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Merge branch 'master' of github.com:JamesEMcClure/LBPM-WIA into merge

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This commit is contained in:
James McClure 2023-01-21 08:48:25 -05:00
commit bf076ca633
18 changed files with 819 additions and 49 deletions
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15
common/Domain.cpp
View File

@ -217,18 +217,25 @@ void Domain::read_swc(const std::string &Filename) {
double z = k*voxel_length + start_z;
double distance;
double s = ((x-xp)*alpha+(y-yp)*beta+(z-zp)*gamma) / (alpha*alpha + beta*beta + gamma*gamma);
if (s > length){
distance = ri - sqrt((x-xi)*(x-xi) + (y-yi)*(y-yi) + (z-zi)*(z-zi));
double s = ((x-xp)*alpha+(y-yp)*beta+(z-zp)*gamma) / (alpha*alpha + beta*beta + gamma*gamma);
double di = ri - sqrt((x-xi)*(x-xi) + (y-yi)*(y-yi) + (z-zi)*(z-zi));
double dp = rp - sqrt((x-xp)*(x-xp) + (y-yp)*(y-yp) + (z-zp)*(z-zp));
if (s > length ){
distance = di;
}
else if (s < 0.0){
distance = rp - sqrt((x-xp)*(x-xp) + (y-yp)*(y-yp) + (z-zp)*(z-zp));
distance = dp;
}
else {
// linear variation for radius
double radius = rp + (ri - rp)*s/length;
distance = radius - sqrt((x-xp-alpha*s)*(x-xp-alpha*s) + (y-yp-beta*s)*(y-yp-beta*s) + (z-zp-gamma*s)*(z-zp-gamma*s));
}
if (distance < di) distance = di;
if (distance < dp) distance = dp;
if ( distance > 0.0 ){
/* label the voxel */
//id[k*Nx*Ny + j*Nx + i] = label;

68
common/Membrane.cpp
View File

@ -667,6 +667,74 @@ int Membrane::Create(DoubleArray &Distance, IntArray &Map){
return mlink;
}
void Membrane::Write(string filename){
int mlink = membraneLinkCount;
std::ofstream ofs (filename, std::ofstream::out);
/* Create local copies of membrane data structures */
double *tmpMembraneCoef; // mass transport coefficient for the membrane
tmpMembraneCoef = new double [2*mlink*sizeof(double)];
ScaLBL_CopyToHost(tmpMembraneCoef, MembraneCoef, 2*mlink*sizeof(double));
int i,j,k;
for (int m=0; m<mlink; m++){
double a1 = tmpMembraneCoef[2*m];
double a2 = tmpMembraneCoef[2*m+1];
int m1 = membraneLinks[2*m]%Np;
int m2 = membraneLinks[2*m+1]%Np;
// map index to global i,j,k
k = m1/(Nx*Ny); j = (m1-Nx*Ny*k)/Nx; i = m1-Nx*Ny*k-Nx*j;
ofs << i << " " << j << " " << k << " "<< a1 ;
k = m2/(Nx*Ny); j = (m2-Nx*Ny*k)/Nx; i = m2-Nx*Ny*k-Nx*j;
ofs << i << " " << j << " " << k << " "<< a2 << endl;
}
ofs.close();
/*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);
*/
delete [] tmpMembraneCoef;
}
void Membrane::Read(string filename){
int mlink = membraneLinkCount;
/* Create local copies of membrane data structures */
double *tmpMembraneCoef; // mass transport coefficient for the membrane
tmpMembraneCoef = new double [2*mlink*sizeof(double)];
FILE *fid = fopen(filename.c_str(), "r");
INSIST(fid != NULL, "Error opening membrane file \n");
//........read the spheres..................
// We will read until a blank like or end-of-file is reached
int count = 0;
int i,j,k;
int ii,jj,kk;
double a1, a2;
while (fscanf(fid, "%i,%i,%i,%lf,%i,%i,%i,%lf,\n", &i, &j, &k, &a1, &ii, &jj, &kk, &a2) == 8){
printf("%i, %i, %i, %lf \n", i,j,k, a2);
count++;
}
if (count != mlink){
printf("WARNING (Membrane::Read): number of file lines does not match number of links \n");
}
fclose(fid);
ScaLBL_CopyToDevice(MembraneCoef, tmpMembraneCoef, 2*mlink*sizeof(double));
/*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);
*/
delete [] tmpMembraneCoef;
}
int Membrane::D3Q7_MapRecv(int Cqx, int Cqy, int Cqz, int *d3q19_recvlist,
int count, int *membraneRecvLabels, DoubleArray &Distance, int *dvcMap){

12
common/Membrane.h
View File

@ -92,6 +92,18 @@ public:
* @param Map - mapping between regular layout and compact layout
*/
int Create(DoubleArray &Distance, IntArray &Map);
/**
* \brief Write membrane data to output file
* @param filename - name of file to save
*/
void Write(string filename);
/**
* \brief Read membrane data from input file
* @param filename - name of file to save
*/
void Read(string filename);
void SendD3Q7AA(double *dist);
void RecvD3Q7AA(double *dist);

23
common/ScaLBL.cpp
View File

@ -2472,6 +2472,29 @@ void ScaLBL_Communicator::D3Q7_Poisson_Potential_BC_Z(int *neighborList, double
}
}
void ScaLBL_Communicator::D3Q19_Poisson_Potential_BC_z(int *neighborList, double *fq, double Vin, int time){
if (kproc == 0) {
if (time%2==0){
ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_z(dvcSendList_z, fq, Vin, sendCount_z, N);
}
else{
ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_z(neighborList, dvcSendList_z, fq, Vin, sendCount_z, N);
}
}
}
void ScaLBL_Communicator::D3Q19_Poisson_Potential_BC_Z(int *neighborList, double *fq, double Vout, int time){
if (kproc == nprocz-1){
if (time%2==0){
ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_Z(dvcSendList_Z, fq, Vout, sendCount_Z, N);
}
else{
ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_Z(neighborList, dvcSendList_Z, fq, Vout, sendCount_Z, N);
}
}
}
void ScaLBL_Communicator::Poisson_D3Q7_BC_z(int *Map, double *Psi, double Vin){
if (kproc == 0) {
ScaLBL_Poisson_D3Q7_BC_z(dvcSendList_z, Map, Psi, Vin, sendCount_z);

