598 lines
27 KiB
C++
598 lines
27 KiB
C++
#include "analysis/ElectroChemistry.h"
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ElectroChemistryAnalyzer::ElectroChemistryAnalyzer(std::shared_ptr<Domain> dm)
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: Dm(dm) {
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Nx = dm->Nx;
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Ny = dm->Ny;
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Nz = dm->Nz;
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Volume = (Nx - 2) * (Ny - 2) * (Nz - 2) * Dm->nprocx() * Dm->nprocy() *
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Dm->nprocz() * 1.0;
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ChemicalPotential.resize(Nx, Ny, Nz);
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ChemicalPotential.fill(0);
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ElectricalPotential.resize(Nx, Ny, Nz);
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ElectricalPotential.fill(0);
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ElectricalField_x.resize(Nx, Ny, Nz);
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ElectricalField_x.fill(0);
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ElectricalField_y.resize(Nx, Ny, Nz);
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ElectricalField_y.fill(0);
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ElectricalField_z.resize(Nx, Ny, Nz);
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ElectricalField_z.fill(0);
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Pressure.resize(Nx, Ny, Nz);
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Pressure.fill(0);
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Rho.resize(Nx, Ny, Nz);
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Rho.fill(0);
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Vel_x.resize(Nx, Ny, Nz);
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Vel_x.fill(0); // Gradient of the phase indicator field
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Vel_y.resize(Nx, Ny, Nz);
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Vel_y.fill(0);
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Vel_z.resize(Nx, Ny, Nz);
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Vel_z.fill(0);
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SDs.resize(Nx, Ny, Nz);
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SDs.fill(0);
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IonFluxDiffusive_x.resize(Nx, Ny, Nz);
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IonFluxDiffusive_x.fill(0);
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IonFluxDiffusive_y.resize(Nx, Ny, Nz);
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IonFluxDiffusive_y.fill(0);
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IonFluxDiffusive_z.resize(Nx, Ny, Nz);
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IonFluxDiffusive_z.fill(0);
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IonFluxAdvective_x.resize(Nx, Ny, Nz);
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IonFluxAdvective_x.fill(0);
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IonFluxAdvective_y.resize(Nx, Ny, Nz);
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IonFluxAdvective_y.fill(0);
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IonFluxAdvective_z.resize(Nx, Ny, Nz);
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IonFluxAdvective_z.fill(0);
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IonFluxElectrical_x.resize(Nx, Ny, Nz);
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IonFluxElectrical_x.fill(0);
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IonFluxElectrical_y.resize(Nx, Ny, Nz);
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IonFluxElectrical_y.fill(0);
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IonFluxElectrical_z.resize(Nx, Ny, Nz);
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IonFluxElectrical_z.fill(0);
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if (Dm->rank() == 0) {
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bool WriteHeader = false;
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TIMELOG = fopen("electrokinetic.csv", "r");
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if (TIMELOG != NULL)
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fclose(TIMELOG);
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else
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WriteHeader = true;
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TIMELOG = fopen("electrokinetic.csv", "a+");
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if (WriteHeader) {
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// If timelog is empty, write a short header to list the averages
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//fprintf(TIMELOG,"--------------------------------------------------------------------------------------\n");
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fprintf(TIMELOG, "TBD TBD\n");
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}
