Merge branch 'Greyscale-devel' of github.com:JamesEMcClure/LBPM-WIA into Greyscale
This commit is contained in:
JamesEMcclure
commit
dd4a317b13
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@ -405,7 +405,7 @@ void Domain::Decomp(std::string Filename)
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for (int idx=0; idx<ReadValues.size(); idx++){
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long int label=ReadValues[idx];
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long int count=LabelCount[idx];
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printf("Label=%d, Count=%d \n",label,count);
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printf("Label=%ld, Count=%ld \n",label,count);
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}
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}
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@ -448,7 +448,7 @@ void Domain::Decomp(std::string Filename)
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}
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if (inlet_layers_z > 0){
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printf("Checkerboard pattern at z inlet for %i layers \n",inlet_layers_z);
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printf("Checkerboard pattern at z inlet for %i layers, saturated with phase label=%i \n",inlet_layers_z,inlet_layers_phase);
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// use checkerboard pattern
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for (int k = zStart; k < zStart+inlet_layers_z; k++){
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for (int j = 0; j<global_Ny; j++){
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@ -507,7 +507,7 @@ void Domain::Decomp(std::string Filename)
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}
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if (outlet_layers_z > 0){
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printf("Checkerboard pattern at z outlet for %i layers \n",outlet_layers_z);
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printf("Checkerboard pattern at z outlet for %i layers, saturated with phase label=%i \n",outlet_layers_z,outlet_layers_phase);
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// use checkerboard pattern
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for (int k = zStart + nz*nprocz - outlet_layers_z; k < zStart + nz*nprocz; k++){
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for (int j = 0; j<global_Ny; j++){
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@ -600,6 +600,60 @@ void Domain::Decomp(std::string Filename)
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MPI_Recv(id,N,MPI_CHAR,0,15,Comm,MPI_STATUS_IGNORE);
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}
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MPI_Barrier(Comm);
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// Compute the porosity
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double sum;
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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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//.........................................................
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// If external boundary conditions are applied remove solid
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if (BoundaryCondition > 0 && kproc() == 0){
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if (inlet_layers_z < 4){
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inlet_layers_z=4;
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if(RANK==0){
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printf("NOTE:Non-periodic BC is applied, but the number of Z-inlet layers is not specified (or is smaller than 3 voxels) \n the number of Z-inlet layer is reset to %i voxels, saturated with phase label=%i \n",inlet_layers_z-1,inlet_layers_phase);
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}
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}
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for (int k=0; k<inlet_layers_z; 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] = inlet_layers_phase;
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}
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}
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}
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}
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if (BoundaryCondition > 0 && kproc() == nprocz-1){
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if (outlet_layers_z < 4){
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outlet_layers_z=4;
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if(RANK==nprocs-1){
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printf("NOTE:Non-periodic BC is applied, but the number of Z-outlet layers is not specified (or is smaller than 3 voxels) \n the number of Z-outlet layer is reset to %i voxels, saturated with phase label=%i \n",outlet_layers_z-1,outlet_layers_phase);
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}
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}
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for (int k=Nz-outlet_layers_z; 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] = outlet_layers_phase;
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}
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}
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}
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}
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for (int k=inlet_layers_z+1; k<Nz-outlet_layers_z-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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}
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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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}
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void Domain::AggregateLabels(char *FILENAME){
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@ -61,6 +61,7 @@ extern "C" void ScaLBL_UnpackDenD3Q7(int *list, int count, double *recvbuf, int
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extern "C" void ScaLBL_D3Q19_Init(double *Dist, int Np);
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extern "C" void ScaLBL_D3Q19_Momentum(double *dist, double *vel, int Np);
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extern "C" void ScaLBL_D3Q19_Pressure(double *dist, double *press, int Np);
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@ -70,6 +71,23 @@ extern "C" void ScaLBL_D3Q19_AAeven_BGK(double *dist, int start, int finish, int
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extern "C" void ScaLBL_D3Q19_AAodd_BGK(int *neighborList, double *dist, int start, int finish, int Np, double rlx, double Fx, double Fy, double Fz);
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// GREYSCALE MODEL
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extern "C" void ScaLBL_D3Q19_GreyIMRT_Init(double *Dist, int Np, double Den);
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extern "C" void ScaLBL_D3Q19_AAeven_Greyscale(double *dist, int start, int finish, int Np, double rlx, double rlx_eff, double Fx, double Fy, double Fz,
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double *Poros,double *Perm, double *Velocity,double *Pressure);
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extern "C" void ScaLBL_D3Q19_AAodd_Greyscale(int *neighborList, double *dist, int start, int finish, int Np, double rlx, double rlx_eff, double Fx, double Fy, double Fz,
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double *Poros,double *Perm, double *Velocity,double *Pressure);
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extern "C" void ScaLBL_D3Q19_AAeven_Greyscale_IMRT(double *dist, int start, int finish, int Np, double rlx, double rlx_eff, double Fx, double Fy, double Fz,
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double *Poros,double *Perm, double *Velocity,double Den,double *Pressure);
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extern "C" void ScaLBL_D3Q19_AAodd_Greyscale_IMRT(int *neighborList, double *dist, int start, int finish, int Np, double rlx, double rlx_eff, double Fx, double Fy, double Fz,
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double *Poros,double *Perm, double *Velocity,double Den,double *Pressure);
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// MRT MODEL
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extern "C" void ScaLBL_D3Q19_AAeven_MRT(double *dist, int start, int finish, int Np, double rlx_setA, double rlx_setB, double Fx,
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double Fy, double Fz);
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@ -99,6 +99,33 @@ extern "C" void ScaLBL_D3Q19_Init(double *dist, int Np)
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}
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}
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extern "C" void ScaLBL_D3Q19_GreyIMRT_Init(double *dist, int Np, double Den)
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{
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int n;
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for (n=0; n<Np; n++){
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dist[n] = Den - 0.6666666666666667;
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dist[Np+n] = 0.055555555555555555; //double(100*n)+1.f;
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dist[2*Np+n] = 0.055555555555555555; //double(100*n)+2.f;
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dist[3*Np+n] = 0.055555555555555555; //double(100*n)+3.f;
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dist[4*Np+n] = 0.055555555555555555; //double(100*n)+4.f;
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dist[5*Np+n] = 0.055555555555555555; //double(100*n)+5.f;
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dist[6*Np+n] = 0.055555555555555555; //double(100*n)+6.f;
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dist[7*Np+n] = 0.0277777777777778; //double(100*n)+7.f;
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dist[8*Np+n] = 0.0277777777777778; //double(100*n)+8.f;
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dist[9*Np+n] = 0.0277777777777778; //double(100*n)+9.f;
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dist[10*Np+n] = 0.0277777777777778; //double(100*n)+10.f;
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dist[11*Np+n] = 0.0277777777777778; //double(100*n)+11.f;
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dist[12*Np+n] = 0.0277777777777778; //double(100*n)+12.f;
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dist[13*Np+n] = 0.0277777777777778; //double(100*n)+13.f;
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dist[14*Np+n] = 0.0277777777777778; //double(100*n)+14.f;
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dist[15*Np+n] = 0.0277777777777778; //double(100*n)+15.f;
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dist[16*Np+n] = 0.0277777777777778; //double(100*n)+16.f;
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dist[17*Np+n] = 0.0277777777777778; //double(100*n)+17.f;
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dist[18*Np+n] = 0.0277777777777778; //double(100*n)+18.f;
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}
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}
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//*************************************************************************
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extern "C" void ScaLBL_D3Q19_Swap(char *ID, double *disteven, double *distodd, int Nx, int Ny, int Nz)
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{
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1567
cpu/Greyscale.cpp
Normal file
1567
cpu/Greyscale.cpp
Normal file
File diff suppressed because it is too large
Load Diff
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@ -7,11 +7,26 @@ ReadSubphase<-function(PATH){
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S<-read.csv(FILE,head=TRUE,sep=" ")
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S$Vw<-S$Vwc+S$Vwd
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S$Vn<-S$Vnc+S$Vnd
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S$Aw<-S$Awc+S$Awd
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S$An<-S$Anc+S$And
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S$Hw<-S$Hwc+S$Hwd
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S$Hn<-S$Hnc+S$Hnd
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S$Xw<-S$Xwc+S$Xwd
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S$Xn<-S$Xnc+S$Xnd
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S$Sw<-S$Vw/(S$Vn+S$Vw)
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S$pw<-(S$pwc*S$Vwc+S$pwd*S$Vwd) / (S$Vwc+S$Vwd)
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S$pn<-(S$pnc*S$Vnc+S$pnd*S$Vnd) / (S$Vnc+S$Vnd)
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S$Qwx<-S$Vw*(S$Pwc_x+S$Pwd_x)/(S$Mwc+S$Mwd)
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S$Qnx<-S$Vn*(S$Pnc_x+S$Pnd_x)/(S$Mnc+S$Mnd)
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S$Krn<-S$nun*S$Qnx/S$Fx
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S$Krw<-S$nuw*S$Qwx/S$Fx
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S$Qwy<-S$Vw*(S$Pwc_y+S$Pwd_y)/(S$Mwc+S$Mwd)
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S$Qny<-S$Vn*(S$Pnc_y+S$Pnd_y)/(S$Mnc+S$Mnd)
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S$Qwz<-S$Vw*(S$Pwc_z+S$Pwd_z)/(S$Mwc+S$Mwd)
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S$Qnz<-S$Vn*(S$Pnc_z+S$Pnd_z)/(S$Mnc+S$Mnd)
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S$Krn<-S$nun*S$Qnz/S$Fz
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S$Krw<-S$nuw*S$Qwz/S$Fz
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S$Case<-PATH
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return(S)
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}
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|
|
|
|||
40
gpu/D3Q19.cu
40
gpu/D3Q19.cu
|
|
@ -282,6 +282,36 @@ __global__ void dvc_ScaLBL_D3Q19_Init(double *dist, int Np)
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|||
}
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}
|
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__global__ void dvc_ScaLBL_D3Q19_GreyIMRT_Init(double *dist, int Np, double Den)
|
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{
|
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int n;
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int S = Np/NBLOCKS/NTHREADS + 1;
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for (int s=0; s<S; s++){
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//........Get 1-D index for this thread....................
