From 5ccb06646d39106c02dc40018a80a0e33cade52b Mon Sep 17 00:00:00 2001
From: James E McClure <jemcclur@gmail.com>
Date: Wed, 20 Feb 2019 18:33:41 -0500
Subject: [PATCH] refactor morphdrain pp

---
 tests/lbpm_morphdrain_pp.cpp | 368 +++++++----------------------------
 1 file changed, 73 insertions(+), 295 deletions(-)

diff --git a/tests/lbpm_morphdrain_pp.cpp b/tests/lbpm_morphdrain_pp.cpp
index 70798e88..3ca4c7a9 100644
--- a/tests/lbpm_morphdrain_pp.cpp
+++ b/tests/lbpm_morphdrain_pp.cpp
@@ -134,6 +134,8 @@ int main(int argc, char **argv)
 	// 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);
 
 	// Solve for the position of the solid phase
 	for (int k=0;k<nz;k++){
@@ -160,318 +162,94 @@ int main(int argc, char **argv)
 	if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
 	CalcDist(SignDist,id_solid,Dm);
 
-/*	// 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);
+	// 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;
+				if (id[n] == 1){
+					phase(i,j,k) = 1.0;
+				}
+				else
+					phase(i,j,k) = -1.0;
+			}
+		}
+	}
 	
-	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
+	// 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;
-					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);
-			        }
+	// 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);
 			}
 		}
-	}
-
-	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;
-										}
-									}
-								}
+		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;
 							}
 						}
-						// 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);
-
-        }
-    }
-
 	sprintf(LocalRankFilename,"ID.%05i",rank);
 	FILE *ID = fopen(LocalRankFilename,"wb");
 	fwrite(id,1,N,ID);