def test_save_load_octree():
np.random.seed(int(0x4d3d3d3))
pos = np.random.normal(0.5, scale=0.05,
size=(NPART, 3)) * (DRE - DLE) + DLE
octree = ParticleOctreeContainer((1, 1, 1), DLE, DRE)
octree.n_ref = 32
for i in range(3):
np.clip(pos[:, i], DLE[i], DRE[i], pos[:, i])
# Convert to integers
pos = np.floor((pos - DLE) / dx).astype("uint64")
morton = get_morton_indices(pos)
morton.sort()
octree.add(morton)
octree.finalize()
saved = octree.save_octree()
loaded = OctreeContainer.load_octree(saved)
always = AlwaysSelector(None)
ir1 = octree.ires(always)
ir2 = loaded.ires(always)
yield assert_equal, ir1, ir2
fc1 = octree.fcoords(always)
fc2 = loaded.fcoords(always)
yield assert_equal, fc1, fc2
fw1 = octree.fwidth(always)
fw2 = loaded.fwidth(always)
yield assert_equal, fw1, fw2
def test_add_particles_random():
np.random.seed(int(0x4d3d3d3))
pos = np.random.normal(0.5, scale=0.05,
size=(NPART, 3)) * (DRE - DLE) + DLE
# Now convert to integers
for i in range(3):
np.clip(pos[:, i], DLE[i], DRE[i], pos[:, i])
# Convert to integers
pos = np.floor((pos - DLE) / dx).astype("uint64")
morton = get_morton_indices(pos)
morton.sort()
for ndom in [1, 2, 4, 8]:
octree = ParticleOctreeContainer((1, 1, 1), DLE, DRE)
octree.n_ref = 32
for dom, split in enumerate(np.array_split(morton, ndom)):
octree.add(split)
octree.finalize()
# This visits every oct.
tc = octree.recursively_count()
total_count = np.zeros(len(tc), dtype="int32")
for i in sorted(tc):
total_count[i] = tc[i]
yield assert_equal, octree.nocts, total_count.sum()
# This visits every cell -- including those covered by octs.
#for dom in range(ndom):
# level_count += octree.count_levels(total_count.size-1, dom, mask)
yield assert_equal, total_count, [1, 8, 64, 64, 256, 536, 1856, 1672]
def test_save_load_octree():
np.random.seed(int(0x4d3d3d3))
pos = np.random.normal(0.5, scale=0.05, size=(NPART,3)) * (DRE-DLE) + DLE
octree = ParticleOctreeContainer((1, 1, 1), DLE, DRE)
octree.n_ref = 32
for i in range(3):
np.clip(pos[:,i], DLE[i], DRE[i], pos[:,i])
# Convert to integers
pos = np.floor((pos - DLE)/dx).astype("uint64")
morton = get_morton_indices(pos)
morton.sort()
octree.add(morton)
octree.finalize()
saved = octree.save_octree()
loaded = OctreeContainer.load_octree(saved)
always = AlwaysSelector(None)
ir1 = octree.ires(always)
ir2 = loaded.ires(always)
yield assert_equal, ir1, ir2
fc1 = octree.fcoords(always)
fc2 = loaded.fcoords(always)
yield assert_equal, fc1, fc2
fw1 = octree.fwidth(always)
fw2 = loaded.fwidth(always)
yield assert_equal, fw1, fw2
def test_add_particles_random():
np.random.seed(int(0x4d3d3d3))
pos = np.random.normal(0.5, scale=0.05, size=(NPART,3)) * (DRE-DLE) + DLE
# Now convert to integers
for i in range(3):
np.clip(pos[:,i], DLE[i], DRE[i], pos[:,i])
# Convert to integers
pos = np.floor((pos - DLE)/dx).astype("uint64")
morton = get_morton_indices(pos)
morton.sort()
for ndom in [1, 2, 4, 8]:
octree = ParticleOctreeContainer((1, 1, 1), DLE, DRE)
octree.n_ref = 32
for dom, split in enumerate(np.array_split(morton, ndom)):
octree.add(split)
octree.finalize()
# This visits every oct.
tc = octree.recursively_count()
total_count = np.zeros(len(tc), dtype="int32")
for i in sorted(tc):
total_count[i] = tc[i]
yield assert_equal, octree.nocts, total_count.sum()
