Fix source

dealii · Apr 17, 2020 · 5502071 · 5502071
1 parent ba5ba4b
commit 5502071
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Showing 21 changed files with 80 additions and 28 deletions.
diff --git a/source/base/index_set.cc b/source/base/index_set.cc
@@ -159,6 +159,7 @@ IndexSet::do_compress() const
 
 
 
+#ifndef DOXYGEN
 IndexSet IndexSet::operator&(const IndexSet &is) const
 {
   Assert(size() == is.size(), ExcDimensionMismatch(size(), is.size()));
@@ -202,6 +203,7 @@ IndexSet IndexSet::operator&(const IndexSet &is) const
   result.compress();
   return result;
 }
+#endif
 
 
 

diff --git a/source/differentiation/ad/ad_drivers.cc b/source/differentiation/ad/ad_drivers.cc
@@ -256,6 +256,7 @@ namespace Differentiation
 
 #  ifdef DEAL_II_WITH_ADOLC
 
+#    ifndef DOXYGEN
     // Specialization for taped ADOL-C auto-differentiable numbers.
 
     template <typename ADNumberType>
@@ -273,6 +274,7 @@ namespace Differentiation
       , vbufsize(0u)
       , tbufsize(0u)
     {}
+#    endif
 
 
     template <typename ADNumberType>
@@ -1464,6 +1466,7 @@ namespace Differentiation
     }
 
 
+#  ifndef DOXYGEN
     template <typename ADNumberType>
     std::vector<double>
     TapedDrivers<
@@ -1477,6 +1480,7 @@ namespace Differentiation
       std::copy(in.begin(), in.end(), out.begin());
       return out;
     }
+#  endif
 
 
     // -------------   TapelessDrivers   -------------
@@ -1715,6 +1719,7 @@ namespace Differentiation
     // reverse mode to compute the first derivatives (and, if supported,
     // forward mode for the second).
 
+#  ifndef DOXYGEN
     template <typename ADNumberType, typename ScalarType>
     TapelessDrivers<
       ADNumberType,
@@ -1725,6 +1730,7 @@ namespace Differentiation
           NumberTypes::sacado_rad_dfad>::type>::TapelessDrivers()
       : dependent_variable_marking_safe(false)
     {}
+#  endif
 
 
     template <typename ADNumberType, typename ScalarType>
@@ -1983,6 +1989,7 @@ namespace Differentiation
     // forward mode to compute the first (and, if supported, second)
     // derivatives.
 
+#  ifndef DOXYGEN
     template <typename ADNumberType, typename ScalarType>
     TapelessDrivers<
       ADNumberType,
@@ -1995,6 +2002,7 @@ namespace Differentiation
           NumberTypes::sacado_dfad_dfad>::type>::TapelessDrivers()
       : dependent_variable_marking_safe(false)
     {}
+#  endif
 
 
     template <typename ADNumberType, typename ScalarType>

diff --git a/source/differentiation/sd/symengine_scalar_operations.cc b/source/differentiation/sd/symengine_scalar_operations.cc
@@ -74,6 +74,7 @@ namespace Differentiation
     /* ---------------- Symbol map creation and manipulation --------------*/
 
 
+#  ifndef DOXYGEN
     namespace internal
     {
       bool
@@ -161,6 +162,7 @@ namespace Differentiation
       for (const auto &entry : symbol_values)
         set_value_in_symbol_map(substitution_map, entry.first, entry.second);
     }
+#  endif
 
 
     /* ------------------ Symbol substitution map creation ----------------*/
@@ -175,6 +177,7 @@ namespace Differentiation
     }
 
 
+#  ifndef DOXYGEN
     /* ---------------- Symbolic substitution map enlargement --------------*/
 
 
@@ -260,6 +263,7 @@ namespace Differentiation
     {
       return expression.substitute(substitution_map);
     }
+#  endif // DOXYGEN
 
   } // namespace SD
 } // namespace Differentiation

diff --git a/source/differentiation/sd/symengine_tensor_operations.cc b/source/differentiation/sd/symengine_tensor_operations.cc
@@ -240,13 +240,15 @@ namespace Differentiation
     }
 
 
+#  ifndef DOXYGEN
     template <int dim>
     Tensor<1, dim, Expression>
     make_vector_of_symbolic_functions(const std::string &            sym,
                                       const types::substitution_map &arguments)
     {
       return internal::Symbol_Function_Tensor<1, dim>::create(sym, arguments);
     }
+#  endif
 
 
     template <int rank, int dim>
@@ -265,6 +267,7 @@ namespace Differentiation
     }
 
 
+#  ifndef DOXYGEN
     template <int rank, int dim>
     Tensor<rank, dim, Expression>
     make_tensor_of_symbolic_functions(const std::string &            sym,
@@ -284,6 +287,7 @@ namespace Differentiation
       return internal::Symbol_Function_SymmetricTensor<rank, dim>::create(
         sym, arguments);
     }
+#  endif // DOXYGEN
 
   } // namespace SD
 } // namespace Differentiation

diff --git a/source/differentiation/sd/symengine_utilities.cc b/source/differentiation/sd/symengine_utilities.cc
@@ -30,6 +30,7 @@ namespace Differentiation
 
     namespace Utilities
     {
+#  ifndef DOXYGEN
       SE::map_basic_basic
       convert_expression_map_to_basic_map(
         const SD::types::substitution_map &substitution_map)
@@ -39,6 +40,7 @@ namespace Differentiation
           sub_map[entry.first.get_RCP()] = entry.second.get_RCP();
         return sub_map;
       }
+#  endif
 
 
       SE::vec_basic
@@ -53,6 +55,7 @@ namespace Differentiation
       }
 
 
+#  ifndef DOXYGEN
       SD::types::symbol_vector
       extract_symbols(const SD::types::substitution_map &substitution_values)
       {
@@ -64,6 +67,7 @@ namespace Differentiation
 
         return symbols;
       }
+#  endif
 
     } // namespace Utilities
 

diff --git a/source/grid/tria_objects.cc b/source/grid/tria_objects.cc
@@ -454,10 +454,12 @@ namespace internal
 
 
     // explicit instantiations
+#ifndef DOXYGEN
     template class TriaObjects<TriaObject<1>>;
     template class TriaObjects<TriaObject<2>>;
 
-#include "tria_objects.inst"
+#  include "tria_objects.inst"
+#endif
   } // namespace TriangulationImplementation
 } // namespace internal
 

diff --git a/source/lac/block_sparsity_pattern.cc b/source/lac/block_sparsity_pattern.cc
@@ -273,6 +273,7 @@ BlockSparsityPatternBase<SparsityPatternBase>::print(std::ostream &out) const
 }
 
 
+#ifndef DOXYGEN
 template <>
 void
 BlockSparsityPatternBase<DynamicSparsityPattern>::print(std::ostream &out) const
@@ -299,6 +300,7 @@ BlockSparsityPatternBase<DynamicSparsityPattern>::print(std::ostream &out) const
       k += block(ib, 0).n_rows();
     }
 }
+#endif
 
 
 template <class SparsityPatternBase>

diff --git a/source/lac/petsc_matrix_base.cc b/source/lac/petsc_matrix_base.cc
@@ -29,6 +29,7 @@ namespace PETScWrappers
 {
   namespace MatrixIterators
   {
+#  ifndef DOXYGEN
     void
     MatrixBase::const_iterator::Accessor::visit_present_row()
     {
@@ -68,6 +69,7 @@ namespace PETScWrappers
       ierr = MatRestoreRow(*matrix, this->a_row, &ncols, &colnums, &values);
       AssertThrow(ierr == 0, ExcPETScError(ierr));
     }
+#  endif
   } // namespace MatrixIterators
 
 

diff --git a/source/lac/petsc_parallel_sparse_matrix.cc b/source/lac/petsc_parallel_sparse_matrix.cc
@@ -607,6 +607,7 @@ namespace PETScWrappers
         }
     }
 
+#  ifndef DOXYGEN
     // explicit instantiations
     //
     template SparseMatrix::SparseMatrix(const MPI_Comm &,
@@ -671,6 +672,7 @@ namespace PETScWrappers
     SparseMatrix::do_reinit(const IndexSet &,
                             const IndexSet &,
                             const DynamicSparsityPattern &);
+#  endif
 
 
     PetscScalar

diff --git a/source/lac/petsc_sparse_matrix.cc b/source/lac/petsc_sparse_matrix.cc
@@ -286,6 +286,7 @@ namespace PETScWrappers
     MatrixBase::Tmmult(C, B, V);
   }
 
+#  ifndef DOXYGEN
   // Explicit instantiations
   //
   template SparseMatrix::SparseMatrix(const SparsityPattern &, const bool);
@@ -301,6 +302,7 @@ namespace PETScWrappers
   SparseMatrix::do_reinit(const SparsityPattern &, const bool);
   template void
   SparseMatrix::do_reinit(const DynamicSparsityPattern &, const bool);
+#  endif
 } // namespace PETScWrappers
 
 

diff --git a/source/lac/petsc_vector_base.cc b/source/lac/petsc_vector_base.cc
@@ -32,6 +32,7 @@ namespace PETScWrappers
 {
   namespace internal
   {
+#  ifndef DOXYGEN
     VectorReference::operator PetscScalar() const
     {
       AssertIndexRange(index, vector.size());
@@ -109,6 +110,7 @@ namespace PETScWrappers
 
       return value;
     }
+#  endif
   } // namespace internal
 
   VectorBase::VectorBase()

diff --git a/source/lac/read_write_vector.cc b/source/lac/read_write_vector.cc
@@ -40,6 +40,7 @@ namespace LinearAlgebra
 