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}
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}
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ElectroChemistryAnalyzer::~ElectroChemistryAnalyzer() {
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if (Dm->rank() == 0) {
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fclose(TIMELOG);
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}
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}
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void ElectroChemistryAnalyzer::SetParams() {}
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void ElectroChemistryAnalyzer::Basic(ScaLBL_IonModel &Ion,
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ScaLBL_Poisson &Poisson,
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ScaLBL_StokesModel &Stokes, int timestep) {
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int i, j, k;
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double Vin = 0.0;
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double Vout = 0.0;
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Poisson.getElectricPotential(ElectricalPotential);
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/* local sub-domain averages */
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double *rho_avg_local;
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double *rho_mu_avg_local;
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double *rho_mu_fluctuation_local;
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double *rho_psi_avg_local;
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double *rho_psi_fluctuation_local;
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/* global averages */
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double *rho_avg_global;
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double *rho_mu_avg_global;
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double *rho_mu_fluctuation_global;
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double *rho_psi_avg_global;
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double *rho_psi_fluctuation_global;
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/* local sub-domain averages */
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rho_avg_local = new double[Ion.number_ion_species];
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rho_mu_avg_local = new double[Ion.number_ion_species];
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rho_mu_fluctuation_local = new double[Ion.number_ion_species];
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rho_psi_avg_local = new double[Ion.number_ion_species];
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rho_psi_fluctuation_local = new double[Ion.number_ion_species];
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/* global averages */
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rho_avg_global = new double[Ion.number_ion_species];
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rho_mu_avg_global = new double[Ion.number_ion_species];
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rho_mu_fluctuation_global = new double[Ion.number_ion_species];
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rho_psi_avg_global = new double[Ion.number_ion_species];
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rho_psi_fluctuation_global = new double[Ion.number_ion_species];
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for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
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rho_avg_local[ion] = 0.0;
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rho_mu_avg_local[ion] = 0.0;
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rho_psi_avg_local[ion] = 0.0;
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Ion.getIonConcentration(Rho, ion);
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/* Compute averages for each ion */
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for (k = 1; k < Nz; k++) {
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for (j = 1; j < Ny; j++) {
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for (i = 1; i < Nx; i++) {
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rho_avg_local[ion] += Rho(i, j, k);
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rho_mu_avg_local[ion] += Rho(i, j, k) * Rho(i, j, k);
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rho_psi_avg_local[ion] +=
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Rho(i, j, k) * ElectricalPotential(i, j, k);
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}
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}
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}
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rho_avg_global[ion] = Dm->Comm.sumReduce(rho_avg_local[ion]) / Volume;
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rho_mu_avg_global[ion] =
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Dm->Comm.sumReduce(rho_mu_avg_local[ion]) / Volume;
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rho_psi_avg_global[ion] =