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n = S*blockIdx.x*blockDim.x + s*blockDim.x + threadIdx.x;
|
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if (n<Np ){
|
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dist[n] = Den - 0.6666666666666667;
|
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dist[Np+n] = 0.055555555555555555; //double(100*n)+1.f;
|
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dist[2*Np+n] = 0.055555555555555555; //double(100*n)+2.f;
|
||||
dist[3*Np+n] = 0.055555555555555555; //double(100*n)+3.f;
|
||||
dist[4*Np+n] = 0.055555555555555555; //double(100*n)+4.f;
|
||||
dist[5*Np+n] = 0.055555555555555555; //double(100*n)+5.f;
|
||||
dist[6*Np+n] = 0.055555555555555555; //double(100*n)+6.f;
|
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dist[7*Np+n] = 0.0277777777777778; //double(100*n)+7.f;
|
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dist[8*Np+n] = 0.0277777777777778; //double(100*n)+8.f;
|
||||
dist[9*Np+n] = 0.0277777777777778; //double(100*n)+9.f;
|
||||
dist[10*Np+n] = 0.0277777777777778; //double(100*n)+10.f;
|
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dist[11*Np+n] = 0.0277777777777778; //double(100*n)+11.f;
|
||||
dist[12*Np+n] = 0.0277777777777778; //double(100*n)+12.f;
|
||||
dist[13*Np+n] = 0.0277777777777778; //double(100*n)+13.f;
|
||||
dist[14*Np+n] = 0.0277777777777778; //double(100*n)+14.f;
|
||||
dist[15*Np+n] = 0.0277777777777778; //double(100*n)+15.f;
|
||||
dist[16*Np+n] = 0.0277777777777778; //double(100*n)+16.f;
|
||||
dist[17*Np+n] = 0.0277777777777778; //double(100*n)+17.f;
|
||||
dist[18*Np+n] = 0.0277777777777778; //double(100*n)+18.f;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
//*************************************************************************
|
||||
__global__ void dvc_ScaLBL_D3Q19_Swap_Compact(int *neighborList, double *disteven, double *distodd, int Np, int q){
|
||||
|
|
@ -2340,7 +2370,15 @@ extern "C" void ScaLBL_D3Q19_Init(double *dist, int Np){
|
|||
dvc_ScaLBL_D3Q19_Init<<<NBLOCKS,NTHREADS >>>(dist, Np);
|
||||
cudaError_t err = cudaGetLastError();
|
||||
if (cudaSuccess != err){
|
||||
printf("CUDA error in ScaLBL_D3Q19_AA_Init: %s \n",cudaGetErrorString(err));
|
||||
printf("CUDA error in ScaLBL_D3Q19_Init: %s \n",cudaGetErrorString(err));
|
||||
}
|
||||
}
|
||||
|
||||
extern "C" void ScaLBL_D3Q19_GreyIMRT_Init(double *dist, int Np, double Den){
|
||||
dvc_ScaLBL_D3Q19_GreyIMRT_Init<<<NBLOCKS,NTHREADS >>>(dist, Np, Den);
|
||||
cudaError_t err = cudaGetLastError();
|
||||
if (cudaSuccess != err){
|
||||
printf("CUDA error in ScaLBL_D3Q19_GreyIMRT_Init: %s \n",cudaGetErrorString(err));
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
1633
gpu/Greyscale.cu
Normal file
1633
gpu/Greyscale.cu
Normal file
File diff suppressed because it is too large
Load Diff
892
models/GreyscaleModel.cpp
Normal file
892
models/GreyscaleModel.cpp
Normal file
|
|
@ -0,0 +1,892 @@
|
|||
/*
|
||||
Greyscale lattice boltzmann model
|
||||
*/
|
||||
#include "models/GreyscaleModel.h"
|
||||
#include "analysis/distance.h"
|
||||
#include "analysis/morphology.h"
|
||||
#include <stdlib.h>
|
||||
#include <time.h>
|
||||
|
||||
template<class TYPE>
|
||||
void DeleteArray( const TYPE *p )
|
||||
{
|
||||
delete [] p;
|
||||
}
|
||||
|
||||
ScaLBL_GreyscaleModel::ScaLBL_GreyscaleModel(int RANK, int NP, MPI_Comm COMM):
|
||||
rank(RANK), nprocs(NP), Restart(0),timestep(0),timestepMax(0),tau(0),tau_eff(0),Den(0),Fx(0),Fy(0),Fz(0),flux(0),din(0),dout(0),GreyPorosity(0),
|
||||
Nx(0),Ny(0),Nz(0),N(0),Np(0),nprocx(0),nprocy(0),nprocz(0),BoundaryCondition(0),Lx(0),Ly(0),Lz(0),comm(COMM)
|
||||
{
|
||||
SignDist.resize(Nx,Ny,Nz);
|
||||
SignDist.fill(0);
|
||||
|
||||
}
|
||||
ScaLBL_GreyscaleModel::~ScaLBL_GreyscaleModel(){
|
||||
|
||||
}
|
||||
|
||||
void ScaLBL_GreyscaleModel::ReadParams(string filename){
|
||||
// read the input database
|
||||
db = std::make_shared<Database>( filename );
|
||||
domain_db = db->getDatabase( "Domain" );
|
||||
greyscale_db = db->getDatabase( "Greyscale" );
|
||||
analysis_db = db->getDatabase( "Analysis" );
|
||||
vis_db = db->getDatabase( "Visualization" );
|
||||
|
||||
// set defaults
|
||||
timestepMax = 100000;
|
||||
tau = 1.0;
|
||||
tau_eff = tau;
|
||||
Den = 1.0;//constant density
|
||||
tolerance = 0.01;
|
||||
Fx = Fy = Fz = 0.0;
|
||||
Restart=false;
|
||||
din=dout=1.0;
|
||||
flux=0.0;
|
||||
dp = 10.0; //unit of 'dp': voxel
|
||||
CollisionType = 1; //1: IMRT; 2: BGK
|
||||
|
||||
// ---------------------- Greyscale Model parameters -----------------------//
|
||||
if (greyscale_db->keyExists( "timestepMax" )){
|
||||
timestepMax = greyscale_db->getScalar<int>( "timestepMax" );
|
||||
}
|
||||
if (greyscale_db->keyExists( "tau" )){
|
||||
tau = greyscale_db->getScalar<double>( "tau" );
|
||||
}
|
||||
tau_eff = greyscale_db->getWithDefault<double>( "tau_eff", tau );
|
||||
if (greyscale_db->keyExists( "Den" )){
|
||||
Den = greyscale_db->getScalar<double>( "Den" );
|
||||
}
|
||||
if (greyscale_db->keyExists( "dp" )){
|
||||
dp = greyscale_db->getScalar<double>( "dp" );
|
||||
}
|
||||
if (greyscale_db->keyExists( "F" )){
|
||||
Fx = greyscale_db->getVector<double>( "F" )[0];
|
||||
Fy = greyscale_db->getVector<double>( "F" )[1];
|
||||
Fz = greyscale_db->getVector<double>( "F" )[2];
|
||||
}
|
||||
if (greyscale_db->keyExists( "Restart" )){
|
||||
Restart = greyscale_db->getScalar<bool>( "Restart" );
|
||||
}
|
||||
if (greyscale_db->keyExists( "din" )){
|
||||
din = greyscale_db->getScalar<double>( "din" );
|
||||
}
|
||||
if (greyscale_db->keyExists( "dout" )){
|
||||
dout = greyscale_db->getScalar<double>( "dout" );
|
||||
}
|
||||
if (greyscale_db->keyExists( "flux" )){
|
||||
flux = greyscale_db->getScalar<double>( "flux" );
|
||||
}
|
||||
if (greyscale_db->keyExists( "tolerance" )){
|
||||
tolerance = greyscale_db->getScalar<double>( "tolerance" );
|
||||
}
|
||||
auto collision = greyscale_db->getWithDefault<std::string>( "collision", "IMRT" );
|
||||
if (collision == "BGK"){
|
||||
CollisionType=2;
|
||||
}
|
||||
// ------------------------------------------------------------------------//
|
||||
|
||||
//------------------------ Other Domain parameters ------------------------//
|
