# IODATA is an input and output module for quantum chemistry.
# Copyright (C) 2011-2019 The IODATA Development Team
#
# This file is part of IODATA.
#
# IODATA is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 3
# of the License, or (at your option) any later version.
#
# IODATA is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>
# --
"""Test iodata.formats.poscar module."""
import os
from importlib.resources import as_file, files
import numpy as np
from numpy.testing import assert_allclose, assert_equal
from ..api import dump_one, load_one
from ..utils import angstrom, volume
[docs]
def test_load_poscar_water():
with as_file(files("iodata.test.data").joinpath("POSCAR.water")) as fn:
mol = load_one(str(fn))
assert mol.title == "Water molecule in a box"
assert_equal(mol.atnums, [8, 1, 1])
coords = np.array([0.074983 * 15, 0.903122 * 15, 0.000000])
assert_allclose(mol.atcoords[1], coords, atol=1e-7)
assert_allclose(volume(mol.cellvecs), 15**3, atol=1.0e-4)
[docs]
def test_load_poscar_cubicbn_cartesian():
with as_file(files("iodata.test.data").joinpath("POSCAR.cubicbn_cartesian")) as fn:
mol = load_one(str(fn))
assert mol.title == "Cubic BN"
assert_equal(mol.atnums, [5, 7])
assert_allclose(mol.atcoords[1], np.array([0.25] * 3) * 3.57 * angstrom, atol=1.0e-10)
assert_allclose(volume(mol.cellvecs), (3.57 * angstrom) ** 3 / 4, atol=1.0e-10)
[docs]
def test_load_poscar_cubicbn_direct():
with as_file(files("iodata.test.data").joinpath("POSCAR.cubicbn_direct")) as fn:
mol = load_one(str(fn))
assert mol.title == "Cubic BN"
assert_equal(mol.atnums, [5, 7])
assert_allclose(mol.atcoords[1], np.array([0.25] * 3) * 3.57 * angstrom, atol=1.0e-10)
assert_allclose(volume(mol.cellvecs), (3.57 * angstrom) ** 3 / 4, 1.0e-10)
[docs]
def test_load_dump_consistency(tmpdir):
with as_file(files("iodata.test.data").joinpath("water_element.xyz")) as fn:
mol0 = load_one(str(fn))
# random matrix generated from a uniform distribution on [0., 5.0)
mol0.cellvecs = np.array(
[
[2.05278155, 0.23284023, 1.59024118],
[4.96430141, 4.73044423, 4.67590975],
[3.48374425, 0.67931228, 0.66281160],
]
)
fn_tmp = os.path.join(tmpdir, "POSCAR")
dump_one(mol0, fn_tmp)
mol1 = load_one(fn_tmp)
assert mol0.title == mol1.title
assert_equal(mol1.atnums, [8, 1, 1])
assert_allclose(mol0.atcoords[1], mol1.atcoords[0], atol=1.0e-10)
assert_allclose(mol0.atcoords[0], mol1.atcoords[1], atol=1.0e-10)
assert_allclose(mol0.atcoords[2], mol1.atcoords[2], atol=1.0e-10)
assert_allclose(mol0.cellvecs, mol1.cellvecs, atol=1.0e-10)