def CircleManifoldMesh(ncells, radius=1, comm=COMM_WORLD):
"""Generated a 1D mesh of the circle, immersed in 2D.
:arg ncells: number of cells the circle should be
divided into (min 3)
:kwarg radius: (optional) radius of the circle to approximate
(defaults to 1).
:kwarg comm: Optional communicator to build the mesh on (defaults to
COMM_WORLD).
"""
if ncells < 3:
raise ValueError("CircleManifoldMesh must have at least three cells")
vertices = radius * np.column_stack(
(np.cos(np.arange(ncells) * (2 * np.pi / ncells)),
np.sin(np.arange(ncells) * (2 * np.pi / ncells))))
cells = np.column_stack((np.arange(0, ncells, dtype=np.int32),
np.roll(np.arange(0, ncells, dtype=np.int32),
-1)))
plex = mesh._from_cell_list(1, cells, vertices, comm)
m = mesh.Mesh(plex, dim=2, reorder=False)
m._circle_manifold = radius
return m
def CubedSphereMesh(radius, refinement_level=0, degree=1,
reorder=None, comm=COMM_WORLD):
"""Generate an cubed approximation to the surface of the
sphere.
:arg radius: The radius of the sphere to approximate.
:kwarg refinement_level: optional number of refinements (0 is a cube).
:kwarg degree: polynomial degree of coordinate space (defaults
to 1: bilinear quads)
:kwarg reorder: (optional), should the mesh be reordered?
"""
if refinement_level < 0 or refinement_level % 1:
raise RuntimeError("Number of refinements must be a non-negative integer")
if degree < 1:
raise ValueError("Mesh coordinate degree must be at least 1")
cells, coords = _cubedsphere_cells_and_coords(radius, refinement_level)
plex = mesh._from_cell_list(2, cells, coords, comm)
m = mesh.Mesh(plex, dim=3, reorder=reorder)
if degree > 1:
new_coords = function.Function(functionspace.VectorFunctionSpace(m, "Q", degree))
new_coords.interpolate(ufl.SpatialCoordinate(m))
# "push out" to sphere
new_coords.dat.data[:] *= (radius / np.linalg.norm(new_coords.dat.data, axis=1)).reshape(-1, 1)
m = mesh.Mesh(new_coords)
m._radius = radius
return m
def TorusMesh(nR, nr, R, r, quadrilateral=False, reorder=None):
"""Generate a toroidal mesh
:arg nR: The number of cells in the major direction (min 3)
:arg nr: The number of cells in the minor direction (min 3)
:arg R: The major radius
:arg r: The minor radius
:kwarg quadrilateral: (optional), creates quadrilateral mesh, defaults to False
:kwarg reorder: (optional), should the mesh be reordered
"""
if nR < 3 or nr < 3:
raise ValueError("Must have at least 3 cells in each direction")
# gives an array [[0, 0], [0, 1], ..., [1, 0], [1, 1], ...]
idx_temp = np.asarray(np.meshgrid(np.arange(nR), np.arange(nr))).swapaxes(0, 2).reshape(-1, 2)
# vertices - standard formula for (x, y, z), see Wikipedia
vertices = np.column_stack((
(R + r*np.cos(idx_temp[:, 1]*(2*np.pi/nr)))*np.cos(idx_temp[:, 0]*(2*np.pi/nR)),
(R + r*np.cos(idx_temp[:, 1]*(2*np.pi/nr)))*np.sin(idx_temp[:, 0]*(2*np.pi/nR)),
r*np.sin(idx_temp[:, 1]*(2*np.pi/nr))))
# cell vertices
i, j = np.meshgrid(np.arange(nR), np.arange(nr))
i = i.reshape(-1) # Miklos's suggestion to make the code
j = j.reshape(-1) # less impenetrable
cells = [i*nr + j, i*nr + (j+1) % nr, ((i+1) % nR)*nr + (j+1) % nr, ((i+1) % nR)*nr + j]
cells = np.column_stack(cells)
if not quadrilateral:
# two cells per cell above...
cells = cells[:, [0, 1, 3, 1, 2, 3]].reshape(-1, 3)
plex = mesh._from_cell_list(2, cells, vertices)
m = mesh.Mesh(plex, dim=3, reorder=reorder)
return m
def TorusMesh(nR, nr, R, r, quadrilateral=False, reorder=None):
"""Generate a toroidal mesh
:arg nR: The number of cells in the major direction (min 3)
:arg nr: The number of cells in the minor direction (min 3)
:arg R: The major radius
:arg r: The minor radius
:kwarg quadrilateral: (optional), creates quadrilateral mesh, defaults to False
:kwarg reorder: (optional), should the mesh be reordered
"""
if nR < 3 or nr < 3:
raise ValueError("Must have at least 3 cells in each direction")
# gives an array [[0, 0], [0, 1], ..., [1, 0], [1, 1], ...]
idx_temp = np.asarray(np.meshgrid(np.arange(nR), np.arange(nr))).swapaxes(0, 2).reshape(-1, 2)
# vertices - standard formula for (x, y, z), see Wikipedia
vertices = np.column_stack((
(R + r*np.cos(idx_temp[:, 1]*(2*np.pi/nr)))*np.cos(idx_temp[:, 0]*(2*np.pi/nR)),
(R + r*np.cos(idx_temp[:, 1]*(2*np.pi/nr)))*np.sin(idx_temp[:, 0]*(2*np.pi/nR)),
r*np.sin(idx_temp[:, 1]*(2*np.pi/nr))))
# cell vertices
i, j = np.meshgrid(np.arange(nR), np.arange(nr))
i = i.reshape(-1) # Miklos's suggestion to make the code
j = j.reshape(-1) # less impenetrable
cells = [i*nr + j, i*nr + (j+1) % nr, ((i+1) % nR)*nr + (j+1) % nr, ((i+1) % nR)*nr + j]
cells = np.column_stack(cells)
if not quadrilateral:
# two cells per cell above...
cells = cells[:, [0, 1, 3, 1, 2, 3]].reshape(-1, 3)
plex = mesh._from_cell_list(2, cells, vertices)
m = mesh.Mesh(plex, dim=3, reorder=reorder)
return m
def RectangleMesh(nx, ny, Lx, Ly, quadrilateral=False, reorder=None):
"""Generate a rectangular mesh
:arg nx: The number of cells in the x direction
:arg ny: The number of cells in the y direction
:arg Lx: The extent in the x direction
:arg Ly: The extent in the y direction
:kwarg quadrilateral: (optional), creates quadrilateral mesh, defaults to False
:kwarg reorder: (optional), should the mesh be reordered
The boundary edges in this mesh are numbered as follows:
* 1: plane x == 0
* 2: plane x == Lx
* 3: plane y == 0
* 4: plane y == Ly
"""
if quadrilateral:
dx = float(Lx) / nx
dy = float(Ly) / ny
xcoords = np.arange(0.0, Lx + 0.01 * dx, dx)
ycoords = np.arange(0.0, Ly + 0.01 * dy, dy)
coords = np.asarray(np.meshgrid(xcoords, ycoords)).swapaxes(0, 2).reshape(-1, 2)
# cell vertices
i, j = np.meshgrid(np.arange(nx), np.arange(ny))
cells = [i*(ny+1) + j, i*(ny+1) + j+1, (i+1)*(ny+1) + j+1, (i+1)*(ny+1) + j]
cells = np.asarray(cells).swapaxes(0, 2).reshape(-1, 4)
plex = mesh._from_cell_list(2, cells, coords)
else:
boundary = PETSc.DMPlex().create(MPI.comm)
boundary.setDimension(1)
boundary.createSquareBoundary([0., 0.], [float(Lx), float(Ly)], [nx, ny])
boundary.setTriangleOptions("pqezQYSl")
plex = PETSc.DMPlex().generate(boundary)
# mark boundary facets
plex.createLabel("boundary_ids")
plex.markBoundaryFaces("boundary_faces")
coords = plex.getCoordinates()
coord_sec = plex.getCoordinateSection()
if plex.getStratumSize("boundary_faces", 1) > 0:
boundary_faces = plex.getStratumIS("boundary_faces", 1).getIndices()
xtol = float(Lx)/(2*nx)
ytol = float(Ly)/(2*ny)
for face in boundary_faces:
face_coords = plex.vecGetClosure(coord_sec, coords, face)
if abs(face_coords[0]) < xtol and abs(face_coords[2]) < xtol:
plex.setLabelValue("boundary_ids", face, 1)
if abs(face_coords[0] - Lx) < xtol and abs(face_coords[2] - Lx) < xtol:
plex.setLabelValue("boundary_ids", face, 2)
if abs(face_coords[1]) < ytol and abs(face_coords[3]) < ytol:
plex.setLabelValue("boundary_ids", face, 3)
if abs(face_coords[1] - Ly) < ytol and abs(face_coords[3] - Ly) < ytol:
plex.setLabelValue("boundary_ids", face, 4)
return mesh.Mesh(plex, reorder=reorder)
def RectangleMesh(nx, ny, Lx, Ly, quadrilateral=False, reorder=None):
"""Generate a rectangular mesh
:arg nx: The number of cells in the x direction
:arg ny: The number of cells in the y direction
:arg Lx: The extent in the x direction
:arg Ly: The extent in the y direction
:kwarg quadrilateral: (optional), creates quadrilateral mesh, defaults to False
:kwarg reorder: (optional), should the mesh be reordered
The boundary edges in this mesh are numbered as follows:
* 1: plane x == 0
* 2: plane x == Lx
* 3: plane y == 0
* 4: plane y == Ly
"""
if quadrilateral:
dx = float(Lx) / nx
dy = float(Ly) / ny
xcoords = np.arange(0.0, Lx + 0.01 * dx, dx)
ycoords = np.arange(0.0, Ly + 0.01 * dy, dy)
coords = np.asarray(np.meshgrid(xcoords, ycoords)).swapaxes(0, 2).reshape(-1, 2)
# cell vertices
i, j = np.meshgrid(np.arange(nx), np.arange(ny))
cells = [i*(ny+1) + j, i*(ny+1) + j+1, (i+1)*(ny+1) + j+1, (i+1)*(ny+1) + j]
cells = np.asarray(cells).swapaxes(0, 2).reshape(-1, 4)
plex = mesh._from_cell_list(2, cells, coords)
else:
boundary = PETSc.DMPlex().create(MPI.comm)
boundary.setDimension(1)
boundary.createSquareBoundary([0., 0.], [float(Lx), float(Ly)], [nx, ny])
boundary.setTriangleOptions("pqezQYSl")
plex = PETSc.DMPlex().generate(boundary)
# mark boundary facets
plex.createLabel("boundary_ids")
plex.markBoundaryFaces("boundary_faces")
coords = plex.getCoordinates()
coord_sec = plex.getCoordinateSection()
if plex.getStratumSize("boundary_faces", 1) > 0:
boundary_faces = plex.getStratumIS("boundary_faces", 1).getIndices()
xtol = float(Lx)/(2*nx)
ytol = float(Ly)/(2*ny)
for face in boundary_faces:
face_coords = plex.vecGetClosure(coord_sec, coords, face)
if abs(face_coords[0]) < xtol and abs(face_coords[2]) < xtol:
plex.setLabelValue("boundary_ids", face, 1)
if abs(face_coords[0] - Lx) < xtol and abs(face_coords[2] - Lx) < xtol:
plex.setLabelValue("boundary_ids", face, 2)
if abs(face_coords[1]) < ytol and abs(face_coords[3]) < ytol:
plex.setLabelValue("boundary_ids", face, 3)
if abs(face_coords[1] - Ly) < ytol and abs(face_coords[3] - Ly) < ytol:
plex.setLabelValue("boundary_ids", face, 4)
return mesh.Mesh(plex, reorder=reorder)
def IcosahedralSphereMesh(radius, refinement_level=0, degree=1, reorder=None):
"""Generate an icosahedral approximation to the surface of the
sphere.
:arg radius: The radius of the sphere to approximate.
For a radius R the edge length of the underlying
icosahedron will be.
.. math::
a = \\frac{R}{\\sin(2 \\pi / 5)}
:kwarg refinement_level: optional number of refinements (0 is an
icosahedron).
:kwarg degree: polynomial degree of coordinate space (defaults
to 1: flat triangles)
:kwarg reorder: (optional), should the mesh be reordered?
"""
if degree < 1:
raise ValueError("Mesh coordinate degree must be at least 1")
from math import sqrt
phi = (1 + sqrt(5)) / 2
# vertices of an icosahedron with an edge length of 2
vertices = np.array([[-1, phi, 0], [1, phi, 0], [-1, -phi,
0], [1, -phi, 0],
[0, -1, phi], [0, 1, phi], [0, -1,
-phi], [0, 1, -phi],
[phi, 0, -1], [phi, 0, 1], [-phi, 0, -1],
[-phi, 0, 1]])
# faces of the base icosahedron
faces = np.array(
[[0, 11, 5], [0, 5, 1], [0, 1, 7], [0, 7, 10], [0, 10, 11], [1, 5, 9],
[5, 11, 4], [11, 10, 2], [10, 7, 6], [7, 1, 8], [3, 9, 4], [3, 4, 2],
[3, 2, 6], [3, 6, 8], [3, 8, 9], [4, 9, 5], [2, 4, 11], [6, 2, 10],
[8, 6, 7], [9, 8, 1]],
dtype=np.int32)
plex = mesh._from_cell_list(2, faces, vertices)
plex.setRefinementUniform(True)
for i in range(refinement_level):
plex = plex.refine()
coords = plex.getCoordinatesLocal().array.reshape(-1, 3)
scale = (radius / np.linalg.norm(coords, axis=1)).reshape(-1, 1)
coords *= scale
m = mesh.Mesh(plex, dim=3, reorder=reorder)
if degree > 1:
new_coords = function.Function(
functionspace.VectorFunctionSpace(m, "CG", degree))
new_coords.interpolate(expression.Expression(("x[0]", "x[1]", "x[2]")))
# "push out" to sphere
new_coords.dat.data[:] *= (
radius / np.linalg.norm(new_coords.dat.data, axis=1)).reshape(
-1, 1)
m = mesh.Mesh(new_coords)
m._icosahedral_sphere = radius
return m
def UnitTetrahedronMesh(comm=COMM_WORLD):
"""Generate a mesh of the reference tetrahedron.
:kwarg comm: Optional communicator to build the mesh on (defaults to
COMM_WORLD).
"""
coords = [[0., 0., 0.], [1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]
cells = [[0, 1, 2, 3]]
plex = mesh._from_cell_list(3, cells, coords, comm)
return mesh.Mesh(plex, reorder=False)
def UnitTetrahedronMesh(comm=COMM_WORLD):
"""Generate a mesh of the reference tetrahedron.
:kwarg comm: Optional communicator to build the mesh on (defaults to
COMM_WORLD).
"""
coords = [[0., 0., 0.], [1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]
cells = [[0, 1, 2, 3]]
plex = mesh._from_cell_list(3, cells, coords, comm)
return mesh.Mesh(plex, reorder=False)
def IntervalMesh(ncells, length_or_left, right=None, comm=COMM_WORLD):
"""
Generate a uniform mesh of an interval.
:arg ncells: The number of the cells over the interval.
:arg length_or_left: The length of the interval (if ``right``
is not provided) or else the left hand boundary point.
:arg right: (optional) position of the right
boundary point (in which case ``length_or_left`` should
be the left boundary point).
:kwarg comm: Optional communicator to build the mesh on (defaults to
COMM_WORLD).
