From: kronbichler Date: Mon, 8 Sep 2008 14:47:42 +0000 (+0000) Subject: Trilinos vector and sparse matrix classes now only store a pointer to a user-provided... X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=f43aea90fc4181abd810c80dc82a75d34d8c0eb8;p=dealii-svn.git Trilinos vector and sparse matrix classes now only store a pointer to a user-provided map, and do not copy the mapping (distribution of data among processors). git-svn-id: https://svn.dealii.org/trunk@16764 0785d39b-7218-0410-832d-ea1e28bc413d --- diff --git a/deal.II/lac/include/lac/trilinos_precondition_amg.h b/deal.II/lac/include/lac/trilinos_precondition_amg.h index 17f38b9b59..0b953b9011 100755 --- a/deal.II/lac/include/lac/trilinos_precondition_amg.h +++ b/deal.II/lac/include/lac/trilinos_precondition_amg.h @@ -54,10 +54,10 @@ namespace TrilinosWrappers * This class implements an algebraic multigrid (AMG) preconditioner * based on the Trilinos ML implementation. What this class does is * twofold. When the initialize() function is invoked, a ML - * preconditioner object is created based on the matrix - * that we want the preconditioner to be based on. A call of the - * respective vmult function does call the respective - * operation in the Trilinos package, where it is called + * preconditioner object is created based on the matrix that we want + * the preconditioner to be based on. A call of the respective + * vmult function does call the respective operation in + * the Trilinos package, where it is called * ApplyInverse. Use of this class is explained in the * @ref step_31 "step-31" tutorial program. * @@ -71,11 +71,12 @@ namespace TrilinosWrappers * fact that some of the entries in the preconditioner matrix are zero * and hence can be neglected. * - * The implementation is able to distinguish between matrices from - * elliptic problems and convection dominated problems. We use the standard - * options provided by Trilinos ML for elliptic problems, except that we use a - * Chebyshev smoother instead of a symmetric Gauss-Seidel smoother. - * For most elliptic problems, Chebyshev is better than Gauss-Seidel (SSOR). + * The implementation is able to distinguish between matrices from + * elliptic problems and convection dominated problems. We use the + * standard options provided by Trilinos ML for elliptic problems, + * except that we use a Chebyshev smoother instead of a symmetric + * Gauss-Seidel smoother. For most elliptic problems, Chebyshev is + * better than Gauss-Seidel (SSOR). * * @ingroup TrilinosWrappers * @ingroup Preconditioners @@ -99,9 +100,9 @@ namespace TrilinosWrappers * multilevel hierarchy for the * solution of a linear system * with the given matrix. The - * function uses the matrix - * format specified in - * TrilinosWrappers::SparseMatrix. + * function uses the matrix + * format specified in + * TrilinosWrappers::SparseMatrix. */ void initialize (const SparseMatrix &matrix, const bool elliptic = true, @@ -115,11 +116,12 @@ namespace TrilinosWrappers * multilevel hierarchy for the * solution of a linear system * with the given matrix. This - * function takes a deal.ii matrix - * and copies the content into a - * Trilinos matrix, so the function - * can be considered rather - * inefficient. + * function takes a deal.ii + * matrix and copies the + * content into a Trilinos + * matrix, so the function can + * be considered rather + * inefficient. */ void initialize (const ::dealii::SparseMatrix &deal_ii_sparse_matrix, const bool elliptic = true, @@ -129,26 +131,29 @@ namespace TrilinosWrappers const bool output_details = false); /** - * This function can be used - * for a faster recalculation of - * the preconditioner construction - * when the matrix entries - * underlying the preconditioner - * have changed, - * but the matrix sparsity pattern - * has remained the same. What this - * function does is to take the - * already generated coarsening - * structure, compute the AMG - * prolongation and restriction - * according to a smoothed aggregation - * strategy and then builds the whole - * multilevel hiearchy. This function - * can be considerably faster in that - * case, since the coarsening pattern - * is usually the most difficult thing - * to do when setting up the - * AMG ML preconditioner. + * This function can be used + * for a faster recalculation + * of the preconditioner + * construction when the matrix + * entries underlying the + * preconditioner have changed, + * but the matrix sparsity + * pattern has remained the + * same. What this function + * does is to take the already + * generated coarsening + * structure, compute the AMG + * prolongation and restriction + * according to a smoothed + * aggregation strategy and + * then builds the whole + * multilevel hiearchy. This + * function can be considerably + * faster in that case, since + * the coarsening pattern is + * usually the most difficult + * thing to do when setting up + * the AMG ML preconditioner. */ void reinit (); @@ -178,11 +183,23 @@ namespace TrilinosWrappers */ boost::shared_ptr multigrid_operator; + /** + * Internal communication + * pattern in case the matrix + * needs to be copied from + * deal.II format. + */ #ifdef DEAL_II_COMPILER_SUPPORTS_MPI Epetra_MpiComm communicator; #else Epetra_SerialComm communicator; #endif + + /** + * Internal Trilinos map in + * case the matrix needs to be + * copied from deal.II format. + */ boost::shared_ptr Map; /** diff --git a/deal.II/lac/include/lac/trilinos_sparse_matrix.h b/deal.II/lac/include/lac/trilinos_sparse_matrix.h index 5cda675d0e..2399203e18 100755 --- a/deal.II/lac/include/lac/trilinos_sparse_matrix.h +++ b/deal.II/lac/include/lac/trilinos_sparse_matrix.h @@ -51,14 +51,14 @@ namespace TrilinosWrappers namespace MatrixIterators { /** - * STL conforming iterator. This class acts as an iterator walking over the - * elements of Trilinos matrices. The implementation of this class is similar - * to the one for PETSc matrices. + * STL conforming iterator. This class acts as an iterator walking + * over the elements of Trilinos matrices. The implementation of this + * class is similar to the one for PETSc matrices. * - * Note that Trilinos does not give any guarantees as to the order of elements - * within each row. Note also that accessing the elements of a full matrix - * surprisingly only shows the nonzero elements of the matrix, not all - * elements. + * Note that Trilinos does not give any guarantees as to the order of + * elements within each row. Note also that accessing the elements of + * a full matrix surprisingly only shows the nonzero elements of the + * matrix, not all elements. * * @ingroup TrilinosWrappers * @author Martin Kronbichler, Wolfgang Bangerth, 2008 @@ -66,55 +66,53 @@ namespace TrilinosWrappers class const_iterator { private: - /** - * Accessor class for iterators - */ + /** + * Accessor class for iterators + */ class Accessor { public: - /** - * Constructor. Since we use - * accessors only for read - * access, a const matrix - * pointer is sufficient. - */ + /** + * Constructor. Since we use + * accessors only for read + * access, a const matrix + * pointer is sufficient. + */ Accessor (const SparseMatrix *matrix, const unsigned int row, const unsigned int index); - /** - * Row number of the element - * represented by this - * object. - */ + /** + * Row number of the element + * represented by this object. + */ unsigned int row() const; - /** - * Index in row of the element - * represented by this - * object. - */ + /** + * Index in row of the element + * represented by this object. + */ unsigned int index() const; - /** - * Column number of the - * element represented by - * this object. - */ + /** + * Column number of the element + * represented by this object. + */ unsigned int column() const; - /** - * Value of this matrix entry. - */ + /** + * Value of this matrix entry. + */ TrilinosScalar value() const; - /** - * Exception - */ + /** + * Exception + */ DeclException0 (ExcBeyondEndOfMatrix); - /** - * Exception - */ + + /** + * Exception + */ DeclException3 (ExcAccessToNonlocalRow, int, int, int, << "You tried to access row " << arg1 @@ -123,126 +121,128 @@ namespace TrilinosWrappers << " are stored locally and can be accessed."); private: - /** - * The matrix accessed. - */ + /** + * The matrix accessed. + */ mutable SparseMatrix *matrix; - /** - * Current row number. - */ + /** + * Current row number. + */ unsigned int a_row; - /** - * Current index in row. - */ + /** + * Current index in row. + */ unsigned int a_index; - /** - * Cache where we store the - * column indices of the present - * row. This is necessary, since - * Trilinos makes access to the - * elements of its matrices - * rather hard, and it is much - * more efficient to copy all - * column entries of a row once - * when we enter it than - * repeatedly asking Trilinos for - * individual ones. This also - * makes some sense since it is - * likely that we will access - * them sequentially anyway. - * - * In order to make copying of - * iterators/accessor of - * acceptable performance, we - * keep a shared pointer to these - * entries so that more than one - * accessor can access this data - * if necessary. - */ + /** + * Cache where we store the + * column indices of the + * present row. This is + * necessary, since Trilinos + * makes access to the elements + * of its matrices rather hard, + * and it is much more + * efficient to copy all column + * entries of a row once when + * we enter it than repeatedly + * asking Trilinos for + * individual ones. This also + * makes some sense since it is + * likely that we will access + * them sequentially anyway. + * + * In order to make copying of + * iterators/accessor of + * acceptable performance, we + * keep a shared pointer to + * these entries so that more + * than one accessor can access + * this data if necessary. + */ boost::shared_ptr > colnum_cache; - /** - * Similar cache for the values - * of this row. - */ + /** + * Similar cache for the values + * of this row. + */ boost::shared_ptr > value_cache; - /** - * Discard the old row caches - * (they may still be used by - * other accessors) and generate - * new ones for the row pointed - * to presently by this accessor. - */ + /** + * Discard the old row caches + * (they may still be used by + * other accessors) and + * generate new ones for the + * row pointed to presently by + * this accessor. + */ void visit_present_row (); - /** - * Make enclosing class a - * friend. - */ + /** + * Make enclosing class a + * friend. + */ friend class const_iterator; }; public: - /** - * Constructor. Create an iterator - * into the matrix @p matrix for the - * given row and the index within it. - */ + /** + * Constructor. Create an + * iterator into the matrix @p + * matrix for the given row and + * the index within it. + */ const_iterator (const SparseMatrix *matrix, const unsigned int row, const unsigned int index); - /** - * Prefix increment. - */ + /** + * Prefix increment. + */ const_iterator& operator++ (); - /** - * Postfix increment. - */ + /** + * Postfix increment. + */ const_iterator operator++ (int); - /** - * Dereferencing operator. - */ + /** + * Dereferencing operator. + */ const Accessor& operator* () const; - /** - * Dereferencing operator. - */ + /** + * Dereferencing operator. + */ const Accessor* operator-> () const; - /** - * Comparison. True, if - * both iterators point to - * the same matrix - * position. - */ + /** + * Comparison. True, if both + * iterators point to the same + * matrix position. + */ bool operator == (const const_iterator&) const; - /** - * Inverse of ==. - */ + + /** + * Inverse of ==. + */ bool operator != (const const_iterator&) const; - /** - * Comparison - * operator. Result is true - * if either the first row - * number is smaller or if - * the row numbers are - * equal and the first - * index is smaller. - */ + /** + * Comparison operator. Result + * is true if either the first + * row number is smaller or if + * the row numbers are equal + * and the first index is + * smaller. + */ bool operator < (const const_iterator&) const; - /** - * Exception - */ + /** + * Exception + */ DeclException2 (ExcInvalidIndexWithinRow, int, int, << "Attempt to access element " << arg2 @@ -250,10 +250,10 @@ namespace TrilinosWrappers << " which doesn't have that many elements."); private: - /** - * Store an object of the - * accessor