How to ensure the displaced mesh is used #29699

keassyguang · 2025-01-17T10:23:27Z

keassyguang
Jan 17, 2025

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 · 2025-01-18T21:09:51Z

GiudGiud
Jan 18, 2025
Collaborator

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

Is that an option for your case?

85 replies

keassyguang Mar 10, 2025
Author

Do not comment out the following code. You must set use_displaced_mesh = false to the indicators

But in the input file you provided, I didn't see any use_displaced_mesh = false'. Do you mean by setting use_displaced_mesh = false` directly in the indicators block so that it overrides the global parameter?

[Adaptivity]
  max_h_level = 5
  initial_marker = combo
  marker = combo

  [Indicators]
    [gradient_jump_T]
      block = 1
      type = GradientJumpIndicator
      variable = Temperature
      use_displaced_mesh = false
    []

    [gradient_jump_von_mises]
      block = 1
      type = GradientJumpIndicator
      variable = von_mises
      use_displaced_mesh = false
    []
  []

  [Markers]
    [marker_error_frac_T]
      block = 1
      type = ErrorFractionMarker
      indicator = gradient_jump_T
      coarsen = 0.2
      refine = 0.1
    []

    [marker_error_frac_von_mises]
      block = 1
      type = ErrorFractionMarker
      indicator = gradient_jump_von_mises
      coarsen = 0.2
      refine = 0.3
    []

    [marker_value_range]
      block = 2
      type = ValueRangeMarker
      variable = layerY
      lower_bound = 0
      upper_bound = 50e-6
      third_state = DO_NOTHING
    []

    [combo]
      type = ComboMarker
      markers = 'marker_error_frac_von_mises marker_value_range'
      # markers = 'marker_error_frac_T marker_error_frac_von_mises marker_value_range'
    []
  []
[]

If we set `skip_execution_outside_variable_domain = true' as the global parameter and comment out the convective BCs, we will probably get the error message as in case 1 above.

GiudGiud Mar 10, 2025
Collaborator

Yes for the first item

The second one, if you set that Boolean you do not need to comment out the BCs

GiudGiud Mar 10, 2025
Collaborator

But in the input file you provided, I didn't see any use_displaced_mesh = false'.

I forgot but it s important. The internal side indicators do not support executing on the displaced mesh, but they can execute on the undisplaced one in a simulartion which has a displaced mesh

keassyguang Mar 10, 2025
Author

The second one, if you set that Boolean you do not need to comment out the BCs

Thanks, got it.

I forgot but it s important. The internal side indicators do not support executing on the displaced mesh, but they can execute on the undisplaced one in a simulartion which has a displaced mesh

Many thanks, I will try it tomorrow morning, hope everything goes well as we spent so much time on it.

keassyguang Mar 11, 2025
Author

Unfortunately, there are still a lots of issues of my simulation even though I have updated to the latest moose and your branch. Also, the use_displaced_mesh = false is added to the indicators.

When I use skip_execution_outside_variable_domain = true as the global parameter and use the convective BCs shown as below

[GlobalParams]
  skip_execution_outside_variable_domain = true
[]

[BCs]
  # BCs for heat transfer
  # Left side is convective
  [Temperature_left]
    type = ADConvectiveHeatFluxBC
    T_infinity = 300
    heat_transfer_coefficient = 20   # W/m^2/K
    variable = Temperature
    boundary = 'left'
  []

  # Right side is convective
  [Temperature_right]
    type = ADConvectiveHeatFluxBC
    T_infinity = 300
    heat_transfer_coefficient = 20   # W/m^2/K
    variable = Temperature
    boundary = 'right'
  []

  # Top surface is convective
  [Convective_top]
    type = ADConvectiveHeatFluxBC
    variable = Temperature
    boundary = 'top_active'
    T_infinity = 300.0
    heat_transfer_coefficient = 5    # W/m^2/K
  []

  # Bottom surface is convective
  [Convective_bottom]
    type = ADConvectiveHeatFluxBC
    variable = Temperature
    boundary = 'bottom'
    T_infinity = 300.0
    heat_transfer_coefficient = 20   # W/m^2/K
  []

  # BCs for mechanics
  # Fixed bottom boundary
  [ux_bottom_fix]
    type = DirichletBC
    variable = disp_x
    boundary = 'bottom'
    value = 0.0
  []

  [uy_bottom_fix]
    type = DirichletBC
    variable = disp_y
    boundary = 'bottom'
    value = 0.0
  []
[]

I got errors shown in below. Am I missing something? #29700 is indeed merged

*** ERROR ***
'Temperature_left' of type 'ADConvectiveHeatFluxBC' depends on variable(s) 'Temperature,disp_x,disp_y'. However, that variable does not appear to be defined on (all of) boundary 'left'.

Then, I commented out the Temperature_left and Temperature_right BCs and ran the simulation. The above error has gone, however, it aborted when time=4.0 again with similar error message.

Time Step 40, time = 4, dt = 0.1
WARNING: At least one element took more than 10 iterations to converge in inverse_map()...
Rerun in devel/dbg mode for more details.
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Arguments are incompatible
[0]PETSC ERROR: Incompatible vector local lengths parameter # 1 local size 15533 != parameter # 2 local size 13729
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR:   Option left: name:--timing (no value) source: command line
[0]PETSC ERROR:   Option left: name:-i value: test_thermal_mechanical_with_AMR_moose_developer.i source: command line
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: unknown  GIT Date: unknown
[0]PETSC ERROR: ../thermal_mechanics_test-opt with 1 MPI process(es) and PETSC_ARCH  on IHP-SPD-C0QH6A1 by liug2 Tue Mar 11 09:52:06 2025
[0]PETSC ERROR: Configure options: --with-64-bit-indices --with-cxx-dialect=C++17 --with-debugging=no --with-fortran-bindings=0 --with-mpi=1 --with-openmp=1 --with-strict-petscerrorcode=1 --with-shared-libraries=1 --with-sowing=0 --download-fblaslapack=1 --download-hpddm=1 --download-hypre=1 --download-metis=1 --download-mumps=1 --download-ptscotch=1 --download-parmetis=1 --download-scalapack=1 --download-slepc=1 --download-strumpack=1 --download-superlu_dist=1 --with-hdf5-dir=/home/liug2/miniforge/envs/moose --with-make-np=16 --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --with-x=0 --with-ssl=0 --with-mpi-dir=/home/liug2/miniforge/envs/moose AR=/home/liug2/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-ar RANLIB=/home/liug2/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-ranlib CFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/liug2/miniforge/envs/moose/include -fdebug-prefix-map=/data/civet2/build/_env/conda-bld/moose-mpi_1735973043613/work=/usr/local/src/conda/moose-mpi-base-2024.12.23 -fdebug-prefix-map=/home/liug2/miniforge/envs/moose=/usr/local/src/conda-prefix " CXXFLAGS="-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/liug2/miniforge/envs/moose/include -fdebug-prefix-map=/data/civet2/build/_env/conda-bld/moose-mpi_1735973043613/work=/usr/local/src/conda/moose-mpi-base-2024.12.23 -fdebug-prefix-map=/home/liug2/miniforge/envs/moose=/usr/local/src/conda-prefix  " CPPFLAGS="-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/liug2/miniforge/envs/moose/include " FFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/liug2/miniforge/envs/moose/include -fdebug-prefix-map=/data/civet2/build/_env/conda-bld/moose-mpi_1735973043613/work=/usr/local/src/conda/moose-mpi-base-2024.12.23 -fdebug-prefix-map=/home/liug2/miniforge/envs/moose=/usr/local/src/conda-prefix " FCFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/liug2/miniforge/envs/moose/include -fdebug-prefix-map=/data/civet2/build/_env/conda-bld/moose-mpi_1735973043613/work=/usr/local/src/conda/moose-mpi-base-2024.12.23 -fdebug-prefix-map=/home/liug2/miniforge/envs/moose=/usr/local/src/conda-prefix " LDFLAGS="-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/liug2/miniforge/envs/moose/lib -Wl,-rpath-link,/home/liug2/miniforge/envs/moose/lib -L/home/liug2/miniforge/envs/moose/lib " --prefix=/home/liug2/miniforge/envs/moose/petsc
[0]PETSC ERROR: #1 VecCopyAsync_Private() at /data/civet2/build/_env/conda-bld/moose-petsc_1735974488891/work/src/vec/vec/interface/vector.c:1719
[0]PETSC ERROR: #2 VecCopy() at /data/civet2/build/_env/conda-bld/moose-petsc_1735974488891/work/src/vec/vec/interface/vector.c:1800
libMesh terminating:
Incompatible vector local lengths parameter # 1 local size 15533 != parameter # 2 local size 13729
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

