Index

A

activation_energy (kinisi.arrhenius.Arrhenius property) (kinisi.arrhenius.VogelFulcherTammann property) activation_energy_high_temperature (kinisi.arrhenius.PiecewiseArrhenius property) (kinisi.arrhenius.PiecewiseSmoothArrhenius property) activation_energy_low_temperature (kinisi.arrhenius.PiecewiseArrhenius property) (kinisi.arrhenius.PiecewiseSmoothArrhenius property)

Analyzer (class in kinisi.analyzer) Arrhenius (class in kinisi.arrhenius) arrhenius() (in module kinisi.arrhenius) ASEParser (class in kinisi.ase)

B

bayesian_regression() (kinisi.diffusion.Diffusion method)

C

calculate_msd() (in module kinisi.displacement) calculate_mstd() (in module kinisi.displacement) compute_covariance_matrix() (kinisi.diffusion.Diffusion method) conductivity() (kinisi.conductivity_analyzer.ConductivityAnalyzer method) ConductivityAnalyzer (class in kinisi.conductivity_analyzer)

consistency_ratio (kinisi.diffusion.Diffusion property) consistency_z (kinisi.diffusion.Diffusion property) coords (kinisi.parser.Parser property) correct_drift() (kinisi.parser.Parser method) covariance_matrix (kinisi.diffusion.Diffusion property) create_integer_dt() (kinisi.parser.Parser method)

D

D (kinisi.diffusion.Diffusion property) (kinisi.diffusion_analyzer.DiffusionAnalyzer property) D_infinite (kinisi.yeh_hummer.YehHummer property) D_J (kinisi.diffusion.Diffusion property) (kinisi.jump_diffusion_analyzer.JumpDiffusionAnalyzer property) da (kinisi.analyzer.Analyzer property) dg (kinisi.analyzer.Analyzer property) Diffusion (class in kinisi.diffusion)

diffusion() (kinisi.diffusion_analyzer.DiffusionAnalyzer method) DiffusionAnalyzer (class in kinisi.diffusion_analyzer) disp (kinisi.parser.Parser property) distribution (kinisi.fitting.FittingBase property) distributions (kinisi.conductivity_analyzer.ConductivityAnalyzer property) (kinisi.diffusion_analyzer.DiffusionAnalyzer property) (kinisi.jump_diffusion_analyzer.JumpDiffusionAnalyzer property) dt (kinisi.analyzer.Analyzer property)

E

eigenvalue_clipping() (in module kinisi.diffusion)

extrapolate() (kinisi.arrhenius.TemperatureDependent method)

F

FittingBase (class in kinisi.fitting) flatchain (kinisi.conductivity_analyzer.ConductivityAnalyzer property) (kinisi.diffusion_analyzer.DiffusionAnalyzer property) (kinisi.fitting.FittingBase property) (kinisi.jump_diffusion_analyzer.JumpDiffusionAnalyzer property) from_ase() (kinisi.conductivity_analyzer.ConductivityAnalyzer class method) (kinisi.diffusion_analyzer.DiffusionAnalyzer class method) (kinisi.jump_diffusion_analyzer.JumpDiffusionAnalyzer class method)

from_hdf5() (kinisi.analyzer.Analyzer class method) from_universe() (kinisi.conductivity_analyzer.ConductivityAnalyzer class method) (kinisi.diffusion_analyzer.DiffusionAnalyzer class method) (kinisi.jump_diffusion_analyzer.JumpDiffusionAnalyzer class method) from_xdatcar() (kinisi.conductivity_analyzer.ConductivityAnalyzer class method) (kinisi.diffusion_analyzer.DiffusionAnalyzer class method) (kinisi.jump_diffusion_analyzer.JumpDiffusionAnalyzer class method)

G

get_drift_indices() (kinisi.ase.ASEParser method) (kinisi.mdanalysis.MDAnalysisParser method) (kinisi.parser.Parser method) (kinisi.pymatgen.PymatgenParser method) get_independent_variable() (kinisi.fitting.FittingBase method) get_indices() (kinisi.ase.ASEParser method) (kinisi.mdanalysis.MDAnalysisParser method) (kinisi.parser.Parser method) (kinisi.pymatgen.PymatgenParser method)

get_molecules() (in module kinisi.parser) get_specie_and_drift_indices() (kinisi.parser.Parser method) get_structure_coords_latt() (kinisi.ase.ASEParser method) (kinisi.mdanalysis.MDAnalysisParser method) (kinisi.pymatgen.PymatgenParser method)

