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add output; CPU version compiled; to be tested

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This commit is contained in:
Rex Zhe Li 2020-08-17 09:59:22 -04:00
parent 85fc59190c
commit 771f679f5c
10 changed files with 151 additions and 20 deletions
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8
common/ScaLBL.h
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@ -49,6 +49,8 @@ extern "C" void ScaLBL_D3Q19_Init(double *Dist, int Np);
extern "C" void ScaLBL_D3Q19_Momentum(double *dist, double *vel, int Np);
extern "C" void ScaLBL_D3Q19_Momentum_Phys(double *dist, double *vel, double h, double time_conv, int Np);
extern "C" void ScaLBL_D3Q19_Pressure(double *dist, double *press, int Np);
// BGK MODEL
@ -89,6 +91,8 @@ extern "C" void ScaLBL_D3Q7_Ion_Init(double *dist, double *Den, double DenInit,
extern "C" void ScaLBL_D3Q7_Ion_ChargeDensity(double *Den, double *ChargeDensity, int IonValence, int ion_component, int start, int finish, int Np);
extern "C" void ScaLBL_IonConcentration_Phys(double *Den, double h, int ion_component, int start, int finish, int Np);
// LBM Poisson solver
extern "C" void ScaLBL_D3Q7_AAodd_Poisson(int *neighborList, double *dist, double *Den_charge, double *Psi, double *ElectricField, double tau, double epsilon_LB,double gamma,
@ -102,10 +106,10 @@ extern "C" void ScaLBL_D3Q7_Poisson_Init(double *dist, int Np);
// LBM Stokes Model (adapted from MRT model)
extern "C" void ScaLBL_D3Q19_AAeven_StokesMRT(double *dist, double *Velocity, double *ChargeDensity, double *ElectricField, double rlx_setA, double rlx_setB,
double Gx, double Gy, double Gz, int start, int finish, int Np);
double Gx, double Gy, double Gz, double Ex, double Ey, double Ez, int start, int finish, int Np);
extern "C" void ScaLBL_D3Q19_AAodd_StokesMRT(int *neighborList, double *dist, double *Velocity, double *ChargeDensity, double *ElectricField, double rlx_setA, double rlx_setB,
double Gx, double Gy, double Gz, int start, int finish, int Np);
double Gx, double Gy, double Gz, double Ex, double Ey, double Ez, int start, int finish, int Np);
// MRT MODEL
extern "C" void ScaLBL_D3Q19_AAeven_MRT(double *dist, int start, int finish, int Np, double rlx_setA, double rlx_setB, double Fx,

10
cpu/Ion.cpp
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@ -235,3 +235,13 @@ extern "C" void ScaLBL_D3Q7_Ion_ChargeDensity(double *Den, double *ChargeDensity
}
}
extern "C" void ScaLBL_IonConcentration_Phys(double *Den, double h, int ion_component, int start, int finish, int Np){
//h: resolution [um/lu]
int n;
double Ci;
for (n=start; n<finish; n++){
Ci = Den[n+ion_component*Np];
Den[n+ion_component*Np] = Ci/(h*h*h*1.0e-18);
}
}