||||
BoundaryCondition = 0;
|
||||
if (domain_db->keyExists( "BC" )){
|
||||
BoundaryCondition = domain_db->getScalar<int>( "BC" );
|
||||
}
|
||||
// ------------------------------------------------------------------------//
|
||||
}
|
||||
|
||||
void ScaLBL_GreyscaleModel::SetDomain(){
|
||||
Dm = std::shared_ptr<Domain>(new Domain(domain_db,comm)); // full domain for analysis
|
||||
Mask = std::shared_ptr<Domain>(new Domain(domain_db,comm)); // mask domain removes immobile phases
|
||||
// domain parameters
|
||||
Nx = Dm->Nx;
|
||||
Ny = Dm->Ny;
|
||||
Nz = Dm->Nz;
|
||||
Lx = Dm->Lx;
|
||||
Ly = Dm->Ly;
|
||||
Lz = Dm->Lz;
|
||||
N = Nx*Ny*Nz;
|
||||
|
||||
SignDist.resize(Nx,Ny,Nz);
|
||||
Velocity_x.resize(Nx,Ny,Nz);
|
||||
Velocity_y.resize(Nx,Ny,Nz);
|
||||
Velocity_z.resize(Nx,Ny,Nz);
|
||||
PorosityMap.resize(Nx,Ny,Nz);
|
||||
Pressure.resize(Nx,Ny,Nz);
|
||||
|
||||
id = new signed char [N];
|
||||
for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = 1; // initialize this way
|
||||
MPI_Barrier(comm);
|
||||
Dm->CommInit();
|
||||
MPI_Barrier(comm);
|
||||
// Read domain parameters
|
||||
rank = Dm->rank();
|
||||
nprocx = Dm->nprocx();
|
||||
nprocy = Dm->nprocy();
|
||||
nprocz = Dm->nprocz();
|
||||
}
|
||||
|
||||
void ScaLBL_GreyscaleModel::ReadInput(){
|
||||
|
||||
sprintf(LocalRankString,"%05d",rank);
|
||||
sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
|
||||
sprintf(LocalRestartFile,"%s%s","Restart.",LocalRankString);
|
||||
|
||||
if (domain_db->keyExists( "Filename" )){
|
||||
auto Filename = domain_db->getScalar<std::string>( "Filename" );
|
||||
Mask->Decomp(Filename);
|
||||
}
|
||||
else{
|
||||
if (rank==0) printf("Filename of input image is not found, reading ID.0* instead.");
|
||||
Mask->ReadIDs();
|
||||
}
|
||||
for (int i=0; i<Nx*Ny*Nz; i++) id[i] = Mask->id[i]; // save what was read
|
||||
|
||||
// Generate the signed distance map
|
||||
// Initialize the domain and communication
|
||||
Array<char> id_solid(Nx,Ny,Nz);
|
||||
int count = 0;
|
||||
// Solve for the position of the solid phase
|
||||
for (int k=0;k<Nz;k++){
|
||||
for (int j=0;j<Ny;j++){
|
||||
for (int i=0;i<Nx;i++){
|
||||
int n = k*Nx*Ny+j*Nx+i;
|
||||
// Initialize the solid phase
|
||||
signed char label = Mask->id[n];
|
||||
if (label > 0) id_solid(i,j,k) = 1;
|
||||
else id_solid(i,j,k) = 0;
|
||||
}
|
||||
}
|
||||
}
|
||||
// Initialize the signed distance function
|
||||
for (int k=0;k<Nz;k++){
|
||||
for (int j=0;j<Ny;j++){
|
||||
for (int i=0;i<Nx;i++){
|
||||
int n=k*Nx*Ny+j*Nx+i;
|
||||
// Initialize distance to +/- 1
|
||||
SignDist(i,j,k) = 2.0*double(id_solid(i,j,k))-1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
// MeanFilter(SignDist);
|
||||
if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
|
||||
CalcDist(SignDist,id_solid,*Mask);
|
||||
|
||||
if (rank == 0) cout << "Domain set." << endl;
|
||||
}
|
||||
|
||||
/********************************************************
|
||||
* AssignComponentLabels *
|
||||
********************************************************/
|
||||
void ScaLBL_GreyscaleModel::AssignComponentLabels(double *Porosity, double *Permeability)
|
||||
{
|
||||
size_t NLABELS=0;
|
||||
signed char VALUE=0;
|
||||
double POROSITY=0.f;
|
||||
double PERMEABILITY=0.f;
|
||||
|
||||
auto LabelList = greyscale_db->getVector<int>( "ComponentLabels" );
|
||||
auto PorosityList = greyscale_db->getVector<double>( "PorosityList" );
|
||||
auto PermeabilityList = greyscale_db->getVector<double>( "PermeabilityList" );
|
||||
|
||||
NLABELS=LabelList.size();
|
||||
if (NLABELS != PorosityList.size()){
|
||||
ERROR("Error: ComponentLabels and PorosityList must be the same length! \n");
|
||||
}
|
||||
|
||||
double label_count[NLABELS];
|
||||
double label_count_global[NLABELS];
|
||||
// Assign the labels
|
||||
|
||||
for (int idx=0; idx<NLABELS; idx++) label_count[idx]=0;
|
||||
|
||||
for (int k=1;k<Nz-1;k++){
|
||||
for (int j=1;j<Ny-1;j++){
|
||||
for (int i=1;i<Nx-1;i++){
|
||||
int n = k*Nx*Ny+j*Nx+i;
|
||||
VALUE=id[n];
|
||||
// Assign the affinity from the paired list
|
||||
for (unsigned int idx=0; idx < NLABELS; idx++){
|
||||
//printf("idx=%i, value=%i, %i, \n",idx, VALUE,LabelList[idx]);
|
||||
if (VALUE == LabelList[idx]){
|
||||
POROSITY=PorosityList[idx];
|
||||
label_count[idx] += 1.0;
|
||||
idx = NLABELS;
|
||||
//Mask->id[n] = 0; // set mask to zero since this is an immobile component
|
||||
}
|
||||
}
|
||||
int idx = Map(i,j,k);
|
||||
if (!(idx < 0)){
|
||||
if (POROSITY<=0.0){
|
||||
ERROR("Error: Porosity for grey voxels must be 0.0 < Porosity <= 1.0 !\n");
|
||||
}
|
||||
else{
|
||||
Porosity[idx] = POROSITY;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (NLABELS != PermeabilityList.size()){
|
||||
ERROR("Error: ComponentLabels and PermeabilityList must be the same length! \n");
|
||||
}
|
||||
for (int k=1;k<Nz-1;k++){
|
||||
for (int j=1;j<Ny-1;j++){
|
||||
for (int i=1;i<Nx-1;i++){
|
||||
int n = k*Nx*Ny+j*Nx+i;
|
||||
VALUE=id[n];
|
||||
// Assign the affinity from the paired list
|
||||
for (unsigned int idx=0; idx < NLABELS; idx++){
|
||||
//printf("idx=%i, value=%i, %i, \n",idx, VALUE,LabelList[idx]);
|
||||
if (VALUE == LabelList[idx]){
|
||||
PERMEABILITY=PermeabilityList[idx];
|
||||
idx = NLABELS;
|
||||
//Mask->id[n] = 0; // set mask to zero since this is an immobile component
|
||||
}
|
||||
}
|
||||
int idx = Map(i,j,k);
|
||||
if (!(idx < 0)){
|
||||
if (PERMEABILITY<=0.0){
|
||||
ERROR("Error: Permeability for grey voxel must be > 0.0 ! \n");
|
||||
}
|
||||
else{
|
||||
Permeability[idx] = PERMEABILITY/Dm->voxel_length/Dm->voxel_length;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// Set Dm to match Mask
|
||||
for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = Mask->id[i];
|
||||
|
||||
for (int idx=0; idx<NLABELS; idx++) label_count_global[idx]=sumReduce( Dm->Comm, label_count[idx]);
|
||||
|
||||
//Initialize a weighted porosity after considering grey voxels
|
||||
GreyPorosity=0.0;
|
||||
for (unsigned int idx=0; idx<NLABELS; idx++){
|
||||
double volume_fraction = double(label_count_global[idx])/double((Nx-2)*(Ny-2)*(Nz-2)*nprocs);
|
||||
GreyPorosity+=volume_fraction*PorosityList[idx];
|
||||
}
|
||||
|
||||
if (rank==0){
|
||||
