# LAMMPS Input File for Grain Boundaries
# Mark Tschopp, Dec2009
# Modified by PM Larsen to demonstrate the use of PTM in LAMMPS
# This file will generate a single Sigma5(310) STGB and run PTM

# ---------- Initialize Simulation ---------------------
clear
units metal
dimension 3
boundary p p p
atom_style atomic

# ---------- Create Sigma5(310) Structure ---------
lattice fcc 4.05
region whole block 0.000000 12.807225 -64.0361225 64.0361225 0.000000 4.050000 units box
create_box 2 whole
region upper block INF INF 0.000000 64.0361225 INF INF units box
lattice fcc 4.05 orient x  0  3  1 orient y  0 -1  3 orient z  1  0  0
create_atoms 1 region upper
region lower block INF INF -64.0361225 0.000000 INF INF units box
lattice fcc 4.05 orient x  0  3 -1 orient y  0  1  3 orient z  1  0  0
create_atoms 2 region lower
group upper type 1
group lower type 2

mass 1 1.0
mass 2 1.0

# ---------- Define Interatomic Potential ---------------------
pair_style	lj/cut 2.5
pair_coeff	* * 1 1
pair_coeff	1 1 1 1.1 2.8

# ---------- Displace atoms and delete overlapping atoms ---------------------
displace_atoms upper move 0 0 0 units lattice
delete_atoms overlap 0.35 lower upper

# ---------- Define PTM settings (default structures, RMSD threshold of 0.1) -------------------
compute ptm all ptm/atom default 0.1

# ---------- Dump data into Data file -------------
reset_timestep 0
dump 		1 all cfg 10000 dump.ptm_example_*.cfg mass type xs ys zs c_ptm[1] c_ptm[2] c_ptm[3] c_ptm[4] c_ptm[5] c_ptm[6] c_ptm[7]
dump_modify     1 element Al Al
run 1

print "All done"