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[Mesh]
  type = GeneratedMesh
  dim = 3
  nx = 10
  ny = 1
  nz = 1
  xmin = 0
  xmax = 1
  ymin = 0
  ymax = 0.1
  zmin = 0
  zmax = 1
[]

[Variables]
  [./disp_x]
  [../]
  [./disp_y]
  [../]
  [./disp_z]
  [../]
  [./pf]
  [../]
[]

[Kernels]
  [./pf_time]
    type = TimeDerivative
    variable = pf
  [../]
  [./pf_diffusion]
    type = LynxHydroDarcy
    variable = pf
  [../]
  [./pf_poro]
    type = LynxHydroPoroMech
    variable = pf
    displacements = 'disp_x disp_y disp_z'
  [../]
  [./mech_x]
    type = LynxSolidMomentum
    variable = disp_x
    component = 0
    displacements = 'disp_x disp_y disp_z'
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    fluid_pressure = 'pf'
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  [../]
  [./mech_y]
    type = LynxSolidMomentum
    variable = disp_y
    component = 1
    displacements = 'disp_x disp_y disp_z'
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    fluid_pressure = 'pf'
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  [../]
  [./mech_z]
    type = LynxSolidMomentum
    variable = disp_z
    component = 2
    displacements = 'disp_x disp_y disp_z'
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    fluid_pressure = 'pf'
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  [../]
[]

[AuxVariables]
  [./porosity]
    order = CONSTANT
    family = MONOMIAL
    initial_condition = 0.1
  [../]
  [./stress_yy]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./tot_force]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

[AuxKernels]
  [./porosity_aux]
    type = ConstantAux
    variable = porosity
    value = 0.1
  [../]
  [./stress_yy_aux]
    type = LynxStressAux
    variable = stress_yy
    index_i = 1
    index_j = 1
  [../]
  [./tot_force]
    type = ParsedAux
    args = 'stress_yy pf'
    execute_on = timestep_end
    variable = tot_force
    function = '-stress_yy+0.6*pf'
  [../]
[]

[Functions]
  [./top_velocity]
    type = PiecewiseLinear
    x = '0 0.002 0.006   0.014   0.03    0.046   0.062   0.078   0.094   0.11    0.126   0.142   0.158   0.174   0.19 0.206 0.222 0.238 0.254 0.27 0.286 0.302 0.318 0.334 0.35 0.366 0.382 0.398 0.414 0.43 0.446 0.462 0.478 0.494 0.51 0.526 0.542 0.558 0.574 0.59 0.606 0.622 0.638 0.654 0.67 0.686 0.702'
    y = '-0.041824842    -0.042730269    -0.043412712    -0.04428867     -0.045509181    -0.04645965     -0.047268246 -0.047974749      -0.048597109     -0.0491467  -0.049632388     -0.050061697      -0.050441198     -0.050776675     -0.051073238      -0.0513354 -0.051567152      -0.051772022     -0.051953128 -0.052113227 -0.052254754 -0.052379865 -0.052490464 -0.052588233 -0.052674662 -0.052751065 -0.052818606 -0.052878312 -0.052931093 -0.052977751 -0.053018997 -0.053055459 -0.053087691 -0.053116185 -0.053141373 -0.05316364 -0.053183324 -0.053200724 -0.053216106 -0.053229704 -0.053241725 -0.053252351 -0.053261745 -0.053270049 -0.053277389 -0.053283879 -0.053289615'
  [../]
[]

[BCs]
  [./no_x_left]
    type = PresetBC
    variable = disp_x
    boundary = left
    value = 0
  [../]
  [./no_y_bottom]
    type = PresetBC
    variable = disp_y
    boundary = bottom
    value = 0
  [../]
  [./no_z_plane_strain]
    type = PresetBC
    variable = disp_z
    boundary = 'back front'
    value = 0
  [../]
  [./drained_right]
    type = DirichletBC
    variable = pf
    boundary = 'right'
    value = 0
  [../]
  [./top_velocity]
    type = FunctionPresetBC
    variable = disp_y
    function = top_velocity
    boundary = top
  [../]
[]

[Materials]
  [./poroelastic_material]
    type = LynxDeformation
    displacements = 'disp_x disp_y disp_z'
    bulk_modulus = 1.0
    shear_modulus = 0.75
  [../]
  [./hydro_mat]
    type = LynxHydroConstant
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    porosity = 'porosity'
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    fluid_modulus = 8
    solid_modulus = 2.5
    permeability = 1.5e-03
    fluid_viscosity = 1.0e-03
  [../]
[]

[Postprocessors]
  [./p0]
    type = PointValue
    outputs = csv
    point = '0.0 0 0'
    variable = pf
  [../]
  [./p1]
    type = PointValue
    outputs = csv
    point = '0.1 0 0'
    variable = pf
  [../]
  [./p2]
    type = PointValue
    outputs = csv
    point = '0.2 0 0'
    variable = pf
  [../]
  [./p3]
    type = PointValue
    outputs = csv
    point = '0.3 0 0'
    variable = pf
  [../]
  [./p4]
    type = PointValue
    outputs = csv
    point = '0.4 0 0'
    variable = pf
  [../]
  [./p5]
    type = PointValue
    outputs = csv
    point = '0.5 0 0'
    variable = pf
  [../]
  [./p6]
    type = PointValue
    outputs = csv
    point = '0.6 0 0'
    variable = pf
  [../]
  [./p7]
    type = PointValue
    outputs = csv
    point = '0.7 0 0'
    variable = pf
  [../]
  [./p8]
    type = PointValue
    outputs = csv
    point = '0.8 0 0'
    variable = pf
  [../]
  [./p9]
    type = PointValue
    outputs = csv
    point = '0.9 0 0'
    variable = pf
  [../]
  [./p99]
    type = PointValue
    outputs = csv
    point = '1 0 0'
    variable = pf
  [../]
  [./xdisp]
    type = PointValue
    outputs = csv
    point = '1 0.1 0'
    variable = disp_x
  [../]
  [./ydisp]
    type = PointValue
    outputs = csv
    point = '1 0.1 0'
    variable = disp_y
  [../]
  [./total_downwards_force]
     type = ElementAverageValue
     outputs = csv
     variable = tot_force
  [../]
  [./dt]
    type = FunctionValuePostprocessor
    function = if(0.15*t<0.01,0.15*t,0.01)
    outputs = console
  [../]
[]

[Preconditioning]
  [./precond]
    type = SMP
    full = true
    petsc_options = '-snes_ksp_ew'
    petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -ksp_max_it -sub_pc_type -sub_pc_factor_shift_type'
    petsc_options_value = 'gmres asm 1E-05 1E-10 200 500 lu NONZERO'
  [../]
[]

[Executioner]
  type = Transient
  solve_type = Newton
  start_time = 0
  end_time = 0.7
  [./TimeStepper]
    type = PostprocessorDT
    postprocessor = dt
    dt = 0.001
  [../]
[]

[Outputs]
  execute_on = 'timestep_end'
  perf_graph = true
  exodus = true
  [./csv]
    interval = 3
    type = CSV
  [../]
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[]