import ScaLBL updates
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@ -50,10 +50,14 @@ public:
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void DummyFluidVelocity();
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void DummyElectricField();
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void Checkpoint();
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void TestGrotthus();
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double CalIonDenConvergence(vector<double> &ci_avg_previous);
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bool Restart;
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int timestep;
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int timestepGlobal;
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vector<int> timestepMax;
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int BoundaryConditionSolid;
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double h; //domain resolution, unit [um/lu]
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@ -63,6 +67,10 @@ public:
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double fluidVelx_dummy, fluidVely_dummy, fluidVelz_dummy;
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double Ex_dummy, Ey_dummy, Ez_dummy;
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bool use_Grotthus;
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size_t pH_ion;
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double IonizationEnergy;
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size_t number_ion_species;
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vector<int> BoundaryConditionInlet;
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vector<int> BoundaryConditionOutlet;
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@ -79,6 +87,8 @@ public:
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vector<double> Cout; //outlet boundary value, can be either concentration [mol/m^3] or flux [mol/m^2/sec]
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vector<double> tau;
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vector<double> time_conv;
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vector<double> BC_frequency;
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vector<double> BC_amplitude;
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int Nx, Ny, Nz, N, Np;
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int rank, nprocx, nprocy, nprocz, nprocs;
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@ -1,5 +1,5 @@
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/*
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* Multi-relaxation time LBM Model
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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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@ -36,6 +36,7 @@ ScaLBL_Poisson::~ScaLBL_Poisson()
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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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@ -66,7 +67,7 @@ void ScaLBL_Poisson::ReadParams(string filename){
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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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Restart = false;
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// LB-Poisson Model parameters
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if (electric_db->keyExists( "Restart" )){
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@ -141,7 +142,7 @@ void ScaLBL_Poisson::ReadParams(string filename){
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/* restart string */
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sprintf(LocalRankString, "%05d", rank);
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sprintf(LocalRestartFile, "%s%s", "Psi.", LocalRankString);
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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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@ -211,7 +212,7 @@ 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","Psi.",LocalRankString);
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sprintf(LocalRestartFile,"%s%s","PoissonSolver.",LocalRankString);
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if (domain_db->keyExists( "Filename" )){
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@ -278,6 +279,44 @@ void ScaLBL_Poisson::AssignSolidBoundary(double *poisson_solid, int *poisson_sol
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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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@ -368,13 +407,14 @@ void ScaLBL_Poisson::Create(){
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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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int dist_mem_size = Np*sizeof(double);
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int neighborSize=18*(Np*sizeof(int));
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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);
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ScaLBL_AllocateDeviceMemory((void **) &Psi, sizeof(double)*Nx*Ny*Nz);
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ScaLBL_AllocateDeviceMemory((void **) &Permittivity, sizeof(double)*Nx*Ny*Nz);
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ScaLBL_AllocateDeviceMemory((void **) &Psi_BCLabel, sizeof(int)*Nx*Ny*Nz);
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ScaLBL_AllocateDeviceMemory((void **) &ElectricField, 3*sizeof(double)*Np);
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ScaLBL_AllocateDeviceMemory((void **) &ResidualError, sizeof(double)*Np);
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@ -443,8 +483,12 @@ void ScaLBL_Poisson::Potential_Init(double *psi_init){
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Vin0 = Vout0 = 1.0; //unit: [V]
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freqIn = freqOut = 50.0; //unit: [Hz]
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PhaseShift_In = PhaseShift_Out = 0.0; //unit: [radian]
