def setUp(self):
self.file_location = os.path.dirname(os.path.abspath(__file__))
self.file_list = list()
self.outcar_parser = Outcar()
# file_list = ["OUTCAR_1", "OUTCAR_2", "OUTCAR_3", "OUTCAR_4", "OUTCAR_5", "OUTCAR_6", "OUTCAR_7"]
file_list = os.listdir(os.path.abspath(os.path.join(self.file_location,
"../static/vasp_test_files/outcar_samples")))
for f in file_list:
direc = os.path.abspath(os.path.join(self.file_location,
"../static/vasp_test_files/outcar_samples"))
filename = posixpath.join(direc, f)
self.file_list.append(filename)
def interactive_fetch(self):
if self._interactive_fetch_completed and self.server.run_mode.interactive_non_modal:
print('First run and then fetch')
else:
self._interactive_check_output()
self._interactive_vasprun = Outcar()
super(VaspInteractive, self).interactive_collect()
self._logger.debug('interactive run - done')
def run_if_interactive(self):
self.run_if_interactive_non_modal()
self._interactive_check_output()
self._interactive_vasprun = Outcar()
self.interactive_collect()
class TestOutcar(unittest.TestCase):
def setUp(self):
self.file_location = os.path.dirname(os.path.abspath(__file__))
self.file_list = list()
self.outcar_parser = Outcar()
# file_list = ["OUTCAR_1", "OUTCAR_2", "OUTCAR_3", "OUTCAR_4", "OUTCAR_5", "OUTCAR_6", "OUTCAR_7"]
file_list = os.listdir(os.path.abspath(os.path.join(self.file_location,
"../static/vasp_test_files/outcar_samples")))
for f in file_list:
direc = os.path.abspath(os.path.join(self.file_location,
"../static/vasp_test_files/outcar_samples"))
filename = posixpath.join(direc, f)
self.file_list.append(filename)
def test_from_file(self):
for filename in self.file_list:
self.outcar_parser.from_file(filename=filename)
type_dict = dict()
type_dict["energies"] = np.ndarray
type_dict["scf_energies"] = list
type_dict["forces"] = np.ndarray
type_dict["positions"] = np.ndarray
type_dict["cells"] = np.ndarray
type_dict["steps"] = np.ndarray
type_dict["temperatures"] = np.ndarray
type_dict["time"] = np.ndarray
type_dict["fermi_level"] = float
type_dict["scf_dipole_moments"] = list
type_dict["kin_energy_error"] = float
type_dict["stresses"] = np.ndarray
type_dict["irreducible_kpoints"] = tuple
type_dict["pressures"] = np.ndarray
type_dict["energies_int"] = np.ndarray
type_dict["energies_zero"] = np.ndarray
parse_keys = self.outcar_parser.parse_dict.keys()
for key, value in type_dict.items():
self.assertTrue(key in parse_keys)
try:
self.assertIsInstance(self.outcar_parser.parse_dict[key], value)
except AssertionError:
if int(filename.split('/OUTCAR_')[-1]) == 8:
self.assertEqual(key, "fermi_level")
else:
print(key, self.outcar_parser.parse_dict[key])
raise AssertionError("{} has the wrong type".format(key))
def test_get_positions_and_forces(self):
for filename in self.file_list:
output = self.outcar_parser.get_positions_and_forces(filename)
self.assertIsInstance(output[0], np.ndarray)
self.assertIsInstance(output[1], np.ndarray)
self.assertEqual(len(output[0]), len(output[1]))
if int(filename.split('/OUTCAR_')[-1]) == 1:
positions = np.array([[[0., 0., 0.], [1.85, 1.85, 0.], [1.85, 0., 1.85], [0., 1.85, 1.85]]])
forces = np.array([[[-0., 0., 0.], [-0., 0., 0.], [0., 0., 0.], [0., -0., -0.]]])
self.assertEqual(positions.__str__(), output[0].__str__())
self.assertEqual(forces.__str__(), output[1].__str__())
if int(filename.split('/OUTCAR_')[-1]) == 2:
positions = np.array([[[0., 0., 0.], [1.4, 1.4, 1.4]]])
forces = np.array([[[-0., 0., 0.], [0., -0., -0.]]])
