From: heltai Date: Mon, 20 Jan 2014 11:28:59 +0000 (+0000) Subject: Merged from trunk r32214 through r32261. X-Git-Url: https://gitweb.dealii.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=cfad29b3a7c45d32fd8573322f4b3f16dde77e11;p=dealii-svn.git Merged from trunk r32214 through r32261. git-svn-id: https://svn.dealii.org/branches/branch_manifold_id@32262 0785d39b-7218-0410-832d-ea1e28bc413d --- diff --git a/deal.II/cmake/macros/macro_deal_ii_invoke_autopilot.cmake b/deal.II/cmake/macros/macro_deal_ii_invoke_autopilot.cmake index bad218f916..323a2b229d 100644 --- a/deal.II/cmake/macros/macro_deal_ii_invoke_autopilot.cmake +++ b/deal.II/cmake/macros/macro_deal_ii_invoke_autopilot.cmake @@ -41,7 +41,7 @@ MACRO(DEAL_II_INVOKE_AUTOPILOT) # Generator specific values: IF(CMAKE_GENERATOR MATCHES "Ninja") # - # Ninja doesn't like a redifinition of the "help" target, so use "info" + # Ninja doesn't like a redefinition of the "help" target, so use "info" # in this case... # SET(_make_command "$ ninja") diff --git a/deal.II/doc/news/changes.h b/deal.II/doc/news/changes.h index 4c21c7596b..c58ef940bd 100644 --- a/deal.II/doc/news/changes.h +++ b/deal.II/doc/news/changes.h @@ -84,6 +84,42 @@ inconvenience this causes.

Specific improvements

    +
  1. Fixed: The method DoFTools::extract_constant_modes only worked for + elements where the constant function 1 is represented by all ones. This + is now fixed by querying the element for its constant modes on each cell. +
    + (Martin Kronbichler, 2014/01/19) +
    2. + +
  2. Fixed: PETScWrappers::MPI::Vector::all_zero() was broken with more than + one processor (illegal memory access) and did not communicate between all + processors. Documentation for many vector types of all_zero() has been extended. +
    + (Timo Heister, 2014/01/17) +
    3. + +
  3. Fixed/new: DoFCellAccessor::set_dof_values_by_interpolation and + DoFCellAccessor::get_interpolated_dof_values could previously be + called for hp::DoFHandler objects on cells that are non-active. This + makes no sense since these cells have no associated finite element + space. Doing so now raises an exception. +
    + However, there are legitimate cases where one may want to interpolate + from children to a parent's finite element space. Since in the hp + case no finite element space is naturally associated with an inactive + cell, it is now possible to pass an explicit finite element index + argument to the function specifying which element of an hp::FECollection + object describes the space onto which you want to interpolate. +
    + (Wolfgang Bangerth, 2014/01/18) +
    4. + +
  4. Fixed: The methods IndexSet::do_compress() and + IndexSet::add_indices(IndexSet&) had quadratic complexity in the number of + ranges. The algorithms have been changed into linear complexity ones. +
    + (Martin Kronbichler, 2014/01/15) +
  5. Fixed: There were several bugs in functions like FEValues::get_function_values() where the code did not properly handle the diff --git a/deal.II/examples/step-16/step-16.cc b/deal.II/examples/step-16/step-16.cc index e03e244297..67b1a5b413 100644 --- a/deal.II/examples/step-16/step-16.cc +++ b/deal.II/examples/step-16/step-16.cc @@ -526,7 +526,7 @@ namespace Step16 // with a gotcha that is easily forgotten: The indices of global // degrees of freedom we want here are the ones for current level, not // for the global matrix. We therefore need the function - // MGDoFAccessorLLget_mg_dof_indices, not + // MGDoFAccessor::get_mg_dof_indices, not // MGDoFAccessor::get_dof_indices as used in the assembly of the // global system: cell->get_mg_dof_indices (local_dof_indices); diff --git a/deal.II/examples/step-32/step-32.cc b/deal.II/examples/step-32/step-32.cc index cd2207025f..882332e1ea 100644 --- a/deal.II/examples/step-32/step-32.cc +++ b/deal.II/examples/step-32/step-32.cc @@ -1,7 +1,7 @@ /* --------------------------------------------------------------------- * $Id$ * - * Copyright (C) 2008 - 2013 by the deal.II authors + * Copyright (C) 2008 - 2014 by the deal.II authors * * This file is part of the deal.II library. * @@ -939,9 +939,12 @@ namespace Step32 // that have been broken out of the ones listed above. Specifically, there // are first three functions that we call from setup_dofs and // then the ones that do the assembling of linear systems: - void setup_stokes_matrix (const std::vector &stokes_partitioning); - void setup_stokes_preconditioner (const std::vector &stokes_partitioning); - void setup_temperature_matrices (const IndexSet &temperature_partitioning); + void setup_stokes_matrix (const std::vector &stokes_partitioning, + const std::vector &stokes_relevant_partitioning); + void setup_stokes_preconditioner (const std::vector &stokes_partitioning, + const std::vector &stokes_relevant_partitioning); + void setup_temperature_matrices (const IndexSet &temperature_partitioning, + const IndexSet &temperature_relevant_partitioning); // Following the @ref MTWorkStream "task-based parallelization" paradigm, @@ -1817,6 +1820,30 @@ namespace Step32 // the globally assembled sparsity pattern available with which the global // matrix can be initialized. // + // There is one important aspect when initializing Trilinos sparsity + // patterns in parallel: In addition to specifying the locally owned rows + // and columns of the matrices via the @p stokes_partitioning index set, we + // also supply information about all the rows we are possibly going to write + // into when assembling on a certain processor. The set of locally relevant + // rows contains all such rows (possibly also a few unnecessary ones, but it + // is difficult to find the exact row indices before actually getting + // indices on all cells and resolving constraints). This additional + // information allows to exactly determine the structure for the + // off-processor data found during assembly. While Trilinos matrices are + // able to collect this information on the fly as well (when initializing + // them from some other reinit method), it is less efficient and leads to + // problems when assembling matrices with multiple threads. In this program, + // we pessimistically assume that only one processor at a time can write + // into the matrix while assembly (whereas the computation is parallel), + // which is fine for Trilinos matrices. In practice, one can do better by + // hinting WorkStream at cells that do not share vertices, allowing for + // parallelism among those cells (see the graph coloring algorithms and + // WorkStream with colored iterators argument). However, that only works + // when only one MPI processor is present because Trilinos' internal data + // structures for accumulating off-processor data on the fly are not thread + // safe. With the initialization presented here, there is no such problem + // and one could safely introduce graph coloring for this algorithm. + // // The only other change we need to make is to tell the // DoFTools::make_sparsity_pattern() function that it is only supposed to // work on a subset of cells, namely the ones whose @@ -1830,15 +1857,16 @@ namespace Step32 // once the matrix has been given the sparsity structure. template void BoussinesqFlowProblem:: - setup_stokes_matrix (const std::vector &stokes_partitioning) + setup_stokes_matrix (const std::vector &stokes_partitioning, + const std::vector &stokes_relevant_partitioning) { stokes_matrix.clear (); - TrilinosWrappers::BlockSparsityPattern sp (stokes_partitioning, - MPI_COMM_WORLD); + TrilinosWrappers::BlockSparsityPattern sp(stokes_partitioning, stokes_partitioning, + stokes_relevant_partitioning, + MPI_COMM_WORLD); Table<2,DoFTools::Coupling> coupling (dim+1, dim+1); - for (unsigned int c=0; c void BoussinesqFlowProblem:: - setup_stokes_preconditioner (const std::vector &stokes_partitioning) + setup_stokes_preconditioner (const std::vector &stokes_partitioning, + const std::vector &stokes_relevant_partitioning) { Amg_preconditioner.reset (); Mp_preconditioner.reset (); stokes_preconditioner_matrix.clear (); - TrilinosWrappers::BlockSparsityPattern sp (stokes_partitioning, - MPI_COMM_WORLD); + TrilinosWrappers::BlockSparsityPattern sp(stokes_partitioning, stokes_partitioning, + stokes_relevant_partitioning, + MPI_COMM_WORLD); Table<2,DoFTools::Coupling> coupling (dim+1, dim+1); for (unsigned int c=0; c void BoussinesqFlowProblem:: - setup_temperature_matrices (const IndexSet &temperature_partitioner) + setup_temperature_matrices (const IndexSet &temperature_partitioner, + const IndexSet &temperature_relevant_partitioner) { T_preconditioner.reset (); temperature_mass_matrix.clear (); temperature_stiffness_matrix.clear (); temperature_matrix.clear (); - TrilinosWrappers::SparsityPattern sp (temperature_partitioner, - MPI_COMM_WORLD); + TrilinosWrappers::SparsityPattern sp(temperature_partitioner, + temperature_partitioner, + temperature_relevant_partitioner, + MPI_COMM_WORLD); DoFTools::make_sparsity_pattern (temperature_dof_handler, sp, temperature_constraints, false, Utilities::MPI:: @@ -2057,16 +2090,31 @@ namespace Step32 // All this done, we can then initialize the various matrix and vector // objects to their proper sizes. At the end, we also record that all // matrices and preconditioners have to be re-computed at the beginning of - // the next time step. - setup_stokes_matrix (stokes_partitioning); - setup_stokes_preconditioner (stokes_partitioning); - setup_temperature_matrices (temperature_partitioning); - - stokes_rhs.reinit (stokes_partitioning, MPI_COMM_WORLD); + // the next time step. Note how we initialize the vectors for the Stokes + // and temperature right hand sides: These are writable vectors (last + // boolean argument set to @p true) that have the correct one-to-one + // partitioning of locally owned elements but are still given the relevant + // partitioning for means of figuring out the vector entries that are + // going to be set right away. As for matrices, this allows for writing + // local contributions into the vector with multiple threads (always + // assuming that the same vector entry is not accessed by multiple threads + // at the same time). The other vectors only allow for read access of + // individual elements, including ghosts, but are not suitable for + // solvers. + setup_stokes_matrix (stokes_partitioning, stokes_relevant_partitioning); + setup_stokes_preconditioner (stokes_partitioning, + stokes_relevant_partitioning); + setup_temperature_matrices (temperature_partitioning, + temperature_relevant_partitioning); + + stokes_rhs.reinit (stokes_partitioning, stokes_relevant_partitioning, + MPI_COMM_WORLD, true); stokes_solution.reinit (stokes_relevant_partitioning, MPI_COMM_WORLD); old_stokes_solution.reinit (stokes_solution); - temperature_rhs.reinit (temperature_partitioning, MPI_COMM_WORLD); + temperature_rhs.reinit (temperature_partitioning, + temperature_relevant_partitioning, + MPI_COMM_WORLD, true); temperature_solution.reinit (temperature_relevant_partitioning, MPI_COMM_WORLD); old_temperature_solution.reinit (temperature_solution); old_old_temperature_solution.reinit (temperature_solution); @@ -2449,7 +2497,8 @@ namespace Step32 Assembly::CopyData:: StokesSystem (stokes_fe)); - stokes_matrix.compress(VectorOperation::add); + if (rebuild_stokes_matrix == true) + stokes_matrix.compress(VectorOperation::add); stokes_rhs.compress(VectorOperation::add); rebuild_stokes_matrix = false; @@ -3660,7 +3709,8 @@ int main (int argc, char *argv[]) using namespace Step32; using namespace dealii; - Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv); + Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, + numbers::invalid_unsigned_int); try { diff --git a/deal.II/include/deal.II/base/data_out_base.h b/deal.II/include/deal.II/base/data_out_base.h index db413f05fd..0d9ee2bbf3 100644 --- a/deal.II/include/deal.II/base/data_out_base.h +++ b/deal.II/include/deal.II/base/data_out_base.h @@ -1,7 +1,7 @@ // --------------------------------------------------------------------- // $Id$ // -// Copyright (C) 1999 - 2013 by the deal.II authors +// Copyright (C) 1999 - 2014 by the deal.II authors // // This file is part of the deal.II library. // @@ -1087,11 +1087,8 @@ public: * of an STL std::map type with a certain number of * elements?), this is only an estimate. however often quite close * to the true value. - */ + */ std::size_t memory_consumption () const; - - private: - }; @@ -1111,6 +1108,7 @@ public: * understand. */ static const unsigned int format_version = 3; + private: /** * Dummy entry to suppress compiler warnings when copying an empty @@ -2308,6 +2306,8 @@ public: using DataOutBase::get_output_format_names; using DataOutBase::determine_intermediate_format_dimensions; + using DataOutBase::Patch; + /** * Constructor. */ diff --git a/deal.II/include/deal.II/base/index_set.h b/deal.II/include/deal.II/base/index_set.h index b5b439d990..166a642a23 100644 --- a/deal.II/include/deal.II/base/index_set.h +++ b/deal.II/include/deal.II/base/index_set.h @@ -66,356 +66,243 @@ public: IndexSet (); /** - * Constructor that also sets the - * overall size of the index - * range. + * Constructor that also sets the overall size of the index range. */ explicit IndexSet (const types::global_dof_index size); /** - * Remove all indices from this - * index set. The index set retains - * its size, however. + * Remove all indices from this index set. The index set retains its size, + * however. */ void clear (); /** - * Set the maximal size of the - * indices upon which this object - * operates. + * Set the maximal size of the indices upon which this object operates. * - * This function can only be - * called if the index set does - * not yet contain any elements. - * This can be achieved by calling - * clear(), for example. + * This function can only be called if the index set does not yet contain + * any elements. This can be achieved by calling clear(), for example. */ void set_size (const types::global_dof_index size); /** - * Return the size of the index - * space of which this index set - * is a subset of. + * Return the size of the index space of which this index set is a subset + * of. * - * Note that the result is not equal to - * the number of indices within this - * set. The latter information is - * returned by n_elements(). + * Note that the result is not equal to the number of indices within this + * set. The latter information is returned by n_elements(). */ types::global_dof_index size () const; /** - * Add the half-open range - * $[\text{begin},\text{end})$ to - * the set of indices represented - * by this class. + * Add the half-open range $[\text{begin},\text{end})$ to the set of indices + * represented by this class. */ void add_range (const types::global_dof_index begin, const types::global_dof_index end); /** - * Add an individual index to the - * set of indices. + * Add an individual index to the set of indices. */ void add_index (const types::global_dof_index index); /** - * Add a whole set of indices - * described by dereferencing - * every element of the the - * iterator range - * [begin,end). + * Add a whole set of indices described by dereferencing every element of + * the the iterator range [begin,end). */ template void add_indices (const ForwardIterator &begin, const ForwardIterator &end); /** - * Add the given IndexSet @p other to the - * current one, constructing the union of - * *this and @p other. + * Add the given IndexSet @p other to the current one, constructing the + * union of *this and @p other. * - * If the @p offset argument is nonzero, then every - * index in @p other is shifted by @p offset before being - * added to the current index set. This allows to construct, - * for example, one index set from several others that are - * supposed to represent index sets corresponding to - * different ranges (e.g., when constructing the set of - * nonzero entries of a block vector from the sets of nonzero - * elements of the individual blocks of a vector). + * If the @p offset argument is nonzero, then every index in @p other is + * shifted by @p offset before being added to the current index set. This + * allows to construct, for example, one index set from several others that + * are supposed to represent index sets corresponding to different ranges + * (e.g., when constructing the set of nonzero entries of a block vector + * from the sets of nonzero elements of the individual blocks of a vector). * - * This function will generate an exception if any of the - * (possibly shifted) indices of the @p other index set - * lie outside the range [0,size()) represented - * by the current object. + * This function will generate an exception if any of the (possibly shifted) + * indices of the @p other index set lie outside the range + * [0,size()) represented by the current object. */ void add_indices(const IndexSet &other, const unsigned int offset = 0); /** - * Return whether the specified - * index is an element of the - * index set. + * Return whether the specified index is an element of the index set. */ bool is_element (const types::global_dof_index index) const; /** - * Return whether the index set - * stored by this object defines - * a contiguous range. This is - * true also if no indices are - * stored at all. + * Return whether the index set stored by this object defines a contiguous + * range. This is true also if no indices are stored at all. */ bool is_contiguous () const; /** - * Return the number of elements - * stored in this index set. + * Return the number of elements stored in this index set. */ types::global_dof_index n_elements () const; /** - * Return the global index of the local - * index with number @p local_index - * stored in this index set. @p - * local_index obviously needs to be less - * than n_elements(). + * Return the global index of the local index with number @p local_index + * stored in this index set. @p local_index obviously needs to be less than + * n_elements(). */ types::global_dof_index nth_index_in_set (const unsigned int local_index) const; /** - * Return the how-manyth element of this - * set (counted in ascending order) @p - * global_index is. @p global_index needs - * to be less than the size(). This - * function throws an exception if the - * index @p global_index is not actually - * a member of this index set, i.e. if - * is_element(global_index) is false. + * Return the how-manyth element of this set (counted in ascending order) @p + * global_index is. @p global_index needs to be less than the size(). This + * function throws an exception if the index @p global_index is not actually + * a member of this index set, i.e. if is_element(global_index) is false. */ types::global_dof_index index_within_set (const types::global_dof_index global_index) const; /** - * Each index set can be - * represented as the union of a - * number of contiguous intervals - * of indices, where if necessary - * intervals may only consist of - * individual elements to - * represent isolated members of - * the index set. + * Each index set can be represented as the union of a number of contiguous + * intervals of indices, where if necessary intervals may only consist of + * individual elements to represent isolated members of the index set. * - * This function returns the - * minimal number of such - * intervals that are needed to - * represent the index set under - * consideration. + * This function returns the minimal number of such intervals that are + * needed to represent the index set under consideration. */ unsigned int n_intervals () const; /** - * Compress the internal - * representation by merging - * individual elements with - * contiguous ranges, etc. This - * function does not have any - * external effect. + * Compress the internal representation by merging individual elements with + * contiguous ranges, etc. This function does not have any external effect. */ void compress () const; /** - * Comparison for equality of - * index sets. This operation is - * only allowed if the size of - * the two sets is the same - * (though of course they do not - * have to have the same number - * of indices). + * Comparison for equality of index sets. This operation is only allowed if + * the size of the two sets is the same (though of course they do not have + * to have the same number of indices). */ bool operator == (const IndexSet &is) const; /** - * Comparison for inequality of - * index sets. This operation is - * only allowed if the size of - * the two sets is the same - * (though of course they do not - * have to have the same number - * of indices). + * Comparison for inequality of index sets. This operation is only allowed + * if the size of the two sets is the same (though of course they do not + * have to have the same number of indices). */ bool operator != (const IndexSet &is) const; /** - * Return the intersection of the - * current index set and the - * argument given, i.e. a set of - * indices that are elements of - * both index sets. The two index - * sets must have the same size - * (though of course they do not - * have to have the same number - * of indices). + * Return the intersection of the current index set and the argument given, + * i.e. a set of indices that are elements of both index sets. The two index + * sets must have the same size (though of course they do not have to have + * the same number of indices). */ IndexSet operator & (const IndexSet &is) const; /** - * This command takes an interval - * [begin, end) and returns - * the intersection of the current - * index set with the interval, shifted - * to the range [0, - * end-begin). + * This command takes an interval [begin, end) and returns the + * intersection of the current index set with the interval, shifted to the + * range [0, end-begin). * - * In other words, the result of this operation is the - * intersection of the set represented by the current object - * and the interval [begin, end), as seen - * within the interval [begin, end) by - * shifting the result of the intersection operation to - * the left by begin. This corresponds to the notion - * of a view: The interval [begin, end) is - * a window through which we see the set represented - * by the current object. + * In other words, the result of this operation is the intersection of the + * set represented by the current object and the interval [begin, + * end), as seen within the interval [begin, end) by + * shifting the result of the intersection operation to the left by + * begin. This corresponds to the notion of a view: The + * interval [begin, end) is a window through which we see + * the set represented by the current object. */ IndexSet get_view (const types::global_dof_index