Here is my input file
input file

[Problem]
  type = FEProblem
  kernel_coverage_check = false
  # material_coverage_check = false
  # boundary_restricted_node_integrity_check = false
  # boundary_restricted_elem_integrity_check = false
[]


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


[Mesh]
  displacements = 'disp_x disp_y'
  [gen]
    type = GeneratedMeshGenerator
    dim = 2
    nx = 10
    ny = 2
    xmin = 0
    ymin = 0
    xmax = 8000e-6
    ymax = 1600e-6
  []

  [refine_bottom] #refine the bottom
    type = RefineSidesetGenerator
    input = 'gen'
    boundaries = 'bottom'
    boundary_side = 'primary'
    refinement = 4
    # enable_neighbor_refinement = false
  []

  [active_domain] #the initially active domain
    type = SubdomainBoundingBoxGenerator
    input = 'refine_bottom'
    block_id = 1
    bottom_left = '0 0 0'
    top_right = '8000e-6 50e-6 0'
  []

  [inactive_domain] #the initially inactive domain
    type = SubdomainBoundingBoxGenerator
    input = 'active_domain'
    block_id = 2
    bottom_left = '0 50e-6 0'
    top_right = '8000e-6 1600e-6 0'
  []

  [sideset_top_active]
    type = SideSetsAroundSubdomainGenerator
    input = inactive_domain
    normal = '0 1 0'
    block = 1
    new_boundary = 'top_active' # top boundary of active domain
  []
[]


[Variables]
  # Temperature
  [Temperature]
    block = 1
    order = FIRST
    family = LAGRANGE
    initial_condition = 300.0             # K
  []

  # ADD the displacement variables for mechanics:
  # Displacement variables
  [disp_x]
    block = 1
    # block = '1 2'
    order = FIRST
    family = LAGRANGE
  []

  [disp_y]
    block = 1
    # block = '1 2'
    order = FIRST
    family = LAGRANGE
  []
[]


[AuxVariables]
  # AuxVariabl used for element activation
  [layerY]
    [AuxKernel]
    type = ParsedAux
    use_xyzt = true
    expression = 'y - 50e-6 * (floor(t/4.0) + 1)'
    execute_on = 'INITIAL TIMESTEP_BEGIN'
    []
  []

  # Processor ID
  [processor_id]
    order = CONSTANT
    family = MONOMIAL
  []

  # Von Mises stress
  [von_mises]
    block = 1
    order = FIRST
    family = MONOMIAL
  []
[]


[Kernels]
  # Kernels belonged to the Heat transfer model
  # (k∇T,∇ψ)
  [Heat_conduction]
    block = 1
    type = ADHeatConduction
    variable = Temperature
  []

  # ρCp∂T/∂t
  [Heat_conduction_time_derivative]
    block = 1
    type = ADHeatConductionTimeDerivative
    variable = Temperature
  []

  # Photopolymerization heat
  [Heat_source]
    block = 1
    type = HeatSource
    variable = Temperature
    function = 'heat_source_function'
  []

  # Kernels belonged to the Mechanical model
  # Mechanics kernels
  [stress_x]
    block = 1
    type = ADStressDivergenceTensors
    displacements = 'disp_x disp_y'
    variable = disp_x
    component = 0
    use_displaced_mesh = true
  []

  [stress_y]
    block = 1
    type = ADStressDivergenceTensors
    displacements = 'disp_x disp_y'
    variable = disp_y
    component = 1
    use_displaced_mesh = true
  []
[]


[AuxKernels]
  # Processor ID
  [processor_id_aux]
    type = ProcessorIDAux
    variable = processor_id
    execute_on = timestep_begin
  []

  # Von Mises stress
  [von_mises_aux]
    block = 1
    type = ADRankTwoScalarAux
    variable = von_mises
    rank_two_tensor = stress
    scalar_type = VonMisesStress
    execute_on = 'initial timestep_end'
  []
[]


[Functions]
  [heat_source_function]
    # block = 1
    type = ParsedFunction
    expression = 'if(x >= 3000e-6 & x <= 5000e-6, 0.5e8 * exp((y - 50e-6 * (floor(t/4.0) + 1)) / 200e-6), 0)'
  []
[]


[MeshModifiers]
  [addLayer]
    type = CoupledVarThresholdElementSubdomainModifier
    coupled_var = 'layerY'
    criterion_type = BELOW
    threshold = 0
    subdomain_id = 1
    moving_boundaries = 'top_active'
    moving_boundary_subdomain_pairs = '1 2'
    execute_on = 'INITIAL TIMESTEP_BEGIN'
  []
[]


[Materials]
  # Thermal properties parameters
  [Thermal_properties]
    block = 1
    type = ADGenericConstantMaterial  # Changed to AD version
    prop_names = 'thermal_conductivity specific_heat'
    prop_values = '0.223 1700'
  []

  # Density
  [Density]
    block = 1
    type = ADGenericConstantMaterial
    prop_names = 'density'
    prop_values = 1120              # kg/m^3
  []

  # Dummy property for block 2
  [dummy_mat_inactive]
    block = 2
    type = GenericConstantMaterial
    prop_names = 'dummy_mat'
    prop_values = '0.0'
  []

  [elasticity]
    block = 1
    type = ADComputeIsotropicElasticityTensor
    poissons_ratio = 0.3
    youngs_modulus = 1e8
  []

  [thermal_expansion_strain]
    block = 1
    type = ADComputeThermalExpansionEigenstrain
    stress_free_temperature = 300
    thermal_expansion_coeff = 100e-6
    temperature = Temperature
    eigenstrain_name = eigenstrain
  []

  [strain]
    block = 1
    type = ADComputeFiniteStrain
    displacements = 'disp_x disp_y'
    eigenstrain_names = eigenstrain
  []

  [stress]
    block = 1
    type = ADComputeFiniteStrainElasticStress
  []
[]

[GlobalParams]
  skip_execution_outside_variable_domain = true
[]

[BCs]
  # BCs for heat transfer
  # Left side is convective
  # [Temperature_left]
  #   type = ADConvectiveHeatFluxBC
  #   T_infinity = 300
  #   heat_transfer_coefficient = 20   # W/m^2/K
  #   variable = Temperature
  #   boundary = 'left'
  # []

  # # Right side is convective
  # [Temperature_right]
  #   type = ADConvectiveHeatFluxBC
  #   T_infinity = 300
  #   heat_transfer_coefficient = 20   # W/m^2/K
  #   variable = Temperature
  #   boundary = 'right'
  # []

  # Top surface is convective
  [Convective_top]
    type = ADConvectiveHeatFluxBC
    variable = Temperature
    boundary = 'top_active'
    T_infinity = 300.0
    heat_transfer_coefficient = 5    # W/m^2/K
  []

  # Bottom surface is convective
  [Convective_bottom]
    type = ADConvectiveHeatFluxBC
    variable = Temperature
    boundary = 'bottom'
    T_infinity = 300.0
    heat_transfer_coefficient = 20   # W/m^2/K
  []

  # BCs for mechanics
  # Fixed bottom boundary
  [ux_bottom_fix]
    type = DirichletBC
    variable = disp_x
    boundary = 'bottom'
    value = 0.0
  []

  [uy_bottom_fix]
    type = DirichletBC
    variable = disp_y
    boundary = 'bottom'
    value = 0.0
  []
[]


[Executioner]
  automatic_scaling = true
  line_search = 'none'

  type = Transient
  solve_type = 'PJFNK'

  [TimeIntegrator]
    type = ImplicitEuler
  []

  start_time = 0.0
  end_time = 80.0
  dt = 1.0e-1

  petsc_options_iname = '-pc_type -snes_type -pc_factor_shift_type'
  petsc_options_value = 'lu vinewtonrsls NONZERO'

  # petsc_options_iname = '-pc_type -pc_hypre_type -snes_type'
  # petsc_options_value = 'hypre boomeramg vinewtonrsls'

  nl_abs_tol = 1e-8
[]

[Outputs]
  exodus = true
  file_base = test_AMR_moose_developer
  # time_step_interval = 4

