Hi,
I am trying to add a single Silicon atom atop a substrate layer with a total of 384 atoms. Of these 192 are fixed and the rest are mobile. Please find attached a VMD input file to get a better understanding. Now, my objective is to add a 385 atom atop the moving atoms and understand how it interacts with the atoms(moving and fixed) below. How can I do this using LAMMPS? I tried creating a config file with the coordinates to the 384 atoms and manually adding the 385th atom in the end and using the read_data command in the LAMMPS input script.
This doesn’t work out and I receive an incomplete log file with an empty movie dump file preventing me from visualizing this atom in VMD. I am using the Stillinger Weber potential. I tried using the Tersoff potential too but to no avail.
Please find attached all the required files. I’d be elated if anyone could give me an apt answer at the earliest.
Regards,
Saketh.
University of Toledo.
Si_TAD.in (1.22 KB)
Si_TADConfig.xyz (9.3 KB)
Si_TADLog.lammps (382 Bytes)
Once you have read a date file (e.g. with 384 atoms) you
can use the create atom single command to add one more atom.
You could also use fix deposit to add one (or more) atoms in a more
random manner.
Steve
Hi Steve, thanks for the reply.
At present, I use the dump xyz args syntax to create a dump file to be
visualized in VMD. I would like to know if VMD takes even vx, vy, vz atom
velocities for visualization and if it does, what is the format for the VMD
input file.
I have been searching for this for a few days not but just do not see
anywhere if VMD takes velocities for visualization.
Regards,
Saketh.
University of Toledo.
Hi Steve, thanks for the reply.
At present, I use the dump xyz args syntax to create a dump file to be
visualized in VMD. I would like to know if VMD takes even vx, vy, vz atom
velocities for visualization and if it does, what is the format for the VMD
input file.
I have been searching for this for a few days not but just do not see
anywhere if VMD takes velocities for visualization.
you haven't been searching very well, since i have discussed that
topic many times on both the LAMMPS and the VMD list. also,
this is the kind of question that you have to ask on the VMD mailing list.
the answer that you would have received there (probably from me, too),
is that the .xyz file format is the lowest common denominator and thus
a very bad idea to use, as you remove a lot of information. there is no
"standard" what is in columns beyond the first four in .xyz (actually
it is the xmol format, tinker has a different .xyz, as have many other
people and software packages).
_however_ the new VMD version 1.9 that was released just yesterday
_does_ support reading verlocities, if you write them to a custom
style dump.
cheers,
axel.