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merging multi-halo

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This commit is contained in:
JamesEMcclure
2021-01-13 21:44:23 -05:00
parent 29e486a1a0 64b49f720e
commit 0fe3125833
184 changed files with 22054 additions and 7588 deletions
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405
models/IonModel.cpp
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@@ -6,11 +6,11 @@
#include "analysis/distance.h"
#include "common/ReadMicroCT.h"
ScaLBL_IonModel::ScaLBL_IonModel(int RANK, int NP, MPI_Comm COMM):
ScaLBL_IonModel::ScaLBL_IonModel(int RANK, int NP, const Utilities::MPI& COMM):
rank(RANK),nprocs(NP),timestep(0),timestepMax(0),time_conv(0),kb(0),electron_charge(0),T(0),Vt(0),k2_inv(0),h(0),
tolerance(0),number_ion_species(0),Nx(0),Ny(0),Nz(0),N(0),Np(0),nprocx(0),nprocy(0),nprocz(0),
fluidVelx_dummy(0),fluidVely_dummy(0),fluidVelz_dummy(0),
BoundaryCondition(0),BoundaryConditionSolid(0),Lx(0),Ly(0),Lz(0),comm(COMM)
BoundaryConditionInlet(0),BoundaryConditionOutlet(0),BoundaryConditionSolid(0),Lx(0),Ly(0),Lz(0),comm(COMM)
{
}
@@ -40,8 +40,6 @@ void ScaLBL_IonModel::ReadParams(string filename,vector<int> &num_iter){
IonDiffusivity.push_back(1.0e-9);//user-input diffusivity has physical unit [m^2/sec]
IonValence.push_back(1);//algebraic valence charge
IonConcentration.push_back(1.0e-3);//user-input ion concentration has physical unit [mol/m^3]
Cin.push_back(1.0e-3);//user-input inlet boundary ion concentration;unit [mol/m^3]
Cout.push_back(1.0e-3);//user-input outlet boundary ion concentration;unit [mol/m^3]
//tau.push_back(0.5+k2_inv*time_conv/(h*1.0e-6)/(h*1.0e-6)*IonDiffusivity[0]);
time_conv.push_back((tau[0]-0.5)/k2_inv*(h*h*1.0e-12)/IonDiffusivity[0]);
fluidVelx_dummy = 0.0;//for debugging, unit [m/sec]
@@ -162,54 +160,78 @@ void ScaLBL_IonModel::ReadParams(string filename,vector<int> &num_iter){
}
// Read boundary condition for ion transport
// BC = 0: normal periodic BC
// BC = 1: fixed inlet and outlet ion concentration
BoundaryCondition = 0;
if (ion_db->keyExists( "BC" )){
BoundaryCondition = ion_db->getScalar<int>( "BC" );
// BC = 1: fixed ion concentration; unit=[mol/m^3]
// BC = 2: fixed ion flux (inward flux); unit=[mol/m^2/sec]
BoundaryConditionInlet.push_back(0);
BoundaryConditionOutlet.push_back(0);
//Inlet
if (ion_db->keyExists( "BC_InletList" )){
BoundaryConditionInlet = ion_db->getVector<int>( "BC_InletList" );
if (BoundaryConditionInlet.size()!=number_ion_species){
ERROR("Error: number_ion_species and BC_InletList must be of the same length! \n");
}
unsigned short int BC_inlet_min = *min_element(BoundaryConditionInlet.begin(),BoundaryConditionInlet.end());
unsigned short int BC_inlet_max = *max_element(BoundaryConditionInlet.begin(),BoundaryConditionInlet.end());
if (BC_inlet_min == 0 && BC_inlet_max>0){
ERROR("Error: BC_InletList: mix of periodic, ion concentration and flux BC is not supported! \n");
}
if (BC_inlet_min>0){
//read in inlet values Cin
if (ion_db->keyExists("InletValueList")){
