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'''
This module contains all the functions related to wrapping NGSolve meshes to
PETSc DMPlex using the petsc4py interface.
'''
import itertools
import numpy as np
from packaging.version import Version
from petsc4py import PETSc
import netgen.meshing as ngm
try:
import ngsolve as ngs
except ImportError:
class ngs:
"dummy class"
class comp:
"dummy class"
Mesh = type(None)
FACE_SETS_LABEL = "Face Sets"
CELL_SETS_LABEL = "Cell Sets"
EDGE_SETS_LABEL = "Edge Sets"
class MeshMapping:
'''
This class creates a mapping between Netgen/NGSolve meshes and PETSc DMPlex
:arg mesh: the mesh object, it can be either a Netgen/NGSolve mesh or a PETSc DMPlex
:arg name: the name of to be assigned to the PETSc DMPlex, by default this is set to "Default"
'''
def __init__(self, mesh=None, comm=PETSc.COMM_WORLD.tompi4py(), name="Default"):
self.name = name
self.comm = comm
if isinstance(mesh,(ngs.comp.Mesh,ngm.Mesh)):
self.createPETScDMPlex(mesh)
elif isinstance(mesh,PETSc.DMPlex):
self.createNGSMesh(mesh)
else:
raise ValueError("Mesh format not recognised.")
def createNGSMesh(self, plex):
'''
This function generate an NGSolve mesh from a PETSc DMPlex
:arg plex: the PETSc DMPlex to be converted in NGSolve mesh object
'''
self.petscPlex = plex
ngMesh = ngm.Mesh(dim=plex.getCoordinateDim())
self.ngMesh = ngMesh
if plex.getDimension() == 2:
coordinates = plex.getCoordinates().getArray().reshape([-1,2])
self.ngMesh.AddPoints(coordinates)
cStart,cEnd = plex.getHeightStratum(0)
vStart, _ = plex.getHeightStratum(2)
cells = []
for i in range(cStart,cEnd):
sIndex = plex.getCone(i)
if len(sIndex)==3:
S = list(itertools.chain.from_iterable([
list(plex.getCone(sIndex[k])-vStart) for k in range(len(sIndex))]))
cell = list(dict.fromkeys(S))
A = np.array([coordinates[cell[1]]-coordinates[cell[0]],
coordinates[cell[2]]-coordinates[cell[1]]])
if np.linalg.det(A) > 0:
cells = cells + [cell]
else:
cells = cells + [[cell[0],cell[2],cell[1]]]
else:
S = [plex.getCone(sIndex[k])-vStart for k in list(range(len(sIndex)))]
k = 0
cell = []
while k < len(sIndex):
if S[k][0] == S[k-1][1]:
cell = cell+[S[k][0]]
else:
if k == 0 and S[k][0] not in list(S[k+1]):
S[-1] = np.array([S[-1][1],S[-1][0]])
else:
S[k] = np.array([S[k][1],S[k][0]])
cell = cell+[S[k][0]]
k = k+1
cells = cells + [cell]
self.ngMesh.Add(ngm.FaceDescriptor(bc=1))
self.ngMesh.AddElements(dim=2, index=1, data=np.asarray(cells, dtype=np.int32), base=0)
for bcLabel in range(1,plex.getLabelSize(FACE_SETS_LABEL)+1):
bcIndices = plex.getStratumIS("Face Sets",bcLabel).indices
for j in bcIndices:
bcIndex = plex.getCone(j)-vStart
if len(bcIndex) == 2:
edge = ngm.Element1D([v+1 for v in bcIndex],index=bcLabel)
self.ngMesh.Add(edge)
elif plex.getDimension() == 3:
coordinates = plex.getCoordinates().getArray().reshape([-1,3])
self.ngMesh.AddPoints(coordinates)
cStart, cEnd = plex.getHeightStratum(0)
vStart, _ = plex.getHeightStratum(3)
cells = []
for i in range(cStart,cEnd):
fIndex = plex.getCone(i)
f1 = plex.getCone(fIndex[0])
f2 = plex.getCone(fIndex[1])
sIndex = [f1[0],f1[1],f1[2],f2[0],f2[1],f2[2]]
if len(fIndex) == 4:
S = list(itertools.chain.from_iterable([
list(plex.getCone(sIndex[k])-vStart) for k in list(range(len(sIndex)))]))
cell = list(dict.fromkeys(S))
A = np.array([coordinates[cell[1]]-coordinates[cell[0]],
coordinates[cell[2]]-coordinates[cell[1]],
coordinates[cell[3]]-coordinates[cell[2]]])
if np.linalg.det(A) > 0:
cells = cells + [cell]
else:
cells = cells + [[cell[0],cell[1],cell[3],cell[2]]]
