ParsedAux

construction:Undocumented Class

The ParsedAux has not been documented. The content listed below should be used as a starting point for documenting the class, which includes the typical automatic documentation associated with a MooseObject; however, what is contained is ultimately determined by what is necessary to make the documentation clear for users.


# ParsedAux

!syntax description /AuxKernels/ParsedAux

## Overview

!! Replace these lines with information regarding the ParsedAux object.

## Example Input File Syntax

!! Describe and include an example of how to use the ParsedAux object.

!syntax parameters /AuxKernels/ParsedAux

!syntax inputs /AuxKernels/ParsedAux

!syntax children /AuxKernels/ParsedAux

Parsed function AuxKernel.

Input Parameters

functionfunction expression
C++ Type:FunctionExpression
Options:
Description:function expression
variableThe name of the variable that this object applies to
C++ Type:AuxVariableName
Options:
Description:The name of the variable that this object applies to

Required Parameters

argscoupled variables
C++ Type:std::vector<VariableName>
Options:
Description:coupled variables
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
boundaryThe list of boundary IDs from the mesh where this boundary condition applies
C++ Type:std::vector<BoundaryName>
Options:
Description:The list of boundary IDs from the mesh where this boundary condition applies
check_boundary_restrictedTrueWhether to check for multiple element sides on the boundary in the case of a boundary restricted, element aux variable. Setting this to false will allow contribution to a single element's elemental value(s) from multiple boundary sides on the same element (example: when the restricted boundary exists on two or more sides of an element, such as at a corner of a mesh
Default:True
C++ Type:bool
Options:
Description:Whether to check for multiple element sides on the boundary in the case of a boundary restricted, element aux variable. Setting this to false will allow contribution to a single element's elemental value(s) from multiple boundary sides on the same element (example: when the restricted boundary exists on two or more sides of an element, such as at a corner of a mesh
constant_expressionsVector of values for the constants in constant_names (can be an FParser expression)
C++ Type:std::vector<std::string>
Options:
Description:Vector of values for the constants in constant_names (can be an FParser expression)
constant_namesVector of constants used in the parsed function (use this for kB etc.)
C++ Type:std::vector<std::string>
Options:
Description:Vector of constants used in the parsed function (use this for kB etc.)
execute_onLINEAR TIMESTEP_ENDThe list of flag(s) indicating when this object should be executed, the available options include NONE, INITIAL, LINEAR, NONLINEAR, TIMESTEP_END, TIMESTEP_BEGIN, FINAL, CUSTOM, PRE_DISPLACE.
Default:LINEAR TIMESTEP_END
C++ Type:ExecFlagEnum
Options:NONE, INITIAL, LINEAR, NONLINEAR, TIMESTEP_END, TIMESTEP_BEGIN, FINAL, CUSTOM, PRE_DISPLACE
Description:The list of flag(s) indicating when this object should be executed, the available options include NONE, INITIAL, LINEAR, NONLINEAR, TIMESTEP_END, TIMESTEP_BEGIN, FINAL, CUSTOM, PRE_DISPLACE.
use_xyztFalseMake coordinate (x,y,z) and time (t) variables available in the function expression.
Default:False
C++ Type:bool
Options:
Description:Make coordinate (x,y,z) and time (t) variables available in the function expression.

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.
disable_fpoptimizerFalseDisable the function parser algebraic optimizer
Default:False
C++ Type:bool
Options:
Description:Disable the function parser algebraic optimizer
enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Options:
Description:Set the enabled status of the MooseObject.
enable_ad_cacheTrueEnable cacheing of function derivatives for faster startup time
Default:True
C++ Type:bool
Options:
Description:Enable cacheing of function derivatives for faster startup time
enable_auto_optimizeTrueEnable automatic immediate optimization of derivatives
Default:True
C++ Type:bool
Options:
Description:Enable automatic immediate optimization of derivatives
enable_jitTrueEnable just-in-time compilation of function expressions for faster evaluation
Default:True
C++ Type:bool
Options:
Description:Enable just-in-time compilation of function expressions for faster evaluation
evalerror_behaviornanWhat to do if evaluation error occurs. Options are to pass a nan, pass a nan with a warning, throw a error, or throw an exception
Default:nan
C++ Type:MooseEnum
Options:nan, nan_warning, error, exception
Description:What to do if evaluation error occurs. Options are to pass a nan, pass a nan with a warning, throw a error, or throw an exception
seed0The seed for the master random number generator
Default:0
C++ Type:unsigned int
Options:
Description:The seed for the master random number generator
use_displaced_meshFalseWhether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.
Default:False
C++ Type:bool
Options:
Description:Whether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.

Advanced Parameters

Input Files

(modules/functional_expansion_tools/test/tests/standard_use/volume_coupling_custom_norm_sub.i)
(test/tests/transfers/multiapp_userobject_transfer/restricted_node_master.i)
(modules/geochemistry/test/tests/kinetics/quartz_deposition.i)
(modules/geochemistry/test/tests/solubilities_and_activities/gypsum_solubility.i)
(modules/porous_flow/examples/tutorial/11.i)
(modules/porous_flow/test/tests/chemistry/dissolution_limited.i)
(modules/navier_stokes/test/tests/finite_volume/ins/boussinesq/boussinesq.i)
(modules/porous_flow/test/tests/poro_elasticity/mandel_fully_saturated.i)
(modules/geochemistry/test/tests/time_dependent_reactions/flushing_case3.i)
(modules/porous_flow/examples/groundwater/ex02_abstraction.i)
(modules/phase_field/examples/interfacekernels/interface_fluxbc.i)
(test/tests/functions/piecewise_multilinear/twoD_const.i)
(modules/combined/examples/geochem-porous_flow/geotes_2D/aquifer_geochemistry.i)
(test/tests/auxkernels/parsed_aux/parsed_aux_test.i)
(modules/functional_expansion_tools/examples/3D_volumetric_cylindrical_subapp_mesh_refine/sub.i)
(modules/geochemistry/test/tests/kinetics/kinetic_albite.i)
(modules/functional_expansion_tools/test/tests/errors/multiapp_sub.i)
(modules/functional_expansion_tools/examples/1D_volumetric_Cartesian/sub.i)
(test/tests/kernels/hfem/robin_displaced.i)
(modules/functional_expansion_tools/test/tests/standard_use/volume_sub.i)
(test/tests/transfers/multiapp_userobject_transfer/restricted_elem_master.i)
(modules/combined/examples/geochem-porous_flow/forge/aquifer_geochemistry.i)
(modules/geochemistry/test/tests/kernels/time_deriv_1.i)
(test/tests/outputs/png/wedge.i)
(test/tests/auxkernels/linear_combination/test.i)
(modules/functional_expansion_tools/examples/2D_volumetric_Cartesian/sub.i)
(modules/tensor_mechanics/test/tests/notched_plastic_block/cmc_planar.i)
(modules/geochemistry/test/tests/time_dependent_reactions/flushing_case1.i)
(modules/geochemistry/test/tests/kernels/dispersion_1.i)
(modules/combined/examples/phase_field-mechanics/kks_mechanics_VTS.i)
(modules/combined/examples/geochem-porous_flow/geotes_weber_tensleep/eqm_model_25_to_92degC.i)
(modules/porous_flow/examples/reservoir_model/regular_grid.i)
(modules/porous_flow/test/tests/chemistry/precipitation.i)
(modules/functional_expansion_tools/examples/3D_volumetric_cylindrical/sub.i)
(modules/porous_flow/test/tests/poro_elasticity/mandel_constM.i)
(modules/combined/test/tests/poro_mechanics/mandel.i)
(modules/functional_expansion_tools/test/tests/standard_use/multiapp_sub.i)
(test/tests/transfers/multiapp_userobject_transfer/restricted_node_sub.i)
(test/tests/auxkernels/parsed_aux/xyzt.i)
(modules/geochemistry/test/tests/time_dependent_reactions/flushing_case2.i)
(modules/porous_flow/examples/groundwater/ex01.i)
(modules/combined/examples/publications/rapid_dev/fig3.i)
(test/tests/transfers/multiapp_userobject_transfer/restricted_elem_sub.i)
(modules/tensor_mechanics/test/tests/action/material_output_order.i)
(modules/combined/examples/geochem-porous_flow/geotes_weber_tensleep/exchanger.i)
(modules/combined/examples/geochem-porous_flow/geotes_2D/exchanger_un_quartz.i)
(modules/porous_flow/test/tests/pressure_pulse/pressure_pulse_1d_MD.i)
(modules/tensor_mechanics/test/tests/notched_plastic_block/biaxial_planar.i)
(modules/tensor_mechanics/test/tests/torque/ad_torque_small.i)
(modules/porous_flow/test/tests/poro_elasticity/mandel_basicthm.i)
(modules/geochemistry/test/tests/sorption_and_surface_complexation/selenate.i)
(modules/fluid_properties/test/tests/water/water.i)
(modules/functional_expansion_tools/examples/3D_volumetric_Cartesian_different_submesh/sub.i)
(modules/combined/examples/mortar/mortar_gradient.i)
(modules/tensor_mechanics/test/tests/torque/torque_small.i)
(modules/combined/examples/geochem-porous_flow/geotes_2D/aquifer_un_quartz_geochemistry.i)
(modules/combined/test/tests/poro_mechanics/borehole_highres.i)
(modules/combined/examples/phase_field-mechanics/kks_mechanics_KHS.i)
(modules/porous_flow/test/tests/poro_elasticity/mandel.i)
(modules/combined/examples/geochem-porous_flow/geotes_weber_tensleep/aquifer_geochemistry.i)
(modules/porous_flow/test/tests/chemistry/precipitation_2phase.i)
(modules/combined/examples/geochem-porous_flow/geotes_2D/exchanger.i)
(modules/porous_flow/examples/reservoir_model/field_model.i)
(modules/porous_flow/examples/thm_example/2D_c.i)
(modules/porous_flow/test/tests/chemistry/dissolution_limited_2phase.i)
(modules/porous_flow/test/tests/poro_elasticity/mandel_fully_saturated_volume.i)
(modules/porous_flow/examples/tutorial/11_2D.i)
(modules/porous_flow/test/tests/chemistry/dissolution.i)
(modules/geochemistry/test/tests/kinetics/quartz_dissolution.i)
(modules/geochemistry/test/tests/kernels/time_deriv_2.i)
(modules/functional_expansion_tools/examples/3D_volumetric_Cartesian_direct/sub.i)
(modules/combined/test/tests/poro_mechanics/borehole_lowres.i)
(modules/functional_expansion_tools/examples/3D_volumetric_Cartesian/sub.i)

(modules/functional_expansion_tools/test/tests/standard_use/volume_coupling_custom_norm_sub.i)

[Mesh]
  type = GeneratedMesh
  dim = 1

  xmin = 0.0
  xmax = 10.0
  nx = 15
[]

[Variables]
  [./empty]
  [../]
[]

[AuxVariables]
  [./s]
    order = FIRST
    family = LAGRANGE
  [../]
  [./m_in]
    order = FIRST
    family = LAGRANGE
  [../]
[]

[Kernels]
  [./null_kernel]
    type = NullKernel
    variable = empty
  [../]
[]

[AuxKernels]
  [./reconstruct_m_in]
    type = FunctionSeriesToAux
    function = FX_Basis_Value_Sub
    variable = m_in
  [../]
  [./calculate_s]
    type = ParsedAux
    variable = s
    args = m_in
    function = '2*exp(-m_in/0.8)'
  [../]
[]

[Functions]
  [./FX_Basis_Value_Sub]
    type = FunctionSeries
    series_type = Cartesian
    orders = '3'
    physical_bounds = '0.0  10.0'
    x = Legendre
    generation_type = 'sqrt_mu'
    expansion_type = 'sqrt_mu'
  [../]
[]

[UserObjects]
  [./FX_Value_UserObject_Sub]
    type = FXVolumeUserObject
    function = FX_Basis_Value_Sub
    variable = s
  [../]
[]

[Executioner]
  type = Transient
  num_steps = 10
  dt = 0.5
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

(test/tests/transfers/multiapp_userobject_transfer/restricted_node_master.i)

num_layers = 2

[Mesh]
  [box]
    type = GeneratedMeshGenerator
    dim = 3
    nx = ${num_layers}
    ny = 3
    nz = 3
    xmin = 0.25
    xmax = 1.25
  []
  # The MultiAppUserObjectTransfer object only works with ReplicatedMesh
  parallel_type = replicated
[]

[Variables]
  [u]
  []
[]

[Kernels]
  [td]
    type = TimeDerivative
    variable = u
  []

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

[AuxVariables]
  [a]
  []

  [s]
  []
[]

[AuxKernels]
  [s_ak]
    type = ParsedAux
    variable = s
    use_xyzt = true
    function = 'x+(z*z)'
  []
[]

[Functions]
[]

[Postprocessors]
  [a_avg]
    type = ElementAverageValue
    variable = a
  []
[]

[UserObjects]
  [S_avg_front]
    type = LayeredSideAverage
    boundary = front
    variable = s
    num_layers = ${num_layers}
    direction = x
  []

  [S_avg_back]
    type = LayeredSideAverage
    boundary = back
    variable = s
    num_layers = ${num_layers}
    direction = x
  []
[]

[MultiApps]
  [ch0]
    type = TransientMultiApp
    input_files = 'restricted_node_sub.i'
    bounding_box_padding = '0 0.5 1'
    positions = '0 0.5 -0.1'
    output_in_position = true
    cli_args = 'yy=0'
  []
  [ch1]
    type = TransientMultiApp
    input_files = 'restricted_node_sub.i'
    bounding_box_padding = '0 0.5 1'
    positions = '0 0.5  1.1'
    output_in_position = true
    cli_args = 'yy=1'
  []
[]

[Transfers]
  [from_ch0]
    type = MultiAppUserObjectTransfer
    boundary = back
    direction = from_multiapp
    multi_app = ch0
    variable = a
    user_object = A_avg
  []

  [from_ch1]
    type = MultiAppUserObjectTransfer
    boundary = front
    direction = from_multiapp
    multi_app = ch1
    variable = a
    user_object = A_avg
  []

  [to_ch0]
    type = MultiAppUserObjectTransfer
    block = 20
    direction = to_multiapp
    multi_app = ch0
    variable = S
    user_object = S_avg_back
  []

  [to_ch1]
    type = MultiAppUserObjectTransfer
    block = 20
    direction = to_multiapp
    multi_app = ch1
    variable = S
    user_object = S_avg_front
  []
[]

[Executioner]
  type = Transient
  num_steps = 2

  dt = 1
  nl_abs_tol = 1e-7
[]

[Outputs]
  exodus = true
[]

(modules/geochemistry/test/tests/kinetics/quartz_deposition.i)

# Example of quartz deposition in a fracture, as the temperature is reduced from 300degC to 25degC
# The initial free molality of SiO2(aq) is determined using quartz_equilibrium_at300degC
[GlobalParams]
  point = '0 0 0'
[]

[TimeDependentReactionSolver]
  model_definition = definition
  geochemistry_reactor_name = reactor
  charge_balance_species = "Cl-"
  constraint_species = "H2O              Na+              Cl-              SiO2(aq)"
  constraint_value = "  1.0              1E-10            1E-10            0.009722905"
  constraint_meaning = "kg_solvent_water bulk_composition bulk_composition free_concentration"
  constraint_unit = "   kg               moles            moles            molal"
  initial_temperature = 300.0
  temperature = temp_controller
  kinetic_species_name = Quartz
  kinetic_species_initial_value = 400
  kinetic_species_unit = g
  ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
  add_aux_pH = false # there is no H+ in this system
  evaluate_kinetic_rates_always = true # implicit time-marching used for stability
  execute_console_output_on = '' # only CSV output used in this example
[]

[UserObjects]
  [rate_quartz]
    type = GeochemistryKineticRate
    kinetic_species_name = Quartz
    intrinsic_rate_constant = 7.4112E2 # 2.35E-5mol/s/cm^2 = 7.411E2mol/yr/cm^2
    multiply_by_mass = true
    area_quantity = 1
    activation_energy = 72800.0
  []
  [definition]
    type = GeochemicalModelDefinition
    database_file = "../../../database/moose_geochemdb.json"
    basis_species = "H2O SiO2(aq) Na+ Cl-"
    kinetic_minerals = "Quartz"
    kinetic_rate_descriptions = "rate_quartz"
  []
[]


[Executioner]
  type = Transient
  dt = 0.02
  end_time = 1 # measured in years
[]

[AuxVariables]
  [temp_controller]
  []
  [diss_rate]
  []
[]
[AuxKernels]
  [temp_controller_auxk]
    type = FunctionAux
    function = '300 - 275 * t'
    variable = temp_controller
    execute_on = 'timestep_begin'
  []
  [diss_rate]
    type = ParsedAux
    args = mol_change_Quartz
    function = '-mol_change_Quartz / 0.02' # 0.02 = timestep size
    variable = diss_rate
  []
[]
[Postprocessors]
  [mg_per_kg_sio2]
    type = PointValue
    variable = "mg_per_kg_SiO2(aq)"
  []
  [rate_mole_per_year]
    type = PointValue
    variable = diss_rate
  []
  [temperature]
    type = PointValue
    variable = "solution_temperature"
  []
[]
[Outputs]
  csv = true
[]

(modules/geochemistry/test/tests/solubilities_and_activities/gypsum_solubility.i)

[TimeDependentReactionSolver]
  model_definition = definition
  swap_out_of_basis = "Ca++"
  swap_into_basis = "Gypsum"
  charge_balance_species = "SO4--"
  constraint_species = "H2O              Cl-                Na+                SO4--            Gypsum"
  constraint_value = "  1.0              1E-10              1E-10              1E-6             0.5814"
  constraint_meaning = "kg_solvent_water free_concentration free_concentration bulk_composition free_mineral"
  constraint_unit = "   kg               molal              molal              moles            moles"
  source_species_names = 'NaCl'
  source_species_rates = '1.0'
  add_aux_pH = false # there is no H+ in the problem
  ramp_max_ionic_strength_initial = 0 # not needed in this simple problem
  stoichiometric_ionic_str_using_Cl_only = true # for comparison with GWB
  abs_tol = 1E-12
  execute_console_output_on = '' # only CSV output in this example
[]

[UserObjects]
  [definition]
    type = GeochemicalModelDefinition
    database_file = "../../../database/moose_geochemdb.json"
    basis_species = "H2O Cl- Na+ SO4-- Ca++"
    equilibrium_minerals = "Gypsum"
    piecewise_linear_interpolation = true # for comparison with GWB
  []
[]

[Functions]
  [timestepper]
    type = PiecewiseLinear
    x = '0    0.1'
    y = '0.01 0.1'
  []
[]

[Executioner]
  type = Transient
  [TimeStepper]
    type = FunctionDT
    function = timestepper
  []
  end_time = 3
[]

[Outputs]
  csv = true
[]

[AuxVariables]
  [dissolved_gypsum_moles]
  []
[]
[AuxKernels]
  [dissolved_gypsum_moles]
    type = ParsedAux
    args = 'bulk_moles_Gypsum free_mg_Gypsum'
    function = 'bulk_moles_Gypsum - free_mg_Gypsum / 1000 / 172.168 '
    variable = dissolved_gypsum_moles
    execute_on = 'timestep_end'
  []
[]

[Postprocessors]
  [cl_molal]
    type = PointValue
    point = '0 0 0'
    variable = 'molal_Cl-'
  []
  [dissolved_gypsum_mol]
    type = PointValue
    point = '0 0 0'
    variable = dissolved_gypsum_moles
  []
[]

(modules/porous_flow/examples/tutorial/11.i)

# Two-phase borehole injection problem
[Mesh]
  [annular]
    type = AnnularMeshGenerator
    nr = 10
    rmin = 1.0
    rmax = 10
    growth_r = 1.4
    nt = 4
    dmin = 0
    dmax = 90
  []
  [make3D]
    input = annular
    type = MeshExtruderGenerator
    extrusion_vector = '0 0 12'
    num_layers = 3
    bottom_sideset = 'bottom'
    top_sideset = 'top'
  []
  [shift_down]
    type = TransformGenerator
    transform = TRANSLATE
    vector_value = '0 0 -6'
    input = make3D
  []
  [aquifer]
    type = SubdomainBoundingBoxGenerator
    block_id = 1
    bottom_left = '0 0 -2'
    top_right = '10 10 2'
    input = shift_down
  []
  [injection_area]
    type = ParsedGenerateSideset
    combinatorial_geometry = 'x*x+y*y<1.01'
    included_subdomain_ids = 1
    new_sideset_name = 'injection_area'
    input = 'aquifer'
  []
  [rename]
    type = RenameBlockGenerator
    old_block_id = '0 1'
    new_block_name = 'caps aquifer'
    input = 'injection_area'
  []
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = 'pwater pgas T disp_x disp_y'
    number_fluid_phases = 2
    number_fluid_components = 2
  []
  [pc]
    type = PorousFlowCapillaryPressureVG
    alpha = 1E-6
    m = 0.6
  []
[]

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
  gravity = '0 0 0'
  biot_coefficient = 1.0
  PorousFlowDictator = dictator
[]

[Variables]
  [pwater]
    initial_condition = 20E6
  []
  [pgas]
    initial_condition = 20.1E6
  []
  [T]
    initial_condition = 330
    scaling = 1E-5
  []
  [disp_x]
    scaling = 1E-5
  []
  [disp_y]
    scaling = 1E-5
  []
[]

[Kernels]
  [mass_water_dot]
    type = PorousFlowMassTimeDerivative
    fluid_component = 0
    use_displaced_mesh = false
    variable = pwater
  []
  [flux_water]
    type = PorousFlowAdvectiveFlux
    fluid_component = 0
    use_displaced_mesh = false
    variable = pwater
  []
  [vol_strain_rate_water]
    type = PorousFlowMassVolumetricExpansion
    fluid_component = 0
    use_displaced_mesh = false
    variable = pwater
  []
  [mass_co2_dot]
    type = PorousFlowMassTimeDerivative
    fluid_component = 1
    use_displaced_mesh = false
    variable = pgas
  []
  [flux_co2]
    type = PorousFlowAdvectiveFlux
    fluid_component = 1
    use_displaced_mesh = false
    variable = pgas
  []
  [vol_strain_rate_co2]
    type = PorousFlowMassVolumetricExpansion
    fluid_component = 1
    use_displaced_mesh = false
    variable = pgas
  []
  [energy_dot]
    type = PorousFlowEnergyTimeDerivative
    use_displaced_mesh = false
    variable = T
  []
  [advection]
    type = PorousFlowHeatAdvection
    use_displaced_mesh = false
    variable = T
  []
  [conduction]
    type = PorousFlowHeatConduction
    use_displaced_mesh = false
    variable = T
  []
  [vol_strain_rate_heat]
    type = PorousFlowHeatVolumetricExpansion
    use_displaced_mesh = false
    variable = T
  []
  [grad_stress_x]
    type = StressDivergenceTensors
    temperature = T
    variable = disp_x
    eigenstrain_names = thermal_contribution
    use_displaced_mesh = false
    component = 0
  []
  [poro_x]
    type = PorousFlowEffectiveStressCoupling
    variable = disp_x
    use_displaced_mesh = false
    component = 0
  []
  [grad_stress_y]
    type = StressDivergenceTensors
    temperature = T
    variable = disp_y
    eigenstrain_names = thermal_contribution
    use_displaced_mesh = false
    component = 1
  []
  [poro_y]
    type = PorousFlowEffectiveStressCoupling
    variable = disp_y
    use_displaced_mesh = false
    component = 1
  []
[]

[AuxVariables]
  [disp_z]
  []
  [effective_fluid_pressure]
    family = MONOMIAL
    order = CONSTANT
  []
  [mass_frac_phase0_species0]
    initial_condition = 1 # all water in phase=0
  []
  [mass_frac_phase1_species0]
    initial_condition = 0 # no water in phase=1
  []
  [sgas]
    family = MONOMIAL
    order = CONSTANT
  []
  [swater]
    family = MONOMIAL
    order = CONSTANT
  []
  [stress_rr]
    family = MONOMIAL
    order = CONSTANT
  []
  [stress_tt]
    family = MONOMIAL
    order = CONSTANT
  []
  [stress_zz]
    family = MONOMIAL
    order = CONSTANT
  []
  [porosity]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[AuxKernels]
  [effective_fluid_pressure]
    type = ParsedAux
    args = 'pwater pgas swater sgas'
    function = 'pwater * swater + pgas * sgas'
    variable = effective_fluid_pressure
  []
  [swater]
    type = PorousFlowPropertyAux
    variable = swater
    property = saturation
    phase = 0
    execute_on = timestep_end
  []
  [sgas]
    type = PorousFlowPropertyAux
    variable = sgas
    property = saturation
    phase = 1
    execute_on = timestep_end
  []
  [stress_rr]
    type = RankTwoScalarAux
    variable = stress_rr
    rank_two_tensor = stress
    scalar_type = RadialStress
    point1 = '0 0 0'
    point2 = '0 0 1'
    execute_on = timestep_end
  []
  [stress_tt]
    type = RankTwoScalarAux
    variable = stress_tt
    rank_two_tensor = stress
    scalar_type = HoopStress
    point1 = '0 0 0'
    point2 = '0 0 1'
    execute_on = timestep_end
  []
  [stress_zz]
    type = RankTwoAux
    variable = stress_zz
    rank_two_tensor = stress
    index_i = 2
    index_j = 2
    execute_on = timestep_end
  []
  [porosity]
    type = PorousFlowPropertyAux
    variable = porosity
    property = porosity
    execute_on = timestep_end
  []
[]


[BCs]
  [roller_tmax]
    type = DirichletBC
    variable = disp_x
    value = 0
    boundary = dmax
  []
  [roller_tmin]
    type = DirichletBC
    variable = disp_y
    value = 0
    boundary = dmin
  []
  [pinned_top_bottom_x]
    type = DirichletBC
    variable = disp_x
    value = 0
    boundary = 'top bottom'
  []
  [pinned_top_bottom_y]
    type = DirichletBC
    variable = disp_y
    value = 0
    boundary = 'top bottom'
  []
  [cavity_pressure_x]
    type = Pressure
    boundary = injection_area
    variable = disp_x
    component = 0
    postprocessor = constrained_effective_fluid_pressure_at_wellbore
    use_displaced_mesh = false
  []
  [cavity_pressure_y]
    type = Pressure
    boundary = injection_area
    variable = disp_y
    component = 1
    postprocessor = constrained_effective_fluid_pressure_at_wellbore
    use_displaced_mesh = false
  []

  [cold_co2]
    type = DirichletBC
    boundary = injection_area
    variable = T
    value = 290  # injection temperature
    use_displaced_mesh = false
  []
  [constant_co2_injection]
    type = PorousFlowSink
    boundary = injection_area
    variable = pgas
    fluid_phase = 1
    flux_function = -1E-4
    use_displaced_mesh = false
  []

  [outer_water_removal]
    type = PorousFlowPiecewiseLinearSink
    boundary = rmax
    variable = pwater
    fluid_phase = 0
    pt_vals = '0 1E9'
    multipliers = '0 1E8'
    PT_shift = 20E6
    use_mobility = true
    use_relperm = true
    use_displaced_mesh = false
  []
  [outer_co2_removal]
    type = PorousFlowPiecewiseLinearSink
    boundary = rmax
    variable = pgas
    fluid_phase = 1
    pt_vals = '0 1E9'
    multipliers = '0 1E8'
    PT_shift = 20.1E6
    use_mobility = true
    use_relperm = true
    use_displaced_mesh = false
  []
[]

[Modules]
  [FluidProperties]
    [true_water]
      type = Water97FluidProperties
    []
    [tabulated_water]
      type = TabulatedFluidProperties
      fp = true_water
      temperature_min = 275
      pressure_max = 1E8
      interpolated_properties = 'density viscosity enthalpy internal_energy'
      fluid_property_file = water97_tabulated_11.csv
    []
    [true_co2]
      type = CO2FluidProperties
    []
    [tabulated_co2]
      type = TabulatedFluidProperties
      fp = true_co2
      temperature_min = 275
      pressure_max = 1E8
      interpolated_properties = 'density viscosity enthalpy internal_energy'
      fluid_property_file = co2_tabulated_11.csv
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
    temperature = T
  []
  [saturation_calculator]
    type = PorousFlow2PhasePP
    phase0_porepressure = pwater
    phase1_porepressure = pgas
    capillary_pressure = pc
  []
  [massfrac]
    type = PorousFlowMassFraction
    mass_fraction_vars = 'mass_frac_phase0_species0 mass_frac_phase1_species0'
  []
  [water]
    type = PorousFlowSingleComponentFluid
    fp = tabulated_water
    phase = 0
  []
  [co2]
    type = PorousFlowSingleComponentFluid
    fp = tabulated_co2
    phase = 1
  []
  [relperm_water]
    type = PorousFlowRelativePermeabilityCorey
    n = 4
    s_res = 0.1
    sum_s_res = 0.2
    phase = 0
  []
  [relperm_co2]
    type = PorousFlowRelativePermeabilityBC
    nw_phase = true
    lambda = 2
    s_res = 0.1
    sum_s_res = 0.2
    phase = 1
  []
  [porosity_mat]
    type = PorousFlowPorosity
    fluid = true
    mechanical = true
    thermal = true
    porosity_zero = 0.1
    reference_temperature = 330
    reference_porepressure = 20E6
    thermal_expansion_coeff = 15E-6 # volumetric
    solid_bulk = 8E9 # unimportant since biot = 1
  []
  [permeability_aquifer]
    type = PorousFlowPermeabilityKozenyCarman
    block = aquifer
    poroperm_function = kozeny_carman_phi0
    phi0 = 0.1
    n = 2
    m = 2
    k0 = 1E-12
  []
  [permeability_caps]
    type = PorousFlowPermeabilityKozenyCarman
    block = caps
    poroperm_function = kozeny_carman_phi0
    phi0 = 0.1
    n = 2
    m = 2
    k0 = 1E-15
    k_anisotropy = '1 0 0  0 1 0  0 0 0.1'
  []
  [rock_thermal_conductivity]
    type = PorousFlowThermalConductivityIdeal
    dry_thermal_conductivity = '2 0 0  0 2 0  0 0 2'
  []
  [rock_internal_energy]
    type = PorousFlowMatrixInternalEnergy
    specific_heat_capacity = 1100
    density = 2300
  []

  [elasticity_tensor]
    type = ComputeIsotropicElasticityTensor
    youngs_modulus = 5E9
    poissons_ratio = 0.0
  []
  [strain]
    type = ComputeSmallStrain
    eigenstrain_names = 'thermal_contribution initial_stress'
  []
  [thermal_contribution]
    type = ComputeThermalExpansionEigenstrain
    temperature = T
    thermal_expansion_coeff = 5E-6 # this is the linear thermal expansion coefficient
    eigenstrain_name = thermal_contribution
    stress_free_temperature = 330
  []
  [initial_strain]
    type = ComputeEigenstrainFromInitialStress
    initial_stress = '20E6 0 0  0 20E6 0  0 0 20E6'
    eigenstrain_name = initial_stress
  []
  [stress]
    type = ComputeLinearElasticStress
  []

  [effective_fluid_pressure_mat]
    type = PorousFlowEffectiveFluidPressure
  []
  [volumetric_strain]
    type = PorousFlowVolumetricStrain
  []
[]

[Postprocessors]
  [effective_fluid_pressure_at_wellbore]
    type = PointValue
    variable = effective_fluid_pressure
    point = '1 0 0'
    execute_on = timestep_begin
    use_displaced_mesh = false
  []
  [constrained_effective_fluid_pressure_at_wellbore]
    type = FunctionValuePostprocessor
    function = constrain_effective_fluid_pressure
    execute_on = timestep_begin
  []
[]

[Functions]
  [constrain_effective_fluid_pressure]
    type = ParsedFunction
    vars = effective_fluid_pressure_at_wellbore
    vals = effective_fluid_pressure_at_wellbore
    value = 'max(effective_fluid_pressure_at_wellbore, 20E6)'
  []
[]

[Preconditioning]
  active = basic
  [basic]
    type = SMP
    full = true
    petsc_options = '-ksp_diagonal_scale -ksp_diagonal_scale_fix'
    petsc_options_iname = '-pc_type -sub_pc_type -sub_pc_factor_shift_type -pc_asm_overlap'
    petsc_options_value = ' asm      lu           NONZERO                   2'
  []
  [preferred_but_might_not_be_installed]
    type = SMP
    full = true
    petsc_options_iname = '-pc_type -pc_factor_mat_solver_package'
    petsc_options_value = ' lu       mumps'
  []
[]

[Executioner]
  type = Transient
  solve_type = Newton
  end_time = 1E3
  [TimeStepper]
    type = IterationAdaptiveDT
    dt = 1E3
    growth_factor = 1.2
    optimal_iterations = 10
  []
  nl_abs_tol = 1E-7
[]

[Outputs]
  exodus = true
[]

(modules/porous_flow/test/tests/chemistry/dissolution_limited.i)

# The dissolution reaction, with limited initial mineral concentration
#
# a <==> mineral
#
# produces "mineral".  Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / porosity)' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is positive for a < 0.25, ie dissolution for a(t=0) < 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
#   = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * porosity
#
# However, c(t=0) is small, so that the reaction only works until c=0, then a and c both remain fixed
#
# This test checks that (a + c / porosity) is time-independent, and that a follows the above solution, until c=0 and thereafter remains fixed.
#
# Aside:
#    The exponential curve is not followed exactly because moose actually solves
#    (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#    which does not give an exponential exactly, except in the limit dt->0
[Mesh]
  type = GeneratedMesh
  dim = 1
[]

[Variables]
  [a]
    initial_condition = 0.05
  []
[]

[AuxVariables]
  [eqm_k]
    initial_condition = 0.5
  []
  [pressure]
  []
  [ini_mineral_conc]
    initial_condition = 0.015
  []
  [mineral]
    family = MONOMIAL
    order = CONSTANT
  []
  [should_be_static]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[AuxKernels]
  [mineral]
    type = PorousFlowPropertyAux
    property = mineral_concentration
    mineral_species = 0
    variable = mineral
  []
  [should_be_static]
    type = ParsedAux
    args = 'mineral a'
    function = 'a + mineral / 0.1'
    variable = should_be_static
  []
[]

[GlobalParams]
  PorousFlowDictator = dictator
[]

[Kernels]
  [mass_a]
    type = PorousFlowMassTimeDerivative
    fluid_component = 0
    variable = a
  []
  [pre_dis]
    type = PorousFlowPreDis
    variable = a
    mineral_density = 1000
    stoichiometry = 1
  []
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = a
    number_fluid_phases = 1
    number_fluid_components = 2
    number_aqueous_kinetic = 1
  []
[]

[Modules]
  [FluidProperties]
    [simple_fluid]
      type = SimpleFluidProperties
      bulk_modulus = 2e9 # huge, so mimic chemical_reactions
      density0 = 1000
      thermal_expansion = 0
      viscosity = 1e-3
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
    temperature = 1
  []
  [ppss]
    type = PorousFlow1PhaseFullySaturated
    porepressure = pressure
  []
  [mass_frac]
    type = PorousFlowMassFraction
    mass_fraction_vars = a
  []
  [predis]
    type = PorousFlowAqueousPreDisChemistry
    primary_concentrations = a
    num_reactions = 1
    equilibrium_constants = eqm_k
    primary_activity_coefficients = 2
    reactions = 1
    specific_reactive_surface_area = 0.5
    kinetic_rate_constant = 0.6065306597126334
    activation_energy = 3
    molar_volume = 2
    gas_constant = 6
    reference_temperature = 0.5
  []
  [mineral_conc]
    type = PorousFlowAqueousPreDisMineral
    initial_concentrations = ini_mineral_conc
  []
  [simple_fluid]
    type = PorousFlowSingleComponentFluid
    fp = simple_fluid
    phase = 0
  []
  [porosity]
    type = PorousFlowPorosityConst
    porosity = 0.1
  []
[]

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

[Executioner]
  type = Transient
  solve_type = Newton
  nl_abs_tol = 1E-10
  dt = 0.01
  end_time = 1
[]

[Postprocessors]
  [a]
    type = PointValue
    point = '0 0 0'
    variable = a
  []
  [should_be_static]
    type = PointValue
    point = '0 0 0'
    variable = should_be_static
  []
[]
[Outputs]
  interval = 10
  csv = true
  perf_graph = true
[]

(modules/navier_stokes/test/tests/finite_volume/ins/boussinesq/boussinesq.i)

mu = 1
rho = 1
k = 1
cp = 1
alpha = 1
vel = 'velocity'
velocity_interp_method = 'rc'
advected_interp_method = 'upwind'
rayleigh=1e3
hot_temp=${rayleigh}
temp_ref=${fparse hot_temp / 2.}

[GlobalParams]
  two_term_boundary_expansion = true
[]

[Mesh]
  [gen]
    type = GeneratedMeshGenerator
    dim = 2
    xmin = 0
    xmax = 1
    ymin = 0
    ymax = 1
    nx = 32
    ny = 32
  []
[]

[Variables]
  [u]
    type = INSFVVelocityVariable
  []
  [v]
    type = INSFVVelocityVariable
  []
  [pressure]
    type = INSFVPressureVariable
  []
  [T]
    type = INSFVEnergyVariable
    scaling = 1e-4
  []
  [lambda]
    family = SCALAR
    order = FIRST
  []
[]

[AuxVariables]
  [U]
    order = CONSTANT
    family = MONOMIAL
    fv = true
  []
  [vel_x]
    order = FIRST
    family = MONOMIAL
  []
  [vel_y]
    order = FIRST
    family = MONOMIAL
  []
  [viz_T]
    order = FIRST
    family = MONOMIAL
  []
[]

[AuxKernels]
  [mag]
    type = VectorMagnitudeAux
    variable = U
    x = u
    y = v
    execute_on = 'initial timestep_end'
  []
  [vel_x]
    type = ParsedAux
    variable = vel_x
    function = 'u'
    execute_on = 'initial timestep_end'
    args = 'u'
  []
  [vel_y]
    type = ParsedAux
    variable = vel_y
    function = 'v'
    execute_on = 'initial timestep_end'
    args = 'v'
  []
  [viz_T]
    type = ParsedAux
    variable = viz_T
    function = 'T'
    execute_on = 'initial timestep_end'
    args = 'T'
  []
[]

[FVKernels]
  [mass]
    type = INSFVMassAdvection
    variable = pressure
    vel = ${vel}
    advected_interp_method = ${advected_interp_method}
    velocity_interp_method = ${velocity_interp_method}
    u = u
    v = v
    pressure = pressure
    mu = ${mu}
    rho = ${rho}
  []
  [mean_zero_pressure]
    type = FVScalarLagrangeMultiplier
    variable = pressure
    lambda = lambda
  []

  [u_advection]
    type = INSFVMomentumAdvection
    variable = u
    advected_quantity = 'rhou'
    vel = ${vel}
    velocity_interp_method = ${velocity_interp_method}
    advected_interp_method = ${advected_interp_method}
    pressure = pressure
    u = u
    v = v
    mu = ${mu}
    rho = ${rho}
  []
  [u_viscosity]
    type = FVDiffusion
    variable = u
    coeff = ${mu}
  []
  [u_pressure]
    type = INSFVMomentumPressure
    variable = u
    momentum_component = 'x'
    p = pressure
  []
  [u_buoyancy]
    type = INSFVMomentumBoussinesq
    variable = u
    temperature = T
    gravity = '0 -1 0'
    rho = ${rho}
    ref_temperature = ${temp_ref}
    momentum_component = 'x'
  []
  [u_gravity]
    type = INSFVMomentumGravity
    variable = u
    gravity = '0 -1 0'
    rho = ${rho}
    momentum_component = 'x'
  []

  [v_advection]
    type = INSFVMomentumAdvection
    variable = v
    advected_quantity = 'rhov'
    vel = ${vel}
    velocity_interp_method = ${velocity_interp_method}
    advected_interp_method = ${advected_interp_method}
    pressure = pressure
    u = u
    v = v
    mu = ${mu}
    rho = ${rho}
  []
  [v_viscosity]
    type = FVDiffusion
    variable = v
    coeff = ${mu}
  []
  [v_pressure]
    type = INSFVMomentumPressure
    variable = v
    momentum_component = 'y'
    p = pressure
  []
  [v_buoyancy]
    type = INSFVMomentumBoussinesq
    variable = v
    temperature = T
    gravity = '0 -1 0'
    rho = ${rho}
    ref_temperature = ${temp_ref}
    momentum_component = 'y'
  []
  [v_gravity]
    type = INSFVMomentumGravity
    variable = v
    gravity = '0 -1 0'
    rho = ${rho}
    momentum_component = 'y'
  []

  [temp_conduction]
    type = FVDiffusion
    coeff = 'k'
    variable = T
  []
  [temp_advection]
    type = INSFVEnergyAdvection
    variable = T
    vel = ${vel}
    velocity_interp_method = ${velocity_interp_method}
    advected_interp_method = ${advected_interp_method}
    pressure = pressure
    u = u
    v = v
    mu = ${mu}
    rho = ${rho}
  []
[]

[FVBCs]
  [top_x]
    type = INSFVNoSlipWallBC
    variable = u
    boundary = 'top'
    function = 'lid_function'
  []

  [no_slip_x]
    type = INSFVNoSlipWallBC
    variable = u
    boundary = 'left right bottom'
    function = 0
  []

  [no_slip_y]
    type = INSFVNoSlipWallBC
    variable = v
    boundary = 'left right top bottom'
    function = 0
  []

  [T_hot]
    type = FVDirichletBC
    variable = T
    boundary = left
    value = ${hot_temp}
  []

  [T_cold]
    type = FVDirichletBC
    variable = T
    boundary = right
    value = 0
  []
[]

[Materials]
  [const]
    type = ADGenericConstantMaterial
    prop_names = 'k cp alpha'
    prop_values = '${k} ${cp} ${alpha}'
  []
  [ins_fv]
    type = INSFVMaterial
    u = 'u'
    v = 'v'
    pressure = 'pressure'
    temperature = 'T'
    rho = ${rho}
  []
[]

[Functions]
  [lid_function]
    type = ParsedFunction
    value = '4*x*(1-x)'
  []
[]


[Executioner]
  type = Steady
  solve_type = 'NEWTON'
  petsc_options_iname = '-pc_type -ksp_gmres_restart -sub_pc_type -sub_pc_factor_shift_type'
  petsc_options_value = 'asm      300                lu           NONZERO'
  nl_rel_tol = 1e-12
[]

[Outputs]
  exodus = true
[]

(modules/porous_flow/test/tests/poro_elasticity/mandel_fully_saturated.i)

# Mandel's problem of consolodation of a drained medium
# Using the FullySaturatedDarcyBase and FullySaturatedMassTimeDerivative kernels
# Note the use of consistent_with_displaced_mesh = false in the calculation of volumetric strain
#
# A sample is in plane strain.
# -a <= x <= a
# -b <= y <= b
# It is squashed with constant force by impermeable, frictionless plattens on its top and bottom surfaces (at y=+/-b)
# Fluid is allowed to leak out from its sides (at x=+/-a)
# The porepressure within the sample is monitored.
#
# As is common in the literature, this is simulated by
# considering the quarter-sample, 0<=x<=a and 0<=y<=b, with
# impermeable, roller BCs at x=0 and y=0 and y=b.
# Porepressure is fixed at zero on x=a.
# Porepressure and displacement are initialised to zero.
# Then the top (y=b) is moved downwards with prescribed velocity,
# so that the total force that is inducing this downwards velocity
# is fixed.  The velocity is worked out by solving Mandel's problem
# analytically, and the total force is monitored in the simulation
# to check that it indeed remains constant.
#
# Here are the problem's parameters, and their values:
# Soil width.  a = 1
# Soil height.  b = 0.1
# Soil's Lame lambda.  la = 0.5
# Soil's Lame mu, which is also the Soil's shear modulus.  mu = G = 0.75
# Soil bulk modulus.  K = la + 2*mu/3 = 1
# Drained Poisson ratio.  nu = (3K - 2G)/(6K + 2G) = 0.2
# Soil bulk compliance.  1/K = 1
# Fluid bulk modulus.  Kf = 8
# Fluid bulk compliance.  1/Kf = 0.125
# Soil initial porosity.  phi0 = 0.1
# Biot coefficient.  alpha = 0.6
# Biot modulus.  M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 4.705882
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.694118
# Undrained Poisson ratio.  nuu = (3Ku - 2G)/(6Ku + 2G) = 0.372627
# Skempton coefficient.  B = alpha*M/Ku = 1.048035
# Fluid mobility (soil permeability/fluid viscosity).  k = 1.5
# Consolidation coefficient.  c = 2*k*B^2*G*(1-nu)*(1+nuu)^2/9/(1-nuu)/(nuu-nu) = 3.821656
# Normal stress on top.  F = 1
#
# The solution for porepressure and displacements is given in
# AHD Cheng and E Detournay "A direct boundary element method for plane strain poroelasticity" International Journal of Numerical and Analytical Methods in Geomechanics 12 (1988) 551-572.
# The solution involves complicated infinite series, so I shall not write it here

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

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
  PorousFlowDictator = dictator
  block = 0
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = 'porepressure disp_x disp_y disp_z'
    number_fluid_phases = 1
    number_fluid_components = 1
  []
[]

[Variables]
  [disp_x]
  []
  [disp_y]
  []
  [disp_z]
  []
  [porepressure]
  []
[]

[BCs]
  [roller_xmin]
    type = DirichletBC
    variable = disp_x
    value = 0
    boundary = 'left'
  []
  [roller_ymin]
    type = DirichletBC
    variable = disp_y
    value = 0
    boundary = 'bottom'
  []
  [plane_strain]
    type = DirichletBC
    variable = disp_z
    value = 0
    boundary = 'back front'
  []
  [xmax_drained]
    type = DirichletBC
    variable = porepressure
    value = 0
    boundary = right
  []
  [top_velocity]
    type = FunctionDirichletBC
    variable = disp_y
    function = top_velocity
    boundary = top
  []
[]

[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'
  []
[]

[AuxVariables]
  [stress_yy]
    order = CONSTANT
    family = MONOMIAL
  []
  [tot_force]
    order = CONSTANT
    family = MONOMIAL
  []
[]

[AuxKernels]
  [stress_yy]
    type = RankTwoAux
    rank_two_tensor = stress
    variable = stress_yy
    index_i = 1
    index_j = 1
  []
  [tot_force]
    type = ParsedAux
    args = 'stress_yy porepressure'
    execute_on = timestep_end
    variable = tot_force
    function = '-stress_yy+0.6*porepressure'
  []
[]

[Kernels]
  [grad_stress_x]
    type = StressDivergenceTensors
    variable = disp_x
    component = 0
  []
  [grad_stress_y]
    type = StressDivergenceTensors
    variable = disp_y
    component = 1
  []
  [grad_stress_z]
    type = StressDivergenceTensors
    variable = disp_z
    component = 2
  []
  [poro_x]
    type = PorousFlowEffectiveStressCoupling
    biot_coefficient = 0.6
    variable = disp_x
    component = 0
  []
  [poro_y]
    type = PorousFlowEffectiveStressCoupling
    biot_coefficient = 0.6
    variable = disp_y
    component = 1
  []
  [poro_z]
    type = PorousFlowEffectiveStressCoupling
    biot_coefficient = 0.6
    component = 2
    variable = disp_z
  []
  [mass0]
    type = PorousFlowFullySaturatedMassTimeDerivative
    biot_coefficient = 0.6
    coupling_type = HydroMechanical
    variable = porepressure
  []
  [flux]
    type = PorousFlowFullySaturatedDarcyBase
    variable = porepressure
    gravity = '0 0 0'
  []
[]

[Modules]
  [FluidProperties]
    [simple_fluid]
      type = SimpleFluidProperties
      bulk_modulus = 8
      density0 = 1
      thermal_expansion = 0
      viscosity = 1
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
  []
  [elasticity_tensor]
    type = ComputeElasticityTensor
    C_ijkl = '0.5 0.75'
    # bulk modulus is lambda + 2*mu/3 = 0.5 + 2*0.75/3 = 1
    fill_method = symmetric_isotropic
  []
  [strain]
    type = ComputeSmallStrain
  []
  [stress]
    type = ComputeLinearElasticStress
  []
  [eff_fluid_pressure_qp]
    type = PorousFlowEffectiveFluidPressure
  []
  [vol_strain]
    type = PorousFlowVolumetricStrain
    consistent_with_displaced_mesh = false
  []
  [ppss]
    type = PorousFlow1PhaseFullySaturated
    porepressure = porepressure
  []
  [massfrac]
    type = PorousFlowMassFraction
  []
  [simple_fluid_qp]
    type = PorousFlowSingleComponentFluid
    fp = simple_fluid
    phase = 0
  []
  [porosity]
    type = PorousFlowPorosityConst # only the initial value of this is ever used
    porosity = 0.1
  []
  [biot_modulus]
    type = PorousFlowConstantBiotModulus
    biot_coefficient = 0.6
    solid_bulk_compliance = 1
    fluid_bulk_modulus = 8
  []
  [permeability]
    type = PorousFlowPermeabilityConst
    permeability = '1.5 0 0   0 1.5 0   0 0 1.5'
  []
[]

[Postprocessors]
  [p0]
    type = PointValue
    outputs = csv
    point = '0.0 0 0'
    variable = porepressure
  []
  [p1]
    type = PointValue
    outputs = csv
    point = '0.1 0 0'
    variable = porepressure
  []
  [p2]
    type = PointValue
    outputs = csv
    point = '0.2 0 0'
    variable = porepressure
  []
  [p3]
    type = PointValue
    outputs = csv
    point = '0.3 0 0'
    variable = porepressure
  []
  [p4]
    type = PointValue
    outputs = csv
    point = '0.4 0 0'
    variable = porepressure
  []
  [p5]
    type = PointValue
    outputs = csv
    point = '0.5 0 0'
    variable = porepressure
  []
  [p6]
    type = PointValue
    outputs = csv
    point = '0.6 0 0'
    variable = porepressure
  []
  [p7]
    type = PointValue
    outputs = csv
    point = '0.7 0 0'
    variable = porepressure
  []
  [p8]
    type = PointValue
    outputs = csv
    point = '0.8 0 0'
    variable = porepressure
  []
  [p9]
    type = PointValue
    outputs = csv
    point = '0.9 0 0'
    variable = porepressure
  []
  [p99]
    type = PointValue
    outputs = csv
    point = '1 0 0'
    variable = porepressure
  []
  [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
    outputs = console
    function = if(0.15*t<0.01,0.15*t,0.01)
  []
[]

[Preconditioning]
  [andy]
    type = SMP
    full = true
    petsc_options_iname = '-ksp_type -pc_type -sub_pc_type -snes_atol -snes_rtol -snes_max_it'
    petsc_options_value = 'gmres asm lu 1E-14 1E-10 10000'
  []
[]

[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'
  file_base = mandel_fully_saturated
  [csv]
    interval = 3
    type = CSV
  []
[]

(modules/geochemistry/test/tests/time_dependent_reactions/flushing_case3.i)

# Alkali flushing of a reservoir (an example of flushing): adding Na2SiO3
# To determine the initial constraint_values, run flushing_equilibrium_at70degC.i
# Note that flushing_equilibrium_at70degC.i will have to be re-run when temperature-dependence has been added to geochemistry
# Note that Dawsonite is currently not included as an equilibrium_mineral, otherwise it is supersaturated in the initial configuration, so precipitates.  Bethke does not report this in Fig30.4, so I assume it is due to temperature dependence
[GlobalParams]
  point = '0 0 0'
[]

