Constraints and Contact explanation needed #29062

mshtx-mdacc · 2024-11-13T13:45:32Z

mshtx-mdacc
Nov 13, 2024

Howdy,

I'm attempting to model the displacement due to gravity of a linear elastic material attached on top of non-moving "stem" encased in a shell that is a frictionless surface. I'm reading in a 3D tetrahedral mesh for the linear elastic material and and another mesh for the surrounding shell that is triangles. Both files were made using GMSH and I'm reading in MSH files. The shell is only there as a constraint and will not displace or deform. There is one section of the shell that is "open" to allow for outward movement in that area, but that is a later problem. There's also no need for thermal properties currently.

I'm read over the constraints source documentation as well as the Contact module and I'm having trouble understanding how to implement my problem. I was hoping someone could point me in the right direction. My input file and error results are below:

I apologize for my lack of understanding.

Cheers,

MSH

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
  volumetric_locking_correction = true
  # uniform_refine = 1
[]

[Mesh]
  construct_side_list_from_node_list = true
  [dura]
    type = FileMeshGenerator
    file = 'cranDura.msh'
    show_info = true
  []
  [duraBoundRename]
    type = RenameBoundaryGenerator
    input = dura
    old_boundary = '1 2'
    new_boundary = 'DuraBoundary CranBoundary'
  []
  [whole]
    type = FileMeshGenerator
    file = 'occMesh.msh'
    show_info = true
  []
  [wholeBoundRename]
    type = RenameBoundaryGenerator
    input = whole
    old_boundary = '3 4 5'
    new_boundary = 'PialBoundary BSBoundary TumorBoundary'
  []
  [combinedMesh]
    type = CombinerGenerator
    inputs = 'duraBoundRename wholeBoundRename'
  []
  [scaled]
    type = TransformGenerator
    input = combinedMesh
    transform = SCALE
    vector_value = '1.0e-3 1.0e-3 1.0e-3'
  []
  [diag]
    type = MeshDiagnosticsGenerator
    input = scaled
    examine_element_overlap = WARNING
    examine_element_types = WARNING
    examine_element_volumes = WARNING
    examine_non_conformality = WARNING
    # examine_nonplanar_sides = INFO
    # examine_sidesets_orientation = WARNING
    # check_for_watertight_sidesets = WARNING
    search_for_adaptivity_nonconformality = WARNING
    check_local_jacobian = WARNING
  []
  patch_update_strategy = iteration
[]

[Kernels]
  [gravity]
    type = Gravity
    value = -9.81
    variable = disp_z
  []
[]

[Physics/SolidMechanics/QuasiStatic]
  [all]
    strain = FINITE
    add_variables = true
    generate_output = 'stress_xx stress_yy stress_zz stress_xy stress_xz stress_yz'
    # use_automatic_differentiation = true
    block = 'pial tumor brainstem'
  []
[]

[BCs]
  [fixedBS_x]
    type = DirichletBC
    preset = false
    variable = disp_x
    boundary = BSBoundary
    value = 0
  []
  [fixedBS_y]
    type = DirichletBC
    preset = false
    variable = disp_y
    boundary = BSBoundary
    value = 0
  []
  [fixedBS_z]
    type = DirichletBC
    preset = false
    variable = disp_z
    boundary = BSBoundary
    value = 0
  []
  [fixedDura_x]
    type = DirichletBC
    preset = false
    variable = disp_x
    boundary = DuraBoundary
    value = 0
  []
  [fixedDura_y]
    type = DirichletBC
    preset = false
    variable = disp_y
    boundary = DuraBoundary
    value = 0
  []
  [fixedDura_z]
    type = DirichletBC
    preset = false
    variable = disp_z
    boundary = DuraBoundary
    value = 0
  []
[]

[Materials]
  [elasticityBrain]
    type = ComputeIsotropicElasticityTensor
    youngs_modulus = 210000.0
    poissons_ratio = 0.45
    block = 'pial brainstem'
  []
  [elasticityTumor]
    type = ComputeIsotropicElasticityTensor
    youngs_modulus = 210000.0
    poissons_ratio = 0.45
    block = 'tumor'
  []
  [stress]
    type = ComputeFiniteStrainElasticStress
    block = 'pial tumor brainstem'
  []
  [density]
    type = GenericConstantMaterial
    prop_names = density
    prop_values = 1000.0
  []
[]

[Contact]
  [duraPial]
    primary = 'PialBoundary'
    secondary = 'DuraBoundary'
    model = frictionless
    formulation = penalty
    penalty = 2e5
    normalize_penalty = true
    # normal_smoothing_distance = 0.01
  []
[]


[Executioner]
  type = Transient
  solve_type = 'NEWTON'
  # line_search = none
  automatic_scaling = True
  petsc_options_iname = '-pc_type'
  petsc_options_value = 'lu'
  end_time = 2.0
  dt = 1
  steady_state_detection = true
  steady_state_tolerance = 1e-04
  l_tol = 1e-04 #1e-05 is default
  # l_abs_tol = 1e-18 # 1e-50 is default
  [Predictor]
    type = SimplePredictor
    scale = 1
  []
[]

[Outputs]
  exodus = true
[]

