#-----INITIALIZATION-----
units		real
dimension	3
boundary	p	p	p
atom_style	full
#-----Atom definition-----
lattice		sc 5
region		whole block 0 10 0 10 0 10
#-----Force Fields-----
pair_style	lj/cut/coul/long 15.0 15.0
pair_modify	tail yes
bond_style	harmonic
angle_style	harmonic
improper_style cvff
kspace_style	pppm 1.0e-4
read_data	cyclopentanol.txt
replicate	5 5 4
#-----Define setting-----
compute eng all pe/atom
compute eatoms all reduce sum c_eng

#-----Equilibriation-----
reset_timestep 0

group	cyclopentanol type 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 
fix		mynpt cyclopentanol npt temp 300.0 300.0 100 iso 1.0 1.0 1000 mtk yes tloop 10 ploop 10
velocity	cyclopentanol create 300.0 13430
#-----Output-----
dump 1 cyclopentanol cfg 20 dump.cyc6.*.cfg mass type xs ys zs c_eng fx fy fz
print "System is equilibiriated"
run		0
velocity	cyclopentanol scale 300.0
thermo 1
thermo_style	custom step temp pe ke etotal press
min_style	cg
minimize	1e-25 1e-25 2000000 2000000
variable	PotentialEnergy equal epair 

timestep	1.0

#-----RDF calculation-----
#rerun dump.cyc2.*.cfg every 1 dump x y z fx fy fz q box yes
#special_bond coul 1e-50 1e-50 1e-50
#compute 13 cyclopentanol rdf 150 cutoff 15
#fix 07 cyclopentanol ave/time 1 10 10 c_myRDF[*] file tmp.rdf mode vector
#print "The end is near . . ."