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LBPM/analysis/morphology.cpp
James E McClure 842d9a01d6 estimate growth better
2018-12-17 18:47:44 -05:00

396 lines
15 KiB
C++
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#include <analysis/morphology.h>
// Implementation of morphological opening routine
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];
}
}
//***************************************************************************************
double MorphOpen(DoubleArray &SignDist, char *id, std::shared_ptr<Domain> Dm, double VoidFraction){
// SignDist is the distance to the object that you want to constaing the morphological opening
// VoidFraction is the the empty space where the object inst
// id is a labeled map
// Dm contains information about the domain structure
int nx = Dm->Nx;
int ny = Dm->Ny;
int nz = Dm->Nz;
int iproc = Dm->iproc();
int jproc = Dm->jproc();
int kproc = Dm->kproc();
int nprocx = Dm->nprocx();
int nprocy = Dm->nprocy();
int nprocz = Dm->nprocz();
int rank = Dm->rank();
int n;
double final_void_fraction;
double count,countGlobal,totalGlobal;
count = 0.f;
double maxdist=-200.f;
double maxdistGlobal;
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;
// extract maximum distance for critical radius
if ( SignDist(i,j,k) > maxdist) maxdist=SignDist(i,j,k);
if ( SignDist(i,j,k) > 0.0 ){
count += 1.0;
id[n] = 2;
}
}
}
}
MPI_Barrier(Dm->Comm);
// total Global is the number of nodes in the pore-space
MPI_Allreduce(&count,&totalGlobal,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
MPI_Allreduce(&maxdist,&maxdistGlobal,1,MPI_DOUBLE,MPI_MAX,Dm->Comm);
double volume=double(nprocx*nprocy*nprocz)*double(nx-2)*double(ny-2)*double(nz-2);
double volume_fraction=totalGlobal/volume;
if (rank==0) printf("Volume fraction for morphological opening: %f \n",volume_fraction);
if (rank==0) printf("Maximum pore size: %f \n",maxdistGlobal);
// 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 void_fraction_old=1.0;
double void_fraction_new=1.0;
double void_fraction_diff_old = 1.0;
double void_fraction_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 GlobalNumber = 1.f;
int imin,jmin,kmin,imax,jmax,kmax;
double Rcrit_new = maxdistGlobal;
//if (argc>2){
// Rcrit_new = strtod(argv[2],NULL);
// if (rank==0) printf("Max. distance =%f, Initial critical radius = %f \n",maxdistGlobal,Rcrit_new);
//}
while (void_fraction_new > VoidFraction)
{
void_fraction_diff_old = void_fraction_diff_new;
void_fraction_old = void_fraction_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(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) > 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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->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,Dm->Comm);
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;
}
}
}
}
MPI_Allreduce(&count,&countGlobal,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
void_fraction_new = countGlobal/totalGlobal;
void_fraction_diff_new = abs(void_fraction_new-VoidFraction);
if (rank==0){
printf(" %f ",void_fraction_new);
printf(" %f\n",Rcrit_new);
}
}
if (void_fraction_diff_new<void_fraction_diff_old){
final_void_fraction=void_fraction_new;
if (rank==0){
printf("Final void fraction =%f\n",void_fraction_new);
printf("Final critical radius=%f\n",Rcrit_new);
}
}
else{
final_void_fraction=void_fraction_old;
if (rank==0){
printf("Final void fraction=%f\n",void_fraction_old);
printf("Final critical radius=%f\n",Rcrit_old);
}
}
return final_void_fraction;
}
double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id, std::shared_ptr<Domain> Dm, double TargetGrowth){
int Nx = Dm->Nx;
int Ny = Dm->Ny;
int Nz = Dm->Nz;
int iproc = Dm->iproc();
int jproc = Dm->jproc();
int kproc = Dm->kproc();
int nprocx = Dm->nprocx();
int nprocy = Dm->nprocy();
int nprocz = Dm->nprocz();
int rank = Dm->rank();
double count=0.0;
for (int k=1; k<Nz-1; k++){
for (int j=1; j<Ny-1; j++){
for (int i=1; i<Nx-1; i++){
if (Dist(i,j,k) < 0.0){
count+=1.0;
}
}
}
}
double count_original=sumReduce( Dm->Comm, count);
// Estimate morph_delta
double morph_delta = 0.0;
if (TargetGrowth > 0.0) morph_delta = 0.1;
else morph_delta = -0.1;
double morph_delta_previous = 0.0;
double GrowthEstimate = 0.0;
double GrowthPrevious = 0.0;
int COUNT_FOR_LOOP = 0;
double ERROR = 100.0;
if (rank == 0) printf("Estimate delta for growth=%f \n",TargetGrowth);
while ( ERROR > 0.01 && COUNT_FOR_LOOP < 10 ){
COUNT_FOR_LOOP++;
count = 0.0;
double MAX_DISPLACEMENT = 0.0;
for (int k=1; k<Nz-1; k++){
for (int j=1; j<Ny-1; j++){
for (int i=1; i<Nx-1; i++){
double walldist=BoundaryDist(i,j,k);
double wallweight = 1.0 / (1+exp(-5.f*(walldist-1.f)));
//wallweight = 1.0;
if (fabs(wallweight*morph_delta) > MAX_DISPLACEMENT) MAX_DISPLACEMENT= fabs(wallweight*morph_delta);
if (Dist(i,j,k) - wallweight*morph_delta < 0.0){
count+=1.0;
}
}
}
}
count=sumReduce( Dm->Comm, count);
MAX_DISPLACEMENT = maxReduce( Dm->Comm, MAX_DISPLACEMENT);
GrowthEstimate = count - count_original;
ERROR = fabs((GrowthEstimate-TargetGrowth) /TargetGrowth);
if (rank == 0) printf(" delta=%f, growth=%f, max. displacement = %f \n",morph_delta, GrowthEstimate, MAX_DISPLACEMENT);
// Now adjust morph_delta
double step_size = (TargetGrowth - GrowthEstimate)*(morph_delta - morph_delta_previous) / (GrowthEstimate - GrowthPrevious);
GrowthPrevious = GrowthEstimate;
morph_delta_previous = morph_delta;
morph_delta += step_size;
if (morph_delta / morph_delta_previous > 2.0 ) morph_delta = morph_delta_previous*2.0;
//MAX_DISPLACEMENT *= max(TargetGrowth/GrowthEstimate,1.25);
if (MAX_DISPLACEMENT > 2.0 ){
morph_delta *= 2.0/morph_delta;
//if (COUNT_FOR_LOOP > 2) COUNT_FOR_LOOP = 100;
COUNT_FOR_LOOP = 100; // exit loop if displacement is too large
}
}
if (rank == 0) printf("Final delta=%f \n",morph_delta);
count = 0.0;
for (int k=1; k<Nz-1; k++){
for (int j=1; j<Ny-1; j++){
for (int i=1; i<Nx-1; i++){
double walldist=BoundaryDist(i,j,k);
double wallweight = 1.0 / (1+exp(-5.f*(walldist-1.f)));
//wallweight = 1.0;
Dist(i,j,k) -= wallweight*morph_delta;
if (Dist(i,j,k) < 0.0) count+=1.0;
}
}
}
count=sumReduce( Dm->Comm, count);
return count;
}
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