Merge branch 'master' of github.com:JamesEMcClure/LBPM-WIA

analysis/analysis.cpp

@@ -515,7 +515,7 @@ static int LocalToGlobalIDs( int nx, int ny, int nz, const RankInfoStruct& rank_
     for (size_t i=0; i<LocalIDs.length(); i++) {
         if ( LocalIDs(i)>=0 ) {
             local.insert(LocalIDs(i));
-            if ( LocalIDs(i)!=IDs(i) )
+            if ( LocalIDs(i)!=IDs(i) && IDs(i)>= 0)
                 map[LocalIDs(i)].remote_ids.insert(IDs(i));
         }
     }

example/CMakeLists.txt

@@ -1,6 +1,7 @@
 # Copy the examples to the install folder
 INSTALL_EXAMPLE( Bubble )
 INSTALL_EXAMPLE( ConstrainedBubble )
+INSTALL_EXAMPLE( Piston )
 INSTALL_EXAMPLE( Sph1896 )
 
 # Create unit tests for each example

example/Piston/Color.in

@@ -1,4 +1,4 @@
-0.7
+1.0
 1.0e-2 0.95 -0.7
 0.7
 0.0 0.0 0.0

example/Piston/Domain.in

@@ -1,4 +1,4 @@
-1 1 4
+1 1 10
-100 100 100
+40 40 40
 229
 1.0 1.0 1.0

example/Piston/Piston.sh

@@ -1,27 +1,37 @@
 #!/bin/bash
 
-# This runscript is for the Virginia Tech supercomputer HokieSpeed
+# Lines assigning various pressure BC for Color.in
-#PBS -l walltime=72:00:00
+echo "0 1 1.01 0.99" > Color.in.pressures
-# Set the number of nodes, and the number of processors per node (generally should be 6)
+echo "0 1 1.0125 0.9875" >> Color.in.pressures
-#PBS -l nodes=1:ppn=12
+echo "0 1 1.015 0.985" >> Color.in.pressures
-##PBS -l nodes=hs195
+echo "0 1 1.02 0.98" >> Color.in.pressures
-#PBS -A arcadm
+echo "0 1 1.025 0.975" >> Color.in.pressures
-# Access group, queue, and accounting project
+echo "0 1 1.03 0.97" >> Color.in.pressures
-#PBS -W group_list=arcadm
-#PBS -q large_q
 
-module purge
+for i in `seq 1 6`; do 
-module load gcc cuda mvapich2/1.9rc1
+    # Set up cases for each boundary pressure pair
+    dir="Case"$i
+    echo $dir
+    mkdir -p $dir
+    # copy the domain file
+    cp Domain.in $dir
 
-cd $PBS_O_WORKDIR
+    # set up each case -- parameters are fixed in Color.in, with multiple cases to set the boundary pressure
+    sed -n '1p' Color.in > $dir/Color.in
+    sed -n '2p' Color.in >> $dir/Color.in
+    sed -n '3p' Color.in >> $dir/Color.in
+    sed -n '4p' Color.in >> $dir/Color.in
+#    sed -n '5p' Color.in >> $dir/Color.in
+    # print the pressure values into the input file
+    sed -n "${i}p" Color.in.pressures >> $dir/Color.in
+    sed -n '6p' Color.in >> $dir/Color.in
 
-cat $PBS_NODEFILE > hostfile
+done
 
-echo "------------------------------------------"
+# simulations should be run using the following syntax
-echo "Running LBM using MPI!" 
+# PRE-PROCESSOR - set the radius to 18 voxel lengths
-echo "Number of processors = " $PBS_NP
+#mpirun -np 10 ~/install-LBPM-WIA/bin/lbpm_captube_pp 18 1
-echo "------------------------------------------"
+# RUN THE SIMULAUTION 
-
+#mpirun -np 10 ~/install-LBPM-WIA/bin/lbpm_color_simulator
-mpirun -np 4 ~/install-LBPM-WIA/bin/lb2_Color_wia_mpi >
 
 exit;

example/Piston/README.piston

@@ -0,0 +1,8 @@
+# This test case sets up a piston displacment example
+# The case is intended to:
+
+1. Verify that the interface and common curve are computed accurately. 
+
+2. Measure the dynamic contact angle and compare to known relationships
+
+Example input files are provided. 

