Reference documentation for deal.II version 8.1.0
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CompressedSetSparsityPattern Class Reference

#include <compressed_set_sparsity_pattern.h>

Inheritance diagram for CompressedSetSparsityPattern:
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Classes

struct  Line
 

Public Types

typedef types::global_dof_index size_type
 
typedef std::set< size_type >
::const_iterator 
row_iterator
 

Public Member Functions

 CompressedSetSparsityPattern ()
 
 CompressedSetSparsityPattern (const CompressedSetSparsityPattern &)
 
 CompressedSetSparsityPattern (const size_type m, const size_type n)
 
 CompressedSetSparsityPattern (const size_type n)
 
CompressedSetSparsityPatternoperator= (const CompressedSetSparsityPattern &)
 
void reinit (const size_type m, const size_type n)
 
void compress ()
 
bool empty () const
 
size_type max_entries_per_row () const
 
void add (const size_type i, const size_type j)
 
template<typename ForwardIterator >
void add_entries (const size_type row, ForwardIterator begin, ForwardIterator end, const bool indices_are_sorted=false)
 
bool exists (const size_type i, const size_type j) const
 
void symmetrize ()
 
void print (std::ostream &out) const
 
void print_gnuplot (std::ostream &out) const
 
size_type n_rows () const
 
size_type n_cols () const
 
size_type row_length (const size_type row) const
 
row_iterator row_begin (const size_type row) const
 
row_iterator row_end (const size_type row) const
 
size_type bandwidth () const
 
size_type n_nonzero_elements () const
 
- Public Member Functions inherited from Subscriptor
 Subscriptor ()
 
 Subscriptor (const Subscriptor &)
 
virtual ~Subscriptor ()
 
Subscriptoroperator= (const Subscriptor &)
 
void subscribe (const char *identifier=0) const
 
void unsubscribe (const char *identifier=0) const
 
unsigned int n_subscriptions () const
 
void list_subscribers () const
 
 DeclException3 (ExcInUse, int, char *, std::string &,<< "Object of class "<< arg2<< " is still used by "<< arg1<< " other objects.\n"<< "(Additional information: "<< arg3<< ")\n"<< "Note the entry in the Frequently Asked Questions of "<< "deal.II (linked to from http://www.dealii.org/) for "<< "more information on what this error means.")
 
 DeclException2 (ExcNoSubscriber, char *, char *,<< "No subscriber with identifier \""<< arg2<< "\" did subscribe to this object of class "<< arg1)
 
template<class Archive >
void serialize (Archive &ar, const unsigned int version)
 

Static Public Member Functions

static bool stores_only_added_elements ()
 

Private Attributes

size_type rows
 
size_type cols
 
std::vector< Linelines
 

Detailed Description

This class acts as an intermediate form of the SparsityPattern class. From the interface it mostly represents a SparsityPattern object that is kept compressed at all times. However, since the final sparsity pattern is not known while constructing it, keeping the pattern compressed at all times can only be achieved at the expense of either increased memory or run time consumption upon use. The main purpose of this class is to avoid some memory bottlenecks, so we chose to implement it memory conservative, but the chosen data format is too unsuited to be used for actual matrices. It is therefore necessary to first copy the data of this object over to an object of type SparsityPattern before using it in actual matrices.

Another viewpoint is that this class does not need up front allocation of a certain amount of memory, but grows as necessary. An extensive description of sparsity patterns can be found in the documentation of the Sparsity patterns module.

This class is an example of the "dynamic" type of Sparsity patterns. It is discussed in the step-27 and step-22 tutorial programs.

Interface

Since this class is intended as an intermediate replacement of the SparsityPattern class, it has mostly the same interface, with small changes where necessary. In particular, the add() function, and the functions inquiring properties of the sparsity pattern are the same.

Usage

Use this class as follows:

CompressedSetSparsityPattern compressed_pattern (dof_handler.n_dofs());
compressed_pattern);
constraints.condense (compressed_pattern);
sp.copy_from (compressed_pattern);

See also step-11 and step-18 for usage patterns of the related CompressedSparsityPattern class, and step-27 of the current class.

Notes

There are several, exchangeable variations of this class, see Sparsity patterns, section '"Dynamic" or "compressed" sparsity patterns' for more information.

This class is a variation of the CompressedSparsityPattern class. Instead of using sorted vectors together with a caching algorithm for storing the column indices of nonzero entries, the std::set container is used. This solution might not be the fastest in all situations, but seems to work much better than the CompressedSparsityPattern in the context of hp-adaptivity (see for example step-27), or generally when there are many nonzero entries in each row of a matrix (see step-22). On the other hand, a benchmark where nonzero entries were randomly inserted into the sparsity pattern revealed that this class is slower by a factor 4-6 in this situation. Hence, currently the suggestion is to carefully analyze which of the CompressedSparsityPattern classes works best in a certain setting. An algorithm which performs equally well in all situations still has to be found.

Author
Oliver Kayser-Herold, 2007

Definition at line 111 of file compressed_set_sparsity_pattern.h.

