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

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This commit is contained in:
James E McClure
2017-08-13 15:04:12 -04:00
parent faf44b3a20 a114d88ed4
commit ee3607224c
8 changed files with 246 additions and 31 deletions
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5
common/Domain.h
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@@ -667,8 +667,8 @@ inline double Eikonal(DoubleArray &Distance, char *ID, Domain &Dm, int timesteps
int n = k*Dm.Nx*Dm.Ny + j*Dm.Nx + i;
sign = -1;
if (ID[n] == 1) sign = 1;
sign = 1;
if (ID[n] == 0) sign = -1;
// local second derivative terms
Dxxp = minmod(Dxx(i,j,k),Dxx(i+1,j,k));
@@ -740,6 +740,7 @@ inline double Eikonal(DoubleArray &Distance, char *ID, Domain &Dm, int timesteps
GlobalVar /= (Dm.Nx-2)*(Dm.Ny-2)*(Dm.Nz-2)*Dm.nprocx*Dm.nprocy*Dm.nprocz;
count++;
if (count%50 == 0 && Dm.rank==0 )
printf("Time=%i, Max variation=%f, Global variation=%f \n",count,GlobalMax,GlobalVar);

47
common/TwoPhase.cpp
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@@ -196,7 +196,7 @@ TwoPhase::~TwoPhase()
void TwoPhase::ColorToSignedDistance(double Beta, DoubleArray &ColorData, DoubleArray &DistData)
{
/* double factor,temp,value;
double factor,temp,value;
factor=0.5/Beta;
// Initialize to -1,1 (segmentation)
for (int k=0; k<Nz; k++){
@@ -205,42 +205,51 @@ void TwoPhase::ColorToSignedDistance(double Beta, DoubleArray &ColorData, Double
value = ColorData(i,j,k);
// Set phase ID field for non-wetting phase
// here NWP is tagged with 1
// all other phases tagged with 0
int n = k*Nx*Ny+j*Nx+i;
if (value > 0) TempID[n] = 1;
else TempID[n] = 0;
else TempID[n] = 0;
//temp = factor*log((1.0+value)/(1.0-value));
//if (value > 0.8) DistData(i,j,k) = 2.94*factor;
//else if (value < -0.8) DistData(i,j,k) = -2.94*factor;
//else DistData(i,j,k) = temp;
// Distance threshhold
// temp -- distance based on analytical form McClure, Prins et al, Comp. Phys. Comm.
// distance should be negative outside the NWP
// distance should be positive inside of the NWP
temp = factor*log((1.0+value)/(1.0-value));
if (value > 0.8) DistData(i,j,k) = 2.94*factor;
else if (value < -0.8) DistData(i,j,k) = -2.94*factor;
else DistData(i,j,k) = temp;
// Basic threshold
//if (value > 0) DistData(i,j,k) = 1.0;
//else DistData(i,j,k) = -1.0;
// distance to the NWP
// negative inside NWP, positive outside
//if (value > 0) DistData(i,j,k) = -0.5;
//else DistData(i,j,k) = 0.5;
// Initialize directly
DistData(i,j,k) = value;
// DistData(i,j,k) = value;
}
}
}
SSO(DistData,TempID,Dm,160);
Eikonal(DistData,TempID,Dm,50);
for (int k=0; k<Nz; k++){
for (int j=0; j<Ny; j++){
for (int i=0; i<Nx; i++){
DistData(i,j,k) += 2.0;
}
}
for (int k=0; k<Nz; k++){
for (int j=0; j<Ny; j++){
for (int i=0; i<Nx; i++){
DistData(i,j,k) += 1.0;
}
}
}
*/
for (int k=0; k<Nz; k++){
/* for (int k=0; k<Nz; k++){
for (int j=0; j<Ny; j++){
for (int i=0; i<Nx; i++){
DistData(i,j,k) = ColorData(i,j,k);
}
}
}
*/
}

1
tests/CMakeLists.txt
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@@ -14,6 +14,7 @@ ADD_LBPM_EXECUTABLE( lbpm_serial_decomp )
ADD_LBPM_EXECUTABLE( lbpm_disc_pp )
ADD_LBPM_EXECUTABLE( lbpm_juanes_bench_disc_pp )
ADD_LBPM_EXECUTABLE( lbpm_captube_pp )
ADD_LBPM_EXECUTABLE( lbpm_plates_pp )
ADD_LBPM_EXECUTABLE( lbpm_squaretube_pp )
ADD_LBPM_EXECUTABLE( lbpm_BlobAnalysis )
ADD_LBPM_EXECUTABLE( TestBubble )

