Issue: A 3D mesh is being imported as 2D mesh

mesh
1

Hi Guys,

I am trying to import a 3D surface mesh of a ship using

mesh = Mesh('barge.xml')

but it is imported as a 2D file.

I also tried in the .xdmf format

mesh = Mesh()
with XDMFFile("barge_fenics.xdmf") as infile:
    infile.read(mesh)

But it also results in the same issue

I created this .xml and .xdmf files from a .stl file using freecad.

Can anyone tell me how to resolve this issue?

Thank you

Here is a part of the barge.xdmf file

<?xml version="1.0"?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf version="3.0"><Domain><Grid GridType="Uniform" Name="base_mesh"><Topology NodesPerElement="6" NumberOfElements="6107" TopologyType="TRIANGLE_6"><DataItem Dimensions="6107 6" Format="XML" NumberType="UInt">0 1 2 3172 3173 3174
0 2 3 3174 3175 3176
4 5 6 3177 3178 3179
4 6 7 3179 3180 3181
: : :  :    :     :
-191.391265 -35.300344</DataItem></Geometry></Grid></Domain></Xdmf>
2

You Need to prune the z-coordinate. See for instance Converting simple 2D mesh from gmsh to dolfin

3

I did run the code

meshio-convert barge.xml barge.xdmf -p -z

It outputted two files .xdmf and .h5

When I ran the above code

it still returning a 2D mesh. But what I need is a 3D surface mesh.

4

Then just do not run prune?

5

Even without pruning, the mesh is still 2D flattened mesh.

6

In xdmf or when using it in dolfin?

7

In the dolfin, it is reading to as 2D mesh but in .xdmf is 3D mesh.

Screenshot from 2020-03-16 15-17-56
Screenshot from 2020-03-16 15-17-56711×624 30.8 KB

it is reading it as a 2D mesh with or without pruning.

But the original mesh is a 3D surface mesh and I want it to read as a 3D mesh.

image
image746×624 25.4 KB

8

Could you print mesh.topology().dim() and mesh.geometry().dim()?
I do not have any issue loading a 3D mesh in 2D (also using a second order geometry).

<Xdmf Version="3.0"><Domain><Grid Name="Grid"><Information Name="Information" Value="0">
<![CDATA[<main />]]>
</Information><Geometry GeometryType="XYZ"><DataItem DataType="Float" Dimensions="23 3" Format="XML" Precision="8">
-7.000000000000000e-01 2.000000000000000e-01 0.000000000000000e+00
3.000000000000000e-01 2.000000000000000e-01 0.000000000000000e+00
3.000000000000000e-01 7.000000000000000e-01 0.000000000000000e+00
-7.000000000000000e-01 7.000000000000000e-01 0.000000000000000e+00
-2.000000000000000e-01 2.000000000000000e-01 0.000000000000000e+00
-4.500000000000000e-01 2.000000000000000e-01 0.000000000000000e+00
5.000000000000004e-02 2.000000000000000e-01 0.000000000000000e+00
3.000000000000000e-01 4.500000000000000e-01 0.000000000000000e+00
-2.000000000000000e-01 7.000000000000000e-01 0.000000000000000e+00
5.000000000000007e-02 7.000000000000000e-01 0.000000000000000e+00
-4.500000000000000e-01 7.000000000000000e-01 0.000000000000000e+00
-7.000000000000000e-01 4.500000000000000e-01 0.000000000000000e+00
-4.500000000000000e-01 4.500000000000000e-01 0.000000000000000e+00
5.000000000000004e-02 4.500000000000000e-01 0.000000000000000e+00
-3.250000000000000e-01 3.250000000000000e-01 0.000000000000000e+00
-5.750000000000000e-01 3.250000000000000e-01 0.000000000000000e+00
1.750000000000000e-01 5.750000000000000e-01 0.000000000000000e+00
1.750000000000000e-01 3.250000000000000e-01 0.000000000000000e+00
-7.499999999999996e-02 3.250000000000000e-01 0.000000000000000e+00
-7.499999999999996e-02 5.750000000000000e-01 0.000000000000000e+00
-5.750000000000000e-01 5.750000000000000e-01 0.000000000000000e+00
-3.250000000000000e-01 5.750000000000000e-01 0.000000000000000e+00
-2.000000000000000e-01 4.500000000000000e-01 0.000000000000000e+00
</DataItem></Geometry><Topology NodesPerElement="6" NumberOfElements="8" TopologyType="Triangle_6"><DataItem DataType="Int" Dimensions="8 6" Format="XML" Precision="8">
4 12 0 14 15 5
2 13 1 16 17 7
1 13 4 17 18 6
8 13 2 19 16 9
3 12 8 20 21 10
8 12 4 21 14 22
0 12 3 15 20 11
4 13 8 18 19 22
</DataItem></Topology></Grid></Domain></Xdmf>