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Dm->Comm.sumReduce(rho_psi_avg_local[ion]) / Volume;
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if (rho_avg_global[ion] > 0.0) {
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rho_mu_avg_global[ion] /= rho_avg_global[ion];
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rho_psi_avg_global[ion] /= rho_avg_global[ion];
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}
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}
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for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
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rho_mu_fluctuation_local[ion] = 0.0;
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rho_psi_fluctuation_local[ion] = 0.0;
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/* Compute averages for each ion */
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for (k = 1; k < Nz; k++) {
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for (j = 1; j < Ny; j++) {
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for (i = 1; i < Nx; i++) {
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rho_mu_fluctuation_local[ion] +=
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(Rho(i, j, k) * Rho(i, j, k) - rho_mu_avg_global[ion]);
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rho_psi_fluctuation_local[ion] +=
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(Rho(i, j, k) * ElectricalPotential(i, j, k) -
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rho_psi_avg_global[ion]);
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}
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}
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}
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rho_mu_fluctuation_global[ion] =
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Dm->Comm.sumReduce(rho_mu_fluctuation_local[ion]);
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rho_psi_fluctuation_global[ion] =
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Dm->Comm.sumReduce(rho_psi_fluctuation_local[ion]);
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}
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if (Dm->rank() == 0) {
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fprintf(TIMELOG, "%i ", timestep);
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for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
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fprintf(TIMELOG, "%.8g ", rho_avg_global[ion]);
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fprintf(TIMELOG, "%.8g ", rho_mu_avg_global[ion]);
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fprintf(TIMELOG, "%.8g ", rho_psi_avg_global[ion]);
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fprintf(TIMELOG, "%.8g ", rho_mu_fluctuation_global[ion]);
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fprintf(TIMELOG, "%.8g ", rho_psi_fluctuation_global[ion]);
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}
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fprintf(TIMELOG, "%.8g %.8g\n", Vin, Vout);
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fflush(TIMELOG);
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}
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/* else{
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fprintf(TIMELOG,"%i ",timestep);
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for (int ion=0; ion<Ion.number_ion_species; ion++){
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fprintf(TIMELOG,"%.8g ",rho_avg_local[ion]);
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fprintf(TIMELOG,"%.8g ",rho_mu_avg_local[ion]);
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fprintf(TIMELOG,"%.8g ",rho_psi_avg_local[ion]);
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fprintf(TIMELOG,"%.8g ",rho_mu_fluctuation_local[ion]);
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fprintf(TIMELOG,"%.8g ",rho_psi_fluctuation_local[ion]);
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}
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fflush(TIMELOG);
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} */
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}
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void ElectroChemistryAnalyzer::WriteVis(ScaLBL_IonModel &Ion,
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ScaLBL_Poisson &Poisson,
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ScaLBL_StokesModel &Stokes,
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std::shared_ptr<Database> input_db,
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int timestep) {
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auto vis_db = input_db->getDatabase("Visualization");
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char VisName[40];
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auto format = vis_db->getWithDefault<string>( "format", "hdf5" );
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std::vector<IO::MeshDataStruct> visData;