*** Info ***
SolidMechanics Action: selecting 'incremental finite strain' formulation.
FileMeshGenerator 'dura':  Mesh Information:
FileMeshGenerator 'dura':   elem_dimensions()={2}
FileMeshGenerator 'dura':   spatial_dimension()=3
FileMeshGenerator 'dura':   n_nodes()=1904
FileMeshGenerator 'dura':     n_local_nodes()=1904
FileMeshGenerator 'dura':   n_elem()=3804
FileMeshGenerator 'dura':     n_local_elem()=3804
FileMeshGenerator 'dura':     n_active_elem()=3804
FileMeshGenerator 'dura':   n_subdomains()=2
FileMeshGenerator 'dura':   n_elemsets()=0
FileMeshGenerator 'dura':   n_partitions()=1
FileMeshGenerator 'dura':   n_processors()=1
FileMeshGenerator 'dura':   n_threads()=20
FileMeshGenerator 'dura':   processor_id()=0
FileMeshGenerator 'dura':   is_prepared()=true
FileMeshGenerator 'dura':   is_replicated()=true
FileMeshGenerator 'dura': 
FileMeshGenerator 'dura':  Mesh Bounding Box:
FileMeshGenerator 'dura':   Minimum: (x,y,z)=(-84.0226, -65.7844, -94.3662)
FileMeshGenerator 'dura':   Maximum: (x,y,z)=( 79.5143,  62.8207,   36.612)
FileMeshGenerator 'dura':   Delta:   (x,y,z)=( 163.537,  128.605,  130.978)
FileMeshGenerator 'dura': 
FileMeshGenerator 'dura':  Mesh Element Type(s):
FileMeshGenerator 'dura':   TRI3
FileMeshGenerator 'dura': 
FileMeshGenerator 'dura':  Mesh Nodesets:
FileMeshGenerator 'dura':   Nodeset 1, 1582 nodes
FileMeshGenerator 'dura':    Bounding box minimum: (x,y,z)=(-84.0226, -65.7844, -94.3662)
FileMeshGenerator 'dura':    Bounding box maximum: (x,y,z)=( 79.5143,  62.8207,   36.612)
FileMeshGenerator 'dura':    Bounding box delta: (x,y,z)=( 163.537,  128.605,  130.978)
FileMeshGenerator 'dura':   Nodeset 2, 243 nodes
FileMeshGenerator 'dura':    Bounding box minimum: (x,y,z)=( -44.929, -60.4617,   -40.44)
FileMeshGenerator 'dura':    Bounding box maximum: (x,y,z)=(-25.2524, -54.2443,  -20.907)
FileMeshGenerator 'dura':    Bounding box delta: (x,y,z)=( 19.6766,  6.21745,   19.533)
FileMeshGenerator 'dura': 
FileMeshGenerator 'dura':  Mesh Sidesets:
FileMeshGenerator 'dura':   Sideset 1, 7232 sides (EDGE2), 3150 elems (TRI3), 1582 nodes
FileMeshGenerator 'dura':    Side volume: 51064
FileMeshGenerator 'dura':    Bounding box minimum: (x,y,z)=(-84.0226, -65.7844, -94.3662)
FileMeshGenerator 'dura':    Bounding box maximum: (x,y,z)=( 79.5143,  62.8207,   36.612)
FileMeshGenerator 'dura':    Bounding box delta: (x,y,z)=( 163.537,  128.605,  130.978)
FileMeshGenerator 'dura':   Sideset 2, 856 sides (EDGE2), 468 elems (TRI3), 243 nodes
FileMeshGenerator 'dura':    Side volume: 1178.86
FileMeshGenerator 'dura':    Bounding box minimum: (x,y,z)=( -44.929, -60.4617,   -40.44)
FileMeshGenerator 'dura':    Bounding box maximum: (x,y,z)=(-25.2524, -54.2443,  -20.907)
FileMeshGenerator 'dura':    Bounding box delta: (x,y,z)=( 19.6766,  6.21745,   19.533)
FileMeshGenerator 'dura': 
FileMeshGenerator 'dura':  Mesh Edgesets:
FileMeshGenerator 'dura':   None
FileMeshGenerator 'dura': 
FileMeshGenerator 'dura':  Mesh Subdomains:
FileMeshGenerator 'dura':   Subdomain 1 (duraSurf): 3262 elems (TRI3, 3262 active), 1654 active nodes
FileMeshGenerator 'dura':    Volume: 61651.4
FileMeshGenerator 'dura':    Bounding box minimum: (x,y,z)=(-84.0226, -65.7844, -94.3662)
FileMeshGenerator 'dura':    Bounding box maximum: (x,y,z)=( 79.5143,  62.8207,   36.612)
FileMeshGenerator 'dura':    Bounding box delta: (x,y,z)=( 163.537,  128.605,  130.978)
FileMeshGenerator 'dura':   Subdomain 2 (cranSurf): 542 elems (TRI3, 542 active), 294 active nodes
FileMeshGenerator 'dura':    Volume: 312.892
FileMeshGenerator 'dura':    Bounding box minimum: (x,y,z)=( -44.929, -60.4617,   -40.44)
FileMeshGenerator 'dura':    Bounding box maximum: (x,y,z)=(-25.2524, -54.2443,  -20.907)
FileMeshGenerator 'dura':    Bounding box delta: (x,y,z)=( 19.6766,  6.21745,   19.533)
FileMeshGenerator 'dura':   Global mesh volume = 61964.3
FileMeshGenerator 'whole':  Mesh Information:
FileMeshGenerator 'whole':   elem_dimensions()={3}
FileMeshGenerator 'whole':   spatial_dimension()=3
FileMeshGenerator 'whole':   n_nodes()=8269
FileMeshGenerator 'whole':     n_local_nodes()=8269
FileMeshGenerator 'whole':   n_elem()=41943
FileMeshGenerator 'whole':     n_local_elem()=41943
FileMeshGenerator 'whole':     n_active_elem()=41943
FileMeshGenerator 'whole':   n_subdomains()=3
FileMeshGenerator 'whole':   n_elemsets()=0
FileMeshGenerator 'whole':   n_partitions()=1
FileMeshGenerator 'whole':   n_processors()=1
FileMeshGenerator 'whole':   n_threads()=20
FileMeshGenerator 'whole':   processor_id()=0
FileMeshGenerator 'whole':   is_prepared()=true
FileMeshGenerator 'whole':   is_replicated()=true
FileMeshGenerator 'whole': 
FileMeshGenerator 'whole':  Mesh Bounding Box:
FileMeshGenerator 'whole':   Minimum: (x,y,z)=(-81.7544, -64.2067, -93.5764)
FileMeshGenerator 'whole':   Maximum: (x,y,z)=( 77.8743,  60.2982,  34.8699)
FileMeshGenerator 'whole':   Delta:   (x,y,z)=( 159.629,  124.505,  128.446)
FileMeshGenerator 'whole': 
FileMeshGenerator 'whole':  Mesh Element Type(s):
FileMeshGenerator 'whole':   TET4
FileMeshGenerator 'whole': 
FileMeshGenerator 'whole':  Mesh Nodesets:
FileMeshGenerator 'whole':   Nodeset 3, 1907 nodes
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-81.7544, -64.2067, -93.5764)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=( 77.8743,  60.2982,  34.8699)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 159.629,  124.505,  128.446)
FileMeshGenerator 'whole':   Nodeset 4, 168 nodes
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-8.54777, -18.4029, -93.2513)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=( 18.0482,  14.0718, -36.3033)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=(  26.596,  32.4747,   56.948)
FileMeshGenerator 'whole':   Nodeset 5, 1156 nodes
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-50.0139, -44.1489, -47.6101)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=(-19.2785, -10.5483, -23.1809)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 30.7354,  33.6006,  24.4292)
FileMeshGenerator 'whole': 
FileMeshGenerator 'whole':  Mesh Sidesets:
FileMeshGenerator 'whole':   Sideset 3, 3799 sides (TRI3), 3799 elems (TET4), 1907 nodes
FileMeshGenerator 'whole':    Side volume: 58627.2
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-81.7544, -64.2067, -93.5764)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=( 77.8743,  60.2982,  34.8699)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 159.629,  124.505,  128.446)
FileMeshGenerator 'whole':   Sideset 4, 639 sides (TRI3), 636 elems (TET4), 168 nodes
FileMeshGenerator 'whole':    Side volume: 7176.75
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-8.54777, -18.4029, -93.2513)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=( 18.0482,  14.0718, -36.3033)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=(  26.596,  32.4747,   56.948)
FileMeshGenerator 'whole':   Sideset 5, 4616 sides (TRI3), 4616 elems (TET4), 1156 nodes
FileMeshGenerator 'whole':    Side volume: 5310.18
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-50.0139, -44.1489, -47.6101)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=(-19.2785, -10.5483, -23.1809)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 30.7354,  33.6006,  24.4292)
FileMeshGenerator 'whole': 
FileMeshGenerator 'whole':  Mesh Edgesets:
FileMeshGenerator 'whole':   None
FileMeshGenerator 'whole': 
FileMeshGenerator 'whole':  Mesh Subdomains:
FileMeshGenerator 'whole':   Subdomain 3 (pial): 34892 elems (TET4, 34892 active), 7635 active nodes
FileMeshGenerator 'whole':    Volume: 1.15877e+06
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-81.7544, -64.2067, -93.5764)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=( 77.8743,  60.2982,  34.8699)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 159.629,  124.505,  128.446)
FileMeshGenerator 'whole':   Subdomain 4 (brainstem): 538 elems (TET4, 538 active), 201 active nodes
FileMeshGenerator 'whole':    Volume: 15008.8
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-8.54777, -18.4029, -93.2513)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=( 18.0482,  14.0718, -36.3033)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=(  26.596,  32.4747,   56.948)
FileMeshGenerator 'whole':   Subdomain 5 (tumor): 6513 elems (TET4, 6513 active), 1750 active nodes
FileMeshGenerator 'whole':    Volume: 11387.5
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-50.0139, -44.1489, -47.6101)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=(-19.2785, -10.5483, -23.1809)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 30.7354,  33.6006,  24.4292)
FileMeshGenerator 'whole':   Global mesh volume = 1.18517e+06


