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Moved double precision Eikonal() function into eikonal.h / .hpp

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This commit is contained in:
James E McClure 2018-01-24 16:19:10 -05:00
parent 2134e560d7
commit 38ceb73cfe
2 changed files with 159 additions and 0 deletions
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2
analysis/eikonal.h
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@ -21,6 +21,8 @@
* @param[in] timesteps Maximum number of timesteps to process
* @return Returns the global variation
*/
inline double Eikonal(DoubleArray &Distance, const char *ID, const Domain &Dm, int timesteps);
float Eikonal3D( Array<float> &Distance, const Array<char> &ID, const Domain &Dm, const int timesteps);

157
analysis/eikonal.hpp
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@ -18,9 +18,166 @@ inline float minmod(float &a, float &b)
}
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;
}
/******************************************************************
* Solve the eikonal equation *
******************************************************************/
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
*/
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);
// 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[n] == 0) 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.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);
if (fabs(GlobalMax) < 1e-5){
if (Dm.rank==0) printf("Exiting with max tolerance of 1e-5 \n");
count=timesteps;
}
}
return GlobalVar;
}
inline float Eikonal3D( Array<float> &Distance, const Array<char> &ID, const Domain &Dm, const int timesteps)
{
PROFILE_START("Eikonal3D");