├── .DS_Store ├── .astylerc ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── project-goal.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ └── main.yml ├── .gitignore ├── .vscode ├── c_cpp_properties.json ├── launch.json ├── settings.json └── tasks.json ├── CMakeLists.txt ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── REPORTING_GUIDELINES.md ├── doc ├── Doxyfile ├── citations.md ├── debug.md ├── design │ └── standards.md ├── dev_team.md ├── ensembles.md ├── indices.md ├── installation.md ├── running_aether.md └── student.md ├── edu └── examples │ ├── Advection │ ├── advect.cpp │ ├── cubesphere_test.cpp │ ├── euler.cpp │ ├── fluid2d.cpp │ ├── plot.py │ ├── plot2d.py │ ├── run.sh │ └── shallow.cpp │ ├── Fortran │ ├── call_msis.f90 │ ├── compile_msis │ ├── main_v2.cpp │ ├── msis2.1_test.F90 │ ├── msis2.1_test_in.txt │ ├── msis2.1_test_out.txt │ ├── msis2.1_test_ref_dp.txt │ ├── msis21.parm │ ├── msis_all.F90 │ ├── msis_calc.F90 │ ├── msis_constants.F90 │ ├── msis_dfn.F90 │ ├── msis_gfn.F90 │ ├── msis_gtd8d.F90 │ ├── msis_init.F90 │ ├── msis_tfn.F90 │ ├── msis_utils.F90 │ ├── nrlmsis2.1_license.txt │ ├── print_hi.f90 │ ├── readme.txt │ ├── run_msis.cpp │ └── subroutine_dir.png │ ├── Mpi │ └── main.cpp │ ├── Netcdf │ ├── PresTemp4dRd.cpp │ ├── PresTemp4dWr.cpp │ ├── SfcPresTempWr.cpp │ ├── SimpleXyWr.cpp │ └── netcdf_cxx4_example │ │ ├── 3DBFI_20110320_000005.nc │ │ └── main.cpp │ ├── OpenMP │ ├── first.cpp │ └── pi.cpp │ ├── Random │ └── test_random.cpp │ ├── arm.cpp │ └── arm_vars.h ├── ext ├── IE │ ├── AMIE_Library.f90 │ ├── EIE_Initialize.f90 │ ├── EIE_IoLibrary.f90 │ ├── EIE_Library.f90 │ ├── EIE_set_inputs.f90 │ ├── ModAMIE_Interface.f90 │ ├── ModCharSize.f90 │ ├── ModConst.f90 │ ├── ModEIEConductance.f90 │ ├── ModEIEFiles.f90 │ ├── ModEIE_Interface.f90 │ ├── ModErrors.f90 │ ├── ModExtras.f90 │ ├── ModFtaModel.f90 │ ├── ModKind.f90 │ ├── ModNumConst.f90 │ ├── ModTimeConvert.f90 │ ├── ModWeimer.f │ ├── ModWeimer05.f90 │ ├── call_ie_from_c.f90 │ ├── hmr89.f │ ├── ihp.f90 │ ├── iz94.f │ ├── merge_str.f90 │ ├── mh86.f │ └── readAMIEoutput.f90 └── MSIS │ ├── call_msis.f90 │ ├── msis_calc.F90 │ ├── msis_constants.F90 │ ├── msis_dfn.F90 │ ├── msis_gfn.F90 │ ├── msis_gtd8d.F90 │ ├── msis_init.F90 │ ├── msis_tfn.F90 │ └── msis_utils.F90 ├── include ├── .DS_Store ├── advance.h ├── aether.h ├── aurora.h ├── bfield.h ├── calc_chemistry.h ├── calc_euv.h ├── calc_grid_derived.h ├── calc_momentum_friction.h ├── chemistry.h ├── collisions.h ├── constants.h ├── cubesphere.h ├── electrodynamics.h ├── euv.h ├── external_msis.h ├── file_input.h ├── fill_grid.h ├── grid.h ├── indices.h ├── init_geo_grid.h ├── inputs.h ├── ions.h ├── logfile.h ├── neutrals.h ├── output.h ├── parallel.h ├── planets.h ├── quadtree.h ├── read_collision_file.h ├── read_indices_files.h ├── report.h ├── sizes.h ├── solvers.h ├── sphere.h ├── time_conversion.h ├── times.h ├── tools.h └── transform.h ├── requirements.linux ├── requirements.mac ├── share ├── FindNetCDF.cmake ├── examples │ ├── README │ ├── aether.json │ ├── aether_20130317.json │ ├── aether_cubesphere.json │ ├── aether_ensemble.json │ ├── aether_partial.json │ ├── aether_sphere.json │ └── aether_stretch_alt.json ├── include │ ├── armadillo │ ├── armadillo_bits │ │ ├── BaseCube_bones.hpp │ │ ├── BaseCube_meat.hpp │ │ ├── Base_bones.hpp │ │ ├── Base_meat.hpp │ │ ├── Col_bones.hpp │ │ ├── Col_meat.hpp │ │ ├── CubeToMatOp_bones.hpp │ │ ├── CubeToMatOp_meat.hpp │ │ ├── Cube_bones.hpp │ │ ├── Cube_meat.hpp │ │ ├── GenCube_bones.hpp │ │ ├── GenCube_meat.hpp │ │ ├── GenSpecialiser.hpp │ │ ├── Gen_bones.hpp │ │ ├── Gen_meat.hpp │ │ ├── GlueCube_bones.hpp │ │ ├── GlueCube_meat.hpp │ │ ├── Glue_bones.hpp │ │ ├── Glue_meat.hpp │ │ ├── MapMat_bones.hpp │ │ ├── MapMat_meat.hpp │ │ ├── Mat_bones.hpp │ │ ├── Mat_meat.hpp │ │ ├── OpCube_bones.hpp │ │ ├── OpCube_meat.hpp │ │ ├── Op_bones.hpp │ │ ├── Op_meat.hpp │ │ ├── Proxy.hpp │ │ ├── ProxyCube.hpp │ │ ├── Row_bones.hpp │ │ ├── Row_meat.hpp │ │ ├── SizeCube_bones.hpp │ │ ├── SizeCube_meat.hpp │ │ ├── SizeMat_bones.hpp │ │ ├── SizeMat_meat.hpp │ │ ├── SpBase_bones.hpp │ │ ├── SpBase_meat.hpp │ │ ├── SpCol_bones.hpp │ │ ├── SpCol_meat.hpp │ │ ├── SpGlue_bones.hpp │ │ ├── SpGlue_meat.hpp │ │ ├── SpMat_bones.hpp │ │ ├── SpMat_iterators_meat.hpp │ │ ├── SpMat_meat.hpp │ │ ├── SpOp_bones.hpp │ │ ├── SpOp_meat.hpp │ │ ├── SpProxy.hpp │ │ ├── SpRow_bones.hpp │ │ ├── SpRow_meat.hpp │ │ ├── SpSubview_bones.hpp │ │ ├── SpSubview_col_list_bones.hpp │ │ ├── SpSubview_col_list_meat.hpp │ │ ├── SpSubview_iterators_meat.hpp │ │ ├── SpSubview_meat.hpp │ │ ├── SpToDOp_bones.hpp │ │ ├── SpToDOp_meat.hpp │ │ ├── SpValProxy_bones.hpp │ │ ├── SpValProxy_meat.hpp │ │ ├── access.hpp │ │ ├── arma_cmath.hpp │ │ ├── arma_config.hpp │ │ ├── arma_forward.hpp │ │ ├── arma_ostream_bones.hpp │ │ ├── arma_ostream_meat.hpp │ │ ├── arma_rel_comparators.hpp │ │ ├── arma_rng.hpp │ │ ├── arma_rng_cxx11.hpp │ │ ├── arma_rng_cxx98.hpp │ │ ├── arma_static_check.hpp │ │ ├── arma_str.hpp │ │ ├── arma_version.hpp │ │ ├── arrayops_bones.hpp │ │ ├── arrayops_meat.hpp │ │ ├── auxlib_bones.hpp │ │ ├── auxlib_meat.hpp │ │ ├── band_helper.hpp │ │ ├── compiler_check.hpp │ │ ├── compiler_setup.hpp │ │ ├── compiler_setup_post.hpp │ │ ├── cond_rel_bones.hpp │ │ ├── cond_rel_meat.hpp │ │ ├── config.hpp │ │ ├── config.hpp.cmake │ │ ├── constants.hpp │ │ ├── constants_old.hpp │ │ ├── csv_name.hpp │ │ ├── debug.hpp │ │ ├── def_arpack.hpp │ │ ├── def_atlas.hpp │ │ ├── def_blas.hpp │ │ ├── def_hdf5.hpp │ │ ├── def_lapack.hpp │ │ ├── def_superlu.hpp │ │ ├── diagmat_proxy.hpp │ │ ├── diagview_bones.hpp │ │ ├── diagview_meat.hpp │ │ ├── diskio_bones.hpp │ │ ├── diskio_meat.hpp │ │ ├── distr_param.hpp │ │ ├── eGlueCube_bones.hpp │ │ ├── eGlueCube_meat.hpp │ │ ├── eGlue_bones.hpp │ │ ├── eGlue_meat.hpp │ │ ├── eOpCube_bones.hpp │ │ ├── eOpCube_meat.hpp │ │ ├── eOp_bones.hpp │ │ ├── eOp_meat.hpp │ │ ├── eglue_core_bones.hpp │ │ ├── eglue_core_meat.hpp │ │ ├── eop_aux.hpp │ │ ├── eop_core_bones.hpp │ │ ├── eop_core_meat.hpp │ │ ├── fft_engine.hpp │ │ ├── field_bones.hpp │ │ ├── field_meat.hpp │ │ ├── fill.hpp │ │ ├── fn_accu.hpp │ │ ├── fn_all.hpp │ │ ├── fn_any.hpp │ │ ├── fn_approx_equal.hpp │ │ ├── fn_as_scalar.hpp │ │ ├── fn_chi2rnd.hpp │ │ ├── fn_chol.hpp │ │ ├── fn_clamp.hpp │ │ ├── fn_cond.hpp │ │ ├── fn_conv.hpp │ │ ├── fn_conv_to.hpp │ │ ├── fn_cor.hpp │ │ ├── fn_cov.hpp │ │ ├── fn_cross.hpp │ │ ├── fn_cumprod.hpp │ │ ├── fn_cumsum.hpp │ │ ├── fn_det.hpp │ │ ├── fn_diagmat.hpp │ │ ├── fn_diagvec.hpp │ │ ├── fn_diff.hpp │ │ ├── fn_dot.hpp │ │ ├── fn_eig_gen.hpp │ │ ├── fn_eig_pair.hpp │ │ ├── fn_eig_sym.hpp │ │ ├── fn_eigs_gen.hpp │ │ ├── fn_eigs_sym.hpp │ │ ├── fn_elem.hpp │ │ ├── fn_eps.hpp │ │ ├── fn_expmat.hpp │ │ ├── fn_eye.hpp │ │ ├── fn_fft.hpp │ │ ├── fn_fft2.hpp │ │ ├── fn_find.hpp │ │ ├── fn_find_unique.hpp │ │ ├── fn_flip.hpp │ │ ├── fn_hess.hpp │ │ ├── fn_hist.hpp │ │ ├── fn_histc.hpp │ │ ├── fn_index_max.hpp │ │ ├── fn_index_min.hpp │ │ ├── fn_inplace_strans.hpp │ │ ├── fn_inplace_trans.hpp │ │ ├── fn_interp1.hpp │ │ ├── fn_interp2.hpp │ │ ├── fn_intersect.hpp │ │ ├── fn_inv.hpp │ │ ├── fn_join.hpp │ │ ├── fn_kmeans.hpp │ │ ├── fn_kron.hpp │ │ ├── fn_log_det.hpp │ │ ├── fn_log_normpdf.hpp │ │ ├── fn_logmat.hpp │ │ ├── fn_lu.hpp │ │ ├── fn_max.hpp │ │ ├── fn_mean.hpp │ │ ├── fn_median.hpp │ │ ├── fn_min.hpp │ │ ├── fn_misc.hpp │ │ ├── fn_mvnrnd.hpp │ │ ├── fn_n_unique.hpp │ │ ├── fn_nonzeros.hpp │ │ ├── fn_norm.hpp │ │ ├── fn_normalise.hpp │ │ ├── fn_normcdf.hpp │ │ ├── fn_normpdf.hpp │ │ ├── fn_numel.hpp │ │ ├── fn_ones.hpp │ │ ├── fn_orth_null.hpp │ │ ├── fn_pinv.hpp │ │ ├── fn_polyfit.hpp │ │ ├── fn_polyval.hpp │ │ ├── fn_powmat.hpp │ │ ├── fn_princomp.hpp │ │ ├── fn_prod.hpp │ │ ├── fn_qr.hpp │ │ ├── fn_quantile.hpp │ │ ├── fn_qz.hpp │ │ ├── fn_randg.hpp │ │ ├── fn_randi.hpp │ │ ├── fn_randn.hpp │ │ ├── fn_randperm.hpp │ │ ├── fn_randu.hpp │ │ ├── fn_range.hpp │ │ ├── fn_rank.hpp │ │ ├── fn_regspace.hpp │ │ ├── fn_repelem.hpp │ │ ├── fn_repmat.hpp │ │ ├── fn_reshape.hpp │ │ ├── fn_resize.hpp │ │ ├── fn_reverse.hpp │ │ ├── fn_roots.hpp │ │ ├── fn_schur.hpp │ │ ├── fn_shift.hpp │ │ ├── fn_shuffle.hpp │ │ ├── fn_size.hpp │ │ ├── fn_solve.hpp │ │ ├── fn_sort.hpp │ │ ├── fn_sort_index.hpp │ │ ├── fn_speye.hpp │ │ ├── fn_spones.hpp │ │ ├── fn_sprandn.hpp │ │ ├── fn_sprandu.hpp │ │ ├── fn_spsolve.hpp │ │ ├── fn_sqrtmat.hpp │ │ ├── fn_stddev.hpp │ │ ├── fn_strans.hpp │ │ ├── fn_sum.hpp │ │ ├── fn_svd.hpp │ │ ├── fn_svds.hpp │ │ ├── fn_sylvester.hpp │ │ ├── fn_symmat.hpp │ │ ├── fn_toeplitz.hpp │ │ ├── fn_trace.hpp │ │ ├── fn_trans.hpp │ │ ├── fn_trapz.hpp │ │ ├── fn_trig.hpp │ │ ├── fn_trimat.hpp │ │ ├── fn_trimat_ind.hpp │ │ ├── fn_trunc_exp.hpp │ │ ├── fn_trunc_log.hpp │ │ ├── fn_unique.hpp │ │ ├── fn_var.hpp │ │ ├── fn_vectorise.hpp │ │ ├── fn_wishrnd.hpp │ │ ├── fn_zeros.hpp │ │ ├── glue_affmul_bones.hpp │ │ ├── glue_affmul_meat.hpp │ │ ├── glue_atan2_bones.hpp │ │ ├── glue_atan2_meat.hpp │ │ ├── glue_conv_bones.hpp │ │ ├── glue_conv_meat.hpp │ │ ├── glue_cor_bones.hpp │ │ ├── glue_cor_meat.hpp │ │ ├── glue_cov_bones.hpp │ │ ├── glue_cov_meat.hpp │ │ ├── glue_cross_bones.hpp │ │ ├── glue_cross_meat.hpp │ │ ├── glue_hist_bones.hpp │ │ ├── glue_hist_meat.hpp │ │ ├── glue_histc_bones.hpp │ │ ├── glue_histc_meat.hpp │ │ ├── glue_hypot_bones.hpp │ │ ├── glue_hypot_meat.hpp │ │ ├── glue_intersect_bones.hpp │ │ ├── glue_intersect_meat.hpp │ │ ├── glue_join_bones.hpp │ │ ├── glue_join_meat.hpp │ │ ├── glue_kron_bones.hpp │ │ ├── glue_kron_meat.hpp │ │ ├── glue_max_bones.hpp │ │ ├── glue_max_meat.hpp │ │ ├── glue_min_bones.hpp │ │ ├── glue_min_meat.hpp │ │ ├── glue_mixed_bones.hpp │ │ ├── glue_mixed_meat.hpp │ │ ├── glue_mvnrnd_bones.hpp │ │ ├── glue_mvnrnd_meat.hpp │ │ ├── glue_polyfit_bones.hpp │ │ ├── glue_polyfit_meat.hpp │ │ ├── glue_polyval_bones.hpp │ │ ├── glue_polyval_meat.hpp │ │ ├── glue_quantile_bones.hpp │ │ ├── glue_quantile_meat.hpp │ │ ├── glue_relational_bones.hpp │ │ ├── glue_relational_meat.hpp │ │ ├── glue_solve_bones.hpp │ │ ├── glue_solve_meat.hpp │ │ ├── glue_times_bones.hpp │ │ ├── glue_times_meat.hpp │ │ ├── glue_toeplitz_bones.hpp │ │ ├── glue_toeplitz_meat.hpp │ │ ├── glue_trapz_bones.hpp │ │ ├── glue_trapz_meat.hpp │ │ ├── gmm_diag_bones.hpp │ │ ├── gmm_diag_meat.hpp │ │ ├── gmm_full_bones.hpp │ │ ├── gmm_full_meat.hpp │ │ ├── gmm_misc_bones.hpp │ │ ├── gmm_misc_meat.hpp │ │ ├── hdf5_misc.hpp │ │ ├── hdf5_name.hpp │ │ ├── include_atlas.hpp │ │ ├── include_hdf5.hpp │ │ ├── include_superlu.hpp │ │ ├── injector_bones.hpp │ │ ├── injector_meat.hpp │ │ ├── memory.hpp │ │ ├── mp_misc.hpp │ │ ├── mtGlueCube_bones.hpp │ │ ├── mtGlueCube_meat.hpp │ │ ├── mtGlue_bones.hpp │ │ ├── mtGlue_meat.hpp │ │ ├── mtOpCube_bones.hpp │ │ ├── mtOpCube_meat.hpp │ │ ├── mtOp_bones.hpp │ │ ├── mtOp_meat.hpp │ │ ├── mtSpGlue_bones.hpp │ │ ├── mtSpGlue_meat.hpp │ │ ├── mtSpOp_bones.hpp │ │ ├── mtSpOp_meat.hpp │ │ ├── mul_gemm.hpp │ │ ├── mul_gemm_mixed.hpp │ │ ├── mul_gemv.hpp │ │ ├── mul_herk.hpp │ │ ├── mul_syrk.hpp │ │ ├── newarp_DenseGenMatProd_bones.hpp │ │ ├── newarp_DenseGenMatProd_meat.hpp │ │ ├── newarp_DoubleShiftQR_bones.hpp │ │ ├── newarp_DoubleShiftQR_meat.hpp │ │ ├── newarp_EigsSelect.hpp │ │ ├── newarp_GenEigsSolver_bones.hpp │ │ ├── newarp_GenEigsSolver_meat.hpp │ │ ├── newarp_SortEigenvalue.hpp │ │ ├── newarp_SparseGenMatProd_bones.hpp │ │ ├── newarp_SparseGenMatProd_meat.hpp │ │ ├── newarp_SparseGenRealShiftSolve_bones.hpp │ │ ├── newarp_SparseGenRealShiftSolve_meat.hpp │ │ ├── newarp_SymEigsShiftSolver_bones.hpp │ │ ├── newarp_SymEigsShiftSolver_meat.hpp │ │ ├── newarp_SymEigsSolver_bones.hpp │ │ ├── newarp_SymEigsSolver_meat.hpp │ │ ├── newarp_TridiagEigen_bones.hpp │ │ ├── newarp_TridiagEigen_meat.hpp │ │ ├── newarp_UpperHessenbergEigen_bones.hpp │ │ ├── newarp_UpperHessenbergEigen_meat.hpp │ │ ├── newarp_UpperHessenbergQR_bones.hpp │ │ ├── newarp_UpperHessenbergQR_meat.hpp │ │ ├── newarp_cx_attrib.hpp │ │ ├── op_all_bones.hpp │ │ ├── op_all_meat.hpp │ │ ├── op_any_bones.hpp │ │ ├── op_any_meat.hpp │ │ ├── op_chi2rnd_bones.hpp │ │ ├── op_chi2rnd_meat.hpp │ │ ├── op_chol_bones.hpp │ │ ├── op_chol_meat.hpp │ │ ├── op_clamp_bones.hpp │ │ ├── op_clamp_meat.hpp │ │ ├── op_cond_bones.hpp │ │ ├── op_cond_meat.hpp │ │ ├── op_cor_bones.hpp │ │ ├── op_cor_meat.hpp │ │ ├── op_cov_bones.hpp │ │ ├── op_cov_meat.hpp │ │ ├── op_cumprod_bones.hpp │ │ ├── op_cumprod_meat.hpp │ │ ├── op_cumsum_bones.hpp │ │ ├── op_cumsum_meat.hpp │ │ ├── op_cx_scalar_bones.hpp │ │ ├── op_cx_scalar_meat.hpp │ │ ├── op_det_bones.hpp │ │ ├── op_det_meat.hpp │ │ ├── op_diagmat_bones.hpp │ │ ├── op_diagmat_meat.hpp │ │ ├── op_diagvec_bones.hpp │ │ ├── op_diagvec_meat.hpp │ │ ├── op_diff_bones.hpp │ │ ├── op_diff_meat.hpp │ │ ├── op_dot_bones.hpp │ │ ├── op_dot_meat.hpp │ │ ├── op_dotext_bones.hpp │ │ ├── op_dotext_meat.hpp │ │ ├── op_expmat_bones.hpp │ │ ├── op_expmat_meat.hpp │ │ ├── op_fft_bones.hpp │ │ ├── op_fft_meat.hpp │ │ ├── op_find_bones.hpp │ │ ├── op_find_meat.hpp │ │ ├── op_find_unique_bones.hpp │ │ ├── op_find_unique_meat.hpp │ │ ├── op_flip_bones.hpp │ │ ├── op_flip_meat.hpp │ │ ├── op_hist_bones.hpp │ │ ├── op_hist_meat.hpp │ │ ├── op_htrans_bones.hpp │ │ ├── op_htrans_meat.hpp │ │ ├── op_index_max_bones.hpp │ │ ├── op_index_max_meat.hpp │ │ ├── op_index_min_bones.hpp │ │ ├── op_index_min_meat.hpp │ │ ├── op_inv_bones.hpp │ │ ├── op_inv_meat.hpp │ │ ├── op_log_det_bones.hpp │ │ ├── op_log_det_meat.hpp │ │ ├── op_logmat_bones.hpp │ │ ├── op_logmat_meat.hpp │ │ ├── op_max_bones.hpp │ │ ├── op_max_meat.hpp │ │ ├── op_mean_bones.hpp │ │ ├── op_mean_meat.hpp │ │ ├── op_median_bones.hpp │ │ ├── op_median_meat.hpp │ │ ├── op_min_bones.hpp │ │ ├── op_min_meat.hpp │ │ ├── op_misc_bones.hpp │ │ ├── op_misc_meat.hpp │ │ ├── op_nonzeros_bones.hpp │ │ ├── op_nonzeros_meat.hpp │ │ ├── op_norm_bones.hpp │ │ ├── op_norm_meat.hpp │ │ ├── op_normalise_bones.hpp │ │ ├── op_normalise_meat.hpp │ │ ├── op_orth_null_bones.hpp │ │ ├── op_orth_null_meat.hpp │ │ ├── op_pinv_bones.hpp │ │ ├── op_pinv_meat.hpp │ │ ├── op_powmat_bones.hpp │ │ ├── op_powmat_meat.hpp │ │ ├── op_princomp_bones.hpp │ │ ├── op_princomp_meat.hpp │ │ ├── op_prod_bones.hpp │ │ ├── op_prod_meat.hpp │ │ ├── op_range_bones.hpp │ │ ├── op_range_meat.hpp │ │ ├── op_relational_bones.hpp │ │ ├── op_relational_meat.hpp │ │ ├── op_repelem_bones.hpp │ │ ├── op_repelem_meat.hpp │ │ ├── op_repmat_bones.hpp │ │ ├── op_repmat_meat.hpp │ │ ├── op_reshape_bones.hpp │ │ ├── op_reshape_meat.hpp │ │ ├── op_resize_bones.hpp │ │ ├── op_resize_meat.hpp │ │ ├── op_reverse_bones.hpp │ │ ├── op_reverse_meat.hpp │ │ ├── op_roots_bones.hpp │ │ ├── op_roots_meat.hpp │ │ ├── op_shift_bones.hpp │ │ ├── op_shift_meat.hpp │ │ ├── op_shuffle_bones.hpp │ │ ├── op_shuffle_meat.hpp │ │ ├── op_sort_bones.hpp │ │ ├── op_sort_index_bones.hpp │ │ ├── op_sort_index_meat.hpp │ │ ├── op_sort_meat.hpp │ │ ├── op_sp_minus_bones.hpp │ │ ├── op_sp_minus_meat.hpp │ │ ├── op_sp_plus_bones.hpp │ │ ├── op_sp_plus_meat.hpp │ │ ├── op_sqrtmat_bones.hpp │ │ ├── op_sqrtmat_meat.hpp │ │ ├── op_stddev_bones.hpp │ │ ├── op_stddev_meat.hpp │ │ ├── op_strans_bones.hpp │ │ ├── op_strans_meat.hpp │ │ ├── op_sum_bones.hpp │ │ ├── op_sum_meat.hpp │ │ ├── op_symmat_bones.hpp │ │ ├── op_symmat_meat.hpp │ │ ├── op_toeplitz_bones.hpp │ │ ├── op_toeplitz_meat.hpp │ │ ├── op_trimat_bones.hpp │ │ ├── op_trimat_meat.hpp │ │ ├── op_unique_bones.hpp │ │ ├── op_unique_meat.hpp │ │ ├── op_var_bones.hpp │ │ ├── op_var_meat.hpp │ │ ├── op_vectorise_bones.hpp │ │ ├── op_vectorise_meat.hpp │ │ ├── op_wishrnd_bones.hpp │ │ ├── op_wishrnd_meat.hpp │ │ ├── operator_cube_div.hpp │ │ ├── operator_cube_minus.hpp │ │ ├── operator_cube_plus.hpp │ │ ├── operator_cube_relational.hpp │ │ ├── operator_cube_schur.hpp │ │ ├── operator_cube_times.hpp │ │ ├── operator_div.hpp │ │ ├── operator_minus.hpp │ │ ├── operator_ostream.hpp │ │ ├── operator_plus.hpp │ │ ├── operator_relational.hpp │ │ ├── operator_schur.hpp │ │ ├── operator_times.hpp │ │ ├── podarray_bones.hpp │ │ ├── podarray_meat.hpp │ │ ├── promote_type.hpp │ │ ├── restrictors.hpp │ │ ├── running_stat_bones.hpp │ │ ├── running_stat_meat.hpp │ │ ├── running_stat_vec_bones.hpp │ │ ├── running_stat_vec_meat.hpp │ │ ├── sp_auxlib_bones.hpp │ │ ├── sp_auxlib_meat.hpp │ │ ├── span.hpp │ │ ├── spdiagview_bones.hpp │ │ ├── spdiagview_meat.hpp │ │ ├── spglue_join_bones.hpp │ │ ├── spglue_join_meat.hpp │ │ ├── spglue_kron_bones.hpp │ │ ├── spglue_kron_meat.hpp │ │ ├── spglue_max_bones.hpp │ │ ├── spglue_max_meat.hpp │ │ ├── spglue_merge_bones.hpp │ │ ├── spglue_merge_meat.hpp │ │ ├── spglue_min_bones.hpp │ │ ├── spglue_min_meat.hpp │ │ ├── spglue_minus_bones.hpp │ │ ├── spglue_minus_meat.hpp │ │ ├── spglue_plus_bones.hpp │ │ ├── spglue_plus_meat.hpp │ │ ├── spglue_relational_bones.hpp │ │ ├── spglue_relational_meat.hpp │ │ ├── spglue_schur_bones.hpp │ │ ├── spglue_schur_meat.hpp │ │ ├── spglue_times_bones.hpp │ │ ├── spglue_times_meat.hpp │ │ ├── spop_diagmat_bones.hpp │ │ ├── spop_diagmat_meat.hpp │ │ ├── spop_htrans_bones.hpp │ │ ├── spop_htrans_meat.hpp │ │ ├── spop_max_bones.hpp │ │ ├── spop_max_meat.hpp │ │ ├── spop_mean_bones.hpp │ │ ├── spop_mean_meat.hpp │ │ ├── spop_min_bones.hpp │ │ ├── spop_min_meat.hpp │ │ ├── spop_misc_bones.hpp │ │ ├── spop_misc_meat.hpp │ │ ├── spop_norm_bones.hpp │ │ ├── spop_norm_meat.hpp │ │ ├── spop_normalise_bones.hpp │ │ ├── spop_normalise_meat.hpp │ │ ├── spop_repmat_bones.hpp │ │ ├── spop_repmat_meat.hpp │ │ ├── spop_reverse_bones.hpp │ │ ├── spop_reverse_meat.hpp │ │ ├── spop_strans_bones.hpp │ │ ├── spop_strans_meat.hpp │ │ ├── spop_sum_bones.hpp │ │ ├── spop_sum_meat.hpp │ │ ├── spop_symmat_bones.hpp │ │ ├── spop_symmat_meat.hpp │ │ ├── spop_trimat_bones.hpp │ │ ├── spop_trimat_meat.hpp │ │ ├── spop_var_bones.hpp │ │ ├── spop_var_meat.hpp │ │ ├── spop_vectorise_bones.hpp │ │ ├── spop_vectorise_meat.hpp │ │ ├── strip.hpp │ │ ├── subview_bones.hpp │ │ ├── subview_cube_bones.hpp │ │ ├── subview_cube_each_bones.hpp │ │ ├── subview_cube_each_meat.hpp │ │ ├── subview_cube_meat.hpp │ │ ├── subview_cube_slices_bones.hpp │ │ ├── subview_cube_slices_meat.hpp │ │ ├── subview_each_bones.hpp │ │ ├── subview_each_meat.hpp │ │ ├── subview_elem1_bones.hpp │ │ ├── subview_elem1_meat.hpp │ │ ├── subview_elem2_bones.hpp │ │ ├── subview_elem2_meat.hpp │ │ ├── subview_field_bones.hpp │ │ ├── subview_field_meat.hpp │ │ ├── subview_meat.hpp │ │ ├── sympd_helper.hpp │ │ ├── traits.hpp │ │ ├── translate_arpack.hpp │ │ ├── translate_atlas.hpp │ │ ├── translate_blas.hpp │ │ ├── translate_lapack.hpp │ │ ├── translate_superlu.hpp │ │ ├── trimat_helper.hpp │ │ ├── typedef_elem.hpp │ │ ├── typedef_elem_check.hpp │ │ ├── typedef_mat.hpp │ │ ├── typedef_mat_fixed.hpp │ │ ├── unwrap.hpp │ │ ├── unwrap_cube.hpp │ │ ├── unwrap_spmat.hpp │ │ ├── upgrade_val.hpp │ │ ├── wall_clock_bones.hpp │ │ ├── wall_clock_meat.hpp │ │ ├── xtrans_mat_bones.hpp │ │ ├── xtrans_mat_meat.hpp │ │ ├── xvec_htrans_bones.hpp │ │ └── xvec_htrans_meat.hpp │ └── nlohmann │ │ └── json.hpp ├── run │ ├── UA │ │ ├── inputs │ │ │ ├── aether.in │ │ │ ├── aether_in.json │ │ │ ├── aurora_earth.csv │ │ │ ├── b20110320n_omni.bin │ │ │ ├── b20110320s_omni.bin │ │ │ ├── chemistry_earth.csv │ │ │ ├── chemistry_earth.xlsx │ │ │ ├── chemistry_earth_richards.csv │ │ │ ├── defaults.json │ │ │ ├── earth.in │ │ │ ├── euv.csv │ │ │ ├── euv_59.csv │ │ │ ├── euv_solomon.csv │ │ │ ├── ext │ │ │ │ ├── ie │ │ │ │ │ ├── FTA │ │ │ │ │ │ ├── fit_coef_21bins_lbhl_r1_b_b.csv │ │ │ │ │ │ ├── fit_coef_21bins_lbhl_r1_b_b.txt │ │ │ │ │ │ ├── fit_coef_21bins_lbhl_r1_b_k.csv │ │ │ │ │ │ ├── fit_coef_21bins_lbhl_r1_b_k.txt │ │ │ │ │ │ ├── fit_coef_21bins_lbhl_r1_k_b.csv │ │ │ │ │ │ ├── fit_coef_21bins_lbhl_r1_k_b.txt │ │ │ │ │ │ ├── fit_coef_21bins_lbhl_r1_k_k.csv │ │ │ │ │ │ ├── fit_coef_21bins_lbhl_r1_k_k.txt │ │ │ │ │ │ ├── fit_coef_21bins_lbhl_r2_k_b.csv │ │ │ │ │ │ ├── fit_coef_21bins_lbhl_r2_k_b.txt │ │ │ │ │ │ ├── fit_coef_21bins_lbhl_r2_k_b_log_4p.txt │ │ │ │ │ │ ├── fit_coef_21bins_lbhl_r2_k_k.csv │ │ │ │ │ │ ├── fit_coef_21bins_lbhl_r2_k_k.txt │ │ │ │ │ │ ├── fit_coef_21bins_lbhl_r2_k_k_log_4p.txt │ │ │ │ │ │ ├── fit_coef_21bins_lbhs_r1_b_b.csv │ │ │ │ │ │ ├── fit_coef_21bins_lbhs_r1_b_b.txt │ │ │ │ │ │ ├── fit_coef_21bins_lbhs_r1_b_k.csv │ │ │ │ │ │ ├── fit_coef_21bins_lbhs_r1_b_k.txt │ │ │ │ │ │ ├── fit_coef_21bins_lbhs_r1_k_b.csv │ │ │ │ │ │ ├── fit_coef_21bins_lbhs_r1_k_b.txt │ │ │ │ │ │ ├── fit_coef_21bins_lbhs_r1_k_k.csv │ │ │ │ │ │ ├── fit_coef_21bins_lbhs_r1_k_k.txt │ │ │ │ │ │ ├── fit_coef_21bins_lbhs_r2_k_b.csv │ │ │ │ │ │ ├── fit_coef_21bins_lbhs_r2_k_b.txt │ │ │ │ │ │ ├── fit_coef_21bins_lbhs_r2_k_b_log_4p.txt │ │ │ │ │ │ ├── fit_coef_21bins_lbhs_r2_k_k.csv │ │ │ │ │ │ ├── fit_coef_21bins_lbhs_r2_k_k.txt │ │ │ │ │ │ └── fit_coef_21bins_lbhs_r2_k_k_log_4p.txt │ │ │ │ │ ├── README │ │ │ │ │ ├── SCHAtable.dat │ │ │ │ │ ├── W05scBndy.dat │ │ │ │ │ ├── W05scEpot.dat │ │ │ │ │ ├── hmr89.cofcnts │ │ │ │ │ ├── hpke.noaa │ │ │ │ │ ├── isoelec_edep.dat │ │ │ │ │ ├── iz94.cofcnts │ │ │ │ │ ├── mhi.cofcnts │ │ │ │ │ ├── mhs.cofcnts │ │ │ │ │ ├── w2k.dat │ │ │ │ │ └── wei96.cofcnts │ │ │ │ └── msis │ │ │ │ │ └── msis21.parm │ │ │ ├── f107.txt │ │ │ ├── indices_lookup.json │ │ │ ├── ion_neutral_collision_frequencies.csv │ │ │ ├── ion_neutral_collision_frequencies.xlsx │ │ │ ├── omni_20110319.txt │ │ │ ├── omni_20110622.txt │ │ │ └── orbits.csv │ │ ├── output │ │ │ └── .dummy │ │ └── restartOut │ │ │ └── .empty │ └── aether.json └── vimrc ├── src ├── add_sources.cpp ├── advance.cpp ├── aurora.cpp ├── bfield.cpp ├── calc_chemical_sources.cpp ├── calc_chemistry.cpp ├── calc_electron_temperature.cpp ├── calc_euv.cpp ├── calc_grid_derived.cpp ├── calc_ion_drift.cpp ├── calc_ion_temperature.cpp ├── calc_neutral_derived.cpp ├── chemistry.cpp ├── collisions.cpp ├── containers_io.cpp ├── cubesphere.cpp ├── dipole.cpp ├── electrodynamics.cpp ├── euv.cpp ├── exchange_messages.cpp ├── exchange_messages_v2.cpp ├── file_input.cpp ├── fill_grid.cpp ├── grid.cpp ├── indices.cpp ├── init_geo_grid.cpp ├── init_parallel.cpp ├── inputs.cpp ├── ions.cpp ├── logfile.cpp ├── main │ ├── file_readinput.cpp │ ├── main.cpp │ ├── main_test_coord.cpp │ ├── main_test_exchange.cpp │ ├── main_test_gradient.cpp │ ├── main_test_interpolation.cpp │ └── test.cpp ├── msis.cpp ├── neutral_ion_collisions.cpp ├── neutrals.cpp ├── neutrals_advect.cpp ├── neutrals_bcs.cpp ├── neutrals_ics.cpp ├── neutrals_momentum_eddy.cpp ├── neutrals_momentum_friction.cpp ├── output.cpp ├── output │ ├── output_binary.cpp │ └── output_netcdf.cpp ├── output_netcdf.cpp ├── planets.cpp ├── quadtree.cpp ├── read_collision_file.cpp ├── read_f107_file.cpp ├── read_input_file.cpp ├── read_netcdf_electrodynamics.cpp ├── read_omni_file.cpp ├── report.cpp ├── solver_chemistry.cpp ├── solver_conduction.cpp ├── solver_coriolis.cpp ├── solver_gradients.cpp ├── solver_grid_interpolation.cpp ├── solver_horizontal_cubesphere.cpp ├── solver_interpolation.cpp ├── solver_limiter.cpp ├── solver_vertical_rusanov.cpp ├── time.cpp ├── time_conversion.cpp ├── tools.cpp └── transform.cpp ├── srcPython ├── amie_read_binary.py ├── amie_routines.py ├── electrodynamics_read.py ├── electrodynamics_write.py ├── kyoto.py ├── logfile_read.py ├── omni_download_write_swmf.py ├── omniweb.py ├── plot_logfiles.py ├── postAether.py ├── satellite_test.py ├── swmf_imf.py └── test_electrodynamics.sh └── tests ├── 2d_alt ├── aether.json.2d └── run_test.sh ├── acheron ├── aether.json.acheron └── run_test.sh ├── advect ├── n2_advect.json ├── n2_advect_earth.in ├── no_advect.json ├── run_test.sh └── some_advect.json ├── centacc ├── aether.json.false ├── aether.json.true └── run_test_centacc.sh ├── check_missing_files.py ├── chemistry ├── aether.json.no_perturb ├── aether.json.w_perturb └── run_test.sh ├── chemistry_check.csv ├── cooling ├── aether.json.all_false ├── aether.json.all_true ├── aether.json.no_true ├── aether.json.o_true └── run_test_cool.sh ├── cubesphere ├── aether_cubesphere.json └── run_test.sh ├── eddy ├── aether.json.v0 ├── aether.json.v1.momentum_f ├── aether.json.v2.energy_f ├── aether.json.v3.uniform └── run_test.sh ├── electrodynamics_unit_tests.cpp ├── error_report └── aether.error.json ├── euv ├── aether.json.22_euvac ├── aether.json.22_hfg ├── aether.json.37_euvac ├── aether.json.59_euvac ├── aether.json.59_neuvac ├── aether.json.59_neuvac_nopei └── run_test.sh ├── exchange ├── aether.json.cubesphere └── run_test.sh ├── global_input_report ├── Temperature_a30_20110320_000000.png ├── Temperature_a30_20110320_001000.png ├── aether1.json └── run_test.sh ├── gradient_cubesphere ├── aether.json.gradient_test └── run_all.sh ├── gravity ├── aether_first.json ├── aether_second.json ├── aether_third.json ├── gravity_test.py ├── output_pngs │ └── .dummy ├── read_routines.py └── run_test.sh ├── hdf5 └── run_test.sh ├── ie_test ├── aether.json.cube.ie_test ├── aether.json.sphere.ie_test └── run_test.sh ├── logfile ├── aether.logfile.json └── run_test.sh ├── msis ├── aether.json.w_msis ├── aether.json.wo_msis ├── results │ ├── w_for_w_msis.png │ ├── w_for_wo_msis.png │ ├── wo_for_w_msis.png │ └── wo_for_wo_msis.png └── run_test.sh ├── nan ├── aether.json.check_nan ├── aether.json.insert_nan └── run_test_nan.sh ├── outputs_pngs ├── var14_alt042_110320_010000.png └── var24_alt006_110320_010000.png ├── partial_planet └── run_test.sh ├── read_chemistry ├── aether.json.errors ├── chemistry_check_0.csv ├── chemistry_check_1.csv ├── chemistry_check_2.csv ├── chemistry_check_3.csv ├── chemistry_check_4.csv ├── chemistry_check_5.csv └── run_test.sh ├── restart_cubesphere ├── aether.first.json ├── aether.second.json ├── aether.whole.json └── run_test.sh ├── restart_ensembles ├── 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