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// $Id: dof_info.h 31076 2013-10-02 17:52:30Z heister $
//
// Copyright (C) 2011 - 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.
//
// ---------------------------------------------------------------------
#ifndef __deal2__matrix_free_dof_info_h
#define __deal2__matrix_free_dof_info_h
#include <deal.II/base/exceptions.h>
#include <deal.II/base/vectorization.h>
#include <deal.II/base/partitioner.h>
#include <deal.II/lac/constraint_matrix.h>
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/matrix_free/helper_functions.h>
#include <deal.II/base/std_cxx1x/array.h>
#include <memory>
DEAL_II_NAMESPACE_OPEN
namespace internal
{
namespace MatrixFreeFunctions
{
/**
* The class that stores the indices of the degrees of freedom for all the
* cells. Essentially, this is a smart number cache in the style of a
* DoFHandler that also embeds the description of constraints directly on
* the cell level without the need to refer to the external
* ConstraintMatrix.
*
* This class only stores index relations. The weights for hanging node
* constraints are stored in a different field. This is because a
* different field allows for the same compressed weight data on different
* DoFHandlers for vector-valued problems. There, the indices might be
* constrained differently on different components (e.g. Dirichlet
* conditions only on selected components), whereas the weights from
* hanging nodes are the same and need to be stored only once. The
* combination will be handled in the MatrixFree class.
*
* @author Katharina Kormann and Martin Kronbichler, 2010, 2011
*/
struct DoFInfo
{
/**
* Default empty constructor.
*/
DoFInfo ();
/**
* Copy constructor.
*/
DoFInfo (const DoFInfo &dof_info);
/**
* Clears all data fields in this class.
*/
void clear ();
/**
* Returns a pointer to the first index in the DoF row @p row.
*/
const unsigned int *begin_indices (const unsigned int row) const;
/**
* Returns a pointer to the one past the last DoF index in the row @p
* row.
*/
const unsigned int *end_indices (const unsigned int row) const;
/**
* Returns the number of entries in the indices field for the given row.
*/
unsigned int row_length_indices (const unsigned int row) const;
/**
* Returns a pointer to the first constraint indicator in the row @p
* row.
*/
const std::pair<unsigned short,unsigned short> *
begin_indicators (const unsigned int row) const;
/**
* Returns a pointer to the one past the last constraint indicator in
* the row @p row.
*/
const std::pair<unsigned short,unsigned short> *
end_indicators (const unsigned int row) const;
/**
* Returns the number of entries in the constraint indicator field for
* the given row.
*/
unsigned int row_length_indicators (const unsigned int row) const;
/**
* Returns a pointer to the first index in the DoF row @p row for plain
* indices (i.e., the entries where constraints are not embedded).
*/
const unsigned int *begin_indices_plain (const unsigned int row) const;
/**
* Returns a pointer to the one past the last DoF index in the row @p
* row (i.e., the entries where constraints are not embedded).
*/
const unsigned int *end_indices_plain (const unsigned int row) const;
/**
* Returns the FE index for a given finite element degree. If not in hp
* mode, this function always returns index 0. If an index is not found
* in hp mode, it returns max_fe_degree, i.e., one index past the last
* valid one.
*/
unsigned int fe_index_from_degree (const unsigned int fe_degree) const;
/**
* Returns the FE index for a given finite element degree. If not in hp
* mode or if the index is not found, this function always returns index
* 0. Hence, this function does not check whether the given degree is
* actually present.
*/
unsigned int
fe_index_from_dofs_per_cell (const unsigned int dofs_per_cell) const;
/**
* This internal method takes the local indices on a cell and fills them
* into this class. It resolves the constraints and distributes the
* results. Ghost indices, i.e., indices that are located on another
* processor, get a temporary number by this function, and will later be
* assigned the correct index after all the ghost indices have been
* collected by the call to @p assign_ghosts.
*/
void read_dof_indices (const std::vector<types::global_dof_index> &local_indices,
const std::vector<unsigned int> &lexicographic_inv,
const ConstraintMatrix &constraints,
const unsigned int cell_number,
ConstraintValues<double> &constraint_values,
bool &cell_at_boundary);
/**
* This method assigns the correct indices to ghost indices from the
* temporary numbering employed by the @p read_dof_indices function. The
* numbers are localized with respect to the MPI process, and ghosts
* start at the end of the locally owned range. This way, we get direct
* access to all vector entries.
