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lammps/lib/atc/SparseMatrix.h
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SparseMatrix.h
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#ifndef SPARSEMATRIX_H
#define SPARSEMATRIX_H
#include <exception>
#include "MatrixLibrary.h"
#include <algorithm>
/**
* @struct TRI_COORD
* @brief Triplet SparseMatrix entry
*/
template <typename T>
struct TRI_COORD
{
TRI_COORD<T>(unsigned row=0, unsigned col=0);
TRI_COORD<T>(unsigned row, unsigned col, T val, bool add_to=0);
unsigned i, j;
T v;
bool add;
};
/**
* @class SparseMatrix
* @brief Stores data in triplet format or CRS format
*/
template<typename T>
class SparseMatrix : public Matrix<T>
{
//* SparseMatrix-Vector multiplication (S * v)
friend DenseVector<T> operator*<T>(const SparseMatrix<T> &A, const Vector<T>& x);
//* SparseMatrix-DenseMatrix multiplication (S * F)
friend DenseMatrix<T> operator*<T>(const SparseMatrix<T> &A, const Matrix<T>& D);
//* SparseMatrix-DiagonalMatrix multiplication (S * D)
friend SparseMatrix<T> operator*<T>(const SparseMatrix<T> &A, const DiagonalMatrix<T>& D);
//* SparseMatrix-SparseMatrix multiplication (S * S)
friend SparseMatrix<T> operator*<T>(const SparseMatrix<T> &A, const SparseMatrix<T> &B);
//* computes the product of a SparseMatrix tranpose with a SparseVector (M'*v).
friend SparseVector<T> operator*<T>(const SparseMatrix<T> &M, const SparseVector<T> &v);
//* computes the product of a SparseMatrix tranpose with a SparseVector (M'*v).
friend SparseVector<T> operator*<T>(const SparseVector<T> &v, const SparseMatrix<T> &M);
public:
SparseMatrix(INDEX rows=0, INDEX cols=0);
SparseMatrix(const SparseMatrix<T>& c);
SparseMatrix(const DenseMatrix<T>& c);
~SparseMatrix();
//* General index by value (requires a binary search on the row)
T operator()(INDEX i, INDEX j) const;
//* General index by reference (requires a binary search on the row)
T& operator()(INDEX i, INDEX j);
//* General flat index by value operator (by nth nonzero)
T operator[](INDEX i) const;
//* General flat index by reference operator (by nth nonzero)
T& operator[](INDEX i);
//* adds a value to index i,j
void set(INDEX i, INDEX j, T v);
//* sets a value to index i,j
void add(INDEX i, INDEX j, T v);
//* return a triplet value of the ith nonzero
TRIPLET<T> get_triplet(INDEX i) const;
//* full reset - completely wipes out all SparseMatrix data
void reset(INDEX rows=0, INDEX cols=0, bool zero=true);
//* only changes the bounds of the matrix, no deletion
void resize(INDEX rows=0, INDEX cols=0, bool zero=true);
//* reset - from DenseMatrix - this will be SLOW
void reset(const DenseMatrix<T>& D, double TOL=-1.0);
//* copy data
void copy(const T * ptr, INDEX rows=0, INDEX cols=0);
void dense_copy(DenseMatrix<T>& D) const;
DenseMatrix<T> dense_copy(void) const;
//* returns true if the matrix has no nonzero elements
bool empty() const;
//* returns the user-specified number of rows
INDEX nRows() const;
//* returns the user-specified number of cols
INDEX nCols() const;
//* returns the number of non-zero elements
INDEX size() const;
//* returns the number of non-zeros in a row
INDEX RowSize(INDEX r) const;
//* returns a pointer to the nonzero data
inline T* get_ptr() const;
//* checks if the index i,j falls in the user-specified range
bool in_range(INDEX i, INDEX j) const;
/*
* \section assignment operators
*/
//* copies SparseMatrix R to this
SparseMatrix<T>& operator=(const SparseMatrix &R);
//* sets all nonzero values to a constant
SparseMatrix<T>& operator=(const T v);
//* scales all nonzero values by a constant
SparseMatrix<T>& operator*=(const T &a);
/*
* \section Multiplication operations
*/
//* S' * F
DenseMatrix<T> transMat(const DenseMatrix<T> &D) const;
//* S' * S
DenseMatrix<T> transMat(const SparseMatrix<T> &S) const;
//* S' * v
DenseVector<T> transMat(const Vector<T> &x) const;
SparseMatrix<T> transpose() const;
SparseMatrix<T>& row_scale(const Vector<T> &v);
SparseMatrix<T>& col_scale(const Vector<T> &v);
DenseVector<T> col_sum() const;
DenseVector<INDEX> column_count() const;
DiagonalMatrix<T> get_diag() const;
void get_row(INDEX i, DenseVector<T>& row, DenseVector<INDEX>& indx) const;
void WeightedLeastSquares(const SparseMatrix<T> &N, const DiagonalMatrix<T> &D);
T get_row_max(INDEX row) const;
T get_row_min(INDEX row) const;
/*
* \section I/O functions
*/
//* outputs this SparseMatrix to a formatted string
string tostring() const;
using Matrix<T>::matlab;
//* writes a command to recreate this matrix in matlab to a stream
void matlab(ostream &o, const string &name="S") const;
//* prints a row histogram for each row
void print_row_histogram(const string &name, INDEX nbins = 10) const;
//* prints a histogram of the values in a row
void print_row_histogram(INDEX row, INDEX nbins) const;
//! Writes the matrix to a binary file (after a compress).
void binary_write(std::fstream& f) const;
//! Reads a SparseMatrix from a binary file. (wipes out any original data)
void binary_read(std::fstream& f);
//* Dump templated type to disk; operation not safe for all types
void write_restart(FILE *f) const;
/*
* \section Utility functions
*/
//* converts all triplets and merges with CRS
void compress();
//* converts T to CRS
static void compress(const SparseMatrix<T> &C);
//* sorts and returns the # of unique triplets
INDEX CountUniqueTriplets();
private:
//* creates a CRS structure
void _create(INDEX size, INDEX nrows);
//* clears all memory and nulls references
void _delete();
//* copys all data from another SparseMatrix
void _copy(const SparseMatrix<T> &C);
//* general sparse matrix assignment
void _set_equal(const Matrix<T> &r);
//* returns the first row with a nonzero in it (from the CRS structure only)
int _first_nonzero_row_crs() const;
/*
* \section CRS storage variables
*/
T * _val; // matrix non-zeros
INDEX *_ia, *_ja; // ptrs to rows, column indexes
INDEX _size, _nRowsCRS; // # of non-zeros, rows
//* new (unsorted triplet values - won't intersect CRS values)
mutable vector<TRI_COORD<T> > _tri;
/*
* \section User specified variables
*/
INDEX _nRows, _nCols;
static T _zero;
};
#include "SparseMatrix-inl.h"
#endif
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