ADTrappingEquilibriumEquation

construction:Undocumented Class

The ADTrappingEquilibriumEquation 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.

Compute the local movement of particles between the mobile phaseand the trapped phase for a specific trap type

Overview

ADTrappingEquilibriumEquation implements the RHS of Eq. (1) which is the trapping reaction equation governing movement of particles between the trapped and mobile phases.

$(1)var element = document.getElementById("moose-equation-74bd6cb6-a6ff-4228-bb59-b8a88d7e63d4");katex.render("\\frac{\\partial C_{t,i}}{\\partial t} = \\nu_m C_m \\left(n_i - C_{t,i} \\right) - \\nu_iC_{t,i} ", element, {displayMode:true,throwOnError:false});$

$var element = document.getElementById("moose-equation-fb5e840f-770d-4316-b27b-632e03605f80");katex.render("C_m", element, {displayMode:false,throwOnError:false});$ and $var element = document.getElementById("moose-equation-0d0f385d-23bb-4d63-9d04-5c6abae7ade4");katex.render("C_t", element, {displayMode:false,throwOnError:false});$ represent the local concentrations of hydrogen isotope in the mobile and trapped phases respecitvely. $var element = document.getElementById("moose-equation-feaefa43-0ea6-4f2c-8ae6-ad4e84f7645d");katex.render("\\nu_m", element, {displayMode:false,throwOnError:false});$ and $var element = document.getElementById("moose-equation-facd6515-c203-43f0-8289-81cf08f7b331");katex.render("\\nu_i", element, {displayMode:false,throwOnError:false});$ are the temperature-dependant reaction rates which are taken from material properties made available through one the TrappingMaterial classes defined in Achlys. $var element = document.getElementById("moose-equation-d55a809f-939a-4207-a87f-a5d8bb05e580");katex.render("n", element, {displayMode:false,throwOnError:false});$ is the trap density such that the term in the brackets is zero when all traps are filled.

Residual is accumulated in the trapped concentration and the mobile concentration is the secondary coupled variable.

Example Input File Syntax

[Kernels]
  [./trapping_equilibrium_equation1]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_1
    v = Mobile
    n_traps = n1
    vi = V1
  [../]
  [./trapping_equilibrium_equation2]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_2
    v = Mobile
    n_traps = n2
    vi = V2
  [../]
  [./trapping_equilibrium_equation3]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_3
    v = Mobile
    n_traps = n3
    vi = V3
  [../]
  [./trapped_time_deriv_couple]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped_1
  [../]
  [./trapped_time_deriv_couple2]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped_2
  [../]
  [./trapped_time_deriv_couple3]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped_3
  [../]
  [./trapped_time_deriv2]
    type = ADTimeDerivative
    variable = Trapped_2
  [../]
  [./trapped_time_deriv3]
    type = ADTimeDerivative
    variable = Trapped_3
  [../]
[]

Input Parameters

vConcentration of mobile particles
C++ Type:std::vector<VariableName>
Options:
Description:Concentration of mobile particles
variableThe name of the variable that this residual object operates on
C++ Type:NonlinearVariableName
Options:
Description:The name of the variable that this residual object operates on

Required Parameters

blockThe list of blocks (ids or names) that this object will be applied
C++ Type:std::vector<SubdomainName>
Options:
Description:The list of blocks (ids or names) that this object will be applied
displacementsThe displacements
C++ Type:std::vector<VariableName>
Options:
Description:The displacements
n_trapsn0material property for trapping density
Default:n0
C++ Type:MaterialPropertyName
Options:
Description:material property for trapping density
prop_getter_suffixAn optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.
C++ Type:MaterialPropertyName
Options:
Description:An optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.
viv0the rate constant for this trap
Default:v0
C++ Type:MaterialPropertyName
Options:
Description:the rate constant for this trap

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.
diag_save_inThe name of auxiliary variables to save this Kernel's diagonal Jacobian contributions to. Everything about that variable must match everything about this variable (the type, what blocks it's on, etc.)
C++ Type:std::vector<AuxVariableName>
Options:
Description:The name of auxiliary variables to save this Kernel's diagonal Jacobian contributions to. Everything about that variable must match everything about this variable (the type, what blocks it's on, etc.)
enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Options:
Description:Set the enabled status of the MooseObject.
implicitTrueDetermines whether this object is calculated using an implicit or explicit form
Default:True
C++ Type:bool
Options:
Description:Determines whether this object is calculated using an implicit or explicit form
save_inThe name of auxiliary variables to save this Kernel's residual contributions to. Everything about that variable must match everything about this variable (the type, what blocks it's on, etc.)
C++ Type:std::vector<AuxVariableName>
Options:
Description:The name of auxiliary variables to save this Kernel's residual contributions to. Everything about that variable must match everything about this variable (the type, what blocks it's on, etc.)
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

extra_matrix_tagsThe extra tags for the matrices this Kernel should fill
C++ Type:std::vector<TagName>
Options:
Description:The extra tags for the matrices this Kernel should fill
extra_vector_tagsThe extra tags for the vectors this Kernel should fill
C++ Type:std::vector<TagName>
Options:
Description:The extra tags for the vectors this Kernel should fill
matrix_tagssystemThe tag for the matrices this Kernel should fill
Default:system
C++ Type:MultiMooseEnum
Options:nontime, system
Description:The tag for the matrices this Kernel should fill
vector_tagsnontimeThe tag for the vectors this Kernel should fill
Default:nontime
C++ Type:MultiMooseEnum
Options:nontime, time
Description:The tag for the vectors this Kernel should fill

Tagging Parameters

Input Files

(test/tests/mms/temporal_convergence/mms_temporal.i)
(problems/thermal_desorption/ogorodnikova/tds_multiapp/desorp_multi.i)
(problems/thermal_desorption/ogorodnikova/tds_multiapp/resting_multi.i)
(test/tests/kernels/one_d_one_trap/one_d_one_trap.i)
(test/tests/mms/spatial_convergence/mms_spatial.i)
(problems/thermal_desorption/ogorodnikova/tds_multiapp/implant_sub.i)

(problems/thermal_desorption/ogorodnikova/tds_multiapp/desorp_multi.i)

