Cleaning up lbpm_segmented_pp, remove comments, re-indent,etc.
This commit is contained in:
James E McClure
parent
4fb098c8c0
commit
84d9fed6e7
@ -40,140 +40,141 @@ inline double minmod(double &a, double &b){
|
||||
|
||||
inline double Eikonal(DoubleArray &Distance, char *ID, Domain &Dm, int timesteps){
|
||||
|
||||
/*
|
||||
* This routine converts the data in the Distance array to a signed distance
|
||||
* by solving the equation df/dt = sign(1-|grad f|), where Distance provides
|
||||
* the values of f on the mesh associated with domain Dm
|
||||
* It has been tested with segmented data initialized to values [-1,1]
|
||||
* and will converge toward the signed distance to the surface bounding the associated phases
|
||||
*
|
||||
* Reference:
|
||||
* Min C (2010) On reinitializing level set functions, Journal of Computational Physics 229
|
||||
*/
|
||||
/*
|
||||
* This routine converts the data in the Distance array to a signed distance
|
||||
* by solving the equation df/dt = sign(1-|grad f|), where Distance provides
|
||||
* the values of f on the mesh associated with domain Dm
|
||||
* It has been tested with segmented data initialized to values [-1,1]
|
||||
* and will converge toward the signed distance to the surface bounding the associated phases
|
||||
*
|
||||
* Reference:
|
||||
* Min C (2010) On reinitializing level set functions, Journal of Computational Physics 229
|
||||
*/
|
||||
|
||||
int i,j,k;
|
||||
double dt=0.1;
|
||||
double Dx,Dy,Dz;
|
||||
double Dxp,Dxm,Dyp,Dym,Dzp,Dzm;
|
||||
double Dxxp,Dxxm,Dyyp,Dyym,Dzzp,Dzzm;
|
||||
double sign,norm;
|
||||
double LocalVar,GlobalVar,LocalMax,GlobalMax;
|
||||
int i,j,k;
|
||||
double dt=0.1;
|
||||
double Dx,Dy,Dz;
|
||||
double Dxp,Dxm,Dyp,Dym,Dzp,Dzm;
|
||||
double Dxxp,Dxxm,Dyyp,Dyym,Dzzp,Dzzm;
|
||||
double sign,norm;
|
||||
double LocalVar,GlobalVar,LocalMax,GlobalMax;
|
||||
|
||||
int xdim,ydim,zdim;
|
||||
xdim=Dm.Nx-2;
|
||||
ydim=Dm.Ny-2;
|
||||
zdim=Dm.Nz-2;
|
||||
fillHalo<double> fillData(Dm.Comm, Dm.rank_info,xdim,ydim,zdim,1,1,1,0,1);
|
||||
int xdim,ydim,zdim;
|
||||
xdim=Dm.Nx-2;
|
||||
ydim=Dm.Ny-2;
|
||||
zdim=Dm.Nz-2;
|
||||
fillHalo<double> fillData(Dm.Comm, Dm.rank_info,xdim,ydim,zdim,1,1,1,0,1);
|
||||
|
||||
// Arrays to store the second derivatives
|
||||
DoubleArray Dxx(Dm.Nx,Dm.Ny,Dm.Nz);
|
||||
DoubleArray Dyy(Dm.Nx,Dm.Ny,Dm.Nz);
|
||||
DoubleArray Dzz(Dm.Nx,Dm.Ny,Dm.Nz);
|
||||
// Arrays to store the second derivatives
|
||||
DoubleArray Dxx(Dm.Nx,Dm.Ny,Dm.Nz);
|
||||
DoubleArray Dyy(Dm.Nx,Dm.Ny,Dm.Nz);
|
