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_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_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())