Issues replicating Example 1 : As Simple as it Gets with a GMSH ASCII input mesh file

[kurtenkera]

I'm trying to reproduce the results of Example 1: As Simple as it Gets (link: https://mooseframework.inl.gov/getting_started/examples_and_tutorials/examples/ex01_inputfile.html). Rather than using the mug.e mesh file which is provided by default, I'm trying to reproduce the figure below using a GMSH ASCII file that I created of a hollow cylinder (the .msh file is contained in here, hollow_cylinder_ascii.zip). This is the figure that I want to reproduce:

The information here on Named Entity Support (link: https://mooseframework.inl.gov/application_usage/mesh_block_type.html) has led me to believe that all I need to do is define two physical surfaces 'top' and 'bottom' that refer to the top and bottom surfaces of my cylinder. I did this in a Python script that imports the gmsh module, and you can also inspect the .msh file in hollow_cylinder_ascii.zip that these names have been implemented in lines 6 and 7 of the .msh file.

However, when I attempt to run the example problem (link: https://mooseframework.inl.gov/getting_started/examples_and_tutorials/examples/ex01_inputfile.html) with ex01.i, but changing the 'Mesh' related code to the following:

[Mesh]
  # This mesh file has 'top' and 'bottom' named boundaries defined inside it.
  file = hollow_cylinder_ascii.msh
[]

I get the following error:

*** ERROR ***
/home/enk001/Documents/PHD/PHD-Code/projects-MOOSE/moose/examples/ex01_inputfile/ex01_cyl.i:26: (BCs/bottom/boundary):
    the following node sets (ids) do not exist on the mesh: bottom (1)

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor

Likewise, if I run the code with the following changes to ex01.i:

[Mesh]
  # This mesh file has 'top' and 'bottom' named boundaries defined inside it.
  file = hollow_cylinder_ascii.msh
  boundary_name = 'bottom top'
[]

I get a slightly different error:

*** ERROR ***
The following error occurred in the object "Mesh", of type "SetupMeshAction".

You must supply the same number of boundary ids and names parameters

Stack frames: 16
0: libMesh::print_trace(std::ostream&)
1: moose::internal::mooseErrorRaw(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
2: callMooseErrorRaw(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, MooseApp*)
3: /home/enk001/Documents/PHD/PHD-Code/projects-MOOSE/moose/framework/libmoose-opt.so.0(+0xaff771) [0x773da7aff771]
4: SetupMeshAction::setupMesh(MooseMesh*)
5: SetupMeshAction::act()
6: Action::timedAct()
7: ActionWarehouse::executeActionsWithAction(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)
8: ActionWarehouse::executeAllActions()
9: MooseApp::runInputFile()
10: MooseApp::run()
11: ./ex01-opt(+0x20dc) [0x617a3052a0dc]
12: main
13: /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x773d9e629d90]
14: __libc_start_main
15: ./ex01-opt(+0x2386) [0x617a3052a386]
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor

Here are my questions: How can I get this simple example working with a .msh (ASCII) file? I believe I've correctly labelled the top and bottom surfaces of my MSH ASCII file, and the documentation here (https://mooseframework.inl.gov/application_usage/mesh_block_type.html) suggests that MOOSE should be able to recognise this?

Thanks in advance!

[GiudGiud]

Hello

Please run with --mesh-only on the command line to get a summary of what MOOSE understood from this mesh file.

The second error:

You must supply the same number of boundary ids and names parameters

is because this parameter is used to (re)name boundaries that only have an id. So you must also pass the id to use this boundary_name parameter

Guillaume

[kurtenkera]

This is the output that I get when running with --mesh-only:

 Mesh Information:
  elem_dimensions()={2}
  spatial_dimension()=3
  n_nodes()=136
    n_local_nodes()=136
  n_elem()=152
    n_local_elem()=152
    n_active_elem()=152
  n_subdomains()=2
  n_elemsets()=0
  n_partitions()=1
  n_processors()=1
  n_threads()=1
  processor_id()=0
  is_prepared()=true
  is_replicated()=true

 Mesh Bounding Box:
  Minimum: (x,y,z)=(    -0.5,     -0.5,        0)
  Maximum: (x,y,z)=(     0.5,      0.5,        1)
  Delta:   (x,y,z)=(       1,        1,        1)

