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# fmt: off
import re
import tempfile
import numpy as np
import numpy.testing as npt
from ase import Atoms
from ase.io.cube import ATOMS, DATA, read_cube, read_cube_data, write_cube
from ase.units import Bohr
# Have some real data to write to a file
file_content = """Generated by octopus maya
git: 5b62360b6ec96e210d8ebbbd817bea74da18dfa8 build: \
Fri Oct 8 14:58:44 CEST 2021
5 -3.779452 -1.889726 -3.779452
5 1.889726 0.000000 0.000000
3 0.000000 1.889726 0.000000
5 0.000000 0.000000 0.000000
6 0.000000 0.000000 0.000000 0.000000
1 0.000000 0.000000 0.000000 2.057912
1 0.000000 1.940220 0.000000 -0.685971
1 0.000000 -0.970110 -1.680269 -0.685971
1 0.000000 -0.970110 1.680269 -0.685971
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
0.000000E+00 0.284545E-01 0.706656E-01 0.000000E+00 0.000000E+00
0.000000E+00 0.000000E+00 0.391115E-01 0.000000E+00 0.000000E+00
0.000000E+00 0.284545E-01 0.706656E-01 0.000000E+00 0.000000E+00
0.000000E+00 0.399121E-01 0.926179E-01 0.000000E+00 0.000000E+00
0.000000E+00 0.325065E-01 0.272831E+00 0.173787E+00 0.149557E-01
0.000000E+00 0.399121E-01 0.926179E-01 0.000000E+00 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
0.000000E+00 0.506939E-01 0.138292E+00 0.000000E+00 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00"""
def test_cube_writing():
d = 1.104 # N2 bondlength
at = Atoms("N2", [(0, 0, 0), (0, 0, d * Bohr)])
dummydata = np.arange(8).reshape((2, 2, 2))
origin_in = (42 * Bohr, 0, 0)
comment_regex = r"(Cube file from ASE, written on )([a-zA-Z ])*([0-9: ])*"
# create output
with tempfile.NamedTemporaryFile(mode="r+") as outfil:
write_cube(outfil, at, data=dummydata, origin=origin_in)
# reset read head
outfil.seek(0)
# Check default comment
comment_line = outfil.readline()
assert re.match(comment_regex, comment_line)
# Check constant string
assert outfil.readline() == ("OUTER LOOP: X, MIDDLE LOOP: Y, "
"INNER LOOP: Z\n")
# Check origin
origin_from_file = outfil.readline().split()[1:]
origin_from_file = tuple(
map(lambda p: float(p) * Bohr, origin_from_file))
assert origin_from_file == origin_in
# skip three lines
outfil.readline()
outfil.readline()
outfil.readline()
# check Atoms and positions
atom1 = outfil.readline().split()
assert atom1 == ["7", "0.000000", "0.000000", "0.000000", "0.000000"]
atom2 = outfil.readline().split()
assert atom2 == ["7", "0.000000", "0.000000",
"0.000000", f"{d:.6f}"]
# Check data
data_lines = list(
map(lambda l: float(l.rstrip("\n")), outfil.readlines()))
for idx, line in enumerate(data_lines):
assert float(idx) == line
def test_cube_reading():
with tempfile.NamedTemporaryFile(mode="r+") as cubefil:
# Write data to a file
cubefil.write(file_content)
cubefil.seek(0)
# read data using cube reading
result = read_cube(cubefil)
npt.assert_equal(
result[ATOMS].get_atomic_numbers(), np.array([6, 1, 1, 1, 1])
)
assert isinstance(result, dict)
# check data
assert result[DATA].shape == (5, 3, 5)
# check spacing
assert result["spacing"].shape == (3, 3)
# check that values are on the diagonal (correctness of order in
# reading)
npt.assert_almost_equal(
result["spacing"].diagonal() / Bohr,
np.array([1.889726, 1.889726, 0.000000]),
)
# check that sum is only 1.889726 for every column (correctness of
# value)
npt.assert_almost_equal(
result["spacing"].sum(axis=0) / Bohr,
