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LBPM/tests/GenerateSphereTest.cpp
James McClure 7f4f74779c fix the build
2021-01-05 18:43:44 -05:00

479 lines
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#include <stdio.h>
#include <stdlib.h>
#include <sys/stat.h>
#include <iostream>
#include <exception>
#include <stdexcept>
#include <fstream>
//#include "common/pmmc.h"
#include "common/Domain.h"
#include "common/SpherePack.h"
#include "common/MPI.h"
#include "common/Communication.h"
/*
* Pre-Processor to generate signed distance function from sphere packing
* to use as an input domain for lattice Boltzmann simulator
* James E. McClure 2014
*/
using namespace std;
inline void PackID(const int *list, int count, char *sendbuf, char *ID){
// Fill in the phase ID values from neighboring processors
// This packs up the values that need to be sent from one processor to another
int idx,n;
for (idx=0; idx<count; idx++){
n = list[idx];
sendbuf[idx] = ID[n];
}
}
//***************************************************************************************
inline void UnpackID(const int *list, int count, char *recvbuf, char *ID){
// Fill in the phase ID values from neighboring processors
// This unpacks the values once they have been recieved from neighbors
int idx,n;
for (idx=0; idx<count; idx++){
n = list[idx];
ID[n] = recvbuf[idx];
}
}
inline void MorphOpen(DoubleArray SignDist, char *id, Domain &Dm, int nx, int ny, int nz, int rank, double SW){
int i,j,k,n;
double count,countGlobal,totalGlobal;
count = 0.f;
double maxdist=0.f;
double maxdistGlobal;
int nprocx=Dm.nprocx();
int nprocy=Dm.nprocy();
int nprocz=Dm.nprocz();
for (int k=0; k<nz; k++){
for (int j=0; j<ny; j++){
for (int i=0; i<nx; i++){
n = k*nx*ny+j*nx+i;
if (SignDist(i,j,k) < 0.0) id[n] = 0;
else{
// initially saturated with wetting phase
id[n] = 2;
count+=1.0;
// extract maximum distance for critical radius
if ( SignDist(i,j,k) > maxdist) maxdist=SignDist(i,j,k);
}
}
}
}
// total Global is the number of nodes in the pore-space
totalGlobal = Dm.Comm.sumReduce( count );
maxdistGlobal = Dm.Comm.sumReduce( maxdist );
double volume=double(nprocx*nprocy*nprocz)*double(nx-2)*double(ny-2)*double(nz-2);
double porosity=totalGlobal/volume;
if (rank==0) printf("Media Porosity: %f \n",porosity);
if (rank==0) printf("Maximum pore size: %f \n",maxdistGlobal);
// Generate the NWP configuration
//if (rank==0) printf("Initializing morphological distribution with critical radius %f \n", Rcrit);
if (rank==0) printf("Performing morphological opening with target saturation %f \n", SW);
// GenerateResidual(id,nx,ny,nz,Saturation);
// Communication buffers
char *sendID_x, *sendID_y, *sendID_z, *sendID_X, *sendID_Y, *sendID_Z;
char *sendID_xy, *sendID_yz, *sendID_xz, *sendID_Xy, *sendID_Yz, *sendID_xZ;
char *sendID_xY, *sendID_yZ, *sendID_Xz, *sendID_XY, *sendID_YZ, *sendID_XZ;
char *recvID_x, *recvID_y, *recvID_z, *recvID_X, *recvID_Y, *recvID_Z;
char *recvID_xy, *recvID_yz, *recvID_xz, *recvID_Xy, *recvID_Yz, *recvID_xZ;
char *recvID_xY, *recvID_yZ, *recvID_Xz, *recvID_XY, *recvID_YZ, *recvID_XZ;
// send buffers
sendID_x = new char [Dm.sendCount("x")];
sendID_y = new char [Dm.sendCount("y")];
sendID_z = new char [Dm.sendCount("z")];
sendID_X = new char [Dm.sendCount("X")];
sendID_Y = new char [Dm.sendCount("Y")];
sendID_Z = new char [Dm.sendCount("Z")];
sendID_xy = new char [Dm.sendCount("xy")];
sendID_yz = new char [Dm.sendCount("yz")];
sendID_xz = new char [Dm.sendCount("xz")];
sendID_Xy = new char [Dm.sendCount("Xy")];
sendID_Yz = new char [Dm.sendCount("Yz")];
sendID_xZ = new char [Dm.sendCount("xZ")];
sendID_xY = new char [Dm.sendCount("xY")];
sendID_yZ = new char [Dm.sendCount("yZ")];
sendID_Xz = new char [Dm.sendCount("Xz")];
sendID_XY = new char [Dm.sendCount("XY")];
sendID_YZ = new char [Dm.sendCount("YZ")];
sendID_XZ = new char [Dm.sendCount("XZ")];
//......................................................................................
