VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Aug 24 2010 - 09:48:26 CDT

hi dan,

On Tue, Aug 24, 2010 at 10:38 AM, Dan Lussier <dtlussier_at_gmail.com> wrote:
> 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.

ok. that means, you have coordinates that somehow manage
to fool the heuristics to tell scaled from unscaled coordinates
for old style dump files. unusual, but not impossible. this is one
of the reasons that prompted the change in the file format.

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

yes.

> 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.

the best way would be to "convert" them to the new dump style.
the fastest is probably to use the sed command. e.g. with:

for s in *.lammpstrj ; do sed -e 's,^ITEM: ATOMS,ITEM: ATOMS id type x
y z,' $s > tmp && tmp $s; done

or something equivalent for the second ITEM string that matches your dump file.

cheers,
    axel.

> 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.
>>
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.