atom recognition

Dear All
I am creating Au(111) hcp lattice surface using create atoms. Everything works well except the atom recognition in xyz file. It recognize as number 1 so when i converting output of this into lammps data using topo in vmd its giving the mass as mass of the hydrogen. I need to combine this surface with SAM monolayers and do the simulation.
Did I missed something?
Here is the input script

units metal
atom_style full
dimension 3
boundary p p p
lattice hcp 2.916 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region box block 0 7 0 4 0 3
create_box 1 box
create_atoms 1 box

set group all type 1

set type 1 charge 0.0

neighbor 2.0 multi
neigh_modify every 1 delay 0 check yes
pair_style eam
pair_coeff 1 1 Au_u3.eam

print ======================================================================
print “500 steps CG Minimization.”
print ======================================================================

dump 1 all atom 25 {sname}_min.lammpstrj dump_modify 1 image yes scale yes dump 2 all xyz 5000 min_{sname}.xyz
min_style sd
minimize 1.0e-4 1.0e-6 500 50000
min_style cg
minimize 1.0e-4 1.0e-6 500 50000
undump 1
undump 2

Thanking you in advance
Mathi

Dear All
I am creating Au(111) hcp lattice surface using create atoms. Everything
works well except the atom recognition in xyz file. It recognize as number 1
so when i converting output of this into lammps data using topo in vmd its
giving the mass as mass of the hydrogen. I need to combine this surface
with SAM monolayers and do the simulation.
Did I missed something?

yes. how can VMD know that a "1" means an Au atom?

it would be better you write a restart, use restart2data and
input the data file. or you can use VMD scripting to override
all the settings that you want to the properties that you need.

axel.

Recently I got the same problem when I tried to view lammps xyz files with Jmol applet.

So I added “dump_modify element” option for dump xyz style. It associates element names with atom types like for cfg and image dump styles in the current lammps version.

I think this modification will be useful in your case.

Try the following to use it:

  1. Replace dump_xyz.cpp and dump_xyz.h files in lammps src directory and recompile lammps
  2. Add “dump_modify 2 element Au” after "dump 2… " line

Grigory Smirnov

2012/4/10 Vasumathi V <vasuphy@…24…>

dump_xyz.h (1.5 KB)

dump_xyz.cpp (3.98 KB)

grigory,

do you mind, if i integrate this into LAMMPS-ICMS and
then, when fully tested, send to steve for inclusion into
the mainline LAMMPS version.

however, i am going to make a modification:
rather than defaulting all atoms to element "C",
i would have them by default have the current
naming scheme, i.e. the type number as default.

there are also a few additional subtleties that
need to be taken care of in order to maintain
full backward compatibility.

cheers,
    axel.

Axel,

Of course, I don’t mind. Furthermore, my modification is based on dump_custom.cpp and there are no specific code in the modified dump_xyz.* files.
I’d be happy it to see it with your modifications in the mainline LAMMPS version

Grigory Smirnov.

2012/4/11 Axel Kohlmeyer <akohlmey@…43…4…>

Axel,

Of course, I don't mind. Furthermore, my modification is based on
dump_custom.cpp and there are no specific code in the modified dump_xyz.*
files.
I'd be happy it to see it with your modifications in the mainline LAMMPS
version

ok. the adjusted version with full backward compatibility is now
in LAMMPS-ICMS. I've also added documentation and changed
the xyz comment line (the second line of each frame) to include
the time step numbers which should be a useful addition.

cheers,
     axel.