[Mesh]
 [./unlabelled]
    file = /Users/sdixon/projects/blue_kite/problems/thermal_desorption/optimisation/ogorodnikova_1k.msh
    type = FileMeshGenerator
    construct_side_list_from_node_list=true
  [../]
  [./block_1]
    type= AllSideSetsByNormalsGenerator
    input = unlabelled
    #fixed_normal = false
  [../]
[]

[Problem]
  type = FEProblem # This is the "normal" type of Finite Element Problem in MOOSE
  coord_type = XYZ # cartesian
[]

[Variables]
  [./Mobile]
  [../]
  [./Trapped_1]
  [../]
  [./Trapped_2]
  []
  [./Trapped_3]
  []
[]

[Functions]
  [./dts]
    type = PiecewiseLinear
    x = '0 1e-4 5e-4 1e-3'
    y = '1e-4 1e-4 5e-4 5e-4'
  [../]
  [./Gaussian_implant]
    type = ParsedFunction
    value = 'scale * exp( -0.5 * ((x - mean) / sd)^2)'
    vars = 'scale mean sd'
    vals = '0.93e8 4.5e-9 4.5e-9'
  [../]
  [./Exponweib_implant]
    type = ParsedFunction
    value = 'peak * (a * c / scale) * (( 1 - exp(-1 * (((x*1e9)-loc)/scale)^c))^(a-1) ) * exp(-1 * (((x*1e9)-loc)/scale)^c)*(((x*1e9)-loc)/scale)^(c-1)'
    vars = 'peak a c loc scale'
    vals = '5.82e8 0.90 1.96 -0.013 4.909'
  [../]
[]

[MultiApps]
  [sub_app]
    type = FullSolveMultiApp
    #app_type = BlueKiteApp
    input_files = 'resting_multi.i'
   # positions = '0   0.029   0
   #              0.015 0.0.029 0
   #              0.015 0.014 0
   #              0.0 0.014 0'
  execute_on = INITIAL
  clone_master_mesh = true
  []
[]

[Transfers]
#   [to_sub] 
#    type = MultiAppCopyTransfer
#    multi_app = sub_app
#    source_variable = 'surface_temp'
#    variable = 'surface_temp'
#    direction = to_multiapp
#  []
  [mobile_transfer]
    type =  MultiAppCopyTransfer #MultiAppScalarToAuxScalarTransfer
    multi_app = sub_app
    source_variable = 'Mobile'
    variable = 'Mobile'
    direction = from_multiapp
  []
  [trap_1_transfer]
    type =  MultiAppCopyTransfer #MultiAppScalarToAuxScalarTransfer
    multi_app = sub_app
    source_variable = 'Trapped_1'
    variable = 'Trapped_1'
    direction = from_multiapp
  []
  [trap_2_transfer]
    type =  MultiAppCopyTransfer #MultiAppScalarToAuxScalarTransfer
    multi_app = sub_app
    source_variable = 'Trapped_2'
    variable = 'Trapped_2'
    direction = from_multiapp
  []
  [trap_3_transfer]
    type =  MultiAppCopyTransfer #MultiAppScalarToAuxScalarTransfer
    multi_app = sub_app
    source_variable = 'Trapped_3'
    variable = 'Trapped_3'
    direction = from_multiapp
  []
[]

[Kernels]
  [./H3_diffusion_eq1]
    type = ADMatDiffusion
    variable = Mobile
    Diffusivity = D
  [../]
  [./mobile_time_deriv]
    type = ADTimeDerivative
    variable = Mobile
  [../]
  [./trapping_equilibrium_equation1]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_1
    v = Mobile
    n_traps = n1
    vi = V1
  [../]
  [./trapping_equilibrium_equation2]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_2
    v = Mobile
    n_traps = n2
    vi = V2
  [../]
  [./trapping_equilibrium_equation3]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_3
    v = Mobile
    n_traps = n3
    vi = V3
  [../]
  [./trapped_time_deriv_couple]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped_1
  [../]
  [./trapped_time_deriv_couple2]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped_2
  [../]
  [./trapped_time_deriv_couple3]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped_3
  [../]
  [./trapped_time_deriv]
    type = ADTimeDerivative
    variable = Trapped_1
  [../]     
  [./trapped_time_deriv2]
    type = ADTimeDerivative
    variable = Trapped_2
  [../]
  [./trapped_time_deriv3]
    type = ADTimeDerivative
    variable = Trapped_3
  [../]
[]

[Postprocessors]
  [/pfc_flux]
    type = ADSideFluxIntegral
    variable = Mobile
    boundary = 1
    diffusivity = D
  [../]
  [/back_flux]
    type = ADSideFluxIntegral
    variable = Mobile
    boundary = 2
    diffusivity = D
  [../]
  [./total_mobile]
    type = VariableIntegral
    variable = Mobile
  [../]
  [./total_trap_1]
    type = VariableIntegral
    variable = Trapped_1
  [../]
    [./total_trap_2]
    type = VariableIntegral
    variable = Trapped_2
  [../]
  [./total_trap_3]
    type = VariableIntegral
    variable = Trapped_3
  [../]
[]

[BCs]
  [./desorption]
    type =  ADDirichletBC
    variable = Mobile
    boundary = 1
    value = 0
  [../]
  [./back_desorption]
    type =  ADDirichletBC
    variable = Mobile
    boundary = 2
    value = 0
  [../]
[]

[Materials]
   [./implant]
    type = ExtrinsicStaticTrappingMaterialRampingT
# Energies
    E_diff = 0.39
    E1 = 0.87
    E2 = 1.0
    E3 = 1.50
    k_boltz = 8.617333E-5
# pre-exponential rate constants
    v0 = 1.0E13
    D0 = 4.1E-7
    lambda = 1.1E-10
# unused
    rho = 1 # unecessary scaling factor, do not use
# site densities
    n_sol = 6
    n1 = 1E-3 #1.0E25
    n2 = 4e-4
    n3a_max = 1e-1
    n3b_max = 1e-2
# trap creation rates
    eta_a = 6e-4
    eta_b = 2e-4
    trap_evolution_time = 400
# flux distribution parameters
    flux = 4e-10
    function = Gaussian_implant
    xp = 1e-6
#Temperature
    initial_T = 300
    beta = 8
    block = 'Tungsten' # 'Stopping_zone' # Plastic_region
# thermal properties
    conductivity = 150 # W/K
    Cp = 137 # J/(kg K)
    density = 19300 # kg/m3
  [../] 
[]
[Executioner]
  type = Transient
  solve_type = NEWTON
  scheme = bdf2
  automatic_scaling=True
 compute_scaling_once=False
  scaling_group_variables = 'Trapped_3; Trapped_2; Trapped_1; Mobile'
  resid_vs_jac_scaling_param = 0.8
 # l_tol = 1e-4
  l_max_its = 100
  nl_max_funcs = 7
  #nl_rel_tol = 1e-7
  nl_abs_tol = 1e-29

