ComboMarker

A marker that converts many markers into a single marker by considering the maximum value of the listed markers (i.e., refinement takes precedent).

Description

The ComboMarker is used to combine multiple markers into a single marker. This is done by taking the maximum value of the marker value from the supplied markers. Therefore, refinement of an element takes precedence.

Example Input Syntax

[Adaptivity]
  [./Markers]
    [./box]
      type = BoxMarker
      bottom_left = '0.3 0.3 0'
      top_right = '0.6 0.6 0'
      inside = refine
      outside = do_nothing
    [../]
    [./combo]
      type = ComboMarker
      markers = 'box box2'
    [../]
    [./box2]
      type = BoxMarker
      bottom_left = '0.5 0.5 0'
      top_right = '0.8 0.8 0'
      inside = refine
      outside = coarsen
    [../]
  [../]
[]

Input Parameters

markersA list of marker names to combine into a single marker.
C++ Type:std::vector<MarkerName>
Options:
Description:A list of marker names to combine into a single marker.

Required Parameters

blockThe list of block ids (SubdomainID) that this object will be applied
C++ Type:std::vector<SubdomainName>
Options:
Description:The list of block ids (SubdomainID) that this object will be applied

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.
outputsVector of output names were you would like to restrict the output of variables(s) associated with this object
C++ Type:std::vector<OutputName>
Options:
Description:Vector of output names were you would like to restrict the output of variables(s) associated with this object

Advanced Parameters

Input Files

(test/tests/executioners/adapt_and_modify/adapt_and_modify_heavy.i)
(test/tests/executioners/adapt_and_modify/adapt_and_modify.i)
(test/tests/markers/dont_mark/dont_mark_test.i)
(test/tests/markers/combo_marker/combo_marker_test.i)
(test/tests/dirackernels/point_caching/point_caching_adaptive_refinement.i)
(modules/phase_field/examples/nucleation/refine.i)

(test/tests/markers/combo_marker/combo_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]
    [./box]
      type = BoxMarker
      bottom_left = '0.3 0.3 0'
      top_right = '0.6 0.6 0'
      inside = refine
      outside = do_nothing
    [../]
    [./combo]
      type = ComboMarker
      markers = 'box box2'
    [../]
    [./box2]
      type = BoxMarker
      bottom_left = '0.5 0.5 0'
      top_right = '0.8 0.8 0'
      inside = refine
      outside = coarsen
    [../]
  [../]
[]

[Outputs]
  exodus = true
[]

(test/tests/executioners/adapt_and_modify/adapt_and_modify_heavy.i)

[Mesh]
  # This example uses Adaptivity Indicators, which are written out as
  # CONSTANT MONOMIAL variables, which don't currently work correctly
  # 2122 for more information.
  type = GeneratedMesh
  dim = 2
  nx = 15
  ny = 15
#  parallel_type = replicated
[]

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

[AuxVariables]
  [./elem]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

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

[AuxKernels]
  [./elem]
    type = UniqueIDAux
    variable = elem
    execute_on = timestep_begin
  [../]
[]

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

[UserObjects]
  [./rh_uo]
    type = RandomHitUserObject
    execute_on = timestep_begin
    num_hits = 1
  [../]
  [./rhsm]
    type = RandomHitSolutionModifier
    execute_on = custom
    modify = u
    random_hits = rh_uo
    amount = 10
  [../]
[]

[Executioner]
  type = AdaptAndModify
  num_steps = 400
  dt = 2e-4
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
  adapt_cycles = 2
[]

[Adaptivity]
  marker = rhm # Switch to combo to get the effect of both
  [./Indicators]
    [./gji]
      type = GradientJumpIndicator
      variable = u
    [../]
  [../]
  [./Markers]
    [./rhm]
      type = RandomHitMarker
      random_hits = rh_uo
    [../]
    [./efm]
      type = ErrorFractionMarker
      coarsen = 0.2
      indicator = gji
      refine = 0.8
    [../]
    [./combo]
      type = ComboMarker
      markers = 'efm rhm'
    [../]
  [../]
[]

[Outputs]
  exodus = true
[]

(test/tests/executioners/adapt_and_modify/adapt_and_modify.i)

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 15
  ny = 15
[]

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

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

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

[UserObjects]
  [./rh_uo]
    type = RandomHitUserObject
    execute_on = 'initial timestep_begin'
    num_hits = 1
  [../]
  [./rhsm]
    type = RandomHitSolutionModifier
    execute_on = 'custom'
    modify = u
    random_hits = rh_uo
    amount = 1000
  [../]
[]

