Meshio does not read Gmsh physical groups

[fen]

Hi All,

I am trying to use Gmsh .msh file in FEniCS. The environment is FEniCS container with meshio 4.3.12 installed. Gmsh is 4.8.0. and not in the container.

I generated a simple model (a unit box with a cylinder hole in y direction), and defined two surface physical groups 1/2, (top/bottom surface of the box). I export the mesh to box.msh in version 2 format. I used the python codes discussed previously, in which meshio reads the msh file and generates two xdmf files. The first one, mesh.xdmf is tetra cells, which is OK. The second mf.xdmf file is triangle cells, supposedly referring to the two physical surfaces 1/2. However, in paraview mf.xdmf is all surfaces of the box and cylinder hole. mesh_from_file.get_cell_data("gmsh:physical", "triangle") gives an array of all 0 elements. It seems the meshio failed to recognize physical groups.

If the mesh is exported as version 4 msh format, the meshio.read(box.msh) throws an error “ValueError: Incompatible cell data. 33 cell blocks, but ‘gmsh:physical’ has 2 blocks.”

Could anyone help? I followed this thread closely (Gmsh 4.4.1 in FEniCS? Meshio) , and also this one Meshio Changelog - pyup.io (meshio ver 4.0 change mesh.cells from dict to list tuples).

Thank you!

The geo code

// Gmsh project created on Fri Apr 09 22:46:46 2021
SetFactory("OpenCASCADE");
//+
Box(1) = {0, 0, 0, 1, 1, 1};
//+
Cylinder(2) = {0.3, 0, 0.5, 0, 1, 0, 0.1, 2*Pi};
//+
BooleanDifference{ Volume{1}; Delete; }{ Volume{2}; Delete; };
//+
Physical Surface("1", 28) = {10};
//+
Physical Surface("2", 29) = {12};

python code

import meshio
import numpy
mesh_from_file = meshio.read("box.msh")

meshio.write("mesh.xdmf", meshio.Mesh(points=mesh_from_file.points, 
                                      cells={"tetra": mesh_from_file.get_cells_type("tetra")}))

meshio.write("mf.xdmf", meshio.Mesh(points=mesh_from_file.points, cells={"triangle": mesh_from_file.get_cells_type("triangle")}, 
                                    cell_data={"name_to_read": [mesh_from_file.get_cell_data("gmsh:physical", "triangle")]}))

My python code and geo codes are attached

[Firemage0520]

I do not know if this will fix your issue or not, I don’t really have time to test it myself, but are you missing a semicolon at the end of the “BooleanDifference” line?

[fen]

Thank you @Firemage0520 . I don’t know why it is missing a semicolon, but it works in gmsh. I have just added a semicolon, and it did not change any behaviors that I mentioned in my original post.

[bhaveshshrimali]

@fen

I generated a simple model (a unit box with a cylinder hole in y direction), and defined two surface physical groups 1/2, (top/bottom surface of the box). I export the mesh to box.msh in version 2 format.

I may have missed something in a hurry, but the following could be of some help as a starting point. I save all the physical entities (volume/surface). Note this is pygmsh-6.1.1 since I prefer to use that over the newer releases.

import numpy as np
import meshio, pygmsh, os

geom = pygmsh.opencascade.Geometry()
b1 = geom.add_box([0.0, 0.0, 0.0], [1.0, 1.0, 1.0])
cyl1 = geom.add_cylinder([0.3, 0.0, 0.5], [0.0, 1.0, 0], 0.1, 2 * np.pi)
final = geom.boolean_difference([b1], [cyl1])
geom.add_raw_code("eps=1.E-3;")
geom.add_raw_code(
    "bottom() = Surface In BoundingBox {-eps, -eps, -eps, 1 + eps, eps, 1 + eps};"
)
geom.add_raw_code(
    "top() = Surface In BoundingBox {-eps, 1-eps, -eps, 1 + eps, 1 + eps, 1 + eps};"
)

geom.add_raw_code('Physical Surface("top") = top();')
geom.add_raw_code('Physical Surface("bottom") = bottom();')
geom.add_raw_code('Physical Volume("domain") = bo1[];')

msh = pygmsh.generate_mesh(geom, geo_filename=os.path.join(os.getcwd(), "testmesh.geo"))

tetramesh = meshio.Mesh(msh.points, cells={"tetra": msh.get_cells_type("tetra")})
cellData = msh.get_cell_data("gmsh:physical", "triangle")
trimesh = meshio.Mesh(
    msh.points,
    cells={"triangle": msh.get_cells_type("triangle")},
    cell_data={"bdry": [cellData]},
)
meshio.xdmf.write("testmesh.xdmf", tetramesh)
meshio.xdmf.write("testmesh_tri.xdmf", trimesh)

and the corresponding geo file:

// This code was created by pygmsh vunknown.
SetFactory("OpenCASCADE");
vol0 = newv;
Box(vol0) = {0.0, 0.0, 0.0, 1.0, 1.0, 1.0};
vol1 = newv;
Cylinder(vol1) = {0.3, 0.0, 0.5, 0.0, 1.0, 0, 0.1, 6.283185307179586};
bo1[] = BooleanDifference{ Volume{vol0}; Delete; } { Volume{vol1}; Delete;};
eps=1.E-3;
bottom() = Surface In BoundingBox {-eps, -eps, -eps, 1 + eps, eps, 1 + eps};
top() = Surface In BoundingBox {-eps, 1-eps, -eps, 1 + eps, 1 + eps, 1 + eps};
Physical Surface("top") = top();
Physical Surface("bottom") = bottom();
Physical Volume("domain") = bo1[];

Please also checkout the meshing tutorials by @dokken https://jsdokken.com/converted_files/tutorial_gmsh.html for a much more comprehensive usage of the gmsh python API and loading the generated meshes into dolfin (or dolfinx), in case if you haven’t.

My understanding of top/bottom corresponds to y=1/y=0, but you can change that according to your definitions.

[fen]

Thank you @bhaveshshrimali for your detailed response. My ultimate goal is to use gmsh API/pygmsh to generate the mesh, and solve in FEniCS. Since I have little to no knowledge of any of them, I had to divide them and learn step by step.

As to your suggestions

1. I tried the geo file. Your geo file opens OK in my Gmsh GUI 4.8.0. However I meshed the model, and exported to .msh. The same problems remain when I ran my python code: Meshio.read() can read ver2 msh file, but does not recognize physical groups; ver4 msh file cannot be properly read by Meshio.

2. I also tried to run your python/pygmsh code. I had to install pygmsh and gmsh to the FEniCS container following this thread (Problem with installation of latest gmsh 4.6.0 via pip - #3 by Nexius). I could import meshio and pygmsh in container’s bash, but not directly in jupyter notebook (Jupyter did not find module of pygmsh). I did the following in Jupyter to be able to import gmsh and pygmsh. However there are errors about opencascade, see below.

import sys
sys.path.append('/usr/local/gmsh-4.6.0-Linux64-sdk/lib')    # have to add path manually to import gmsh
sys.path.append('/usr/local/gmsh-4.6.0-Linux64-sdk/bin')
import meshio
import gmsh
import pygmsh, os
import numpy as np

#geom = pygmsh.opencascade.Geometry()     # pygmsh has no opencascade attribute
geom = pygmsh.geo.Geometry()                      # pygmsh.geo.Geometry() works
b1 = geom.add_box([0.0, 0.0, 0.0], [1.0, 1.0, 1.0])     # error: add_box() missing 4 required positional arguments: 'y0', 'y1', 'z0', and 'z1'

It seems pygmsh (v7.1.8) has no .opencascade, but .geo attribute. ‘add_box’ needs 4 arguments. I have not yet started studying pygmsh/gmsh API but your code provides me a good point to start with.

At this point I will try to stick to 1), i.e. generate a mesh from Gmsh GUI with physical groups, and then use my python code to read (via meshio) and export to separate xdmf files. Any insights?

[bhaveshshrimali]

@fen

The same problems remain when I ran my python code: Meshio.read() can read ver2 msh file, but does not recognize physical groups;

I am not sure if I follow. pygmsh-6.1.1 in my case does exactly what you are doing (except for the GUI). It writes the geo file, spawns a process on the command line and calls gmsh. If you take the above geo file (say test.geo), and then simply run from the terminal:

gmsh -3 test.geo -o test.msh

and then read your test.msh using the code snippet above, it should work. Also, I think that the default format when saving as .msh is indeed MSH 4.1 and not MSH 2.0. I have checked this just now.

@fen

I also tried to run your python/pygmsh code

Yes, so you should uninstall the latest pygmsh and instead do

pip3 install pygmsh==6.1.1

if you want to run the above code. I think the link that I posted above also has updated tutorials on using the later versions of pygmsh. pygmsh-7 onwards uses the gmsh python API and hence I directly use that instead.

[Nexius]

Dear all.