  # Set PETSc parameters to optimize solver efficiency
  petsc_options_iname = '-ksp_type -pc_type -pc_factor_shift_type'
  petsc_options_value = 'bcgs lu  NONZERO'
#  dt = 0.25 #0.001 #5e-2
  end_time = 62.5
  timestep_tolerance = 0.01
    [TimeStepper]
    type = IterationAdaptiveDT
    optimal_iterations = 5
    cutback_factor = 0.5
    growth_factor = 1.1
    dt = 0.1
  []
[]


[Outputs]
  #execute_on = 'timestep_end'
  exodus = false # Output Exodus format
  csv = true
[]
[Debug]
  show_material_props = true
  show_var_residual_norms = true
[]

(test/tests/mms/temporal_convergence/mms_temporal.i)

[Mesh]
  type = GeneratedMesh # Can generate simple lines, rectangles and rectangular prisms
  dim = 1 # Dimension of the mesh
  nx = 10 # Number of elements in the x direction
  xmax = 1.0 # Length of test chamber
[]

[Problem]
  type = FEProblem # This is the "normal" type of Finite Element Problem in MOOSE
  coord_type = XYZ # cartesian
[]

[Variables]
  [./Mobile]
    initial_condition = 0.0
  [../]
  [./Trapped]
    initial_condition = 0.0
#    scaling = 1e18
  [../]
[]

#[ICs]
#  [./Mobile]
#    type = FunctionIC
#    function = '1 + ( x * x)'
#    variable = Mobile
#  [../]
#  [./Trapped]
#    type = FunctionIC
#    function = '2 + ( x * x)'
#    variable = Trapped
#  [../]
#[]

[Functions]
  [spatial_convergence_f]
    type = ParsedFunction
    value = '(1/tau) * sin(2*pi*x/l) + D*((2*pi/l)^2) * sin(2*pi*x/l)*(t/tau) + (1/tau)*(x/l)^3'
    vars = 'l D tau'
    vals = '1.0 1.0 1.0' #4.4e-9
  []
  [spatial_convergence_g]
    type = ParsedFunction
    value = '(1/tau) * (x/l)^3 - (vm * sin(2*pi*x/l) * t * (n - (t*(x/l)^3))) + (vi*(t*(x/l)^3))'
    vars = 'l D vm vi n tau'
    vals = '1.0 1.0 0.5 1.0 2.0 1.0'
  []
  [exact_spatial]
    type = ParsedFunction
    value = 'sin(2*pi*x/l) * (t/tau)'
    vars = 'l tau'
    vals = '1.0 1.0'
  []
  [exact_u]
    type = ParsedFunction
    value = '(x/(3*l))*(t/tau)^3'
    vars = 'l tau'
    vals = '1.0 1.0'
  []
  [exact_v]
    type = ParsedFunction
    value = '(x/l) * ( 1 / ( 2 * pi) ) * sin ( 2 * pi * t / tau)'
    vars = 'l tau'
    vals = '1.0 1.0'
  []
  [temporal_convergence_f]
    type = ParsedFunction
    value = '( x / (tau * l) ) * ((t/tau)^2 + cos(2*pi*t/tau))'
    vars = 'l tau'
    vals = '1.0 1.0'
  []
  [temporal_convergence_g]
    type = ParsedFunction
    value = '(x/ (tau * l)) * cos(2*pi*t/tau) - (vm * (x/(3*l))*(t/tau)^3 * (n - (x/(2*pi*l))*sin(2*pi*t/tau))) + (vi * (x/(2*pi*l))*sin(2*pi*t/tau) )'
    vars = 'l tau vi vm n'
    vals = '1.0 1.0 1.0 0.5 2'
  []
  [temporal_bc_u]
    type = ParsedFunction
    value = '(1 / 3) * ( t / tau ) ^ 3'
    vars = 'tau'
    vals = '1.0'
  []
  [temporal_bc_v]
    type = ParsedFunction
    value = '( 1 / ( 2 * pi) ) * sin ( 2 * pi * t / tau)'
    vars = 'tau l'
    vals = '1.0 1.0'
  []
[]

[Postprocessors]
#[error]
#    type = ElementL2Error
#    function = exact_u
#    variable = Mobile
#  []
[error]
    type = ElementL2Error
    function = exact_v
    variable = Trapped
  []
#  [h]
#    type = AverageElementSize
#  []
[]

[Kernels]
  [./H3_diffusion_eq1]
    type = ADMatDiffusion
    variable = Mobile
    diffusivity = D
  [../]
  [./mobile_time_deriv]
    type = ADTimeDerivative
    variable = Mobile
  [../]
  [./trapping_equilibrium_equation]
    type = ADTrappingEquilibriumEquation
    variable = Trapped
    v = Mobile
    vi = V1
    n_traps = n1
  [../]
  [./trapped_time_deriv_couple]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped
  [../]
  [./trapped_time_deriv]
    type = ADTimeDerivative
    variable = Trapped
  [../]
# EXTRA MMS SOURCE TERMS
 [./eq1_mms_source]
   variable = Mobile
   type = ADBodyForce
   function = temporal_convergence_f
   value = 1
 [../]
 [./eq2_mms_source]
   variable = Trapped
   type = ADBodyForce
   function = temporal_convergence_g
   value = 1
 [../]
[]

