def threefry_random_bits(key: jnp.ndarray, bit_width, shape):
"""Sample uniform random bits of given width and shape using PRNG key."""
if not _is_threefry_prng_key(key):
raise TypeError("_random_bits got invalid prng key.")
if bit_width not in (8, 16, 32, 64):
raise TypeError("requires 8-, 16-, 32- or 64-bit field width.")
shape = core.as_named_shape(shape)
for name, size in shape.named_items:
real_size = lax.psum(1, name)
if real_size != size:
raise ValueError(
f"The shape of axis {name} was specified as {size}, "
f"but it really is {real_size}")
axis_index = lax.axis_index(name)
key = threefry_fold_in(key, axis_index)
size = prod(shape.positional)
# Compute ceil(bit_width * size / 32) in a way that is friendly to shape
# polymorphism
max_count, r = divmod(bit_width * size, 32)
if r > 0:
max_count += 1
if core.is_constant_dim(max_count):
nblocks, rem = divmod(max_count, jnp.iinfo(np.uint32).max)
else:
nblocks, rem = 0, max_count
if not nblocks:
bits = threefry_2x32(key, lax.iota(np.uint32, rem))
else:
keys = threefry_split(key, nblocks + 1)
subkeys, last_key = keys[:-1], keys[-1]
blocks = vmap(threefry_2x32,
in_axes=(0, None))(subkeys,
lax.iota(np.uint32,
jnp.iinfo(np.uint32).max))
last = threefry_2x32(last_key, lax.iota(np.uint32, rem))
bits = lax.concatenate([blocks.ravel(), last], 0)
dtype = UINT_DTYPES[bit_width]
if bit_width == 64:
bits = [lax.convert_element_type(x, dtype) for x in jnp.split(bits, 2)]
bits = lax.shift_left(bits[0], dtype(32)) | bits[1]
elif bit_width in [8, 16]:
# this is essentially bits.view(dtype)[:size]
bits = lax.bitwise_and(
np.uint32(np.iinfo(dtype).max),
lax.shift_right_logical(
lax.broadcast(bits, (1, )),
lax.mul(
np.uint32(bit_width),
lax.broadcasted_iota(np.uint32, (32 // bit_width, 1), 0))))
bits = lax.reshape(bits, (np.uint32(max_count * 32 // bit_width), ),
(1, 0))
bits = lax.convert_element_type(bits, dtype)[:size]
return lax.reshape(bits, shape)
def linspace(start,
stop,
num=50,
endpoint=True,
retstep=False,
dtype=None,
axis=0):
"""Implementation of linspace differentiable w.r.t. start and stop args."""
lax._check_user_dtype_supported(dtype, "linspace")
dtype = np.float32 if dtype is None else dtype
bounds_shape = list(lax.broadcast_shapes(np.shape(start), np.shape(stop)))
axis = len(bounds_shape) if axis == -1 else axis
bounds_shape.insert(axis, 1)
iota_shape = [
1,
] * len(bounds_shape)
iota_shape[axis] = num
delta = (stop - start) / num
if endpoint:
delta *= num / (num - 1)
out = (jnp.reshape(start, bounds_shape) +
jnp.reshape(lax.iota(dtype, num), iota_shape) *
jnp.reshape(delta, bounds_shape))
if retstep:
return jnp.array(out, dtype=dtype), delta
else:
return jnp.array(out, dtype=dtype)
def body_fn(i, permutation):
j = swaps[..., i]
iotas = np.ix_(*(lax.iota(np.int32, b) for b in batch_dims))
x = permutation[..., i]
y = permutation[iotas + (j, )]
permutation = ops.index_update(permutation, ops.index[..., i], y)
return ops.index_update(permutation, ops.index[iotas + (j, )], x)
def _lu_jvp_rule(primals, tangents):
a, = primals
a_dot, = tangents
lu, pivots = lu_p.bind(a)
if a_dot is ad_util.zero:
return (core.pack(
