open_dataset error "conflicting sizes" with gmsh extruded mesh

[manu0600]

Hello,

I have experienced an error when loading a Nek5000 output file with a mesh created from GMSH. A similar case with a mesh from genbox works flowlessly.

when running the following command :
open_dataset('channel3D_0.f00001')
I get the following error :
conflicting sizes for dimension 'y': length 8 on 'xmesh' and length 9 on 'y'

Could you help me resolve this issue ?

(Visualizing it with paraview works fine in both cases, as a check)

[ashwinvis]

open_dataset works only for cubes or cuboids. Is your mesh like that? This is because I have not found a nice way to extract the 1D coordinates from the 3D position arrays. See:

pymech/pymech/dataset.py

Lines 181 to 187 in 3a87b03

	def meshgrid_to_dim(self, mesh):
	"""Reverse of np.meshgrid. This method extracts one-dimensional
	coordinates from a cubical array format for every direction
	"""
	dim = np.unique(np.round(mesh, 8))
	return dim

and

pymech/pymech/dataset.py

Lines 206 to 212 in 3a87b03

	data_vars = {
	ax[2]: self.meshgrid_to_dim(elem.pos[0]), # x
	ax[1]: self.meshgrid_to_dim(elem.pos[1]), # y
	ax[0]: self.meshgrid_to_dim(elem.pos[2]), # z
	"xmesh": (ax, elem.pos[0]),
	"ymesh": (ax, elem.pos[1]),
	"zmesh": (ax, elem.pos[2]),

If open_dataset does not work for your case, you can use readnek and exa2vtk to visualize.

[ashwinvis]

I could help you more if you can generate a minimal example to reproduce.

[ashwinvis]

See also #13 if you are interested in non-cubical geometries.

[manu0600]

Here are two similar cases based on the turbChannel example, but with 2 different meshed from GMSH :
https://we.tl/t-iCenFDPVpw

The case turbChannel_GMSH appears to work well, but the other one turbChannel_GMSH_1 gives the error I mentionned. Both are one box, so I am not sure why one works and not the other.

Hope this helps

[ashwinvis]

We need to check if this was a duplicate of #56 which was fixed

[ashwinvis]

Some source code to reproduce this exists here, but the field files need to be generated

https://github.com/eX-Mech/pymech-test-data/blob/gmsh-bug