Cin = ion_db->getVector<double>( "InletValueList" );
if (Cin.size()!=number_ion_species){
ERROR("Error: number_ion_species and InletValueList must be the same length! \n");
}
}
else {
ERROR("Error: Non-periodic BCs are specified but InletValueList cannot be found! \n");
}
for (unsigned int i=0;i<BoundaryConditionInlet.size();i++){
switch (BoundaryConditionInlet[i]){
case 1://fixed boundary ion concentration [mol/m^3]
Cin[i] = Cin[i]*(h*h*h*1.0e-18);//LB ion concentration has unit [mol/lu^3]
break;
case 2://fixed boundary ion flux [mol/m^2/sec]
Cin[i] = Cin[i]*(h*h*1.0e-12)*time_conv[i];//LB ion flux has unit [mol/lu^2/lt]
break;
}
}
}
}
if (BoundaryCondition==1){
//read boundary ion concentration list; INPUT unit [mol/m^3]
//it must be converted to LB unit [mol/lu^3]
//inlet
if (ion_db->keyExists("CinList")){
Cin.clear();
Cin = ion_db->getVector<double>( "CinList" );
if (Cin.size()!=number_ion_species){
ERROR("Error: number_ion_species and CinList must be the same length! \n");
//Outlet
if (ion_db->keyExists( "BC_OutletList" )){
BoundaryConditionOutlet = ion_db->getVector<int>( "BC_OutletList" );
if (BoundaryConditionOutlet.size()!=number_ion_species){
ERROR("Error: number_ion_species and BC_OutletList must be of the same length! \n");
}
unsigned short int BC_outlet_min = *min_element(BoundaryConditionOutlet.begin(),BoundaryConditionOutlet.end());
unsigned short int BC_outlet_max = *max_element(BoundaryConditionOutlet.begin(),BoundaryConditionOutlet.end());
if (BC_outlet_min == 0 && BC_outlet_max>0){
ERROR("Error: BC_OutletList: mix of periodic, ion concentration and flux BC is not supported! \n");
}
if (BC_outlet_min>0){
//read in outlet values Cout
if (ion_db->keyExists("OutletValueList")){
Cout = ion_db->getVector<double>( "OutletValueList" );
if (Cout.size()!=number_ion_species){
ERROR("Error: number_ion_species and OutletValueList must be the same length! \n");
}
}
else{
for (int i=0; i<Cin.size();i++){
Cin[i] = Cin[i]*(h*h*h*1.0e-18);//LB ion concentration has unit [mol/lu^3]
else {
ERROR("Error: Non-periodic BCs are specified but OutletValueList cannot be found! \n");
}
for (unsigned int i=0;i<BoundaryConditionOutlet.size();i++){
switch (BoundaryConditionOutlet[i]){
case 1://fixed boundary ion concentration [mol/m^3]
Cout[i] = Cout[i]*(h*h*h*1.0e-18);//LB ion concentration has unit [mol/lu^3]
break;
case 2://fixed boundary ion flux [mol/m^2/sec]
Cout[i] = Cout[i]*(h*h*1.0e-12)*time_conv[i];//LB ion flux has unit [mol/lu^2/lt]
break;
}
}
}
else {
for (int i=0; i<Cin.size();i++){
Cin[i] = Cin[i]*(h*h*h*1.0e-18);//LB ion concentration has unit [mol/lu^3]
}
}
//outlet
if (ion_db->keyExists("CoutList")){
Cout.clear();
Cout = ion_db->getVector<double>( "CoutList" );
if (Cout.size()!=number_ion_species){
ERROR("Error: number_ion_species and CoutList must be the same length! \n");
}
else{
for (int i=0; i<Cout.size();i++){
Cout[i] = Cout[i]*(h*h*h*1.0e-18);//LB ion concentration has unit [mol/lu^3]
}
}
}
else {
for (int i=0; i<Cout.size();i++){
