NumbatPerturbationIC|Numbat

examples/3D/isotropic/3DddcSF_Ra5000.i

# Density-driven convective mixing in a 3D model using the streamfunction
# formulation for Ra = 5000
#
# Uses an unstructured mesh generated by Gmsh
# To generate the mesh, run 'gmsh -3 Ra5000.geo'
#
# Note: this mesh has approximately 8.4 million elements and takes about
# 8 hours to run using 200 processors

[Mesh]
  type = FileMesh
  file = Ra5000.e
[]

[Numbat]
  [./Dimensionless]
  [../]
[]

[ICs]
  [./concentration]
    type = NumbatPerturbationIC
    variable = concentration
    amplitude = 0.1
    seed = 1
  [../]
  [./streamfunctionx]
    type = ConstantIC
    variable = streamfunction_x
    value = 0.0
  [../]
  [./streamfunctiony]
    type = ConstantIC
    variable = streamfunction_y
    value = 0.0
  [../]
[]

[Functions]
  [./timesteps]
    type = PiecewiseConstant
    x = '0 10 500 1e3 1e4 6e4'
    y = '9 10 50 100 200 200'
  [../]
[]

[Executioner]
  type = Transient
  end_time = 6e4
  start_time = 1
  solve_type = NEWTON
  petsc_options = -snes_ksp_ew
  petsc_options_iname = '-ksp_type -pc_type -pc_asm_overlap -sub_pc_type -pc_factor_levels -ksp_atol'
  petsc_options_value = 'gmres asm 10 ilu 4 1e-12'
  nl_abs_tol = 1e-9
  l_max_its = 200
  [./TimeStepper]
    type = FunctionDT
    function = timesteps
  [../]
[]

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

[Outputs]
  perf_graph = true
  [./exodus]
    type = Exodus
    execute_on = 'INITIAL TIMESTEP_END'
    interval = 4
  [../]
  [./csvoutput]
    type = CSV
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
  [./checkpoint]
    type = Checkpoint
    num_files = 2
    interval = 10
  [../]
[]

tests/1D/1DSF_error.i

[Mesh]
  type = GeneratedMesh
  dim = 1
  xmax = 10
  nx = 20
  nz = 0
[]

[Variables]
  [./concentration]
    order = FIRST
    family = LAGRANGE
    [./InitialCondition]
      type = NumbatPerturbationIC
      variable = concentration
      amplitude = 0.01
      seed = 1
    [../]
  [../]
  [./streamfunction]
    order = FIRST
    family = LAGRANGE
    initial_condition = 0.0
  [../]
[]

[Kernels]
  [./Darcy]
    type = NumbatDarcySF
    variable = streamfunction
    concentration = concentration
  [../]
  [./Convection]
    type = NumbatConvectionSF
    variable = concentration
    streamfunction = streamfunction
  [../]
  [./Diffusion]
    type = NumbatDiffusionSF
    variable = concentration
  [../]
  [./TimeDerivative]
    type = TimeDerivative
    variable = concentration
  [../]
[]

[AuxVariables]
  [./u]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./w]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

[AuxKernels]
  [./uAux]
    type = NumbatDarcyVelocitySF
    variable = u
    component = x
    streamfunction = streamfunction
  [../]
  [./wAux]
    type = NumbatDarcyVelocitySF
    variable = w
    component = y
    streamfunction = streamfunction
  [../]
[]

[BCs]
  [./conctop]
    type = DirichletBC
    variable = concentration
    boundary = top
    value = 1.0
  [../]
  [./concbottom]
    type = DirichletBC
    variable = concentration
    boundary = bottom
    value = 0.0
  [../]
  [./streamfuntop]
    type = DirichletBC
    variable = streamfunction
    boundary = top
    value = 0.0
  [../]
  [./streamfunbottom]
    type = DirichletBC
    variable = streamfunction
    boundary = bottom
    value = 0.0
  [../]
  [./Periodic]
    [./x]
      variable = 'concentration streamfunction'
      auto_direction = x
    [../]
  [../]
[]