*/
void assign_ghosts(const std::vector<unsigned int> &boundary_cells);
/**
* Reorganizes cells for serial (non-thread-parallelized) such that
* boundary cells are places in the middle. This way, computations and
* communication can be overlapped. Should only be called by one DoFInfo
* object when used on a system of several DoFHandlers.
*/
void compute_renumber_serial (const std::vector<unsigned int> &boundary_cells,
const SizeInfo &size_info,
std::vector<unsigned int> &renumbering);
/**
* Reorganizes cells in the hp case without parallelism such that all
* cells with the same FE index are placed consecutively. Should only be
* called by one DoFInfo object when used on a system of several
* DoFHandlers.
*/
void compute_renumber_hp_serial (SizeInfo &size_info,
std::vector<unsigned int> &renumbering,
std::vector<unsigned int> &irregular_cells);
/**
* Computes the initial renumbering of cells such that all cells with
* ghosts are put first. This is the first step before building the
* thread graph and used to overlap computations and communication.
*/
void compute_renumber_parallel (const std::vector<unsigned int> &boundary_cells,
SizeInfo &size_info,
std::vector<unsigned int> &renumbering);
/**
* This method reorders the way cells are gone through based on a given
* renumbering of the cells. It also takes @p vectorization_length cells
* together and interprets them as one cell only, as is needed for
* vectorization.
*/
void reorder_cells (const SizeInfo &size_info,
const std::vector<unsigned int> &renumbering,
const std::vector<unsigned int> &constraint_pool_row_index,
const std::vector<unsigned int> &irregular_cells,
const unsigned int vectorization_length);
/**
* This helper function determines a block size if the user decided not
* to force a block size through MatrixFree::AdditionalData. This is
* computed based on the number of hardware threads on the system
* and the number of macro cells that we should work on.
*/
void guess_block_size (const SizeInfo &size_info,
TaskInfo &task_info);
/**
* This method goes through all cells that have been filled into @p
* dof_indices and finds out which cells can be worked on independently
* and which ones are neighboring and need to be done at different times
* when used in parallel.
*
* The strategy is based on a two-level approach. The outer level is
* subdivided into partitions similar to the type of neighbors in
* Cuthill-McKee, and the inner level is subdivided via colors (for
* chunks within the same color, can work independently). One task is
* represented by a chunk of cells. The cell chunks are formed before
* subdivision into partitions and colors.
*/
void
make_thread_graph_partition_color (SizeInfo &size_info,
TaskInfo &task_info,
std::vector<unsigned int> &renumbering,
std::vector<unsigned int> &irregular_cells,
const bool hp_bool);
/**
* This function goes through all cells that have been filled into @p
* dof_indices and finds out which cells can be worked on independently
* and which ones are neighboring and need to be done at different times
* when used in parallel.
*
* The strategy is based on a two-level approach. The outer level is
* subdivided into partitions similar to the type of neighbors in
* Cuthill-McKee, and the inner level is again subdivided into
* Cuthill-McKee-like partitions (partitions whose level differs by more
* than 2 can be worked on independently). One task is represented by a
* chunk of cells. The cell chunks are formed after subdivision into the
* two levels of partitions.
*/
void
make_thread_graph_partition_partition (SizeInfo &size_info,
TaskInfo &task_info,
std::vector<unsigned int> &renumbering,
std::vector<unsigned int> &irregular_cells,
const bool hp_bool);
/**
* This function computes the connectivity of the currently stored
* indices and fills the structure into a sparsity pattern. The
* parameter block_size can be used to specify whether several cells
* should be treated as one.
*/
void
make_connectivity_graph (const SizeInfo &size_info,
const TaskInfo &task_info,
const std::vector<unsigned int> &renumbering,
const std::vector<unsigned int> &irregular_cells,
const bool do_blocking,
CompressedSimpleSparsityPattern &connectivity) const;
/**
* Renumbers the degrees of freedom to give good access for this class.
