Index

_

__call__() (sisl.constant.PhysicalConstant method) (sisl.mixing.AdaptiveDIISMixer method) (sisl.mixing.AdaptivePulayMixer method) (sisl.mixing.AndersonMixer method) (sisl.mixing.BaseHistoryWeightMixer method) (sisl.mixing.BaseMixer method) (sisl.mixing.BaseWeightMixer method) (sisl.mixing.DIISMixer method) (sisl.mixing.LinearMixer method) (sisl.mixing.PulayMixer method) (sisl.mixing.StepMixer method) (sisl.physics.Bloch method) (sisl.viz.AtomicMatrixPlot method) (sisl.viz.BandsPlot method) (sisl.viz.FatbandsPlot method) (sisl.viz.GeometryPlot method) (sisl.viz.GridPlot method) (sisl.viz.PdosPlot method) (sisl.viz.Plot method) (sisl.viz.SitesPlot method) (sisl.viz.WavefunctionPlot method) (sisl_toolbox.siesta.atom.AtomInput method)

_densitymatrix (class in sisl.physics.densitymatrix) _electron_State (class in sisl.physics.electron)

A

a2isc() (sisl.Geometry method) a2o() (sisl.Geometry method) a2p() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) a2sc() (sisl.Geometry method) a2transpose() (sisl.Geometry method) a_buf (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) a_dev (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) a_down() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) a_elec() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) accuracy_reached() (sisl.io.vasp.outcarSileVASP method) AdaptiveDIISMixer (class in sisl.mixing) AdaptivePulayMixer (class in sisl.mixing) add() (in module sisl) (sisl.Atoms method) (sisl.Geometry method) (sisl.Lattice method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseOrbital method) add_group() (sisl.viz.FatbandsPlot method) (sisl.viz.PdosPlot method) add_note() (sisl.io.SileError method) (sisl.io.SileInfo method) (sisl.io.SileWarning method) add_section() (sisl.geom.CompositeGeometrySection method) add_sile() (in module sisl.io) add_vacuum() (sisl.Geometry method) (sisl.Lattice method) Adensity_matrix() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) adjust_weight() (sisl.mixing.AdaptiveDIISMixer method) (sisl.mixing.AdaptivePulayMixer method) ADOS() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) ae() (sisl_toolbox.siesta.atom.AtomInput method) agnr() (in module sisl.geom) ahc() (in module sisl.physics.electron) align() (sisl.SparseCSR method) align_norm() (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.State method) (sisl.physics.StateC method) align_phase() (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.State method) (sisl.physics.StateC method) alpha (sisl.GTOrbital property) (sisl.STOrbital property) AndersonMixer (class in sisl.mixing) angle (sisl.Quaternion property) angle() (in module sisl.utils) (sisl.Geometry method) (sisl.Lattice method) animation() (in module sisl.viz) aniSileSiesta (class in sisl.io.siesta) AnyAxes (in module sisl.typing) AnyAxis (in module sisl.typing) append() (in module sisl) (sisl.Atoms method) (sisl.Geometry method) (sisl.Grid method) (sisl.Lattice method) (sisl.mixing.History method) (sisl.oplist method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseOrbital method)

apply (sisl.physics.BandStructure attribute) (sisl.physics.BrillouinZone attribute) (sisl.physics.MonkhorstPack attribute) apply() (in module sisl) (sisl.Geometry method) (sisl.Grid method) apply_newton() (sisl.physics.DynamicalMatrix method) area() (sisl.Geometry method) (sisl.Grid method) (sisl.Lattice method) args (sisl.io.SileError attribute) (sisl.io.SileInfo attribute) (sisl.io.SileWarning attribute) array() (sisl.physics.BandStructure.apply method) (sisl.physics.BrillouinZone.apply method) (sisl.physics.MonkhorstPack.apply method) as_integer_ratio() (sisl.BoundaryCondition method) (sisl.constant.PhysicalConstant method) as_primary() (sisl.Geometry method) as_supercell() (sisl.Geometry method) asc2uc() (sisl.Geometry method) asciiSileBigDFT (class in sisl.io.bigdft) asCoefficient() (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.StateC method) ase() (sisl.Geometry.new method) (sisl.Geometry.to method) (sisl.Lattice.new method) (sisl.Lattice.to method) assert_consistency() (sisl.geom.NeighborFinder method) asState() (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.StateC method) atom Atom (class in sisl) atom (sisl.Atoms property) (sisl.geom.AtomNeighborList attribute) atom_ACOHP() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) atom_ACOOP() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) atom_COHP (sisl.io.tbtrans.phtprojncSilePHtrans attribute) (sisl.io.tbtrans.tbtprojncSileTBtrans attribute) atom_COHP() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) atom_COOP (sisl.io.tbtrans.phtprojncSilePHtrans attribute) (sisl.io.tbtrans.tbtprojncSileTBtrans attribute) atom_COOP() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) atom_current() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) atom_transmission() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) AtomCategory (class in sisl.geom) atomic-orbital atomic_mass() (sisl.PeriodicTable method) atomicmatrix() (sisl.physics.densitymatrix._densitymatrix.plot method) (sisl.physics.DensityMatrix.plot method) (sisl.physics.DynamicalMatrix.plot method) (sisl.physics.EnergyDensityMatrix.plot method) (sisl.physics.Hamiltonian.plot method) (sisl.physics.Overlap.plot method) (sisl.physics.SparseOrbitalBZ.plot method) (sisl.physics.SparseOrbitalBZSpin.plot method) (sisl.SparseAtom.plot method) (sisl.SparseCSR.plot method) (sisl.SparseOrbital.plot method) AtomicMatrixPlot (class in sisl.viz) AtomicOrbital (class in sisl) AtomInput (class in sisl_toolbox.siesta.atom) AtomLike (in module sisl.typing) AtomNeighborList (class in sisl.geom) Atoms (class in sisl) atoms (sisl.geom.PartialNeighborList attribute) (sisl.Geometry property) AtomsIndex (in module sisl.typing) AtomsLike (in module sisl.typing) attach() (sisl.Geometry method) auc2sc() (sisl.Geometry method) average() (sisl.Grid method) (sisl.physics.BandStructure.apply method) (sisl.physics.BrillouinZone.apply method) (sisl.physics.MonkhorstPack.apply method) AxisIntLiteral (in module sisl.typing) axyz() (sisl.Geometry method)

B

bands() (sisl.io.siesta.bandsSileSiesta.plot method) (sisl.io.siesta.fdfSileSiesta.plot method) (sisl.io.siesta.wfsxSileSiesta.plot method) (sisl.physics.BandStructure.plot method) (sisl.physics.BrillouinZone.plot method) (sisl.physics.MonkhorstPack.plot method) BandsPlot (class in sisl.viz) bandsSileSiesta (class in sisl.io.siesta) BandStructure (class in sisl.physics) base_directory() (sisl.io.BaseSile method) (sisl.io.bigdft.asciiSileBigDFT method) (sisl.io.bigdft.SileBigDFT method) (sisl.io.bigdft.SileBinBigDFT method) (sisl.io.cubeSile method) (sisl.io.dftb.hamrealSileDFTB method) (sisl.io.dftb.overrealSileDFTB method) (sisl.io.dftb.SileBinDFTB method) (sisl.io.dftb.SileDFTB method) (sisl.io.fhiaims.inSileFHIaims method) (sisl.io.fhiaims.SileBinFHIaims method) (sisl.io.fhiaims.SileFHIaims method) (sisl.io.gulp.fcSileGULP method) (sisl.io.gulp.gotSileGULP method) (sisl.io.gulp.SileBinGULP method) (sisl.io.gulp.SileGULP method) (sisl.io.moldenSile method) (sisl.io.openmx.mdSileOpenMX method) (sisl.io.openmx.omxSileOpenMX method) (sisl.io.openmx.SileBinOpenMX method) (sisl.io.openmx.SileCDFOpenMX method) (sisl.io.openmx.SileOpenMX method) (sisl.io.orca.SileBinORCA method) (sisl.io.orca.SileORCA method) (sisl.io.orca.stdoutSileORCA method) (sisl.io.orca.txtSileORCA method) (sisl.io.pdbSile method) (sisl.io.scaleup.orboccSileScaleUp method) (sisl.io.scaleup.refSileScaleUp method) (sisl.io.scaleup.rhamSileScaleUp method) (sisl.io.scaleup.SileBinScaleUp method) (sisl.io.scaleup.SileScaleUp method) (sisl.io.siesta.aniSileSiesta method) (sisl.io.siesta.bandsSileSiesta method) (sisl.io.siesta.dmSileSiesta method) (sisl.io.siesta.eigSileSiesta method) (sisl.io.siesta.faSileSiesta method) (sisl.io.siesta.fcSileSiesta method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.gridncSileSiesta method) (sisl.io.siesta.gridSileSiesta method) (sisl.io.siesta.hsxSileSiesta method) (sisl.io.siesta.ionncSileSiesta method) (sisl.io.siesta.ionxmlSileSiesta method) (sisl.io.siesta.kpSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.onlysSileSiesta method) (sisl.io.siesta.orbindxSileSiesta method) (sisl.io.siesta.pdosSileSiesta method) (sisl.io.siesta.rkpSileSiesta method) (sisl.io.siesta.SileBinSiesta method) (sisl.io.siesta.SileCDFSiesta method) (sisl.io.siesta.SileSiesta method) (sisl.io.siesta.stdoutSileSiesta method) (sisl.io.siesta.structSileSiesta method) (sisl.io.siesta.timesSileSiesta method) (sisl.io.siesta.tsdeSileSiesta method) (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.siesta.tshsSileSiesta method) (sisl.io.siesta.tsvncSileSiesta method) (sisl.io.siesta.wfsxSileSiesta method) (sisl.io.siesta.xvSileSiesta method) (sisl.io.Sile method) (sisl.io.SileBin method) (sisl.io.SileCDF method) (sisl.io.tableSile method) (sisl.io.tbtrans.deltancSileTBtrans method) (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.SileBinTBtrans method) (sisl.io.tbtrans.SileCDFTBtrans method) (sisl.io.tbtrans.SileTBtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtgfSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) (sisl.io.vasp.carSileVASP method) (sisl.io.vasp.chgSileVASP method) (sisl.io.vasp.doscarSileVASP method) (sisl.io.vasp.eigenvalSileVASP method) (sisl.io.vasp.locpotSileVASP method) (sisl.io.vasp.outcarSileVASP method) (sisl.io.vasp.SileBinVASP method) (sisl.io.vasp.SileVASP method) (sisl.io.wannier90.centresSileWannier90 method) (sisl.io.wannier90.hrSileWannier90 method) (sisl.io.wannier90.SileBinWannier90 method) (sisl.io.wannier90.SileWannier90 method) (sisl.io.wannier90.tbSileWannier90 method) (sisl.io.wannier90.winSileWannier90 method) (sisl.io.xsfSile method) (sisl.io.xyzSile method) base_file (sisl.io.BaseSile property) (sisl.io.bigdft.asciiSileBigDFT property) (sisl.io.bigdft.SileBigDFT property) (sisl.io.bigdft.SileBinBigDFT property) (sisl.io.cubeSile property) (sisl.io.dftb.hamrealSileDFTB property) (sisl.io.dftb.overrealSileDFTB property) (sisl.io.dftb.SileBinDFTB property) (sisl.io.dftb.SileDFTB property) (sisl.io.fhiaims.inSileFHIaims property) (sisl.io.fhiaims.SileBinFHIaims property) (sisl.io.fhiaims.SileFHIaims property) (sisl.io.gulp.fcSileGULP property) (sisl.io.gulp.gotSileGULP property) (sisl.io.gulp.SileBinGULP property) (sisl.io.gulp.SileGULP property) (sisl.io.moldenSile property) (sisl.io.openmx.mdSileOpenMX property) (sisl.io.openmx.omxSileOpenMX property) (sisl.io.openmx.SileBinOpenMX property) (sisl.io.openmx.SileCDFOpenMX property) (sisl.io.openmx.SileOpenMX property) (sisl.io.orca.SileBinORCA property) (sisl.io.orca.SileORCA property) (sisl.io.orca.stdoutSileORCA property) (sisl.io.orca.txtSileORCA property) (sisl.io.pdbSile property) (sisl.io.scaleup.orboccSileScaleUp property) (sisl.io.scaleup.refSileScaleUp property) (sisl.io.scaleup.rhamSileScaleUp property) (sisl.io.scaleup.SileBinScaleUp property) (sisl.io.scaleup.SileScaleUp property) (sisl.io.siesta.aniSileSiesta property) (sisl.io.siesta.bandsSileSiesta property) (sisl.io.siesta.dmSileSiesta property) (sisl.io.siesta.eigSileSiesta property) (sisl.io.siesta.faSileSiesta property) (sisl.io.siesta.fcSileSiesta property) (sisl.io.siesta.fdfSileSiesta property) (sisl.io.siesta.gridncSileSiesta property) (sisl.io.siesta.gridSileSiesta property) (sisl.io.siesta.hsxSileSiesta property) (sisl.io.siesta.ionncSileSiesta property) (sisl.io.siesta.ionxmlSileSiesta property) (sisl.io.siesta.kpSileSiesta property) (sisl.io.siesta.ncSileSiesta property) (sisl.io.siesta.onlysSileSiesta property) (sisl.io.siesta.orbindxSileSiesta property) (sisl.io.siesta.pdosSileSiesta property) (sisl.io.siesta.rkpSileSiesta property) (sisl.io.siesta.SileBinSiesta property) (sisl.io.siesta.SileCDFSiesta property) (sisl.io.siesta.SileSiesta property) (sisl.io.siesta.stdoutSileSiesta property) (sisl.io.siesta.structSileSiesta property) (sisl.io.siesta.timesSileSiesta property) (sisl.io.siesta.tsdeSileSiesta property) (sisl.io.siesta.tsgfSileSiesta property) (sisl.io.siesta.tshsSileSiesta property) (sisl.io.siesta.tsvncSileSiesta property) (sisl.io.siesta.wfsxSileSiesta property) (sisl.io.siesta.xvSileSiesta property) (sisl.io.Sile property) (sisl.io.SileBin property) (sisl.io.SileCDF property) (sisl.io.tableSile property) (sisl.io.tbtrans.deltancSileTBtrans property) (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.SileBinTBtrans property) (sisl.io.tbtrans.SileCDFTBtrans property) (sisl.io.tbtrans.SileTBtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtgfSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) (sisl.io.vasp.carSileVASP property) (sisl.io.vasp.chgSileVASP property) (sisl.io.vasp.doscarSileVASP property) (sisl.io.vasp.eigenvalSileVASP property) (sisl.io.vasp.locpotSileVASP property) (sisl.io.vasp.outcarSileVASP property) (sisl.io.vasp.SileBinVASP property) (sisl.io.vasp.SileVASP property) (sisl.io.wannier90.centresSileWannier90 property) (sisl.io.wannier90.hrSileWannier90 property) (sisl.io.wannier90.SileBinWannier90 property) (sisl.io.wannier90.SileWannier90 property) (sisl.io.wannier90.tbSileWannier90 property) (sisl.io.wannier90.winSileWannier90 property) (sisl.io.xsfSile property) (sisl.io.xyzSile property)

BaseHistoryWeightMixer (class in sisl.mixing) BaseMixer (class in sisl.mixing) BaseSile (class in sisl.io) BaseWeightMixer (class in sisl.mixing) basic batched_indices() (in module sisl.utils) BC (sisl.Lattice attribute) bcc() (in module sisl.geom) bcc_slab() (in module sisl.geom) BDOS() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) berry_curvature() (in module sisl.physics) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.StateCElectron method) berry_phase() (in module sisl.physics.electron) bilayer() (in module sisl.geom) bit_count() (sisl.BoundaryCondition method) bit_length() (sisl.BoundaryCondition method) Bloch (class in sisl.physics) bloch (sisl.physics.Bloch property) bloch() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) bond_correct() (sisl.Geometry method) bond_current (sisl.io.tbtrans.phtavncSilePHtrans attribute) (sisl.io.tbtrans.phtncSilePHtrans attribute) bond_current() (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) bond_order() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.EnergyDensityMatrix method) bond_transmission() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) bose_einstein() (in module sisl.physics) boundary_condition (sisl.Geometry property) (sisl.Grid property) (sisl.Lattice property) BoundaryCondition (class in sisl) BrillouinZone (class in sisl.physics) broadening_matrix() (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) (sisl.physics.RealSpaceSE method) (sisl.physics.RealSpaceSI method) (sisl.physics.RecursiveSI method) (sisl.physics.SelfEnergy method) (sisl.physics.SemiInfinite method) (sisl.physics.WideBandSE method) (sisl_toolbox.btd.DownfoldSelfEnergy method) (sisl_toolbox.btd.PivotSelfEnergy method) btd() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) build_section() (sisl.geom.CompositeGeometrySection method)

