def test_set_distance_noadjust(four_particle_45_twist):
mol = four_particle_45_twist
origpos = mol.positions.copy()
olddist = mdt.distance(mol.atoms[1], mol.atoms[2])
mdt.set_distance(mol.atoms[1],
mol.atoms[2],
2.0 * olddist,
adjustmol=False)
assert abs(mdt.distance(mol.atoms[1], mol.atoms[2]) -
2.0 * olddist) <= 1e-9 * u.angstrom
assert (origpos[0]
== mol.positions[0]).all() and (origpos[-1]
== mol.positions[-1]).all()
def test_atomic_distance_measures_are_consistent(objkey, request):
mol = request.getfuncargvalue(objkey)
distance_array = mol.calc_distance_array()
for i, j in itertools.product(xrange(3), xrange(3)):
ai, aj = mol.atoms[i], mol.atoms[j]
assert ai.distance(aj) == distance_array[i, j]
assert mdt.distance(ai, aj) == distance_array[i, j]
np.testing.assert_almost_equal(np.sum((ai.position - aj.position)**2).defunits_value(),
(distance_array[i, j]**2).defunits_value(),
decimal=10)
def test_set_distance_and_adjust(four_particle_45_twist):
mol = four_particle_45_twist
origpos = mol.positions.copy()
distance = mdt.DistanceMonitor(mol.atoms[1], mol.atoms[2])
olddist = distance.value
distance.value *= 2.0
displacement = np.sqrt(((origpos[0] - mol.positions[0])**2).sum()) + \
np.sqrt(((origpos[-1] - mol.positions[-1])**2).sum())
assert abs(mdt.distance(mol.atoms[1], mol.atoms[2]) -
2.0 * olddist) <= 1e-9 * u.angstrom
assert abs(displacement - olddist) < 1.0e-9 * u.angstrom
def test_atomic_distance_measures_are_consistent(objkey, request):
mol = request.getfixturevalue(objkey)
distance_array = mol.calc_distance_array()
for i, j in itertools.product(range(3), range(3)):
ai, aj = mol.atoms[i], mol.atoms[j]
assert ai.distance(aj) == distance_array[i, j]
assert mdt.distance(ai, aj) == distance_array[i, j]
np.testing.assert_almost_equal(np.sum(
(ai.position - aj.position)**2).defunits_value(),
(distance_array[i,
j]**2).defunits_value(),
decimal=10)
def distance(self, a1, a2):
a1, a2 = list(map(self._get_traj_atom, (a1, a2)))
return mdt.distance(a1, a2)