[TimeDependentReactionSolver]
  model_definition = definition
  geochemistry_reactor_name = reactor
  charge_balance_species = "Cl-"
  swap_into_basis = "Calcite Dolomite-ord Muscovite Kaolinite"
  swap_out_of_basis = "HCO3- Mg++ K+ Al+++"
  constraint_species = "H2O H+   Cl-       Na+       Ca++       Calcite   Dolomite-ord Muscovite Kaolinite SiO2(aq)"
  constraint_value = "  1.0 1E-5 2.1716946 1.0288941 0.21650572 10.177537 3.6826177    1.320907  1.1432682 6.318e-05"
  constraint_meaning = "kg_solvent_water activity bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition free_concentration"
  constraint_unit = "   kg              dimensionless moles          moles              moles              moles              moles              moles              moles              molal"
  initial_temperature = 70.0
  temperature = 70.0
  kinetic_species_name = Quartz
  kinetic_species_initial_value = 226.992243
  kinetic_species_unit = moles
  evaluate_kinetic_rates_always = true # implicit time-marching used for stability
  ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
  close_system_at_time = 0.0
  remove_fixed_activity_name = "H+"
  remove_fixed_activity_time = 0.0
  mode = 3 # flush through the NaOH solution specified below:
  source_species_names = "H2O    H+  Na+   SiO2(aq)"
  source_species_rates = "27.88 -0.25 0.25 0.125" # 1kg water/2days = 27.755moles/day.  0.25mol Na2O/2days = 0.25*(--2mol H+ + 2mol Na+ + 1mol H2O)/2days
[]

[UserObjects]
  [rate_quartz]
    type = GeochemistryKineticRate
    kinetic_species_name = Quartz
    intrinsic_rate_constant = 1.3824E-13 # 1.6E-19mol/s/cm^2 = 1.3824E-13mol/day/cm^2
    multiply_by_mass = true
    area_quantity = 1000
    promoting_species_names = "H+"
    promoting_species_indices = "-0.5"
  []
  [definition]
    type = GeochemicalModelDefinition
    database_file = "../../../database/moose_geochemdb.json"
    basis_species = "H2O H+ Cl- Na+ Ca++ HCO3- Mg++ K+ Al+++ SiO2(aq)"
    equilibrium_minerals = "Calcite Dolomite-ord Muscovite Kaolinite Paragonite Analcime Phlogopite Tridymite" # Dawsonite
    kinetic_minerals = "Quartz"
    kinetic_rate_descriptions = "rate_quartz"
  []
[]

[AuxVariables]
  [diss_rate]
  []
[]
[AuxKernels]
  [diss_rate]
    type = ParsedAux
    args = mol_change_Quartz
    function = '-mol_change_Quartz / 1.0' # 1.0 = timestep size
    variable = diss_rate
  []
[]

[Postprocessors]
  [pH]
    type = PointValue
    variable = "pH"
  []
  [rate_mole_per_day]
    type = PointValue
    variable = diss_rate
  []
  [cm3_Calcite]
    type = PointValue
    variable = free_cm3_Calcite
  []
  [cm3_Dolomite]
    type = PointValue
    variable = free_cm3_Dolomite-ord
  []
  [cm3_Muscovite]
    type = PointValue
    variable = free_cm3_Muscovite
  []
  [cm3_Kaolinite]
    type = PointValue
    variable = free_cm3_Kaolinite
  []
  [cm3_Quartz]
    type = PointValue
    variable = free_cm3_Quartz
  []
  [cm3_Paragonite]
    type = PointValue
    variable = free_cm3_Paragonite
  []
  [cm3_Analcime]
    type = PointValue
    variable = free_cm3_Analcime
  []
  [cm3_Phlogopite]
    type = PointValue
    variable = free_cm3_Phlogopite
  []
  [cm3_Tridymite]
    type = PointValue
    variable = free_cm3_Tridymite
  []
[]

[Executioner]
  type = Transient
  dt = 0.1
  end_time = 20E-1 # measured in days
[]

[Outputs]
  csv = true
[]

(modules/porous_flow/examples/groundwater/ex02_abstraction.i)

# Abstraction groundwater model.  See groundwater_models.md for a detailed description
[Mesh]
  [from_steady_state]
    type = FileMeshGenerator
    file = gold/ex02_steady_state_ex.e
  []
[]

[GlobalParams]
  PorousFlowDictator = dictator
[]

[Variables]
  [pp]
  []
[]

[ICs]
  [pp]
    type = FunctionIC
    variable = pp
    function = steady_state_pp
  []
[]

[BCs]
  [rainfall_recharge]
    type = PorousFlowSink
    boundary = zmax
    variable = pp
    flux_function = -1E-6  # recharge of 0.1mm/day = 1E-4m3/m2/day = 0.1kg/m2/day ~ 1E-6kg/m2/s
  []
  [evapotranspiration]
    type = PorousFlowHalfCubicSink
    boundary = zmax
    variable = pp
    center = 0.0
    cutoff = -5E4 # roots of depth 5m.  5m of water = 5E4 Pa
    use_mobility = true
    fluid_phase = 0
    # Assume pan evaporation of 4mm/day = 4E-3m3/m2/day = 4kg/m2/day ~ 4E-5kg/m2/s
    # Assume that if permeability was 1E-10m^2 and water table at topography then ET acts as pan strength
    # Because use_mobility = true, then 4E-5 = maximum_flux = max * perm * density / visc = max * 1E-4, so max = 40
    max = 40
  []
[]

[DiracKernels]
  inactive = polyline_sink_borehole
  [river]
    type = PorousFlowPolyLineSink
    SumQuantityUO = baseflow
    point_file = ex02_river.bh
    # Assume a perennial river.
    # Assume the river has an incision depth of 1m and a stage height of 1.5m, and these are constant in time and uniform over the whole model.  Hence, if groundwater head is 0.5m (5000Pa) there will be no baseflow and leakage.
    p_or_t_vals = '-999995000 5000 1000005000'
    # Assume the riverbed conductance, k_zz*density*river_segment_length*river_width/riverbed_thickness/viscosity = 1E-6*river_segment_length kg/Pa/s
    fluxes = '-1E3 0 1E3'
    variable = pp
  []
  [horizontal_borehole]
    type = PorousFlowPeacemanBorehole
    SumQuantityUO = abstraction
    bottom_p_or_t = -1E5
    unit_weight = '0 0 -1E4'
    character = 1.0
    point_file = ex02.bh
    variable = pp
  []
  [polyline_sink_borehole]
    type = PorousFlowPolyLineSink
    SumQuantityUO = abstraction
    fluxes = '-0.4 0 0.4'
    p_or_t_vals = '-1E8 0 1E8'
    point_file = ex02.bh
    variable = pp
  []
[]

[Functions]
  [steady_state_pp]
    type = SolutionFunction
    from_variable = pp
    solution = steady_state_solution
  []
  [baseflow_rate]
    type = ParsedFunction
    vars = 'baseflow_kg dt'
    vals = 'baseflow_kg dt'
    value = 'baseflow_kg / dt * 24.0 * 3600.0 / 400.0'
  []
  [abstraction_rate]
    type = ParsedFunction
    vars = 'abstraction_kg dt'
    vals = 'abstraction_kg dt'
    value = 'abstraction_kg / dt * 24.0 * 3600.0'
  []
[]

[AuxVariables]
  [ini_pp]
  []
  [pp_change]
  []
[]

[AuxKernels]
  [ini_pp]
    type = FunctionAux
    variable = ini_pp
    function = steady_state_pp
    execute_on = INITIAL
  []
  [pp_change]
    type = ParsedAux
    variable = pp_change
    args = 'pp ini_pp'
    function = 'pp - ini_pp'
  []
[]

[PorousFlowUnsaturated]
  fp = simple_fluid
  porepressure = pp
[]

[Modules]
  [FluidProperties]
    [simple_fluid]
      type = SimpleFluidProperties
    []
  []
[]

[Materials]
  [porosity_everywhere]
    type = PorousFlowPorosityConst
    porosity = 0.05
  []
  [permeability_aquifers]
    type = PorousFlowPermeabilityConst
    block = 'top_aquifer bot_aquifer'
    permeability = '1E-12 0 0 0 1E-12 0 0 0 1E-13'
  []
  [permeability_aquitard]
    type = PorousFlowPermeabilityConst
    block = aquitard
    permeability = '1E-16 0 0 0 1E-16 0 0 0 1E-17'
  []
[]

[UserObjects]
  [steady_state_solution]
    type = SolutionUserObject
    execute_on = INITIAL
    mesh = gold/ex02_steady_state_ex.e
    timestep = LATEST
    system_variables = pp
  []
  [baseflow]
    type = PorousFlowSumQuantity
  []
  [abstraction]
    type = PorousFlowSumQuantity
  []
[]

[Postprocessors]
  [baseflow_kg]
    type = PorousFlowPlotQuantity
    uo = baseflow
    outputs = 'none'
  []
  [dt]
    type = TimestepSize
    outputs = 'none'
  []
  [baseflow_l_per_m_per_day]
    type = FunctionValuePostprocessor
    function = baseflow_rate
  []
  [abstraction_kg]
    type = PorousFlowPlotQuantity
    uo = abstraction
    outputs = 'none'
  []
  [abstraction_kg_per_day]
    type = FunctionValuePostprocessor
    function = abstraction_rate
  []
[]

[Preconditioning]
  [smp]
    type = SMP
    full = true
    # following 2 lines are not mandatory, but illustrate a popular preconditioner choice in groundwater models
    petsc_options_iname = '-pc_type -sub_pc_type  -pc_asm_overlap'
    petsc_options_value = ' asm      ilu           2              '
  []
[]

[Executioner]
  type = Transient
  solve_type = Newton
  dt = 100
  [TimeStepper]
    type = FunctionDT
    function = 'max(100, t)'
  []
  end_time = 8.64E5 # 10 days
  nl_abs_tol = 1E-11
[]

[Outputs]
  print_linear_residuals = false
  [ex]
    type = Exodus
    execute_on = final
  []
  [csv]
    type = CSV
  []
[]

(modules/phase_field/examples/interfacekernels/interface_fluxbc.i)

#
# This test demonstrates an InterfaceKernel (InterfaceDiffusionFlux) that can
# replace a pair of integrated DiffusionFluxBC boundary conditions.
#
# The AuxVariable 'diff' shows the difference between the BC and the InterfaceKernel
# approach.
#

[Mesh]
  [gen]
    type = GeneratedMeshGenerator
    dim = 2
    nx = 50
    ny = 50
  []
  [./box1]
    input = gen
    type = SubdomainBoundingBoxGenerator
    block_id = 1
    bottom_left = '0 0 0'
    top_right = '0.51 1 0'
  [../]
  [./box2]
    input = box1
    type = SubdomainBoundingBoxGenerator
    block_id = 2
    bottom_left = '0.49 0 0'
    top_right = '1 1 0'
  [../]
  [./iface_u]
    type = SideSetsBetweenSubdomainsGenerator
    primary_block = 1
    paired_block = 2
    new_boundary = 10
    input = box2
  [../]
  [./iface_v]
    type = SideSetsBetweenSubdomainsGenerator
    primary_block = 2
    paired_block = 1
    new_boundary = 11
    input = iface_u
  [../]
[]

[Variables]
  [./u1]
    block = 1
    [./InitialCondition]
      type = FunctionIC
      function = 'r:=sqrt((x-0.4)^2+(y-0.5)^2);if(r<0.05,5,1)'
    [../]
  [../]
  [./v1]
    block = 2
    [./InitialCondition]
      type = FunctionIC
      function = 'r:=sqrt((x-0.7)^2+(y-0.5)^2);if(r<0.05,5,1)'
    [../]
  [../]
  [./u2]
    block = 1
    [./InitialCondition]
      type = FunctionIC
      function = 'r:=sqrt((x-0.4)^2+(y-0.5)^2);if(r<0.05,5,1)'
    [../]
  [../]
  [./v2]
    block = 2
    [./InitialCondition]
      type = FunctionIC
      function = 'r:=sqrt((x-0.7)^2+(y-0.5)^2);if(r<0.05,5,1)'
    [../]
  [../]
[]

[Kernels]
  [./u1_diff]
    type = Diffusion
    variable = u1
    block = 1
  [../]
  [./u1_dt]
    type = TimeDerivative
    variable = u1
    block = 1
  [../]
  [./v1_diff]
    type = Diffusion
    variable = v1
    block = 2
  [../]
  [./v1_dt]
    type = TimeDerivative
    variable = v1
    block = 2
  [../]

  [./u2_diff]
    type = Diffusion
    variable = u2
    block = 1
  [../]
  [./u2_dt]
    type = TimeDerivative
    variable = u2
    block = 1
  [../]
  [./v2_diff]
    type = Diffusion
    variable = v2
    block = 2
  [../]
  [./v2_dt]
    type = TimeDerivative
    variable = v2
    block = 2
  [../]
[]

[AuxVariables]
  [./diff]
  [../]
[]

[AuxKernels]
  [./u_side]
    type = ParsedAux
    variable = diff
    block = 1
    args = 'u1 u2'
    function = 'u1 - u2'
  [../]
  [./v_side]
    type = ParsedAux
    variable = diff
    block = 2
    args = 'v1 v2'
    function = 'v1 - v2'
  [../]
[]

[InterfaceKernels]
  [./iface]
    type = InterfaceDiffusionBoundaryTerm
    boundary = 10
    variable = u2
    neighbor_var = v2
  [../]
[]

[BCs]
  [./u_boundary_term]
    type = DiffusionFluxBC
    variable = u1
    boundary = 10
  [../]
  [./v_boundary_term]
    type = DiffusionFluxBC
    variable = v1
    boundary = 11
  [../]
[]

[Executioner]
  type = Transient
  dt = 0.001
  num_steps = 20
[]

[Outputs]
  exodus = true
  print_linear_residuals = false
[]

(test/tests/functions/piecewise_multilinear/twoD_const.i)

# PiecewiseMultilinear function tests in 2D
# See [Functions] block for a description of the tests
# The functions are compared with ParsedFunctions using postprocessors

[Mesh]
  type = GeneratedMesh
  dim = 2
  xmin = 0
  xmax = 2
  nx = 4
  ymin = -1
  ymax =  1
  ny = 4
[]

[Variables]
  [./dummy]
  [../]
[]

[Kernels]
  [./dummy_u]
    type = TimeDerivative
    variable = dummy
  [../]
[]


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

  [./constant_ref]
    family = MONOMIAL
    order = CONSTANT
  [../]

  [./diff]
    family = MONOMIAL
    order = CONSTANT
  [../]
[]

[AuxKernels]
  [./const_AuxK]
    type = FunctionAux
    variable = constant
    function = const_fcn
  [../]

  [./const_ref_AuxK]
    type = FunctionAux
    variable = constant_ref
    function = const_ref
  [../]

  [./diff]
    type = ParsedAux
    variable = diff
    function = 'constant - constant_ref'
    args = 'constant constant_ref'
  [../]
[]


[Functions]
  [./const_fcn]
    type = PiecewiseMulticonstant
    direction = 'left right'
    data_file = twoD_const.txt
  [../]

  [./const_ref]
    type = ParsedFunction
    value = '
            ix := if(x < 0.5, 0, if(x < 1, 1, 2));
            iy := if(y > 0, 2, if(y > -0.5, 1, 0));
            iy * 3 + ix
            '
  [../]
[]


[Postprocessors]
  [./diff_pp]
    type = ElementIntegralVariablePostprocessor
    variable = diff
  [../]
[]

[Executioner]
  type = Transient
  dt = 1
  end_time = 1
[]

[Outputs]
  execute_on = 'timestep_end'
  file_base = twoD_const
  hide = dummy
  exodus = true
[]

(modules/combined/examples/geochem-porous_flow/geotes_2D/aquifer_geochemistry.i)

# Simulates geochemistry in the aquifer.  This input file may be run in standalone fashion but it does not do anything of interest.  To simulate something interesting, run the porous_flow.i simulation which couples to this input file using MultiApps.
# This file receives pf_rate_H2O, pf_rate_Na, pf_rate_Cl, pf_rate_SiO2 and temperature as AuxVariables from porous_flow.i.
# The pf_rate quantities are kg/s changes of fluid-component mass at each node, but the geochemistry module expects rates-of-changes of moles at every node.  Secondly, since this input file considers just 1 litre of aqueous solution at every node, the nodal_void_volume is used to convert pf_rate_* into rate_*_per_1l, which is measured in mol/s/1_litre_of_aqueous_solution.
# This file sends massfrac_Na, massfrac_Cl and massfrac_SiO2 to porous_flow.i.  These are computed from the corresponding transported_* quantities.
[Mesh]
  [gen]
    type = GeneratedMeshGenerator
    dim = 2
    nx = 14 # for better resolution, use 56 or 112
    ny = 8  # for better resolution, use 32 or 64
    xmin = -70
    xmax = 70
    ymin = -40
    ymax = 40
  []
[]

[GlobalParams]
  point = '0 0 0'
  reactor = reactor
[]

[SpatialReactionSolver]
  model_definition = definition
  geochemistry_reactor_name = reactor
  charge_balance_species = "Cl-"
  constraint_species = "H2O              Na+              Cl-              SiO2(aq)"
# ASSUME that 1 litre of solution contains:
  constraint_value = "  1.0              0.1              0.1              0.000555052386"
  constraint_meaning = "kg_solvent_water bulk_composition bulk_composition free_concentration"
  constraint_unit = "   kg               moles            moles            molal"
  initial_temperature = 50.0
  kinetic_species_name = QuartzLike
# Per 1 litre (1000cm^3) of aqueous solution (1kg of solvent water), there is 9000cm^3 of QuartzLike, which means the initial porosity is 0.1.
  kinetic_species_initial_value = 9000
  kinetic_species_unit = cm3
  temperature = temperature
  source_species_names = 'H2O    Na+   Cl-   SiO2(aq)'
  source_species_rates = 'rate_H2O_per_1l rate_Na_per_1l rate_Cl_per_1l rate_SiO2_per_1l'
  ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
  add_aux_pH = false # there is no H+ in this system
  evaluate_kinetic_rates_always = true # implicit time-marching used for stability
  execute_console_output_on = ''
[]

[UserObjects]
  [rate_quartz]
    type = GeochemistryKineticRate
    kinetic_species_name = QuartzLike
    intrinsic_rate_constant = 1.0E-2
    multiply_by_mass = true
    area_quantity = 1
    activation_energy = 72800.0
  []
  [definition]
    type = GeochemicalModelDefinition
    database_file = "small_database.json"
    basis_species = "H2O SiO2(aq) Na+ Cl-"
    kinetic_minerals = "QuartzLike"
    kinetic_rate_descriptions = "rate_quartz"
  []
  [nodal_void_volume_uo]
    type = NodalVoidVolume
    porosity = porosity
    execute_on = 'initial timestep_end' # "initial" means this is evaluated properly for the first timestep
  []
[]


[Executioner]
  type = Transient
  dt = 1E5
  end_time = 7.76E6 # 90 days
[]

[AuxVariables]
  [temperature]
    initial_condition = 50.0
  []
  [porosity]
    initial_condition = 0.1
  []
  [nodal_void_volume]
  []
  [pf_rate_H2O] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Na] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Cl] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_SiO2] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
  []
  [rate_H2O_per_1l] # rate per 1 litre of aqueous solution that we consider at each node
  []
  [rate_Na_per_1l]
  []
  [rate_Cl_per_1l]
  []
  [rate_SiO2_per_1l]
  []
  [transported_H2O]
  []
  [transported_Na]
  []
  [transported_Cl]
  []
  [transported_SiO2]
  []
  [transported_mass]
  []
  [massfrac_Na]
  []
  [massfrac_Cl]
  []
  [massfrac_SiO2]
  []
  [massfrac_H2O]
  []
[]
[AuxKernels]
  [porosity]
    type = ParsedAux
    args = free_cm3_QuartzLike
    function = '1000.0 / (1000.0 + free_cm3_QuartzLike)'
    variable = porosity
    execute_on = 'timestep_end'
  []
  [nodal_void_volume_auxk]
    type = NodalVoidVolumeAux
    variable = nodal_void_volume
    nodal_void_volume_uo = nodal_void_volume_uo
    execute_on = 'initial timestep_end' # "initial" to ensure it is properly evaluated for the first timestep
  []
  [rate_H2O_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_H2O nodal_void_volume'
    variable = rate_H2O_per_1l
# pf_rate = change in kg at every node
# pf_rate * 1000 / molar_mass_in_g_per_mole = change in moles at every node
# pf_rate * 1000 / molar_mass / (nodal_void_volume_in_m^3 * 1000) = change in moles per litre of aqueous solution
    function = 'pf_rate_H2O / 18.0152 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_Na_per_1l]
    type = ParsedAux
    args = 'pf_rate_Na nodal_void_volume'
    variable = rate_Na_per_1l
    function = 'pf_rate_Na / 22.9898 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_Cl_per_1l]
    type = ParsedAux
    args = 'pf_rate_Cl nodal_void_volume'
    variable = rate_Cl_per_1l
    function = 'pf_rate_Cl / 35.453 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_SiO2_per_1l]
    type = ParsedAux
    args = 'pf_rate_SiO2 nodal_void_volume'
    variable = rate_SiO2_per_1l
    function = 'pf_rate_SiO2 / 60.0843 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [transported_H2O_auxk]
    type = GeochemistryQuantityAux
    variable = transported_H2O
    species = H2O
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_Na]
    type = GeochemistryQuantityAux
    variable = transported_Na
    species = Na+
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_Cl]
    type = GeochemistryQuantityAux
    variable = transported_Cl
    species = Cl-
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_SiO2]
    type = GeochemistryQuantityAux
    variable = transported_SiO2
    species = 'SiO2(aq)'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_mass_auxk]
    type = ParsedAux
    args = 'transported_H2O transported_Na transported_Cl transported_SiO2'
    variable = transported_mass
    function = 'transported_H2O * 18.0152 + transported_Na * 22.9898 + transported_Cl * 35.453 + transported_SiO2 * 60.0843'
    execute_on = 'timestep_end'
  []
  [massfrac_H2O]
    type = ParsedAux
    args = 'transported_H2O transported_mass'
    variable = massfrac_H2O
    function = 'transported_H2O * 18.0152 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Na]
    type = ParsedAux
    args = 'transported_Na transported_mass'
    variable = massfrac_Na
    function = 'transported_Na * 22.9898 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Cl]
    type = ParsedAux
    args = 'transported_Cl transported_mass'
    variable = massfrac_Cl
    function = 'transported_Cl * 35.453 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_SiO2]
    type = ParsedAux
    args = 'transported_SiO2 transported_mass'
    variable = massfrac_SiO2
    function = 'transported_SiO2 * 60.0843 / transported_mass'
    execute_on = 'timestep_end'
  []
[]
[Postprocessors]
  [cm3_quartz]
    type = PointValue
    variable = free_cm3_QuartzLike
  []
  [porosity]
    type = PointValue
    variable = porosity
  []
  [solution_temperature]
    type = PointValue
    variable = solution_temperature
  []
  [massfrac_H2O]
    type = PointValue
    variable = massfrac_H2O
  []
  [massfrac_Na]
    type = PointValue
    variable = massfrac_Na
  []
  [massfrac_Cl]
    type = PointValue
    variable = massfrac_Cl
  []
  [massfrac_SiO2]
    type = PointValue
    variable = massfrac_SiO2
  []
[]

[Outputs]
  exodus = true
  csv = true
[]

(test/tests/auxkernels/parsed_aux/parsed_aux_test.i)

[Mesh]
  type = GeneratedMesh

  dim = 2

  xmin = 0
  xmax = 1

  ymin = 0
  ymax = 1

  nx = 10
  ny = 10
[]

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

  [v]
    order = FIRST
    family = LAGRANGE
  []
[]

[AuxVariables]
  [parsed]
    order = FIRST
    family = LAGRANGE
  []
[]

[Kernels]
  [diff_u]
    type = Diffusion
    variable = u
  []

  [diff_v]
    type = Diffusion
    variable = v
  []
[]

[BCs]
  [left_u]
    type = DirichletBC
    variable = u
    boundary = 2
    value = 0
  []

  [right_u]
    type = DirichletBC
    variable = u
    boundary = 0
    value = 1
  []

  [left_v]
    type = DirichletBC
    variable = v
    boundary = 3
    value = 0
  []

  [right_v]
    type = DirichletBC
    variable = v
    boundary = 1
    value = 1
  []
[]

[Bounds]
  [u_bounds]
    type = ParsedAux
    variable = parsed
    args = 'u v'
    function = '(u-0.5)^3*v'
  []
[]

[Executioner]
  type = Steady

  solve_type = 'PJFNK'
[]

[Outputs]
  file_base = out
  exodus = true
[]

(modules/functional_expansion_tools/examples/3D_volumetric_cylindrical_subapp_mesh_refine/sub.i)

# Derived from the example '3D_volumetric_cylindrical' with the following differences:
#
#   1) The model mesh is refined in the MasterApp by 1
#   2) Mesh adaptivity is enabled for the SubApp
#   3) Output from the SubApp is enabled so that the mesh changes can be visualized
[Mesh]
  type = FileMesh
  file = cyl-tet.e
[]

[Adaptivity]
  marker = errorfrac
  steps = 2
  [./Indicators]
    [./error]
      type = GradientJumpIndicator
      variable = s
      outputs = none
    [../]
  [../]
  [./Markers]
    [./errorfrac]
      type = ErrorFractionMarker
      refine = 0.4
      coarsen = 0.1
      indicator = error
      outputs = none
    [../]
  [../]
[]

# Non-copy transfers only work with AuxVariable, but nothing will be solved without a variable
# defined. The solution is to define an empty variable tha does nothing, but causes MOOSE to solve
# the AuxKernels that we need.
[Variables]
  [./empty]
  [../]
[]

[AuxVariables]
  [./s]
    order = FIRST
    family = LAGRANGE
  [../]
  [./m_in]
    order = FIRST
    family = LAGRANGE
  [../]
[]

# We must have a kernel for every variable, hence this null kernel to match the variable 'empty'
[Kernels]
  [./null_kernel]
    type = NullKernel
    variable = empty
  [../]
[]

[AuxKernels]
  [./reconstruct_m_in]
    type = FunctionSeriesToAux
    function = FX_Basis_Value_Sub
    variable = m_in
  [../]
  [./calculate_s] # Something to make 's' change each time, but allow a converging solution
    type = ParsedAux
    variable = s
    args = m_in
    function = '2*exp(-m_in/0.8)'
  [../]
[]

[Functions]
  [./FX_Basis_Value_Sub]
    type = FunctionSeries
    series_type = CylindricalDuo
    orders = '5   3' # Axial first, then (r, t) FX
    physical_bounds = '-2.5 2.5   0 0 1' # z_min z_max   x_center y_center radius
    z = Legendre # Axial in z
    disc = Zernike # (r, t) default to unit disc in x-y plane
  [../]
[]

[UserObjects]
  [./FX_Value_UserObject_Sub]
    type = FXVolumeUserObject
    function = FX_Basis_Value_Sub
    variable = s
  [../]
[]

[Executioner]
  type = Transient
  num_steps = 10
  dt = 0.5
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

[Outputs]
  exodus = true
  file_base = sub
[]

(modules/geochemistry/test/tests/kinetics/kinetic_albite.i)

# Example of kinetically-controlled dissolution of albite into an acidic solution
[TimeDependentReactionSolver]
  model_definition = definition
  geochemistry_reactor_name = reactor
  charge_balance_species = "Cl-"
  constraint_species = "H2O              H+            Cl-              Na+              SiO2(aq)           Al+++"
  constraint_value = "  1.0              -1.5          0.1              0.1              1E-6               1E-6"
  constraint_meaning = "kg_solvent_water log10activity bulk_composition bulk_composition free_concentration free_concentration"
  constraint_unit = "   kg               dimensionless moles            moles            molal              molal"
  initial_temperature = 70.0
  temperature = 70.0
  kinetic_species_name = Albite
  kinetic_species_initial_value = 250
  kinetic_species_unit = g
  evaluate_kinetic_rates_always = true # implicit time-marching used for stability
  ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
  stoichiometric_ionic_str_using_Cl_only = true # for comparison with GWB
  execute_console_output_on = '' # only CSV output for this example
[]

[UserObjects]
  [rate_albite]
    type = GeochemistryKineticRate
    kinetic_species_name = Albite
    intrinsic_rate_constant = 5.4432E-8 # 6.3E-13mol/s/cm^2 = 5.4432E-8mol/day/cm^2
    multiply_by_mass = true
    area_quantity = 1000
    promoting_species_names = "H+"
    promoting_species_indices = "1.0"
  []
  [definition]
    type = GeochemicalModelDefinition
    database_file = "../../../database/moose_geochemdb.json"
    basis_species = "H2O H+ Cl- Na+ SiO2(aq) Al+++"
    kinetic_minerals = "Albite"
    kinetic_rate_descriptions = "rate_albite"
  []
[]

[Executioner]
  type = Transient
  dt = 5
  end_time = 30 # measured in days
[]

[AuxVariables]
  [mole_change_albite]
  []
[]
[AuxKernels]
  [mole_change_albite]
    type = ParsedAux
    args = moles_Albite
    function = 'moles_Albite - 0.953387'
    variable = mole_change_albite
  []
[]
[Postprocessors]
  [mole_change_Albite]
    type = PointValue
    point = '0 0 0'
    variable = "mole_change_albite"
  []
[]
[Outputs]
  csv = true
[]

(modules/functional_expansion_tools/test/tests/errors/multiapp_sub.i)

[Mesh]
  type = GeneratedMesh
  dim = 1

  xmin = 0.0
  xmax = 10.0
  nx = 15
[]

[Variables]
  [./empty]
  [../]
[]

[AuxVariables]
  [./s]
    order = FIRST
    family = LAGRANGE
  [../]
  [./m_in]
    order = FIRST
    family = LAGRANGE
  [../]
[]

[Kernels]
  [./null_kernel]
    type = NullKernel
    variable = empty
  [../]
[]

[AuxKernels]
  [./reconstruct_m_in]
    type = FunctionSeriesToAux
    function = FX_Basis_Value_Sub
    variable = m_in
  [../]
  [./calculate_s]
    type = ParsedAux
    variable = s
    args = m_in
    function = '2*exp(-m_in/0.8)'
  [../]
[]

[Functions]
  [./FX_Basis_Value_Sub]
    type = FunctionSeries
    series_type = Cartesian
    orders = '3'
    physical_bounds = '0.0  10.0'
    x = Legendre
  [../]
[]

[UserObjects]
  [./FX_Value_UserObject_Sub]
    type = FXVolumeUserObject
    function = FX_Basis_Value_Sub
    variable = s
  [../]
[]

[Executioner]
  type = Transient
  num_steps = 10
  dt = 0.5
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

(modules/functional_expansion_tools/examples/1D_volumetric_Cartesian/sub.i)

# Basic example coupling a master and sub app in a 1D Cartesian volume.
#
# The master app provides field values to the sub app via Functional Expansions, which then performs
# its calculations. The sub app's solution field values are then transferred back to the master app
# and coupled into the solution of the master app solution.
#
# This example couples Functional Expansions via AuxVariable.
[Mesh]
  type = GeneratedMesh
  dim = 1

  xmin = 0.0
  xmax = 10.0
  nx = 15
[]

# Non-copy transfers only work with AuxVariable, but nothing will be solved without a variable
# defined. The solution is to define an empty variable tha does nothing, but causes MOOSE to solve
# the AuxKernels that we need.
[Variables]
  [./empty]
  [../]
[]

[AuxVariables]
  [./s]
    order = FIRST
    family = LAGRANGE
  [../]
  [./m_in]
    order = FIRST
    family = LAGRANGE
  [../]
[]

# We must have a kernel for every variable, hence this null kernel to match the variable 'empty'
[Kernels]
  [./null_kernel]
    type = NullKernel
    variable = empty
  [../]
[]

[AuxKernels]
  [./reconstruct_m_in]
    type = FunctionSeriesToAux
    function = FX_Basis_Value_Sub
    variable = m_in
  [../]
  [./calculate_s] # Something to make 's' change each time, but allow a converging solution
    type = ParsedAux
    variable = s
    args = m_in
    function = '2*exp(-m_in/0.8)'
  [../]
[]

[Functions]
  [./FX_Basis_Value_Sub]
    type = FunctionSeries
    series_type = Cartesian
    orders = '3'
    physical_bounds = '0.0  10.0'
    x = Legendre
  [../]
[]

[UserObjects]
  [./FX_Value_UserObject_Sub]
    type = FXVolumeUserObject
    function = FX_Basis_Value_Sub
    variable = s
  [../]
[]

[Executioner]
  type = Transient
  num_steps = 10
  dt = 0.5
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

(test/tests/kernels/hfem/robin_displaced.i)

[Mesh]
  [square]
    type = CartesianMeshGenerator
    dx = '0.3125 0.3125 0.3125'
    dy = '0.3333333333333 0.3333333333333 0.3333333333333'
    dim = 2
  []
  displacements = 'x_disp y_disp'
  build_all_side_lowerd_mesh = true
[]

[Variables]
  [u]
    order = THIRD
    family = MONOMIAL
    block = 0
    components = 2
  []
  [lambda]
    order = CONSTANT
    family = MONOMIAL
    block = INTERNAL_SIDE_LOWERD_SUBDOMAIN
    components = 2
  []
[]

[AuxVariables]
  [v]
    order = CONSTANT
    family = MONOMIAL
    block = 0
    initial_condition = '1'
  []
  [x_disp]
    block = 0
  []
  [y_disp]
    block = 0
    initial_condition = 0
  []
[]

[AuxKernels]
  [x_disp]
    type = ParsedAux
    variable = x_disp
    use_xyzt = true
    function = 'x/15'
  []
[]

[Kernels]
  [diff]
    type = ArrayDiffusion
    variable = u
    block = 0
    diffusion_coefficient = dc
    use_displaced_mesh = true
  []
  [source]
    type = ArrayCoupledForce
    variable = u
    v = v
    coef = '1 2'
    block = 0
    use_displaced_mesh = true
  []
[]

[DGKernels]
  [surface]
    type = ArrayHFEMDiffusion
    variable = u
    lowerd_variable = lambda
    use_displaced_mesh = true
  []
[]

[BCs]
  [all]
    type = ArrayVacuumBC
    boundary = 'left right top bottom'
    variable = u
    use_displaced_mesh = true
  []
[]

[Materials]
  [dc]
    type = GenericConstantArray
    prop_name = dc
    prop_value = '1 1'
  []
[]

[Postprocessors]
  [intu]
    type = ElementIntegralArrayVariablePostprocessor
    variable = u
    block = 0
    use_displaced_mesh = true
  []
  [lambdanorm]
    type = ElementArrayL2Norm
    variable = lambda
    block = INTERNAL_SIDE_LOWERD_SUBDOMAIN
    use_displaced_mesh = true
  []
[]

[Executioner]
  type = Steady
  solve_type = 'NEWTON'
  petsc_options_iname = '-pc_type -snes_linesearch_type -pc_factor_mat_solver_type'
  petsc_options_value = 'lu       basic                 mumps'
[]

[Outputs]
  [out]
    # we hide lambda because it may flip sign due to element
    # renumbering with distributed mesh
    type = Exodus
    hide = lambda
  []
  csv = true
[]

(modules/functional_expansion_tools/test/tests/standard_use/volume_sub.i)

[Mesh]
  type = GeneratedMesh
  dim = 1

  xmin = 0.0
  xmax = 10.0
  nx = 15
[]

[Variables]
  [./empty]
  [../]
[]

[AuxVariables]
  [./s]
    order = FIRST
    family = LAGRANGE
  [../]
  [./m_in]
    order = FIRST
    family = LAGRANGE
  [../]
[]

[Kernels]
  [./null_kernel]
    type = NullKernel
    variable = empty
  [../]
[]

[AuxKernels]
  [./reconstruct_m_in]
    type = FunctionSeriesToAux
    function = FX_Basis_Value_Sub
    variable = m_in
  [../]
  [./calculate_s]
    type = ParsedAux
    variable = s
    args = m_in
    function = '2*exp(-m_in/0.8)'
  [../]
[]

[Functions]
  [./FX_Basis_Value_Sub]
    type = FunctionSeries
    series_type = Cartesian
    orders = '3'
    physical_bounds = '0.0  10.0'
    x = Legendre
  [../]
[]

[UserObjects]
  [./FX_Value_UserObject_Sub]
    type = FXVolumeUserObject
    function = FX_Basis_Value_Sub
    variable = s
  [../]
[]

[Executioner]
  type = Transient
  num_steps = 10
  dt = 0.5
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

(test/tests/transfers/multiapp_userobject_transfer/restricted_elem_master.i)

num_layers = 2

[Mesh]
  [box]
    type = GeneratedMeshGenerator
    dim = 3
    nx = ${num_layers}
    ny = 3
    nz = 3
  []
  # The MultiAppUserObjectTransfer object only works with ReplicatedMesh
  parallel_type = replicated
[]

[Variables]
  [u]
  []
[]

[Kernels]
  [td]
    type = TimeDerivative
    variable = u
  []

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

[AuxVariables]
  [a]
    family = MONOMIAL
    order = CONSTANT
  []

  [s]
  []
[]

[AuxKernels]
  [s_ak]
    type = ParsedAux
    variable = s
    use_xyzt = true
    function = 'x+(z*z)'
  []
[]

[Functions]
[]

[Postprocessors]
  [a_avg]
    type = ElementAverageValue
    variable = a
  []
[]

[UserObjects]
  [S_avg_front]
    type = LayeredSideAverage
    boundary = front
    variable = s
    num_layers = ${num_layers}
    direction = x
  []

  [S_avg_back]
    type = LayeredSideAverage
    boundary = back
    variable = s
    num_layers = ${num_layers}
    direction = x
  []
[]

[MultiApps]
  [ch0]
    type = TransientMultiApp
    input_files = 'restricted_elem_sub.i'
    bounding_box_padding = '0 0.5 1'
    positions = '0 0.5 -0.1'
    output_in_position = true
    cli_args = 'yy=0'
  []
  [ch1]
    type = TransientMultiApp
    input_files = 'restricted_elem_sub.i'
    bounding_box_padding = '0 0.5 1'
    positions = '0 0.5  1.1'
    output_in_position = true
    cli_args = 'yy=1'
  []
[]

[Transfers]
  [from_ch0]
    type = MultiAppUserObjectTransfer
    boundary = back
    direction = from_multiapp
    multi_app = ch0
    variable = a
    user_object = A_avg
  []

  [from_ch1]
    type = MultiAppUserObjectTransfer
    boundary = front
    direction = from_multiapp
    multi_app = ch1
    variable = a
    user_object = A_avg
  []

  [to_ch0]
    type = MultiAppUserObjectTransfer
    block = 20
    direction = to_multiapp
    multi_app = ch0
    variable = S
    user_object = S_avg_back
  []

  [to_ch1]
    type = MultiAppUserObjectTransfer
    block = 20
    direction = to_multiapp
    multi_app = ch1
    variable = S
    user_object = S_avg_front
  []
[]

[Executioner]
  type = Transient
  num_steps = 2

  dt = 1
  nl_abs_tol = 1e-7
[]

[Outputs]
  exodus = true
[]

(modules/combined/examples/geochem-porous_flow/forge/aquifer_geochemistry.i)

# Simulates geochemistry in the aquifer.  This input file may be run in standalone fashion, which will study the natural kinetically-controlled mineral changes in the same way as natural_reservoir.i.  To simulate the FORGE injection scenario, run the porous_flow.i simulation which couples to this input file using MultiApps.
# This file receives pf_rate_H pf_rate_Na pf_rate_K pf_rate_Ca pf_rate_Mg pf_rate_SiO2 pf_rate_Al pf_rate_Cl pf_rate_SO4 pf_rate_HCO3 pf_rate_H2O and temperature as AuxVariables from porous_flow.i
# The pf_rate quantities are kg/s changes of fluid-component mass at each node, but the geochemistry module expects rates-of-changes of moles at every node.  Secondly, since this input file considers just 1 litre of aqueous solution at every node, the nodal_void_volume is used to convert pf_rate_* into rate_*_per_1l, which is measured in mol/s/1_litre_of_aqueous_solution.
# This file sends massfrac_H massfrac_Na massfrac_K massfrac_Ca massfrac_Mg massfrac_SiO2 massfrac_Al massfrac_Cl massfrac_SO4 massfrac_HCO3 to porous_flow.i.  These are computed from the corresponding transported_* quantities.
# The results depend on the kinetic rates used and these are recognised to be poorly constrained by experiment
[UserObjects]
  [rate_Albite]
    type = GeochemistryKineticRate
    kinetic_species_name = Albite
    intrinsic_rate_constant = 1E-17
    multiply_by_mass = true
    area_quantity = 10
    activation_energy = 69.8E3
    one_over_T0 = 0.003354
  []
  [rate_Anhydrite]
    type = GeochemistryKineticRate
    kinetic_species_name = Anhydrite
    intrinsic_rate_constant = 1.0E-7
    multiply_by_mass = true
    area_quantity = 10
    activation_energy = 14.3E3
    one_over_T0 = 0.003354
  []
  [rate_Anorthite]
    type = GeochemistryKineticRate
    kinetic_species_name = Anorthite
    intrinsic_rate_constant = 1.0E-13
    multiply_by_mass = true
    area_quantity = 10
    activation_energy = 17.8E3
    one_over_T0 = 0.003354
  []
  [rate_Calcite]
    type = GeochemistryKineticRate
    kinetic_species_name = Calcite
    intrinsic_rate_constant = 1.0E-10
    multiply_by_mass = true
    area_quantity = 10
    activation_energy = 23.5E3
    one_over_T0 = 0.003354
  []
  [rate_Chalcedony]
    type = GeochemistryKineticRate
    kinetic_species_name = Chalcedony
    intrinsic_rate_constant = 1.0E-18
    multiply_by_mass = true
    area_quantity = 10
    activation_energy = 90.1E3
    one_over_T0 = 0.003354
  []
  [rate_Clinochl-7A]
    type = GeochemistryKineticRate
    kinetic_species_name = Clinochl-7A
    intrinsic_rate_constant = 1.0E-17
    multiply_by_mass = true
    area_quantity = 10
    activation_energy = 88.0E3
    one_over_T0 = 0.003354
  []
  [rate_Illite]
    type = GeochemistryKineticRate
    kinetic_species_name = Illite
    intrinsic_rate_constant = 1E-17
    multiply_by_mass = true
    area_quantity = 10
    activation_energy = 29E3
    one_over_T0 = 0.003354
  []
  [rate_K-feldspar]
    type = GeochemistryKineticRate
    kinetic_species_name = K-feldspar
    intrinsic_rate_constant = 1E-17
    multiply_by_mass = true
    area_quantity = 10
    activation_energy = 38E3
    one_over_T0 = 0.003354
  []
  [rate_Kaolinite]
    type = GeochemistryKineticRate
    kinetic_species_name = Kaolinite
    intrinsic_rate_constant = 1E-18
    multiply_by_mass = true
    area_quantity = 10
    activation_energy = 22.2E3
    one_over_T0 = 0.003354
  []
  [rate_Quartz]
    type = GeochemistryKineticRate
    kinetic_species_name = Quartz
    intrinsic_rate_constant = 1E-18
    multiply_by_mass = true
    area_quantity = 10
    activation_energy = 90.1E3
    one_over_T0 = 0.003354
  []
  [rate_Paragonite]
    type = GeochemistryKineticRate
    kinetic_species_name = Paragonite
    intrinsic_rate_constant = 1E-17
    multiply_by_mass = true
    area_quantity = 10
    activation_energy = 22E3
    one_over_T0 = 0.003354
  []
  [rate_Phlogopite]
    type = GeochemistryKineticRate
    kinetic_species_name = Phlogopite
    intrinsic_rate_constant = 1E-17
    multiply_by_mass = true
    area_quantity = 10
    activation_energy = 22E3
    one_over_T0 = 0.003354
  []
  [rate_Laumontite]
    type = GeochemistryKineticRate
    kinetic_species_name = Laumontite
    intrinsic_rate_constant = 1.0E-15
    multiply_by_mass = true
    area_quantity = 10
    activation_energy = 17.8E3
    one_over_T0 = 0.003354
  []
  [rate_Zoisite]
    type = GeochemistryKineticRate
    kinetic_species_name = Zoisite
    intrinsic_rate_constant = 1E-16
    multiply_by_mass = true
    area_quantity = 10
    activation_energy = 66.1E3
    one_over_T0 = 0.003354
  []
  [definition]
    type = GeochemicalModelDefinition
    database_file = '../../../../geochemistry/database/moose_geochemdb.json'
    basis_species = 'H2O H+ Na+ K+ Ca++ Mg++ SiO2(aq) Al+++ Cl- SO4-- HCO3-'
    remove_all_extrapolated_secondary_species = true
    kinetic_minerals = 'Albite Anhydrite Anorthite Calcite Chalcedony Clinochl-7A Illite K-feldspar Kaolinite Quartz Paragonite Phlogopite Zoisite Laumontite'
    kinetic_rate_descriptions = 'rate_Albite rate_Anhydrite rate_Anorthite rate_Calcite rate_Chalcedony rate_Clinochl-7A rate_Illite rate_K-feldspar rate_Kaolinite rate_Quartz rate_Paragonite rate_Phlogopite rate_Zoisite rate_Laumontite'
  []
  [nodal_void_volume_uo]
    type = NodalVoidVolume
    porosity = porosity
    execute_on = 'initial timestep_end' # "initial" means this is evaluated properly for the first timestep
  []
[]

[SpatialReactionSolver]
  model_definition = definition
  geochemistry_reactor_name = reactor
  charge_balance_species = 'Cl-'
  constraint_species = 'H2O              H+                  Na+              K+                 Ca++              Mg++                SiO2(aq)           Al+++               Cl-                SO4--               HCO3-'
# Following numbers are from water_60_to_220degC_out.csv
  constraint_value = '  1.0006383866109  9.5165072498215e-07 0.100020379171   0.0059389061065    0.011570884507621 4.6626763057447e-06 0.0045110404925255 5.8096968688789e-17 0.13500708594394   6.6523540147676e-05 7.7361407898089e-05'
  constraint_meaning = 'kg_solvent_water free_concentration       free_concentration    free_concentration      free_concentration     free_concentration       free_concentration      free_concentration       bulk_composition free_concentration       free_concentration'
  constraint_unit = '   kg               molal               molal            molal              molal             molal               molal              molal               moles              molal               molal'
  initial_temperature = 220
  temperature = temperature
  kinetic_species_name = '         Albite             Anorthite          K-feldspar         Quartz             Phlogopite         Paragonite         Calcite            Anhydrite          Chalcedony         Illite             Kaolinite          Clinochl-7A        Zoisite            Laumontite'
  kinetic_species_initial_value = '4.324073236492E+02 4.631370307325E+01 2.685015418378E+02 7.720095013956E+02 1.235192062541E+01 7.545461404965E-01 4.234651808835E-04 4.000485907930E-04 4.407616361072E+00 1.342524904876E+01 1.004823151125E+00 4.728132387707E-01 7.326007326007E-01 4.818116116598E-01'
  kinetic_species_unit = '         moles              moles              moles              moles              moles              moles              moles              moles              moles              moles              moles              moles              moles              moles'
  evaluate_kinetic_rates_always = true # otherwise will easily "run out" of dissolving species
  source_species_names = 'H2O H+ Na+ K+ Ca++ Mg++ SiO2(aq) Al+++ Cl- SO4-- HCO3-'
  source_species_rates = 'rate_H2O_per_1l rate_H_per_1l rate_Na_per_1l rate_K_per_1l rate_Ca_per_1l rate_Mg_per_1l rate_SiO2_per_1l rate_Al_per_1l rate_Cl_per_1l rate_SO4_per_1l rate_HCO3_per_1l'
  ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
  execute_console_output_on = ''
  add_aux_molal = false # save some memory and reduce variables in output exodus
  add_aux_mg_per_kg = false # save some memory and reduce variables in output exodus
  add_aux_free_mg = false # save some memory and reduce variables in output exodus
  add_aux_activity = false # save some memory and reduce variables in output exodus
  add_aux_bulk_moles = false # save some memory and reduce variables in output exodus
  adaptive_timestepping = true
[]

[Mesh]
  [gen]
    type = GeneratedMeshGenerator
    dim = 2
    nx = 15
    ny = 10
    xmin = -100
    xmax = 200
    ymin = -100
    ymax = 100
  []
  [injection_node]
    input = gen
    type = ExtraNodesetGenerator
    new_boundary = injection_node
    coord = '0 0 0'
  []
[]

[Executioner]
  type = Transient
  [TimeStepper]
    type = FunctionDT
    function = 'max(1E6, 0.3 * t)'
  []
  end_time = 4E12
[]

[AuxVariables]
  [temperature]
    initial_condition = 220.0
  []
  [porosity]
    initial_condition = 0.01
  []
  [nodal_void_volume]
  []
  [free_cm3_Kfeldspar] # necessary because of the minus sign in K-feldspar which does not parse correctly in the porosity AuxKernel
  []
  [free_cm3_Clinochl7A] # necessary because of the minus sign in Clinochl-7A which does not parse correctly in the porosity AuxKernel
  []
  [pf_rate_H] # change in H mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Na]
  []
  [pf_rate_K]
  []
  [pf_rate_Ca]
  []
  [pf_rate_Mg]
  []
  [pf_rate_SiO2]
  []
  [pf_rate_Al]
  []
  [pf_rate_Cl]
  []
  [pf_rate_SO4]
  []
  [pf_rate_HCO3]
  []
  [pf_rate_H2O] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
  []
  [rate_H_per_1l]
  []
  [rate_Na_per_1l]
  []
  [rate_K_per_1l]
  []
  [rate_Ca_per_1l]
  []
  [rate_Mg_per_1l]
  []
  [rate_SiO2_per_1l]
  []
  [rate_Al_per_1l]
  []
  [rate_Cl_per_1l]
  []
  [rate_SO4_per_1l]
  []
  [rate_HCO3_per_1l]
  []
  [rate_H2O_per_1l]
  []
  [transported_H]
  []
  [transported_Na]
  []
  [transported_K]
  []
  [transported_Ca]
  []
  [transported_Mg]
  []
  [transported_SiO2]
  []
  [transported_Al]
  []
  [transported_Cl]
  []
  [transported_SO4]
  []
  [transported_HCO3]
  []
  [transported_H2O]
  []
  [transported_mass]
  []
  [massfrac_H]
  []
  [massfrac_Na]
  []
  [massfrac_K]
  []
  [massfrac_Ca]
  []
  [massfrac_Mg]
  []
  [massfrac_SiO2]
  []
  [massfrac_Al]
  []
  [massfrac_Cl]
  []
  [massfrac_SO4]
  []
  [massfrac_HCO3]
  []
  [massfrac_H2O]
  []
[]

