EBSDReaderPointDataAux

construction:Undocumented Class

The EBSDReaderPointDataAux has not been documented. The content listed below should be used as a starting point for documenting the class, which includes the typical automatic documentation associated with a MooseObject; however, what is contained is ultimately determined by what is necessary to make the documentation clear for users.

Outputs the requested EBSD reader point data.

Overview

Example Input File Syntax

Input Parameters

data_nameThe data to be extracted from the EBSD data by this AuxKernel
C++ Type:MooseEnum
Options:phi1, phi, phi2, feature_id, phase, symmetry
Controllable:No
Description:The data to be extracted from the EBSD data by this AuxKernel
ebsd_readerThe EBSDReader GeneralUserObject
C++ Type:UserObjectName
Controllable:No
Description:The EBSDReader GeneralUserObject
variableThe name of the variable that this object applies to
C++ Type:AuxVariableName
Unit:(no unit assumed)
Controllable:No
Description:The name of the variable that this object applies to

Required Parameters

blockThe list of blocks (ids or names) that this object will be applied
C++ Type:std::vector<SubdomainName>
Controllable:No
Description:The list of blocks (ids or names) that this object will be applied
boundaryThe list of boundaries (ids or names) from the mesh where this object applies
C++ Type:std::vector<BoundaryName>
Controllable:No
Description:The list of boundaries (ids or names) from the mesh where this object applies
check_boundary_restrictedTrueWhether to check for multiple element sides on the boundary in the case of a boundary restricted, element aux variable. Setting this to false will allow contribution to a single element's elemental value(s) from multiple boundary sides on the same element (example: when the restricted boundary exists on two or more sides of an element, such as at a corner of a mesh
Default:True
C++ Type:bool
Controllable:No
Description:Whether to check for multiple element sides on the boundary in the case of a boundary restricted, element aux variable. Setting this to false will allow contribution to a single element's elemental value(s) from multiple boundary sides on the same element (example: when the restricted boundary exists on two or more sides of an element, such as at a corner of a mesh
execute_onLINEAR TIMESTEP_ENDThe list of flag(s) indicating when this object should be executed. For a description of each flag, see https://mooseframework.inl.gov/source/interfaces/SetupInterface.html.
Default:LINEAR TIMESTEP_END
C++ Type:ExecFlagEnum
Options:XFEM_MARK, FORWARD, ADJOINT, HOMOGENEOUS_FORWARD, ADJOINT_TIMESTEP_BEGIN, ADJOINT_TIMESTEP_END, NONE, INITIAL, LINEAR, LINEAR_CONVERGENCE, NONLINEAR, NONLINEAR_CONVERGENCE, POSTCHECK, TIMESTEP_END, TIMESTEP_BEGIN, MULTIAPP_FIXED_POINT_END, MULTIAPP_FIXED_POINT_BEGIN, MULTIAPP_FIXED_POINT_CONVERGENCE, FINAL, CUSTOM, PRE_DISPLACE
Controllable:No
Description:The list of flag(s) indicating when this object should be executed. For a description of each flag, see https://mooseframework.inl.gov/source/interfaces/SetupInterface.html.

Optional Parameters

control_tagsAdds user-defined labels for accessing object parameters via control logic.
C++ Type:std::vector<std::string>
Controllable:No
Description:Adds user-defined labels for accessing object parameters via control logic.
enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Controllable:Yes
Description:Set the enabled status of the MooseObject.
seed0The seed for the master random number generator
Default:0
C++ Type:unsigned int
Controllable:No
Description:The seed for the master random number generator
use_displaced_meshFalseWhether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.
Default:False
C++ Type:bool
Controllable:No
Description:Whether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.

Advanced Parameters

prop_getter_suffixAn optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.
C++ Type:MaterialPropertyName
Unit:(no unit assumed)
Controllable:No
Description:An optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.
use_interpolated_stateFalseFor the old and older state use projected material properties interpolated at the quadrature points. To set up projection use the ProjectedStatefulMaterialStorageAction.
Default:False
C++ Type:bool
Controllable:No
Description:For the old and older state use projected material properties interpolated at the quadrature points. To set up projection use the ProjectedStatefulMaterialStorageAction.

