1644 lines
68 KiB
C++
1644 lines
68 KiB
C++
/*
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* Gauss's Law solver
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*/
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#include "models/PoissonSolver.h"
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#include "analysis/distance.h"
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#include "common/ReadMicroCT.h"
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static inline bool fileExists( const std::string &filename )
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{
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std::ifstream ifile( filename.c_str() );
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return ifile.good();
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}
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ScaLBL_Poisson::ScaLBL_Poisson(int RANK, int NP, const Utilities::MPI& COMM):
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rank(RANK), TIMELOG(nullptr), nprocs(NP),timestep(0),timestepMax(0),tau(0),k2_inv(0),tolerance(0),h(0),
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epsilon0(0),epsilon0_LB(0),epsilonR(0),epsilon_LB(0),Vin(0),Vout(0),Nx(0),Ny(0),Nz(0),N(0),Np(0),analysis_interval(0),
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chargeDen_dummy(0),WriteLog(0),nprocx(0),nprocy(0),nprocz(0),
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BoundaryConditionInlet(0),BoundaryConditionOutlet(0),BoundaryConditionSolidList(0),Lx(0),Ly(0),Lz(0),
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Vin0(0),freqIn(0),PhaseShift_In(0),Vout0(0),freqOut(0),PhaseShift_Out(0),
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TestPeriodic(0),TestPeriodicTime(0),TestPeriodicTimeConv(0),TestPeriodicSaveInterval(0),
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comm(COMM)
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{
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if ( rank == 0 ) {
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bool WriteHeader = !fileExists( "PoissonSolver_Convergence.csv" );
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TIMELOG = fopen("PoissonSolver_Convergence.csv","a+");
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if (WriteHeader)
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fprintf(TIMELOG,"Timestep Error\n");
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}
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}
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ScaLBL_Poisson::~ScaLBL_Poisson()
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{
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ScaLBL_FreeDeviceMemory(NeighborList);
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ScaLBL_FreeDeviceMemory(dvcMap);
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ScaLBL_FreeDeviceMemory(Psi);
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ScaLBL_FreeDeviceMemory(Psi_BCLabel);
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ScaLBL_FreeDeviceMemory(Permittivity);
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ScaLBL_FreeDeviceMemory(ElectricField);
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ScaLBL_FreeDeviceMemory(ResidualError);
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ScaLBL_FreeDeviceMemory(fq);
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if ( TIMELOG )
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fclose( TIMELOG );
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}
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void ScaLBL_Poisson::ReadParams(string filename){
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// read the input database
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db = std::make_shared<Database>( filename );
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domain_db = db->getDatabase( "Domain" );
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electric_db = db->getDatabase( "Poisson" );
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k2_inv = 3.0;//speed of sound for D3Q19 lattice
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tau = 0.5+k2_inv;
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timestepMax = 100000;
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tolerance = 1.0e-6;//stopping criterion for obtaining steady-state electricla potential
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h = 1.0;//resolution; unit: um/lu
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epsilon0 = 8.85e-12;//electric permittivity of vaccum; unit:[C/(V*m)]
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epsilon0_LB = epsilon0*(h*1.0e-6);//unit:[C/(V*lu)]
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epsilonR = 78.4;//default dielectric constant of water
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epsilon_LB = epsilon0_LB*epsilonR;//electric permittivity
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analysis_interval = 1000;
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chargeDen_dummy = 1.0e-3;//For debugging;unit=[C/m^3]
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WriteLog = false;
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TestPeriodic = false;
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TestPeriodicTime = 1.0;//unit: [sec]
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TestPeriodicTimeConv = 0.01; //unit [sec/lt]
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TestPeriodicSaveInterval = 0.1; //unit [sec]
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Restart = false;
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// LB-Poisson Model parameters
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if (electric_db->keyExists( "Restart" )){
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Restart = electric_db->getScalar<bool>("Restart");
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}
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if (electric_db->keyExists( "timestepMax" )){
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timestepMax = electric_db->getScalar<int>( "timestepMax" );
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}
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if (electric_db->keyExists( "tau" )){
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tau = electric_db->getScalar<double>( "tau" );
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}
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if (electric_db->keyExists( "analysis_interval" )){
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analysis_interval = electric_db->getScalar<int>( "analysis_interval" );
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}
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if (electric_db->keyExists( "tolerance" )){
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tolerance = electric_db->getScalar<double>( "tolerance" );
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}
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//'tolerance_method' can be {"MSE","MSE_max"}
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tolerance_method = electric_db->getWithDefault<std::string>( "tolerance_method", "MSE" );
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lattice_scheme = electric_db->getWithDefault<std::string>( "lattice_scheme", "D3Q19" );
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if (electric_db->keyExists( "epsilonR" )){
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epsilonR = electric_db->getScalar<double>( "epsilonR" );
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}
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if (electric_db->keyExists( "DummyChargeDen" )){
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chargeDen_dummy = electric_db->getScalar<double>( "DummyChargeDen" );
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}
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if (electric_db->keyExists( "WriteLog" )){
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WriteLog = electric_db->getScalar<bool>( "WriteLog" );
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}
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if (electric_db->keyExists( "TestPeriodic" )){
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TestPeriodic = electric_db->getScalar<bool>( "TestPeriodic" );
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}
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if (electric_db->keyExists( "TestPeriodicTime" )){
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TestPeriodicTime = electric_db->getScalar<double>( "TestPeriodicTime" );
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}
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if (electric_db->keyExists( "TestPeriodicTimeConv" )){
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TestPeriodicTimeConv = electric_db->getScalar<double>( "TestPeriodicTimeConv" );
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}
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if (electric_db->keyExists( "TestPeriodicSaveInterval" )){
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TestPeriodicSaveInterval = electric_db->getScalar<double>( "TestPeriodicSaveInterval" );
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}
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// Read solid boundary condition specific to Poisson equation
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// BC_solid=1: Dirichlet-type surfacen potential
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// BC_solid=2: Neumann-type surfacen charge density
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BoundaryConditionSolidList.push_back(1);
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if (electric_db->keyExists( "BC_SolidList" )){
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BoundaryConditionSolidList.clear();
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BoundaryConditionSolidList = electric_db->getVector<int>( "BC_SolidList" );
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}
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// Read boundary condition for electric potential
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// BC = 0: normal periodic BC
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// BC = 1: fixed electric potential
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// BC = 2: sine/cosine periodic electric potential (need extra input parameters)
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BoundaryConditionInlet = 0;
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BoundaryConditionOutlet = 0;
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if (electric_db->keyExists( "BC_Inlet" )){
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BoundaryConditionInlet = electric_db->getScalar<int>( "BC_Inlet" );
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}
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if (electric_db->keyExists( "BC_Outlet" )){
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BoundaryConditionOutlet = electric_db->getScalar<int>( "BC_Outlet" );
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}
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// Read domain parameters
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if (domain_db->keyExists( "voxel_length" )){//default unit: um/lu
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h = domain_db->getScalar<double>( "voxel_length" );
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}
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//Re-calcualte model parameters if user updates input
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epsilon0_LB = epsilon0*(h*1.0e-6);//unit:[C/(V*lu)]
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epsilon_LB = epsilon0_LB*epsilonR;//electric permittivity
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/* restart string */
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sprintf(LocalRankString, "%05d", rank);
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sprintf(LocalRestartFile, "%s%s", "PoissonSolver.", LocalRankString);
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if (rank==0) printf("***********************************************************************************\n");
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if (rank==0) printf("LB-Poisson Solver: steady-state MaxTimeStep = %i; steady-state tolerance = %.3g \n", timestepMax,tolerance);
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if (rank==0) printf(" LB relaxation tau = %.5g \n", tau);
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if (rank==0) printf("***********************************************************************************\n");
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if (tolerance_method.compare("MSE")==0){
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if (rank==0) printf("LB-Poisson Solver: Use averaged MSE to check solution convergence.\n");
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}
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else if (tolerance_method.compare("MSE_max")==0){
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if (rank==0) printf("LB-Poisson Solver: Use maximum MSE to check solution convergence.\n");
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}
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else{
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if (rank==0) printf("LB-Poisson Solver: tolerance_method=%s cannot be identified!\n",tolerance_method.c_str());
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}
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if (lattice_scheme.compare("D3Q7")==0){
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if (rank==0) printf("LB-Poisson Solver: Use D3Q7 lattice structure.\n");
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}
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else if (lattice_scheme.compare("D3Q19")==0){
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if (rank==0) printf("LB-Poisson Solver: Use D3Q19 lattice structure.\n");
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}
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else{
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if (rank==0) printf("LB-Poisson Solver: lattice_scheme=%s cannot be identified!\n",lattice_scheme.c_str());
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}
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}
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void ScaLBL_Poisson::SetDomain(){
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Dm = std::shared_ptr<Domain>(new Domain(domain_db,comm)); // full domain for analysis
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Mask = std::shared_ptr<Domain>(new Domain(domain_db,comm)); // mask domain removes immobile phases
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// domain parameters
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Nx = Dm->Nx;
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Ny = Dm->Ny;
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Nz = Dm->Nz;
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Lx = Dm->Lx;
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Ly = Dm->Ly;
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Lz = Dm->Lz;
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N = Nx*Ny*Nz;
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Distance.resize(Nx,Ny,Nz);
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Psi_host.resize(Nx,Ny,Nz);
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Psi_previous.resize(Nx,Ny,Nz);
