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SparseMatrix.h
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rLAMMPS lammps
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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