reorganize solveIncrement

Broke solveIncrement into four smaller sections:
1. Aux vars that are not nonlinear (sequential)
2. Explicit vars (concurrent)
3. Linear solves (sequential)
4. Nonlinear solve (concurrent)

TODO/NOTES:
I broke the skip_time_dependent thing.
Changes not yet propogated.
Need some documentation.
Prefer to pass var_index into solver rather than use member variable currentFieldIndex.
Maybe removed need for member variable currentIncrement.
computeExplicitRHS-like functions are commented with "HERE" to be replaced

include/core/matrixFreePDE.h

@@ -19,6 +19,7 @@
 #include <deal.II/grid/tria_iterator.h>
 #include <deal.II/lac/affine_constraints.h>
 #include <deal.II/lac/la_parallel_vector.h>
+#include <deal.II/lac/solver_control.h>
 #include <deal.II/lac/vector.h>
 #include <deal.II/matrix_free/fe_evaluation.h>
 #include <deal.II/matrix_free/matrix_free.h>
@@ -32,6 +33,7 @@
 #include <core/variableValueContainer.h>
 #include <grains/SimplifiedGrainRepresentation.h>
 #include <nucleation/nucleus.h>
+#include <sys/types.h>
 #include <utilities/computeStress.h>
 #include <utilities/utilities.h>
 
@@ -171,6 +173,10 @@ class MatrixFreePDE : public Subscriptor
 
   std::vector<SimplifiedGrainRepresentation<dim>> simplified_grain_representations;
 
+  // ===========================================================================
+  // METHODS FOR SOLVING
+  // ===========================================================================
+
   /**
    * Method to solve each time increment of a time-dependent problem. For
    * time-independent problems this method is called only once. This method
@@ -179,7 +185,51 @@ class MatrixFreePDE : public Subscriptor
    * problems, Implicit (matrix-free) solver for Elliptic problems.
    */
   virtual void
-  solveIncrement(bool skip_time_dependent);
+  solveIncrement(uint current_increment, bool skip_time_dependent);
+
+  void
+  linearSolveOnce(unsigned int var_index, SolverControl &solver_control);
+  void
+  auxiliaryOnce(unsigned int var_index, uint current_increment);
+  bool
+  nonlinearIncrement(unsigned int   var_index,
+                     SolverControl &solver_control,
+                     uint           current_increment);
+  bool
+  auxiliaryIncrement(unsigned int var_index, uint current_increment);
+  void
+  print_explicit_update(uint var_index, uint current_increment);
+  void
+  print_linear_update(uint           var_index,
+                      uint           current_increment,
+                      SolverControl &solver_control);
+  void
+  print_nonlinear_update(uint var_index, uint current_increment);
+  void
+  print_nonlinear_status(uint   var_index,
+                         uint   current_increment,
+                         uint   nonlinear_iteration_index,
+                         double diff);
+
+  /*Method to compute an explicit timestep*/
+  void
+  updateExplicitSolution(unsigned int var_index);
+
+  void
+  updateLinearSolution(unsigned int var_index);
+
+  /*Method to compute an implicit timestep*/
+  bool
+  updateImplicitSolution(unsigned int fieldIndex, unsigned int nonlinear_iteration_index);
+
+  /*Method to apply boundary conditions*/
+  void
+  applyBCs(unsigned int var_index);
+
+  // ===========================================================================
+  //
+  // ===========================================================================
+
   /* Method to write solution fields to vtu and pvtu (parallel) files.
    *
    * This method can be enabled/disabled by setting the flag writeOutput to
@@ -263,18 +313,6 @@ class MatrixFreePDE : public Subscriptor
   void
   computeInvM();
 
-  /*Method to compute an explicit timestep*/
-  void
-  updateExplicitSolution(unsigned int fieldIndex);
-
-  /*Method to compute an implicit timestep*/
-  bool
-  updateImplicitSolution(unsigned int fieldIndex, unsigned int nonlinear_iteration_index);
-
-  /*Method to apply boundary conditions*/
-  void
-  applyBCs(unsigned int fieldIndex);
-
   /**
    * \brief Compute element volume for the triangulation
    */