PDynA

Module contents

PDyna is a package for analysing dynamic properties of perovskite.

Submodules

• pdyna.core module
  • Dataset
    • Dataset.data_format
    • Dataset.data_path
    • Dataset.featurize()
  • Frame
    • Frame.analysis()
    • Frame.data_format
    • Frame.data_path
    • Frame.tilting_and_distortion()
  • Trajectory
    • Trajectory.Allpos
    • Trajectory.latmat
    • Trajectory.uniname
    • Trajectory.st0
    • Trajectory.at0
    • Trajectory.Xindex
    • Trajectory.natom
    • Trajectory.species_set
    • Trajectory.formula
    • Trajectory.nframe
    • Trajectory.atomic_symbols
    • Trajectory.MDsetting
    • Trajectory.MDTimestep
    • Trajectory.Tgrad
    • Trajectory.allow_equil
    • Trajectory.read_every
    • Trajectory.timing
    • Trajectory.octahedra
    • Trajectory.prop_lib
    • Trajectory.Lat
    • Trajectory.Distortion
    • Trajectory.Tilting
    • Trajectory.Tilting_Corr
    • Trajectory.MOvec
    • Trajectory.spatialCorr
    • Trajectory.spatialCorrLength
    • Trajectory.data_format
    • Trajectory.data_path
    • Trajectory.dynamics()
    • Trajectory.lattice_parameter()
    • Trajectory.molecular_orientation()
    • Trajectory.property_processing()
    • Trajectory.radial_distribution()
    • Trajectory.site_displacement()
    • Trajectory.system_test()
    • Trajectory.tilting_and_distortion()
• pdyna.structural module
  • apply_pbc_cart_vecs()
  • apply_pbc_cart_vecs_single_frame()
  • calc_displacement()
  • calc_displacement_full()
  • calc_distortion_from_order_manual()
  • calc_distortions_from_bond_vectors()
  • calc_distortions_from_bond_vectors_full()
  • calc_rotation_from_arbitrary_order()
  • centmass_organic()
  • centmass_organic_vec()
  • convert_xb_to_bx()
  • distance_matrix()
  • distance_matrix_ase()
  • distance_matrix_ase_replace()
  • distance_matrix_handler()
  • find_B_cage_and_disp()
  • find_polytype_network()
  • find_population_gap()
  • fit_octahedral_network_defect_tol()
  • fit_octahedral_network_defect_tol_non_orthogonal()
  • fit_octahedral_network_frame()
  • get_cart_from_frac()
  • get_frac_from_cart()
  • get_volume()
  • match_bx_arbitrary()
  • match_bx_orthogonal()
  • match_bx_orthogonal_rotated()
  • match_mixed_halide_octa_dot()
  • match_molecules_extra()
  • octahedra_coords_into_bond_vectors()
  • periodicity_fold()
  • pseudocubic_lat()
  • quick_match_octahedron()
  • resolve_octahedra()
  • simply_calc_distortion()
  • structure_time_average_ase()
  • structure_time_average_ase_organic()
  • tqdm_joblib()
  • traj_time_average()
• pdyna.analysis module
  • MO_correlation()
  • Tilt_correlation()
  • abs_sqrt()
  • compute_tilt_density()
  • compute_tilt_domain()
  • defect_3D_scatter()
  • draw_MO_order_time()
  • draw_MO_spatial_corr()
  • draw_MO_spatial_corr_NN12()
  • draw_MO_spatial_corr_norm()
  • draw_MO_spatial_corr_norm_var()
  • draw_MO_spatial_corr_time()
  • draw_RDF()
  • draw_conntype_tilt_density()
  • draw_dist_density()
  • draw_dist_density_frame()
  • draw_dist_evolution()
  • draw_dist_evolution_time()
  • draw_distortion_evolution_sca()
  • draw_halideconc_dist_density()
  • draw_halideconc_lat_density()
  • draw_halideconc_tilt_density()
  • draw_halideconc_tilt_density_transient()
  • draw_hetero_dist_density()
  • draw_hetero_lat_density()
  • draw_hetero_tilt_density()
  • draw_lattice_density()
  • draw_lattice_evolution()
  • draw_lattice_evolution_time()
  • draw_octatype_dist_density()
  • draw_octatype_lat_density()
  • draw_octatype_tilt_density()
  • draw_octatype_tilt_density_transient()
  • draw_tilt_and_corr_density_full()
  • draw_tilt_and_corr_density_shade()
  • draw_tilt_and_corr_density_shade_frame()
  • draw_tilt_and_corr_density_shade_longarray()
  • draw_tilt_and_corr_density_shade_non3D()
  • draw_tilt_coaxial()
  • draw_tilt_corr_density_time()
  • draw_tilt_corr_evolution_sca()
  • draw_tilt_density()
  • draw_tilt_evolution()
  • draw_tilt_evolution_sca()
  • draw_tilt_evolution_time()
  • draw_tilt_prediction()
  • draw_tilt_spatial_corr()
  • draw_transient_properties()
  • fit_3D_disp_atomwise()
  • fit_3D_disp_total()
  • fit_damped_oscillator()
  • fit_exp_decay()
  • fit_exp_decay_both()
  • fit_exp_decay_both_correct()
  • fit_exp_decay_fixed()
  • fit_exp_decay_single()
  • get_cube()
  • get_norm_corr()
  • get_tcp_from_list()
  • if_arrays_are_different()
  • orientation_density()
  • orientation_density_2pan()
  • orientation_density_3D_dots()
  • orientation_density_3D_sphere()
  • peaks_3D_scatter()
  • print_partition()
  • properties_to_binned_grid()
  • quantify_halideconc_tilt_domain()
  • quantify_hetero_tilt_domain()
  • quantify_octatype_tilt_domain()
  • quantify_tilt_domain()
  • savitzky_golay()
  • set_axes_equal()
  • sphere_bin_count()
  • sphere_mesh()
  • spherical_coordinates()
  • vis3D_domain_anime()
  • vis3D_domain_frame()
• pdyna.io module
  • chemical_from_formula()
  • construct_cell()
  • display_A_sites()
  • get_max_index()
  • lammps_data_to_ase_atoms()
  • print_time()
  • process_lammps_data()
  • process_lat()
  • process_lat_reverse()
  • read_ase_md_settings()
  • read_ase_traj()
  • read_lammps_dir()
  • read_lammps_dump()
  • read_lammps_settings()
  • read_pdb()
  • read_xdatcar()
  • read_xyz()
• pdyna.basis module