Fix iounits

[grhawk]

Fixing the issue #147

• the pdb is printed in the right way and match exactly the xyz.
• the cell is initialized even with an xyz file. If the cell is present in the xml too, the last one which is read is used.
• a warning message is printed when the units for cell and position are specified in the xml file. The standard way should be to specify the units of the cell and the units of the contents directly in the comment line of the xyz or in the TITLE line of the pdb using the keywords quantity{units} and cell{units}. The needed of specifying cell and contents units in a different place is necessary since the file contents can be everything, not only "length".

Check the warning message they could probably be shorter...

Still todo:

• [ ] Update the documentation
• [ ] Update the examples
• [ ] Move the output units conversion machinery into the io module

@ceriottm Despite the "Still todo" it would be important to merge this fix.

[ceriottm]

So I merged but not deleted the branch. Please open a new pull request for the other parts of the fix.