[Executioner]
  type = Transient
  end_time = 100
  solve_type = PJFNK
  petsc_options_iname = '-ksp_type -pc_type -pc_sub_type'
  petsc_options_value = 'gmres asm lu'
[]

[Postprocessors]
  [./boundaryfluxint]
    type = NumbatSideFlux
    variable = concentration
    boundary = top
  [../]
[]

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

[Outputs]
  perf_graph = true
[]

tests/ics/2D.i

# Density-driven convective mixing
# Test the initial condition

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 1000
  ny = 2
  xmax = 10
[]

[Variables]
  [./concentration]
    [./InitialCondition]
      type = NumbatPerturbationIC
      variable = concentration
      amplitude = 0.5
      seed = 0
    [../]
  [../]
[]

[Executioner]
  type = Transient
  end_time = 2
  start_time = 1
  solve_type = PJFNK
[]

[Problem]
  type = FEProblem
  solve = False
[]

[VectorPostprocessors]
  [./conc]
    type = NodalValueSampler
    variable = concentration
    sort_by = id
    execute_on = initial
  [../]
[]

[Outputs]
  perf_graph = true
  [./csvoutput]
    type = CSV
    file_base = 2D
    execute_on = 'INITIAL'
  [../]
[]

examples/inputfiles/2DSF.i

# Sample input file for 2D density-driven convective mixing using the streamfunction formulation
# Note: this input file is primarily used to generate documentation
# PLEASE DO NOT ALTER THIS FILE

[Mesh]
  type = GeneratedMesh
  dim = 2
  xmax = 1000
  ymin = -500
  ymax = 0
  nx = 80
  ny = 25
  bias_y = 0.9
[]

[Adaptivity]
  marker = errormarker
  max_h_level = 1
  [./Indicators]
    [./gradjumpindicator]
      type = GradientJumpIndicator
      variable = concentration
    [../]
  [../]
  [./Markers]
    [./errormarker]
      type = ErrorToleranceMarker
      refine = 0.005
      indicator = gradjumpindicator
    [../]
  [../]
[]

[Variables]
  [./concentration]
    order = FIRST
    family = LAGRANGE
  [../]
  [./streamfunction]
    order = FIRST
    family = LAGRANGE
    initial_condition = 0.0
  [../]
[]

[ICs]
  [./concentration]
    type = NumbatPerturbationIC
    variable = concentration
    amplitude = 0.1
    seed = 1
  [../]
[]

[Kernels]
  [./Darcy]
    type = NumbatDarcySF
    variable = streamfunction
    concentration = concentration
  [../]
  [./Convection]
    type = NumbatConvectionSF
    variable = concentration
    streamfunction = streamfunction
  [../]
  [./Diffusion]
    type = NumbatDiffusionSF
    variable = concentration
  [../]
  [./TimeDerivative]
    type = TimeDerivative
    variable = concentration
  [../]
[]

[AuxVariables]
  [./u]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./w]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

[AuxKernels]
  [./uAux]
    type = NumbatDarcyVelocitySF
    variable = u
    component = x
    streamfunction = streamfunction
  [../]
  [./wAux]
    type = NumbatDarcyVelocitySF
    variable = w
    component = y
    streamfunction = streamfunction
  [../]
[]

[BCs]
  [./conctop]
    type = DirichletBC
    variable = concentration
    boundary = top
    value = 1.0
  [../]
  [./streamfuntop]
    type = DirichletBC
    variable = streamfunction
    boundary = top
    value = 0.0
  [../]
  [./streamfunbottom]
    type = DirichletBC
    variable = streamfunction
    boundary = bottom
    value = 0.0
  [../]
  [./Periodic]
    [./x]
      variable = 'concentration streamfunction'
      auto_direction = x
    [../]
  [../]
[]

[Executioner]
  type = Transient
  dtmax = 100
  end_time = 5000
  start_time = 1
  solve_type = PJFNK
  nl_abs_tol = 1e-10
  [./TimeStepper]
    type = IterationAdaptiveDT
    dt = 1
    cutback_factor = 0.5
    growth_factor = 2
  [../]
  [./TimeIntegrator]
    type = LStableDirk2
  [../]
[]

