def test_3dmesher_par_adapt():
fname = os.path.join(os.path.dirname(__file__), "test3D.bin")
nz, nx, ny = 20, 10, 10
bbox = (-2000.0, 0.0, 0.0, 1000.0, 0.0, 1000.0)
cube = Cube(bbox)
hmin = 50
wl = 10
freq = 4
grade = 0.15
ef = get_sizing_function_from_segy(
fname,
bbox,
hmin=hmin,
wl=wl,
freq=freq,
grade=grade,
nx=nx,
ny=ny,
nz=nz,
byte_order="little",
)
points, cells = generate_mesh(
cube,
ef,
max_iter=10,
)
points = comm.bcast(points, 0)
points, cells = generate_mesh(
points=points,
domain=cube,
edge_length=ef,
axis=1,
max_iter=10,
)
points = comm.bcast(points, 0)
points, cells = generate_mesh(
points=points,
edge_length=ef,
domain=cube,
axis=2,
max_iter=10,
)
if comm.rank == 0:
import meshio
meshio.write_points_cells(
"foo3D_V3.vtk",
points,
[("tetra", cells)],
)
vol = geometry.simp_vol(points / 1000, cells)
assert np.abs(2 - np.sum(vol)) < 0.10 # km2
def run_SeismicMesh(ef, HMIN=75.0):
bbox = (-12000.0, 0.0, 0.0, 67000.0)
rectangle = Rectangle(bbox)
t1 = time.time()
points, cells = generate_mesh(
domain=rectangle,
edge_length=ef,
verbose=0,
max_iter=25,
)
elapsed = time.time() - t1
# import meshio
# meshio.write_points_cells(
# "BP2004_sm" + str(HMIN) + ".vtk",
# points,
# [("triangle", cells)],
# file_format="vtk",
# )
plex = meshplex.MeshTri(points, cells)
quality = numpy.abs(plex.cell_quality)
num_cells = len(cells)
num_vertices = len(points)
return quality, elapsed, num_vertices, num_cells
def test_2dmesher_SDF():
"""Unit disk"""
hmin = 0.2
bbox = (-1.0, 1.0, -1.0, 1.0)
disk = geometry.Disk([0.0, 0.0], 1)
def EF(p):
d = disk.eval(p)
return hmin - d * 0.15
points, cells = generate_mesh(
bbox=bbox,
domain=disk,
h0=hmin,
edge_length=EF,
max_iter=100,
)
# print(len(points), len(cells))
assert allclose([len(points), len(cells)], [63, 93], atol=10)
assert allclose(sum(geometry.simp_vol(points, cells)), 3.14, atol=hmin)
import meshio
meshio.write_points_cells(
"blah.vtk",
points[:, [1, 0]] / 1000,
[("triangle", cells)],
file_format="vtk",
)
def test_2dmesher():
fname = os.path.join(os.path.dirname(__file__), "testing.segy")
bbox = (-10000.0, 0.0, 0.0, 10000.0)
wl = 5
freq = 5.0
hmin = 100
hmax = 10e6
grade = 0.005
grad = 50.0
rectangle = Rectangle(bbox)
ef = get_sizing_function_from_segy(
fname,
bbox=bbox,
grade=grade,
grad=grad,
wl=wl,
freq=freq,
hmin=hmin,
hmax=hmax,
)
plot_sizing_function(ef)
write_velocity_model(fname)
points, cells = generate_mesh(
rectangle,
ef,
h0=hmin,
perform_checks=True,
)
# should have: 7690 vertices and 15045 cells
print(len(points), len(cells))
allclose([len(points), len(cells)], [7690, 15045], atol=100)
def run_SeismicMesh(ef, HMIN=75.0):
bbox = (-12000, 0.0, 0.0, 67000.0)
rectangle = Rectangle(bbox)
t1 = time.time()
points, cells = generate_mesh(
domain=rectangle,
edge_length=ef,
h0=HMIN,
max_iter=25,
delta_t=0.3,
)
points, cells = geometry.delete_boundary_entities(points,
cells,
dim=2,
min_qual=0.10)
elapsed = time.time() - t1
# meshio.write_points_cells(
# "BP2004_sm.vtk",
# points,
# [("triangle", cells)],
# file_format="vtk",
# )
plex = meshplex.MeshTri(points, cells)
quality = numpy.abs(plex.cell_quality)
num_cells = len(cells)
num_vertices = len(points)
return quality, elapsed, num_vertices, num_cells
def run_SeismicMesh(ef, HMIN=75.0):
cube = Cube(bbox)
t1 = time.time()
points, cells = generate_mesh(
domain=cube,
edge_length=ef,
max_iter=25,
)
