How to ensure the displaced mesh is used

[keassyguang]

Hello MOOSE Community,

I'm developing a custom material class that inherits from ADMaterial. The coordinates of the current quadrature point will be used as a condition to assign a specific value to some created variables. What I want to know is whether the coordinates of _q_point[_qp](0), _q_point[_qp](1) and _q_point[_qp](2) return the displaced mesh or the undisplaced mesh. Since I need the coordinates of the quadrature point under the displaced mesh, what should I do to ensure that the displaced mesh is always used?

[GiudGiud]

For many objects, all you need to do is setting use_displaced_mesh = true

Is that an option for your case?

[keassyguang]

I have uploaded three input files to create working and non-working examples:
To run these simulations, you need to comment out the condition code related to the isSNESVi in the BoundsBase constructor.

1. test.i: The simulation can be run with a displaced mesh, but the refined mesh cannot be coarsened;
2. test_without_displaced_mesh.i: Both the GlobalParams block and displacements = 'disp_x disp_y' in the Mesh block are commented out, the adaptivity works well;
3. test_without_displaced_mesh_segfault.i: keep everything the same as test 2, but change refinement = 5 to refinement = 4 in the mesh block, the simulation aborted with a segmentation fault (signal 11).

I have checked some of the outputs. It seems that the GradientJumpIndicator cannot return a correct value as I saw that all the calculated values are almost zero (~1e-38).
Thank you so much.

[GiudGiud]

Thanks. I ll take a look soon.

It seems that the GradientJumpIndicator cannot return a correct value as I saw that all the calculated values are almost zero (~1e-38).

This is probably due to not using the displaced mesh correctly in the code. Should be an easy fix

you need to comment out the condition code related to the isSNESVi in the BoundsBase constructor.

this is fixed in moose already now. I dont need to do this with an updated moose :)

I recommend you keep moving with this non-optimal adaptivity setup.

[keassyguang]

Thanks. I ll take a look soon.

Thank you very much.

This is probably due to not using the displaced mesh correctly in the code. Should be an easy fix

Hopefully it is.

this is fixed in moose already now. I dont need to do this with an updated moose :)

Good, I didn't update it yet.

I recommend you keep moving with this non-optimal adaptivity setup.

Yes, I can continue my research with the non-optimal adaptivity setup, but I really want to know the time reduction using adaptivity, especially for the large scale 3D models.

[GiudGiud]

These inputs dont run without using your app. I ll have to use a machine on which I can install an external app. I ll be delayed

[keassyguang]

These inputs dont run without using your app. I ll have to use a machine on which I can install an external app. I ll be delayed

Thanks a lot.

I have created another non-working example that doesn't require my app. This example can only run the first two or three steps, but I think it is enough to illustrate the problem as the adaptivity does not work and the calculated gradient jump is also close to zero with the displaced mesh.

Key results:

1. with use_displaced_mesh = true, the adaptivity does not work, gradient jump value close to zero;
2. comment out use_displaced_mesh = true, the adaptivity works but is aborted with a converge issue.

Cannot take square root of a number less than or equal to zero in the calculation of C3_test for the Rashid approximation for the rotation tensor. This zero or negative number may occur when elements become heavily distorted.
To recover, the solution will fail and then be re-attempted with a reduced time step.

  Nonlinear solve did not converge due to DIVERGED_FNORM_NAN iterations 3
 Solve Did NOT Converge!
Aborting as solve did not converge

Input file

[Mesh]
  type = GeneratedMesh
  displacements = 'disp_x disp_y'
  dim = 2
  xmin = 0
  ymin = 0
  xmax = 2
  ymax = 1
  nx = 10
  ny = 5
[]

[GlobalParams]
  displacements = 'disp_x disp_y'
  use_displaced_mesh = true
[]

[Variables]
  [./disp_x]
  [../]
  [./disp_y]
  [../]
[]

[AuxVariables]
  [von_mises]
    order = FIRST
    family = MONOMIAL
  []
[]

[AuxKernels]
  [von_mises]
    type = ADRankTwoScalarAux
    variable = von_mises
    rank_two_tensor = stress
    scalar_type = VonMisesStress
    execute_on = 'INITIAL TIMESTEP_END'
  []
[]

[Kernels]
  [./stress_x]
    type = ADStressDivergenceTensors
    displacements = 'disp_x disp_y'
    component = 0
    variable = disp_x
  [../]
  [./stress_y]
    type = ADStressDivergenceTensors
    displacements = 'disp_x disp_y'
    component = 1
    variable = disp_y
  [../]
[]

[BCs]
  [./fix_bottom_x]
    type = ADDirichletBC
    variable = disp_x
    boundary = bottom
    value = 0
  [../]
  [./fix_bottom_y]
    type = ADDirichletBC
    variable = disp_y
    boundary = bottom
    value = 0
  [../]
  [top_pull_y]
    type = FunctionDirichletBC
    variable = disp_y
    function = 't'
    boundary = 'top'
  []
[]

[Materials]
  [./elasticity]
    type = ADComputeIsotropicElasticityTensor
    poissons_ratio = 0.3
    youngs_modulus = 10e9
  [../]
  [./strain]
    type = ADComputeFiniteStrain
    displacements = 'disp_x disp_y'
  [../]
  [./stress]
    type = ADComputeFiniteStrainElasticStress
  [../]
[]
  
[Executioner]
  type = Transient
  dt = 0.05
  solve_type = 'PJFNK'

  petsc_options_iname = -pc_hypre_type
  petsc_options_value = boomeramg

  dtmin = 0.01
  num_steps = 10
[]

[Outputs]
  exodus = true
[]

[Adaptivity]
  max_h_level = 4
  initial_marker = combo
  marker = combo
  
  [Indicators]
    [jump_von_mises]
      type = GradientJumpIndicator
      variable = von_mises
    []
  []

  [Markers]
    [errorfrac]
      type = ErrorFractionMarker
      indicator = jump_von_mises
      refine = 0.7
      coarsen = 0.2
    []

    [boundary_marker]
      type = BoundaryMarker
      next_to = 'bottom'
      mark = refine
    []

    [boundary_marker_1]
      type = BoundaryMarker
      next_to = 'top'
      mark = refine
    []

    [combo]
      type = ComboMarker
      markers = 'errorfrac'
      # markers = 'boundary_marker boundary_marker_1'
      # markers = 'errorfrac boundary_marker boundary_marker_1'
    []
  []
[]