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from compyle.api import declare, annotate
from compyle.parallel import serial
from compyle.low_level import atomic_inc, cast
from math import floor
import numpy as np
@annotate
def find_cell_id(x, y, z, h, eps, c):
c[0] = cast(floor((x + eps) / h), "int")
c[1] = cast(floor((y + eps) / h), "int")
c[2] = cast(floor((z + eps) / h), "int")
@annotate
def flatten(p, q, r, qmax, rmax):
return (p * qmax + q) * rmax + r
@serial
@annotate
def count_bins(i, x, y, z, h, eps, qmax, rmax, keys, bin_counts,
sort_offsets):
c = declare('matrix(3, "int")')
find_cell_id(x[i], y[i], z[i], h, eps, c)
key = flatten(c[0], c[1], c[2], qmax, rmax)
keys[i] = key
idx = atomic_inc(bin_counts[key])
sort_offsets[i] = idx
@annotate
def sort_indices(i, keys, sort_offsets, start_indices, sorted_indices):
key = keys[i]
offset = sort_offsets[i]
start_idx = start_indices[key]
sorted_indices[start_idx + offset] = i
@annotate
def input_start_indices(i, counts):
return 0 if i == 0 else counts[i - 1]
@annotate
def output_start_indices(i, item, indices):
indices[i] = item
@annotate
def fill_keys(i, x, y, z, h, eps, qmax, rmax, indices, keys):
c = declare('matrix(3, "int")')
find_cell_id(x[i], y[i], z[i], h, eps, c)
key = flatten(c[0], c[1], c[2], qmax, rmax)
keys[i] = key
indices[i] = i
@annotate
def input_scan_keys(i, keys):
return 1 if i == 0 or keys[i] != keys[i - 1] else 0
@annotate
def output_scan_keys(i, item, prev_item, keys, start_indices):
key = keys[i]
if item != prev_item:
start_indices[key] = i
@annotate
def fill_bin_counts(i, keys, start_indices, bin_counts, num_particles):
if i == num_particles - 1:
last_key = keys[num_particles - 1]
bin_counts[last_key] = num_particles - start_indices[last_key]
if i == 0 or keys[i] == keys[i - 1]:
return
key = keys[i]
prev_key = keys[i - 1]
bin_counts[prev_key] = start_indices[key] - start_indices[prev_key]
@annotate
def find_neighbor_lengths_knl(i, x, y, z, h, eps, qmax, rmax, start_indices,
sorted_indices, bin_counts, nbr_lengths,
max_key):
d = h * h
q_c = declare('matrix(3, "int")')
find_cell_id(x[i], y[i], z[i], h, eps, q_c)
for p in range(-1, 2):
for q in range(-1, 2):
for r in range(-1, 2):
cx = q_c[0] + p
cy = q_c[1] + q
cz = q_c[2] + r
key = flatten(cx, cy, cz, qmax, rmax)
if key >= max_key or key < 0:
continue
start_idx = start_indices[key]
np = bin_counts[key]
for k in range(np):
j = sorted_indices[start_idx + k]
xij = x[i] - x[j]
yij = y[i] - y[j]
zij = z[i] - z[j]
rij2 = xij * xij + yij * yij + zij * zij
if rij2 < d:
nbr_lengths[i] += 1
@annotate
def find_neighbors_knl(i, x, y, z, h, eps, qmax, rmax, start_indices, sorted_indices,
bin_counts, nbr_starts, nbrs, max_key):
d = h * h
q_c = declare('matrix(3, "int")')
find_cell_id(x[i], y[i], z[i], h, eps, q_c)
length = 0
nbr_start_idx = nbr_starts[i]
for p in range(-1, 2):
for q in range(-1, 2):
for r in range(-1, 2):
cx = q_c[0] + p
cy = q_c[1] + q
cz = q_c[2] + r
key = flatten(cx, cy, cz, qmax, rmax)
if key >= max_key or key < 0:
continue
start_idx = start_indices[key]
np = bin_counts[key]
for k in range(np):
j = sorted_indices[start_idx + k]
xij = x[i] - x[j]
yij = y[i] - y[j]
zij = z[i] - z[j]
rij2 = xij * xij + yij * yij + zij * zij
if rij2 < d:
nbrs[nbr_start_idx + length] = j
length += 1
@annotate
def find_neighbor_lengths_periodic_knl(i, x, y, z, h, eps, xmax, ymax, zmax,
pmax, qmax, rmax, start_indices,
sorted_indices, bin_counts, nbr_lengths,
max_key):
d = h * h
q_c = declare('matrix(3, "int")')
xij, yij, zij = declare('double', 3)
find_cell_id(x[i], y[i], z[i], h, eps, q_c)
for p in range(-1, 2):
for q in range(-1, 2):
for r in range(-1, 2):
cx = q_c[0] + p
cy = q_c[1] + q
cz = q_c[2] + r
cx_f = cast(cx, "float")
cy_f = cast(cy, "float")
cz_f = cast(cz, "float")
xoffset = cast(floor(cx_f / pmax), "int")
yoffset = cast(floor(cy_f / qmax), "int")
zoffset = cast(floor(cz_f / rmax), "int")
cx -= xoffset * pmax
cy -= yoffset * qmax
cz -= zoffset * rmax
key = flatten(cx, cy, cz, qmax, rmax)
if key >= max_key or key < 0:
continue
start_idx = start_indices[key]
np = bin_counts[key]
for k in range(np):
j = sorted_indices[start_idx + k]
xij = abs(x[i] - x[j])
yij = abs(y[i] - y[j])
zij = abs(z[i] - z[j])
xij = min(xij, xmax - xij)
yij = min(yij, ymax - yij)
zij = min(zij, zmax - zij)
rij2 = xij * xij + yij * yij + zij * zij
if rij2 < d:
nbr_lengths[i] += 1
@annotate
def find_neighbors_periodic_knl(i, x, y, z, h, eps, xmax, ymax, zmax,
pmax, qmax, rmax, start_indices, sorted_indices,
bin_counts, nbr_starts, nbrs, max_key):
d = h * h
q_c = declare('matrix(3, "int")')
xij, yij, zij = declare('double', 3)
find_cell_id(x[i], y[i], z[i], h, eps, q_c)
length = 0
nbr_start_idx = nbr_starts[i]
for p in range(-1, 2):
for q in range(-1, 2):
for r in range(-1, 2):
cx = q_c[0] + p
cy = q_c[1] + q
cz = q_c[2] + r
cx_f = cast(cx, "float")
cy_f = cast(cy, "float")
cz_f = cast(cz, "float")
xoffset = cast(floor(cx_f / pmax), "int")
yoffset = cast(floor(cy_f / qmax), "int")
zoffset = cast(floor(cz_f / rmax), "int")
cx -= xoffset * pmax
cy -= yoffset * qmax
cz -= zoffset * rmax
key = flatten(cx, cy, cz, qmax, rmax)
if key >= max_key or key < 0:
continue
start_idx = start_indices[key]
np = bin_counts[key]
for k in range(np):
j = sorted_indices[start_idx + k]
xij = abs(x[i] - x[j])
yij = abs(y[i] - y[j])
zij = abs(z[i] - z[j])
xij = min(xij, xmax - xij)
yij = min(yij, ymax - yij)
zij = min(zij, zmax - zij)
rij2 = xij * xij + yij * yij + zij * zij
if rij2 < d:
nbrs[nbr_start_idx + length] = j
length += 1
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