8
common/ScaLBL.h
View File

@ -396,6 +396,12 @@ extern "C" void ScaLBL_D3Q19_AAeven_Poisson(int *Map, double *dist,
extern "C" void ScaLBL_D3Q19_Poisson_getElectricField(double *dist, double *ElectricField, double tau, int Np);
extern "C" void ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_Z(int *d_neighborList, int *list, double *dist, double Vin, int count, int Np);
extern "C" void ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_z(int *d_neighborList, int *list, double *dist, double Vin, int count, int Np);
extern "C" void ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_Z(int *list, double *dist, double Vout, int count, int Np);
extern "C" void ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_z(int *list, double *dist, double Vout, int count, 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,double rho0, double den_scale, double h, double time_conv, bool UseSlippingVelBC, int start, int finish, int Np);
@ -806,6 +812,8 @@ public:
double D3Q19_Flux_BC_z(int *neighborList, double *fq, double flux, int time);
void D3Q7_Poisson_Potential_BC_z(int *neighborList, double *fq, double Vin, int time);
void D3Q7_Poisson_Potential_BC_Z(int *neighborList, double *fq, double Vout, int time);
void D3Q19_Poisson_Potential_BC_z(int *neighborList, double *fq, double Vin, int time);
void D3Q19_Poisson_Potential_BC_Z(int *neighborList, double *fq, double Vout, int time);
void Poisson_D3Q7_BC_z(int *Map, double *Psi, double Vin);
void Poisson_D3Q7_BC_Z(int *Map, double *Psi, double Vout);
void D3Q7_Ion_Concentration_BC_z(int *neighborList, double *fq, double Cin, int time);

3
cpu/D3Q7BC.cpp
View File

@ -181,6 +181,7 @@ extern "C" void ScaLBL_D3Q7_AAodd_Poisson_Potential_BC_z(int *d_neighborList,
}
}
extern "C" void ScaLBL_D3Q7_AAodd_Poisson_Potential_BC_Z(int *d_neighborList,
int *list,
double *dist,
@ -213,6 +214,8 @@ extern "C" void ScaLBL_D3Q7_AAodd_Poisson_Potential_BC_Z(int *d_neighborList,
}
}
extern "C" void ScaLBL_Poisson_D3Q7_BC_z(int *list, int *Map, double *Psi,
double Vin, int count) {
int idx, n, nm;

88
cpu/Poisson.cpp
View File

@ -631,6 +631,8 @@ extern "C" void ScaLBL_D3Q19_AAeven_Poisson_ElectricPotential(
}
}
extern "C" void ScaLBL_D3Q19_AAodd_Poisson(int *neighborList, int *Map,
double *dist, double *Den_charge,
double *Psi, double *ElectricField,
@ -915,6 +917,92 @@ extern "C" void ScaLBL_D3Q19_AAeven_Poisson(int *Map, double *dist,
}
}
extern "C" void ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_z(int *list, double *dist, double Vin, int count, int Np) {
double W1 = 1.0/24.0;
double W2 = 1.0/48.0;
int nread, nr5;
for (int idx = 0; idx < count; idx++) {
int n = list[idx];
dist[6 * Np + n] = W1*Vin;
dist[12 * Np + n] = W2*Vin;
dist[13 * Np + n] = W2*Vin;
dist[16 * Np + n] = W2*Vin;
dist[17 * Np + n] = W2*Vin;
}
}
extern "C" void ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_Z(int *list,
double *dist,
double Vout,
int count, int Np) {
double W1 = 1.0/24.0;
double W2 = 1.0/48.0;
for (int idx = 0; idx < count; idx++) {
int n = list[idx];
dist[5 * Np + n] = W1*Vout;
dist[11 * Np + n] = W2*Vout;
dist[14 * Np + n] = W2*Vout;
dist[15 * Np + n] = W2*Vout;
dist[18 * Np + n] = W2*Vout;
}
}
extern "C" void ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_z(int *d_neighborList,
int *list,
double *dist,
double Vin, int count,
int Np) {
double W1 = 1.0/24.0;
double W2 = 1.0/48.0;
int nr5, nr11, nr14, nr15, nr18;
for (int idx = 0; idx < count; idx++) {
int n = list[idx];
// Unknown distributions
nr5 = d_neighborList[n + 4 * Np];
nr11 = d_neighborList[n + 10 * Np];
nr15 = d_neighborList[n + 14 * Np];
nr14 = d_neighborList[n + 13 * Np];
nr18 = d_neighborList[n + 17 * Np];
dist[nr5] = W1*Vin;
dist[nr11] = W2*Vin;
dist[nr15] = W2*Vin;
dist[nr14] = W2*Vin;
dist[nr18] = W2*Vin;
}
}
extern "C" void ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_Z(int *d_neighborList, int *list, double *dist, double Vout, int count, int Np) {
double W1 = 1.0/24.0;
double W2 = 1.0/48.0;
int nr6, nr12, nr13, nr16, nr17;
for (int idx = 0; idx < count; idx++) {
int n = list[idx];
// unknown distributions
nr6 = d_neighborList[n + 5 * Np];
nr12 = d_neighborList[n + 11 * Np];
nr16 = d_neighborList[n + 15 * Np];
nr17 = d_neighborList[n + 16 * Np];
nr13 = d_neighborList[n + 12 * Np];
dist[nr6] = W1*Vout;
dist[nr12] = W2*Vout;
dist[nr16] = W2*Vout;
dist[nr17] = W2*Vout;
dist[nr13] = W2*Vout;
}
}
extern "C" void ScaLBL_D3Q19_Poisson_Init(int *Map, double *dist, double *Psi,
int start, int finish, int Np) {
int n;

