void UMFPackMatrix::alloc() {
_F_
assert(pages != NULL);
assert(size > 0);
// initialize the arrays Ap and Ai
Ap = new int [size + 1];
MEM_CHECK(Ap);
int aisize = get_num_indices();
Ai = new int [aisize];
MEM_CHECK(Ai);
// sort the indices and remove duplicities, insert into Ai
int i, pos = 0;
for (i = 0; i < size; i++) {
Ap[i] = pos;
pos += sort_and_store_indices(pages[i], Ai + pos, Ai + aisize);
}
Ap[i] = pos;
delete [] pages;
pages = NULL;
nnz = Ap[size];
Ax = new scalar [nnz];
MEM_CHECK(Ax);
memset(Ax, 0, sizeof(scalar) * nnz);
}
void PetscMatrix::alloc() {
_F_
#ifdef WITH_PETSC
assert(pages != NULL);
// calc nnz
int *nnz_array = new int[size];
MEM_CHECK(nnz_array);
// fill in nnz_array
int aisize = get_num_indices();
int *ai = new int[aisize];
MEM_CHECK(ai);
// sort the indices and remove duplicities, insert into ai
int pos = 0;
for (unsigned int i = 0; i < size; i++) {
nnz_array[i] = sort_and_store_indices(pages[i], ai + pos, ai + aisize);
pos += nnz_array[i];
}
// stote the number of nonzeros
nnz = pos;
delete [] pages; pages = NULL;
delete [] ai;
//
MatCreateSeqAIJ(PETSC_COMM_SELF, size, size, 0, nnz_array, &matrix);
// MatSetOption(matrix, MAT_ROW_ORIENTED);
// MatSetOption(matrix, MAT_ROWS_SORTED);
delete [] nnz_array;
inited = true;
#endif
}
void CSCMatrix::alloc() {
_F_
assert(pages != NULL);
if (size <= 0)
error("UMFPack failed, matrix size must be greater than 0.");
// initialize the arrays Ap and Ai
Ap = new int [size + 1];
MEM_CHECK(Ap);
int aisize = get_num_indices();
Ai = new int [aisize];
MEM_CHECK(Ai);
// sort the indices and remove duplicities, insert into Ai
unsigned int i;
int pos = 0;
for (i = 0; i < size; i++) {
Ap[i] = pos;
pos += sort_and_store_indices(pages[i], Ai + pos, Ai + aisize);
}
Ap[i] = pos;
delete [] pages;
pages = NULL;
nnz = Ap[size];
Ax = new scalar [nnz];
MEM_CHECK(Ax);
memset(Ax, 0, sizeof(scalar) * nnz);
}
void DiscreteProblem::create_matrix()
{
// remove any previous matrix
free_matrix_indices();
free_matrix_values();
// calculate the total number of DOFs
ndofs = 0;
for (int i = 0; i < neq; i++)
ndofs += spaces[i]->get_num_dofs();
if (!quiet) verbose("Ndofs: %d", ndofs);
if (!ndofs) return;
// get row and column indices of nonzero matrix elements
Page** pages = new Page*[ndofs];
memset(pages, 0, sizeof(Page*) * ndofs);
if (!quiet) { verbose("Calculating matrix sparse structure..."); begin_time(); }
precalculate_sparse_structure(pages);
// initialize the arrays Ap and Ai
Ap = (int*) malloc(sizeof(int) * (ndofs+1));
int aisize = get_num_indices(pages, ndofs);
Ai = (int*) malloc(sizeof(int) * aisize);
if (Ai == NULL) error("Out of memory. Could not allocate the array Ai.");
// sort the indices and remove duplicities, insert into Ai
int i, pos = 0, num;
for (i = 0; i < ndofs; i++)
{
Ap[i] = pos;
pos += sort_and_store_indices(pages[i], Ai + pos, Ai + aisize);
}
Ap[i] = pos;
if (!quiet) verbose(" Nonzeros: %d\n Total matrix size: %0.1lf MB\n (time: %g sec)",
pos, (double) get_matrix_size() / (1024*1024), end_time());
delete [] pages;
// shrink Ai to the actual size
int* oldAi = Ai;
Ai = (int*) realloc(Ai, sizeof(int) * pos);
if (oldAi != Ai) warn("Realloc moved Ai when shrinking."); // this should not happen
// UMFPACK: perform symbolic analysis of the matrix
if (!quiet) { verbose("Performing UMFPACK symbolic analysis..."); begin_time(); }
int status = umfpack_symbolic(ndofs, ndofs, Ap, Ai, NULL, &Symbolic, NULL, NULL);
if (status != UMFPACK_OK) umfpack_status(status);
if (!quiet) verbose(" (time: %g sec)", end_time());
equi = (double*) malloc(sizeof(double) * ndofs);
if (equi == NULL) error("Out of memory. Error allocating the equilibration vector.");
for (int i = 0; i < ndofs; i++)
equi[i] = 1.0;
is_equi = false;
}
