Changing the order of atoms in velocity.dat

[tsuyoshi38]

It is sometimes useful if we can set the initial velocity of atoms manually to start MD simulations.
In principle, we can do it by reading these values from the file velocity.dat.
However, the order of atoms in this file are weird and different from that in coordinate file, because it follows the old-CONQUEST format (partition labeling).
We (Lionel and I) believe it should be changed and I would like to do it soon.

Note that md.checkpoints, which is used in restarting MD ,also has the same problem.
But, as many users may have already stored the data in this format, I wonder we should change it later.
(Probably before a major version up.)