Just a small note: instead of using pygmsh and opencascade one can also use the built-in functions in gmsh! Here is a small example of how to fragment two cylinders:

# Done with gmsh 4.6.0
import numpy as np
import scipy.constants as const

import gmsh

gmsh.initialize()

cyl1_x    =   0.0
cyl1_y    =   0.0
cyl1_z    =   0.0
cyl1_vx   =   0.0
cyl1_vy   =   0.0
cyl1_vz   =  50.0
cyl1_size = 100.0

cyl2_x    =  0.0
cyl2_y    =  0.0
cyl2_z    = 40.0
cyl2_vx   =  0.0
cyl2_vy   =  0.0
cyl2_vz   = 50.0
cyl2_size = 50.0

cyl1_1 = gmsh.model.occ.addCylinder(cyl1_x,
                                    cyl1_y,
                                    cyl1_z,
                                    cyl1_vx,
                                    cyl1_vy,
                                    cyl1_vz,
                                    cyl1_size,
                                    angle=2.0*const.pi)

cyl2_1 = gmsh.model.occ.addCylinder(cyl2_x,
                                    cyl2_y,
                                    cyl2_z,
                                    cyl2_vx,
                                    cyl2_vy,
                                    cyl2_vz,
                                    cyl2_size,
                                    angle=2.0*const.pi)

gmsh.model.occ.fragment([(3, cyl1_1)], [(3, cyl2_1)],
                                 removeObject=True,
                                 removeTool=False)

gmsh.model.occ.removeAllDuplicates()

gmsh.model.occ.synchronize()
gmsh.model.mesh.generate(3)
gmsh.write("mesh.msh")

Other objects: gmsh.model.occ.addCylinder, gmsh.model.occ.addCone, gmsh.model.occ.addSphere and so on …

[Nexius]

… and, because this might get important: once created a gmsh file, you have an interest for the import of the gmsh mesh into FEniCS. Below you find two definitions, how I import 2D or 3D meshes into FEniCS (this was derived, e.g., from here and so on).

First you use convert_mesh_xdmf and then load_mesh_to_fenics. It is written such that you can use MPI (see, e.g., here).

Greetings … .

import os
import numpy as np
import meshio
from fenics import *


# _________________________________________________________________ Definitions

# Convert the 'gmsh' specific mesh into a XDMF mesh. This is done for MPI
#
# i             => process number (MPI)
# file_mesh     => gmsh file
# dir_data      => directory of the mesh files
# dimension     => either "2D" or "3D"
#
def convert_mesh_xdmf(i, file_mesh, dir_data, dimension):

    mesh = meshio.read(file_mesh)

    string_nr = "{:04d}".format(i)

    tetra_cells    = None # For 3D only
    tetra_data     = None # For 3D only
    triangle_cells = None # For 2D and 3D
    triangle_data  = None # For 2D and 3D
    line_cells     = None # For 2D only
    line_data      = None # For 2D only

    for key in mesh.cell_data_dict["gmsh:physical"].keys():
        if key == "triangle":
            triangle_data = mesh.cell_data_dict["gmsh:physical"][key]
        elif key == "tetra":
            tetra_data = mesh.cell_data_dict["gmsh:physical"][key]
        elif key == "line":
            line_data = mesh.cell_data_dict["gmsh:physical"][key]

    for cell in mesh.cells:
        if cell.type == "tetra":
            if tetra_cells is None:
                tetra_cells = cell.data
            else:
                tetra_cells = np.vstack([tetra_cells, cell.data])
        elif cell.type == "triangle":
            if triangle_cells is None:
                triangle_cells = cell.data
            else:
                triangle_cells = np.vstack([triangle_cells, cell.data])
        elif cell.type == "line":
            if line_cells is None:
                line_cells = cell.data
            else:
                line_cells = np.vstack([line_cells, cell.data])

    line_mesh  = meshio.Mesh(points=mesh.points,
                             cells={"line": line_cells},
                             cell_data={"name_to_read":[line_data]})
    tetra_mesh = meshio.Mesh(points=mesh.points,
                             cells={"tetra": tetra_cells},
                             cell_data={"name_to_read":[tetra_data]})

    triangle_mesh =meshio.Mesh(points=mesh.points,
                               cells=[("triangle", triangle_cells)],
                               cell_data={"name_to_read":[triangle_data]})

    file_msh_subd = os.path.join(dir_data, "Data_"+string_nr+"_msh_subd.xdmf")
    file_bound    = os.path.join(dir_data, "Data_"+string_nr+"_bound.xdmf")

    if dimension == "2D":
        meshio.write(file_msh_subd, triangle_mesh)
        meshio.write(file_bound,    line_mesh)
    if dimension == "3D":
        meshio.write(file_msh_subd, tetra_mesh)
        meshio.write(file_bound,    triangle_mesh)


# Import the mesh, boundaries and subdomains into FEniCS.
#
# i             => process number (MPI)
# dir_data      => directory of the mesh files
#
def load_mesh_to_fenics(i, dir_data):

    string_nr = "{:04d}".format(i)

    file_msh_subd = os.path.join(dir_data, "Data_"+string_nr+"_msh_subd.xdmf")
    file_bound    = os.path.join(dir_data, "Data_"+string_nr+"_bound.xdmf")