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for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = 1; // initialize this way
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//Averages = std::shared_ptr<TwoPhase> ( new TwoPhase(Dm) ); // TwoPhase analysis object
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comm.barrier();
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if (BoundaryConditionInlet==0 && BoundaryConditionOutlet==0){
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Dm->BoundaryCondition = 0;
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Mask->BoundaryCondition = 0;
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}
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else if (BoundaryConditionInlet>0 && BoundaryConditionOutlet>0){
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Dm->BoundaryCondition = 1;
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Mask->BoundaryCondition = 1;
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}
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else {//i.e. non-periodic and periodic BCs are mixed
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ERROR("Error: check the type of inlet and outlet boundary condition! Mixed periodic and non-periodic BCs are found!\n");
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}
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Dm->CommInit();
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comm.barrier();
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rank = Dm->rank();
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nprocx = Dm->nprocx();
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nprocy = Dm->nprocy();
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nprocz = Dm->nprocz();
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}
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void ScaLBL_Poisson::ReadInput(){
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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","PoissonSolver.",LocalRankString);
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if (domain_db->keyExists( "Filename" )){
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auto Filename = domain_db->getScalar<std::string>( "Filename" );
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Mask->Decomp(Filename);
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}
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else if (domain_db->keyExists( "GridFile" )){
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// Read the local domain data
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auto input_id = readMicroCT( *domain_db, comm );
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// Fill the halo (assuming GCW of 1)
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array<int,3> size0 = { (int) input_id.size(0), (int) input_id.size(1), (int) input_id.size(2) };
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ArraySize size1 = { (size_t) Mask->Nx, (size_t) Mask->Ny, (size_t) Mask->Nz };
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ASSERT( (int) size1[0] == size0[0]+2 && (int) size1[1] == size0[1]+2 && (int) size1[2] == size0[2]+2 );
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fillHalo<signed char> fill( comm, Mask->rank_info, size0, { 1, 1, 1 }, 0, 1 );
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Array<signed char> id_view;
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id_view.viewRaw( size1, Mask->id.data() );
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fill.copy( input_id, id_view );
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fill.fill( id_view );
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}
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else{
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Mask->ReadIDs();
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}
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// Generate the signed distance map
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// Initialize the domain and communication
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Array<char> id_solid(Nx,Ny,Nz);
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// Solve for the position of the solid phase
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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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// Initialize the solid phase
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if (Mask->id[n] > 0) id_solid(i,j,k) = 1;
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else id_solid(i,j,k) = 0;
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}
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}
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}
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// Initialize the signed distance function
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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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// Initialize distance to +/- 1
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Distance(i,j,k) = 2.0*double(id_solid(i,j,k))-1.0;
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}
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}
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}
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// MeanFilter(Averages->SDs);
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if (rank==0) printf("LB-Poisson Solver: Initialized solid phase & converting to Signed Distance function \n");
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CalcDist(Distance,id_solid,*Dm);
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if (rank == 0) cout << " Domain set." << endl;
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}
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void ScaLBL_Poisson::AssignSolidBoundary(double *poisson_solid, int *poisson_solid_BClabel)
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{
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signed char VALUE=0;
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double AFFINITY=0.f;
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int BoundaryConditionSolid=0;
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auto LabelList = electric_db->getVector<int>( "SolidLabels" );
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auto AffinityList = electric_db->getVector<double>( "SolidValues" );
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size_t NLABELS = LabelList.size();
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if (NLABELS != AffinityList.size() || NLABELS != BoundaryConditionSolidList.size()){
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ERROR("Error: LB-Poisson Solver: BC_SolidList, SolidLabels and SolidValues all must be of the same length! \n");
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}
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if (electric_db->keyExists( "PermittivityValues" ))
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{
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/* assign the permittivity based on the material*/
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double *Permittivity_host;
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Permittivity_host = new double[Nx*Ny*Nz];
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double PERMITTIVITY = epsilon_LB;
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auto LabelList = electric_db->getVector<int>( "SolidLabels" );
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auto PermittivityList = electric_db->getVector<double>( "PermittivityValues" );
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size_t NLABELS = LabelList.size();
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if (NLABELS != PermittivityList.size()){
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ERROR("Error: LB-Poisson Solver: SolidLabels and PermittivityList all must be of the same length! \n");
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}
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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=Mask->id[n];
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PERMITTIVITY=epsilon_LB;
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// Assign the affinity from the paired list
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for (unsigned int idx=0; idx < NLABELS; idx++){
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if (VALUE == LabelList[idx]){
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PERMITTIVITY=PermittivityList[idx];
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//label_count[idx] += 1.0;
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idx = NLABELS;
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}
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}
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int idx=Map(i,j,k);
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if (!(idx<0)) Permittivity_host[n] = PERMITTIVITY;
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}
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}
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}
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ScaLBL_CopyToDevice(Permittivity, Permittivity_host, sizeof(double)*Nx*Ny*Nz);
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delete [] Permittivity_host;
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}
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std::vector<double> label_count( NLABELS, 0.0 );
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std::vector<double> label_count_global( NLABELS, 0.0 );
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// Assign the labels
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for (size_t idx=0; idx<NLABELS; idx++) label_count[idx]=0;
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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=Mask->id[n];
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AFFINITY=0.f;
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BoundaryConditionSolid=0;
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// Assign the affinity from the paired list
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for (unsigned int idx=0; idx < NLABELS; idx++){
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if (VALUE == LabelList[idx]){
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AFFINITY=AffinityList[idx];
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BoundaryConditionSolid=BoundaryConditionSolidList[idx];
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if (BoundaryConditionSolid!=1 && BoundaryConditionSolid!=2){
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ERROR("Error: LB-Poisson Solver: Note only BC_SolidList of 1 or 2 is supported!\n");
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}
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//NOTE need to convert the user input phys unit to LB unit
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if (BoundaryConditionSolid==2){
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//for BCS=1, i.e. Dirichlet-type, no need for unit conversion
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AFFINITY = AFFINITY*(h*h*1.0e-12)/epsilon_LB;
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}
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label_count[idx] += 1.0;
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idx = NLABELS;
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//Mask->id[n] = 0; // set mask to zero since this is an immobile component
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}
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}
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poisson_solid[n] = AFFINITY;
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poisson_solid_BClabel[n] = BoundaryConditionSolid;
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}
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}
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}
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for (size_t idx=0; idx<NLABELS; idx++)
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label_count_global[idx]=Dm->Comm.sumReduce( label_count[idx]);
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if (rank==0){
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printf("LB-Poisson Solver: number of Poisson solid labels: %lu \n",NLABELS);
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for (unsigned int idx=0; idx<NLABELS; idx++){
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VALUE=LabelList[idx];
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AFFINITY=AffinityList[idx];
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BoundaryConditionSolid=BoundaryConditionSolidList[idx];
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double volume_fraction = double(label_count_global[idx])/double((Nx-2)*(Ny-2)*(Nz-2)*nprocs);
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if (BoundaryConditionSolid==1){
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printf(" label=%d, surface potential=%.3g [V], volume fraction=%.2g\n",VALUE,AFFINITY,volume_fraction);
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}
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else if (BoundaryConditionSolid==2){
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printf(" label=%d, surface charge density=%.3g [C/m^2], volume fraction=%.2g\n",VALUE,AFFINITY,volume_fraction);
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}
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else{
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ERROR("Error: LB-Poisson Solver: Note only BC_SolidList of 1 or 2 is supported!\n");
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}
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}
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}
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}
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void ScaLBL_Poisson::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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int rank=Mask->rank();
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//.........................................................
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// Initialize communication structures in averaging domain
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for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = Mask->id[i];
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Mask->CommInit();
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Np=Mask->PoreCount();
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//...........................................................................
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if (rank==0) printf ("LB-Poisson Solver: 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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ScaLBL_Comm_Regular = std::shared_ptr<ScaLBL_Communicator>(new ScaLBL_Communicator(Mask));
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int Npad=(Np/16 + 2)*16;
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if (rank==0) printf ("LB-Poisson Solver: 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.data(),Npad,1);
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comm.barrier();
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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 ("LB-Poisson Solver: Allocating distributions \n");
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//......................device distributions.................................