60
cpu/Stokes.cpp
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@ -1,7 +1,7 @@
#include <stdio.h>
extern "C" void ScaLBL_D3Q19_AAeven_StokesMRT(double *dist, double *Velocity, double *ChargeDensity, double *ElectricField, double rlx_setA, double rlx_setB,
double Gx, double Gy, double Gz, int start, int finish, int Np)
double Gx, double Gy, double Gz, double Ex_const, double Ey_const, double Ez_const, int start, int finish, int Np)
{
double fq;
// conserved momemnts
@ -32,9 +32,9 @@ extern "C" void ScaLBL_D3Q19_AAeven_StokesMRT(double *dist, double *Velocity, do
//Load data
rhoE = ChargeDensity[n];
Ex = ElectricField[n+0*Np];
Ey = ElectricField[n+1*Np];
Ez = ElectricField[n+2*Np];
Ex = ElectricField[n+0*Np]+Ex_const;
Ey = ElectricField[n+1*Np]+Ey_const;
Ez = ElectricField[n+2*Np]+Ez_const;
//compute total body force, including input body force (Gx,Gy,Gz)
Fx = Gx + rhoE*Ex;
Fy = Gy + rhoE*Ey;
@ -455,7 +455,7 @@ extern "C" void ScaLBL_D3Q19_AAeven_StokesMRT(double *dist, double *Velocity, do
}
extern "C" void ScaLBL_D3Q19_AAodd_StokesMRT(int *neighborList, double *dist, double *Velocity, double *ChargeDensity, double *ElectricField, double rlx_setA, double rlx_setB,
double Gx, double Gy, double Gz, int start, int finish, int Np)
double Gx, double Gy, double Gz, double Ex_const, double Ey_const, double Ez_const, int start, int finish, int Np)
{
double fq;
// conserved momemnts
@ -487,9 +487,9 @@ extern "C" void ScaLBL_D3Q19_AAodd_StokesMRT(int *neighborList, double *dist, do
//Load data
rhoE = ChargeDensity[n];
Ex = ElectricField[n+0*Np];
Ey = ElectricField[n+1*Np];
Ez = ElectricField[n+2*Np];
Ex = ElectricField[n+0*Np]+Ex_const;
Ey = ElectricField[n+1*Np]+Ey_const;
Ez = ElectricField[n+2*Np]+Ez_const;
//compute total body force, including input body force (Gx,Gy,Gz)
Fx = Gx + rhoE*Ex;
Fy = Gy + rhoE*Ey;
@ -955,3 +955,47 @@ extern "C" void ScaLBL_D3Q19_AAodd_StokesMRT(int *neighborList, double *dist, do
}
}
extern "C" void ScaLBL_D3Q19_Momentum_Phys(double *dist, double *vel, double h, double time_conv, int Np)
{
//h: resolution [um/lu]
//time_conv: time conversion factor [sec/lt]
int n;
// distributions
double f1,f2,f3,f4,f5,f6,f7,f8,f9;
double f10,f11,f12,f13,f14,f15,f16,f17,f18;
double vx,vy,vz;
for (n=0; n<Np; n++){
//........................................................................
// Registers to store the distributions
//........................................................................
f2 = dist[2*Np+n];
f4 = dist[4*Np+n];
f6 = dist[6*Np+n];
f8 = dist[8*Np+n];
f10 = dist[10*Np+n];
f12 = dist[12*Np+n];
f14 = dist[14*Np+n];
f16 = dist[16*Np+n];
f18 = dist[18*Np+n];
//........................................................................
f1 = dist[Np+n];
f3 = dist[3*Np+n];
f5 = dist[5*Np+n];
f7 = dist[7*Np+n];
f9 = dist[9*Np+n];
f11 = dist[11*Np+n];
f13 = dist[13*Np+n];
f15 = dist[15*Np+n];
f17 = dist[17*Np+n];
//.................Compute the velocity...................................
vx = f1-f2+f7-f8+f9-f10+f11-f12+f13-f14;
vy = f3-f4+f7-f8-f9+f10+f15-f16+f17-f18;
vz = f5-f6+f11-f12-f13+f14+f15-f16-f17+f18;
//..................Write the velocity.....................................
vel[0*Np+n] = vx*(h*1.0e-6)/time_conv;
vel[1*Np+n] = vy*(h*1.0e-6)/time_conv;
vel[2*Np+n] = vz*(h*1.0e-6)/time_conv;
//........................................................................
}
}

19
models/IonModel.cpp
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@ -457,3 +457,22 @@ void ScaLBL_IonModel::Run(double *Velocity, double *ElectricField){
}
void ScaLBL_IonModel::getIonConcentration(){
for (int ic=0; ic<number_ion_species; ic++){
ScaLBL_IonConcentration_Phys(Ci, h, ic, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
}
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);
FILE *OUTFILE;
sprintf(LocalRankFilename,"Ion%02i.%05i.raw",ic+1,rank);
OUTFILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,OUTFILE);
fclose(OUTFILE);
}
}