#fd = self.ngmesh.Add(ngm.FaceDescriptor(bc=plex.getLabelSize(FACE_SETS_LABEL)+1))
self.ngMesh.Add(ngm.FaceDescriptor(bc=plex.getLabelSize(FACE_SETS_LABEL)+1))
self.ngMesh.AddElements(dim=3, index=plex.getLabelSize(FACE_SETS_LABEL)+1,
data=np.asarray(cells,dtype=np.int32), base=0)
for bcLabel in range(1,plex.getLabelSize(FACE_SETS_LABEL)+1):
faces = []
bcIndices = plex.getStratumIS("Face Sets",bcLabel).indices
for j in bcIndices:
sIndex = plex.getCone(j)
if len(sIndex)==3:
S = list(itertools.chain.from_iterable([
list(plex.getCone(sIndex[k])-vStart) for k in range(len(sIndex))]))
face = list(dict.fromkeys(S))
A = np.array([coordinates[face[1]]-coordinates[face[0]],
coordinates[face[2]]-coordinates[face[1]],
coordinates[face[0]]-coordinates[face[2]]])
eig = np.linalg.eig(A)[0].real
if eig[1]*eig[2] > 0:
faces = faces + [face]
else:
faces = faces + [[face[0],face[2],face[1]]]
#fd = self.ngmesh.Add(ngm.FaceDescriptor(bc=bcLabel))
self.ngMesh.Add(ngm.FaceDescriptor(bc=bcLabel))
self.ngMesh.AddElements(dim=2, index=bcLabel,
data=np.asarray(faces,dtype=np.int32), base=0)
else:
raise NotImplementedError("No implementation for dimension greater than 3.")
def createPETScDMPlex(self, mesh):
'''
This function generate an PETSc DMPlex from a Netgen/NGSolve mesh object
:arg plex: the Netgen/NGSolve mesh object to be converted into a PETSc
DMPlex.
'''
if isinstance(mesh,ngs.comp.Mesh):
self.ngMesh = mesh.ngmesh
else:
self.ngMesh = mesh
comm = self.comm
if self.ngMesh.dim == 3:
if comm.rank == 0:
V = self.ngMesh.Coordinates()
T = self.ngMesh.Elements3D().NumPy()["nodes"]
surfMesh, dim = False, 3
if len(T) == 0:
surfMesh, dim = True, 2
T = self.ngMesh.Elements2D().NumPy()["nodes"]
if Version(np.__version__) >= Version("2.2"):
T = np.trim_zeros(T, "b", axis=1).astype(np.int32) - 1
else:
T = (
np.array(
[list(np.trim_zeros(a, "b")) for a in list(T)],
dtype=np.int32,
)
- 1
)
plex = PETSc.DMPlex().createFromCellList(dim, T, V, comm=comm)
plex.setName(self.name)
vStart, _ = plex.getDepthStratum(0)
if surfMesh:
for e in self.ngMesh.Elements1D():
join = plex.getJoin([vStart+v.nr-1 for v in e.vertices])
plex.setLabelValue(FACE_SETS_LABEL, join[0], int(e.surfaces[1]))
else:
for e in self.ngMesh.Elements2D():
join = plex.getFullJoin([vStart+v.nr-1 for v in e.vertices])
plex.setLabelValue(FACE_SETS_LABEL, join[0], int(e.index))
for e in self.ngMesh.Elements1D():
join = plex.getJoin([vStart+v.nr-1 for v in e.vertices])
plex.setLabelValue(EDGE_SETS_LABEL, join[0], int(e.index))
self.petscPlex = plex
else:
plex = PETSc.DMPlex().createFromCellList(3,
np.zeros((0, 4), dtype=np.int32),
np.zeros((0, 3), dtype=np.double),
comm=comm)
self.petscPlex = plex
elif self.ngMesh.dim == 2:
if comm.rank == 0:
V = self.ngMesh.Coordinates()
T = self.ngMesh.Elements2D().NumPy()["nodes"]
T = np.array([list(np.trim_zeros(a, 'b')) for a in list(T)])-1
plex = PETSc.DMPlex().createFromCellList(2, T, V, comm=comm)
plex.setName(self.name)
vStart, _ = plex.getDepthStratum(0) # vertices
for e in self.ngMesh.Elements1D():
join = plex.getJoin([vStart+v.nr-1 for v in e.vertices])
plex.setLabelValue(FACE_SETS_LABEL, join[0], int(e.index))
if not (1 == self.ngMesh.Elements2D().NumPy()["index"]).all():
for e in self.ngMesh.Elements2D():
join = plex.getFullJoin([vStart+v.nr-1 for v in e.vertices])
plex.setLabelValue(CELL_SETS_LABEL, join[0], int(e.index))
self.petscPlex = plex
else:
plex = PETSc.DMPlex().createFromCellList(2,
np.zeros((0, 3), dtype=np.int32),
np.zeros((0, 2), dtype=np.double),
comm=comm)
self.petscPlex = plex
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