begin, const types::global_dof_index end) const; /** - * Removes all elements contained in @p - * other from this set. In other words, - * if $x$ is the current object and $o$ - * the argument, then we compute $x + * Removes all elements contained in @p other from this set. In other words, + * if $x$ is the current object and $o$ the argument, then we compute $x * \leftarrow x \backslash o$. */ void subtract_set (const IndexSet &other); /** - * Fills the given vector with all - * indices contained in this IndexSet. + * Fills the given vector with all indices contained in this IndexSet. */ void fill_index_vector(std::vector &indices) const; /** - * Fill the given vector with either - * zero or one elements, providing - * a binary representation of this - * index set. The given vector is - * assumed to already have the correct - * size. + * Fill the given vector with either zero or one elements, providing a + * binary representation of this index set. The given vector is assumed to + * already have the correct size. * - * The given argument is filled with - * integer values zero and one, using - * vector.operator[]. Thus, - * any object that has such an operator - * can be used as long as it allows - * conversion of integers zero and one to - * elements of the vector. Specifically, - * this is the case for classes Vector, - * BlockVector, but also - * std::vector@, - * std::vector@, and - * std::vector@. + * The given argument is filled with integer values zero and one, using + * vector.operator[]. Thus, any object that has such an + * operator can be used as long as it allows conversion of integers zero and + * one to elements of the vector. Specifically, this is the case for classes + * Vector, BlockVector, but also std::vector@, std::vector@, + * and std::vector@. */ template void fill_binary_vector (Vector &vector) const; /** - * Outputs a text representation of this - * IndexSet to the given stream. Used for - * testing. + * Outputs a text representation of this IndexSet to the given stream. Used + * for testing. */ template void print(STREAM &out) const; /** - * Writes the IndexSet into a text based - * file format, that can be read in again - * using the read() function. + * Writes the IndexSet into a text based file format, that can be read in + * again using the read() function. */ void write(std::ostream &out) const; /** - * Constructs the IndexSet from a text - * based representation given by the - * stream @param in written by the - * write() function. + * Constructs the IndexSet from a text based representation given by the + * stream @param in written by the write() function. */ void read(std::istream &in); /** - * Writes the IndexSet into a binary, - * compact representation, that can be - * read in again using the block_read() - * function. + * Writes the IndexSet into a binary, compact representation, that can be + * read in again using the block_read() function. */ void block_write(std::ostream &out) const; /** - * Constructs the IndexSet from a binary - * representation given by the stream - * @param in written by the write_block() - * function. + * Constructs the IndexSet from a binary representation given by the stream + * @param in written by the write_block() function. */ void block_read(std::istream &in); #ifdef DEAL_II_WITH_TRILINOS /** - * Given an MPI communicator, - * create a Trilinos map object - * that represents a distribution - * of vector elements or matrix - * rows in which we will locally - * store those elements or rows - * for which we store the index - * in the current index set, and - * all the other elements/rows - * elsewhere on one of the other + * Given an MPI communicator, create a Trilinos map object that represents a + * distribution of vector elements or matrix rows in which we will locally + * store those elements or rows for which we store the index in the current + * index set, and all the other elements/rows elsewhere on one of the other * MPI processes. * - * The last argument only plays a - * role if the communicator is a - * parallel one, distributing - * computations across multiple - * processors. In that case, if - * the last argument is false, - * then it is assumed that the - * index sets this function is - * called on on all processors - * are mutually exclusive but - * together enumerate each index - * exactly once. In other words, - * if you call this function on - * two processors, then the index - * sets this function is called - * with must together have all - * possible indices from zero to - * size()-1, and no index must - * appear in both index - * sets. This corresponds, for - * example, to the case where we - * want to split the elements of - * vectors into unique subsets to - * be stored on different - * processors -- no element - * should be owned by more than - * one processor, but each - * element must be owned by one. + * The last argument only plays a role if the communicator is a parallel + * one, distributing computations across multiple processors. In that case, + * if the last argument is false, then it is assumed that the index sets + * this function is called on on all processors are mutually exclusive but + * together enumerate each index exactly once. In other words, if you call + * this function on two processors, then the index sets this function is + * called with must together have all possible indices from zero to + * size()-1, and no index must appear in both index sets. This corresponds, + * for example, to the case where we want to split the elements of vectors + * into unique subsets to be stored on different processors -- no element + * should be owned by more than one processor, but each element must be + * owned by one. * - * On the other hand, if the - * second argument is true, then - * the index sets can be - * overlapping, though they still - * need to contain each index - * exactly once on all processors - * taken together. This is a - * useful operation if we want to - * create vectors that not only - * contain the locally owned - * indices, but for example also - * the elements that correspond - * to degrees of freedom located - * on ghost cells. + * On the other hand, if the second argument is true, then the index sets + * can be overlapping, though they still need to contain each index exactly + * once on all processors taken together. This is a useful operation if we + * want to create vectors that not only contain the locally owned indices, + * but for example also the elements that correspond to degrees of freedom + * located on ghost cells. */ Epetra_Map make_trilinos_map (const MPI_Comm &communicator = MPI_COMM_WORLD, const bool overlapping = false) const; @@ -423,8 +310,7 @@ public: /** - * Determine an estimate for the memory - * consumption (in bytes) of this + * Determine an estimate for the memory consumption (in bytes) of this * object. */ std::size_t memory_consumption () const; @@ -442,18 +328,11 @@ public: private: /** - * A type that denotes the half - * open index range - * [begin,end). + * A type that denotes the half open index range [begin,end). * - * The nth_index_in_set denotes - * the how many-th index within - * this IndexSet the first - * element of the current range - * is. This information is only - * accurate if - * IndexSet::compress() has been - * called after the last + * The nth_index_in_set denotes the how many-th index within this IndexSet + * the first element of the current range is. This information is only + * accurate if IndexSet::compress() has been called after the last * insertion. */ struct Range @@ -521,72 +400,52 @@ private: } /** - * Write or read the data of this object to or - * from a stream for the purpose of serialization + * Write or read the data of this object to or from a stream for the + * purpose of serialization */ template void serialize (Archive &ar, const unsigned int version); }; /** - * A set of contiguous ranges of - * indices that make up (part of) - * this index set. This variable - * is always kept sorted. + * A set of contiguous ranges of indices that make up (part of) this index + * set. This variable is always kept sorted. * - * The variable is marked - * "mutable" so that it can be - * changed by compress(), though - * this of course doesn't change - * anything about the external - * representation of this index - * set. + * The variable is marked "mutable" so that it can be changed by compress(), + * though this of course doesn't change anything about the external + * representation of this index set. */ mutable std::vector ranges; /** - * True if compress() has been - * called after the last change - * in the set of indices. + * True if compress() has been called after the last change in the set of + * indices. * - * The variable is marked - * "mutable" so that it can be - * changed by compress(), though - * this of course doesn't change - * anything about the external - * representation of this index - * set. + * The variable is marked "mutable" so that it can be changed by compress(), + * though this of course doesn't change anything about the external + * representation of this index set. */ mutable bool is_compressed; /** - * The overall size of the index - * range. Elements of this index - * set have to have a smaller - * number than this value. + * The overall size of the index range. Elements of this index set have to + * have a smaller number than this value. */ types::global_dof_index index_space_size; /** - * This integer caches the index of the - * largest range in @p ranges. This gives - * O(1) access to the range with - * most elements, while general access - * costs O(log(n_ranges)). The - * largest range is needed for the - * methods @p is_element(), @p - * index_within_set(), @p - * nth_index_in_set. In many - * applications, the largest range - * contains most elements (the locally - * owned range), whereas there are only a - * few other elements (ghosts). + * This integer caches the index of the largest range in @p ranges. This + * gives O(1) access to the range with most elements, while general + * access costs O(log(n_ranges)). The largest range is needed for + * the methods @p is_element(), @p index_within_set(), @p + * nth_index_in_set. In many applications, the largest range contains most + * elements (the locally owned range), whereas there are only a few other + * elements (ghosts). */ mutable types::global_dof_index largest_range; /** - * Actually perform the compress() - * operation. + * Actually perform the compress() operation. */ void do_compress() const; }; @@ -701,40 +560,6 @@ IndexSet::compress () const -inline -void -IndexSet::add_range (const types::global_dof_index begin, - const types::global_dof_index end) -{ - Assert ((begin < index_space_size) - || - ((begin == index_space_size) && (end == index_space_size)), - ExcIndexRangeType (begin, 0, index_space_size)); - Assert (end <= index_space_size, - ExcIndexRangeType (end, 0, index_space_size+1)); - Assert (begin <= end, - ExcIndexRangeType (begin, 0, end)); - - if (begin != end) - { - const Range new_range(begin,end); - - // the new index might be larger than the last - // index present in the ranges. Then we can - // skip the binary search - if (ranges.size() == 0 || begin > ranges.back().end) - ranges.push_back(new_range); - else - ranges.insert (Utilities::lower_bound (ranges.begin(), - ranges.end(), - new_range), - new_range); - is_compressed = false; - } -} - - - inline void IndexSet::add_index (const types::global_dof_index index) @@ -763,10 +588,8 @@ void IndexSet::add_indices (const ForwardIterator &begin, const ForwardIterator &end) { - // insert each element of the - // range. if some of them happen to - // be consecutive, merge them to a - // range + // insert each element of the range. if some of them happen to be + // consecutive, merge them to a range for (ForwardIterator p=begin; p!=end;) { const types::global_dof_index begin_index = *p; @@ -786,26 +609,6 @@ IndexSet::add_indices (const ForwardIterator &begin, -inline -void -IndexSet::add_indices(const IndexSet &other, - const unsigned int offset) -{ - if ((this == &other) && (offset == 0)) - return; - - for (std::vector::iterator range = other.ranges.begin(); - range != other.ranges.end(); - ++range) - { - add_range(range->begin+offset, range->end+offset); - } - - compress(); -} - - - inline bool IndexSet::is_element (const types::global_dof_index index) const @@ -814,38 +617,24 @@ IndexSet::is_element (const types::global_dof_index index) const { compress (); - // fast check whether the index is in the - // largest range + // fast check whether the index is in the largest range Assert (largest_range < ranges.size(), ExcInternalError()); if (index >= ranges[largest_range].begin && index < ranges[largest_range].end) return true; - // get the element after which - // we would have to insert a - // range that consists of all - // elements from this element - // to the end of the index - // range plus one. after this - // call we know that if - // p!=end() then - // p->begin<=index unless there - // is no such range at all + // get the element after which we would have to insert a range that + // consists of all elements from this element to the end of the index + // range plus one. after this call we know that if p!=end() then + // p->begin<=index unless there is no such range at all // - // if the searched for element - // is an element of this range, - // then we're done. otherwise, - // the element can't be in one - // of the following ranges - // because otherwise p would be - // a different iterator + // if the searched for element is an element of this range, then we're + // done. otherwise, the element can't be in one of the following ranges + // because otherwise p would be a different iterator // - // since we already know the position - // relative to the largest range (we - // called compress!), we can perform - // the binary search on ranges with - // lower/higher number compared to the - // largest range + // since we already know the position relative to the largest range (we + // called compress!), we can perform the binary search on ranges with + // lower/higher number compared to the largest range std::vector::const_iterator p = std::upper_bound (ranges.begin() + (indexbegin > index), ExcInternalError()); - // now move to that previous - // range + // now move to that previous range --p; Assert (p->begin <= index, ExcInternalError()); return (p->end > index); } - // didn't find this index, so it's - // not in the set + // didn't find this index, so it's not in the set return false; } @@ -889,8 +676,7 @@ inline types::global_dof_index IndexSet::n_elements () const { - // make sure we have - // non-overlapping ranges + // make sure we have non-overlapping ranges compress (); types::global_dof_index v = 0; @@ -914,28 +700,35 @@ IndexSet::n_elements () const +inline +unsigned int +IndexSet::n_intervals () const +{ + compress (); + return ranges.size(); +} + + + inline types::global_dof_index IndexSet::nth_index_in_set (const unsigned int n) const { - // to make this call thread-safe, compress() - // must not be called through this function + // to make this call thread-safe, compress() must not be called through this + // function Assert (is_compressed == true, ExcMessage ("IndexSet must be compressed.")); Assert (n < n_elements(), ExcIndexRangeType (n, 0, n_elements())); - // first check whether the index is in the - // largest range + // first check whether the index is in the largest range Assert (largest_range < ranges.size(), ExcInternalError()); std::vector::const_iterator main_range=ranges.begin()+largest_range; if (n>=main_range->nth_index_in_set && nnth_index_in_set+(main_range->end-main_range->begin)) return main_range->begin + (n-main_range->nth_index_in_set); - // find out which chunk the local index n - // belongs to by using a binary search. the - // comparator is based on the end of the - // ranges. Use the position relative to main_range to - // subdivide the ranges + // find out which chunk the local index n belongs to by using a binary + // search. the comparator is based on the end of the ranges. Use the + // position relative to main_range to subdivide the ranges Range r (n,n+1); r.nth_index_in_set = n; std::vector::const_iterator range_begin, range_end; @@ -969,15 +762,14 @@ inline types::global_dof_index IndexSet::index_within_set (const types::global_dof_index n) const { - // to make this call thread-safe, compress() - // must not be called through this function + // to make this call thread-safe, compress() must not be called through this + // function Assert (is_compressed == true, ExcMessage ("IndexSet must be compressed.")); Assert (is_element(n) == true, ExcIndexNotPresent (n)); Assert (n < size(), ExcIndexRangeType (n, 0, size())); - // check whether the index is in the largest - // range. use the result to perform a - // one-sided binary search afterward + // check whether the index is in the largest range. use the result to + // perform a one-sided binary search afterward Assert (largest_range < ranges.size(), ExcInternalError()); std::vector::const_iterator main_range=ranges.begin()+largest_range; if (n >= main_range->begin && n < main_range->end) @@ -1046,12 +838,11 @@ IndexSet::fill_binary_vector (Vector &vector) const ExcDimensionMismatch (vector.size(), size())); compress(); - // first fill all elements of the vector - // with zeroes. + // first fill all elements of the vector with zeroes. std::fill (vector.begin(), vector.end(), 0); - // then write ones into the elements whose - // indices are contained in the index set + // then write ones into the elements whose indices are contained in the + // index set for (std::vector::iterator it = ranges.begin(); it != ranges.end(); ++it) diff --git a/deal.II/include/deal.II/dofs/dof_accessor.h b/deal.II/include/deal.II/dofs/dof_accessor.h index 461d8d912a..885eeff0ee 100644 --- a/deal.II/include/deal.II/dofs/dof_accessor.h +++ b/deal.II/include/deal.II/dofs/dof_accessor.h @@ -1407,27 +1407,42 @@ public: /** * Return the interpolation of the given finite element function to * the present cell. In the simplest case, the cell is a terminal - * one, i.e. has no children; then, the returned value is the vector - * of nodal values on that cell. You could then as well get the + * one, i.e., it has no children; then, the returned value is the vector + * of nodal values on that cell. You could as well get the * desired values through the @p get_dof_values function. In the * other case, when the cell has children, we use the restriction * matrices provided by the finite element class to compute the * interpolation from the children to the present cell. * - * It is assumed that both vectors already have the right size + * If the cell is part of a hp::DoFHandler object, cells only have an + * associated finite element space if they are active. However, this + * function is supposed to also provide information on inactive cells + * with children. Consequently, it carries a third argument that can be + * used in the hp context that denotes the finite element space we are + * supposed to interpolate onto. If the cell is active, this function + * then obtains the finite element function from the values + * vector on this cell and interpolates it onto the space described + * by the fe_indexth element of the hp::FECollection associated + * with the hp::DoFHandler of which this cell is a part of. If the cell + * is not active, then we first perform this interpolation on all of its + * terminal children and then interpolate this function down to the + * cell requested keeping the function space the same. + * + * It is assumed that both input vectors already have the right size * beforehand. * - * Unlike the get_dof_values() function, this function works on - * cells rather than to lines, quads, and hexes, since interpolation + * @note Unlike the get_dof_values() function, this function is only available + * on cells, rather than on lines, quads, and hexes, since interpolation * is presently only provided for cells by the finite element * classes. */ template void get_interpolated_dof_values (const InputVector &values, - Vector &interpolated_values) const; + Vector &interpolated_values, + const unsigned int fe_index = DH::default_fe_index) const; /** - * This, again, is the counterpart to get_interpolated_dof_values(): + * This function is the counterpart to get_interpolated_dof_values(): * you specify the dof values on a cell and these are interpolated * to the children of the present cell and set on the terminal * cells. @@ -1476,7 +1491,8 @@ public: */ template void set_dof_values_by_interpolation (const Vector &local_values, - OutputVector &values) const; + OutputVector &values, + const unsigned int fe_index = DH::default_fe_index) const; /** * Distribute a local (cell based) vector to a global one by mapping diff --git a/deal.II/include/deal.II/dofs/dof_accessor.templates.h b/deal.II/include/deal.II/dofs/dof_accessor.templates.h index 327146e3f5..2c9af2dcc0 100644 --- a/deal.II/include/deal.II/dofs/dof_accessor.templates.h +++ b/deal.II/include/deal.II/dofs/dof_accessor.templates.h @@ -80,7 +80,12 @@ DoFAccessor::DoFAccessor (const DoFAccessor & : BaseClass(other), dof_handler(0) { - Assert (false, ExcInvalidObject()); + Assert (false, ExcMessage("You are trying to assign iterators that are incompatible. " + "Reasons for incompatibility are that they point to different " + "types of DoFHandlers (e.g., dealii::DoFHandler and " + "dealii::hp::DoFHandler) or that the refer to objects of " + "different dimensionality (e.g., assigning a line iterator " + "to a quad iterator).")); } diff --git a/deal.II/include/deal.II/fe/fe.h b/deal.II/include/deal.II/fe/fe.h index fda2a7fef3..def12dd29c 100644 --- a/deal.II/include/deal.II/fe/fe.h +++ b/deal.II/include/deal.II/fe/fe.h @@ -1313,6 +1313,15 @@ public: BlockMask block_mask (const ComponentMask &component_mask) const; + /** + * Returns a list of constant modes of the element. The returns table has as + * many rows as there are components in the element and dofs_per_cell + * columns. To each component of the finite element, the row in the returned + * table contains a basis representation of the constant function 1 on the + * element. + */ + virtual Table<2,bool> get_constant_modes () const; + //@} /** diff --git a/deal.II/include/deal.II/fe/fe_dgp.h b/deal.II/include/deal.II/fe/fe_dgp.h index 7ea266a45e..6343a7c637 100644 --- a/deal.II/include/deal.II/fe/fe_dgp.h +++ b/deal.II/include/deal.II/fe/fe_dgp.h @@ -327,6 +327,12 @@ public: static const unsigned int n_projection_matrices; }; + /** + * Returns a list of constant