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Moving to a new signed distance function

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This commit is contained in:
Mark Berrill
2018-05-17 12:07:20 -04:00
parent 5a686278bf
commit 195481f615
20 changed files with 502 additions and 659 deletions
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156
tests/TestSegDist.cpp
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@@ -11,8 +11,8 @@
#include <fstream>
#include "common/Array.h"
#include "common/Domain.h"
#include "analysis/eikonal.h"
#include "IO/Writer.h"
#include "analysis/distance.h"
std::shared_ptr<Database> loadInputs( int nprocs )
@@ -21,7 +21,7 @@ std::shared_ptr<Database> loadInputs( int nprocs )
auto db = std::make_shared<Database>( );
db->putScalar<int>( "BC", 0 );
db->putVector<int>( "nproc", { 2, 2, 2 } );
db->putVector<int>( "n", { 50, 50, 50 } );
db->putVector<int>( "n", { 100, 100, 100 } );
db->putScalar<int>( "nspheres", 0 );
db->putVector<double>( "L", { 1, 1, 1 } );
return db;
@@ -31,13 +31,13 @@ std::shared_ptr<Database> loadInputs( int nprocs )
//***************************************************************************************
int main(int argc, char **argv)
{
// Initialize MPI
int rank, nprocs;
MPI_Init(&argc,&argv);
// 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);
{
MPI_Comm_rank(comm,&rank);
MPI_Comm_size(comm,&nprocs);
{
// Load inputs
@@ -49,99 +49,81 @@ int main(int argc, char **argv)
// Get the rank info
Domain Dm(db);
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;
Dm.id[n] = 1;
}
}
}
Dm.CommInit(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;
Dm.id[n] = 1;
}
}
}
Dm.CommInit(comm);
int nx = Nx+2;
int nx = Nx+2;
int ny = Ny+2;
int nz = Nz+2;
double BubbleRadius = 25;
double BubbleRadius = 0.3*nx;
// Initialize the bubble
double Cx = 1.0*nx;
double Cy = 1.0*ny;
double Cz = 1.0*nz;
// Initialize the bubble
double Cx = 1.0*nx;
double Cy = 1.0*ny;
double Cz = 1.0*nz;
DoubleArray Distance(nx,ny,nz);
DoubleArray TrueDist(nx,ny,nz);
DoubleArray TrueDist(nx,ny,nz);
Array<char> id(nx,ny,nz);
id.fill(0);
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=1;k<nz-1;k++){
for (int j=1;j<ny-1;j++){
for (int i=1;i<nx-1;i++){
// True signed distance
double x = (nx-2)*Dm.iproc()+i-1;
double y = (ny-2)*Dm.jproc()+j-1;
double z = (nz-2)*Dm.kproc()+k-1;
TrueDist(i,j,k) = sqrt((x-Cx)*(x-Cx)+(y-Cy)*(y-Cy)+(z-Cz)*(z-Cz)) - BubbleRadius;
// True signed distance
double x = (nx-2)*Dm.iproc()+i-1;
double y = (ny-2)*Dm.jproc()+j-1;
double z = (nz-2)*Dm.kproc()+k-1;
TrueDist(i,j,k) = sqrt((x-Cx)*(x-Cx)+(y-Cy)*(y-Cy)+(z-Cz)*(z-Cz)) - BubbleRadius;
// Initialize phase positions
if (TrueDist(i,j,k) < 0.0){
id(i,j,k) = 0;
} else{
id(i,j,k)=1;
}
// Initialize phase positions
if (TrueDist(i,j,k) < 0.0){
id(i,j,k) = 0;
} else{
id(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++){
// Initialize distance to +/- 1
Distance(i,j,k) = 2.0*id(i,j,k)-1.0;
}
}
}
}
}
}
if (rank==0) printf("Nx = %i \n",(int)Distance.size(0));
if (rank==0) printf("Ny = %i \n",(int)Distance.size(1));
