pybec.analysis

analysis.py Module for manipulating data from QuantumEspresso Output after Parsing

Contains all functions for calculating Born Effective Charges

Functions

apply_chunks(interpolator, grid_x, grid_y, ...)
apply_kriging_chunks(krig_interp, grid_x, ...)
ave_BEC_dict(elements, BECs)	Create a dictionary where the keys are the element symbols and the values are the average Born Effective Charges for that element.
correct_jumps(arr[, x, jump_quantum, ...])	Correct discontinuities in trajectory
correct_jumps_between_arr(arr1, arr2, ...)	Shift the start value of one array to align with the end value of another.
dipole_field(R, p_vec, centroid)
find_jumps(arr[, thresh])	Detect where the trajectory has anomolous values.
find_np_atoms(df_matrix, df_np)
gen_BEC_df(no_efield, clamped_ion, xyz[, ...])	Generate a pandas dataframe containing the Born Effective Charges of the ions in the unit cell
get_BECs(for_0, for_1, e_field, ...)	Calculate the born effective charges for an array of ions.
get_centroid(atoms_dict[, key])	Calculate the centroid of the atoms of a certian element in a unit cell.
get_dipole_field(coords[, dipole_loc, ...])	Returns the electric field from a point dipole.
get_dipole_field_displaced(coords[, ...])	Returns the electric field from a point dipole.
get_dist_to_centroid(atoms_dict, centroid)	Calculate the centroid of the atoms of a certian element in a unit cell.
get_field_along_d(field_dict[, ...])	Calculate the electric field along a specific direction from the FE results.
get_full_pol(directory)	Gets the trajectory of the polarization.
get_spherical_coords_to_centroid(atoms_dict, ...)	Calculate the centroid of the atoms of a certian element in a unit cell.
grid_krig_execute(krig_execute)
infer_e_field(for_0, for_1, z_exp[, ...])	Calculate the born effective charges for an array of ions.
infer_local_field(for_0, for_1, z_exp[, ...])	Calculate the born effective charges for an array of ions.
interp_3d(coord_arr, val_arr[, resolution, ...])
krige_grid_search(BEC_df)
pad_cell(cell_df, lattice[, pad])
point_in_hull(point, hull[, tolerance, inc])	https://stackoverflow.com/questions/16750618/whats-an-efficient-way-to-find-if-a-point-lies-in-the-convex-hull-of-a-point-cl/42165596#42165596
points_in_hull(points, hull[, tolerance, inc])
select_cell_segment(cell_df, lattice, frac_dir)	Select a portion of the unit cell along a given set of directions.
to_Bohr(coords)	Convert a coordinate dictionary from Angstroms to Bohr
volume(lattice)	Calculate the volume of a 3D unit cell.