  The Navier-Stokes equations in a finite cylinder are written in terms of
poloidal and toroidal potentials in order to impose incompressibility.
Regularity of the solutions is ensured in several ways: First, the potentials
are represented using a spectral basis which is analytic at the cylindrical
axis. Second, the non-physical discontinuous boundary conditions at the
cylindrical corners are smoothed using a polynomial approximation to a steep
exponential profile. Third, the nonlinear term is evaluated in such a way as to
eliminate singularities. The resulting pseudo-spectral code is tested using
exact polynomial solutions and the spectral convergence of the coefficients is
demonstrated. Our solutions are shown to agree with exact polynomial solutions
and with previous axisymmetric calculations of vortex breakdown and of
nonaxisymmetric calculations of onset of helical spirals. Parallelization by
azimuthal wavenumber is shown to be highly effective.
