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"""Tests of VASP calculator interface."""
import tarfile
import tempfile
from io import StringIO
from pathlib import Path
import numpy as np
import pytest
from phonopy.file_IO import parse_FORCE_SETS
from phonopy.interface.phonopy_yaml import read_cell_yaml
from phonopy.interface.vasp import (
Vasprun,
VasprunxmlExpat,
get_vasp_structure_lines,
parse_set_of_forces,
read_vasp,
read_vasp_from_strings,
read_XDATCAR,
write_XDATCAR,
)
cwd = Path(__file__).parent
def test_read_vasp():
"""Test read_vasp."""
cell = read_vasp(cwd / ".." / "POSCAR_NaCl")
filename = cwd / "NaCl-vasp.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
@pytest.mark.parametrize(
"first_line_str, is_vasp4",
[(None, True), (None, False), ("my_comment", True), ("my_comment", False)],
)
def test_get_vasp_structure_lines(helper_methods, is_vasp4, first_line_str):
"""Test get_vasp_structure_lines (almost write_vasp)."""
filename = cwd / "NaCl-vasp.yaml"
cell_ref = read_cell_yaml(filename)
lines = get_vasp_structure_lines(
cell_ref, direct=True, is_vasp4=is_vasp4, first_line_str=first_line_str
)
cell = read_vasp_from_strings("\n".join(lines))
helper_methods.compare_cells_with_order(cell, cell_ref)
if is_vasp4:
# is_vasp4 is True, first_line_str is ignored.
assert lines[0] == "Na Cl"
elif first_line_str:
assert lines[0] == first_line_str
def test_get_vasp_structure_lines_shuffled_positions(helper_methods):
"""Test get_vasp_structure_lines with a cell having shuffled positions.
Order of atoms is sorted by chemical symbols. Therefore,
helper_methods.compare_cells_with_order fails.
"""
poscar_yaml = """lattice:
- [ 5.690301476175672, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 5.690301476175672, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 5.690301476175672 ] # c
points:
- symbol: Na # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 22.989769
- symbol: Cl # 2
coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 35.453000
- symbol: Na # 3
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 22.989769
- symbol: Cl # 4
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 35.453000
- symbol: Na # 5
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 22.989769
- symbol: Cl # 6
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 35.453000
- symbol: Na # 7
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 22.989769
- symbol: Cl # 8
coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 35.453000
"""
cell_ref = read_cell_yaml(StringIO(poscar_yaml))
lines = get_vasp_structure_lines(cell_ref, direct=True)
cell = read_vasp_from_strings("\n".join(lines))
with pytest.raises(AssertionError):
helper_methods.compare_cells_with_order(cell, cell_ref)
helper_methods.compare_cells(cell, cell_ref)
perm = []
for p_i in cell.scaled_positions:
diff = cell_ref.scaled_positions - p_i
diff -= np.rint(diff)
dists = np.linalg.norm(diff @ cell.cell, axis=1)
perm.append(np.where(dists < 1e-8)[0][0])
np.testing.assert_array_equal(perm, [0, 2, 4, 6, 1, 3, 5, 7])
np.testing.assert_array_equal(cell.numbers, [11, 11, 11, 11, 17, 17, 17, 17])
def test_parse_vasprun_xml():
"""Test parsing vasprun.xml with expat."""
filename_vasprun = cwd / "vasprun.xml.tar.bz2"
_tar = tarfile.open(filename_vasprun)
filename = cwd / ".." / "FORCE_SETS_NaCl"
dataset = parse_FORCE_SETS(filename=filename)
energy_ref = [-216.82820693, -216.82817843]
for i, member in enumerate(_tar.getmembers()):
vr = Vasprun(_tar.extractfile(member), use_expat=True)
# for force in vr.read_forces():
# print("% 15.8f % 15.8f % 15.8f" % tuple(force))
# print("")
ref = dataset["first_atoms"][i]["forces"]
np.testing.assert_allclose(ref, vr.read_forces(), atol=1e-8)
np.testing.assert_allclose(energy_ref[i], vr.read_energy(), atol=1e-8)
def test_VasprunxmlExpat():
"""Test VasprunxmlExpat."""
filename_vasprun = cwd / "vasprun.xml.tar.bz2"
_tar = tarfile.open(filename_vasprun)
for member in _tar.getmembers():
vasprun = VasprunxmlExpat(_tar.extractfile(member))
vasprun.parse()
np.testing.assert_equal(vasprun.fft_grid, [64, 64, 64])
np.testing.assert_equal(vasprun.fft_fine_grid, [128, 128, 128])
assert vasprun.efermi is None
assert vasprun.symbols == ["Na"] * 32 + ["Cl"] * 32
np.testing.assert_almost_equal(vasprun.NELECT, 448)
np.testing.assert_almost_equal(vasprun.volume, 1473.99433936)
break
def test_parse_set_of_forces():
"""Test parse_set_of_forces."""
filename_vasprun = cwd / "vasprun.xml.tar.bz2"
_tar = tarfile.open(filename_vasprun)
fps = [_tar.extractfile(member) for member in _tar.getmembers()]
calc_dataset = parse_set_of_forces(64, fps)
filename = cwd / ".." / "FORCE_SETS_NaCl"
dataset = parse_FORCE_SETS(filename=filename)
force_sets = [dataset["first_atoms"][i]["forces"] for i in (0, 1)]
energy_ref = [-216.82820693, -216.82817843]
np.testing.assert_allclose(
calc_dataset["points"][0][0], [0.00087869, 0.0, 0.0], atol=1e-5
)
np.testing.assert_allclose(
calc_dataset["points"][1][32], [0.25087869, 0.25, 0.25], atol=1e-5
)
np.testing.assert_allclose(force_sets, calc_dataset["forces"], atol=1e-8)
np.testing.assert_allclose(
energy_ref, calc_dataset["supercell_energies"], atol=1e-8
)
def test_read_XDATCAR():
"""Test read_XDATCAR."""
filename_xdatcar = cwd / "XDATCAR-NaCl"
lattice, positions = read_XDATCAR(filename_xdatcar)
np.testing.assert_allclose(lattice, np.eye(3) * 22.562240, atol=1e-8)
np.testing.assert_allclose(
positions[0, 0], [0.99854664, 0.00265936, 0.00701660], atol=1e-8
)
np.testing.assert_allclose(
positions[-1, -1], [0.75034458, 0.74972945, 0.87262656], atol=1e-8
)
def test_write_XDATCAR():
"""Test write_XDATCAR."""
filename_vasprun = cwd / "vasprun.xml.tar.bz2"
_tar = tarfile.open(filename_vasprun)
for _, member in enumerate(_tar.getmembers()):
vasprun = VasprunxmlExpat(_tar.extractfile(member))
vasprun.parse()
break
with tempfile.TemporaryFile() as fp:
write_XDATCAR(vasprunxml_expat=vasprun, fileptr=fp)
fp.seek(0)
lattice, positions = read_XDATCAR(fileptr=fp)
np.testing.assert_allclose(lattice, np.eye(3) * 11.38060295, atol=1e-8)
np.testing.assert_allclose(positions[0, 0], [0.00087869, 0, 0], atol=1e-8)
np.testing.assert_allclose(positions[-1, -1], [0.5, 0.5, 0.75], atol=1e-8)
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