Merge branch 'master' of https://github.com/JamesEMcClure/LBPM-WIA
This commit is contained in:
James E McClure
commit
ac797709ce
@ -21,6 +21,7 @@ using namespace std;
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// Reading the domain information file
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void read_domain( int rank, int nprocs, MPI_Comm comm,
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int& nprocx, int& nprocy, int& nprocz, int& nx, int& ny, int& nz,
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155
common/Domain.h
155
common/Domain.h
@ -24,7 +24,6 @@ void read_domain( int rank, int nprocs, MPI_Comm comm,
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int& nprocx, int& nprocy, int& nprocz, int& nx, int& ny, int& nz,
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int& nspheres, double& Lx, double& Ly, double& Lz );
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//! Class to hold domain info
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struct Domain{
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// Default constructor
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@ -597,6 +596,160 @@ inline void ReadBinaryFile(char *FILENAME, double *Data, int N)
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File.close();
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}
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inline double minmod(double &a, double &b){
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double value;
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value = a;
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if ( a*b < 0.0) value=0.0;
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else if (fabs(a) > fabs(b)) value = b;
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return value;
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}
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inline 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 Physics 229
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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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else Dx = Dxm*Dxm;
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if (Dyp + Dym > 0.f) Dy = Dyp*Dyp;
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else Dy = Dym*Dym;
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if (Dzp + Dzm > 0.f) Dz = Dzp*Dzp;
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else Dz = 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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else Dx = Dxm*Dxm;
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if (Dyp + Dym < 0.f) Dy = Dyp*Dyp;
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else Dy = Dym*Dym;
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if (Dzp + Dzm < 0.f) Dz = Dzp*Dzp;
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else Dz = 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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#endif
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@ -24,8 +24,12 @@ int main(int argc, char **argv)
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MPI_Comm_size(comm,&nprocs);
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{
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int SOLID=atoi(argv[1]);
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int NWP=atoi(argv[2]);
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bool MULTINPUT=false;
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int NWP,SOLID,rank_offset;
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SOLID=atoi(argv[1]);
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NWP=atoi(argv[2]);
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//char NWP,SOLID;
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//SOLID=argv[1][0];
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//NWP=argv[2][0];
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@ -33,6 +37,13 @@ int main(int argc, char **argv)
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printf("Solid Label: %i \n",SOLID);
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printf("NWP Label: %i \n",NWP);
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}
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if (argc > 3){
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rank_offset = atoi(argv[3]);
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}
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else{
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MULTINPUT=true;
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rank_offset=0;
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}
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//.......................................................................
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// Reading the domain information file
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@ -274,12 +285,14 @@ int main(int argc, char **argv)
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char LocalRankFilename[40];
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sprintf(LocalRankFilename,"ID.%05i",rank);
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sprintf(LocalRankFilename,"ID.%05i",rank+rank_offset);
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FILE *ID = fopen(LocalRankFilename,"wb");
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fwrite(Dm.id,1,N,ID);
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// fwrite(Distance.get(),8,Distance.length(),ID);
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fclose(ID);
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if (!MULTINPUT){
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if (rank==0) printf("Writing symmetric domain reflection\n");
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MPI_Barrier(comm);
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int symrank,sympz;
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@ -306,6 +319,7 @@ int main(int argc, char **argv)
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fwrite(symid,1,N,SYMID);
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fclose(SYMID);
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}
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}
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MPI_Barrier(comm);
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MPI_Finalize();
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}
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@ -26,162 +26,6 @@ inline void MeanFilter(DoubleArray &Mesh){
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}
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}
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inline double minmod(double &a, double &b){
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double value;
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value = a;
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if ( a*b < 0.0) value=0.0;
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else if (fabs(a) > fabs(b)) value = b;
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return value;
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}
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inline 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 Physics 229
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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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else Dx = Dxm*Dxm;
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if (Dyp + Dym > 0.f) Dy = Dyp*Dyp;
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else Dy = Dym*Dym;
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if (Dzp + Dzm > 0.f) Dz = Dzp*Dzp;
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else Dz = 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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else Dx = Dxm*Dxm;
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if (Dyp + Dym < 0.f) Dy = Dyp*Dyp;
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else Dy = Dym*Dym;
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if (Dzp + Dzm < 0.f) Dz = Dzp*Dzp;
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else Dz = 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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int main(int argc, char **argv)
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{
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