modes of the element. For this element, the + * first entry is true, all other are false. + */ + virtual Table<2,bool> get_constant_modes () const; + protected: /** diff --git a/deal.II/include/deal.II/fe/fe_dgq.h b/deal.II/include/deal.II/fe/fe_dgq.h index a07cf4f32d..c10aaa8ad8 100644 --- a/deal.II/include/deal.II/fe/fe_dgq.h +++ b/deal.II/include/deal.II/fe/fe_dgq.h @@ -280,6 +280,12 @@ public: virtual bool has_support_on_face (const unsigned int shape_index, const unsigned int face_index) const; + /** + * Returns a list of constant modes of the element. For this element, it + * simply returns one row with all entries set to true. + */ + virtual Table<2,bool> get_constant_modes () const; + /** * Determine an estimate for the * memory consumption (in bytes) diff --git a/deal.II/include/deal.II/fe/fe_face.h b/deal.II/include/deal.II/fe/fe_face.h index af7b702cfa..6e80608548 100644 --- a/deal.II/include/deal.II/fe/fe_face.h +++ b/deal.II/include/deal.II/fe/fe_face.h @@ -124,6 +124,13 @@ public: FiniteElementDomination::Domination compare_for_face_domination (const FiniteElement &fe_other) const; + + /** + * Returns a list of constant modes of the element. For this element, it + * simply returns one row with all entries set to true. + */ + virtual Table<2,bool> get_constant_modes () const; + private: /** * Return vector with dofs per vertex, line, quad, hex. @@ -234,6 +241,14 @@ public: FiniteElementDomination::Domination compare_for_face_domination (const FiniteElement &fe_other) const; + /** + * Returns a list of constant modes of the element. For this element, the + * first entry on each face is true, all other are false (as the constant + * function is represented by the first base function of Legendre + * polynomials. + */ + virtual Table<2,bool> get_constant_modes () const; + private: /** * Return vector with dofs per vertex, line, quad, hex. diff --git a/deal.II/include/deal.II/fe/fe_nedelec.h b/deal.II/include/deal.II/fe/fe_nedelec.h index 6b15aa1be6..81dad103af 100644 --- a/deal.II/include/deal.II/fe/fe_nedelec.h +++ b/deal.II/include/deal.II/fe/fe_nedelec.h @@ -281,6 +281,12 @@ public: virtual void interpolate (std::vector &local_dofs, const VectorSlice > > &values) const; + + /** + * Returns a list of constant modes of the element. + */ + virtual Table<2,bool> get_constant_modes () const; + virtual std::size_t memory_consumption () const; virtual FiniteElement *clone() const; diff --git a/deal.II/include/deal.II/fe/fe_poly.h b/deal.II/include/deal.II/fe/fe_poly.h index 0cee69105c..a6aa46f8a9 100644 --- a/deal.II/include/deal.II/fe/fe_poly.h +++ b/deal.II/include/deal.II/fe/fe_poly.h @@ -162,6 +162,7 @@ public: virtual Tensor<2,dim> shape_grad_grad_component (const unsigned int i, const Point &p, const unsigned int component) const; + protected: virtual diff --git a/deal.II/include/deal.II/fe/fe_q_base.h b/deal.II/include/deal.II/fe/fe_q_base.h index 15b6701171..6870f28fd2 100644 --- a/deal.II/include/deal.II/fe/fe_q_base.h +++ b/deal.II/include/deal.II/fe/fe_q_base.h @@ -195,6 +195,12 @@ public: const bool face_flip = false, const bool face_rotation = false) const; + /** + * Returns a list of constant modes of the element. For this element, the + * list consists of true arguments for all components. + */ + virtual Table<2,bool> get_constant_modes () const; + /** * @name Functions to support hp * @{ diff --git a/deal.II/include/deal.II/fe/fe_q_hierarchical.h b/deal.II/include/deal.II/fe/fe_q_hierarchical.h index bed960dcc2..54fe8b4e63 100644 --- a/deal.II/include/deal.II/fe/fe_q_hierarchical.h +++ b/deal.II/include/deal.II/fe/fe_q_hierarchical.h @@ -379,6 +379,13 @@ public: */ std::vector get_embedding_dofs (const unsigned int sub_degree) const; + /** + * Returns a list of constant modes of the element. For this element, the + * list consists of true arguments for the first vertex shape functions and + * false for the remaining ones. + */ + virtual Table<2,bool> get_constant_modes () const; + protected: /** * @p clone function instead of diff --git a/deal.II/include/deal.II/fe/fe_raviart_thomas.h b/deal.II/include/deal.II/fe/fe_raviart_thomas.h index 8f46f9f577..bda93239da 100644 --- a/deal.II/include/deal.II/fe/fe_raviart_thomas.h +++ b/deal.II/include/deal.II/fe/fe_raviart_thomas.h @@ -146,6 +146,13 @@ public: virtual void interpolate( std::vector &local_dofs, const VectorSlice > > &values) const; + + /** + * Returns a list of constant modes of the element. For this element, the + * list consists of true arguments for all components. + */ + virtual Table<2,bool> get_constant_modes () const; + virtual std::size_t memory_consumption () const; virtual FiniteElement *clone() const; diff --git a/deal.II/include/deal.II/fe/fe_system.h b/deal.II/include/deal.II/fe/fe_system.h index 0705632bac..7022cdd694 100644 --- a/deal.II/include/deal.II/fe/fe_system.h +++ b/deal.II/include/deal.II/fe/fe_system.h @@ -469,6 +469,15 @@ public: Point unit_face_support_point (const unsigned int index) const; + /** + * Returns a list of constant modes of the element. The returns table has as + * many rows as there are components in the element and dofs_per_cell + * columns. To each component of the finite element, the row in the returned + * table contains a basis representation of the constant function 1 on the + * element. Concatenates the constant modes of each base element. + */ + virtual Table<2,bool> get_constant_modes () const; + /** * @name Functions to support hp * @{ diff --git a/deal.II/include/deal.II/grid/grid_generator.h b/deal.II/include/deal.II/grid/grid_generator.h index 0ad8634481..56194984fe 100644 --- a/deal.II/include/deal.II/grid/grid_generator.h +++ b/deal.II/include/deal.II/grid/grid_generator.h @@ -385,10 +385,12 @@ namespace GridGenerator const double half_length = 1.0); /** - * Initialize the given triangulation with a hyper-L consisting of exactly + * Initialize the given triangulation with a hyper-L (in 2d or 3d) + * consisting of exactly * 2^dim-1 cells. It produces the hypercube with the interval * [left,right] without the hypercube made out of the interval - * [(a+b)/2,b]. + * [(a+b)/2,b]. This will result in the classical L-shape in 2d. + * The shape will look like the following in 3d: * * @image html hyper_l.png * @@ -436,12 +438,12 @@ namespace GridGenerator * indicator 1, while the inner boundary has id zero. If the flag is @p * false, both have indicator zero. * - * In 2D, the number n_cells of elements for this initial + * In 2d, the number n_cells of elements for this initial * triangulation can be chosen arbitrarily. If the number of initial cells * is zero (as is the default), then it is computed adaptively such that the * resulting elements have the least aspect ratio. * - * In 3D, only two different numbers are meaningful, 6 for a surface based + * In 3d, only two different numbers are meaningful, 6 for a surface based * on a hexahedron (i.e. 6 panels on the inner sphere extruded in radial * direction to form 6 cells) and 12 for the rhombic dodecahedron. These * give rise to the following meshes upon one refinement: @@ -614,7 +616,7 @@ namespace GridGenerator const bool colorize = false); /** - * Produce a ring of cells in 3D that is cut open, twisted and glued + * Produce a ring of cells in 3d that is cut open, twisted and glued * together again. This results in a kind of moebius-loop. * * @param tria The triangulation to be worked on. diff --git a/deal.II/include/deal.II/lac/compressed_simple_sparsity_pattern.h b/deal.II/include/deal.II/lac/compressed_simple_sparsity_pattern.h index 6257f4733a..fa745dcd53 100644 --- a/deal.II/include/deal.II/lac/compressed_simple_sparsity_pattern.h +++ b/deal.II/include/deal.II/lac/compressed_simple_sparsity_pattern.h @@ -98,139 +98,96 @@ public: typedef types::global_dof_index size_type; /** - * An iterator that can be used to - * iterate over the elements of a single - * row. The result of dereferencing such - * an iterator is a column index. + * An iterator that can be used to iterate over the elements of a single + * row. The result of dereferencing such an iterator is a column index. */ typedef std::vector::const_iterator row_iterator; /** - * Initialize the matrix empty, - * that is with no memory - * allocated. This is useful if - * you want such objects as - * member variables in other - * classes. You can make the - * structure usable by calling - * the reinit() function. + * Initialize the matrix empty, that is with no memory allocated. This is + * useful if you want such objects as member variables in other classes. You + * can make the structure usable by calling the reinit() function. */ CompressedSimpleSparsityPattern (); /** - * Copy constructor. This constructor is - * only allowed to be called if the - * matrix structure to be copied is - * empty. This is so in order to prevent - * involuntary copies of objects for - * temporaries, which can use large - * amounts of computing time. However, - * copy constructors are needed if you - * want to use the STL data types on - * classes like this, e.g. to write such - * statements like v.push_back - * (CompressedSparsityPattern());, - * with @p v a vector of @p - * CompressedSparsityPattern objects. + * Copy constructor. This constructor is only allowed to be called if the + * matrix structure to be copied is empty. This is so in order to prevent + * involuntary copies of objects for temporaries, which can use large + * amounts of computing time. However, copy constructors are needed if you + * want to use the STL data types on classes like this, e.g. to write such + * statements like v.push_back (CompressedSparsityPattern());, with + * @p v a vector of @p CompressedSparsityPattern objects. */ CompressedSimpleSparsityPattern (const CompressedSimpleSparsityPattern &); /** - * Initialize a rectangular - * matrix with @p m rows and - * @p n columns. The @p rowset - * restricts the storage to - * elements in rows of this set. - * Adding elements outside of - * this set has no effect. The - * default argument keeps all - * entries. + * Initialize a rectangular matrix with @p m rows and @p n columns. The @p + * rowset restricts the storage to elements in rows of this set. Adding + * elements outside of this set has no effect. The default argument keeps + * all entries. */ CompressedSimpleSparsityPattern (const size_type m, const size_type n, const IndexSet &rowset = IndexSet()); /** - * Create a square SparsityPattern using - * the index set. + * Create a square SparsityPattern using the index set. */ CompressedSimpleSparsityPattern (const IndexSet &indexset); /** - * Initialize a square matrix of - * dimension @p n. + * Initialize a square matrix of dimension @p n. */ CompressedSimpleSparsityPattern (const size_type n); /** - * Copy operator. For this the - * same holds as for the copy - * constructor: it is declared, - * defined and fine to be called, - * but the latter only for empty + * Copy operator. For this the same holds as for the copy constructor: it is + * declared, defined and fine to be called, but the latter only for empty * objects. */ CompressedSimpleSparsityPattern &operator = (const CompressedSimpleSparsityPattern &); /** - * Reallocate memory and set up - * data structures for a new - * matrix with @p m rows and - * @p n columns, with at most - * max_entries_per_row() nonzero - * entries per row. The @p rowset - * restricts the storage to - * elements in rows of this set. - * Adding elements outside of - * this set has no effect. The - * default argument keeps all - * entries. + * Reallocate memory and set up data structures for a new matrix with @p m + * rows and @p n columns, with at most max_entries_per_row() nonzero entries + * per row. The @p rowset restricts the storage to elements in rows of this + * set. Adding elements outside of this set has no effect. The default + * argument keeps all entries. */ void reinit (const size_type m, const size_type n, const IndexSet &rowset = IndexSet()); /** - * Since this object is kept - * compressed at all times anway, - * this function does nothing, - * but is declared to make the - * interface of this class as - * much alike as that of the - * SparsityPattern class. + * Since this object is kept compressed at all times anway, this function + * does nothing, but is declared to make the interface of this class as much + * alike as that of the SparsityPattern class. */ void compress (); /** - * Return whether the object is - * empty. It is empty if no - * memory is allocated, which is - * the same as that both - * dimensions are zero. + * Return whether the object is empty. It is empty if no memory is + * allocated, which is the same as that both dimensions are zero. */ bool empty () const; /** - * Return the maximum number of - * entries per row. Note that - * this number may change as - * entries are added. + * Return the maximum number of entries per row. Note that this number may + * change as entries are added. */ size_type max_entries_per_row () const; /** - * Add a nonzero entry to the - * matrix. If the entry already - * exists, nothing bad happens. + * Add a nonzero entry to the matrix. If the entry already exists, nothing + * bad happens. */ void add (const size_type i, const size_type j); /** - * Add several nonzero entries to the - * specified row of the matrix. If the - * entries already exist, nothing bad - * happens. + * Add several nonzero entries to the specified row of the matrix. If the + * entries already exist, nothing bad happens. */ template void add_entries (const size_type row, @@ -239,98 +196,70 @@ public: const bool indices_are_unique_and_sorted = false); /** - * Check if a value at a certain - * position may be non-zero. + * Check if a value at a certain position may be non-zero. */ bool exists (const size_type i, const size_type j) const; /** - * Make the sparsity pattern - * symmetric by adding the - * sparsity pattern of the + * Make the sparsity pattern symmetric by adding the sparsity pattern of the * transpose object. * - * This function throws an - * exception if the sparsity - * pattern does not represent a - * square matrix. + * This function throws an exception if the sparsity pattern does not + * represent a square matrix. */ void symmetrize (); /** - * Print the sparsity of the - * matrix. The output consists of - * one line per row of the format - * [i,j1,j2,j3,...]. i - * is the row number and - * jn are the allocated - * columns in this row. + * Print the sparsity of the matrix. The output consists of one line per row + * of the format [i,j1,j2,j3,...]. i is the row number and + * jn are the allocated columns in this row. */ void print (std::ostream &out) const; /** - * Print the sparsity of the matrix in a - * format that @p gnuplot understands and - * which can be used to plot the sparsity - * pattern in a graphical way. The format - * consists of pairs i j of - * nonzero elements, each representing - * one entry of this matrix, one per line - * of the output file. Indices are - * counted from zero on, as usual. Since - * sparsity patterns are printed in the - * same way as matrices are displayed, we - * print the negative of the column - * index, which means that the - * (0,0) element is in the top - * left rather than in the bottom left - * corner. + * Print the sparsity of the matrix in a format that @p gnuplot understands + * and which can be used to plot the sparsity pattern in a graphical + * way. The format consists of pairs i j of nonzero elements, each + * representing one entry of this matrix, one per line of the output + * file. Indices are counted from zero on, as usual. Since sparsity patterns + * are printed in the same way as matrices are displayed, we print the + * negative of the column index, which means that the (0,0) element + * is in the top left rather than in the bottom left corner. * - * Print the sparsity pattern in - * gnuplot by setting the data style - * to dots or points and use the - * @p plot command. + * Print the sparsity pattern in gnuplot by setting the data style to dots + * or points and use the @p plot command. */ void print_gnuplot (std::ostream &out) const; /** - * Return number of rows of this - * matrix, which equals the dimension - * of the image space. + * Return number of rows of this matrix, which equals the dimension of the + * image space. */ size_type n_rows () const; /** - * Return number of columns of this - * matrix, which equals the dimension - * of the range space. + * Return number of columns of this matrix, which equals the dimension of + * the range space. */ size_type n_cols () const; /** - * Number of entries in a - * specific row. This function - * can only be called if the - * given row is a member of the - * index set of rows that we want - * to store. + * Number of entries in a specific row. This function can only be called if + * the given row is a member of the index set of rows that we want to store. */ size_type row_length (const size_type row) const; /** - * Access to column number field. - * Return the column number of - * the @p indexth entry in @p row. + * Access to column number field. Return the column number of the @p + * indexth entry in @p row. */ size_type column_number (const size_type row, const size_type index) const; /** - * Return an iterator that can loop over - * all entries in the given - * row. Dereferencing the iterator yields - * a column index. + * Return an iterator that can loop over all entries in the given + * row. Dereferencing the iterator yields a column index. */ row_iterator row_begin (const size_type row) const; @@ -339,65 +268,52 @@ public: */ row_iterator row_end (const size_type row) const; /** - * Compute the bandwidth of the matrix - * represented by this structure. The - * bandwidth is the maximum of - * $|i-j|$ for which the index pair - * $(i,j)$ represents a nonzero entry - * of the matrix. + * Compute the bandwidth of the matrix represented by this structure. The + * bandwidth is the maximum of $|i-j|$ for which the index pair $(i,j)$ + * represents a nonzero entry of the matrix. */ size_type bandwidth () const; /** - * Return the number of nonzero elements - * allocated through this sparsity pattern. + * Return the number of nonzero elements allocated through this sparsity + * pattern. */ size_type n_nonzero_elements () const; /** - * Return the IndexSet that sets which - * rows are active on the current - * processor. It corresponds to the - * IndexSet given to this class in the + * Return the IndexSet that sets which rows are active on the current + * processor. It corresponds to the IndexSet given to this class in the * constructor or in the reinit function. */ const IndexSet &row_index_set () const; /** - * return whether this object stores only - * those entries that have been added - * explicitly, or if the sparsity pattern - * contains elements that have been added - * through other means (implicitly) while - * building it. For the current class, - * the result is always true. + * return whether this object stores only those entries that have been added + * explicitly, or if the sparsity pattern contains elements that have been + * added through other means (implicitly) while building it. For the current + * class, the result is always true. * - * This function mainly serves the - * purpose of describing the current - * class in cases where several kinds of - * sparsity patterns can be passed as + * This function mainly serves the purpose of describing the current class + * in cases where several kinds of sparsity patterns can be passed as * template arguments. */ static bool stores_only_added_elements (); /** - * Determine an estimate for the - * memory consumption (in bytes) - * of this object. + * Determine an estimate for the memory consumption (in bytes) of this + * object. */ size_type memory_consumption () const; private: /** - * Number of rows that this sparsity - * structure shall represent. + * Number of rows that this sparsity structure shall represent. */ size_type rows; /** - * Number of columns that this sparsity - * structure shall represent. + * Number of columns that this sparsity structure shall represent. */ size_type cols; @@ -409,21 +325,17 @@ private: /** - * Store some data for each row - * describing which entries of this row - * are nonzero. Data is stored sorted in - * the @p entries std::vector. - * The vector per row is dynamically - * growing upon insertion doubling its - * memory each time. + * Store some data for each row describing which entries of this row are + * nonzero. Data is stored sorted in the @p entries std::vector. The vector + * per row is dynamically growing upon insertion doubling its memory each + * time. */ struct Line { public: /** - * Storage for the column indices of - * this row. This array is always - * kept sorted. + * Storage for the column indices of this row. This array is always kept + * sorted. */ std::vector entries; @@ -433,14 +345,12 @@ private: Line (); /** - * Add the given column number to - * this line. + * Add the given column number to this line. */ void add (const size_type col_num); /** - * Add the columns specified by the - * iterator range to this line. + * Add the columns specified by the iterator range to this line. */ template void add_entries (ForwardIterator begin, @@ -455,9 +365,7 @@ private: /** - * Actual data: store for each - * row the set of nonzero - * entries. + * Actual data: store for each row the set of nonzero entries. */ std::vector lines; }; @@ -470,28 +378,24 @@ inline void CompressedSimpleSparsityPattern::Line::add (const size_type j) { - // first check the last element (or if line - // is still empty) + // first check the last element (or if line is still empty) if ( (entries.size()==0) || ( entries.back() < j) ) { entries.push_back(j); return; } - // do a binary search to find the place - // where to insert: + // do a binary search to find the place where to insert: std::vector::iterator it = Utilities::lower_bound(entries.begin(), entries.end(), j); - // If this entry is a duplicate, exit - // immediately + // If this entry is a duplicate, exit immediately if (*it == j) return; - // Insert at the right place in the - // vector. Vector grows automatically to + // Insert at the right place in the vector. Vector grows automatically to // fit elements. Always doubles its size. entries.insert(it, j); } diff --git a/deal.II/include/deal.II/lac/constraint_matrix.h b/deal.II/include/deal.II/lac/constraint_matrix.h index d46d327d6b..3219015fa1 100644 --- a/deal.II/include/deal.II/lac/constraint_matrix.h +++ b/deal.II/include/deal.II/lac/constraint_matrix.h @@ -1,7 +1,7 @@ // --------------------------------------------------------------------- // $Id$ // -// Copyright (C) 1998 - 2013 by the deal.II authors +// Copyright (C) 1998 - 2014 by the deal.II authors // // This file is part of the deal.II library. // @@ -1737,7 +1737,7 @@ distribute_local_to_global (const FullMatrix &local_matrix, // the actual implementation follows in the cm.templates.h file. distribute_local_to_global (local_matrix, local_vector, local_dof_indices, global_matrix, global_vector, use_inhomogeneities_for_rhs, - internal::bool2type::value>()); + dealii::internal::bool2type::value>()); } diff --git a/deal.II/include/deal.II/lac/parallel_vector.h b/deal.II/include/deal.II/lac/parallel_vector.h index db837d4983..7ccb1f9743 100644 --- a/deal.II/include/deal.II/lac/parallel_vector.h +++ b/deal.II/include/deal.II/lac/parallel_vector.h @@ -71,8 +71,11 @@ namespace parallel * Functions related to parallel functionality: * - The function compress() goes through the data associated * with ghost indices and communicates it to the owner process, which can - * then add/set it to the correct position. This can be used e.g. after + * then add it to the correct position. This can be used e.g. after * having run an assembly routine involving ghosts that fill this vector. + * Note that the @p insert mode of @p compress() does not set the + * elements included in ghost entries but simply discards them, assuming + * that the owning processor has set them to the desired value already. * - The update_ghost_values() function imports the data from * the owning processor to the ghost indices in order to provide read * access to the data associated with ghosts. @@ -92,7 +95,7 @@ namespace parallel * writing into ghost elements but only reading from them. This is in * order to avoid undesired ghost data artifacts when calling compress() * after modifying some vector entries. - * The current statues of the ghost entries (read mode or write mode) can + * The current status of the ghost entries (read mode or write mode) can * be queried by the method has_ghost_elements(), which returns * true exactly when ghost elements have been updated and * false otherwise, irrespective of the actual number of @@ -301,9 +304,9 @@ namespace parallel * both the element on the ghost site as well as the owning site), this * operation makes the assumption that all data is set correctly on the * owning processor. Upon call of compress(VectorOperation::insert), all - * ghost entries are therefore simply zeroed out (using - * zero_ghost_values()). In debug mode, a check is performed that makes - * sure that the data set is actually consistent between processors, + * ghost entries are thus simply zeroed out (using + * zero_ghost_values()). In debug mode, a check is performed for whether + * the data set is actually consistent between processors, * i.e., whenever a non-zero ghost element is found, it is compared to * the value on the owning processor and an exception is thrown if these * elements do not agree. @@ -424,9 +427,8 @@ namespace parallel /** * Return whether the vector contains only elements with value - * zero. This function is mainly for internal consistency checks and - * should seldom be used when not in debug mode since it uses quite some - * time. + * zero. This is a collective operation. This function is expensive, because + * potentially all elements have to be checked. */ bool all_zero () const; diff --git a/deal.II/include/deal.II/lac/petsc_parallel_vector.h b/deal.II/include/deal.II/lac/petsc_parallel_vector.h index bc3ee07627..eaf007917a 100644 --- a/deal.II/include/deal.II/lac/petsc_parallel_vector.h +++ b/deal.II/include/deal.II/lac/petsc_parallel_vector.h @@ -502,6 +502,14 @@ namespace PETScWrappers const bool scientific = true, const bool across = true) const; + /** + * @copydoc PETScWrappers::VectorBase::all_zero() + * + * @note This function overloads the one in the base class + * to make this a collective operation. + */ + bool all_zero () const; + protected: /** * Create a vector of length diff --git a/deal.II/include/deal.II/lac/petsc_vector_base.h b/deal.II/include/deal.II/lac/petsc_vector_base.h index 6de405f3b5..403a8ec8eb 100644 --- a/deal.II/include/deal.II/lac/petsc_vector_base.h +++ b/deal.II/include/deal.II/lac/petsc_vector_base.h @@ -626,12 +626,9 @@ namespace PETScWrappers const VectorBase &v); /** - * Return whether the vector contains - * only elements with value zero. This - * function is mainly for internal - * consistency checks and should - * seldom be used when not in debug - * mode since it uses quite some time. + * Return whether the vector contains only elements with value + * zero. This is a collective operation. This function is expensive, because + * potentially all elements have to be checked. */ bool all_zero () const; diff --git a/deal.II/include/deal.II/lac/sparsity_tools.h b/deal.II/include/deal.II/lac/sparsity_tools.h index 89b4a2b21c..55baf88362 100644 --- a/deal.II/include/deal.II/lac/sparsity_tools.h +++ b/deal.II/include/deal.II/lac/sparsity_tools.h @@ -52,152 +52,89 @@ namespace SparsityTools typedef types::global_dof_index size_type; /** - * Use the METIS partitioner to generate - * a partitioning of the degrees of - * freedom represented by this sparsity - * pattern. In effect, we view this - * sparsity pattern as a graph of - * connections between various degrees of - * freedom, where each nonzero entry in - * the sparsity pattern corresponds to an - * edge between two nodes in the - * connection graph. The goal is then to - * decompose this graph into groups of - * nodes so that a minimal number of - * edges are cut by the boundaries - * between node groups. This partitioning - * is done by METIS. Note that METIS can - * only partition symmetric sparsity - * patterns, and that of course the - * sparsity pattern has to be square. We - * do not check for symmetry of the - * sparsity pattern, since this is an - * expensive operation, but rather leave - * this as the responsibility of caller - * of this function. + * Use the METIS partitioner to generate a partitioning of the degrees of + * freedom represented by this sparsity pattern. In effect, we view this + * sparsity pattern as a graph of connections between various degrees of + * freedom, where each nonzero entry in the sparsity pattern corresponds to + * an edge between two nodes in the connection graph. The goal is then to + * decompose this graph into groups of nodes so that a minimal number of + * edges are cut by the boundaries between node groups. This partitioning is + * done by METIS. Note that METIS can only partition symmetric sparsity + * patterns, and that of course the sparsity pattern has to be square. We do + * not check for symmetry of the sparsity pattern, since this is an + * expensive operation, but rather leave this as the responsibility of + * caller of this function. * - * After calling this function, the - * output array will have values between - * zero and @p n_partitions-1 for each - * node (i.e. row or column of the + * After calling this function, the output array will have values between + * zero and @p n_partitions-1 for each node (i.e. row or column of the * matrix). * - * This function will generate an error - * if METIS is not installed unless - * @p n_partitions is one. I.e., you can - * write a program so that it runs in the - * single-processor single-partition case - * without METIS installed, and only - * requires METIS when multiple - * partitions are required. + * This function will generate an error if METIS is not installed unless @p + * n_partitions is one. I.e., you can write a program so that it runs in the + * single-processor single-partition case without METIS installed, and only + * requires METIS when multiple partitions are required. * - * Note that the sparsity pattern itself - * is not changed by calling this - * function. However, you will likely use - * the information generated by calling - * this function to renumber degrees of - * freedom, after which you will of - * course have to regenerate the sparsity - * pattern. + * Note that the sparsity pattern itself is not changed by calling this + * function. However, you will likely use the information generated by + * calling this function to renumber degrees of freedom, after which you + * will of course have to regenerate the sparsity pattern. * - * This function will rarely be called - * separately, since in finite element - * methods you will want to partition the - * mesh, not the matrix. This can be done - * by calling - * @p GridTools::partition_triangulation. + * This function will rarely be called separately, since in finite element + * methods you will want to partition the mesh, not the matrix. This can be + * done by calling @p GridTools::partition_triangulation. */ void partition (const SparsityPattern &sparsity_pattern, const unsigned int n_partitions, std::vector &partition_indices); /** - * For a given sparsity pattern, compute a - * re-enumeration of row/column indices - * based on the algorithm by Cuthill-McKee. + * For a given sparsity pattern, compute a re-enumeration of row/column + * indices based on the algorithm by Cuthill-McKee. * - * This algorithm is a graph renumbering - * algorithm in which we attempt to find a - * new numbering of all nodes of a graph - * based on their connectivity to other - * nodes (i.e. the edges that connect - * nodes). This connectivity is here - * represented by the sparsity pattern. In - * many cases within the library, the nodes - * represent degrees of freedom and edges - * are nonzero entries in a matrix, - * i.e. pairs of degrees of freedom that - * couple through the action of a bilinear - * form. + * This algorithm is a graph renumbering algorithm in which we attempt to + * find a new numbering of all nodes of a graph based on their connectivity + * to other nodes (i.e. the edges that connect nodes). This connectivity is + * here represented by the sparsity pattern. In many cases within the + * library, the nodes represent degrees of freedom and edges are nonzero + * entries in a matrix, i.e. pairs of degrees of freedom that couple through + * the action of a bilinear form. * - * The algorithms starts at a node, - * searches the other nodes for - * those which are coupled with the one we - * started with and numbers these in a - * certain way. It then finds the second - * level of nodes, namely those that couple - * with those of the previous level (which - * were those that coupled with the initial - * node) and numbers these. And so on. For - * the details of the algorithm, especially - * the numbering within each level, we - * refer the reader to the book of Schwarz - * (H. R. Schwarz: Methode der finiten + * The algorithms starts at a node, searches the other nodes for those which + * are coupled with the one we started with and numbers these in a certain + * way. It then finds the second level of nodes, namely those that couple + * with those of the previous level (which were those that coupled with the + * initial node) and numbers these. And so on. For the details of the + * algorithm, especially the numbering within each level, we refer the + * reader to the book of Schwarz (H. R. Schwarz: Methode der finiten * Elemente). * - * These algorithms have one major - * drawback: they require a good starting - * node, i.e. node that will have number - * zero in the output array. A starting - * node forming the initial level of nodes - * can thus be given by the user, e.g. by - * exploiting knowledge of the actual - * topology of the domain. It is also - * possible to give several starting - * indices, which may be used to simulate a - * simple upstream numbering (by giving the - * inflow nodes as starting values) or to - * make preconditioning faster (by letting - * the Dirichlet boundary indices be - * starting points). + * These algorithms have one major drawback: they require a good starting + * node, i.e. node that will have number zero in the output array. A + * starting node forming the initial level of nodes can thus be given by the + * user, e.g. by exploiting knowledge of the actual topology of the + * domain. It is also possible to give several starting indices, which may + * be used to simulate a simple upstream numbering (by giving the inflow + * nodes as starting values) or to make preconditioning faster (by letting + * the Dirichlet boundary indices be starting points). * - * If no starting index is given, one is - * chosen automatically, namely one with - * the smallest coordination number (the - * coordination number is the number of - * other nodes this node couples - * with). This node is usually located on - * the boundary of the domain. There is, - * however, large ambiguity in this when - * using the hierarchical meshes used in - * this library, since in most cases the - * computational domain is not approximated - * by tilting and deforming elements and by - * plugging together variable numbers of - * elements at vertices, but rather by - * hierarchical refinement. There is - * therefore a large number of nodes with - * equal coordination numbers. The - * renumbering algorithms will therefore - * not give optimal results. + * If no starting index is given, one is chosen automatically, namely one + * with the smallest coordination number (the coordination number is the + * number of other nodes this node couples with). This node is usually + * located on the boundary of the domain. There is, however, large ambiguity + * in this when using the hierarchical meshes used in this library, since in + * most cases the computational domain is not approximated by tilting and + * deforming elements and by plugging together variable numbers of elements + * at vertices, but rather by hierarchical refinement. There is therefore a + * large number of nodes with equal coordination numbers. The renumbering + * algorithms will therefore not give optimal results. * - * If the graph has two or more - * unconnected components and if no - * starting indices are given, the - * algorithm will number each - * component - * consecutively. However, this - * requires the determination of a - * starting index for each - * component; as a consequence, the - * algorithm will produce an - * exception if starting indices - * are given, taking the latter as - * an indication that the caller of - * the function would like to - * override the part of the - * algorithm that chooses starting - * indices. + * If the graph has two or more unconnected components and if no starting + * indices are given, the algorithm will number each component + * consecutively. However, this requires the determination of a starting + * index for each component; as a consequence, the algorithm will produce an + * exception if starting indices are given, taking the latter as an + * indication that the caller of the function would like to override the + * part of the algorithm that chooses starting indices. */ void reorder_Cuthill_McKee (const SparsityPattern &sparsity, @@ -207,45 +144,26 @@ namespace SparsityTools #ifdef DEAL_II_WITH_MPI /** - * Communciate rows in a compressed - * sparsity pattern over MPI. + * Communciate rows in a compressed sparsity pattern over MPI. * - * @param csp is the sparsity - * pattern that has been built - * locally and for which we need to - * exchange entries with other - * processors to make sure that - * each processor knows all the - * elements of the rows of a matrix - * it stores and that may - * eventually be written to. This - * sparsity pattern will be changed - * as a result of this function: - * All entries in rows that belong - * to a different processor are - * sent to them and added there. + * @param csp is the sparsity pattern that has been built locally and for + * which we need to exchange entries with other processors to make sure that + * each processor knows all the elements of the rows of a matrix it stores + * and that may eventually be written to. This sparsity pattern will be + * changed as a result of this function: All entries in rows that belong to + * a different processor are sent to them and added there. * * @param rows_per_cpu determines ownership of rows. * - * @param mpi_comm is the MPI - * communicator that is shared - * between the processors that all - * participate in this operation. + * @param mpi_comm is the MPI communicator that is shared between the + * processors that all participate in this operation. * - * @param myrange indicates the - * range of elements stored locally - * and should be the one used in - * the constructor of the - * CompressedSimpleSparsityPattern. - * This should be the locally relevant set. - * Only - * rows contained in myrange are - * checked in csp for transfer. - * This function needs to be used - * with - * PETScWrappers::MPI::SparseMatrix - * for it to work correctly in a - * parallel computation. + * @param myrange indicates the range of elements stored locally and should + * be the one used in the constructor of the + * CompressedSimpleSparsityPattern. This should be the locally relevant + * set. Only rows contained in myrange are checked in csp for transfer. + * This function needs to be used with PETScWrappers::MPI::SparseMatrix for + * it to work correctly in a parallel computation. */ template void distribute_sparsity_pattern(CSP_t &csp, diff --git a/deal.II/include/deal.II/lac/trilinos_block_sparse_matrix.h b/deal.II/include/deal.II/lac/trilinos_block_sparse_matrix.h index 99d19b118a..1464bff090 100644 --- a/deal.II/include/deal.II/lac/trilinos_block_sparse_matrix.h +++ b/deal.II/include/deal.II/lac/trilinos_block_sparse_matrix.h @@ -194,7 +194,8 @@ namespace TrilinosWrappers */ template void reinit (const std::vector &input_maps, - const BlockSparsityType &block_sparsity_pattern); + const BlockSparsityType &block_sparsity_pattern, + const bool exchange_data = false); /** * Resize the matrix, by using an @@ -207,7 +208,8 @@ namespace TrilinosWrappers template void reinit (const std::vector &input_maps, const BlockSparsityType &block_sparsity_pattern, - const MPI_Comm &communicator = MPI_COMM_WORLD); + const MPI_Comm &communicator = MPI_COMM_WORLD, + const bool exchange_data = false); /** * Resize the matrix and initialize it diff --git a/deal.II/include/deal.II/lac/trilinos_sparse_matrix.h b/deal.II/include/deal.II/lac/trilinos_sparse_matrix.h index 2a21d5daa9..c5ab727b66 100644 --- a/deal.II/include/deal.II/lac/trilinos_sparse_matrix.h +++ b/deal.II/include/deal.II/lac/trilinos_sparse_matrix.h @@ -46,6 +46,8 @@ # include "Epetra_SerialComm.h" # endif +class Epetra_Export; + DEAL_II_NAMESPACE_OPEN // forward declarations @@ -54,6 +56,7 @@ template class BlockMatrixBase; template class SparseMatrix; class SparsityPattern; + namespace TrilinosWrappers { // forward declarations @@ -456,21 +459,26 @@ namespace TrilinosWrappers * matrix row at the same time can lead to data races and must be explicitly * avoided by the user. However, it is possible to access different * rows of the matrix from several threads simultaneously under the - * following two conditions: + * following three conditions: *
      *
    • The matrix uses only one MPI process. + *
    • The matrix has been initialized with the reinit() method + * with a CompressedSimpleSparsityPattern (that includes the set of locally + * relevant rows, i.e., the rows that an assembly routine will possibly + * write into). *
    • The matrix has been initialized from a * TrilinosWrappers::SparsityPattern object that in turn has been * initialized with the reinit function specifying three index sets, one * for the rows, one for the columns and for the larger set of @p - * writeable_rows, and the operation is an addition. Note that all other - * reinit methods and constructors of TrilinosWrappers::SparsityPattern - * will result in a matrix that needs to allocate off-processor entries on - * demand, which breaks thread-safety. Of course, using the respective - * reinit method for the block Trilinos sparsity pattern and block matrix - * also results in thread-safety. + * writeable_rows, and the operation is an addition. *
