Merge pull request #72 from hugary1995/gb_cavitation

Refactor grain boundary cavitation model

.gitignore

@@ -19,4 +19,5 @@ build
 *.csv
 *.previous_test_results.json
 *~
+.vscode
 *.yaml

Makefile

@@ -37,7 +37,7 @@ RDG                 := no
 RICHARDS            := no
 SOLID_MECHANICS     := no
 STOCHASTIC_TOOLS    := no
-TENSOR_MECHANICS    := yes
+SOLID_MECHANICS     := yes
 WATER_STEAM_EOS     := no
 XFEM                := no
 POROUS_FLOW         := no

examples/CPFE_with_GBcavitation/cpfem_with_GBcavitation_example.i

@@ -27,22 +27,20 @@
   displacements = 'disp_x disp_y disp_z'
 []
 
-[Modules]
-  [TensorMechanics]
-    [Master]
+[Physics]
+  [SolidMechanics]
+    [QuasiStatic]
       [all]
         strain = FINITE
         new_system = true
         add_variables = true
         formulation = TOTAL
         volumetric_locking_correction = false
-        generate_output = 'cauchy_stress_xx cauchy_stress_yy cauchy_stress_zz cauchy_stress_xy '
-                          'cauchy_stress_xz cauchy_stress_yz mechanical_strain_xx mechanical_strain_yy mechanical_strain_zz mechanical_strain_xy '
-                          'mechanical_strain_xz mechanical_strain_yz'
+        generate_output = 'cauchy_stress_xx cauchy_stress_yy cauchy_stress_zz cauchy_stress_xy cauchy_stress_xz cauchy_stress_yz mechanical_strain_xx mechanical_strain_yy mechanical_strain_zz mechanical_strain_xy mechanical_strain_xz mechanical_strain_yz'
       []
     []
   []
-[] 
+[]
 
 #output some material propertiy from the cavitation model
 [AuxVariables]
@@ -61,42 +59,41 @@
 []
 
 [AuxKernels]
-[a]
-  type = MaterialRealAux
-  boundary = 'interface'
-  property = a
-  execute_on = 'TIMESTEP_END'
-  variable = a
-  check_boundary_restricted = false #this is important
-[]
-[b]
-  type = MaterialRealAux
-  boundary = 'interface'
-  property = b
-  execute_on = 'TIMESTEP_END'
-  variable = b
-  check_boundary_restricted = false #this is important
-[]
-[D]
-  type = MaterialRealAux
-  boundary = 'interface'
-  property = interface_damage
-  execute_on = 'TIMESTEP_END'
-  variable = D
-  check_boundary_restricted = false #this is important
-[]
+  [a]
+    type = MaterialRealAux
+    boundary = 'interface'
+    property = a
+    execute_on = 'TIMESTEP_END'
+    variable = a
+    check_boundary_restricted = false #this is important
+  []
+  [b]
+    type = MaterialRealAux
+    boundary = 'interface'
+    property = b
+    execute_on = 'TIMESTEP_END'
+    variable = b
+    check_boundary_restricted = false #this is important
+  []
+  [D]
+    type = MaterialRealAux
+    boundary = 'interface'
+    property = interface_damage
+    execute_on = 'TIMESTEP_END'
+    variable = D
+    check_boundary_restricted = false #this is important
+  []
 []
 
-[Modules/TensorMechanics/CohesiveZoneMaster]
-  [./czm_ik]
+[Physics/SolidMechanics/CohesiveZone]
+  [czm_ik]
     # add the proper cohesive interface kernels
     boundary = 'interface'
     strain = FINITE # use finite strins, total lagrangian formulation
-    generate_output='traction_x traction_y traction_z jump_x jump_y jump_z normal_traction tangent_traction normal_jump tangent_jump' #output traction and jump
-  [../]
+    generate_output = 'traction_x traction_y traction_z jump_x jump_y jump_z normal_traction tangent_traction normal_jump tangent_jump' #output traction and jump
+  []
 []
 
-
 [Functions]
   # loading functions for each direction
   [applied_load_x]
@@ -116,7 +113,6 @@
   []
 []
 
-
 [BCs]
   [x0]
     type = DirichletBC
@@ -186,7 +182,7 @@
     read_type = block
     nblock = 10
     use_zero_based_block_indexing = false
-  [../]
+  []
 []
 [Materials]
   [stress]
@@ -228,7 +224,7 @@
   start_time = 0.0
   dtmin = 1e-4
   dtmax = 1e3
-  end_time =  10
+  end_time = 10
   n_max_nonlinear_pingpong = 1
   nl_forced_its = 2
 
