26 size =
sizeof(double);
29 size = 2*
sizeof(double);
66 int *ia =
A->ia, *ja =
A->ja, *ib, *jb, nz =
A->nz, m =
A->m, n =
A->n,
type =
A->type,
format =
A->format;
77 for (i = 0; i <= n; i++) ib[i] = 0;
78 for (i = 0; i < m; i++){
79 for (j = ia[i]; j < ia[i+1]; j++){
84 for (i = 0; i < n; i++) ib[i+1] += ib[i];
90 for (i = 0; i < m; i++){
91 for (j = ia[i]; j < ia[i+1]; j++){
93 b[ib[ja[j]]++] = a[j];
101 for (i = 0; i < m; i++){
102 for (j = ia[i]; j < ia[i+1]; j++){
104 b[2*ib[ja[j]]] = a[2*j];
105 b[2*ib[ja[j]]+1] = a[2*j+1];
114 for (i = 0; i < m; i++){
115 for (j = ia[i]; j < ia[i+1]; j++){
117 bi[ib[ja[j]]++] = ai[j];
123 for (i = 0; i < m; i++){
124 for (j = ia[i]; j < ia[i+1]; j++){
138 for (i = n-1; i >= 0; i--) ib[i+1] = ib[i];
146 bool pattern_symmetric_only) {
159 if (!
A)
return false;
163 int *ia, *ja, *ib, *jb,
type, m;
172 if (
A->m !=
A->n)
return false;
175 if (!
B)
return false;
183 mask =
gv_calloc((
size_t)m,
sizeof(
int));
184 for (i = 0; i < m; i++) mask[i] = -1;
193 for (i = 0; i <= m; i++)
if (ia[i] != ib[i])
goto RETURN;
194 for (i = 0; i < m; i++){
195 for (j = ia[i]; j < ia[i+1]; j++){
198 for (j = ib[i]; j < ib[i+1]; j++){
199 if (mask[jb[j]] < ia[i])
goto RETURN;
201 for (j = ib[i]; j < ib[i+1]; j++){
211 for (i = 0; i <= m; i++)
if (ia[i] != ib[i])
goto RETURN;
212 for (i = 0; i < m; i++){
213 for (j = ia[i]; j < ia[i+1]; j++){
216 for (j = ib[i]; j < ib[i+1]; j++){
217 if (mask[jb[j]] < ia[i])
goto RETURN;
219 for (j = ib[i]; j < ib[i+1]; j++){
230 for (i = 0; i < m; i++){
231 for (j = ia[i]; j < ia[i+1]; j++){
234 for (j = ib[i]; j < ib[i+1]; j++){
235 if (mask[jb[j]] < ia[i])
goto RETURN;
237 for (j = ib[i]; j < ib[i+1]; j++){
238 if (bi[j] != ai[mask[jb[j]]])
goto RETURN;
245 for (i = 0; i < m; i++){
246 for (j = ia[i]; j < ia[i+1]; j++){
249 for (j = ib[i]; j < ib[i+1]; j++){
250 if (mask[jb[j]] < ia[i])
goto RETURN;
263 if (test_pattern_symmetry_only){
290 A->ia =
gv_calloc((
size_t)(m + 1),
sizeof(
int));
301 size_t nz_t = (size_t) nz;
313 if (
A->size > 0 && nz_t > 0) {
324 size_t nz_t = (size_t) nz;
397 fprintf(f,
"%%%%MatrixMarket matrix coordinate real general\n");
400 fprintf(f,
"%%%%MatrixMarket matrix coordinate complex general\n");
403 fprintf(f,
"%%%%MatrixMarket matrix coordinate integer general\n");
406 fprintf(f,
"%%%%MatrixMarket matrix coordinate pattern general\n");
414 fprintf(f,
"%d %d %d\n",
A->m,
A->n,
A->nz);
421 for (i = 0; i < m; i++){
422 for (j = ia[i]; j < ia[i+1]; j++){
423 fprintf(f,
"%d %d %16.8g\n",i+1, ja[j]+1, a[j]);
429 for (i = 0; i < m; i++){
430 for (j = ia[i]; j < ia[i+1]; j++){
431 fprintf(f,