[AuxKernels]
  [free_cm3_Kfeldspar]
    type = GeochemistryQuantityAux
    variable = free_cm3_Kfeldspar
    species = 'K-feldspar'
    quantity = free_cm3
    execute_on = 'timestep_begin timestep_end'
  []
  [free_cm3_Clinochl7A]
    type = GeochemistryQuantityAux
    variable = free_cm3_Clinochl7A
    species = 'Clinochl-7A'
    quantity = free_cm3
    execute_on = 'timestep_begin timestep_end'
  []
  [porosity_auxk]
    type = ParsedAux
    args = 'free_cm3_Albite free_cm3_Anhydrite free_cm3_Anorthite free_cm3_Calcite free_cm3_Chalcedony free_cm3_Clinochl7A free_cm3_Illite free_cm3_Kfeldspar free_cm3_Kaolinite free_cm3_Quartz free_cm3_Paragonite free_cm3_Phlogopite free_cm3_Zoisite free_cm3_Laumontite'
    function = '1000.0 / (1000.0 + free_cm3_Albite + free_cm3_Anhydrite + free_cm3_Anorthite + free_cm3_Calcite + free_cm3_Chalcedony + free_cm3_Clinochl7A + free_cm3_Illite + free_cm3_Kfeldspar + free_cm3_Kaolinite + free_cm3_Quartz + free_cm3_Paragonite + free_cm3_Phlogopite + free_cm3_Zoisite + free_cm3_Laumontite)'
    variable = porosity
    execute_on = 'timestep_end'
  []
  [nodal_void_volume_auxk]
    type = NodalVoidVolumeAux
    variable = nodal_void_volume
    nodal_void_volume_uo = nodal_void_volume_uo
    execute_on = 'initial timestep_end' # "initial" to ensure it is properly evaluated for the first timestep
  []
  [rate_H_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_H nodal_void_volume'
    variable = rate_H_per_1l
    function = 'pf_rate_H / 1.0079 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_Na_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Na nodal_void_volume'
    variable = rate_Na_per_1l
    function = 'pf_rate_Na / 22.9898 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_K_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_K nodal_void_volume'
    variable = rate_K_per_1l
    function = 'pf_rate_K / 39.0983 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_Ca_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Ca nodal_void_volume'
    variable = rate_Ca_per_1l
    function = 'pf_rate_Ca / 40.08 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_Mg_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Mg nodal_void_volume'
    variable = rate_Mg_per_1l
    function = 'pf_rate_Mg / 24.305 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_SiO2_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_SiO2 nodal_void_volume'
    variable = rate_SiO2_per_1l
    function = 'pf_rate_SiO2 / 60.0843 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_Al_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Al nodal_void_volume'
    variable = rate_Al_per_1l
    function = 'pf_rate_Al / 26.9815 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_Cl_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Cl nodal_void_volume'
    variable = rate_Cl_per_1l
    function = 'pf_rate_Cl / 35.453 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_SO4_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_SO4 nodal_void_volume'
    variable = rate_SO4_per_1l
    function = 'pf_rate_SO4 / 96.0576 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_HCO3_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_HCO3 nodal_void_volume'
    variable = rate_HCO3_per_1l
    function = 'pf_rate_HCO3 / 61.0171 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_H2O_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_H2O nodal_void_volume'
    variable = rate_H2O_per_1l
    function = 'pf_rate_H2O / 18.01801802 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [transported_H_auxk]
    type = GeochemistryQuantityAux
    variable = transported_H
    species = 'H+'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_begin'
  []
  [transported_Na_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Na
    species = 'Na+'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_begin'
  []
  [transported_K_auxk]
    type = GeochemistryQuantityAux
    variable = transported_K
    species = 'K+'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_begin'
  []
  [transported_Ca_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Ca
    species = 'Ca++'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_begin'
  []
  [transported_Mg_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Mg
    species = 'Mg++'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_begin'
  []
  [transported_SiO2_auxk]
    type = GeochemistryQuantityAux
    variable = transported_SiO2
    species = 'SiO2(aq)'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_begin'
  []
  [transported_Al_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Al
    species = 'Al+++'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_begin'
  []
  [transported_Cl_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Cl
    species = 'Cl-'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_begin'
  []
  [transported_SO4_auxk]
    type = GeochemistryQuantityAux
    variable = transported_SO4
    species = 'SO4--'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_begin'
  []
  [transported_HCO3_auxk]
    type = GeochemistryQuantityAux
    variable = transported_HCO3
    species = 'HCO3-'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_begin'
  []
  [transported_H2O_auxk]
    type = GeochemistryQuantityAux
    variable = transported_H2O
    species = 'H2O'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_begin'
  []
  [transported_mass_auxk]
    type = ParsedAux
    args = ' transported_H transported_Na transported_K transported_Ca transported_Mg transported_SiO2 transported_Al transported_Cl transported_SO4 transported_HCO3 transported_H2O'
    variable = transported_mass
    function = 'transported_H * 1.0079 + transported_Cl * 35.453 + transported_SO4 * 96.0576 + transported_HCO3 * 61.0171 + transported_SiO2 * 60.0843 + transported_Al * 26.9815 + transported_Ca * 40.08 + transported_Mg * 24.305 + transported_K * 39.0983 + transported_Na * 22.9898 + transported_H2O * 18.01801802'
    execute_on = 'timestep_end'
  []
  [massfrac_H_auxk]
    type = ParsedAux
    args = 'transported_H transported_mass'
    variable = massfrac_H
    function = 'transported_H * 1.0079 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Na_auxk]
    type = ParsedAux
    args = 'transported_Na transported_mass'
    variable = massfrac_Na
    function = 'transported_Na * 22.9898 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_K_auxk]
    type = ParsedAux
    args = 'transported_K transported_mass'
    variable = massfrac_K
    function = 'transported_K * 39.0983 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Ca_auxk]
    type = ParsedAux
    args = 'transported_Ca transported_mass'
    variable = massfrac_Ca
    function = 'transported_Ca * 40.08 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Mg_auxk]
    type = ParsedAux
    args = 'transported_Mg transported_mass'
    variable = massfrac_Mg
    function = 'transported_Mg * 24.305 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_SiO2_auxk]
    type = ParsedAux
    args = 'transported_SiO2 transported_mass'
    variable = massfrac_SiO2
    function = 'transported_SiO2 * 60.0843 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Al_auxk]
    type = ParsedAux
    args = 'transported_Al transported_mass'
    variable = massfrac_Al
    function = 'transported_Al * 26.9815 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Cl_auxk]
    type = ParsedAux
    args = 'transported_Cl transported_mass'
    variable = massfrac_Cl
    function = 'transported_Cl * 35.453 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_SO4_auxk]
    type = ParsedAux
    args = 'transported_SO4 transported_mass'
    variable = massfrac_SO4
    function = 'transported_SO4 * 96.0576 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_HCO3_auxk]
    type = ParsedAux
    args = 'transported_HCO3 transported_mass'
    variable = massfrac_HCO3
    function = 'transported_HCO3 * 61.0171 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_H2O_auxk]
    type = ParsedAux
    args = 'transported_H2O transported_mass'
    variable = massfrac_H2O
    function = 'transported_H2O * 18.01801802 / transported_mass'
    execute_on = 'timestep_end'
  []
[]

[GlobalParams]
  point = '0 0 0'
  reactor = reactor
[]

[Postprocessors]
  [temperature]
    type = PointValue
    variable = 'solution_temperature'
  []
  [porosity]
    type = PointValue
    variable = porosity
  []
  [solution_temperature]
    type = PointValue
    variable = solution_temperature
  []
  [massfrac_H]
    type = PointValue
    variable = massfrac_H
  []
  [massfrac_Na]
    type = PointValue
    variable = massfrac_Na
  []
  [massfrac_K]
    type = PointValue
    variable = massfrac_K
  []
  [massfrac_Ca]
    type = PointValue
    variable = massfrac_Ca
  []
  [massfrac_Mg]
    type = PointValue
    variable = massfrac_Mg
  []
  [massfrac_SiO2]
    type = PointValue
    variable = massfrac_SiO2
  []
  [massfrac_Al]
    type = PointValue
    variable = massfrac_Al
  []
  [massfrac_Cl]
    type = PointValue
    variable = massfrac_Cl
  []
  [massfrac_SO4]
    type = PointValue
    variable = massfrac_SO4
  []
  [massfrac_HCO3]
    type = PointValue
    variable = massfrac_HCO3
  []
  [massfrac_H2O]
    type = PointValue
    variable = massfrac_H2O
  []
  [cm3_Albite]
    type = PointValue
    variable = 'free_cm3_Albite'
  []
  [cm3_Anhydrite]
    type = PointValue
    variable = 'free_cm3_Anhydrite'
  []
  [cm3_Anorthite]
    type = PointValue
    variable = 'free_cm3_Anorthite'
  []
  [cm3_Calcite]
    type = PointValue
    variable = 'free_cm3_Calcite'
  []
  [cm3_Chalcedony]
    type = PointValue
    variable = 'free_cm3_Chalcedony'
  []
  [cm3_Clinochl-7A]
    type = PointValue
    variable = 'free_cm3_Clinochl-7A'
  []
  [cm3_Illite]
    type = PointValue
    variable = 'free_cm3_Illite'
  []
  [cm3_K-feldspar]
    type = PointValue
    variable = 'free_cm3_K-feldspar'
  []
  [cm3_Kaolinite]
    type = PointValue
    variable = 'free_cm3_Kaolinite'
  []
  [cm3_Quartz]
    type = PointValue
    variable = 'free_cm3_Quartz'
  []
  [cm3_Paragonite]
    type = PointValue
    variable = 'free_cm3_Paragonite'
  []
  [cm3_Phlogopite]
    type = PointValue
    variable = 'free_cm3_Phlogopite'
  []
  [cm3_Zoisite]
    type = PointValue
    variable = 'free_cm3_Zoisite'
  []
  [cm3_Laumontite]
    type = PointValue
    variable = 'free_cm3_Laumontite'
  []
  [cm3_mineral]
    type = LinearCombinationPostprocessor
    pp_names = 'cm3_Albite cm3_Anhydrite cm3_Anorthite cm3_Calcite cm3_Chalcedony cm3_Clinochl-7A cm3_Illite cm3_K-feldspar cm3_Kaolinite cm3_Quartz cm3_Paragonite cm3_Phlogopite cm3_Zoisite cm3_Laumontite'
    pp_coefs = '1 1 1 1 1 1 1 1 1 1 1 1 1 1'
  []
  [pH]
    type = PointValue
    variable = 'pH'
  []
[]

[Outputs]
  [exo]
    type = Exodus
    execute_on = final
  []
  csv = true
[]

(modules/geochemistry/test/tests/kernels/time_deriv_1.i)

# An initial concentration field in a material with constant porosity is subjected to a constant source
# porosity * d(concentration)/dt = source
# The result is checked vs the expected solution, which is conc = conc_old + dt * source / porosity
[Mesh]
  type = GeneratedMesh
  dim = 3
  nx = 2
  ny = 4
  nz = 2
[]

[Variables]
  [conc]
  []
[]

[Kernels]
  [dot]
    type = GeochemistryTimeDerivative
    porosity = porosity
    variable = conc
  []
  [source]
    type = BodyForce
    function = 3.0
    variable = conc
  []
[]

[ICs]
  [conc]
    type = FunctionIC
    function = 'z * z + 4 * x * x * x + y'
    variable = conc
  []
[]

[AuxVariables]
  [porosity]
  []
  [expected]
  []
  [should_be_zero]
  []
[]

[AuxKernels]
  [porosity]
    type = FunctionAux
    function = '6.0'
    variable = porosity
  []
  [expected]
    type = FunctionAux
    function = 'z * z + 4 * x * x * x + y + 2.0 * 3.0 / 6.0'
    variable = expected
  []
  [should_be_zero]
    type = ParsedAux
    args = 'expected conc'
    function = 'expected - conc'
    variable = should_be_zero
  []
[]

[Postprocessors]
  [error]
    type = NodalL2Norm
    variable = should_be_zero
  []
[]

[Executioner]
  type = Transient
  solve_type = Newton
  dt = 2
  end_time = 2
[]

[Outputs]
  csv = true
[]

(test/tests/outputs/png/wedge.i)

[Mesh]
  file = wedge.e
  uniform_refine = 1
[]

[Functions]
  active = 'tr_x tr_y'

  [./tr_x]
    type = ParsedFunction
    value = -x
  [../]

  [./tr_y]
    type = ParsedFunction
    value = y
  [../]
[]

[AuxVariables]
  [two_u]
  []
[]

[AuxKernels]
  [two_u]
    type = ParsedAux
    variable = two_u
    args = 'u'
    function = '2*u'
  []
[]

[Variables]
  active = 'u'

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

[Kernels]
  active = 'diff forcing dot'

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

  [./forcing]
    type = GaussContForcing
    variable = u
    x_center = -0.5
    y_center = 3.0
    x_spread = 0.2
    y_spread = 0.2
  [../]

  [./dot]
    type = TimeDerivative
    variable = u
  [../]
[]

[BCs]
  #active = ' '

  [./Periodic]
    [./x]
      primary = 1
      secondary = 2
      transform_func = 'tr_x tr_y'
      inv_transform_func = 'tr_x tr_y'
    [../]
  [../]
[]

[Executioner]
  type = Transient
  dt = 0.5
  num_steps = 6
  solve_type = NEWTON
[]

[Outputs]
  [png]
    type = PNGOutput
    resolution = 25
    color = RWB
    variable = 'two_u'
  []
[]

(test/tests/auxkernels/linear_combination/test.i)

# All tested logic is in the aux system
# The non-linear problem is unrelated

[Mesh]
  type = GeneratedMesh
  dim = 1
  xmin = -1
  xmax =  1
  nx = 10
[]

[Functions]
  [./v1_func]
    type = ParsedFunction
    value = (1-x)/2
  [../]
  [./v2_func]
    type = ParsedFunction
    value = (1+x)/2
  [../]
[]

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

[AuxVariables]
  [./lc]
  [../]

  [./v1]
  [../]
  [./v2]
  [../]

  [./w1]
  [../]
  [./w2]
  [../]
[]

[ICs]
  [./v1_ic]
    type = FunctionIC
    variable = v1
    function = v1_func
  [../]
  [./v2_ic]
    type = FunctionIC
    variable = v2
    function = v2_func
  [../]

  [./w1_ic]
    type = ConstantIC
    variable = w1
    value = 0.3
  [../]
  [./w2_ic]
    type = ConstantIC
    variable = w2
    value = 0.5
  [../]
[]

[AuxKernels]
  [./lc-aux]
    type = ParsedAux
    variable = lc
    function = 'v1*w1+v2*w2'
    args = 'v1 w1 v2 w2'
    execute_on = 'timestep_end'
  [../]
[]


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

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

  [./right]
    type = DirichletBC
    variable = u
    boundary = right
    value = 2
  [../]
[]

[Executioner]
  type = Steady
  solve_type = 'PJFNK'
[]

[Outputs]
  [./out]
    type = Exodus
  [../]
[]

(modules/functional_expansion_tools/examples/2D_volumetric_Cartesian/sub.i)

# Basic example coupling a master and sub app in a 2D Cartesian volume.
#
# The master app provides field values to the sub app via Functional Expansions, which then performs
# its calculations. The sub app's solution field values are then transferred back to the master app
# and coupled into the solution of the master app solution.
#
# This example couples Functional Expansions via AuxVariable.
[Mesh]
  type = GeneratedMesh
  dim = 2

  xmin = 0.0
  xmax = 10.0
  nx = 15

  ymin = 1.0
  ymax = 11.0
  ny = 25
[]

# Non-copy transfers only work with AuxVariable, but nothing will be solved without a variable
# defined. The solution is to define an empty variable tha does nothing, but causes MOOSE to solve
# the AuxKernels that we need.
[Variables]
  [./empty]
  [../]
[]

[AuxVariables]
  [./s]
    order = FIRST
    family = LAGRANGE
  [../]
  [./m_in]
    order = FIRST
    family = LAGRANGE
  [../]
[]

# We must have a kernel for every variable, hence this null kernel to match the variable 'empty'
[Kernels]
  [./null_kernel]
    type = NullKernel
    variable = empty
  [../]
[]

[AuxKernels]
  [./reconstruct_m_in]
    type = FunctionSeriesToAux
    function = FX_Basis_Value_Sub
    variable = m_in
  [../]
  [./calculate_s] # Something to make 's' change each time, but allow a converging solution
    type = ParsedAux
    variable = s
    args = m_in
    function = '2*exp(-m_in/0.8)'
  [../]
[]

[Functions]
  [./FX_Basis_Value_Sub]
    type = FunctionSeries
    series_type = Cartesian
    orders = '3   4'
    physical_bounds = '0.0  10.0    1.0 11.0'
    x = Legendre
    y = Legendre
  [../]
[]

[UserObjects]
  [./FX_Value_UserObject_Sub]
    type = FXVolumeUserObject
    function = FX_Basis_Value_Sub
    variable = s
  [../]
[]

[Executioner]
  type = Transient
  num_steps = 10
  dt = 0.5
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

(modules/tensor_mechanics/test/tests/notched_plastic_block/cmc_planar.i)

# Uses an unsmoothed version of capped-Mohr-Coulomb (via ComputeMultiPlasticityStress with TensorMechanicsPlasticTensileMulti and TensorMechanicsPlasticMohrCoulombMulti) to simulate the following problem.
# A cubical block is notched around its equator.
# All of its outer surfaces have roller BCs, but the notched region is free to move as needed
# The block is initialised with a high hydrostatic tensile stress
# Without the notch, the BCs do not allow contraction of the block, and this stress configuration is admissible
# With the notch, however, the interior parts of the block are free to move in order to relieve stress, and this causes plastic failure
# The top surface is then pulled upwards (the bottom is fixed because of the roller BCs)
# This causes more failure
[Mesh]
  [generated_mesh]
    type = GeneratedMeshGenerator
    dim = 3
    nx = 9
    ny = 9
    nz = 9
    xmin = 0
    xmax = 0.1
    ymin = 0
    ymax = 0.1
    zmin = 0
    zmax = 0.1
  []
  [block_to_remove_xmin]
    type = SubdomainBoundingBoxGenerator
    bottom_left = '-0.01 -0.01 0.045'
    top_right = '0.01 0.11 0.055'
    location = INSIDE
    block_id = 1
    input = generated_mesh
  []
  [block_to_remove_xmax]
    type = SubdomainBoundingBoxGenerator
    bottom_left = '0.09 -0.01 0.045'
    top_right = '0.11 0.11 0.055'
    location = INSIDE
    block_id = 1
    input = block_to_remove_xmin
  []
  [block_to_remove_ymin]
    type = SubdomainBoundingBoxGenerator
    bottom_left = '-0.01 -0.01 0.045'
    top_right = '0.11 0.01 0.055'
    location = INSIDE
    block_id = 1
    input = block_to_remove_xmax
  []
  [block_to_remove_ymax]
    type = SubdomainBoundingBoxGenerator
    bottom_left = '-0.01 0.09 0.045'
    top_right = '0.11 0.11 0.055'
    location = INSIDE
    block_id = 1
    input = block_to_remove_ymin
  []
  [remove_block]
    type = BlockDeletionGenerator
    block = 1
    input = block_to_remove_ymax
  []
[]

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
[]

[Modules/TensorMechanics/Master]
  [./all]
    add_variables = true
    incremental = true
    generate_output = 'max_principal_stress mid_principal_stress min_principal_stress stress_zz'
    eigenstrain_names = ini_stress
  [../]
[]

[Postprocessors]
  [./uz]
    type = PointValue
    point = '0 0 0.1'
    use_displaced_mesh = false
    variable = disp_z
  [../]
  [./s_zz]
    type = ElementAverageValue
    use_displaced_mesh = false
    variable = stress_zz
  [../]
  [./num_res]
    type = NumResidualEvaluations
  [../]
  [./nr_its]
    type = ElementAverageValue
    variable = num_iters
  [../]
  [./max_nr_its]
    type = ElementExtremeValue
    variable = num_iters
  [../]
  [./runtime]
    type = PerfGraphData
    data_type = TOTAL
    section_name = 'Root'
  [../]
[]

[BCs]
  # back=zmin, front=zmax, bottom=ymin, top=ymax, left=xmin, right=xmax
  [./xmin_xzero]
    type = DirichletBC
    variable = disp_x
    boundary = left
    value = 0.0
  [../]
  [./xmax_xzero]
    type = DirichletBC
    variable = disp_x
    boundary = right
    value = 0.0
  [../]
  [./ymin_yzero]
    type = DirichletBC
    variable = disp_y
    boundary = bottom
    value = 0.0
  [../]
  [./ymax_yzero]
    type = DirichletBC
    variable = disp_y
    boundary = top
    value = 0.0
  [../]
  [./zmin_zzero]
    type = DirichletBC
    variable = disp_z
    boundary = back
    value = '0'
  [../]
  [./zmax_disp]
    type = FunctionDirichletBC
    variable = disp_z
    boundary = front
    function = '1E-6*max(t,0)'
  [../]
[]

[AuxVariables]
  [./mc_int]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./plastic_strain]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./num_iters]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./yield_fcn]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

[AuxKernels]
  [./mc_int_auxk]
    type = MaterialStdVectorAux
    index = 0
    property = plastic_internal_parameter
    variable = mc_int
  [../]
  [./plastic_strain_aux]
    type = MaterialRankTwoTensorAux
    i = 2
    j = 2
    property = plastic_strain
    variable = plastic_strain
  [../]
  [./num_iters_auxk] # cannot use plastic_NR_iterations directly as this is zero, since no NR iterations are actually used, since we use a custom algorithm to do the return
    type = ParsedAux
    args = plastic_strain
    function = 'if(plastic_strain>0,1,0)'
    variable = num_iters
  [../]
  [./yield_fcn_auxk]
    type = MaterialStdVectorAux
    index = 0
    property = plastic_yield_function
    variable = yield_fcn
  [../]
[]

[UserObjects]
  [./ts]
    type = TensorMechanicsHardeningConstant
    value = 3E6
  [../]
  [./tensile]
    type = TensorMechanicsPlasticTensileMulti
    tensile_strength = ts
    yield_function_tolerance = 1
    internal_constraint_tolerance = 1.0E-6
    #shift = 1
    use_custom_returnMap = false
    use_custom_cto = false
  [../]

  [./mc_coh]
    type = TensorMechanicsHardeningConstant
    value = 5E6
  [../]
  [./mc_phi]
    type = TensorMechanicsHardeningConstant
    value = 35
    convert_to_radians = true
  [../]
  [./mc_psi]
    type = TensorMechanicsHardeningConstant
    value = 10
    convert_to_radians = true
  [../]
  [./mc]
    type = TensorMechanicsPlasticMohrCoulombMulti
    cohesion = mc_coh
    friction_angle = mc_phi
    dilation_angle = mc_psi
    yield_function_tolerance = 1E-5
    internal_constraint_tolerance = 1E-11
    use_custom_returnMap = false
  [../]
[]

[Materials]
  [./elasticity_tensor]
    type = ComputeIsotropicElasticityTensor
    youngs_modulus = 16E9
    poissons_ratio = 0.25
  [../]
  [./mc]
    type = ComputeMultiPlasticityStress
    ep_plastic_tolerance = 1E-6
    plastic_models = 'tensile mc'
    max_NR_iterations = 50
    specialIC = rock
    deactivation_scheme = safe_to_dumb
    debug_fspb = crash
  [../]
  [./strain_from_initial_stress]
    type = ComputeEigenstrainFromInitialStress
    initial_stress = '2.5E6 0 0  0 2.5E6 0  0 0 2.5E6'
    eigenstrain_name = ini_stress
  [../]
[]

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

[Executioner]
  start_time = -1
  end_time = 10
  dt = 1
  solve_type = NEWTON
  type = Transient

  l_tol = 1E-2
  nl_abs_tol = 1E-5
  nl_rel_tol = 1E-7
  l_max_its = 200
  nl_max_its = 400

  petsc_options_iname = '-pc_type -pc_asm_overlap -sub_pc_type -ksp_type -ksp_gmres_restart'
  petsc_options_value = ' asm      2              lu            gmres     200'
[]


[Outputs]
  file_base = cmc_planar
  perf_graph = true
  exodus = false
  csv = true
[]

(modules/geochemistry/test/tests/time_dependent_reactions/flushing_case1.i)

# Alkali flushing of a reservoir (an example of flushing): adding NaOH
# To determine the initial constraint_values, run flushing_equilibrium_at70degC.i
# Note that flushing_equilibrium_at70degC.i will have to be re-run when temperature-dependence has been added to geochemistry
# Note that Dawsonite is currently not included as an equilibrium_mineral, otherwise it is supersaturated in the initial configuration, so precipitates.  Bethke does not report this in Fig30.4, so I assume it is due to temperature dependence
[GlobalParams]
  point = '0 0 0'
[]

[TimeDependentReactionSolver]
  model_definition = definition
  geochemistry_reactor_name = reactor
  charge_balance_species = "Cl-"
  swap_into_basis = "Calcite Dolomite-ord Muscovite Kaolinite"
  swap_out_of_basis = "HCO3- Mg++ K+ Al+++"
  constraint_species = "H2O H+   Cl-       Na+       Ca++       Calcite   Dolomite-ord Muscovite Kaolinite SiO2(aq)"
  constraint_value = "  1.0 1E-5 2.1716946 1.0288941 0.21650572 10.177537 3.6826177    1.320907  1.1432682 6.318e-05"
  constraint_meaning = "kg_solvent_water activity bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition free_concentration"
  constraint_unit = "   kg              dimensionless moles          moles              moles              moles              moles              moles              moles              molal"
  initial_temperature = 70.0
  temperature = 70.0
  kinetic_species_name = Quartz
  kinetic_species_initial_value = 226.992243
  kinetic_species_unit = moles
  evaluate_kinetic_rates_always = true # implicit time-marching used for stability
  ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
  close_system_at_time = 0.0
  remove_fixed_activity_name = "H+"
  remove_fixed_activity_time = 0.0
  mode = 3 # flush through the NaOH solution specified below:
  source_species_names = "H2O    Na+  OH-"
  source_species_rates = "27.755 0.25 0.25" # 1kg water/2days = 27.755moles/day.  0.5mol Na+/2days = 0.25mol/day
[]

[UserObjects]
  [rate_quartz]
    type = GeochemistryKineticRate
    kinetic_species_name = Quartz
    intrinsic_rate_constant = 1.3824E-13 # 1.6E-19mol/s/cm^2 = 1.3824E-13mol/day/cm^2
    multiply_by_mass = true
    area_quantity = 1000
    promoting_species_names = "H+"
    promoting_species_indices = "-0.5"
  []
  [definition]
    type = GeochemicalModelDefinition
    database_file = "../../../database/moose_geochemdb.json"
    basis_species = "H2O H+ Cl- Na+ Ca++ HCO3- Mg++ K+ Al+++ SiO2(aq)"
    equilibrium_minerals = "Calcite Dolomite-ord Muscovite Kaolinite Paragonite Analcime Phlogopite Tridymite" # Dawsonite
    kinetic_minerals = "Quartz"
    kinetic_rate_descriptions = "rate_quartz"
  []
[]

[AuxVariables]
  [diss_rate]
  []
[]
[AuxKernels]
  [diss_rate]
    type = ParsedAux
    args = mol_change_Quartz
    function = '-mol_change_Quartz / 1.0' # 1.0 = timestep size
    variable = diss_rate
  []
[]

[Postprocessors]
  [pH]
    type = PointValue
    variable = "pH"
  []
  [rate_mole_per_day]
    type = PointValue
    variable = diss_rate
  []
  [cm3_Calcite]
    type = PointValue
    variable = free_cm3_Calcite
  []
  [cm3_Dolomite]
    type = PointValue
    variable = free_cm3_Dolomite-ord
  []
  [cm3_Muscovite]
    type = PointValue
    variable = free_cm3_Muscovite
  []
  [cm3_Kaolinite]
    type = PointValue
    variable = free_cm3_Kaolinite
  []
  [cm3_Quartz]
    type = PointValue
    variable = free_cm3_Quartz
  []
  [cm3_Paragonite]
    type = PointValue
    variable = free_cm3_Paragonite
  []
  [cm3_Analcime]
    type = PointValue
    variable = free_cm3_Analcime
  []
  [cm3_Phlogopite]
    type = PointValue
    variable = free_cm3_Phlogopite
  []
  [cm3_Tridymite]
    type = PointValue
    variable = free_cm3_Tridymite
  []
[]

[Executioner]
  type = Transient
  dt = 1
  end_time = 20 # measured in days
[]

[Outputs]
  csv = true
[]

(modules/geochemistry/test/tests/kernels/dispersion_1.i)

# Dispersion of a step-function front of concentration
# The initial condition is such that the theoretical result is exactly
# c = erf(x/sqrt(4*t*D)), where D = hydrodynamic_dispersion
#
# The finite mesh resolution and large time-step size means this is only achieved approximately (increasing nx and decreasing results in the error decreasing, but note the series approximation to the error function means that the error should never be exactly zero)

por = 2.0 # this is the porosity.  The result should not depend on por in this example since it appears in both terms of the PDE
[Mesh]
  type = GeneratedMesh
  dim = 1
  nx = 100
  xmin = -5
  xmax = 5
[]

[Variables]
  [conc]
  []
[]

[ICs]
  [spike]
    type = FunctionIC
    variable = conc
    function = 'if(x<=0.0, -1.0, 1.0)'
  []
[]

[Kernels]
  [dot]
    type = GeochemistryTimeDerivative
    porosity = ${por}
    variable = conc
  []
  [disp]
    type = GeochemistryDispersion
    variable = conc
    porosity = ${por}
    tensor_coeff = '0.3 0 0  0 0 0  0 0 0'
  []
[]

[Executioner]
  type = Transient
  solve_type = Newton
  dt = 0.5
  end_time = 1.0
[]

[AuxVariables]
  [expected]
  []
  [should_be_zero]
  []
[]

[AuxKernels]
  [expected]
    type = FunctionAux
    variable = expected
    function = erf
  []
  [should_be_zero]
    type = ParsedAux
    args = 'expected conc'
    function = 'expected - conc'
    variable = should_be_zero
  []
[]

[Postprocessors]
  [error]
    type = ElementL2Norm
    variable = should_be_zero
  []
[]

[Functions]
  [erf]
    type = ParsedFunction
    # series expansion for evaluating the error function
    value = 'xi := x / sqrt(4 * t * 0.3); expxi := exp(-xi * xi); if(x < 0.0, -1.0, if(x > 0.0, 1.0, 0.0)) * 2 / sqrt(pi) * sqrt(1 - expxi) * (sqrt(pi) / 2.0 + 31.0 * expxi / 200.0 - 341.0 * expxi * expxi / 8000.0)'
  []
[]

[Outputs]
  exodus = true
  execute_on = final
[]

(modules/combined/examples/phase_field-mechanics/kks_mechanics_VTS.i)

# KKS phase-field model coupled with elasticity using the Voigt-Taylor scheme as
# described in L.K. Aagesen et al., Computational Materials Science, 140, 10-21 (2017)
# Original run #170329e

[Mesh]
  type = GeneratedMesh
  dim = 3
  nx = 640
  ny = 1
  nz = 1
  xmin = -10
  xmax = 10
  ymin = 0
  ymax = 0.03125
  zmin = 0
  zmax = 0.03125
  elem_type = HEX8
[]


[Variables]
  # order parameter
  [./eta]
    order = FIRST
    family = LAGRANGE
  [../]

  # solute concentration
  [./c]
    order = FIRST
    family = LAGRANGE
  [../]

  # chemical potential
  [./w]
    order = FIRST
    family = LAGRANGE
  [../]

  # solute phase concentration (matrix)
  [./cm]
    order = FIRST
    family = LAGRANGE
  [../]
  # solute phase concentration (precipitate)
  [./cp]
    order = FIRST
    family = LAGRANGE
  [../]
  [./disp_x]
    order = FIRST
    family = LAGRANGE
  [../]
  [./disp_y]
    order = FIRST
    family = LAGRANGE
  [../]
  [./disp_z]
    order = FIRST
    family = LAGRANGE
  [../]
[]

[ICs]
  [./eta_ic]
    variable = eta
    type = FunctionIC
    function = ic_func_eta
    block = 0
  [../]
  [./c_ic]
    variable = c
    type = FunctionIC
    function = ic_func_c
    block = 0
  [../]
  [./w_ic]
    variable = w
    type = ConstantIC
    value = 0.00991
    block = 0
  [../]
  [./cm_ic]
    variable = cm
    type = ConstantIC
    value = 0.131
    block = 0
  [../]
  [./cp_ic]
    variable = cp
    type = ConstantIC
    value = 0.236
    block = 0
  [../]
[]

[Functions]
  [./ic_func_eta]
    type = ParsedFunction
    value = '0.5*(1.0+tanh((x)/delta_eta/sqrt(2.0)))'
    vars = 'delta_eta'
    vals = '0.8034'
  [../]
  [./ic_func_c]
    type = ParsedFunction
    value = '0.2388*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^3*(6*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^2-15*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))+10)+0.1338*(1-(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^3*(6*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^2-15*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))+10))'
    vars = 'delta'
    vals = '0.8034'
  [../]
  [./psi_eq_int]
    type = ParsedFunction
    value = 'volume*psi_alpha'
    vars = 'volume psi_alpha'
    vals = 'volume psi_alpha'
  [../]
  [./gamma]
    type = ParsedFunction
    value = '(psi_int - psi_eq_int) / dy / dz'
    vars = 'psi_int psi_eq_int dy       dz'
    vals = 'psi_int psi_eq_int 0.03125  0.03125'
  [../]
[]

[AuxVariables]
  [./sigma11]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./sigma22]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./sigma33]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./e11]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./e12]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./e22]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./e33]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./e_el11]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./e_el12]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./e_el22]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./f_el]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./eigen_strain00]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./Fglobal]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./psi]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

[AuxKernels]
  [./matl_sigma11]
    type = RankTwoAux
    rank_two_tensor = stress
    index_i = 0
    index_j = 0
    variable = sigma11
  [../]
  [./matl_sigma22]
    type = RankTwoAux
    rank_two_tensor = stress
    index_i = 1
    index_j = 1
    variable = sigma22
  [../]
  [./matl_sigma33]
    type = RankTwoAux
    rank_two_tensor = stress
    index_i = 2
    index_j = 2
    variable = sigma33
  [../]
  [./matl_e11]
    type = RankTwoAux
    rank_two_tensor = total_strain
    index_i = 0
    index_j = 0
    variable = e11
  [../]
  [./matl_e12]
    type = RankTwoAux
    rank_two_tensor = total_strain
    index_i = 0
    index_j = 1
    variable = e12
  [../]
  [./matl_e22]
    type = RankTwoAux
    rank_two_tensor = total_strain
    index_i = 1
    index_j = 1
    variable = e22
  [../]
  [./matl_e33]
    type = RankTwoAux
    rank_two_tensor = total_strain
    index_i = 2
    index_j = 2
    variable = e33
  [../]
  [./f_el]
    type = MaterialRealAux
    variable = f_el
    property = f_el_mat
    execute_on = timestep_end
  [../]
  [./GlobalFreeEnergy]
    variable = Fglobal
    type = KKSGlobalFreeEnergy
    fa_name = fm
    fb_name = fp
    w = 0.0264
    kappa_names = kappa
    interfacial_vars = eta
  [../]
  [./psi_potential]
    variable = psi
    type = ParsedAux
    args = 'Fglobal w c f_el sigma11 e11'
    function = 'Fglobal - w*c + f_el - sigma11*e11'
  [../]
[]


[BCs]
  [./left_x]
    type = DirichletBC
    variable = disp_x
    boundary = left
    value = 0
  [../]
  [./right_x]
    type = DirichletBC
    variable = disp_x
    boundary = right
    value = 0
  [../]
  [./front_y]
    type = DirichletBC
    variable = disp_y
    boundary = front
    value = 0
  [../]
  [./back_y]
    type = DirichletBC
    variable = disp_y
    boundary = back
    value = 0
  [../]
  [./top_z]
    type = DirichletBC
    variable = disp_z
    boundary = top
    value = 0
  [../]
  [./bottom_z]
    type = DirichletBC
    variable = disp_z
    boundary = bottom
    value = 0
  [../]
[]

[Materials]
  # Chemical free energy of the matrix
  [./fm]
    type = DerivativeParsedMaterial
    f_name = fm
    args = 'cm'
    function = '6.55*(cm-0.13)^2'
  [../]
# Elastic energy of the matrix
  [./elastic_free_energy_m]
    type = ElasticEnergyMaterial
    base_name = matrix
    f_name = fe_m
    args = ' '
    outputs = exodus
  [../]
# Total free energy of the matrix
  [./Total_energy_matrix]
    type = DerivativeSumMaterial
    f_name = f_total_matrix
    sum_materials = 'fm fe_m'
    args = 'cm'
  [../]

  # Free energy of the precipitate phase
  [./fp]
    type = DerivativeParsedMaterial
    f_name = fp
    args = 'cp'
    function = '6.55*(cp-0.235)^2'
  [../]

# Elastic energy of the precipitate
  [./elastic_free_energy_p]
    type = ElasticEnergyMaterial
    base_name = ppt
    f_name = fe_p
    args = ' '
    outputs = exodus
  [../]

# Total free energy of the precipitate
  [./Total_energy_ppt]
    type = DerivativeSumMaterial
    f_name = f_total_ppt
    sum_materials = 'fp fe_p'
    args = 'cp'
  [../]

  # Total elastic energy
    [./Total_elastic_energy]
      type = DerivativeTwoPhaseMaterial
      eta = eta
      f_name = f_el_mat
      fa_name = fe_m
      fb_name = fe_p
      outputs = exodus
      W = 0
    [../]

  # h(eta)
  [./h_eta]
    type = SwitchingFunctionMaterial
    h_order = HIGH
    eta = eta
  [../]

  # g(eta)
  [./g_eta]
    type = BarrierFunctionMaterial
    g_order = SIMPLE
    eta = eta
  [../]

  # constant properties
  [./constants]
    type = GenericConstantMaterial
    prop_names  = 'M   L   kappa     misfit'
    prop_values = '0.7 0.7 0.01704   0.00377'
  [../]

  #Mechanical properties
  [./Stiffness_matrix]
    type = ComputeElasticityTensor
    C_ijkl = '103.3 74.25 74.25 103.3 74.25 103.3 46.75 46.75 46.75'
    base_name = matrix
    fill_method = symmetric9
  [../]
  [./Stiffness_ppt]
    type = ComputeElasticityTensor
    C_ijkl = '100.7 71.45 71.45 100.7 71.45 100.7 50.10 50.10 50.10'
    base_name = ppt
    fill_method = symmetric9
  [../]
  [./stress_matrix]
    type = ComputeLinearElasticStress
    base_name = matrix
  [../]
  [./stress_ppt]
    type = ComputeLinearElasticStress
    base_name = ppt
  [../]
  [./strain_matrix]
    type = ComputeSmallStrain
    displacements = 'disp_x disp_y disp_z'
    base_name = matrix
  [../]
  [./strain_ppt]
    type = ComputeSmallStrain
    displacements = 'disp_x disp_y disp_z'
    base_name = ppt
    eigenstrain_names = 'eigenstrain_ppt'
  [../]
  [./eigen_strain]
    type = ComputeEigenstrain
    base_name = ppt
    eigen_base = '1 1 1 0 0 0'
    prefactor = misfit
    eigenstrain_name = 'eigenstrain_ppt'
  [../]
  [./global_stress]
    type = TwoPhaseStressMaterial
    base_A = matrix
    base_B = ppt
  [../]
  [./global_strain]
    type = ComputeSmallStrain
    displacements = 'disp_x disp_y disp_z'
  [../]
[]

[Kernels]
  [./TensorMechanics]
    displacements = 'disp_x disp_y disp_z'
  [../]

  # enforce c = (1-h(eta))*cm + h(eta)*cp
  [./PhaseConc]
    type = KKSPhaseConcentration
    ca       = cm
    variable = cp
    c        = c
    eta      = eta
  [../]

  # enforce pointwise equality of chemical potentials
  [./ChemPotVacancies]
    type = KKSPhaseChemicalPotential
    variable = cm
    cb       = cp
    fa_name  = f_total_matrix
    fb_name  = f_total_ppt
  [../]

  #
  # Cahn-Hilliard Equation
  #
  [./CHBulk]
    type = KKSSplitCHCRes
    variable = c
    ca       = cm
    fa_name  = f_total_matrix
    w        = w
  [../]

  [./dcdt]
    type = CoupledTimeDerivative
    variable = w
    v = c
  [../]
  [./ckernel]
    type = SplitCHWRes
    mob_name = M
    variable = w
  [../]

  #
  # Allen-Cahn Equation
  #
  [./ACBulkF]
    type = KKSACBulkF
    variable = eta
    fa_name  = f_total_matrix
    fb_name  = f_total_ppt
    w        = 0.0264
    args = 'cp cm'
  [../]
  [./ACBulkC]
    type = KKSACBulkC
    variable = eta
    ca       = cm
    cb       = cp
    fa_name  = f_total_matrix
  [../]
  [./ACInterface]
    type = ACInterface
    variable = eta
    kappa_name = kappa
  [../]
  [./detadt]
    type = TimeDerivative
    variable = eta
  [../]
[]

[Executioner]
  type = Transient
  solve_type = 'PJFNK'
  petsc_options_iname = '-pc_type -sub_pc_type   -sub_pc_factor_shift_type'
  petsc_options_value = 'asm       ilu            nonzero'

  l_max_its = 30
  nl_max_its = 10
  l_tol = 1.0e-4
  nl_rel_tol = 1.0e-8
  nl_abs_tol = 1.0e-11
  num_steps = 200

  [./TimeStepper]
    type = SolutionTimeAdaptiveDT
    dt = 0.5
  [../]
[]

[VectorPostprocessors]
  #[./eta]
  #  type =  LineValueSampler
  #  start_point = '-10 0 0'
  #  end_point = '10 0 0'
  #  variable = eta
  #  num_points = 321
  #  sort_by =  id
  #[../]
  #[./eta_position]
  #  type = FindValueOnLineSample
  #  vectorpostprocessor = eta
  #  variable_name = eta
  #  search_value = 0.5
  #[../]
#  [./f_el]
#    type =  LineMaterialRealSampler
#    start = '-20 0 0'
#    end   = '20 0 0'
#    sort_by = id
#    property = f_el
#  [../]
#  [./f_el_a]
#    type =  LineMaterialRealSampler
#    start = '-20 0 0'
#    end   = '20 0 0'
#    sort_by = id
#    property = fe_m
#  [../]
#  [./f_el_b]
#    type =  LineMaterialRealSampler
#    start = '-20 0 0'
#    end   = '20 0 0'
#    sort_by = id
#    property = fe_p
#  [../]
#  [./h_out]
#    type =  LineMaterialRealSampler
#    start = '-20 0 0'
#    end   = '20 0 0'
#    sort_by = id
#    property = h
#  [../]
#  [./fm_out]
#    type =  LineMaterialRealSampler
#    start = '-20 0 0'
#    end   = '20 0 0'
#    sort_by = id
#    property = fm
#  [../]
[]

[Postprocessors]
  [./f_el_int]
    type = ElementIntegralMaterialProperty
    mat_prop = f_el_mat
  [../]
  [./c_alpha]
    type =  SideAverageValue
    boundary = left
    variable = c
  [../]
  [./c_beta]
    type =  SideAverageValue
    boundary = right
    variable = c
  [../]
  [./e11_alpha]
    type =  SideAverageValue
    boundary = left
    variable = e11
  [../]
  [./e11_beta]
    type =  SideAverageValue
    boundary = right
    variable = e11
  [../]
  [./s11_alpha]
    type =  SideAverageValue
    boundary = left
    variable = sigma11
  [../]
  [./s22_alpha]
    type =  SideAverageValue
    boundary = left
    variable = sigma22
  [../]
  [./s33_alpha]
    type =  SideAverageValue
    boundary = left
    variable = sigma33
  [../]
  [./s11_beta]
    type =  SideAverageValue
    boundary = right
    variable = sigma11
  [../]
  [./s22_beta]
    type =  SideAverageValue
    boundary = right
    variable = sigma22
  [../]
  [./s33_beta]
    type =  SideAverageValue
    boundary = right
    variable = sigma33
  [../]
  [./f_el_alpha]
    type =  SideAverageValue
    boundary = left
    variable = f_el
  [../]
  [./f_el_beta]
    type =  SideAverageValue
    boundary = right
    variable = f_el
  [../]
  [./f_c_alpha]
    type =  SideAverageValue
    boundary = left
    variable = Fglobal
  [../]
  [./f_c_beta]
    type =  SideAverageValue
    boundary = right
    variable = Fglobal
  [../]
  [./chem_pot_alpha]
    type =  SideAverageValue
    boundary = left
    variable = w
  [../]
  [./chem_pot_beta]
    type =  SideAverageValue
    boundary = right
    variable = w
  [../]
  [./psi_alpha]
    type =  SideAverageValue
    boundary = left
    variable = psi
  [../]
  [./psi_beta]
    type =  SideAverageValue
    boundary = right
    variable = psi
  [../]
  [./total_energy]
    type = ElementIntegralVariablePostprocessor
    variable = Fglobal
  [../]
  # Get simulation cell size from postprocessor
  [./volume]
    type = ElementIntegralMaterialProperty
    mat_prop = 1
  [../]
  [./psi_eq_int]
    type = FunctionValuePostprocessor
    function = psi_eq_int
  [../]
  [./psi_int]
    type = ElementIntegralVariablePostprocessor
    variable = psi
  [../]
  [./gamma]
    type = FunctionValuePostprocessor
    function = gamma
  [../]
[]

#
# Precondition using handcoded off-diagonal terms
#
[Preconditioning]
  [./full]
    type = SMP
    full = true
  [../]
[]


[Outputs]
  [./exodus]
    type = Exodus
    interval = 20
  [../]
  [./csv]
    type = CSV
    execute_on = 'final'
  [../]
#[./console]
#    type = Console
#    output_file = true
#  [../]
[]

(modules/combined/examples/geochem-porous_flow/geotes_weber_tensleep/eqm_model_25_to_92degC.i)

[UserObjects]
  [definition]
    type = GeochemicalModelDefinition
    database_file = "../../../../geochemistry/database/moose_geochemdb.json"
    basis_species = "H2O H+ Cl- SO4-- HCO3- SiO2(aq) Al+++ Ca++ Mg++ Fe++ K+ Na+ Sr++ F- B(OH)3 Br- Ba++ Li+ NO3- O2(aq)"
    equilibrium_minerals = "Siderite Pyrrhotite Dolomite Illite Anhydrite Calcite Quartz K-feldspar Kaolinite Barite Celestite Fluorite Albite Chalcedony Goethite"
  []
[]

[TimeDependentReactionSolver]
  model_definition = definition
  geochemistry_reactor_name = reactor
  swap_out_of_basis = "NO3- O2(aq)"
  swap_into_basis = "  NH3  HS-"
  charge_balance_species = "Cl-"
  constraint_species = "H2O H+          Cl-         SO4--       HCO3-       HS-         SiO2(aq)    Al+++       Ca++        Mg++        Fe++        K+          Na+         Sr++        F-         B(OH)3      Br-         Ba++        Li+         NH3"
  constraint_value = "  1.0 0.019675774 1.619044933 0.062774835 0.065489838 0.003840583 0.001597755 0.000129719 0.013448104 0.001851471 0.000787867 0.048851229 1.587660615 0.000159781 0.00032108 0.006663119 0.001238987 0.000101944 0.013110503 0.001937302"
  constraint_meaning = "kg_solvent_water bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition"
  constraint_unit = "kg moles moles moles moles moles moles moles moles moles moles moles moles moles moles moles moles moles moles moles"
  prevent_precipitation = "Celestite Fluorite Albite Chalcedony Goethite"
  ramp_max_ionic_strength_initial = 0 # not needed in this simple problem
  initial_temperature = 25
  temperature = 95 # so final temp = 92
  execute_console_output_on = 'initial timestep_end'
  source_species_names = "Siderite    Pyrrhotite  Dolomite    Illite      Anhydrite   Calcite    Quartz     K-feldspar  Kaolinite   Barite"
  source_species_rates = "6.287111422 0.510783201 2.796550921 0.647761624 1.175446234 12.1838956 322.504833 6.613392119 5.96865E-05 8.46449E-05"
  solver_info = true
  stoichiometric_ionic_str_using_Cl_only = true
[]

[Executioner]
  type = Transient
  dt = 1
  end_time = 1
[]

[AuxVariables]
  [total_mineral_volume]
  []
  [free_cm3_Kfeldspar] # necessary because of the minus sign in K-feldspar which does not parse correctly in the total_mineral_volume AuxKernel
  []
[]

[AuxKernels]
  [free_cm3_Kfeldspar]
    type = GeochemistryQuantityAux
    reactor = reactor
    variable = free_cm3_Kfeldspar
    species = 'K-feldspar'
    quantity = free_cm3
    execute_on = 'timestep_begin timestep_end'
  []
  [total_mineral_volume_auxk]
    type = ParsedAux
    args = 'free_cm3_Siderite free_cm3_Pyrrhotite free_cm3_Dolomite free_cm3_Illite free_cm3_Anhydrite free_cm3_Calcite free_cm3_Quartz free_cm3_Kfeldspar free_cm3_Kaolinite free_cm3_Barite free_cm3_Celestite free_cm3_Fluorite free_cm3_Albite free_cm3_Chalcedony free_cm3_Goethite'
    function = 'free_cm3_Siderite + free_cm3_Pyrrhotite + free_cm3_Dolomite + free_cm3_Illite + free_cm3_Anhydrite + free_cm3_Calcite + free_cm3_Quartz + free_cm3_Kfeldspar + free_cm3_Kaolinite + free_cm3_Barite + free_cm3_Celestite + free_cm3_Fluorite + free_cm3_Albite + free_cm3_Chalcedony + free_cm3_Goethite'
    variable = total_mineral_volume
    execute_on = 'timestep_begin timestep_end'
  []
[]

[Postprocessors]
  [total_mineral_volume]
    type = PointValue
    point = '0 0 0'
    variable = total_mineral_volume
  []
[]

[Outputs]
  csv = true
[]

(modules/porous_flow/examples/reservoir_model/regular_grid.i)

# SPE 10 comparative problem - model 1
# Data and description from https://www.spe.org/web/csp/datasets/set01.htm
# Simple input file that just establishes gravity equilibrium in the model
#
# Heterogeneous permeability is included by reading data from an external file
# using the PiecewiseMultilinear function, and saving that data to an elemental
# AuxVariable that is then used in PorousFlowPermeabilityConstFromVar

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 100
  ny = 20
  xmax = 762
  ymax = 15.24
[]

[GlobalParams]
  PorousFlowDictator = dictator
  gravity = '0 -9.81 0'
  temperature_unit = Celsius
[]

[Variables]
  [porepressure]
    initial_condition = 20e6
  []
[]

[Functions]
  [perm_md_fcn]
    type = PiecewiseMultilinear
    data_file = spe10_case1.data
  []
[]

[BCs]
  [top]
    type = DirichletBC
    variable = porepressure
    value = 20e6
    boundary = top
  []
[]

[AuxVariables]
  [temperature]
    initial_condition = 50
  []
  [xnacl]
    initial_condition = 0.1
  []
  [porosity]
    family = MONOMIAL
    order = CONSTANT
    initial_condition = 0.2
  []
  [perm_md]
    family = MONOMIAL
    order = CONSTANT
  []
  [perm]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[Kernels]
  [mass0]
    type = PorousFlowMassTimeDerivative
    variable = porepressure
  []
  [flux0]
    type = PorousFlowFullySaturatedDarcyFlow
    variable = porepressure
  []
[]

[AuxKernels]
  [perm_md]
    type = FunctionAux
    function = perm_md_fcn
    variable = perm_md
    execute_on = initial
  []
  [perm]
    type = ParsedAux
    variable = perm
    args = perm_md
    function = '9.869233e-16*perm_md'
    execute_on = initial
  []
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = porepressure
    number_fluid_phases = 1
    number_fluid_components = 1
  []
[]