148
cuda/Poisson.cu
View File

@ -3,7 +3,7 @@
//#include <cuda_profiler_api.h>
#define NBLOCKS 1024
#define NTHREADS 256
#define NTHREADS 512
__global__ void dvc_ScaLBL_D3Q7_AAodd_Poisson_ElectricPotential(int *neighborList,int *Map, double *dist, double *Psi, int start, int finish, int Np){
int n;
@ -328,7 +328,7 @@ __global__ void dvc_ScaLBL_D3Q19_AAodd_Poisson(int *neighborList, int *Map,
f16, f17, f18;
int nr1, nr2, nr3, nr4, nr5, nr6, nr7, nr8, nr9, nr10, nr11, nr12, nr13,
nr14, nr15, nr16, nr17, nr18;
double error,sum_q;
double sum_q;
double rlx = 1.0 / tau;
int idx;
@ -421,7 +421,7 @@ __global__ void dvc_ScaLBL_D3Q19_AAodd_Poisson(int *neighborList, int *Map,
f18 = dist[nr18];
sum_q = f1+f2+f3+f4+f5+f6+f7+f8+f9+f10+f11+f12+f13+f14+f15+f16+f17+f18;
error = 8.0*(sum_q - f0) + rho_e;
//error = 8.0*(sum_q - f0) + rho_e;
psi = 2.0*(f0*(1.0 - rlx) + rlx*(sum_q + 0.125*rho_e));
@ -545,6 +545,12 @@ __global__ void dvc_ScaLBL_D3Q19_AAeven_Poisson(int *Map, double *dist,
f17 = dist[18 * Np + n];
f18 = dist[17 * Np + n];
/* Ex = (f1 - f2) * rlx *
4.0; //NOTE the unit of electric field here is V/lu
Ey = (f3 - f4) * rlx *
4.0; //factor 4.0 is D3Q7 lattice squared speed of sound
Ez = (f5 - f6) * rlx * 4.0;
*/
Ex = (f1 - f2 + 0.5*(f7 - f8 + f9 - f10 + f11 - f12 + f13 - f14))*4.0; //NOTE the unit of electric field here is V/lu
Ey = (f3 - f4 + 0.5*(f7 - f8 - f9 + f10 + f15 - f16 + f17 - f18))*4.0;
Ez = (f5 - f6 + 0.5*(f11 - f12 - f13 + f14 + f15 - f16 - f17 + f18))*4.0;
@ -554,12 +560,14 @@ __global__ void dvc_ScaLBL_D3Q19_AAeven_Poisson(int *Map, double *dist,
sum_q = f1+f2+f3+f4+f5+f6+f7+f8+f9+f10+f11+f12+f13+f14+f15+f16+f17+f18;
error = 8.0*(sum_q - f0) + rho_e;
Error[n] = error;
psi = 2.0*(f0*(1.0 - rlx) + rlx*(sum_q + 0.125*rho_e));
idx = Map[n];
Psi[idx] = psi;
idx = Map[n];
Psi[idx] = psi;
// q = 0
dist[n] = W0*psi;//
@ -593,7 +601,6 @@ __global__ void dvc_ScaLBL_D3Q19_AAeven_Poisson(int *Map, double *dist,
dist[16 * Np + n] = W2*psi;//f16 * (1.0 - rlx) +W2* (rlx * psi) - (1.0-0.5*rlx)*0.02777777777777778*rho_e;
dist[17 * Np + n] = W2*psi;//f17 * (1.0 - rlx) +W2* (rlx * psi) - (1.0-0.5*rlx)*0.02777777777777778*rho_e;
dist[18 * Np + n] = W2*psi;//f18 * (1.0 - rlx) +W2* (rlx * psi) - (1.0-0.5*rlx)*0.02777777777777778*rho_e;
//........................................................................
}
}
@ -635,6 +642,131 @@ __global__ void dvc_ScaLBL_D3Q19_Poisson_Init(int *Map, double *dist, double *P
}
}
__global__ void dvc_ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_z(int *list, double *dist, double Vin, int count, int Np) {
double W1 = 1.0/24.0;
double W2 = 1.0/48.0;
int idx = blockIdx.x*blockDim.x + threadIdx.x;
if (idx < count){
int n = list[idx];
dist[6 * Np + n] = W1*Vin;
dist[12 * Np + n] = W2*Vin;
dist[13 * Np + n] = W2*Vin;
dist[16 * Np + n] = W2*Vin;
dist[17 * Np + n] = W2*Vin;
}
}
__global__ void dvc_ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_Z(int *list, double *dist, double Vout, int count, int Np) {
double W1 = 1.0/24.0;
double W2 = 1.0/48.0;
int idx = blockIdx.x*blockDim.x + threadIdx.x;
if (idx < count){
int n = list[idx];
dist[5 * Np + n] = W1*Vout;
dist[11 * Np + n] = W2*Vout;
dist[14 * Np + n] = W2*Vout;
dist[15 * Np + n] = W2*Vout;
dist[18 * Np + n] = W2*Vout;
}
}
__global__ void dvc_ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_z(int *d_neighborList, int *list, double *dist, double Vin, int count, int Np) {
double W1 = 1.0/24.0;
double W2 = 1.0/48.0;
int nr5, nr11, nr14, nr15, nr18;
int idx = blockIdx.x*blockDim.x + threadIdx.x;
if (idx < count){
int n = list[idx];
// Unknown distributions
nr5 = d_neighborList[n + 4 * Np];
nr11 = d_neighborList[n + 10 * Np];
nr15 = d_neighborList[n + 14 * Np];
nr14 = d_neighborList[n + 13 * Np];
nr18 = d_neighborList[n + 17 * Np];
dist[nr5] = W1*Vin;
dist[nr11] = W2*Vin;
dist[nr15] = W2*Vin;
dist[nr14] = W2*Vin;
dist[nr18] = W2*Vin;
}
}
__global__ void dvc_ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_Z(int *d_neighborList, int *list, double *dist, double Vout, int count, int Np) {
double W1 = 1.0/24.0;
double W2 = 1.0/48.0;
int nr6, nr12, nr13, nr16, nr17;
int idx = blockIdx.x*blockDim.x + threadIdx.x;
if (idx < count){
int n = list[idx];
// unknown distributions
nr6 = d_neighborList[n + 5 * Np];
nr12 = d_neighborList[n + 11 * Np];
nr16 = d_neighborList[n + 15 * Np];
nr17 = d_neighborList[n + 16 * Np];
nr13 = d_neighborList[n + 12 * Np];
dist[nr6] = W1*Vout;
dist[nr12] = W2*Vout;
dist[nr16] = W2*Vout;
dist[nr17] = W2*Vout;
dist[nr13] = W2*Vout;
}
}
/* wrapper functions to launch kernels */
extern "C" void ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_z(int *list, double *dist, double Vin, int count, int Np){
int GRID = count / 512 + 1;
dvc_ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_z<<<GRID,512>>>(list, dist, Vin, count, Np);
cudaError_t err = cudaGetLastError();
if (cudaSuccess != err){
printf("CUDA error in ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_z (kernel): %s \n",cudaGetErrorString(err));
}
}
//
extern "C" void ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_Z(int *list, double *dist, double Vout, int count, int Np){
int GRID = count / 512 + 1;
dvc_ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_Z<<<GRID,512>>>(list, dist, Vout, count, Np);
cudaError_t err = cudaGetLastError();
if (cudaSuccess != err){
printf("CUDA error in ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_Z (kernel): %s \n",cudaGetErrorString(err));
}
}
extern "C" void ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_z(int *d_neighborList, int *list, double *dist, double Vin, int count,int Np) {
int GRID = count / 512 + 1;
dvc_ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_z<<<GRID,512>>>(d_neighborList, list, dist, Vin, count, Np);
cudaError_t err = cudaGetLastError();
if (cudaSuccess != err){
printf("CUDA error in ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_z (kernel): %s \n",cudaGetErrorString(err));
}
}
//
extern "C" void ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_Z(int *d_neighborList, int *list, double *dist, double Vout, int count, int Np) {
int GRID = count / 512 + 1;
dvc_ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_Z<<<GRID,512>>>(d_neighborList, list, dist, Vout, count, Np);
cudaError_t err = cudaGetLastError();
if (cudaSuccess != err){
printf("CUDA error in ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_Z (kernel): %s \n",cudaGetErrorString(err));
}
}
extern "C" void ScaLBL_D3Q19_AAodd_Poisson(int *neighborList, int *Map,
double *dist, double *Den_charge,
double *Psi, double *ElectricField,