    * + * Note that all other reinit methods and constructors of + * TrilinosWrappers::SparsityPattern will result in a matrix that needs to + * allocate off-processor entries on demand, which breaks thread-safety. Of + * course, using the respective reinit method for the block Trilinos + * sparsity pattern and block matrix also results in thread-safety. + * * @ingroup TrilinosWrappers * @ingroup Matrix1 * @author Martin Kronbichler, Wolfgang Bangerth, 2008, 2009 @@ -720,6 +728,11 @@ namespace TrilinosWrappers * set, each processor just sets the elements in the sparsity pattern that * belong to its rows. * + * If the sparsity pattern given to this function is of type + * CompressedSimpleSparsity pattern, then a matrix will be created that + * allows several threads to write into different rows of the matrix at + * the same also with MPI, as opposed to most other reinit() methods. + * * This is a collective operation that needs to be called on all * processors in order to avoid a dead lock. */ @@ -1844,6 +1857,11 @@ namespace TrilinosWrappers */ std_cxx1x::shared_ptr nonlocal_matrix; + /** + * An export object used to communicate the nonlocal matrix. + */ + std_cxx1x::shared_ptr nonlocal_matrix_exporter; + /** * Trilinos doesn't allow to mix additions to matrix entries and * overwriting them (to make synchronisation of %parallel computations @@ -2737,11 +2755,21 @@ namespace TrilinosWrappers for (TrilinosWrappers::types::int_type i=0; i(row)), - n_indices, - indices); + std::cout << "Matrix row " + << (row_partitioner().MyGID(static_cast(row)) == false ? "(nonlocal part)" : "") + << " has the following indices:" << std::endl; + std::vector indices; + const Epetra_CrsGraph* graph = + (nonlocal_matrix.get() != 0 && + row_partitioner().MyGID(static_cast(row)) == false) ? + &nonlocal_matrix->Graph() : &matrix->Graph(); + + indices.resize(graph->NumGlobalIndices(static_cast(row))); + int n_indices = 0; + graph->ExtractGlobalRowCopy(static_cast(row), + indices.size(), n_indices, &indices[0]); + AssertDimension(static_cast(n_indices), indices.size()); + for (TrilinosWrappers::types::int_type i=0; i*> (&fe) != 0) && (line * fe.degree <= i) && (i < (line + 1) * fe.degree))) { diff --git a/deal.II/source/base/index_set.cc b/deal.II/source/base/index_set.cc index ce4b5bcfb7..17d1c555b7 100644 --- a/deal.II/source/base/index_set.cc +++ b/deal.II/source/base/index_set.cc @@ -28,16 +28,48 @@ DEAL_II_NAMESPACE_OPEN + +void +IndexSet::add_range (const types::global_dof_index begin, + const types::global_dof_index end) +{ + Assert ((begin < index_space_size) + || + ((begin == index_space_size) && (end == index_space_size)), + ExcIndexRangeType (begin, 0, index_space_size)); + Assert (end <= index_space_size, + ExcIndexRangeType (end, 0, index_space_size+1)); + Assert (begin <= end, + ExcIndexRangeType (begin, 0, end)); + + if (begin != end) + { + const Range new_range(begin,end); + + // the new index might be larger than the last index present in the + // ranges. Then we can skip the binary search + if (ranges.size() == 0 || begin > ranges.back().end) + ranges.push_back(new_range); + else + ranges.insert (Utilities::lower_bound (ranges.begin(), + ranges.end(), + new_range), + new_range); + is_compressed = false; + } +} + + + void IndexSet::do_compress () const { - // see if any of the - // contiguous ranges can be - // merged. since they are sorted by - // their first index, determining + // see if any of the contiguous ranges can be merged. do not use + // std::vector::erase in-place as it is quadratic in the number of + // ranges. since the ranges are sorted by their first index, determining // overlap isn't all that hard - for (std::vector::iterator - i = ranges.begin(); + std::vector::iterator store = ranges.begin(); + for (std::vector::iterator i = ranges.begin(); i != ranges.end(); ) { std::vector::iterator @@ -47,37 +79,29 @@ IndexSet::do_compress () const types::global_dof_index first_index = i->begin; types::global_dof_index last_index = i->end; - // see if we can merge any of - // the following ranges - bool can_merge = false; + // see if we can merge any of the following ranges while (next != ranges.end() && (next->begin <= last_index)) { last_index = std::max (last_index, next->end); ++next; - can_merge = true; } + i = next; - if (can_merge == true) - { - // delete the old ranges - // and insert the new range - // in place of the previous - // one - *i = Range(first_index, last_index); - i = ranges.erase (i+1, next); - } - else - ++i; + // store the new range in the slot we last occupied + *store = Range(first_index, last_index); + ++store; + } + // use a compact array with exactly the right amount of storage + if (store != ranges.end()) + { + std::vector new_ranges(ranges.begin(), store); + ranges.swap(new_ranges); } - - // now compute indices within set and the - // range with most elements + // now compute indices within set and the range with most elements types::global_dof_index next_index = 0, largest_range_size = 0; - for (std::vector::iterator - i = ranges.begin(); - i != ranges.end(); + for (std::vector::iterator i = ranges.begin(); i != ranges.end(); ++i) { Assert(i->begin < i->end, ExcInternalError()); @@ -92,11 +116,8 @@ IndexSet::do_compress () const } is_compressed = true; - // check that next_index is - // correct. needs to be after the - // previous statement because we - // otherwise will get into an - // endless loop + // check that next_index is correct. needs to be after the previous + // statement because we otherwise will get into an endless loop Assert (next_index == n_elements(), ExcInternalError()); } @@ -119,18 +140,15 @@ IndexSet::operator & (const IndexSet &is) const && (r2 != is.ranges.end())) { - // if r1 and r2 do not overlap - // at all, then move the - // pointer that sits to the - // left of the other up by one + // if r1 and r2 do not overlap at all, then move the pointer that sits + // to the left of the other up by one if (r1->end <= r2->begin) ++r1; else if (r2->end <= r1->begin) ++r2; else { - // the ranges must overlap - // somehow + // the ranges must overlap somehow Assert (((r1->begin <= r2->begin) && (r1->end > r2->begin)) || @@ -138,21 +156,15 @@ IndexSet::operator & (const IndexSet &is) const (r2->end > r1->begin)), ExcInternalError()); - // add the overlapping - // range to the result + // add the overlapping range to the result result.add_range (std::max (r1->begin, r2->begin), std::min (r1->end, r2->end)); - // now move that iterator - // that ends earlier one - // up. note that it has to - // be this one because a - // subsequent range may - // still have a chance of - // overlapping with the - // range that ends later + // now move that iterator that ends earlier one up. note that it has + // to be this one because a subsequent range may still have a chance + // of overlapping with the range that ends later if (r1->end <= r2->end) ++r1; else @@ -166,15 +178,6 @@ IndexSet::operator & (const IndexSet &is) const -unsigned int -IndexSet::n_intervals () const -{ - compress (); - return ranges.size(); -} - - - IndexSet IndexSet::get_view (const types::global_dof_index begin, const types::global_dof_index end) const @@ -209,6 +212,131 @@ IndexSet::get_view (const types::global_dof_index begin, +void +IndexSet::subtract_set (const IndexSet &other) +{ + compress(); + other.compress(); + is_compressed = false; + + + // we save new ranges to be added to our IndexSet in an temporary list and + // add all of them in one go at the end. This is necessary because a growing + // ranges vector invalidates iterators. + std::list temp_list; + + std::vector::iterator own_it = ranges.begin(); + std::vector::iterator other_it = other.ranges.begin(); + + while (own_it != ranges.end() && other_it != other.ranges.end()) + { + //advance own iterator until we get an overlap + if (own_it->end <= other_it->begin) + { + ++own_it; + continue; + } + //we are done with other_it, so advance + if (own_it->begin >= other_it->end) + { + ++other_it; + continue; + } + + //Now own_it and other_it overlap. First save the part of own_it that + //is before other_it (if not empty). + if (own_it->begin < other_it->begin) + { + Range r(own_it->begin, other_it->begin); + r.nth_index_in_set = 0; //fix warning of unused variable + temp_list.push_back(r); + } + // change own_it to the sub range behind other_it. Do not delete own_it + // in any case. As removal would invalidate iterators, we just shrink + // the range to an empty one. + own_it->begin = other_it->end; + if (own_it->begin > own_it->end) + { + own_it->begin = own_it->end; + ++own_it; + } + + // continue without advancing iterators, the right one will be advanced + // next. + } + + // Now delete all empty ranges we might + // have created. + for (std::vector::iterator it = ranges.begin(); + it != ranges.end(); ) + { + if (it->begin >= it->end) + it = ranges.erase(it); + else + ++it; + } + + // done, now add the temporary ranges + for (std::list::iterator it = temp_list.begin(); + it != temp_list.end(); + ++it) + add_range(it->begin, it->end); + + compress(); +} + + + +void +IndexSet::add_indices(const IndexSet &other, + const unsigned int offset) +{ + if ((this == &other) && (offset == 0)) + return; + + compress(); + other.compress(); + + std::vector::const_iterator r1 = ranges.begin(), + r2 = other.ranges.begin(); + + std::vector new_ranges; + // just get the start and end of the ranges right in this method, everything + // else will be done in compress() + while (r1 != ranges.end() || r2 != other.ranges.end()) + { + // the two ranges do not overlap or we are at the end of one of the + // ranges + if (r2 == other.ranges.end() || + (r1 != ranges.end() && r1->end < (r2->begin+offset))) + { + new_ranges.push_back(*r1); + ++r1; + } + else if (r1 == ranges.end() || (r2->end+offset) < r1->begin) + { + new_ranges.push_back(Range(r2->begin+offset,r2->end+offset)); + ++r2; + } + else + { + // ok, we do overlap, so just take the combination of the current + // range (do not bother to merge with subsequent ranges) + Range next(std::min(r1->begin, r2->begin+offset), + std::max(r1->end, r2->end+offset)); + new_ranges.push_back(next); + ++r1; + ++r2; + } + } + ranges.swap(new_ranges); + + is_compressed = false; + compress(); +} + + + void IndexSet::write(std::ostream &out) const { @@ -277,87 +405,6 @@ IndexSet::block_read(std::istream &in) -void -IndexSet::subtract_set (const IndexSet &other) -{ - compress(); - other.compress(); - is_compressed = false; - - - // we save new ranges to be added to our - // IndexSet in an temporary list and add - // all of them in one go at the end. This - // is necessary because a growing ranges - // vector invalidates iterators. - std::list temp_list; - - std::vector::iterator own_it = ranges.begin(); - std::vector::iterator other_it = other.ranges.begin(); - - while (own_it != ranges.end() && other_it != other.ranges.end()) - { - //advance own iterator until we get an - //overlap - if (own_it->end <= other_it->begin) - { - ++own_it; - continue; - } - //we are done with other_it, so advance - if (own_it->begin >= other_it->end) - { - ++other_it; - continue; - } - - //Now own_it and other_it overlap. - //First save the part of own_it that is - //before other_it (if not empty). - if (own_it->begin < other_it->begin) - { - Range r(own_it->begin, other_it->begin); - r.nth_index_in_set = 0; //fix warning of unused variable - temp_list.push_back(r); - } - // change own_it to the sub range - // behind other_it. Do not delete - // own_it in any case. As removal would - // invalidate iterators, we just shrink - // the range to an empty one. - own_it->begin = other_it->end; - if (own_it->begin > own_it->end) - { - own_it->begin = own_it->end; - ++own_it; - } - - // continue without advancing - // iterators, the right one will be - // advanced next. - } - - // Now delete all empty ranges we might - // have created. - for (std::vector::iterator it = ranges.begin(); - it != ranges.end(); ) - { - if (it->begin >= it->end) - it = ranges.erase(it); - else - ++it; - } - - // done, now add the temporary ranges - for (std::list::iterator it = temp_list.begin(); - it != temp_list.end(); - ++it) - add_range(it->begin, it->end); - - compress(); -} - - void IndexSet::fill_index_vector(std::vector &indices) const { compress(); diff --git a/deal.II/source/dofs/dof_accessor_get.cc b/deal.II/source/dofs/dof_accessor_get.cc index 9b9ca8b7b8..427e7e9f2c 100644 --- a/deal.II/source/dofs/dof_accessor_get.cc +++ b/deal.II/source/dofs/dof_accessor_get.cc @@ -1,7 +1,7 @@ // --------------------------------------------------------------------- // $Id$ // -// Copyright (C) 1998 - 2013 by the deal.II authors +// Copyright (C) 1998 - 2014 by the deal.II authors // // This file is part of the deal.II library. // @@ -43,27 +43,72 @@ template void DoFCellAccessor:: get_interpolated_dof_values (const InputVector &values, - Vector &interpolated_values) const + Vector &interpolated_values, + const unsigned int fe_index) const { - const FiniteElement &fe = this->get_fe(); - const unsigned int dofs_per_cell = fe.dofs_per_cell; - - Assert (this->dof_handler != 0, - typename BaseClass::ExcInvalidObject()); - Assert (&fe != 0, - typename BaseClass::ExcInvalidObject()); - Assert (interpolated_values.size() == dofs_per_cell, - typename BaseClass::ExcVectorDoesNotMatch()); - Assert (values.size() == this->dof_handler->n_dofs(), - typename BaseClass::ExcVectorDoesNotMatch()); - if (!this->has_children()) // if this cell has no children: simply return the exact values on this - // cell - this->get_dof_values (values, interpolated_values); + // cell unless the finite element we need to interpolate to is different than + // the one we have on the current cell + { + if ((dynamic_cast*> + (this->dof_handler) + != 0) + || + (fe_index == this->active_fe_index()) + || + (fe_index == DH::default_fe_index)) + this->get_dof_values (values, interpolated_values); + else + { + // well, here we need to first get the values from the current + // cell and then interpolate it to the element requested. this + // can clearly only happen for hp::DoFHandler objects + Vector tmp (this->get_fe().dofs_per_cell); + this->get_dof_values (values, tmp); + + FullMatrix interpolation (this->dof_handler->get_fe()[fe_index].dofs_per_cell, + this->get_fe().dofs_per_cell); + this->dof_handler->get_fe()[fe_index].get_interpolation_matrix (this->get_fe(), + interpolation); + interpolation.vmult (interpolated_values, tmp); + } + } else - // otherwise clobber them from the children + // otherwise obtain them from the children { + // we are on a non-active cell. these do not have any finite + // element associated with them in the hp context (in the non-hp + // context, we can simply assume that the FE space to which we + // want to interpolate is the same as for all elements in the + // mesh). consequently, we cannot interpolate from children's FE + // space to this cell's (unknown) FE space unless an explicit + // fe_index is given + Assert ((dynamic_cast*> + (this->dof_handler) + != 0) + || + (fe_index != DH::default_fe_index), + ExcMessage ("You cannot call this function on non-active cells " + "of hp::DoFHandler objects unless you provide an explicit " + "finite element index because they do not have naturally " + "associated finite element spaces associated: degrees " + "of freedom are only distributed on active cells for which " + "the active_fe_index has been set.")); + + const FiniteElement &fe = this->get_dof_handler().get_fe()[fe_index]; + const unsigned int dofs_per_cell = fe.dofs_per_cell; + + Assert (this->dof_handler != 0, + typename BaseClass::ExcInvalidObject()); + Assert (&fe != 0, + typename BaseClass::ExcInvalidObject()); + Assert (interpolated_values.size() == dofs_per_cell, + typename BaseClass::ExcVectorDoesNotMatch()); + Assert (values.size() == this->dof_handler->n_dofs(), + typename BaseClass::ExcVectorDoesNotMatch()); + + Vector tmp1(dofs_per_cell); Vector tmp2(dofs_per_cell); @@ -101,9 +146,12 @@ get_interpolated_dof_values (const InputVector &values, for (unsigned int child=0; childn_children(); ++child) { // get the values from the present child, if necessary by - // interpolation itself + // interpolation itself either from its own children or + // by interpolating from the finite element on an active + // child to the finite element space requested here this->child(child)->get_interpolated_dof_values (values, - tmp1); + tmp1, + fe_index); // interpolate these to the mother cell fe.get_restriction_matrix(child, this->refinement_case()).vmult (tmp2, tmp1); diff --git a/deal.II/source/dofs/dof_accessor_get.inst.in b/deal.II/source/dofs/dof_accessor_get.inst.in index 75d1009f06..c2e4b79151 100644 --- a/deal.II/source/dofs/dof_accessor_get.inst.in +++ b/deal.II/source/dofs/dof_accessor_get.inst.in @@ -21,14 +21,16 @@ for (VEC : SERIAL_VECTORS; SCALAR : REAL_SCALARS; deal_II_dimension : DIMENSIONS template void DoFCellAccessor, lda>::get_interpolated_dof_values - (const VEC&, Vector&) const; + (const VEC&, Vector&, + const unsigned int fe_index) const; #if deal_II_dimension != 3 template void DoFCellAccessor, lda>::get_interpolated_dof_values - (const VEC&, Vector&) const; + (const VEC&, Vector&, + const unsigned int fe_index) const; #endif @@ -37,7 +39,8 @@ for (VEC : SERIAL_VECTORS; SCALAR : REAL_SCALARS; deal_II_dimension : DIMENSIONS template void DoFCellAccessor, lda>::get_interpolated_dof_values - (const VEC&, Vector&) const; + (const VEC&, Vector&, + const unsigned int fe_index) const; #endif @@ -49,14 +52,16 @@ for (VEC : SERIAL_VECTORS; SCALAR : REAL_SCALARS; deal_II_dimension : DIMENSIONS template void DoFCellAccessor, lda>::get_interpolated_dof_values - (const VEC&, Vector&) const; + (const VEC&, Vector&, + const unsigned int fe_index) const; #if deal_II_dimension != 3 template void DoFCellAccessor, lda>::get_interpolated_dof_values - (const VEC&, Vector&) const; + (const VEC&, Vector&, + const unsigned int fe_index) const; #endif @@ -65,7 +70,8 @@ for (VEC : SERIAL_VECTORS; SCALAR : REAL_SCALARS; deal_II_dimension : DIMENSIONS template void DoFCellAccessor, lda>::get_interpolated_dof_values - (const VEC&, Vector&) const; + (const VEC&, Vector&, + const unsigned int fe_index) const; #endif } diff --git a/deal.II/source/dofs/dof_accessor_set.cc b/deal.II/source/dofs/dof_accessor_set.cc index f11fc845a0..bfbedda11c 100644 --- a/deal.II/source/dofs/dof_accessor_set.cc +++ b/deal.II/source/dofs/dof_accessor_set.cc @@ -1,7 +1,7 @@ // --------------------------------------------------------------------- // $Id$ // -// Copyright (C) 1998 - 2013 by the deal.II authors +// Copyright (C) 1998 - 2014 by the deal.II authors // // This file is part of the deal.II library. // @@ -44,25 +44,45 @@ template void DoFCellAccessor:: set_dof_values_by_interpolation (const Vector &local_values, - OutputVector &values) const + OutputVector &values, + const unsigned int fe_index) const { - const unsigned int dofs_per_cell = this->get_fe().dofs_per_cell; - - Assert (this->dof_handler != 0, - typename BaseClass::ExcInvalidObject()); - Assert (&this->get_fe() != 0, - typename BaseClass::ExcInvalidObject()); - Assert (local_values.size() == dofs_per_cell, - typename BaseClass::ExcVectorDoesNotMatch()); - Assert (values.size() == this->dof_handler->n_dofs(), - typename BaseClass::ExcVectorDoesNotMatch()); - if (!this->has_children()) // if this cell has no children: simply set the values on this cell this->set_dof_values (local_values, values); else // otherwise distribute them to the children { + // we are on a non-active cell. these do not have any finite + // element associated with them in the hp context (in the non-hp + // context, we can simply assume that the FE space to from which we + // want to interpolate is the same as for all elements in the + // mesh). consequently, we cannot interpolate to children's FE + // space from this cell's (unknown) FE space unless an explicit + // fe_index is given + Assert ((dynamic_cast*> + (this->dof_handler) + != 0) + || + (fe_index != DH::default_fe_index), + ExcMessage ("You cannot call this function on non-active cells " + "of hp::DoFHandler objects unless you provide an explicit " + "finite element index because they do not have naturally " + "associated finite element spaces associated: degrees " + "of freedom are only distributed on active cells for which " + "the active_fe_index has been set.")); + + const unsigned int dofs_per_cell = this->get_fe().dofs_per_cell; + + Assert (this->dof_handler != 0, + typename BaseClass::ExcInvalidObject()); + Assert (&this->get_fe() != 0, + typename BaseClass::ExcInvalidObject()); + Assert (local_values.size() == dofs_per_cell, + typename BaseClass::ExcVectorDoesNotMatch()); + Assert (values.size() == this->dof_handler->n_dofs(), + typename BaseClass::ExcVectorDoesNotMatch()); + Vector tmp(dofs_per_cell); for (unsigned int child=0; childn_children(); ++child) diff --git a/deal.II/source/dofs/dof_accessor_set.inst.in b/deal.II/source/dofs/dof_accessor_set.inst.in index 74948318e8..4b54558287 100644 --- a/deal.II/source/dofs/dof_accessor_set.inst.in +++ b/deal.II/source/dofs/dof_accessor_set.inst.in @@ -21,14 +21,16 @@ for (VEC : SERIAL_VECTORS; SCALAR : REAL_SCALARS; deal_II_dimension : DIMENSIONS template void DoFCellAccessor, lda>::set_dof_values_by_interpolation - (const Vector&, VEC&) const; + (const Vector&, VEC&, + const unsigned int fe_index) const; #if deal_II_dimension != 3 template void DoFCellAccessor, lda>::set_dof_values_by_interpolation - (const Vector&, VEC&) const; + (const Vector&, VEC&, + const unsigned int fe_index) const; #endif @@ -37,7 +39,8 @@ for (VEC : SERIAL_VECTORS; SCALAR : REAL_SCALARS; deal_II_dimension : DIMENSIONS template void DoFCellAccessor, lda>::set_dof_values_by_interpolation - (const Vector&, VEC&) const; + (const Vector&, VEC&, + const unsigned int fe_index) const; #endif @@ -49,14 +52,16 @@ for (VEC : SERIAL_VECTORS; SCALAR : REAL_SCALARS; deal_II_dimension : DIMENSIONS template void DoFCellAccessor, lda>::set_dof_values_by_interpolation - (const Vector&, VEC&) const; + (const Vector&, VEC&, + const unsigned int fe_index) const; #if deal_II_dimension != 3 template void DoFCellAccessor, lda>::set_dof_values_by_interpolation - (const Vector&, VEC&) const; + (const Vector&, VEC&, + const unsigned int fe_index) const; #endif @@ -65,7 +70,8 @@ for (VEC : SERIAL_VECTORS; SCALAR : REAL_SCALARS; deal_II_dimension : DIMENSIONS template void DoFCellAccessor, lda>::set_dof_values_by_interpolation - (const Vector&, VEC&) const; + (const Vector&, VEC&, + const unsigned int fe_index) const; #endif } diff --git a/deal.II/source/dofs/dof_handler_policy.cc b/deal.II/source/dofs/dof_handler_policy.cc index 3e71bbd9c1..c8bb6d84f0 100644 --- a/deal.II/source/dofs/dof_handler_policy.cc +++ b/deal.II/source/dofs/dof_handler_policy.cc @@ -1892,8 +1892,8 @@ namespace internal unsigned int sent=needs_to_get_cells.size(); unsigned int recv=senders.size(); - MPI_Reduce(&sent, &sum_send, 1, MPI_UNSIGNED, MPI_SUM, 56345, tr->get_communicator()); - MPI_Reduce(&recv, &sum_recv, 1, MPI_UNSIGNED, MPI_SUM, 56346, tr->get_communicator()); + MPI_Allreduce(&sent, &sum_send, 1, MPI_UNSIGNED, MPI_SUM, tr->get_communicator()); + MPI_Allreduce(&recv, &sum_recv, 1, MPI_UNSIGNED, MPI_SUM, tr->get_communicator()); Assert(sum_send==sum_recv, ExcInternalError()); } #endif diff --git a/deal.II/source/dofs/dof_tools.cc b/deal.II/source/dofs/dof_tools.cc index 15beb53ea5..e0315e5533 100644 --- a/deal.II/source/dofs/dof_tools.cc +++ b/deal.II/source/dofs/dof_tools.cc @@ -1000,19 +1000,44 @@ namespace DoFTools n_selected_dofs += std::count (dofs_by_component.begin(), dofs_by_component.end(), i); + // Find local numbering within the selected components + const IndexSet &locally_owned_dofs = dof_handler.locally_owned_dofs(); + std::vector component_numbering(locally_owned_dofs.n_elements(), + numbers::invalid_unsigned_int); + for (unsigned int i=0, count=0; i(n_selected_dofs, false)); - std::vector component_list (n_components, 0); - for (unsigned int d=0; d + fe_collection (dof_handler.get_fe()); + std::vector > element_constant_modes; + for (unsigned int f=0; f dof_indices; + for (; cell!