From 2b88b63ac54ba970e3f0eca8247e0eecc9514828 Mon Sep 17 00:00:00 2001
From: Markus Holzer <markus.holzer@fau.de>
Date: Fri, 18 Jun 2021 10:07:27 +0000
Subject: [PATCH] Use closest normal for boundary index list with single_link
---
pystencils/boundaries/createindexlist.py | 81 ++++++++------
.../boundaries/createindexlistcython.pyx | 104 +++++++++++++++---
.../test_boundary_indexlist_creation.py | 55 +++++++--
3 files changed, 183 insertions(+), 57 deletions(-)
diff --git a/pystencils/boundaries/createindexlist.py b/pystencils/boundaries/createindexlist.py
index 51bd5464f..be8fee7e5 100644
--- a/pystencils/boundaries/createindexlist.py
+++ b/pystencils/boundaries/createindexlist.py
@@ -1,4 +1,3 @@
-import itertools
import warnings
import numpy as np
@@ -35,45 +34,67 @@ def numpy_data_type_for_boundary_object(boundary_object, dim):
+ [(i[0], i[1].numpy_dtype) for i in boundary_object.additional_data], align=True)
-def _create_boundary_neighbor_index_list_python(flag_field_arr, nr_of_ghost_layers, boundary_mask,
- fluid_mask, stencil, single_link):
+def _create_index_list_python(flag_field_arr, boundary_mask,
+ fluid_mask, stencil, single_link, inner_or_boundary=False, nr_of_ghost_layers=None):
+
+ if inner_or_boundary and nr_of_ghost_layers is None:
+ raise ValueError("If inner_or_boundary is set True the number of ghost layers "
+ "around the inner domain has to be specified")
+
+ if nr_of_ghost_layers is None:
+ nr_of_ghost_layers = 0
+
coordinate_names = boundary_index_array_coordinate_names[:len(flag_field_arr.shape)]
index_arr_dtype = np.dtype([(name, np.int32) for name in coordinate_names] + [(direction_member_name, np.int32)])
- result = []
- gl = nr_of_ghost_layers
- for cell in itertools.product(*reversed([range(gl, i - gl) for i in flag_field_arr.shape])):
- cell = cell[::-1]
- if not flag_field_arr[cell] & fluid_mask:
- continue
+ # boundary cells are extracted via np.where. To ensure continous memory access in the compute kernel these cells
+ # have to be sorted.
+ boundary_cells = np.transpose(np.nonzero(flag_field_arr == boundary_mask))
+ for i in range(len(flag_field_arr.shape)):
+ boundary_cells = boundary_cells[boundary_cells[:, i].argsort(kind='mergesort')]
+
+ # First a set is created to save all fluid cells which are near boundary
+ fluid_cells = set()
+ for cell in boundary_cells:
+ cell = tuple(cell)
for dir_idx, direction in enumerate(stencil):
neighbor_cell = tuple([cell_i + dir_i for cell_i, dir_i in zip(cell, direction)])
- if flag_field_arr[neighbor_cell] & boundary_mask:
- result.append(cell + (dir_idx,))
- if single_link:
- break
-
- return np.array(result, dtype=index_arr_dtype)
+ # prevent out ouf bounds access. If boundary cell is at the border, some stencil directions would be out.
+ if any(not 0 + nr_of_ghost_layers <= e < upper - nr_of_ghost_layers
+ for e, upper in zip(neighbor_cell, flag_field_arr.shape)):
+ continue
+ if flag_field_arr[neighbor_cell] & fluid_mask:
+ fluid_cells.add(neighbor_cell)
+ # then this is set is transformed to a list to make it sortable. This ensures continoous memory access later.
+ fluid_cells = list(fluid_cells)
+ if len(flag_field_arr.shape) == 3:
+ fluid_cells.sort(key=lambda tup: (tup[-1], tup[-2], tup[0]))
+ else:
+ fluid_cells.sort(key=lambda tup: (tup[-1], tup[0]))
-def _create_boundary_cell_index_list_python(flag_field_arr, boundary_mask,
- fluid_mask, stencil, single_link):
- coordinate_names = boundary_index_array_coordinate_names[:len(flag_field_arr.shape)]
- index_arr_dtype = np.dtype([(name, np.int32) for name in coordinate_names] + [(direction_member_name, np.int32)])
+ cells_to_iterate = fluid_cells if inner_or_boundary else boundary_cells
+ checkmask = boundary_mask if inner_or_boundary else fluid_mask
result = []
- for cell in itertools.product(*reversed([range(0, i) for i in flag_field_arr.shape])):
- cell = cell[::-1]
- if not flag_field_arr[cell] & boundary_mask:
- continue
+ for cell in cells_to_iterate:
+ cell = tuple(cell)
+ sum_cells = np.zeros(len(cell))
for dir_idx, direction in enumerate(stencil):
neighbor_cell = tuple([cell_i + dir_i for cell_i, dir_i in zip(cell, direction)])
+ # prevent out ouf bounds access. If boundary cell is at the border, some stencil directions would be out.
