├── .LICENSE_header ├── .binder ├── apt.txt └── postBuild ├── .codecov.yml ├── .git-blame-ignore-revs ├── .git_archival.txt ├── .gitattributes ├── .github ├── FUNDING.yml ├── ISSUE_TEMPLATE │ ├── 005_bug.md │ ├── 010_feature.md │ ├── 015_contribute.md │ ├── 020_issue.md │ ├── 100_publication.md │ └── config.yml ├── PULL_REQUEST_TEMPLATE.md ├── dependabot.yaml └── workflows │ ├── codeql.yml │ ├── codeql │ └── config.yml │ ├── documentation_ghpages.yaml │ ├── linter.yml │ ├── test.yaml │ └── wheels.yaml ├── .gitignore ├── .gitmodules ├── .mailmap ├── .pre-commit-config.yaml ├── .readthedocs-pre_install.sh ├── .readthedocs.yml ├── CITATION.cff ├── CMakeLists.txt ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── DEPLOY.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── benchmarks ├── bloch.py ├── bz_parallel.py ├── bz_replace.py ├── comparisons │ └── neighbors.py ├── graphene.py ├── graphene_io.py ├── graphene_repeat.py ├── graphene_tile.py ├── graphene_within.py ├── lprofile3.sh ├── optimizations │ ├── array_arange.ipynb │ ├── bloch.ipynb │ └── hamiltonian.ipynb ├── run.sh ├── sparse_matrices.py ├── sparse_matrices_ufunc.py └── stats.py ├── changes ├── 924.fix.rst ├── 927.change.rst ├── 929.fix.rst ├── 947.fix.rst ├── 949.doc.rst ├── 951.change.1.rst ├── 951.change.rst ├── 954.change.rst ├── README.rst ├── orphan.1.change.rst ├── orphan.2.change.rst ├── orphan.3.change.rst ├── orphan.4.change.rst ├── orphan.5.fix.rst └── toolbox │ └── .gitignore ├── data └── atomic_radii.dat ├── developments ├── distributions.py ├── miller.py ├── spin.ipynb └── test_numpy_installs.sh ├── docs ├── Makefile ├── _static │ ├── css │ │ └── custom_styles.css │ └── visualization │ │ └── plotly │ │ └── basic-tutorials │ │ └── GUIScreenshot.png ├── _templates │ └── autosummary │ │ ├── class.rst │ │ ├── function.rst │ │ └── module.rst ├── api │ ├── basic.rst │ ├── core.rst │ ├── geom │ │ ├── building.rst │ │ ├── index.rst │ │ ├── indexing.rst │ │ └── neighbors.rst │ ├── index.rst │ ├── io │ │ ├── basic.rst │ │ ├── bigdft-hidden.rst │ │ ├── bigdft.rst │ │ ├── dftb-hidden.rst │ │ ├── dftb.rst │ │ ├── fhiaims-hidden.rst │ │ ├── fhiaims.rst │ │ ├── generic.rst │ │ ├── gulp-hidden.rst │ │ ├── gulp.rst │ │ ├── index.rst │ │ ├── openmx-hidden.rst │ │ ├── openmx.rst │ │ ├── orca-hidden.rst │ │ ├── orca.rst │ │ ├── scaleup-hidden.rst │ │ ├── scaleup.rst │ │ ├── siesta-hidden.rst │ │ ├── siesta.rst │ │ ├── tbtrans-hidden.rst │ │ ├── tbtrans.rst │ │ ├── vasp-hidden.rst │ │ ├── vasp.rst │ │ ├── wannier90-hidden.rst │ │ └── wannier90.rst │ ├── mixing.rst │ ├── physics.brillouinzone.rst │ ├── physics.distribution.rst │ ├── physics.electron-hidden.rst │ ├── physics.electron.rst │ ├── physics.matrix-hidden.rst │ ├── physics.matrix.rst │ ├── physics.phonon.rst │ ├── physics.rst │ ├── typing.rst │ ├── unit_constant.constant.rst │ ├── unit_constant.rst │ ├── unit_constant.unit.rst │ ├── utilities.misc.rst │ ├── utilities.rst │ ├── utilities.shape.rst │ └── viz │ │ └── index.rst ├── build_docs.sh ├── changelog │ ├── index.rst │ ├── v0.10.0.rst │ ├── v0.11.0.rst │ ├── v0.12.0.rst │ ├── v0.12.1.rst │ ├── v0.12.2.rst │ ├── v0.13.0.rst │ ├── v0.14.0.rst │ ├── v0.14.2.rst │ ├── v0.14.3.rst │ ├── v0.15.0.rst │ ├── v0.15.1.rst │ ├── v0.15.2.rst │ ├── v0.8.0.rst │ ├── v0.8.1.rst │ ├── v0.8.2.rst │ ├── v0.8.3.rst │ ├── v0.8.4.rst │ ├── v0.8.5.rst │ ├── v0.9.0.rst │ ├── v0.9.1.rst │ ├── v0.9.2.rst │ ├── v0.9.3.rst │ ├── v0.9.4.rst │ ├── v0.9.5.rst │ ├── v0.9.6.rst │ ├── v0.9.7.rst │ └── v0.9.8.rst ├── cite.rst ├── conf.py ├── conventions.rst ├── dev │ └── index.rst ├── environment.rst ├── index.rst ├── introduction.rst ├── other.rst ├── quickstart │ ├── basic_deps.dot │ ├── basic_deps.svg │ ├── index.rst │ ├── install.rst │ ├── intro_tutorials │ │ ├── 01_geometry.ipynb │ │ ├── 02_geometry_orbitals.ipynb │ │ └── 03_geometry_sile.ipynb │ └── overview.rst ├── references.bib ├── references.rst ├── release.rst ├── release │ ├── 0.16.0-notes.rst │ ├── 0.16.1-notes.rst │ ├── 0.16.2-notes.rst │ └── template.rst ├── scripts │ ├── index.rst │ ├── sdata.rst │ ├── sgeom.rst │ ├── sgrid.rst │ └── stoolbox.rst ├── sisl_modules │ ├── __init__.py │ └── github_links.py ├── sisl_uses.bib ├── spelling_wordlist.txt ├── toolbox │ ├── btd │ │ └── btd.rst │ ├── index.rst │ ├── siesta │ │ ├── atom_plot.rst │ │ └── atom_plot_output.png │ └── transiesta │ │ └── ts_fft.rst ├── tutorials │ ├── convert.bash │ ├── figures │ │ ├── 04_graphene_couplings.png │ │ ├── 04_supercell.png │ │ ├── 05_graphene_bs.png │ │ └── 05_square_bs.png │ ├── index.rst │ ├── siesta_1 │ │ ├── H.psf │ │ ├── O.psf │ │ └── siesta_1.nc │ ├── siesta_2 │ │ ├── C.psf │ │ └── siesta_2.nc │ ├── tutorial_01.rst │ ├── tutorial_02.rst │ ├── tutorial_04.rst │ ├── tutorial_04.tex │ ├── tutorial_05.rst │ ├── tutorial_05_graphene.py │ ├── tutorial_05_square.py │ ├── tutorial_06.rst │ ├── tutorial_06_square.py │ ├── tutorial_es_1.ipynb │ ├── tutorial_es_2.ipynb │ ├── tutorial_setup.tex │ ├── tutorial_siesta_1.ipynb │ ├── tutorial_siesta_2.ipynb │ └── tutorial_siesta_2_ahc.ipynb └── visualization │ ├── ase │ └── index.rst │ ├── basic-tutorials │ └── Demo.ipynb │ ├── blender │ ├── First animation.rst │ └── Getting started.rst │ ├── combining-plots │ └── Intro to combining plots.ipynb │ ├── diy │ ├── Adding new backends.ipynb │ └── Building a new plot.ipynb │ ├── index.rst │ ├── showcase │ ├── AtomicMatrixPlot.ipynb │ ├── BandsPlot.ipynb │ ├── FatbandsPlot.ipynb │ ├── GeometryPlot.ipynb │ ├── GridPlot.ipynb │ ├── PdosPlot.ipynb │ ├── SitesPlot.ipynb │ ├── WavefunctionPlot.ipynb │ └── _template │ │ ├── Showcase template.ipynb │ │ └── create.py │ └── tests │ └── test_tutorials.py ├── examples ├── ex_01.py ├── ex_02.py └── ex_03.py ├── pyproject.toml ├── src ├── CMakeLists.txt ├── sisl │ ├── CMakeLists.txt │ ├── __init__.py │ ├── __main__.py │ ├── _array.py │ ├── _category.py │ ├── _common.py │ ├── _core │ │ ├── CMakeLists.txt │ │ ├── __init__.py │ │ ├── _dtypes.pxd │ │ ├── _dtypes.pyx │ │ ├── _lattice.pyx │ │ ├── _sparse.pxd │ │ ├── _sparse.pyx │ │ ├── _ufuncs_atom.py │ │ ├── _ufuncs_geometry.py │ │ ├── _ufuncs_grid.py │ │ ├── _ufuncs_lattice.py │ │ ├── _ufuncs_orbital.py │ │ ├── _ufuncs_sparse.py │ │ ├── _ufuncs_sparse_geometry.py │ │ ├── atom.py │ │ ├── geometry.py │ │ ├── grid.py │ │ ├── lattice.py │ │ ├── oplist.py │ │ ├── orbital.py │ │ ├── periodictable.py │ │ ├── quaternion.py │ │ ├── sparse.py │ │ ├── sparse_geometry.