Material Property Retrieval Parameters

Input Files

(modules/phase_field/test/tests/reconstruction/2phase_reconstruction3.i)
(modules/phase_field/test/tests/reconstruction/2phase_reconstruction.i)
(modules/phase_field/test/tests/grain_tracker_test/split_grain.i)
(modules/phase_field/examples/ebsd_reconstruction/IN100-111grn.i)
(modules/phase_field/test/tests/reconstruction/1phase_reconstruction.i)
(modules/phase_field/test/tests/reconstruction/EulerAngleVariables2RGBAux.i)
(modules/phase_field/test/tests/grain_tracker_test/grain_tracker_ebsd.i)
(modules/combined/examples/phase_field-mechanics/EBSD_reconstruction_grain_growth_mech.i)

(modules/phase_field/test/tests/reconstruction/2phase_reconstruction3.i)

#
# In this test , which is set up similarly to 2phase_reconstruction_test2.i
# we demonstrate that the feature numbers in the EBSD file can be chosen arbitrarily.
# There is no need for then to start at a certain index or even to be contiguous!
# The EBSDReaderPointDataAux AuxKernel outputs the original feature IDs (grain numbers)
#

[Problem]
  type = FEProblem
  solve = false
  kernel_coverage_check = false
[]

[Mesh]
  [ebsd_mesh]
    type = EBSDMeshGenerator
    filename = Renumbered.txt
  []
[]

[GlobalParams]
  op_num = 2
  var_name_base = gr
[]

[UserObjects]
  [ebsd_reader]
    type = EBSDReader
  []
  [ebsd]
    type = PolycrystalEBSD
    coloring_algorithm = bt
    ebsd_reader = ebsd_reader
    phase = 1
    output_adjacency_matrix = true
  []
[]

[ICs]
  [PolycrystalICs]
    [PolycrystalColoringIC]
      polycrystal_ic_uo = ebsd
    []
  []
[]

[AuxVariables]
  [GRAIN]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[AuxKernels]
  [grain_aux]
    type = EBSDReaderPointDataAux
    variable = GRAIN
    ebsd_reader = ebsd_reader
    data_name = 'feature_id'
    execute_on = 'initial'
  []
[]

[Variables]
  [PolycrystalVariables]
  []
[]

[Executioner]
  type = Transient
  num_steps = 0
[]

[Outputs]
  exodus = true
[]

(modules/phase_field/test/tests/reconstruction/2phase_reconstruction.i)

#
# In this test we set the initial condition of two variables
# based on solely the phase information in a given EBSD data file,
# ignoring the feature IDs entirely
#

[Problem]
  type = FEProblem
  solve = false
  kernel_coverage_check = false
[]

# The following sections are extracted in the documentation in
# moose/docs/content/modules/phase_field/ICs/EBSD.md

[Mesh]
  # Create a mesh representing the EBSD data
  [ebsd_mesh]
    type = EBSDMeshGenerator
    filename = 'Ti_2Phase_28x28_ebsd.txt'
  []
[]

[UserObjects]
  [ebsd]
    # Read in the EBSD data. Uses the filename given in the mesh block.
    type = EBSDReader
  []
[]

[Variables]
  # Creates the two variables being initialized
  [c1]
  []
  [c2]
  []
[]

[ICs]
  [phase1_recon]
    # Initializes the variable info from the ebsd data
    type = ReconPhaseVarIC
    ebsd_reader = ebsd
    phase = 1
    variable = c1
  []
  [phase2_recon]
    type = ReconPhaseVarIC
    ebsd_reader = ebsd
    phase = 2
    variable = c2
  []
[]
#ENDDOC - End of the file section that is included in the documentation. Do not change this line!

[AuxVariables]
  [PHI1]
    family = MONOMIAL
    order = CONSTANT
  []
  [PHI]
    family = MONOMIAL
    order = CONSTANT
  []
  [APHI2]
    family = MONOMIAL
    order = CONSTANT
  []
  [PHI2]
    family = MONOMIAL
    order = CONSTANT
  []
  [PHASE]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[AuxKernels]
  [phi1_aux]
    type = EBSDReaderPointDataAux
    variable = PHI1
    ebsd_reader = ebsd
    data_name = 'phi1'
    execute_on = 'initial'
  []
  [phi_aux]
    type = EBSDReaderPointDataAux
    variable = PHI
    ebsd_reader = ebsd
    data_name = 'phi'
    execute_on = 'initial'
  []
  [phi2_aux]
    type = EBSDReaderPointDataAux
    variable = PHI2
    ebsd_reader = ebsd
    data_name = 'phi2'
    execute_on = 'initial'
  []
  [phase_aux]
    type = EBSDReaderPointDataAux
    variable = PHASE
    ebsd_reader = ebsd
    data_name = 'phase'
    execute_on = 'initial'
  []
[]

