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39 #include "sparsematrix.h"
46 #include "gromacs/utility/smalloc.h"
49 gmx_sparsematrix_init(int nrow
)
52 gmx_sparsematrix_t
*A
;
58 snew(A
->nalloc
, nrow
);
61 for (i
= 0; i
< nrow
; i
++)
73 gmx_sparsematrix_destroy(gmx_sparsematrix_t
* A
)
77 /* Release each row */
78 for (i
= 0; i
< A
->nrow
; i
++)
80 if (A
->data
[i
] != nullptr)
85 /* Release the rowdata arrays */
89 /* Release matrix structure itself */
96 gmx_sparsematrix_print(FILE * stream
,
97 gmx_sparsematrix_t
* A
)
101 for (i
= 0; i
< A
->nrow
; i
++)
103 if (A
->ndata
[i
] == 0)
105 for (j
= 0; j
< A
->nrow
; j
++)
107 fprintf(stream
, " %6.3f", 0.0);
113 for (j
= 0; j
< A
->ndata
[i
]; j
++)
115 while (k
++ < A
->data
[i
][j
].col
)
117 fprintf(stream
, " %6.3f", 0.0);
119 fprintf(stream
, " %6.3f", A
->data
[i
][j
].value
);
121 while (k
++ < A
->nrow
)
123 fprintf(stream
, " %6.3f", 0.0);
126 fprintf(stream
, "\n");
133 gmx_sparsematrix_value(gmx_sparsematrix_t
* A
,
137 gmx_bool found
= FALSE
;
141 assert(row
< A
->nrow
);
145 /* Find previous value */
146 for (i
= 0; i
< A
->ndata
[row
] && (found
== FALSE
); i
++)
148 if (A
->data
[row
][i
].col
== col
)
151 value
= A
->data
[row
][i
].value
;
155 /* value=0 if we didn't find any match */
162 gmx_sparsematrix_increment_value(gmx_sparsematrix_t
* A
,
167 gmx_bool found
= FALSE
;
170 assert(row
< A
->nrow
);
172 /* Try to find a previous entry with this row/col */
173 for (i
= 0; i
< A
->ndata
[row
] && !found
; i
++)
175 if (A
->data
[row
][i
].col
== col
)
178 A
->data
[row
][i
].value
+= difference
;
182 /* Add a new entry if nothing was found */
185 /* add the value at the end of the row */
186 if (A
->ndata
[row
] == A
->nalloc
[row
])
188 A
->nalloc
[row
] += 100;
189 if (A
->data
[row
] == nullptr)
191 snew(A
->data
[row
], A
->nalloc
[row
]);
195 srenew(A
->data
[row
], A
->nalloc
[row
]);
198 A
->data
[row
][A
->ndata
[row
]].col
= col
;
199 /* Previous value was 0.0 */
200 A
->data
[row
][A
->ndata
[row
]].value
= difference
;
206 /* Routine to compare column values of two entries, used for quicksort of each row.
208 * The data entries to compare are of the type gmx_sparsematrix_entry_t, but quicksort
209 * uses void pointers as arguments, so we cast them back internally.
212 compare_columns(const void *v1
, const void *v2
)
214 int c1
= ((gmx_sparsematrix_entry_t
*)v1
)->col
;
215 int c2
= ((gmx_sparsematrix_entry_t
*)v2
)->col
;
233 gmx_sparsematrix_compress(gmx_sparsematrix_t
* A
)
237 for (i
= 0; i
< A
->nrow
; i
++)
239 /* Remove last value on this row while it is zero */
240 while (A
->ndata
[i
] > 0 && A
->data
[i
][A
->ndata
[i
]-1].value
== 0)
245 /* Go through values on this row and look for more zero elements */
246 for (j
= 0; j
< A
->ndata
[i
]; j
++)
248 /* If this element was zero, exchange it with the last non-zero
249 * element on the row (yes, this will invalidate the sort order)
251 if (A
->data
[i
][j
].value
== 0)
253 A
->data
[i
][j
].value
= A
->data
[i
][A
->ndata
[i
]-1].value
;
254 A
->data
[i
][j
].col
= A
->data
[i
][A
->ndata
[i
]-1].col
;
258 /* Only non-zero elements remaining on this row. Sort them after column index */
259 qsort((void *)(A
->data
[i
]),
261 sizeof(gmx_sparsematrix_entry_t
),
268 gmx_sparsematrix_vector_multiply(gmx_sparsematrix_t
* A
,
274 gmx_sparsematrix_entry_t
* data
; /* pointer to simplify data access */
276 for (i
= 0; i
< A
->nrow
; i
++)
281 if (A
->compressed_symmetric
)
283 for (i
= 0; i
< A
->nrow
; i
++)
289 for (k
= 0; k
< A
->ndata
[i
]; k
++)
304 /* not compressed symmetric storage */
305 for (i
= 0; i
< A
->nrow
; i
++)
310 for (k
= 0; k
< A
->ndata
[i
]; k
++)