def test_temperature(self):
mf = MolecularFrame('Li crystal').import_from(make_supercell_li())
mf.temperature = 50.0
self.assertAlmostEqual(mf.temperature, 50.0)
with self.assertRaises(AssertionError):
mf.temperature = 0 # T > 0
def test_center_of_mass(self):
mf = MolecularFrame('Li crystal').import_from(make_supercell_li())
for i in range(3):
self.assertAlmostEqual(mf.center_of_mass[i], 16.672499, 5)
# Set COM to center
mf.center_of_mass = (0, 0, 0)
for i in range(3):
self.assertAlmostEqual(mf.center_of_mass[i], 0)
def test_molecular_frame_clone(self):
mf = MolecularFrame('Li crystal').import_from(make_supercell_li())
mf_clone = mf.clone()
mf.atoms_section.atoms[
0].x = 1.0 # make a change to the first atom in mf
self.assertIsInstance(mf_clone, MolecularFrame)
self.assertTrue(not mf_clone.atoms_section.atoms[0].x ==
mf.atoms_section.atoms[0].x)
self.assertEqual(mf_clone.atoms_section.atoms[0].y,
mf.atoms_section.atoms[0].y)
def test_molecular_frame_equal(self):
mf = MolecularFrame('Cu crystal').import_from(make_supercell_cu())
new_mf = mf # equal operator
self.assertEqual(new_mf.get_number_of_atoms(),
mf.get_number_of_atoms())
self.assertEqual(new_mf.name, mf.name)
self.assertEqual(new_mf.atoms_section.atoms[1].x,
mf.atoms_section.atoms[1].x) # atom x position
self.assertEqual(
new_mf.atoms_section.atoms[1].symbol,
mf.atoms_section.atoms[1].symbol) # second atom symbol
def test_molecular_frame_select_region(self):
def sphere(x, y, z):
"""sphere region"""
if np.sqrt(x**2 + y**2 + z**2) < 7.0:
return True
else:
return False
mf = MolecularFrame('Li crystal').import_from(make_supercell_li())
sel_mf = mf.select(SelectRegion(sphere))
self.assertIsInstance(sel_mf, MolecularFrame)
self.assertEqual(sel_mf.get_number_of_atoms(), 12)
def test_molecular_frame_formatter(self):
mf1 = MolecularFrame('Cu crystal').import_from(make_supercell_cu())
filename = "cu_pytest.xyz"
mf1.write(filename)
mf2 = MolecularFrame().read(filename)
self.assertEqual(mf1.get_number_of_atoms(), mf2.get_number_of_atoms())
os.system("rm -f %s" % filename)
def test_molecular_frame_plus(self):
mf1 = MolecularFrame('Cu crystal').import_from(make_supercell_cu())
mf2 = MolecularFrame('Li crystal').import_from(make_supercell_li())
mf = mf1 + mf2 # plus operator
self.assertIsInstance(mf, MolecularFrame)
self.assertTrue(mf1.name in mf.name and mf2.name in mf.name)
self.assertEqual(mf.get_number_of_atoms(),
mf1.get_number_of_atoms() + mf2.get_number_of_atoms())
def test_molecular_frame_import_ase(self):
mf = MolecularFrame('Cu crystal')
mf.import_from(package_instance=make_supercell_cu(),
package_name="ASE")
self.assertEqual(mf.get_number_of_atoms(),
make_supercell_cu().get_number_of_atoms())
self.assertEqual(mf.name, 'Cu crystal')
self.assertAlmostEqual(
mf.atoms_section.atoms[1].x,
make_supercell_cu().get_positions()[1][0]) # 2nd atom
self.assertEqual(mf.get_atoms_section().atoms[1].symbol,
'Cu') # second atom symbol
def test_molecular_frame_adaptor(self):
mf1 = MolecularFrame('Cu crystal').import_from(make_supercell_cu())
mf2 = MolecularFrame().import_from(mf1.export())
self.assertEqual(mf1.get_number_of_atoms(), mf2.get_number_of_atoms())
self.assertTrue(Atoms().name in mf2.get_sections_name())
self.assertTrue(Box().name in mf2.get_sections_name())
def test_molecular_frame(self):
mf = MolecularFrame()
self.assertIsInstance(mf, MolecularFrame)
self.assertEqual(mf.name, 'Molecular Frame')