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# Copyright (c) 2024, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Unit tests for utilities."""
from cclib.parser import utils
import numpy
import scipy.spatial.transform
class FloatTest:
def test_float_basic(self) -> None:
"""Are floats converted from strings correctly?"""
assert utils.float("0.0") == 0.0
assert utils.float("1.0") == 1.0
assert utils.float("-1.0") == -1.0
def test_float_numeric_format(self) -> None:
"""Does numeric formatting get converted correctly?"""
assert utils.float("1.2345E+02") == 123.45
assert utils.float("1.2345D+02") == 123.45
def test_float_stars(self) -> None:
"""Does the function return nan for stars?"""
assert numpy.isnan(utils.float("*"))
assert numpy.isnan(utils.float("*****"))
class ConvertorTest:
def test_convertor(self) -> None:
assert f"{utils.convertor(8.0, 'eV', 'wavenumber'):.3f}" == "64524.354"
class GetRotationTest:
delta = 1e-14
@classmethod
def setup_class(cls) -> None:
cls.r = scipy.spatial.transform.Rotation.from_euler("xyz", [15, 25, 35], degrees=True)
cls.t = numpy.array([-1, 0, 2])
cls.a = numpy.array([[1.0, 1.0, 1.0], [0.0, 1.0, 2.0], [0.0, 0.0, 0.0], [0.0, 0.0, 4.0]])
cls.b = cls.r.apply(cls.a + cls.t)
def test_default(self) -> None:
"""Is the rotation is correct?"""
_r = utils.get_rotation(self.a, self.b)
# as_dcm is renamed to from_matrix in scipy 1.4.0 and will be removed in sicpy 1.6.0
if hasattr(self.r, "as_matrix"):
numpy.testing.assert_allclose(self.r.as_matrix(), _r.as_matrix(), atol=self.delta)
else:
numpy.testing.assert_allclose(self.r.as_dcm(), _r.as_dcm(), atol=self.delta)
def test_two_atoms(self) -> None:
"""Is the rotation is correct for 2 atoms?"""
a2 = self.a[:2]
b2 = self.b[:2]
rotated_diff = self.r.apply(a2) - utils.get_rotation(a2, b2).apply(a2)
# rotated_diff should be translation
numpy.testing.assert_allclose(rotated_diff[0], rotated_diff[1], atol=self.delta)
def test_one_atom(self) -> None:
"""Is the rotation is identity for 1 atom?"""
a1 = self.a[:1]
b1 = self.b[:1]
if hasattr(self.r, "as_matrix"):
numpy.testing.assert_allclose(
numpy.eye(3), utils.get_rotation(a1, b1).as_matrix(), atol=self.delta
)
else:
numpy.testing.assert_allclose(
numpy.eye(3), utils.get_rotation(a1, b1).as_dcm(), atol=self.delta
)
class PeriodicTableTest:
def test_periodictable(self) -> None:
t = utils.PeriodicTable()
assert t.element[6] == "C"
assert t.number["C"] == 6
assert t.element[44] == "Ru"
assert t.number["Au"] == 79
class WidthSplitterTest:
def test_default(self) -> None:
"""Does the splitter remove empty fields by default properly?"""
fixed_splitter = utils.WidthSplitter((4, 3, 5, 6, 10, 10, 10, 10, 10, 10))
line_full = " 60 H 10 s 0.14639 0.00000 0.00000 -0.00000 -0.00000 0.00000"
line_truncated = " 1 C 1 s -0.00000 -0.00000 0.00000"
ref_full = [
"60",
"H",
"10",
"s",
"0.14639",
"0.00000",
"0.00000",
"-0.00000",
"-0.00000",
"0.00000",
]
ref_truncated = ["1", "C", "1", "s", "-0.00000", "-0.00000", "0.00000"]
tokens_full = fixed_splitter.split(line_full)
tokens_truncated = fixed_splitter.split(line_truncated)
assert ref_full == tokens_full
assert ref_truncated == tokens_truncated
def test_no_truncation(self) -> None:
"""Does the splitter return even the empty fields when asked?"""
fixed_splitter = utils.WidthSplitter((4, 3, 5, 6, 10, 10, 10, 10, 10, 10))
line = " 1 C 1 s -0.00000 -0.00000 0.00000"
ref_not_truncated = ["1", "C", "1", "s", "-0.00000", "-0.00000", "0.00000", "", "", ""]
tokens_not_truncated = fixed_splitter.split(line, truncate=False)
assert ref_not_truncated == tokens_not_truncated
class SymmetrizeTest:
def test_dim_from_tblock_size(self) -> None:
assert utils._dim_from_tblock_size(1) == 1
# This isn't possible until we fully move to pytest.
# with pytest.raises(
# RuntimeError,
# match="The number of elements (2) isn't possible for a matrix triangle"
# ):
# assert utils._dim_from_tblock_size(2)
assert utils._dim_from_tblock_size(3) == 2
assert utils._dim_from_tblock_size(6) == 3
assert utils._dim_from_tblock_size(10) == 4
def test_block_to_matrix(self) -> None:
inp = numpy.array([1, 2, 3, 4, 5, 6], dtype=int)
ref = numpy.array([[1, 2, 4], [2, 3, 5], [4, 5, 6]], dtype=int)
numpy.testing.assert_equal(utils.block_to_matrix(inp), ref)
def test_symmetrize(self) -> None:
inp = numpy.array([[1, 9, 7], [4, 8, 3], [6, 2, 5]], dtype=int)
ref_lower = numpy.array([[1, 4, 6], [4, 8, 2], [6, 2, 5]], dtype=int)
ref_upper = numpy.array([[1, 9, 7], [9, 8, 3], [7, 3, 5]], dtype=int)
numpy.testing.assert_equal(utils.symmetrize(inp, "lower"), ref_lower)
numpy.testing.assert_equal(utils.symmetrize(inp, "upper"), ref_upper)
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