C

c (in module sisl.constant) (sisl.physics.Coefficient attribute) (sisl.physics.electron.CoefficientElectron attribute) (sisl.physics.electron.EigenstateElectron attribute) (sisl.physics.electron.EigenvalueElectron attribute) (sisl.physics.electron.StateCElectron attribute) (sisl.physics.phonon.CoefficientPhonon attribute) (sisl.physics.phonon.EigenmodePhonon attribute) (sisl.physics.phonon.EigenvaluePhonon attribute) (sisl.physics.phonon.ModeCPhonon attribute) (sisl.physics.StateC attribute) carSileVASP (class in sisl.io.vasp) CartesianAxes (in module sisl.typing) CartesianAxis (in module sisl.typing) CartesianAxisLiteral (in module sisl.typing) CartesianAxisStrLiteral (in module sisl.typing) categorize() (sisl.geom.AtomCategory method) cell (sisl.Geometry property) (sisl.Grid property) (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) (sisl.Lattice attribute) (sisl.physics.BandStructure property) (sisl.physics.BrillouinZone property) (sisl.physics.MonkhorstPack property) cell2length() (sisl.Lattice method) CellAxes (in module sisl.typing) CellAxis (in module sisl.typing) CellAxisLiteral (in module sisl.typing) CellAxisStrLiteral (in module sisl.typing) CellLike (in module sisl.typing) center (sisl.shape.Cube property) (sisl.shape.Cuboid property) (sisl.shape.Ellipsoid property) (sisl.shape.EllipticalCylinder property) (sisl.shape.NullShape property) (sisl.shape.Shape property) (sisl.shape.Sphere property) center() (in module sisl) (sisl.Geometry method) (sisl.Lattice method) centresSileWannier90 (class in sisl.io.wannier90) cgnr() (in module sisl.geom) change_gauge() (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.State method) (sisl.physics.StateC method) characters_written (sisl.io.SileError attribute) chemical_potential (sisl.io.tbtrans.phtavncSilePHtrans attribute) (sisl.io.tbtrans.phtncSilePHtrans attribute) chemical_potential() (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) chgSileVASP (class in sisl.io.vasp) clear() (sisl.mixing.History method) (sisl.oplist method) (sisl.physics.RealSpaceSE method) (sisl.physics.RealSpaceSI method) (sisl.utils.PropertyDict method) (sisl.viz.Figure method) close() (sisl.Geometry method) (sisl.io.bigdft.asciiSileBigDFT method) (sisl.io.bigdft.SileBigDFT method) (sisl.io.cubeSile method) (sisl.io.dftb.hamrealSileDFTB method) (sisl.io.dftb.overrealSileDFTB method) (sisl.io.dftb.SileDFTB method) (sisl.io.fhiaims.inSileFHIaims method) (sisl.io.fhiaims.SileFHIaims method) (sisl.io.gulp.fcSileGULP method) (sisl.io.gulp.gotSileGULP method) (sisl.io.gulp.SileGULP method) (sisl.io.moldenSile method) (sisl.io.openmx.mdSileOpenMX method) (sisl.io.openmx.omxSileOpenMX method) (sisl.io.openmx.SileCDFOpenMX method) (sisl.io.openmx.SileOpenMX method) (sisl.io.orca.SileORCA method) (sisl.io.orca.stdoutSileORCA method) (sisl.io.orca.txtSileORCA method) (sisl.io.pdbSile method) (sisl.io.scaleup.orboccSileScaleUp method) (sisl.io.scaleup.refSileScaleUp method) (sisl.io.scaleup.rhamSileScaleUp method) (sisl.io.scaleup.SileScaleUp method) (sisl.io.siesta.aniSileSiesta method) (sisl.io.siesta.bandsSileSiesta method) (sisl.io.siesta.eigSileSiesta method) (sisl.io.siesta.faSileSiesta method) (sisl.io.siesta.fcSileSiesta method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.gridncSileSiesta method) (sisl.io.siesta.ionncSileSiesta method) (sisl.io.siesta.ionxmlSileSiesta method) (sisl.io.siesta.kpSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.orbindxSileSiesta method) (sisl.io.siesta.pdosSileSiesta method) (sisl.io.siesta.rkpSileSiesta method) (sisl.io.siesta.SileCDFSiesta method) (sisl.io.siesta.SileSiesta method) (sisl.io.siesta.stdoutSileSiesta method) (sisl.io.siesta.structSileSiesta method) (sisl.io.siesta.timesSileSiesta method) (sisl.io.siesta.tsvncSileSiesta method) (sisl.io.siesta.xvSileSiesta method) (sisl.io.Sile method) (sisl.io.SileCDF method) (sisl.io.tableSile method) (sisl.io.tbtrans.deltancSileTBtrans method) (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.SileCDFTBtrans method) (sisl.io.tbtrans.SileTBtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) (sisl.io.vasp.carSileVASP method) (sisl.io.vasp.chgSileVASP method) (sisl.io.vasp.doscarSileVASP method) (sisl.io.vasp.eigenvalSileVASP method) (sisl.io.vasp.locpotSileVASP method) (sisl.io.vasp.outcarSileVASP method) (sisl.io.vasp.SileVASP method) (sisl.io.wannier90.centresSileWannier90 method) (sisl.io.wannier90.hrSileWannier90 method) (sisl.io.wannier90.SileWannier90 method) (sisl.io.wannier90.tbSileWannier90 method) (sisl.io.wannier90.winSileWannier90 method) (sisl.io.xsfSile method) (sisl.io.xyzSile method)

close_sc() (sisl.Geometry method) coeff (sisl.GTOrbital property) (sisl.STOrbital property) Coefficient (class in sisl.physics) CoefficientElectron (class in sisl.physics.electron) CoefficientPhonon (class in sisl.physics.phonon) coefficients() (sisl.mixing.AdaptiveDIISMixer method) (sisl.mixing.AdaptivePulayMixer method) (sisl.mixing.DIISMixer method) (sisl.mixing.PulayMixer method) COHP() (sisl.physics.electron.EigenstateElectron method) col (sisl.SparseCSR attribute) cold() (in module sisl.physics) completed() (sisl.io.orca.stdoutSileORCA method) (sisl.io.siesta.stdoutSileSiesta method) (sisl.io.vasp.outcarSileVASP method) composite_geometry() (in module sisl.geom) CompositeGeometrySection (class in sisl.geom) conductivity() (in module sisl.physics.electron) conj() (sisl.Quaternion method) conjugate() (sisl.BoundaryCondition method) (sisl.constant.PhysicalConstant method) construct() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseOrbital method) context (sisl.viz.AtomicMatrixPlot attribute) (sisl.viz.BandsPlot attribute) (sisl.viz.FatbandsPlot attribute) (sisl.viz.GeometryPlot attribute) (sisl.viz.GridPlot attribute) (sisl.viz.PdosPlot attribute) (sisl.viz.Plot attribute) (sisl.viz.SitesPlot attribute) (sisl.viz.WavefunctionPlot attribute) COOP() (sisl.physics.electron.EigenstateElectron method) Coord (in module sisl.typing) CoordOrScalar (in module sisl.typing) COP() (in module sisl.physics.electron) (sisl.physics.electron.EigenstateElectron method) copy() (in module sisl) (sisl.Atom method) (sisl.AtomicOrbital method) (sisl.Atoms method) (sisl.Geometry method) (sisl.Grid method) (sisl.GTOrbital method) (sisl.HydrogenicOrbital method) (sisl.Lattice method) (sisl.oplist method) (sisl.Orbital method) (sisl.physics.BandStructure method) (sisl.physics.BrillouinZone method) (sisl.physics.Coefficient method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.electron.CoefficientElectron method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvalueElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.MonkhorstPack method) (sisl.physics.Overlap method) (sisl.physics.phonon.CoefficientPhonon method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvaluePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.physics.Spin method) (sisl.physics.State method) (sisl.physics.StateC method) (sisl.Quaternion method) (sisl.shape.Cube method) (sisl.shape.Cuboid method) (sisl.shape.Ellipsoid method) (sisl.shape.EllipticalCylinder method) (sisl.shape.NullShape method) (sisl.shape.Shape method) (sisl.shape.Sphere method) (sisl.SparseAtom method) (sisl.SparseCSR method) (sisl.SparseOrbital method) (sisl.SphericalOrbital method) (sisl.STOrbital method) (sisl.utils.PropertyDict method) count() (sisl.oplist method) cpu_time() (sisl.io.vasp.outcarSileVASP method) create_construct() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseOrbital method) cross_section() (sisl.Grid method) Cube (class in sisl.shape) cubeSile (class in sisl.io) Cuboid (class in sisl.shape) Cuboid() (sisl.Lattice.to method) (sisl.shape.Cube.to method) (sisl.shape.Cuboid.to method) (sisl.shape.Ellipsoid.to method) (sisl.shape.EllipticalCylinder.to method) (sisl.shape.NullShape.to method) (sisl.shape.Shape.to method) (sisl.shape.Sphere.to method) current (sisl.io.tbtrans.phtavncSilePHtrans attribute) (sisl.io.tbtrans.phtncSilePHtrans attribute) (sisl.io.tbtrans.phtprojncSilePHtrans attribute) (sisl.io.tbtrans.tbtprojncSileTBtrans attribute) current() (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) current_parameter (sisl.io.tbtrans.phtavncSilePHtrans attribute) (sisl.io.tbtrans.phtncSilePHtrans attribute) (sisl.io.tbtrans.phtprojncSilePHtrans attribute) (sisl.io.tbtrans.tbtprojncSileTBtrans attribute) current_parameter() (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method)

D

D (sisl.physics.DensityMatrix property) (sisl.physics.DynamicalMatrix property) data (sisl.SparseCSR property) dataarray() (sisl.physics.BandStructure.apply method) (sisl.physics.BrillouinZone.apply method) (sisl.physics.MonkhorstPack.apply method) dataframe() (sisl.Geometry.to method) dcell (sisl.Grid property) ddDk() (sisl.physics.DensityMatrix method) (sisl.physics.DynamicalMatrix method) ddEk() (sisl.physics.EnergyDensityMatrix method) ddHk() (sisl.physics.Hamiltonian method) dDk() (sisl.physics.DensityMatrix method) (sisl.physics.DynamicalMatrix method) ddSk() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) decorate() (sisl.oplist class method) default_inputs (sisl.viz.AtomicMatrixPlot property) (sisl.viz.BandsPlot property) (sisl.viz.FatbandsPlot property) (sisl.viz.GeometryPlot property) (sisl.viz.GridPlot property) (sisl.viz.PdosPlot property) (sisl.viz.Plot property) (sisl.viz.SitesPlot property) (sisl.viz.WavefunctionPlot property) degenerate() (sisl.physics.Coefficient method) (sisl.physics.electron.CoefficientElectron method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvalueElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.phonon.CoefficientPhonon method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvaluePhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.StateC method) degenerate_decouple() (in module sisl.physics) degree (sisl.Quaternion property) dEk() (sisl.physics.EnergyDensityMatrix method) delete_columns() (sisl.SparseCSR method) DELETE_KWARG (sisl.viz.AtomicMatrixPlot attribute) (sisl.viz.BandsPlot attribute) (sisl.viz.FatbandsPlot attribute) (sisl.viz.GeometryPlot attribute) (sisl.viz.GridPlot attribute) (sisl.viz.PdosPlot attribute) (sisl.viz.Plot attribute) (sisl.viz.SitesPlot attribute) (sisl.viz.WavefunctionPlot attribute) deltancSileTBtrans (class in sisl.io.tbtrans) denominator (sisl.BoundaryCondition attribute) density() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.EnergyDensityMatrix method) density_matrix (sisl.io.tbtrans.phtprojncSilePHtrans attribute) (sisl.io.tbtrans.tbtprojncSileTBtrans attribute) density_matrix() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) DensityMatrix (class in sisl.physics) derivative() (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.StateC method) DeviceGreen (class in sisl_toolbox.btd) dHk() (sisl.physics.Hamiltonian method) diagonal() (sisl.SparseCSR method) diags() (sisl.SparseCSR method) diamond() (in module sisl.geom) dihedral() (sisl.Geometry method) DIISMixer (class in sisl.mixing) dim (sisl.physics.DensityMatrix property) (sisl.physics.densitymatrix._densitymatrix property) (sisl.physics.DynamicalMatrix property) (sisl.physics.EnergyDensityMatrix property) (sisl.physics.Hamiltonian property) (sisl.physics.Overlap property) (sisl.physics.SparseOrbitalBZ property) (sisl.physics.SparseOrbitalBZSpin property) (sisl.SparseAtom property) (sisl.SparseCSR property) (sisl.SparseOrbital property) dir_file() (sisl.io.BaseSile method) (sisl.io.bigdft.asciiSileBigDFT method) (sisl.io.bigdft.SileBigDFT method) (sisl.io.bigdft.SileBinBigDFT method) (sisl.io.cubeSile method) (sisl.io.dftb.hamrealSileDFTB method) (sisl.io.dftb.overrealSileDFTB method) (sisl.io.dftb.SileBinDFTB method) (sisl.io.dftb.SileDFTB method) (sisl.io.fhiaims.inSileFHIaims method) (sisl.io.fhiaims.SileBinFHIaims method) (sisl.io.fhiaims.SileFHIaims method) (sisl.io.gulp.fcSileGULP method) (sisl.io.gulp.gotSileGULP method) (sisl.io.gulp.SileBinGULP method) (sisl.io.gulp.SileGULP method) (sisl.io.moldenSile method) (sisl.io.openmx.mdSileOpenMX method) (sisl.io.openmx.omxSileOpenMX method) (sisl.io.openmx.SileBinOpenMX method) (sisl.io.openmx.SileCDFOpenMX method) (sisl.io.openmx.SileOpenMX method) (sisl.io.orca.SileBinORCA method) (sisl.io.orca.SileORCA method) (sisl.io.orca.stdoutSileORCA method) (sisl.io.orca.txtSileORCA method) (sisl.io.pdbSile method) (sisl.io.scaleup.orboccSileScaleUp method) (sisl.io.scaleup.refSileScaleUp method) (sisl.io.scaleup.rhamSileScaleUp method) (sisl.io.scaleup.SileBinScaleUp method) (sisl.io.scaleup.SileScaleUp method) (sisl.io.siesta.aniSileSiesta method) (sisl.io.siesta.bandsSileSiesta method) (sisl.io.siesta.dmSileSiesta method) (sisl.io.siesta.eigSileSiesta method) (sisl.io.siesta.faSileSiesta method) (sisl.io.siesta.fcSileSiesta method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.gridncSileSiesta method) (sisl.io.siesta.gridSileSiesta method) (sisl.io.siesta.hsxSileSiesta method) (sisl.io.siesta.ionncSileSiesta method) (sisl.io.siesta.ionxmlSileSiesta method) (sisl.io.siesta.kpSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.onlysSileSiesta method) (sisl.io.siesta.orbindxSileSiesta method) (sisl.io.siesta.pdosSileSiesta method) (sisl.io.siesta.rkpSileSiesta method) (sisl.io.siesta.SileBinSiesta method) (sisl.io.siesta.SileCDFSiesta method) (sisl.io.siesta.SileSiesta method) (sisl.io.siesta.stdoutSileSiesta method) (sisl.io.siesta.structSileSiesta method) (sisl.io.siesta.timesSileSiesta method) (sisl.io.siesta.tsdeSileSiesta method) (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.siesta.tshsSileSiesta method) (sisl.io.siesta.tsvncSileSiesta method) (sisl.io.siesta.wfsxSileSiesta method) (sisl.io.siesta.xvSileSiesta method) (sisl.io.Sile method) (sisl.io.SileBin method) (sisl.io.SileCDF method) (sisl.io.tableSile method) (sisl.io.tbtrans.deltancSileTBtrans method) (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.SileBinTBtrans method) (sisl.io.tbtrans.SileCDFTBtrans method) (sisl.io.tbtrans.SileTBtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtgfSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) (sisl.io.vasp.carSileVASP method) (sisl.io.vasp.chgSileVASP method) (sisl.io.vasp.doscarSileVASP method) (sisl.io.vasp.eigenvalSileVASP method) (sisl.io.vasp.locpotSileVASP method) (sisl.io.vasp.outcarSileVASP method) (sisl.io.vasp.SileBinVASP method) (sisl.io.vasp.SileVASP method) (sisl.io.wannier90.centresSileWannier90 method) (sisl.io.wannier90.hrSileWannier90 method) (sisl.io.wannier90.SileBinWannier90 method) (sisl.io.wannier90.SileWannier90 method) (sisl.io.wannier90.tbSileWannier90 method) (sisl.io.wannier90.winSileWannier90 method) (sisl.io.xsfSile method) (sisl.io.xyzSile method)

