SparseMatrix.cpp

Go to the documentation of this file.

///////////////////////////////////////////////////////////////////////////////
//
// File: SparseMatrix.cpp
//
// For more information, please see: http://www.nektar.info
//
// The MIT License
//
// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
// Department of Aeronautics, Imperial College London (UK), and Scientific
// Computing and Imaging Institute, University of Utah (USA).
//
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this software and associated documentation files (the "Software"),
// to deal in the Software without restriction, including without limitation
// the rights to use, copy, modify, merge, publish, distribute, sublicense,
// and/or sell copies of the Software, and to permit persons to whom the
// Software is furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
// DEALINGS IN THE SOFTWARE.
//
// Description: Generic sparse matrix class templated by underlying sparse
//              storage format
//
///////////////////////////////////////////////////////////////////////////////
 
#include <algorithm>
#include <fstream>
#include <map>
#include <utility>
#include <vector>
 
#include <LibUtilities/LinearAlgebra/MatrixStorageType.h>
#include <LibUtilities/LinearAlgebra/NistSparseDescriptors.hpp>
#include <LibUtilities/LinearAlgebra/SparseMatrix.hpp>
#include <LibUtilities/LinearAlgebra/StorageSmvBsr.hpp>
 
using std::max;
using std::min;
 
namespace Nektar
{
 
template <typename SparseStorageType>
NekSparseMatrix<SparseStorageType>::NekSparseMatrix(
    const SparseStorageSharedPtr &sparseStoragePtr)
    : m_mulCallsCounter(0), m_sparseStorage(sparseStoragePtr)
{
}
 
template <typename SparseStorageType>
NekSparseMatrix<SparseStorageType>::NekSparseMatrix(const NekSparseMatrix &src)
    : m_mulCallsCounter(src.m_mulCallsCounter),
      m_sparseStorage(src.m_sparseStorage)
{
}
 
template <typename SparseStorageType>
NekSparseMatrix<SparseStorageType>::~NekSparseMatrix()
{
}
 
template <typename SparseStorageType>
IndexType NekSparseMatrix<SparseStorageType>::GetRows() const
{
    return m_sparseStorage->GetRows();
}
 
template <typename SparseStorageType>
IndexType NekSparseMatrix<SparseStorageType>::GetColumns() const
{
    return m_sparseStorage->GetColumns();
}
 
template <typename SparseStorageType>
IndexType NekSparseMatrix<SparseStorageType>::GetNumNonZeroEntries() const
{
    return m_sparseStorage->GetNumNonZeroEntries();
}
 
template <typename SparseStorageType>
const typename NekSparseMatrix<SparseStorageType>::DataType NekSparseMatrix<
    SparseStorageType>::GetFillInRatio() const
{
    return m_sparseStorage->GetFillInRatio();
}
 
template <typename SparseStorageType>
typename boost::call_traits<
    typename SparseStorageType::DataType>::const_reference
NekSparseMatrix<SparseStorageType>::operator()(unsigned int row,
                                               unsigned int column) const
{
    return m_sparseStorage->GetValue(row, column);
}
 
template <typename SparseStorageType>
typename SparseStorageType::const_iterator NekSparseMatrix<
    SparseStorageType>::begin() const
{
    return m_sparseStorage->begin();
}
 
template <typename SparseStorageType>
typename SparseStorageType::const_iterator NekSparseMatrix<
    SparseStorageType>::end() const
{
    return m_sparseStorage->end();
}
 
template <typename SparseStorageType>
void NekSparseMatrix<SparseStorageType>::Multiply(const DataVectorType &in,
                                                  DataVectorType &out)
{
    m_sparseStorage->Multiply(in, out);
    m_mulCallsCounter++;
}
 
template <typename SparseStorageType>
void NekSparseMatrix<SparseStorageType>::Multiply(const DataType *in,
                                                  DataType *out)
{
    m_sparseStorage->Multiply(in, out);
    m_mulCallsCounter++;
}
 
template <typename SparseStorageType>
size_t NekSparseMatrix<SparseStorageType>::GetMemoryFootprint() const
{
    return m_sparseStorage->GetMemoryUsage() + sizeof(SparseStorageSharedPtr) +
           sizeof(unsigned long); // mulCallsCounter
}
 
