OilfieldToolsNet/LBPM
4
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Improving CalcDist

Browse Source
This commit is contained in:
Mark Berrill 2018-05-17 16:03:30 -04:00
parent 195481f615
commit fa42b83efd
6 changed files with 184 additions and 197 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
IO/Reader.cpp
View File

@ -44,7 +44,6 @@ std::vector<std::string> IO::readTimesteps( const std::string& filename )
FILE *fid= fopen(filename.c_str(),"rb");
if ( fid==NULL )
ERROR("Error opening file");
auto pos = std::min(filename.find_last_of(47),filename.find_last_of(90));
std::vector<std::string> timesteps;
char buf[1000];
while (fgets(buf,sizeof(buf),fid) != NULL) {
@ -160,7 +159,6 @@ std::shared_ptr<IO::Mesh> IO::getMesh( const std::string& path, const std::strin
#ifdef USE_SILO
const DatabaseEntry& database = meshDatabase.domains[domain];
std::string filename = path + "/" + timestep + "/" + database.file;
int rank = std::stoi(database.file.substr(0,database.file.find(".silo")).c_str());
auto fid = silo::open( filename, silo::READ );
if ( meshDatabase.meshClass=="PointList" ) {
Array<double> coords = silo::readPointMesh<double>( fid, database.name );
@ -262,7 +260,6 @@ std::shared_ptr<IO::Variable> IO::getVariable( const std::string& path, const st
const auto& database = meshDatabase.domains[domain];
auto variableDatabase = meshDatabase.getVariableDatabase( variable );
std::string filename = path + "/" + timestep + "/" + database.file;
int rank = std::stoi(database.file.substr(0,database.file.find(".silo")).c_str());
auto fid = silo::open( filename, silo::READ );
var.reset( new Variable( variableDatabase.dim, variableDatabase.type, variable ) );
if ( meshDatabase.meshClass=="PointList" ) {

2
IO/silo.hpp
View File

@ -322,9 +322,7 @@ void readTriMesh( DBfile* fid, const std::string& meshname, Array<TYPE>& coords,
}
auto zones = mesh->zones;
int N_zones = zones->nzones;
int ndim_zones = zones->ndims;
ASSERT( zones->nshapes==1 );
int shape_type = zones->shapetype[0];
int shapesize = zones->shapesize[0];
tri.resize(N_zones,shapesize);
for (int i=0; i<N_zones; i++) {

288
analysis/distance.cpp
View File

@ -1,60 +1,12 @@
#include "analysis/distance.h"
// Check if we need to recompute distance after updating ghose values
static bool checkUpdate( const Array<Vec> &d, double dx, double dy, double dz )
{
auto s = d.size();
bool test[3] = { false, false, false };
// Check x-direction
Vec v1, v2;
for (size_t k=1; k<s[2]-1; k++) {
for (size_t j=1; j<s[1]-1; j++) {
v1 = d(1,j,k);
v2 = d(0,j,k);
v2.x += dx;
test[0] = test[0] || v2 < v1;
v1 = d(s[0]-2,j,k);
v2 = d(s[0]-1,j,k);
v2.x -= dx;
test[0] = test[0] || v2 < v1;
}
}
// Check y-direction
for (size_t k=1; k<s[2]-1; k++) {
for (size_t i=1; i<s[0]-1; i++) {
v1 = d(i,1,k);
v2 = d(i,0,k);
v2.y += dy;
test[1] = test[1] || v2 < v1;
v1 = d(i,s[1]-2,k);
v2 = d(i,s[1]-1,k);
v2.y -= dy;
test[1] = test[1] || v2 < v1;
}
}
// Check z-direction
for (size_t j=1; j<s[1]-1; j++) {
for (size_t i=1; i<s[0]-1; i++) {
v1 = d(i,j,1);
v2 = d(i,j,0);
v2.z += dz;
test[2] = test[2] || v2 < v1;
v1 = d(i,j,s[2]-2);
v2 = d(i,j,s[2]-1);
v2.z -= dz;
test[2] = test[2] || v2 < v1;
}
}
return test[0] || test[1] || test[2];
}
/******************************************************************
* A fast distance calculation *
******************************************************************/
template<class TYPE>
void CalcDist( Array<TYPE> &Distance, const Array<char> &ID, const Domain &Dm, const std::array<bool,3>& periodic )
void CalcDist( Array<TYPE> &Distance, const Array<char> &ID, const Domain &Dm,
const std::array<bool,3>& periodic, const std::array<double,3>& dx )
{
ASSERT( Distance.size() == ID.size() );
std::array<int,3> n = { Dm.Nx-2, Dm.Ny-2, Dm.Nz-2 };
@ -64,15 +16,121 @@ void CalcDist( Array<TYPE> &Distance, const Array<char> &ID, const Domain &Dm, c
for (size_t i=0; i<ID.length(); i++)
id(i) = ID(i) == 0 ? -1:1;
fillData.fill( id );
CalcVecDist( vecDist, id, Dm, periodic );
CalcVecDist( vecDist, id, Dm, periodic, dx );
for (size_t i=0; i<Distance.length(); i++)
Distance(i) = id(i)*vecDist(i).norm();
}
void CalcVecDist( Array<Vec> &d, const Array<int> &ID0, const Domain &Dm, const std::array<bool,3>& periodic )
/******************************************************************
* Vector-based distance calculation *
* Initialize cells adjacent to boundaries *
******************************************************************/
static void calcVecInitialize( Array<Vec> &d, const Array<int> &ID, double dx, double dy, double dz )
{
d.fill( Vec( 1e50, 1e50, 1e50 ) );
const double dx0 = 0.5*dx;
const double dy0 = 0.5*dy;
const double dz0 = 0.5*dz;
//const double dxy0 = 0.25*sqrt( dx*dx + dy*dy );
//const double dxz0 = 0.25*sqrt( dx*dx + dz*dz );
//const double dyz0 = 0.25*sqrt( dy*dy + dz*dz );
//const double dxyz0 = sqrt( dx*dx + dy*dy + dz*dz );
int Nx = d.size(0);
int Ny = d.size(1);
int Nz = d.size(2);
for (int k=1; k<Nz-1; k++) {
for (int j=1; j<Ny-1; j++) {
for (int i=1; i<Nx-1; i++) {
int id = ID(i,j,k);
bool x[2] = { id != ID(i-1,j,k), id != ID(i+1,j,k) };
bool y[2] = { id != ID(i,j-1,k), id != ID(i,j+1,k) };
bool z[2] = { id != ID(i,j,k-1), id != ID(i,j,k+1) };
if ( x[0] ) d(i,j,k) = Vec( dx0, 0, 0 );
if ( x[1] ) d(i,j,k) = Vec( -dx0, 0, 0 );
if ( y[0] ) d(i,j,k) = Vec( 0, dy0, 0 );
if ( y[1] ) d(i,j,k) = Vec( 0, -dy0, 0 );
if ( z[0] ) d(i,j,k) = Vec( 0, 0, dz0 );
if ( z[1] ) d(i,j,k) = Vec( 0, 0, -dz0 );
/*if ( x[0] && y[0] ) d(i,j,k) = Vec( dxy0, dxy0, 0 );
if ( x[0] && y[1] ) d(i,j,k) = Vec( dxy0, -dxy0, 0 );
if ( x[1] && y[0] ) d(i,j,k) = Vec( -dxy0, dxy0, 0 );
if ( x[1] && y[1] ) d(i,j,k) = Vec( -dxy0, -dxy0, 0 );
if ( x[0] && z[0] ) d(i,j,k) = Vec( dxz0, 0, dxz0 );
if ( x[0] && z[1] ) d(i,j,k) = Vec( dxz0, 0, -dxz0 );
if ( x[1] && z[0] ) d(i,j,k) = Vec( -dxz0, 0, dxz0 );
if ( x[1] && z[1] ) d(i,j,k) = Vec( -dxz0, 0, -dxz0 );
if ( y[0] && z[0] ) d(i,j,k) = Vec( 0, dyz0, dyz0 );
if ( y[0] && z[1] ) d(i,j,k) = Vec( 0, dyz0, -dyz0 );
if ( y[1] && z[0] ) d(i,j,k) = Vec( 0, -dyz0, dyz0 );
if ( y[1] && z[1] ) d(i,j,k) = Vec( 0, -dyz0, -dyz0 );*/
}
}
}
}
/******************************************************************
* Vector-based distance calculation *
* Update interior cells *
******************************************************************/
static double calcVecUpdateInterior( Array<Vec> &d, double dx, double dy, double dz )
{
double err = 0;
int Nx = d.size(0);
int Ny = d.size(1);
int Nz = d.size(2);
// Propagate (+,+,+)
for (int k=1; k<Nz; k++) {
for (int j=1; j<Ny; j++) {
for (int i=1; i<Nx; i++) {
auto vx = d(i-1,j,k);
auto vy = d(i,j-1,k);
auto vz = d(i,j,k-1);
vx.x += dx;
vy.y += dy;
vz.z += dz;
auto v = std::min( std::min(vx,vy), vz );
double d1 = v.norm2();
double d2 = d(i,j,k).norm2();
if ( d1 < d2 ) {
d(i,j,k) = v;
err = std::max( err, sqrt(d2)-sqrt(d1) );
}
}
}
}
// Propagate (-,-,-)
for (int k=Nz-2; k>=0; k--) {
for (int j=Ny-2; j>=0; j--) {
for (int i=Nx-2; i>=0; i--) {
auto vx = d(i+1,j,k);
auto vy = d(i,j+1,k);