[Executioner]
  type = Transient
  num_steps = 0
[]

[Outputs]
  exodus = true
[]

(modules/phase_field/test/tests/grain_tracker_test/split_grain.i)

[Mesh]
  [ebsd_mesh]
    type = EBSDMeshGenerator
    filename = EBSD_split_grain.txt
  []
[]

[GlobalParams]
  op_num = 4
  var_name_base = gr
[]

[UserObjects]
  [ebsd_reader]
    type = EBSDReader
  []
  [ebsd]
    type = PolycrystalEBSD
    coloring_algorithm = bt
    ebsd_reader = ebsd_reader
    enable_var_coloring = true
    output_adjacency_matrix = true
  []
  [grain_tracker]
    type = GrainTracker
    flood_entity_type = ELEMENTAL
    compute_halo_maps = true # For displaying HALO fields
    polycrystal_ic_uo = ebsd
  []
[]

[ICs]
  [PolycrystalICs]
    [PolycrystalColoringIC]
      polycrystal_ic_uo = ebsd
    []
  []
[]

[Variables]
  [PolycrystalVariables]
  []
[]

[AuxVariables]
  [bnds]
  []
  [unique_grains]
    order = CONSTANT
    family = MONOMIAL
  []
  [ghost_elements]
    order = CONSTANT
    family = MONOMIAL
  []
  [halos]
    order = CONSTANT
    family = MONOMIAL
  []
  [var_indices]
    order = CONSTANT
    family = MONOMIAL
  []
  [ebsd_grains]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[Kernels]
  [PolycrystalKernel]
  []
[]

[AuxKernels]
  [BndsCalc]
    type = BndsCalcAux
    variable = bnds
    execute_on = 'initial timestep_end'
  []
  [ghost_elements]
    type = FeatureFloodCountAux
    variable = ghost_elements
    field_display = GHOSTED_ENTITIES
    execute_on = 'initial timestep_end'
    flood_counter = grain_tracker
  []
  [halos]
    type = FeatureFloodCountAux
    variable = halos
    field_display = HALOS
    execute_on = 'initial timestep_end'
    flood_counter = grain_tracker
  []
  [var_indices]
    type = FeatureFloodCountAux
    variable = var_indices
    execute_on = 'initial timestep_end'
    flood_counter = grain_tracker
    field_display = VARIABLE_COLORING
  []
  [unique_grains]
    type = FeatureFloodCountAux
    variable = unique_grains
    execute_on = 'initial timestep_end'
    flood_counter = grain_tracker
    field_display = UNIQUE_REGION
  []
  [grain_aux]
    type = EBSDReaderPointDataAux
    variable = ebsd_grains
    ebsd_reader = ebsd_reader
    data_name = 'feature_id'
    execute_on = 'initial timestep_end'
  []
[]

[Modules]
  [PhaseField]
    [EulerAngles2RGB]
      crystal_structure = cubic
      euler_angle_provider = ebsd_reader
      grain_tracker = grain_tracker
    []
  []
[]

[Materials]
  [Copper]
    # T = 500 # K
    type = GBEvolution
    T = 500
    wGB = 0.6 # um
    GBmob0 = 2.5e-6 # m^4/(Js) from Schoenfelder 1997
    Q = 0.23 # Migration energy in eV
    GBenergy = 0.708 # GB energy in J/m^2
    molar_volume = 7.11e-6 # Molar volume in m^3/mol
    length_scale = 1.0e-6
    time_scale = 1.0e-6
  []
[]

[Postprocessors]
  [n_elements]
    type = NumElements
    execute_on = 'initial timestep_end'
  []
  [n_nodes]
    type = NumNodes
    execute_on = 'initial timestep_end'
  []
  [DOFs]
    type = NumDOFs
  []
[]

[Executioner]
  type = Transient
  scheme = bdf2
  solve_type = PJFNK

  petsc_options_iname = '-pc_type -pc_hypre_type -pc_hypre_boomeramg_strong_threshold'
  petsc_options_value = 'hypre    boomeramg      0.7'

  l_tol = 1.0e-4
  l_max_its = 20
  nl_max_its = 20
  nl_rel_tol = 1.0e-8

  start_time = 0.0
  num_steps = 2

  [TimeStepper]
    type = IterationAdaptiveDT
    cutback_factor = 0.9
    dt = 10.0
    growth_factor = 1.1
    optimal_iterations = 7
  []
[]

[Outputs]
  exodus = true
  csv = true
  perf_graph = true
[]

