I would like to re-start a simulation with initial conditions for positions and velocities and have a reference set of positions, different from the initial positions, to calculate displacements from. I don't think this is currently possible; it looks like the new capability to calculate displacements uses the initial positions. Is there a way around this? Adding another keyword/optional section to the "read data" is the first thing that comes to mind.
btw the application is setting up a traveling wave packet in lattice where displacements from the undeformed configuration are needed to visualize its passage.. amongst other things..
You could have a new section of the data file with this info,
but the question is where would it be stored. In the current
implementation of compute displace/atom and fix coord/original
that info is stored with the atom via fix coord/original which manages
the memory needed.
So I think the better solution is to have an option on fix coord/original
to specify a file that lists the original coords as one line per atom.
Thus when the fix is invoked in your input script, the file would be read,
and the info stored by the fix. Kind of like fix tmd does.