points, cells = sliver_removal(
points=points,
domain=cube,
edge_length=ef,
)
elapsed = time.time() - t1
# meshio.write_points_cells(
# "sm_EAGE.vtk",
# points,
# [("tetra", cells)],
# file_format="vtk",
# )
plex = meshplex.MeshTetra(points, cells)
angles = plex.q_min_sin_dihedral_angles
quality = plex.q_radius_ratio
num_cells = len(cells)
num_vertices = len(points)
return angles, quality, elapsed, num_vertices, num_cells
def test_rotations2d():
bbox = (0.0, 1.0, 0.0, 1.0)
geo = []
geo.append(Disk((0.5, 0.5), 0.1, rotate=0.2 * 3.14))
geo.append(Rectangle(bbox, rotate=0.3 * 3.14))
for domain in geo:
p, c = generate_mesh(domain=domain, edge_length=0.1)
def test_3dmesher_par():
fname = os.path.join(os.path.dirname(__file__), "test3D.bin")
nz, nx, ny = 20, 10, 10
bbox = (-2e3, 0.0, 0.0, 1e3, 0.0, 1e3)
hmin = 50
wl = 10
freq = 4
grade = 0.15
grad = 50.0
cube = Cube(bbox)
ef = get_sizing_function_from_segy(
fname,
bbox,
hmin=hmin,
grade=grade,
grad=grad,
wl=wl,
freq=freq,
nz=nz,
nx=nx,
ny=ny,
byte_order="little",
axes_order=(2, 0,
1), # order for EAGE (x, y, z) to default order (z,x,y)
)
points, cells = generate_mesh(
h0=hmin,
edge_length=ef,
domain=cube,
perform_checks=False,
)
points, cells = sliver_removal(
points=points,
domain=cube,
edge_length=ef,
h0=hmin,
perform_checks=False,
)
if comm.rank == 0:
import meshio
meshio.write_points_cells(
"foo3D_V3.vtk",
points,
[("tetra", cells)],
)
vol = geometry.simp_vol(points / 1000, cells)
assert np.abs(2 - np.sum(vol)) < 0.10 # km2
print(len(points), len(cells))
assert np.abs(9220 - len(points)) < 5000
assert np.abs(49156 - len(cells)) < 5000
def test_2dmesher_par_adapt():
fname = os.path.join(os.path.dirname(__file__), "testing.segy")
bbox = (-10e3, 0.0, 0.0, 10e3)
wl = 5
freq = 5
hmin = 100
grade = 0.005
ef = get_sizing_function_from_segy(
fname,
bbox,
hmin=hmin,
wl=wl,
freq=freq,
grade=grade,
)
rectangle = Rectangle(bbox)
points, cells = generate_mesh(
edge_length=ef,
domain=rectangle,
h0=hmin,
perform_checks=False,
)
points = comm.bcast(points, 0)
# pass the points and restart with a different axis
points, cells = generate_mesh(
points=points,
edge_length=ef,
h0=hmin,
domain=rectangle,
perform_checks=False,
)
if comm.rank == 0:
import meshio
meshio.write_points_cells("test2d.vtk",
points / 1000, [("triangle", cells)],
file_format="vtk")
area = geometry.simp_vol(points / 1000, cells)
assert np.abs(100 - np.sum(area)) < 0.60 # km2
def test_rotations3d():
bbox = (0.0, 1.0, 0.0, 1.0, 0.0, 1.0)
geo = []
geo.append(Ball((0.5, 0.5, 0.5), 0.1, rotate=0.0 * 3.14))
geo.append(Cube(bbox, rotate=0.4 * 3.14))
geo.append(Torus(1.0, 0.5, rotate=0.4 * 3.14))
geo.append(Prism(0.5, 0.5, rotate=0.5 * 3.14))
geo.append(Cylinder(1.0, 0.5, rotate=0.6 * 3.14))
for domain in geo:
p, c = generate_mesh(domain=domain, edge_length=0.1)
def test_3dmesher_domain_extension(style_answer):
style, answer = style_answer
fname = os.path.join(os.path.dirname(__file__), "test3D.bin")
wl = 5
freq = 2
hmin = 150
grade = 0.005
bbox = (-2e3, 0.0, 0.0, 1e3, 0.0, 1e3)
cube = Cube(bbox)
ef = get_sizing_function_from_segy(
fname,
bbox,
grade=grade,
grad=hmin,
freq=freq,
wl=wl,
hmin=hmin,
nz=20,
nx=10,
ny=10,
byte_order="little",
domain_pad=200,
pad_style=style,
axes_order=(2, 0, 1),
)
write_velocity_model(fname,
nz=20,
nx=10,
ny=10,
byte_order="little",
ofname="testing",
bbox=bbox)
points, cells = generate_mesh(
