/
test_outputs.py
1008 lines (877 loc) · 49.1 KB
/
test_outputs.py
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# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
import json
import numpy as np
import warnings
import xml.etree.cElementTree as ET
from pymatgen.core.periodic_table import Element
from pymatgen.electronic_structure.core import OrbitalType
from pymatgen.io.vasp.inputs import Kpoints
from pymatgen.io.vasp.outputs import Chgcar, Locpot, Oszicar, Outcar, \
Vasprun, Procar, Xdatcar, Dynmat, BSVasprun, UnconvergedVASPWarning
from pymatgen import Spin, Orbital, Lattice, Structure
from pymatgen.entries.compatibility import MaterialsProjectCompatibility
from pymatgen.electronic_structure.core import Magmom
from pymatgen.util.testing import PymatgenTest
"""
Created on Jul 16, 2012
"""
__author__ = "Shyue Ping Ong, Stephen Dacek"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyue@mit.edu"
__date__ = "Jul 16, 2012"
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
'test_files')
class VasprunTest(unittest.TestCase):
def test_multiple_dielectric(self):
v = Vasprun(os.path.join(test_dir, "vasprun.GW0.xml"))
self.assertEqual(len(v.other_dielectric), 3)
def test_charge_charge_dielectric(self):
"""
VASP 5.4.4 writes out two dielectric functions to vasprun.xml
These are the "density-density" and "velocity-velocity" linear response functions.
See the comments in `linear_optics.F` for details.
"""
v = Vasprun(os.path.join(test_dir, "vasprun.xml.dielectric_5.4.4"),
parse_potcar_file=False)
self.assertEqual( v.dielectric is not None, True )
self.assertEqual( 'density' in v.dielectric_data, True )
self.assertEqual( 'velocity' in v.dielectric_data, True )
def test_vasprun_with_more_than_two_unlabelled_dielectric_functions(self):
with self.assertRaises(NotImplementedError):
Vasprun(os.path.join(test_dir, "vasprun.xml.dielectric_bad"),
parse_potcar_file=False)
def test_bad_vasprun(self):
self.assertRaises(ET.ParseError,
Vasprun, os.path.join(test_dir, "bad_vasprun.xml"))
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
# Trigger a warning.
v = Vasprun(os.path.join(test_dir, "bad_vasprun.xml"),
exception_on_bad_xml=False)
# Verify some things
self.assertEqual(len(v.ionic_steps), 1)
self.assertAlmostEqual(v.final_energy, -269.00551374)
self.assertTrue(issubclass(w[-1].category,
UserWarning))
def test_vdw(self):
v = Vasprun(os.path.join(test_dir, "vasprun.xml.vdw"))
self.assertAlmostEqual(v.final_energy, -9.78310677)
def test_properties(self):
filepath = os.path.join(test_dir, 'vasprun.xml.nonlm')
vasprun = Vasprun(filepath, parse_potcar_file=False)
orbs = list(vasprun.complete_dos.pdos[vasprun.final_structure[
0]].keys())
self.assertIn(OrbitalType.s, orbs)
filepath = os.path.join(test_dir, 'vasprun.xml')
vasprun = Vasprun(filepath, parse_potcar_file=False)
# Test NELM parsing.
self.assertEqual(vasprun.parameters["NELM"], 60)
# test pdos parsing
pdos0 = vasprun.complete_dos.pdos[vasprun.final_structure[0]]
self.assertAlmostEqual(pdos0[Orbital.s][Spin.up][16], 0.0026)
self.assertAlmostEqual(pdos0[Orbital.pz][Spin.down][16], 0.0012)
self.assertEqual(pdos0[Orbital.s][Spin.up].shape, (301,))
filepath2 = os.path.join(test_dir, 'lifepo4.xml')
vasprun_ggau = Vasprun(filepath2, parse_projected_eigen=True,
parse_potcar_file=False)
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, parse_potcar_file=False)
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, parse_potcar_file=False)
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][0], 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')
