ValueThresholdMarker

The refinement state based on a threshold value compared to the specified variable.

Description

The ValueThresholdMarker requires an estimate of error be provided from an Indicator. Using this indicator an element is marked for refinement or coarsening if the element error value above or below the coarsening and refinement thresholds.

By default elements with error greater than the threshold defined in the "refine" parameter will be marked for refinement. Element with error less than the threshold defined in the "coarsen" parameters will be marked for coarsening. This behavior can be inverted using the "invert" parameter.

Additionally, a third buffer region can be defined. Elements in this region may be marked to a different state. Typically, this buffer region is used to define a region of elements that are marked with "DO_NOTHING" to avoid having elements marked for refinement directly adjacent to elements marked for refinement.

Example Input Syntax

[Adaptivity]
  [./Markers]
    [./marker]
      type = ValueThresholdMarker
      coarsen = 0.3
      variable = u
      refine = 0.7
    [../]
    [./inverted_marker]
      type = ValueThresholdMarker
      invert = true
      coarsen = 0.7
      refine = 0.3
      variable = u
      third_state = DO_NOTHING
    [../]
  [../]
[]

Input Parameters

variableThe values of this variable will be compared to 'refine' and 'coarsen' to see what should be done with the element
C++ Type:VariableName
Controllable:No
Description:The values of this variable will be compared to 'refine' and 'coarsen' to see what should be done with the element

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
coarsenThe threshold value for coarsening. Elements with variable values beyond this will be marked for coarsening.
C++ Type:double
Controllable:No
Description:The threshold value for coarsening. Elements with variable values beyond this will be marked for coarsening.
invertFalseIf this is true then values _below_ 'refine' will be refined and _above_ 'coarsen' will be coarsened.
Default:False
C++ Type:bool
Controllable:No
Description:If this is true then values _below_ 'refine' will be refined and _above_ 'coarsen' will be coarsened.
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
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.
refineThe threshold value for refinement. Elements with variable values beyond this will be marked for refinement.
C++ Type:double
Controllable:No
Description:The threshold value for refinement. Elements with variable values beyond this will be marked for refinement.
third_stateDONT_MARKThe Marker state to apply to values falling in-between the coarsen and refine thresholds.
Default:DONT_MARK
C++ Type:MooseEnum
Options:DONT_MARK, COARSEN, DO_NOTHING, REFINE
Controllable:No
Description:The Marker state to apply to values falling in-between the coarsen and refine thresholds.
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.

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:No
Description:Set the enabled status of the MooseObject.
outputsVector of output names where you would like to restrict the output of variables(s) associated with this object
C++ Type:std::vector<OutputName>
Controllable:No
Description:Vector of output names where you would like to restrict the output of variables(s) associated with this object

Advanced Parameters

Input Files

(modules/phase_field/test/tests/GBType/GB_Type_Phase1.i)
(modules/phase_field/test/tests/grain_tracker_test/grain_tracker_test_elemental.i)
(modules/phase_field/examples/nucleation/refine.i)
(modules/phase_field/examples/grain_growth/grain_growth_2D_voronoi_newadapt.i)
(test/tests/markers/value_threshold_marker/value_threshold_marker_test.i)
(test/tests/outputs/output_interface/marker.i)

(test/tests/markers/value_threshold_marker/value_threshold_marker_test.i)

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 10
  ny = 10
  nz = 0
  zmax = 0
  elem_type = QUAD4
[]

[Variables]
  [./u]
    order = FIRST
    family = LAGRANGE
  [../]
[]

[Kernels]
  [./diff]
    type = Diffusion
    variable = u
  [../]
[]

[BCs]
  [./left]
    type = DirichletBC
    variable = u
    boundary = 1
    value = 0
  [../]
  [./right]
    type = DirichletBC
    variable = u
    boundary = 2
    value = 1
  [../]
[]

[Executioner]
  type = Steady

  solve_type = 'PJFNK'
[]

[Adaptivity]
  [./Markers]
    [./marker]
      type = ValueThresholdMarker
      coarsen = 0.3
      variable = u
      refine = 0.7
    [../]
    [./inverted_marker]
      type = ValueThresholdMarker
      invert = true
      coarsen = 0.7
      refine = 0.3
      variable = u
      third_state = DO_NOTHING
    [../]
  [../]
[]

[Outputs]
  exodus = true
[]

(modules/phase_field/test/tests/GBType/GB_Type_Phase1.i)

# MOOSE input file
# Written by Pierre-Clement Simon - Idaho National Laboratory
#
# Project:
# TRISO fuel fission gas transport: Silver diffusion in silicon carbide
#
# Published with:
# ---
#
# Phase Field Model:   Isotropic diffusion equation
# type:                Transient
# Grain structure:     Single grain
# BCs:                 Fixed value on the right, flux on the left
#
#
# Info:
# - Input file used to generate polycrystals for SiC
#
# Updates from previous file:
# -
#
# Units
# length: --
# time: --
# energy: --
# quantity: --

# This simulation predicts GB migration of a 2D copper polycrystal with 15 grains
# Mesh adaptivity (new system) 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
# We are not using the GrainTracker in this example so the number
# of order paramaters must match the number of grains.

[Mesh]
  [ebsd_mesh]
    type = EBSDMeshGenerator
    # Two Parallel Grains
    filename = 'EBSD_ThreeGrains.txt'
  []
[]

[GlobalParams]
  # Parameters used by several kernels that are defined globally to simplify input file
  op_num = 6 # Number of grains
  var_name_base = gr # Base name of grains
[]

[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
    threshold = 0.001
    connecting_threshold = 0.008
    compute_var_to_feature_map = true
    compute_halo_maps = true # For displaying HALO fields
    remap_grains = true
    polycrystal_ic_uo = ebsd
  []
[]

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

[Variables]
  # Variable block, where all variables in the simulation are declared
  [./PolycrystalVariables]
    # Custom action that created all of the grain variables and sets their initial condition
  [../]
[]

[AuxVariables]
  # Dependent variables
  [./bnds]
    # Variable used to visualize the grain boundaries in the simulation
  [../]
  [./unique_grains]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./aphi1]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./bPhi]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./cphi2]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./ebsd_numbers]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

[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'
  [../]
  # generate the unique ID from grain_tracker
  [./unique_grains]
    type = FeatureFloodCountAux
    variable = unique_grains
    execute_on = 'initial timestep_end'
    flood_counter = grain_tracker
    field_display = UNIQUE_REGION
  [../]
  # The phi will output the Euler angle from EBSD data, and the data structure
  # will change with the guide from grain_tracker
  [./aphi1]
    type = OutputEulerAngles
    variable = aphi1
    euler_angle_provider = ebsd_reader
    grain_tracker = grain_tracker
    output_euler_angle = 'phi1'
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
  [./bPhi]
    type = OutputEulerAngles
    variable = bPhi
    euler_angle_provider = ebsd_reader
    grain_tracker = grain_tracker
    output_euler_angle = 'Phi'
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
  [./cphi2]
    type = OutputEulerAngles
    variable = cphi2
    euler_angle_provider = ebsd_reader
    grain_tracker = grain_tracker
    output_euler_angle = 'phi2'
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
  # Import the unique grain ID from ebsd data, and the data structure
  # will change with the guide from grain_tracker
  [ebsd_numbers]
    type = EBSDReaderAvgDataAux
    data_name = feature_id
    ebsd_reader = ebsd_reader
    grain_tracker = grain_tracker
    variable = ebsd_numbers
    execute_on = 'initial timestep_end'
  [../]
[]

[BCs]
  # Boundary Condition block
  [./Periodic]
    [./top_bottom]
      auto_direction = 'x y' # Makes problem periodic in the x and y directions
    [../]
  [../]
[]

[Materials]
  [./CuGrGr]
    # Material properties
    type = GBEvolution # Quantitative material properties for copper grain growth.  Dimensions are nm and ns
    GBmob0 = 2.5e-6 # Mobility prefactor for Cu from schonfelder1997molecular bibtex entry
    GBenergy = 0.708 # GB energy for Cu from schonfelder1997molecular bibtex entry
    Q = 0.23 # Activation energy for grain growth from Schonfelder 1997
    T = 450 # Constant temperature of the simulation (for mobility calculation)
    wGB = 6 # Width of the diffuse GB
  [../]
  [./GB_type]
    # The new developed Miso Bnds Aux Kernel
    type = ComputeGBMisorientationType
    ebsd_reader = ebsd_reader
    grain_tracker = grain_tracker
    output_properties = 'gb_type'
    outputs = exodus
  [../]
[]

[Postprocessors]
  # Scalar postprocessors
  [./dt]
    # Outputs the current time step
    type = TimestepSize
  [../]
  [n_elements]
    type = NumElems
    execute_on = 'initial timestep_end'
  []
  [n_nodes]
    type = NumNodes
    execute_on = 'initial timestep_end'
  []
  [DOFs]
    type = NumDOFs
  []
[]

[Adaptivity]
  initial_steps = 1
  max_h_level = 1
  marker = combined
  [./Indicators]
    [./error]
      type = GradientJumpIndicator
      variable = bnds
    [../]
  [../]
  [./Markers]
    [./bound_adapt]
      type = ValueThresholdMarker
      third_state = DO_NOTHING
      coarsen = 0.999 #1.0
      refine = 0.95 #0.95
      variable = bnds
      invert = true
    [../]
    [./errorfrac]
      type = ErrorFractionMarker
      coarsen = 0.1
      indicator = error
      refine = 0.7
    [../]
    [./combined]
      type = ComboMarker
      markers = 'bound_adapt errorfrac'
    [../]
  [../]
[]

[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 = 'PJFNK'

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

  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_abs_tol = 1e-11 # Relative tolerance for nonlienar solves
  nl_rel_tol = 1e-10 # Absolute tolerance for nonlienar solves

  [TimeStepper]
    type = IterationAdaptiveDT
    cutback_factor = 0.9
    dt = 1
    growth_factor = 1.1
    optimal_iterations = 7
  []

  start_time = 0.0
  num_steps = 2
[]

[Outputs]
  perf_graph = true
  exodus = true
 [./console]
    type = Console
    max_rows = 10
  [../]
[]

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

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 25
  ny = 25
  nz = 0
  xmax = 1000
  ymax = 1000
  zmax = 0
  elem_type = QUAD4
[]

[GlobalParams]
  op_num = 12 # Should match grain_num so we can test with FauxGrainTracker too
  var_name_base = gr
[]

[Variables]
  [./PolycrystalVariables]
  [../]
[]

[UserObjects]
  [./voronoi]
    type = PolycrystalVoronoi
    grain_num = 12 # Number of grains
    coloring_algorithm = bt # bt will assign one grain to each op if they are the same
    rand_seed = 8675
  [../]
  [./grain_tracker]
    type = GrainTracker
  [../]
[]

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

[AuxVariables]
  [./bnds]
    order = FIRST
    family = LAGRANGE
  [../]
  [./unique_grains]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./var_indices]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

[Kernels]
  [./PolycrystalKernel]
  [../]
[]

[AuxKernels]
  [./BndsCalc]
    type = BndsCalcAux
    variable = bnds
  [../]
  [./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
  [../]
[]

[BCs]
  [./Periodic]
    [./all]
      auto_direction = 'x y'
    [../]
  [../]
[]

[Materials]
  [./CuGrGr]
    type = GBEvolution
    T = 500 # K
    wGB = 100 # nm
    GBmob0 = 2.5e-6
    Q = 0.23
    GBenergy = 0.708
    molar_volume = 7.11e-6
  [../]
[]

[Postprocessors]
  [./DOFs]
    type = NumDOFs
  [../]
[]

[Executioner]
  type = Transient
  scheme = bdf2
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
  petsc_options_value = 'hypre boomeramg 31'
  l_tol = 1.0e-4
  l_max_its = 30
  nl_max_its = 20
  nl_rel_tol = 1.0e-9
  start_time = 0.0
  num_steps = 2
  dt = 100.0
[]

[Adaptivity]
  marker = error_marker
  max_h_level = 1
  [./Markers]
    active = 'error_marker'
    [./bnds_marker]
      type = ValueThresholdMarker
      invert = true
      refine = 0.85
      coarsen = 0.975
      third_state = DO_NOTHING
      variable = bnds
    [../]
    [./error_marker]
      type = ErrorFractionMarker
      coarsen = 0.1
      indicator = bnds_error
      refine = 0.7
    [../]
  [../]
  [./Indicators]
    [./bnds_error]
      type = GradientJumpIndicator
      variable = bnds
    [../]
  [../]
[]

[Outputs]
  exodus = true
[]

(modules/phase_field/examples/nucleation/refine.i)

#
# Example derived from cahn_hilliard.i demonstrating the use of Adaptivity
# with the DiscreteNucleation system. The DiscreteNucleationMarker triggers
# mesh refinement for the nucleus geometry. It is up to the user to specify
# refinement for the physics. In this example this is done using a GradientJumpIndicator
# with a ValueThresholdMarker. The nucleation system marker and the physics marker
# must be combined using a ComboMarker to combine their effect.
#

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 10
  ny = 10
  xmax = 500
  ymax = 500
  elem_type = QUAD
[]

[Modules]
  [./PhaseField]
    [./Conserved]
      [./c]
        free_energy = F
        mobility = M
        kappa = kappa_c
        solve_type = REVERSE_SPLIT
      [../]
    [../]
  [../]
[]

[ICs]
  [./c_IC]
    type = ConstantIC
    variable = c
    value = 0.2
  [../]
[]

[Materials]
  [./pfmobility]
    type = GenericConstantMaterial
    prop_names  = 'M kappa_c'
    prop_values = '1 25'
  [../]
  [./chemical_free_energy]
    # simple double well free energy
    type = DerivativeParsedMaterial
    property_name = Fc
    coupled_variables = 'c'
    constant_names       = 'barr_height  cv_eq'
    constant_expressions = '0.1          0'
    expression = 16*barr_height*c^2*(1-c)^2 # +0.01*(c*plog(c,0.005)+(1-c)*plog(1-c,0.005))
    derivative_order = 2
    outputs = exodus
  [../]
  [./probability]
    # This is a made up toy nucleation rate it should be replaced by
    # classical nucleation theory in a real simulation.
    type = ParsedMaterial
    property_name = P
    coupled_variables = c
    expression = 'if(c<0.21,c*1e-8,0)'
    outputs = exodus
  [../]
  [./nucleation]
    # The nucleation material is configured to insert nuclei into the free energy
    # tht force the concentration to go to 0.95, and holds this enforcement for 500
    # time units.
    type = DiscreteNucleation
    property_name = Fn
    op_names  = c
    op_values = 0.90
    penalty = 5
    penalty_mode = MIN
    map = map
    outputs = exodus
  [../]
  [./free_energy]
    # add the chemical and nucleation free energy contributions together
    type = DerivativeSumMaterial
    derivative_order = 2
    coupled_variables = c
    sum_materials = 'Fc Fn'
  [../]
[]

[UserObjects]
  [./inserter]
    # The inserter runs at the end of each time step to add nucleation events
    # that happened during the timestep (if it converged) to the list of nuclei
    type = DiscreteNucleationInserter
    hold_time = 50
    probability = P
    radius = 10
  [../]
  [./map]
    # The map UO runs at the beginning of a timestep and generates a per-element/qp
    # map of nucleus locations. The map is only regenerated if the mesh changed or
    # the list of nuclei was modified.
    # The map converts the nucleation points into finite area objects with a given radius.
    type = DiscreteNucleationMap
    periodic = c
    inserter = inserter
  [../]
[]

[Preconditioning]
  [./SMP]
    type = SMP
    full = true
  [../]
[]

