def test_as_dict(self): filepath = os.path.join(test_dir, 'vasprun.xml') vasprun = Vasprun(filepath) #Test that as_dict() is json-serializable self.assertIsNotNone(json.dumps(vasprun.as_dict())) self.assertEqual( vasprun.as_dict()["input"]["potcar_type"], ['PAW_PBE', 'PAW_PBE', 'PAW_PBE', 'PAW_PBE', 'PAW_PBE'])
def test_properties(self): filepath = os.path.join(test_dir, 'vasprun.xml') vasprun = Vasprun(filepath) #test pdos parsing pdos0 = vasprun.complete_dos.pdos[vasprun.final_structure[0]] self.assertAlmostEqual(pdos0[Orbital.s][1][16], 0.0026) self.assertAlmostEqual(pdos0[Orbital.pz][-1][16], 0.0012) self.assertEqual(pdos0[Orbital.s][1].shape, (301, )) filepath2 = os.path.join(test_dir, 'lifepo4.xml') vasprun_ggau = Vasprun(filepath2, parse_projected_eigen=True) totalscsteps = sum([len(i['electronic_steps']) for i in vasprun.ionic_steps]) self.assertEqual(29, len(vasprun.ionic_steps)) self.assertEqual(len(vasprun.structures), len(vasprun.ionic_steps)) self.assertEqual(vasprun.lattice, vasprun.lattice_rec.reciprocal_lattice) for i, step in enumerate(vasprun.ionic_steps): self.assertEqual(vasprun.structures[i], step["structure"]) self.assertTrue(all([vasprun.structures[i] == vasprun.ionic_steps[i][ "structure"] for i in range(len(vasprun.ionic_steps))])) self.assertEqual(308, totalscsteps, "Incorrect number of energies read from vasprun.xml") self.assertEqual(['Li'] + 4 * ['Fe'] + 4 * ['P'] + 16 * ["O"], vasprun.atomic_symbols) self.assertEqual(vasprun.final_structure.composition.reduced_formula, "LiFe4(PO4)4") self.assertIsNotNone(vasprun.incar, "Incar cannot be read") self.assertIsNotNone(vasprun.kpoints, "Kpoints cannot be read") self.assertIsNotNone(vasprun.eigenvalues, "Eigenvalues cannot be read") self.assertAlmostEqual(vasprun.final_energy, -269.38319884, 7) self.assertAlmostEqual(vasprun.tdos.get_gap(), 2.0589, 4) expectedans = (2.539, 4.0906, 1.5516, False) (gap, cbm, vbm, direct) = vasprun.eigenvalue_band_properties self.assertAlmostEqual(gap, expectedans[0]) self.assertAlmostEqual(cbm, expectedans[1]) self.assertAlmostEqual(vbm, expectedans[2]) self.assertEqual(direct, expectedans[3]) self.assertFalse(vasprun.is_hubbard) self.assertEqual(vasprun.potcar_symbols, ['PAW_PBE Li 17Jan2003', 'PAW_PBE Fe 06Sep2000', 'PAW_PBE Fe 06Sep2000', 'PAW_PBE P 17Jan2003', 'PAW_PBE O 08Apr2002']) self.assertIsNotNone(vasprun.kpoints, "Kpoints cannot be read") self.assertIsNotNone(vasprun.actual_kpoints, "Actual kpoints cannot be read") self.assertIsNotNone(vasprun.actual_kpoints_weights, "Actual kpoints weights cannot be read") for atomdoses in vasprun.pdos: for orbitaldos in atomdoses: self.assertIsNotNone(orbitaldos, "Partial Dos cannot be read") #test skipping ionic steps. vasprun_skip = Vasprun(filepath, 3) self.assertEqual(vasprun_skip.nionic_steps, 29) self.assertEqual(len(vasprun_skip.ionic_steps), int(vasprun.nionic_steps / 3) + 