[BCs]
  [./left_face_u]
    type = ADDirichletBC
    variable = Mobile
    boundary = left
    value = 0
  [../]
  [./right_face_u]
    type = ADFunctionDirichletBC
    variable = Mobile
    boundary = right
    function = temporal_bc_u
  [../]
  [./left_face_v]
    type = ADDirichletBC
    variable = Trapped
    boundary = left
    value = 0
  [../]
  [./right_face_v]
    type = ADFunctionDirichletBC
    variable = Trapped
    boundary = right
    function = temporal_bc_v
  [../]
[]
[Materials]
  [./mat1]
    type = TrappingMaterialConstT
    v0 = 1.0
    E1 = 0.0
    E2 = 0.0
    E3 = 0.0
    k_boltz = 8.6E-5
    D0 = 1.0 #2.1019185 #4.1e-7
    E_diff = 0.0
    lambda = 0.4472135954999579
    n_sol = 10
    n1 = 2
    n2 = 0.0
    n3 = 0.0
    const_T = 1000
  [../]
[]
[Executioner]
  type = Transient # Steady state problem
  solve_type = NEWTON #'PJFNK' #NEWTON # Perform a Newton solve
  compute_scaling_once = False
  automatic_scaling = True
  #  l_tol = 1e-4
 #   nl_rel_tol = 1e-4
  #  nl_abs_tol = 5e-30
#  resid_vs_jac_scaling_param = 1.0
  nl_max_funcs = 7
  petsc_options_iname = '-ksp_type -pc_type -pc_factor_shift_type'
  petsc_options_value = 'bcgs lu NONZERO'
  dt = 0.2
  end_time = 1.0
  timestep_tolerance = 1e-5
[]
[Preconditioning]
  [./smp]
    type = SMP
    full = true
  [../]
[]
[Outputs]
  exodus = true # Output Exodus format
  csv = true
   #[./prov]
  #  type = Provenance
  #[../]
[]
#[Debug]
#  show_material_props = true
#  show_var_residual_norms = true
#[]

(problems/thermal_desorption/ogorodnikova/tds_multiapp/desorp_multi.i)

[Mesh]
 [./unlabelled]
    file = /Users/sdixon/projects/blue_kite/problems/thermal_desorption/optimisation/ogorodnikova_1k.msh
    type = FileMeshGenerator
    construct_side_list_from_node_list=true
  [../]
  [./block_1]
    type= AllSideSetsByNormalsGenerator
    input = unlabelled
    #fixed_normal = false
  [../]
[]

[Problem]
  type = FEProblem # This is the "normal" type of Finite Element Problem in MOOSE
  coord_type = XYZ # cartesian
[]

[Variables]
  [./Mobile]
  [../]
  [./Trapped_1]
  [../]
  [./Trapped_2]
  []
  [./Trapped_3]
  []
[]

[Functions]
  [./dts]
    type = PiecewiseLinear
    x = '0 1e-4 5e-4 1e-3'
    y = '1e-4 1e-4 5e-4 5e-4'
  [../]
  [./Gaussian_implant]
    type = ParsedFunction
    value = 'scale * exp( -0.5 * ((x - mean) / sd)^2)'
    vars = 'scale mean sd'
    vals = '0.93e8 4.5e-9 4.5e-9'
  [../]
  [./Exponweib_implant]
    type = ParsedFunction
    value = 'peak * (a * c / scale) * (( 1 - exp(-1 * (((x*1e9)-loc)/scale)^c))^(a-1) ) * exp(-1 * (((x*1e9)-loc)/scale)^c)*(((x*1e9)-loc)/scale)^(c-1)'
    vars = 'peak a c loc scale'
    vals = '5.82e8 0.90 1.96 -0.013 4.909'
  [../]
[]

[MultiApps]
  [sub_app]
    type = FullSolveMultiApp
    #app_type = BlueKiteApp
    input_files = 'resting_multi.i'
   # positions = '0   0.029   0
   #              0.015 0.0.029 0
   #              0.015 0.014 0
   #              0.0 0.014 0'
  execute_on = INITIAL
  clone_master_mesh = true
  []
[]

[Transfers]
#   [to_sub] 
#    type = MultiAppCopyTransfer
#    multi_app = sub_app
#    source_variable = 'surface_temp'
#    variable = 'surface_temp'
#    direction = to_multiapp
#  []
  [mobile_transfer]
    type =  MultiAppCopyTransfer #MultiAppScalarToAuxScalarTransfer
    multi_app = sub_app
    source_variable = 'Mobile'
    variable = 'Mobile'
    direction = from_multiapp
  []
  [trap_1_transfer]
    type =  MultiAppCopyTransfer #MultiAppScalarToAuxScalarTransfer
    multi_app = sub_app
    source_variable = 'Trapped_1'
    variable = 'Trapped_1'
    direction = from_multiapp
  []
  [trap_2_transfer]
    type =  MultiAppCopyTransfer #MultiAppScalarToAuxScalarTransfer
    multi_app = sub_app
    source_variable = 'Trapped_2'
    variable = 'Trapped_2'
    direction = from_multiapp
  []
  [trap_3_transfer]
    type =  MultiAppCopyTransfer #MultiAppScalarToAuxScalarTransfer
    multi_app = sub_app
    source_variable = 'Trapped_3'
    variable = 'Trapped_3'
    direction = from_multiapp
  []
[]

[Kernels]
  [./H3_diffusion_eq1]
    type = ADMatDiffusion
    variable = Mobile
    Diffusivity = D
  [../]
  [./mobile_time_deriv]
    type = ADTimeDerivative
    variable = Mobile
  [../]
  [./trapping_equilibrium_equation1]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_1
    v = Mobile
    n_traps = n1
    vi = V1
  [../]
  [./trapping_equilibrium_equation2]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_2
    v = Mobile
    n_traps = n2
    vi = V2
  [../]
  [./trapping_equilibrium_equation3]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_3
    v = Mobile
    n_traps = n3
    vi = V3
  [../]
  [./trapped_time_deriv_couple]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped_1
  [../]
  [./trapped_time_deriv_couple2]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped_2
  [../]
  [./trapped_time_deriv_couple3]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped_3
  [../]
  [./trapped_time_deriv]
    type = ADTimeDerivative
    variable = Trapped_1
  [../]     
  [./trapped_time_deriv2]
    type = ADTimeDerivative
    variable = Trapped_2
  [../]
  [./trapped_time_deriv3]
    type = ADTimeDerivative
    variable = Trapped_3
  [../]
[]

