refactor morphdrain pp
This commit is contained in:
James E McClure
parent
d9ba9f322e
commit
223f17883d
@ -16,207 +16,99 @@
|
||||
#include "analysis/runAnalysis.h"
|
||||
|
||||
//*************************************************************************
|
||||
// Morpohological drainage pre-processor
|
||||
// Generate states on primary drainage using morphological approach
|
||||
// Morpohologica pre-processor
|
||||
// Initialize phase distribution 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 comm = MPI_COMM_WORLD;
|
||||
MPI_Comm_rank(comm,&rank);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
{
|
||||
//.......................................................................
|
||||
// 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;
|
||||
// char fluidValue,solidValue;
|
||||
int MAXTIME=1000;
|
||||
int READ_FROM_BLOCK=0;
|
||||
|
||||
//.......................................................................
|
||||
// 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;
|
||||
char LocalRankString[8];
|
||||
char LocalRankFilename[40];
|
||||
|
||||
string filename;
|
||||
if (argc > 1){
|
||||
filename=argv[1];
|
||||
}
|
||||
else ERROR("No input database provided\n");
|
||||
// read the input database
|
||||
auto db = std::make_shared<Database>( filename );
|
||||
auto domain_db = db->getDatabase( "Domain" );
|
||||
|
||||
// Read domain parameters
|
||||
auto L = domain_db->getVector<double>( "L" );
|
||||
auto size = domain_db->getVector<int>( "n" );
|
||||
auto nproc = domain_db->getVector<int>( "nproc" );
|
||||
double SW = domain_db->getScalar<double>( "Sw" );
|
||||
|
||||
nx = size[0];
|
||||
ny = size[1];
|
||||
nz = size[2];
|
||||
nprocx = nproc[0];
|
||||
nprocy = nproc[1];
|
||||
nprocz = nproc[2];
|
||||
|
||||
// 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(domain_db,comm);
|
||||
|
||||
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;
|
||||
}
|
||||
string filename;
|
||||
double Rcrit_new, SW;
|
||||
if (argc > 1){
|
||||
filename=argv[1];
|
||||
Rcrit_new=0.f;
|
||||
//SW=strtod(argv[2],NULL);
|
||||
}
|
||||
}
|
||||
else ERROR("No input database provided\n");
|
||||
// read the input database
|
||||
auto db = std::make_shared<Database>( filename );
|
||||
auto domain_db = db->getDatabase( "Domain" );
|
||||
|
||||
Dm.CommInit();
|
||||
// Read domain parameters
|
||||
auto L = domain_db->getVector<double>( "L" );
|
||||
auto size = domain_db->getVector<int>( "n" );
|
||||
auto nproc = domain_db->getVector<int>( "nproc" );
|
||||
auto ReadValues = domain_db->getVector<char>( "ReadValues" );
|
||||
auto WriteValues = domain_db->getVector<char>( "WriteValues" );
|
||||
SW = domain_db->getScalar<double>("Sw");
|
||||
|
||||
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_morphdrain_pp: Error reading ID (rank=%i) \n",rank);
|
||||
fclose(IDFILE);
|
||||
// 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);
|
||||
|
||||
nx = size[0];
|
||||
ny = size[1];
|
||||
nz = size[2];
|
||||
nprocx = nproc[0];
|
||||
nprocy = nproc[1];
|
||||
nprocz = nproc[2];
|
||||
|
||||
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);
|
||||
|
||||
// Generate the signed distance map
|
||||
// Initialize the domain and communication
|
||||
Array<char> id_solid(nx,ny,nz);
|
||||
DoubleArray SignDist(nx,ny,nz);
|
||||
DoubleArray phase(nx,ny,nz);
|
||||
IntArray phase_label(nx,ny,nz);
|
||||
int N = (nx+2)*(ny+2)*(nz+2);
|
||||
|