 Mesh Element Type(s):
  TRI3

 Mesh Nodesets:
  None

 Mesh Sidesets:
  None

 Mesh Edgesets:
  None

 Mesh Subdomains:
  Subdomain 1 (bottom): 76 elems (TRI3, 76 active), 68 active nodes
   Volume: 0.281914
   Bounding box minimum: (x,y,z)=(    -0.5,     -0.5,        0)
   Bounding box maximum: (x,y,z)=(     0.5,      0.5,        0)
   Bounding box delta: (x,y,z)=(       1,        1,        0)
  Subdomain 2 (top): 76 elems (TRI3, 76 active), 68 active nodes
   Volume: 0.281914
   Bounding box minimum: (x,y,z)=(    -0.5,     -0.5,        1)
   Bounding box maximum: (x,y,z)=(     0.5,      0.5,        1)
   Bounding box delta: (x,y,z)=(       1,        1,        0)
  Global mesh volume = 0.563829

WARNING! There are options you set that were not used!
WARNING! could be spelling mistake, etc!
There are 2 unused database options. They are:
Option left: name:--mesh-only (no value) source: command line
Option left: name:-i value: ex01_cyl.i source: command line

Evidently, there are no recognised Mesh sidesets. Is there any documentation that explains how to clearly label sidesets in Gmsh that are recognisable by MOOSE? I thought I accomplished this by assigning the top and bottom surfaces of my hollow cylinder to two distinct "physical groups" (see https://gmsh.info/doc/texinfo/gmsh.html#Elementary-entities-vs-physical-groups for more on defining physical groups in Gmsh) 'top' and 'bottom' respectively?

[GiudGiud]

I would look at other posts here. There are other examples of people using gmsh who have imported boundary ids

maybe the test input there is helpful as an example?
https://github.com/idaholab/moose/tree/next/test/tests/meshgenerators/gmsh_bcs

[navier-rgb]

How are you exporting the gmsh, @kurtenkera ? make sure you don't save all elements or parametric coordinates when exporting the mesh to .msh format.

[kurtenkera]

Here is my hollow_cylinder_ascii.msh file below (see below). Is there any clear documentation in MOOSE regarding using gmsh for meshing? I can't seem to find any. Why would we not save all elements? And by 'parametric coordinates', do you mean coordinates of nodes?

$MeshFormat
4.1 0 8
$EndMeshFormat
$PhysicalNames
2
2 1 "bottom"
2 2 "top"
$EndPhysicalNames
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1 -0.5 -0.5 0 0.5 0.5 1 0 10 -1 50 21 25 29 33 -37 -41 -45 -49 
$EndEntities
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[navier-rgb]

Hi @kurtenkera. I assume your simulation is 3D. If you check the box next to 'all elements' when exporting/saving your gmsh file to .msh file, moose will select and try to use all lower-dimensional elements. You don't want to do that. That might be the cause of your issue. Yes, that's what I meant by parametric coordinates.

[sreihani]

Hi there,

I am wondering what tool is used to create the file "mug.e". Is it an exodus type file created by Paraview? Also, can MOOSE read any drawing files, for instance created by SolidWorks? If not, what features are available in MOOSE environment to create complex geometries.
Thanks.

[GiudGiud]

I am wondering what tool is used to create the file "mug.e". Is it an exodus type file created by Paraview?

you need to use a meshing tool. This problem is very common so you ll find examples in Gmsh or Cubit

Also, can MOOSE read any drawing files, for instance created by SolidWorks

No we need to read a mesh, not a CAD file. You can use a mesher (cubit, gmsh, openfoam's hex utility, ...) to turn a CAD into a mesh

[sreihani]

Thanks for the quick response.

Is there any recommendation for cubit vs. gmsh? For instance, more compatibility with MOOSE environment, if exists.

[GiudGiud]

cubit open version is limited in the element count but it is definitely nicer to use
cubit paid version has no limits

[sreihani]

Could you let me know which one (cubit or gmsh) was used to create "mug.e" file?

[GiudGiud]

where is this file In moose?

[sreihani]

~/projects/moose/examples/ex01_inputfile/mug.e

[GiudGiud]

ok it doesnt say.
Either software can do it. This can be done in MOOSE too with a little bit more work

[GiudGiud]

see this
https://mooseframework.inl.gov/syntax/Mesh/index.html#06c829ee-a157-4b26-9d9b-e3f359e0d061
and use the MeshGenerator objects.