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fillHalo<double> fillData(Dm->Comm, Dm->rank_info,
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{Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2}, {1, 1, 1},
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0, 1);
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IO::initialize("",format,"false");
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// Create the MeshDataStruct
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visData.resize(1);
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visData[0].meshName = "domain";
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visData[0].mesh =
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std::make_shared<IO::DomainMesh>(Dm->rank_info, Dm->Nx - 2, Dm->Ny - 2,
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Dm->Nz - 2, Dm->Lx, Dm->Ly, Dm->Lz);
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//electric potential
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auto ElectricPotentialVar = std::make_shared<IO::Variable>();
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//electric field
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auto ElectricFieldVar_x = std::make_shared<IO::Variable>();
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auto ElectricFieldVar_y = std::make_shared<IO::Variable>();
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auto ElectricFieldVar_z = std::make_shared<IO::Variable>();
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//ion concentration
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std::vector<shared_ptr<IO::Variable>> IonConcentration;
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for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
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IonConcentration.push_back(std::make_shared<IO::Variable>());
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}
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//fluid velocity
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auto VxVar = std::make_shared<IO::Variable>();
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auto VyVar = std::make_shared<IO::Variable>();
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auto VzVar = std::make_shared<IO::Variable>();
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// diffusive ion flux
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std::vector<shared_ptr<IO::Variable>> IonFluxDiffusive;
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for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
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//push in x-,y-, and z-component for each ion species
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IonFluxDiffusive.push_back(std::make_shared<IO::Variable>());
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IonFluxDiffusive.push_back(std::make_shared<IO::Variable>());
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IonFluxDiffusive.push_back(std::make_shared<IO::Variable>());
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}
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// advective ion flux
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std::vector<shared_ptr<IO::Variable>> IonFluxAdvective;
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for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
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//push in x-,y-, and z-component for each ion species
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IonFluxAdvective.push_back(std::make_shared<IO::Variable>());
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IonFluxAdvective.push_back(std::make_shared<IO::Variable>());
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IonFluxAdvective.push_back(std::make_shared<IO::Variable>());
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}
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// electro-migrational ion flux
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std::vector<shared_ptr<IO::Variable>> IonFluxElectrical;
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for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
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//push in x-,y-, and z-component for each ion species
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IonFluxElectrical.push_back(std::make_shared<IO::Variable>());
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IonFluxElectrical.push_back(std::make_shared<IO::Variable>());
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IonFluxElectrical.push_back(std::make_shared<IO::Variable>());
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}
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//--------------------------------------------------------------------------------------------------------------------
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//-------------------------------------Create Names for Variables------------------------------------------------------
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if (vis_db->getWithDefault<bool>("save_electric_potential", true)) {
