Spectral routines tested and output improved.

Cleanup of the output routines, and also added HDF5 grid output for the
simulation. The spectral routines (differentiation, streamfunction calculation,
vorticity calculation, and velocity calculation) have been tested with a simple
formula for the streamfunction. Things appear to be coming out as expected.
Updated time integration and file IO.

The time integration routine has been updated to use the new spectral module
routines. The main code's time loop has also been updated for these changes.
File IO was slightly adjusted to give 0,1,2,3,... numbering for restart files,
with the current simulation step and time stored in the restart file as
attributes.
Added XMF output file for HDF5 restart files.

In order to open HDF5 data using the Xdmf format, we need an XMF file that marks
up the grid and restart file data in a way that post-processors can open them
properly. This functionality has now been added to the HDF5 restart writer.
Added TG vortex for convergence analysis.

The Taylor-Green vortex problem has been added to test for the convergence order
of the time integration scheme. A post-processing python script checks a series
of results to obtain the convergence order.