[Executioner]
  type = AdaptAndModify
  num_steps = 4
  dt = 1e-3

  solve_type = 'PJFNK'
  nl_rel_tol = 1e-15

  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
  adapt_cycles = 2
[]

[Adaptivity]
  marker = rhm # Switch to combo to get the effect of both
  [./Indicators]
    [./gji]
      type = GradientJumpIndicator
      variable = u
    [../]
  [../]
  [./Markers]
    [./rhm]
      type = RandomHitMarker
      random_hits = rh_uo
    [../]
    [./efm]
      type = ErrorFractionMarker
      coarsen = 0.001
      indicator = gji
      refine = 0.8
    [../]
    [./combo]
      type = ComboMarker
      markers = 'efm rhm'
    [../]
  [../]
[]

[Outputs]
  exodus = true
[]

(test/tests/markers/dont_mark/dont_mark_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]
    [./box]
      type = BoxMarker
      bottom_left = '0.3 0.3 0'
      top_right = '0.6 0.6 0'
      inside = refine
      outside = coarsen
    [../]
    [./combo]
      type = ComboMarker
      markers = 'box box2'
    [../]
    [./box2]
      type = BoxMarker
      bottom_left = '0.5 0.5 0'
      top_right = '0.8 0.8 0'
      inside = dont_mark
      outside = refine
    [../]
  [../]
[]

[Outputs]
  exodus = true
[]

(test/tests/markers/combo_marker/combo_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]
    [./box]
      type = BoxMarker
      bottom_left = '0.3 0.3 0'
      top_right = '0.6 0.6 0'
      inside = refine
      outside = do_nothing
    [../]
    [./combo]
      type = ComboMarker
      markers = 'box box2'
    [../]
    [./box2]
      type = BoxMarker
      bottom_left = '0.5 0.5 0'
      top_right = '0.8 0.8 0'
      inside = refine
      outside = coarsen
    [../]
  [../]
[]

[Outputs]
  exodus = true
[]

(test/tests/dirackernels/point_caching/point_caching_adaptive_refinement.i)

[Mesh]
  type = GeneratedMesh
  dim = 2
  xmin = 0
  xmax = 1
  ymin = 0
  ymax = 1
  nx = 2
  ny = 2
  elem_type = QUAD4
  uniform_refine = 2
[]

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

[Kernels]
  active = 'diff'

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

[DiracKernels]
  active = 'point_source'

  [./point_source]
    type = CachingPointSource
    variable = u
  [../]
[]

[BCs]
  [./left]
    type = DirichletBC
    variable = u
    boundary = 3
    value = 0
  [../]

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

[Executioner]
  type = Steady

  solve_type = 'PJFNK'
[]

[Adaptivity]
  steps = 3
  marker = 'combo'

  [./Markers]
    [./combo]
      # In a real problem you would want to mark based on an error
      # indicator, but we want this test to run consistently in
      # parallel, so we just mark elements within a box for
      # refinement.  The boxes here are based on the 8x8
      # uniformly-refined initial grid.
      type = ComboMarker
      markers = 'box1 box2 box3'
    [../]

    [./box1]
      type = BoxMarker
      bottom_left = '0.125 0.625 0'
      top_right = '0.375 0.875 0'
      inside = refine
      outside = dont_mark
    [../]

    [./box2]
      type = BoxMarker
      bottom_left = '0.625 0.625 0'
      top_right = '0.875 0.875 0'
      inside = refine
      outside = dont_mark
    [../]

    [./box3]
      type = BoxMarker
      bottom_left = '0.625 0.125 0'
      top_right = '0.875 0.375 0'
      inside = refine
      outside = dont_mark
    [../]
  [../]
[]

[Outputs]
  execute_on = 'timestep_end'
  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
    f_name = Fc
    args = 'c'
    constant_names       = 'barr_height  cv_eq'
    constant_expressions = '0.1          0'
    function = 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
    f_name = P
    args = c
    function = '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
    f_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
    args = 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
[]

Description
Example Input Syntax
Input Parameters
Input Files

Install MOOSE

New Users

Examples and Tutorials

Application Usage

Physics and Syntax

Application Development

Framework Development

MOOSEDocs

Infrastructure

Questions

Information and Tools

INL Applications and Remote Access