if any(not 0 <= e < upper for e, upper in zip(neighbor_cell, flag_field_arr.shape)):
continue
- if flag_field_arr[neighbor_cell] & fluid_mask:
- result.append(cell + (dir_idx,))
+ if flag_field_arr[neighbor_cell] & checkmask:
if single_link:
- break
+ sum_cells += np.array(direction)
+ else:
+ result.append(tuple(cell) + (dir_idx,))
+
+ # the discrete normal direction is the one which gives the maximum inner product to the stencil direction
+ if single_link and any(sum_cells != 0):
+ idx = np.argmax(np.inner(sum_cells, stencil))
+ result.append(tuple(cell) + (idx,))
return np.array(result, dtype=index_arr_dtype)
@@ -91,7 +112,7 @@ def create_boundary_index_list(flag_field, stencil, boundary_mask, fluid_mask,
nr_of_ghost_layers: only relevant if neighbors is True
inner_or_boundary: if true, the result contains the cell coordinates of the domain cells -
if false the boundary cells are listed
- single_link: if true only the first link is reported from this cell
+ single_link: if true only the link in normal direction to this cell is reported
"""
dim = len(flag_field.shape)
@@ -119,10 +140,8 @@ def create_boundary_index_list(flag_field, stencil, boundary_mask, fluid_mask,
else:
if flag_field.size > 1e6:
warnings.warn("Boundary setup may take very long! Consider installing cython to speed it up")
- if inner_or_boundary:
- return _create_boundary_neighbor_index_list_python(*args)
- else:
- return _create_boundary_cell_index_list_python(*args_no_gl)
+ return _create_index_list_python(*args_no_gl, inner_or_boundary=inner_or_boundary,
+ nr_of_ghost_layers=nr_of_ghost_layers)
def create_boundary_index_array(flag_field, stencil, boundary_mask, fluid_mask, boundary_object,
diff --git a/pystencils/boundaries/createindexlistcython.pyx b/pystencils/boundaries/createindexlistcython.pyx
index 0931fdc7f..bd30fc1ba 100644
--- a/pystencils/boundaries/createindexlistcython.pyx
+++ b/pystencils/boundaries/createindexlistcython.pyx
@@ -22,20 +22,37 @@ def create_boundary_neighbor_index_list_2d(object[IntegerType, ndim=2] flag_fiel
cdef int xs, ys, x, y
cdef int dirIdx, num_directions, dx, dy
+ cdef int sum_x, sum_y
+ cdef float dot, maxn
+ cdef int calculated_idx
+
xs, ys = flag_field.shape
boundary_index_list = []
num_directions = stencil.shape[0]
for y in range(nr_of_ghost_layers, ys - nr_of_ghost_layers):
for x in range(nr_of_ghost_layers, xs - nr_of_ghost_layers):
+ sum_x = 0; sum_y = 0;
if flag_field[x, y] & fluid_mask:
for dirIdx in range(num_directions):
- dx = stencil[dirIdx,0]
- dy = stencil[dirIdx,1]
+ dx = stencil[dirIdx,0]; dy = stencil[dirIdx,1]
if flag_field[x + dx, y + dy] & boundary_mask:
- boundary_index_list.append((x,y, dirIdx))
if single_link:
- break
+ sum_x += dx; sum_y += dy;
+ else:
+ boundary_index_list.append((x, y, dirIdx))
+
+ dot = 0; maxn = 0; calculated_idx = 0
+ if single_link and (sum_x != 0 or sum_y != 0):
+ for dirIdx in range(num_directions):
+ dx = stencil[dirIdx, 0]; dy = stencil[dirIdx, 1];
+
+ dot = dx * sum_x + dy * sum_y
+ if dot > maxn:
+ maxn = dot
+ calculated_idx = dirIdx
+
+ boundary_index_list.append((x, y, calculated_idx))
return boundary_index_list
@@ -47,6 +64,10 @@ def create_boundary_neighbor_index_list_3d(object[IntegerType, ndim=3] flag_fiel
cdef int xs, ys, zs, x, y, z
cdef int dirIdx, num_directions, dx, dy, dz
+ cdef int sum_x, sum_y, sum_z
+ cdef float dot, maxn
+ cdef int calculated_idx
+
xs, ys, zs = flag_field.shape
boundary_index_list = []
num_directions = stencil.shape[0]
@@ -54,15 +75,27 @@ def create_boundary_neighbor_index_list_3d(object[IntegerType, ndim=3] flag_fiel
