PolycrystalColoringICAction

Action to create ICs for polycrystal variables from a UserObject

Overview

This simplifies the syntax for creating polycrystal ICs. It automatically creates an IC for each variable used in the grain growth model. It works for both the traditional phase field grain growth model and the linearized interface grain growth model. Depending on the value of linearized_interface, two different ICs are used for each variable:

For linearized_interface = false, PolycrystalColoringIC is used.
For linearized_interface = true, PolycrystalColoringICLinearizedInterface is used.

Both of these ICs require a UserObject to define the actual polycrystal geometry. See Polycrystal ICs for more information and a full list of the options.

Example Input File Syntax

For linearized_interface = false

[GlobalParams]
  # Parameters used by several kernels that are defined globally to simplify input file
  op_num = '8' # Number of order parameters used
  var_name_base = 'gr' # Base name of grains
  order = 'CONSTANT'
  family = 'MONOMIAL'
[]

[ICs]
  [PolycrystalICs]
    [PolycrystalColoringIC]
      polycrystal_ic_uo = voronoi
    []
  []
[]

For linearized_interface = true

[GlobalParams]
  bound_value = 5.0
  op_num = 5
  var_name_base = phi
[]

[ICs]
  [PolycrystalICs]
    [PolycrystalColoringIC]
      polycrystal_ic_uo = RandomVoronoi
      linearized_interface = true
    []
  []
[]

Input Parameters

op_numnumber of order parameters to create
C++ Type:unsigned int
Controllable:No
Description:number of order parameters to create
polycrystal_ic_uoOptional: TODO
C++ Type:UserObjectName
Controllable:No
Description:Optional: TODO
var_name_basespecifies the base name of the variables
C++ Type:std::string
Controllable:No
Description:specifies the base name of the variables

Required Parameters

active__all__ If specified only the blocks named will be visited and made active
Default:__all__
C++ Type:std::vector<std::string>
Controllable:No
Description:If specified only the blocks named will be visited and made active
blockBlock restriction for the initial condition
C++ Type:std::vector<SubdomainName>
Controllable:No
Description:Block restriction for the initial condition
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.
inactiveIf specified blocks matching these identifiers will be skipped.
C++ Type:std::vector<std::string>
Controllable:No
Description:If specified blocks matching these identifiers will be skipped.

Optional Parameters

bound_value5Bound value used to keep variable between +/-bound. Must be positive.
Default:5
C++ Type:double
Controllable:No
Description:Bound value used to keep variable between +/-bound. Must be positive.
linearized_interfaceFalseWhether to use linearized interface or the standard model
Default:False
C++ Type:bool
Controllable:No
Description:Whether to use linearized interface or the standard model

Linearizedinterface Parameters

(../moose/modules/phase_field/test/tests/grain_tracker_test/distributed_poly_ic.i)

[Mesh]
  # Mesh block.  Meshes can be read in or automatically generated
  type = GeneratedMesh
  uniform_refine = 1 # Initial uniform refinement of the mesh
  dim = 2 # Problem dimension
  nx = 12 # Number of elements in the x-direction
  ny = 12 # Number of elements in the y-direction
  xmax = 1000 # maximum x-coordinate of the mesh
  ymax = 1000 # maximum y-coordinate of the mesh
  elem_type = QUAD4 # Type of elements used in the mesh
  parallel_type = distributed
[]

[GlobalParams]
  # Parameters used by several kernels that are defined globally to simplify input file
  op_num = '8' # Number of order parameters used
  var_name_base = 'gr' # Base name of grains
  order = 'CONSTANT'
  family = 'MONOMIAL'
[]

[Variables]
  # Variable block, where all variables in the simulation are declared
  [PolycrystalVariables]
    order = FIRST
    family = LAGRANGE
  []
[]

[UserObjects]
  [voronoi]
    type = PolycrystalVoronoi
    grain_num = 12 # Number of grains
    coloring_algorithm = jp
    rand_seed = 10
  []
  [grain_tracker]
    type = GrainTracker
    threshold = 0.2
    verbosity_level = 1
    connecting_threshold = 0.08
    flood_entity_type = ELEMENTAL
    compute_halo_maps = true # For displaying HALO fields
    execute_on = 'initial timestep_end'
    polycrystal_ic_uo = voronoi
  []
[]

