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save the work;CPU version compiled; to be tested

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This commit is contained in:
Rex Zhe Li committed 2020-08-16 11:20:11 -04:00
1 parent 3adde14ecf
commit 85fc59190c
13 files changed
+361 -101
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models/PoissonSolver.cpp
+108 -14
View File
@@ -6,9 +6,9 @@
#include "common/ReadMicroCT.h"
ScaLBL_Poisson::ScaLBL_Poisson(int RANK, int NP, MPI_Comm 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),
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)
rank(RANK), nprocs(NP),timestep(0),timestepMax(0),tau(0),k2_inv(0),gamma(0),tolerance(0),h(0),
epsilon0(0),epsilon0_LB(0),epsilonR(0),epsilon_LB(0),Nx(0),Ny(0),Nz(0),N(0),Np(0),analysis_interval(0),
nprocx(0),nprocy(0),nprocz(0),BoundaryCondition(0),BoundaryConditionSolid(0),Lx(0),Ly(0),Lz(0),comm(COMM)
{
}
@@ -54,9 +54,16 @@ void ScaLBL_Poisson::ReadParams(string filename){
if (domain_db->keyExists( "voxel_length" )){//default unit: um/lu
h = domain_db->getScalar<double>( "voxel_length" );
}
BoundaryCondition = 0;
if (domain_db->keyExists( "BC" )){
BoundaryCondition = domain_db->getScalar<int>( "BC" );
}
BoundaryConditionSolid = 1;
if (domain_db->keyExists( "BC_Solid" )){
BoundaryConditionSolid = domain_db->getScalar<int>( "BC_Solid" );
}
//Re-calcualte model parameters if user updates input
epsilon0_LB = epsilon0*(h*1.0e-6);//unit:[C/(V*lu)]
epsilon_LB = epsilon0_LB*epsilonR;//electrical permittivity
@@ -66,6 +73,18 @@ void ScaLBL_Poisson::ReadParams(string filename){
if (rank==0) printf("LB-Poisson Solver: steady-state MaxTimeStep = %i; steady-state tolerance = %.3g \n", timestepMax,tolerance);
if (rank==0) printf(" LB relaxation tau = %.5g \n", tau);
if (rank==0) printf("***********************************************************************************\n");
switch (BoundaryConditionSolid){
case 1:
if (rank==0) printf("LB-Poisson Solver: solid boundary: Dirichlet-type surfacen potential is assigned");
break;
case 2:
if (rank==0) printf("LB-Poisson Solver: solid boundary: Neumann-type surfacen charge density is assigned");
break;
default:
if (rank==0) printf("LB-Poisson Solver: solid boundary: Dirichlet-type surfacen potential is assigned");
break;
}
}
void ScaLBL_Poisson::SetDomain(){
Dm = std::shared_ptr<Domain>(new Domain(domain_db,comm)); // full domain for analysis
@@ -152,6 +171,77 @@ void ScaLBL_Poisson::ReadInput(){
if (rank == 0) cout << " Domain set." << endl;
}
void ScaLBL_Poisson::AssignSolidBoundary(double *poisson_solid)
{
size_t NLABELS=0;
signed char VALUE=0;
double AFFINITY=0.f;
auto LabelList = electric_db->getVector<int>( "SolidLabels" );
auto AffinityList = electric_db->getVector<double>( "SolidValues" );
NLABELS=LabelList.size();
if (NLABELS != AffinityList.size()){
ERROR("Error: LB-Poisson Solver: SolidLabels and SolidValues must be the same length! \n");
}
double label_count[NLABELS];
double label_count_global[NLABELS];
// Assign the labels
for (size_t idx=0; idx<NLABELS; idx++) label_count[idx]=0;
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++){
//printf("idx=%i, value=%i, %i, \n",idx, VALUE,LabelList[idx]);
if (VALUE == LabelList[idx]){
AFFINITY=AffinityList[idx];
//NOTE need to convert the user input phys unit to LB unit
if (BoundaryConditionSolid==2){
//for BCS=1, i.e. Dirichlet-type, no need for unit conversion
AFFINITY = AFFINITY*(h*h*1.0e-12);