[Postprocessors]
  [./boundaryfluxint]
    type = NumbatSideFluxSF
    variable = concentration
    boundary = top
  [../]
  [./numdofs]
    type = NumDOFs
  [../]
[]

[Preconditioning]
  [./smp]
    type = SMP
    full = true
    petsc_options = -snes_ksp_ew
    petsc_options_iname = '-pc_type -sub_pc_type -ksp_atol'
    petsc_options_value = 'asm ilu 1e-12'
  [../]
[]

[Outputs]
  perf_graph = true
  [./exodus]
    type = Exodus
    file_base = 2DddcSF
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
  [./csvoutput]
    type = CSV
    file_base = 2DddcSF
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
[]

examples/3D/anisotropic/3DddcSF.i

# Density-driven convective mixing with permeability anisotropy
# Example with gamma = kv/kh = 0.5
# To implement anisotropy, must change the gamma and coeff_tensor parameters in the kernels

[Mesh]
  type = GeneratedMesh
  dim = 3
  xmax = 200
  ymax = 200
  zmin = -200
  zmax = 0
  nx = 10
  ny = 10
  nz = 10
[]

[Adaptivity]
  max_h_level = 2
  initial_marker = boxmarker
  initial_steps = 1
  marker = combomarker
  [./Indicators]
    [./gradjumpindicator]
      type = GradientJumpIndicator
      variable = concentration
    [../]
  [../]
  [./Markers]
    [./errormarker]
      type = ErrorToleranceMarker
      coarsen = 2.5
      refine = 1
      indicator = gradjumpindicator
    [../]
    [./boxmarker]
      type = BoxMarker
      bottom_left = '0 0 -10'
      top_right = '1000 1000 0'
      inside = refine
      outside = dont_mark
    [../]
    [./combomarker]
      type = ComboMarker
      markers = 'boxmarker errormarker'
    [../]
  [../]
[]

[Numbat]
  [./Dimensionless]
    gamma = 0.5
  [../]
[]

[ICs]
  [./concentration]
    type = NumbatPerturbationIC
    variable = concentration
    amplitude = 0.1
    seed = 1
  [../]
  [./streamfunctionx]
    type = ConstantIC
    variable = streamfunction_x
    value = 0.0
  [../]
  [./streamfunctiony]
    type = ConstantIC
    variable = streamfunction_y
    value = 0.0
  [../]
[]

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

[Executioner]
  type = Transient
  scheme = bdf2
  dtmin = 0.1
  dtmax = 1000
  end_time = 3000
  solve_type = NEWTON
  [./TimeStepper]
    type = IterationAdaptiveDT
    dt = 1
  [../]
[]

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

[Outputs]
  perf_graph = true
  [./exodus]
    type = Exodus
    file_base = 3Dddc2
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
  [./csvoutput]
    type = CSV
    file_base = 3Dddc2
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
[]

examples/2D/anisotropic/2DddcSF.i

# Density-driven convective mixing with permeability anisotropy using the
# streamfunction formulation in 2D.
# Example with gamma = kv/kh = 0.75
# Density-driven convective mixing
# The dimensionless Numbat action is used to add all variables, kernels etc.
# Mesh adaptivity used to refine mesh wround fingers
# A coarse grid and time stepping used to allow this model to run in ~ 2 minutes

[Mesh]
  type = NumbatBiasedMesh
  dim = 2
  xmax = 1000
  ymin = -500
  ymax = 0
  nx = 100
  ny = 25
  refined_edge = top
  refined_resolution = 10
[]

[Numbat]
  [./Dimensionless]
    gamma = 0.75
    periodic_bcs = true
  [../]
[]

[Adaptivity]
  marker = errormarker
  max_h_level = 1
  [./Indicators]
    [./gradjumpindicator]
      type = GradientJumpIndicator
      variable = concentration
    [../]
  [../]
  [./Markers]
    [./errormarker]
      type = ErrorFractionMarker
      refine = 0.25
      indicator = gradjumpindicator
    [../]
  [../]
[]