  [console]
    type = Console
    output_linear = true
    output_nonlinear = true
    time_step_interval = 40
  []
[]


[Adaptivity]
  max_h_level = 5
  initial_marker = combo
  marker = combo

  [Indicators]
    [gradient_jump_T]
      block = 1
      type = GradientJumpIndicator
      variable = Temperature
      use_displaced_mesh = false
    []

    [gradient_jump_von_mises]
      block = 1
      type = GradientJumpIndicator
      variable = von_mises
      use_displaced_mesh = false
    []
  []

  [Markers]
    [marker_error_frac_T]
      block = 1
      type = ErrorFractionMarker
      indicator = gradient_jump_T
      coarsen = 0.2
      refine = 0.1
    []

    [marker_error_frac_von_mises]
      block = 1
      type = ErrorFractionMarker
      indicator = gradient_jump_von_mises
      coarsen = 0.2
      refine = 0.3
    []

    [marker_value_range]
      block = 2
      type = ValueRangeMarker
      variable = layerY
      lower_bound = 0
      upper_bound = 50e-6
      third_state = DO_NOTHING
    []

    # [marker_boundary]
    #   type = BoundaryMarker
    #   next_to = 'bottom'
    #   mark = refine
    # []

    [combo]
      type = ComboMarker
      # block = '1 2'
      # markers = 'marker_error_frac_T marker_value_range'
      markers = 'marker_error_frac_von_mises marker_value_range'
      # markers = 'marker_error_frac_T marker_error_frac_von_mises marker_value_range'
      # markers = 'marker_error_frac_T marker_error_frac_von_mises marker_value_range marker_boundary'
    []
  []
[]

It seems that the variable const bool _use_nodal_values; defined in InternalSideIndicator.h isn't used in InternalSideIndicator.C.
Could you please try to run the simulation with one processor (even if it takes some time to reach time=4.0) instead of in parallel? Because the simulation can pass time=4.0 when I run with parallel, but it aborted when I use one processor. In the parallel case, the simulation finally aborted at some point far away from end_time.
I think there might be something wrong with the ComboMarker when the block restriction is used in the Markers block. The current code of ComboMarker seems to ignore the block restriction and treat it as one block (initial). As a result, the combo results become a mess.

    [combo]
      type = ComboMarker
      # block = '1 2'
      markers = 'marker_error_frac_T marker_error_frac_von_mises marker_value_range'
    []

GiudGiud · 2025-03-11T14:09:31Z

GiudGiud
Mar 11, 2025
Collaborator

Am I missing something? #29700 is indeed merged

yes you forgot to turn off the variable boundary integrity checks in the Problem.

70 replies

GiudGiud Apr 24, 2025
Collaborator

Dont use subdomain modification. Vary the material properties instead by making them depend on variable values

keassyguang May 1, 2025
Author

Dont use subdomain modification. Vary the material properties instead by making them depend on variable values

Thank you very much. In this case I would have to solve the whole mesh and it could be very expensive.

I have reviewed our discussions over the last three or four months on this topic. The results below were obtained several months ago without considering the displaced mesh, but the convective heat transfer condition at the moving boundary was considered. However, with the latest MOOSE, the simulation aborted when we used the same input file. I have noticed that both MOOSE and libmesh are updated regularly, will the problems not only come from MOOSE but also from libmesh?

GiudGiud May 2, 2025
Collaborator

It can come from anywhere but it s generally most likely to come from a moose update.

If you can make a minimal example with the commit number when it worked I can take a look at what changed

keassyguang May 3, 2025
Author

Sorry, I forgot the commit number. Where can I find the commit number for the whole history of MOOSE, I think I need to try one by one, September last year to December.

GiudGiud May 3, 2025
Collaborator

You can use git log, with additional arguments like "since" to see the commits from a date range

GiudGiud · 2025-05-08T18:45:46Z

GiudGiud
May 8, 2025
Collaborator

@keassyguang the fix got merged into MOOSE.
Where are you now in terms of problems with the moving boundaries?

5 replies

keassyguang May 12, 2025
Author

Sorry for the late reply, I am travelling.
We are still having problems with the moving boundaries when using the displaced mesh. When the displaced mesh is not used, I can reproduce my previous results. I will do further tests after the 19th of May.

keassyguang May 21, 2025
Author

I updated MOOSE to the latest version and reran our previous model. It failed during the material mapping stage after adaptive mesh refinement. The error message, back trace, and input file are below. Do you have any suggestions on where to look?

Error message

Time Step 13, time = 1.3, dt = 0.1
 Solve Converged!
Segmentation fault (core dumped)

Back trace

*** Info ***
/home/liug2/projects/thermal_mechanics_test/problems_new/moose_developer.i:431: (Adaptivity/Markers/combo/markers):
    Combo marker and markers 'marker_error_frac_T, marker_error_frac_von_mises' do not share the same block restrictions. Markers outside their block restriction will not mark.
Using EXPERIMENTAL Stateful Material Property projection with Adaptivity!
Framework Information:
MOOSE Version:           git commit cc3575724a on 2025-05-19
LibMesh Version:         
PETSc Version:           3.23.0
SLEPc Version:           3.23.0
Current Time:            Wed May 21 16:58:52 2025
Executable Timestamp:    Wed May 21 16:49:46 2025

Input File(s):
  /home/liug2/projects/thermal_mechanics_test/problems_new/moose_developer.i

Checkpoint:
  Wall Time Interval:      Every 3600 s
  User Checkpoint:         Disabled
  # Checkpoints Kept:      2
  Execute On:              TIMESTEP_END 

Parallelism:
  Num Processors:          1
  Num Threads:             1

Mesh: 
  Parallel Type:           replicated
  Mesh Dimension:          2
  Spatial Dimension:       2
  Nodes:                   637
  Elems:                   470
  Max h-Refinement Level:  4
  Num Subdomains:          2

Nonlinear System:
  Num DOFs:                966
  Num Local DOFs:          966
  Variables:               { "Temperature" "disp_x" "disp_y" } 
  Finite Element Types:    "LAGRANGE" 
  Approximation Orders:    "FIRST" 

Auxiliary System:
  Num DOFs:                3167
  Num Local DOFs:          3167
  Num Constrained DOFs:    150
  Local Constrained DOFs:  150
  Variables:               "layerY" "processor_id" "von_mises" { "gradient_jump_T" "gradient_jump_von_mises" 
                             "marker_error_frac_T" "marker_error_frac_von_mises" } { "marker_value_range" 
                             "combo" } 
  Finite Element Types:    "LAGRANGE" "MONOMIAL" "MONOMIAL" "MONOMIAL" "MONOMIAL" 
  Approximation Orders:    "FIRST" "CONSTANT" "FIRST" "CONSTANT" "CONSTANT" 

Execution Information:
  Executioner:             Transient
  TimeStepper:             ConstantDT
  TimeIntegrator(s):       ImplicitEuler
  Solver Mode:             Preconditioned JFNK 
  PETSc Preconditioner:    lu 



Time Step 13, time = 1.3, dt = 0.1
Still Executing
  Finished Computing User Objects                                                        [  5.68 s] [  234 MB]

    Computing Jacobian                                                                   [  9.71 s] [  234 MB]
    Computing Jacobian                                                                   [  9.74 s] [  235 MB]
 Solve Converged!
  Finished Solving                                                                       [ 36.54 s] [  236 MB]
  Computing Markers                                                                      [  5.83 s] [  236 MB]


