potential of CNT

Daer All

I used VMD software and topotools to create my CNT model, and used some code to obtain potential energy, there is one problem. when I impose a strain to simulation box as below code,at first end boundary expand then start to compress and never the pressure be equal to zero. what is my problem ? and how long should i wait as pressure value alternate ?

thermo 100
thermo_style custom step press lx lz pe
thermo_modify norm no

fix 1 all box/relax aniso 0 dilate partial
displace_box all z delta 0 0.01 units box

minimize 0 0 10000 10000

regard

Daer All

I used VMD software and topotools to create my CNT model, and used some code to obtain potential energy, there is one problem. when I impose a strain to simulation box as below code,at first end boundary expand then start to compress and never the pressure be equal to zero. what is my problem ? and how long should i wait as pressure value alternate ?

thermo 100
thermo_style custom step press lx lz pe
thermo_modify norm no

fix 1 all box/relax aniso 0 dilate partial
displace_box all z delta 0 0.01 units box

minimize 0 0 10000 10000

regard

fix 1 all box/relax aniso 0 dilate partial
displace_box all z delta 0 0.01 units box
minimize 0 0 10000 10000

I used VMD software and topotools to create my CNT model, and used some code
to obtain potential energy, there is one problem. when I impose a strain to
simulation box as below code,at first end boundary expand then start to
compress and never the pressure be equal to zero. what is my problem ? and
how long should i wait as pressure value alternate ?

1) Are you sure you want to use "aniso" for a carbon nanotube? You
probably only want to adjust the volume of your simulation box in the
direction that the tube is pointing in. (For example, if your
nanotube points in the Z direction, then replace "aniso" with "z".
See below. Otherwise your simulation box may explode or collapse in
the x and y directions.)
2) Comment: Although this is not the source of your problem, you don't
really need "dilate partial" if you are using group "all" in the fix
box/relax command.
3) The displace_box command does not exist any more. (It's been
replaced by "change_box".
LAMMPS Molecular Dynamics Simulator) You may want to upgrade
to a more recent version of LAMMPS.
4) I've read strange things can happen with the minimize command.
(Some of LAMMPS' features break using that command.) Does the strange
behaviour persist if you simply run the system at zero temperature and
pressure? In other words, instead of using "minimize", try running
regular molecular dynamics using something like this:

fix 1 mobile npt temp 400.0 0.0 100 z 0.0 0.0 1000.0 drag 1
run 20000
  --- or this ---
fix fxlan all langevin 400.0 0.0 100 48279
fix fxnph all nph z 0.0 0.0 1000.0 drag 1
run 20000

(The temperature begins at 400 Kelvin (assuming you are using "real"
units) and is cooled to zero. Of coarse, these numbers may not work
for your system. Instead of "aniso" I am using "z", assuming that
your nanotube is parallel to the Z axis. You probably want to use a
small timestep., significantly less than 1fs. In case I screwed up
those commands, check these web pages:

LAMMPS Molecular Dynamics Simulator)

5) Try this if everything else fails (because I doubt this is the
problem). If it's not too difficult, try simplifying your system by
commenting out the "displace_box" command. (If necessary, make
modifications to the beginning of your data file to compensate.)

If that does not work, then you may have a problem with your
force-field, units, or the initial boundary-box dimensions and tube
orientation, or some other physics problem. I hope this helps.

Andrew