[Modules]
  [FluidProperties]
    [water]
      type = Water97FluidProperties
    []
    [watertab]
      type = TabulatedFluidProperties
      fp = water
      save_file = false
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
    temperature = temperature
  []
  [ps]
    type = PorousFlow1PhaseFullySaturated
    porepressure = porepressure
  []
  [massfrac]
    type = PorousFlowMassFraction
  []
  [brine]
    type = PorousFlowBrine
    compute_enthalpy = false
    compute_internal_energy = false
    xnacl = xnacl
    phase = 0
    water_fp = watertab
  []
  [porosity]
    type = PorousFlowPorosityConst
    porosity = porosity
  []
  [permeability]
    type = PorousFlowPermeabilityConstFromVar
    perm_xx = perm
    perm_yy = perm
    perm_zz = perm
  []
[]

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

[Executioner]
  type = Transient
  solve_type = Newton
  end_time = 1e5
  nl_abs_tol = 1e-12
  nl_rel_tol = 1e-06
  steady_state_detection = true
  steady_state_tolerance = 1e-12
  [TimeStepper]
    type = IterationAdaptiveDT
    dt = 1e2
  []
[]

[Outputs]
  execute_on = 'initial timestep_end'
  exodus = true
  perf_graph = true
[]

(modules/porous_flow/test/tests/chemistry/precipitation.i)

# The precipitation reaction
#
# a <==> mineral
#
# produces "mineral".  Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / porosity)' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is negative for a > 0.25, ie precipitation for a(t=0) > 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
#   = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * porosity
#
# This test checks that (a + c / porosity) is time-independent, and that a follows the above solution
#
# Aside:
#    The exponential curve is not followed exactly because moose actually solves
#    (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#    which does not give an exponential exactly, except in the limit dt->0
[Mesh]
  type = GeneratedMesh
  dim = 1
[]

[Variables]
  [a]
    initial_condition = 0.9
  []
[]

[AuxVariables]
  [pressure]
  []
  [ini_mineral_conc]
    initial_condition = 0.2
  []
  [k]
    initial_condition = 0.5
  []
  [mineral]
    family = MONOMIAL
    order = CONSTANT
  []
  [should_be_static]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[AuxKernels]
  [mineral]
    type = PorousFlowPropertyAux
    property = mineral_concentration
    mineral_species = 0
    variable = mineral
  []
  [should_be_static]
    type = ParsedAux
    args = 'mineral a'
    function = 'a + mineral / 0.1'
    variable = should_be_static
  []
[]

[GlobalParams]
  PorousFlowDictator = dictator
[]

[Kernels]
  [mass_a]
    type = PorousFlowMassTimeDerivative
    fluid_component = 0
    variable = a
  []
  [pre_dis]
    type = PorousFlowPreDis
    variable = a
    mineral_density = 1000
    stoichiometry = 1
  []
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = a
    number_fluid_phases = 1
    number_fluid_components = 2
    number_aqueous_kinetic = 1
  []
[]

[Modules]
  [FluidProperties]
    [simple_fluid]
      type = SimpleFluidProperties
      bulk_modulus = 2e9 # huge, so mimic chemical_reactions
      density0 = 1000
      thermal_expansion = 0
      viscosity = 1e-3
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
    temperature = 1
  []
  [ppss]
    type = PorousFlow1PhaseFullySaturated
    porepressure = pressure
  []
  [mass_frac]
    type = PorousFlowMassFraction
    mass_fraction_vars = a
  []
  [predis]
    type = PorousFlowAqueousPreDisChemistry
    primary_concentrations = a
    num_reactions = 1
    equilibrium_constants = k
    primary_activity_coefficients = 2
    reactions = 1
    specific_reactive_surface_area = 0.5
    kinetic_rate_constant = 0.6065306597126334
    activation_energy = 3
    molar_volume = 2
    gas_constant = 6
    reference_temperature = 0.5
  []
  [mineral_conc]
    type = PorousFlowAqueousPreDisMineral
    initial_concentrations = ini_mineral_conc
  []
  [simple_fluid]
    type = PorousFlowSingleComponentFluid
    fp = simple_fluid
    phase = 0
  []
  [porosity]
    type = PorousFlowPorosityConst
    porosity = 0.1
  []
[]

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

[Executioner]
  type = Transient
  solve_type = Newton
  nl_abs_tol = 1E-10
  dt = 0.01
  end_time = 1
[]

[Postprocessors]
  [a]
    type = PointValue
    point = '0 0 0'
    variable = a
  []
  [should_be_static]
    type = PointValue
    point = '0 0 0'
    variable = should_be_static
  []
[]
[Outputs]
  interval = 10
  csv = true
  perf_graph = true
[]

(modules/functional_expansion_tools/examples/3D_volumetric_cylindrical/sub.i)

# Basic example coupling a master and sub app in a 3D cylindrical mesh from an input file
#
# The master app provides field values to the sub app via Functional Expansions, which then performs
# its calculations. The sub app's solution field values are then transferred back to the master app
# and coupled into the solution of the master app solution.
#
# This example couples Functional Expansions via AuxVariable, the recommended approach.
#
# Note: this problem is not light, and may take a few minutes to solve.
[Mesh]
  type = FileMesh
  file = cyl-tet.e
[]

# Non-copy transfers only work with AuxVariable, but nothing will be solved without a variable
# defined. The solution is to define an empty variable tha does nothing, but causes MOOSE to solve
# the AuxKernels that we need.
[Variables]
  [./empty]
  [../]
[]

[AuxVariables]
  [./s]
    order = FIRST
    family = LAGRANGE
  [../]
  [./m_in]
    order = FIRST
    family = LAGRANGE
  [../]
[]

# We must have a kernel for every variable, hence this null kernel to match the variable 'empty'
[Kernels]
  [./null_kernel]
    type = NullKernel
    variable = empty
  [../]
[]

[AuxKernels]
  [./reconstruct_m_in]
    type = FunctionSeriesToAux
    function = FX_Basis_Value_Sub
    variable = m_in
  [../]
  [./calculate_s] # Something to make 's' change each time, but allow a converging solution
    type = ParsedAux
    variable = s
    args = m_in
    function = '2*exp(-m_in/0.8)'
  [../]
[]

[Functions]
  [./FX_Basis_Value_Sub]
    type = FunctionSeries
    series_type = CylindricalDuo
    orders = '5   3' # Axial first, then (r, t) FX
    physical_bounds = '-2.5 2.5   0 0 1' # z_min z_max   x_center y_center radius
    z = Legendre # Axial in z
    disc = Zernike # (r, t) default to unit disc in x-y plane
  [../]
[]

[UserObjects]
  [./FX_Value_UserObject_Sub]
    type = FXVolumeUserObject
    function = FX_Basis_Value_Sub
    variable = s
  [../]
[]

[Executioner]
  type = Transient
  num_steps = 10
  dt = 0.5
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

(modules/porous_flow/test/tests/poro_elasticity/mandel_constM.i)

# Mandel's problem of consolodation of a drained medium
#
# A sample is in plane strain.
# -a <= x <= a
# -b <= y <= b
# It is squashed with constant force by impermeable, frictionless plattens on its top and bottom surfaces (at y=+/-b)
# Fluid is allowed to leak out from its sides (at x=+/-a)
# The porepressure within the sample is monitored.
#
# As is common in the literature, this is simulated by
# considering the quarter-sample, 0<=x<=a and 0<=y<=b, with
# impermeable, roller BCs at x=0 and y=0 and y=b.
# Porepressure is fixed at zero on x=a.
# Porepressure and displacement are initialised to zero.
# Then the top (y=b) is moved downwards with prescribed velocity,
# so that the total force that is inducing this downwards velocity
# is fixed.  The velocity is worked out by solving Mandel's problem
# analytically, and the total force is monitored in the simulation
# to check that it indeed remains constant.
#
# Here are the problem's parameters, and their values:
# Soil width.  a = 1
# Soil height.  b = 0.1
# Soil's Lame lambda.  la = 0.5
# Soil's Lame mu, which is also the Soil's shear modulus.  mu = G = 0.75
# Soil bulk modulus.  K = la + 2*mu/3 = 1
# Drained Poisson ratio.  nu = (3K - 2G)/(6K + 2G) = 0.2
# Soil bulk compliance.  1/K = 1
# Fluid bulk modulus.  Kf = 8
# Fluid bulk compliance.  1/Kf = 0.125
# Soil initial porosity.  phi0 = 0.1
# Biot coefficient.  alpha = 0.6
# Biot modulus.  M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 4.705882
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.694118
# Undrained Poisson ratio.  nuu = (3Ku - 2G)/(6Ku + 2G) = 0.372627
# Skempton coefficient.  B = alpha*M/Ku = 1.048035
# Fluid mobility (soil permeability/fluid viscosity).  k = 1.5
# Consolidation coefficient.  c = 2*k*B^2*G*(1-nu)*(1+nuu)^2/9/(1-nuu)/(nuu-nu) = 3.821656
# Normal stress on top.  F = 1
#
# The solution for porepressure and displacements is given in
# AHD Cheng and E Detournay "A direct boundary element method for plane strain poroelasticity" International Journal of Numerical and Analytical Methods in Geomechanics 12 (1988) 551-572.
# The solution involves complicated infinite series, so I shall not write it here

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

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
  PorousFlowDictator = dictator
  block = 0
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = 'porepressure disp_x disp_y disp_z'
    number_fluid_phases = 1
    number_fluid_components = 1
  []
  [pc]
    type = PorousFlowCapillaryPressureVG
    m = 0.8
    alpha = 1e-5
  []
[]

[Variables]
  [disp_x]
  []
  [disp_y]
  []
  [disp_z]
  []
  [porepressure]
  []
[]

[BCs]
  [roller_xmin]
    type = DirichletBC
    variable = disp_x
    value = 0
    boundary = 'left'
  []
  [roller_ymin]
    type = DirichletBC
    variable = disp_y
    value = 0
    boundary = 'bottom'
  []
  [plane_strain]
    type = DirichletBC
    variable = disp_z
    value = 0
    boundary = 'back front'
  []
  [xmax_drained]
    type = DirichletBC
    variable = porepressure
    value = 0
    boundary = right
  []
  [top_velocity]
    type = FunctionDirichletBC
    variable = disp_y
    function = top_velocity
    boundary = top
  []
[]

[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'
  []
[]

[AuxVariables]
  [stress_yy]
    order = CONSTANT
    family = MONOMIAL
  []
  [tot_force]
    order = CONSTANT
    family = MONOMIAL
  []
[]

[AuxKernels]
  [stress_yy]
    type = RankTwoAux
    rank_two_tensor = stress
    variable = stress_yy
    index_i = 1
    index_j = 1
  []
  [tot_force]
    type = ParsedAux
    args = 'stress_yy porepressure'
    execute_on = timestep_end
    variable = tot_force
    function = '-stress_yy+0.6*porepressure'
  []
[]

[Kernels]
  [grad_stress_x]
    type = StressDivergenceTensors
    variable = disp_x
    component = 0
  []
  [grad_stress_y]
    type = StressDivergenceTensors
    variable = disp_y
    component = 1
  []
  [grad_stress_z]
    type = StressDivergenceTensors
    variable = disp_z
    component = 2
  []
  [poro_x]
    type = PorousFlowEffectiveStressCoupling
    biot_coefficient = 0.6
    variable = disp_x
    component = 0
  []
  [poro_y]
    type = PorousFlowEffectiveStressCoupling
    biot_coefficient = 0.6
    variable = disp_y
    component = 1
  []
  [poro_z]
    type = PorousFlowEffectiveStressCoupling
    biot_coefficient = 0.6
    component = 2
    variable = disp_z
  []
  [poro_vol_exp]
    type = PorousFlowMassVolumetricExpansion
    variable = porepressure
    fluid_component = 0
  []
  [mass0]
    type = PorousFlowMassTimeDerivative
    fluid_component = 0
    variable = porepressure
  []
  [flux]
    type = PorousFlowAdvectiveFlux
    variable = porepressure
    gravity = '0 0 0'
    fluid_component = 0
  []
[]

[Modules]
  [FluidProperties]
    [simple_fluid]
      type = SimpleFluidProperties
      bulk_modulus = 8
      density0 = 1
      thermal_expansion = 0
      viscosity = 1
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
  []
  [elasticity_tensor]
    type = ComputeElasticityTensor
    C_ijkl = '0.5 0.75'
    # bulk modulus is lambda + 2*mu/3 = 0.5 + 2*0.75/3 = 1
    fill_method = symmetric_isotropic
  []
  [strain]
    type = ComputeSmallStrain
  []
  [stress]
    type = ComputeLinearElasticStress
  []
  [eff_fluid_pressure]
    type = PorousFlowEffectiveFluidPressure
  []
  [vol_strain]
    type = PorousFlowVolumetricStrain
  []
  [ppss]
    type = PorousFlow1PhaseP
    porepressure = porepressure
    capillary_pressure = pc
  []
  [massfrac]
    type = PorousFlowMassFraction
  []
  [simple_fluid]
    type = PorousFlowSingleComponentFluid
    fp = simple_fluid
    phase = 0
  []
  [porosity]
    type = PorousFlowPorosityHMBiotModulus
    porosity_zero = 0.1
    biot_coefficient = 0.6
    solid_bulk = 1
    constant_fluid_bulk_modulus = 8
    constant_biot_modulus = 4.7058823529
  []
  [permeability]
    type = PorousFlowPermeabilityConst
    permeability = '1.5 0 0   0 1.5 0   0 0 1.5'
  []
  [relperm]
    type = PorousFlowRelativePermeabilityCorey
    n = 0 # unimportant in this fully-saturated situation
    phase = 0
  []
[]

[Postprocessors]
  [p0]
    type = PointValue
    outputs = csv
    point = '0.0 0 0'
    variable = porepressure
  []
  [p1]
    type = PointValue
    outputs = csv
    point = '0.1 0 0'
    variable = porepressure
  []
  [p2]
    type = PointValue
    outputs = csv
    point = '0.2 0 0'
    variable = porepressure
  []
  [p3]
    type = PointValue
    outputs = csv
    point = '0.3 0 0'
    variable = porepressure
  []
  [p4]
    type = PointValue
    outputs = csv
    point = '0.4 0 0'
    variable = porepressure
  []
  [p5]
    type = PointValue
    outputs = csv
    point = '0.5 0 0'
    variable = porepressure
  []
  [p6]
    type = PointValue
    outputs = csv
    point = '0.6 0 0'
    variable = porepressure
  []
  [p7]
    type = PointValue
    outputs = csv
    point = '0.7 0 0'
    variable = porepressure
  []
  [p8]
    type = PointValue
    outputs = csv
    point = '0.8 0 0'
    variable = porepressure
  []
  [p9]
    type = PointValue
    outputs = csv
    point = '0.9 0 0'
    variable = porepressure
  []
  [p99]
    type = PointValue
    outputs = csv
    point = '1 0 0'
    variable = porepressure
  []
  [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
    outputs = console
    function = if(0.15*t<0.01,0.15*t,0.01)
  []
[]

[Preconditioning]
  [andy]
    type = SMP
    full = true
    petsc_options_iname = '-ksp_type -pc_type -sub_pc_type -snes_atol -snes_rtol -snes_max_it'
    petsc_options_value = 'gmres asm lu 1E-14 1E-10 10000'
  []
[]

[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'
  file_base = mandel_constM
  [csv]
    interval = 3
    type = CSV
  []
[]

(modules/combined/test/tests/poro_mechanics/mandel.i)

# Mandel's problem of consolodation of a drained medium
#
# A sample is in plane strain.
# -a <= x <= a
# -b <= y <= b
# It is squashed with constant force by impermeable, frictionless plattens on its top and bottom surfaces (at y=+/-b)
# Fluid is allowed to leak out from its sides (at x=+/-a)
# The porepressure within the sample is monitored.
#
# As is common in the literature, this is simulated by
# considering the quarter-sample, 0<=x<=a and 0<=y<=b, with
# impermeable, roller BCs at x=0 and y=0 and y=b.
# Porepressure is fixed at zero on x=a.
# Porepressure and displacement are initialised to zero.
# Then the top (y=b) is moved downwards with prescribed velocity,
# so that the total force that is inducing this downwards velocity
# is fixed.  The velocity is worked out by solving Mandel's problem
# analytically, and the total force is monitored in the simulation
# to check that it indeed remains constant.
#
# Here are the problem's parameters, and their values:
# Soil width.  a = 1
# Soil height.  b = 0.1
# Soil's Lame lambda.  la = 0.5
# Soil's Lame mu, which is also the Soil's shear modulus.  mu = G = 0.75
# Soil bulk modulus.  K = la + 2*mu/3 = 1
# Drained Poisson ratio.  nu = (3K - 2G)/(6K + 2G) = 0.2
# Soil bulk compliance.  1/K = 1
# Fluid bulk modulus.  Kf = 8
# Fluid bulk compliance.  1/Kf = 0.125
# Soil initial porosity.  phi0 = 0.1
# Biot coefficient.  alpha = 0.6
# Biot modulus.  M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 4.705882
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.694118
# Undrained Poisson ratio.  nuu = (3Ku - 2G)/(6Ku + 2G) = 0.372627
# Skempton coefficient.  B = alpha*M/Ku = 1.048035
# Fluid mobility (soil permeability/fluid viscosity).  k = 1.5
# Consolidation coefficient.  c = 2*k*B^2*G*(1-nu)*(1+nuu)^2/9/(1-nuu)/(nuu-nu) = 3.821656
# Normal stress on top.  F = 1
#
# The solution for porepressure and displacements is given in
# AHD Cheng and E Detournay "A direct boundary element method for plane strain poroelasticity" International Journal of Numerical and Analytical Methods in Geomechanics 12 (1988) 551-572.
# The solution involves complicated infinite series, so I shall not write it here

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

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
  porepressure = porepressure
  block = 0
[]

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

[BCs]
  [./roller_xmin]
    type = DirichletBC
    variable = disp_x
    value = 0
    boundary = 'left'
  [../]
  [./roller_ymin]
    type = DirichletBC
    variable = disp_y
    value = 0
    boundary = 'bottom'
  [../]
  [./plane_strain]
    type = DirichletBC
    variable = disp_z
    value = 0
    boundary = 'back front'
  [../]
  [./xmax_drained]
    type = DirichletBC
    variable = porepressure
    value = 0
    boundary = right
  [../]
  [./top_velocity]
    type = FunctionDirichletBC
    variable = disp_y
    function = top_velocity
    boundary = top
  [../]
[]

[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'
  [../]
[]


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

[AuxKernels]
  [./stress_yy]
    type = RankTwoAux
    rank_two_tensor = stress
    variable = stress_yy
    index_i = 1
    index_j = 1
  [../]
  [./tot_force]
    type = ParsedAux
    args = 'stress_yy porepressure'
    execute_on = timestep_end
    variable = tot_force
    function = '-stress_yy+0.6*porepressure'
  [../]
[]



[Kernels]
  [./grad_stress_x]
    type = StressDivergenceTensors
    variable = disp_x
    component = 0
  [../]
  [./grad_stress_y]
    type = StressDivergenceTensors
    variable = disp_y
    component = 1
  [../]
  [./grad_stress_z]
    type = StressDivergenceTensors
    variable = disp_z
    component = 2
  [../]
    [./poro_x]
    type = PoroMechanicsCoupling
    variable = disp_x
    component = 0
  [../]
  [./poro_y]
    type = PoroMechanicsCoupling
    variable = disp_y
    component = 1
  [../]
  [./poro_z]
    type = PoroMechanicsCoupling
    variable = disp_z
    component = 2
  [../]
  [./poro_timederiv]
    type = PoroFullSatTimeDerivative
    variable = porepressure
  [../]
  [./darcy_flow]
    type = CoefDiffusion
    variable = porepressure
    coef = 1.5
  [../]
[]


[Materials]
  [./elasticity_tensor]
    type = ComputeElasticityTensor
    C_ijkl = '0.5 0.75'
    # bulk modulus is lambda + 2*mu/3 = 0.5 + 2*0.75/3 = 1
    fill_method = symmetric_isotropic
  [../]
  [./strain]
    type = ComputeSmallStrain
    displacements = 'disp_x disp_y disp_z'
  [../]
  [./stress]
    type = ComputeLinearElasticStress
  [../]
  [./poro_material]
    type = PoroFullSatMaterial
    porosity0 = 0.1
    biot_coefficient = 0.6
    solid_bulk_compliance = 1
    fluid_bulk_compliance = 0.125
    constant_porosity = true
  [../]
[]

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


[Preconditioning]
  [./andy]
    type = SMP
    full = true
    petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it'
    petsc_options_value = 'bcgs bjacobi 1E-14 1E-10 10000'
  [../]
[]

[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'
  file_base = mandel
  [./csv]
    interval = 3
    type = CSV
  [../]
[]

(modules/functional_expansion_tools/test/tests/standard_use/multiapp_sub.i)

[Mesh]
  type = GeneratedMesh
  dim = 1

  xmin = 0.0
  xmax = 10.0
  nx = 15
[]

[Variables]
  [./empty]
  [../]
[]

[AuxVariables]
  [./s]
    order = FIRST
    family = LAGRANGE
  [../]
  [./m_in]
    order = FIRST
    family = LAGRANGE
  [../]
[]

[Kernels]
  [./null_kernel]
    type = NullKernel
    variable = empty
  [../]
[]

[AuxKernels]
  [./reconstruct_m_in]
    type = FunctionSeriesToAux
    function = FX_Basis_Value_Sub
    variable = m_in
  [../]
  [./calculate_s]
    type = ParsedAux
    variable = s
    args = m_in
    function = '2*exp(-m_in/0.8)'
  [../]
[]

[Functions]
  [./FX_Basis_Value_Sub]
    type = FunctionSeries
    series_type = Cartesian
    orders = '3'
    physical_bounds = '0.0  10.0'
    x = Legendre
  [../]
[]

[UserObjects]
  [./FX_Value_UserObject_Sub]
    type = FXVolumeUserObject
    function = FX_Basis_Value_Sub
    variable = s
  [../]
[]

[Executioner]
  type = Transient
  num_steps = 10
  dt = 0.5
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

(test/tests/transfers/multiapp_userobject_transfer/restricted_node_sub.i)

# yy is passed in from the master app

[Mesh]
  [line]
    type = GeneratedMeshGenerator
    dim = 1
    nx = 5
    xmax = 2.5
  []
  [box]
    type = SubdomainBoundingBoxGenerator
    input = line
    bottom_left = '0 -0.1 -0.1'
    top_right = '1.5 0.1 0.1'
    # need a different block ID than what is in the master app to make sure the transfer works properly
    block_id = 20
  []
[]

[AuxVariables]
  [A]
  []

  [S]
  []
[]

[AuxKernels]
  [A_ak]
    type = ParsedAux
    variable = A
    use_xyzt = true
    function = '2*x+4*${yy}'
    execute_on = 'TIMESTEP_BEGIN'
  []
[]

[Variables]
  [u]
  []
[]

[Kernels]
  [td]
    type = TimeDerivative
    variable = u
  []

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

[UserObjects]
  [A_avg]
    type = LayeredAverage
    block = 20
    num_layers = 2
    direction = x
    variable = A
    execute_on = TIMESTEP_END
  []
[]

[Executioner]
  type = Transient
[]

[Outputs]
  exodus = true
[]

(test/tests/auxkernels/parsed_aux/xyzt.i)

[Mesh]
  type = GeneratedMesh
  dim = 3
  nx = 4
  ny = 4
  nz = 4
[]

# [Variables]
#   [u]
#   []
# []
#
# [Kernels]
#   [diff]
#     type = CoefDiffusion
#     variable = u
#     coef = 0.1
#   []
#   [dt]
#     type = TimeDerivative
#     variable = u
#   []
# []

[AuxVariables]
  [xvar]
    family = MONOMIAL
    order = FIRST
  []
  [yvar]
  []
  [zvar]
    family = MONOMIAL
    order = CONSTANT
  []
  [tvar]
  []
[]

[AuxKernels]
  [xvar]
    type = ParsedAux
    variable = xvar
    use_xyzt = true
    function = 'x+1'
  []
  [yvar]
    type = ParsedAux
    variable = yvar
    use_xyzt = true
    function = 'y+2'
  []
  [zvar]
    type = ParsedAux
    variable = zvar
    use_xyzt = true
    function = 'z+3'
  []
  [tvar]
    type = ParsedAux
    variable = tvar
    use_xyzt = true
    function = 't+0.1*(x+y+z)'
    execute_on = 'INITIAL TIMESTEP_END'
  []
[]

[Problem]
  solve = false
  kernel_coverage_check = false
[]

[Executioner]
  type = Transient
  num_steps = 3
[]

[Outputs]
  exodus = true
[]

(modules/geochemistry/test/tests/time_dependent_reactions/flushing_case2.i)

# Alkali flushing of a reservoir (an example of flushing): adding Na2CO3
# To determine the initial constraint_values, run flushing_equilibrium_at70degC.i
# Note that flushing_equilibrium_at70degC.i will have to be re-run when temperature-dependence has been added to geochemistry
# Note that Dawsonite is currently not included as an equilibrium_mineral, otherwise it is supersaturated in the initial configuration, so precipitates.  Bethke does not report this in Fig30.4, so I assume it is due to temperature dependence
[GlobalParams]
  point = '0 0 0'
[]

[TimeDependentReactionSolver]
  model_definition = definition
  geochemistry_reactor_name = reactor
  charge_balance_species = "Cl-"
  swap_into_basis = "Calcite Dolomite-ord Muscovite Kaolinite"
  swap_out_of_basis = "HCO3- Mg++ K+ Al+++"
  constraint_species = "H2O H+   Cl-       Na+       Ca++       Calcite   Dolomite-ord Muscovite Kaolinite SiO2(aq)"
  constraint_value = "  1.0 1E-5 2.1716946 1.0288941 0.21650572 10.177537 3.6826177    1.320907  1.1432682 6.318e-05"
  constraint_meaning = "kg_solvent_water activity bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition free_concentration"
  constraint_unit = "   kg              dimensionless moles          moles              moles              moles              moles              moles              moles              molal"
  initial_temperature = 70.0
  temperature = 70.0
  kinetic_species_name = Quartz
  kinetic_species_initial_value = 226.992243
  kinetic_species_unit = moles
  evaluate_kinetic_rates_always = true # implicit time-marching used for stability
  ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
  close_system_at_time = 0.0
  remove_fixed_activity_name = "H+"
  remove_fixed_activity_time = 0.0
  mode = 3 # flush through the NaOH solution specified below:
  source_species_names = "H2O    Na+  CO3--"
  source_species_rates = "27.755 0.25 0.125" # 1kg water/2days = 27.755moles/day.  0.5mol Na+/2days = 0.25mol/day
[]

[UserObjects]
  [rate_quartz]
    type = GeochemistryKineticRate
    kinetic_species_name = Quartz
    intrinsic_rate_constant = 1.3824E-13 # 1.6E-19mol/s/cm^2 = 1.3824E-13mol/day/cm^2
    multiply_by_mass = true
    area_quantity = 1000
    promoting_species_names = "H+"
    promoting_species_indices = "-0.5"
  []
  [definition]
    type = GeochemicalModelDefinition
    database_file = "../../../database/moose_geochemdb.json"
    basis_species = "H2O H+ Cl- Na+ Ca++ HCO3- Mg++ K+ Al+++ SiO2(aq)"
    equilibrium_minerals = "Calcite Dolomite-ord Muscovite Kaolinite Paragonite Analcime Phlogopite Tridymite" # Dawsonite
    kinetic_minerals = "Quartz"
    kinetic_rate_descriptions = "rate_quartz"
  []
[]

[AuxVariables]
  [diss_rate]
  []
[]
[AuxKernels]
  [diss_rate]
    type = ParsedAux
    args = mol_change_Quartz
    function = '-mol_change_Quartz / 1.0' # 1.0 = timestep size
    variable = diss_rate
  []
[]

[Postprocessors]
  [pH]
    type = PointValue
    variable = "pH"
  []
  [rate_mole_per_day]
    type = PointValue
    variable = diss_rate
  []
  [cm3_Calcite]
    type = PointValue
    variable = free_cm3_Calcite
  []
  [cm3_Dolomite]
    type = PointValue
    variable = free_cm3_Dolomite-ord
  []
  [cm3_Muscovite]
    type = PointValue
    variable = free_cm3_Muscovite
  []
  [cm3_Kaolinite]
    type = PointValue
    variable = free_cm3_Kaolinite
  []
  [cm3_Quartz]
    type = PointValue
    variable = free_cm3_Quartz
  []
  [cm3_Paragonite]
    type = PointValue
    variable = free_cm3_Paragonite
  []
  [cm3_Analcime]
    type = PointValue
    variable = free_cm3_Analcime
  []
  [cm3_Phlogopite]
    type = PointValue
    variable = free_cm3_Phlogopite
  []
  [cm3_Tridymite]
    type = PointValue
    variable = free_cm3_Tridymite
  []
[]

[Executioner]
  type = Transient
  dt = 1
  end_time = 20 # measured in days
[]

[Outputs]
  csv = true
[]

(modules/porous_flow/examples/groundwater/ex01.i)

# Groundwater extraction example.
# System consists of two confined aquifers separated by an aquitard
# There is a hydraulic gradient in the upper aquifer
# A well extracts water from the lower aquifer, and the impact on the upper aquifer is observed
# In the center of the model, the roof of the upper aquifer sits 70m below the local water table

[Mesh]
  [basic_mesh]
    type = GeneratedMeshGenerator
    dim = 3
    xmin = -50
    xmax = 50
    nx = 20
    ymin = -25
    ymax = 25
    ny = 10
    zmin = -100
    zmax = -70
    nz = 3
  []
  [lower_aquifer]
    type = SubdomainBoundingBoxGenerator
    input = basic_mesh
    block_id = 1
    block_name = lower_aquifer
    bottom_left = '-1000 -500 -100'
    top_right = '1000 500 -90'
  []
  [aquitard]
    type = SubdomainBoundingBoxGenerator
    input = lower_aquifer
    block_id = 2
    block_name = aquitard
    bottom_left = '-1000 -500 -90'
    top_right = '1000 500 -80'
  []
  [upper_aquifer]
    type = SubdomainBoundingBoxGenerator
    input = aquitard
    block_id = 3
    block_name = upper_aquifer
    bottom_left = '-1000 -500 -80'
    top_right = '1000 500 -70'
  []
[]

[GlobalParams]
  PorousFlowDictator = dictator
[]

[Variables]
  [pp]
  []
[]

[ICs]
  [pp]
    type = FunctionIC
    variable = pp
    function = insitu_pp
  []
[]

[BCs]
  [pp]
    type = FunctionDirichletBC
    variable = pp
    function = insitu_pp
    boundary = 'left right top bottom front back'
  []
[]

[Functions]
  [upper_aquifer_head]
    type = ParsedFunction
    value = '10 + x / 200'
  []
  [lower_aquifer_head]
    type = ParsedFunction
    value = '20'
  []
  [insitu_head]
    type = ParsedFunction
    vals = 'lower_aquifer_head upper_aquifer_head'
    vars = 'low up'
    value = 'if(z <= -90, low, if(z >= -80, up, (up * (z + 90) - low * (z + 80)) / (10.0)))'
  []
  [insitu_pp]
    type = ParsedFunction
    vals = 'insitu_head'
    vars = 'h'
    value = '(h - z) * 1E4'
  []
  [l_rate]
    type = ParsedFunction
    vals = 'm3_produced dt'
    vars = 'm3_produced dt'
    value = '1000 * m3_produced / dt'
  []
[]

[AuxVariables]
  [insitu_head]
  []
  [head_change]
  []
[]

[AuxKernels]
  [insitu_head]
    type = FunctionAux
    variable = insitu_head
    function = insitu_head
  []
  [head_change]
    type = ParsedAux
    args = 'pp insitu_head'
    use_xyzt = true
    function = 'pp / 1E4 + z - insitu_head'
    variable = head_change
  []
[]

[Postprocessors]
  [m3_produced]
    type = PorousFlowPlotQuantity
    uo = volume_extracted
    outputs = 'none'
  []
  [dt]
    type = TimestepSize
    outputs = 'none'
  []
  [l_per_s]
    type = FunctionValuePostprocessor
    function = l_rate
  []
[]

[VectorPostprocessors]
  [drawdown]
    type = LineValueSampler
    variable = head_change
    start_point = '-50 0 -75'
    end_point = '50 0 -75'
    num_points = 101
    sort_by = x
  []
[]

[PorousFlowBasicTHM]
  fp = simple_fluid
  gravity = '0 0 -10'
  porepressure = pp
  multiply_by_density = false
[]

[Modules]
  [FluidProperties]
    [simple_fluid]
      type = SimpleFluidProperties
      # the following mean that density = 1000 * exp(P / 1E15) ~ 1000
      thermal_expansion = 0
      bulk_modulus = 1E15
    []
  []
[]

[Materials]
  [porosity_aquifers]
    type = PorousFlowPorosityConst
    porosity = 0.05
    block = 'upper_aquifer lower_aquifer'
  []
  [porosity_aquitard]
    type = PorousFlowPorosityConst
    porosity = 0.2
    block = aquitard
  []
  [biot_mod]
    type = PorousFlowConstantBiotModulus
    fluid_bulk_modulus = 2E9
    biot_coefficient = 1.0
  []
  [permeability_aquifers]
    type = PorousFlowPermeabilityConst
    permeability = '1E-12 0 0 0 1E-12 0 0 0 1E-12'
    block = 'upper_aquifer lower_aquifer'
  []
  [permeability_aquitard]
    type = PorousFlowPermeabilityConst
    permeability = '1E-16 0 0 0 1E-16 0 0 0 1E-17'
    block = aquitard
  []
[]

[DiracKernels]
  [sink]
    type = PorousFlowPolyLineSink
    SumQuantityUO = volume_extracted
    point_file = ex01.bh_lower
    line_length = 10
    variable = pp
    # following produces a flux of 0 m^3(water)/m(borehole length)/s if porepressure = 0, and a flux of 1 m^3/m/s if porepressure = 1E9
    p_or_t_vals = '0 1E9'
    fluxes = '0 1'
  []
[]

[UserObjects]
  [volume_extracted]
    type = PorousFlowSumQuantity
  []
[]

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

[Executioner]
  type = Transient
  solve_type = Newton
  [TimeStepper]
    type = SolutionTimeAdaptiveDT
    dt = 1.1E5
  []
  end_time = 3.456E5 # 4 days
  nl_abs_tol = 1E-13
[]

[Outputs]
  [csv]
    type = CSV
    file_base = ex01_lower_extraction
    execute_on = final
  []
[]

(modules/combined/examples/publications/rapid_dev/fig3.i)

#
# Fig. 3 input for 10.1016/j.commatsci.2017.02.017
# D. Schwen et al./Computational Materials Science 132 (2017) 36-45
# Comparison of an analytical (ca) and numerical (c) phase field interface
# profile. Supply the L parameter on the command line to gather the data for
# the inset plot.
#

[Mesh]
  type = GeneratedMesh
  dim = 1
  nx = ${L}
  xmin = -30
  xmax = 30
[]

[Functions]
  [./solution]
    type = ParsedFunction
    value = 0.5*(1+tanh(x/2^0.5))
  [../]
[]

[Variables]
  [./c]
    [./InitialCondition]
      type = FunctionIC
      function = solution
      #type = FunctionIC
      #function = if(x>0,1,0)
    [../]
  [../]
  [./w]
  [../]
[]

[AuxVariables]
  [./diff]
  [../]
  [./ca]
    [./InitialCondition]
      type = FunctionIC
      function = '0.5*(1+tanh(x/2^0.5))'
    [../]
  [../]
[]

[AuxKernels]
  [./diff]
    type = ParsedAux
    variable = diff
    function = c-ca
    args = 'c ca'
  [../]
[]

[Materials]
  [./F]
    type = DerivativeParsedMaterial
    f_name = F
    function = 'c^2*(1-c)^2'
    args = c
  [../]
[]

[Kernels]
  # Split Cahn-Hilliard kernels
  [./c_res]
    type = SplitCHParsed
    variable = c
    f_name = F
    kappa_name = 1
    w = w
  [../]
  [./wres]
    type = SplitCHWRes
    variable = w
    mob_name = 1
  [../]
  [./time]
    type = CoupledTimeDerivative
    variable = w
    v = c
  [../]
[]

[Postprocessors]
  [./L2]
    type = ElementL2Error
    function = solution
    variable = c
  [../]
[]

[VectorPostprocessors]
  [./c]
    type = LineValueSampler
    variable = 'c ca diff'
    start_point = '-10 0 0'
    end_point = '10 0 0'
    num_points = 200
    sort_by = x
  [../]
[]

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

[Executioner]
  type = Transient
  solve_type = NEWTON

  nl_rel_tol = 1e-10
  nl_abs_tol = 1e-12
  end_time = 1e+6

  [./TimeStepper]
    type = IterationAdaptiveDT
    dt = 1
    optimal_iterations = 5
    iteration_window = 1
  [../]
[]

[Outputs]
  csv = true
  execute_on = final
[]

(test/tests/transfers/multiapp_userobject_transfer/restricted_elem_sub.i)

# yy is passed in from the master app

[Mesh]
  [line]
    type = GeneratedMeshGenerator
    dim = 1
    nx = 4
    xmax = 2
  []
  [box]
    type = SubdomainBoundingBoxGenerator
    input = line
    bottom_left = '0 -0.1 -0.1'
    top_right = '1 0.1 0.1'
    # need a different block ID than what is in the master app to make sure the transfer works properly
    block_id = 20
  []
[]

[AuxVariables]
  [A]
    family = MONOMIAL
    order = CONSTANT
  []

  [S]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[AuxKernels]
  [A_ak]
    type = ParsedAux
    variable = A
    use_xyzt = true
    function = '2*x+4*${yy}'
    execute_on = 'TIMESTEP_BEGIN'
  []
[]

[Variables]
  [u]
  []
[]

[Kernels]
  [td]
    type = TimeDerivative
    variable = u
  []

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

[UserObjects]
  [A_avg]
    type = LayeredAverage
    block = 20
    num_layers = 2
    direction = x
    variable = A
    execute_on = TIMESTEP_END
  []
[]

[Executioner]
  type = Transient
[]

[Outputs]
  exodus = true
[]

(modules/tensor_mechanics/test/tests/action/material_output_order.i)

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
  origin = '0 0 2'
  direction = '0 0 1'
  polar_moment_of_inertia = pmi
  factor = t
[]

[Mesh]
  [ring]
    type = AnnularMeshGenerator
    nr = 1
    nt = 30
    rmin = 0.95
    rmax = 1
  []
  [extrude]
    type = MeshExtruderGenerator
    input = ring
    extrusion_vector = '0 0 2'
    bottom_sideset = 'bottom'
    top_sideset = 'top'
    num_layers = 5
  []
[]

[AuxVariables]
  [alpha_var]
  []
  [shear_stress_var]
    order = CONSTANT
    family = MONOMIAL
  []
[]

[AuxKernels]
  [alpha]
    type = RotationAngle
    variable = alpha_var
  []
  [shear_stress]
    type = ParsedAux
    variable = shear_stress_var
    args = 'stress_yz stress_xz'
    function = 'sqrt(stress_yz^2 + stress_xz^2)'
  []
[]

[BCs]
  # fix bottom
  [fix_x]
    type = DirichletBC
    boundary = bottom
    variable = disp_x
    value = 0
  []
  [fix_y]
    type = DirichletBC
    boundary = bottom
    variable = disp_y
    value = 0
  []
  [fix_z]
    type = DirichletBC
    boundary = bottom
    variable = disp_z
    value = 0
  []

  # twist top
  [twist_x]
    type = Torque
    boundary = top
    variable = disp_x
  []
  [twist_y]
    type = Torque
    boundary = top
    variable = disp_y
  []
  [twist_z]
    type = Torque
    boundary = top
    variable = disp_z
  []
[]

[Modules/TensorMechanics/Master]
  [all]
    add_variables = true
    strain = SMALL
    generate_output = 'vonmises_stress stress_yz stress_xz'
  []
[]

[Postprocessors]
  [pmi]
    type = PolarMomentOfInertia
    boundary = top
    # execute_on = 'INITIAL NONLINEAR'
    execute_on = 'INITIAL'
  []
  [alpha]
    type = SideAverageValue
    variable = alpha_var
    boundary = top
  []
  [shear_stress]
    type = ElementAverageValue
    variable = shear_stress_var
  []
[]

[Materials]
  [stress]
    type = ComputeLinearElasticStress
  []
  [elastic]
    type = ComputeIsotropicElasticityTensor
    youngs_modulus = 0.3
    shear_modulus = 100
  []
[]

[Executioner]
  # type = Steady
  type = Transient
  num_steps = 1
  solve_type = PJFNK
  petsc_options_iname = '-pctype'
  petsc_options_value = 'lu'
  nl_max_its = 150
[]

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

(modules/combined/examples/geochem-porous_flow/geotes_weber_tensleep/exchanger.i)

#########################################
#                                       #
# File written by create_input_files.py #
#                                       #
#########################################
# Model of the heat-exchanger
# The input fluid to the heat exchanger is determined by AuxVariables called production_temperature, production_rate_H, production_rate_Cl, production_rate_SO4, production_rate_HCO3, production_rate_SiO2aq, production_rate_Al, production_rate_Ca, production_rate_Mg, production_rate_Fe, production_rate_K, production_rate_Na, production_rate_Sr, production_rate_F, production_rate_BOH, production_rate_Br, production_rate_Ba, production_rate_Li, production_rate_NO3, production_rate_O2aq, production_rate_H2O.  These come from Postprocessors in the porous_flow.i simulation that measure the fluid composition at the production well.
# Given the input fluid, the exchanger cools/heats the fluid, removing any precipitates, and injects fluid back to porous_flow.i at temperature output_temperature and composition given by massfrac_H, etc.

[UserObjects]
  [definition]
    type = GeochemicalModelDefinition
    database_file = '../../../../geochemistry/database/moose_geochemdb.json'
    basis_species = 'H2O H+ Cl- SO4-- HCO3- SiO2(aq) Al+++ Ca++ Mg++ Fe++ K+ Na+ Sr++ F- B(OH)3 Br- Ba++ Li+ NO3- O2(aq)'
    equilibrium_minerals = 'Siderite Pyrrhotite Dolomite Illite Anhydrite Calcite Quartz K-feldspar Kaolinite Barite Celestite Fluorite Albite Chalcedony Goethite'
  []
[]

[TimeDependentReactionSolver]
  model_definition = definition
  include_moose_solve = false
  geochemistry_reactor_name = reactor
  swap_out_of_basis = 'NO3- O2(aq)'
  swap_into_basis = '  NH3  HS-'
  charge_balance_species = 'Cl-'
# initial conditions are unimportant because in exchanger mode all existing fluid is flushed from the system before adding the produced water
  constraint_species = 'H2O H+ Cl- SO4-- HCO3- SiO2(aq) Al+++ Ca++ Mg++ Fe++ K+ Na+ Sr++ F- B(OH)3 Br- Ba++ Li+ NH3 HS-'
  constraint_value = '1.0 1E-6 1E-6 1E-18 1E-18 1E-18    1E-18 1E-18 1E-18 1E-18 1E-18 1E-18 1E-18 1E-18 1E-18 1E-18 1E-18 1E-18 1E-18 1E-18'
  constraint_meaning = 'kg_solvent_water bulk_composition bulk_composition free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration free_concentration'
  constraint_unit = "kg moles moles molal molal molal molal molal molal molal molal molal molal molal molal molal molal molal molal molal"
  prevent_precipitation = 'Fluorite Albite Goethite'
  initial_temperature = 92
  mode = 4
  temperature = ramp_temperature # ramp up to 160degC over ~1 day so that aquifer geochemistry simulation can easily converge
  cold_temperature = 92
  heating_increments = 10
  source_species_names = ' H+ Cl- SO4-- HCO3- SiO2(aq) Al+++ Ca++ Mg++ Fe++ K+ Na+ Sr++ F- B(OH)3 Br- Ba++ Li+ NO3- O2(aq) H2O'
  source_species_rates = ' production_rate_H production_rate_Cl production_rate_SO4 production_rate_HCO3 production_rate_SiO2aq production_rate_Al production_rate_Ca production_rate_Mg production_rate_Fe production_rate_K production_rate_Na production_rate_Sr production_rate_F production_rate_BOH production_rate_Br production_rate_Ba production_rate_Li production_rate_NO3 production_rate_O2aq production_rate_H2O'
  ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
[]

[GlobalParams]
  point = '0 0 0'
  reactor = reactor
[]

[AuxVariables]
  [ramp_temperature]
    initial_condition = 92
  []
  [production_temperature]
    initial_condition = 92 # the production_T Transfer lags one timestep behind for some reason, so give this a reasonable initial condition
  []
  [transported_H]
  []
  [transported_Cl]
  []
  [transported_SO4]
  []
  [transported_HCO3]
  []
  [transported_SiO2aq]
  []
  [transported_Al]
  []
  [transported_Ca]
  []
  [transported_Mg]
  []
  [transported_Fe]
  []
  [transported_K]
  []
  [transported_Na]
  []
  [transported_Sr]
  []
  [transported_F]
  []
  [transported_BOH]
  []
  [transported_Br]
  []
  [transported_Ba]
  []
  [transported_Li]
  []
  [transported_NO3]
  []
  [transported_O2aq]
  []
  [transported_H2O]
  []
  [transported_mass]
  []
  [massfrac_H]
  []
  [massfrac_Cl]
  []
  [massfrac_SO4]
  []
  [massfrac_HCO3]
  []
  [massfrac_SiO2aq]
  []
  [massfrac_Al]
  []
  [massfrac_Ca]
  []
  [massfrac_Mg]
  []
  [massfrac_Fe]
  []
  [massfrac_K]
  []
  [massfrac_Na]
  []
  [massfrac_Sr]
  []
  [massfrac_F]
  []
  [massfrac_BOH]
  []
  [massfrac_Br]
  []
  [massfrac_Ba]
  []
  [massfrac_Li]
  []
  [massfrac_NO3]
  []
  [massfrac_O2aq]
  []
  [massfrac_H2O]
  []
  [dumped_Siderite]
  []
  [dumped_Pyrrhotite]
  []
  [dumped_Dolomite]
  []
  [dumped_Illite]
  []
  [dumped_Anhydrite]
  []
  [dumped_Calcite]
  []
  [dumped_Quartz]
  []
  [dumped_K-feldspar]
  []
  [dumped_Kaolinite]
  []
  [dumped_Barite]
  []
  [dumped_Celestite]
  []
  [dumped_Fluorite]
  []
  [dumped_Albite]
  []
  [dumped_Chalcedony]
  []
  [dumped_Goethite]
  []
# The production_* Transfers lag one timestep behind for some reason (when the porous_flow simulation has finished, it correctly computes mole_rate_*_produced, but the Transfer gets the mole_rate_*_produced from the previous timestep), so give the production_rate_* reasonable initial conditions, otherwise they will be zero at the start of the simulation.
  [production_rate_H]
    initial_condition = -0.00058596786807342
  []
  [production_rate_Cl]
    initial_condition = 0.274767413291287
  []
  [production_rate_SO4]
    initial_condition = 0.012567456786868922
  []
  [production_rate_HCO3]
    initial_condition = 0.0001668295857850308
  []
  [production_rate_SiO2aq]
    initial_condition = 0.00010068057668449495
  []
  [production_rate_Al]
    initial_condition = 2.4224219572143877e-07
  []
  [production_rate_Ca]
    initial_condition = 0.0040997718654983036
  []
  [production_rate_Mg]
    initial_condition = 0.00015261342984691217
  []
  [production_rate_Fe]
    initial_condition = 0.0001550375425863269
  []
  [production_rate_K]
    initial_condition = 0.0003500651859998926
  []
  [production_rate_Na]
    initial_condition = 0.2896767602995328
  []
  [production_rate_Sr]
    initial_condition = 2.915285700108879e-05
  []
  [production_rate_F]
    initial_condition = 5.8582680830041476e-05
  []
  [production_rate_BOH]
    initial_condition = 0.0012157199878760335
  []
  [production_rate_Br]
    initial_condition = 0.00022605948665165203
  []
  [production_rate_Ba]
    initial_condition = 2.2773554030672105e-07
  []
  [production_rate_Li]
    initial_condition = 0.0023920780265869763
  []
  [production_rate_NO3]
    initial_condition = 0.000353470613973057
  []
  [production_rate_O2aq]
    initial_condition = -0.00044255942331181803
  []
  [production_rate_H2O]
    initial_condition = 10.10458252764496
  []
[]

