Move from fenics to fenicsX

[je-cook]

Description of issue / requirement to address

At some point in the future we need to move to fenicsX as fenics is unmaintained and had its last update in 2019

Proposed solution

Update to fenicsX https://fenicsproject.org

Alternative solutions

N/A

Additional context

Add any other context or screenshots about the feature request here.

[je-cook]

Here is the install script for fenicsx linked from #701

https://github.com/Fusion-Power-Plant-Framework/bluemira/blob/4c42b1c5b874c29f092c77e4a8dd9169290dc66b/scripts/fenicsx/install-fenicsx-deps.sh

https://github.com/Fusion-Power-Plant-Framework/bluemira/blob/4c42b1c5b874c29f092c77e4a8dd9169290dc66b/scripts/fenicsx/install-fenicsx.sh

fyi @ivanmaione this will overwrite fencis-ufl everything else could be installed side by side

[je-cook]

The labelling of the mesh in dolfinx seems to pull over the same information as our gmsh importer and test_override_lcar_surf but test_mesh_poly fails and gives the same result instead of half the node number but if I double lcars for the second half I get the expected result... @ivanmaione @oliverfunk :

from bluemira.geometry import tools
from bluemira.geometry.face import BluemiraFace
import bluemira.mesh.meshing as msh
from bluemira.base.look_and_feel import bluemira_print
import inspect
import gmsh
from mpi4py import MPI

import dolfinx.io.gmshio as gmshio

def test_override_lcar_surf_and_mesh_poly(lcar, nodes_num, half):
    poly = tools.make_polygon(
        [[0, 0, 0], [1, 0, 0], [1, 0, 1], [0, 0, 1]], closed=True, label="poly"
    )

    poly.mesh_options = {"lcar": lcar, "physical_group": "poly"}

    surf = BluemiraFace(poly, label="surf")
    if half:
        surf.mesh_options = {"lcar": lcar / 2, "physical_group": "coil"}
    else:
        surf.mesh_options = {"physical_group": "coil"}

    m = msh.Mesh()
    m(surf)

    mesh, *meshtags = gmshio.model_to_mesh(
        gmsh.model, comm=MPI.COMM_WORLD, rank=0, gdim=2
    )

    msh._FreeCADGmsh._finalize_mesh(m.logfile)
    return mesh, meshtags

def mesh_call(self, obj, dim=2):
    """
    Generate the mesh and save it to file.
    """
    bluemira_print("Starting mesh process...")

    if "Component" in [c.__name__ for c in inspect.getmro(type(obj))]:
        from bluemira.base.tools import create_compound_from_component

        obj = create_compound_from_component(obj)

    if isinstance(obj, msh.Meshable):
        # gmsh is initialized
        msh._FreeCADGmsh._initialize_mesh(self.terminal, self.modelname)
        # Mesh the object. A dictionary with the geometrical and internal
        # information that are used by gmsh is returned. In particular,
        # a gmsh key is added to any meshed entity.
        buffer = self._Mesh__mesh_obj(obj, dim=dim)
        # Check for possible intersection (only allowed at the boundary to adjust
        # the gmsh_dictionary
        msh.Mesh._Mesh__iterate_gmsh_dict(buffer, msh.Mesh._check_intersections)

        # Create the physical groups
        self._apply_physical_group(buffer)

        # apply the mesh size
        self._apply_mesh_size(buffer)

        # generate the mesh
        msh._FreeCADGmsh._generate_mesh()
        return
        # save the mesh file
        # for file in self.meshfile:
        #     _FreeCADGmsh._save_mesh(file)

        # # close gmsh
        # _FreeCADGmsh._finalize_mesh(self.logfile)
    else:
        raise ValueError("Only Meshable objects can be meshed")

    bluemira_print("Mesh process completed.")

    return buffer

# hack out the gmsh closing for now
msh.Mesh.__call__ = mesh_call

lcars = [0.1, 0.25, 0.5, 0.1, 0.25, 0.5]
#  lcars = [0.1, 0.25, 0.5, 0.1 * 2, 0.25 * 2, 0.5 * 2]  # This works...
half = [True, True, True, False, False, False]
nodes_num = [80, 32, 16, 40, 16, 8]

meshes, meshtags = [], []
for lcar, nn in zip(lcars, nodes_num):
    mesh, _meshtags = test_override_lcar_surf_and_mesh_poly(lcar, nn, half=half)
    meshes += [mesh]
    meshtags += [_meshtags]
    assert _meshtags[-1].indices.size == nn
    assert all(_meshtags[0].values == 1)
    assert all(_meshtags[1].values == 2)

[je-cook]

Accomplished in #2872 will go into develop with the python3.10 upgrade