tests/CMakeLists.txt

@@ -7,6 +7,7 @@ INSTALL_LBPM_EXE( lbpm_random_pp )
 INSTALL_LBPM_EXE( lbpm_segmented_pp )
 INSTALL_LBPM_EXE( lbpm_segmented_decomp )
 INSTALL_LBPM_EXE( lbpm_disc_pp )
+INSTALL_LBPM_EXE( lbpm_captube_pp )
 INSTALL_LBPM_EXE( lbpm_BlobAnalysis )
 INSTALL_LBPM_EXE( TestBubble )
 INSTALL_LBPM_EXE( BasicSimulator )

tests/lbpm_captube_pp.cpp

@@ -0,0 +1,217 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/stat.h>
+#include <iostream>
+#include <exception>
+#include <stdexcept>
+#include <fstream>
+
+#include "ScaLBL.h"
+#include "Communication.h"
+#include "TwoPhase.h"
+#include "common/MPI_Helpers.h"
+
+int main(int argc, char **argv)
+{
+	//*****************************************
+	// ***** MPI STUFF ****************
+	//*****************************************
+	// Initialize MPI
+	int rank,nprocs;
+	MPI_Init(&argc,&argv);
+	MPI_Comm_rank(MPI_COMM_WORLD,&rank);
+	MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
+	// parallel domain size (# of sub-domains)
+	int nprocx,nprocy,nprocz;
+	int iproc,jproc,kproc;
+	int sendtag,recvtag;
+	//*****************************************
+	// MPI ranks for all 18 neighbors
+	//**********************************
+	int rank_x,rank_y,rank_z,rank_X,rank_Y,rank_Z;
+	int rank_xy,rank_XY,rank_xY,rank_Xy;
+	int rank_xz,rank_XZ,rank_xZ,rank_Xz;
+	int rank_yz,rank_YZ,rank_yZ,rank_Yz;
+	//**********************************
+	MPI_Request req1[18],req2[18];
+	MPI_Status stat1[18],stat2[18];
+
+	double TubeRadius =15.0;
+	int BC;
+	TubeRadius=strtod(argv[1],NULL);
+	BC=atoi(argv[2]);
+
+	if (rank == 0){
+		printf("********************************************************\n");
+		printf("Generate 3D cylindrical capillary tube geometry with radius = %f voxels \n",TubeRadius);
+		printf("********************************************************\n");
+	}
+
+	// Variables that specify the computational domain  
+	string FILENAME;
+	int Nx,Ny,Nz;		// local sub-domain size
+	int nspheres;		// number of spheres in the packing
+	double Lx,Ly,Lz;	// Domain length
+	int i,j,k,n;
+
+	// pmmc threshold values
+	double fluid_isovalue,solid_isovalue;
+	fluid_isovalue = 0.0;
+	solid_isovalue = 0.0;
+
+	if (rank==0){
+		//.......................................................................
+		// Reading the domain information file
+		//.......................................................................
+		ifstream domain("Domain.in");
+		domain >> nprocx;
+		domain >> nprocy;
+		domain >> nprocz;
+		domain >> Nx;
+		domain >> Ny;
+		domain >> Nz;
+		domain >> nspheres;
+		domain >> Lx;
+		domain >> Ly;
+		domain >> Lz;
+		//.......................................................................
+	}
+	// **************************************************************
+	// Broadcast simulation parameters from rank 0 to all other procs
+	MPI_Barrier(MPI_COMM_WORLD);
+	// Computational domain
+	MPI_Bcast(&Nx,1,MPI_INT,0,MPI_COMM_WORLD);
+	MPI_Bcast(&Ny,1,MPI_INT,0,MPI_COMM_WORLD);
+	MPI_Bcast(&Nz,1,MPI_INT,0,MPI_COMM_WORLD);
+	MPI_Bcast(&nprocx,1,MPI_INT,0,MPI_COMM_WORLD);
+	MPI_Bcast(&nprocy,1,MPI_INT,0,MPI_COMM_WORLD);
+	MPI_Bcast(&nprocz,1,MPI_INT,0,MPI_COMM_WORLD);
+	MPI_Bcast(&nspheres,1,MPI_INT,0,MPI_COMM_WORLD);
+	MPI_Bcast(&Lx,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
+	MPI_Bcast(&Ly,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
+	MPI_Bcast(&Lz,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
+	//.................................................
+	MPI_Barrier(MPI_COMM_WORLD);
+	
+	// **************************************************************
+	if (nprocs != nprocx*nprocy*nprocz){
+		printf("nprocx =  %i \n",nprocx);
+		printf("nprocy =  %i \n",nprocy);
+		printf("nprocz =  %i \n",nprocz);