auto vz = d(i,j,k+1);
vx.x -= dx;
vy.y -= dy;
vz.z -= dz;
auto v = std::min( std::min(vx,vy), vz );
double d1 = v.norm2();
double d2 = d(i,j,k).norm2();
if ( d1 < d2 ) {
d(i,j,k) = v;
err = std::max( err, sqrt(d2)-sqrt(d1) );
}
}
}
}
return err;
}
/******************************************************************
* Vector-based distance calculation *
******************************************************************/
void CalcVecDist( Array<Vec> &d, const Array<int> &ID0, const Domain &Dm,
const std::array<bool,3>& periodic, const std::array<double,3>& dx )
{
const double dx = 1.0;
const double dy = 1.0;
const double dz = 1.0;
std::array<int,3> N = { Dm.Nx, Dm.Ny, Dm.Nz };
std::array<int,3> n = { Dm.Nx-2, Dm.Ny-2, Dm.Nz-2 };
// Create ID with ghosts
@ -102,112 +160,30 @@ void CalcVecDist( Array<Vec> &d, const Array<int> &ID0, const Domain &Dm, const
fillDataID.fill( ID );
// Create communicator for distance
fillHalo<Vec> fillData( Dm.Comm, Dm.rank_info, n, {1,1,1}, 50, 1, {true,false,false}, periodic );
// Initialize the vector distance
d.fill( Vec( 1e50, 1e50, 1e50 ) );
const double dx0 = 0.5*dx;
const double dy0 = 0.5*dy;
const double dz0 = 0.5*dz;
//const double dxy0 = 0.25*sqrt( dx*dx + dy*dy );
//const double dxz0 = 0.25*sqrt( dx*dx + dz*dz );
//const double dyz0 = 0.25*sqrt( dy*dy + dz*dz );
//const double dxyz0 = sqrt( dx*dx + dy*dy + dz*dz );
for (int k=1; k<Dm.Nz-1; k++) {
for (int j=1; j<Dm.Ny-1; j++) {
for (int i=1; i<Dm.Nx-1; i++) {
int id = ID(i,j,k);
bool x[2] = { id != ID(i-1,j,k), id != ID(i+1,j,k) };
bool y[2] = { id != ID(i,j-1,k), id != ID(i,j+1,k) };
bool z[2] = { id != ID(i,j,k-1), id != ID(i,j,k+1) };
if ( x[0] ) d(i,j,k) = Vec( dx0, 0, 0 );
if ( x[1] ) d(i,j,k) = Vec( -dx0, 0, 0 );
if ( y[0] ) d(i,j,k) = Vec( 0, dy0, 0 );
if ( y[1] ) d(i,j,k) = Vec( 0, -dy0, 0 );
if ( z[0] ) d(i,j,k) = Vec( 0, 0, dz0 );
if ( z[1] ) d(i,j,k) = Vec( 0, 0, -dz0 );
/*if ( x[0] && y[0] ) d(i,j,k) = Vec( dxy0, dxy0, 0 );
if ( x[0] && y[1] ) d(i,j,k) = Vec( dxy0, -dxy0, 0 );
if ( x[1] && y[0] ) d(i,j,k) = Vec( -dxy0, dxy0, 0 );
if ( x[1] && y[1] ) d(i,j,k) = Vec( -dxy0, -dxy0, 0 );
if ( x[0] && z[0] ) d(i,j,k) = Vec( dxz0, 0, dxz0 );
if ( x[0] && z[1] ) d(i,j,k) = Vec( dxz0, 0, -dxz0 );
if ( x[1] && z[0] ) d(i,j,k) = Vec( -dxz0, 0, dxz0 );
if ( x[1] && z[1] ) d(i,j,k) = Vec( -dxz0, 0, -dxz0 );
if ( y[0] && z[0] ) d(i,j,k) = Vec( 0, dyz0, dyz0 );
if ( y[0] && z[1] ) d(i,j,k) = Vec( 0, dyz0, -dyz0 );
if ( y[1] && z[0] ) d(i,j,k) = Vec( 0, -dyz0, dyz0 );
if ( y[1] && z[1] ) d(i,j,k) = Vec( 0, -dyz0, -dyz0 );*/
}
}
// Calculate the local distances
calcVecInitialize( d, ID, dx[0], dx[1], dx[2] );
double err = 1e100;
double tol = 0.5 * std::min( std::min(dx[0],dx[1]), dx[2] );
for (int it=0; it<=50 && err>tol; it++) {
err = calcVecUpdateInterior( d, dx[0], dx[1], dx[2] );
}
int N_it = Dm.nprocx() + Dm.nprocy() + Dm.nprocz() + 3;
// Calculate the global distances
int N_it = Dm.nprocx() + Dm.nprocy() + Dm.nprocz() + 100;
for ( int it=0; it<N_it; it++ ) {
//if ( Dm.rank() == 0 )
// printf("Runing iteration %i\n",it+1);
// Propagate +/- x-direction
for (int k=0; k<Dm.Nz; k++) {
for (int j=0; j<Dm.Ny; j++) {
for (int i=1; i<Dm.Nx; i++) {
auto v1 = d(i,j,k);
auto v2 = d(i-1,j,k);
v2.x += dx;
if ( v2 < v1 )
d(i,j,k) = v2;
}
for (int i=Dm.Nx-2; i>=0; i--) {
auto v1 = d(i,j,k);
auto v2 = d(i+1,j,k);
v2.x -= dx;
if ( v2 < v1 )
d(i,j,k) = v2;
}
}
}
// Propagate +/- y-direction
for (int k=0; k<Dm.Nz; k++) {
for (int i=0; i<Dm.Nx; i++) {
for (int j=1; j<Dm.Ny; j++) {
auto v1 = d(i,j,k);
auto v2 = d(i,j-1,k);
v2.y += dy;
if ( v2 < v1 )
d(i,j,k) = v2;
}
for (int j=Dm.Ny-2; j>=0; j--) {
auto v1 = d(i,j,k);
auto v2 = d(i,j+1,k);
v2.y -= dy;
if ( v2 < v1 )
d(i,j,k) = v2;
}
}
}
// Propagate +/- z-direction
for (int j=0; j<Dm.Ny; j++) {
for (int i=0; i<Dm.Nx; i++) {
for (int k=1; k<Dm.Nz; k++) {
auto v1 = d(i,j,k);
auto v2 = d(i,j,k-1);
v2.z += dz;
if ( v2 < v1 )
d(i,j,k) = v2;
}
for (int k=Dm.Nz-2; k>=0; k--) {
auto v1 = d(i,j,k);
auto v2 = d(i,j,k+1);
v2.z -= dz;
if ( v2 < v1 )
d(i,j,k) = v2;
}
}
}
// Update ghosts
fillData.fill( d );
bool test = checkUpdate( d, dx, dy, dz );
test = sumReduce( Dm.Comm, test );
if ( !test )
// Update distance
double err = calcVecUpdateInterior( d, dx[0], dx[1], dx[2] );
// Check if we are finished
err = maxReduce( Dm.Comm, err );
if ( err < tol )
break;
}
}
template void CalcDist<float>( Array<float>&, const Array<char>&, const Domain&, const std::array<bool,3>& );
template void CalcDist<double>( Array<double>&, const Array<char>&, const Domain&, const std::array<bool,3>& );
// Explicit instantiations
template void CalcDist<float>( Array<float>&, const Array<char>&, const Domain&, const std::array<bool,3>&, const std::array<double,3>& );
template void CalcDist<double>( Array<double>&, const Array<char>&, const Domain&, const std::array<bool,3>&, const std::array<double,3>& );