Member Typedef Documentation

Declare the type for container size.

Definition at line 117 of file compressed_set_sparsity_pattern.h.

typedef std::set<size_type>::const_iterator CompressedSetSparsityPattern::row_iterator

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.

Definition at line 125 of file compressed_set_sparsity_pattern.h.

Constructor & Destructor Documentation

CompressedSetSparsityPattern::CompressedSetSparsityPattern ( )

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.

CompressedSetSparsityPattern::CompressedSetSparsityPattern ( const CompressedSetSparsityPattern )

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 yo want to use the STL data types on classes like this, e.g. to write such statements like v.push_back (CompressedSetSparsityPattern());, with v a vector of CompressedSetSparsityPattern objects.

CompressedSetSparsityPattern::CompressedSetSparsityPattern ( const size_type  m,
const size_type  n 
)

Initialize a rectangular matrix with m rows and n columns.

CompressedSetSparsityPattern::CompressedSetSparsityPattern ( const size_type  n)

Initialize a square matrix of dimension n.

Member Function Documentation

CompressedSetSparsityPattern& CompressedSetSparsityPattern::operator= ( const CompressedSetSparsityPattern )

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.

void CompressedSetSparsityPattern::reinit ( const size_type  m,
const size_type  n 
)

Reallocate memory and set up data structures for a new matrix with m rows and n columns, with at most max_entries_per_row() nonzero entries per row.

void CompressedSetSparsityPattern::compress ( )

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.

bool CompressedSetSparsityPattern::empty ( ) const

Return whether the object is empty. It is empty if no memory is allocated, which is the same as that both dimensions are zero.

size_type CompressedSetSparsityPattern::max_entries_per_row ( ) const

Return the maximum number of entries per row. Note that this number may change as entries are added.

void CompressedSetSparsityPattern::add ( const size_type  i,
const size_type  j 
)
inline

Add a nonzero entry to the matrix. If the entry already exists, nothing bad happens.

Definition at line 468 of file compressed_set_sparsity_pattern.h.

template<typename ForwardIterator >
void CompressedSetSparsityPattern::add_entries ( const size_type  row,
ForwardIterator  begin,
ForwardIterator  end,
const bool  indices_are_sorted = false 
)
inline

Add several nonzero entries to the specified row of the matrix. If the entries already exist, nothing bad happens.

Definition at line 482 of file compressed_set_sparsity_pattern.h.

bool CompressedSetSparsityPattern::exists ( const size_type  i,
const size_type  j 
) const

Check if a value at a certain position may be non-zero.

void CompressedSetSparsityPattern::symmetrize ( )

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.

void CompressedSetSparsityPattern::print ( std::ostream &  out) const

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 CompressedSetSparsityPattern::print_gnuplot ( std::ostream &  out) const

Print the sparsity of the matrix in a format that 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 plot command.

CompressedSetSparsityPattern::size_type CompressedSetSparsityPattern::n_rows ( ) const
inline

Return number of rows of this matrix, which equals the dimension of the image space.

Definition at line 450 of file compressed_set_sparsity_pattern.h.

CompressedSetSparsityPattern::size_type CompressedSetSparsityPattern::n_cols ( ) const
inline

Return number of columns of this matrix, which equals the dimension of the range space.

Definition at line 459 of file compressed_set_sparsity_pattern.h.

CompressedSetSparsityPattern::size_type CompressedSetSparsityPattern::row_length ( const size_type  row) const
inline

Number of entries in a specific row.

Definition at line 496 of file compressed_set_sparsity_pattern.h.

CompressedSetSparsityPattern::row_iterator CompressedSetSparsityPattern::row_begin ( const size_type  row) const
inline

Return an iterator that can loop over all entries in the given row. Dereferencing the iterator yields a column index.

Definition at line 507 of file compressed_set_sparsity_pattern.h.

CompressedSetSparsityPattern::row_iterator CompressedSetSparsityPattern::row_end ( const size_type  row) const
inline

End iterator for the given row.

Definition at line 516 of file compressed_set_sparsity_pattern.h.

size_type CompressedSetSparsityPattern::bandwidth ( ) 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.

size_type CompressedSetSparsityPattern::n_nonzero_elements ( ) const

Return the number of nonzero elements allocated through this sparsity pattern.

bool CompressedSetSparsityPattern::stores_only_added_elements ( )
inlinestatic

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 template arguments.

Definition at line 525 of file compressed_set_sparsity_pattern.h.

Member Data Documentation

size_type CompressedSetSparsityPattern::rows
private

Number of rows that this sparsity structure shall represent.

Definition at line 370 of file compressed_set_sparsity_pattern.h.

size_type CompressedSetSparsityPattern::cols
private

Number of columns that this sparsity structure shall represent.

Definition at line 376 of file compressed_set_sparsity_pattern.h.

std::vector<Line> CompressedSetSparsityPattern::lines
private

Actual data: store for each row the set of nonzero entries.

Definition at line 415 of file compressed_set_sparsity_pattern.h.


The documentation for this class was generated from the following file: