Files
LBPM/tests/lbpm_morphdrain_pp.cpp
2018-05-19 07:49:32 -04:00

496 lines
16 KiB
C++

/*
* Pre-processor to generate signed distance function from segmented data
* segmented data should be stored in a raw binary file as 1-byte integer (type char)
* will output distance functions for phases
*/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <iostream>
#include <fstream>
#include <sstream>
#include "common/Array.h"
#include "common/Domain.h"
//*************************************************************************
// Morpohological drainage pre-processor
// Generate states on primary drainage using morphological approach
// Signed distance function is used to determine fluid configuration
//*************************************************************************
inline void PackID(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(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];
}
}
//***************************************************************************************
int main(int argc, char **argv)
{
// Initialize MPI
int rank, nprocs;
MPI_Init(&argc,&argv);
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Comm_rank(comm,&rank);
MPI_Comm_size(comm,&nprocs);
//double Rcrit;
double SW=strtod(argv[1],NULL);
if (rank==0){
//printf("Critical radius %f (voxels)\n",Rcrit);
printf("Target saturation %f \n",SW);
}
// }
//.......................................................................
// Reading the domain information file
//.......................................................................
int nprocx, nprocy, nprocz, nx, ny, nz, nspheres;
double Lx, Ly, Lz;
int i,j,k,n;
int BC=0;
if (rank==0){
ifstream domain("Domain.in");
domain >> nprocx;
domain >> nprocy;
domain >> nprocz;
domain >> nx;
domain >> ny;
domain >> nz;
domain >> nspheres;
domain >> Lx;
domain >> Ly;
domain >> Lz;
}
MPI_Barrier(comm);
// Computational domain
MPI_Bcast(&nx,1,MPI_INT,0,comm);
MPI_Bcast(&ny,1,MPI_INT,0,comm);
MPI_Bcast(&nz,1,MPI_INT,0,comm);
MPI_Bcast(&nprocx,1,MPI_INT,0,comm);
MPI_Bcast(&nprocy,1,MPI_INT,0,comm);
MPI_Bcast(&nprocz,1,MPI_INT,0,comm);
MPI_Bcast(&nspheres,1,MPI_INT,0,comm);
MPI_Bcast(&Lx,1,MPI_DOUBLE,0,comm);
MPI_Bcast(&Ly,1,MPI_DOUBLE,0,comm);
MPI_Bcast(&Lz,1,MPI_DOUBLE,0,comm);
//.................................................
MPI_Barrier(comm);
// Check that the number of processors >= the number of ranks
if ( rank==0 ) {
printf("Number of MPI ranks required: %i \n", nprocx*nprocy*nprocz);
printf("Number of MPI ranks used: %i \n", nprocs);
printf("Full domain size: %i x %i x %i \n",nx*nprocx,ny*nprocy,nz*nprocz);
}
if ( nprocs < nprocx*nprocy*nprocz ){
ERROR("Insufficient number of processors");
}
char LocalRankFilename[40];
int BoundaryCondition=1;
Domain Dm(nx,ny,nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BoundaryCondition);
nx+=2; ny+=2; nz+=2;
int N = nx*ny*nz;
char *id;
id = new char[N];
// Define 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;
}
}
}
/*// Exclude the maximum / minimum z rows
if (rank/(nprocx*nprocy)==0){
int k=0;
for (int j=0; j<ny; j++){
for (int i=0; i<nx; i++){
n = k*nx*ny+j*nx+i;
Dm.id[n] = 0;
}
}
}
if (rank/(nprocx*nprocy)==nprocz-1){
int k=nz-1;
for (int j=0; j<ny; j++){
for (int i=0; i<nx; i++){
n = k*nx*ny+j*nx+i;
Dm.id[n] = 0;
}
}
}
*/
Dm.CommInit();
int xdim,ydim,zdim;
xdim=Dm.Nx-2;
ydim=Dm.Ny-2;
zdim=Dm.Nz-2;
fillHalo<double> fillData(Dm.Comm, Dm.rank_info,{xdim,ydim,zdim},{1,1,1},0,1);
DoubleArray SignDist(nx,ny,nz);
// Read the signed distance from file
sprintf(LocalRankFilename,"SignDist.%05i",rank);
FILE *DIST = fopen(LocalRankFilename,"rb");
size_t ReadSignDist;
ReadSignDist=fread(SignDist.data(),8,N,DIST);
if (ReadSignDist != size_t(N)) printf("lbpm_morphdrain_pp: Error reading signed distance function (rank=%i)\n",rank);
fclose(DIST);
fillData.fill(SignDist);
sprintf(LocalRankFilename,"ID.%05i",rank);
size_t readID;
FILE *IDFILE = fopen(LocalRankFilename,"rb");
if (IDFILE==NULL) ERROR("Error opening file: ID.xxxxx");
readID=fread(id,1,N,IDFILE);
if (readID != size_t(N)) printf("lbpm_segmented_pp: Error reading ID (rank=%i) \n",rank);
fclose(IDFILE);
Dm.CommInit();
int iproc = Dm.iproc();
int jproc = Dm.jproc();
int kproc = Dm.kproc();
// Generate the NWP configuration
//if (rank==0) printf("Performing morphological drainage with critical radius %f \n", Rcrit);
if (rank==0) printf("Performing morphological drainage 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 x,y,z;
int ii,jj,kk;
int Nx = nx;
int Ny = ny;
int Nz = nz;
double GlobalNumber = 1.f;
double count,countGlobal,totalGlobal;
count = 0.f;
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;
}
}
}
}
// total Global is the number of nodes in the pore-space
MPI_Allreduce(&count,&totalGlobal,1,MPI_DOUBLE,MPI_SUM,comm);
double porosity=totalGlobal/(double(nprocx*nprocy*nprocz)*double(nx-2)*double(ny-2)*double(nz-2));
if (rank==0) printf("Media Porosity: %f \n",porosity);
double radius,Rcrit_new;
radius = 0.0;
// Layer the inlet with NWP
if (kproc == 0){
for(j=0; j<Ny; j++){
for(i=0; i<Nx; i++){
n = j*nx+i;
// n = nx*ny + j*nx+i;
id[n]=1;
if (SignDist(i,j,0) > radius){
radius=SignDist(i,j,0);
}
}
}
}
MPI_Allreduce(&radius,&Rcrit_new,1,MPI_DOUBLE,MPI_MAX,comm);
if (rank==0) printf("Starting morhpological drainage with critical radius = %f \n",Rcrit_new);
int imin,jmin,kmin,imax,jmax,kmax;
// Decrease the critical radius until the target saturation is met
double deltaR=0.01; // amount to change the radius in voxel units
double Rcrit_old;
double sw_old=1.0; // initial WP saturation set to one
double sw_new=1.0; // initial WP saturation set to one
double sw_diff_old = 1.0;
double sw_diff_new = 1.0;
while (sw_new > SW && Rcrit_new > 0.99){
Rcrit_old = Rcrit_new;
Rcrit_new -= deltaR*Rcrit_old;// decrease critical radius
sw_old = sw_new;
sw_diff_old = sw_diff_new;
int Window=round(Rcrit_new);
GlobalNumber = 1.0;
while (GlobalNumber > 0){
//if (rank==0) printf("GlobalNumber=%f \n",GlobalNumber);
double LocalNumber=GlobalNumber=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 (id[n] == 1 && 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);
//......................................................................................
MPI_Sendrecv(sendID_x,Dm.sendCount_x,MPI_CHAR,Dm.rank_x(),sendtag,
recvID_X,Dm.recvCount_X,MPI_CHAR,Dm.rank_X(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_X,Dm.sendCount_X,MPI_CHAR,Dm.rank_X(),sendtag,
recvID_x,Dm.recvCount_x,MPI_CHAR,Dm.rank_x(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_y,Dm.sendCount_y,MPI_CHAR,Dm.rank_y(),sendtag,
recvID_Y,Dm.recvCount_Y,MPI_CHAR,Dm.rank_Y(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_Y,Dm.sendCount_Y,MPI_CHAR,Dm.rank_Y(),sendtag,
recvID_y,Dm.recvCount_y,MPI_CHAR,Dm.rank_y(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_z,Dm.sendCount_z,MPI_CHAR,Dm.rank_z(),sendtag,
recvID_Z,Dm.recvCount_Z,MPI_CHAR,Dm.rank_Z(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_Z,Dm.sendCount_Z,MPI_CHAR,Dm.rank_Z(),sendtag,
recvID_z,Dm.recvCount_z,MPI_CHAR,Dm.rank_z(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_xy,Dm.sendCount_xy,MPI_CHAR,Dm.rank_xy(),sendtag,
recvID_XY,Dm.recvCount_XY,MPI_CHAR,Dm.rank_XY(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_XY,Dm.sendCount_XY,MPI_CHAR,Dm.rank_XY(),sendtag,
recvID_xy,Dm.recvCount_xy,MPI_CHAR,Dm.rank_xy(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_Xy,Dm.sendCount_Xy,MPI_CHAR,Dm.rank_Xy(),sendtag,
recvID_xY,Dm.recvCount_xY,MPI_CHAR,Dm.rank_xY(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_xY,Dm.sendCount_xY,MPI_CHAR,Dm.rank_xY(),sendtag,
recvID_Xy,Dm.recvCount_Xy,MPI_CHAR,Dm.rank_Xy(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_xz,Dm.sendCount_xz,MPI_CHAR,Dm.rank_xz(),sendtag,
recvID_XZ,Dm.recvCount_XZ,MPI_CHAR,Dm.rank_XZ(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_XZ,Dm.sendCount_XZ,MPI_CHAR,Dm.rank_XZ(),sendtag,
recvID_xz,Dm.recvCount_xz,MPI_CHAR,Dm.rank_xz(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_Xz,Dm.sendCount_Xz,MPI_CHAR,Dm.rank_Xz(),sendtag,
recvID_xZ,Dm.recvCount_xZ,MPI_CHAR,Dm.rank_xZ(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_xZ,Dm.sendCount_xZ,MPI_CHAR,Dm.rank_xZ(),sendtag,
recvID_Xz,Dm.recvCount_Xz,MPI_CHAR,Dm.rank_Xz(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_yz,Dm.sendCount_yz,MPI_CHAR,Dm.rank_yz(),sendtag,
recvID_YZ,Dm.recvCount_YZ,MPI_CHAR,Dm.rank_YZ(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_YZ,Dm.sendCount_YZ,MPI_CHAR,Dm.rank_YZ(),sendtag,
recvID_yz,Dm.recvCount_yz,MPI_CHAR,Dm.rank_yz(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_Yz,Dm.sendCount_Yz,MPI_CHAR,Dm.rank_Yz(),sendtag,
recvID_yZ,Dm.recvCount_yZ,MPI_CHAR,Dm.rank_yZ(),recvtag,comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendID_yZ,Dm.sendCount_yZ,MPI_CHAR,Dm.rank_yZ(),sendtag,
recvID_Yz,Dm.recvCount_Yz,MPI_CHAR,Dm.rank_Yz(),recvtag,comm,MPI_STATUS_IGNORE);
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);
//......................................................................................
MPI_Allreduce(&LocalNumber,&GlobalNumber,1,MPI_DOUBLE,MPI_SUM,comm);
// Layer the inlet with NWP
if (kproc == 0){
for(j=0; j<Ny; j++){
for(i=0; i<Nx; i++){
n = j*nx+i;
// n = nx*ny + j*nx+i;
id[n]=1;
}
}
}
// Layer the outlet with WP
if (kproc == nprocz-1){
for(j=0; j<Ny; j++){
for(i=0; i<Nx; i++){
n = (nz-1)*nx*ny+j*nx+i;
// n = nx*ny + j*nx+i;
id[n]=2;
}
}
}
}
count = 1.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;
}
}
}
}
MPI_Allreduce(&count,&countGlobal,1,MPI_DOUBLE,MPI_SUM,comm);
sw_new= countGlobal/totalGlobal;
sw_diff_new = abs(sw_new-SW);
// 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);
}
}
// if (rank==0){
// printf("Final saturation=%f\n",sw);
// printf("Final critical radius=%f\n",Rcrit);
//
// }
sprintf(LocalRankFilename,"ID.%05i",rank);
FILE *ID = fopen(LocalRankFilename,"wb");
fwrite(id,1,N,ID);
fclose(ID);
MPI_Barrier(comm);
MPI_Finalize();
}