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_atom.py │ │ │ ├── test_atoms.py │ │ │ ├── test_geometry.py │ │ │ ├── test_geometry_return.py │ │ │ ├── test_grid.py │ │ │ ├── test_lattice.py │ │ │ ├── test_oplist.py │ │ │ ├── test_orbital.py │ │ │ ├── test_quaternion.py │ │ │ ├── test_sgeom.py │ │ │ ├── test_sgrid.py │ │ │ ├── test_sparse.py │ │ │ ├── test_sparse_geometry.py │ │ │ └── test_sparse_orbital.py │ ├── _dispatch_class.py │ ├── _dispatcher.py │ ├── _environ.py │ ├── _help.py │ ├── _indices.pxd │ ├── _indices.pyx │ ├── _internal.py │ ├── _lazy_viz.py │ ├── _lib │ │ ├── _argparse.py │ │ └── _docscrape.py │ ├── _math_small.pyx │ ├── _namedindex.py │ ├── _nodify.py │ ├── _sparse_grid.py │ ├── _sparse_grid_ops.py │ ├── _ufuncs.py │ ├── conftest.py │ ├── constant.py │ ├── geom │ │ ├── CMakeLists.txt │ │ ├── __init__.py │ │ ├── _category │ │ │ ├── __init__.py │ │ │ ├── _coord.py │ │ │ ├── _kind.py │ │ │ ├── _neighbors.py │ │ │ ├── base.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ └── test_geom_category.py │ │ ├── _common.py │ │ ├── _composite.py │ │ ├── _neighbors │ │ │ ├── CMakeLists.txt │ │ │ ├── __init__.py │ │ │ ├── _finder.py │ │ │ ├── _neighborlists.py │ │ │ ├── _operations.py │ │ │ └── tests │ │ │ │ └── test_finder.py │ │ ├── basic.py │ │ ├── bilayer.py │ │ ├── flat.py │ │ ├── nanoribbon.py │ │ ├── nanotube.py │ │ ├── special.py │ │ ├── surfaces.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ └── test_geom.py │ ├── io │ │ ├── CMakeLists.txt │ │ ├── __init__.py │ │ ├── _except_base.py │ │ ├── _except_objects.py │ │ ├── _help.py │ │ ├── _multiple.py │ │ ├── _zipfile.py │ │ ├── bigdft │ │ │ ├── __init__.py │ │ │ ├── ascii.py │ │ │ └── sile.py │ │ ├── cube.py │ │ ├── dftb │ │ │ ├── __init__.py │ │ │ ├── realdat.py │ │ │ ├── sile.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ └── test_realdat.py │ │ ├── fhiaims │ │ │ ├── __init__.py │ │ │ ├── _geometry.py │ │ │ ├── sile.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ └── test_in.py │ │ ├── gulp │ │ │ ├── __init__.py │ │ │ ├── fc.py │ │ │ ├── got.py │ │ │ ├── sile.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ └── test_gout.py │ │ ├── ham.py │ │ ├── molden.py │ │ ├── openmx │ │ │ ├── __init__.py │ │ │ ├── md.py │ │ │ ├── omx.py │ │ │ └── sile.py │ │ ├── orca │ │ │ ├── __init__.py │ │ │ ├── sile.py │ │ │ ├── stdout.py │ │ │ ├── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_stdout.py │ │ │ │ └── test_txt.py │ │ │ └── txt.py │ │ ├── pdb.py │ │ ├── scaleup │ │ │ ├── __init__.py │ │ │ ├── orbocc.py │ │ │ ├── ref.py │ │ │ ├── rham.py │ │ │ └── sile.py │ │ ├── siesta │ │ │ ├── CMakeLists.txt │ │ │ ├── __init__.py │ │ │ ├── _help.py │ │ │ ├── _src │ │ │ │ ├── dm_read.f90 │ │ │ │ ├── dm_write.f90 │ │ │ │ ├── gf_read.f90 │ │ │ │ ├── gf_write.f90 │ │ │ │ ├── grid_read.f90 │ │ │ │ ├── grid_write.f90 │ │ │ │ ├── hsx_read.f90 │ │ │ │ ├── hsx_write.f90 │ │ │ │ ├── io_m.f90 │ │ │ │ ├── precision.f90 │ │ │ │ ├── siesta_sc_off.f90 │ │ │ │ ├── sparse_io.f90 │ │ │ │ ├── tsde_read.f90 │ │ │ │ ├── tsde_write.f90 │ │ │ │ ├── tshs_read.f90 │ │ │ │ ├── tshs_write.f90 │ │ │ │ └── wfsx_read.f90 │ │ │ ├── ani.py │ │ │ ├── bands.py │ │ │ ├── basis.py │ │ │ ├── binaries.py │ │ │ ├── eig.py │ │ │ ├── fa.py │ │ │ ├── fc.py │ │ │ ├── fdf.py │ │ │ ├── kp.py │ │ │ ├── orb_indx.py │ │ │ ├── pdos.py │ │ │ ├── siesta_grid.py │ │ │ ├── siesta_nc.py │ │ │ ├── sile.py │ │ │ ├── stdout.py │ │ │ ├── struct.py │ │ │ ├── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_ani.py │ │ │ │ ├── test_bands.py │ │ │ │ ├── test_basis.py │ │ │ │ ├── test_dm.py │ │ │ │ ├── test_eig.py │ │ │ │ ├── test_fa.py │ │ │ │ ├── test_fc.py │ │ │ │ ├── test_fdf.py │ │ │ │ ├── test_gf.py │ │ │ │ ├── test_grid.py │ │ │ │ ├── test_hsx.py │ │ │ │ ├── test_kp.py │ │ │ │ ├── test_matrices.py │ │ │ │ ├── test_orb_indx.py │ │ │ │ ├── test_pdos.py │ │ │ │ ├── test_siesta.py │ │ │ │ ├── test_stdout.py │ │ │ │ ├── test_stdout_charges.py │ │ │ │ ├── test_struct.py │ │ │ │ ├── test_times.py │ │ │ │ ├── test_tsde.py │ │ │ │ ├── test_tshs.py │ │ │ │ ├── test_vibra.py │ │ │ │ ├── test_wfsx.py │ │ │ │ └── test_xv.py │ │ │ ├── times.py │ │ │ ├── transiesta_grid.py │ │ │ ├── vibra.py │ │ │ └── xv.py │ │ ├── sile.py │ │ ├── table.py │ │ ├── tbtrans │ │ │ ├── __init__.py │ │ │ ├── _cdf.py │ │ │ ├── binaries.py │ │ │ ├── delta.py │ │ │ ├── pht.py │ │ │ ├── phtproj.py │ │ │ ├── se.py │ │ │ ├── sile.py │ │ │ ├── tbt.py │ │ │ ├── tbtproj.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_delta.py │ │ │ │ ├── test_tbt.py │ │ │ │ └── test_tbtproj.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_buffers.py │ │ │ ├── test_cube.py │ │ │ ├── test_ham.py │ │ │ ├── test_object.py │ │ │ ├── test_table.py │ │ │ ├── test_xsf.py │ │ │ ├── test_xyz.py │ │ │ └── test_zipfile.py │ │ ├── vasp │ │ │ ├── __init__.py │ │ │ ├── car.py │ │ │ ├── chg.py │ │ │ ├── doscar.py │ │ │ ├── eigenval.py │ │ │ ├── locpot.py │ │ │ ├── outcar.py │ │ │ ├── sile.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_car.py │ │ │ │ ├── test_chg.py │ │ │ │ ├── test_doscar.py │ │ │ │ ├── test_eigenval.py │ │ │ │ ├── test_locpot.py │ │ │ │ └── test_outcar.py │ │ ├── wannier90 │ │ │ ├── __init__.py │ │ │ ├── seedname.py │ │ │ ├── sile.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ └── test_seedname.py │ │ ├── xsf.py │ │ └── xyz.py │ ├── linalg │ │ ├── __init__.py │ │ ├── base.py │ │ ├── special.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_eig.py │ │ │ ├── test_inv.py │ │ │ ├── test_solve.py │ │ │ └── test_special.py │ ├── messages.py │ ├── mixing │ │ ├── __init__.py │ │ ├── base.py │ │ ├── diis.py │ │ ├── linear.