printf("Image resolution: %.5g [um/voxel]\n",Dm->voxel_length);
|
||||
printf("Component labels: %lu \n",NLABELS);
|
||||
for (unsigned int idx=0; idx<NLABELS; idx++){
|
||||
VALUE=LabelList[idx];
|
||||
POROSITY=PorosityList[idx];
|
||||
PERMEABILITY=PermeabilityList[idx];
|
||||
double volume_fraction = double(label_count_global[idx])/double((Nx-2)*(Ny-2)*(Nz-2)*nprocs);
|
||||
printf(" label=%d: porosity=%.3g, permeability=%.3g [um^2] (=%.3g [voxel^2]), volume fraction=%.3g\n",
|
||||
VALUE,POROSITY,PERMEABILITY,PERMEABILITY/Dm->voxel_length/Dm->voxel_length,volume_fraction);
|
||||
printf(" effective porosity=%.3g\n",volume_fraction*POROSITY);
|
||||
}
|
||||
printf("The weighted porosity, considering both open and grey voxels, is %.3g\n",GreyPorosity);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
void ScaLBL_GreyscaleModel::Create(){
|
||||
/*
|
||||
* This function creates the variables needed to run a LBM
|
||||
*/
|
||||
//.........................................................
|
||||
// don't perform computations at the eight corners
|
||||
//id[0] = id[Nx-1] = id[(Ny-1)*Nx] = id[(Ny-1)*Nx + Nx-1] = 0;
|
||||
//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;
|
||||
|
||||
//.........................................................
|
||||
// Initialize communication structures in averaging domain
|
||||
for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = Mask->id[i];
|
||||
Mask->CommInit();
|
||||
Np=Mask->PoreCount();
|
||||
//...........................................................................
|
||||
if (rank==0) printf ("Create ScaLBL_Communicator \n");
|
||||
// Create a communicator for the device (will use optimized layout)
|
||||
// ScaLBL_Communicator ScaLBL_Comm(Mask); // original
|
||||
ScaLBL_Comm = std::shared_ptr<ScaLBL_Communicator>(new ScaLBL_Communicator(Mask));
|
||||
|
||||
int Npad=(Np/16 + 2)*16;
|
||||
if (rank==0) printf ("Set up memory efficient layout, %i | %i | %i \n", Np, Npad, N);
|
||||
Map.resize(Nx,Ny,Nz); Map.fill(-2);
|
||||
auto neighborList= new int[18*Npad];
|
||||
Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Mask->id,Np);
|
||||
MPI_Barrier(comm);
|
||||
|
||||
//...........................................................................
|
||||
// MAIN VARIABLES ALLOCATED HERE
|
||||
//...........................................................................
|
||||
// LBM variables
|
||||
if (rank==0) printf ("Allocating distributions \n");
|
||||
//......................device distributions.................................
|
||||
dist_mem_size = Np*sizeof(double);
|
||||
neighborSize=18*(Np*sizeof(int));
|
||||
//...........................................................................
|
||||
ScaLBL_AllocateDeviceMemory((void **) &NeighborList, neighborSize);
|
||||
ScaLBL_AllocateDeviceMemory((void **) &dvcMap, sizeof(int)*Np);
|
||||
ScaLBL_AllocateDeviceMemory((void **) &fq, 19*dist_mem_size);
|
||||
ScaLBL_AllocateDeviceMemory((void **) &Permeability, sizeof(double)*Np);
|
||||
ScaLBL_AllocateDeviceMemory((void **) &Porosity, sizeof(double)*Np);
|
||||
ScaLBL_AllocateDeviceMemory((void **) &Pressure_dvc, sizeof(double)*Np);
|
||||
ScaLBL_AllocateDeviceMemory((void **) &Velocity, 3*sizeof(double)*Np);
|
||||
//...........................................................................
|
||||
// Update GPU data structures
|
||||
if (rank==0) printf ("Setting up device map and neighbor list \n");
|
||||
fflush(stdout);
|
||||
int *TmpMap;
|
||||
TmpMap=new int[Np];
|
||||
for (int k=1; k<Nz-1; k++){
|
||||
for (int j=1; j<Ny-1; j++){
|
||||
for (int i=1; i<Nx-1; i++){
|
||||
int idx=Map(i,j,k);
|
||||
if (!(idx < 0))
|
||||
TmpMap[idx] = k*Nx*Ny+j*Nx+i;
|
||||
}
|
||||
}
|
||||
}
|
||||
// check that TmpMap is valid
|
||||
for (int idx=0; idx<ScaLBL_Comm->LastExterior(); idx++){
|
||||
int n = TmpMap[idx];
|
||||
if (n > Nx*Ny*Nz){
|
||||
printf("Bad value! idx=%i \n");
|
||||
TmpMap[idx] = Nx*Ny*Nz-1;
|
||||
}
|
||||
}
|
||||
for (int idx=ScaLBL_Comm->FirstInterior(); idx<ScaLBL_Comm->LastInterior(); idx++){
|
||||
int n = TmpMap[idx];
|
||||
if (n > Nx*Ny*Nz){
|
||||
printf("Bad value! idx=%i \n");
|
||||
TmpMap[idx] = Nx*Ny*Nz-1;
|
||||
}
|
||||
}
|
||||
ScaLBL_CopyToDevice(dvcMap, TmpMap, sizeof(int)*Np);
|
||||
ScaLBL_DeviceBarrier();
|
||||
delete [] TmpMap;
|
||||
|
||||
// copy the neighbor list
|
||||
ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
|
||||
// initialize phi based on PhaseLabel (include solid component labels)
|
||||
double *Poros, *Perm;
|
||||
Poros = new double[Np];
|
||||
Perm = new double[Np];
|
||||
AssignComponentLabels(Poros,Perm);
|
||||
ScaLBL_CopyToDevice(Porosity, Poros, Np*sizeof(double));
|
||||
ScaLBL_CopyToDevice(Permeability, Perm, Np*sizeof(double));
|
||||
}
|
||||
|
||||
|
||||
void ScaLBL_GreyscaleModel::Initialize(){
|
||||
if (rank==0) printf ("Initializing distributions \n");
|
||||
//TODO: for BGK, you need to consider voxel porosity
|
||||
// for IMRT, the whole set of feq is different
|
||||
// if in the future you have different collison mode, need to write two set of initialization functions
|
||||
if (CollisionType==1){
|
||||
ScaLBL_D3Q19_GreyIMRT_Init(fq, Np, Den);
|
||||
if (rank==0) printf("Collision model: Incompressible MRT.\n");
|
||||
}
|
||||
else if (CollisionType==2){
|
||||
ScaLBL_D3Q19_Init(fq, Np);
|
||||
if (rank==0) printf("Collision model: BGK.\n");
|
||||
}
|
||||
else{
|
||||
if (rank==0) printf("Unknown collison type! IMRT collision is used.\n");
|
||||
ScaLBL_D3Q19_GreyIMRT_Init(fq, Np, Den);
|
||||
CollisionType=1;
|
||||
greyscale_db->putScalar<std::string>( "collision", "IMRT" );
|
||||
}
|
||||
|
||||
if (Restart == true){
|
||||
if (rank==0){
|
||||
printf("Initializing distributions from Restart! \n");
|
||||
}
|
||||
// Read in the restart file to CPU buffers
|
||||
std::shared_ptr<double> cfq;
|
||||
cfq = std::shared_ptr<double>(new double[19*Np],DeleteArray<double>);
|
||||
FILE *File;
|
||||
File=fopen(LocalRestartFile,"rb");
|
||||
fread(cfq.get(),sizeof(double),19*Np,File);
|
||||
fclose(File);
|
||||
|
||||
// Copy the restart data to the GPU
|
||||
ScaLBL_CopyToDevice(fq,cfq.get(),19*Np*sizeof(double));
|
||||
ScaLBL_DeviceBarrier();
|
||||
|
||||
MPI_Barrier(comm);
|
||||