    # Open the latter files and obtain the mesh, subdomains, boundaries,
    # dx and ds.
    mesh = Mesh(MPI.comm_self)
    with XDMFFile(MPI.comm_self, file_msh_subd) as infile:
        infile.read(mesh)

    mvc = MeshValueCollection("size_t", mesh, 2)
    with XDMFFile(MPI.comm_self, file_bound) as infile:
        infile.read(mvc, "name_to_read")
    boundaries = cpp.mesh.MeshFunctionSizet(mesh, mvc)

    mvc2 = MeshValueCollection("size_t", mesh, 3)
    with XDMFFile(MPI.comm_self, file_msh_subd) as infile:
        infile.read(mvc2, "name_to_read")
    subdomains = cpp.mesh.MeshFunctionSizet(mesh, mvc2)

    dx = Measure("dx", domain=mesh, subdomain_data=subdomains)
    ds = Measure("ds", domain=mesh, subdomain_data=boundaries)
    dS = Measure("dS", domain=mesh, subdomain_data=boundaries)

    # We note some statistical information into the parameter class
    n_cells     = mesh.num_cells()
    n_facets    = mesh.num_faces()
    n_vertices  = mesh.num_vertices()
    n_edges     = mesh.num_edges()

    # We print out this info on the terminal for the case that we decide to
    # eventually stop the calculations.
    print("Mesh information")
    print("================")
    print("No. of cells   : ", n_cells)
    print("No. of faces   : ", n_facets)
    print("No. of vertices: ", n_vertices)
    print("No. of edges   : ", n_edges)

    return n_cells, n_facets, n_vertices, n_edges, mesh, subdomains, boundaries, dx, ds, dS

[fen]

@bhaveshshrimali what you have done is absolutely correct, as evident by the plots. @Nexius , thank you for the gmsh build-in codes. They actually ran well on my system. I have not studied gmsh API yet but will do so.

I tend to believe there are some conflicts between Gmsh (in Win10) and FEniCS+Meshio+pygmsh container in my system. I have tried ver 6.1.1 and 7.8 of pygmsh, but both seem not to connect to the gmsh in the docker container. I have also tried Meshio 3.1 and 4.7; again neither of them read Gmsh(Win 10 GUI)'s .msh in ver4 format; while they both can read msh in ver2, they failed to recognize the physical groups (msh.get_cell_data("gmsh:physical", "triangle") gives all 0 array).

At this point my system is a mess. I will remove the fenics docker container completely, and start from scratch. I will also get a linux computer (my old laptop) to run Gmsh in linux to see if I can solve (or reproduce) the problem. Will report here later in few days.

BTW, it would be appreciated if any of you can provide a 3d .msh file with physical surface groups generated from this thread. It would help me narrow down the problem. Thank you so much!

[bhaveshshrimali]