}
label_count[idx] += 1.0;
idx = NLABELS;
//Mask->id[n] = 0; // set mask to zero since this is an immobile component
}
}
poisson_solid[n] = AFFINITY;
}
}
}
for (size_t idx=0; idx<NLABELS; idx++)
label_count_global[idx]=sumReduce( Dm->Comm, label_count[idx]);
if (rank==0){
printf("LB-Poisson Solver: Poisson 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);
switch (BoundaryConditionSolid){
case 1:
printf(" label=%d, surface potential=%.3g [V], volume fraction=%.2g\n",VALUE,AFFINITY,volume_fraction);
break;
case 2:
printf(" label=%d, surface charge density=%.3g [C/m^2], volume fraction=%.2g\n",VALUE,AFFINITY,volume_fraction);
break;
default:
printf(" label=%d, surface potential=%.3g [V], volume fraction=%.2g\n",VALUE,AFFINITY,volume_fraction);
break;
}
}
}
}
void ScaLBL_Poisson::Create(){
/*
* This function creates the variables needed to run a LBM
@@ -187,22 +277,26 @@ void ScaLBL_Poisson::Create(){
ScaLBL_AllocateDeviceMemory((void **) &fq, 7*dist_mem_size);
ScaLBL_AllocateDeviceMemory((void **) &Psi, sizeof(double)*Np);
ScaLBL_AllocateDeviceMemory((void **) &ElectricField, 3*sizeof(double)*Np);
ScaLBL_AllocateDeviceMemory((void **) &zeta, sizeof(double)*ScaLBL_Comm->n_bb_d3q7);
ScaLBL_AllocateDeviceMemory((void **) &PoissonSolid, sizeof(double)*Nx*Ny*Nz);
//...........................................................................
// initialize the zeta function (example is zeta is constant on solid surface)
double *tmpZeta = new double[ScaLBL_Comm->n_bb_d3q7];
for int (i=0; i<ScaLBL_Comm->n_bb_d3q7; i++){
tmpZeta[i] = 1.0/k2_inv; // this has to be read from input file
}
ScaLBL_CopyToDevice(zeta, tmpZeta, sizeof(double)*ScaLBL_Comm->n_bb_d3q7);
delete [] tmpZeta;
// Update GPU data structures
if (rank==0) printf ("LB-Poisson Solver: Setting up device map and neighbor list \n");
// copy the neighbor list
ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
//Initialize solid boundary for electrical potential
ScaLBL_Comm->SetupBounceBackList(Map, Mask->id, Np);
MPI_Barrier(comm);
double *PoissonSolid_host;
PoissonSolid_host = new double[Nx*Ny*Nz];
AssignSolidBoundary(PoissonSolid_host);
ScaLBL_CopyToDevice(PoissonSolid, PoissonSolid_host, Nx*Ny*Nz*sizeof(double));
ScaLBL_DeviceBarrier();
delete [] PoissonSolid_host;
}
void ScaLBL_Poisson::Initialize(){
@@ -233,7 +327,7 @@ void ScaLBL_Poisson::Run(double *ChargeDensity){
// Set boundary conditions
/* ... */
ScaLBL_D3Q7_AAodd_Poisson(NeighborList, fq, ChargeDensity, Psi, ElectricField, tau, epsilon_LB, gamma, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_Comm->SolidDirichletD3Q7(fq, zeta);
ScaLBL_Comm->SolidDirichletD3Q7(fq, PoissonSolid);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
// *************EVEN TIMESTEP*************//
@@ -244,14 +338,14 @@ void ScaLBL_Poisson::Run(double *ChargeDensity){
// Set boundary conditions
/* ... */
ScaLBL_D3Q7_AAeven_Poisson(fq, ChargeDensity, Psi, ElectricField, tau, epsilon_LB, gamma, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_Comm->SolidDirichletD3Q7(fq, zeta);
ScaLBL_Comm->SolidDirichletD3Q7(fq, PoissonSolid);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
//************************************************************************/
// Check convergence of steady-state solution
if (timestep%analysis_interval==0){
ScaLBL_Comm->RegularLayout(Map,&Psi,Psi_host);
ScaLBL_Comm->RegularLayout(Map,Psi,Psi_host);
double count_loc=0;
double count;
double psi_avg;