def test_shortest_vector(self):
raise SkipTest
# simple cases
uc = UnitCell(numpy.identity(3,float)*3)
self.assertArraysAlmostEqual(uc.shortest_vector([3, 0, 1]), numpy.array([0, 0, 1]))
self.assertArraysAlmostEqual(uc.shortest_vector([-3, 0, 1]), numpy.array([0, 0, 1]))
self.assertArraysAlmostEqual(uc.shortest_vector([-2, 0, 1]), numpy.array([1, 0, 1]))
self.assertArraysAlmostEqual(uc.shortest_vector([-1.6, 1, 1]), numpy.array([1.4, 1, 1]))
self.assertArraysAlmostEqual(uc.shortest_vector([-1.4, 1, 1]), numpy.array([-1.4, 1, 1]))
# simple cases
uc = UnitCell(numpy.identity(3,float)*3, numpy.array([True, False, False]))
self.assertArraysAlmostEqual(uc.shortest_vector([3, 0, 1]), numpy.array([0, 0, 1]))
self.assertArraysAlmostEqual(uc.shortest_vector([3, 0, 3]), numpy.array([0, 0, 3]))
# random tests
for uc_counter in xrange(1000):
uc = self.get_random_uc(full=False)
for r_counter in xrange(10):
r0 = numpy.random.normal(0, 10, 3)
r1 = uc.shortest_vector(r0)
change = r1 - r0
self.assert_(numpy.dot(change, r0) <= 0)
#self.assert_(numpy.linalg.norm(r0) >= numpy.linalg.norm(r1))
index = uc.to_fractional(r0-r1)
self.assertArraysAlmostEqual(index, numpy.round(index), doabs=True)
index = uc.to_fractional(r1)
self.assert_(index.max()<0.5)
self.assert_(index.max()>=-0.5)
r0 = numpy.random.normal(0, 10, (10,3))
r1 = uc.shortest_vector(r0)
for i in xrange(10):
r1_row_bis = uc.shortest_vector(r0[i])
self.assertArraysAlmostEqual(r1_row_bis, r1[i], doabs=True)
def test_distance_matrix_periodic(self):
for i in xrange(1000):
N = 6
unit_cell = UnitCell(
numpy.random.uniform(0,1,(3,3)),
numpy.random.randint(0,2,3).astype(bool),
)
fractional = numpy.random.uniform(0,1,(N,3))
coordinates = unit_cell.to_cartesian(fractional)
from molmod.ext import molecules_distance_matrix
dm = molecules_distance_matrix(coordinates, unit_cell.matrix,
unit_cell.reciprocal)
for i in xrange(N):
for j in xrange(i,N):
delta = coordinates[j]-coordinates[i]
delta = unit_cell.shortest_vector(delta)
distance = numpy.linalg.norm(delta)
self.assertAlmostEqual(dm[i,j], distance)
def test_shortest_vector_aperiodic(self):
unit_cell = UnitCell(numpy.identity(3, float), numpy.zeros(3, bool))
shortest = unit_cell.shortest_vector(numpy.ones(3, float))
expected = numpy.ones(3, float)
self.assertArraysAlmostEqual(shortest, expected)
def test_shortest_vector_trivial(self):
uc = UnitCell(numpy.identity(3, float))
half = numpy.array([0.5,0.5,0.5])
self.assertArraysEqual(uc.shortest_vector(half), -half)
self.assertArraysEqual(uc.shortest_vector(-half), -half)
