mad tea party
This commit is contained in:
James E McClure
@@ -75,16 +75,16 @@ void ScaLBL_ColorModel::ReadParams(string filename){
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void ScaLBL_ColorModel::ReadInput(){
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int rank=Dm->rank();
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size_t readID;
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//.......................................................................
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if (rank == 0) printf("Read input media... \n");
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//.......................................................................
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sprintf(LocalRankString,"%05d",Dm->rank());
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sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
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sprintf(LocalRestartFile,"%s%s","Restart.",LocalRankString);
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// .......... READ THE INPUT FILE .......................................
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//...........................................................................
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if (rank == 0) cout << "Reading in domain from signed distance function..." << endl;
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if (rank == 0) cout << "Reading in signed distance function..." << endl;
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//.......................................................................
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sprintf(LocalRankString,"%05d",rank);
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sprintf(LocalRankFilename,"%s%s","SignDist.",LocalRankString);
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@@ -92,17 +92,10 @@ void ScaLBL_ColorModel::ReadInput(){
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MPI_Barrier(comm);
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if (rank == 0) cout << "Domain set." << endl;
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if (rank==0) printf("Initialize from segmented data: solid=0, NWP=1, WP=2 \n");
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sprintf(LocalRankFilename,"ID.%05i",rank);
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FILE *IDFILE = fopen(LocalRankFilename,"rb");
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if (IDFILE==NULL) ERROR("lbpm_color_simulator: Error opening file: ID.xxxxx");
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readID=fread(id,1,N,IDFILE);
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if (readID != size_t(N)) printf("lbpm_color_simulator: Error reading ID (rank=%i) \n",Dm->rank());
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fclose(IDFILE);
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// Read restart file
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if (Restart == true){
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if (Dm->rank()==0){
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size_t readID;
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printf("Reading restart file! \n");
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ifstream restart("Restart.txt");
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if (restart.is_open()){
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@@ -124,132 +117,170 @@ void ScaLBL_ColorModel::ReadInput(){
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MPI_Barrier(comm);
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}
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}
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void Domain::AssignComponentLabels(double *phase)
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{
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int NLABELS=0;
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char VALUE=0;
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double AFFINITY=0.f;
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vector <char> Label;
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vector <double> Affinity;
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// Read the labels
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if (rank()==0){
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printf("Component labels:\n");
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ifstream iFILE("ComponentLabels.csv");
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if (iFILE.good()){
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int value;
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while (!iFILE.eof()){
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iFILE>>value;
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iFILE>>AFFINITY;
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VALUE=char(value);
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Label.push_back(value);
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Affinity.push_back(AFFINITY);
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NLABELS++;
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printf("%i %f\n",VALUE,AFFINITY);
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}
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}
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else{
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printf("Using default labels: Solid (0 --> -1.0), NWP (1 --> 1.0), WP (2 --> -1.0)\n");
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// Set default values
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VALUE=0; AFFINITY=-1.0;
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Label.push_back(VALUE);
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Affinity.push_back(AFFINITY);
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NLABELS++;
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VALUE=1; AFFINITY=1.0;
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Label.push_back(VALUE);
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Affinity.push_back(AFFINITY);
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NLABELS++;
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VALUE=2; AFFINITY=-1.0;
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Label.push_back(VALUE);
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Affinity.push_back(AFFINITY);
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NLABELS++;
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}
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}
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MPI_Barrier(Comm);
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// Broadcast the list
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MPI_Bcast(&NLABELS,1,MPI_INT,0,Comm);
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//printf("rank=%i, NLABELS=%i \n ",rank(),NLABELS);
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// Copy into contiguous buffers
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char *LabelList;
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double * AffinityList;
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LabelList=new char[NLABELS];
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AffinityList=new double[NLABELS];
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if (rank()==0){
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for (int idx=0; idx < NLABELS; idx++){
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VALUE=Label[idx];
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AFFINITY=Affinity[idx];
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printf("rank=%i, idx=%i, value=%d, affinity=%f \n",rank(),idx,VALUE,AFFINITY);
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LabelList[idx]=VALUE;
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AffinityList[idx]=AFFINITY;
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}
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}
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MPI_Barrier(Comm);
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MPI_Bcast(LabelList,NLABELS,MPI_CHAR,0,Comm);
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MPI_Bcast(AffinityList,NLABELS,MPI_DOUBLE,0,Comm);
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// Assign the labels
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for (int k=0;k<Nz;k++){
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for (int j=0;j<Ny;j++){
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for (int i=0;i<Nx;i++){
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int n = k*Nx*Ny+j*Nx+i;
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VALUE=id[n];
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// Assign the affinity from the paired list
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for (int idx=0; idx < NLABELS; idx++){
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//printf("rank=%i, idx=%i, value=%i, %i, \n",rank(),idx, VALUE,LabelList[idx]);
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if (VALUE == LabelList[idx]){
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AFFINITY=AffinityList[idx];
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idx = NLABELS;
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}
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}
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phase[n] = AFFINITY;
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}
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}
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}
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}
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void ScaLBL_ColorModel::Create(){
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/*
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* This function creates the variables needed to run a LBM
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*/
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//.......................................................................