[AuxKernels]
  [ramp_temperature]
    type = FunctionAux
    variable = ramp_temperature
    function = 'min(160, max(92, 92 + (160 - 92) * t / 1E5))'
  []
  [transported_H_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_H
    species = 'H+'
  []
  [transported_Cl_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_Cl
    species = 'Cl-'
  []
  [transported_SO4_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_SO4
    species = 'SO4--'
  []
  [transported_HCO3_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_HCO3
    species = 'HCO3-'
  []
  [transported_SiO2aq_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_SiO2aq
    species = 'SiO2(aq)'
  []
  [transported_Al_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_Al
    species = 'Al+++'
  []
  [transported_Ca_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_Ca
    species = 'Ca++'
  []
  [transported_Mg_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_Mg
    species = 'Mg++'
  []
  [transported_Fe_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_Fe
    species = 'Fe++'
  []
  [transported_K_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_K
    species = 'K+'
  []
  [transported_Na_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_Na
    species = 'Na+'
  []
  [transported_Sr_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_Sr
    species = 'Sr++'
  []
  [transported_F_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_F
    species = 'F-'
  []
  [transported_BOH_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_BOH
    species = 'B(OH)3'
  []
  [transported_Br_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_Br
    species = 'Br-'
  []
  [transported_Ba_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_Ba
    species = 'Ba++'
  []
  [transported_Li_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_Li
    species = 'Li+'
  []
  [transported_NO3_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_NO3
    species = 'NO3-'
  []
  [transported_O2aq_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_O2aq
    species = 'O2(aq)'
  []
  [transported_H2O_auxk]
    type = GeochemistryQuantityAux
    quantity = transported_moles_in_original_basis
    variable = transported_H2O
    species = 'H2O'
  []
  [transported_mass_auxk]
    type = ParsedAux
    args = ' transported_H transported_Cl transported_SO4 transported_HCO3 transported_SiO2aq transported_Al transported_Ca transported_Mg transported_Fe transported_K transported_Na transported_Sr transported_F transported_BOH transported_Br transported_Ba transported_Li transported_NO3 transported_O2aq transported_H2O'
    variable = transported_mass
    function = ' transported_H * 1.0079 + transported_Cl * 35.453 + transported_SO4 * 96.0576 + transported_HCO3 * 61.0171 + transported_SiO2aq * 60.0843 + transported_Al * 26.9815 + transported_Ca * 40.08 + transported_Mg * 24.305 + transported_Fe * 55.847 + transported_K * 39.0983 + transported_Na * 22.9898 + transported_Sr * 87.62 + transported_F * 18.9984 + transported_BOH * 61.8329 + transported_Br * 79.904 + transported_Ba * 137.33 + transported_Li * 6.941 + transported_NO3 * 62.0049 + transported_O2aq * 31.9988 + transported_H2O * 18.01801802'
  []
  [massfrac_H_auxk]
    type = ParsedAux
    args = 'transported_mass transported_H'
    variable = massfrac_H
    function = '1.0079 * transported_H / transported_mass'
  []
  [massfrac_Cl_auxk]
    type = ParsedAux
    args = 'transported_mass transported_Cl'
    variable = massfrac_Cl
    function = '35.453 * transported_Cl / transported_mass'
  []
  [massfrac_SO4_auxk]
    type = ParsedAux
    args = 'transported_mass transported_SO4'
    variable = massfrac_SO4
    function = '96.0576 * transported_SO4 / transported_mass'
  []
  [massfrac_HCO3_auxk]
    type = ParsedAux
    args = 'transported_mass transported_HCO3'
    variable = massfrac_HCO3
    function = '61.0171 * transported_HCO3 / transported_mass'
  []
  [massfrac_SiO2aq_auxk]
    type = ParsedAux
    args = 'transported_mass transported_SiO2aq'
    variable = massfrac_SiO2aq
    function = '60.0843 * transported_SiO2aq / transported_mass'
  []
  [massfrac_Al_auxk]
    type = ParsedAux
    args = 'transported_mass transported_Al'
    variable = massfrac_Al
    function = '26.9815 * transported_Al / transported_mass'
  []
  [massfrac_Ca_auxk]
    type = ParsedAux
    args = 'transported_mass transported_Ca'
    variable = massfrac_Ca
    function = '40.08 * transported_Ca / transported_mass'
  []
  [massfrac_Mg_auxk]
    type = ParsedAux
    args = 'transported_mass transported_Mg'
    variable = massfrac_Mg
    function = '24.305 * transported_Mg / transported_mass'
  []
  [massfrac_Fe_auxk]
    type = ParsedAux
    args = 'transported_mass transported_Fe'
    variable = massfrac_Fe
    function = '55.847 * transported_Fe / transported_mass'
  []
  [massfrac_K_auxk]
    type = ParsedAux
    args = 'transported_mass transported_K'
    variable = massfrac_K
    function = '39.0983 * transported_K / transported_mass'
  []
  [massfrac_Na_auxk]
    type = ParsedAux
    args = 'transported_mass transported_Na'
    variable = massfrac_Na
    function = '22.9898 * transported_Na / transported_mass'
  []
  [massfrac_Sr_auxk]
    type = ParsedAux
    args = 'transported_mass transported_Sr'
    variable = massfrac_Sr
    function = '87.62 * transported_Sr / transported_mass'
  []
  [massfrac_F_auxk]
    type = ParsedAux
    args = 'transported_mass transported_F'
    variable = massfrac_F
    function = '18.9984 * transported_F / transported_mass'
  []
  [massfrac_BOH_auxk]
    type = ParsedAux
    args = 'transported_mass transported_BOH'
    variable = massfrac_BOH
    function = '61.8329 * transported_BOH / transported_mass'
  []
  [massfrac_Br_auxk]
    type = ParsedAux
    args = 'transported_mass transported_Br'
    variable = massfrac_Br
    function = '79.904 * transported_Br / transported_mass'
  []
  [massfrac_Ba_auxk]
    type = ParsedAux
    args = 'transported_mass transported_Ba'
    variable = massfrac_Ba
    function = '137.33 * transported_Ba / transported_mass'
  []
  [massfrac_Li_auxk]
    type = ParsedAux
    args = 'transported_mass transported_Li'
    variable = massfrac_Li
    function = '6.941 * transported_Li / transported_mass'
  []
  [massfrac_NO3_auxk]
    type = ParsedAux
    args = 'transported_mass transported_NO3'
    variable = massfrac_NO3
    function = '62.0049 * transported_NO3 / transported_mass'
  []
  [massfrac_O2aq_auxk]
    type = ParsedAux
    args = 'transported_mass transported_O2aq'
    variable = massfrac_O2aq
    function = '31.9988 * transported_O2aq / transported_mass'
  []
  [massfrac_H2O_auxk]
    type = ParsedAux
    args = 'transported_mass transported_H2O'
    variable = massfrac_H2O
    function = '18.01801802 * transported_H2O / transported_mass'
  []
  [dumped_Siderite_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_Siderite
    species = Siderite
    quantity = moles_dumped
  []
  [dumped_Pyrrhotite_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_Pyrrhotite
    species = Pyrrhotite
    quantity = moles_dumped
  []
  [dumped_Dolomite_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_Dolomite
    species = Dolomite
    quantity = moles_dumped
  []
  [dumped_Illite_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_Illite
    species = Illite
    quantity = moles_dumped
  []
  [dumped_Anhydrite_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_Anhydrite
    species = Anhydrite
    quantity = moles_dumped
  []
  [dumped_Calcite_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_Calcite
    species = Calcite
    quantity = moles_dumped
  []
  [dumped_Quartz_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_Quartz
    species = Quartz
    quantity = moles_dumped
  []
  [dumped_K-feldspar_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_K-feldspar
    species = K-feldspar
    quantity = moles_dumped
  []
  [dumped_Kaolinite_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_Kaolinite
    species = Kaolinite
    quantity = moles_dumped
  []
  [dumped_Barite_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_Barite
    species = Barite
    quantity = moles_dumped
  []
  [dumped_Celestite_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_Celestite
    species = Celestite
    quantity = moles_dumped
  []
  [dumped_Fluorite_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_Fluorite
    species = Fluorite
    quantity = moles_dumped
  []
  [dumped_Albite_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_Albite
    species = Albite
    quantity = moles_dumped
  []
  [dumped_Chalcedony_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_Chalcedony
    species = Chalcedony
    quantity = moles_dumped
  []
  [dumped_Goethite_auxk]
    type = GeochemistryQuantityAux
    variable = dumped_Goethite
    species = Goethite
    quantity = moles_dumped
  []
[]

[Postprocessors]
  [cumulative_moles_precipitated_Siderite]
    type = PointValue
    variable = dumped_Siderite
  []
  [cumulative_moles_precipitated_Pyrrhotite]
    type = PointValue
    variable = dumped_Pyrrhotite
  []
  [cumulative_moles_precipitated_Dolomite]
    type = PointValue
    variable = dumped_Dolomite
  []
  [cumulative_moles_precipitated_Illite]
    type = PointValue
    variable = dumped_Illite
  []
  [cumulative_moles_precipitated_Anhydrite]
    type = PointValue
    variable = dumped_Anhydrite
  []
  [cumulative_moles_precipitated_Calcite]
    type = PointValue
    variable = dumped_Calcite
  []
  [cumulative_moles_precipitated_Quartz]
    type = PointValue
    variable = dumped_Quartz
  []
  [cumulative_moles_precipitated_K-feldspar]
    type = PointValue
    variable = dumped_K-feldspar
  []
  [cumulative_moles_precipitated_Kaolinite]
    type = PointValue
    variable = dumped_Kaolinite
  []
  [cumulative_moles_precipitated_Barite]
    type = PointValue
    variable = dumped_Barite
  []
  [cumulative_moles_precipitated_Celestite]
    type = PointValue
    variable = dumped_Celestite
  []
  [cumulative_moles_precipitated_Fluorite]
    type = PointValue
    variable = dumped_Fluorite
  []
  [cumulative_moles_precipitated_Albite]
    type = PointValue
    variable = dumped_Albite
  []
  [cumulative_moles_precipitated_Chalcedony]
    type = PointValue
    variable = dumped_Chalcedony
  []
  [cumulative_moles_precipitated_Goethite]
    type = PointValue
    variable = dumped_Goethite
  []
  [production_temperature]
    type = PointValue
    variable = production_temperature
  []
  [mass_heated_this_timestep]
    type = PointValue
    variable = transported_mass
  []
[]

[Outputs]
  csv = true
[]

[Executioner]
  type = Transient
  solve_type = Newton
  end_time = 7.76E6 # 90 days
  [TimeStepper]
    type = FunctionDT
    function = 'min(3E4, max(1E4, 0.2 * t))'
  []
[]

[MultiApps]
  [porous_flow_sim]
    type = TransientMultiApp
    input_files = porous_flow.i
    execute_on = 'timestep_end'
  []
[]

[Transfers]
  [injection_T]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'solution_temperature'
    variable = 'injection_temperature'
  []
  [injection_H]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_H'
    variable = 'injection_rate_massfrac_H'
  []
  [injection_Cl]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_Cl'
    variable = 'injection_rate_massfrac_Cl'
  []
  [injection_SO4]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_SO4'
    variable = 'injection_rate_massfrac_SO4'
  []
  [injection_HCO3]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_HCO3'
    variable = 'injection_rate_massfrac_HCO3'
  []
  [injection_SiO2aq]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_SiO2aq'
    variable = 'injection_rate_massfrac_SiO2aq'
  []
  [injection_Al]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_Al'
    variable = 'injection_rate_massfrac_Al'
  []
  [injection_Ca]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_Ca'
    variable = 'injection_rate_massfrac_Ca'
  []
  [injection_Mg]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_Mg'
    variable = 'injection_rate_massfrac_Mg'
  []
  [injection_Fe]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_Fe'
    variable = 'injection_rate_massfrac_Fe'
  []
  [injection_K]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_K'
    variable = 'injection_rate_massfrac_K'
  []
  [injection_Na]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_Na'
    variable = 'injection_rate_massfrac_Na'
  []
  [injection_Sr]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_Sr'
    variable = 'injection_rate_massfrac_Sr'
  []
  [injection_F]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_F'
    variable = 'injection_rate_massfrac_F'
  []
  [injection_BOH]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_BOH'
    variable = 'injection_rate_massfrac_BOH'
  []
  [injection_Br]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_Br'
    variable = 'injection_rate_massfrac_Br'
  []
  [injection_Ba]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_Ba'
    variable = 'injection_rate_massfrac_Ba'
  []
  [injection_Li]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_Li'
    variable = 'injection_rate_massfrac_Li'
  []
  [injection_NO3]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_NO3'
    variable = 'injection_rate_massfrac_NO3'
  []
  [injection_O2aq]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_O2aq'
    variable = 'injection_rate_massfrac_O2aq'
  []
  [injection_H2O]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_H2O'
    variable = 'injection_rate_massfrac_H2O'
  []

  [production_T]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = production_temperature
    variable = production_temperature
  []
  [production_H]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_H_produced
    variable = production_rate_H
  []
  [production_Cl]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_Cl_produced
    variable = production_rate_Cl
  []
  [production_SO4]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_SO4_produced
    variable = production_rate_SO4
  []
  [production_HCO3]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_HCO3_produced
    variable = production_rate_HCO3
  []
  [production_SiO2aq]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_SiO2aq_produced
    variable = production_rate_SiO2aq
  []
  [production_Al]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_Al_produced
    variable = production_rate_Al
  []
  [production_Ca]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_Ca_produced
    variable = production_rate_Ca
  []
  [production_Mg]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_Mg_produced
    variable = production_rate_Mg
  []
  [production_Fe]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_Fe_produced
    variable = production_rate_Fe
  []
  [production_K]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_K_produced
    variable = production_rate_K
  []
  [production_Na]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_Na_produced
    variable = production_rate_Na
  []
  [production_Sr]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_Sr_produced
    variable = production_rate_Sr
  []
  [production_F]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_F_produced
    variable = production_rate_F
  []
  [production_BOH]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_BOH_produced
    variable = production_rate_BOH
  []
  [production_Br]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_Br_produced
    variable = production_rate_Br
  []
  [production_Ba]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_Ba_produced
    variable = production_rate_Ba
  []
  [production_Li]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_Li_produced
    variable = production_rate_Li
  []
  [production_NO3]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_NO3_produced
    variable = production_rate_NO3
  []
  [production_O2aq]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_O2aq_produced
    variable = production_rate_O2aq
  []
  [production_H2O]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_H2O_produced
    variable = production_rate_H2O
  []
[]

(modules/combined/examples/geochem-porous_flow/geotes_2D/exchanger_un_quartz.i)

# Model of the heat-exchanger
# The input fluid to the heat exchanger is determined by AuxVariables called production_temperature, production_rate_Na, production_rate_Cl, production_rate_SiO2 and production_rate_H2O.  These come from Postprocessors in the porous-flow simulation that measure the fluid composition at the production well.
# Given the input fluid, the exchanger cools/heats the fluid, removing any precipitates, and injects fluid back to the porous-flow simulation at temperature output_temperature and composition given by massfrac_Na, etc.
# In the absence of data concerning Quartz precipitation rates in heat exchangers, do not treat Quartz as kinetic
[GlobalParams]
  point = '0 0 0'
  reactor = reactor
[]

[TimeDependentReactionSolver]
  model_definition = definition
  include_moose_solve = false
  geochemistry_reactor_name = reactor
  charge_balance_species = "Cl-"
  swap_out_of_basis = "SiO2(aq)"
  swap_into_basis = "QuartzUnlike"
  constraint_species = "H2O              Na+                Cl-                QuartzUnlike"
  constraint_value = "  1.0E-2           0.1E-2             0.1E-2             1E-10"
  constraint_meaning = "kg_solvent_water bulk_composition bulk_composition free_mineral"
  constraint_unit = "   kg               moles              moles              moles"
  initial_temperature = 50.0
  mode = 4
  temperature = 200
  cold_temperature = 40.0
  source_species_names = 'H2O    Na+   Cl-   SiO2(aq)'
  source_species_rates = 'production_rate_H2O production_rate_Na production_rate_Cl production_rate_SiO2'
  ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
  add_aux_pH = false # there is no H+ in this system
  evaluate_kinetic_rates_always = true # implicit time-marching used for stability
  execute_console_output_on = '' # only CSV output used in this example
[]

[UserObjects]
  [definition]
    type = GeochemicalModelDefinition
    database_file = "small_database.json"
    basis_species = "H2O SiO2(aq) Na+ Cl-"
    equilibrium_minerals = "QuartzUnlike"
  []
[]


[Executioner]
  type = Transient
  dt = 1E5
  end_time = 2E6 #7.76E6 # 90 days
[]

[AuxVariables]
  [production_temperature]
    initial_condition = 50 # the production_T Transfer lags one timestep behind for some reason, so give this a reasonable initial condition
  []
  [transported_H2O]
  []
  [transported_Na]
  []
  [transported_Cl]
  []
  [transported_SiO2]
  []
  [transported_mass]
  []
  [massfrac_H2O]
  []
  [massfrac_Na]
  []
  [massfrac_Cl]
  []
  [massfrac_SiO2]
  []
  [dumped_quartz]
  []
  [production_rate_H2O]
    initial_condition = 5.518533e+01 # the production_H2O Transfer lags one timestep behind for some reason (when the porous_flow simulation has finished, it correctly computes mole_rate_H2O_produced, but the Transfer gets the mole_rate_H2O_produced from the previous timestep), so give this a reasonable initial condition, otherwise this will be zero at the start of the simulation!
  []
  [production_rate_Na]
    initial_condition = 9.943302e-02
  []
  [production_rate_Cl]
    initial_condition = 9.943302e-02
  []
  [production_rate_SiO2]
    initial_condition = 2.340931e-04
  []
[]
[AuxKernels]
  [transported_H2O]
    type = GeochemistryQuantityAux
    variable = transported_H2O
    species = H2O
    quantity = transported_moles_in_original_basis
  []
  [transported_Na]
    type = GeochemistryQuantityAux
    variable = transported_Na
    species = Na+
    quantity = transported_moles_in_original_basis
  []
  [transported_Cl]
    type = GeochemistryQuantityAux
    variable = transported_Cl
    species = Cl-
    quantity = transported_moles_in_original_basis
  []
  [transported_SiO2]
    type = GeochemistryQuantityAux
    variable = transported_SiO2
    species = 'SiO2(aq)'
    quantity = transported_moles_in_original_basis
  []
  [transported_mass]
    type = ParsedAux
    args = 'transported_H2O transported_Na transported_Cl transported_SiO2'
    variable = transported_mass
    function = 'transported_H2O * 18.0152 + transported_Na * 22.9898 + transported_Cl * 35.453 + transported_SiO2 * 60.0843'
  []
  [massfrac_H2O]
    type = ParsedAux
    args = 'transported_mass transported_H2O'
    variable = massfrac_H2O
    function = '18.0152 * transported_H2O / transported_mass'
  []
  [massfrac_Na]
    type = ParsedAux
    args = 'transported_mass transported_Na'
    variable = massfrac_Na
    function = '22.9898 * transported_Na / transported_mass'
  []
  [massfrac_Cl]
    type = ParsedAux
    args = 'transported_mass transported_Cl'
    variable = massfrac_Cl
    function = '35.453 * transported_Cl / transported_mass'
  []
  [massfrac_SiO2]
    type = ParsedAux
    args = 'transported_mass transported_SiO2'
    variable = massfrac_SiO2
    function = '60.0843 * transported_SiO2 / transported_mass'
  []
  [dumped_quartz]
    type = GeochemistryQuantityAux
    variable = dumped_quartz
    species = QuartzUnlike
    quantity = moles_dumped
  []
[]
[Postprocessors]
  [cumulative_moles_precipitated_quartz]
    type = PointValue
    variable = dumped_quartz
  []
  [production_temperature]
    type = PointValue
    variable = production_temperature
  []
  [mass_heated_this_timestep]
    type = PointValue
    variable = transported_mass
  []
[]
[Outputs]
  csv = true
[]

[MultiApps]
  [porous_flow_sim]
    type = TransientMultiApp
    input_files = porous_flow.i
    cli_args = 'MultiApps/react/input_files=aquifer_un_quartz_geochemistry.i'
    execute_on = 'timestep_end'
  []
[]

[Transfers]
  [injection_T]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'solution_temperature'
    variable = 'injection_temperature'
  []
  [injection_Na]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_Na'
    variable = 'injection_rate_massfrac_Na'
  []
  [injection_Cl]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_Cl'
    variable = 'injection_rate_massfrac_Cl'
  []
  [injection_SiO2]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_SiO2'
    variable = 'injection_rate_massfrac_SiO2'
  []
  [injection_H2O]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_H2O'
    variable = 'injection_rate_massfrac_H2O'
  []

  [production_T]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = production_temperature
    variable = production_temperature
  []
  [production_Na]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_Na_produced
    variable = production_rate_Na
  []
  [production_Cl]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_Cl_produced
    variable = production_rate_Cl
  []
  [production_SiO2]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_SiO2_produced
    variable = production_rate_SiO2
  []
  [production_H2O]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_H2O_produced
    variable = production_rate_H2O
  []
[]

(modules/porous_flow/test/tests/pressure_pulse/pressure_pulse_1d_MD.i)

# Pressure pulse in 1D with 1 phase - transient
# Using the "MD" formulation (where primary variable is log(mass-density
[Mesh]
  type = GeneratedMesh
  dim = 1
  nx = 10
  xmin = 0
  xmax = 100
[]

[GlobalParams]
  PorousFlowDictator = dictator
[]

[Variables]
  [md]
    # initial porepressure = 2E6
    # so initial md = log(density_P0) + porepressure/bulk_modulus =
    initial_condition = 6.90875527898214
  []
[]

[Kernels]
  [mass0]
    type = PorousFlowMassTimeDerivative
    fluid_component = 0
    variable = md
  []
  [flux]
    type = PorousFlowAdvectiveFlux
    variable = md
    gravity = '0 0 0'
    fluid_component = 0
  []
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = 'md'
    number_fluid_phases = 1
    number_fluid_components = 1
  []
[]

[Modules]
  [FluidProperties]
    [simple_fluid]
      type = SimpleFluidProperties
      bulk_modulus = 2e9
      density0 = 1000
      thermal_expansion = 0
      viscosity = 1e-3
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
  []
  [ppss]
    type = PorousFlow1PhaseMD_Gaussian
    mass_density = md
    al = 1E-6 # this is irrelevant in this example
    density_P0 = 1000
    bulk_modulus = 2E9
  []
  [massfrac]
    type = PorousFlowMassFraction
  []
  [simple_fluid]
    type = PorousFlowSingleComponentFluid
    fp = simple_fluid
    phase = 0
  []
  [porosity]
    type = PorousFlowPorosityConst
    porosity = 0.1
  []
  [permeability]
    type = PorousFlowPermeabilityConst
    permeability = '1E-15 0 0 0 1E-15 0 0 0 1E-15'
  []
  [relperm]
    type = PorousFlowRelativePermeabilityCorey
    n = 0
    phase = 0
  []
[]

[BCs]
  [left]
    type = DirichletBC
    boundary = left
    # BC porepressure = 3E6
    # so boundary md = log(density_P0) + porepressure/bulk_modulus =
    value = 6.90925527898214
    variable = md
  []
[]

[Preconditioning]
  [andy]
    type = SMP
    full = true
  []
[]

[Executioner]
  type = Transient
  solve_type = Newton
  dt = 1E3
  end_time = 1E4
[]

[AuxVariables]
  [pp]
  []
[]

[AuxKernels]
  [pp]
    type = ParsedAux
    function = '(md-6.9077552789821)*2.0E9'
    args = 'md'
    variable = pp
  []
[]


[Postprocessors]
  [p000]
    type = PointValue
    variable = pp
    point = '0 0 0'
    execute_on = 'initial timestep_end'
  []
  [p010]
    type = PointValue
    variable = pp
    point = '10 0 0'
    execute_on = 'initial timestep_end'
  []
  [p020]
    type = PointValue
    variable = pp
    point = '20 0 0'
    execute_on = 'initial timestep_end'
  []
  [p030]
    type = PointValue
    variable = pp
    point = '30 0 0'
    execute_on = 'initial timestep_end'
  []
  [p040]
    type = PointValue
    variable = pp
    point = '40 0 0'
    execute_on = 'initial timestep_end'
  []
  [p050]
    type = PointValue
    variable = pp
    point = '50 0 0'
    execute_on = 'initial timestep_end'
  []
  [p060]
    type = PointValue
    variable = pp
    point = '60 0 0'
    execute_on = 'initial timestep_end'
  []
  [p070]
    type = PointValue
    variable = pp
    point = '70 0 0'
    execute_on = 'initial timestep_end'
  []
  [p080]
    type = PointValue
    variable = pp
    point = '80 0 0'
    execute_on = 'initial timestep_end'
  []
  [p090]
    type = PointValue
    variable = pp
    point = '90 0 0'
    execute_on = 'initial timestep_end'
  []
  [p100]
    type = PointValue
    variable = pp
    point = '100 0 0'
    execute_on = 'initial timestep_end'
  []
[]

[Outputs]
  file_base = pressure_pulse_1d_MD
  print_linear_residuals = false
  csv = true
[]

(modules/tensor_mechanics/test/tests/notched_plastic_block/biaxial_planar.i)

# Uses non-smoothed Mohr-Coulomb (via ComputeMultiPlasticityStress and TensorMechanicsPlasticMohrCoulombMulti) to simulate the following problem.
# A cubical block is notched around its equator.
# All of its outer surfaces have roller BCs, but the notched region is free to move as needed
# The block is initialised with a high hydrostatic tensile stress
# Without the notch, the BCs do not allow contraction of the block, and this stress configuration is admissible
# With the notch, however, the interior parts of the block are free to move in order to relieve stress, and this causes plastic failure
# The top surface is then pulled upwards (the bottom is fixed because of the roller BCs)
# This causes more failure
[Mesh]
  [generated_mesh]
    type = GeneratedMeshGenerator
    dim = 3
    nx = 9
    ny = 9
    nz = 9
    xmin = 0
    xmax = 0.1
    ymin = 0
    ymax = 0.1
    zmin = 0
    zmax = 0.1
  []
  [block_to_remove_xmin]
    type = SubdomainBoundingBoxGenerator
    bottom_left = '-0.01 -0.01 0.045'
    top_right = '0.01 0.11 0.055'
    location = INSIDE
    block_id = 1
    input = generated_mesh
  []
  [block_to_remove_xmax]
    type = SubdomainBoundingBoxGenerator
    bottom_left = '0.09 -0.01 0.045'
    top_right = '0.11 0.11 0.055'
    location = INSIDE
    block_id = 1
    input = block_to_remove_xmin
  []
  [block_to_remove_ymin]
    type = SubdomainBoundingBoxGenerator
    bottom_left = '-0.01 -0.01 0.045'
    top_right = '0.11 0.01 0.055'
    location = INSIDE
    block_id = 1
    input = block_to_remove_xmax
  []
  [block_to_remove_ymax]
    type = SubdomainBoundingBoxGenerator
    bottom_left = '-0.01 0.09 0.045'
    top_right = '0.11 0.11 0.055'
    location = INSIDE
    block_id = 1
    input = block_to_remove_ymin
  []
  [remove_block]
    type = BlockDeletionGenerator
    block = 1
    input = block_to_remove_ymax
  []
[]

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
[]

[Modules/TensorMechanics/Master]
  [./all]
    add_variables = true
    incremental = true
    generate_output = 'max_principal_stress mid_principal_stress min_principal_stress stress_zz'
    eigenstrain_names = ini_stress
  [../]
[]

[Postprocessors]
  [./uz]
    type = PointValue
    point = '0 0 0.1'
    use_displaced_mesh = false
    variable = disp_z
  [../]
  [./s_zz]
    type = ElementAverageValue
    use_displaced_mesh = false
    variable = stress_zz
  [../]
  [./num_res]
    type = NumResidualEvaluations
  [../]
  [./nr_its]
    type = ElementAverageValue
    variable = num_iters
  [../]
  [./max_nr_its]
    type = ElementExtremeValue
    variable = num_iters
  [../]
  [./runtime]
    type = PerfGraphData
    data_type = TOTAL
    section_name = 'Root'
  [../]
[]

[BCs]
  # back=zmin, front=zmax, bottom=ymin, top=ymax, left=xmin, right=xmax
  [./xmin_xzero]
    type = DirichletBC
    variable = disp_x
    boundary = left
    value = 0.0
  [../]
  [./xmax_xzero]
    type = DirichletBC
    variable = disp_x
    boundary = right
    value = 0.0
  [../]
  [./ymin_yzero]
    type = DirichletBC
    variable = disp_y
    boundary = bottom
    value = 0.0
  [../]
  [./ymax_yzero]
    type = DirichletBC
    variable = disp_y
    boundary = top
    value = 0.0
  [../]
  [./zmin_zzero]
    type = DirichletBC
    variable = disp_z
    boundary = back
    value = '0'
  [../]
  [./zmax_disp]
    type = FunctionDirichletBC
    variable = disp_z
    boundary = front
    function = '1E-6*max(t,0)'
  [../]
[]

[AuxVariables]
  [./mc_int]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./plastic_strain]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./num_iters]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./yield_fcn]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

[AuxKernels]
  [./mc_int_auxk]
    type = MaterialStdVectorAux
    index = 0
    property = plastic_internal_parameter
    variable = mc_int
  [../]
  [./plastic_strain_aux]
    type = MaterialRankTwoTensorAux
    i = 2
    j = 2
    property = plastic_strain
    variable = plastic_strain
  [../]
  [./num_iters_auxk] # cannot use plastic_NR_iterations directly as this is zero, since no NR iterations are actually used, since we use a custom algorithm to do the return
    type = ParsedAux
    args = plastic_strain
    function = 'if(plastic_strain>0,1,0)'
    variable = num_iters
  [../]
  [./yield_fcn_auxk]
    type = MaterialStdVectorAux
    index = 0
    property = plastic_yield_function
    variable = yield_fcn
  [../]
[]

[UserObjects]
  [./mc_coh]
    type = TensorMechanicsHardeningConstant
    value = 5E6
  [../]
  [./mc_phi]
    type = TensorMechanicsHardeningConstant
    value = 35
    convert_to_radians = true
  [../]
  [./mc_psi]
    type = TensorMechanicsHardeningConstant
    value = 10
    convert_to_radians = true
  [../]
  [./mc]
    type = TensorMechanicsPlasticMohrCoulombMulti
    cohesion = mc_coh
    friction_angle = mc_phi
    dilation_angle = mc_psi
    yield_function_tolerance = 1E-5
    internal_constraint_tolerance = 1E-11
  [../]
[]

[Materials]
  [./elasticity_tensor]
    type = ComputeIsotropicElasticityTensor
    youngs_modulus = 16E9
    poissons_ratio = 0.25
  [../]
  [./mc]
    type = ComputeMultiPlasticityStress
    ep_plastic_tolerance = 1E-11
    plastic_models = mc
    max_NR_iterations = 1000
    debug_fspb = crash
  [../]
  [./strain_from_initial_stress]
    type = ComputeEigenstrainFromInitialStress
    initial_stress = '6E6 0 0  0 6E6 0  0 0 6E6'
    eigenstrain_name = ini_stress
  [../]
[]

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

[Executioner]
  start_time = -1
  end_time = 10
  dt = 1
  solve_type = NEWTON
  type = Transient

  l_tol = 1E-2
  nl_abs_tol = 1E-5
  nl_rel_tol = 1E-7
  l_max_its = 200
  nl_max_its = 400

  petsc_options_iname = '-pc_type -pc_asm_overlap -sub_pc_type -ksp_type -ksp_gmres_restart'
  petsc_options_value = ' asm      2              lu            gmres     200'
[]


[Outputs]
  file_base = biaxial_planar
  perf_graph = true
  exodus = false
  csv = true
[]

(modules/tensor_mechanics/test/tests/torque/ad_torque_small.i)

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
  origin = '0 0 2'
  direction = '0 0 1'
  polar_moment_of_inertia = pmi
  factor = t
[]

[Mesh]
  [ring]
    type = AnnularMeshGenerator
    nr = 1
    nt = 30
    rmin = 0.95
    rmax = 1
  []
  [extrude]
    type = MeshExtruderGenerator
    input = ring
    extrusion_vector = '0 0 2'
    bottom_sideset = 'bottom'
    top_sideset = 'top'
    num_layers = 5
  []
[]

[AuxVariables]
  [alpha_var]
  []
  [shear_stress_var]
    order = CONSTANT
    family = MONOMIAL
  []
[]

[AuxKernels]
  [alpha]
    type = RotationAngle
    variable = alpha_var
  []
  [shear_stress]
    type = ParsedAux
    variable = shear_stress_var
    args = 'stress_yz stress_xz'
    function = 'sqrt(stress_yz^2 + stress_xz^2)'
  []
[]

[BCs]
  # fix bottom
  [fix_x]
    type = DirichletBC
    boundary = bottom
    variable = disp_x
    value = 0
  []
  [fix_y]
    type = DirichletBC
    boundary = bottom
    variable = disp_y
    value = 0
  []
  [fix_z]
    type = DirichletBC
    boundary = bottom
    variable = disp_z
    value = 0
  []

  # twist top
  [twist_x]
    type = ADTorque
    boundary = top
    variable = disp_x
  []
  [twist_y]
    type = ADTorque
    boundary = top
    variable = disp_y
  []
  [twist_z]
    type = ADTorque
    boundary = top
    variable = disp_z
  []
[]

[Modules/TensorMechanics/Master]
  [all]
    add_variables = true
    strain = SMALL
    use_automatic_differentiation = true
    generate_output = 'vonmises_stress stress_yz stress_xz'
  []
[]

[Postprocessors]
  [pmi]
    type = PolarMomentOfInertia
    boundary = top
    # execute_on = 'INITIAL NONLINEAR'
    execute_on = 'INITIAL'
  []
  [alpha]
    type = SideAverageValue
    variable = alpha_var
    boundary = top
  []
  [shear_stress]
    type = ElementAverageValue
    variable = shear_stress_var
  []
[]

[Materials]
  [stress]
    type = ADComputeLinearElasticStress
  []
  [elastic]
    type = ADComputeIsotropicElasticityTensor
    youngs_modulus = 0.3
    shear_modulus = 100
  []
[]

[Executioner]
  # type = Steady
  type = Transient
  num_steps = 1
  solve_type = NEWTON
  petsc_options_iname = '-pctype'
  petsc_options_value = 'lu'
  nl_max_its = 150
[]

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

(modules/porous_flow/test/tests/poro_elasticity/mandel_basicthm.i)

# using a BasicTHM Action
#
# Mandel's problem of consolodation of a drained medium
# Using the FullySaturatedDarcyBase and FullySaturatedFullySaturatedMassTimeDerivative kernels
# with multiply_by_density = false, so that this problem becomes linear
# Note the use of consistent_with_displaced_mesh = false in the calculation of volumetric strain
#
# A sample is in plane strain.
# -a <= x <= a
# -b <= y <= b
# It is squashed with constant force by impermeable, frictionless plattens on its top and bottom surfaces (at y=+/-b)
# Fluid is allowed to leak out from its sides (at x=+/-a)
# The porepressure within the sample is monitored.
#
# As is common in the literature, this is simulated by
# considering the quarter-sample, 0<=x<=a and 0<=y<=b, with
# impermeable, roller BCs at x=0 and y=0 and y=b.
# Porepressure is fixed at zero on x=a.
# Porepressure and displacement are initialised to zero.
# Then the top (y=b) is moved downwards with prescribed velocity,
# so that the total force that is inducing this downwards velocity
# is fixed.  The velocity is worked out by solving Mandel's problem
# analytically, and the total force is monitored in the simulation
# to check that it indeed remains constant.
#
# Here are the problem's parameters, and their values:
# Soil width.  a = 1
# Soil height.  b = 0.1
# Soil's Lame lambda.  la = 0.5
# Soil's Lame mu, which is also the Soil's shear modulus.  mu = G = 0.75
# Soil bulk modulus.  K = la + 2*mu/3 = 1
# Drained Poisson ratio.  nu = (3K - 2G)/(6K + 2G) = 0.2
# Soil bulk compliance.  1/K = 1
# Fluid bulk modulus.  Kf = 8
# Fluid bulk compliance.  1/Kf = 0.125
# Soil initial porosity.  phi0 = 0.1
# Biot coefficient.  alpha = 0.6
# Biot modulus.  M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 4.705882
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.694118
# Undrained Poisson ratio.  nuu = (3Ku - 2G)/(6Ku + 2G) = 0.372627
# Skempton coefficient.  B = alpha*M/Ku = 1.048035
# Fluid mobility (soil permeability/fluid viscosity).  k = 1.5
# Consolidation coefficient.  c = 2*k*B^2*G*(1-nu)*(1+nuu)^2/9/(1-nuu)/(nuu-nu) = 3.821656
# Normal stress on top.  F = 1
#
# The solution for porepressure and displacements is given in
# AHD Cheng and E Detournay "A direct boundary element method for plane strain poroelasticity" International Journal of Numerical and Analytical Methods in Geomechanics 12 (1988) 551-572.
# The solution involves complicated infinite series, so I shall not write it here

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

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
  PorousFlowDictator = dictator
  block = 0
[]

[Variables]
  [disp_x]
  []
  [disp_y]
  []
  [disp_z]
  []
  [porepressure]
  []
[]

[BCs]
  [roller_xmin]
    type = DirichletBC
    variable = disp_x
    value = 0
    boundary = 'left'
  []
  [roller_ymin]
    type = DirichletBC
    variable = disp_y
    value = 0
    boundary = 'bottom'
  []
  [plane_strain]
    type = DirichletBC
    variable = disp_z
    value = 0
    boundary = 'back front'
  []
  [xmax_drained]
    type = DirichletBC
    variable = porepressure
    value = 0
    boundary = right
  []
  [top_velocity]
    type = FunctionDirichletBC
    variable = disp_y
    function = top_velocity
    boundary = top
  []
[]

[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'
  []
[]

[AuxVariables]
  [tot_force]
    order = CONSTANT
    family = MONOMIAL
  []
[]

[AuxKernels]
  [tot_force]
    type = ParsedAux
    args = 'stress_yy porepressure'
    execute_on = timestep_end
    variable = tot_force
    function = '-stress_yy+0.6*porepressure'
  []
[]

[Modules]
  [FluidProperties]
    [the_simple_fluid]
      type = SimpleFluidProperties
      thermal_expansion = 0.0
      bulk_modulus = 8.0
      viscosity = 1.0
      density0 = 1.0
    []
  []
[]

[PorousFlowBasicTHM]
  coupling_type = HydroMechanical
  displacements = 'disp_x disp_y disp_z'
  multiply_by_density = false
  porepressure = porepressure
  biot_coefficient = 0.6
  gravity = '0 0 0'
  fp = the_simple_fluid
[]

[Materials]
  [elasticity_tensor]
    type = ComputeElasticityTensor
    C_ijkl = '0.5 0.75'
    # bulk modulus is lambda + 2*mu/3 = 0.5 + 2*0.75/3 = 1
    fill_method = symmetric_isotropic
  []
  [strain]
    type = ComputeSmallStrain
  []
  [stress]
    type = ComputeLinearElasticStress
  []
  [porosity]
    type = PorousFlowPorosityConst # only the initial value of this is ever used
    porosity = 0.1
  []
  [biot_modulus]
    type = PorousFlowConstantBiotModulus
    biot_coefficient = 0.6
    solid_bulk_compliance = 1
    fluid_bulk_modulus = 8
  []
  [permeability]
    type = PorousFlowPermeabilityConst
    permeability = '1.5 0 0   0 1.5 0   0 0 1.5'
  []
[]

[Postprocessors]
  [p0]
    type = PointValue
    outputs = csv
    point = '0.0 0 0'
    variable = porepressure
  []
  [p1]
    type = PointValue
    outputs = csv
    point = '0.1 0 0'
    variable = porepressure
  []
  [p2]
    type = PointValue
    outputs = csv
    point = '0.2 0 0'
    variable = porepressure
  []
  [p3]
    type = PointValue
    outputs = csv
    point = '0.3 0 0'
    variable = porepressure
  []
  [p4]
    type = PointValue
    outputs = csv
    point = '0.4 0 0'
    variable = porepressure
  []
  [p5]
    type = PointValue
    outputs = csv
    point = '0.5 0 0'
    variable = porepressure
  []
  [p6]
    type = PointValue
    outputs = csv
    point = '0.6 0 0'
    variable = porepressure
  []
  [p7]
    type = PointValue
    outputs = csv
    point = '0.7 0 0'
    variable = porepressure
  []
  [p8]
    type = PointValue
    outputs = csv
    point = '0.8 0 0'
    variable = porepressure
  []
  [p9]
    type = PointValue
    outputs = csv
    point = '0.9 0 0'
    variable = porepressure
  []
  [p99]
    type = PointValue
    outputs = csv
    point = '1 0 0'
    variable = porepressure
  []
  [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
    outputs = console
    function = if(0.15*t<0.01,0.15*t,0.01)
  []
[]


[Preconditioning]
  [andy]
    type = SMP
    full = true
    petsc_options_iname = '-ksp_type -pc_type -sub_pc_type -snes_atol -snes_rtol -snes_max_it'
    petsc_options_value = 'gmres asm lu 1E-14 1E-10 10000'
  []
[]

[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'
  file_base = mandel_basicthm
  [csv]
    interval = 3
    type = CSV
  []
[]

(modules/geochemistry/test/tests/sorption_and_surface_complexation/selenate.i)

# Langmuir sorption of Selenate
[TimeIndependentReactionSolver]
  model_definition = definition
  charge_balance_species = "Na+"
  constraint_species = "H2O              H+            Na+              SorbingSite      SeO4--"
  constraint_value = "  1.0              -7.5          10E-6            310E-9           5E-6"
  constraint_meaning = "kg_solvent_water log10activity bulk_composition bulk_composition free_concentration"
  constraint_unit = "   kg               dimensionless moles            moles            molal"
  ramp_max_ionic_strength_initial = 0 # not needed in this simple problem
  execute_console_output_on = '' # only CSV output for this problem
[]

[UserObjects]
  [definition]
    type = GeochemicalModelDefinition
    database_file = "../../database/selenate_sorption.json"
    basis_species = "H2O H+ Na+ SeO4-- SorbingSite"
  []
[]

[AuxVariables]
  [mol_sorbed_selenate_per_g_dry_soil]
  []
[]
[AuxKernels]
  [mol_sorbed_selenate_per_g_dry_soil]
    type = ParsedAux
    args = molal_SorbedSelenate
    function = 'molal_SorbedSelenate / 500.0'
    variable = mol_sorbed_selenate_per_g_dry_soil
  []
[]
[Postprocessors]
  [mol_sorbed_selenate_per_g_dry_soil]
    type = PointValue
    point = '0 0 0'
    variable = mol_sorbed_selenate_per_g_dry_soil
  []
[]

[Outputs]
  csv = true
[]

(modules/fluid_properties/test/tests/water/water.i)

# Example of using Water97FluidProperties module in Region 1 by recovering the values
# in Table 5 of Revised Release on the IAPWS Industrial Formulation 1997 for the
# Thermodynamic Properties of Water and Steam

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 3
  xmax = 3
  # This test uses ElementalVariableValue postprocessors on specific
  # elements, so element numbering needs to stay unchanged
  allow_renumbering = false
[]

[Variables]
  [./dummy]
  [../]
[]

[AuxVariables]
  [./pressure]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./temperature]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./rho]
    family = MONOMIAL
    order = CONSTANT
  [../]
  [./v]
    family = MONOMIAL
    order = CONSTANT
  [../]
  [./e]
    family = MONOMIAL
    order = CONSTANT
  [../]
  [./h]
    family = MONOMIAL
    order = CONSTANT
  [../]
  [./s]
    family = MONOMIAL
    order = CONSTANT
  [../]
  [./cp]
    family = MONOMIAL
    order = CONSTANT
  [../]
  [./cv]
    family = MONOMIAL
    order = CONSTANT
  [../]
  [./c]
    family = MONOMIAL
    order = CONSTANT
  [../]
  [./mu]
    family = MONOMIAL
    order = CONSTANT
  [../]
  [./k]
    family = MONOMIAL
    order = CONSTANT
  [../]
[]

[Functions]
  [./tic]
    type = ParsedFunction
    value = 'if(x<2, 300, 500)'
  [../]
  [./pic]
    type = ParsedFunction
    value = 'if(x<1,3e6, if(x<2, 80e6, 3e6))'
  [../]
[]

[ICs]
  [./p_ic]
    type = FunctionIC
    function = pic
    variable = pressure
  [../]
  [./t_ic]
    type = FunctionIC
    function = tic
    variable = temperature
  [../]
[]

[AuxKernels]
  [./rho]
    type = MaterialRealAux
    variable = rho
    property = density
  [../]
  [./v]
    type = ParsedAux
    args = rho
    function = 1/rho
    variable = v
  [../]
  [./e]
    type = MaterialRealAux
    variable = e
    property = e
  [../]
  [./h]
    type = MaterialRealAux
    variable = h
    property = h
  [../]
  [./s]
    type = MaterialRealAux
    variable = s
    property = s
  [../]
  [./cp]
    type = MaterialRealAux
    variable = cp
    property = cp
  [../]
  [./cv]
    type = MaterialRealAux
    variable = cv
    property = cv
  [../]
  [./c]
    type = MaterialRealAux
    variable = c
    property = c
  [../]
  [./mu]
    type = MaterialRealAux
    variable = mu
    property = viscosity
  [../]
  [./k]
    type = MaterialRealAux
    variable = k
    property = k
  [../]
[]

[Modules]
  [./FluidProperties]
    [./water]
      type = Water97FluidProperties
    [../]
  [../]
[]

[Materials]
  [./fp_mat]
    type = FluidPropertiesMaterialPT
    pressure = pressure
    temperature = temperature
    fp = water
  [../]
[]

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

[Postprocessors]
  [./density0]
    type = ElementalVariableValue
    variable = rho
    elementid = 0
  [../]
  [./density1]
    type = ElementalVariableValue
    variable = rho
    elementid = 1
  [../]
  [./density2]
    type = ElementalVariableValue
    variable = rho
    elementid = 2
  [../]
  [./v0]
    type = ElementalVariableValue
    variable = v
    elementid = 0
  [../]
  [./v1]
    type = ElementalVariableValue
    variable = v
    elementid = 1
  [../]
  [./v2]
    type = ElementalVariableValue
    variable = v
    elementid = 2
  [../]
  [./e0]
    type = ElementalVariableValue
    variable = e
    elementid = 0
  [../]
  [./e1]
    type = ElementalVariableValue
    variable = e
    elementid = 1
  [../]
  [./e2]
    type = ElementalVariableValue
    variable = e
    elementid = 2
  [../]
  [./h0]
    type = ElementalVariableValue
    variable = h
    elementid = 0
  [../]
  [./h1]
    type = ElementalVariableValue
    variable = h
    elementid = 1
  [../]
  [./h2]
    type = ElementalVariableValue
    variable = h
    elementid = 2
  [../]
  [./s0]
    type = ElementalVariableValue
    variable = s
    elementid = 0
  [../]
  [./s1]
    type = ElementalVariableValue
    variable = s
    elementid = 1
  [../]
  [./s2]
    type = ElementalVariableValue
    variable = s
    elementid = 2
  [../]
  [./cp0]
    type = ElementalVariableValue
    variable = cp
    elementid = 0
  [../]
  [./cp1]
    type = ElementalVariableValue
    variable = cp
    elementid = 1
  [../]
  [./cp2]
    type = ElementalVariableValue
    variable = cp
    elementid = 2
  [../]
  [./cv0]
    type = ElementalVariableValue
    variable = cv
    elementid = 0
  [../]
  [./cv1]
    type = ElementalVariableValue
    variable = cv
    elementid = 1
  [../]
  [./cv2]
    type = ElementalVariableValue
    variable = cv
    elementid = 2
  [../]
  [./c0]
    type = ElementalVariableValue
    variable = c
    elementid = 0
  [../]
  [./c1]
    type = ElementalVariableValue
    variable = c
    elementid = 1
  [../]
  [./c2]
    type = ElementalVariableValue
    variable = c
    elementid = 2
  [../]
  [./mu0]
    type = ElementalVariableValue
    variable = mu
    elementid = 0
  [../]
  [./mu1]
    type = ElementalVariableValue
    variable = mu
    elementid = 1
  [../]
  [./mu2]
    type = ElementalVariableValue
    variable = mu
    elementid = 2
  [../]
  [./k0]
    type = ElementalVariableValue
    variable = k
    elementid = 0
  [../]
  [./k1]
    type = ElementalVariableValue
    variable = k
    elementid = 1
  [../]
  [./k2]
    type = ElementalVariableValue
    variable = k
    elementid = 2
  [../]
[]

[Executioner]
  type = Steady
  solve_type = NEWTON
[]

[Outputs]
  csv = true
[]

(modules/functional_expansion_tools/examples/3D_volumetric_Cartesian_different_submesh/sub.i)

# Derived from the example '3D_volumetric_Cartesian' with the following differences:
#
#   1) The number of x and y divisions in the sub app is not the same as the master app
#   2) The subapp mesh is skewed in x and z
[Mesh]
  type = GeneratedMesh
  dim = 3

  xmin = 0.0
  xmax = 10.0
  nx = 23
  bias_x = 1.2

  ymin = 1.0
  ymax = 11.0
  ny = 33

  zmin = 2.0
  zmax = 12.0
  nz = 35
  bias_z = 0.8
[]

# Non-copy transfers only work with AuxVariable, but nothing will be solved without a variable
# defined. The solution is to define an empty variable tha does nothing, but causes MOOSE to solve
# the AuxKernels that we need.
[Variables]
  [./empty]
  [../]
[]

[AuxVariables]
  [./s]
    order = FIRST
    family = LAGRANGE
  [../]
  [./m_in]
    order = FIRST
    family = LAGRANGE
  [../]
[]

# We must have a kernel for every variable, hence this null kernel to match the variable 'empty'
[Kernels]
  [./null_kernel]
    type = NullKernel
    variable = empty
  [../]
[]

[AuxKernels]
  [./reconstruct_m_in]
    type = FunctionSeriesToAux
    function = FX_Basis_Value_Sub
    variable = m_in
  [../]
  [./calculate_s] # Something to make 's' change each time, but allow a converging solution
    type = ParsedAux
    variable = s
    args = m_in
    function = '2*exp(-m_in/0.8)'
  [../]
[]

[Functions]
  [./FX_Basis_Value_Sub]
    type = FunctionSeries
    series_type = Cartesian
    orders = '3   4   5'
    physical_bounds = '0.0  10.0    1.0 11.0    2.0 12.0'
    x = Legendre
    y = Legendre
    z = Legendre
  [../]
[]

[UserObjects]
  [./FX_Value_UserObject_Sub]
    type = FXVolumeUserObject
    function = FX_Basis_Value_Sub
    variable = s
  [../]
[]

[Executioner]
  type = Transient
  num_steps = 10
  dt = 0.5
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

(modules/combined/examples/mortar/mortar_gradient.i)

#
# Compare a diffusion equation with (c) and without (v) periodic gradient
# constraints and a ramped sloped initial condition and value-periodic diffusion (p)
# without a slope.
#

[Mesh]
  [gen]
    type = GeneratedMeshGenerator
    dim = 2
    nx = 40
    ny = 40
  []
  [secondary_x]
    input = gen
    type = LowerDBlockFromSidesetGenerator
    sidesets = '3'
    new_block_id = 10
    new_block_name = "secondary_x"
  []
  [primary_x]
    input = secondary_x
    type = LowerDBlockFromSidesetGenerator
    sidesets = '1'
    new_block_id = 12
    new_block_name = "primary_x"
  []
  [secondary_y]
    input = primary_x
    type = LowerDBlockFromSidesetGenerator
    sidesets = '0'
    new_block_id = 11
    new_block_name = "secondary_y"
  []
  [primary_y]
    input = secondary_y
    type = LowerDBlockFromSidesetGenerator
    sidesets = '2'
    new_block_id = 13
    new_block_name = "primary_y"
  []
[]

[Functions]
  [./init_slope]
    # slope with a concentration spike close to the lower interface
    type = ParsedFunction
    value = 'if(x>0.4 & x<0.6 & y>0.1 & y<0.3, 3+y, y)'
  [../]
  [./init_flat]
    # no-slope and the same spike
    type = ParsedFunction
    value = 'if(x>0.4 & x<0.6 & y>0.1 & y<0.3, 3, 0)'
  [../]
[]

[Variables]
  # gradient constrained concentration
  [./c]
    order = FIRST
    family = LAGRANGE
    block = 0
    [./InitialCondition]
      type = FunctionIC
      function = init_slope
    [../]
  [../]

  # unconstrained concentrarion
  [./v]
    order = FIRST
    family = LAGRANGE
    block = 0
    [./InitialCondition]
      type = FunctionIC
      function = init_slope
    [../]
  [../]

  # flat value periodic diffusion
  [./p]
    order = FIRST
    family = LAGRANGE
    block = 0
    [./InitialCondition]
      type = FunctionIC
      function = init_flat
    [../]
  [../]

  # Lagrange multipliers for gradient component in the horizontal directon
  [./lm_left_right_x]
    order = FIRST
    family = LAGRANGE
    block = "secondary_x"
  [../]
  [./lm_left_right_y]
    order = FIRST
    family = LAGRANGE
    block = "secondary_x"
  [../]

  # Lagrange multipliers for gradient component in the vertical directon
  [./lm_up_down_x]
    order = FIRST
    family = LAGRANGE
    block = "secondary_y"
  [../]
  [./lm_up_down_y]
    order = FIRST
    family = LAGRANGE
    block = "secondary_y"
  [../]
[]

[Kernels]
  # the gradient constrained concentration
  [./diff]
    type = Diffusion
    variable = c
    block = 0
  [../]
  [./dt]
    type = TimeDerivative
    variable = c
    block = 0
  [../]

  # the un-constrained concentration
  [./diff2]
    type = Diffusion
    variable = v
    block = 0
  [../]
  [./dt2]
    type = TimeDerivative
    variable = v
    block = 0
  [../]

  # the value periodic concentration
  [./diff3]
    type = Diffusion
    variable = p
    block = 0
  [../]
  [./dt3]
    type = TimeDerivative
    variable = p
    block = 0
  [../]
[]

[Constraints]
  [./equaly_grad_x]
    type = EqualGradientConstraint
    variable = lm_up_down_x
    component = 0
    secondary_variable = c
    secondary_boundary = bottom
    primary_boundary = top
    secondary_subdomain = secondary_y
    primary_subdomain = primary_y
    periodic = true
  [../]
  [./equaly_grad_y]
    type = EqualGradientConstraint
    variable = lm_up_down_y
    component = 1
    secondary_variable = c
    secondary_boundary = bottom
    primary_boundary = top
    secondary_subdomain = secondary_y
    primary_subdomain = primary_y
    periodic = true
  [../]