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_diis.py │ │ │ ├── test_history.py │ │ │ ├── test_linear.py │ │ │ └── test_step.py │ ├── physics │ │ ├── CMakeLists.txt │ │ ├── __init__.py │ │ ├── _bloch.pyx │ │ ├── _brillouinzone_apply.py │ │ ├── _common.py │ │ ├── _feature.py │ │ ├── _matrix_ddk.pyx │ │ ├── _matrix_dk.pyx │ │ ├── _matrix_k.pyx │ │ ├── _matrix_phase.pyx │ │ ├── _matrix_phase3.pyx │ │ ├── _matrix_phase_sc.pyx │ │ ├── _matrix_utils.pxd │ │ ├── _matrix_utils.pyx │ │ ├── _phase.pxd │ │ ├── _phase.pyx │ │ ├── _ufuncs_brillouinzone.py │ │ ├── _ufuncs_densitymatrix.py │ │ ├── _ufuncs_dynamicalmatrix.py │ │ ├── _ufuncs_electron.py │ │ ├── _ufuncs_energydensitymatrix.py │ │ ├── _ufuncs_hamiltonian.py │ │ ├── _ufuncs_matrix.py │ │ ├── _ufuncs_overlap.py │ │ ├── _ufuncs_state.py │ │ ├── bloch.py │ │ ├── brillouinzone.py │ │ ├── densitymatrix.py │ │ ├── distribution.py │ │ ├── dynamicalmatrix.py │ │ ├── electron.py │ │ ├── energydensitymatrix.py │ │ ├── hamiltonian.py │ │ ├── overlap.py │ │ ├── phonon.py │ │ ├── self_energy.py │ │ ├── sparse.py │ │ ├── spin.py │ │ ├── state.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_bloch.py │ │ │ ├── test_brillouinzone.py │ │ │ ├── test_density_matrix.py │ │ │ ├── test_distribution.py │ │ │ ├── test_dynamical_matrix.py │ │ │ ├── test_electron.py │ │ │ ├── test_energy_density_matrix.py │ │ │ ├── test_feature.py │ │ │ ├── test_hamiltonian.py │ │ │ ├── test_overlap.py │ │ │ ├── test_physics_sparse.py │ │ │ ├── test_self_energy.py │ │ │ ├── test_spin.py │ │ │ └── test_state.py │ ├── shape │ │ ├── __init__.py │ │ ├── _cylinder.py │ │ ├── base.py │ │ ├── ellipsoid.py │ │ ├── prism4.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_cylinder.py │ │ │ ├── test_ellipsoid.py │ │ │ ├── test_prism4.py │ │ │ └── test_shape.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_help.py │ │ ├── test_messages.py │ │ ├── test_namedindex.py │ │ ├── test_package.py │ │ └── test_sparse_grid.py │ ├── typing │ │ ├── __init__.py │ │ ├── _atom.py │ │ ├── _common.py │ │ ├── _core.py │ │ ├── _indices.py │ │ ├── _physics.py │ │ ├── _units.py │ │ └── tests │ │ │ └── test_typing.py │ ├── unit │ │ ├── __init__.py │ │ ├── base.py │ │ ├── codata.py │ │ ├── codata_2010.txt │ │ ├── codata_2014.txt │ │ ├── codata_2018.txt │ │ ├── codata_2022.txt │ │ ├── siesta.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_codata.py │ │ │ ├── test_unit.py │ │ │ └── test_unit_siesta.py │ ├── utils │ │ ├── __init__.py │ │ ├── _arrays.py │ │ ├── _search_mro.py │ │ ├── _sisl_cmd.py │ │ ├── cmd.py │ │ ├── mathematics.py │ │ ├── misc.py │ │ ├── ranges.