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Vin = 1.0; //Boundary-z (inlet) electric potential
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Vout = 1.0; //Boundary-Z (outlet) electric potential
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Vin = 0.0; //Boundary-z (inlet) electric potential
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Vout = 0.0; //Boundary-Z (outlet) electric potential
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/* Assign permittivity value to the solid */
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signed char VALUE=0;
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double AFFINITY=0.f;
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if (BoundaryConditionInlet==0 && BoundaryConditionOutlet==0){
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@ -453,6 +497,7 @@ void ScaLBL_Poisson::Potential_Init(double *psi_init){
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auto LabelList = electric_db->getVector<int>( "InitialValueLabels" );
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auto AffinityList = electric_db->getVector<double>( "InitialValues" );
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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 != AffinityList.size()){
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@ -549,17 +594,27 @@ void ScaLBL_Poisson::Potential_Init(double *psi_init){
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if (BoundaryConditionOutlet==2) Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,0);
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//initialize a linear electrical potential between inlet and outlet
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double slope = (Vout-Vin)/(Nz-2);
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double psi_linearized;
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double slope = (Vout-Vin)/((Nz-2)*Dm->nprocz());
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double psi_linearized = Vin;
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for (int k=0;k<Nz;k++){
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if (Dm->kproc() == 0){
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if (k==0 || k==1){
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psi_linearized = Vin;
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}
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else if (k==Nz-1 || k==Nz-2){
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else{
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psi_linearized = slope*(Dm->kproc()*(Nz-2) + (k-1)) + Vin;
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}
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}
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if (Dm->kproc() == Dm->nprocz()-1){
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if (k==Nz-1 || k==Nz-2){
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psi_linearized = Vout;
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}
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else{
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psi_linearized = slope*(k-1)+Vin;
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psi_linearized = slope*(Dm->kproc()*(Nz-2) + (k-1)) + Vin;
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}
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}
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else{
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psi_linearized = slope*(Dm->kproc()*(Nz-2) + (k-1)) + Vin;
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}
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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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@ -643,79 +698,6 @@ void ScaLBL_Poisson::Initialize(double time_conv_from_Study){
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//}
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}
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//void ScaLBL_Poisson::Run(double *ChargeDensity, bool UseSlippingVelBC, int timestep_from_Study){
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//
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// //.......create and start timer............
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// //double starttime,stoptime,cputime;
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// //comm.barrier();
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// //auto t1 = std::chrono::system_clock::now();
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// double *host_Error;
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// host_Error = new double [Np];
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//
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// timestep=0;
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// double error = 1.0;
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// while (timestep < timestepMax && error > tolerance) {
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// //************************************************************************/
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// // *************ODD TIMESTEP*************//
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// timestep++;
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// //SolveElectricPotentialAAodd(timestep_from_Study,ChargeDensity, UseSlippingVelBC);//update electric potential
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// SolvePoissonAAodd(ChargeDensity, UseSlippingVelBC);//perform collision
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// ScaLBL_Comm->Barrier(); comm.barrier();
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//
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// // *************EVEN TIMESTEP*************//
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// timestep++;
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// //SolveElectricPotentialAAeven(timestep_from_Study,ChargeDensity, UseSlippingVelBC);//update electric potential