  [./equalx_grad_x]
    type = EqualGradientConstraint
    variable = lm_left_right_x
    component = 0
    secondary_variable = c
    secondary_boundary = left
    primary_boundary = right
    secondary_subdomain = secondary_x
    primary_subdomain = primary_x
    periodic = true
  [../]
  [./equalx_grad_y]
    type = EqualGradientConstraint
    variable = lm_left_right_y
    component = 1
    secondary_variable = c
    secondary_boundary = left
    primary_boundary = right
    secondary_subdomain = secondary_x
    primary_subdomain = primary_x
    periodic = true
  [../]
[]

[BCs]
  # DiffusionFluxBC is the surface term in the weak form of the Diffusion equation
  [./surface]
    type = DiffusionFluxBC
    boundary = 'top bottom left right'
    variable = c
  [../]
  [./surface2]
    type = DiffusionFluxBC
    boundary = 'top bottom left right'
    variable = v
  [../]

  # for the value periodic diffusion we skip the surface term and apply value PBCs
  [./Periodic]
    [./up_down]
      variable = p
      primary = 0
      secondary = 2
      translation = '0 1 0'
    [../]
    [./left_right]
      variable = p
      primary = 1
      secondary = 3
      translation = '-1 0 0'
    [../]
  [../]
[]

[AuxVariables]
  [./diff_constraint]
    block = 0
  [../]
  [./diff_periodic]
    block = 0
  [../]
  [./diff_slope]
    block = 0
  [../]
  [./slope]
    block = 0
    [./InitialCondition]
      type = FunctionIC
      function = y
    [../]
  [../]
[]

[AuxKernels]
  # difference between the constrained and unconstrained sloped diffusions
  [./diff_constraint]
    type = ParsedAux
    variable = diff_constraint
    function = 'c-v'
    args = 'c v'
    block = 0
  [../]

  # difference between the periodic gradient constrained diffusion and the flat
  # value period diffusien with a constant slope added. This should be the same,
  # but they aren't quite because the gradient constraint affects the gradient in
  # the entire elements (i.e. a larger volume is affected by the gradient constraint
  # compared to the nodal value periodicity)
  [./diff_periodic]
    type = ParsedAux
    variable = diff_periodic
    function = 'c-p-slope'
    args = 'c p slope'
    block = 0
  [../]

  # subtract the constant slope from the gradient periodic simulation (should yield
  # almost p - per the argument above)
  [./diff_slope]
    type = ParsedAux
    variable = diff_slope
    function = 'c-slope'
    args = 'c slope'
    block = 0
  [../]
[]

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

[Executioner]
  type = Transient
  solve_type = NEWTON

  # the shift is necessary to facilitate the solve. The Lagrange multipliers
  # introduce zero-on diaginal blocks, which make the matrix hard to invert.
  petsc_options_iname = '-pc_type -pc_factor_shift_type -pc_factor_shift_amount'
  petsc_options_value = ' lu       NONZERO               1e-10'

  nl_rel_tol = 1e-11
  nl_abs_tol = 1e-10
  l_tol = 1e-10
  dt = 0.01
  num_steps = 20
[]

[Outputs]
  exodus = true
[]

(modules/tensor_mechanics/test/tests/torque/torque_small.i)

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
  origin = '0 0 2'
  direction = '0 0 1'
  polar_moment_of_inertia = pmi
  factor = t
[]

[Mesh]
  [ring]
    type = AnnularMeshGenerator
    nr = 1
    nt = 30
    rmin = 0.95
    rmax = 1
  []
  [extrude]
    type = MeshExtruderGenerator
    input = ring
    extrusion_vector = '0 0 2'
    bottom_sideset = 'bottom'
    top_sideset = 'top'
    num_layers = 5
  []
[]

[AuxVariables]
  [alpha_var]
  []
  [shear_stress_var]
    order = CONSTANT
    family = MONOMIAL
  []
[]

[AuxKernels]
  [alpha]
    type = RotationAngle
    variable = alpha_var
  []
  [shear_stress]
    type = ParsedAux
    variable = shear_stress_var
    args = 'stress_yz stress_xz'
    function = 'sqrt(stress_yz^2 + stress_xz^2)'
  []
[]

[BCs]
  # fix bottom
  [fix_x]
    type = DirichletBC
    boundary = bottom
    variable = disp_x
    value = 0
  []
  [fix_y]
    type = DirichletBC
    boundary = bottom
    variable = disp_y
    value = 0
  []
  [fix_z]
    type = DirichletBC
    boundary = bottom
    variable = disp_z
    value = 0
  []

  # twist top
  [twist_x]
    type = Torque
    boundary = top
    variable = disp_x
  []
  [twist_y]
    type = Torque
    boundary = top
    variable = disp_y
  []
  [twist_z]
    type = Torque
    boundary = top
    variable = disp_z
  []
[]

[Modules/TensorMechanics/Master]
  [all]
    add_variables = true
    strain = SMALL
    generate_output = 'vonmises_stress stress_yz stress_xz'
  []
[]

[Postprocessors]
  [pmi]
    type = PolarMomentOfInertia
    boundary = top
    # execute_on = 'INITIAL NONLINEAR'
    execute_on = 'INITIAL'
  []
  [alpha]
    type = SideAverageValue
    variable = alpha_var
    boundary = top
  []
  [shear_stress]
    type = ElementAverageValue
    variable = shear_stress_var
  []
[]

[Materials]
  [stress]
    type = ComputeLinearElasticStress
  []
  [elastic]
    type = ComputeIsotropicElasticityTensor
    youngs_modulus = 0.3
    shear_modulus = 100
  []
  []

[Executioner]
  # type = Steady
  type = Transient
  num_steps = 1
  solve_type = PJFNK
  petsc_options_iname = '-pctype'
  petsc_options_value = 'lu'
  nl_max_its = 150
[]

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

(modules/combined/examples/geochem-porous_flow/geotes_2D/aquifer_un_quartz_geochemistry.i)

[Mesh]
  [gen]
    type = GeneratedMeshGenerator
    dim = 2
    nx = 56
    ny = 32
    xmin = -70
    xmax = 70
    ymin = -40
    ymax = 40
  []
[]

[GlobalParams]
  point = '0 0 0'
  reactor = reactor
[]

[SpatialReactionSolver]
  model_definition = definition
  geochemistry_reactor_name = reactor
  charge_balance_species = "Cl-"
  constraint_species = "H2O              Na+                Cl-                SiO2(aq)"
# ASSUME that 1 litre of solution contains:
  constraint_value = "  1.0              0.1                0.1                0.00172249633"
  constraint_meaning = "kg_solvent_water bulk_composition bulk_composition free_concentration"
  constraint_unit = "   kg               moles              moles              molal"
  initial_temperature = 50.0
  kinetic_species_name = QuartzUnlike
# Per 1 litre (1000cm^3) of aqueous solution (1kg of solvent water), there is 9000cm^3 of QuartzUnlike, which means the initial porosity is 0.1.
  kinetic_species_initial_value = 9000
  kinetic_species_unit = cm3
  temperature = temperature
  source_species_names = 'H2O    Na+   Cl-   SiO2(aq)'
  source_species_rates = 'rate_H2O_per_1l rate_Na_per_1l rate_Cl_per_1l rate_SiO2_per_1l'
  ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
  add_aux_pH = false # there is no H+ in this system
  evaluate_kinetic_rates_always = true # implicit time-marching used for stability
  execute_console_output_on = '' # only CSV and exodus output used in this example
[]

[UserObjects]
  [rate_quartz]
    type = GeochemistryKineticRate
    kinetic_species_name = QuartzUnlike
    intrinsic_rate_constant = 1.0E-2
    multiply_by_mass = true
    area_quantity = 1
    activation_energy = 72800.0
  []
  [definition]
    type = GeochemicalModelDefinition
    database_file = "small_database.json"
    basis_species = "H2O SiO2(aq) Na+ Cl-"
    kinetic_minerals = "QuartzUnlike"
    kinetic_rate_descriptions = "rate_quartz"
  []
[]


[Executioner]
  type = Transient
  dt = 1E5
  end_time = 7.76E6 # 90 days
[]

[AuxVariables]
  [temperature]
    initial_condition = 50.0
  []
  [nodal_volume]
  []
  [porosity]
  []
  [nodal_void_volume]
  []
  [pf_rate_H2O] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Na] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Cl] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_SiO2] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
  []
  [rate_H2O_per_1l] # rate per 1 litre of aqueous solution that we consider at each node
  []
  [rate_Na_per_1l]
  []
  [rate_Cl_per_1l]
  []
  [rate_SiO2_per_1l]
  []
  [transported_H2O]
  []
  [transported_Na]
  []
  [transported_Cl]
  []
  [transported_SiO2]
  []
  [transported_mass]
  []
  [massfrac_Na]
  []
  [massfrac_Cl]
  []
  [massfrac_SiO2]
  []
  [massfrac_H2O]
  []
[]
[AuxKernels]
  [nodal_volume] # TODO: change this hard-coded version once PR is merged
    type = FunctionAux
    variable = nodal_volume
    function = 'if(abs(x) = 70 & abs(y) = 40, 2.5, if(abs(x) = 70 | abs(y) = 40, 5, 10))'
    execute_on = 'initial'
  []
  [porosity]
    type = ParsedAux
    args = free_cm3_QuartzUnlike
    function = '1000.0 / (1000.0 + free_cm3_QuartzUnlike)'
    variable = porosity
    execute_on = 'timestep_begin timestep_end'
  []
  [nodal_void_volume]
    type = ParsedAux
    args = 'porosity nodal_volume'
    variable = nodal_void_volume
    function = 'porosity * nodal_volume'
    execute_on = 'timestep_begin'
  []
  [rate_H2O_per_1l]
    type = ParsedAux
    args = 'pf_rate_H2O nodal_void_volume'
    variable = rate_H2O_per_1l
# pf_rate = change in kg at every node
# pf_rate * 1000 / molar_mass_in_g_per_mole = change in moles at every node
# pf_rate * 1000 / molar_mass / (nodal_void_volume_in_m^3 * 1000) = change in moles per litre of aqueous solution
    function = 'pf_rate_H2O / 18.0152 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_Na_per_1l]
    type = ParsedAux
    args = 'pf_rate_Na nodal_void_volume'
    variable = rate_Na_per_1l
    function = 'pf_rate_Na / 22.9898 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_Cl_per_1l]
    type = ParsedAux
    args = 'pf_rate_Cl nodal_void_volume'
    variable = rate_Cl_per_1l
    function = 'pf_rate_Cl / 35.453 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [rate_SiO2_per_1l]
    type = ParsedAux
    args = 'pf_rate_SiO2 nodal_void_volume'
    variable = rate_SiO2_per_1l
    function = 'pf_rate_SiO2 / 60.0843 / nodal_void_volume'
    execute_on = 'timestep_begin'
  []
  [transported_H2O]
    type = GeochemistryQuantityAux
    variable = transported_H2O
    species = H2O
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_Na]
    type = GeochemistryQuantityAux
    variable = transported_Na
    species = Na+
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_Cl]
    type = GeochemistryQuantityAux
    variable = transported_Cl
    species = Cl-
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_SiO2]
    type = GeochemistryQuantityAux
    variable = transported_SiO2
    species = 'SiO2(aq)'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_mass]
    type = ParsedAux
    args = 'transported_H2O transported_Na transported_Cl transported_SiO2'
    variable = transported_mass
    function = 'transported_H2O * 18.0152 + transported_Na * 22.9898 + transported_Cl * 35.453 + transported_SiO2 * 60.0843'
    execute_on = 'timestep_end'
  []
  [massfrac_H2O]
    type = ParsedAux
    args = 'transported_H2O transported_mass'
    variable = massfrac_H2O
    function = 'transported_H2O * 18.0152 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Na]
    type = ParsedAux
    args = 'transported_Na transported_mass'
    variable = massfrac_Na
    function = 'transported_Na * 22.9898 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Cl]
    type = ParsedAux
    args = 'transported_Cl transported_mass'
    variable = massfrac_Cl
    function = 'transported_Cl * 35.453 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_SiO2]
    type = ParsedAux
    args = 'transported_SiO2 transported_mass'
    variable = massfrac_SiO2
    function = 'transported_SiO2 * 60.0843 / transported_mass'
    execute_on = 'timestep_end'
  []
[]
[Postprocessors]
  [cm3_quartz]
    type = PointValue
    variable = free_cm3_QuartzUnlike
  []
  [porosity]
    type = PointValue
    variable = porosity
  []
  [solution_temperature]
    type = PointValue
    variable = solution_temperature
  []
  [massfrac_H2O]
    type = PointValue
    variable = massfrac_H2O
  []
  [massfrac_Na]
    type = PointValue
    variable = massfrac_Na
  []
  [massfrac_Cl]
    type = PointValue
    variable = massfrac_Cl
  []
  [massfrac_SiO2]
    type = PointValue
    variable = massfrac_SiO2
  []
[]
[Outputs]
  exodus = true
  csv = true
[]

(modules/combined/test/tests/poro_mechanics/borehole_highres.i)

# Poroelastic response of a borehole.
#
# HIGHRES VERSION: this version gives good agreement with the analytical solution, but it takes a while so is a "heavy" test
#
# A fully-saturated medium contains a fluid with a homogeneous porepressure,
# but an anisitropic insitu stress.  A infinitely-long borehole aligned with
# the $$z$$ axis is instanteously excavated.  The borehole boundary is
# stress-free and allowed to freely drain.  This problem is analysed using
# plane-strain conditions (no $$z$$ displacement).
#
# The solution in Laplace space is found in E Detournay and AHD Cheng "Poroelastic response of a borehole in a non-hydrostatic stress field".  International Journal of Rock Mechanics and Mining Sciences and Geomechanics Abstracts 25 (1988) 171-182.  In the small-time limit, the Laplace transforms may be performed.  There is one typo in the paper.  Equation (A4)'s final term should be -(a/r)\sqrt(4ct/(a^2\pi)), and not +(a/r)\sqrt(4ct/(a^2\pi)).
#
# Because realistic parameters are chosen (below),
# the residual for porepressure is much smaller than
# the residuals for the displacements.  Therefore the
# scaling parameter is chosen.  Also note that the
# insitu stresses are effective stresses, not total
# stresses, but the solution in the above paper is
# expressed in terms of total stresses.
#
# Here are the problem's parameters, and their values:
# Borehole radius.  a = 1
# Rock's Lame lambda.  la = 0.5E9
# Rock's Lame mu, which is also the Rock's shear modulus.  mu = G = 1.5E9
# Rock bulk modulus.  K = la + 2*mu/3 = 1.5E9
# Drained Poisson ratio.  nu = (3K - 2G)/(6K + 2G) = 0.125
# Rock bulk compliance.  1/K = 0.66666666E-9
# Fluid bulk modulus.  Kf = 0.7171315E9
# Fluid bulk compliance.  1/Kf = 1.39444444E-9
# Rock initial porosity.  phi0 = 0.3
# Biot coefficient.  alpha = 0.65
# Biot modulus.  M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 2E9
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.345E9
# Undrained Poisson ratio.  nuu = (3Ku - 2G)/(6Ku + 2G) = 0.2364
# Skempton coefficient.  B = alpha*M/Ku = 0.554
# Fluid mobility (rock permeability/fluid viscosity).  k = 1E-12

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

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
  porepressure = porepressure
  block = 1
[]

[Variables]
  [./disp_x]
  [../]
  [./disp_y]
  [../]
  [./disp_z]
  [../]
  [./porepressure]
    scaling = 1E9  # Notice the scaling, to make porepressure's kernels roughly of same magnitude as disp's kernels
  [../]
[]

[GlobalParams]
  volumetric_locking_correction=true
[]

[ICs]
  [./initial_p]
    type = ConstantIC
    variable = porepressure
    value = 1E6
  [../]
[]

[BCs]
  [./fixed_outer_x]
    type = DirichletBC
    variable = disp_x
    value = 0
    boundary = outer
  [../]
  [./fixed_outer_y]
    type = DirichletBC
    variable = disp_y
    value = 0
    boundary = outer
  [../]
  [./plane_strain]
    type = DirichletBC
    variable = disp_z
    value = 0
    boundary = 'zmin zmax'
  [../]
  [./borehole_wall]
    type = DirichletBC
    variable = porepressure
    value = 0
    boundary = bh_wall
  [../]
[]



[AuxVariables]
  [./stress_yy]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./tot_yy]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

[AuxKernels]
  [./stress_yy]
    type = RankTwoAux
    rank_two_tensor = stress
    variable = stress_yy
    index_i = 1
    index_j = 1
  [../]
  [./tot_yy]
    type = ParsedAux
    args = 'stress_yy porepressure'
    execute_on = timestep_end
    variable = tot_yy
    function = 'stress_yy-0.65*porepressure'
  [../]
[]



[Kernels]
  [./grad_stress_x]
    type = StressDivergenceTensors
    variable = disp_x
    component = 0
  [../]
  [./grad_stress_y]
    type = StressDivergenceTensors
    variable = disp_y
    component = 1
  [../]
  [./grad_stress_z]
    type = StressDivergenceTensors
    variable = disp_z
    component = 2
  [../]
  [./poro_x]
    type = PoroMechanicsCoupling
    variable = disp_x
    component = 0
  [../]
  [./poro_y]
    type = PoroMechanicsCoupling
    variable = disp_y
    component = 1
  [../]
  [./poro_z]
    type = PoroMechanicsCoupling
    variable = disp_z
    component = 2
  [../]
  [./poro_timederiv]
    type = PoroFullSatTimeDerivative
    variable = porepressure
  [../]
  [./darcy_flow]
    type = CoefDiffusion
    variable = porepressure
    coef = 1E-12
  [../]
[]

[Materials]
  [./elasticity_tensor]
    type = ComputeElasticityTensor
    C_ijkl = '0.5E9 1.5E9'
    # bulk modulus is lambda + 2*mu/3 = 0.5 + 2*1.5/3 = 1.5E9
    fill_method = symmetric_isotropic
  [../]
  [./strain]
    type = ComputeFiniteStrain
    displacements = 'disp_x disp_y disp_z'
    eigenstrain_names = ini_stress
  [../]
  [./ini_stress]
    type = ComputeEigenstrainFromInitialStress
    initial_stress = '-1.35E6 0 0  0 -3.35E6 0  0 0 0' # remember this is the effective stress
    eigenstrain_name = ini_stress
  [../]
  [./no_plasticity]
    type = ComputeFiniteStrainElasticStress
  [../]
  [./poro_material]
    type = PoroFullSatMaterial
    porosity0 = 0.3
    biot_coefficient = 0.65
    solid_bulk_compliance = 0.6666666666667E-9
    fluid_bulk_compliance = 1.3944444444444E-9
    constant_porosity = false
  [../]
[]

[Postprocessors]
  [./p00]
    type = PointValue
    variable = porepressure
    point = '1.00 0 0'
    outputs = csv_p
  [../]
  [./p01]
    type = PointValue
    variable = porepressure
    point = '1.01 0 0'
    outputs = csv_p
  [../]
  [./p02]
    type = PointValue
    variable = porepressure
    point = '1.02 0 0'
    outputs = csv_p
  [../]
  [./p03]
    type = PointValue
    variable = porepressure
    point = '1.03 0 0'
    outputs = csv_p
  [../]
  [./p04]
    type = PointValue
    variable = porepressure
    point = '1.04 0 0'
    outputs = csv_p
  [../]
  [./p05]
    type = PointValue
    variable = porepressure
    point = '1.05 0 0'
    outputs = csv_p
  [../]
  [./p06]
    type = PointValue
    variable = porepressure
    point = '1.06 0 0'
    outputs = csv_p
  [../]
  [./p07]
    type = PointValue
    variable = porepressure
    point = '1.07 0 0'
    outputs = csv_p
  [../]
  [./p08]
    type = PointValue
    variable = porepressure
    point = '1.08 0 0'
    outputs = csv_p
  [../]
  [./p09]
    type = PointValue
    variable = porepressure
    point = '1.09 0 0'
    outputs = csv_p
  [../]
  [./p10]
    type = PointValue
    variable = porepressure
    point = '1.10 0 0'
    outputs = csv_p
  [../]
  [./p11]
    type = PointValue
    variable = porepressure
    point = '1.11 0 0'
    outputs = csv_p
  [../]
  [./p12]
    type = PointValue
    variable = porepressure
    point = '1.12 0 0'
    outputs = csv_p
  [../]
  [./p13]
    type = PointValue
    variable = porepressure
    point = '1.13 0 0'
    outputs = csv_p
  [../]
  [./p14]
    type = PointValue
    variable = porepressure
    point = '1.14 0 0'
    outputs = csv_p
  [../]
  [./p15]
    type = PointValue
    variable = porepressure
    point = '1.15 0 0'
    outputs = csv_p
  [../]
  [./p16]
    type = PointValue
    variable = porepressure
    point = '1.16 0 0'
    outputs = csv_p
  [../]
  [./p17]
    type = PointValue
    variable = porepressure
    point = '1.17 0 0'
    outputs = csv_p
  [../]
  [./p18]
    type = PointValue
    variable = porepressure
    point = '1.18 0 0'
    outputs = csv_p
  [../]
  [./p19]
    type = PointValue
    variable = porepressure
    point = '1.19 0 0'
    outputs = csv_p
  [../]
  [./p20]
    type = PointValue
    variable = porepressure
    point = '1.20 0 0'
    outputs = csv_p
  [../]
  [./p21]
    type = PointValue
    variable = porepressure
    point = '1.21 0 0'
    outputs = csv_p
  [../]
  [./p22]
    type = PointValue
    variable = porepressure
    point = '1.22 0 0'
    outputs = csv_p
  [../]
  [./p23]
    type = PointValue
    variable = porepressure
    point = '1.23 0 0'
    outputs = csv_p
  [../]
  [./p24]
    type = PointValue
    variable = porepressure
    point = '1.24 0 0'
    outputs = csv_p
  [../]
  [./p25]
    type = PointValue
    variable = porepressure
    point = '1.25 0 0'
    outputs = csv_p
  [../]

  [./s00]
    type = PointValue
    variable = disp_x
    point = '1.00 0 0'
    outputs = csv_s
  [../]
  [./s01]
    type = PointValue
    variable = disp_x
    point = '1.01 0 0'
    outputs = csv_s
  [../]
  [./s02]
    type = PointValue
    variable = disp_x
    point = '1.02 0 0'
    outputs = csv_s
  [../]
  [./s03]
    type = PointValue
    variable = disp_x
    point = '1.03 0 0'
    outputs = csv_s
  [../]
  [./s04]
    type = PointValue
    variable = disp_x
    point = '1.04 0 0'
    outputs = csv_s
  [../]
  [./s05]
    type = PointValue
    variable = disp_x
    point = '1.05 0 0'
    outputs = csv_s
  [../]
  [./s06]
    type = PointValue
    variable = disp_x
    point = '1.06 0 0'
    outputs = csv_s
  [../]
  [./s07]
    type = PointValue
    variable = disp_x
    point = '1.07 0 0'
    outputs = csv_s
  [../]
  [./s08]
    type = PointValue
    variable = disp_x
    point = '1.08 0 0'
    outputs = csv_s
  [../]
  [./s09]
    type = PointValue
    variable = disp_x
    point = '1.09 0 0'
    outputs = csv_s
  [../]
  [./s10]
    type = PointValue
    variable = disp_x
    point = '1.10 0 0'
    outputs = csv_s
  [../]
  [./s11]
    type = PointValue
    variable = disp_x
    point = '1.11 0 0'
    outputs = csv_s
  [../]
  [./s12]
    type = PointValue
    variable = disp_x
    point = '1.12 0 0'
    outputs = csv_s
  [../]
  [./s13]
    type = PointValue
    variable = disp_x
    point = '1.13 0 0'
    outputs = csv_s
  [../]
  [./s14]
    type = PointValue
    variable = disp_x
    point = '1.14 0 0'
    outputs = csv_s
  [../]
  [./s15]
    type = PointValue
    variable = disp_x
    point = '1.15 0 0'
    outputs = csv_s
  [../]
  [./s16]
    type = PointValue
    variable = disp_x
    point = '1.16 0 0'
    outputs = csv_s
  [../]
  [./s17]
    type = PointValue
    variable = disp_x
    point = '1.17 0 0'
    outputs = csv_s
  [../]
  [./s18]
    type = PointValue
    variable = disp_x
    point = '1.18 0 0'
    outputs = csv_s
  [../]
  [./s19]
    type = PointValue
    variable = disp_x
    point = '1.19 0 0'
    outputs = csv_s
  [../]
  [./s20]
    type = PointValue
    variable = disp_x
    point = '1.20 0 0'
    outputs = csv_s
  [../]
  [./s21]
    type = PointValue
    variable = disp_x
    point = '1.21 0 0'
    outputs = csv_s
  [../]
  [./s22]
    type = PointValue
    variable = disp_x
    point = '1.22 0 0'
    outputs = csv_s
  [../]
  [./s23]
    type = PointValue
    variable = disp_x
    point = '1.23 0 0'
    outputs = csv_s
  [../]
  [./s24]
    type = PointValue
    variable = disp_x
    point = '1.24 0 0'
    outputs = csv_s
  [../]
  [./s25]
    type = PointValue
    variable = disp_x
    point = '1.25 0 0'
    outputs = csv_s
  [../]

  [./t00]
    type = PointValue
    variable = tot_yy
    point = '1.00 0 0'
    outputs = csv_t
  [../]
  [./t01]
    type = PointValue
    variable = tot_yy
    point = '1.01 0 0'
    outputs = csv_t
  [../]
  [./t02]
    type = PointValue
    variable = tot_yy
    point = '1.02 0 0'
    outputs = csv_t
  [../]
  [./t03]
    type = PointValue
    variable = tot_yy
    point = '1.03 0 0'
    outputs = csv_t
  [../]
  [./t04]
    type = PointValue
    variable = tot_yy
    point = '1.04 0 0'
    outputs = csv_t
  [../]
  [./t05]
    type = PointValue
    variable = tot_yy
    point = '1.05 0 0'
    outputs = csv_t
  [../]
  [./t06]
    type = PointValue
    variable = tot_yy
    point = '1.06 0 0'
    outputs = csv_t
  [../]
  [./t07]
    type = PointValue
    variable = tot_yy
    point = '1.07 0 0'
    outputs = csv_t
  [../]
  [./t08]
    type = PointValue
    variable = tot_yy
    point = '1.08 0 0'
    outputs = csv_t
  [../]
  [./t09]
    type = PointValue
    variable = tot_yy
    point = '1.09 0 0'
    outputs = csv_t
  [../]
  [./t10]
    type = PointValue
    variable = tot_yy
    point = '1.10 0 0'
    outputs = csv_t
  [../]
  [./t11]
    type = PointValue
    variable = tot_yy
    point = '1.11 0 0'
    outputs = csv_t
  [../]
  [./t12]
    type = PointValue
    variable = tot_yy
    point = '1.12 0 0'
    outputs = csv_t
  [../]
  [./t13]
    type = PointValue
    variable = tot_yy
    point = '1.13 0 0'
    outputs = csv_t
  [../]
  [./t14]
    type = PointValue
    variable = tot_yy
    point = '1.14 0 0'
    outputs = csv_t
  [../]
  [./t15]
    type = PointValue
    variable = tot_yy
    point = '1.15 0 0'
    outputs = csv_t
  [../]
  [./t16]
    type = PointValue
    variable = tot_yy
    point = '1.16 0 0'
    outputs = csv_t
  [../]
  [./t17]
    type = PointValue
    variable = tot_yy
    point = '1.17 0 0'
    outputs = csv_t
  [../]
  [./t18]
    type = PointValue
    variable = tot_yy
    point = '1.18 0 0'
    outputs = csv_t
  [../]
  [./t19]
    type = PointValue
    variable = tot_yy
    point = '1.19 0 0'
    outputs = csv_t
  [../]
  [./t20]
    type = PointValue
    variable = tot_yy
    point = '1.20 0 0'
    outputs = csv_t
  [../]
  [./t21]
    type = PointValue
    variable = tot_yy
    point = '1.21 0 0'
    outputs = csv_t
  [../]
  [./t22]
    type = PointValue
    variable = tot_yy
    point = '1.22 0 0'
    outputs = csv_t
  [../]
  [./t23]
    type = PointValue
    variable = tot_yy
    point = '1.23 0 0'
    outputs = csv_t
  [../]
  [./t24]
    type = PointValue
    variable = tot_yy
    point = '1.24 0 0'
    outputs = csv_t
  [../]
  [./t25]
    type = PointValue
    variable = tot_yy
    point = '1.25 0 0'
    outputs = csv_t
  [../]

  [./dt]
    type = FunctionValuePostprocessor
    outputs = console
    function = 2*t
  [../]
[]


[Preconditioning]
  [./andy]
    type = SMP
    full = true
    petsc_options = '-snes_monitor -snes_linesearch_monitor'
    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 1E0 1E-10 200 500 lu NONZERO'
  [../]
[]

[Executioner]
  type = Transient
  solve_type = Newton
  start_time = 0
  end_time = 0.3
  dt = 0.1
  #[./TimeStepper]
  #  type = PostprocessorDT
  #  postprocessor = dt
  #  dt = 0.003
  #[../]
[]

[Outputs]
  execute_on = 'timestep_end'
  file_base = borehole_highres
  exodus = true
  sync_times = '0.003 0.3'
  [./csv_p]
    file_base = borehole_highres_p
    type = CSV
  [../]
  [./csv_s]
    file_base = borehole_highres_s
    type = CSV
  [../]
  [./csv_t]
    file_base = borehole_highres_t
    type = CSV
  [../]
[]

(modules/combined/examples/phase_field-mechanics/kks_mechanics_KHS.i)

# KKS phase-field model coupled with elasticity using Khachaturyan's scheme as
# described in L.K. Aagesen et al., Computational Materials Science, 140, 10-21 (2017)
# Original run #170403a

[Mesh]
  type = GeneratedMesh
  dim = 3
  nx = 640
  ny = 1
  nz = 1
  xmin = -10
  xmax = 10
  ymin = 0
  ymax = 0.03125
  zmin = 0
  zmax = 0.03125
  elem_type = HEX8
[]


[Variables]
  # order parameter
  [./eta]
    order = FIRST
    family = LAGRANGE
  [../]

  # solute concentration
  [./c]
    order = FIRST
    family = LAGRANGE
  [../]

  # chemical potential
  [./w]
    order = FIRST
    family = LAGRANGE
  [../]

  # solute phase concentration (matrix)
  [./cm]
    order = FIRST
    family = LAGRANGE
  [../]
  # solute phase concentration (precipitate)
  [./cp]
    order = FIRST
    family = LAGRANGE
  [../]
  [./disp_x]
    order = FIRST
    family = LAGRANGE
  [../]
  [./disp_y]
    order = FIRST
    family = LAGRANGE
  [../]
  [./disp_z]
    order = FIRST
    family = LAGRANGE
  [../]
[]

[ICs]
  [./eta_ic]
    variable = eta
    type = FunctionIC
    function = ic_func_eta
    block = 0
  [../]
  [./c_ic]
    variable = c
    type = FunctionIC
    function = ic_func_c
    block = 0
  [../]
  [./w_ic]
    variable = w
    type = ConstantIC
    value = 0.00991
    block = 0
  [../]
  [./cm_ic]
    variable = cm
    type = ConstantIC
    value = 0.131
    block = 0
  [../]
  [./cp_ic]
    variable = cp
    type = ConstantIC
    value = 0.236
    block = 0
  [../]
[]

[Functions]
  [./ic_func_eta]
    type = ParsedFunction
    value = '0.5*(1.0+tanh((x)/delta_eta/sqrt(2.0)))'
    vars = 'delta_eta'
    vals = '0.8034'
  [../]
  [./ic_func_c]
    type = ParsedFunction
    value = '0.2389*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^3*(6*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^2-15*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))+10)+0.1339*(1-(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^3*(6*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^2-15*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))+10))'
    vars = 'delta'
    vals = '0.8034'
  [../]
  [./psi_eq_int]
    type = ParsedFunction
    value = 'volume*psi_alpha'
    vars = 'volume psi_alpha'
    vals = 'volume psi_alpha'
  [../]
  [./gamma]
    type = ParsedFunction
    value = '(psi_int - psi_eq_int) / dy / dz'
    vars = 'psi_int psi_eq_int dy       dz'
    vals = 'psi_int psi_eq_int 0.03125  0.03125'
  [../]
[]

[AuxVariables]
  [./sigma11]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./sigma22]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./sigma33]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./e11]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./e12]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./e22]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./e33]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./e_el11]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./e_el12]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./e_el22]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./f_el]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./eigen_strain00]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./Fglobal]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./psi]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

[AuxKernels]
  [./matl_sigma11]
    type = RankTwoAux
    rank_two_tensor = stress
    index_i = 0
    index_j = 0
    variable = sigma11
  [../]
  [./matl_sigma22]
    type = RankTwoAux
    rank_two_tensor = stress
    index_i = 1
    index_j = 1
    variable = sigma22
  [../]
  [./matl_sigma33]
    type = RankTwoAux
    rank_two_tensor = stress
    index_i = 2
    index_j = 2
    variable = sigma33
  [../]
  [./matl_e11]
    type = RankTwoAux
    rank_two_tensor = total_strain
    index_i = 0
    index_j = 0
    variable = e11
  [../]
  [./f_el]
    type = MaterialRealAux
    variable = f_el
    property = f_el_mat
    execute_on = timestep_end
  [../]
  [./GlobalFreeEnergy]
    variable = Fglobal
    type = KKSGlobalFreeEnergy
    fa_name = fm
    fb_name = fp
    w = 0.0264
    kappa_names = kappa
    interfacial_vars = eta
  [../]
  [./psi_potential]
    variable = psi
    type = ParsedAux
    args = 'Fglobal w c f_el sigma11 e11'
    function = 'Fglobal - w*c + f_el - sigma11*e11'
  [../]
[]


[BCs]
  [./left_x]
    type = DirichletBC
    variable = disp_x
    boundary = left
    value = 0
  [../]
  [./right_x]
    type = DirichletBC
    variable = disp_x
    boundary = right
    value = 0
  [../]
  [./front_y]
    type = DirichletBC
    variable = disp_y
    boundary = front
    value = 0
  [../]
  [./back_y]
    type = DirichletBC
    variable = disp_y
    boundary = back
    value = 0
  [../]
  [./top_z]
    type = DirichletBC
    variable = disp_z
    boundary = top
    value = 0
  [../]
  [./bottom_z]
    type = DirichletBC
    variable = disp_z
    boundary = bottom
    value = 0
  [../]
[]

[Materials]
  # Chemical free energy of the matrix
  [./fm]
    type = DerivativeParsedMaterial
    f_name = fm
    args = 'cm'
    function = '6.55*(cm-0.13)^2'
  [../]

  # Chemical Free energy of the precipitate phase
  [./fp]
    type = DerivativeParsedMaterial
    f_name = fp
    args = 'cp'
    function = '6.55*(cp-0.235)^2'
  [../]

# Elastic energy of the precipitate
  [./elastic_free_energy_p]
    type = ElasticEnergyMaterial
    f_name = f_el_mat
    args = 'eta'
    outputs = exodus
  [../]


  # h(eta)
  [./h_eta]
    type = SwitchingFunctionMaterial
    h_order = HIGH
    eta = eta
  [../]

  # 1- h(eta), putting in function explicitly
  [./one_minus_h_eta_explicit]
    type = DerivativeParsedMaterial
    f_name = one_minus_h_explicit
    args = eta
    function = 1-eta^3*(6*eta^2-15*eta+10)
    outputs = exodus
  [../]

  # g(eta)
  [./g_eta]
    type = BarrierFunctionMaterial
    g_order = SIMPLE
    eta = eta
  [../]

  # constant properties
  [./constants]
    type = GenericConstantMaterial
    prop_names  = 'M   L   kappa      misfit'
    prop_values = '0.7 0.7 0.01704    0.00377'
  [../]

  #Mechanical properties
  [./Stiffness_matrix]
    type = ComputeElasticityTensor
    base_name = C_matrix
    C_ijkl = '103.3 74.25 74.25 103.3 74.25 103.3 46.75 46.75 46.75'
    fill_method = symmetric9
  [../]
  [./Stiffness_ppt]
    type = ComputeElasticityTensor
    C_ijkl = '100.7 71.45 71.45 100.7 71.45 100.7 50.10 50.10 50.10'
    base_name = C_ppt
    fill_method = symmetric9
  [../]
  [./C]
    type = CompositeElasticityTensor
    args = eta
    tensors = 'C_matrix               C_ppt'
    weights = 'one_minus_h_explicit   h'
  [../]
  [./stress]
    type = ComputeLinearElasticStress
  [../]
  [./strain]
    type = ComputeSmallStrain
    displacements = 'disp_x disp_y disp_z'
    eigenstrain_names = 'eigenstrain_ppt'
  [../]
  [./eigen_strain]
    type = ComputeVariableEigenstrain
    eigen_base = '0.00377 0.00377 0.00377 0 0 0'
    prefactor = h
    args = eta
    eigenstrain_name = 'eigenstrain_ppt'
  [../]
[]

[Kernels]
  [./TensorMechanics]
    displacements = 'disp_x disp_y disp_z'
  [../]

  # enforce c = (1-h(eta))*cm + h(eta)*cp
  [./PhaseConc]
    type = KKSPhaseConcentration
    ca       = cm
    variable = cp
    c        = c
    eta      = eta
  [../]

  # enforce pointwise equality of chemical potentials
  [./ChemPotVacancies]
    type = KKSPhaseChemicalPotential
    variable = cm
    cb       = cp
    fa_name  = fm
    fb_name  = fp
  [../]

  #
  # Cahn-Hilliard Equation
  #
  [./CHBulk]
    type = KKSSplitCHCRes
    variable = c
    ca       = cm
    fa_name  = fm
    w        = w
  [../]

  [./dcdt]
    type = CoupledTimeDerivative
    variable = w
    v = c
  [../]
  [./ckernel]
    type = SplitCHWRes
    mob_name = M
    variable = w
  [../]

  #
  # Allen-Cahn Equation
  #
  [./ACBulkF]
    type = KKSACBulkF
    variable = eta
    fa_name  = fm
    fb_name  = fp
    w        = 0.0264
    args = 'cp cm'
  [../]
  [./ACBulkC]
    type = KKSACBulkC
    variable = eta
    ca       = cm
    cb       = cp
    fa_name  = fm
  [../]
  [./ACBulk_el] #This adds df_el/deta for strain interpolation
    type = AllenCahn
    variable = eta
    f_name = f_el_mat
  [../]
  [./ACInterface]
    type = ACInterface
    variable = eta
    kappa_name = kappa
  [../]
  [./detadt]
    type = TimeDerivative
    variable = eta
  [../]
[]

[Executioner]
  type = Transient
  solve_type = 'PJFNK'
  petsc_options_iname = '-pc_type -sub_pc_type   -sub_pc_factor_shift_type'
  petsc_options_value = 'asm       ilu            nonzero'

  l_max_its = 30
  nl_max_its = 10
  l_tol = 1.0e-4
  nl_rel_tol = 1.0e-8
  nl_abs_tol = 1.0e-11
  num_steps = 200

  [./TimeStepper]
    type = SolutionTimeAdaptiveDT
    dt = 0.5
  [../]
[]

[Postprocessors]
  [./f_el_int]
    type = ElementIntegralMaterialProperty
    mat_prop = f_el_mat
  [../]
  [./c_alpha]
    type =  SideAverageValue
    boundary = left
    variable = c
  [../]
  [./c_beta]
    type =  SideAverageValue
    boundary = right
    variable = c
  [../]
  [./e11_alpha]
    type =  SideAverageValue
    boundary = left
    variable = e11
  [../]
  [./e11_beta]
    type =  SideAverageValue
    boundary = right
    variable = e11
  [../]
  [./s11_alpha]
    type =  SideAverageValue
    boundary = left
    variable = sigma11
  [../]
  [./s22_alpha]
    type =  SideAverageValue
    boundary = left
    variable = sigma22
  [../]
  [./s33_alpha]
    type =  SideAverageValue
    boundary = left
    variable = sigma33
  [../]
  [./s11_beta]
    type =  SideAverageValue
    boundary = right
    variable = sigma11
  [../]
  [./s22_beta]
    type =  SideAverageValue
    boundary = right
    variable = sigma22
  [../]
  [./s33_beta]
    type =  SideAverageValue
    boundary = right
    variable = sigma33
  [../]
  [./f_el_alpha]
    type =  SideAverageValue
    boundary = left
    variable = f_el
  [../]
  [./f_el_beta]
    type =  SideAverageValue
    boundary = right
    variable = f_el
  [../]
  [./f_c_alpha]
    type =  SideAverageValue
    boundary = left
    variable = Fglobal
  [../]
  [./f_c_beta]
    type =  SideAverageValue
    boundary = right
    variable = Fglobal
  [../]
  [./chem_pot_alpha]
    type =  SideAverageValue
    boundary = left
    variable = w
  [../]
  [./chem_pot_beta]
    type =  SideAverageValue
    boundary = right
    variable = w
  [../]
  [./psi_alpha]
    type =  SideAverageValue
    boundary = left
    variable = psi
  [../]
  [./psi_beta]
    type =  SideAverageValue
    boundary = right
    variable = psi
  [../]
  [./total_energy]
    type = ElementIntegralVariablePostprocessor
    variable = Fglobal
  [../]
  # Get simulation cell size from postprocessor
  [./volume]
    type = ElementIntegralMaterialProperty
    mat_prop = 1
  [../]
  [./psi_eq_int]
    type = FunctionValuePostprocessor
    function = psi_eq_int
  [../]
  [./psi_int]
    type = ElementIntegralVariablePostprocessor
    variable = psi
  [../]
  [./gamma]
    type = FunctionValuePostprocessor
    function = gamma
  [../]
  [./int_position]
    type = FindValueOnLine
    start_point = '-10 0 0'
    end_point = '10 0 0'
    v = eta
    target = 0.5
  [../]
[]

#
# Precondition using handcoded off-diagonal terms
#
[Preconditioning]
  [./full]
    type = SMP
    full = true
  [../]
[]


[Outputs]
  [./exodus]
    type = Exodus
    interval = 20
  [../]
  checkpoint = true
  [./csv]
    type = CSV
    execute_on = 'final'
  [../]
[]

(modules/porous_flow/test/tests/poro_elasticity/mandel.i)

# Mandel's problem of consolodation of a drained medium
#
# A sample is in plane strain.
# -a <= x <= a
# -b <= y <= b
# It is squashed with constant force by impermeable, frictionless plattens on its top and bottom surfaces (at y=+/-b)
# Fluid is allowed to leak out from its sides (at x=+/-a)
# The porepressure within the sample is monitored.
#
# As is common in the literature, this is simulated by
# considering the quarter-sample, 0<=x<=a and 0<=y<=b, with
# impermeable, roller BCs at x=0 and y=0 and y=b.
# Porepressure is fixed at zero on x=a.
# Porepressure and displacement are initialised to zero.
# Then the top (y=b) is moved downwards with prescribed velocity,
# so that the total force that is inducing this downwards velocity
# is fixed.  The velocity is worked out by solving Mandel's problem
# analytically, and the total force is monitored in the simulation
# to check that it indeed remains constant.
#
# Here are the problem's parameters, and their values:
# Soil width.  a = 1
# Soil height.  b = 0.1
# Soil's Lame lambda.  la = 0.5
# Soil's Lame mu, which is also the Soil's shear modulus.  mu = G = 0.75
# Soil bulk modulus.  K = la + 2*mu/3 = 1
# Drained Poisson ratio.  nu = (3K - 2G)/(6K + 2G) = 0.2
# Soil bulk compliance.  1/K = 1
# Fluid bulk modulus.  Kf = 8
# Fluid bulk compliance.  1/Kf = 0.125
# Soil initial porosity.  phi0 = 0.1
# Biot coefficient.  alpha = 0.6
# Biot modulus.  M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 4.705882
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.694118
# Undrained Poisson ratio.  nuu = (3Ku - 2G)/(6Ku + 2G) = 0.372627
# Skempton coefficient.  B = alpha*M/Ku = 1.048035
# Fluid mobility (soil permeability/fluid viscosity).  k = 1.5
# Consolidation coefficient.  c = 2*k*B^2*G*(1-nu)*(1+nuu)^2/9/(1-nuu)/(nuu-nu) = 3.821656
# Normal stress on top.  F = 1
#
# The solution for porepressure and displacements is given in
# AHD Cheng and E Detournay "A direct boundary element method for plane strain poroelasticity" International Journal of Numerical and Analytical Methods in Geomechanics 12 (1988) 551-572.
# The solution involves complicated infinite series, so I shall not write it here
#
# FINAL NOTE: The above solution assumes constant Biot Modulus.
# In porous_flow this is not true.  Therefore the solution is
# a little different than in the paper.  This test was therefore
# validated against MOOSE's poromechanics, which can choose either
# a constant Biot Modulus (which has been shown to agree with
# the analytic solution), or a non-constant Biot Modulus (which
# gives the same results as porous_flow).

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

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
  PorousFlowDictator = dictator
  block = 0
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = 'porepressure disp_x disp_y disp_z'
    number_fluid_phases = 1
    number_fluid_components = 1
  []
  [pc]
    type = PorousFlowCapillaryPressureVG
    m = 0.8
    alpha = 1e-5
  []
[]

[Variables]
  [disp_x]
  []
  [disp_y]
  []
  [disp_z]
  []
  [porepressure]
  []
[]

[BCs]
  [roller_xmin]
    type = DirichletBC
    variable = disp_x
    value = 0
    boundary = 'left'
  []
  [roller_ymin]
    type = DirichletBC
    variable = disp_y
    value = 0
    boundary = 'bottom'
  []
  [plane_strain]
    type = DirichletBC
    variable = disp_z
    value = 0
    boundary = 'back front'
  []
  [xmax_drained]
    type = DirichletBC
    variable = porepressure
    value = 0
    boundary = right
  []
  [top_velocity]
    type = FunctionDirichletBC
    variable = disp_y
    function = top_velocity
    boundary = top
  []
[]

[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'
  []
[]

[AuxVariables]
  [stress_yy]
    order = CONSTANT
    family = MONOMIAL
  []
  [tot_force]
    order = CONSTANT
    family = MONOMIAL
  []
[]

[AuxKernels]
  [stress_yy]
    type = RankTwoAux
    rank_two_tensor = stress
    variable = stress_yy
    index_i = 1
    index_j = 1
  []
  [tot_force]
    type = ParsedAux
    args = 'stress_yy porepressure'
    execute_on = timestep_end
    variable = tot_force
    function = '-stress_yy+0.6*porepressure'
  []
[]

[Kernels]
  [grad_stress_x]
    type = StressDivergenceTensors
    variable = disp_x
    component = 0
  []
  [grad_stress_y]
    type = StressDivergenceTensors
    variable = disp_y
    component = 1
  []
  [grad_stress_z]
    type = StressDivergenceTensors
    variable = disp_z
    component = 2
  []
  [poro_x]
    type = PorousFlowEffectiveStressCoupling
    biot_coefficient = 0.6
    variable = disp_x
    component = 0
  []
  [poro_y]
    type = PorousFlowEffectiveStressCoupling
    biot_coefficient = 0.6
    variable = disp_y
    component = 1
  []
  [poro_z]
    type = PorousFlowEffectiveStressCoupling
    biot_coefficient = 0.6
    component = 2
    variable = disp_z
  []
  [poro_vol_exp]
    type = PorousFlowMassVolumetricExpansion
    variable = porepressure
    fluid_component = 0
  []
  [mass0]
    type = PorousFlowMassTimeDerivative
    fluid_component = 0
    variable = porepressure
  []
  [flux]
    type = PorousFlowAdvectiveFlux
    variable = porepressure
    gravity = '0 0 0'
    fluid_component = 0
  []
[]

[Modules]
  [FluidProperties]
    [simple_fluid]
      type = SimpleFluidProperties
      bulk_modulus = 8
      density0 = 1
      thermal_expansion = 0
      viscosity = 1
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
  []
  [elasticity_tensor]
    type = ComputeElasticityTensor
    C_ijkl = '0.5 0.75'
    # bulk modulus is lambda + 2*mu/3 = 0.5 + 2*0.75/3 = 1
    fill_method = symmetric_isotropic
  []
  [strain]
    type = ComputeSmallStrain
  []
  [stress]
    type = ComputeLinearElasticStress
  []
  [eff_fluid_pressure]
    type = PorousFlowEffectiveFluidPressure
  []
  [vol_strain]
    type = PorousFlowVolumetricStrain
  []
  [ppss]
    type = PorousFlow1PhaseP
    porepressure = porepressure
    capillary_pressure = pc
  []
  [massfrac]
    type = PorousFlowMassFraction
  []
  [simple_fluid]
    type = PorousFlowSingleComponentFluid
    fp = simple_fluid
    phase = 0
  []
  [porosity]
    type = PorousFlowPorosity
    fluid = true
    mechanical = true
    ensure_positive = false
    porosity_zero = 0.1
    biot_coefficient = 0.6
    solid_bulk = 1
  []
  [permeability]
    type = PorousFlowPermeabilityConst
    permeability = '1.5 0 0   0 1.5 0   0 0 1.5'
  []
  [relperm]
    type = PorousFlowRelativePermeabilityCorey
    n = 0 # unimportant in this fully-saturated situation
    phase = 0
  []
[]

[Postprocessors]
  [p0]
    type = PointValue
    outputs = csv
    point = '0.0 0 0'
    variable = porepressure
  []
  [p1]
    type = PointValue
    outputs = csv
    point = '0.1 0 0'
    variable = porepressure
  []
  [p2]
    type = PointValue
    outputs = csv
    point = '0.2 0 0'
    variable = porepressure
  []
  [p3]
    type = PointValue
    outputs = csv
    point = '0.3 0 0'
    variable = porepressure
  []
  [p4]
    type = PointValue
    outputs = csv
    point = '0.4 0 0'
    variable = porepressure
  []
  [p5]
    type = PointValue
    outputs = csv
    point = '0.5 0 0'
    variable = porepressure
  []
  [p6]
    type = PointValue
    outputs = csv
    point = '0.6 0 0'
    variable = porepressure
  []
  [p7]
    type = PointValue
    outputs = csv
    point = '0.7 0 0'
    variable = porepressure
  []
  [p8]
    type = PointValue
    outputs = csv
    point = '0.8 0 0'
    variable = porepressure
  []
  [p9]
    type = PointValue
    outputs = csv
    point = '0.9 0 0'
    variable = porepressure
  []
  [p99]
    type = PointValue
    outputs = csv
    point = '1 0 0'
    variable = porepressure
  []
  [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
    outputs = console
    function = if(0.15*t<0.01,0.15*t,0.01)
  []
[]


[Preconditioning]
  [andy]
    type = SMP
    full = true
    petsc_options_iname = '-ksp_type -pc_type -sub_pc_type -snes_atol -snes_rtol -snes_max_it'
    petsc_options_value = 'gmres asm lu 1E-14 1E-10 10000'
  []
[]

[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'
  file_base = mandel
  [csv]
    interval = 3
    type = CSV
  []
[]

(modules/combined/examples/geochem-porous_flow/geotes_weber_tensleep/aquifer_geochemistry.i)

#########################################
#                                       #
# File written by create_input_files.py #
#                                       #
#########################################
# Simulates geochemistry in the aquifer.  This input file may be run in standalone fashion but it does not do anything of interest.  To simulate something interesting, run the porous_flow.i simulation which couples to this input file using MultiApps.
# This file receives pf_rate_H pf_rate_Cl pf_rate_SO4 pf_rate_HCO3 pf_rate_SiO2aq pf_rate_Al pf_rate_Ca pf_rate_Mg pf_rate_Fe pf_rate_K pf_rate_Na pf_rate_Sr pf_rate_F pf_rate_BOH pf_rate_Br pf_rate_Ba pf_rate_Li pf_rate_NO3 pf_rate_O2aq pf_rate_H2O and temperature as AuxVariables from porous_flow.i
# The pf_rate quantities are kg/s changes of fluid-component mass at each node, but the geochemistry module expects rates-of-changes of moles at every node.  Secondly, since this input file considers just 1 litre of aqueous solution at every node, the nodal_void_volume is used to convert pf_rate_* into rate_*_per_1l, which is measured in mol/s/1_litre_of_aqueous_solution.
# This file sends massfrac_H massfrac_Cl massfrac_SO4 massfrac_HCO3 massfrac_SiO2aq massfrac_Al massfrac_Ca massfrac_Mg massfrac_Fe massfrac_K massfrac_Na massfrac_Sr massfrac_F massfrac_BOH massfrac_Br massfrac_Ba massfrac_Li massfrac_NO3 massfrac_O2aq to porous_flow.i.  These are computed from the corresponding transported_* quantities.

