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
<[email protected]>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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--
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world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
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