HELP

Hello Sir,

I want to simulate a 1 dimensional chain of Argon (in solid phase) at different temperatures (10, 20, 30, 40 Kelvin, as I have chosen them) and then calculate the average chain length at each temperature and then calculate the thermal expansion coefficient from that. But as I am running my script, the length of the chain keeps on increasing with time which should happen because in that case there is no average length of the chain. The length should oscillate.

I shall be highly thankful to you if you have a look at the script and the data file and help me figure out what is wrong. I am attaching the script and the data file herewith.

Thanking you

script.txt (822 Bytes)

position_and_vel.txt (8.36 KB)

Hello Sir,
                  I want to simulate a 1 dimensional chain of Argon (in
solid phase) at different temperatures (10, 20, 30, 40 Kelvin, as I have
chosen them) and then calculate the average chain length at each temperature
and then calculate the thermal expansion coefficient from that. But as I am
running my script, the length of the chain keeps on increasing with time
which should happen because in that case there is no average length of the
chain. The length should oscillate.
                   I shall be highly thankful to you if you have a look at
the script and the data file and help me figure out what is wrong. I am
attaching the script and the data file herewith.

wouldn't it be better you discuss this with teacher of your class,
rather than have somebody else do your homework assignment for you?

axel.

I started to reply, and then I realized something.
I confess to be lousy and chemistry. But even I am confident enough
to ask why argon would naturally form chains? Isn't it a noble gas?

   ------ standard reply (written before carefully reading what you posted) ----

Assuming that what you are trying to do makes sense...
Have you tried visually looking at what your system is doing?

I have attached some general instructions for viewing LAMMPS data
files and trajectories in VMD using Axel's topotools program. ( Axel
wrote a useful program which allows you to import (and export and
manipulate) LAMMPS data files into VMD (among other features). This
also allows you to create LAMMPS trajectories in VMD and see what is
going on.

At the beginning of the instructions, where it tells you to type this
into the Extensions->Tk Console window:

   topo readlammpsdata system.data full
   animate write psf system.psf

Type this instead

   topo readlammpsdata position_and_vel.txt full
   animate write psf system.psf

---- bonds ----

I'm not sure if there are supposed to be bonds in your system.
(Probably not if it's Argon.) If so, they should be visible in VMD at
this point. Check and make sure that they are.

I would change your "dump" command to something like:
dump 2b all custom 500 dump-position.lammpstrj id mol type x y z ix iy iz

and then run a short simulation, perhaps:
run 20000

The extra information (mol ix iy iz) helps VMD figure out how to wrap
coordinates without splitting molecules. (Not sure if you need that
feature.)
If you name your trajectory file "dump-position.lammpstrj" instead of
"dump-position.txt", VMD will have an easier time automatically
detecting its format.
You can save as frequently or infrequently as you like, but 500 should
be frequent enough to see what is going on, assuming the timestep is
reasonable.

Cheers

Andrew

README_visualize.txt (2.85 KB)