The left hand boundary point has boundary marker 1,
while the right hand point has marker 2.
"""
if right is None:
left = 0
right = length_or_left
else:
left = length_or_left
if ncells <= 0 or ncells % 1:
raise ValueError("Number of cells must be a postive integer")
length = right - left
if length < 0:
raise ValueError("Requested mesh has negative length")
dx = length / ncells
# This ensures the rightmost point is actually present.
coords = np.arange(left, right + 0.01 * dx, dx,
dtype=np.double).reshape(-1, 1)
cells = np.dstack(
(np.arange(0, len(coords) - 1,
dtype=np.int32), np.arange(1, len(coords),
dtype=np.int32))).reshape(-1, 2)
plex = mesh._from_cell_list(1, cells, coords, comm)
# Apply boundary IDs
plex.createLabel("boundary_ids")
coordinates = plex.getCoordinates()
coord_sec = plex.getCoordinateSection()
vStart, vEnd = plex.getDepthStratum(0) # vertices
for v in range(vStart, vEnd):
vcoord = plex.vecGetClosure(coord_sec, coordinates, v)
if vcoord[0] == coords[0]:
plex.setLabelValue("boundary_ids", v, 1)
if vcoord[0] == coords[-1]:
plex.setLabelValue("boundary_ids", v, 2)
return mesh.Mesh(plex, reorder=False)
def IntervalMesh(ncells, length_or_left, right=None, comm=COMM_WORLD):
"""
Generate a uniform mesh of an interval.
:arg ncells: The number of the cells over the interval.
:arg length_or_left: The length of the interval (if ``right``
is not provided) or else the left hand boundary point.
:arg right: (optional) position of the right
boundary point (in which case ``length_or_left`` should
be the left boundary point).
:kwarg comm: Optional communicator to build the mesh on (defaults to
COMM_WORLD).
The left hand boundary point has boundary marker 1,
while the right hand point has marker 2.
"""
if right is None:
left = 0
right = length_or_left
else:
left = length_or_left
if ncells <= 0 or ncells % 1:
raise ValueError("Number of cells must be a postive integer")
length = right - left
if length < 0:
raise ValueError("Requested mesh has negative length")
dx = float(length) / ncells
# This ensures the rightmost point is actually present.
coords = np.arange(left, right + 0.01 * dx, dx).reshape(-1, 1)
cells = np.dstack((np.arange(0, len(coords) - 1, dtype=np.int32),
np.arange(1, len(coords), dtype=np.int32))).reshape(-1, 2)
plex = mesh._from_cell_list(1, cells, coords, comm)
# Apply boundary IDs
plex.createLabel("boundary_ids")
coordinates = plex.getCoordinates()
coord_sec = plex.getCoordinateSection()
vStart, vEnd = plex.getDepthStratum(0) # vertices
for v in range(vStart, vEnd):
vcoord = plex.vecGetClosure(coord_sec, coordinates, v)
if vcoord[0] == coords[0]:
plex.setLabelValue("boundary_ids", v, 1)
if vcoord[0] == coords[-1]:
plex.setLabelValue("boundary_ids", v, 2)
return mesh.Mesh(plex, reorder=False)
def CircleManifoldMesh(ncells, radius=1):
"""Generated a 1D mesh of the circle, immersed in 2D.
:arg ncells: number of cells the circle should be
divided into (min 3)
:kwarg radius: (optional) radius of the circle to approximate
(defaults to 1).
"""
if ncells < 3:
raise ValueError("CircleManifoldMesh must have at least three cells")
vertices = radius*np.column_stack((np.cos(np.arange(ncells)*(2*np.pi/ncells)),
np.sin(np.arange(ncells)*(2*np.pi/ncells))))
cells = np.column_stack((np.arange(0, ncells, dtype=np.int32),
np.roll(np.arange(0, ncells, dtype=np.int32), -1)))
plex = mesh._from_cell_list(1, cells, vertices)
m = mesh.Mesh(plex, dim=2, reorder=False)
m._circle_manifold = radius
return m
def IcosahedralSphereMesh(radius, refinement_level=0, degree=1, reorder=None,
comm=COMM_WORLD):
"""Generate an icosahedral approximation to the surface of the
sphere.
:arg radius: The radius of the sphere to approximate.
For a radius R the edge length of the underlying
icosahedron will be.
.. math::
a = \\frac{R}{\\sin(2 \\pi / 5)}
:kwarg refinement_level: optional number of refinements (0 is an
icosahedron).
:kwarg degree: polynomial degree of coordinate space (defaults
to 1: flat triangles)
:kwarg reorder: (optional), should the mesh be reordered?
:kwarg comm: Optional communicator to build the mesh on (defaults to
COMM_WORLD).
"""
if refinement_level < 0 or refinement_level % 1:
raise RuntimeError("Number of refinements must be a non-negative integer")
if degree < 1:
raise ValueError("Mesh coordinate degree must be at least 1")
from math import sqrt
phi = (1 + sqrt(5)) / 2
# vertices of an icosahedron with an edge length of 2
vertices = np.array([[-1, phi, 0],
[1, phi, 0],
[-1, -phi, 0],
[1, -phi, 0],
[0, -1, phi],
[0, 1, phi],
[0, -1, -phi],
[0, 1, -phi],
[phi, 0, -1],
[phi, 0, 1],
[-phi, 0, -1],
[-phi, 0, 1]])
# faces of the base icosahedron
faces = np.array([[0, 11, 5],
[0, 5, 1],
[0, 1, 7],
[0, 7, 10],
[0, 10, 11],
[1, 5, 9],
[5, 11, 4],
[11, 10, 2],
[10, 7, 6],
[7, 1, 8],
[3, 9, 4],
[3, 4, 2],
[3, 2, 6],
[3, 6, 8],
[3, 8, 9],
[4, 9, 5],
[2, 4, 11],
[6, 2, 10],
[8, 6, 7],
[9, 8, 1]], dtype=np.int32)
plex = mesh._from_cell_list(2, faces, vertices, comm)
plex.setRefinementUniform(True)
for i in range(refinement_level):
plex = plex.refine()
coords = plex.getCoordinatesLocal().array.reshape(-1, 3)
scale = (radius / np.linalg.norm(coords, axis=1)).reshape(-1, 1)
coords *= scale
m = mesh.Mesh(plex, dim=3, reorder=reorder)
if degree > 1:
new_coords = function.Function(functionspace.VectorFunctionSpace(m, "CG", degree))
new_coords.interpolate(expression.Expression(("x[0]", "x[1]", "x[2]")))
# "push out" to sphere
new_coords.dat.data[:] *= (radius / np.linalg.norm(new_coords.dat.data, axis=1)).reshape(-1, 1)
m = mesh.Mesh(new_coords)
m._icosahedral_sphere = radius
return m
def UnitTriangleMesh():
"""Generate a mesh of the reference triangle"""
coords = [[0., 0.], [1., 0.], [0., 1.]]
cells = [[0, 1, 2]]
plex = mesh._from_cell_list(2, cells, coords)
return mesh.Mesh(plex, reorder=False)
def UnitTetrahedronMesh():
"""Generate a mesh of the reference tetrahedron"""
coords = [[0., 0., 0.], [1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]
cells = [[0, 1, 2, 3]]
plex = mesh._from_cell_list(3, cells, coords)
return mesh.Mesh(plex, reorder=False)
def UnitTriangleMesh():
"""Generate a mesh of the reference triangle"""
coords = [[0., 0.], [1., 0.], [0., 1.]]
cells = [[0, 1, 2]]
plex = mesh._from_cell_list(2, cells, coords)
return mesh.Mesh(plex, reorder=False)
def UnitTetrahedronMesh():
"""Generate a mesh of the reference tetrahedron"""
coords = [[0., 0., 0.], [1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]
cells = [[0, 1, 2, 3]]
plex = mesh._from_cell_list(3, cells, coords)
return mesh.Mesh(plex, reorder=False)
def CubedSphereMesh(radius, refinement_level=0, degree=1,
reorder=None, use_dmplex_refinement=False):
"""Generate an cubed approximation to the surface of the
sphere.