class. - */ + /** + * Store an object of the + * accessor class. + */ Accessor accessor; }; @@ -261,33 +261,34 @@ namespace TrilinosWrappers /** - * This class implements a wrapper to use the Trilinos distributed sparse matrix - * class Epetra_FECrsMatrix. This is precisely the kind of matrix we deal with - * all the time - we most likely get it from some assembly process, where also - * entries not locally owned might need to be written and hence need to be - * forwarded to the owner process. - * This class is designed to be used in a distributed - * memory architecture with an MPI compiler on the bottom, but works equally - * well also for serial processes. The only requirement for this class to - * work is that Trilinos has been installed with the same compiler as is used - * for generating deal.II. + * This class implements a wrapper to use the Trilinos distributed + * sparse matrix class Epetra_FECrsMatrix. This is precisely the kind + * of matrix we deal with all the time - we most likely get it from + * some assembly process, where also entries not locally owned might + * need to be written and hence need to be forwarded to the owner + * process. This class is designed to be used in a distributed memory + * architecture with an MPI compiler on the bottom, but works equally + * well also for serial processes. The only requirement for this class + * to work is that Trilinos has been installed with the same compiler + * as is used for generating deal.II. * * The interface of this class is modeled after the existing * SparseMatrix class in deal.II. It has almost the same member - * functions, and is often exchangable. However, since Trilinos only supports a - * single scalar type (double), it is not templated, and only works with - * doubles. + * functions, and is often exchangable. However, since Trilinos only + * supports a single scalar type (double), it is not templated, and + * only works with doubles. * - * Note that Trilinos only guarantees that operations do what you expect if the - * functions @p GlobalAssemble has been called after matrix assembly. - * Therefore, you need to call - * SparseMatrix::compress() before you actually use the matrix. This also - * calls @p FillComplete that compresses the storage format for sparse - * matrices by discarding unused elements. Trilinos allows to continue with - * assembling the matrix after calls to these functions, but since there are - * no more free entries available after that any more, it is better to only - * call SparseMatrix::compress() once at the end of the assembly stage and - * before the matrix is actively used. + * Note that Trilinos only guarantees that operations do what you + * expect if the functions @p GlobalAssemble has been called after + * matrix assembly. Therefore, you need to call + * SparseMatrix::compress() before you actually use the matrix. This + * also calls @p FillComplete that compresses the storage format for + * sparse matrices by discarding unused elements. Trilinos allows to + * continue with assembling the matrix after calls to these functions, + * but since there are no more free entries available after that any + * more, it is better to only call SparseMatrix::compress() once at + * the end of the assembly stage and before the matrix is actively + * used. * * @ingroup TrilinosWrappers * @ingroup Matrix1 @@ -297,23 +298,25 @@ namespace TrilinosWrappers { public: /** - * A structure that describes some of - * the traits of this class in terms of - * its run-time behavior. Some other - * classes (such as the block matrix - * classes) that take one or other of - * the matrix classes as its template - * parameters can tune their behavior - * based on the variables in this - * class. + * A structure that describes + * some of the traits of this + * class in terms of its + * run-time behavior. Some + * other classes (such as the + * block matrix classes) that + * take one or other of the + * matrix classes as its + * template parameters can tune + * their behavior based on the + * variables in this class. */ struct Traits { - /** - * It is safe to elide additions of - * zeros to individual elements of - * this matrix. - */ + /** + * It is safe to elide additions of + * zeros to individual elements of + * this matrix. + */ static const bool zero_addition_can_be_elided = true; }; @@ -324,8 +327,9 @@ namespace TrilinosWrappers typedef MatrixIterators::const_iterator const_iterator; /** - * Declare a typedef in analogy to all - * the other container classes. + * Declare a typedef in analogy + * to all the other container + * classes. */ typedef TrilinosScalar value_type; @@ -335,134 +339,152 @@ namespace TrilinosWrappers SparseMatrix (); /** - * Constructor using an Epetra_Map - * and a maximum number of nonzero - * matrix entries. Note that this - * number does not need to be exact, - * and it is even allowed that - * the actual matrix structure - * has more nonzero entries than - * specified in the constructor. - * However it is still advantageous to - * provide good estimates here since - * this will considerably increase - * the performance of the matrix. + * Constructor using an + * Epetra_Map and a maximum + * number of nonzero matrix + * entries. Note that this + * number does not need to be + * exact, and it is even + * allowed that the actual + * matrix structure has more + * nonzero entries than + * specified in the + * constructor. However it is + * still advantageous to + * provide good estimates here + * since this will considerably + * increase the performance of + * the matrix. */ SparseMatrix (const Epetra_Map &InputMap, const unsigned int n_max_entries_per_row); /** - * Same as before, but now use the - * exact number of nonzeros in each - * matrix row. Since we know the - * number of elements in the matrix - * exactly in this case, we can - * already allocate the right amount - * of memory, which makes the - * creation process including the - * insertion of nonzero elements - * by the respective - * SparseMatrix::reinit call + * Same as before, but now use + * the exact number of nonzeros + * in each matrix row. Since we + * know the number of elements + * in the matrix exactly in + * this case, we can already + * allocate the right amount of + * memory, which makes the + * creation process including + * the insertion of nonzero + * elements by the respective + * SparseMatrix::reinit call * considerably faster. */ SparseMatrix (const Epetra_Map &InputMap, const std::vector &n_entries_per_row); /** - * This function is similar to the - * one above, but it now takes two - * different Epetra maps for rows - * and columns. This interface is - * meant to be used for generating - * rectangular matrices, where one - * map specifies the parallel - * distribution of rows and the other - * the one of the columns. This is - * in contrast to the first - * constructor, where the same map - * is used for both the number of - * rows and the number of columns. - * The number - * of columns per row is specified - * by the maximum number of entries. + * This function is similar to + * the one above, but it now + * takes two different Epetra + * maps for rows and + * columns. This interface is + * meant to be used for + * generating rectangular + * matrices, where one map + * specifies the parallel + * distribution of rows and the + * other the one of the + * columns. This is in contrast + * to the first constructor, + * where the same map is used + * for both the number of rows + * and the number of columns. + * The number of columns per + * row is specified by the + * maximum number of entries. */ SparseMatrix (const Epetra_Map &InputRowMap, const Epetra_Map &InputColMap, const unsigned int n_max_entries_per_row); /** - * This function is similar to the - * one above, but it now takes two - * different Epetra maps for rows - * and columns. This interface is - * meant to be used for generating - * rectangular matrices, where one - * map specifies the parallel - * distribution of rows and the other - * the one of the columns. The - * vector n_entries_per_row specifies - * the number of entries in each - * row of the newly generated matrix. + * This function is similar to + * the one above, but it now + * takes two different Epetra + * maps for rows and + * columns. This interface is + * meant to be used for + * generating rectangular + * matrices, where one map + * specifies the parallel + * distribution of rows and the + * other the one of the + * columns. The vector + * n_entries_per_row specifies + * the number of entries in + * each row of the newly + * generated matrix. */ SparseMatrix (const Epetra_Map &InputRowMap, const Epetra_Map &InputColMap, const std::vector &n_entries_per_row); /** - * Destructor. Made virtual so that one - * can use pointers to this class. + * Destructor. Made virtual so + * that one can use pointers to + * this class. */ virtual ~SparseMatrix (); /** - * Copy the given matrix to this - * one. + * Copy the given matrix to + * this one. * - * The function returns a reference to - * *this. + * The function returns a + * reference to *this. */ SparseMatrix & copy_from (const SparseMatrix &source); /** - * This function initializes the - * Trilinos matrix with a deal.II - * sparsity pattern, i.e. it - * makes the Trilinos Epetra - * matrix know the position of - * nonzero entries according to - * the sparsity pattern. Note that, - * when using this function, the - * matrix must already be initialized - * with a suitable Epetra_Map that - * describes the distribution of - * the matrix among the MPI + * This function initializes + * the Trilinos matrix with a + * deal.II sparsity pattern, + * i.e. it makes the Trilinos + * Epetra matrix know the + * position of nonzero entries + * according to the sparsity + * pattern. Note that, when + * using this function, the + * matrix must already be + * initialized with a suitable + * Epetra_Map that describes + * the distribution of the + * matrix among the MPI * processes. Otherwise, an * error will be thrown. */ void reinit (const SparsityPattern &sparsity_pattern); /** - * This function is initializes the - * Trilinos Epetra matrix according - * to the specified sparsity_pattern, - * and also reassigns the matrix - * rows to different processes + * This function is initializes + * the Trilinos Epetra matrix + * according to the specified + * sparsity_pattern, and also + * reassigns the matrix rows to + * different processes * according to a user-supplied - * Epetra map. This might be useful - * when the matrix structure changes, - * e.g. when the grid is refined. + * Epetra map. This might be + * useful when the matrix + * structure changes, e.g. when + * the grid is refined. */ void reinit (const Epetra_Map &input_map, const SparsityPattern &sparsity_pattern); /** - * This function is similar to the - * other initialization function above, - * but now also reassigns the matrix - * rows and columns according to - * two user-supplied Epetra maps. - * To be used for rectangular + * This function is similar to + * the other initialization + * function above, but now also + * reassigns the matrix rows + * and columns according to two + * user-supplied Epetra maps. + * To be used for rectangular * matrices. */ void reinit (const Epetra_Map &input_row_map, @@ -470,36 +492,38 @@ namespace TrilinosWrappers const SparsityPattern &sparsity_pattern); /** - * This function copies the - * content in sparse_matrix - * to the current matrix. + * This function copies the + * content in + * sparse_matrix to + * the current matrix. */ void reinit (const SparseMatrix &sparse_matrix); /** - * This function initializes the - * Trilinos matrix using the deal.II - * sparse matrix and the entries stored - * therein. It uses a threshold - * to copy only elements with - * modulus larger than the - * threshold (so zeros in the - * deal.II matrix can be filtered - * away). + * This function initializes + * the Trilinos matrix using + * the deal.II sparse matrix + * and the entries stored + * therein. It uses a threshold + * to copy only elements with + * modulus larger than the + * threshold (so zeros in the + * deal.II matrix can be + * filtered away). */ void reinit (const Epetra_Map &input_map, const ::dealii::SparseMatrix &dealii_sparse_matrix, const double drop_tolerance=1e-13); /** - * This function is similar to the - * other