[lammps-users] dumping unwrapped coordinates

Venkat,

If you use the dump atop style, and give the file an ending of .lammpstrj,
VMD should be able to read the file:

dump 1 all atom 1000 sim.lammpstrj
dump_modify 1 scale no

In the newer version of LAMMPS you can also dump directly to dcd, although
in this case you must dump all your atoms

dump 1 all dcd 1000 sim.dcd

Then you can load in your trajectory. However, VMD cannot yet read lammps
data files, so it won't have any bond connectivity information - unless
you generate a psf file for your system (psf being CHARMM's standard
structure file format).

Naveen

Dear Lammps users,

I'm having trouble obtaining equilibrium on my system. I've been trying to
follow several papers that deal with a slab of metallic atoms in the way
equilibrium at a certain temperature is achieved but they don't seem to work
in lammps for the bulk (periodic boundary conditions) or a free surface.
I've noticed that even though the velocities oscillate slowly at a given
temperature the msd seems to oscillate a lot.

I'm trying two schemes:

1. setting the temperature of the system at 0 K using velocity create and
then very slowly (in 200 ps increasing the temperature in 25 K intervals)
using temp/rescale. Doing velocity rescaling for 20 ps using temp/rescale to
make sure that the system oscillates around a certain temperature, and then
a 50 ps run without constraints using time integration according to the
microcanonical ensemble (at this point I unfix the temp/rescale command).

2. setting the temperature of the system at the desired temperature (instead
of 0 K) and then repeating the same procedure as 1.

Any suggestions?

Jaime Sanchez

Hi Jaime,

if the slab is a solid, I think you may obtain an oscillating MSD (with maximum amplitude less than sigma^2)
even if the system is equilibrated. May be if you run it for a very long time, you end up smoothing the oscillations
to an almost constant very small value, but I would not consider one or the other as an indication that the system
is or not in equilibrium.

If msd oscillates with an amplitude that is bigger than sigma^2, that may be an indication of something wrong and
I do not know what it may be.
vale

Dear Lammps users,

I'm having trouble obtaining equilibrium on my system. I've been trying to
follow several papers that deal with a slab of metallic atoms in the way
equilibrium at a certain temperature is achieved but they don't seem to work
in lammps for the bulk (periodic boundary conditions) or a free surface.
I've noticed that even though the velocities oscillate slowly at a given
temperature the msd seems to oscillate a lot.

I'm trying two schemes:

1. setting the temperature of the system at 0 K using velocity create and
then very slowly (in 200 ps increasing the temperature in 25 K intervals)
using temp/rescale. Doing velocity rescaling for 20 ps using temp/rescale to
make sure that the system oscillates around a certain temperature, and then
a 50 ps run without constraints using time integration according to the
microcanonical ensemble (at this point I unfix the temp/rescale command).

2. setting the temperature of the system at the desired temperature (instead
of 0 K) and then repeating the same procedure as 1.

Any suggestions?

Jaime Sanchez

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Valeria Molinero
Materials and Process Simulation Center [email protected]
139-74 Beckman Institute Phone: +1-626-395 2724
California Institute of Technology Fax: +1-626-585 0918
Pasadena, California 91125, U.S.A.

Hi Valeria,

How much would you say is "a very long time" for the oscillations to smooth
out?

On my oscillation problem I find that even though the temperature
oscillates, let's say, between 24.9 to 25.1 K at some points during the 50
ps run it seems that the msd increases; not by small amount but actually
increases to values that are 2 to 3 times larger than the previous ones.
This is actually what I don't understand that's happening.

Jaime

I'll post a patch soon that allows you to dump unwrapped
coords directly ... it's a pretty simple addition to dump.cpp

Steve