direction() (in module sisl.utils) DIRICHLET (sisl.BoundaryCondition attribute) (sisl.Grid attribute) disk_usage() (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.tbtrans.tbtgfSileTBtrans method) displacement (sisl.physics.MonkhorstPack property) displacement() (sisl.physics.phonon.EigenmodePhonon method) distance() (sisl.Geometry method) Dk() (sisl.physics.DensityMatrix method) (sisl.physics.DynamicalMatrix method) dkind (sisl.Grid property) (sisl.physics.Coefficient property) (sisl.physics.DensityMatrix property) (sisl.physics.densitymatrix._densitymatrix property) (sisl.physics.DynamicalMatrix property) (sisl.physics.electron.CoefficientElectron property) (sisl.physics.electron.EigenstateElectron property) (sisl.physics.electron.EigenvalueElectron property) (sisl.physics.electron.EigenvectorElectron property) (sisl.physics.electron.StateCElectron property) (sisl.physics.electron.StateElectron property) (sisl.physics.EnergyDensityMatrix property) (sisl.physics.Hamiltonian property) (sisl.physics.Overlap property) (sisl.physics.phonon.CoefficientPhonon property) (sisl.physics.phonon.EigenmodePhonon property) (sisl.physics.phonon.EigenvaluePhonon property) (sisl.physics.phonon.EigenvectorPhonon property) (sisl.physics.phonon.ModeCPhonon property) (sisl.physics.phonon.ModePhonon property) (sisl.physics.SparseOrbitalBZ property) (sisl.physics.SparseOrbitalBZSpin property) (sisl.physics.Spin property) (sisl.physics.State property) (sisl.physics.StateC property) (sisl.SparseAtom property) (sisl.SparseCSR property) (sisl.SparseOrbital property) dmSileSiesta (class in sisl.io.siesta) DOS() (in module sisl.physics.electron) (in module sisl.physics.phonon) (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvalueElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvaluePhonon method) doscarSileVASP (class in sisl.io.vasp) DownfoldSelfEnergy (class in sisl_toolbox.btd) draw_area_line() (sisl.viz.Figure method) draw_arrows() (sisl.viz.Figure method) draw_arrows_3D() (sisl.viz.Figure method) draw_balls_3D() (sisl.viz.Figure method) draw_heatmap() (sisl.viz.Figure method) draw_line() (sisl.viz.Figure method) draw_line_3D() (sisl.viz.Figure method) draw_mesh_3D() (sisl.viz.Figure method) draw_multicolor_area_line() (sisl.viz.Figure method) draw_multicolor_balls_3D() (sisl.viz.Figure method) draw_multicolor_line() (sisl.viz.Figure method) draw_multicolor_line_3D() (sisl.viz.Figure method) draw_multicolor_scatter() (sisl.viz.Figure method) draw_multicolor_scatter_3D() (sisl.viz.Figure method) draw_multisize_area_line() (sisl.viz.Figure method) draw_multisize_balls_3D() (sisl.viz.Figure method) draw_multisize_line() (sisl.viz.Figure method) draw_multisize_line_3D() (sisl.viz.Figure method) draw_multisize_scatter() (sisl.viz.Figure method) draw_multisize_scatter_3D() (sisl.viz.Figure method) draw_scatter() (sisl.viz.Figure method) draw_scatter_3D() (sisl.viz.Figure method) dryrun_nodes (sisl.viz.AtomicMatrixPlot attribute) (sisl.viz.BandsPlot attribute) (sisl.viz.FatbandsPlot attribute) (sisl.viz.GeometryPlot attribute) (sisl.viz.GridPlot attribute) (sisl.viz.PdosPlot attribute) (sisl.viz.Plot attribute) (sisl.viz.SitesPlot attribute) (sisl.viz.WavefunctionPlot attribute) dSk() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) dtype (sisl.Grid property) (sisl.physics.Coefficient property) (sisl.physics.DensityMatrix property) (sisl.physics.densitymatrix._densitymatrix property) (sisl.physics.DynamicalMatrix property) (sisl.physics.electron.CoefficientElectron property) (sisl.physics.electron.EigenstateElectron property) (sisl.physics.electron.EigenvalueElectron property) (sisl.physics.electron.EigenvectorElectron property) (sisl.physics.electron.StateCElectron property) (sisl.physics.electron.StateElectron property) (sisl.physics.EnergyDensityMatrix property) (sisl.physics.Hamiltonian property) (sisl.physics.Overlap property) (sisl.physics.phonon.CoefficientPhonon property) (sisl.physics.phonon.EigenmodePhonon property) (sisl.physics.phonon.EigenvaluePhonon property) (sisl.physics.phonon.EigenvectorPhonon property) (sisl.physics.phonon.ModeCPhonon property) (sisl.physics.phonon.ModePhonon property) (sisl.physics.SparseOrbitalBZ property) (sisl.physics.SparseOrbitalBZSpin property) (sisl.physics.Spin property) (sisl.physics.State property) (sisl.physics.StateC property) (sisl.SparseAtom property) (sisl.SparseCSR property) (sisl.SparseOrbital property) dvolume (sisl.Grid property) DynamicalMatrix (class in sisl.physics)

E

E (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) (sisl.physics.EnergyDensityMatrix property) edge_length (sisl.shape.Cube property) (sisl.shape.Cuboid property) edges() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseCSR method) (sisl.SparseOrbital method) effective_mass() (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.StateCElectron method) eig (sisl.physics.electron.EigenstateElectron property) (sisl.physics.electron.EigenvalueElectron property) eig() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) eigenchannel() (sisl_toolbox.btd.DeviceGreen method) eigenmode() (sisl.physics.DynamicalMatrix method) EigenmodePhonon (class in sisl.physics.phonon) eigenstate() (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.physics.Hamiltonian method) EigenstateElectron (class in sisl.physics.electron) eigenvalSileVASP (class in sisl.io.vasp) eigenvalue() (sisl.physics.DynamicalMatrix method) (sisl.physics.Hamiltonian method) EigenvalueElectron (class in sisl.physics.electron) EigenvaluePhonon (class in sisl.physics.phonon) EigenvectorElectron (class in sisl.physics.electron) EigenvectorPhonon (class in sisl.physics.phonon) eigh() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) eigsh() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) eigSileSiesta (class in sisl.io.siesta) Eindex() (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtgfSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) Ek() (sisl.physics.EnergyDensityMatrix method) elecs (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property)

electron_temperature (sisl.io.tbtrans.phtavncSilePHtrans attribute) (sisl.io.tbtrans.phtncSilePHtrans attribute) electron_temperature() (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) elements (sisl.mixing.History property) eliminate_zeros() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseCSR method) (sisl.SparseOrbital method) Ellipsoid (class in sisl.shape) Ellipsoid() (sisl.shape.Cube.to method) (sisl.shape.Cuboid.to method) (sisl.shape.Ellipsoid.to method) (sisl.shape.EllipticalCylinder.to method) (sisl.shape.NullShape.to method) (sisl.shape.Shape.to method) (sisl.shape.Sphere.to method) EllipticalCylinder (class in sisl.shape) empty() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseCSR method) (sisl.SparseOrbital method) EnergyDensityMatrix (class in sisl.physics) equal() (sisl.Atom method) (sisl.AtomicOrbital method) (sisl.Atoms method) (sisl.Geometry method) (sisl.GTOrbital method) (sisl.HydrogenicOrbital method) (sisl.Lattice method) (sisl.Orbital method) (sisl.SphericalOrbital method) (sisl.STOrbital method) erange() (in module sisl.utils) errno (sisl.io.SileError attribute) eta() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) evaluate_input_node() (sisl.viz.AtomicMatrixPlot static method) (sisl.viz.BandsPlot static method) (sisl.viz.FatbandsPlot static method) (sisl.viz.GeometryPlot static method) (sisl.viz.GridPlot static method) (sisl.viz.PdosPlot static method) (sisl.viz.Plot static method) (sisl.viz.SitesPlot static method) (sisl.viz.WavefunctionPlot static method) excite() (sisl_toolbox.siesta.atom.AtomInput method) expand() (sisl.shape.Cube method) (sisl.shape.Cuboid method) (sisl.shape.Ellipsoid method) (sisl.shape.EllipticalCylinder method) (sisl.shape.NullShape method) (sisl.shape.Sphere method) extend() (sisl.oplist method)

F

f (sisl.SphericalOrbital attribute) fano (sisl.io.tbtrans.phtavncSilePHtrans attribute) (sisl.io.tbtrans.phtprojncSilePHtrans attribute) (sisl.io.tbtrans.tbtavncSileTBtrans attribute) (sisl.io.tbtrans.tbtprojncSileTBtrans attribute) fano() (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) faSileSiesta (class in sisl.io.siesta) fatbands() (sisl.io.siesta.wfsxSileSiesta.plot method) (sisl.physics.BandStructure.plot method) (sisl.physics.BrillouinZone.plot method) (sisl.physics.MonkhorstPack.plot method) FatbandsPlot (class in sisl.viz) fcc() (in module sisl.geom) fcc_slab() (in module sisl.geom) fcSileGULP (class in sisl.io.gulp) fcSileSiesta (class in sisl.io.siesta) fdfSileSiesta (class in sisl.io.siesta) fermi_dirac() (in module sisl.physics) fermi_level() (sisl.physics.Hamiltonian method) fig_has_attr() (sisl.viz.Figure class method) Figure (class in sisl.viz) file (sisl.io.BaseSile property) (sisl.io.bigdft.asciiSileBigDFT property) (sisl.io.bigdft.SileBigDFT property) (sisl.io.bigdft.SileBinBigDFT property) (sisl.io.cubeSile property) (sisl.io.dftb.hamrealSileDFTB property) (sisl.io.dftb.overrealSileDFTB property) (sisl.io.dftb.SileBinDFTB property) (sisl.io.dftb.SileDFTB property) (sisl.io.fhiaims.inSileFHIaims property) (sisl.io.fhiaims.SileBinFHIaims property) (sisl.io.fhiaims.SileFHIaims property) (sisl.io.gulp.fcSileGULP property) (sisl.io.gulp.gotSileGULP property) (sisl.io.gulp.SileBinGULP property) (sisl.io.gulp.SileGULP property) (sisl.io.moldenSile property) (sisl.io.openmx.mdSileOpenMX property) (sisl.io.openmx.omxSileOpenMX property) (sisl.io.openmx.SileBinOpenMX property) (sisl.io.openmx.SileCDFOpenMX property) (sisl.io.openmx.SileOpenMX property) (sisl.io.orca.SileBinORCA property) (sisl.io.orca.SileORCA property) (sisl.io.orca.stdoutSileORCA property) (sisl.io.orca.txtSileORCA property) (sisl.io.pdbSile property) (sisl.io.scaleup.orboccSileScaleUp property) (sisl.io.scaleup.refSileScaleUp property) (sisl.io.scaleup.rhamSileScaleUp property) (sisl.io.scaleup.SileBinScaleUp property) (sisl.io.scaleup.SileScaleUp property) (sisl.io.siesta.aniSileSiesta property) (sisl.io.siesta.bandsSileSiesta property) (sisl.io.siesta.dmSileSiesta property) (sisl.io.siesta.eigSileSiesta property) (sisl.io.siesta.faSileSiesta property) (sisl.io.siesta.fcSileSiesta property) (sisl.io.siesta.fdfSileSiesta property) (sisl.io.siesta.gridncSileSiesta property) (sisl.io.siesta.gridSileSiesta property) (sisl.io.siesta.hsxSileSiesta property) (sisl.io.siesta.ionncSileSiesta property) (sisl.io.siesta.ionxmlSileSiesta property) (sisl.io.siesta.kpSileSiesta property) (sisl.io.siesta.ncSileSiesta property) (sisl.io.siesta.onlysSileSiesta property) (sisl.io.siesta.orbindxSileSiesta property) (sisl.io.siesta.pdosSileSiesta property) (sisl.io.siesta.rkpSileSiesta property) (sisl.io.siesta.SileBinSiesta property) (sisl.io.siesta.SileCDFSiesta property) (sisl.io.siesta.SileSiesta property) (sisl.io.siesta.stdoutSileSiesta property) (sisl.io.siesta.structSileSiesta property) (sisl.io.siesta.timesSileSiesta property) (sisl.io.siesta.tsdeSileSiesta property) (sisl.io.siesta.tsgfSileSiesta property) (sisl.io.siesta.tshsSileSiesta property) (sisl.io.siesta.tsvncSileSiesta property) (sisl.io.siesta.wfsxSileSiesta property) (sisl.io.siesta.xvSileSiesta property) (sisl.io.Sile property) (sisl.io.SileBin property) (sisl.io.SileCDF property) (sisl.io.tableSile property) (sisl.io.tbtrans.deltancSileTBtrans property) (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.SileBinTBtrans property) (sisl.io.tbtrans.SileCDFTBtrans property) (sisl.io.tbtrans.SileTBtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtgfSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) (sisl.io.vasp.carSileVASP property) (sisl.io.vasp.chgSileVASP property) (sisl.io.vasp.doscarSileVASP property) (sisl.io.vasp.eigenvalSileVASP property) (sisl.io.vasp.locpotSileVASP property) (sisl.io.vasp.outcarSileVASP property) (sisl.io.vasp.SileBinVASP property) (sisl.io.vasp.SileVASP property) (sisl.io.wannier90.centresSileWannier90 property) (sisl.io.wannier90.hrSileWannier90 property) (sisl.io.wannier90.SileBinWannier90 property) (sisl.io.wannier90.SileWannier90 property) (sisl.io.wannier90.tbSileWannier90 property) (sisl.io.wannier90.winSileWannier90 property) (sisl.io.xsfSile property) (sisl.io.xyzSile property)

fileindex() (in module sisl.utils) filename (sisl.io.SileError attribute) filename2 (sisl.io.SileError attribute) fill() (sisl.Grid method) final_node_key() (sisl.viz.AtomicMatrixPlot class method) (sisl.viz.BandsPlot class method) (sisl.viz.FatbandsPlot class method) (sisl.viz.GeometryPlot class method) (sisl.viz.GridPlot class method) (sisl.viz.PdosPlot class method) (sisl.viz.Plot class method) (sisl.viz.SitesPlot class method) (sisl.viz.WavefunctionPlot class method) finalize() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseCSR method) (sisl.SparseOrbital method) finalized (sisl.physics.DensityMatrix property) (sisl.physics.densitymatrix._densitymatrix property) (sisl.physics.DynamicalMatrix property) (sisl.physics.EnergyDensityMatrix property) (sisl.physics.Hamiltonian property) (sisl.physics.Overlap property) (sisl.physics.SparseOrbitalBZ property) (sisl.physics.SparseOrbitalBZSpin property) (sisl.SparseAtom property) (sisl.SparseCSR property) (sisl.SparseOrbital property) find_close() (sisl.geom.NeighborFinder method) find_neighbors() (sisl.geom.NeighborFinder method) find_node_key() (sisl.viz.AtomicMatrixPlot class method) (sisl.viz.BandsPlot class method) (sisl.viz.FatbandsPlot class method) (sisl.viz.GeometryPlot class method) (sisl.viz.GridPlot class method) (sisl.viz.PdosPlot class method) (sisl.viz.Plot class method) (sisl.viz.SitesPlot class method) (sisl.viz.WavefunctionPlot class method) find_nsc() (sisl.Geometry method) find_unique_pairs() (sisl.geom.NeighborFinder method) firsto (sisl.Atoms property) (sisl.Geometry property) fit() (sisl.Lattice method) formula() (sisl.Atoms method) from_bytes() (sisl.BoundaryCondition method) from_fdf() (sisl_toolbox.btd.DeviceGreen class method) from_func() (sisl.viz.AtomicMatrixPlot class method) (sisl.viz.BandsPlot class method) (sisl.viz.FatbandsPlot class method) (sisl.viz.GeometryPlot class method) (sisl.viz.GridPlot class method) (sisl.viz.PdosPlot class method) (sisl.viz.Plot class method) (sisl.viz.SitesPlot class method) (sisl.viz.WavefunctionPlot class method) from_input() (sisl_toolbox.siesta.atom.AtomInput class method) from_node_tree() (sisl.viz.AtomicMatrixPlot class method) (sisl.viz.BandsPlot class method) (sisl.viz.FatbandsPlot class method) (sisl.viz.GeometryPlot class method) (sisl.viz.GridPlot class method) (sisl.viz.PdosPlot class method) (sisl.viz.Plot class method) (sisl.viz.SitesPlot class method) (sisl.viz.WavefunctionPlot class method) from_yaml() (sisl_toolbox.siesta.atom.AtomInput class method) fromhex() (sisl.constant.PhysicalConstant method) fromkeys() (sisl.utils.PropertyDict method) fromsp() (sisl.physics.DensityMatrix class method) (sisl.physics.densitymatrix._densitymatrix class method) (sisl.physics.DynamicalMatrix class method) (sisl.physics.EnergyDensityMatrix class method) (sisl.physics.Hamiltonian class method) (sisl.physics.Overlap class method) (sisl.physics.SparseOrbitalBZ class method) (sisl.physics.SparseOrbitalBZSpin class method) (sisl.SparseAtom class method) (sisl.SparseCSR class method) (sisl.SparseOrbital class method) FullNeighborList (class in sisl.geom) function (sisl.viz.Plot attribute) function() (sisl.viz.AtomicMatrixPlot static method) (sisl.viz.BandsPlot static method) (sisl.viz.FatbandsPlot static method) (sisl.viz.GeometryPlot static method) (sisl.viz.GridPlot static method) (sisl.viz.PdosPlot static method) (sisl.viz.SitesPlot static method) (sisl.viz.WavefunctionPlot static method) FuncType (in module sisl.typing) fxyz (sisl.Geometry property)

G

G (in module sisl.constant) G0 (in module sisl.constant) GaugeType (in module sisl.typing) gaussian() (in module sisl.physics) geom (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) geometry Geometry (class in sisl) geometry (sisl.geom.NeighborFinder attribute) (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) (sisl.physics.DensityMatrix property) (sisl.physics.densitymatrix._densitymatrix property) (sisl.physics.DynamicalMatrix property) (sisl.physics.EnergyDensityMatrix property) (sisl.physics.Hamiltonian property) (sisl.physics.Overlap property) (sisl.physics.SparseOrbitalBZ property) (sisl.physics.SparseOrbitalBZSpin property) (sisl.SparseAtom property) (sisl.SparseOrbital property) (sisl.viz.GeometryPlot property) geometry() (sisl.Geometry.plot method) (sisl.io.bigdft.asciiSileBigDFT.plot method) (sisl.io.cubeSile.plot method) (sisl.io.fhiaims.inSileFHIaims.plot method) (sisl.io.gulp.gotSileGULP.plot method) (sisl.io.openmx.mdSileOpenMX.plot method) (sisl.io.openmx.omxSileOpenMX.plot method) (sisl.io.orca.txtSileORCA.plot method) (sisl.io.pdbSile.plot method) (sisl.io.scaleup.refSileScaleUp.plot method) (sisl.io.siesta.aniSileSiesta.plot method) (sisl.io.siesta.fdfSileSiesta.plot method) (sisl.io.siesta.hsxSileSiesta.plot method) (sisl.io.siesta.ncSileSiesta.plot method) (sisl.io.siesta.onlysSileSiesta.plot method) (sisl.io.siesta.pdosSileSiesta.plot method) (sisl.io.siesta.stdoutSileSiesta.plot method) (sisl.io.siesta.structSileSiesta.plot method) (sisl.io.siesta.tshsSileSiesta.plot method) (sisl.io.siesta.xvSileSiesta.plot method) (sisl.io.tbtrans.deltancSileTBtrans.plot method) (sisl.io.tbtrans.phtavncSilePHtrans.plot method) (sisl.io.tbtrans.phtncSilePHtrans.plot method) (sisl.io.tbtrans.phtprojncSilePHtrans.plot method) (sisl.io.tbtrans.phtsencSilePHtrans.plot method) (sisl.io.tbtrans.tbtavncSileTBtrans.plot method) (sisl.io.tbtrans.tbtncSileTBtrans.plot method) (sisl.io.tbtrans.tbtprojncSileTBtrans.plot method) (sisl.io.tbtrans.tbtsencSileTBtrans.plot method) (sisl.io.vasp.carSileVASP.plot method) (sisl.io.vasp.chgSileVASP.plot method) (sisl.io.vasp.locpotSileVASP.plot method) (sisl.io.wannier90.centresSileWannier90.plot method) (sisl.io.wannier90.tbSileWannier90.plot method) (sisl.io.wannier90.winSileWannier90.plot method) (sisl.io.xsfSile.plot method) (sisl.io.xyzSile.plot method) geometry_group() (sisl.io.vasp.carSileVASP static method) (sisl.io.vasp.chgSileVASP static method) (sisl.io.vasp.doscarSileVASP static method) (sisl.io.vasp.eigenvalSileVASP static method) (sisl.io.vasp.locpotSileVASP static method) (sisl.io.vasp.outcarSileVASP static method) (sisl.io.vasp.SileBinVASP static method) (sisl.io.vasp.SileVASP static method) GeometryLike (in module sisl.typing) GeometryPlot (class in sisl.viz) get() (sisl.io.openmx.omxSileOpenMX method) (sisl.io.siesta.fdfSileSiesta method) (sisl.utils.PropertyDict method) (sisl.viz.AtomicMatrixPlot method) (sisl.viz.BandsPlot method) (sisl.viz.FatbandsPlot method) (sisl.viz.GeometryPlot method) (sisl.viz.GridPlot method) (sisl.viz.PdosPlot method) (sisl.viz.Plot method) (sisl.viz.SitesPlot method) (sisl.viz.WavefunctionPlot method)

get_diagram_label() (sisl.viz.AtomicMatrixPlot method) (sisl.viz.BandsPlot method) (sisl.viz.FatbandsPlot method) (sisl.viz.GeometryPlot method) (sisl.viz.GridPlot method) (sisl.viz.PdosPlot method) (sisl.viz.Plot method) (sisl.viz.SitesPlot method) (sisl.viz.WavefunctionPlot method) get_distribution() (in module sisl.physics) get_figure() (in module sisl.viz) get_input() (sisl.viz.AtomicMatrixPlot method) (sisl.viz.BandsPlot method) (sisl.viz.FatbandsPlot method) (sisl.viz.GeometryPlot method) (sisl.viz.GridPlot method) (sisl.viz.PdosPlot method) (sisl.viz.Plot method) (sisl.viz.SitesPlot method) (sisl.viz.WavefunctionPlot method) get_sile() (in module sisl.io) get_sile_class() (in module sisl.io) get_siles() (in module sisl.io) get_syntax (sisl.viz.AtomicMatrixPlot attribute) (sisl.viz.BandsPlot attribute) (sisl.viz.FatbandsPlot attribute) (sisl.viz.GeometryPlot attribute) (sisl.viz.GridPlot attribute) (sisl.viz.PdosPlot attribute) (sisl.viz.Plot attribute) (sisl.viz.SitesPlot attribute) (sisl.viz.WavefunctionPlot attribute) get_tree() (sisl.viz.AtomicMatrixPlot method) (sisl.viz.BandsPlot method) (sisl.viz.FatbandsPlot method) (sisl.viz.GeometryPlot method) (sisl.viz.GridPlot method) (sisl.viz.PdosPlot method) (sisl.viz.Plot method) (sisl.viz.SitesPlot method) (sisl.viz.WavefunctionPlot method) getitem() (sisl.BoundaryCondition class method) goldene() (in module sisl.geom) gotSileGULP (class in sisl.io.gulp) graphene() (in module sisl.geom) graphene_flake() (in module sisl.geom) graphene_heteroribbon() (in module sisl.geom) graphene_nanoribbon() (in module sisl.geom) green() (sisl.physics.RealSpaceSE method) (sisl.physics.RealSpaceSI method) (sisl.physics.RecursiveSI method) (sisl_toolbox.btd.DeviceGreen method) Grid (class in sisl) grid() (sisl.Grid.plot method) (sisl.io.cubeSile.plot method) (sisl.io.siesta.fdfSileSiesta.plot method) (sisl.io.siesta.gridncSileSiesta.plot method) (sisl.io.siesta.ncSileSiesta.plot method) (sisl.io.siesta.tsvncSileSiesta.plot method) (sisl.io.vasp.chgSileVASP.plot method) (sisl.io.vasp.locpotSileVASP.plot method) (sisl.physics.BandStructure.apply method) (sisl.physics.BrillouinZone.apply method) (sisl.physics.MonkhorstPack class method) (sisl.physics.MonkhorstPack.apply method) grid_unit (sisl.io.siesta.gridSileSiesta attribute) GridLike (in module sisl.typing) gridncSileSiesta (class in sisl.io.siesta) GridPlot (class in sisl.viz) grids (sisl.io.siesta.ncSileSiesta property) gridSileSiesta (class in sisl.io.siesta) group_atom_data() (sisl.Atoms method) groups() (sisl.viz.FatbandsPlot method) (sisl.viz.PdosPlot method) GTOrbital (class in sisl)

H

h (in module sisl.constant) H (sisl.physics.Hamiltonian property) Hamiltonian (class in sisl.physics) hamrealSileDFTB (class in sisl.io.dftb) has_level() (sisl.io.tbtrans.deltancSileTBtrans method) hassame() (sisl.Atoms method) hbar (in module sisl.constant) hcp() (in module sisl.geom) heaviside() (in module sisl.physics) height (sisl.shape.EllipticalCylinder property) height_vector (sisl.shape.EllipticalCylinder property) heteroribbon() (in module sisl.geom) hex() (sisl.constant.PhysicalConstant method) hexagonal() (in module sisl.geom) History (class in sisl.mixing) history (sisl.mixing.AdaptiveDIISMixer property) (sisl.mixing.AdaptivePulayMixer property) (sisl.mixing.AndersonMixer property) (sisl.mixing.BaseHistoryWeightMixer property) (sisl.mixing.DIISMixer property) (sisl.mixing.LinearMixer property) (sisl.mixing.PulayMixer property)

history_max (sisl.mixing.History attribute) Hk() (sisl.physics.Hamiltonian method) (sisl_toolbox.btd.DeviceGreen method) HkSk() (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.tbtrans.tbtgfSileTBtrans method) honeycomb() (in module sisl.geom) honeycomb_flake() (in module sisl.geom) hrSileWannier90 (class in sisl.io.wannier90) hsxSileSiesta (class in sisl.io.siesta) hw (sisl.physics.phonon.EigenmodePhonon property) (sisl.physics.phonon.EigenvaluePhonon property) hydrogenic-orbital HydrogenicOrbital (class in sisl)

I

i (sisl.geom.AtomNeighborList property) (sisl.geom.FullNeighborList property) (sisl.geom.PartialNeighborList property) (sisl.geom.PointNeighborList property) (sisl.geom.PointsNeighborList property) (sisl.geom.UniqueNeighborList property) icell (sisl.Geometry property) (sisl.Grid property) (sisl.Lattice property) imag (sisl.BoundaryCondition attribute) (sisl.constant.PhysicalConstant attribute) in_primitive() (sisl.physics.BandStructure static method) (sisl.physics.BrillouinZone static method) (sisl.physics.MonkhorstPack static method) includes() (sisl.io.siesta.fdfSileSiesta method) index() (sisl.Atom method) (sisl.Atoms method) (sisl.Grid method) (sisl.oplist method) index2xyz() (sisl.Grid method) index_fold() (sisl.Grid method) index_truncate() (sisl.Grid method) info (sisl.physics.Coefficient attribute) (sisl.physics.electron.CoefficientElectron attribute) (sisl.physics.electron.EigenstateElectron attribute) (sisl.physics.electron.EigenvalueElectron attribute) (sisl.physics.electron.EigenvectorElectron attribute) (sisl.physics.electron.StateCElectron attribute) (sisl.physics.electron.StateElectron attribute) (sisl.physics.phonon.CoefficientPhonon attribute) (sisl.physics.phonon.EigenmodePhonon attribute) (sisl.physics.phonon.EigenvaluePhonon attribute) (sisl.physics.phonon.EigenvectorPhonon attribute) (sisl.physics.phonon.ModeCPhonon attribute) (sisl.physics.phonon.ModePhonon attribute) (sisl.physics.State attribute) (sisl.physics.StateC attribute) info() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) init_3D() (sisl.viz.Figure method) init_coloraxis() (sisl.viz.Figure method) init_figure() (sisl.viz.Figure method) initialize() (sisl.physics.RealSpaceSE method) (sisl.physics.RealSpaceSI method) inner() (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.State method) (sisl.physics.StateC method) inputs (sisl.viz.AtomicMatrixPlot property) (sisl.viz.BandsPlot property) (sisl.viz.FatbandsPlot property) (sisl.viz.GeometryPlot property) (sisl.viz.GridPlot property) (sisl.viz.PdosPlot property) (sisl.viz.Plot property) (sisl.viz.SitesPlot property) (sisl.viz.WavefunctionPlot property) insert() (in module sisl) (sisl.Atoms method) (sisl.Geometry method) (sisl.oplist method) insert_jump() (sisl.physics.BandStructure method) inSileFHIaims (class in sisl.io.fhiaims) interp() (sisl.Grid method) ionncSileSiesta (class in sisl.io.siesta) ionxmlSileSiesta (class in sisl.io.siesta) ipr() (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.State method) (sisl.physics.StateC method) iR() (sisl.Geometry method) is_cartesian() (sisl.Lattice method) is_class() (sisl.geom.AtomCategory class method) is_colinear (sisl.physics.Spin property) is_diagonal (sisl.physics.Spin property)

is_integer() (sisl.BoundaryCondition method) (sisl.constant.PhysicalConstant method) is_noncolinear (sisl.physics.Spin property) is_orthogonal() (sisl.Lattice method) is_output_outdated() (sisl.viz.AtomicMatrixPlot method) (sisl.viz.BandsPlot method) (sisl.viz.FatbandsPlot method) (sisl.viz.GeometryPlot method) (sisl.viz.GridPlot method) (sisl.viz.PdosPlot method) (sisl.viz.Plot method) (sisl.viz.SitesPlot method) (sisl.viz.WavefunctionPlot method) is_polarized (sisl.physics.Spin property) is_spinorbit (sisl.physics.Spin property) is_unpolarized (sisl.physics.Spin property) isc (sisl.geom.AtomNeighborList property) (sisl.geom.FullNeighborList property) (sisl.geom.PartialNeighborList property) (sisl.geom.PointNeighborList property) (sisl.geom.PointsNeighborList property) (sisl.geom.UniqueNeighborList property) isc_off (sisl.Geometry property) (sisl.Grid property) (sisl.Lattice property) isosurface() (sisl.Grid method) items() (sisl.utils.PropertyDict method) iter() (sisl.Atom method) (sisl.Atoms method) (sisl.Geometry method) (sisl.io.openmx.SileCDFOpenMX method) (sisl.io.siesta.gridncSileSiesta method) (sisl.io.siesta.ionncSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.SileCDFSiesta method) (sisl.io.siesta.tsvncSileSiesta method) (sisl.io.SileCDF method) (sisl.io.tbtrans.deltancSileTBtrans method) (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.SileCDFTBtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) (sisl.physics.BandStructure method) (sisl.physics.BandStructure.apply method) (sisl.physics.BrillouinZone method) (sisl.physics.BrillouinZone.apply method) (sisl.physics.Coefficient method) (sisl.physics.electron.CoefficientElectron method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvalueElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.MonkhorstPack method) (sisl.physics.MonkhorstPack.apply method) (sisl.physics.phonon.CoefficientPhonon method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvaluePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.State method) (sisl.physics.StateC method) iter_block() (sisl.Geometry method) iter_block_rand() (sisl.Geometry method) iter_block_shape() (sisl.Geometry method) iter_nnz() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseCSR method) (sisl.SparseOrbital method) iter_orbitals() (sisl.Geometry method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) iter_shape() (in module sisl.utils) iter_species() (sisl.Geometry method)

J

j (sisl.geom.AtomNeighborList property) (sisl.geom.FullNeighborList property) (sisl.geom.PartialNeighborList property) (sisl.geom.PointNeighborList property) (sisl.geom.PointsNeighborList property) (sisl.geom.UniqueNeighborList property)

K

k (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) (sisl.physics.BandStructure property) (sisl.physics.BrillouinZone property) (sisl.physics.MonkhorstPack property) keys() (sisl.utils.PropertyDict method) kind (sisl.physics.Spin property) kindex() (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtgfSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method)

KPoint (in module sisl.typing) kpSileSiesta (class in sisl.io.siesta) kpt (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) kT (sisl.io.tbtrans.phtavncSilePHtrans attribute) (sisl.io.tbtrans.phtncSilePHtrans attribute) kT() (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) kw() (sisl.geom.AtomCategory class method)

L

l (sisl.AtomicOrbital property) (sisl.GTOrbital property) (sisl.HydrogenicOrbital property) (sisl.SphericalOrbital property) (sisl.STOrbital property) last_log (sisl.viz.AtomicMatrixPlot property) (sisl.viz.BandsPlot property) (sisl.viz.FatbandsPlot property) (sisl.viz.GeometryPlot property) (sisl.viz.GridPlot property) (sisl.viz.PdosPlot property) (sisl.viz.Plot property) (sisl.viz.SitesPlot property) (sisl.viz.WavefunctionPlot property) lasto (sisl.Atoms property) (sisl.Geometry property) (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) lattice Lattice (class in sisl)

LatticeLike (in module sisl.typing) LatticeOrGeometry (in module sisl.typing) LatticeOrGeometryLike (in module sisl.typing) length (sisl.Geometry property) (sisl.Grid property) (sisl.Lattice property) lengthf() (sisl.Lattice method) lineark() (sisl.physics.BandStructure method) LinearMixer (class in sisl.mixing) lineartick() (sisl.physics.BandStructure method) list() (sisl.physics.BandStructure.apply method) (sisl.physics.BrillouinZone.apply method) (sisl.physics.MonkhorstPack.apply method) list2str() (in module sisl.utils) listify (in module sisl.utils) locpotSileVASP (class in sisl.io.vasp) logs (sisl.viz.AtomicMatrixPlot attribute) (sisl.viz.BandsPlot attribute) (sisl.viz.FatbandsPlot attribute) (sisl.viz.GeometryPlot attribute) (sisl.viz.GridPlot attribute) (sisl.viz.PdosPlot attribute) (sisl.viz.Plot attribute) (sisl.viz.SitesPlot attribute) (sisl.viz.WavefunctionPlot attribute) lorentzian() (in module sisl.physics) lstranges() (in module sisl.utils)

