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"""Module to read atoms in chemical json file format.
https://wiki.openchemistry.org/Chemical_JSON
"""
import json
import numpy as np
from ase import Atoms
from ase.cell import Cell
# contract and lower case string
def contract(dictionary):
dcopy = {}
for key in dictionary:
dcopy[key.replace(' ', '').lower()] = dictionary[key]
return dcopy
def read_cml(fileobj):
data = contract(json.load(fileobj))
atoms = Atoms()
datoms = data['atoms']
atoms = Atoms(datoms['elements']['number'])
if 'unitcell' in data:
cell = data['unitcell']
a = cell['a']
b = cell['b']
c = cell['c']
alpha = cell['alpha']
beta = cell['beta']
gamma = cell['gamma']
atoms.cell = Cell.fromcellpar([a, b, c, alpha, beta, gamma])
atoms.pbc = True
coords = contract(datoms['coords'])
if '3d' in coords:
positions = np.array(coords['3d']).reshape(len(atoms), 3)
atoms.set_positions(positions)
else:
positions = np.array(coords['3dfractional']).reshape(len(atoms), 3)
atoms.set_scaled_positions(positions)
yield atoms
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