From: Dan Lussier (dtlussier_at_gmail.com)
Date: Tue Aug 24 2010 - 09:38:11 CDT

Hi Axel,

Ok - that is good to know. One off the reasons I asked at all was
because when I load my LAMMPS dump I am observing a strange (or at
least it appears strange to me) behaviour.

In my case the x coordinate is limited from [0,160] but when the data
is loaded into VMD and I look at the range of x I find something like
[0,25000]. The same thing is seen in both y and x so the overall
effect appears to be applied evenly to all the coordinates such that
the geometry is simply scaled rather than mangled.

I am using unscaled coordinates if this is of consequence to the way
the reader works.

It usually isn't a big deal - but it makes interacting with the data
via selections and scripting more tricky, so if there was a way to
avoid this I'd love to hear.

Thanks again,

Dan

On 23-Aug-10, at 8:04 PM, Axel Kohlmeyer wrote:

> On Mon, 2010-08-23 at 19:08 -0500, Dan Lussier wrote:
>> Hi,
>
> dan,
>
>> I have some old (i.e. not self-describing) LAMMPS ASCII dump files
>> that I would like to look at again in VMD.
>
>> Is it possible to simply add the necessary column definitions (i.e.
>> id
>> type x y z vx vy vz ..) to the 9th line of the dump file (i.e. ITEM:
>> ATOMS) so that it can be read properly by the newest version of the
>> LAMMPS reader plugin?
>
> the current lammps plugin should still support old style dump files
> in the same way it was supporting them before. i've recently
> fixed some bugs and added support for triclinic cells, so you may
> want to try one of the latest VMD alpha test versions or download and
> compile the plugin from the sources posted here (only tested on
> linux):
> http://sites.google.com/site/akohlmey/software/lammps-icms
>
> if you want to also read in velocities, which was previously not
> supported, you would have to add the description list, but only
> for the first frame in each file.
>
> cheers,
> axel.
>
>> Thanks.
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>