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use FOM morphology

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This commit is contained in:
James McClure
2021-01-04 22:30:05 -05:00
parent 2f5fc9ead1
commit 00e6d0f2da
1 changed files with 26 additions and 27 deletions
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53
analysis/morphology.cpp
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@@ -58,11 +58,11 @@ double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain>
}
}
}
MPI_Barrier(Dm->Comm);
Dm->Comm.barrier();
// 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);
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);
@@ -131,9 +131,8 @@ double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain>
// 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=0.0;
double Rcrit_old;
double GlobalNumber = 1.f;
int imin,jmin,kmin,imax,jmax,kmax;
if (ErodeLabel == 1){
@@ -220,7 +219,7 @@ double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain>
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);
@@ -241,7 +240,7 @@ double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain>
UnpackID(Dm->recvList("YZ"), Dm->recvCount("YZ") ,recvID_YZ, id);
//......................................................................................
MPI_Allreduce(&LocalNumber,&GlobalNumber,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
//double GlobalNumber = Dm->Comm.sumReduce( LocalNumber );
count = 0.f;
for (int k=1; k<Nz-1; k++){
@@ -254,7 +253,7 @@ double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain>
}
}
}
MPI_Allreduce(&count,&countGlobal,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
countGlobal = Dm->Comm.sumReduce( count );
void_fraction_new = countGlobal/totalGlobal;
void_fraction_diff_new = abs(void_fraction_new-VoidFraction);
/* if (rank==0){
@@ -286,7 +285,7 @@ double morph_open()
fillHalo<char> fillChar(Dm->Comm,Dm->rank_info,{Nx-2,Ny-2,Nz-2},{1,1,1},0,1);
MPI_Allreduce(&LocalNumber,&GlobalNumber,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
GlobalNumber = Dm->Comm.sumReduce( LocalNumber );
count = 0.f;
for (int k=1; k<Nz-1; k++){
@@ -299,7 +298,7 @@ double morph_open()
}
}
}
MPI_Allreduce(&count,&countGlobal,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
countGlobal = Dm->Comm.sumReduce( count );
return countGlobal;
}
*/
@@ -342,11 +341,11 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
}
}
MPI_Barrier(Dm->Comm);
Dm->Comm.barrier();
// 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);
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);
@@ -416,7 +415,6 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
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;
@@ -424,7 +422,7 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
// Rcrit_new = strtod(argv[2],NULL);
// if (rank==0) printf("Max. distance =%f, Initial critical radius = %f \n",maxdistGlobal,Rcrit_new);
//}
MPI_Barrier(Dm->Comm);
Dm->Comm.barrier();
FILE *DRAIN = fopen("morphdrain.csv","w");
@@ -528,7 +526,7 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
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);
// double GlobalNumber = Dm->Comm.sumReduce( LocalNumber );
for (int k=0; k<nz; k++){
for (int j=0; j<ny; j++){
@@ -547,7 +545,7 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
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(Dm->Comm);
Dm->Comm.barrier();
for (int k=0; k<nz; k++){
for (int j=0; j<ny; j++){
@@ -583,7 +581,7 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
}
ComputeGlobalBlobIDs(nx-2,ny-2,nz-2,Dm->rank_info,phase,SignDist,vF,vS,phase_label,Dm->Comm);
MPI_Barrier(Dm->Comm);
Dm->Comm.barrier();
for (int k=1; k<nz-1; k++){
for (int j=1; j<ny-1; j++){
@@ -609,7 +607,7 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
}
}
}
MPI_Allreduce(&count,&countGlobal,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
countGlobal = Dm->Comm.sumReduce( count );
void_fraction_new = countGlobal/totalGlobal;
void_fraction_diff_new = abs(void_fraction_new-VoidFraction);
if (rank==0){
@@ -649,13 +647,13 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
return final_void_fraction;
}
double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id, std::shared_ptr<Domain> Dm, double TargetGrowth, double WallFactor)
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 rank = Dm->rank();
double count=0.0;
for (int k=1; k<Nz-1; k++){
for (int j=1; j<Ny-1; j++){
@@ -666,7 +664,7 @@ double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id,
}
}
}
double count_original=sumReduce( Dm->Comm, count);
double count_original = Dm->Comm.sumReduce( count);
// Estimate morph_delta
double morph_delta = 0.0;
@@ -686,7 +684,8 @@ double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id,
for (int j=1; j<Ny-1; j++){
for (int i=1; i<Nx-1; i++){
double walldist=BoundaryDist(i,j,k);
double wallweight = WallFactor/ (1+exp(-5.f*(walldist-1.f)));
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){
@@ -695,8 +694,8 @@ double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id,
}
}
}
count=sumReduce( Dm->Comm, count);
MAX_DISPLACEMENT = maxReduce( Dm->Comm, MAX_DISPLACEMENT);
count = Dm->Comm.sumReduce( count );
MAX_DISPLACEMENT = Dm->Comm.maxReduce( MAX_DISPLACEMENT );
GrowthEstimate = count - count_original;
ERROR = fabs((GrowthEstimate-TargetGrowth) /TargetGrowth);
@@ -732,14 +731,14 @@ double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id,
for (int j=1; j<Ny-1; j++){
for (int i=1; i<Nx-1; i++){
double walldist=BoundaryDist(i,j,k);
double wallweight = WallFactor / (1+exp(-5.f*(walldist-1.f)));
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);
count = Dm->Comm.sumReduce( count );
return count;
}