def explore_mesh(mesh, name):
print("Nb vertices:", mesh.nb_vertices)
print("Nb cells:", mesh.nb_cells)
print("Nb faces:", mesh.nb_faces)
print("Vertices")
print_collection(mesh.vertices)
print("Cell nodes")
print_collection(mesh.connectivity.cells.nodes)
print("Cell face")
print_collection(mesh.connectivity.cells.faces)
print("Face nodes")
print_collection(mesh.connectivity.faces.nodes)
print("Boundary faces:", mesh.boundary_faces())
fcenters = MT.as_coordinate_array(mesh.face_centers())
print("All face centers: (with shape", fcenters.shape, ")")
print(fcenters)
ccenters = MT.as_coordinate_array(mesh.cell_centers())
print("All cell centers: (with shape", ccenters.shape, ")")
print(ccenters)
vertices = MT.as_coordinate_array(mesh.vertices)
cellnodes = np.array(
[np.array(cell) for cell in mesh.connectivity.cells.nodes])
print(cellnodes)
vtkw.write_vtu(vtkw.vtu_doc(vertices, cellnodes), name + ".vtu")
vtkw.write_vtu(
vtkw.vtu_doc(fcenters, np.reshape(np.arange(fcenters.shape[0]),
(-1, 1))),
name + "_face_centers.vtu",
)
node_color = np.empty(mesh.nb_vertices, dtype="i")
face_color = np.empty(mesh.nb_faces, dtype="i")
for proc, dist in enumerate(distribution):
cells, nodes, faces = [v.array_view() for v in dist[0]]
ghost_cells_index, ghost_nodes_index, ghost_faces_index = dist[1]
node_color[nodes[:ghost_nodes_index]] = proc
face_color[faces[:ghost_faces_index]] = proc
offsets, cellsnodes = mesh.cells_nodes_as_COC()
vtkw.write_vtu(
vtkw.vtu_doc_from_COC(
mesh.vertices_array(),
np.array(offsets[1:], copy=False), # no first zero offset for wtk
np.array(cellsnodes, copy=False),
mesh.cells_vtk_ids(),
pointdata={"color": node_color},
celldata={"color": cell_color},
),
"distribution.vtu",
)
offsets, facesnodes = mesh.faces_nodes_as_COC()
vtkw.write_vtu(
vtkw.vtu_doc_from_COC(
mesh.vertices_array(),
np.array(offsets[1:], copy=False), # no first zero offset for wtk
np.array(facesnodes, copy=False),
mesh.faces_vtk_ids(),
pointdata={"color": node_color},
celldata={"color": face_color},
def retrieve(filename, dtype):
return np.loadtxt(os.path.join(dirname, filename), dtype=dtype)
vertices = retrieve("vertices", np.double)
cells = retrieve("cells", MT.idtype())
faces = retrieve("faces", MT.idtype())
fault_faces = retrieve("faces_fault", MT.idtype())
fault_faces_nodes = faces[fault_faces]
mesh = MT.tetmesh(vertices, cells)
fault_faces_id = mesh.faces_ids(fault_faces_nodes)
vtkw.write_vtu(vtkw.vtu_doc(vertices, cells),
os.path.join(dirname, "mesh.vtu"))
ffcenters = mesh.face_centers(fault_faces_id)
vtkw.write_vtu(
vtkw.vtu_doc(ffcenters, np.reshape(np.arange(ffcenters.shape[0]),
(-1, 1))),
os.path.join(dirname, "fault_faces_centers.vtu"),
)
fcenters = mesh.face_centers(mesh.faces_ids(faces))
patches = retrieve("patches", np.int)
assert fcenters.shape[0] == patches.shape[0]
vtkw.write_vtu(
vtkw.vtu_doc(
def create_and_distribute_mesh(
mesh_constructor, constructor_arguments, coloring_algorithm
):
# retrieve mesh class from underlying MeshTools module
mesh_module_name = mesh_constructor.__module__.split(".")[-1]
assert hasattr(MT, mesh_module_name)
start = datetime.datetime.now()
if rank == 0:
global_mesh = mesh_constructor(*constructor_arguments)
print("coloring after", (datetime.datetime.now() - start).total_seconds())
cell_color = coloring_algorithm(global_mesh)
print("distributing after", (datetime.datetime.now() - start).total_seconds())
