Atomic Simulation Environment (ASE) - ase.py

This page documents MatSimPy functions for modifying and analyzing ASE atoms objects.

vacuum_adjust

def vacuum_adjust(ASE_xtract, rm_vac)

Removes a user-specified amount of vacuum from an ASE atoms object and centres the object.

Parameters:

• ASE_xtract (ASE atoms object): The atoms object to adjust.
• rm_vac (float): A positive float value, the amount of vacuum to remove from the Atoms object.

Returns:

• ASE_xtract (ASE Atoms object): the centred and modified ASE atoms object.

composition_identifier

def composition_identifier(ASE_obj)

Defines the composition of an ASE atoms object in a paired list output for chemical numbers and symbols.

Parameters:

• ASE_obj (ASE atoms object): The molecule/atom to be analyzed.

Returns:

• [elem_list, num_list] (list): Paired lists of element symbols and element #’s’.

Example:

  elem_list, num_list = composition_identifier(ASE_obj)