├── .gitignore ├── Dockerfile ├── LICENSE.txt ├── README.md ├── backend ├── data │ ├── .log │ ├── .mail │ ├── .msh │ ├── ASTMG173.txt │ ├── Ag_JC.txt │ ├── Ag_Palik.txt │ ├── Al.txt │ ├── Al2O3.txt │ ├── Al2O3_PV.txt │ ├── AlGaAs.txt │ ├── AlN.txt │ ├── AlN_PV.txt │ ├── Al_CRC.txt │ ├── Al_Palik.txt │ ├── Au_CRC.txt │ ├── Au_JC.txt │ ├── Au_Palik.txt │ ├── CH3NH3PbI3.txt │ ├── CdTe.txt │ ├── CuO.txt │ ├── Cu_JC.txt │ ├── Cu_Palik.txt │ ├── FTO_Wenger.txt │ ├── FTO_Wengerk5.txt │ ├── FeS2.txt │ ├── GO_2014.txt │ ├── GO_2015.txt │ ├── GaAs.txt │ ├── GaN.txt │ ├── GaP.txt │ ├── Ge.txt │ ├── Ge_Doped.txt │ ├── H2O.txt │ ├── ITO.txt │ ├── ITO_anneal_Gen_Osc.txt │ ├── InAs.txt │ ├── InGaAs.txt │ ├── InP.txt │ ├── Low_Fe_Glass_Pil.txt │ ├── MgF2.txt │ ├── MoO3.txt │ ├── Perovskite_E_u_00.txt │ ├── Perovskite_Loper_E_u_080.txt │ ├── Perovskite_b2b_nk.txt │ ├── Sb2S3.txt │ ├── Sb2S3_ANU2014.txt │ ├── Sb2S3_ANU2015.txt │ ├── Si3N4.txt │ ├── SiO2.txt │ ├── SiON_High.txt │ ├── SiON_Low.txt │ ├── Si_a.txt │ ├── Si_c.txt │ ├── SnO2.txt │ ├── Soda_lime_glass_nk_Pil.txt │ ├── Spiro.txt │ ├── Spiro_nk_Filipic.txt │ ├── TiO2.txt │ ├── TiO2_anatase.txt │ ├── Zn3P2.txt │ ├── ZnO.txt │ ├── ZnS.txt │ └── rGO_2015.txt ├── fortran │ ├── Completeness.f │ ├── J_dagger_overlap.f │ ├── J_dagger_overlap_1d.f │ ├── J_overlap.f │ ├── J_overlap_1d.f │ ├── K_overlap.f.bak │ ├── Makefile │ ├── Makefile-pre_compiled_libs │ ├── Makefile-silliac │ ├── __init__.py │ ├── array_sol.f │ ├── array_sol_1d.f │ ├── array_sol_P2_1d.f │ ├── asmbly.f │ ├── asmbly_1d.f │ ├── basis_ls.f │ ├── basis_vec.f │ ├── bound_cond.f │ ├── conv_gmsh.f │ ├── conv_gmsh_subroutines.f │ ├── csr_length.f │ ├── csr_max_length.f │ ├── curved_elem_tri.f │ ├── debug.h │ ├── field_value_plane.f │ ├── geometry.f │ ├── geometry_1d.f.bak │ ├── get_coord_p3.f │ ├── gmsh_interface_c4.f │ ├── gmsh_interface_cyl.f │ ├── gmsh_plot_PW.f │ ├── gmsh_plot_field.f │ ├── gmsh_plot_field_3d.f │ ├── gmsh_plot_slice.f │ ├── gmsh_plot_slice_1d.f.bak │ ├── gmsh_post_process.f │ ├── gmsh_post_process_1d.f.bak │ ├── interp_nod_2d.f │ ├── ivalue.f │ ├── jacobian_p1_2d.f │ ├── jacobian_p2_2d.f │ ├── lattice_vec.f │ ├── lib │ │ ├── libamd.a │ │ ├── libcamd.a │ │ ├── libccolamd.a │ │ ├── libcholmod.a │ │ ├── libcolamd.a │ │ ├── libmetis.a │ │ ├── libsuitesparseconfig.a │ │ ├── libumfpack.a │ │ ├── umf4_f77zwrapper64.o │ │ ├── umf4_f77zwrapper_SS_3.7.1.c │ │ └── umf4_f77zwrapper_SS_4.2.0.c │ ├── list_edge.f │ ├── list_face.f │ ├── list_node_P3.f │ ├── mail_to_gmsh.f.bak │ ├── matrix_kxy_1d.f │ ├── matrix_kyx_1d.f │ ├── matrix_kyy_1d.f │ ├── matrix_mxx_1d.f │ ├── matrix_myy_1d.f │ ├── mesh_1d_p2.f.bak │ ├── mode_energy.f │ ├── msh │ │ ├── 16_msh_template.geo │ │ ├── 1D_1_msh_template-horizontal.geo.bak │ │ ├── 1D_1_msh_template-vertical.geo.bak │ │ ├── 1D_1_msh_template.geo.bak │ │ ├── 1D_2_msh_template-horizontal.geo.bak │ │ ├── 1D_2_msh_template.geo.bak │ │ ├── 1_2strip_msh_template.geo │ │ ├── 1_msh_template.geo │ │ ├── 1_strip_msh_template.geo │ │ ├── 2_msh_template.geo │ │ ├── 3_msh_template.geo │ │ ├── 4_msh_template.geo │ │ ├── 4testing-600_120.geo │ │ ├── 4testing-600_120.mail │ │ ├── 4testing-940_266_sq.geo │ │ ├── 4testing-940_266_sq.mail │ │ ├── 9_msh_template.geo │ │ ├── L_msh_template.geo │ │ ├── SRR_msh_template.geo │ │ ├── chiral_slits_msh_template.geo │ │ ├── cross1_msh_template.geo │ │ ├── cross_shell1_msh_template.geo │ │ ├── dimer1_msh_template.geo │ │ ├── egg_inclusion_msh_template.geo │ │ ├── egg_msh_template.geo │ │ ├── elle_msh_template.geo │ │ ├── ellipse_msh_template.geo │ │ ├── hex_msh_template.geo │ │ ├── rect1_msh_template.geo │ │ ├── rect_shell1_msh_template.geo │ │ ├── ring1_msh_template.geo │ │ ├── row_2_msh_template.geo │ │ ├── row_5_msh_template.geo │ │ ├── square_dimer1_msh_template.geo │ │ └── square_shell_dimer1_msh_template.geo │ ├── normalisation.f │ ├── normalisation_1d.f │ ├── orthogonal.f │ ├── orthogonal_1d.f │ ├── periodic_N_E_F.f │ ├── periodic_cond.f │ ├── periodic_cond_1d.f │ ├── periodic_node.f │ ├── phi1_2d_mat.f │ ├── phi2_2d_mat.f │ ├── phi2_2d_mat_J.f │ ├── phi3_2d_mat.f │ ├── pw_matrix_1d_to_2d.f │ ├── pw_ordering.f │ ├── pw_ordering_1d.f │ ├── py_calc_modes.f │ ├── py_calc_modes_1d.f │ ├── py_plot_field.f.bak │ ├── quad_triangle.f │ ├── slice_interp.f │ ├── sort_csr.f │ ├── sort_int.f │ ├── sort_n.f │ ├── stat.h │ ├── type_node_edge_face.f │ ├── valpr_lapack_1d.f │ ├── valpr_umf_64.f │ ├── vector_p2_exp_1d.f │ ├── vector_p3_exp_1d.f │ ├── write_param.f.bak │ ├── write_sol.f │ ├── write_sol_P2_1d.f │ ├── z_indexx.f │ ├── z_mxv_csc_64.f │ ├── zarpack.f │ └── zarpack_util.f ├── materials.py ├── mode_calcs.py ├── objects.py ├── paths.py ├── plotting.py └── stack.py ├── dependencies.txt ├── docker_install.md ├── docs ├── Makefile ├── build │ └── latex │ │ └── EMUstack.pdf ├── requirements.txt └── source │ ├── conf.py │ ├── fem_1d.rst │ ├── fem_2d.rst │ ├── index.rst │ ├── install.rst │ ├── intro.rst │ ├── materials.rst │ ├── mode_calcs.rst │ ├── objects.rst │ ├── plotting.rst │ ├── screen_sesh.rst │ ├── stack.rst │ └── tutorial.rst ├── examples ├── Au Nanodisk Array with Interpolators.ipynb ├── Elliptical Nanohole Array (custom target interface).ipynb ├── simo_010-single_interface.py ├── simo_011-single_interface-dispersive.py ├── simo_020-thin_film_multilayered_stack.py ├── simo_021-thin_film_mirror.py ├── simo_030-1D_grating.py ├── simo_031-1D_grating-2_inclusions.py ├── simo_032-1D_grating-3_inclusions.py ├── simo_040-2D_array.py ├── simo_041-combining_1D_and_2D_array.py ├── simo_042-eliptical_holes-CD.py ├── simo_050-plotting_fields_1d.py ├── simo_051-plotting_fields_2d.py ├── simo_052-plotting_amplitudes.py ├── simo_053-plotting_k_space_amps.py ├── simo_060-shear_transformations.py ├── simo_070-ultrathin_limit.py ├── simo_071-many_substrates.py ├── simo_080-convergence-stacked_gratings.py ├── simo_090-EOT.py └── simo_091-slab_mode_finding.py ├── overrides.json ├── reload_simo └── simo_reload.py ├── setup.sh └── tests ├── ref ├── case_0.npz ├── case_0 │ ├── Absorptance_stack0001.txt │ ├── Efficiency_stack0001.txt │ ├── Lay_Absorb_0_stack0001.txt │ ├── Lay_Absorb_1_stack0001.txt │ ├── Lay_Absorb_2_stack0001.txt │ ├── Lay_Absorb_3_stack0001.txt │ ├── Lay_Absorb_4_stack0001.txt │ ├── Lay_Trans_0_stack0001.txt │ ├── Lay_Trans_1_stack0001.txt │ ├── Lay_Trans_2_stack0001.txt │ ├── Lay_Trans_3_stack0001.txt │ ├── Lay_Trans_4_stack0001.txt │ ├── Reflectance_stack0001.txt │ └── Transmittance_stack0001.txt ├── case_1.npz ├── case_1 │ ├── Absorptance_stack0001.txt │ ├── Efficiency_stack0001.txt │ ├── Lay_Absorb_0_stack0001.txt │ ├── Lay_Trans_0_stack0001.txt │ ├── Reflectance_stack0001.txt │ └── Transmittance_stack0001.txt ├── case_2.npz ├── case_2 │ ├── Absorptance_stack0001.txt │ ├── Lay_Absorb_0_stack0001.txt │ ├── Lay_Trans_0_stack0001.txt │ ├── Reflectance_stack0001.txt │ └── Transmittance_stack0001.txt ├── case_3.npz ├── case_3 │ ├── Absorptance_stack0001.txt │ ├── 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