def test_lines_no_crossing(self):
p = np.array([[-1, 1, 0, 0],
[0, 0, -1, 1]])
lines = np.array([[0, 1],
[2, 3]])
box = np.array([[2], [2]])
new_pts, new_lines = basics.remove_edge_crossings(p, lines, box=box)
assert np.allclose(new_pts, p)
assert np.allclose(new_lines, lines)
def test_three_lines_no_crossing(self):
# This test gave an error at some point
p = np.array([[ 0., 0., 0.3, 1., 1., 0.5],
[2/3, 1/.7, 0.3, 2/3, 1/.7, 0.5]])
lines = np.array([[0, 3], [1, 4], [2, 5]]).T
box = np.array([[1], [2]])
new_pts, new_lines = basics.remove_edge_crossings(p, lines, box=box)
p_known = basics.snap_to_grid(p, box=box)
assert np.allclose(new_pts, p_known)
assert np.allclose(new_lines, lines)
def test_split_segment_partly_overlapping(self):
p = np.array([[0, 1, 2, 3],
[0, 0, 0, 0]])
lines = np.array([[0, 2], [1, 3]]).T
box = np.array([[1], [1]])
new_pts, new_lines = basics.remove_edge_crossings(p, lines, box=box)
p_known = basics.snap_to_grid(p, box=box)
lines_known = np.array([[0, 1], [1, 2], [2, 3]]).T
assert np.allclose(new_pts, p_known)
assert np.allclose(new_lines, lines_known)
def test_three_lines_one_crossing(self):
# This test gave an error at some point
p = np.array([[ 0., 0.5, 0.3, 1., 0.3, 0.5],
[2/3, 0.3, 0.3, 2/3, 0.5, 0.5]])
lines = np.array([[0, 3], [2, 5], [1, 4]]).T
box = np.array([[1], [2]])
new_pts, new_lines = basics.remove_edge_crossings(p, lines, box=box)
p_known = np.hstack((p, np.array([[0.4], [0.4]])))
p_known = basics.snap_to_grid(p_known, box=box)
lines_known = np.array([[0, 3], [2, 6], [6, 5], [1, 6], [6, 4]]).T
assert np.allclose(new_pts, p_known)
assert np.allclose(new_lines, lines_known)
def test_split_segment_fully_overlapping_switched_order(self):
p = np.array([[0, 1, 2, 3],
[0, 0, 0, 0]])
lines = np.array([[0, 3], [2, 1]]).T
box = np.array([[1], [1]])
new_pts, new_lines = basics.remove_edge_crossings(p, lines, box=box)
new_lines = np.sort(new_lines, axis=0)
p_known = basics.snap_to_grid(p, box=box)
lines_known = np.array([[0, 1], [1, 2], [2, 3]]).T
assert np.allclose(new_pts, p_known)
assert np.allclose(new_lines, lines_known)
def test_split_segment_partly_overlapping_switched_order(self):
# Same partly overlapping test, but switch order of edge-point
# connection. Should make no difference
p = np.array([[0, 1, 2, 3],
[0, 0, 0, 0]])
lines = np.array([[0, 2], [3, 1]]).T
box = np.array([[1], [1]])
new_pts, new_lines = basics.remove_edge_crossings(p, lines, box=box)
new_lines = np.sort(new_lines, axis=0)
p_known = basics.snap_to_grid(p, box=box)
lines_known = np.array([[0, 1], [1, 2], [2, 3]]).T
assert np.allclose(new_pts, p_known)
assert np.allclose(new_lines, lines_known)
def test_lines_crossing_origin(self):
p = np.array([[-1, 1, 0, 0],
[0, 0, -1, 1]])
lines = np.array([[0, 2],
[1, 3],
[1, 2],
[3, 4]])
box = np.array([[2], [2]])
new_pts, new_lines = basics.remove_edge_crossings(p, lines, box=box)
p_known = np.hstack((p, np.array([[0], [0]])))
p_known = basics.snap_to_grid(p_known, box=box)
lines_known = np.array([[0, 4, 2, 4],
[4, 1, 4, 3],
[1, 1, 2, 2],
[3, 3, 4, 4]])
assert np.allclose(new_pts, p_known)
assert np.allclose(new_lines, lines_known)
def triangle_grid(fracs, domain, **kwargs):
"""
Generate a gmsh grid in a 2D domain with fractures.
