[lammps-users] fix evaporate visualization

Hey Lammps users,

I am using fix evaporate for a simulation. Unfortunately, I can't use dump
xyz because the atom list is no longer sequential.

It is not clear to me how to use VMD to visualize the output because the
number of atoms is not constant. I took a look at Axel K.'s topotool but
unfortunately it relies on xyz file formats. Pizza.py is also giving me a
lot of trouble during installation.

Any advice on packages or strategies to visualize lammps output format and
a variable number of atoms?

Thanks,
John

You could dump out output in formats which are sequential and then write a short tcl or gawk script to convert it in xyz format. Then use Axel’s tool. May be this helps.

Hey Lammps users,

I am using fix evaporate for a simulation. Unfortunately, I can't use dump
xyz because the atom list is no longer sequential.

It is not clear to me how to use VMD to visualize the output because the
number of atoms is not constant. I took a look at Axel K.'s topotool but
unfortunately it relies on xyz file formats. Pizza.py is also giving me a
lot of trouble during installation.

john,

is there a specific reason that you need your atoms
to be sorted in a special way for visualization?

the varxyz reader will internally shuffle atoms around in
order to save space. as far as VMD is concerned, it only
cares about atom types.

it would be straightforward to add a reader to lammps
dump files, but the resorting will happen in any case.

cheers,
    axel.

Hey Lammps users,

I am using fix evaporate for a simulation. Unfortunately, I can't use dump
xyz because the atom list is no longer sequential.

It is not clear to me how to use VMD to visualize the output because the
number of atoms is not constant. I took a look at Axel K.'s topotool but
unfortunately it relies on xyz file formats. Pizza.py is also giving me a
lot of trouble during installation.

Any advice on packages or strategies to visualize lammps output format and
a variable number of atoms?

i forgot.

many lammps users seem to be using atomeye for visualization,
perhaps that would be an alternative?

axel.

Pizza.py is also giving me a
lot of trouble during installation.

Just a comment on this. Pizza.py is a collection of many
tools. Some of them are hard to install, like the graphics viz one.
But Pizza.py should just ignore the tools it can't install, so you
can use the ones it did. The tools for reading dump files
and converting them to other formats should install easily.
The only thing the dump tool needs is Numeric. The dump
tool has a sort method.

Steve