[Postprocessors]
  [/pfc_flux]
    type = ADSideFluxIntegral
    variable = Mobile
    boundary = 1
    diffusivity = D
  [../]
  [/back_flux]
    type = ADSideFluxIntegral
    variable = Mobile
    boundary = 2
    diffusivity = D
  [../]
  [./total_mobile]
    type = VariableIntegral
    variable = Mobile
  [../]
  [./total_trap_1]
    type = VariableIntegral
    variable = Trapped_1
  [../]
    [./total_trap_2]
    type = VariableIntegral
    variable = Trapped_2
  [../]
  [./total_trap_3]
    type = VariableIntegral
    variable = Trapped_3
  [../]
[]

[BCs]
  [./desorption]
    type =  ADDirichletBC
    variable = Mobile
    boundary = 1
    value = 0
  [../]
  [./back_desorption]
    type =  ADDirichletBC
    variable = Mobile
    boundary = 2
    value = 0
  [../]
[]

[Materials]
   [./implant]
    type = ExtrinsicStaticTrappingMaterialRampingT
# Energies
    E_diff = 0.39
    E1 = 0.87
    E2 = 1.0
    E3 = 1.50
    k_boltz = 8.617333E-5
# pre-exponential rate constants
    v0 = 1.0E13
    D0 = 4.1E-7
    lambda = 1.1E-10
# unused
    rho = 1 # unecessary scaling factor, do not use
# site densities
    n_sol = 6
    n1 = 1E-3 #1.0E25
    n2 = 4e-4
    n3a_max = 1e-1
    n3b_max = 1e-2
# trap creation rates
    eta_a = 6e-4
    eta_b = 2e-4
    trap_evolution_time = 400
# flux distribution parameters
    flux = 4e-10
    function = Gaussian_implant
    xp = 1e-6
#Temperature
    initial_T = 300
    beta = 8
    block = 'Tungsten' # 'Stopping_zone' # Plastic_region
# thermal properties
    conductivity = 150 # W/K
    Cp = 137 # J/(kg K)
    density = 19300 # kg/m3
  [../] 
[]
[Executioner]
  type = Transient
  solve_type = NEWTON
  scheme = bdf2
  automatic_scaling=True
 compute_scaling_once=False
  scaling_group_variables = 'Trapped_3; Trapped_2; Trapped_1; Mobile'
  resid_vs_jac_scaling_param = 0.8
 # l_tol = 1e-4
  l_max_its = 100
  nl_max_funcs = 7
  #nl_rel_tol = 1e-7
  nl_abs_tol = 1e-29

  # Set PETSc parameters to optimize solver efficiency
  petsc_options_iname = '-ksp_type -pc_type -pc_factor_shift_type'
  petsc_options_value = 'bcgs lu  NONZERO'
#  dt = 0.25 #0.001 #5e-2
  end_time = 62.5
  timestep_tolerance = 0.01
    [TimeStepper]
    type = IterationAdaptiveDT
    optimal_iterations = 5
    cutback_factor = 0.5
    growth_factor = 1.1
    dt = 0.1
  []
[]


[Outputs]
  #execute_on = 'timestep_end'
  exodus = false # Output Exodus format
  csv = true
[]
[Debug]
  show_material_props = true
  show_var_residual_norms = true
[]

(problems/thermal_desorption/ogorodnikova/tds_multiapp/resting_multi.i)

[Mesh]
 [./unlabelled]
    file = /Users/sdixon/projects/blue_kite/problems/thermal_desorption/optimisation/ogorodnikova_1k.msh
    type = FileMeshGenerator
    construct_side_list_from_node_list=true
  [../]
  [./block_1]
    type= AllSideSetsByNormalsGenerator
    input = unlabelled
    #fixed_normal = false
  [../]
[]

[Problem]
  type = FEProblem # This is the "normal" type of Finite Element Problem in MOOSE
  coord_type = XYZ # cartesian
[]

[Variables]
  [./Mobile]
    initial_condition = 0.0
  [../]
  [./Trapped_1]
    initial_condition = 0.0
  [../]
  [./Trapped_2]
    initial_condition = 0.0
  []
  [./Trapped_3]
    initial_condition = 0.0
  []
[]

[Functions]
  [./dts]
    type = PiecewiseLinear
    x = '0 1e-4 5e-4 1e-3'
    y = '1e-4 1e-4 5e-4 5e-4'
  [../]
  [./Gaussian_implant]
    type = ParsedFunction
    value = 'scale * exp( -0.5 * ((x - mean) / sd)^2)'
    vars = 'scale mean sd'
    vals = '0.93e8 4.5e-9 4.5e-9'
  [../]
  [./Exponweib_implant]
    type = ParsedFunction
    value = 'peak * (a * c / scale) * (( 1 - exp(-1 * (((x*1e9)-loc)/scale)^c))^(a-1) ) * exp(-1 * (((x*1e9)-loc)/scale)^c)*(((x*1e9)-loc)/scale)^(c-1)'
    vars = 'peak a c loc scale'
    vals = '5.82e8 0.90 1.96 -0.013 4.909'
  [../]
[]

[MultiApps]
  [sub_app]
    type = FullSolveMultiApp
    #app_type = BlueKiteApp
    input_files = 'implant_sub.i'
   # positions = '0   0.029   0
   #              0.015 0.0.029 0
   #              0.015 0.014 0
   #              0.0 0.014 0'
  execute_on = INITIAL
  clone_master_mesh = true
  []
[]

[Transfers]
#   [to_sub] 
#    type = MultiAppCopyTransfer
#    multi_app = sub_app
#    source_variable = 'surface_temp'
#    variable = 'surface_temp'
#    direction = to_multiapp
#  []
  [mobile_transfer]
    type =  MultiAppCopyTransfer #MultiAppScalarToAuxScalarTransfer
    multi_app = sub_app
    source_variable = 'Mobile'
    variable = 'Mobile'
    direction = from_multiapp
  []
  [trap_1_transfer]
    type =  MultiAppCopyTransfer #MultiAppScalarToAuxScalarTransfer
    multi_app = sub_app
    source_variable = 'Trapped_1'
    variable = 'Trapped_1'
    direction = from_multiapp
  []
  [trap_2_transfer]
    type =  MultiAppCopyTransfer #MultiAppScalarToAuxScalarTransfer
    multi_app = sub_app
    source_variable = 'Trapped_2'
    variable = 'Trapped_2'
    direction = from_multiapp
  []
  [trap_3_transfer]
    type =  MultiAppCopyTransfer #MultiAppScalarToAuxScalarTransfer
    multi_app = sub_app
    source_variable = 'Trapped_3'
    variable = 'Trapped_3'
    direction = from_multiapp
  []
[]

