Dear all,
I am creating a simulation in LAMMPS for FCC Nickel system. checkout the command file attached. I am dividing the simulation box into two halves, top and bottom, to do further transformations.
The problem is when I am dividing the box into two halves, I am missing a layer in the top region.
clear
log perfect.lammps
units metal
dimension 3
boundary p p p
atom_style atomic
variable lp equal 3.52395413816153
variable factor equal 8
lattice fcc ${lp} orient x -1 1 0 orient y -1 -1 2 orient z 1 1 1
variable xdim equal ${lp}*sqrt(2)
variable ydim equal ${lp}*sqrt(6)
variable zdim equal (${lp}*sqrt(3)*${factor})+${lp}*sqrt(3)*(2) #This number because this is 6 layers (2 stacks of ABC stacking). Creating Vacuum of this size to make things periodic.
#12.2073353333=a*sqrt(3)*(2) where a is lattice parameter.
variable atoms_end equal ${lp}*sqrt(3)*${factor}
variable length equal (${atoms_end}/2) #which is ${lp}*sqrt(3)*4
region full_box block 0 ${xdim} 0 ${ydim} 0 ${zdim} units box
region atoms block 0 ${xdim} 0 ${ydim} 0 ${atoms_end} units box
region top block 0 ${xdim} 0 ${ydim} ${length} ${zdim} units box
region bottom block 0 ${xdim} 0 ${ydim} 0 ${length} units box
lattice fcc ${lp} orient x -1 1 0 orient y -1 -1 2 orient z 1 1 1
create_box 1 full_box
create_atoms 1 region atoms
group top_atoms region top
group bottom_atoms region bottom
I hope reason for having the variable atoms_end is intuitive. I am not filling any atoms above it,leaving it as vacuum. Checkout the dump files attached. Is this not the right approach to divide the box?
I have consulted my professor and he asked me to create top and bottom atoms separately to avoid confusion.
But I want to know why my method doesn’t work. Would be very helpful if someone can explain the mistake I am making.
perfect.txt (2.5 KB)
Modified command
perfect_modified.txt (2.6 KB)
(The difference is the change in magnitude of variable “length”)
Dump Files
pefect.dat (1.3 MB)
perfect_bottom.dat (749.7 KB)
perfect_top.dat (635.6 KB)
Modified
pefect.dat (1.3 MB)
perfect_bottom_modified.dat (697.9 KB)
perfect_top_modified.dat (687.3 KB)
Thank You.
PS: If I use variable atoms_end equal ${lp}*sqrt(3)*${factor} - (1/6)(${lp}*sqrt(3)) instead of
variable atoms_end equal ${lp}*sqrt(3)*${factor}, I am able to get ABCABCABCABC in top and bottom layers by some basic mathematics. I have attached their dump files as well below. But I am not convinced with the way the structures were created.
