def test_default_graph_periodic(self):
molecule = Molecule.from_file("input/lau.xyz")
uc = UnitCell.from_parameters3(
numpy.array([14.587, 12.877, 7.613])*angstrom,
numpy.array([90.000, 111.159, 90.000])*deg
)
uc = uc.alignment_c*uc
molecule = molecule.copy_with(unit_cell=uc)
molecule.set_default_graph()
self.assertEqual(molecule.graph.num_edges, 4*molecule.size/3)
def test_parameters(self):
for counter in xrange(100):
in_lengths = numpy.random.uniform(0.5, 1, (3,))
in_angles = numpy.random.uniform(0.3, numpy.pi/2, (3,))
try:
uc = UnitCell.from_parameters3(in_lengths, in_angles)
except ValueError, e:
continue
out_lengths, out_angles = uc.parameters
self.assertArraysAlmostEqual(in_lengths, out_lengths)
self.assertArraysAlmostEqual(in_angles, out_angles)
def iter_unit_cells(unit_cell_str, sub=None):
sub = fix_slice(sub)
if len(unit_cell_str) == 0:
uc = UnitCell(
numpy.array([[1,0,0],[0,1,0],[0,0,1]], float),
numpy.array([False,False,False]),
)
while True:
yield uc
if "," in unit_cell_str:
parameters = list(parse_unit(word) for word in unit_cell_str.split(",") if len(word) > 0)
if len(parameters) == 1:
a= parameters[0]
uc = UnitCell(
numpy.array([[a,0,0],[0,a,0],[0,0,a]], float),
numpy.array([True, True, True]),
)
elif len(parameters) == 3:
a,b,c = parameters
uc = UnitCell(
numpy.array([[a,0,0],[0,b,0],[0,0,c]], float),
numpy.array([True, True, True]),
)
elif len(parameters) == 6:
a,b,c,alpha,beta,gamma = parameters
uc = UnitCell.from_parameters3(
numpy.array([a,b,c]),
numpy.array([alpha,beta,gamma])
)
elif len(parameters) == 9:
uc = UnitCell(
numpy.array(parameters, float).reshape((3,3)),
numpy.array([True, True, True]),
)
else:
raise ValueError("If the --cell option contains comma's, one, three, six or nine value(s) are expected.")
while True:
yield uc
else:
filenames = ["%s.%s" % (unit_cell_str, suffix) for suffix in ["a.x", "a.y", "a.z", "b.x", "b.y", "b.z", "c.x", "c.y", "c.z"]]
dtype = numpy.dtype([("cell", float, (3,3))])
mtr = MultiTracksReader(filenames, dtype, sub=sub)
for row in mtr:
yield UnitCell(
numpy.array(row["cell"], float),
numpy.array([True, True, True]),
)
def test_distances_intra_lau_periodic(self):
coordinates = XYZFile("input/lau.xyz").geometries[0]
cutoff = periodic.max_radius*2
unit_cell = UnitCell.from_parameters3(
numpy.array([14.59, 12.88, 7.61])*angstrom,
numpy.array([ 90.0, 111.0, 90.0])*deg,
)
pair_search = PairSearchIntra(coordinates, cutoff, unit_cell)
self.verify_bins_intra_periodic(pair_search.bins)
distances = [
(frozenset([i0, i1]), distance)
for i0, i1, delta, distance
in pair_search
]
self.verify_distances_intra(coordinates, cutoff, distances, unit_cell)