distribution = global_mesh.distribute(cell_color)
node_color = np.empty(global_mesh.nb_vertices, dtype="i")
face_color = np.empty(global_mesh.nb_faces, dtype="i")
face_location = []
# we make a first loop to locate faces with relatively to cell
for proc, dist in enumerate(distribution):
cells, nodes, faces = [v.array_view() for v in dist[0]]
# ghost_cells_index, ghost_nodes_index, ghost_faces_index = dist[1]
# node_color[nodes[:ghost_nodes_index]] = proc
# face_color[faces[:ghost_faces_index]] = proc
face_location.append(global_mesh.locate_faces_with_cell(cells, faces))
vertices = global_mesh.vertices_array()
cellnodes = global_mesh.connectivity.cells.nodes.raw_array()
print(
"starting distribution after",
(datetime.datetime.now() - start).total_seconds(),
)
nbparts = len(distribution)
assert nbparts == comm.size
for proc in range(1, nbparts):
cells, nodes, faces = [v.array_view() for v in distribution[proc][0]]
# ?? send owns or deduce owns from color ?
comm.send(
(cells.shape[0], nodes.shape[0], faces.shape[0], cellnodes.shape[1]),
dest=proc,
tag=11,
)
comm.send(distribution[proc][1], dest=proc, tag=111)
# send global ids ->
assert cells.dtype == MT.idtype()
comm.Send([cells, mpi_id_type], dest=proc, tag=12)
assert nodes.dtype == MT.idtype()
comm.Send([nodes, mpi_id_type], dest=proc, tag=13)
assert faces.dtype == MT.idtype()
comm.Send([faces, mpi_id_type], dest=proc, tag=14)
# send part elements ->
assert vertices.dtype == np.double
comm.Send([vertices[nodes], np2mpi(np.double)], dest=proc, tag=15)
comm.Send([cellnodes[cells], MPI.BYTE], dest=proc, tag=16)
face_cell, face_position = face_location[proc]
assert face_cell.dtype == MT.idtype()
comm.Send([face_cell, mpi_id_type], dest=proc, tag=17)
assert face_position.dtype == np.uint8
comm.Send([face_position, np2mpi(np.uint8)], dest=proc, tag=18)
# part that stays on master proc
cells_gid, nodes_gid, unsorted_faces_gid = [
v.array_view() for v in distribution[0][0]
]
ghost_indexes = distribution[0][1]
vertices = np.copy(vertices[nodes_gid])
cellnodes = cellnodes[cells_gid]
face_cell, face_position = face_location[0]
else:
nbcells, nbnodes, nbfaces, raw_cell_size = comm.recv(source=0, tag=11)
ghost_indexes = comm.recv(source=0, tag=111)
# -> receive global ids
cells_gid = np.empty((nbcells,), dtype=MT.idtype())
comm.Recv([cells_gid, mpi_id_type], source=0, tag=12)
nodes_gid = np.empty((nbnodes,), dtype=MT.idtype())
comm.Recv([nodes_gid, mpi_id_type], source=0, tag=13)
unsorted_faces_gid = np.empty((nbfaces,), dtype=MT.idtype())
comm.Recv([unsorted_faces_gid, mpi_id_type], source=0, tag=14)
# -> receive part elements
vertices = np.empty((nbnodes, 3), dtype=np.double)
comm.Recv([vertices, np2mpi(np.double)], source=0, tag=15)
# print('proc', comm.rank, ':', vertices.min(axis=0), vertices.max(axis=0))
cellnodes = np.empty((nbcells, raw_cell_size), dtype=np.byte)
comm.Recv([cellnodes, MPI.BYTE], source=0, tag=16)
face_cell = np.empty((nbfaces,), dtype=MT.idtype())
comm.Recv([face_cell, mpi_id_type], source=0, tag=17)
face_position = np.empty((nbfaces,), dtype=np.uint8)
comm.Recv([face_position, np2mpi(np.uint8)], source=0, tag=18)
# Rebuild local meshes
print(
"rebuilding on",
rank,
"after",
(datetime.datetime.now() - start).total_seconds(),
)
Mesh = getattr(MT, mesh_module_name)
mesh = Mesh.create_from_remap(vertices, cellnodes, nodes_gid)
