ATC version 2.0, date: Aug7
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10557 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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rjones
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#ifndef SPARSEMATRIX_H
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#define SPARSEMATRIX_H
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#include <exception>
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#include "MatrixLibrary.h"
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#include <algorithm>
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/**
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* @struct TRI_COORD
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* @brief Triplet SparseMatrix entry
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*/
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template <typename T>
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struct TRI_COORD
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{
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TRI_COORD<T>(unsigned row=0, unsigned col=0);
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TRI_COORD<T>(unsigned row, unsigned col, T val, bool add_to=0);
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unsigned i, j;
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T v;
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bool add;
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};
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/**
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* @class SparseMatrix
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* @brief Stores data in triplet format or CRS format
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*/
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template<typename T>
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class SparseMatrix : public Matrix<T>
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{
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//* SparseMatrix-Vector multiplication (S * v)
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friend DenseVector<T> operator*<T>(const SparseMatrix<T> &A, const Vector<T>& x);
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//* SparseMatrix-DenseMatrix multiplication (S * F)
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friend DenseMatrix<T> operator*<T>(const SparseMatrix<T> &A, const Matrix<T>& D);
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//* SparseMatrix-DiagonalMatrix multiplication (S * D)
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friend SparseMatrix<T> operator*<T>(const SparseMatrix<T> &A, const DiagonalMatrix<T>& D);
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//* SparseMatrix-SparseMatrix multiplication (S * S)
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friend SparseMatrix<T> operator*<T>(const SparseMatrix<T> &A, const SparseMatrix<T> &B);
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//* computes the product of a SparseMatrix tranpose with a SparseVector (M'*v).
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friend SparseVector<T> operator*<T>(const SparseMatrix<T> &M, const SparseVector<T> &v);
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//* computes the product of a SparseMatrix tranpose with a SparseVector (M'*v).
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friend SparseVector<T> operator*<T>(const SparseVector<T> &v, const SparseMatrix<T> &M);
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public:
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SparseMatrix(INDEX rows=0, INDEX cols=0);
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SparseMatrix(const SparseMatrix<T>& c);
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SparseMatrix(const DenseMatrix<T>& c);
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~SparseMatrix();
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//* General index by value (requires a binary search on the row)
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T operator()(INDEX i, INDEX j) const;
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//* General index by reference (requires a binary search on the row)
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T& operator()(INDEX i, INDEX j);
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//* General flat index by value operator (by nth nonzero)
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T operator[](INDEX i) const;
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//* General flat index by reference operator (by nth nonzero)
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T& operator[](INDEX i);
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//* adds a value to index i,j
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void set(INDEX i, INDEX j, T v);
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//* sets a value to index i,j
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void add(INDEX i, INDEX j, T v);
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//* return a triplet value of the ith nonzero
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TRIPLET<T> get_triplet(INDEX i) const;
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//* full reset - completely wipes out all SparseMatrix data
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void reset(INDEX rows=0, INDEX cols=0, bool zero=true);
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//* only changes the bounds of the matrix, no deletion
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void resize(INDEX rows=0, INDEX cols=0, bool zero=true);
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//* reset - from DenseMatrix - this will be SLOW
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void reset(const DenseMatrix<T>& D, double TOL=-1.0);
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//* copy data
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void copy(const T * ptr, INDEX rows=0, INDEX cols=0);
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void dense_copy(DenseMatrix<T>& D) const;
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DenseMatrix<T> dense_copy(void) const;
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//* returns true if the matrix has no nonzero elements
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bool empty() const;
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//* returns the user-specified number of rows
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INDEX nRows() const;
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//* returns the user-specified number of cols
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INDEX nCols() const;
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//* returns the number of non-zero elements
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INDEX size() const;
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//* returns the number of non-zeros in a row
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INDEX RowSize(INDEX r) const;
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//* returns a pointer to the nonzero data
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inline T* get_ptr() const;
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//* checks if the index i,j falls in the user-specified range
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bool in_range(INDEX i, INDEX j) const;
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/*
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* \section assignment operators
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*/
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//* copies SparseMatrix R to this
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SparseMatrix<T>& operator=(const SparseMatrix &R);
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//* sets all nonzero values to a constant
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SparseMatrix<T>& operator=(const T v);
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//* scales all nonzero values by a constant
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SparseMatrix<T>& operator*=(const T &a);
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/*
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* \section Multiplication operations
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*/
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//* S' * F
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DenseMatrix<T> transMat(const DenseMatrix<T> &D) const;
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//* S' * S
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DenseMatrix<T> transMat(const SparseMatrix<T> &S) const;
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//* S' * v
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DenseVector<T> transMat(const Vector<T> &x) const;
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SparseMatrix<T> transpose() const;
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SparseMatrix<T>& row_scale(const Vector<T> &v);
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SparseMatrix<T>& col_scale(const Vector<T> &v);
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DenseVector<T> col_sum() const;
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DenseVector<INDEX> column_count() const;
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DiagonalMatrix<T> get_diag() const;
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void get_row(INDEX i, DenseVector<T>& row, DenseVector<INDEX>& indx) const;
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void WeightedLeastSquares(const SparseMatrix<T> &N, const DiagonalMatrix<T> &D);
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T get_row_max(INDEX row) const;
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T get_row_min(INDEX row) const;
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/*
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* \section I/O functions
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*/
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//* outputs this SparseMatrix to a formatted string
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string tostring() const;
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using Matrix<T>::matlab;
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//* writes a command to recreate this matrix in matlab to a stream
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void matlab(ostream &o, const string &name="S") const;
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//* prints a row histogram for each row
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void print_row_histogram(const string &name, INDEX nbins = 10) const;
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//* prints a histogram of the values in a row
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void print_row_histogram(INDEX row, INDEX nbins) const;
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//! Writes the matrix to a binary file (after a compress).
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void binary_write(std::fstream& f) const;
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//! Reads a SparseMatrix from a binary file. (wipes out any original data)
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void binary_read(std::fstream& f);
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//* Dump templated type to disk; operation not safe for all types
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void write_restart(FILE *f) const;
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/*
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* \section Utility functions
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*/
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//* converts all triplets and merges with CRS
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void compress();
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//* converts T to CRS
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static void compress(const SparseMatrix<T> &C);
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//* sorts and returns the # of unique triplets
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INDEX CountUniqueTriplets();
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private:
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//* creates a CRS structure
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void _create(INDEX size, INDEX nrows);
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//* clears all memory and nulls references
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void _delete();
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//* copys all data from another SparseMatrix
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void _copy(const SparseMatrix<T> &C);
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//* general sparse matrix assignment
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void _set_equal(const Matrix<T> &r);
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//* returns the first row with a nonzero in it (from the CRS structure only)
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int _first_nonzero_row_crs() const;
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/*
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* \section CRS storage variables
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*/
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T * _val; // matrix non-zeros
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INDEX *_ia, *_ja; // ptrs to rows, column indexes
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INDEX _size, _nRowsCRS; // # of non-zeros, rows
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//* new (unsorted triplet values - won't intersect CRS values)
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mutable vector<TRI_COORD<T> > _tri;
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/*
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* \section User specified variables
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*/
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INDEX _nRows, _nCols;
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static T _zero;
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};
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#include "SparseMatrix-inl.h"
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#endif
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