:arg radius: The radius of the sphere to approximate.
:kwarg refinement_level: optional number of refinements (0 is a cube).
:kwarg degree: polynomial degree of coordinate space (defaults
to 1: bilinear quads)
:kwarg reorder: (optional), should the mesh be reordered?
:kwarg use_dmplex_refinement: (optional), use dmplex to apply
the refinement.
"""
if degree < 1:
raise ValueError("Mesh coordinate degree must be at least 1")
if use_dmplex_refinement:
# vertices of a cube with an edge length of 2
vertices = np.array([[-1., -1., -1.],
[1., -1., -1.],
[-1., 1., -1.],
[1., 1., -1.],
[-1., -1., 1.],
[1., -1., 1.],
[-1., 1., 1.],
[1., 1., 1.]])
# faces of the base cube
# bottom face viewed from above
# 2 3
# 0 1
# top face viewed from above
# 6 7
# 4 5
faces = np.array([[0, 1, 3, 2], # bottom
[4, 5, 7, 6], # top
[0, 1, 5, 4],
[2, 3, 7, 6],
[0, 2, 6, 4],
[1, 3, 7, 5]], dtype=np.int32)
plex = mesh._from_cell_list(2, faces, vertices)
plex.setRefinementUniform(True)
for i in range(refinement_level):
plex = plex.refine()
# rescale points to the sphere
# this is not the same as the gnonomic transformation
coords = plex.getCoordinatesLocal().array.reshape(-1, 3)
scale = (radius / np.linalg.norm(coords, axis=1)).reshape(-1, 1)
coords *= scale
else:
cells, coords = _cubedsphere_cells_and_coords(radius, refinement_level)
plex = mesh._from_cell_list(2, cells, coords)
m = mesh.Mesh(plex, dim=3, reorder=reorder)
if degree > 1:
new_coords = function.Function(functionspace.VectorFunctionSpace(m, "Q", degree))
new_coords.interpolate(expression.Expression(("x[0]", "x[1]", "x[2]")))
# "push out" to sphere
new_coords.dat.data[:] *= (radius / np.linalg.norm(new_coords.dat.data, axis=1)).reshape(-1, 1)
m = mesh.Mesh(new_coords)
return m
def export_mesh_to_firedrake(mesh, group_nr=None, comm=None):
r"""
Create a firedrake mesh corresponding to one
:class:`~meshmode.mesh.Mesh`'s
:class:`~meshmode.mesh.SimplexElementGroup`.
:param mesh: A :class:`~meshmode.mesh.Mesh` to convert with
at least one :class:`~meshmode.mesh.SimplexElementGroup`.
'mesh.is_conforming' must evaluate to *True*.
'mesh' must have vertices supplied, i.e.
'mesh.vertices' must not be *None*.
:param group_nr: The group number to be converted into a firedrake
mesh. The corresponding group must be of type
:class:`~meshmode.mesh.SimplexElementGroup`. If *None* and
*mesh* has only one group, that group is used. Otherwise,
a *ValueError* is raised.
:param comm: The communicator to build the dmplex mesh on
:return: A tuple *(fdrake_mesh, fdrake_cell_ordering, perm2cell)*
where
* *fdrake_mesh* is a :mod:`firedrake`
`firedrake.mesh.MeshGeometry` corresponding to
*mesh*
* *fdrake_cell_ordering* is a numpy array whose *i*\ th
element in *mesh* (i.e. the *i*\ th element in
*mesh.groups[group_nr].vertex_indices*) corresponds to the
*fdrake_cell_ordering[i]*\ th :mod:`firedrake` cell
* *perm2cell* is a dictionary, mapping tuples to
1-D numpy arrays of meshmode element indices.
Each meshmode element index
appears in exactly one of these arrays. The corresponding
tuple describes how firedrake reordered the local vertex
indices on that cell. In particular, if *c*
is in the list *perm2cell[p]* for a tuple *p*, then
the *p[i]*\ th local vertex of the *fdrake_cell_ordering[c]*\ th
firedrake cell corresponds to the *i*\ th local vertex
of the *c*\ th meshmode element.
.. warning::
Currently, no custom boundary tags are exported along with the mesh.
:mod:`firedrake` seems to only allow one marker on each facet, whereas
:mod:`meshmode` allows many.
"""
if not isinstance(mesh, Mesh):
raise TypeError("'mesh' must of type meshmode.mesh.Mesh,"
" not '%s'." % type(mesh))
if group_nr is None:
if len(mesh.groups) != 1:
raise ValueError("'group_nr' is *None* but 'mesh' has "
"more than one group.")
group_nr = 0
if not isinstance(group_nr, int):
raise TypeError("Expecting 'group_nr' to be of type int, not "
f"'{type(group_nr)}'")
if group_nr < 0 or group_nr >= len(mesh.groups):
raise ValueError("'group_nr' is an invalid group index:"
f" '{group_nr}' fails to satisfy "
f"0 <= {group_nr} < {len(mesh.groups)}")
if not isinstance(mesh.groups[group_nr], SimplexElementGroup):
raise TypeError("Expecting 'mesh.groups[group_nr]' to be of type "
"meshmode.mesh.SimplexElementGroup, not "
f"'{type(mesh.groups[group_nr])}'")
if mesh.vertices is None:
raise ValueError("'mesh' has no vertices "
"('mesh.vertices' is *None*)")
if not mesh.is_conforming:
raise ValueError(f"'mesh.is_conforming' is {mesh.is_conforming} "
"instead of *True*. Converting non-conforming "
" meshes to Firedrake is not supported")
# Get the vertices and vertex indices of the requested group
with ProcessLogger(logger, "Obtaining vertices from selected group"):
group = mesh.groups[group_nr]
fd2mm_indices = np.unique(group.vertex_indices.flatten())
coords = mesh.vertices[:, fd2mm_indices].T
mm2fd_indices = dict(zip(fd2mm_indices, np.arange(np.size(fd2mm_indices))))
cells = np.vectorize(mm2fd_indices.__getitem__)(group.vertex_indices)
# Get a dmplex object and then a mesh topology
with ProcessLogger(logger, "Building dmplex object and MeshTopology"):
if comm is None:
from pyop2.mpi import COMM_WORLD
comm = COMM_WORLD
# FIXME : not sure how to get around the private accesses
import firedrake.mesh as fd_mesh
plex = fd_mesh._from_cell_list(group.dim, cells, coords, comm)
# Nb : One might be tempted to pass reorder=False and thereby save some
# hassle in exchange for forcing firedrake to have slightly
# less efficient caching. Unfortunately, that only prevents
# the cells from being reordered, and does not prevent the
# vertices from being (locally) reordered on each cell...
# the tl;dr is we don't actually save any hassle
top = fd_mesh.Mesh(plex, dim=mesh.ambient_dim) # mesh topology
top.init()
# Get new element ordering:
with ProcessLogger(logger, "Determining permutations applied"
" to local vertex numbers"):
c_start, c_end = top._topology_dm.getHeightStratum(0)
cell_index_mm2fd = np.vectorize(top._cell_numbering.getOffset)(
np.arange(c_start, c_end))
v_start, v_end = top._topology_dm.getDepthStratum(0)
