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Merge pull request #142 from ajnonaka/fix_PEC_layer2
Fix pec layer2
2 parents 3bf4acc + d9abc3e commit a7ffad4

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‎Examples/Tests/circuits/Candice/inputs_candice20‎

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# See parameters in https://github.com/ECP-WarpX/artemis/pull/43
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################################
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####### GENERAL PARAMETERS ######
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#################################
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max_step = 1
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amr.n_cell = n_cellx n_celly n_cellz
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amr.max_grid_size = max_grid_sizex max_grid_sizey max_grid_sizez
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amr.blocking_factor = blocking_factor
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amr.refine_grid_layout = 1 # if n_MPI > n_grids, the grids will be successively divided in half until n_MPI <= n_grids
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geometry.dims = 3
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geometry.prob_lo = prob_lox prob_loy prob_loz
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geometry.prob_hi = prob_hix prob_hiy prob_hiz
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amr.max_level = 0
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# use pec instead of pml overlaying current source so you don't get a reflection
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boundary.field_lo = pml pml pml
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boundary.field_hi = pml pml pml
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my_constants.offset_y = -1100.e-6
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#################################
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############ NUMERICS ###########
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#################################
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warpx.verbose = 1
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warpx.cfl = 0.8
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# vacuum or macroscopic
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algo.em_solver_medium = macroscopic
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# laxwendroff or backwardeuler
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algo.macroscopic_sigma_method = laxwendroff
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macroscopic.sigma_function(x,y,z) = "sigma_0 + (sigma_si - sigma_0) * (z <= h_si)"
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macroscopic.epsilon_function(x,y,z) = "eps_0 + eps_0 * (eps_r_si - 1.) * (z <= h_si)"
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macroscopic.mu_function(x,y,z) = "mu_0 + mu_0 * (mu_r_si - 1.) * (z <= h_si)"
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macroscopic.npy_k_index = 0
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macroscopic.npy_k_index2 = 3
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# comment for PEC, uncomment these for GDS-PEC
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macroscopic.sigma_npy_file = "voyageurs_layer1.npy"
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macroscopic.sigma_npy_file2 = "voyageurs_layer2.npy"
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macroscopic.sigma_npy_value = 1.e11
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algo.use_PEC_mask = 1
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macroscopic.mu_npy_file = "voyageurs_layer1.npy"
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macroscopic.mu_npy_file2 = "voyageurs_layer2.npy"
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macroscopic.mu_npy_value = 1.25663706e-06
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#################################
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############ FIELDS #############
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#################################
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###############
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# domain size
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# n_cellx/y/z and Lx/y/z are needed to calculate dx/dy/dz
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###############
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my_constants.n_cellx = 7544
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my_constants.n_celly = 7544
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my_constants.n_cellz = 4
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my_constants.max_grid_sizex = 92
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my_constants.max_grid_sizey = 92
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my_constants.max_grid_sizez = 4
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my_constants.blocking_factor = 2
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my_constants.prob_lox = 0.
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my_constants.prob_loy = 0.
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my_constants.prob_loz = 0.
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my_constants.prob_hix = 9430.e-6
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my_constants.prob_hiy = 9430.e-6
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my_constants.prob_hiz = 300.e-6
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my_constants.Lx = prob_hix - prob_lox
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my_constants.Ly = prob_hiy - prob_loy
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my_constants.Lz = prob_hiz - prob_loz
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###############
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# material properties
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###############
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my_constants.sigma_0 = 0.0
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my_constants.sigma_si = 0.
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my_constants.eps_0 = 8.8541878128e-12
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my_constants.eps_r_si = 11.7
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my_constants.mu_0 = 1.25663706212e-06
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my_constants.mu_r_si = 1.0
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###############
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# silicon and palladium cross section
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###############
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my_constants.h_si = 150.e-6
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###############
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# derived quantities and fundamental constants - don't touch these
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###############
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my_constants.pi = 3.14159265358979
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my_constants.freq = 8.6e9
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my_constants.TP = 1./freq
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# grid spacing
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my_constants.dx = Lx / n_cellx
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my_constants.dy = Ly / n_celly
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my_constants.dz = Lz / n_cellz
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my_constants.ddx = dx/1.e6
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my_constants.ddy = dy/1.e6
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my_constants.ddz = dz/1.e6
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my_constants.flag_none = 0
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my_constants.flag_hs = 1
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my_constants.flag_ss = 2
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###############
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# excitation
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###############
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warpx.E_excitation_on_grid_style = parse_E_excitation_grid_function
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warpx.Ex_excitation_flag_function(x,y,z) = "flag_none"
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warpx.Ey_excitation_flag_function(x,y,z) = "flag_ss * 0"
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warpx.Ez_excitation_flag_function(x,y,z) = "flag_none"
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# This is a source on a qubit control line
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warpx.Ex_excitation_grid_function(x,y,z,t) = "0."
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warpx.Ey_excitation_grid_function(x,y,z,t) = "0."
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warpx.Ez_excitation_grid_function(x,y,z,t) = "0."
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###############
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# diagnostics
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###############
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warpx.field_io_nfiles=64
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warpx.particle_io_nfiles=64
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diagnostics.diags_names = plt
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###############
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# full plotfiles
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plt.intervals = 1
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plt.fields_to_plot = Ex Ey Ez Bx By Bz mu
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plt.diag_type = Full
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plt.file_min_digits = 7

