1

2
b1

System dimensionality: 2, units: lj

Input data:
Atom types : 2 (1 and 2 in the above figure, each atom is of different type)
Number of atoms : 2
Number of bonds : 1 (the bond b1 above)
Set the atom 1 at the origin
set the atom 2 at the distance equal to the bond length, |b1|
the input data can be the following:
LAMMPS data file
2 atoms #the total number of atoms
1 bonds # the total number of bonds
2
1

atom types
bond types

-1.0
-1.0
-0.1

1.0
1.0
0.1

# no of atom types
# no of bond types
xlo xhi
ylo yhi
zlo zhi

#box size
#box size
# you have to define the z-size, even for 2D systems, the defauls is -0.5,0.5

Masses
1
2

1.000000
1

#masses of atom TYPES (the first column)

Atoms
1 1 1
2 1 2

0
0

0
0.5

0
0

#coorinates. The first column: atom number, the second- MOLECLE

#number, the third- atom TYPE, fourth- x, fifth -y, sixth -z

Bonds
1112

#first column-the bond number, second bond TYPE, third and fourth the
#numbers of atoms connected by that bond.

Store the above data in the signgle.dat file

All the details about types are in the input script.
The input script
#INITIALIZATION
dimension 2
boundary p p p
# (periodic bc, even in the z direction, default)
atom_style bond
# check http://lammps.sandia.gov/doc/angle_style.html
units lj
#check http://lammps.sandia.gov/doc/units.html
read_data single.dat
#read this file for the first time

#read_restart restart1
#read_data multi.dat

#read one of the files below during next runs

# check http://lammps.sandia.gov/doc/read_data.html

# explanations for each command: http://lammps.sandia.gov/doc/Section_commands.html#comm

replicate 50 50 1
neighbor 2.0 bin

#builts larger system, comment this line in the next runs

#define the list of neighbours

velocity all create 1.0 1234

velocity all zero linear

#create the initial velocity

#remove the momentum

reset_timestep 0
timestep 0.01
#sets the timestep. If the program fails decrease it, try to make it larger (default for
# lj units =0.05).
# INTERACTION PARAMETERS
pair_style lj/cut 1 (global cut-off =1, any definition below changes it)
pair_coeff 1 1 1.0 1.0
#usage: i,j types of atoms, epsilon, sigma (and, optionally cut-off)
pair_coeff 1 2 1.0 0.5 0.5
pair_coeff 2 2 3.0 0.1
special_bonds lj 0.0 1.0 1.0
#tuns on/off the interactions between the atomscontributingto bonds,reead manual
bond_style harmonic
# harmonic bond
bond_coeff 1 500.0 0.5
# bond type, energy, equilibrium distance. 500 a huge energy
# try also fixed bond lengths
#fix bonf all shake 0.0001 1 100 b 1 #read the description for fix shake
#MD RUN
fix integrate all nve
#nve simulation
fix 3 all temp/rescale 1 1.0 1.0 0.00005 1.0
#rescale temperature
fix 111 all momentum 1 linear 1 1 1 angular #remove momentum, comment this line after performing
# preliminary calculations
#fix 13ID all temp/berendsen 2 2 10
#berendsen thermostat, comment temperature rescalling
#fix 1a all press/berendsen iso 0.5 0.5 50.0
#berendsen barostat
#ADDITIONAL CALCULATIONS
# be sure that the numbers 10 100 1000 and 10 1000 10000 are correct
# their meaning ( 10 1000 10000): the output after 10000,20000,etc timesteps, each time the averaging
# is over 1000 values obtained after 10,20,30,.....9980,9990 and 10000 timesteps (10010, 10020,...19990,20000, etc)
compute BOND all bond/local dist
compute T all temp
compute P all pressure thermo_temp
compute MSD all msd com yes
fix TempAve all ave/time 10 100 1000 c_T c_P c_MSD[4] file temp.txt #file temp.txt contains themo data
fix length all ave/histo 10 1000 10000 0.4 0.6 50 c_BOND mode vector file l.txt
#file l.txt histograms of bond lengths)
#RUN, OUTPUTS
thermo 200
thermo_style custom step temp pe epair ebond
dump d1 all custom 500 dump.lammpstrj id type x y z
run 20000
write_restart restart1
write_data multi.dat nocoeff