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Reference documentation for deal.II version 9.6.0
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Reference documentation for deal.II version 9.6.0
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#include <deal.II/base/index_set.h>
Classes | |
| class | ElementIterator |
| class | IntervalAccessor |
| class | IntervalIterator |
| struct | Range |
Public Types | |
| using | size_type = types::global_dof_index |
| using | value_type = signed int |
Public Member Functions | |
| IndexSet () | |
| IndexSet (const size_type size) | |
| IndexSet (const IndexSet &)=default | |
| IndexSet & | operator= (const IndexSet &)=default |
| IndexSet (IndexSet &&is) noexcept | |
| IndexSet & | operator= (IndexSet &&is) noexcept |
| template<typename NodeType > | |
| IndexSet (const Teuchos::RCP< const Tpetra::Map< int, types::signed_global_dof_index, NodeType > > &map) | |
| IndexSet (const Epetra_BlockMap &map) | |
| void | clear () |
| void | set_size (const size_type size) |
| size_type | size () const |
| void | add_range (const size_type begin, const size_type end) |
| void | add_index (const size_type index) |
| template<typename ForwardIterator > | |
| void | add_indices (const ForwardIterator &begin, const ForwardIterator &end) |
| void | add_indices (const IndexSet &other, const size_type offset=0) |
| bool | is_element (const size_type index) const |
| bool | is_contiguous () const |
| bool | is_empty () const |
| bool | is_ascending_and_one_to_one (const MPI_Comm communicator) const |
| size_type | n_elements () const |
| size_type | nth_index_in_set (const size_type local_index) const |
| size_type | index_within_set (const size_type global_index) const |
| unsigned int | n_intervals () const |
| size_type | largest_range_starting_index () const |
| void | compress () const |
| bool | operator== (const IndexSet &is) const |
| bool | operator!= (const IndexSet &is) const |
| IndexSet | operator& (const IndexSet &is) const |
| IndexSet | get_view (const size_type begin, const size_type end) const |
| IndexSet | get_view (const IndexSet &mask) const |
| std::vector< IndexSet > | split_by_block (const std::vector< types::global_dof_index > &n_indices_per_block) const |
| void | subtract_set (const IndexSet &other) |
| IndexSet | tensor_product (const IndexSet &other) const |
| size_type | pop_back () |
| size_type | pop_front () |
| std::vector< size_type > | get_index_vector () const |
| void | fill_index_vector (std::vector< size_type > &indices) const |
| template<typename VectorType > | |
| void | fill_binary_vector (VectorType &vector) const |
| bool | is_subset_of (const IndexSet &other) const |
| template<typename StreamType > | |
| void | print (StreamType &out) const |
| void | write (std::ostream &out) const |
| void | read (std::istream &in) |
| void | block_write (std::ostream &out) const |
| void | block_read (std::istream &in) |
| Epetra_Map | make_trilinos_map (const MPI_Comm communicator=MPI_COMM_WORLD, const bool overlapping=false) const |
| template<typename NodeType = LinearAlgebra::TpetraWrappers::TpetraTypes::NodeType<MemorySpace::Host>> | |
| Tpetra::Map< int, types::signed_global_dof_index, NodeType > | make_tpetra_map (const MPI_Comm communicator=MPI_COMM_WORLD, const bool overlapping=false) const |
| template<typename NodeType = LinearAlgebra::TpetraWrappers::TpetraTypes::NodeType<MemorySpace::Host>> | |
| Teuchos::RCP< Tpetra::Map< int, types::signed_global_dof_index, NodeType > > | make_tpetra_map_rcp (const MPI_Comm communicator=MPI_COMM_WORLD, const bool overlapping=false) const |
| IS | make_petsc_is (const MPI_Comm communicator=MPI_COMM_WORLD) const |
| std::size_t | memory_consumption () const |
| template<class Archive > | |
| void | serialize (Archive &ar, const unsigned int version) |
| template<typename Vector > | |
| void | fill_binary_vector (Vector &vector) const |
Iterators | |
| ElementIterator | begin () const |
| ElementIterator | at (const size_type global_index) const |
| ElementIterator | end () const |
| IntervalIterator | begin_intervals () const |
| IntervalIterator | end_intervals () const |
Static Public Member Functions | |
| static ::ExceptionBase & | ExcIndexNotPresent (size_type arg1) |
Private Member Functions | |
| void | do_compress () const |
| bool | is_element_binary_search (const size_type local_index) const |
| size_type | nth_index_in_set_binary_search (const size_type local_index) const |
| size_type | index_within_set_binary_search (const size_type global_index) const |
| void | add_range_lower_bound (const Range &range) |
| void | add_ranges_internal (boost::container::small_vector< std::pair< size_type, size_type >, 200 > &tmp_ranges, const bool ranges_are_sorted) |
Private Attributes | |
| std::vector< Range > | ranges |
| bool | is_compressed |
| size_type | index_space_size |
| size_type | largest_range |
| Threads::Mutex | compress_mutex |
Related Symbols | |
(Note that these are not member symbols.) | |
| IndexSet | complete_index_set (const IndexSet::size_type N) |
A class that represents a subset of indices among a larger set. For example, it can be used to denote the set of degrees of freedom within the range \([0,\mathrm{dof\_handler.n\_dofs()})\) that belongs to a particular subdomain, or those among all degrees of freedom that are stored on a particular processor in a distributed parallel computation.