40
docs/source/userGuide/models/color/index.rst
View File

@ -176,42 +176,70 @@ The non-zero equilibrium moments are defined as
:nowrap:
$$
m_1^{eq} = (j_x^2+j_y^2+j_z^2) - \alpha |\textbf{C}|, \\
m_1^{eq} = 19\frac{ j_x^2+j_y^2+j_z^2}{\rho_0} - 11\rho - 19 \alpha |\textbf{C}|, \\
$$
.. math::
:nowrap:
$$
m_2^{eq} = 3\rho - \frac{11( j_x^2+j_y^2+j_z^2)}{2\rho_0}, \\
$$
.. math::
:nowrap:
$$
m_4^{eq} = -\frac{2 j_x}{3}, \\
$$
.. math::
:nowrap:
$$
m_6^{eq} = -\frac{2 j_y}{3}, \\
$$
.. math::
:nowrap:
$$
m_8^{eq} = -\frac{2 j_z}{3}, \\
$$
.. math::
:nowrap:
$$
m_9^{eq} = (2j_x^2-j_y^2-j_z^2)+ \alpha \frac{|\textbf{C}|}{2}(2n_x^2-n_y^2-n_z^2), \\
m_9^{eq} = \frac{2j_x^2-j_y^2-j_z^2}{\rho_0}+ \alpha \frac{|\textbf{C}|}{2}(2n_x^2-n_y^2-n_z^2), \\
$$
.. math::
:nowrap:
$$
m_{11}^{eq} = (j_y^2-j_z^2) + \alpha \frac{|\textbf{C}|}{2}(n_y^2-n_z^2), \\
m_{11}^{eq} = \frac{j_y^2-j_z^2}{\rho_0} + \alpha \frac{|\textbf{C}|}{2}(n_y^2-n_z^2), \\
$$
.. math::
:nowrap:
$$
m_{13}^{eq} = j_x j_y + \alpha \frac{|\textbf{C}|}{2} n_x n_y\;, \\
m_{13}^{eq} = \frac{j_x j_y}{\rho_0} + \alpha \frac{|\textbf{C}|}{2} n_x n_y\;, \\
$$
.. math::
:nowrap:
$$
m_{14}^{eq} = j_y j_z + \alpha \frac{|\textbf{C}|}{2} n_y n_z\;, \\
m_{14}^{eq} = \frac{j_y j_z}{\rho_0} + \alpha \frac{|\textbf{C}|}{2} n_y n_z\;, \\
$$
.. math::
:nowrap:
$$
m_{15}^{eq} = j_x j_z + \alpha \frac{|\textbf{C}|}{2} n_x n_z\;,
m_{15}^{eq} = \frac{j_x j_z}{\rho_0} + \alpha \frac{|\textbf{C}|}{2} n_x n_z\;.
$$
where the color gradient is determined from the phase indicator field

41
docs/source/userGuide/models/greyscaleColor/greyscaleColor.rst
View File

@ -241,46 +241,75 @@ The relaxation parameters are determined from the relaxation time:
The non-zero equilibrium moments are defined as
.. math::
:nowrap:
$$
m_1^{eq} = (j_x^2+j_y^2+j_z^2) - \alpha |\textbf{C}|, \\
m_1^{eq} = 19\frac{ j_x^2+j_y^2+j_z^2}{\rho_0} - 11\rho - 19 \alpha |\textbf{C}|, \\
$$
.. math::
:nowrap:
$$
m_2^{eq} = 3\rho - \frac{11( j_x^2+j_y^2+j_z^2)}{2\rho_0}, \\
$$
.. math::
:nowrap:
$$
m_4^{eq} = -\frac{2 j_x}{3}, \\
$$
.. math::
:nowrap:
$$
m_6^{eq} = -\frac{2 j_y}{3}, \\
$$
.. math::
:nowrap:
$$
m_8^{eq} = -\frac{2 j_z}{3}, \\
$$
.. math::
:nowrap:
$$
m_9^{eq} = (2j_x^2-j_y^2-j_z^2)+ \alpha \frac{|\textbf{C}|}{2}(2n_x^2-n_y^2-n_z^2), \\
m_9^{eq} = \frac{2j_x^2-j_y^2-j_z^2}{\rho_0}+ \alpha \frac{|\textbf{C}|}{2}(2n_x^2-n_y^2-n_z^2), \\
$$
.. math::
:nowrap:
$$
m_{11}^{eq} = (j_y^2-j_z^2) + \alpha \frac{|\textbf{C}|}{2}(n_y^2-n_z^2), \\
m_{11}^{eq} = \frac{j_y^2-j_z^2}{\rho_0} + \alpha \frac{|\textbf{C}|}{2}(n_y^2-n_z^2), \\
$$
.. math::
:nowrap:
$$
m_{13}^{eq} = j_x j_y + \alpha \frac{|\textbf{C}|}{2} n_x n_y\;, \\
m_{13}^{eq} = \frac{j_x j_y}{\rho_0} + \alpha \frac{|\textbf{C}|}{2} n_x n_y\;, \\
$$
.. math::
:nowrap:
$$
m_{14}^{eq} = j_y j_z + \alpha \frac{|\textbf{C}|}{2} n_y n_z\;, \\
m_{14}^{eq} = \frac{j_y j_z}{\rho_0} + \alpha \frac{|\textbf{C}|}{2} n_y n_z\;, \\
$$
.. math::
:nowrap:
$$
m_{15}^{eq} = j_x j_z + \alpha \frac{|\textbf{C}|}{2} n_x n_z\;,
m_{15}^{eq} = \frac{j_x j_z}{\rho_0} + \alpha \frac{|\textbf{C}|}{2} n_x n_z\;.
$$
where the color gradient is determined from the phase indicator field