=endc; ++cell) + if (cell->is_locally_owned()) { - constant_modes[localized_component[dofs_by_component[i]]][counter] = true; - ++counter; + dof_indices.resize(cell->get_fe().dofs_per_cell); + cell->get_dof_indices(dof_indices); + + for (unsigned int i=0; iactive_fe_index()](comp,i); + } } } diff --git a/deal.II/source/dofs/dof_tools_sparsity.cc b/deal.II/source/dofs/dof_tools_sparsity.cc index c48bf2f677..6f97a33e9a 100644 --- a/deal.II/source/dofs/dof_tools_sparsity.cc +++ b/deal.II/source/dofs/dof_tools_sparsity.cc @@ -584,17 +584,20 @@ namespace DoFTools constraints.add_entries_local_to_global (dofs_on_other_cell, dofs_on_this_cell, sparsity, keep_constrained_dofs); + // only need to add this when the neighbor is not + // owned by the current processor, otherwise we add + // the entries for the neighbor there + if (sub_neighbor->subdomain_id() != cell->subdomain_id()) + constraints.add_entries_local_to_global + (dofs_on_other_cell, sparsity, keep_constrained_dofs); } } else { // Refinement edges are taken care of by coarser // cells - - // TODO: in the distributed case, we miss out the - // constraints when the neighbor cell is coarser, but - // only the current cell is owned locally! - if (cell->neighbor_is_coarser(face)) + if (cell->neighbor_is_coarser(face) && + neighbor->subdomain_id() == cell->subdomain_id()) continue; const unsigned int n_dofs_on_neighbor @@ -613,11 +616,15 @@ namespace DoFTools // around if (!cell->neighbor(face)->active() || - (cell->neighbor(face)->subdomain_id() != - cell->subdomain_id())) - constraints.add_entries_local_to_global - (dofs_on_other_cell, dofs_on_this_cell, - sparsity, keep_constrained_dofs); + (neighbor->subdomain_id() != cell->subdomain_id())) + { + constraints.add_entries_local_to_global + (dofs_on_other_cell, dofs_on_this_cell, + sparsity, keep_constrained_dofs); + if (neighbor->subdomain_id() != cell->subdomain_id()) + constraints.add_entries_local_to_global + (dofs_on_other_cell, sparsity, keep_constrained_dofs); + } } } } diff --git a/deal.II/source/fe/fe.cc b/deal.II/source/fe/fe.cc index 43db5378c1..165e5da3ab 100644 --- a/deal.II/source/fe/fe.cc +++ b/deal.II/source/fe/fe.cc @@ -1087,6 +1087,7 @@ FiniteElement::unit_face_support_point (const unsigned int index) } + template bool FiniteElement::has_support_on_face ( @@ -1097,6 +1098,17 @@ FiniteElement::has_support_on_face ( } + +template +Table<2,bool> +FiniteElement::get_constant_modes () const +{ + Assert (false, ExcNotImplemented()); + return Table<2,bool>(this->n_components(), this->dofs_per_cell); +} + + + template void FiniteElement::interpolate( diff --git a/deal.II/source/fe/fe_dgp.cc b/deal.II/source/fe/fe_dgp.cc index 1c4d07bc3e..ca52e4f149 100644 --- a/deal.II/source/fe/fe_dgp.cc +++ b/deal.II/source/fe/fe_dgp.cc @@ -237,6 +237,17 @@ FE_DGP::has_support_on_face (const unsigned int, +template +Table<2,bool> +FE_DGP::get_constant_modes () const +{ + Table<2,bool> constant_modes(1, this->dofs_per_cell); + constant_modes(0,0) = true; + return constant_modes; +} + + + template std::size_t FE_DGP::memory_consumption () const diff --git a/deal.II/source/fe/fe_dgq.cc b/deal.II/source/fe/fe_dgq.cc index 7b23f08e94..c3a5c523d5 100644 --- a/deal.II/source/fe/fe_dgq.cc +++ b/deal.II/source/fe/fe_dgq.cc @@ -671,6 +671,19 @@ FE_DGQ::has_support_on_face (const unsigned int shape_index, +template +Table<2,bool> +FE_DGQ::get_constant_modes () const +{ + Table<2,bool> constant_modes(1, this->dofs_per_cell); + for (unsigned int i=0; idofs_per_cell; ++i) + constant_modes(0,i) = true; + return constant_modes; +} + + + + template std::size_t FE_DGQ::memory_consumption () const diff --git a/deal.II/source/fe/fe_face.cc b/deal.II/source/fe/fe_face.cc index 1a21a6802d..728a6d2498 100644 --- a/deal.II/source/fe/fe_face.cc +++ b/deal.II/source/fe/fe_face.cc @@ -288,6 +288,18 @@ compare_for_face_domination (const FiniteElement &fe_other) const +template +Table<2,bool> +FE_FaceQ::get_constant_modes () const +{ + Table<2,bool> constant_modes(1, this->dofs_per_cell); + for (unsigned int i=0; idofs_per_cell; ++i) + constant_modes(0,i) = true; + return constant_modes; +} + + + // --------------------------------------- FE_FaceP -------------------------- template @@ -500,6 +512,19 @@ get_subface_interpolation_matrix (const FiniteElement &x_source_fe } + +template +Table<2,bool> +FE_FaceP::get_constant_modes () const +{ + Table<2,bool> constant_modes(1, this->dofs_per_cell); + for (unsigned int face=0; face::faces_per_cell; ++face) + constant_modes(0, face*this->dofs_per_face) = true; + return constant_modes; +} + + + // explicit instantiations #include "fe_face.inst" diff --git a/deal.II/source/fe/fe_nedelec.cc b/deal.II/source/fe/fe_nedelec.cc index f14d895076..61111bb018 100644 --- a/deal.II/source/fe/fe_nedelec.cc +++ b/deal.II/source/fe/fe_nedelec.cc @@ -5469,6 +5469,19 @@ const } + +template +Table<2,bool> +FE_Nedelec::get_constant_modes() const +{ + Table<2,bool> constant_modes(dim, this->dofs_per_cell); + for (unsigned int d=0; ddofs_per_cell; ++i) + constant_modes(d,i) = true; + return constant_modes; +} + + template std::size_t FE_Nedelec::memory_consumption () const diff --git a/deal.II/source/fe/fe_q_base.cc b/deal.II/source/fe/fe_q_base.cc index 10db7b4839..7212212063 100644 --- a/deal.II/source/fe/fe_q_base.cc +++ b/deal.II/source/fe/fe_q_base.cc @@ -1494,6 +1494,18 @@ FE_Q_Base::has_support_on_face (const unsigned int shape_inde +template +Table<2,bool> +FE_Q_Base::get_constant_modes () const +{ + Table<2,bool> constant_modes(1, this->dofs_per_cell); + // leave out last component + for (unsigned int i=0; i(this->degree+1); ++i) + constant_modes(0, i) = true; + return constant_modes; +} + + // explicit instantiations #include "fe_q_base.inst" diff --git a/deal.II/source/fe/fe_q_hierarchical.cc b/deal.II/source/fe/fe_q_hierarchical.cc index 7185ee76b0..b1800b6311 100644 --- a/deal.II/source/fe/fe_q_hierarchical.cc +++ b/deal.II/source/fe/fe_q_hierarchical.cc @@ -1861,6 +1861,20 @@ FE_Q_Hierarchical::get_embedding_dofs (const unsigned int sub_degree) const +template +Table<2,bool> +FE_Q_Hierarchical::get_constant_modes () const +{ + Table<2,bool> constant_modes(1, this->dofs_per_cell); + for (unsigned int i=0; i::vertices_per_cell; ++i) + constant_modes(0,i) = true; + for (unsigned int i=GeometryInfo::vertices_per_cell; idofs_per_cell; ++i) + constant_modes(0,i) = false; + return constant_modes; +} + + + template std::size_t FE_Q_Hierarchical::memory_consumption () const diff --git a/deal.II/source/fe/fe_raviart_thomas.cc b/deal.II/source/fe/fe_raviart_thomas.cc index bf82030640..22208bae95 100644 --- a/deal.II/source/fe/fe_raviart_thomas.cc +++ b/deal.II/source/fe/fe_raviart_thomas.cc @@ -403,6 +403,19 @@ FE_RaviartThomas::get_dpo_vector (const unsigned int deg) +template +Table<2,bool> +FE_RaviartThomas::get_constant_modes() const +{ + Table<2,bool> constant_modes(dim, this->dofs_per_cell); + for (unsigned int d=0; ddofs_per_cell; ++i) + constant_modes(d,i) = true; + return constant_modes; +} + + + //--------------------------------------------------------------------------- // Data field initialization //--------------------------------------------------------------------------- @@ -532,6 +545,7 @@ FE_RaviartThomas::interpolate( } + template std::size_t FE_RaviartThomas::memory_consumption () const diff --git a/deal.II/source/fe/fe_system.cc b/deal.II/source/fe/fe_system.cc index 8683136e66..84d0af0ef5 100644 --- a/deal.II/source/fe/fe_system.cc +++ b/deal.II/source/fe/fe_system.cc @@ -2982,6 +2982,33 @@ FESystem::unit_face_support_point (const unsigned int index) const +template +Table<2,bool> +FESystem::get_constant_modes () const +{ + Table<2,bool> constant_modes(this->n_components(), this->dofs_per_cell); + unsigned int comp=0; + for (unsigned int i=0; i base_table = base_elements[i].first->get_constant_modes(); + const unsigned int n_base_components = base_elements[i].first->n_components(); + for (unsigned int k=0; kdofs_per_cell; ++k) + { + std::pair, unsigned int> ind + = this->system_to_base_index(k); + if (ind.first.first == i) + for (unsigned int c=0; cn_components()); + return constant_modes; +} + + + template std::size_t FESystem::memory_consumption () const diff --git a/deal.II/source/lac/petsc_parallel_vector.cc b/deal.II/source/lac/petsc_parallel_vector.cc index 848ba3eec1..ce866b663d 100644 --- a/deal.II/source/lac/petsc_parallel_vector.cc +++ b/deal.II/source/lac/petsc_parallel_vector.cc @@ -359,6 +359,21 @@ namespace PETScWrappers + bool + Vector::all_zero() const + { + unsigned int has_nonzero = VectorBase::all_zero()?0:1; +#ifdef DEAL_II_WITH_MPI + // in parallel, check that the vector + // is zero on _all_ processors. + unsigned int num_nonzero = Utilities::MPI::sum(has_nonzero, communicator); + return num_nonzero == 0; +#else + return has_nonzero == 0; +#endif + } + + void Vector::print (std::ostream &out, const unsigned int precision, diff --git a/deal.II/source/lac/petsc_vector_base.cc b/deal.II/source/lac/petsc_vector_base.cc index 4166708d98..5f4bd0118c 100644 --- a/deal.II/source/lac/petsc_vector_base.cc +++ b/deal.II/source/lac/petsc_vector_base.cc @@ -662,7 +662,7 @@ namespace PETScWrappers AssertThrow (ierr == 0, ExcPETScError(ierr)); const PetscScalar *ptr = start_ptr, - *eptr = start_ptr + size(); + *eptr = start_ptr + local_size(); bool flag = true; while (ptr != eptr) { @@ -715,7 +715,7 @@ namespace PETScWrappers AssertThrow (ierr == 0, ExcPETScError(ierr)); const PetscScalar *ptr = start_ptr, - *eptr = start_ptr + size(); + *eptr = start_ptr + local_size(); bool flag = true; while (ptr != eptr) { diff --git a/deal.II/source/lac/sparsity_tools.cc b/deal.II/source/lac/sparsity_tools.cc index 57a04430c0..afa8e0fa3d 100644 --- a/deal.II/source/lac/sparsity_tools.cc +++ b/deal.II/source/lac/sparsity_tools.cc @@ -477,7 +477,7 @@ namespace SparsityTools Assert (status.MPI_TAG==124, ExcInternalError()); MPI_Get_count(&status, MPI_BYTE, &len); - Assert( len%sizeof(unsigned int)==0, ExcInternalError()); + Assert( len%sizeof(size_type)==0, ExcInternalError()); recv_buf.resize(len/sizeof(size_type)); @@ -500,8 +500,7 @@ namespace SparsityTools } } - // complete all sends, so that we can - // safely destroy the buffers. + // complete all sends, so that we can safely destroy the buffers. MPI_Waitall(requests.size(), &requests[0], MPI_STATUSES_IGNORE); } @@ -625,8 +624,7 @@ namespace SparsityTools } } - // complete all sends, so that we can - // safely destroy the buffers. + // complete all sends, so that we can safely destroy the buffers. MPI_Waitall(requests.size(), &requests[0], MPI_STATUSES_IGNORE); } diff --git a/deal.II/source/lac/trilinos_block_sparse_matrix.cc b/deal.II/source/lac/trilinos_block_sparse_matrix.cc index b338de4186..79cc8aa3c5 100644 --- a/deal.II/source/lac/trilinos_block_sparse_matrix.cc +++ b/deal.II/source/lac/trilinos_block_sparse_matrix.cc @@ -84,7 +84,8 @@ namespace TrilinosWrappers void BlockSparseMatrix:: reinit (const std::vector ¶llel_partitioning, - const BlockSparsityType &block_sparsity_pattern) + const BlockSparsityType &block_sparsity_pattern, + const bool exchange_data) { Assert (parallel_partitioning.size() == block_sparsity_pattern.n_block_rows(), ExcDimensionMismatch (parallel_partitioning.size(), @@ -118,7 +119,8 @@ namespace TrilinosWrappers { this->sub_objects[r][c]->reinit (parallel_partitioning[r], parallel_partitioning[c], - block_sparsity_pattern.block(r,c)); + block_sparsity_pattern.block(r,c), + exchange_data); } } @@ -129,14 +131,15 @@ namespace TrilinosWrappers BlockSparseMatrix:: reinit (const std::vector ¶llel_partitioning, const BlockSparsityType &block_sparsity_pattern, - const MPI_Comm &communicator) + const MPI_Comm &communicator, + const bool exchange_data) { std::vector epetra_maps; for (size_type i=0; i &, - const dealii::BlockSparsityPattern &); + const dealii::BlockSparsityPattern &, + const bool); template void BlockSparseMatrix::reinit (const std::vector &, - const dealii::BlockCompressedSparsityPattern &); + const dealii::BlockCompressedSparsityPattern &, + const bool); template void BlockSparseMatrix::reinit (const std::vector &, - const dealii::BlockCompressedSetSparsityPattern &); + const dealii::BlockCompressedSetSparsityPattern &, + const bool); template void BlockSparseMatrix::reinit (const std::vector &, - const dealii::BlockCompressedSimpleSparsityPattern &); + const dealii::BlockCompressedSimpleSparsityPattern &, + const bool); template void BlockSparseMatrix::reinit (const std::vector &, const dealii::BlockCompressedSimpleSparsityPattern &, - const MPI_Comm &); + const MPI_Comm &, + const bool); } diff --git a/deal.II/source/lac/trilinos_sparse_matrix.cc b/deal.II/source/lac/trilinos_sparse_matrix.cc index c486406f7f..88e828f356 100644 --- a/deal.II/source/lac/trilinos_sparse_matrix.cc +++ b/deal.II/source/lac/trilinos_sparse_matrix.cc @@ -1,7 +1,7 @@ // --------------------------------------------------------------------- // $Id$ // -// Copyright (C) 2008 - 2013 by the deal.II authors +// Copyright (C) 2008 - 2014 by the deal.II authors // // This file is part of the deal.II library. // @@ -25,6 +25,7 @@ # include # include # include +# include # include # include @@ -390,6 +391,7 @@ namespace TrilinosWrappers SparseMatrix::copy_from (const SparseMatrix &m) { nonlocal_matrix.reset(); + nonlocal_matrix_exporter.reset(); // check whether we need to update the // partitioner or can just copy the data: @@ -480,6 +482,7 @@ namespace TrilinosWrappers // release memory before reallocation matrix.reset(); nonlocal_matrix.reset(); + nonlocal_matrix_exporter.reset(); // if we want to exchange data, build a usual Trilinos sparsity pattern // and let that handle the exchange. otherwise, manually create a @@ -575,10 +578,193 @@ namespace TrilinosWrappers + // specialization for CompressedSimpleSparsityPattern which can provide us + // with more information about the non-locally owned rows + template <> + void + SparseMatrix::reinit (const Epetra_Map &input_row_map, + const Epetra_Map &input_col_map, + const CompressedSimpleSparsityPattern &sparsity_pattern, + const bool exchange_data) + { + matrix.reset(); + nonlocal_matrix.reset(); + nonlocal_matrix_exporter.reset(); + + AssertDimension (sparsity_pattern.n_rows(), + static_cast(n_global_elements(input_row_map))); + + // exchange data if requested with deal.II's own function +#ifdef DEAL_II_WITH_MPI + const Epetra_MpiComm* communicator = + dynamic_cast(&input_row_map.Comm()); + if (exchange_data && communicator != 0) + { + std::vector + owned_per_proc(communicator->NumProc(), -1); + size_type my_elements = input_row_map.NumMyElements(); + MPI_Allgather(&my_elements, 1, + Utilities::MPI::internal::mpi_type_id(&my_elements), + &owned_per_proc[0], 1, + Utilities::MPI::internal::mpi_type_id(&my_elements), + communicator->Comm()); + + AssertDimension(std::accumulate(owned_per_proc.begin(), + owned_per_proc.end(), size_type()), sparsity_pattern.n_rows()); + + SparsityTools::distribute_sparsity_pattern + (const_cast(sparsity_pattern), + owned_per_proc, communicator->Comm(), sparsity_pattern.row_index_set()); + } +#endif + + if (input_row_map.Comm().MyPID() == 0) + { + AssertDimension (sparsity_pattern.n_rows(), + static_cast(n_global_elements(input_row_map))); + AssertDimension (sparsity_pattern.n_cols(), + static_cast(n_global_elements(input_col_map))); + } + + column_space_map.reset (new Epetra_Map (input_col_map)); + + IndexSet relevant_rows (sparsity_pattern.row_index_set()); + // serial case + if (relevant_rows.size() == 0) + { + relevant_rows.set_size(n_global_elements(input_row_map)); + relevant_rows.add_range(0, n_global_elements(input_row_map)); + } + relevant_rows.compress(); + Assert(relevant_rows.n_elements() >= static_cast(input_row_map.NumMyElements()), + ExcMessage("Locally relevant rows of sparsity pattern must contain " + "all locally owned rows")); + + // check whether the relevant rows correspond to exactly the same map as + // the owned rows. In that case, do not create the nonlocal graph and fill + // the columns by demand + bool have_ghost_rows = false; + { + std::vector indices; + relevant_rows.fill_index_vector(indices); + Epetra_Map relevant_map (TrilinosWrappers::types::int_type(-1), + TrilinosWrappers::types::int_type(relevant_rows.n_elements()), + (indices.empty() ? 0 : + reinterpret_cast(&indices[0])), + 0, input_row_map.Comm()); + if (relevant_map.SameAs(input_row_map)) + have_ghost_rows = false; + else + have_ghost_rows = true; + } + + const unsigned int n_rows = relevant_rows.n_elements(); + std::vector ghost_rows; + std::vector n_entries_per_row(input_row_map.NumMyElements()); + std::vector n_entries_per_ghost_row; + for (unsigned int i=0, own=0; i 0) + { + ghost_rows.push_back(global_row); + n_entries_per_ghost_row.push_back(sparsity_pattern.row_length(global_row)); + } + } + + // make sure all processors create an off-processor matrix with at least + // one entry + if (have_ghost_rows == true && ghost_rows.empty() == true) + { + ghost_rows.push_back(0); + n_entries_per_ghost_row.push_back(1); + } + + Epetra_Map off_processor_map(-1, ghost_rows.size(), &ghost_rows[0], + 0, input_row_map.Comm()); + + std_cxx1x::shared_ptr graph, nonlocal_graph; + if (input_row_map.Comm().NumProc() > 1) + { + graph.reset (new Epetra_CrsGraph (Copy, input_row_map, + &n_entries_per_row[0], true)); + if (have_ghost_rows == true) + nonlocal_graph.reset (new Epetra_CrsGraph (Copy, off_processor_map, + &n_entries_per_ghost_row[0], + true)); + } + else + graph.reset (new Epetra_CrsGraph (Copy, input_row_map, input_col_map, + &n_entries_per_row[0], true)); + + // now insert the indices, select between the right matrix + std::vector row_indices; + + for (unsigned int i=0; iInsertGlobalIndices (global_row, row_length, &row_indices[0]); + else + { + Assert(nonlocal_graph.get() != 0, ExcInternalError()); + nonlocal_graph->InsertGlobalIndices (global_row, row_length, + &row_indices[0]); + } + } + + graph->FillComplete(input_col_map, input_row_map); + graph->OptimizeStorage(); + + AssertDimension (sparsity_pattern.n_cols(),static_cast( + n_global_cols(*graph))); + + matrix.reset (new Epetra_FECrsMatrix(Copy, *graph, false)); + + // and now the same operations for the nonlocal graph and matrix + if (nonlocal_graph.get() != 0) + { + if (nonlocal_graph->IndicesAreGlobal() == false && + nonlocal_graph->RowMap().NumMyElements() > 0) + { + // insert dummy element + TrilinosWrappers::types::int_type row = + nonlocal_graph->RowMap().MyGID(TrilinosWrappers::types::int_type(0)); + nonlocal_graph->InsertGlobalIndices(row, 1, &row); + } + Assert(nonlocal_graph->IndicesAreGlobal() == true, + ExcInternalError()); + nonlocal_graph->FillComplete(input_col_map, input_row_map); + nonlocal_graph->OptimizeStorage(); + + nonlocal_matrix.reset (new Epetra_CrsMatrix(Copy, *nonlocal_graph)); + } + last_action = Zero; + + // In the end, the matrix needs to be compressed in order to be really + // ready. + compress(); + } + + + + void SparseMatrix::reinit (const SparsityPattern &sparsity_pattern) { matrix.reset (); + nonlocal_matrix_exporter.reset(); // reinit with a (parallel) Trilinos sparsity pattern. column_space_map.reset (new Epetra_Map @@ -602,6 +788,7 @@ namespace TrilinosWrappers { column_space_map.reset (new Epetra_Map (sparse_matrix.domain_partitioner())); matrix.reset (); + nonlocal_matrix_exporter.reset(); matrix.reset (new Epetra_FECrsMatrix (Copy, sparse_matrix.trilinos_sparsity_pattern(), false)); if (sparse_matrix.nonlocal_matrix != 0) @@ -767,6 +954,7 @@ namespace TrilinosWrappers const Epetra_CrsGraph *graph = &input_matrix.Graph(); nonlocal_matrix.reset(); + nonlocal_matrix_exporter.reset(); matrix.reset (); matrix.reset (new Epetra_FECrsMatrix(Copy, *graph, false)); @@ -818,8 +1006,10 @@ namespace TrilinosWrappers // do only export in case of an add() operation, otherwise the owning // processor must have set the correct entry nonlocal_matrix->FillComplete(*column_space_map, matrix->RowMap()); - Epetra_Export exporter(nonlocal_matrix->RowMap(), matrix->RowMap()); - ierr = matrix->Export(*nonlocal_matrix, exporter, mode); + if (nonlocal_matrix_exporter.get() == 0) + nonlocal_matrix_exporter.reset + (new Epetra_Export(nonlocal_matrix->RowMap(), matrix->RowMap())); + ierr = matrix->Export(*nonlocal_matrix, *nonlocal_matrix_exporter, mode); AssertThrow(ierr == 0, ExcTrilinosError(ierr)); ierr = matrix->FillComplete(*column_space_map, matrix->RowMap()); nonlocal_matrix->PutScalar(0); @@ -850,6 +1040,7 @@ namespace TrilinosWrappers Utilities::Trilinos::comm_self())); matrix.reset (new Epetra_FECrsMatrix(View, *column_space_map, 0)); nonlocal_matrix.reset(); + nonlocal_matrix_exporter.reset(); matrix->FillComplete(); @@ -1615,11 +1806,6 @@ namespace TrilinosWrappers const CompressedSparsityPattern &, const bool); template void - SparseMatrix::reinit (const Epetra_Map &, - const Epetra_Map &, - const CompressedSimpleSparsityPattern &, - const bool); - template void SparseMatrix::reinit (const Epetra_Map &, const Epetra_Map &, const CompressedSetSparsityPattern &, diff --git a/deal.II/source/multigrid/mg_tools.cc b/deal.II/source/multigrid/mg_tools.cc index 7321c64d2e..62589b793f 100644 --- a/deal.II/source/multigrid/mg_tools.cc +++ b/deal.II/source/multigrid/mg_tools.cc @@ -611,9 +611,9 @@ namespace MGTools typename DoFHandler::cell_iterator neighbor = cell->neighbor(face); neighbor->get_mg_dof_indices (dofs_on_other_cell); - // only add one direction - // The other is taken care of - // by neighbor. + // only add one direction The other is taken care of by + // neighbor (except when the neighbor is not owned by the same + // processor) for (unsigned int i=0; iis_locally_owned_on_level() == false) + for (unsigned int i=0; i > + tmp_interface_dofs(interface_dofs.size()); + std::vector > + tmp_boundary_interface_dofs(interface_dofs.size()); const FiniteElement &fe = mg_dof_handler.get_fe(); @@ -1633,12 +1641,14 @@ namespace MGTools } } - if (has_coarser_neighbor == true) - for (unsigned int face_nr=0; face_nr::faces_per_cell; ++face_nr) - if (cell->at_boundary(face_nr)) - for (unsigned int j=0; j::faces_per_cell; ++face_nr) + if (cell->at_boundary(face_nr)) + for (unsigned int j=0; jlevel(); @@ -1647,12 +1657,31 @@ namespace MGTools for (unsigned int i=0; i &/*mapping*/, const std::vector &/*solutions*/, std::vector*> &/*errors*/, const ComponentMask &/*component_mask_*/, - const Function */*coefficient*/, + const Function * /*coefficient*/, const unsigned int, const types::subdomain_id /*subdomain_id*/, const types::material_id /*material_id*/) diff --git a/tests/fe/element_constant_modes.cc b/tests/fe/element_constant_modes.cc new file mode 100644 index 0000000000..4ae2eab1fa --- /dev/null +++ b/tests/fe/element_constant_modes.cc @@ -0,0 +1,85 @@ +// --------------------------------------------------------------------- +// $Id$ +// +// Copyright (C) 2014 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +#include "../tests.