# Input file for uniaxial compressive loading of PU
# Arunjyoti, November 2010

# ------------------------ INPUT  FILE -------------------------------
# VARIABLES
variable fname index PU_1000_Model.txt
variable simname index PU_1000_Model


# ------------------------ INITIALIZATION ----------------------------
units 		nano
dimension	3
boundary	p	p	p
atom_style	molecular
log 		log.${simname}.txt
read_data	${fname}

# ------------------------ FORCE FIELDS ------------------------------
pair_style nm/cut 5.0     #set LJ style and cutoff
pair_modify shift yes        	#shift energy at cutoff
pair_coeff 1 1 9.3  1.67  12.0 6.0  		#set LJ parameters for H-H
pair_coeff 1 2 7.2  1.94  12.0 6.0  		#set LJ parameters for H-S
pair_coeff 2 2 5.6  2.12  12.0 6.0   		#set LJ parameters for S-S


# ----------------------- BOND DEFINITION ----------------------------
bond_style harmonic		#set bond style
bond_coeff 1 6530.0  2.768	#set harmonic bond parameters
bond_coeff 2 5818.5  2.516	#set harmonic bond parameters

# ----------------------- ANGLE DEFINITION ----------------------------
angle_style cosine/squared
angle_coeff 1 285.0  146.89
angle_coeff 2 160.0  153.09
angle_coeff 3 470.0  142.12

# ------------------------- SETTINGS ---------------------------------
compute peratom all pe/atom 

######################################
# COMPRESSION
reset_timestep	0
timestep 0.000001
variable T1 equal 500
velocity all create ${T1} 123456 mom yes rot yes
#################################################
#########################################################
fix		1 all nvt temp 500 500 200e-5
min_style cg
minimize 1.0e-4 1.0e-6 100 1000


dump 		1 all cfg 10000 dump.PU_1000.comp_*.cfg mass type xs ys zs c_peratom fx fy fz
dump_modify     1 element H, S
thermo 	100
thermo_style	custom step temp lx ly lz ke pe pxx pyy pzz density

run 1000000
unfix 1
undump 1
#########################################################
fix		1 all nvt temp 500 298 200e-5
min_style cg
minimize 1.0e-4 1.0e-6 100 1000


dump 		1 all cfg 10000 dump.PU_1000.comp_*.cfg mass type xs ys zs c_peratom fx fy fz
dump_modify     1 element H, S
thermo 	100
thermo_style	custom step temp lx ly lz ke pe pxx pyy pzz density

run 1000000
unfix 1
undump 1
#########################################################
fix		1 all nvt temp 298 298 200e-5
min_style cg
minimize 1.0e-4 1.0e-6 100 1000


dump 		1 all cfg 20000 dump.PU_1000.comp_*.cfg mass type xs ys zs c_peratom fx fy fz
dump_modify     1 element H, S
thermo 	100
thermo_style	custom step temp lx ly lz ke pe pxx pyy pzz density

run 2000000
unfix 1
undump 1
write_restart 	restart.PU_1000_OUTPUT.dreiding4
#############################################################
# SIMULATION DONE
print "All done"