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save unfinished work; to be built and tested

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This commit is contained in:
Rex Zhe Li
2021-05-11 22:25:05 -04:00
parent e97dfa78df
commit fee3d9eadc
6 changed files with 457 additions and 7 deletions
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212
models/StokesModel.cpp
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@@ -8,6 +8,7 @@
ScaLBL_StokesModel::ScaLBL_StokesModel(int RANK, int NP, const Utilities::MPI& COMM):
rank(RANK), nprocs(NP), Restart(0),timestep(0),timestepMax(0),tau(0),
Fx(0),Fy(0),Fz(0),flux(0),din(0),dout(0),mu(0),h(0),nu_phys(0),rho_phys(0),rho0(0),den_scale(0),time_conv(0),tolerance(0),
epsilon0(0),epsilon0_LB(0),epsilonR(0),epsilon_LB(0),UseSlippingVelBC(0),
Nx(0),Ny(0),Nz(0),N(0),Np(0),nprocx(0),nprocy(0),nprocz(0),BoundaryCondition(0),Lx(0),Ly(0),Lz(0),comm(COMM)
{
@@ -38,6 +39,12 @@ void ScaLBL_StokesModel::ReadParams(string filename,int num_iter){
tolerance = 1.0e-8;
Fx = Fy = 0.0;
Fz = 1.0e-5;
//Stokes solver also needs the following parameters for slipping velocity BC
epsilon0 = 8.85e-12;//electric permittivity of vaccum; unit:[C/(V*m)]
epsilon0_LB = epsilon0*(h*1.0e-6);//unit:[C/(V*lu)]
epsilonR = 78.4;//default dielectric constant of water
epsilon_LB = epsilon0_LB*epsilonR;//electric permittivity
UseSlippingVelBC = false;
//--------------------------------------------------------------------------//
// Read domain parameters
@@ -85,12 +92,18 @@ void ScaLBL_StokesModel::ReadParams(string filename,int num_iter){
if (stokes_db->keyExists( "flux" )){
flux = stokes_db->getScalar<double>( "flux" );
}
if (stokes_db->keyExists( "UseElectroosmoticVelocityBC" )){
UseSlippingVelBC = stokes_db->getScalar<bool>( "UseElectroosmoticVelocityBC" );
}
if (electric_db->keyExists( "epsilonR" )){
epsilonR = electric_db->getScalar<double>( "epsilonR" );
}
// Re-calculate model parameters due to parameter read
mu=(tau-0.5)/3.0;
time_conv = (h*h*1.0e-12)*mu/nu_phys;//time conversion factor from physical to LB unit; [sec/lt]
den_scale = rho_phys/rho0*(h*h*h*1.0e-18);//scale factor for density
epsilon_LB = epsilon0_LB*epsilonR;//electric permittivity
}
void ScaLBL_StokesModel::ReadParams(string filename){
@@ -100,7 +113,6 @@ void ScaLBL_StokesModel::ReadParams(string filename){
db = std::make_shared<Database>( filename );
domain_db = db->getDatabase( "Domain" );
stokes_db = db->getDatabase( "Stokes" );
//---------------------- Default model parameters --------------------------//
rho_phys = 1000.0; //by default use water density; unit [kg/m^3]
@@ -114,6 +126,12 @@ void ScaLBL_StokesModel::ReadParams(string filename){
tolerance = 1.0e-8;
Fx = Fy = 0.0;
Fz = 1.0e-5;
//Stokes solver also needs the following parameters for slipping velocity BC
epsilon0 = 8.85e-12;//electric permittivity of vaccum; unit:[C/(V*m)]
epsilon0_LB = epsilon0*(h*1.0e-6);//unit:[C/(V*lu)]
epsilonR = 78.4;//default dielectric constant of water
epsilon_LB = epsilon0_LB*epsilonR;//electric permittivity
UseSlippingVelBC = false;
//--------------------------------------------------------------------------//
// Read domain parameters
@@ -161,12 +179,18 @@ void ScaLBL_StokesModel::ReadParams(string filename){
if (stokes_db->keyExists( "flux" )){