Cout[i] = Cout[i]*(h*h*h*1.0e-18);//LB ion concentration has unit [mol/lu^3]
}
}
}
}
}
void ScaLBL_IonModel::ReadParams(string filename){
@@ -236,8 +258,6 @@ void ScaLBL_IonModel::ReadParams(string filename){
IonDiffusivity.push_back(1.0e-9);//user-input diffusivity has physical unit [m^2/sec]
IonValence.push_back(1);//algebraic valence charge
IonConcentration.push_back(1.0e-3);//user-input ion concentration has physical unit [mol/m^3]
Cin.push_back(1.0e-3);//user-input inlet boundary ion concentration;unit [mol/m^3]
Cout.push_back(1.0e-3);//user-input outlet boundary ion concentration;unit [mol/m^3]
//tau.push_back(0.5+k2_inv*time_conv/(h*1.0e-6)/(h*1.0e-6)*IonDiffusivity[0]);
time_conv.push_back((tau[0]-0.5)/k2_inv*(h*h*1.0e-12)/IonDiffusivity[0]);
fluidVelx_dummy = 0.0;//for debugging, unit [m/sec]
@@ -350,54 +370,78 @@ void ScaLBL_IonModel::ReadParams(string filename){
}
// Read boundary condition for ion transport
// BC = 0: normal periodic BC
// BC = 1: fixed inlet and outlet ion concentration
BoundaryCondition = 0;
if (ion_db->keyExists( "BC" )){
BoundaryCondition = ion_db->getScalar<int>( "BC" );
// BC = 1: fixed ion concentration; unit=[mol/m^3]
// BC = 2: fixed ion flux (inward flux); unit=[mol/m^2/sec]
BoundaryConditionInlet.push_back(0);
BoundaryConditionOutlet.push_back(0);
//Inlet
if (ion_db->keyExists( "BC_InletList" )){
BoundaryConditionInlet = ion_db->getVector<int>( "BC_InletList" );
if (BoundaryConditionInlet.size()!=number_ion_species){
ERROR("Error: number_ion_species and BC_InletList must be of the same length! \n");
}
unsigned short int BC_inlet_min = *min_element(BoundaryConditionInlet.begin(),BoundaryConditionInlet.end());
unsigned short int BC_inlet_max = *max_element(BoundaryConditionInlet.begin(),BoundaryConditionInlet.end());
if (BC_inlet_min == 0 && BC_inlet_max>0){
ERROR("Error: BC_InletList: mix of periodic, ion concentration and flux BC is not supported! \n");
}
if (BC_inlet_min>0){
//read in inlet values Cin
if (ion_db->keyExists("InletValueList")){
Cin = ion_db->getVector<double>( "InletValueList" );
if (Cin.size()!=number_ion_species){
ERROR("Error: number_ion_species and InletValueList must be the same length! \n");
}
}
else {
ERROR("Error: Non-periodic BCs are specified but InletValueList cannot be found! \n");
}
for (unsigned int i=0;i<BoundaryConditionInlet.size();i++){
switch (BoundaryConditionInlet[i]){
case 1://fixed boundary ion concentration [mol/m^3]
Cin[i] = Cin[i]*(h*h*h*1.0e-18);//LB ion concentration has unit [mol/lu^3]
break;
case 2://fixed boundary ion flux [mol/m^2/sec]
Cin[i] = Cin[i]*(h*h*1.0e-12)*time_conv[i];//LB ion flux has unit [mol/lu^2/lt]
break;
}
}
}
}
if (BoundaryCondition==1){
//read boundary ion concentration list; INPUT unit [mol/m^3]
//it must be converted to LB unit [mol/lu^3]
//inlet
if (ion_db->keyExists("CinList")){
Cin.clear();
Cin = ion_db->getVector<double>( "CinList" );
if (Cin.size()!=number_ion_species){
ERROR("Error: number_ion_species and CinList must be the same length! \n");
//Outlet
if (ion_db->keyExists( "BC_OutletList" )){