"%d %d %16.8g %16.8g\n",i+1, ja[j]+1, a[2*j], a[2*j+1]);
437 for (i = 0; i < m; i++){
438 for (j = ia[i]; j < ia[i+1]; j++){
439 fprintf(f,
"%d %d %d\n",i+1, ja[j]+1, ai[j]);
444 for (i = 0; i < m; i++){
445 for (j = ia[i]; j < ia[i+1]; j++){
446 fprintf(f,
"%d %d\n",i+1, ja[j]+1);
466 fprintf(f,
"%%%%MatrixMarket matrix coordinate real general\n");
469 fprintf(f,
"%%%%MatrixMarket matrix coordinate complex general\n");
472 fprintf(f,
"%%%%MatrixMarket matrix coordinate integer general\n");
475 fprintf(f,
"%%%%MatrixMarket matrix coordinate pattern general\n");
483 fprintf(f,
"%d %d %d\n",
A->m,
A->n,
A->nz);
490 for (i = 0; i <
A->nz; i++){
491 fprintf(f,
"%d %d %16.8g\n",ia[i]+1, ja[i]+1, a[i]);
496 for (i = 0; i <
A->nz; i++){
497 fprintf(f,
"%d %d %16.8g %16.8g\n",ia[i]+1, ja[i]+1, a[2*i], a[2*i+1]);
502 for (i = 0; i <
A->nz; i++){
503 fprintf(f,
"%d %d %d\n",ia[i]+1, ja[i]+1, ai[i]);
507 for (i = 0; i <
A->nz; i++){
508 fprintf(f,
"%d %d\n",ia[i]+1, ja[i]+1);
580 assert(m > 0 && n > 0 && nz >= 0);
582 if (m <=0 || n <= 0 || nz < 0)
return NULL;
589 for (i = 0; i <= m; i++){
597 for (i = 0; i < nz; i++){
598 if (irn[i] < 0 || irn[i] >= m || jcn[i] < 0 || jcn[i] >= n) {
604 for (i = 0; i < m; i++) ia[i+1] += ia[i];
605 for (i = 0; i < nz; i++){
606 a[ia[irn[i]]] = val[i];
607 ja[ia[irn[i]]++] = jcn[i];
609 for (i = m; i > 0; i--) ia[i] = ia[i - 1];
615 for (i = 0; i < nz; i++){
616 if (irn[i] < 0 || irn[i] >= m || jcn[i] < 0 || jcn[i] >= n) {
622 for (i = 0; i < m; i++) ia[i+1] += ia[i];
623 for (i = 0; i < nz; i++){
624 a[2*ia[irn[i]]] = *(val++);
625 a[2*ia[irn[i]]+1] = *(val++);
626 ja[ia[irn[i]]++] = jcn[i];
628 for (i = m; i > 0; i--) ia[i] = ia[i - 1];
634 for (i = 0; i < nz; i++){
635 if (irn[i] < 0 || irn[i] >= m || jcn[i] < 0 || jcn[i] >= n) {
641 for (i = 0; i < m; i++) ia[i+1] += ia[i];
642 for (i = 0; i < nz; i++){
643 ai[ia[irn[i]]] = vali[i];
644 ja[ia[irn[i]]++] = jcn[i];
646 for (i = m; i > 0; i--) ia[i] = ia[i - 1];
650 for (i = 0; i < nz; i++){
651 if (irn[i] < 0 || irn[i] >= m || jcn[i] < 0 || jcn[i] >= n) {
657 for (i = 0; i < m; i++) ia[i+1] += ia[i];
658 for (i = 0; i < nz; i++){
659 ja[ia[irn[i]]++] = jcn[i];
661 for (i = m; i > 0; i--) ia[i] = ia[i - 1];
665 for (i = 0; i < nz; i++){
666 if (irn[i] < 0 || irn[i] >= m || jcn[i] < 0 || jcn[i] >= n) {
672 for (i = 0; i < m; i++) ia[i+1] += ia[i];
673 memcpy(
A->a, val0,
A->size*((
size_t)nz));
674 for (i = 0; i < nz; i++){
675 ja[ia[irn[i]]++] = jcn[i];
677 for (i = m; i > 0; i--) ia[i] = ia[i - 1];
707 int *ia =
A->ia, *ja =
A->ja, *ib =
B->ia, *jb =
B->ja, *ic, *jc;
712 assert(
A->type ==
B->type);
715 if (m !=
B->m || n !=
B->n)
return NULL;
717 nzmax =
A->nz +
B->nz;
724 mask =
gv_calloc((
size_t)n,
sizeof(
int));
726 for (i = 0; i < n; i++) mask[i] = -1;
735 for (i = 0; i < m; i++){
736 for (j = ia[i]; j < ia[i+1]; j++){
742 for (j = ib[i]; j < ib[i+1]; j++){
743 if (mask[jb[j]] < ic[i]){
747 c[mask[jb[j]]] += b[j];
758 for (i = 0; i < m; i++){
759 for (j = ia[i]; j < ia[i+1]; j++){
763 c[2*nz+1] = a[2*j+1];
766 for (j = ib[i]; j < ib[i+1]; j++){
767 if (mask[jb[j]] < ic[i]){
770 c[2*nz+1] = b[2*j+1];
773 c[2*mask[jb[j]]] += b[2*j];
774 c[2*mask[jb[j]]+1] += b[2*j+1];
785 for (i = 0; i < m; i++){
786 for (j = ia[i]; j < ia[i+1]; j++){
792 for (j = ib[i]; j < ib[i+1]; j++){
793 if (mask[jb[j]] < ic[i]){
798 c[mask[jb[j]]] += b[j];
806 for (i = 0; i < m; i++){
807 for (j = ia[i]; j < ia[i+1]; j++){
812 for (j = ib[i]; j < ib[i+1]; j++){
813 if (mask[jb[j]] < ic[i]){
839 int i, j, k, *ia, *ja, m;
850 for (i = 0; i < m; i++){
851 for (k = 0; k < dim; k++) res[i * dim + k] = 0;
852 for (j = ia[i]; j < ia[i+1]; j++){
853 for (k = 0; k < dim; k++) res[i * dim + k] += a[j] * v[ja[j] *dim + k];
860 int i, j, *ia, *ja, m;
861 double *a, *u =
NULL;
875 if (!u) u =
gv_calloc((
size_t)m,
sizeof(
double));
876 for (i = 0; i < m; i++){
878 for (j = ia[i]; j < ia[i+1]; j++){
879 u[i] += a[j]*v[ja[j]];
884 if (!u) u =
gv_calloc((
size_t)m,
sizeof(
double));
885 for (i = 0; i < m; i++){
887 for (j = ia[i]; j < ia[i+1]; j++){
896 if (!u) u =
gv_calloc((
size_t)m,
sizeof(
double));
897 for (i = 0; i < m; i++){
899 for (j = ia[i]; j < ia[i+1]; j++){
900 u[i] += ai[j]*v[ja[j]];
905 if (!u) u =
gv_calloc((
size_t)m,
sizeof(
double));
906 for (i = 0; i < m; i++){
908 for (j = ia[i]; j < ia[i+1]; j++){
926 int *ia =
A->ia, *ja =
A->ja, *ib =
B->ia, *jb =
B->ja, *ic, *jc;
927 int i, j, k, jj,
type, nz;
932 if (
A->n !=
B->m)
return NULL;
933 if (
A->type !=
B->type){
935 printf(
"in SparseMatrix_multiply, the matrix types do not match, right now only multiplication of matrices of the same type is supported\n");
941 mask = calloc((
size_t)
B->n,
sizeof(
int));
942 if (!mask)
return NULL;
944 for (i = 0; i <
B->n; i++) mask[i] = -1;
947 for (i = 0; i < m; i++){
948 for (j = ia[i]; j < ia[i+1]; j++){
950 for (k = ib[jj]; k < ib[jj+1]; k++){
951 if (mask[jb[k]] != -i - 2){
954 fprintf(stderr,
"overflow in SparseMatrix_multiply !!!\n");
960 mask[jb[k]] = -i - 2;
980 for (i = 0; i < m; i++){
981 for (j = ia[i]; j < ia[i+1]; j++){
983 for (k = ib[jj]; k < ib[jj+1]; k++){
984 if (mask[jb[k]] < ic[i]){
990 assert(jc[mask[jb[k]]] == jb[k]);
991 c[mask[jb[k]]] += a[j]*b[k];
1005 for (i = 0; i < m; i++){