Here you go

$MeshFormat
4.1 0 8
$EndMeshFormat
$PhysicalNames
3
2 1 "top"
2 2 "bottom"
3 3 "domain"
$EndPhysicalNames
$Entities
10 15 7 1
9 0.2999999999999999 1 0.6 0 
10 0.2999999999999999 0 0.6 0 
11 0 0 1 0 
12 0 0 0 0 
13 0 1 1 0 
14 0 1 0 0 
15 1 0 0 0 
16 1 0 1 0 
17 1 1 1 0 
18 1 1 0 0 
13 0.1999999 0.9999999000000001 0.3999999 0.4000001 1.0000001 0.6000000999999999 0 2 9 -9 
14 0.2999998999999999 -9.999999994736442e-08 0.5999999 0.3000000999999999 1.0000001 0.6000000999999999 0 2 10 -9 
15 0.1999999 -1e-07 0.3999999 0.4000001 1e-07 0.6000000999999999 0 2 10 -10 
16 -1e-07 -1e-07 -9.999999994736442e-08 1e-07 1e-07 1.0000001 0 2 12 -11 
17 -1e-07 -9.999999994736442e-08 0.9999999000000001 1e-07 1.0000001 1.0000001 0 2 11 -13 
18 -1e-07 0.9999999000000001 -9.999999994736442e-08 1e-07 1.0000001 1.0000001 0 2 14 -13 
19 -1e-07 -9.999999994736442e-08 -1e-07 1e-07 1.0000001 1e-07 0 2 12 -14 
20 -9.999999994736442e-08 -1e-07 -1e-07 1.0000001 1e-07 1e-07 0 2 12 -15 
21 0.9999999000000001 -1e-07 -9.999999994736442e-08 1.0000001 1e-07 1.0000001 0 2 15 -16 
22 -9.999999994736442e-08 -1e-07 0.9999999000000001 1.0000001 1e-07 1.0000001 0 2 11 -16 
23 -9.999999994736442e-08 0.9999999000000001 0.9999999000000001 1.0000001 1.0000001 1.0000001 0 2 13 -17 
24 0.9999999000000001 -9.999999994736442e-08 0.9999999000000001 1.0000001 1.0000001 1.0000001 0 2 16 -17 
25 -9.999999994736442e-08 0.9999999000000001 -1e-07 1.0000001 1.0000001 1e-07 0 2 14 -18 
26 0.9999999000000001 0.9999999000000001 -9.999999994736442e-08 1.0000001 1.0000001 1.0000001 0 2 18 -17 
27 0.9999999000000001 -9.999999994736442e-08 -1e-07 1.0000001 1.0000001 1e-07 0 2 15 -18 
7 0.1999999 -9.999999994736442e-08 0.3999999 0.4000001 1.0000001 0.6000000999999999 0 4 13 -14 15 14 
8 -1e-07 -9.999999994736442e-08 -9.999999994736442e-08 1e-07 1.0000001 1.0000001 0 4 16 17 -18 -19 
9 -9.999999994736442e-08 -1e-07 -9.999999994736442e-08 1.0000001 1e-07 1.0000001 1 2 5 20 21 -22 -16 15 
10 -9.999999994736442e-08 -9.999999994736442e-08 0.9999999000000001 1.0000001 1.0000001 1.0000001 0 4 17 23 -24 -22 
11 -9.999999994736442e-08 0.9999999000000001 -9.999999994736442e-08 1.0000001 1.0000001 1.0000001 1 1 5 25 26 -23 -18 13 
12 -9.999999994736442e-08 -9.999999994736442e-08 -1e-07 1.0000001 1.0000001 1e-07 0 4 19 25 -27 -20 
13 0.9999999000000001 -9.999999994736442e-08 -9.999999994736442e-08 1.0000001 1.0000001 1.0000001 0 4 21 24 -26 -27 
1 -9.999999994736442e-08 -9.999999994736442e-08 -9.999999994736442e-08 1.0000001 1.0000001 1.0000001 1 3 7 8 9 10 11 12 13 7 
$EndEntities
$Nodes
33 189 1 189
0 9 0 1
1
0.2999999999999999 1 0.6
0 10 0 1
2
0.2999999999999999 0 0.6
0 11 0 1
3
0 0 1
0 12 0 1
4
0 0 0
0 13 0 1
5
0 1 1
0 14 0 1
6
0 1 0
0 15 0 1
7
1 0 0
0 16 0 1
8
1 0 1
0 17 0 1
9
1 1 1
0 18 0 1
10
1 1 0
1 13 0 13
11
12
13
14
15
16
17
18
19
20
21
22
23
0.3433883739117558 1 0.5900968867902419
0.378183148246803 1 0.5623489801858733
0.3974927912181824 1 0.5222520933956314
0.3974927912181824 1 0.4777479066043686
0.378183148246803 1 0.4376510198141266
0.3433883739117558 1 0.4099031132097581
0.3 1 0.4
0.2566116260882442 1 0.4099031132097581
0.221816851753197 1 0.4376510198141266
0.2025072087818176 1 0.4777479066043686
0.2025072087818176 1 0.5222520933956314
0.221816851753197 1 0.5623489801858733
0.2566116260882442 1 0.5900968867902419
1 14 0 3
24
25
26
0.2999999999999999 0.25 0.6
0.2999999999999999 0.5 0.6
0.2999999999999999 0.75 0.6
1 15 0 13
27
28
29
30
31
32
33
34
35
36
37
38
39
0.3433883739117558 0 0.5900968867902419
0.378183148246803 0 0.5623489801858733
0.3974927912181824 0 0.5222520933956314
0.3974927912181824 0 0.4777479066043686
0.378183148246803 0 0.4376510198141266
0.3433883739117558 0 0.4099031132097581
0.3 0 0.4
0.2566116260882442 0 0.4099031132097581
0.221816851753197 0 0.4376510198141266
0.2025072087818176 0 0.4777479066043686
0.2025072087818176 0 0.5222520933956314
0.221816851753197 0 0.5623489801858733
0.2566116260882442 0 0.5900968867902419
1 16 0 1
40
0 0 0.5
1 17 0 1
41
0 0.5 1
1 18 0 1
42
0 1 0.5
1 19 0 1
43
0 0.5 0
1 20 0 1
44
0.5 0 0
1 21 0 1
45
1 0 0.5
1 22 0 1
46
0.5 0 1
1 23 0 1
47
0.5 1 1
1 24 0 1
48
1 0.5 1
1 25 0 1
49
0.5 1 0
1 26 0 1
50
1 1 0.5
1 27 0 1
51
1 0.5 0
2 7 0 72
52
53
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0.2158831334920706 0.3923495142414911 0.4459227148528406
0.2761961584839044 0.9604106880638535 0.4028744259781359
0.3634869330403887 0.03831174889097004 0.422738047312243
0.2386231727844231 0.04358306987508974 0.4210513769534312
0.3570097700799455 0.9643020440273072 0.4178423094565594
0.2099031132097581 0.9615398792819613 0.4566116260882442
0.3998149979341919 0.0402335755485877 0.5060799825161972
0.2006387343456938 0.04463611509859518 0.5112844533573588
0.3998332397898698 0.9498469300850713 0.5057727145311671
0.2077926391976693 0.9320092890222652 0.5387014549321962
0.3623489801858734 0.03846012071803868 0.5781831482468029
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$EndElements