BoundaryConditionOutlet = ion_db->getVector<int>( "BC_OutletList" );
if (BoundaryConditionOutlet.size()!=number_ion_species){
ERROR("Error: number_ion_species and BC_OutletList must be of the same length! \n");
}
unsigned short int BC_outlet_min = *min_element(BoundaryConditionOutlet.begin(),BoundaryConditionOutlet.end());
unsigned short int BC_outlet_max = *max_element(BoundaryConditionOutlet.begin(),BoundaryConditionOutlet.end());
if (BC_outlet_min == 0 && BC_outlet_max>0){
ERROR("Error: BC_OutletList: mix of periodic, ion concentration and flux BC is not supported! \n");
}
if (BC_outlet_min>0){
//read in outlet values Cout
if (ion_db->keyExists("OutletValueList")){
Cout = ion_db->getVector<double>( "OutletValueList" );
if (Cout.size()!=number_ion_species){
ERROR("Error: number_ion_species and OutletValueList must be the same length! \n");
}
}
else{
for (int i=0; i<Cin.size();i++){
Cin[i] = Cin[i]*(h*h*h*1.0e-18);//LB ion concentration has unit [mol/lu^3]
else {
ERROR("Error: Non-periodic BCs are specified but OutletValueList cannot be found! \n");
}
for (unsigned int i=0;i<BoundaryConditionOutlet.size();i++){
switch (BoundaryConditionOutlet[i]){
case 1://fixed boundary ion concentration [mol/m^3]
Cout[i] = Cout[i]*(h*h*h*1.0e-18);//LB ion concentration has unit [mol/lu^3]
break;
case 2://fixed boundary ion flux [mol/m^2/sec]
Cout[i] = Cout[i]*(h*h*1.0e-12)*time_conv[i];//LB ion flux has unit [mol/lu^2/lt]
break;
}
}
}
else {
for (int i=0; i<Cin.size();i++){
Cin[i] = Cin[i]*(h*h*h*1.0e-18);//LB ion concentration has unit [mol/lu^3]
}
}
//outlet
if (ion_db->keyExists("CoutList")){
Cout.clear();
Cout = ion_db->getVector<double>( "CoutList" );
if (Cout.size()!=number_ion_species){
ERROR("Error: number_ion_species and CoutList must be the same length! \n");
}
else{
for (int i=0; i<Cout.size();i++){
Cout[i] = Cout[i]*(h*h*h*1.0e-18);//LB ion concentration has unit [mol/lu^3]
}
}
}
else {
for (int i=0; i<Cout.size();i++){
Cout[i] = Cout[i]*(h*h*h*1.0e-18);//LB ion concentration has unit [mol/lu^3]
}
}
}
}
}
void ScaLBL_IonModel::SetDomain(){
@@ -417,11 +461,24 @@ void ScaLBL_IonModel::SetDomain(){
for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = 1; // initialize this way
//Averages = std::shared_ptr<TwoPhase> ( new TwoPhase(Dm) ); // TwoPhase analysis object
MPI_Barrier(comm);
Dm->BoundaryCondition = BoundaryCondition;
Mask->BoundaryCondition = BoundaryCondition;
comm.barrier();
unsigned short int BC_inlet_min = *min_element(BoundaryConditionInlet.begin(),BoundaryConditionInlet.end());
unsigned short int BC_outlet_min = *min_element(BoundaryConditionOutlet.begin(),BoundaryConditionOutlet.end());
if (BC_inlet_min==0 && BC_outlet_min==0){
Dm->BoundaryCondition = 0;
Mask->BoundaryCondition = 0;
}
else if (BC_inlet_min>0 && BC_outlet_min>0){
Dm->BoundaryCondition = 1;
Mask->BoundaryCondition = 1;
}
else { //i.e. periodic and non-periodic BCs are mixed
ERROR("Error: check the type of inlet and outlet boundary condition! Mixed periodic and non-periodic BCs are found. \n");