// recv buffers
recvID_x = new char [Dm.recvCount("x")];
recvID_y = new char [Dm.recvCount("y")];
recvID_z = new char [Dm.recvCount("z")];
recvID_X = new char [Dm.recvCount("X")];
recvID_Y = new char [Dm.recvCount("Y")];
recvID_Z = new char [Dm.recvCount("Z")];
recvID_xy = new char [Dm.recvCount("xy")];
recvID_yz = new char [Dm.recvCount("yz")];
recvID_xz = new char [Dm.recvCount("xz")];
recvID_Xy = new char [Dm.recvCount("Xy")];
recvID_xZ = new char [Dm.recvCount("xZ")];
recvID_xY = new char [Dm.recvCount("xY")];
recvID_yZ = new char [Dm.recvCount("yZ")];
recvID_Yz = new char [Dm.recvCount("Yz")];
recvID_Xz = new char [Dm.recvCount("Xz")];
recvID_XY = new char [Dm.recvCount("XY")];
recvID_YZ = new char [Dm.recvCount("YZ")];
recvID_XZ = new char [Dm.recvCount("XZ")];
//......................................................................................
int sendtag,recvtag;
sendtag = recvtag = 7;
int ii,jj,kk;
int Nx = nx;
int Ny = ny;
int Nz = nz;
double sw_old=1.0;
double sw_new=1.0;
double sw_diff_old = 1.0;
double sw_diff_new = 1.0;
// Increase the critical radius until the target saturation is met
double deltaR=0.05; // amount to change the radius in voxel units
double Rcrit_old;
double Rcrit_new;
int imin,jmin,kmin,imax,jmax,kmax;
Rcrit_new = maxdistGlobal;
while (sw_new > SW)
{
sw_diff_old = sw_diff_new;
sw_old = sw_new;
Rcrit_old = Rcrit_new;
Rcrit_new -= deltaR*Rcrit_old;
int Window=round(Rcrit_new);
if (Window == 0) Window = 1; // If Window = 0 at the begining, after the following process will have sw=1.0
// and sw<Sw will be immediately broken
double LocalNumber=0.f;
for(k=0; k<Nz; k++){
for(j=0; j<Ny; j++){
for(i=0; i<Nx; i++){
n = k*nx*ny + j*nx+i;
if (SignDist(i,j,k) > Rcrit_new){
// loop over the window and update
imin=max(1,i-Window);
jmin=max(1,j-Window);
kmin=max(1,k-Window);
imax=min(Nx-1,i+Window);
jmax=min(Ny-1,j+Window);
kmax=min(Nz-1,k+Window);
for (kk=kmin; kk<kmax; kk++){
for (jj=jmin; jj<jmax; jj++){
for (ii=imin; ii<imax; ii++){
int nn = kk*nx*ny+jj*nx+ii;
double dsq = double((ii-i)*(ii-i)+(jj-j)*(jj-j)+(kk-k)*(kk-k));
if (id[nn] == 2 && dsq <= Rcrit_new*Rcrit_new){
LocalNumber+=1.0;
id[nn]=1;
}
}
}
}
}
// move on
}
}
}
// Pack and send the updated ID values
PackID(Dm.sendList("x"), Dm.sendCount("x") ,sendID_x, id);
PackID(Dm.sendList("X"), Dm.sendCount("X") ,sendID_X, id);
PackID(Dm.sendList("y"), Dm.sendCount("y") ,sendID_y, id);
PackID(Dm.sendList("Y"), Dm.sendCount("Y") ,sendID_Y, id);
PackID(Dm.sendList("z"), Dm.sendCount("z") ,sendID_z, id);
PackID(Dm.sendList("Z"), Dm.sendCount("Z") ,sendID_Z, id);
PackID(Dm.sendList("xy"), Dm.sendCount("xy") ,sendID_xy, id);
PackID(Dm.sendList("Xy"), Dm.sendCount("Xy") ,sendID_Xy, id);
PackID(Dm.sendList("xY"), Dm.sendCount("xY") ,sendID_xY, id);
PackID(Dm.sendList("XY"), Dm.sendCount("XY") ,sendID_XY, id);
PackID(Dm.sendList("xz"), Dm.sendCount("xz") ,sendID_xz, id);
PackID(Dm.sendList("Xz"), Dm.sendCount("Xz") ,sendID_Xz, id);
PackID(Dm.sendList("xZ"), Dm.sendCount("xZ") ,sendID_xZ, id);
PackID(Dm.sendList("XZ"), Dm.sendCount("XZ") ,sendID_XZ, id);
PackID(Dm.sendList("yz"), Dm.sendCount("yz") ,sendID_yz, id);
PackID(Dm.sendList("Yz"), Dm.sendCount("Yz") ,sendID_Yz, id);
PackID(Dm.sendList("yZ"), Dm.sendCount("yZ") ,sendID_yZ, id);
PackID(Dm.sendList("YZ"), Dm.sendCount("YZ") ,sendID_YZ, id);
//......................................................................................