[BCs]
  [./Periodic]
    [./all]
      auto_direction = 'x y'
    [../]
  [../]
[]

[Postprocessors]
  [./dt]
    type = TimestepSize
  [../]
  [./ndof]
    type = NumDOFs
  [../]
  [./rate]
    type = DiscreteNucleationData
    value = RATE
    inserter = inserter
  [../]
  [./dtnuc]
    type = DiscreteNucleationTimeStep
    inserter = inserter
    p2nucleus = 0.0005
    dt_max = 10
  [../]
  [./update]
    type = DiscreteNucleationData
    value = UPDATE
    inserter = inserter
  [../]
  [./count]
    type = DiscreteNucleationData
    value = COUNT
    inserter = inserter
  [../]
[]

[Adaptivity]
  [./Indicators]
    [./jump]
      type = GradientJumpIndicator
      variable = c
    [../]
  [../]
  [./Markers]
    [./nuc]
      type = DiscreteNucleationMarker
      map = map
    [../]
    [./grad]
      type = ValueThresholdMarker
      variable = jump
      coarsen = 0.1
      refine = 0.2
    [../]
    [./combo]
      type = ComboMarker
      markers = 'nuc grad'
    [../]
  [../]
  marker = combo
  cycles_per_step = 3
  recompute_markers_during_cycles = true
  max_h_level = 3
[]

[Executioner]
  type = Transient
  scheme = bdf2
  solve_type = 'PJFNK'
  petsc_options_iname = '-pc_type -sub_pc_type'
  petsc_options_value = 'asm      lu          '

  nl_max_its = 20
  l_tol = 1.0e-4
  nl_rel_tol = 1.0e-10
  nl_abs_tol = 1.0e-10
  start_time = 0.0
  num_steps = 120

  [./TimeStepper]
    type = IterationAdaptiveDT
    dt = 10
    growth_factor = 1.5
    cutback_factor = 0.5
    optimal_iterations = 8
    iteration_window = 2
    timestep_limiting_postprocessor = dtnuc
  [../]
[]

[Outputs]
  exodus = true
  csv = true
  print_linear_residuals = false
[]

(modules/phase_field/examples/grain_growth/grain_growth_2D_voronoi_newadapt.i)

# This simulation predicts GB migration of a 2D copper polycrystal with 15 grains
# Mesh adaptivity (new system) 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
# We are not using the GrainTracker in this example so the number
# of order paramaters must match the number of grains.

[Mesh]
  # Mesh block.  Meshes can be read in or automatically generated
  type = GeneratedMesh
  dim = 2 # Problem dimension
  nx = 12 # Number of elements in the x-direction
  ny = 12 # Number of elements in the y-direction
  nz = 0 # Number of elements in the z-direction
  xmin = 0    # minimum x-coordinate of the mesh
  xmax = 1000 # maximum x-coordinate of the mesh
  ymin = 0    # minimum y-coordinate of the mesh
  ymax = 1000 # maximum y-coordinate of the mesh
  zmin = 0
  zmax = 0
  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 = 15 # Number of grains
  var_name_base = gr # Base name of grains
[]

[UserObjects]
  [./voronoi]
    type = PolycrystalVoronoi
    grain_num = 15
    rand_seed = 42
    coloring_algorithm = bt # We must use bt to force the UserObject to assign one grain to each op
  [../]
[]

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

[Variables]
  # Variable block, where all variables in the simulation are declared
  [./PolycrystalVariables]
    # Custom action that created all of the grain variables and sets their initial condition
  [../]
[]

[AuxVariables]
  # Dependent variables
  [./bnds]
    # Variable used to visualize the grain boundaries in the simulation
  [../]
[]

[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 = timestep_end
  [../]
[]

[BCs]
  # Boundary Condition block
  [./Periodic]
    [./top_bottom]
      auto_direction = 'x y' # Makes problem periodic in the x and y directions
    [../]
  [../]
[]

