EBSDMeshGenerator

Mesh generated from a specified DREAM.3D EBSD data file.

The mesh is generated from the EBSD information, to get an optimal reconstruction of the data. This is accomplished in the mesh block using the EBSDMeshGenerator type. The same data file used with the EBSD reader is used in the EBSDReader UserObject. The mesh is created with one node per data point in the EBSD data file. If you wish to use mesh adaptivity and allow the mesh to get coarser during the simulation, the "uniform_refine" parameter is used to set how many times the mesh can be coarsened. For this to work the number of elements along _each_ dimension has to be divisible by $var element = document.getElementById("moose-equation-f52e5bf4-f1e2-447f-bdc6-a4b2bacaa382");katex.render("2^u", element, {displayMode:false,throwOnError:false,macros:{"\\pf":"\\frac{\\partial #1}{\\partial #2}"}});$ where $var element = document.getElementById("moose-equation-606c414d-49c6-4572-81b3-698acce75d30");katex.render("u", element, {displayMode:false,throwOnError:false,macros:{"\\pf":"\\frac{\\partial #1}{\\partial #2}"}});$ is the value of the "uniform_refine" parameter.

warning:"uniform_refine" parameter

Contrary to other mesh objects the "uniform_refine" parameter will not affect the resolution of the final mesh. It sets the levels of coarsening that can be applied to the EBSD data.

Input Parameters

filenameThe name of the file containing the EBSD data
C++ Type:FileName
Options:
Description:The name of the file containing the EBSD data

Required Parameters

bias_x1The amount by which to grow (or shrink) the cells in the x-direction.
Default:1
C++ Type:double
Options:
Description:The amount by which to grow (or shrink) the cells in the x-direction.
bias_y1The amount by which to grow (or shrink) the cells in the y-direction.
Default:1
C++ Type:double
Options:
Description:The amount by which to grow (or shrink) the cells in the y-direction.
bias_z1The amount by which to grow (or shrink) the cells in the z-direction.
Default:1
C++ Type:double
Options:
Description:The amount by which to grow (or shrink) the cells in the z-direction.
boundary_id_offset0This offset is added to the generated boundary IDs
Default:0
C++ Type:short
Options:
Description:This offset is added to the generated boundary IDs
boundary_name_prefixIf provided, prefix the built in boundary names with this string
C++ Type:std::string
Options:
Description:If provided, prefix the built in boundary names with this string
elem_typeThe type of element from libMesh to generate (default: linear element for requested dimension)
C++ Type:MooseEnum
Options:EDGE, EDGE2, EDGE3, EDGE4, QUAD, QUAD4, QUAD8, QUAD9, TRI3, TRI6, HEX, HEX8, HEX20, HEX27, TET4, TET10, PRISM6, PRISM15, PRISM18, PYRAMID5, PYRAMID13, PYRAMID14
Description:The type of element from libMesh to generate (default: linear element for requested dimension)
extra_element_integersNames of extra element integers
C++ Type:std::vector<ExtraElementIDName>
Options:
Description:Names of extra element integers
gauss_lobatto_gridFalseGrade mesh into boundaries according to Gauss-Lobatto quadrature spacing.
Default:False
C++ Type:bool
Options:
Description:Grade mesh into boundaries according to Gauss-Lobatto quadrature spacing.
show_infoFalseWhether or not to show mesh info after generating the mesh (bounding box, element types, sidesets, nodesets, subdomains, etc)
Default:False
C++ Type:bool
Options:
Description:Whether or not to show mesh info after generating the mesh (bounding box, element types, sidesets, nodesets, subdomains, etc)
uniform_refine0Number of coarsening levels available in adaptive mesh refinement.
Default:0
C++ Type:unsigned int
Options:
Description:Number of coarsening levels available in adaptive mesh refinement.

Optional Parameters

control_tagsAdds user-defined labels for accessing object parameters via control logic.
C++ Type:std::vector<std::string>
Options:
Description:Adds user-defined labels for accessing object parameters via control logic.
enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Options:
Description:Set the enabled status of the MooseObject.