This class can represent a collection of half-open ranges of indices as well as individual elements. For practical purposes it also stores the overall range these indices can assume. In other words, you need to specify the size of the index space \([0,\text{size})\) of which objects of this class are a subset.
There are two ways to iterate over the IndexSets: First, begin() and end() allow iteration over individual indices in the set. Second, begin_interval() and end_interval() allow iteration over the half-open ranges as described above.
The data structures used in this class along with a rationale can be found in the Distributed Computing paper.
Definition at line 69 of file index_set.h.
size_type is the type used for storing the size and the individual entries in the IndexSet.
Definition at line 80 of file index_set.h.
| using IndexSet::value_type = signed int |
One can see an IndexSet as a container of size size(), where the elements of the containers are bool values that are either false or true, depending on whether a particular index is an element of the IndexSet or not. In other words, an IndexSet is a bit like a vector in which the elements we store are booleans. In this view, the correct local alias indicating the type of the elements of the vector would then be bool.
On the other hand, bool has the disadvantage that it is not a numerical type that, for example, allows multiplication with a double. In other words, one can not easily use a vector of booleans in a place where other vectors are allowed. Consequently, we declare the type of the elements of such a vector as a signed integer. This uses the fact that in the C++ language, booleans are implicitly convertible to integers. In other words, declaring the type of the elements of the vector as a signed integer is only a small lie, but it is a useful one.
Definition at line 99 of file index_set.h.
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Default constructor.
Definition at line 1657 of file index_set.h.
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inlineexplicit |
Constructor that also sets the overall size of the index range.
Definition at line 1665 of file index_set.h.
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Copy constructor.
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inlinenoexcept |
Move constructor. Create a new IndexSet by transferring the internal data of the input set.
Definition at line 1673 of file index_set.h.
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explicit |
Constructor from a Trilinos Teuchos::RCP<Tpetra::Map>.
Definition at line 44 of file index_set.cc.
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explicit |
Constructor from a Trilinos Epetra_BlockMap.
Definition at line 109 of file index_set.cc.
Move assignment operator. Transfer the internal data of the input set into the current one.
Definition at line 1690 of file index_set.h.
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Remove all indices from this index set. The index set retains its size, however.
Definition at line 1752 of file index_set.h.
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inline |
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.
Definition at line 1764 of file index_set.h.
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inline |
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().
Definition at line 1776 of file index_set.h.
Add the half-open range \([\text{begin},\text{end})\) to the set of indices represented by this class.
| [in] | begin | The first element of the range to be added. |
| [in] | end | The past-the-end element of the range to be added. |
Definition at line 1803 of file index_set.h.
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Add an individual index to the set of indices.
If you have many indices to add to the set, consider calling the add_indices() function below. It is considerably more efficient, particularly if the indices to be added are stored in an array that is already sorted.
Definition at line 1795 of file index_set.h.
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Add a whole set of indices described by dereferencing every element of the iterator range [begin,end).
| [in] | begin | Iterator to the first element of range of indices to be added. |
| [in] | end | The past-the-end iterator for the range of elements to be added. |
begin<=end needs to be satisfied. They also obviously have to point into the same container.(1,1,1,2,2,4,6,8,8,8)). In other words, it is very useful to call std::sort() on the range of indices you are about to add, but it is not necessary to call the usual combination of std::unique and std::erase to reduce the list of indices to only a set of unique elements. Definition at line 1831 of file index_set.h.
