Lloyd Aggregation and Dirichlet Nodes

[Alexey-Voronin]

Some of the matrices that I deal with contain rows with only 1's not diagonal, corresponding to Dirichlet boundary conditions. I found that Lloyd aggregation randomly picks some of them to be the seeds for the aggregates, which is not desirable behavior.

pyamg/pyamg/graph.py

Lines 191 to 201 in 83b4851

	G = asgraph(G)
	N = G.shape[0]
	if G.dtype.kind == 'c':
	# complex dtype
	G = np.abs(G)
	# interpret seeds argument
	if np.isscalar(seeds):
	seeds = np.random.permutation(N)[:seeds]
	seeds = seeds.astype('intc')

I included a couple of lines of code on line 199 to help avoid this behavior.

     if np.isscalar(seeds):
         indptr = G.indptr
         nodes = np.where(indptr[1:]-indptr[:-1] > 1)[0]
         seeds = np.random.permutation(nodes)[:seeds]
         seeds = seeds.astype('intc')