[UserObjects]
  [definition]
    type = GeochemicalModelDefinition
    database_file = '../../../../geochemistry/database/moose_geochemdb.json'
    basis_species = 'H2O H+ Cl- SO4-- HCO3- SiO2(aq) Al+++ Ca++ Mg++ Fe++ K+ Na+ Sr++ F- B(OH)3 Br- Ba++ Li+ NO3- O2(aq)'
    equilibrium_minerals = 'Siderite Pyrrhotite Dolomite Illite Anhydrite Calcite Quartz K-feldspar Kaolinite Barite Celestite Fluorite Albite Chalcedony Goethite'
  []
  [nodal_void_volume_uo]
    type = NodalVoidVolume
    porosity = porosity
    execute_on = 'initial timestep_end' # initial means this is evaluated properly for the first timestep
  []
[]

[SpatialReactionSolver]
  model_definition = definition
  geochemistry_reactor_name = reactor
  charge_balance_species = 'Cl-'
  swap_out_of_basis = 'NO3- H+         Fe++       Ba++   SiO2(aq) Mg++     O2(aq)   Al+++   K+     Ca++      HCO3-'
  swap_into_basis = '  NH3  Pyrrhotite K-feldspar Barite Quartz   Dolomite Siderite Calcite Illite Anhydrite Kaolinite'
# ASSUME that 1 litre of solution contains:
  constraint_species = 'H2O        Quartz     Calcite   K-feldspar Siderite  Dolomite  Anhydrite Pyrrhotite Illite    Kaolinite  Barite       Na+       Cl-       SO4--       Li+         B(OH)3      Br-         F-         Sr++        NH3'
  constraint_value = '  0.99778351 322.177447 12.111108 6.8269499  6.2844304 2.8670301 1.1912027 0.51474767 0.3732507 0.20903322 0.0001865889 1.5876606 1.5059455 0.046792579 0.013110503 0.006663119 0.001238987 0.00032108 0.000159781 0.001937302'
  constraint_meaning = 'kg_solvent_water bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition bulk_composition'
  constraint_unit = "kg moles moles moles moles moles moles moles moles moles moles moles moles moles moles moles moles moles moles moles"
  prevent_precipitation = 'Fluorite Albite Goethite'
  initial_temperature = 92
  temperature = temperature
  source_species_names = 'H+ Cl- SO4-- HCO3- SiO2(aq) Al+++ Ca++ Mg++ Fe++ K+ Na+ Sr++ F- B(OH)3 Br- Ba++ Li+ NO3- O2(aq) H2O'
  source_species_rates = ' rate_H_per_1l rate_Cl_per_1l rate_SO4_per_1l rate_HCO3_per_1l rate_SiO2aq_per_1l rate_Al_per_1l rate_Ca_per_1l rate_Mg_per_1l rate_Fe_per_1l rate_K_per_1l rate_Na_per_1l rate_Sr_per_1l rate_F_per_1l rate_BOH_per_1l rate_Br_per_1l rate_Ba_per_1l rate_Li_per_1l rate_NO3_per_1l rate_O2aq_per_1l rate_H2O_per_1l'
  ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
  execute_console_output_on = '' # only CSV and exodus output for this simulation
  add_aux_molal = false # save some memory and reduce variables in output exodus
  add_aux_mg_per_kg = false # save some memory and reduce variables in output exodus
  add_aux_free_mg = false # save some memory and reduce variables in output exodus
  add_aux_activity = false # save some memory and reduce variables in output exodus
  add_aux_bulk_moles = false # save some memory and reduce variables in output exodus
  adaptive_timestepping = true
[]

[Mesh]
  [gen]
    type = GeneratedMeshGenerator
    dim = 3
    xmin = -75
    xmax = 75
    ymin = 0
    ymax = 40
    zmin = -25
    zmax = 25
    nx = 15
    ny = 4
    nz = 5
  []
  [aquifer]
    type = ParsedSubdomainMeshGenerator
    input = gen
    block_id = 1
    block_name = aquifer
    combinatorial_geometry = 'z >= -5 & z <= 5'
  []
  [injection_nodes]
    input = aquifer
    type = ExtraNodesetGenerator
    new_boundary = injection_nodes
    coord = '-25 0 -5; -25 0 5'
  []
  [production_nodes]
    input = injection_nodes
    type = ExtraNodesetGenerator
    new_boundary = production_nodes
    coord = '25 0 -5; 25 0 5'
  []
[]
[GlobalParams]
  point = '-25 0 0'
  reactor = reactor
[]
[Executioner]
  type = Transient
  solve_type = Newton
  end_time = 7.76E6 # 90 days
  [TimeStepper]
    type = FunctionDT
    function = 'min(3E4, max(1E4, 0.2 * t))'
  []
[]
[AuxVariables]
  [temperature]
    initial_condition = 92.0
  []
  [porosity]
    initial_condition = 0.1
  []
  [nodal_void_volume]
  []
  [free_cm3_Kfeldspar] # necessary because of the minus sign in K-feldspar which does not parse correctly in the porosity AuxKernel
  []
  [pf_rate_H] # change in H mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Cl] # change in Cl mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_SO4] # change in SO4 mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_HCO3] # change in HCO3 mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_SiO2aq] # change in SiO2aq mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Al] # change in Al mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Ca] # change in Ca mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Mg] # change in Mg mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Fe] # change in Fe mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_K] # change in K mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Na] # change in Na mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Sr] # change in Sr mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_F] # change in F mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_BOH] # change in BOH mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Br] # change in Br mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Ba] # change in Ba mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_Li] # change in Li mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_NO3] # change in NO3 mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_O2aq] # change in O2aq mass (kg/s) at each node provided by the porous-flow simulation
  []
  [pf_rate_H2O] # change in H2O mass (kg/s) at each node provided by the porous-flow simulation
  []
  [rate_H_per_1l]
  []
  [rate_Cl_per_1l]
  []
  [rate_SO4_per_1l]
  []
  [rate_HCO3_per_1l]
  []
  [rate_SiO2aq_per_1l]
  []
  [rate_Al_per_1l]
  []
  [rate_Ca_per_1l]
  []
  [rate_Mg_per_1l]
  []
  [rate_Fe_per_1l]
  []
  [rate_K_per_1l]
  []
  [rate_Na_per_1l]
  []
  [rate_Sr_per_1l]
  []
  [rate_F_per_1l]
  []
  [rate_BOH_per_1l]
  []
  [rate_Br_per_1l]
  []
  [rate_Ba_per_1l]
  []
  [rate_Li_per_1l]
  []
  [rate_NO3_per_1l]
  []
  [rate_O2aq_per_1l]
  []
  [rate_H2O_per_1l]
  []
  [transported_H]
  []
  [transported_Cl]
  []
  [transported_SO4]
  []
  [transported_HCO3]
  []
  [transported_SiO2aq]
  []
  [transported_Al]
  []
  [transported_Ca]
  []
  [transported_Mg]
  []
  [transported_Fe]
  []
  [transported_K]
  []
  [transported_Na]
  []
  [transported_Sr]
  []
  [transported_F]
  []
  [transported_BOH]
  []
  [transported_Br]
  []
  [transported_Ba]
  []
  [transported_Li]
  []
  [transported_NO3]
  []
  [transported_O2aq]
  []
  [transported_H2O]
  []
  [transported_mass]
  []
  [massfrac_H]
  []
  [massfrac_Cl]
  []
  [massfrac_SO4]
  []
  [massfrac_HCO3]
  []
  [massfrac_SiO2aq]
  []
  [massfrac_Al]
  []
  [massfrac_Ca]
  []
  [massfrac_Mg]
  []
  [massfrac_Fe]
  []
  [massfrac_K]
  []
  [massfrac_Na]
  []
  [massfrac_Sr]
  []
  [massfrac_F]
  []
  [massfrac_BOH]
  []
  [massfrac_Br]
  []
  [massfrac_Ba]
  []
  [massfrac_Li]
  []
  [massfrac_NO3]
  []
  [massfrac_O2aq]
  []
  [massfrac_H2O]
  []
[]

[AuxKernels]
  [free_cm3_Kfeldspar]
    type = GeochemistryQuantityAux
    variable = free_cm3_Kfeldspar
    species = 'K-feldspar'
    quantity = free_cm3
    execute_on = 'timestep_end'
  []
  [porosity_auxk]
    type = ParsedAux
    args = 'free_cm3_Siderite free_cm3_Pyrrhotite free_cm3_Dolomite free_cm3_Illite free_cm3_Anhydrite free_cm3_Calcite free_cm3_Quartz free_cm3_Kfeldspar free_cm3_Kaolinite free_cm3_Barite free_cm3_Celestite free_cm3_Fluorite free_cm3_Albite free_cm3_Chalcedony free_cm3_Goethite'
    function = '1000.0 / (1000.0 + free_cm3_Siderite + free_cm3_Pyrrhotite + free_cm3_Dolomite + free_cm3_Illite + free_cm3_Anhydrite + free_cm3_Calcite + free_cm3_Quartz + free_cm3_Kfeldspar + free_cm3_Kaolinite + free_cm3_Barite + free_cm3_Celestite + free_cm3_Fluorite + free_cm3_Albite + free_cm3_Chalcedony + free_cm3_Goethite)'
    variable = porosity
    execute_on = 'timestep_end'
  []
  [nodal_void_volume_auxk]
    type = NodalVoidVolumeAux
    variable = nodal_void_volume
    nodal_void_volume_uo = nodal_void_volume_uo
    execute_on = 'initial timestep_end' # initial to ensure it is properly evaluated for the first timestep
  []
  [rate_H_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_H nodal_void_volume'
    variable = rate_H_per_1l
    function = 'pf_rate_H / 1.0079 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_Cl_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Cl nodal_void_volume'
    variable = rate_Cl_per_1l
    function = 'pf_rate_Cl / 35.453 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_SO4_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_SO4 nodal_void_volume'
    variable = rate_SO4_per_1l
    function = 'pf_rate_SO4 / 96.0576 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_HCO3_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_HCO3 nodal_void_volume'
    variable = rate_HCO3_per_1l
    function = 'pf_rate_HCO3 / 61.0171 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_SiO2aq_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_SiO2aq nodal_void_volume'
    variable = rate_SiO2aq_per_1l
    function = 'pf_rate_SiO2aq / 60.0843 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_Al_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Al nodal_void_volume'
    variable = rate_Al_per_1l
    function = 'pf_rate_Al / 26.9815 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_Ca_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Ca nodal_void_volume'
    variable = rate_Ca_per_1l
    function = 'pf_rate_Ca / 40.08 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_Mg_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Mg nodal_void_volume'
    variable = rate_Mg_per_1l
    function = 'pf_rate_Mg / 24.305 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_Fe_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Fe nodal_void_volume'
    variable = rate_Fe_per_1l
    function = 'pf_rate_Fe / 55.847 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_K_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_K nodal_void_volume'
    variable = rate_K_per_1l
    function = 'pf_rate_K / 39.0983 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_Na_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Na nodal_void_volume'
    variable = rate_Na_per_1l
    function = 'pf_rate_Na / 22.9898 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_Sr_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Sr nodal_void_volume'
    variable = rate_Sr_per_1l
    function = 'pf_rate_Sr / 87.62 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_F_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_F nodal_void_volume'
    variable = rate_F_per_1l
    function = 'pf_rate_F / 18.9984 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_BOH_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_BOH nodal_void_volume'
    variable = rate_BOH_per_1l
    function = 'pf_rate_BOH / 61.8329 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_Br_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Br nodal_void_volume'
    variable = rate_Br_per_1l
    function = 'pf_rate_Br / 79.904 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_Ba_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Ba nodal_void_volume'
    variable = rate_Ba_per_1l
    function = 'pf_rate_Ba / 137.33 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_Li_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_Li nodal_void_volume'
    variable = rate_Li_per_1l
    function = 'pf_rate_Li / 6.941 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_NO3_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_NO3 nodal_void_volume'
    variable = rate_NO3_per_1l
    function = 'pf_rate_NO3 / 62.0049 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_O2aq_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_O2aq nodal_void_volume'
    variable = rate_O2aq_per_1l
    function = 'pf_rate_O2aq / 31.9988 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [rate_H2O_per_1l_auxk]
    type = ParsedAux
    args = 'pf_rate_H2O nodal_void_volume'
    variable = rate_H2O_per_1l
    function = 'pf_rate_H2O / 18.01801802 / nodal_void_volume'
    execute_on = 'timestep_end'
  []
  [transported_H_auxk]
    type = GeochemistryQuantityAux
    variable = transported_H
    species = 'H+'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_Cl_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Cl
    species = 'Cl-'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_SO4_auxk]
    type = GeochemistryQuantityAux
    variable = transported_SO4
    species = 'SO4--'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_HCO3_auxk]
    type = GeochemistryQuantityAux
    variable = transported_HCO3
    species = 'HCO3-'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_SiO2aq_auxk]
    type = GeochemistryQuantityAux
    variable = transported_SiO2aq
    species = 'SiO2(aq)'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_Al_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Al
    species = 'Al+++'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_Ca_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Ca
    species = 'Ca++'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_Mg_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Mg
    species = 'Mg++'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_Fe_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Fe
    species = 'Fe++'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_K_auxk]
    type = GeochemistryQuantityAux
    variable = transported_K
    species = 'K+'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_Na_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Na
    species = 'Na+'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_Sr_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Sr
    species = 'Sr++'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_F_auxk]
    type = GeochemistryQuantityAux
    variable = transported_F
    species = 'F-'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_BOH_auxk]
    type = GeochemistryQuantityAux
    variable = transported_BOH
    species = 'B(OH)3'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_Br_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Br
    species = 'Br-'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_Ba_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Ba
    species = 'Ba++'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_Li_auxk]
    type = GeochemistryQuantityAux
    variable = transported_Li
    species = 'Li+'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_NO3_auxk]
    type = GeochemistryQuantityAux
    variable = transported_NO3
    species = 'NO3-'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_O2aq_auxk]
    type = GeochemistryQuantityAux
    variable = transported_O2aq
    species = 'O2(aq)'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_H2O_auxk]
    type = GeochemistryQuantityAux
    variable = transported_H2O
    species = 'H2O'
    quantity = transported_moles_in_original_basis
    execute_on = 'timestep_end'
  []
  [transported_mass_auxk]
    type = ParsedAux
    args = ' transported_H transported_Cl transported_SO4 transported_HCO3 transported_SiO2aq transported_Al transported_Ca transported_Mg transported_Fe transported_K transported_Na transported_Sr transported_F transported_BOH transported_Br transported_Ba transported_Li transported_NO3 transported_O2aq transported_H2O'
    variable = transported_mass
    function = 'transported_H * 1.0079 + transported_Cl * 35.453 + transported_SO4 * 96.0576 + transported_HCO3 * 61.0171 + transported_SiO2aq * 60.0843 + transported_Al * 26.9815 + transported_Ca * 40.08 + transported_Mg * 24.305 + transported_Fe * 55.847 + transported_K * 39.0983 + transported_Na * 22.9898 + transported_Sr * 87.62 + transported_F * 18.9984 + transported_BOH * 61.8329 + transported_Br * 79.904 + transported_Ba * 137.33 + transported_Li * 6.941 + transported_NO3 * 62.0049 + transported_O2aq * 31.9988 + transported_H2O * 18.01801802'
    execute_on = 'timestep_end'
  []
  [massfrac_H_auxk]
    type = ParsedAux
    args = 'transported_H transported_mass'
    variable = massfrac_H
    function = 'transported_H * 1.0079 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Cl_auxk]
    type = ParsedAux
    args = 'transported_Cl transported_mass'
    variable = massfrac_Cl
    function = 'transported_Cl * 35.453 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_SO4_auxk]
    type = ParsedAux
    args = 'transported_SO4 transported_mass'
    variable = massfrac_SO4
    function = 'transported_SO4 * 96.0576 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_HCO3_auxk]
    type = ParsedAux
    args = 'transported_HCO3 transported_mass'
    variable = massfrac_HCO3
    function = 'transported_HCO3 * 61.0171 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_SiO2aq_auxk]
    type = ParsedAux
    args = 'transported_SiO2aq transported_mass'
    variable = massfrac_SiO2aq
    function = 'transported_SiO2aq * 60.0843 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Al_auxk]
    type = ParsedAux
    args = 'transported_Al transported_mass'
    variable = massfrac_Al
    function = 'transported_Al * 26.9815 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Ca_auxk]
    type = ParsedAux
    args = 'transported_Ca transported_mass'
    variable = massfrac_Ca
    function = 'transported_Ca * 40.08 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Mg_auxk]
    type = ParsedAux
    args = 'transported_Mg transported_mass'
    variable = massfrac_Mg
    function = 'transported_Mg * 24.305 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Fe_auxk]
    type = ParsedAux
    args = 'transported_Fe transported_mass'
    variable = massfrac_Fe
    function = 'transported_Fe * 55.847 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_K_auxk]
    type = ParsedAux
    args = 'transported_K transported_mass'
    variable = massfrac_K
    function = 'transported_K * 39.0983 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Na_auxk]
    type = ParsedAux
    args = 'transported_Na transported_mass'
    variable = massfrac_Na
    function = 'transported_Na * 22.9898 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Sr_auxk]
    type = ParsedAux
    args = 'transported_Sr transported_mass'
    variable = massfrac_Sr
    function = 'transported_Sr * 87.62 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_F_auxk]
    type = ParsedAux
    args = 'transported_F transported_mass'
    variable = massfrac_F
    function = 'transported_F * 18.9984 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_BOH_auxk]
    type = ParsedAux
    args = 'transported_BOH transported_mass'
    variable = massfrac_BOH
    function = 'transported_BOH * 61.8329 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Br_auxk]
    type = ParsedAux
    args = 'transported_Br transported_mass'
    variable = massfrac_Br
    function = 'transported_Br * 79.904 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Ba_auxk]
    type = ParsedAux
    args = 'transported_Ba transported_mass'
    variable = massfrac_Ba
    function = 'transported_Ba * 137.33 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_Li_auxk]
    type = ParsedAux
    args = 'transported_Li transported_mass'
    variable = massfrac_Li
    function = 'transported_Li * 6.941 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_NO3_auxk]
    type = ParsedAux
    args = 'transported_NO3 transported_mass'
    variable = massfrac_NO3
    function = 'transported_NO3 * 62.0049 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_O2aq_auxk]
    type = ParsedAux
    args = 'transported_O2aq transported_mass'
    variable = massfrac_O2aq
    function = 'transported_O2aq * 31.9988 / transported_mass'
    execute_on = 'timestep_end'
  []
  [massfrac_H2O_auxk]
    type = ParsedAux
    args = 'transported_H2O transported_mass'
    variable = massfrac_H2O
    function = 'transported_H2O * 18.01801802 / transported_mass'
    execute_on = 'timestep_end'
  []
[]

[Postprocessors]
  [memory]
    type = MemoryUsage
    outputs = 'console'
  []
  [porosity]
    type = PointValue
    variable = porosity
  []
  [solution_temperature]
    type = PointValue
    variable = solution_temperature
  []
  [massfrac_H]
    type = PointValue
    variable = massfrac_H
  []
  [massfrac_Cl]
    type = PointValue
    variable = massfrac_Cl
  []
  [massfrac_SO4]
    type = PointValue
    variable = massfrac_SO4
  []
  [massfrac_HCO3]
    type = PointValue
    variable = massfrac_HCO3
  []
  [massfrac_SiO2aq]
    type = PointValue
    variable = massfrac_SiO2aq
  []
  [massfrac_Al]
    type = PointValue
    variable = massfrac_Al
  []
  [massfrac_Ca]
    type = PointValue
    variable = massfrac_Ca
  []
  [massfrac_Mg]
    type = PointValue
    variable = massfrac_Mg
  []
  [massfrac_Fe]
    type = PointValue
    variable = massfrac_Fe
  []
  [massfrac_K]
    type = PointValue
    variable = massfrac_K
  []
  [massfrac_Na]
    type = PointValue
    variable = massfrac_Na
  []
  [massfrac_Sr]
    type = PointValue
    variable = massfrac_Sr
  []
  [massfrac_F]
    type = PointValue
    variable = massfrac_F
  []
  [massfrac_BOH]
    type = PointValue
    variable = massfrac_BOH
  []
  [massfrac_Br]
    type = PointValue
    variable = massfrac_Br
  []
  [massfrac_Ba]
    type = PointValue
    variable = massfrac_Ba
  []
  [massfrac_Li]
    type = PointValue
    variable = massfrac_Li
  []
  [massfrac_NO3]
    type = PointValue
    variable = massfrac_NO3
  []
  [massfrac_O2aq]
    type = PointValue
    variable = massfrac_O2aq
  []
  [massfrac_H2O]
    type = PointValue
    variable = massfrac_H2O
  []
  [free_cm3_Siderite]
    type = PointValue
    variable = free_cm3_Siderite
  []
  [free_cm3_Pyrrhotite]
    type = PointValue
    variable = free_cm3_Pyrrhotite
  []
  [free_cm3_Dolomite]
    type = PointValue
    variable = free_cm3_Dolomite
  []
  [free_cm3_Illite]
    type = PointValue
    variable = free_cm3_Illite
  []
  [free_cm3_Anhydrite]
    type = PointValue
    variable = free_cm3_Anhydrite
  []
  [free_cm3_Calcite]
    type = PointValue
    variable = free_cm3_Calcite
  []
  [free_cm3_Quartz]
    type = PointValue
    variable = free_cm3_Quartz
  []
  [free_cm3_K-feldspar]
    type = PointValue
    variable = free_cm3_K-feldspar
  []
  [free_cm3_Kaolinite]
    type = PointValue
    variable = free_cm3_Kaolinite
  []
  [free_cm3_Barite]
    type = PointValue
    variable = free_cm3_Barite
  []
  [free_cm3_Celestite]
    type = PointValue
    variable = free_cm3_Celestite
  []
  [free_cm3_Fluorite]
    type = PointValue
    variable = free_cm3_Fluorite
  []
  [free_cm3_Albite]
    type = PointValue
    variable = free_cm3_Albite
  []
  [free_cm3_Chalcedony]
    type = PointValue
    variable = free_cm3_Chalcedony
  []
  [free_cm3_Goethite]
    type = PointValue
    variable = free_cm3_Goethite
  []
[]
[Outputs]
  exodus = true
  csv = true
[]

(modules/porous_flow/test/tests/chemistry/precipitation_2phase.i)

# Using a two-phase system (see precipitation.i for the single-phase)
# The saturation and porosity are chosen so that the results are identical to precipitation.i
#
# The precipitation reaction
#
# a <==> mineral
#
# produces "mineral".  Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / (porosity * saturation))' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is negative for a > 0.25, ie precipitation for a(t=0) > 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
#   = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * (porosity * saturation)
#
# This test checks that (a + c / (porosity * saturation)) is time-independent, and that a follows the above solution
#
# Aside:
#    The exponential curve is not followed exactly because moose actually solves
#    (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#    which does not give an exponential exactly, except in the limit dt->0
[Mesh]
  type = GeneratedMesh
  dim = 1
[]

[Variables]
  [a]
    initial_condition = 0.9
  []
[]

[AuxVariables]
  [eqm_k]
    initial_condition = 0.5
  []
  [pressure0]
  []
  [saturation1]
    initial_condition = 0.25
  []
  [b]
    initial_condition = 0.123
  []
  [ini_mineral_conc]
    initial_condition = 0.2
  []
  [mineral]
    family = MONOMIAL
    order = CONSTANT
  []
  [should_be_static]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[AuxKernels]
  [mineral]
    type = PorousFlowPropertyAux
    property = mineral_concentration
    mineral_species = 0
    variable = mineral
  []
  [should_be_static]
    type = ParsedAux
    args = 'mineral a'
    function = 'a + mineral / 0.1'
    variable = should_be_static
  []
[]

[GlobalParams]
  PorousFlowDictator = dictator
[]

[Kernels]
  [mass_a]
    type = PorousFlowMassTimeDerivative
    fluid_component = 0
    variable = a
  []
  [pre_dis]
    type = PorousFlowPreDis
    variable = a
    mineral_density = 1000
    stoichiometry = 1
  []
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = a
    number_fluid_phases = 2
    number_fluid_components = 2
    number_aqueous_kinetic = 1
    aqueous_phase_number = 1
  []
  [pc]
    type = PorousFlowCapillaryPressureConst
  []
[]

[Modules]
  [FluidProperties]
    [simple_fluid]
      type = SimpleFluidProperties
      bulk_modulus = 2e9 # huge, so mimic chemical_reactions
      density0 = 1000
      thermal_expansion = 0
      viscosity = 1e-3
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
    temperature = 1
  []
  [ppss]
    type = PorousFlow2PhasePS
    capillary_pressure = pc
    phase0_porepressure = pressure0
    phase1_saturation = saturation1
  []
  [mass_frac]
    type = PorousFlowMassFraction
    mass_fraction_vars = 'b a'
  []
  [predis]
    type = PorousFlowAqueousPreDisChemistry
    primary_concentrations = a
    num_reactions = 1
    equilibrium_constants = eqm_k
    primary_activity_coefficients = 2
    reactions = 1
    specific_reactive_surface_area = 0.5
    kinetic_rate_constant = 0.6065306597126334
    activation_energy = 3
    molar_volume = 2
    gas_constant = 6
    reference_temperature = 0.5
  []
  [mineral_conc]
    type = PorousFlowAqueousPreDisMineral
    initial_concentrations = ini_mineral_conc
  []
  [simple_fluid0]
    type = PorousFlowSingleComponentFluid
    fp = simple_fluid
    phase = 0
  []
  [simple_fluid1]
    type = PorousFlowSingleComponentFluid
    fp = simple_fluid
    phase = 1
  []
  [porosity]
    type = PorousFlowPorosityConst
    porosity = 0.4
  []
[]

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

[Executioner]
  type = Transient
  solve_type = Newton
  nl_abs_tol = 1E-10
  dt = 0.01
  end_time = 1
[]

[Postprocessors]
  [a]
    type = PointValue
    point = '0 0 0'
    variable = a
  []
  [should_be_static]
    type = PointValue
    point = '0 0 0'
    variable = should_be_static
  []
[]
[Outputs]
  interval = 10
  csv = true
  perf_graph = true
[]

(modules/combined/examples/geochem-porous_flow/geotes_2D/exchanger.i)

# Model of the heat-exchanger
# The input fluid to the heat exchanger is determined by AuxVariables called production_temperature, production_rate_Na, production_rate_Cl, production_rate_SiO2 and production_rate_H2O.  These come from Postprocessors in the porous-flow simulation that measure the fluid composition at the production well.
# Given the input fluid, the exchanger cools/heats the fluid, removing any precipitates, and injects fluid back to the porous-flow simulation at temperature output_temperature and composition given by massfrac_Na, etc.
# In the absence of data concerning Quartz precipitation rates in heat exchangers, do not treat Quartz as kinetic
[GlobalParams]
  point = '0 0 0'
  reactor = reactor
[]

[TimeDependentReactionSolver]
  model_definition = definition
  include_moose_solve = false
  geochemistry_reactor_name = reactor
  charge_balance_species = "Cl-"
  swap_out_of_basis = "SiO2(aq)"
  swap_into_basis = "QuartzLike"
  constraint_species = "H2O              Na+              Cl-              QuartzLike"
  constraint_value = "  1.0E-2           0.1E-2           0.1E-2           1E-10"
  constraint_meaning = "kg_solvent_water bulk_composition bulk_composition free_mineral"
  constraint_unit = "   kg               moles            moles            moles"
  initial_temperature = 50.0
  mode = 4
  temperature = 200
  cold_temperature = 40.0
  source_species_names = 'H2O    Na+   Cl-   SiO2(aq)'
  source_species_rates = 'production_rate_H2O production_rate_Na production_rate_Cl production_rate_SiO2'
  ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
  add_aux_pH = false # there is no H+ in this system
  evaluate_kinetic_rates_always = true # implicit time-marching used for stability
  execute_console_output_on = '' # only CSV output used in this example
[]

[UserObjects]
  [definition]
    type = GeochemicalModelDefinition
    database_file = "small_database.json"
    basis_species = "H2O SiO2(aq) Na+ Cl-"
    equilibrium_minerals = "QuartzLike"
  []
[]

[Executioner]
  type = Transient
  dt = 1E5
  end_time = 2E6 #7.76E6 # 90 days
[]

[AuxVariables]
  [production_temperature]
    initial_condition = 50 # the production_T Transfer lags one timestep behind for some reason, so give this a reasonable initial condition
  []
  [transported_H2O]
  []
  [transported_Na]
  []
  [transported_Cl]
  []
  [transported_SiO2]
  []
  [transported_mass]
  []
  [massfrac_H2O]
  []
  [massfrac_Na]
  []
  [massfrac_Cl]
  []
  [massfrac_SiO2]
  []
  [dumped_quartz]
  []
  [production_rate_H2O]
    initial_condition = 5.518533e+01 # the production_H2O Transfer lags one timestep behind for some reason (when the porous_flow simulation has finished, it correctly computes mole_rate_H2O_produced, but the Transfer gets the mole_rate_H2O_produced from the previous timestep), so give this a reasonable initial condition, otherwise this will be zero at the start of the simulation!
  []
  [production_rate_Na]
    initial_condition = 9.943302e-02
  []
  [production_rate_Cl]
    initial_condition = 9.943302e-02
  []
  [production_rate_SiO2]
    initial_condition = 2.340931e-04
  []
[]
[AuxKernels]
  [transported_H2O_auxk]
    type = GeochemistryQuantityAux
    variable = transported_H2O
    species = H2O
    quantity = transported_moles_in_original_basis
  []
  [transported_Na]
    type = GeochemistryQuantityAux
    variable = transported_Na
    species = Na+
    quantity = transported_moles_in_original_basis
  []
  [transported_Cl]
    type = GeochemistryQuantityAux
    variable = transported_Cl
    species = Cl-
    quantity = transported_moles_in_original_basis
  []
  [transported_SiO2]
    type = GeochemistryQuantityAux
    variable = transported_SiO2
    species = 'SiO2(aq)'
    quantity = transported_moles_in_original_basis
  []
  [transported_mass_auxk]
    type = ParsedAux
    args = 'transported_H2O transported_Na transported_Cl transported_SiO2'
    variable = transported_mass
    function = 'transported_H2O * 18.0152 + transported_Na * 22.9898 + transported_Cl * 35.453 + transported_SiO2 * 60.0843'
  []
  [massfrac_H2O]
    type = ParsedAux
    args = 'transported_mass transported_H2O'
    variable = massfrac_H2O
    function = '18.0152 * transported_H2O / transported_mass'
  []
  [massfrac_Na]
    type = ParsedAux
    args = 'transported_mass transported_Na'
    variable = massfrac_Na
    function = '22.9898 * transported_Na / transported_mass'
  []
  [massfrac_Cl]
    type = ParsedAux
    args = 'transported_mass transported_Cl'
    variable = massfrac_Cl
    function = '35.453 * transported_Cl / transported_mass'
  []
  [massfrac_SiO2]
    type = ParsedAux
    args = 'transported_mass transported_SiO2'
    variable = massfrac_SiO2
    function = '60.0843 * transported_SiO2 / transported_mass'
  []
  [dumped_quartz]
    type = GeochemistryQuantityAux
    variable = dumped_quartz
    species = QuartzLike
    quantity = moles_dumped
  []
[]
[Postprocessors]
  [cumulative_moles_precipitated_quartz]
    type = PointValue
    variable = dumped_quartz
  []
  [production_temperature]
    type = PointValue
    variable = production_temperature
  []
  [mass_heated_this_timestep]
    type = PointValue
    variable = transported_mass
  []
[]
[Outputs]
  csv = true
[]

[MultiApps]
  [porous_flow_sim]
    type = TransientMultiApp
    input_files = porous_flow.i
    execute_on = 'timestep_end'
  []
[]

[Transfers]
  [injection_T]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'solution_temperature'
    variable = 'injection_temperature'
  []
  [injection_Na]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_Na'
    variable = 'injection_rate_massfrac_Na'
  []
  [injection_Cl]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_Cl'
    variable = 'injection_rate_massfrac_Cl'
  []
  [injection_SiO2]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_SiO2'
    variable = 'injection_rate_massfrac_SiO2'
  []
  [injection_H2O]
    type = MultiAppNearestNodeTransfer
    direction = TO_MULTIAPP
    multi_app = porous_flow_sim
    fixed_meshes = true
    source_variable = 'massfrac_H2O'
    variable = 'injection_rate_massfrac_H2O'
  []

  [production_T]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = production_temperature
    variable = production_temperature
  []
  [production_Na]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_Na_produced
    variable = production_rate_Na
  []
  [production_Cl]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_Cl_produced
    variable = production_rate_Cl
  []
  [production_SiO2]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_SiO2_produced
    variable = production_rate_SiO2
  []
  [production_H2O]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = FROM_MULTIAPP
    multi_app = porous_flow_sim
    postprocessor = mole_rate_H2O_produced
    variable = production_rate_H2O
  []
[]

(modules/porous_flow/examples/reservoir_model/field_model.i)

# Field model generated using geophysical modelling tool

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

[GlobalParams]
  PorousFlowDictator = dictator
  gravity = '0 0 -9.81'
  temperature_unit = Celsius
[]

[Variables]
  [porepressure]
    initial_condition = 20e6
  []
[]

[AuxVariables]
  [temperature]
    initial_condition = 50
  []
  [xnacl]
    initial_condition = 0.1
  []
  [porosity]
    family = MONOMIAL
    order = CONSTANT
    initial_from_file_var = poro
  []
  [permx_md]
    family = MONOMIAL
    order = CONSTANT
    initial_from_file_var = permX
  []
  [permy_md]
    family = MONOMIAL
    order = CONSTANT
    initial_from_file_var = permY
  []
  [permz_md]
    family = MONOMIAL
    order = CONSTANT
    initial_from_file_var = permZ
  []
  [permx]
    family = MONOMIAL
    order = CONSTANT
  []
  [permy]
    family = MONOMIAL
    order = CONSTANT
  []
  [permz]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[AuxKernels]
  [permx]
    type = ParsedAux
    variable = permx
    args = permx_md
    function = '9.869233e-16*permx_md'
    execute_on = initial
  []
  [permy]
    type = ParsedAux
    variable = permy
    args = permy_md
    function = '9.869233e-16*permy_md'
    execute_on = initial
  []
  [permz]
    type = ParsedAux
    variable = permz
    args = permz_md
    function = '9.869233e-16*permz_md'
    execute_on = initial
  []
[]

[Kernels]
  [mass0]
    type = PorousFlowMassTimeDerivative
    variable = porepressure
  []
  [flux0]
    type = PorousFlowFullySaturatedDarcyFlow
    variable = porepressure
  []
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = porepressure
    number_fluid_phases = 1
    number_fluid_components = 1
  []
[]

[Modules]
  [FluidProperties]
    [water]
      type = Water97FluidProperties
    []
    [watertab]
      type = TabulatedFluidProperties
      fp = water
      save_file = false
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
    temperature = temperature
  []
  [ps]
    type = PorousFlow1PhaseFullySaturated
    porepressure = porepressure
  []
  [massfrac]
    type = PorousFlowMassFraction
  []
  [brine]
    type = PorousFlowBrine
    compute_enthalpy = false
    compute_internal_energy = false
    xnacl = xnacl
    phase = 0
    water_fp = watertab
  []
  [porosity]
    type = PorousFlowPorosityConst
    porosity = porosity
  []
  [permeability]
    type = PorousFlowPermeabilityConstFromVar
    perm_xx = permx
    perm_yy = permy
    perm_zz = permz
  []
[]

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

[Executioner]
  type = Transient
  solve_type = Newton
  dt = 1e2
  end_time = 1e2
[]

[Outputs]
  execute_on = 'initial timestep_end'
  exodus = true
  perf_graph = true
[]

(modules/porous_flow/examples/thm_example/2D_c.i)

# Two phase, temperature-dependent, with mechanics and chemistry, radial with fine mesh, constant injection of cold co2 into a overburden-reservoir-underburden containing mostly water
# species=0 is water
# species=1 is co2
# phase=0 is liquid, and since massfrac_ph0_sp0 = 1, this is all water
# phase=1 is gas, and since massfrac_ph1_sp0 = 0, this is all co2
#
# The mesh used below has very high resolution, so the simulation takes a long time to complete.
# Some suggested meshes of different resolution:
# nx=50, bias_x=1.2
# nx=100, bias_x=1.1
# nx=200, bias_x=1.05
# nx=400, bias_x=1.02
# nx=1000, bias_x=1.01
# nx=2000, bias_x=1.003
[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 2000
  bias_x = 1.003
  xmin = 0.1
  xmax = 5000
  ny = 1
  ymin = 0
  ymax = 11
[]

[Problem]
  coord_type = RZ
[]

[GlobalParams]
  displacements = 'disp_r disp_z'
  PorousFlowDictator = dictator
  gravity = '0 0 0'
  biot_coefficient = 1.0
[]

[Variables]
  [pwater]
    initial_condition = 18.3e6
  []
  [sgas]
    initial_condition = 0.0
  []
  [temp]
    initial_condition = 358
  []
  [disp_r]
  []
[]

[AuxVariables]
  [rate]
  []
  [disp_z]
  []
  [massfrac_ph0_sp0]
    initial_condition = 1 # all H20 in phase=0
  []
  [massfrac_ph1_sp0]
    initial_condition = 0 # no H2O in phase=1
  []
  [pgas]
    family = MONOMIAL
    order = FIRST
  []
  [swater]
    family = MONOMIAL
    order = FIRST
  []
  [stress_rr]
    order = CONSTANT
    family = MONOMIAL
  []
  [stress_tt]
    order = CONSTANT
    family = MONOMIAL
  []
  [stress_zz]
    order = CONSTANT
    family = MONOMIAL
  []
  [mineral_conc_m3_per_m3]
    family = MONOMIAL
    order = CONSTANT
    initial_condition = 0.1
  []
  [eqm_const]
    initial_condition = 0.0
  []
  [porosity]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[Kernels]
  [mass_water_dot]
    type = PorousFlowMassTimeDerivative
    fluid_component = 0
    use_displaced_mesh = false
    variable = pwater
  []
  [flux_water]
    type = PorousFlowAdvectiveFlux
    fluid_component = 0
    use_displaced_mesh = false
    variable = pwater
  []
  [mass_co2_dot]
    type = PorousFlowMassTimeDerivative
    fluid_component = 1
    use_displaced_mesh = false
    variable = sgas
  []
  [flux_co2]
    type = PorousFlowAdvectiveFlux
    fluid_component = 1
    use_displaced_mesh = false
    variable = sgas
  []
  [energy_dot]
    type = PorousFlowEnergyTimeDerivative
    use_displaced_mesh = false
    variable = temp
  []
  [advection]
    type = PorousFlowHeatAdvection
    use_displaced_mesh = false
    variable = temp
  []
  [conduction]
    type = PorousFlowExponentialDecay
    use_displaced_mesh = false
    variable = temp
    reference = 358
    rate = rate
  []
  [grad_stress_r]
    type = StressDivergenceRZTensors
    temperature = temp
    eigenstrain_names = thermal_contribution
    variable = disp_r
    use_displaced_mesh = false
    component = 0
  []
  [poro_r]
    type = PorousFlowEffectiveStressCoupling
    variable = disp_r
    use_displaced_mesh = false
    component = 0
  []
[]

[AuxKernels]
  [rate]
    type = FunctionAux
    variable = rate
    execute_on = timestep_begin
    function = decay_rate
  []
  [pgas]
    type = PorousFlowPropertyAux
    property = pressure
    phase = 1
    variable = pgas
  []
  [swater]
    type = PorousFlowPropertyAux
    property = saturation
    phase = 0
    variable = swater
  []
  [stress_rr]
    type = RankTwoAux
    rank_two_tensor = stress
    variable = stress_rr
    index_i = 0
    index_j = 0
  []
  [stress_tt]
    type = RankTwoAux
    rank_two_tensor = stress
    variable = stress_tt
    index_i = 2
    index_j = 2
  []
  [stress_zz]
    type = RankTwoAux
    rank_two_tensor = stress
    variable = stress_zz
    index_i = 1
    index_j = 1
  []
  [mineral]
    type = PorousFlowPropertyAux
    property = mineral_concentration
    mineral_species = 0
    variable = mineral_conc_m3_per_m3
  []
  [eqm_const_auxk]
    type = ParsedAux
    variable = eqm_const
    args = temp
    function = '(358 - temp) / (358 - 294)'
  []
  [porosity_auxk]
    type = PorousFlowPropertyAux
    property = porosity
    variable = porosity
  []
[]

[Functions]
  [decay_rate]
# Eqn(26) of the first paper of LaForce et al.
# Ka * (rho C)_a = 10056886.914
# h = 11
    type = ParsedFunction
    value = 'sqrt(10056886.914/t)/11.0'
  []
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = 'temp pwater sgas disp_r'
    number_fluid_phases = 2
    number_fluid_components = 2
    number_aqueous_kinetic = 1
    aqueous_phase_number = 1
  []
  [pc]
    type = PorousFlowCapillaryPressureConst
    pc = 0
  []
[]

[Modules]
  [FluidProperties]
    [water]
      type = SimpleFluidProperties
      bulk_modulus = 2.27e14
      density0 = 970.0
      viscosity = 0.3394e-3
      cv = 4149.0
      cp = 4149.0
      porepressure_coefficient = 0.0
      thermal_expansion = 0
    []
    [co2]
      type = SimpleFluidProperties
      bulk_modulus = 2.27e14
      density0 = 516.48
      viscosity = 0.0393e-3
      cv = 2920.5
      cp = 2920.5
      porepressure_coefficient = 0.0
      thermal_expansion = 0
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
    temperature = temp
  []
  [ppss]
    type = PorousFlow2PhasePS
    phase0_porepressure = pwater
    phase1_saturation = sgas
    capillary_pressure = pc
  []
  [massfrac]
    type = PorousFlowMassFraction
    mass_fraction_vars = 'massfrac_ph0_sp0 massfrac_ph1_sp0'
  []
  [water]
    type = PorousFlowSingleComponentFluid
    fp = water
    phase = 0
  []
  [gas]
    type = PorousFlowSingleComponentFluid
    fp = co2
    phase = 1
  []
  [porosity_reservoir]
    type = PorousFlowPorosity
    porosity_zero = 0.2
    chemical = true
    reference_chemistry = 0.1
    initial_mineral_concentrations = 0.1
  []
  [permeability_reservoir]
    type = PorousFlowPermeabilityConst
    permeability = '2e-12 0 0  0 0 0  0 0 0'
  []
  [relperm_liquid]
    type = PorousFlowRelativePermeabilityCorey
    n = 4
    phase = 0
    s_res = 0.200
    sum_s_res = 0.405
  []
  [relperm_gas]
    type = PorousFlowRelativePermeabilityBC
    phase = 1
    s_res = 0.205
    sum_s_res = 0.405
    nw_phase = true
    lambda = 2
  []
  [thermal_conductivity_reservoir]
    type = PorousFlowThermalConductivityIdeal
    dry_thermal_conductivity = '0 0 0  0 1.320 0  0 0 0'
    wet_thermal_conductivity = '0 0 0  0 3.083 0  0 0 0'
  []
  [internal_energy_reservoir]
    type = PorousFlowMatrixInternalEnergy
    specific_heat_capacity = 1100
    density = 2350.0
  []
  [elasticity_tensor]
    type = ComputeIsotropicElasticityTensor
    shear_modulus = 6.0E9
    poissons_ratio = 0.2
  []
  [strain]
    type = ComputeAxisymmetricRZSmallStrain
    eigenstrain_names = 'thermal_contribution ini_stress'
  []
  [ini_strain]
    type = ComputeEigenstrainFromInitialStress
    initial_stress = '-12.8E6 0 0  0 -51.3E6 0  0 0 -12.8E6'
    eigenstrain_name = ini_stress
  []
  [thermal_contribution]
    type = ComputeThermalExpansionEigenstrain
    temperature = temp
    stress_free_temperature = 358
    thermal_expansion_coeff = 5E-6
    eigenstrain_name = thermal_contribution
  []
  [stress]
    type = ComputeLinearElasticStress
  []
  [eff_fluid_pressure]
    type = PorousFlowEffectiveFluidPressure
  []
  [vol_strain]
    type = PorousFlowVolumetricStrain
  []
  [predis]
    type = PorousFlowAqueousPreDisChemistry
    num_reactions = 1
    primary_concentrations = 1.0 # fixed activity
    equilibrium_constants_as_log10 = true
    equilibrium_constants = eqm_const
    primary_activity_coefficients = 1.0 # fixed activity
    reactions = 1
    kinetic_rate_constant = 1E-6
    molar_volume = 1.0
    specific_reactive_surface_area = 1.0
    activation_energy = 0.0 # no Arrhenius
  []
  [mineral_conc]
    type = PorousFlowAqueousPreDisMineral
    initial_concentrations = 0.1
  []
  [predis_nodes]
    type = PorousFlowAqueousPreDisChemistry
    at_nodes = true
    num_reactions = 1
    primary_concentrations = 1.0 # fixed activity
    equilibrium_constants_as_log10 = true
    equilibrium_constants = eqm_const
    primary_activity_coefficients = 1.0 # fixed activity
    reactions = 1
    kinetic_rate_constant = 1E-6
    molar_volume = 1.0
    specific_reactive_surface_area = 1.0
    activation_energy = 0.0 # no Arrhenius
  []
  [mineral_conc_nodes]
    type = PorousFlowAqueousPreDisMineral
    at_nodes = true
    initial_concentrations = 0.1
  []
[]

[BCs]
  [outer_pressure_fixed]
    type = DirichletBC
    boundary = right
    value = 18.3e6
    variable = pwater
  []
  [outer_saturation_fixed]
    type = DirichletBC
    boundary = right
    value = 0.0
    variable = sgas
  []
  [outer_temp_fixed]
    type = DirichletBC
    boundary = right
    value = 358
    variable = temp
  []
  [fixed_outer_r]
    type = DirichletBC
    variable = disp_r
    value = 0
    boundary = right
  []
  [co2_injection]
    type = PorousFlowSink
    boundary = left
    variable = sgas
    use_mobility = false
    use_relperm = false
    fluid_phase = 1
    flux_function = 'min(t/100.0,1)*(-2.294001475)' # 5.0E5 T/year = 15.855 kg/s, over area of 2Pi*0.1*11
  []
  [cold_co2]
    type = DirichletBC
    boundary = left
    variable = temp
    value = 294
  []
  [cavity_pressure_x]
    type = Pressure
    boundary = left
    variable = disp_r
    component = 0
    postprocessor = p_bh # note, this lags
    use_displaced_mesh = false
  []
[]

[Postprocessors]
  [p_bh]
    type = PointValue
    variable = pwater
    point = '0.1 0 0'
    execute_on = timestep_begin
    use_displaced_mesh = false
  []
  [mineral_bh] # mineral concentration (m^3(mineral)/m^3(rock)) at the borehole
    type = PointValue
    variable = mineral_conc_m3_per_m3
    point = '0.1 0 0'
    use_displaced_mesh = false
  []
[]

[VectorPostprocessors]
  [ptsuss]
    type = LineValueSampler
    use_displaced_mesh = false
    start_point = '0.1 0 0'
    end_point = '5000 0 0'
    sort_by = x
    num_points = 50000
    outputs = csv
    variable = 'pwater temp sgas disp_r stress_rr stress_tt mineral_conc_m3_per_m3 porosity'
  []
[]

[Preconditioning]
  active = 'smp'
  [smp]
    type = SMP
    full = true
    #petsc_options = '-snes_converged_reason -ksp_diagonal_scale -ksp_diagonal_scale_fix -ksp_gmres_modifiedgramschmidt -snes_linesearch_monitor'
    petsc_options_iname = '-ksp_type -pc_type -sub_pc_type -sub_pc_factor_shift_type -pc_asm_overlap -snes_atol -snes_rtol -snes_max_it'
    petsc_options_value = 'gmres      asm      lu           NONZERO                   2               1E2       1E-5        50'
  []
  [mumps]
    type = SMP
    full = true
    petsc_options = '-snes_converged_reason -ksp_diagonal_scale -ksp_diagonal_scale_fix -ksp_gmres_modifiedgramschmidt -snes_linesearch_monitor'
    petsc_options_iname = '-ksp_type -pc_type -pc_factor_mat_solver_package -pc_factor_shift_type -snes_rtol -snes_atol -snes_max_it'
    petsc_options_value = 'gmres      lu       mumps                         NONZERO               1E-5       1E2       50'
  []
[]

[Executioner]
  type = Transient
  solve_type = NEWTON
  end_time = 1.5768e8
  #dtmax = 1e6
  [TimeStepper]
    type = IterationAdaptiveDT
    dt = 1
    growth_factor = 1.1
  []
[]

[Outputs]
  print_linear_residuals = false
  sync_times = '3600 86400 2.592E6 1.5768E8'
  perf_graph = true
  exodus = true
  [csv]
    type = CSV
    sync_only = true
  []
[]

(modules/porous_flow/test/tests/chemistry/dissolution_limited_2phase.i)

# Using a two-phase system (see dissolution_limited.i for the single-phase)
# The saturation and porosity are chosen so that the results are identical to dissolution_limited.i
#
# The dissolution reaction, with limited initial mineral concentration
#
# a <==> mineral
#
# produces "mineral".  Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / (porosity * saturation))' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is positive for a < 0.25, ie dissolution for a(t=0) < 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
#   = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * porosity * saturation
#
# However, c(t=0) is small, so that the reaction only works until c=0, then a and c both remain fixed
#
# This test checks that (a + c / (porosity * saturation)) is time-independent, and that a follows the above solution, until c=0 and thereafter remains fixed.
#
# Aside:
#    The exponential curve is not followed exactly because moose actually solves
#    (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#    which does not give an exponential exactly, except in the limit dt->0
[Mesh]
  type = GeneratedMesh
  dim = 1
[]

[Variables]
  [a]
    initial_condition = 0.05
  []
[]

[AuxVariables]
  [eqm_k]
    initial_condition = 0.5
  []
  [pressure0]
  []
  [saturation1]
    initial_condition = 0.25
  []
  [b]
    initial_condition = 0.123
  []
  [ini_mineral_conc]
    initial_condition = 0.015
  []
  [mineral]
    family = MONOMIAL
    order = CONSTANT
  []
  [should_be_static]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[AuxKernels]
  [mineral]
    type = PorousFlowPropertyAux
    property = mineral_concentration
    mineral_species = 0
    variable = mineral
  []
  [should_be_static]
    type = ParsedAux
    args = 'mineral a'
    function = 'a + mineral / 0.1'
    variable = should_be_static
  []
[]

[GlobalParams]
  PorousFlowDictator = dictator
[]

[Kernels]
  [mass_a]
    type = PorousFlowMassTimeDerivative
    fluid_component = 0
    variable = a
  []
  [pre_dis]
    type = PorousFlowPreDis
    variable = a
    mineral_density = 1000
    stoichiometry = 1
  []
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = a
    number_fluid_phases = 2
    number_fluid_components = 2
    number_aqueous_kinetic = 1
    aqueous_phase_number = 1
  []
  [pc]
    type = PorousFlowCapillaryPressureConst
  []
[]

[Modules]
  [FluidProperties]
    [simple_fluid]
      type = SimpleFluidProperties
      bulk_modulus = 2e9 # huge, so mimic chemical_reactions
      density0 = 1000
      thermal_expansion = 0
      viscosity = 1e-3
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
    temperature = 1
  []
  [ppss]
    type = PorousFlow2PhasePS
    capillary_pressure = pc
    phase0_porepressure = pressure0
    phase1_saturation = saturation1
  []
  [mass_frac]
    type = PorousFlowMassFraction
    mass_fraction_vars = 'b a'
  []
  [predis]
    type = PorousFlowAqueousPreDisChemistry
    primary_concentrations = a
    num_reactions = 1
    equilibrium_constants = eqm_k
    primary_activity_coefficients = 2
    reactions = 1
    specific_reactive_surface_area = 0.5
    kinetic_rate_constant = 0.6065306597126334
    activation_energy = 3
    molar_volume = 2
    gas_constant = 6
    reference_temperature = 0.5
  []
  [mineral_conc]
    type = PorousFlowAqueousPreDisMineral
    initial_concentrations = ini_mineral_conc
  []
  [simple_fluid0]
    type = PorousFlowSingleComponentFluid
    fp = simple_fluid
    phase = 0
  []
  [simple_fluid1]
    type = PorousFlowSingleComponentFluid
    fp = simple_fluid
    phase = 1
  []
  [porosity]
    type = PorousFlowPorosityConst
    porosity = 0.4
  []
[]

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

[Executioner]
  type = Transient
  solve_type = Newton
  nl_abs_tol = 1E-10
  dt = 0.01
  end_time = 1
[]

[Postprocessors]
  [a]
    type = PointValue
    point = '0 0 0'
    variable = a
  []
  [should_be_static]
    type = PointValue
    point = '0 0 0'
    variable = should_be_static
  []
[]
[Outputs]
  interval = 10
  csv = true
  perf_graph = true
[]

(modules/porous_flow/test/tests/poro_elasticity/mandel_fully_saturated_volume.i)

# Mandel's problem of consolodation of a drained medium
# Using the FullySaturatedDarcyBase and FullySaturatedFullySaturatedMassTimeDerivative kernels
# with multiply_by_density = false, so that this problem becomes linear
# Note the use of consistent_with_displaced_mesh = false in the calculation of volumetric strain
#
# A sample is in plane strain.
# -a <= x <= a
# -b <= y <= b
# It is squashed with constant force by impermeable, frictionless plattens on its top and bottom surfaces (at y=+/-b)
# Fluid is allowed to leak out from its sides (at x=+/-a)
# The porepressure within the sample is monitored.
#
# As is common in the literature, this is simulated by
# considering the quarter-sample, 0<=x<=a and 0<=y<=b, with
# impermeable, roller BCs at x=0 and y=0 and y=b.
# Porepressure is fixed at zero on x=a.
# Porepressure and displacement are initialised to zero.
# Then the top (y=b) is moved downwards with prescribed velocity,
# so that the total force that is inducing this downwards velocity
# is fixed.  The velocity is worked out by solving Mandel's problem
# analytically, and the total force is monitored in the simulation
# to check that it indeed remains constant.
#
# Here are the problem's parameters, and their values:
# Soil width.  a = 1
# Soil height.  b = 0.1
# Soil's Lame lambda.  la = 0.5
# Soil's Lame mu, which is also the Soil's shear modulus.  mu = G = 0.75
# Soil bulk modulus.  K = la + 2*mu/3 = 1
# Drained Poisson ratio.  nu = (3K - 2G)/(6K + 2G) = 0.2
# Soil bulk compliance.  1/K = 1
# Fluid bulk modulus.  Kf = 8
# Fluid bulk compliance.  1/Kf = 0.125
# Soil initial porosity.  phi0 = 0.1
# Biot coefficient.  alpha = 0.6
# Biot modulus.  M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 4.705882
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.694118
# Undrained Poisson ratio.  nuu = (3Ku - 2G)/(6Ku + 2G) = 0.372627
# Skempton coefficient.  B = alpha*M/Ku = 1.048035
# Fluid mobility (soil permeability/fluid viscosity).  k = 1.5
# Consolidation coefficient.  c = 2*k*B^2*G*(1-nu)*(1+nuu)^2/9/(1-nuu)/(nuu-nu) = 3.821656
# Normal stress on top.  F = 1
#
# The solution for porepressure and displacements is given in
# AHD Cheng and E Detournay "A direct boundary element method for plane strain poroelasticity" International Journal of Numerical and Analytical Methods in Geomechanics 12 (1988) 551-572.
# The solution involves complicated infinite series, so I shall not write it here

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

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
  PorousFlowDictator = dictator
  block = 0
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = 'porepressure disp_x disp_y disp_z'
    number_fluid_phases = 1
    number_fluid_components = 1
  []
[]

[Variables]
  [disp_x]
  []
  [disp_y]
  []
  [disp_z]
  []
  [porepressure]
  []
[]

[BCs]
  [roller_xmin]
    type = DirichletBC
    variable = disp_x
    value = 0
    boundary = 'left'
  []
  [roller_ymin]
    type = DirichletBC
    variable = disp_y
    value = 0
    boundary = 'bottom'
  []
  [plane_strain]
    type = DirichletBC
    variable = disp_z
    value = 0
    boundary = 'back front'
  []
  [xmax_drained]
    type = DirichletBC
    variable = porepressure
    value = 0
    boundary = right
  []
  [top_velocity]
    type = FunctionDirichletBC
    variable = disp_y
    function = top_velocity
    boundary = top
  []
[]

[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'
  []
[]

[AuxVariables]
  [stress_yy]
    order = CONSTANT
    family = MONOMIAL
  []
  [tot_force]
    order = CONSTANT
    family = MONOMIAL
  []
[]

[AuxKernels]
  [stress_yy]
    type = RankTwoAux
    rank_two_tensor = stress
    variable = stress_yy
    index_i = 1
    index_j = 1
  []
  [tot_force]
    type = ParsedAux
    args = 'stress_yy porepressure'
    execute_on = timestep_end
    variable = tot_force
    function = '-stress_yy+0.6*porepressure'
  []
[]

[Kernels]
  [grad_stress_x]
    type = StressDivergenceTensors
    variable = disp_x
    component = 0
  []
  [grad_stress_y]
    type = StressDivergenceTensors
    variable = disp_y
    component = 1
  []
  [grad_stress_z]
    type = StressDivergenceTensors
    variable = disp_z
    component = 2
  []
  [poro_x]
    type = PorousFlowEffectiveStressCoupling
    biot_coefficient = 0.6
    variable = disp_x
    component = 0
  []
  [poro_y]
    type = PorousFlowEffectiveStressCoupling
    biot_coefficient = 0.6
    variable = disp_y
    component = 1
  []
  [poro_z]
    type = PorousFlowEffectiveStressCoupling
    biot_coefficient = 0.6
    component = 2
    variable = disp_z
  []
  [mass0]
    type = PorousFlowFullySaturatedMassTimeDerivative
    biot_coefficient = 0.6
    multiply_by_density = false
    coupling_type = HydroMechanical
    variable = porepressure
  []
  [flux]
    type = PorousFlowFullySaturatedDarcyBase
    multiply_by_density = false
    variable = porepressure
    gravity = '0 0 0'
  []
[]

[Modules]
  [FluidProperties]
    [simple_fluid]
      type = SimpleFluidProperties
      bulk_modulus = 8
      density0 = 1
      thermal_expansion = 0
      viscosity = 1
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
  []
  [elasticity_tensor]
    type = ComputeElasticityTensor
    C_ijkl = '0.5 0.75'
    # bulk modulus is lambda + 2*mu/3 = 0.5 + 2*0.75/3 = 1
    fill_method = symmetric_isotropic
  []
  [strain]
    type = ComputeSmallStrain
  []
  [stress]
    type = ComputeLinearElasticStress
  []
  [eff_fluid_pressure_qp]
    type = PorousFlowEffectiveFluidPressure
  []
  [vol_strain]
    type = PorousFlowVolumetricStrain
    consistent_with_displaced_mesh = false
  []
  [ppss]
    type = PorousFlow1PhaseFullySaturated
    porepressure = porepressure
  []
  [massfrac]
    type = PorousFlowMassFraction
  []
  [simple_fluid_qp]
    type = PorousFlowSingleComponentFluid
    fp = simple_fluid
    phase = 0
  []
  [porosity]
    type = PorousFlowPorosityConst # only the initial value of this is ever used
    porosity = 0.1
  []
  [biot_modulus]
    type = PorousFlowConstantBiotModulus
    biot_coefficient = 0.6
    solid_bulk_compliance = 1
    fluid_bulk_modulus = 8
  []
  [permeability]
    type = PorousFlowPermeabilityConst
    permeability = '1.5 0 0   0 1.5 0   0 0 1.5'
  []
[]

[Postprocessors]
  [p0]
    type = PointValue
    outputs = csv
    point = '0.0 0 0'
    variable = porepressure
  []
  [p1]
    type = PointValue
    outputs = csv
    point = '0.1 0 0'
    variable = porepressure
  []
  [p2]
    type = PointValue
    outputs = csv
    point = '0.2 0 0'
    variable = porepressure
  []
  [p3]
    type = PointValue
    outputs = csv
    point = '0.3 0 0'
    variable = porepressure
  []
  [p4]
    type = PointValue
    outputs = csv
    point = '0.4 0 0'
    variable = porepressure
  []
  [p5]
    type = PointValue
    outputs = csv
    point = '0.5 0 0'
    variable = porepressure
  []
  [p6]
    type = PointValue
    outputs = csv
    point = '0.6 0 0'
    variable = porepressure
  []
  [p7]
    type = PointValue
    outputs = csv
    point = '0.7 0 0'
    variable = porepressure
  []
  [p8]
    type = PointValue
    outputs = csv
    point = '0.8 0 0'
    variable = porepressure
  []
  [p9]
    type = PointValue
    outputs = csv
    point = '0.9 0 0'
    variable = porepressure
  []
  [p99]
    type = PointValue
    outputs = csv
    point = '1 0 0'
    variable = porepressure
  []
  [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
    outputs = console
    function = if(0.15*t<0.01,0.15*t,0.01)
  []
[]

[Preconditioning]
  [andy]
    type = SMP
    full = true
    petsc_options_iname = '-ksp_type -pc_type -sub_pc_type -snes_atol -snes_rtol -snes_max_it'
    petsc_options_value = 'gmres asm lu 1E-14 1E-10 10000'
  []
[]

[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'
  file_base = mandel_fully_saturated_volume
  [csv]
    interval = 3
    type = CSV
  []
[]

(modules/porous_flow/examples/tutorial/11_2D.i)

# Two-phase borehole injection problem in RZ coordinates
[Mesh]
  [gen]
    type = GeneratedMeshGenerator
    dim = 2
    nx = 10
    xmin = 1.0
    xmax = 10
    bias_x = 1.4
    ny = 3
    ymin = -6
    ymax = 6
  []
  [aquifer]
    input = gen
    type = SubdomainBoundingBoxGenerator
    block_id = 1
    bottom_left = '0 -2 0'
    top_right = '10 2 0'
  []
  [injection_area]
    type = ParsedGenerateSideset
    combinatorial_geometry = 'x<1.0001'
    included_subdomain_ids = 1
    new_sideset_name = 'injection_area'
    input = 'aquifer'
  []
  [rename]
    type = RenameBlockGenerator
    old_block_id = '0 1'
    new_block_name = 'caps aquifer'
    input = 'injection_area'
  []
[]

[Problem]
  coord_type = RZ
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = 'pwater pgas T disp_r'
    number_fluid_phases = 2
    number_fluid_components = 2
  []
  [pc]
    type = PorousFlowCapillaryPressureVG
    alpha = 1E-6
    m = 0.6
  []
[]

[GlobalParams]
  displacements = 'disp_r disp_z'
  gravity = '0 0 0'
  biot_coefficient = 1.0
  PorousFlowDictator = dictator
[]

[Variables]
  [pwater]
    initial_condition = 20E6
  []
  [pgas]
    initial_condition = 20.1E6
  []
  [T]
    initial_condition = 330
    scaling = 1E-5
  []
  [disp_r]
    scaling = 1E-5
  []
[]

[Kernels]
  [mass_water_dot]
    type = PorousFlowMassTimeDerivative
    fluid_component = 0
    use_displaced_mesh = false
    variable = pwater
  []
  [flux_water]
    type = PorousFlowAdvectiveFlux
    fluid_component = 0
    use_displaced_mesh = false
    variable = pwater
  []
  [vol_strain_rate_water]
    type = PorousFlowMassVolumetricExpansion
    fluid_component = 0
    use_displaced_mesh = false
    variable = pwater
  []
  [mass_co2_dot]
    type = PorousFlowMassTimeDerivative
    fluid_component = 1
    use_displaced_mesh = false
    variable = pgas
  []
  [flux_co2]
    type = PorousFlowAdvectiveFlux
    fluid_component = 1
    use_displaced_mesh = false
    variable = pgas
  []
  [vol_strain_rate_co2]
    type = PorousFlowMassVolumetricExpansion
    fluid_component = 1
    use_displaced_mesh = false
    variable = pgas
  []
  [energy_dot]
    type = PorousFlowEnergyTimeDerivative
    use_displaced_mesh = false
    variable = T
  []
  [advection]
    type = PorousFlowHeatAdvection
    use_displaced_mesh = false
    variable = T
  []
  [conduction]
    type = PorousFlowHeatConduction
    use_displaced_mesh = false
    variable = T
  []
  [vol_strain_rate_heat]
    type = PorousFlowHeatVolumetricExpansion
    use_displaced_mesh = false
    variable = T
  []
  [grad_stress_r]
    type = StressDivergenceRZTensors
    temperature = T
    variable = disp_r
    eigenstrain_names = thermal_contribution
    use_displaced_mesh = false
    component = 0
  []
  [poro_r]
    type = PorousFlowEffectiveStressCoupling
    variable = disp_r
    use_displaced_mesh = false
    component = 0
  []
[]

[AuxVariables]
  [disp_z]
  []
  [effective_fluid_pressure]
    family = MONOMIAL
    order = CONSTANT
  []
  [mass_frac_phase0_species0]
    initial_condition = 1 # all water in phase=0
  []
  [mass_frac_phase1_species0]
    initial_condition = 0 # no water in phase=1
  []
  [sgas]
    family = MONOMIAL
    order = CONSTANT
  []
  [swater]
    family = MONOMIAL
    order = CONSTANT
  []
  [stress_rr]
    family = MONOMIAL
    order = CONSTANT
  []
  [stress_tt]
    family = MONOMIAL
    order = CONSTANT
  []
  [stress_zz]
    family = MONOMIAL
    order = CONSTANT
  []
  [porosity]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[AuxKernels]
  [effective_fluid_pressure]
    type = ParsedAux
    args = 'pwater pgas swater sgas'
    function = 'pwater * swater + pgas * sgas'
    variable = effective_fluid_pressure
  []
  [swater]
    type = PorousFlowPropertyAux
    variable = swater
    property = saturation
    phase = 0
    execute_on = timestep_end
  []
  [sgas]
    type = PorousFlowPropertyAux
    variable = sgas
    property = saturation
    phase = 1
    execute_on = timestep_end
  []
  [stress_rr_aux]
    type = RankTwoAux
    variable = stress_rr
    rank_two_tensor = stress
    index_i = 0
    index_j = 0
  []
  [stress_tt]
    type = RankTwoAux
    rank_two_tensor = stress
    variable = stress_tt
    index_i = 2
    index_j = 2
  []
  [stress_zz]
    type = RankTwoAux
    rank_two_tensor = stress
    variable = stress_zz
    index_i = 1
    index_j = 1
  []
  [porosity]
    type = PorousFlowPropertyAux
    variable = porosity
    property = porosity
    execute_on = timestep_end
  []
[]


[BCs]
  [pinned_top_bottom_r]
    type = DirichletBC
    variable = disp_r
    value = 0
    boundary = 'top bottom'
  []
  [cavity_pressure_r]
    type = Pressure
    boundary = injection_area
    variable = disp_r
    component = 0
    postprocessor = constrained_effective_fluid_pressure_at_wellbore
    use_displaced_mesh = false
  []

  [cold_co2]
    type = DirichletBC
    boundary = injection_area
    variable = T
    value = 290  # injection temperature
    use_displaced_mesh = false
  []
  [constant_co2_injection]
    type = PorousFlowSink
    boundary = injection_area
    variable = pgas
    fluid_phase = 1
    flux_function = -1E-4
    use_displaced_mesh = false
  []

  [outer_water_removal]
    type = PorousFlowPiecewiseLinearSink
    boundary = right
    variable = pwater
    fluid_phase = 0
    pt_vals = '0 1E9'
    multipliers = '0 1E8'
    PT_shift = 20E6
    use_mobility = true
    use_relperm = true
    use_displaced_mesh = false
  []
  [outer_co2_removal]
    type = PorousFlowPiecewiseLinearSink
    boundary = right
    variable = pgas
    fluid_phase = 1
    pt_vals = '0 1E9'
    multipliers = '0 1E8'
    PT_shift = 20.1E6
    use_mobility = true
    use_relperm = true
    use_displaced_mesh = false
  []
[]

[Modules]
  [FluidProperties]
    [true_water]
      type = Water97FluidProperties
    []
    [tabulated_water]
      type = TabulatedFluidProperties
      fp = true_water
      temperature_min = 275
      pressure_max = 1E8
      fluid_property_file = water97_tabulated_11.csv
    []
    [true_co2]
      type = CO2FluidProperties
    []
    [tabulated_co2]
      type = TabulatedFluidProperties
      fp = true_co2
      temperature_min = 275
      pressure_max = 1E8
      fluid_property_file = co2_tabulated_11.csv
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
    temperature = T
  []
  [saturation_calculator]
    type = PorousFlow2PhasePP
    phase0_porepressure = pwater
    phase1_porepressure = pgas
    capillary_pressure = pc
  []
  [massfrac]
    type = PorousFlowMassFraction
    mass_fraction_vars = 'mass_frac_phase0_species0 mass_frac_phase1_species0'
  []
  [water]
    type = PorousFlowSingleComponentFluid
    fp = tabulated_water
    phase = 0
  []
  [co2]
    type = PorousFlowSingleComponentFluid
    fp = tabulated_co2
    phase = 1
  []
  [relperm_water]
    type = PorousFlowRelativePermeabilityCorey
    n = 4
    s_res = 0.1
    sum_s_res = 0.2
    phase = 0
  []
  [relperm_co2]
    type = PorousFlowRelativePermeabilityBC
    nw_phase = true
    lambda = 2
    s_res = 0.1
    sum_s_res = 0.2
    phase = 1
  []
  [porosity]
    type = PorousFlowPorosity
    fluid = true
    mechanical = true
    thermal = true
    porosity_zero = 0.1
    reference_temperature = 330
    reference_porepressure = 20E6
    thermal_expansion_coeff = 15E-6 # volumetric
    solid_bulk = 8E9 # unimportant since biot = 1
  []
  [permeability_aquifer]
    type = PorousFlowPermeabilityKozenyCarman
    block = aquifer
    poroperm_function = kozeny_carman_phi0
    phi0 = 0.1
    n = 2
    m = 2
    k0 = 1E-12
  []
  [permeability_caps]
    type = PorousFlowPermeabilityKozenyCarman
    block = caps
    poroperm_function = kozeny_carman_phi0
    phi0 = 0.1
    n = 2
    m = 2
    k0 = 1E-15
    k_anisotropy = '1 0 0  0 1 0  0 0 0.1'
  []
  [rock_thermal_conductivity]
    type = PorousFlowThermalConductivityIdeal
    dry_thermal_conductivity = '2 0 0  0 2 0  0 0 2'
  []
  [rock_internal_energy]
    type = PorousFlowMatrixInternalEnergy
    specific_heat_capacity = 1100
    density = 2300
  []

  [elasticity_tensor]
    type = ComputeIsotropicElasticityTensor
    youngs_modulus = 5E9
    poissons_ratio = 0.0
  []
  [strain]
    type = ComputeAxisymmetricRZSmallStrain
    eigenstrain_names = 'thermal_contribution initial_stress'
  []
  [thermal_contribution]
    type = ComputeThermalExpansionEigenstrain
    temperature = T
    thermal_expansion_coeff = 5E-6 # this is the linear thermal expansion coefficient
    eigenstrain_name = thermal_contribution
    stress_free_temperature = 330
  []
  [initial_strain]
    type = ComputeEigenstrainFromInitialStress
    initial_stress = '20E6 0 0  0 20E6 0  0 0 20E6'
    eigenstrain_name = initial_stress
  []
  [stress]
    type = ComputeLinearElasticStress
  []

  [effective_fluid_pressure]
    type = PorousFlowEffectiveFluidPressure
  []
  [volumetric_strain]
    type = PorousFlowVolumetricStrain
  []
[]

[Postprocessors]
  [effective_fluid_pressure_at_wellbore]
    type = PointValue
    variable = effective_fluid_pressure
    point = '1 0 0'
    execute_on = timestep_begin
    use_displaced_mesh = false
  []
  [constrained_effective_fluid_pressure_at_wellbore]
    type = FunctionValuePostprocessor
    function = constrain_effective_fluid_pressure
    execute_on = timestep_begin
  []
[]

[Functions]
  [constrain_effective_fluid_pressure]
    type = ParsedFunction
    vars = effective_fluid_pressure_at_wellbore
    vals = effective_fluid_pressure_at_wellbore
    value = 'max(effective_fluid_pressure_at_wellbore, 20E6)'
  []
[]

[Preconditioning]
  active = basic
  [basic]
    type = SMP
    full = true
    petsc_options = '-ksp_diagonal_scale -ksp_diagonal_scale_fix'
    petsc_options_iname = '-pc_type -sub_pc_type -sub_pc_factor_shift_type -pc_asm_overlap'
    petsc_options_value = ' asm      lu           NONZERO                   2'
  []
  [preferred_but_might_not_be_installed]
    type = SMP
    full = true
    petsc_options_iname = '-pc_type -pc_factor_mat_solver_package'
    petsc_options_value = ' lu       mumps'
  []
[]

[Executioner]
  type = Transient
  solve_type = Newton
  end_time = 1E3
  [TimeStepper]
    type = IterationAdaptiveDT
    dt = 1E3
    growth_factor = 1.2
    optimal_iterations = 10
  []
  nl_abs_tol = 1E-7
[]

[Outputs]
  exodus = true
[]

(modules/porous_flow/test/tests/chemistry/dissolution.i)

# The dissolution reaction
#
# a <==> mineral
#
# produces "mineral".  Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / porosity)' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is positive for a < 0.25, ie dissolution for a(t=0) < 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
#   = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * porosity
#
# This test checks that (a + c / porosity) is time-independent, and that a follows the above solution
#
# Aside:
#    The exponential curve is not followed exactly because moose actually solves
#    (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#    which does not give an exponential exactly, except in the limit dt->0
[Mesh]
  type = GeneratedMesh
  dim = 1
[]

[Variables]
  [a]
    initial_condition = 0.05
  []
[]

[AuxVariables]
  [eqm_k]
    initial_condition = 0.5
  []
  [pressure]
  []
  [ini_mineral_conc]
    initial_condition = 0.3
  []
  [mineral]
    family = MONOMIAL
    order = CONSTANT
  []
  [should_be_static]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[AuxKernels]
  [mineral]
    type = PorousFlowPropertyAux
    property = mineral_concentration
    mineral_species = 0
    variable = mineral
  []
  [should_be_static]
    type = ParsedAux
    args = 'mineral a'
    function = 'a + mineral / 0.1'
    variable = should_be_static
  []
[]

[GlobalParams]
  PorousFlowDictator = dictator
[]

[Kernels]
  [mass_a]
    type = PorousFlowMassTimeDerivative
    fluid_component = 0
    variable = a
  []
  [pre_dis]
    type = PorousFlowPreDis
    variable = a
    mineral_density = 1000
    stoichiometry = 1
  []
[]

[UserObjects]
  [dictator]
    type = PorousFlowDictator
    porous_flow_vars = a
    number_fluid_phases = 1
    number_fluid_components = 2
    number_aqueous_kinetic = 1
  []
[]

[Modules]
  [FluidProperties]
    [simple_fluid]
      type = SimpleFluidProperties
      bulk_modulus = 2e9 # huge, so mimic chemical_reactions
      density0 = 1000
      thermal_expansion = 0
      viscosity = 1e-3
    []
  []
[]

[Materials]
  [temperature]
    type = PorousFlowTemperature
    temperature = 1
  []
  [ppss]
    type = PorousFlow1PhaseFullySaturated
    porepressure = pressure
  []
  [mass_frac]
    type = PorousFlowMassFraction
    mass_fraction_vars = a
  []
  [predis]
    type = PorousFlowAqueousPreDisChemistry
    primary_concentrations = a
    num_reactions = 1
    equilibrium_constants = eqm_k
    primary_activity_coefficients = 2
    reactions = 1
    specific_reactive_surface_area = 0.5
    kinetic_rate_constant = 0.6065306597126334
    activation_energy = 3
    molar_volume = 2
    gas_constant = 6
    reference_temperature = 0.5
  []
  [mineral_conc]
    type = PorousFlowAqueousPreDisMineral
    initial_concentrations = ini_mineral_conc
  []
  [simple_fluid]
    type = PorousFlowSingleComponentFluid
    fp = simple_fluid
    phase = 0
  []
  [porosity]
    type = PorousFlowPorosityConst
    porosity = 0.1
  []
[]


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

[Executioner]
  type = Transient
  solve_type = Newton
  nl_abs_tol = 1E-10
  dt = 0.01
  end_time = 1
[]

[Postprocessors]
  [a]
    type = PointValue
    point = '0 0 0'
    variable = a
  []
  [should_be_static]
    type = PointValue
    point = '0 0 0'
    variable = should_be_static
  []
[]
[Outputs]
  interval = 10
  csv = true
  perf_graph = true
[]

(modules/geochemistry/test/tests/kinetics/quartz_dissolution.i)

# Example of quartz dissolution.
[TimeDependentReactionSolver]
  model_definition = definition
  geochemistry_reactor_name = reactor
  charge_balance_species = "Cl-"
  constraint_species = "H2O              H+               Cl-              SiO2(aq)"
  constraint_value = "  1.0              1E-10            1E-10            1E-9"
  constraint_meaning = "kg_solvent_water bulk_composition bulk_composition free_concentration"
  constraint_unit = "   kg               moles            moles            molal"
  initial_temperature = 100.0
  temperature = 100.0
  kinetic_species_name = Quartz
  kinetic_species_initial_value = 5
  kinetic_species_unit = kg
  ramp_max_ionic_strength_initial = 0 # max_ionic_strength in such a simple problem does not need ramping
  stoichiometric_ionic_str_using_Cl_only = true # for comparison with GWB
  execute_console_output_on = '' # only CSV output for this example
[]

[UserObjects]
  [rate_quartz]
    type = GeochemistryKineticRate
    kinetic_species_name = Quartz
    intrinsic_rate_constant = 1.728E-10 # 2.0E-15mol/s/cm^2 = 1.728E-10mol/day/cm^2
    multiply_by_mass = true
    area_quantity = 1000
  []
  [definition]
    type = GeochemicalModelDefinition
    database_file = "../../../database/moose_geochemdb.json"
    basis_species = "H2O SiO2(aq) H+ Cl-"
    kinetic_minerals = "Quartz"
    kinetic_rate_descriptions = "rate_quartz"
    piecewise_linear_interpolation = true # for comparison with GWB
  []
[]

[Functions]
  [timestepper]
    type = PiecewiseLinear
    x = '0 0.5 3'
    y = '0.01 0.05 0.1'
  []
[]

[Executioner]
  type = Transient
  [TimeStepper]
    type = FunctionDT
    function = timestepper
  []
  end_time = 5.0
[]

[AuxVariables]
  [diss]
  []
[]
[AuxKernels]
  [diss]
    type = ParsedAux
    args = moles_Quartz
    function = '83.216414271 - moles_Quartz'
    variable = diss
  []
[]
[Postprocessors]
  [dissolved_moles]
    type = PointValue
    point = '0 0 0'
    variable = diss
  []
[]
[Outputs]
  csv = true
[]

(modules/geochemistry/test/tests/kernels/time_deriv_2.i)

# A point-source is added to fluid in a material with spatially-varying porosity
# porosity * d(concentration)/dt = 3.0 * delta(x - 1.0)
# where delta is the Dirac delta function (a ConstantPointSource DiracKernel)
# The solution, at x = 1.0 is
# concentration = concentration_old + 3 * dt / porosity
# while concentration is unchanged elsewhere.
# Note that since GeochemistryTimeDerivative is mass-lumped, it produces this solution.
# If mass lumping had not been used, concentration would have decreased at x != 1.0
[Mesh]
  type = GeneratedMesh
  dim = 1
  nx = 2
  xmax = 2
[]

[Variables]
  [conc]
  []
[]

[Kernels]
  [dot]
    type = GeochemistryTimeDerivative
    porosity = porosity
    variable = conc
  []
[]

[DiracKernels]
  [source]
    type = ConstantPointSource
    point = '1.0 0 0'
    variable = conc
    value = 12.0
  []
[]

[ICs]
  [conc]
    type = FunctionIC
    function = 'x * x'
    variable = conc
  []
[]

[AuxVariables]
  [porosity]
  []
  [expected]
  []
  [should_be_zero]
  []
[]

[AuxKernels]
  [porosity]
    type = FunctionAux
    function = '6.0 + x'
    variable = porosity
  []
  [expected]
    type = FunctionAux
   function = 'if(x > 0.5 & x < 1.5, x * x + 2.0 * 12.0 / (6.0 + x), x * x)'
    variable = expected
  []
  [should_be_zero]
    type = ParsedAux
    args = 'expected conc'
    function = 'expected - conc'
    variable = should_be_zero
  []
[]

[Postprocessors]
  [error]
    type = NodalL2Norm
    variable = should_be_zero
  []
[]

[Executioner]
  type = Transient
  solve_type = Newton
  dt = 2
  end_time = 2
[]

[Outputs]
  csv = true
[]

(modules/functional_expansion_tools/examples/3D_volumetric_Cartesian_direct/sub.i)

# Derived from the example '3D_volumetric_Cartesian' with the following differences:
#
#   1) The coupling is performed via BodyForce instead of the
#      FunctionSeriesToAux+CoupledForce approach
[Mesh]
  type = GeneratedMesh
  dim = 3

  xmin = 0.0
  xmax = 10.0
  nx = 15

  ymin = 1.0
  ymax = 11.0
  ny = 25

  zmin = 2.0
  zmax = 12.0
  nz = 35
[]

# Non-copy transfers only work with AuxVariable, but nothing will be solved without a variable
# defined. The solution is to define an empty variable tha does nothing, but causes MOOSE to solve
# the AuxKernels that we need.
[Variables]
  [./empty]
  [../]
[]

[AuxVariables]
  [./s]
    order = FIRST
    family = LAGRANGE
  [../]
  [./m_in]
    order = FIRST
    family = LAGRANGE
  [../]
[]

# We must have a kernel for every variable, hence this null kernel to match the variable 'empty'
[Kernels]
  [./null_kernel]
    type = NullKernel
    variable = empty
  [../]
[]

[AuxKernels]
  [./reconstruct_m_in]
    type = FunctionSeriesToAux
    function = FX_Basis_Value_Sub
    variable = m_in
  [../]
  [./calculate_s] # Something to make 's' change each time, but allow a converging solution
    type = ParsedAux
    variable = s
    args = m_in
    function = '2*exp(-m_in/0.8)'
  [../]
[]

[Functions]
  [./FX_Basis_Value_Sub]
    type = FunctionSeries
    series_type = Cartesian
    orders = '3   4   5'
    physical_bounds = '0.0  10.0    1.0 11.0    2.0 12.0'
    x = Legendre
    y = Legendre
    z = Legendre
  [../]
[]

[UserObjects]
  [./FX_Value_UserObject_Sub]
    type = FXVolumeUserObject
    function = FX_Basis_Value_Sub
    variable = s
  [../]
[]

[Executioner]
  type = Transient
  num_steps = 10
  dt = 0.5
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

(modules/combined/test/tests/poro_mechanics/borehole_lowres.i)

# Poroelastic response of a borehole.
#
# LOWRES VERSION: this version does not give perfect agreement with the analytical solution
#
# A fully-saturated medium contains a fluid with a homogeneous porepressure,
# but an anisitropic insitu stress.  A infinitely-long borehole aligned with
# the $$z$$ axis is instanteously excavated.  The borehole boundary is
# stress-free and allowed to freely drain.  This problem is analysed using
# plane-strain conditions (no $$z$$ displacement).
#
# The solution in Laplace space is found in E Detournay and AHD Cheng "Poroelastic response of a borehole in a non-hydrostatic stress field".  International Journal of Rock Mechanics and Mining Sciences and Geomechanics Abstracts 25 (1988) 171-182.  In the small-time limit, the Laplace transforms may be performed.  There is one typo in the paper.  Equation (A4)'s final term should be -(a/r)\sqrt(4ct/(a^2\pi)), and not +(a/r)\sqrt(4ct/(a^2\pi)).
#
# Because realistic parameters are chosen (below),
# the residual for porepressure is much smaller than
# the residuals for the displacements.  Therefore the
# scaling parameter is chosen.  Also note that the
# insitu stresses are effective stresses, not total
# stresses, but the solution in the above paper is
# expressed in terms of total stresses.
#
# Here are the problem's parameters, and their values:
# Borehole radius.  a = 1
# Rock's Lame lambda.  la = 0.5E9
# Rock's Lame mu, which is also the Rock's shear modulus.  mu = G = 1.5E9
# Rock bulk modulus.  K = la + 2*mu/3 = 1.5E9
# Drained Poisson ratio.  nu = (3K - 2G)/(6K + 2G) = 0.125
# Rock bulk compliance.  1/K = 0.66666666E-9
# Fluid bulk modulus.  Kf = 0.7171315E9
# Fluid bulk compliance.  1/Kf = 1.39444444E-9
# Rock initial porosity.  phi0 = 0.3
# Biot coefficient.  alpha = 0.65
# Biot modulus.  M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 2E9
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.345E9
# Undrained Poisson ratio.  nuu = (3Ku - 2G)/(6Ku + 2G) = 0.2364
# Skempton coefficient.  B = alpha*M/Ku = 0.554
# Fluid mobility (rock permeability/fluid viscosity).  k = 1E-12

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

[GlobalParams]
  displacements = 'disp_x disp_y disp_z'
  porepressure = porepressure
  block = 1
[]

[GlobalParams]
  volumetric_locking_correction=true
[]

[Variables]
  [./disp_x]
  [../]
  [./disp_y]
  [../]
  [./disp_z]
  [../]
  [./porepressure]
    scaling = 1E9  # Notice the scaling, to make porepressure's kernels roughly of same magnitude as disp's kernels
  [../]
[]

[ICs]
  [./initial_p]
    type = ConstantIC
    variable = porepressure
    value = 1E6
  [../]
[]

[BCs]
  [./fixed_outer_x]
    type = DirichletBC
    variable = disp_x
    value = 0
    boundary = outer
  [../]
  [./fixed_outer_y]
    type = DirichletBC
    variable = disp_y
    value = 0
    boundary = outer
  [../]
  [./plane_strain]
    type = DirichletBC
    variable = disp_z
    value = 0
    boundary = 'zmin zmax'
  [../]
  [./borehole_wall]
    type = DirichletBC
    variable = porepressure
    value = 0
    boundary = bh_wall
  [../]
[]



[AuxVariables]
  [./stress_yy]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./tot_yy]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

[AuxKernels]
  [./stress_yy]
    type = RankTwoAux
    rank_two_tensor = stress
    variable = stress_yy
    index_i = 1
    index_j = 1
  [../]
  [./tot_yy]
    type = ParsedAux
    args = 'stress_yy porepressure'
    execute_on = timestep_end
    variable = tot_yy
    function = 'stress_yy-0.65*porepressure'
  [../]
[]



[Kernels]
  [./grad_stress_x]
    type = StressDivergenceTensors
    variable = disp_x
    component = 0
  [../]
  [./grad_stress_y]
    type = StressDivergenceTensors
    variable = disp_y
    component = 1
  [../]
  [./grad_stress_z]
    type = StressDivergenceTensors
    variable = disp_z
    component = 2
  [../]
  [./poro_x]
    type = PoroMechanicsCoupling
    variable = disp_x
    component = 0
  [../]
  [./poro_y]
    type = PoroMechanicsCoupling
    variable = disp_y
    component = 1
  [../]
  [./poro_z]
    type = PoroMechanicsCoupling
    variable = disp_z
    component = 2
  [../]
  [./poro_timederiv]
    type = PoroFullSatTimeDerivative
    variable = porepressure
  [../]
  [./darcy_flow]
    type = CoefDiffusion
    variable = porepressure
    coef = 1E-12
  [../]
[]

[Materials]
  [./elasticity_tensor]
    type = ComputeElasticityTensor
    C_ijkl = '0.5E9 1.5E9'
    # bulk modulus is lambda + 2*mu/3 = 0.5 + 2*1.5/3 = 1.5E9
    fill_method = symmetric_isotropic
  [../]
  [./strain]
    type = ComputeFiniteStrain
    displacements = 'disp_x disp_y disp_z'
    eigenstrain_names = ini_stress
  [../]
  [./ini_stress]
    type = ComputeEigenstrainFromInitialStress
    initial_stress = '-1.35E6 0 0  0 -3.35E6 0  0 0 0' # remember this is the effective stress
    eigenstrain_name = ini_stress
  [../]
  [./no_plasticity]
    type = ComputeFiniteStrainElasticStress
  [../]
  [./poro_material]
    type = PoroFullSatMaterial
    porosity0 = 0.3
    biot_coefficient = 0.65
    solid_bulk_compliance = 0.6666666666667E-9
    fluid_bulk_compliance = 1.3944444444444E-9
    constant_porosity = false
  [../]
[]

[Postprocessors]
  [./p00]
    type = PointValue
    variable = porepressure
    point = '1.00 0 0'
    outputs = csv_p
  [../]
  [./p01]
    type = PointValue
    variable = porepressure
    point = '1.01 0 0'
    outputs = csv_p
  [../]
  [./p02]
    type = PointValue
    variable = porepressure
    point = '1.02 0 0'
    outputs = csv_p
  [../]
  [./p03]
    type = PointValue
    variable = porepressure
    point = '1.03 0 0'
    outputs = csv_p
  [../]
  [./p04]
    type = PointValue
    variable = porepressure
    point = '1.04 0 0'
    outputs = csv_p
  [../]
  [./p05]
    type = PointValue
    variable = porepressure
    point = '1.05 0 0'
    outputs = csv_p
  [../]
  [./p06]
    type = PointValue
    variable = porepressure
    point = '1.06 0 0'
    outputs = csv_p
  [../]
  [./p07]
    type = PointValue
    variable = porepressure
    point = '1.07 0 0'
    outputs = csv_p
  [../]
  [./p08]
    type = PointValue
    variable = porepressure
    point = '1.08 0 0'
    outputs = csv_p
  [../]
  [./p09]
    type = PointValue
    variable = porepressure
    point = '1.09 0 0'
    outputs = csv_p
  [../]
  [./p10]
    type = PointValue
    variable = porepressure
    point = '1.10 0 0'
    outputs = csv_p
  [../]
  [./p11]
    type = PointValue
    variable = porepressure
    point = '1.11 0 0'
    outputs = csv_p
  [../]
  [./p12]
    type = PointValue
    variable = porepressure
    point = '1.12 0 0'
    outputs = csv_p
  [../]
  [./p13]
    type = PointValue
    variable = porepressure
    point = '1.13 0 0'
    outputs = csv_p
  [../]
  [./p14]
    type = PointValue
    variable = porepressure
    point = '1.14 0 0'
    outputs = csv_p
  [../]
  [./p15]
    type = PointValue
    variable = porepressure
    point = '1.15 0 0'
    outputs = csv_p
  [../]
  [./p16]
    type = PointValue
    variable = porepressure
    point = '1.16 0 0'
    outputs = csv_p
  [../]
  [./p17]
    type = PointValue
    variable = porepressure
    point = '1.17 0 0'
    outputs = csv_p
  [../]
  [./p18]
    type = PointValue
    variable = porepressure
    point = '1.18 0 0'
    outputs = csv_p
  [../]
  [./p19]
    type = PointValue
    variable = porepressure
    point = '1.19 0 0'
    outputs = csv_p
  [../]
  [./p20]
    type = PointValue
    variable = porepressure
    point = '1.20 0 0'
    outputs = csv_p
  [../]
  [./p21]
    type = PointValue
    variable = porepressure
    point = '1.21 0 0'
    outputs = csv_p
  [../]
  [./p22]
    type = PointValue
    variable = porepressure
    point = '1.22 0 0'
    outputs = csv_p
  [../]
  [./p23]
    type = PointValue
    variable = porepressure
    point = '1.23 0 0'
    outputs = csv_p
  [../]
  [./p24]
    type = PointValue
    variable = porepressure
    point = '1.24 0 0'
    outputs = csv_p
  [../]
  [./p25]
    type = PointValue
    variable = porepressure
    point = '1.25 0 0'
    outputs = csv_p
  [../]

  [./s00]
    type = PointValue
    variable = disp_x
    point = '1.00 0 0'
    outputs = csv_s
  [../]
  [./s01]
    type = PointValue
    variable = disp_x
    point = '1.01 0 0'
    outputs = csv_s
  [../]
  [./s02]
    type = PointValue
    variable = disp_x
    point = '1.02 0 0'
    outputs = csv_s
  [../]
  [./s03]
    type = PointValue
    variable = disp_x
    point = '1.03 0 0'
    outputs = csv_s
  [../]
  [./s04]
    type = PointValue
    variable = disp_x
    point = '1.04 0 0'
    outputs = csv_s
  [../]
  [./s05]
    type = PointValue
    variable = disp_x
    point = '1.05 0 0'
    outputs = csv_s
  [../]
  [./s06]
    type = PointValue
    variable = disp_x
    point = '1.06 0 0'
    outputs = csv_s
  [../]
  [./s07]
    type = PointValue
    variable = disp_x
    point = '1.07 0 0'
    outputs = csv_s
  [../]
  [./s08]
    type = PointValue
    variable = disp_x
    point = '1.08 0 0'
    outputs = csv_s
  [../]
  [./s09]
    type = PointValue
    variable = disp_x
    point = '1.09 0 0'
    outputs = csv_s
  [../]
  [./s10]
    type = PointValue
    variable = disp_x
    point = '1.10 0 0'
    outputs = csv_s
  [../]
  [./s11]
    type = PointValue
    variable = disp_x
    point = '1.11 0 0'
    outputs = csv_s
  [../]
  [./s12]
    type = PointValue
    variable = disp_x
    point = '1.12 0 0'
    outputs = csv_s
  [../]
  [./s13]
    type = PointValue
    variable = disp_x
    point = '1.13 0 0'
    outputs = csv_s
  [../]
  [./s14]
    type = PointValue
    variable = disp_x
    point = '1.14 0 0'
    outputs = csv_s
  [../]
  [./s15]
    type = PointValue
    variable = disp_x
    point = '1.15 0 0'
    outputs = csv_s
  [../]
  [./s16]
    type = PointValue
    variable = disp_x
    point = '1.16 0 0'
    outputs = csv_s
  [../]
  [./s17]
    type = PointValue
    variable = disp_x
    point = '1.17 0 0'
    outputs = csv_s
  [../]
  [./s18]
    type = PointValue
    variable = disp_x
    point = '1.18 0 0'
    outputs = csv_s
  [../]
  [./s19]
    type = PointValue
    variable = disp_x
    point = '1.19 0 0'
    outputs = csv_s
  [../]
  [./s20]
    type = PointValue
    variable = disp_x
    point = '1.20 0 0'
    outputs = csv_s
  [../]
  [./s21]
    type = PointValue
    variable = disp_x
    point = '1.21 0 0'
    outputs = csv_s
  [../]
  [./s22]
    type = PointValue
    variable = disp_x
    point = '1.22 0 0'
    outputs = csv_s
  [../]
  [./s23]
    type = PointValue
    variable = disp_x
    point = '1.23 0 0'
    outputs = csv_s
  [../]
  [./s24]
    type = PointValue
    variable = disp_x
    point = '1.24 0 0'
    outputs = csv_s
  [../]
  [./s25]
    type = PointValue
    variable = disp_x
    point = '1.25 0 0'
    outputs = csv_s
  [../]

  [./t00]
    type = PointValue
    variable = tot_yy
    point = '1.00 0 0'
    outputs = csv_t
  [../]
  [./t01]
    type = PointValue
    variable = tot_yy
    point = '1.01 0 0'
    outputs = csv_t
  [../]
  [./t02]
    type = PointValue
    variable = tot_yy
    point = '1.02 0 0'
    outputs = csv_t
  [../]
  [./t03]
    type = PointValue
    variable = tot_yy
    point = '1.03 0 0'
    outputs = csv_t
  [../]
  [./t04]
    type = PointValue
    variable = tot_yy
    point = '1.04 0 0'
    outputs = csv_t
  [../]
  [./t05]
    type = PointValue
    variable = tot_yy
    point = '1.05 0 0'
    outputs = csv_t
  [../]
  [./t06]
    type = PointValue
    variable = tot_yy
    point = '1.06 0 0'
    outputs = csv_t
  [../]
  [./t07]
    type = PointValue
    variable = tot_yy
    point = '1.07 0 0'
    outputs = csv_t
  [../]
  [./t08]
    type = PointValue
    variable = tot_yy
    point = '1.08 0 0'
    outputs = csv_t
  [../]
  [./t09]
    type = PointValue
    variable = tot_yy
    point = '1.09 0 0'
    outputs = csv_t
  [../]
  [./t10]
    type = PointValue
    variable = tot_yy
    point = '1.10 0 0'
    outputs = csv_t
  [../]
  [./t11]
    type = PointValue
    variable = tot_yy
    point = '1.11 0 0'
    outputs = csv_t
  [../]
  [./t12]
    type = PointValue
    variable = tot_yy
    point = '1.12 0 0'
    outputs = csv_t
  [../]
  [./t13]
    type = PointValue
    variable = tot_yy
    point = '1.13 0 0'
    outputs = csv_t
  [../]
  [./t14]
    type = PointValue
    variable = tot_yy
    point = '1.14 0 0'
    outputs = csv_t
  [../]
  [./t15]
    type = PointValue
    variable = tot_yy
    point = '1.15 0 0'
    outputs = csv_t
  [../]
  [./t16]
    type = PointValue
    variable = tot_yy
    point = '1.16 0 0'
    outputs = csv_t
  [../]
  [./t17]
    type = PointValue
    variable = tot_yy
    point = '1.17 0 0'
    outputs = csv_t
  [../]
  [./t18]
    type = PointValue
    variable = tot_yy
    point = '1.18 0 0'
    outputs = csv_t
  [../]
  [./t19]
    type = PointValue
    variable = tot_yy
    point = '1.19 0 0'
    outputs = csv_t
  [../]
  [./t20]
    type = PointValue
    variable = tot_yy
    point = '1.20 0 0'
    outputs = csv_t
  [../]
  [./t21]
    type = PointValue
    variable = tot_yy
    point = '1.21 0 0'
    outputs = csv_t
  [../]
  [./t22]
    type = PointValue
    variable = tot_yy
    point = '1.22 0 0'
    outputs = csv_t
  [../]
  [./t23]
    type = PointValue
    variable = tot_yy
    point = '1.23 0 0'
    outputs = csv_t
  [../]
  [./t24]
    type = PointValue
    variable = tot_yy
    point = '1.24 0 0'
    outputs = csv_t
  [../]
  [./t25]
    type = PointValue
    variable = tot_yy
    point = '1.25 0 0'
    outputs = csv_t
  [../]

  [./dt]
    type = FunctionValuePostprocessor
    outputs = console
    function = 2*t
  [../]
[]


[Preconditioning]
  [./andy]
    type = SMP
    full = true
    petsc_options = '-snes_monitor -snes_linesearch_monitor'
    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 1E0 1E-10 200 500 lu NONZERO'
  [../]
[]

[Executioner]
  type = Transient
  solve_type = Newton
  start_time = 0
  end_time = 0.3
  dt = 0.3
  #[./TimeStepper]
  #  type = PostprocessorDT
  #  postprocessor = dt
  #  dt = 0.003
  #[../]
[]

[Outputs]
  execute_on = 'timestep_end'
  file_base = borehole_lowres
  exodus = true
  sync_times = '0.003 0.3'
  [./csv_p]
    file_base = borehole_lowres_p
    type = CSV
  [../]
  [./csv_s]
    file_base = borehole_lowres_s
    type = CSV
  [../]
  [./csv_t]
    file_base = borehole_lowres_t
    type = CSV
  [../]
[]

(modules/functional_expansion_tools/examples/3D_volumetric_Cartesian/sub.i)

# Basic example coupling a master and sub app in a 3D Cartesian volume.
#
# The master app provides field values to the sub app via Functional Expansions, which then performs
# its calculations. The sub app's solution field values are then transferred back to the master app
# and coupled into the solution of the master app solution.
#
# This example couples Functional Expansions via AuxVariable.
#
# Note: this problem is not light, and may take a few minutes to solve.
[Mesh]
  type = GeneratedMesh
  dim = 3

  xmin = 0.0
  xmax = 10.0
  nx = 15

  ymin = 1.0
  ymax = 11.0
  ny = 25

  zmin = 2.0
  zmax = 12.0
  nz = 35
[]

# Non-copy transfers only work with AuxVariable, but nothing will be solved without a variable
# defined. The solution is to define an empty variable tha does nothing, but causes MOOSE to solve
# the AuxKernels that we need.
[Variables]
  [./empty]
  [../]
[]

[AuxVariables]
  [./s]
    order = FIRST
    family = LAGRANGE
  [../]
  [./m_in]
    order = FIRST
    family = LAGRANGE
  [../]
[]

# We must have a kernel for every variable, hence this null kernel to match the variable 'empty'
[Kernels]
  [./null_kernel]
    type = NullKernel
    variable = empty
  [../]
[]

[AuxKernels]
  [./reconstruct_m_in]
    type = FunctionSeriesToAux
    function = FX_Basis_Value_Sub
    variable = m_in
  [../]
  [./calculate_s] # Something to make 's' change each time, but allow a converging solution
    type = ParsedAux
    variable = s
    args = m_in
    function = '2*exp(-m_in/0.8)'
  [../]
[]

[Functions]
  [./FX_Basis_Value_Sub]
    type = FunctionSeries
    series_type = Cartesian
    orders = '3   4   5'
    physical_bounds = '0.0  10.0    1.0 11.0    2.0 12.0'
    x = Legendre
    y = Legendre
    z = Legendre
  [../]
[]

[UserObjects]
  [./FX_Value_UserObject_Sub]
    type = FXVolumeUserObject
    function = FX_Basis_Value_Sub
    variable = s
  [../]
[]

[Executioner]
  type = Transient
  num_steps = 10
  dt = 0.5
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

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