*** Info ***
Number of elements below prescribed minimum volume : 0


*** Info ***
Number of elements with negative volume : 0


*** Info ***
Number of elements above prescribed maximum volume : 0
Element type in subdomain duraSurf (1) : TRI3
Element type in subdomain cranSurf (2) : TRI3
Element type in subdomain pial (3) : TET4
Element type in subdomain brainstem (4) : TET4
Element type in subdomain tumor (5) : TET4
Element overlap detected at :   Node id()=3687, processor_id()=0, Point=(x,y,z)=(0.0154507, -0.00702446, -0.0935352)
    DoFs=

Element overlap detected at :   Node id()=3737, processor_id()=0, Point=(x,y,z)=(0.0154763, -0.00731964, -0.0934313)
    DoFs=

Element overlap detected at :   Node id()=4218, processor_id()=0, Point=(x,y,z)=(0.0163035, -0.00716439, -0.0933583)
    DoFs=

Element overlap detected at :   Node id()=4221, processor_id()=0, Point=(x,y,z)=(-0.0419385, -0.0319768, -0.0474792)
    DoFs=

Element overlap detected at :   Node id()=4335, processor_id()=0, Point=(x,y,z)=(-0.0463072, -0.0223911, -0.0472151)
    DoFs=

Element overlap detected at :   Node id()=4461, processor_id()=0, Point=(x,y,z)=(0.0119511, -0.0378783, -0.0590096)
    DoFs=

Element overlap detected at :   Node id()=5313, processor_id()=0, Point=(x,y,z)=(-0.0392629, -0.0252479, -0.0491522)
    DoFs=

Element overlap detected at :   Node id()=5316, processor_id()=0, Point=(x,y,z)=(-0.0469305, -0.0205409, -0.0473713)
    DoFs=

Element overlap detected at :   Node id()=5338, processor_id()=0, Point=(x,y,z)=(0.0156101, -0.00683169, -0.0935764)
    DoFs=

Maximum output reached, log is silenced


*** Warning ***
/projects/brain_shift/problems/brainshift.i:41.3:
The following warning occurred in the MeshGenerator 'diag' of type MeshDiagnosticsGenerator.

Number of elements overlapping (node-based heuristics): 75
Element overlap detected with element : 545 near point (x,y,z)=(0.015999, -0.00673049, -0.0935516)
Element overlap detected with element : 585 near point (x,y,z)=(0.0254182, 0.0250946, -0.0927013)
Element overlap detected with element : 741 near point (x,y,z)=(0.0215615, -0.0381008, -0.0792992)
Element overlap detected with element : 839 near point (x,y,z)=(0.00435568, 0.0420025, -0.07475)
Element overlap detected with element : 1037 near point (x,y,z)=(-0.00623083, 0.0172514, -0.0661587)
Element overlap detected with element : 1707 near point (x,y,z)=(-0.0405893, -0.0298933, -0.0485796)
Element overlap detected with element : 1712 near point (x,y,z)=(-0.0411144, -0.0254104, -0.048033)
Element overlap detected with element : 1713 near point (x,y,z)=(-0.0385833, -0.0265844, -0.0497375)
Element overlap detected with element : 1714 near point (x,y,z)=(-0.0404277, -0.0278381, -0.0487592)
Maximum output reached, log is silenced


*** Warning ***
/projects/brain_shift/problems/brainshift.i:41.3:
The following warning occurred in the MeshGenerator 'diag' of type MeshDiagnosticsGenerator.

