def test_random_lattice():
'''Testing random made box'''
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
wat = Molecule.from_arrays(type_array=['O', 'H', 'H'])
s = random_lattice_box([na, cl, wat], [160, 160, 160], [4, 4, 4])
eq_(s.dimensions['molecule'], 160 * 3)
eq_(s.dimensions['atom'], 160 * 5)
def test_sort():
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
[na, cl],
225,
repetitions=[3, 3, 3])
tsys.sort()
assert_npequal(tsys.type_array[:tsys.n_mol // 2], ['Cl'] * (tsys.n_mol // 2))
def test_crystal():
'''Building a crystal by using spacegroup module'''
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
[na, cl],
225,
repetitions=[13, 13, 13])
eq_(tsys.r_array.min(), 0.0)
eq_(tsys.r_array.max(), 12.5)
def test_serialization():
cl = Molecule([Atom.from_fields(type="Cl", r=[0.0, 0.0, 0.0])])
jsonstr = cl.to_json()
m = Molecule.from_json(jsonstr)
eq_(Molecule.from_json(jsonstr).to_json(), jsonstr)
na = Molecule([Atom("Na", [0.0, 0.0, 0.0])])
cl = Molecule([Atom("Cl", [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl], 225, repetitions=[3, 3, 3])
jsonstr = tsys.to_json()
eq_(System.from_json(jsonstr).to_json(), jsonstr)
def test_bonds():
# TODO: deprecate this shit
from chemlab.io import datafile
bz = datafile("tests/data/benzene.mol").read('molecule')
na = Molecule([Atom('O', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]), ])
# Adding bonds
s = System()
with s.batch() as b:
b.append(bz)
assert_npequal(s.bonds, bz.bonds)
assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2])
assert_npequal(s.bond_orders, bz.bond_orders)
s.add(bz)
assert_npequal(s.type_array, ['C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
'C', 'C', 'C'])
eq_(s.dimensions['atom'], 12)
assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 7)))
# Reordering
s.bonds = np.array([[0, 1], [6, 8]])
s.reorder_molecules([1, 0])
assert_eqbonds(s.bonds, np.array([[6, 7], [0, 2]]))
# Selection
ss = subsystem_from_molecules(s, [1])
assert_npequal(ss.bonds, np.array([[0, 1]]))
def _make_water():
mol = Molecule([Atom("O", [-4.99, 2.49, 0.0]),
Atom("H", [-4.02, 2.49, 0.0]),
Atom("H", [-5.32, 1.98, 1.0])],
bonds=[[0, 1], [0, 2]],
export={'hello': 1.0})
return mol
def test_random_lattice():
"""Testing random made box"""
na = Molecule([Atom("Na", [0.0, 0.0, 0.0])])
cl = Molecule([Atom("Cl", [0.0, 0.0, 0.0])])
wat = Molecule.from_arrays(type_array=["O", "H", "H"])
s = random_lattice_box([na, cl, wat], [160, 160, 160], [4, 4, 4])
eq_(s.dimensions["molecule"], 160 * 3)
eq_(s.dimensions["atom"], 160 * 5)
def test_init(self):
mol = _make_water()
eq_(mol.export, {'hello': 1.0})
assert_npequal(mol.get_attribute('type_array').value, ['O', 'H', 'H'])
assert_npequal(mol.type_array, ['O', 'H', 'H'])
assert_npequal(mol.bonds, [[0, 1], [0, 2]])
mol = Molecule.empty()
eq_(mol.dimensions['atom'], 0)
eq_(mol.dimensions['bond'], 0)
def test_init(self):
mol = _make_water()
eq_(mol.export, {"hello": 1.0})
assert_npequal(mol.get_attribute("type_array").value, ["O", "H", "H"])
assert_npequal(mol.type_array, ["O", "H", "H"])
assert_npequal(mol.bonds, [[0, 1], [0, 2]])
mol = Molecule.empty()
eq_(mol.dimensions["atom"], 0)
eq_(mol.dimensions["bond"], 0)
def test_serialization():
cl = Molecule([Atom.from_fields(type='Cl', r=[0.0, 0.0, 0.0])])
jsonstr = cl.to_json()
m = Molecule.from_json(jsonstr)
eq_(Molecule.from_json(jsonstr).to_json(), jsonstr)
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
[na, cl],
225,
repetitions=[3, 3, 3])
jsonstr = tsys.to_json()
eq_(System.from_json(jsonstr).to_json(), jsonstr)