Dm.Comm.sendrecv(sendID_x,Dm.sendCount("x"),Dm.rank_x(),sendtag,recvID_X,Dm.recvCount("X"),Dm.rank_X(),recvtag);
Dm.Comm.sendrecv(sendID_X,Dm.sendCount("X"),Dm.rank_X(),sendtag,recvID_x,Dm.recvCount("x"),Dm.rank_x(),recvtag);
Dm.Comm.sendrecv(sendID_y,Dm.sendCount("y"),Dm.rank_y(),sendtag,recvID_Y,Dm.recvCount("Y"),Dm.rank_Y(),recvtag);
Dm.Comm.sendrecv(sendID_Y,Dm.sendCount("Y"),Dm.rank_Y(),sendtag,recvID_y,Dm.recvCount("y"),Dm.rank_y(),recvtag);
Dm.Comm.sendrecv(sendID_z,Dm.sendCount("z"),Dm.rank_z(),sendtag,recvID_Z,Dm.recvCount("Z"),Dm.rank_Z(),recvtag);
Dm.Comm.sendrecv(sendID_Z,Dm.sendCount("Z"),Dm.rank_Z(),sendtag,recvID_z,Dm.recvCount("z"),Dm.rank_z(),recvtag);
Dm.Comm.sendrecv(sendID_xy,Dm.sendCount("xy"),Dm.rank_xy(),sendtag,recvID_XY,Dm.recvCount("XY"),Dm.rank_XY(),recvtag);
Dm.Comm.sendrecv(sendID_XY,Dm.sendCount("XY"),Dm.rank_XY(),sendtag,recvID_xy,Dm.recvCount("xy"),Dm.rank_xy(),recvtag);
Dm.Comm.sendrecv(sendID_Xy,Dm.sendCount("Xy"),Dm.rank_Xy(),sendtag,recvID_xY,Dm.recvCount("xY"),Dm.rank_xY(),recvtag);
Dm.Comm.sendrecv(sendID_xY,Dm.sendCount("xY"),Dm.rank_xY(),sendtag,recvID_Xy,Dm.recvCount("Xy"),Dm.rank_Xy(),recvtag);
Dm.Comm.sendrecv(sendID_xz,Dm.sendCount("xz"),Dm.rank_xz(),sendtag,recvID_XZ,Dm.recvCount("XZ"),Dm.rank_XZ(),recvtag);
Dm.Comm.sendrecv(sendID_XZ,Dm.sendCount("XZ"),Dm.rank_XZ(),sendtag,recvID_xz,Dm.recvCount("xz"),Dm.rank_xz(),recvtag);
Dm.Comm.sendrecv(sendID_Xz,Dm.sendCount("Xz"),Dm.rank_Xz(),sendtag,recvID_xZ,Dm.recvCount("xZ"),Dm.rank_xZ(),recvtag);
Dm.Comm.sendrecv(sendID_xZ,Dm.sendCount("xZ"),Dm.rank_xZ(),sendtag,recvID_Xz,Dm.recvCount("Xz"),Dm.rank_Xz(),recvtag);
Dm.Comm.sendrecv(sendID_yz,Dm.sendCount("yz"),Dm.rank_yz(),sendtag,recvID_YZ,Dm.recvCount("YZ"),Dm.rank_YZ(),recvtag);
Dm.Comm.sendrecv(sendID_YZ,Dm.sendCount("YZ"),Dm.rank_YZ(),sendtag,recvID_yz,Dm.recvCount("yz"),Dm.rank_yz(),recvtag);
Dm.Comm.sendrecv(sendID_Yz,Dm.sendCount("Yz"),Dm.rank_Yz(),sendtag,recvID_yZ,Dm.recvCount("yZ"),Dm.rank_yZ(),recvtag);
Dm.Comm.sendrecv(sendID_yZ,Dm.sendCount("yZ"),Dm.rank_yZ(),sendtag,recvID_Yz,Dm.recvCount("Yz"),Dm.rank_Yz(),recvtag);
//......................................................................................
