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_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])