‎Source/BoundaryConditions/PML.cpp‎

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Original file line numberDiff line numberDiff line change
@@ -723,6 +723,13 @@ PML::PML (const int lev, const BoxArray& grid_ba, const DistributionMapping& gri
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lev,
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macroscopic_properties->m_npy_k_index,
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macroscopic_properties->m_sigma_npy_value);
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if (!macroscopic_properties->m_sigma_npy_filename2.empty()) {
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macroscopic_properties->InitializeMacroMultiFabFromNumpy(pml_sigma_fp.get(),
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macroscopic_properties->m_sigma_npy_filename2,
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lev,
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macroscopic_properties->m_npy_k_index2,
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macroscopic_properties->m_sigma_npy_value);
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}
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}
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if (warpx.use_PEC_mask) {
@@ -732,6 +739,10 @@ PML::PML (const int lev, const BoxArray& grid_ba, const DistributionMapping& gri
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macroscopic_properties->InitializePECFromSigma(pml_sigma_fp.get(), pml_PEC_fp[0].get(), pml_PEC_fp[1].get(),
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macroscopic_properties->m_npy_k_index);
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if (!macroscopic_properties->m_sigma_npy_filename2.empty()) {
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macroscopic_properties->InitializePECFromSigma(pml_sigma_fp.get(), pml_PEC_fp[0].get(), pml_PEC_fp[1].get(),
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macroscopic_properties->m_npy_k_index2);
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}
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// no need for sigma anymore
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pml_sigma_fp.get()->setVal(0.);
@@ -755,6 +766,13 @@ PML::PML (const int lev, const BoxArray& grid_ba, const DistributionMapping& gri
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lev,
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macroscopic_properties->m_npy_k_index,
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macroscopic_properties->m_epsilon_npy_value);
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if (!macroscopic_properties->m_epsilon_npy_filename2.empty()) {
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macroscopic_properties->InitializeMacroMultiFabFromNumpy(pml_eps_fp.get(),
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macroscopic_properties->m_epsilon_npy_filename2,
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lev,
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macroscopic_properties->m_npy_k_index2,
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macroscopic_properties->m_epsilon_npy_value);
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}
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}
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// Initialize mu, permeability
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lev,
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macroscopic_properties->m_npy_k_index,
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macroscopic_properties->m_mu_npy_value);
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if (!macroscopic_properties->m_mu_npy_filename2.empty()) {
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macroscopic_properties->InitializeMacroMultiFabFromNumpy(pml_mu_fp.get(),
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macroscopic_properties->m_mu_npy_filename2,
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lev,
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macroscopic_properties->m_npy_k_index2,
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macroscopic_properties->m_mu_npy_value);
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}
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}
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}

‎Source/FieldSolver/FiniteDifferenceSolver/MacroscopicProperties/MacroscopicProperties.H‎

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@@ -100,10 +100,14 @@ public:
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amrex::Real m_mu = PhysConst::mu0;
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/** index to insert the mask */
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int m_npy_k_index = 0;
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int m_npy_k_index2 = 0;
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/** numpy arrays for layer */
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std::string m_sigma_npy_filename;
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std::string m_sigma_npy_filename2;
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std::string m_epsilon_npy_filename;
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std::string m_epsilon_npy_filename2;
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std::string m_mu_npy_filename;
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std::string m_mu_npy_filename2;
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/** numerical value of sigma, epsilon, and mu for gds numpy array layer */
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amrex::Real m_sigma_npy_value = 0.;
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amrex::Real m_epsilon_npy_value = 0.;