Add the given IndexSet other to the current one, constructing the union of *this and other.
If the offset argument is nonzero, then every index in other is shifted by 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 other index set lie outside the range [0,size()) represented by the current object.
Definition at line 652 of file index_set.cc.
Return whether the specified index is an element of the index set.
Definition at line 1894 of file index_set.h.
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Return whether the index set stored by this object defines a contiguous range. This is true also if no indices are stored at all.
Definition at line 1917 of file index_set.h.
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Return whether the index set stored by this object contains no elements. This is similar, but faster than checking n_elements() == 0.
Note that a set being empty does not imply that the size of the index space must be zero. Rather, this function returns true if the subset of indices in the index space is the empty set, regardless of the size of the index space.
Definition at line 1926 of file index_set.h.
Return whether the IndexSets are ascending with respect to MPI process number and 1:1, i.e., each index is contained in exactly one IndexSet (among those stored on the different processes), each process stores contiguous subset of indices, and the index set on process \(p+1\) starts at the index one larger than the last one stored on process \(p\). In case there is only one MPI process, this just means that the IndexSet is complete.
Definition at line 1130 of file index_set.cc.
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Return the number of elements stored in this index set.
Definition at line 1934 of file index_set.h.
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Return the global index of the local index with number local_index stored in this index set. local_index obviously needs to be less than n_elements().
Definition at line 1982 of file index_set.h.
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inline |
Return the how-manyth element of this set (counted in ascending order) global_index is. global_index needs to be less than the size(). This function returns numbers::invalid_dof_index if the index global_index is not actually a member of this index set, i.e. if is_element(global_index) is false.
Definition at line 2001 of file index_set.h.
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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.
Definition at line 1959 of file index_set.h.
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inline |
This function returns the local index of the beginning of the largest range.
In other words, the return value is nth_index_in_set(x), where x is the first index of the largest contiguous range of indices in the IndexSet. The return value is therefore equal to the number of elements in the set that come before the largest range.
This call assumes that the IndexSet is nonempty.
Definition at line 1968 of file index_set.h.
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Compress the internal representation by merging individual elements with contiguous ranges, etc. This function does not have any external effect.
Definition at line 1784 of file index_set.h.
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), or if one of the two objects being compared is empty. The comparison between two objects of different sizes would of course, intuitively, result in a false outcome, but it is often a sign of a programming mistake to compare index sets of different sizes against each other, and the comparison is consequently not allowed. On the other hand, the comparison against an empty object makes sense to ensure, for example, that an IndexSet object has been initialized.
Definition at line 2027 of file index_set.h.
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), or if one of the two objects being compared is empty. The comparison between two objects of different sizes would of course, intuitively, result in a false outcome, but it is often a sign of a programming mistake to compare index sets of different sizes against each other, and the comparison is consequently not allowed. On the other hand, the comparison against an empty object makes sense to ensure, for example, that an IndexSet object has been initialized.
Definition at line 2048 of file index_set.h.
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).
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.
A more general function of the same name, taking a mask instead of just an interval to define the view, is below.
Definition at line 273 of file index_set.cc.
This command takes a "mask", i.e., a second index set of same size as the current one and returns the intersection of the current index set the mask, shifted to the index of an entry within the given mask. For example, if the current object is a an IndexSet object representing an index space [0,100) containing indices [20,40), and if the mask represents an index space of the same size but containing all 50 odd indices in this range, then the result will be an index set for a space of size 50 that contains those indices that correspond to the question "the how many'th entry in the mask are the indices [20,40). This will result in an index set of size 50 that contains the indices {11,12,13,14,15,16,17,18,19,20} (because, for example, the index 20 in the original set is not in the mask, but 21 is and corresponds to the 11th entry of the mask – the mask contains the elements {1,3,5,7,9,11,13,15,17,19,21,...}).
In other words, the result of this operation is the intersection of the set represented by the current object and the mask, as seen within the mask. This corresponds to the notion of a view: The mask is a window through which we see the set represented by the current object.
