Minimization problem

LAMMPS LAMMPS General Discussion
1

After minimizing a CSL grain boundary structure surface defects come , how to remove this?
I am using this

units metal
echo both
atom_style atomic
dimension 3
boundary p p p

read_data final.lmp

timestep 0.002
pair_style eam/alloy
pair_coeff * * NAME Element

#-------------------------SIMULATION PROCESS---------------------------------

Initial velocities at a given temperature

velocity all create 100 458273253 dist gaussian

Timestep to make the integration of the motion equation

timestep 0.002

Parameters to print out on the screen and log.lammps file

thermo_style custom step temp etotal vol lx ly lz press pxx pyy pzz cpu

thermo 100

Saving atomic coordinates

dump 1 all custom 1000 Alpoly*.lammpstrj id type x y z

Energy minimization parameters

fix 1 all box/relax iso 0.0 vmax 0.01

minimize 1.0e-10 1.0e-12 1000 1000

equilibration of sample at 300 K in NPT

this fix is only for equilibration/sample prep

fix 1 all npt temp 100 100 0.01 iso 0.0 0.0 0.1

run 1000

#-----SIMULATION DONE-------
print “Simulation complete”

2

Not sure about your grain boundary problem, but your thermostat and barostat relaxation times look awfully fast. Your fix npt has a thermostat damping time of 5 timesteps, which is too short for stable temperature control in most cases. Similarly, your barostat time constant is 50 timesteps, which is probably far too few for accurate pressure control.

3

What happens is determined by the forces and the initial geometry. Both are parameters that you control via the data file and the pair style and potential file.