(modules/phase_field/examples/ebsd_reconstruction/IN100-111grn.i)

[Mesh]
  [ebsd_mesh]
    type = EBSDMeshGenerator
    filename = IN100_120x120.txt
    pre_refine = 2
  []
[]

[GlobalParams]
  op_num = 8
  var_name_base = gr
[]

[UserObjects]
  [ebsd_reader]
    type = EBSDReader
  []
  [ebsd]
    type = PolycrystalEBSD
    coloring_algorithm = bt
    ebsd_reader = ebsd_reader
    enable_var_coloring = true
  []
  [grain_tracker]
    type = GrainTracker
    flood_entity_type = ELEMENTAL
    compute_halo_maps = true # For displaying HALO fields
    polycrystal_ic_uo = ebsd
  []
[]

[ICs]
  [PolycrystalICs]
    [PolycrystalColoringIC]
      polycrystal_ic_uo = ebsd
    []
  []
[]

[Variables]
  [PolycrystalVariables]
  []
[]

[AuxVariables]
  [bnds]
  []
  [unique_grains_ic]
    order = CONSTANT
    family = MONOMIAL
  []
  [unique_grains]
    order = CONSTANT
    family = MONOMIAL
  []
  [ghost_elements]
    order = CONSTANT
    family = MONOMIAL
  []
  [halos]
    order = CONSTANT
    family = MONOMIAL
  []
  [var_indices_ic]
    order = CONSTANT
    family = MONOMIAL
  []
  [var_indices]
    order = CONSTANT
    family = MONOMIAL
  []
  [ebsd_grains]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[Kernels]
  [PolycrystalKernel]
  []
[]

[AuxKernels]
  [BndsCalc]
    type = BndsCalcAux
    variable = bnds
    execute_on = 'initial timestep_end'
  []
  [ghost_elements]
    type = FeatureFloodCountAux
    variable = ghost_elements
    field_display = GHOSTED_ENTITIES
    execute_on = 'initial timestep_end'
    flood_counter = grain_tracker
  []
  [halos]
    type = FeatureFloodCountAux
    variable = halos
    field_display = HALOS
    execute_on = 'initial timestep_end'
    flood_counter = grain_tracker
  []
  [var_indices_ic]
    type = FeatureFloodCountAux
    variable = var_indices_ic
    execute_on = 'initial'
    flood_counter = ebsd
    field_display = VARIABLE_COLORING
  []
  [unique_grains_ic]
    type = FeatureFloodCountAux
    variable = unique_grains_ic
    execute_on = 'initial'
    flood_counter = ebsd
    field_display = UNIQUE_REGION
  []
  [var_indices]
    type = FeatureFloodCountAux
    variable = var_indices
    execute_on = 'initial timestep_end'
    flood_counter = grain_tracker
    field_display = VARIABLE_COLORING
  []
  [unique_grains]
    type = FeatureFloodCountAux
    variable = unique_grains
    execute_on = 'initial timestep_end'
    flood_counter = grain_tracker
    field_display = UNIQUE_REGION
  []
  [grain_aux]
    type = EBSDReaderPointDataAux
    variable = ebsd_grains
    ebsd_reader = ebsd_reader
    data_name = 'feature_id'
    execute_on = 'initial timestep_end'
  []
[]

[Modules]
  [PhaseField]
    [EulerAngles2RGB]
      crystal_structure = cubic
      euler_angle_provider = ebsd_reader
      grain_tracker = grain_tracker
    []
  []
[]

[Materials]
  [Copper]
    # T = 500 # K
    type = GBEvolution
    T = 500
    wGB = 0.6 # um
    GBmob0 = 2.5e-6 # m^4/(Js) from Schoenfelder 1997
    Q = 0.23 # Migration energy in eV
    GBenergy = 0.708 # GB energy in J/m^2
    molar_volume = 7.11e-6 # Molar volume in m^3/mol
    length_scale = 1.0e-6
    time_scale = 1.0e-6
  []
[]

[Postprocessors]
  [dt]
    type = TimestepSize
  []
  [n_elements]
    type = NumElements
    execute_on = 'initial timestep_end'
  []
  [n_nodes]
    type = NumNodes
    execute_on = 'initial timestep_end'
  []
  [DOFs]
    type = NumDOFs
  []
[]