||||
DoubleArray Dzz(Dm.Nx,Dm.Ny,Dm.Nz);
|
||||
|
||||
int count = 0;
|
||||
while (count < timesteps){
|
||||
int count = 0;
|
||||
while (count < timesteps){
|
||||
|
||||
// Communicate the halo of values
|
||||
fillData.fill(Distance);
|
||||
// Communicate the halo of values
|
||||
fillData.fill(Distance);
|
||||
|
||||
// Compute second order derivatives
|
||||
for (k=1;k<Dm.Nz-1;k++){
|
||||
for (j=1;j<Dm.Ny-1;j++){
|
||||
for (i=1;i<Dm.Nx-1;i++){
|
||||
Dxx(i,j,k) = Distance(i+1,j,k) + Distance(i-1,j,k) - 2*Distance(i,j,k);
|
||||
Dyy(i,j,k) = Distance(i,j+1,k) + Distance(i,j-1,k) - 2*Distance(i,j,k);
|
||||
Dzz(i,j,k) = Distance(i,j,k+1) + Distance(i,j,k-1) - 2*Distance(i,j,k);
|
||||
}
|
||||
}
|
||||
}
|
||||
fillData.fill(Dxx);
|
||||
fillData.fill(Dyy);
|
||||
fillData.fill(Dzz);
|
||||
// Compute second order derivatives
|
||||
for (k=1;k<Dm.Nz-1;k++){
|
||||
for (j=1;j<Dm.Ny-1;j++){
|
||||
for (i=1;i<Dm.Nx-1;i++){
|
||||
Dxx(i,j,k) = Distance(i+1,j,k) + Distance(i-1,j,k) - 2*Distance(i,j,k);
|
||||
Dyy(i,j,k) = Distance(i,j+1,k) + Distance(i,j-1,k) - 2*Distance(i,j,k);
|
||||
Dzz(i,j,k) = Distance(i,j,k+1) + Distance(i,j,k-1) - 2*Distance(i,j,k);
|
||||
}
|
||||
}
|
||||
}
|
||||
fillData.fill(Dxx);
|
||||
fillData.fill(Dyy);
|
||||
fillData.fill(Dzz);
|
||||
|
||||
LocalMax=LocalVar=0.0;
|
||||
// Execute the next timestep
|
||||
for (k=1;k<Dm.Nz-1;k++){
|
||||
for (j=1;j<Dm.Ny-1;j++){
|
||||
for (i=1;i<Dm.Nx-1;i++){
|
||||
LocalMax=LocalVar=0.0;
|
||||
// Execute the next timestep
|
||||
for (k=1;k<Dm.Nz-1;k++){
|
||||
for (j=1;j<Dm.Ny-1;j++){
|
||||
for (i=1;i<Dm.Nx-1;i++){
|
||||
|
||||
int n = k*Dm.Nx*Dm.Ny + j*Dm.Nx + i;
|
||||
int n = k*Dm.Nx*Dm.Ny + j*Dm.Nx + i;
|
||||
|
||||
sign = -1;
|
||||
if (ID[n] == 1) sign = 1;
|
||||
sign = -1;
|
||||
if (ID[n] == 1) sign = 1;
|
||||
|
||||
// local second derivative terms
|
||||
Dxxp = minmod(Dxx(i,j,k),Dxx(i+1,j,k));
|
||||
Dyyp = minmod(Dyy(i,j,k),Dyy(i,j+1,k));
|
||||
Dzzp = minmod(Dzz(i,j,k),Dzz(i,j,k+1));
|
||||
Dxxm = minmod(Dxx(i,j,k),Dxx(i-1,j,k));
|
||||
Dyym = minmod(Dyy(i,j,k),Dyy(i,j-1,k));
|
||||
Dzzm = minmod(Dzz(i,j,k),Dzz(i,j,k-1));
|
||||
// local second derivative terms
|
||||
Dxxp = minmod(Dxx(i,j,k),Dxx(i+1,j,k));
|
||||
Dyyp = minmod(Dyy(i,j,k),Dyy(i,j+1,k));
|
||||
Dzzp = minmod(Dzz(i,j,k),Dzz(i,j,k+1));
|
||||
Dxxm = minmod(Dxx(i,j,k),Dxx(i-1,j,k));
|
||||
Dyym = minmod(Dyy(i,j,k),Dyy(i,j-1,k));
|
||||
Dzzm = minmod(Dzz(i,j,k),Dzz(i,j,k-1));
|
||||
|
||||
/* //............Compute upwind derivatives ...................