flux = stokes_db->getScalar<double>( "flux" );
}
if (stokes_db->keyExists( "UseElectroosmoticVelocityBC" )){
UseSlippingVelBC = stokes_db->getScalar<bool>( "UseElectroosmoticVelocityBC" );
}
if (electric_db->keyExists( "epsilonR" )){
epsilonR = electric_db->getScalar<double>( "epsilonR" );
}
// Re-calculate model parameters due to parameter read
mu=(tau-0.5)/3.0;
time_conv = (h*h*1.0e-12)*mu/nu_phys;//time conversion factor from physical to LB unit; [sec/lt]
den_scale = rho_phys/rho0*(h*h*h*1.0e-18);//scale factor for density
epsilon_LB = epsilon0_LB*epsilonR;//electric permittivity
}
void ScaLBL_StokesModel::SetDomain(){
@@ -258,6 +282,157 @@ void ScaLBL_StokesModel::ReadInput(){
if (rank == 0) cout << " Domain set." << endl;
}
void ScaLBL_IonModel::AssignZetaPotentialSolid(double *zeta_potential_solid)
{
size_t NLABELS=0;
signed char VALUE=0;
double AFFINITY=0.f;
auto LabelList = ion_db->getVector<int>( "SolidLabels" );
auto AffinityList = ion_db->getVector<double>( "ZetaPotentialSolidList" );
NLABELS=LabelList.size();
if (NLABELS != AffinityList.size()){
ERROR("Error: LB Stokes Solver: SolidLabels and ZetaPotentialSolidList must be the same length! \n");
}
double label_count[NLABELS];
double label_count_global[NLABELS];
for (size_t idx=0; idx<NLABELS; idx++) label_count[idx]=0;
// Assign the labels
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];//no need to convert unit for zeta potential (i.e. volt)
label_count[idx] += 1.0;
idx = NLABELS;
}
}
zeta_potential_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 Stokes Solver: number of 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);
printf(" label=%d, zeta potential=%.3g [V], volume fraction=%.2g\n",VALUE,AFFINITY,volume_fraction);
}
}
}
void ScaLBL_IonModel::AssignSolidGrad(double *solid_grad)
{
//TODO need to normalize the computed solid grad!!!
double *Dst;
Dst = new double [3*3*3];
for (int kk=0; kk<3; kk++){
for (int jj=0; jj<3; jj++){
for (int ii=0; ii<3; ii++){
int index = kk*9+jj*3+ii;
Dst[index] = sqrt(double(ii-1)*double(ii-1) + double(jj-1)*double(jj-1)+ double(kk-1)*double(kk-1));
}
}
}
//implement a D3Q19 lattice
double w_face = 1.0/18.0;
double w_edge = 0.5*w_face;
double w_corner = 0.0;
//local
Dst[13] = 0.f;
//faces
Dst[4] = w_face;
Dst[10] = w_face;
Dst[12] = w_face;
Dst[14] = w_face;
Dst[16] = w_face;
Dst[22] = w_face;
// corners
Dst[0] = w_corner;
Dst[2] = w_corner;
Dst[6] = w_corner;
Dst[8] = w_corner;
Dst[18] = w_corner;
Dst[20] = w_corner;
Dst[24] = w_corner;
Dst[26] = w_corner;
// edges
Dst[1] = w_edge;
Dst[3] = w_edge;
Dst[5] = w_edge;
Dst[7] = w_edge;
Dst[9] = w_edge;
Dst[11] = w_edge;
Dst[15] = w_edge;
Dst[17] = w_edge;
Dst[19] = w_edge;
Dst[21] = w_edge;
Dst[23] = w_edge;
Dst[25] = w_edge;
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)){
double phi_x = 0.f;
double phi_y = 0.f;
double phi_z = 0.f;
for (int kk=0; kk<3; kk++){
for (int jj=0; jj<3; jj++){
for (int ii=0; ii<3; ii++){
int index = kk*9+jj*3+ii;
double weight= Dst[index];
int idi=i+ii-1;
int idj=j+jj-1;
int idk=k+kk-1;
if (idi < 0) idi=0;
if (idj < 0) idj=0;
if (idk < 0) idk=0;
if (!(idi < Nx)) idi=Nx-1;
if (!(idj < Ny)) idj=Ny-1;
if (!(idk < Nz)) idk=Nz-1;
int nn = idk*Nx*Ny + idj*Nx + idi;
double vec_x = double(ii-1);
double vec_y = double(jj-1);
