dear tamara,
please always keep the lammps list in cc:
so that others get to see the resolution
of issues and can look it up in the archives.
[...]
Does this work for per-atom computes/fixes as well? i.e. can I do:
LAMMPSREMAPFILEDS=vx=c_tempAtom....?
yes, this should work. the replacement is done without any knowledge
of lammps as a simple string replace (i think i have to pat myself on
the back for implementing it this hack in such a generic way. at the
time it was just the most straightforward solution).
I don't want to waste you time, so if there is documentation for the
trajectory reader api, could you point me to it?
some very generic documentation is here.
http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/molfileplugins.html#molfileplugins
it has some doxygen generated links to embedded documentation, but this
is not very up-to-date and not very complete. the best is probably to
download the vmd plugin sources (or better get read-only cvs access)
and read some well written plugins as examples and learn from them.
>hope this helps,
> axel.
This was tremendously helpful. I was dreading getting into the weeds of
tcl programming.
tcl programming is not that bad. it can be quite elegant, after you get
the hang of it. only its learning curve is much steeper than for other
script languages; at least at the beginning.
well, with tcl programming it would be easier to pass custom information
to VMD, since you don't have go through the molfile plugin API. the
topotools plugin as a couple of examples. it can read and write many
variants of LAMMPS data files and has a way to handle .xyz files with
varying numbers of atoms. but this comes at a price of a much reduced
performance.
cheers,
axel.