# LAMMPS Input File for creating Grain Boundary in the sample
# By Anand Mathew
# UH
# Date: Apr 15 2023

# ---------- Initialize Simulation --------------------- 

# Clear the simulation environment
clear 

# Set units for the simulation 
units metal 

# Set the dimensions of the simulation to 3D
dimension 3 

# Set the boundary conditions
boundary s s p 

# Set the atom style 
atom_style atomic 

# ---------- Create Atomistic Structure --------------------- 

read_data cylindrical_sample_coal1.lmp

# ---------- Define Interatomic Potential --------------------- 
pair_style eam/alloy													# Define potential style
pair_coeff * * Mishin_updated-Ni-Al-Co-2013.eam.alloy Co Al
				# Set potential file and elements

neighbor 2.0 bin                        										# Define neighbor list settings
neigh_modify delay 10 check yes											# Modify neighbor list settings



# ---------- Define Settings --------------------- 
compute csym all centro/atom fcc   										# Compute centering parameter for atoms based on fcc lattice structure
compute eng all pe/atom            										# Compute potential energy of each atom
compute eatoms all reduce sum c_eng 										# Compute total potential energy of the system

# ---------- Run Minimization --------------------- 
reset_timestep 0            											# Reset timestep counter to 0
thermo 10                   											# Print output every 10 timesteps
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms  						# Specify what to print in the output
dump 1 all cfg 500 dump.CoAl_Al_cylinder_*.cfg mass type xs ys zs c_csym c_eng fx fy fz 				# Write atomic positions, energy, and force data to file every 50 timesteps


min_style cg          												# Specify minimization algorithm
minimize 1e-15 1e-15 5000 5000 											# Perform energy minimization --> Max iterations are 5000

undump 1            													# Stop writing output to file


# ---------- Run Minimization 2--------------------- 
# Now allow the box to expand/contract perpendicular to the grain boundary

reset_timestep 0 													# set the timestep to 0
thermo 10 														# print thermo output every 10 steps
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms 						# define the thermo output

# apply a fix to allow the box to relax in the z direction, while constraining the x-y plane
fix 1 all box/relax z 0 vmax 0.001

min_style cg 														# use conjugate gradient for minimization
minimize 1e-15 1e-15 5000 5000 											# minimize the energy until the force is below 1e-15 and energy is below 1e-15, up to 5000 iterations

# ---------- Calculate GB Energy --------------------- 

  										# print the grain boundary energy

# ---------- Dump data into Data file ------------- 

reset_timestep 0 													# set the timestep to 0
dump 1 all custom 500 dump.GB_CoAL_AL_sig13_*.txt id type xs ys zs c_csym 					# dump data every 100 steps
#dump_modify     1 element Al Co
minimize 1e-15 1e-15 5000 5000 											# minimize the energy until the force is below 1e-15 and energy is below 1e-15, up to 5000 iterations
undump 1 # stop dumping data

write_restart restart.alco_sig61_stgb 										# write a restart file
write_data CoAl_AL_sig13.txt 											# write a data file
print "All done" 													# print a message to indicate completion