initialization function with - * deal.II sparse matrix input above, - * but now takes Epetra maps for both - * the rows and the columns of the - * matrix. - * To be used for rectangular - * matrices. + * This function is similar to + * the other initialization + * function with deal.II sparse + * matrix input above, but now + * takes Epetra maps for both + * the rows and the columns of + * the matrix. To be used for + * rectangular matrices. */ void reinit (const Epetra_Map &input_row_map, const Epetra_Map &input_col_map, @@ -507,41 +531,49 @@ namespace TrilinosWrappers const double drop_tolerance=1e-13); /** - * Release all memory and return - * to a state just like after - * having called the default - * constructor. + * Release all memory and + * return to a state just like + * after having called the + * default constructor. */ void clear (); /** - * Trilinos matrices store their own - * sparsity patterns. So, in analogy to - * our own SparsityPattern class, - * this function compresses the - * sparsity pattern and allows the - * resulting matrix to be used in all - * other operations where before only - * assembly functions were - * allowed. This function must - * therefore be called once you have + * Trilinos matrices store + * their own sparsity + * patterns. So, in analogy to + * our own SparsityPattern + * class, this function + * compresses the sparsity + * pattern and allows the + * resulting matrix to be used + * in all other operations + * where before only assembly + * functions were allowed. This + * function must therefore be + * called once you have * assembled the matrix. */ void compress (); /** - * This operator assigns a scalar to a - * matrix. Since this does usually not - * make much sense (should we set all - * matrix entries to this value? Only - * the nonzero entries of the sparsity - * pattern?), this operation is only - * allowed if the actual value to be - * assigned is zero. This operator only - * exists to allow for the obvious - * notation matrix=0, which - * sets all elements of the matrix to - * zero, but keeps the sparsity pattern + * This operator assigns a + * scalar to a matrix. Since + * this does usually not make + * much sense (should we set + * all matrix entries to this + * value? Only the nonzero + * entries of the sparsity + * pattern?), this operation is + * only allowed if the actual + * value to be assigned is + * zero. This operator only + * exists to allow for the + * obvious notation + * matrix=0, which + * sets all elements of the + * matrix to zero, but keeps + * the sparsity pattern * previously used. */ SparseMatrix & @@ -551,14 +583,14 @@ namespace TrilinosWrappers * Set the element (i,j) * to @p value. * - * This function - * adds a new entry to the - * matrix if it didn't exist - * before, very much in - * contrast to the SparseMatrix - * class which throws an error - * if the entry does not exist. - * If value is not a + * This function adds a new + * entry to the matrix if it + * didn't exist before, very + * much in contrast to the + * SparseMatrix class which + * throws an error if the entry + * does not exist. If + * value is not a * finite number an exception * is thrown. */ @@ -567,17 +599,17 @@ namespace TrilinosWrappers const TrilinosScalar value); /** - * Add @p value to the - * element (i,j). + * Add @p value to the element + * (i,j). * - * This function - * adds a new entry to the - * matrix if it didn't exist - * before, very much in - * contrast to the SparseMatrix - * class which throws an error - * if the entry does not exist. - * If value is not a + * This function adds a new + * entry to the matrix if it + * didn't exist before, very + * much in contrast to the + * SparseMatrix class which + * throws an error if the entry + * does not exist. If + * value is not a * finite number an exception * is thrown. */ @@ -597,79 +629,96 @@ namespace TrilinosWrappers * pattern, though (but retains * the allocated memory in case * new entries are again added - * later). Note that this - * is a global operation, so this - * needs to be done on all - * MPI processes. + * later). Note that this is a + * global operation, so this + * needs to be done on all MPI + * processes. * * This operation is used in - * eliminating constraints (e.g. due to - * hanging nodes) and makes sure that - * we can write this modification to - * the matrix without having to read - * entries (such as the locations of - * non-zero elements) from it -- - * without this o peration, removing - * constraints on parallel matrices is - * a rather complicated procedure. + * eliminating constraints + * (e.g. due to hanging nodes) + * and makes sure that we can + * write this modification to + * the matrix without having to + * read entries (such as the + * locations of non-zero + * elements) from it -- without + * this o peration, removing + * constraints on parallel + * matrices is a rather + * complicated procedure. * - * The second parameter can be used to - * set the diagonal entry of this row - * to a value different from zero. The - * default is to set it to zero. + * The second parameter can be + * used to set the diagonal + * entry of this row to a value + * different from zero. The + * default is to set it to + * zero. */ void clear_row (const unsigned int row, const TrilinosScalar new_diag_value = 0); /** - * Same as clear_row(), except that it - * works on a number of rows at once. + * Same as clear_row(), except + * that it works on a number of + * rows at once. * - * The second parameter can be used to - * set the diagonal entries of all - * cleared rows to something different - * from zero. Note that all of these - * diagonal entries get the same value - * -- if you want different values for - * the diagonal entries, you have to - * set them by hand. + * The second parameter can be + * used to set the diagonal + * entries of all cleared rows + * to something different from + * zero. Note that all of these + * diagonal entries get the + * same value -- if you want + * different values for the + * diagonal entries, you have + * to set them by hand. */ void clear_rows (const std::vector &rows, const TrilinosScalar new_diag_value = 0); /** - * Return the value of the entry - * (i,j). This may be an - * expensive operation and you should - * always take care where to call this - * function. In contrast to the - * respective function in the - * @p SparseMatrix class, we don't - * throw an exception if the respective - * entry doesn't exist in the sparsity - * pattern of this class, since Trilinos - * does not transmit this information. - * On the other hand, an exception - * will be thrown when the requested - * element is not saved on the calling - * process. + * Return the value of the + * entry (i,j). This + * may be an expensive + * operation and you should + * always take care where to + * call this function. In + * contrast to the respective + * function in the @p + * SparseMatrix class, we don't + * throw an exception if the + * respective entry doesn't + * exist in the sparsity + * pattern of this class, since + * Trilinos does not transmit + * this information. On the + * other hand, an exception + * will be thrown when the + * requested element is not + * saved on the calling + * process. * - * This function is therefore exactly - * equivalent to the el() function. + * This function is therefore + * exactly equivalent to the + * el() function. */ TrilinosScalar operator () (const unsigned int i, const unsigned int j) const; /** - * Return the value of the matrix entry - * (i,j). If this entry does not - * exist in the sparsity pattern, then - * zero is returned. While this may be - * convenient in some cases, note that - * it is simple to write algorithms - * that are slow compared to an optimal - * solution, since the sparsity of the - * matrix is not used. + * Return the value of the + * matrix entry + * (i,j). If this entry + * does not exist in the + * sparsity pattern, then zero + * is returned. While this may + * be convenient in some cases, + * note that it is simple to + * write algorithms that are + * slow compared to an optimal + * solution, since the sparsity + * of the matrix is not used. */ TrilinosScalar el (const unsigned int i, const unsigned int j) const; @@ -680,32 +729,30 @@ namespace TrilinosWrappers * row. This function throws an * error if the matrix is not * quadratic. - * - * TODO: Trilinos can access the - * diagonal faster. Implement this! */ TrilinosScalar diag_element (const unsigned int i) const; /** - * Return the number of rows in this - * matrix. + * Return the number of rows in + * this matrix. */ unsigned int m () const; /** - * Return the number of columns in this - * matrix. + * Return the number of columns + * in this matrix. */ unsigned int n () const; /** - * Return the local dimension of the - * matrix, i.e. the number of rows - * stored on the present MPI - * process. For sequential matrices, - * this number is the same as m(), - * but for parallel matrices it may be - * smaller. + * Return the local dimension + * of the matrix, i.e. the + * number of rows stored on the + * present MPI process. For + * sequential matrices, this + * number is the same as m(), + * but for parallel matrices it + * may be smaller. * * To figure out which elements * exactly are stored locally, @@ -718,15 +765,15 @@ namespace TrilinosWrappers * indicating which rows of * this matrix are stored * locally. The first number is - * the index of the first - * row stored, the second - * the index of the one past - * the last one that is stored - * locally. If this is a - * sequential matrix, then the - * result will be the pair - * (0,m()), otherwise it will be - * a pair (i,i+n), where + * the index of the first row + * stored, the second the index + * of the one past the last one + * that is stored locally. If + * this is a sequential matrix, + * then the result will be the + * pair (0,m()), otherwise it + * will be a pair (i,i+n), + * where * n=local_size(). */ std::pair @@ -741,24 +788,25 @@ namespace TrilinosWrappers /** * Return the number of nonzero - * elements of this - * matrix. + * elements of this matrix. */ unsigned int n_nonzero_elements () const; /** - * Number of entries in a specific row. + * Number of entries in a + * specific row. */ unsigned int row_length (const unsigned int row) const; /** - * Return the l1-norm of the matrix, that is - * $|M|_1=max_{all columns j}\sum_{all - * rows i} |M_ij|$, - * (max. sum of columns). - * This is the - * natural matrix norm that is compatible - * to the l1-norm for vectors, i.e. + * Return the l1-norm of the + * matrix, that is + * $|M|_1=max_{all columns + * j}\sum_{all rows i} |M_ij|$, + * (max. sum of columns). This + * is the natural matrix norm + * that is compatible to the + * l1-norm for vectors, i.e. * $|Mv|_1\leq |M|_1 |v|_1$. * (cf. Haemmerlin-Hoffmann: * Numerische Mathematik) @@ -766,76 +814,87 @@ namespace TrilinosWrappers TrilinosScalar l1_norm () const; /** - * Return the linfty-norm of the - * matrix, that is - * $|M|_infty=max_{all rows i}\sum_{all - * columns j} |M_ij|$, - * (max. sum of rows). - * This is the - * natural matrix norm that is compatible - * to the linfty-norm of vectors, i.e. - * $|Mv|_infty \leq |M|_infty |v|_infty$. + * Return the linfty-norm of + * the matrix, that is + * $|M|_infty=max_{all rows + * i}\sum_{all columns j} + * |M_ij|$, (max. sum of rows). + * This is the natural matrix + * norm that is compatible to + * the linfty-norm of vectors, + * i.e. $|Mv|_infty \leq + * |M|_infty |v|_infty$. * (cf. Haemmerlin-Hoffmann: * Numerische Mathematik) */ TrilinosScalar linfty_norm () const; /** - * Return the frobenius norm of the - * matrix, i.e. the square root of the - * sum of squares of all entries in the + * Return the frobenius norm of + * the matrix, i.e. the square + * root of the sum of squares + * of all entries in the * matrix. */ TrilinosScalar frobenius_norm () const; /** - * Multiply the entire matrix by a - * fixed factor. + * Multiply the entire matrix + * by a fixed factor. */ SparseMatrix & operator *= (const TrilinosScalar factor); /** - * Divide the entire matrix by a - * fixed factor. + * Divide the entire matrix by + * a fixed factor. */ SparseMatrix & operator /= (const TrilinosScalar factor); /** - * Matrix-vector multiplication: - * let dst = M*src with - * M being this