Added serial domain decomposition tool
This commit is contained in:
James E McClure
@@ -10,6 +10,7 @@ ADD_LBPM_EXECUTABLE( lbpm_morphdrain_pp )
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ADD_LBPM_EXECUTABLE( lbpm_morphopen_pp )
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ADD_LBPM_EXECUTABLE( lbpm_segmented_pp )
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ADD_LBPM_EXECUTABLE( lbpm_segmented_decomp )
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ADD_LBPM_EXECUTABLE( lbpm_serial_decomp )
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ADD_LBPM_EXECUTABLE( lbpm_disc_pp )
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ADD_LBPM_EXECUTABLE( lbpm_captube_pp )
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ADD_LBPM_EXECUTABLE( lbpm_squaretube_pp )
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159
tests/lbpm_serial_decomp.cpp
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159
tests/lbpm_serial_decomp.cpp
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@@ -0,0 +1,159 @@
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/*
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* Pre-processor to generate signed distance function from segmented data
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* segmented data should be stored in a raw binary file as 1-byte integer (type char)
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* will output distance functions for phases
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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/Domain.h"
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int main(int argc, char **argv)
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{
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int rank=0;
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bool MULTINPUT=false;
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int NWP,SOLID,rank_offset;
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SOLID=atoi(argv[1]);
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NWP=atoi(argv[2]);
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if (rank==0){
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printf("Solid Label: %i \n",SOLID);
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printf("NWP Label: %i \n",NWP);
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}
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if (argc > 3){
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rank_offset = atoi(argv[3]);
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}
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else{
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MULTINPUT=true;
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rank_offset=0;
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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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int Nx,Ny,Nz;
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int i,j,k,n;
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int BC=0;
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char Filename[40];
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int xStart,yStart,zStart;
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// char fluidValue,solidValue;
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std::vector<char> solidValues;
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std::vector<char> nwpValues;
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std::string line;
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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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ifstream image("Segmented.in");
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image >> Filename; // Name of data file containing segmented data
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image >> Nx; // size of the binary file
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image >> Ny;
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image >> Nz;
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image >> xStart; // offset for the starting voxel
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image >> yStart;
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image >> zStart;
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}
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char *SegData = NULL;
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// Rank=0 reads the entire segmented data and distributes to worker processes
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if (rank==0){
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printf("Dimensions of segmented image: %i x %i x %i \n",Nx,Ny,Nz);
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SegData = new char[Nx*Ny*Nz];
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FILE *SEGDAT = fopen(Filename,"rb");
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if (SEGDAT==NULL) ERROR("Error reading segmented data");
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size_t ReadSeg;
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ReadSeg=fread(SegData,1,Nx*Ny*Nz,SEGDAT);
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if (ReadSeg != size_t(Nx*Ny*Nz)) printf("lbpm_segmented_decomp: Error reading segmented data (rank=%i)\n",rank);
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fclose(SEGDAT);
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printf("Read segmented data from %s \n",Filename);
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}
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// Get the rank info
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int N = (nx+2)*(ny+2)*(nz+2);
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// number of sites to use for periodic boundary condition transition zone
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int z_transition_size = (nprocz*nz - (Nz - zStart))/2;
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if (z_transition_size < 0) z_transition_size=0;
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char LocalRankFilename[40];
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char *loc_id;
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loc_id = new char [(nx+2)*(ny+2)*(nz+2)];
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// Set up the sub-domains
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if (rank==0){
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printf("Distributing subdomains across %i processors \n",nprocs);
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printf("Process grid: %i x %i x %i \n",nprocx,nprocy,nprocz);
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printf("Subdomain size: %i \n",N);
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printf("Size of transition region: %i \n", z_transition_size);
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char *tmp;
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tmp = new char[N];
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for (int kp=0; kp<nprocz; kp++){
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for (int jp=0; jp<nprocy; jp++){
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for (int ip=0; ip<nprocx; ip++){
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// rank of the process that gets this subdomain
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int rnk = kp*nprocx*nprocy + jp*nprocx + ip;
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// Pack and send the subdomain for rnk
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for (k=0;k<nz+2;k++){
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for (j=0;j<ny+2;j++){
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for (i=0;i<nx+2;i++){
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int x = xStart + ip*nx + i-1;
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int y = yStart + jp*ny + j-1;
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// int z = zStart + kp*nz + k-1;
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int z = zStart + kp*nz + k-1 - z_transition_size;
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if (z<zStart) z=zStart;
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if (!(z<Nz)) z=Nz-1;
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int nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
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int nglobal = z*Nx*Ny+y*Nx+x;
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loc_id[nlocal] = SegData[nglobal];
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}
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}
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}
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// relabel the data
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for (k=0;k<nz+2;k++){
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for (j=0;j<ny+2;j++){
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for (i=0;i<nx+2;i++){
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n = k*(nx+2)*(ny+2) + j*(nx+2) + i;;
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if (loc_id[n]==char(SOLID)) loc_id[n] = 0;
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else if (loc_id[n]==char(NWP)) loc_id[n] = 1;
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else loc_id[n] = 2;
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}
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}
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}
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// Write the data for this rank data
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sprintf(LocalRankFilename,"ID.%05i",rnk+rank_offset);
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FILE *ID = fopen(LocalRankFilename,"wb");
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fwrite(loc_id,1,(nx+2)*(ny+2)*(nz+2),ID);
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fclose(ID);
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}
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}
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}
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}
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printf("Domain decomposition completed successfully \n");
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return 0;
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}
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