np.array([1.889726, 1.889726, 0.000000]),
)
# check origin
assert result["origin"].shape == (3,)
npt.assert_almost_equal(
result["origin"], np.array([-3.779452, -1.889726, -3.779452]) * Bohr
)
# check PBC
assert (result[ATOMS].get_pbc() == (True, True, False)).all()
file_content_multiple = """ Benzene_Opt_Freq_B3LYP_6_31G_d_p_ MO=HOMO,LUMO
MO coefficients
-12 -8.797610 -9.151024 -6.512752 2
3 8.063676 0.000000 0.000000
3 0.000000 8.063676 0.000000
3 0.000000 0.000000 8.063676
6 6.000000 -2.284858 -1.319192 0.000000
6 6.000000 -2.284825 1.319137 0.000000
6 6.000000 0.000000 -2.638272 0.000000
6 6.000000 2.284845 -1.319103 0.000000
6 6.000000 -0.000008 2.638273 0.000000
6 6.000000 2.284870 1.319165 0.000000
1 1.000000 -4.062255 -2.345299 0.000000
1 1.000000 -0.000025 -4.690600 0.000000
1 1.000000 -4.062297 2.345119 0.000000
1 1.000000 0.000075 4.690601 0.000000
1 1.000000 4.062174 2.345444 0.000000
1 1.000000 4.062187 -2.345312 0.000000
2 21 22
-2.74760E-12 -8.90988E-12 5.59016E-10 1.81277E-09 8.76453E-16 2.84215E-15
-1.43957E-07 -2.02610E-07 2.92889E-05 4.12223E-05 4.59206E-11 6.46303E-11
-6.71453E-10 9.41323E-10 1.36612E-07 -1.91518E-07 2.14186E-13 -3.00272E-13
5.12861E-08 6.37111E-08 -1.04345E-05 -1.29624E-05 -1.63597E-11 -2.03231E-11
-3.53200E-05 -7.80160E-05 1.33966E-02 3.06849E-02 1.12667E-08 2.48862E-08
-3.26637E-06 4.17535E-06 6.66354E-04 -8.51133E-04 1.04193E-09 -1.33189E-09
8.90476E-11 1.24804E-10 -1.81173E-08 -2.53921E-08 -2.84052E-14 -3.98110E-14
3.14350E-06 1.73228E-06 -6.39634E-04 -3.52493E-04 -1.00274E-09 -5.52577E-10
6.74853E-09 -2.18944E-08 -1.37303E-06 4.45455E-06 -2.15271E-12 6.98406E-12
"""
def test_cube_reading_multiple():
with tempfile.NamedTemporaryFile(mode="r+") as cubefil:
# Write data to a file
cubefil.write(file_content_multiple)
cubefil.seek(0)
# read data using cube reading
result = read_cube(cubefil)
npt.assert_equal(
result[ATOMS].get_atomic_numbers(),
[6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1]
)
assert isinstance(result, dict)
# check data
assert result[DATA].shape == (3, 3, 3)
# and datas
assert len(result["datas"]) == 2
assert (
result[DATA].shape
== result["datas"][0].shape
== result["datas"][1].shape
)
# check labels
assert result["labels"] == [21, 22]
# check spacing
assert result["spacing"].shape == (3, 3)
# check that values are on the diagonal
# (correctness of order in reading)
npt.assert_almost_equal(
result["spacing"].diagonal() / Bohr,
np.array([8.063676, 8.063676, 8.063676]),
)
# check that sum is only 8.063676 for every column
# (correctness of value)
npt.assert_almost_equal(
result["spacing"].sum(axis=0) / Bohr,
np.array([8.063676, 8.063676, 8.063676]),
)
# check origin
assert result["origin"].shape == (3,)
npt.assert_almost_equal(
result["origin"], np.array([-8.797610, -9.151024, -6.512752]) * Bohr
)
# check PBC
# I don't know what this does so please check...
assert (result[ATOMS].get_pbc() == (True, True, True)).all()
def test_reading_using_io():
with tempfile.NamedTemporaryFile(mode="r+") as cubefil:
# Write data to a file
cubefil.write(file_content)
cubefil.seek(0)
result = read_cube_data(cubefil)
assert isinstance(result, tuple)
assert len(result) == 2
assert result[0].shape == (5, 3, 5)
assert isinstance(result[1], Atoms)
npt.assert_equal(result[1].get_atomic_numbers(),
np.array([6, 1, 1, 1, 1]))
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