self.assertEqual(positions.__str__(), output[0].__str__())
self.assertEqual(forces.__str__(), output[1].__str__())
if int(filename.split('/OUTCAR_')[-1]) == 3 \
or int(filename.split('/OUTCAR_')[-1]) == 5 \
or int(filename.split('/OUTCAR_')[-1]) == 6:
positions = np.array([[[0., 0., 0.], [1.4, 1.4, 1.4]]])
forces = np.array([[[0., -0., 0.], [-0., 0., -0.]]])
self.assertEqual(positions.__str__(), output[0].__str__())
self.assertEqual(forces.__str__(), output[1].__str__())
if int(filename.split('/OUTCAR_')[-1]) == 4:
positions = np.array([[[0., 0., 0.], [1.4, 1.4, 1.4]]])
forces = np.array([[[-0., -0., 0.], [0., 0., 0.]]])
self.assertEqual(positions.__str__(), output[0].__str__())
self.assertEqual(forces.__str__(), output[1].__str__())
def test_get_positions(self):
for filename in self.file_list:
output = self.outcar_parser.get_positions(filename)
self.assertIsInstance(output, np.ndarray)
if int(filename.split('/OUTCAR_')[-1]) == 1:
positions = np.array([[[0., 0., 0.], [1.85, 1.85, 0.], [1.85, 0., 1.85], [0., 1.85, 1.85]]])
self.assertEqual(positions.__str__(), output.__str__())
if int(filename.split('/OUTCAR_')[-1]) in [2, 3, 4, 5, 6]:
positions = np.array([[[0., 0., 0.], [1.4, 1.4, 1.4]]])
self.assertEqual(positions.__str__(), output.__str__())
def test_get_forces(self):
for filename in self.file_list:
output = self.outcar_parser.get_forces(filename)
self.assertIsInstance(output, np.ndarray)
if int(filename.split('/OUTCAR_')[-1]) == 1:
forces = np.array([[[-0., 0., 0.], [-0., 0., 0.], [0., 0., 0.], [0., -0., -0.]]])
self.assertEqual(forces.__str__(), output.__str__())
if int(filename.split('/OUTCAR_')[-1]) == 2:
forces = np.array([[[-0., 0., 0.], [0., -0., -0.]]])
self.assertEqual(forces.__str__(), output.__str__())
if int(filename.split('/OUTCAR_')[-1]) in [3, 5, 6]:
forces = np.array([[[0., -0., 0.], [-0., 0., -0.]]])
self.assertEqual(forces.__str__(), output.__str__())
if int(filename.split('/OUTCAR_')[-1]) == 4:
forces = np.array([[[-0., -0., 0.], [0., 0., 0.]]])
self.assertEqual(forces.__str__(), output.__str__())
def test_get_cells(self):
for filename in self.file_list:
output = self.outcar_parser.get_cells(filename)
self.assertIsInstance(output, np.ndarray)
if int(filename.split('/OUTCAR_')[-1]) == 1:
cells = np.array([[[3.7, 0., 0.], [0., 3.7, 0.], [0., 0., 3.7]]])
self.assertEqual(cells.__str__(), output.__str__())
if int(filename.split('/OUTCAR_')[-1]) in [2, 4, 5, 6]:
cells = np.array([[[2.8, 0., 0.], [0., 2.8, 0.], [0., 0., 2.8]]])
self.assertEqual(cells.__str__(), output.__str__())
def test_get_total_energies(self):
for filename in self.file_list:
output = self.outcar_parser.get_total_energies(filename)
self.assertIsInstance(output, np.ndarray)
if int(filename.split('/OUTCAR_')[-1]) == 1:
energies = np.array([-24.59765979])
self.assertEqual(energies.__str__(), output.__str__())
if int(filename.split('/OUTCAR_')[-1]) == 2:
energies = np.array([-17.73798679])
self.assertEqual(energies.__str__(), output.__str__())
if int(filename.split('/OUTCAR_')[-1]) in [3, 4]:
energies = np.array([-18.40140804])
self.assertEqual(energies.__str__(), output.__str__())