147
hip/Poisson.hip
View File

@ -301,7 +301,7 @@ __global__ void dvc_ScaLBL_D3Q19_AAodd_Poisson(int *neighborList, int *Map,
//........Get 1-D index for this thread....................
n = S*blockIdx.x*blockDim.x + s*blockDim.x + threadIdx.x + start;
if (n<finish) {
//Load data
//Load data
//When Helmholtz-Smoluchowski slipping velocity BC is used, the bulk fluid is considered as electroneutral
//and thus the net space charge density is zero.
rho_e = (UseSlippingVelBC==1) ? 0.0 : Den_charge[n] / epsilon_LB;
@ -451,7 +451,8 @@ __global__ void dvc_ScaLBL_D3Q19_AAodd_Poisson(int *neighborList, int *Map,
dist[nr18] = W2*psi; //f17 * (1.0 - rlx) +W2* (rlx * psi) - (1.0-0.5*rlx)*0.02777777777777778*rho_e;
// q = 18
dist[nr17] = W2*psi;
dist[nr17] = W2*psi; //f18 * (1.0 - rlx) +W2* (rlx * psi) - (1.0-0.5*rlx)*0.02777777777777778*rho_e;
}
}
}
@ -479,7 +480,7 @@ __global__ void dvc_ScaLBL_D3Q19_AAeven_Poisson(int *Map, double *dist,
//........Get 1-D index for this thread....................
n = S*blockIdx.x*blockDim.x + s*blockDim.x + threadIdx.x + start;
if (n<finish) {
//Load data
//Load data
//When Helmholtz-Smoluchowski slipping velocity BC is used, the bulk fluid is considered as electroneutral
//and thus the net space charge density is zero.
rho_e = (UseSlippingVelBC==1) ? 0.0 : Den_charge[n] / epsilon_LB;
@ -505,6 +506,12 @@ __global__ void dvc_ScaLBL_D3Q19_AAeven_Poisson(int *Map, double *dist,
f17 = dist[18 * Np + n];
f18 = dist[17 * Np + n];
/* Ex = (f1 - f2) * rlx *
4.0; //NOTE the unit of electric field here is V/lu
Ey = (f3 - f4) * rlx *
4.0; //factor 4.0 is D3Q7 lattice squared speed of sound
Ez = (f5 - f6) * rlx * 4.0;
*/
Ex = (f1 - f2 + 0.5*(f7 - f8 + f9 - f10 + f11 - f12 + f13 - f14))*4.0; //NOTE the unit of electric field here is V/lu
Ey = (f3 - f4 + 0.5*(f7 - f8 - f9 + f10 + f15 - f16 + f17 - f18))*4.0;
Ez = (f5 - f6 + 0.5*(f11 - f12 - f13 + f14 + f15 - f16 - f17 + f18))*4.0;
@ -514,12 +521,14 @@ __global__ void dvc_ScaLBL_D3Q19_AAeven_Poisson(int *Map, double *dist,
sum_q = f1+f2+f3+f4+f5+f6+f7+f8+f9+f10+f11+f12+f13+f14+f15+f16+f17+f18;
error = 8.0*(sum_q - f0) + rho_e;
Error[n] = error;
psi = 2.0*(f0*(1.0 - rlx) + rlx*(sum_q + 0.125*rho_e));
idx = Map[n];
Psi[idx] = psi;
idx = Map[n];
Psi[idx] = psi;
// q = 0
dist[n] = W0*psi;//
@ -553,7 +562,6 @@ __global__ void dvc_ScaLBL_D3Q19_AAeven_Poisson(int *Map, double *dist,
dist[16 * Np + n] = W2*psi;//f16 * (1.0 - rlx) +W2* (rlx * psi) - (1.0-0.5*rlx)*0.02777777777777778*rho_e;
dist[17 * Np + n] = W2*psi;//f17 * (1.0 - rlx) +W2* (rlx * psi) - (1.0-0.5*rlx)*0.02777777777777778*rho_e;
dist[18 * Np + n] = W2*psi;//f18 * (1.0 - rlx) +W2* (rlx * psi) - (1.0-0.5*rlx)*0.02777777777777778*rho_e;
//........................................................................
}
}
@ -594,6 +602,129 @@ __global__ void dvc_ScaLBL_D3Q19_Poisson_Init(int *Map, double *dist, double *P
}
}
}
__global__ void dvc_ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_z(int *list, double *dist, double Vin, int count, int Np) {
double W1 = 1.0/24.0;
double W2 = 1.0/48.0;
int idx = blockIdx.x*blockDim.x + threadIdx.x;
if (idx < count){
int n = list[idx];
dist[6 * Np + n] = W1*Vin;
dist[12 * Np + n] = W2*Vin;
dist[13 * Np + n] = W2*Vin;
dist[16 * Np + n] = W2*Vin;
dist[17 * Np + n] = W2*Vin;
}
}
__global__ void dvc_ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_Z(int *list, double *dist, double Vout, int count, int Np) {
double W1 = 1.0/24.0;
double W2 = 1.0/48.0;
int idx = blockIdx.x*blockDim.x + threadIdx.x;
if (idx < count){
int n = list[idx];
dist[5 * Np + n] = W1*Vout;
dist[11 * Np + n] = W2*Vout;
dist[14 * Np + n] = W2*Vout;
dist[15 * Np + n] = W2*Vout;
dist[18 * Np + n] = W2*Vout;
}
}
__global__ void dvc_ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_z(int *d_neighborList, int *list, double *dist, double Vin, int count, int Np) {
double W1 = 1.0/24.0;
double W2 = 1.0/48.0;
int nr5, nr11, nr14, nr15, nr18;
int idx = blockIdx.x*blockDim.x + threadIdx.x;
if (idx < count){
int n = list[idx];
// Unknown distributions
nr5 = d_neighborList[n + 4 * Np];
nr11 = d_neighborList[n + 10 * Np];
nr15 = d_neighborList[n + 14 * Np];
nr14 = d_neighborList[n + 13 * Np];
nr18 = d_neighborList[n + 17 * Np];
dist[nr5] = W1*Vin;
dist[nr11] = W2*Vin;
dist[nr15] = W2*Vin;
dist[nr14] = W2*Vin;
dist[nr18] = W2*Vin;
}
}
__global__ void dvc_ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_Z(int *d_neighborList, int *list, double *dist, double Vout, int count, int Np) {
double W1 = 1.0/24.0;
double W2 = 1.0/48.0;
int nr6, nr12, nr13, nr16, nr17;
int idx = blockIdx.x*blockDim.x + threadIdx.x;
if (idx < count){
int n = list[idx];
// unknown distributions
nr6 = d_neighborList[n + 5 * Np];
nr12 = d_neighborList[n + 11 * Np];
nr16 = d_neighborList[n + 15 * Np];
nr17 = d_neighborList[n + 16 * Np];
nr13 = d_neighborList[n + 12 * Np];
dist[nr6] = W1*Vout;
dist[nr12] = W2*Vout;
dist[nr16] = W2*Vout;
dist[nr17] = W2*Vout;
dist[nr13] = W2*Vout;
}
}
/* wrapper functions to launch kernels */
extern "C" void ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_z(int *list, double *dist, double Vin, int count, int Np){
int GRID = count / 512 + 1;
dvc_ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_z<<<GRID,512>>>(list, dist, Vin, count, Np);
cudaError_t err = cudaGetLastError();
if (cudaSuccess != err){
printf("Hip error in ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_z (kernel): %s \n",cudaGetErrorString(err));
}
}
//
extern "C" void ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_Z(int *list, double *dist, double Vout, int count, int Np){
int GRID = count / 512 + 1;
dvc_ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_Z<<<GRID,512>>>(list, dist, Vout, count, Np);
cudaError_t err = cudaGetLastError();
if (cudaSuccess != err){
printf("Hip error in ScaLBL_D3Q19_AAeven_Poisson_Potential_BC_Z (kernel): %s \n",cudaGetErrorString(err));
}
}
extern "C" void ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_z(int *d_neighborList, int *list, double *dist, double Vin, int count,int Np) {
int GRID = count / 512 + 1;
dvc_ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_z<<<GRID,512>>>(d_neighborList, list, dist, Vin, count, Np);
cudaError_t err = cudaGetLastError();
if (cudaSuccess != err){
printf("Hip error in ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_z (kernel): %s \n",cudaGetErrorString(err));
}
}
//
extern "C" void ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_Z(int *d_neighborList, int *list, double *dist, double Vout, int count, int Np) {
int GRID = count / 512 + 1;
dvc_ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_Z<<<GRID,512>>>(d_neighborList, list, dist, Vout, count, Np);
cudaError_t err = cudaGetLastError();
if (cudaSuccess != err){
printf("Hip error in ScaLBL_D3Q19_AAodd_Poisson_Potential_BC_Z (kernel): %s \n",cudaGetErrorString(err));
}
}
extern "C" void ScaLBL_D3Q19_AAodd_Poisson(int *neighborList, int *Map,
double *dist, double *Den_charge,

