Added pre-processor for 2D disc packs test/lbpm_disc_pp.cpp
This commit is contained in:
James McClure
parent
79a4f16b78
commit
1f93d49662
@ -2,6 +2,7 @@
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INSTALL_LBPM_EXE( lb2_Color_wia_mpi )
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INSTALL_LBPM_EXE( lbpm_color_simulator )
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INSTALL_LBPM_EXE( lbpm_sphere_pp )
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INSTALL_LBPM_EXE( lbpm_disc_pp )
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INSTALL_LBPM_EXE( TestBubble )
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INSTALL_LBPM_EXE( BasicSimulator )
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INSTALL_LBPM_EXE( BlobAnalysis )
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363
tests/lbpm_disc_pp.cpp
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363
tests/lbpm_disc_pp.cpp
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@ -0,0 +1,363 @@
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#include <stdio.h>
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#include <stdlib.h>
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#include <sys/stat.h>
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#include <iostream>
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#include <exception>
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#include <stdexcept>
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#include <fstream>
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#include <mpi.h>
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#include "pmmc.h"
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#include "Domain.h"
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#include "Extras.h"
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#include "Communication.h"
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/*
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* Pre-Processor to generate signed distance function from disc packing
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* to use as an input domain for lattice Boltzmann simulator
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* James E. McClure 2014
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*/
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using namespace std;
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inline void ReadDiscPacking(int ndiscs, double *List_cx, double *List_cy, double *List_rad)
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{
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// Read in the full disc pack
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//...... READ IN THE DISCS...................................
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cout << "Reading the packing file..." << endl;
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FILE *fid = fopen("DiscPack.in","rb");
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INSIST(fid!=NULL,"Error opening DistPack.in");
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//............................................
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// We will read until a blank like or end-of-file is reached
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int count = 0;
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while ( !feof(fid) && fgets(line,100,fid)>0 ) {
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char* line2 = line;
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List_cx[count] = strtod(line2,&line2);
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List_cy[count] = strtod(line2,&line2);
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List_rad[count] = strtod(line2,&line2);
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count++;
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}
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cout << "Number of spheres extracted is: " << count << endl;
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INSIST( count==ndiscs, "Specified number of discs is probably incorrect!" );
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// .............................................................
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}
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inline void SignedDistanceDiscPack(double *Distance, int ndiscs, double *List_cx, double *List_cy, double *List_rad,
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double Lx, double Ly, double Lz, int Nx, int Ny, int Nz,
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int iproc, int jproc, int kproc, int nprocx, int nprocy, int nprocz)
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{
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// Use sphere lists to determine which nodes are in porespace
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// Write out binary file for nodes
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int N = Nx*Ny*Nz; // Domain size, including the halo
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double hx,hy,hz;
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double x,y,z;
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double cx,cy,cz,r;
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int imin,imax,jmin,jmax,kmin,kmax;
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int p,i,j,k,n;
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//............................................
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double min_x,min_y,min_z;
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double distance;
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//............................................
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// Lattice spacing for the entire domain
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// It should generally be true that hx=hy=hz
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// Otherwise, you will end up with ellipsoids
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hx = Lx/((Nx-2)*nprocx-1);
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hy = Ly/((Ny-2)*nprocy-1);
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hz = Lz/((Nz-2)*nprocz-1);
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//............................................
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// Get maximum and minimum for this domain
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// Halo is included !
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min_x = double(iproc*(Nx-2)-1)*hx;
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min_y = double(jproc*(Ny-2)-1)*hy;
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min_z = double(kproc*(Nz-2)-1)*hz;
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//............................................
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//............................................
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// Pre-initialize Distance
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for (n=0;n<N;n++){
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Distance[n]=100.0;
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}
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//............................................
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//............................................
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// .........Loop over the spheres.............