Running:

from dolfin import *

mesh = Mesh()
with XDMFFile("mesh.xdmf") as infile:
    infile.read(mesh)
print(mesh.geometry().dim(), mesh.topology().dim())

yields the print 3, 2

9 
mesh = Mesh()
with XDMFFile("barge.xdmf") as infile:
    infile.read(mesh)

mesh2 = Mesh('barge.xml')
print(mesh.geometry().dim(), mesh.topology().dim())
print(mesh2.geometry().dim(), mesh2.topology().dim())

Output

2 2
2 2
10

Then you are not writing your XML/XDMF-files correctly. For instance, what is in the corresponding: </Information><Geometry GeometryType="XYZ"><DataItem DataType="Float" Dimensions="23 3" Format="XML" Precision="8">

Also, what happens if you read in the file I sent you?

11

For your file I am getting 3, 2 output.

12

And what is the GeometryType=“XYZ” (as shown above in my case) in your case?

13

In my file, the information is
<Xdmf version="3.0"><Domain><Grid GridType="Uniform" Name="base_mesh"><Topology NodesPerElement="6" NumberOfElements="6107" TopologyType="TRIANGLE_6"><DataItem Dimensions="6107 6" Format="XML" NumberType="UInt">0 1 2 3172 3173 3174

14

@ckesanapalli

It has to have a geometry type as well, like:
</Information><Geometry GeometryType="XYZ"><DataItem DataType="Float" Dimensions="23 3" Format="XML" Precision="8">
This contains all the nodes of the mesh

15

when I added geometry <Geometry GeometryType="XYZ"> to the xdmf file, I am getting error saying

*** -------------------------------------------------------------------------
*** DOLFIN encountered an error. If you are not able to resolve this issue
*** using the information listed below, you can ask for help at
***
***     fenics-support@googlegroups.com
***
*** Remember to include the error message listed below and, if possible,
*** include a *minimal* running example to reproduce the error.
***
*** -------------------------------------------------------------------------
*** Error:   Unable to determine geometric dimension.
*** Reason:  GeometryType "" in XDMF file is unknown or unsupported.
*** Where:   This error was encountered inside XDMFFile.cpp.
*** Process: 0
*** 
*** DOLFIN version: 2019.1.0
*** Git changeset:  77c758717da1cb8017bf95109363bb1a91a4f8e5
*** -------------------------------------------------------------------------

I think I resolved the issue.

In .xml format, the dimension is saved as 2. I changed it to 3 and now it is importing as 3D mesh.

Maybe I should be careful and inspect the mesh files after converting them from one to another.

Thanks a lot for the help.

16

That is likely the issue. Above I gave you a reference mesh that contains the two parts of information that is required to read in a second order 2D geometry embedded in a 3D space. When converting from xmlto xdmf your xdmffile has to include a geometry (the nodes of the mesh), and a topology (the connectivity of the nodes where each row is a cell).