if int(filename.split('/OUTCAR_')[-1]) in [5, 6]:
energies = np.array([-18.40218607])
self.assertEqual(energies.__str__(), output.__str__())
def test_get_all_total_energies(self):
for filename in self.file_list:
output = self.outcar_parser.get_all_total_energies(filename)
self.assertIsInstance(output, list)
self.assertIsInstance(output[-1], np.ndarray)
if int(filename.split('/OUTCAR_')[-1]) == 1:
energies = np.array([164.50346113, -22.34826105, -29.05044151, -29.09407035, -29.0944954, -27.08800718,
-24.63733705, -24.60427656, -24.59776189, -24.59765131, -24.59765979])
self.assertEqual(energies.__str__(), output[0].__str__())
if int(filename.split('/OUTCAR_')[-1]) == 2:
energies = np.array([49.31292902, -18.6411937, -20.8983855, -20.92056153, -20.92073722,
-17.95357529, -17.76756585, -17.739524, -17.7379502, -17.73798679])
self.assertEqual(energies.__str__(), output[0].__str__())
if int(filename.split('/OUTCAR_')[-1]) in [3, 4]:
energies = np.array([44.19769573, -19.71777011, -20.86598567, -20.87149728, -20.87156762, -18.51206993,
-18.43794441, -18.41311659, -18.40310749, -18.4014402, -18.40140804])
self.assertEqual(energies.__str__(), output[0].__str__())
if int(filename.split('/OUTCAR_')[-1]) in [5, 6]:
energies = np.array([ 69.15405871, -18.00103756, -20.85032272, -20.87198829, -20.87222361, -18.51305208,
-18.43873509, -18.41390999, -18.40387841, -18.40222137, -18.40218607])
self.assertEqual(energies.__str__(), output[0].__str__())
def test_get_energy_without_entropy(self):
for filename in self.file_list:
output = self.outcar_parser.get_energy_without_entropy(filename)
energy_tot = self.outcar_parser.get_total_energies(filename)
self.assertIsInstance(output, np.ndarray)
self.assertEqual(len(energy_tot), len(output))
def test_get_energy_sigma_0(self):
for filename in self.file_list:
output = self.outcar_parser.get_energy_sigma_0(filename)
energy_tot = self.outcar_parser.get_total_energies(filename)
self.assertIsInstance(output, np.ndarray)
self.assertEqual(len(energy_tot), len(output))
def test_get_temperatures(self):
for filename in self.file_list:
output = self.outcar_parser.get_temperatures(filename)
self.assertIsInstance(output, np.ndarray)
if int(filename.split('/OUTCAR_')[-1]) in [1, 2, 3, 4, 5, 6]:
temperatures = np.array([ 0.])
self.assertEqual(temperatures.__str__(), output.__str__())
def test_get_steps(self):
for filename in self.file_list:
output = self.outcar_parser.get_steps(filename)
self.assertIsInstance(output, np.ndarray)
if int(filename.split('/OUTCAR_')[-1]) in [1, 2, 3, 4, 5, 6]:
steps = np.array([0., 0.02040816, 0.04081633, 0.06122449, 0.08163265, 0.10204082, 0.12244898, 0.14285714,
0.16326531, 0.18367347, 0.20408163, 0.2244898, 0.24489796, 0.26530612, 0.28571429,
0.30612245, 0.32653061, 0.34693878, 0.36734694, 0.3877551, 0.40816327, 0.42857143,
0.44897959, 0.46938776, 0.48979592, 0.51020408, 0.53061224, 0.55102041, 0.57142857,
0.59183673, 0.6122449, 0.63265306, 0.65306122, 0.67346939, 0.69387755, 0.71428571,
0.73469388, 0.75510204, 0.7755102, 0.79591837, 0.81632653, 0.83673469, 0.85714286,
0.87755102, 0.89795918, 0.91836735, 0.93877551, 0.95918367, 0.97959184, 1.])