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
# Trigger a warning.
vasprun_unconverged = Vasprun(filepath, parse_potcar_file=False)
# Verify some things
self.assertEqual(len(w), 1)
self.assertTrue(issubclass(w[-1].category,
UnconvergedVASPWarning))
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, parse_potcar_file=False)
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(
check_potcar_hash=False).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, parse_potcar_file=False)
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, parse_potcar_file=False)
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"),
parse_potcar_file=False)
self.assertEqual(vasprun_uniform.kpoints.style,
Kpoints.supported_modes.Reciprocal)
vasprun_no_pdos = Vasprun(os.path.join(test_dir, "Li_no_projected.xml"),
parse_potcar_file=False)
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"),
parse_potcar_file=False)
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])
v = Vasprun(os.path.join(test_dir, "vasprun.xml.indirect.gz"))
(gap, cbm, vbm, direct) = v.eigenvalue_band_properties
self.assertFalse(direct)
vasprun_optical = Vasprun(
os.path.join(test_dir, "vasprun.xml.opticaltransitions"),
parse_potcar_file=False)
self.assertAlmostEqual(3.084, vasprun_optical.optical_transition[0][0])
self.assertAlmostEqual(3.087, vasprun_optical.optical_transition[3][0])
self.assertAlmostEqual(0.001, vasprun_optical.optical_transition[0][1])
self.assertAlmostEqual(0.001, vasprun_optical.optical_transition[1][1])
self.assertAlmostEqual(0.001, vasprun_optical.optical_transition[7][1])
self.assertAlmostEqual(0.001, vasprun_optical.optical_transition[19][1])
self.assertAlmostEqual(3.3799999999,
vasprun_optical.optical_transition[54][0])
self.assertAlmostEqual(3.381, vasprun_optical.optical_transition[55][0])
self.assertAlmostEqual(3.381, vasprun_optical.optical_transition[56][0])
self.assertAlmostEqual(10554.9860,
vasprun_optical.optical_transition[54][1])
self.assertAlmostEqual(0.0, vasprun_optical.optical_transition[55][1])
self.assertAlmostEqual(0.001, vasprun_optical.optical_transition[56][1])
def test_force_constants(self):
vasprun_fc = Vasprun(os.path.join(test_dir, "vasprun.xml.dfpt.phonon"),
parse_potcar_file=False)
fc_ans = [[-0.00184451, -0., -0.],
[-0., -0.00933824, -0.03021279],
[-0., -0.03021279, 0.01202547]]
nm_ans = [[0.0884346, -0.08837289, -0.24995639],
[-0.0884346, 0.08837289, 0.24995639],
[0.15306645, -0.05105771, -0.14441306],
[-0.15306645, 0.05105771, 0.14441306],
[-0.0884346, 0.08837289, 0.24995639],
[0.0884346, -0.08837289, -0.24995639],
[-0.15306645, 0.05105771, 0.14441306],
[0.15306645, -0.05105771, -0.14441306],
[-0.0884346, 0.08837289, 0.24995639],
[0.0884346, -0.08837289, -0.24995639],
[-0.15306645, 0.05105771, 0.14441306],
[0.15306645, -0.05105771, -0.14441306],
[0.0884346, -0.08837289, -0.24995639],
[-0.0884346, 0.08837289, 0.24995639],
[0.15306645, -0.05105771, -0.14441306],
[-0.15306645, 0.05105771, 0.14441306]]
nm_eigenval_ans = [-0.59067079, -0.59067079, -0.59067003, -0.59067003,
-0.59067003, -0.59067003, -0.585009, -0.585009,
-0.58500895, -0.58500883, -0.5062956, -0.5062956]
self.assertEqual(vasprun_fc.force_constants.shape, (16, 16, 3, 3))
self.assertTrue(np.allclose(vasprun_fc.force_constants[8, 9], fc_ans))
self.assertEqual(vasprun_fc.normalmode_eigenvals.size, 48)
self.assertTrue(np.allclose(vasprun_fc.normalmode_eigenvals[17:29],
nm_eigenval_ans))
self.assertEqual(vasprun_fc.normalmode_eigenvecs.shape, (48, 16, 3))
self.assertTrue(
np.allclose(vasprun_fc.normalmode_eigenvecs[33], nm_ans))
def test_Xe(self):
vr = Vasprun(os.path.join(test_dir, 'vasprun.xml.xe'),
parse_potcar_file=False)
self.assertEqual(vr.atomic_symbols, ['Xe'])
def test_invalid_element(self):
self.assertRaises(ValueError, Vasprun,
os.path.join(test_dir, 'vasprun.xml.wrong_sp'))
def test_selective_dynamics(self):
vsd = Vasprun(os.path.join(test_dir, 'vasprun.xml.indirect.gz'))
np.testing.assert_array_equal(
vsd.final_structure.site_properties.get('selective_dynamics'),
[[True] * 3, [False] * 3], "Selective dynamics parsing error")
def test_as_dict(self):
filepath = os.path.join(test_dir, 'vasprun.xml')