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for (p=0;p<ndiscs;p++){
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// Get the sphere from the list, map to local min
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cx = List_cx[p] - min_x;
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cy = List_cy[p] - min_y;
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r = List_rad[p];
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// Check if
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// Range for this sphere in global indexing
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imin = int ((cx-2*r)/hx);
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imax = int ((cx+2*r)/hx)+2;
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jmin = int ((cy-2*r)/hy);
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// Obviously we have to do something at the edges
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if (imin<0) imin = 0;
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if (imin>Nx) imin = Nx;
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if (imax<0) imax = 0;
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if (imax>Nx) imax = Nx;
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if (jmin<0) jmin = 0;
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if (jmin>Ny) jmin = Ny;
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if (jmax<0) jmax = 0;
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if (jmax>Ny) jmax = Ny;
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// Loop over the domain for this sphere (may be null)
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for (i=imin;i<imax;i++){
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for (j=jmin;j<jmax;j++){
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for (k=0;k<Nz;k++){
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// x,y,z is distance in physical units
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x = i*hx;
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y = j*hy;
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z = k*hz;
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// if inside sphere, set to zero
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// get the position in the list
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n = k*Nx*Ny+j*Nx+i;
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// Compute the distance
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distance = sqrt((cx-x)*(cx-x)+(cy-y)*(cy-y)) - r;
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// Assign the minimum distance
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if (distance < Distance[n]) Distance[n] = distance;
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}
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}
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}
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}
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// Map the distance to lattice units
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for (n=0; n<N; n++) Distance[n] = Distance[n]/hx;
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}
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int main(int argc, char **argv)
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{
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//*****************************************
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// ***** MPI STUFF ****************
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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_rank(MPI_COMM_WORLD,&rank);
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MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
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// parallel domain size (# of sub-domains)
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int nprocx,nprocy,nprocz;
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int iproc,jproc,kproc;
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int sendtag,recvtag;
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//*****************************************
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// MPI ranks for all 18 neighbors
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//**********************************
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int rank_x,rank_y,rank_z,rank_X,rank_Y,rank_Z;
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int rank_xy,rank_XY,rank_xY,rank_Xy;
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int rank_xz,rank_XZ,rank_xZ,rank_Xz;
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int rank_yz,rank_YZ,rank_yZ,rank_Yz;
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//**********************************
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MPI_Request req1[18],req2[18];
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MPI_Status stat1[18],stat2[18];
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if (rank == 0){
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printf("********************************************************\n");
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printf("Running Disc Packing Pre-Processor for LBPM-WIA \n");
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printf("********************************************************\n");
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}
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// Variables that specify the computational domain
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string FILENAME;
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unsigned int nBlocks, nthreads;
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int Nx,Ny,Nz; // local sub-domain size
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int ndiscs; // number of spheres in the packing
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double Lx,Ly,Lz; // Domain length
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double D = 1.0; // reference length for non-dimensionalization
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int i,j,k,n;
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if (rank==0){
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//.......................................................................
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// Reading the domain information file
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//.......................................................................
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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 >> ndiscs;
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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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}
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// **************************************************************
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// Broadcast simulation parameters from rank 0 to all other procs
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MPI_Barrier(MPI_COMM_WORLD);
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//.................................................
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// Computational domain
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MPI_Bcast(&Nx,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&Ny,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&Nz,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&nprocx,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&nprocy,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&nprocz,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&ndiscs,1,MPI_INT,0,MPI_COMM_WORLD);
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MPI_Bcast(&Lx,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
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MPI_Bcast(&Ly,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
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MPI_Bcast(&Lz,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
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//.................................................
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MPI_Barrier(MPI_COMM_WORLD);
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// **************************************************************
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if (nprocs != nprocx*nprocy*nprocz){
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printf("nprocx = %i \n",nprocx);
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printf("nprocy = %i \n",nprocy);
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printf("nprocz = %i \n",nprocz);
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INSIST(nprocs == nprocx*nprocy*nprocz,"Fatal error in processor count!");
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}
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InitializeRanks( rank, nprocx, nprocy, nprocz, iproc, jproc, kproc,
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rank_x, rank_y, rank_z, rank_X, rank_Y, rank_Z,
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rank_xy, rank_XY, rank_xY, rank_Xy, rank_xz, rank_XZ, rank_xZ, rank_Xz,
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rank_yz, rank_YZ, rank_yZ, rank_Yz );
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MPI_Barrier(MPI_COMM_WORLD);
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Nz += 2;
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Nx = Ny = Nz; // Cubic domain
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int N = Nx*Ny*Nz;
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int dist_mem_size = N*sizeof(double);
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if (rank==0) printf("Number of nodes per side = %i \n", Nx);
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if (rank==0) printf("Total Number of nodes = %i \n", N);
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if (rank==0) printf("********************************************************\n");
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//.......................................................................
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if (rank == 0) printf("Read input media... \n");
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//.......................................................................
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//.......................................................................
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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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// printf("Local File Name = %s \n",LocalRankFilename);
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// .......... READ THE INPUT FILE .......................................
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// char value;
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char *id;
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id = new char[N];
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int sum = 0;
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double sum_local;
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double iVol_global = 1.0/(1.0*(Nx-2)*(Ny-2)*(Nz-2)*nprocs);
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double porosity, pore_vol;
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//...........................................................................