+		INSIST(nprocs == nprocx*nprocy*nprocz,"Fatal error in processor count!");
+	}
+
+	if (rank==0){
+		printf("********************************************************\n");
+		printf("Sub-domain size = %i x %i x %i\n",Nz,Nz,Nz);
+		printf("Parallel domain size = %i x %i x %i\n",nprocx,nprocy,nprocz);
+		printf("********************************************************\n");
+	}
+
+	// Initialized domain and averaging framework for Two-Phase Flow
+	Domain Dm(Nx,Ny,Nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BC);
+	Dm.CommInit(MPI_COMM_WORLD);
+	TwoPhase Averages(Dm);
+
+	InitializeRanks( rank, nprocx, nprocy, nprocz, iproc, jproc, kproc,
+			 	 	 rank_x, rank_y, rank_z, rank_X, rank_Y, rank_Z,
+			 	 	 rank_xy, rank_XY, rank_xY, rank_Xy, rank_xz, rank_XZ, rank_xZ, rank_Xz,
+			 	 	 rank_yz, rank_YZ, rank_yZ, rank_Yz );
+	 
+	MPI_Barrier(MPI_COMM_WORLD);
+
+	Nz += 2;
+	Nx = Ny = Nz;	// Cubic domain
+
+	int N = Nx*Ny*Nz;
+	int dist_mem_size = N*sizeof(double);
+
+	//.......................................................................
+	// Filenames used
+	char LocalRankString[8];
+	char LocalRankFilename[40];
+	char LocalRestartFile[40];
+	char tmpstr[10];
+	sprintf(LocalRankString,"%05d",rank);
+	sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
+	sprintf(LocalRestartFile,"%s%s","Restart.",LocalRankString);
+	
+//	printf("Local File Name =  %s \n",LocalRankFilename);
+	// .......... READ THE INPUT FILE .......................................
+//	char value;
+	char *id;
+	id = new char[N];
+	int sum = 0;
+	double sum_local;
+	double iVol_global = 1.0/(1.0*(Nx-2)*(Ny-2)*(Nz-2)*nprocs);
+	//if (pBC) iVol_global = 1.0/(1.0*(Nx-2)*nprocx*(Ny-2)*nprocy*((Nz-2)*nprocz-6));
+	double porosity, pore_vol;
+
+	// Initializes a constrained bubble test
+	double BubbleBot = 20.0;  // How big to make the NWP bubble
+	double BubbleTop = 60.0;  // How big to make the NWP bubble
+	//double TubeRadius = 15.5; // Radius of the capillary tube
+	sum=0;
+	for (k=0;k<Nz;k++){
+		for (j=0;j<Ny;j++){
+			for (i=0;i<Nx;i++){
+				n = k*Nx*Ny + j*Nz + i;
+				// Cylindrical capillary tube aligned with the z direction
+				Averages.SDs(i,j,k) = TubeRadius-sqrt(1.0*((i-Nx/2)*(i-Nx/2)
+									+ (j-Ny/2)*(j-Ny/2)));
+				// Initialize phase positions field
+				if (Averages.SDs(i,j,k) < 0.0){
+					id[n] = 0;
+				}
+	/*			else if (k<BubbleBot){
+					id[n] = 2;
+					sum++;
+				}
+				else if (k<BubbleTop && rank == 0 && pBC == 0){
+					id[n] = 1;
+					sum++;
+				}
+*/
+				else{
+					id[n] = 2;
+					sum++;
+				}
+			}
+		}
+	}
+	porosity = double(sum)/double(1.0*N);
+	// Compute the pore volume
+	sum_local = 0.0;
+	for ( k=1;k<Nz-1;k++){
+		for ( j=1;j<Ny-1;j++){
+			for ( i=1;i<Nx-1;i++){
+				n = k*Nx*Ny+j*Nx+i;
+				if (id[n] > 0){
+					sum_local += 1.0;
+				}
+			}
+		}
+	}
+	MPI_Allreduce(&sum_local,&pore_vol,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
+
+	//.........................................................
+	// don't perform computations at the eight corners
+	id[0] = id[Nx-1] = id[(Ny-1)*Nx] = id[(Ny-1)*Nx + Nx-1] = 0;
+	id[(Nz-1)*Nx*Ny] = id[(Nz-1)*Nx*Ny+Nx-1] = id[(Nz-1)*Nx*Ny+(Ny-1)*Nx] = id[(Nz-1)*Nx*Ny+(Ny-1)*Nx + Nx-1] = 0;
+	//.........................................................
+
+    sprintf(LocalRankFilename,"SignDist.%05i",rank);
+    FILE *DIST = fopen(LocalRankFilename,"wb");
+    fwrite(Averages.SDs.get(),8,Averages.SDs.length(),DIST);
+    fclose(DIST);
+
+	sprintf(LocalRankFilename,"ID.%05i",rank);
+	FILE *ID = fopen(LocalRankFilename,"wb");
+	fwrite(id,1,N,ID);
+	fclose(ID);
+
+	// ****************************************************
+	MPI_Barrier(MPI_COMM_WORLD);
+	MPI_Finalize();
+	// ****************************************************
+}

