def test_cube_parse_angstrom():
name = 'cube_angstrom'
target = ["Comment 1\n",
"Comment 2\n",
" 8 0.5000 0.5000 0.5000\n",
" -5 1.0000 0.0000 0.0000\n",
" -5 0.0000 1.0000 0.0000\n",
" -5 0.0000 0.0000 1.0000\n",
" 11 0.0000 0.0000 0.0000 0.0000\n",
" 17 0.0000 4.7243 0.0000 0.0000\n",
" 11 0.0000 4.7243 4.7243 0.0000\n",
" 17 0.0000 0.0000 4.7243 0.0000\n",
" 17 0.0000 0.0000 0.0000 4.7243\n",
" 11 0.0000 4.7243 0.0000 4.7243\n",
" 17 0.0000 4.7243 4.7243 4.7243\n",
" 11 0.0000 0.0000 4.7243 4.7243\n",
" 0.000 1.000 2.000 5.196 8.000\n",
" 1.000 1.414 2.236 5.292 8.062\n",
" 2.000 2.236 2.828 5.568 8.246\n",
" 3.000 3.162 3.606 6.000 8.544\n",
" 4.000 4.123 4.472 6.557 8.944\n",
"\n",
" 1.000 1.414 2.236 5.292 8.062\n",
" 1.414 1.732 2.449 5.385 8.124\n",
" 2.236 2.449 3.000 5.657 8.307\n",
" 3.162 3.317 3.742 6.083 8.602\n",
" 4.123 4.243 4.583 6.633 9.000\n",
"\n",
" 2.000 2.236 2.828 5.568 8.246\n",
" 2.236 2.449 3.000 5.657 8.307\n",
" 2.828 3.000 3.464 5.916 8.485\n",
" 3.606 3.742 4.123 6.325 8.775\n",
" 4.472 4.583 4.899 6.856 9.165\n",
"\n",
" 3.000 3.162 3.606 6.000 8.544\n",
" 3.162 3.317 3.742 6.083 8.602\n",
" 3.606 3.742 4.123 6.325 8.775\n",
" 4.243 4.359 4.690 6.708 9.055\n",
" 5.000 5.099 5.385 7.211 9.434\n",
"\n",
" 4.000 4.123 4.472 6.557 8.944\n",
" 4.123 4.243 4.583 6.633 9.000\n",
" 4.472 4.583 4.899 6.856 9.165\n",
" 5.000 5.099 5.385 7.211 9.434\n",
" 5.657 5.745 6.000 7.681 9.798\n"]
Mol, _ = cube.parser(name, target)
assert Mol.name == name
assert Mol.nat == 8
assert Mol.ntyp == 2
assert Mol.getTypes() == ['Na', 'Cl']
assert Mol.getFmt() == 'angstrom'
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 5, 0), (0, 0, 5)))
assert list(map(len, Mol.getBonds(1.1))) == [12, 4, 4, 0, 4, 0, 0, 0]
assert vec_equal(Mol.getVolOffset(), [0.5, 0.5, 0.5])
def test_cube_parse_bohr():
name = 'cube_angstrom'
target = ["Comment 1\n",
"Comment 2\n",
" 8 0.0000 0.0000 0.0000\n",
" 3 5.0000 0.0000 0.0000\n",
" 3 0.0000 5.0000 0.0000\n",
" 3 0.0000 0.0000 5.0000\n",
" 11 1.0000 0.0000 0.0000 0.0000\n",
" 17 -1.0000 4.7243 0.0000 0.0000\n",
" 11 1.0000 4.7243 4.7243 0.0000\n",
" 17 -1.0000 0.0000 4.7243 0.0000\n",
" 17 -1.0000 0.0000 0.0000 4.7243\n",
" 11 1.0000 4.7243 0.0000 4.7243\n",
" 17 -1.0000 4.7243 4.7243 4.7243\n",
" 11 1.0000 0.0000 4.7243 4.7243\n",
" 0.000 1.000 2.000 3.000 4.000\n",
" 5.000 6.000 7.000 8.000 9.000\n",
" 10.000 11.000 12.000 13.000 14.000\n",
" 15.000 16.000 17.000 18.000 19.000\n",
" 20.000 21.000 22.000 23.000 24.000\n",
" 25.000 26.000\n"]
Mol, _ = cube.parser(name, target)
assert Mol.name == name
assert Mol.nat == 8
assert Mol.ntyp == 2
assert Mol.getTypes() == ['Na', 'Cl']
assert Mol.getFmt() == 'bohr'
assert vec_equal(Mol.getVec(), ((15, 0, 0), (0, 15, 0), (0, 0, 15)))
assert list(map(len, Mol.getBonds(1.1))) == [12, 0, 0, 0, 0, 0, 0, 0]
assert vec_equal(Mol.getVolOffset(), [0, 0, 0])
assert vec_equal(Mol.getVol(),
(((0, 1, 2), (3, 4, 5), (6, 7, 8)),
((9, 10, 11), (12, 13, 14), (15, 16, 17)),
((18, 19, 20), (21, 22, 23), (24, 25, 26))))
assert vec_equal(Mol.getVolGradient(),
((((9, 9, 9), (9, 9, 9), (9, 9, 9)),
((-18, -18, -18), (-18, -18, -18), (-18, -18, -18)),
((9, 9, 9), (9, 9, 9), (9, 9, 9))),
(((3, 3, 3), (-6, -6, -6), (3, 3, 3)),
((3, 3, 3), (-6, -6, -6), (3, 3, 3)),
((3, 3, 3), (-6, -6, -6), (3, 3, 3))),
(((1, -2, 1), (1, -2, 1), (1, -2, 1)),
((1, -2, 1), (1, -2, 1), (1, -2, 1)),
((1, -2, 1), (1, -2, 1), (1, -2, 1)))))
assert atom_equal(Mol.getAtom(0, charge=True), ['Na', (0, 0, 0), 1.0])