(lu, pivots)), ad.TangentTuple((ad_util.zero, ad_util.zero)))
a_shape = np.shape(a)
m, n = a_shape[-2:]
dtype = lax.dtype(a)
k = min(m, n)
permutation = lu_pivots_to_permutation(pivots, m)
batch_dims = a_shape[:-2]
iotas = np.ix_(*(lax.iota(np.int32, b) for b in batch_dims + (1, )))
x = a_dot[iotas[:-1] + (permutation, slice(None))]
# Differentiation of Matrix Functionals Using Triangular Factorization
# F. R. De Hoog, R. S. Anderssen, and M. A. Lukas
#
# LU = A
# ==> L'U + LU' = A'
# ==> inv(L) . L' + U' . inv(U) = inv(L) A' inv(U)
# ==> L' = L . tril(inv(L) . A' . inv(U), -1)
# U' = triu(inv(L) . A' . inv(U)) . U
ndims = len(a_shape)
l_padding = [(0, 0, 0)] * ndims
l_padding[-1] = (0, m - k, 0)
zero = np._constant_like(lu, 0)
l = lax.pad(np.tril(lu[..., :, :k], -1), zero, l_padding)
l = l + np.eye(m, m, dtype=dtype)
u_eye = lax.pad(np.eye(n - k, n - k, dtype=dtype), zero,
((k, 0, 0), (k, 0, 0)))
u_padding = [(0, 0, 0)] * ndims
u_padding[-2] = (0, n - k, 0)
u = lax.pad(np.triu(lu[..., :k, :]), zero, u_padding) + u_eye
la = triangular_solve(l,
x,
left_side=True,
transpose_a=False,
lower=True,
unit_diagonal=True)
lau = triangular_solve(u,
la,
left_side=False,
transpose_a=False,
lower=False)
l_dot = np.matmul(l, np.tril(lau, -1))
u_dot = np.matmul(np.triu(lau), u)
lu_dot = l_dot + u_dot
return (lu, pivots), (lu_dot, ad_util.zero)
def _lu_pivots_body_fn(i, permutation_and_swaps):
permutation, swaps = permutation_and_swaps
batch_dims = swaps.shape[:-1]
j = swaps[..., i]
iotas = np.ix_(*(lax.iota(np.int32, b) for b in batch_dims))
x = permutation[..., i]
y = permutation[iotas + (j, )]
permutation = ops.index_update(permutation, ops.index[..., i], y)
return ops.index_update(permutation, ops.index[iotas + (j, )], x), swaps
def init(key, shape, dtype=np.float32):
# assume shape is (horizon, num_state_dims, num_action_dims)
T, n, m = shape
def generate_lqr(key, _):
new_key, p_key, a_key, b_key, q_key, r_key = random.split(key, 6)
pmat = pmat_initializer(p_key, (n, n), dtype=dtype)
lqr = LQR(
A=amat_initializer(a_key, (n, n), dtype=dtype),
B=bmat_initializer(b_key, (n, m), dtype=dtype),
Q=qmat_initializer(q_key, (n, n), dtype=dtype),
R=rmat_initializer(r_key, (m, m), dtype=dtype),
)
return new_key, (pmat, lqr)
return lax.scan(generate_lqr, key, lax.iota(T))[1]
def rollout(x_init, lqr, policy, num_steps):
def timevarying_step(x_t, inputs):
t, lqr = inputs
u_t = policy(x_t, t)
x_tp1 = lqr.A @ x_t + lqr.B @ u_t
c_t = x_t @ (lqr.Q @ x_t) + u_t @ (lqr.R @ u_t)
return x_tp1, (x_t, u_t, c_t)
def nonvarying_step(x_t, t):
return timevarying_step(x_t, (t, lqr))
step_rollout = nonvarying_step
values = lax.iota(np.int32, num_steps)
if lqr.A.ndim == 3:
step_rollout = timevarying_step
values = (values, lqr)
return lax.scan(step_rollout, x_init, values)
def cell_list_fn(position: Array,
capacity_overflow_update: Optional[Tuple[
int, bool, Callable[..., CellList]]] = None,
extra_capacity: int = 0,
**kwargs) -> CellList:
N = position.shape[0]
dim = position.shape[1]
if dim != 2 and dim != 3:
# NOTE(schsam): Do we want to check this in compute_fn as well?
raise ValueError(
f'Cell list spatial dimension must be 2 or 3. Found {dim}.')