# Firedrake goes crazy reordering local vertex numbers,
# we've got to work to figure out what changes they made.
#
# *perm2cells* will map permutations of local vertex numbers to
# the list of all the meshmode cells
# which firedrake reordered according to that permutation
#
# Permutations on *n* vertices are stored as a tuple
# containing all of the integers *0*, *1*, *2*, ..., *n-1*
# exactly once. A permutation *p*
# represents relabeling the *i*\ th local vertex
# of a meshmode element as the *p[i]*\ th local vertex
# in the corresponding firedrake cell.
#
# *perm2cells[p]* is a list of all the meshmode element indices
# for which *p* represents the reordering applied by firedrake
perm2cells = {}
for mm_cell_id, dmp_ids in enumerate(top.cell_closure[cell_index_mm2fd]):
# look at order of vertices in firedrake cell
vert_dmp_ids = \
dmp_ids[np.logical_and(v_start <= dmp_ids, dmp_ids < v_end)]
fdrake_order = vert_dmp_ids - v_start
# get original order
mm_order = mesh.groups[group_nr].vertex_indices[mm_cell_id]
# want permutation p so that mm_order[p] = fdrake_order
# To do so, look at permutations acting by composition.
#
# mm_order \circ argsort(mm_order) =
# fdrake_order \circ argsort(fdrake_order)
# so
# mm_order \circ argsort(mm_order) \circ inv(argsort(fdrake_order))
# = fdrake_order
#
# argsort acts as an inverse, so the desired permutation is:
perm = tuple(np.argsort(mm_order)[np.argsort(np.argsort(fdrake_order))])
perm2cells.setdefault(perm, [])
perm2cells[perm].append(mm_cell_id)
# Make perm2cells map to numpy arrays instead of lists
perm2cells = {perm: np.array(cells)
for perm, cells in perm2cells.items()}
# Now make a coordinates function
with ProcessLogger(logger, "Building firedrake function "
"space for mesh coordinates"):
from firedrake import VectorFunctionSpace, Function
coords_fspace = VectorFunctionSpace(top, "CG", group.order,
dim=mesh.ambient_dim)
coords = Function(coords_fspace)
# get firedrake unit nodes and map onto meshmode reference element
fd_ref_cell_to_mm = get_affine_reference_simplex_mapping(group.dim, True)
fd_unit_nodes = get_finat_element_unit_nodes(coords_fspace.finat_element)
fd_unit_nodes = fd_ref_cell_to_mm(fd_unit_nodes)
basis = simplex_best_available_basis(group.dim, group.order)
resampling_mat = resampling_matrix(basis,
new_nodes=fd_unit_nodes,
old_nodes=group.unit_nodes)
# Store the meshmode data resampled to firedrake unit nodes
# (but still in meshmode order)
resampled_group_nodes = np.matmul(group.nodes, resampling_mat.T)
# Now put the nodes in the right local order
# nodes is shaped *(ambient dim, nelements, nunit nodes)*
with ProcessLogger(logger, "Storing meshmode mesh coordinates"
" in firedrake nodal order"):
from meshmode.mesh.processing import get_simplex_element_flip_matrix
for perm, cells in perm2cells.items():
flip_mat = get_simplex_element_flip_matrix(group.order,
fd_unit_nodes,
perm)
flip_mat = np.rint(flip_mat).astype(np.int32)
resampled_group_nodes[:, cells, :] = \
np.matmul(resampled_group_nodes[:, cells, :], flip_mat.T)
# store resampled data in right cell ordering
with ProcessLogger(logger, "resampling mesh coordinates to "
"firedrake unit nodes"):
reordered_cell_node_list = coords_fspace.cell_node_list[cell_index_mm2fd]
coords.dat.data[reordered_cell_node_list, :] = \
resampled_group_nodes.transpose((1, 2, 0))
return fd_mesh.Mesh(coords), cell_index_mm2fd, perm2cells
def OneElementThickMesh(ncells, Lx, Ly, comm=COMM_WORLD):
"""
Generate a rectangular mesh in the domain with corners [0,0]
and [Lx, Ly] with ncells, that is periodic in the x-direction.
:arg ncells: The number of cells in the mesh.
:arg Lx: The width of the domain in the x-direction.
:arg Ly: The width of the domain in the y-direction.
:kwarg comm: Optional communicator to build the mesh on (defaults to
COMM_WORLD).
"""
left = np.arange(ncells, dtype='int32')
right = np.roll(left, -1)
cells = np.array([left, left, right, right]).T
dx = Lx/ncells
X = np.arange(1.0*ncells)*dx
Y = 0.*X
coords = np.array([X, Y]).T
# a line of coordinates, with a looped topology
plex = mesh._from_cell_list(2, cells, coords, comm)
mesh1 = mesh.Mesh(plex)
mesh1.topology.init()
cell_numbering = mesh1._cell_numbering
cell_range = plex.getHeightStratum(0)
cell_closure = np.zeros((cell_range[1], 9), dtype=int)
# Get the coordinates for this process
coords = plex.getCoordinatesLocal().array_r
# get the PETSc section
coords_sec = plex.getCoordinateSection()
for e in range(*cell_range):
closure, orient = plex.getTransitiveClosure(e)
# get the row for this cell
row = cell_numbering.getOffset(e)
# run some checks
assert(closure[0] == e)
assert len(closure) == 7, closure
edge_range = plex.getHeightStratum(1)
assert(all(closure[1:5] >= edge_range[0]))
assert(all(closure[1:5] < edge_range[1]))
vertex_range = plex.getHeightStratum(2)
assert(all(closure[5:] >= vertex_range[0]))
assert(all(closure[5:] < vertex_range[1]))
# enter the cell number
cell_closure[row][8] = e
# Get a list of unique edges
edge_set = list(set(closure[1:5]))
# there are two vertices in the cell
cell_vertices = closure[5:]
cell_X = np.array([0., 0.])
for i, v in enumerate(cell_vertices):
cell_X[i] = coords[coords_sec.getOffset(v)]
# Add in the edges
for i in range(3):
# count up how many times each edge is repeated
repeats = list(closure[1:5]).count(edge_set[i])
if repeats == 2:
# we have a y-periodic edge
cell_closure[row][6] = edge_set[i]
cell_closure[row][7] = edge_set[i]
elif repeats == 1:
# in this code we check if it is a right edge, or a left edge
# by inspecting the x coordinates of the edge vertex (1)
# and comparing with the x coordinates of the cell vertices (2)
# there is only one vertex on the edge in this case
edge_vertex = plex.getCone(edge_set[i])[0]
# get X coordinate for this edge
edge_X = coords[coords_sec.getOffset(edge_vertex)]
# get X coordinates for this cell
if(cell_X.min() < dx/2):
if cell_X.max() < 3*dx/2:
# We are in the first cell
if(edge_X.min() < dx/2):
# we are on left hand edge
cell_closure[row][4] = edge_set[i]
else:
# we are on right hand edge
cell_closure[row][5] = edge_set[i]
else:
# We are in the last cell
if(edge_X.min() < dx/2):
# we are on right hand edge
cell_closure[row][5] = edge_set[i]
else:
# we are on left hand edge
cell_closure[row][4] = edge_set[i]
else:
if(abs(cell_X.min()-edge_X.min()) < dx/2):
# we are on left hand edge
cell_closure[row][4] = edge_set[i]
else:
# we are on right hand edge
cell_closure[row][5] = edge_set[i]
# Add in the vertices
vertices = closure[5:]
v1 = vertices[0]
v2 = vertices[1]
x1 = coords[coords_sec.getOffset(v1)]
x2 = coords[coords_sec.getOffset(v2)]
# Fix orientations
if(x1 > x2):
if(x1 - x2 < dx*1.5):
# we are not on the rightmost cell and need to swap
v1, v2 = v2, v1
elif(x2 - x1 > dx*1.5):
# we are on the rightmost cell and need to swap
v1, v2 = v2, v1
cell_closure[row][0:4] = [v1, v1, v2, v2]
mesh1.topology.cell_closure = np.array(cell_closure, dtype=np.int32)
mesh1.init()
Vc = VectorFunctionSpace(mesh1, 'DQ', 1)
fc = Function(Vc).interpolate(mesh1.coordinates)
mash = mesh.Mesh(fc)
topverts = Vc.cell_node_list[:, 1::2].flatten()
mash.coordinates.dat.data_with_halos[topverts, 1] = Ly
# search for the last cell
mcoords_ro = mash.coordinates.dat.data_ro_with_halos
mcoords = mash.coordinates.dat.data_with_halos
for e in range(*cell_range):
cell = cell_numbering.getOffset(e)
cell_nodes = Vc.cell_node_list[cell, :]
Xvals = mcoords_ro[cell_nodes, 0]
if(Xvals.max() - Xvals.min() > Lx/2):
mcoords[cell_nodes[2:], 0] = Lx
else:
mcoords
local_facet_dat = mash.topology.interior_facets.local_facet_dat
local_facet_number = mash.topology.interior_facets.local_facet_number
lfd_ro = local_facet_dat.data_ro
for i in range(lfd_ro.shape[0]):
if all(lfd_ro[i, :] == np.array([3, 3])):
local_facet_dat.data[i, :] = [2, 3]
local_facet_number[i, :] = [2, 3]
return mash
def CylinderMesh(nr, nl, radius=1, depth=1, longitudinal_direction="z",
quadrilateral=False, reorder=None, comm=COMM_WORLD):
"""Generates a cylinder mesh.