1006 for (j = ia[i]; j < ia[i+1]; j++){
1008 for (k = ib[jj]; k < ib[jj+1]; k++){
1009 if (mask[jb[k]] < ic[i]){
1012 c[2*nz] = a[2*j]*b[2*k] - a[2*j+1]*b[2*k+1];
1013 c[2*nz+1] = a[2*j]*b[2*k+1] + a[2*j+1]*b[2*k];
1016 assert(jc[mask[jb[k]]] == jb[k]);
1017 c[2*mask[jb[k]]] += a[2*j]*b[2*k] - a[2*j+1]*b[2*k+1];
1018 c[2*mask[jb[k]]+1] += a[2*j]*b[2*k+1] + a[2*j+1]*b[2*k];
1032 for (i = 0; i < m; i++){
1033 for (j = ia[i]; j < ia[i+1]; j++){
1035 for (k = ib[jj]; k < ib[jj+1]; k++){
1036 if (mask[jb[k]] < ic[i]){
1042 assert(jc[mask[jb[k]]] == jb[k]);
1043 c[mask[jb[k]]] += a[j]*b[k];
1053 for (i = 0; i < m; i++){
1054 for (j = ia[i]; j < ia[i+1]; j++){
1056 for (k = ib[jj]; k < ib[jj+1]; k++){
1057 if (mask[jb[k]] < ic[i]){
1062 assert(jc[mask[jb[k]]] == jb[k]);
1089 int *ia =
A->ia, *ja =
A->ja, *ib =
B->ia, *jb =
B->ja, *ic =
C->ia, *jc =
C->ja, *
id, *jd;
1090 int i, j, k, l, ll, jj,
type, nz;
1095 if (
A->n !=
B->m)
return NULL;
1096 if (
B->n !=
C->m)
return NULL;
1098 if (
A->type !=
B->type ||
B->type !=
C->type){
1100 printf(
"in SparseMatrix_multiply, the matrix types do not match, right now only multiplication of matrices of the same type is supported\n");
1108 mask = calloc((
size_t)
C->n,
sizeof(
int));
1109 if (!mask)
return NULL;
1111 for (i = 0; i <
C->n; i++) mask[i] = -1;
1114 for (i = 0; i < m; i++){
1115 for (j = ia[i]; j < ia[i+1]; j++){
1117 for (l = ib[jj]; l < ib[jj+1]; l++){
1119 for (k = ic[ll]; k < ic[ll+1]; k++){
1120 if (mask[jc[k]] != -i - 2){
1123 fprintf(stderr,
"overflow in SparseMatrix_multiply !!!\n");
1128 mask[jc[k]] = -i - 2;
1147 for (i = 0; i < m; i++){
1148 for (j = ia[i]; j < ia[i+1]; j++){
1150 for (l = ib[jj]; l < ib[jj+1]; l++){
1152 for (k = ic[ll]; k < ic[ll+1]; k++){
1153 if (mask[jc[k]] <
id[i]){
1156 d[nz] = a[j]*b[l]*c[k];
1159 assert(jd[mask[jc[k]]] == jc[k]);
1160 d[mask[jc[k]]] += a[j]*b[l]*c[k];
1177 int *ia =
A->
ia, *ja =
A->ja,
type =
A->type, n =
A->n;
1178 int *mask =
NULL, nz = 0, i, j, sta;
1180 mask =
gv_calloc((
size_t)n,
sizeof(
int));
1181 for (i = 0; i < n; i++) mask[i] = -1;
1189 for (i = 0; i <
A->m; i++){
1190 for (j = sta; j < ia[i+1]; j++){
1191 if (mask[ja[j]] < ia[i]){
1196 assert(ja[mask[ja[j]]] == ja[j]);
1197 a[mask[ja[j]]] += a[j];
1210 for (i = 0; i <
A->m; i++) {
1211 for (j = sta; j < ia[i+1]; j++) {
1212 if (mask[ja[j]] < ia[i]) {
1214 a[2 * nz] = a[2 * j];
1215 a[2 * nz + 1] = a[2 * j + 1];
1218 assert(ja[mask[ja[j]]] == ja[j]);
1219 a[2 * mask[ja[j]]] += a[2 * j];
1220 a[2 * mask[ja[j]]+1] += a[2 * j + 1];
1233 for (i = 0; i <
A->m; i++){
1234 for (j = sta; j < ia[i+1]; j++){