UnpackID(Dm.recvList("x"), Dm.recvCount("x") ,recvID_x, id);
UnpackID(Dm.recvList("X"), Dm.recvCount("X") ,recvID_X, id);
UnpackID(Dm.recvList("y"), Dm.recvCount("y") ,recvID_y, id);
UnpackID(Dm.recvList("Y"), Dm.recvCount("Y") ,recvID_Y, id);
UnpackID(Dm.recvList("z"), Dm.recvCount("z") ,recvID_z, id);
UnpackID(Dm.recvList("Z"), Dm.recvCount("Z") ,recvID_Z, id);
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("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);
//......................................................................................
//double GlobalNumber = Dm.Comm.sumReduce( LocalNumber );
count = 0.f;
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] == 2){
count+=1.0;
}
}
}
}
countGlobal = Dm.Comm.sumReduce( count );
sw_new = countGlobal/totalGlobal;
sw_diff_new = abs(sw_new-SW);
// for test only
if (rank==0){
//printf("Final saturation=%f\n",sw_new);
// printf("Final critical radius=%f\n",Rcrit_new);
}
}
if (sw_diff_new<sw_diff_old){
if (rank==0){
printf("Final saturation=%f\n",sw_new);
printf("Final critical radius=%f\n",Rcrit_new);
}
}
else{
if (rank==0){
printf("Final saturation=%f\n",sw_old);
printf("Final critical radius=%f\n",Rcrit_old);
}
}
}
int main(int argc, char **argv)
{
// Initialize MPI
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
{
// parallel domain size (# of sub-domains)
int nprocx,nprocy,nprocz;
int iproc,jproc,kproc;
//*****************************************
if (rank == 0){
printf("********************************************************\n");
printf("Running Sphere Packing pre-processor for LBPM-WIA \n");
printf("********************************************************\n");
}
// Variables that specify the computational domain
string filename;
int Nx,Ny,Nz; // local sub-domain size
int nspheres; // number of spheres in the packing
double Lx,Ly,Lz; // Domain length
double D = 1.0; // reference length for non-dimensionalization
int i,j,k,n;
filename = argv[1];
auto db = std::make_shared<Database>( filename );
auto domain_db = db->getDatabase( "Domain" );
auto Dm = std::shared_ptr<Domain>(new Domain(domain_db,comm)); // full domain for analysis
Nx = Dm->Nx;
Ny = Dm->Ny;
Nz = Dm->Nz;
Lx = Dm->Lx;
Ly = Dm->Ly;
Lz = Dm->Lz;
iproc = Dm->iproc();
jproc = Dm->jproc();
kproc = Dm->kproc();
nprocx = Dm->nprocx();
nprocy = Dm->nprocy();
nprocz = Dm->nprocz();
nspheres = domain_db->getScalar<int>( "nspheres");
//printf("Set domain \n");
//int BoundaryCondition=1;
//Nz += 2;
//Nx = Ny = Nz; // Cubic domain
int N = Nx*Ny*Nz;
// Define Dm.Communication sub-domain -- everywhere
for (int k=0; k<Nz; k++){
for (int j=0; j<Ny; j++){
for (int i=0; i<Nx; i++){
n = k*Nx*Ny+j*Nx+i;
Dm->id[n] = 1;
}
}
}
Dm->CommInit();
//.......................................................................
