From 908d198db35e1aaad18b22507102ece2608ca7af Mon Sep 17 00:00:00 2001
From: Stephen Dixon <sdixon@Ivans-iMac.home>
Date: Thu, 12 Aug 2021 03:26:24 +0100
Subject: [PATCH 1/3] Adding thermal desorption example

---
 .../ogorodnikova/tds_multiapp/desorp_multi.i  |  285 ++
 .../ogorodnikova/tds_multiapp/implant_sub.i   |  234 ++
 .../tds_multiapp/ogorodnikova_1k.msh          | 3022 +++++++++++++++++
 .../ogorodnikova/tds_multiapp/resting_multi.i |  288 ++
 4 files changed, 3829 insertions(+)
 create mode 100644 problems/thermal_desorption/ogorodnikova/tds_multiapp/desorp_multi.i
 create mode 100644 problems/thermal_desorption/ogorodnikova/tds_multiapp/implant_sub.i
 create mode 100644 problems/thermal_desorption/ogorodnikova/tds_multiapp/ogorodnikova_1k.msh
 create mode 100644 problems/thermal_desorption/ogorodnikova/tds_multiapp/resting_multi.i

diff --git a/problems/thermal_desorption/ogorodnikova/tds_multiapp/desorp_multi.i b/problems/thermal_desorption/ogorodnikova/tds_multiapp/desorp_multi.i
new file mode 100644
index 0000000..bca9314
--- /dev/null
+++ b/problems/thermal_desorption/ogorodnikova/tds_multiapp/desorp_multi.i
@@ -0,0 +1,285 @@
+[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
+[]
diff --git a/problems/thermal_desorption/ogorodnikova/tds_multiapp/implant_sub.i b/problems/thermal_desorption/ogorodnikova/tds_multiapp/implant_sub.i
new file mode 100644
index 0000000..ddef8da
--- /dev/null
+++ b/problems/thermal_desorption/ogorodnikova/tds_multiapp/implant_sub.i
@@ -0,0 +1,234 @@
+[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
+[]
diff --git a/problems/thermal_desorption/ogorodnikova/tds_multiapp/ogorodnikova_1k.msh b/problems/thermal_desorption/ogorodnikova/tds_multiapp/ogorodnikova_1k.msh
new file mode 100644
index 0000000..8e804ef
--- /dev/null
+++ b/problems/thermal_desorption/ogorodnikova/tds_multiapp/ogorodnikova_1k.msh
@@ -0,0 +1,3022 @@
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+999 1000 2 
+$EndElements
diff --git a/problems/thermal_desorption/ogorodnikova/tds_multiapp/resting_multi.i b/problems/thermal_desorption/ogorodnikova/tds_multiapp/resting_multi.i
new file mode 100644
index 0000000..b13f897
--- /dev/null
+++ b/problems/thermal_desorption/ogorodnikova/tds_multiapp/resting_multi.i
@@ -0,0 +1,288 @@
+[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
+[]

From 16f7a8a9dba7e19129f62e1a39ccb0cc5cc5fece Mon Sep 17 00:00:00 2001
From: Stephen Dixon <sdixon@Ivans-iMac.home>
Date: Thu, 12 Aug 2021 04:06:52 +0100
Subject: [PATCH 2/3] testing updated CI script

---
 docker/achlys-ubuntu/Dockerfile | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/docker/achlys-ubuntu/Dockerfile b/docker/achlys-ubuntu/Dockerfile
index 28ca621..9ebd8a3 100644
--- a/docker/achlys-ubuntu/Dockerfile
+++ b/docker/achlys-ubuntu/Dockerfile
@@ -7,7 +7,12 @@
 
 FROM helenbrooks/moose-ubuntu
 ARG compile_cores=1
-ARG build_git_sha="release/0.1.0"
+ARG build_git_sha="master"
+
+RUN apt-get update && \
+  apt-get -y install pip && \
+  pip3 install sympy && \
+  pip3 install pandas
 
 RUN cd /home && \
     git clone https://github.com/aurora-multiphysics/achlys.git && \

From 5d01d1d039df1316ce850fdd9f2d7ace15e3e4ce Mon Sep 17 00:00:00 2001
From: Stephen Dixon <sdixon@Ivans-iMac.home>
Date: Thu, 12 Aug 2021 04:29:03 +0100
Subject: [PATCH 3/3] adding more python dependencies to CI dockerfile

---
 docker/achlys-ubuntu/Dockerfile | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/docker/achlys-ubuntu/Dockerfile b/docker/achlys-ubuntu/Dockerfile
index 9ebd8a3..4faaba4 100644
--- a/docker/achlys-ubuntu/Dockerfile
+++ b/docker/achlys-ubuntu/Dockerfile
@@ -11,8 +11,11 @@ ARG build_git_sha="master"
 
 RUN apt-get update && \
   apt-get -y install pip && \
-  pip3 install sympy && \
-  pip3 install pandas
+  pip3 install sympy  \
+   pandas \ 
+   matplotlib \
+   pyyaml \ 
+   mock
 
 RUN cd /home && \
     git clone https://github.com/aurora-multiphysics/achlys.git && \