Changing mesh coordinates in fenicsx

[scaramouche]

Hi all,

I’ve just upgraded from legacy Fenics to Fenicsx. I used to be able to generate a linearly spaced mesh, apply a transformation to its coordinates, and get a new nonlinearly-spaced mesh that I knew would work well for my problem.

It used to work as follows:
mesh = IntervalMesh( num_cells, x_min, x_max )
new_coordinates = some_nonlinear_function( mesh.coordinates()[:,0] )
mesh.coordinates()[:,0] = new_coordinates[:]

I would like to get the same to work. Now I’m generating an interval mesh as follows:
mesh = create_interval( comm=MPI.COMM_WORLD, nx=num_cells, points=(x_min, x_max) )

But this mesh doesn’t have any coordinates() attributes. I would really like to use the transformation I have, and that I know works, as opposed to learning lots of new mesh code from scratch that may not do what I want.

Please let me know if it’s possible. Thanks!

[nate]

See dolfinx/cpp/dolfinx/mesh/Geometry.h at main · FEniCS/dolfinx · GitHub. From the python layer, something like mesh.geometry.x.

Edit: Updated permalink to relevant C++ code dolfinx/cpp/dolfinx/mesh/Geometry.h at d04eba8996a51a5e0c2d02691577da81302ab0fe · FEniCS/dolfinx · GitHub

[dokken]

You can also have a look at:

Changing the shape in the surface normal directions

The simplest mesh deformation can be described as follows: import dolfinx from mpi4py import MPI from typing import List import numpy as np def deform_mesh(V, bcs: List[dolfinx.fem.DirichletBCMetaClass]): mesh = V.mesh u = dolfinx.fem.Function(V) dolfinx.fem.petsc.set_bc(u.vector, bcs) deformation_array = u.x.array.reshape((-1, mesh.geometry.dim)) mesh.geometry.x[:, :mesh.geometry.dim] += deformation_array mesh = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, 10, 10) …

[scaramouche]

Thank you both, that helps!