domain=cube,
edge_length=ef,
h0=hmin,
perform_checks=False,
)
points, cells = sliver_removal(points=points,
domain=cube,
edge_length=ef,
h0=hmin)
print(len(points), len(cells))
allclose([len(points), len(cells)], answer, atol=100)
import meshio
meshio.write_points_cells("foo3D" + style + ".vtk", points,
[("tetra", cells)])
def test_3dmesher_SDF():
"""Unit cylinder"""
hmin = 0.10
bbox = (-1.0, 1.0, -1.0, 1.0, -1.0, 1.0)
def cylinder(p):
r, z = sqrt(p[:, 0] ** 2 + p[:, 1] ** 2), p[:, 2]
d1, d2, d3 = r - 1.0, z - 1.0, -z - 1.0
d4, d5 = sqrt(d1 ** 2 + d2 ** 2), sqrt(d1 ** 2 + d3 ** 2)
d = maximum.reduce([d1, d2, d3])
ix = (d1 > 0) * (d2 > 0)
d[ix] = d4[ix]
ix = (d1 > 0) * (d3 > 0)
d[ix] = d5[ix]
return d
def EF(p):
return array(
[
hmin,
]
* len(p)
)
points, cells = generate_mesh(
bbox=bbox,
domain=cylinder,
h0=hmin,
edge_length=EF,
max_iter=100,
)
points, cells = sliver_removal(
points=points, domain=cylinder, edge_length=EF, h0=hmin, bbox=bbox
)
assert allclose(sum(geometry.simp_vol(points, cells)), 6.28, atol=hmin)
print(len(points), len(cells))
allclose([len(points), len(cells)], [6825, 36206], atol=100)
import meshio
meshio.write_points_cells(
"blah.vtk",
points / 1000,
[("tetra", cells)],
file_format="vtk",
)
def test_3dmesher():
fname = os.path.join(os.path.dirname(__file__), "test3D.bin")
wl = 10
freq = 2
hmin = 50
grade = 0.005
bbox = (-2e3, 0.0, 0.0, 1e3, 0.0, 1e3)
cube = Cube(bbox)
ef = get_sizing_function_from_segy(
fname,
bbox,
grade=grade,
grad=hmin,
freq=freq,
wl=wl,
hmin=hmin,
nz=20,
nx=10,
ny=10,
byte_order="little",
domain_pad=0.0,
axes_order=(2, 0, 1),
)
write_velocity_model(fname,
nz=20,
nx=10,
ny=10,
byte_order="little",
ofname="testing")
points, cells = generate_mesh(
domain=cube,
edge_length=ef,
h0=hmin,
max_iter=25,
perform_checks=False,
)
points, cells = sliver_removal(points=points,
edge_length=ef,
domain=cube,
h0=hmin)
print(len(points), len(cells))
allclose([len(points), len(cells)], [16459, 89240], atol=100)
def test_2dmesher_domain_extension(style_answer):
style, answer = style_answer
fname = os.path.join(os.path.dirname(__file__), "testing.segy")
bbox = (-10e3, 0.0, 0.0, 10e3)
wl = 5
freq = 5.0
hmin = 100
hmax = 10e6
grade = 0.005
grad = 50.0
rectangle = Rectangle(bbox)
ef = get_sizing_function_from_segy(
fname,
bbox=bbox,
grade=grade,
grad=grad,
stencil_size=100,
wl=wl,
freq=freq,
hmin=hmin,
hmax=hmax,
pad_style=style,
domain_pad=1e3,
)
plot_sizing_function(ef)
write_velocity_model(fname, bbox=bbox)
points, cells = generate_mesh(
rectangle,
ef,
h0=hmin,
perform_checks=True,
)
# import meshio
# meshio.write_points_cells(
# "TEST.vtk", points, [("triangle", cells)], file_format="vtk"
# )
print(len(points), len(cells))
assert allclose([len(points), len(cells)], answer, atol=100)
def test_2dmesher_par():
fname = os.path.join(os.path.dirname(__file__), "testing.segy")
bbox = (-10e3, 0.0, 0.0, 10e3)
freq = 2
wl = 10
hmin = 75
grade = 0.005
rectangle = Rectangle(bbox)
ef = get_sizing_function_from_segy(fname,
bbox,
hmin=hmin,
wl=wl,
freq=freq,
grade=grade)
points, cells = generate_mesh(
rectangle,
ef,
h0=hmin,
max_iter=100,
perform_checks=False,
)
if comm.rank == 0:
import meshio
meshio.write_points_cells(
"test2d.vtk",
points / 1000,
[("triangle", cells)],
file_format="vtk",
)
area = geometry.simp_vol(points / 1000, cells)
assert np.abs(100 - np.sum(area)) < 0.50 # km2
