Reftraj ensemble

[Ondrej Marsalek]

Hi,

I am trying to use the reftraj ensemble and there are two things that
I find slightly inconvenient.

1) You need to provide coordinates in the input file, although they
are not needed, as you get them from the reference trajectory. They
are probably (at least I hope) ignored. If they are, it would be nice
say that in the input manual at the reftraj entry. It would be even
better not to require them at all and use whatever is the first frame
requested instead.

2) If you want to get consistent step numbers everywhere, you need to
remove the frame with i=0 from CP2K xyz trajectory output that you use
as a reference trajectory. Seems to be due to some mixing of
zero-based and one-based indexing.

As usual with my messages here, nothing critical, but I think it is
worth mentioning. Either for people trying to make sense of the
numbers (like me a while ago) or for a developer who is really bored
;-)

Best,
Ondrej