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merging multi-halo

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This commit is contained in:
JamesEMcclure
2021-01-13 21:44:23 -05:00
parent 29e486a1a0 64b49f720e
commit 0fe3125833
184 changed files with 22054 additions and 7588 deletions
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106
models/GreyscaleModel.cpp
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@@ -13,7 +13,7 @@ void DeleteArray( const TYPE *p )
delete [] p;
}
ScaLBL_GreyscaleModel::ScaLBL_GreyscaleModel(int RANK, int NP, MPI_Comm COMM):
ScaLBL_GreyscaleModel::ScaLBL_GreyscaleModel(int RANK, int NP, const Utilities::MPI& 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)
{
@@ -121,9 +121,9 @@ void ScaLBL_GreyscaleModel::SetDomain(){
id = new signed char [N];
for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = 1; // initialize this way
MPI_Barrier(comm);
comm.barrier();
Dm->CommInit();
MPI_Barrier(comm);
comm.barrier();
// Read domain parameters
rank = Dm->rank();
nprocx = Dm->nprocx();
@@ -267,7 +267,7 @@ void ScaLBL_GreyscaleModel::AssignComponentLabels(double *Porosity, double *Perm
// 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]);
for (int idx=0; idx<NLABELS; idx++) label_count_global[idx]=Dm->Comm.sumReduce( label_count[idx]);
//Initialize a weighted porosity after considering grey voxels
GreyPorosity=0.0;
for (unsigned int idx=0; idx<NLABELS; idx++){
@@ -291,6 +291,56 @@ void ScaLBL_GreyscaleModel::AssignComponentLabels(double *Porosity, double *Perm
}
}
void ScaLBL_GreyscaleModel::AssignComponentLabels(double *Porosity,double *Permeability,const vector<std::string> &File_poro,const vector<std::string> &File_perm)
{
double *Porosity_host, *Permeability_host;
Porosity_host = new double[N];
Permeability_host = new double[N];
double POROSITY=0.f;
double PERMEABILITY=0.f;
//Initialize a weighted porosity after considering grey voxels
double GreyPorosity_loc=0.0;
GreyPorosity=0.0;
//double label_count_loc = 0.0;
//double label_count_glb = 0.0;
Mask->ReadFromFile(File_poro[0],File_poro[1],Porosity_host);
Mask->ReadFromFile(File_perm[0],File_perm[1],Permeability_host);
for (int k=0;k<Nz;k++){
for (int j=0;j<Ny;j++){
for (int i=0;i<Nx;i++){
int idx = Map(i,j,k);
if (!(idx < 0)){
int n = k*Nx*Ny+j*Nx+i;
POROSITY = Porosity_host[n];
PERMEABILITY = Permeability_host[n];
if (POROSITY<=0.0){
ERROR("Error: Porosity for grey voxels must be 0.0 < Porosity <= 1.0 !\n");
}
else if (PERMEABILITY<=0.0){
ERROR("Error: Permeability for grey voxel must be > 0.0 ! \n");
}
else{
Porosity[idx] = POROSITY;
Permeability[idx] = PERMEABILITY;
GreyPorosity_loc += POROSITY;
//label_count_loc += 1.0;
}
}
}
}
}
GreyPorosity = Dm->Comm.sumReduce( GreyPorosity_loc);
GreyPorosity = GreyPorosity/double((Nx-2)*(Ny-2)*(Nz-2)*nprocs);
if (rank==0){
printf("Image resolution: %.5g [um/voxel]\n",Dm->voxel_length);
printf("The weighted porosity, considering both open and grey voxels, is %.3g\n",GreyPorosity);
}
delete [] Porosity_host;
delete [] Permeability_host;
}
void ScaLBL_GreyscaleModel::Create(){
/*
@@ -316,8 +366,8 @@ void ScaLBL_GreyscaleModel::Create(){
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,1);
MPI_Barrier(comm);
Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Mask->id.data(),Np,1);
comm.barrier();
//...........................................................................