@@ -244,5 +240,5 @@
 
 [Outputs]
   sync_times = '0 0.1 1 10'
-  exodus=true
+  exodus = true
 []

examples/euler_angle-reader/cpfem_eulerTest.i

@@ -8,147 +8,144 @@
 []
 
 [Variables]
-      [./disp_x]
-            order = second
-      [../]
-      [./disp_y]
-            order = second
-      [../]
-      [./disp_z]
-            order = second
-      [../]
+  [disp_x]
+    order = second
+  []
+  [disp_y]
+    order = second
+  []
+  [disp_z]
+    order = second
+  []
 []
 
 [Functions]
-  [./pfn]
+  [pfn]
     type = PiecewiseLinear
     x = '0    100'
     y = '0.00 0.01'
-  [../]
+  []
 []
 
 [AuxVariables]
-  [./orientation_q1]
+  [orientation_q1]
     order = CONSTANT
     family = MONOMIAL
-  [../]
-  [./orientation_q2]
+  []
+  [orientation_q2]
     order = CONSTANT
     family = MONOMIAL
-  [../]
-  [./orientation_q3]
+  []
+  [orientation_q3]
     order = CONSTANT
     family = MONOMIAL
-  [../]
-  [./orientation_q4]
+  []
+  [orientation_q4]
     order = CONSTANT
     family = MONOMIAL
-  [../]
+  []
 []
 
 [AuxKernels]
   [q1]
     type = MaterialStdVectorAux
-    property  = orientation
+    property = orientation
     index = 0
-    variable  = orientation_q1
-  [../]
+    variable = orientation_q1
+  []
   [q2]
     type = MaterialStdVectorAux
-    property  = orientation
+    property = orientation
     index = 1
-    variable  = orientation_q2
-  [../]
+    variable = orientation_q2
+  []
   [q3]
     type = MaterialStdVectorAux
-    property  = orientation
+    property = orientation
     index = 2
-    variable  = orientation_q3
-  [../]
+    variable = orientation_q3
+  []
   [q4]
     type = MaterialStdVectorAux
-    property  = orientation
+    property = orientation
     index = 3
-    variable  = orientation_q4
-  [../]
+    variable = orientation_q4
+  []
 []
 
-[Modules]
-  [TensorMechanics]
-    [Master]
+[Physics]
+  [SolidMechanics]
+    [QuasiStatic]
       [all]
         strain = FINITE
         new_system = true
         formulation = TOTAL
         volumetric_locking_correction = false
-        generate_output = 'cauchy_stress_xx cauchy_stress_yy cauchy_stress_zz cauchy_stress_xy '
-                          'cauchy_stress_xz cauchy_stress_yz mechanical_strain_xx mechanical_strain_yy mechanical_strain_zz mechanical_strain_xy '
-                          'mechanical_strain_xz mechanical_strain_yz'
+        generate_output = 'cauchy_stress_xx cauchy_stress_yy cauchy_stress_zz cauchy_stress_xy cauchy_stress_xz cauchy_stress_yz mechanical_strain_xx mechanical_strain_yy mechanical_strain_zz mechanical_strain_xy mechanical_strain_xz mechanical_strain_yz'
       []
     []
   []
-[] 
+[]
 
 [UserObjects]
-  [./euler_angle_file]
+  [euler_angle_file]
     type = ElementPropertyReadFile
     nprop = 3
     prop_file_name = grn_10_rand.tex
     read_type = block
     nblock = 10
     use_zero_based_block_indexing = false
-  [../]
+  []
 []
 [BCs]
-  [./left]
-     type = DirichletBC
-     preset = true
-     variable = disp_x
-     boundary = left
-     value = 0.0
-  [../]
-
-  [./bottom]
+  [left]
     type = DirichletBC
-     preset = true
+    preset = true
+    variable = disp_x
+    boundary = left
+    value = 0.0
+  []
+
+  [bottom]
+    type = DirichletBC
+    preset = true
     variable = disp_y
     boundary = bottom
     value = 0.0
-  [../]
+  []
 
-  [./back]
+  [back]
     type = DirichletBC
-     preset = true
+    preset = true
     variable = disp_z
     boundary = back
     value = 0.0
-  [../]
+  []
 
-  [./front]
+  [front]
     type = FunctionDirichletBC
     variable = disp_y
     boundary = top
     function = pfn
     preset = true
-  [../]
+  []
 []
 
 [Materials]
-  [./stress]
+  [stress]
     type = NEMLCrystalPlasticity
     database = "test.xml"
     model = "grain_1"
     large_kinematics = true
     euler_angle_reader = euler_angle_file
-  [../]
+  []
 []
 
-
 [Preconditioning]
-  [./smp]
+  [smp]
     type = SMP
     full = true
-  [../]
+  []
 []
 
 [Executioner]