vasprun = Vasprun(filepath,
parse_potcar_file=False)
# 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_get_band_structure(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
filepath = os.path.join(test_dir, 'vasprun_Si_bands.xml')
vasprun = Vasprun(filepath,
parse_projected_eigen=True,
parse_potcar_file=False)
bs = vasprun.get_band_structure(kpoints_filename=
os.path.join(test_dir,
'KPOINTS_Si_bands'))
cbm = bs.get_cbm()
vbm = bs.get_vbm()
self.assertEqual(cbm['kpoint_index'], [13],
"wrong cbm kpoint index")
self.assertAlmostEqual(cbm['energy'], 6.2301, "wrong cbm energy")
self.assertEqual(cbm['band_index'], {Spin.up: [4], Spin.down: [4]},
"wrong cbm bands")
self.assertEqual(vbm['kpoint_index'], [0, 63, 64])
self.assertAlmostEqual(vbm['energy'], 5.6158, "wrong vbm energy")
self.assertEqual(vbm['band_index'], {Spin.up: [1, 2, 3],
Spin.down: [1, 2, 3]},
"wrong vbm bands")
self.assertEqual(vbm['kpoint'].label, "\\Gamma", "wrong vbm label")
self.assertEqual(cbm['kpoint'].label, None, "wrong cbm label")
projected = bs.get_projection_on_elements()
self.assertAlmostEqual(projected[Spin.up][0][0]["Si"], 0.4238)
projected = bs.get_projections_on_elements_and_orbitals(
{"Si": ["s"]})
self.assertAlmostEqual(projected[Spin.up][0][0]["Si"]["s"], 0.4238)
def test_sc_step_overflow(self):
filepath = os.path.join(test_dir, 'vasprun.xml.sc_overflow')
# with warnings.catch_warnings(record=True) as w:
# warnings.simplefilter("always")
# vasprun = Vasprun(filepath)
# self.assertEqual(len(w), 3)
vasprun = Vasprun(filepath)
estep = vasprun.ionic_steps[0]['electronic_steps'][29]
self.assertTrue(np.isnan(estep['e_wo_entrp']))
def test_update_potcar(self):
filepath = os.path.join(test_dir, 'vasprun.xml')
potcar_path = os.path.join(test_dir, 'POTCAR.LiFePO4.gz')
potcar_path2 = os.path.join(test_dir, 'POTCAR2.LiFePO4.gz')
vasprun = Vasprun(filepath, parse_potcar_file=False)
self.assertEqual(vasprun.potcar_spec,
[{"titel": "PAW_PBE Li 17Jan2003", "hash": None},
{"titel": "PAW_PBE Fe 06Sep2000", "hash": None},
{"titel": "PAW_PBE Fe 06Sep2000", "hash": None},
{"titel": "PAW_PBE P 17Jan2003", "hash": None},
{"titel": "PAW_PBE O 08Apr2002", "hash": None}])
vasprun.update_potcar_spec(potcar_path)
self.assertEqual(vasprun.potcar_spec, [{"titel": "PAW_PBE Li 17Jan2003",
"hash": "65e83282d1707ec078c1012afbd05be8"},
{"titel": "PAW_PBE Fe 06Sep2000",
"hash": "9530da8244e4dac17580869b4adab115"},
{"titel": "PAW_PBE Fe 06Sep2000",
"hash": "9530da8244e4dac17580869b4adab115"},
{"titel": "PAW_PBE P 17Jan2003",
"hash": "7dc3393307131ae67785a0cdacb61d5f"},
{"titel": "PAW_PBE O 08Apr2002",
"hash": "7a25bc5b9a5393f46600a4939d357982"}])
vasprun2 = Vasprun(filepath, parse_potcar_file=False)
self.assertRaises(ValueError, vasprun2.update_potcar_spec, potcar_path2)
vasprun = Vasprun(filepath, parse_potcar_file=potcar_path)
self.assertEqual(vasprun.potcar_spec, [{"titel": "PAW_PBE Li 17Jan2003",
"hash": "65e83282d1707ec078c1012afbd05be8"},
{"titel": "PAW_PBE Fe 06Sep2000",
"hash": "9530da8244e4dac17580869b4adab115"},
{"titel": "PAW_PBE Fe 06Sep2000",
"hash": "9530da8244e4dac17580869b4adab115"},
{"titel": "PAW_PBE P 17Jan2003",
"hash": "7dc3393307131ae67785a0cdacb61d5f"},
{"titel": "PAW_PBE O 08Apr2002",
"hash": "7a25bc5b9a5393f46600a4939d357982"}])
self.assertRaises(ValueError, Vasprun, filepath,
parse_potcar_file=potcar_path2)
def test_search_for_potcar(self):
filepath = os.path.join(test_dir, 'vasprun.xml')
vasprun = Vasprun(filepath, parse_potcar_file=True)
self.assertEqual(vasprun.potcar_spec, [{"titel": "PAW_PBE Li 17Jan2003",
"hash": "65e83282d1707ec078c1012afbd05be8"},
{"titel": "PAW_PBE Fe 06Sep2000",
"hash": "9530da8244e4dac17580869b4adab115"},
{"titel": "PAW_PBE Fe 06Sep2000",
"hash": "9530da8244e4dac17580869b4adab115"},
{"titel": "PAW_PBE P 17Jan2003",
"hash": "7dc3393307131ae67785a0cdacb61d5f"},
{"titel": "PAW_PBE O 08Apr2002",
"hash": "7a25bc5b9a5393f46600a4939d357982"}])
def test_potcar_not_found(self):
filepath = os.path.join(test_dir, 'vasprun.xml')
# Ensure no potcar is found and nothing is updated
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
vasprun = Vasprun(filepath, parse_potcar_file='.')