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// SolvePoissonAAeven(ChargeDensity, UseSlippingVelBC);//perform collision
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// ScaLBL_Comm->Barrier(); comm.barrier();
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// //************************************************************************/
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//
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//
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// // Check convergence of steady-state solution
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// if (timestep==2){
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// //save electric potential for convergence check
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// }
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// if (timestep%analysis_interval==0){
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// /* get the elecric potential */
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// ScaLBL_CopyToHost(Psi_host.data(),Psi,sizeof(double)*Nx*Ny*Nz);
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// if (rank==0) printf(" ... getting Poisson solver error \n");
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// double err = 0.0;
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// double max_error = 0.0;
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// ScaLBL_CopyToHost(host_Error,ResidualError,sizeof(double)*Np);
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// for (int idx=0; idx<Np; idx++){
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// err = host_Error[idx]*host_Error[idx];
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// if (err > max_error ){
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// max_error = err;
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// }
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// }
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// error=Dm->Comm.maxReduce(max_error);
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//
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// /* compute the eletric field */
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// //ScaLBL_D3Q19_Poisson_getElectricField(fq, ElectricField, tau, Np);
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//
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// }
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// }
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// if(WriteLog==true){
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// getConvergenceLog(timestep,error);
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// }
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//
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// //************************************************************************/
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// ////if (rank==0) printf("LB-Poission Solver: a steady-state solution is obtained\n");
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// ////if (rank==0) printf("---------------------------------------------------------------------------\n");
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// //// Compute the walltime per timestep
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// //auto t2 = std::chrono::system_clock::now();
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// //double cputime = std::chrono::duration<double>( t2 - t1 ).count() / timestep;
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// //// Performance obtained from each node
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// //double MLUPS = double(Np)/cputime/1000000;
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//
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// //if (rank==0) printf("******************* LB-Poisson Solver Statistics ********************\n");
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// //if (rank==0) printf("CPU time = %f \n", cputime);
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// //if (rank==0) printf("Lattice update rate (per core)= %f MLUPS \n", MLUPS);
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// //MLUPS *= nprocs;
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// //if (rank==0) printf("Lattice update rate (total)= %f MLUPS \n", MLUPS);
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// //if (rank==0) printf("*********************************************************************\n");
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//
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//}
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void ScaLBL_Poisson::Run(double *ChargeDensity, bool UseSlippingVelBC, int timestep_from_Study){
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double error = 1.0;
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@ -791,23 +773,100 @@ void ScaLBL_Poisson::Run(double *ChargeDensity, bool UseSlippingVelBC, int times
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double *host_Error;
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host_Error = new double [Np];
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timestep=0;
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auto t1 = std::chrono::system_clock::now();
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while (timestep < timestepMax && error > tolerance) {
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// Universal constant
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double kb = 1.38e-23; //Boltzmann constant;unit [J/K]
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double electron_charge = 1.6e-19; //electron charge;unit [C]
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double T = 300.0; //temperature; unit [K]
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double Vt = kb * T / electron_charge; //thermal voltage; unit [Vy]
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double Cp = 1.014e-7; // proton concentration