}
|
||||
}
|
||||
|
||||
void ScaLBL_GreyscaleModel::Run(){
|
||||
int nprocs=nprocx*nprocy*nprocz;
|
||||
const RankInfoStruct rank_info(rank,nprocx,nprocy,nprocz);
|
||||
|
||||
int analysis_interval = 1000; // number of timesteps in between in situ analysis
|
||||
int visualization_interval = 1000;
|
||||
int restart_interval = 10000; // number of timesteps in between in saving distributions for restart
|
||||
if (analysis_db->keyExists( "analysis_interval" )){
|
||||
analysis_interval = analysis_db->getScalar<int>( "analysis_interval" );
|
||||
}
|
||||
if (analysis_db->keyExists( "visualization_interval" )){
|
||||
visualization_interval = analysis_db->getScalar<int>( "visualization_interval" );
|
||||
}
|
||||
if (analysis_db->keyExists( "restart_interval" )){
|
||||
restart_interval = analysis_db->getScalar<int>( "restart_interval" );
|
||||
}
|
||||
if (greyscale_db->keyExists( "timestep" )){
|
||||
timestep = greyscale_db->getScalar<int>( "timestep" );
|
||||
}
|
||||
|
||||
if (rank==0){
|
||||
printf("********************************************************\n");
|
||||
printf("No. of timesteps: %i \n", timestepMax);
|
||||
fflush(stdout);
|
||||
}
|
||||
|
||||
//.......create and start timer............
|
||||
double starttime,stoptime,cputime;
|
||||
ScaLBL_DeviceBarrier();
|
||||
MPI_Barrier(comm);
|
||||
starttime = MPI_Wtime();
|
||||
//.........................................
|
||||
|
||||
Minkowski Morphology(Mask);
|
||||
|
||||
//************ MAIN ITERATION LOOP ***************************************/
|
||||
PROFILE_START("Loop");
|
||||
auto current_db = db->cloneDatabase();
|
||||
double rlx = 1.0/tau;
|
||||
double rlx_eff = 1.0/tau_eff;
|
||||
double error = 1.0;
|
||||
double flow_rate_previous = 0.0;
|
||||
while (timestep < timestepMax && error > tolerance) {
|
||||
//************************************************************************/
|
||||
// *************ODD TIMESTEP*************//
|
||||
timestep++;
|
||||
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
|
||||
switch (CollisionType){
|
||||
case 1:
|
||||
ScaLBL_D3Q19_AAodd_Greyscale_IMRT(NeighborList, fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
|
||||
break;
|
||||
case 2:
|
||||
ScaLBL_D3Q19_AAodd_Greyscale(NeighborList, fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Pressure_dvc);
|
||||
break;
|
||||
default:
|
||||
ScaLBL_D3Q19_AAodd_Greyscale_IMRT(NeighborList, fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
|
||||
break;
|
||||
}
|
||||
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
|
||||
ScaLBL_DeviceBarrier();
|
||||
// Set BCs
|
||||
if (BoundaryCondition == 3){
|
||||
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, din, timestep);
|
||||
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
|
||||
}
|
||||
switch (CollisionType){
|
||||
case 1:
|
||||
ScaLBL_D3Q19_AAodd_Greyscale_IMRT(NeighborList, fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
|
||||
break;
|
||||
case 2:
|
||||
ScaLBL_D3Q19_AAodd_Greyscale(NeighborList, fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Pressure_dvc);
|
||||
break;
|
||||
default:
|
||||
ScaLBL_D3Q19_AAodd_Greyscale_IMRT(NeighborList, fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
|
||||
break;
|
||||
}
|
||||
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
|
||||
|
||||
// *************EVEN TIMESTEP*************//
|
||||
timestep++;
|
||||
ScaLBL_Comm->SendD3Q19AA(fq); //READ FORM NORMAL
|
||||
switch (CollisionType){
|
||||
case 1:
|
||||
ScaLBL_D3Q19_AAeven_Greyscale_IMRT(fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
|
||||
break;
|
||||
case 2:
|
||||
ScaLBL_D3Q19_AAeven_Greyscale(fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Pressure_dvc);
|
||||
break;
|
||||
default:
|
||||
ScaLBL_D3Q19_AAeven_Greyscale_IMRT(fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
|
||||
break;
|
||||
}
|
||||
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
|
||||
ScaLBL_DeviceBarrier();
|
||||
// Set BCs
|
||||
if (BoundaryCondition == 3){
|
||||
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, din, timestep);
|
||||
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
|
||||
}
|
||||
switch (CollisionType){
|
||||
case 1:
|
||||
ScaLBL_D3Q19_AAeven_Greyscale_IMRT(fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
|
||||
break;
|
||||
case 2:
|
||||
ScaLBL_D3Q19_AAeven_Greyscale(fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Pressure_dvc);
|
||||
break;
|
||||
default:
|
||||
ScaLBL_D3Q19_AAeven_Greyscale_IMRT(fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
|
||||
break;
|
||||
}
|
||||
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
|
||||
//************************************************************************/
|
||||
|
||||
if (timestep%analysis_interval==0){
|
||||
ScaLBL_Comm->RegularLayout(Map,&Velocity[0],Velocity_x);
|
||||
ScaLBL_Comm->RegularLayout(Map,&Velocity[Np],Velocity_y);
|
||||
ScaLBL_Comm->RegularLayout(Map,&Velocity[2*Np],Velocity_z);
|
||||
//ScaLBL_Comm->RegularLayout(Map,Porosity,PorosityMap);
|
||||
//ScaLBL_Comm->RegularLayout(Map,Pressure_dvc,Pressure);
|
||||
|
||||
double count_loc=0;
|
||||
double count;
|
||||
double vax,vay,vaz;
|
||||
double vax_loc,vay_loc,vaz_loc;
|
||||
//double px_loc,py_loc,pz_loc;
|
||||
//double px,py,pz;
|
||||
//double mass_loc,mass_glb;
|
||||
|
||||
//parameters for domain average
|
||||
int64_t i,j,k,n,imin,jmin,kmin,kmax;
|
||||
// If external boundary conditions are set, do not average over the inlet and outlet
|
||||
kmin=1; kmax=Nz-1;
|
||||
//In case user forgets to specify the inlet/outlet buffer layers for BC>0
|
||||
if (BoundaryCondition > 0 && Dm->kproc() == 0) kmin=4;
|
||||
if (BoundaryCondition > 0 && Dm->kproc() == Dm->nprocz()-1) kmax=Nz-4;
|
||||
|
||||
imin=jmin=1;
|
||||
// If inlet/outlet layers exist use these as default
|
||||
//if (Dm->inlet_layers_x > 0) imin = Dm->inlet_layers_x;
|
||||
//if (Dm->inlet_layers_y > 0) jmin = Dm->inlet_layers_y;
|
||||
if (BoundaryCondition > 0 && Dm->inlet_layers_z > 0 && Dm->kproc() == 0) kmin = 1 + Dm->inlet_layers_z;//"1" indicates the halo layer
|
||||
if (BoundaryCondition > 0 && Dm->outlet_layers_z > 0 && Dm->kproc() == Dm->nprocz()-1) kmax = Nz-1 - Dm->outlet_layers_z;
|
||||
|
||||
