2D Mesh w/ quads only

[ryancoe]

I'm interested in using pygmsh to generate a surface (2D) mesh with only quads. I figured out how to do this in gmsh using the Mesh.SubdivisionAlgorithm and Mesh.RecombineAll via the gmsh command line interace:

gmsh -2 test.geo -format vtk -bin -o test.vtk -clscale 0.25 -clcurv 7.2 \
-setnumber Mesh.SubdivisionAlgorithm 1 -setnumber Mesh.RecombineAll 1

However, when I pass these options to pygmsh.generate_mesh via the extra_gmsh_arguments they don't seem to work. Even more odd, I can see from the log what pygmsh is calling -- when I copy this to my command line I get the desired result.

MWE below:

import pygmsh
import numpy as np
import os

geom = pygmsh.opencascade.Geometry()

fbname = 'test'
ofst = 0.1
geom.add_cylinder(x0=[0.0, 0.0, 0+ofst],
                         axis=[0.0, 0.0, -2],
                         radius=1,
                         angle=2 * np.pi,
                         char_length=1)

mshRefFactor = 0.25
mshArgs = ['-clscale', str(mshRefFactor),
           '-clcurv', str(360/50),
           '-setnumber', 'Mesh.SubdivisionAlgorithm 1',
           '-setnumber', 'Mesh.RecombineAll 1']
mesh = pygmsh.generate_mesh(geom,
                            dim=2,
                            extra_gmsh_arguments=mshArgs,
                            remove_lower_dim_cells=True,
                            gmsh_path='/usr/local/bin/gmsh',
                            geo_filename=fbname + '.geo',
                            msh_filename=fbname + '.vtk',
                            mesh_file_type='vtk')

os.system('gmsh -2 test.geo -format vtk -bin -o testCLI.vtk -clscale 0.25 \
          -clcurv 7.2 -setnumber Mesh.SubdivisionAlgorithm 1 \
              -setnumber Mesh.RecombineAll 1')

$ python mwePygmsh.py 
Info    : Running '/usr/local/bin/gmsh -2 test.geo -format vtk -bin -o test.vtk -clscale 0.25 -clcurv 7.2 -setnumber Mesh.SubdivisionAlgorithm 1 -setnumber Mesh.RecombineAll 1' [Gmsh 4.5.6, 1 node, max. 1 thread]
Info    : Started on Tue Apr 28 13:47:42 2020
Info    : Reading 'test.geo'...
Info    : Done reading 'test.geo'
Info    : Meshing 1D...
Info    : [  0 %] Meshing curve 1 (Circle)
Info    : [ 40 %] Meshing curve 2 (Line)
Info    : [ 70 %] Meshing curve 3 (Circle)
Info    : Done meshing 1D (0.000661 s)
Info    : Meshing 2D...
Info    : [  0 %] Meshing surface 1 (Cylinder, Frontal-Delaunay)
Info    : [ 40 %] Meshing surface 2 (Plane, Frontal-Delaunay)
Info    : [ 70 %] Meshing surface 3 (Plane, Frontal-Delaunay)
Info    : Done meshing 2D (0.022969 s)
Info    : 465 nodes 993 elements
Info    : Writing 'test.vtk'...
Info    : Done writing 'test.vtk'
Info    : Stopped on Tue Apr 28 13:47:42 2020

msh file: test.vtk

geo file: test.geo
Info    : Running 'gmsh -2 test.geo -format vtk -bin -o testCLI.vtk -clscale 0.25 -clcurv 7.2 -setnumber Mesh.SubdivisionAlgorithm 1 -setnumber Mesh.RecombineAll 1' [Gmsh 4.5.6, 1 node, max. 1 thread]
Info    : Started on Tue Apr 28 13:47:42 2020
Info    : Reading 'test.geo'...
Info    : Done reading 'test.geo'
Info    : Meshing 1D...
Info    : [  0 %] Meshing curve 1 (Circle)
Info    : [ 40 %] Meshing curve 2 (Line)
Info    : [ 70 %] Meshing curve 3 (Circle)
Info    : Done meshing 1D (0.000738 s)
Info    : Meshing 2D...
Info    : [  0 %] Meshing surface 1 (Cylinder, Frontal-Delaunay)
Info    : [  0 %] Blossom: 856 internal 56 closed
Info    : [  0 %] Blossom recombination completed (0.003377 s): 296 quads, 0 triangles, 0 invalid quads, 0 quads with Q < 0.1, avg Q = 0.651414, min Q = 0.315895
Info    : [ 40 %] Meshing surface 2 (Plane, Frontal-Delaunay)
Info    : [ 40 %] Blossom: 226 internal 28 closed
Info    : [ 40 %] Blossom recombination completed (0.001559 s): 80 quads, 0 triangles, 0 invalid quads, 0 quads with Q < 0.1, avg Q = 0.740646, min Q = 0.524194
Info    : [ 70 %] Meshing surface 3 (Plane, Frontal-Delaunay)
Info    : [ 70 %] Blossom: 235 internal 28 closed
Info    : [ 70 %] Blossom recombination completed (0.002262 s): 80 quads, 0 triangles, 0 invalid quads, 0 quads with Q < 0.1, avg Q = 0.771524, min Q = 0.488293
Info    : Done meshing 2D (0.028026 s)
Info    : Refining mesh...
Info    : Meshing order 2 (curvilinear on)...
Info    : [  0 %] Meshing curve 1 order 2
Info    : [ 20 %] Meshing curve 2 order 2
Info    : [ 30 %] Meshing curve 3 order 2
Info    : [ 50 %] Meshing surface 1 order 2
Info    : [ 60 %] Meshing surface 2 order 2
Info    : [ 80 %] Meshing surface 3 order 2
Info    : [ 90 %] Meshing volume 1 order 2
Info    : Done meshing order 2 (0.012253 s)
Info    : Done refining mesh (0.012763 s)
Info    : 1826 nodes 1958 elements
Info    : Writing 'testCLI.vtk'...
Info    : Done writing 'testCLI.vtk'
Info    : Stopped on Tue Apr 28 13:47:42 2020

From pygmsh:

From gmsh:

[gdmcbain]

Try separating the arguments of -setnumber:

mshArgs = ['-clscale', str(mshRefFactor),
           '-clcurv', str(360/50),
           '-setnumber', 'Mesh.SubdivisionAlgorithm', '1',
           '-setnumber', 'Mesh.RecombineAll', '1']

[ryancoe]

Ahh, thanks!

[nschloe]

@ryancoe +1 on the good bug report. I wish they were all like this.