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continue the work of storing ion diffusive flux;incomplete.

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This commit is contained in:
Rex Zhe Li
2021-09-29 15:41:38 +10:00
parent 6c262b53e5
commit 01499e672d
7 changed files with 166 additions and 14 deletions
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80
models/IonModel.cpp
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@@ -692,6 +692,7 @@ void ScaLBL_IonModel::Create(){
ScaLBL_AllocateDeviceMemory((void **) &fq, number_ion_species*7*dist_mem_size);
ScaLBL_AllocateDeviceMemory((void **) &Ci, number_ion_species*sizeof(double)*Np);
ScaLBL_AllocateDeviceMemory((void **) &ChargeDensity, sizeof(double)*Np);
ScaLBL_AllocateDeviceMemory((void **) &FluxDiffusive, number_ion_species*3*sizeof(double)*Np);
//...........................................................................
// Update GPU data structures
if (rank==0) printf ("LB Ion Solver: Setting up device map and neighbor list \n");
@@ -877,9 +878,9 @@ void ScaLBL_IonModel::Run(double *Velocity, double *ElectricField){
//LB-Ion collison
ScaLBL_D3Q7_AAodd_Ion(NeighborList, &fq[ic*Np*7],&Ci[ic*Np],Velocity,ElectricField,IonDiffusivity[ic],IonValence[ic],
ScaLBL_D3Q7_AAodd_Ion(NeighborList, &fq[ic*Np*7],&Ci[ic*Np],&FluxDiffusive[3*ic*Np],Velocity,ElectricField,IonDiffusivity[ic],IonValence[ic],
rlx[ic],Vt,ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_D3Q7_AAodd_Ion(NeighborList, &fq[ic*Np*7],&Ci[ic*Np],Velocity,ElectricField,IonDiffusivity[ic],IonValence[ic],
ScaLBL_D3Q7_AAodd_Ion(NeighborList, &fq[ic*Np*7],&Ci[ic*Np],&FluxDiffusive[3*ic*Np],Velocity,ElectricField,IonDiffusivity[ic],IonValence[ic],
rlx[ic],Vt,0, ScaLBL_Comm->LastExterior(), Np);
if (BoundaryConditionSolid==1){
@@ -933,9 +934,9 @@ void ScaLBL_IonModel::Run(double *Velocity, double *ElectricField){
//LB-Ion collison
ScaLBL_D3Q7_AAeven_Ion(&fq[ic*Np*7],&Ci[ic*Np],Velocity,ElectricField,IonDiffusivity[ic],IonValence[ic],
ScaLBL_D3Q7_AAeven_Ion(&fq[ic*Np*7],&Ci[ic*Np],&FluxDiffusive[3*ic*Np],Velocity,ElectricField,IonDiffusivity[ic],IonValence[ic],
rlx[ic],Vt,ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_D3Q7_AAeven_Ion(&fq[ic*Np*7],&Ci[ic*Np],Velocity,ElectricField,IonDiffusivity[ic],IonValence[ic],
ScaLBL_D3Q7_AAeven_Ion(&fq[ic*Np*7],&Ci[ic*Np],&FluxDiffusive[3*ic*Np],Velocity,ElectricField,IonDiffusivity[ic],IonValence[ic],
rlx[ic],Vt,0, ScaLBL_Comm->LastExterior(), Np);
if (BoundaryConditionSolid==1){
@@ -973,7 +974,22 @@ void ScaLBL_IonModel::getIonConcentration(DoubleArray &IonConcentration, const s
ScaLBL_Comm->RegularLayout(Map,&Ci[ic*Np],IonConcentration);
ScaLBL_Comm->Barrier(); comm.barrier();
IonConcentration_LB_to_Phys(IonConcentration);
}