// px_loc = py_loc = pz_loc = 0.f;
|
||||
// mass_loc = 0.f;
|
||||
// for (int k=kmin; k<kmax; k++){
|
||||
// for (int j=jmin; j<Ny-1; j++){
|
||||
// for (int i=imin; i<Nx-1; i++){
|
||||
// if (SignDist(i,j,k) > 0){
|
||||
// px_loc += Velocity_x(i,j,k)*Den*PorosityMap(i,j,k);
|
||||
// py_loc += Velocity_y(i,j,k)*Den*PorosityMap(i,j,k);
|
||||
// pz_loc += Velocity_z(i,j,k)*Den*PorosityMap(i,j,k);
|
||||
// mass_loc += Den*PorosityMap(i,j,k);
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
// MPI_Allreduce(&px_loc, &px, 1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
||||
// MPI_Allreduce(&py_loc, &py, 1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
||||
// MPI_Allreduce(&pz_loc, &pz, 1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
||||
// MPI_Allreduce(&mass_loc,&mass_glb,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
||||
//
|
||||
// vax = px/mass_glb;
|
||||
// vay = py/mass_glb;
|
||||
// vaz = pz/mass_glb;
|
||||
|
||||
vax_loc = vay_loc = vaz_loc = 0.f;
|
||||
for (int k=kmin; k<kmax; k++){
|
||||
for (int j=jmin; j<Ny-1; j++){
|
||||
for (int i=imin; i<Nx-1; i++){
|
||||
if (SignDist(i,j,k) > 0){
|
||||
vax_loc += Velocity_x(i,j,k);
|
||||
vay_loc += Velocity_y(i,j,k);
|
||||
vaz_loc += Velocity_z(i,j,k);
|
||||
count_loc+=1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
MPI_Allreduce(&vax_loc,&vax,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
||||
MPI_Allreduce(&vay_loc,&vay,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
||||
MPI_Allreduce(&vaz_loc,&vaz,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
||||
MPI_Allreduce(&count_loc,&count,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
||||
|
||||
vax /= count;
|
||||
vay /= count;
|
||||
vaz /= count;
|
||||
|
||||
double force_mag = sqrt(Fx*Fx+Fy*Fy+Fz*Fz);
|
||||
double dir_x = Fx/force_mag;
|
||||
double dir_y = Fy/force_mag;
|
||||
double dir_z = Fz/force_mag;
|
||||
if (force_mag == 0.0){
|
||||
// default to z direction
|
||||
dir_x = 0.0;
|
||||
dir_y = 0.0;
|
||||
dir_z = 1.0;
|
||||
force_mag = 1.0;
|
||||
}
|
||||
//double flow_rate = (px*dir_x + py*dir_y + pz*dir_z)/mass_glb;
|
||||
double flow_rate = (vax*dir_x + vay*dir_y + vaz*dir_z);
|
||||
|
||||
error = fabs(flow_rate - flow_rate_previous) / fabs(flow_rate);
|
||||
flow_rate_previous = flow_rate;
|
||||
|
||||
//if (rank==0) printf("Computing Minkowski functionals \n");
|
||||
Morphology.ComputeScalar(SignDist,0.f);
|
||||
//Morphology.PrintAll();
|
||||
double mu = (tau-0.5)/3.f;
|
||||
double Vs = Morphology.V();
|
||||
double As = Morphology.A();
|
||||
double Hs = Morphology.H();
|
||||
double Xs = Morphology.X();
|
||||
Vs=sumReduce( Dm->Comm, Vs);
|
||||
As=sumReduce( Dm->Comm, As);
|
||||
Hs=sumReduce( Dm->Comm, Hs);
|
||||
Xs=sumReduce( Dm->Comm, Xs);
|
||||
double h = Dm->voxel_length;
|
||||
//double absperm = h*h*mu*Mask->Porosity()*flow_rate / force_mag;
|
||||
double absperm = h*h*mu*GreyPorosity*flow_rate / force_mag;
|
||||
|
||||
if (rank==0){
|
||||
printf(" AbsPerm = %.5g [micron^2]\n",absperm);
|
||||
bool WriteHeader=false;
|
||||
FILE * log_file = fopen("Permeability.csv","r");
|
||||
if (log_file != NULL)
|
||||
fclose(log_file);
|
||||
else
|
||||
WriteHeader=true;
|
||||
log_file = fopen("Permeability.csv","a");
|
||||
if (WriteHeader)
|
||||
fprintf(log_file,"timestep Fx Fy Fz mu Vs As Hs Xs vax vay vaz AbsPerm \n",
|
||||
timestep,Fx,Fy,Fz,mu,h*h*h*Vs,h*h*As,h*Hs,Xs,vax,vay,vaz,absperm);
|
||||
|
||||
fprintf(log_file,"%i %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g\n",timestep, Fx, Fy, Fz, mu,
|
||||
h*h*h*Vs,h*h*As,h*Hs,Xs,vax,vay,vaz, absperm);
|
||||
fclose(log_file);
|
||||
}
|
||||
}
|
||||
|
||||
if (timestep%visualization_interval==0){
|
||||
VelocityField();
|
||||
}
|
||||
|
||||
if (timestep%restart_interval==0){
|
||||
//Use rank=0 write out Restart.db
|
||||
if (rank==0) {
|
||||
greyscale_db->putScalar<int>("timestep",timestep);
|
||||
greyscale_db->putScalar<bool>( "Restart", true );
|
||||
current_db->putDatabase("Greyscale", greyscale_db);
|
||||
std::ofstream OutStream("Restart.db");
|
||||
current_db->print(OutStream, "");
|
||||
OutStream.close();
|
||||
|
||||
}
|
||||
//Write out Restart data.
|
||||
std::shared_ptr<double> cfq;
|
||||
cfq = std::shared_ptr<double>(new double[19*Np],DeleteArray<double>);
|
||||
ScaLBL_CopyToHost(cfq.get(),fq,19*Np*sizeof(double));// Copy restart data to the CPU
|
||||
|
||||
FILE *RESTARTFILE;
|
||||
RESTARTFILE=fopen(LocalRestartFile,"wb");
|
||||
fwrite(cfq.get(),sizeof(double),19*Np,RESTARTFILE);
|
||||
fclose(RESTARTFILE);
|
||||
MPI_Barrier(comm);
|
||||
}
|
||||
}
|
||||
|
||||
PROFILE_STOP("Loop");
|
||||
PROFILE_SAVE("lbpm_greyscale_simulator",1);
|
||||
//************************************************************************
|
||||
ScaLBL_DeviceBarrier();
|
||||
MPI_Barrier(comm);
|
||||
stoptime = MPI_Wtime();
|
||||
if (rank==0) printf("-------------------------------------------------------------------\n");
|
||||
// Compute the walltime per timestep
|
||||
cputime = (stoptime - starttime)/timestep;
|
||||
// Performance obtained from each node
|
||||
double MLUPS = double(Np)/cputime/1000000;
|
||||
|
||||
if (rank==0) printf("********************************************************\n");
|
||||
if (rank==0) printf("CPU time = %f \n", cputime);
|
||||
if (rank==0) printf("Lattice update rate (per core)= %f MLUPS \n", MLUPS);
|
||||
MLUPS *= nprocs;
|
||||
if (rank==0) printf("Lattice update rate (total)= %f MLUPS \n", MLUPS);
|
||||
if (rank==0) printf("********************************************************\n");
|
||||
|
||||
// ************************************************************************
|
||||
}
|
||||
|
||||
void ScaLBL_GreyscaleModel::VelocityField(){
|
||||
|
||||
/* Minkowski Morphology(Mask);
|
||||
int SIZE=Np*sizeof(double);
|
||||
ScaLBL_D3Q19_Momentum(fq,Velocity, Np);
|
||||
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
|
||||
ScaLBL_CopyToHost(&VELOCITY[0],&Velocity[0],3*SIZE);
|
||||
|
||||
memcpy(Morphology.SDn.data(), Distance.data(), Nx*Ny*Nz*sizeof(double));
|
||||
Morphology.Initialize();
|
||||
Morphology.UpdateMeshValues();
|
||||
Morphology.ComputeLocal();
|
||||
Morphology.Reduce();
|
||||
|
||||
double count_loc=0;
