Add multi-scale-grain-growth inputs

problems/physics/multi-scale-grain-growth/grain_growth_2D_bottom.i

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+# This simulation predicts GB migration of a 2D copper polycrystal with 100 grains represented with 18 order parameters
+# Mesh adaptivity and time step adaptivity are used
+# An AuxVariable is used to calculate the grain boundary locations
+# Postprocessors are used to record time step and the number of grains
+
+[Mesh]
+  # Mesh block.  Meshes can be read in or automatically generated
+  type = GeneratedMesh
+  dim = 2 # Problem dimension
+  nx = 11 # Number of elements in the x-direction
+  ny = 11 # Number of elements in the y-direction
+  xmin = 0    # minimum x-coordinate of the mesh
+  xmax = 1e5 # maximum x-coordinate of the mesh
+  ymin = 0    # minimum y-coordinate of the mesh
+  ymax = 1e5 # maximum y-coordinate of the mesh
+  elem_type = QUAD4  # Type of elements used in the mesh
+  uniform_refine = 3 # Initial uniform refinement of the mesh
+
+  parallel_type = replicated # Periodic BCs
+[]
+
+[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
+[]
+
+[Variables]
+  # Variable block, where all variables in the simulation are declared
+  [./PolycrystalVariables]
+  [../]
+[]
+
+[UserObjects]
+  [./voronoi]
+    type = PolycrystalVoronoi
+    grain_num = 100 # Number of grains
+    rand_seed = 20
+  [../]
+  [./grain_tracker]
+    type = GrainTracker
+    threshold = 0.2
+    connecting_threshold = 0.08
+    compute_halo_maps = true # Only necessary for displaying HALOS
+  [../]
+[]
+
+[ICs]
+  [./PolycrystalICs]
+    [./PolycrystalColoringIC]
+      polycrystal_ic_uo = voronoi
+    [../]
+  [../]
+[]
+
+[AuxVariables]
+  # Dependent variables
+  [./bnds]
+    # Variable used to visualize the grain boundaries in the simulation
+  [../]
+  [./unique_grains]
+    order = CONSTANT
+    family = MONOMIAL
+  [../]
+  [./var_indices]
+    order = CONSTANT
+    family = MONOMIAL
+  [../]
+  [./ghost_regions]
+    order = CONSTANT
+    family = MONOMIAL
+  [../]
+  [./halos]
+    order = CONSTANT
+    family = MONOMIAL
+  [../]
+  [./T_1000K]
+    initial_condition = 0.298
+  [../]
+  [./T]
+    initial_condition = 298
+  [../]
+[]
+
+[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'
+  [../]
+  [./temp_conversion]
+    type = ParsedAux
+    args = 'T_1000K'
+    function = '1000 * T_1000K'
+    variable = T
+  [../]
+[]
+
+[BCs]
+  # Boundary Condition block
+  [./Periodic]
+    [./top_bottom]
+      auto_direction = 'x y'
+    [../]
+  [../]
+[]
+
+[Materials]
+  [./CuGrGr]
+    # Material properties
+    type = GBEvolution
+    T = T # Specified temperature profile
+    wGB = 1e3 # Width of the diffuse GB
+    GBmob0 = 3.19e-4 #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
+  [../]
+  [./num_dofs]
+    type = NumDOFs
+  [../]
+[]
+
+[Preconditioning]
+  [smp]
+    type = SMP
+    full = true
+  []
+[]
+
+[Executioner]
+  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
+
+  #Preconditioned JFNK (default)
+  solve_type = 'NEWTON'
+
+  # Uses newton iteration to solve the problem.
+  petsc_options_iname = '-pc_type -ksp_gmres_restart'
+  petsc_options_value = 'asm 101'
+
+  l_max_its = 30 # Max number of linear iterations
+  l_tol = 1e-4 # Relative tolerance for linear solves
+  nl_max_its = 12 # Max number of nonlinear iterations
+  nl_rel_tol = 1e-10 # Absolute tolerance for nonlienar solves
+
+  start_time = 0.0
+  end_time = 4800
+
+  [./TimeStepper]
+    type = IterationAdaptiveDT
+    dt = 25 # Initial time step.  In this simulation it changes.
+    optimal_iterations = 8 # Time step will adapt to maintain this number of nonlinear iterations
+  [../]
+
+  [./Adaptivity]
+    # Block that turns on mesh adaptivity. Note that mesh will never coarsen beyond initial mesh (before uniform refinement)
+    initial_adaptivity = 2 # Number of times mesh is adapted to initial condition
+    refine_fraction = 0.7 # Fraction of high error that will be refined
+    coarsen_fraction = 0.1 # Fraction of low error that will coarsened
+    max_h_level = 4 # Max number of refinements used, starting from initial mesh (before uniform refinement)
+  [../]
+[]
+
+[Outputs]
+  exodus = true # Exodus file will be outputted
+  csv = true
+  [./console]
+    type = Console
+    max_rows = 20 # Will print the 20 most recent postprocessor values to the screen
+  [../]
+[]