Add option to control boundary addition during generate
- add_boundaries= True or False
Minor fixups to tools
- all methods now accept return_indices rather than just indices
Added some domain size calculations to Cubic
Clean up of some query methods
- Added 'none' option to _find_indices, which finds pores/throats with NONE of the given labels
- Fixed num_neighbors, which still accepted labels, and added a flatten option which gives the sum total neighbors (pnums excluded)
Added find_interface_throats method
- included method on the run_script to find interface between 'GDL' and 'MPL'
Moved save_object_tocsv() method to Utilities module.
Minor changes to _calc_eff_prop in LinearSolver.

Just to make it more user friendly!
Added info dictionaries to VTK file.

throat_info and throat_data have been added too, but since the
coordinates for them have not been defined, the visual results of them
may not be correct.
Removed throat data from VTK file.

The data are still there, but we don't want to visualize them, because
the VTK file can show only Np items. (it has been designed for pores).
We can visualize throats by adding some methods inside VTK file for
throat coordinates and connection. Even after that, I'm  not still sure
that we can show both pore and throat data on one VTK file .
But in the meantime, since they do not represent correct values, we
should remove them from final visualization.
Merge branch 'develop' of https://github.com/PMEAL/OpenPNM into Documentation

Conflicts:
	run_script.py