# CHECKME: invert cell_gid, would this be faster in C++?
gid2lid = {cells_gid[k]: k for k in range(cells_gid.shape[0])}
local_face_cell = np.array([gid2lid[gci] for gci in face_cell])
faces_gid_order = mesh.identify_faces_from_positions(local_face_cell, face_position)
faces_gid = unsorted_faces_gid[faces_gid_order]
sys.stdout.flush()
comm.Barrier()
print(
"total processing time on",
rank,
":",
(datetime.datetime.now() - start).total_seconds(),
)
offsets, cellsnodes = mesh.cells_nodes_as_COC()
ghost_tag = np.zeros(mesh.nb_cells, dtype="i")
ghost_tag[ghost_indexes[0] :] = 1
vtkw.write_vtu(
vtkw.vtu_doc_from_COC(
mesh.vertices_array(),
np.array(offsets[1:], copy=False), # no first zero offset for vtk
np.array(cellsnodes, copy=False),
mesh.cells_vtk_ids(),
celldata={"ghost": ghost_tag},
),
"localmesh-%03d.vtu" % rank,
)
return mesh
import numpy as np
import vtkwriters as vtkw
vtkw.write_vtu(
vtkw.polyhedra_vtu_doc(
vertices=np.array(
[
(-1, -1, 0),
(1, -1, 0),
(0, 1, 0),
(0, 0, 1),
(0, -1, 0),
],
dtype="d",
),
cells_faces=[[
(0, 4, 1, 2),
(0, 1, 3),
(1, 2, 3),
(2, 0, 3),
]],
),
"tet_as_polyhedron",
)
Point((1.0, 0.0, 1.0)),
Point((1.0, 1.0, 1.0)),
Point((0.0, 1.0, 1.0)),
]
hexas = [
Hexa((0, 1, 2, 3, 4, 5, 6, 7)),
]
mesh = MeshTools.HybridMesh.Mesh()
vertices = mesh.vertices
for P in pts:
vertices.append(P)
cellnodes = mesh.connectivity.cells.nodes
for elt in hexas:
cellnodes.append(elt)
mesh.connectivity.update_from_cellnodes()
offsets, cellsnodes = mesh.cells_nodes_as_COC()
vtkw.write_vtu(
vtkw.vtu_doc_from_COC(
mesh.vertices_array(),
np.array(offsets[1:], copy=False), # no first zero offset for vtk
np.array(cellsnodes, copy=False),
mesh.cells_vtk_ids(),
),
"hexa.vtu",
)
import numpy as np
import MeshTools as MT
import GridTools as GT
import vtkwriters as vtkw
vertices, cells = GT.grid2hexs((3, 2, 4))
cells = np.ascontiguousarray(cells, dtype=MT.idtype())
mesh = MT.HexMesh.make(vertices, cells)
vertices = MT.as_coordinate_array(mesh.vertices)
cellnodes = np.array(
[np.array(nodes) for nodes in mesh.connectivity.cells.nodes])
vtkw.write_vtu(vtkw.vtu_doc(vertices, cellnodes), "hexs.vtu")
vertices[j * nr:(j + 1) * nr, 1] = y[0]
for k, yk in enumerate(y[1:]):
vertices[(k + 1) * (nr * ntheta):(k + 2) *
(nr * ntheta)] = vertices[k * (nr * ntheta):(k + 1) *
(nr * ntheta)]
vertices[(k + 1) * (nr * ntheta):(k + 2) * (nr * ntheta), 1] = yk
ncr, ncth, ncy = nr - 1, nsectors, nslices
ncells = ncr * ncth * ncy
cells = np.zeros((ncells, 8), dtype=MT.idtype())
tmp = np.arange(ncr)