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size_t dist_mem_size = Np*sizeof(double);
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size_t 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 **) &dvcID, sizeof(signed char)*Nx*Ny*Nz);
|
|
ScaLBL_AllocateDeviceMemory((void **) &Psi, sizeof(double)*Nx*Ny*Nz);
|
|
ScaLBL_AllocateDeviceMemory((void **) &Permittivity, sizeof(double)*Nx*Ny*Nz);
|
|
ScaLBL_AllocateDeviceMemory((void **) &Psi_BCLabel, sizeof(int)*Nx*Ny*Nz);
|
|
ScaLBL_AllocateDeviceMemory((void **) &ElectricField, 3*sizeof(double)*Np);
|
|
ScaLBL_AllocateDeviceMemory((void **) &ResidualError, sizeof(double)*Np);
|
|
if (lattice_scheme.compare("D3Q7")==0){
|
|
ScaLBL_AllocateDeviceMemory((void **) &fq, 7*dist_mem_size);
|
|
}
|
|
else if (lattice_scheme.compare("D3Q19")==0){
|
|
ScaLBL_AllocateDeviceMemory((void **) &fq, 19*dist_mem_size);
|
|
}
|
|
//...........................................................................
|
|
|
|
// Update GPU data structures
|
|
if (rank==0) printf ("LB-Poisson Solver: 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;
|
|
}
|
|
}
|
|
}
|
|
comm.barrier();
|
|
if (rank==0) printf (" .... LB-Poisson Solver: check neighbor list \n");
|
|
// check that TmpMap is valid
|
|
for (int idx=0; idx<ScaLBL_Comm->LastExterior(); idx++){
|
|
auto n = TmpMap[idx];
|
|
if (n > Nx*Ny*Nz){
|
|
printf("Bad value! idx=%i \n", n);
|
|
TmpMap[idx] = Nx*Ny*Nz-1;
|
|
}
|
|
}
|
|
for (int idx=ScaLBL_Comm->FirstInterior(); idx<ScaLBL_Comm->LastInterior(); idx++){
|
|
auto n = TmpMap[idx];
|
|
if ( n > Nx*Ny*Nz ){
|
|
printf("Bad value! idx=%i \n",n);
|
|
TmpMap[idx] = Nx*Ny*Nz-1;
|
|
}
|
|
}
|
|
comm.barrier();
|
|
if (rank==0) printf (" .... LB-Poisson Solver: copy neighbor list to GPU \n");
|
|
ScaLBL_CopyToDevice(dvcMap, TmpMap, sizeof(int)*Np);
|
|
ScaLBL_Comm->Barrier();
|
|
delete [] TmpMap;
|
|
// copy the neighbor list
|
|
ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
|
|
ScaLBL_Comm->Barrier();
|
|
comm.barrier();
|
|
delete [] neighborList;
|
|
// copy node ID
|
|
//ScaLBL_CopyToDevice(dvcID, Mask->id, sizeof(signed char)*Nx*Ny*Nz);
|
|
//ScaLBL_Comm->Barrier();
|
|
|
|
//Initialize solid boundary for electric potential
|
|
// DON'T USE WITH CELLULAR SYSTEM (NO SOLID -- NEED Membrane SOLUTION)
|
|
ScaLBL_Comm->SetupBounceBackList(Map, Mask->id.data(), Np);
|
|
comm.barrier();
|
|
}
|
|
|
|
void ScaLBL_Poisson::Potential_Init(double *psi_init){
|
|
|
|
//set up default boundary input parameters
|
|
Vin0 = Vout0 = 1.0; //unit: [V]
|
|
freqIn = freqOut = 50.0; //unit: [Hz]
|
|
PhaseShift_In = PhaseShift_Out = 0.0; //unit: [radian]
|
|
Vin = 0.0; //Boundary-z (inlet) electric potential
|
|
Vout = 0.0; //Boundary-Z (outlet) electric potential
|
|
|
|
/* Assign permittivity value to the solid */
|
|
signed char VALUE=0;
|
|
double AFFINITY=0.f;
|
|
|
|
if (BoundaryConditionInlet==0 && BoundaryConditionOutlet==0){
|
|
|
|
signed char VALUE=0;
|
|
double AFFINITY=0.f;
|
|
|
|
auto LabelList = electric_db->getVector<int>( "InitialValueLabels" );
|
|
auto AffinityList = electric_db->getVector<double>( "InitialValues" );
|
|
auto PermittivityList = electric_db->getVector<double>( "PermittivityValues" );
|
|
|
|
size_t NLABELS = LabelList.size();
|
|
if (NLABELS != AffinityList.size()){
|
|
ERROR("Error: LB-Poisson Solver: InitialValueLabels and InitialValues must be of the same length! \n");
|
|
}
|
|
|
|
std::vector<double> label_count( NLABELS, 0.0 );
|
|
std::vector<double> label_count_global( NLABELS, 0.0 );
|
|
|
|
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;
|
|
VALUE=Mask->id[n];
|
|
AFFINITY=0.f;
|
|
// Assign the affinity from the paired list
|
|
for (unsigned int idx=0; idx < NLABELS; idx++){
|
|
if (VALUE == LabelList[idx]){
|
|
AFFINITY=AffinityList[idx];
|
|
label_count[idx] += 1.0;
|
|
idx = NLABELS;
|
|
}
|
|
}
|
|
int idx=Map(i,j,k);
|
|
if (!(idx<0)) psi_init[n] = AFFINITY;
|
|
}
|
|
}
|
|
}
|
|
|
|
for (size_t idx=0; idx<NLABELS; idx++)
|
|
label_count_global[idx]=Dm->Comm.sumReduce( label_count[idx]);
|
|
|
|
if (rank==0){
|
|
printf("LB-Poisson Solver: number of Poisson initial-value labels: %lu \n",NLABELS);
|
|
for (unsigned int idx=0; idx<NLABELS; idx++){
|
|
VALUE=LabelList[idx];
|
|
AFFINITY=AffinityList[idx];
|
|
double volume_fraction = double(label_count_global[idx])/double((Nx-2)*(Ny-2)*(Nz-2)*nprocs);
|
|
printf(" label=%d, initial potential=%.3g [V], volume fraction=%.2g\n",VALUE,AFFINITY,volume_fraction);
|
|
}
|
|
}
|
|
}
|
|
else if (BoundaryConditionInlet>0 && BoundaryConditionOutlet>0){
|
|
//read input parameters for inlet
|
|
switch (BoundaryConditionInlet){
|
|
case 1:
|
|
if (electric_db->keyExists( "Vin" )){
|
|
Vin = electric_db->getScalar<double>( "Vin" );
|
|
}
|
|
if (rank==0) printf("LB-Poisson Solver: inlet boundary; fixed electric potential Vin = %.3g [V]\n",Vin);
|
|
break;
|
|
case 2:
|
|
if (electric_db->keyExists( "Vin0" )){//voltage amplitude; unit: Volt
|
|
Vin0 = electric_db->getScalar<double>( "Vin0" );
|
|
}
|
|
if (electric_db->keyExists( "freqIn" )){//unit: Hz
|
|
freqIn = electric_db->getScalar<double>( "freqIn" );
|
|
}
|
|
if (electric_db->keyExists( "PhaseShift_In" )){//phase shift, unit: radian
|
|
PhaseShift_In = electric_db->getScalar<double>( "PhaseShift_In" );
|
|
}
|
|
if (rank==0){
|
|
printf("LB-Poisson Solver: inlet boundary; periodic electric potential Vin = %.3g*Cos[2*pi*%.3g*t+%.3g] [V] \n",Vin0,freqIn,PhaseShift_In);
|
|
printf(" V0 = %.3g [V], frequency = %.3g [Hz], phase shift = %.3g [radian] \n",Vin0,freqIn,PhaseShift_In);
|
|
}
|
|
break;
|
|
}
|
|
//read input parameters for outlet
|
|
switch (BoundaryConditionOutlet){
|
|
case 1:
|
|
if (electric_db->keyExists( "Vout" )){
|
|
Vout = electric_db->getScalar<double>( "Vout" );
|
|
}
|
|
if (rank==0) printf("LB-Poisson Solver: outlet boundary; fixed electric potential Vout = %.3g [V] \n",Vout);
|
|
break;
|
|
case 2:
|
|
if (electric_db->keyExists( "Vout0" )){//voltage amplitude; unit: Volt
|
|
Vout0 = electric_db->getScalar<double>( "Vout0" );
|
|
}
|
|
if (electric_db->keyExists( "freqOut" )){//unit: Hz
|
|
freqOut = electric_db->getScalar<double>( "freqOut" );
|
|
}
|
|
if (electric_db->keyExists( "PhaseShift_Out" )){//timestep shift, unit: lt
|
|
PhaseShift_Out = electric_db->getScalar<double>( "PhaseShift_Out" );
|
|
}
|
|
if (rank==0){
|
|
printf("LB-Poisson Solver: outlet boundary; periodic electric potential Vout = %.3g*Cos[2*pi*%.3g*t+%.3g] [V]\n",Vout0,freqOut,PhaseShift_Out);
|
|
printf(" V0 = %.3g [V], frequency = %.3g [Hz], timestep shift = %.3g [radian] \n",Vout0,freqOut,PhaseShift_Out);
|
|
}
|
|
break;
|
|
}
|
|
//calcualte inlet/outlet voltage for the case of BCInlet/Outlet=2
|
|
if (BoundaryConditionInlet==2) Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,0);
|
|
if (BoundaryConditionOutlet==2) Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,0);
|
|
|
|
//initialize a linear electrical potential between inlet and outlet
|
|
double slope = (Vout-Vin)/((Nz-2)*Dm->nprocz());
|
|
double psi_linearized = Vin;
|
|
for (int k=0;k<Nz;k++){
|
|
if (Dm->kproc() == 0){
|
|
if (k==0 || k==1){
|
|
psi_linearized = Vin;
|
|
}
|
|
else{
|
|
psi_linearized = slope*(Dm->kproc()*(Nz-2) + (k-1)) + Vin;
|
|
}
|
|
}
|
|
if (Dm->kproc() == Dm->nprocz()-1){
|
|
if (k==Nz-1 || k==Nz-2){
|
|
psi_linearized = Vout;
|
|
}
|
|
else{
|
|
psi_linearized = slope*(Dm->kproc()*(Nz-2) + (k-1)) + Vin;
|
|
}
|
|
}
|
|
else{
|
|
psi_linearized = slope*(Dm->kproc()*(Nz-2) + (k-1)) + Vin;
|
|
}
|
|
for (int j=0;j<Ny;j++){
|
|
for (int i=0;i<Nx;i++){
|
|
int n = k*Nx*Ny+j*Nx+i;
|
|
if (Mask->id[n]>0){
|
|
psi_init[n] = psi_linearized;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
else{//mixed periodic and non-periodic BCs are not supported!
