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

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

Browse Source
This commit is contained in:
James E McClure
2020-07-22 11:58:02 -04:00
parent a1f3375911 4d2174cedb
commit 418ba77751
6 changed files with 228 additions and 7 deletions
Download Patch File Download Diff File Expand all files Collapse all files

15
analysis/Minkowski.cpp
View File

@@ -91,7 +91,19 @@ void Minkowski::ComputeScalar(const DoubleArray& Field, const double isovalue)
Xi -= 0.5;
}
// Euler characteristic -- each vertex shared by four cubes
Xi += 0.25*double(object.VertexCount);
//Xi += 0.25*double(object.VertexCount);
// check if vertices are at corners
for (int idx=0; idx<object.VertexCount; idx++){
auto P1 = object.vertex.coords(idx);
if ( remainder(P1.x,1.0)==0.0 && remainder(P1.y,1.0)==0.0 && remainder(P1.z,1.0)==0.0 ){
Xi += 0.125;
}
else Xi += 0.25;
}
/*double nside_extern = double(npts);
double nside_intern = double(npts)-3.0;
EulerChar=0.0;
if (npts > 0) EulerChar = (0.25*nvert - nside_intern - 0.5*nside_extern + nface); */
}
}
}
@@ -137,6 +149,7 @@ void Minkowski::MeasureObject(){
}
}
CalcDist(distance,id,*Dm);
Eikonal(distance, id, *Dm, 10, {true, true, true});
ComputeScalar(distance,0.0);
}

18
analysis/dcel.cpp
View File

@@ -388,16 +388,22 @@ void iso_surface(const Array<double>&Field, const double isovalue)
auto P1 = object.vertex.coords(object.halfedge.v1(e1));
auto P2 = object.vertex.coords(object.halfedge.v1(e2));
auto P3 = object.vertex.coords(object.halfedge.v1(e3));
P1.x += 1.0*i; P1.y += 1.0*j; P1.z +=1.0*k;
P2.x += 1.0*i; P2.y += 1.0*j; P2.z +=1.0*k;
P3.x += 1.0*i; P3.y += 1.0*j; P3.z +=1.0*k;
fprintf(TRIANGLES,"vertex %f %f %f\n",P1.x,P1.y,P1.z);
fprintf(TRIANGLES,"vertex %f %f %f\n",P2.x,P2.y,P2.z);
fprintf(TRIANGLES,"vertex %f %f %f\n",P3.x,P3.y,P3.z);
auto Normal = object.TriNormal(e1);
// P1.x += 1.0*i; P1.y += 1.0*j; P1.z +=1.0*k;
//P2.x += 1.0*i; P2.y += 1.0*j; P2.z +=1.0*k;
//P3.x += 1.0*i; P3.y += 1.0*j; P3.z +=1.0*k;
fprintf(TRIANGLES,"facet normal %f %f %f\n",Normal.x,Normal.y,Normal.z);
fprintf(TRIANGLES," outer loop\n");
fprintf(TRIANGLES," vertex %f %f %f\n",P1.x,P1.y,P1.z);
fprintf(TRIANGLES," vertex %f %f %f\n",P2.x,P2.y,P2.z);
fprintf(TRIANGLES," vertex %f %f %f\n",P3.x,P3.y,P3.z);
fprintf(TRIANGLES," endloop\n");
fprintf(TRIANGLES,"endfacet\n");
}
}
}
}
fprintf(TRIANGLES,"endsolid isosurface\n");
fclose(TRIANGLES);
}

142
analysis/distance.cpp
View File

@@ -182,6 +182,148 @@ void CalcVecDist( Array<Vec> &d, const Array<int> &ID0, const Domain &Dm,
}
}
double Eikonal(DoubleArray &Distance, const Array<char> &ID, Domain &Dm, int timesteps, const std::array<bool,3>& periodic){
/*
* 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 Physics229
*/
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);
fillHalo<double> fillData( Dm.Comm, Dm.rank_info, {xdim, ydim, zdim}, {1,1,1}, 50, 1, {true,true,true}, periodic );
// 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){
// 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);
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;
sign = -1;
if (ID(i,j,k) == 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));
/* //............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)- 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;
// Compute upwind derivatives for Godunov Hamiltonian
if (sign < 0.0){
if (Dxp + Dxm > 0.f) Dx = Dxp*Dxp;
else Dx = Dxm*Dxm;
if (Dyp + Dym > 0.f) Dy = Dyp*Dyp;
else Dy = Dym*Dym;
if (Dzp + Dzm > 0.f) Dz = Dzp*Dzp;
else Dz = Dzm*Dzm;
}
else{
if (Dxp + Dxm < 0.f) Dx = Dxp*Dxp;
else Dx = Dxm*Dxm;
if (Dyp + Dym < 0.f) Dy = Dyp*Dyp;
else Dy = Dym*Dym;
if (Dzp + Dzm < 0.f) Dz = Dzp*Dzp;
else Dz = Dzm*Dzm;
}
//Dx = max(Dxp*Dxp,Dxm*Dxm);
//Dy = max(Dyp*Dyp,Dym*Dym);
//Dz = max(Dzp*Dzp,Dzm*Dzm);
norm=sqrt(Dx + Dy + Dz);
if (norm > 1.0) norm=1.0;
Distance(i,j,k) += dt*sign*(1.0 - norm);
LocalVar += dt*sign*(1.0 - norm);
if (fabs(dt*sign*(1.0 - norm)) > LocalMax)
LocalMax = fabs(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.Volume;
count++;
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;
}
// Explicit instantiations
template void CalcDist<float>( Array<float>&, const Array<char>&, const Domain&, const std::array<bool,3>&, const std::array<double,3>& );

22
analysis/distance.h
View File

@@ -16,6 +16,16 @@ struct Vec {
};
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; }
inline double minmod(double &a, double &b){
double value;
value = a;
if ( a*b < 0.0) value=0.0;
else if (fabs(a) > fabs(b)) value = b;
return value;
}
/*!
* @brief Calculate the distance using a simple method
@@ -40,4 +50,16 @@ void CalcDist( Array<TYPE> &Distance, const Array<char> &ID, const Domain &Dm,
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} );
/*!
* @brief Calculate the distance based on solution of Eikonal equation
* @details This routine calculates the signed distance to the nearest domain surface.
* @param[out] Distance Distance function
* @param[in] ID Domain id
* @param[in] Dm Domain information
* @param[in] timesteps number of timesteps to run for Eikonal solver
* @param[in] periodic Directions that are periodic
*/
double Eikonal(DoubleArray &Distance, const Array<char> &ID, Domain &Dm, int timesteps, const std::array<bool,3>& periodic);
#endif

1
tests/CMakeLists.txt
View File

@@ -70,6 +70,7 @@ ADD_LBPM_TEST_PARALLEL( TestCommD3Q19 8 )
ADD_LBPM_TEST_1_2_4( testCommunication )
ADD_LBPM_TEST( TestWriter )
ADD_LBPM_TEST( TestDatabase )
ADD_LBPM_TEST( TestSetDevice )
ADD_LBPM_PROVISIONAL_TEST( TestMicroCTReader )
IF ( USE_NETCDF )
ADD_LBPM_TEST_PARALLEL( TestNetcdf 8 )

37
tests/TestSetDevice.cpp Normal file
View File

@@ -0,0 +1,37 @@
#include <iostream>
#include "common/MPI_Helpers.h"
#include "common/Utilities.h"
#include "common/ScaLBL.h"
int main (int argc, char **argv)
{
MPI_Init(&argc,&argv);
int rank = MPI_WORLD_RANK();
int nprocs = MPI_WORLD_SIZE();
for (int i=0; i<nprocs; i++) {
if ( rank==i )
printf("%i of %i: Hello world\n",rank,nprocs);
MPI_Barrier(MPI_COMM_WORLD);
}
// Initialize compute device
ScaLBL_SetDevice(rank);
ScaLBL_DeviceBarrier();
MPI_Barrier(MPI_COMM_WORLD);
// Create a memory leak for valgrind to find
if ( nprocs==1 ) {
double *x = new double[1];
ASSERT(x!=NULL);
}
// set the error code
// Note: the error code should be consistent across all processors
int error = 0;
// Finished
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
return error;
}