4
models/IonModel.cpp
View File

@ -300,7 +300,8 @@ void ScaLBL_IonModel::ReadParams(string filename, vector<int> &num_iter) {
void ScaLBL_IonModel::ReadParams(string filename) {
//NOTE: the maximum iteration timesteps for ions are left unspecified
// it relies on the multiphys controller to compute the max timestep
USE_MEMBRANE = true;
USE_MEMBRANE = false;
Restart = false;
// read the input database
db = std::make_shared<Database>(filename);
domain_db = db->getDatabase("Domain");
@ -1549,7 +1550,6 @@ void ScaLBL_IonModel::RunMembrane(double *Velocity, double *ElectricField, doubl
IonMembrane->IonTransport(&fq[ic * Np * 7],&Ci[ic * Np]);
/* if (BoundaryConditionSolid == 1) {
//TODO IonSolid may also be species-dependent
ScaLBL_Comm->SolidDirichletD3Q7(&fq[ic * Np * 7], IonSolid);

254
models/PoissonSolver.cpp
View File

@ -86,7 +86,7 @@ void ScaLBL_Poisson::ReadParams(string filename){
}
//'tolerance_method' can be {"MSE","MSE_max"}
tolerance_method = electric_db->getWithDefault<std::string>( "tolerance_method", "MSE" );
lattice_scheme = electric_db->getWithDefault<std::string>( "lattice_scheme", "D3Q7" );
lattice_scheme = electric_db->getWithDefault<std::string>( "lattice_scheme", "D3Q19" );
if (electric_db->keyExists( "epsilonR" )){
epsilonR = electric_db->getScalar<double>( "epsilonR" );
}
@ -726,13 +726,13 @@ void ScaLBL_Poisson::Run(double *ChargeDensity, bool UseSlippingVelBC, int times
// *************ODD TIMESTEP*************//
timestep++;
SolveElectricPotentialAAodd(timestep_from_Study);//update electric potential
SolvePoissonAAodd(ChargeDensity, UseSlippingVelBC);//perform collision
SolvePoissonAAodd(ChargeDensity, UseSlippingVelBC,timestep);//perform collision
ScaLBL_Comm->Barrier(); comm.barrier();
// *************EVEN TIMESTEP*************//
timestep++;
SolveElectricPotentialAAeven(timestep_from_Study);//update electric potential
SolvePoissonAAeven(ChargeDensity, UseSlippingVelBC);//perform collision
SolvePoissonAAeven(ChargeDensity, UseSlippingVelBC,timestep);//perform collision
ScaLBL_Comm->Barrier(); comm.barrier();
//************************************************************************/
@ -797,18 +797,17 @@ void ScaLBL_Poisson::Run(double *ChargeDensity, bool UseSlippingVelBC, int times
//************************************************************************/
// *************ODD TIMESTEP*************//
timestep++;
//SolveElectricPotentialAAodd(timestep_from_Study,ChargeDensity, UseSlippingVelBC);//update electric potential
SolvePoissonAAodd(ChargeDensity, UseSlippingVelBC);//perform collision
//SolveElectricPotentialAAodd(timestep_from_Study);//,ChargeDensity, UseSlippingVelBC);//update electric potential
SolvePoissonAAodd(ChargeDensity, UseSlippingVelBC,timestep);//perform collision
ScaLBL_Comm->Barrier(); comm.barrier();
// *************EVEN TIMESTEP*************//
timestep++;
//SolveElectricPotentialAAeven(timestep_from_Study,ChargeDensity, UseSlippingVelBC);//update electric potential
SolvePoissonAAeven(ChargeDensity, UseSlippingVelBC);//perform collision
//SolveElectricPotentialAAeven(timestep_from_Study);//,ChargeDensity, UseSlippingVelBC);//update electric potential
SolvePoissonAAeven(ChargeDensity, UseSlippingVelBC,timestep);//perform collision
ScaLBL_Comm->Barrier(); comm.barrier();
//************************************************************************/
// Check convergence of steady-state solution
if (timestep==2){
//save electric potential for convergence check
@ -863,6 +862,145 @@ void ScaLBL_Poisson::Run(double *ChargeDensity, bool UseSlippingVelBC, int times
}
}
void ScaLBL_Poisson::Run(double *ChargeDensity, DoubleArray MembraneDistance, bool UseSlippingVelBC, int timestep_from_Study){
double error = 1.0;
double threshold = 10000000.0;
bool SET_THRESHOLD = false;
if (electric_db->keyExists( "rescale_at_distance" )){
SET_THRESHOLD = true;
threshold = electric_db->getScalar<double>( "rescale_at_distance" );
}
if (BoundaryConditionInlet > 0) SET_THRESHOLD = false;
if (BoundaryConditionOutlet > 0) SET_THRESHOLD = false;
double *host_Error;
host_Error = new double [Np];
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();
// *************EVEN TIMESTEP*************//
timestep++;
//SolveElectricPotentialAAeven(timestep_from_Study,ChargeDensity, UseSlippingVelBC);//update electric potential
SolvePoissonAAeven(ChargeDensity, UseSlippingVelBC,timestep);//perform collision
ScaLBL_Comm->Barrier(); comm.barrier();
//************************************************************************/
// Check convergence of steady-state solution
if (timestep==2){
//save electric potential for convergence check
}
if (timestep%analysis_interval==0){
/* get the elecric potential */
ScaLBL_CopyToHost(Psi_host.data(),Psi,sizeof(double)*Nx*Ny*Nz);
if (rank==0) printf(" ... getting Poisson solver error \n");
double err = 0.0;
double max_error = 0.0;
ScaLBL_CopyToHost(host_Error,ResidualError,sizeof(double)*Np);
for (int idx=0; idx<Np; idx++){
err = host_Error[idx]*host_Error[idx];
if (err > max_error ){
max_error = err;
}
}
error=Dm->Comm.maxReduce(max_error);
if (error > tolerance && SET_THRESHOLD){
/* don't use this with an external BC */
// cpompute the far-field electric potential
double inside_local = 0.0;
double outside_local = 0.0;
double inside_count_local = 0.0;
double outside_count_local = 0.0;
/* global values */
double inside_global = 0.0;
double outside_global = 0.0;
double inside_count_global = 0.0;
double outside_count_global = 0.0;
for (int k=1; k<Nz; k++){
for (int j=1; j<Ny; j++){
for (int i=1; i<Nx; i++){
int n = k*Nx*Ny + j*Nx + i;
double distance = MembraneDistance(i,j,k);
if (distance > threshold && distance < (threshold + 1.0)){
outside_count_local += 1.0;
outside_local += Psi_host(n);
}
else if (distance < (-1.0)*threshold && distance > (-1.0)*(threshold + 1.0)){
inside_count_local += 1.0;
inside_local += Psi_host(n);
}
}
}
}
