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vis capabilities for poisson, default d3q19

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This commit is contained in:
James McClure 2022-10-26 16:17:23 -04:00
parent f1ceb930ee
commit 613a43c309
3 changed files with 51 additions and 2 deletions
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1
models/IonModel.cpp
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@ -1549,7 +1549,6 @@ 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);

50
models/PoissonSolver.cpp
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@ -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" );
}
@ -1320,6 +1320,54 @@ void ScaLBL_Poisson::ElectricField_LB_to_Phys(DoubleArray &Efield_reg){
}
}
void ScaLBL_Poisson::WriteVis( int timestep) {
auto vis_db = db->getDatabase("Visualization");
char VisName[40];
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,

2
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);
@ -43,6 +44,7 @@ public:
DoubleArray &Values_z);
void getElectricField_debug(int timestep);
void Checkpoint();
void WriteVis( int timestep);
void DummyChargeDensity(); //for debugging