[ICs]
  [./concentration]
    type = NumbatPerturbationIC
    variable = concentration
    amplitude = 0.1
    seed = 1
  [../]
[]

[Executioner]
  type = Transient
  dtmax = 100
  end_time = 3000
  start_time = 1
  solve_type = NEWTON
  nl_abs_tol = 1e-10
  [./TimeStepper]
    type = IterationAdaptiveDT
    dt = 1
    cutback_factor = 0.5
    growth_factor = 2
  [../]
[]

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

[Preconditioning]
  [./smp]
    type = SMP
    full = true
    petsc_options = -snes_ksp_ew
    petsc_options_iname = '-pc_type -sub_pc_type -ksp_atol'
    petsc_options_value = 'asm ilu 1e-12'
  [../]
[]

[Outputs]
  perf_graph = true
  [./exodus]
    type = Exodus
    file_base = 2DddcSF
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
  [./csvoutput]
    type = CSV
    file_base = 2DddcSF
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
[]

examples/3D/isotropic/3DddcSF.i

# Density-driven convective mixing in a 3D model using the streamfunction
# formulation.
#
# Note: do not run this on a laptop!

[Mesh]
  type = NumbatBiasedMesh
  dim = 3
  xmax = 500
  ymax = 500
  zmin = -200
  zmax = 0
  nx = 40
  ny = 40
  nz = 20
  refined_edge = top
  refined_resolution = 2
[]

[Adaptivity]
  max_h_level = 1
  initial_marker = boxmarker
  initial_steps = 1
  marker = errormarker
  [./Indicators]
    [./gradjumpindicator]
      type = GradientJumpIndicator
      variable = concentration
    [../]
  [../]
  [./Markers]
    [./errormarker]
      type = ErrorToleranceMarker
      refine = 0.05
      indicator = gradjumpindicator
    [../]
    [./boxmarker]
      type = BoxMarker
      bottom_left = '0 0 -10'
      top_right = '500 500 0'
      inside = refine
      outside = dont_mark
    [../]
  [../]
[]

[Numbat]
  [./Dimensionless]
  [../]
[]

[ICs]
  [./concentration]
    type = NumbatPerturbationIC
    variable = concentration
    amplitude = 0.1
    seed = 1
  [../]
  [./streamfunctionx]
    type = ConstantIC
    variable = streamfunction_x
    value = 0.0
  [../]
  [./streamfunctiony]
    type = ConstantIC
    variable = streamfunction_y
    value = 0.0
  [../]
[]

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

[Executioner]
  type = Transient
  dtmax = 100
  end_time = 2500
  start_time = 1
  solve_type = NEWTON
  petsc_options = -snes_ksp_ew
  petsc_options_iname = '-pc_type -sub_pc_type -ksp_atol -pc_asm_overlap'
  petsc_options_value = 'asm ilu 1e-12 4'
  nl_abs_tol = 1e-10
  [./TimeStepper]
    type = IterationAdaptiveDT
    dt = 1
    cutback_factor = 0.5
    growth_factor = 2
  [../]
[]

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

[Outputs]
  perf_graph = true
  [./exodus]
    type = Exodus
    file_base = 3DddcSF
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
  [./csvoutput]
    type = CSV
    file_base = 3DddcSF
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
[]

examples/inputfiles/3DSF.i

# Sample input file for 3D density-driven convective mixing using the streamfunction formulation
# Note: this input file is primarily used to generate documentation
# PLEASE DO NOT ALTER THIS FILE

[Mesh]
  type = GeneratedMesh
  dim = 3
  xmax = 500
  ymax = 500
  zmin = -200
  zmax = 0
  nx = 40
  ny = 40
  nz = 20
  bias_z = 0.7
[]