inside_count_global = Dm->Comm.sumReduce(inside_count_local);
outside_count_global = Dm->Comm.sumReduce(outside_count_local);
outside_global = Dm->Comm.sumReduce(outside_local);
inside_global = Dm->Comm.sumReduce(inside_local);
outside_global /= outside_count_global;
inside_global /= inside_count_global;
if (rank==0) printf(" Rescaling far-field electric potential to value (outside): %f \n",outside_global);
if (rank==0) printf(" Rescaling far-field electric potential to value (inside): %f \n",inside_global);
// rescale the far-field electric potential
for (int k=1; k<Nz; k++){
for (int j=1; j<Ny; j++){
for (int i=1; i<Nx; i++){
int n = k*Nx*Ny + j*Nx + i;
double distance = MembraneDistance(i,j,k);
if ( distance > (threshold + 1.0)){
Psi_host(n) = outside_global;
}
else if ( distance < (-1.0)*(threshold + 1.0)){
Psi_host(n) = inside_global;
}
}
}
}
ScaLBL_CopyToDevice(Psi,Psi_host.data(),sizeof(double)*Nx*Ny*Nz);
}
/* compute the eletric field */
//ScaLBL_D3Q19_Poisson_getElectricField(fq, ElectricField, tau, Np);
}
}
if (rank == 0)
printf("---------------------------------------------------------------"
"----\n");
// Compute the walltime per timestep
auto t2 = std::chrono::system_clock::now();
double cputime = std::chrono::duration<double>(t2 - t1).count() / timestep;
// Performance obtained from each node
double MLUPS = double(Np) / cputime / 1000000;
if (rank == 0)
printf("********************************************************\n");
if (rank == 0)
printf("CPU time = %f \n", cputime);
if (rank == 0)
printf("Lattice update rate (per core)= %f MLUPS \n", MLUPS);
MLUPS *= nprocs;
if (rank == 0)
printf("Lattice update rate (total)= %f MLUPS \n", MLUPS);
if (rank == 0)
printf("********************************************************\n");
delete [] host_Error;
//************************************************************************/
if(WriteLog==true){
getConvergenceLog(timestep,error);
}
}
void ScaLBL_Poisson::getConvergenceLog(int timestep,double error){
if ( rank == 0 ) {
fprintf(TIMELOG,"%i %.5g\n",timestep,error);
@ -1008,7 +1146,7 @@ void ScaLBL_Poisson::SolveElectricPotentialAAeven(int timestep_from_Study){
}
}
void ScaLBL_Poisson::SolvePoissonAAodd(double *ChargeDensity, bool UseSlippingVelBC){
void ScaLBL_Poisson::SolvePoissonAAodd(double *ChargeDensity, bool UseSlippingVelBC, int timestep){
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);
@ -1029,6 +1167,30 @@ void ScaLBL_Poisson::SolvePoissonAAodd(double *ChargeDensity, bool UseSlippingVe
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_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
// Set boundary conditions
if (BoundaryConditionInlet > 0){
switch (BoundaryConditionInlet){
case 1:
ScaLBL_Comm->D3Q7_Poisson_Potential_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);
break;
}
}
if (BoundaryConditionOutlet > 0){
switch (BoundaryConditionOutlet){
case 1:
ScaLBL_Comm->D3Q7_Poisson_Potential_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);
break;
}
}
ScaLBL_D3Q19_AAodd_Poisson(NeighborList, dvcMap, fq, ChargeDensity, Psi, ElectricField, tau, epsilon_LB, UseSlippingVelBC, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_Comm->Barrier();
@ -1038,7 +1200,7 @@ void ScaLBL_Poisson::SolvePoissonAAodd(double *ChargeDensity, bool UseSlippingVe
}
}
void ScaLBL_Poisson::SolvePoissonAAeven(double *ChargeDensity, bool UseSlippingVelBC){
void ScaLBL_Poisson::SolvePoissonAAeven(double *ChargeDensity, bool UseSlippingVelBC, int timestep){
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);
@ -1056,6 +1218,31 @@ void ScaLBL_Poisson::SolvePoissonAAeven(double *ChargeDensity, bool UseSlippingV
ScaLBL_D3Q19_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, ResidualError, tau, 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){
switch (BoundaryConditionInlet){
case 1:
ScaLBL_Comm->D3Q7_Poisson_Potential_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);
break;
}
}
if (BoundaryConditionOutlet > 0){
switch (BoundaryConditionOutlet){
case 1:
ScaLBL_Comm->D3Q7_Poisson_Potential_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);
break;
}
}
ScaLBL_D3Q19_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, ResidualError, tau, epsilon_LB, UseSlippingVelBC, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_Comm->Barrier();
@ -1182,6 +1369,53 @@ void ScaLBL_Poisson::ElectricField_LB_to_Phys(DoubleArray &Efield_reg){
}
}
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);
IO::initialize("",format,"false");
// Create the MeshDataStruct
visData.resize(1);
visData[0].meshName = "domain";
visData[0].mesh =
std::make_shared<IO::DomainMesh>(Dm->rank_info, Dm->Nx - 2, Dm->Ny - 2,
Dm->Nz - 2, Dm->Lx, Dm->Ly, Dm->Lz);
//electric potential
auto ElectricPotentialVar = std::make_shared<IO::Variable>();
//--------------------------------------------------------------------------------------------------------------------
//-------------------------------------Create Names for Variables------------------------------------------------------
if (vis_db->getWithDefault<bool>("save_electric_potential", true)) {
ElectricPotentialVar->name = "ElectricPotential";
ElectricPotentialVar->type = IO::VariableType::VolumeVariable;
ElectricPotentialVar->dim = 1;
ElectricPotentialVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
visData[0].vars.push_back(ElectricPotentialVar);
}
//--------------------------------------------------------------------------------------------------------------------
//------------------------------------Save All Variables--------------------------------------------------------------
if (vis_db->getWithDefault<bool>("save_electric_potential", true)) {
ASSERT(visData[0].vars[0]->name == "ElectricPotential");
getElectricPotential(ElectricalPotential);
Array<double> &ElectricPotentialData = visData[0].vars[0]->data;
fillData.copy(ElectricalPotential, ElectricPotentialData);
}
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,