1235 if (mask[ja[j]] < ia[i]){
1240 assert(ja[mask[ja[j]]] == ja[j]);
1241 a[mask[ja[j]]] += a[j];
1253 for (i = 0; i <
A->m; i++){
1254 for (j = sta; j < ia[i+1]; j++){
1255 if (mask[ja[j]] < ia[i]){
1259 assert(ja[mask[ja[j]]] == ja[j]);
1277 int jcn,
const void *val) {
1280 static const int nentries = 1;
1285 if (nz + nentries >=
A->nzmax){
1286 nzmax = nz + nentries;
1292 if (
A->size) memcpy((
char*)
A->a + ((
size_t)nz)*
A->size/
sizeof(
char), val,
A->size*((
size_t)nentries));
1293 if (irn >=
A->m)
A->m = irn + 1;
1294 if (jcn >=
A->n)
A->n = jcn + 1;
1301 int i, j, *ia, *ja, nz, sta;
1312 for (i = 0; i <
A->m; i++){
1313 for (j = sta; j < ia[i+1]; j++){
1327 for (i = 0; i <
A->m; i++){
1328 for (j = sta; j < ia[i+1]; j++){
1332 a[2*nz+1] = a[2*j+1];
1344 for (i = 0; i <
A->m; i++){
1345 for (j = sta; j < ia[i+1]; j++){
1358 for (i = 0; i <
A->m; i++){
1359 for (j = sta; j < ia[i+1]; j++){
1381 int i, j, *ia, *ja, nz, sta;
1392 for (i = 0; i <
A->m; i++){
1393 for (j = sta; j < ia[i+1]; j++){
1407 for (i = 0; i <
A->m; i++){
1408 for (j = sta; j < ia[i+1]; j++){
1412 a[2*nz+1] = a[2*j+1];
1424 for (i = 0; i <
A->m; i++){
1425 for (j = sta; j < ia[i+1]; j++){
1438 for (i = 0; i <
A->m; i++){
1439 for (j = sta; j < ia[i+1]; j++){
1475 for (i = 0; i <
A->m; i++){
1476 deg = ia[i+1] - ia[i];
1477 for (j = ia[i]; j < ia[i+1]; j++){
1485 for (i = 0; i <
A->m; i++){
1486 deg = ia[i+1] - ia[i];
1487 for (j = ia[i]; j < ia[i+1]; j++){
1489 a[2*j] = a[2*j]/deg;
1490 a[2*j+1] = a[2*j+1]/deg;
1515 int i, *ia, *ja, nz, m, n;
1527 if (n != m)
return NULL;
1531 memcpy(
B->ia, ia,
sizeof(
int)*((
size_t)(m+1)));
1532 memcpy(
B->ja, ja,
sizeof(
int)*((
size_t)nz));
1540 for (i = 0; i <
A->nz; i++) a[i] = 1.;
1542 A->size =
sizeof(double);
1554 printf(
"only CSR and real matrix supported.\n");
1561 for (i = 0; i <
A->m; i++){
1562 for (j =
A->ia[i]; j <
A->ia[i+1]; j++){
1573 memcpy(
B->ia,
A->ia,
sizeof(
int)*((
size_t)(
A->m+1)));
1574 if (
A->ia[
A->m] != 0) {
1575 memcpy(
B->ja,
A->ja,
sizeof(
int)*((
size_t)(
A->ia[
A->m])));
1577 if (
A->a) memcpy(
B->a,
A->a,
A->size*((
size_t)
A->nz));
1578 B->property =
A->property;
1585 int i, j, m =
A->m, *ia =
A->ia, *ja =
A->ja;
1587 for (i = 0; i < m; i++){
1588 for (j = ia[i]; j < ia[i+1]; j++){
1589 if (i == ja[j])
return true;
1596 int **levelset_ptr,
int **levelset,
1597 int **mask,
bool reinitialize_mask) {
1606 int i, j, sta = 0, sto = 1, nz, ii;
1607 int m =
A->m, *ia =
A->ia, *ja =
A->ja;
1609 if (!(*levelset_ptr)) *levelset_ptr =
gv_calloc((
size_t)(m + 2),
sizeof(
int));
1610 if (!(*levelset)) *levelset =
gv_calloc((
size_t)m,
sizeof(
