Binary generate.lmp

# Binary polycrystal site-by-site substitution energy scan
# This script reads a relaxed Al polycrystal, temporarily replaces each site
# with Cu, evaluates the total energy, and writes one energy value per site.

units           metal
atom_style      atomic
boundary        p p p
read_data       70+5.lmp extra/atom/types 1

# Atomic masses (type 1 = Al, type 2 = Cu)
mass            1 26.98
mass            2 63.55

# Interatomic potential
pair_style      eam/alloy
pair_coeff      * * AlCU.eam Al Cu
# Basic settings
variable        total_atoms equal atoms
variable        atom_id loop ${total_atoms}
variable        totalenergy equal pe

timestep        0.001
thermo          1000
thermo_style    custom step pe

# Relax the initial structure before the substitution scan
minimize        0 1.0e-12 10000 10000

label           loop_start

# Substitute the current site with Cu (type 2)
set             atom ${atom_id} type 2
minimize        0 1.0e-12 1000 1000
# Recompute the energy without additional time integration
run             0
print           "${atom_id} ${totalenergy}" append binary_site_substitution_energies.txt

# Restore the original Al atom (type 1)
set             atom ${atom_id} type 1

next            atom_id
jump            SELF loop_start

run             0
print           "Done."

# Example run command:
# mpiexec -np 4 lmp -in in.lmp -pk omp 4 -sf omp