def test_array_shape(at):
# Check that unashable data type in info does not break output
at.info['bad-info'] = [[1, np.array([0, 1])], [2, np.array([0, 1])]]
with no_warn():
ase.io.write('to.xyz', at, format='extxyz')
del at.info['bad-info']
at.arrays['ns_extra_data'] = np.zeros((len(at), 1))
assert at.arrays['ns_extra_data'].shape == (2, 1)
ase.io.write('to_new.xyz', at, format='extxyz')
at_new = ase.io.read('to_new.xyz')
assert at_new.arrays['ns_extra_data'].shape == (2, )
import os
import numpy as np
import ase.io
from ase.io import extxyz
from ase.atoms import Atoms
from ase.build import bulk
from ase.test.testsuite import no_warn
# array data of shape (N, 1) squeezed down to shape (N, ) -- bug fixed
# in commit r4541
at = bulk('Si')
# Check that unashable data type in info does not break output
at.info['bad-info'] = [[1, np.array([0, 1])], [2, np.array([0, 1])]]
with no_warn():
ase.io.write('to.xyz', at, format='extxyz', tolerant=True)
del at.info['bad-info']
at.arrays['ns_extra_data'] = np.zeros((len(at), 1))
assert at.arrays['ns_extra_data'].shape == (2, 1)
ase.io.write('to_new.xyz', at, format='extxyz')
at_new = ase.io.read('to_new.xyz')
assert at_new.arrays['ns_extra_data'].shape == (2, )
os.unlink('to.xyz')
os.unlink('to_new.xyz')
#test comment read/write with vec_cell
at.info['comment'] = 'test comment'
ase.io.write('comment.xyz', at, comment=at.info['comment'], vec_cell=True)