From: Axel Kohlmeyer (
Date: Fri Jan 08 2010 - 08:19:15 CST

On Fri, 2010-01-08 at 14:12 +0100, MyLinkka wrote:

> The data columns are in a style: id type xu yu zu
> But because it's in the "old style", there is no such a self-description
> string specified there.

> I import that old style dump file into VMD. The lammpstrj plugin tried
> to guess and map the column types. But it seems that a style "id type x
> y z" was determined instead of the desired "id type xu yu zu". That's
> why I suspected there is some logic problem in the implementation of
> smart format guess algorithm. (most probably to change j>4 to j>5 will
> correct it, I hope. )

no. strictly speaking, it is impossible to determine from the little
information contained in an old style dump files what it contains in
the columns. the idea of this test is to establish a minimum requirement
for a (3d) atom style output.

> The problem should be reproduced if you load the two attached lammpstrj
> files. The only difference between these two files are the
> self-description string.

ok. i see what your problem is. this is _not_ due to the test that you
are describing, but rather due to the guess that the plugin makes to
tell trajectories with fractional coordinates apart from trajectories
with regular coordinates. since your initial structure is "flat", it
triggers the test and the plugin assumes fractional coordinates.
have a look at the text output in the vmd console when loading the
two files. for this reason i added code to the plugin print to the
console which guess it is making.

> However, as a simple solution, I could use sed to add column labels to each
> frame, then no ambiguity is there any more.

that is probably the best way to proceed. in principle the plugin could
be changes to work correctly for your old files, but since your case is
very exotic i would prefer not to do this for fear of breaking the
compatibility for other, more common cases of old lammps trajectories.


> Ting Li (KULeuven)

Dr. Axel Kohlmeyer 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.