[ICs]
  [PolycrystalICs]
    [PolycrystalColoringIC]
      polycrystal_ic_uo = voronoi
    []
  []
[]

[AuxVariables]
  # Dependent variables
  [bnds]
    # Variable used to visualize the grain boundaries in the simulation
    order = FIRST
    family = LAGRANGE
  []
  [unique_grains]
  []
  [var_indices]
  []
  [ghost_regions]
  []
  [halos]
  []
  [halo0]
  []
  [halo1]
  []
  [halo2]
  []
  [halo3]
  []
  [halo4]
  []
  [halo5]
  []
  [halo6]
  []
  [halo7]
  []
  [centroids]
    order = CONSTANT
    family = MONOMIAL
  []
  [proc_id]
  []
  [voronoi_id]
  []
  [evaluable_elems]
  []
[]

[Kernels]
  # Kernel block, where the kernels defining the residual equations are set up.
  [PolycrystalKernel]
    # Custom action creating all necessary kernels for grain growth.  All input parameters are up in GlobalParams
  []
[]

[AuxKernels]
  # AuxKernel block, defining the equations used to calculate the auxvars
  [bnds_aux]
    # AuxKernel that calculates the GB term
    type = BndsCalcAux
    variable = bnds
    execute_on = 'initial timestep_end'
  []
  [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'
  []
  [ghosted_entities]
    type = FeatureFloodCountAux
    variable = ghost_regions
    flood_counter = grain_tracker
    field_display = GHOSTED_ENTITIES
    execute_on = 'initial timestep_end'
  []
  [halos]
    type = FeatureFloodCountAux
    variable = halos
    flood_counter = grain_tracker
    field_display = HALOS
    execute_on = 'initial timestep_end'
  []
  [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
  []
  [halo4]
    type = FeatureFloodCountAux
    variable = halo4
    map_index = 4
    field_display = HALOS
    flood_counter = grain_tracker
  []
  [halo5]
    type = FeatureFloodCountAux
    variable = halo5
    map_index = 5
    field_display = HALOS
    flood_counter = grain_tracker
  []
  [halo6]
    type = FeatureFloodCountAux
    variable = halo6
    map_index = 6
    field_display = HALOS
    flood_counter = grain_tracker
  []
  [halo7]
    type = FeatureFloodCountAux
    variable = halo7
    map_index = 7
    field_display = HALOS
    flood_counter = grain_tracker
  []
  [centroids]
    type = FeatureFloodCountAux
    variable = centroids
    execute_on = 'timestep_end'
    field_display = CENTROID
    flood_counter = grain_tracker
  []
  [proc_id]
    type = ProcessorIDAux
    variable = proc_id
    execute_on = 'initial'
  []
  [voronoi_id]
    type = VoronoiICAux
    variable = voronoi_id
    execute_on = 'initial'
    polycrystal_ic_uo = voronoi
  []
[]

[Materials]
  [CuGrGr]
    # Material properties
    type = GBEvolution
    T = '450' # Constant temperature of the simulation (for mobility calculation)
    wGB = 125 # Width of the diffuse GB
    GBmob0 = 2.5e-6 # m^4(Js) for copper from Schoenfelder1997
    Q = 0.23 # eV for copper from Schoenfelder1997
    GBenergy = 0.708 # J/m^2 from Schoenfelder1997
  []
[]

[Postprocessors]
  # Scalar postprocessors
  [dt]
    # Outputs the current time step
    type = TimestepSize
  []
[]

[Executioner]
  # Uses newton iteration to solve the problem.
  type = Transient # Type of executioner, here it is transient with an adaptive time step
  scheme = bdf2 # Type of time integration (2nd order backward euler), defaults to 1st order backward euler
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -mat_mffd_type'
  petsc_options_value = 'hypre boomeramg 101 ds'
  l_max_its = 30 # Max number of linear iterations
  l_tol = 1e-4 # Relative tolerance for linear solves
  nl_max_its = 40 # Max number of nonlinear iterations
  nl_rel_tol = 1e-10 # Absolute tolerance for nonlienar solves
  start_time = 0.0
  num_steps = 2
  dt = 300
[]

[Outputs]
  csv = true
[]

