Merge pull request #47 from micahjohnson150/spatial_rescale-45

Spatial rescale 45

include/kernels/PhaseTransition.h

@@ -21,6 +21,12 @@ class PhaseTransition :
 
 protected:
   virtual Real computeDFDOP(PFFunctionType type);
+/**
+ * Compute off-diagonal jacobain
+ * The off-diagonal jacobain term, i.e., the derivative of the coupled time derivative with respect
+ * to the coupled variable.
+ */
+//  virtual Real computeQpOffDiagJacobian(unsigned int jvar);
 
 private:
   VariableValue & _s;
@@ -29,5 +35,7 @@ class PhaseTransition :
 
   MaterialProperty<Real> & _s_eq;
 
+  unsigned int _v_var;
+
 };
 #endif // PHASETRANSITION_H

problems/1D_full/1D_full.i

@@ -1,15 +1,10 @@
 [Mesh]
-  type = GeneratedMesh
+  type = FileMesh
+  file = phi_diffusion_0021_mesh.xdr
   dim = 2
-  nx = 100
-  ny = 2
-  xmax = .005
-  ymax = .0002
-  elem_type = QUAD4
 []
 
 [Variables]
-  active = 'phi T'
   [./T]
   [../]
   [./u]
@@ -18,24 +13,25 @@
   [../]
 []
 
-[AuxVariables]
-  [./u]
-  [../]
-[]
-
 [Functions]
   [./T_func]
-    type = ParsedFunction
-    value = -200*x+261
+    type = SolutionFunction
+    from_variable = T
+    solution = intial_T
+  [../]
+  [./phi_func]
+    type = SolutionFunction
+    from_variable = phi
+    solution = initial_phi
   [../]
 []
 
 [Kernels]
-  active = 'phi_transition heat_diffusion phi_double_well heat_phi_time heat_time phi_time phi_square_gradient'
   [./heat_diffusion]
-    type = MatDiffusion
+    type = PikaDiffusion
     variable = T
-    D_name = conductivity
+    use_temporal_scaling = true
+    property = conductivity
   [../]
   [./heat_time]
     type = PikaTimeDerivative
@@ -44,11 +40,12 @@
     scale = 1.0
   [../]
   [./heat_phi_time]
-    type = PikaScaledTimeDerivative
+    type = PikaCoupledTimeDerivative
     variable = T
     property = latent_heat
     scale = -0.5
-    differentiated_variable = phi
+    use_temporal_scaling = true
+    coupled_variable = phi
   [../]
   [./vapor_time]
     type = PikaTimeDerivative
@@ -57,15 +54,18 @@
     scale = 1.0
   [../]
   [./vapor_diffusion]
-    type = MatDiffusion
+    type = PikaDiffusion
     variable = u
-    D_name = diffusion_coefficient
+    use_temporal_scaling = true
+    property = diffusion_coefficient
   [../]
   [./vapor_phi_time]
-    type = PikaScaledTimeDerivative
+    type = PikaCoupledTimeDerivative
     variable = u
     coefficient = 0.5
     differentiated_variable = phi
+    use_temporal_scaling = true
+    coupled_variable = phi
   [../]
   [./phi_time]
     type = PikaTimeDerivative
@@ -93,6 +93,7 @@
 []
 
 [BCs]
+  active = 'T_hot T_cold phi_bc'
   [./T_hot]
     type = DirichletBC
     variable = T
@@ -110,75 +111,99 @@
     variable = T
     boundary = 'top bottom'
   [../]
+  [./phi_bc]
+    type = DirichletBC
+    variable = phi
+    boundary = 'left right'
+    value = 1
+  [../]
 []
 
 [Postprocessors]
 []
 
 [UserObjects]
-  [./property_uo]
-    type = PropertyUserObject
+  [./intial_T]
+    type = SolutionUserObject
+    system = nl0
+    mesh = temp_diffusion_0003_mesh.xdr
+    nodal_variables = T
+    es = temp_diffusion_0003.xdr
+  [../]
+  [./initial_phi]
+    type = SolutionUserObject
+    system = nl0
+    mesh = phi_diffusion_0021_mesh.xdr
+    nodal_variables = phi
+    es = phi_diffusion_0021.xdr
+  [../]
+[]
+
+[Preconditioning]
+  [./smp_precond]
+    type = SMP
+    full = true
   [../]
 []
 
 [Executioner]
   # Preconditioned JFNK (default)
   type = Transient
-  dt = 5
   solve_type = PJFNK
   petsc_options_iname = '-ksp_gmres_restart -pc_type -pc_hypre_type'
-  petsc_options_value = '500 hypre boomeramg'
-  end_time = 10
+  petsc_options_value = '100 hypre boomeramg'
+  end_time = 1300
 []
 
 [Adaptivity]
-  max_h_level = 3
-  initial_steps = 3
+  max_h_level = 5
+  initial_steps = 2
+  marker = combo
   initial_marker = phi_marker
-  marker = combo_mark
   [./Indicators]
-    [./phi_grad_indicator]
+    [./phi_grad_jump]
       type = GradientJumpIndicator
       variable = phi
     [../]
-    [./u_jump_indicator]
+    [./u_grad_jump]
       type = GradientJumpIndicator
       variable = u
-      block = 0
+    [../]
+    [./T_grad_jump]
+      type = GradientJumpIndicator
+      variable = T
     [../]
   [../]
   [./Markers]
-    active = 'phi_marker combo_mark u_marker'
     [./phi_marker]
       type = ErrorFractionMarker
-      coarsen = 0.2
-      indicator = phi_grad_indicator
-      refine = .8
-    [../]
-    [./T_marker]
-      type = ErrorFractionMarker
-      coarsen = 0.2
-      indicator = T_jump_indicator
-      refine = 0.7
+      coarsen = .01
+      indicator = phi_grad_jump
+      refine = .6
     [../]
     [./u_marker]
       type = ErrorFractionMarker
-      indicator = u_jump_indicator
-      coarsen = 0.2
-      refine = 0.8
-      block = 0
+      coarsen = .01
+      indicator = u_grad_jump
+      refine = 0.6
     [../]
-    [./combo_mark]
+    [./combo]
       type = ComboMarker
-      block = 0
-      markers = 'u_marker phi_marker'
+      markers = 'phi_marker u_marker t_marker'
+    [../]
+    [./t_marker]
+      type = ErrorFractionMarker
+      coarsen = .01
+      indicator = T_grad_jump
+      refine = .5
     [../]
   [../]
 []
 
 [Outputs]
   output_initial = true
   exodus = true
+  file_base = phi_diffusion
   [./console]
     type = Console
     perf_log = true
@@ -189,14 +214,9 @@
 
 [ICs]
   [./phase_ic]
-    x1 = 0.00214285714
     variable = phi
-    type = KaempferAnalyticPhaseIC
-    x2 = 0.00285714285
-    phi_new = -1
-    phi_old = 1
-    x3 = 0.00357142857
-    x4 = 0.00428571428
+    type = FunctionIC
+    function = phi_func
   [../]
   [./temperature_ic]
     variable = T
@@ -215,8 +235,9 @@
 [PikaMaterials]
   phi = phi
   temperature = T
-  interface_thickness = 1e-6
-  reference_temperature = 263.15
+  interface_thickness = 8e-5
+  output_properties = 'tau equilibrium_concentration heat_capacity conductivity diffusion_coefficient latent_heat lambda'
+  outputs = all
   temporal_scaling = 1e-4
 []