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include + + +template +void print_constant_modes(const FiniteElement &fe) +{ + Table<2,bool> constant_modes = fe.get_constant_modes(); + deallog << "Testing " << fe.get_name() << std::endl; + + for (unsigned int r=0; r +void test() +{ + print_constant_modes(FE_Q(1)); + print_constant_modes(FE_Q(2)); + print_constant_modes(FE_DGQ(1)); + print_constant_modes(FE_DGP(2)); + print_constant_modes(FE_Q_Hierarchical(1)); + print_constant_modes(FE_Q_Hierarchical(2)); + print_constant_modes(FE_FaceQ(1)); + print_constant_modes(FE_FaceP(1)); + print_constant_modes(FESystem(FE_Q(1), 2, FE_Q(2), 1)); + print_constant_modes(FESystem(FE_DGP(1), 1, FE_Q_iso_Q1(2), 1)); +} + +template <> +void test<1>() +{ + print_constant_modes(FE_Q<1>(1)); + print_constant_modes(FESystem<1>(FE_Q<1>(1), 2, FE_Q<1>(2), 1)); + print_constant_modes(FESystem<1>(FE_DGP<1>(1), 1, FE_Q_iso_Q1<1>(2), 1)); +} + + +int +main() +{ + std::ofstream logfile ("output"); + deallog.attach(logfile); + deallog.depth_console(0); + + test<1>(); + test<2>(); + test<3>(); + + return 0; +} + + + diff --git a/tests/fe/element_constant_modes.output b/tests/fe/element_constant_modes.output new file mode 100644 index 0000000000..428dbf5c6e --- /dev/null +++ b/tests/fe/element_constant_modes.output @@ -0,0 +1,79 @@ + +DEAL::Testing FE_Q<1>(1) +DEAL::1 1 +DEAL:: +DEAL::Testing FESystem<1>[FE_Q<1>(1)^2-FE_Q<1>(2)] +DEAL::1 0 0 1 0 0 0 +DEAL::0 1 0 0 1 0 0 +DEAL::0 0 1 0 0 1 1 +DEAL:: +DEAL::Testing FESystem<1>[FE_DGP<1>(1)-FE_Q_iso_Q1<1>(2)] +DEAL::0 0 1 0 0 +DEAL::1 1 0 0 1 +DEAL:: +DEAL::Testing FE_Q<2>(1) +DEAL::1 1 1 1 +DEAL:: +DEAL::Testing FE_Q<2>(2) +DEAL::1 1 1 1 1 1 1 1 1 +DEAL:: +DEAL::Testing FE_DGQ<2>(1) +DEAL::1 1 1 1 +DEAL:: +DEAL::Testing FE_DGP<2>(2) +DEAL::1 0 0 0 0 0 +DEAL:: +DEAL::Testing FE_Q_Hierarchical<2>(1) +DEAL::1 1 1 1 +DEAL:: +DEAL::Testing FE_Q_Hierarchical<2>(2) +DEAL::1 1 1 1 0 0 0 0 0 +DEAL:: +DEAL::Testing FE_FaceQ<2>(1) +DEAL::1 1 1 1 1 1 1 1 +DEAL:: +DEAL::Testing FE_FaceP<2>(1) +DEAL::1 0 1 0 1 0 1 0 +DEAL:: +DEAL::Testing FESystem<2>[FE_Q<2>(1)^2-FE_Q<2>(2)] +DEAL::1 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 +DEAL::0 1 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 +DEAL::0 0 1 0 0 1 0 0 1 0 0 1 1 1 1 1 1 +DEAL:: +DEAL::Testing FESystem<2>[FE_DGP<2>(1)-FE_Q_iso_Q1<2>(2)] +DEAL::0 0 0 0 0 0 0 0 1 0 0 0 +DEAL::1 1 1 1 1 1 1 1 0 0 0 1 +DEAL:: +DEAL::Testing FE_Q<3>(1) +DEAL::1 1 1 1 1 1 1 1 +DEAL:: +DEAL::Testing FE_Q<3>(2) +DEAL::1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +DEAL:: +DEAL::Testing FE_DGQ<3>(1) +DEAL::1 1 1 1 1 1 1 1 +DEAL:: +DEAL::Testing FE_DGP<3>(2) +DEAL::1 0 0 0 0 0 0 0 0 0 +DEAL:: +DEAL::Testing FE_Q_Hierarchical<3>(1) +DEAL::1 1 1 1 1 1 1 1 +DEAL:: +DEAL::Testing FE_Q_Hierarchical<3>(2) +DEAL::1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +DEAL:: +DEAL::Testing FE_FaceQ<3>(1) +DEAL::1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +DEAL:: +DEAL::Testing FE_FaceP<3>(1) +DEAL::1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 +DEAL:: +DEAL::Testing FESystem<3>[FE_Q<3>(1)^2-FE_Q<3>(2)] +DEAL::1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +DEAL::0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +DEAL::0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +DEAL:: +DEAL::Testing FESystem<3>[FE_DGP<3>(1)-FE_Q_iso_Q1<3>(2)] +DEAL::0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 +DEAL::1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 1 +DEAL:: diff --git a/tests/gla/gla.h b/tests/gla/gla.h index 9f48457f40..b7a9ece8e5 100644 --- a/tests/gla/gla.h +++ b/tests/gla/gla.h @@ -55,6 +55,11 @@ public: void compress(VectorOperation::values op) {} + bool all_zero() + { + return false; + } + bool has_ghost_elements() { return false; diff --git a/tests/gla/mat_01.cc b/tests/gla/mat_01.cc index 84bd19afc9..2e4711a081 100644 --- a/tests/gla/mat_01.cc +++ b/tests/gla/mat_01.cc @@ -43,7 +43,7 @@ void test () IndexSet local_active(numproc*2); local_active.add_range(myid*2,myid*2+2); IndexSet local_relevant= local_active; - local_relevant.add_range(1,2); + local_relevant.add_range(0,1); CompressedSimpleSparsityPattern csp (local_relevant); @@ -51,8 +51,7 @@ void test () if (local_relevant.is_element(i)) csp.add(i,i); - if (myid==0) - csp.add(0,1); + csp.add(0,1); typename LA::MPI::SparseMatrix mat; diff --git a/tests/gla/vec_all_zero_01.cc b/tests/gla/vec_all_zero_01.cc new file mode 100644 index 0000000000..00d4bcb417 --- /dev/null +++ b/tests/gla/vec_all_zero_01.cc @@ -0,0 +1,86 @@ +// --------------------------------------------------------------------- +// $Id: vec_00.cc 31681 2013-11-16 08:04:28Z maier $ +// +// Copyright (C) 2004 - 2013 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + + +// check that all_zero is working correctly (as a collective operation) + +#include "../tests.h" +#include +#include +#include +#include +#include +#include + +#include "gla.h" + +template +void test () +{ + unsigned int myid = Utilities::MPI::this_mpi_process (MPI_COMM_WORLD); + unsigned int numproc = Utilities::MPI::n_mpi_processes (MPI_COMM_WORLD); + + if (myid==0) + deallog << "numproc=" << numproc << std::endl; + + // each processor owns 2 indices and all + // are ghosting Element 1 (the second) + + IndexSet local_active(numproc*2); + local_active.add_range(myid*2,myid*2+2); + IndexSet local_relevant(numproc*2); + local_relevant.add_range(1,2); + + + typename LA::MPI::Vector x; + x.reinit(local_active, MPI_COMM_WORLD); + x=0; + typename LA::MPI::Vector g(local_active, local_relevant, MPI_COMM_WORLD); + g=x; + deallog << "all_zero? " << g.all_zero() << " (should be true)" << std::endl; + if (myid==0) + x(0)=1.0; + x.compress(VectorOperation::insert); + g=x; + deallog << "all_zero? " << g.all_zero() << " (should be false)" << std::endl; + + // done + if (myid==0) + deallog << "OK" << std::endl; +} + + + +int main (int argc, char **argv) +{ + Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv); + MPILogInitAll log; + unsigned int myid = Utilities::MPI::this_mpi_process (MPI_COMM_WORLD); + + { + deallog.push("PETSc"); + test(); + deallog.pop(); + deallog.push("Trilinos"); + test(); + deallog.pop(); + } + + if (myid==9999) + test(); // don't execute + +} diff --git a/tests/gla/vec_all_zero_01.mpirun=3.output b/tests/gla/vec_all_zero_01.mpirun=3.output new file mode 100644 index 0000000000..437293a1e6 --- /dev/null +++ b/tests/gla/vec_all_zero_01.mpirun=3.output @@ -0,0 +1,21 @@ + +DEAL:0:PETSc::numproc=3 +DEAL:0:PETSc::all_zero? 1 (should be true) +DEAL:0:PETSc::all_zero? 0 (should be false) +DEAL:0:PETSc::OK +DEAL:0:Trilinos::numproc=3 +DEAL:0:Trilinos::all_zero? 1 (should be true) +DEAL:0:Trilinos::all_zero? 0 (should be false) +DEAL:0:Trilinos::OK + +DEAL:1:PETSc::all_zero? 1 (should be true) +DEAL:1:PETSc::all_zero? 0 (should be false) +DEAL:1:Trilinos::all_zero? 1 (should be true) +DEAL:1:Trilinos::all_zero? 0 (should be false) + + +DEAL:2:PETSc::all_zero? 1 (should be true) +DEAL:2:PETSc::all_zero? 0 (should be false) +DEAL:2:Trilinos::all_zero? 1 (should be true) +DEAL:2:Trilinos::all_zero? 0 (should be false) + diff --git a/tests/hp/get_interpolated_dof_values_01.cc b/tests/hp/get_interpolated_dof_values_01.cc new file mode 100644 index 0000000000..743e8a75ea --- /dev/null +++ b/tests/hp/get_interpolated_dof_values_01.cc @@ -0,0 +1,107 @@ +// --------------------------------------------------------------------- +// $Id$ +// +// Copyright (C) 1998 - 2014 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +// cell->get_interpolated_dof_values can not work properly in the hp +// context when called on non-active cells because these do not have a +// finite element associated with them + +#include "../tests.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include + +#define PRECISION 2 + + + + +template +void test () +{ + // create a hp::DoFHandler with different finite elements on the + // cells. note that we assign active_fe_indices also to inactive + // elements + Triangulation tr; + GridGenerator::hyper_cube(tr, 0., 1.); + tr.refine_global (2); + + hp::FECollection fe; + for (unsigned int i=1; i<5; ++i) + fe.push_back (FE_Q(i)); + + hp::DoFHandler dof_handler(tr); + for (typename hp::DoFHandler::cell_iterator cell=dof_handler.begin(); + cell!=dof_handler.end(); ++cell) + cell->set_active_fe_index (cell->index() % fe.size()); + + dof_handler.distribute_dofs (fe); + + // create a mostly arbitrary FE field + Vector solution(dof_handler.n_dofs()); + for (unsigned int i=0; i::cell_iterator cell=dof_handler.begin(0); + Vector local (cell->get_fe().dofs_per_cell); + + try + { + cell->get_interpolated_dof_values (solution, local); + } + catch (const ExceptionBase &e) + { + deallog << "Yes, exception!" << std::endl; + deallog << e.get_exc_name() << std::endl; + } +} + + +int +main() +{ + std::ofstream logfile ("output"); + logfile.precision (PRECISION); + logfile.setf(std::ios::fixed); + deallog.attach(logfile); + deallog.depth_console(0); + deallog.threshold_double(1.e-10); + + deal_II_exceptions::disable_abort_on_exception(); + + test<1>(); + test<2>(); + test<3>(); + + return 0; +} + + + diff --git a/tests/hp/get_interpolated_dof_values_01.debug.output b/tests/hp/get_interpolated_dof_values_01.debug.output new file mode 100644 index 0000000000..ba7953b18d --- /dev/null +++ b/tests/hp/get_interpolated_dof_values_01.debug.output @@ -0,0 +1,7 @@ + +DEAL::Yes, exception! +DEAL::ExcMessage ("You cannot call this function on non-active cells " "of hp::DoFHandler objects unless you provide an explicit " "finite element index because they do not have naturally " "associated finite element spaces associated: degrees " "of freedom are only distributed on active cells for which " "the active_fe_index has been set.") +DEAL::Yes, exception! +DEAL::ExcMessage ("You cannot call this function on non-active cells " "of hp::DoFHandler objects unless you provide an explicit " "finite element index because they do not have naturally " "associated finite element spaces associated: degrees " "of freedom are only distributed on active cells for which " "the active_fe_index has been set.") +DEAL::Yes, exception! +DEAL::ExcMessage ("You cannot call this function on non-active cells " "of hp::DoFHandler objects unless you provide an explicit " "finite element index because they do not have naturally " "associated finite element spaces associated: degrees " "of freedom are only distributed on active cells for which " "the active_fe_index has been set.") diff --git a/tests/hp/get_interpolated_dof_values_02.cc b/tests/hp/get_interpolated_dof_values_02.cc new file mode 100644 index 0000000000..c97e8aafce --- /dev/null +++ b/tests/hp/get_interpolated_dof_values_02.cc @@ -0,0 +1,123 @@ +// --------------------------------------------------------------------- +// $Id$ +// +// Copyright (C) 1998 - 2014 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +// cell->get_interpolated_dof_values can not work properly in the hp +// context when called on non-active cells because these do not have a +// finite element associated with them +// +// this test verifies that if we call the function on active cells with no +// explicitly given fe_index that we get the same result as from +// cell->get_dof_values, and that if we call it with an fe_index for a Q1 +// element that we simply get the vertex dof values + +#include "../tests.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include + +#define PRECISION 2 + + + + +template +void test () +{ + // create a hp::DoFHandler with different finite elements on the + // cells. note that we assign active_fe_indices also to inactive + // elements + Triangulation tr; + GridGenerator::hyper_cube(tr, 0., 1.); + tr.refine_global (2); + + hp::FECollection fe; + for (unsigned int i=1; i<5; ++i) + fe.push_back (FE_Q(i)); + + hp::DoFHandler dof_handler(tr); + for (typename hp::DoFHandler::cell_iterator cell=dof_handler.begin(); + cell!=dof_handler.end(); ++cell) + cell->set_active_fe_index (cell->index() % fe.size()); + + dof_handler.distribute_dofs (fe); + + // create a mostly arbitrary FE field + Vector solution(dof_handler.n_dofs()); + for (unsigned int i=0; i::active_cell_iterator cell=dof_handler.begin_active(); + cell!=dof_handler.end(); ++cell) + { + // get values without specifying an explicit fe_index + Vector local1 (cell->get_fe().dofs_per_cell); + cell->get_interpolated_dof_values (solution, local1); + + // then do the same with the "correct", local fe_index + Vector local2 (cell->get_fe().dofs_per_cell); + cell->get_interpolated_dof_values (solution, local2, + cell->active_fe_index()); + + // and do it a third time with the fe_index for a Q1 element + Vector local3 (fe[0].dofs_per_cell); + cell->get_interpolated_dof_values (solution, local3, + 0); + + // now verify correctness + Assert (local1 == local2, ExcInternalError()); + + // also for the second test. note that vertex dofs always come first in + // local1, so we can easily compare + for (unsigned int i=0; i(); + test<2>(); + test<3>(); + + return 0; +} + + + diff --git a/tests/hp/get_interpolated_dof_values_02.output b/tests/hp/get_interpolated_dof_values_02.output new file mode 100644 index 0000000000..fb71de2867 --- /dev/null +++ b/tests/hp/get_interpolated_dof_values_02.output @@ -0,0 +1,4 @@ + +DEAL::OK +DEAL::OK +DEAL::OK diff --git a/tests/hp/get_interpolated_dof_values_03.cc b/tests/hp/get_interpolated_dof_values_03.cc new file mode 100644 index 0000000000..0a4e142cbd --- /dev/null +++ b/tests/hp/get_interpolated_dof_values_03.cc @@ -0,0 +1,113 @@ +// --------------------------------------------------------------------- +// $Id$ +// +// Copyright (C) 1998 - 2014 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +// cell->get_interpolated_dof_values can not work properly in the hp +// context when called on non-active cells because these do not have a +// finite element associated with them +// +// this test verifies that if we call the function on active cells with an +// explicitly given fe_index that we can interpolate from children to the +// so-specified FE space + +#include "../tests.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include + + +template +void test () +{ + deallog << dim << "D" << std::endl; + + // create a hp::DoFHandler with different finite elements on the + // cells. note that we assign active_fe_indices also to inactive + // elements + Triangulation tr; + GridGenerator::hyper_cube(tr, 0., 1.); + tr.refine_global (2); + + hp::FECollection fe; + for (unsigned int i=1; i<5; ++i) + fe.push_back (FE_Q(i)); + + hp::DoFHandler dof_handler(tr); + for (typename hp::DoFHandler::cell_iterator cell=dof_handler.begin(); + cell!=dof_handler.end(); ++cell) + cell->set_active_fe_index (cell->index() % fe.size()); + + dof_handler.distribute_dofs (fe); + + // create a mostly arbitrary FE field + Vector solution(dof_handler.n_dofs()); + for (unsigned int i=0; i::cell_iterator cell=dof_handler.begin(0); + Vector local (fe[0].dofs_per_cell); + cell->get_interpolated_dof_values (solution, local, + 0); + for (unsigned int i=0; i::active_cell_iterator cell=dof_handler.begin_active(); + cell!=dof_handler.end(); ++cell) + { + Vector x (cell->get_fe().dofs_per_cell); + cell->get_dof_values (solution, x); + deallog << "cell =" << cell << ": "; + for (unsigned int i=0; i(); + test<2>(); + test<3>(); + + return 0; +} + + + diff --git a/tests/hp/get_interpolated_dof_values_03.output b/tests/hp/get_interpolated_dof_values_03.output new file mode 100644 index 0000000000..c6835e5c7c --- /dev/null +++ b/tests/hp/get_interpolated_dof_values_03.output @@ -0,0 +1,91 @@ + +DEAL::1D +DEAL::0 7.00000 +DEAL::cell =2.0: 0 1.00000 +DEAL::cell =2.1: 1.00000 2.00000 3.00000 +DEAL::cell =2.2: 2.00000 4.00000 5.00000 6.00000 +DEAL::cell =2.3: 4.00000 7.00000 8.00000 9.00000 10.0000 +DEAL::2D +DEAL::0 44.0000 91.0000 150.000 +DEAL::cell =2.0: 0 1.00000 2.00000 3.00000 +DEAL::cell =2.1: 1.00000 40.0000 3.00000 42.0000 4.00000 5.00000 6.00000 7.00000 8.00000 +DEAL::cell =2.2: 2.00000 3.00000 82.0000 83.0000 9.00000 10.0000 11.0000 12.0000 13.0000 14.0000 15.0000 16.0000 17.0000 18.0000 19.0000 20.0000 +DEAL::cell =2.3: 3.00000 42.0000 83.0000 125.000 21.0000 22.0000 23.0000 24.0000 25.0000 26.0000 27.0000 7.00000 28.0000 29.0000 88.0000 30.0000 31.0000 32.0000 33.0000 34.0000 35.0000 36.0000 37.0000 38.0000 39.0000 +DEAL::cell =2.4: 40.0000 41.0000 42.0000 43.0000 +DEAL::cell =2.5: 41.0000 44.0000 43.0000 45.0000 46.0000 47.0000 48.0000 49.0000 50.0000 +DEAL::cell =2.6: 42.0000 43.0000 125.000 126.000 51.0000 52.0000 53.0000 54.0000 55.0000 56.0000 57.0000 58.0000 59.0000 60.0000 61.0000 62.0000 +DEAL::cell =2.7: 43.0000 45.0000 126.000 129.000 63.0000 64.0000 65.0000 66.0000 67.0000 68.0000 69.0000 49.0000 70.0000 71.0000 133.000 72.0000 73.0000 74.0000 75.0000 76.0000 77.0000 78.0000 79.0000 80.0000 81.0000 +DEAL::cell =2.8: 82.0000 83.0000 84.0000 85.0000 +DEAL::cell =2.9: 83.0000 125.000 85.0000 127.000 86.0000 87.0000 88.0000 89.0000 90.0000 +DEAL::cell =2.10: 84.0000 85.0000 91.0000 92.0000 93.0000 94.0000 95.0000 96.0000 97.0000 98.0000 99.0000 100.000 101.000 102.000 103.000 104.000 +DEAL::cell =2.11: 85.0000 127.000 92.0000 136.000 105.000 106.000 107.000 108.000 109.000 110.000 111.000 89.0000 112.000 113.000 114.000 115.000 116.000 117.000 118.000 119.000 120.000 121.000 122.000 123.000 124.000 +DEAL::cell =2.12: 125.000 126.000 127.000 128.000 +DEAL::cell =2.13: 126.000 129.000 128.000 130.000 131.000 132.000 133.000 134.000 135.000 +DEAL::cell =2.14: 127.000 128.000 136.000 137.000 138.000 139.000 140.000 141.000 142.000 143.000 144.000 145.000 146.000 147.000 148.000 149.000 +DEAL::cell =2.15: 128.000 130.000 137.000 150.000 151.000 152.000 153.000 154.000 155.000 156.000 157.000 134.000 158.000 159.000 160.000 161.000 162.000 163.000 164.000 165.000 166.000 167.000 168.000 169.000 170.000 +DEAL::3D +DEAL::0 362.000 741.000 1167.00 1603.00 1921.00 2252.00 2621.00 +DEAL::cell =2.0: 0 1.00000 2.00000 3.00000 4.00000 5.00000 6.00000 7.00000 +DEAL::cell =2.1: 1.00000 354.000 3.00000 356.000 5.00000 358.000 7.00000 360.000 8.00000 9.00000 10.0000 11.0000 12.0000 13.0000 14.0000 15.0000 16.0000 17.0000 18.0000 19.0000 20.0000 21.0000 22.0000 23.0000 24.0000 25.0000 26.0000 +DEAL::cell =2.2: 2.00000 3.00000 714.000 715.000 6.00000 7.00000 718.000 719.000 27.0000 28.0000 29.0000 30.0000 31.0000 32.0000 33.0000 34.0000 35.0000 36.0000 37.0000 38.0000 39.0000 40.0000 41.0000 42.0000 43.0000 44.0000 45.0000 46.0000 47.0000 48.0000 49.0000 50.0000 51.0000 52.0000 53.0000 54.0000 55.0000 56.0000 57.0000 58.0000 59.0000 60.0000 61.0000 62.0000 63.0000 64.0000 65.0000 66.0000 67.0000 68.0000 69.0000 70.0000 71.0000 72.0000 73.0000 74.0000 75.0000 76.0000 77.0000 78.0000 79.0000 80.0000 81.0000 82.0000 +DEAL::cell =2.3: 3.00000 356.000 715.000 1076.00 7.00000 360.000 719.000 1080.00 83.0000 84.0000 85.0000 86.0000 87.0000 88.0000 89.0000 90.0000 91.0000 92.0000 93.0000 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2370.00 2371.00 2372.00 2373.00 2374.00 2375.00 2376.00 2377.00 2378.00 2379.00 2380.00 2381.00 2382.00 2383.00 2384.00 2385.00 2386.00 2387.00 2388.00 2389.00 2390.00 2391.00 2392.00 +DEAL::cell =2.56: 1285.00 1286.00 1287.00 1288.00 2393.00 2394.00 2395.00 2396.00 +DEAL::cell =2.57: 1286.00 1289.00 1288.00 1290.00 2394.00 2397.00 2396.00 2398.00 1291.00 1292.00 1293.00 1294.00 2399.00 2400.00 2401.00 2402.00 2403.00 2404.00 2405.00 2406.00 2407.00 2408.00 2409.00 2410.00 1303.00 2411.00 2412.00 +DEAL::cell =2.58: 1287.00 1288.00 1305.00 1306.00 2395.00 2396.00 2413.00 2414.00 1307.00 1308.00 1309.00 1310.00 1311.00 1312.00 1313.00 1314.00 2415.00 2416.00 2417.00 2418.00 2419.00 2420.00 2421.00 2422.00 2423.00 2424.00 2425.00 2426.00 2427.00 2428.00 2429.00 2430.00 2431.00 2432.00 2433.00 2434.00 2435.00 2436.00 2437.00 2438.00 2439.00 2440.00 2441.00 2442.00 2443.00 2444.00 2445.00 2446.00 1339.00 1340.00 1341.00 1342.00 2447.00 2448.00 2449.00 2450.00 2451.00 2452.00 2453.00 2454.00 2455.00 2456.00 2457.00 2458.00 +DEAL::cell =2.59: 1288.00 1290.00 1306.00 1351.00 2396.00 2398.00 2414.00 2459.00 1352.00 1353.00 1354.00 1355.00 1356.00 1357.00 1358.00 1359.00 1360.00 1361.00 1362.00 1363.00 2460.00 2461.00 2462.00 2463.00 2464.00 2465.00 2466.00 2467.00 2468.00 2469.00 2470.00 2471.00 2472.00 2473.00 2474.00 2475.00 2476.00 2477.00 2478.00 2479.00 2480.00 2481.00 2482.00 2483.00 2484.00 2485.00 2486.00 2487.00 2488.00 2489.00 2490.00 2491.00 2492.00 2493.00 2494.00 2495.00 2496.00 2497.00 2498.00 2499.00 2500.00 2501.00 2502.00 2503.00 2504.00 2505.00 2410.00 2506.00 2507.00 2508.00 2509.00 2510.00 2511.00 2512.00 2513.00 2514.00 2515.00 2516.00 2517.00 2518.00 1411.00 1412.00 1413.00 1414.00 1415.00 1416.00 1417.00 1418.00 1419.00 2519.00 2520.00 2521.00 2522.00 2523.00 2524.00 2525.00 2526.00 2527.00 2528.00 2529.00 2530.00 2531.00 2532.00 2533.00 2534.00 2535.00 2536.00 2537.00 2538.00 2539.00 2540.00 2541.00 2542.00 2543.00 2544.00 2545.00 2546.00 2547.00 2548.00 2549.00 2550.00 2551.00 2552.00 2553.00 2554.00 +DEAL::cell =2.60: 2393.00 2394.00 2395.00 2396.00 2555.00 2556.00 2557.00 2558.00 +DEAL::cell =2.61: 2394.00 2397.00 2396.00 2398.00 2556.00 2559.00 2558.00 2560.00 2399.00 2400.00 2401.00 2402.00 2561.00 2562.00 2563.00 2564.00 2565.00 2566.00 2567.00 2568.00 2569.00 2570.00 2571.00 2572.00 2411.00 2573.00 2574.00 +DEAL::cell =2.62: 2395.00 2396.00 2413.00 2414.00 2557.00 2558.00 2575.00 2576.00 2415.00 2416.00 2417.00 2418.00 2419.00 2420.00 2421.00 2422.00 2577.00 2578.00 2579.00 2580.00 2581.00 2582.00 2583.00 2584.00 2585.00 2586.00 2587.00 2588.00 2589.00 2590.00 2591.00 2592.00 2593.00 2594.00 2595.00 2596.00 2597.00 2598.00 2599.00 2600.00 2601.00 2602.00 2603.00 2604.00 2605.00 2606.00 2607.00 2608.00 2447.00 2448.00 2449.00 2450.00 2609.00 2610.00 2611.00 2612.00 2613.00 2614.00 2615.00 2616.00 2617.00 2618.00 2619.00 2620.00 +DEAL::cell =2.63: 2396.00 2398.00 2414.00 2459.00 2558.00 2560.00 2576.00 2621.00 2460.00 2461.00 2462.00 2463.00 2464.00 2465.00 2466.00 2467.00 2468.00 2469.00 2470.00 2471.00 2622.00 2623.00 2624.00 2625.00 2626.00 2627.00 2628.00 2629.00 2630.00 2631.00 2632.00 2633.00 2634.00 2635.00 2636.00 2637.00 2638.00 2639.00 2640.00 2641.00 2642.00 2643.00 2644.00 2645.00 2646.00 2647.00 2648.00 2649.00 2650.00 2651.00 2652.00 2653.00 2654.00 2655.00 2656.00 2657.00 2658.00 2659.00 2660.00 2661.00 2662.00 2663.00 2664.00 2665.00 2666.00 2667.00 2572.00 2668.00 2669.00 2670.00 2671.00 2672.00 2673.00 2674.00 2675.00 2676.00 2677.00 2678.00 2679.00 2680.00 2519.00 2520.00 2521.00 2522.00 2523.00 2524.00 2525.00 2526.00 2527.00 2681.00 2682.00 2683.00 2684.00 2685.00 2686.00 2687.00 2688.00 2689.00 2690.00 2691.00 2692.00 2693.00 2694.00 2695.00 2696.00 2697.00 2698.00 2699.00 2700.00 2701.00 2702.00 2703.00 2704.00 2705.00 2706.00 2707.00 2708.00 2709.00 2710.00 2711.00 2712.00 2713.00 2714.00 2715.00 2716.00 diff --git a/tests/hp/set_dof_values_by_interpolation_01.cc b/tests/hp/set_dof_values_by_interpolation_01.cc new file mode 100644 index 0000000000..323033ad07 --- /dev/null +++ b/tests/hp/set_dof_values_by_interpolation_01.cc @@ -0,0 +1,107 @@ +// --------------------------------------------------------------------- +// $Id$ +// +// Copyright (C) 1998 - 2014 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +// cell->set_dof_values_by_interpolation can not work properly in the hp +// context when called on non-active cells because these do not have a +// finite element associated with them + +#include "../tests.