Assertion `find_side != find_elem->second.end()' failed
Material property does not have side entry
at /home/liug2/projects/moose/framework/build/header_symlinks/MaterialPropertyStorage.h, line 465
Stack frames: 17
0: libMesh::print_trace(std::ostream&)
1: /home/liug2/projects/moose/framework/libmoose-dbg.so.0(+0x213fdbd) [0x7ffff533fdbd]
2: MaterialPropertyStorage::restrictStatefulProps(std::vector<std::pair<unsigned int, QpMap>, std::allocator<std::pair<unsigned int, QpMap> > > const&, std::vector<libMesh::Elem const*, std::allocator<libMesh::Elem const*> > const&, libMesh::QBase const&, libMesh::QBase const&, unsigned int, libMesh::Elem const&, int)
3: ProjectMaterialProperties::onBoundary(libMesh::Elem const*, unsigned int, short, libMesh::Elem const*)
4: ThreadedElementLoopBase<libMesh::StoredRange<__gnu_cxx::__normal_iterator<libMesh::Elem const**, std::vector<libMesh::Elem const*, std::allocator<libMesh::Elem const*> > >, libMesh::Elem const*> >::operator()(libMesh::StoredRange<__gnu_cxx::__normal_iterator<libMesh::Elem const**, std::vector<libMesh::Elem const*, std::allocator<libMesh::Elem const*> > >, libMesh::Elem const*> const&, bool)
5: /home/liug2/projects/moose/framework/libmoose-dbg.so.0(+0x29fa5bd) [0x7ffff5bfa5bd]
6: FEProblemBase::meshChangedHelper(bool)
7: FEProblemBase::adaptMesh()
8: TransientBase::incrementStepOrReject()
9: TransientBase::execute()
10: MooseApp::executeExecutioner()
11: MooseApp::run()
12: /home/liug2/projects/thermal_mechanics_test/thermal_mechanics_test-dbg(+0x7d92) [0x55555555bd92]
13: main
14: /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7fffdfe29d90]
15: __libc_start_main
16: /home/liug2/projects/thermal_mechanics_test/thermal_mechanics_test-dbg(+0x606e) [0x55555555a06e]
[0] /home/liug2/projects/moose/framework/build/header_symlinks/MaterialPropertyStorage.h, line 465, compiled May 21 2025 at 16:41:37

Thread 1 "thermal_mechani" hit Breakpoint 1, 0x00007fffe034a4f0 in PMPI_Abort () from /home/liug2/miniforge/envs/moose/lib/libmpi.so.12
(gdb) bt
#0  0x00007fffe034a4f0 in PMPI_Abort () from /home/liug2/miniforge/envs/moose/lib/libmpi.so.12
#1  0x00007ffff533fe16 in MaterialPropertyStorage::props (this=0x555555889590, elem=0x555557371560, side=2, state=0)
    at /home/liug2/projects/moose/framework/build/header_symlinks/MaterialPropertyStorage.h:465
#2  0x00007ffff534bd02 in MaterialPropertyStorage::restrictStatefulProps (this=0x555555889590, coarsening_map=..., coarsened_element_children=..., qrule=..., 
    qrule_face=..., tid=0, elem=..., input_side=2) at /home/liug2/projects/moose/framework/src/materials/MaterialPropertyStorage.C:262
#3  0x00007ffff409a872 in ProjectMaterialProperties::onBoundary (this=0x7fffffffb040, elem=0x555555dcaf10, side=2, bnd_id=4)
    at /home/liug2/projects/moose/framework/src/loops/ProjectMaterialProperties.C:197
#4  0x00007ffff41827d2 in ThreadedElementLoopBase<libMesh::StoredRange<__gnu_cxx::__normal_iterator<libMesh::Elem const**, std::vector<libMesh::Elem const*, std::allocator<libMesh::Elem const*> > >, libMesh::Elem const*> >::operator() (this=0x7fffffffb040, range=..., bypass_threading=false)
    at /home/liug2/projects/moose/framework/build/header_symlinks/ThreadedElementLoopBase.h:277
#5  0x00007ffff5bfa5bd in libMesh::Threads::parallel_reduce<libMesh::StoredRange<__gnu_cxx::__normal_iterator<libMesh::Elem const**, std::vector<libMesh::Elem const*, std::allocator<libMesh::Elem const*> > >, libMesh::Elem const*>, ProjectMaterialProperties> (range=..., body=...)
    at /home/liug2/miniforge/envs/moose/libmesh/include/libmesh/threads_pthread.h:367
#6  0x00007ffff5bbe096 in FEProblemBase::meshChangedHelper (this=0x555555de11b0, intermediate_change=true)
    at /home/liug2/projects/moose/framework/src/problems/FEProblemBase.C:8108
#7  0x00007ffff5bbb431 in FEProblemBase::adaptMesh (this=0x555555de11b0) at /home/liug2/projects/moose/framework/src/problems/FEProblemBase.C:7915
#8  0x00007ffff5e10887 in TransientBase::incrementStepOrReject (this=0x555555f1e870) at /home/liug2/projects/moose/framework/src/executioners/TransientBase.C:344
#9  0x00007ffff5e0f93f in TransientBase::execute (this=0x555555f1e870) at /home/liug2/projects/moose/framework/src/executioners/TransientBase.C:283
#10 0x00007ffff4e0da00 in MooseApp::executeExecutioner (this=0x55555584ea20) at /home/liug2/projects/moose/framework/src/base/MooseApp.C:1678
#11 0x00007ffff4e14e69 in MooseApp::run (this=0x55555584ea20) at /home/liug2/projects/moose/framework/src/base/MooseApp.C:2062
#12 0x000055555555bd92 in Moose::main<ThermalMechanicsTestTestApp> (argc=3, argv=0x7fffffffc148)
    at /home/liug2/projects/moose/framework/build/header_symlinks/MooseMain.h:41
#13 0x000055555555b2bb in main (argc=3, argv=0x7fffffffc148) at /home/liug2/projects/thermal_mechanics_test/src/main.C:17

Input file

[Problem]
    type = FEProblem
    kernel_coverage_check = false
    # material_coverage_check = false
    # boundary_restricted_node_integrity_check = false
    # boundary_restricted_elem_integrity_check = false
  []
  
  
  [GlobalParams]
    displacements = 'disp_x disp_y'
    use_displaced_mesh = true
    skip_execution_outside_variable_domain = true
  []

  
  [Mesh]
    displacements = 'disp_x disp_y'
    [gen]
      type = GeneratedMeshGenerator
      dim = 2
      nx = 10
      ny = 2
      xmin = 0
      ymin = 0
      xmax = 8000e-6
      ymax = 1600e-6
    []
  
    [refine_bottom] #refine the bottom
      type = RefineSidesetGenerator
      input = 'gen'
      boundaries = 'bottom'
      boundary_side = 'primary'
      refinement = 4
      # enable_neighbor_refinement = false
    []
  
    [active_domain] #the initially active domain
      type = SubdomainBoundingBoxGenerator
      input = 'refine_bottom'
      block_id = 1
      bottom_left = '0 0 0'
      top_right = '8000e-6 50e-6 0'
    []
  
    [inactive_domain] #the initially inactive domain
      type = SubdomainBoundingBoxGenerator
      input = 'active_domain'
      block_id = 2
      bottom_left = '0 50e-6 0'
      top_right = '8000e-6 1600e-6 0'
    []
  
    [sideset_top_active]
      type = SideSetsAroundSubdomainGenerator
      input = inactive_domain
      normal = '0 1 0'
      block = 1
      new_boundary = 'top_active' # top boundary of active domain
    []
  []
  
  
  [Variables]
    # Temperature
    [Temperature]
      block = 1
      order = FIRST
      family = LAGRANGE
      initial_condition = 300.0             # K
    []
  
    # ADD the displacement variables for mechanics:
    # Displacement variables
    [disp_x]
      block = 1
      # block = '1 2'
      order = FIRST
      family = LAGRANGE
    []
  
    [disp_y]
      block = 1
      # block = '1 2'
      order = FIRST
      family = LAGRANGE
    []
  []
  
  
  [AuxVariables]
    # AuxVariabl used for element activation
    [layerY]
      [AuxKernel]
      type = ParsedAux
      use_xyzt = true
      expression = 'y - 50e-6 * (floor(t/4.0) + 1)'
      execute_on = 'INITIAL TIMESTEP_BEGIN'
      []
    []
  
    # Processor ID
    [processor_id]
      order = CONSTANT
      family = MONOMIAL
    []
  
    # Von Mises stress
    [von_mises]
      block = 1
      order = FIRST
      family = MONOMIAL
    []
  []
  
  
  [Kernels]
    # Kernels belonged to the Heat transfer model
    # (k∇T,∇ψ)
    [Heat_conduction]
      block = 1
      type = ADHeatConduction
      variable = Temperature
    []
  
    # ρCp∂T/∂t
    [Heat_conduction_time_derivative]
      block = 1
      type = ADHeatConductionTimeDerivative
      variable = Temperature
    []
  
    # Photopolymerization heat
    [Heat_source]
      block = 1
      type = HeatSource
      variable = Temperature
      function = 'heat_source_function'
    []
  
    # Kernels belonged to the Mechanical model
    # Mechanics kernels
    [stress_x]
      block = 1
      type = ADStressDivergenceTensors
      displacements = 'disp_x disp_y'
      variable = disp_x
      component = 0
      use_displaced_mesh = true
    []
  
