Fix semantics of permeability assignment

Calling code relies on permeability tensors being stored in column
major order (row index cycling the most rapidly).  Honour that
requirement.  The previous assignment implied row major ordering
(column index cycling the most rapidly).  This, however, is a
pedantic rather than visible change because the surrounding code
enforces symmetric tensors whence both orderings produce the same
results when the array is viewed contiguously.
Remove obsolete comment

This comment was needed when the code was first developed, but
subsequent development has rendered it obsolete.  Remove it to avoid
confusion.
Simplify diagonal component thresholding

This commit switches the assignment

    diagonal = max(diagonal, minval)

to using a reference in the "diagonal" expression.  This guarantees
that the indexing is done once which eases maintainability.  While
here, replace the hard-coded dimension stride ('3') with the current
run-time dimension.  This is mostly for symmetry because the overall
code is only really supported in three space dimension.
Merge pull request #635 from bska/fix-perm-assignment

Fix permeability assignment