The function uses modified versions of pygmsh and mesh_io,
both downloaded from github.
To be added:
Functionality for tuning gmsh, including grid size, refinements, etc.
Examples
>>> p = np.array([[-1, 1, 0, 0], [0, 0, -1, 1]])
>>> lines = np.array([[0, 2], [1, 3]])
>>> char_h = 0.5 * np.ones(p.shape[1])
>>> tags = np.array([1, 3])
>>> fracs = {'points': p, 'edges': lines}
>>> box = {'xmin': -2, 'xmax': 2, 'ymin': -2, 'ymax': 2}
>>> path_to_gmsh = '~/gmsh/bin/gmsh'
>>> g = create_grid(fracs, box, gmsh_path=path_to_gmsh)
>>> plot_grid.plot_grid(g)
Parameters
----------
fracs: (dictionary) Two fields: points (2 x num_points) np.ndarray,
lines (2 x num_lines) connections between points, defines fractures.
box: (dictionary) keys xmin, xmax, ymin, ymax, [together bounding box
for the domain]
**kwargs: To be explored. Must contain the key 'gmsh_path'
Returns
-------
list (length 3): For each dimension (2 -> 0), a list of all grids in
that dimension.
"""
# Verbosity level
verbose = kwargs.get('verbose', 1)
# File name for communication with gmsh
file_name = kwargs.get('file_name', 'gmsh_frac_file')
in_file = file_name + '.geo'
out_file = file_name + '.msh'
# Pick out fracture points, and their connections
frac_pts = fracs['points']
frac_con = fracs['edges']
# Unified description of points and lines for domain, and fractures
pts_all, lines = __merge_domain_fracs_2d(domain, frac_pts, frac_con)
# We split all fracture intersections so that the new lines do not
# intersect, except possible at the end points
dx = np.array([[domain['xmax'] - domain['xmin']],
[domain['ymax'] - domain['ymin']]])
pts_split, lines_split = cg.remove_edge_crossings(pts_all, lines, box=dx)
# We find the end points that is shared by more than one intersection
intersections = __find_intersection_points(lines_split)
# Constants used in the gmsh.geo-file
const = constants.GmshConstants()
# Gridding size
lchar_dom = kwargs.get('lchar_dom', None)
lchar_frac = kwargs.get('lchar_frac', lchar_dom)
# gmsh options
gmsh_path = kwargs.get('gmsh_path')
gmsh_verbose = kwargs.get('gmsh_verbose', verbose)
gmsh_opts = {'-v': gmsh_verbose}
# Create a writer of gmsh .geo-files
gw = gmsh_interface.GmshWriter(pts_split,
lines_split,
domain=domain,
mesh_size=lchar_dom,
mesh_size_bound=lchar_frac,
intersection_points=intersections)
gw.write_geo(in_file)
# Run gmsh
gmsh_status = gmsh_interface.run_gmsh(gmsh_path,
in_file,
out_file,
dims=2,
**gmsh_opts)
if verbose > 0:
start_time = time.time()
if gmsh_status == 0:
print('Gmsh processed file successfully')
else:
print('Gmsh failed with status ' + str(gmsh_status))
pts, cells, phys_names, cell_info = mesh_io.read(out_file)
# Create grids from gmsh mesh.
g_2d = mesh_2_grid.create_2d_grids(pts, cells, is_embedded=False)
g_1d, _ = mesh_2_grid.create_1d_grids(
pts,
cells,
phys_names,
cell_info,
line_tag=const.PHYSICAL_NAME_FRACTURES)
g_0d = mesh_2_grid.create_0d_grids(pts, cells)
grids = [g_2d, g_1d, g_0d]
if verbose > 0:
print('\n')
print('Grid creation completed. Elapsed time ' +
str(time.time() - start_time))
print('\n')
for g_set in grids:
if len(g_set) > 0:
s = 'Created ' + str(len(g_set)) + ' ' + str(g_set[0].dim) + \
'-d grids with '
num = 0
for g in g_set:
num += g.num_cells
s += str(num) + ' cells'
print(s)
print('\n')
return grids