if (rank==0) printf("Nz = %i \n",(int)Distance.size(2));
MPI_Barrier(comm);
if (rank==0) printf("Initialized! Converting to Signed Distance function \n");
MPI_Barrier(comm);
if (rank==0) printf("Initialized! Converting to Signed Distance function \n");
double t1 = MPI_Wtime();
DoubleArray Distance(nx,ny,nz);
CalcDist(Distance,id,Dm,{false,false,false});
double t2 = MPI_Wtime();
if (rank==0)
printf("Total time: %f seconds \n",t2-t1);
double starttime,stoptime,cputime;
starttime = MPI_Wtime();
double err1 = Eikonal(Distance,id,Dm,1000);
stoptime = MPI_Wtime();
cputime = (stoptime - starttime);
if (rank==0) printf("Total time: %f seconds \n",cputime);
double localError=0.0;
int localCount = 0;
for (int k=0;k<nz;k++){
for (int j=0;j<ny;j++){
for (int i=0;i<nx;i++){
if (fabs(TrueDist(i,j,k)) < 3.0){
localError += (Distance(i,j,k)-TrueDist(i,j,k))*(Distance(i,j,k)-TrueDist(i,j,k));
localCount++;
}
}
}
}
double localError=0.0;
int localCount = 0;
for (int k=0;k<nz;k++){
for (int j=0;j<ny;j++){
for (int i=0;i<nx;i++){
if (fabs(TrueDist(i,j,k)) < 3.0){
localError += (Distance(i,j,k)-TrueDist(i,j,k))*(Distance(i,j,k)-TrueDist(i,j,k));
localCount++;
}
}
}
}
double globalError;
int globalCount;
MPI_Allreduce(&localError,&globalError,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
MPI_Allreduce(&localCount,&globalCount,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
double err2 = sqrt(globalError)/(double (globalCount));
if (rank==0) printf("global variation %f \n", err1);
if (rank==0) printf("Mean error %f \n", err2);
double err2 = sqrt(globalError)/(double (globalCount));
if (rank==0) printf("Mean error %f \n", err2);
// Write the results to visit
Array<int> ID0(id.size());
@@ -149,17 +131,17 @@ int main(int argc, char **argv)
Array<double> ID(Nx,Ny,Nz);
Array<double> dist1(Nx,Ny,Nz);
Array<double> dist2(Nx,Ny,Nz);
fillHalo<double> fillData(Dm.Comm, Dm.rank_info,Nx,Ny,Nz,1,1,1,0,1);
fillHalo<double> fillData(Dm.Comm, Dm.rank_info,{Nx,Ny,Nz},{1,1,1},0,1);
fillData.copy( ID0, ID );
fillData.copy( Distance, dist1 );
fillData.copy( TrueDist, dist2 );
fillData.copy( TrueDist, dist1 );
fillData.copy( Distance, dist2 );
std::vector<IO::MeshDataStruct> data(1);
data[0].meshName = "mesh";
data[0].mesh.reset( new IO::DomainMesh( Dm.rank_info, Nx, Ny, Nz, Dm.Lx, Dm.Ly, Dm.Lz ) );
data[0].vars.emplace_back( new IO::Variable( 1, IO::VariableType::VolumeVariable, "ID", ID ) );
data[0].vars.emplace_back( new IO::Variable( 1, IO::VariableType::VolumeVariable, "Distance", dist1 ) );
data[0].vars.emplace_back( new IO::Variable( 1, IO::VariableType::VolumeVariable, "TrueDist", dist2 ) );
data[0].vars.emplace_back( new IO::Variable( 1, IO::VariableType::VolumeVariable, "error", dist1-dist2 ) );
data[0].vars.emplace_back( new IO::Variable( 1, IO::VariableType::VolumeVariable, "TrueDist", dist1 ) );
data[0].vars.emplace_back( new IO::Variable( 1, IO::VariableType::VolumeVariable, "Distance", dist2 ) );
data[0].vars.emplace_back( new IO::Variable( 1, IO::VariableType::VolumeVariable, "error", dist2-dist1 ) );
IO::initialize( "", "silo", false );
IO::writeData( "testSegDist", data, MPI_COMM_WORLD );