Eikonal solver in distance
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JamesEMcclure
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4fd74a78a7
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@ -182,6 +182,147 @@ void CalcVecDist( Array<Vec> &d, const Array<int> &ID0, const Domain &Dm,
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double Eikonal(DoubleArray &Distance, char *ID, Domain &Dm, int timesteps){
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/*
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* This routine converts the data in the Distance array to a signed distance
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* by solving the equation df/dt = sign(1-|grad f|), where Distance provides
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* the values of f on the mesh associated with domain Dm
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* It has been tested with segmented data initialized to values [-1,1]
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* and will converge toward the signed distance to the surface bounding the associated phases
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*
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* Reference:
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* Min C (2010) On reinitializing level set functions, Journal of Computational Physics229
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*/
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int i,j,k;
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double dt=0.1;
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double Dx,Dy,Dz;
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double Dxp,Dxm,Dyp,Dym,Dzp,Dzm;
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double Dxxp,Dxxm,Dyyp,Dyym,Dzzp,Dzzm;
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double sign,norm;
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double LocalVar,GlobalVar,LocalMax,GlobalMax;
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int xdim,ydim,zdim;
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xdim=Dm.Nx-2;
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ydim=Dm.Ny-2;
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zdim=Dm.Nz-2;
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fillHalo<double> fillData(Dm.Comm, Dm.rank_info,xdim,ydim,zdim,1,1,1,0,1);
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// Arrays to store the second derivatives
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DoubleArray Dxx(Dm.Nx,Dm.Ny,Dm.Nz);
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DoubleArray Dyy(Dm.Nx,Dm.Ny,Dm.Nz);
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DoubleArray Dzz(Dm.Nx,Dm.Ny,Dm.Nz);
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int count = 0;
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while (count < timesteps){
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// Communicate the halo of values
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fillData.fill(Distance);
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// Compute second order derivatives
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for (k=1;k<Dm.Nz-1;k++){
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for (j=1;j<Dm.Ny-1;j++){
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for (i=1;i<Dm.Nx-1;i++){
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Dxx(i,j,k) = Distance(i+1,j,k) + Distance(i-1,j,k) - 2*Distance(i,j,k);
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Dyy(i,j,k) = Distance(i,j+1,k) + Distance(i,j-1,k) - 2*Distance(i,j,k);
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Dzz(i,j,k) = Distance(i,j,k+1) + Distance(i,j,k-1) - 2*Distance(i,j,k);
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}
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}
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}
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fillData.fill(Dxx);
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fillData.fill(Dyy);
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fillData.fill(Dzz);
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LocalMax=LocalVar=0.0;
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// Execute the next timestep
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for (k=1;k<Dm.Nz-1;k++){
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for (j=1;j<Dm.Ny-1;j++){
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for (i=1;i<Dm.Nx-1;i++){
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int n = k*Dm.Nx*Dm.Ny + j*Dm.Nx + i;
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sign = -1;
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if (ID[n] == 1) sign = 1;
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// local second derivative terms
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Dxxp = minmod(Dxx(i,j,k),Dxx(i+1,j,k));
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Dyyp = minmod(Dyy(i,j,k),Dyy(i,j+1,k));
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Dzzp = minmod(Dzz(i,j,k),Dzz(i,j,k+1));
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Dxxm = minmod(Dxx(i,j,k),Dxx(i-1,j,k));
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Dyym = minmod(Dyy(i,j,k),Dyy(i,j-1,k));
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Dzzm = minmod(Dzz(i,j,k),Dzz(i,j,k-1));
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/* //............Compute upwind derivatives ...................