Number of elements overlapping (centroid-based heuristics): 14
Non-conformality detected at  :   Node id()=386, processor_id()=0, Point=(x,y,z)=(0.00410082,  0.03949, -0.0766449)
    DoFs=

Non-conformality detected at  :   Node id()=386, processor_id()=0, Point=(x,y,z)=(0.00410082,  0.03949, -0.0766449)
    DoFs=

Non-conformality detected at  :   Node id()=423, processor_id()=0, Point=(x,y,z)=(0.0238497, -0.0394382, -0.078978)
    DoFs=

Non-conformality detected at  :   Node id()=423, processor_id()=0, Point=(x,y,z)=(0.0238497, -0.0394382, -0.078978)
    DoFs=

Non-conformality detected at  :   Node id()=423, processor_id()=0, Point=(x,y,z)=(0.0238497, -0.0394382, -0.078978)
    DoFs=

Non-conformality detected at  :   Node id()=931, processor_id()=0, Point=(x,y,z)=(-0.0400146, -0.0261689, -0.0488047)
    DoFs=

Non-conformality detected at  :   Node id()=932, processor_id()=0, Point=(x,y,z)=(-0.0401632, -0.0225636, -0.0482625)
    DoFs=

Non-conformality detected at  :   Node id()=932, processor_id()=0, Point=(x,y,z)=(-0.0401632, -0.0225636, -0.0482625)
    DoFs=

Non-conformality detected at  :   Node id()=932, processor_id()=0, Point=(x,y,z)=(-0.0401632, -0.0225636, -0.0482625)
    DoFs=

Maximum output reached, log is silenced


*** Warning ***
/projects/brain_shift/problems/brainshift.i:41.3:
The following warning occurred in the MeshGenerator 'diag' of type MeshDiagnosticsGenerator.

Number of non-conformal nodes: 189


*** Info ***
Number of non-conformal nodes likely due to mesh refinement detected by heuristic: 0


*** Info ***
Number of elements with a negative Jacobian: 0


*** Info ***
Number of element sides with negative Jacobians: 0
Currently Setting Up
  Initializing
    Finished Initializing Equation Systems                                               [  2.15 s] [  676 MB]
  Finished Initializing                                                                  [  2.39 s] [  678 MB]
Finished Setting Up                                                                      [  6.95 s] [  678 MB]
Framework Information:
MOOSE Version:           git commit e1a48104b91 on 2024-10-30
LibMesh Version:         5483644b60cc538a4b54d312f28835bd94107627
PETSc Version:           3.21.5
SLEPc Version:           3.21.1
Current Time:            Wed Nov 13 13:40:08 2024
Executable Timestamp:    Wed Nov  6 16:49:09 2024

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

Parallelism:
  Num Processors:          1
  Num Threads:             20

Mesh: 
  Parallel Type:           replicated
  Mesh Dimension:          3
  Spatial Dimension:       3
  Nodes:                   10173
  Elems:                   45747
  Num Subdomains:          5

Nonlinear System:
  Num DOFs:                30519
  Num Local DOFs:          30519
  Variables:               { "disp_x" "disp_y" "disp_z" } 
  Finite Element Types:    "LAGRANGE" 
  Approximation Orders:    "FIRST" 

Auxiliary System:
  Num DOFs:                305001
  Num Local DOFs:          305001
  Variables:               { "stress_xx" "stress_yy" "stress_zz" "stress_xy" "stress_xz" "stress_yz" 
                             } { "penetration" "contact_pressure" "nodal_area" } 
  Finite Element Types:    "MONOMIAL" "LAGRANGE" 
  Approximation Orders:    "CONSTANT" "FIRST" 

Execution Information:
  Executioner:             Transient
  TimeStepper:             ConstantDT
  TimeIntegrator(s):       ImplicitEuler
  Solver Mode:             NEWTON
  PETSc Preconditioner:    lu 
  MOOSE Preconditioner:    SMP (auto)

Currently Executing
  Performing Initial Setup
    Setting Up Materials
      Finished Computing Initial Material Values                                         [  0.19 s] [  846 MB]
    Finished Setting Up Materials                                                        [  0.20 s] [  846 MB]
    Finished Reinitializing Because of Geometric Search Objects                          [  6.91 s] [  982 MB]
  Finished Performing Initial Setup                                                      [  9.36 s] [  983 MB]

Time Step 0, time = 0

Time Step 1, time = 1, dt = 1

    Rebuilding Geometric Search Patches
      Finished Reinitializing Because of Geometric Search Objects                        [  6.79 s] [  993 MB]
    Finished Rebuilding Geometric Search Patches                                         [  6.82 s] [  993 MB]
 Skipping predictor this step

Performing automatic scaling calculation

 0 Nonlinear |R| = 3.121542e-05
    Computing Jacobian.....................................                              [199.28 s] [ 1017 MB]
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Object is in wrong state
[0]PETSC ERROR: Matrix is missing diagonal entry 0
[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:--n-threads=20 (no value) source: command line
[0]PETSC ERROR:   Option left: name:-i value: brainshift.i source: command line
[0]PETSC ERROR:   Option left: name:-ksp_converged_reason value: ::failed source: code
[0]PETSC ERROR:   Option left: name:-snes_converged_reason value: ::failed source: code
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.21.5, unknown 
[0]PETSC ERROR: ../brain_shift-opt on a  named 39bbf6a0da85 by root Wed Nov 13 13:40:01 2024
[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 --download-hdf5=1 --with-hdf5-fortran-bindings=0 --download-hdf5-configure-arguments="--with-zlib" --with-make-np=16 --prefix=/opt/petsc
[0]PETSC ERROR: #1 MatLUFactorSymbolic_SeqAIJ() at /root/build/petsc/src/mat/impls/aij/seq/aijfact.c:309
[0]PETSC ERROR: #2 MatLUFactorSymbolic() at /root/build/petsc/src/mat/interface/matrix.c:3200
[0]PETSC ERROR: #3 PCSetUp_LU() at /root/build/petsc/src/ksp/pc/impls/factor/lu/lu.c:87
[0]PETSC ERROR: #4 PCSetUp() at /root/build/petsc/src/ksp/pc/interface/precon.c:1079
[0]PETSC ERROR: #5 KSPSetUp() at /root/build/petsc/src/ksp/ksp/interface/itfunc.c:415
[0]PETSC ERROR: #6 KSPSolve_Private() at /root/build/petsc/src/ksp/ksp/interface/itfunc.c:831
[0]PETSC ERROR: #7 KSPSolve() at /root/build/petsc/src/ksp/ksp/interface/itfunc.c:1078
[0]PETSC ERROR: #8 SNESSolve_NEWTONLS() at /root/build/petsc/src/snes/impls/ls/ls.c:221
[0]PETSC ERROR: #9 SNESSolve() at /root/build/petsc/src/snes/interface/snes.c:4753
libMesh terminating:
Matrix is missing diagonal entry 0
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

