Created a morphological drainage pre-processor in lbpm_morphdrain_pp (not in CMake or project, code not implemented)
This commit is contained in:
James E McClure
parent
6db20f8761
commit
f94f6df3d1
384
tests/lbpm_morphdrain_pp.cpp
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384
tests/lbpm_morphdrain_pp.cpp
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@ -0,0 +1,384 @@
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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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//*************************************************************************
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// Morpohological drainage pre-processor
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// Generate states on primary drainage using morphological approach
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// Signed distance function is used to determine fluid configuration
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//*************************************************************************
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inline void PackID(int *list, int count, char *sendbuf, char *ID){
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// Fill in the phase ID values from neighboring processors
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// This packs up the values that need to be sent from one processor to another
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int idx,n;
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for (idx=0; idx<count; idx++){
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n = list[idx];
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sendbuf[idx] = ID[n];
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}
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}
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//***************************************************************************************
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inline void UnpackID(int *list, int count, char *recvbuf, char *ID){
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// Fill in the phase ID values from neighboring processors
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// This unpacks the values once they have been recieved from neighbors
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int idx,n;
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for (idx=0; idx<count; idx++){
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n = list[idx];
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ID[n] = recvbuf[idx];
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}
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}
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//***************************************************************************************
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int main(int argc, char **argv)
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{
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// Initialize MPI
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int rank, nprocs;
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MPI_Init(&argc,&argv);
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MPI_Comm 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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double Rcrit;
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Rcrit=strtod(argv[1],NULL);
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if (rank==0){
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printf("Critical radius %f (voxels)\n",Rcrit);
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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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int nprocx, nprocy, nprocz, nx, ny, nz, nspheres;
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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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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 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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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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// 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(comm);
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DoubleArray SignDist(nx,ny,nz);
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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.get(),8,N,DIST);
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if (ReadSignDist != size_t(N)) printf("lbpm_morphdrain_pp: Error reading signed distance function (rank=%i)\n",rank);
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fclose(DIST);
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int count,countGlobal,totalGlobal;
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count = 0;
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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) id[n] = 0;
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else{
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// initially saturated with wetting phase
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id[n] = 2;
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count++;
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}
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}
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}
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}
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// total Global is the number of nodes in the pore-space
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MPI_Allreduce(&count,&totalGlobal,1,MPI_INT,MPI_SUM,comm);
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float porosity=float(totalGlobal)/(nprocx*nprocy*nprocz*(nx-2)*(ny-2)*(nz-2));
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if (rank==0) printf("Media Porosity: %f \n",porosity);
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Dm.CommInit(comm);
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int iproc = Dm.iproc;
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int jproc = Dm.jproc;
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int kproc = Dm.kproc;
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// Generate the NWP configuration
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if (rank==0) printf("Performing morphological drainage with critical radius %f \n", Rcrit);
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// GenerateResidual(id,nx,ny,nz,Saturation);
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int count=1;
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int x,y,z;
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int ii,jj,kk;
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int Nx = nx;
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int Ny = ny;
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int Nz = nz;
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float sat = 0.f;
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int Number = 0; // number of features
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while (count != 0){
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for(k=0; k<Nz; k++){
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for(j=0; j<Ny; j++){
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for(i=0; i<Nx; i++){
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}
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}
