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"""Tests related to QBOX"""
import numpy as np
import pytest
from ase import Atoms
from ase.io import qbox
from ase.io import formats
@pytest.fixture
def qboxfile(datadir):
return datadir / 'qbox_test.xml'
@pytest.fixture
def qballfile(datadir):
return datadir / 'qbox_04_md_ntc.reference.xml'
def test_read_output(qboxfile):
"""Test reading the output file"""
# Read only one frame
atoms = qbox.read_qbox(qboxfile)
assert isinstance(atoms, Atoms)
assert np.allclose(atoms.cell, np.diag([16, 16, 16]))
assert len(atoms) == 4
assert np.allclose(atoms[0].position,
[3.70001108, -0.00000000, -0.00000003],
atol=1e-7) # Last frame
assert np.allclose(atoms.get_velocities()[2],
[-0.00000089, -0.00000000, -0.00000000],
atol=1e-9) # Last frame
assert np.allclose(atoms.get_forces()[3],
[-0.00000026, -0.01699708, 0.00000746],
atol=1e-7) # Last frame
assert np.isclose(-15.37294664, atoms.get_potential_energy())
assert np.allclose(atoms.get_stress(),
[-0.40353661, -1.11698386, -1.39096418,
0.00001786, -0.00002405, -0.00000014])
# Read all the frames
atoms = qbox.read_qbox(qboxfile, slice(None))
assert isinstance(atoms, list)
assert len(atoms) == 5
assert len(atoms[1]) == 4
assert np.allclose(atoms[1][0].position,
[3.70001108, -0.00000000, -0.00000003],
atol=1e-7) # 2nd frame
assert np.allclose(atoms[1].get_forces()[3],
[-0.00000029, -0.01705361, 0.00000763],
atol=1e-7) # 2nd frame
def test_format(qboxfile, qballfile):
"""Make sure the `formats.py` operations work"""
atoms = formats.read(qboxfile)
assert len(atoms) == 4
atoms = formats.read(qboxfile, index=slice(None), format='qbox')
assert len(atoms) == 5
atoms = formats.read(qballfile)
assert len(atoms) == 32
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