OilfieldToolsNet/LBPM
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cleanup with help from valgrind

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This commit is contained in:
James McClure
2022-05-06 16:21:37 -04:00
parent ba6d438630
commit c424e1d984
5 changed files with 340 additions and 292 deletions
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31
models/IonModel.cpp
View File

@@ -13,7 +13,20 @@ ScaLBL_IonModel::ScaLBL_IonModel(int RANK, int NP, const Utilities::MPI &COMM)
nprocy(0), nprocz(0), fluidVelx_dummy(0), fluidVely_dummy(0),
fluidVelz_dummy(0), BoundaryConditionInlet(0), BoundaryConditionOutlet(0),
BoundaryConditionSolid(0), Lx(0), Ly(0), Lz(0), comm(COMM) {}
ScaLBL_IonModel::~ScaLBL_IonModel() {}
ScaLBL_IonModel::~ScaLBL_IonModel() {
ScaLBL_FreeDeviceMemory(NeighborList);
ScaLBL_FreeDeviceMemory(dvcMap);
ScaLBL_FreeDeviceMemory(fq);
ScaLBL_FreeDeviceMemory(Ci);
ScaLBL_FreeDeviceMemory(ChargeDensity);
ScaLBL_FreeDeviceMemory(FluxDiffusive);
ScaLBL_FreeDeviceMemory(FluxAdvective);
ScaLBL_FreeDeviceMemory(FluxElectrical);
ScaLBL_FreeDeviceMemory(IonSolid);
ScaLBL_FreeDeviceMemory(FluidVelocityDummy);
}
void ScaLBL_IonModel::ReadParams(string filename, vector<int> &num_iter) {
@@ -50,6 +63,8 @@ void ScaLBL_IonModel::ReadParams(string filename, vector<int> &num_iter) {
Ez_dummy = 0.0; //for debugging, unit [V/m]
//--------------------------------------------------------------------------//
BoundaryConditionSolid = 0;
// Read domain parameters
if (domain_db->keyExists("voxel_length")) { //default unit: um/lu
h = domain_db->getScalar<double>("voxel_length");
@@ -685,7 +700,6 @@ void ScaLBL_IonModel::SetDomain() {
}
void ScaLBL_IonModel::SetMembrane() {
size_t NLABELS = 0;
membrane_db = db->getDatabase("Membrane");
@@ -693,7 +707,7 @@ void ScaLBL_IonModel::SetMembrane() {
auto MembraneLabels = membrane_db->getVector<int>("MembraneLabels");
IonMembrane = std::shared_ptr<Membrane>(new Membrane(Dm, NeighborList, Np));
size_t NLABELS = MembraneLabels.size();
signed char LABEL = 0;
double *label_count;
double *label_count_global;
@@ -1020,7 +1034,6 @@ void ScaLBL_IonModel::Create() {
}
ScaLBL_CopyToDevice(dvcMap, TmpMap, sizeof(int) * Np);
ScaLBL_Comm->Barrier();
delete[] TmpMap;
ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
comm.barrier();
@@ -1042,6 +1055,13 @@ void ScaLBL_IonModel::Create() {
ScaLBL_Comm->Barrier();
delete[] IonSolid_host;
}
else {
IonSolid = NULL;
}
delete[] TmpMap;
delete[] neighborList;
}
void ScaLBL_IonModel::Initialize() {
@@ -1444,6 +1464,7 @@ void ScaLBL_IonModel::RunMembrane(double *Velocity, double *ElectricField, doubl
//auto t1 = std::chrono::system_clock::now();
for (size_t ic = 0; ic < number_ion_species; ic++) {
/* set the mass transfer coefficients for the membrane */
IonMembrane->AssignCoefficients(dvcMap, Psi, ThresholdVoltage[ic],MassFractionIn[ic],
MassFractionOut[ic],ThresholdMassFractionIn[ic],ThresholdMassFractionOut[ic]);
@@ -1525,8 +1546,6 @@ void ScaLBL_IonModel::RunMembrane(double *Velocity, double *ElectricField, doubl
//Compute charge density for Poisson equation
for (size_t ic = 0; ic < number_ion_species; ic++) {
int Valence = IonValence[ic];
if (rank==0) printf("compute charge density for ion %i, Valence =%i \n", ic,Valence);
ScaLBL_D3Q7_Ion_ChargeDensity(Ci, ChargeDensity, Valence, ic,
ScaLBL_Comm->FirstInterior(),
ScaLBL_Comm->LastInterior(), Np);

9
models/PoissonSolver.cpp
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@@ -32,6 +32,14 @@ ScaLBL_Poisson::ScaLBL_Poisson(int RANK, int NP, const Utilities::MPI& COMM):
}
ScaLBL_Poisson::~ScaLBL_Poisson()
{
ScaLBL_FreeDeviceMemory(NeighborList);
ScaLBL_FreeDeviceMemory(dvcMap);
ScaLBL_FreeDeviceMemory(Psi);
ScaLBL_FreeDeviceMemory(Psi_BCLabel);
ScaLBL_FreeDeviceMemory(ElectricField);
ScaLBL_FreeDeviceMemory(ResidualError);
ScaLBL_FreeDeviceMemory(fq);
if ( TIMELOG )
fclose( TIMELOG );
}
@@ -416,6 +424,7 @@ void ScaLBL_Poisson::Create(){
//ScaLBL_Comm->Barrier();
//Initialize solid boundary for electric potential
// DON'T USE WITH CELLULAR SYSTEM (NO SOLID -- NEED Membrane SOLUTION)
ScaLBL_Comm->SetupBounceBackList(Map, Mask->id.data(), Np);
comm.barrier();
}