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// Compute the media porosity, assign phase labels and solid composition
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//.......................................................................
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int nprocs=nprocx*nprocy*nprocz;
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int rank=Dm->rank();
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double sum;
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double porosity;
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double sum_local=0.0;
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double iVol_global = 1.0/(1.0*(Nx-2)*(Ny-2)*(Nz-2)*nprocs);
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if (BoundaryCondition > 0) iVol_global = 1.0/(1.0*(Nx-2)*nprocx*(Ny-2)*nprocy*((Nz-2)*nprocz-6));
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Np=0; // number of local pore nodes
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//.......................................................................
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for (int k=1;k<Nz-1;k++){
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for (int j=1;j<Ny-1;j++){
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for (int i=1;i<Nx-1;i++){
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int n = k*Nx*Ny+j*Nx+i;
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if (id[n] > 0){
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sum_local+=1.0;
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Np++;
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}
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}
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}
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}
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MPI_Allreduce(&sum_local,&sum,1,MPI_DOUBLE,MPI_SUM,comm);
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porosity = sum*iVol_global;
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if (rank==0) printf("Media porosity = %f \n",porosity);
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//.........................................................
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// If external boundary conditions are applied remove solid
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if (BoundaryCondition > 0 && Dm->kproc() == 0){
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for (int k=0; k<3; k++){
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for (int j=0;j<Ny;j++){
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for (int i=0;i<Nx;i++){
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int n = k*Nx*Ny+j*Nx+i;
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//id[n] = 1;
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Averages->SDs(n) = max(Averages->SDs(n),1.0*(2.5-k));
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}
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}
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}
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}
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if (BoundaryCondition > 0 && Dm->kproc() == nprocz-1){
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for (int k=Nz-3; k<Nz; k++){
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for (int j=0;j<Ny;j++){
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for (int i=0;i<Nx;i++){
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int n = k*Nx*Ny+j*Nx+i;
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//id[n] = 2;
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Averages->SDs(n) = max(Averages->SDs(n),1.0*(k-Nz+2.5));
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}
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}
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}
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}
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//.........................................................
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// don't perform computations at the eight corners
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id[0] = id[Nx-1] = id[(Ny-1)*Nx] = id[(Ny-1)*Nx + Nx-1] = 0;
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id[(Nz-1)*Nx*Ny] = id[(Nz-1)*Nx*Ny+Nx-1] = id[(Nz-1)*Nx*Ny+(Ny-1)*Nx] = id[(Nz-1)*Nx*Ny+(Ny-1)*Nx + Nx-1] = 0;
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//.........................................................
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int nprocs=nprocx*nprocy*nprocz;
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int rank=Dm->rank();
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//.........................................................
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// don't perform computations at the eight corners
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id[0] = id[Nx-1] = id[(Ny-1)*Nx] = id[(Ny-1)*Nx + Nx-1] = 0;
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id[(Nz-1)*Nx*Ny] = id[(Nz-1)*Nx*Ny+Nx-1] = id[(Nz-1)*Nx*Ny+(Ny-1)*Nx] = id[(Nz-1)*Nx*Ny+(Ny-1)*Nx + Nx-1] = 0;
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//.........................................................
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// Initialize communication structures in averaging domain
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for (int i=0; i<Mask->Nx*Mask->Ny*Mask->Nz; i++) Mask->id[i] = id[i];
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Mask->CommInit(comm);
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// Initialize communication structures in averaging domain
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for (int i=0; i<Mask->Nx*Mask->Ny*Mask->Nz; i++) Mask->id[i] = id[i];
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Mask->CommInit(comm);
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double *PhaseLabel;
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PhaseLabel = new double[N];
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Mask->AssignComponentLabels(PhaseLabel);
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//...........................................................................
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if (rank==0) printf ("Create ScaLBL_Communicator \n");
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// Create a communicator for the device (will use optimized layout)
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// ScaLBL_Communicator ScaLBL_Comm(Mask); // original
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ScaLBL_Comm = std::shared_ptr<ScaLBL_Communicator>(new ScaLBL_Communicator(Mask));
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//...........................................................................
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if (rank==0) printf ("Create ScaLBL_Communicator \n");
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// Create a communicator for the device (will use optimized layout)
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// ScaLBL_Communicator ScaLBL_Comm(Mask); // original
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ScaLBL_Comm = std::shared_ptr<ScaLBL_Communicator>(new ScaLBL_Communicator(Mask));
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//Create a second communicator based on the regular data layout
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//ScaLBL_Communicator ScaLBL_Comm_Regular(Mask);
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int Npad=(Np/16 + 2)*16;
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if (rank==0) printf ("Set up memory efficient layout \n");
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Map.resize(Nx,Ny,Nz); Map.fill(-2);
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auto neighborList= new int[18*Npad];
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Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Mask->id,Np);
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MPI_Barrier(comm);
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int Npad=(Np/16 + 2)*16;
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if (rank==0) printf ("Set up memory efficient layout \n");
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Map.resize(Nx,Ny,Nz); Map.fill(-2);
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auto neighborList= new int[18*Npad];
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Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Mask->id,Np);
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MPI_Barrier(comm);
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//...........................................................................