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timestep=0;
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auto t1 = std::chrono::system_clock::now();
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while (timestep < timestepMax && error > tolerance) {
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//************************************************************************/
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// *************ODD TIMESTEP*************//
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// Set boundary conditions
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timestep++;
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//SolveElectricPotentialAAodd(timestep_from_Study);//,ChargeDensity, UseSlippingVelBC);//update electric potential
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SolvePoissonAAodd(ChargeDensity, UseSlippingVelBC,timestep);//perform collision
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ScaLBL_Comm->Barrier(); comm.barrier();
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//SolvePoissonAAodd(ChargeDensity, UseSlippingVelBC, timestep);//perform collision
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ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
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ScaLBL_D3Q19_AAodd_Poisson(NeighborList, dvcMap, fq, ChargeDensity, Psi, ElectricField,
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tau, Vt, Cp, epsilon_LB, UseSlippingVelBC,
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ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
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ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
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if (BoundaryConditionInlet > 0 && Dm->kproc()==0){
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switch (BoundaryConditionInlet){
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case 1:
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ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
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break;
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case 2:
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Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,timestep_from_Study);
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ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
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break;
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}
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}
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if (BoundaryConditionOutlet > 0 && Dm->kproc() == nprocz-1){
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switch (BoundaryConditionOutlet){
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case 1:
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ScaLBL_Comm->D3Q19_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
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break;
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case 2:
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Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,timestep_from_Study);
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ScaLBL_Comm->D3Q19_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
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break;
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}
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}
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ScaLBL_D3Q19_AAodd_Poisson(NeighborList, dvcMap, fq, ChargeDensity, Psi, ElectricField,
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tau, Vt, Cp, epsilon_LB, UseSlippingVelBC,
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0, ScaLBL_Comm->LastExterior(), Np);
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// *************EVEN TIMESTEP*************//
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timestep++;
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//SolveElectricPotentialAAeven(timestep_from_Study);//,ChargeDensity, UseSlippingVelBC);//update electric potential
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SolvePoissonAAeven(ChargeDensity, UseSlippingVelBC,timestep);//perform collision
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//SolvePoissonAAeven(ChargeDensity, UseSlippingVelBC, timestep);//perform collision
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//ScaLBL_Comm->Barrier(); comm.barrier();
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ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
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ScaLBL_D3Q19_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, ResidualError,
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tau, Vt, Cp, epsilon_LB, UseSlippingVelBC,
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ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
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ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
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// Set boundary conditions
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if (BoundaryConditionInlet > 0 && Dm->kproc()==0){
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switch (BoundaryConditionInlet){
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case 1:
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ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
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break;
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case 2:
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Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,timestep_from_Study);
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ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
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break;
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}
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}
