Meeting issue when load mesh created by gmsh

dolfinx
1

I want to create and load a mesh using gmsh to dolfinx mesh. However, I meet an unexpected crush. Here is my code:

import gmsh
# Define the geometry

LX = 1.1
LY = 1.1
nx = 11
ny = 11
# Initialize GMSH
gmsh.initialize()

# Create a new model
gmsh.model.add("mixed_mesh")
gmsh.option.setNumber("General.Terminal", 1)

#a0 = gmsh.model.geo.addPoint(0, LY, 0)
a1 = gmsh.model.geo.addPoint(0, LY-LY/ny, 0)
a2 = gmsh.model.geo.addPoint(LX/nx, LY-LY/ny, 0)
#a3 = gmsh.model.geo.addPoint(LX/nx, LY, 0)

#b0 = gmsh.model.geo.addPoint(0, 0, 0)
b1 = gmsh.model.geo.addPoint(LX/nx,0, 0)
b2 = gmsh.model.geo.addPoint(LX/nx, LY/ny, 0)
b3 = gmsh.model.geo.addPoint(0, LY/ny, 0)


# F
f = gmsh.model.geo.addPoint(LX/nx/2, LY/2, 0)
f0 = gmsh.model.geo.addPoint(0, LY/2+LY/ny/2, 0)
f1 = gmsh.model.geo.addPoint(0, LY/2-LY/ny/2, 0)
f2 = gmsh.model.geo.addPoint(LX/nx, LY/2-LY/ny/2, 0)
f3 = gmsh.model.geo.addPoint(LX/nx, LY/2+LY/ny/2, 0)
# Create lines
S1_l0 = gmsh.model.geo.addLine(a1, f0)
S1_l1 = gmsh.model.geo.addLine(f0, f3) # S10
S1_l2 = gmsh.model.geo.addLine(f3, a2)
S1_l3 = gmsh.model.geo.addLine(a2, a1)


S2_l1 = gmsh.model.geo.addLine(f0, f)
S2_l2 = gmsh.model.geo.addLine(f, f3)
S2_l3 = gmsh.model.geo.addLine(f3, f0)

S3_l1 = gmsh.model.geo.addLine(f, f1)
S3_l2 = gmsh.model.geo.addLine(f1, f2)
S3_l3 = gmsh.model.geo.addLine(f2, f)

S4_l1 = gmsh.model.geo.addLine(f1, b3)
S4_l2 = gmsh.model.geo.addLine(b3, b2)
S4_l3 = gmsh.model.geo.addLine(b2, f2)
S4_l4 = gmsh.model.geo.addLine(f2, f1)



# Create a line loop
S1_loop = gmsh.model.geo.addCurveLoop([S1_l0, S1_l1, S1_l2, S1_l3])
S2_loop = gmsh.model.geo.addCurveLoop([S2_l1, S2_l2, S2_l3])
S3_loop = gmsh.model.geo.addCurveLoop([S3_l1, S3_l2, S3_l3])
S4_loop = gmsh.model.geo.addCurveLoop([S4_l1, S4_l2, S4_l3, S4_l4])



# Create a plane surface
S1 = gmsh.model.geo.addPlaneSurface([S1_loop])
S2 = gmsh.model.geo.addPlaneSurface([S2_loop])
S3 = gmsh.model.geo.addPlaneSurface([S3_loop])
S4 = gmsh.model.geo.addPlaneSurface([S4_loop])

gmsh.model.addPhysicalGroup(2, [S1], 1)
gmsh.model.addPhysicalGroup(2, [S2], 2)
gmsh.model.addPhysicalGroup(2, [S3], 3)
gmsh.model.addPhysicalGroup(2, [S4], 4)



# Divide 4 parts
for i in [S1_l0,S1_l2,S4_l1,S4_l3]:
     gmsh.model.geo.mesh.setTransfiniteCurve(i, 5)   


gmsh.model.geo.mesh.setTransfiniteSurface(S1, "Left",[])
gmsh.model.geo.mesh.setTransfiniteSurface(S4, "Left",[])
gmsh.model.geo.mesh.setRecombine(2,S1) # If comment this, everything went well
gmsh.model.geo.mesh.setRecombine(2,S4) # If comment this, everything went well

# Synchronize the model with GMSH
# Generate the 2D mesh

gmsh.model.geo.synchronize()
gmsh.model.mesh.generate(2)
#gmsh.option.setNumber("Mesh.SaveAll", 1)
gmsh.fltk.run()

from dolfinx.io import gmshio
from mpi4py import MPI
mesh, cell_tags, facet_tags = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0)

And the error is:

Invalid rank, error stack:
internal_Issend(61644): MPI_Issend(buf=0x17ff6d001, count=1, MPI_BYTE, 1, 1, comm=0x84000005, request=0x17ff106a4) failed
internal_Issend(61605): Invalid rank has value 1 but must be nonnegative and less than 1
Abort(866780422) on node 0 (rank 0 in comm 416): application called MPI_Abort(comm=0x84000005, 866780422) - process 0

My fenicsx version is 0.9 and the system is MocOS.

I found that everything works fine if I don’t use quadrilateral meshes. I am a beginner in FEniCSx and don’t know how to handle this issue. I hope someone can provide a solution.

2

This command is in general not adviced. This can result in duplicate points, facets and cells being stored in the mesh file. Could you turn it off?

3

Thanks for your reply. This was off already. It still can’t work.

4

How are you expecting the triangular ends to be meshed with quadrilateral elements with your current code?

image
image309×535 1.83 KB

If you use:

gmsh.option.setNumber("Mesh.Algorithm", 8)
gmsh.option.setNumber("Mesh.RecombinationAlgorithm", 2)
gmsh.option.setNumber("Mesh.RecombineAll", 1)
gmsh.option.setNumber("Mesh.SubdivisionAlgorithm", 1)

from my tutorial
https://jsdokken.com/dolfinx-tutorial/chapter2/ns_code2.html#generating-the-mesh
you get

image
image326×607 2.52 KB

However, please note that cells connected by vertex only is not well-adviced, as it:

  1. Can cause singular behavior for some PDEs (such as elasticity equations).
  2. Is not supported in DOLFINx in parallel.

Could you provide some context about why you want this mesh?

5

It works for me. Thank you very much. Actually, I want to define a hinge between two components but haven’t found a good way to express it. Therefore, I used a single point between two elements to connect them. Since there is still elastic deformation, is there any other method to define a hinge? Regardless, thank you for your help and advice.

6

I would probably use an MPC:

7

Thanks for your advice! I will try it.