self.assertEqual(len(w), 2)
self.assertEqual(vasprun.potcar_spec, [{"titel": "PAW_PBE Li 17Jan2003", "hash": None},
{"titel": "PAW_PBE Fe 06Sep2000", "hash": None},
{"titel": "PAW_PBE Fe 06Sep2000", "hash": None},
{"titel": "PAW_PBE P 17Jan2003", "hash": None},
{"titel": "PAW_PBE O 08Apr2002", "hash": None}])
def test_parsing_chemical_shift_calculations(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
filepath = os.path.join(test_dir, "nmr", "cs", "basic",
'vasprun.xml.chemical_shift.scstep')
vasprun = Vasprun(filepath)
nestep = len(vasprun.ionic_steps[-1]['electronic_steps'])
self.assertEqual(nestep, 10)
self.assertTrue(vasprun.converged)
def test_charged_structure(self):
vpath = os.path.join(test_dir, 'vasprun.charged.xml')
potcar_path = os.path.join(test_dir, 'POT_GGA_PAW_PBE', 'POTCAR.Si.gz')
vasprun = Vasprun(vpath, parse_potcar_file=False)
vasprun.update_charge_from_potcar(potcar_path)
self.assertEqual(vasprun.parameters.get("NELECT", 8), 9)
self.assertEqual(vasprun.structures[0].charge, 1)
class OutcarTest(unittest.TestCase):
def test_init(self):
for f in ['OUTCAR', 'OUTCAR.gz']:
filepath = os.path.join(test_dir, f)
outcar = Outcar(filepath)
expected_mag = ({'d': 0.0, 'p': 0.003, 's': 0.002, 'tot': 0.005},
{'d': 0.798, 'p': 0.008, 's': 0.007, 'tot': 0.813},
{'d': 0.798, 'p': 0.008, 's': 0.007, 'tot': 0.813},
{'d': 0.0, 'p': -0.117, 's': 0.005, 'tot': -0.112},
{'d': 0.0, 'p': -0.165, 's': 0.004, 'tot': -0.162},
{'d': 0.0, 'p': -0.117, 's': 0.005, 'tot': -0.112},
{'d': 0.0, 'p': -0.165, 's': 0.004, 'tot': -0.162})
expected_chg = ({'p': 0.154, 's': 0.078, 'd': 0.0, 'tot': 0.232},
{'p': 0.707, 's': 0.463, 'd': 8.316, 'tot': 9.486},
{'p': 0.707, 's': 0.463, 'd': 8.316, 'tot': 9.486},
{'p': 3.388, 's': 1.576, 'd': 0.0, 'tot': 4.964},
{'p': 3.365, 's': 1.582, 'd': 0.0, 'tot': 4.947},
{'p': 3.388, 's': 1.576, 'd': 0.0, 'tot': 4.964},
{'p': 3.365, 's': 1.582, 'd': 0.0, 'tot': 4.947})
self.assertAlmostEqual(outcar.magnetization, expected_mag, 5,
"Wrong magnetization read from Outcar")
self.assertAlmostEqual(outcar.charge, expected_chg, 5,
"Wrong charge read from Outcar")
self.assertFalse(outcar.is_stopped)
self.assertEqual(outcar.run_stats, {'System time (sec)': 0.938,
'Total CPU time used (sec)': 545.142,
'Elapsed time (sec)': 546.709,
'Maximum memory used (kb)': 0.0,
'Average memory used (kb)': 0.0,
'User time (sec)': 544.204,
'cores': '8'})
self.assertAlmostEqual(outcar.efermi, 2.0112)
self.assertAlmostEqual(outcar.nelect, 44.9999991)
self.assertAlmostEqual(outcar.total_mag, 0.9999998)
self.assertIsNotNone(outcar.as_dict())
self.assertFalse(outcar.lepsilon)
filepath = os.path.join(test_dir, 'OUTCAR.stopped')
outcar = Outcar(filepath)
self.assertTrue(outcar.is_stopped)
for f in ['OUTCAR.lepsilon', 'OUTCAR.lepsilon.gz']:
filepath = os.path.join(test_dir, f)
outcar = Outcar(filepath)
self.assertTrue(outcar.lepsilon)
self.assertAlmostEqual(outcar.dielectric_tensor[0][0], 3.716432)
self.assertAlmostEqual(outcar.dielectric_tensor[0][1], -0.20464)
self.assertAlmostEqual(outcar.dielectric_tensor[1][2], -0.20464)
self.assertAlmostEqual(outcar.dielectric_ionic_tensor[0][0],
0.001419)
self.assertAlmostEqual(outcar.dielectric_ionic_tensor[0][2],
0.001419)
self.assertAlmostEqual(outcar.dielectric_ionic_tensor[2][2],
0.001419)
self.assertAlmostEqual(outcar.piezo_tensor[0][0], 0.52799)
self.assertAlmostEqual(outcar.piezo_tensor[1][3], 0.35998)
self.assertAlmostEqual(outcar.piezo_tensor[2][5], 0.35997)
self.assertAlmostEqual(outcar.piezo_ionic_tensor[0][0], 0.05868)
self.assertAlmostEqual(outcar.piezo_ionic_tensor[1][3], 0.06241)
self.assertAlmostEqual(outcar.piezo_ionic_tensor[2][5], 0.06242)
self.assertAlmostEqual(outcar.born[0][1][2], -0.385)
self.assertAlmostEqual(outcar.born[1][2][0], 0.36465)
filepath = os.path.join(test_dir, 'OUTCAR.NiO_SOC.gz')
outcar = Outcar(filepath)
expected_mag = (
{'s': Magmom([0.0, 0.0, -0.001]), 'p': Magmom([0.0, 0.0, -0.003]),
'd': Magmom([0.0, 0.0, 1.674]), 'tot': Magmom([0.0, 0.0, 1.671])},
{'s': Magmom([0.0, 0.0, 0.001]), 'p': Magmom([0.0, 0.0, 0.003]),
'd': Magmom([0.0, 0.0, -1.674]),
'tot': Magmom([0.0, 0.0, -1.671])},
{'s': Magmom([0.0, 0.0, 0.0]), 'p': Magmom([0.0, 0.0, 0.0]),