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// MAIN VARIABLES ALLOCATED HERE
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//...........................................................................
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// LBM variables
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if (rank==0) printf ("Allocating distributions \n");
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//......................device distributions.................................
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int dist_mem_size = Np*sizeof(double);
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int neighborSize=18*(Np*sizeof(int));
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//...........................................................................
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// MAIN VARIABLES ALLOCATED HERE
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//...........................................................................
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// LBM variables
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if (rank==0) printf ("Allocating distributions \n");
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//......................device distributions.................................
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int dist_mem_size = Np*sizeof(double);
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int neighborSize=18*(Np*sizeof(int));
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//...........................................................................
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ScaLBL_AllocateDeviceMemory((void **) &NeighborList, neighborSize);
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ScaLBL_AllocateDeviceMemory((void **) &dvcMap, sizeof(int)*Np);
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ScaLBL_AllocateDeviceMemory((void **) &fq, 19*dist_mem_size);
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ScaLBL_AllocateDeviceMemory((void **) &Aq, 7*dist_mem_size);
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ScaLBL_AllocateDeviceMemory((void **) &Bq, 7*dist_mem_size);
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ScaLBL_AllocateDeviceMemory((void **) &Den, 2*dist_mem_size);
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ScaLBL_AllocateDeviceMemory((void **) &Phi, sizeof(double)*Np);
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ScaLBL_AllocateDeviceMemory((void **) &Pressure, sizeof(double)*Np);
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ScaLBL_AllocateDeviceMemory((void **) &Velocity, 3*sizeof(double)*Np);
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ScaLBL_AllocateDeviceMemory((void **) &Gradient, 3*sizeof(double)*Np);
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ScaLBL_AllocateDeviceMemory((void **) &SolidPotential, 3*sizeof(double)*Np);
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//...........................................................................
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// Update GPU data structures
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if (rank==0) printf ("Setting up device map and neighbor list \n");
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//...........................................................................
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ScaLBL_AllocateDeviceMemory((void **) &NeighborList, neighborSize);
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ScaLBL_AllocateDeviceMemory((void **) &dvcMap, sizeof(int)*Np);
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ScaLBL_AllocateDeviceMemory((void **) &fq, 19*dist_mem_size);
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ScaLBL_AllocateDeviceMemory((void **) &Aq, 7*dist_mem_size);
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ScaLBL_AllocateDeviceMemory((void **) &Bq, 7*dist_mem_size);
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ScaLBL_AllocateDeviceMemory((void **) &Den, 2*dist_mem_size);
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ScaLBL_AllocateDeviceMemory((void **) &Phi, sizeof(double)*Np);
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ScaLBL_AllocateDeviceMemory((void **) &Pressure, sizeof(double)*Np);
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ScaLBL_AllocateDeviceMemory((void **) &Velocity, 3*sizeof(double)*Np);
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ScaLBL_AllocateDeviceMemory((void **) &Gradient, 3*sizeof(double)*Np);
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ScaLBL_AllocateDeviceMemory((void **) &SolidPotential, 3*sizeof(double)*Np);
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//...........................................................................
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// Update GPU data structures
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if (rank==0) printf ("Setting up device map and neighbor list \n");
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// copy the neighbor list
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ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
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int *TmpMap;
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TmpMap=new int[Np];
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for (int k=1; k<Nz-1; k++){
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for (int j=1; j<Ny-1; j++){
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for (int i=1; i<Nx-1; i++){
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int idx=Map(i,j,k);
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if (!(idx < 0))
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TmpMap[idx] = k*Nx*Ny+j*Nx+i;
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}
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}
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}
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ScaLBL_CopyToDevice(dvcMap, TmpMap, sizeof(int)*Np);
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ScaLBL_DeviceBarrier();
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delete [] TmpMap;
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int *TmpMap;
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TmpMap=new int[Np];
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for (int k=1; k<Nz-1; k++){
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for (int j=1; j<Ny-1; j++){
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for (int i=1; i<Nx-1; i++){
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int idx=Map(i,j,k);
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if (!(idx < 0))
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TmpMap[idx] = k*Nx*Ny+j*Nx+i;
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}
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}
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}
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ScaLBL_CopyToDevice(dvcMap, TmpMap, sizeof(int)*Np);
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ScaLBL_DeviceBarrier();
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delete [] TmpMap;
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}
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/********************************************************
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* AssignComponentLabels *
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********************************************************/
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void ScaLBL_ColorModel::Initialize(){
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/*
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* This function initializes model (includes both mobile and immobile components)
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@@ -24,6 +24,7 @@ public:
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// functions in they should be run
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void ReadParams(string filename);
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void ReadParams(std::shared_ptr<Database> db0);
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void AssignComponentLabels(double *phase);
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void ReadInput();
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void Create();
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void Initialize();
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