Index

A

accept() (hylight.mode.Mask method) add_interval() (hylight.mode.Mask method) angle() (in module hylight.mode)

archive_modes() (in module hylight.npz) as_bool() (hylight.mode.Mask method) atoms (hylight.phonopy.loader.PPStruct attribute) (hylight.struct.Struct property)

C

CellMismatch (class in hylight.mode) compute_delta_R() (in module hylight.multi_modes) compute_spectrum() (in module hylight.mono_mode) (in module hylight.multi_modes)

copy() (hylight.struct.Struct method) CrystalOut (class in hylight.crystal.common)

D

DISP (hylight.guess_width.OmegaEff attribute) dropwhile_err() (in module hylight.findiff.collect) duschinsky() (in module hylight.guess_width) (in module hylight.multi_modes)

dynamical_matrix() (in module hylight.mode) dynmatshow() (in module hylight.multi_modes)

E

effective_phonon_energy() (in module hylight.guess_width) energies() (hylight.mode.Mode method) energy_cm1 (hylight.mode.Mode property) energy_eV (hylight.mode.Mode property)

energy_meV (hylight.mode.Mode property) energy_si (hylight.mode.Mode property) expected_width() (in module hylight.guess_width) export() (in module hylight.jmol) export_disp() (in module hylight.jmol)

F

FC_MEAN (hylight.guess_width.OmegaEff attribute) FC_RMS (hylight.guess_width.OmegaEff attribute) fc_spectrum() (in module hylight.multi_modes) format_v() (in module hylight.jmol) freq_from_finite_diff() (in module hylight.multi_modes)

from_bias() (hylight.mode.Mask class method) from_file() (hylight.crystal.common.CrystalOut class method) (hylight.vasp.common.Poscar class method) from_mode() (hylight.struct.Struct class method) from_yaml_cell() (hylight.phonopy.loader.PPStruct class method) FULL_ND (hylight.guess_width.WidthModel attribute)

G

GAUSSIAN (hylight.multi_modes.LineShape attribute) gaussian() (in module hylight.utils) gen_disp() (in module hylight.findiff.gen) gen_translat() (in module hylight.utils) generate_basis() (in module hylight.mode) get_energies() (in module hylight.mode) get_forces() (in module hylight.findiff.collect)

get_forces_and_pos() (in module hylight.findiff.collect) get_HR_factors() (in module hylight.mode) get_offset() (hylight.struct.Struct method) get_ref_info() (in module hylight.findiff.collect) get_struct() (in module hylight.phonopy.loader) GRAD (hylight.guess_width.OmegaEff attribute) gradiant_at() (in module hylight.guess_width) guess_width() (in module hylight.guess_width)

H

HR_MEAN (hylight.guess_width.OmegaEff attribute) HR_RMS (hylight.guess_width.OmegaEff attribute) hr_spectrum() (in module hylight.multi_modes) huang_rhys() (hylight.mode.Mode method) (in module hylight.mono_mode) hylight module hylight.constants module hylight.crystal module hylight.crystal.common module hylight.crystal.loader module hylight.findiff module hylight.findiff.collect module hylight.findiff.gen module hylight.guess_width module hylight.jmol module hylight.loader module

hylight.mode module hylight.mono_mode module hylight.multi_modes module hylight.npz module hylight.phonopy module hylight.phonopy.loader module hylight.struct module hylight.typing module hylight.utils module hylight.vasp module hylight.vasp.common module hylight.vasp.loader module hylight.vasp.utils module

I

InputError

integrate() (in module hylight.guess_width)

L

lattice (hylight.phonopy.loader.PPStruct attribute) LineShape (class in hylight.multi_modes) load_phonons() (in module hylight.crystal.loader) (in module hylight.npz) (in module hylight.phonopy.loader) (in module hylight.vasp.loader) load_phonons_bandsh5() (in module hylight.phonopy.loader)

load_phonons_bandyaml() (in module hylight.phonopy.loader) load_phonons_qpointsh5() (in module hylight.phonopy.loader) load_phonons_qpointsyaml() (in module hylight.phonopy.loader) load_poscar() (in module hylight.vasp.loader) load_poscar_latt() (in module hylight.vasp.loader) localization_ratio() (hylight.mode.Mode method) LORENTZIAN (hylight.multi_modes.LineShape attribute)

M

make_finite_diff_poscar() (in module hylight.vasp.utils) make_line_shape() (in module hylight.multi_modes) Mask (class in hylight.mode) masses (hylight.phonopy.loader.PPStruct attribute) measure_fwhm() (in module hylight.utils) Mode (class in hylight.mode) modes_from_dynmat() (in module hylight.mode) module hylight hylight.constants hylight.crystal hylight.crystal.common hylight.crystal.loader hylight.findiff hylight.findiff.collect hylight.findiff.gen hylight.guess_width hylight.jmol hylight.loader hylight.mode hylight.mono_mode hylight.multi_modes hylight.npz hylight.phonopy hylight.phonopy.loader hylight.struct hylight.typing hylight.utils hylight.vasp hylight.vasp.common hylight.vasp.loader hylight.vasp.utils

N

NONE (hylight.multi_modes.LineShape attribute)

normalize() (in module hylight.crystal.loader)

O

OmegaEff (class in hylight.guess_width)

ONED (hylight.guess_width.WidthModel attribute) orthonormalize() (in module hylight.mode)

P

parse_formatted_table() (in module hylight.utils) participation_ratio() (hylight.mode.Mode method) per_species_n_eff() (hylight.mode.Mode method) per_species_pr() (hylight.mode.Mode method) periodic_diff() (in module hylight.utils) periodic_dist() (in module hylight.utils) plot() (hylight.mode.Mask method) plot_spectral_function() (in module hylight.multi_modes)

pops (hylight.phonopy.loader.PPStruct attribute) pops_and_masses() (in module hylight.npz) Poscar (class in hylight.vasp.common) PPStruct (class in hylight.phonopy.loader) process_phonons() (in module hylight.findiff.collect) project() (hylight.mode.Mode method) project_coef2() (hylight.mode.Mode method) project_coef2_R() (hylight.mode.Mode method) project_on_asr() (in module hylight.mode)

R

random_basis() (in module hylight.findiff.gen) raw (hylight.struct.Struct property) rect() (in module hylight.multi_modes)

ref (hylight.phonopy.loader.PPStruct attribute) reject() (hylight.mode.Mask method) rot_c_to_v() (in module hylight.mode)

S

same_cell() (in module hylight.mode) save_disp() (in module hylight.findiff.gen) save_disp_from_basis() (in module hylight.findiff.gen) save_random_disp() (in module hylight.findiff.gen) select_interval() (in module hylight.utils) set_lattice() (hylight.mode.Mode method) setup_logging() (in module hylight)

sigma() (in module hylight.guess_width) sigma_full_nd() (in module hylight.guess_width) sigma_hybrid() (in module hylight.guess_width) SINGLE_ES_FREQ (hylight.guess_width.WidthModel attribute) sp_at() (hylight.struct.Struct method) species_names (hylight.struct.Struct property) Struct (class in hylight.struct) system_name (hylight.struct.Struct property)

T

to_file() (hylight.vasp.common.Poscar method) to_jmol() (hylight.mode.Mode method)

to_stream() (hylight.vasp.common.Poscar method) to_traj() (hylight.mode.Mode method)

V

variance() (in module hylight.guess_width)

W

WidthModel (class in hylight.guess_width)

write_jmol_options() (in module hylight.jmol) write_xyz() (in module hylight.jmol)