tests/lbpm_segmented_pp.cpp

@@ -144,7 +144,7 @@ int main(int argc, char **argv)
 	MeanFilter(Averages.SDs);
 
 	if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
-	SSO(Averages.SDs,id,Dm,20);
+	SSO(Averages.SDs,id,Dm,25);
 
     sprintf(LocalRankFilename,"SignDist.%05i",rank);
     FILE *DIST = fopen(LocalRankFilename,"wb");
@@ -175,18 +175,13 @@ int main(int argc, char **argv)
 	MeanFilter(Averages.Phase);
 
 	if (rank==0) printf("Initialized non-wetting phase -- Converting to Signed Distance function \n");
-	SSO(Averages.Phase,id,Dm,20);
+	SSO(Averages.Phase,id,Dm,25);
 
-    sprintf(LocalRankFilename,"Phase.%05i",rank);
-    FILE *PHASE = fopen(LocalRankFilename,"wb");
-    fwrite(Averages.Phase.get(),8,Averages.Phase.length(),PHASE);
-    fclose(PHASE);
-/*
 	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;
-				Averages.Phase(i,j,k) += 1.0;
+				Averages.Phase(i,j,k) -= 1.0;
 				if (Averages.SDs(i,j,k) > 0.0){
 					if (Averages.Phase(i,j,k) > 0.0){
 						Dm.id[n] = 2;
@@ -200,7 +195,7 @@ int main(int argc, char **argv)
 				}
 				// Initialize distance to +/- 1
 				// Dilation of the non-wetting phase
-				Averages.SDn(i,j,k) = Averages.Phase(i,j,k)+1.0;
+				Averages.SDn(i,j,k) = -Averages.Phase(i,j,k);
 				Averages.Phase(i,j,k) = Averages.SDn(i,j,k);
 				Averages.Phase_tplus(i,j,k) = Averages.SDn(i,j,k);
 				Averages.Phase_tminus(i,j,k) = Averages.SDn(i,j,k);
@@ -213,91 +208,30 @@ int main(int argc, char **argv)
 		}
 	}
 
+
+    sprintf(LocalRankFilename,"Phase.%05i",rank);
+    FILE *PHASE = fopen(LocalRankFilename,"wb");
+    fwrite(Averages.Phase.get(),8,Averages.Phase.length(),PHASE);
+    fclose(PHASE);
+
 	double vF,vS;
 	vF = vS = 0.0;
 
     double beta = 0.95;
 	if (rank==0) printf("initializing the system \n");
-    Averages.SetupCubes(Dm);
     Averages.UpdateSolid();
-    Averages.Initialize();
     Averages.UpdateMeshValues();
     Dm.CommunicateMeshHalo(Averages.Phase);
     Dm.CommunicateMeshHalo(Averages.SDn);
+    Dm.CommunicateMeshHalo(Averages.SDs);
 