_, cell_size, cells_per_side, cell_count = \
_cell_dimensions(dim, box_size, minimum_cell_size)
if capacity_overflow_update is None:
cell_capacity = _estimate_cell_capacity(position, box_size,
cell_size,
buffer_size_multiplier)
cell_capacity += extra_capacity
overflow = False
update_fn = cell_list_fn
else:
cell_capacity, overflow, update_fn = capacity_overflow_update
hash_multipliers = _compute_hash_constants(dim, cells_per_side)
# Create cell list data.
particle_id = lax.iota(i32, N)
# NOTE(schsam): We use the convention that particles that are successfully,
# copied have their true id whereas particles empty slots have id = N.
# Then when we copy data back from the grid, copy it to an array of shape
# [N + 1, output_dimension] and then truncate it to an array of shape
# [N, output_dimension] which ignores the empty slots.
cell_position = jnp.zeros((cell_count * cell_capacity, dim),
dtype=position.dtype)
cell_id = N * jnp.ones((cell_count * cell_capacity, 1), dtype=i32)
# It might be worth adding an occupied mask. However, that will involve
# more compute since often we will do a mask for species that will include
# an occupancy test. It seems easier to design around this empty_data_value
# for now and revisit the issue if it comes up later.
empty_kwarg_value = 10**5
cell_kwargs = {}
# pytype: disable=attribute-error
for k, v in kwargs.items():
if not util.is_array(v):
raise ValueError(
(f'Data must be specified as an ndarray. Found "{k}" '
f'with type {type(v)}.'))
if v.shape[0] != position.shape[0]:
raise ValueError(
('Data must be specified per-particle (an ndarray '
f'with shape ({N}, ...)). Found "{k}" with '
f'shape {v.shape}.'))
kwarg_shape = v.shape[1:] if v.ndim > 1 else (1, )
cell_kwargs[k] = empty_kwarg_value * jnp.ones(
(cell_count * cell_capacity, ) + kwarg_shape, v.dtype)
# pytype: enable=attribute-error
indices = jnp.array(position / cell_size, dtype=i32)
hashes = jnp.sum(indices * hash_multipliers, axis=1)
# Copy the particle data into the grid. Here we use a trick to allow us to
# copy into all cells simultaneously using a single lax.scatter call. To do
# this we first sort particles by their cell hash. We then assign each
# particle to have a cell id = hash * cell_capacity + grid_id where
# grid_id is a flat list that repeats 0, .., cell_capacity. So long as
# there are fewer than cell_capacity particles per cell, each particle is
# guarenteed to get a cell id that is unique.
sort_map = jnp.argsort(hashes)
sorted_position = position[sort_map]
sorted_hash = hashes[sort_map]
sorted_id = particle_id[sort_map]
sorted_kwargs = {}
for k, v in kwargs.items():
sorted_kwargs[k] = v[sort_map]
sorted_cell_id = jnp.mod(lax.iota(i32, N), cell_capacity)
sorted_cell_id = sorted_hash * cell_capacity + sorted_cell_id
cell_position = cell_position.at[sorted_cell_id].set(sorted_position)
sorted_id = jnp.reshape(sorted_id, (N, 1))
cell_id = cell_id.at[sorted_cell_id].set(sorted_id)
cell_position = _unflatten_cell_buffer(cell_position, cells_per_side,
dim)
cell_id = _unflatten_cell_buffer(cell_id, cells_per_side, dim)
for k, v in sorted_kwargs.items():
if v.ndim == 1:
v = jnp.reshape(v, v.shape + (1, ))
cell_kwargs[k] = cell_kwargs[k].at[sorted_cell_id].set(v)
cell_kwargs[k] = _unflatten_cell_buffer(cell_kwargs[k],
cells_per_side, dim)
occupancy = ops.segment_sum(jnp.ones_like(hashes), hashes, cell_count)
max_occupancy = jnp.max(occupancy)
overflow = overflow | (max_occupancy >= cell_capacity)
return CellList(cell_position, cell_id, cell_kwargs, overflow,
cell_capacity, update_fn) # pytype: disable=wrong-arg-count
[RandArg((3, 4, 5), _f32), np.array([1, 2], np.int32)],
poly_axes=[0, None]),
_make_harness("jnp_getitem", "",
lambda a, i: a[i],
[RandArg((3, 4), _f32), np.array([2, 2], np.int32)],
poly_axes=[None, 0]),
# TODO(necula): not supported yet
# _make_harness("jnp_getitem", "",
# lambda a, i: a[i],
# [RandArg((3, 4), _f32), np.array([2, 2], np.int32)],
# poly_axes=[0, 0]),
_make_harness("iota", "",
lambda x: x + lax.iota(_f32, x.shape[0]),
[RandArg((3,), _f32)],
poly_axes=[0]),
_make_harness("jnp_matmul", "0",
jnp.matmul,
[RandArg((7, 8, 4), _f32), RandArg((7, 4, 5), _f32)],
poly_axes=[0, 0],
tol=1e-5),
_make_harness("jnp_matmul", "1",
jnp.matmul,
[RandArg((7, 8, 4), _f32), RandArg((4, 5), _f32)],
poly_axes=[0, None],
tol=1e-5),
def build_cells(R, **kwargs):
N = R.shape[0]
dim = R.shape[1]
if dim != 2 and dim != 3:
# NOTE(schsam): Do we want to check this in compute_fn as well?
raise ValueError(
'Cell list spatial dimension must be 2 or 3. Found {}'.format(dim))
neighborhood_tile_count = 3 ** dim
_, cell_size, cells_per_side, cell_count = \
_cell_dimensions(dim, box_size, minimum_cell_size)
hash_multipliers = _compute_hash_constants(dim, cells_per_side)
# Create cell list data.
particle_id = lax.iota(np.int64, N)
# NOTE(schsam): We use the convention that particles that are successfully,
# copied have their true id whereas particles empty slots have id = N.
# Then when we copy data back from the grid, copy it to an array of shape
# [N + 1, output_dimension] and then truncate it to an array of shape
# [N, output_dimension] which ignores the empty slots.
mask_id = np.ones((N,), np.int64) * N
cell_R = np.zeros((cell_count * cell_capacity, dim), dtype=R.dtype)
cell_id = N * np.ones((cell_count * cell_capacity, 1), dtype=i32)
# It might be worth adding an occupied mask. However, that will involve
# more compute since often we will do a mask for species that will include
# an occupancy test. It seems easier to design around this empty_data_value
# for now and revisit the issue if it comes up later.
empty_kwarg_value = 10 ** 5
cell_kwargs = {}
for k, v in kwargs.items():
if not isinstance(v, np.ndarray):
raise ValueError((
'Data must be specified as an ndarry. Found "{}" with '
'type {}'.format(k, type(v))))
if v.shape[0] != R.shape[0]:
raise ValueError(
('Data must be specified per-particle (an ndarray with shape '
'(R.shape[0], ...)). Found "{}" with shape {}'.format(k, v.shape)))
kwarg_shape = v.shape[1:] if v.ndim > 1 else (1,)
cell_kwargs[k] = empty_kwarg_value * np.ones(
(cell_count * cell_capacity,) + kwarg_shape, v.dtype)
indices = np.array(R / cell_size, dtype=i32)
hashes = np.sum(indices * hash_multipliers, axis=1)