‎Source/FieldSolver/FiniteDifferenceSolver/MacroscopicProperties/MacroscopicProperties.cpp‎

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@@ -44,6 +44,7 @@ MacroscopicProperties::ReadParameters ()
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// Query mask index
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pp_macroscopic.query("npy_k_index", m_npy_k_index);
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pp_macroscopic.query("npy_k_index2", m_npy_k_index2);
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// Query input for material conductivity, sigma.
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pp_macroscopic.query("sigma_npy_value", m_sigma_npy_value);
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m_sigma_s = "parse_sigma_npy_file";
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sigma_specified = true;
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sigma_npy_specified = true;
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// parse second layer
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pp_macroscopic.query("sigma_npy_file2", m_sigma_npy_filename2);
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}
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if (sigma_func_specified && sigma_npy_specified) {
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// initialize both later in InitData
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m_epsilon_s = "parse_epsilon_npy_file";
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epsilon_specified = true;
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epsilon_npy_specified = true;
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pp_macroscopic.query("epsilon_npy_file2", m_epsilon_npy_filename2);
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}
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if (epsilon_func_specified && epsilon_npy_specified) {
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// initialize both later in InitData
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m_mu_s = "parse_mu_npy_file";
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mu_specified = true;
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mu_npy_specified = true;
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pp_macroscopic.query("mu_npy_file2", m_mu_npy_filename2);
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}
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if (mu_func_specified && mu_npy_specified) {
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// initialize both later in InitData
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// Step 2: Overwrite with numpy mask in valid region if provided
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if (m_sigma_s == "parse_sigma_npy_file" || m_sigma_s == "parse_sigma_both") {
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InitializeMacroMultiFabFromNumpy(m_sigma_mf.get(), m_sigma_npy_filename, lev, m_npy_k_index, m_sigma_npy_value);
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if (!m_sigma_npy_filename2.empty()) {
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InitializeMacroMultiFabFromNumpy(m_sigma_mf.get(), m_sigma_npy_filename2, lev, m_npy_k_index2, m_sigma_npy_value);
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}
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}
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274282
if (warpx.use_PEC_mask) {
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PECz->setVal(1.);
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InitializePECFromSigma(m_sigma_mf.get(), PECx, PECy, m_npy_k_index);
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if (!m_sigma_npy_filename2.empty()) {
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InitializePECFromSigma(m_sigma_mf.get(), PECx, PECy, m_npy_k_index2);
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}
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// no need for sigma anymore
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m_sigma_mf->setVal(0.);
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}
@@ -301,6 +312,9 @@ MacroscopicProperties::InitData ()
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// Step 2: Overwrite with numpy mask in valid region if provided
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if (m_epsilon_s == "parse_epsilon_npy_file" || m_epsilon_s == "parse_epsilon_both") {
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InitializeMacroMultiFabFromNumpy(m_eps_mf.get(), m_epsilon_npy_filename, lev, m_npy_k_index, m_epsilon_npy_value);
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if (!m_epsilon_npy_filename2.empty()) {
316+
InitializeMacroMultiFabFromNumpy(m_eps_mf.get(), m_epsilon_npy_filename2, lev, m_npy_k_index2, m_epsilon_npy_value);
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}
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}
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306320
////////////////////////
@@ -318,6 +332,9 @@ MacroscopicProperties::InitData ()
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// Step 2: Overwrite with numpy mask in valid region if provided
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if (m_mu_s == "parse_mu_npy_file" || m_mu_s == "parse_mu_both") {
320334
InitializeMacroMultiFabFromNumpy(m_mu_mf.get(), m_mu_npy_filename, lev, m_npy_k_index, m_mu_npy_value);
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if (!m_mu_npy_filename2.empty()) {
336+
InitializeMacroMultiFabFromNumpy(m_mu_mf.get(), m_mu_npy_filename2, lev, m_npy_k_index2, m_mu_npy_value);
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}
321338
}
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#ifdef WARPX_MAG_LLG

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