M

m (sisl.AtomicOrbital property) (sisl.GTOrbital property) (sisl.HydrogenicOrbital property) (sisl.STOrbital property) m_e (in module sisl.constant) m_p (in module sisl.constant) map_inputs() (sisl.viz.AtomicMatrixPlot method) (sisl.viz.BandsPlot method) (sisl.viz.FatbandsPlot method) (sisl.viz.GeometryPlot method) (sisl.viz.GridPlot method) (sisl.viz.PdosPlot method) (sisl.viz.Plot method) (sisl.viz.SitesPlot method) (sisl.viz.WavefunctionPlot method) mass (sisl.Atom property) (sisl.Atoms property) (sisl.Geometry property) math_eval() (in module sisl.utils) matrix max_elements (sisl.mixing.History property) maxR() (sisl.Atom method) (sisl.Atoms method) (sisl.Geometry method) mdSileOpenMX (class in sisl.io.openmx) mean() (sisl.Grid method) memory (sisl.geom.NeighborFinder attribute) merge() (sisl.io.tbtrans.deltancSileTBtrans class method) (sisl.physics.BandStructure static method) (sisl.physics.BrillouinZone static method) (sisl.physics.MonkhorstPack static method) (sisl.viz.AtomicMatrixPlot method) (sisl.viz.BandsPlot method) (sisl.viz.FatbandsPlot method) (sisl.viz.GeometryPlot method) (sisl.viz.GridPlot method) (sisl.viz.PdosPlot method) (sisl.viz.Plot method) (sisl.viz.SitesPlot method) (sisl.viz.WavefunctionPlot method) merge_plots() (in module sisl.viz) mgrid() (sisl.Grid class method) min_nsc (sisl.geom.AtomNeighborList property) (sisl.geom.FullNeighborList property) (sisl.geom.PartialNeighborList property) (sisl.geom.PointNeighborList property) (sisl.geom.PointsNeighborList property) (sisl.geom.UniqueNeighborList property) mirror() (sisl.Geometry method) mix() (sisl.mixing.AdaptiveDIISMixer method) (sisl.mixing.AdaptivePulayMixer method) (sisl.mixing.DIISMixer method) (sisl.mixing.PulayMixer method)

mixer (sisl.mixing.StepMixer property) mode (sisl.physics.phonon.EigenmodePhonon property) (sisl.physics.phonon.EigenvectorPhonon property) (sisl.physics.phonon.ModeCPhonon property) (sisl.physics.phonon.ModePhonon property) ModeCPhonon (class in sisl.physics.phonon) ModePhonon (class in sisl.physics.phonon) module sisl sisl.constant sisl.geom sisl.io sisl.io.bigdft sisl.io.dftb sisl.io.fhiaims sisl.io.gulp sisl.io.openmx sisl.io.orca sisl.io.scaleup sisl.io.siesta sisl.io.tbtrans sisl.io.vasp sisl.io.wannier90 sisl.mixing sisl.physics sisl.physics.electron sisl.physics.phonon sisl.shape sisl.typing sisl.unit sisl.unit.siesta sisl.utils sisl.viz sisl_toolbox sisl_toolbox.btd sisl_toolbox.siesta.atom sisl_toolbox.transiesta.poisson moldenSile (class in sisl.io) molecules (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) MonkhorstPack (class in sisl.physics) move() (sisl.Geometry method) mu() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) mulliken() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.EnergyDensityMatrix method)

N

n (sisl.AtomicOrbital property) (sisl.GTOrbital property) (sisl.HydrogenicOrbital property) (sisl.STOrbital property) n_btd() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) n_neighbors (sisl.geom.AtomNeighborList property) (sisl.geom.FullNeighborList property) (sisl.geom.PartialNeighborList property) (sisl.geom.PointNeighborList property) (sisl.geom.PointsNeighborList property) (sisl.geom.UniqueNeighborList property) n_s (sisl.Geometry property) (sisl.Grid property) (sisl.Lattice attribute) na (sisl.Geometry property) (sisl.io.orca.stdoutSileORCA property) (sisl.io.orca.txtSileORCA property) (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) na_b (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) na_buffer (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) na_d (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) na_dev (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) na_down() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) na_s (sisl.Geometry property) na_u (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) name (sisl.geom.AtomCategory property) name() (sisl.AtomicOrbital method) (sisl.GTOrbital method) (sisl.HydrogenicOrbital method) (sisl.Orbital method) (sisl.SphericalOrbital method) (sisl.STOrbital method) names (sisl.Geometry property) nanoribbon() (in module sisl.geom) nanotube() (in module sisl.geom) nbins (sisl.geom.NeighborFinder attribute) ncol (sisl.SparseCSR attribute) ncSileSiesta (class in sisl.io.siesta) ndarray() (sisl.Lattice.new method) (sisl.physics.BandStructure.apply method) (sisl.physics.BrillouinZone.apply method) (sisl.physics.MonkhorstPack.apply method) nE (sisl.io.tbtrans.phtavncSilePHtrans property) ne (sisl.io.tbtrans.phtavncSilePHtrans property) nE (sisl.io.tbtrans.phtncSilePHtrans property) ne (sisl.io.tbtrans.phtncSilePHtrans property) nE (sisl.io.tbtrans.phtprojncSilePHtrans property) ne (sisl.io.tbtrans.phtprojncSilePHtrans property) nE (sisl.io.tbtrans.phtsencSilePHtrans property) ne (sisl.io.tbtrans.phtsencSilePHtrans property) nE (sisl.io.tbtrans.tbtavncSileTBtrans property) ne (sisl.io.tbtrans.tbtavncSileTBtrans property) nE (sisl.io.tbtrans.tbtncSileTBtrans property) ne (sisl.io.tbtrans.tbtncSileTBtrans property) nE (sisl.io.tbtrans.tbtprojncSileTBtrans property) ne (sisl.io.tbtrans.tbtprojncSileTBtrans property) nE (sisl.io.tbtrans.tbtsencSileTBtrans property) ne (sisl.io.tbtrans.tbtsencSileTBtrans property) NeighborFinder (class in sisl.geom) network (sisl.viz.AtomicMatrixPlot attribute) (sisl.viz.BandsPlot attribute) (sisl.viz.FatbandsPlot attribute) (sisl.viz.GeometryPlot attribute) (sisl.viz.GridPlot attribute) (sisl.viz.PdosPlot attribute) (sisl.viz.Plot attribute) (sisl.viz.SitesPlot attribute) (sisl.viz.WavefunctionPlot attribute) NEUMANN (sisl.BoundaryCondition attribute) (sisl.Grid attribute) new (sisl.Geometry attribute) (sisl.Grid attribute) (sisl.Lattice attribute) next() (sisl.mixing.StepMixer method) nk (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) nkpt (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property)

nnz (sisl.physics.DensityMatrix property) (sisl.physics.densitymatrix._densitymatrix property) (sisl.physics.DynamicalMatrix property) (sisl.physics.EnergyDensityMatrix property) (sisl.physics.Hamiltonian property) (sisl.physics.Overlap property) (sisl.physics.SparseOrbitalBZ property) (sisl.physics.SparseOrbitalBZSpin property) (sisl.SparseAtom property) (sisl.SparseCSR property) (sisl.SparseOrbital property) no (sisl.Atom property) (sisl.Atoms property) (sisl.Geometry property) (sisl.io.orca.stdoutSileORCA property) (sisl.io.orca.txtSileORCA property) (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) no_d (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) no_down() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) no_e() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) no_s (sisl.Geometry property) no_u (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) nodes (sisl.viz.AtomicMatrixPlot attribute) (sisl.viz.BandsPlot attribute) (sisl.viz.FatbandsPlot attribute) (sisl.viz.GeometryPlot attribute) (sisl.viz.GridPlot attribute) (sisl.viz.PdosPlot attribute) (sisl.viz.Plot attribute) (sisl.viz.SitesPlot attribute) (sisl.viz.WavefunctionPlot attribute) noise_power (sisl.io.tbtrans.phtavncSilePHtrans attribute) (sisl.io.tbtrans.phtncSilePHtrans attribute) (sisl.io.tbtrans.phtprojncSilePHtrans attribute) (sisl.io.tbtrans.tbtavncSileTBtrans attribute) (sisl.io.tbtrans.tbtprojncSileTBtrans attribute) noise_power() (sisl.io.tbtrans.tbtncSileTBtrans method) non_orthogonal (sisl.physics.DensityMatrix property) (sisl.physics.densitymatrix._densitymatrix property) (sisl.physics.DynamicalMatrix property) (sisl.physics.EnergyDensityMatrix property) (sisl.physics.Hamiltonian property) (sisl.physics.Overlap property) (sisl.physics.SparseOrbitalBZ property) (sisl.physics.SparseOrbitalBZSpin property) NONCOLINEAR (sisl.physics.Spin attribute) none() (sisl.physics.BandStructure.apply method) (sisl.physics.BrillouinZone.apply method) (sisl.physics.MonkhorstPack.apply method) nonzero() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseCSR method) (sisl.SparseOrbital method) norm() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.State method) (sisl.physics.StateC method) (sisl.Quaternion method) norm2() (sisl.physics.electron._electron_State method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.State method) (sisl.physics.StateC method) normalize() (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.State method) (sisl.physics.StateC method) nsc (sisl.Geometry property) (sisl.Grid property) (sisl.Lattice attribute) nspecie (sisl.Atoms property) nspecies (sisl.Atoms property) NullShape (class in sisl.shape) numerator (sisl.BoundaryCondition attribute)

O

o2a() (sisl.Geometry method) o2isc() (sisl.Geometry method) o2p() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) o2sc() (sisl.Geometry method) o2transpose() (sisl.Geometry method) o_dev (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) occupation() (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvalueElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvaluePhonon method) offset() (sisl.Lattice method) omxSileOpenMX (class in sisl.io.openmx) onlysSileSiesta (class in sisl.io.siesta) OPEN (sisl.BoundaryCondition attribute) (sisl.Grid attribute) oplist (class in sisl) oplist() (sisl.physics.BandStructure.apply method) (sisl.physics.BrillouinZone.apply method) (sisl.physics.MonkhorstPack.apply method) optimize_nsc() (sisl.Geometry method) orb (sisl.AtomicOrbital property) (sisl.HydrogenicOrbital property) orbindxSileSiesta (class in sisl.io.siesta) orbital Orbital (class in sisl) orbital() (sisl.Atoms method) orbital_ACOHP() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) orbital_ACOOP() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) orbital_COHP (sisl.io.tbtrans.phtprojncSilePHtrans attribute) (sisl.io.tbtrans.tbtprojncSileTBtrans attribute) orbital_COHP() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method)

orbital_COOP (sisl.io.tbtrans.phtprojncSilePHtrans attribute) (sisl.io.tbtrans.tbtprojncSileTBtrans attribute) orbital_COOP() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) orbital_current (sisl.io.tbtrans.phtavncSilePHtrans attribute) (sisl.io.tbtrans.phtncSilePHtrans attribute) orbital_current() (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) orbital_momentum() (sisl.physics.DensityMatrix method) orbital_transmission() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) orbitals (sisl.Atom property) (sisl.Atoms property) (sisl.Geometry property) OrbitalsIndex (in module sisl.typing) orboccSileScaleUp (class in sisl.io.scaleup) origin (sisl.Geometry property) (sisl.Grid property) (sisl.Lattice property) (sisl.shape.Cube property) (sisl.shape.Cuboid property) oRij() (sisl.Geometry method) orij() (sisl.Geometry method) orthogonal (sisl.physics.DensityMatrix property) (sisl.physics.densitymatrix._densitymatrix property) (sisl.physics.DynamicalMatrix property) (sisl.physics.EnergyDensityMatrix property) (sisl.physics.Hamiltonian property) (sisl.physics.Overlap property) (sisl.physics.SparseOrbitalBZ property) (sisl.physics.SparseOrbitalBZSpin property) osc2uc() (sisl.Geometry method) ouc2sc() (sisl.Geometry method) outcarSileVASP (class in sisl.io.vasp) outer() (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.State method) (sisl.physics.StateC method) Overlap (class in sisl.physics) overlap() (sisl.Geometry method) overrealSileDFTB (class in sisl.io.dftb)

P

P (sisl.AtomicOrbital property) (sisl.HydrogenicOrbital property) parallel() (sisl.Lattice method) param_circle() (sisl.physics.BandStructure class method) (sisl.physics.BrillouinZone class method) (sisl.physics.MonkhorstPack class method) parameters() (sisl.Lattice method) parametrize() (sisl.physics.BandStructure static method) (sisl.physics.BrillouinZone static method) (sisl.physics.MonkhorstPack static method) parent (sisl.physics.Coefficient attribute) (sisl.physics.electron.CoefficientElectron attribute) (sisl.physics.electron.EigenstateElectron attribute) (sisl.physics.electron.EigenvalueElectron attribute) (sisl.physics.electron.EigenvectorElectron attribute) (sisl.physics.electron.StateCElectron attribute) (sisl.physics.electron.StateElectron attribute) (sisl.physics.phonon.CoefficientPhonon attribute) (sisl.physics.phonon.EigenmodePhonon attribute) (sisl.physics.phonon.EigenvaluePhonon attribute) (sisl.physics.phonon.EigenvectorPhonon attribute) (sisl.physics.phonon.ModeCPhonon attribute) (sisl.physics.phonon.ModePhonon attribute) (sisl.physics.State attribute) (sisl.physics.StateC attribute) PartialNeighborList (class in sisl.geom) Path() (sisl.Geometry.to method) (sisl.Grid.to method) (sisl.Lattice.to method) pbc (sisl.Geometry property) (sisl.Grid property) (sisl.Lattice property) pdbSile (class in sisl.io) PDOS() (in module sisl.physics.electron) (in module sisl.physics.phonon) pdos() (sisl.io.siesta.fdfSileSiesta.plot method) (sisl.io.siesta.pdosSileSiesta.plot method) (sisl.io.siesta.wfsxSileSiesta.plot method) (sisl.io.tbtrans.phtavncSilePHtrans.plot method) (sisl.io.tbtrans.phtncSilePHtrans.plot method) (sisl.io.tbtrans.phtprojncSilePHtrans.plot method) (sisl.io.tbtrans.tbtavncSileTBtrans.plot method) (sisl.io.tbtrans.tbtncSileTBtrans.plot method) (sisl.io.tbtrans.tbtprojncSileTBtrans.plot method) PDOS() (sisl.physics.electron.EigenstateElectron method) pdos() (sisl.physics.Hamiltonian.plot method) PDOS() (sisl.physics.phonon.EigenmodePhonon method) PdosPlot (class in sisl.viz) pdosSileSiesta (class in sisl.io.siesta) PERIODIC (sisl.BoundaryCondition attribute) (sisl.Grid attribute) PeriodicTable (class in sisl) pg() (sisl_toolbox.siesta.atom.AtomInput method) phase() (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.State method) (sisl.physics.StateC method) phonon_temperature() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) phtavncSilePHtrans (class in sisl.io.tbtrans) phtncSilePHtrans (class in sisl.io.tbtrans) phtprojncSilePHtrans (class in sisl.io.tbtrans) phtsencSilePHtrans (class in sisl.io.tbtrans) PhysicalConstant (class in sisl.constant) pivot() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) pivot_down() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) PivotSelfEnergy (class in sisl_toolbox.btd) plane() (sisl.Lattice method) Plot (class in sisl.viz) plot (sisl.Geometry attribute) (sisl.Grid attribute) (sisl.io.bigdft.asciiSileBigDFT attribute) (sisl.io.cubeSile attribute) (sisl.io.fhiaims.inSileFHIaims attribute) (sisl.io.gulp.gotSileGULP attribute) (sisl.io.openmx.mdSileOpenMX attribute) (sisl.io.openmx.omxSileOpenMX attribute) (sisl.io.orca.txtSileORCA attribute) (sisl.io.pdbSile attribute) (sisl.io.scaleup.refSileScaleUp attribute) (sisl.io.siesta.aniSileSiesta attribute) (sisl.io.siesta.bandsSileSiesta attribute) (sisl.io.siesta.fdfSileSiesta attribute) (sisl.io.siesta.gridncSileSiesta attribute) (sisl.io.siesta.hsxSileSiesta attribute) (sisl.io.siesta.ncSileSiesta attribute) (sisl.io.siesta.onlysSileSiesta attribute) (sisl.io.siesta.pdosSileSiesta attribute) (sisl.io.siesta.stdoutSileSiesta attribute) (sisl.io.siesta.structSileSiesta attribute) (sisl.io.siesta.tshsSileSiesta attribute) (sisl.io.siesta.tsvncSileSiesta attribute) (sisl.io.siesta.wfsxSileSiesta attribute) (sisl.io.siesta.xvSileSiesta attribute) (sisl.io.tbtrans.deltancSileTBtrans attribute) (sisl.io.tbtrans.phtavncSilePHtrans attribute) (sisl.io.tbtrans.phtncSilePHtrans attribute) (sisl.io.tbtrans.phtprojncSilePHtrans attribute) (sisl.io.tbtrans.phtsencSilePHtrans attribute) (sisl.io.tbtrans.tbtavncSileTBtrans attribute) (sisl.io.tbtrans.tbtncSileTBtrans attribute) (sisl.io.tbtrans.tbtprojncSileTBtrans attribute) (sisl.io.tbtrans.tbtsencSileTBtrans attribute) (sisl.io.vasp.carSileVASP attribute) (sisl.io.vasp.chgSileVASP attribute) (sisl.io.vasp.locpotSileVASP attribute) (sisl.io.wannier90.centresSileWannier90 attribute) (sisl.io.wannier90.tbSileWannier90 attribute) (sisl.io.wannier90.winSileWannier90 attribute) (sisl.io.xsfSile attribute) (sisl.io.xyzSile attribute) (sisl.physics.BandStructure attribute) (sisl.physics.BrillouinZone attribute) (sisl.physics.DensityMatrix attribute) (sisl.physics.densitymatrix._densitymatrix attribute) (sisl.physics.DynamicalMatrix attribute) (sisl.physics.electron.EigenstateElectron attribute) (sisl.physics.EnergyDensityMatrix attribute) (sisl.physics.Hamiltonian attribute) (sisl.physics.MonkhorstPack attribute) (sisl.physics.Overlap attribute) (sisl.physics.SparseOrbitalBZ attribute) (sisl.physics.SparseOrbitalBZSpin attribute) (sisl.SparseAtom attribute) (sisl.SparseCSR attribute) (sisl.SparseOrbital attribute)

plot() (sisl_toolbox.siesta.atom.AtomInput method) plot_actions (sisl.viz.Figure attribute) plot_class_key() (sisl.viz.AtomicMatrixPlot class method) (sisl.viz.BandsPlot class method) (sisl.viz.FatbandsPlot class method) (sisl.viz.GeometryPlot class method) (sisl.viz.GridPlot class method) (sisl.viz.PdosPlot class method) (sisl.viz.Plot class method) (sisl.viz.SitesPlot class method) (sisl.viz.WavefunctionPlot class method) point (sisl.geom.PointNeighborList attribute) PointNeighborList (class in sisl.geom) PointsNeighborList (class in sisl.geom) POLARIZED (sisl.physics.Spin attribute) pop() (sisl.oplist method) (sisl.utils.PropertyDict method) popitem() (sisl.utils.PropertyDict method) prepend() (in module sisl) (sisl.Atoms method) (sisl.Geometry method) (sisl.Lattice method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseOrbital method) print() (sisl.io.siesta.fdfSileSiesta static method) projections() (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) PropertyDict (class in sisl.utils) psi() (sisl.AtomicOrbital method) (sisl.GTOrbital method) (sisl.HydrogenicOrbital method) (sisl.Orbital method) (sisl.SphericalOrbital method) (sisl.STOrbital method) psi_spher() (sisl.AtomicOrbital method) (sisl.GTOrbital method) (sisl.HydrogenicOrbital method) (sisl.SphericalOrbital method) (sisl.STOrbital method) ptr (sisl.SparseCSR attribute) PulayMixer (class in sisl.mixing) pyamg() (sisl.Grid.to method) pyamg_boundary_condition() (sisl.Grid method) pyamg_fix() (sisl.Grid method) pyamg_index() (sisl.Grid method) pyamg_source() (sisl.Grid class method) pymatgen() (sisl.Geometry.new method) (sisl.Geometry.to method)

