# From .vtk to .xdmf. Reading mesh infos and setting up boundaries

**URL:** <https://fenicsproject.discourse.group/t/from-vtk-to-xdmf-reading-mesh-infos-and-setting-up-boundaries/6068>\
**Category:** mesh\
**Created:** [June 22, 2021, 4:53pm UTC](https://fenicsproject.discourse.group/t/from-vtk-to-xdmf-reading-mesh-infos-and-setting-up-boundaries/6068 "2021-06-22T16:53:53Z")\
**Posts on this page:** 1\
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**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\
**Post date:** [June 22, 2021, 5:20pm UTC](https://fenicsproject.discourse.group/t/from-vtk-to-xdmf-reading-mesh-infos-and-setting-up-boundaries/6068/2 "2021-06-22T17:20:04Z")

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I would suggest using `meshio`, as shown in

> [@Accessing and marking imported boundaries](https://fenicsproject.discourse.group/t/accessing-and-marking-imported-boundaries/5753/8):
>
> As you are using a stp file I do not have access to, I cannot really do much more than showing you a minimal working example. Here is a minimal geo file (taken from the gmsh tutorial, called tutorial\_t1.geo lc = 1e-1; Point(1) = {0, 0, 0, lc}; Point(2) = {.1, 0, 0, lc}; Point(3) = {.1, .3, 0, lc}; Point(4) = {0, .3, 0, lc}; Line(1) = {1, 2}; Line(2) = {3, 2}; Line(3) = {3, 4}; Line(4) = {4, 1}; Curve Loop(1) = {4, 1, -2, 3}; Plane Surface(1) = {1}; Physical Curve(666) = {1, 2, 4}; Physical S…

To be slightly more specific, read in your `vtk` mesh (and data ) with `meshio.read("filename.vtk")`, then create a mesh with each of the data

```auto
    mesh = meshio.read("filename.vtk")
    cells = mesh.get_cells_type(cell_type)
    # Code for extracting fibers from the read in mesh goes here 
    strain_data = ....
    fibers_data = ....
    sheets_data = ...
    out_mesh = meshio.Mesh(points=mesh.points, cells={
                           cell_type: cells}, cell_data={"strain": [strain_data], "fibers":[fibers_data], ....]})
    if prune_z:
        out_mesh.prune_z_0()
   out_mesh.write("mesh.xdmf")  

```

which can be read into dolfin as

```auto
mesh = Mesh()

with XDMFFile("mesh.xdmf") as infile:
    infile.read(mesh)
    mvc = MeshValueCollection("size_t", mesh, mesh.topology().dim())
    infile.read(mvc, "strain")
strain_func = cpp.mesh.MeshFunctionSizet(mesh, mvc) # boundary_parts

```

The code above is pseudo-code, as I do not use the `vtk` format, and do not have any minimal examples at hand to test the code. Therefore, this might require modification. Note that there are many posts about how to read in meshes and external data on this forum.

For your last question, how is your rho field defined? is it defined as a function of x,y,z? if so, use subdomain on the following form:

```auto
 class rho0_boundary(SubDomain):
        def inside(self, x, on_boundary):
            return on_boundary and near(rho(x), 0)

```

and use the subdomain as shown in: [https://fenicsproject.org/olddocs/dolfin/latest/python/demos/subdomains-poisson/documentation.html?highlight=measure](https://fenicsproject.org/olddocs/dolfin/latest/python/demos/subdomains-poisson/documentation.html?highlight=measure)

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