[Kernels]
  [./H3_diffusion_eq1]
    type = ADMatDiffusion
    variable = Mobile
    Diffusivity = D
  [../]
  [./mobile_time_deriv]
    type = ADTimeDerivative
    variable = Mobile
  [../]
  [./trapping_equilibrium_equation1]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_1
    v = Mobile
    n_traps = n1
    vi = V1
  [../]
  [./trapping_equilibrium_equation2]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_2
    v = Mobile
    n_traps = n2
    vi = V2
  [../]
  [./trapping_equilibrium_equation3]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_3
    v = Mobile
    n_traps = n3
    vi = V3
  [../]
  [./trapped_time_deriv_couple]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped_1
  [../]
  [./trapped_time_deriv_couple2]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped_2
  [../]
  [./trapped_time_deriv_couple3]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped_3
  [../]
  [./trapped_time_deriv]
    type = ADTimeDerivative
    variable = Trapped_1
  [../]     
  [./trapped_time_deriv2]
    type = ADTimeDerivative
    variable = Trapped_2
  [../]
  [./trapped_time_deriv3]
    type = ADTimeDerivative
    variable = Trapped_3
  [../]
[]

[Postprocessors]
  [/pfc_flux]
    type = ADSideFluxIntegral
    variable = Mobile
    boundary = 1
    diffusivity = D
  [../]
  [/back_flux]
    type = ADSideFluxIntegral
    variable = Mobile
    boundary = 2
    diffusivity = D
  [../]
  [./total_mobile]
    type = VariableIntegral
    variable = Mobile
  [../]
  [./total_trap_1]
    type = VariableIntegral
    variable = Trapped_1
  [../]
    [./total_trap_2]
    type = VariableIntegral
    variable = Trapped_2
  [../]
  [./total_trap_3]
    type = VariableIntegral
    variable = Trapped_3
  [../]
[]

[BCs]
  [./desorption]
    type =  ADDirichletBC
    variable = Mobile
    boundary = 1
    value = 0
  [../]
  [./back_desorption]
    type =  ADDirichletBC
    variable = Mobile
    boundary = 2
    value = 0
  [../]
[]

[Materials]
   [./implant]
    type = ExtrinsicStaticTrappingMaterial
# Energies
    E_diff = 0.39
    E1 = 0.87
    E2 = 1.0
    E3 = 1.5
    k_boltz = 8.617333E-5
# pre-exponential rate constants
    v0 = 1.0E13
    D0 = 4.1E-7
    lambda = 1.1E-10
# unused
    rho = 1 # unecessary scaling factor, do not use
# site densities
    n_sol = 6
    n1 = 1E-3 #1.0E25
    n2 = 4e-4
    n3a_max = 1e-1
    n3b_max = 1e-2
# trap creation rates
    eta_a = 6e-4
    eta_b = 2e-4
    trap_evolution_time = 400
# flux distribution parameters
    flux = 4e-10
    function = Gaussian_implant
    xp = 1e-6
#Temperature
    const_T = 300
    block = 'Tungsten' #'Implantation_region'
# thermal properties
    conductivity = 150 # W/K
    Cp = 137 # J/(kg K)
    density = 19300 # kg/m3
  [../]
[]

[Executioner]
  type = Transient
  solve_type = NEWTON
  scheme = bdf2
  automatic_scaling=True
 compute_scaling-once=False
  scaling_group_variables = 'Trapped_3; Trapped_2; Trapped_1; Mobile'
  resid_vs_jac_scaling_param = 0.8
  l_tol = 1e-4
  l_max_its = 100
  nl_max_funcs = 7
#  nl_rel_tol = 1e-7
  nl_abs_tol = 1e-29

  # Set PETSc parameters to optimize solver efficiency
  petsc_options_iname = '-ksp_type -pc_type -pc_factor_shift_type'
  petsc_options_value = 'bcgs lu  NONZERO'
  end_time = 50
  timestep_tolerance = 0.01
  [TimeStepper]
    type = IterationAdaptiveDT
    optimal_iterations = 4
    cutback_factor = 0.8
    growth_factor = 1.5
    dt = 0.05
  []
[]


[Outputs]
  #execute_on = 'timestep_end'
  exodus = false # Output Exodus format
  csv = true
[]
[Debug]
  show_material_props = true
  show_var_residual_norms = true
[]

(test/tests/kernels/one_d_one_trap/one_d_one_trap.i)

[Mesh]
  type = GeneratedMesh
  dim = 1 
  nx = 20
  xmax = 5e-5
[]

[Problem]
  type = FEProblem # This is the "normal" type of Finite Element Problem in MOOSE
  coord_type = XYZ # cartesian
[]

[Variables]
  [./Mobile]
    initial_condition = 0.0
  [../]
  [./Trapped]
    initial_condition = 0.0
  [../]
[]

[Kernels]
  [./H3_diffusion_eq1]
    type = ADMatDiffusion
    variable = Mobile
    diffusivity = D
  [../]
  [./mobile_time_deriv]
    type = ADTimeDerivative
    variable = Mobile
  [../]
  [./trapping_equilibrium_equation]
    type = ADTrappingEquilibriumEquation
    variable = Trapped
    v = Mobile
    vi = V1
    n_traps = n1
  [../]
  [./trapped_time_deriv_couple]
    type = ADCoupledTimeDerivative 
    variable = Mobile
    v = Trapped
  [../]
  [./trapped_time_deriv]
    type = ADTimeDerivative
    variable = Trapped
  [../]
[]

[BCs]
  [./left_face]
    type = ADDirichletBC
    variable = Mobile
    boundary = left
    value = 1e-4
  [../]
  [./right_face]
    type = ADDirichletBC #DiffusionFluxBC
    variable = Mobile
    boundary = right
    value = 0
  [../]
[]

