def test_1(self):
a = np.arange(30).reshape(10, 3).astype(np.float32)
n = 10
res = np.zeros(n * (n-1) // 2, dtype=np.float32)
box = np.ones(3).astype(np.float32) * 30
cgmath.intra_distance_array_withpbc(a, box, res)
ref = util.slow_intra_distance_withpbc(a, box)
assert_array_almost_equal(ref, res)
def test_1(self):
for prec in self.precs:
a = np.arange(30).reshape(10, 3).astype(prec)
n = 10
res = np.zeros(n * (n-1) // 2, dtype=prec)
box = np.ones(3).astype(prec) * 30
cgmath.intra_distance_array_withpbc(a, box, res)
ref = util.slow_intra_distance_withpbc(a, box)
assert_array_almost_equal(ref, res)
def cellgrid_self_distance_array(cg1):
"""Calculate all pairwise distances within a certain CellGrid
:Returns:
indices, distances
indices - (n, 2)
distances (n)
"""
box = cg1.box
Nreq = _calculate_self_distance_array_size(cg1)
indices = np.empty((Nreq, 2), dtype=np.int)
dist = np.empty(Nreq, dtype=np.float32)
pos = 0
for cell in cg1:
n = len(cell)
if n > 1:
# Do own cell as a self distance comparison
cgmath.intra_distance_array_withpbc(
cell.coordinates,
box,
dist[pos:]
)
cgmath.intra_index_array(
cell.indices,
indices[pos:]
)
pos += n * (n - 1) // 2
# Then all half neighbours as a full comparison
for addr in cell.half_neighbours:
other = cg1[addr]
if not other:
continue
cgmath.inter_distance_array_withpbc(
cell.coordinates,
other.coordinates,
box,
dist[pos:]
)
cgmath.inter_index_array(
cell.indices,
other.indices,
indices[pos:]
)
pos += n * len(other)
return indices, dist
def cellgrid_self_distance_array(cg1):
"""Calculate all pairwise distances within a certain CellGrid
:Returns:
indices, distances
indices - (n, 2)
distances (n)
"""
box = cg1.box
Nreq = _calculate_self_distance_array_size(cg1)
indices = np.empty((Nreq, 2), dtype=np.int)
dist = np.empty(Nreq, dtype=cg1.datatype)
pos = 0
for cell in cg1:
n = len(cell)
if n > 1:
# Do own cell as a self distance comparison
cgmath.intra_distance_array_withpbc(cell.coordinates, box,
dist[pos:])
cgmath.intra_index_array(cell.indices, indices[pos:])
pos += n * (n - 1) // 2
# Then all half neighbours as a full comparison
for addr in cell.half_neighbours:
other = cg1[addr]
if not other:
continue
cgmath.inter_distance_array_withpbc(cell.coordinates,
other.coordinates, box,
dist[pos:])
cgmath.inter_index_array(cell.indices, other.indices,
indices[pos:])
pos += n * len(other)
return indices, dist