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_arrays.py │ │ │ ├── test_cmd.py │ │ │ ├── test_mathematics.py │ │ │ ├── test_misc.py │ │ │ └── test_ranges.py │ └── viz │ │ ├── __init__.py │ │ ├── _plotables.py │ │ ├── _plotables_register.py │ │ ├── _presets.py │ │ ├── _single_dispatch.py │ │ ├── _splot.py │ │ ├── _xarray_accessor.py │ │ ├── data │ │ ├── __init__.py │ │ ├── bands.py │ │ ├── data.py │ │ ├── eigenstate.py │ │ ├── pdos.py │ │ ├── sisl_objs.py │ │ ├── tests │ │ │ ├── .coverage │ │ │ ├── test_bands.py │ │ │ └── test_pdos.py │ │ └── xarray.py │ │ ├── data_sources │ │ ├── __init__.py │ │ ├── atom_data.py │ │ ├── bond_data.py │ │ ├── data_source.py │ │ ├── eigenstate_data.py │ │ ├── file │ │ │ ├── __init__.py │ │ │ ├── file_source.py │ │ │ └── siesta.py │ │ ├── hamiltonian_source.py │ │ └── orbital_data.py │ │ ├── figure │ │ ├── __init__.py │ │ ├── blender.py │ │ ├── figure.py │ │ ├── matplotlib.py │ │ ├── plotly.py │ │ └── py3dmol.py │ │ ├── plot.py │ │ ├── plots │ │ ├── __init__.py │ │ ├── bands.py │ │ ├── geometry.py │ │ ├── grid.py │ │ ├── matrix.py │ │ ├── merged.py │ │ ├── orbital_groups_plot.py │ │ ├── pdos.py │ │ └── tests │ │ │ ├── .coverage │ │ │ ├── __init__.py │ │ │ ├── test_bands.py │ │ │ ├── test_geometry.py │ │ │ ├── test_grid.py │ │ │ ├── test_matrix.py │ │ │ └── test_pdos.py │ │ ├── plotters │ │ ├── __init__.py │ │ ├── cell.py │ │ ├── grid.py │ │ ├── matrix.py │ │ ├── plot_actions.py │ │ ├── tests │ │ │ ├── test_matrix.py │ │ │ └── test_xarray.py │ │ └── xarray.py │ │ ├── plotutils.py │ │ ├── processors │ │ ├── __init__.py │ │ ├── atom.py │ │ ├── axes.py │ │ ├── bands.py │ │ ├── cell.py │ │ ├── coords.py │ │ ├── data.py │ │ ├── eigenstate.py │ │ ├── geometry.py │ │ ├── grid.py │ │ ├── logic.py │ │ ├── math.py │ │ ├── matrix.py │ │ ├── orbital.py │ │ ├── spin.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_axes.py │ │ │ ├── test_bands.py │ │ │ ├── test_cell.py │ │ │ ├── test_coords.py │ │ │ ├── test_data.py │ │ │ ├── test_eigenstate.py │ │ │ ├── test_geometry.py │ │ │ ├── test_grid.py │ │ │ ├── test_groupreduce.py │ │ │ ├── test_logic.py │ │ │ ├── test_math.py │ │ │ ├── test_matrix.py │ │ │ ├── test_orbital.py │ │ │ ├── test_sci_groupreduce.py │ │ │ └── test_spin.py │ │ ├── wavefunction.py │ │ └── xarray.py │ │ └── types.py └── sisl_toolbox │ ├── README │ ├── btd │ ├── __init__.py │ ├── _btd.py │ ├── _electrode.py │ ├── _green.py │ └── _help.py │ ├── cli │ ├── __init__.py │ ├── _cli.py │ └── _cli_imports.py │ ├── models │ ├── __init__.py │ ├── _base.py │ └── _graphene │ │ ├── __init__.py │ │ ├── _base.py │ │ └── _hamiltonian.py │ ├── siesta │ ├── atom │ │ ├── __init__.py │ │ └── _atom.py │ └── minimizer │ │ ├── __init__.py │ │ ├── _atom_basis.py │ │ ├── _atom_pseudo.py │ │ ├── _metric.py │ │ ├── _metric_siesta.py │ │ ├── _minimize.py │ │ ├── _minimize_siesta.py │ │ ├── _path.py │ │ ├── _runner.py │ │ ├── _variable.py │ │ ├── _yaml_reader.py │ │ └── optimize.yaml │ └── transiesta │ └── poisson │ ├── __init__.py │ └── fftpoisson_fix.py └── tools ├── _debug_info.py.conf ├── add_header.sh ├── build_tools ├── build_wheels.sh └── test_wheels.sh ├── changelog.py ├── codata.py ├── pep8.sh ├── runlint.bash └── tag.sh /.LICENSE_header: -------------------------------------------------------------------------------- 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