Bug corrections:

1. Changing wrong preprocessor definition to compile using the parallel HDF5 library.
2. Reverting the order of the parallel HDF5 file writing: the output is correct now, but opening the files using the Xmdf format is still swaping the Z and X coordinates. We need to save the output file using the ZYX order, but this requires additional work. For the moment the tool is working fine to have a quick look at the results, and we have other tools for postprocessing.
3. The Xdmf tool writes the necessary file to view the HDF5 results in Paraview and VisIt. I corrected a few bugs and added a 3D extension. WARNING: this format still uses the column-major system swaping the last and first dimensions.