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Re: [lammps-users] Reg. anatase nanorod structure stabilization
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Re: [lammps-users] Reg. anatase nanorod structure stabilization

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Thu, 12 Apr 2018 04:57:03 -0400

On Wed, Apr 11, 2018 at 5:02 PM, ABHINAV SHUKLA <as37@...7325...> wrote:
Dear all,

I am trying to stabilize a cross nanorod system of anatase. However during equilibration atoms are getting off the nanorods (screenshots attached for reference). It would be of great help if somebody can explain the reason behind it. 

​the reason is your input. LAMMPS will read and execute the computations (e.g. evaluate the forces and update velocities and positions) for the atom positions and force field parameters you provide it with.
what you see is what happens for the particular settings, geometry and parameters you input.

so now you have to ask yourself (and run the corresponding tests):
- is the geometry correct? what happens, if you use just one read_data command instead of two?
- is the force field correct? are the parameters suitable to model a system like yours (or only bulk crystals where atoms cannot "escape")?
​- is your relaxation/equilibration/simulation protocol correct?

it is very unlikely, that somebody here has the time to look into it, and it *is* part of the job of doing simulations to test, validate and debug all input and settings. basically, for as long as LAMMPS is doing what it says in the documentation, it should be doing, then any problem is your problem. if there is a conflict or contradiction, then the mailing list is a place to ask people for help.

a couple of obvious things as a starting point to consider:
a) most people do a minimization first; and b) there is no point in using a barostat on such a system.​



Following is the input script:

dimension 3
units metal
atom_style full
newton on
boundary p s p 

region simbox block -300 300 -300 300 -100 300
create_box      2 simbox 
read_data add append 
read_data add append

set type 1 charge 2.196
set type 2  charge -1.098

#------------int​​eratomic potential
pair_style buck/coul/cut 8.0
pair_coeff   1 1   31393.4364 0.154 5.2929
pair_coeff   1 2   17106.4193 0.194 12.7031
pair_coeff   2 2   11886.2131 0.234 30.4873

neighbor 2.0 bin 
neigh_modify every 1 delay 0 check yes

timestep 0.001
thermo 100
thermo_style custom step cpu temp ke pe etotal pyy lx ly lz
dump config all custom 200 anatase.config.* id type x y z vx vy vz
dump_modify config format line "%8d %5d %25.18g %25.18g %25.18g %20.13g %20.13g %20.13g"

velocity all create 300 12345 mom yes rot no

fix 2 all nvt temp 300.0 300.0 1.0
run 50000
unfix 2

fix 1 all npt temp 300.0 300.0 0.1 x 1.0 1.0 1.0 z 1.0 1.0 1.0
run 50000
unfix 1

fix 3 all nve
run 50000
unfix 3

Thanks & Regards,
Abhinav Shukla

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Dr. Axel Kohlmeyer  akohlmey@...12...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.