1) self.assertEqual(len(vasprun_skip.ionic_steps), len(vasprun_skip.structures)) self.assertEqual(len(vasprun_skip.ionic_steps), int(vasprun.nionic_steps / 3) + 1) #Check that nionic_steps is preserved no matter what. self.assertEqual(vasprun_skip.nionic_steps, vasprun.nionic_steps) self.assertNotAlmostEqual(vasprun_skip.final_energy, vasprun.final_energy) #Test with ionic_step_offset vasprun_offset = Vasprun(filepath, 3, 6) self.assertEqual(len(vasprun_offset.ionic_steps), int(len(vasprun.ionic_steps) / 3) - 1) self.assertEqual(vasprun_offset.structures[0], vasprun_skip.structures[2]) self.assertTrue(vasprun_ggau.is_hubbard) self.assertEqual(vasprun_ggau.hubbards["Fe"], 4.3) self.assertAlmostEqual(vasprun_ggau.projected_eigenvalues[(Spin.up, 0, 0, 96, Orbital.s)], 0.0032) d = vasprun_ggau.as_dict() self.assertEqual(d["elements"], ["Fe", "Li", "O", "P"]) self.assertEqual(d["nelements"], 4) filepath = os.path.join(test_dir, 'vasprun.xml.unconverged') vasprun_unconverged = Vasprun(filepath) self.assertTrue(vasprun_unconverged.converged_ionic) self.assertFalse(vasprun_unconverged.converged_electronic) self.assertFalse(vasprun_unconverged.converged) filepath = os.path.join(test_dir, 'vasprun.xml.dfpt') vasprun_dfpt = Vasprun(filepath) self.assertAlmostEqual(vasprun_dfpt.epsilon_static[0][0], 3.26105533) self.assertAlmostEqual(vasprun_dfpt.epsilon_static[0][1], -0.00459066) self.assertAlmostEqual(vasprun_dfpt.epsilon_static[2][2], 3.24330517) self.assertAlmostEqual(vasprun_dfpt.epsilon_static_wolfe[0][0], 3.33402531) self.assertAlmostEqual(vasprun_dfpt.epsilon_static_wolfe[0][1], -0.00559998) self.assertAlmostEqual(vasprun_dfpt.epsilon_static_wolfe[2][2], 3.31237357) self.assertTrue(vasprun_dfpt.converged) entry = vasprun_dfpt.get_computed_entry() entry = MaterialsProjectCompatibility().process_entry(entry) self.assertAlmostEqual(entry.uncorrected_energy + entry.correction, entry.energy) filepath = os.path.join(test_dir, 'vasprun.xml.dfpt.ionic') vasprun_dfpt_ionic = Vasprun(filepath) self.assertAlmostEqual(vasprun_dfpt_ionic.epsilon_ionic[0][0], 515.73485838) self.assertAlmostEqual(vasprun_dfpt_ionic.epsilon_ionic[0][1], -0.00263523) self.assertAlmostEqual(vasprun_dfpt_ionic.epsilon_ionic[2][2], 19.02110169) filepath = os.path.join(test_dir, 'vasprun.xml.dfpt.unconverged') vasprun_dfpt_unconv = Vasprun(filepath) self.assertFalse(vasprun_dfpt_unconv.converged_electronic) self.assertTrue(vasprun_dfpt_unconv.converged_ionic) self.assertFalse(vasprun_dfpt_unconv.converged) vasprun_uniform = Vasprun(os.path.join(test_dir, "vasprun.xml.uniform")) self.assertEqual(vasprun_uniform.kpoints.style, "Reciprocal") vasprun_no_pdos = Vasprun(os.path.join(test_dir, "Li_no_projected.xml")) self.assertIsNotNone(vasprun_no_pdos.complete_dos) self.assertFalse(vasprun_no_pdos.dos_has_errors)
