def test_set(self):
#print
for counter in xrange(100):
#print counter
uc = UnitCell()
uc.cell = numpy.random.uniform(-1, 1, (3, 3))
in_lengths = numpy.random.uniform(0.5, 1, (3,))
in_angles = numpy.random.uniform(0.3, math.pi/2, (3,))
#print
#print " === IN === "
#print in_lengths
#print in_angles
det_before = numpy.linalg.det(uc.cell)
try:
uc.set_parameters(in_lengths, in_angles)
except ValueError, e:
#print
#print e.__class__
#print e
#print in_lengths
#print in_angles/math.pi*180
#print "-"*20
continue
det_after = numpy.linalg.det(uc.cell)
#print " === OUT === "
out_lengths, out_angles = uc.get_parameters()
#print out_lengths
#print out_angles
self.assertAlmostEqual(sum((in_lengths - out_lengths)**2), 0.0, 5, "Lengths mismatch.")
self.assertAlmostEqual(sum((in_angles - out_angles)**2), 0.0, 5, "Angles mismatch: %s and %s" % (in_angles, out_angles))
self.assert_(det_before * det_after > 0, "Handedness has changed.")
def test_radius_indexes(self):
cell = numpy.array([
[1.5, 0, 0],
[0, 1.5, 0],
[0, 0, 1.5],
], float)
uc = UnitCell(cell, numpy.array([True, True, True]))
self.assert_((uc.get_radius_ranges(3.1)==3).all())
self.assertEqual(len(uc.get_radius_indexes(3.1)), 81)
def test_radius_indexes(self):
cell = numpy.array([
[1.5, 0, 0],
[0, 1.5, 0],
[0, 0, 1.5],
], float)
uc = UnitCell(cell, numpy.array([True, True, True]))
self.assert_((uc.get_radius_ranges(3.1) == 3).all())
self.assertEqual(len(uc.get_radius_indexes(3.1)), 81)
def test_shortest_vector(self):
for uc_counter in xrange(10):
#print counter
uc = UnitCell()
uc.cell = numpy.random.uniform(-1, 1, (3, 3))
uc.update_reciproke()
for r_counter in xrange(10):
r0 = numpy.random.normal(0, 10, 3)
r1 = uc.shortest_vector(r0)
self.assert_(numpy.linalg.norm(r0) <= numpy.linalg.norm(r1))
def create_pattern():
"Read the atom positions and transform them to the flat coordinates"
active, inactive = universe.get_active_inactive()
tmp_cell = UnitCell()
tmp_cell.add_cell_vector(universe.cell[:,active[0]])
tmp_cell.add_cell_vector(universe.cell[:,active[1]])
r = tmp_cell.calc_align_rotation_matrix()
return [
(atom.number, numpy.dot(r, atom.get_absolute_frame().t))
for atom in yield_atoms([universe])
]
def test_distances_intra_periodic(self):
molecule, binned_atoms = self.load_binned_atoms("lau.xyz")
unit_cell = UnitCell()
unit_cell.set_parameters(
numpy.array([14.59, 12.88, 7.61])*angstrom,
numpy.array([ 90.0, 111.0, 90.0])*degree,
)
distances = dict(
(frozenset([positioned1.id, positioned2.id]), result)
for (positioned1, positioned2), result
in IntraAnalyseNeighboringObjects(binned_atoms, self.compare_function)(unit_cell)
)
self.verify_intra(molecule, distances, unit_cell)
def test_add_periodicities(self):
for counter in xrange(100):
#print counter
uc = UnitCell()
uc.cell = numpy.random.uniform(-1, 1, (3, 3))
uc.cell_active[:] = False
uc.add_cell_vector(numpy.random.uniform(-2, 2, 3))
uc.add_cell_vector(numpy.random.uniform(-2, 2, 3))
uc.add_cell_vector(numpy.random.uniform(-2, 2, 3))
def test_add_periodicities(self):
for counter in xrange(100):
#print counter
uc = UnitCell()
uc.cell = numpy.random.uniform(-1, 1, (3, 3))
uc.cell_active[:] = False
uc.add_cell_vector(numpy.random.uniform(-2,2,3))
uc.add_cell_vector(numpy.random.uniform(-2,2,3))
uc.add_cell_vector(numpy.random.uniform(-2,2,3))
def test_set(self):
#print
for counter in xrange(100):
#print counter
uc = UnitCell()
uc.cell = numpy.random.uniform(-1, 1, (3, 3))
in_lengths = numpy.random.uniform(0.5, 1, (3, ))
in_angles = numpy.random.uniform(0.3, math.pi / 2, (3, ))
#print
#print " === IN === "
#print in_lengths
#print in_angles
det_before = numpy.linalg.det(uc.cell)
try:
uc.set_parameters(in_lengths, in_angles)
except ValueError, e:
#print
#print e.__class__
#print e
#print in_lengths
#print in_angles/math.pi*180
#print "-"*20
continue
det_after = numpy.linalg.det(uc.cell)
#print " === OUT === "
out_lengths, out_angles = uc.get_parameters()
#print out_lengths
#print out_angles
self.assertAlmostEqual(sum((in_lengths - out_lengths)**2), 0.0, 5,
"Lengths mismatch.")
self.assertAlmostEqual(
sum((in_angles - out_angles)**2), 0.0, 5,
"Angles mismatch: %s and %s" % (in_angles, out_angles))
self.assert_(det_before * det_after > 0, "Handedness has changed.")
def test_shortest_vector(self):
for uc_counter in xrange(10):
#print counter
uc = UnitCell()
uc.cell = numpy.random.uniform(-1, 1, (3, 3))
uc.update_reciproke()
for r_counter in xrange(10):
r0 = numpy.random.normal(0, 10, 3)
r1 = uc.shortest_vector(r0)
self.assert_(numpy.linalg.norm(r0) <= numpy.linalg.norm(r1))
def convert_to_value(self, representation):
lengths, angles = ComposedInTable.convert_to_value(self, representation)
unit_cell = UnitCell(self.saved_value)
unit_cell.set_parameters(lengths, angles)
return unit_cell.cell
def convert_to_representation(self, value):
unit_cell = UnitCell(value)
self.saved_value = value
lengths, angles = unit_cell.get_parameters()
return ComposedInTable.convert_to_representation(self, (lengths, angles))