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include + +#define PRECISION 2 + + + + +template +void test () +{ + // create a hp::DoFHandler with different finite elements on the + // cells. note that we assign active_fe_indices also to inactive + // elements + Triangulation tr; + GridGenerator::hyper_cube(tr, 0., 1.); + tr.refine_global (2); + + hp::FECollection fe; + for (unsigned int i=1; i<5; ++i) + fe.push_back (FE_Q(i)); + + hp::DoFHandler dof_handler(tr); + for (typename hp::DoFHandler::cell_iterator cell=dof_handler.begin(); + cell!=dof_handler.end(); ++cell) + cell->set_active_fe_index (cell->index() % fe.size()); + + dof_handler.distribute_dofs (fe); + + // create a mostly arbitrary FE field + Vector solution(dof_handler.n_dofs()); + for (unsigned int i=0; i::cell_iterator cell=dof_handler.begin(0); + Vector local (cell->get_fe().dofs_per_cell); + + try + { + cell->get_interpolated_dof_values (solution, local); + } + catch (const ExceptionBase &e) + { + deallog << "Yes, exception!" << std::endl; + deallog << e.get_exc_name() << std::endl; + } +} + + +int +main() +{ + std::ofstream logfile ("output"); + logfile.precision (PRECISION); + logfile.setf(std::ios::fixed); + deallog.attach(logfile); + deallog.depth_console(0); + deallog.threshold_double(1.e-10); + + deal_II_exceptions::disable_abort_on_exception(); + + test<1>(); + test<2>(); + test<3>(); + + return 0; +} + + + diff --git a/tests/hp/set_dof_values_by_interpolation_01.debug.output b/tests/hp/set_dof_values_by_interpolation_01.debug.output new file mode 100644 index 0000000000..2aca68e01e --- /dev/null +++ b/tests/hp/set_dof_values_by_interpolation_01.debug.output @@ -0,0 +1,7 @@ + +DEAL::Yes, exception! +DEAL::ExcMessage ("You cannot call this function on non-active cells " "of hp::DoFHandler objects because they do not have " "associated finite element spaces associated: degrees " "of freedom are only distributed on active cells for which " "the active_fe_index has been set.") +DEAL::Yes, exception! +DEAL::ExcMessage ("You cannot call this function on non-active cells " "of hp::DoFHandler objects because they do not have " "associated finite element spaces associated: degrees " "of freedom are only distributed on active cells for which " "the active_fe_index has been set.") +DEAL::Yes, exception! +DEAL::ExcMessage ("You cannot call this function on non-active cells " "of hp::DoFHandler objects because they do not have " "associated finite element spaces associated: degrees " "of freedom are only distributed on active cells for which " "the active_fe_index has been set.") diff --git a/tests/trilinos/assemble_matrix_parallel_05.cc b/tests/trilinos/assemble_matrix_parallel_05.cc new file mode 100644 index 0000000000..f39a906e1a --- /dev/null +++ b/tests/trilinos/assemble_matrix_parallel_05.cc @@ -0,0 +1,454 @@ +// --------------------------------------------------------------------- +// $Id$ +// +// Copyright (C) 2009 - 2013 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + + +// tests thread safety of parallel Trilinos matrices. Same test as +// parallel_matrix_assemble_02 but initializing the matrix from +// CompressedSimpleSparsityPattern instead of a Trilinos sparsity pattern. + +#include "../tests.h" + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include + +std::ofstream logfile("output"); + +using namespace dealii; + + +namespace Assembly +{ + namespace Scratch + { + template + struct Data + { + Data (const FiniteElement &fe, + const Quadrature &quadrature) + : + fe_values(fe, + quadrature, + update_values | update_gradients | + update_quadrature_points | update_JxW_values) + {} + + Data (const Data &data) + : + fe_values(data.fe_values.get_mapping(), + data.fe_values.get_fe(), + data.fe_values.get_quadrature(), + data.fe_values.get_update_flags()) + {} + + FEValues fe_values; + }; + } + + namespace Copy + { + struct Data + { + Data(const bool assemble_reference) + : + assemble_reference(assemble_reference) + {} + std::vector local_dof_indices; + FullMatrix local_matrix; + Vector local_rhs; + const bool assemble_reference; + }; + } +} + +template +class LaplaceProblem +{ +public: + LaplaceProblem (); + ~LaplaceProblem (); + + void run (); + +private: + void setup_system (); + void test_equality (); + void assemble_reference (); + void assemble_test (); + void solve (); + void create_coarse_grid (); + void postprocess (); + + void local_assemble (const FilteredIterator::active_cell_iterator> &cell, + Assembly::Scratch::Data &scratch, + Assembly::Copy::Data &data); + void copy_local_to_global (const Assembly::Copy::Data &data); + + std::vector + get_conflict_indices (FilteredIterator::active_cell_iterator> const &cell) const; + + parallel::distributed::Triangulation triangulation; + + DoFHandler dof_handler; + FE_Q fe; + QGauss quadrature; + + ConstraintMatrix constraints; + + TrilinosWrappers::SparseMatrix reference_matrix; + TrilinosWrappers::SparseMatrix test_matrix; + + TrilinosWrappers::MPI::Vector reference_rhs; + TrilinosWrappers::MPI::Vector test_rhs; + + std::vector::active_cell_iterator> > > graph; +}; + + + +template +class BoundaryValues : public Function +{ +public: + BoundaryValues () : Function () {} + + virtual double value (const Point &p, + const unsigned int component) const; +}; + + +template +double +BoundaryValues::value (const Point &p, + const unsigned int /*component*/) const +{ + double sum = 0; + for (unsigned int d=0; d +class RightHandSide : public Function +{ +public: + RightHandSide () : Function () {} + + virtual double value (const Point &p, + const unsigned int component) const; +}; + + +template +double +RightHandSide::value (const Point &p, + const unsigned int /*component*/) const +{ + double product = 1; + for (unsigned int d=0; d +LaplaceProblem::LaplaceProblem () + : + triangulation (MPI_COMM_WORLD), + dof_handler (triangulation), + fe (1), + quadrature(fe.degree+1) +{ +} + + +template +LaplaceProblem::~LaplaceProblem () +{ + dof_handler.clear (); +} + + + +template +std::vector +LaplaceProblem:: +get_conflict_indices (FilteredIterator::active_cell_iterator> const &cell) const +{ + std::vector local_dof_indices(cell->get_fe().dofs_per_cell); + cell->get_dof_indices(local_dof_indices); + + constraints.resolve_indices(local_dof_indices); + return local_dof_indices; +} + +template +void LaplaceProblem::setup_system () +{ + reference_matrix.clear(); + test_matrix.clear(); + dof_handler.distribute_dofs (fe); + + constraints.clear (); + + DoFTools::make_hanging_node_constraints (dof_handler, constraints); + + // add boundary conditions as inhomogeneous constraints here, do it after + // having added the hanging node constraints in order to be consistent and + // skip dofs that are already constrained (i.e., are hanging nodes on the + // boundary in 3D). In contrast to step-27, we choose a sine function. + VectorTools::interpolate_boundary_values (dof_handler, + 0, + BoundaryValues(), + constraints); + constraints.close (); + + typedef FilteredIterator::active_cell_iterator> CellFilter; + CellFilter begin(IteratorFilters::LocallyOwnedCell(),dof_handler.begin_active()); + CellFilter end(IteratorFilters::LocallyOwnedCell(),dof_handler.end()); + graph = GraphColoring::make_graph_coloring(begin,end, + static_cast + (FilteredIterator::active_cell_iterator> const &)> > + (std_cxx1x::bind(&LaplaceProblem::get_conflict_indices, this,std_cxx1x::_1))); + + IndexSet locally_owned = dof_handler.locally_owned_dofs(); + { + TrilinosWrappers::SparsityPattern csp; + csp.reinit(locally_owned, locally_owned, MPI_COMM_WORLD); + DoFTools::make_sparsity_pattern (dof_handler, csp, + constraints, false); + csp.compress(); + reference_matrix.reinit (csp); + reference_rhs.reinit (locally_owned, MPI_COMM_WORLD); + } + { + IndexSet relevant_set; + DoFTools::extract_locally_relevant_dofs (dof_handler, relevant_set); + CompressedSimpleSparsityPattern csp(dof_handler.n_dofs(), dof_handler.n_dofs(), + relevant_set); + DoFTools::make_sparsity_pattern (dof_handler, csp, + constraints, false); + test_matrix.reinit (locally_owned, csp, MPI_COMM_WORLD, true); + test_rhs.reinit (locally_owned, relevant_set, MPI_COMM_WORLD, true); + } +} + + + +template +void +LaplaceProblem::local_assemble (const FilteredIterator::active_cell_iterator> &cell, + Assembly::Scratch::Data &scratch, + Assembly::Copy::Data &data) +{ + const unsigned int dofs_per_cell = cell->get_fe().dofs_per_cell; + + data.local_matrix.reinit (dofs_per_cell, dofs_per_cell); + data.local_matrix = 0; + + data.local_rhs.reinit (dofs_per_cell); + data.local_rhs = 0; + + scratch.fe_values.reinit (cell); + + const FEValues &fe_values = scratch.fe_values; + + const RightHandSide rhs_function; + + for (unsigned int q_point=0; + q_pointget_dof_indices (data.local_dof_indices); +} + + + +template +void +LaplaceProblem::copy_local_to_global (const Assembly::Copy::Data &data) +{ + if (data.assemble_reference) + constraints.distribute_local_to_global(data.local_matrix, data.local_rhs, + data.local_dof_indices, + reference_matrix, reference_rhs); + else + constraints.distribute_local_to_global(data.local_matrix, data.local_rhs, + data.local_dof_indices, + test_matrix, test_rhs); +} + + + +template +void LaplaceProblem::assemble_reference () +{ + reference_matrix = 0; + reference_rhs = 0; + + Assembly::Copy::Data copy_data(true); + Assembly::Scratch::Data assembly_data(fe, quadrature); + + for (unsigned int color=0; color::active_cell_iterator> >::const_iterator p = graph[color].begin(); + p != graph[color].end(); ++p) + { + local_assemble(*p, assembly_data, copy_data); + copy_local_to_global(copy_data); + } + reference_matrix.compress(VectorOperation::add); + reference_rhs.compress(VectorOperation::add); +} + + + +template +void LaplaceProblem::assemble_test () +{ + test_matrix = 0; + test_rhs = 0; + + WorkStream:: + run (graph, + std_cxx1x::bind (&LaplaceProblem:: + local_assemble, + this, + std_cxx1x::_1, + std_cxx1x::_2, + std_cxx1x::_3), + std_cxx1x::bind (&LaplaceProblem:: + copy_local_to_global, + this, + std_cxx1x::_1), + Assembly::Scratch::Data(fe, quadrature), + Assembly::Copy::Data (false), + 2*multithread_info.n_threads(), + 1); + test_matrix.compress(VectorOperation::add); + test_rhs.compress(VectorOperation::add); + + test_matrix.add(-1, reference_matrix); + + // there should not even be roundoff difference between matrices + deallog.threshold_double(1.e-30); + deallog << "error in matrix: " << test_matrix.frobenius_norm() << std::endl; + test_rhs.add(-1., reference_rhs); + deallog << "error in vector: " << test_rhs.l2_norm() << std::endl; +} + + + +template +void LaplaceProblem::postprocess () +{ + Vector estimated_error_per_cell (triangulation.n_active_cells()); + for (unsigned int i=0; i +void LaplaceProblem::run () +{ + for (unsigned int cycle=0; cycle<3; ++cycle) + { + if (cycle == 0) + { + GridGenerator::hyper_cube(triangulation, 0, 1); + triangulation.refine_global(6); + } + + setup_system (); + + assemble_reference (); + assemble_test (); + + if (cycle < 2) + postprocess (); + } +} + + + +int main (int argc, char **argv) +{ + deallog << std::setprecision (2); + logfile << std::setprecision (2); + deallog.attach(logfile); + deallog.depth_console(0); + + Utilities::MPI::MPI_InitFinalize init(argc, argv, numbers::invalid_unsigned_int); + + { + deallog.push("2d"); + LaplaceProblem<2> laplace_problem; + laplace_problem.run (); + deallog.pop(); + } +} + diff --git a/tests/trilinos/assemble_matrix_parallel_05.mpirun=1.output b/tests/trilinos/assemble_matrix_parallel_05.mpirun=1.output new file mode 100644 index 0000000000..6e5eabc7ba --- /dev/null +++ b/tests/trilinos/assemble_matrix_parallel_05.mpirun=1.output @@ -0,0 +1,7 @@ + +DEAL:2d::error in matrix: 0 +DEAL:2d::error in vector: 0 +DEAL:2d::error in matrix: 0 +DEAL:2d::error in vector: 0 +DEAL:2d::error in matrix: 0 +DEAL:2d::error in vector: 0 diff --git a/tests/trilinos/assemble_matrix_parallel_05.mpirun=4.output b/tests/trilinos/assemble_matrix_parallel_05.mpirun=4.output new file mode 100644 index 0000000000..6e5eabc7ba --- /dev/null +++ b/tests/trilinos/assemble_matrix_parallel_05.mpirun=4.output @@ -0,0 +1,7 @@ + +DEAL:2d::error in matrix: 0 +DEAL:2d::error in vector: 0 +DEAL:2d::error in matrix: 0 +DEAL:2d::error in vector: 0 +DEAL:2d::error in matrix: 0 +DEAL:2d::error in vector: 0 diff --git a/tests/trilinos/assemble_matrix_parallel_06.cc b/tests/trilinos/assemble_matrix_parallel_06.cc new file mode 100644 index 0000000000..592f21a821 --- /dev/null +++ b/tests/trilinos/assemble_matrix_parallel_06.cc @@ -0,0 +1,479 @@ +// --------------------------------------------------------------------- +// $Id$ +// +// Copyright (C) 2009 - 2013 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + + +// tests thread safety of parallel Trilinos block matrices. Same test as +// parallel_matrix_assemble_04 but initializing the matrix from +// BlockCompressedSimpleSparsityPattern instead of a Trilinos sparsity pattern. + +#include "../tests.h" + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include + +std::ofstream logfile("output"); + +using namespace dealii; + + +namespace Assembly +{ + namespace Scratch + { + template + struct Data + { + Data (const FiniteElement &fe, + const Quadrature &quadrature) + : + fe_values(fe, + quadrature, + update_values | update_gradients | + update_quadrature_points | update_JxW_values) + {} + + Data (const Data &data) + : + fe_values(data.fe_values.get_mapping(), + data.fe_values.get_fe(), + data.fe_values.get_quadrature(), + data.fe_values.get_update_flags()) + {} + + FEValues fe_values; + }; + } + + namespace Copy + { + struct Data + { + Data(const bool assemble_reference) + : + assemble_reference(assemble_reference) + {} + std::vector local_dof_indices; + FullMatrix local_matrix; + Vector local_rhs; + const bool assemble_reference; + }; + } +} + +template +class LaplaceProblem +{ +public: + LaplaceProblem (); + ~LaplaceProblem (); + + void run (); + +private: + void setup_system (); + void test_equality (); + void assemble_reference (); + void assemble_test (); + void solve (); + void create_coarse_grid (); + void postprocess (); + + void local_assemble (const FilteredIterator::active_cell_iterator> &cell, + Assembly::Scratch::Data &scratch, + Assembly::Copy::Data &data); + void copy_local_to_global (const Assembly::Copy::Data &data); + + std::vector + get_conflict_indices (FilteredIterator::active_cell_iterator> const &cell) const; + + parallel::distributed::Triangulation triangulation; + + DoFHandler dof_handler; + FESystem fe; + QGauss quadrature; + + ConstraintMatrix constraints; + + TrilinosWrappers::BlockSparseMatrix reference_matrix; + TrilinosWrappers::BlockSparseMatrix test_matrix; + + TrilinosWrappers::MPI::BlockVector reference_rhs; + TrilinosWrappers::MPI::BlockVector test_rhs; + + std::vector::active_cell_iterator> > > graph; +}; + + + +template +class BoundaryValues : public Function +{ +public: + BoundaryValues () : Function (2) {} + + virtual double value (const Point &p, + const unsigned int component) const; +}; + + +template +double +BoundaryValues::value (const Point &p, + const unsigned int /*component*/) const +{ + double sum = 0; + for (unsigned int d=0; d +class RightHandSide : public Function +{ +public: + RightHandSide () : Function () {} + + virtual double value (const Point &p, + const unsigned int component) const; +}; + + +template +double +RightHandSide::value (const Point &p, + const unsigned int /*component*/) const +{ + double product = 1; + for (unsigned int d=0; d +LaplaceProblem::LaplaceProblem () + : + triangulation (MPI_COMM_WORLD), + dof_handler (triangulation), + fe (FE_Q(1),1, FE_Q(2),1), + quadrature(3) +{ +} + + +template +LaplaceProblem::~LaplaceProblem () +{ + dof_handler.clear (); +} + + + +template +std::vector +LaplaceProblem:: +get_conflict_indices (FilteredIterator::active_cell_iterator> const &cell) const +{ + std::vector local_dof_indices(cell->get_fe().dofs_per_cell); + cell->get_dof_indices(local_dof_indices); + + constraints.resolve_indices(local_dof_indices); + return local_dof_indices; +} + +template +void LaplaceProblem::setup_system () +{ + reference_matrix.clear(); + test_matrix.clear(); + dof_handler.distribute_dofs (fe); + std::vector blocks(2,0); + blocks[1] = 1; + DoFRenumbering::component_wise(dof_handler, blocks); + + constraints.clear (); + + DoFTools::make_hanging_node_constraints (dof_handler, constraints); + + // add boundary conditions as inhomogeneous constraints here, do it after + // having added the hanging node constraints in order to be consistent and + // skip dofs that are already constrained (i.e., are hanging nodes on the + // boundary in 3D). In contrast to step-27, we choose a sine function. + VectorTools::interpolate_boundary_values (dof_handler, + 0, + BoundaryValues(), + constraints); + constraints.close (); + + typedef FilteredIterator::active_cell_iterator> CellFilter; + CellFilter begin(IteratorFilters::LocallyOwnedCell(),dof_handler.begin_active()); + CellFilter end(IteratorFilters::LocallyOwnedCell(),dof_handler.end()); + graph = GraphColoring::make_graph_coloring(begin,end, + static_cast + (FilteredIterator::active_cell_iterator> const &)> > + (std_cxx1x::bind(&LaplaceProblem::get_conflict_indices, this,std_cxx1x::_1))); + + TrilinosWrappers::BlockSparsityPattern csp(2,2); + std::vector locally_owned(2), relevant_set(2); + IndexSet locally_owned_total = dof_handler.locally_owned_dofs(), relevant_total; + DoFTools::extract_locally_relevant_dofs (dof_handler, relevant_total); + + std::vector dofs_per_block (2); + DoFTools::count_dofs_per_block (dof_handler, dofs_per_block, blocks); + locally_owned[0] = locally_owned_total.get_view(0, dofs_per_block[0]); + locally_owned[1] = locally_owned_total.get_view(dofs_per_block[0], + dof_handler.n_dofs()); + relevant_set[0] = relevant_total.get_view(0, dofs_per_block[0]); + relevant_set[1] = relevant_total.get_view(dofs_per_block[0], + dof_handler.n_dofs()); + + { + csp.reinit(locally_owned, locally_owned, MPI_COMM_WORLD); + DoFTools::make_sparsity_pattern (dof_handler, csp, + constraints, false); + csp.compress(); + reference_matrix.reinit (csp); + reference_rhs.reinit (locally_owned, MPI_COMM_WORLD); + } + { + BlockCompressedSimpleSparsityPattern csp(relevant_set); + DoFTools::make_sparsity_pattern (dof_handler, csp, + constraints, false); + test_matrix.reinit (locally_owned, csp, MPI_COMM_WORLD, true); + test_rhs.reinit (locally_owned, relevant_set, MPI_COMM_WORLD, true); + } +} + + + +template +void +LaplaceProblem::local_assemble (const FilteredIterator::active_cell_iterator> &cell, + Assembly::Scratch::Data &scratch, + Assembly::Copy::Data &data) +{ + const unsigned int dofs_per_cell = cell->get_fe().dofs_per_cell; + + data.local_matrix.reinit (dofs_per_cell, dofs_per_cell); + data.local_matrix = 0; + + data.local_rhs.reinit (dofs_per_cell); + data.local_rhs = 0; + + scratch.fe_values.reinit (cell); + + const FEValues &fe_values = scratch.fe_values; + + const RightHandSide rhs_function; + + // this does not make a lot of sense physically but it serves the purpose of + // the test well + for (unsigned int q_point=0; + q_pointget_dof_indices (data.local_dof_indices); +} + + + +template +void +LaplaceProblem::copy_local_to_global (const Assembly::Copy::Data &data) +{ + if (data.assemble_reference) + constraints.distribute_local_to_global(data.local_matrix, data.local_rhs, + data.local_dof_indices, + reference_matrix, reference_rhs); + else + constraints.distribute_local_to_global(data.local_matrix, data.local_rhs, + data.local_dof_indices, + test_matrix, test_rhs); +} + + + +template +void LaplaceProblem::assemble_reference () +{ + reference_matrix = 0; + reference_rhs = 0; + + Assembly::Copy::Data copy_data(true); + Assembly::Scratch::Data assembly_data(fe, quadrature); + + for (unsigned int color=0; color::active_cell_iterator> >::const_iterator p = graph[color].begin(); + p != graph[color].end(); ++p) + { + local_assemble(*p, assembly_data, copy_data); + copy_local_to_global(copy_data); + } + reference_matrix.compress(VectorOperation::add); + reference_rhs.compress(VectorOperation::add); +} + + + +template +void LaplaceProblem::assemble_test () +{ + test_matrix = 0; + test_rhs = 0; + + WorkStream:: + run (graph, + std_cxx1x::bind (&LaplaceProblem:: + local_assemble, + this, + std_cxx1x::_1, + std_cxx1x::_2, + std_cxx1x::_3), + std_cxx1x::bind (&LaplaceProblem:: + copy_local_to_global, + this, + std_cxx1x::_1), + Assembly::Scratch::Data(fe, quadrature), + Assembly::Copy::Data (false), + 2*multithread_info.n_threads(), + 1); + test_matrix.compress(VectorOperation::add); + test_rhs.compress(VectorOperation::add); + + test_matrix.add(-1, reference_matrix); + + // there should not even be roundoff difference between matrices + deallog.threshold_double(1.e-30); + double frobenius_norm = 0; + for (unsigned int i=0; i<2; ++i) + for (unsigned int j=0; j<2; ++j) + frobenius_norm += numbers::NumberTraits::abs_square(test_matrix.block(i,j).frobenius_norm()); + deallog << "error in matrix: " << std::sqrt(frobenius_norm) << std::endl; + test_rhs.add(-1., reference_rhs); + deallog << "error in vector: " << test_rhs.l2_norm() << std::endl; +} + + + +template +void LaplaceProblem::postprocess () +{ + Vector estimated_error_per_cell (triangulation.n_active_cells()); + for (unsigned int i=0; i +void LaplaceProblem::run () +{ + for (unsigned int cycle=0; cycle<3; ++cycle) + { + if (cycle == 0) + { + GridGenerator::hyper_shell(triangulation, + Point(), + 0.5, 1., (dim==3) ? 96 : 12, false); +#ifdef DEBUG + triangulation.refine_global(3); +#else + triangulation.refine_global(5); +#endif + } + + setup_system (); + + assemble_reference (); + assemble_test (); + + if (cycle < 2) + postprocess (); + } +} + + + +int main (int argc, char **argv) +{ + deallog << std::setprecision (2); + logfile << std::setprecision (2); + deallog.attach(logfile); + deallog.depth_console(0); + + Utilities::MPI::MPI_InitFinalize init(argc, argv, numbers::invalid_unsigned_int); + + { + deallog.push("2d"); + LaplaceProblem<2> laplace_problem; + laplace_problem.run (); + deallog.pop(); + } +} + diff --git a/tests/trilinos/assemble_matrix_parallel_06.mpirun=4.output b/tests/trilinos/assemble_matrix_parallel_06.mpirun=4.output new file mode 100644 index 0000000000..6e5eabc7ba --- /dev/null +++ b/tests/trilinos/assemble_matrix_parallel_06.mpirun=4.output @@ -0,0 +1,7 @@ + +DEAL:2d::error in matrix: 0 +DEAL:2d::error in vector: 0 +DEAL:2d::error in matrix: 0 +DEAL:2d::error in vector: 0 +DEAL:2d::error in matrix: 0 +DEAL:2d::error in vector: 0