[fen]

@bhaveshshrimali Thank you ! My python code can read (Meshio 4.3.12) your .msh file, and correctly generates xdmf files recognizing the physical surface groups!

Thank you so much!

Now the problem has to be Gmsh, either I did something wrong or it’s not properly installed.
Will post my updates here.

[Kei_Yamamoto]

Hi @fen
I have the same problem. I have 3d msh file that looks similar but does not read physical groups. Could you summarize your solution ??

[Kei_Yamamoto]

Hi, I am trying to create coiled pipe using gmsh. I have the following python script for generating msh file

import gmsh
import math
import os
import sys

gmsh.initialize()

gmsh.model.add("coiled_pipe")

# define a spline curve:
nturns = 5.
npts = 20
r = 1.
h = 1. * nturns
p = []
for i in range(0, npts):
    theta = i * 2 * math.pi * nturns / npts
    gmsh.model.occ.addPoint(r * math.cos(theta), r * math.sin(theta),
                            i * h / npts, 1, 1000 + i)
    p.append(1000 + i)
gmsh.model.occ.addSpline(p, 1000)

# A wire is like a curve loop, but open:
gmsh.model.occ.addWire([1000], 1000)

# We define the shape we would like to extrude along the spline (a disk):
gmsh.model.occ.addDisk(1, 0, 0, 0.2, 0.2, 1000)
gmsh.model.occ.rotate([(2, 1000)], 0, 0, 0, 1, 0, 0, math.pi / 2)

# We extrude the disk along the spline to create a pipe (other sweeping types
# can be specified; try e.g. 'Frenet' instead of 'DiscreteTrihedron'):
gmsh.model.occ.addPipe([(2, 1000)], 1000, 'DiscreteTrihedron')

# We delete the source surface, and increase the number of sub-edges for a
# nicer display of the geometry:
gmsh.model.occ.remove([(2, 1000)])
gmsh.option.setNumber("Geometry.NumSubEdges", 1000)

gmsh.model.occ.synchronize()

# We can activate the calculation of mesh element sizes based on curvature
# (here with a target of 20 elements per 2*Pi radians):
gmsh.option.setNumber("Mesh.MeshSizeFromCurvature", 20)

# We can constraint the min and max element sizes to stay within reasonnable
# values (see `t10.py' for more details):
gmsh.option.setNumber("Mesh.MeshSizeMin", 0.001)
gmsh.option.setNumber("Mesh.MeshSizeMax", 0.3)

#  Physical groups
gmsh.model.addPhysicalGroup(dim=2, tags=[1001], tag=1)
gmsh.model.setPhysicalName(dim=2, tag=1, name="inlet")
gmsh.model.addPhysicalGroup(dim=2, tags=[1003], tag=2)
gmsh.model.setPhysicalName(dim=2, tag=2, name="outlet")
gmsh.model.addPhysicalGroup(dim=2, tags=[1002], tag=3)
gmsh.model.setPhysicalName(dim=2, tag=3, name="boundary")
gmsh.model.addPhysicalGroup(dim=3, tags=[1], tag=1)
gmsh.model.setPhysicalName(dim=3, tag=1, name="Volume")

gmsh.model.mesh.generate(3)
gmsh.write("coiled_pipe.msh")

# Launch the GUI to see the results:
if '-nopopup' not in sys.argv:
    gmsh.fltk.run()

gmsh.finalize()

but meshio does not seem to recognize physical groups. I am fairly new to gmsh so I may have problems in my above code, but at least it seems correct when I open the msh file with gmsh GUI.
I used the following code to read msh file and generate xdmf file.

