Address comments

geodynamics · Nov 22, 2017 · 3e76d7e · 3e76d7e
1 parent f93c011
commit 3e76d7e
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Showing 13 changed files with 59 additions and 67 deletions.
diff --git a/include/aspect/free_surface.h b/include/aspect/free_surface.h
@@ -41,8 +41,13 @@ namespace aspect
     class ApplyStabilization: public Assemblers::Interface<dim>,
       public SimulatorAccess<dim>
     {
-        void execute (internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
-                      internal::Assembly::CopyData::CopyDataBase<dim> &data) const;
+      public:
+        virtual ~ApplyStabilization () {};
+
+        virtual
+        void
+        execute (internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
+                 internal::Assembly::CopyData::CopyDataBase<dim> &data) const;
     };
   }
 

diff --git a/include/aspect/melt.h b/include/aspect/melt.h
@@ -146,8 +146,6 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~MeltInterface () {};
-
         /**
          * Attach melt outputs. Since most melt assemblers require the
          * melt material model properties they are created in this base class
@@ -166,8 +164,6 @@ namespace aspect
     class MeltStokesPreconditioner : public MeltInterface<dim>
     {
       public:
-        virtual ~MeltStokesPreconditioner () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
@@ -182,8 +178,6 @@ namespace aspect
     class MeltStokesSystem : public MeltInterface<dim>
     {
       public:
-        virtual ~MeltStokesSystem () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
@@ -200,8 +194,6 @@ namespace aspect
     class MeltStokesSystemBoundary : public MeltInterface<dim>
     {
       public:
-        virtual ~MeltStokesSystemBoundary () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
@@ -216,8 +208,6 @@ namespace aspect
     class MeltAdvectionSystem : public MeltInterface<dim>
     {
       public:
-        virtual ~MeltAdvectionSystem () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
@@ -241,8 +231,6 @@ namespace aspect
     class MeltPressureRHSCompatibilityModification : public MeltInterface<dim>
     {
       public:
-        virtual ~MeltPressureRHSCompatibilityModification () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
@@ -256,8 +244,6 @@ namespace aspect
     class MeltBoundaryTraction : public MeltInterface<dim>
     {
       public:
-        virtual ~MeltBoundaryTraction () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,

diff --git a/include/aspect/newton.h b/include/aspect/newton.h
@@ -140,7 +140,7 @@ namespace aspect
     class NewtonStokesPreconditioner : public NewtonInterface<dim>
     {
       public:
-        virtual ~NewtonStokesPreconditioner () {};
+        virtual ~NewtonStokesPreconditioner () {}
 
         void
         execute (internal::Assembly::Scratch::ScratchBase<dim>  &scratch,
@@ -155,7 +155,7 @@ namespace aspect
     class NewtonStokesIncompressibleTerms : public NewtonInterface<dim>
     {
       public:
-        virtual ~NewtonStokesIncompressibleTerms () {};
+        virtual ~NewtonStokesIncompressibleTerms () {}
 
         void
         execute (internal::Assembly::Scratch::ScratchBase<dim>  &scratch,
@@ -171,7 +171,7 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~NewtonStokesCompressibleStrainRateViscosityTerm () {};
+        virtual ~NewtonStokesCompressibleStrainRateViscosityTerm () {}
 
         virtual
         void
@@ -190,7 +190,7 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~NewtonStokesReferenceDensityCompressibilityTerm () {};
+        virtual ~NewtonStokesReferenceDensityCompressibilityTerm () {}
 
         virtual
         void
@@ -211,7 +211,7 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~NewtonStokesImplicitReferenceDensityCompressibilityTerm () {};
+        virtual ~NewtonStokesImplicitReferenceDensityCompressibilityTerm () {}
 
         virtual
         void
@@ -230,7 +230,7 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~NewtonStokesIsothermalCompressionTerm () {};
+        virtual ~NewtonStokesIsothermalCompressionTerm () {}
 
         virtual
         void

diff --git a/include/aspect/simulator/assemblers/advection.h b/include/aspect/simulator/assemblers/advection.h
@@ -38,8 +38,6 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~AdvectionSystem () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>  &scratch,
@@ -59,8 +57,6 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~AdvectionSystemBoundaryFace () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>  &scratch,
@@ -76,8 +72,6 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~AdvectionSystemInteriorFace () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>  &scratch,

diff --git a/include/aspect/simulator/assemblers/interface.h b/include/aspect/simulator/assemblers/interface.h
@@ -62,13 +62,13 @@ namespace aspect
             :
             cell(),
             face_number(numbers::invalid_unsigned_int)
-          {};
+          {}
 
           ScratchBase(const ScratchBase &scratch)
             :
             cell(scratch.cell),
             face_number(scratch.face_number)
-          {};
+          {}
 
           virtual ~ScratchBase () {};
 
@@ -333,8 +333,6 @@ namespace aspect
         template <int dim>
         struct CopyDataBase
         {
-          CopyDataBase() {};
-
           virtual ~CopyDataBase () {};
         };
 
@@ -486,7 +484,7 @@ namespace aspect
     class Interface
     {
       public:
-        virtual ~Interface () {}
+        virtual ~Interface ();
 
         /**
          * Execute this assembler object. This function performs the primary work
@@ -504,7 +502,7 @@ namespace aspect
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim> &scratch,
-                internal::Assembly::CopyData::CopyDataBase<dim> &data) const =0;
+                internal::Assembly::CopyData::CopyDataBase<dim> &data) const = 0;
 
