How to use the pyiron.atomistics.structure.atoms.CrystalStructure function in pyiron

def test_get_positions(self):
        basis_Mg = CrystalStructure("Mg", bravais_basis="fcc", lattice_constant=4.2)
        self.assertTrue(np.array_equal(basis_Mg.positions, basis_Mg.get_positions()))

def test_apply_strain(self):
        basis_Fe = CrystalStructure("Fe", bravais_basis="bcc", lattice_constants=2.85)
        with self.assertRaises(ValueError):
            basis_Fe.apply_strain(-2)
        basis_new = basis_Fe.apply_strain(0.01, return_box=True)
        self.assertAlmostEqual(basis_new.cell[0,0], 2.85*1.01)
        self.assertAlmostEqual(basis_new.positions[1,0], 0.5*2.85*1.01)
        self.assertAlmostEqual(basis_Fe.cell[0,0], 2.85)
        basis_Fe.apply_strain(0.01)
        self.assertAlmostEqual(basis_Fe.cell[0,0], 2.85*1.01)

self.assertEqual(self.C3[2].position.tolist(), [0, 2, 0])
        self.assertTrue(
            (self.C3[1:].positions == np.array([[0, 0, 2], [0, 2, 0]])).all()
        )
        short_basis = self.CO2[0]
        self.assertIsInstance(short_basis, Atom)
        short_basis = self.CO2[[0]]
        self.assertIsInstance(short_basis, Atoms)
        self.assertEqual(short_basis.indices[0], 0)
        self.assertEqual(len(short_basis.species), 1)
        short_basis = self.CO2[[2]]
        self.assertIsInstance(short_basis, Atoms)
        self.assertEqual(short_basis.indices[0], 0)
        self.assertEqual(len(short_basis.species), 1)
        basis_Mg = CrystalStructure("Mg", bravais_basis="fcc", lattice_constant=4.2)
        basis_O = CrystalStructure("O", bravais_basis="fcc", lattice_constant=4.2)
        basis_O.positions += [0.0, 0.0, 0.5]
        basis = basis_Mg + basis_O
        basis.center_coordinates_in_unit_cell()
        basis.set_repeat([3, 3, 3])
        mg_indices = basis.select_index("Mg")
        o_indices = basis.select_index("O")
        basis_new = basis[mg_indices] + basis[o_indices]
        self.assertEqual(
            len(basis_new._tag_list), len(basis[mg_indices]) + len(basis[o_indices])
        )
        self.assertEqual(basis_new.get_spacegroup()["Number"], 225)

def test_parent_index(self):
        basis_Mg = CrystalStructure("Mg", bravais_basis="fcc", lattice_constant=4.2)
        basis_O = CrystalStructure("O", bravais_basis="fcc", lattice_constant=4.2)
        basis_O.positions += [0.0, 0.0, 0.5]
        basis = basis_Mg + basis_O
        basis.center_coordinates_in_unit_cell()
        basis.set_repeat([2, 2, 2])
        o_indices = basis.select_index("O")
        pse = PeriodicTable()
        pse.add_element("O", "O_up", spin="up")
        o_up = pse.element("O_up")
        basis[o_indices] = o_up
        self.assertTrue(np.array_equal(o_indices, basis.select_index(o_up)))
        self.assertEqual(len(basis.select_index("O")), 0)
        self.assertTrue(np.array_equal(o_indices, basis.select_parent_index("O")))

def test_set_structure(self):
        self.assertEqual(self.job.structure, None)
        atoms = CrystalStructure("Pt", BravaisBasis="fcc", a=3.98)
        self.job.structure = atoms
        self.assertEqual(self.job.structure, atoms)
        self.job.structure = None
        self.assertEqual(self.job.structure, None)
        self.job.structure = atoms
        self.assertEqual(self.job.structure, atoms)

def test_apply_strain(self):
        basis_Fe = CrystalStructure("Fe", bravais_basis="bcc", lattice_constants=2.85)
        with self.assertRaises(ValueError):
            basis_Fe.apply_strain(-2)
        basis_new = basis_Fe.apply_strain(0.01, return_box=True)
        self.assertAlmostEqual(basis_new.cell[0,0], 2.85*1.01)
        self.assertAlmostEqual(basis_new.positions[1,0], 0.5*2.85*1.01)
        self.assertAlmostEqual(basis_Fe.cell[0,0], 2.85)
        basis_Fe.apply_strain(0.01)
        self.assertAlmostEqual(basis_Fe.cell[0,0], 2.85*1.01)