# Copy the particle data into the grid. Here we use a trick to allow us to
# copy into all cells simultaneously using a single lax.scatter call. To do
# this we first sort particles by their cell hash. We then assign each
# particle to have a cell id = hash * cell_capacity + grid_id where grid_id
# is a flat list that repeats 0, .., cell_capacity. So long as there are
# fewer than cell_capacity particles per cell, each particle is guarenteed
# to get a cell id that is unique.
sort_map = np.argsort(hashes)
sorted_R = R[sort_map]
sorted_hash = hashes[sort_map]
sorted_id = particle_id[sort_map]
sorted_kwargs = {}
for k, v in kwargs.items():
sorted_kwargs[k] = v[sort_map]
sorted_cell_id = np.mod(lax.iota(np.int64, N), cell_capacity)
sorted_cell_id = sorted_hash * cell_capacity + sorted_cell_id
cell_R = ops.index_update(cell_R, sorted_cell_id, sorted_R)
sorted_id = np.reshape(sorted_id, (N, 1))
cell_id = ops.index_update(
cell_id, sorted_cell_id, sorted_id)
cell_R = _unflatten_cell_buffer(cell_R, cells_per_side, dim)
cell_id = _unflatten_cell_buffer(cell_id, cells_per_side, dim)
for k, v in sorted_kwargs.items():
if v.ndim == 1:
v = np.reshape(v, v.shape + (1,))
cell_kwargs[k] = ops.index_update(cell_kwargs[k], sorted_cell_id, v)
cell_kwargs[k] = _unflatten_cell_buffer(
cell_kwargs[k], cells_per_side, dim)
return CellList(cell_R, cell_id, cell_kwargs)
def range_like(x):
return lax.iota(np.int32, x.shape[0])
def f_jax(x):
x + lax.iota(np.float32, x.shape[0])
def testShapeUsesBuiltinInt(self):
x = lax.iota(np.int32, 3) + 1
self.assertIsInstance(x.shape[0], int) # not np.int64
def build_cells(R):
N = R.shape[0]
dim = R.shape[1]
neighborhood_tile_count = 3**dim
_, cell_size, cells_per_side, cell_count = \
_cell_dimensions(dim, box_size, minimum_cell_size)
if species is None:
_species = np.zeros((N, ), dtype=i32)
else:
_species = species
hash_multipliers = _compute_hash_constants(dim, cells_per_side)
# Create grid data.
particle_id = lax.iota(np.int64, N)
# NOTE(schsam): We use the convention that particles that come from the
# center cell have their true id copied, whereas particles that come from
# the halo have an id = N. Then when we copy data back from the grid,
# we copy it to an array of shape [N + 1, output_dimension] and then
# truncate it to an array of shape [N, output_dimension] which ignores the
# halo particles.
mask_id = np.ones((N, ), np.int64) * N
cell_R = np.zeros((cell_count * cell_capacity, dim), dtype=R.dtype)
# NOTE(schsam): empty_species_index is just supposed to be large enough that
# we will never run into it. However, there might be a more robust way to do
# this.
empty_species_index = i16(1000)
cell_species = empty_species_index * np.ones(
(cell_count * cell_capacity, 1), dtype=_species.dtype)
cell_id = N * np.ones((cell_count * cell_capacity, 1), dtype=i32)
indices = np.array(R / cell_size, dtype=i32)
# Create a copy of particle data for each neighboring cell shifting the hash
# appropriately.
# TODO(schsam): Replace with np.tile() when it gets implemented.
tiled_R = R
tiled_species = _species
for _ in range(neighborhood_tile_count - 1):
tiled_R = np.concatenate((tiled_R, R), axis=0)
tiled_species = np.concatenate((tiled_species, _species), axis=0)
tiled_hash = np.array([], dtype=i32)
tiled_id = np.array([], dtype=i32)
for dindex in _neighboring_cells(dim):
tiled_indices = np.mod(indices + dindex, cells_per_side)
tiled_hash = np.concatenate(
(tiled_hash, np.sum(tiled_indices * hash_multipliers, axis=1)),
axis=0)
if np.all(dindex == 0):
tiled_id = np.concatenate((tiled_id, particle_id), axis=0)
else:
tiled_id = np.concatenate((tiled_id, mask_id), axis=0)