 #undef TEMPL_COPY_CONSTRUCTOR
 
+#ifndef DOXYGEN
   template void
   ReadWriteVector<float>::import(
     const distributed::Vector<float, ::dealii::MemorySpace::Host> &,
@@ -51,7 +52,7 @@ namespace LinearAlgebra
     const distributed::Vector<double, ::dealii::MemorySpace::Host> &,
     VectorOperation::values,
     const std::shared_ptr<const CommunicationPatternBase> &);
-#ifdef DEAL_II_WITH_COMPLEX_VALUES
+#  ifdef DEAL_II_WITH_COMPLEX_VALUES
   template void
   ReadWriteVector<std::complex<float>>::import(
     const distributed::Vector<std::complex<float>, ::dealii::MemorySpace::Host>
@@ -65,6 +66,7 @@ namespace LinearAlgebra
       &,
     VectorOperation::values,
     const std::shared_ptr<const CommunicationPatternBase> &);
+#  endif
 #endif
 } // namespace LinearAlgebra
 

diff --git a/source/lac/sparsity_pattern.cc b/source/lac/sparsity_pattern.cc
@@ -1043,6 +1043,7 @@ SparsityPattern::memory_consumption() const
 
 
 
+#ifndef DOXYGEN
 // explicit instantiations
 template void
 SparsityPattern::copy_from<float>(const FullMatrix<float> &);
@@ -1055,20 +1056,21 @@ SparsityPattern::add_entries<const SparsityPattern::size_type *>(
   const size_type *,
   const size_type *,
   const bool);
-#ifndef DEAL_II_VECTOR_ITERATOR_IS_POINTER
+#  ifndef DEAL_II_VECTOR_ITERATOR_IS_POINTER
 template void
 SparsityPattern::add_entries<
   std::vector<SparsityPattern::size_type>::const_iterator>(
   const size_type,
   std::vector<size_type>::const_iterator,
   std::vector<size_type>::const_iterator,
   const bool);
-#endif
+#  endif
 template void
 SparsityPattern::add_entries<std::vector<SparsityPattern::size_type>::iterator>(
   const size_type,
   std::vector<size_type>::iterator,
   std::vector<size_type>::iterator,
   const bool);
+#endif
 
 DEAL_II_NAMESPACE_CLOSE
diff --git a/source/lac/trilinos_block_sparse_matrix.cc b/source/lac/trilinos_block_sparse_matrix.cc
@@ -38,6 +38,7 @@ namespace TrilinosWrappers
 
 
 
+#  ifndef DOXYGEN
   void
   BlockSparseMatrix::reinit(const size_type n_block_rows,
                             const size_type n_block_columns)
@@ -63,6 +64,7 @@ namespace TrilinosWrappers
           this->sub_objects[r][c] = p;
         }
   }
+#  endif
 
 
 
@@ -366,6 +368,7 @@ namespace TrilinosWrappers
 
 
 
+#  ifndef DOXYGEN
   // -------------------- explicit instantiations -----------------------
   //
   template void
@@ -387,6 +390,7 @@ namespace TrilinosWrappers
                             const dealii::BlockDynamicSparsityPattern &,
                             const MPI_Comm &,
                             const bool);
+#  endif // DOXYGEN
 
 } // namespace TrilinosWrappers
 

diff --git a/source/lac/trilinos_precondition.cc b/source/lac/trilinos_precondition.cc
@@ -788,6 +788,7 @@ namespace TrilinosWrappers
     dst = src;
   }
 
+#  ifndef DOXYGEN
   void
   PreconditionIdentity::vmult(
     LinearAlgebra::distributed::Vector<double> &      dst,
@@ -803,6 +804,7 @@ namespace TrilinosWrappers
   {
     dst = src;
   }
+#  endif // DOXYGEN
 } // namespace TrilinosWrappers
 
 DEAL_II_NAMESPACE_CLOSE

diff --git a/source/lac/trilinos_precondition_ml.cc b/source/lac/trilinos_precondition_ml.cc
@@ -339,6 +339,7 @@ namespace TrilinosWrappers
 
 
 
+#  ifndef DOXYGEN
   // explicit instantiations
   template void
   PreconditionAMG::initialize(const ::dealii::SparseMatrix<double> &,
@@ -350,6 +351,7 @@ namespace TrilinosWrappers
                               const AdditionalData &,
                               const double,
                               const ::dealii::SparsityPattern *);
+#  endif