[Materials]
  [./mat1]
    type = TrappingMaterialConstT
    v0 = 1.0E13
    v1 = 1.0E13
    v2 = 1.0E13
    v3 = 1.0E13
    E1 = 8.6e-3
    E2 = 0.0
    E3 = 0.0
    k_boltz = 8.6E-5
    D0 = 1.0
    E_diff = 0.0
    lambda = 3.16E-8
    n_sol = 2
    n1 = 0.1
    n2 = 0.0
    n3 = 0.0
    const_T = 1000
  [../]
[]

[Executioner]
  type = Transient
  solve_type = NEWTON 
  # Set PETSc parameters to optimize solver efficiency
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = ' hypre    boomeramg'
  dt = 1e-9
  num_steps = 10
[]

[Outputs]
  console = false
  exodus = true # Output Exodus format
[]

(test/tests/mms/spatial_convergence/mms_spatial.i)

[Mesh]
  type = GeneratedMesh # Can generate simple lines, rectangles and rectangular prisms
  dim = 1 # Dimension of the mesh
  nx = 4 # Number of elements in the x direction
  xmax = 1.0 # Length of test chamber
[]

[Problem]
  type = FEProblem # This is the "normal" type of Finite Element Problem in MOOSE
  coord_type = XYZ # cartesian
[]

[Variables]
  [./Mobile]
    initial_condition = 0.0
  [../]
  [./Trapped]
    initial_condition = 0.0
#    scaling = 1e18
  [../]
[]

#[ICs]
#  [./Mobile]
#    type = FunctionIC
#    function = '1 + ( x * x)'
#    variable = Mobile
#  [../]
#  [./Trapped]
#    type = FunctionIC
#    function = '2 + ( x * x)'
#    variable = Trapped
#  [../]
#[]

[Functions]
  [spatial_convergence_f]
    type = ParsedFunction
    value = '(1/tau) * sin(2*pi*x/l) + D*((2*pi/l)^2) * sin(2*pi*x/l)*(t/tau) + (1/tau)*(x/l)^3'
    vars = 'l D tau'
    vals = '1.0 1.0 1.0' #4.4e-9
  []
  [spatial_convergence_g]
    type = ParsedFunction
    value = '(1/tau) * (x/l)^3 - (vm * sin(2*pi*x/l) * t * (n - (t*(x/l)^3))) + (vi*(t*(x/l)^3))'
    vars = 'l D vm vi n tau'
    vals = '1.0 1.0 0.5 1.0 2.0 1.0'
  []
  [exact]
    type = ParsedFunction
    value = 'sin(2*pi*x/l) * (t/tau)'
    vars = 'l tau'
    vals = '1.0 1.0'
  []
  #[temporal_convergence_f]
  #  type = ParsedFunction
  #  value = ''
  #  vars = 'l D'
  #  vals = '0.02 4.4e-9'
  #[]
  #[temporal_convergence_g]
  #  type = ParsedFunction
  #  value = ''
  #  vars = 'l D'
  #  vals = '0.02 4.4e-9'
  #[]
[]

[Postprocessors]
[error]
    type = ElementL2Error
    function = exact
    variable = Mobile
  []
  [h]
    type = AverageElementSize
  []
[]

[Kernels]
  [./H3_diffusion_eq1]
    type = ADMatDiffusion
    variable = Mobile
    diffusivity = D
  [../]
  [./mobile_time_deriv]
    type = ADTimeDerivative
    variable = Mobile
  [../]
  [./trapping_equilibrium_equation]
    type = ADTrappingEquilibriumEquation
    variable = Trapped
    v = Mobile
    vi = V1
    n_traps = n1
  [../]
  [./trapped_time_deriv_couple]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped
  [../]
  [./trapped_time_deriv]
    type = ADTimeDerivative
    variable = Trapped
  [../]
# EXTRA MMS SOURCE TERMS
 [./eq1_mms_source]
   variable = Mobile
   type = ADBodyForce
   function = spatial_convergence_f
   value = 1
 [../]
 [./eq2_mms_source]
   variable = Trapped
   type = ADBodyForce
   function = spatial_convergence_g
   value = 1
 [../]
[]

[BCs]
  [./left_face]
    type = ADDirichletBC
    variable = Mobile
    boundary = left
    value = 0
  [../]
  [./right_face]
    type = ADDirichletBC
    variable = Mobile
    boundary = right
    value = 0
  [../]
  [./left_face_t]
    type = ADDirichletBC
    variable = Trapped
    boundary = left
    value = 0
  [../]
  [./right_face_t]
    type = ADFunctionDirichletBC
    variable = Trapped
    boundary = right
    function = 't'
  [../]
[]
[Materials]
  [./mat1]
    type = TrappingMaterialConstT
    v0 = 1.0
    E1 = 0.0
    E2 = 0.0
    E3 = 0.0
    k_boltz = 8.6E-5
    D0 = 1.0 #2.1019185 #4.1e-7
    E_diff = 0.0
    lambda = 0.4472135954999579
    n_sol = 10
    n1 = 2
    n2 = 0.0
    n3 = 0.0
    const_T = 1000
  [../]
[]
[Executioner]
  type = Transient # Steady state problem
  solve_type = NEWTON #'PJFNK' #NEWTON # Perform a Newton solve
  compute_scaling_once = False
  automatic_scaling = True
  #  l_tol = 1e-4
 #   nl_rel_tol = 1e-4
  #  nl_abs_tol = 5e-30
#  resid_vs_jac_scaling_param = 1.0
  nl_max_funcs = 7
  petsc_options_iname = '-ksp_type -pc_type -pc_factor_shift_type'
  petsc_options_value = 'bcgs lu NONZERO'
  dt = 1e-2
  end_time = 1.0
  timestep_tolerance = 1e-5
[]
[Preconditioning]
  [./smp]
    type = SMP
    full = true
  [../]
[]
[Outputs]
  exodus = true # Output Exodus format
  csv = true
   #[./prov]
  #  type = Provenance
  #[../]
[]
#[Debug]
#  show_material_props = true
#  show_var_residual_norms = true
#[]

(problems/thermal_desorption/ogorodnikova/tds_multiapp/implant_sub.i)