def create_mesh(mesh, cell_type):

    cells = mesh.get_cells_type(cell_type)
    cell_data = mesh.get_cell_data("gmsh:physical", cell_type)
    points = mesh.points
    # Create output mesh
    out_mesh = meshio.Mesh(points=points, cells={cell_type: cells},
                           cell_data={"name_to_read": [cell_data]})
    return out_mesh

mesh3D_from_msh = meshio.read("coiled_pipe.msh")
tetra_mesh = create_mesh(mesh3D_from_msh, "tetra")

meshio.write("coiled_pipe.xdmf", tetra_mesh)

There is no error message when I run them, but xdmf file does not contain any of physical group names (inlet, outlet, volume, boundary), but has “name_to_read” name.
I can not find what is wrong with my code, so I appreciate any help.

Update : This is how my mesh looks like with Gmsh GUI

Best,

[fen]

Update: I use Gmsh 4.8.0 on linux Mint. It opens @bhaveshshrimali 's geo file OK. Under GUI I export to box_bh.msh in ver4 format (checked the option save all elements). My code in docker is simply as follows:

import meshio
mesh_from_file = meshio.read("box_bh.msh")

This generates an error of ValueError: Incompatible cell data. 33 cell blocks, but 'gmsh:physical' has 3 blocks.

Instead I use command gmsh -3 box.geo -o box_bh_com.msh to generate msh file. And this file can be correctly read by the same python code.

It appears Gmsh GUI exports a msh file that is incompatible with Meshio. The command line is fine.

@Kei_Yamamoto I am not sure if I know the solution yet, but I can summarize my problem as above. FYI, originally I used Gmsh 4.8.0. GUI on native Win10 and got the same problem.

It appears to be a Gmsh question rather than a FEniCS question now.

[Kei_Yamamoto]

@fen Thank you for the update. I do not use Gmsh GUI to generate geo file, but used the python API for creating msh file direclty. I just used Gmsh GUI for checking if the physical groups are actually embedded. However, I might try using geo file and use the gmsh -3 box.geo -o box_bh_com.msh as you mentioned. Thank you for your help. Other comments or help are very much welcomed.

[fen]

Hi @Nexius , thank you for your contribution to reading XDMF in parallel! Without any knowledge of MPI, I dared to try it just now for fun. My system is FEniCS docker on WIN10, on an I-7 4core system with 16GB (docker can use 4-core 8GB). Could you please address how to save results to XDMF file(s) in parallel computing. Following your example I added the following line to save the results.

file_results = fn.XDMFFile(MPI.COMM_SELF, "test_mpi.xdmf")
file_results.parameters['flush_output'] = True
file_results.parameters['functions_share_mesh'] = True
...
file_results.write(u, t)            #write u(displacement) at time-step t

I must have been wrong, and notice the following issues and successes:

1. I have to use MPI.COMM_SELF instead of MPI.comm_self, otherwise it raises no attribute 'comm_self'. Out of curiosity, is it a version issue of mpi4py?
2. With export HDF5_USE_FILE_LOCKING=FALSE, I run mpirun -np 4 python3 test.py. The code DOES run the FEA analysis MANY times (as I can see it prints the ‘u’ results many times). But in the end it halts and raises many blocks of errors as follows.

HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) MPI-process 1:
  #000: ../../../src/H5F.c line 579 in H5Fopen(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #001: ../../../src/H5Fint.c line 1168 in H5F_open(): unable to lock the file or initialize file structure
    major: File accessibilty
    minor: Unable to open file
  #002: ../../../src/H5FD.c line 1821 in H5FD_lock(): driver lock request failed
    major: Virtual File Layer
    minor: Can't update object
  #003: ../../../src/H5FDsec2.c line 939 in H5FD_sec2_lock(): unable to flock file, errno = 11, error message = 'Resource temporarily unavailable'
    major: File accessibilty
    minor: Bad file ID accessed

3. with export HDF5_USE_FILE_LOCKING=TRUE, it raises error without performing any FEA analysis.

Traceback (most recent call last):
  File "test.py", line 66, in <module>
    infile.read(mvc, "name_to_read")
RuntimeError:

*** -------------------------------------------------------------------------
*** 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 find entity in map.
*** Reason:  Error reading MeshValueCollection.
*** Where:   This error was encountered inside HDF5File.cpp.
*** Process: 2
***
*** DOLFIN version: 2019.1.0
*** Git changeset:  74d7efe1e84d65e9433fd96c50f1d278fa3e3f3f
*** -------------------------------------------------------------------------

Do you have any insights? I can clean up my codes to provide a minimal working code if needed. Thank you!