8
analysis/distance.h
View File

@ -11,6 +11,7 @@ struct Vec {
inline Vec(): x(0), y(0), z(0) {}
inline Vec( double x_, double y_, double z_ ): x(x_), y(y_), z(z_) {}
inline double norm() const { return sqrt(x*x+y*y+z*z); }
inline double norm2() const { return x*x+y*y+z*z; }
};
inline bool operator<(const Vec& l, const Vec& r){ return l.x*l.x+l.y*l.y+l.z*l.z < r.x*r.x+r.y*r.y+r.z*r.z; }
@ -24,7 +25,8 @@ inline bool operator<(const Vec& l, const Vec& r){ return l.x*l.x+l.y*l.y+l.z*l.
* @param[in] periodic Directions that are periodic
*/
template<class TYPE>
void CalcDist( Array<TYPE> &Distance, const Array<char> &ID, const Domain &Dm, const std::array<bool,3>& periodic = {true,true,true} );
void CalcDist( Array<TYPE> &Distance, const Array<char> &ID, const Domain &Dm,
const std::array<bool,3>& periodic = {true,true,true}, const std::array<double,3>& dx = {1,1,1} );
/*!
* @brief Calculate the distance using a simple method
@ -34,7 +36,7 @@ void CalcDist( Array<TYPE> &Distance, const Array<char> &ID, const Domain &Dm, c
* @param[in] Dm Domain information
* @param[in] periodic Directions that are periodic
*/
void CalcVecDist( Array<Vec> &Distance, const Array<int> &ID, const Domain &Dm, const std::array<bool,3>& periodic );
void CalcVecDist( Array<Vec> &Distance, const Array<int> &ID, const Domain &Dm,
const std::array<bool,3>& periodic = {true,true,true}, const std::array<double,3>& dx = {1,1,1} );
#endif

