Index

A

abs_sqrt() (in module pdyna.analysis) allow_equil (pdyna.core.Trajectory attribute) Allpos (pdyna.core.Trajectory attribute) analysis() (pdyna.core.Frame method)

apply_pbc_cart_vecs() (in module pdyna.structural) apply_pbc_cart_vecs_single_frame() (in module pdyna.structural) at0 (pdyna.core.Trajectory attribute) atomic_symbols (pdyna.core.Trajectory attribute)

C

calc_displacement() (in module pdyna.structural) calc_displacement_full() (in module pdyna.structural) calc_distortion_from_order_manual() (in module pdyna.structural) calc_distortions_from_bond_vectors() (in module pdyna.structural) calc_distortions_from_bond_vectors_full() (in module pdyna.structural) calc_rotation_from_arbitrary_order() (in module pdyna.structural)

centmass_organic() (in module pdyna.structural) centmass_organic_vec() (in module pdyna.structural) chemical_from_formula() (in module pdyna.io) compute_tilt_density() (in module pdyna.analysis) compute_tilt_domain() (in module pdyna.analysis) construct_cell() (in module pdyna.io) convert_xb_to_bx() (in module pdyna.structural)

D

data_format (pdyna.core.Dataset attribute) (pdyna.core.Frame attribute) (pdyna.core.Trajectory attribute) data_path (pdyna.core.Dataset attribute) (pdyna.core.Frame attribute) (pdyna.core.Trajectory attribute) Dataset (class in pdyna.core) defect_3D_scatter() (in module pdyna.analysis) display_A_sites() (in module pdyna.io) distance_matrix() (in module pdyna.structural) distance_matrix_ase() (in module pdyna.structural) distance_matrix_ase_replace() (in module pdyna.structural) distance_matrix_handler() (in module pdyna.structural) Distortion (pdyna.core.Trajectory attribute) draw_conntype_tilt_density() (in module pdyna.analysis) draw_dist_density() (in module pdyna.analysis) draw_dist_density_frame() (in module pdyna.analysis) draw_dist_evolution() (in module pdyna.analysis) draw_dist_evolution_time() (in module pdyna.analysis) draw_distortion_evolution_sca() (in module pdyna.analysis) draw_halideconc_dist_density() (in module pdyna.analysis) draw_halideconc_lat_density() (in module pdyna.analysis) draw_halideconc_tilt_density() (in module pdyna.analysis) draw_halideconc_tilt_density_transient() (in module pdyna.analysis) draw_hetero_dist_density() (in module pdyna.analysis) draw_hetero_lat_density() (in module pdyna.analysis) draw_hetero_tilt_density() (in module pdyna.analysis) draw_lattice_density() (in module pdyna.analysis)

draw_lattice_evolution() (in module pdyna.analysis) draw_lattice_evolution_time() (in module pdyna.analysis) draw_MO_order_time() (in module pdyna.analysis) draw_MO_spatial_corr() (in module pdyna.analysis) draw_MO_spatial_corr_NN12() (in module pdyna.analysis) draw_MO_spatial_corr_norm() (in module pdyna.analysis) draw_MO_spatial_corr_norm_var() (in module pdyna.analysis) draw_MO_spatial_corr_time() (in module pdyna.analysis) draw_octatype_dist_density() (in module pdyna.analysis) draw_octatype_lat_density() (in module pdyna.analysis) draw_octatype_tilt_density() (in module pdyna.analysis) draw_octatype_tilt_density_transient() (in module pdyna.analysis) draw_RDF() (in module pdyna.analysis) draw_tilt_and_corr_density_full() (in module pdyna.analysis) draw_tilt_and_corr_density_shade() (in module pdyna.analysis) draw_tilt_and_corr_density_shade_frame() (in module pdyna.analysis) draw_tilt_and_corr_density_shade_longarray() (in module pdyna.analysis) draw_tilt_and_corr_density_shade_non3D() (in module pdyna.analysis) draw_tilt_coaxial() (in module pdyna.analysis) draw_tilt_corr_density_time() (in module pdyna.analysis) draw_tilt_corr_evolution_sca() (in module pdyna.analysis) draw_tilt_density() (in module pdyna.analysis) draw_tilt_evolution() (in module pdyna.analysis) draw_tilt_evolution_sca() (in module pdyna.analysis) draw_tilt_evolution_time() (in module pdyna.analysis) draw_tilt_prediction() (in module pdyna.analysis) draw_tilt_spatial_corr() (in module pdyna.analysis) draw_transient_properties() (in module pdyna.analysis) dynamics() (pdyna.core.Trajectory method)

F

featurize() (pdyna.core.Dataset method) find_B_cage_and_disp() (in module pdyna.structural) find_polytype_network() (in module pdyna.structural) find_population_gap() (in module pdyna.structural) fit_3D_disp_atomwise() (in module pdyna.analysis) fit_3D_disp_total() (in module pdyna.analysis) fit_damped_oscillator() (in module pdyna.analysis) fit_exp_decay() (in module pdyna.analysis)

fit_exp_decay_both() (in module pdyna.analysis) fit_exp_decay_both_correct() (in module pdyna.analysis) fit_exp_decay_fixed() (in module pdyna.analysis) fit_exp_decay_single() (in module pdyna.analysis) fit_octahedral_network_defect_tol() (in module pdyna.structural) fit_octahedral_network_defect_tol_non_orthogonal() (in module pdyna.structural) fit_octahedral_network_frame() (in module pdyna.structural) formula (pdyna.core.Trajectory attribute) Frame (class in pdyna.core)