// Filenames used
char LocalRankString[8];
char LocalRankFilename[40];
char LocalRestartFile[40];
sprintf(LocalRankString,"%05d",rank);
sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
sprintf(LocalRestartFile,"%s%s","Restart.",LocalRankString);
// printf("Local File Name = %s \n",LocalRankFilename);
// .......... READ THE INPUT FILE .......................................
// char value;
char *id;
id = new char[N];
int sum = 0;
double sum_local;
double iVol_global = 1.0/(1.0*(Nx-2)*(Ny-2)*(Nz-2)*nprocs);
double porosity;
//...........................................................................
DoubleArray SignDist(Nx,Ny,Nz);
//.......................................................................
// Read in sphere pack
//if (rank==1) printf("nspheres =%i \n",nspheres);
//.......................................................................
double *cx,*cy,*cz,*rad;
cx = new double[nspheres];
cy = new double[nspheres];
cz = new double[nspheres];
rad = new double[nspheres];
//.......................................................................
if (rank == 0) printf("Reading the sphere packing \n");
if (rank == 0) ReadSpherePacking(nspheres,cx,cy,cz,rad);
comm.barrier();
// Broadcast the sphere packing to all processes
comm.bcast(cx,nspheres,0);
comm.bcast(cy,nspheres,0);
comm.bcast(cz,nspheres,0);
comm.bcast(rad,nspheres,0);
//...........................................................................
comm.barrier();
if (rank == 0) cout << "Domain set." << endl;
if (rank == 0){
// Compute the Sauter mean diameter
double totVol = 0.0;
double totArea = 0.0;
// Compute the total volume and area of all spheres
for (i=0; i<nspheres; i++){
totVol += 1.3333333333333*3.14159265359*rad[i]*rad[i]*rad[i];
totArea += 4.0*3.14159265359*rad[i]*rad[i];
}
D = 6.0*(Nx-2)*nprocx*totVol / totArea / Lx;
printf("Sauter Mean Diameter (computed from sphere packing) = %f \n",D);
}
comm.bcast(&D,1,0);
//.......................................................................
SignedDistance(SignDist.data(),nspheres,cx,cy,cz,rad,Lx,Ly,Lz,Nx,Ny,Nz,
iproc,jproc,kproc,nprocx,nprocy,nprocz);
//.......................................................................
// Assign the phase ID field based on the signed distance
//.......................................................................
for (k=0;k<Nz;k++){
for (j=0;j<Ny;j++){
for (i=0;i<Nx;i++){
n = k*Nx*Ny+j*Nx+i;
id[n] = 0;
}
}
}
sum=0;
for ( k=1;k<Nz-1;k++){
for ( j=1;j<Ny-1;j++){
for ( i=1;i<Nx-1;i++){
n = k*Nx*Ny+j*Nx+i;
if (SignDist(n) > 0.0){
id[n] = 2;
}
// compute the porosity (actual interface location used)
if (SignDist(n) > 0.0){
sum++;
}
}
}
}
sum_local = 1.0*sum;
porosity = comm.sumReduce(sum_local);
porosity = porosity*iVol_global;
if (rank==0) printf("Media porosity = %f \n",porosity);
// Run Morphological opening to initialize 50% saturation
double SW=0.50;
if (rank==0) printf("MorphOpen: Initializing with saturation %f \n",SW);
MorphOpen(SignDist, id, *Dm, Nx, Ny, Nz, rank, SW);
//.........................................................
// don't perform computations at the eight corners
id[0] = id[Nx-1] = id[(Ny-1)*Nx] = id[(Ny-1)*Nx + Nx-1] = 0;
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;
//.........................................................
/* //.......................................................................
sprintf(LocalRankString,"%05d",rank);
sprintf(LocalRankFilename,"%s%s","SignDist.",LocalRankString);
FILE *DIST = fopen(LocalRankFilename,"wb");
if (DIST==NULL) ERROR("Error opening file: ID.xxxxx");
fwrite(SignDist.data(),1,N*sizeof(double),DIST);
fclose(DIST);
//......................................................................
*/
//.......................................................................
sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
FILE *IDFILE = fopen(LocalRankFilename,"wb");
if (IDFILE==NULL) ERROR("Error opening file: ID.xxxxx");
fwrite(id,1,N,IDFILE);
fclose(IDFILE);
//......................................................................
}
Utilities::shutdown();
}
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