int));
1612 *mask =
gv_calloc((
size_t)m,
sizeof(
int));
1613 for (i = 0; i < m; i++) (*mask)[i] =
UNMASKED;
1617 assert(root >= 0 && root < m);
1618 (*levelset_ptr)[0] = 0;
1619 (*levelset_ptr)[1] = 1;
1620 (*levelset)[0] = root;
1626 for (i = sta; i < sto; i++){
1627 ii = (*levelset)[i];
1628 for (j = ia[ii]; j < ia[ii+1]; j++){
1629 if (ii == ja[j])
continue;
1630 if ((*mask)[ja[j]] < 0){
1631 (*levelset)[nz++] = ja[j];
1632 (*mask)[ja[j]] = *nlevel + 1;
1636 (*levelset_ptr)[++(*nlevel)] = nz;
1641 if (reinitialize_mask)
for (i = 0; i < (*levelset_ptr)[*nlevel]; i++) (*mask)[(*levelset)[i]] =
UNMASKED;
1647 int *levelset_ptr =
NULL, *levelset =
NULL, *mask =
NULL, nlevel;
1648 int m =
A->m, i, nn;
1653 int *comps_ptr =
gv_calloc((
size_t)(m + 1),
sizeof(
int));
1657 for (i = 0; i < m; i++){
1658 if (i == 0 || mask[i] < 0) {
1660 if (i == 0) *comps = levelset;
1661 nn = levelset_ptr[nlevel];
1663 comps_ptr[(*ncomp)+1] = comps_ptr[(*ncomp)] + nn;
1679 int *ia =
A->ia, *ja =
A->ja, n =
A->n, m =
A->m;
1680 int *super =
NULL, *nsuper =
NULL, i, j, *mask =
NULL, isup, *newmap, isuper;
1682 super =
gv_calloc((
size_t)n,
sizeof(
int));
1683 nsuper =
gv_calloc((
size_t)(n + 1),
sizeof(
int));
1684 mask =
gv_calloc((
size_t)n,
sizeof(
int));
1685 newmap =
gv_calloc((
size_t)n,
sizeof(
int));
1689 for (i = 0; i < n; i++) super[i] = isup;
1691 for (i = 0; i < n; i++) mask[i] = -1;
1694 for (i = 0; i < m; i++){
1697 printf(
"doing row %d-----\n",i+1);
1699 for (j = ia[i]; j < ia[i+1]; j++){
1700 isuper = super[ja[j]];
1703 for (j = ia[i]; j < ia[i+1]; j++){
1704 isuper = super[ja[j]];
1705 if (mask[isuper] < i){
1707 if (nsuper[isuper] == 0){
1709 printf(
"node %d keep super node id %d\n",ja[j]+1,isuper+1);
1712 newmap[isuper] = isuper;
1714 newmap[isuper] = isup;
1717 printf(
"make node %d into supernode %d\n",ja[j]+1,isup+1);
1719 super[ja[j]] = isup++;
1723 printf(
"node %d join super node %d\n",ja[j]+1,newmap[isuper]+1);
1725 super[ja[j]] = newmap[isuper];
1726 nsuper[newmap[isuper]]++;
1731 for (j = 0; j < isup; j++) printf(
"(%d,%d),",j+1,nsuper[j]);
1736 for (i = 0; i < n; i++){
1737 printf(
"node %d is in supernode %d\n",i, super[i]);
1741 fprintf(stderr,
"n = %d, nsup = %d\n",n,isup);
1746 for (i = 0; i < isup; i++) nsuper[i+1] += nsuper[i];
1749 for (i = 0; i < n; i++){
1751 (*cluster)[nsuper[isuper]++] = i;
1753 for (i = isup; i > 0; i--) nsuper[i] = nsuper[i-1];
1759 for (i = 0; i < *ncluster; i++){
1761 for (j = (*clusterp)[i]; j < (*clusterp)[i+1]; j++){
1762 printf(
"%d, ",(*cluster)[j]);
1777 int nz =
A->nz,
type =
A->type;
1778 int m =
A->m, n =
A->n, i, j;
1780 if (!