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ElectricPotentialVar->name = "ElectricPotential";
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ElectricPotentialVar->type = IO::VariableType::VolumeVariable;
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ElectricPotentialVar->dim = 1;
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ElectricPotentialVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
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visData[0].vars.push_back(ElectricPotentialVar);
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}
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if (vis_db->getWithDefault<bool>("save_concentration", true)) {
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for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
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sprintf(VisName, "IonConcentration_%zu", ion + 1);
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IonConcentration[ion]->name = VisName;
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IonConcentration[ion]->type = IO::VariableType::VolumeVariable;
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IonConcentration[ion]->dim = 1;
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IonConcentration[ion]->data.resize(Dm->Nx - 2, Dm->Ny - 2,
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Dm->Nz - 2);
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visData[0].vars.push_back(IonConcentration[ion]);
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}
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}
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if (vis_db->getWithDefault<bool>("save_velocity", false)) {
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VxVar->name = "Velocity_x";
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VxVar->type = IO::VariableType::VolumeVariable;
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VxVar->dim = 1;
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VxVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
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visData[0].vars.push_back(VxVar);
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VyVar->name = "Velocity_y";
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VyVar->type = IO::VariableType::VolumeVariable;
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VyVar->dim = 1;
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VyVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
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visData[0].vars.push_back(VyVar);
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VzVar->name = "Velocity_z";
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VzVar->type = IO::VariableType::VolumeVariable;
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VzVar->dim = 1;
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VzVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
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visData[0].vars.push_back(VzVar);
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}
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if (vis_db->getWithDefault<bool>("save_ion_flux_diffusive", false)) {
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for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
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// x-component of diffusive flux
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sprintf(VisName, "Ion%zu_FluxDiffusive_x", ion + 1);
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IonFluxDiffusive[3 * ion + 0]->name = VisName;
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IonFluxDiffusive[3 * ion + 0]->type =
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IO::VariableType::VolumeVariable;
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IonFluxDiffusive[3 * ion + 0]->dim = 1;
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IonFluxDiffusive[3 * ion + 0]->data.resize(Dm->Nx - 2, Dm->Ny - 2,
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Dm->Nz - 2);
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visData[0].vars.push_back(IonFluxDiffusive[3 * ion + 0]);
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// y-component of diffusive flux
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sprintf(VisName, "Ion%zu_FluxDiffusive_y", ion + 1);
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IonFluxDiffusive[3 * ion + 1]->name = VisName;
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IonFluxDiffusive[3 * ion + 1]->type =
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IO::VariableType::VolumeVariable;
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IonFluxDiffusive[3 * ion + 1]->dim = 1;
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IonFluxDiffusive[3 * ion + 1]->data.resize(Dm->Nx - 2, Dm->Ny - 2,
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Dm->Nz - 2);
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visData[0].vars.push_back(IonFluxDiffusive[3 * ion + 1]);