|
|
ERROR("Error: check the type of inlet and outlet boundary condition! Mixed periodic and non-periodic BCs are found!\n");
|
|
}
|
|
/** RESTART **/
|
|
if (Restart == true) {
|
|
if (rank == 0) {
|
|
printf(" POISSON MODEL: Reading restart file! \n");
|
|
}
|
|
ifstream File(LocalRestartFile, ios::binary);
|
|
double value;
|
|
// Read the distributions
|
|
for (int n = 0; n < Nx*Ny*Nz; n++) {
|
|
File.read((char *)&value, sizeof(value));
|
|
psi_init[n] = value;
|
|
}
|
|
File.close();
|
|
}
|
|
/** END RESTART **/
|
|
}
|
|
|
|
double ScaLBL_Poisson::getBoundaryVoltagefromPeriodicBC(double V0, double freq, double phase_shift, int time_step){
|
|
return V0*cos(2.0*M_PI*freq*time_conv*time_step+phase_shift);
|
|
}
|
|
|
|
void ScaLBL_Poisson::Initialize(double time_conv_from_Study){
|
|
/*
|
|
* This function initializes model
|
|
* "time_conv_from_Study" is the phys to LB time conversion factor, unit=[sec/lt]
|
|
* which is used for periodic voltage input for inlet and outlet boundaries
|
|
*/
|
|
if (lattice_scheme.compare("D3Q7")==0){
|
|
if (rank==0) printf ("LB-Poisson Solver: initializing D3Q7 distributions\n");
|
|
}
|
|
else if (lattice_scheme.compare("D3Q19")==0){
|
|
if (rank==0) printf ("LB-Poisson Solver: initializing D3Q19 distributions\n");
|
|
}
|
|
//NOTE the initialization involves two steps:
|
|
//1. assign solid boundary value (surface potential or surface change density)
|
|
//2. Initialize electric potential for pore nodes
|
|
double *psi_host;
|
|
int *psi_BCLabel_host;
|
|
psi_host = new double [Nx*Ny*Nz];
|
|
psi_BCLabel_host = new int [Nx*Ny*Nz];
|
|
time_conv = time_conv_from_Study;
|
|
AssignSolidBoundary(psi_host,psi_BCLabel_host);//step1
|
|
Potential_Init(psi_host);//step2
|
|
ScaLBL_CopyToDevice(Psi, psi_host, Nx*Ny*Nz*sizeof(double));
|
|
ScaLBL_CopyToDevice(Psi_BCLabel, psi_BCLabel_host, Nx*Ny*Nz*sizeof(int));
|
|
ScaLBL_Comm->Barrier();
|
|
if (lattice_scheme.compare("D3Q7")==0){
|
|
ScaLBL_D3Q7_Poisson_Init(dvcMap, fq, Psi, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
|
ScaLBL_D3Q7_Poisson_Init(dvcMap, fq, Psi, 0, ScaLBL_Comm->LastExterior(), Np);
|
|
}
|
|
else if (lattice_scheme.compare("D3Q19")==0){
|
|
/* switch to d3Q19 model */
|
|
ScaLBL_D3Q19_Poisson_Init(dvcMap, fq, Psi, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
|
ScaLBL_D3Q19_Poisson_Init(dvcMap, fq, Psi, 0, ScaLBL_Comm->LastExterior(), Np);
|
|
}
|
|
delete [] psi_host;
|
|
delete [] psi_BCLabel_host;
|
|
|
|
//extra treatment for halo layer
|
|
//if (BoundaryCondition==1){
|
|
// if (Dm->kproc()==0){
|
|
// ScaLBL_SetSlice_z(Psi,Vin,Nx,Ny,Nz,0);
|
|
// }
|
|
// if (Dm->kproc() == nprocz-1){
|
|
// ScaLBL_SetSlice_z(Psi,Vout,Nx,Ny,Nz,Nz-1);
|
|
// }
|
|
//}
|
|
}
|
|
|
|
void ScaLBL_Poisson::Run(double *ChargeDensity, bool UseSlippingVelBC, int timestep_from_Study){
|
|
|
|
double error = 1.0;
|
|
if (lattice_scheme.compare("D3Q7")==0){
|
|
timestep=0;
|
|
while (timestep < timestepMax && error > tolerance) {
|
|
//************************************************************************/
|
|
// *************ODD TIMESTEP*************//
|
|
timestep++;
|
|
SolveElectricPotentialAAodd(timestep_from_Study);//update electric potential
|
|
SolvePoissonAAodd(ChargeDensity, UseSlippingVelBC,timestep);//perform collision
|
|
ScaLBL_Comm->Barrier(); comm.barrier();
|
|
|
|
// *************EVEN TIMESTEP*************//
|
|
timestep++;
|
|
SolveElectricPotentialAAeven(timestep_from_Study);//update electric potential
|
|
SolvePoissonAAeven(ChargeDensity, UseSlippingVelBC,timestep);//perform collision
|
|
ScaLBL_Comm->Barrier(); comm.barrier();
|
|
//************************************************************************/
|
|
|
|
// Check convergence of steady-state solution
|
|
if (timestep==2){
|
|
//save electric potential for convergence check
|
|
ScaLBL_CopyToHost(Psi_previous.data(),Psi,sizeof(double)*Nx*Ny*Nz);
|
|
}
|
|
if (timestep%analysis_interval==0){
|
|
if (tolerance_method.compare("MSE")==0){
|
|
double count_loc=0;
|
|
double count;
|
|
double MSE_loc=0.0;
|
|
ScaLBL_CopyToHost(Psi_host.data(),Psi,sizeof(double)*Nx*Ny*Nz);
|
|
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){
|
|
MSE_loc += (Psi_host(i,j,k) - Psi_previous(i,j,k))*(Psi_host(i,j,k) - Psi_previous(i,j,k));
|
|
count_loc+=1.0;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
error=Dm->Comm.sumReduce(MSE_loc);
|
|
count=Dm->Comm.sumReduce(count_loc);
|
|
error /= count;
|
|
}
|
|
else if (tolerance_method.compare("MSE_max")==0){
|
|
vector<double>MSE_loc;
|
|
double MSE_loc_max;
|
|
ScaLBL_CopyToHost(Psi_host.data(),Psi,sizeof(double)*Nx*Ny*Nz);
|
|
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){
|
|
MSE_loc.push_back((Psi_host(i,j,k) - Psi_previous(i,j,k))*(Psi_host(i,j,k) - Psi_previous(i,j,k)));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
vector<double>::iterator it_max = max_element(MSE_loc.begin(),MSE_loc.end());
|
|
unsigned int idx_max=distance(MSE_loc.begin(),it_max);
|
|
MSE_loc_max=MSE_loc[idx_max];
|
|
error=Dm->Comm.maxReduce(MSE_loc_max);
|
|
}
|
|
else{
|
|
ERROR("Error: user-specified tolerance_method cannot be identified; check you input database! \n");
|
|
}
|
|
ScaLBL_CopyToHost(Psi_previous.data(),Psi,sizeof(double)*Nx*Ny*Nz);
|
|
}
|
|
}
|
|
}
|
|
else if (lattice_scheme.compare("D3Q19")==0){
|
|
|
|
double *host_Error;
|
|
host_Error = new double [Np];
|
|
|
|
timestep=0;
|
|
auto t1 = std::chrono::system_clock::now();
|
|
while (timestep < timestepMax && error > tolerance) {
|
|
// Universal constant
|
|
double kb = 1.38e-23; //Boltzmann constant;unit [J/K]
|
|
double electron_charge = 1.6e-19; //electron charge;unit [C]
|
|
double T = 300.0; //temperature; unit [K]
|
|
double Vt = kb * T / electron_charge; //thermal voltage; unit [Vy]
|
|
double Cp = 1.014e-7; // proton concentration
|
|
|
|
timestep=0;
|
|
auto t1 = std::chrono::system_clock::now();
|
|
while (timestep < timestepMax && error > tolerance) {
|
|
//************************************************************************/
|
|
// *************ODD TIMESTEP*************//
|
|
// Set boundary conditions
|
|
timestep++;
|
|
|
|
//SolvePoissonAAodd(ChargeDensity, UseSlippingVelBC, timestep);//perform collision
|
|
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
|
|
ScaLBL_D3Q19_AAodd_Poisson(NeighborList, dvcMap, fq, ChargeDensity, Psi, ElectricField,
|
|
tau, Vt, Cp, epsilon_LB, UseSlippingVelBC,
|
|
ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
|
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
|
|
|
|
if (BoundaryConditionInlet > 0 && Dm->kproc()==0){
|
|
switch (BoundaryConditionInlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
case 2:
|
|
Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
}
|
|
}
|
|
if (BoundaryConditionOutlet > 0 && Dm->kproc() == nprocz-1){
|
|
