Lammps input file

#LAMMPS Input file generated by Avogadro
# Mos2

# Intialization
units          real
dimension      3
boundary       p p p
atom_style     full
kspace_style pppm 1.0e-4
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes

# Atom Definition
read_data small_mos2_ctab_water.data

pair_style lj/cut/coul/long 10 15
angle_style harmonic
bond_style harmonic
improper_style none
dihedral_style fourier
special_bonds amber

group MovingAtoms type 1 2 3 4 6 7  #Br C H Hw N O
group MoS2Atoms type 5 8            #Mo S


#coefficients
##############################################################
#angle
# C-N-C
angle_coeff  4 62.84 110.64
# C-C-C
angle_coeff  1 63.21 110.63
# C-C-H
angle_coeff  2 46.37 110.05
# C-C-N
angle_coeff  3 64.45 114.32
# H-C-H
angle_coeff  5 39.43 108.35
# N-C-H
angle_coeff  6 49.01 107.90
# H-O-H
angle_coeff  7 55.0  104.52
# Mo-S-Mo
angle_coeff 8 2.5163 82.0
# S-Mo-S
angle_coeff 9 2.5163 82.0




#bonds
#C-C
bond_coeff 1 303.1 1.5350
#C-H
bond_coeff 2 337.3 1.0920
#C-N
bond_coeff 3  293.6 1.4990
#O-H
bond_coeff 4 450.0 0.9572
#Mo-S
bond_coeff 5 4.3213 2.41

#dihedrals
# C -C -C -N
dihedral_coeff 3 1  0.155555555556 3 0.0
dihedral_coeff 6 1 0.155555555556 3 0.0
dihedral_coeff 7 1 0.155555555556 3 0.0
# C -N -C -C
dihedral_coeff 4 1 0.155555555556 3 0.0
# H -C -C -H
dihedral_coeff 5 1 0.15 3 0.0
# C -C -C -H
dihedral_coeff 2 1 0.16 3 0.0
# C -C -C -C
dihedral_coeff 1 3 0.18 3 0.0 0.25 2 180.0 0.2 1 180.0

#Mo -S -Mo -S dihedral or any interaction with MoS2 will be ignored hence no deen for this
#dihedral_coeff 8  none



#pair coefficients

pair_coeff 1 1 0.420       3.59923082129
pair_coeff 1 2 0.214       3.49945016486
pair_coeff 1 3 0.0812      3.12438180452
pair_coeff 1 4 0.00        1.99961541064
pair_coeff 1 5 .29663      3.0751
pair_coeff 1 6 0.2672      3.42461467254
pair_coeff 1 7 0.2070      3.39361541065
pair_coeff 1 8 0.0799      3.4844
pair_coeff 2 2 0.1094      3.39966950842
pair_coeff 2 3 0.0414      3.02460114808
pair_coeff 2 4 0.00        1.89983475421
pair_coeff 2 5 0.15139     2.9753
pair_coeff 2 6 0.1364      3.3248340161
pair_coeff 2 7 0.1056      3.29383475421
pair_coeff 2 8 0.04078     3.3846
pair_coeff 3 3 0.0157      2.64953278775
pair_coeff 3 4 0.00        1.52476639388
pair_coeff 3 5 0.0574      2.6003
pair_coeff 3 6 0.0517      2.94976565576
pair_coeff 3 7 0.0400      2.91876639387
pair_coeff 3 8 0.01545     3.0095
pair_coeff 4 4 0.00        0.4000
pair_coeff 4 5 0.00        1.4755
pair_coeff 4 6 0.00        1.82499926189
pair_coeff 4 7 0.00        1.7753
pair_coeff 4 8 0.00        1.8847
pair_coeff 5 5 0.2095      2.5510
pair_coeff 5 6 0.1887      2.9005
pair_coeff 5 7 0.1462      2.8695
pair_coeff 5 8 0.0085      2.9318
pair_coeff 6 6 0.1700      3.24999852378
pair_coeff 6 7 0.1317      3.21899926189
pair_coeff 6 8 0.0508      3.3097
pair_coeff 7 7 0.102       3.188
pair_coeff 7 8 0.03937     3.2788
pair_coeff 8 8 0.0152      3.3695
####################################################################


# Settings
dump num1 all atom 10000 mos2_water_ctab.lammpstrj

fix mos2 MoS2Atoms rigid single
velocity       MovingAtoms create 300 492459 rot yes mom yes dist gaussian

fix vol MovingAtoms nvt temp 300 300 100 tchain 1
##To fill out any _vacuum_ gaps and make system homogenous


timestep      .1

thermo_style   custom step etotal evdwl ecoul lx ly lz temp
thermo         10000

run 100000
unfix vol


fix NPT MovingAtoms npt temp 300 300 100 x 1.013 1.013 10 y 1.013 1.013 10 z 1.013 1.013 10 couple none drag 1
run 5000000