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"""Tests for QE calculater interface."""
from __future__ import annotations
import pathlib
import numpy as np
from phonopy.file_IO import get_io_module_to_decompress
from phonopy.interface.phonopy_yaml import read_cell_yaml
from phonopy.interface.qe import PH_Q2R, read_pwscf
from phonopy.structure.symmetry import Symmetry
cwd = pathlib.Path(__file__).parent
def test_read_pwscf():
"""Test of read_pwscf with default scaled positions.
Keywords appear in the following order:
ATOMIC_SPECIES
ATOMIC_POSITIONS
CELL_PARAMETERS
K_POINTS
"""
_test_read_pwscf("NaCl-pwscf.in")
def test_read_pwscf_2():
"""Test of read_pwscf with default scaled positions.
Keywords appear in different order from test_read_pwscf.
ATOMIC_SPECIES
ATOMIC_POSITIONS
K_POINTS
CELL_PARAMETERS
"""
_test_read_pwscf("NaCl-pwscf-2.in")
def test_read_pwscf_angstrom():
"""Test of read_pwscf with angstrom coordinates."""
_test_read_pwscf("NaCl-pwscf-angstrom.in")
def test_read_pwscf_bohr():
"""Test of read_pwscf with bohr coordinates."""
_test_read_pwscf("NaCl-pwscf-bohr.in")
def test_read_pwscf_NaCl_Xn():
"""Test of read_pwscf."""
cell, pp_filenames = read_pwscf(cwd / "NaCl-pwscf-Xn.in")
print(cell)
symnums = pp_filenames.keys()
assert set(symnums) == {"Na", "Cl", "Cl1"}
np.testing.assert_allclose(
cell.masses,
[
22.98976928,
22.98976928,
22.98976928,
22.98976928,
35.453,
35.453,
70.0,
70.0,
],
)
assert ["Na", "Na", "Na", "Na", "Cl", "Cl", "Cl1", "Cl1"] == cell.symbols
cell_ref, pp_filenames = read_pwscf(cwd / "NaCl-pwscf.in")
symops = Symmetry(cell).symmetry_operations
symops_ref = Symmetry(cell_ref).symmetry_operations
np.testing.assert_allclose(symops["translations"], symops_ref["translations"])
np.testing.assert_array_equal(symops["rotations"], symops_ref["rotations"])
def test_make_fc_q2r():
"""Test make_fc_q2r."""
fc_0_10 = [
[6.06001648e-05, -3.48358667e-05, -8.14194922e-05],
[-3.48358667e-05, 1.21530469e-05, -1.65827117e-04],
[-8.14194922e-05, -1.65827117e-04, -1.14989696e-04],
]
fc_1_10 = [
[-4.05313258e-04, 1.92325415e-10, -9.48168187e-11],
[5.67066085e-11, -3.30626094e-04, 1.06319726e-03],
[-7.34782548e-11, 3.68433780e-04, 8.99705485e-04],
]
fc_filename = cwd / "NaCl-q2r.fc.xz"
myio = get_io_module_to_decompress(fc_filename)
with myio.open(fc_filename) as f:
primcell_filename = cwd / "NaCl-q2r.in"
cell, _ = read_pwscf(primcell_filename)
q2r = PH_Q2R(f)
q2r.run(cell)
assert q2r.fc is not None
np.testing.assert_allclose(fc_0_10, q2r.fc[0, 10], atol=1e-8)
np.testing.assert_allclose(fc_1_10, q2r.fc[1, 10], atol=1e-8)
def _test_read_pwscf(filename):
"""Test of read_pwscf."""
cell, pp_filenames = read_pwscf(cwd / filename)
filename = cwd / "NaCl-abinit-pwscf.yaml"
cell_ref = read_cell_yaml(filename)
assert (np.abs(cell.cell - cell_ref.cell) < 1e-5).all()
diff_pos = cell.scaled_positions - cell_ref.scaled_positions
diff_pos -= np.rint(diff_pos)
assert (np.abs(diff_pos) < 1e-5).all()
for s, s_r in zip(cell.symbols, cell_ref.symbols):
assert s == s_r
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