    [stress_y]
      block = 1
      type = ADStressDivergenceTensors
      displacements = 'disp_x disp_y'
      variable = disp_y
      component = 1
      use_displaced_mesh = true
    []
  []
  
  
  [AuxKernels]
    # Processor ID
    [processor_id_aux]
      type = ProcessorIDAux
      variable = processor_id
      execute_on = timestep_begin
    []
  
    # Von Mises stress
    [von_mises_aux]
      block = 1
      type = ADRankTwoScalarAux
      variable = von_mises
      rank_two_tensor = stress
      scalar_type = VonMisesStress
      execute_on = 'initial timestep_end'
    []
  []
  
  
  [Functions]
    [heat_source_function]
      # block = 1
      type = ParsedFunction
      expression = 'if(x >= 3000e-6 & x <= 5000e-6, 0.5e8 * exp((y - 50e-6 * (floor(t/4.0) + 1)) / 200e-6), 0)'
    []
  []
  
  
  [MeshModifiers]
    [addLayer]
      type = CoupledVarThresholdElementSubdomainModifier
      coupled_var = 'layerY'
      criterion_type = BELOW
      threshold = 0
      subdomain_id = 1
      moving_boundaries = 'top_active'
      moving_boundary_subdomain_pairs = '1 2'
      execute_on = 'INITIAL TIMESTEP_BEGIN'
    []
  []
  
  
  [Materials]
    # Thermal properties parameters
    [Thermal_properties]
      block = 1
      type = ADGenericConstantMaterial  # Changed to AD version
      prop_names = 'thermal_conductivity specific_heat'
      prop_values = '0.223 1700'
    []
  
    # Density
    [Density]
      block = 1
      type = ADGenericConstantMaterial
      prop_names = 'density'
      prop_values = 1120              # kg/m^3
    []
  
    # Dummy property for block 2
    [dummy_mat_inactive]
      block = 2
      type = GenericConstantMaterial
      prop_names = 'dummy_mat'
      prop_values = '0.0'
    []
  
    [elasticity]
      block = 1
      type = ADComputeIsotropicElasticityTensor
      poissons_ratio = 0.3
      youngs_modulus = 1e8
    []
  
    [thermal_expansion_strain]
      block = 1
      type = ADComputeThermalExpansionEigenstrain
      stress_free_temperature = 300
      thermal_expansion_coeff = 100e-6
      temperature = Temperature
      eigenstrain_name = eigenstrain
    []
  
    [strain]
      block = 1
      type = ADComputeFiniteStrain
      displacements = 'disp_x disp_y'
      eigenstrain_names = eigenstrain
    []
  
    [stress]
      block = 1
      type = ADComputeFiniteStrainElasticStress
    []
  []
  
  [BCs]
    # BCs for heat transfer
    # Left side is convective
    # [Temperature_left]
    #   type = ADConvectiveHeatFluxBC
    #   T_infinity = 300
    #   heat_transfer_coefficient = 20   # W/m^2/K
    #   variable = Temperature
    #   boundary = 'left'
    # []
  
    # # Right side is convective
    # [Temperature_right]
    #   type = ADConvectiveHeatFluxBC
    #   T_infinity = 300
    #   heat_transfer_coefficient = 20   # W/m^2/K
    #   variable = Temperature
    #   boundary = 'right'
    # []
  
    # Top surface is convective
    [Convective_top]
      type = ADConvectiveHeatFluxBC
      variable = Temperature
      boundary = 'top_active'
      T_infinity = 300.0
      heat_transfer_coefficient = 5    # W/m^2/K
    []
  
    # [DirichletBC_top]
    #     type = DirichletBC
    #     variable = Temperature
    #     boundary = 'top_active'
    #     value = 330.0
    #     # use_displaced_mesh = false
    #   []

    # Bottom surface is convective
    [Convective_bottom]
      type = ADConvectiveHeatFluxBC
      variable = Temperature
      boundary = 'bottom'
      T_infinity = 300.0
      heat_transfer_coefficient = 20   # W/m^2/K
    []
  
    # BCs for mechanics
    # Fixed bottom boundary
    [ux_bottom_fix]
      type = DirichletBC
      variable = disp_x
      boundary = 'bottom'
      value = 0.0
    []
  
    [uy_bottom_fix]
      type = DirichletBC
      variable = disp_y
      boundary = 'bottom'
      value = 0.0
    []
  []
  
  
  [Executioner]
    automatic_scaling = true
    line_search = 'none'
  
    type = Transient
    solve_type = 'PJFNK'
  
    [TimeIntegrator]
      type = ImplicitEuler
    []
  
    start_time = 0.0
    end_time = 80.0
    dt = 1.0e-1
  
    petsc_options_iname = '-pc_type -snes_type -pc_factor_shift_type'
    petsc_options_value = 'lu vinewtonrsls NONZERO'
  
    # petsc_options_iname = '-pc_type -pc_hypre_type -snes_type'
    # petsc_options_value = 'hypre boomeramg vinewtonrsls'
  
    nl_abs_tol = 1e-8
  []
  
  [Outputs]
    exodus = true
    file_base = test_AMR_moose_developer
    # time_step_interval = 4
  
    [console]
      type = Console
      output_linear = true
      output_nonlinear = true
      time_step_interval = 40
    []
  []
  
  
  [Adaptivity]
    max_h_level = 5
    initial_marker = combo
    marker = combo
  
    [Indicators]
      [gradient_jump_T]
        block = 1
        type = GradientJumpIndicator
        variable = Temperature
        use_displaced_mesh = false
      []
  
      [gradient_jump_von_mises]
        block = 1
        type = GradientJumpIndicator
        variable = von_mises
        use_displaced_mesh = false
      []
    []
  
    [Markers]
      [marker_error_frac_T]
        block = 1
        type = ErrorFractionMarker
        indicator = gradient_jump_T
        coarsen = 0.2
        refine = 0.1
      []
  
      [marker_error_frac_von_mises]
        block = 1
        type = ErrorFractionMarker
        indicator = gradient_jump_von_mises
        coarsen = 0.2
        refine = 0.3
      []
  
      [marker_value_range]
        # block = '2'
        type = ValueRangeMarker
        variable = layerY
        lower_bound = -0e-6
        upper_bound = 50e-6
        third_state = DO_NOTHING
      []
  
      [combo]
        type = ComboMarker
        markers = 'marker_error_frac_T marker_error_frac_von_mises marker_value_range'
      []
    []
  []

GiudGiud May 21, 2025
Collaborator

hello

my guess is that you are using a material property in a boundary condition on a boundary near which the material property is not defined due to its block restriction.
since it's a stateful property it's one of the mechanical ones.

But the only BCs using material properties are for temperature.
Maybe try to switch these BCs to something that uses a constant instead of a material property, and see if the error goes away.

GiudGiud May 21, 2025
Collaborator

also please try to set use-displaced_mesh = false to the ADConvectiveHeatFluxBC.

keassyguang May 22, 2025
Author

also please try to set use-displaced_mesh = false to the ADConvectiveHeatFluxBC.

The same result as we didn't set.

keassyguang · 2025-05-22T11:23:58Z

keassyguang
May 22, 2025
Author

my guess is that you are using a material property in a boundary condition on a boundary near which the material property is not defined due to its block restriction.
since it's a stateful property it's one of the mechanical ones.

Most of the variables, kernels, and materials are only defined in Block 1 because the problem only needs to be solved in the active domain. I have checked the input file again, and everything appears to be defined correctly.

Maybe try to switch these BCs to something that uses a constant instead of a material property, and see if the error goes away.

I removed the ADConvectiveHeatFluxBC BCs on the moving boundary and ran the simulation. The simulation aborted after several hundred steps. I also have tried other cases.

The convective BCs were considered.

Modifying the computational domain to a smaller one, the simulation can be run successfully.
Modify the threshold of the markers; sometimes the simulation can be run successfully.
Try using different CPUs in parallel or a single CPU. Sometimes the simulation is successful and sometimes it fails.
Restricting indicators and markers to block 1 seems to make it easier to run successfully.

In this simple example, we can sometimes run it successfully and sometimes we cannot. However, when I try these approaches with my own app, the simulation always fails to run.

Here is the input file I tested which can be run successfully with 20 CPUs in parallel.