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if (BoundaryConditionOutlet > 0 && Dm->kproc() == nprocz-1){
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switch (BoundaryConditionOutlet){
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case 1:
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ScaLBL_Comm->D3Q19_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
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break;
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case 2:
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Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,timestep_from_Study);
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ScaLBL_Comm->D3Q19_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
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break;
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}
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}
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ScaLBL_D3Q19_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, ResidualError,
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tau, Vt, Cp, epsilon_LB, UseSlippingVelBC,
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0, ScaLBL_Comm->LastExterior(), Np);
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ScaLBL_Comm->Barrier(); comm.barrier();
|
||||
//************************************************************************/
|
||||
|
||||
}
|
||||
// Check convergence of steady-state solution
|
||||
if (timestep==2){
|
||||
//save electric potential for convergence check
|
||||
|
@ -826,12 +885,11 @@ void ScaLBL_Poisson::Run(double *ChargeDensity, bool UseSlippingVelBC, int times
|
|||
}
|
||||
}
|
||||
error=Dm->Comm.maxReduce(max_error);
|
||||
|
||||
/* compute the eletric field */
|
||||
//ScaLBL_D3Q19_Poisson_getElectricField(fq, ElectricField, tau, Np);
|
||||
|
||||
if (rank==0) printf(" error = %0.5g \n",error);
|
||||
}
|
||||
}
|
||||
// SetMeanZeroVoltage();
|
||||
|
||||
if (rank == 0)
|
||||
printf("---------------------------------------------------------------"
|
||||
"----\n");
|
||||
|
@ -841,6 +899,9 @@ void ScaLBL_Poisson::Run(double *ChargeDensity, bool UseSlippingVelBC, int times
|
|||
// 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)
|
||||
|
@ -877,20 +938,93 @@ void ScaLBL_Poisson::Run(double *ChargeDensity, DoubleArray MembraneDistance, bo
|
|||
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++;
|
||||
//SolveElectricPotentialAAodd(timestep_from_Study,ChargeDensity, UseSlippingVelBC);//update electric potential
|
||||
SolvePoissonAAodd(ChargeDensity, UseSlippingVelBC,timestep);//perform collision
|
||||
ScaLBL_Comm->Barrier(); comm.barrier();
|
||||
//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++;
|
||||
//SolveElectricPotentialAAeven(timestep_from_Study,ChargeDensity, UseSlippingVelBC);//update electric potential
|
||||
SolvePoissonAAeven(ChargeDensity, UseSlippingVelBC,timestep);//perform collision
|
||||
|
||||
|
||||
//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();
|
||||
//************************************************************************/
|
||||
|
||||
|
@ -972,6 +1106,8 @@ void ScaLBL_Poisson::Run(double *ChargeDensity, DoubleArray MembraneDistance, bo
|
|||
//ScaLBL_D3Q19_Poisson_getElectricField(fq, ElectricField, tau, Np);
|
||||
}
|
||||
}
|
||||
// SetMeanZeroVoltage();
|
||||
|
||||
if (rank == 0)
|
||||
printf("---------------------------------------------------------------"
|
||||
"----\n");
|
||||
|
@ -1000,6 +1136,43 @@ void ScaLBL_Poisson::Run(double *ChargeDensity, DoubleArray MembraneDistance, bo
|
|||
}
|
||||
}
|
||||
|
||||
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);
|
||||
|
@ -1120,22 +1293,22 @@ void ScaLBL_Poisson::SolveElectricPotentialAAeven(int timestep_from_Study){
|
|||
if (BoundaryConditionInlet > 0){
|
||||
switch (BoundaryConditionInlet){
|
||||
case 1:
|
||||
ScaLBL_Comm->D3Q19_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
||||
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_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
||||
ScaLBL_Comm->D3Q19_Pressure_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);
|
||||
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_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
||||
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, Vin, timestep);
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
@ -1147,6 +1320,14 @@ void ScaLBL_Poisson::SolveElectricPotentialAAeven(int timestep_from_Study){
|
|||
|
||||
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);
|
||||
|
@ -1163,35 +1344,35 @@ void ScaLBL_Poisson::SolvePoissonAAodd(double *ChargeDensity, bool UseSlippingVe
|
|||
}
|
||||
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, epsilon_LB, UseSlippingVelBC, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
||||
//ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
|
||||
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){
|
||||
if (BoundaryConditionInlet > 0 && Dm->kproc()==0){
|
||||
switch (BoundaryConditionInlet){
|
||||
case 1:
|
||||
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
||||
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, Vin, timestep);
|
||||
break;
|
||||
case 2:
|
||||
Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,timestep);
|
||||
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
||||
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, Vin, timestep);
|
||||
break;
|
||||
}
|
||||
}
|
||||
if (BoundaryConditionOutlet > 0){
|
||||
if (BoundaryConditionOutlet > 0 && Dm->kproc() == nprocz-1){
|
||||
switch (BoundaryConditionOutlet){
|
||||
case 1:
|
||||
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
||||
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, Vout, timestep);
|
||||
break;
|
||||
case 2:
|
||||
Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,timestep);
|
||||
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
||||
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, Vout, timestep);
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