[Adaptivity]
  max_h_level = 1
  initial_marker = boxmarker
  initial_steps = 1
  marker = errormarker
  [./Indicators]
    [./gradjumpindicator]
      type = GradientJumpIndicator
      variable = concentration
    [../]
  [../]
  [./Markers]
    [./errormarker]
      type = ErrorToleranceMarker
      refine = 0.05
      indicator = gradjumpindicator
    [../]
    [./boxmarker]
      type = BoxMarker
      bottom_left = '0 0 -10'
      top_right = '500 500 0'
      inside = refine
      outside = dont_mark
    [../]
  [../]
[]

[Variables]
  [./concentration]
    order = FIRST
    family = LAGRANGE
    [./InitialCondition]
      type = NumbatPerturbationIC
      variable = concentration
      amplitude = 0.1
      seed = 1
    [../]
  [../]
  [./streamfunctionx]
    order = FIRST
    family = LAGRANGE
    initial_condition = 0.0
  [../]
  [./streamfunctiony]
    order = FIRST
    family = LAGRANGE
    initial_condition = 0.0
  [../]
[]

[Kernels]
  [./Darcy_x]
    type = NumbatDarcySF
    variable = streamfunctionx
    concentration = concentration
    component = x
  [../]
  [./Darcy_y]
    type = NumbatDarcySF
    variable = streamfunctiony
    concentration = concentration
    component = y
  [../]
  [./Convection]
    type = NumbatConvectionSF
    variable = concentration
    streamfunction = 'streamfunctionx streamfunctiony'
  [../]
  [./Diffusion]
    type = NumbatDiffusionSF
    variable = concentration
  [../]
  [./TimeDerivative]
    type = TimeDerivative
    variable = concentration
  [../]
[]

[AuxVariables]
  [./u]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./v]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./w]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

[AuxKernels]
  [./uAux]
    type = NumbatDarcyVelocitySF
    variable = u
    component = x
    streamfunction = 'streamfunctionx streamfunctiony'
  [../]
  [./vAux]
    type = NumbatDarcyVelocitySF
    variable = v
    component = y
    streamfunction = 'streamfunctionx streamfunctiony'
  [../]
  [./wAux]
    type = NumbatDarcyVelocitySF
    variable = w
    component = z
    streamfunction = 'streamfunctionx streamfunctiony'
  [../]
[]

[BCs]
  [./conctop]
    type = DirichletBC
    variable = concentration
    boundary = front
    value = 1.0
  [../]
  [./streamfunxtop]
    type = DirichletBC
    variable = streamfunctionx
    boundary = front
    value = 0.0
  [../]
  [./streamfunxbottom]
    type = DirichletBC
    variable = streamfunctionx
    boundary = back
    value = 0.0
  [../]
  [./streamfunytop]
    type = DirichletBC
    variable = streamfunctiony
    boundary = front
    value = 0.0
  [../]
  [./streamfunybottom]
    type = DirichletBC
    variable = streamfunctiony
    boundary = back
    value = 0.0
  [../]
  [./Periodic]
    [./xy]
      variable = 'concentration streamfunctionx streamfunctiony'
      auto_direction = 'x y'
    [../]
  [../]
[]

[Preconditioning]
  [./smp]
    type = SMP
    full = true
    petsc_options = -snes_ksp_ew
    petsc_options_iname = '-pc_type -sub_pc_type -ksp_atol'
    petsc_options_value = 'asm lu 1e-12'
  [../]
[]

[Executioner]
  type = Transient
  dtmax = 100
  end_time = 2500
  start_time = 1
  solve_type = NEWTON
  nl_abs_tol = 1e-10
  [./TimeStepper]
    type = IterationAdaptiveDT
    dt = 1
    cutback_factor = 0.5
    growth_factor = 2
  [../]
  [./TimeIntegrator]
    type = LStableDirk2
  [../]
[]

[Postprocessors]
  [./boundaryfluxint]
    type = NumbatSideFluxSF
    variable = concentration
    boundary = front
  [../]
  [./numdofs]
    type = NumDOFs
  [../]
[]

[Outputs]
  perf_graph = true
  [./exodus]
    type = Exodus
    file_base = 3DddcSF
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
  [./csvoutput]
    type = CSV
    file_base = 3DddcSF
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
[]

tests/ics/3D.i

# Density-driven convective mixing
# Test the initial condition

[Mesh]
  type = GeneratedMesh
  dim = 3
  nx = 50
  ny = 50
  nz = 2
  xmax = 10
  ymax = 10
[]

