[lammps-users] xyz output

Hello,

Using below commands, I still don’t get an xyz file readable in VMD:

dump main all atom 100 main.xyz
dump_modify main sort id

I think there is a way to make output file (dump) readable in VMD or other visualization software.
Could anyone let me know?

Please don’t say “use pizza.py”.
FYI, pizza.py is very difficult for me to handle. I spent too much time setting it and I eventually failed. So, I decided not to use it.

Maybe a VMD person can comment. You can also
use native dump atom or dump custom formats out
of LAMMPS that VMD can read directly.

Steve

Hello,

hello edward,

Using below commands, I still don't get an xyz file readable in VMD:
dump main all atom 100 main.xyz
dump_modify main sort id
I think there is a way to make output file (dump) readable in VMD or other
visualization software.

vmd reads .xyz files produced by lammps just fine. the format
is trivial and easy to parse.

you have to provide more details as to why and how it doesn't work
for you so that we can track down where the problem is. i can only
assume that it is a case of PEBCAC.

Could anyone let me know?
Please don't say "use pizza.py".
FYI, pizza.py is very difficult for me to handle. I spent too much time
setting it and I eventually failed. So, I decided not to use it.

perhaps you didn't reads its documentation well enough,
or your python skills are insufficient and you would need to
beef them up before continuing. in any case, there is no use
in complaining about something unless you can provide
specific examples that don't work as expected and sufficient
detail so that somebody can reproduce step-by-step of
what you have been doing.

axel.

Hello,
Using below commands, I still don't get an xyz file readable in VMD:
dump main all atom 100 main.xyz

...wait. this is not at all creating an .xyz format file.
this will still create a lammps format trajectory file.

however, since you give it the name .xyz, VMD will
think that it is a xyz format file (which it isn't) and then
- of course - refuse to load it.
if you name this file, e.g. main.lammpstrj it will load just fine.

remember: the filename does _not_ determine the file format,
but for convenience people have established conventions that
a file name indicates a format. if you go against those conventions,
then you get what you deserve.

axel.