matrix. + * Matrix-vector + * multiplication: let dst = + * M*src with M + * being this matrix. * * Source and destination must * not be the same vector. * - * Note that both vectors have to be - * distributed vectors generated using - * the same Map as was used for the - * matrix in case you work on a - * distributed memory architecture, - * using the interface of the - * TrilinosWrappers::Vector class. + * Note that both vectors have + * to be distributed vectors + * generated using the same Map + * as was used for the matrix + * in case you work on a + * distributed memory + * architecture, using the + * interface of the + * TrilinosWrappers::Vector + * class. */ void vmult (Vector &dst, const Vector &src) const; /** - * Matrix-vector multiplication: let - * dst = MT*src with - * M being this matrix. This - * function does the same as vmult() - * but takes the transposed matrix. + * Matrix-vector + * multiplication: let dst = + * MT*src with + * M being this + * matrix. This function does + * the same as vmult() but + * takes the transposed matrix. * * Source and destination must * not be the same vector. * - * Note that both vectors have to be - * distributed vectors generated using - * the same Map as was used for the - * matrix in case you work on a - * distributed memory architecture, - * using the interface of the - * TrilinosWrappers::Vector class. + * Note that both vectors have + * to be distributed vectors + * generated using the same Map + * as was used for the matrix + * in case you work on a + * distributed memory + * architecture, using the + * interface of the + * TrilinosWrappers::Vector + * class. */ void Tvmult (Vector &dst, const Vector &src) const; @@ -850,13 +909,16 @@ namespace TrilinosWrappers * Source and destination must * not be the same vector. * - * Note that both vectors have to be - * distributed vectors generated using - * the same Map as was used for the - * matrix in case you work on a - * distributed memory architecture, - * using the interface of the - * TrilinosWrappers::Vector class. + * Note that both vectors have + * to be distributed vectors + * generated using the same Map + * as was used for the matrix + * in case you work on a + * distributed memory + * architecture, using the + * interface of the + * TrilinosWrappers::Vector + * class. */ void vmult_add (Vector &dst, const Vector &src) const; @@ -865,59 +927,70 @@ namespace TrilinosWrappers * Adding Matrix-vector * multiplication. Add * MT*src to - * dst with M being - * this matrix. This function - * does the same as vmult_add() - * but takes the transposed - * matrix. + * dst with M + * being this matrix. This + * function does the same as + * vmult_add() but takes the + * transposed matrix. * * Source and destination must * not be the same vector. * - * Note that both vectors have to be - * distributed vectors generated using - * the same Map as was used for the - * matrix in case you work on a - * distributed memory architecture, - * using the interface of the - * TrilinosWrappers::Vector class. + * Note that both vectors have + * to be distributed vectors + * generated using the same Map + * as was used for the matrix + * in case you work on a + * distributed memory + * architecture, using the + * interface of the + * TrilinosWrappers::Vector + * class. */ void Tvmult_add (Vector &dst, const Vector &src) const; /** - * Return the square of the norm - * of the vector $v$ with respect - * to the norm induced by this - * matrix, + * Return the square of the + * norm of the vector $v$ with + * respect to the norm induced + * by this matrix, * i.e. $\left(v,Mv\right)$. This - * is useful, e.g. in the finite - * element context, where the - * $L_2$ norm of a function - * equals the matrix norm with - * respect to the mass matrix of - * the vector representing the - * nodal values of the finite - * element function. + * is useful, e.g. in the + * finite element context, + * where the $L_2$ norm of a + * function equals the matrix + * norm with respect to the + * mass matrix of the vector + * representing the nodal + * values of the finite element + * function. * - * Obviously, the matrix needs to - * be quadratic for this operation. + * Obviously, the matrix needs + * to be quadratic for this + * operation. * - * The implementation of this function - * is not as efficient as the one in - * the @p SparseMatrix class used in - * deal.II (i.e. the original one, not - * the Trilinos wrapper class) since Trilinos - * doesn't support this operation and - * needs a temporary vector. + * The implementation of this + * function is not as efficient + * as the one in the @p + * SparseMatrix class used in + * deal.II (i.e. the original + * one, not the Trilinos + * wrapper class) since + * Trilinos doesn't support + * this operation and needs a + * temporary vector. * - * Note that both vectors have to be - * distributed vectors generated using - * the same Map as was used for the - * matrix in case you work on a - * distributed memory architecture, - * using the interface of the - * TrilinosWrappers::Vector class. + * Note that both vectors have + * to be distributed vectors + * generated using the same Map + * as was used for the matrix + * in case you work on a + * distributed memory + * architecture, using the + * interface of the + * TrilinosWrappers::Vector + * class. */ TrilinosScalar matrix_norm_square (const Vector &v) const; @@ -925,21 +998,27 @@ namespace TrilinosWrappers * Compute the matrix scalar * product $\left(u,Mv\right)$. * - * The implementation of this function - * is not as efficient as the one in - * the @p SparseMatrix class used in - * deal.II (i.e. the original one, not - * the Trilinos wrapper class) since Trilinos - * doesn't support this operation and - * needs a temporary vector. + * The implementation of this + * function is not as efficient + * as the one in the @p + * SparseMatrix class used in + * deal.II (i.e. the original + * one, not the Trilinos + * wrapper class) since + * Trilinos doesn't support + * this operation and needs a + * temporary vector. * - * Note that both vectors have to be - * distributed vectors generated using - * the same Map as was used for the - * matrix in case you work on a - * distributed memory architecture, - * using the interface of the - * TrilinosWrappers::Vector class. + * Note that both vectors have + * to be distributed vectors + * generated using the same Map + * as was used for the matrix + * in case you work on a + * distributed memory + * architecture, using the + * interface of the + * TrilinosWrappers::Vector + * class. */ TrilinosScalar matrix_scalar_product (const Vector &u, const Vector &v) const; @@ -947,35 +1026,38 @@ namespace TrilinosWrappers /** * Compute the residual of an * equation Mx=b, where - * the residual is defined to be - * r=b-Mx. Write the - * residual into - * @p dst. The + * the residual is defined to + * be r=b-Mx. Write the + * residual into @p dst. The * l2 norm of * the residual vector is * returned. * - * Source x and destination - * dst must not be the same - * vector. + * Source x and + * destination dst must + * not be the same vector. * - * Note that both vectors have to be - * distributed vectors generated using - * the same Map as was used for the - * matrix in case you work on a - * distributed memory architecture, - * using the interface of the - * TrilinosWrappers::Vector class. + * Note that both vectors have + * to be distributed vectors + * generated using the same Map + * as was used for the matrix + * in case you work on a + * distributed memory + * architecture, using the + * interface of the + * TrilinosWrappers::Vector + * class. */ TrilinosScalar residual (Vector &dst, const Vector &x, const Vector &b) const; /** - * Add matrix scaled by - * factor to this matrix, - * i.e. the matrix factor*matrix - * is added to this. + * Add matrix scaled + * by factor to this + * matrix, i.e. the matrix + * factor*matrix is + * added to this. */ void add (const TrilinosScalar factor, const SparseMatrix &matrix); @@ -995,64 +1077,75 @@ namespace TrilinosWrappers * STL-like iterator with the * first entry of row @p r. * - * Note that if the given row is empty, - * i.e. does not contain any nonzero - * entries, then the iterator returned by - * this function equals - * end(r). Note also that the - * iterator may not be dereferencable in - * that case. + * Note that if the given row + * is empty, i.e. does not + * contain any nonzero entries, + * then the iterator returned + * by this function equals + * end(r). Note also + * that the iterator may not be + * dereferencable in that case. */ const_iterator begin (const unsigned int r) const; /** - * Final iterator of row r. It - * points to the first element past the - * end of line @p r, or past the end of - * the entire sparsity pattern. + * Final iterator of row + * r. It points to the + * first element past the end + * of line @p r, or past the + * end of the entire sparsity + * pattern. * - * Note that the end iterator is not - * necessarily dereferencable. This is in - * particular the case if it is the end - * iterator for the last row of a matrix. + * Note that the end iterator + * is not necessarily + * dereferencable. This is in + * particular the case if it is + * the end iterator for the + * last row of a matrix. */ const_iterator end (const unsigned int r) const; - /** - * Make an in-place transpose of a - * matrix. - */ + /** + * Make an in-place transpose + * of a matrix. + */ void transpose (); - /** - * Test whether a matrix is symmetric. - * Default tolerance is zero. - * TODO: Not implemented. - */ + /** + * Test whether a matrix is + * symmetric. Default + * tolerance is zero. TODO: + * Not implemented. + */ bool is_symmetric (const double tol = 0.0); - /** - * Test whether a matrix is Hermitian, - * i.e. it is the complex conjugate - * of its transpose. - * TODO: Not implemented. - */ + /** + * Test whether a matrix is + * Hermitian, i.e. it is the + * complex conjugate of its + * transpose. TODO: Not + * implemented. + */ bool is_hermitian (); - /** - * Abstract Trilinos object that helps view - * in ASCII other Trilinos objects. Currently - * this function is not implemented. - * TODO: Not implemented. - */ + /** + * Abstract Trilinos object + * that helps view in ASCII + * other Trilinos + * objects. Currently this + * function is not + * implemented. TODO: Not + * implemented. + */ void write_ascii (); /** - * Print the matrix to the given - * stream, using the format - * (line,col) value, - * i.e. one nonzero entry of the - * matrix per line. + * Print the matrix to the + * given stream, using the + * format (line,col) + * value, i.e. one nonzero + * entry of the matrix per + * line. */ void print (std::ostream &out) const; @@ -1098,55 +1191,71 @@ namespace TrilinosWrappers private: /** - * Epetra Trilinos mapping of the - * matrix rows that - * assigns parts of the matrix to - * the individual processes. - * TODO: is it possible to only use - * a pointer? - */ - Epetra_Map row_map; + * Dummy pointer that is used + * internally in the + * constructor for empty + * matrices. + */ + const Epetra_Map *dummy_map; /** - * Pointer to the user-supplied - * Epetra Trilinos mapping of the - * matrix columns that - * assigns parts of the matrix to - * the individual processes. + * Pointer to Epetra Trilinos + * mapping of the matrix rows + * that assigns parts of the + * matrix to the individual + * processes. This map is + * provided either via the + * constructor or in a reinit + * function. */ - Epetra_Map col_map; + Epetra_Map *row_map; /** - * Trilinos doesn't allow to mix additions - * to matrix entries and overwriting - * them (to make synchronisation of + * Pointer to the user-supplied + * Epetra Trilinos mapping of + * the matrix columns that + * assigns parts of the matrix + * to the individual processes. + */ + Epetra_Map *col_map; + + /** + * Trilinos doesn't allow to + * mix additions to matrix + * entries and overwriting them + * (to make synchronisation of * parallel computations - * simpler). The way we do it is to, - * for each access operation, store - * whether it is an insertion or an - * addition. If the previous one was of - * different type, then we first have - * to flush the Trilinos buffers; - * otherwise, we can simply go on. - * Luckily, Trilinos has an object - * for this which does