18
common/MPI_Helpers.h
View File

@ -170,6 +170,12 @@ void unpack( std::set<TYPE>& data, const char *buffer );
// Helper functions
inline double sumReduce( MPI_Comm comm, double x )
{
double y = 0;
MPI_Allreduce(&x,&y,1,MPI_DOUBLE,MPI_SUM,comm);
return y;
}
inline float sumReduce( MPI_Comm comm, float x )
{
float y = 0;
@ -199,12 +205,24 @@ inline std::vector<int> sumReduce( MPI_Comm comm, const std::vector<int>& x )
MPI_Allreduce(x.data(),y.data(),x.size(),MPI_INT,MPI_SUM,comm);
return y;
}
inline double maxReduce( MPI_Comm comm, double x )
{
double y = 0;
MPI_Allreduce(&x,&y,1,MPI_DOUBLE,MPI_MAX,comm);
return y;
}
inline float maxReduce( MPI_Comm comm, float x )
{
float y = 0;
MPI_Allreduce(&x,&y,1,MPI_FLOAT,MPI_MAX,comm);
return y;
}
inline int maxReduce( MPI_Comm comm, int x )
{
int y = 0;
MPI_Allreduce(&x,&y,1,MPI_INT,MPI_MAX,comm);
return y;
}
#endif

62
tests/TestSegDist.cpp
View File

@ -17,11 +17,18 @@
std::shared_ptr<Database> loadInputs( int nprocs )
{
INSIST(nprocs==8, "TestSegDist: Number of MPI processes must be equal to 8");
std::vector<int> nproc;
if ( nprocs == 1 ) {
nproc = { 1, 1, 1 };
} else if ( nprocs == 8 ) {
nproc = { 2, 2, 2 };
} else {
ERROR("TestSegDist: Unsupported number of processors");
}
auto db = std::make_shared<Database>( );
db->putScalar<int>( "BC", 0 );
db->putVector<int>( "nproc", { 2, 2, 2 } );
db->putVector<int>( "n", { 100, 100, 100 } );
db->putVector<int>( "nproc", nproc );
db->putVector<int>( "n", { 200, 200, 200 } );
db->putScalar<int>( "nspheres", 0 );
db->putVector<double>( "L", { 1, 1, 1 } );
return db;
@ -63,35 +70,30 @@ int main(int argc, char **argv)
int ny = Ny+2;
int nz = Nz+2;
double BubbleRadius = 0.3*nx;
// Initialize the bubble
double Cx = 1.0*nx;
double Cy = 1.0*ny;
double Cz = 1.0*nz;
double BubbleRadius = 0.15*Nx*Dm.nprocx();
double Cx = 0.40*Nx*Dm.nprocx();
double Cy = 0.45*Nx*Dm.nprocy();
double Cz = 0.50*Nx*Dm.nprocy();
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++) {
double z = k - 0.5 + Dm.kproc()*Nz;
for (int j=1; j<ny-1; j++) {
double y = j - 0.5 + Dm.jproc()*Ny;
for (int i=1; i<nx-1; i++) {
double x = i - 0.5 + Dm.iproc()*Nx;
// 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;
}
}
}
}
@ -106,24 +108,18 @@ int main(int argc, char **argv)
if (rank==0)
printf("Total time: %f seconds \n",t2-t1);
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 err = 0.0;
for (int i=1; i<Nx-1; i++) {
for (int j=1; j<Ny-1; j++) {
for (int k=1; k<Nz-1; k++) {
err += (Distance(i,j,k)-TrueDist(i,j,k))*(Distance(i,j,k)-TrueDist(i,j,k));
}
}
}
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("Mean error %f \n", err2);
err = sumReduce( Dm.Comm, err );
err = sqrt( err / (nx*ny*nz*nprocs) );
if (rank==0)
printf("Mean error %0.4f \n", err);
// Write the results to visit
Array<int> ID0(id.size());