  Boundary integral methods are highly suited for problems with complicated
geometries, but require special quadrature methods to accurately compute the
singular and nearly singular layer potentials that appear in them. This paper
presents a boundary integral method that can be used to study the motion of
rigid particles in three-dimensional periodic Stokes flow with confining walls.
A centrepiece of our method is the highly accurate special quadrature method,
which is based on a combination of upsampled quadrature and quadrature by
expansion (QBX), accelerated using a precomputation scheme. The method is
demonstrated for rodlike and spheroidal particles, with the confining geometry
given by a pipe or a pair of flat walls. A parameter selection strategy for the
special quadrature method is presented and tested. Periodic interactions are
computed using the Spectral Ewald (SE) fast summation method, which allows our
method to run in O(n log n) time for n grid points, assuming the number of
geometrical objects grows while the grid point concentration is kept fixed.