'd': Magmom([0.0, 0.0, 0.0]), 'tot': Magmom([0.0, 0.0, 0.0])},
{'s': Magmom([0.0, 0.0, 0.0]), 'p': Magmom([0.0, 0.0, 0.0]),
'd': Magmom([0.0, 0.0, 0.0]), 'tot': Magmom([0.0, 0.0, 0.0])}
)
# test note: Magmom class uses np.allclose() when testing for equality
# so fine to use assertEqual here
self.assertEqual(outcar.magnetization, expected_mag,
"Wrong vector magnetization read from Outcar for SOC calculation")
def test_polarization(self):
filepath = os.path.join(test_dir, "OUTCAR.BaTiO3.polar")
outcar = Outcar(filepath)
self.assertEqual(outcar.spin, True)
self.assertEqual(outcar.noncollinear, False)
self.assertAlmostEqual(outcar.p_ion[0], 0.0)
self.assertAlmostEqual(outcar.p_ion[1], 0.0)
self.assertAlmostEqual(outcar.p_ion[2], -5.56684)
self.assertAlmostEqual(outcar.p_sp1[0], 2.00068)
self.assertAlmostEqual(outcar.p_sp2[0], -2.00044)
self.assertAlmostEqual(outcar.p_elec[0], 0.00024)
self.assertAlmostEqual(outcar.p_elec[1], 0.00019)
self.assertAlmostEqual(outcar.p_elec[2], 3.61674)
def test_pseudo_zval(self):
filepath = os.path.join(test_dir, "OUTCAR.BaTiO3.polar")
outcar = Outcar(filepath)
self.assertDictEqual({'Ba': 10.00, 'Ti': 10.00, 'O': 6.00},
outcar.zval_dict)
def test_dielectric(self):
filepath = os.path.join(test_dir, "OUTCAR.dielectric")
outcar = Outcar(filepath)
outcar.read_corrections()
self.assertAlmostEqual(outcar.data["dipol_quadrupol_correction"],
0.03565)
self.assertAlmostEqual(outcar.final_energy, -797.46760559)
def test_freq_dielectric(self):
filepath = os.path.join(test_dir, "OUTCAR.LOPTICS")
outcar = Outcar(filepath)
outcar.read_freq_dielectric()
self.assertAlmostEqual(outcar.frequencies[0], 0)
self.assertAlmostEqual(outcar.frequencies[-1], 39.826101)
self.assertAlmostEqual(outcar.dielectric_tensor_function[0][0, 0],
8.96938800)
self.assertAlmostEqual(outcar.dielectric_tensor_function[-1][0, 0],
7.36167000e-01 + 1.53800000e-03j)
self.assertEqual(len(outcar.frequencies),
len(outcar.dielectric_tensor_function))
np.testing.assert_array_equal(outcar.dielectric_tensor_function[0],
outcar.dielectric_tensor_function[
0].transpose())
def test_freq_dielectric_vasp544(self):
filepath = os.path.join(test_dir, "OUTCAR.LOPTICS.vasp544")
outcar = Outcar(filepath)
outcar.read_freq_dielectric()
self.assertAlmostEqual(outcar.frequencies[0], 0)
self.assertAlmostEqual(outcar.frequencies[-1], 39.63964)
self.assertAlmostEqual(outcar.dielectric_tensor_function[0][0, 0],
12.769435 + 0j)
self.assertAlmostEqual(outcar.dielectric_tensor_function[-1][0, 0],
0.828615 + 0.016594j)
self.assertEqual(len(outcar.frequencies),
len(outcar.dielectric_tensor_function))
np.testing.assert_array_equal(outcar.dielectric_tensor_function[0],
outcar.dielectric_tensor_function[
0].transpose())
def test_read_elastic_tensor(self):
filepath = os.path.join(test_dir, "OUTCAR.total_tensor.Li2O.gz")
outcar = Outcar(filepath)
outcar.read_elastic_tensor()
self.assertAlmostEqual(outcar.data["elastic_tensor"][0][0], 1986.3391)
self.assertAlmostEqual(outcar.data["elastic_tensor"][0][1], 187.8324)
self.assertAlmostEqual(outcar.data["elastic_tensor"][3][3], 586.3034)
def test_read_piezo_tensor(self):
filepath = os.path.join(test_dir, "OUTCAR.lepsilon.gz")
outcar = Outcar(filepath)
outcar.read_piezo_tensor()
self.assertAlmostEqual(outcar.data["piezo_tensor"][0][0], 0.52799)
self.assertAlmostEqual(outcar.data["piezo_tensor"][1][3], 0.35998)
self.assertAlmostEqual(outcar.data["piezo_tensor"][2][5], 0.35997)
def test_core_state_eigen(self):
filepath = os.path.join(test_dir, "OUTCAR.CL")
cl = Outcar(filepath).read_core_state_eigen()
self.assertAlmostEqual(cl[6]["2s"][-1], -174.4779)
filepath = os.path.join(test_dir, "OUTCAR.icorelevel")
cl = Outcar(filepath).read_core_state_eigen()
self.assertAlmostEqual(cl[4]["3d"][-1], -31.4522)
def test_avg_core_poten(self):
filepath = os.path.join(test_dir, "OUTCAR.lepsilon")
cp = Outcar(filepath).read_avg_core_poten()
self.assertAlmostEqual(cp[-1][1], -90.0487)
filepath = os.path.join(test_dir, "OUTCAR")
cp = Outcar(filepath).read_avg_core_poten()
self.assertAlmostEqual(cp[0][6], -73.1068)
def test_single_atom(self):
filepath = os.path.join(test_dir, "OUTCAR.Al")
outcar = Outcar(filepath)