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// z-component of diffusive flux
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sprintf(VisName, "Ion%zu_FluxDiffusive_z", ion + 1);
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IonFluxDiffusive[3 * ion + 2]->name = VisName;
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IonFluxDiffusive[3 * ion + 2]->type =
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IO::VariableType::VolumeVariable;
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IonFluxDiffusive[3 * ion + 2]->dim = 1;
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IonFluxDiffusive[3 * ion + 2]->data.resize(Dm->Nx - 2, Dm->Ny - 2,
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Dm->Nz - 2);
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visData[0].vars.push_back(IonFluxDiffusive[3 * ion + 2]);
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}
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}
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if (vis_db->getWithDefault<bool>("save_ion_flux_advective", false)) {
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for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
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// x-component of advective flux
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sprintf(VisName, "Ion%zu_FluxAdvective_x", ion + 1);
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IonFluxAdvective[3 * ion + 0]->name = VisName;
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IonFluxAdvective[3 * ion + 0]->type =
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IO::VariableType::VolumeVariable;
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IonFluxAdvective[3 * ion + 0]->dim = 1;
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IonFluxAdvective[3 * ion + 0]->data.resize(Dm->Nx - 2, Dm->Ny - 2,
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Dm->Nz - 2);
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visData[0].vars.push_back(IonFluxAdvective[3 * ion + 0]);
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// y-component of advective flux
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sprintf(VisName, "Ion%zu_FluxAdvective_y", ion + 1);
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IonFluxAdvective[3 * ion + 1]->name = VisName;
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IonFluxAdvective[3 * ion + 1]->type =
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IO::VariableType::VolumeVariable;
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IonFluxAdvective[3 * ion + 1]->dim = 1;
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IonFluxAdvective[3 * ion + 1]->data.resize(Dm->Nx - 2, Dm->Ny - 2,
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Dm->Nz - 2);
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visData[0].vars.push_back(IonFluxAdvective[3 * ion + 1]);
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// z-component of advective flux
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sprintf(VisName, "Ion%zu_FluxAdvective_z", ion + 1);
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IonFluxAdvective[3 * ion + 2]->name = VisName;
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IonFluxAdvective[3 * ion + 2]->type =
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IO::VariableType::VolumeVariable;
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IonFluxAdvective[3 * ion + 2]->dim = 1;
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IonFluxAdvective[3 * ion + 2]->data.resize(Dm->Nx - 2, Dm->Ny - 2,
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Dm->Nz - 2);
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visData[0].vars.push_back(IonFluxAdvective[3 * ion + 2]);
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}
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}
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if (vis_db->getWithDefault<bool>("save_ion_flux_electrical", false)) {
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for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
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// x-component of electro-migrational flux
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sprintf(VisName, "Ion%zu_FluxElectrical_x", ion + 1);
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IonFluxElectrical[3 * ion + 0]->name = VisName;
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IonFluxElectrical[3 * ion + 0]->type =
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IO::VariableType::VolumeVariable;
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IonFluxElectrical[3 * ion + 0]->dim = 1;
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IonFluxElectrical[3 * ion + 0]->data.resize(Dm->Nx - 2, Dm->Ny - 2,
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Dm->Nz - 2);
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visData[0].vars.push_back(IonFluxElectrical[3 * ion + 0]);
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// y-component of electro-migrational flux
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sprintf(VisName, "Ion%zu_FluxElectrical_y", ion + 1);