Q

q (in module sisl.constant) q0 (sisl.AtomicOrbital property) (sisl.Atoms property) (sisl.Geometry property) (sisl.GTOrbital property) (sisl.HydrogenicOrbital property) (sisl.Orbital property) (sisl.SphericalOrbital property) (sisl.STOrbital property)

Quaternion (class in sisl)

R

R (sisl.AtomicOrbital property) (sisl.geom.NeighborFinder attribute) (sisl.GTOrbital property) (sisl.HydrogenicOrbital property) (sisl.Orbital property) (sisl.SphericalOrbital property) (sisl.STOrbital property) radial() (sisl.AtomicOrbital method) (sisl.GTOrbital method) (sisl.HydrogenicOrbital method) (sisl.SphericalOrbital method) (sisl.STOrbital method) radial_vector (sisl.shape.Ellipsoid property) (sisl.shape.EllipticalCylinder property) (sisl.shape.Sphere property) radian (sisl.Quaternion property) radius (sisl.shape.Ellipsoid property) (sisl.shape.EllipticalCylinder property) (sisl.shape.Sphere property) radius() (sisl.Atom method) (sisl.PeriodicTable method) rcell (sisl.Geometry property) (sisl.Grid property) (sisl.Lattice property) (sisl.physics.BandStructure property) (sisl.physics.BrillouinZone property) (sisl.physics.MonkhorstPack property) read() (sisl.Geometry static method) (sisl.Grid static method) (sisl.io.BaseSile method) (sisl.io.bigdft.asciiSileBigDFT method) (sisl.io.bigdft.SileBigDFT method) (sisl.io.bigdft.SileBinBigDFT method) (sisl.io.cubeSile method) (sisl.io.dftb.hamrealSileDFTB method) (sisl.io.dftb.overrealSileDFTB method) (sisl.io.dftb.SileBinDFTB method) (sisl.io.dftb.SileDFTB method) (sisl.io.fhiaims.inSileFHIaims method) (sisl.io.fhiaims.SileBinFHIaims method) (sisl.io.fhiaims.SileFHIaims method) (sisl.io.gulp.fcSileGULP method) (sisl.io.gulp.gotSileGULP method) (sisl.io.gulp.SileBinGULP method) (sisl.io.gulp.SileGULP method) (sisl.io.moldenSile method) (sisl.io.openmx.mdSileOpenMX method) (sisl.io.openmx.omxSileOpenMX method) (sisl.io.openmx.SileBinOpenMX method) (sisl.io.openmx.SileCDFOpenMX method) (sisl.io.openmx.SileOpenMX method) (sisl.io.orca.SileBinORCA method) (sisl.io.orca.SileORCA method) (sisl.io.orca.stdoutSileORCA method) (sisl.io.orca.txtSileORCA method) (sisl.io.pdbSile method) (sisl.io.scaleup.orboccSileScaleUp method) (sisl.io.scaleup.refSileScaleUp method) (sisl.io.scaleup.rhamSileScaleUp method) (sisl.io.scaleup.SileBinScaleUp method) (sisl.io.scaleup.SileScaleUp method) (sisl.io.siesta.aniSileSiesta method) (sisl.io.siesta.bandsSileSiesta method) (sisl.io.siesta.dmSileSiesta method) (sisl.io.siesta.eigSileSiesta method) (sisl.io.siesta.faSileSiesta method) (sisl.io.siesta.fcSileSiesta method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.gridncSileSiesta method) (sisl.io.siesta.gridSileSiesta method) (sisl.io.siesta.hsxSileSiesta method) (sisl.io.siesta.ionncSileSiesta method) (sisl.io.siesta.ionxmlSileSiesta method) (sisl.io.siesta.kpSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.onlysSileSiesta method) (sisl.io.siesta.orbindxSileSiesta method) (sisl.io.siesta.pdosSileSiesta method) (sisl.io.siesta.rkpSileSiesta method) (sisl.io.siesta.SileBinSiesta method) (sisl.io.siesta.SileCDFSiesta method) (sisl.io.siesta.SileSiesta method) (sisl.io.siesta.stdoutSileSiesta method) (sisl.io.siesta.structSileSiesta method) (sisl.io.siesta.timesSileSiesta method) (sisl.io.siesta.tsdeSileSiesta method) (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.siesta.tshsSileSiesta method) (sisl.io.siesta.tsvncSileSiesta method) (sisl.io.siesta.wfsxSileSiesta method) (sisl.io.siesta.xvSileSiesta method) (sisl.io.Sile method) (sisl.io.SileBin method) (sisl.io.SileCDF method) (sisl.io.tableSile method) (sisl.io.tbtrans.deltancSileTBtrans method) (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.SileBinTBtrans method) (sisl.io.tbtrans.SileCDFTBtrans method) (sisl.io.tbtrans.SileTBtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtgfSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) (sisl.io.vasp.carSileVASP method) (sisl.io.vasp.chgSileVASP method) (sisl.io.vasp.doscarSileVASP method) (sisl.io.vasp.eigenvalSileVASP method) (sisl.io.vasp.locpotSileVASP method) (sisl.io.vasp.outcarSileVASP method) (sisl.io.vasp.SileBinVASP method) (sisl.io.vasp.SileVASP method) (sisl.io.wannier90.centresSileWannier90 method) (sisl.io.wannier90.hrSileWannier90 method) (sisl.io.wannier90.SileBinWannier90 method) (sisl.io.wannier90.SileWannier90 method) (sisl.io.wannier90.tbSileWannier90 method) (sisl.io.wannier90.winSileWannier90 method) (sisl.io.xsfSile method) (sisl.io.xyzSile method) (sisl.Lattice static method) (sisl.physics.DensityMatrix static method) (sisl.physics.DynamicalMatrix static method) (sisl.physics.EnergyDensityMatrix static method) (sisl.physics.Hamiltonian static method) (sisl.physics.Overlap static method) read_basis() (sisl.io.cubeSile method) (sisl.io.openmx.mdSileOpenMX method) (sisl.io.openmx.omxSileOpenMX method) (sisl.io.scaleup.orboccSileScaleUp method) (sisl.io.siesta.aniSileSiesta method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.hsxSileSiesta method) (sisl.io.siesta.ionncSileSiesta method) (sisl.io.siesta.ionxmlSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.orbindxSileSiesta method) (sisl.io.siesta.stdoutSileSiesta method) (sisl.io.siesta.wfsxSileSiesta method) (sisl.io.xsfSile method) (sisl.io.xyzSile method) read_brillouinzone() (sisl.io.siesta.kpSileSiesta method) (sisl.io.siesta.rkpSileSiesta method) (sisl.io.siesta.wfsxSileSiesta method) read_charge() (sisl.io.orca.stdoutSileORCA method) (sisl.io.siesta.stdoutSileSiesta method) read_data() (sisl.io.siesta.bandsSileSiesta method) (sisl.io.siesta.eigSileSiesta method) (sisl.io.siesta.faSileSiesta method) (sisl.io.siesta.kpSileSiesta method) (sisl.io.siesta.pdosSileSiesta method) (sisl.io.siesta.rkpSileSiesta method) (sisl.io.siesta.stdoutSileSiesta method) (sisl.io.siesta.timesSileSiesta method) (sisl.io.siesta.xvSileSiesta method) (sisl.io.tableSile method) (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.vasp.doscarSileVASP method) (sisl.io.vasp.eigenvalSileVASP method) read_delta() (sisl.io.tbtrans.deltancSileTBtrans method) read_density_matrix() (sisl.io.siesta.dmSileSiesta method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.tsdeSileSiesta method) read_dynamical_matrix() (sisl.io.gulp.gotSileGULP method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.ncSileSiesta method) read_eigenstate() (sisl.io.siesta.wfsxSileSiesta method) read_electrons() (sisl.io.orca.stdoutSileORCA method) (sisl.io.orca.txtSileORCA method) read_energy() (sisl.io.orca.stdoutSileORCA method) (sisl.io.orca.txtSileORCA method) (sisl.io.siesta.stdoutSileSiesta method) (sisl.io.vasp.outcarSileVASP method) read_energy_density_matrix() (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.tsdeSileSiesta method) read_fermi_level() (sisl.io.siesta.bandsSileSiesta method) (sisl.io.siesta.eigSileSiesta method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.hsxSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.onlysSileSiesta method) (sisl.io.siesta.pdosSileSiesta method) (sisl.io.siesta.tsdeSileSiesta method) (sisl.io.siesta.tshsSileSiesta method) (sisl.io.vasp.doscarSileVASP method) read_force() (sisl.io.siesta.faSileSiesta method) (sisl.io.siesta.fcSileSiesta method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.stdoutSileSiesta method) read_force_constant() (sisl.io.gulp.fcSileGULP method) (sisl.io.siesta.fcSileSiesta method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.ncSileSiesta method) read_geometry() (sisl.io.bigdft.asciiSileBigDFT method) (sisl.io.cubeSile method) (sisl.io.fhiaims.inSileFHIaims method) (sisl.io.gulp.gotSileGULP method) (sisl.io.openmx.mdSileOpenMX method) (sisl.io.openmx.omxSileOpenMX method) (sisl.io.orca.txtSileORCA method) (sisl.io.pdbSile method) (sisl.io.scaleup.refSileScaleUp method) (sisl.io.siesta.aniSileSiesta method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.hsxSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.onlysSileSiesta method) (sisl.io.siesta.pdosSileSiesta method) (sisl.io.siesta.stdoutSileSiesta method) (sisl.io.siesta.structSileSiesta method) (sisl.io.siesta.tshsSileSiesta method) (sisl.io.siesta.xvSileSiesta method) (sisl.io.tbtrans.deltancSileTBtrans method) (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) (sisl.io.vasp.carSileVASP method) (sisl.io.vasp.chgSileVASP method) (sisl.io.vasp.locpotSileVASP method) (sisl.io.wannier90.centresSileWannier90 method) (sisl.io.wannier90.tbSileWannier90 method) (sisl.io.wannier90.winSileWannier90 method) (sisl.io.xsfSile method) (sisl.io.xyzSile method)

read_grid() (sisl.io.cubeSile method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.gridncSileSiesta method) (sisl.io.siesta.gridSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.tsvncSileSiesta method) (sisl.io.vasp.chgSileVASP method) (sisl.io.vasp.locpotSileVASP method) read_grid_size() (sisl.io.siesta.gridSileSiesta method) read_gtensor() (sisl.io.orca.txtSileORCA method) read_hamiltonian() (sisl.io.dftb.hamrealSileDFTB method) (sisl.io.scaleup.rhamSileScaleUp method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.hsxSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.siesta.tshsSileSiesta method) (sisl.io.tbtrans.tbtgfSileTBtrans method) (sisl.io.wannier90.hrSileWannier90 method) (sisl.io.wannier90.tbSileWannier90 method) (sisl.io.wannier90.winSileWannier90 method) read_header() (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.tbtrans.tbtgfSileTBtrans method) read_hessian() (sisl.io.gulp.fcSileGULP method) (sisl.io.siesta.fcSileSiesta method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.ncSileSiesta method) read_hyperfine_coupling() (sisl.io.orca.txtSileORCA method) read_info() (sisl.io.siesta.wfsxSileSiesta method) read_lattice() (sisl.io.cubeSile method) (sisl.io.fhiaims.inSileFHIaims method) (sisl.io.gulp.gotSileGULP method) (sisl.io.openmx.mdSileOpenMX method) (sisl.io.openmx.omxSileOpenMX method) (sisl.io.pdbSile method) (sisl.io.scaleup.refSileScaleUp method) (sisl.io.siesta.aniSileSiesta method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.gridncSileSiesta method) (sisl.io.siesta.gridSileSiesta method) (sisl.io.siesta.hsxSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.onlysSileSiesta method) (sisl.io.siesta.structSileSiesta method) (sisl.io.siesta.tshsSileSiesta method) (sisl.io.siesta.tsvncSileSiesta method) (sisl.io.siesta.xvSileSiesta method) (sisl.io.tbtrans.deltancSileTBtrans method) (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) (sisl.io.vasp.carSileVASP method) (sisl.io.vasp.chgSileVASP method) (sisl.io.vasp.locpotSileVASP method) (sisl.io.wannier90.tbSileWannier90 method) (sisl.io.wannier90.winSileWannier90 method) (sisl.io.xsfSile method) (sisl.io.xyzSile method) read_lattice_nsc() (sisl.io.gulp.gotSileGULP method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.orbindxSileSiesta method) read_moment() (sisl.io.fhiaims.inSileFHIaims method) (sisl.io.siesta.stdoutSileSiesta method) read_orbital_energies() (sisl.io.orca.stdoutSileORCA method) read_overlap() (sisl.io.dftb.hamrealSileDFTB method) (sisl.io.dftb.overrealSileDFTB method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.hsxSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.onlysSileSiesta method) (sisl.io.siesta.tshsSileSiesta method) read_scf() (sisl.io.siesta.stdoutSileSiesta method) read_self_energy() (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.tbtrans.tbtgfSileTBtrans method) read_sizes() (sisl.io.siesta.wfsxSileSiesta method) read_stress() (sisl.io.siesta.stdoutSileSiesta method) read_trajectory() (sisl.io.vasp.outcarSileVASP method) read_velocity() (sisl.io.fhiaims.inSileFHIaims method) (sisl.io.siesta.xvSileSiesta method) real (sisl.BoundaryCondition attribute) (sisl.constant.PhysicalConstant attribute) real_space_coupling() (sisl.physics.RealSpaceSE method) (sisl.physics.RealSpaceSI method) real_space_parent() (sisl.physics.RealSpaceSE method) (sisl.physics.RealSpaceSI method) RealSpaceSE (class in sisl.physics) RealSpaceSI (class in sisl.physics) recursive_update_inputs() (sisl.viz.AtomicMatrixPlot method) (sisl.viz.BandsPlot method) (sisl.viz.FatbandsPlot method) (sisl.viz.GeometryPlot method) (sisl.viz.GridPlot method) (sisl.viz.PdosPlot method) (sisl.viz.Plot method) (sisl.viz.SitesPlot method) (sisl.viz.WavefunctionPlot method) RecursiveSI (class in sisl.physics) reduce() (sisl.Atoms method) (sisl.Geometry method) reflection() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) refSileScaleUp (class in sisl.io.scaleup) remove() (in module sisl) (sisl.Atom method) (sisl.Atoms method) (sisl.Geometry method) (sisl.Grid method) (sisl.oplist method) (sisl.physics.Coefficient method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.electron.CoefficientElectron method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvalueElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.phonon.CoefficientPhonon method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvaluePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.physics.State method) (sisl.physics.StateC method) (sisl.SparseAtom method) (sisl.SparseCSR method) (sisl.SparseOrbital method) remove_groups() (sisl.viz.FatbandsPlot method) (sisl.viz.PdosPlot method) remove_orbital() (sisl.Geometry method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseOrbital method) remove_part() (sisl.Grid method) reorder() (sisl.Atoms method) (sisl.Geometry method) repeat() (in module sisl) (sisl.Atoms method) (sisl.Geometry method) (sisl.Lattice method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseOrbital method) replace() (sisl.Atoms method) (sisl.Geometry method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.MonkhorstPack method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseOrbital method) replace_atom() (sisl.Atoms method) reset() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseOrbital method) (sisl_toolbox.btd.DeviceGreen method) reverse() (sisl.Atoms method) (sisl.Geometry method) (sisl.oplist method) rhamSileScaleUp (class in sisl.io.scaleup) Rij() (sisl.Geometry method) rij() (sisl.Geometry method) Rij() (sisl.physics.DensityMatrix method) rij() (sisl.physics.DensityMatrix method) Rij() (sisl.physics.densitymatrix._densitymatrix method) rij() (sisl.physics.densitymatrix._densitymatrix method) Rij() (sisl.physics.DynamicalMatrix method) rij() (sisl.physics.DynamicalMatrix method) Rij() (sisl.physics.EnergyDensityMatrix method) rij() (sisl.physics.EnergyDensityMatrix method) Rij() (sisl.physics.Hamiltonian method) rij() (sisl.physics.Hamiltonian method) Rij() (sisl.physics.Overlap method) rij() (sisl.physics.Overlap method) Rij() (sisl.physics.SparseOrbitalBZ method) rij() (sisl.physics.SparseOrbitalBZ method) Rij() (sisl.physics.SparseOrbitalBZSpin method) rij() (sisl.physics.SparseOrbitalBZSpin method) Rij() (sisl.SparseAtom method) rij() (sisl.SparseAtom method) Rij() (sisl.SparseOrbital method) rij() (sisl.SparseOrbital method) rkpSileSiesta (class in sisl.io.siesta) rocksalt() (in module sisl.geom) rocksalt_slab() (in module sisl.geom) rotate() (in module sisl) (sisl.Geometry method) (sisl.Lattice method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.State method) (sisl.physics.StateC method) (sisl.Quaternion method) rotate_miller() (sisl.Geometry method)

