Merge pull request #192 from asartori86/split

Split pidomus.cc in several files + fixed doxygen

Author: asartori86

Doxyfile.in

@@ -109,6 +109,7 @@ class BaseInterface : public ParameterAcceptor, public SimulatorAccess<dim,space
    * must be called inside the constructor of the derived class.
    */
   void init ();
+  /** @} */
 
   /**
    * Override this function in your derived interface in order to
@@ -221,10 +222,10 @@ class BaseInterface : public ParameterAcceptor, public SimulatorAccess<dim,space
    * in the case the problem does not converge using @p prec_op .
    *
    * To clarify the difference between @p prec_op and @p prec_op_finer
-   * consider the case where you have a matrix @var A and you want to
+   * consider the case where you have a matrix A and you want to
    * provide an 'inverse' using AMG.  A possible strategy consist in
    * using the linear operator associated to AMG and a further
-   * strategy is to invert @var A using AMG.  In detail, @p prec_op
+   * strategy is to invert A using AMG.  In detail, @p prec_op
    * should be
    * \code{.cpp}
    *   auto A_inv = linear_operator(A, AMG)
@@ -234,12 +235,12 @@ class BaseInterface : public ParameterAcceptor, public SimulatorAccess<dim,space
    *   auto A_inv = inverse_operator(A, solver, AMG)
    * \endcode
    *
-   * In the @var .prm file it is possible to specify the maximum
+   * In the .prm file it is possible to specify the maximum
    * number of iterations allowed for the solver in the case we are
    * using @p prec_op or @p prec_op_finer.
    *
    * To enable the finer preconditioner it is sufficient to set
-   * "Enable finer preconditioner" equals to @var true.
+   * "Enable finer preconditioner" equals to true.
    */
   virtual void compute_system_operators(const std::vector<shared_ptr<typename LATrilinos::BlockMatrix> >,
                                         LinearOperator<LATrilinos::VectorType> &system_op,
@@ -402,6 +403,7 @@ class BaseInterface : public ParameterAcceptor, public SimulatorAccess<dim,space
    *   couplings[0] = "1,1;1,0"; // first block is the velocity, the second is the pressure
    *   couplings[1] = "1,0;0,1";
    * }
+   * @endcode
    */
   virtual void set_matrix_couplings(std::vector<std::string> &couplings) const;
 

include/base_interface.h

@@ -30,7 +30,7 @@
 
 // #include <deal.II/lac/precondition.h>
 
-#include "copy_data.h"
+
 #include "base_interface.h"
 #include "simulator_access.h"
 #include "pidomus_signals.h"
@@ -409,11 +409,6 @@ class piDoMUS : public ParameterAcceptor, public SundialsInterface<typename LAC:
    */
   double second_to_last_dt;
 
-
-  /**
-   * Show timer statistics
-   */
-  bool                     output_timer;
   /**
    * Teucos timer file
    */

include/pidomus.h

@@ -93,7 +93,7 @@ class SimulatorAccess
 
   /**
    * Return the current alpha in the expression
-   * $\dot{y}=\alpha y + \beta \bar{y}$
+   * \f$\dot{y}=\alpha y + \beta \bar{y}\f$
    */
   double get_alpha () const;
 
@@ -190,6 +190,7 @@ class SimulatorAccess
   /** @} */
 
 private:
+
   /**
    * A pointer to the simulator object to which we want to get
    * access.