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45 #include "sparsematrix.h"
51 gmx_sparsematrix_init(int nrow)
54 gmx_sparsematrix_t *A;
75 gmx_sparsematrix_destroy(gmx_sparsematrix_t * A)
79 /* Release each row */
80 for(i=0;i<A->nrow;i++)
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++)
105 for(j=0;j<A->nrow;j++)
106 fprintf(stream," %6.3f",0.0);
112 for(j=0;j<A->ndata[i];j++)
114 while(k++<A->data[i][j].col)
115 fprintf(stream," %6.3f",0.0);
116 fprintf(stream," %6.3f",A->data[i][j].value);
119 fprintf(stream," %6.3f",0.0);
121 fprintf(stream,"\n");
128 gmx_sparsematrix_value(gmx_sparsematrix_t * A,
132 gmx_bool found = FALSE;
140 /* Find previous value */
141 for(i=0;i<A->ndata[row] && (found==FALSE);i++)
143 if(A->data[row][i].col==col)
146 value = A->data[row][i].value;
150 /* value=0 if we didn't find any match */
157 gmx_sparsematrix_increment_value(gmx_sparsematrix_t * A,
162 gmx_bool found = FALSE;
167 /* Try to find a previous entry with this row/col */
168 for(i=0;i<A->ndata[row] && !found;i++)
170 if(A->data[row][i].col==col)
173 A->data[row][i].value += difference;
177 /* Add a new entry if nothing was found */
180 /* add the value at the end of the row */
181 if(A->ndata[row] == A->nalloc[row])
183 A->nalloc[row] += 100;
184 if(A->data[row]==NULL)
186 snew(A->data[row],A->nalloc[row]);
190 srenew(A->data[row],A->nalloc[row]);
193 A->data[row][A->ndata[row]].col = col;
194 /* Previous value was 0.0 */
195 A->data[row][A->ndata[row]].value = difference;
201 /* Routine to compare column values of two entries, used for quicksort of each row.
203 * The data entries to compare are of the type gmx_sparsematrix_entry_t, but quicksort
204 * uses void pointers as arguments, so we cast them back internally.
207 compare_columns(const void *v1, const void *v2)
209 int c1 = ((gmx_sparsematrix_entry_t *)v1)->col;
210 int c2 = ((gmx_sparsematrix_entry_t *)v2)->col;
222 gmx_sparsematrix_compress(gmx_sparsematrix_t * A)
226 for (i=0;i<A->nrow;i++)
228 /* Remove last value on this row while it is zero */
229 while(A->ndata[i]>0 && A->data[i][A->ndata[i]-1].value==0)
232 /* Go through values on this row and look for more zero elements */
233 for(j=0;j<A->ndata[i];j++)
235 /* If this element was zero, exchange it with the last non-zero
236 * element on the row (yes, this will invalidate the sort order)
238 if(A->data[i][j].value==0)
240 A->data[i][j].value = A->data[i][A->ndata[i]-1].value;
241 A->data[i][j].col = A->data[i][A->ndata[i]-1].col;
245 /* Only non-zero elements remaining on this row. Sort them after column index */
246 qsort((void *)(A->data[i]),
248 sizeof(gmx_sparsematrix_entry_t),
255 gmx_sparsematrix_vector_multiply(gmx_sparsematrix_t * A,
261 gmx_sparsematrix_entry_t * data; /* pointer to simplify data access */
263 for (i = 0; i < A->nrow; i ++)
266 if(A->compressed_symmetric)
268 for (i = 0; i < A->nrow; i ++)
274 for (k=0;k<A->ndata[i];k++)
287 /* not compressed symmetric storage */
288 for (i = 0; i < A->nrow; i ++)
294 for (k=0;k<A->ndata[i];k++)