[Variables]
  [./concentration]
    [./InitialCondition]
      type = NumbatPerturbationIC
      variable = concentration
      amplitude = 0.5
      seed = 0
    [../]
  [../]
[]

[Executioner]
  type = Transient
  end_time = 2
  start_time = 1
  solve_type = PJFNK
[]

[Problem]
  type = FEProblem
  solve = False
[]

[VectorPostprocessors]
  [./conc]
    type = NodalValueSampler
    variable = concentration
    sort_by = id
    execute_on = initial
  [../]
[]

[Outputs]
  perf_graph = true
  [./csvoutput]
    type = CSV
    file_base = 3D
    execute_on = 'INITIAL'
  [../]
[]

examples/3D/pseudo2D/3Dddcp.i

# Density-driven convective mixing in a 3D representation of a 2D model. Only a single element is
# used in the y direction.
#
# Note: This example may take some time to run. At least 8 processors are recommended.

[Mesh]
  type = NumbatBiasedMesh
  dim = 3
  xmax = 1000
  zmin = -200
  zmax = 0
  nx = 80
  nz = 20
  ymax = 1
  ny = 1
  refined_edge = top
  refined_resolution = 2
[]

[Adaptivity]
  marker = combomarker
  max_h_level = 1
  initial_marker = boxmarker
  initial_steps = 1
  [./Indicators]
    [./gradjumpindicator]
      type = GradientJumpIndicator
      variable = concentration
    [../]
  [../]
  [./Markers]
    [./errormarker]
      type = ErrorToleranceMarker
      refine = 0.005
      indicator = gradjumpindicator
    [../]
    [./boxmarker]
      type = BoxMarker
      bottom_left = '0 0.0 -1.0'
      top_right = '1000 1 0'
      inside = refine
      outside = dont_mark
    [../]
    [./combomarker]
      type = ComboMarker
      markers = 'boxmarker errormarker'
    [../]
  [../]
[]

[Numbat]
  [./Dimensionless]
  [../]
[]

[ICs]
  [./concentration]
    type = NumbatPerturbationIC
    variable = concentration
    amplitude = 0.1
    seed = 1
  [../]
  [./streamfunctionx]
    type = ConstantIC
    variable = streamfunction_x
    value = 0.0
  [../]
  [./streamfunctiony]
    type = ConstantIC
    variable = streamfunction_y
    value = 0.0
  [../]
[]

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

[Executioner]
  type = Transient
  dtmax = 100
  end_time = 2500
  start_time = 1
  solve_type = NEWTON
  petsc_options = -snes_ksp_ew
  nl_abs_tol = 1e-10
  [./TimeStepper]
    type = IterationAdaptiveDT
    dt = 1
    cutback_factor = 0.5
    growth_factor = 2
  [../]
[]

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

[Outputs]
  perf_graph = true
  [./exodus]
    type = Exodus
    file_base = 3Dddcp
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
  [./csvoutput]
    type = CSV
    file_base = 3Dddcp
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
[]

examples/3D/barriers/3DddcSF.i

# Density-driven convective mixing in a 3D model using the streamfunction
# formulation in a mesh with elliptical barriers
#
# The mesh is created in Gmsh (barrier.geo). To generate the mesh, run 'gmsh -3 barrier.geo'
#
# Ra = 5000

[Mesh]
  type = FileMesh
  file = barrier.msh
[]

[Numbat]
  [./Dimensionless]
    periodic_bcs = false
  [../]
[]

[ICs]
  [./concentration]
    type = NumbatPerturbationIC
    variable = concentration
    amplitude = 0.1
    seed = 1
  [../]
  [./streamfunction_x]
    type = ConstantIC
    variable = streamfunction_x
    value = 0
  [../]
  [./streamfunction_y]
    type = ConstantIC
    variable = streamfunction_y
    value = 0
  [../]
[]