I

intercept (kinisi.analyzer.Analyzer property)

is_orthorhombic() (in module kinisi.parser) is_subset_approx() (in module kinisi.parser)

J

jump_diffusion() (kinisi.jump_diffusion_analyzer.JumpDiffusionAnalyzer method)

JumpDiffusionAnalyzer (class in kinisi.jump_diffusion_analyzer)

K

kinisi.analyze module kinisi.analyzer module kinisi.arrhenius module kinisi.ase module kinisi.conductivity_analyzer module kinisi.diffusion module kinisi.diffusion_analyzer module kinisi.displacement module

kinisi.fitting module kinisi.jump_diffusion_analyzer module kinisi.mdanalysis module kinisi.parser module kinisi.pymatgen module kinisi.samples module kinisi.yeh_hummer module

L

log_likelihood() (kinisi.fitting.FittingBase method) log_posterior() (kinisi.fitting.FittingBase method)

log_prior() (kinisi.fitting.FittingBase method) logz (kinisi.fitting.FittingBase property)

M

marchenkopastur() (in module kinisi.diffusion) max_aposteriori() (kinisi.fitting.FittingBase method) (kinisi.yeh_hummer.YehHummer method) max_likelihood() (kinisi.fitting.FittingBase method) (kinisi.yeh_hummer.YehHummer method) mcmc() (kinisi.fitting.FittingBase method) MDAnalysisParser (class in kinisi.mdanalysis) minimum_eigenvalue_method() (in module kinisi.diffusion) module kinisi.analyze kinisi.analyzer kinisi.arrhenius kinisi.ase kinisi.conductivity_analyzer kinisi.diffusion kinisi.diffusion_analyzer kinisi.displacement kinisi.fitting kinisi.jump_diffusion_analyzer kinisi.mdanalysis kinisi.parser kinisi.pymatgen kinisi.samples kinisi.yeh_hummer

mscd (kinisi.conductivity_analyzer.ConductivityAnalyzer property) msd (kinisi.diffusion_analyzer.DiffusionAnalyzer property) mstd (kinisi.jump_diffusion_analyzer.JumpDiffusionAnalyzer property)

N

n_atoms (kinisi.analyzer.Analyzer property) nested_sampling() (kinisi.fitting.FittingBase method)

nll() (kinisi.fitting.FittingBase method) nlp() (kinisi.fitting.FittingBase method) non_orthorhombic_calculate_displacements() (kinisi.parser.Parser static method)

O

orthorhombic_calculate_displacements() (kinisi.parser.Parser static method)

P

Parser (class in kinisi.parser) piecewise_equation() (in module kinisi.arrhenius) piecewise_smooth_equation() (in module kinisi.arrhenius) PiecewiseArrhenius (class in kinisi.arrhenius) PiecewiseSmoothArrhenius (class in kinisi.arrhenius) posterior_predictive() (kinisi.analyzer.Analyzer method) (kinisi.diffusion.Diffusion method)

preexponential_factor (kinisi.arrhenius.Arrhenius property) (kinisi.arrhenius.PiecewiseArrhenius property) (kinisi.arrhenius.PiecewiseSmoothArrhenius property) (kinisi.arrhenius.VogelFulcherTammann property) prior_transform() (kinisi.fitting.FittingBase method) PymatgenParser (class in kinisi.pymatgen)

S

Samples (class in kinisi.samples) shear_viscosity (kinisi.yeh_hummer.YehHummer property)

sigma (kinisi.conductivity_analyzer.ConductivityAnalyzer property) (kinisi.diffusion.Diffusion property)

T

T0 (kinisi.arrhenius.PiecewiseArrhenius property) (kinisi.arrhenius.PiecewiseSmoothArrhenius property) (kinisi.arrhenius.VogelFulcherTammann property)

TemperatureDependent (class in kinisi.arrhenius) to_hdf5() (kinisi.analyzer.Analyzer method) to_unit() (kinisi.samples.Samples method)

V

viscosity_to_slope() (kinisi.yeh_hummer.YehHummer method)

VogelFulcherTammann (class in kinisi.arrhenius) vtf_equation() (in module kinisi.arrhenius)

W

width (kinisi.arrhenius.PiecewiseSmoothArrhenius property)

Y

YehHummer (class in kinisi.yeh_hummer)