def test_lmp_parse_image_skew_fail():
name = 'lmp_parse_other'
target = ["\n",
"4 atoms\n",
"2 atom types\n",
"\n",
"0 5 xlo xhi\n",
"0 5 ylo yhi\n",
"0 5 zlo zhi\n",
"1 2 3 xy xz yz\n",
"\n",
"Masses\n",
"\n",
"1 22.99 #Na\n",
"2 34.99 #Cl\n",
"\n",
"Atoms\n",
"\n",
"1 1 0.0 0.0 0.0 0 0 0\n",
"2 1 2.5 2.5 0.0 0 0 0\n",
"3 2 0.0 2.5 0.0 0 0 0\n",
"4 2 2.5 0.0 0.0 0 0 0\n",
"\n"]
Mol, _ = lammpsData.parser(name, target)
assert Mol.nat == 4
assert float_equal(Mol.getCellDim(fmt='angstrom'), 1)
assert vec_equal(Mol.getVec(), ((5, 0, 0), (1, 5, 0), (2, 3, 5)))
failtarget = ["\n",
"4 atoms\n",
"2 atom types\n",
"\n",
"0 5 xlo xhi\n",
"0 5 ylo yhi\n",
"0 5 zlo zhi\n",
"1 2 3 xy xz yz\n",
"\n",
"Masses\n",
"\n",
"1 22.99\n",
"2 34.99\n",
"\n",
"Atoms\n",
"\n",
"1 1 0.0 0.0 0.0 0 0 0\n",
"2 1 2.5 2.5 0.0 0 0 0\n",
"3 2 0.0 2.5 0.0 0 0 0\n",
"4 2 2.5 0.0 0.0 0 0 0\n",
"\n"]
try:
Mol, _ = lammpsData.parser(name, failtarget)
except NotImplementedError:
assert True
except:
assert False
else:
assert False
def test_lmp_parse_atomstyles():
name = "lmp_parse"
head = ["\n",
"4 atoms\n",
"2 atom types\n",
"\n",
"0 5 xlo xhi\n",
"0 5 ylo yhi\n",
"0 5 zlo zhi\n",
"\n",
"Masses\n",
"\n",
"1 22.99 #Na\n",
"2 34.99 #Cl\n",
"\n"]
atoms = [["Atoms # atomic\n",
"\n",
"1 1 0.0 0.0 0.0\n",
"2 1 2.5 2.5 0.0\n",
"3 2 0.0 2.5 0.0\n",
"4 2 2.5 0.0 0.0\n",
"\n"],
["Atoms\n",
"\n",
"1 1 0.0 0.0 0.0\n",
"2 1 2.5 2.5 0.0\n",
"3 2 0.0 2.5 0.0\n",
"4 2 2.5 0.0 0.0\n",
"\n"],
["Atoms\n",
"\n",
"1 1 1 0.0 0.0 0.0\n",
"2 1 1 2.5 2.5 0.0\n",
"3 1 2 0.0 2.5 0.0\n",
"4 1 2 2.5 0.0 0.0\n",
"\n"],
["Atoms # bond\n",
"\n",
"1 1 1 0.0 0.0 0.0\n",
"2 1 1 2.5 2.5 0.0\n",
"3 1 2 0.0 2.5 0.0\n",
"4 1 2 2.5 0.0 0.0\n",
"\n"],
["Atoms\n",
"\n",
"1 1 1 1 0.0 0.0 0.0\n",
"2 1 1 1 2.5 2.5 0.0\n",
"3 1 2 -1 0.0 2.5 0.0\n",
"4 1 2 -1 2.5 0.0 0.0\n",
"\n"],
["Atoms # full\n",
"\n",
"1 1 1 1 0.0 0.0 0.0\n",
"2 1 1 1 2.5 2.5 0.0\n",
"3 1 2 -1 0.0 2.5 0.0\n",
"4 1 2 -1 2.5 0.0 0.0\n",
"\n"],
]
for a in atoms:
Mol, _ = lammpsData.parser(name, head + a)
assert Mol.nat == 4
assert Mol.ntyp == 2
assert Mol.getTypes() == ['Na', 'Cl']
assert Mol.pse['Cl']['m'] == 34.99
assert float_equal(Mol.getCellDim(fmt='angstrom'), 1)
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 5, 0), (0, 0, 5)))
assert list(map(len, Mol.getBonds(1.1))) == [4, 2, 2, 0, 0, 0, 0, 0]
assert atom_equal(Mol.getAtom(0), ['Na', [0, 0, 0]])
assert atom_equal(Mol.getAtom(1), ['Na', [2.5, 2.5, 0]])
assert atom_equal(Mol.getAtom(2), ['Cl', [0, 2.5, 0]])
assert atom_equal(Mol.getAtom(3), ['Cl', [2.5, 0, 0]])
assert atom_equal(Mol.getAtom(0, charge=True), ['Na', [0, 0, 0], 1.])
assert atom_equal(Mol.getAtom(2, charge=True), ['Cl', [0, 2.5, 0], -1.0])