[Problem]
  type = FEProblem
  kernel_coverage_check = false
  material_coverage_check = false
  boundary_restricted_node_integrity_check = false
  boundary_restricted_elem_integrity_check = false
[]


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


[Mesh]
  displacements = 'disp_x disp_y'
  [gen]
    type = GeneratedMeshGenerator
    dim = 2
    nx = 10
    ny = 2
    xmin = 0
    ymin = 0
    xmax = 8000e-6
    ymax = 1600e-6
  []

  [refine_bottom] #refine the bottom
    type = RefineSidesetGenerator
    input = 'gen'
    boundaries = 'bottom'
    boundary_side = 'primary'
    refinement = 4
    enable_neighbor_refinement = false
  []

  [active_domain] #the initially active domain
    type = SubdomainBoundingBoxGenerator
    input = 'refine_bottom'
    block_id = 1
    bottom_left = '0 0 0'
    top_right = '8000e-6 50e-6 0'
  []

  [inactive_domain] #the initially inactive domain
    type = SubdomainBoundingBoxGenerator
    input = 'active_domain'
    block_id = 2
    bottom_left = '0 50e-6 0'
    top_right = '8000e-6 1600e-6 0'
  []

  [sideset_top_active]
    type = SideSetsAroundSubdomainGenerator
    input = inactive_domain
    normal = '0 1 0'
    block = 1
    new_boundary = 'top_active' # top boundary of active domain
  []
[]


[Variables]
  # Temperature
  [Temperature]
    block = 1
    order = FIRST
    family = LAGRANGE
    initial_condition = 300.0             # K
  []

  # ADD the displacement variables for mechanics:
  # Displacement variables
  [disp_x]
    block = 1
    # block = '1 2'
    order = FIRST
    family = LAGRANGE
  []

  [disp_y]
    block = 1
    # block = '1 2'
    order = FIRST
    family = LAGRANGE
  []
[]


[AuxVariables]
  # AuxVariabl used for element activation
  [layerY]
    block = '1 2'
    [AuxKernel]
    type = ParsedAux
    use_xyzt = true
    expression = 'y - 50e-6 * (floor(t/4.00001) + 1)'
    execute_on = 'INITIAL TIMESTEP_BEGIN'
    []
  []

  # AuxVariable used for bounds control
  [bounds_dummy]
    # block = 1
    block = '1 2'
    order = FIRST
    family = LAGRANGE
  []

  # Processor ID
  [processor_id]
    order = CONSTANT
    family = MONOMIAL
  []

  # Von Mises stress
  [von_mises]
    block = 1
    order = FIRST
    family = MONOMIAL
  []
[]


[Kernels]
  # Kernels belonged to the Heat transfer model
  # (k∇T,∇ψ)
  [Heat_conduction]
    block = 1
    type = ADHeatConduction
    variable = Temperature
  []

  # ρCp∂T/∂t
  [Heat_conduction_time_derivative]
    block = 1
    type = ADHeatConductionTimeDerivative
    variable = Temperature
  []

  # Photopolymerization heat
  [Heat_source]
    block = 1
    type = HeatSource
    variable = Temperature
    function = 'heat_source_function'
  []

  # Kernels belonged to the Mechanical model
  # Mechanics kernels
  [stress_x]
    block = 1
    type = ADStressDivergenceTensors
    displacements = 'disp_x disp_y'
    variable = disp_x
    component = 0
    # use_displaced_mesh = true
  []

  [stress_y]
    block = 1
    type = ADStressDivergenceTensors
    displacements = 'disp_x disp_y'
    variable = disp_y
    component = 1
    # use_displaced_mesh = true
  []
[]


[AuxKernels]
  # Processor ID
  [processor_id_aux]
    type = ProcessorIDAux
    variable = processor_id
    execute_on = timestep_begin
  []

  # Von Mises stress
  [von_mises_aux]
    block = 1
    type = ADRankTwoScalarAux
    variable = von_mises
    rank_two_tensor = stress
    scalar_type = VonMisesStress
    execute_on = 'initial timestep_end'
  []
[]


[Functions]
  [heat_source_function]
    # block = 1
    type = ParsedFunction
    expression = 'if(x >= 3000e-6 & x <= 5000e-6, 0.5e8 * exp((y - 50e-6 * (floor(t/4.00001) + 1)) / 200e-6), 0)'
  []
[]


[MeshModifiers]
  [addLayer]
    type = CoupledVarThresholdElementSubdomainModifier
    coupled_var = 'layerY'
    criterion_type = BELOW
    threshold = 0
    subdomain_id = 1
    moving_boundaries = 'top_active'
    moving_boundary_subdomain_pairs = '1 2'
    # execute_on = 'TIMESTEP_BEGIN'
    # execute_on = 'TIMESTEP_END'
    execute_on = 'INITIAL TIMESTEP_BEGIN'
    execution_order_group = 1
  []

  # [side_updater]
  #   type                 = SidesetBetweenSubdomainUpdater
  #   # type                 = SidesetAroundSubdomainUpdater
  #   inner_subdomains     = '1'
  #   outer_subdomains     = '2'
  #   update_sideset_name  = 'top_active'
  #   execute_on = 'INITIAL TIMESTEP_BEGIN'
  #   # execute_on = 'TIMESTEP_BEGIN'
  #   # execute_on = 'TIMESTEP_END'
  #   execution_order_group = 2
  # []
[]


[Materials]
  # Thermal properties parameters
  [Thermal_properties]
    block = 1
    type = ADGenericConstantMaterial  # Changed to AD version
    prop_names = 'thermal_conductivity specific_heat'
    prop_values = '0.223 1700'
  []

  # Density
  [Density]
    block = 1
    type = ADGenericConstantMaterial
    prop_names = 'density'
    prop_values = 1120              # kg/m^3
  []

  # Dummy property for block 2
  [dummy_mat_inactive]
    block = 2
    type = GenericConstantMaterial
    prop_names = 'dummy_mat'
    prop_values = '0.0'
  []

  [elasticity]
    block = 1
    type = ADComputeIsotropicElasticityTensor
    poissons_ratio = 0.3
    youngs_modulus = 1e8
  []

  [thermal_expansion_strain]
    block = 1
    type = ADComputeThermalExpansionEigenstrain
    stress_free_temperature = 300
    thermal_expansion_coeff = 100e-6
    temperature = Temperature
    eigenstrain_name = eigenstrain
  []

  [strain]
    block = 1
    type = ADComputeFiniteStrain
    displacements = 'disp_x disp_y'
    eigenstrain_names = eigenstrain
  []

  [stress]
    block = 1
    type = ADComputeFiniteStrainElasticStress
  []
[]

[Bounds]
  # Bounds of initiator concentration
  [T_upper_bound]
    block = 1
    # block = '1 2'
    type = ConstantBounds
    variable = bounds_dummy
    bounded_variable = Temperature
    bound_type = upper
    bound_value = 600           # K
  []
  [T_lower_bound]
    block = 1
    # block = '1 2'
    type = ConstantBounds
    variable = bounds_dummy
    bounded_variable = Temperature
    bound_type = lower
    bound_value = 300
  []
[]


[BCs]
  # BCs for heat transfer
  # Left side is convective
  [Temperature_left]
    type = ADConvectiveHeatFluxBC
    T_infinity = 300
    heat_transfer_coefficient = 20   # W/m^2/K
    variable = Temperature
    boundary = 'left'
  []

  # Right side is convective
  [Temperature_right]
    type = ADConvectiveHeatFluxBC
    T_infinity = 300
    heat_transfer_coefficient = 20   # W/m^2/K
    variable = Temperature
    boundary = 'right'
  []

  # Top surface is convective
  [Convective_top]
    type = ADConvectiveHeatFluxBC
    variable = Temperature
    boundary = 'top_active'
    T_infinity = 300.0
    heat_transfer_coefficient = 5    # W/m^2/K
    # use_displaced_mesh = false
  []
  # [DirichletBC_top]
  #   type = DirichletBC
  #   variable = Temperature
  #   boundary = 'top_active'
  #   value = 330.0
  #   # use_displaced_mesh = false
  # []

  # Bottom surface is convective
  [Convective_bottom]
    type = ADConvectiveHeatFluxBC
    variable = Temperature
    boundary = 'bottom'
    T_infinity = 300.0
    heat_transfer_coefficient = 20   # W/m^2/K
  []