|
||||
double count;
|
||||
double vax,vay,vaz;
|
||||
double vax_loc,vay_loc,vaz_loc;
|
||||
vax_loc = vay_loc = vaz_loc = 0.f;
|
||||
for (int n=0; n<ScaLBL_Comm->LastExterior(); n++){
|
||||
vax_loc += VELOCITY[n];
|
||||
vay_loc += VELOCITY[Np+n];
|
||||
vaz_loc += VELOCITY[2*Np+n];
|
||||
count_loc+=1.0;
|
||||
}
|
||||
|
||||
for (int n=ScaLBL_Comm->FirstInterior(); n<ScaLBL_Comm->LastInterior(); n++){
|
||||
vax_loc += VELOCITY[n];
|
||||
vay_loc += VELOCITY[Np+n];
|
||||
vaz_loc += VELOCITY[2*Np+n];
|
||||
count_loc+=1.0;
|
||||
}
|
||||
MPI_Allreduce(&vax_loc,&vax,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
||||
MPI_Allreduce(&vay_loc,&vay,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
||||
MPI_Allreduce(&vaz_loc,&vaz,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
||||
MPI_Allreduce(&count_loc,&count,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
||||
|
||||
vax /= count;
|
||||
vay /= count;
|
||||
vaz /= count;
|
||||
|
||||
double mu = (tau-0.5)/3.f;
|
||||
if (rank==0) printf("Fx Fy Fz mu Vs As Js Xs vx vy vz\n");
|
||||
if (rank==0) printf("%.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g\n",Fx, Fy, Fz, mu,
|
||||
Morphology.V(),Morphology.A(),Morphology.J(),Morphology.X(),vax,vay,vaz);
|
||||
*/
|
||||
|
||||
std::vector<IO::MeshDataStruct> visData;
|
||||
fillHalo<double> fillData(Dm->Comm,Dm->rank_info,{Dm->Nx-2,Dm->Ny-2,Dm->Nz-2},{1,1,1},0,1);
|
||||
|
||||
auto VxVar = std::make_shared<IO::Variable>();
|
||||
auto VyVar = std::make_shared<IO::Variable>();
|
||||
auto VzVar = std::make_shared<IO::Variable>();
|
||||
auto SignDistVar = std::make_shared<IO::Variable>();
|
||||
auto PressureVar = std::make_shared<IO::Variable>();
|
||||
|
||||
IO::initialize("","silo","false");
|
||||
// Create the MeshDataStruct
|
||||
visData.resize(1);
|
||||
visData[0].meshName = "domain";
|
||||
visData[0].mesh = std::make_shared<IO::DomainMesh>( Dm->rank_info,Dm->Nx-2,Dm->Ny-2,Dm->Nz-2,Dm->Lx,Dm->Ly,Dm->Lz );
|
||||
SignDistVar->name = "SignDist";
|
||||
SignDistVar->type = IO::VariableType::VolumeVariable;
|
||||
SignDistVar->dim = 1;
|
||||
SignDistVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
|
||||
visData[0].vars.push_back(SignDistVar);
|
||||
|
||||
VxVar->name = "Velocity_x";
|
||||
VxVar->type = IO::VariableType::VolumeVariable;
|
||||
VxVar->dim = 1;
|
||||
VxVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
|
||||
visData[0].vars.push_back(VxVar);
|
||||
VyVar->name = "Velocity_y";
|
||||
VyVar->type = IO::VariableType::VolumeVariable;
|
||||
VyVar->dim = 1;
|
||||
VyVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
|
||||
visData[0].vars.push_back(VyVar);
|
||||
VzVar->name = "Velocity_z";
|
||||
VzVar->type = IO::VariableType::VolumeVariable;
|
||||
VzVar->dim = 1;
|
||||
VzVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
|
||||
visData[0].vars.push_back(VzVar);
|
||||
|
||||
PressureVar->name = "Pressure";
|
||||
PressureVar->type = IO::VariableType::VolumeVariable;
|
||||
PressureVar->dim = 1;
|
||||
PressureVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
|
||||
visData[0].vars.push_back(PressureVar);
|
||||
|
||||
Array<double>& SignData = visData[0].vars[0]->data;
|
||||
Array<double>& VelxData = visData[0].vars[1]->data;
|
||||
Array<double>& VelyData = visData[0].vars[2]->data;
|
||||
Array<double>& VelzData = visData[0].vars[3]->data;
|
||||
Array<double>& PressureData = visData[0].vars[4]->data;
|
||||
|
||||
ASSERT(visData[0].vars[0]->name=="SignDist");
|
||||
ASSERT(visData[0].vars[1]->name=="Velocity_x");
|
||||
ASSERT(visData[0].vars[2]->name=="Velocity_y");
|
||||
ASSERT(visData[0].vars[3]->name=="Velocity_z");
|
||||
ASSERT(visData[0].vars[4]->name=="Pressure");
|
||||
|
||||
ScaLBL_Comm->RegularLayout(Map,&Velocity[0],Velocity_x);
|
||||
ScaLBL_Comm->RegularLayout(Map,&Velocity[Np],Velocity_y);
|
||||
ScaLBL_Comm->RegularLayout(Map,&Velocity[2*Np],Velocity_z);
|
||||
ScaLBL_Comm->RegularLayout(Map,Pressure_dvc,Pressure);
|
||||
|
||||
fillData.copy(SignDist,SignData);
|
||||
fillData.copy(Velocity_x,VelxData);
|
||||
fillData.copy(Velocity_y,VelyData);
|
||||
fillData.copy(Velocity_z,VelzData);
|
||||
fillData.copy(Pressure,PressureData);
|
||||
|
||||
IO::writeData( timestep, visData, Dm->Comm );
|
||||
|
||||
}
|
||||
|
||||
void ScaLBL_GreyscaleModel::WriteDebug(){
|
||||
// Copy back final phase indicator field and convert to regular layout
|
||||
DoubleArray PhaseField(Nx,Ny,Nz);
|
||||
|
||||
//ScaLBL_CopyToHost(Porosity.data(), Poros, sizeof(double)*N);
|
||||
|
||||
// FILE *OUTFILE;
|
||||
// sprintf(LocalRankFilename,"Phase.%05i.raw",rank);
|
||||
// OUTFILE = fopen(LocalRankFilename,"wb");
|
||||
// fwrite(PhaseField.data(),8,N,OUTFILE);
|
||||
// fclose(OUTFILE);
|
||||
//
|
||||
// ScaLBL_Comm->RegularLayout(Map,&Den[0],PhaseField);
|
||||
// FILE *AFILE;
|
||||
// sprintf(LocalRankFilename,"A.%05i.raw",rank);
|
||||
// AFILE = fopen(LocalRankFilename,"wb");
|
||||
// fwrite(PhaseField.data(),8,N,AFILE);
|
||||
// fclose(AFILE);
|
||||
//
|
||||
// ScaLBL_Comm->RegularLayout(Map,&Den[Np],PhaseField);
|
||||
// FILE *BFILE;
|
||||
// sprintf(LocalRankFilename,"B.%05i.raw",rank);
|
||||
// BFILE = fopen(LocalRankFilename,"wb");
|
||||
// fwrite(PhaseField.data(),8,N,BFILE);
|
||||
// fclose(BFILE);
|
||||
//
|
||||
// ScaLBL_Comm->RegularLayout(Map,Pressure,PhaseField);
|
||||
// FILE *PFILE;
|
||||
// sprintf(LocalRankFilename,"Pressure.%05i.raw",rank);
|
||||
// PFILE = fopen(LocalRankFilename,"wb");
|
||||
// fwrite(PhaseField.data(),8,N,PFILE);
|
||||
// fclose(PFILE);
|
||||
|
||||
ScaLBL_Comm->RegularLayout(Map,&Velocity[0],PhaseField);
|
||||
FILE *VELX_FILE;
|
||||
sprintf(LocalRankFilename,"Velocity_X.%05i.raw",rank);
|
||||
VELX_FILE = fopen(LocalRankFilename,"wb");
|
||||
fwrite(PhaseField.data(),8,N,VELX_FILE);
|
||||
fclose(VELX_FILE);
|
||||
|
||||
ScaLBL_Comm->RegularLayout(Map,&Velocity[Np],PhaseField);
|
||||
FILE *VELY_FILE;
|
||||
sprintf(LocalRankFilename,"Velocity_Y.%05i.raw",rank);
|
||||
VELY_FILE = fopen(LocalRankFilename,"wb");
|
||||
fwrite(PhaseField.data(),8,N,VELY_FILE);
|
||||
fclose(VELY_FILE);
|
||||
|
||||
ScaLBL_Comm->RegularLayout(Map,&Velocity[2*Np],PhaseField);
|
||||
FILE *VELZ_FILE;
|
||||