expected_mag = ({u'p': 0.0, u's': 0.0, u'd': 0.0, u'tot': 0.0},)
expected_chg = ({u'p': 0.343, u's': 0.425, u'd': 0.0, u'tot': 0.768},)
self.assertAlmostEqual(outcar.magnetization, expected_mag)
self.assertAlmostEqual(outcar.charge, expected_chg)
self.assertFalse(outcar.is_stopped)
self.assertEqual(outcar.run_stats, {'System time (sec)': 0.592,
'Total CPU time used (sec)': 50.194,
'Elapsed time (sec)': 52.337,
'Maximum memory used (kb)': 62900.0,
'Average memory used (kb)': 0.0,
'User time (sec)': 49.602,
'cores': '32'})
self.assertAlmostEqual(outcar.efermi, 8.0942)
self.assertAlmostEqual(outcar.nelect, 3)
self.assertAlmostEqual(outcar.total_mag, 8.2e-06)
self.assertIsNotNone(outcar.as_dict())
def test_chemical_shifts(self):
filename = os.path.join(test_dir, "nmr", "cs", "core.diff",
"hydromagnesite", "OUTCAR")
outcar = Outcar(filename)
outcar.read_chemical_shifts()
expected_chemical_shifts = [[191.9974, 69.5232, 0.6342],
[195.0808, 68.183, 0.833],
[192.0389, 69.5762, 0.6329],
[195.0844, 68.1756, 0.8336],
[192.005, 69.5289, 0.6339],
[195.0913, 68.1859, 0.833],
[192.0237, 69.565, 0.6333],
[195.0788, 68.1733, 0.8337]]
self.assertAlmostEqual(
len(outcar.data["chemical_shifts"]["valence_only"][20: 28]),
len(expected_chemical_shifts))
for c1, c2 in zip(
outcar.data["chemical_shifts"]["valence_only"][20: 28],
expected_chemical_shifts):
for x1, x2 in zip(list(c1.maryland_values), c2):
self.assertAlmostEqual(x1, x2, places=5)
def test_chemical_shifts_with_different_core_contribution(self):
filename = os.path.join(test_dir, "nmr", "cs", "core.diff",
"core.diff.chemical.shifts.OUTCAR")
outcar = Outcar(filename)
outcar.read_chemical_shifts()
c_vo = outcar.data["chemical_shifts"]["valence_only"][7].maryland_values
for x1, x2 in zip(list(c_vo),
[198.7009, 73.7484, 1.0000]):
self.assertAlmostEqual(x1, x2)
c_vc = outcar.data["chemical_shifts"]["valence_and_core"][
7].maryland_values
for x1, x2 in zip(list(c_vc),
[-1.9406, 73.7484, 1.0000]):
self.assertAlmostEqual(x1, x2)
def test_cs_raw_tensors(self):
filename = os.path.join(test_dir, "nmr", "cs", "core.diff",
"core.diff.chemical.shifts.OUTCAR")
outcar = Outcar(filename)
unsym_tensors = outcar.read_cs_raw_symmetrized_tensors()
self.assertEqual(unsym_tensors[0],
[[-145.814605, -4.263425, 0.000301],
[4.263434, -145.812238, -8.7e-05],
[0.000136, -0.000189, -142.794068]])
self.assertEqual(unsym_tensors[29],
[[287.789318, -53.799325, 30.900024],
[-53.799571, 225.668117, -17.839598],
[3.801103, -2.195218, 88.896756]])
def test_cs_g0_contribution(self):
filename = os.path.join(test_dir, "nmr", "cs", "core.diff",
"core.diff.chemical.shifts.OUTCAR")
outcar = Outcar(filename)
g0_contrib = outcar.read_cs_g0_contribution()
self.assertEqual(g0_contrib,
[[-8.773535, 9e-06, 1e-06],
[1.7e-05, -8.773536, -0.0792],
[-6e-06, -0.008328, -9.320237]])
def test_cs_core_contribution(self):
filename = os.path.join(test_dir, "nmr", "cs", "core.diff",
"core.diff.chemical.shifts.OUTCAR")
outcar = Outcar(filename)
core_contrib = outcar.read_cs_core_contribution()
self.assertEqual(core_contrib,
{'Mg': -412.8248405,
'C': -200.5098812,
'O': -271.0766979})
def test_nmr_efg(self):
filename = os.path.join(test_dir, "nmr", "efg", "AlPO4", "OUTCAR")
outcar = Outcar(filename)
outcar.read_nmr_efg()
expected_efg = [
{'eta': 0.465, 'nuclear_quadrupole_moment': 146.6, 'cq': -5.573},
{'eta': 0.465, 'nuclear_quadrupole_moment': 146.6, 'cq': -5.573},
{'eta': 0.137, 'nuclear_quadrupole_moment': 146.6, 'cq': 6.327},
{'eta': 0.137, 'nuclear_quadrupole_moment': 146.6, 'cq': 6.327},
{'eta': 0.112, 'nuclear_quadrupole_moment': 146.6, 'cq': -7.453},
{'eta': 0.112, 'nuclear_quadrupole_moment': 146.6, 'cq': -7.453},
{'eta': 0.42, 'nuclear_quadrupole_moment': 146.6, 'cq': -5.58},
{'eta': 0.42, 'nuclear_quadrupole_moment': 146.6, 'cq': -5.58}]
self.assertEqual(len(outcar.data["efg"][2:10]), len(expected_efg))
for e1, e2 in zip(outcar.data["efg"][2:10], expected_efg):
for k in e1.keys():
self.assertAlmostEqual(e1[k], e2[k], places=5)
def test_read_fermi_contact_shift(self):
filepath = os.path.join(test_dir, "OUTCAR_fc")
outcar = Outcar(filepath)
outcar.read_fermi_contact_shift()
self.assertAlmostEqual(outcar.data["fermi_contact_shift"][u'fch'][0][0],