Advanced Parameters

Input Files

(modules/phase_field/test/tests/reconstruction/2phase_reconstruction4.i)
(modules/phase_field/test/tests/reconstruction/2phase_reconstruction3.i)
(modules/phase_field/examples/ebsd_reconstruction/IN100-111grn.i)
(modules/phase_field/test/tests/reconstruction/EulerAngleVariables2RGBAux.i)
(modules/phase_field/test/tests/grain_tracker_test/grain_tracker_ebsd.i)
(modules/phase_field/test/tests/reconstruction/2phase_reconstruction.i)
(modules/phase_field/test/tests/reconstruction/1phase_evolution.i)
(modules/phase_field/test/tests/reconstruction/euler2rgb_no_grain_region.i)
(modules/phase_field/test/tests/reconstruction/2phase_reconstruction2.i)
(modules/combined/examples/phase_field-mechanics/EBSD_reconstruction_grain_growth_mech.i)
(modules/phase_field/test/tests/reconstruction/1phase_reconstruction.i)
(modules/phase_field/test/tests/reconstruction/euler2rgb_non_uniform_orientation.i)
(modules/phase_field/test/tests/grain_tracker_test/split_grain.i)

(modules/phase_field/test/tests/reconstruction/2phase_reconstruction4.i)

#
# In this test we set the initial condition of a set of order parameters
# by pulling out the only grains from given EBSD data file that belong to a specified phase
#

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

[Mesh]
  [ebsd_mesh]
    type = EBSDMeshGenerator
    filename = ebsd_40x40_2_phase.txt
  []
[]

[GlobalParams]
  op_num = 6
  var_name_base = gr
[]

[UserObjects]
  [ebsd_reader]
    type = EBSDReader
  []
  [ebsd]
    type = PolycrystalEBSD
    coloring_algorithm = bt
    ebsd_reader = ebsd_reader
    phase = 2
    output_adjacency_matrix = true
  []
  [grain_tracker]
    type = GrainTracker
    polycrystal_ic_uo = ebsd
    remap_grains = false
  []
[]

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

[AuxKernels]
  [var_indices]
    type = FeatureFloodCountAux
    variable = var_indices
    flood_counter = grain_tracker
    field_display = VARIABLE_COLORING
  []
[]

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

[Variables]
  [PolycrystalVariables]
  []
[]

[Executioner]
  type = Transient
  num_steps = 0
[]

[Outputs]
  exodus = true
[]

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

[Mesh]
  [ebsd_mesh]
    type = EBSDMeshGenerator
    filename = IN100_120x120.txt
    uniform_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 = NumElems
    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/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 = 'test.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/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/reconstruction/1phase_evolution.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.
#

[Mesh]
  [ebsd_mesh]
    type = EBSDMeshGenerator
    filename = IN100_001_28x28_Marmot.txt
  []
[]

[GlobalParams]
  op_num = 5
  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
    polycrystal_ic_uo = ebsd
  []
[]

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

[Variables]
  [PolycrystalVariables]
  []
[]

[Kernels]
  [PolycrystalKernel]
  []
[]

[AuxVariables]
  [feature]
    family = MONOMIAL
    order = CONSTANT
  []
  [bnds]
  []
[]

[AuxKernels]
  [feature]
    type = EBSDReaderAvgDataAux
    variable = feature
    ebsd_reader = ebsd_reader
    grain_tracker = grain_tracker
    data_name = feature_id
    execute_on = 'initial timestep_end'
  []
  [bnds]
    type = BndsCalcAux
    variable = bnds
    execute_on = 'initial timestep_end'
  []
[]

[Materials]
  [CuGrGr]
    # Material properties
    type = GBEvolution # Quantitative material properties for copper grain growth.  Dimensions are nm and ns
    block = 0 # Block ID (only one block in this problem)
    GBmob0 = 2.5e-6 #Mobility prefactor for Cu from Schonfelder1997
    GBenergy = 0.708 # GB energy in J/m^2
    Q = 0.23 #Activation energy for grain growth from Schonfelder 1997
    T = 500 # K   #Constant temperature of the simulation (for mobility calculation)
    wGB = 1 # nm    #Width of the diffuse GB
    #outputs = exodus
    length_scale = 1e-06
    time_scale = 1e-6
  []
[]

[Executioner]
  type = Transient
  num_steps = 2
  dt = 10
[]

[Outputs]
  exodus = true
[]

(modules/phase_field/test/tests/reconstruction/euler2rgb_no_grain_region.i)

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

[GlobalParams]
  op_num = 8
  var_name_base = gr
[]

[UserObjects]
  [ebsd_reader]
    type = EBSDReader
    execute_on = initial
  []
  [ebsd]
    type = PolycrystalEBSD
    coloring_algorithm = bt
    ebsd_reader = ebsd_reader
    phase = 2
    output_adjacency_matrix = true
  []
  [grain_tracker]
    type = GrainTracker
    polycrystal_ic_uo = ebsd
  []
[]

[ICs]
  [PolycrystalICs]
    [PolycrystalColoringIC]
      polycrystal_ic_uo = ebsd
    []
  []
  [void_phase]
    type = ReconPhaseVarIC
    variable = c
    ebsd_reader = ebsd_reader
    phase = 1
  []
[]

