def test_1(self):
for prec in self.precs:
# 2 sets of 100 points in 10*10*10 box
n = 100
boxsize = 10.0
d_max = 2.0
a = (np.random.random(n * 3).reshape(n, 3) * boxsize).astype(prec)
b = (np.random.random(n * 3).reshape(n, 3) * boxsize).astype(prec)
box = (np.ones(3) * boxsize).astype(prec)
idx, dists = capped_distance_array(a, b, d_max, box)
# Brute force approach, do all n * n comparisons
ref = np.zeros(n * n, dtype=prec)
cgmath.inter_distance_array_withpbc(a, b, box, ref)
ref = ref.reshape(n, n)
# Check all distances under 2.0 were caught
ref_idx = np.where(ref < d_max)
for x, y in zip(ref_idx[0], ref_idx[1]):
# Order can be reversed
assert (x, y in idx) or (y, x in idx)
# Check all reported distances were accurate
# ie, ref[idx[i]] == dists[i]
for (i, j), d in zip(idx, dists):
assert ref[i, j] == d
def test_1(self):
a = np.arange(30).reshape(10, 3).astype(np.float32)
b = np.arange(30).reshape(10, 3).astype(np.float32)
res = np.zeros(100).astype(np.float32)
box = np.ones(3).astype(np.float32) * 30
cgmath.inter_distance_array_withpbc(a, b, box, res)
ref = np.ravel(util.slow_inter_distance_withpbc(a, b, 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)
b = np.arange(30).reshape(10, 3).astype(prec)
res = np.zeros(100).astype(prec)
box = np.ones(3).astype(prec) * 30
cgmath.inter_distance_array_withpbc(a, b, box, res)
ref = np.ravel(util.slow_inter_distance_withpbc(a, b, 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_distance_array(cg1, cg2):
"""Calculate all pairwise distances between pairs in cg1 and cg2
:Returns:
indices, distances
indices - (n, 2) array of indices
The first index refers to coordinates within cg1
The second index from cg2
distances - (n) Array of distances
"""
if not cg1 == cg2:
raise ValueError("CellGrids are not compatible")
# calculate required size of array
Nreq = _calculate_distance_array_size(cg1, cg2)
dist = np.empty(Nreq, dtype=np.float32)
indices = np.empty((Nreq, 2), dtype=np.int)
box = cg1.box
# Calculate distances cell by cell
pos = 0
# For each cell in cg1
for cell in cg1:
# Iterate over all neighbours in other cellgrid
for addr in itertools.chain([cell.address], cell.all_neighbours):
other = cg2[addr]
cgmath.inter_distance_array_withpbc(
cell.coordinates,
other.coordinates,
box,
dist[pos:]
)
cgmath.inter_index_array(
cell.indices,
other.indices,
indices[pos:]
)
pos += len(cell) * len(other)
return indices, dist
def test_1(self):
for prec in self.precs:
n = 100
boxsize = 10.0
d_max = 2.0
a = (np.random.random(n * 3).reshape(n, 3) * boxsize).astype(prec)
box = (np.ones(3) * boxsize).astype(prec)
idx, dists = capped_self_distance_array(a, d_max, box)
ref = np.zeros(n * n, dtype=prec)
cgmath.inter_distance_array_withpbc(a, a, box, ref)
ref = ref.reshape(n, n)
# Mask out coordinates seeing themselves
ref[np.diag_indices_from(ref)] = d_max + 1.0
ref_idx = np.where(ref < d_max)
for x, y in zip(ref_idx[0], ref_idx[1]):
assert (x, y in idx) or (y, x in idx)
for (i, j), d in zip(idx, dists):
assert ref[i, j] == d
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
def cellgrid_distance_array(cg1, cg2):
"""Calculate all pairwise distances between pairs in cg1 and cg2
:Returns:
indices, distances
indices - (n, 2) array of indices
The first index refers to coordinates within cg1
The second index from cg2
distances - (n) Array of distances
"""
if not cg1 == cg2:
raise ValueError("CellGrids are not compatible")
# calculate required size of array
Nreq = _calculate_distance_array_size(cg1, cg2)
dist = np.empty(Nreq, dtype=cg1.datatype)
indices = np.empty((Nreq, 2), dtype=np.int)
box = cg1.box
# Calculate distances cell by cell
pos = 0
# For each cell in cg1
for cell in cg1:
# Iterate over all neighbours in other cellgrid
for addr in itertools.chain([cell.address], cell.all_neighbours):
other = cg2[addr]
cgmath.inter_distance_array_withpbc(cell.coordinates,
other.coordinates, box,
dist[pos:])
cgmath.inter_index_array(cell.indices, other.indices,
indices[pos:])
pos += len(cell) * len(other)
return indices, dist
def brute_force_method(a, b, box):
res = np.zeros((a.shape[0] * b.shape[0]), dtype=PREC)
return inter_distance_array_withpbc(a, b, box, res)
def brute_force_method(a, b, box):
res = np.zeros((a.shape[0] * b.shape[0]), dtype=PREC)
return inter_distance_array_withpbc(a, b, box, res)