[Materials]
  [./CuGrGr]
    # Material properties
    type = GBEvolution # Quantitative material properties for copper grain growth.  Dimensions are nm and ns
    GBmob0 = 2.5e-6 # Mobility prefactor for Cu from schonfelder1997molecular bibtex entry
    GBenergy = 0.708 # GB energy for Cu from schonfelder1997molecular bibtex entry
    Q = 0.23 # Activation energy for grain growth from Schonfelder 1997
    T = 450 # Constant temperature of the simulation (for mobility calculation)
    wGB = 14 # Width of the diffuse GB
  [../]
[]

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

[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 = '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_abs_tol = 1e-11 # Relative tolerance for nonlienar solves
  nl_rel_tol = 1e-10 # Absolute tolerance for nonlienar solves

  [./TimeStepper]
    type = SolutionTimeAdaptiveDT
    dt = 25 # Initial time step.  In this simulation it changes.
  [../]

  start_time = 0.0
  end_time = 4000
  num_steps = 3
[]

[Adaptivity]
  marker = errorfrac
  max_h_level = 4
  [./Indicators]
    [./error]
      type = GradientJumpIndicator
      variable = bnds
    [../]
  [../]
  [./Markers]
    [./bound_adapt]
      type = ValueThresholdMarker
      third_state = DO_NOTHING
      coarsen = 1.0
      refine = 0.99
      variable = bnds
      invert = true
    [../]
    [./errorfrac]
      type = ErrorFractionMarker
      coarsen = 0.1
      indicator = error
      refine = 0.7
    [../]
  [../]
[]

[Outputs]
  exodus = true
  csv = true
  [./console]
    type = Console
    max_rows = 20
  [../]
[]

(test/tests/markers/value_threshold_marker/value_threshold_marker_test.i)

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 10
  ny = 10
  nz = 0
  zmax = 0
  elem_type = QUAD4
[]

[Variables]
  [./u]
    order = FIRST
    family = LAGRANGE
  [../]
[]

[Kernels]
  [./diff]
    type = Diffusion
    variable = u
  [../]
[]

[BCs]
  [./left]
    type = DirichletBC
    variable = u
    boundary = 1
    value = 0
  [../]
  [./right]
    type = DirichletBC
    variable = u
    boundary = 2
    value = 1
  [../]
[]

[Executioner]
  type = Steady

  solve_type = 'PJFNK'
[]

[Adaptivity]
  [./Markers]
    [./marker]
      type = ValueThresholdMarker
      coarsen = 0.3
      variable = u
      refine = 0.7
    [../]
    [./inverted_marker]
      type = ValueThresholdMarker
      invert = true
      coarsen = 0.7
      refine = 0.3
      variable = u
      third_state = DO_NOTHING
    [../]
  [../]
[]

[Outputs]
  exodus = true
[]

(test/tests/outputs/output_interface/marker.i)

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 10
  ny = 10
[]

[Variables]
  [./u]
  [../]
[]

[Kernels]
  [./diff]
    type = Diffusion
    variable = u
  [../]
[]

[BCs]
  [./left]
    type = DirichletBC
    variable = u
    boundary = left
    value = 0
  [../]
  [./right]
    type = DirichletBC
    variable = u
    boundary = right
    value = 1
  [../]
[]

[Executioner]
  type = Steady
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

[Adaptivity]
  [./Indicators]
    [./indicator_0]
      type = GradientJumpIndicator
      variable = u
      outputs = none
    [../]
    [./indicator_1]
      type = GradientJumpIndicator
      variable = u
      outputs = none
    [../]
  [../]
  [./Markers]
    [./marker_0]
      type = ValueThresholdMarker
      outputs = markers
      refine = 0.5
      variable = u
    [../]
    [./marker_1]
      type = BoxMarker
      bottom_left = '0.25 0.25 0'
      top_right = '0.75 0.75 0'
      inside = REFINE
      outside = DONT_MARK
      outputs = markers
    [../]
  [../]
[]

[Outputs]
  [./markers]
    type = Exodus
  [../]
  [./no_markers]
    type = Exodus
  [../]
[]

Description
Example Input Syntax
Input Parameters
Input Files