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IonFluxElectrical[3 * ion + 1]->name = VisName;
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IonFluxElectrical[3 * ion + 1]->type =
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IO::VariableType::VolumeVariable;
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IonFluxElectrical[3 * ion + 1]->dim = 1;
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IonFluxElectrical[3 * ion + 1]->data.resize(Dm->Nx - 2, Dm->Ny - 2,
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Dm->Nz - 2);
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visData[0].vars.push_back(IonFluxElectrical[3 * ion + 1]);
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// z-component of electro-migrational flux
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sprintf(VisName, "Ion%zu_FluxElectrical_z", ion + 1);
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IonFluxElectrical[3 * ion + 2]->name = VisName;
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IonFluxElectrical[3 * ion + 2]->type =
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IO::VariableType::VolumeVariable;
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IonFluxElectrical[3 * ion + 2]->dim = 1;
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IonFluxElectrical[3 * ion + 2]->data.resize(Dm->Nx - 2, Dm->Ny - 2,
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Dm->Nz - 2);
|
|
visData[0].vars.push_back(IonFluxElectrical[3 * ion + 2]);
|
|
}
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_electric_field", false)) {
|
|
ElectricFieldVar_x->name = "ElectricField_x";
|
|
ElectricFieldVar_x->type = IO::VariableType::VolumeVariable;
|
|
ElectricFieldVar_x->dim = 1;
|
|
ElectricFieldVar_x->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
|
|
visData[0].vars.push_back(ElectricFieldVar_x);
|
|
ElectricFieldVar_y->name = "ElectricField_y";
|
|
ElectricFieldVar_y->type = IO::VariableType::VolumeVariable;
|
|
ElectricFieldVar_y->dim = 1;
|
|
ElectricFieldVar_y->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
|
|
visData[0].vars.push_back(ElectricFieldVar_y);
|
|
ElectricFieldVar_z->name = "ElectricField_z";
|
|
ElectricFieldVar_z->type = IO::VariableType::VolumeVariable;
|
|
ElectricFieldVar_z->dim = 1;
|
|
ElectricFieldVar_z->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
|
|
visData[0].vars.push_back(ElectricFieldVar_z);
|
|
}
|
|
//--------------------------------------------------------------------------------------------------------------------
|
|
|
|
//------------------------------------Save All Variables--------------------------------------------------------------
|
|
if (vis_db->getWithDefault<bool>("save_electric_potential", true)) {
|
|
ASSERT(visData[0].vars[0]->name == "ElectricPotential");
|
|
Poisson.getElectricPotential(ElectricalPotential);
|
|
Array<double> &ElectricPotentialData = visData[0].vars[0]->data;
|
|
fillData.copy(ElectricalPotential, ElectricPotentialData);
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_concentration", true)) {
|
|
for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
|
|
sprintf(VisName, "IonConcentration_%zu", ion + 1);
|
|
//IonConcentration[ion]->name = VisName;
|
|
ASSERT(visData[0].vars[1 + ion]->name == VisName);
|
|
Array<double> &IonConcentrationData =
|
|
visData[0].vars[1 + ion]->data;
|
|
Ion.getIonConcentration(Rho, ion);
|
|
fillData.copy(Rho, IonConcentrationData);
|
|
}
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_velocity", false)) {
|
|
ASSERT(visData[0].vars[1 + Ion.number_ion_species + 0]->name ==
|
|
"Velocity_x");
|
|
ASSERT(visData[0].vars[1 + Ion.number_ion_species + 1]->name ==
|
|
"Velocity_y");
|
|
ASSERT(visData[0].vars[1 + Ion.number_ion_species + 2]->name ==
|
|
"Velocity_z");
|
|
Stokes.getVelocity(Vel_x, Vel_y, Vel_z);
|
|
Array<double> &VelxData =
|
|
visData[0].vars[1 + Ion.number_ion_species + 0]->data;
|
|
Array<double> &VelyData =
|
|
visData[0].vars[1 + Ion.number_ion_species + 1]->data;
|
|
Array<double> &VelzData =
|
|
visData[0].vars[1 + Ion.number_ion_species + 2]->data;
|
|
fillData.copy(Vel_x, VelxData);
|
|
fillData.copy(Vel_y, VelyData);
|
|
fillData.copy(Vel_z, VelzData);
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_ion_flux_diffusive", false)) {
|
|
for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
|
|
|
|
// x-component of diffusive flux
|
|
sprintf(VisName, "Ion%zu_FluxDiffusive_x", ion + 1);
|
|
//IonFluxDiffusive[3*ion+0]->name = VisName;
|
|
ASSERT(visData[0]
|
|
.vars[4 + Ion.number_ion_species + 3 * ion + 0]
|
|
->name == VisName);
|
|
// y-component of diffusive flux
|
|
sprintf(VisName, "Ion%zu_FluxDiffusive_y", ion + 1);
|
|
//IonFluxDiffusive[3*ion+1]->name = VisName;
|
|
ASSERT(visData[0]
|
|
.vars[4 + Ion.number_ion_species + 3 * ion + 1]
|
|
->name == VisName);
|
|
// z-component of diffusive flux
|
|
sprintf(VisName, "Ion%zu_FluxDiffusive_z", ion + 1);
|
|
//IonFluxDiffusive[3*ion+2]->name = VisName;
|
|
ASSERT(visData[0]
|
|
.vars[4 + Ion.number_ion_species + 3 * ion + 2]
|
|
->name == VisName);
|
|
|
|
