Index

A

a (vachoppy.trajectory.CalculatorEnsemble attribute) (vachoppy.trajectory.CalculatorSingle attribute) animate_occupation() (vachoppy.trajectory.Trajectory method)

animate_vacancy_trajectory() (vachoppy.trajectory.Trajectory method) atom_count (vachoppy.trajectory.TrajectoryBundle attribute) atom_counts (vachoppy.utils.Snapshots attribute) AttemptFrequency (class in vachoppy.frequency)

C

calculate() (vachoppy.einstein.MSDCalculator method) (vachoppy.einstein.MSDEnsemble method) (vachoppy.fingerprint.FingerPrint method) (vachoppy.trajectory.CalculatorEnsemble method) (vachoppy.trajectory.CalculatorSingle method) (vachoppy.vibration.Vibration method) calculate_attempt_frequency() (vachoppy.trajectory.CalculatorEnsemble method) Calculator() (in module vachoppy.core) CalculatorEnsemble (class in vachoppy.trajectory)

calculators (vachoppy.einstein.MSDEnsemble attribute) (vachoppy.trajectory.CalculatorEnsemble attribute) CalculatorSingle (class in vachoppy.trajectory) concat_traj() (in module vachoppy.utils) cosine_distance() (in module vachoppy.fingerprint) counts (vachoppy.trajectory.CalculatorSingle attribute) (vachoppy.trajectory.TrajectoryAnalyzer attribute) counts_unknown (vachoppy.trajectory.TrajectoryAnalyzer attribute) cut_traj() (in module vachoppy.utils)

D

D (vachoppy.einstein.MSDEnsemble attribute) (vachoppy.trajectory.CalculatorEnsemble attribute) (vachoppy.trajectory.CalculatorSingle attribute) D0 (vachoppy.einstein.MSDEnsemble attribute) (vachoppy.trajectory.CalculatorEnsemble attribute) D0_x (vachoppy.trajectory.CalculatorEnsemble attribute) D0_y (vachoppy.trajectory.CalculatorEnsemble attribute) D0_z (vachoppy.trajectory.CalculatorEnsemble attribute) D_rand (vachoppy.trajectory.CalculatorEnsemble attribute) (vachoppy.trajectory.CalculatorSingle attribute)

D_rand0 (vachoppy.trajectory.CalculatorEnsemble attribute) decompose_diffusivity() (vachoppy.trajectory.CalculatorEnsemble method) diffusivity (vachoppy.einstein.MSDCalculator attribute) displacements (vachoppy.vibration.Vibration attribute) distance_PBC() (vachoppy.trajectory.Trajectory method) dt (vachoppy.einstein.MSDCalculator attribute) (vachoppy.utils.Snapshots attribute) Dx (vachoppy.trajectory.CalculatorEnsemble attribute) Dy (vachoppy.trajectory.CalculatorEnsemble attribute) Dz (vachoppy.trajectory.CalculatorEnsemble attribute)

E

Ea_D (vachoppy.einstein.MSDEnsemble attribute) (vachoppy.trajectory.CalculatorEnsemble attribute) Ea_D_rand (vachoppy.trajectory.CalculatorEnsemble attribute) Ea_f (vachoppy.trajectory.CalculatorEnsemble attribute) Ea_path (vachoppy.frequency.AttemptFrequency attribute) Ea_tau (vachoppy.trajectory.CalculatorEnsemble attribute)

Ea_x (vachoppy.trajectory.CalculatorEnsemble attribute) Ea_y (vachoppy.trajectory.CalculatorEnsemble attribute) Ea_z (vachoppy.trajectory.CalculatorEnsemble attribute) Einstein() (in module vachoppy.einstein) Encounter (class in vachoppy.trajectory) encounter_complete (vachoppy.trajectory.Encounter attribute) encounter_in_process (vachoppy.trajectory.Encounter attribute)

F

f (vachoppy.trajectory.CalculatorEnsemble attribute) (vachoppy.trajectory.CalculatorSingle attribute) f0 (vachoppy.trajectory.CalculatorEnsemble attribute)

f_cor (vachoppy.trajectory.Encounter attribute) FingerPrint (class in vachoppy.fingerprint) fingerprint (vachoppy.fingerprint.FingerPrint attribute) frequencies (vachoppy.vibration.Vibration attribute)

G

get_fingerprint() (in module vachoppy.fingerprint)

H

hopping_history (vachoppy.trajectory.CalculatorSingle attribute) (vachoppy.trajectory.Trajectory attribute) (vachoppy.trajectory.TrajectoryAnalyzer attribute)

hopping_sequence (vachoppy.trajectory.Trajectory attribute)

I

intercept (vachoppy.einstein.MSDCalculator attribute)

L

lattice (vachoppy.einstein.MSDCalculator attribute) (vachoppy.trajectory.TrajectoryBundle attribute) (vachoppy.utils.Snapshots attribute)

lattice_parameter (vachoppy.core.Site attribute) lattice_sites (vachoppy.core.Site attribute)

M

mean_frequency (vachoppy.vibration.Vibration attribute) module vachoppy.core vachoppy.einstein vachoppy.fingerprint vachoppy.frequency vachoppy.trajectory vachoppy.utils vachoppy.vibration

monitor_performance() (in module vachoppy.utils) msd (vachoppy.einstein.MSDCalculator attribute) (vachoppy.trajectory.Encounter attribute) msd_rand (vachoppy.trajectory.TrajectoryAnalyzer attribute) MSDCalculator (class in vachoppy.einstein) MSDEnsemble (class in vachoppy.einstein)