switch (BoundaryConditionOutlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
case 2:
|
|
Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
}
|
|
}
|
|
|
|
ScaLBL_D3Q19_AAodd_Poisson(NeighborList, dvcMap, fq, ChargeDensity, Psi, ElectricField,
|
|
tau, Vt, Cp, epsilon_LB, UseSlippingVelBC,
|
|
0, ScaLBL_Comm->LastExterior(), Np);
|
|
|
|
// *************EVEN TIMESTEP*************//
|
|
|
|
timestep++;
|
|
|
|
//SolvePoissonAAeven(ChargeDensity, UseSlippingVelBC, timestep);//perform collision
|
|
//ScaLBL_Comm->Barrier(); comm.barrier();
|
|
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
|
|
ScaLBL_D3Q19_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, ResidualError,
|
|
tau, Vt, Cp, epsilon_LB, UseSlippingVelBC,
|
|
ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
|
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
|
|
|
|
// Set boundary conditions
|
|
if (BoundaryConditionInlet > 0 && Dm->kproc()==0){
|
|
switch (BoundaryConditionInlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
case 2:
|
|
Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
}
|
|
}
|
|
if (BoundaryConditionOutlet > 0 && Dm->kproc() == nprocz-1){
|
|
switch (BoundaryConditionOutlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
case 2:
|
|
Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
}
|
|
}
|
|
|
|
ScaLBL_D3Q19_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, ResidualError,
|
|
tau, Vt, Cp, epsilon_LB, UseSlippingVelBC,
|
|
0, ScaLBL_Comm->LastExterior(), Np);
|
|
ScaLBL_Comm->Barrier(); comm.barrier();
|
|
//************************************************************************/
|
|
}
|
|
// Check convergence of steady-state solution
|
|
if (timestep==2){
|
|
//save electric potential for convergence check
|
|
}
|
|
if (timestep%analysis_interval==0){
|
|
/* get the elecric potential */
|
|
ScaLBL_CopyToHost(Psi_host.data(),Psi,sizeof(double)*Nx*Ny*Nz);
|
|
if (rank==0) printf(" ... getting Poisson solver error \n");
|
|
double err = 0.0;
|
|
double max_error = 0.0;
|
|
ScaLBL_CopyToHost(host_Error,ResidualError,sizeof(double)*Np);
|
|
for (int idx=0; idx<Np; idx++){
|
|
err = host_Error[idx]*host_Error[idx];
|
|
if (err > max_error ){
|
|
max_error = err;
|
|
}
|
|
}
|
|
error=Dm->Comm.maxReduce(max_error);
|
|
if (rank==0) printf(" error = %0.5g \n",error);
|
|
}
|
|
}
|
|
// SetMeanZeroVoltage();
|
|
|
|
if (rank == 0)
|
|
printf("---------------------------------------------------------------"
|
|
"----\n");
|
|
// Compute the walltime per timestep
|
|
auto t2 = std::chrono::system_clock::now();
|
|
double cputime = std::chrono::duration<double>(t2 - t1).count() / timestep;
|
|
// Performance obtained from each node
|
|
double MLUPS = double(Np) / cputime / 1000000;
|
|
|
|
if(WriteLog==true){
|
|
getConvergenceLog(timestep,error);
|
|
}
|
|
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");
|
|
delete [] host_Error;
|
|
|
|
}
|
|
//************************************************************************/
|
|
|
|
if(WriteLog==true){
|
|
getConvergenceLog(timestep,error);
|
|
}
|
|
}
|
|
|
|
void ScaLBL_Poisson::Run(double *ChargeDensity, DoubleArray MembraneDistance, bool UseSlippingVelBC, int timestep_from_Study){
|
|
|
|
double error = 1.0;
|
|
double threshold = 10000000.0;
|
|
bool SET_THRESHOLD = false;
|
|
if (electric_db->keyExists( "rescale_at_distance" )){
|
|
SET_THRESHOLD = true;
|
|
threshold = electric_db->getScalar<double>( "rescale_at_distance" );
|
|
}
|
|
if (BoundaryConditionInlet > 0) SET_THRESHOLD = false;
|
|
if (BoundaryConditionOutlet > 0) SET_THRESHOLD = false;
|
|
|
|
double *host_Error;
|
|
host_Error = new double [Np];
|
|
|
|
// Universal constant
|
|
double kb = 1.38e-23; //Boltzmann constant;unit [J/K]
|
|
double electron_charge = 1.6e-19; //electron charge;unit [C]
|
|
double T = 300.0; //temperature; unit [K]
|
|
double Vt = kb * T / electron_charge; //thermal voltage; unit [Vy]
|
|
double Cp = 1.014e-7; // proton concentration
|
|
|
|
timestep=0;
|
|
auto t1 = std::chrono::system_clock::now();
|
|
while (timestep < timestepMax && error > tolerance) {
|
|
//************************************************************************/
|
|
// *************ODD TIMESTEP*************//
|
|
timestep++;
|
|
//SolvePoissonAAodd(ChargeDensity, UseSlippingVelBC, timestep);//perform collision
|
|
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
|
|
ScaLBL_D3Q19_AAodd_Poisson(NeighborList, dvcMap, fq, ChargeDensity, Psi, ElectricField,
|
|
tau, Vt, Cp, epsilon_LB, UseSlippingVelBC,
|
|
ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
|
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
|
|
// Set boundary conditions
|
|
if (BoundaryConditionInlet > 0 && Dm->kproc()==0){
|
|
switch (BoundaryConditionInlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
case 2:
|
|
Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
}
|
|
}
|
|
if (BoundaryConditionOutlet > 0 && Dm->kproc() == nprocz-1){
|
|
switch (BoundaryConditionOutlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
case 2:
|
|
Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
}
|
|
}
|
|
|
|
ScaLBL_D3Q19_AAodd_Poisson(NeighborList, dvcMap, fq, ChargeDensity, Psi, ElectricField,
|
|
tau, Vt, Cp, epsilon_LB, UseSlippingVelBC,
|
|
0, ScaLBL_Comm->LastExterior(), Np);
|
|
|
|
// *************EVEN TIMESTEP*************//
|
|
timestep++;
|
|
|
|
|
|
//SolvePoissonAAeven(ChargeDensity, UseSlippingVelBC, timestep);//perform collision
|
|
//ScaLBL_Comm->Barrier(); comm.barrier();
|
|
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
|
|
ScaLBL_D3Q19_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, ResidualError,
|
|
tau, Vt, Cp, epsilon_LB, UseSlippingVelBC,
|
|
ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
|
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
|
|
|
|
// Set boundary conditions
|
|
if (BoundaryConditionInlet > 0 && Dm->kproc()==0){
|
|
switch (BoundaryConditionInlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
case 2:
|
|
Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
}
|
|
}
|
|
if (BoundaryConditionOutlet > 0 && Dm->kproc() == nprocz-1){
|
|
switch (BoundaryConditionOutlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
case 2:
|
|
Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
}
|
|
}
|
|
ScaLBL_D3Q19_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, ResidualError,
|
|
tau, Vt, Cp, epsilon_LB, UseSlippingVelBC,
|
|
0, ScaLBL_Comm->LastExterior(), Np);
|
|
|
|
|
|
ScaLBL_Comm->Barrier(); comm.barrier();
|
|
//************************************************************************/
|
|
|
|
// Check convergence of steady-state solution
|
|
if (timestep==2){
|
|
//save electric potential for convergence check
|
|
}
|
|
if (timestep%analysis_interval==0){
|
|
/* get the elecric potential */
|
|
ScaLBL_CopyToHost(Psi_host.data(),Psi,sizeof(double)*Nx*Ny*Nz);