void ScaLBL_IonModel::getIonFluxDiffusive(DoubleArray &IonFlux_x,DoubleArray &IonFlux_y,DoubleArray &IonFlux_z,const size_t ic){
//This function wirte out the data in a normal layout (by aggregating all decomposed domains)
ScaLBL_Comm->RegularLayout(Map,&FluxDiffusive[ic*3*Np+0*Np],IonFlux_x);
IonFlux_LB_to_Phys(IonFlux_x,ic);
ScaLBL_Comm->Barrier(); comm.barrier();
ScaLBL_Comm->RegularLayout(Map,&FluxDiffusive[ic*3*Np+1*Np],IonFlux_y);
IonFlux_LB_to_Phys(IonFlux_y,ic);
ScaLBL_Comm->Barrier(); comm.barrier();
ScaLBL_Comm->RegularLayout(Map,&FluxDiffusive[ic*3*Np+2*Np],IonFlux_z);
IonFlux_LB_to_Phys(IonFlux_z,ic);
ScaLBL_Comm->Barrier(); comm.barrier();
}
void ScaLBL_IonModel::getIonConcentration_debug(int timestep){
@@ -992,13 +1008,67 @@ void ScaLBL_IonModel::getIonConcentration_debug(int timestep){
}
}
void ScaLBL_IonModel::getIonFluxDiffusive_debug(int timestep){
//This function write out decomposed data
DoubleArray PhaseField(Nx,Ny,Nz);
for (size_t ic=0; ic<number_ion_species; ic++){
//x-component
ScaLBL_Comm->RegularLayout(Map,&FluxDiffusive[ic*3*Np+0*Np],PhaseField);
ScaLBL_Comm->Barrier(); comm.barrier();
IonFlux_LB_to_Phys(PhaseField);
FILE *OUTFILE_X;
sprintf(LocalRankFilename,"IonFluxDiffusive_X_%02zu_Time_%i.%05i.raw",ic+1,timestep,rank);
OUTFILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,OUTFILE_X);
fclose(OUTFILE_X);
//y-component
ScaLBL_Comm->RegularLayout(Map,&FluxDiffusive[ic*3*Np+1*Np],PhaseField);
ScaLBL_Comm->Barrier(); comm.barrier();
IonFlux_LB_to_Phys(PhaseField);
FILE *OUTFILE_Y;
sprintf(LocalRankFilename,"IonFluxDiffusive_Y_%02zu_Time_%i.%05i.raw",ic+1,timestep,rank);
OUTFILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,OUTFILE_Y);
fclose(OUTFILE_Y);
//z-component
ScaLBL_Comm->RegularLayout(Map,&FluxDiffusive[ic*3*Np+2*Np],PhaseField);
ScaLBL_Comm->Barrier(); comm.barrier();
IonFlux_LB_to_Phys(PhaseField);
FILE *OUTFILE_Z;
sprintf(LocalRankFilename,"IonFluxDiffusive_Z_%02zu_Time_%i.%05i.raw",ic+1,timestep,rank);
OUTFILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,OUTFILE_Z);
fclose(OUTFILE_Z);
}
}
void ScaLBL_IonModel::IonConcentration_LB_to_Phys(DoubleArray &Den_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)){
Den_reg(i,j,k) = Den_reg(i,j,k)/(h*h*h*1.0e-18);
Den_reg(i,j,k) = Den_reg(i,j,k)/(h*h*h*1.0e-18);//this converts the unit to [mol/m^3]
}
}
}
}
}
void ScaLBL_IonModel::IonFlux_LB_to_Phys(DoubleArray &Den_reg, const size_t ic){
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)){
Den_reg(i,j,k) = Den_reg(i,j,k)/(h*h*1.0e-12*time_conv[ic]);//this converts the unit to [mol/m^2/s]
}
}
}

1
models/IonModel.h
View File

@@ -83,6 +83,7 @@ public:
double *IonSolid;
double *FluidVelocityDummy;
double *ElectricFieldDummy;
double *FluxDiffusive;
private:
Utilities::MPI comm;