// MAIN VARIABLES ALLOCATED HERE
@@ -344,7 +394,19 @@ void ScaLBL_GreyscaleModel::Create(){
double *Poros, *Perm;
Poros = new double[Np];
Perm = new double[Np];
AssignComponentLabels(Poros,Perm);
if (greyscale_db->keyExists("FileVoxelPorosityMap")){
//NOTE: FileVoxel**Map is a vector, including "file_name, datatype"
auto File_poro = greyscale_db->getVector<std::string>( "FileVoxelPorosityMap" );
auto File_perm = greyscale_db->getVector<std::string>( "FileVoxelPermeabilityMap" );
AssignComponentLabels(Poros,Perm,File_poro,File_perm);
}
else if (greyscale_db->keyExists("PorosityList")){
//initialize voxel porosity and perm from the input list
AssignComponentLabels(Poros,Perm);
}
else {
ERROR("Error: PorosityList or FilenameVoxelPorosityMap cannot be found! \n");
}
ScaLBL_CopyToDevice(Porosity, Poros, Np*sizeof(double));
ScaLBL_CopyToDevice(Permeability, Perm, Np*sizeof(double));
delete [] Poros;
@@ -392,7 +454,7 @@ void ScaLBL_GreyscaleModel::Initialize(){
ScaLBL_CopyToDevice(fq,cfq.get(),19*Np*sizeof(double));
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
comm.barrier();
}
}
@@ -425,7 +487,7 @@ void ScaLBL_GreyscaleModel::Run(){
//.......create and start timer............
double starttime,stoptime,cputime;
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
comm.barrier();
starttime = MPI_Wtime();
//.........................................
@@ -478,7 +540,7 @@ void ScaLBL_GreyscaleModel::Run(){
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);
ScaLBL_DeviceBarrier(); comm.barrier();
// *************EVEN TIMESTEP*************//
timestep++;
@@ -518,7 +580,7 @@ void ScaLBL_GreyscaleModel::Run(){
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);
ScaLBL_DeviceBarrier(); comm.barrier();
//************************************************************************/
if (timestep%analysis_interval==0){
@@ -587,10 +649,10 @@ void ScaLBL_GreyscaleModel::Run(){
}
}
}
vax = sumReduce( Mask->Comm, vax_loc);
vay = sumReduce( Mask->Comm, vay_loc);
vaz = sumReduce( Mask->Comm, vaz_loc);
count = sumReduce( Mask->Comm, count_loc);
vax = Dm->Comm.sumReduce( vax_loc);
vay = Dm->Comm.sumReduce( vay_loc);
vaz = Dm->Comm.sumReduce( vaz_loc);
count = Dm->Comm.sumReduce( count_loc);
vax /= count;
vay /= count;
@@ -621,10 +683,10 @@ void ScaLBL_GreyscaleModel::Run(){
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);
Vs = Dm->Comm.sumReduce( Vs);
As = Dm->Comm.sumReduce( As);
Hs = Dm->Comm.sumReduce( Hs);
Xs = Dm->Comm.sumReduce( Xs);
double h = Dm->voxel_length;
//double absperm = h*h*mu*Mask->Porosity()*flow_rate / force_mag;
@@ -673,7 +735,7 @@ void ScaLBL_GreyscaleModel::Run(){
RESTARTFILE=fopen(LocalRestartFile,"wb");
fwrite(cfq.get(),sizeof(double),19*Np,RESTARTFILE);
fclose(RESTARTFILE);
MPI_Barrier(comm);
comm.barrier();
}
}
@@ -681,7 +743,7 @@ void ScaLBL_GreyscaleModel::Run(){
PROFILE_SAVE("lbpm_greyscale_simulator",1);
//************************************************************************
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
comm.barrier();
stoptime = MPI_Wtime();
if (rank==0) printf("-------------------------------------------------------------------\n");
// Compute the walltime per timestep
@@ -704,7 +766,7 @@ void ScaLBL_GreyscaleModel::VelocityField(){
/* Minkowski Morphology(Mask);
int SIZE=Np*sizeof(double);
ScaLBL_D3Q19_Momentum(fq,Velocity, Np);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_DeviceBarrier(); comm.barrier();
ScaLBL_CopyToHost(&VELOCITY[0],&Velocity[0],3*SIZE);
memcpy(Morphology.SDn.data(), Distance.data(), Nx*Ny*Nz*sizeof(double));