|
|
if (rank==0) printf(" ... getting Poisson solver error \n");
|
|
double err = 0.0;
|
|
double max_error = 0.0;
|
|
ScaLBL_CopyToHost(host_Error,ResidualError,sizeof(double)*Np);
|
|
for (int idx=0; idx<Np; idx++){
|
|
err = host_Error[idx]*host_Error[idx];
|
|
if (err > max_error ){
|
|
max_error = err;
|
|
}
|
|
}
|
|
error=Dm->Comm.maxReduce(max_error);
|
|
|
|
if (error > tolerance && SET_THRESHOLD){
|
|
/* don't use this with an external BC */
|
|
// cpompute the far-field electric potential
|
|
double inside_local = 0.0;
|
|
double outside_local = 0.0;
|
|
double inside_count_local = 0.0;
|
|
double outside_count_local = 0.0;
|
|
/* global values */
|
|
double inside_global = 0.0;
|
|
double outside_global = 0.0;
|
|
double inside_count_global = 0.0;
|
|
double outside_count_global = 0.0;
|
|
for (int k=1; k<Nz; k++){
|
|
for (int j=1; j<Ny; j++){
|
|
for (int i=1; i<Nx; i++){
|
|
int n = k*Nx*Ny + j*Nx + i;
|
|
double distance = MembraneDistance(i,j,k);
|
|
if (distance > threshold && distance < (threshold + 1.0)){
|
|
outside_count_local += 1.0;
|
|
outside_local += Psi_host(n);
|
|
}
|
|
else if (distance < (-1.0)*threshold && distance > (-1.0)*(threshold + 1.0)){
|
|
inside_count_local += 1.0;
|
|
inside_local += Psi_host(n);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
inside_count_global = Dm->Comm.sumReduce(inside_count_local);
|
|
outside_count_global = Dm->Comm.sumReduce(outside_count_local);
|
|
outside_global = Dm->Comm.sumReduce(outside_local);
|
|
inside_global = Dm->Comm.sumReduce(inside_local);
|
|
outside_global /= outside_count_global;
|
|
inside_global /= inside_count_global;
|
|
|
|
if (rank==0) printf(" Rescaling far-field electric potential to value (outside): %f \n",outside_global);
|
|
if (rank==0) printf(" Rescaling far-field electric potential to value (inside): %f \n",inside_global);
|
|
|
|
// rescale the far-field electric potential
|
|
for (int k=1; k<Nz; k++){
|
|
for (int j=1; j<Ny; j++){
|
|
for (int i=1; i<Nx; i++){
|
|
int n = k*Nx*Ny + j*Nx + i;
|
|
double distance = MembraneDistance(i,j,k);
|
|
if ( distance > (threshold + 1.0)){
|
|
Psi_host(n) = outside_global;
|
|
}
|
|
else if ( distance < (-1.0)*(threshold + 1.0)){
|
|
Psi_host(n) = inside_global;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
ScaLBL_CopyToDevice(Psi,Psi_host.data(),sizeof(double)*Nx*Ny*Nz);
|
|
}
|
|
/* compute the eletric field */
|
|
//ScaLBL_D3Q19_Poisson_getElectricField(fq, ElectricField, tau, Np);
|
|
}
|
|
}
|
|
// SetMeanZeroVoltage();
|
|
|
|
if (rank == 0)
|
|
printf("---------------------------------------------------------------"
|
|
"----\n");
|
|
// Compute the walltime per timestep
|
|
auto t2 = std::chrono::system_clock::now();
|
|
double cputime = std::chrono::duration<double>(t2 - t1).count() / 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");
|
|
delete [] host_Error;
|
|
|
|
//************************************************************************/
|
|
if(WriteLog==true){
|
|
getConvergenceLog(timestep,error);
|
|
}
|
|
}
|
|
|
|
void ScaLBL_Poisson::SetMeanZeroVoltage(){
|
|
/* get the elecric potential */
|
|
ScaLBL_CopyToHost(Psi_host.data(),Psi,sizeof(double)*Nx*Ny*Nz);
|
|
|
|
double local_mean_voltage = 0.0;
|
|
double global_mean_voltage = 0.0;
|
|
double local_count = 0.0;
|
|
double global_count = 0.0;
|
|
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;
|
|
local_mean_voltage += Psi_host(n);
|
|
local_count += 1.0;
|
|
}
|
|
}
|
|
}
|
|
global_mean_voltage = Dm->Comm.sumReduce(local_mean_voltage);
|
|
global_count = Dm->Comm.sumReduce(local_count);
|
|
global_mean_voltage /= global_count;
|
|
// rescale the far-field electric potential
|
|
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;
|
|
double value = Psi_host(n);
|
|
value -= global_mean_voltage;
|
|
Psi_host(n) = value;
|
|
}
|
|
}
|
|
}
|
|
ScaLBL_CopyToDevice(Psi,Psi_host.data(),sizeof(double)*Nx*Ny*Nz);
|
|
|
|
if (rank == 0)
|
|
printf("Rescale voltage (average was %.5g) \n", global_mean_voltage);
|
|
}
|
|
|
|
void ScaLBL_Poisson::getConvergenceLog(int timestep,double error){
|
|
if ( rank == 0 ) {
|
|
fprintf(TIMELOG,"%i %.5g\n",timestep,error);
|
|
fflush(TIMELOG);
|
|
}
|
|
}
|
|
|
|
void ScaLBL_Poisson::SolveElectricPotentialAAodd(int timestep_from_Study){
|
|
|
|
if (lattice_scheme.compare("D3Q7")==0){
|
|
ScaLBL_Comm->SendD3Q7AA(fq, 0); //READ FROM NORMAL
|
|
ScaLBL_D3Q7_AAodd_Poisson_ElectricPotential(NeighborList, dvcMap, fq, Psi, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
|
ScaLBL_Comm->RecvD3Q7AA(fq, 0); //WRITE INTO OPPOSITE
|
|
ScaLBL_Comm->Barrier();
|
|
// Set boundary conditions
|
|
if (BoundaryConditionInlet > 0){
|
|
switch (BoundaryConditionInlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
case 2:
|
|
Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
}
|
|
}
|
|
if (BoundaryConditionOutlet > 0){
|
|
switch (BoundaryConditionOutlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
case 2:
|
|
Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
}
|
|
}
|
|
//-------------------------//
|
|
ScaLBL_D3Q7_AAodd_Poisson_ElectricPotential(NeighborList, dvcMap, fq, Psi, 0, ScaLBL_Comm->LastExterior(), Np);
|
|
}
|
|
else if (lattice_scheme.compare("D3Q19")==0){
|
|
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
|
|
//ScaLBL_D3Q19_AAodd_Poisson_ElectricPotential(NeighborList, dvcMap, fq, ChargeDensity, Psi, epsilon_LB, UseSlippingVelBC, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
|
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
|
|
ScaLBL_Comm->Barrier();
|
|
|
|
// Set boundary conditions
|
|
if (BoundaryConditionInlet > 0){
|
|
switch (BoundaryConditionInlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
case 2:
|
|
Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
}
|
|
}
|
|
if (BoundaryConditionOutlet > 0){
|
|
switch (BoundaryConditionOutlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
case 2:
|
|
Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
}
|
|
}
|
|
//-------------------------//
|
|
|
|
//ScaLBL_D3Q19_AAodd_Poisson_ElectricPotential(NeighborList, dvcMap, fq, ChargeDensity, Psi, epsilon_LB, UseSlippingVelBC, 0, ScaLBL_Comm->LastExterior(), Np);
|
|
}
|
|
}
|
|
|
|
void ScaLBL_Poisson::SolveElectricPotentialAAeven(int timestep_from_Study){
|
|
|
|
if (lattice_scheme.compare("D3Q7")==0){
|
|
ScaLBL_Comm->SendD3Q7AA(fq, 0); //READ FORM NORMAL
|
|
ScaLBL_D3Q7_AAeven_Poisson_ElectricPotential(dvcMap, fq, Psi, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
|
ScaLBL_Comm->RecvD3Q7AA(fq, 0); //WRITE INTO OPPOSITE
|
|
ScaLBL_Comm->Barrier();
|
|
// Set boundary conditions
|
|
if (BoundaryConditionInlet > 0){
|
|
switch (BoundaryConditionInlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
case 2:
|
|
Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
}