}
Dm->CommInit();
MPI_Barrier(comm);
comm.barrier();
rank = Dm->rank();
nprocx = Dm->nprocx();
@@ -449,7 +506,7 @@ void ScaLBL_IonModel::ReadInput(){
ASSERT( (int) size1[0] == size0[0]+2 && (int) size1[1] == size0[1]+2 && (int) size1[2] == size0[2]+2 );
fillHalo<signed char> fill( comm, Mask->rank_info, size0, { 1, 1, 1 }, 0, 1 );
Array<signed char> id_view;
id_view.viewRaw( size1, Mask->id );
id_view.viewRaw( size1, Mask->id.data() );
fill.copy( input_id, id_view );
fill.fill( id_view );
}
@@ -531,7 +588,7 @@ void ScaLBL_IonModel::AssignSolidBoundary(double *ion_solid)
}
for (size_t idx=0; idx<NLABELS; idx++)
label_count_global[idx]=sumReduce( Dm->Comm, label_count[idx]);
label_count_global[idx]=Dm->Comm.sumReduce( label_count[idx]);
if (rank==0){
printf("LB Ion Solver: number of ion solid labels: %lu \n",NLABELS);
@@ -593,8 +650,9 @@ void ScaLBL_IonModel::Create(){
if (rank==0) printf ("LB Ion Solver: Set up memory efficient layout \n");
Map.resize(Nx,Ny,Nz); Map.fill(-2);
auto neighborList= new int[18*Npad];
Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Mask->id,Np,1);
MPI_Barrier(comm);
Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Mask->id.data(),Np,1);
comm.barrier();
//...........................................................................
// MAIN VARIABLES ALLOCATED HERE
//...........................................................................
@@ -613,21 +671,21 @@ void ScaLBL_IonModel::Create(){
if (rank==0) printf ("LB Ion Solver: Setting up device map and neighbor list \n");
// copy the neighbor list
ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
MPI_Barrier(comm);
comm.barrier();
//Initialize solid boundary for electrical potential
//if ion concentration at solid surface is specified
if (BoundaryConditionSolid==1){
ScaLBL_AllocateDeviceMemory((void **) &IonSolid, sizeof(double)*Nx*Ny*Nz);
ScaLBL_Comm->SetupBounceBackList(Map, Mask->id, Np);
MPI_Barrier(comm);
ScaLBL_AllocateDeviceMemory((void **) &IonSolid, sizeof(double)*Nx*Ny*Nz);
ScaLBL_Comm->SetupBounceBackList(Map, Mask->id.data(), Np);
comm.barrier();
double *IonSolid_host;
IonSolid_host = new double[Nx*Ny*Nz];
AssignSolidBoundary(IonSolid_host);
ScaLBL_CopyToDevice(IonSolid, IonSolid_host, Nx*Ny*Nz*sizeof(double));
ScaLBL_DeviceBarrier();
ScaLBL_Comm->Barrier();
delete [] IonSolid_host;
}
}
@@ -647,7 +705,7 @@ void ScaLBL_IonModel::Initialize(){
AssignIonConcentration_FromFile(&Ci_host[ic*Np],File_ion);
}
ScaLBL_CopyToDevice(Ci, Ci_host, number_ion_species*sizeof(double)*Np);
MPI_Barrier(comm);
comm.barrier();
for (int ic=0; ic<number_ion_species; ic++){
ScaLBL_D3Q7_Ion_Init_FromFile(&fq[ic*Np*7],&Ci[ic*Np],Np);
}
@@ -664,15 +722,6 @@ void ScaLBL_IonModel::Initialize(){
ScaLBL_D3Q7_Ion_ChargeDensity(Ci, ChargeDensity, IonValence[ic], ic, 0, ScaLBL_Comm->LastExterior(), Np);
}
if (rank==0) printf("*****************************************************\n");
if (rank==0) printf("LB Ion Transport Solver: \n");
for (int i=0; i<number_ion_species;i++){
