add_subdomain_ids and Exodus output

[Wendy-Ji]

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Question

Hello,

I am using add_subdomain_ids to add an empty subdomain (see below code). I need this for my simulations which start off with empty subdomains and have elements later added to them.

When I turn on the Exodus output, I get the below error. If the variable isn't MONOMIAL and CONSTANT, then this error won't appear. The same problem occurs if I use add_subdomain_names. I'm not sure if I did something wrong with the setup, or if you can't have an Exodus output for this particular setup.

Thank you.

Wendy

[Problem]
  solve = false
[]

[Mesh]
  [generated]
    type = GeneratedMeshGenerator
    dim = 2
    nx = 10
    ny = 10
  []
  add_subdomain_ids = 1
[]

[Variables]
  [dummy]
    family = MONOMIAL
    order = CONSTANT
    block = '0 1'
  []
[]

[Preconditioning]
  [SMP]
    type = SMP
    full = true
  []
[]

[Executioner]
  type = Transient
  end_time = 2
[]

[Outputs]
  exodus = True
[]

[GiudGiud]

hello

this is a known issue, you need to actually have an element in subdomain 1 before outputting to exodus (for now)

Guillaume

[jmeier]

Dear Guillaume, I have the same problem right now (ExodusII_IO_Helper: block id XXX not found in block_ids.). It makes it difficult for us to use the TimedSubdomainModifier .

You wrote there must be at least one element in each subdomain before outputting to exodus. In each timstep? Or just the first one?

The error message states the error is thrown in libmesh. According to a backtrace I did with gdb Moose is calling libmesh in line 343 of Exodus.C (method Exodus::outputElementalVariables()). Could we insert some kind of if-condition to avoid the error? What should be checked?

moose/framework/src/outputs/Exodus.C

Lines 333 to 343 in 82b674a

	Exodus::outputElementalVariables()
	{
	// Make sure the the file is ready for writing of elemental data
	if (!_exodus_initialized || !hasNodalVariableOutput())
	outputEmptyTimestep();
	// Write the elemental data
	std::vector<std::string> elemental(getElementalVariableOutput().begin(),
	getElementalVariableOutput().end());
	_exodus_io_ptr->set_output_variables(elemental);
	_exodus_io_ptr->write_element_data(*_es_ptr);

[GiudGiud]

We have no investigated it further.

We could remove the non-existing block from the element data before sending it to the exodus writer. That would be fine imo but it s a little hacky. The better fix is in libmesh, modifying write_element_data to not die on missing subdomains

[jmeier]

Should I create an issue over there? Or do you have better connections with the guys there?

[GiudGiud]

Sure

[jmeier]

Please find the issue with libmesh here: libMesh/libmesh#3949