[lammps-users] Problem with Equilibration

LAMMPS LAMMPS Mailing List Mirror
#1

Dear All,

I am a new LAMMPS user.
I am trying to equilibrate a box of Nickel atoms.
When I use periodic boundary conditions (p p p) , atoms fly off.
When any one of the boundary conditions is shrink-wrapped (for example “s p p”), atoms do not fly off after equilibration.
I am giving the input script below
Can anyone help me.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

units metal
boundary p p p

atom_style atomic
lattice fcc 3.52
region box block 0 4 0 10.0 0 4
create_box 3 box

lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 &
origin 0.5 0 0
create_atoms 1 box

pair_style eam
pair_coeff * * Ni_u3.eam

neighbor 0.3 bin
neigh_modify delay 1

region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
group upper region upper
group boundary union lower upper
group mobile subtract all boundary

set group lower type 2
set group upper type 3

compute new3d mobile temp

equilibrate

minimize 1e-4 1e-6 1000 1000
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0

fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d

dump 1 all xyz 100 dump.shear
thermo 25
thermo_modify temp new3d

timestep 0.001
run 10000

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Thanks in advance
sivashankar

#2

Dear sivasankar,
Try minimizing your system first before running the dynamics engine. Does your potential energy at timestep 0 make sense to you?

#3

It sounds to me like the crystal wasn't built well at the boundary. Try calculating the distance between two atoms across the boundary. I bet they are overlapping a bit.
Matt

Quoting Vikas Varshney <[email protected]>:

#4

lattice fcc 3.52
region box block 0 4 0 10.0 0 4
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 &
      origin 0.5 0 0

These commands are not likely to give a periodic system, since you
defined your box before you changed the lattice to something that
isn't axis aligned. Read the doc
page for the lattice command and about how to choose box sizes that
will be periodic for oriented lattices. Even then you need to carefully
check that you generate atoms that are correct near the boundaries.

Steve