def test_properties(self): filepath = os.path.join(test_dir, 'vasprun.xml') vasprun = Vasprun(filepath) #test pdos parsing pdos0 = vasprun.complete_dos.pdos[vasprun.final_structure[0]] self.assertAlmostEqual(pdos0[Orbital.s][1][16], 0.0026) self.assertAlmostEqual(pdos0[Orbital.pz][-1][16], 0.0012) self.assertEqual(pdos0[Orbital.s][1].shape, (301, )) filepath2 = os.path.join(test_dir, 'lifepo4.xml') vasprun_ggau = Vasprun(filepath2, parse_projected_eigen=True) totalscsteps = sum( [len(i['electronic_steps']) for i in vasprun.ionic_steps]) self.assertEqual(29, len(vasprun.ionic_steps)) self.assertEqual(len(vasprun.structures), len(vasprun.ionic_steps)) self.assertEqual(vasprun.lattice, vasprun.lattice_rec.reciprocal_lattice) for i, step in enumerate(vasprun.ionic_steps): self.assertEqual(vasprun.structures[i], step["structure"]) self.assertTrue( all([ vasprun.structures[i] == vasprun.ionic_steps[i]["structure"] for i in range(len(vasprun.ionic_steps)) ])) self.assertEqual(308, totalscsteps, "Incorrect number of energies read from vasprun.xml") self.assertEqual(['Li'] + 4 * ['Fe'] + 4 * ['P'] + 16 * ["O"], vasprun.atomic_symbols) self.assertEqual(vasprun.final_structure.composition.reduced_formula, "LiFe4(PO4)4") self.assertIsNotNone(vasprun.incar, "Incar cannot be read") self.assertIsNotNone(vasprun.kpoints, "Kpoints cannot be read") self.assertIsNotNone(vasprun.eigenvalues, "Eigenvalues cannot be read") self.assertAlmostEqual(vasprun.final_energy, -269.38319884, 7) self.assertAlmostEqual(vasprun.tdos.get_gap(), 2.0589, 4) expectedans = (2.539, 4.0906, 1.5516, False) (gap, cbm, vbm, direct) = vasprun.eigenvalue_band_properties self.assertAlmostEqual(gap, expectedans[0]) self.assertAlmostEqual(cbm, expectedans[1]) self.assertAlmostEqual(vbm, expectedans[2]) self.assertEqual(direct, expectedans[3]) self.assertFalse(vasprun.is_hubbard) self.assertEqual(vasprun.potcar_symbols, [ 'PAW_PBE Li 17Jan2003', 'PAW_PBE Fe 06Sep2000', 'PAW_PBE Fe 06Sep2000', 'PAW_PBE P 17Jan2003', 'PAW_PBE O 08Apr2002' ]) self.assertIsNotNone(vasprun.kpoints, "Kpoints cannot be read") self.assertIsNotNone(vasprun.actual_kpoints, "Actual kpoints cannot be read") self.assertIsNotNone(vasprun.actual_kpoints_weights, "Actual kpoints weights cannot be read") for atomdoses in vasprun.pdos: for orbitaldos in atomdoses: self.assertIsNotNone(orbitaldos, "Partial Dos cannot be read") #test skipping ionic steps. vasprun_skip = Vasprun(filepath, 3) self.assertEqual(vasprun_skip.nionic_steps, 29) self.assertEqual(len(vasprun_skip.ionic_steps), int(vasprun.nionic_steps / 3) + 1) self.assertEqual(len(vasprun_skip.ionic_steps), len(vasprun_skip.structures)) self.assertEqual(len(vasprun_skip.ionic_steps), int(vasprun.nionic_steps / 3) + 1) #Check that nionic_steps is preserved no matter what. self.assertEqual(vasprun_skip.nionic_steps, vasprun.nionic_steps) self.assertNotAlmostEqual(vasprun_skip.final_energy, vasprun.final_energy) #Test with ionic_step_offset vasprun_offset = Vasprun(filepath, 3, 6) self.assertEqual(len(vasprun_offset.ionic_steps), int(len(vasprun.ionic_steps) / 3) - 