Problem in reading LAMMPS .xyz trajectory file using VOTCA

[Sanjeet Singh]

Hi Christoph,

I am trying to generate the radial distribution function using the following command:

csg_stat --top topology.xml --trj Trajectory2.xyz --cg PEO-10.xml --options setting-BON-RDF.xml --nt 2

But, i am getting the following error.

an error occurred:

First line of xyz file should contain number of atoms/beads, nothing else.

Can you please help me with this.

Thank you.

Sanjeet

[Christoph Junghans]

Can you do the following:
$ head Trajectory2.xyz

Christoph
>
> Thank you.
>
> Sanjeet
>
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Christoph Junghans
Web: http://www.compphys.de

[Sanjeet Singh]

Hi Christoph,

Thank you for your reply.

I did "head Trajectory2.xyz", and it gives me the following output.

ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
360
ITEM: BOX BOUNDS pp pp pp
0.0000000000000000e+00 1.5430965000000000e+01
0.0000000000000000e+00 1.5430965000000000e+01
0.0000000000000000e+00 1.5430965000000000e+01
ITEM: ATOMS id mol type q xs ys zs
199 3 4 0.053 0.358814 0.135826 0.17584

But, i think i have figured out the solution. I went through the different post in the group and noticed that csg_stat command is able to read trajectory.dump file. So, i just compared my file, Trajectory2.xyz, with one of the .dump file available on the group post and noticed that the format of the .dump file is exactly similar to my .xyz file. So, i just changed the extension of my file from .xyz to .dump, and now csg_stat is able to read this file.

Thank you. 

Sanjeet

[Christoph Junghans]

On Wed, Sep 7, 2022 at 10:15 AM Sanjeet Singh <sanje...@gmail.com> wrote:
>
> Hi Christoph,
>

> Thank you for your reply.
>
> I did "head Trajectory2.xyz", and it gives me the following output.
>
> ITEM: TIMESTEP
> 0
> ITEM: NUMBER OF ATOMS
> 360
> ITEM: BOX BOUNDS pp pp pp
> 0.0000000000000000e+00 1.5430965000000000e+01
> 0.0000000000000000e+00 1.5430965000000000e+01
> 0.0000000000000000e+00 1.5430965000000000e+01
> ITEM: ATOMS id mol type q xs ys zs
> 199 3 4 0.053 0.358814 0.135826 0.17584
>
> But, i think i have figured out the solution. I went through the different post in the group and noticed that csg_stat command is able to read trajectory.dump file. So, i just compared my file, Trajectory2.xyz, with one of the .dump file available on the group post and noticed that the format of the .dump file is exactly similar to my .xyz file. So, i just changed the extension of my file from .xyz to .dump, and now csg_stat is able to read this file.

Yes, the above is not an xyz file, but a dump file, thier formats are
very different, hence you will have to rename Trajectory2.xyz to
something like Trajectory2.dump as VOTCA is using the file extension
to figure out which format a trajectory file is.

Christoph

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/40d7039e-600d-4f7a-8a35-803a72dc7f11n%40googlegroups.com.