# Copy the particle data into the grid. Here we use a trick to allow us to
# copy into all cells simultaneously using a single lax.scatter call. To do
# this we first sort particles by their cell hash. We then assign each
# particle to have a cell id = hash * cell_capacity + grid_id where grid_id
# is a flat list that repeats 0, .., cell_capacity. So long as there are
# fewer than cell_capacity particles per cell, each particle is guarenteed
# to get a cell id that is unique.
sort_map = np.argsort(tiled_hash)
sorted_R = tiled_R[sort_map]
sorted_species = tiled_species[sort_map]
sorted_hash = tiled_hash[sort_map]
sorted_id = tiled_id[sort_map]
tiled_size = neighborhood_tile_count * N
sorted_cell_id = np.mod(lax.iota(np.int64, tiled_size), cell_capacity)
sorted_cell_id = sorted_hash * cell_capacity + sorted_cell_id
def copy_values_to_cell(cell_value, value, ids):
scatter_indices = np.reshape(ids, (tiled_size, 1))
dnums = lax.ScatterDimensionNumbers(
update_window_dims=tuple([1]),
inserted_window_dims=tuple([0]),
scatter_dims_to_operand_dims=tuple([0]),
)
return lax.scatter(cell_value, scatter_indices, value, dnums)
cell_R = copy_values_to_cell(cell_R, sorted_R, sorted_cell_id)
sorted_species = np.reshape(sorted_species, (tiled_size, 1))
cell_species = copy_values_to_cell(cell_species, sorted_species,
sorted_cell_id)
sorted_id = np.reshape(sorted_id, (tiled_size, 1))
cell_id = copy_values_to_cell(cell_id, sorted_id, sorted_cell_id)
cell_R = np.reshape(cell_R, (cell_count, cell_capacity, dim))
cell_species = np.reshape(cell_species, (cell_count, cell_capacity))
cell_id = np.reshape(cell_id, (cell_count, cell_capacity))
return Grid(N, dim, cell_count, cell_R, cell_species, cell_id)
def build_cells(R):
N = R.shape[0]
dim = R.shape[1]
if dim != 2 and dim != 3:
# NOTE(schsam): Do we want to check this in compute_fn as well?
raise ValueError(
'Cell list spatial dimension must be 2 or 3. Found {}'.format(
dim))
neighborhood_tile_count = 3**dim
_, cell_size, cells_per_side, cell_count = \
_cell_dimensions(dim, box_size, minimum_cell_size)
if species is None:
_species = np.zeros((N, ), dtype=i32)
else:
_species = species
hash_multipliers = _compute_hash_constants(dim, cells_per_side)
# Create cell list data.
particle_id = lax.iota(np.int64, N)
# NOTE(schsam): We use the convention that particles that are successfully,
# copied have their true id whereas particles empty slots have id = N.
# Then when we copy data back from the grid, copy it to an array of shape
# [N + 1, output_dimension] and then truncate it to an array of shape
# [N, output_dimension] which ignores the empty slots.
mask_id = np.ones((N, ), np.int64) * N
cell_R = np.zeros((cell_count * cell_capacity, dim), dtype=R.dtype)
# NOTE(schsam): empty_species_index is just supposed to be large enough that
# we will never run into it. However, there might be a more robust way to do
# this.
empty_species_index = i32(1000)
cell_species = empty_species_index * np.ones(
(cell_count * cell_capacity, 1), dtype=_species.dtype)
cell_id = N * np.ones((cell_count * cell_capacity, 1), dtype=i32)
indices = np.array(R / cell_size, dtype=i32)
hashes = np.sum(indices * hash_multipliers, axis=1)
