More fundamental testing of the Jacobian. (idaholab#5913)

- Turned off currently_computing_jacobian flag in ExampleShapeElementUserObject
  because the storage was not getting assigned before the executeJacobian
  functions were getting called resulting in an index out-of-bounds error.
- Added hasActiveBlocks check to avoid segmentation faults
- Perform a dynamic pointer cast to test whether an elemental_object is a
  shape_elemental_object before performing executeJacobianWrapper
- Simplified jacobian.i test while trying to probe what's causing the wrong
  Jacobian
- I believe it's in the kernel: the kernel only loops over local _j when the
  ith residual is a function of dof's outside the local j's

framework/include/base/FEProblem.h

@@ -340,7 +340,7 @@ class FEProblem :
   /**
    * Returns true if we are currently computing Jacobian
    */
-  virtual const bool & currentlyComputingJacobian() { return _currently_computing_jacobian; }
+  virtual bool currentlyComputingJacobian() { return _currently_computing_jacobian; }
 
   /**
    * Returns true if we are in or beyond the initialSetup stage

framework/src/base/ComputeUserObjectsThread.C

@@ -67,6 +67,7 @@ ComputeUserObjectsThread::subdomainChanged()
   _fe_problem.prepareMaterials(_subdomain, _tid);
 
   // ShapeElementUserObject requested Jacobian variables
+  if (_elemental_user_objects.hasActiveBlockObjects(_subdomain, _tid))
   {
     std::set<MooseVariable *> jacobian_moose_vars;
 
@@ -79,9 +80,9 @@ ComputeUserObjectsThread::subdomainChanged()
         const std::set<MooseVariable *> & mv_deps = shape_element_uo->jacobianMooseVariables();
         jacobian_moose_vars.insert(mv_deps.begin(), mv_deps.end());
       }
-    }
 
-    _jacobian_moose_vars.assign(jacobian_moose_vars.begin(), jacobian_moose_vars.end());
+      _jacobian_moose_vars.assign(jacobian_moose_vars.begin(), jacobian_moose_vars.end());
+    }
   }
 }
 

test/src/userobjects/ExampleShapeElementUserObject.C

@@ -41,7 +41,7 @@ ExampleShapeElementUserObject::initialize()
   // Jacobian term storage is up to the user. One option is using an std::vector
   // We resize it to the total number of DOFs in the system and zero it out.
   // WARNING: this can be large number (smart sparse storage could be a future improvement)
-  if (_currently_computing_jacobian)
+  // if (_currently_computing_jacobian)
     _jacobian_storage.assign(_subproblem.es().n_dofs(), 0.0);
 }
 

test/tests/userobjects/shape_element_user_object/jacobian.i

@@ -1,8 +1,8 @@
 [Mesh]
   type = GeneratedMesh
-  dim = 2
-  nx = 3
-  ny = 3
+  dim = 1
+  nx = 2
+  # ny = 3
 []
 
 [Variables]
@@ -15,11 +15,11 @@
     [../]
   [../]
   [./v]
-    order = THIRD
-    family = HERMITE
+    order = FIRST
+    family = LAGRANGE
     [./InitialCondition]
       type = FunctionIC
-      function = (y-0.5)^2
+      function = (x-0.5)^2
     [../]
   [../]
   [./w]
@@ -52,10 +52,10 @@
     type = TimeDerivative
     variable = v
   [../]
-  [./time_w]
-    type = TimeDerivative
-    variable = w
-  [../]
+  # [./time_w]
+  #   type = TimeDerivative
+  #   variable = w
+  # [../]
 []
 
 [UserObjects]
@@ -79,6 +79,9 @@
 [Executioner]
   type = Transient
   solve_type = NEWTON
+  petsc_options = '-snes_test_display'
+  petsc_options_iname = '-snes_type'
+  petsc_options_value = 'test'
   dt = 0.1
   num_steps = 2
 []