|
||||
/* //............Compute upwind derivatives ...................
|
||||
Dxp = Distance(i+1,j,k) - Distance(i,j,k) + 0.5*Dxxp;
|
||||
Dyp = Distance(i,j+1,k) - Distance(i,j,k) + 0.5*Dyyp;
|
||||
Dzp = Distance(i,j,k+1) - Distance(i,j,k) + 0.5*Dzzp;
|
||||
|
||||
|
||||
Dxm = Distance(i,j,k) - Distance(i-1,j,k) + 0.5*Dxxm;
|
||||
Dym = Distance(i,j,k) - Distance(i,j-1,k) + 0.5*Dyym;
|
||||
Dzm = Distance(i,j,k) - Distance(i,j,k-1) + 0.5*Dzzm;
|
||||
*/
|
||||
Dxp = Distance(i+1,j,k);
|
||||
Dyp = Distance(i,j+1,k);
|
||||
Dzp = Distance(i,j,k+1);
|
||||
*/
|
||||
Dxp = Distance(i+1,j,k);
|
||||
Dyp = Distance(i,j+1,k);
|
||||
Dzp = Distance(i,j,k+1);
|
||||
|
||||
Dxm = Distance(i-1,j,k);
|
||||
Dym = Distance(i,j-1,k);
|
||||
Dzm = Distance(i,j,k-1);
|
||||
Dxm = Distance(i-1,j,k);
|
||||
Dym = Distance(i,j-1,k);
|
||||
Dzm = Distance(i,j,k-1);
|
||||
|
||||
// Compute upwind derivatives for Godunov Hamiltonian
|
||||
if (sign < 0.0){
|
||||
if (Dxp > Dxm) Dx = Dxp - Distance(i,j,k) + 0.5*Dxxp;
|
||||
else Dx = Distance(i,j,k) - Dxm + 0.5*Dxxm;
|
||||
// Compute upwind derivatives for Godunov Hamiltonian
|
||||
if (sign < 0.0){
|
||||
if (Dxp > Dxm) Dx = Dxp - Distance(i,j,k) + 0.5*Dxxp;
|
||||
else Dx = Distance(i,j,k) - Dxm + 0.5*Dxxm;
|
||||
|
||||
if (Dyp > Dym) Dy = Dyp - Distance(i,j,k) + 0.5*Dyyp;
|
||||
else Dy = Distance(i,j,k) - Dym + 0.5*Dyym;
|
||||
if (Dyp > Dym) Dy = Dyp - Distance(i,j,k) + 0.5*Dyyp;
|
||||
else Dy = Distance(i,j,k) - Dym + 0.5*Dyym;
|
||||
|
||||
if (Dzp > Dzm) Dz = Dzp - Distance(i,j,k) + 0.5*Dzzp;
|
||||
else Dz = Distance(i,j,k) - Dzm + 0.5*Dzzm;
|
||||
}
|
||||
else{
|
||||
if (Dxp < Dxm) Dx = Dxp - Distance(i,j,k) + 0.5*Dxxp;
|
||||
else Dx = Distance(i,j,k) - Dxm + 0.5*Dxxm;
|
||||
if (Dzp > Dzm) Dz = Dzp - Distance(i,j,k) + 0.5*Dzzp;
|
||||
else Dz = Distance(i,j,k) - Dzm + 0.5*Dzzm;
|
||||
}
|
||||
else{
|
||||
if (Dxp < Dxm) Dx = Dxp - Distance(i,j,k) + 0.5*Dxxp;
|
||||
else Dx = Distance(i,j,k) - Dxm + 0.5*Dxxm;
|
||||
|
||||
if (Dyp < Dym) Dy = Dyp - Distance(i,j,k) + 0.5*Dyyp;
|
||||
else Dy = Distance(i,j,k) - Dym + 0.5*Dyym;
|
||||
if (Dyp < Dym) Dy = Dyp - Distance(i,j,k) + 0.5*Dyyp;
|
||||
else Dy = Distance(i,j,k) - Dym + 0.5*Dyym;
|
||||
|
||||
if (Dzp < Dzm) Dz = Dzp - Distance(i,j,k) + 0.5*Dzzp;
|
||||
