Add CylinderMesh

[tkarna]

Adds CylinderMesh which enables RectangleMesh that is periodic only in x or y direction.

[tkarna]

Boundary definition is missing. How to add that? Presumably 1 is y==0 and 2 is y==Ly.

[wence-]

I think you need to do it after creating the CylinderMesh. Something like:

...
    plex = mesh._from_cell_list(2, cells, vertices)
    plex.createLabel("boundary_ids")
    plex.markBoundaryFaces("boundary_faces")
    coords = plex.getCoordinates()
    coord_sec = plex.getCoordinateSection()
    if plex.getStratumSize("boundary_faces", 1) > 0:
        boundary_faces = plex.getStratumIS("boundary_faces", 1).getIndices()
        for face in boundary_faces:
            face_coords = plex.vecGetClosure(coord_sec, coords, face)
            if abs(face_coords[2]) < eps and abs(face_coords[5]) < eps:
                # bottom of cylinder (z is longitudinal direction)
                plex.setLabelValue("boundary_ids", face, 1)
            if abs(face_coords[2] - depth) < eps and abs(face_coords[5] - depth) < eps:
                # top of cylinder
                plex.setLabelValue("boundary_ids", face, 2)

[wence-]

I've added support for cylinders that have x, y, or z longitudinal directions, and change the interface to PeriodicRectangleMesh. My brain broke when doing the y periodic PartiallyPeriodicRectangleMesh, so I didn't support that.

[tkarna]

Looks good. I've added boundary ids for CylinderMesh and y periodicity for PartiallyPeriodicRectangleMesh. Needs testing I guess.

[wence-]

Thanks. We can adapt the periodic interval advection tests to 2d I think.

[wence-]

I've added a test, let's wait for the green light then I'll merge.

[tkarna]

Nice. This doesn't test the boundaries, should we add one for that too (e.g. diffusion with dirichlet bcs)?

[wence-]

Oh yes. that's a good idea.

[wence-]

OK, and now with more test.