if (rank==0) printf(" Ion %i: LB relaxation tau = %.5g\n", i+1,tau[i]);
if (rank==0) printf(" Time conversion factor: %.5g [sec/lt]\n", time_conv[i]);
if (rank==0) printf(" Internal iteration: %i [lt]\n", timestepMax[i]);
}
if (rank==0) printf("*****************************************************\n");
switch (BoundaryConditionSolid){
case 0:
if (rank==0) printf("LB Ion Solver: solid boundary: non-flux boundary is assigned\n");
@@ -684,6 +733,40 @@ void ScaLBL_IonModel::Initialize(){
if (rank==0) printf("LB Ion Solver: solid boundary: non-flux boundary is assigned\n");
break;
}
for (int i=0; i<number_ion_species;i++){
switch (BoundaryConditionInlet[i]){
case 0:
if (rank==0) printf("LB Ion Solver: inlet boundary for Ion %i is periodic \n",i+1);
break;
case 1:
if (rank==0) printf("LB Ion Solver: inlet boundary for Ion %i is concentration = %.5g [mol/m^3] \n",i+1,Cin[i]/(h*h*h*1.0e-18));
break;
case 2:
if (rank==0) printf("LB Ion Solver: inlet boundary for Ion %i is (inward) flux = %.5g [mol/m^2/sec] \n",i+1,Cin[i]/(h*h*1.0e-12)/time_conv[i]);
break;
}
switch (BoundaryConditionOutlet[i]){
case 0:
if (rank==0) printf("LB Ion Solver: outlet boundary for Ion %i is periodic \n",i+1);
break;
case 1:
if (rank==0) printf("LB Ion Solver: outlet boundary for Ion %i is concentration = %.5g [mol/m^3] \n",i+1,Cout[i]/(h*h*h*1.0e-18));
break;
case 2:
if (rank==0) printf("LB Ion Solver: outlet boundary for Ion %i is (inward) flux = %.5g [mol/m^2/sec] \n",i+1,Cout[i]/(h*h*1.0e-12)/time_conv[i]);
break;
}
}
if (rank==0) printf("*****************************************************\n");
if (rank==0) printf("LB Ion Transport Solver: \n");
for (int i=0; i<number_ion_species;i++){
if (rank==0) printf(" Ion %i: LB relaxation tau = %.5g\n", i+1,tau[i]);
if (rank==0) printf(" Time conversion factor: %.5g [sec/lt]\n", time_conv[i]);
if (rank==0) printf(" Internal iteration: %i [lt]\n", timestepMax[i]);
}
if (rank==0) printf("*****************************************************\n");
}
void ScaLBL_IonModel::Run(double *Velocity, double *ElectricField){
@@ -700,7 +783,7 @@ void ScaLBL_IonModel::Run(double *Velocity, double *ElectricField){
//.......create and start timer............
//double starttime,stoptime,cputime;
//ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
//ScaLBL_Comm->Barrier(); comm.barrier();
//starttime = MPI_Wtime();
for (int ic=0; ic<number_ion_species; ic++){
@@ -713,13 +796,29 @@ void ScaLBL_IonModel::Run(double *Velocity, double *ElectricField){
ScaLBL_Comm->SendD3Q7AA(fq, ic); //READ FROM NORMAL
ScaLBL_D3Q7_AAodd_IonConcentration(NeighborList, &fq[ic*Np*7],&Ci[ic*Np],ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_Comm->RecvD3Q7AA(fq, ic); //WRITE INTO OPPOSITE
ScaLBL_DeviceBarrier();
// Set boundary conditions
if (BoundaryCondition == 1){
ScaLBL_Comm->D3Q7_Ion_Concentration_BC_z(NeighborList, &fq[ic*Np*7], Cin[ic], timestep);
ScaLBL_Comm->D3Q7_Ion_Concentration_BC_Z(NeighborList, &fq[ic*Np*7], Cout[ic], timestep);
ScaLBL_Comm->Barrier();
//--------------------------------------- Set boundary conditions -------------------------------------//
if (BoundaryConditionInlet[ic]>0){
switch (BoundaryConditionInlet[ic]){
case 1:
ScaLBL_Comm->D3Q7_Ion_Concentration_BC_z(NeighborList, &fq[ic*Np*7], Cin[ic], timestep);
break;
case 2:
ScaLBL_Comm->D3Q7_Ion_Flux_BC_z(NeighborList, &fq[ic*Np*7], Cin[ic], tau[ic], &Velocity[2*Np], timestep);
break;
}
}
//-------------------------//
if (BoundaryConditionOutlet[ic]>0){
switch (BoundaryConditionOutlet[ic]){
case 1:
ScaLBL_Comm->D3Q7_Ion_Concentration_BC_Z(NeighborList, &fq[ic*Np*7], Cout[ic], timestep);
break;
case 2:
ScaLBL_Comm->D3Q7_Ion_Flux_BC_Z(NeighborList, &fq[ic*Np*7], Cout[ic], tau[ic], &Velocity[2*Np], timestep);
break;
}
}
//----------------------------------------------------------------------------------------------------//
ScaLBL_D3Q7_AAodd_IonConcentration(NeighborList, &fq[ic*Np*7],&Ci[ic*Np], 0, ScaLBL_Comm->LastExterior(), Np);
@@ -732,7 +831,7 @@ void ScaLBL_IonModel::Run(double *Velocity, double *ElectricField){
if (BoundaryConditionSolid==1){
//TODO IonSolid may also be species-dependent
ScaLBL_Comm->SolidDirichletD3Q7(&fq[ic*Np*7], IonSolid);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_Comm->Barrier(); comm.barrier();
}
// *************EVEN TIMESTEP*************//
@@ -741,13 +840,29 @@ void ScaLBL_IonModel::Run(double *Velocity, double *ElectricField){
ScaLBL_Comm->SendD3Q7AA(fq, ic); //READ FORM NORMAL
ScaLBL_D3Q7_AAeven_IonConcentration(&fq[ic*Np*7],&Ci[ic*Np],ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_Comm->RecvD3Q7AA(fq, ic); //WRITE INTO OPPOSITE
ScaLBL_DeviceBarrier();
// Set boundary conditions
if (BoundaryCondition == 1){
ScaLBL_Comm->D3Q7_Ion_Concentration_BC_z(NeighborList, &fq[ic*Np*7], Cin[ic], timestep);
ScaLBL_Comm->D3Q7_Ion_Concentration_BC_Z(NeighborList, &fq[ic*Np*7], Cout[ic], timestep);
ScaLBL_Comm->Barrier();
//--------------------------------------- Set boundary conditions -------------------------------------//
if (BoundaryConditionInlet[ic]>0){
switch (BoundaryConditionInlet[ic]){
case 1:
ScaLBL_Comm->D3Q7_Ion_Concentration_BC_z(NeighborList, &fq[ic*Np*7], Cin[ic], timestep);
break;
case 2:
ScaLBL_Comm->D3Q7_Ion_Flux_BC_z(NeighborList, &fq[ic*Np*7], Cin[ic], tau[ic], &Velocity[2*Np], timestep);
break;
}
}
//-------------------------//
if (BoundaryConditionOutlet[ic]>0){
switch (BoundaryConditionOutlet[ic]){
case 1:
ScaLBL_Comm->D3Q7_Ion_Concentration_BC_Z(NeighborList, &fq[ic*Np*7], Cout[ic], timestep);
break;
case 2:
ScaLBL_Comm->D3Q7_Ion_Flux_BC_Z(NeighborList, &fq[ic*Np*7], Cout[ic], tau[ic], &Velocity[2*Np], timestep);
break;
}
}
//----------------------------------------------------------------------------------------------------//
ScaLBL_D3Q7_AAeven_IonConcentration(&fq[ic*Np*7],&Ci[ic*Np], 0, ScaLBL_Comm->LastExterior(), Np);
@@ -760,7 +875,7 @@ void ScaLBL_IonModel::Run(double *Velocity, double *ElectricField){
if (BoundaryConditionSolid==1){
//TODO IonSolid may also be species-dependent