A typical case where this function is useful is as follows. Say, you have a block linear system in which you have blocks corresponding to variables \((u,p,T,c)\) (which you can think of as velocity, pressure, temperature, and chemical composition – or whatever other kind of problem you are currently considering in your own work). We solve this in parallel, so every MPI process has its own locally_owned_dofs index set that describes which among all \(N_\text{dofs}\) degrees of freedom this process owns. Let's assume we have developed a linear solver or preconditioner that first solves the coupled \(u\)- \(T\) system, and once that is done, solves the \(p\)- \(c\) system. In this case, it is often useful to set up block vectors with only two components corresponding to the \(u\) and \(T\) components, and later for only the \(p\)- \(c\) components of the solution. The question is which of the components of these 2-block vectors are locally owned? The answer is that we need to get a view of the locally_owned_dofs index set in which we apply a mask that corresponds to the variables we're currently interested in. For the \(u\)- \(T\) system, we need a mask (corresponding to an index set of size \(N_\text{dofs}\)) that contains all indices of \(u\) degrees of freedom as well as all indices of \(T\) degrees of freedom. The resulting view is an index set of size \(N_u+N_T\) that contains the indices of the locally owned \(u\) and \(T\) degrees of freedom.
Definition at line 308 of file index_set.cc.
| std::vector< IndexSet > IndexSet::split_by_block | ( | const std::vector< types::global_dof_index > & | n_indices_per_block | ) | const |
Split the set indices represented by this object into blocks given by the n_indices_per_block structure. The sum of its entries must match the global size of the current object.
Definition at line 444 of file index_set.cc.
| void IndexSet::subtract_set | ( | const IndexSet & | other | ) |
Remove all elements contained in other from this set. In other words, if \(x\) is the current object and \(o\) the argument, then we compute \(x
\leftarrow x \backslash o\).
Definition at line 473 of file index_set.cc.
Return a new IndexSet, with global size equal to this->size()*other.size(), containing for every element n of this IndexSet, the entries in the half open range [n*other.size(), (n+1)*other.size()) of the other IndexSet.
The name results from the perspective that one starts with an IndexSet and takes the tensor product with another IndexSet with other.size() elements; this results in a matrix of size this->size() times other.size() that has ones in exactly the rows for which this IndexSet contained an index and in the columns for which the other IndexSet contained an index. This matrix is then "unrolled" again by going through each row one by one and reindexing the entries of the matrix in consecutive order. A one in the matrix then corresponds to an entry in the reindexed IndexSet that is returned by this function.
Definition at line 542 of file index_set.cc.
| IndexSet::size_type IndexSet::pop_back | ( | ) |
Remove and return the last element of the last range. This function throws an exception if the IndexSet is empty.
Definition at line 554 of file index_set.cc.
| IndexSet::size_type IndexSet::pop_front | ( | ) |
Remove and return the first element of the first range. This function throws an exception if the IndexSet is empty.
Definition at line 572 of file index_set.cc.
| std::vector< IndexSet::size_type > IndexSet::get_index_vector | ( | ) | const |
Return a vector with all indices contained in this IndexSet. This vector may of course be quite large if the IndexSet stores many indices. (This may be true even if the IndexSet itself does not take up much memory: IndexSet stores indices in a compressed format in which contiguous ranges of indices are only stored using pairs of indices.)
Definition at line 926 of file index_set.cc.
| void IndexSet::fill_index_vector | ( | std::vector< size_type > & | indices | ) | const |
Fill the given vector with all indices contained in this IndexSet.
This function is equivalent to calling get_index_vector() and assigning the result to the indices argument.
Definition at line 945 of file index_set.cc.
| void IndexSet::fill_binary_vector | ( | VectorType & | vector | ) | 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.
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<bool>, std::vector<int>, and std::vector<double>.
Determine whether the current object represents a set of indices that is a subset of the set represented by the argument. This function returns true if the two sets are the same, that is, it considers the "subset" comparison typically used in set theory, rather than the "strict subset" comparison.
Definition at line 706 of file index_set.cc.
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Output a text representation of this IndexSet to the given stream. Used for testing.
Definition at line 2089 of file index_set.h.
| void IndexSet::write | ( | std::ostream & | out | ) | const |
Write the IndexSet into a text based file format, that can be read in again using the read() function.
Definition at line 730 of file index_set.cc.
| void IndexSet::read | ( | std::istream & | in | ) |
Construct the IndexSet from a text based representation given by the stream in written by the write() function.
Definition at line 745 of file index_set.cc.
| void IndexSet::block_write | ( | std::ostream & | out | ) | const |
Write the IndexSet into a binary, compact representation, that can be read in again using the block_read() function.
