Files
LBPM/models/MRTModel.cpp
James McClure 7f4f74779c fix the build
2021-01-05 18:43:44 -05:00

469 lines
16 KiB
C++

/*
* Multi-relaxation time LBM Model
*/
#include "models/MRTModel.h"
#include "analysis/distance.h"
#include "common/ReadMicroCT.h"
ScaLBL_MRTModel::ScaLBL_MRTModel(int RANK, int NP, const Utilities::MPI& COMM):
rank(RANK), nprocs(NP), Restart(0),timestep(0),timestepMax(0),tau(0),
Fx(0),Fy(0),Fz(0),flux(0),din(0),dout(0),mu(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)
{
}
ScaLBL_MRTModel::~ScaLBL_MRTModel(){
}
void ScaLBL_MRTModel::ReadParams(string filename){
// read the input database
db = std::make_shared<Database>( filename );
domain_db = db->getDatabase( "Domain" );
mrt_db = db->getDatabase( "MRT" );
tau = 1.0;
timestepMax = 100000;
tolerance = 1.0e-8;
Fx = Fy = 0.0;
Fz = 1.0e-5;
// Color Model parameters
if (mrt_db->keyExists( "timestepMax" )){
timestepMax = mrt_db->getScalar<int>( "timestepMax" );
}
if (mrt_db->keyExists( "tolerance" )){
tolerance = mrt_db->getScalar<double>( "tolerance" );
}
if (mrt_db->keyExists( "tau" )){
tau = mrt_db->getScalar<double>( "tau" );
}
if (mrt_db->keyExists( "F" )){
Fx = mrt_db->getVector<double>( "F" )[0];
Fy = mrt_db->getVector<double>( "F" )[1];
Fz = mrt_db->getVector<double>( "F" )[2];
}
if (mrt_db->keyExists( "Restart" )){
Restart = mrt_db->getScalar<bool>( "Restart" );
}
if (mrt_db->keyExists( "din" )){
din = mrt_db->getScalar<double>( "din" );
}
if (mrt_db->keyExists( "dout" )){
dout = mrt_db->getScalar<double>( "dout" );
}
if (mrt_db->keyExists( "flux" )){
flux = mrt_db->getScalar<double>( "flux" );
}
// Read domain parameters
if (mrt_db->keyExists( "BoundaryCondition" )){
BoundaryCondition = mrt_db->getScalar<int>( "BC" );
}
else if (domain_db->keyExists( "BC" )){
BoundaryCondition = domain_db->getScalar<int>( "BC" );
}
mu=(tau-0.5)/3.0;
}
void ScaLBL_MRTModel::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;
Distance.resize(Nx,Ny,Nz);
Velocity_x.resize(Nx,Ny,Nz);
Velocity_y.resize(Nx,Ny,Nz);
Velocity_z.resize(Nx,Ny,Nz);
for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = 1; // initialize this way
//Averages = std::shared_ptr<TwoPhase> ( new TwoPhase(Dm) ); // TwoPhase analysis object
comm.barrier();
Dm->CommInit();
comm.barrier();
rank = Dm->rank();
nprocx = Dm->nprocx();
nprocy = Dm->nprocy();
nprocz = Dm->nprocz();
}
void ScaLBL_MRTModel::ReadInput(){
sprintf(LocalRankString,"%05d",Dm->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 (domain_db->keyExists( "GridFile" )){
// Read the local domain data
auto input_id = readMicroCT( *domain_db, comm );
// Fill the halo (assuming GCW of 1)
array<int,3> size0 = { (int) input_id.size(0), (int) input_id.size(1), (int) input_id.size(2) };
ArraySize size1 = { (size_t) Mask->Nx, (size_t) Mask->Ny, (size_t) Mask->Nz };
ASSERT( (int) size1[0] == size0[0]+2 && (int) size1[1] == size0[1]+2 && (int) size1[2] == size0[2]+2 );
fillHalo<signed char> fill( comm, Mask->rank_info, size0, { 1, 1, 1 }, 0, 1 );
Array<signed char> id_view;
id_view.viewRaw( size1, Mask->id.data() );
fill.copy( input_id, id_view );
fill.fill( id_view );
}
else{
Mask->ReadIDs();
}
// Generate the signed distance map
// Initialize the domain and communication
Array<char> id_solid(Nx,Ny,Nz);
// 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
if (Mask->id[n] > 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++){
// Initialize distance to +/- 1
Distance(i,j,k) = 2.0*double(id_solid(i,j,k))-1.0;
}
}
}
// MeanFilter(Averages->SDs);
if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
CalcDist(Distance,id_solid,*Dm);
if (rank == 0) cout << "Domain set." << endl;
}
void ScaLBL_MRTModel::Create(){
/*
* This function creates the variables needed to run a LBM
*/
int rank=Mask->rank();
//.........................................................