GiudGiud · 2024-11-13T14:31:27Z

GiudGiud
Nov 13, 2024
Collaborator

Hello

I can understand these two for a contact problem

Number of elements overlapping (node-based heuristics): 75
Number of non-conformal nodes: 189

but that one seems excessive

Number of elements overlapping (centroid-based heuristics): 14

some elements have their centroid inside another element.

Are you sure the mesh is well formed?

5 replies

mshtx-mdacc Nov 13, 2024
Author

The problem comes when I try to combine the two meshes. I only want to use the Dura surface mesh as a boundary to restrict the movement of the 3D mesh. Unfortunately the surfaces of the pial (surface of the 3D Mesh) and the dura (Surface only mesh) will sometimes overlap. I've tried to combine the 2 in GMSH but ran into problems. I thought I could combine the two in MOOSE.

GiudGiud Nov 13, 2024
Collaborator

Maybe shrink or move one using the TransformGenerator before combining?

MOOSE will let you combine any two mesh with zero checks but that does not mean it can perform a simulation with overlapping meshes

lynnmunday Nov 13, 2024

There is an embedded constraint for rebar in concrete. That might work for tying the brain to the skull. It requires the rebar to be embedded completely in the concrete in order to apply the nodal constraint.
https://mooseframework.inl.gov/source/constraints/EqualValueEmbeddedConstraint.html

mshtx-mdacc Dec 2, 2024
Author

I've been able to dilate the dura mesh in GMSH so that it no longer has any overlap. I'm getting the same error as before. I'm sure I don't have this setup right. I've changed the tag numbers for edge, surface, and volume to be unique. I've also changed the Young's modulus to be more realistic, but I don't think that would matter.

Do I need the dura boundary to be fixed?

Do the dura and cran boundaries actually need any physics or material properties on them?

Sorry for all of the questions, my background is in low frequency EM and my meshes don't usually move. I've posted the input file and results below:

input:

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
  volumetric_locking_correction = true
  # uniform_refine = 1
  # block = 'pial tumor brainstem'
[]

[Mesh]
  # construct_side_list_from_node_list = true
  [dura]
    type = FileMeshGenerator
    file = 'cranDura.msh'
    show_info = true
  []
  [duraBoundRename]
    type = RenameBoundaryGenerator
    input = dura
    old_boundary = '1001 1002'
    new_boundary = 'DuraBoundary CranBoundary'
  []
  [whole]
    type = FileMeshGenerator
    file = 'occMesh.msh'
    show_info = true
  []
  [wholeBoundRename]
    type = RenameBoundaryGenerator
    input = whole
    old_boundary = '1003 1004 1005'
    new_boundary = 'PialBoundary BSBoundary TumorBoundary'
  []
  [combinedMesh]
    type = CombinerGenerator
    inputs = 'duraBoundRename wholeBoundRename'
  []
  [scaled]
    type = TransformGenerator
    input = combinedMesh
    transform = SCALE
    vector_value = '1.0e-3 1.0e-3 1.0e-3'
  []
  [diag]
    type = MeshDiagnosticsGenerator
    input = scaled
    examine_element_overlap = WARNING
    examine_element_types = WARNING
    examine_element_volumes = WARNING
    examine_non_conformality = WARNING
    # examine_nonplanar_sides = INFO
    # examine_sidesets_orientation = WARNING
    # check_for_watertight_sidesets = WARNING
    search_for_adaptivity_nonconformality = WARNING
    check_local_jacobian = WARNING
  []
  patch_update_strategy = iteration
[]

[Kernels]
  [gravity]
    type = Gravity
    value = -9.81
    variable = disp_z
  []
[]

[Physics/SolidMechanics/QuasiStatic]
  [all]
    strain = FINITE
    add_variables = true
    generate_output = 'stress_xx stress_yy stress_zz stress_xy stress_xz stress_yz'
    # use_automatic_differentiation = true
    block = 'pial tumor brainstem'
  []
[]

[BCs]
  [fixedBS_x]
    type = DirichletBC
    preset = false
    variable = disp_x
    boundary = BSBoundary
    value = 0
  []
  [fixedBS_y]
    type = DirichletBC
    preset = false
    variable = disp_y
    boundary = BSBoundary
    value = 0
  []
  [fixedBS_z]
    type = DirichletBC
    preset = false
    variable = disp_z
    boundary = BSBoundary
    value = 0
  []
  [fixedDura_x]
    type = DirichletBC
    preset = false
    variable = disp_x
    boundary = DuraBoundary
    value = 0
  []
  [fixedDura_y]
    type = DirichletBC
    preset = false
    variable = disp_y
    boundary = DuraBoundary
    value = 0
  []
  [fixedDura_z]
    type = DirichletBC
    preset = false
    variable = disp_z
    boundary = DuraBoundary
    value = 0
  []
[]

[Materials]
  [elasticityBrain]
    type = ComputeIsotropicElasticityTensor
    youngs_modulus = 2100.0
    poissons_ratio = 0.45
    block = 'pial brainstem'
  []
  [elasticityTumor]
    type = ComputeIsotropicElasticityTensor
    youngs_modulus = 100000.0
    poissons_ratio = 0.45
    block = 'tumor'
  []
  [stress]
    type = ComputeFiniteStrainElasticStress
    block = 'pial tumor brainstem'
  []
  [density]
    type = GenericConstantMaterial
    prop_names = density
    prop_values = 1000.0
  []
[]