Definition at line 767 of file index_set.cc.
| void IndexSet::block_read | ( | std::istream & | in | ) |
Construct the IndexSet from a binary representation given by the stream in written by the write_block() function.
Definition at line 781 of file index_set.cc.
| Epetra_Map IndexSet::make_trilinos_map | ( | const MPI_Comm | communicator = MPI_COMM_WORLD, |
| const bool | overlapping = false ) const |
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 with 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, and they also do not need to span the whole index set. 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. Another application of this method is to select a subset of the elements of a vector, e.g. for extracting only certain solution components.
Definition at line 1041 of file index_set.cc.
| Tpetra::Map< int, types::signed_global_dof_index, NodeType > IndexSet::make_tpetra_map | ( | const MPI_Comm | communicator = MPI_COMM_WORLD, |
| const bool | overlapping = false ) const |
Definition at line 957 of file index_set.cc.
| Teuchos::RCP< Tpetra::Map< int, types::signed_global_dof_index, NodeType > > IndexSet::make_tpetra_map_rcp | ( | const MPI_Comm | communicator = MPI_COMM_WORLD, |
| const bool | overlapping = false ) const |
Definition at line 967 of file index_set.cc.
| IS IndexSet::make_petsc_is | ( | const MPI_Comm | communicator = MPI_COMM_WORLD | ) | const |
Definition at line 1110 of file index_set.cc.
| std::size_t IndexSet::memory_consumption | ( | ) | const |
Determine an estimate for the memory consumption (in bytes) of this object.
Definition at line 1196 of file index_set.cc.
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Write or read the data of this object to or from a stream for the purpose of serialization using the BOOST serialization library.
Definition at line 2120 of file index_set.h.
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Return an iterator that points at the first index that is contained in this IndexSet.
Definition at line 1710 of file index_set.h.
| IndexSet::ElementIterator IndexSet::at | ( | const size_type | global_index | ) | const |
Return an element iterator pointing to the element with global index global_index or the next larger element if the index is not in the set. This is equivalent to
If there is no element in this IndexSet at or behind global_index, this method will return end().
Definition at line 876 of file index_set.cc.
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Return an iterator that points one after the last index that is contained in this IndexSet.
Definition at line 1722 of file index_set.h.
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Return an Iterator that points at the first interval of this IndexSet.
Definition at line 1731 of file index_set.h.
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Return an Iterator that points one after the last interval of this IndexSet.
Definition at line 1743 of file index_set.h.
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Actually perform the compress() operation.
Definition at line 139 of file index_set.cc.
Expensive part of is_element() that does a binary search in case we did not find the index in the largest range. Kept separate to avoid pulling in a binary search in the header and make it easy for the compiler to inline the fast path.
Definition at line 801 of file index_set.cc.
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private |
Expensive part of nth_index_in_set() that does the binary search in case we did not find the index in the largest range. Kept separate to avoid using a binary search in the header and make it easy for the compiler to inline the fast path.
Definition at line 837 of file index_set.cc.
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Expensive part of index_within_set() that does the binary search in case we did not find the index in the largest range. Kept separate to avoid using a binary search in the header and make it easy for the compiler to inline the fast path.
Definition at line 854 of file index_set.cc.
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Expensive part of add_index() and add_range(). Defined in separate function to avoid using a binary search in the header and make it easy for the compiler to inline the fast path.
Definition at line 594 of file index_set.cc.
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Expensive part of add_indices().
Definition at line 610 of file index_set.cc.
Definition at line 2070 of file index_set.h.
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Create and return an index set of size \(N\) that contains every single index within this range. In essence, this function returns an index set created by
This function exists so that one can create and initialize index sets that are complete in one step, or so one can write code like
Definition at line 1204 of file index_set.h.
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mutableprivate |
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.
Definition at line 1098 of file index_set.h.
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mutableprivate |
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.
Definition at line 1108 of file index_set.h.
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The overall size of the index range. Elements of this index set have to have a smaller number than this value.
Definition at line 1114 of file index_set.h.
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This integer caches the index of the largest range in 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 is_element(), index_within_set(), 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).
Definition at line 1125 of file index_set.h.
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A mutex that is used to synchronize operations of the do_compress() function that is called from many 'const' functions via compress().
Definition at line 1131 of file index_set.h.
1.11.0