||||
// Solve for the position of the solid phase
|
||||
for (int k=0;k<nz;k++){
|
||||
for (int j=0;j<ny;j++){
|
||||
for (int i=0;i<nx;i++){
|
||||
int n = k*nx*ny+j*nx+i;
|
||||
// Initialize the solid phase
|
||||
if (id[n] > 0) id_solid(i,j,k) = 1;
|
||||
else id_solid(i,j,k) = 0;
|
||||
}
|
||||
}
|
||||
}
|
||||
// Initialize the signed distance function
|
||||
for (int k=0;k<nz;k++){
|
||||
for (int j=0;j<ny;j++){
|
||||
for (int i=0;i<nx;i++){
|
||||
int n = k*nx*ny+j*nx+i;
|
||||
// Initialize distance to +/- 1
|
||||
SignDist(i,j,k) = 2.0*double(id_solid(i,j,k))-1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
std::shared_ptr<Domain> Dm (new Domain(domain_db,comm));
|
||||
// std::shared_ptr<Domain> Dm (new Domain(nx,ny,nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BC));
|
||||
for (n=0; n<N; n++) Dm->id[n]=1;
|
||||
Dm->CommInit();
|
||||
|
||||
if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
|
||||
CalcDist(SignDist,id_solid,Dm);
|
||||
char *id;
|
||||
id = new char [N];
|
||||
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_morphopen_pp: Error reading ID (rank=%i) \n",rank);
|
||||
fclose(IDFILE);
|
||||
|
||||
// Run the morphological opening
|
||||
MorphOpen(SignDist, id, *Dm, SW);
|
||||
nx+=2; ny+=2; nz+=2;
|
||||
// Generate the signed distance map
|
||||
// Initialize the domain and communication
|
||||
Array<char> id_solid(nx,ny,nz);
|
||||
DoubleArray SignDist(nx,ny,nz);
|
||||
DoubleArray phase(nx,ny,nz);
|
||||
IntArray phase_label(nx,ny,nz);
|
||||
|
||||
for (int k=0;k<nz;k++){
|
||||
for (int j=0;j<ny;j++){
|
||||
for (int i=0;i<nx;i++){
|
||||
int n = k*nx*ny+j*nx+i;
|
||||
if (id[n] == 1){
|
||||
phase(i,j,k) = 1.0;
|
||||
}
|
||||
else
|
||||
phase(i,j,k) = -1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Extract only the connected part
|
||||
BlobIDstruct new_index;
|
||||
double vF=0.0; double vS=0.0;
|
||||
ComputeGlobalBlobIDs(nx-2,ny-2,nz-2,Dm.rank_info,phase,SignDist,vF,vS,phase_label,Dm.Comm);
|
||||
MPI_Barrier(comm);
|
||||
|
||||
for (int k=0;k<nz;k++){
|
||||
for (int j=0;j<ny;j++){
|
||||
for (int i=0;i<nx;i++){
|
||||
int n = k*nx*ny+j*nx+i;
|
||||
if (id[n] == 1 && phase_label(i,j,k) > 1){
|
||||
id[n] = 2;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// calculate distance to non-wetting fluid
|
||||
if (domain_db->keyExists( "HistoryLabels" )){
|
||||
if (rank==0) printf("Relabel solid components that touch fluid 1 \n");
|
||||
auto LabelList = domain_db->getVector<char>( "ComponentLabels" );
|
||||
auto HistoryLabels = domain_db->getVector<char>( "HistoryLabels" );
|
||||
size_t NLABELS=LabelList.size();
|
||||
if (rank==0){
|
||||
for (unsigned int idx=0; idx < NLABELS; idx++){
|
||||
char VALUE = LabelList[idx];
|
||||
char NEWVAL = HistoryLabels[idx];
|
||||
printf(" Relabel component %d as %d \n", VALUE, NEWVAL);
|
||||
}
|
||||
}
|
||||
// Solve for the position of the solid phase
|
||||
for (int k=0;k<nz;k++){
|
||||
for (int j=0;j<ny;j++){
|
||||
for (int i=0;i<nx;i++){
|
||||
int n = k*nx*ny+j*nx+i;
|
||||
// Initialize the solid phase
|
||||
if (id[n] == 1) id_solid(i,j,k) = 0;
|
||||
else id_solid(i,j,k) = 1;
|
||||
if (id[n] > 0) id_solid(i,j,k) = 1;
|
||||
else id_solid(i,j,k) = 0;
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -230,32 +122,108 @@ int main(int argc, char **argv)
|
||||
}
|
||||
}
|
||||
}
|
||||
CalcDist(SignDist,id_solid,Dm);
|
||||
// re-label IDs near the non-wetting fluid