ScaLBL_Comm->SolidDirichletD3Q7(&fq[ic*Np*7], IonSolid);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_Comm->Barrier(); comm.barrier();
}
}
}
@@ -786,17 +901,13 @@ void ScaLBL_IonModel::Run(double *Velocity, double *ElectricField){
//if (rank==0) printf("********************************************************\n");
}
void ScaLBL_IonModel::getIonConcentration(int timestep){
//This function wirte out the data in a normal layout (by aggregating all decomposed domains)
DoubleArray PhaseField(Nx,Ny,Nz);
for (int ic=0; ic<number_ion_species; ic++){
ScaLBL_Comm->RegularLayout(Map,&Ci[ic*Np],PhaseField);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
IonConcentration_LB_to_Phys(PhaseField);
void ScaLBL_IonModel::getIonConcentration(DoubleArray &IonConcentration, const int ic){
//This function wirte out the data in a normal layout (by aggregating all decomposed domains)
ScaLBL_Comm->RegularLayout(Map,&Ci[ic*Np],IonConcentration);
ScaLBL_Comm->Barrier(); comm.barrier();
IonConcentration_LB_to_Phys(IonConcentration);
sprintf(OutputFilename,"Ion%02i_Time_%i.raw",ic+1,timestep);
Mask->AggregateLabels(OutputFilename,PhaseField);
}
}
void ScaLBL_IonModel::getIonConcentration_debug(int timestep){
@@ -804,7 +915,7 @@ void ScaLBL_IonModel::getIonConcentration_debug(int timestep){
DoubleArray PhaseField(Nx,Ny,Nz);
for (int ic=0; ic<number_ion_species; ic++){
ScaLBL_Comm->RegularLayout(Map,&Ci[ic*Np],PhaseField);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_Comm->Barrier(); comm.barrier();
IonConcentration_LB_to_Phys(PhaseField);
FILE *OUTFILE;
@@ -845,7 +956,7 @@ void ScaLBL_IonModel::DummyFluidVelocity(){
}
ScaLBL_AllocateDeviceMemory((void **) &FluidVelocityDummy, sizeof(double)*3*Np);
ScaLBL_CopyToDevice(FluidVelocityDummy, FluidVelocity_host, sizeof(double)*3*Np);
ScaLBL_DeviceBarrier();
ScaLBL_Comm->Barrier();
delete [] FluidVelocity_host;
}
@@ -866,7 +977,7 @@ void ScaLBL_IonModel::DummyElectricField(){
}
ScaLBL_AllocateDeviceMemory((void **) &ElectricFieldDummy, sizeof(double)*3*Np);
ScaLBL_CopyToDevice(ElectricFieldDummy, ElectricField_host, sizeof(double)*3*Np);
ScaLBL_DeviceBarrier();
ScaLBL_Comm->Barrier();
delete [] ElectricField_host;
}
@@ -891,10 +1002,8 @@ double ScaLBL_IonModel::CalIonDenConvergence(vector<double> &ci_avg_previous){
ci_loc +=Ci_host[idx];
count_loc+=1.0;
}
MPI_Allreduce(&ci_loc,&ci_avg,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
MPI_Allreduce(&count_loc,&count,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
ci_avg = Mask->Comm.sumReduce( ci_loc);
count = Mask->Comm.sumReduce( count_loc);
ci_avg /= count;
double ci_avg_mag=ci_avg;
if (ci_avg==0.0) ci_avg_mag=1.0;
@@ -918,7 +1027,7 @@ double ScaLBL_IonModel::CalIonDenConvergence(vector<double> &ci_avg_previous){
// DoubleArray PhaseField(Nx,Ny,Nz);
// for (int ic=0; ic<number_ion_species; ic++){
// ScaLBL_Comm->RegularLayout(Map,&Ci[ic*Np],PhaseField);
// ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
// ScaLBL_Comm->Barrier(); comm.barrier();
//
// FILE *OUTFILE;
// sprintf(LocalRankFilename,"Ion%02i.%05i.raw",ic+1,rank);