|
|
}
|
|
if (BoundaryConditionOutlet > 0){
|
|
switch (BoundaryConditionOutlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
case 2:
|
|
Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
}
|
|
}
|
|
//-------------------------//
|
|
ScaLBL_D3Q7_AAeven_Poisson_ElectricPotential(dvcMap, fq, Psi, 0, ScaLBL_Comm->LastExterior(), Np);
|
|
}
|
|
else if (lattice_scheme.compare("D3Q19")==0){
|
|
ScaLBL_Comm->SendD3Q19AA(fq); //READ FORM NORMAL
|
|
//ScaLBL_D3Q19_AAeven_Poisson_ElectricPotential(dvcMap, fq, ChargeDensity, Psi, epsilon_LB, UseSlippingVelBC,
|
|
// ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
|
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
|
|
ScaLBL_Comm->Barrier();
|
|
|
|
|
|
// Set boundary conditions
|
|
if (BoundaryConditionInlet > 0){
|
|
switch (BoundaryConditionInlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
case 2:
|
|
Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
}
|
|
}
|
|
if (BoundaryConditionOutlet > 0){
|
|
switch (BoundaryConditionOutlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
case 2:
|
|
Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,timestep_from_Study);
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
}
|
|
}
|
|
|
|
//-------------------------//
|
|
//ScaLBL_D3Q19_AAeven_Poisson_ElectricPotential(dvcMap, fq, ChargeDensity, Psi, epsilon_LB, UseSlippingVelBC, 0, ScaLBL_Comm->LastExterior(), Np);
|
|
}
|
|
}
|
|
|
|
void ScaLBL_Poisson::SolvePoissonAAodd(double *ChargeDensity, bool UseSlippingVelBC, int timestep){
|
|
|
|
// Universal constant
|
|
double kb = 1.38e-23; //Boltzmann constant;unit [J/K]
|
|
double electron_charge = 1.6e-19; //electron charge;unit [C]
|
|
double T = 300.0; //temperature; unit [K]
|
|
double Vt = kb * T / electron_charge; //thermal voltage; unit [Vy]
|
|
double Cp = 1.014e-7; // proton concentration
|
|
|
|
|
|
if (lattice_scheme.compare("D3Q7")==0){
|
|
ScaLBL_D3Q7_AAodd_Poisson(NeighborList, dvcMap, fq, ChargeDensity, Psi, ElectricField, tau, epsilon_LB, UseSlippingVelBC, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
|
ScaLBL_D3Q7_AAodd_Poisson(NeighborList, dvcMap, fq, ChargeDensity, Psi, ElectricField, tau, epsilon_LB, UseSlippingVelBC, 0, ScaLBL_Comm->LastExterior(), Np);
|
|
//TODO: perhaps add another ScaLBL_Comm routine to update Psi values on solid boundary nodes.
|
|
//something like:
|
|
//ScaLBL_Comm->SolidDirichletBoundaryUpdates(Psi, Psi_BCLabel, timestep);
|
|
ScaLBL_Comm->SolidDirichletAndNeumannD3Q7(fq, Psi, Psi_BCLabel);
|
|
//if (BoundaryConditionSolid==1){
|
|
// ScaLBL_Comm->SolidDirichletD3Q7(fq, Psi);
|
|
//}
|
|
//else if (BoundaryConditionSolid==2){
|
|
// ScaLBL_Comm->SolidNeumannD3Q7(fq, Psi);
|
|
//}
|
|
}
|
|
else if (lattice_scheme.compare("D3Q19")==0){
|
|
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
|
|
ScaLBL_D3Q19_AAodd_Poisson(NeighborList, dvcMap, fq, ChargeDensity, Psi, ElectricField, tau, Vt, Cp, epsilon_LB, UseSlippingVelBC,
|
|
ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
|
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
|
|
|
|
// Set boundary conditions
|
|
if (BoundaryConditionInlet > 0 && Dm->kproc()==0){
|
|
switch (BoundaryConditionInlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
case 2:
|
|
Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,timestep);
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
}
|
|
}
|
|
if (BoundaryConditionOutlet > 0 && Dm->kproc() == nprocz-1){
|
|
switch (BoundaryConditionOutlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
case 2:
|
|
Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,timestep);
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
}
|
|
}
|
|
|
|
ScaLBL_D3Q19_AAodd_Poisson(NeighborList, dvcMap, fq, ChargeDensity, Psi, ElectricField, tau, Vt, Cp, epsilon_LB, UseSlippingVelBC, 0, ScaLBL_Comm->LastExterior(), Np);
|
|
ScaLBL_Comm->Barrier();
|
|
//TODO: perhaps add another ScaLBL_Comm routine to update Psi values on solid boundary nodes.
|
|
//something like:
|
|
//ScaLBL_Comm->SolidDirichletAndNeumannD3Q7(fq, Psi, Psi_BCLabel);
|
|
}
|
|
}
|
|
|
|
void ScaLBL_Poisson::SolvePoissonAAeven(double *ChargeDensity, bool UseSlippingVelBC, int timestep){
|
|
|
|
// Universal constant
|
|
double kb = 1.38e-23; //Boltzmann constant;unit [J/K]
|
|
double electron_charge = 1.6e-19; //electron charge;unit [C]
|
|
double T = 300.0; //temperature; unit [K]
|
|
double Vt = kb * T / electron_charge; //thermal voltage; unit [Vy]
|
|
double Cp = 1.014e-7; // proton concentration
|
|
|
|
if (lattice_scheme.compare("D3Q7")==0){
|
|
ScaLBL_D3Q7_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, tau, epsilon_LB, UseSlippingVelBC, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
|
ScaLBL_D3Q7_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, tau, epsilon_LB, UseSlippingVelBC, 0, ScaLBL_Comm->LastExterior(), Np);
|
|
ScaLBL_Comm->SolidDirichletAndNeumannD3Q7(fq, Psi, Psi_BCLabel);
|
|
//if (BoundaryConditionSolid==1){
|
|
// ScaLBL_Comm->SolidDirichletD3Q7(fq, Psi);
|
|
//}
|
|
//else if (BoundaryConditionSolid==2){
|
|
// ScaLBL_Comm->SolidNeumannD3Q7(fq, Psi);
|
|
//}
|
|
}
|
|
else if (lattice_scheme.compare("D3Q19")==0){
|
|
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
|
|
ScaLBL_D3Q19_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, ResidualError, tau, Vt, Cp, epsilon_LB, UseSlippingVelBC, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
|
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
|
|
|
|
// Set boundary conditions
|
|
if (BoundaryConditionInlet > 0 && Dm->kproc()==0){
|
|
switch (BoundaryConditionInlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
case 2:
|
|
Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,timestep);
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, Vin, timestep);
|
|
break;
|
|
}
|
|
}
|
|
if (BoundaryConditionOutlet > 0 && Dm->kproc() == nprocz-1){
|
|
switch (BoundaryConditionOutlet){
|
|
case 1:
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
case 2:
|
|
Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,timestep);
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, Vout, timestep);
|
|
break;
|
|
}
|
|
}
|
|
|
|
ScaLBL_D3Q19_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, ResidualError, tau, Vt, Cp, epsilon_LB, UseSlippingVelBC, 0, ScaLBL_Comm->LastExterior(), Np);
|
|
ScaLBL_Comm->Barrier();
|
|
|
|
//ScaLBL_Comm->SolidDirichletAndNeumannD3Q7(fq, Psi, Psi_BCLabel);
|
|
}
|
|
}
|
|
|
|
void ScaLBL_Poisson::Checkpoint(){
|
|
|
|
if (rank == 0) {
|
|
printf(" POISSON MODEL: Writing restart file! \n");
|
|
}
|
|
double value;
|
|
double *cPsi;
|
|
cPsi = new double[Nx*Ny*Nz];
|
|
ScaLBL_CopyToHost(cPsi, Psi, Nx*Ny*Nz *sizeof(double));
|
|
|
|
ofstream File(LocalRestartFile, ios::binary);
|
|
for (int n = 0; n < Nx*Ny*Nz; n++) {
|
|
value = cPsi[n];
|
|
