A problem in using dump2data.py

Hello everyone,

I need to extract xyz of particles in different frames from file.lammpstrj. In order to that i used dump2data.py

  • dump2data.py -xyz -t 1000 <file.lammpstrj> coords.xyx

but i got the following error:

  • NameError: global name ‘xlo_str’ is not defined.

Would you please guide me?

Regards
Katerina

Hello everyone,

I need to extract xyz of particles in different frames from file.lammpstrj. In order to that i used dump2data.py

- dump2data.py -xyz -t 1000 <file.lammpstrj> coords.xyx

but i got the following error:

- NameError: global name 'xlo_str' is not defined.

Would you please guide me?

the most significant guidance i can give you, is that this is a
problem with a tool that is part of moltemplate, *not* a LAMMPS (we
simply bundle moltemplate for convenience). so you are not using the
best communication channels to get help.

for complete information about moltemplate, please see the moltemplate
home page at: www.moltemplate.org
you can report bugs like this one seems to be at its github issues
page at: https://github.com/jewettaij/moltemplate/issues
but before doing that, i would first check out the latest version. the
version bundled with LAMMPS is likely outdated.

axel.

Dear Katerina
   Actually, posting the question on the LAMMPS mailing list probably
is the best way to reach me. Unfortunately, I've been in China for
the last month, and haven't been able to read gmail or reply to
moltemplate questions very easily. I've got a backlog of moltemplate
related questions and bug reports to deal with.
   Please email me the trajectory file you are using. (Or,
preferably, send me a short version of that file that has the same
error. I can only receive attachments up to 25mb.)
   Thanks for posting the problem. Hopefully we can get it resolved.
Andrew

Dear Katerina
So I attempted to fix the bug you reported… I think it occurred because I forgot to test it on trajectory files which use scaled coordinates (xs, ys, zs), and it seems like you are using this kind of trajectory.
Hopefully, the new version of “dump2data.py” solves this problem. It can be downloaded from:
https://github.com/jewettaij/moltemplate

(it’s bundled with version 2.10.5 or later of moltemplate)
Again, thank you very much, again for reporting the error.
I never received any trajectory files from you. It would help me further if you could try downloading this new version, see if it works on your files, and post a reply to let me know what happened.

Andrew

(You don’t need to CC ongoing debugging discussions to the lammps mailing list, but I might post a message there once we know it’s working.)