else Dz = Distance(i,j,k) - Dzm + 0.5*Dzzm;
|
||||
}
|
||||
if (Dzp < Dzm) Dz = Dzp - Distance(i,j,k) + 0.5*Dzzp;
|
||||
else Dz = Distance(i,j,k) - Dzm + 0.5*Dzzm;
|
||||
}
|
||||
|
||||
norm=sqrt(Dx*Dx+Dy*Dy+Dz*Dz);
|
||||
if (norm > 1.0) norm=1.0;
|
||||
|
||||
Distance(i,j,k) += dt*sign*(1.0 - norm);
|
||||
LocalVar += dt*sign*(1.0 - norm);
|
||||
norm=sqrt(Dx*Dx+Dy*Dy+Dz*Dz);
|
||||
if (norm > 1.0) norm=1.0;
|
||||
|
||||
if (fabs(dt*sign*(1.0 - norm)) > LocalMax)
|
||||
LocalMax = fabs(dt*sign*(1.0 - norm));
|
||||
}
|
||||
}
|
||||
}
|
||||
Distance(i,j,k) += dt*sign*(1.0 - norm);
|
||||
LocalVar += dt*sign*(1.0 - norm);
|
||||
|
||||
MPI_Allreduce(&LocalVar,&GlobalVar,1,MPI_DOUBLE,MPI_SUM,Dm.Comm);
|
||||
MPI_Allreduce(&LocalMax,&GlobalMax,1,MPI_DOUBLE,MPI_MAX,Dm.Comm);
|
||||
GlobalVar /= (Dm.Nx-2)*(Dm.Ny-2)*(Dm.Nz-2)*Dm.nprocx*Dm.nprocy*Dm.nprocz;
|
||||
count++;
|
||||
if (fabs(dt*sign*(1.0 - norm)) > LocalMax)
|
||||
LocalMax = fabs(dt*sign*(1.0 - norm));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (count%50 == 0 && Dm.rank==0 )
|
||||
printf("Time=%i, Max variation=%f, Global variation=%f \n",count,GlobalMax,GlobalVar);
|
||||
MPI_Allreduce(&LocalVar,&GlobalVar,1,MPI_DOUBLE,MPI_SUM,Dm.Comm);
|
||||
MPI_Allreduce(&LocalMax,&GlobalMax,1,MPI_DOUBLE,MPI_MAX,Dm.Comm);
|
||||
GlobalVar /= (Dm.Nx-2)*(Dm.Ny-2)*(Dm.Nz-2)*Dm.nprocx*Dm.nprocy*Dm.nprocz;
|
||||
count++;
|
||||
|
||||
if (fabs(GlobalMax) < 1e-5){
|
||||
if (Dm.rank==0) printf("Exiting with max tolerance of 1e-5 \n");
|
||||
count=timesteps;
|
||||
if (count%50 == 0 && Dm.rank==0 )
|
||||
printf("Time=%i, Max variation=%f, Global variation=%f \n",count,GlobalMax,GlobalVar);
|
||||
|
||||
if (fabs(GlobalMax) < 1e-5){
|
||||
if (Dm.rank==0) printf("Exiting with max tolerance of 1e-5 \n");
|
||||
count=timesteps;
|
||||
}
|
||||
}
|
||||
}
|
||||
return GlobalVar;
|
||||
return GlobalVar;
|
||||
}
|
||||
|
||||
|
||||
@ -182,270 +183,163 @@ int main(int argc, char **argv)
|
||||
// Initialize MPI
|
||||
int rank, nprocs;
|
||||
MPI_Init(&argc,&argv);
|
||||
MPI_Comm comm = MPI_COMM_WORLD;
|
||||
MPI_Comm comm = MPI_COMM_WORLD;
|
||||
MPI_Comm_rank(comm,&rank);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
{
|
||||
//.......................................................................