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}
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for (k=z;k<z+sizeZ;k++){
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for (j=y;j<y+sizeY;j++){
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for (i=x;i<x+sizeX;i++){
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// Identify nodes in the domain (periodic BC)
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ii = i;
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jj = j;
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kk = k;
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if (ii>nprocx*(Nx-2)) ii-=nprocx*(Nx-2);
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if (jj>nprocy*(Ny-2)) jj-=nprocy*(Ny-2);
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if (kk>nprocz*(Nz-2)) kk-=nprocz*(Nz-2);
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// Check if this is in the subdomain
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if (ii < (iproc+1)*(Nx-2)+1 && jj < (jproc+1)*(Ny-2)+1 && kk < (kproc+1)*(Nz-2)+1 &&
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ii > iproc*(Nx-2) && jj > jproc*(Ny-2) && kk > kproc*(Nz-2) ){
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// Map from global to local coordinates
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ii -= iproc*(Nx-2);
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jj -= jproc*(Ny-2);
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kk -= kproc*(Nz-2);
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n = kk*Nx*Ny+jj*Nx+ii;
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if (id[n] == 2){
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id[n] = 1;
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//count++;
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}
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}
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}
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}
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}
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count = 0;
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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 (id[n] == 1){
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count++;
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}
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}
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}
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}
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MPI_Allreduce(&count,&countGlobal,1,MPI_INT,MPI_SUM,comm);
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sat = float(countGlobal)/totalGlobal;
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//if (rank==0) printf("New count=%i\n",countGlobal);
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//if (rank==0) printf("New saturation=%f\n",sat);
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}
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// Fill in the phase ID from neighboring processors
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char *sendID_x, *sendID_y, *sendID_z, *sendID_X, *sendID_Y, *sendID_Z;
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char *sendID_xy, *sendID_yz, *sendID_xz, *sendID_Xy, *sendID_Yz, *sendID_xZ;
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char *sendID_xY, *sendID_yZ, *sendID_Xz, *sendID_XY, *sendID_YZ, *sendID_XZ;
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char *recvID_x, *recvID_y, *recvID_z, *recvID_X, *recvID_Y, *recvID_Z;
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char *recvID_xy, *recvID_yz, *recvID_xz, *recvID_Xy, *recvID_Yz, *recvID_xZ;
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char *recvID_xY, *recvID_yZ, *recvID_Xz, *recvID_XY, *recvID_YZ, *recvID_XZ;
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// send buffers
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sendID_x = new char [Dm.sendCount_x];
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sendID_y = new char [Dm.sendCount_y];
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sendID_z = new char [Dm.sendCount_z];
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sendID_X = new char [Dm.sendCount_X];
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sendID_Y = new char [Dm.sendCount_Y];
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sendID_Z = new char [Dm.sendCount_Z];
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sendID_xy = new char [Dm.sendCount_xy];
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sendID_yz = new char [Dm.sendCount_yz];
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sendID_xz = new char [Dm.sendCount_xz];
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sendID_Xy = new char [Dm.sendCount_Xy];
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sendID_Yz = new char [Dm.sendCount_Yz];
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sendID_xZ = new char [Dm.sendCount_xZ];
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sendID_xY = new char [Dm.sendCount_xY];
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sendID_yZ = new char [Dm.sendCount_yZ];
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sendID_Xz = new char [Dm.sendCount_Xz];
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sendID_XY = new char [Dm.sendCount_XY];
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sendID_YZ = new char [Dm.sendCount_YZ];
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sendID_XZ = new char [Dm.sendCount_XZ];
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//......................................................................................
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// recv buffers
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recvID_x = new char [Dm.recvCount_x];
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recvID_y = new char [Dm.recvCount_y];
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recvID_z = new char [Dm.recvCount_z];
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recvID_X = new char [Dm.recvCount_X];
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recvID_Y = new char [Dm.recvCount_Y];
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recvID_Z = new char [Dm.recvCount_Z];
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recvID_xy = new char [Dm.recvCount_xy];
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recvID_yz = new char [Dm.recvCount_yz];
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recvID_xz = new char [Dm.recvCount_xz];
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recvID_Xy = new char [Dm.recvCount_Xy];
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recvID_xZ = new char [Dm.recvCount_xZ];
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recvID_xY = new char [Dm.recvCount_xY];
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recvID_yZ = new char [Dm.recvCount_yZ];
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recvID_Yz = new char [Dm.recvCount_Yz];
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recvID_Xz = new char [Dm.recvCount_Xz];
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recvID_XY = new char [Dm.recvCount_XY];
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recvID_YZ = new char [Dm.recvCount_YZ];
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recvID_XZ = new char [Dm.recvCount_XZ];
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//......................................................................................
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int sendtag,recvtag;
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sendtag = recvtag = 7;
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PackID(Dm.sendList_x, Dm.sendCount_x ,sendID_x, id);
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PackID(Dm.sendList_X, Dm.sendCount_X ,sendID_X, id);
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PackID(Dm.sendList_y, Dm.sendCount_y ,sendID_y, id);
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PackID(Dm.sendList_Y, Dm.sendCount_Y ,sendID_Y, id);
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PackID(Dm.sendList_z, Dm.sendCount_z ,sendID_z, id);
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PackID(Dm.sendList_Z, Dm.sendCount_Z ,sendID_Z, id);
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PackID(Dm.sendList_xy, Dm.sendCount_xy ,sendID_xy, id);
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PackID(Dm.sendList_Xy, Dm.sendCount_Xy ,sendID_Xy, id);
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PackID(Dm.sendList_xY, Dm.sendCount_xY ,sendID_xY, id);
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PackID(Dm.sendList_XY, Dm.sendCount_XY ,sendID_XY, id);
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PackID(Dm.sendList_xz, Dm.sendCount_xz ,sendID_xz, id);
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PackID(Dm.sendList_Xz, Dm.sendCount_Xz ,sendID_Xz, id);
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PackID(Dm.sendList_xZ, Dm.sendCount_xZ ,sendID_xZ, id);
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PackID(Dm.sendList_XZ, Dm.sendCount_XZ ,sendID_XZ, id);
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PackID(Dm.sendList_yz, Dm.sendCount_yz ,sendID_yz, id);
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PackID(Dm.sendList_Yz, Dm.sendCount_Yz ,sendID_Yz, id);
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PackID(Dm.sendList_yZ, Dm.sendCount_yZ ,sendID_yZ, id);
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PackID(Dm.sendList_YZ, Dm.sendCount_YZ ,sendID_YZ, id);
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//......................................................................................
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MPI_Sendrecv(sendID_x,Dm.sendCount_x,MPI_CHAR,Dm.rank_x,sendtag,
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recvID_X,Dm.recvCount_X,MPI_CHAR,Dm.rank_X,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_X,Dm.sendCount_X,MPI_CHAR,Dm.rank_X,sendtag,
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recvID_x,Dm.recvCount_x,MPI_CHAR,Dm.rank_x,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_y,Dm.sendCount_y,MPI_CHAR,Dm.rank_y,sendtag,
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recvID_Y,Dm.recvCount_Y,MPI_CHAR,Dm.rank_Y,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Y,Dm.sendCount_Y,MPI_CHAR,Dm.rank_Y,sendtag,
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recvID_y,Dm.recvCount_y,MPI_CHAR,Dm.rank_y,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_z,Dm.sendCount_z,MPI_CHAR,Dm.rank_z,sendtag,
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recvID_Z,Dm.recvCount_Z,MPI_CHAR,Dm.rank_Z,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Z,Dm.sendCount_Z,MPI_CHAR,Dm.rank_Z,sendtag,
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recvID_z,Dm.recvCount_z,MPI_CHAR,Dm.rank_z,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_xy,Dm.sendCount_xy,MPI_CHAR,Dm.rank_xy,sendtag,
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recvID_XY,Dm.recvCount_XY,MPI_CHAR,Dm.rank_XY,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_XY,Dm.sendCount_XY,MPI_CHAR,Dm.rank_XY,sendtag,
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recvID_xy,Dm.recvCount_xy,MPI_CHAR,Dm.rank_xy,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Xy,Dm.sendCount_Xy,MPI_CHAR,Dm.rank_Xy,sendtag,
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recvID_xY,Dm.recvCount_xY,MPI_CHAR,Dm.rank_xY,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_xY,Dm.sendCount_xY,MPI_CHAR,Dm.rank_xY,sendtag,
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recvID_Xy,Dm.recvCount_Xy,MPI_CHAR,Dm.rank_Xy,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_xz,Dm.sendCount_xz,MPI_CHAR,Dm.rank_xz,sendtag,
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recvID_XZ,Dm.recvCount_XZ,MPI_CHAR,Dm.rank_XZ,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_XZ,Dm.sendCount_XZ,MPI_CHAR,Dm.rank_XZ,sendtag,
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recvID_xz,Dm.recvCount_xz,MPI_CHAR,Dm.rank_xz,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Xz,Dm.sendCount_Xz,MPI_CHAR,Dm.rank_Xz,sendtag,
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recvID_xZ,Dm.recvCount_xZ,MPI_CHAR,Dm.rank_xZ,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_xZ,Dm.sendCount_xZ,MPI_CHAR,Dm.rank_xZ,sendtag,
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recvID_Xz,Dm.recvCount_Xz,MPI_CHAR,Dm.rank_Xz,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_yz,Dm.sendCount_yz,MPI_CHAR,Dm.rank_yz,sendtag,
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recvID_YZ,Dm.recvCount_YZ,MPI_CHAR,Dm.rank_YZ,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_YZ,Dm.sendCount_YZ,MPI_CHAR,Dm.rank_YZ,sendtag,
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recvID_yz,Dm.recvCount_yz,MPI_CHAR,Dm.rank_yz,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Yz,Dm.sendCount_Yz,MPI_CHAR,Dm.rank_Yz,sendtag,
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recvID_yZ,Dm.recvCount_yZ,MPI_CHAR,Dm.rank_yZ,recvtag,comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_yZ,Dm.sendCount_yZ,MPI_CHAR,Dm.rank_yZ,sendtag,
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recvID_Yz,Dm.recvCount_Yz,MPI_CHAR,Dm.rank_Yz,recvtag,comm,MPI_STATUS_IGNORE);
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//......................................................................................
