This number
is np.uintc(-1)
which I would interpret as the algorithm returning its input:
https://bitbucket.org/fenics-project/dolfin/src/74a6ac2095059ea6582fe4ea11686c1c723e14f5/dolfin/geometry/GenericBoundingBoxTree.cpp?at=master#lines-282
which means that the point found in Bitbucket
is as close as any point in the mesh (i.e. a vertex/mipoint is the closest entity).
This seems like a bug to me, and you could consider adding an issue on fenics-project / DOLFIN / issues — Bitbucket
However, as DOLFINx is now the recommened version to use, ref: The new DOLFINx solver is now recommended over DOLFIN
it is unlikely that it will be fixed in the old version.
For DOLFINx, the syntax would be:
from IPython import embed
import dolfinx
import numpy as np
import ufl
from mpi4py import MPI
mesh_path = "./"
with dolfinx.io.XDMFFile(MPI.COMM_WORLD, mesh_path + "circle_mesh.xdmf", "r") as infile:
mesh_sphere = infile.read_mesh(name="Grid")
L1_sph = ufl.FiniteElement("Lagrange", mesh_sphere.ufl_cell(), 1)
V_sph = dolfinx.fem.FunctionSpace(mesh_sphere, L1_sph)
dim = mesh_sphere.topology.dim
tree_sph = dolfinx.geometry.BoundingBoxTree(mesh_sphere, dim)
num_entities_local = mesh_sphere.topology.index_map(
dim).size_local + mesh_sphere.topology.index_map(dim).num_ghosts
entities = np.arange(num_entities_local, dtype=np.int32)
midpoint_tree = dolfinx.geometry.create_midpoint_tree(
mesh_sphere, dim, entities)
points = np.array([[.5, .86602541, 0]])
closest_entities = dolfinx.geometry.compute_closest_entity(
tree_sph, midpoint_tree, mesh_sphere, points)
squared_distance = dolfinx.geometry.squared_distance(
mesh_sphere, dim, closest_entities, points)
print(closest_entities, squared_distance)
coords = mesh_sphere.geometry.x
x_dofmap = mesh_sphere.geometry.dofmap
coordinate_dofs = coords[x_dofmap.links(closest_entities[0])]
distance_vec = dolfinx.geometry.compute_distance_gjk(
coordinate_dofs, points[0])
print(f"Point {points[0]} Closest point on mesh {points[0] + distance_vec}")
which yields you the following image:
