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LBPM/analysis/morphology.cpp
James McClure d7fc677435 refactor morphology
2021-01-05 16:03:15 -05:00

750 lines
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#include <analysis/morphology.h>
// Implementation of morphological opening routine
inline void PackID(const int *list, int count, signed char *sendbuf, signed 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, signed char *recvbuf, signed 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, signed char *id, std::shared_ptr<Domain> Dm, double VoidFraction, signed char ErodeLabel, signed char NewLabel){
// 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 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 ( id[n] == ErodeLabel){
count += 1.0;
//id[n] = 2;
}
}
}
}
Dm->Comm.barrier();
// 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 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);
final_void_fraction = volume_fraction; //initialize
// Communication buffers
signed char *sendID_x, *sendID_y, *sendID_z, *sendID_X, *sendID_Y, *sendID_Z;
signed char *sendID_xy, *sendID_yz, *sendID_xz, *sendID_Xy, *sendID_Yz, *sendID_xZ;
signed char *sendID_xY, *sendID_yZ, *sendID_Xz, *sendID_XY, *sendID_YZ, *sendID_XZ;
signed char *recvID_x, *recvID_y, *recvID_z, *recvID_X, *recvID_Y, *recvID_Z;
signed char *recvID_xy, *recvID_yz, *recvID_xz, *recvID_Xy, *recvID_Yz, *recvID_xZ;
signed char *recvID_xY, *recvID_yZ, *recvID_Xz, *recvID_XY, *recvID_YZ, *recvID_XZ;
// send buffers
sendID_x = new signed char [Dm->sendCount("x")];
sendID_y = new signed char [Dm->sendCount("y")];
sendID_z = new signed char [Dm->sendCount("z")];
sendID_X = new signed char [Dm->sendCount("X")];
sendID_Y = new signed char [Dm->sendCount("Y")];
sendID_Z = new signed char [Dm->sendCount("Z")];
sendID_xy = new signed char [Dm->sendCount("xy")];
sendID_yz = new signed char [Dm->sendCount("yz")];
sendID_xz = new signed char [Dm->sendCount("xz")];
sendID_Xy = new signed char [Dm->sendCount("Xy")];
sendID_Yz = new signed char [Dm->sendCount("Yz")];
sendID_xZ = new signed char [Dm->sendCount("xZ")];
sendID_xY = new signed char [Dm->sendCount("xY")];
sendID_yZ = new signed char [Dm->sendCount("yZ")];
sendID_Xz = new signed char [Dm->sendCount("Xz")];
sendID_XY = new signed char [Dm->sendCount("XY")];
sendID_YZ = new signed char [Dm->sendCount("YZ")];
sendID_XZ = new signed char [Dm->sendCount("XZ")];
//......................................................................................
// recv buffers
recvID_x = new signed char [Dm->recvCount("x")];
recvID_y = new signed char [Dm->recvCount("y")];
recvID_z = new signed char [Dm->recvCount("z")];
recvID_X = new signed char [Dm->recvCount("X")];
recvID_Y = new signed char [Dm->recvCount("Y")];
recvID_Z = new signed char [Dm->recvCount("Z")];
recvID_xy = new signed char [Dm->recvCount("xy")];
recvID_yz = new signed char [Dm->recvCount("yz")];
recvID_xz = new signed char [Dm->recvCount("xz")];
recvID_Xy = new signed char [Dm->recvCount("Xy")];
recvID_xZ = new signed char [Dm->recvCount("xZ")];
recvID_xY = new signed char [Dm->recvCount("xY")];
recvID_yZ = new signed char [Dm->recvCount("yZ")];
recvID_Yz = new signed char [Dm->recvCount("Yz")];
recvID_Xz = new signed char [Dm->recvCount("Xz")];
recvID_XY = new signed char [Dm->recvCount("XY")];
recvID_YZ = new signed char [Dm->recvCount("YZ")];
recvID_XZ = new signed char [Dm->recvCount("XZ")];
//......................................................................................
int sendtag,recvtag;
sendtag = recvtag = 7;
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;
int imin,jmin,kmin,imax,jmax,kmax;
if (ErodeLabel == 1){
VoidFraction = 1.0 - VoidFraction;
}
double Rcrit_new = maxdistGlobal;
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] == ErodeLabel && dsq <= Rcrit_new*Rcrit_new){
LocalNumber+=1.0;
id[nn]=NewLabel;
}
}
}
}
}
// 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] == ErodeLabel){
count+=1.0;
}
}
}
}
countGlobal = Dm->Comm.sumReduce( count );
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 morph_open()
{
fillHalo<char> fillChar(Dm->Comm,Dm->rank_info,{Nx-2,Ny-2,Nz-2},{1,1,1},0,1);
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 );
return countGlobal;
}
*/
//***************************************************************************************
double MorphDrain(DoubleArray &SignDist, signed 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 nprocx = Dm->nprocx();
int nprocy = Dm->nprocy();
int nprocz = Dm->nprocz();
int rank = Dm->rank();
DoubleArray phase(nx,ny,nz);
IntArray phase_label(nx,ny,nz);
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;
}
}
}
}
Dm->Comm.barrier();
// 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 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
signed char *sendID_x, *sendID_y, *sendID_z, *sendID_X, *sendID_Y, *sendID_Z;
signed char *sendID_xy, *sendID_yz, *sendID_xz, *sendID_Xy, *sendID_Yz, *sendID_xZ;
signed char *sendID_xY, *sendID_yZ, *sendID_Xz, *sendID_XY, *sendID_YZ, *sendID_XZ;
signed char *recvID_x, *recvID_y, *recvID_z, *recvID_X, *recvID_Y, *recvID_Z;
signed char *recvID_xy, *recvID_yz, *recvID_xz, *recvID_Xy, *recvID_Yz, *recvID_xZ;
signed char *recvID_xY, *recvID_yZ, *recvID_Xz, *recvID_XY, *recvID_YZ, *recvID_XZ;
// send buffers
sendID_x = new signed char [Dm->sendCount("x")];
sendID_y = new signed char [Dm->sendCount("y")];
sendID_z = new signed char [Dm->sendCount("z")];
sendID_X = new signed char [Dm->sendCount("X")];
sendID_Y = new signed char [Dm->sendCount("Y")];
sendID_Z = new signed char [Dm->sendCount("Z")];
sendID_xy = new signed char [Dm->sendCount("xy")];
sendID_yz = new signed char [Dm->sendCount("yz")];
sendID_xz = new signed char [Dm->sendCount("xz")];
sendID_Xy = new signed char [Dm->sendCount("Xy")];
sendID_Yz = new signed char [Dm->sendCount("Yz")];
sendID_xZ = new signed char [Dm->sendCount("xZ")];
sendID_xY = new signed char [Dm->sendCount("xY")];
sendID_yZ = new signed char [Dm->sendCount("yZ")];
sendID_Xz = new signed char [Dm->sendCount("Xz")];
sendID_XY = new signed char [Dm->sendCount("XY")];
sendID_YZ = new signed char [Dm->sendCount("YZ")];
sendID_XZ = new signed char [Dm->sendCount("XZ")];
//......................................................................................