# Boundary condition for barriers (not set up by action)
[BCs]
  [./streamfunxbarrier]
    type = PresetBC
    variable = streamfunction_x
    boundary = barriers
    value = 0
  [../]
  [./streamfunybarrier]
    type = PresetBC
    variable = streamfunction_y
    boundary = barriers
    value = 0
  [../]
  [./Periodic]
    [./x]
      variable = 'concentration streamfunction_x streamfunction_y'
      primary = left
      secondary = right
      translation = '100 0 0'
    [../]
    [./y]
      variable = 'concentration streamfunction_x streamfunction_y'
      primary = front
      secondary = back
      translation = '0 100 0'
    [../]
  [../]
[]

[Preconditioning]
  [./smp]
    type = SMP
    full = true
    petsc_options = '-snes_ksp_ew'
    petsc_options_iname = '-ksp_type -pc_type -pc_asm_overlap -sub_pc_type -pc_factor_levels -ksp_atol'
    petsc_options_value = 'gmres asm 10 ilu 4 1e-12'
  [../]
[]

[Functions]
  [./timesteps]
    type = PiecewiseConstant
    x = '0 10 500 1e3 1e4 6e4'
    y = '9 10 50 100 200 200'
  [../]
[]

[Executioner]
  type = Transient
  end_time = 6e4
  start_time = 1
  solve_type = NEWTON
  nl_abs_tol = 1e-9
  l_max_its = 200
  [./TimeStepper]
    type = FunctionDT
    function = timesteps
  [../]
[]

[Outputs]
  perf_graph = true
  [./exodus]
    type = Exodus
    execute_on = 'INITIAL TIMESTEP_END'
    interval = 4
  [../]
  [./csvoutput]
    type = CSV
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
  [./checkpoint]
    type = Checkpoint
    num_files = 2
    interval = 10
  [../]
[]

examples/2D/isotropic/2DddcSF.i

# Density-driven convective mixing using the streamfunction formulation in 2D.
# The dimensionless Numbat action is used to add all variables, kernels etc.
# Mesh adaptivity used to refine mesh wround fingers
# A coarse grid and time stepping used to allow this model to run in ~ 2 minutes

[Mesh]
  type = NumbatBiasedMesh
  dim = 2
  xmax = 1000
  ymin = -500
  ymax = 0
  nx = 100
  ny = 25
  refined_edge = top
  refined_resolution = 10
[]

[Numbat]
  [./Dimensionless]
    periodic_bcs = true
  [../]
[]

[Adaptivity]
  marker = errormarker
  max_h_level = 1
  [./Indicators]
    [./gradjumpindicator]
      type = GradientJumpIndicator
      variable = concentration
    [../]
  [../]
  [./Markers]
    [./errormarker]
      type = ErrorFractionMarker
      refine = 0.25
      indicator = gradjumpindicator
    [../]
  [../]
[]

[ICs]
  [./concentration]
    type = NumbatPerturbationIC
    variable = concentration
    amplitude = 0.1
    seed = 1
  [../]
[]

[Executioner]
  type = Transient
  dtmax = 100
  end_time = 3000
  start_time = 1
  solve_type = NEWTON
  nl_abs_tol = 1e-10
  [./TimeStepper]
    type = IterationAdaptiveDT
    dt = 1
    cutback_factor = 0.5
    growth_factor = 2
  [../]
[]

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

[Preconditioning]
  [./smp]
    type = SMP
    full = true
    petsc_options = -snes_ksp_ew
    petsc_options_iname = '-pc_type -sub_pc_type -ksp_atol'
    petsc_options_value = 'asm ilu 1e-12'
  [../]
[]

[Outputs]
  perf_graph = true
  [./exodus]
    type = Exodus
    file_base = 2DddcSF
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
  [./csvoutput]
    type = CSV
    file_base = 2DddcSF
    execute_on = 'INITIAL TIMESTEP_END'
  [../]
[]

NumbatPerturbationIC

Input Parameters

Required Parameters

Optional Parameters

Advanced Parameters

Input Files