Array<double> &IonFluxData_x =
|
|
visData[0].vars[4 + Ion.number_ion_species + 3 * ion + 0]->data;
|
|
Array<double> &IonFluxData_y =
|
|
visData[0].vars[4 + Ion.number_ion_species + 3 * ion + 1]->data;
|
|
Array<double> &IonFluxData_z =
|
|
visData[0].vars[4 + Ion.number_ion_species + 3 * ion + 2]->data;
|
|
Ion.getIonFluxDiffusive(IonFluxDiffusive_x, IonFluxDiffusive_y,
|
|
IonFluxDiffusive_z, ion);
|
|
fillData.copy(IonFluxDiffusive_x, IonFluxData_x);
|
|
fillData.copy(IonFluxDiffusive_y, IonFluxData_y);
|
|
fillData.copy(IonFluxDiffusive_z, IonFluxData_z);
|
|
}
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_ion_flux_advective", false)) {
|
|
for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
|
|
|
|
// x-component of diffusive flux
|
|
sprintf(VisName, "Ion%zu_FluxAdvective_x", ion + 1);
|
|
//IonFluxDiffusive[3*ion+0]->name = VisName;
|
|
ASSERT(visData[0]
|
|
.vars[4 + Ion.number_ion_species * (1 + 3) + 3 * ion + 0]
|
|
->name == VisName);
|
|
// y-component of diffusive flux
|
|
sprintf(VisName, "Ion%zu_FluxAdvective_y", ion + 1);
|
|
//IonFluxDiffusive[3*ion+1]->name = VisName;
|
|
ASSERT(visData[0]
|
|
.vars[4 + Ion.number_ion_species * (1 + 3) + 3 * ion + 1]
|
|
->name == VisName);
|
|
// z-component of diffusive flux
|
|
sprintf(VisName, "Ion%zu_FluxAdvective_z", ion + 1);
|
|
//IonFluxDiffusive[3*ion+2]->name = VisName;
|
|
ASSERT(visData[0]
|
|
.vars[4 + Ion.number_ion_species * (1 + 3) + 3 * ion + 2]
|
|
->name == VisName);
|
|
|
|
Array<double> &IonFluxData_x =
|
|
visData[0]
|
|
.vars[4 + Ion.number_ion_species * (1 + 3) + 3 * ion + 0]
|
|
->data;
|
|
Array<double> &IonFluxData_y =
|
|
visData[0]
|
|
.vars[4 + Ion.number_ion_species * (1 + 3) + 3 * ion + 1]
|
|
->data;
|
|
Array<double> &IonFluxData_z =
|
|
visData[0]
|
|
.vars[4 + Ion.number_ion_species * (1 + 3) + 3 * ion + 2]
|
|
->data;
|
|
Ion.getIonFluxAdvective(IonFluxAdvective_x, IonFluxAdvective_y,
|
|
IonFluxAdvective_z, ion);
|
|
fillData.copy(IonFluxAdvective_x, IonFluxData_x);
|
|
fillData.copy(IonFluxAdvective_y, IonFluxData_y);
|
|
fillData.copy(IonFluxAdvective_z, IonFluxData_z);
|
|
}
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_ion_flux_electrical", false)) {
|
|
for (size_t ion = 0; ion < Ion.number_ion_species; ion++) {
|
|
|
|
// x-component of diffusive flux
|
|
sprintf(VisName, "Ion%zu_FluxElectrical_x", ion + 1);
|
|
//IonFluxDiffusive[3*ion+0]->name = VisName;
|
|
ASSERT(visData[0]
|
|
.vars[4 + Ion.number_ion_species * (1 + 6) + 3 * ion + 0]
|
|
->name == VisName);
|
|
// y-component of diffusive flux
|
|
sprintf(VisName, "Ion%zu_FluxElectrical_y", ion + 1);
|
|
//IonFluxDiffusive[3*ion+1]->name = VisName;
|
|
ASSERT(visData[0]
|
|
.vars[4 + Ion.number_ion_species * (1 + 6) + 3 * ion + 1]
|
|
->name == VisName);
|
|
// z-component of diffusive flux
|
|
sprintf(VisName, "Ion%zu_FluxElectrical_z", ion + 1);
|
|
//IonFluxDiffusive[3*ion+2]->name = VisName;
|
|
ASSERT(visData[0]
|
|
.vars[4 + Ion.number_ion_species * (1 + 6) + 3 * ion + 2]
|
|
->name == VisName);
|
|
|
|
Array<double> &IonFluxData_x =
|
|
visData[0]
|
|
.vars[4 + Ion.number_ion_species * (1 + 6) + 3 * ion + 0]
|
|
->data;
|
|
Array<double> &IonFluxData_y =
|
|
visData[0]
|
|
.vars[4 + Ion.number_ion_species * (1 + 6) + 3 * ion + 1]
|
|
->data;
|
|
Array<double> &IonFluxData_z =
|
|
visData[0]
|
|
.vars[4 + Ion.number_ion_species * (1 + 6) + 3 * ion + 2]
|
|
->data;
|
|
Ion.getIonFluxElectrical(IonFluxElectrical_x, IonFluxElectrical_y,
|
|
IonFluxElectrical_z, ion);
|
|
fillData.copy(IonFluxElectrical_x, IonFluxData_x);
|
|
fillData.copy(IonFluxElectrical_y, IonFluxData_y);
|
|
fillData.copy(IonFluxElectrical_z, IonFluxData_z);
|
|
}
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("save_electric_field", false)) {
|
|
ASSERT(
|
|
visData[0].vars[4 + Ion.number_ion_species * (1 + 9) + 0]->name ==
|
|
"ElectricField_x");
|
|
ASSERT(
|
|
visData[0].vars[4 + Ion.number_ion_species * (1 + 9) + 1]->name ==
|
|
"ElectricField_y");
|
|
ASSERT(
|
|
visData[0].vars[4 + Ion.number_ion_species * (1 + 9) + 2]->name ==
|
|
"ElectricField_z");
|
|
Poisson.getElectricField(ElectricalField_x, ElectricalField_y,
|
|
ElectricalField_z);
|
|
Array<double> &ElectricalFieldxData =
|
|
visData[0].vars[4 + Ion.number_ion_species * (1 + 9) + 0]->data;
|
|
Array<double> &ElectricalFieldyData =
|
|
visData[0].vars[4 + Ion.number_ion_species * (1 + 9) + 1]->data;
|
|
Array<double> &ElectricalFieldzData =
|
|
visData[0].vars[4 + Ion.number_ion_species * (1 + 9) + 2]->data;
|
|
fillData.copy(ElectricalField_x, ElectricalFieldxData);
|
|
fillData.copy(ElectricalField_y, ElectricalFieldyData);
|
|
fillData.copy(ElectricalField_z, ElectricalFieldzData);
|
|
}
|
|
|
|
if (vis_db->getWithDefault<bool>("write_silo", true))
|
|
IO::writeData(timestep, visData, Dm->Comm);
|
|
//--------------------------------------------------------------------------------------------------------------------
|
|
/* if (vis_db->getWithDefault<bool>( "save_8bit_raw", true )){
|
|
char CurrentIDFilename[40];
|
|
sprintf(CurrentIDFilename,"id_t%d.raw",timestep);
|
|
Averages.AggregateLabels(CurrentIDFilename);
|
|
}
|
|
*/
|
|
}
|