  # BCs for mechanics
  # Fixed bottom boundary
  [ux_bottom_fix]
    type = DirichletBC
    variable = disp_x
    boundary = 'bottom'
    value = 0.0
  []

  [uy_bottom_fix]
    type = DirichletBC
    variable = disp_y
    boundary = 'bottom'
    value = 0.0
  []
[]


[Executioner]
  automatic_scaling = true
  line_search = 'none'

  type = Transient
  solve_type = 'PJFNK'

  [TimeIntegrator]
    type = ImplicitEuler
  []

  start_time = 0.0
  end_time = 80.0
  dt = 1.0e-1

  petsc_options_iname = '-pc_type -snes_type -pc_factor_shift_type'
  petsc_options_value = 'lu vinewtonrsls NONZERO'

  # petsc_options_iname = '-pc_type -pc_hypre_type -snes_type'
  # petsc_options_value = 'hypre boomeramg vinewtonrsls'

  nl_abs_tol = 1e-12
[]

[Outputs]
  exodus = true
  # file_base = test_AMR_moose_developer_combo_with_T_BCs
  file_base = bbb
  # time_step_interval = 4

  # [./exodus]
  #   type = Exodus
  #   file_base = failed_output
  #   execute_on = 'TIMESTEP_END FAILED'
  # [../]

  [console]
    type = Console
    output_linear = true
    output_nonlinear = true
    time_step_interval = 40
  []
[]


[Adaptivity]
  max_h_level = 5
  initial_marker = combo
  marker = combo

  [Indicators]
    [gradient_jump_T]
      block = 1
      type = GradientJumpIndicator
      variable = Temperature
      use_displaced_mesh = false
    []

    [gradient_jump_von_mises]
      block = 1
      type = GradientJumpIndicator
      variable = von_mises
      use_displaced_mesh = false
    []
  []

  [Markers]
    [marker_error_frac_T]
      block = 1
      type = ErrorFractionMarker
      indicator = gradient_jump_T
      # coarsen = 0.3
      # refine = 0.6
      # coarsen = 0
      coarsen = 0.5
      refine = 0.2
    []

    [marker_error_frac_von_mises]
      block = 1
      type = ErrorFractionMarker
      indicator = gradient_jump_von_mises
      # coarsen = 0.3
      # refine = 0.6
      # coarsen = 0
      coarsen = 0.5
      refine = 0.2
    []

    [marker_value_range]
      block = '1'
      type = ValueRangeMarker
      variable = layerY
      lower_bound = -50e-6
      # lower_bound = 0
      upper_bound = 0e-6
      third_state = DO_NOTHING
    []

    # [marker_boundary]
    #   type = BoundaryMarker
    #   next_to = 'bottom'
    #   mark = refine
    # []

    # [marker_boundary]
    #   block = 1
    #   type = BoundaryMarker
    #   next_to = 'top_active'
    #   mark = refine
    # []

    # [marker_boundary_preserve]
    #   block = 1
    #   type = BoundaryPreservedMarker
    #   preserved_boundary = 'top_active'
    #   marker = 'marker_error_frac_von_mises'
    # []

    [combo]
      type = ComboMarker
      block = '1'
      # markers = 'marker_error_frac_T marker_value_range'
      # markers = 'marker_error_frac_von_mises marker_value_range'
      markers = 'marker_error_frac_T marker_error_frac_von_mises marker_value_range'
      # markers = 'marker_error_frac_T marker_error_frac_von_mises marker_value_range marker_boundary'

      # markers = 'marker_error_frac_T marker_error_frac_von_mises marker_boundary'

      # markers = 'marker_error_frac_T marker_error_frac_von_mises marker_boundary_preserve'
      # markers = 'marker_error_frac_T marker_error_frac_von_mises marker_boundary marker_boundary_preserve'
      # markers = 'marker_error_frac_T marker_error_frac_von_mises marker_value_range marker_boundary_preserve'
    []
  []
[]

Here is a gif showing the mesh change.

46 replies

GiudGiud Oct 27, 2025
Collaborator

weird. Well you can always output the dofmap instead (in Outputs) it has the number of DoFs.
something else about this PP must be off

keassyguang Oct 27, 2025
Author

Well you can always output the dofmap instead (in Outputs) it has the number of DoFs.

Thank you. It works, but it would be better if we could output the DOFs of NL, AUX and ALL in one CSV file.

keassyguang Nov 1, 2025
Author

Hi @GiudGiud,
Even after updating to the latest Moose, I still haven't solved the mesh clone issue. No matter what the number I set for the refinement parameter using the RefineSidesetGenerator, the debug mode would throw the same error. I checked the past error reports and found that this has been happening for six months.

I also checked line 109 of the replicated_mesh.h file in my Macbook, as indicated by the backtrace information, to see where the issue might have arisen.
/projects/moose/libmesh/include/mesh

lines 105-111:

  virtual std::unique_ptr<MeshBase> clone () const override
  { return std::make_unique<ReplicatedMesh>(*this); }

  /**
   * Destructor.
   */
  virtual ~ReplicatedMesh();

In this case, there should be no problem with debug mode, since line 109 has been commented out.

However, when I checked the libmesh repository from
https://github.com/libMesh/libmesh/blob/5e6cdb491a6cb72a9b87c05e434303afcff5d0a1/include/mesh/replicated_mesh.h

lines 105-112

virtual std::unique_ptr<MeshBase> clone () const override
  {
    auto returnval = std::make_unique<ReplicatedMesh>(*this);
#ifdef DEBUG
    libmesh_assert(*returnval == *this);
#endif
    return returnval;
  }

I'm really confused about how replicated_mesh.h works in Moose. I am wondering if there is a way to comment out libmesh_assert(*returnVal == *this); and recompile libmesh so that I can bypass this issue and continue debugging.

keassyguang Nov 12, 2025
Author

I just generated a mesh with refinements=5 and did not get an error. Did you update the dbg binary as well?

Hi @GiudGiud,
Can you try the below input file? You will need to turn on the heat transfer and solid mechanics modules to run.

[Problem]
  type = FEProblem
  kernel_coverage_check = false
  material_coverage_check = false
  boundary_restricted_node_integrity_check = false
  boundary_restricted_elem_integrity_check = false
[]


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


[Mesh]
  displacements = 'disp_x disp_y'
  [gen]
    type = GeneratedMeshGenerator
    dim = 2
    nx = 6
    ny = 2
    xmin = 0
    ymin = 0
    xmax = 4800e-6
    ymax = 1600e-6
  []

  [refine_bottom] #refine the bottom
    type = RefineSidesetGenerator
    input = 'gen'
    boundaries = 'bottom'
    boundary_side = 'primary'
    refinement = 5
  []

  [active_domain] #the initially active domain
    type = SubdomainBoundingBoxGenerator
    input = 'refine_bottom'
    block_id = 1
    bottom_left = '0 0 0'
    top_right = '4800e-6 50e-6 0'
  []

  [inactive_domain] #the initially inactive domain
    type = SubdomainBoundingBoxGenerator
    input = 'active_domain'
    block_id = 2
    bottom_left = '0 50e-6 0'
    top_right = '4800e-6 1600e-6 0'
  []

  [sideset_top_active]
    type = SideSetsAroundSubdomainGenerator
    input = inactive_domain
    normal = '0 1 0'
    block = 1
    new_boundary = 'top_active' # top boundary of active domain
  []
[]


[Variables]
  # Temperature
  [Temperature]
    block = 1
    order = FIRST
    family = LAGRANGE
    initial_condition = 300.0             # K
  []

  # ADD the displacement variables for mechanics:
  # Displacement variables z
  [disp_x]
    block = 1
    order = FIRST
    family = LAGRANGE
  []

  [disp_y]
    block = 1
    order = FIRST
    family = LAGRANGE
  []
[]


[AuxVariables]
  # AuxVariabl used for element activation
  [layerY]
    [AuxKernel]
      type = ParsedAux
      use_xyzt = true
      expression = 'y - 50e-6 * (floor(t/2.0) + 1)'
      execute_on = 'INITIAL TIMESTEP_BEGIN'
    []
  []

  # Processor ID
  [processor_id]
    order = CONSTANT
    family = MONOMIAL
  []

  # Von Mises stress
  [von_mises]
    block = 1
    order = FIRST
    family = MONOMIAL
  []
[]


[Kernels]
  # Kernels belonged to the Heat transfer model
  # (k∇T,∇ψ)
  [Heat_conduction]
    block = 1
    type = ADHeatConduction
    variable = Temperature
  []