(../moose/modules/phase_field/test/tests/grain_tracker_test/distributed_poly_ic.i)

[Mesh]
  # Mesh block.  Meshes can be read in or automatically generated
  type = GeneratedMesh
  uniform_refine = 1 # Initial uniform refinement of the mesh
  dim = 2 # Problem dimension
  nx = 12 # Number of elements in the x-direction
  ny = 12 # Number of elements in the y-direction
  xmax = 1000 # maximum x-coordinate of the mesh
  ymax = 1000 # maximum y-coordinate of the mesh
  elem_type = QUAD4 # Type of elements used in the mesh
  parallel_type = distributed
[]

[GlobalParams]
  # Parameters used by several kernels that are defined globally to simplify input file
  op_num = '8' # Number of order parameters used
  var_name_base = 'gr' # Base name of grains
  order = 'CONSTANT'
  family = 'MONOMIAL'
[]

[Variables]
  # Variable block, where all variables in the simulation are declared
  [PolycrystalVariables]
    order = FIRST
    family = LAGRANGE
  []
[]

[UserObjects]
  [voronoi]
    type = PolycrystalVoronoi
    grain_num = 12 # Number of grains
    coloring_algorithm = jp
    rand_seed = 10
  []
  [grain_tracker]
    type = GrainTracker
    threshold = 0.2
    verbosity_level = 1
    connecting_threshold = 0.08
    flood_entity_type = ELEMENTAL
    compute_halo_maps = true # For displaying HALO fields
    execute_on = 'initial timestep_end'
    polycrystal_ic_uo = voronoi
  []
[]

[ICs]
  [PolycrystalICs]
    [PolycrystalColoringIC]
      polycrystal_ic_uo = voronoi
    []
  []
[]

[AuxVariables]
  # Dependent variables
  [bnds]
    # Variable used to visualize the grain boundaries in the simulation
    order = FIRST
    family = LAGRANGE
  []
  [unique_grains]
  []
  [var_indices]
  []
  [ghost_regions]
  []
  [halos]
  []
  [halo0]
  []
  [halo1]
  []
  [halo2]
  []
  [halo3]
  []
  [halo4]
  []
  [halo5]
  []
  [halo6]
  []
  [halo7]
  []
  [centroids]
    order = CONSTANT
    family = MONOMIAL
  []
  [proc_id]
  []
  [voronoi_id]
  []
  [evaluable_elems]
  []
[]

[Kernels]
  # Kernel block, where the kernels defining the residual equations are set up.
  [PolycrystalKernel]
    # Custom action creating all necessary kernels for grain growth.  All input parameters are up in GlobalParams
  []
[]

[AuxKernels]
  # AuxKernel block, defining the equations used to calculate the auxvars
  [bnds_aux]
    # AuxKernel that calculates the GB term
    type = BndsCalcAux
    variable = bnds
    execute_on = 'initial timestep_end'
  []
  [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'
  []
  [ghosted_entities]
    type = FeatureFloodCountAux
    variable = ghost_regions
    flood_counter = grain_tracker
    field_display = GHOSTED_ENTITIES
    execute_on = 'initial timestep_end'
  []
  [halos]
    type = FeatureFloodCountAux
    variable = halos
    flood_counter = grain_tracker
    field_display = HALOS
    execute_on = 'initial timestep_end'
  []
  [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
  []
  [halo4]
    type = FeatureFloodCountAux
    variable = halo4
    map_index = 4
    field_display = HALOS
    flood_counter = grain_tracker
  []
  [halo5]
    type = FeatureFloodCountAux
    variable = halo5
    map_index = 5
    field_display = HALOS
    flood_counter = grain_tracker
  []
  [halo6]
    type = FeatureFloodCountAux
    variable = halo6
    map_index = 6
    field_display = HALOS
    flood_counter = grain_tracker
  []
  [halo7]
    type = FeatureFloodCountAux
    variable = halo7
    map_index = 7
    field_display = HALOS
    flood_counter = grain_tracker
  []
  [centroids]
    type = FeatureFloodCountAux
    variable = centroids
    execute_on = 'timestep_end'
    field_display = CENTROID
    flood_counter = grain_tracker
  []
  [proc_id]
    type = ProcessorIDAux
    variable = proc_id
    execute_on = 'initial'
  []
  [voronoi_id]
    type = VoronoiICAux
    variable = voronoi_id
    execute_on = 'initial'
    polycrystal_ic_uo = voronoi
  []
[]