:arg nr: number of cells the cylinder circumference should be
divided into (min 3)
:arg nl: number of cells along the longitudinal axis of the cylinder
:kwarg radius: (optional) radius of the cylinder to approximate
(default 1).
:kwarg depth: (optional) depth of the cylinder to approximate
(default 1).
:kwarg longitudinal_direction: (option) direction for the
longitudinal axis of the cylinder.
:kwarg quadrilateral: (optional), creates quadrilateral mesh, defaults to False
:kwarg comm: Optional communicator to build the mesh on (defaults to
COMM_WORLD).
The boundary edges in this mesh are numbered as follows:
* 1: plane l == 0 (bottom)
* 2: plane l == depth (top)
"""
if nr < 3:
raise ValueError("CylinderMesh must have at least three cells")
coord_xy = radius*np.column_stack((np.cos(np.arange(nr)*(2*np.pi/nr)),
np.sin(np.arange(nr)*(2*np.pi/nr))))
coord_z = depth*np.linspace(0.0, 1.0, nl + 1).reshape(-1, 1)
vertices = np.asarray(np.column_stack((np.tile(coord_xy, (nl + 1, 1)),
np.tile(coord_z, (1, nr)).reshape(-1, 1))),
dtype=np.double)
# intervals on circumference
ring_cells = np.column_stack((np.arange(0, nr, dtype=np.int32),
np.roll(np.arange(0, nr, dtype=np.int32), -1)))
# quads in the first layer
ring_cells = np.column_stack((ring_cells, np.roll(ring_cells, 1, axis=1) + nr))
offset = np.arange(nl, dtype=np.int32)*nr
cells = np.row_stack((ring_cells + i for i in offset))
if not quadrilateral:
# two cells per cell above...
cells = cells[:, [0, 1, 3, 1, 2, 3]].reshape(-1, 3)
if longitudinal_direction == "x":
rotation = np.asarray([[0, 0, 1],
[0, 1, 0],
[-1, 0, 0]], dtype=np.double)
vertices = np.dot(vertices, rotation.T)
elif longitudinal_direction == "y":
rotation = np.asarray([[1, 0, 0],
[0, 0, 1],
[0, -1, 0]], dtype=np.double)
vertices = np.dot(vertices, rotation.T)
elif longitudinal_direction != "z":
raise ValueError("Unknown longitudinal direction '%s'" % longitudinal_direction)
plex = mesh._from_cell_list(2, cells, vertices, comm)
plex.createLabel("boundary_ids")
plex.markBoundaryFaces("boundary_faces")
coords = plex.getCoordinates()
coord_sec = plex.getCoordinateSection()
if plex.getStratumSize("boundary_faces", 1) > 0:
boundary_faces = plex.getStratumIS("boundary_faces", 1).getIndices()
eps = depth/(2*nl)
for face in boundary_faces:
face_coords = plex.vecGetClosure(coord_sec, coords, face)
# index of x/y/z coordinates of the face element
axis_ix = {"x": 0, "y": 1, "z": 2}
i = axis_ix[longitudinal_direction]
j = i + 3
if abs(face_coords[i]) < eps and abs(face_coords[j]) < eps:
# bottom of cylinder
plex.setLabelValue("boundary_ids", face, 1)
if abs(face_coords[i] - depth) < eps and abs(face_coords[j] - depth) < eps:
# top of cylinder
plex.setLabelValue("boundary_ids", face, 2)
m = mesh.Mesh(plex, dim=3, reorder=reorder)
return m
def CubedSphereMesh(radius, refinement_level=0, degree=1,
reorder=None, use_dmplex_refinement=False,
comm=COMM_WORLD):
"""Generate an cubed approximation to the surface of the
sphere.
:arg radius: The radius of the sphere to approximate.
:kwarg refinement_level: optional number of refinements (0 is a cube).
:kwarg degree: polynomial degree of coordinate space (defaults
to 1: bilinear quads)
:kwarg reorder: (optional), should the mesh be reordered?
:kwarg use_dmplex_refinement: (optional), use dmplex to apply
the refinement.
"""
if refinement_level < 0 or refinement_level % 1:
raise RuntimeError("Number of refinements must be a non-negative integer")
if degree < 1:
raise ValueError("Mesh coordinate degree must be at least 1")
if use_dmplex_refinement:
# vertices of a cube with an edge length of 2
vertices = np.array([[-1., -1., -1.],
[1., -1., -1.],
[-1., 1., -1.],
[1., 1., -1.],
[-1., -1., 1.],
[1., -1., 1.],
[-1., 1., 1.],
[1., 1., 1.]])
# faces of the base cube
# bottom face viewed from above
# 2 3
# 0 1
# top face viewed from above
# 6 7
# 4 5
faces = np.array([[0, 1, 3, 2], # bottom
[4, 5, 7, 6], # top
[0, 1, 5, 4],
[2, 3, 7, 6],
[0, 2, 6, 4],
[1, 3, 7, 5]], dtype=np.int32)
plex = mesh._from_cell_list(2, faces, vertices, comm)
plex.setRefinementUniform(True)
for i in range(refinement_level):
plex = plex.refine()
# rescale points to the sphere
# this is not the same as the gnonomic transformation
coords = plex.getCoordinatesLocal().array.reshape(-1, 3)
scale = (radius / np.linalg.norm(coords, axis=1)).reshape(-1, 1)
coords *= scale
else:
cells, coords = _cubedsphere_cells_and_coords(radius, refinement_level)
plex = mesh._from_cell_list(2, cells, coords, comm)
m = mesh.Mesh(plex, dim=3, reorder=reorder)
if degree > 1:
new_coords = function.Function(functionspace.VectorFunctionSpace(m, "Q", degree))
new_coords.interpolate(expression.Expression(("x[0]", "x[1]", "x[2]")))
# "push out" to sphere
new_coords.dat.data[:] *= (radius / np.linalg.norm(new_coords.dat.data, axis=1)).reshape(-1, 1)
m = mesh.Mesh(new_coords)
return m
def RectangleMesh(nx, ny, Lx, Ly, quadrilateral=False, reorder=None,
diagonal="left", comm=COMM_WORLD):
"""Generate a rectangular mesh
:arg nx: The number of cells in the x direction
:arg ny: The number of cells in the y direction
:arg Lx: The extent in the x direction
:arg Ly: The extent in the y direction
:kwarg quadrilateral: (optional), creates quadrilateral mesh, defaults to False
:kwarg reorder: (optional), should the mesh be reordered
:kwarg comm: Optional communicator to build the mesh on (defaults to
COMM_WORLD).
:kwarg diagonal: For triangular meshes, should the diagonal got
from bottom left to top right (``"right"``), or top left to
bottom right (``"left"``).
The boundary edges in this mesh are numbered as follows:
* 1: plane x == 0
* 2: plane x == Lx
* 3: plane y == 0
* 4: plane y == Ly
"""
for n in (nx, ny):
if n <= 0 or n % 1:
raise ValueError("Number of cells must be a postive integer")
xcoords = np.linspace(0.0, Lx, nx + 1, dtype=np.double)
ycoords = np.linspace(0.0, Ly, ny + 1, dtype=np.double)
coords = np.asarray(np.meshgrid(xcoords, ycoords)).swapaxes(0, 2).reshape(-1, 2)
# cell vertices
i, j = np.meshgrid(np.arange(nx, dtype=np.int32), np.arange(ny, dtype=np.int32))
cells = [i*(ny+1) + j, i*(ny+1) + j+1, (i+1)*(ny+1) + j+1, (i+1)*(ny+1) + j]
cells = np.asarray(cells).swapaxes(0, 2).reshape(-1, 4)
if not quadrilateral:
if diagonal == "left":
idx = [0, 1, 3, 1, 2, 3]
elif diagonal == "right":
idx = [0, 1, 2, 0, 2, 3]
else:
raise ValueError("Unrecognised value for diagonal '%r'", diagonal)
# two cells per cell above...
cells = cells[:, idx].reshape(-1, 3)
plex = mesh._from_cell_list(2, cells, coords, comm)
# mark boundary facets
plex.createLabel("boundary_ids")
plex.markBoundaryFaces("boundary_faces")
coords = plex.getCoordinates()
coord_sec = plex.getCoordinateSection()
if plex.getStratumSize("boundary_faces", 1) > 0:
boundary_faces = plex.getStratumIS("boundary_faces", 1).getIndices()
xtol = Lx/(2*nx)
ytol = Ly/(2*ny)
for face in boundary_faces:
face_coords = plex.vecGetClosure(coord_sec, coords, face)
if abs(face_coords[0]) < xtol and abs(face_coords[2]) < xtol:
plex.setLabelValue("boundary_ids", face, 1)
if abs(face_coords[0] - Lx) < xtol and abs(face_coords[2] - Lx) < xtol:
plex.setLabelValue("boundary_ids", face, 2)
if abs(face_coords[1]) < ytol and abs(face_coords[3]) < ytol:
plex.setLabelValue("boundary_ids", face, 3)
if abs(face_coords[1] - Ly) < ytol and abs(face_coords[3] - Ly) < ytol:
plex.setLabelValue("boundary_ids", face, 4)
return mesh.Mesh(plex, reorder=reorder)
def OneElementThickMesh(ncells, Lx, Ly, comm=COMM_WORLD):
"""
Generate a rectangular mesh in the domain with corners [0,0]
and [Lx, Ly] with ncells, that is periodic in the x-direction.
:arg ncells: The number of cells in the mesh.
:arg Lx: The width of the domain in the x-direction.
:arg Ly: The width of the domain in the y-direction.
:kwarg comm: Optional communicator to build the mesh on (defaults to
COMM_WORLD).
"""
left = np.arange(ncells, dtype=np.int32)
right = np.roll(left, -1)
cells = np.array([left, left, right, right]).T
dx = Lx/ncells
X = np.arange(1.0*ncells, dtype=np.double)*dx
Y = 0.*X
coords = np.array([X, Y]).T
# a line of coordinates, with a looped topology
plex = mesh._from_cell_list(2, cells, coords, comm)
mesh1 = mesh.Mesh(plex)
mesh1.topology.init()
cell_numbering = mesh1._cell_numbering
cell_range = plex.getHeightStratum(0)
cell_closure = np.zeros((cell_range[1], 9), dtype=IntType)
# Get the coordinates for this process
coords = plex.getCoordinatesLocal().array_r
# get the PETSc section
coords_sec = plex.getCoordinateSection()
for e in range(*cell_range):
closure, orient = plex.getTransitiveClosure(e)
# get the row for this cell
row = cell_numbering.getOffset(e)
# run some checks
assert(closure[0] == e)
assert len(closure) == 7, closure
edge_range = plex.getHeightStratum(1)
assert(all(closure[1:5] >= edge_range[0]))
assert(all(closure[1:5] < edge_range[1]))
vertex_range = plex.getHeightStratum(2)
assert(all(closure[5:] >= vertex_range[0]))
assert(all(closure[5:] < vertex_range[1]))
# enter the cell number
cell_closure[row][8] = e
# Get a list of unique edges
edge_set = list(set(closure[1:5]))
# there are two vertices in the cell
cell_vertices = closure[5:]
cell_X = np.array([0., 0.])
for i, v in enumerate(cell_vertices):
cell_X[i] = coords[coords_sec.getOffset(v)]
# Add in the edges
for i in range(3):
# count up how many times each edge is repeated
repeats = list(closure[1:5]).count(edge_set[i])
if repeats == 2:
# we have a y-periodic edge
cell_closure[row][6] = edge_set[i]
cell_closure[row][7] = edge_set[i]
elif repeats == 1:
# in this code we check if it is a right edge, or a left edge
# by inspecting the x coordinates of the edge vertex (1)
# and comparing with the x coordinates of the cell vertices (2)
# there is only one vertex on the edge in this case
edge_vertex = plex.getCone(edge_set[i])[0]
# get X coordinate for this edge
edge_X = coords[coords_sec.getOffset(edge_vertex)]
# get X coordinates for this cell
if(cell_X.min() < dx/2):
if cell_X.max() < 3*dx/2:
# We are in the first cell
if(edge_X.min() < dx/2):
# we are on left hand edge
cell_closure[row][4] = edge_set[i]
else:
# we are on right hand edge
cell_closure[row][5] = edge_set[i]
else:
# We are in the last cell
if(edge_X.min() < dx/2):
# we are on right hand edge
cell_closure[row][5] = edge_set[i]
else:
# we are on left hand edge
cell_closure[row][4] = edge_set[i]
else:
if(abs(cell_X.min()-edge_X.min()) < dx/2):
# we are on left hand edge
cell_closure[row][4] = edge_set[i]
else:
# we are on right hand edge
cell_closure[row][5] = edge_set[i]
# Add in the vertices
vertices = closure[5:]
v1 = vertices[0]
v2 = vertices[1]
x1 = coords[coords_sec.getOffset(v1)]
x2 = coords[coords_sec.getOffset(v2)]
# Fix orientations
if(x1 > x2):
if(x1 - x2 < dx*1.5):
# we are not on the rightmost cell and need to swap
v1, v2 = v2, v1
elif(x2 - x1 > dx*1.5):
# we are on the rightmost cell and need to swap
v1, v2 = v2, v1
cell_closure[row][0:4] = [v1, v1, v2, v2]
mesh1.topology.cell_closure = np.array(cell_closure, dtype=IntType)
mesh1.init()
Vc = VectorFunctionSpace(mesh1, 'DQ', 1)
fc = Function(Vc).interpolate(mesh1.coordinates)
mash = mesh.Mesh(fc)
topverts = Vc.cell_node_list[:, 1::2].flatten()
mash.coordinates.dat.data_with_halos[topverts, 1] = Ly
# search for the last cell
mcoords_ro = mash.coordinates.dat.data_ro_with_halos
mcoords = mash.coordinates.dat.data_with_halos
for e in range(*cell_range):
cell = cell_numbering.getOffset(e)
cell_nodes = Vc.cell_node_list[cell, :]
Xvals = mcoords_ro[cell_nodes, 0]
if(Xvals.max() - Xvals.min() > Lx/2):
mcoords[cell_nodes[2:], 0] = Lx
else:
mcoords
local_facet_dat = mash.topology.interior_facets.local_facet_dat
local_facet_number = mash.topology.interior_facets.local_facet_number
lfd_ro = local_facet_dat.data_ro
for i in range(lfd_ro.shape[0]):
if all(lfd_ro[i, :] == np.array([3, 3])):
local_facet_dat.data[i, :] = [2, 3]
local_facet_number[i, :] = [2, 3]
return mash
def CylinderMesh(nr, nl, radius=1, depth=1, longitudinal_direction="z",
quadrilateral=False, reorder=None, comm=COMM_WORLD):
"""Generates a cylinder mesh.
:arg nr: number of cells the cylinder circumference should be
divided into (min 3)
:arg nl: number of cells along the longitudinal axis of the cylinder
:kwarg radius: (optional) radius of the cylinder to approximate
(default 1).
:kwarg depth: (optional) depth of the cylinder to approximate
(default 1).
:kwarg longitudinal_direction: (option) direction for the
longitudinal axis of the cylinder.
:kwarg quadrilateral: (optional), creates quadrilateral mesh, defaults to False
:kwarg comm: Optional communicator to build the mesh on (defaults to
COMM_WORLD).
The boundary edges in this mesh are numbered as follows:
* 1: plane l == 0 (bottom)
* 2: plane l == depth (top)
"""
if nr < 3:
raise ValueError("CylinderMesh must have at least three cells")
coord_xy = radius*np.column_stack((np.cos(np.arange(nr)*(2*np.pi/nr)),
np.sin(np.arange(nr)*(2*np.pi/nr))))
coord_z = depth*np.linspace(0.0, 1.0, nl + 1).reshape(-1, 1)
vertices = np.column_stack((np.tile(coord_xy, (nl + 1, 1)),
np.tile(coord_z, (1, nr)).reshape(-1, 1)))
# intervals on circumference
ring_cells = np.column_stack((np.arange(0, nr, dtype=np.int32),
np.roll(np.arange(0, nr, dtype=np.int32), -1)))
# quads in the first layer
ring_cells = np.column_stack((ring_cells, np.roll(ring_cells, 1, axis=1) + nr))
offset = np.arange(nl)*nr
cells = np.row_stack((ring_cells + i for i in offset))
if not quadrilateral:
# two cells per cell above...
cells = cells[:, [0, 1, 3, 1, 2, 3]].reshape(-1, 3)
if longitudinal_direction == "x":
rotation = np.asarray([[0, 0, 1],
[0, 1, 0],
[-1, 0, 0]])
vertices = np.dot(vertices, rotation.T)
elif longitudinal_direction == "y":
rotation = np.asarray([[1, 0, 0],
[0, 0, 1],
[0, -1, 0]])
vertices = np.dot(vertices, rotation.T)
elif longitudinal_direction != "z":
raise ValueError("Unknown longitudinal direction '%s'" % longitudinal_direction)
plex = mesh._from_cell_list(2, cells, vertices, comm)
plex.createLabel("boundary_ids")
plex.markBoundaryFaces("boundary_faces")
coords = plex.getCoordinates()
coord_sec = plex.getCoordinateSection()
if plex.getStratumSize("boundary_faces", 1) > 0:
boundary_faces = plex.getStratumIS("boundary_faces", 1).getIndices()
eps = float(depth)/(2*nl)
for face in boundary_faces:
face_coords = plex.vecGetClosure(coord_sec, coords, face)
# index of x/y/z coordinates of the face element
axis_ix = {"x": 0, "y": 1, "z": 2}
i = axis_ix[longitudinal_direction]
j = i + 3
if abs(face_coords[i]) < eps and abs(face_coords[j]) < eps:
# bottom of cylinder
plex.setLabelValue("boundary_ids", face, 1)
if abs(face_coords[i] - depth) < eps and abs(face_coords[j] - depth) < eps:
# top of cylinder
plex.setLabelValue("boundary_ids", face, 2)
m = mesh.Mesh(plex, dim=3, reorder=reorder)
return m
def BoxMesh(nx, ny, nz, Lx, Ly, Lz, reorder=None, comm=COMM_WORLD):
"""Generate a mesh of a 3D box.
:arg nx: The number of cells in the x direction
:arg ny: The number of cells in the y direction
:arg nz: The number of cells in the z direction
:arg Lx: The extent in the x direction
:arg Ly: The extent in the y direction
:arg Lz: The extent in the z direction
:kwarg reorder: (optional), should the mesh be reordered?
:kwarg comm: Optional communicator to build the mesh on (defaults to
COMM_WORLD).
The boundary surfaces are numbered as follows:
* 1: plane x == 0
* 2: plane x == Lx
* 3: plane y == 0
* 4: plane y == Ly
* 5: plane z == 0
* 6: plane z == Lz
"""
for n in (nx, ny, nz):
if n <= 0 or n % 1:
raise ValueError("Number of cells must be a postive integer")
xcoords = np.linspace(0, Lx, nx + 1, dtype=np.double)
ycoords = np.linspace(0, Ly, ny + 1, dtype=np.double)
zcoords = np.linspace(0, Lz, nz + 1, dtype=np.double)
# X moves fastest, then Y, then Z
coords = np.asarray(np.meshgrid(xcoords, ycoords, zcoords)).swapaxes(0, 3).reshape(-1, 3)
i, j, k = np.meshgrid(np.arange(nx, dtype=np.int32),
np.arange(ny, dtype=np.int32),
np.arange(nz, dtype=np.int32))
v0 = k*(nx + 1)*(ny + 1) + j*(nx + 1) + i
v1 = v0 + 1
v2 = v0 + (nx + 1)
v3 = v1 + (nx + 1)
v4 = v0 + (nx + 1)*(ny + 1)
v5 = v1 + (nx + 1)*(ny + 1)
v6 = v2 + (nx + 1)*(ny + 1)
v7 = v3 + (nx + 1)*(ny + 1)
cells = [v0, v1, v3, v7,
v0, v1, v7, v5,
v0, v5, v7, v4,
v0, v3, v2, v7,
v0, v6, v4, v7,
v0, v2, v6, v7]
cells = np.asarray(cells).swapaxes(0, 3).reshape(-1, 4)
plex = mesh._from_cell_list(3, cells, coords, comm)
# Apply boundary IDs
plex.createLabel("boundary_ids")
plex.markBoundaryFaces("boundary_faces")
coords = plex.getCoordinates()
coord_sec = plex.getCoordinateSection()
if plex.getStratumSize("boundary_faces", 1) > 0:
boundary_faces = plex.getStratumIS("boundary_faces", 1).getIndices()
xtol = Lx/(2*nx)
ytol = Ly/(2*ny)
ztol = Lz/(2*nz)
for face in boundary_faces:
face_coords = plex.vecGetClosure(coord_sec, coords, face)
if abs(face_coords[0]) < xtol and abs(face_coords[3]) < xtol and abs(face_coords[6]) < xtol:
plex.setLabelValue("boundary_ids", face, 1)
if abs(face_coords[0] - Lx) < xtol and abs(face_coords[3] - Lx) < xtol and abs(face_coords[6] - Lx) < xtol:
plex.setLabelValue("boundary_ids", face, 2)
if abs(face_coords[1]) < ytol and abs(face_coords[4]) < ytol and abs(face_coords[7]) < ytol:
plex.setLabelValue("boundary_ids", face, 3)
if abs(face_coords[1] - Ly) < ytol and abs(face_coords[4] - Ly) < ytol and abs(face_coords[7] - Ly) < ytol:
plex.setLabelValue("boundary_ids", face, 4)
if abs(face_coords[2]) < ztol and abs(face_coords[5]) < ztol and abs(face_coords[8]) < ztol:
plex.setLabelValue("boundary_ids", face, 5)
if abs(face_coords[2] - Lz) < ztol and abs(face_coords[5] - Lz) < ztol and abs(face_coords[8] - Lz) < ztol:
plex.setLabelValue("boundary_ids", face, 6)
return mesh.Mesh(plex, reorder=reorder)