A)
return NULL;
1782 irn =
gv_calloc((
size_t)nz * 2,
sizeof(
int));
1783 jcn =
gv_calloc((
size_t)nz * 2,
sizeof(
int));
1787 assert(
A->size != 0 && nz > 0);
1789 memcpy(val,
A->a,
A->size*((
size_t)nz));
1790 memcpy(((
char*) val) + ((
size_t)nz)*
A->size,
A->a,
A->size*((
size_t)nz));
1794 for (i = 0; i < m; i++){
1795 for (j = (
A->ia)[i]; j < (
A->ia)[i+1]; j++){
1797 jcn[nz++] = (
A->ja)[j] + m;
1800 for (i = 0; i < m; i++){
1801 for (j = (
A->ia)[i]; j < (
A->ia)[i+1]; j++){
1803 irn[nz++] = (
A->ja)[j] + m;
1818 switch (bipartite_options){
1820 if (
A->m ==
A->n)
return A;
1844 int nz = 0, i, j, *irn, *jcn, *ia =
A->
ia, *ja =
A->ja, m =
A->m, n =
A->n;
1848 int irow = 0, icol = 0;
1850 if (nrow <= 0 || ncol <= 0)
return NULL;
1854 rmask =
gv_calloc((
size_t)m,
sizeof(
int));
1855 cmask =
gv_calloc((
size_t)n,
sizeof(
int));
1856 for (i = 0; i < m; i++) rmask[i] = -1;
1857 for (i = 0; i < n; i++) cmask[i] = -1;
1860 for (i = 0; i < nrow; i++) {
1861 if (rindices[i] >= 0 && rindices[i] < m){
1862 rmask[rindices[i]] = irow++;
1866 for (i = 0; i < nrow; i++) {
1872 for (i = 0; i < ncol; i++) {
1873 if (cindices[i] >= 0 && cindices[i] < n){
1874 cmask[cindices[i]] = icol++;
1878 for (i = 0; i < ncol; i++) {
1883 for (i = 0; i < m; i++){
1884 if (rmask[i] < 0)
continue;
1885 for (j = ia[i]; j < ia[i+1]; j++){
1886 if (cmask[ja[j]] < 0)
continue;
1896 irn =
gv_calloc((
size_t)nz,
sizeof(
int));
1897 jcn =
gv_calloc((
size_t)nz,
sizeof(
int));
1898 val =
gv_calloc((
size_t)nz,
sizeof(
double));
1901 for (i = 0; i < m; i++){
1902 if (rmask[i] < 0)
continue;
1903 for (j = ia[i]; j < ia[i+1]; j++){
1904 if (cmask[ja[j]] < 0)
continue;
1906 jcn[nz] = cmask[ja[j]];
1917 irn =
gv_calloc((
size_t)nz,
sizeof(
int));
1918 jcn =
gv_calloc((
size_t)nz,
sizeof(
int));
1919 val =
gv_calloc(2 * (
size_t)nz,
sizeof(
double));
1922 for (i = 0; i < m; i++){
1923 if (rmask[i] < 0)
continue;
1924 for (j = ia[i]; j < ia[i+1]; j++){
1925 if (cmask[ja[j]] < 0)
continue;
1927 jcn[nz] = cmask[ja[j]];
1929 val[2*nz+1] = a[2*j+1];
1940 irn =
gv_calloc((
size_t)nz,
sizeof(
int));
1941 jcn =
gv_calloc((
size_t)nz,
sizeof(
int));
1942 val =
gv_calloc((
size_t)nz,
sizeof(
int));
1945 for (i = 0; i < m; i++){
1946 if (rmask[i] < 0)
continue;
1947 for (j = ia[i]; j < ia[i+1]; j++){
1948 if (cmask[ja[j]] < 0)
continue;
1950 jcn[nz] = cmask[ja[j]];
1959 irn =
gv_calloc((
size_t)nz,
sizeof(
int));
1960 jcn =
gv_calloc((
size_t)nz,
sizeof(
int));
1962 for (i = 0; i < m; i++){
1963 if (rmask[i] < 0)
continue;
1964 for (j = ia[i]; j < ia[i+1]; j++){
1965 if (cmask[ja[j]] < 0)
continue;
1967 jcn[nz++] = cmask[ja[j]];
2000 for (i = 0; i <
A->nz; i++) a[i] = 1.;
2002 A->size =
sizeof(double);
2014 for (i = 1; i <= m; i++) (
A->ia)[i] = (
A->ia)[i-1] + n;
2018 for (i = 0; i < m; i++){
2019 for (j = 0; j < n; j++) {
2038 int m =
D->
m, n =
D->n;
2039 int *levelset_ptr =
NULL, *levelset =
NULL, *mask =
NULL;
2040 int i, j, k, nlevel;
2049 if (!(*dist0)) *dist0 =
gv_calloc(n * n,
sizeof(
double));
2050 for (i = 0; i < n*n; i++) (*dist0)[i] = -1;
2052 for (k = 0; k < n; k++) {
2054 assert(levelset_ptr[nlevel] == n);
2055 for (i = 0; i < nlevel; i++) {
2056 for (j = levelset_ptr[i]; j < levelset_ptr[i+1]; j++) {
2057 (*dist0)[k*n+levelset[j]] = i;
void SparseMatrix_distance_matrix(SparseMatrix D0, double **dist0)
static SparseMatrix SparseMatrix_realloc(SparseMatrix A, int nz)
void SparseMatrix_decompose_to_supervariables(SparseMatrix A, int *ncluster, int **cluster, int **clusterp)
SparseMatrix SparseMatrix_from_coordinate_format(SparseMatrix A)
