Hi, I am new on Fenics and i face a problem when I want to import meshes. I use Fenics on Google Colaboratory. In the following lines, i present what i have done : step 1. I created the geometry (.geo) of my mesh using the script which follows… Jt = 0.2 ; Ht = 0.2 ; D = 1. ; B = 3*D ; L = 5*D ; …

This is dependent on your original mesh, that you have converted to xdmf format. You should inspect the facet_mesh file in for instance paraview, to see if you spot anything. I would also suggest to look at the generated mesh, mesh.xdmf with paraview to make sure it looks Like what you expect. See …

Thank you. I tried this like you said : # import and plot mesh !meshio-convert perfect_contact.msh perfect_contact.xdmf mesh = Mesh() with XDMFFile("perfect_contact.xdmf") as infile: infile.read(mesh) but I faced this issue: ------------------------------------------------------------------…

You need to split the mesh data into one file for the cells, and one for the facets, see: Extracting mesh regions for gmsh mesh - #16 by dokken You can load the facet data as described here: How to extract and use physical labels from GMSH surfaces on FEniCS (2D mesh) - #12 by dokken

I wrote : # import and plot mesh # part 1 mesh_from_file = !meshio-read("perfect_contact.msh") def create_mesh(mesh, cell_type, prune_z=False): cells = np.vstack([cell.data for cell in mesh.cells if cell.type==cell_type]) cell_data = np.hstack([mesh.cell_data_dict["gmsh:physical"][key] …

Why doesn’t import meshio and meshio.read work? You claim that your other command works, But it clearly doesn’t as it does not read in the mesh. Try for instance: print(mesh_from_file) What does this yield you? Does it give you a meshio.Mesh object?

with : print(mesh_from_file) I got : [‘/bin/bash: -c: line 0: syntax error near unexpected token "perfect_contact.msh"\'', '/bin/bash: -c: line 0: meshio-read(“perfect_contact.msh”)'’] I think my other command didn’t work as you said. I tried back what you sent me and I have this issue: ---…

I saw two solutions: This one FROM quay.io/fenicsproject/stable:current USER root RUN apt-get -qq update && \ apt-get -y upgrade && \ apt-get clean && \ apt-get -y install python3-h5py && \ pip install --upgrade pip && \ pip install meshio[all] && \ rm -rf /var/lib/apt/list…

So first of all you need to get your installation right. I have made a minimal recipe on how to use google co-lab with fenics and meshio (using a smaller mesh called mesh.msh. See: https://colab.research.google.com/drive/1OBhNSF_EcmVaLiLnkcWJ4nNAi0kx6cXa?usp=sharing

Thank you. I think I didn’t get this point : mesh = Mesh() with XDMFFile("mesh.xdmf") as infile: infile.read(mesh) mvc = MeshValueCollection("size_t", mesh, 1) with XDMFFile("facet_mesh.xdmf") as infile: infile.read(mvc, "name_to_read") mf = cpp.mesh.MeshFunctionSizet(mesh, mvc) print(mesh…

Thank you, I would be able to fix my program with all your hints !

How to define a mesh in colab as the one imported?

mesh

dokken February 12, 2021, 11:34pm 8

The solution to this error message can be found at: Gmsh 4.4.1 in FEniCS? Meshio - #9 by SantiagoOrtiz

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How to define a mesh in colab as the one imported?

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