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DoubleArray SignDist(Nx,Ny,Nz);
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//.......................................................................
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// Read in sphere pack
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if (rank==1) printf("ndiscs =%i \n",ndiscs);
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//.......................................................................
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double *cx,*cy,*cz,*rad;
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cx = new double[ndiscs];
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cy = new double[ndiscs];
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cz = new double[ndiscs];
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rad = new double[ndiscs];
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//.......................................................................
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if (rank == 0) printf("Reading the sphere packing \n");
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if (rank == 0) ReadDiscPacking(ndiscs,cx,cy,rad);
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MPI_Barrier(MPI_COMM_WORLD);
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// Broadcast the sphere packing to all processes
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MPI_Bcast(cx,ndiscs,MPI_DOUBLE,0,MPI_COMM_WORLD);
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MPI_Bcast(cy,ndiscs,MPI_DOUBLE,0,MPI_COMM_WORLD);
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MPI_Bcast(cz,ndiscs,MPI_DOUBLE,0,MPI_COMM_WORLD);
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MPI_Bcast(rad,ndiscs,MPI_DOUBLE,0,MPI_COMM_WORLD);
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//...........................................................................
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MPI_Barrier(MPI_COMM_WORLD);
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if (rank == 0) cout << "Domain set." << endl;
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//.......................................................................
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SignedDistanceDiscPack(SignDist.data,ndiscs,cx,cy,rad,Lx,Ly,Lz,Nx,Ny,Nz,
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iproc,jproc,kproc,nprocx,nprocy,nprocz);
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//.......................................................................
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// Assign walls in the signed distance functions (x,y boundaries)
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double dst;
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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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dst = (iproc*(Nx-2)+i-2)*1.0;
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if ((Nx-2)*nprocx-dst < dst) dst = Nx*nprocx-dst;
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if (dst < (jproc*(Ny-2)+j-2)*1.0)) dst = (jproc*(Ny-2)+j-2)*1.0);
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if (dst < (Ny-2)*nprocx-(jproc*(Ny-2)+j-2)*1.0)) (Ny-2)*nprocx-(jproc*(Ny-2)+j-2)*1.0);
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if (dst < SignDist(i,j,k)) SignDist(i,j,k) = dst;
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n = k*Nx*Ny+j*Nx+i;
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id[n] = 0;
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}
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}
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}
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//.......................................................................
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// Assign the phase ID field based on the signed distance
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//.......................................................................
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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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n = k*Nx*Ny+j*Nx+i;
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id[n] = 0;
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}
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}
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}
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sum=0;
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pore_vol = 0.0;
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for ( k=1;k<Nz-1;k++){
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for ( j=1;j<Ny-1;j++){
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for ( i=1;i<Nx-1;i++){
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n = k*Nx*Ny+j*Nx+i;
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if (SignDist.data[n] > 0.0){
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id[n] = 2;
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}
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// compute the porosity (actual interface location used)
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if (SignDist.data[n] > 0.0){
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sum++;
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}
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}
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}
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}
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sum_local = 1.0*sum;
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MPI_Allreduce(&sum_local,&porosity,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
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porosity = porosity*iVol_global;
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if (rank==0) printf("Media porosity = %f \n",porosity);
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// Compute the pore volume
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sum_local = 0.0;
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for ( k=1;k<Nz-1;k++){
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for ( j=1;j<Ny-1;j++){
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for ( i=1;i<Nx-1;i++){
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n = k*Nx*Ny+j*Nx+i;
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if (id[n] > 0){
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sum_local += 1.0;
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}
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}
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}
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}
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MPI_Allreduce(&sum_local,&pore_vol,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
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//.........................................................
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// don't perform computations at the eight corners
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id[0] = id[Nx-1] = id[(Ny-1)*Nx] = id[(Ny-1)*Nx + Nx-1] = 0;
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id[(Nz-1)*Nx*Ny] = id[(Nz-1)*Nx*Ny+Nx-1] = id[(Nz-1)*Nx*Ny+(Ny-1)*Nx] = id[(Nz-1)*Nx*Ny+(Ny-1)*Nx + Nx-1] = 0;
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//.........................................................
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//.......................................................................
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sprintf(LocalRankString,"%05d",rank);
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sprintf(LocalRankFilename,"%s%s","SignDist.",LocalRankString);
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WriteLocalSolidDistance(LocalRankFilename, SignDist.data, N);
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//......................................................................
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// ****************************************************
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MPI_Barrier(MPI_COMM_WORLD);
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MPI_Finalize();
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// ****************************************************
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}
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