# This visits every cell -- including those covered by octs.
#for dom in range(ndom):
# level_count += octree.count_levels(total_count.size-1, dom, mask)
yield assert_equal, total_count, [1, 8, 64, 64, 256, 536, 1856, 1672]
def test_get_morton_indices():
from yt.utilities.lib.geometry_utils import get_morton_indices, get_morton_indices_unravel
INDEX_MAX_64 = np.uint64(2097151)
li = np.arange(6, dtype=np.uint64).reshape((2, 3))
mi_ans = np.array([10, 229], dtype=np.uint64)
mi_out = get_morton_indices(li)
mi_out2 = get_morton_indices_unravel(li[:, 0], li[:, 1], li[:, 2])
assert_array_equal(mi_out, mi_ans)
assert_array_equal(mi_out2, mi_ans)
li[0, :] = INDEX_MAX_64 * np.ones(3, dtype=np.uint64)
assert_raises(ValueError, get_morton_indices, li)
assert_raises(ValueError, get_morton_indices_unravel, li[:, 0], li[:, 1],
li[:, 2])
def test_morton_neighbor():
from yt.utilities.lib.geometry_utils import get_morton_indices, morton_neighbor
order = 20
imax = np.uint64(1 << order)
p = np.array(
[
[imax / 2, imax / 2, imax / 2],
[imax / 2, imax / 2, 0],
[imax / 2, imax / 2, imax],
],
dtype=np.uint64,
)
p_ans = np.array(
[
[imax / 2, imax / 2, imax / 2 + 1],
[imax / 2, imax / 2, imax / 2 - 1],
[imax / 2, imax / 2, imax - 1],
[imax / 2, imax / 2, 1],
[imax / 2, imax / 2 + 1, imax / 2 + 1],
[imax / 2 - 1, imax / 2 - 1, imax / 2],
[imax / 2 - 1, imax / 2, imax / 2 + 1],
[imax / 2, imax / 2 - 1, imax - 1],
[imax / 2, imax / 2 + 1, 1],
],
dtype=np.uint64,
)
mi_ans = get_morton_indices(p_ans)
assert_equal(morton_neighbor(p[0, :], [2], [+1], imax), mi_ans[0])
assert_equal(morton_neighbor(p[0, :], [2], [-1], imax), mi_ans[1])
assert_equal(morton_neighbor(p[1, :], [2], [-1], imax, periodic=False), -1)
assert_equal(morton_neighbor(p[2, :], [2], [+1], imax, periodic=False), -1)
assert_equal(morton_neighbor(p[1, :], [2], [-1], imax, periodic=True),
mi_ans[2])
assert_equal(morton_neighbor(p[2, :], [2], [+1], imax, periodic=True),
mi_ans[3])
assert_equal(morton_neighbor(p[0, :], [1, 2], [+1, +1], imax), mi_ans[4])
assert_equal(morton_neighbor(p[0, :], [0, 1], [-1, -1], imax), mi_ans[5])
assert_equal(morton_neighbor(p[0, :], [0, 2], [-1, +1], imax), mi_ans[6])
assert_equal(
morton_neighbor(p[1, :], [1, 2], [-1, -1], imax, periodic=False), -1)
assert_equal(
morton_neighbor(p[2, :], [1, 2], [+1, +1], imax, periodic=False), -1)
assert_equal(
morton_neighbor(p[1, :], [1, 2], [-1, -1], imax, periodic=True),
mi_ans[7])
assert_equal(
morton_neighbor(p[2, :], [1, 2], [+1, +1], imax, periodic=True),
mi_ans[8])
def test_get_morton_neighbors():
from yt.utilities.lib.geometry_utils import get_morton_indices, get_morton_neighbors
order = 20
imax = 1 << order
p = np.array(
[
[imax / 2, imax / 2, imax / 2],
[imax / 2, imax / 2, 0],
[imax / 2, imax / 2, imax],
],
dtype=np.uint64,
)
pn_non = [
np.array(
[
# x +/- 1
[imax / 2 + 1, imax / 2, imax / 2],
[imax / 2 + 1, imax / 2 + 1, imax / 2],
[imax / 2 + 1, imax / 2 + 1, imax / 2 + 1],
[imax / 2 + 1, imax / 2 + 1, imax / 2 - 1],
[imax / 2 + 1, imax / 2 - 1, imax / 2],
[imax / 2 + 1, imax / 2 - 1, imax / 2 + 1],
[imax / 2 + 1, imax / 2 - 1, imax / 2 - 1],
[imax / 2 + 1, imax / 2, imax / 2 + 1],
[imax / 2 + 1, imax / 2, imax / 2 - 1],
[imax / 2 - 1, imax / 2, imax / 2],
[imax / 2 - 1, imax / 2 + 1, imax / 2],
[imax / 2 - 1, imax / 2 + 1, imax / 2 + 1],
[imax / 2 - 1, imax / 2 + 1, imax / 2 - 1],
[imax / 2 - 1, imax / 2 - 1, imax / 2],
[imax / 2 - 1, imax / 2 - 1, imax / 2 + 1],
[imax / 2 - 1, imax / 2 - 1, imax / 2 - 1],
[imax / 2 - 1, imax / 2, imax / 2 + 1],
[imax / 2 - 1, imax / 2, imax / 2 - 1],
# y +/- 1
[imax / 2, imax / 2 + 1, imax / 2],
[imax / 2, imax / 2 + 1, imax / 2 + 1],
[imax / 2, imax / 2 + 1, imax / 2 - 1],
[imax / 2, imax / 2 - 1, imax / 2],
[imax / 2, imax / 2 - 1, imax / 2 + 1],
[imax / 2, imax / 2 - 1, imax / 2 - 1],
# x +/- 1
[imax / 2, imax / 2, imax / 2 + 1],
[imax / 2, imax / 2, imax / 2 - 1],
],
dtype=np.uint64,
),
np.array(
[
# x +/- 1
[imax / 2 + 1, imax / 2, 0],
[imax / 2 + 1, imax / 2 + 1, 0],
[imax / 2 + 1, imax / 2 + 1, 1],
[imax / 2 + 1, imax / 2 - 1, 0],
[imax / 2 + 1, imax / 2 - 1, 1],
[imax / 2 + 1, imax / 2, 1],
[imax / 2 - 1, imax / 2, 0],
[imax / 2 - 1, imax / 2 + 1, 0],
[imax / 2 - 1, imax / 2 + 1, 1],
[imax / 2 - 1, imax / 2 - 1, 0],
[imax / 2 - 1, imax / 2 - 1, 1],
[imax / 2 - 1, imax / 2, 1],
# y +/- 1
[imax / 2, imax / 2 + 1, 0],
[imax / 2, imax / 2 + 1, 1],
[imax / 2, imax / 2 - 1, 0],
[imax / 2, imax / 2 - 1, 1],
# z +/- 1
[imax / 2, imax / 2, 0 + 1],
],
dtype=np.uint64,
),
np.array(
[
# x +/- 1
[imax / 2 + 1, imax / 2, imax],
[imax / 2 + 1, imax / 2 + 1, imax],
[imax / 2 + 1, imax / 2 + 1, imax - 1],
[imax / 2 + 1, imax / 2 - 1, imax],
[imax / 2 + 1, imax / 2 - 1, imax - 1],
[imax / 2 + 1, imax / 2, imax - 1],
[imax / 2 - 1, imax / 2, imax],
[imax / 2 - 1, imax / 2 + 1, imax],
[imax / 2 - 1, imax / 2 + 1, imax - 1],
[imax / 2 - 1, imax / 2 - 1, imax],
[imax / 2 - 1, imax / 2 - 1, imax - 1],
[imax / 2 - 1, imax / 2, imax - 1],
# y +/- 1
[imax / 2, imax / 2 + 1, imax],
[imax / 2, imax / 2 + 1, imax - 1],
[imax / 2, imax / 2 - 1, imax],
[imax / 2, imax / 2 - 1, imax - 1],
# z +/- 1
[imax / 2, imax / 2, imax - 1],
],
dtype=np.uint64,
),
]
pn_per = [
np.array(
[
# x +/- 1
[imax / 2 + 1, imax / 2, imax / 2],
[imax / 2 + 1, imax / 2 + 1, imax / 2],
[imax / 2 + 1, imax / 2 + 1, imax / 2 + 1],
[imax / 2 + 1, imax / 2 + 1, imax / 2 - 1],
[imax / 2 + 1, imax / 2 - 1, imax / 2],
[imax / 2 + 1, imax / 2 - 1, imax / 2 + 1],
[imax / 2 + 1, imax / 2 - 1, imax / 2 - 1],
[imax / 2 + 1, imax / 2, imax / 2 + 1],
[imax / 2 + 1, imax / 2, imax / 2 - 1],
[imax / 2 - 1, imax / 2, imax / 2],
[imax / 2 - 1, imax / 2 + 1, imax / 2],
[imax / 2 - 1, imax / 2 + 1, imax / 2 + 1],
[imax / 2 - 1, imax / 2 + 1, imax / 2 - 1],
[imax / 2 - 1, imax / 2 - 1, imax / 2],
[imax / 2 - 1, imax / 2 - 1, imax / 2 + 1],
[imax / 2 - 1, imax / 2 - 1, imax / 2 - 1],
[imax / 2 - 1, imax / 2, imax / 2 + 1],
[imax / 2 - 1, imax / 2, imax / 2 - 1],
# y +/- 1
[imax / 2, imax / 2 + 1, imax / 2],
[imax / 2, imax / 2 + 1, imax / 2 + 1],
[imax / 2, imax / 2 + 1, imax / 2 - 1],
[imax / 2, imax / 2 - 1, imax / 2],
[imax / 2, imax / 2 - 1, imax / 2 + 1],
[imax / 2, imax / 2 - 1, imax / 2 - 1],
# z +/- 1
[imax / 2, imax / 2, imax / 2 + 1],
[imax / 2, imax / 2, imax / 2 - 1],
],
dtype=np.uint64,
),
np.array(
[
# x +/- 1
[imax / 2 + 1, imax / 2, 0],
[imax / 2 + 1, imax / 2 + 1, 0],
[imax / 2 + 1, imax / 2 + 1, 1],
[imax / 2 + 1, imax / 2 + 1, imax - 1],
[imax / 2 + 1, imax / 2 - 1, 0],
[imax / 2 + 1, imax / 2 - 1, 1],
[imax / 2 + 1, imax / 2 - 1, imax - 1],
[imax / 2 + 1, imax / 2, 1],
[imax / 2 + 1, imax / 2, imax - 1],
[imax / 2 - 1, imax / 2, 0],
[imax / 2 - 1, imax / 2 + 1, 0],
[imax / 2 - 1, imax / 2 + 1, 1],
[imax / 2 - 1, imax / 2 + 1, imax - 1],
[imax / 2 - 1, imax / 2 - 1, 0],
[imax / 2 - 1, imax / 2 - 1, 1],
[imax / 2 - 1, imax / 2 - 1, imax - 1],
[imax / 2 - 1, imax / 2, 1],
[imax / 2 - 1, imax / 2, imax - 1],
# y +/- 1
[imax / 2, imax / 2 + 1, 0],
[imax / 2, imax / 2 + 1, 1],
[imax / 2, imax / 2 + 1, imax - 1],
[imax / 2, imax / 2 - 1, 0],
[imax / 2, imax / 2 - 1, 1],
[imax / 2, imax / 2 - 1, imax - 1],
# z +/- 1
[imax / 2, imax / 2, 0 + 1],
[imax / 2, imax / 2, imax - 1],
],
dtype=np.uint64,
),
np.array(
[
# x +/- 1
[imax / 2 + 1, imax / 2, imax],
[imax / 2 + 1, imax / 2 + 1, imax],
[imax / 2 + 1, imax / 2 + 1, 1],
[imax / 2 + 1, imax / 2 + 1, imax - 1],
[imax / 2 + 1, imax / 2 - 1, imax],
[imax / 2 + 1, imax / 2 - 1, 1],
[imax / 2 + 1, imax / 2 - 1, imax - 1],
[imax / 2 + 1, imax / 2, 1],
[imax / 2 + 1, imax / 2, imax - 1],
[imax / 2 - 1, imax / 2, imax],
[imax / 2 - 1, imax / 2 + 1, imax],
[imax / 2 - 1, imax / 2 + 1, 1],
[imax / 2 - 1, imax / 2 + 1, imax - 1],
[imax / 2 - 1, imax / 2 - 1, imax],
[imax / 2 - 1, imax / 2 - 1, 1],
[imax / 2 - 1, imax / 2 - 1, imax - 1],
[imax / 2 - 1, imax / 2, 1],
[imax / 2 - 1, imax / 2, imax - 1],
# y +/- 1
[imax / 2, imax / 2 + 1, imax],
[imax / 2, imax / 2 + 1, 1],
[imax / 2, imax / 2 + 1, imax - 1],
[imax / 2, imax / 2 - 1, imax],
[imax / 2, imax / 2 - 1, 1],
[imax / 2, imax / 2 - 1, imax - 1],
# z +/- 1
[imax / 2, imax / 2, 1],
[imax / 2, imax / 2, imax - 1],
],
dtype=np.uint64,
),
]
mi = get_morton_indices(p)
N = mi.shape[0]
# Non-periodic
for i in range(N):
out = get_morton_neighbors(np.array([mi[i]], dtype=np.uint64),
order=order,
periodic=False)
ans = get_morton_indices(np.vstack([p[i, :], pn_non[i]]))
assert_array_equal(np.unique(out),
np.unique(ans),
err_msg=f"Non-periodic: {i}")
# Periodic
for i in range(N):
out = get_morton_neighbors(np.array([mi[i]], dtype=np.uint64),
order=order,
periodic=True)
ans = get_morton_indices(np.vstack([p[i, :], pn_per[i]]))
assert_array_equal(np.unique(out),
np.unique(ans),
err_msg=f"Periodic: {i}")