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Dxp = Distance(i+1,j,k) - Distance(i,j,k) + 0.5*Dxxp;
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Dyp = Distance(i,j+1,k) - Distance(i,j,k) + 0.5*Dyyp;
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Dzp = Distance(i,j,k+1) - Distance(i,j,k) + 0.5*Dzzp;
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Dxm = Distance(i,j,k) - Distance(i-1,j,k) + 0.5*Dxxm;
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Dym = Distance(i,j,k) - Distance(i,j-1,k) + 0.5*Dyym;
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Dzm = Distance(i,j,k) - Distance(i,j,k-1) + 0.5*Dzzm;
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*/
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Dxp = Distance(i+1,j,k)- Distance(i,j,k) - 0.5*Dxxp;
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Dyp = Distance(i,j+1,k)- Distance(i,j,k) - 0.5*Dyyp;
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Dzp = Distance(i,j,k+1)- Distance(i,j,k) - 0.5*Dzzp;
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Dxm = Distance(i,j,k) - Distance(i-1,j,k) + 0.5*Dxxm;
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Dym = Distance(i,j,k) - Distance(i,j-1,k) + 0.5*Dyym;
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Dzm = Distance(i,j,k) - Distance(i,j,k-1) + 0.5*Dzzm;
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// Compute upwind derivatives for Godunov Hamiltonian
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if (sign < 0.0){
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if (Dxp + Dxm > 0.f) Dx = Dxp*Dxp;
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elseDx = Dxm*Dxm;
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if (Dyp + Dym > 0.f) Dy = Dyp*Dyp;
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elseDy = Dym*Dym;
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if (Dzp + Dzm > 0.f) Dz = Dzp*Dzp;
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elseDz = Dzm*Dzm;
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}
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else{
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if (Dxp + Dxm < 0.f) Dx = Dxp*Dxp;
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elseDx = Dxm*Dxm;
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if (Dyp + Dym < 0.f) Dy = Dyp*Dyp;
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elseDy = Dym*Dym;
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if (Dzp + Dzm < 0.f) Dz = Dzp*Dzp;
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elseDz = Dzm*Dzm;
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}
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//Dx = max(Dxp*Dxp,Dxm*Dxm);
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//Dy = max(Dyp*Dyp,Dym*Dym);
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//Dz = max(Dzp*Dzp,Dzm*Dzm);
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norm=sqrt(Dx + Dy + Dz);
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if (norm > 1.0) norm=1.0;
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Distance(i,j,k) += dt*sign*(1.0 - norm);
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LocalVar += dt*sign*(1.0 - norm);
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if (fabs(dt*sign*(1.0 - norm)) > LocalMax)
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LocalMax = fabs(dt*sign*(1.0 - norm));
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}
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}
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}
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MPI_Allreduce(&LocalVar,&GlobalVar,1,MPI_DOUBLE,MPI_SUM,Dm.Comm);
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MPI_Allreduce(&LocalMax,&GlobalMax,1,MPI_DOUBLE,MPI_MAX,Dm.Comm);
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GlobalVar /= (Dm.Nx-2)*(Dm.Ny-2)*(Dm.Nz-2)*Dm.nprocx*Dm.nprocy*Dm.nprocz;
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count++;
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if (count%50 == 0 && Dm.rank==0 )
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printf("Time=%i, Max variation=%f, Global variation=%f \n",count,GlobalMax,GlobalVar);
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if (fabs(GlobalMax) < 1e-5){
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if (Dm.rank==0) printf("Exiting with max tolerance of 1e-5 \n");
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count=timesteps;
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}
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}
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return GlobalVar;
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}
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// Explicit instantiations
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// Explicit instantiations
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template void CalcDist<float>( Array<float>&, const Array<char>&, const Domain&, const std::array<bool,3>&, const std::array<double,3>& );
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template void CalcDist<float>( Array<float>&, const Array<char>&, const Domain&, const std::array<bool,3>&, const std::array<double,3>& );
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@ -40,4 +40,15 @@ void CalcDist( Array<TYPE> &Distance, const Array<char> &ID, const Domain &Dm,
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void CalcVecDist( Array<Vec> &Distance, const Array<int> &ID, const Domain &Dm,
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void CalcVecDist( Array<Vec> &Distance, const Array<int> &ID, const Domain &Dm,
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const std::array<bool,3>& periodic = {true,true,true}, const std::array<double,3>& dx = {1,1,1} );
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const std::array<bool,3>& periodic = {true,true,true}, const std::array<double,3>& dx = {1,1,1} );
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/*!
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* @brief Calculate the distance based on solution of Eikonal equation
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* @details This routine calculates the signed distance to the nearest domain surface.
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* @param[out] Distance Distance function
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* @param[in] ID Domain id
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* @param[in] Dm Domain information
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* @param[in] timesteps number of timesteps to run for Eikonal solver
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*/
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double Eikonal(DoubleArray &Distance, char *ID, Domain &Dm, int timesteps);
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#endif
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#endif
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