4
tests/TestSegDist.cpp
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@@ -102,7 +102,7 @@ int main(int argc, char **argv)
for (i=0;i<nx;i++){
n=k*nx*ny+j*nx+i;
// Initialize distance to +/- 1
Distance(i,j,k) = 2.0*id[n]-1.0;
Distance(i,j,k) = 1.0*id[n]-0.5;
}
}
}
@@ -113,7 +113,7 @@ int main(int argc, char **argv)
MPI_Barrier(comm);
if (rank==0) printf("Initialized! Converting to Signed Distance function \n");
SSO(Distance,id,Dm,10);
Eikonal(Distance,id,Dm,10);
double Error=0.0;
int Count = 0;

2
tests/lbpm_color_simulator.cpp
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@@ -612,7 +612,7 @@ int main(int argc, char **argv)
MPI_Barrier(comm);
//.......................................................................
// Once phase has been initialized, map solid to account for 'smeared' interface
for (i=0; i<N; i++) Averages->SDs(i) -= (1.0);
//for (i=0; i<N; i++) Averages->SDs(i) -= (1.0);
// Make sure the id match for the two domains
for (i=0; i<N; i++) Dm.id[i] = Mask.id[i];
//.......................................................................

6
tests/lbpm_morphdrain_pp.cpp
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@@ -236,9 +236,9 @@ int main(int argc, char **argv)
double count,countGlobal,totalGlobal;
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++){
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{

8
tests/lbpm_morphopen_pp.cpp
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@@ -139,16 +139,16 @@ int main(int argc, char **argv)
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);
if (ReadSignDist != size_t(N)) printf("lbpm_morphopen_pp: Error reading signed distance function (rank=%i)\n",rank);
fclose(DIST);
double count,countGlobal,totalGlobal;
count = 0.f;
double maxdist=0.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++){
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{

204
tests/lbpm_plates_pp.cpp Normal file
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@@ -0,0 +1,204 @@
#include <stdio.h>
#include <stdlib.h>
#include <sys/stat.h>
#include <iostream>
#include <exception>
#include <stdexcept>
#include <fstream>
#include "common/ScaLBL.h"
#include "common/Communication.h"
#include "common/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 comm = MPI_COMM_WORLD;
MPI_Comm_rank(comm,&rank);
MPI_Comm_size(comm,&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;
double WIDTH;
TubeRadius=strtod(argv[1],NULL);
WIDTH=strtod(argv[2],NULL);
int BC = 0;
if (rank == 0){
printf("********************************************************\n");
printf("Generate 3D parallel plates 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
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(comm);
// Computational domain
MPI_Bcast(&Nx,1,MPI_INT,0,comm);
MPI_Bcast(&Ny,1,MPI_INT,0,comm);
MPI_Bcast(&Nz,1,MPI_INT,0,comm);
MPI_Bcast(&nprocx,1,MPI_INT,0,comm);
MPI_Bcast(&nprocy,1,MPI_INT,0,comm);
MPI_Bcast(&nprocz,1,MPI_INT,0,comm);
MPI_Bcast(&nspheres,1,MPI_INT,0,comm);
MPI_Bcast(&Lx,1,MPI_DOUBLE,0,comm);
MPI_Bcast(&Ly,1,MPI_DOUBLE,0,comm);
MPI_Bcast(&Lz,1,MPI_DOUBLE,0,comm);
//.................................................
MPI_Barrier(comm);
// **************************************************************
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(comm);
TwoPhase Averages(Dm);
MPI_Barrier(comm);
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 pore_vol;
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)));
// Initialize phase positions
if (Averages.SDs(i,j,k) < 0.0){
id[n] = 0;
}
else if (Averages.SDs(i,j,k) < WIDTH){
id[n] = 2;
sum++;
}
else {
id[n] = 1;
sum++;
}
}
}
}
// 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,comm);
//.........................................................
// 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.data(),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(comm);
MPI_Finalize();
// ****************************************************
}