1
models/IonModel.h
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@ -29,6 +29,7 @@ public:
void Create();
void Initialize();
void Run(double *Velocity, double *ElectricField);
void getIonConcentration();
//bool Restart,pBC;
int timestep,timestepMax;

11
models/PoissonSolver.cpp
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@ -390,3 +390,14 @@ void ScaLBL_Poisson::Run(double *ChargeDensity){
}
void ScaLBL_Poisson::getElectricalPotential(){
DoubleArray PhaseField(Nx,Ny,Nz);
ScaLBL_Comm->RegularLayout(Map,Psi,PhaseField);
//ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
FILE *OUTFILE;
sprintf(LocalRankFilename,"Electrical_Potential.%05i.raw",rank);
OUTFILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,OUTFILE);
fclose(OUTFILE);
}

1
models/PoissonSolver.h
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@ -28,6 +28,7 @@ public:
void Create();
void Initialize();
void Run(double *ChargeDensity);
void getElectricalPotential();
//bool Restart,pBC;
int timestep,timestepMax;

53
models/StokesModel.cpp
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@ -35,6 +35,9 @@ void ScaLBL_StokesModel::ReadParams(string filename,int num_iter){
tolerance = 1.0e-8;
Fx = Fy = 0.0;
Fz = 1.0e-5;
//Body electric field [V/lu]
Ex = Ey = 0.0;
Ez = 1.0e-3;
//--------------------------------------------------------------------------//
// Single-fluid Navier-Stokes Model parameters
@ -55,6 +58,11 @@ void ScaLBL_StokesModel::ReadParams(string filename,int num_iter){
Fy = stokes_db->getVector<double>( "F" )[1];
Fz = stokes_db->getVector<double>( "F" )[2];
}
if (stokes_db->keyExists( "ElectricField" )){//NOTE user-input has physical unit [V/m]
Ex = stokes_db->getVector<double>( "ElectricField" )[0];
Ey = stokes_db->getVector<double>( "ElectricField" )[1];
Ez = stokes_db->getVector<double>( "ElectricField" )[2];
}
if (stokes_db->keyExists( "Restart" )){
Restart = stokes_db->getScalar<bool>( "Restart" );
}
@ -79,6 +87,11 @@ void ScaLBL_StokesModel::ReadParams(string filename,int num_iter){
// Re-calculate model parameters due to parameter read
mu=(tau-0.5)/3.0;
time_conv = h*h*mu/nu_phys;//time conversion factor from physical to LB unit; [sec/lt]
// convert user-input electric field ([V/m]) from physical unit to LB unit
Ex = Ex*(h*1.0e-6);//LB electric field: V/lu
Ey = Ey*(h*1.0e-6);
Ez = Ez*(h*1.0e-6);
if (rank==0) printf("*****************************************************\n");
if (rank==0) printf("LB Single-Fluid Navier-Stokes Solver: \n");
if (rank==0) printf(" Time conversion factor: %.5g [sec/lt]\n", time_conv);
@ -232,7 +245,7 @@ void ScaLBL_StokesModel::Run_Lite(double *ChargeDensity, double *ElectricField){
while (timestep < timestepMax) {
//************************************************************************/
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
ScaLBL_D3Q19_AAodd_StokesMRT(NeighborList, fq, Velocity, ChargeDensity, ElectricField, rlx_setA, rlx_setB, Fx, Fy, Fz,
ScaLBL_D3Q19_AAodd_StokesMRT(NeighborList, fq, Velocity, ChargeDensity, ElectricField, rlx_setA, rlx_setB, Fx, Fy, Fz, Ex, Ey, Ez,
ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
// Set boundary conditions
@ -248,12 +261,12 @@ void ScaLBL_StokesModel::Run_Lite(double *ChargeDensity, double *ElectricField){
ScaLBL_Comm->D3Q19_Reflection_BC_z(fq);
