purpose. Now as time goes i need to look the bond dynamics. that is why
if you use bonds defined in the data file,
how is there going to be bond dynamics?
Alas this is one of the few things missing from a dump file. (I don't
know how hard it would be to add the option to include bond
information in a dump file, but even if Steve did it, I don't know how
long before VMD would support it.) Restart files have this
information but you need to make many of them (one for each moment in
time you wish to examine).
please remember, that for practically all simulations
that *do* define bonds in a lammps data file, the bonding
information doesn't change over the course of a trajectory.
hence it doesn't really need to be stored in the trajectory.
you can just read it in once, e.g. from the data file, or
even better with additional per-atom non-varying info:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks#TOC-Reconstruct-a-.pdb-.psf-files-from-a-LAMMPS-data-file-for-use-with-visualization-programs
VMD's internal data structure don't support changing
of the topology during a trajectory anyway. so anything
that goes beyond that, would have to be implemented
in add-on scripts that hook into the animation loop.
LAMMPS already supports dumping the bond information
into a special format dump file (for cases using bond/swap,
bond/create and so on).
however, for cases where you would want recompute
bonds dynamically based on a distance criterion (as
indicated by the OP), you can just use one or more of
the "DynamicBonds" representation in VMD and be
done with it
You could use the new "rerun" lammps command to read an existing dump
file. Then (I think) you can use the "restart" command to generate
restart files at regular intervals. (Would that work?) Then, outside
of lammps (using the bash or tcsh shell) you could create a loop which
converts each restart file to a DATA file (using the "restart2data"
utility).
yes, this would work, and it would also be supported by VMD
by reading each data file into a new molecule and then using
the "multimolanim" plugin/extension, which animates the display
by switching individual restart files on and off. but this is needlessly
complicated. it can be even done from within LAMMPS using "shell"
command.
Then you could read each DATA file with your program.
i think there may be a confusion may be about what is
understood by a "data" file. within lammps 'slang' it is
yet another well defined file format, but it seems the
OP expected the dump to just have a list of coordinates
without any additional info or structure.
axel.