|
||||
// Reading the domain information file
|
||||
//.......................................................................
|
||||
int nprocx, nprocy, nprocz, nx, ny, nz, nspheres;
|
||||
double Lx, Ly, Lz;
|
||||
int Nx,Ny,Nz;
|
||||
int i,j,k,n;
|
||||
int BC=0;
|
||||
char Filename[40];
|
||||
int xStart,yStart,zStart;
|
||||
// char fluidValue,solidValue;
|
||||
//.......................................................................
|
||||
// Reading the domain information file
|
||||
//.......................................................................
|
||||
int nprocx, nprocy, nprocz, nx, ny, nz, nspheres;
|
||||
double Lx, Ly, Lz;
|
||||
int Nx,Ny,Nz;
|
||||
int i,j,k,n;
|
||||
int BC=0;
|
||||
char Filename[40];
|
||||
int xStart,yStart,zStart;
|
||||
// char fluidValue,solidValue;
|
||||
|
||||
std::vector<char> solidValues;
|
||||
std::vector<char> nwpValues;
|
||||
std::string line;
|
||||
std::vector<char> solidValues;
|
||||
std::vector<char> nwpValues;
|
||||
std::string line;
|
||||
|
||||
if (rank==0){
|
||||
ifstream domain("Domain.in");
|
||||
domain >> nprocx;
|
||||
domain >> nprocy;
|
||||
domain >> nprocz;
|
||||
domain >> nx;
|
||||
domain >> ny;
|
||||
domain >> nz;
|
||||
domain >> nspheres;
|
||||
domain >> Lx;
|
||||
domain >> Ly;
|
||||
domain >> Lz;
|
||||
if (rank==0){
|
||||
ifstream domain("Domain.in");
|
||||
domain >> nprocx;
|
||||
domain >> nprocy;
|
||||
domain >> nprocz;
|
||||
domain >> nx;
|
||||
domain >> ny;
|
||||
domain >> nz;
|
||||
domain >> nspheres;
|
||||
domain >> Lx;
|
||||
domain >> Ly;
|
||||
domain >> Lz;
|
||||
|
||||
ifstream image("Segmented.in");
|
||||
image >> Filename; // Name of data file containing segmented data
|
||||
image >> Nx; // size of the binary file
|
||||
image >> Ny;
|
||||
image >> Nz;
|
||||
image >> xStart; // offset for the starting voxel
|
||||
image >> yStart;
|
||||
image >> zStart;
|
||||
ifstream image("Segmented.in");
|
||||
image >> Filename; // Name of data file containing segmented data
|
||||
image >> Nx; // size of the binary file
|
||||
image >> Ny;
|
||||
image >> Nz;
|
||||
image >> xStart; // offset for the starting voxel
|
||||
image >> yStart;
|
||||
image >> zStart;
|
||||
|
||||
}
|
||||
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);
|
||||
}
|
||||
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);
|
||||
|
||||
// Check that the number of processors >= the number of ranks
|
||||
if ( rank==0 ) {
|
||||
printf("Number of MPI ranks required: %i \n", nprocx*nprocy*nprocz);
|
||||
printf("Number of MPI ranks used: %i \n", nprocs);
|
||||
printf("Full domain size: %i x %i x %i \n",nx*nprocx,ny*nprocy,nz*nprocz);
|
||||
}
|
||||
if ( nprocs < nprocx*nprocy*nprocz ){
|
||||
ERROR("Insufficient number of processors");
|
||||
}
|
||||
// Check that the number of processors >= the number of ranks
|
||||
if ( rank==0 ) {
|
||||