ScaLBL_D3Q19_AAodd_Poisson(NeighborList, dvcMap, fq, ChargeDensity, Psi, ElectricField, tau, epsilon_LB, UseSlippingVelBC, 0, ScaLBL_Comm->LastExterior(), Np);
|
||||
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:
|
||||
|
@ -1201,6 +1382,13 @@ void ScaLBL_Poisson::SolvePoissonAAodd(double *ChargeDensity, bool UseSlippingVe
|
|||
|
||||
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);
|
||||
|
@ -1214,35 +1402,34 @@ void ScaLBL_Poisson::SolvePoissonAAeven(double *ChargeDensity, bool UseSlippingV
|
|||
}
|
||||
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, epsilon_LB, UseSlippingVelBC, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
||||
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
|
||||
// ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
|
||||
|
||||
// Set boundary conditions
|
||||
if (BoundaryConditionInlet > 0){
|
||||
if (BoundaryConditionInlet > 0 && Dm->kproc()==0){
|
||||
switch (BoundaryConditionInlet){
|
||||
case 1:
|
||||
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
||||
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, Vin, timestep);
|
||||
break;
|
||||
case 2:
|
||||
Vin = getBoundaryVoltagefromPeriodicBC(Vin0,freqIn,PhaseShift_In,timestep);
|
||||
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_z(NeighborList, fq, Vin, timestep);
|
||||
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, Vin, timestep);
|
||||
break;
|
||||
}
|
||||
}
|
||||
if (BoundaryConditionOutlet > 0){
|
||||
if (BoundaryConditionOutlet > 0 && Dm->kproc() == nprocz-1){
|
||||
switch (BoundaryConditionOutlet){
|
||||
case 1:
|
||||
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
||||
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, Vout, timestep);
|
||||
break;
|
||||
case 2:
|
||||
Vout = getBoundaryVoltagefromPeriodicBC(Vout0,freqOut,PhaseShift_Out,timestep);
|
||||
ScaLBL_Comm->D3Q7_Poisson_Potential_BC_Z(NeighborList, fq, Vout, timestep);
|
||||
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, Vout, timestep);
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
ScaLBL_D3Q19_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, ResidualError, tau, epsilon_LB, UseSlippingVelBC, 0, ScaLBL_Comm->LastExterior(), Np);
|
||||
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);
|
||||
|
@ -1279,7 +1466,8 @@ void ScaLBL_Poisson::DummyChargeDensity(){
|
|||
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] = 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);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
@ -1302,6 +1490,11 @@ void ScaLBL_Poisson::getElectricPotential_debug(int timestep){
|
|||
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);
|
||||
|
@ -1373,12 +1566,15 @@ void ScaLBL_Poisson::WriteVis( int timestep) {
|
|||
auto vis_db = db->getDatabase("Visualization");
|
||||
auto format = vis_db->getWithDefault<string>( "format", "hdf5" );
|
||||
|
||||
DoubleArray ElectricalPotential(Nx, Ny, Nz);
|
||||
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);
|
||||
|
@ -1389,8 +1585,22 @@ void ScaLBL_Poisson::WriteVis( int timestep) {
|
|||
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)) {
|
||||
|
@ -1400,6 +1610,14 @@ void ScaLBL_Poisson::WriteVis( int timestep) {
|
|||
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--------------------------------------------------------------
|
||||
|
@ -1410,140 +1628,16 @@ void ScaLBL_Poisson::WriteVis( int timestep) {
|
|||
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);
|
||||
//--------------------------------------------------------------------------------------------------------------------
|
||||
}
|
||||
|
||||
//void ScaLBL_Poisson::SolveElectricField(){
|
||||
// ScaLBL_Comm_Regular->SendHalo(Psi);
|
||||
// ScaLBL_D3Q7_Poisson_ElectricField(NeighborList, dvcMap, dvcID, Psi, ElectricField, BoundaryConditionSolid,
|
||||
// Nx, Nx*Ny, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
|
||||
// ScaLBL_Comm_Regular->RecvHalo(Psi);
|
||||
// ScaLBL_Comm->Barrier();
|
||||
// if (BoundaryCondition == 1){
|
||||
// ScaLBL_Comm->Poisson_D3Q7_BC_z(dvcMap,Psi,Vin);
|
||||
// ScaLBL_Comm->Poisson_D3Q7_BC_Z(dvcMap,Psi,Vout);
|
||||
// }
|
||||
// ScaLBL_D3Q7_Poisson_ElectricField(NeighborList, dvcMap, dvcID, Psi, ElectricField, BoundaryConditionSolid, Nx, Nx*Ny, 0, ScaLBL_Comm->LastExterior(), Np);
|
||||
//
|
||||
//}
|
||||
|
||||
//void ScaLBL_Poisson::getElectricPotential(){
|
||||
//
|
||||
// DoubleArray PhaseField(Nx,Ny,Nz);
|
||||
// ScaLBL_Comm->RegularLayout(Map,Psi,PhaseField);
|
||||
// //ScaLBL_Comm->Barrier(); comm.barrier();
|
||||
// FILE *OUTFILE;
|
||||
// sprintf(LocalRankFilename,"Electric_Potential.%05i.raw",rank);
|
||||
// OUTFILE = fopen(LocalRankFilename,"wb");
|
||||
// fwrite(PhaseField.data(),8,N,OUTFILE);
|
||||
// fclose(OUTFILE);
|
||||
//}
|
||||
|
||||
//old version where Psi is of size Np
|
||||
//void ScaLBL_Poisson::AssignSolidBoundary(double *poisson_solid)
|
||||
//{
|
||||
// size_t NLABELS=0;
|
||||
// signed char VALUE=0;
|
||||
// double AFFINITY=0.f;
|
||||
//
|
||||
// auto LabelList = electric_db->getVector<int>( "SolidLabels" );
|
||||
// auto AffinityList = electric_db->getVector<double>( "SolidValues" );
|
||||
//
|
||||
// NLABELS=LabelList.size();
|
||||
// if (NLABELS != AffinityList.size()){
|
||||
// ERROR("Error: LB-Poisson Solver: SolidLabels and SolidValues must be the same length! \n");
|
||||
// }
|
||||
//
|
||||
// double label_count[NLABELS];
|
||||
// double label_count_global[NLABELS];
|
||||
// // Assign the labels
|
||||
//
|
||||
// for (size_t idx=0; idx<NLABELS; idx++) label_count[idx]=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++){
|
||||
// //printf("idx=%i, value=%i, %i, \n",idx, VALUE,LabelList[idx]);
|
||||
// if (VALUE == LabelList[idx]){
|
||||
// AFFINITY=AffinityList[idx];
|
||||
// //NOTE need to convert the user input phys unit to LB unit
|
||||
// if (BoundaryConditionSolid==2){
|
||||
// //for BCS=1, i.e. Dirichlet-type, no need for unit conversion
|
||||
// //TODO maybe there is a factor of gamm missing here ?