double vec_z = double(kk-1);
double GWNS = double(Mask->id[nn]);
//Since the solid unit normal vector is wanted, treat
//wet node as 0.0 and solid node as 1.0
GWNS = (GWNS>0.0) ? 0.0:1.0;
phi_x += GWNS*weight*vec_x;
phi_y += GWNS*weight*vec_y;
phi_z += GWNS*weight*vec_z;
}
}
}
solid_grad[idx+0*Np] = phi_x;
solid_grad[idx+1*Np] = phi_y;
solid_grad[idx+2*Np] = phi_z;
}
}
}
}
}
void ScaLBL_StokesModel::Create(){
/*
* This function creates the variables needed to run a LBM
@@ -301,6 +476,26 @@ void ScaLBL_StokesModel::Create(){
ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
comm.barrier();
if (UseSlippingVelBC==true){
ScaLBL_Comm->SetupBounceBackList(Map, Mask->id.data(), Np,1);
comm.barrier();
//For slipping velocity BC, need zeta potential and solid unit normal vector
ScaLBL_AllocateDeviceMemory((void **) &ZetaPotentialSolid, sizeof(double)*Nx*Ny*Nz);
ScaLBL_AllocateDeviceMemory((void **) &SolidGrad, sizeof(double)*Np); //unit normal vector of solid nodes
double *ZetaPotentialSolid_host;
ZetaPotentialSolid_host = new double[Nx*Ny*Nz];
AssignZetaPotentialSolid(ZetaPotentialSolid_host);
double *SolidGrad_host;
SolidGrad_host = new double[3*Np];
AssignSolidGrad(SolidGrad_host);
ScaLBL_CopyToDevice(ZetaPotentialSolid, ZetaPotentialSolid_host, Nx*Ny*Nz*sizeof(double));
ScaLBL_CopyToDevice(SolidGrad, SolidGrad_host, 3*Np*sizeof(double));
ScaLBL_Comm->Barrier();
delete [] ZetaPotentialSolid_host;
delete [] SolidGrad_host;
}
}
void ScaLBL_StokesModel::Initialize(){
@@ -324,6 +519,7 @@ void ScaLBL_StokesModel::Run_Lite(double *ChargeDensity, double *ElectricField){
timestep = 0;
while (timestep < timestepMax) {
//************************************************************************/
//**************ODD TIMESTEP*************//
timestep++;
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
ScaLBL_D3Q19_AAodd_StokesMRT(NeighborList, fq, Velocity, ChargeDensity, ElectricField, rlx_setA, rlx_setB, Fx, Fy, Fz,rho0,den_scale,h,time_conv,
@@ -344,8 +540,14 @@ void ScaLBL_StokesModel::Run_Lite(double *ChargeDensity, double *ElectricField){
}
ScaLBL_D3Q19_AAodd_StokesMRT(NeighborList, fq, Velocity, ChargeDensity, ElectricField, rlx_setA, rlx_setB, Fx, Fy, Fz,rho0,den_scale,h,time_conv,
0, ScaLBL_Comm->LastExterior(), Np);
if (UseSlippingVelBC==true){
ScaLBL_Comm->SolidSlippingVelocityBCD3Q19(fq, ZetaPotentialSolid, ElectricField, SolidGrad,
epslion_LB, 1.0/rlx_setA, rho0, den_scale, h, time_conv);
}
ScaLBL_Comm->Barrier(); comm.barrier();
//**************EVEN TIMESTEP*************//
timestep++;
ScaLBL_Comm->SendD3Q19AA(fq); //READ FORM NORMAL
ScaLBL_D3Q19_AAeven_StokesMRT(fq, Velocity, ChargeDensity, ElectricField, rlx_setA, rlx_setB, Fx, Fy, Fz,rho0,den_scale,h,time_conv,
@@ -366,6 +568,10 @@ void ScaLBL_StokesModel::Run_Lite(double *ChargeDensity, double *ElectricField){
}
ScaLBL_D3Q19_AAeven_StokesMRT(fq, Velocity, ChargeDensity, ElectricField, rlx_setA, rlx_setB, Fx, Fy, Fz,rho0,den_scale,h,time_conv,
0, ScaLBL_Comm->LastExterior(), Np);
if (UseSlippingVelBC==true){
ScaLBL_Comm->SolidSlippingVelocityBCD3Q19(fq, ZetaPotentialSolid, ElectricField, SolidGrad,
epslion_LB, 1.0/rlx_setA, rho0, den_scale, h, time_conv);
}
ScaLBL_Comm->Barrier(); comm.barrier();
//************************************************************************/
}