Please ignore (remove) this bit of code:

  if exterior:
        if Rcut == None:
            raise Exception("Rcut needs to be specified!")
        out = split_mesh_spheres(Rcut, data, mesh)

as it is not relevant here.

Hugo

Le ven. 20 oct. 2023 à 15:04, Hugo Lévy <hugo.levy@gmail.com> a écrit :

Hi Himalaya Singh,

I also happen to work with Sfepy for the FEM part and Gmsh for the meshing part. A while ago I faced the same problem as the one you describe. My solution is the following:

1. Define Physical Groups for your different regions in Gmsh
2. Save the mesh as a .vtk file
3. "Convert" this file into a new .vtk that is more friendly for Sfepy

For the latter step, I use the following bit of Python code:

def converter4sfepy(fullfilename, ignoreTags=[]):
    """
    @author: Hugo Lévy
    Converts the .vtk mesh written by Gmsh into a new .vtk which
facilitates
    topological entity selection with Sfepy. Vertices are given a unique
group
    id following the convention:
        [0 - 99]    --> vertex tag (i.e. entity of dimension 0)
        [100 - 199] --> edge tag (i.e. entity of dimension 1)
        [200 - 299] --> facet tag (i.e. entity of dimension D-1)
        [300 - xxx] --> cell tag (i.e. entity of dimension D)
    If one node belong to several topological entities, it will be tagged
with
    the lowest dimension group id. For instance, a vertex belonging to a
facet
    of tag 200 and a subvolume of tag 300 will be tagged 200. This is
    problematic for subvolume selection. This difficulty is overcome by
taking
    advantage of the 'mat_ids' field that is readable by Sfepy.

    Parameters
    ----------
    fullfilename : str
        Absolute pathname of the .vtk mesh.
    ignoreTags : list, optional
        List of tags to be ignored in the new .vtk mesh. The default is [].

    """

    from sfepy.discrete.fem import Mesh # Sfepy I/O utilities
    mesh = Mesh.from_file(fullfilename)
    cell_dim = mesh.dim

    # All the necessary & sufficient info for defining a mesh
    data = list(mesh._get_io_data(cell_dim_only=cell_dim))

    # Managing vertex groups
    ngroups = np.array([None for _ in range(mesh.n_nod)])
    reader = meshio.read(fullfilename)
    for key in reader.cells_dict.keys():
        conn = reader.cells_dict[key]
        formerTags = list(reader.cell_data_dict.values())[0][key]
        for k, tag in enumerate(formerTags):
            if tag not in ignoreTags:
                for idx in conn[k]:
                    if ngroups[idx] is None:
                        ngroups[idx] = int(tag)
    ngroups[np.where(ngroups==None)] = 400 # default marker for untagged
    data[1] = ngroups.astype(dtype=np.int32)

    # Managing cell groups
    conns = list(reader.cells_dict.values())[-1] # entities of highest dim
    mat_ids = np.max(ngroups[conns], axis=1)
    data[3] = [mat_ids.astype(dtype=np.int32)]

    # Overwrite the former mesh
    if exterior:
        if Rcut == None:
            raise Exception("Rcut needs to be specified!")
        out = split_mesh_spheres(Rcut, data, mesh)
    else:
        mesh = Mesh.from_data(mesh.name, *data)
        mesh.write(fullfilename, None, binary=False)
        out = fullfilename

    return out

Hope that helps!

Cheers, Hugo

Le ven. 20 oct. 2023 à 13:50, Robert Cimrman <cimrman3@ntc.zcu.cz> a écrit :

...

Forwarding to ML...

-------- Forwarded Message -------- Subject: Wanted help in defining Gmsh files regions created in Gmsh itself(No defining as x> or x< like this) Date: Fri, 20 Oct 2023 17:00:59 +0530 From: Himalaya singh <aayusingh05@gmail.com> To: sfepy-owner@python.org

I am new to this tool, and I have been exploring it for some time. I got some issues related to the microstructure Regions defining problem directly from Gmsh(.msh file) using Sfepy.

Actually, I am working on lithium ion batteries(Electrode Microstructure) and I am confused how I can make sfepy to read two different regions directly From Gmsh file (where there are grain and grain boundaries having different properties ).

I want some help so my microstructure and created regions will be read by sfepy.

Also, if i will create a simple square domain in Gmsh having three different regions as i already defined as physical group region_1, region_2,region_3 in Gmsh. How can I implement codes for these domains? I just want it to read directly from: mesh = Mesh.from_file('Region.msh').

Any lead or help will be highly appreciated Thank you for your help!

Himalaya Singh Machine Design Department of Mechanical Engineering, IIT Madras

---

SfePy mailing list -- sfepy@python.org To unsubscribe send an email to sfepy-leave@python.org https://mail.python.org/mailman3/lists/sfepy.python.org/ Member address: hugo.levy@gmail.com