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# type: ignore
import os
import numpy as np
import numpy.testing
import unittest
import ase
import ase.build
import ase.io
from ase.io.vasp import write_vasp_xdatcar
from ase.calculators.calculator import compare_atoms
class TestXdatcarRoundtrip(unittest.TestCase):
def setUp(self):
self.outfile = 'NaCl.XDATCAR'
self.NaCl = ase.build.bulk('NaCl', 'rocksalt', a=5.64)
def tearDown(self):
if os.path.isfile(self.outfile):
os.remove(self.outfile)
def assert_atoms_almost_equal(self, atoms, other, tol=1e-15):
"""Compare two Atoms objects, raising AssertionError if different"""
system_changes = compare_atoms(atoms, other, tol=tol)
if len(system_changes) > 0:
raise AssertionError(
"Atoms objects differ by {}".format(', '.join(system_changes)))
def assert_trajectory_almost_equal(self, traj1, traj2):
self.assertEqual(len(traj1), len(traj2))
for image, other in zip(traj1, traj2):
self.assert_atoms_almost_equal(image, other)
def test_roundtrip(self):
# Create a series of translated cells
trajectory = [self.NaCl.copy() for i in range(5)]
for i, atoms in enumerate(trajectory):
atoms.set_scaled_positions(atoms.get_scaled_positions()
+ i * np.array([0.05, 0, 0.02]))
atoms.wrap()
ase.io.write(self.outfile, trajectory, format='vasp-xdatcar')
roundtrip_trajectory = ase.io.read(self.outfile, index=':')
self.assert_trajectory_almost_equal(trajectory, roundtrip_trajectory)
def test_roundtrip_single_atoms(self):
atoms = ase.build.bulk('Ge')
ase.io.write(self.outfile, atoms, format='vasp-xdatcar')
roundtrip_atoms = ase.io.read(self.outfile)
self.assert_atoms_almost_equal(atoms, roundtrip_atoms)
def test_typeerror(self):
with self.assertRaises(TypeError):
atoms = ase.build.bulk('Ge')
write_vasp_xdatcar(self.outfile, atoms)
with self.assertRaises(TypeError):
not_atoms = 1
ase.io.write(self.outfile, not_atoms, format='vasp-xdatcar')
with self.assertRaises(TypeError):
not_traj = [True, False, False]
ase.io.write(self.outfile, not_traj, format='vasp-xdatcar')
def test_wrap():
atoms = ase.build.bulk('Ge')
# Shift atomic positions to get negative coordinates
atoms.wrap(center=(-1, -1, -1))
atoms.write('POSCAR', direct=True, wrap=False)
new_atoms = ase.io.read('POSCAR')
assert np.allclose(atoms.positions, new_atoms.positions)
atoms.write('POSCAR', direct=True, wrap=True)
new_atoms = ase.io.read('POSCAR')
atoms.wrap()
assert np.allclose(atoms.positions, new_atoms.positions)
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