[Executioner]
  type = Transient
  scheme = bdf2
  solve_type = PJFNK

  petsc_options_iname = '-pc_type -pc_hypre_type -pc_hypre_boomeramg_strong_threshold'
  petsc_options_value = 'hypre    boomeramg      0.7'

  l_tol = 1.0e-4
  l_max_its = 20
  nl_max_its = 20
  nl_rel_tol = 1.0e-8

  start_time = 0.0
  num_steps = 30

  [TimeStepper]
    type = IterationAdaptiveDT
    cutback_factor = 0.9
    dt = 10.0
    growth_factor = 1.1
    optimal_iterations = 7
  []

  [Adaptivity]
    initial_adaptivity = 2
    refine_fraction = 0.7
    coarsen_fraction = 0.1
    max_h_level = 2
  []
[]

[Outputs]
  exodus = true
  checkpoint = true
  perf_graph = true
[]

(modules/phase_field/test/tests/reconstruction/1phase_reconstruction.i)

#
# In this test we set the initial condition of a set of order parameters
# by pulling out the grain data from given EBSD data file ignoring the phase completely.
#

[Problem]
  type = FEProblem
  solve = false
  kernel_coverage_check = false
[]

# The following sections are extracted in the documentation in
# moose/docs/content/modules/phase_field/ICs/EBSD.md

[Mesh]
  # Create a mesh representing the EBSD data
  [ebsd_mesh]
    type = EBSDMeshGenerator
    filename = IN100_001_28x28_Marmot.txt
  []
[]

[GlobalParams]
  # Define the number and names of the order parameters used to represent the grains
  op_num = 4
  var_name_base = gr
[]

[UserObjects]
  [ebsd_reader]
    # Read in the EBSD data. Uses the filename given in the mesh block.
    type = EBSDReader
  []
  [ebsd]
    type = PolycrystalEBSD
    coloring_algorithm = bt
    ebsd_reader = ebsd_reader
    output_adjacency_matrix = true
  []
  [grain_tracker]
    type = GrainTracker
    # For displaying HALO fields
    compute_halo_maps = true
    # Link in the ebsd userobject here so that grain tracker can extract info from it
    polycrystal_ic_uo = ebsd
  []
[]

[Variables]
  [PolycrystalVariables]
    # Create all the order parameters
    order = FIRST
    family = LAGRANGE
  []
[]

[ICs]
  [PolycrystalICs]
    [PolycrystalColoringIC]
      # Uses the data from the user object 'ebsd' to initialize the variables for all the order parameters.
      polycrystal_ic_uo = ebsd
    []
  []
[]
#ENDDOC - End of the file section that is included in the documentation. Do not change this line!

[GlobalParams]
  execute_on = 'initial'
  family = MONOMIAL
  order = CONSTANT
[]

[AuxVariables]
  [PHI1]
  []
  [PHI]
  []
  [PHI2]
  []
  [GRAIN]
  []
  [unique_grains]
  []
  [var_indices]
  []
  [halo0]
  []
  [halo1]
  []
  [halo2]
  []
  [halo3]
  []
[]

[AuxKernels]
  [phi1_aux]
    type = EBSDReaderPointDataAux
    variable = PHI1
    ebsd_reader = ebsd_reader
    data_name = 'phi1'
  []
  [phi_aux]
    type = EBSDReaderPointDataAux
    variable = PHI
    ebsd_reader = ebsd_reader
    data_name = 'phi'
  []
  [phi2_aux]
    type = EBSDReaderPointDataAux
    variable = PHI2
    ebsd_reader = ebsd_reader
    data_name = 'phi2'
  []
  [grain_aux]
    type = EBSDReaderPointDataAux
    variable = GRAIN
    ebsd_reader = ebsd_reader
    data_name = 'feature_id'
  []
  [unique_grains]
    type = FeatureFloodCountAux
    variable = unique_grains
    flood_counter = grain_tracker
    field_display = UNIQUE_REGION
  []
  [var_indices]
    type = FeatureFloodCountAux
    variable = var_indices
    flood_counter = grain_tracker
    field_display = VARIABLE_COLORING
  []
  [halo0]
    type = FeatureFloodCountAux
    variable = halo0
    map_index = 0
    field_display = HALOS
    flood_counter = grain_tracker
  []
  [halo1]
    type = FeatureFloodCountAux
    variable = halo1
    map_index = 1
    field_display = HALOS
    flood_counter = grain_tracker
  []
  [halo2]
    type = FeatureFloodCountAux
    variable = halo2
    map_index = 2
    field_display = HALOS
    flood_counter = grain_tracker
  []
  [halo3]
    type = FeatureFloodCountAux
    variable = halo3
    map_index = 3
    field_display = HALOS
    flood_counter = grain_tracker
  []
[]