N

nsw (vachoppy.einstein.MSDCalculator attribute) nu (vachoppy.frequency.AttemptFrequency attribute) (vachoppy.trajectory.CalculatorEnsemble attribute) nu_path (vachoppy.frequency.AttemptFrequency attribute) (vachoppy.trajectory.CalculatorEnsemble attribute)

num_A (vachoppy.fingerprint.FingerPrint attribute) num_atoms (vachoppy.utils.Snapshots attribute) num_B (vachoppy.fingerprint.FingerPrint attribute) num_encounter (vachoppy.trajectory.Encounter attribute) num_steps (vachoppy.utils.Snapshots attribute)

O

occupation (vachoppy.trajectory.Trajectory attribute)

P

parse_lammps() (in module vachoppy.core) parse_md() (in module vachoppy.core) path (vachoppy.core.Site attribute) path_count (vachoppy.trajectory.Encounter attribute) path_name (vachoppy.core.Site attribute) plot_a() (vachoppy.trajectory.CalculatorEnsemble method) plot_cosine_distance() (in module vachoppy.fingerprint) plot_counts() (vachoppy.trajectory.CalculatorEnsemble method) (vachoppy.trajectory.CalculatorSingle method) plot_D() (vachoppy.einstein.MSDEnsemble method) (vachoppy.trajectory.CalculatorEnsemble method) plot_D_rand() (vachoppy.trajectory.CalculatorEnsemble method) plot_D_xyz() (vachoppy.trajectory.CalculatorEnsemble method)

plot_displacements() (vachoppy.vibration.Vibration method) plot_f() (vachoppy.trajectory.CalculatorEnsemble method) plot_fingerprint() (vachoppy.fingerprint.FingerPrint method) plot_frequencies() (vachoppy.vibration.Vibration method) plot_msd() (vachoppy.einstein.MSDCalculator method) (vachoppy.einstein.MSDEnsemble method) plot_msd_xyz() (vachoppy.trajectory.CalculatorEnsemble method) plot_nu() (vachoppy.frequency.AttemptFrequency method) (vachoppy.trajectory.CalculatorEnsemble method) plot_tau() (vachoppy.trajectory.CalculatorEnsemble method) plot_vacancy_trajectory() (vachoppy.trajectory.Trajectory method) plot_z() (vachoppy.frequency.AttemptFrequency method) (vachoppy.trajectory.CalculatorEnsemble method) pos (vachoppy.utils.Snapshots attribute)

R

R (vachoppy.fingerprint.FingerPrint attribute)

R2 (vachoppy.einstein.MSDEnsemble attribute) residence_time (vachoppy.trajectory.TrajectoryAnalyzer attribute)

S

save_parameters() (vachoppy.einstein.MSDEnsemble method) (vachoppy.trajectory.CalculatorEnsemble method) save_snapshots() (vachoppy.utils.Snapshots method) save_trajectory() (vachoppy.trajectory.CalculatorEnsemble method) (vachoppy.trajectory.CalculatorSingle method) show_hopping_history() (vachoppy.trajectory.CalculatorEnsemble method) (vachoppy.trajectory.CalculatorSingle method) show_hopping_paths() (vachoppy.trajectory.CalculatorEnsemble method) (vachoppy.trajectory.CalculatorSingle method) show_traj() (in module vachoppy.utils) Site (class in vachoppy.core) site_name (vachoppy.core.Site attribute) site_radius (vachoppy.vibration.Vibration attribute)

Snapshots (class in vachoppy.utils) structure (vachoppy.core.Site attribute) summary() (vachoppy.core.Site method) (vachoppy.einstein.MSDCalculator method) (vachoppy.einstein.MSDEnsemble method) (vachoppy.fingerprint.FingerPrint method) (vachoppy.frequency.AttemptFrequency method) (vachoppy.trajectory.CalculatorEnsemble method) (vachoppy.trajectory.CalculatorSingle method) (vachoppy.trajectory.Encounter method) (vachoppy.trajectory.TrajectoryAnalyzer method) (vachoppy.trajectory.TrajectoryBundle method) (vachoppy.vibration.Vibration method) symbol (vachoppy.core.Site attribute)

T

tau (vachoppy.trajectory.CalculatorEnsemble attribute) (vachoppy.trajectory.CalculatorSingle attribute) tau0 (vachoppy.trajectory.CalculatorEnsemble attribute) temperature (vachoppy.einstein.MSDCalculator attribute) temperatures (vachoppy.einstein.MSDEnsemble attribute) (vachoppy.frequency.AttemptFrequency attribute) (vachoppy.trajectory.CalculatorEnsemble attribute) (vachoppy.trajectory.TrajectoryBundle attribute)

timestep (vachoppy.einstein.MSDCalculator attribute) traj (vachoppy.trajectory.TrajectoryBundle attribute) Trajectory (class in vachoppy.trajectory) TrajectoryAnalyzer (class in vachoppy.trajectory) TrajectoryBundle (class in vachoppy.trajectory)

U

unwrapped_vacancy_trajectory_coord_cart (vachoppy.trajectory.Trajectory attribute)

update_json() (vachoppy.frequency.AttemptFrequency method)

V

vacancy_trajectory_coord_cart (vachoppy.trajectory.Trajectory attribute) vacancy_trajectory_index (vachoppy.trajectory.Trajectory attribute) vachoppy.core module vachoppy.einstein module vachoppy.fingerprint module

vachoppy.frequency module vachoppy.trajectory module vachoppy.utils module vachoppy.vibration module Vibration (class in vachoppy.vibration)

Z

z (vachoppy.frequency.AttemptFrequency attribute) (vachoppy.trajectory.CalculatorEnsemble attribute)