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UnpackID(Dm.recvList_x, Dm.recvCount_x ,recvID_x, id);
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UnpackID(Dm.recvList_X, Dm.recvCount_X ,recvID_X, id);
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UnpackID(Dm.recvList_y, Dm.recvCount_y ,recvID_y, id);
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UnpackID(Dm.recvList_Y, Dm.recvCount_Y ,recvID_Y, id);
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UnpackID(Dm.recvList_z, Dm.recvCount_z ,recvID_z, id);
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UnpackID(Dm.recvList_Z, Dm.recvCount_Z ,recvID_Z, id);
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UnpackID(Dm.recvList_xy, Dm.recvCount_xy ,recvID_xy, id);
|
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UnpackID(Dm.recvList_Xy, Dm.recvCount_Xy ,recvID_Xy, id);
|
||||
UnpackID(Dm.recvList_xY, Dm.recvCount_xY ,recvID_xY, id);
|
||||
UnpackID(Dm.recvList_XY, Dm.recvCount_XY ,recvID_XY, id);
|
||||
UnpackID(Dm.recvList_xz, Dm.recvCount_xz ,recvID_xz, id);
|
||||
UnpackID(Dm.recvList_Xz, Dm.recvCount_Xz ,recvID_Xz, id);
|
||||
UnpackID(Dm.recvList_xZ, Dm.recvCount_xZ ,recvID_xZ, id);
|
||||
UnpackID(Dm.recvList_XZ, Dm.recvCount_XZ ,recvID_XZ, id);
|
||||
UnpackID(Dm.recvList_yz, Dm.recvCount_yz ,recvID_yz, id);
|
||||
UnpackID(Dm.recvList_Yz, Dm.recvCount_Yz ,recvID_Yz, id);
|
||||
UnpackID(Dm.recvList_yZ, Dm.recvCount_yZ ,recvID_yZ, id);
|
||||
UnpackID(Dm.recvList_YZ, Dm.recvCount_YZ ,recvID_YZ, id);
|
||||
//......................................................................................
|
||||
count = 0;
|
||||
for (int k=1; k<Nz-1; k++){
|
||||
for (int j=1; j<Ny-1; j++){
|
||||
for (int i=1; i<Nx-1; i++){
|
||||
n=k*Nx*Ny+j*Nx+i;
|
||||
if (id[n] == 1){
|
||||
count++;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
MPI_Allreduce(&count,&countGlobal,1,MPI_INT,MPI_SUM,comm);
|
||||
sat = float(countGlobal)/totalGlobal;
|
||||
if (rank==0) printf("Final saturation=%f\n",sat);
|
||||
|
||||
sprintf(LocalRankFilename,"ID.%05i",rank);
|
||||
FILE *ID = fopen(LocalRankFilename,"wb");
|
||||
fwrite(id,1,N,ID);
|
||||
fclose(ID);
|
||||
|
||||
MPI_Barrier(comm);
|
||||
MPI_Finalize();
|
||||
return 0;
|
||||
}
|
||||
Loading…
Reference in New Issue
Block a user