Steve,
Does 'write_restart' saves the coordinates folded in the central
simulation box (for periodic boundaries) ? 'dump' documentation says
that the coordinates may be slightly outside the box!!
I have this peculiar problem, I use 'boundary p p f', and don't fold
the coordinate in z direction (as it's fixed) while converting binary
to ascii data file. When I restart from the ascii data file, it gives
"bond atoms missing" error which means atoms are too far away. Might
be due to bonded atoms are sitting at opposite sides of the box. I
tried also using the x,y,z unfolded data, still having the same
problem!!
Monojoy
Whenver a restart file is written, a reneighboring is
done immediately before to insure atom coords are
inside the perioidic box. So you shouldn't have
a problem. If the atom was about to move across
a fixed boundary, it would be lost in either the
original simulation or the restarted one. If that's
a bad event (e.g. you lose an atom in a bonded
molecule), then you shouldn't use "f" as a boundary
condition.
Steve
One follow-up - you said this:
I use 'boundary p p f', and don't fold
the coordinate in z direction (as it's fixed) while converting binary
to ascii data file
I presume you are using tools/restart2data.cpp to convert
a restart file to a data file. It will do the right
thing - if you are doing the conversion yourself,
all bets are off.
Steve
Thanks Steve for the info.
Yes, I am using restart2data.cpp file to convert the bin file. Then
change the converted input myself (using my code) to accomodate the
system I am looking for. It works fine for all other cases, just this
case when using 'boundary p p f' does not work. Something might be
wrong, let me check it first!
Monojoy
If you can run with the data file restart2data produced,
then the issue must be with the changes you made to
the data file ...
Steve