[Variables]
  [PolycrystalVariables]
  []
[]

[AuxVariables]
  #  active = 'c bnds'

  [c]
  []
  [bnds]
  []
  [ebsd_numbers]
    family = MONOMIAL
    order = CONSTANT
  []

  # Note: Not active
  [unique_grains]
    family = MONOMIAL
    order = CONSTANT
  []
  [var_indices]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[Kernels]
  [PolycrystalKernel]
    c = c
  []
[]

[AuxKernels]
  #  active = 'BndsCalc'

  [BndsCalc]
    type = BndsCalcAux
    variable = bnds
    execute_on = 'initial timestep_end'
  []
  [ebsd_numbers]
    type = EBSDReaderAvgDataAux
    data_name = feature_id
    ebsd_reader = ebsd_reader
    grain_tracker = grain_tracker
    variable = ebsd_numbers
    phase = 2
    execute_on = 'initial timestep_end'
  []

  # Note: Not active
  [unique_grains]
    type = FeatureFloodCountAux
    variable = unique_grains
    flood_counter = grain_tracker
    field_display = UNIQUE_REGION
    execute_on = 'initial timestep_end'
  []
  [var_indices]
    type = FeatureFloodCountAux
    variable = var_indices
    flood_counter = grain_tracker
    field_display = VARIABLE_COLORING
    execute_on = 'initial timestep_end'
  []
[]

[Modules]
  [PhaseField]
    [EulerAngles2RGB]
      crystal_structure = cubic
      grain_tracker = grain_tracker
      euler_angle_provider = ebsd_reader
      no_grain_color = '.1 .1 .1'
      phase = 2
    []
  []
[]

[Materials]
  [bulk]
    type = GBEvolution
    block = 0
    T = 2273
    wGB = 10.0
    GBenergy = 1.58
    GBmob0 = 9.2124e-9
    Q = 2.77
    length_scale = 1.0e-6
    time_scale = 60.0
  []
[]

[Executioner]
  type = Transient
  scheme = bdf2
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -sub_pc_type -pc_asm_overlap -ksp_grmres_restart '
  petsc_options_value = '   asm        lu            1               21'
  start_time = 0.0
  dt = 0.2
  num_steps = 1
[]

[Outputs]
  csv = true
  exodus = true
  execute_on = 'INITIAL TIMESTEP_END'
  perf_graph = true
[]

(modules/phase_field/test/tests/reconstruction/2phase_reconstruction2.i)

#
# In this test we set the initial condition of a set of order parameters
# by pulling out the only grains from given EBSD data file that belong to a specified phase
#

[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]
  [ebsd_mesh]
    type = EBSDMeshGenerator
    filename = Ti_2Phase_28x28_ebsd.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
  []
[]

[Variables]
  [PolycrystalVariables]
  []
[]

[ICs]
  [PolycrystalICs]
    [PolycrystalColoringIC]
      # select only data for phase 1 from the EBSD file
      polycrystal_ic_uo = ebsd
    []
  []
[]
#ENDDOC - End of the file section that is included in the documentation. Do not change this line!

[Executioner]
  type = Transient
  num_steps = 0
[]

[Outputs]
  exodus = 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 = NumElems
    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
[]

(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/euler2rgb_non_uniform_orientation.i)

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

[GlobalParams]
  op_num = 10
  var_name_base = gr
[]

[UserObjects]
  [ebsd_reader]
    type = EBSDReader
    bins = 40
  []
  [ebsd]
    type = PolycrystalEBSD
    coloring_algorithm = jp
    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]
  []
[]

[Kernels]
  [PolycrystalKernel]
  []
[]

[AuxKernels]
  [BndsCalc]
    type = BndsCalcAux
    variable = bnds
    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 = NumElems
    execute_on = 'initial timestep_end'
  []
  [n_nodes]
    type = NumNodes
    execute_on = 'initial timestep_end'
  []
  [DOFs]
    type = NumDOFs
  []
[]

[Executioner]
  type = Transient
  scheme = bdf2
  solve_type = Newton
  petsc_options_iname = '-pc_type -pc_hypre_type -pc_hypre_boomeramg_strong_threshold'
  petsc_options_value = 'hypre    boomeramg      0.7'
  l_tol = 1.0e-6
  l_max_its = 100
  nl_max_its = 20
  nl_rel_tol = 1.0e-8
  start_time = 0.0
  num_steps = 0
[]

[Outputs]
  exodus = true
  perf_graph = 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 = NumElems
    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
[]

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