self.assertEqual(steps.__str__(), output.__str__())
def test_get_time(self):
for filename in self.file_list:
output = self.outcar_parser.get_time(filename)
self.assertIsInstance(output, np.ndarray)
if int(filename.split('/OUTCAR_')[-1]) in [1, 2, 3, 4, 5, 6]:
time = np.array([0., 0.02040816, 0.04081633, 0.06122449, 0.08163265, 0.10204082, 0.12244898, 0.14285714,
0.16326531, 0.18367347, 0.20408163, 0.2244898, 0.24489796, 0.26530612, 0.28571429,
0.30612245, 0.32653061, 0.34693878, 0.36734694, 0.3877551, 0.40816327, 0.42857143,
0.44897959, 0.46938776, 0.48979592, 0.51020408, 0.53061224, 0.55102041, 0.57142857,
0.59183673, 0.6122449, 0.63265306, 0.65306122, 0.67346939, 0.69387755, 0.71428571,
0.73469388, 0.75510204, 0.7755102, 0.79591837, 0.81632653, 0.83673469, 0.85714286,
0.87755102, 0.89795918, 0.91836735, 0.93877551, 0.95918367, 0.97959184, 1.])
self.assertEqual(time.__str__(), output.__str__())
def test_get_fermi_level(self):
for filename in self.file_list:
output = self.outcar_parser.get_fermi_level(filename)
try:
self.assertIsInstance(output, float)
except AssertionError:
self.assertEqual(int(filename.split('/OUTCAR_')[-1]), 8)
if int(filename.split('/OUTCAR_')[-1]) == 1:
fermi_level = 2.9738
self.assertEqual(fermi_level, output)
if int(filename.split('/OUTCAR_')[-1]) == 2:
fermi_level = 5.9788
self.assertEqual(fermi_level, output)
if int(filename.split('/OUTCAR_')[-1]) in [3, 4]:
fermi_level = 5.9613
self.assertEqual(fermi_level, output)
if int(filename.split('/OUTCAR_')[-1]) in [5, 6]:
fermi_level = 5.9614
self.assertEqual(fermi_level, output)
def test_get_magnetization(self):
for filename in self.file_list:
output, final_magmoms = self.outcar_parser.get_magnetization(filename)
positions = self.outcar_parser.get_positions(filename)
if int(filename.split('/OUTCAR_')[-1]) == 1:
magnetization = [np.array([])]
self.assertEqual(magnetization.__str__(), output.__str__())
self.assertFalse(final_magmoms)
if int(filename.split('/OUTCAR_')[-1]) == 2:
magnetization = [np.array([])]
self.assertEqual(magnetization.__str__(), output.__str__())
self.assertFalse(final_magmoms)
if int(filename.split('/OUTCAR_')[-1]) == 3:
magnetization = [np.array([4., 4., 4., 4., 3.1349091, 4.1157043, 4.2255076, 4.2514329, 4.2041297,
4.2125079, 4.2125079])]
self.assertEqual(magnetization.__str__(), output.__str__())
self.assertFalse(final_magmoms)
if int(filename.split('/OUTCAR_')[-1]) == 4:
magnetization = [np.array([4., 4., 4., 4., 3.1349091, 4.1157043, 4.2255076, 4.2514329, 4.2041297,
4.2125079, 4.2125079])]
final_mag_lst = [[2.111, 2.111]]
self.assertEqual(magnetization.__str__(), output.__str__())
self.assertEqual(final_magmoms, final_mag_lst)
if int(filename.split('/OUTCAR_')[-1]) == 5:
magnetization = [np.array([[0., 4., 0.], [0., 4., 0.], [0., 4., 0.], [0., 4., 0.], [-0., 3.1360688, -0.],
[-0., 4.1168471, 0.], [0., 4.2261074, -0.], [-0., 4.2517361, 0.],
[-0., 4.2043676, 0.], [0., 4.2128061, 0.], [0., 4.2128061, 0.]])]
self.assertEqual(magnetization.__str__(), output.__str__())
self.assertFalse(final_magmoms)
if int(filename.split('/OUTCAR_')[-1]) == 6:
magnetization = [np.array([[0., 4., 0.], [0., 4., 0.], [0., 4., 0.], [0., 4., 0.], [-0., 3.1360688, -0.],
[-0., 4.1168471, 0.], [0., 4.2261074, -0.], [-0., 4.2517361, 0.],
[-0., 4.2043676, 0.], [0., 4.2128061, 0.], [0., 4.2128061, 0.]])]
