How to open a result?

I/O
1

I am new to fenics and want to do a quite simple task, but having some troubles.

I solved a lot of pressure/velocity fields in a permanent regime and saved them in XMDF/H5 format.
I have only saved the velocity field (2 dimensional).

Now, I want to open it in python to generate a visualization (yes, I want to do it with python since I have an issue with the files to open them all in paraview).

However, I don’t know how to open a file. I’ve tried some internet found solutions, but they didn’t work.
I would appreciate it if someone could share a bit of code, so I could open those files. It would also be nice if you could tell me how to get the coordinates (x,y) and velocity (U) from this file.

Many thanks

2

Are you using legacy fenics or fenicsx?

If you are using legacy fenics, the 2 ways to do this are

  1. Saving the solution in an XDMFFile with write_checkpoint and reading it back in with read_checkpoint. Some useful info can be found in this post.
  2. Saving the solution in a HDF5File with the 'w' (write) argument, which can then be read back into python using the 'r' (read) argument. Some relevant info is in this post.
3

For dolfinx, the best way I’ve found is to use meshio to read the DOF arrays. e.g.

import meshio

mesh_meshio = meshio.read(xdmf_filename)
u = mesh_meshio.point_data["name"]

or

u = mesh_meshio.cell_data["name"]

for DG0 functions.

If you need to construct a dolfinx function from this, you will need to reorder the cell indices to match the dolfinx ordering.

def permute_array(array, perm_indices):
    output = array.copy()
    for i in range(len(array)):
        output[i] = array[perm_indices[i]]
    return output

CG1 = dolfinx.fem.VectorFunctionSpace(mesh, ("CG", 1))
u_dolfinx = dolfinx.fem.Function(CG1)
u_dolfinx.x.array[:] = permute_array(u, mesh.geometry.input_global_indices).flatten()

or for DG0 functions

DG0 = dolfinx.fem.VectorFunctionSpace(mesh, ("DG", 0))
u_dolfinx = dolfinx.fem.Function(DG0)
u_dolfinx.x.array[:] = permute_array(u, mesh.topology.original_cell_index).flatten()

Please note that this will only work on a single process.

1 Like
4

Thank you. This is the simplest solution Ive found.