already all - * the parallel communications in - * such a case, so we simply use their - * model, which stores whether the - * last operation was an addition - * or an insertion. + * simpler). The way we do it + * is to, for each access + * operation, store whether it + * is an insertion or an + * addition. If the previous + * one was of different type, + * then we first have to flush + * the Trilinos buffers; + * otherwise, we can simply go + * on. Luckily, Trilinos has + * an object for this which + * does already all the + * parallel communications in + * such a case, so we simply + * use their model, which + * stores whether the last + * operation was an addition or + * an insertion. */ Epetra_CombineMode last_action; public: /** * A sparse matrix object in - * Trilinos to be used for - * finite element based problems - * which allows for assembling into - * non-local elements. - * The actual type, a sparse - * matrix, is set in the constructor. + * Trilinos to be used for + * finite element based + * problems which allows for + * assembling into non-local + * elements. The actual type, + * a sparse matrix, is set in + * the constructor. */ std::auto_ptr matrix; @@ -1163,7 +1272,7 @@ namespace TrilinosWrappers inline const_iterator::Accessor:: - Accessor (const SparseMatrix *matrix, + Accessor (const SparseMatrix *matrix, const unsigned int row, const unsigned int index) : diff --git a/deal.II/lac/include/lac/trilinos_vector.h b/deal.II/lac/include/lac/trilinos_vector.h index 4e3fe40250..7871e248db 100755 --- a/deal.II/lac/include/lac/trilinos_vector.h +++ b/deal.II/lac/include/lac/trilinos_vector.h @@ -51,113 +51,124 @@ namespace TrilinosWrappers // forward declaration class Vector; - /** - * @cond internal - */ + /** + * @cond internal + */ /** - * A namespace for internal implementation details of the TrilinosWrapper - * members. - * @ingroup TrilinosWrappers + * A namespace for internal implementation details of the + * TrilinosWrapper members. @ingroup TrilinosWrappers */ namespace internal { - /** - * This class implements a wrapper for - * accessing the Trilinos vector - * in the same way as we access - * deal.II objects: - * it is initialized with a vector and an - * element within it, and has a - * conversion operator to extract the - * scalar value of this element. It also - * has a variety of assignment operator - * for writing to this one element. - * @ingroup TrilinosWrappers - */ + /** + * This class implements a + * wrapper for accessing the + * Trilinos vector in the same + * way as we access deal.II + * objects: it is initialized + * with a vector and an element + * within it, and has a + * conversion operator to + * extract the scalar value of + * this element. It also has a + * variety of assignment + * operator for writing to this + * one element. @ingroup + * TrilinosWrappers + */ class VectorReference { private: - /** - * Constructor. It is made private so - * as to only allow the actual vector - * class to create it. - */ + /** + * Constructor. It is made + * private so as to only allow + * the actual vector class to + * create it. + */ VectorReference (Vector &vector, const unsigned int index); public: - /** - * This looks like a copy operator, - * but does something different than - * usual. In particular, it does not - * copy the member variables of this - * reference. Rather, it handles the - * situation where we have two - * vectors @p v and @p w, and assign - * elements like in - * v(i)=w(i). Here, both - * left and right hand side of the - * assignment have data type - * VectorReference, but what we - * really mean is to assign the - * vector elements represented by the - * two references. This operator - * implements this operation. Note - * also that this allows us to make - * the assignment operator const. - */ + /** + * This looks like a copy + * operator, but does something + * different than usual. In + * particular, it does not copy + * the member variables of this + * reference. Rather, it + * handles the situation where + * we have two vectors @p v and + * @p w, and assign elements + * like in + * v(i)=w(i). Here, + * both left and right hand + * side of the assignment have + * data type VectorReference, + * but what we really mean is + * to assign the vector + * elements represented by the + * two references. This + * operator implements this + * operation. Note also that + * this allows us to make the + * assignment operator const. + */ const VectorReference & operator = (const VectorReference &r) const; - /** - * Set the referenced element of the - * vector to s. - */ + /** + * Set the referenced element of the + * vector to s. + */ const VectorReference & operator = (const TrilinosScalar &s) const; - /** - * Add s to the referenced - * element of the vector-> - */ + /** + * Add s to the + * referenced element of the + * vector-> + */ const VectorReference & operator += (const TrilinosScalar &s) const; - /** - * Subtract s from the - * referenced element of the vector-> - */ + /** + * Subtract s from the + * referenced element of the + * vector-> + */ const VectorReference & operator -= (const TrilinosScalar &s) const; - /** - * Multiply the referenced element of - * the vector by s. - */ + /** + * Multiply the referenced + * element of the vector by + * s. + */ const VectorReference & operator *= (const TrilinosScalar &s) const; - /** - * Divide the referenced element of - * the vector by s. - */ + /** + * Divide the referenced + * element of the vector by + * s. + */ const VectorReference & operator /= (const TrilinosScalar &s) const; - /** - * Convert the reference to an actual - * value, i.e. return the value of - * the referenced element of the - * vector. - */ + /** + * Convert the reference to an + * actual value, i.e. return + * the value of the referenced + * element of the vector. + */ operator TrilinosScalar () const; - /** - * Exception - */ + /** + * Exception + */ DeclException1 (ExcTrilinosError, int, << "An error with error number " << arg1 << " occured while calling a Trilinos function"); - /** - * Exception - */ + /** + * Exception + */ DeclException3 (ExcAccessToNonLocalElement, int, int, int, << "You tried to access element " << arg1 @@ -166,111 +177,116 @@ namespace TrilinosWrappers << " are stored locally and can be accessed."); private: - /** - * Point to the vector we are - * referencing. - */ + /** + * Point to the vector we are + * referencing. + */ Vector &vector; - /** - * Index of the referenced element - * of the vector. - */ + /** + * Index of the referenced element + * of the vector. + */ const unsigned int index; - /** - * Make the vector class a friend, so - * that it can create objects of the - * present type. - */ + /** + * Make the vector class a + * friend, so that it can + * create objects of the + * present type. + */ friend class ::dealii::TrilinosWrappers::Vector; }; } - /** - * @endcond - */ + /** + * @endcond + */ /** - * This class implements a wrapper to use the Trilinos distributed vector - * class Epetra_FEVector. This is precisely the kind of vector we deal with - * all the time - we probably get it from some assembly process, where also - * entries not locally owned might need to written and hence need to be - * forwarded to the owner. This class is designed to be used in a distributed - * memory architecture with an MPI compiler on the bottom, but works equally - * well also for serial processes. The only requirement for this class to - * work is that Trilinos is installed with the respective compiler as a - * basis. + * This class implements a wrapper to use the Trilinos distributed + * vector class Epetra_FEVector. This is precisely the kind of vector + * we deal with all the time - we probably get it from some assembly + * process, where also entries not locally owned might need to written + * and hence need to be forwarded to the owner. This class is designed + * to be used in a distributed memory architecture with an MPI + * compiler on the bottom, but works equally well also for serial + * processes. The only requirement for this class to work is that + * Trilinos is installed with the respective compiler as a basis. * * The interface of this class is modeled after the existing Vector - * class in deal.II. It has almost the same member functions, and is often - * exchangable. However, since Trilinos only supports a single scalar type - * (double), it is not templated, and only works with that type. + * class in deal.II. It has almost the same member functions, and is + * often exchangable. However, since Trilinos only supports a single + * scalar type (double), it is not templated, and only works with that + * type. * - * Note that Trilinos only guarantees that operations do what you expect if the - * function @p GlobalAssemble has been called after vector assembly in order to - * distribute the data. Therefore, you need to call Vector::compress() - * before you actually use the vectors. + * Note that Trilinos only guarantees that operations do what you + * expect if the function @p GlobalAssemble has been called after + * vector assembly in order to distribute the data. Therefore, you + * need to call Vector::compress() before you actually use the + * vectors. * *

Parallel communication model

* - * The parallel functionality of Trilinos is built on top of the Message Passing - * Interface (MPI). MPI's communication model is built on collective - * communications: if one process wants something from another, that other - * process has to be willing to accept this communication. A process cannot - * query data from another process by calling a remote function, without that - * other process expecting such a transaction. The consequence is that most of - * the operations in the base class of this class have to be called - * collectively. For example, if you want to compute the l2 norm of a parallel - * vector, @em all processes across which this vector is shared have to call - * the @p l2_norm function. If you don't do this, but instead only call the @p - * l2_norm function on one process, then the following happens: This one - * process will call one of the collective MPI functions and wait for all the - * other processes to join in on this. Since the other processes don't call - * this function, you will either get a time-out on the first process, or, - * worse, by the time the next a callto a Trilinos function generates an MPI - * message on the other processes , you will get a cryptic message that only a - * subset of processes attempted a communication. These bugs can be very hard - * to figure out, unless you are well-acquainted with the communication model - * of MPI, and know which functions may generate MPI messages. + * The parallel functionality of Trilinos is built on top of the + * Message Passing Interface (MPI). MPI's communication model is built + * on collective communications: if one process wants something from + * another, that other process has to be willing to accept this + * communication. A process cannot query data from another process by + * calling a remote function, without that other process expecting + * such a transaction. The consequence is that most of the operations + * in the base class of this class have to be called collectively. For + * example, if you want to compute the l2 norm of a parallel vector, + * @em all processes across which this vector is shared have to call + * the @p l2_norm function. If you don't do this, but instead only + * call the @p l2_norm function on one process, then the following + * happens: This one process will call one of the collective MPI + * functions and wait for all the other processes to join in on + * this. Since the other processes don't call this function, you will + * either get a time-out on the first process, or, worse, by the time + * the next a callto a Trilinos function generates an MPI message on + * the other processes , you will get a cryptic message that only a + * subset of processes attempted a communication. These bugs can be + * very hard to figure out, unless you are well-acquainted with the + * communication model of MPI, and know which functions may generate + * MPI messages. * - * One particular case, where an MPI message may be generated unexpectedly is - * discussed below. + * One particular case, where an MPI message may be generated + * unexpectedly is discussed below. * *