printf("Number of MPI ranks required: %i \n", nprocx*nprocy*nprocz);
|
||||
printf("Number of MPI ranks used: %i \n", nprocs);
|
||||
printf("Full domain size: %i x %i x %i \n",nx*nprocx,ny*nprocy,nz*nprocz);
|
||||
}
|
||||
if ( nprocs < nprocx*nprocy*nprocz ){
|
||||
ERROR("Insufficient number of processors");
|
||||
}
|
||||
|
||||
char LocalRankFilename[40];
|
||||
char LocalRankFilename[40];
|
||||
|
||||
int N = (nx+2)*(ny+2)*(nz+2);
|
||||
Domain Dm(nx,ny,nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BC);
|
||||
for (n=0; n<N; n++) Dm.id[n]=1;
|
||||
Dm.CommInit(comm);
|
||||
int N = (nx+2)*(ny+2)*(nz+2);
|
||||
Domain Dm(nx,ny,nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BC);
|
||||
for (n=0; n<N; n++) Dm.id[n]=1;
|
||||
Dm.CommInit(comm);
|
||||
|
||||
// Read the phase ID
|
||||
size_t readID;
|
||||
sprintf(LocalRankFilename,"ID.%05i",rank);
|
||||
FILE *ID = fopen(LocalRankFilename,"rb");
|
||||
readID=fread(Dm.id,1,N,ID);
|
||||
if (readID != size_t(N)) printf("lbpm_segmented_pp: Error reading ID \n");
|
||||
fclose(ID);
|
||||
// make sure communication
|
||||
// Set up layers in x direction
|
||||
for (k=0; k<nz; k++){
|
||||
for (j=0; j<ny; j++){
|
||||
Dm.id[k*nx*ny+j*nx]=1;
|
||||
Dm.id[k*nx*ny+j*nx+nx-1] = 1;
|
||||
}
|
||||
}
|
||||
|
||||
for (k=0; k<nz; k++){
|
||||
for (i=0; i<nx; i++){
|
||||
Dm.id[k*nx*ny+i]=1;
|
||||
Dm.id[k*nx*ny+(ny-1)*nx+i] = 1;
|
||||
}
|
||||
}
|
||||
|
||||
for (j=0; j<ny; j++){
|
||||
for (i=0; i<nx; i++){
|
||||
Dm.id[j*nx+i]=1;
|
||||
Dm.id[nx*ny*(nz-1)+j*nx+i] = 1;
|
||||
}
|
||||
}
|
||||
|
||||
// Initialize the domain and communication
|
||||
|
||||
nx+=2; ny+=2; nz+=2;
|
||||
int count = 0;
|
||||
N=nx*ny*nz;
|
||||
|
||||
char *id;
|
||||
id = new char [N];
|
||||
TwoPhase Averages(Dm);
|
||||
// DoubleArray Distance(nx,ny,nz);
|
||||
// DoubleArray Phase(nx,ny,nz);
|
||||
|
||||
// Solve for the position of the solid 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;
|
||||
// Initialize the solid phase
|
||||
if (Dm.id[n] == 0) id[n] = 0;
|
||||
else id[n] = 1;
|
||||
// Read the phase ID
|
||||
size_t readID;
|
||||
sprintf(LocalRankFilename,"ID.%05i",rank);
|
||||
FILE *ID = fopen(LocalRankFilename,"rb");
|
||||
readID=fread(Dm.id,1,N,ID);
|
||||
if (readID != size_t(N)) printf("lbpm_segmented_pp: Error reading ID \n");
|
||||
fclose(ID);
|
||||
// make sure communication
|
||||
// Set up layers in x direction
|
||||
for (k=0; k<nz; k++){
|
||||
for (j=0; j<ny; j++){
|
||||
Dm.id[k*nx*ny+j*nx]=1;
|
||||
Dm.id[k*nx*ny+j*nx+nx-1] = 1;
|
||||
}
|
||||
}
|
||||
}
|
||||
// Initialize the signed distance function
|
||||
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;
|
||||
// Initialize distance to +/- 1
|
||||
Averages.SDs(i,j,k) = 2.0*id[n]-1.0;
|
||||
|
||||
for (k=0; k<nz; k++){
|
||||
for (i=0; i<nx; i++){
|
||||
Dm.id[k*nx*ny+i]=1;
|
||||
Dm.id[k*nx*ny+(ny-1)*nx+i] = 1;
|
||||
}
|
||||
}
|
||||
}
|
||||
MeanFilter(Averages.SDs);
|
||||
|
||||
double LocalVar, TotalVar;
|
||||
if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
|
||||
int Maxtime=10*max(max(Dm.Nx*Dm.nprocx,Dm.Ny*Dm.nprocy),Dm.Nz*Dm.nprocz);
|
||||
LocalVar = Eikonal(Averages.SDs,id,Dm,Maxtime);
|
||||
|
||||
MPI_Allreduce(&LocalVar,&TotalVar,1,MPI_DOUBLE,MPI_SUM,comm);
|
||||
TotalVar /= nprocs;
|
||||
if (rank==0) printf("Final variation in signed distance function %f \n",TotalVar);
|
||||
|
||||
sprintf(LocalRankFilename,"SignDist.%05i",rank);
|
||||
FILE *DIST = fopen(LocalRankFilename,"wb");
|
||||
fwrite(Averages.SDs.data(),8,Averages.SDs.length(),DIST);
|
||||
fclose(DIST);
|
||||
|
||||
/* // Solve for the position of the non-wetting 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;
|
||||
// Initialize the non-wetting phase
|
||||
if (Dm.id[n] == 1) id[n] = 1;
|
||||
else id[n] = 0;
|
||||
for (j=0; j<ny; j++){
|
||||
for (i=0; i<nx; i++){
|
||||
Dm.id[j*nx+i]=1;
|
||||
Dm.id[nx*ny*(nz-1)+j*nx+i] = 1;
|
||||
}
|
||||
}
|
||||
}
|
||||
// Initialize the signed distance function
|
||||
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;
|
||||
// Initialize distance to +/- 1
|
||||
Averages.Phase(i,j,k) = 2.0*id[n]-1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
MeanFilter(Averages.Phase);
|
||||
|
||||
if (rank==0) printf("Initialized non-wetting phase -- Converting to Signed Distance function \n");
|
||||
SSO(Averages.Phase,id,Dm,100);
|
||||
// Initialize the domain and communication
|
||||
|
||||
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;
|
||||
// Initialize distance to +/- 1
|
||||
// Dilation of the non-wetting phase
|
||||
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);
|
||||
Averages.DelPhi(i,j,k) = 0.0;
|
||||
Averages.Press(i,j,k) = 0.0;
|
||||
Averages.Vel_x(i,j,k) = 0.0;
|
||||
Averages.Vel_y(i,j,k) = 0.0;
|
||||
Averages.Vel_z(i,j,k) = 0.0;
|
||||
if (Averages.SDs(i,j,k) > 0.0){
|
||||
if (Averages.Phase(i,j,k) > 0.0){
|
||||
Dm.id[n] = 2;
|
||||
}
|
||||
else{
|
||||
Dm.id[n] = 1;
|
||||
}
|
||||
}
|
||||
else{
|
||||
Dm.id[n] = 0;
|
||||
nx+=2; ny+=2; nz+=2;
|
||||
int count = 0;
|
||||
N=nx*ny*nz;
|
||||
|
||||
char *id;
|
||||
id = new char [N];
|
||||
TwoPhase Averages(Dm);
|
||||
// DoubleArray Distance(nx,ny,nz);
|
||||
// DoubleArray Phase(nx,ny,nz);
|
||||
|
||||
// Solve for the position of the solid 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;
|
||||
// Initialize the solid phase
|
||||
if (Dm.id[n] == 0) id[n] = 0;
|
||||
else id[n] = 1;
|
||||
}
|
||||
}
|
||||
}
|
||||
// Initialize the signed distance function
|
||||
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;
|
||||
// Initialize distance to +/- 1
|
||||
Averages.SDs(i,j,k) = 2.0*id[n]-1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
MeanFilter(Averages.SDs);
|
||||
|
||||
double LocalVar, TotalVar;
|
||||
if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
|
||||
int Maxtime=10*max(max(Dm.Nx*Dm.nprocx,Dm.Ny*Dm.nprocy),Dm.Nz*Dm.nprocz);
|
||||
LocalVar = Eikonal(Averages.SDs,id,Dm,Maxtime);
|
||||
|
||||
MPI_Allreduce(&LocalVar,&TotalVar,1,MPI_DOUBLE,MPI_SUM,comm);
|
||||
TotalVar /= nprocs;
|
||||
if (rank==0) printf("Final variation in signed distance function %f \n",TotalVar);
|
||||
|
||||
sprintf(LocalRankFilename,"SignDist.%05i",rank);
|
||||
FILE *DIST = fopen(LocalRankFilename,"wb");
|
||||
fwrite(Averages.SDs.data(),8,Averages.SDs.length(),DIST);
|
||||
fclose(DIST);
|
||||
|
||||
}
|
||||
|
||||
// Create the MeshDataStruct
|
||||
fillHalo<double> fillData(Dm.Comm,Dm.rank_info,Nx-2,Ny-2,Nz-2,1,1,1,0,1);
|
||||
std::vector<IO::MeshDataStruct> meshData(1);
|
||||
meshData[0].meshName = "domain";
|
||||
meshData[0].mesh = std::shared_ptr<IO::DomainMesh>( new IO::DomainMesh(Dm.rank_info,Nx-2,Ny-2,Nz-2,Lx,Ly,Lz) );
|
||||
std::shared_ptr<IO::Variable> PhaseVar( new IO::Variable() );
|
||||
std::shared_ptr<IO::Variable> SolidVar( new IO::Variable() );
|
||||
std::shared_ptr<IO::Variable> BlobIDVar( new IO::Variable() );
|
||||
PhaseVar->name = "Fluid";
|
||||
PhaseVar->type = IO::VolumeVariable;
|
||||
PhaseVar->dim = 1;
|
||||
PhaseVar->data.resize(Nx-2,Ny-2,Nz-2);
|
||||
meshData[0].vars.push_back(PhaseVar);
|
||||
SolidVar->name = "Solid";
|
||||
SolidVar->type = IO::VolumeVariable;
|
||||
SolidVar->dim = 1;
|
||||
SolidVar->data.resize(Nx-2,Ny-2,Nz-2);
|
||||
meshData[0].vars.push_back(SignDistVar);
|
||||
BlobIDVar->name = "BlobID";
|
||||
BlobIDVar->type = IO::VolumeVariable;
|
||||
BlobIDVar->dim = 1;
|
||||
BlobIDVar->data.resize(Nx-2,Ny-2,Nz-2);
|
||||
meshData[0].vars.push_back(BlobIDVar);
|
||||
|
||||
fillData.copy(Averages.SDn,PhaseVar->data);
|
||||
fillData.copy(Averages.SDs,SolidVar->data);
|
||||
fillData.copy(Averages.Label_NWP,BlobIDVar->data);
|
||||
IO::writeData( 0, meshData, 2, comm );
|
||||
|
||||
// sprintf(LocalRankFilename,"Phase.%05i",rank);
|
||||
// FILE *PHASE = fopen(LocalRankFilename,"wb");
|
||||
// fwrite(Averages.Phase.get(),8,Averages.Phase.length(),PHASE);
|
||||
// fclose(PHASE);
|
||||
|
||||
double beta = 0.95;
|
||||
if (rank==0) printf("initializing the system \n");
|
||||
Averages.UpdateSolid();
|
||||
Averages.UpdateMeshValues();
|
||||
Dm.CommunicateMeshHalo(Averages.Phase);
|
||||
Dm.CommunicateMeshHalo(Averages.SDn);
|
||||
Dm.CommunicateMeshHalo(Averages.SDs);
|
||||
|
||||
int timestep=5;
|
||||
Averages.Initialize();
|
||||
if (rank==0) printf("computing phase components \n");
|
||||
Averages.ComponentAverages();
|
||||
if (rank==0) printf("sorting phase components \n");
|
||||
Averages.SortBlobs();
|
||||
Averages.PrintComponents(timestep);
|
||||
*/
|
||||
}
|
||||
MPI_Barrier(comm);
|
||||
MPI_Barrier(comm);
|
||||
MPI_Finalize();
|
||||
return 0;
|
||||
return 0;
|
||||
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user