*/
void renumber_dofs (std::vector<types::global_dof_index> &renumbering);
/**
* Returns the memory consumption in bytes of this class.
*/
std::size_t memory_consumption() const;
/**
* Prints a detailed summary of memory consumption in the different
* structures of this class to the given output stream.
*/
template <typename STREAM>
void print_memory_consumption(STREAM &out,
const SizeInfo &size_info) const;
/**
* Prints a representation of the indices in the class to the given
* output stream.
*/
template <typename Number>
void print (const std::vector<Number> &constraint_pool_data,
const std::vector<unsigned int> &constraint_pool_row_index,
std::ostream &out) const;
/**
* Stores the rowstart indices of the compressed row storage in the @p
* dof_indices and @p constraint_indicator fields. These two fields are
* always accessed together, so it is simpler to keep just one variable
* for them. This also obviates keeping two rowstart vectors in synch.
*
* In addition, the third field stores whether a particular cell has a
* certain structure in the indices, like indices for vector-valued
* problems or for cells where not all vector components are filled.
*/
std::vector<std_cxx1x::array<unsigned int, 3> > row_starts;
/**
* Stores the indices of the degrees of freedom for each cell. These
* indices are computed in MPI-local index space, i.e., each processor
* stores the locally owned indices as numbers between <tt>0</tt> and
* <tt>n_locally_owned_dofs-1</tt> and ghost indices in the range
* <tt>n_locally_owned_dofs</tt> to
* <tt>n_locally_owned_dofs+n_ghost_dofs</tt>. The translation between
* this MPI-local index space and the global numbering of degrees of
* freedom is stored in the @p vector_partitioner data structure.
* This array also includes the indirect contributions from constraints,
* which are described by the @p constraint_indicator field. Because of
* variable lengths of rows, this would be a vector of a
* vector. However, we use one contiguous memory region and store the
* rowstart in the variable @p row_starts.
*/
std::vector<unsigned int> dof_indices;
/**
* This variable describes the position of constraints in terms of the
* local numbering of degrees of freedom on a cell. The first number
* stores the distance from one constrained degree of freedom to the
* next. This allows to identify the position of constrained DoFs as we
* loop through the local degrees of freedom of the cell when reading
* from or writing to a vector. The second number stores the index of
* the constraint weights, stored in the variable constraint_pool_data.
*/
std::vector<std::pair<unsigned short,unsigned short> > constraint_indicator;
/**
* This stores the parallel partitioning that can be used to set up
* vectors. The partitioner includes the description of the local range
* in the vector, and also includes how the ghosts look like. This
* enables initialization of vectors based on the DoFInfo field.
*/
std_cxx1x::shared_ptr<const Utilities::MPI::Partitioner> vector_partitioner;
/**
* This stores a (sorted) list of all locally owned degrees of freedom
* that are constrained.
*/
std::vector<unsigned int> constrained_dofs;
/**
* Stores the rowstart indices of the compressed row storage in the @p
* plain_dof_indices fields.
*/
std::vector<unsigned int> row_starts_plain_indices;
/**
* Stores the indices of the degrees of freedom for each cell. This
* array does not include the indirect contributions from constraints,
* which are included in @p dof_indices. Because of variable lengths of
* rows, this would be a vector of a vector. However, we use one
* contiguous memory region and store the rowstart in the variable @p
* row_starts_plain_indices.
*/
std::vector<unsigned int> plain_dof_indices;
/**
* Stores the dimension of the underlying DoFHandler. Since the indices
* are not templated, this is the variable that makes the dimension
* accessible in the (rare) cases it is needed inside this class.
*/
unsigned int dimension;
/**
* Stores the number of components in the DoFHandler where the indices
* have been read from.
*/
unsigned int n_components;
/**
* Stores the number of degrees of freedom per cell.
*/
std::vector<unsigned int> dofs_per_cell;
/**
* Stores the number of degrees of freedom per face.
*/
std::vector<unsigned int> dofs_per_face;
/**
* Informs on whether plain indices are cached.
*/
bool store_plain_indices;
/**
* Stores the index of the active finite element in the hp case.