-0.002)
self.assertAlmostEqual(outcar.data["fermi_contact_shift"][u'th'][0][0],
-0.052)
self.assertAlmostEqual(outcar.data["fermi_contact_shift"][u'dh'][0][0],
0.0)
def test_drift(self):
outcar = Outcar(os.path.join(test_dir, "OUTCAR"))
self.assertEqual(len(outcar.drift), 5)
self.assertAlmostEqual(np.sum(outcar.drift), 0)
outcar = Outcar(os.path.join(test_dir, "OUTCAR.CL"))
self.assertEqual(len(outcar.drift), 79)
self.assertAlmostEqual(np.sum(outcar.drift), 0.448010)
def test_electrostatic_potential(self):
outcar = Outcar(os.path.join(test_dir, "OUTCAR"))
self.assertEqual(outcar.ngf, [54, 30, 54])
self.assertTrue(
np.allclose(outcar.sampling_radii, [0.9748, 0.9791, 0.7215]))
self.assertTrue(np.allclose(outcar.electrostatic_potential,
[-26.0704, -45.5046, -45.5046, -72.9539,
-73.0621, -72.9539, -73.0621]))
class BSVasprunTest(unittest.TestCase):
def test_get_band_structure(self):
filepath = os.path.join(test_dir, 'vasprun_Si_bands.xml')
vasprun = BSVasprun(filepath, parse_potcar_file=False)
bs = vasprun.get_band_structure(kpoints_filename=
os.path.join(test_dir,
'KPOINTS_Si_bands'))
cbm = bs.get_cbm()
vbm = bs.get_vbm()
self.assertEqual(cbm['kpoint_index'], [13], "wrong cbm kpoint index")
self.assertAlmostEqual(cbm['energy'], 6.2301, "wrong cbm energy")
self.assertEqual(cbm['band_index'], {Spin.up: [4], Spin.down: [4]},
"wrong cbm bands")
self.assertEqual(vbm['kpoint_index'], [0, 63, 64])
self.assertAlmostEqual(vbm['energy'], 5.6158, "wrong vbm energy")
self.assertEqual(vbm['band_index'], {Spin.up: [1, 2, 3],
Spin.down: [1, 2, 3]},
"wrong vbm bands")
self.assertEqual(vbm['kpoint'].label, "\\Gamma", "wrong vbm label")
self.assertEqual(cbm['kpoint'].label, None, "wrong cbm label")
d = vasprun.as_dict()
self.assertIn("eigenvalues", d["output"])
class OszicarTest(unittest.TestCase):
def test_init(self):
filepath = os.path.join(test_dir, 'OSZICAR')
oszicar = Oszicar(filepath)
self.assertEqual(len(oszicar.electronic_steps),
len(oszicar.ionic_steps))
self.assertEqual(len(oszicar.all_energies), 60)
self.assertAlmostEqual(oszicar.final_energy, -526.63928)
class LocpotTest(unittest.TestCase):
def test_init(self):
filepath = os.path.join(test_dir, 'LOCPOT')
locpot = Locpot.from_file(filepath)
self.assertAlmostEqual(-217.05226954,
sum(locpot.get_average_along_axis(0)))
self.assertAlmostEqual(locpot.get_axis_grid(0)[-1], 2.87629, 2)
self.assertAlmostEqual(locpot.get_axis_grid(1)[-1], 2.87629, 2)
self.assertAlmostEqual(locpot.get_axis_grid(2)[-1], 2.87629, 2)
class ChgcarTest(PymatgenTest):
def test_init(self):
filepath = os.path.join(test_dir, 'CHGCAR.nospin')
chg = Chgcar.from_file(filepath)
self.assertAlmostEqual(chg.get_integrated_diff(0, 2)[0, 1], 0)
filepath = os.path.join(test_dir, 'CHGCAR.spin')
chg = Chgcar.from_file(filepath)
self.assertAlmostEqual(chg.get_integrated_diff(0, 1)[0, 1],
-0.0043896932237534022)
# test sum
chg += chg
self.assertAlmostEqual(chg.get_integrated_diff(0, 1)[0, 1],
-0.0043896932237534022 * 2)
filepath = os.path.join(test_dir, 'CHGCAR.Fe3O4')
chg = Chgcar.from_file(filepath)
ans = [1.56472768, 3.25985108, 3.49205728, 3.66275028, 3.8045896,
5.10813352]
myans = chg.get_integrated_diff(0, 3, 6)
self.assertTrue(np.allclose(myans[:, 1], ans))
def test_write(self):
filepath = os.path.join(test_dir, 'CHGCAR.spin')
chg = Chgcar.from_file(filepath)
chg.write_file("CHGCAR_pmg")
with open("CHGCAR_pmg") as f:
for i, line in enumerate(f):
if i == 22130:
self.assertEqual("augmentation occupancies 1 15\n", line)
if i == 44255:
self.assertEqual("augmentation occupancies 1 15\n", line)
os.remove("CHGCAR_pmg")
def test_soc_chgcar(self):
filepath = os.path.join(test_dir, "CHGCAR.NiO_SOC.gz")
chg = Chgcar.from_file(filepath)
self.assertEqual(set(chg.data.keys()),
{'total', 'diff_x', 'diff_y', 'diff_z', 'diff'})
self.assertTrue(chg.is_soc)
self.assertEqual(chg.data['diff'].shape, chg.data['diff_y'].shape)
# check our construction of chg.data['diff'] makes sense
# this has been checked visually too and seems reasonable
self.assertEqual(abs(chg.data['diff'][0][0][0]),
np.linalg.norm([chg.data['diff_x'][0][0][0],
chg.data['diff_y'][0][0][0],
chg.data['diff_z'][0][0][0]]))