[Mesh]
 [./unlabelled] 
    file = /Users/sdixon/projects/blue_kite/problems/thermal_desorption/optimisation/ogorodnikova_1k.msh
    type = FileMeshGenerator
    construct_side_list_from_node_list=true
  [../]
  [./block_1]
    type= AllSideSetsByNormalsGenerator
    input = unlabelled
    #fixed_normal = false
  [../]
[]

[Problem]
  type = FEProblem # This is the "normal" type of Finite Element Problem in MOOSE
  coord_type = XYZ # cartesian
[]

[Variables]
  [./Mobile]
    initial_condition = 0.0
  [../]
  [./Trapped_1]
    initial_comdition = 0.0
    scaling = 1e2
  [../]
  [./Trapped_2]
    initial_condition = 0.0
    scaling = 1e3
  []
  [./Trapped_3]
    initial_condition = 0.0
    scaling = 1e3
  []
[]

[Functions]
  [./dts]
    type = PiecewiseLinear
    x = '0 1e-4 5e-4 1e-3'
    y = '1e-4 1e-4 5e-4 5e-4'
  [../]
  [./Gaussian_implant]
    type = ParsedFunction
    value = 'scale * exp( -0.5 * ((x - mean) / sd)^2)'
    vars = 'scale mean sd'
    vals = '0.93e8 4.5e-9 4.5e-9'
  [../]
  [./Exponweib_implant]
    type = ParsedFunction
    value = 'peak * (a * c / scale) * (( 1 - exp(-1 * (((x*1e9)-loc)/scale)^c))^(a-1) ) * exp(-1 * (((x*1e9)-loc)/scale)^c)*(((x*1e9)-loc)/scale)^(c-1)'
    vars = 'peak a c loc scale'
    vals = '5.82e8 0.90 1.96 -0.013 4.909'
  [../]
[]


[Kernels]
  [./H3_source]
    type = ADBodyForce
    variable = Mobile
    value = 4e-10
    function = Gaussian_implant
  []
  [./H3_diffusion_eq1]
    type = ADMatDiffusion
    variable = Mobile
    Diffusivity = D
  [../]
  [./mobile_time_deriv]
    type = ADTimeDerivative 
    variable = Mobile
  [../]
  [./trapping_equilibrium_equation1]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_1
    v = Mobile
    n_traps = n1
    vi = V1
  [../]
  [./trapping_equilibrium_equation2]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_2
    v = Mobile
    n_traps = n2
    vi = V2
  [../]
  [./trapping_equilibrium_equation3]
    type = ADTrappingEquilibriumEquation
    variable = Trapped_3
    v = Mobile
    n_traps = n3
    vi = V3
  [../]
  [./trapped_time_deriv_couple]
    type = ADCoupledTimeDerivative
    variable = Mobile
    v = Trapped_1
  [../]
  [./trapped_time_deriv_couple2]
    type = ADCoupledTimeDerivative 
    variable = Mobile
    v = Trapped_2
  [../]
  [./trapped_time_deriv_couple3]
    type = ADCoupledTimeDerivative 
    variable = Mobile
    v = Trapped_3
  [../]
  [./trapped_time_deriv]
    type = ADTimeDerivative 
    variable = Trapped_1
  [../]     
  [./trapped_time_deriv2]
    type = ADTimeDerivative
    variable = Trapped_2
  [../]
  [./trapped_time_deriv3]
    type = ADTimeDerivative
    variable = Trapped_3
  [../]
[]

[BCs]
  [./PFC]
    type = ADDirichletBC
    variable = Mobile
    boundary = 1
    value = 0
  [../]
[]

[Materials]
   [./implant]
    type = ExtrinsicTransientTrappingMaterial2
# Energies    
    E_diff = 0.39
    E1 = 0.87
    E2 = 1.0
    E3 = 1.5
    k_boltz = 8.617333E-5
# pre-exponential rate constants    
    v0 = 1e13 
    D0 = 4.1e-7
    lambda = 1.1E-10
# unused    
    rho = 1 # unecessary scaling factor, do not use
# site densities    
    n_sol = 6
    n1 = 1e-3
    n2 = 4e-4
    n3a_max = 1e-1
    n3b_max = 1e-2
# trap creation rates    
    eta_a = 6e-4
    eta_b = 2e-4
# flux distribution parameters    
    flux = 4e-10
    function = Gaussian_implant
    xp = 1e-6
#Temperature    
    const_T = 300
    block = 'Tungsten'
# thermal properties
    conductivity = 150 # W/K
    Cp = 137 # J/(kg K)
    density = 19300 # kg/m3
  [../]
[]

[Postprocessors]
  [./total_mobile]
    type = VariableIntegral
    variable = Mobile
  [../]
  [./total_trap_1]
    type = VariableIntegral
    variable = Trapped_1
  [../]
    [./total_trap_2]
    type = VariableIntegral
    variable = Trapped_2
  [../]
  [./total_trap_3]
    type = VariableIntegral
    variable = Trapped_3
  [../]
[]

[Executioner]
  type = Transient
  solve_type = NEWTON 
  scheme = bdf2
  automatic_scaling=True
#  compute_scaling_once=False
#  scaling_group_variables = 'Trapped_3 Trapped_2 Trapped_1 Mobile'
  resid_vs_jac_scaling_param = 0.8
  l_max_its = 100
  nl_max_funcs = 7
#  nl_rel_tol = 1e-7
  nl_abs_tol = 1e-29
  
  # Set PETSc parameters to optimize solver efficiency
  timestep_tolerance = 0.01
  petsc_options_iname = '-ksp_type -pc_type -pc_factor_shift_type'
  petsc_options_value = 'bcgs lu  NONZERO'
  end_time = 400
  [TimeStepper]
    type = IterationAdaptiveDT
    optimal_iterations = 4
    cutback_factor = 0.8
    growth_factor = 1.2
    dt = 5e-4
  []
[]

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


[Outputs]
  exodus = true
  csv = true
#  console = false
[]

[Debug]
#  show_material_props = true
  show_var_residual_norms = true
[]

Overview
Example Input File Syntax
Input Parameters
Input Files

Module

Examples

Source Code

Comparison to Analytical Solution

Thermal Desorption Spectrum

Kernels

BCs

Materials

Postprocessors