// 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 \n");
Map.resize(Nx,Ny,Nz); Map.fill(-2);
auto neighborList= new int[18*Npad];
Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Mask->id.data(),Np);
comm.barrier();
//...........................................................................
// MAIN VARIABLES ALLOCATED HERE
//...........................................................................
// LBM variables
if (rank==0) printf ("Allocating distributions \n");
//......................device distributions.................................
int dist_mem_size = Np*sizeof(double);
int neighborSize=18*(Np*sizeof(int));
//...........................................................................
ScaLBL_AllocateDeviceMemory((void **) &NeighborList, neighborSize);
ScaLBL_AllocateDeviceMemory((void **) &fq, 19*dist_mem_size);
ScaLBL_AllocateDeviceMemory((void **) &Pressure, 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");
// copy the neighbor list
ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
comm.barrier();
}
void ScaLBL_MRTModel::Initialize(){
/*
* This function initializes model
*/
if (rank==0) printf ("Initializing distributions \n");
ScaLBL_D3Q19_Init(fq, Np);
}
void ScaLBL_MRTModel::Run(){
double rlx_setA=1.0/tau;
double rlx_setB = 8.f*(2.f-rlx_setA)/(8.f-rlx_setA);
Minkowski Morphology(Mask);
if (rank==0){
bool WriteHeader=false;
FILE *log_file = fopen("Permeability.csv","r");
if (log_file != NULL)
fclose(log_file);
else
WriteHeader=true;
if (WriteHeader){
log_file = fopen("Permeability.csv","a+");
fprintf(log_file,"time Fx Fy Fz mu Vs As Js Xs vx vy vz k\n");
fclose(log_file);
}
}
//.......create and start timer............
double starttime,stoptime,cputime;
ScaLBL_DeviceBarrier(); comm.barrier();
starttime = MPI_Wtime();
if (rank==0) printf("Beginning AA timesteps, timestepMax = %i \n", timestepMax);
if (rank==0) printf("********************************************************\n");
timestep=0;
double error = 1.0;
double flow_rate_previous = 0.0;
while (timestep < timestepMax && error > tolerance) {
//************************************************************************/
timestep++;
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
ScaLBL_D3Q19_AAodd_MRT(NeighborList, fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
// Set boundary conditions
if (BoundaryCondition == 3){
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, din, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
}
else if (BoundaryCondition == 4){
din = ScaLBL_Comm->D3Q19_Flux_BC_z(NeighborList, fq, flux, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
}
else if (BoundaryCondition == 5){
ScaLBL_Comm->D3Q19_Reflection_BC_z(fq);
ScaLBL_Comm->D3Q19_Reflection_BC_Z(fq);
}
ScaLBL_D3Q19_AAodd_MRT(NeighborList, fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
ScaLBL_DeviceBarrier(); comm.barrier();
timestep++;
ScaLBL_Comm->SendD3Q19AA(fq); //READ FORM NORMAL
ScaLBL_D3Q19_AAeven_MRT(fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
// Set boundary conditions
if (BoundaryCondition == 3){
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, din, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
}
else if (BoundaryCondition == 4){
din = ScaLBL_Comm->D3Q19_Flux_BC_z(NeighborList, fq, flux, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
}
else if (BoundaryCondition == 5){
ScaLBL_Comm->D3Q19_Reflection_BC_z(fq);
ScaLBL_Comm->D3Q19_Reflection_BC_Z(fq);
}
ScaLBL_D3Q19_AAeven_MRT(fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
ScaLBL_DeviceBarrier(); comm.barrier();
//************************************************************************/
if (timestep%1000==0){
ScaLBL_D3Q19_Momentum(fq,Velocity, Np);
ScaLBL_DeviceBarrier(); comm.barrier();
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);
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 k=1; k<Nz-1; k++){
for (int j=1; j<Ny-1; j++){
for (int i=1; i<Nx-1; i++){
if (Distance(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;
}
}
}
}
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;
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 = (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(Distance,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=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;
if (rank==0) {
printf(" %f\n",absperm);
FILE * log_file = fopen("Permeability.csv","a");
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);
}
}
}
//************************************************************************/
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_MRTModel::VelocityField(){
/* Minkowski Morphology(Mask);
int SIZE=Np*sizeof(double);
ScaLBL_D3Q19_Momentum(fq,Velocity, Np);
ScaLBL_DeviceBarrier(); comm.barrier();
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>();
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);
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;
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");
fillData.copy(Distance,SignData);
fillData.copy(Velocity_x,VelxData);
fillData.copy(Velocity_y,VelyData);
fillData.copy(Velocity_z,VelzData);
IO::writeData( timestep, visData, Dm->Comm );
}