  # ρCp∂T/∂t
  [Heat_conduction_time_derivative]
    block = 1
    type = ADHeatConductionTimeDerivative
    variable = Temperature
  []

  # Photopolymerization heat
  [Heat_source]
    block = 1
    type = HeatSource
    variable = Temperature
    function = 'heat_source_function'
  []

  # Kernels belonged to the Mechanical model
  # Mechanics kernels
  [stress_x]
    block = 1
    type = ADStressDivergenceTensors
    displacements = 'disp_x disp_y'
    variable = disp_x
    component = 0
    use_displaced_mesh = true
  []

  [stress_y]
    block = 1
    type = ADStressDivergenceTensors
    displacements = 'disp_x disp_y'
    variable = disp_y
    component = 1
    use_displaced_mesh = true
  []
[]


[AuxKernels]
  # Processor ID
  [processor_id_aux]
    type = ProcessorIDAux
    variable = processor_id
    execute_on = timestep_begin
  []

  # Von Mises stress
  [von_mises_aux]
    block = 1
    type = ADRankTwoScalarAux
    variable = von_mises
    rank_two_tensor = stress
    scalar_type = VonMisesStress
    execute_on = 'initial timestep_end'
  []
[]


[Functions]
  [heat_source_function]
    type = ParsedFunction
    expression = 'if(x >= 1800e-6 & x <= 3000e-6, 0.5e8 * exp((y - 50e-6 * (floor(t/2.0) + 1)) / 200e-6), 0)'
  []
[]


[MeshModifiers]
  [addLayer]
    type = CoupledVarThresholdElementSubdomainModifier
    coupled_var = 'layerY'
    criterion_type = BELOW
    threshold = 0
    subdomain_id = 1
    moving_boundaries = 'top_active'
    moving_boundary_subdomain_pairs = '1 2'
    execute_on = 'INITIAL TIMESTEP_BEGIN'
    execution_order_group = 0
  []
[]


[Materials]
  # Thermal properties parameters
  [Thermal_properties]
    block = 1
    type = ADGenericConstantMaterial  # Changed to AD version
    prop_names = 'thermal_conductivity specific_heat'
    prop_values = '0.223 1700'
  []

  # Density
  [Density]
    block = 1
    type = ADGenericConstantMaterial
    prop_names = 'density'
    prop_values = 1120              # kg/m^3
  []

  # Dummy property for block 2
  [dummy_mat_inactive]
    block = 2
    type = GenericConstantMaterial
    prop_names = 'dummy_mat'
    prop_values = '0.0'
  []

  [elasticity]
    block = 1
    type = ADComputeIsotropicElasticityTensor
    poissons_ratio = 0.3
    youngs_modulus = 1e8
  []

  [thermal_expansion_strain]
    block = 1
    type = ADComputeThermalExpansionEigenstrain
    stress_free_temperature = 300
    thermal_expansion_coeff = 100e-6
    temperature = Temperature
    eigenstrain_name = eigenstrain
  []

  [strain]
    block = 1
    type = ADComputeFiniteStrain
    displacements = 'disp_x disp_y'
    eigenstrain_names = eigenstrain
  []

  [stress]
    block = 1
    type = ADComputeFiniteStrainElasticStress
  []
[]


[BCs]
  # BCs for heat transfer
  # Left side is convective
  [Temperature_left]
    type = ADConvectiveHeatFluxBC
    T_infinity = 300
    heat_transfer_coefficient = 20   # W/m^2/K
    variable = Temperature
    boundary = 'left'
  []

  # Right side is convective
  [Temperature_right]
    type = ADConvectiveHeatFluxBC
    T_infinity = 300
    heat_transfer_coefficient = 20   # W/m^2/K
    variable = Temperature
    boundary = 'right'
  []

  # Top surface is convective
  [Convective_top]
    type = ADConvectiveHeatFluxBC
    variable = Temperature
    boundary = 'top_active'
    T_infinity_functor = 300.0
    heat_transfer_coefficient_functor = 5
    use_displaced_mesh = false
  []

  # Bottom surface is convective
  [Convective_bottom]
    type = ADConvectiveHeatFluxBC
    variable = Temperature
    boundary = 'bottom'
    T_infinity_functor = 300.0
    heat_transfer_coefficient_functor = 5
  []

  # BCs for mechanics
  # Fixed bottom boundary
  [ux_bottom_fix]
    type = DirichletBC
    variable = disp_x
    boundary = 'bottom'
    value = 0.0
  []

  [uy_bottom_fix]
    type = DirichletBC
    variable = disp_y
    boundary = 'bottom'
    value = 0.0
  []
[]


[Executioner]
  automatic_scaling = true
  line_search = 'none'

  type = Transient
  solve_type = 'PJFNK'

  [TimeIntegrator]
    type = ImplicitEuler
  []

  start_time = 0.0
  end_time = 40.0
  dt = 1.0e-1

  petsc_options_iname = '-pc_type     -snes_type     -pc_factor_shift_type'
  petsc_options_value = 'lu           vinewtonrsls   NONZERO'

  nl_abs_tol = 1e-8
[]

[Outputs]
  exodus = true
  csv = true

  [console]
    type = Console
    output_linear = true
    output_nonlinear = true
    time_step_interval = 20
  []

  # [dof]
  #   type = DOFMap
  #   execute_on = 'initial timestep_end'
  # []
[]


[Adaptivity]
  max_h_level = 5
  initial_marker = combo
  marker = combo

  [Indicators]
    [gradient_jump_T]
      block = 1
      type = GradientJumpIndicator
      variable = Temperature
      use_displaced_mesh = false
    []

    [gradient_jump_von_mises]
      block = 1
      type = GradientJumpIndicator
      variable = von_mises
      use_displaced_mesh = false
    []
  []

  [Markers]
    [marker_error_frac_T]
      block = 1
      type = ErrorFractionMarker
      indicator = gradient_jump_T
      coarsen = 0.3
      refine = 0.2
    []

    [marker_error_frac_von_mises]
      block = 1
      type = ErrorFractionMarker
      indicator = gradient_jump_von_mises
      coarsen = 0.3
      refine = 0.2
    []

    [marker_value_range]
      block = '2'
      type = ValueRangeMarker
      variable = layerY
      lower_bound = 0e-6
      upper_bound = 50e-6
      third_state = DO_NOTHING
    []

    [combo]
      type = ComboMarker
      block = '1 2'

      markers = 'marker_error_frac_T marker_error_frac_von_mises marker_value_range'
    []
  []
[]

# [Postprocessors]
#   [./num_dofs_nl]
#     type = NumDOFs
#     system = NL
#   [../]

#   [./num_dofs_aux]
#     type = NumDOFs
#     system = AUX
#   [../]

#   # default
#   [./num_dofs_all]
#     type = NumDOFs
#     system = ALL
#   [../]
# []

GiudGiud Nov 12, 2025
Collaborator

hello

I can reproduce the bug with this!
Thanks for making this minimal example.
I ll take a look. The crash is happening in libmesh clone()

How to ensure the displaced mesh is used #29699

Uh oh!

Uh oh!

keassyguang Jan 17, 2025

Replies: 4 comments · 206 replies

Uh oh!

GiudGiud Jan 18, 2025 Collaborator

Uh oh!

keassyguang Mar 10, 2025 Author

Uh oh!

GiudGiud Mar 10, 2025 Collaborator

Uh oh!

GiudGiud Mar 10, 2025 Collaborator

Uh oh!

keassyguang Mar 10, 2025 Author

Uh oh!

Uh oh!

keassyguang Mar 11, 2025 Author

Uh oh!

GiudGiud Mar 11, 2025 Collaborator

Uh oh!

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keassyguang May 12, 2025 Author

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GiudGiud May 21, 2025 Collaborator

Uh oh!

keassyguang May 22, 2025 Author

Uh oh!

Uh oh!

keassyguang May 22, 2025 Author

Uh oh!

GiudGiud Oct 27, 2025 Collaborator

Uh oh!

keassyguang Oct 27, 2025 Author

Uh oh!

keassyguang Nov 1, 2025 Author

Uh oh!

keassyguang Nov 12, 2025 Author

Uh oh!

GiudGiud Nov 12, 2025 Collaborator

keassyguang
Jan 17, 2025

Replies: 4 comments 206 replies

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