[Executioner]
  type = Steady
[]

[Outputs]
  exodus = true
[]

(modules/phase_field/test/tests/reconstruction/EulerAngleVariables2RGBAux.i)

[Mesh]
  [ebsd_mesh]
    type = EBSDMeshGenerator
    filename = IN100_001_28x28_Clean_Marmot.txt
  []
[]

[UserObjects]
  [ebsd]
    type = EBSDReader
  []
[]

[AuxVariables]
  [phi1]
    family = MONOMIAL
    order = CONSTANT
  []
  [phi]
    family = MONOMIAL
    order = CONSTANT
  []
  [phi2]
    family = MONOMIAL
    order = CONSTANT
  []

  [phase]
    order = CONSTANT
    family = MONOMIAL
  []
  [symmetry]
    order = CONSTANT
    family = MONOMIAL
  []

  [rgb]
    order = CONSTANT
    family = MONOMIAL
  []
[]

[AuxKernels]
  [phi1_aux]
    type = EBSDReaderPointDataAux
    variable = phi1
    ebsd_reader = ebsd
    data_name = phi1
    execute_on = initial
  []
  [phi_aux]
    type = EBSDReaderPointDataAux
    variable = phi
    ebsd_reader = ebsd
    data_name = phi
    execute_on = initial
  []
  [phi2_aux]
    type = EBSDReaderPointDataAux
    variable = phi2
    ebsd_reader = ebsd
    data_name = phi2
    execute_on = initial
  []

  [phase_aux]
    type = EBSDReaderPointDataAux
    variable = phase
    ebsd_reader = ebsd
    data_name = phase
    execute_on = initial
  []

  [symmetry_aux]
    type = EBSDReaderPointDataAux
    variable = symmetry
    ebsd_reader = ebsd
    data_name = symmetry
    execute_on = initial
  []

  [rgb]
    type = EulerAngleVariables2RGBAux
    variable = rgb
    phi1 = phi1
    phi = phi
    phi2 = phi2
    phase = phase
    symmetry = symmetry
    execute_on = initial
  []
[]

[Executioner]
  type = Steady
[]

[Problem]
  solve = false
  kernel_coverage_check = false
[]

[Outputs]
  exodus = true
  show = 'rgb'
[]

(modules/phase_field/test/tests/grain_tracker_test/grain_tracker_ebsd.i)

[Mesh]
  [ebsd_mesh]
    type = EBSDMeshGenerator
    filename = 'ebsd_9.txt'
  []
[]

[GlobalParams]
  op_num = 4
  var_name_base = gr
[]

[UserObjects]
  [ebsd_reader]
    type = EBSDReader
  []
  [ebsd]
    type = PolycrystalEBSD
    coloring_algorithm = bt
    ebsd_reader = ebsd_reader
    output_adjacency_matrix = true
  []
  [grain_tracker]
    type = GrainTracker
    threshold = 0.2
    connecting_threshold = 0.08
    flood_entity_type = ELEMENTAL
    compute_halo_maps = true # For displaying HALO fields
    polycrystal_ic_uo = ebsd
    execute_on = 'initial timestep_end'
  []
[]

[ICs]
  [PolycrystalICs]
    [PolycrystalColoringIC]
      polycrystal_ic_uo = ebsd
    []
  []
[]

[Variables]
  [PolycrystalVariables]
  []
[]

[AuxVariables]
  [bnds]
  []
  [unique_grains]
    family = MONOMIAL
    order = CONSTANT
  []
  [var_indices]
    family = MONOMIAL
    order = CONSTANT
  []
  [ebsd_grains]
    family = MONOMIAL
    order = CONSTANT
  []
  [phi1]
    family = MONOMIAL
    order = CONSTANT
  []
  [halo0]
    order = CONSTANT
    family = MONOMIAL
  []
  [halo1]
    order = CONSTANT
    family = MONOMIAL
  []
  [halo2]
    order = CONSTANT
    family = MONOMIAL
  []
  [halo3]
    order = CONSTANT
    family = MONOMIAL
  []
[]

[Kernels]
  [PolycrystalKernel]
  []
[]