S

S (sisl.physics.DensityMatrix property) (sisl.physics.densitymatrix._densitymatrix property) (sisl.physics.DynamicalMatrix property) (sisl.physics.EnergyDensityMatrix property) (sisl.physics.Hamiltonian property) (sisl.physics.Overlap property) (sisl.physics.SparseOrbitalBZ property) (sisl.physics.SparseOrbitalBZSpin property) sc (sisl.Geometry property) (sisl.Grid property) sc() (in module sisl.geom) sc2uc() (sisl.Geometry method) sc_index() (sisl.Geometry method) (sisl.Grid method) (sisl.Lattice method) sc_off (sisl.Geometry property) (sisl.Grid property) (sisl.Lattice property) scale() (in module sisl) (sisl.Atom method) (sisl.AtomicOrbital method) (sisl.Atoms method) (sisl.Geometry method) (sisl.GTOrbital method) (sisl.HydrogenicOrbital method) (sisl.Lattice method) (sisl.Orbital method) (sisl.shape.Cube method) (sisl.shape.Cuboid method) (sisl.shape.Ellipsoid method) (sisl.shape.EllipticalCylinder method) (sisl.shape.NullShape method) (sisl.shape.Shape method) (sisl.shape.Sphere method) (sisl.SphericalOrbital method) (sisl.STOrbital method) scale_columns() (sisl.SparseCSR method) scattering_matrix() (sisl_toolbox.btd.DeviceGreen method) scattering_state() (sisl_toolbox.btd.DeviceGreen method) se2broadening() (sisl.physics.RealSpaceSE static method) (sisl.physics.RealSpaceSI static method) (sisl.physics.RecursiveSI static method) (sisl.physics.SelfEnergy static method) (sisl.physics.SemiInfinite static method) (sisl.physics.WideBandSE static method) (sisl_toolbox.btd.DownfoldSelfEnergy static method) (sisl_toolbox.btd.PivotSelfEnergy static method) self_energy() (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtgfSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) (sisl.physics.RealSpaceSE method) (sisl.physics.RealSpaceSI method) (sisl.physics.RecursiveSI method) (sisl.physics.SelfEnergy method) (sisl.physics.SemiInfinite method) (sisl.physics.WideBandSE method) (sisl_toolbox.btd.DownfoldSelfEnergy method) (sisl_toolbox.btd.PivotSelfEnergy method) self_energy_average() (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) self_energy_lr() (sisl.physics.RecursiveSI method) SelfEnergy (class in sisl.physics) SemiInfinite (class in sisl.physics) set() (sisl.io.siesta.fdfSileSiesta method) set_axes_equal() (sisl.viz.Figure method) set_axis() (sisl.viz.Figure method) set_bc() (sisl.Grid method) set_boundary() (sisl.Grid method) set_boundary_condition() (sisl.Grid method) (sisl.Lattice method) set_dyn_key() (sisl.io.gulp.gotSileGULP method) set_dynamical_matrix_key() (sisl.io.gulp.gotSileGULP method) set_geometry() (sisl.Grid method) set_geometry_key() (sisl.io.gulp.gotSileGULP method) set_grid() (sisl.Grid method) set_history() (sisl.mixing.AdaptiveDIISMixer method) (sisl.mixing.AdaptivePulayMixer method) (sisl.mixing.AndersonMixer method) (sisl.mixing.BaseHistoryWeightMixer method) (sisl.mixing.DIISMixer method) (sisl.mixing.LinearMixer method) (sisl.mixing.PulayMixer method) set_key() (sisl.io.gulp.gotSileGULP method) set_lattice() (sisl.Geometry method) (sisl.Grid method) set_lattice_key() (sisl.io.gulp.gotSileGULP method) set_nsc() (sisl.Geometry method) (sisl.Grid method) (sisl.Lattice method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseOrbital method) set_options() (sisl.physics.RealSpaceSE method) (sisl.physics.RealSpaceSI method) set_parent() (sisl.physics.BandStructure method) (sisl.physics.BrillouinZone method) (sisl.physics.MonkhorstPack method) set_radial() (sisl.AtomicOrbital method) (sisl.HydrogenicOrbital method) (sisl.SphericalOrbital method) set_supercell() (sisl.Geometry method) (sisl.Grid method) set_supercell_key() (sisl.io.gulp.gotSileGULP method) set_weight() (sisl.mixing.AdaptiveDIISMixer method) (sisl.mixing.AdaptivePulayMixer method) (sisl.mixing.AndersonMixer method) (sisl.mixing.BaseHistoryWeightMixer method) (sisl.mixing.BaseWeightMixer method) (sisl.mixing.DIISMixer method) (sisl.mixing.LinearMixer method) (sisl.mixing.PulayMixer method) setdefault() (sisl.utils.PropertyDict method) setup() (sisl.geom.NeighborFinder method) (sisl.physics.RealSpaceSE method) (sisl.physics.RealSpaceSI method) (sisl.viz.AtomicMatrixPlot method) (sisl.viz.BandsPlot method) (sisl.viz.FatbandsPlot method) (sisl.viz.GeometryPlot method) (sisl.viz.GridPlot method) (sisl.viz.PdosPlot method) (sisl.viz.Plot method) (sisl.viz.SitesPlot method) (sisl.viz.WavefunctionPlot method) Shape (class in sisl.shape) shape (sisl.Grid property) (sisl.physics.Coefficient property) (sisl.physics.DensityMatrix property) (sisl.physics.densitymatrix._densitymatrix property) (sisl.physics.DynamicalMatrix property) (sisl.physics.electron.CoefficientElectron property) (sisl.physics.electron.EigenstateElectron property) (sisl.physics.electron.EigenvalueElectron property) (sisl.physics.electron.EigenvectorElectron property) (sisl.physics.electron.StateCElectron property) (sisl.physics.electron.StateElectron property) (sisl.physics.EnergyDensityMatrix property) (sisl.physics.Hamiltonian property) (sisl.physics.Overlap property) (sisl.physics.phonon.CoefficientPhonon property) (sisl.physics.phonon.EigenmodePhonon property) (sisl.physics.phonon.EigenvaluePhonon property) (sisl.physics.phonon.EigenvectorPhonon property) (sisl.physics.phonon.ModeCPhonon property) (sisl.physics.phonon.ModePhonon property) (sisl.physics.SparseOrbitalBZ property) (sisl.physics.SparseOrbitalBZSpin property) (sisl.physics.State property) (sisl.physics.StateC property) (sisl.SparseAtom property) (sisl.SparseCSR property) (sisl.SparseOrbital property) shc() (in module sisl.physics.electron) shift() (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) shot_noise (sisl.io.tbtrans.phtavncSilePHtrans attribute) (sisl.io.tbtrans.phtncSilePHtrans attribute) (sisl.io.tbtrans.phtprojncSilePHtrans attribute) (sisl.io.tbtrans.tbtavncSileTBtrans attribute) (sisl.io.tbtrans.tbtprojncSileTBtrans attribute) shot_noise() (sisl.io.tbtrans.tbtncSileTBtrans method) show() (sisl.viz.Figure method) Sile (class in sisl.io) Sile() (sisl.Geometry.new method) (sisl.Geometry.to method) (sisl.Lattice.new method) (sisl.Lattice.to method) SileBigDFT (class in sisl.io.bigdft) SileBin (class in sisl.io) SileBinBigDFT (class in sisl.io.bigdft) SileBinDFTB (class in sisl.io.dftb) SileBinFHIaims (class in sisl.io.fhiaims) SileBinGULP (class in sisl.io.gulp) SileBinOpenMX (class in sisl.io.openmx) SileBinORCA (class in sisl.io.orca) SileBinScaleUp (class in sisl.io.scaleup) SileBinSiesta (class in sisl.io.siesta) SileBinTBtrans (class in sisl.io.tbtrans) SileBinVASP (class in sisl.io.vasp) SileBinWannier90 (class in sisl.io.wannier90) SileCDF (class in sisl.io) SileCDFOpenMX (class in sisl.io.openmx) SileCDFSiesta (class in sisl.io.siesta) SileCDFTBtrans (class in sisl.io.tbtrans) SileDFTB (class in sisl.io.dftb) SileError SileFHIaims (class in sisl.io.fhiaims) SileGULP (class in sisl.io.gulp) SileInfo SileLike (in module sisl.typing) SileOpenMX (class in sisl.io.openmx) SileORCA (class in sisl.io.orca) SileScaleUp (class in sisl.io.scaleup) SileSiesta (class in sisl.io.siesta) SileTBtrans (class in sisl.io.tbtrans) SileVASP (class in sisl.io.vasp) SileWannier90 (class in sisl.io.wannier90) SileWarning SimpleIndex (in module sisl.typing) sisl module sisl.constant module sisl.geom module sisl.io module sisl.io.bigdft module sisl.io.dftb module sisl.io.fhiaims module sisl.io.gulp module sisl.io.openmx module sisl.io.orca module sisl.io.scaleup module sisl.io.siesta module sisl.io.tbtrans module sisl.io.vasp module sisl.io.wannier90 module sisl.mixing module sisl.physics module sisl.physics.electron module sisl.physics.phonon module sisl.shape module sisl.typing module sisl.unit module

sisl.unit.siesta module sisl.utils module sisl.viz module sisl_toolbox module sisl_toolbox.btd module sisl_toolbox.siesta.atom module sisl_toolbox.transiesta.poisson module sites() (sisl.physics.BandStructure.plot method) (sisl.physics.BrillouinZone.plot method) (sisl.physics.MonkhorstPack.plot method) SitesPlot (class in sisl.viz) size (sisl.Grid property) (sisl.physics.Spin property) Sk() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.electron._electron_State method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl_toolbox.btd.DeviceGreen method) smooth() (sisl.Grid method) solve_lagrange() (sisl.mixing.AdaptiveDIISMixer method) (sisl.mixing.AdaptivePulayMixer method) (sisl.mixing.DIISMixer method) (sisl.mixing.PulayMixer method) solve_poisson() (in module sisl_toolbox.transiesta.poisson) sort() (in module sisl) (sisl.Geometry method) (sisl.oplist method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.StateC method) spalign() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseOrbital method) sparse-matrix sparse_atom_to_vector() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) sparse_orbital_to_atom() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) sparse_orbital_to_scalar() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) sparse_orbital_to_vector() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) SparseAtom (class in sisl) SparseCSR (class in sisl) SparseMatrix (in module sisl.typing) SparseMatrixExt (in module sisl.typing) SparseOrbital (class in sisl) SparseOrbitalBZ (class in sisl.physics) SparseOrbitalBZSpin (class in sisl.physics) sparserij() (sisl.Geometry method) sparsity_union() (sisl.SparseCSR class method) specie (sisl.Atoms property) specie_index() (sisl.Atoms method) species (sisl.Atoms property) species_index() (sisl.Atoms method) spectral() (sisl_toolbox.btd.DeviceGreen method) spher() (sisl.AtomicOrbital method) (sisl.GTOrbital method) (sisl.HydrogenicOrbital method) (sisl.SphericalOrbital method) (sisl.STOrbital method) Sphere (class in sisl.shape) Sphere() (sisl.Atom.to method) (sisl.shape.Cube.to method) (sisl.shape.Cuboid.to method) (sisl.shape.Ellipsoid.to method) (sisl.shape.EllipticalCylinder.to method) (sisl.shape.NullShape.to method) (sisl.shape.Sphere.to method) spherical-orbital SphericalOrbital (class in sisl) Spin (class in sisl.physics) spin (sisl.physics.DensityMatrix property) (sisl.physics.densitymatrix._densitymatrix property) (sisl.physics.EnergyDensityMatrix property) (sisl.physics.Hamiltonian property) (sisl.physics.SparseOrbitalBZSpin property) spin_align() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.EnergyDensityMatrix method) spin_berry_curvature() (in module sisl.physics) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.StateCElectron method) spin_contamination() (in module sisl.physics.electron) spin_moment() (in module sisl.physics.electron) (sisl.physics.electron._electron_State method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) spin_rotate() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.EnergyDensityMatrix method) spinor (sisl.physics.Spin property) SPINORBIT (sisl.physics.Spin attribute) split_DOS() (sisl.viz.PdosPlot method) split_groups() (sisl.viz.FatbandsPlot method) (sisl.viz.PdosPlot method) split_indices (sisl.geom.AtomNeighborList property) (sisl.geom.FullNeighborList property) (sisl.geom.PartialNeighborList property) (sisl.geom.PointNeighborList property) (sisl.geom.PointsNeighborList property) (sisl.geom.UniqueNeighborList property) split_orbs() (sisl.viz.FatbandsPlot method) (sisl.viz.PdosPlot method) spsame() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseCSR method) (sisl.SparseOrbital method) State (class in sisl.physics) state (sisl.physics.electron.EigenstateElectron attribute) (sisl.physics.electron.EigenvectorElectron attribute) (sisl.physics.electron.StateCElectron attribute) (sisl.physics.electron.StateElectron attribute) (sisl.physics.phonon.EigenmodePhonon attribute) (sisl.physics.phonon.EigenvectorPhonon attribute) (sisl.physics.phonon.ModeCPhonon attribute) (sisl.physics.phonon.ModePhonon attribute) (sisl.physics.State attribute) (sisl.physics.StateC attribute) StateC (class in sisl.physics) StateCElectron (class in sisl.physics.electron) StateElectron (class in sisl.physics.electron) stdoutSileORCA (class in sisl.io.orca) stdoutSileSiesta (class in sisl.io.siesta) step_function() (in module sisl.physics) StepMixer (class in sisl.mixing) STOrbital (class in sisl) str() (sisl.Geometry.to method) (sisl.Grid.to method) (sisl.Lattice.to method) str_spec() (in module sisl.utils) strerror (sisl.io.SileError attribute) strmap() (in module sisl.utils) strseq() (in module sisl.utils) structSileSiesta (class in sisl.io.siesta) sub() (in module sisl) (sisl.Atom method) (sisl.Atoms method) (sisl.Geometry method) (sisl.Grid method) (sisl.physics.Coefficient method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.electron.CoefficientElectron method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvalueElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.phonon.CoefficientPhonon method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvaluePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.physics.State method) (sisl.physics.StateC method) (sisl.SparseAtom method) (sisl.SparseCSR method) (sisl.SparseOrbital method) sub_orbital() (sisl.Geometry method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseOrbital method) sub_part() (sisl.Grid method) subplots() (in module sisl.viz) sum() (sisl.Grid method) (sisl.physics.BandStructure.apply method) (sisl.physics.BrillouinZone.apply method) (sisl.physics.MonkhorstPack.apply method) supercell swap() (in module sisl) (sisl.Atoms method) (sisl.Geometry method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseOrbital method) swap_atom() (sisl.Atoms method) swapaxes() (in module sisl) (sisl.Geometry method) (sisl.Grid method) (sisl.Lattice method) symbol (sisl.Atom property)