*/
std::vector<unsigned int> cell_active_fe_index;
/**
* Stores the maximum degree of different finite elements for the hp
* case.
*/
unsigned int max_fe_index;
/**
* This variable stores the dofs per cell and the finite element degree
* associated for all fe indices in the underlying element for easier
* access to data in the hp case.
*/
std::vector<std::pair<unsigned int,unsigned int> > fe_index_conversion;
/**
* Temporarily stores the numbers of ghosts during setup. Cleared when
* calling @p assign_ghosts. Then, all information is collected by the
* partitioner.
*/
std::vector<types::global_dof_index> ghost_dofs;
};
/*----------------------- Inline functions ----------------------------------*/
#ifndef DOXYGEN
inline
const unsigned int *
DoFInfo::begin_indices (const unsigned int row) const
{
AssertIndexRange (row, row_starts.size()-1);
const unsigned int index = row_starts[row][0];
AssertIndexRange(index, dof_indices.size()+1);
return dof_indices.empty() ? 0 : &dof_indices[0] + index;
}
inline
const unsigned int *
DoFInfo::end_indices (const unsigned int row) const
{
AssertIndexRange (row, row_starts.size()-1);
const unsigned int index = row_starts[row+1][0];
AssertIndexRange(index, dof_indices.size()+1);
return dof_indices.empty() ? 0 : &dof_indices[0] + index;
}
inline
unsigned int
DoFInfo::row_length_indices (const unsigned int row) const
{
AssertIndexRange (row, row_starts.size()-1);
return (row_starts[row+1][0] - row_starts[row][0]);
}
inline
const std::pair<unsigned short,unsigned short> *
DoFInfo::begin_indicators (const unsigned int row) const
{
AssertIndexRange (row, row_starts.size()-1);
const unsigned int index = row_starts[row][1];
AssertIndexRange (index, constraint_indicator.size()+1);
return constraint_indicator.empty() ? 0 : &constraint_indicator[0] + index;
}
inline
const std::pair<unsigned short,unsigned short> *
DoFInfo::end_indicators (const unsigned int row) const
{
AssertIndexRange (row, row_starts.size()-1);
const unsigned int index = row_starts[row+1][1];
AssertIndexRange (index, constraint_indicator.size()+1);
return constraint_indicator.empty() ? 0 : &constraint_indicator[0] + index;
}
inline
unsigned int
DoFInfo::row_length_indicators (const unsigned int row) const
{
AssertIndexRange (row, row_starts.size()-1);
return (row_starts[row+1][1] - row_starts[row][1]);
}
inline
const unsigned int *
DoFInfo::begin_indices_plain (const unsigned int row) const
{
// if we have no constraints, should take the data from dof_indices
if (row_length_indicators(row) == 0)
{
Assert (row_starts_plain_indices[row]==numbers::invalid_unsigned_int,
ExcInternalError());
return begin_indices(row);
}
else
{
AssertDimension (row_starts.size(), row_starts_plain_indices.size());
const unsigned int index = row_starts_plain_indices[row];
AssertIndexRange(index, plain_dof_indices.size()+1);
return plain_dof_indices.empty() ? 0 : &plain_dof_indices[0] + index;
}
}
inline
const unsigned int *
DoFInfo::end_indices_plain (const unsigned int row) const
{
return begin_indices_plain(row) +
dofs_per_cell[(cell_active_fe_index.size()==0)?
0:cell_active_fe_index[row]];
}
inline
unsigned int
DoFInfo::fe_index_from_degree (const unsigned int fe_degree) const
{
const unsigned int n_indices = fe_index_conversion.size();
for (unsigned int i=0; i<n_indices; ++i)
if (fe_index_conversion[i].first == fe_degree)
return i;
return n_indices;
}
inline
unsigned int
DoFInfo::fe_index_from_dofs_per_cell (const unsigned int dofs_per_cell) const
{
for (unsigned int i=0; i<fe_index_conversion.size(); ++i)
if (fe_index_conversion[i].second == dofs_per_cell)
return i;
return 0;
}
} // end of namespace MatrixFreeFunctions
} // end of namespace internal
#endif // ifndef DOXYGEN
DEAL_II_NAMESPACE_CLOSE
#endif
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