sprintf(LocalRankFilename,"Velocity_Z.%05i.raw",rank);
|
||||
VELZ_FILE = fopen(LocalRankFilename,"wb");
|
||||
fwrite(PhaseField.data(),8,N,VELZ_FILE);
|
||||
fclose(VELZ_FILE);
|
||||
|
||||
ScaLBL_Comm->RegularLayout(Map,&Porosity[0],PhaseField);
|
||||
FILE *POROS_FILE;
|
||||
sprintf(LocalRankFilename,"Porosity.%05i.raw",rank);
|
||||
POROS_FILE = fopen(LocalRankFilename,"wb");
|
||||
fwrite(PhaseField.data(),8,N,POROS_FILE);
|
||||
fclose(POROS_FILE);
|
||||
|
||||
ScaLBL_Comm->RegularLayout(Map,&Permeability[0],PhaseField);
|
||||
FILE *PERM_FILE;
|
||||
sprintf(LocalRankFilename,"Permeability.%05i.raw",rank);
|
||||
PERM_FILE = fopen(LocalRankFilename,"wb");
|
||||
fwrite(PhaseField.data(),8,N,PERM_FILE);
|
||||
fclose(PERM_FILE);
|
||||
}
|
||||
92
models/GreyscaleModel.h
Normal file
92
models/GreyscaleModel.h
Normal file
|
|
@ -0,0 +1,92 @@
|
|||
/*
|
||||
Implementation of color lattice boltzmann model
|
||||
*/
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <sys/stat.h>
|
||||
#include <iostream>
|
||||
#include <exception>
|
||||
#include <stdexcept>
|
||||
#include <fstream>
|
||||
|
||||
#include "common/Communication.h"
|
||||
#include "common/MPI_Helpers.h"
|
||||
#include "common/Database.h"
|
||||
#include "common/ScaLBL.h"
|
||||
#include "ProfilerApp.h"
|
||||
#include "threadpool/thread_pool.h"
|
||||
|
||||
class ScaLBL_GreyscaleModel{
|
||||
public:
|
||||
ScaLBL_GreyscaleModel(int RANK, int NP, MPI_Comm COMM);
|
||||
~ScaLBL_GreyscaleModel();
|
||||
|
||||
// functions in they should be run
|
||||
void ReadParams(string filename);
|
||||
void ReadParams(std::shared_ptr<Database> db0);
|
||||
void SetDomain();
|
||||
void ReadInput();
|
||||
void Create();
|
||||
void Initialize();
|
||||
void Run();
|
||||
void WriteDebug();
|
||||
void VelocityField();
|
||||
|
||||
bool Restart,pBC;
|
||||
int timestep,timestepMax;
|
||||
int BoundaryCondition;
|
||||
int CollisionType;
|
||||
double tau;
|
||||
double tau_eff;
|
||||
double Den;//constant density
|
||||
double tolerance;
|
||||
double Fx,Fy,Fz,flux;
|
||||
double din,dout;
|
||||
double dp;//solid particle diameter, unit in voxel
|
||||
double GreyPorosity;
|
||||
|
||||
int Nx,Ny,Nz,N,Np;
|
||||
int rank,nprocx,nprocy,nprocz,nprocs;
|
||||
double Lx,Ly,Lz;
|
||||
|
||||
std::shared_ptr<Domain> Dm; // this domain is for analysis
|
||||
std::shared_ptr<Domain> Mask; // this domain is for lbm
|
||||
std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm;
|
||||
|
||||
// input database
|
||||
std::shared_ptr<Database> db;
|
||||
std::shared_ptr<Database> domain_db;
|
||||
std::shared_ptr<Database> greyscale_db;
|
||||
std::shared_ptr<Database> analysis_db;
|
||||
std::shared_ptr<Database> vis_db;
|
||||
|
||||
signed char *id;
|
||||
int *NeighborList;
|
||||
int *dvcMap;
|
||||
double *fq;
|
||||
double *Permeability;//grey voxel permeability
|
||||
double *Porosity;
|
||||
double *Velocity;
|
||||
double *Pressure_dvc;
|
||||
IntArray Map;
|
||||
DoubleArray SignDist;
|
||||
DoubleArray Velocity_x;
|
||||
DoubleArray Velocity_y;
|
||||
DoubleArray Velocity_z;
|
||||
DoubleArray PorosityMap;
|
||||
DoubleArray Pressure;
|
||||
|
||||
private:
|
||||
MPI_Comm comm;
|
||||
|
||||
int dist_mem_size;
|
||||
int neighborSize;
|
||||
// filenames
|
||||
char LocalRankString[8];
|
||||
char LocalRankFilename[40];
|
||||
char LocalRestartFile[40];
|
||||
|
||||
void AssignComponentLabels(double *Porosity, double *Permeablity);
|
||||
|
||||
};
|
||||
|
||||
|
|
@ -3,6 +3,7 @@
|
|||
#ADD_LBPM_EXECUTABLE( lbpm_nondarcy_simulator )
|
||||
ADD_LBPM_EXECUTABLE( lbpm_color_simulator )
|
||||
ADD_LBPM_EXECUTABLE( lbpm_permeability_simulator )
|
||||
ADD_LBPM_EXECUTABLE( lbpm_greyscale_simulator )
|
||||
#ADD_LBPM_EXECUTABLE( lbpm_BGK_simulator )
|
||||
#ADD_LBPM_EXECUTABLE( lbpm_color_macro_simulator )
|
||||
ADD_LBPM_EXECUTABLE( lbpm_dfh_simulator )
|
||||
|
|
|
|||
64
tests/lbpm_greyscale_simulator.cpp
Normal file
64
tests/lbpm_greyscale_simulator.cpp
Normal file
|
|
@ -0,0 +1,64 @@
|
|||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <sys/stat.h>
|
||||
#include <iostream>
|
||||
#include <exception>
|
||||
#include <stdexcept>
|
||||
#include <fstream>
|
||||
|
||||
#include "common/ScaLBL.h"
|
||||
#include "common/Communication.h"
|
||||
#include "common/MPI_Helpers.h"
|
||||
#include "models/GreyscaleModel.h"
|
||||
//#define WRITE_SURFACES
|
||||
|
||||
/*
|
||||
* Simulator for two-phase flow in porous media
|
||||
* James E. McClure 2013-2014
|
||||
*/
|
||||
|
||||
using namespace std;
|
||||
|
||||
|
||||
int main(int argc, char **argv)
|
||||
{
|
||||
//*****************************************
|
||||
// ***** MPI STUFF ****************
|
||||
//*****************************************
|
||||
// Initialize MPI
|
||||
int rank,nprocs;
|
||||
MPI_Init(&argc,&argv);
|
||||
MPI_Comm comm = MPI_COMM_WORLD;
|
||||
MPI_Comm_rank(comm,&rank);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
{
|
||||
// parallel domain size (# of sub-domains)
|
||||
int nprocx,nprocy,nprocz;
|
||||
int iproc,jproc,kproc;
|
||||
|
||||
if (rank == 0){
|
||||
printf("********************************************************\n");
|
||||
printf("Running Greyscale Single Phase Permeability Calculation \n");
|
||||
printf("********************************************************\n");
|
||||
}
|
||||
// Initialize compute device
|
||||
int device=ScaLBL_SetDevice(rank);
|
||||
ScaLBL_DeviceBarrier();
|
||||
MPI_Barrier(comm);
|
||||
|
||||
ScaLBL_GreyscaleModel Greyscale(rank,nprocs,comm);
|
||||
auto filename = argv[1];
|
||||
Greyscale.ReadParams(filename);
|
||||
Greyscale.SetDomain(); // this reads in the domain
|
||||
Greyscale.ReadInput();
|
||||
Greyscale.Create(); // creating the model will create data structure to match the pore structure and allocate variables
|
||||
Greyscale.Initialize(); // initializing the model will set initial conditions for variables
|
||||
Greyscale.Run();
|
||||
//Greyscale.VelocityField();
|
||||
//Greyscale.WriteDebug();
|
||||
}
|
||||
// ****************************************************
|
||||
MPI_Barrier(comm);
|
||||
MPI_Finalize();
|
||||
// ****************************************************
|
||||
}
|
||||
Loading…
Reference in New Issue
Block a user