Source code for aiida_castep.parsers.utils
"""
Utility functions
"""
import copy
import numpy as np
from aiida.common import OutputParsingError
from aiida.orm import StructureData
from aiida.plugins import DataFactory
[docs]def structure_from_input(cell, positions, symbols):
"""
Receives the dictionary cell parsed from CASTEP
Convert it into an AiiDA structure object
"""
out_structure = StructureData(cell=cell)
for symbol, position in zip(symbols, positions):
out_structure.append_atom(symbols=symbol, position=position)
return out_structure
[docs]def add_last_if_exists(dict_of_sequence, key, dict_to_be_added):
"""
Added the last term of a sequence to a dictionary.
This is used for collecting final values in a dictionary of 'trajectory'
"""
try:
last = dict_of_sequence[key][-1]
except (KeyError, IndexError):
return
# Check if last exist - in case of DefaultDict being passed
if last:
dict_to_be_added[key] = last
[docs]def desort_structure(structure, original_structure):
"""
Recover the order of structure. CASTEP will sort the input structure
according to the atomic numbers
"""
new_structure = copy.deepcopy(structure)
rsort = get_desort_args(original_structure)
new_sites = np.array(structure.sites)[rsort]
# Map back to the original order
new_structure.clear_sites()
for site in new_sites:
new_structure.append_site(site)
# Check for sure
assert [site.kind_name for site in original_structure.sites] == [
site.kind_name for site in new_structure.sites
]
return new_structure
[docs]def get_desort_args(original_structure):
"""
Return an index array for desorting the structure
:return: An array used to recovery the original order
"""
numbers = original_structure.get_ase().numbers
isort = np.argsort(numbers, kind="mergesort")
rsort = [-1] * len(numbers)
for idx, value in enumerate(isort):
rsort[value] = idx
assert -1 not in rsort
return rsort