def test_distances_periodic():
coords = np.array([[0.0, 0.0, 0.0],
[0.0, 0.9, 0.0],
[0.0, 0.2, 0.0]])
coords = np.random.random((1000, 3))
periodic = np.array([1.0, 1.0, 1.0])
cutoff = 0.1
# Consistency checks
print "Simple"
t = time.time()
dist_simple = distance_matrix(coords, coords, cutoff, method="simple",
periodic=periodic)
print -t + time.time()
print "Cell-lists"
t = time.time()
dist_clist = distance_matrix(coords, coords, cutoff,
method="cell-lists", periodic=periodic)
print -t + time.time()
#print dist_simple
#print dist_clist
# errors = (dist_simple != dist_clist.todense()).nonzero()
# iderr = (errors[0][0, 0], errors[1][0,0])
# print iderr
# print coords[iderr[0]], coords[iderr[1]]
# print dist_simple[iderr]
# print dist_clist[iderr]
assert np.allclose(dist_simple, dist_clist.todense())
def test_distances(coords, coords_b, cutoff):
# Consistency checks
print "Simple"
t = time.time()
dist_simple = distance_matrix(coords, coords_b, cutoff, method="simple")
print -t + time.time()
print "Cell-lists"
t = time.time()
dist_clist = distance_matrix(coords, coords_b, cutoff, method="cell-lists")
print -t + time.time()
print dist_simple
print dist_clist.todense()
assert np.allclose(dist_simple, dist_clist.todense())
def test_distances(coords, coords_b, cutoff):
# Consistency checks
print "Simple"
t = time.time()
dist_simple = distance_matrix(coords, coords_b, cutoff, method="simple")
print -t + time.time()
print "Cell-lists"
t = time.time()
dist_clist = distance_matrix(coords, coords_b, cutoff, method="cell-lists")
print -t + time.time()
print dist_simple
print dist_clist.todense()
assert np.allclose(dist_simple, dist_clist.todense())
def test_distances_periodic():
coords = np.array([[0.0, 0.0, 0.0], [0.0, 0.9, 0.0], [0.0, 0.2, 0.0]])
coords = np.random.random((1000, 3))
periodic = np.array([1.0, 1.0, 1.0])
cutoff = 0.1
# Consistency checks
print "Simple"
t = time.time()
dist_simple = distance_matrix(coords,
coords,
cutoff,
method="simple",
periodic=periodic)
print -t + time.time()
print "Cell-lists"
t = time.time()
dist_clist = distance_matrix(coords,
coords,
cutoff,
method="cell-lists",
periodic=periodic)
print -t + time.time()
#print dist_simple
#print dist_clist
# errors = (dist_simple != dist_clist.todense()).nonzero()
# iderr = (errors[0][0, 0], errors[1][0,0])
# print iderr
# print coords[iderr[0]], coords[iderr[1]]
# print dist_simple[iderr]
# print dist_clist[iderr]
assert np.allclose(dist_simple, dist_clist.todense())
def test_distances_periodic():
coords = np.array([[0.0, 0.0, 0.0],
[0.0, 0.9, 0.0],
[0.0, 0.2, 0.0]])
coords = np.random.random((1000, 3))
periodic = np.array([1.0, 1.0, 1.0])
cutoff = 0.1
# Consistency checks
print "Simple"
t = time.time()
dist_simple = distance_matrix(coords, coords, cutoff, method="simple",
periodic=periodic)
print -t + time.time()
print "Cell-lists"
t = time.time()
dist_clist = distance_matrix(coords, coords, cutoff,
method="cell-lists", periodic=periodic)
print -t + time.time()
assert np.allclose(dist_simple, dist_clist.todense())
def test_distances_periodic():
coords = np.array([[0.0, 0.0, 0.0],
[0.0, 0.9, 0.0],
[0.0, 0.2, 0.0]])
coords = np.random.random((1000, 3))
periodic = np.array([1.0, 1.0, 1.0])
cutoff = 0.1
# Consistency checks
print "Simple"
t = time.time()
dist_simple = distance_matrix(coords, coords, cutoff, method="simple",
periodic=periodic)
print -t + time.time()
print "Cell-lists"
t = time.time()
dist_clist = distance_matrix(coords, coords, cutoff,
method="cell-lists", periodic=periodic)
print -t + time.time()
assert np.allclose(dist_simple, dist_clist.todense())