G

get_cart_from_frac() (in module pdyna.structural) get_cube() (in module pdyna.analysis) get_frac_from_cart() (in module pdyna.structural)

get_max_index() (in module pdyna.io) get_norm_corr() (in module pdyna.analysis) get_tcp_from_list() (in module pdyna.analysis) get_volume() (in module pdyna.structural)

I

if_arrays_are_different() (in module pdyna.analysis)

L

lammps_data_to_ase_atoms() (in module pdyna.io) Lat (pdyna.core.Trajectory attribute)

latmat (pdyna.core.Trajectory attribute) lattice_parameter() (pdyna.core.Trajectory method)

M

match_bx_arbitrary() (in module pdyna.structural) match_bx_orthogonal() (in module pdyna.structural) match_bx_orthogonal_rotated() (in module pdyna.structural) match_mixed_halide_octa_dot() (in module pdyna.structural) match_molecules_extra() (in module pdyna.structural) MDsetting (pdyna.core.Trajectory attribute) MDTimestep (pdyna.core.Trajectory attribute) MO_correlation() (in module pdyna.analysis)

module pdyna pdyna.analysis pdyna.basis pdyna.core pdyna.io pdyna.structural molecular_orientation() (pdyna.core.Trajectory method) MOvec (pdyna.core.Trajectory attribute)

N

natom (pdyna.core.Trajectory attribute)

nframe (pdyna.core.Trajectory attribute)

O

octahedra (pdyna.core.Trajectory attribute) octahedra_coords_into_bond_vectors() (in module pdyna.structural) orientation_density() (in module pdyna.analysis)

orientation_density_2pan() (in module pdyna.analysis) orientation_density_3D_dots() (in module pdyna.analysis) orientation_density_3D_sphere() (in module pdyna.analysis)

P

pdyna module pdyna.analysis module pdyna.basis module pdyna.core module pdyna.io module pdyna.structural module

peaks_3D_scatter() (in module pdyna.analysis) periodicity_fold() (in module pdyna.structural) print_partition() (in module pdyna.analysis) print_time() (in module pdyna.io) process_lammps_data() (in module pdyna.io) process_lat() (in module pdyna.io) process_lat_reverse() (in module pdyna.io) prop_lib (pdyna.core.Trajectory attribute) properties_to_binned_grid() (in module pdyna.analysis) property_processing() (pdyna.core.Trajectory method) pseudocubic_lat() (in module pdyna.structural)

Q

quantify_halideconc_tilt_domain() (in module pdyna.analysis) quantify_hetero_tilt_domain() (in module pdyna.analysis)

quantify_octatype_tilt_domain() (in module pdyna.analysis) quantify_tilt_domain() (in module pdyna.analysis) quick_match_octahedron() (in module pdyna.structural)

R

radial_distribution() (pdyna.core.Trajectory method) read_ase_md_settings() (in module pdyna.io) read_ase_traj() (in module pdyna.io) read_every (pdyna.core.Trajectory attribute) read_lammps_dir() (in module pdyna.io)

read_lammps_dump() (in module pdyna.io) read_lammps_settings() (in module pdyna.io) read_pdb() (in module pdyna.io) read_xdatcar() (in module pdyna.io) read_xyz() (in module pdyna.io) resolve_octahedra() (in module pdyna.structural)

S

savitzky_golay() (in module pdyna.analysis) set_axes_equal() (in module pdyna.analysis) simply_calc_distortion() (in module pdyna.structural) site_displacement() (pdyna.core.Trajectory method) spatialCorr (pdyna.core.Trajectory attribute) spatialCorrLength (pdyna.core.Trajectory attribute) species_set (pdyna.core.Trajectory attribute)

sphere_bin_count() (in module pdyna.analysis) sphere_mesh() (in module pdyna.analysis) spherical_coordinates() (in module pdyna.analysis) st0 (pdyna.core.Trajectory attribute) structure_time_average_ase() (in module pdyna.structural) structure_time_average_ase_organic() (in module pdyna.structural) system_test() (pdyna.core.Trajectory method)

T

Tgrad (pdyna.core.Trajectory attribute) Tilt_correlation() (in module pdyna.analysis) Tilting (pdyna.core.Trajectory attribute) tilting_and_distortion() (pdyna.core.Frame method) (pdyna.core.Trajectory method)

Tilting_Corr (pdyna.core.Trajectory attribute) timing (pdyna.core.Trajectory attribute) tqdm_joblib() (in module pdyna.structural) traj_time_average() (in module pdyna.structural) Trajectory (class in pdyna.core)

U

uniname (pdyna.core.Trajectory attribute)

V

vis3D_domain_anime() (in module pdyna.analysis)

vis3D_domain_frame() (in module pdyna.analysis)

X

Xindex (pdyna.core.Trajectory attribute)