8
models/PoissonSolver.h
View File

@ -22,6 +22,7 @@
#ifndef ScaLBL_POISSON_INC
#define ScaLBL_POISSON_INC
class ScaLBL_Poisson {
public:
ScaLBL_Poisson(int RANK, int NP, const Utilities::MPI &COMM);
@ -35,12 +36,15 @@ public:
void Create();
void Initialize(double time_conv_from_Study);
void Run(double *ChargeDensity, bool UseSlippingVelBC, int timestep_from_Study);
void Run(double *ChargeDensity, DoubleArray MembraneDistance,
bool UseSlippingVelBC, int timestep_from_Study);
void getElectricPotential(DoubleArray &ReturnValues);
void getElectricPotential_debug(int timestep);
void getElectricField(DoubleArray &Values_x, DoubleArray &Values_y,
DoubleArray &Values_z);
void getElectricField_debug(int timestep);
void Checkpoint();
void WriteVis( int timestep);
void DummyChargeDensity(); //for debugging
@ -114,8 +118,8 @@ private:
void SolveElectricPotentialAAeven(int timestep_from_Study);
void SolveElectricPotentialAAodd(int timestep_from_Study);
//void SolveElectricField();
void SolvePoissonAAodd(double *ChargeDensity, bool UseSlippingVelBC);
void SolvePoissonAAeven(double *ChargeDensity, bool UseSlippingVelBC);
void SolvePoissonAAodd(double *ChargeDensity, bool UseSlippingVelBC, int timestep);
void SolvePoissonAAeven(double *ChargeDensity, bool UseSlippingVelBC, int timestep);
void getConvergenceLog(int timestep,double error);
double getBoundaryVoltagefromPeriodicBC(double V0,double freq,double t0,int time_step);

1
sample_scripts/configure_arden
View File

@ -13,6 +13,7 @@ cmake -D CMAKE_C_COMPILER:PATH=/opt/arden/openmpi/3.1.2/bin/mpicc \
-D CUDA_HOST_COMPILER="/usr/bin/gcc" \
-D USE_HDF5=1 \
-D HDF5_DIRECTORY="/opt/arden/hdf5/1.8.12" \
-D USE_DOXYGEN=true \
-D USE_CUDA=0 \
-D USE_TIMER=0 \
~/Programs/LBPM

3
tests/TestPoissonSolver.cpp
View File

@ -76,11 +76,14 @@ int main(int argc, char **argv)
PoissonSolver.getElectricField_debug(timestep);
}
}
PoissonSolver.WriteVis(timestep);
}
else {
int timestep = 1;
PoissonSolver.Run(PoissonSolver.ChargeDensityDummy,false,1);
PoissonSolver.getElectricPotential_debug(1);
PoissonSolver.getElectricField_debug(1);
PoissonSolver.WriteVis(timestep);
}
if (rank==0) printf("Maximum timestep is reached and the simulation is completed\n");

4
tests/lbpm_nernst_planck_cell_simulator.cpp
View File

@ -125,7 +125,7 @@ int main(int argc, char **argv)
while (timestep < Study.timestepMax){
timestep++;
PoissonSolver.Run(IonModel.ChargeDensity,SlipBC,timestep);//solve Poisson equtaion to get steady-state electrical potental
PoissonSolver.Run(IonModel.ChargeDensity,IonModel.MembraneDistance,SlipBC,timestep);//solve Poisson equtaion to get steady-state electrical potental
//comm.barrier();
//if (rank == 0) printf(" Poisson step %i \n",timestep);
//StokesModel.Run_Lite(IonModel.ChargeDensity, PoissonSolver.ElectricField);// Solve the N-S equations to get velocity
@ -133,7 +133,7 @@ int main(int argc, char **argv)
IonModel.RunMembrane(IonModel.FluidVelocityDummy,PoissonSolver.ElectricField,PoissonSolver.Psi); //solve for ion transport with membrane
//comm.barrier();
if (rank == 0) printf(" Membrane step %i \n",timestep);
//if (rank == 0) printf(" Membrane step %i \n",timestep);
fflush(stdout);

1
tests/lbpm_nernst_planck_simulator.cpp
View File

@ -104,7 +104,6 @@ int main(int argc, char **argv)
//StokesModel.Run_Lite(IonModel.ChargeDensity, PoissonSolver.ElectricField);// Solve the N-S equations to get velocity
IonModel.Run(IonModel.FluidVelocityDummy,PoissonSolver.ElectricField); //solve for ion transport and electric potential
//if (timestep%Study.analysis_interval==0){
// Analysis.Basic(IonModel,PoissonSolver,StokesModel,timestep);
//}