def normalize_adj(adj : sp.csr_matrix):
"""Normalize adjacency matrix and convert it to a sparse tensor."""
if sp.isspmatrix(adj):
adj = adj.tolil()
adj.setdiag(1)
adj = adj.tocsr()
deg = np.ravel(adj.sum(1))
deg_sqrt_inv = 1 / np.sqrt(deg)
adj_norm = adj.multiply(deg_sqrt_inv[:, None]).multiply(deg_sqrt_inv[None, :])
elif torch.is_tensor(adj):
deg = adj.sum(1)
deg_sqrt_inv = 1 / torch.sqrt(deg)
adj_norm = adj * deg_sqrt_inv[:, None] * deg_sqrt_inv[None, :]
return to_sparse_tensor(adj_norm)
def _assemble_neumann_common(
self,
g: pp.Grid,
data: Dict,
M: sps.csr_matrix,
mass: sps.csr_matrix,
bc_weight: float = None,
) -> Tuple[sps.csr_matrix, np.ndarray]:
""" Impose Neumann boundary discretization on an already assembled
system matrix.
Common implementation for VEM and RT0. The parameter mass should be
adapted to the discretization method in question
"""
norm = sps.linalg.norm(mass, np.inf) if bc_weight else 1
parameter_dictionary = data[pp.PARAMETERS][self.keyword]
bc = parameter_dictionary["bc"]
# assign the Neumann boundary conditions
# For dual discretizations, internal boundaries
# are handled by assigning Dirichlet conditions. THus, we remove them
# from the is_neu (where they belong by default) and add them in
# is_dir.
is_neu = np.logical_and(bc.is_neu, np.logical_not(bc.is_internal))
if bc and np.any(is_neu):
is_neu = np.hstack((is_neu, np.zeros(g.num_cells, dtype=np.bool)))
is_neu = np.where(is_neu)[0]
# set in an efficient way the essential boundary conditions, by
# clear the rows and put norm in the diagonal
for row in is_neu:
M.data[M.indptr[row]:M.indptr[row + 1]] = 0.0
d = M.diagonal()
d[is_neu] = norm
M.setdiag(d)
return M, norm
def removeEye(adj: sp.csr_matrix):
adj = adj.tolil(copy=True)
adj.setdiag(0)
return adj.tocsr()
def addEye(adj: sp.csr_matrix):
adj = adj.tolil(copy=True)
adj.setdiag(1)
return adj.tocsr()