for z in range(nr_of_ghost_layers, zs - nr_of_ghost_layers):
for y in range(nr_of_ghost_layers, ys - nr_of_ghost_layers):
for x in range(nr_of_ghost_layers, xs - nr_of_ghost_layers):
+ sum_x = 0; sum_y = 0; sum_z = 0
if flag_field[x, y, z] & fluid_mask:
for dirIdx in range(num_directions):
- dx = stencil[dirIdx,0]
- dy = stencil[dirIdx,1]
- dz = stencil[dirIdx,2]
+ dx = stencil[dirIdx,0]; dy = stencil[dirIdx,1]; dz = stencil[dirIdx,2]
if flag_field[x + dx, y + dy, z + dz] & boundary_mask:
- boundary_index_list.append((x,y,z, dirIdx))
if single_link:
- break
+ sum_x += dx; sum_y += dy; sum_z += dz
+ else:
+ boundary_index_list.append((x, y, z, dirIdx))
+
+ dot = 0; maxn = 0; calculated_idx = 0
+ if single_link and (sum_x != 0 or sum_y != 0 or sum_z != 0):
+ for dirIdx in range(num_directions):
+ dx = stencil[dirIdx, 0]; dy = stencil[dirIdx, 1]; dz = stencil[dirIdx, 2]
+
+ dot = dx * sum_x + dy * sum_y + dz * sum_z
+ if dot > maxn:
+ maxn = dot
+ calculated_idx = dirIdx
+
+ boundary_index_list.append((x, y, z, calculated_idx))
return boundary_index_list
@@ -75,21 +108,39 @@ def create_boundary_cell_index_list_2d(object[IntegerType, ndim=2] flag_field,
cdef int xs, ys, x, y
cdef int dirIdx, num_directions, dx, dy
+ cdef int sum_x, sum_y
+ cdef float dot, maxn
+ cdef int calculated_idx
+
xs, ys = flag_field.shape
boundary_index_list = []
num_directions = stencil.shape[0]
for y in range(0, ys):
for x in range(0, xs):
+ sum_x = 0; sum_y = 0;
if flag_field[x, y] & boundary_mask:
for dirIdx in range(num_directions):
- dx = stencil[dirIdx,0]
- dy = stencil[dirIdx,1]
+ dx = stencil[dirIdx,0]; dy = stencil[dirIdx,1]
if 0 <= x + dx < xs and 0 <= y + dy < ys:
if flag_field[x + dx, y + dy] & fluid_mask:
- boundary_index_list.append((x,y, dirIdx))
if single_link:
- break
+ sum_x += dx; sum_y += dy
+ else:
+ boundary_index_list.append((x, y, dirIdx))
+
+ dot = 0; maxn = 0; calculated_idx = 0
+ if single_link and (sum_x != 0 or sum_y != 0):
+ for dirIdx in range(num_directions):
+ dx = stencil[dirIdx, 0]; dy = stencil[dirIdx, 1]
+
+ dot = dx * sum_x + dy * sum_y
+ if dot > maxn:
+ maxn = dot
+ calculated_idx = dirIdx
+
+ boundary_index_list.append((x, y, calculated_idx))
+
return boundary_index_list
@@ -101,6 +152,10 @@ def create_boundary_cell_index_list_3d(object[IntegerType, ndim=3] flag_field,
cdef int xs, ys, zs, x, y, z
cdef int dirIdx, num_directions, dx, dy, dz
+ cdef int sum_x, sum_y, sum_z
+ cdef float dot, maxn
+ cdef int calculated_idx
+
xs, ys, zs = flag_field.shape
boundary_index_list = []
num_directions = stencil.shape[0]
@@ -108,14 +163,27 @@ def create_boundary_cell_index_list_3d(object[IntegerType, ndim=3] flag_field,
for z in range(0, zs):
for y in range(0, ys):
for x in range(0, xs):
+ sum_x = 0; sum_y = 0; sum_z = 0
if flag_field[x, y, z] & boundary_mask:
for dirIdx in range(num_directions):
- dx = stencil[dirIdx,0]
- dy = stencil[dirIdx,1]
- dz = stencil[dirIdx,2]
+ dx = stencil[dirIdx, 0]; dy = stencil[dirIdx, 1]; dz = stencil[dirIdx, 2]
if 0 <= x + dx < xs and 0 <= y + dy < ys and 0 <= z + dz < zs:
if flag_field[x + dx, y + dy, z + dz] & fluid_mask:
- boundary_index_list.append((x,y,z, dirIdx))
if single_link:
- break
+ sum_x += dx; sum_y += dy; sum_z += dz
+ else:
+ boundary_index_list.append((x, y, z, dirIdx))
+
+ dot = 0; maxn = 0; calculated_idx=0
+ if single_link and (sum_x != 0 or sum_y !=0 or sum_z !=0):
+ for dirIdx in range(num_directions):
+ dx = stencil[dirIdx, 0]; dy = stencil[dirIdx, 1]; dz = stencil[dirIdx, 2]
+
+ dot = dx*sum_x + dy*sum_y + dz*sum_z
+ if dot > maxn:
+ maxn = dot
+ calculated_idx = dirIdx
+
+ boundary_index_list.append((x, y, z, calculated_idx))