final_mag_lst = [[[0.0, 2.111, -0.0], [0.0, 2.111, 0.0]]]
self.assertEqual(magnetization.__str__(), output.__str__())
self.assertEqual(final_magmoms, final_mag_lst)
final_magmoms = np.array(final_magmoms)
final_magmoms[:, np.arange(len(positions[0]), dtype=int), :] = final_magmoms.copy()
self.assertEqual(np.array(final_magmoms).shape[1], positions.shape[1])
if int(filename.split('/OUTCAR_')[-1]) == 7:
self.assertEqual((1, 49, 3), np.array(output).shape)
self.assertEqual((11, 32, 3), np.array(final_magmoms).shape)
final_magmoms = np.array(final_magmoms)
final_magmoms[:, np.arange(len(positions[0]), dtype=int), :] = final_magmoms.copy()
self.assertEqual(np.array(final_magmoms).shape[1], positions.shape[1])
def test_get_broyden_mixing_mesh(self):
for filename in self.file_list:
output = self.outcar_parser.get_broyden_mixing_mesh(filename)
if int(filename.split('/OUTCAR_')[-1]) == 1:
mixing = 729
self.assertEqual(mixing, output)
if int(filename.split('/OUTCAR_')[-1]) in [2, 3, 4, 5, 6]:
mixing = 343
self.assertEqual(mixing, output)
def test_get_dipole_moments(self):
for filename in self.file_list:
output = self.outcar_parser.get_dipole_moments(filename)
self.assertTrue(output)
self.assertIsInstance(output, list)
if len(output) > 1:
self.assertIsInstance(output[-1], np.ndarray)
self.assertIsInstance(output[-1][-1], np.ndarray)
self.assertEqual(len(output[-1][-1]), 3)
def test_get_stresses(self):
for filename in self.file_list:
output_si = self.outcar_parser.get_stresses(filename, si_unit=True)
output_kb = self.outcar_parser.get_stresses(filename, si_unit=False)
self.assertIsInstance(output_si, np.ndarray)
self.assertIsInstance(output_kb, np.ndarray)
if int(filename.split('/OUTCAR_')[-1]) == 1:
pullay_si = np.array([[-14.41433, -14.41433, -14.41433, 0., 0., 0.]])
pullay_kb = np.array([[-455.93181, -455.93181, -455.93181, 0., 0., 0.]])
self.assertEqual(output_si.__str__(), pullay_si.__str__())
self.assertEqual(output_kb.__str__(), pullay_kb.__str__())
if int(filename.split('/OUTCAR_')[-1]) == 2:
pullay_si = np.array([[-5.38507, -5.38507, -5.38507, -0., 0., -0.]])
pullay_kb = np.array([[-393.032, -393.032, -393.032, -0., 0., -0.]])
self.assertEqual(output_si.__str__(), pullay_si.__str__())
self.assertEqual(output_kb.__str__(), pullay_kb.__str__())
if int(filename.split('/OUTCAR_')[-1]) == 3:
pullay_si = np.array([[-3.29441, -3.29441, -3.29441, 0., -0., 0.]])
pullay_kb = np.array([[-240.44384, -240.44384, -240.44384, 0., -0., 0.]])
self.assertEqual(output_si.__str__(), pullay_si.__str__())
self.assertEqual(output_kb.__str__(), pullay_kb.__str__())
if int(filename.split('/OUTCAR_')[-1]) == 4:
pullay_si = np.array([[-3.29441, -3.29441, -3.29441, -0., -0., -0.]])
pullay_kb = np.array([[-240.44384, -240.44384, -240.44384, -0., -0., -0.]])
self.assertEqual(output_si.__str__(), pullay_si.__str__())
self.assertEqual(output_kb.__str__(), pullay_kb.__str__())
if int(filename.split('/OUTCAR_')[-1]) in [5, 6]:
pullay_si = np.array([[-3.3066, -3.3066, -3.3066, 0., -0., 0.]])
pullay_kb = np.array([[-241.33405, -241.33409, -241.33405, 0., -0., 0.]])