def test_repeat(self):
        basis_Mg = CrystalStructure("Mg", bravais_basis="fcc", lattice_constant=4.2)
        basis_O = CrystalStructure("O", bravais_basis="fcc", lattice_constant=4.2)
        basis_O.set_scaled_positions(basis_O.get_scaled_positions() + [0.0, 0.0, 0.5])
        basis = basis_Mg + basis_O
        basis.center_coordinates_in_unit_cell()
        basis.add_tag(selective_dynamics=[True, True, True])
        basis.selective_dynamics[basis.select_index("O")] = [False, False, False]
        len_before = len(basis)
        sel_dyn_before = np.array(basis.selective_dynamics.list())
        self.assertTrue(
            np.alltrue(
                np.logical_not(
                    np.alltrue(sel_dyn_before[basis.select_index("O")], axis=1)
                )
            )
        )
        self.assertTrue(
            np.alltrue(np.alltrue(sel_dyn_before[basis.select_index("Mg")], axis=1))

def setUpClass(cls):
        cls.file_location = os.path.dirname(os.path.abspath(__file__))
        cls.project = Project(os.path.join(cls.file_location, 'testing_murnaghan_non_modal'))
        cls.basis = CrystalStructure(element="Fe", bravais_basis='bcc', lattice_constant=2.8)
        cls.project.remove_jobs(recursive=True)
        # cls.project.remove_jobs(recursive=True)

def test_get_scaled_positions(self):
        basis_Mg = CrystalStructure("Mg", bravais_basis="fcc", lattice_constant=4.2)
        basis_Mg.set_cell(basis_Mg.cell+0.1 * np.random.random((3, 3)))
        basis_Mg = basis_Mg.center_coordinates_in_unit_cell()
        self.assertTrue(
            np.allclose(
                np.dot(np.linalg.inv(basis_Mg.cell).T, basis_Mg.positions.T).T,
                basis_Mg.get_scaled_positions(),
            )

lat_0[:] = "V"
        self.assertEqual(lat_0.get_chemical_formula(), "V108")
        lat_0[[1, 3, 5]] = "Mg"  # direct occupation
        self.assertEqual(lat_0.get_chemical_formula(), "Mg3V105")
        # lat_0[[0]] = 'V'                     # vacancy (note: do not delete atom)
        lat_1 = lat_0.copy()
        lat_1.set_scaled_positions(1 / 4 + lat_1.get_scaled_positions())
        lat_1[:] = "V"
        self.assertEqual(lat_1.get_chemical_formula(), "V108")
        lat_1[[1, 4, 9]] = "H"
        lat_1[[2, 5, 8]] = "C"
        self.assertEqual(lat_1.get_chemical_formula(), "C3H3V102")
        lat_1.set_scaled_positions(1 / 4 + lat_1.get_scaled_positions())
        lat_1[:] = "V"  # vacancies
        self.assertEqual(lat_1.get_chemical_formula(), "V108")
        basis_Mg = CrystalStructure("Mg", bravais_basis="fcc", lattice_constant=4.2)
        basis_Mg.set_repeat(3)
        basis_Mg[:-3] = "Al"
        self.assertEqual(basis_Mg.get_chemical_formula(), 'Al105Mg3')
        basis_Mg[4:-len(basis_Mg)+7] = "C"
        self.assertEqual(basis_Mg.get_chemical_formula(), 'Al102C3Mg3')
        basis_Mg[4:] = "C"
        self.assertEqual(basis_Mg.get_chemical_formula(), 'Al4C104')
        basis_Mg[:] = "Mg"
        self.assertEqual(basis_Mg.get_chemical_formula(), 'Mg108')
        basis_Mg[::2] = "Al"
        self.assertEqual(basis_Mg.get_chemical_formula(), 'Al54Mg54')
        struct = CrystalStructure("Al", bravais_basis="fcc", lattice_constant=4.2, bravais_lattice="cubic")
        struct[0] = 'Mg'
        self.assertEqual(struct.get_chemical_formula(), 'Al3Mg')
        struct[1] = 'Cu'
        self.assertEqual(struct.get_chemical_formula(), 'Al2CuMg')