|
||||
// AFFINITY = AFFINITY*(h*h*1.0e-12)/epsilon_LB;
|
||||
// }
|
||||
// label_count[idx] += 1.0;
|
||||
// idx = NLABELS;
|
||||
// //Mask->id[n] = 0; // set mask to zero since this is an immobile component
|
||||
// }
|
||||
// }
|
||||
// poisson_solid[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 solid 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);
|
||||
// switch (BoundaryConditionSolid){
|
||||
// case 1:
|
||||
// printf(" label=%d, surface potential=%.3g [V], volume fraction=%.2g\n",VALUE,AFFINITY,volume_fraction);
|
||||
// break;
|
||||
// case 2:
|
||||
// printf(" label=%d, surface charge density=%.3g [C/m^2], volume fraction=%.2g\n",VALUE,AFFINITY,volume_fraction);
|
||||
// break;
|
||||
// default:
|
||||
// printf(" label=%d, surface potential=%.3g [V], volume fraction=%.2g\n",VALUE,AFFINITY,volume_fraction);
|
||||
// break;
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
//}
|
||||
|
||||
// old version where Psi is of size Np
|
||||
//void ScaLBL_Poisson::Potential_Init(double *psi_init){
|
||||
//
|
||||
// if (BoundaryCondition==1){
|
||||
// if (electric_db->keyExists( "Vin" )){
|
||||
// Vin = electric_db->getScalar<double>( "Vin" );
|
||||
// }
|
||||
// if (electric_db->keyExists( "Vout" )){
|
||||
// Vout = electric_db->getScalar<double>( "Vout" );
|
||||
// }
|
||||
// }
|
||||
// //By default only periodic BC is applied and Vin=Vout=1.0, i.e. there is no potential gradient along Z-axis
|
||||
// double slope = (Vout-Vin)/(Nz-2);
|
||||
// double psi_linearized;
|
||||
// for (int k=0;k<Nz;k++){
|
||||
// if (k==0 || k==1){
|
||||
// psi_linearized = Vin;
|
||||
// }
|
||||
// else if (k==Nz-1 || k==Nz-2){
|
||||
// psi_linearized = Vout;
|
||||
// }
|
||||
// else{
|
||||
// psi_linearized = slope*(k-1)+Vin;
|
||||
// }
|
||||
// for (int j=0;j<Ny;j++){
|
||||
// for (int i=0;i<Nx;i++){
|
||||
// int idx = Map(i,j,k);
|
||||
// if (!(idx < 0)){
|
||||
// psi_init[idx] = psi_linearized;
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
//}
|
||||
|
|
|
@ -39,6 +39,7 @@ public:
|
|||
void Run(double *ChargeDensity, DoubleArray MembraneDistance,
|
||||
bool UseSlippingVelBC, int timestep_from_Study);
|
||||
void getElectricPotential(DoubleArray &ReturnValues);
|
||||
void getSolverError(DoubleArray &ReturnValues);
|
||||
void getElectricPotential_debug(int timestep);
|
||||
void getElectricField(DoubleArray &Values_x, DoubleArray &Values_y,
|
||||
DoubleArray &Values_z);
|
||||
|
@ -96,6 +97,7 @@ public:
|
|||
double *Psi;
|
||||
int *Psi_BCLabel;
|
||||
double *ElectricField;
|
||||
double *Permittivity;
|
||||
double *ChargeDensityDummy; // for debugging
|
||||
double *ResidualError;
|
||||
|
||||
|
@ -120,6 +122,7 @@ private:
|
|||
//void SolveElectricField();
|
||||
void SolvePoissonAAodd(double *ChargeDensity, bool UseSlippingVelBC, int timestep);
|
||||
void SolvePoissonAAeven(double *ChargeDensity, bool UseSlippingVelBC, int timestep);
|
||||
void SetMeanZeroVoltage();
|
||||
void getConvergenceLog(int timestep,double error);
|
||||
double getBoundaryVoltagefromPeriodicBC(double V0,double freq,double t0,int time_step);
|
||||
|
||||
|
|
|
@ -34,6 +34,7 @@ int main(int argc, char **argv)
|
|||
{
|
||||
|
||||
int i,j,k,n;
|
||||
bool Bounceback = false;
|
||||
|
||||
int rank = comm.getRank();
|
||||
if (rank == 0){
|
||||
|
@ -300,7 +301,7 @@ int main(int argc, char **argv)
|
|||
ScaLBL_CopyToDevice(fq, fq_host, sizeof(double)*7*Np);
|
||||
|
||||
M.SendD3Q7AA(&fq[0]);
|
||||
M.RecvD3Q7AA(&gq[0]);
|
||||
M.RecvD3Q7AA(&gq[0],Bounceback);
|
||||
// this has only the communicated values
|
||||
//ScaLBL_CopyToHost(fq_host, gq, sizeof(double)*7*Np);
|
||||
if (rank==0) printf ("Sum result \n");
|
||||
|
|
Loading…
Reference in New Issue
Block a user