+
return boundary_index_list
\ No newline at end of file
diff --git a/pystencils_tests/test_boundary_indexlist_creation.py b/pystencils_tests/test_boundary_indexlist_creation.py
index 58c6a18f6..970a2b1de 100644
--- a/pystencils_tests/test_boundary_indexlist_creation.py
+++ b/pystencils_tests/test_boundary_indexlist_creation.py
@@ -26,11 +26,11 @@ def test_equivalence_cython_python_version(single_link):
flag_field_3d[-1, :, :] = mask
flag_field_3d[7, 7, 7] = mask
- result_python_2d = cil._create_boundary_neighbor_index_list_python(flag_field_2d, 1, mask, fluid_mask,
- stencil_2d, single_link)
+ result_python_2d = cil._create_index_list_python(flag_field_2d, mask, fluid_mask,
+ stencil_2d, single_link, True, 1)
- result_python_3d = cil._create_boundary_neighbor_index_list_python(flag_field_3d, 1, mask, fluid_mask,
- stencil_3d, single_link)
+ result_python_3d = cil._create_index_list_python(flag_field_3d, mask, fluid_mask,
+ stencil_3d, single_link, True, 1)
result_cython_2d = cil.create_boundary_index_list(flag_field_2d, stencil_2d, mask,
fluid_mask, 1, True, single_link)
@@ -62,11 +62,11 @@ def test_equivalence_cell_idx_list_cython_python_version(single_link):
flag_field_3d[-1, :, :] = mask
flag_field_3d[7, 7, 7] = mask
- result_python_2d = cil._create_boundary_cell_index_list_python(flag_field_2d, mask, fluid_mask,
- stencil_2d, single_link)
+ result_python_2d = cil._create_index_list_python(flag_field_2d, mask, fluid_mask,
+ stencil_2d, single_link, False)
- result_python_3d = cil._create_boundary_cell_index_list_python(flag_field_3d, mask, fluid_mask,
- stencil_3d, single_link)
+ result_python_3d = cil._create_index_list_python(flag_field_3d, mask, fluid_mask,
+ stencil_3d, single_link, False)
result_cython_2d = cil.create_boundary_index_list(flag_field_2d, stencil_2d, mask, fluid_mask, None,
False, single_link)
@@ -75,3 +75,42 @@ def test_equivalence_cell_idx_list_cython_python_version(single_link):
np.testing.assert_equal(result_python_2d, result_cython_2d)
np.testing.assert_equal(result_python_3d, result_cython_3d)
+
+@pytest.mark.parametrize('inner_or_boundary', [False, True])
+def test_normal_calculation(inner_or_boundary):
+ stencil = tuple((x,y) for x,y in product([-1, 0, 1], [-1, 0, 1]))
+ domain_size = (32, 32)
+ dtype = np.uint32
+ fluid_mask = dtype(1)
+ mask = dtype(2)
+ flag_field = np.ones([domain_size[0], domain_size[1]], dtype=dtype) * fluid_mask
+
+ radius_inner = domain_size[0] // 4
+ radius_outer = domain_size[0] // 2
+ y_mid = domain_size[1] / 2
+ x_mid = domain_size[0] / 2
+
+ for x in range(0, domain_size[0]):
+ for y in range(0, domain_size[1]):
+ if (y - y_mid) ** 2 + (x - x_mid) ** 2 < radius_inner ** 2:
+ flag_field[x, y] = mask
+ if (x - x_mid) ** 2 + (y - y_mid) ** 2 > radius_outer ** 2:
+ flag_field[x, y] = mask
+
+ args_no_gl = (flag_field, mask, fluid_mask, np.array(stencil, dtype=np.int32), True)
+ index_list = cil._create_index_list_python(*args_no_gl, inner_or_boundary=inner_or_boundary, nr_of_ghost_layers=1)
+
+ checkmask = mask if inner_or_boundary else fluid_mask
+
+ for cell in index_list:
+ idx = cell[2]
+ cell = tuple((cell[0], cell[1]))
+ sum_cells = np.zeros(len(cell))
+ for dir_idx, direction in enumerate(stencil):
+ neighbor_cell = tuple([cell_i + dir_i for cell_i, dir_i in zip(cell, direction)])
+ if any(not 0 <= e < upper for e, upper in zip(neighbor_cell, flag_field.shape)):
+ continue
+ if flag_field[neighbor_cell] & checkmask:
+ sum_cells += np.array(direction)
+
+ assert np.argmax(np.inner(sum_cells, stencil)) == idx
--
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