SparseMatrix SparseMatrix_transpose(SparseMatrix A)
SparseMatrix SparseMatrix_remove_upper(SparseMatrix A)
SparseMatrix SparseMatrix_get_submatrix(SparseMatrix A, int nrow, int ncol, int *rindices, int *cindices)
SparseMatrix SparseMatrix_symmetrize(SparseMatrix A, bool pattern_symmetric_only)
SparseMatrix SparseMatrix_general_new(int m, int n, int nz, int type, size_t sz, int format)
SparseMatrix SparseMatrix_get_augmented(SparseMatrix A)
static size_t size_of_matrix_type(int type)
void SparseMatrix_multiply_dense(SparseMatrix A, const double *v, double *res, int dim)
SparseMatrix SparseMatrix_coordinate_form_add_entry(SparseMatrix A, int irn, int jcn, const void *val)
bool SparseMatrix_is_symmetric(SparseMatrix A, bool test_pattern_symmetry_only)
SparseMatrix SparseMatrix_to_square_matrix(SparseMatrix A, int bipartite_options)
void SparseMatrix_multiply_vector(SparseMatrix A, double *v, double **res)
SparseMatrix SparseMatrix_multiply(SparseMatrix A, SparseMatrix B)
SparseMatrix SparseMatrix_divide_row_by_degree(SparseMatrix A)
void SparseMatrix_export(FILE *f, SparseMatrix A)
static void SparseMatrix_export_csr(FILE *f, SparseMatrix A)
SparseMatrix SparseMatrix_from_coordinate_arrays(int nz, int m, int n, int *irn, int *jcn, void *val0, int type, size_t sz)
SparseMatrix SparseMatrix_from_coordinate_arrays_not_compacted(int nz, int m, int n, int *irn, int *jcn, void *val0, int type, size_t sz)
static SparseMatrix SparseMatrix_from_coordinate_arrays_internal(int nz, int m, int n, int *irn, int *jcn, void *val0, int type, size_t sz, int sum_repeated)
static void SparseMatrix_export_coord(FILE *f, SparseMatrix A)
void SparseMatrix_delete(SparseMatrix A)
SparseMatrix SparseMatrix_make_undirected(SparseMatrix A)
static SparseMatrix SparseMatrix_alloc(SparseMatrix A, int nz)
SparseMatrix SparseMatrix_copy(SparseMatrix A)
SparseMatrix SparseMatrix_set_entries_to_real_one(SparseMatrix A)
static void SparseMatrix_level_sets(SparseMatrix A, int root, int *nlevel, int **levelset_ptr, int **levelset, int **mask, bool reinitialize_mask)
SparseMatrix SparseMatrix_get_real_adjacency_matrix_symmetrized(SparseMatrix A)
SparseMatrix SparseMatrix_sort(SparseMatrix A)
SparseMatrix SparseMatrix_sum_repeat_entries(SparseMatrix A)
SparseMatrix SparseMatrix_add(SparseMatrix A, SparseMatrix B)
SparseMatrix SparseMatrix_multiply3(SparseMatrix A, SparseMatrix B, SparseMatrix C)
SparseMatrix SparseMatrix_apply_fun(SparseMatrix A, double(*fun)(double x))
bool SparseMatrix_has_diagonal(SparseMatrix A)
static SparseMatrix SparseMatrix_init(int m, int n, int type, size_t sz, int format)
int * SparseMatrix_weakly_connected_components(SparseMatrix A0, int *ncomp, int **comps)
SparseMatrix SparseMatrix_from_coordinate_format_not_compacted(SparseMatrix A)
SparseMatrix SparseMatrix_remove_diagonal(SparseMatrix A)
SparseMatrix SparseMatrix_new(int m, int n, int nz, int type, int format)
SparseMatrix SparseMatrix_from_dense(int m, int n, double *x)
#define SparseMatrix_set_pattern_symmetric(A)
#define SparseMatrix_known_strucural_symmetric(A)
#define SparseMatrix_set_symmetric(A)
@ MATRIX_PATTERN_SYMMETRIC
#define SparseMatrix_set_undirected(A)
#define SparseMatrix_known_symmetric(A)
@ BIPARTITE_PATTERN_UNSYM
Memory allocation wrappers that exit on failure.
static void * gv_recalloc(void *ptr, size_t old_nmemb, size_t new_nmemb, size_t size)
static void * gv_calloc(size_t nmemb, size_t size)
static void * gv_alloc(size_t size)
#define clear_flag(a, flag)
GVIO_API const char * format