[Materials]
  [CuGrGr]
    # Material properties
    type = GBEvolution
    T = '450' # Constant temperature of the simulation (for mobility calculation)
    wGB = 125 # Width of the diffuse GB
    GBmob0 = 2.5e-6 # m^4(Js) for copper from Schoenfelder1997
    Q = 0.23 # eV for copper from Schoenfelder1997
    GBenergy = 0.708 # J/m^2 from Schoenfelder1997
  []
[]

[Postprocessors]
  # Scalar postprocessors
  [dt]
    # Outputs the current time step
    type = TimestepSize
  []
[]

[Executioner]
  # Uses newton iteration to solve the problem.
  type = Transient # Type of executioner, here it is transient with an adaptive time step
  scheme = bdf2 # Type of time integration (2nd order backward euler), defaults to 1st order backward euler
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -mat_mffd_type'
  petsc_options_value = 'hypre boomeramg 101 ds'
  l_max_its = 30 # Max number of linear iterations
  l_tol = 1e-4 # Relative tolerance for linear solves
  nl_max_its = 40 # Max number of nonlinear iterations
  nl_rel_tol = 1e-10 # Absolute tolerance for nonlienar solves
  start_time = 0.0
  num_steps = 2
  dt = 300
[]

[Outputs]
  csv = true
[]

(../moose/modules/phase_field/test/tests/grain_growth_w_linearized_interface/voronoi_linearized_interface.i)

[GlobalParams]
  bound_value = 5.0
  op_num = 5
  var_name_base = phi
[]

[Mesh]
  type = GeneratedMesh
  dim = 2
  xmax = 100
  ymax = 100
  nx = 20
  ny = 20
[]

[Modules]
  [PhaseField]
    [GrainGrowthLinearizedInterface]
      op_name_base = gr
      mobility = L
      kappa = kappa_op
    []
  []
[]

[ICs]
  [PolycrystalICs]
    [PolycrystalColoringIC]
      polycrystal_ic_uo = RandomVoronoi
      linearized_interface = true
    []
  []
[]

[UserObjects]
  [RandomVoronoi]
    type = PolycrystalVoronoi
    grain_num = 5
    int_width = 10
    rand_seed = 103838
  []
[]

[Materials]
  [GBEovlution]
    type = GBEvolution
    GBenergy = 0.97
    GBMobility = 0.6e-6
    T = 300
    wGB = 10
  []
[]

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

  petsc_options_iname = '-pc_type -ksp_type -snes_type'
  petsc_options_value = 'bjacobi gmres vinewtonrsls'

  dt = 0.05
  num_steps = 1
[]

[Outputs]
  exodus = true
[]

(../moose/modules/phase_field/test/tests/grain_growth_w_linearized_interface/voronoi_linearized_interface.i)

[GlobalParams]
  bound_value = 5.0
  op_num = 5
  var_name_base = phi
[]

[Mesh]
  type = GeneratedMesh
  dim = 2
  xmax = 100
  ymax = 100
  nx = 20
  ny = 20
[]

[Modules]
  [PhaseField]
    [GrainGrowthLinearizedInterface]
      op_name_base = gr
      mobility = L
      kappa = kappa_op
    []
  []
[]

[ICs]
  [PolycrystalICs]
    [PolycrystalColoringIC]
      polycrystal_ic_uo = RandomVoronoi
      linearized_interface = true
    []
  []
[]

[UserObjects]
  [RandomVoronoi]
    type = PolycrystalVoronoi
    grain_num = 5
    int_width = 10
    rand_seed = 103838
  []
[]

[Materials]
  [GBEovlution]
    type = GBEvolution
    GBenergy = 0.97
    GBMobility = 0.6e-6
    T = 300
    wGB = 10
  []
[]

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

  petsc_options_iname = '-pc_type -ksp_type -snes_type'
  petsc_options_value = 'bjacobi gmres vinewtonrsls'

  dt = 0.05
  num_steps = 1
[]

[Outputs]
  exodus = true
[]