[AuxKernels]
  [BndsCalc]
    type = BndsCalcAux
    variable = bnds
    execute_on = timestep_end
  []
  [unique_grains]
    type = FeatureFloodCountAux
    variable = unique_grains
    execute_on = 'initial timestep_end'
    flood_counter = grain_tracker
    field_display = UNIQUE_REGION
  []
  [var_indices]
    type = FeatureFloodCountAux
    variable = var_indices
    execute_on = 'initial timestep_end'
    flood_counter = grain_tracker
    field_display = VARIABLE_COLORING
  []
  [grain_aux]
    type = EBSDReaderPointDataAux
    variable = ebsd_grains
    ebsd_reader = ebsd_reader
    data_name = 'feature_id'
    execute_on = 'initial timestep_end'
  []
  [phi1]
    type = OutputEulerAngles
    euler_angle_provider = ebsd_reader
    output_euler_angle = phi1
    grain_tracker = grain_tracker
    variable = phi1
  []
  [halo0]
    type = FeatureFloodCountAux
    variable = halo0
    map_index = 0
    field_display = HALOS
    flood_counter = grain_tracker
  []
  [halo1]
    type = FeatureFloodCountAux
    variable = halo1
    map_index = 1
    field_display = HALOS
    flood_counter = grain_tracker
  []
  [halo2]
    type = FeatureFloodCountAux
    variable = halo2
    map_index = 2
    field_display = HALOS
    flood_counter = grain_tracker
  []
  [halo3]
    type = FeatureFloodCountAux
    variable = halo3
    map_index = 3
    field_display = HALOS
    flood_counter = grain_tracker
  []
[]

[Materials]
  [CuGrGr]
    type = GBEvolution
    T = 500 #K
    wGB = 0.75 #micron
    length_scale = 1.0e-6
    time_scale = 1.0e-4

    GBmob0 = 2.5e-6
    Q = 0.23
    GBenergy = 0.708
    molar_volume = 7.11e-6
  []
[]

[Postprocessors]
  [n_nodes]
    type = NumNodes
    execute_on = timestep_end
  []

  [DOFs]
    type = NumDOFs
  []
[]

[Executioner]
  type = Transient
  scheme = 'bdf2'

  #Preconditioned JFNK (default)
  solve_type = 'PJFNK'
  petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart '
                        '-pc_hypre_boomeramg_strong_threshold'
  petsc_options_value = 'hypre boomeramg 31 0.7'
  l_tol = 1.0e-4
  l_max_its = 20
  nl_rel_tol = 1.0e-9
  nl_max_its = 20
  start_time = 0.0
  num_steps = 1
  dt = 0.05
[]

[Outputs]
  execute_on = 'initial'
  exodus = true
  perf_graph = true
[]

(modules/combined/examples/phase_field-mechanics/EBSD_reconstruction_grain_growth_mech.i)

# This example reconstructs the grain structure from an EBSD data file
# Then, an isotropic grain model is run with linear elasticity and an anisotropic
# elasticity tensor that uses the measured EBSD angles.
[Mesh]
  [ebsd_mesh]
    type = EBSDMeshGenerator
    uniform_refine = 2 #Mesh can go two levels coarser than the EBSD grid
    filename = IN100_128x128.txt
  []
[]

[GlobalParams]
  op_num = 8
  var_name_base = gr
  displacements = 'disp_x disp_y'
[]

[Variables]
  [PolycrystalVariables] #Polycrystal variable generation (30 order parameters)
  []
  [disp_x]
  []
  [disp_y]
  []
[]

[AuxVariables]
  [bnds]
  []
  [gt_indices]
    order = CONSTANT
    family = MONOMIAL
  []
  [unique_grains]
    order = CONSTANT
    family = MONOMIAL
  []
  [vonmises_stress]
    order = CONSTANT
    family = MONOMIAL
  []
  [C1111]
    order = CONSTANT
    family = MONOMIAL
  []
  [phi1]
    order = CONSTANT
    family = MONOMIAL
  []
  [Phi]
    order = CONSTANT
    family = MONOMIAL
  []
  [phi2]
    order = CONSTANT
    family = MONOMIAL
  []
  [EBSD_grain]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[ICs]
  [PolycrystalICs]
    [ReconVarIC]
      ebsd_reader = ebsd
      coloring_algorithm = bt
    []
  []
[]

[Kernels]
  [PolycrystalKernel]
  []
  [PolycrystalElasticDrivingForce]
  []
  [TensorMechanics]
  []
[]

[AuxKernels]
  [BndsCalc]
    type = BndsCalcAux
    variable = bnds
    execute_on = 'initial timestep_end'
  []
  [gt_indices]
    type = FeatureFloodCountAux
    variable = gt_indices
    execute_on = 'initial timestep_end'
    flood_counter = grain_tracker
    field_display = VARIABLE_COLORING
  []
  [unique_grains]
    type = FeatureFloodCountAux
    variable = unique_grains
    execute_on = 'initial timestep_end'
    flood_counter = grain_tracker
    field_display = UNIQUE_REGION
  []
  [C1111]
    type = RankFourAux
    variable = C1111
    rank_four_tensor = elasticity_tensor
    index_l = 0
    index_j = 0
    index_k = 0
    index_i = 0
    execute_on = timestep_end
  []
  [vonmises_stress]
    type = RankTwoScalarAux
    variable = vonmises_stress
    rank_two_tensor = stress
    scalar_type = VonMisesStress
    execute_on = timestep_end
  []
  [phi1]
    type = OutputEulerAngles
    variable = phi1
    euler_angle_provider = ebsd
    grain_tracker = grain_tracker
    output_euler_angle = 'phi1'
    execute_on = 'initial'
  []
  [Phi]
    type = OutputEulerAngles
    variable = Phi
    euler_angle_provider = ebsd
    grain_tracker = grain_tracker
    output_euler_angle = 'Phi'
    execute_on = 'initial'
  []
  [phi2]
    type = OutputEulerAngles
    variable = phi2
    euler_angle_provider = ebsd
    grain_tracker = grain_tracker
    output_euler_angle = 'phi2'
    execute_on = 'initial'
  []
  [grain_aux]
    type = EBSDReaderPointDataAux
    variable = EBSD_grain
    ebsd_reader = ebsd
    data_name = 'feature_id'
    execute_on = 'initial'
  []
[]

[BCs]
  [top_displacement]
    type = DirichletBC
    variable = disp_y
    boundary = top
    value = -2.0
  []
  [x_anchor]
    type = DirichletBC
    variable = disp_x
    boundary = 'left right'
    value = 0.0
  []
  [y_anchor]
    type = DirichletBC
    variable = disp_y
    boundary = bottom
    value = 0.0
  []
[]

[Modules]
  [PhaseField]
    [EulerAngles2RGB]
      crystal_structure = cubic
      euler_angle_provider = ebsd
      grain_tracker = grain_tracker
    []
  []
[]

[Materials]
  [Copper]
    # T = 500 # K
    type = GBEvolution
    block = 0
    T = 500
    wGB = 0.6 # um
    GBmob0 = 2.5e-6 # m^4/(Js) from Schoenfelder 1997
    Q = 0.23 # Migration energy in eV
    GBenergy = 0.708 # GB energy in J/m^2
    molar_volume = 7.11e-6; # Molar volume in m^3/mol
    length_scale = 1.0e-6
    time_scale = 1.0e-6
  []
  [ElasticityTensor]
    type = ComputePolycrystalElasticityTensor
    grain_tracker = grain_tracker
  []
  [strain]
    type = ComputeSmallStrain
    block = 0
    displacements = 'disp_x disp_y'
  []
  [stress]
    type = ComputeLinearElasticStress
    block = 0
  []
[]

[Postprocessors]
  [dt]
    type = TimestepSize
  []
  [n_elements]
    type = NumElements
    execute_on = 'initial timestep_end'
  []
  [n_nodes]
    type = NumNodes
    execute_on = 'initial timestep_end'
  []
  [DOFs]
    type = NumDOFs
  []
[]

[UserObjects]
  [ebsd]
    type = EBSDReader
  []
  [grain_tracker]
    type = GrainTrackerElasticity
    compute_var_to_feature_map = true
    ebsd_reader = ebsd

    fill_method = symmetric9
    C_ijkl = '1.27e5 0.708e5 0.708e5 1.27e5 0.708e5 1.27e5 0.7355e5 0.7355e5 0.7355e5'
    euler_angle_provider = ebsd
  []
[]

[Executioner]
  type = Transient
  scheme = bdf2
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type -pc_hypre_boomeramg_strong_threshold'
  petsc_options_value = '  hypre    boomeramg                   0.7'
  l_tol = 1.0e-4
  l_max_its = 20
  nl_max_its = 20
  nl_rel_tol = 1.0e-8
  start_time = 0.0
  num_steps = 30
  dt = 10
  [Adaptivity]
    initial_adaptivity = 0
    refine_fraction = 0.7
    coarsen_fraction = 0.1
    max_h_level = 2
  []
  [TimeStepper]
    type = IterationAdaptiveDT
    cutback_factor = 0.9
    dt = 10.0
    growth_factor = 1.1
    optimal_iterations = 7
  []
[]

[Outputs]
  csv = true
  exodus = true
[]

Overview
Example Input File Syntax
Input Parameters
Input Files