         /**
          * This function gets called if a MaterialModelOutputs is created
@@ -539,7 +537,7 @@ namespace aspect
          * This ensures the additional material model output is available when
          * execute() is called.
          */
-        virtual void create_additional_material_model_outputs(MaterialModel::MaterialModelOutputs<dim> &) const {}
+        virtual void create_additional_material_model_outputs(MaterialModel::MaterialModelOutputs<dim> &) const;
 
         /**
          * A required function for objects that implement the assembly of terms
@@ -551,16 +549,12 @@ namespace aspect
          * equation). Thus different objects compute different residuals (i.e.
          * the residual for a melt advection equation looks different from the
          * residual for a passive compositional field).
+         * For assemblers for the Stokes system, an implementation of this
+         * function is not necessary.
          */
         virtual
         std::vector<double>
-        compute_residual(internal::Assembly::Scratch::ScratchBase<dim> &) const
-        {
-          AssertThrow(false, ExcMessage("This function should either be implemented "
-                                        "(if this is an assembler that has to compute a residual, or not be called "
-                                        "(if this is an assembler that has not to compute a residual)."));
-          return std::vector<double>();
-        }
+        compute_residual(internal::Assembly::Scratch::ScratchBase<dim> &) const;
     };
 
     /**

diff --git a/include/aspect/simulator/assemblers/stokes.h b/include/aspect/simulator/assemblers/stokes.h
@@ -37,8 +37,6 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~StokesPreconditioner () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
@@ -54,8 +52,6 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~StokesCompressiblePreconditioner () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
@@ -71,8 +67,6 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~StokesIncompressibleTerms () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
@@ -93,8 +87,6 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~StokesCompressibleStrainRateViscosityTerm () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
@@ -115,8 +107,6 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~StokesReferenceDensityCompressibilityTerm () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
@@ -137,8 +127,6 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~StokesImplicitReferenceDensityCompressibilityTerm () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
@@ -159,8 +147,6 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~StokesIsothermalCompressionTerm () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
@@ -176,8 +162,6 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~StokesBoundaryTraction () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,
@@ -196,8 +180,6 @@ namespace aspect
       public SimulatorAccess<dim>
     {
       public:
-        virtual ~StokesPressureRHSCompatibilityModification () {};
-
         virtual
         void
         execute(internal::Assembly::Scratch::ScratchBase<dim>   &scratch,

diff --git a/include/aspect/simulator_access.h b/include/aspect/simulator_access.h
@@ -640,8 +640,8 @@ namespace aspect
       get_newton_handler () const;
 
       /**
-       * Return a set of boundary indicators that describes which of the
-       * boundaries have a free surface boundary condition
+       * Return a reference to the free surface handler. This function will
+       * throw an exception if no free surface is activated.
        */
       const FreeSurfaceHandler<dim> &
       get_free_surface_handler () const;

diff --git a/source/simulator/assemblers/interface.cc b/source/simulator/assemblers/interface.cc
@@ -461,6 +461,33 @@ namespace aspect
 
   namespace Assemblers
   {
+    template <int dim>
+    Interface<dim>::~Interface()
+    {}
+
+
+
+    template <int dim>
+    void
+    Interface<dim>::create_additional_material_model_outputs(MaterialModel::MaterialModelOutputs<dim> &) const
+    {}
+
+
+
+    template <int dim>
+    std::vector<double>
+    Interface<dim>::compute_residual(internal::Assembly::Scratch::ScratchBase<dim> &) const
+    {
+      AssertThrow(false,
+                  ExcMessage("If this is an assembler that has to compute a residual"
+                             "then this function should be implemented. "
+                             "If this is an assembler that does not have to compute a residual, it should not be called."));
+
+      return std::vector<double>();
+    }
+
+
+
     template <int dim>
     Manager<dim>::Properties::Properties ()
       :
@@ -492,7 +519,8 @@ namespace aspect
     } \
   } \
   namespace Assemblers { \
-    template struct Manager<dim>::Properties; \
+    template class Interface<dim>; \
+    template class Manager<dim>; \
   }
   ASPECT_INSTANTIATE(INSTANTIATE)
 }
diff --git a/source/simulator/assemblers/newton_stokes.cc b/source/simulator/assemblers/newton_stokes.cc
@@ -584,6 +584,7 @@ namespace aspect
   namespace Assemblers
   {
 #define INSTANTIATE(dim) \
+  template class NewtonInterface<dim>; \
   template class NewtonStokesPreconditioner<dim>; \
   template class NewtonStokesIncompressibleTerms<dim>; \
   template class NewtonStokesCompressibleStrainRateViscosityTerm<dim>; \

diff --git a/source/simulator/assembly.cc b/source/simulator/assembly.cc
@@ -109,7 +109,7 @@ namespace aspect
     // lines in set_assemblers(), where this operation appears multiple times.
     template <int dim, class AssemblerType>
     void
-    initialize_simulator(Simulator<dim> &simulator,
+    initialize_simulator(const Simulator<dim> &simulator,
                          std::vector<std_cxx11::unique_ptr<AssemblerType> > &assemblers)
     {
       for (unsigned int i=0; i<assemblers.size(); ++i)

diff --git a/source/simulator/entropy_viscosity.cc b/source/simulator/entropy_viscosity.cc
@@ -132,9 +132,9 @@ namespace aspect
 
     for (unsigned int i=1; i<assemblers->advection_system.size(); ++i)
       {
-        std::vector<double> new_residual = assemblers->advection_system[i]->compute_residual(scratch);
-        for (unsigned int i=0; i<residual.size(); ++i)
-          residual[i] += new_residual[i];
+        const std::vector<double> new_residual = assemblers->advection_system[i]->compute_residual(scratch);
+        for (unsigned int j=0; j<residual.size(); ++j)
+          residual[j] += new_residual[j];
       }