// recv buffers
recvID_x = new signed char [Dm->recvCount("x")];
recvID_y = new signed char [Dm->recvCount("y")];
recvID_z = new signed char [Dm->recvCount("z")];
recvID_X = new signed char [Dm->recvCount("X")];
recvID_Y = new signed char [Dm->recvCount("Y")];
recvID_Z = new signed char [Dm->recvCount("Z")];
recvID_xy = new signed char [Dm->recvCount("xy")];
recvID_yz = new signed char [Dm->recvCount("yz")];
recvID_xz = new signed char [Dm->recvCount("xz")];
recvID_Xy = new signed char [Dm->recvCount("Xy")];
recvID_xZ = new signed char [Dm->recvCount("xZ")];
recvID_xY = new signed char [Dm->recvCount("xY")];
recvID_yZ = new signed char [Dm->recvCount("yZ")];
recvID_Yz = new signed char [Dm->recvCount("Yz")];
recvID_Xz = new signed char [Dm->recvCount("Xz")];
recvID_XY = new signed char [Dm->recvCount("XY")];
recvID_YZ = new signed char [Dm->recvCount("YZ")];
recvID_XZ = new signed char [Dm->recvCount("XZ")];
//......................................................................................
int sendtag,recvtag;
sendtag = recvtag = 7;
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;
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);
//}
Dm->Comm.barrier();
FILE *DRAIN = fopen("morphdrain.csv","w");
fprintf(DRAIN,"sw radius\n");
while (void_fraction_new > VoidFraction && Rcrit_new > 0.5)
{
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=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 (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+1)*(Rcrit_new+1)){
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 );
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 (id[n] == 1){
phase(i,j,k) = 1.0;
}
else
phase(i,j,k) = -1.0;
}
}
}
// Extract only the connected part of NWP
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);
Dm->Comm.barrier();
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 (id[n] == 1 && phase_label(i,j,k) > 1){
id[n] = 2;
}
}
}
}
/*
* Extract only the connected part of NWP
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){
phase(i,j,k) = 1.0;
}
else if (id[n] == 1){
// nwp
phase(i,j,k) = -1.0;
}
else{
// treat solid as WP since films can connect
phase(i,j,k) = 1.0;
}
}
}
}
ComputeGlobalBlobIDs(nx-2,ny-2,nz-2,Dm->rank_info,phase,SignDist,vF,vS,phase_label,Dm->Comm);
Dm->Comm.barrier();
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 && phase_label(i,j,k) > 1){
id[n] = 20;
}
}
}
}
// done
*/
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] > 1){
count+=1.0;
}
}
}
}
countGlobal = Dm->Comm.sumReduce( count );
void_fraction_new = countGlobal/totalGlobal;
void_fraction_diff_new = abs(void_fraction_new-VoidFraction);
if (rank==0){
fprintf(DRAIN,"%f ",void_fraction_new);
fprintf(DRAIN,"%f\n",Rcrit_new);
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);
}
}
// label all WP components as 2
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] > 1){
id[n] = 2;
}
}
}
}
return final_void_fraction;
}
//double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id, std::shared_ptr<Domain> Dm, double TargetGrowth)
double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id, std::shared_ptr<Domain> Dm, double TargetGrowth, double WallFactor)
{
int Nx = Dm->Nx;
int Ny = Dm->Ny;
int Nz = Dm->Nz;
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 = Dm->Comm.sumReduce( 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)));
double wallweight = WallFactor/ (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 = Dm->Comm.sumReduce( count );
MAX_DISPLACEMENT = Dm->Comm.maxReduce( 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 (morph_delta > 0.0 ){
// object is growing
if (MAX_DISPLACEMENT > 3.0 ){
morph_delta = 3.0;
COUNT_FOR_LOOP = 100; // exit loop if displacement is too large
}
}
else{
// object is shrinking
if (MAX_DISPLACEMENT > 1.0 ){
morph_delta = -1.0;
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;
double wallweight = WallFactor / (1+exp(-5.f*(walldist-1.f)));
Dist(i,j,k) -= wallweight*morph_delta;
if (Dist(i,j,k) < 0.0) count+=1.0;
}
}
}
count = Dm->Comm.sumReduce( count );
return count;
}
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