# Copy the particle data into the grid. Here we use a trick to allow us to
# copy into all cells simultaneously using a single lax.scatter call. To do
# this we first sort particles by their cell hash. We then assign each
# particle to have a cell id = hash * cell_capacity + grid_id where grid_id
# is a flat list that repeats 0, .., cell_capacity. So long as there are
# fewer than cell_capacity particles per cell, each particle is guarenteed
# to get a cell id that is unique.
sort_map = np.argsort(hashes)
sorted_R = R[sort_map]
sorted_species = _species[sort_map]
sorted_hash = hashes[sort_map]
sorted_id = particle_id[sort_map]
sorted_cell_id = np.mod(lax.iota(np.int64, N), cell_capacity)
sorted_cell_id = sorted_hash * cell_capacity + sorted_cell_id
cell_R = ops.index_update(cell_R, sorted_cell_id, sorted_R)
sorted_species = np.reshape(sorted_species, (N, 1))
cell_species = ops.index_update(cell_species, sorted_cell_id,
sorted_species)
sorted_id = np.reshape(sorted_id, (N, 1))
cell_id = ops.index_update(cell_id, sorted_cell_id, sorted_id)
cell_R = _unflatten_cell_buffer(cell_R, cells_per_side, dim)
cell_species = _unflatten_cell_buffer(cell_species, cells_per_side,
dim)
cell_id = _unflatten_cell_buffer(cell_id, cells_per_side, dim)
return CellList(N, dim, cell_count, cell_R, cell_species, cell_id)
def padded_add(x):
return x + lax.iota(x.shape[0])
def _threefry_split(key, num) -> jnp.ndarray:
counts = lax.iota(np.uint32, num * 2)
return lax.reshape(threefry_2x32(key, counts), (num, 2))
def _cofactor_solve(a, b):
"""Equivalent to det(a)*solve(a, b) for nonsingular mat.
Intermediate function used for jvp and vjp of det.
This function borrows heavily from jax.numpy.linalg.solve and
jax.numpy.linalg.slogdet to compute the gradient of the determinant
in a way that is well defined even for low rank matrices.
This function handles two different cases:
* rank(a) == n or n-1
* rank(a) < n-1
For rank n-1 matrices, the gradient of the determinant is a rank 1 matrix.
Rather than computing det(a)*solve(a, b), which would return NaN, we work
directly with the LU decomposition. If a = p @ l @ u, then
det(a)*solve(a, b) =
prod(diag(u)) * u^-1 @ l^-1 @ p^-1 b =
prod(diag(u)) * triangular_solve(u, solve(p @ l, b))
If a is rank n-1, then the lower right corner of u will be zero and the
triangular_solve will fail.
Let x = solve(p @ l, b) and y = det(a)*solve(a, b).
Then y_{n}
x_{n} / u_{nn} * prod_{i=1...n}(u_{ii}) =
x_{n} * prod_{i=1...n-1}(u_{ii})
So by replacing the lower-right corner of u with prod_{i=1...n-1}(u_{ii})^-1
we can avoid the triangular_solve failing.
To correctly compute the rest of y_{i} for i != n, we simply multiply
x_{i} by det(a) for all i != n, which will be zero if rank(a) = n-1.
For the second case, a check is done on the matrix to see if `solve`
returns NaN or Inf, and gives a matrix of zeros as a result, as the
gradient of the determinant of a matrix with rank less than n-1 is 0.
This will still return the correct value for rank n-1 matrices, as the check
is applied *after* the lower right corner of u has been updated.
Args:
a: A square matrix or batch of matrices, possibly singular.
b: A matrix, or batch of matrices of the same dimension as a.
Returns:
det(a) and cofactor(a)^T*b, aka adjugate(a)*b
"""
a = _promote_arg_dtypes(jnp.asarray(a))
b = _promote_arg_dtypes(jnp.asarray(b))
a_shape = jnp.shape(a)
b_shape = jnp.shape(b)
a_ndims = len(a_shape)
if not (a_ndims >= 2 and a_shape[-1] == a_shape[-2]
and b_shape[-2:] == a_shape[-2:]):
msg = ("The arguments to _cofactor_solve must have shapes "
"a=[..., m, m] and b=[..., m, m]; got a={} and b={}")
raise ValueError(msg.format(a_shape, b_shape))
if a_shape[-1] == 1:
return a[..., 0, 0], b
# lu contains u in the upper triangular matrix and l in the strict lower
# triangular matrix.
# The diagonal of l is set to ones without loss of generality.
lu, pivots, permutation = lax_linalg.lu(a)
dtype = lax.dtype(a)
batch_dims = lax.broadcast_shapes(lu.shape[:-2], b.shape[:-2])
x = jnp.broadcast_to(b, batch_dims + b.shape[-2:])
lu = jnp.broadcast_to(lu, batch_dims + lu.shape[-2:])
# Compute (partial) determinant, ignoring last diagonal of LU
diag = jnp.diagonal(lu, axis1=-2, axis2=-1)
parity = jnp.count_nonzero(pivots != jnp.arange(a_shape[-1]), axis=-1)
sign = jnp.asarray(-2 * (parity % 2) + 1, dtype=dtype)
