Image Function Capabilities

[agorgogi]

Hello,
I would like to use Moose for simulating heterogeneous materials. I have input images of microstructures, an example is attached, which I want to mesh with Moose so as to accurately capture the geometry of the phases, and create different block IDs for the finite elements belonging to a different phase ( each phase is shown with different color in the image). I could then refer to finite elements based on their block ID, and assign the corresponding phase material properties to them.

My first approach was the following:
Create a uniform mesh with finite element size matching the pixel/voxel size of the image, and then passing this mesh as the input to ImageSubdomain Generator, as follows

[Mesh]
    [mesh_define]
        type = GeneratedMeshGenerator
        dim = 2
        nx = 320 # = number of image pixels in x
        ny = 320 # = number of image pixels in y
    []
    [image]
        input = mesh_define
        type = ImageSubdomainGenerator
        file_base = microstructure396_3D_png/0  # all images filenames start with 0
        file_suffix = png
        file_range = '0000' # read only one image from the stack for now
        threshold = 255 # everything above 255 will be assigned to block 1, everything below to block 0
        upper_value = 1
        lower_value = 0
    []  
[]

This results in accurate geometry representation and assignment of block IDs to the different phases, as shown below.

The problem with this approach is that it is very computationally expensive, because of the uniform mesh.

So my second approach was to use adaptive mesh refinement with Moose ImageFunction. Moose image function will sample the values of the image (the values of the different pixel colors), and will adaptively refine the mesh until it adequetely captures the geometrical features in the image. In the Moose documentation, it is mentioned that I can then use the result of the Image Function to set the values of a variable, e.g. displacements. However, I do not want that. Instead, what I want is to use the result of the ImageFunction to set the block IDs of the corresponding finite elements. Is there any possible way I could do that? Or is there any other possible way I could create a non-uniform (adaptive) mesh that accurately captures the image geometry, and correctly assigns different block IDs to finite elements belonging to different phases?

[Mesh]
    type = GeneratedMesh
    dim = 2
    nx = 10
    ny = 10
[]

[Functions]
    [image_func]
      type = ImageFunction
      file_base = microstructure396_3D_png/0
      file_suffix = png
      file_range = '0000'
      threshold = 255
      upper_value = 1
      lower_value = 0
    []
[]
  
[Variables]
    [u]
    []
[]

[ICs]
    [u_ic]
      type = FunctionIC
      function = image_func
      variable = u
    []
[]
  
[Problem]
    type = FEProblem
    solve = false  # that was the other way no to solve the problem, but only generate the mesh
[]
  
[Executioner]
    type = Transient
    num_steps = 1
    dt = 0.1
[]
  
[Adaptivity]
    max_h_level = 5
    initial_steps = 5
    initial_marker = marker
    [Indicators]
      [indicator]
        type = GradientJumpIndicator
        variable = u
      []
    []
    [Markers]
      [marker]
        type = ErrorFractionMarker
        indicator = indicator
        refine = 0.9
      []
    []
[]
  
[Outputs]
    exodus = true
[]

Looking forward to any suggestions, thank you!

[GiudGiud]

Hello

This might be a little convoluted but you could :

• use a FunctionAux to set an auxiliary variable to the local value of the function (executed on INITIAL)
  https://mooseframework.inl.gov/source/auxkernels/FunctionAux.html

• use this user object on INITIAL to change the subdomain
  https://mooseframework.inl.gov/source/userobjects/CoupledVarThresholdElementSubdomainModifier.html

[GiudGiud]

Are you plotting those at the end of the simulation or after a time step? Parlaview will plot the initial state by default

[Rahim-Habibi]

@GiudGiud it is at the end of simulation, the simulation time is just 0.1s.
[Executioner]
type = Transient
num_steps = 1
dt = 0.1
[]

[GiudGiud]

in paraview did you change the time to select the end of the simulation.
in MOOSE you should be fine, we output all time steps to the exodus file

[Rahim-Habibi]

@GiudGiud,
yes i selected the end of simulation in paraview.

[GiudGiud]

ok then ImageFunction isnt working as expected here