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Merge branch 'electrokinetic' of github.com:JamesEMcClure/LBPM-WIA into electrokinetic
This commit is contained in:
James McClure 2021-01-04 00:07:23 -05:00
commit 5c914a5719
1 changed files with 21 additions and 17 deletions
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38
analysis/ElectroChemistry.cpp
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@ -140,7 +140,10 @@ void ElectroChemistryAnalyzer::WriteVis( ScaLBL_IonModel &Ion, ScaLBL_Poisson &P
visData[0].meshName = "domain"; 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 ); 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 );
auto ElectricPotential = std::make_shared<IO::Variable>(); auto ElectricPotential = std::make_shared<IO::Variable>();
auto IonConcentration = std::make_shared<IO::Variable>(); std::vector<shared_ptr<IO::Variable>> IonConcentration;
for (int ion=0; ion<Ion.number_ion_species; ion++){
IonConcentration.push_back(std::make_shared<IO::Variable>());
}
auto VxVar = std::make_shared<IO::Variable>(); auto VxVar = std::make_shared<IO::Variable>();
auto VyVar = std::make_shared<IO::Variable>(); auto VyVar = std::make_shared<IO::Variable>();
auto VzVar = std::make_shared<IO::Variable>(); auto VzVar = std::make_shared<IO::Variable>();
@ -155,14 +158,15 @@ void ElectroChemistryAnalyzer::WriteVis( ScaLBL_IonModel &Ion, ScaLBL_Poisson &P
if (vis_db->getWithDefault<bool>( "save_concentration", true )){ if (vis_db->getWithDefault<bool>( "save_concentration", true )){
for (int ion=0; ion<Ion.number_ion_species; ion++){ for (int ion=0; ion<Ion.number_ion_species; ion++){
sprintf(VisName,"IonConcentration_%i",ion); sprintf(VisName,"IonConcentration_%i",ion+1);
IonConcentration->name = VisName; IonConcentration[ion]->name = VisName;
IonConcentration->type = IO::VariableType::VolumeVariable; IonConcentration[ion]->type = IO::VariableType::VolumeVariable;
IonConcentration->dim = 1; IonConcentration[ion]->dim = 1;
IonConcentration->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2); IonConcentration[ion]->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
visData[0].vars.push_back(IonConcentration); visData[0].vars.push_back(IonConcentration[ion]);
} }
} }
if (vis_db->getWithDefault<bool>( "save_velocity", false )){ if (vis_db->getWithDefault<bool>( "save_velocity", false )){
VxVar->name = "Velocity_x"; VxVar->name = "Velocity_x";
VxVar->type = IO::VariableType::VolumeVariable; VxVar->type = IO::VariableType::VolumeVariable;
@ -190,23 +194,23 @@ void ElectroChemistryAnalyzer::WriteVis( ScaLBL_IonModel &Ion, ScaLBL_Poisson &P
if (vis_db->getWithDefault<bool>( "save_concentration", true )){ if (vis_db->getWithDefault<bool>( "save_concentration", true )){
for (int ion=0; ion<Ion.number_ion_species; ion++){ for (int ion=0; ion<Ion.number_ion_species; ion++){
sprintf(VisName,"IonConcentration_%i",ion); sprintf(VisName,"IonConcentration_%i",ion+1);
IonConcentration->name = VisName; IonConcentration[ion]->name = VisName;
ASSERT(visData[0].vars[1]->name==VisName); ASSERT(visData[0].vars[1+ion]->name==VisName);
Array<double>& IonConcentrationData = visData[0].vars[1]->data; Array<double>& IonConcentrationData = visData[0].vars[1+ion]->data;
Ion.getIonConcentration(Rho,ion); Ion.getIonConcentration(Rho,ion);
fillData.copy(Rho,IonConcentrationData); fillData.copy(Rho,IonConcentrationData);
} }
} }
if (vis_db->getWithDefault<bool>( "save_velocity", false )){ if (vis_db->getWithDefault<bool>( "save_velocity", false )){
ASSERT(visData[0].vars[2]->name=="Velocity_x"); ASSERT(visData[0].vars[1+Ion.number_ion_species+0]->name=="Velocity_x");
ASSERT(visData[0].vars[3]->name=="Velocity_y"); ASSERT(visData[0].vars[1+Ion.number_ion_species+1]->name=="Velocity_y");
ASSERT(visData[0].vars[4]->name=="Velocity_z"); ASSERT(visData[0].vars[1+Ion.number_ion_species+2]->name=="Velocity_z");
Stokes.getVelocity(Vel_x,Vel_y,Vel_z); Stokes.getVelocity(Vel_x,Vel_y,Vel_z);
Array<double>& VelxData = visData[0].vars[2]->data; Array<double>& VelxData = visData[0].vars[1+Ion.number_ion_species+0]->data;
Array<double>& VelyData = visData[0].vars[3]->data; Array<double>& VelyData = visData[0].vars[1+Ion.number_ion_species+1]->data;
Array<double>& VelzData = visData[0].vars[4]->data; Array<double>& VelzData = visData[0].vars[1+Ion.number_ion_species+2]->data;
fillData.copy(Vel_x,VelxData); fillData.copy(Vel_x,VelxData);
fillData.copy(Vel_y,VelyData); fillData.copy(Vel_y,VelyData);
fillData.copy(Vel_z,VelzData); fillData.copy(Vel_z,VelzData);