[Contact]
  [duraPial]
    primary = 'PialBoundary'
    secondary = 'DuraBoundary'
    model = frictionless
    formulation = penalty
    penalty = 2e3
    normalize_penalty = true
    # normal_smoothing_distance = 0.01
  []
[]


[Executioner]
  type = Transient
  solve_type = 'NEWTON'
  line_search = none
  automatic_scaling = True
  petsc_options_iname = '-pc_type'
  petsc_options_value = 'lu'
  end_time = 2.0
  dt = 1
  steady_state_detection = true
  steady_state_tolerance = 1e-04
  l_tol = 1e-04 #1e-05 is default
  # l_abs_tol = 1e-18 # 1e-50 is default
  [Predictor]
    type = SimplePredictor
    scale = 1
  []
[]

[Outputs]
  exodus = true
[]

Results:

*** Info ***
SolidMechanics Action: selecting 'incremental finite strain' formulation.
FileMeshGenerator 'dura':  Mesh Information:
FileMeshGenerator 'dura':   elem_dimensions()={2}
FileMeshGenerator 'dura':   spatial_dimension()=3
FileMeshGenerator 'dura':   n_nodes()=4746
FileMeshGenerator 'dura':     n_local_nodes()=4746
FileMeshGenerator 'dura':   n_elem()=9488
FileMeshGenerator 'dura':     n_local_elem()=9488
FileMeshGenerator 'dura':     n_active_elem()=9488
FileMeshGenerator 'dura':   n_subdomains()=2
FileMeshGenerator 'dura':   n_elemsets()=0
FileMeshGenerator 'dura':   n_partitions()=1
FileMeshGenerator 'dura':   n_processors()=1
FileMeshGenerator 'dura':   n_threads()=20
FileMeshGenerator 'dura':   processor_id()=0
FileMeshGenerator 'dura':   is_prepared()=true
FileMeshGenerator 'dura':   is_replicated()=true
FileMeshGenerator 'dura': 
FileMeshGenerator 'dura':  Mesh Bounding Box:
FileMeshGenerator 'dura':   Minimum: (x,y,z)=(-84.3797, -66.4979, -95.4167)
FileMeshGenerator 'dura':   Maximum: (x,y,z)=( 81.3309,  63.0385,   35.259)
FileMeshGenerator 'dura':   Delta:   (x,y,z)=( 165.711,  129.536,  130.676)
FileMeshGenerator 'dura': 
FileMeshGenerator 'dura':  Mesh Element Type(s):
FileMeshGenerator 'dura':   TRI3
FileMeshGenerator 'dura': 
FileMeshGenerator 'dura':  Mesh Nodesets:
FileMeshGenerator 'dura':   Nodeset 1001, 4345 nodes
FileMeshGenerator 'dura':    Bounding box minimum: (x,y,z)=(-84.3797, -66.4979, -95.4167)
FileMeshGenerator 'dura':    Bounding box maximum: (x,y,z)=( 81.3309,  63.0385,   35.259)
FileMeshGenerator 'dura':    Bounding box delta: (x,y,z)=( 165.711,  129.536,  130.676)
FileMeshGenerator 'dura':   Nodeset 1002, 422 nodes
FileMeshGenerator 'dura':    Bounding box minimum: (x,y,z)=(-42.0643, -59.9799, -43.3222)
FileMeshGenerator 'dura':    Bounding box maximum: (x,y,z)=(-22.4669, -52.4347, -23.8568)
FileMeshGenerator 'dura':    Bounding box delta: (x,y,z)=( 19.5974,  7.54517,  19.4654)
FileMeshGenerator 'dura': 
FileMeshGenerator 'dura':  Mesh Sidesets:
FileMeshGenerator 'dura':   Sideset 1001 (duraEdge), 25476 sides (EDGE2), 8694 elems (TRI3), 4345 nodes
FileMeshGenerator 'dura':    Side volume: 105197
FileMeshGenerator 'dura':    Bounding box minimum: (x,y,z)=(-84.3797, -66.4979, -95.4167)
FileMeshGenerator 'dura':    Bounding box maximum: (x,y,z)=( 81.3309,  63.0385,   35.259)
FileMeshGenerator 'dura':    Bounding box delta: (x,y,z)=( 165.711,  129.536,  130.676)
FileMeshGenerator 'dura':   Sideset 1002 (cranEdge), 1740 sides (EDGE2), 776 elems (TRI3), 422 nodes
FileMeshGenerator 'dura':    Side volume: 1884.95
FileMeshGenerator 'dura':    Bounding box minimum: (x,y,z)=(-42.0643, -59.9799, -43.3222)
FileMeshGenerator 'dura':    Bounding box maximum: (x,y,z)=(-22.4669, -52.4347, -23.8568)
FileMeshGenerator 'dura':    Bounding box delta: (x,y,z)=( 19.5974,  7.54517,  19.4654)
FileMeshGenerator 'dura': 
FileMeshGenerator 'dura':  Mesh Edgesets:
FileMeshGenerator 'dura':   None
FileMeshGenerator 'dura': 
FileMeshGenerator 'dura':  Mesh Subdomains:
FileMeshGenerator 'dura':   Subdomain 101 (duraSurf): 8687 elems (TRI3, 8687 active), 4382 active nodes
FileMeshGenerator 'dura':    Volume: 62531.2
FileMeshGenerator 'dura':    Bounding box minimum: (x,y,z)=(-84.3797, -66.4979, -95.4167)
FileMeshGenerator 'dura':    Bounding box maximum: (x,y,z)=( 81.3309,  63.0385,   35.259)
FileMeshGenerator 'dura':    Bounding box delta: (x,y,z)=( 165.711,  129.536,  130.676)
FileMeshGenerator 'dura':   Subdomain 102 (cranSurf): 801 elems (TRI3, 801 active), 439 active nodes
FileMeshGenerator 'dura':    Volume: 315.733
FileMeshGenerator 'dura':    Bounding box minimum: (x,y,z)=(-42.0643, -59.9799, -43.3222)
FileMeshGenerator 'dura':    Bounding box maximum: (x,y,z)=(-22.4669, -52.4347, -23.8568)
FileMeshGenerator 'dura':    Bounding box delta: (x,y,z)=( 19.5974,  7.54517,  19.4654)
FileMeshGenerator 'dura':   Global mesh volume = 62846.9
FileMeshGenerator 'whole':  Mesh Information:
FileMeshGenerator 'whole':   elem_dimensions()={3}
FileMeshGenerator 'whole':   spatial_dimension()=3
FileMeshGenerator 'whole':   n_nodes()=8386
FileMeshGenerator 'whole':     n_local_nodes()=8386
FileMeshGenerator 'whole':   n_elem()=42774
FileMeshGenerator 'whole':     n_local_elem()=42774
FileMeshGenerator 'whole':     n_active_elem()=42774
FileMeshGenerator 'whole':   n_subdomains()=3
FileMeshGenerator 'whole':   n_elemsets()=0
FileMeshGenerator 'whole':   n_partitions()=1
FileMeshGenerator 'whole':   n_processors()=1
FileMeshGenerator 'whole':   n_threads()=20
FileMeshGenerator 'whole':   processor_id()=0
FileMeshGenerator 'whole':   is_prepared()=true
FileMeshGenerator 'whole':   is_replicated()=true
FileMeshGenerator 'whole': 
FileMeshGenerator 'whole':  Mesh Bounding Box:
FileMeshGenerator 'whole':   Minimum: (x,y,z)=(-81.6497, -64.1349, -93.4483)
FileMeshGenerator 'whole':   Maximum: (x,y,z)=( 78.3783,  60.5591,  33.4434)
FileMeshGenerator 'whole':   Delta:   (x,y,z)=( 160.028,  124.694,  126.892)
FileMeshGenerator 'whole': 
FileMeshGenerator 'whole':  Mesh Element Type(s):
FileMeshGenerator 'whole':   TET4
FileMeshGenerator 'whole': 
FileMeshGenerator 'whole':  Mesh Nodesets:
FileMeshGenerator 'whole':   Nodeset 103, 1878 nodes
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-81.6497, -64.1349, -93.4483)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=( 78.3783,  60.5591,  33.4434)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 160.028,  124.694,  126.892)
FileMeshGenerator 'whole':   Nodeset 104, 181 nodes
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-10.0568, -19.1267, -92.8687)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=( 19.0618,  15.5251, -35.7652)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 29.1186,  34.6518,  57.1035)
FileMeshGenerator 'whole':   Nodeset 105, 1271 nodes
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-50.0455, -45.0358, -47.7942)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=(-18.9423, -9.63433, -21.2255)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 31.1032,  35.4015,  26.5687)
FileMeshGenerator 'whole':   Nodeset 1003, 1672 nodes
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-81.6497, -64.1349, -93.4483)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=( 78.3783,  60.5591,  33.4434)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 160.028,  124.694,  126.892)
FileMeshGenerator 'whole':   Nodeset 1004, 172 nodes
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-10.0568, -19.1267, -92.8687)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=( 19.0618,  15.5251, -35.7652)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 29.1186,  34.6518,  57.1035)
FileMeshGenerator 'whole':   Nodeset 1005, 730 nodes
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-50.0455, -45.0358, -47.7942)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=(-18.9423, -9.63433, -21.2255)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 31.1032,  35.4015,  26.5687)
FileMeshGenerator 'whole': 
FileMeshGenerator 'whole':  Mesh Sidesets:
FileMeshGenerator 'whole':   Sideset 103 (pialSurf), 3736 sides (TRI3), 3736 elems (TET4), 1878 nodes
FileMeshGenerator 'whole':    Side volume: 58619
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-81.6497, -64.1349, -93.4483)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=( 78.3783,  60.5591,  33.4434)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 160.028,  124.694,  126.892)
FileMeshGenerator 'whole':   Sideset 104 (brainstemSurf), 694 sides (TRI3), 691 elems (TET4), 181 nodes
FileMeshGenerator 'whole':    Side volume: 7997.49
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-10.0568, -19.1267, -92.8687)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=( 19.0618,  15.5251, -35.7652)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 29.1186,  34.6518,  57.1035)
FileMeshGenerator 'whole':   Sideset 105 (tumorSurf), 5076 sides (TRI3), 5076 elems (TET4), 1271 nodes
FileMeshGenerator 'whole':    Side volume: 5877.59
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-50.0455, -45.0358, -47.7942)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=(-18.9423, -9.63433, -21.2255)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 31.1032,  35.4015,  26.5687)
FileMeshGenerator 'whole': 
FileMeshGenerator 'whole':  Mesh Edgesets:
FileMeshGenerator 'whole':   None
FileMeshGenerator 'whole': 
FileMeshGenerator 'whole':  Mesh Subdomains:
FileMeshGenerator 'whole':   Subdomain 3 (pial): 34678 elems (TET4, 34678 active), 7637 active nodes
FileMeshGenerator 'whole':    Volume: 1.15209e+06
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-81.6497, -64.1349, -93.4483)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=( 78.3783,  60.5591,  33.4434)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 160.028,  124.694,  126.892)
FileMeshGenerator 'whole':   Subdomain 4 (brainstem): 619 elems (TET4, 619 active), 221 active nodes
FileMeshGenerator 'whole':    Volume: 16616.1
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-10.0568, -19.1267, -92.8687)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=( 19.0618,  15.5251, -35.7652)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 29.1186,  34.6518,  57.1035)
FileMeshGenerator 'whole':   Subdomain 5 (tumor): 7477 elems (TET4, 7477 active), 1977 active nodes
FileMeshGenerator 'whole':    Volume: 13161.4
FileMeshGenerator 'whole':    Bounding box minimum: (x,y,z)=(-50.0455, -45.0358, -47.7942)
FileMeshGenerator 'whole':    Bounding box maximum: (x,y,z)=(-18.9423, -9.63433, -21.2255)
FileMeshGenerator 'whole':    Bounding box delta: (x,y,z)=( 31.1032,  35.4015,  26.5687)
FileMeshGenerator 'whole':   Global mesh volume = 1.18187e+06


*** Info ***
Number of elements below prescribed minimum volume : 0


*** Info ***
Number of elements with negative volume : 0


*** Info ***
Number of elements above prescribed maximum volume : 0
Element type in subdomain pial (3) : TET4
Element type in subdomain brainstem (4) : TET4
Element type in subdomain tumor (5) : TET4
Element type in subdomain duraSurf (101) : TRI3
Element type in subdomain cranSurf (102) : TRI3


