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from ase.io.jsonio import encode, decode
from ase.build import bulk, molecule
import numpy as np
def test_jsonio_atoms():
def assert_equal(atoms1, atoms2):
assert atoms1 == atoms2
assert set(atoms1.arrays) == set(atoms2.arrays)
for name in atoms1.arrays:
assert np.array_equal(atoms1.arrays[name], atoms2.arrays[name]), name
atoms = bulk('Ti')
print('atoms', atoms)
txt = encode(atoms)
print('encoded', txt)
atoms1 = decode(txt)
print('decoded', atoms1)
txt1 = encode(atoms1)
assert txt == txt1
assert_equal(atoms, atoms1)
BeH = molecule('BeH')
assert BeH.has('initial_magmoms')
new_BeH = decode(encode(BeH))
assert_equal(BeH, new_BeH)
assert new_BeH.has('initial_magmoms')
from ase.constraints import FixAtoms
atoms = bulk('Ti')
atoms.constraints = FixAtoms(indices=[0])
newatoms = decode(encode(atoms))
c1 = atoms.constraints
c2 = newatoms.constraints
assert len(c1) == len(c2) == 1
# Can we check constraint equality somehow?
# Would make sense for FixAtoms
assert np.array_equal(c1[0].index, c2[0].index)
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