# partial_det[:, -1] contains the full determinant and
# partial_det[:, -2] contains det(u) / u_{nn}.
partial_det = jnp.cumprod(diag, axis=-1) * sign[..., None]
lu = lu.at[..., -1, -1].set(1.0 / partial_det[..., -2])
permutation = jnp.broadcast_to(permutation, batch_dims + (a_shape[-1], ))
iotas = jnp.ix_(*(lax.iota(jnp.int32, b) for b in batch_dims + (1, )))
# filter out any matrices that are not full rank
d = jnp.ones(x.shape[:-1], x.dtype)
d = lax_linalg.triangular_solve(lu, d, left_side=True, lower=False)
d = jnp.any(jnp.logical_or(jnp.isnan(d), jnp.isinf(d)), axis=-1)
d = jnp.tile(d[..., None, None], d.ndim * (1, ) + x.shape[-2:])
x = jnp.where(d, jnp.zeros_like(x), x) # first filter
x = x[iotas[:-1] + (permutation, slice(None))]
x = lax_linalg.triangular_solve(lu,
x,
left_side=True,
lower=True,
unit_diagonal=True)
x = jnp.concatenate(
(x[..., :-1, :] * partial_det[..., -1, None, None], x[..., -1:, :]),
axis=-2)
x = lax_linalg.triangular_solve(lu, x, left_side=True, lower=False)
x = jnp.where(d, jnp.zeros_like(x), x) # second filter
return partial_det[..., -1], x
def build_cells(R):
N = R.shape[0]
dim = R.shape[1]
if dim != 2 and dim != 3:
raise ValueError(
'Cell list spatial dimension must be 2 or 3. Found {}'.format(dim))
neighborhood_tile_count = 3 ** dim
_, cell_size, cells_per_side, cell_count = \
_cell_dimensions(dim, box_size, minimum_cell_size)
if species is None:
_species = np.zeros((N,), dtype=i32)
else:
_species = species
hash_multipliers = _compute_hash_constants(dim, cells_per_side)
# Create cell list data.
particle_id = lax.iota(np.int64, N)
mask_id = np.ones((N,), np.int64) * N
cell_R = np.zeros((cell_count * cell_capacity, dim), dtype=R.dtype)
empty_species_index = i32(1000)
cell_species = empty_species_index * np.ones(
(cell_count * cell_capacity, 1), dtype=_species.dtype)
cell_id = N * np.ones((cell_count * cell_capacity, 1), dtype=i32)
indices = np.array(R / cell_size, dtype=i32)
hashes = np.sum(indices * hash_multipliers, axis=1)
# Copy the particle data into the grid. Here we use a trick to allow us to
# copy into all cells simultaneously using a single lax.scatter call. To do
# this we first sort particles by their cell hash. We then assign each
# particle to have a cell id = hash * cell_capacity + grid_id where grid_id
# is a flat list that repeats 0, .., cell_capacity. So long as there are
# fewer than cell_capacity particles per cell, each particle is guarenteed
# to get a cell id that is unique.
sort_map = np.argsort(hashes)
sorted_R = R[sort_map]
sorted_species = _species[sort_map]
sorted_hash = hashes[sort_map]
sorted_id = particle_id[sort_map]
sorted_cell_id = np.mod(lax.iota(np.int64, N), cell_capacity)
sorted_cell_id = sorted_hash * cell_capacity + sorted_cell_id
cell_R = ops.index_update(cell_R, sorted_cell_id, sorted_R)
sorted_species = np.reshape(sorted_species, (N, 1))
cell_species = ops.index_update(
cell_species, sorted_cell_id, sorted_species)
sorted_id = np.reshape(sorted_id, (N, 1))
cell_id = ops.index_update(
cell_id, sorted_cell_id, sorted_id)
cell_R = _unflatten_cell_buffer(cell_R, cells_per_side, dim)
cell_species = _unflatten_cell_buffer(cell_species, cells_per_side, dim)
cell_id = _unflatten_cell_buffer(cell_id, cells_per_side, dim)
return CellList(N, dim, cell_count, cell_R, cell_species, cell_id)