|
||||
|
||||
if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
|
||||
CalcDist(SignDist,id_solid,*Dm);
|
||||
|
||||
MPI_Barrier(comm);
|
||||
|
||||
// Run the morphological opening
|
||||
MorphOpen(SignDist, id, Dm, SW);
|
||||
|
||||
for (int k=0;k<nz;k++){
|
||||
for (int j=0;j<ny;j++){
|
||||
for (int i=0;i<nx;i++){
|
||||
int n = k*nx*ny+j*nx+i;
|
||||
signed char LOCVAL = id[n];
|
||||
for (unsigned int idx=0; idx < NLABELS; idx++){
|
||||
char VALUE=LabelList[idx];
|
||||
char NEWVALUE=HistoryLabels[idx];
|
||||
if (LOCVAL == VALUE){
|
||||
idx = NLABELS;
|
||||
if (SignDist(i,j,k) < 1.0){
|
||||
id[n] = NEWVALUE;
|
||||
if (id[n] == 1){
|
||||
phase(i,j,k) = 1.0;
|
||||
}
|
||||
else
|
||||
phase(i,j,k) = -1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Extract only the connected part
|
||||
BlobIDstruct new_index;
|
||||
double vF=0.0; double vS=0.0;
|
||||
ComputeGlobalBlobIDs(nx-2,ny-2,nz-2,Dm.rank_info,phase,SignDist,vF,vS,phase_label,Dm.Comm);
|
||||
MPI_Barrier(comm);
|
||||
|
||||
for (int k=0;k<nz;k++){
|
||||
for (int j=0;j<ny;j++){
|
||||
for (int i=0;i<nx;i++){
|
||||
int n = k*nx*ny+j*nx+i;
|
||||
if (id[n] == 1 && phase_label(i,j,k) > 1){
|
||||
id[n] = 2;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// calculate distance to non-wetting fluid
|
||||
if (domain_db->keyExists( "HistoryLabels" )){
|
||||
if (rank==0) printf("Relabel solid components that touch fluid 1 \n");
|
||||
auto LabelList = domain_db->getVector<char>( "ComponentLabels" );
|
||||
auto HistoryLabels = domain_db->getVector<char>( "HistoryLabels" );
|
||||
size_t NLABELS=LabelList.size();
|
||||
if (rank==0){
|
||||
for (unsigned int idx=0; idx < NLABELS; idx++){
|
||||
char VALUE = LabelList[idx];
|
||||
char NEWVAL = HistoryLabels[idx];
|
||||
printf(" Relabel component %d as %d \n", VALUE, NEWVAL);
|
||||
}
|
||||
}
|
||||
for (int k=0;k<nz;k++){
|
||||
for (int j=0;j<ny;j++){
|
||||
for (int i=0;i<nx;i++){
|
||||
int n = k*nx*ny+j*nx+i;
|
||||
// Initialize the solid phase
|
||||
if (id[n] == 1) id_solid(i,j,k) = 0;
|
||||
else id_solid(i,j,k) = 1;
|
||||
}
|
||||
}
|
||||
}
|
||||
// Initialize the signed distance function
|
||||
for (int k=0;k<nz;k++){
|
||||
for (int j=0;j<ny;j++){
|
||||
for (int i=0;i<nx;i++){
|
||||
int n = k*nx*ny+j*nx+i;
|
||||
// Initialize distance to +/- 1
|
||||
SignDist(i,j,k) = 2.0*double(id_solid(i,j,k))-1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
CalcDist(SignDist,id_solid,*Dm);
|
||||
// re-label IDs near the non-wetting fluid
|
||||
for (int k=0;k<nz;k++){
|
||||
for (int j=0;j<ny;j++){
|
||||
for (int i=0;i<nx;i++){
|
||||
int n = k*nx*ny+j*nx+i;
|
||||
signed char LOCVAL = id[n];
|
||||
for (unsigned int idx=0; idx < NLABELS; idx++){
|
||||
char VALUE=LabelList[idx];
|
||||
char NEWVALUE=HistoryLabels[idx];
|
||||
if (LOCVAL == VALUE){
|
||||
idx = NLABELS;
|
||||
if (SignDist(i,j,k) < 1.0){
|
||||
id[n] = NEWVALUE;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
sprintf(LocalRankFilename,"ID.%05i",rank);
|
||||
FILE *ID = fopen(LocalRankFilename,"wb");
|
||||
fwrite(id,1,N,ID);
|
||||
fclose(ID);
|
||||
if (rank==0) printf("Writing ID file \n");
|
||||
sprintf(LocalRankFilename,"ID.%05i",rank);
|
||||
|
||||
FILE *ID = fopen(LocalRankFilename,"wb");
|
||||
fwrite(id,1,N,ID);
|
||||
fclose(ID);
|
||||
}
|
||||
|
||||
MPI_Barrier(comm);
|
||||
MPI_Finalize();
|
||||
|
||||
Loading…
Reference in New Issue
Block a user