template <typename SparseStorageType>
unsigned long NekSparseMatrix<SparseStorageType>::GetMulCallsCounter() const
{
    return m_mulCallsCounter;
}
 
template <typename SparseStorageType>
const typename SparseStorageType::DataType NekSparseMatrix<
    SparseStorageType>::GetAvgRowDensity() const
{
    return (DataType)m_sparseStorage->GetNumNonZeroEntries() /
           (DataType)m_sparseStorage->GetRows();
}
 
template <typename SparseStorageType>
IndexType NekSparseMatrix<SparseStorageType>::GetBandwidth()
{
    int bandwidth = 0;
 
    typename SparseStorageType::const_iterator entry = m_sparseStorage->begin();
 
    for (; entry != m_sparseStorage->end(); ++entry)
    {
        bandwidth = (std::max)(
            bandwidth,
            2 * std::abs((int)(entry->first.first - entry->first.second + 1)));
    }
    return bandwidth;
}
 
template <typename SparseStorageType>
COOMatTypeSharedPtr NekSparseMatrix<SparseStorageType>::GetCooStorage()
{
    COOMatTypeSharedPtr coo(new COOMatType());
 
    typename SparseStorageType::const_iterator entry = m_sparseStorage->begin();
    for (; entry != m_sparseStorage->end(); entry++)
    {
        (*coo)[std::make_pair(entry->first.first, entry->first.second)] =
            entry->second;
    }
    return coo;
}
 
// Generates a matrix each element of which is a number of
// nonzero entries to block-matrix associated with *this object.
// E.g. for unit 6x6 matrix and block size = 2 it will generate
// 3x3 matrix with elements 2 along the diagonal.
//
// The output can be visualised with Python's matplotlib's spy().
//
template <typename SparseStorageType>
void NekSparseMatrix<SparseStorageType>::writeSparsityPatternTo(
    std::ostream &out, IndexType blockSize)
{
    const int matRows  = m_sparseStorage->GetRows();
    const int gridRows = matRows / blockSize + (matRows % blockSize > 0);
    const int gridCols = gridRows;
 
    std::vector<std::vector<int>> grid(gridRows);
    for (int row = 0; row < gridRows; row++)
    {
        grid[row].resize(gridCols, 0);
    }
 
    typename SparseStorageType::const_iterator entry = m_sparseStorage->begin();
    for (; entry != m_sparseStorage->end(); entry++)
    {
        const IndexType row = entry->first.first;
        const IndexType col = entry->first.second;
        const int gridRow   = row / blockSize;
        const int gridCol   = col / blockSize;
        grid[gridRow][gridCol]++;
    }
 
    for (int row = 0; row < gridRows; row++)
    {
        for (int col = 0; col < gridCols; col++)
        {
            out << grid[row][col] << " ";
        }
        out << std::endl;
    }
}
 
/// Complementary routine to the previous. It generates
/// exact non-zero pattern of a given block matrix entry
/// to *this object. E.g., for a 6x6 matrix defined as
/// A(i,i):=i, A(i,j):=0, block size = 2 and
/// blk_row=blk_col=2 it produces 2x2 matrix with 5 and 6
/// along the diagonal.
template <typename SparseStorageType>
void NekSparseMatrix<SparseStorageType>::writeBlockSparsityPatternTo(
    std::ostream &out, const IndexType blk_row, const IndexType blk_col,
    IndexType blockSize)
{
    blockSize = (std::min)(blockSize, m_sparseStorage->GetRows());
    std::vector<std::vector<int>> grid(blockSize);
    for (int row = 0; row < blockSize; row++)
    {
        grid[row].resize(blockSize, 0);
    }
 
    typename SparseStorageType::const_iterator entry = m_sparseStorage->begin();
    for (; entry != m_sparseStorage->end(); entry++)
    {
        const IndexType row = entry->first.first;
        const IndexType col = entry->first.second;
 
        if (blk_row != row / blockSize)
        {
            continue;
        }
        if (blk_col != col / blockSize)
        {
            continue;
        }
        grid[row % blockSize][col % blockSize]++;
    }
 
    for (int row = 0; row < blockSize; row++)
    {
        for (int col = 0; col < blockSize; col++)
        {
            out << grid[row][col] << " ";
        }
        out << std::endl;
    }
}
 
// explicit instantiation
template class NekSparseMatrix<StorageSmvBsr<NekDouble>>;
 
} // namespace Nektar