cells[:ncr, 0] = tmp
cells[:ncr, 1] = tmp + 1
cells[:ncr, 2] = tmp + 1 + nr
cells[:ncr, 3] = tmp + nr
for j in range(1, ncth - 1):
cells[j * ncr:(j + 1) * ncr, :4] = cells[(j - 1) * ncr:j * ncr, :4] + nr
cells[(ncth - 1) * ncr:ncth * ncr, :2] = cells[(ncth - 2) * ncr:(ncth - 1) *
ncr, 3:1:-1]
cells[(ncth - 1) * ncr:ncth * ncr, 2:4] = cells[:ncr, 1::-1]
cells[:(ncr * ncth), 4:] = cells[:(ncr * ncth), :4] + nr * ntheta
for k in range(1, ncy):
cells[k * (ncr * ncth):(k + 1) *
(ncr * ncth), :] = (cells[(k - 1) * (ncr * ncth):k *
(ncr * ncth), :] + nr * ntheta)
mesh = MT.hexmesh(vertices, cells)
vtkw.write_vtu(vtkw.vtu_doc(mesh.vertices, mesh.cellnodes), "andra.vtu")
mesh = MT.TetMesh.make(vertices, MT.idarray(tets))
print("Nb vertices:", mesh.nb_vertices)
print("Nb cells:", mesh.nb_cells)
print("Nb faces:", mesh.nb_faces)
def print_collection(iterable):
for item in iterable:
print(item)
print("Vertices")
print_collection(mesh.vertices)
print("Cell face")
print_collection(mesh.connectivity.cells.faces)
print("Cell nodes")
print_collection(mesh.connectivity.cells.nodes)
print("Face nodes")
print_collection(mesh.connectivity.faces.nodes)
print("All cell centers:")
print_collection(mesh.cell_centers())
vtkw.write_vtu(
vtkw.vtu_doc(vertices,
tets,
celldata={"id": np.arange(1, tets.shape[0] + 1)}),
"cubes.vtu",
)
import numpy as np
import vtkwriters as vtkw
vertices = np.array([
[0, 0, 0],
[1, 0, 0],
[1, 1, 0],
[0, 1, 0],
], dtype="d")
triangles = np.array([
[0, 1, 2],
[0, 2, 3],
], dtype="i")
vtkw.write_vtu(
vtkw.vtu_doc(
vertices,
triangles,
celldata={"cell property": np.arange(2)},
fielddata={"color": (0, 255, 0)}, # green
),
"two_triangles",
)
import vtkwriters as vtkw
import gmsh_reader
filename = "case-tests/andra/andra_gallery.msh"
nodes, elements = gmsh_reader.retrieve_mesh_elements(filename)
# select heaxedra only
hexaedra = [elt for elt, tags in elements if type(elt) is MT.Hexahedron]
mesh = MT.HexMesh.create(nodes, hexaedra)
vertices = MT.as_coordinate_array(mesh.vertices)
cellnodes = np.array([np.array(nodes) for nodes in mesh.connectivity.cells.nodes])
vtkw.write_vtu(
vtkw.vtu_doc(vertices, cellnodes), filename.replace(".msh", "_hexaedra_only.vtu")
)
# filter out 2D elements
elements_3D = [
(elt, tags)
for elt, tags in elements
if type(elt) in (MT.Tetrahedron, MT.Wedge, MT.Hexahedron)
]
mesh = MT.HybridMesh.create(nodes, [elt for elt, tags in elements_3D])
physical = np.array([tags[0] for elt, tags in elements_3D])
offsets, cellnodes = mesh.cells_nodes_as_COC()
vtkw.write_vtu(