ScaLBL_Comm->D3Q19_Reflection_BC_Z(fq);
}
ScaLBL_D3Q19_AAodd_StokesMRT(NeighborList, fq, Velocity, ChargeDensity, ElectricField, rlx_setA, rlx_setB, Fx, Fy, Fz, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_D3Q19_AAodd_StokesMRT(NeighborList, fq, Velocity, ChargeDensity, ElectricField, rlx_setA, rlx_setB, Fx, Fy, Fz, Ex, Ey, Ez, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
timestep++;
ScaLBL_Comm->SendD3Q19AA(fq); //READ FORM NORMAL
ScaLBL_D3Q19_AAeven_StokesMRT(fq, Velocity, ChargeDensity, ElectricField, rlx_setA, rlx_setB, Fx, Fy, Fz, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_D3Q19_AAeven_StokesMRT(fq, Velocity, ChargeDensity, ElectricField, rlx_setA, rlx_setB, Fx, Fy, Fz, Ex, Ey, Ez, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
// Set boundary conditions
if (BoundaryCondition == 3){
@ -268,16 +281,40 @@ void ScaLBL_StokesModel::Run_Lite(double *ChargeDensity, double *ElectricField){
ScaLBL_Comm->D3Q19_Reflection_BC_z(fq);
ScaLBL_Comm->D3Q19_Reflection_BC_Z(fq);
}
ScaLBL_D3Q19_AAeven_StokesMRT(fq, Velocity, ChargeDensity, ElectricField, rlx_setA, rlx_setB, Fx, Fy, Fz, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_D3Q19_AAeven_StokesMRT(fq, Velocity, ChargeDensity, ElectricField, rlx_setA, rlx_setB, Fx, Fy, Fz, Ex, Ey, Ez, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
//************************************************************************/
}
}
//void ScaLBL_StokesModel::computeVelocity_phys(){
// ScaLBL_D3Q19_Momentum(fq,Velocity, Np);
// ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
//}
void ScaLBL_StokesModel::getVelocity(){
//get velocity in physical unit [m/sec]
ScaLBL_D3Q19_Momentum_Phys(fq, Velocity, h, time_conv, Np);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
DoubleArray PhaseField(Nx,Ny,Nz);
ScaLBL_Comm->RegularLayout(Map,&Velocity[0],PhaseField);
FILE *VELX_FILE;
sprintf(LocalRankFilename,"Velocity_X.%05i.raw",rank);
VELX_FILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,VELX_FILE);
fclose(VELX_FILE);
ScaLBL_Comm->RegularLayout(Map,&Velocity[Np],PhaseField);
FILE *VELY_FILE;
sprintf(LocalRankFilename,"Velocity_Y.%05i.raw",rank);
VELY_FILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,VELY_FILE);
fclose(VELY_FILE);
ScaLBL_Comm->RegularLayout(Map,&Velocity[2*Np],PhaseField);
FILE *VELZ_FILE;
sprintf(LocalRankFilename,"Velocity_Z.%05i.raw",rank);
VELZ_FILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,VELZ_FILE);
fclose(VELZ_FILE);
}
void ScaLBL_StokesModel::Run(){
double rlx_setA=1.0/tau;

2
models/StokesModel.h
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@ -30,12 +30,14 @@ public:
void Run();
void Run_Lite(double *ChargeDensity, double *ElectricField);
void VelocityField();
void getVelocity();
bool Restart,pBC;
int timestep,timestepMax;
int BoundaryCondition;
double tau,mu;
double Fx,Fy,Fz,flux;
double Ex,Ey,Ez;
double din,dout;
double tolerance;
double nu_phys;

4
tests/lbpm_electrokinetic_dfh_simulator.cpp
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@ -89,7 +89,9 @@ int main(int argc, char **argv)
//--------------------------------------------
}
//StokesModel.WriteDebug();
StokesModel.getVelocity();
PoissonSolver.getElectricalPotential();
IonModel.getIonConcentration();
PROFILE_STOP("Main");
PROFILE_SAVE("lbpm_electrokinetic_simulator",1);