1) self.assertEqual(vasprun_offset.structures[0], vasprun_skip.structures[2]) self.assertTrue(vasprun_ggau.is_hubbard) self.assertEqual(vasprun_ggau.hubbards["Fe"], 4.3) self.assertAlmostEqual( vasprun_ggau.projected_eigenvalues[(Spin.up, 0, 0, 96, Orbital.s)], 0.0032) d = vasprun_ggau.as_dict() self.assertEqual(d["elements"], ["Fe", "Li", "O", "P"]) self.assertEqual(d["nelements"], 4) filepath = os.path.join(test_dir, 'vasprun.xml.unconverged') vasprun_unconverged = Vasprun(filepath) self.assertTrue(vasprun_unconverged.converged_ionic) self.assertFalse(vasprun_unconverged.converged_electronic) self.assertFalse(vasprun_unconverged.converged) filepath = os.path.join(test_dir, 'vasprun.xml.dfpt') vasprun_dfpt = Vasprun(filepath) self.assertAlmostEqual(vasprun_dfpt.epsilon_static[0][0], 3.26105533) self.assertAlmostEqual(vasprun_dfpt.epsilon_static[0][1], -0.00459066) self.assertAlmostEqual(vasprun_dfpt.epsilon_static[2][2], 3.24330517) self.assertAlmostEqual(vasprun_dfpt.epsilon_static_wolfe[0][0], 3.33402531) self.assertAlmostEqual(vasprun_dfpt.epsilon_static_wolfe[0][1], -0.00559998) self.assertAlmostEqual(vasprun_dfpt.epsilon_static_wolfe[2][2], 3.31237357) self.assertTrue(vasprun_dfpt.converged) entry = vasprun_dfpt.get_computed_entry() entry = MaterialsProjectCompatibility().process_entry(entry) self.assertAlmostEqual(entry.uncorrected_energy + entry.correction, entry.energy) filepath = os.path.join(test_dir, 'vasprun.xml.dfpt.ionic') vasprun_dfpt_ionic = Vasprun(filepath) self.assertAlmostEqual(vasprun_dfpt_ionic.epsilon_ionic[0][0], 515.73485838) self.assertAlmostEqual(vasprun_dfpt_ionic.epsilon_ionic[0][1], -0.00263523) self.assertAlmostEqual(vasprun_dfpt_ionic.epsilon_ionic[2][2], 19.02110169) filepath = os.path.join(test_dir, 'vasprun.xml.dfpt.unconverged') vasprun_dfpt_unconv = Vasprun(filepath) self.assertFalse(vasprun_dfpt_unconv.converged_electronic) self.assertTrue(vasprun_dfpt_unconv.converged_ionic) self.assertFalse(vasprun_dfpt_unconv.converged) vasprun_uniform = Vasprun(os.path.join(test_dir, "vasprun.xml.uniform")) self.assertEqual(vasprun_uniform.kpoints.style, "Reciprocal") vasprun_no_pdos = Vasprun(os.path.join(test_dir, "Li_no_projected.xml")) self.assertIsNotNone(vasprun_no_pdos.complete_dos) self.assertFalse(vasprun_no_pdos.dos_has_errors) vasprun_diel = Vasprun(os.path.join(test_dir, "vasprun.xml.dielectric")) self.assertAlmostEqual(0.4294, vasprun_diel.dielectric[0][10]) self.assertAlmostEqual(19.941, vasprun_diel.dielectric[1][51][0]) self.assertAlmostEqual(19.941, vasprun_diel.dielectric[1][51][1]) self.assertAlmostEqual(19.941, vasprun_diel.dielectric[1][51][2]) self.assertAlmostEqual(0.0, vasprun_diel.dielectric[1][51][3]) self.assertAlmostEqual(34.186, vasprun_diel.dielectric[2][85][0]) self.assertAlmostEqual(34.186, vasprun_diel.dielectric[2][85][1]) self.assertAlmostEqual(34.186, vasprun_diel.dielectric[2][85][2]) self.assertAlmostEqual(0.0, vasprun_diel.dielectric[2][85][3])