Accessing individual elements of a vector

* - * Trilinos does allow read access to individual elements of a vector, but in the - * distributed case only to elements that are stored locally. We implement - * this through calls like d=vec(i). However, if you access an - * element outside the locally stored range, an exception is generated. + * Trilinos does allow read access to individual elements of a vector, + * but in the distributed case only to elements that are stored + * locally. We implement this through calls like + * d=vec(i). However, if you access an element outside the + * locally stored range, an exception is generated. * - * In contrast to read access, Trilinos (and the respective deal.II wrapper - * classes) allow to write (or add) to individual elements of vectors, even if - * they are stored on a different process. You can do this writing, for - * example, vec(i)=d or vec(i)+=d, or similar - * operations. There is one catch, however, that may lead to very confusing - * error messages: Trilinos requires application programs to call the compress() - * function when they switch from adding, to elements to writing to - * elements. The reasoning is that all processes might accumulate addition - * operations to elements, even if multiple processes write to the same - * elements. By the time we call compress() the next time, all these additions - * are executed. However, if one process adds to an element, and another - * overwrites to it, the order of execution would yield non-deterministic - * behavior if we don't make sure that a synchronisation with compress() - * happens in between. + * In contrast to read access, Trilinos (and the respective deal.II + * wrapper classes) allow to write (or add) to individual elements of + * vectors, even if they are stored on a different process. You can do + * this writing, for example, vec(i)=d or vec(i)+=d, + * or similar operations. There is one catch, however, that may lead + * to very confusing error messages: Trilinos requires application + * programs to call the compress() function when they switch from + * adding, to elements to writing to elements. The reasoning is that + * all processes might accumulate addition operations to elements, + * even if multiple processes write to the same elements. By the time + * we call compress() the next time, all these additions are + * executed. However, if one process adds to an element, and another + * overwrites to it, the order of execution would yield + * non-deterministic behavior if we don't make sure that a + * synchronisation with compress() happens in between. * - * In order to make sure these calls to compress() happen at the appropriate - * time, the deal.II wrappers keep a state variable that store which is the - * presently allowed operation: additions or writes. If it encounters an - * operation of the opposite kind, it calls compress() and flips the - * state. This can sometimes lead to very confusing behavior, in code that may - * for example look like this: - * @verbatim - * TrilinosWrappers::Vector vector; - * ... - * // do some write operations on the vector - * for (unsigned int i=0; isize(); ++i) - * vector(i) = i; + * In order to make sure these calls to compress() happen at the + * appropriate time, the deal.II wrappers keep a state variable that + * store which is the presently allowed operation: additions or + * writes. If it encounters an operation of the opposite kind, it + * calls compress() and flips the state. This can sometimes lead to + * very confusing behavior, in code that may for example look like + * this: @verbatim TrilinosWrappers::Vector vector; ... // do some + * write operations on the vector for (unsigned int i=0; + * isize(); ++i) vector(i) = i; * * // do some additions to vector elements, but * // only for some elements @@ -282,23 +298,24 @@ namespace TrilinosWrappers * const double norm = vector->l2_norm(); * @endverbatim * - * This code can run into trouble: by the time we see the first addition - * operation, we need to flush the overwrite buffers for the vector, and the - * deal.II library will do so by calling compress(). However, it will only do - * so for all processes that actually do an addition -- if the condition is - * never true for one of the processes, then this one will not get to the - * actual compress() call, whereas all the other ones do. This gets us into - * trouble, since all the other processes hang in the call to flush the write - * buffers, while the one other process advances to the call to compute the l2 - * norm. At this time, you will get an error that some operation was attempted - * by only a subset of processes. This behavior may seem surprising, unless - * you know that write/addition operations on single elements may trigger this - * behavior. + * This code can run into trouble: by the time we see the first + * addition operation, we need to flush the overwrite buffers for the + * vector, and the deal.II library will do so by calling + * compress(). However, it will only do so for all processes that + * actually do an addition -- if the condition is never true for one + * of the processes, then this one will not get to the actual + * compress() call, whereas all the other ones do. This gets us into + * trouble, since all the other processes hang in the call to flush + * the write buffers, while the one other process advances to the call + * to compute the l2 norm. At this time, you will get an error that + * some operation was attempted by only a subset of processes. This + * behavior may seem surprising, unless you know that write/addition + * operations on single elements may trigger this behavior. * - * The problem described here may be avoided by placing additional calls to - * compress(), or making sure that all processes do the same type of - * operations at the same time, for example by placing zero additions if - * necessary. + * The problem described here may be avoided by placing additional + * calls to compress(), or making sure that all processes do the same + * type of operations at the same time, for example by placing zero + * additions if necessary. * * @ingroup TrilinosWrappers * @ingroup Vectors @@ -309,11 +326,13 @@ namespace TrilinosWrappers { public: /** - * Declare some of the standard types - * used in all containers. These types - * parallel those in the C - * standard libraries vector<...> - * class. + * Declare some of the standard + * types used in all + * containers. These types + * parallel those in the + * C standard + * libraries + * vector<...> class. */ typedef TrilinosScalar value_type; typedef TrilinosScalar real_type; @@ -322,47 +341,35 @@ namespace TrilinosWrappers typedef const internal::VectorReference const_reference; /** - * Default constructor. It doesn't do - * anything, derived classes will have - * to initialize the data. + * Default constructor. It + * doesn't do anything, derived + * classes will have to + * initialize the data. */ Vector (); - /** - * One of the constructors that - * actually builds a vector. This - * one requires prior knowledge - * of the size of the vector and - * a communicator from - * Epetra_CommSerial or Epetra_CommMpi, - * depending on whether we use a - * serial or parallel MPI-based program. - * This command distributes the - * vector linearly among the processes, - * from the beginning to the end, - * so you might want to use some - * more advanced mapping and the - * constructor with argument - * Epetra_Map. - */ - Vector (unsigned int GlobalSize, Epetra_Comm &Comm); /** * This constructor takes an - * Epetra_Map that already knows how - * to distribute the individual - * components among the MPI processors, - * including the size of the vector. + * Epetra_Map that already + * knows how to distribute the + * individual components among + * the MPI processors, + * including the size of the + * vector. */ Vector (const Epetra_Map &InputMap); /** - * Copy constructor. Sets the dimension - * to that of the given vector and uses - * the map of that vector, but - * does not copy any element. Instead, - * the memory will remain untouched - * in case fast is false and - * initialized with zero otherwise. + * Copy constructor. Sets the + * dimension to that of the + * given vector and uses the + * map of that vector, but does + * not copy any + * element. Instead, the memory + * will remain untouched in + * case fast is false + * and initialized with zero + * otherwise. */ Vector (const Vector &v, const bool fast = false); @@ -673,55 +680,61 @@ namespace TrilinosWrappers Vector & operator += (const Vector &V); /** - * Subtract the given vector from the - * present one. + * Subtract the given vector + * from the present one. */ Vector & operator -= (const Vector &V); /** * Addition of @p s to all - * components. Note that @p s is a - * scalar and not a vector. + * components. Note that @p s + * is a scalar and not a + * vector. */ void add (const TrilinosScalar s); /** - * Simple vector addition, equal to the - * operator +=. + * Simple vector addition, + * equal to the operator + * +=. */ void add (const Vector &V); /** - * Simple addition of a multiple of a - * vector, i.e. *this = a*V. + * Simple addition of a + * multiple of a vector, + * i.e. *this = a*V. */ void add (const TrilinosScalar a, const Vector &V); /** - * Multiple addition of scaled vectors, - * i.e. *this = a*V + b*W. + * Multiple addition of scaled + * vectors, i.e. *this = + * a*V + b*W. */ void add (const TrilinosScalar a, const Vector &V, const TrilinosScalar b, const Vector &W); /** - * Scaling and simple vector addition, - * i.e. - * *this = s*(*this) + V. + * Scaling and simple vector + * addition, i.e. *this = + * s*(*this) + V. */ void sadd (const TrilinosScalar s, const Vector &V); /** - * Scaling and simple addition, i.e. - * *this = s*(*this) + a*V. + * Scaling and simple addition, + * i.e. *this = s*(*this) + * + a*V. */ void sadd (const TrilinosScalar s, const TrilinosScalar a, const Vector &V); /** - * Scaling and multiple addition. + * Scaling and multiple + * addition. */ void sadd (const TrilinosScalar s, const TrilinosScalar a, @@ -730,8 +743,10 @@ namespace TrilinosWrappers const Vector &W); /** - * Scaling and multiple addition. - * *this = s*(*this) + a*V + b*W + c*X. + * Scaling and multiple + * addition. *this = + * s*(*this) + a*V + b*W + + * c*X. */ void sadd (const TrilinosScalar s, const TrilinosScalar a, @@ -744,64 +759,72 @@ namespace TrilinosWrappers /** * Scale each element of this * vector by the corresponding - * element in the argument. This - * function is mostly meant to - * simulate multiplication (and - * immediate re-assignment) by a - * diagonal scaling matrix. + * element in the + * argument. This function is + * mostly meant to simulate + * multiplication (and + * immediate re-assignment) by + * a diagonal scaling matrix. */ void scale (const Vector &scaling_factors); /** - * Assignment *this = a*V. + * Assignment *this = + * a*V. */ void equ (const TrilinosScalar a, const Vector &V); /** - * Assignment *this = a*V + b*W. + * Assignment *this = a*V + + * b*W. */ void equ (const TrilinosScalar a, const Vector &V, const TrilinosScalar b, const Vector &W); /** - * Compute the elementwise ratio of the - * two given vectors, that is let - * this[i] = a[i]/b[i]. This is - * useful for example if you want to - * compute the cellwise ratio of true to - * estimated error. + * Compute the elementwise + * ratio of the two given + * vectors, that is let + * this[i] = + * a[i]/b[i]. This is + * useful for example if you + * want to compute the cellwise + * ratio of true to estimated + * error. * * This vector is appropriately * scaled to hold the result. * - * If any of the b[i] is - * zero, the result is - * undefined. No attempt is made - * to catch such situations. + * If any of the b[i] + * is zero, the result is + * undefined. No attempt is + * made to catch such + * situations. */ void ratio (const Vector &a, const Vector &b); /** - * Output of vector in user-defined - * format in analogy to the + * Output of vector in + * user-defined format in + * analogy to the * dealii::Vector class. */ void print (const char* format = 0) const; /** - * Print to a - * stream. @p precision denotes - * the desired precision with - * which values shall be printed, - * @p scientific whether + * Print to a stream. @p + * precision denotes the + * desired precision with which + * values shall be printed, @p + * scientific whether * scientific notation shall be - * used. If @p across is - * @p true then the vector is + * used. If @p across is @p + * true then the vector is * printed in a line, while if * @p false then the elements - * are printed on a separate line - * each. + * are printed on a separate + * line each. */ void print (std::ostream &out, const unsigned int precision = 3, @@ -813,18 +836,18 @@ namespace TrilinosWrappers * vector and the other vector * @p v. One could do this * operation with a temporary - * variable and copying over the - * data elements, but this - * function is significantly more - * efficient since it only swaps - * the pointers to the data of - * the two vectors and therefore - * does not need to allocate - * temporary storage and move - * data around. Note that the - * vectors need to be of the same - * size and base on the same - * map. + * variable and copying over + * the data elements, but this + * function is significantly + * more efficient since it only + * swaps the pointers to the + * data of the two vectors and + * therefore does not need to + * allocate temporary storage + * and move data around. Note + * that the vectors need to be + * of the same size and base on + * the same map. * * This function is analog to the * the @p swap function of all C @@ -864,49 +887,65 @@ namespace TrilinosWrappers private: /** - * An Epetra map used to map vector data - * accross multiple processes. This is - * the communicator and data distribution - * object common to all - * Trilinos objects used by deal.II. + * A dummy pointer to an + * Epetra_Map to be used for + * the default constructor. + */ + Epetra_Map *dummy_map; + + /** + * A pointer to an Epetra map + * used to map vector data + * accross multiple + * processes. This is the + * communicator and data + * distribution object common + * to all Trilinos objects used + * by deal.II. */ - Epetra_Map map; + Epetra_Map *map; /** - * Trilinos doesn't allow to mix additions - * to matrix entries and overwriting - * them (to make synchronisation of + * Trilinos doesn't allow to + * mix additions to matrix + * entries and overwriting them + * (to make synchronisation of * parallel computations - * simpler). The way we do it is to, - * for each access operation, store - * whether it is an insertion or an - * addition. If the previous one was of - * different type, then we first have - * to flush the Trilinos buffers; - * otherwise, we can simply go on. - * Luckily, Trilinos has an object - * for this which does already all - * the parallel communications in - * such a case, so we simply use their - * model, which stores whether the - * last operation was an addition - * or an insertion. + * simpler). The way we do it + * is to, for each access + * operation, store whether it + * is an insertion or an + * addition. If the previous + * one was of different type, + * then we first have to flush + * the Trilinos buffers; + * otherwise, we can simply go + * on. Luckily, Trilinos has + * an object for this which + * does already all the + * parallel communications in + * such a case, so we simply + * use their model, which + * stores whether the last + * operation was an addition or + * an insertion. */ Epetra_CombineMode last_action; public: /** - * An Epetra distibuted vector type. - * Requires an existing Epetra_Map for - * storing data. - * TODO: Should become private at some - * point. + * An Epetra distibuted vector + * type. Requires an existing + * Epetra_Map for storing data. + * TODO: Should become private + * at some point. */ std::auto_ptr vector; /** - * Make the reference class a friend. + * Make the reference class a + * friend. */ friend class internal::VectorReference; @@ -917,9 +956,9 @@ namespace TrilinosWrappers // ------------------- inline and template functions -------------- /** - * Global function swap which overloads the default implementation - * of the C standard library which uses a temporary object. The - * function simply exchanges the data of the two vectors. + * Global function swap which overloads the default implementation of + * the C standard library which uses a temporary object. The function + * simply exchanges the data of the two vectors. * * @ingroup TrilinosWrappers * @relates TrilinosWrappers::Vector @@ -947,10 +986,10 @@ namespace TrilinosWrappers const VectorReference & VectorReference::operator = (const VectorReference &r) const { - // as explained in the class - // documentation, this is not the copy - // operator. so simply pass on to the - // "correct" assignment operator + // as explained in the class + // documentation, this is not the copy + // operator. so simply pass on to the + // "correct" assignment operator *this = static_cast (r); return *this; @@ -1029,10 +1068,10 @@ namespace TrilinosWrappers { // if the vectors have different sizes, // then first resize the present one - if (!map.SameAs(v.map)) + if (! map->SameAs(*v.map)) { map = v.map; - vector = std::auto_ptr + vector = std::auto_ptr (new Epetra_FEVector(*v.vector)); } else diff --git a/deal.II/lac/source/trilinos_precondition_amg.cc b/deal.II/lac/source/trilinos_precondition_amg.cc index d9c44149a1..c265a76b12 100755 --- a/deal.II/lac/source/trilinos_precondition_amg.cc +++ b/deal.II/lac/source/trilinos_precondition_amg.cc @@ -53,7 +53,7 @@ namespace TrilinosWrappers const unsigned int n_rows = matrix.m(); const unsigned int null_space_dimension = null_space.size(); - // Build the AMG preconditioner. + // Build the AMG preconditioner. Teuchos::ParameterList parameter_list; if (elliptic) @@ -87,9 +87,10 @@ namespace TrilinosWrappers ExcDimensionMismatch(n_rows, null_space[0].size())); - // Reshape null space as a contiguous - // vector of doubles so that Trilinos - // can read from it. + // Reshape null space as a + // contiguous vector of + // doubles so that Trilinos + // can read from it. null_space_modes.resize (n_rows * null_space_dimension, 0.); for (unsigned int d=0; dvmult function we - // note that invoking a call of - // the Trilinos preconditioner - // requires us to use Epetra vectors - // as well. It is faster - // to provide a view, i.e., feed - // Trilinos with a pointer to the - // data, so we avoid copying the - // content of the vectors during - // the iteration. In the declaration - // of the right hand side, we need - // to cast the source vector (that - // is const in all deal.II - // calls) to non-constant value, as - // this is the way Trilinos wants to - // have them. + // For the implementation of + // the vmult + // function we note that + // invoking a call of the + // Trilinos preconditioner + // requires us to use Epetra + // vectors as well. It is + // faster to provide a view, + // i.e., feed Trilinos with a + // pointer to the data, so we + // avoid copying the content + // of the vectors during the + // iteration. In the + // declaration of the right + // hand side, we need to cast + // the source vector (that is + // const in all + // deal.II calls) to + // non-constant value, as this + // is the way Trilinos wants + // to have them. void PreconditionAMG::vmult (dealii::Vector &dst, const dealii::Vector &src) const { diff --git a/deal.II/lac/source/trilinos_sparse_matrix.cc b/deal.II/lac/source/trilinos_sparse_matrix.cc index 9ed483cdfb..d224a27364 100755 --- a/deal.II/lac/source/trilinos_sparse_matrix.cc +++ b/deal.II/lac/source/trilinos_sparse_matrix.cc @@ -60,7 +60,7 @@ namespace TrilinosWrappers // would it point to?) Assert (ncols != 0, ExcInternalError()); colnum_cache.reset (new std::vector (colnums, - colnums+ncols)); + colnums+ncols)); value_cache.reset (new std::vector (values, values+ncols)); } } @@ -80,35 +80,46 @@ namespace TrilinosWrappers SparseMatrix::SparseMatrix () : #ifdef DEAL_II_COMPILER_SUPPORTS_MPI - row_map (0, 0, Epetra_MpiComm(MPI_COMM_WORLD)), + dummy_map (new Epetra_Map (0, 0, Epetra_MpiComm(MPI_COMM_WORLD))), #else - row_map (0, 0, Epetra_SerialComm()), + dummy_map (new Epetra_Map (0, 0, Epetra_SerialComm())), #endif + row_map (const_cast(dummy_map)), col_map (row_map), last_action (Insert), matrix (std::auto_ptr - (new Epetra_FECrsMatrix(Copy, row_map, 0))) + (new Epetra_FECrsMatrix(Copy, *row_map, 0))) {} SparseMatrix::SparseMatrix (const Epetra_Map &InputMap, const unsigned int n_max_entries_per_row) : - row_map (InputMap), +#ifdef DEAL_II_COMPILER_SUPPORTS_MPI + dummy_map (new Epetra_Map (0, 0, Epetra_MpiComm(MPI_COMM_WORLD))), +#else + dummy_map (new Epetra_Map (0, 0, Epetra_SerialComm())), +#endif + row_map (const_cast(&InputMap)), col_map (row_map), last_action (Insert), matrix (std::auto_ptr - (new Epetra_FECrsMatrix(Copy, row_map, + (new Epetra_FECrsMatrix(Copy, *row_map, int(n_max_entries_per_row), false))) {} - SparseMatrix::SparseMatrix (const Epetra_Map &InputMap, + SparseMatrix::SparseMatrix (const Epetra_Map &InputMap, const std::vector &n_entries_per_row) : - row_map (InputMap), +#ifdef DEAL_II_COMPILER_SUPPORTS_MPI + dummy_map (new Epetra_Map (0, 0, Epetra_MpiComm(MPI_COMM_WORLD))), +#else + dummy_map (new Epetra_Map (0, 0, Epetra_SerialComm())), +#endif + row_map (const_cast(&InputMap)), col_map (row_map), last_action (Insert), matrix (std::auto_ptr - (new Epetra_FECrsMatrix(Copy, row_map, + (new Epetra_FECrsMatrix(Copy, *row_map, (int*)const_cast(&(n_entries_per_row[0])), true))) {} @@ -117,23 +128,33 @@ namespace TrilinosWrappers const Epetra_Map &InputColMap, const unsigned int n_max_entries_per_row) : - row_map (InputRowMap), - col_map (InputColMap), +#ifdef DEAL_II_COMPILER_SUPPORTS_MPI + dummy_map (new Epetra_Map (0, 0, Epetra_MpiComm(MPI_COMM_WORLD))), +#else + dummy_map (new Epetra_Map (0, 0, Epetra_SerialComm())), +#endif + row_map (const_cast(&InputRowMap)), + col_map (const_cast(&InputColMap)), last_action (Insert), matrix (std::auto_ptr - (new Epetra_FECrsMatrix(Copy, row_map, col_map, + (new Epetra_FECrsMatrix(Copy, *row_map, *col_map, int(n_max_entries_per_row), false))) {} - SparseMatrix::SparseMatrix (const Epetra_Map &InputRowMap, - const Epetra_Map &InputColMap, + SparseMatrix::SparseMatrix (const Epetra_Map &InputRowMap, + const Epetra_Map &InputColMap, const std::vector &n_entries_per_row) : - row_map (InputRowMap), - col_map (InputColMap), +#ifdef DEAL_II_COMPILER_SUPPORTS_MPI + dummy_map (new Epetra_Map (0, 0, Epetra_MpiComm(MPI_COMM_WORLD))), +#else + dummy_map (new Epetra_Map (0, 0, Epetra_SerialComm())), +#endif + row_map (const_cast(&InputRowMap)), + col_map (const_cast(&InputColMap)), last_action (Insert), matrix (std::auto_ptr - (new Epetra_FECrsMatrix(Copy, row_map, col_map, + (new Epetra_FECrsMatrix(Copy, *row_map, *col_map, (int*)const_cast(&(n_entries_per_row[0])), true))) {} @@ -142,6 +163,7 @@ namespace TrilinosWrappers SparseMatrix::~SparseMatrix () { + delete dummy_map; } @@ -167,7 +189,7 @@ namespace TrilinosWrappers // sparsity pattern on that // processor, and only broadcast the // pattern afterwards. - if (row_map.Comm().MyPID() == 0) + if (row_map->Comm().MyPID() == 0) { Assert (matrix->NumGlobalRows() == (int)sparsity_pattern.n_rows(), ExcDimensionMismatch (matrix->NumGlobalRows(), @@ -228,11 +250,12 @@ namespace TrilinosWrappers // column map. Maybe find something // more out about this... //reinit (input_map, input_map, sparsity_pattern); - matrix.reset(); + + matrix.reset(); unsigned int n_rows = sparsity_pattern.n_rows(); - if (row_map.Comm().MyPID() == 0) + if (row_map->Comm().MyPID() == 0) { Assert (input_map.NumGlobalElements() == (int)sparsity_pattern.n_rows(), ExcDimensionMismatch (input_map.NumGlobalElements(), @@ -242,8 +265,8 @@ namespace TrilinosWrappers sparsity_pattern.n_cols())); } - row_map = input_map; - col_map = input_map; + row_map = const_cast(&input_map); + col_map = row_map; std::vector n_entries_per_row(n_rows); @@ -251,7 +274,7 @@ namespace TrilinosWrappers n_entries_per_row[(int)row] = sparsity_pattern.row_length(row); matrix = std::auto_ptr - (new Epetra_FECrsMatrix(Copy, row_map, &n_entries_per_row[0], + (new Epetra_FECrsMatrix(Copy, *row_map, &n_entries_per_row[0], false)); reinit (sparsity_pattern); @@ -268,7 +291,7 @@ namespace TrilinosWrappers unsigned int n_rows = sparsity_pattern.n_rows(); - if (row_map.Comm().MyPID() == 0) + if (input_row_map.Comm().MyPID() == 0) { Assert (input_row_map.NumGlobalElements() == (int)sparsity_pattern.n_rows(), ExcDimensionMismatch (input_row_map.NumGlobalElements(), @@ -278,8 +301,8 @@ namespace TrilinosWrappers sparsity_pattern.n_cols())); } - row_map = input_row_map; - col_map = input_col_map; + row_map = const_cast(&input_row_map); + col_map = const_cast(&input_col_map); std::vector n_entries_per_row(n_rows); @@ -287,7 +310,7 @@ namespace TrilinosWrappers n_entries_per_row[(int)row] = sparsity_pattern.row_length(row); matrix = std::auto_ptr - (new Epetra_FECrsMatrix(Copy, row_map, col_map, + (new Epetra_FECrsMatrix(Copy, *row_map, *col_map, &n_entries_per_row[0], false)); reinit (sparsity_pattern); @@ -334,8 +357,8 @@ namespace TrilinosWrappers ExcDimensionMismatch (input_col_map.NumGlobalElements(), dealii_sparse_matrix.n())); - row_map = input_row_map; - col_map = input_col_map; + row_map = const_cast(&input_row_map); + col_map = const_cast(&input_col_map); std::vector n_entries_per_row(n_rows); @@ -344,7 +367,7 @@ namespace TrilinosWrappers dealii_sparse_matrix.get_sparsity_pattern().row_length(row); matrix = std::auto_ptr - (new Epetra_FECrsMatrix(Copy, row_map, col_map, + (new Epetra_FECrsMatrix(Copy, *row_map, *col_map, &n_entries_per_row[0], true)); std::vector values; @@ -382,14 +405,12 @@ namespace TrilinosWrappers // the pointer and generate an // empty matrix. matrix.reset(); -#ifdef DEAL_II_COMPILER_SUPPORTS_MPI - row_map = Epetra_Map (0,0,Epetra_MpiComm(MPI_COMM_WORLD)), -#else - row_map = Epetra_Map (0,0,Epetra_SerialComm()), -#endif + + row_map = const_cast(dummy_map); + col_map = row_map; matrix = std::auto_ptr - (new Epetra_FECrsMatrix(Copy, row_map, 0)); + (new Epetra_FECrsMatrix(Copy, *row_map, 0)); } @@ -399,10 +420,10 @@ namespace TrilinosWrappers { // flush buffers int ierr; - if (row_map.SameAs(col_map)) + if (row_map->SameAs(*col_map)) ierr = matrix->GlobalAssemble (); else - ierr = matrix->GlobalAssemble (col_map, row_map); + ierr = matrix->GlobalAssemble (*col_map, *row_map); AssertThrow (ierr == 0, ExcTrilinosError(ierr)); @@ -440,10 +461,10 @@ namespace TrilinosWrappers if (last_action == Add) { int ierr; - if (row_map.SameAs(col_map)) + if (row_map->SameAs(*col_map)) ierr = matrix->GlobalAssemble (false); else - ierr = matrix->GlobalAssemble(col_map, row_map, false); + ierr = matrix->GlobalAssemble(*col_map, *row_map, false); AssertThrow (ierr == 0, ExcTrilinosError(ierr)); last_action = Insert; @@ -475,10 +496,10 @@ namespace TrilinosWrappers if (last_action == Insert) { int ierr; - if (row_map.SameAs(col_map)) + if (row_map->SameAs(*col_map)) ierr = matrix->GlobalAssemble (false); else - ierr = matrix->GlobalAssemble(col_map, row_map, false); + ierr = matrix->GlobalAssemble(*col_map, *row_map, false); AssertThrow (ierr == 0, ExcTrilinosError(ierr)); @@ -623,6 +644,10 @@ namespace TrilinosWrappers { Assert (m() == n(), ExcNotQuadratic()); + // Trilinos doesn't seem to have a + // more efficient way to access the + // diagonal than by just using the + // standard el(i,j) function. return el(i,i); } @@ -684,14 +709,14 @@ namespace TrilinosWrappers { Assert (row < m(), ExcInternalError()); - // get a representation of the present - // row + // get a representation of the + // present row int ncols = -1; int local_row = matrix->RowMap().LID(row); - // on the processor who owns this - // row, we'll have a non-negative - // value. + // on the processor who owns this + // row, we'll have a non-negative + // value. if (local_row >= 0) { int ierr = matrix->NumMyRowEntries (local_row, ncols); @@ -772,9 +797,9 @@ namespace TrilinosWrappers { Assert (&src != &dst, ExcSourceEqualsDestination()); - Assert (col_map.SameAs(src.vector->Map()), + Assert (col_map->SameAs(src.vector->Map()), ExcMessage ("Column map of matrix does not fit with vector map!")); - Assert (row_map.SameAs(dst.vector->Map()), + Assert (row_map->SameAs(dst.vector->Map()), ExcMessage ("Row map of matrix does not fit with vector map!")); if (!matrix->Filled()) @@ -792,9 +817,9 @@ namespace TrilinosWrappers { Assert (&src != &dst, ExcSourceEqualsDestination()); - Assert (row_map.SameAs(src.vector->Map()), + Assert (row_map->SameAs(src.vector->Map()), ExcMessage ("Row map of matrix does not fit with vector map!")); - Assert (col_map.SameAs(dst.vector->Map()), + Assert (col_map->SameAs(dst.vector->Map()), ExcMessage ("Column map of matrix does not fit with vector map!")); if (!matrix->Filled()) @@ -876,13 +901,15 @@ namespace TrilinosWrappers Assert (rhs.m() == m(), ExcDimensionMismatch (rhs.m(), m())); Assert (rhs.n() == n(), ExcDimensionMismatch (rhs.n(), n())); - // I bet that there must be a better way - // to do this but it has not been found: - // currently, we simply go through each - // row of the argument matrix, copy it, - // scale it, and add it to the current - // matrix. that's probably not the most - // efficient way to do things. + // I bet that there must be a + // better way to do this but it + // has not been found: currently, + // we simply go through each row + // of the argument matrix, copy + // it, scale it, and add it to + // the current matrix. that's + // probably not the most + // efficient way to do things. const std::pair local_range = rhs.local_range(); @@ -917,11 +944,12 @@ namespace TrilinosWrappers - // TODO: Currently this only flips - // a flag that tells Trilinos that - // any application should be done with - // the transpose. However, the matrix - // structure is not reset. + // TODO: Currently this only flips a + // flag that tells Trilinos that any + // application should be done with + // the transpose. However, the + // matrix structure is not + // reset. Can we leave it like this? void SparseMatrix::transpose () { @@ -973,7 +1001,7 @@ namespace TrilinosWrappers // As of now, no particularly neat - // ouput is generated in case of + // ouput is generated in case of // multiple processors. void SparseMatrix::print (std::ostream &out) const { diff --git a/deal.II/lac/source/trilinos_vector.cc b/deal.II/lac/source/trilinos_vector.cc index d57c9afd14..4d7ae7d37f 100755 --- a/deal.II/lac/source/trilinos_vector.cc +++ b/deal.II/lac/source/trilinos_vector.cc @@ -29,63 +29,74 @@ namespace TrilinosWrappers Assert (index < vector.size(), ExcIndexRange (index, 0, vector.size())); - // Trilinos allows for vectors to be - // referenced by the [] or () operators - // but only () checks index bounds - // Also, can only get local values + // Trilinos allows for vectors + // to be referenced by the [] + // or () operators but only () + // checks index bounds Also, + // can only get local values - AssertThrow ((static_cast(index) >= vector.map.MinMyGID()) && - (static_cast(index) <= vector.map.MaxMyGID()), - ExcAccessToNonLocalElement (index, vector.map.MinMyGID(), - vector.map.MaxMyGID()-1)); + AssertThrow ((static_cast(index) >= vector.map->MinMyGID()) && + (static_cast(index) <= vector.map->MaxMyGID()), + ExcAccessToNonLocalElement (index, vector.map->MinMyGID(), + vector.map->MaxMyGID()-1)); return (*(vector.vector))[0][index]; } } + + Vector::Vector () : #ifdef DEAL_II_COMPILER_SUPPORTS_MPI - map (0,0,Epetra_MpiComm(MPI_COMM_WORLD)), + dummy_map (new Epetra_Map (0,0,Epetra_MpiComm(MPI_COMM_WORLD))), #else - map (0,0,Epetra_SerialComm()), + dummy_map (new Epetra_Map (0,0,Epetra_SerialComm())), #endif + map (const_cast(dummy_map)), last_action (Insert), vector(std::auto_ptr - (new Epetra_FEVector(map))) + (new Epetra_FEVector(*map))) {} - Vector::Vector (unsigned int GlobalSize, Epetra_Comm &Comm) - : - map (GlobalSize, 0, Comm), - last_action (Insert), - vector (std::auto_ptr - (new Epetra_FEVector(map))) - {} Vector::Vector (const Epetra_Map &InputMap) : - map (InputMap), +#ifdef DEAL_II_COMPILER_SUPPORTS_MPI + dummy_map (new Epetra_Map (0,0,Epetra_MpiComm(MPI_COMM_WORLD))), +#else + dummy_map (new Epetra_Map (0,0,Epetra_SerialComm())), +#endif + map (const_cast(&InputMap)), last_action (Insert), vector (std::auto_ptr - (new Epetra_FEVector(map))) + (new Epetra_FEVector(*map))) {} + Vector::Vector (const Vector &v, const bool fast) : +#ifdef DEAL_II_COMPILER_SUPPORTS_MPI + dummy_map (new Epetra_Map (0,0,Epetra_MpiComm(MPI_COMM_WORLD))), +#else + dummy_map (new Epetra_Map (0,0,Epetra_SerialComm())), +#endif map (v.map), last_action (Insert), vector(std::auto_ptr - (new Epetra_FEVector(v.map,!fast))) + (new Epetra_FEVector(*map,!fast))) {} Vector::~Vector () - {} + { + vector.reset(); + delete dummy_map; + } @@ -93,9 +104,9 @@ namespace TrilinosWrappers Vector::reinit (const Epetra_Map &input_map) { vector.reset(); - map = input_map; + map = const_cast (&input_map); - vector = std::auto_ptr (new Epetra_FEVector(input_map)); + vector = std::auto_ptr (new Epetra_FEVector(*map)); last_action = Insert; } @@ -107,10 +118,9 @@ namespace TrilinosWrappers { vector.reset(); - if (!map.SameAs(v.map)) - map = v.map; + map = v.map; - vector = std::auto_ptr (new Epetra_FEVector(v.map,!fast)); + vector = std::auto_ptr (new Epetra_FEVector(*map,!fast)); last_action = Insert; } @@ -119,17 +129,13 @@ namespace TrilinosWrappers void Vector::clear () { - // When we clear the matrix, - // reset the pointer and - // generate an empty matrix. + // When we clear the vector, + // reset the pointer and generate + // an empty vector. vector.reset(); -#ifdef DEAL_II_COMPILER_SUPPORTS_MPI - map = Epetra_Map (0,0,Epetra_MpiComm(MPI_COMM_WORLD)), -#else - map = Epetra_Map (0,0,Epetra_SerialComm()), -#endif + map = dummy_map; - vector = std::auto_ptr (new Epetra_FEVector(map)); + vector = std::auto_ptr (new Epetra_FEVector(*map)); last_action = Insert; } @@ -218,9 +224,9 @@ namespace TrilinosWrappers TrilinosScalar Vector::el (const unsigned int index) const { - // Extract local indices in - // the vector. - int trilinos_i = map.LID(index); + // Extract local indices in + // the vector. + int trilinos_i = map->LID(index); TrilinosScalar value = 0.; if (trilinos_i == -1 ) { @@ -388,8 +394,9 @@ namespace TrilinosWrappers Vector::real_type Vector::lp_norm (const TrilinosScalar p) const { - // get a representation of the vector and - // loop over all the elements + // get a representation of the + // vector and loop over all + // the elements TrilinosScalar *start_ptr; int leading_dimension; int ierr = vector->ExtractView (&start_ptr, &leading_dimension); @@ -399,6 +406,7 @@ namespace TrilinosWrappers TrilinosScalar sum=0; const TrilinosScalar * ptr = start_ptr; + // add up elements while (ptr != start_ptr+size()) sum += std::pow(std::fabs(*ptr++), p); @@ -686,9 +694,9 @@ namespace TrilinosWrappers ExcMessage("The given value is not finite but " "either infinite or Not A Number (NaN)")); - // Update member can only input - // two other vectors so - // do it in two steps + // Update member can only + // input two other vectors so + // do it in two steps const int ierr = vector->Update(a, *(v.vector), b, *(w.vector), s); AssertThrow (ierr == 0, ExcTrilinosError(ierr)); @@ -766,9 +774,10 @@ namespace TrilinosWrappers - // TODO: up to now only local data - // printed out! Find a way to neatly - // output distributed data... + // TODO: up to now only local + // data printed out! Find a + // way to neatly output + // distributed data... void Vector::print (const char *format) const { @@ -796,11 +805,12 @@ namespace TrilinosWrappers { AssertThrow (out, ExcIO()); - // get a representation of the vector and - // loop over all the elements - // TODO: up to now only local data - // printed out! Find a way to neatly - // output distributed data... + // get a representation of the + // vector and loop over all + // the elements TODO: up to + // now only local data printed + // out! Find a way to neatly + // output distributed data... TrilinosScalar *val; int leading_dimension; int ierr = vector->ExtractView (&val, &leading_dimension); @@ -820,8 +830,8 @@ namespace TrilinosWrappers out << static_cast(val[i]) << std::endl; out << std::endl; - // restore the representation of the - // vector + // restore the representation + // of the vector AssertThrow (out, ExcIO()); } @@ -830,9 +840,9 @@ namespace TrilinosWrappers void Vector::swap (Vector &v) { - // Just swap the pointers to the - // two Epetra vectors that hold all - // the data. + // Just swap the pointers to + // the two Epetra vectors that + // hold all the data. Vector *p_v = &v, *p_this = this; Vector* tmp = p_v; p_v = p_this; @@ -840,6 +850,7 @@ namespace TrilinosWrappers } + unsigned int Vector::memory_consumption () const {