLabel(i+nx-2,j+ny-2,k);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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sprintf(LocalRankFilename,"RefineID.%05i",writerank);
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WRITEID = fopen(LocalRankFilename,"wb");
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fwrite(id,1,nx*ny*nz,WRITEID);
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fclose(WRITEID);
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writerank = (2*Dm.kproc())*4*nprocx*nprocy + (2*Dm.jproc()+1)*2*nprocx + 2*Dm.iproc();
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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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BlockDist(i,j,k) = RefinedSignDist(i,j+ny-2,k);
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if (BlockDist(i,j,k) > 0) id[k*nx*ny + j*nx + i]=2;
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else id[k*nx*ny + j*nx + i] = RefineLabel(i,j+ny-2,k);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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sprintf(LocalRankFilename,"RefineID.%05i",writerank);
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WRITEID = fopen(LocalRankFilename,"wb");
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fwrite(id,1,nx*ny*nz,WRITEID);
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fclose(WRITEID);
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writerank = (2*Dm.kproc()+1)*4*nprocx*nprocy + (2*Dm.jproc())*2*nprocx + 2*Dm.iproc();
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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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BlockDist(i,j,k) = RefinedSignDist(i,j,k+nz-2);
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if (BlockDist(i,j,k) > 0) id[k*nx*ny + j*nx + i]=2;
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else id[k*nx*ny + j*nx + i] = RefineLabel(i,j,k+nz-2);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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sprintf(LocalRankFilename,"RefineID.%05i",writerank);
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WRITEID = fopen(LocalRankFilename,"wb");
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fwrite(id,1,nx*ny*nz,WRITEID);
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fclose(WRITEID);
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writerank = (2*Dm.kproc()+1)*4*nprocx*nprocy + (2*Dm.jproc())*2*nprocx + 2*Dm.iproc()+1;
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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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BlockDist(i,j,k) = RefinedSignDist(i+nx-2,j,k+nz-2);
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if (BlockDist(i,j,k) > 0) id[k*nx*ny + j*nx + i]=2;
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else id[k*nx*ny + j*nx + i] = RefineLabel(i+nx-2,j,k+nz-2);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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sprintf(LocalRankFilename,"RefineID.%05i",writerank);
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WRITEID = fopen(LocalRankFilename,"wb");
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fwrite(id,1,nx*ny*nz,WRITEID);
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fclose(WRITEID);
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writerank = (2*Dm.kproc()+1)*4*nprocx*nprocy + (2*Dm.jproc()+1)*2*nprocx + 2*Dm.iproc();
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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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BlockDist(i,j,k) = RefinedSignDist(i,j+ny-2,k+nz-2);
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if (BlockDist(i,j,k) > 0) id[k*nx*ny + j*nx + i]=2;
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else id[k*nx*ny + j*nx + i] = RefineLabel(i,j+ny-2,k+nz-2);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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sprintf(LocalRankFilename,"RefineID.%05i",writerank);
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WRITEID = fopen(LocalRankFilename,"wb");
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fwrite(id,1,nx*ny*nz,WRITEID);
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fclose(WRITEID);
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writerank = (2*Dm.kproc()+1)*4*nprocx*nprocy + (2*Dm.jproc()+1)*2*nprocx + 2*Dm.iproc()+1;
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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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BlockDist(i,j,k) = RefinedSignDist(i+nx-2,j+ny-2,k+nz-2);
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if (BlockDist(i,j,k) > 0) id[k*nx*ny + j*nx + i]=2;
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else id[k*nx*ny + j*nx + i] = RefineLabel(i+nx-2,j+ny-2,k+nz-2);
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}
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}
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}
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sprintf(LocalRankFilename,"RefineDist.%05i",writerank);
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REFINEDIST = fopen(LocalRankFilename,"wb");
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fwrite(BlockDist.data(),8,nx*ny*nz,REFINEDIST);
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fclose(REFINEDIST);
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sprintf(LocalRankFilename,"RefineID.%05i",writerank);
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WRITEID = fopen(LocalRankFilename,"wb");
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fwrite(id,1,nx*ny*nz,WRITEID);
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fclose(WRITEID);
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}
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}
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Utilities::shutdown();
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return 0;
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}
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