[jojo3000]

Hello !
If that’s of any relevance to people reading this topic, I had the same error which led me here.
The root cause was the saveAll gmsh parameter that I used for debugging purposes with the python API. It saves unused nodes, etc. to the mesh so meshio is confused. Solved it like this
gmsh.option.setNumber("Mesh.SaveAll", 0)

[nareniitr]

Hello.
I am also little confused about how to properly retrieve physical names from GMSH mesh to XDMF format for use with FEniCS. I followed the same script as https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/172?u=nareniitr provided earlier for a simple 2D rectangular geometry. I convert .msh file to two xdmf files. When I tried to integrate over area dx and boundary ds, I get correct values. However, when I tried to integrate on just one boundary (e.g. Inlet), the integral value is zero. It appears that subdomain_id is not being recognized. Below is a minimum working example.

import meshio
msh = meshio.read("Rectangle.msh")

def create_mesh(mesh, cell_type, prune_z=False):
    cells = mesh.get_cells_type(cell_type)
    cell_data = mesh.get_cell_data("gmsh:physical", cell_type)
    out_mesh = meshio.Mesh(points=mesh.points, cells={cell_type: cells}, cell_data={"name_to_read":[cell_data]})
    if prune_z:
        out_mesh.prune_z_0()
    return out_mesh

line_mesh = create_mesh(msh, "line", prune_z=True)
meshio.write("mf2D.xdmf", line_mesh)

triangle_mesh = create_mesh(msh, "triangle", prune_z=True)
meshio.write("mesh2D.xdmf", triangle_mesh)
# fenics imported later to avoid compatibilty issue with h5
from fenics import *
mesh = Mesh()
with XDMFFile("mesh2D.xdmf") as infile:
    infile.read(mesh)
mvc = MeshValueCollection("size_t", mesh, 1)

with XDMFFile("mf2D.xdmf") as infile:
    infile.read(mvc, "name_to_read")
mf = cpp.mesh.MeshFunctionSizet(mesh, mvc)

print('num_cells   :', mesh.num_cells())
print('num_vertices:', mesh.num_vertices())
print('cell_type   :', mesh.ufl_cell())

dx=Measure("dx", domain=mesh, subdomain_data=mf)
print(assemble(1*dx))

ds=Measure("ds", domain=mesh, subdomain_data=mf)
print(assemble(1*ds))

ds_1=Measure("ds", domain=mesh, subdomain_data=mf, subdomain_id=5)
print(assemble(1*ds_1))

I have also attached geo file I got from GMSH attached here.

//+
Point(1) = {0, 0, 0, 1.0};
//+
Point(2) = {1, 0, 0, 1.0};
//+
Point(3) = {1, 1, 0, 1.0};
//+
Point(4) = {0, 1, 0, 1.0};
//+
Line(1) = {1, 2};
//+
Line(2) = {2, 3};
//+
Line(3) = {4, 1};
//+
Line(4) = {3, 4};
//+
Curve Loop(1) = {4, 3, 1, 2};
//+
Plane Surface(1) = {1};
//+
Physical Curve("Inlet", 5) = {3};
//+
Physical Curve("Outlet", 6) = {2};
//+
Physical Curve("Top", 7) = {4};
//+
Physical Curve("Bottom", 8) = {1};

//+
MeshSize {1, 2, 3, 4} = 0.05;

Can you please help me understand what is the problem here?

[dokken]

You need to define the surface as a physical surface as well:

Physical Surface("Area", 10) = {1};

with this addition I get:

num_cells   : 944
num_vertices: 513
cell_type   : triangle
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
1.0000000000000007
Calling FFC just-in-time (JIT) compiler, this may take some time.
4.000000000000001
Calling FFC just-in-time (JIT) compiler, this may take some time.
0.9999999999999999

[nareniitr]

@nareniitr

from fenics import *
mesh = Mesh()
with XDMFFile("mesh2D.xdmf") as infile:
    infile.read(mesh)
mvc = MeshValueCollection("size_t", mesh, 1)

with XDMFFile("mf2D.xdmf") as infile:
    infile.read(mvc, "name_to_read")
mf = cpp.mesh.MeshFunctionSizet(mesh, mvc)

print('num_cells   :', mesh.num_cells())
print('num_vertices:', mesh.num_vertices())
print('cell_type   :', mesh.ufl_cell())

dx=Measure("dx", domain=mesh, subdomain_data=mf)
print(assemble(1*dx))

ds=Measure("ds", domain=mesh, subdomain_data=mf)
print(assemble(1*ds))

ds_1=Measure("ds", domain=mesh, subdomain_data=mf, subdomain_id=5)
print(assemble(1*ds_1))

Thank you @dokken . That resolved my issue. Just wanted to add for reference that I saved my mesh with Version 4 ASCII format with Save all elements unchecked if anyone else faces the same issue.