T

tableSile (class in sisl.io) tag (sisl.Atom property) (sisl.AtomicOrbital property) (sisl.GTOrbital property) (sisl.HydrogenicOrbital property) (sisl.Orbital property) (sisl.SphericalOrbital property) (sisl.STOrbital property) tbSileWannier90 (class in sisl.io.wannier90) tbtavncSileTBtrans (class in sisl.io.tbtrans) tbtgfSileTBtrans (class in sisl.io.tbtrans) tbtncSileTBtrans (class in sisl.io.tbtrans) tbtprojncSileTBtrans (class in sisl.io.tbtrans) tbtsencSileTBtrans (class in sisl.io.tbtrans) tile() (in module sisl) (sisl.Atoms method) (sisl.Geometry method) (sisl.Grid method) (sisl.Lattice method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.physics.State method) (sisl.physics.StateC method) (sisl.SparseAtom method) (sisl.SparseOrbital method) timesSileSiesta (class in sisl.io.siesta) to (sisl.Atom attribute) (sisl.Geometry attribute) (sisl.Grid attribute) (sisl.Lattice attribute) (sisl.shape.Cube attribute) (sisl.shape.Cuboid attribute) (sisl.shape.Ellipsoid attribute) (sisl.shape.EllipticalCylinder attribute) (sisl.shape.NullShape attribute) (sisl.shape.Shape attribute) (sisl.shape.Sphere attribute) to() (sisl.viz.Figure method) to_bytes() (sisl.BoundaryCondition method) to_full() (sisl.geom.UniqueNeighborList method) to_unique() (sisl.geom.FullNeighborList method) toarray() (sisl.SparseCSR method) toAtomicOrbital() (sisl.SphericalOrbital method) tocartesian() (sisl.physics.BandStructure method) (sisl.physics.BrillouinZone method) (sisl.physics.MonkhorstPack method) tocell() (sisl.Lattice class method) tocsr() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseCSR method) (sisl.SparseOrbital method) toCuboid() (sisl.Lattice method) (sisl.shape.Cube method) (sisl.shape.Cuboid method) (sisl.shape.Ellipsoid method) (sisl.shape.EllipticalCylinder method) (sisl.shape.NullShape method) (sisl.shape.Shape method) (sisl.shape.Sphere method) todense() (sisl.SparseCSR method) toEllipsoid() (sisl.shape.Cube method) (sisl.shape.Cuboid method) (sisl.shape.Ellipsoid method) (sisl.shape.EllipticalCylinder method) (sisl.shape.NullShape method) (sisl.shape.Shape method) (sisl.shape.Sphere method) toGrid() (sisl.AtomicOrbital method) (sisl.GTOrbital method) (sisl.HydrogenicOrbital method) (sisl.Orbital method) (sisl.SphericalOrbital method) (sisl.STOrbital method) tolinear() (sisl.physics.BandStructure method) topyamg() (sisl.Grid method) toreduced() (sisl.physics.BandStructure method) (sisl.physics.BrillouinZone method) (sisl.physics.MonkhorstPack method) toSparseAtom() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseOrbital method)

toSphere() (sisl.Atom method) (sisl.AtomicOrbital method) (sisl.GTOrbital method) (sisl.HydrogenicOrbital method) (sisl.Orbital method) (sisl.shape.Cube method) (sisl.shape.Cuboid method) (sisl.shape.Ellipsoid method) (sisl.shape.EllipticalCylinder method) (sisl.shape.NullShape method) (sisl.shape.Shape method) (sisl.shape.Sphere method) (sisl.SphericalOrbital method) (sisl.STOrbital method) total_nbins (sisl.geom.NeighborFinder attribute) transform() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseCSR method) translate() (in module sisl) (sisl.Geometry method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.EigenvectorPhonon method) (sisl.physics.phonon.ModeCPhonon method) (sisl.physics.phonon.ModePhonon method) (sisl.physics.State method) (sisl.physics.StateC method) (sisl.shape.Cube method) (sisl.shape.Cuboid method) (sisl.shape.Ellipsoid method) (sisl.shape.EllipticalCylinder method) (sisl.shape.NullShape method) (sisl.shape.Shape method) (sisl.shape.Sphere method) translate2uc() (sisl.Geometry method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseOrbital method) translate_columns() (sisl.SparseCSR method) transmission() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) transmission_bulk() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) transmission_eig() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) transpose() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseCSR method) (sisl.SparseOrbital method) triangulene() (in module sisl.geom) trs() (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.SparseOrbitalBZSpin method) tsdeSileSiesta (class in sisl.io.siesta) tsgfSileSiesta (class in sisl.io.siesta) tshsSileSiesta (class in sisl.io.siesta) tsvncSileSiesta (class in sisl.io.siesta) txtSileORCA (class in sisl.io.orca) type() (sisl.io.openmx.omxSileOpenMX method) (sisl.io.siesta.fdfSileSiesta method)

U

uc2sc() (sisl.Geometry method) unfold() (sisl.physics.Bloch method) unfold_points() (sisl.physics.Bloch method) UniqueNeighborList (class in sisl.geom) unit (sisl.constant.PhysicalConstant property) unit_convert() (in module sisl.unit) unit_default() (in module sisl.unit) unit_group() (in module sisl.unit) units (in module sisl.unit) UnitsVar (in module sisl.typing) UNKNOWN (sisl.BoundaryCondition attribute) UNPOLARIZED (sisl.physics.Spin attribute) unrepeat() (in module sisl) (sisl.Geometry method) (sisl.Lattice method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseOrbital method) untile() (in module sisl) (sisl.Geometry method) (sisl.Lattice method) (sisl.physics.DensityMatrix method) (sisl.physics.densitymatrix._densitymatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.Overlap method) (sisl.physics.SparseOrbitalBZ method) (sisl.physics.SparseOrbitalBZSpin method) (sisl.SparseAtom method) (sisl.SparseOrbital method)

update() (sisl.utils.PropertyDict method) update_groups() (sisl.viz.FatbandsPlot method) (sisl.viz.PdosPlot method) update_inputs() (sisl.viz.AtomicMatrixPlot method) (sisl.viz.BandsPlot method) (sisl.viz.FatbandsPlot method) (sisl.viz.GeometryPlot method) (sisl.viz.GridPlot method) (sisl.viz.PdosPlot method) (sisl.viz.Plot method) (sisl.viz.SitesPlot method) (sisl.viz.WavefunctionPlot method) update_settings() (sisl.viz.AtomicMatrixPlot method) (sisl.viz.BandsPlot method) (sisl.viz.FatbandsPlot method) (sisl.viz.GeometryPlot method) (sisl.viz.GridPlot method) (sisl.viz.PdosPlot method) (sisl.viz.Plot method) (sisl.viz.SitesPlot method) (sisl.viz.WavefunctionPlot method)

V

values() (sisl.utils.PropertyDict method) vector_current (sisl.io.tbtrans.phtavncSilePHtrans attribute) (sisl.io.tbtrans.phtncSilePHtrans attribute) vector_current() (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) vector_transmission() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) velocity() (in module sisl.physics) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.phonon.EigenmodePhonon method) (sisl.physics.phonon.ModeCPhonon method)

version (sisl.io.siesta.hsxSileSiesta property) (sisl.io.siesta.onlysSileSiesta property) (sisl.io.siesta.tshsSileSiesta property) vertices() (sisl.Lattice method) volume (sisl.Geometry property) (sisl.Grid property) (sisl.Lattice property) (sisl.shape.Cube property) (sisl.shape.Cuboid property) (sisl.shape.Ellipsoid property) (sisl.shape.EllipticalCylinder property) (sisl.shape.NullShape property) (sisl.shape.Sphere property) volume() (sisl.physics.BandStructure method) (sisl.physics.BrillouinZone method) (sisl.physics.MonkhorstPack method) volumef() (sisl.Lattice method)

W

wavefunction() (in module sisl.physics.electron) (sisl.io.siesta.fdfSileSiesta.plot method) (sisl.io.siesta.wfsxSileSiesta.plot method) (sisl.physics.electron._electron_State method) (sisl.physics.electron.EigenstateElectron method) (sisl.physics.electron.EigenstateElectron.plot method) (sisl.physics.electron.EigenvectorElectron method) (sisl.physics.electron.StateCElectron method) (sisl.physics.electron.StateElectron method) (sisl.physics.Hamiltonian.plot method) WavefunctionPlot (class in sisl.viz) weight (sisl.mixing.AdaptiveDIISMixer property) (sisl.mixing.AdaptivePulayMixer property) (sisl.mixing.AndersonMixer property) (sisl.mixing.BaseHistoryWeightMixer property) (sisl.mixing.BaseWeightMixer property) (sisl.mixing.DIISMixer property) (sisl.mixing.LinearMixer property) (sisl.mixing.PulayMixer property) (sisl.physics.BandStructure property) (sisl.physics.BrillouinZone property) (sisl.physics.MonkhorstPack property) wfsxSileSiesta (class in sisl.io.siesta) WideBandSE (class in sisl.physics) winSileWannier90 (class in sisl.io.wannier90) with_traceback() (sisl.io.SileError method) (sisl.io.SileInfo method) (sisl.io.SileWarning method) within() (sisl.Geometry method) (sisl.shape.Cube method) (sisl.shape.Cuboid method) (sisl.shape.Ellipsoid method) (sisl.shape.EllipticalCylinder method) (sisl.shape.NullShape method) (sisl.shape.Shape method) (sisl.shape.Sphere method) within_index() (sisl.shape.Cube method) (sisl.shape.Cuboid method) (sisl.shape.Ellipsoid method) (sisl.shape.EllipticalCylinder method) (sisl.shape.NullShape method) (sisl.shape.Shape method) (sisl.shape.Sphere method) within_inf() (sisl.Geometry method) within_sc() (sisl.Geometry method) wk (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) wkpt (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) write() (in module sisl) (sisl.Geometry method) (sisl.Grid method) (sisl.io.BaseSile method) (sisl.io.bigdft.asciiSileBigDFT method) (sisl.io.bigdft.SileBigDFT method) (sisl.io.bigdft.SileBinBigDFT method) (sisl.io.cubeSile method) (sisl.io.dftb.hamrealSileDFTB method) (sisl.io.dftb.overrealSileDFTB method) (sisl.io.dftb.SileBinDFTB method) (sisl.io.dftb.SileDFTB method) (sisl.io.fhiaims.inSileFHIaims method) (sisl.io.fhiaims.SileBinFHIaims method) (sisl.io.fhiaims.SileFHIaims method) (sisl.io.gulp.fcSileGULP method) (sisl.io.gulp.gotSileGULP method) (sisl.io.gulp.SileBinGULP method) (sisl.io.gulp.SileGULP method) (sisl.io.moldenSile method) (sisl.io.openmx.mdSileOpenMX method) (sisl.io.openmx.omxSileOpenMX method) (sisl.io.openmx.SileBinOpenMX method) (sisl.io.openmx.SileCDFOpenMX method) (sisl.io.openmx.SileOpenMX method) (sisl.io.orca.SileBinORCA method) (sisl.io.orca.SileORCA method) (sisl.io.orca.stdoutSileORCA method) (sisl.io.orca.txtSileORCA method) (sisl.io.pdbSile method) (sisl.io.scaleup.orboccSileScaleUp method) (sisl.io.scaleup.refSileScaleUp method) (sisl.io.scaleup.rhamSileScaleUp method) (sisl.io.scaleup.SileBinScaleUp method) (sisl.io.scaleup.SileScaleUp method) (sisl.io.siesta.aniSileSiesta method) (sisl.io.siesta.bandsSileSiesta method) (sisl.io.siesta.dmSileSiesta method) (sisl.io.siesta.eigSileSiesta method) (sisl.io.siesta.faSileSiesta method) (sisl.io.siesta.fcSileSiesta method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.gridncSileSiesta method) (sisl.io.siesta.gridSileSiesta method) (sisl.io.siesta.hsxSileSiesta method) (sisl.io.siesta.ionncSileSiesta method) (sisl.io.siesta.ionxmlSileSiesta method) (sisl.io.siesta.kpSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.onlysSileSiesta method) (sisl.io.siesta.orbindxSileSiesta method) (sisl.io.siesta.pdosSileSiesta method) (sisl.io.siesta.rkpSileSiesta method) (sisl.io.siesta.SileBinSiesta method) (sisl.io.siesta.SileCDFSiesta method) (sisl.io.siesta.SileSiesta method) (sisl.io.siesta.stdoutSileSiesta method) (sisl.io.siesta.structSileSiesta method) (sisl.io.siesta.timesSileSiesta method) (sisl.io.siesta.tsdeSileSiesta method) (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.siesta.tshsSileSiesta method) (sisl.io.siesta.tsvncSileSiesta method) (sisl.io.siesta.wfsxSileSiesta method) (sisl.io.siesta.xvSileSiesta method) (sisl.io.Sile method) (sisl.io.SileBin method) (sisl.io.SileCDF method) (sisl.io.tableSile method) (sisl.io.tbtrans.deltancSileTBtrans method) (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.phtsencSilePHtrans method) (sisl.io.tbtrans.SileBinTBtrans method) (sisl.io.tbtrans.SileCDFTBtrans method) (sisl.io.tbtrans.SileTBtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtgfSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) (sisl.io.tbtrans.tbtsencSileTBtrans method) (sisl.io.vasp.carSileVASP method) (sisl.io.vasp.chgSileVASP method) (sisl.io.vasp.doscarSileVASP method) (sisl.io.vasp.eigenvalSileVASP method) (sisl.io.vasp.locpotSileVASP method) (sisl.io.vasp.outcarSileVASP method) (sisl.io.vasp.SileBinVASP method) (sisl.io.vasp.SileVASP method) (sisl.io.wannier90.centresSileWannier90 method) (sisl.io.wannier90.hrSileWannier90 method) (sisl.io.wannier90.SileBinWannier90 method) (sisl.io.wannier90.SileWannier90 method) (sisl.io.wannier90.tbSileWannier90 method) (sisl.io.wannier90.winSileWannier90 method) (sisl.io.xsfSile method) (sisl.io.xyzSile method) (sisl.Lattice method) (sisl.physics.BandStructure method) (sisl.physics.BrillouinZone method) (sisl.physics.DensityMatrix method) (sisl.physics.DynamicalMatrix method) (sisl.physics.EnergyDensityMatrix method) (sisl.physics.Hamiltonian method) (sisl.physics.MonkhorstPack method) (sisl.physics.Overlap method)

write_all_electron() (sisl_toolbox.siesta.atom.AtomInput method) write_basis() (sisl.io.siesta.ncSileSiesta method) write_brillouinzone() (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.kpSileSiesta method) (sisl.io.siesta.rkpSileSiesta method) write_data() (sisl.io.siesta.faSileSiesta method) (sisl.io.siesta.kpSileSiesta method) (sisl.io.siesta.rkpSileSiesta method) (sisl.io.tableSile method) write_delta() (sisl.io.tbtrans.deltancSileTBtrans method) write_density_matrices() (sisl.io.siesta.tsdeSileSiesta method) write_density_matrix() (sisl.io.siesta.dmSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.tsdeSileSiesta method) write_dynamical_matrix() (sisl.io.siesta.ncSileSiesta method) write_energy_density_matrix() (sisl.io.siesta.ncSileSiesta method) write_force() (sisl.io.siesta.faSileSiesta method) write_generation() (sisl_toolbox.siesta.atom.AtomInput method) write_geometry() (sisl.io.bigdft.asciiSileBigDFT method) (sisl.io.cubeSile method) (sisl.io.fhiaims.inSileFHIaims method) (sisl.io.moldenSile method) (sisl.io.openmx.mdSileOpenMX method) (sisl.io.pdbSile method) (sisl.io.scaleup.refSileScaleUp method) (sisl.io.siesta.aniSileSiesta method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.structSileSiesta method) (sisl.io.siesta.xvSileSiesta method) (sisl.io.tbtrans.deltancSileTBtrans method) (sisl.io.vasp.carSileVASP method) (sisl.io.vasp.chgSileVASP method) (sisl.io.vasp.locpotSileVASP method) (sisl.io.wannier90.winSileWannier90 method) (sisl.io.xsfSile method) (sisl.io.xyzSile method) write_grid() (sisl.io.cubeSile method) (sisl.io.siesta.gridncSileSiesta method) (sisl.io.siesta.gridSileSiesta method) (sisl.io.siesta.tsvncSileSiesta method) (sisl.io.xsfSile method) write_hamiltonian() (sisl.io.siesta.ncSileSiesta method) (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.siesta.tshsSileSiesta method) (sisl.io.tbtrans.tbtgfSileTBtrans method) write_header() (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.tbtrans.tbtgfSileTBtrans method) (sisl_toolbox.siesta.atom.AtomInput method) write_lattice() (sisl.io.cubeSile method) (sisl.io.fhiaims.inSileFHIaims method) (sisl.io.moldenSile method) (sisl.io.pdbSile method) (sisl.io.siesta.fdfSileSiesta method) (sisl.io.siesta.gridncSileSiesta method) (sisl.io.siesta.tsvncSileSiesta method) (sisl.io.tbtrans.deltancSileTBtrans method) (sisl.io.wannier90.winSileWannier90 method) (sisl.io.xsfSile method) write_overlap() (sisl.io.siesta.ncSileSiesta method) write_self_energy() (sisl.io.siesta.tsgfSileSiesta method) (sisl.io.tbtrans.tbtgfSileTBtrans method) write_tbtav() (sisl.io.tbtrans.phtavncSilePHtrans method) (sisl.io.tbtrans.phtncSilePHtrans method) (sisl.io.tbtrans.phtprojncSilePHtrans method) (sisl.io.tbtrans.tbtavncSileTBtrans method) (sisl.io.tbtrans.tbtncSileTBtrans method) (sisl.io.tbtrans.tbtprojncSileTBtrans method) write_test() (sisl_toolbox.siesta.atom.AtomInput method)

X

X (sisl.physics.Spin attribute) xa (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) xarray() (sisl.physics.BandStructure.apply method) (sisl.physics.BrillouinZone.apply method) (sisl.physics.MonkhorstPack.apply method)

xsfSile (class in sisl.io) xvSileSiesta (class in sisl.io.siesta) xyz (sisl.io.tbtrans.phtavncSilePHtrans property) (sisl.io.tbtrans.phtncSilePHtrans property) (sisl.io.tbtrans.phtprojncSilePHtrans property) (sisl.io.tbtrans.phtsencSilePHtrans property) (sisl.io.tbtrans.tbtavncSileTBtrans property) (sisl.io.tbtrans.tbtncSileTBtrans property) (sisl.io.tbtrans.tbtprojncSileTBtrans property) (sisl.io.tbtrans.tbtsencSileTBtrans property) xyzSile (class in sisl.io)

Y

Y (sisl.physics.Spin attribute) yield_chain() (sisl.mixing.StepMixer class method)

yield_eigenstate() (sisl.io.siesta.wfsxSileSiesta method) yield_repeat() (sisl.mixing.StepMixer class method)

Z

Z (sisl.Atom property) (sisl.Atoms property) (sisl.physics.Spin attribute) Z() (sisl.PeriodicTable method) Z_int() (sisl.PeriodicTable method)

Z_label() (sisl.PeriodicTable method) Z_short() (sisl.PeriodicTable method) zeta (sisl.AtomicOrbital property) (sisl.HydrogenicOrbital property) zgnr() (in module sisl.geom)