*** Info ***
Number of elements overlapping (node-based heuristics): 0


*** Info ***
Number of elements overlapping (centroid-based heuristics): 0


*** Info ***
Number of non-conformal nodes: 0


*** Info ***
Number of non-conformal nodes likely due to mesh refinement detected by heuristic: 0


*** Info ***
Number of elements with a negative Jacobian: 0


*** Info ***
Number of element sides with negative Jacobians: 0
Currently Setting Up
  Initializing
    Initializing Equation Systems                                                        [  5.60 s] [  691 MB]
  Finished Initializing                                                                  [  5.90 s] [  693 MB]
Finished Setting Up                                                                      [ 10.84 s] [  693 MB]
Framework Information:
MOOSE Version:           git commit 2e75e9d1e3c on 2024-11-26
LibMesh Version:         5483644b60cc538a4b54d312f28835bd94107627
PETSc Version:           3.22.1
SLEPc Version:           3.22.1
Current Time:            Mon Dec  2 14:13:07 2024
Executable Timestamp:    Wed Nov 27 15:04:31 2024

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

Parallelism:
  Num Processors:          1
  Num Threads:             20

Mesh: 
  Parallel Type:           replicated
  Mesh Dimension:          3
  Spatial Dimension:       3
  Nodes:                   13132
  Elems:                   52262
  Num Subdomains:          5

Nonlinear System:
  Num DOFs:                39396
  Num Local DOFs:          39396
  Variables:               { "disp_x" "disp_y" "disp_z" } 
  Finite Element Types:    "LAGRANGE" 
  Approximation Orders:    "FIRST" 

Auxiliary System:
  Num DOFs:                352968
  Num Local DOFs:          352968
  Variables:               { "stress_xx" "stress_yy" "stress_zz" "stress_xy" "stress_xz" "stress_yz" 
                             } { "penetration" "contact_pressure" "nodal_area" } 
  Finite Element Types:    "MONOMIAL" "LAGRANGE" 
  Approximation Orders:    "CONSTANT" "FIRST" 

Execution Information:
  Executioner:             Transient
  TimeStepper:             ConstantDT
  TimeIntegrator(s):       ImplicitEuler
  Solver Mode:             NEWTON
  PETSc Preconditioner:    lu 
  MOOSE Preconditioner:    SMP (auto)

Currently Executing
  Performing Initial Setup
    Setting Up Materials
      Finished Computing Initial Material Values                                         [  0.29 s] [  920 MB]
    Finished Setting Up Materials                                                        [  0.30 s] [  920 MB]
    Reinitializing Because of Geometric Search Objects                                   [ 10.70 s] [ 1015 MB]
  Finished Performing Initial Setup                                                      [ 14.02 s] [ 1016 MB]

Time Step 0, time = 0

Time Step 1, time = 1, dt = 1

    Rebuilding Geometric Search Patches
      Reinitializing Because of Geometric Search Objects                                 [ 11.23 s] [ 1046 MB]
    Finished Rebuilding Geometric Search Patches                                         [ 11.28 s] [ 1046 MB]
 Skipping predictor this step

Performing automatic scaling calculation

 0 Nonlinear |R| = 9.494046e-05
    Computing Jacobian...................................................................................................................................................................................................................................................... [1241.43 s] [ 1184 MB]
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Object is in wrong state
[0]PETSC ERROR: Matrix is missing diagonal entry 12
[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:--n-threads=20 (no value) source: command line
[0]PETSC ERROR:   Option left: name:-i value: brainshift.i source: command line
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.22.1-193-g72c1e49ee3d  GIT Date: 2024-11-14 11:28:54 -0600
[0]PETSC ERROR: ../brain_shift-opt with 1 MPI process(es) and PETSC_ARCH  on 90cc70e882c7 by root Mon Dec  2 14:12:56 2024
[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 --download-hdf5=1 --with-hdf5-fortran-bindings=0 --download-hdf5-configure-arguments="--with-zlib" --with-make-np=16 --prefix=/opt/petsc
[0]PETSC ERROR: #1 MatLUFactorSymbolic_SeqAIJ() at /root/build/petsc/src/mat/impls/aij/seq/aijfact.c:305
[0]PETSC ERROR: #2 MatLUFactorSymbolic() at /root/build/petsc/src/mat/interface/matrix.c:3318
[0]PETSC ERROR: #3 PCSetUp_LU() at /root/build/petsc/src/ksp/pc/impls/factor/lu/lu.c:87
[0]PETSC ERROR: #4 PCSetUp() at /root/build/petsc/src/ksp/pc/interface/precon.c:1071
[0]PETSC ERROR: #5 KSPSetUp() at /root/build/petsc/src/ksp/ksp/interface/itfunc.c:415
[0]PETSC ERROR: #6 KSPSolve_Private() at /root/build/petsc/src/ksp/ksp/interface/itfunc.c:826
[0]PETSC ERROR: #7 KSPSolve() at /root/build/petsc/src/ksp/ksp/interface/itfunc.c:1075
[0]PETSC ERROR: #8 SNESSolve_NEWTONLS() at /root/build/petsc/src/snes/impls/ls/ls.c:221
[0]PETSC ERROR: #9 SNESSolve() at /root/build/petsc/src/snes/interface/snes.c:4837
libMesh terminating:
Matrix is missing diagonal entry 12
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
  Proc: [[55243,0],0]
  Errorcode: 1

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

GiudGiud Dec 2, 2024
Collaborator

set a solve_type of PJFNK for now maybe. I dont know whether Contact has 100% implemented Jacobian contributions

Do I need the dura boundary to be fixed?

no, contact boundaries can move

Do the dura and cran boundaries actually need any physics or material properties on them?

They need the properties to solve the solid mechanics equations i think. I dont know if it makes sense to solve a contact problem on the surface without solving the solid mechanics equations in the volume

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Constraints and Contact explanation needed #29062

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Constraints and Contact explanation needed #29062

mshtx-mdacc Nov 13, 2024

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GiudGiud Nov 13, 2024 Collaborator

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mshtx-mdacc Dec 2, 2024
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