VMD-L Mailing List

From: Marco Kalweit (m.kalweit_at_cranfield.ac.uk)
Date: Thu Oct 05 2006 - 16:48:28 CDT

Lutz,

I think you are right,
thanks for the correction.

Marco

Lutz Maibaum wrote:

>On Thursday 05 October 2006 08:06, Marco Kalweit wrote:
>
>
>>If I remember correctly then following this, I had a look at the dump
>>files and found that the types were messed up.
>>So I thought that this was a Lammps bug and did not care about it futher
>>at the moment.
>>
>>
>
>I don't think it's a bug in LAMMPS. Please take a look at the sample file I
>posted a few days ago:
>
>http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-7959/np2.lammpstrj
>
>In gnuplot you can display the positions of the different atom types with the
>following command:
>
>splot "np2.lammpstrj" u 3:4:($2 == 1 ? $5 : 1/0) w p, "" u 3:4:($2 == 2 ? $5 :
>1/0) w p, "" u 3:4:($2 == 3 ? $5 : 1/0) w p
>
>You see five parallel planar layers as expected. If you load the same file
>into vmd and choose "type" as the coloring method, you get atoms at the same
>positions, but the type assignment is incorrect.
>
>
>
>>The change you made will stop reading the file in as soon as it finds an
>>error. So I do not quite understand how it reads in correctly, following
>>a problem with the type or the id.
>>
>>
>
>In the current version of the LAMMPS plugin the function read_lammps_structue
>basically looks like
>
> for(i=0;i<data->numatoms;i++) {
> j = sscanf(szBuffer, "%d %s %f %f %f", &atomid, atom_type, &x, &y, &z);
> atom = atoms + i;
> strncpy(atom->type, atom_type, sizeof(atom->type));
> }
>
>For the i-th line in the LAMMPS trajectory file, the atom type is assigned to
>the atom with index i in the vmd data structure. On the other hand, in
>read_lammps_timestep, we have
>
> for (i=0; i<natoms; i++) {
> j = sscanf(szBuffer, "%d %s %f %f %f", &atomid, atom_name, &x, &y, &z);
> if (atomid > 0 && atomid <= natoms) {
> int addr = 3 * (atomid - 1);
> ts->coords[addr ] = x * l[0];
> ts->coords[addr + 1] = y * l[1];
> ts->coords[addr + 2] = z * l[2];
> }
> }
>
>so that the position of each atom is assign to the atom with index atomid in
>the vmd data structure. This is inconsistent with type assignment, unless the
>trajectory file is ordered by increasing atomid. By simply changing
>
> atom = atoms + i;
>
>to
>
> atom = atoms + atomid - 1;
>
>in read_lammps_structure, the assignment of atom type to an atom in the vmd
>data structure is based on the atomid rather than the position in the
>trajectory file, which makes it consistent with the assignment of the atom
>coordinates.
>
>Hope this helps,
>
> Lutz
>
>