Solution given on the lammps list already! As long as you write away the
group 'all' (the whole system) in xyz, it makes sure it puts it in the right
order. Or by using a different file format from xyz... I have to admit that
this is perfectly documented behavior of lammps, sorry for disturbing ;)
Greetings, Pim
On Mon, Jan 18, 2010 at 5:36 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> That would be crucial for sure. Not necessary, though to load as a
> trajectory if you only want a few models. Just load the file normally.
>
>
> On Mon, Jan 18, 2010 at 9:35 AM, pim schravendijk <pimli...@googlemail.com
> > wrote:
>
>> Hi there! I will send this to the lammps and the jmol list, because any
>> solution will probably involve either of the programs :)
>>
>> I have problems when reading a lammps xyz trajectory with jmol :(
>>
>> It's a system consisting of LJ particles and a metal, in different parts
>> of the box, obviously
>>
>> pair_style hybrid eam lj/cut 10.0
>> pair_coeff 1 1 eam Pt_u3.eam
>> pair_coeff * 2 lj/cut 0.00673850588 3.165648
>>
>> ...
>>
>> dump 1 gbigbox xyz 10000 rawdump.1.xyz
>>
>> I run this as a parallel job on 8 processors.
>>
>> Afterwards I substitute the atom types 1, 2 with awk into something that
>> jmol can read (Se is chosen for its nice color ;):
>>
>> awk '{if ($1 == '1'){print "Pt ",$2," ",$3," ",$4}else if($1 ==
>> '2'){print "Se ",$2," ",$3," ",$4} else{print $0}}' $1 > tempdump.$1.xyz
>>
>> I make a file with the 10 last snapshots. From that file I make another
>> file, containing the first of those 10 snapshots.
>> This opens correctly in jmol, so far so good.
>>
>> Then, I try to open the file with all 10 last snapshots, and open it with
>> 'load trajectory'
>>
>> The last snapshot is correct:
>>
>> http://www.molmod.com/~schraven/jmol/last_frame_out_of_ten__ten_frame_file.jpg<http://www.molmod.com/%7Eschraven/jmol/last_frame_out_of_ten__ten_frame_file.jpg>
>>
>> But it created a misrepresentation of the first 9 of these 10 snapshots:
>> some of the atoms within the metal and the LJ layer seem all mixed up :(
>>
>> http://www.molmod.com/~schraven/jmol/first_frame_out_of_ten__ten_frame_file.jpg<http://www.molmod.com/%7Eschraven/jmol/first_frame_out_of_ten__ten_frame_file.jpg>
>>
>> That happening is not very possible due to the quite solid nature of the
>> metal ;)
>>
>> I also checked by just reading the first snapshot of the 10 from a file
>> with only this snapshot in it:
>>
>> http://www.molmod.com/~schraven/jmol/first_frame_out_of_ten__single_frame_file.jpg<http://www.molmod.com/%7Eschraven/jmol/first_frame_out_of_ten__single_frame_file.jpg>
>>
>> That is the same structure as the previous picture, but with the correct
>> distribution of atom types.
>>
>> My conclusion is that jmol assumes that the atom order in the last frame
>> of a trajectory is the order in all frames, and that lammps does not keep
>> the atom order constant in the printing of xyz files. For all practical
>> purposes, is there a way to make lammps always use the same order of atoms?
>>
>> I hope anyone can shed some light on this issue!
>>
>> Greetings, Pim
>>
>>
>>
>>
>>
>>
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>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
------------------------------------------------------------------------------
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attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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