# and that the net magnetization is about zero
# note: we get ~ 0.08 here, seems a little high compared to
# vasp output, but might be due to chgcar limitations?
self.assertAlmostEqual(chg.net_magnetization, 0.0, places=0)
chg.write_file("CHGCAR_pmg_soc")
chg_from_file = Chgcar.from_file("CHGCAR_pmg_soc")
self.assertTrue(chg_from_file.is_soc)
os.remove("CHGCAR_pmg_soc")
def test_hdf5(self):
chgcar = Chgcar.from_file(os.path.join(test_dir, "CHGCAR.NiO_SOC.gz"))
chgcar.to_hdf5("chgcar_test.hdf5")
import h5py
with h5py.File("chgcar_test.hdf5", "r") as f:
self.assertArrayAlmostEqual(np.array(f["vdata"]["total"]),
chgcar.data["total"])
self.assertArrayAlmostEqual(np.array(f["vdata"]["diff"]),
chgcar.data["diff"])
self.assertArrayAlmostEqual(np.array(f["lattice"]),
chgcar.structure.lattice.matrix)
self.assertArrayAlmostEqual(np.array(f["fcoords"]),
chgcar.structure.frac_coords)
for z in f["Z"]:
self.assertIn(z, [Element.Ni.Z, Element.O.Z])
for sp in f["species"]:
self.assertIn(sp, ["Ni", "O"])
chgcar2 = Chgcar.from_hdf5("chgcar_test.hdf5")
self.assertArrayAlmostEqual(chgcar2.data["total"],
chgcar.data["total"])
os.remove("chgcar_test.hdf5")
class ProcarTest(unittest.TestCase):
def test_init(self):
filepath = os.path.join(test_dir, 'PROCAR.simple')
p = Procar(filepath)
self.assertAlmostEqual(p.get_occupation(0, 'd')[Spin.up], 0)
self.assertAlmostEqual(p.get_occupation(0, 's')[Spin.up],
0.35381249999999997)
self.assertAlmostEqual(p.get_occupation(0, 'p')[Spin.up], 1.19540625)
self.assertRaises(ValueError, p.get_occupation, 1, 'm')
self.assertEqual(p.nbands, 10)
self.assertEqual(p.nkpoints, 10)
self.assertEqual(p.nions, 3)
lat = Lattice.cubic(3.)
s = Structure(lat, ["Li", "Na", "K"], [[0., 0., 0.],
[0.25, 0.25, 0.25],
[0.75, 0.75, 0.75]])
d = p.get_projection_on_elements(s)
self.assertAlmostEqual(d[Spin.up][2][2],
{'Na': 0.042, 'K': 0.646, 'Li': 0.042})
filepath = os.path.join(test_dir, 'PROCAR')
p = Procar(filepath)
self.assertAlmostEqual(p.get_occupation(0, 'dxy')[Spin.up],
0.96214813853000025)
self.assertAlmostEqual(p.get_occupation(0, 'dxy')[Spin.down],
0.85796295426000124)
def test_phase_factors(self):
filepath = os.path.join(test_dir, 'PROCAR.phase')
p = Procar(filepath)
self.assertAlmostEqual(p.phase_factors[Spin.up][0, 0, 0, 0],
-0.746 + 0.099j)
self.assertAlmostEqual(p.phase_factors[Spin.down][0, 0, 0, 0],
0.372 - 0.654j)
# Two Li should have same phase factor.
self.assertAlmostEqual(p.phase_factors[Spin.up][0, 0, 0, 0],
p.phase_factors[Spin.up][0, 0, 1, 0])
self.assertAlmostEqual(p.phase_factors[Spin.up][0, 0, 2, 0],
-0.053 + 0.007j)
self.assertAlmostEqual(p.phase_factors[Spin.down][0, 0, 2, 0],
0.027 - 0.047j)
class XdatcarTest(unittest.TestCase):
def test_init(self):
filepath = os.path.join(test_dir, 'XDATCAR_4')
x = Xdatcar(filepath)
structures = x.structures
self.assertEqual(len(structures), 4)
for s in structures:
self.assertEqual(s.formula, "Li2 O1")
filepath = os.path.join(test_dir, 'XDATCAR_5')
x = Xdatcar(filepath)
structures = x.structures
self.assertEqual(len(structures), 4)
for s in structures:
self.assertEqual(s.formula, "Li2 O1")
x.concatenate(os.path.join(test_dir, 'XDATCAR_4'))
self.assertEqual(len(x.structures), 8)
self.assertIsNotNone(x.get_string())
class DynmatTest(unittest.TestCase):
def test_init(self):
# nosetests pymatgen/io/vasp/tests/test_outputs.py:DynmatTest.test_init
filepath = os.path.join(test_dir, 'DYNMAT')
d = Dynmat(filepath)
self.assertEqual(d.nspecs, 2)
self.assertEqual(d.natoms, 6)
self.assertEqual(d.ndisps, 3)
self.assertTrue(np.allclose(d.masses, [63.546, 196.966]))
self.assertTrue(4 in d.data)
self.assertTrue(2 in d.data[4])
self.assertTrue(np.allclose(
d.data[4][2]['dispvec'], [0., 0.05, 0.]
))