# octadecanol density estimation

units		real
atom_style	full
dimension	3
variable        x    equal temp
variable        t    equal 298


read_data       octadecanol.data


# initial velocity 
velocity	all create 500 200 loop geom

# multi neighbor and comm for efficiency

neighbor	4 bin
#neigh_modify	delay 1
#comm_modify    mode multi

#octadecanol potential

pair_style lj/cut/coul/long 9.0 

pair_coeff 1 1 0.066 3.5          # c-c
pair_coeff 2 2 0.066 3.5          # c2-c2
pair_coeff 3 3 0.066 3.5          # c3-c3
pair_coeff 4 4 0.030 2.42         # H-H
pair_coeff 5 5 0    0            # H2-H2 o-h
pair_coeff 6 6 0.030 2.5          # h3-h3 ch3oh
pair_coeff 7 7 0.170 3.12         # O-O
special_bonds lj/coul 0.5 0.5 0.5 
pair_modify mix  geometric

bond_style harmonic
bond_coeff 1 268.0 1.529 # 4  C-C
bond_coeff 2 268.0 1.529 # 4  C-C2
bond_coeff 3 268.0 1.529 # 4  C-C3
bond_coeff 4 340.0 1.090 # 2  C-H
bond_coeff 5 340.0 1.090 # 2  C2-H3
bond_coeff 6 320.0 1.380 # 3  C2-O
bond_coeff 7 340.0 1.090 # 2  C3-H
bond_coeff 8 553.0 0.945 # 1  H2-O

angle_style harmonic

angle_coeff 1 58.35 112.70 # 6  C-C-C
angle_coeff 2 58.35 112.70 # 6  C-C-C2
angle_coeff 3 58.35 112.70 # 6  C-C-C3
angle_coeff 4 37.5 110.70 # 3  C-C-H
angle_coeff 5 37.5 110.70 # 3  C-C2-H3
angle_coeff 6 50 109.50   # 5  C-C2-O
angle_coeff 7 37.5 110.70 # 3  C-C3-H
angle_coeff 8 37.5 110.70 # 3  C2-C-H
angle_coeff 9 55 108.50  # 1  C2-O-H2
angle_coeff 10 37.5 110.70 # 3  C3-C-H
angle_coeff 11 33 107.80   # 4  H-C-H
angle_coeff 12 33 107.80   # 4  H-C3-H
angle_coeff 13 33 107.80   # 4  H3-C2-H3 danger
angle_coeff 14 35 109.50  # 2  H3-C2-O

dihedral_style opls
dihedral_coeff 1 1.74   -0.157 0.279 0.000 # C-C-C-C danger
dihedral_coeff 2 1.74   -0.157 0.279 0.000 # C-C-C-C2
dihedral_coeff 3 1.74   -0.157 0.279 0.000 # C-C-C-C3
dihedral_coeff 4 0.000 0.000 0.366 0.000 # C-C-C-H
dihedral_coeff 5 0.000 0.000 0.366 0.000 # C-C-C2-H3
dihedral_coeff 6 1.711 -0.500 0    0.663 # C-C-C2-O
dihedral_coeff 7 0.000 0.000 0.366 0.000 #  C-C-C3-H
dihedral_coeff 8 -0.356 -0.174 0.492 0.00 # C-C2-O-H2
dihedral_coeff 9 0.000 0.000 0.366 0.000 # C2-C-C-H
dihedral_coeff 10 0.000 0.000 0.366 0.000 # C3-C-C-H
dihedral_coeff 11 0.000 0.000 0.318 0.000 # H-C-C-H
dihedral_coeff 12 0.000 0.000 0.318 0.000 # H-C-C2-H3
dihedral_coeff 13 0.000 0.000 0.468 0.000 # H-C-C2-O
dihedral_coeff 14 0.000 0.000 0.318 0.000 # H-C-C3-H
dihedral_coeff 15 0.000 0.000 0.450 0.000 # H3-C2-O-H2

set		type 6 charge 0.060

kspace_style    ewald 1.0e-6

min_style	sd
minimize        1.0e-4 1.0e-6 100 1000
thermo_style	custom step  density temp  etotal press #v_h2o_num
thermo		100
dump		1 all atom 1000 dump.colloid
compute		diff all msd
#compute 	diff2 all rdf 10 1 1 2 2 1 2
fix             1 all nvt temp 380.0 380.0 20.0 
fix             11 all temp/berendsen 380.0 380.0 20.0
restart		10000	poly.restart
run		200000
unfix           1
unfix           11
fix		1 all npt temp 380.0 $t 10.0 iso 10 1 500.0
fix             11 all temp/berendsen 380.0 $t 10.0
run		1000000
unfix           1
unfix           11
fix		1 all npt temp $t $t 20.0 iso 1 1 1000.0
fix             11 all temp/berendsen $t $t 20.0
fix             22 all ave/time 10 10 500 c_diff file msd.xls mode vector
#fix            222 all ave/time 10 10 500 c_diff2 file rdf.xls mode vector

#fix            3 all print 100 "$x " file results.txt
timestep        1


#unfix           111

run             3000000
write_data      octa1_run.data