-	if (rank==0) printf("computing blobs \n");
+	int timestep=5;
- //   int nblobs_global = ComputeGlobalBlobIDs(Dm.Nx-2,Dm.Ny-2,Dm.Nz-2,Dm.rank_info,
+	Averages.Initialize();
-  //  		Averages.Phase,Averages.SDs,vF,vS,Averages.BlobLabel);
+	if (rank==0) printf("computing phase components \n");
-//	if (Dm.rank==0) printf("Number of blobs is %i \n",nblobs_global);
+	Averages.ComponentAverages();
-
+	if (rank==0) printf("sorting phase components \n");
-//     int nblobs_global = ComputeGlobalBlobIDs(Dm.Nx-2,Dm.Ny-2,Dm.Nz-2,Dm.rank_info,
+	Averages.SortBlobs();
-//					 Averages.SDn,Averages.SDs,vF,vS,Averages.BlobLabel);
+	Averages.PrintComponents(timestep);
-
-	if (rank==0) printf("computing local averages  \n");
-	Averages.ComputeLocalBlob();
-	if (rank==0) printf("reducing averages  \n");
-	Averages.Reduce();
-
-	if (rank==0) printf("Writing blobs \n");
-    // Write the local blob ids
-    sprintf(LocalRankFilename,"BlobLabel.%05i",rank);
-    FILE *BLOBLOCAL = fopen(LocalRankFilename,"wb");
-    fwrite(Averages.BlobLabel.get(),4,Averages.BlobLabel.length(),BLOBLOCAL);
-    fclose(BLOBLOCAL);
-    printf("Wrote BlobLabel.%05i \n",rank);
-
-	if (rank==0) printf("Sorting averages \n");
-    //  Blobs.Set(Averages.BlobAverages.NBLOBS);
-    int dimx = (int)Averages.BlobAverages.size(0);
-    int dimy = (int)Averages.BlobAverages.size(1);
-    int TotalBlobInfoSize=dimx*dimy;
-
-    //      BlobContainer Blobs;
-    DoubleArray RecvBuffer(dimx);
-    //    MPI_Allreduce(&Averages.BlobAverages.get(),&Blobs.get(),1,MPI_DOUBLE,MPI_SUM,Dm.Comm);
-    MPI_Barrier(MPI_COMM_WORLD);
-    if (rank==0) printf("Number of components is %i \n",dimy);
-
-    for (int b=0; b<dimy; b++){
-
-    	MPI_Allreduce(&Averages.BlobAverages(0,b),&RecvBuffer(0),dimx,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
-    	for (int idx=0; idx<dimx-1; idx++) Averages.BlobAverages(idx,b)=RecvBuffer(idx);
-    	MPI_Barrier(MPI_COMM_WORLD);
-
-    	if (Averages.BlobAverages(0,b) > 0.0){
-    		double Vn,pn,awn,ans,Jwn,Kwn,lwns,cwns,trawn,trJwn;
-    		Vn = Averages.BlobAverages(1,b);
-    		pn = Averages.BlobAverages(2,b)/Averages.BlobAverages(0,b);
-    		awn = Averages.BlobAverages(3,b);
-    		ans = Averages.BlobAverages(4,b);
-    		if (awn != 0.0){
-    			Jwn = Averages.BlobAverages(5,b)/Averages.BlobAverages(3,b);
-    			Kwn = Averages.BlobAverages(6,b)/Averages.BlobAverages(3,b);
-    		}
-    		else Jwn=Kwn=0.0;
-
-    		trawn = Averages.BlobAverages(12,b);
-    		if (trawn != 0.0){
-    			trJwn = Averages.BlobAverages(13,b)/trawn;
-    		}
-    		else trJwn=0.0;
-
-    		lwns = Averages.BlobAverages(7,b);
-    		if (lwns != 0.0) cwns = Averages.BlobAverages(8,b)/Averages.BlobAverages(7,b);
-    		else  cwns=0.0;
-    		Averages.BlobAverages(2,b) = pn;
-    		Averages.BlobAverages(5,b) = trJwn;
-    		Averages.BlobAverages(6,b) = Kwn;
-    		Averages.BlobAverages(8,b) = cwns;
-    		//	Averages.BlobAverages(13,b) = trJwn;
-    	}
-    }
-
-    if (rank==0) printf("Sorting blobs by volume \n");
-    Averages.SortBlobs();
-
-    if (rank==0)   WriteBlobs(Averages);
-    */
 
     MPI_Barrier(MPI_COMM_WORLD);
 	MPI_Finalize();