File.write((char *)&value, sizeof(value));
|
|
}
|
|
|
|
File.close();
|
|
|
|
delete[] cPsi;
|
|
}
|
|
|
|
void ScaLBL_Poisson::DummyChargeDensity(){
|
|
double *ChargeDensity_host;
|
|
ChargeDensity_host = new double[Np];
|
|
|
|
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))
|
|
//ChargeDensity_host[idx] = chargeDen_dummy*(h*h*h*1.0e-18);
|
|
ChargeDensity_host[idx] = cos(2.0*M_PI*double(k-1)/double(Nz-2))*(h*h*h*1.0e-18);
|
|
}
|
|
}
|
|
}
|
|
ScaLBL_AllocateDeviceMemory((void **) &ChargeDensityDummy, sizeof(double)*Np);
|
|
ScaLBL_CopyToDevice(ChargeDensityDummy, ChargeDensity_host, sizeof(double)*Np);
|
|
ScaLBL_Comm->Barrier();
|
|
delete [] ChargeDensity_host;
|
|
}
|
|
|
|
void ScaLBL_Poisson::getElectricPotential_debug(int timestep){
|
|
//This function write out decomposed data
|
|
DoubleArray PhaseField(Nx,Ny,Nz);
|
|
//ScaLBL_Comm->RegularLayout(Map,Psi,PhaseField);
|
|
ScaLBL_CopyToHost(PhaseField.data(),Psi,sizeof(double)*Nx*Ny*Nz);
|
|
//ScaLBL_Comm->Barrier(); comm.barrier();
|
|
FILE *OUTFILE;
|
|
sprintf(LocalRankFilename,"Electric_Potential_Time_%i.%05i.raw",timestep,rank);
|
|
OUTFILE = fopen(LocalRankFilename,"wb");
|
|
fwrite(PhaseField.data(),8,N,OUTFILE);
|
|
fclose(OUTFILE);
|
|
}
|
|
|
|
void ScaLBL_Poisson::getSolverError(DoubleArray &ReturnValues){
|
|
//This function wirte out the data in a normal layout (by aggregating all decomposed domains)
|
|
ScaLBL_Comm->RegularLayout(Map,ResidualError,ReturnValues);
|
|
}
|
|
|
|
void ScaLBL_Poisson::getElectricPotential(DoubleArray &ReturnValues){
|
|
//This function wirte out the data in a normal layout (by aggregating all decomposed domains)
|
|
//ScaLBL_Comm->RegularLayout(Map,Psi,PhaseField);
|
|
ScaLBL_CopyToHost(ReturnValues.data(),Psi,sizeof(double)*Nx*Ny*Nz);
|
|
}
|
|
|
|
void ScaLBL_Poisson::getElectricField(DoubleArray &Values_x, DoubleArray &Values_y, DoubleArray &Values_z){
|
|
|
|
ScaLBL_Comm->RegularLayout(Map,&ElectricField[0*Np],Values_x);
|
|
ElectricField_LB_to_Phys(Values_x);
|
|
ScaLBL_Comm->Barrier(); comm.barrier();
|
|
|
|
ScaLBL_Comm->RegularLayout(Map,&ElectricField[1*Np],Values_y);
|
|
ElectricField_LB_to_Phys(Values_y);
|
|
ScaLBL_Comm->Barrier(); comm.barrier();
|
|
|
|
ScaLBL_Comm->RegularLayout(Map,&ElectricField[2*Np],Values_z);
|
|
ElectricField_LB_to_Phys(Values_z);
|
|
ScaLBL_Comm->Barrier(); comm.barrier();
|
|
|
|
}
|
|
|
|
void ScaLBL_Poisson::getElectricField_debug(int timestep){
|
|
|
|
//ScaLBL_D3Q7_Poisson_getElectricField(fq,ElectricField,tau,Np);
|
|
//ScaLBL_Comm->Barrier(); comm.barrier();
|
|
|
|
DoubleArray PhaseField(Nx,Ny,Nz);
|
|
ScaLBL_Comm->RegularLayout(Map,&ElectricField[0*Np],PhaseField);
|
|
ElectricField_LB_to_Phys(PhaseField);
|
|
FILE *EX;
|
|
sprintf(LocalRankFilename,"ElectricField_X_Time_%i.%05i.raw",timestep,rank);
|
|
EX = fopen(LocalRankFilename,"wb");
|
|
fwrite(PhaseField.data(),8,N,EX);
|
|
fclose(EX);
|
|
|
|
ScaLBL_Comm->RegularLayout(Map,&ElectricField[1*Np],PhaseField);
|
|
ElectricField_LB_to_Phys(PhaseField);
|
|
FILE *EY;
|
|
sprintf(LocalRankFilename,"ElectricField_Y_Time_%i.%05i.raw",timestep,rank);
|
|
EY = fopen(LocalRankFilename,"wb");
|
|
fwrite(PhaseField.data(),8,N,EY);
|
|
fclose(EY);
|
|
|
|
ScaLBL_Comm->RegularLayout(Map,&ElectricField[2*Np],PhaseField);
|
|
ElectricField_LB_to_Phys(PhaseField);
|
|
FILE *EZ;
|
|
sprintf(LocalRankFilename,"ElectricField_Z_Time_%i.%05i.raw",timestep,rank);
|
|
EZ = fopen(LocalRankFilename,"wb");
|
|
fwrite(PhaseField.data(),8,N,EZ);
|
|
fclose(EZ);
|
|
}
|
|
|
|
void ScaLBL_Poisson::ElectricField_LB_to_Phys(DoubleArray &Efield_reg){
|
|
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)){
|
|
Efield_reg(i,j,k) = Efield_reg(i,j,k)/(h*1.0e-6);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
void ScaLBL_Poisson::WriteVis( int timestep) {
|
|
|
|
auto vis_db = db->getDatabase("Visualization");
|
|
auto format = vis_db->getWithDefault<string>( "format", "hdf5" );
|
|
|
|
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);
|
|
|
|
DoubleArray ElectricalPotential(Nx, Ny, Nz);
|
|
|
|
DoubleArray SolverError(Nx, Ny, Nz);
|
|
|
|
IO::initialize("",format,"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);
|
|
//electric potential
|
|
auto ElectricPotentialVar = std::make_shared<IO::Variable>();
|
|
auto SolverErrorVar = std::make_shared<IO::Variable>();
|
|
|
|
//--------------------------------------------------------------------------------------------------------------------
|
|
DoubleArray Analytical(Nx, Ny, Nz);
|
|
|
|
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))
|
|
//ChargeDensity_host[idx] = chargeDen_dummy*(h*h*h*1.0e-18);
|
|
Analytical(i,j,k) = (2.0*M_PI/double(Nz-2))*(2.0*M_PI/double(Nz-2))*cos(2.0*M_PI*double(k-1)/double(Nz-2))*(h*h*h*1.0e-18)/epsilon_LB;
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
//-------------------------------------Create Names for Variables------------------------------------------------------
|
|
if (vis_db->getWithDefault<bool>("save_electric_potential", true)) {
|
|
ElectricPotentialVar->name = "ElectricPotential";
|
|
ElectricPotentialVar->type = IO::VariableType::VolumeVariable;
|
|
ElectricPotentialVar->dim = 1;
|
|
ElectricPotentialVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
|
|
visData[0].vars.push_back(ElectricPotentialVar);
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_error", true)) {
|
|
SolverErrorVar->name = "SolverError";
|
|
SolverErrorVar->type = IO::VariableType::VolumeVariable;
|
|
SolverErrorVar->dim = 1;
|
|
SolverErrorVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
|
|
visData[0].vars.push_back(SolverErrorVar);
|
|
}
|
|
//--------------------------------------------------------------------------------------------------------------------
|
|
|
|
//------------------------------------Save All Variables--------------------------------------------------------------
|
|
if (vis_db->getWithDefault<bool>("save_electric_potential", true)) {
|
|
ASSERT(visData[0].vars[0]->name == "ElectricPotential");
|
|
getElectricPotential(ElectricalPotential);
|
|
Array<double> &ElectricPotentialData = visData[0].vars[0]->data;
|
|
fillData.copy(ElectricalPotential, ElectricPotentialData);
|
|
}
|
|
|
|
//------------------------------------Save All Variables--------------------------------------------------------------
|
|
if (vis_db->getWithDefault<bool>("save_error", true)) {
|
|
ASSERT(visData[0].vars[1]->name == "SolverError");
|
|
getSolverError(SolverError);
|
|
Array<double> &SolverErrorData = visData[0].vars[1]->data;
|
|
fillData.copy(SolverError, SolverErrorData);
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("write_silo", true))
|
|
IO::writeData(timestep, visData, Dm->Comm);
|
|
//--------------------------------------------------------------------------------------------------------------------
|
|
}
|
|
|