self.assertEqual(output_si.__str__(), pullay_si.__str__())
self.assertEqual(output_kb.__str__(), pullay_kb.__str__())
def test_get_kinetic_energy_error(self):
for filename in self.file_list:
output_total = self.outcar_parser.get_kinetic_energy_error(filename)
self.assertIsInstance(output_total, float)
if int(filename.split('/OUTCAR_')[-1]) == 1:
kinetic_energy_error = 0.0774
self.assertEqual(4 * kinetic_energy_error, output_total)
if int(filename.split('/OUTCAR_')[-1]) in [2, 3, 4, 5, 6]:
kinetic_energy_error = 0.0664
self.assertEqual(2 * kinetic_energy_error, output_total)
if int(filename.split('/OUTCAR_')[-1]) == 7:
kinetic_energy_error = 16.0 * 0.0088 + 16.0 * 0.002
self.assertEqual(kinetic_energy_error, output_total)
if int(filename.split('/OUTCAR_')[-1]) == 8:
kinetic_energy_error = 1.0 * 0.0236 + 32.0 * 0.0091
self.assertEqual(kinetic_energy_error, output_total)
def test_get_kpoints_irreducible_reciprocal(self):
for filename in self.file_list:
output_all = self.outcar_parser.get_irreducible_kpoints(filename, reciprocal=True, weight=True,
planewaves=True)
output_w = self.outcar_parser.get_irreducible_kpoints(filename, reciprocal=True, weight=True,
planewaves=False)
output_p = self.outcar_parser.get_irreducible_kpoints(filename, reciprocal=True, weight=False,
planewaves=True)
output_k = self.outcar_parser.get_irreducible_kpoints(filename, reciprocal=True, weight=False,
planewaves=False)
self.assertIsInstance(output_all[0], np.ndarray)
self.assertIsInstance(output_all[1], np.ndarray)
self.assertIsInstance(output_all[2], np.ndarray)
self.assertIsInstance(output_w[0], np.ndarray)
self.assertIsInstance(output_w[1], np.ndarray)
self.assertIsInstance(output_p[0], np.ndarray)
self.assertIsInstance(output_p[1], np.ndarray)
self.assertIsInstance(output_k, np.ndarray)
self.assertEqual(output_all[0].__str__(), output_w[0].__str__())
self.assertEqual(output_all[1].__str__(), output_w[1].__str__())
self.assertEqual(output_all[0].__str__(), output_p[0].__str__())
self.assertEqual(output_all[2].__str__(), output_p[1].__str__())
self.assertEqual(output_all[0].__str__(), output_k.__str__())
if int(filename.split('/OUTCAR_')[-1]) == 1:
output = (np.array([[0.125, 0.125, 0.125], [0.375, 0.125, 0.125], [0.375, 0.375, 0.125],
[0.375, 0.375, 0.375]]),
np.array([8.0, 24.0, 24.0, 8.0]), np.array([452.0, 457.0, 451.0, 459.0]))
self.assertEqual(output_all.__str__(), output.__str__())
if int(filename.split('/OUTCAR_')[-1]) in [2, 3, 4]:
output = (np.array([[0.125, 0.125, 0.125], [0.375, 0.125, 0.125], [0.375, 0.375, 0.125],
[0.375, 0.375, 0.375]]),
np.array([8.0, 24.0, 24.0, 8.0]), np.array([196., 199., 196., 190.]))
self.assertEqual(output_all.__str__(), output.__str__())
if int(filename.split('/OUTCAR_')[-1]) in [5, 6]:
output = (np.array([[0.125, 0.125, 0.125], [0.375, 0.125, 0.125], [-0.375, 0.125, 0.125],
[0.125, 0.375, 0.125], [0.375, 0.375, 0.125], [-0.375, 0.375, 0.125],
[0.375, 0.125, 0.375], [0.375, 0.375, 0.375]]),
np.array([8., 8., 8., 8., 8., 8., 8., 8.]),
np.array([392., 398., 398., 398., 392., 392., 392., 380.]))
self.assertEqual(output_all.__str__(), output.__str__())
def test_get_nelect(self):
n_elect_list = [40.0, 16.0, 16.0, 16.0, 16.0, 16.0, 224.0, 358.0]
for filename in self.file_list:
i = int(filename.split("_")[-1]) - 1
self.assertEqual(n_elect_list[i], self.outcar_parser.get_nelect(filename))